1
|
Marcionetti A, Bertrand JAM, Cortesi F, Donati GFA, Heim S, Huyghe F, Kochzius M, Pellissier L, Salamin N. Recurrent gene flow events occurred during the diversification of clownfishes of the skunk complex. Mol Ecol 2024; 33:e17347. [PMID: 38624248 DOI: 10.1111/mec.17347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/15/2024] [Accepted: 03/26/2024] [Indexed: 04/17/2024]
Abstract
Clownfish (subfamily Amphiprioninae) are an iconic group of coral reef fish that evolved a mutualistic interaction with sea anemones, which triggered the adaptive radiation of the clade. Within clownfishes, the "skunk complex" is particularly interesting. Besides ecological speciation, interspecific gene flow and hybrid speciation are thought to have shaped the evolution of the group. We investigated the mechanisms characterizing the diversification of this complex. By taking advantage of their disjunct geographical distribution, we obtained whole-genome data of sympatric and allopatric populations of the three main species of the complex (Amphiprion akallopisos, A. perideraion and A. sandaracinos). We examined population structure, genomic divergence and introgression signals and performed demographic modelling to identify the most realistic diversification scenario. We excluded scenarios of strict isolation or hybrid origin of A. sandaracinos. We discovered moderate gene flow from A. perideraion to the ancestor of A. akallopisos + A. sandaracinos and weak gene flow between the species in the Indo-Australian Archipelago throughout the diversification of the group. We identified introgressed regions in A. sandaracinos and detected in A. perideraion two large regions of high divergence from the two other species. While we found that gene flow has occurred throughout the species' diversification, we also observed that recent admixture was less pervasive than initially thought, suggesting a role of host repartition or behavioural barriers in maintaining the genetic identity of the species in sympatry.
Collapse
Affiliation(s)
- Anna Marcionetti
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland
| | - Joris A M Bertrand
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland
- Laboratoire Génome et Développement Des Plantes (UMR 5096 UPVD/CNRS), University of Perpignan via Domitia, Perpignan, France
| | - Fabio Cortesi
- School of the Environment and Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Giulia F A Donati
- EAWAG Swiss Federal Institute of Aquatic Science & Technology, Dübendorf, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Sara Heim
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland
| | - Filip Huyghe
- Marine Biology - Ecology, Evolution and Genetics, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Brussels, Belgium
| | - Marc Kochzius
- Marine Biology - Ecology, Evolution and Genetics, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Brussels, Belgium
| | - Loïc Pellissier
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
- Ecosystems and Landscape Evolution, Department of Environmental System Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich, Switzerland
| | - Nicolas Salamin
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
2
|
Musher LJ, Del-Rio G, Marcondes RS, Brumfield RT, Bravo GA, Thom G. Geogenomic Predictors of Genetree Heterogeneity Explain Phylogeographic and Introgression History: A Case Study in an Amazonian Bird (Thamnophilus aethiops). Syst Biol 2024; 73:36-52. [PMID: 37804132 DOI: 10.1093/sysbio/syad061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 09/14/2023] [Accepted: 10/04/2023] [Indexed: 10/08/2023] Open
Abstract
Can knowledge about genome architecture inform biogeographic and phylogenetic inference? Selection, drift, recombination, and gene flow interact to produce a genomic landscape of divergence wherein patterns of differentiation and genealogy vary nonrandomly across the genomes of diverging populations. For instance, genealogical patterns that arise due to gene flow should be more likely to occur on smaller chromosomes, which experience high recombination, whereas those tracking histories of geographic isolation (reduced gene flow caused by a barrier) and divergence should be more likely to occur on larger and sex chromosomes. In Amazonia, populations of many bird species diverge and introgress across rivers, resulting in reticulated genomic signals. Herein, we used reduced representation genomic data to disentangle the evolutionary history of 4 populations of an Amazonian antbird, Thamnophilus aethiops, whose biogeographic history was associated with the dynamic evolution of the Madeira River Basin. Specifically, we evaluate whether a large river capture event ca. 200 Ka, gave rise to reticulated genealogies in the genome by making spatially explicit predictions about isolation and gene flow based on knowledge about genomic processes. We first estimated chromosome-level phylogenies and recovered 2 primary topologies across the genome. The first topology (T1) was most consistent with predictions about population divergence and was recovered for the Z-chromosome. The second (T2), was consistent with predictions about gene flow upon secondary contact. To evaluate support for these topologies, we trained a convolutional neural network to classify our data into alternative diversification models and estimate demographic parameters. The best-fit model was concordant with T1 and included gene flow between non-sister taxa. Finally, we modeled levels of divergence and introgression as functions of chromosome length and found that smaller chromosomes experienced higher gene flow. Given that (1) genetrees supporting T2 were more likely to occur on smaller chromosomes and (2) we found lower levels of introgression on larger chromosomes (and especially the Z-chromosome), we argue that T1 represents the history of population divergence across rivers and T2 the history of secondary contact due to barrier loss. Our results suggest that a significant portion of genomic heterogeneity arises due to extrinsic biogeographic processes such as river capture interacting with intrinsic processes associated with genome architecture. Future phylogeographic studies would benefit from accounting for genomic processes, as different parts of the genome reveal contrasting, albeit complementary histories, all of which are relevant for disentangling the intricate geogenomic mechanisms of biotic diversification. [Amazonia; biogeography; demographic modeling; gene flow; gene tree; genome architecture; geogenomics; introgression; linked selection; neural network; phylogenomic; phylogeography; reproductive isolation; speciation; species tree.].
Collapse
Affiliation(s)
- Lukas J Musher
- Department of Ornithology, The Academy of Natural Sciences of Drexel University, Philadelphia, PA 19103, USA
- Department of Ornithology, American Museum of Natural History, New York, NY 10024, USA
| | - Glaucia Del-Rio
- Cornell Laboratory of Ornithology and Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Rafael S Marcondes
- Department of Biology and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Robb T Brumfield
- Department of Biology and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Gustavo A Bravo
- Sección de Ornitología, Colecciones Biológicas, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Claustro de San Agustín, Villa de Leyva, Boyacá 111311, Colombia
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Gregory Thom
- Department of Biology and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
| |
Collapse
|
3
|
Yang Z, Liang L, Xiang W, Wang L, Ma Q, Wang Z. Conservation genomics provides insights into genetic resilience and adaptation of the endangered Chinese hazelnut, Corylus chinensis. PLANT DIVERSITY 2024; 46:294-308. [PMID: 38798732 PMCID: PMC11119545 DOI: 10.1016/j.pld.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/23/2024] [Accepted: 03/25/2024] [Indexed: 05/29/2024]
Abstract
Global climate change has increased concerns regarding biodiversity loss. However, many key conservation issues still required further research, including demographic history, deleterious mutation load, adaptive evolution, and putative introgression. Here we generated the first chromosome-level genome of the endangered Chinese hazelnut, Corylus chinensis, and compared the genomic signatures with its sympatric widespread C. kwechowensis-C. yunnanensis complex. We found large genome rearrangements across all Corylus species and identified species-specific expanded gene families that may be involved in adaptation. Population genomics revealed that both C. chinensis and the C. kwechowensis-C. yunnanensis complex had diverged into two genetic lineages, forming a consistent pattern of southwestern-northern differentiation. Population size of the narrow southwestern lineages of both species have decreased continuously since the late Miocene, whereas the widespread northern lineages have remained stable (C. chinensis) or have even recovered from population bottlenecks (C. kwechowensis-C. yunnanensis complex) during the Quaternary. Compared with C. kwechowensis-C. yunnanensis complex, C. chinensis showed significantly lower genomic diversity and higher inbreeding level. However, C. chinensis carried significantly fewer deleterious mutations than C. kwechowensis-C. yunnanensis complex, as more effective purging selection reduced the accumulation of homozygous variants. We also detected signals of positive selection and adaptive introgression in different lineages, which facilitated the accumulation of favorable variants and formation of local adaptation. Hence, both types of selection and exogenous introgression could have mitigated inbreeding and facilitated survival and persistence of C. chinensis. Overall, our study provides critical insights into lineage differentiation, local adaptation, and the potential for future recovery of endangered trees.
Collapse
Affiliation(s)
- Zhen Yang
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Lisong Liang
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Weibo Xiang
- National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, China Three Gorges Corporation, Beijing 100083, China
- Rare Plants Research Institute of Yangtze River, China Three Gorges Corporation, Yichang 443133, China
| | - Lujun Wang
- Research Institute of Economic Forest Cultivation and Processing, Anhui Academy of Forestry, Hefei 230031, China
| | - Qinghua Ma
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Zhaoshan Wang
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| |
Collapse
|
4
|
Dai X, Xiang S, Zhang Y, Yang S, Hu Q, Wu Z, Zhou T, Xiang J, Chen G, Tan X, Wang J, Ding J. Genomic evidence for evolutionary history and local adaptation of two endemic apricots: Prunus hongpingensis and P. zhengheensis. HORTICULTURE RESEARCH 2024; 11:uhad215. [PMID: 38689695 PMCID: PMC11059793 DOI: 10.1093/hr/uhad215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 10/16/2023] [Indexed: 05/02/2024]
Abstract
Apricot, belonging to the Armeniaca section of Rosaceae, is one of the economically important crop fruits that has been extensively cultivated. The natural wild apricots offer valuable genetic resources for crop improvement. However, some of them are endemic, with small populations, and are even at risk of extinction. In this study we unveil chromosome-level genome assemblies for two southern China endemic apricots, Prunus hongpingensis (PHP) and P. zhengheensis (PZH). We also characterize their evolutionary history and the genomic basis of their local adaptation using whole-genome resequencing data. Our findings reveal that PHP and PZH are closely related to Prunus armeniaca and form a distinct lineage. Both species experienced a decline in effective population size following the Last Glacial Maximum (LGM), which likely contributed to their current small population sizes. Despite the observed decrease in genetic diversity and heterozygosity, we do not observe an increased accumulation of deleterious mutations in these two endemic apricots. This is likely due to the combined effects of a low inbreeding coefficient and strong purifying selection. Furthermore, we identify a set of genes that have undergone positive selection and are associated with local environmental adaptation in PHP and PZH, respectively. These candidate genes can serve as valuable genetic resources for targeted breeding and improvement of cultivated apricots. Overall, our study not only enriches our comprehension of the evolutionary history of apricot species but also offers crucial insights for the conservation and future breeding of other endemic species amidst rapid climate changes.
Collapse
Affiliation(s)
- Xiaokang Dai
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Hubei Hongshan Laboratory, Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Songzhu Xiang
- Shennongjia Academy of Forestry, 442499, Shennongjia Forestry District, Hubei, China
| | - Yulin Zhang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, China
| | - Siting Yang
- Shennongjia Academy of Forestry, 442499, Shennongjia Forestry District, Hubei, China
| | - Qianqian Hu
- Shennongjia Academy of Forestry, 442499, Shennongjia Forestry District, Hubei, China
| | - Zhihao Wu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Hubei Hongshan Laboratory, Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Tingting Zhou
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Hubei Hongshan Laboratory, Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Jingsong Xiang
- Shennongjia Academy of Forestry, 442499, Shennongjia Forestry District, Hubei, China
| | - Gongyou Chen
- Shennongjia Academy of Forestry, 442499, Shennongjia Forestry District, Hubei, China
| | - Xiaohua Tan
- Shennongjia Academy of Forestry, 442499, Shennongjia Forestry District, Hubei, China
| | - Jing Wang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, China
| | - Jihua Ding
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Hubei Hongshan Laboratory, Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| |
Collapse
|
5
|
Dumont BL, Gatti DM, Ballinger MA, Lin D, Phifer-Rixey M, Sheehan MJ, Suzuki TA, Wooldridge LK, Frempong HO, Lawal RA, Churchill GA, Lutz C, Rosenthal N, White JK, Nachman MW. Into the Wild: A novel wild-derived inbred strain resource expands the genomic and phenotypic diversity of laboratory mouse models. PLoS Genet 2024; 20:e1011228. [PMID: 38598567 PMCID: PMC11034653 DOI: 10.1371/journal.pgen.1011228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/22/2024] [Accepted: 03/18/2024] [Indexed: 04/12/2024] Open
Abstract
The laboratory mouse has served as the premier animal model system for both basic and preclinical investigations for over a century. However, laboratory mice capture only a subset of the genetic variation found in wild mouse populations, ultimately limiting the potential of classical inbred strains to uncover phenotype-associated variants and pathways. Wild mouse populations are reservoirs of genetic diversity that could facilitate the discovery of new functional and disease-associated alleles, but the scarcity of commercially available, well-characterized wild mouse strains limits their broader adoption in biomedical research. To overcome this barrier, we have recently developed, sequenced, and phenotyped a set of 11 inbred strains derived from wild-caught Mus musculus domesticus. Each of these "Nachman strains" immortalizes a unique wild haplotype sampled from one of five environmentally distinct locations across North and South America. Whole genome sequence analysis reveals that each strain carries between 4.73-6.54 million single nucleotide differences relative to the GRCm39 mouse reference, with 42.5% of variants in the Nachman strain genomes absent from current classical inbred mouse strain panels. We phenotyped the Nachman strains on a customized pipeline to assess the scope of disease-relevant neurobehavioral, biochemical, physiological, metabolic, and morphological trait variation. The Nachman strains exhibit significant inter-strain variation in >90% of 1119 surveyed traits and expand the range of phenotypic diversity captured in classical inbred strain panels. These novel wild-derived inbred mouse strain resources are set to empower new discoveries in both basic and preclinical research.
Collapse
Affiliation(s)
- Beth L. Dumont
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
- Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
- Graduate School of Biomedical Science and Engineering, The University of Maine, Orono, Maine, United States of America
| | - Daniel M. Gatti
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Mallory A. Ballinger
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, United States of America
| | - Dana Lin
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Megan Phifer-Rixey
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Michael J. Sheehan
- Department of Neurobiology and Behavior, Cornell University, Ithaca, New York, United States of America
| | - Taichi A. Suzuki
- College of Health Solutions and Biodesign Center for Health Through Microbiomes, Arizona State University, Tempe, Arizona, United States of America
| | - Lydia K. Wooldridge
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Hilda Opoku Frempong
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
- Graduate School of Biomedical Science and Engineering, The University of Maine, Orono, Maine, United States of America
| | - Raman Akinyanju Lawal
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Gary A. Churchill
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
- Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
- Graduate School of Biomedical Science and Engineering, The University of Maine, Orono, Maine, United States of America
| | - Cathleen Lutz
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Nadia Rosenthal
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
- Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
- Graduate School of Biomedical Science and Engineering, The University of Maine, Orono, Maine, United States of America
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Jacqueline K. White
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Michael W. Nachman
- Department of Integrative Biology, Museum of Vertebrate Zoology, and Center for Computational Biology, University of California, Berkeley, Berkeley, California, United States of America
| |
Collapse
|
6
|
Zhao X, Wen J, Zhang X, Zhang J, Zhu T, Wang H, Yang W, Cao G, Xiong W, Liu Y, Qu C, Ning Z, Qu L. Significant genomic introgression from grey junglefowl (Gallus sonneratii) to domestic chickens (Gallus gallus domesticus). J Anim Sci Biotechnol 2024; 15:45. [PMID: 38556896 PMCID: PMC10983685 DOI: 10.1186/s40104-024-01006-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/31/2024] [Indexed: 04/02/2024] Open
Abstract
BACKGROUND Chicken is one of the most numerous and widely distributed species around the world, and many studies support the multiple ancestral origins of domestic chickens. The research regarding the yellow skin phenotype in domestic chickens (regulated by BCO2) likely originating from the grey junglefowl serves as crucial evidence for demonstrating the multiple origins of chickens. However, beyond the BCO2 gene region, much remains unknown about the introgression from the grey junglefowl into domestic chickens. Therefore, in this study, based on whole-genome data of 149 samples including 4 species of wild junglefowls and 13 local domestic chicken breeds, we explored the introgression events from the grey junglefowl to domestic chickens. RESULTS We successfully detected introgression regions besides BCO2, including two associated with growth trait (IGFBP2 and TKT), one associated with angiogenesis (TIMP3) and two members of the heat shock protein family (HSPB2 and CRYAB). Our findings suggest that the introgression from the grey junglefowl may impact the growth performance of chickens. Furthermore, we revealed introgression events from grey junglefowl at the BCO2 region in multiple domestic chicken breeds, indicating a phenomenon where the yellow skin phenotype likely underwent strong selection and was retained. Additionally, our haplotype analysis shed light on BCO2 introgression event from different sources of grey junglefowl into domestic chickens, possibly suggesting multiple genetic flows between the grey junglefowl and domestic chickens. CONCLUSIONS In summary, our findings provide evidences of the grey junglefowl contributing to the genetic diversity of domestic chickens, laying the foundation for a deeper understanding of the genetic composition within domestic chickens, and offering new perspectives on the impact of introgression on domestic chickens.
Collapse
Affiliation(s)
- Xiurong Zhao
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Junhui Wen
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xinye Zhang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jinxin Zhang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Tao Zhu
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Huie Wang
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production and Construction Corps, Tarim University, Alar, 843300, China
| | - Weifang Yang
- Beijing Municipal General Station of Animal Science, Beijing, 100107, China
| | - Guomin Cao
- Animal husbandry station of Fangchenggang, Fangchenggang, Guangxi Province, 538001, China
| | - Wenjie Xiong
- Animal Disease Prevention and Control Center of Fangchenggang, Fangchenggang, Guangxi Province, 538001, China
| | - Yong Liu
- Beijing Agricultural Effect Poultry Industry Co., Ltd., Beijing, 101100, China
| | - Changqing Qu
- Engineering Technology Research Center of Anti-aging Chinese Herbal Medicine of Anhui Province, Fuyang Normal University, Fuyang, Anhui, 236037, China
| | - Zhonghua Ning
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Lujiang Qu
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
7
|
Rossi M, Hausmann AE, Alcami P, Moest M, Roussou R, Van Belleghem SM, Wright DS, Kuo CY, Lozano-Urrego D, Maulana A, Melo-Flórez L, Rueda-Muñoz G, McMahon S, Linares M, Osman C, McMillan WO, Pardo-Diaz C, Salazar C, Merrill RM. Adaptive introgression of a visual preference gene. Science 2024; 383:1368-1373. [PMID: 38513020 DOI: 10.1126/science.adj9201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/30/2024] [Indexed: 03/23/2024]
Abstract
Visual preferences are important drivers of mate choice and sexual selection, but little is known of how they evolve at the genetic level. In this study, we took advantage of the diversity of bright warning patterns displayed by Heliconius butterflies, which are also used during mate choice. Combining behavioral, population genomic, and expression analyses, we show that two Heliconius species have evolved the same preferences for red patterns by exchanging genetic material through hybridization. Neural expression of regucalcin1 correlates with visual preference across populations, and disruption of regucalcin1 with CRISPR-Cas9 impairs courtship toward conspecific females, providing a direct link between gene and behavior. Our results support a role for hybridization during behavioral evolution and show how visually guided behaviors contributing to adaptation and speciation are encoded within the genome.
Collapse
Affiliation(s)
- Matteo Rossi
- Faculty of Biology, LMU, Munich, Germany
- Smithsonian Tropical Research Institute, Gamboa, Panama
| | | | | | - Markus Moest
- Department of Ecology and Research Department for Limnology, Mondsee, University of Innsbruck, Innsbruck, Austria
| | | | | | | | - Chi-Yun Kuo
- Faculty of Biology, LMU, Munich, Germany
- Smithsonian Tropical Research Institute, Gamboa, Panama
| | - Daniela Lozano-Urrego
- Faculty of Biology, LMU, Munich, Germany
- Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | | | - Lina Melo-Flórez
- Faculty of Biology, LMU, Munich, Germany
- Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Geraldine Rueda-Muñoz
- Faculty of Biology, LMU, Munich, Germany
- Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | | | - Mauricio Linares
- Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | | | | | | | - Camilo Salazar
- Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Richard M Merrill
- Faculty of Biology, LMU, Munich, Germany
- Smithsonian Tropical Research Institute, Gamboa, Panama
| |
Collapse
|
8
|
Sianta SA, Moeller DA, Brandvain Y. The extent of introgression between incipient Clarkia species is determined by temporal environmental variation and mating system. Proc Natl Acad Sci U S A 2024; 121:e2316008121. [PMID: 38466849 PMCID: PMC10963018 DOI: 10.1073/pnas.2316008121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 02/07/2024] [Indexed: 03/13/2024] Open
Abstract
Introgression is pervasive across the tree of life but varies across taxa, geography, and genomic regions. However, the factors modulating this variation and how they may be affected by global change are not well understood. Here, we used 200 genomes and a 15-y site-specific environmental dataset to investigate the effects of environmental variation and mating system divergence on the magnitude of introgression between a recently diverged outcrosser-selfer pair of annual plants in the genus Clarkia. These sister taxa diverged very recently and subsequently came into secondary sympatry where they form replicated contact zones. Consistent with observations of other outcrosser-selfer pairs, we found that introgression was asymmetric between taxa, with substantially more introgression from the selfer to the outcrosser. This asymmetry was caused by a bias in the direction of initial F1 hybrid formation and subsequent backcrossing. We also found extensive variation in the outcrosser's admixture proportion among contact zones, which was predicted nearly entirely by interannual variance in spring precipitation. Greater fluctuations in spring precipitation resulted in higher admixture proportions, likely mediated by the effects of spring precipitation on the expression of traits that determine premating reproductive isolation. Climate-driven hybridization dynamics may be particularly affected by global change, potentially reshaping species boundaries and adaptation to novel environments.
Collapse
Affiliation(s)
- Shelley A. Sianta
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN55108
| | - David A. Moeller
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN55108
| | - Yaniv Brandvain
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN55108
| |
Collapse
|
9
|
Ward CM, Onetto CA, Van Den Heuvel S, Cuijvers KM, Hale LJ, Borneman AR. Recombination, admixture and genome instability shape the genomic landscape of Saccharomyces cerevisiae derived from spontaneous grape ferments. PLoS Genet 2024; 20:e1011223. [PMID: 38517929 PMCID: PMC10990190 DOI: 10.1371/journal.pgen.1011223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 04/03/2024] [Accepted: 03/12/2024] [Indexed: 03/24/2024] Open
Abstract
Cultural exchange of fermentation techniques has driven the spread of Saccharomyces cerevisiae across the globe, establishing natural populations in many countries. Despite this, Oceania is thought to lack native populations of S. cerevisiae, only being introduced after colonisation. Here we investigate the genomic landscape of 411 S. cerevisiae isolated from spontaneous grape fermentations in Australia across multiple locations, years, and grape cultivars. Spontaneous fermentations contained highly recombined mosaic strains that exhibited high levels of genome instability. Assigning genomic windows to putative ancestral origin revealed that few closely related starter lineages have come to dominate the genetic landscape, contributing most of the genetic variation. Fine-scale phylogenetic analysis of loci not observed in strains of commercial wine origin identified widespread admixture with European derived beer yeast along with three independent admixture events from potentially endemic Oceanic lineages that was associated with genome instability. Finally, we investigated Australian ecological niches for basal isolates, identifying phylogenetically distinct S. cerevisiae of non-European, non-domesticated origin associated with admixture loci. Our results illustrate the effect commercial use of microbes may have on local microorganism genetic diversity and demonstrates the presence of non-domesticated, potentially endemic lineages of S. cerevisiae in Australian niches that are actively admixing.
Collapse
Affiliation(s)
- Chris M. Ward
- Australian Wine Research Institute, Urrbrae, South Australia, Australia
| | - Cristobal A. Onetto
- Australian Wine Research Institute, Urrbrae, South Australia, Australia
- University of Adelaide, Adelaide, South Australia, Australia
| | | | | | - Laura J. Hale
- Australian Wine Research Institute, Urrbrae, South Australia, Australia
| | - Anthony R. Borneman
- Australian Wine Research Institute, Urrbrae, South Australia, Australia
- University of Adelaide, Adelaide, South Australia, Australia
| |
Collapse
|
10
|
Jiang Z, Zang W, Ericson PGP, Song G, Wu S, Feng S, Drovetski SV, Liu G, Zhang D, Saitoh T, Alström P, Edwards SV, Lei F, Qu Y. Gene flow and an anomaly zone complicate phylogenomic inference in a rapidly radiated avian family (Prunellidae). BMC Biol 2024; 22:49. [PMID: 38413944 PMCID: PMC10900574 DOI: 10.1186/s12915-024-01848-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Resolving the phylogeny of rapidly radiating lineages presents a challenge when building the Tree of Life. An Old World avian family Prunellidae (Accentors) comprises twelve species that rapidly diversified at the Pliocene-Pleistocene boundary. RESULTS Here we investigate the phylogenetic relationships of all species of Prunellidae using a chromosome-level de novo assembly of Prunella strophiata and 36 high-coverage resequenced genomes. We use homologous alignments of thousands of exonic and intronic loci to build the coalescent and concatenated phylogenies and recover four different species trees. Topology tests show a large degree of gene tree-species tree discordance but only 40-54% of intronic gene trees and 36-75% of exonic genic trees can be explained by incomplete lineage sorting and gene tree estimation errors. Estimated branch lengths for three successive internal branches in the inferred species trees suggest the existence of an empirical anomaly zone. The most common topology recovered for species in this anomaly zone was not similar to any coalescent or concatenated inference phylogenies, suggesting presence of anomalous gene trees. However, this interpretation is complicated by the presence of gene flow because extensive introgression was detected among these species. When exploring tree topology distributions, introgression, and regional variation in recombination rate, we find that many autosomal regions contain signatures of introgression and thus may mislead phylogenetic inference. Conversely, the phylogenetic signal is concentrated to regions with low-recombination rate, such as the Z chromosome, which are also more resistant to interspecific introgression. CONCLUSIONS Collectively, our results suggest that phylogenomic inference should consider the underlying genomic architecture to maximize the consistency of phylogenomic signal.
Collapse
Affiliation(s)
- Zhiyong Jiang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wenqing Zang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, Stockholm, SE-104 05, Sweden
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Shaoyuan Wu
- Jiangsu International Joint Center of Genomics, Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu, China
| | - Shaohong Feng
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou, 311121, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, 314102, China
| | - Sergei V Drovetski
- National Museum of Natural History, Smithsonian Institution, Washington, DC, 20004, USA
- Present address: U.S. Geological Survey, Eastern Ecological Science Center at Patuxent Research Refuge, Laurel, MD, 20708, USA
| | - Gang Liu
- Chinese Academy of Forestry, Institute of Ecological Conservation and Restoration, Beijing, 100091, China
| | - Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Takema Saitoh
- Yamashina Institute for Ornithology, Abiko, Chiba, Japan
| | - Per Alström
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, 752 36, Uppsala, Sweden
| | - Scott V Edwards
- Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, Stockholm, SE-104 05, Sweden.
| |
Collapse
|
11
|
Foley NM, Harris AJ, Bredemeyer KR, Ruedi M, Puechmaille SJ, Teeling EC, Criscitiello MF, Murphy WJ. Karyotypic stasis and swarming influenced the evolution of viral tolerance in a species-rich bat radiation. CELL GENOMICS 2024; 4:100482. [PMID: 38237599 PMCID: PMC10879000 DOI: 10.1016/j.xgen.2023.100482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 09/17/2023] [Accepted: 12/10/2023] [Indexed: 02/17/2024]
Abstract
The emergence of COVID-19 and severe acute respiratory syndrome (SARS) has prioritized understanding bats' viral tolerance. Myotis bats are exceptionally species rich and have evolved viral tolerance. They also exhibit swarming, a cryptic behavior where large, multi-species assemblages gather for mating, which has been hypothesized to promote interspecific hybridization. To resolve the coevolution of genome architecture and their unusual antiviral tolerance, we undertook a phylogenomic analysis of 60 Old World Myotis genomes. We demonstrate an extensive history of introgressive hybridization that has replaced the species phylogeny across 17%-93% of the genome except for pericentromeric regions of macrochromosomes. Introgression tracts were enriched on microchromosome regions containing key antiviral pathway genes overexpressed during viral challenge experiments. Together, these results suggest that the unusual Myotis karyotype may have evolved to selectively position immune-related genes in high recombining genomic regions prone to introgression of divergent alleles, including a diversity of interleukin loci responsible for the release of pro-inflammatory cytokines.
Collapse
Affiliation(s)
- Nicole M Foley
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.
| | - Andrew J Harris
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA; Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - Kevin R Bredemeyer
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA; Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - Manuel Ruedi
- Department of Mammalogy and Ornithology, Natural History Museum of Geneva, Route de Malagnou 1, BP 6434, 1211 Geneva 6, Switzerland
| | - Sebastien J Puechmaille
- Institut des Sciences de l'Évolution, Montpellier (ISEM), Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France; Institut Universitaire de France, Paris, France
| | - Emma C Teeling
- School of Biology and Environmental, Science, Science Centre West, University College Dublin, Belfield, Ireland
| | - Michael F Criscitiello
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA; Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843, USA
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA; Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA.
| |
Collapse
|
12
|
Guo N, Wang S, Wang T, Duan M, Zong M, Miao L, Han S, Wang G, Liu X, Zhang D, Jiao C, Xu H, Chen L, Fei Z, Li J, Liu F. A graph-based pan-genome of Brassica oleracea provides new insights into its domestication and morphotype diversification. PLANT COMMUNICATIONS 2024; 5:100791. [PMID: 38168637 PMCID: PMC10873912 DOI: 10.1016/j.xplc.2023.100791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/08/2023] [Accepted: 12/30/2023] [Indexed: 01/05/2024]
Abstract
The domestication of Brassica oleracea has resulted in diverse morphological types with distinct patterns of organ development. Here we report a graph-based pan-genome of B. oleracea constructed from high-quality genome assemblies of different morphotypes. The pan-genome harbors over 200 structural variant hotspot regions enriched in auxin- and flowering-related genes. Population genomic analyses revealed that early domestication of B. oleracea focused on leaf or stem development. Gene flows resulting from agricultural practices and variety improvement were detected among different morphotypes. Selective-sweep and pan-genome analyses identified an auxin-responsive small auxin up-regulated RNA gene and a CLAVATA3/ESR-RELATED family gene as crucial players in leaf-stem differentiation during the early stage of B. oleracea domestication and the BoKAN1 gene as instrumental in shaping the leafy heads of cabbage and Brussels sprouts. Our pan-genome and functional analyses further revealed that variations in the BoFLC2 gene play key roles in the divergence of vernalization and flowering characteristics among different morphotypes, and variations in the first intron of BoFLC3 are involved in fine-tuning the flowering process in cauliflower. This study provides a comprehensive understanding of the pan-genome of B. oleracea and sheds light on the domestication and differential organ development of this globally important crop species.
Collapse
Affiliation(s)
- Ning Guo
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Shenyun Wang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Vegetable Research Institute, Jiangsu Academy of Agricultural Science, Nanjing, Jiangsu, China
| | - Tianyi Wang
- Smartgenomics Technology Institute, Tianjin 301700, China
| | - Mengmeng Duan
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Mei Zong
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Liming Miao
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Shuo Han
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Guixiang Wang
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Xin Liu
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Deshuang Zhang
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Chengzhi Jiao
- Smartgenomics Technology Institute, Tianjin 301700, China
| | - Hongwei Xu
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Liyang Chen
- Smartgenomics Technology Institute, Tianjin 301700, China.
| | | | - Jianbin Li
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Vegetable Research Institute, Jiangsu Academy of Agricultural Science, Nanjing, Jiangsu, China.
| | - Fan Liu
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China.
| |
Collapse
|
13
|
Feng X, Merilä J, Löytynoja A. Secondary Contact, Introgressive Hybridization, and Genome Stabilization in Sticklebacks. Mol Biol Evol 2024; 41:msae031. [PMID: 38366566 PMCID: PMC10903534 DOI: 10.1093/molbev/msae031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/20/2023] [Accepted: 02/09/2024] [Indexed: 02/18/2024] Open
Abstract
Advances in genomic studies have revealed that hybridization in nature is pervasive and raised questions about the dynamics of different genetic and evolutionary factors following the initial hybridization event. While recent research has proposed that the genomic outcomes of hybridization might be predictable to some extent, many uncertainties remain. With comprehensive whole-genome sequence data, we investigated the genetic introgression between 2 divergent lineages of 9-spined sticklebacks (Pungitius pungitius) in the Baltic Sea. We found that the intensity and direction of selection on the introgressed variation has varied across different genomic elements: while functionally important regions displayed reduced rates of introgression, promoter regions showed enrichment. Despite the general trend of negative selection, we identified specific genomic regions that were enriched for introgressed variants, and within these regions, we detected footprints of selection, indicating adaptive introgression. Geographically, we found the selection against the functional changes to be strongest in the vicinity of the secondary contact zone and weaken as a function of distance from the initial contact. Altogether, the results suggest that the stabilization of introgressed variation in the genomes is a complex, multistage process involving both negative and positive selection. In spite of the predominance of negative selection against introgressed variants, we also found evidence for adaptive introgression variants likely associated with adaptation to Baltic Sea environmental conditions.
Collapse
Affiliation(s)
- Xueyun Feng
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki 00014, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Juha Merilä
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki 00014, Finland
- Area of Ecology and Biodiversity, The School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Ari Löytynoja
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| |
Collapse
|
14
|
Dalapicolla J, Rodrigues do Prado J, Lacey Knowles L, Reis Percequillo A. Phylogenomics and species delimitation of an abundant and little-studied Amazonian forest spiny rat. Mol Phylogenet Evol 2024; 191:107992. [PMID: 38092321 DOI: 10.1016/j.ympev.2023.107992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 12/01/2023] [Accepted: 12/09/2023] [Indexed: 12/21/2023]
Abstract
Species delimitation studies based on integrating different datasets such as genomic, morphometric, and cytogenetics data are rare in studies focused on Neotropical rodents. As a consequence, the evolutionary history of most of these genera remains poorly understood. Proechimys is a highly diverse and widely distributed genus of Neotropical spiny rats with unique traits like multiple sympatry, micro-habitat segregation, and fuzzy species limits. Here, we applied RAD-Seq to infer the phylogenetic relationships, estimate the species boundaries, and estimate the divergence times for Proechimys, one of the most common and least studied small mammals in the Amazon. We tested whether inferred lineages in the phylogenetic trees could be considered distinct species based on the genomic dataset and morphometric data. Analyses revealed the genus is not monophyletic, with Proechimys hoplomyoides sister to a group of Hoplomys gymnurus + all other Proechimys species, contesting the generic status of Hoplomys. There are five main clades in Proechimys stricto sensu (excluding H. gymnurus and P. hoplomyoides). Species delimitation analyses supported 25 species within the genus Proechimys. The five main clades in Proechimys stricto sensu also showed similar ages for their origins, and two rapid diversification events were identified in the Early Pliocene and in the Early Pleistocene. Most cases of sympatry in Proechimys occur among species from the different main clades, and although Proechimys is an inhabitant of the Amazon, three species occupied the Cerrado biome during the Pleistocene. We could associate available nominal taxon, cytogenetics information, and DNA sequences in Genbank to most of the 25 species we hypothesized from our delimitation analyses. Based on our analyses, we estimate that eight forms represent putative new species that need a taxonomic revision.
Collapse
Affiliation(s)
- Jeronymo Dalapicolla
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil; Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, São Paulo, Brazil; Instituto Tecnológico Vale, Belém, Pará, Brazil.
| | | | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
| | - Alexandre Reis Percequillo
- Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, São Paulo, Brazil
| |
Collapse
|
15
|
van der Valk T, Jensen A, Caillaud D, Guschanski K. Comparative genomic analyses provide new insights into evolutionary history and conservation genomics of gorillas. BMC Ecol Evol 2024; 24:14. [PMID: 38273244 PMCID: PMC10811819 DOI: 10.1186/s12862-023-02195-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 12/22/2023] [Indexed: 01/27/2024] Open
Abstract
Genome sequencing is a powerful tool to understand species evolutionary history, uncover genes under selection, which could be informative of local adaptation, and infer measures of genetic diversity, inbreeding and mutational load that could be used to inform conservation efforts. Gorillas, critically endangered primates, have received considerable attention and with the recently sequenced Bwindi mountain gorilla population, genomic data is now available from all gorilla subspecies and both mountain gorilla populations. Here, we reanalysed this rich dataset with a focus on evolutionary history, local adaptation and genomic parameters relevant for conservation. We estimate a recent split between western and eastern gorillas of 150,000-180,000 years ago, with gene flow around 20,000 years ago, primarily between the Cross River and Grauer's gorilla subspecies. This gene flow event likely obscures evolutionary relationships within eastern gorillas: after excluding putatively introgressed genomic regions, we uncover a sister relationship between Virunga mountain gorillas and Grauer's gorillas to the exclusion of Bwindi mountain gorillas. This makes mountain gorillas paraphyletic. Eastern gorillas are less genetically diverse and more inbred than western gorillas, yet we detected lower genetic load in the eastern species. Analyses of indels fit remarkably well with differences in genetic diversity across gorilla taxa as recovered with nucleotide diversity measures. We also identified genes under selection and unique gene variants specific for each gorilla subspecies, encoding, among others, traits involved in immunity, diet, muscular development, hair morphology and behavior. The presence of this functional variation suggests that the subspecies may be locally adapted. In conclusion, using extensive genomic resources we provide a comprehensive overview of gorilla genomic diversity, including a so-far understudied Bwindi mountain gorilla population, identify putative genes involved in local adaptation, and detect population-specific gene flow across gorilla species.
Collapse
Affiliation(s)
- Tom van der Valk
- Centre for Palaeogenetics, Stockholm, Sweden.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
- SciLifeLab, Stockholm, Sweden.
- Department of Zoology, Stockholm University, Stockholm, Sweden.
| | - Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
| | - Damien Caillaud
- Department of Anthropology, University of CA - Davis, Davis, California, USA
| | - Katerina Guschanski
- SciLifeLab, Stockholm, Sweden
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
16
|
Du W, Wang Y, Xie D, Li E, Bai Y, Shang C, Zhang Z. Phylogenomics reveal Populusgonggaensis as a hybrid between P.lasiocarpa and P.cathayana (Salicaceae). PHYTOKEYS 2024; 237:161-177. [PMID: 38298498 PMCID: PMC10829108 DOI: 10.3897/phytokeys.237.103012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 01/01/2024] [Indexed: 02/02/2024]
Abstract
High levels of intra-specific polymorphism and frequent hybridisation make it difficult to define species and correctly apply their scientific names. Populus L. is a challenging genus with plentiful natural and artificial hybrids. This study is a part of the project 'Flora of Pan-Himalaya' and aims to determine the taxonomic identity of P.gonggaensis N. Chao & J.R. He and to find out whether it is of hybrid origin. Whole-genome sequencing data were obtained from 57 samples. The SNP matrix was developed for phylogenetic reconstruction, ABBA-BABA statistics, PCA and ADMIXTURE analysis. The results indicate that P.gonggaensis is a spontaneous hybrid between P.lasiocarpa and P.cathayana. This study points out the importance of SNP data and comprehensive analyses for discovering the potential interspecific hybridisation and clarifies the usage of the name. In addition, the lectotype of P.gonggaensis was designated.
Collapse
Affiliation(s)
- Wenyan Du
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, ChinaBeijing Forestry UniversityBeijingChina
| | - Yachao Wang
- School of Life Science, Fudan University, Shanghai 200433, ChinaFudan UniversityShanghaiChina
| | - Dajun Xie
- Sichuan Academy of Forestry, Chengdu 610000, ChinaSichuan Academy of ForestryChengduChina
| | - Enze Li
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, ChinaBeijing Forestry UniversityBeijingChina
| | - Yuran Bai
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, ChinaBeijing Forestry UniversityBeijingChina
| | - Ce Shang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, ChinaBeijing Forestry UniversityBeijingChina
| | - Zhixiang Zhang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, ChinaBeijing Forestry UniversityBeijingChina
| |
Collapse
|
17
|
Chase MA, Vilcot M, Mugal CF. Evidence that genetic drift not adaptation drives fast-Z and large-Z effects in Ficedula flycatchers. Mol Ecol 2024:e17262. [PMID: 38193599 DOI: 10.1111/mec.17262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 12/01/2023] [Accepted: 12/22/2023] [Indexed: 01/10/2024]
Abstract
The sex chromosomes have been hypothesized to play a key role in driving adaptation and speciation across many taxa. The reason for this is thought to be the hemizygosity of the heteromorphic part of sex chromosomes in the heterogametic sex, which exposes recessive mutations to natural and sexual selection. The exposure of recessive beneficial mutations increases their rate of fixation on the sex chromosomes, which results in a faster rate of evolution. In addition, genetic incompatibilities between sex-linked loci are exposed faster in the genomic background of hybrids of divergent lineages, which makes sex chromosomes contribute disproportionately to reproductive isolation. However, in birds, which show a Z/W sex determination system, the role of adaptation versus genetic drift as the driving force of the faster differentiation of the Z chromosome (fast-Z effect) and the disproportionate role of the Z chromosome in reproductive isolation (large-Z effect) are still debated. Here, we address this debate in the bird genus Ficedula flycatchers based on population-level whole-genome sequencing data of six species. Our analysis provides evidence for both faster lineage sorting and reduced gene flow on the Z chromosome than the autosomes. However, these patterns appear to be driven primarily by the increased role of genetic drift on the Z chromosome, rather than an increased rate of adaptive evolution. Genomic scans of selective sweeps and fixed differences in fact suggest a reduced action of positive selection on the Z chromosome.
Collapse
Affiliation(s)
- Madeline A Chase
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- Swiss Ornithological Institute, Sempach, Switzerland
| | - Maurine Vilcot
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- CEFE, University of Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Carina F Mugal
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- Laboratory of Biometry and Evolutionary Biology, University of Lyon 1, CNRS UMR 5558, Villeurbanne, France
| |
Collapse
|
18
|
Stankowski S, Zagrodzka ZB, Garlovsky MD, Pal A, Shipilina D, Castillo DG, Lifchitz H, Le Moan A, Leder E, Reeve J, Johannesson K, Westram AM, Butlin RK. The genetic basis of a recent transition to live-bearing in marine snails. Science 2024; 383:114-119. [PMID: 38175895 DOI: 10.1126/science.adi2982] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 10/25/2023] [Indexed: 01/06/2024]
Abstract
Key innovations are fundamental to biological diversification, but their genetic basis is poorly understood. A recent transition from egg-laying to live-bearing in marine snails (Littorina spp.) provides the opportunity to study the genetic architecture of an innovation that has evolved repeatedly across animals. Individuals do not cluster by reproductive mode in a genome-wide phylogeny, but local genealogical analysis revealed numerous small genomic regions where all live-bearers carry the same core haplotype. Candidate regions show evidence for live-bearer-specific positive selection and are enriched for genes that are differentially expressed between egg-laying and live-bearing reproductive systems. Ages of selective sweeps suggest that live-bearer-specific alleles accumulated over more than 200,000 generations. Our results suggest that new functions evolve through the recruitment of many alleles rather than in a single evolutionary step.
Collapse
Affiliation(s)
- Sean Stankowski
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
- Department of Ecology and Evolution, University of Sussex, Brighton BN1 9RH, UK
| | - Zuzanna B Zagrodzka
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Martin D Garlovsky
- Department of Applied Zoology, Faculty of Biology, Technische Universität Dresden, 01069 Dresden, Germany
| | - Arka Pal
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
| | - Daria Shipilina
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
- Department of Ecology and Genetics, Program of Evolutionary Biology, Uppsala University, SE-752 36 Uppsala, Sweden
| | | | - Hila Lifchitz
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
| | - Alan Le Moan
- CNRS and Sorbonne Université, Station Biologique de Roscoff, 29680 Roscoff, France
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, 452 96 Strömstad, Sweden
| | - Erica Leder
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, 452 96 Strömstad, Sweden
- Natural History Museum, University of Oslo, 0562 Oslo, Norway
| | - James Reeve
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, 452 96 Strömstad, Sweden
| | - Kerstin Johannesson
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, 452 96 Strömstad, Sweden
| | - Anja M Westram
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
- Faculty of Biosciences and Aquaculture, Nord University, N-8049 Bodø, Norway
| | - Roger K Butlin
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, 452 96 Strömstad, Sweden
| |
Collapse
|
19
|
Thom G, Moreira LR, Batista R, Gehara M, Aleixo A, Smith BT. Genomic Architecture Predicts Tree Topology, Population Structuring, and Demographic History in Amazonian Birds. Genome Biol Evol 2024; 16:evae002. [PMID: 38236173 PMCID: PMC10823491 DOI: 10.1093/gbe/evae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 10/26/2023] [Accepted: 12/12/2023] [Indexed: 01/19/2024] Open
Abstract
Geographic barriers are frequently invoked to explain genetic structuring across the landscape. However, inferences on the spatial and temporal origins of population variation have been largely limited to evolutionary neutral models, ignoring the potential role of natural selection and intrinsic genomic processes known as genomic architecture in producing heterogeneity in differentiation across the genome. To test how variation in genomic characteristics (e.g. recombination rate) impacts our ability to reconstruct general patterns of differentiation between species that cooccur across geographic barriers, we sequenced the whole genomes of multiple bird populations that are distributed across rivers in southeastern Amazonia. We found that phylogenetic relationships within species and demographic parameters varied across the genome in predictable ways. Genetic diversity was positively associated with recombination rate and negatively associated with species tree support. Gene flow was less pervasive in genomic regions of low recombination, making these windows more likely to retain patterns of population structuring that matched the species tree. We further found that approximately a third of the genome showed evidence of selective sweeps and linked selection, skewing genome-wide estimates of effective population sizes and gene flow between populations toward lower values. In sum, we showed that the effects of intrinsic genomic characteristics and selection can be disentangled from neutral processes to elucidate spatial patterns of population differentiation.
Collapse
Affiliation(s)
- Gregory Thom
- Department of Ornithology, American Museum of Natural History, New York, NY, USA
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Lucas Rocha Moreira
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Vertebrate Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Romina Batista
- Programa de Coleções Biológicas, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
- School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Marcelo Gehara
- Department of Earth and Environmental Sciences, Rutgers University, Newark, NJ, USA
| | - Alexandre Aleixo
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
- Department of Environmental Genomics, Instituto Tecnológico Vale, Belém, Brazil
| | - Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, New York, NY, USA
| |
Collapse
|
20
|
Stone BW, Wessinger CA. Ecological Diversification in an Adaptive Radiation of Plants: The Role of De Novo Mutation and Introgression. Mol Biol Evol 2024; 41:msae007. [PMID: 38232726 PMCID: PMC10826641 DOI: 10.1093/molbev/msae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/01/2024] [Accepted: 01/10/2024] [Indexed: 01/19/2024] Open
Abstract
Adaptive radiations are characterized by rapid ecological diversification and speciation events, leading to fuzzy species boundaries between ecologically differentiated species. Adaptive radiations are therefore key systems for understanding how species are formed and maintained, including the role of de novo mutations versus preexisting variation in ecological adaptation and the genome-wide consequences of hybridization events. For example, adaptive introgression, where beneficial alleles are transferred between lineages through hybridization, may fuel diversification in adaptive radiations and facilitate adaptation to new environments. In this study, we employed whole-genome resequencing data to investigate the evolutionary origin of hummingbird-pollinated flowers and to characterize genome-wide patterns of phylogenetic discordance and introgression in Penstemon subgenus Dasanthera, a small and diverse adaptive radiation of plants. We found that magenta hummingbird-adapted flowers have apparently evolved twice from ancestral blue-violet bee-pollinated flowers within this radiation. These shifts in flower color are accompanied by a variety of inactivating mutations to a key anthocyanin pathway enzyme, suggesting that independent de novo loss-of-function mutations underlie the parallel evolution of this trait. Although patterns of introgression and phylogenetic discordance were heterogenous across the genome, a strong effect of gene density suggests that, in general, natural selection opposes introgression and maintains genetic differentiation in gene-rich genomic regions. Our results highlight the importance of both de novo mutation and introgression as sources of evolutionary change and indicate a role for de novo mutation in driving parallel evolution in adaptive radiations.
Collapse
Affiliation(s)
- Benjamin W Stone
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208-3401, USA
| | - Carolyn A Wessinger
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208-3401, USA
| |
Collapse
|
21
|
Stone BW, Wessinger CA. Ecological diversification in an adaptive radiation of plants: the role of de novo mutation and introgression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.01.565185. [PMID: 37961506 PMCID: PMC10635055 DOI: 10.1101/2023.11.01.565185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Adaptive radiations are characterized by rapid ecological diversification and speciation events, leading to fuzzy species boundaries between ecologically differentiated species. Adaptive radiations are therefore key systems for understanding how species are formed and maintained, including the role of de novo mutations vs. pre-existing variation in ecological adaptation and the genome-wide consequences of hybridization events. For example, adaptive introgression, where beneficial alleles are transferred between lineages through hybridization, may fuel diversification in adaptive radiations and facilitate adaptation to new environments. In this study, we employed whole-genome resequencing data to investigate the evolutionary origin of hummingbird-pollinated flowers and to characterize genome-wide patterns of phylogenetic discordance and introgression in Penstemon subgenus Dasanthera, a small and diverse adaptive radiation of plants. We found that magenta hummingbird-adapted flowers have apparently evolved twice from ancestral blue-violet bee-pollinated flowers within this radiation. These shifts in flower color are accompanied by a variety of inactivating mutations to a key anthocyanin pathway enzyme, suggesting that independent de novo loss-of-function mutations underlie parallel evolution of this trait. Although patterns of introgression and phylogenetic discordance were heterogenous across the genome, a strong effect of gene density suggests that, in general, natural selection opposes introgression and maintains genetic differentiation in gene-rich genomic regions. Our results highlight the importance of both de novo mutation and introgression as sources of evolutionary change and indicate a role for de novo mutation in driving parallel evolution in adaptive radiations.
Collapse
Affiliation(s)
- Benjamin W. Stone
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208-3401, USA
| | - Carolyn A. Wessinger
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208-3401, USA
| |
Collapse
|
22
|
Zhang X, Guan J, Zou M, He P, Zhang L, Chen Y, Li W, Wang D, Yu E, Zhong F, Zhu P, Yan X, Xu Y, Luo B, Huang T, Jiang L, Wei P, Peng J. Whole genome sequencing of Crassostrea ariakensis (Mollusca: Ostreidae) and C. hongkongensis expands understandings of stress resistance in sessile oysters. Genomics 2024; 116:110757. [PMID: 38061482 DOI: 10.1016/j.ygeno.2023.110757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/28/2023] [Accepted: 12/04/2023] [Indexed: 12/17/2023]
Abstract
To understand the environmental adaptations among sessile bivalves lacking adaptive immunity, a series of analyses were conducted, with special emphasis on the widely distributed C. ariakensis. Employing Pacbio sequencing and Hi-C technologies, whole genome for each of a C. ariakensis (southern China) and C. hongkongensis individual was generated, with the contig N50 reaching 6.2 and 13.0 Mb, respectively. Each genome harbored over 30,000 protein-coding genes, with approximately half of each genome consisting of repeats. Genome alignment suggested possible introgression between C. gigas and C. ariakensis (northern China), and re-sequencing data corroborated this result and indicated significant gene flow between C. gigas and C. ariakensis. These introgressed candidates, well-represented by genes related to immunity and osmotic pressure, may be associated with environmental stresses. Gene family dynamics modeling suggested immune-related genes were well represented among the expanded genes in C. ariakensis. These outcomes could be attributed to the spread of C. ariakensis.
Collapse
Affiliation(s)
- Xingzhi Zhang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Key Laboratory of Comprehensive Development and Utilization of Aquatic Germplasm Resources of China (Guangxi) and ASEAN (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fisheries Sciences, Nanning 530021, China
| | - Junliang Guan
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Key Laboratory of Comprehensive Development and Utilization of Aquatic Germplasm Resources of China (Guangxi) and ASEAN (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fisheries Sciences, Nanning 530021, China
| | - Ming Zou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Pingping He
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Key Laboratory of Comprehensive Development and Utilization of Aquatic Germplasm Resources of China (Guangxi) and ASEAN (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fisheries Sciences, Nanning 530021, China
| | - Li Zhang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Key Laboratory of Comprehensive Development and Utilization of Aquatic Germplasm Resources of China (Guangxi) and ASEAN (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fisheries Sciences, Nanning 530021, China
| | - Yongxian Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Key Laboratory of Comprehensive Development and Utilization of Aquatic Germplasm Resources of China (Guangxi) and ASEAN (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fisheries Sciences, Nanning 530021, China.
| | - Wei Li
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Key Laboratory of Comprehensive Development and Utilization of Aquatic Germplasm Resources of China (Guangxi) and ASEAN (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fisheries Sciences, Nanning 530021, China
| | - Dapeng Wang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Key Laboratory of Comprehensive Development and Utilization of Aquatic Germplasm Resources of China (Guangxi) and ASEAN (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fisheries Sciences, Nanning 530021, China
| | - Ermeng Yu
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Key Laboratory of Comprehensive Development and Utilization of Aquatic Germplasm Resources of China (Guangxi) and ASEAN (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fisheries Sciences, Nanning 530021, China.
| | | | - Peng Zhu
- Beibu Gulf University, Qinzhou 535000, China
| | - Xueyu Yan
- Beibu Gulf University, Qinzhou 535000, China.
| | - Youhou Xu
- Beibu Gulf University, Qinzhou 535000, China
| | - Bang Luo
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Key Laboratory of Comprehensive Development and Utilization of Aquatic Germplasm Resources of China (Guangxi) and ASEAN (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fisheries Sciences, Nanning 530021, China
| | - Ting Huang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Key Laboratory of Comprehensive Development and Utilization of Aquatic Germplasm Resources of China (Guangxi) and ASEAN (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fisheries Sciences, Nanning 530021, China
| | - Linyuan Jiang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Key Laboratory of Comprehensive Development and Utilization of Aquatic Germplasm Resources of China (Guangxi) and ASEAN (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fisheries Sciences, Nanning 530021, China.
| | - Pinyuan Wei
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Key Laboratory of Comprehensive Development and Utilization of Aquatic Germplasm Resources of China (Guangxi) and ASEAN (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fisheries Sciences, Nanning 530021, China.
| | - Jinxia Peng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Key Laboratory of Comprehensive Development and Utilization of Aquatic Germplasm Resources of China (Guangxi) and ASEAN (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fisheries Sciences, Nanning 530021, China.
| |
Collapse
|
23
|
Stubbs RL, Theodoridis S, Mora-Carrera E, Keller B, Potente G, Yousefi N, Jay P, Léveillé-Bourret É, Choudhury RR, Celep F, Kochjarová J, Conti E. The genomes of Darwin's primroses reveal chromosome-scale adaptive introgression and differential permeability of species boundaries. THE NEW PHYTOLOGIST 2024; 241:911-925. [PMID: 37921572 DOI: 10.1111/nph.19361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/05/2023] [Indexed: 11/04/2023]
Abstract
Introgression is an important source of genetic variation that can determine species adaptation to environmental conditions. Yet, definitive evidence of the genomic and adaptive implications of introgression in nature remains scarce. The widespread hybrid zones of Darwin's primroses (Primula elatior, Primula veris, and Primula vulgaris) provide a unique natural laboratory for studying introgression in flowering plants and the varying permeability of species boundaries. Through analysis of 650 genomes, we provide evidence of an introgressed genomic region likely to confer adaptive advantage in conditions of soil toxicity. We also document unequivocal evidence of chloroplast introgression, an important precursor to species-wide chloroplast capture. Finally, we provide the first evidence that the S-locus supergene, which controls heterostyly in primroses, does not introgress in this clade. Our results contribute novel insights into the adaptive role of introgression and demonstrate the importance of extensive genomic and geographical sampling for illuminating the complex nature of species boundaries.
Collapse
Affiliation(s)
- Rebecca L Stubbs
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, 8008, Switzerland
| | - Spyros Theodoridis
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, 60325, Germany
| | - Emiliano Mora-Carrera
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, 8008, Switzerland
| | - Barbara Keller
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, 8008, Switzerland
| | - Giacomo Potente
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, 8008, Switzerland
| | - Narjes Yousefi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, 8008, Switzerland
| | - Paul Jay
- Center for GeoGenetics, University of Copenhagen, Copenhagen, 1350, Denmark
| | - Étienne Léveillé-Bourret
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, Montreal, QC, H1X 2B2, Canada
| | | | - Ferhat Celep
- Department of Biology, Faculty of Arts and Sciences, Kırıkkale University, Kırıkkale, 71450, Turkey
| | - Judita Kochjarová
- Department of Phytology, Faculty of Forestry, Technical University in Zvolen, Zvolen, 96001, Slovak Republic
| | - Elena Conti
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, 8008, Switzerland
| |
Collapse
|
24
|
Lopez Fang L, Peede D, Ortega-Del Vecchyo D, McTavish EJ, Huerta-Sánchez E. Leveraging shared ancestral variation to detect local introgression. PLoS Genet 2024; 20:e1010155. [PMID: 38190420 PMCID: PMC10798638 DOI: 10.1371/journal.pgen.1010155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 01/19/2024] [Accepted: 12/04/2023] [Indexed: 01/10/2024] Open
Abstract
Introgression is a common evolutionary phenomenon that results in shared genetic material across non-sister taxa. Existing statistical methods such as Patterson's D statistic can detect introgression by measuring an excess of shared derived alleles between populations. The D statistic is effective to detect genome-wide patterns of introgression but can give spurious inferences of introgression when applied to local regions. We propose a new statistic, D+, that leverages both shared ancestral and derived alleles to infer local introgressed regions. Incorporating both shared derived and ancestral alleles increases the number of informative sites per region, improving our ability to identify local introgression. We use a coalescent framework to derive the expected value of this statistic as a function of different demographic parameters under an instantaneous admixture model and use coalescent simulations to compute the power and precision of D+. While the power of D and D+ is comparable, D+ has better precision than D. We apply D+ to empirical data from the 1000 Genome Project and Heliconius butterflies to infer local targets of introgression in humans and in butterflies.
Collapse
Affiliation(s)
- Lesly Lopez Fang
- Department of Life & Environmental Sciences, University of California, Merced, Merced, California, United States of America
- Quantitative & Systems Biology Graduate Group, University of California, Merced, Merced, California, United States of America
| | - David Peede
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Biology, Brown University, Providence, Rhode Island, United States of America
- Institute at Brown for Environment and Society, Brown University, Providence, Rhode Island, United States of America
| | - Diego Ortega-Del Vecchyo
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Santiago de Querétaro, Querétaro, México
| | - Emily Jane McTavish
- Department of Life & Environmental Sciences, University of California, Merced, Merced, California, United States of America
- Quantitative & Systems Biology Graduate Group, University of California, Merced, Merced, California, United States of America
| | - Emilia Huerta-Sánchez
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Biology, Brown University, Providence, Rhode Island, United States of America
| |
Collapse
|
25
|
Langdon QK, Groh JS, Aguillon SM, Powell DL, Gunn T, Payne C, Baczenas JJ, Donny A, Dodge TO, Du K, Schartl M, Ríos-Cárdenas O, Gutierrez-Rodríguez C, Morris M, Schumer M. Genome evolution is surprisingly predictable after initial hybridization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.21.572897. [PMID: 38187753 PMCID: PMC10769416 DOI: 10.1101/2023.12.21.572897] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Over the past two decades, evolutionary biologists have come to appreciate that hybridization, or genetic exchange between distinct lineages, is remarkably common - not just in particular lineages but in taxonomic groups across the tree of life. As a result, the genomes of many modern species harbor regions inherited from related species. This observation has raised fundamental questions about the degree to which the genomic outcomes of hybridization are repeatable and the degree to which natural selection drives such repeatability. However, a lack of appropriate systems to answer these questions has limited empirical progress in this area. Here, we leverage independently formed hybrid populations between the swordtail fish Xiphophorus birchmanni and X. cortezi to address this fundamental question. We find that local ancestry in one hybrid population is remarkably predictive of local ancestry in another, demographically independent hybrid population. Applying newly developed methods, we can attribute much of this repeatability to strong selection in the earliest generations after initial hybridization. We complement these analyses with time-series data that demonstrates that ancestry at regions under selection has remained stable over the past ~40 generations of evolution. Finally, we compare our results to the well-studied X. birchmanni×X. malinche hybrid populations and conclude that deeper evolutionary divergence has resulted in stronger selection and higher repeatability in patterns of local ancestry in hybrids between X. birchmanni and X. cortezi.
Collapse
Affiliation(s)
- Quinn K. Langdon
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California
| | - Jeffrey S. Groh
- Center for Population Biology and Department of Evolution and Ecology, University of California, Davis
| | - Stepfanie M. Aguillon
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles
| | - Daniel L. Powell
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
| | - Theresa Gunn
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
| | - Cheyenne Payne
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
| | | | - Alex Donny
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
| | - Tristram O. Dodge
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
| | - Kang Du
- Xiphophorus Genetic Stock Center, Texas State University San Marcos
| | - Manfred Schartl
- Xiphophorus Genetic Stock Center, Texas State University San Marcos
- Developmental Biochemistry, Biocenter, University of Würzburg
| | | | | | | | - Molly Schumer
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
- Freeman Hrabowski Fellow, Howard Hughes Medical Institute
| |
Collapse
|
26
|
Kato S, Arakaki S, Nagano AJ, Kikuchi K, Hirase S. Genomic landscape of introgression from the ghost lineage in a gobiid fish uncovers the generality of forces shaping hybrid genomes. Mol Ecol 2023. [PMID: 38047388 DOI: 10.1111/mec.17216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/23/2023] [Accepted: 10/26/2023] [Indexed: 12/05/2023]
Abstract
Extinct lineages can leave legacies in the genomes of extant lineages through ancient introgressive hybridization. The patterns of genomic survival of these extinct lineages provide insight into the role of extinct lineages in current biodiversity. However, our understanding on the genomic landscape of introgression from extinct lineages remains limited due to challenges associated with locating the traces of unsampled 'ghost' extinct lineages without ancient genomes. Herein, we conducted population genomic analyses on the East China Sea (ECS) lineage of Chaenogobius annularis, which was suspected to have originated from ghost introgression, with the aim of elucidating its genomic origins and characterizing its landscape of introgression. By combining phylogeographic analysis and demographic modelling, we demonstrated that the ECS lineage originated from ancient hybridization with an extinct ghost lineage. Forward simulations based on the estimated demography indicated that the statistic γ of the HyDe analysis can be used to distinguish the differences in local introgression rates in our data. Consistent with introgression between extant organisms, we found reduced introgression from extinct lineage in regions with low recombination rates and with functional importance, thereby suggesting a role of linked selection that has eliminated the extinct lineage in shaping the hybrid genome. Moreover, we identified enrichment of repetitive elements in regions associated with ghost introgression, which was hitherto little known but was also observed in the re-analysis of published data on introgression between extant organisms. Overall, our findings underscore the unexpected similarities in the characteristics of introgression landscapes across different taxa, even in cases of ghost introgression.
Collapse
Affiliation(s)
- Shuya Kato
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Hamamatsu, Shizuoka, Japan
| | - Seiji Arakaki
- Amakusa Marine Biological Laboratory, Kyushu University, Amakusa, Kumamoto, Japan
| | - Atsushi J Nagano
- Department of Life Sciences, Faculty of Agriculture, Ryukoku University, Ōtsu, Shiga, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Kiyoshi Kikuchi
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Hamamatsu, Shizuoka, Japan
| | - Shotaro Hirase
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Hamamatsu, Shizuoka, Japan
| |
Collapse
|
27
|
Jensen A, Swift F, de Vries D, Beck RMD, Kuderna LFK, Knauf S, Chuma IS, Keyyu JD, Kitchener AC, Farh K, Rogers J, Marques-Bonet T, Detwiler KM, Roos C, Guschanski K. Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation. Mol Biol Evol 2023; 40:msad247. [PMID: 37987553 PMCID: PMC10691879 DOI: 10.1093/molbev/msad247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/17/2023] [Accepted: 11/09/2023] [Indexed: 11/22/2023] Open
Abstract
Understanding the drivers of speciation is fundamental in evolutionary biology, and recent studies highlight hybridization as an important evolutionary force. Using whole-genome sequencing data from 22 species of guenons (tribe Cercopithecini), one of the world's largest primate radiations, we show that rampant gene flow characterizes their evolutionary history and identify ancient hybridization across deeply divergent lineages that differ in ecology, morphology, and karyotypes. Some hybridization events resulted in mitochondrial introgression between distant lineages, likely facilitated by cointrogression of coadapted nuclear variants. Although the genomic landscapes of introgression were largely lineage specific, we found that genes with immune functions were overrepresented in introgressing regions, in line with adaptive introgression, whereas genes involved in pigmentation and morphology may contribute to reproductive isolation. In line with reports from other systems that hybridization might facilitate diversification, we find that some of the most species-rich guenon clades are of admixed origin. This study provides important insights into the prevalence, role, and outcomes of ancestral hybridization in a large mammalian radiation.
Collapse
Affiliation(s)
- Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala SE-75236, Sweden
| | - Frances Swift
- School of Biological Sciences, Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Robin M D Beck
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Lukas F K Kuderna
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald – Insel Riems 17493, Germany
| | | | - Julius D Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Arusha, Tanzania
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Edinburgh EH1 1JF, UK
- School of Geosciences, University of Edinburgh, Edinburgh EH8 9XP, UK
| | - Kyle Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona 08003, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra, Barcelona 08010, Spain
| | - Kate M Detwiler
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL, USA
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen 37077, Germany
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala SE-75236, Sweden
- School of Biological Sciences, Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
28
|
Askelson KK, Spellman GM, Irwin D. Genomic divergence and introgression between cryptic species of a widespread North American songbird. Mol Ecol 2023; 32:6839-6853. [PMID: 37916530 DOI: 10.1111/mec.17169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 09/20/2023] [Indexed: 11/03/2023]
Abstract
Analysis of genomic variation among related populations can sometimes reveal distinct species that were previously undescribed due to similar morphological appearances, and close examination of such cases can provide much insight regarding speciation. Genomic data can also reveal the role of reticulate evolution in differentiation and speciation. White-breasted nuthatches (Sitta carolinensis) are widely distributed North American songbirds that are currently classified as a single species but have been suspected to represent a case of cryptic speciation. Previous genetic analyses suggested four divergent groups, but it was unclear whether these represented multiple reproductively isolated species. Using extensive genomic sampling of over 350 white-breasted nuthatches from across North America and a new chromosome-level reference genome, we asked if white-breasted nuthatches are comprised of multiple species and whether introgression has occurred between divergent populations. Genomic variation of over 300,000 loci revealed four highly differentiated populations (Pacific, n = 45; Eastern, n = 23; Rocky Mountains North, n = 138; and Rocky Mountains South, n = 150) with geographic ranges that are adjacent. We observed a moderate degree of admixture between Rocky Mountain populations but only a small number of hybrids between the Rockies and the Eastern population. The rarity of hybrids together with high levels of differentiation between populations is supportive of populations having some level of reproductive isolation. Between populations, we show evidence for introgression from a divergent ghost lineage of white-breasted nuthatches into the Rocky Mountains South population, which is otherwise closely related to Rocky Mountains North. We conclude that white-breasted nuthatches are best considered at least three species and that ghost lineage introgression has contributed to differentiation between the two Rocky Mountain populations. White-breasted nuthatches provide a dramatic case of morphological similarity despite high genomic differentiation, and the varying levels of reproductive isolation among the four groups provide an example of the speciation continuum.
Collapse
Affiliation(s)
- Kenneth K Askelson
- Biodiversity Research Centre and Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Garth M Spellman
- Department of Zoology, Denver Museum of Nature & Science, Denver, Colorado, USA
| | - Darren Irwin
- Biodiversity Research Centre and Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
29
|
Williams MP, Flegontov P, Maier R, Huber CD. Testing Times: Challenges in Disentangling Admixture Histories in Recent and Complex Demographies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566841. [PMID: 38014190 PMCID: PMC10680674 DOI: 10.1101/2023.11.13.566841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Paleogenomics has expanded our knowledge of human evolutionary history. Since the 2020s, the study of ancient DNA has increased its focus on reconstructing the recent past. However, the accuracy of paleogenomic methods in answering questions of historical and archaeological importance amidst the increased demographic complexity and decreased genetic differentiation within the historical period remains an open question. We used two simulation approaches to evaluate the limitations and behavior of commonly used methods, qpAdm and the f 3 -statistic, on admixture inference. The first is based on branch-length data simulated from four simple demographic models of varying complexities and configurations. The second, an analysis of Eurasian history composed of 59 populations using whole-genome data modified with ancient DNA conditions such as SNP ascertainment, data missingness, and pseudo-haploidization. We show that under conditions resembling historical populations, qpAdm can identify a small candidate set of true sources and populations closely related to them. However, in typical ancient DNA conditions, qpAdm is unable to further distinguish between them, limiting its utility for resolving fine-scaled hypotheses. Notably, we find that complex gene-flow histories generally lead to improvements in the performance of qpAdm and observe no bias in the estimation of admixture weights. We offer a heuristic for admixture inference that incorporates admixture weight estimate and P -values of qpAdm models, and f 3 -statistics to enhance the power to distinguish between multiple plausible candidates. Finally, we highlight the future potential of qpAdm through whole-genome branch-length f 2 -statistics, demonstrating the improved demographic inference that could be achieved with advancements in f -statistic estimations.
Collapse
|
30
|
Tan X, Qi J, Liu Z, Fan P, Liu G, Zhang L, Shen Y, Li J, Roos C, Zhou X, Li M. Phylogenomics Reveals High Levels of Incomplete Lineage Sorting at the Ancestral Nodes of the Macaque Radiation. Mol Biol Evol 2023; 40:msad229. [PMID: 37823401 PMCID: PMC10638670 DOI: 10.1093/molbev/msad229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/06/2023] [Accepted: 10/08/2023] [Indexed: 10/13/2023] Open
Abstract
The genus Macaca includes 23 species assigned into 4 to 7 groups. It exhibits the largest geographic range and represents the most successful example of adaptive radiation of nonhuman primates. However, intrageneric phylogenetic relationships among species remain controversial and have not been resolved so far. In this study, we conducted a phylogenomic analysis on 16 newly generated and 8 published macaque genomes. We found strong evidence supporting the division of this genus into 7 species groups. Incomplete lineage sorting (ILS) was the primary factor contributing to the discordance observed among gene trees; however, we also found evidence of hybridization events, specifically between the ancestral arctoides/sinica and silenus/nigra lineages that resulted in the hybrid formation of the fascicularis/mulatta group. Combined with fossil data, our phylogenomic data were used to establish a scenario for macaque radiation. These findings provide insights into ILS and potential ancient introgression events that were involved in the radiation of macaques, which will lead to a better understanding of the rapid speciation occurring in nonhuman primates.
Collapse
Affiliation(s)
- Xinxin Tan
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Geneplus-Beijing Institute, Beijing 102206, China
| | - Jiwei Qi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhijin Liu
- College of Life Sciences, Capital Normal University, Beijing 100049, China
| | - Pengfei Fan
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Gaoming Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Liye Zhang
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen 37077, Germany
| | - Ying Shen
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Li
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen 37077, Germany
- Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, Göttingen 37077, Germany
| | - Xuming Zhou
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ming Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| |
Collapse
|
31
|
Zhang Y, Zhu Q, Shao Y, Jiang Y, Ouyang Y, Zhang L, Zhang W. Inferring Historical Introgression with Deep Learning. Syst Biol 2023; 72:1013-1038. [PMID: 37257491 DOI: 10.1093/sysbio/syad033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 05/28/2023] [Accepted: 05/30/2023] [Indexed: 06/02/2023] Open
Abstract
Resolving phylogenetic relationships among taxa remains a challenge in the era of big data due to the presence of genetic admixture in a wide range of organisms. Rapidly developing sequencing technologies and statistical tests enable evolutionary relationships to be disentangled at a genome-wide level, yet many of these tests are computationally intensive and rely on phased genotypes, large sample sizes, restricted phylogenetic topologies, or hypothesis testing. To overcome these difficulties, we developed a deep learning-based approach, named ERICA, for inferring genome-wide evolutionary relationships and local introgressed regions from sequence data. ERICA accepts sequence alignments of both population genomic data and multiple genome assemblies, and efficiently identifies discordant genealogy patterns and exchanged regions across genomes when compared with other methods. We further tested ERICA using real population genomic data from Heliconius butterflies that have undergone adaptive radiation and frequent hybridization. Finally, we applied ERICA to characterize hybridization and introgression in wild and cultivated rice, revealing the important role of introgression in rice domestication and adaptation. Taken together, our findings demonstrate that ERICA provides an effective method for teasing apart evolutionary relationships using whole genome data, which can ultimately facilitate evolutionary studies on hybridization and introgression.
Collapse
Affiliation(s)
- Yubo Zhang
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Qingjie Zhu
- Chinese Institute for Brain Research, Beijing 102206, China
| | - Yi Shao
- Chinese Institute for Brain Research, Beijing 102206, China
| | - Yanchen Jiang
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Li Zhang
- Chinese Institute for Brain Research, Beijing 102206, China
| | - Wei Zhang
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| |
Collapse
|
32
|
Montazeaud G, Helleu Q, Wuest SE, Keller L. Indirect genetic effects are shaped by demographic history and ecology in Arabidopsis thaliana. Nat Ecol Evol 2023; 7:1878-1891. [PMID: 37749402 DOI: 10.1038/s41559-023-02189-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 08/07/2023] [Indexed: 09/27/2023]
Abstract
The phenotype of an individual can be affected by the genes of its conspecifics through indirect genetic effects (IGEs). IGEs have been studied across different organisms including wild and domesticated animals and plants, but little is known about their genetic architecture. Here, in a large-scale intraspecific interaction experiment, we show that the contribution of IGEs to the biomass variation of Arabidopsis thaliana is comparable to values classically reported in animals. Moreover, we identify 11 loci explaining 85.1% of the variability in IGEs. We find that positive IGE alleles (that is, those with positive effects on neighbour biomass) occur both in relict accessions from southern Eurasia and in post-glacial colonizers from northern Scandinavia, and that they are likely to have two divergent origins: for nine loci, they evolved in the post-glacial colonizers independently from the relicts, while the two others were introgressed in the post-glacial colonizer from the relicts. Finally, we find that variation in IGEs probably reflects divergent adaptations to the contrasting environments of the edges and the centre of the native range of the species. These findings reveal a surprisingly tractable genetic basis of IGEs in A. thaliana that is shaped by the ecology and the demographic history of the species.
Collapse
Affiliation(s)
- Germain Montazeaud
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
| | - Quentin Helleu
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Structure et Instabilité des Génomes, Muséum National d'Histoire Naturelle, CNRS UMR7196, INSERM U1154, Paris, France
| | - Samuel E Wuest
- Group Breeding Research, Division Plant Breeding, Agroscope, Wädenswil, Switzerland
| | - Laurent Keller
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
- Social Evolution Unit, Chesières, Switzerland.
| |
Collapse
|
33
|
Yüncü E, Işıldak U, Williams MP, Huber CD, Flegontova O, Vyazov LA, Changmai P, Flegontov P. False discovery rates of qpAdm-based screens for genetic admixture. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.25.538339. [PMID: 37904998 PMCID: PMC10614728 DOI: 10.1101/2023.04.25.538339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Although a broad range of methods exists for reconstructing population history from genome-wide single nucleotide polymorphism data, just a few methods gained popularity in archaeogenetics: principal component analysis (PCA); ADMIXTURE, an algorithm that models individuals as mixtures of multiple ancestral sources represented by actual or inferred populations; formal tests for admixture such as f3-statistics and D/f4-statistics; and qpAdm, a tool for fitting two-component and more complex admixture models to groups or individuals. Despite their popularity in archaeogenetics, which is explained by modest computational requirements and ability to analyze data of various types and qualities, protocols relying on qpAdm that screen numerous alternative models of varying complexity and find "fitting" models (often considering both estimated admixture proportions and p-values as a composite criterion of model fit) remain untested on complex simulated population histories in the form of admixture graphs of random topology. We analyzed genotype data extracted from such simulations and tested various types of high-throughput qpAdm protocols ("rotating" and "non-rotating", with or without temporal stratification of target groups and proxy ancestry sources, and with or without a "model competition" step). We caution that high-throughput qpAdm protocols may be inappropriate for exploratory analyses in poorly studied regions/periods since their false discovery rates varied between 12% and 68% depending on the details of the protocol and on the amount and quality of simulated data (i.e., >12% of fitting two-way admixture models imply gene flows that were not simulated). We demonstrate that for reducing false discovery rates of qpAdm protocols to nearly 0% it is advisable to use large SNP sets with low missing data rates, the rotating qpAdm protocol with a strictly enforced rule that target groups do not pre-date their proxy sources, and an unsupervised ADMIXTURE analysis as a way to verify feasible qpAdm models. Our study has a number of limitations: for instance, these recommendations depend on the assumption that the underlying genetic history is a complex admixture graph and not a stepping-stone model.
Collapse
Affiliation(s)
- Eren Yüncü
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Ulaş Işıldak
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Matthew P. Williams
- Department of Biology, Eberly College of Science, Pennsylvania State University, PA, USA
| | - Christian D. Huber
- Department of Biology, Eberly College of Science, Pennsylvania State University, PA, USA
| | - Olga Flegontova
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
| | - Leonid A. Vyazov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Piya Changmai
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| |
Collapse
|
34
|
Peng MS, Liu YH, Shen QK, Zhang XH, Dong J, Li JX, Zhao H, Zhang H, Zhang X, He Y, Shi H, Cui C, Ouzhuluobu, Wu TY, Liu SM, Gonggalanzi, Baimakangzhuo, Bai C, Duojizhuoma, Liu T, Dai SS, Murphy RW, Qi XB, Dong G, Su B, Zhang YP. Genetic and cultural adaptations underlie the establishment of dairy pastoralism in the Tibetan Plateau. BMC Biol 2023; 21:208. [PMID: 37798721 PMCID: PMC10557253 DOI: 10.1186/s12915-023-01707-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/20/2023] [Indexed: 10/07/2023] Open
Abstract
BACKGROUND Domestication and introduction of dairy animals facilitated the permanent human occupation of the Tibetan Plateau. Yet the history of dairy pastoralism in the Tibetan Plateau remains poorly understood. Little is known how Tibetans adapted to milk and dairy products. RESULTS We integrated archeological evidence and genetic analysis to show the picture that the dairy ruminants, together with dogs, were introduced from West Eurasia into the Tibetan Plateau since ~ 3600 years ago. The genetic admixture between the exotic and indigenous dogs enriched the candidate lactase persistence (LP) allele 10974A > G of West Eurasian origin in Tibetan dogs. In vitro experiments demonstrate that - 13838G > A functions as a LP allele in Tibetans. Unlike multiple LP alleles presenting selective signatures in West Eurasians and South Asians, the de novo origin of Tibetan-specific LP allele - 13838G > A with low frequency (~ 6-7%) and absence of selection corresponds - 13910C > T in pastoralists across eastern Eurasia steppe. CONCLUSIONS Results depict a novel scenario of genetic and cultural adaptations to diet and expand current understanding of the establishment of dairy pastoralism in the Tibetan Plateau.
Collapse
Affiliation(s)
- Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan-Hu Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Quan-Kuan Shen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Hua Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, 650091, China
- Institute of Medical Biology, Chinese Academy of Medical Science, Peking Union Medical College, Kunming, 650118, China
| | - Jiajia Dong
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Jin-Xiu Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Hui Zhao
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, 650091, China
| | - Hui Zhang
- State Key Laboratory of Primate Biomedical Research (LPBR), School of Primate Translational Medicine, Kunming University of Science and Technology (KUST), Kunming, 650000, China
| | - Xiaoming Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yaoxi He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong Shi
- State Key Laboratory of Primate Biomedical Research (LPBR), School of Primate Translational Medicine, Kunming University of Science and Technology (KUST), Kunming, 650000, China
| | - Chaoying Cui
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa, 850000, China
| | - Ouzhuluobu
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa, 850000, China
| | - Tian-Yi Wu
- National Key Laboratory of High Altitude Medicine, High Altitude Medical Research Institute, Xining, 810000, China
| | - Shi-Ming Liu
- National Key Laboratory of High Altitude Medicine, High Altitude Medical Research Institute, Xining, 810000, China
| | - Gonggalanzi
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa, 850000, China
| | - Baimakangzhuo
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa, 850000, China
| | - Caijuan Bai
- The First People's Hospital of Gansu Province, Lanzhou, 730000, China
| | - Duojizhuoma
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa, 850000, China
| | - Ti Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, 650091, China
| | - Shan-Shan Dai
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON, M5S 2C6, Canada
| | - Xue-Bin Qi
- State Key Laboratory of Primate Biomedical Research (LPBR), School of Primate Translational Medicine, Kunming University of Science and Technology (KUST), Kunming, 650000, China.
- Tibetan Fukang Hospital, Lhasa, 850000, China.
| | - Guanghui Dong
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, 730000, China.
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
- Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, 650091, China.
| |
Collapse
|
35
|
Cerca J. Understanding natural selection and similarity: Convergent, parallel and repeated evolution. Mol Ecol 2023; 32:5451-5462. [PMID: 37724599 DOI: 10.1111/mec.17132] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/26/2023] [Accepted: 08/30/2023] [Indexed: 09/21/2023]
Abstract
Parallel and convergent evolution offer some of the most compelling evidence for the significance of natural selection in evolution, as the emergence of similar adaptive solutions is unlikely to occur by random chance alone. However, these terms are often employed inconsistently, leading to misinterpretation and confusion, and recently proposed definitions have unintentionally diminished the emphasis on the evolution of similar adaptive solutions. Here, I examine various conceptual frameworks and definitions related to parallel and convergent evolution and propose a consolidated framework that enhances our comprehension of these evolutionary patterns. The primary aim of this framework is to harmonize the concepts of parallel and convergent evolution together with natural selection and the idea of similarity. Both concepts involve the evolution of similar adaptive solutions as a result of environmental challenges. The distinction lies in ancestral phenotypes. Parallel evolution takes place when the ancestral phenotypes (before selection) of the lineages are similar. Convergent evolution happens when the lineages have distinct ancestral phenotypes (before selection). Because an ancestral-based distinction will inevitably lead to cases where uncertainty in the distinction may arise, the framework includes a general term, repeated evolution, which can be used as a term applying to the evolution of similar phenotypes and genotypes as well as similar responses to environmental pressures. Based on the argument that genetic similarity may frequently arise without selection, the framework posits that the similarity of genetic sequences is not of great interest unless linked to the actions of natural selection or to the origins (mutation, standing genetic variation, gene flow) and locations of the similar sequences.
Collapse
Affiliation(s)
- José Cerca
- CEES - Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| |
Collapse
|
36
|
Short AW, Streisfeld MA. Ancient hybridization leads to the repeated evolution of red flowers across a monkeyflower radiation. Evol Lett 2023; 7:293-304. [PMID: 37829500 PMCID: PMC10565894 DOI: 10.1093/evlett/qrad024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/14/2023] [Accepted: 05/12/2023] [Indexed: 10/14/2023] Open
Abstract
The reuse of old genetic variation can promote rapid diversification in evolutionary radiations, but in most cases, the historical events underlying this divergence are not known. For example, ancient hybridization can generate new combinations of alleles that sort into descendant lineages, potentially providing the raw material to initiate divergence. In the Mimulus aurantiacus species complex, there is evidence for widespread gene flow among members of this radiation. In addition, allelic variation in the MaMyb2 gene is responsible for differences in flower color between the closely related ecotypes of subspecies puniceus, contributing to reproductive isolation by pollinators. Previous work suggested that MaMyb2 was introgressed into the red-flowered ecotype of puniceus. However, additional taxa within the radiation have independently evolved red flowers from their yellow-flowered ancestors, raising the possibility that this introgression had a more ancient origin. In this study, we used repeated tests of admixture from whole-genome sequence data across this diverse radiation to demonstrate that there has been both ancient and recurrent hybridization in this group. However, most of the signal of this ancient introgression has been removed due to selection, suggesting that widespread barriers to gene flow are in place between taxa. Yet, a roughly 30 kb region that contains the MaMyb2 gene is currently shared only among the red-flowered taxa. Patterns of admixture, sequence divergence, and extended haplotype homozygosity across this region confirm a history of ancient hybridization, where functional variants have been preserved due to positive selection in red-flowered taxa but lost in their yellow-flowered counterparts. The results of this study reveal that selection against gene flow can reduce genomic signatures of ancient hybridization, but that historical introgression can provide essential genetic variation that facilitates the repeated evolution of phenotypic traits between lineages.
Collapse
Affiliation(s)
- Aidan W Short
- Institute of Ecology and Evolution, 5289 University of Oregon, Eugene, OR 97403-5289, United States
| | - Matthew A Streisfeld
- Institute of Ecology and Evolution, 5289 University of Oregon, Eugene, OR 97403-5289, United States
| |
Collapse
|
37
|
Yang C, Zhou Y, Song Y, Wu D, Zeng Y, Nie L, Liu P, Zhang S, Chen G, Xu J, Zhou H, Zhou L, Qian X, Liu C, Tan S, Zhou C, Dai W, Xu M, Qi Y, Wang X, Guo L, Fan G, Wang A, Deng Y, Zhang Y, Jin J, He Y, Guo C, Guo G, Zhou Q, Xu X, Yang H, Wang J, Xu S, Mao Y, Jin X, Ruan J, Zhang G. The complete and fully-phased diploid genome of a male Han Chinese. Cell Res 2023; 33:745-761. [PMID: 37452091 PMCID: PMC10542383 DOI: 10.1038/s41422-023-00849-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023] Open
Abstract
Since the release of the complete human genome, the priority of human genomic study has now been shifting towards closing gaps in ethnic diversity. Here, we present a fully phased and well-annotated diploid human genome from a Han Chinese male individual (CN1), in which the assemblies of both haploids achieve the telomere-to-telomere (T2T) level. Comparison of this diploid genome with the CHM13 haploid T2T genome revealed significant variations in the centromere. Outside the centromere, we discovered 11,413 structural variations, including numerous novel ones. We also detected thousands of CN1 alleles that have accumulated high substitution rates and a few that have been under positive selection in the East Asian population. Further, we found that CN1 outperforms CHM13 as a reference genome in mapping and variant calling for the East Asian population owing to the distinct structural variants of the two references. Comparison of SNP calling for a large cohort of 8869 Chinese genomes using CN1 and CHM13 as reference respectively showed that the reference bias profoundly impacts rare SNP calling, with nearly 2 million rare SNPs miss-called with different reference genomes. Finally, applying the CN1 as a reference, we discovered 5.80 Mb and 4.21 Mb putative introgression sequences from Neanderthal and Denisovan, respectively, including many East Asian specific ones undetected using CHM13 as the reference. Our analyses reveal the advances of using CN1 as a reference for population genomic studies and paleo-genomic studies. This complete genome will serve as an alternative reference for future genomic studies on the East Asian population.
Collapse
Affiliation(s)
- Chentao Yang
- Center for Genomic Research, International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
- Center for Evolutionary & Organismal Biology, & Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Yang Zhou
- BGI-Shenzhen, Shenzhen, Guangdong, China
- BGI Research-Wuhan, BGI, Wuhan, Hubei, China
| | - Yanni Song
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Dongya Wu
- Center for Genomic Research, International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
- Center for Evolutionary & Organismal Biology, & Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang, China
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yan Zeng
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Lei Nie
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | | | - Shilong Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Guangji Chen
- BGI-Shenzhen, Shenzhen, Guangdong, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jinjin Xu
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Hongling Zhou
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Long Zhou
- Center for Evolutionary & Organismal Biology, & Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaobo Qian
- BGI-Shenzhen, Shenzhen, Guangdong, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chenlu Liu
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | | | | | - Wei Dai
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Mengyang Xu
- BGI-Shenzhen, Shenzhen, Guangdong, China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong, China
| | - Yanwei Qi
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong, China
| | - Xiaobo Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Lidong Guo
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong, China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong, China
| | - Aijun Wang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong, China
| | - Yuan Deng
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Yong Zhang
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | | | - Yunqiu He
- Center for Genomic Research, International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
- Center for Evolutionary & Organismal Biology, & Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Chunxue Guo
- BGI-Shenzhen, Shenzhen, Guangdong, China
- BGI-Hangzhou, Hangzhou, Zhejiang, China
| | - Guoji Guo
- School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qing Zhou
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang, China
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | | | - Jian Wang
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
- Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, China
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, International Joint Center of Genomics of Jiangsu Province School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
- Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yafei Mao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Xin Jin
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Jue Ruan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China.
| | - Guojie Zhang
- Center for Genomic Research, International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China.
- Center for Evolutionary & Organismal Biology, & Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang, China.
- Innovation Center of Yangtze River Delta, Zhejiang University, Hangzhou, Zhejiang, China.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
| |
Collapse
|
38
|
Meier JI, McGee MD, Marques DA, Mwaiko S, Kishe M, Wandera S, Neumann D, Mrosso H, Chapman LJ, Chapman CA, Kaufman L, Taabu-Munyaho A, Wagner CE, Bruggmann R, Excoffier L, Seehausen O. Cycles of fusion and fission enabled rapid parallel adaptive radiations in African cichlids. Science 2023; 381:eade2833. [PMID: 37769075 DOI: 10.1126/science.ade2833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 08/21/2023] [Indexed: 09/30/2023]
Abstract
Although some lineages of animals and plants have made impressive adaptive radiations when provided with ecological opportunity, the propensities to radiate vary profoundly among lineages for unknown reasons. In Africa's Lake Victoria region, one cichlid lineage radiated in every lake, with the largest radiation taking place in a lake less than 16,000 years old. We show that all of its ecological guilds evolved in situ. Cycles of lineage fusion through admixture and lineage fission through speciation characterize the history of the radiation. It was jump-started when several swamp-dwelling refugial populations, each of which were of older hybrid descent, met in the newly forming lake, where they fused into a single population, resuspending old admixture variation. Each population contributed a different set of ancient alleles from which a new adaptive radiation assembled in record time, involving additional fusion-fission cycles. We argue that repeated fusion-fission cycles in the history of a lineage make adaptive radiation fast and predictable.
Collapse
Affiliation(s)
- Joana I Meier
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
- Department of Zoology, University of Cambridge, Cambridge, UK
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Matthew D McGee
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - David A Marques
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
- Natural History Museum Basel, Basel, Switzerland
| | - Salome Mwaiko
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
| | - Mary Kishe
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania
| | - Sylvester Wandera
- National Fisheries Resources Research Institute (NAFIRRI), Jinja, Uganda
| | - Dirk Neumann
- Leipniz Institute for Biodiversity Change, Hamburg, Germany
| | - Hilary Mrosso
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania
| | - Lauren J Chapman
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Colin A Chapman
- Wilson Center, Washington, DC, USA
- Biology Department, Vancouver Island University, Nanaimo, British Columbia, Canada
- School of Life Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi'an, China
- Biology Department, Vancouver Island University, Nanaimo, British Columbia, Canada
| | - Les Kaufman
- Boston University Marine Program, Department of Biology, Boston University, Boston, MA, USA
| | | | | | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Laurent Excoffier
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ole Seehausen
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
| |
Collapse
|
39
|
Dumont BL, Gatti D, Ballinger MA, Lin D, Phifer-Rixey M, Sheehan MJ, Suzuki TA, Wooldridge LK, Frempong HO, Churchill G, Lutz C, Rosenthal N, White JK, Nachman MW. Into the Wild: A novel wild-derived inbred strain resource expands the genomic and phenotypic diversity of laboratory mouse models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.21.558738. [PMID: 37790321 PMCID: PMC10542534 DOI: 10.1101/2023.09.21.558738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The laboratory mouse has served as the premier animal model system for both basic and preclinical investigations for a century. However, laboratory mice capture a narrow subset of the genetic variation found in wild mouse populations. This consideration inherently restricts the scope of potential discovery in laboratory models and narrows the pool of potentially identified phenotype-associated variants and pathways. Wild mouse populations are reservoirs of predicted functional and disease-associated alleles, but the sparsity of commercially available, well-characterized wild mouse strains limits their broader adoption in biomedical research. To overcome this barrier, we have recently imported, sequenced, and phenotyped a set of 11 wild-derived inbred strains developed from wild-caught Mus musculus domesticus. Each of these "Nachman strains" immortalizes a unique wild haplotype sampled from five environmentally diverse locations across North and South America: Saratoga Springs, New York, USA; Gainesville, Florida, USA; Manaus, Brazil; Tucson, Arizona, USA; and Edmonton, Alberta, Canada. Whole genome sequence analysis reveals that each strain carries between 4.73-6.54 million single nucleotide differences relative to the mouse reference assembly, with 42.5% of variants in the Nachman strain genomes absent from classical inbred mouse strains. We phenotyped the Nachman strains on a customized pipeline to assess the scope of disease-relevant neurobehavioral, biochemical, physiological, metabolic, and morphological trait variation. The Nachman strains exhibit significant inter-strain variation in >90% of 1119 surveyed traits and expand the range of phenotypic diversity captured in classical inbred strain panels alone. Taken together, our work introduces a novel wild-derived inbred mouse strain resource that will enable new discoveries in basic and preclinical research. These strains are currently available through The Jackson Laboratory Repository under laboratory code NachJ.
Collapse
Affiliation(s)
- Beth L Dumont
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
- Tufts University, Graduate School of Biomedical Sciences, 136 Harrison Ave, Boston, MA, 02111, USA
- The University of Maine, Graduate School of Biomedical Science and Engineering, 5775 Stodder Hall, Room 46, Orono, ME, 04469, USA
| | - Daniel Gatti
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Mallory A Ballinger
- Department of Integrative Biology, Center for Computational Biology, and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Dana Lin
- Department of Integrative Biology, Center for Computational Biology, and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
| | | | - Michael J Sheehan
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | - Taichi A Suzuki
- College of Health Solutions and Biodesign Center for Health Through Microbiomes, Arizona State University, Tempe, AZ, USA 85281
| | | | - Hilda Opoku Frempong
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
- The University of Maine, Graduate School of Biomedical Science and Engineering, 5775 Stodder Hall, Room 46, Orono, ME, 04469, USA
| | - Gary Churchill
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
- Tufts University, Graduate School of Biomedical Sciences, 136 Harrison Ave, Boston, MA, 02111, USA
- The University of Maine, Graduate School of Biomedical Science and Engineering, 5775 Stodder Hall, Room 46, Orono, ME, 04469, USA
| | - Cathleen Lutz
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Nadia Rosenthal
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
- Tufts University, Graduate School of Biomedical Sciences, 136 Harrison Ave, Boston, MA, 02111, USA
- The University of Maine, Graduate School of Biomedical Science and Engineering, 5775 Stodder Hall, Room 46, Orono, ME, 04469, USA
| | | | - Michael W Nachman
- Department of Integrative Biology, Center for Computational Biology, and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
| |
Collapse
|
40
|
Liu F, Zhao J, Sun H, Xiong C, Sun X, Wang X, Wang Z, Jarret R, Wang J, Tang B, Xu H, Hu B, Suo H, Yang B, Ou L, Li X, Zhou S, Yang S, Liu Z, Yuan F, Pei Z, Ma Y, Dai X, Wu S, Fei Z, Zou X. Genomes of cultivated and wild Capsicum species provide insights into pepper domestication and population differentiation. Nat Commun 2023; 14:5487. [PMID: 37679363 PMCID: PMC10484947 DOI: 10.1038/s41467-023-41251-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/28/2023] [Indexed: 09/09/2023] Open
Abstract
Pepper (Capsicum spp.) is one of the earliest cultivated crops and includes five domesticated species, C. annuum var. annuum, C. chinense, C. frutescens, C. baccatum var. pendulum and C. pubescens. Here, we report a pepper graph pan-genome and a genome variation map of 500 accessions from the five domesticated Capsicum species and close wild relatives. We identify highly differentiated genomic regions among the domesticated peppers that underlie their natural variations in flowering time, characteristic flavors, and unique resistances to biotic and abiotic stresses. Domestication sweeps detected in C. annuum var. annuum and C. baccatum var. pendulum are mostly different, and the common domestication traits, including fruit size, shape and pungency, are achieved mainly through the selection of distinct genomic regions between these two cultivated species. Introgressions from C. baccatum into C. chinense and C. frutescens are detected, including those providing genetic sources for various biotic and abiotic stress tolerances.
Collapse
Affiliation(s)
- Feng Liu
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Jiantao Zhao
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
- Boyce Thompson Institute, Ithaca, NY, USA
| | - Honghe Sun
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Cheng Xiong
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Xuepeng Sun
- Boyce Thompson Institute, Ithaca, NY, USA
- College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
| | - Xin Wang
- Boyce Thompson Institute, Ithaca, NY, USA
- Department of Vegetable Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, China
| | - Zhongyi Wang
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Robert Jarret
- U.S. Department of Agriculture-Agricultural Research Service, Plant Genetic Resources Conservation Unit, Griffin, GA, USA
| | - Jin Wang
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Bingqian Tang
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Hao Xu
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Bowen Hu
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Huan Suo
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Bozhi Yang
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Lijun Ou
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Xuefeng Li
- Institute of Vegetable Research, Hunan Academy of Agricultural Science, Changsha, China
| | - Shudong Zhou
- Institute of Vegetable Research, Hunan Academy of Agricultural Science, Changsha, China
| | - Sha Yang
- Institute of Vegetable Research, Hunan Academy of Agricultural Science, Changsha, China
| | - Zhoubing Liu
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Fang Yuan
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Zhenming Pei
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Yanqing Ma
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Xiongze Dai
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Shan Wu
- Boyce Thompson Institute, Ithaca, NY, USA.
| | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, NY, USA.
- U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, USA.
| | - Xuexiao Zou
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China.
| |
Collapse
|
41
|
Wang XF, Zhang YX, Niu YQ, Sha Y, Wang ZH, Zhang ZB, Yang J, Liu B, Li LF. Post-hybridization introgression and natural selection promoted genomic divergence of Aegilops speltoides and the four S*-genome diploid species. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1500-1513. [PMID: 37313760 DOI: 10.1111/tpj.16334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/15/2023]
Abstract
Understanding how different driving forces have promoted biological divergence and speciation is one of the central issues in evolutionary biology. The Triticum/Aegilops species complex contains 13 diploid species belonging to the A-, B- and D-lineages and offers an ideal system to address the evolutionary dynamics of lineage fusion and splitting. Here, we sequenced the whole genomes of one S-genome species (Aegilops speltoides) of the B-lineage and four S*-genome diploid species (Aegilops bicornis, Aegilops longissima, Aegilops sharonensis and Aegilops searsii) of the D-lineage at the population level. We performed detailed comparisons of the five species and with the other four representative A-, B- and D-lineage species. Our estimates identified frequent genetic introgressions from A- and B-lineages to the D-lineage species. A remarkable observation is the contrasting distributions of putative introgressed loci by the A- and B-lineages along all the seven chromosomes to the extant D-lineage species. These genetic introgressions resulted in high levels of genetic divergence at centromeric regions between Ae. speltoides (B-lineage) and the other four S*-genome diploid species (D-lineage), while natural selection is a potential contributor to divergence among the four S*-genome species at telomeric regions. Our study provides a genome-wide view on how genetic introgression and natural selection acted together yet chromosome-regionally divided to promote genomic divergence among the five S- and S*-genome diploid species, which provides new and nuanced insights into the evolutionary history of the Triticum/Aegilops species complex.
Collapse
Affiliation(s)
- Xin-Feng Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yu-Xin Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yu-Qian Niu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yan Sha
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zhen-Hui Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, 130118, China
| | - Zhi-Bin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ji Yang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Lin-Feng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| |
Collapse
|
42
|
Westbury MV, Cabrera AA, Rey-Iglesia A, De Cahsan B, Duchêne DA, Hartmann S, Lorenzen ED. A genomic assessment of the marine-speciation paradox within the toothed whale superfamily Delphinoidea. Mol Ecol 2023; 32:4829-4843. [PMID: 37448145 DOI: 10.1111/mec.17069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 06/21/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023]
Abstract
The impact of post-divergence gene flow in speciation has been documented across a range of taxa in recent years, and may have been especially widespread in highly mobile, wide-ranging marine species, such as cetaceans. Here, we studied individual genomes from nine species across the three families of the toothed whale superfamily Delphinoidea (Delphinidae, Phocoenidae and Monodontidae). To investigate the role of post-divergence gene flow in the speciation process, we used a multifaceted approach, including (i) phylogenomics, (ii) the distribution of shared derived alleles and (iii) demographic inference. We found the divergence of lineages within Delphinoidea did not follow a process of pure bifurcation, but was much more complex. Sliding-window phylogenomics reveal a high prevalence of discordant topologies within the superfamily, with further analyses indicating these discordances arose due to both incomplete lineage sorting and gene flow. D-statistics and f-branch analyses supported gene flow between members of Delphinoidea, with the vast majority of gene flow occurring as ancient interfamilial events. Demographic analyses provided evidence that introgressive gene flow has likely ceased between all species pairs tested, despite reports of contemporary interspecific hybrids. Our study provides the first steps towards resolving the large complexity of speciation within Delphinoidea; we reveal the prevalence of ancient interfamilial gene flow events prior to the diversification of each family, and suggest that contemporary hybridisation events may be disadvantageous, as hybrid individuals do not appear to contribute to the parental species' gene pools.
Collapse
Affiliation(s)
| | | | | | - Binia De Cahsan
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - David A Duchêne
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Stefanie Hartmann
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | |
Collapse
|
43
|
Tumendemberel O, Hendricks SA, Hohenlohe PA, Sullivan J, Zedrosser A, Saebø M, Proctor MF, Koprowski JL, Waits LP. Range-wide evolutionary relationships and historical demography of brown bears (Ursus arctos) revealed by whole-genome sequencing of isolated central Asian populations. Mol Ecol 2023; 32:5156-5169. [PMID: 37528604 DOI: 10.1111/mec.17091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 07/02/2023] [Accepted: 07/19/2023] [Indexed: 08/03/2023]
Abstract
Phylogeographic studies uncover hidden pathways of divergence and inform conservation. Brown bears (Ursus arctos) have one of the broadest distributions of all land mammals, ranging from Eurasia to North America, and are an important model for evolutionary studies. Although several whole genomes were available for individuals from North America, Europe and Asia, limited whole-genome data were available from Central Asia, including the highly imperilled brown bears in the Gobi Desert. To fill this knowledge gap, we sequenced whole genomes from nine Asian brown bears from the Gobi Desert of Mongolia, Northern Mongolia and the Himalayas of Pakistan. We combined these data with published brown bear sequences from Europe, Asia and North America, as well as other bear species. Our goals were to determine the evolutionary relationships among brown bear populations worldwide, their genetic diversity and their historical demography. Our analyses revealed five major lineages of brown bears based on a filtered set of 684,081 single nucleotide polymorphisms. We found distinct evolutionary lineages of brown bears in the Gobi, Himalayas, northern Mongolia, Europe and North America. The lowest level of genetic diversity and the highest level of inbreeding were found in Pakistan, the Gobi Desert and Central Italy. Furthermore, the effective population size (Ne ) for all brown bears decreased over the last 70,000 years. Our results confirm the genetic distinctiveness and ancient lineage of brown bear subspecies in the Gobi Desert of Mongolia and the Himalayas of Pakistan and highlight their importance for conservation.
Collapse
Affiliation(s)
- Odbayar Tumendemberel
- Haub School of Environment and Natural Resources, University of Wyoming, Laramie, Wyoming, USA
- Department of Natural Science and Environmental Health, University of South-Eastern Norway, Bø i Telemark, Norway
| | - Sarah A Hendricks
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, Idaho, USA
| | - Paul A Hohenlohe
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, Idaho, USA
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | - Jack Sullivan
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, Idaho, USA
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | - Andreas Zedrosser
- Department of Natural Science and Environmental Health, University of South-Eastern Norway, Bø i Telemark, Norway
| | - Mona Saebø
- Department of Natural Science and Environmental Health, University of South-Eastern Norway, Bø i Telemark, Norway
| | | | - John L Koprowski
- Haub School of Environment and Natural Resources, University of Wyoming, Laramie, Wyoming, USA
| | - Lisette P Waits
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, Idaho, USA
| |
Collapse
|
44
|
Wang T, van Dijk ADJ, Bucher J, Liang J, Wu J, Bonnema G, Wang X. Interploidy Introgression Shaped Adaptation during the Origin and Domestication History of Brassica napus. Mol Biol Evol 2023; 40:msad199. [PMID: 37707440 PMCID: PMC10504873 DOI: 10.1093/molbev/msad199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/15/2023] Open
Abstract
Polyploidy is recurrent across the tree of life and known as an evolutionary driving force in plant diversification and crop domestication. How polyploid plants adapt to various habitats has been a fundamental question that remained largely unanswered. Brassica napus is a major crop cultivated worldwide, resulting from allopolyploidy between unknown accessions of diploid B. rapa and B. oleracea. Here, we used whole-genome resequencing data of accessions representing the majority of morphotypes and ecotypes from the species B. rapa, B. oleracea, and B. napus to investigate the role of polyploidy during domestication. To do so, we first reconstructed the phylogenetic history of B. napus, which supported the hypothesis that the emergence of B. napus derived from the hybridization of European turnip of B. rapa and wild B. oleracea. These analyses also showed that morphotypes of swede and Siberian kale (used as vegetable and fodder) were domesticated before rapeseed (oil crop). We next observed that frequent interploidy introgressions from sympatric diploids were prominent throughout the domestication history of B. napus. Introgressed genomic regions were shown to increase the overall genetic diversity and tend to be localized in regions of high recombination. We detected numerous candidate adaptive introgressed regions and found evidence that some of the genes in these regions contributed to phenotypic diversification and adaptation of different morphotypes. Overall, our results shed light on the origin and domestication of B. napus and demonstrate interploidy introgression as an important mechanism that fuels rapid diversification in polyploid species.
Collapse
Affiliation(s)
- Tianpeng Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Aalt D J van Dijk
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Johan Bucher
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Jianli Liang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian Wu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guusje Bonnema
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Xiaowu Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
45
|
Wogan GOU, Yuan ML, Mahler DL, Wang IJ. Hybridization and Transgressive Evolution Generate Diversity in an Adaptive Radiation of Anolis Lizards. Syst Biol 2023; 72:874-884. [PMID: 37186031 PMCID: PMC10687355 DOI: 10.1093/sysbio/syad026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 04/01/2023] [Accepted: 04/24/2023] [Indexed: 05/17/2023] Open
Abstract
Interspecific hybridization may act as a major force contributing to the evolution of biodiversity. Although generally thought to reduce or constrain divergence between 2 species, hybridization can, paradoxically, promote divergence by increasing genetic variation or providing novel combinations of alleles that selection can act upon to move lineages toward new adaptive peaks. Hybridization may, then, play a key role in adaptive radiation by allowing lineages to diversify into new ecological space. Here, we test for signatures of historical hybridization in the Anolis lizards of Puerto Rico and evaluate 2 hypotheses for the role of hybridization in facilitating adaptive radiation-the hybrid swarm origins hypothesis and the syngameon hypothesis. Using whole genome sequences from all 10 species of Puerto Rican anoles, we calculated D and f-statistics (from ABBA-BABA tests) to test for introgression across the radiation and employed multispecies network coalescent methods to reconstruct phylogenetic networks that allow for hybridization. We then analyzed morphological data for these species to test for patterns consistent with transgressive evolution, a phenomenon in which the trait of a hybrid lineage is found outside of the range of its 2 parents. Our analyses uncovered strong evidence for introgression at multiple stages of the radiation, including support for an ancient hybrid origin of a clade comprising half of the extant Puerto Rican anole species. Moreover, we detected significant signals of transgressive evolution for 2 ecologically important traits, head length and toepad width, the latter of which has been described as a key innovation in Anolis. [Adaptive radiation; introgression; multispecies network coalescent; phenotypic evolution; phylogenetic network; reticulation; syngameon; transgressive segregation.].
Collapse
Affiliation(s)
- Guinevere O U Wogan
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Michael L Yuan
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
| | - D Luke Mahler
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Ian J Wang
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
| |
Collapse
|
46
|
Wu D, Xie L, Sun Y, Huang Y, Jia L, Dong C, Shen E, Ye CY, Qian Q, Fan L. A syntelog-based pan-genome provides insights into rice domestication and de-domestication. Genome Biol 2023; 24:179. [PMID: 37537691 PMCID: PMC10401782 DOI: 10.1186/s13059-023-03017-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 07/19/2023] [Indexed: 08/05/2023] Open
Abstract
BACKGROUND Asian rice is one of the world's most widely cultivated crops. Large-scale resequencing analyses have been undertaken to explore the domestication and de-domestication genomic history of Asian rice, but the evolution of rice is still under debate. RESULTS Here, we construct a syntelog-based rice pan-genome by integrating and merging 74 high-accuracy genomes based on long-read sequencing, encompassing all ecotypes and taxa of Oryza sativa and Oryza rufipogon. Analyses of syntelog groups illustrate subspecies divergence in gene presence-and-absence and haplotype composition and identify massive genomic regions putatively introgressed from ancient Geng/japonica to ancient Xian/indica or its wild ancestor, including almost all well-known domestication genes and a 4.5-Mbp centromere-spanning block, supporting a single domestication event in main rice subspecies. Genomic comparisons between weedy and cultivated rice highlight the contribution from wild introgression to the emergence of de-domestication syndromes in weedy rice. CONCLUSIONS This work highlights the significance of inter-taxa introgression in shaping diversification and divergence in rice evolution and provides an exploratory attempt by utilizing the advantages of pan-genomes in evolutionary studies.
Collapse
Affiliation(s)
- Dongya Wu
- Hainan Institute of Zhejiang University, Sanya, 572025, China
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
- Center for Evolutionary & Organismal Biology, Zhejiang University, Hangzhou, 310058, China
| | - Lingjuan Xie
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Yanqing Sun
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Yujie Huang
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Lei Jia
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Chenfeng Dong
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Enhui Shen
- Hainan Institute of Zhejiang University, Sanya, 572025, China
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Chu-Yu Ye
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
| | - Longjiang Fan
- Hainan Institute of Zhejiang University, Sanya, 572025, China.
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China.
| |
Collapse
|
47
|
L Rocha J, Silva P, Santos N, Nakamura M, Afonso S, Qninba A, Boratynski Z, Sudmant PH, Brito JC, Nielsen R, Godinho R. North African fox genomes show signatures of repeated introgression and adaptation to life in deserts. Nat Ecol Evol 2023; 7:1267-1286. [PMID: 37308700 PMCID: PMC10527534 DOI: 10.1038/s41559-023-02094-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 04/26/2023] [Indexed: 06/14/2023]
Abstract
Elucidating the evolutionary process of animal adaptation to deserts is key to understanding adaptive responses to climate change. Here we generated 82 individual whole genomes of four fox species (genus Vulpes) inhabiting the Sahara Desert at different evolutionary times. We show that adaptation of new colonizing species to a hot arid environment has probably been facilitated by introgression and trans-species polymorphisms shared with older desert resident species, including a putatively adaptive 25 Mb genomic region. Scans for signatures of selection implicated genes affecting temperature perception, non-renal water loss and heat production in the recent adaptation of North African red foxes (Vulpes vulpes), after divergence from Eurasian populations approximately 78 thousand years ago. In the extreme desert specialists, Rueppell's fox (V. rueppellii) and fennec (V. zerda), we identified repeated signatures of selection in genes affecting renal water homeostasis supported by gene expression and physiological differences. Our study provides insights into the mechanisms and genetic underpinnings of a natural experiment of repeated adaptation to extreme conditions.
Collapse
Affiliation(s)
- Joana L Rocha
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal.
- Department of Integrative Biology and Department of Statistics, University of California Berkeley, Berkeley, CA, USA.
| | - Pedro Silva
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Nuno Santos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Mónia Nakamura
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Sandra Afonso
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Abdeljebbar Qninba
- Laboratory of Geophysics and Natural Hazards, Geophysics, Natural Patrimony and Green Chemistry Research Center (GEOPAC), Institut Scientifique, Mohammed V University of Rabat, Rabat, Morocco
| | - Zbyszek Boratynski
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Peter H Sudmant
- Department of Integrative Biology and Department of Statistics, University of California Berkeley, Berkeley, CA, USA
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - José C Brito
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Rasmus Nielsen
- Department of Integrative Biology and Department of Statistics, University of California Berkeley, Berkeley, CA, USA.
- Center for Computational Biology, University of California, Berkeley, CA, USA.
- Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Raquel Godinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal.
- Department of Zoology, University of Johannesburg, Auckland Park, South Africa.
| |
Collapse
|
48
|
Kinneberg VB, Lü DS, Peris D, Ravinet M, Skrede I. Introgression between highly divergent fungal sister species. J Evol Biol 2023; 36:1133-1149. [PMID: 37363874 DOI: 10.1111/jeb.14190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 06/28/2023]
Abstract
To understand how species evolve and adapt to changing environments, it is important to study gene flow and introgression due to their influence on speciation and radiation events. Here, we apply a novel experimental system for investigating these mechanisms using natural populations. The system is based on two fungal sister species with morphological and ecological similarities occurring in overlapping habitats. We examined introgression between these species by conducting whole genome sequencing of individuals from populations in North America and Europe. We assessed genome-wide nucleotide divergence and performed crossing experiments to study reproductive barriers. We further used ABBA-BABA statistics together with a network analysis to investigate introgression, and conducted demographic modelling to gain insight into divergence times and introgression events. The results revealed that the species are highly divergent and incompatible in vitro. Despite this, small regions of introgression were scattered throughout the genomes and one introgression event likely involves a ghost population (extant or extinct). This study demonstrates that introgression can be found among divergent species and that population histories can be studied without collections of all the populations involved. Moreover, the experimental system is shown to be a useful tool for research on reproductive isolation in natural populations.
Collapse
Affiliation(s)
- Vilde Bruhn Kinneberg
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
- Evolution and Paleobiology, Natural History Museum, University of Oslo, Oslo, Norway
| | - Dabao Sun Lü
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - David Peris
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Valencia, Spain
| | - Mark Ravinet
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Inger Skrede
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| |
Collapse
|
49
|
Wu B, Meng J, Liu H, Mao D, Yin H, Zhang Z, Zhou X, Zhang B, Sherif A, Liu H, Li X, Xiao J, Yan W, Wang L, Li X, Chen W, Xie W, Yin P, Zhang Q, Xing Y. Suppressing a phosphohydrolase of cytokinin nucleotide enhances grain yield in rice. Nat Genet 2023; 55:1381-1389. [PMID: 37500729 DOI: 10.1038/s41588-023-01454-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 06/21/2023] [Indexed: 07/29/2023]
Abstract
One-step and two-step pathways are proposed to synthesize cytokinin in plants. The one-step pathway is mediated by LONELY GUY (LOG) proteins. However, the enzyme for the two-step pathway remains to be identified. Here, we show that quantitative trait locus GY3 may boost grain yield by more than 20% through manipulating a two-step pathway. Locus GY3 encodes a LOG protein that acts as a 5'-ribonucleotide phosphohydrolase by excessively consuming the cytokinin precursors, which contrasts with the activity of canonical LOG members as phosphoribohydrolases in a one-step pathway. The residue S41 of GY3 is crucial for the dephosphorylation of iPRMP to produce iPR. A solo-LTR insertion within the promoter of GY3 suppressed its expression and resulted in a higher content of active cytokinins in young panicles. Introgression of GY302428 increased grain yield per plot by 7.4% to 16.3% in all investigated indica backgrounds, which demonstrates the great value of GY302428 in indica rice production.
Collapse
Affiliation(s)
- Bi Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Jianghu Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Hongbo Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Donghai Mao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Huanran Yin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Zhanyi Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xiangchun Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Bo Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Ahmed Sherif
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Haiyang Liu
- Hubei collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Wenhao Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Lei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Xingwang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
- Hubei Hongshan Laboratory, Wuhan, China.
| |
Collapse
|
50
|
Wang N, Cao S, Liu Z, Xiao H, Hu J, Xu X, Chen P, Ma Z, Ye J, Chai L, Guo W, Larkin RM, Xu Q, Morrell PL, Zhou Y, Deng X. Genomic conservation of crop wild relatives: A case study of citrus. PLoS Genet 2023; 19:e1010811. [PMID: 37339133 DOI: 10.1371/journal.pgen.1010811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 06/01/2023] [Indexed: 06/22/2023] Open
Abstract
Conservation of crop wild relatives is critical for plant breeding and food security. The lack of clarity on the genetic factors that lead to endangered status or extinction create difficulties when attempting to develop concrete recommendations for conserving a citrus wild relative: the wild relatives of crops. Here, we evaluate the conservation of wild kumquat (Fortunella hindsii) using genomic, geographical, environmental, and phenotypic data, and forward simulations. Genome resequencing data from 73 accessions from the Fortunella genus were combined to investigate population structure, demography, inbreeding, introgression, and genetic load. Population structure was correlated with reproductive type (i.e., sexual and apomictic) and with a significant differentiation within the sexually reproducing population. The effective population size for one of the sexually reproducing subpopulations has recently declined to ~1,000, resulting in high levels of inbreeding. In particular, we found that 58% of the ecological niche overlapped between wild and cultivated populations and that there was extensive introgression into wild samples from cultivated populations. Interestingly, the introgression pattern and accumulation of genetic load may be influenced by the type of reproduction. In wild apomictic samples, the introgressed regions were primarily heterozygous, and genome-wide deleterious variants were hidden in the heterozygous state. In contrast, wild sexually reproducing samples carried a higher recessive deleterious burden. Furthermore, we also found that sexually reproducing samples were self-incompatible, which prevented the reduction of genetic diversity by selfing. Our population genomic analyses provide specific recommendations for distinct reproductive types and monitoring during conservation. This study highlights the genomic landscape of a wild relative of citrus and provides recommendations for the conservation of crop wild relatives.
Collapse
Affiliation(s)
- Nan Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shuo Cao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhongjie Liu
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hua Xiao
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jianbing Hu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Xiaodong Xu
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Peng Chen
- Institute of Horticultural Research, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Zhiyao Ma
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Junli Ye
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Lijun Chai
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Wenwu Guo
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Robert M Larkin
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Qiang Xu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Yongfeng Zhou
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- State Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xiuxin Deng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| |
Collapse
|