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Kremer A, Chen J, Lascoux M. 'Chimes of resilience': what makes forest trees genetically resilient? THE NEW PHYTOLOGIST 2025; 246:1934-1951. [PMID: 40190135 PMCID: PMC12059515 DOI: 10.1111/nph.70108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2024] [Accepted: 02/28/2025] [Indexed: 05/10/2025]
Abstract
Forest trees are foundation species of many ecosystems and are challenged by global environmental changes. We assemble genetic facts and arguments supporting or undermining resilient responses of forest trees to those changes. Genetic resilience is understood here as the capacity of a species to restore its adaptive potential following environmental changes and disturbances. Importantly, the data come primarily from European temperate tree species with large distributions and consider only marginally species with small distributions. We first examine historical trajectories of trees during repeated climatic changes. Species that survived the Pliocene-Pleistocene transition and underwent the oscillations of glacial and interglacial periods were equipped with life history traits enhancing persistence and resilience. Evidence of their resilience also comes from the maintenance of large effective population sizes across time and rapid microevolutionary responses to recent climatic events. We then review genetic mechanisms and attributes shaping resilient responses. Usually, invoked constraints to resilience, such as genetic load or generation time and overlap, have limited consequences or are offset by positive impacts. Conversely, genetic plasticity, gene flow, introgression, genetic architecture of fitness-related traits and demographic dynamics strengthen resilience by accelerating adaptive responses. Finally, we address the limitations of this review and highlight critical research gaps.
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Affiliation(s)
- Antoine Kremer
- UMR BIOGECO, INRAEUniversité de BordeauxCestas33612France
| | - Jun Chen
- College of Life SciencesZhejiang UniversityHangzhou310058China
| | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityUppsalaSE‐75236Sweden
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2
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Chai MW, Lu HP, Liao PC. A Historical Misstep: Niche Shift to Specialisation Is Pushing Insular Ginger Towards an Evolutionary Dead End. Mol Ecol 2025; 34:e17765. [PMID: 40192449 DOI: 10.1111/mec.17765] [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: 05/23/2024] [Revised: 03/10/2025] [Accepted: 04/01/2025] [Indexed: 05/06/2025]
Abstract
Niche specialisation is a double-edged sword as it aids species in adapting to a particular environment but makes them more susceptible to environmental change, which may result in species extinction. Although it has long been debated whether niche specialisation necessarily falls into an 'evolutionary dead end', empirical evidence from a population genetics perspective remains scant, especially when comparing both ecological generalists and specialists simultaneously. In this study, we scrutinised two Taiwan endemic gingers (Zingiber pleiostachyum and Z. shuanglongense) to evaluate how their contrasting patterns in niche breadth evolution have shaped their evolutionary trajectories. We utilised a genome-wide sequencing approach to investigate the demographic histories of each species, assess their maladaptation to future climate change, and estimate their mutational loads. Our results revealed distinct demographic histories between these two gingers. Z. shuanglongense, as the specialist, despite an initial increase during the Last Glacial Maximum (~22 Kya), has been subjected to a long-term decrease in effective population size (Ne), while Z. pleiostachyum is on the contrary increasing, leading to a significantly larger current Ne. Furthermore, ecological specialists are much more vulnerable to future climate change and exhibit greater drift-associated deleterious mutations compared to generalists, directly affecting species' fitness. This study strongly supports the idea that the transition in niche breadth towards specialisation will push Z. shuanglongense perilously close to extinction and also sheds light on species conservation within limited migratory space.
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Affiliation(s)
- Min-Wei Chai
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Hsin-Pei Lu
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Pei-Chun Liao
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
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3
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Chang Y, Zhang R, Liu Y, Liu Y, Tao L, Liu D, Ma Y, Sun W. Conservation genomics of a threatened subtropical Rhododendron species highlights the distinct conservation actions required in marginal and admixed populations. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2025; 122:e70175. [PMID: 40287966 PMCID: PMC12034323 DOI: 10.1111/tpj.70175] [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: 09/20/2024] [Revised: 04/03/2025] [Accepted: 04/10/2025] [Indexed: 04/29/2025]
Abstract
With the impact of climate change and anthropogenic activities, the underlying threats facing populations with different evolutionary histories and distributions, and the associated conservation strategies necessary to ensure their survival, may vary within a species. This is particularly true for marginal populations and/or those showing admixture. Here, we re-sequence genomes of 102 individuals from 21 locations for Rhododendron vialii, a threatened species distributed in the subtropical forests of southwestern China that has suffered from habitat fragmentation due to deforestation. Population structure results revealed that R. vialii can be divided into five genetic lineages using neutral single-nucleotide polymorphisms (SNPs), whereas selected SNPs divide the species into six lineages. This is due to the Guigu (GG) population, which is identified as admixed using neutral SNPs, but is assigned to a distinct genetic cluster using non-neutral loci. R. vialii has experienced multiple genetic bottlenecks, and different demographic histories have been suggested among populations. Ecological niche modeling combined with genomic offset analysis suggests that the marginal population (Northeast, NE) harboring the highest genetic diversity is likely to have the highest risk of maladaptation in the future. The marginal population therefore needs urgent ex situ conservation in areas where the influence of future climate change is predicted to be well buffered. Alternatively, the GG population may have the potential for local adaptation, and will need in situ conservation. The Puer population, which carries the heaviest genetic load, needs genetic rescue. Our findings highlight how population genomics, genomic offset analysis, and ecological niche modeling can be integrated to inform targeted conservation.
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Affiliation(s)
- Yuhang Chang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of BotanyChinese Academy of SciencesKunming650201China
- University of Chinese Academy of SciencesBeijing101408China
| | - Rengang Zhang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of BotanyChinese Academy of SciencesKunming650201China
- University of Chinese Academy of SciencesBeijing101408China
| | - Yang Liu
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of BotanyChinese Academy of SciencesKunming650201China
- University of Chinese Academy of SciencesBeijing101408China
| | - Yuhang Liu
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of BotanyChinese Academy of SciencesKunming650201China
| | - Lidan Tao
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of BotanyChinese Academy of SciencesKunming650201China
- University of Chinese Academy of SciencesBeijing101408China
| | - Detuan Liu
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of BotanyChinese Academy of SciencesKunming650201China
| | - Yongpeng Ma
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of BotanyChinese Academy of SciencesKunming650201China
- University of Chinese Academy of SciencesBeijing101408China
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of BotanyChinese Academy of SciencesKunming650201China
| | - Weibang Sun
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of BotanyChinese Academy of SciencesKunming650201China
- University of Chinese Academy of SciencesBeijing101408China
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of BotanyChinese Academy of SciencesKunming650201China
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4
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Jiang J, Chen JF, Li XT, Wang L, Mao JF, Wang BS, Guo YL. Incorporating genetic load contributes to predicting Arabidopsis thaliana's response to climate change. Nat Commun 2025; 16:2752. [PMID: 40113777 PMCID: PMC11926394 DOI: 10.1038/s41467-025-58021-z] [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: 10/30/2023] [Accepted: 03/06/2025] [Indexed: 03/22/2025] Open
Abstract
Understanding how species respond to climate change can facilitate species conservation and crop breeding. Current prediction frameworks about population vulnerability focused on predicting range shifts or local adaptation but ignored genetic load, which is also crucial for adaptation. By analyzing 1115 globally distributed Arabidopsis thaliana natural accessions, we find that effective population size (Ne) is the major contributor of genetic load variation, both along genome and among populations, and can explain 74-94% genetic load variation in natural populations. Intriguingly, Ne affects genetic load by changing both effectiveness of purifying selection and GC biased gene conversion strength. In particular, by incorporating genetic load, genetic offset and species distribution models (SDM), we predict that, the populations at species' range edge are generally at higher risk. The populations at the eastern range perform poorer in all aspects, southern range have higher genetic offset and lower SDM suitability, while northern range have higher genetic load. Among the diverse natural populations, the Yangtze River basin population is the most vulnerable population under future climate change. Overall, here we deciphered the driving forces of genetic load in A. thaliana, and incorporated SDM, local adaptation and genetic load to predict the fate of populations under future climate change.
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Affiliation(s)
- Juan Jiang
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jia-Fu Chen
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xin-Tong Li
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Li Wang
- Agricultural Synthetic Biology Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jian-Feng Mao
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Bao-Sheng Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Ya-Long Guo
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
- China National Botanical Garden, Beijing, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
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5
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Piot A, El‐Kassaby YA, Porth I. Exon disruptive variants in Populus trichocarpa associated with wood properties exhibit distinct gene expression patterns. THE PLANT GENOME 2025; 18:e20541. [PMID: 39632472 PMCID: PMC11726415 DOI: 10.1002/tpg2.20541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 11/07/2024] [Accepted: 11/10/2024] [Indexed: 12/07/2024]
Abstract
Forest trees may harbor naturally occurring exon disruptive variants (DVs) in their gene sequences, which potentially impact important ecological and economic phenotypic traits. However, the abundance and molecular regulation of these variants remain largely unexplored. Here, 24,420 DVs were identified by screening 1014 Populus trichocarpa full genomes. The identified DVs were predominantly heterozygous with allelic frequencies below 5% (only 26% of DVs had frequencies greater than 5%). Using common garden-grown trees, DVs were assessed for gene expression variation in the developing xylem, revealing that their gene expression can be significantly altered, particularly for homozygous DVs (in the range of 27%-38% of cases depending on the studied common garden). DVs were further investigated for their correlations with 13 wood quality traits, revealing that, among the 148 discovered DV associations, 15 correlated with more than one wood property and six genes had more than one DV in their coding sequences associated with wood traits. Approximately one-third of DVs correlated with wood property variation also showed significant gene expression variation, confirming their non-spurious impact. These findings offer potential avenues for targeted introduction of homozygous mutations using tree biotechnology, and while the exact mechanisms by which DVs may directly influence wood formation remain to be unraveled, this study lays the groundwork for further investigation.
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Affiliation(s)
- Anthony Piot
- Department of Wood and Forest SciencesUniversité LavalQuebec CityQuebecCanada
- Institute for System and Integrated Biology (IBIS)Université LavalQuebec CityQuebecCanada
- Centre for Forest ResearchUniversité LavalQuebec CityQuebecCanada
| | - Yousry A. El‐Kassaby
- Department of Forest and Conservation Sciences, Faculty of ForestryThe University of British ColumbiaVancouverBritish ColumbiaCanada
| | - Ilga Porth
- Department of Wood and Forest SciencesUniversité LavalQuebec CityQuebecCanada
- Institute for System and Integrated Biology (IBIS)Université LavalQuebec CityQuebecCanada
- Centre for Forest ResearchUniversité LavalQuebec CityQuebecCanada
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6
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Long EM, Stitzer MC, Monier B, Schulz AJ, Romay MC, Robbins KR, Buckler ES. Evolutionary signatures of the erosion of sexual reproduction genes in domesticated cassava (Manihot esculenta). G3 (BETHESDA, MD.) 2025; 15:jkae282. [PMID: 39673428 PMCID: PMC11797036 DOI: 10.1093/g3journal/jkae282] [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: 09/18/2024] [Revised: 11/14/2024] [Accepted: 11/18/2024] [Indexed: 12/16/2024]
Abstract
Centuries of clonal propagation in cassava (Manihot esculenta) have reduced sexual recombination, leading to the accumulation of deleterious mutations. This has resulted in both inbreeding depression affecting yield and a significant decrease in reproductive performance, creating hurdles for contemporary breeding programs. Cassava is a member of the Euphorbiaceae family, including notable species such as rubber tree (Hevea brasiliensis) and poinsettia (Euphorbia pulcherrima). Expanding upon preliminary draft genomes, we annotated 7 long-read genome assemblies and aligned a total of 52 genomes, to analyze selection across the genome and the phylogeny. Through this comparative genomic approach, we identified 48 genes under relaxed selection in cassava. Notably, we discovered an overrepresentation of floral expressed genes, especially focused at 6 pollen-related genes. Our results indicate that domestication and a transition to clonal propagation have reduced selection pressures on sexually reproductive functions in cassava leading to an accumulation of mutations in pollen-related genes. This relaxed selection and the genome-wide deleterious mutations responsible for inbreeding depression are potential targets for improving cassava breeding, where the generation of new varieties relies on recombining favorable alleles through sexual reproduction.
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Affiliation(s)
- Evan M Long
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
- Department of Plant Sciences, University of California Davis, Davis, CA 95616, USA
| | - Michelle C Stitzer
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA
| | - Brandon Monier
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA
| | - Aimee J Schulz
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Maria Cinta Romay
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA
| | - Kelly R Robbins
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Edward S Buckler
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA
- United States Department of Agriculture-Agricultural Research Service, Robert W. Holley, Center for Agriculture and Health, Ithaca, NY 14853, USA
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7
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Wilkinson MJ, McLay K, Kainer D, Elphinstone C, Dillon NL, Webb M, Wijesundara UK, Ali A, Bally ISE, Munyengwa N, Furtado A, Henry RJ, Hardner CM, Ortiz-Barrientos D. Centromeres are hotspots for chromosomal inversions and breeding traits in mango. THE NEW PHYTOLOGIST 2025; 245:899-913. [PMID: 39548673 DOI: 10.1111/nph.20252] [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: 07/22/2024] [Accepted: 10/15/2024] [Indexed: 11/18/2024]
Abstract
Chromosomal inversions can preserve combinations of favorable alleles by suppressing recombination. Simultaneously, they reduce the effectiveness of purifying selection enabling deleterious alleles to accumulate. This study explores how areas of low recombination, including centromeric regions and chromosomal inversions, contribute to the accumulation of deleterious and favorable loci in 225 Mangifera indica genomes from the Australian Mango Breeding Program. Here, we identify 17 chromosomal inversions that cover 7.7% (29.7 Mb) of the M. indica genome: eight pericentric (inversion includes the centromere) and nine paracentric (inversion is on one arm of the chromosome). Our results show that these large pericentric inversions are accumulating deleterious loci, while the paracentric inversions show deleterious levels above and below the genome wide average. We find that despite their deleterious load, chromosomal inversions contain small effect loci linked to variation in crucial breeding traits. These results indicate that chromosomal inversions have likely facilitated the evolution of key mango breeding traits. Our study has important implications for selective breeding of favorable combinations of alleles in regions of low recombination.
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Affiliation(s)
- Melanie J Wilkinson
- School of the Environment, The University of Queensland, Brisbane, Qld, 4072, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, Qld, 4072, Australia
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Kathleen McLay
- School of the Environment, The University of Queensland, Brisbane, Qld, 4072, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - David Kainer
- School of the Environment, The University of Queensland, Brisbane, Qld, 4072, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Cassandra Elphinstone
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Natalie L Dillon
- Queensland Department of Agriculture and Fisheries, Mareeba, Qld, 4880, Australia
| | - Matthew Webb
- Queensland Department of Agriculture and Fisheries, Brisbane, Qld, 4001, Australia
| | - Upendra K Wijesundara
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Asjad Ali
- Queensland Department of Agriculture and Fisheries, Mareeba, Qld, 4880, Australia
| | - Ian S E Bally
- Queensland Department of Agriculture and Fisheries, Mareeba, Qld, 4880, Australia
| | - Norman Munyengwa
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Robert J Henry
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, Qld, 4072, Australia
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Craig M Hardner
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Daniel Ortiz-Barrientos
- School of the Environment, The University of Queensland, Brisbane, Qld, 4072, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, Qld, 4072, Australia
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8
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Zhu X, Wang J, Chen H, Kang M. Lineage Differentiation and Genomic Vulnerability in a Relict Tree From Subtropical Forests. Evol Appl 2024; 17:e70033. [PMID: 39494192 PMCID: PMC11530410 DOI: 10.1111/eva.70033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 10/09/2024] [Accepted: 10/11/2024] [Indexed: 11/05/2024] Open
Abstract
The subtropical forests of East Asia are renowned for their high plant diversity, particularly the abundance of ancient relict species. However, both the evolutionary history of these relict species and their capacity for resilience in the face of impending climatic changes remain unclear. Using whole-genome resequencing data, we investigated the lineage differentiation and demographic history of the relict and endangered tree, Bretschneidera sinensis (Akaniaceae). We employed a combination of population genomic and landscape genomic approaches to evaluate variation in mutation load and genomic offset, aiming to predict how different populations may respond to climate change. Our analysis revealed a profound genomic divergence between the East and West lineages, likely as the result of recurrent bottlenecks due to climatic fluctuations during the glacial period. Furthermore, we identified several genes potentially linked to growth characteristics and hypoxia response that had been subjected to positive selection during the lineage differentiation. Our assessment of genomic vulnerability uncovered a significantly higher mutation load and genomic offset in the edge populations of B. sinensis compared to their core counterparts. This implies that the edge populations are likely to experience the most significant impact from the predicted climate conditions. Overall, our research sheds light on the historical lineage differentiation and contemporary genomic vulnerability of B. sinensis. Broadening our understanding of the speciation history and future resilience of relict and endangered species such as B. sinensis, is crucial in developing effective conservation strategies in anticipation of future climatic changes.
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Affiliation(s)
- Xian‐Liang Zhu
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern ChinaGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jing Wang
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern ChinaGuangzhouChina
- South China National Botanical GardenGuangzhouChina
| | - Hong‐Feng Chen
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern ChinaGuangzhouChina
- South China National Botanical GardenGuangzhouChina
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
| | - Ming Kang
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern ChinaGuangzhouChina
- South China National Botanical GardenGuangzhouChina
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
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9
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Chen XY, Zhou BF, Shi Y, Liu H, Liang YY, Ingvarsson PK, Wang B. Evolution of the Correlated Genomic Variation Landscape Across a Divergence Continuum in the Genus Castanopsis. Mol Biol Evol 2024; 41:msae191. [PMID: 39248185 PMCID: PMC11421576 DOI: 10.1093/molbev/msae191] [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: 04/14/2024] [Revised: 08/27/2024] [Accepted: 09/03/2024] [Indexed: 09/10/2024] Open
Abstract
The heterogeneous landscape of genomic variation has been well documented in population genomic studies. However, disentangling the intricate interplay of evolutionary forces influencing the genetic variation landscape over time remains challenging. In this study, we assembled a chromosome-level genome for Castanopsis eyrei and sequenced the whole genomes of 276 individuals from 12 Castanopsis species, spanning a broad divergence continuum. We found highly correlated genomic variation landscapes across these species. Furthermore, variations in genetic diversity and differentiation along the genome were strongly associated with recombination rates and gene density. These results suggest that long-term linked selection and conserved genomic features have contributed to the formation of a common genomic variation landscape. By examining how correlations between population summary statistics change throughout the species divergence continuum, we determined that background selection alone does not fully explain the observed patterns of genomic variation; the effects of recurrent selective sweeps must be considered. We further revealed that extensive gene flow has significantly influenced patterns of genomic variation in Castanopsis species. The estimated admixture proportion correlated positively with recombination rate and negatively with gene density, supporting a scenario of selection against gene flow. Additionally, putative introgression regions exhibited strong signals of positive selection, an enrichment of functional genes, and reduced genetic burdens, indicating that adaptive introgression has played a role in shaping the genomes of hybridizing species. This study provides insights into how different evolutionary forces have interacted in driving the evolution of the genomic variation landscape.
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Affiliation(s)
- Xue-Yan Chen
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Biao-Feng Zhou
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
| | - Yong Shi
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
| | - Hui Liu
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
| | - Yi-Ye Liang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
| | - Pär K Ingvarsson
- Linnean Center for Plant Biology, Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Baosheng Wang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
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10
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Kou YX, Liu ML, López-Pujol J, Zhang QJ, Zhang ZY, Li ZH. Contrasting demographic history and mutational load in three threatened whitebark pines (Pinus subsect. Gerardianae): implications for conservation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:2967-2981. [PMID: 39115017 DOI: 10.1111/tpj.16965] [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: 03/22/2024] [Revised: 07/12/2024] [Accepted: 07/25/2024] [Indexed: 11/15/2024]
Abstract
Demographic history and mutational load are of paramount importance for the adaptation of the endangered species. However, the effects of population evolutionary history and genetic load on the adaptive potential in endangered conifers remain unclear. Here, using population transcriptome sequencing, whole chloroplast genomes and mitochondrial DNA markers, combined with niche analysis, we determined the demographic history and mutational load for three threatened whitebark pines having different endangered statuses, Pinus bungeana, P. gerardiana and P. squamata. Demographic inference indicated that severe bottlenecks occurred in all three pines at different times, coinciding with periods of major climate and geological changes; in contrast, while P. bungeana experienced a recent population expansion, P. gerardiana and P. squamata maintained small population sizes after bottlenecking. Abundant homozygous-derived variants accumulated in the three pines, particularly in P. squamata, while the species with most heterozygous variants was P. gerardiana. Abundant moderately and few highly deleterious variants accumulated in the pine species that have experienced the most severe demographic bottlenecks (P. gerardiana and P. squamata), most likely because of purging effects. Finally, niche modeling showed that the distribution of P. bungeana might experience a significant expansion in the future, and the species' identified genetic clusters are also supported by differences in the ecological niche. The integration of genomic, demographic and niche data has allowed us to prove that the three threatened pines have contrasting patterns of demographic history and mutational load, which may have important implications in their adaptive potential and thus are also key for informing conservation planning.
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Affiliation(s)
- Yi-Xuan Kou
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, Guangxi, 541006, China
| | - Mi-Li Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Jordi López-Pujol
- Botanic Institute of Barcelona (IBB), CSIC-CMCNB, Barcelona, Catalonia, 08038, Spain
- Escuela de Ciencias Ambientales, Universidad Espíritu Santo (UEES), Samborondón, 091650, Ecuador
| | - Qi-Jing Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Zhi-Yong Zhang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, Guangxi, 541006, China
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
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11
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Urquhart-Cronish M, Angert AL, Otto SP, MacPherson A. Density-Dependent Selection during Range Expansion Affects Expansion Load in Life History Traits. Am Nat 2024; 203:382-392. [PMID: 38358811 DOI: 10.1086/728599] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
AbstractModels of range expansion have independently explored fitness consequences of life history trait evolution and increased rates of genetic drift-or "allele surfing"-during spatial spread, but no previous model has examined the interactions between these two processes. Here, using spatially explicit simulations, we explore an ecologically complex range expansion scenario that combines density-dependent selection with allele surfing to asses the genetic and fitness consequences of density-dependent selection on the evolution of life history traits. We demonstrate that density-dependent selection on the range edge acts differently depending on the life history trait and can either diminish or enhance allele surfing. Specifically, we show that selection at the range edge is always weaker at sites affecting competitive ability (K-selected traits) than at sites affecting birth rate (r-selected traits). We then link differences in the frequency of deleterious mutations to differences in the efficacy of selection and rate of mutation accumulation across distinct life history traits. Finally, we demonstrate that the observed fitness consequences of allele surfing depend on the population density in which expansion load is measured. Our work highlights the complex relationship between ecology and expressed genetic load, which will be important to consider when interpreting both experimental and field studies of range expansion.
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12
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Aihara T, Araki K, Onuma Y, Cai Y, Paing AMM, Goto S, Hisamoto Y, Tomaru N, Homma K, Takagi M, Yoshida T, Iio A, Nagamatsu D, Kobayashi H, Hirota M, Uchiyama K, Tsumura Y. Divergent mechanisms of reduced growth performance in Betula ermanii saplings from high-altitude and low-latitude range edges. Heredity (Edinb) 2023; 131:387-397. [PMID: 37940658 PMCID: PMC10673911 DOI: 10.1038/s41437-023-00655-0] [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: 05/10/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 11/10/2023] Open
Abstract
The reduced growth performance of individuals from range edges is a common phenomenon in various taxa, and considered to be an evolutionary factor that limits the species' range. However, most studies did not distinguish between two mechanisms that can lead to this reduction: genetic load and adaptive selection to harsh conditions. To address this lack of understanding, we investigated the climatic and genetic factors underlying the growth performance of Betula ermanii saplings transplanted from 11 populations including high-altitude edge and low-latitude edge population. We estimated the climatic position of the populations within the overall B. ermanii's distribution, and the genetic composition and diversity using restriction-site associated DNA sequencing, and measured survival, growth rates and individual size of the saplings. The high-altitude edge population (APW) was located below the 95% significance interval for the mean annual temperature range, but did not show any distinctive genetic characteristics. In contrast, the low-latitude edge population (SHK) exhibited a high level of linkage disequilibrium, low genetic diversity, a distinct genetic composition from the other populations, and a high relatedness coefficient. Both APW and SHK saplings displayed lower survival rates, heights and diameters, while SHK saplings also exhibited lower growth rates than the other populations' saplings. The low heights and diameters of APW saplings was likely the result of adaptive selection to harsh conditions, while the low survival and growth rates of SHK saplings was likely the result of genetic load. Our findings shed light on the mechanisms underlying the reduced growth performance of range-edge populations.
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Affiliation(s)
- Takaki Aihara
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Kyoko Araki
- Garden Division, Maintenance and Works Department, the Imperial Household Agency, 1-1, Chiyoda, Chiyoda-ku, Tokyo, 100-8111, Japan
- Graduate School of Science and Technology, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Yunosuke Onuma
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Yihan Cai
- Graduate School of Environmental Science, Hokkaido University, Kita 10 Nishi 5, Kita-ku, Sapporo, 060-0810, Japan
| | - Aye Myat Myat Paing
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Susumu Goto
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yoko Hisamoto
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Nobuhiro Tomaru
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Cikusa-ku, Nagoya, Aichi, 464-0804, Japan
| | - Kosuke Homma
- Sado Island Center for Ecological Sustainability, Niigata University, 1101-1, Niibokatagami, Sado, Niigata, 952-0103, Japan
| | - Masahiro Takagi
- Faculty of Agriculture, University of Miyazaki, 1-1, Gakuen kibanadai nishi, Miyazaki, Miyazaki, 889-2192, Japan
| | - Toshiya Yoshida
- Field Science Center for Northern Biosphere, Hokkaido University, Kita 10 Nishi 5, Kita-ku, Sapporo, 060-0810, Japan
| | - Atsuhiro Iio
- Graduate School of Integrated Science and Technology, Shizuoka University, 836, Ohtani, Suruga-ku, Shizuoka, Shizuoka, 422-8017, Japan
| | - Dai Nagamatsu
- Faculty of Agriculture, Tottori University, 4-101, Koyama-cho, Tottori, Tottori, 680-8553, Japan
| | - Hajime Kobayashi
- Faculty of Agriculture, Shinshu University, 8304, Minamiminowa-mura, Kamiina-gun, Nagano, 399-4598, Japan
| | - Mitsuru Hirota
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Kentaro Uchiyama
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, 1, Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan
| | - Yoshihiko Tsumura
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki, 305-8577, Japan.
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13
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Sun S, Wang B, Li C, Xu G, Yang J, Hufford MB, Ross-Ibarra J, Wang H, Wang L. Unraveling Prevalence and Effects of Deleterious Mutations in Maize Elite Lines across Decades of Modern Breeding. Mol Biol Evol 2023; 40:msad170. [PMID: 37494285 PMCID: PMC10414807 DOI: 10.1093/molbev/msad170] [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: 12/20/2022] [Revised: 07/12/2023] [Accepted: 07/21/2023] [Indexed: 07/28/2023] Open
Abstract
Future breeding is likely to involve the detection and removal of deleterious alleles, which are mutations that negatively affect crop fitness. However, little is known about the prevalence of such mutations and their effects on phenotypic traits in the context of modern crop breeding. To address this, we examined the number and frequency of deleterious mutations in 350 elite maize inbred lines developed over the past few decades in China and the United States. Our findings reveal an accumulation of weakly deleterious mutations and a decrease in strongly deleterious mutations, indicating the dominant effects of genetic drift and purifying selection for the two types of mutations, respectively. We also discovered that slightly deleterious mutations, when at lower frequencies, were more likely to be heterozygous in the developed hybrids. This is consistent with complementation as a potential explanation for heterosis. Subsequently, we found that deleterious mutations accounted for more of the variation in phenotypic traits than nondeleterious mutations with matched minor allele frequencies, especially for traits related to leaf angle and flowering time. Moreover, we detected fewer deleterious mutations in the promoter and gene body regions of differentially expressed genes across breeding eras than in nondifferentially expressed genes. Overall, our results provide a comprehensive assessment of the prevalence and impact of deleterious mutations in modern maize breeding and establish a useful baseline for future maize improvement efforts.
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Affiliation(s)
- Shichao Sun
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Baobao Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Changyu Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Gen Xu
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jinliang Yang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Jeffrey Ross-Ibarra
- Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - Haiyang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Li Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
- Kunpeng Institute of Modern Agriculture at Foshan, Chinese Academy of Agricultural Sciences, Foshan, China
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14
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Yuan S, Shi Y, Zhou BF, Liang YY, Chen XY, An QQ, Fan YR, Shen Z, Ingvarsson PK, Wang B. Genomic vulnerability to climate change in Quercus acutissima, a dominant tree species in East Asian deciduous forests. Mol Ecol 2023; 32:1639-1655. [PMID: 36626136 DOI: 10.1111/mec.16843] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 12/30/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023]
Abstract
Understanding the evolutionary processes that shape the landscape of genetic variation and influence the response of species to future climate change is critical for biodiversity conservation. Here, we sampled 27 populations across the distribution range of a dominant forest tree, Quercus acutissima, in East Asia, and applied genome-wide analyses to track the evolutionary history and predict the fate of populations under future climate. We found two genetic groups (East and West) in Q. acutissima that diverged during Pliocene. We also found a heterogeneous landscape of genomic variation in this species, which may have been shaped by population demography and linked selections. Using genotype-environment association analyses, we identified climate-associated SNPs in a diverse set of genes and functional categories, indicating a model of polygenic adaptation in Q. acutissima. We further estimated three genetic offset metrics to quantify genomic vulnerability of this species to climate change due to the complex interplay between local adaptation and migration. We found that marginal populations are under higher risk of local extinction because of future climate change, and may not be able to track suitable habitats to maintain the gene-environment relationships observed under the current climate. We also detected higher reverse genetic offsets in northern China, indicating that genetic variation currently present in the whole range of Q. acutissima may not adapt to future climate conditions in this area. Overall, this study illustrates how evolutionary processes have shaped the landscape of genomic variation, and provides a comprehensive genome-wide view of climate maladaptation in Q. acutissima.
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Affiliation(s)
- Shuai Yuan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
| | - Yong Shi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
| | - Biao-Feng Zhou
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
| | - Yi-Ye Liang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
| | - Xue-Yan Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
| | - Qing-Qing An
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
| | - Yan-Ru Fan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
| | - Zhao Shen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
| | - Pär K Ingvarsson
- Department of Plant Biology, Linnean Center for Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Baosheng Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
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15
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Perrier A, Sánchez‐Castro D, Willi Y. Environment dependence of the expression of mutational load and species' range limits. J Evol Biol 2022; 35:731-741. [PMID: 35290676 PMCID: PMC9314787 DOI: 10.1111/jeb.13997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/10/2022] [Accepted: 02/21/2022] [Indexed: 12/21/2022]
Abstract
Theoretical and empirical research on the causes of species' range limits suggest the contribution of several intrinsic and extrinsic factors, with potentially complex interactions among them. An intrinsic factor proposed by recent theory is mutational load increasing towards range edges because of genetic drift. Furthermore, environmental quality may decline towards range edges and enhance the expression of load. Here, we tested whether the expression of mutational load associated with range limits in the North American plant Arabidopsis lyrata was enhanced under stressful environmental conditions by comparing the performance of within- versus between-population crosses at common garden sites across the species' distribution and beyond. Heterosis, reflecting the expression of load, increased with heightened estimates of genomic load and with environmental stress caused by warming, but the interaction was not significant. We conclude that range-edge populations suffer from a twofold genetic Allee effect caused by increased mutational load and stress-dependent load linked to general heterozygote deficiency, but there is no synergistic effect between them.
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Affiliation(s)
- Antoine Perrier
- Department of BiologyUniversity of VirginiaCharlottesvilleVirginiaUSA
- Department of Environmental SciencesUniversity of BaselBaselSwitzerland
| | | | - Yvonne Willi
- Department of Environmental SciencesUniversity of BaselBaselSwitzerland
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16
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Pujolar JM, Jacobsen MW, Bertolini F. Comparative genomics and signatures of selection in North Atlantic eels. Mar Genomics 2022; 62:100933. [PMID: 35182837 DOI: 10.1016/j.margen.2022.100933] [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: 11/11/2021] [Revised: 02/04/2022] [Accepted: 02/04/2022] [Indexed: 11/17/2022]
Abstract
Comparative genomic approaches can identify putative private and shared signatures of selection. We performed a comparative genomic study of North Atlantic eels, European eel (Anguilla Anguilla) and American eel (A. rostrata). The two sister species are nearly undistinguishable at the phenotypic level and despite a wide non-overlapping continental distribution, they spawn in partial sympatry in the Sargasso Sea. Taking advantage of the newly assembled and annotated genome, we used genome wide RAD sequencing data of 359 individuals retrieved from Sequence Nucleotide Archive and state-of-the-art statistic tests to identify putative genomic signatures of selection in North Atlantic eels. First, using the FST and XP-EHH methods, we detected apparent islands of divergence on a total of 7 chromosomes, particularly on chromosomes 6 and 10. Gene ontology analyses suggested candidate genes mainly related to energy production, development and regulation, which could reflect strong selection on traits related to eel migration and larval duration time. Gene effect prediction using SNPeff showed a high number of SNPs in noncoding regions, pointing to a possible regulatory role. Second, using the iHS method we detected shared regions under selection on a total of 11 chromosomes. Several hypotheses might account for the detection of shared islands of selection in North Atlantic eels, including parallel evolution due to adaptation to similar environments and introgression. Future comparative genomic studies will be needed to further clarify the causes and consequences of introgression, including the directionality of these introgression events.
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Affiliation(s)
- Jose Martin Pujolar
- Centre for Gelatinous Plankton Ecology and Evolution, National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Magnus Wulff Jacobsen
- Section for Marine Living Resources, National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - Francesca Bertolini
- Section for Marine Living Resources, National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark.
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17
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Ackiss AS, Magee MR, Sass GG, Turnquist K, McIntyre PB, Larson WA. Genomic and environmental influences on resilience in a cold-water fish near the edge of its range. Evol Appl 2021; 14:2794-2814. [PMID: 34950230 PMCID: PMC8674893 DOI: 10.1111/eva.13313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 10/05/2021] [Accepted: 10/07/2021] [Indexed: 02/06/2023] Open
Abstract
Small, isolated populations present a challenge for conservation. The dueling effects of selection and drift in a limited pool of genetic diversity make the responses of small populations to environmental perturbations erratic and difficult to predict. This is particularly true at the edge of a species range, where populations often persist at the limits of their environmental tolerances. Populations of cisco, Coregonus artedi, in inland lakes have experienced numerous extirpations along the southern edge of their range in recent decades, which are thought to result from environmental degradation and loss of cold, well-oxygenated habitat as lakes warm. Yet, cisco extirpations do not show a clear latitudinal pattern, suggesting that local environmental factors and potentially local adaptation may influence resilience. Here, we used genomic tools to investigate the nature of this pattern of resilience. We used restriction site-associated DNA capture (Rapture) sequencing to survey genomic diversity and differentiation in southern inland lake cisco populations and compared the frequency of deleterious mutations that potentially influence fitness across lakes. We also examined haplotype diversity in a region of the major histocompatibility complex involved in stress and immune system response. We correlated these metrics to spatial and environmental factors including latitude, lake size, and measures of oxythermal habitat and found significant relationships between genetic metrics and broad and local factors. High levels of genetic differentiation among populations were punctuated by a phylogeographic break and residual patterns of isolation-by-distance. Although the prevalence of deleterious mutations and inbreeding coefficients was significantly correlated with latitude, neutral and non-neutral genetic diversity were most strongly correlated with lake surface area. Notably, differences among lakes in the availability of estimated oxythermal habitat left no clear population genomic signature. Our results shed light on the complex dynamics influencing these isolated populations and provide valuable information for their conservation.
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Affiliation(s)
- Amanda S. Ackiss
- Wisconsin Cooperative Fishery Research UnitCollege of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWisconsinUSA
- U.S. Geological SurveyGreat Lakes Science CenterAnn ArborMichiganUSA
| | | | - Greg G. Sass
- Escanaba Lake Research StationWisconsin Department of Natural ResourcesBoulder JunctionWisconsinUSA
| | - Keith Turnquist
- Wisconsin Cooperative Fishery Research UnitCollege of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWisconsinUSA
| | - Peter B. McIntyre
- Department of Natural Resources and the EnvironmentCornell UniversityIthacaNew YorkUSA
| | - Wesley A. Larson
- U.S. Geological SurveyWisconsin Cooperative Fishery Research UnitCollege of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWisconsinUSA
- National Oceanographic and Atmospheric AdministrationNational Marine Fisheries ServiceAlaska Fisheries Science CenterAuke Bay LaboratoriesJuneauAlaskaUSA
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18
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Ma Y, Liu D, Wariss HM, Zhang R, Tao L, Milne RI, Sun W. Demographic history and identification of threats revealed by population genomic analysis provide insights into conservation for an endangered maple. Mol Ecol 2021; 31:767-779. [PMID: 34826164 DOI: 10.1111/mec.16289] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/17/2021] [Accepted: 11/22/2021] [Indexed: 12/01/2022]
Abstract
Recent advancements in whole genome sequencing techniques capable of covering nearly all the nucleotide variations of a genome would make it possible to set up a conservation framework for threatened plants at the genomic level. Here we applied a whole genome resequencing approach to obtain genome-wide data from 105 individuals sampled from the 10 currently known extant populations of Acer yangbiense, an endangered species with fragmented habitats and restricted distribution in Yunnan, China. To inform meaningful conservation action, we investigated what factors might have contributed to the formation of its extremely small population sizes and what threats it currently suffers at a genomic level. Our results revealed that A. yangbiense has low genetic diversity and comprises different numbers of genetic groups based on neutral (seven) and selected loci (13), with frequent gene flow between populations. Repeated bottleneck events, particularly the most recent one occurring within ~10,000 years before present, which decreased its effective population size (Ne ) < 200, and severe habitat fragmentation resulting from anthropogenic activities as well as a biased gender ratio of mature individuals in its natural habitat, might have together contributed to the currently fragmented and endangered status of A. yangbiense. The species has suffered from inbreeding and deleterious mutation load, both of which varied among populations but had similar patterns; that is, populations with higher FROH (frequency of runs of homozygosity) always carried a larger number of deleterious mutations in the homozygous state than in populations with lower FROH. In addition, based on our genetic differentiation results, and the distribution patterns of homozygous deleterious mutations in individuals, we recommend certain conservation actions regarding the genetic rescue of A. yangbiense. Overall, our study provides meaningful insights into the conservation genetics and a framework for the further conservation for the endangered A. yangbiense.
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Affiliation(s)
- Yongpeng Ma
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Chinese Academy of Sciences, Kunming Institute of Botany, Kunming, China.,Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming Institute of Botany, Kunming, China
| | - Detuan Liu
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Chinese Academy of Sciences, Kunming Institute of Botany, Kunming, China.,Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming Institute of Botany, Kunming, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hafiz Muhammad Wariss
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Chinese Academy of Sciences, Kunming Institute of Botany, Kunming, China.,Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming Institute of Botany, Kunming, China
| | - Rengang Zhang
- Beijing Ori-Gene Science and Technology Co. Ltd, Beijing, China
| | - Lidan Tao
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Chinese Academy of Sciences, Kunming Institute of Botany, Kunming, China.,Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming Institute of Botany, Kunming, China
| | - Richard I Milne
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, UK
| | - Weibang Sun
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Chinese Academy of Sciences, Kunming Institute of Botany, Kunming, China.,Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming Institute of Botany, Kunming, China.,Kunming Botanical Garden, Chinese Academy of Sciences, Kunming Institute of Botany, Kunming, China
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19
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Ma Y, Wariss HM, Liao R, Zhang R, Yun Q, Olmstead RG, Chau JH, Milne RI, Van de Peer Y, Sun W. Genome-wide analysis of butterfly bush (Buddleja alternifolia) in three uplands provides insights into biogeography, demography and speciation. THE NEW PHYTOLOGIST 2021; 232:1463-1476. [PMID: 34292587 PMCID: PMC9291457 DOI: 10.1111/nph.17637] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/19/2021] [Indexed: 05/06/2023]
Abstract
Understanding processes that generate and maintain large disjunctions within plant species can provide valuable insights into plant diversity and speciation. The butterfly bush Buddleja alternifolia has an unusual disjunct distribution, occurring in the Himalaya, Hengduan Mountains (HDM) and the Loess Plateau (LP) in China. We generated a high-quality, chromosome-level genome assembly of B. alternifolia, the first within the family Scrophulariaceae. Whole-genome re-sequencing data from 48 populations plus morphological and petal colour reflectance data covering its full distribution range were collected. Three distinct genetic lineages of B. alternifolia were uncovered, corresponding to Himalayan, HDM and LP populations, with the last also differentiated morphologically and phenologically, indicating occurrence of allopatric speciation likely to be facilitated by geographic isolation and divergent adaptation to distinct ecological niches. Moreover, speciation with gene flow between populations from either side of a mountain barrier could be under way within LP. The current disjunctions within B. alternifolia might result from vicariance of a once widespread distribution, followed by several past contraction and expansion events, possibly linked to climate fluctuations promoted by the Kunlun-Yellow river tectonic movement. Several adaptive genes are likely to be either uniformly or diversely selected among regions, providing a footprint of local adaptations. These findings provide new insights into plant biogeography, adaptation and different processes of allopatric speciation.
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Affiliation(s)
- Yong‐Peng Ma
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small PopulationsKunming Institute of BotanyChinese Academy of SciencesKunming650201China
| | - Hafiz Muhammad Wariss
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small PopulationsKunming Institute of BotanyChinese Academy of SciencesKunming650201China
| | - Rong‐Li Liao
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small PopulationsKunming Institute of BotanyChinese Academy of SciencesKunming650201China
- Fuzhou Botanical GardenFuzhou350012China
| | - Ren‐Gang Zhang
- Beijing Ori‐Gene Science and Technology Co. LtdBeijing102206China
| | - Quan‐Zheng Yun
- Beijing Ori‐Gene Science and Technology Co. LtdBeijing102206China
| | - Richard G. Olmstead
- Department of Biology and Burke MuseumUniversity of WashingtonBox 351800SeattleWA98195USA
| | - John H. Chau
- Centre for Ecological Genomics and Wildlife ConservationDepartment of ZoologyUniversity of JohannesburgPO Box 524Auckland Park2006South Africa
| | - Richard I. Milne
- Institute of Molecular Plant SciencesUniversity of EdinburghEdinburghEH9 3JHUK
| | - Yves Van de Peer
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentB‐9052Belgium
- VIB Center for Plant Systems BiologyGhentB‐9052Belgium
- College of HorticultureNanjing Agricultural UniversityNanjing210095China
- Department of Biochemistry, Genetics and MicrobiologyUniversity of PretoriaArcadia0007South Africa
| | - Wei‐Bang Sun
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small PopulationsKunming Institute of BotanyChinese Academy of SciencesKunming650201China
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20
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Ma H, Liu Y, Liu D, Sun W, Liu X, Wan Y, Zhang X, Zhang R, Yun Q, Wang J, Li Z, Ma Y. Chromosome-level genome assembly and population genetic analysis of a critically endangered rhododendron provide insights into its conservation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1533-1545. [PMID: 34189793 DOI: 10.1111/tpj.15399] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 06/23/2021] [Indexed: 05/25/2023]
Abstract
Rhododendrons are woody plants, famous throughout the world as having high horticultural value. However, many wild species are currently threatened with extinction. Here, we report for the first time a high-quality, chromosome-level genome of Rhododendron griersonianum, which has contributed to approximately 10% of all horticultural rhododendron varieties but which in its wild form has been evaluated as critically endangered. The final genome assembly, which has a contig N50 size of approximately 34 M and a total length of 677 M, is the highest-quality genome sequenced within the genus to date, in part due to its low heterozygosity (0.18%). Identified repeats constitute approximately 57% of the genome, and 38 280 protein-coding genes were predicted with high support. We further resequenced 31 individuals of R. griersonianum as well as 30 individuals of its widespread relative R. delavayi, and performed additional conservation genomic analysis. The results showed that R. griersonianum had lower genetic diversity (θ = 2.58e-3; π = 1.94e-3) when compared not only to R. delavayi (θ = 11.61e-3, π = 12.97e-3), but also to most other woody plants. Furthermore, three severe genetic bottlenecks were detected using both the Stairway plot and fastsimcoal2 analysis, which are thought to have occurred in the late Middle Pleistocene and the Last Glacial Maximum (LGM) period. After these bottlenecks, R. griersonianum recovered and maintained a constant effective population size (>25 000) until now. Intriguingly, R. griersonianum has accumulated significantly more deleterious mutations in the homozygous state than R. delavayi, and several deleterious mutations (e.g., in genes involved in the response to heat stress) are likely to have harmed the adaptation of this plant to its surroundings. This high-quality, chromosome-level genome and the population genomic analysis of the critically endangered R. griersonianum will provide an invaluable resource as well as insights for future study in this species to facilitate conservation and in the genus Rhododendron in general.
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Affiliation(s)
- Hong Ma
- Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, 650233, China
| | - Yongbo Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Detuan Liu
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Weibang Sun
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Xiongfang Liu
- Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, 650233, China
| | - Youming Wan
- Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, 650233, China
| | - Xiujiao Zhang
- Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, 650233, China
| | - Rengang Zhang
- Beijing Ori-Gene Science and Technology Co. Ltd, Beijing, 102206, China
| | - Quanzheng Yun
- Beijing Ori-Gene Science and Technology Co. Ltd, Beijing, 102206, China
| | - Jihua Wang
- The Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
- National Engineering Research Center for Ornamental Horticulture, Kunming, 650205, China
| | - Zhenghong Li
- Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, 650233, China
| | - Yongpeng Ma
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
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21
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Bontrager M, Usui T, Lee-Yaw JA, Anstett DN, Branch HA, Hargreaves AL, Muir CD, Angert AL. Adaptation across geographic ranges is consistent with strong selection in marginal climates and legacies of range expansion. Evolution 2021; 75:1316-1333. [PMID: 33885152 DOI: 10.1111/evo.14231] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 03/14/2021] [Indexed: 12/27/2022]
Abstract
Every species experiences limits to its geographic distribution. Some evolutionary models predict that populations at range edges are less well adapted to their local environments due to drift, expansion load, or swamping gene flow from the range interior. Alternatively, populations near range edges might be uniquely adapted to marginal environments. In this study, we use a database of transplant studies that quantify performance at broad geographic scales to test how local adaptation, site quality, and population quality change from spatial and climatic range centers toward edges. We find that populations from poleward edges perform relatively poorly, both on average across all sites (15% lower population quality) and when compared to other populations at home (31% relative fitness disadvantage), consistent with these populations harboring high genetic load. Populations from equatorial edges also perform poorly on average (18% lower population quality) but, in contrast, outperform foreign populations (16% relative fitness advantage), suggesting that populations from equatorial edges have strongly adapted to unique environments. Finally, we find that populations from sites that are thermally extreme relative to the species' niche demonstrate strong local adaptation, regardless of their geographic position. Our findings indicate that both nonadaptive processes and adaptive evolution contribute to variation in adaptation across species' ranges.
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Affiliation(s)
- Megan Bontrager
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, V6T 1Z4, Canada.,Current Address: Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, M5S 3B2, Canada
| | - Takuji Usui
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Julie A Lee-Yaw
- Department of Biological Sciences, University of Lethbridge, Lethbridge, T1K 3M4, Canada
| | - Daniel N Anstett
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Haley A Branch
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | | | - Christopher D Muir
- School of Life Sciences, University of Hawaii, Honolulu, Hawaii, 96822, United States
| | - Amy L Angert
- Departments of Botany and Zoology and the Biodiversity Research Centre, University of British Columbia, Vancouver, V6T 1Z4, Canada
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22
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de Pedro M, Riba M, González-Martínez SC, Seoane P, Bautista R, Claros MG, Mayol M. Demography, genetic diversity and expansion load in the colonizing species Leontodon longirostris (Asteraceae) throughout its native range. Mol Ecol 2021; 30:1190-1205. [PMID: 33452714 DOI: 10.1111/mec.15802] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/12/2020] [Accepted: 01/08/2021] [Indexed: 12/25/2022]
Abstract
Unravelling the evolutionary processes underlying range expansions is fundamental to understand the distribution of organisms, as well as to predict their future responses to environmental change. Predictions for range expansions include a loss of genetic diversity and an accumulation of deleterious alleles along the expansion axis, which can decrease fitness at the range-front (expansion load). In plants, empirical studies supporting expansion load are scarce, and its effects remain to be tested outside a few model species. Leontodon longirostris is a colonizing Asteraceae with a widespread distribution in the Western Mediterranean, providing a particularly interesting system to gain insight into the factors that can enhance or mitigate expansion load. In this study, we produced a first genome draft for the species, covering 418 Mbp (~53% of the genome). Although incomplete, this draft was suitable to design a targeted sequencing of ~1.5 Mbp in 238 L. longirostris plants from 21 populations distributed along putative colonization routes in the Iberian Peninsula. Inferred demographic history supports a range expansion from southern Iberia around 40,000 years ago, reaching northern Iberia around 25,000 years ago. The expansion was accompanied by a loss of genetic diversity and a significant increase in the proportion of putatively deleterious mutations. However, levels of expansion load in L. longirostris were smaller than those found in other plant species, which can be explained, at least partially, by its high dispersal ability, the self-incompatible mating system, and the fact that the expansion occurred along a strong environmental cline.
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Affiliation(s)
| | - Miquel Riba
- CREAF, Cerdanyola del Vallès, Spain.,Univ. Autònoma Barcelona, Cerdanyola del Vallès, Spain
| | | | - Pedro Seoane
- Department of Molecular Biology and Biochemistry, Universidad de Málaga, and Institute for Mediterranean and Subtropical Horticulture (IHSM-CSIC-UMA), Málaga, Spain.,CIBER de Enfermedades Raras (CIBERER), Málaga, Spain.,Institute of Biomedical Research in Malaga (IBIMA), IBIMA-RARE, Málaga, Spain
| | - Rocío Bautista
- Institute of Biomedical Research in Malaga (IBIMA), IBIMA-RARE, Málaga, Spain.,Andalusian Platform for Bioinformatics-SCBI, Universidad de Málaga, Málaga, Spain
| | - Manuel Gonzalo Claros
- Department of Molecular Biology and Biochemistry, Universidad de Málaga, and Institute for Mediterranean and Subtropical Horticulture (IHSM-CSIC-UMA), Málaga, Spain.,CIBER de Enfermedades Raras (CIBERER), Málaga, Spain.,Institute of Biomedical Research in Malaga (IBIMA), IBIMA-RARE, Málaga, Spain.,Andalusian Platform for Bioinformatics-SCBI, Universidad de Málaga, Málaga, Spain.,Institute for Mediterranean and Subtropical Horticulture "La Mayora" (IHSM-UMA-CSIC), Málaga, Spain
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23
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Lozano R, Gazave E, Dos Santos JPR, Stetter MG, Valluru R, Bandillo N, Fernandes SB, Brown PJ, Shakoor N, Mockler TC, Cooper EA, Taylor Perkins M, Buckler ES, Ross-Ibarra J, Gore MA. Comparative evolutionary genetics of deleterious load in sorghum and maize. NATURE PLANTS 2021; 7:17-24. [PMID: 33452486 DOI: 10.1038/s41477-020-00834-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 12/09/2020] [Indexed: 06/12/2023]
Abstract
Sorghum and maize share a close evolutionary history that can be explored through comparative genomics1,2. To perform a large-scale comparison of the genomic variation between these two species, we analysed ~13 million variants identified from whole-genome resequencing of 499 sorghum lines together with 25 million variants previously identified in 1,218 maize lines. Deleterious mutations in both species were prevalent in pericentromeric regions, enriched in non-syntenic genes and present at low allele frequencies. A comparison of deleterious burden between sorghum and maize revealed that sorghum, in contrast to maize, departed from the domestication-cost hypothesis that predicts a higher deleterious burden among domesticates compared with wild lines. Additionally, sorghum and maize population genetic summary statistics were used to predict a gene deleterious index with an accuracy greater than 0.5. This research represents a key step towards understanding the evolutionary dynamics of deleterious variants in sorghum and provides a comparative genomics framework to start prioritizing these variants for removal through genome editing and breeding.
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Affiliation(s)
- Roberto Lozano
- Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Elodie Gazave
- Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
- Institute of Biotechnology, Cornell University, Ithaca, NY, USA
| | - Jhonathan P R Dos Santos
- Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Markus G Stetter
- Botanical Institute, Biozentrum, University of Cologne, Cologne, Germany
| | - Ravi Valluru
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA
- University of Lincoln, Lincoln, UK
| | - Nonoy Bandillo
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
| | - Samuel B Fernandes
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Patrick J Brown
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Nadia Shakoor
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Todd C Mockler
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Elizabeth A Cooper
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - M Taylor Perkins
- Department of Evolution and Ecology, University of California Davis, Davis, CA, USA
| | - Edward S Buckler
- Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS) R. W. Holley Center for Agriculture and Health, Ithaca, NY, USA
| | - Jeffrey Ross-Ibarra
- Department of Evolution and Ecology, University of California Davis, Davis, CA, USA.
- Center for Population Biology and Genome Center, University of California Davis, Davis, CA, USA.
| | - Michael A Gore
- Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.
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24
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Jaramillo-Correa JP, Bagnoli F, Grivet D, Fady B, Aravanopoulos FA, Vendramin GG, González-Martínez SC. Evolutionary rate and genetic load in an emblematic Mediterranean tree following an ancient and prolonged population collapse. Mol Ecol 2020; 29:4797-4811. [PMID: 33063352 DOI: 10.1111/mec.15684] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 12/18/2022]
Abstract
Severe bottlenecks significantly diminish the amount of genetic diversity and the speed at which it accumulates (i.e., evolutionary rate). They further compromise the efficiency of natural selection to eliminate deleterious variants, which may reach fixation in the surviving populations. Consequently, expanding and adapting to new environments may pose a significant challenge when strong bottlenecks result in genetic pauperization. Herein, we surveyed the patterns of nucleotide diversity, molecular adaptation and genetic load across 177 gene-loci in a circum-Mediterranean conifer (Pinus pinea L.) that represents one of the most extreme cases of genetic pauperization in widespread outbreeding taxa. We found very little genetic variation in both hypervariable nuclear microsatellites (SSRs) and gene-loci, which translated into genetic diversity estimates one order of magnitude lower than those previously reported for pines. Such values were consistent with a strong population decline that began some ~1 Ma. Comparisons with the related and parapatric maritime pine (Pinus pinaster Ait.) revealed reduced rates of adaptive evolution (α and ωa ) and a significant accumulation of genetic load. It is unlikely that these are the result from differences in mutation rate or linkage disequilibrium between the two species; instead they are the presumable outcome of contrasting demographic histories affecting both the speed at which these taxa accumulate genetic diversity, and the global efficacy of selection. Future studies, and programs for conservation and management, should thus start testing for the effects of genetic load on fitness, and integrating such effects into predictive models.
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Affiliation(s)
- Juan P Jaramillo-Correa
- Department of Evolutionary Ecology, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Francesca Bagnoli
- Division of Florence, Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino, Italy
| | - Delphine Grivet
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA-CIFOR, Madrid, Spain
| | - Bruno Fady
- INRAE, Unité de Recherche Écologie des Forêts Méditerranéennes (URFM), Avignon, France
| | - Filippos A Aravanopoulos
- Laboratory of Forest Genetics and Tree Breeding, Department of Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Giovanni G Vendramin
- Division of Florence, Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino, Italy
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25
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Angert AL, Bontrager MG, Ågren J. What Do We Really Know About Adaptation at Range Edges? ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-012120-091002] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Recent theory and empirical evidence have provided new insights regarding how evolutionary forces interact to shape adaptation at stable and transient range margins. Predictions regarding trait divergence at leading edges are frequently supported. However, declines in fitness at and beyond edges show that trait divergence has sometimes been insufficient to maintain high fitness, so identifying constraints to adaptation at range edges remains a key challenge. Indirect evidence suggests that range expansion may be limited by adaptive genetic variation, but direct estimates of genetic constraints at and beyond range edges are still scarce. Sequence data suggest increased genetic load in edge populations in several systems, but its causes and fitness consequences are usually poorly understood. The balance between maladaptive and positive effects of gene flow on fitness at range edges deserves further study. It is becoming increasingly clear that characterizations about degree of adaptation based solely on geographical peripherality are unsupported.
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Affiliation(s)
- Amy L. Angert
- Departments of Botany and Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Megan G. Bontrager
- Department of Evolution and Ecology, University of California, Davis, California 95616, USA
| | - Jon Ågren
- Department of Ecology and Genetics, Uppsala University, SE-752 36 Uppsala, Sweden
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26
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Hämälä T, Tiffin P. Biased Gene Conversion Constrains Adaptation in Arabidopsis thaliana. Genetics 2020; 215:831-846. [PMID: 32414868 PMCID: PMC7337087 DOI: 10.1534/genetics.120.303335] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 05/14/2020] [Indexed: 02/01/2023] Open
Abstract
Reduction of fitness due to deleterious mutations imposes a limit to adaptive evolution. By characterizing features that influence this genetic load we may better understand constraints on responses to both natural and human-mediated selection. Here, using whole-genome, transcriptome, and methylome data from >600 Arabidopsis thaliana individuals, we set out to identify important features influencing selective constraint. Our analyses reveal that multiple factors underlie the accumulation of maladaptive mutations, including gene expression level, gene network connectivity, and gene-body methylation. We then focus on a feature with major effect, nucleotide composition. The ancestral vs. derived status of segregating alleles suggests that GC-biased gene conversion, a recombination-associated process that increases the frequency of G and C nucleotides regardless of their fitness effects, shapes sequence patterns in A. thaliana Through estimation of mutational effects, we present evidence that biased gene conversion hinders the purging of deleterious mutations and contributes to a genome-wide signal of decreased efficacy of selection. By comparing these results to two outcrossing relatives, Arabidopsis lyrata and Capsella grandiflora, we find that protein evolution in A. thaliana is as strongly affected by biased gene conversion as in the outcrossing species. Last, we perform simulations to show that natural levels of outcrossing in A. thaliana are sufficient to facilitate biased gene conversion despite increased homozygosity due to selfing. Together, our results show that even predominantly selfing taxa are susceptible to biased gene conversion, suggesting that it may constitute an important constraint to adaptation among plant species.
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Affiliation(s)
- Tuomas Hämälä
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
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27
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Turner-Hissong SD, Mabry ME, Beissinger TM, Ross-Ibarra J, Pires JC. Evolutionary insights into plant breeding. CURRENT OPINION IN PLANT BIOLOGY 2020; 54:93-100. [PMID: 32325397 DOI: 10.1016/j.pbi.2020.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/20/2020] [Accepted: 03/04/2020] [Indexed: 06/11/2023]
Abstract
Crop domestication is a fascinating area of study, as shown by a multitude of recent reviews. Coupled with the increasing availability of genomic and phenomic resources in numerous crop species, insights from evolutionary biology will enable a deeper understanding of the genetic architecture and short-term evolution of complex traits, which can be used to inform selection strategies. Future advances in crop improvement will rely on the integration of population genetics with plant breeding methodology, and the development of community resources to support research in a variety of crop life histories and reproductive strategies. We highlight recent advances related to the role of selective sweeps and demographic history in shaping genetic architecture, how these breakthroughs can inform selection strategies, and the application of precision gene editing to leverage these connections.
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Affiliation(s)
- Sarah D Turner-Hissong
- Center for Population Biology, University of California, Davis, CA, USA; Department of Evolution and Ecology, University of California, Davis, CA, USA.
| | - Makenzie E Mabry
- Bond Life Science Center and Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Timothy M Beissinger
- Division of Plant Breeding Methodology, Department of Crop Science, Georg-August-Universtät, Göttingen, Germany; Center for Integrated Breeding Research, Georg-August-Universtät, Göttingen, Germany
| | - Jeffrey Ross-Ibarra
- Center for Population Biology, University of California, Davis, CA, USA; Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - J Chris Pires
- Bond Life Science Center and Division of Biological Sciences, University of Missouri, Columbia, MO, USA
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28
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Zhang M, Suren H, Holliday JA. Phenotypic and Genomic Local Adaptation across Latitude and Altitude in Populus trichocarpa. Genome Biol Evol 2020; 11:2256-2272. [PMID: 31298685 PMCID: PMC6735766 DOI: 10.1093/gbe/evz151] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2019] [Indexed: 12/14/2022] Open
Abstract
Local adaptation to climate allows plants to cope with temporally and spatially heterogeneous environments, and parallel phenotypic clines provide a natural experiment to uncover the genomic architecture of adaptation. Though extensive effort has been made to investigate the genomic basis of local adaptation to climate across the latitudinal range of tree species, less is known for altitudinal clines. We used exome capture to genotype 451 Populus trichocarpa genotypes across altitudinal and latitudinal gradients spanning the natural species range, and phenotyped these trees for a variety of adaptive traits in two common gardens. We observed clinal variation in phenotypic traits across the two transects, which indicates climate-driven selection, and coupled gene-based genotype–phenotype and genotype–environment association scans to identify imprints of climatic adaptation on the genome. Although many of the phenotype- and climate-associated genes were unique to one transect, we found evidence of parallelism between latitude and altitude, as well as significant convergence when we compared our outlier genes with those putatively involved in climatic adaptation in two gymnosperm species. These results suggest that not only genomic constraint during adaptation to similar environmental gradients in poplar but also different environmental contexts, spatial scale, and perhaps redundant function among potentially adaptive genes and polymorphisms lead to divergent adaptive architectures.
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Affiliation(s)
- Man Zhang
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, Virginia.,National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University, China
| | - Haktan Suren
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, Virginia
| | - Jason A Holliday
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, Virginia
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29
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Hämälä T, Guiltinan MJ, Marden JH, Maximova SN, dePamphilis CW, Tiffin P. Gene Expression Modularity Reveals Footprints of Polygenic Adaptation in Theobroma cacao. Mol Biol Evol 2020; 37:110-123. [PMID: 31501906 DOI: 10.1093/molbev/msz206] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Separating footprints of adaptation from demography is challenging. When selection has acted on a single locus with major effect, this issue can be alleviated through signatures left by selective sweeps. However, as adaptation is often driven by small allele frequency shifts at many loci, studies focusing on single genes are able to identify only a small portion of genomic variants responsible for adaptation. In face of this challenge, we utilize coexpression information to search for signals of polygenetic adaptation in Theobroma cacao, a tropical tree species that is the source of chocolate. Using transcriptomics and a weighted correlation network analysis, we group genes with similar expression patterns into functional modules. We then ask whether modules enriched for specific biological processes exhibit cumulative effects of differential selection in the form of high FST and dXY between populations. Indeed, modules putatively involved in protein modification, flowering, and water transport show signs of polygenic adaptation even though individual genes that are members of those groups do not bear strong signatures of selection. Modeling of demography, background selection, and the effects of genomic features reveal that these patterns are unlikely to arise by chance. We also find that specific modules are enriched for signals of strong or relaxed purifying selection, with one module bearing signs of adaptive differentiation and an excess of deleterious mutations. Our results provide insight into polygenic adaptation and contribute to understanding of population structure, demographic history, and genome evolution in T. cacao.
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Affiliation(s)
- Tuomas Hämälä
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN
| | - Mark J Guiltinan
- Department of Plant Sciences, The Pennsylvania State University, University Park, PA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA
| | - James H Marden
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA.,Department of Biology, The Pennsylvania State University, University Park, PA
| | - Siela N Maximova
- Department of Plant Sciences, The Pennsylvania State University, University Park, PA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA
| | - Claude W dePamphilis
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA.,Department of Biology, The Pennsylvania State University, University Park, PA
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN
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30
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Bortoluzzi C, Bosse M, Derks MFL, Crooijmans RPMA, Groenen MAM, Megens H. The type of bottleneck matters: Insights into the deleterious variation landscape of small managed populations. Evol Appl 2020; 13:330-341. [PMID: 31993080 PMCID: PMC6976952 DOI: 10.1111/eva.12872] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 09/06/2019] [Accepted: 09/11/2019] [Indexed: 12/19/2022] Open
Abstract
Predictions about the consequences of a small population size on genetic and deleterious variation are fundamental to population genetics. As small populations are more affected by genetic drift, purifying selection acting against deleterious alleles is predicted to be less efficient, therefore increasing the risk of inbreeding depression. However, the extent to which small populations are subjected to genetic drift depends on the nature and time frame in which the bottleneck occurs. Domesticated species are an excellent model to investigate the consequences of population bottlenecks on genetic and deleterious variation in small populations. This is because their history is dominated by known bottlenecks associated with domestication, breed formation and intense selective breeding. Here, we use whole-genome sequencing data from 97 chickens representing 39 traditional fancy breeds to directly examine the consequences of two types of bottlenecks for deleterious variation: the severe domestication bottleneck and the recent population decline accompanying breed formation. We find that recently bottlenecked populations have a higher proportion of deleterious variants relative to populations that have been kept at small population sizes since domestication. We also observe that long tracts of homozygous genotypes (runs of homozygosity) are proportionally more enriched in deleterious variants than the rest of the genome. This enrichment is particularly evident in recently bottlenecked populations, suggesting that homozygosity of these variants is likely to occur due to genetic drift and recent inbreeding. Our results indicate that the timing and nature of population bottlenecks can substantially shape the deleterious variation landscape in small populations.
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Affiliation(s)
- Chiara Bortoluzzi
- Department of Animal Sciences, Animal Breeding and GenomicsWageningen University & ResearchGelderlandThe Netherlands
| | - Mirte Bosse
- Department of Animal Sciences, Animal Breeding and GenomicsWageningen University & ResearchGelderlandThe Netherlands
| | - Martijn F. L. Derks
- Department of Animal Sciences, Animal Breeding and GenomicsWageningen University & ResearchGelderlandThe Netherlands
| | - Richard P. M. A. Crooijmans
- Department of Animal Sciences, Animal Breeding and GenomicsWageningen University & ResearchGelderlandThe Netherlands
| | - Martien A. M. Groenen
- Department of Animal Sciences, Animal Breeding and GenomicsWageningen University & ResearchGelderlandThe Netherlands
| | - Hendrik‐Jan Megens
- Department of Animal Sciences, Animal Breeding and GenomicsWageningen University & ResearchGelderlandThe Netherlands
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31
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Pyhäjärvi T, Kujala ST, Savolainen O. 275 years of forestry meets genomics in Pinus sylvestris. Evol Appl 2020; 13:11-30. [PMID: 31988655 PMCID: PMC6966708 DOI: 10.1111/eva.12809] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 04/05/2019] [Accepted: 04/24/2019] [Indexed: 12/12/2022] Open
Abstract
Pinus sylvestris has a long history of basic and applied research that is relevant for both forestry and evolutionary studies. Its patterns of adaptive variation and role in forest economic and ecological systems have been studied extensively for nearly 275 years, detailed demography for a 100 years and mating system more than 50 years. However, its reference genome sequence is not yet available and genomic studies have been lagging compared to, for example, Pinus taeda and Picea abies, two other economically important conifers. Despite the lack of reference genome, many modern genomic methods are applicable for a more detailed look at its biological characteristics. For example, RNA-seq has revealed a complex transcriptional landscape and targeted DNA sequencing displays an excess of rare variants and geographically homogenously distributed molecular genetic diversity. Current DNA and RNA resources can be used as a reference for gene expression studies, SNP discovery, and further targeted sequencing. In the future, specific consequences of the large genome size, such as functional effects of regulatory open chromatin regions and transposable elements, should be investigated more carefully. For forest breeding and long-term management purposes, genomic data can help in assessing the genetic basis of inbreeding depression and the application of genomic tools for genomic prediction and relatedness estimates. Given the challenges of breeding (long generation time, no easy vegetative propagation) and the economic importance, application of genomic tools has a potential to have a considerable impact. Here, we explore how genomic characteristics of P. sylvestris, such as rare alleles and the low extent of linkage disequilibrium, impact the applicability and power of the tools.
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Affiliation(s)
- Tanja Pyhäjärvi
- Department of Ecology and GeneticsUniversity of OuluOuluFinland
- Biocenter OuluUniversity of OuluOuluFinland
| | | | - Outi Savolainen
- Department of Ecology and GeneticsUniversity of OuluOuluFinland
- Biocenter OuluUniversity of OuluOuluFinland
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32
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A comprehensive genomic scan reveals gene dosage balance impacts on quantitative traits in Populus trees. Proc Natl Acad Sci U S A 2019; 116:13690-13699. [PMID: 31213538 DOI: 10.1073/pnas.1903229116] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Gene dosage variation and the associated changes in gene expression influence a wide variety of traits, ranging from cancer in humans to yield in plants. It is also expected to affect important traits of ecological and agronomic importance in forest trees, but this variation has not been systematically characterized or exploited. Here we performed a comprehensive scan of the Populus genome for dosage-sensitive loci affecting quantitative trait variation for spring and fall phenology and biomass production. The study population was a large collection of clonally propagated F1 hybrid lines of Populus that saturate the genome 10-fold with deletions and insertions (indels) of known sizes and positions. As a group, the phenotypic means of the indel lines consistently differed from control nonindel lines, with an overall negative effect of both insertions and deletions on all biomass-related traits but more diverse effects and an overall wider phenotypic distribution of the indel lines for the phenology-related traits. We also investigated the correlation between gene dosage at specific chromosomal locations and phenotype, to identify dosage quantitative trait loci (dQTL). Such dQTL were detected for most phenotypes examined, but stronger effect dQTL were identified for the phenology-related traits than for the biomass traits. Our genome-wide screen for dosage sensitivity in a higher eukaryote demonstrates the importance of global genomic balance and the impact of dosage on life history traits.
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33
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Willi Y. The relevance of mutation load for species range limits. AMERICAN JOURNAL OF BOTANY 2019; 106:757-759. [PMID: 31162640 DOI: 10.1002/ajb2.1296] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 03/26/2019] [Indexed: 06/09/2023]
Affiliation(s)
- Yvonne Willi
- Department of Environmental Sciences, University of Basel, 4056, Basel, Switzerland
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34
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Wang J, Li X, Do Kim K, Scanlon MJ, Jackson SA, Springer NM, Yu J. Genome-wide nucleotide patterns and potential mechanisms of genome divergence following domestication in maize and soybean. Genome Biol 2019; 20:74. [PMID: 31018867 PMCID: PMC6482504 DOI: 10.1186/s13059-019-1683-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 03/28/2019] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Plant domestication provides a unique model to study genome evolution. Many studies have been conducted to examine genes, genetic diversity, genome structure, and epigenome changes associated with domestication. Interestingly, domesticated accessions have significantly higher [A] and [T] values across genome-wide polymorphic sites than accessions sampled from the corresponding progenitor species. However, the relative contributions of different genomic regions to this genome divergence pattern and underlying mechanisms have not been well characterized. RESULTS Here, we investigate the genome-wide base-composition patterns by analyzing millions of SNPs segregating among 100 accessions from a teosinte-maize comparison set and among 302 accessions from a wild-domesticated soybean comparison set. We show that non-genic part of the genome has a greater contribution than genic SNPs to the [AT]-increase observed between wild and domesticated accessions in maize and soybean. The separation between wild and domesticated accessions in [AT] values is significantly enlarged in non-genic and pericentromeric regions. Motif frequency and sequence context analyses show the motifs (PyCG) related to solar-UV signature are enriched in these regions, particularly when they are methylated. Additional analysis using population-private SNPs also implicates the role of these motifs in relatively recent mutations. With base-composition across polymorphic sites as a genome phenotype, genome scans identify a set of putative candidate genes involved in UV damage repair pathways. CONCLUSIONS The [AT]-increase is more pronounced in genomic regions that are non-genic, pericentromeric, transposable elements; methylated; and with low recombination. Our findings establish important links among UV radiation, mutation, DNA repair, methylation, and genome evolution.
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Affiliation(s)
- Jinyu Wang
- Department of Agronomy, Iowa State University, Ames, IA 50011 USA
| | - Xianran Li
- Department of Agronomy, Iowa State University, Ames, IA 50011 USA
| | - Kyung Do Kim
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602 USA
| | - Michael J. Scanlon
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853 USA
| | - Scott A. Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602 USA
| | - Nathan M. Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108 USA
| | - Jianming Yu
- Department of Agronomy, Iowa State University, Ames, IA 50011 USA
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Abstract
Factors that limit the geographic distribution of species are broadly important in ecology and evolutionary biology, and understanding distribution limits is imperative for predicting how species will respond to environmental change. Good data indicate that factors such as dispersal limitation, small effective population size, and isolation are sometimes important. But empirical research highlights no single factor that explains the ubiquity of distribution limits. In this article, we outline a guide to tackling distribution limits that integrates established causes, such as dispersal limitation and spatial environmental heterogeneity, with understudied causes, such as mutational load and genetic or developmental integration of traits limiting niche expansion. We highlight how modeling and quantitative genetic and genomic analyses can provide insight into sources of distribution limits. Our practical guide provides a framework for considering the many factors likely to determine species distributions and how the different approaches can be integrated to predict distribution limits using eco-evolutionary modeling. The framework should also help predict distribution limits of invasive species and of species under climate change.
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36
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Yang Y, Ma T, Wang Z, Lu Z, Li Y, Fu C, Chen X, Zhao M, Olson MS, Liu J. Genomic effects of population collapse in a critically endangered ironwood tree Ostrya rehderiana. Nat Commun 2018; 9:5449. [PMID: 30575743 PMCID: PMC6303402 DOI: 10.1038/s41467-018-07913-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 12/03/2018] [Indexed: 12/30/2022] Open
Abstract
Increased human activity and climate change are driving numerous tree species to endangered status, and in the worst cases extinction. Here we examine the genomic signatures of the critically endangered ironwood tree Ostrya rehderiana and its widespread congener O. chinensis. Both species have similar demographic histories prior to the Last Glacial Maximum (LGM); however, the effective population size of O. rehderiana continued to decrease through the last 10,000 years, whereas O. chinensis recovered to Pre-LGM numbers. O. rehderiana accumulated more deleterious mutations, but purged more severely deleterious recessive variations than in O. chinensis. This purging and the gradually reduced inbreeding depression together may have mitigated extinction and contributed to the possible future survival of the outcrossing O. rehderiana. Our findings provide critical insights into the evolutionary history of population collapse and the potential for future recovery of the endangered trees.
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Affiliation(s)
- Yongzhi Yang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, China
- State Key Laboratory of Grassland Agro-Ecosystem, College of Life Sciences, Lanzhou University, 730000, Lanzhou, China
| | - Tao Ma
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, China
| | - Zefu Wang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, China
| | - Zhiqiang Lu
- State Key Laboratory of Grassland Agro-Ecosystem, College of Life Sciences, Lanzhou University, 730000, Lanzhou, China
| | - Ying Li
- State Key Laboratory of Grassland Agro-Ecosystem, College of Life Sciences, Lanzhou University, 730000, Lanzhou, China
| | - Chengxin Fu
- Key Laboratory of Conservation Biology for Endangered Wildlife of Ministry of Education, and College of Life Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Xiaoyong Chen
- School of Ecological & Environmental Sciences, East China Normal University, Dongchuan Road 500, 200241, Shanghai, China
| | - Mingshui Zhao
- Zhejiang Tianmushan National Nature Reserve Management Bureau, 310058, Hangzhou, China
| | - Matthew S Olson
- Department of Biological Sciences, Texas Tech University, Box 43131, Lubbock, TX, 79409-3131, USA
| | - Jianquan Liu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, China.
- State Key Laboratory of Grassland Agro-Ecosystem, College of Life Sciences, Lanzhou University, 730000, Lanzhou, China.
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37
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Kono TJY, Lei L, Shih CH, Hoffman PJ, Morrell PL, Fay JC. Comparative Genomics Approaches Accurately Predict Deleterious Variants in Plants. G3 (BETHESDA, MD.) 2018; 8:3321-3329. [PMID: 30139765 PMCID: PMC6169392 DOI: 10.1534/g3.118.200563] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 08/10/2018] [Indexed: 12/11/2022]
Abstract
Recent advances in genome resequencing have led to increased interest in prediction of the functional consequences of genetic variants. Variants at phylogenetically conserved sites are of particular interest, because they are more likely than variants at phylogenetically variable sites to have deleterious effects on fitness and contribute to phenotypic variation. Numerous comparative genomic approaches have been developed to predict deleterious variants, but the approaches are nearly always assessed based on their ability to identify known disease-causing mutations in humans. Determining the accuracy of deleterious variant predictions in nonhuman species is important to understanding evolution, domestication, and potentially to improving crop quality and yield. To examine our ability to predict deleterious variants in plants we generated a curated database of 2,910 Arabidopsis thaliana mutants with known phenotypes. We evaluated seven approaches and found that while all performed well, their relative ranking differed from prior benchmarks in humans. We conclude that deleterious mutations can be reliably predicted in A. thaliana and likely other plant species, but that the relative performance of various approaches does not necessarily translate from one species to another.
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Affiliation(s)
- Thomas J Y Kono
- Department of Agronomy & Plant Genetics, University of Minnesota, St. Paul, MN 551085
| | - Li Lei
- Department of Agronomy & Plant Genetics, University of Minnesota, St. Paul, MN 551085
| | - Ching-Hua Shih
- Department of Genetics, Washington University, St. Louis, MO 63110
| | - Paul J Hoffman
- Department of Agronomy & Plant Genetics, University of Minnesota, St. Paul, MN 551085
| | - Peter L Morrell
- Department of Agronomy & Plant Genetics, University of Minnesota, St. Paul, MN 551085
| | - Justin C Fay
- Department of Genetics, Washington University, St. Louis, MO 63110
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38
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Ferchaud A, Laporte M, Perrier C, Bernatchez L. Impact of supplementation on deleterious mutation distribution in an exploited salmonid. Evol Appl 2018; 11:1053-1065. [PMID: 30026797 PMCID: PMC6050184 DOI: 10.1111/eva.12660] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 05/31/2018] [Accepted: 06/01/2018] [Indexed: 01/03/2023] Open
Abstract
Deleterious mutations have important implications for the evolutionary trajectories of populations. While several studies recently investigated the dynamics of deleterious mutations in wild populations, no study has yet explored the fate of deleterious mutations in a context of populations managed by supplementation. Here, based on a dataset of nine wild and 15 supplemented Lake Trout populations genotyped at 4,982 single nucleotide polymorphisms (SNP)s by means of genotype by sequencing (GBS), we explored the effect of supplementation on the frequency of putatively deleterious variants. Three main findings are consequential for the management of fish populations. First, an increase in neutral genetic diversity in stocked populations compared with unstocked ones was observed. Second, putatively deleterious mutations were more likely to be found in unstocked than in stocked populations, suggesting a lower efficiency to purge deleterious mutations in unstocked lakes. Third, a population currently used as a major source for supplementation is characterized by several fixed putatively deleterious alleles. Therefore, other source populations with lower abundance of putatively deleterious mutations should be favored as sources of supplementation. We discuss management implications of our results, especially pertaining to the joint identification of neutral and deleterious mutations that could help refining the choice of source and sink populations for supplementation in order to maximize their evolutionary potential and to limit their mutation load.
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Affiliation(s)
- Anne‐Laure Ferchaud
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Martin Laporte
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Charles Perrier
- Centre d’Écologie Fonctionnelle et ÉvolutiveUnité Mixte de Recherche CNRS 5175Montpellier Cedex 5France
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
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Wang XJ, Hu QJ, Guo XY, Wang K, Ru DF, German DA, Weretilnyk EA, Abbott RJ, Lascoux M, Liu JQ. Demographic expansion and genetic load of the halophyte model plantEutrema salsugineum. Mol Ecol 2018; 27:2943-2955. [DOI: 10.1111/mec.14738] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 05/16/2018] [Accepted: 05/24/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Xiao-Juan Wang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education; College of Life Sciences; Sichuan University; Chengdu China
| | - Quan-Jun Hu
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education; College of Life Sciences; Sichuan University; Chengdu China
| | - Xin-Yi Guo
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education; College of Life Sciences; Sichuan University; Chengdu China
| | - Kun Wang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education; College of Life Sciences; Sichuan University; Chengdu China
| | - Da-Fu Ru
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education; College of Life Sciences; Sichuan University; Chengdu China
| | - Dmitry A. German
- Department of Biodiversity and Plant Systematics; Centre for Organismal Studies (COS Heidelberg); Heidelberg University; Heidelberg Germany
- South-Siberian Botanical Garden; Altai State University; Barnaul Russia
| | | | | | - Martin Lascoux
- Department of Ecology and Genetics; Evolutionary Biology Center and Science for Life Laboratory; Uppsala University; Uppsala Sweden
| | - Jian-quan Liu
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education; College of Life Sciences; Sichuan University; Chengdu China
- State Key Laboratory of Grassland Agro-Ecosystem; College of Life Science; Lanzhou University; Lanzhou China
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40
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A survey of functional genomic variation in domesticated chickens. Genet Sel Evol 2018; 50:17. [PMID: 29661130 PMCID: PMC5902831 DOI: 10.1186/s12711-018-0390-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 04/04/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Deleterious genetic variation can increase in frequency as a result of mutations, genetic drift, and genetic hitchhiking. Although individual effects are often small, the cumulative effect of deleterious genetic variation can impact population fitness substantially. In this study, we examined the genome of commercial purebred chicken lines for deleterious and functional variations, combining genotype and whole-genome sequence data. RESULTS We analysed over 22,000 animals that were genotyped on a 60 K SNP chip from four purebred lines (two white egg and two brown egg layer lines) and two crossbred lines. We identified 79 haplotypes that showed a significant deficit in homozygous carriers. This deficit was assumed to stem from haplotypes that potentially harbour lethal recessive variations. To identify potentially deleterious mutations, a catalogue of over 10 million variants was derived from 250 whole-genome sequenced animals from three purebred white-egg layer lines. Out of 4219 putative deleterious variants, 152 mutations were identified that likely induce embryonic lethality in the homozygous state. Inferred deleterious variation showed evidence of purifying selection and deleterious alleles were generally overrepresented in regions of low recombination. Finally, we found evidence that mutations, which were inferred to be evolutionally intolerant, likely have positive effects in commercial chicken populations. CONCLUSIONS We present a comprehensive genomic perspective on deleterious and functional genetic variation in egg layer breeding lines, which are under intensive selection and characterized by a small effective population size. We show that deleterious variation is subject to purifying selection and that there is a positive relationship between recombination rate and purging efficiency. In addition, multiple putative functional coding variants were discovered in selective sweep regions, which are likely under positive selection. Together, this study provides a unique molecular perspective on functional and deleterious variation in commercial egg-laying chickens, which can enhance current genomic breeding practices to lower the frequency of undesirable variants in the population.
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41
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Liang P, Saqib HSA, Zhang X, Zhang L, Tang H. Single-Base Resolution Map of Evolutionary Constraints and Annotation of Conserved Elements across Major Grass Genomes. Genome Biol Evol 2018; 10:473-488. [PMID: 29378032 PMCID: PMC5798027 DOI: 10.1093/gbe/evy006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2018] [Indexed: 12/20/2022] Open
Abstract
Conserved noncoding sequences (CNSs) are evolutionarily conserved DNA sequences that do not encode proteins but may have potential regulatory roles in gene expression. CNS in crop genomes could be linked to many important agronomic traits and ecological adaptations. Compared with the relatively mature exon annotation protocols, efficient methods are lacking to predict the location of noncoding sequences in the plant genomes. We implemented a computational pipeline that is tailored to the comparisons of plant genomes, yielding a large number of conserved sequences using rice genome as the reference. In this study, we used 17 published grass genomes, along with five monocot genomes as well as the basal angiosperm genome of Amborella trichopoda. Genome alignments among these genomes suggest that at least 12.05% of the rice genome appears to be evolving under constraints in the Poaceae lineage, with close to half of the evolutionarily constrained sequences located outside protein-coding regions. We found evidence for purifying selection acting on the conserved sequences by analyzing segregating SNPs within the rice population. Furthermore, we found that known functional motifs were significantly enriched within CNS, with many motifs associated with the preferred binding of ubiquitous transcription factors. The conserved elements that we have curated are accessible through our public database and the JBrowse server. In-depth functional annotations and evolutionary dynamics of the identified conserved sequences provide a solid foundation for studying gene regulation, genome evolution, as well as to inform gene isolation for cereal biologists.
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Affiliation(s)
- Pingping Liang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Center for Genomics and Biotechnology, Ministry of Education; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, China
| | - Hafiz Sohaib Ahmed Saqib
- Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xingtan Zhang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Center for Genomics and Biotechnology, Ministry of Education; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liangsheng Zhang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Center for Genomics and Biotechnology, Ministry of Education; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Haibao Tang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Center for Genomics and Biotechnology, Ministry of Education; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
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42
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Makino T, Rubin CJ, Carneiro M, Axelsson E, Andersson L, Webster MT. Elevated Proportions of Deleterious Genetic Variation in Domestic Animals and Plants. Genome Biol Evol 2018; 10:276-290. [PMID: 29325102 PMCID: PMC5786255 DOI: 10.1093/gbe/evy004] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2018] [Indexed: 12/12/2022] Open
Abstract
A fraction of genetic variants segregating in any population are deleterious, which negatively impacts individual fitness. The domestication of animals and plants is associated with population bottlenecks and artificial selection, which are predicted to increase the proportion of deleterious variants. However, the extent to which this is a general feature of domestic species is unclear. Here, we examine the effects of domestication on the prevalence of deleterious variation using pooled whole-genome resequencing data from five domestic animal species (dog, pig, rabbit, chicken, and silkworm) and two domestic plant species (rice and soybean) compared with their wild ancestors. We find significantly reduced genetic variation and increased proportion of nonsynonymous amino acid changes in all but one of the domestic species. These differences are observable across a range of allele frequencies, both common and rare. We find proportionally more single nucleotide polymorphisms in highly conserved elements in domestic species and a tendency for domestic species to harbor a higher proportion of changes classified as damaging. Our findings most likely reflect an increased incidence of deleterious variants in domestic species, which is most likely attributable to population bottlenecks that lead to a reduction in the efficacy of selection. An exception to this pattern is displayed by European domestic pigs, which do not show traces of a strong population bottleneck and probably continued to exchange genes with wild boar populations after domestication. The results presented here indicate that an elevated proportion of deleterious variants is a common, but not ubiquitous, feature of domestic species.
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Affiliation(s)
- Takashi Makino
- Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, Japan
| | - Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Sweden
| | - Miguel Carneiro
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Portugal
| | - Erik Axelsson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Sweden
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Sweden
| | - Matthew T Webster
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Sweden
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Conte GL, Hodgins KA, Yeaman S, Degner JC, Aitken SN, Rieseberg LH, Whitlock MC. Bioinformatically predicted deleterious mutations reveal complementation in the interior spruce hybrid complex. BMC Genomics 2017; 18:970. [PMID: 29246191 PMCID: PMC5731209 DOI: 10.1186/s12864-017-4344-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 11/21/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Mutation load is expected to be reduced in hybrids via complementation of deleterious alleles. While local adaptation of hybrids confounds phenotypic tests for reduced mutation load, it may be possible to assess variation in load by analyzing the distribution of putatively deleterious alleles. Here, we use this approach in the interior spruce (Picea glauca x P. engelmannii) hybrid complex, a group likely to suffer from high mutation load and in which hybrids exhibit local adaptation to intermediate conditions. We used PROVEAN to bioinformatically predict whether non-synonymous alleles are deleterious, based on conservation of the position and abnormality of the amino acid change. RESULTS As expected, we found that predicted deleterious alleles were at lower average allele frequencies than alleles not predicted to be deleterious. We were unable to detect a phenotypic effect on juvenile growth rate of the many rare alleles predicted to be deleterious. Both the proportion of alleles predicted to be deleterious and the proportion of loci homozygous for predicted deleterious alleles were higher in P. engelmannii (Engelmann spruce) than in P. glauca (white spruce), due to higher diversity and frequencies of rare alleles in Engelmann. Relative to parental species, the proportion of alleles predicted to be deleterious was intermediate in hybrids, and the proportion of loci homozygous for predicted deleterious alleles was lowest. CONCLUSION Given that most deleterious alleles are recessive, this suggests that mutation load is reduced in hybrids due to complementation of deleterious alleles. This effect may enhance the fitness of hybrids.
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Affiliation(s)
- Gina L Conte
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada. .,Department of Botany, University of British Columbia, 3200-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada.
| | - Kathryn A Hodgins
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada.,Present Address: School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, 3800, Australia
| | - Sam Yeaman
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada.,Present Address: Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada
| | - Jon C Degner
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Sally N Aitken
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Loren H Rieseberg
- Department of Botany, University of British Columbia, 3200-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
| | - Michael C Whitlock
- Department of Zoology, University of British Columbia, 4200-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
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44
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Wang L, Beissinger TM, Lorant A, Ross-Ibarra C, Ross-Ibarra J, Hufford MB. The interplay of demography and selection during maize domestication and expansion. Genome Biol 2017; 18:215. [PMID: 29132403 PMCID: PMC5683586 DOI: 10.1186/s13059-017-1346-4] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 10/19/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The history of maize has been characterized by major demographic events, including population size changes associated with domestication and range expansion, and gene flow with wild relatives. The interplay between demographic history and selection has shaped diversity across maize populations and genomes. RESULTS We investigate these processes using high-depth resequencing data from 31 maize landraces spanning the pre-Columbian distribution of maize, and four wild teosinte individuals (Zea mays ssp. parviglumis). Genome-wide demographic analyses reveal that maize experienced pronounced declines in effective population size due to both a protracted domestication bottleneck and serial founder effects during post-domestication spread, while parviglumis in the Balsas River Valley experienced population growth. The domestication bottleneck and subsequent spread led to an increase in deleterious alleles in the domesticate compared to the wild progenitor. This cost is particularly pronounced in Andean maize, which has experienced a more dramatic founder event compared to other maize populations. Additionally, we detect introgression from the wild teosinte Zea mays ssp. mexicana into maize in the highlands of Mexico, Guatemala, and the southwestern USA, which reduces the prevalence of deleterious alleles likely due to the higher long-term effective population size of teosinte. CONCLUSIONS These findings underscore the strong interaction between historical demography and the efficiency of selection and illustrate how domesticated species are particularly useful for understanding these processes. The landscape of deleterious alleles and therefore evolutionary potential is clearly influenced by recent demography, a factor that could bear importantly on many species that have experienced recent demographic shifts.
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Affiliation(s)
- Li Wang
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, USA
- Genome Informatics Facility, Iowa State University, Ames, USA
| | - Timothy M. Beissinger
- Department of Plant Sciences, University of California, Davis, USA
- USDA-ARS Plant Genetics Research Unit, Columbia, USA
- Divisions of Plant and Biological Sciences, University of Missouri, Columbia, USA
| | - Anne Lorant
- Department of Plant Sciences, University of California, Davis, USA
| | | | - Jeffrey Ross-Ibarra
- Department of Plant Sciences, University of California, Davis, USA
- Genome Center and Center for Population Biology, University of California, Davis, USA
| | - Matthew B. Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, USA
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45
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Wang L, Beissinger TM, Lorant A, Ross-Ibarra C, Ross-Ibarra J, Hufford MB. The interplay of demography and selection during maize domestication and expansion. Genome Biol 2017. [PMID: 29132403 DOI: 10.1101/114579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
BACKGROUND The history of maize has been characterized by major demographic events, including population size changes associated with domestication and range expansion, and gene flow with wild relatives. The interplay between demographic history and selection has shaped diversity across maize populations and genomes. RESULTS We investigate these processes using high-depth resequencing data from 31 maize landraces spanning the pre-Columbian distribution of maize, and four wild teosinte individuals (Zea mays ssp. parviglumis). Genome-wide demographic analyses reveal that maize experienced pronounced declines in effective population size due to both a protracted domestication bottleneck and serial founder effects during post-domestication spread, while parviglumis in the Balsas River Valley experienced population growth. The domestication bottleneck and subsequent spread led to an increase in deleterious alleles in the domesticate compared to the wild progenitor. This cost is particularly pronounced in Andean maize, which has experienced a more dramatic founder event compared to other maize populations. Additionally, we detect introgression from the wild teosinte Zea mays ssp. mexicana into maize in the highlands of Mexico, Guatemala, and the southwestern USA, which reduces the prevalence of deleterious alleles likely due to the higher long-term effective population size of teosinte. CONCLUSIONS These findings underscore the strong interaction between historical demography and the efficiency of selection and illustrate how domesticated species are particularly useful for understanding these processes. The landscape of deleterious alleles and therefore evolutionary potential is clearly influenced by recent demography, a factor that could bear importantly on many species that have experienced recent demographic shifts.
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Affiliation(s)
- Li Wang
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, USA
- Genome Informatics Facility, Iowa State University, Ames, USA
| | - Timothy M Beissinger
- Department of Plant Sciences, University of California, Davis, USA
- USDA-ARS Plant Genetics Research Unit, Columbia, USA
- Divisions of Plant and Biological Sciences, University of Missouri, Columbia, USA
| | - Anne Lorant
- Department of Plant Sciences, University of California, Davis, USA
| | | | - Jeffrey Ross-Ibarra
- Department of Plant Sciences, University of California, Davis, USA.
- Genome Center and Center for Population Biology, University of California, Davis, USA.
| | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, USA.
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Holliday JA, Aitken SN, Cooke JEK, Fady B, González-Martínez SC, Heuertz M, Jaramillo-Correa JP, Lexer C, Staton M, Whetten RW, Plomion C. Advances in ecological genomics in forest trees and applications to genetic resources conservation and breeding. Mol Ecol 2017; 26:706-717. [PMID: 27997049 DOI: 10.1111/mec.13963] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 12/07/2016] [Accepted: 12/14/2016] [Indexed: 12/25/2022]
Abstract
Forest trees are an unparalleled group of organisms in their combined ecological, economic and societal importance. With widespread distributions, predominantly random mating systems and large population sizes, most tree species harbour extensive genetic variation both within and among populations. At the same time, demographic processes associated with Pleistocene climate oscillations and land-use change have affected contemporary range-wide diversity and may impinge on the potential for future adaptation. Understanding how these adaptive and neutral processes have shaped the genomes of trees species is therefore central to their management and conservation. As for many other taxa, the advent of high-throughput sequencing methods is expected to yield an understanding of the interplay between the genome and environment at a level of detail and depth not possible only a few years ago. An international conference entitled 'Genomics and Forest Tree Genetics' was held in May 2016, in Arcachon (France), and brought together forest geneticists with a wide range of research interests to disseminate recent efforts that leverage contemporary genomic tools to probe the population, quantitative and evolutionary genomics of trees. An important goal of the conference was to discuss how such data can be applied to both genome-enabled breeding and the conservation of forest genetic resources under land use and climate change. Here, we report discoveries presented at the meeting and discuss how the ecological genomic toolkit can be used to address both basic and applied questions in tree biology.
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Affiliation(s)
- Jason A Holliday
- Department of Forest Resources and Environmental Conservation, Virginia Tech, 304 Cheatham Hall, Blacksburg, VA 24061, USA
| | - Sally N Aitken
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC V6T1Z4, Canada
| | - Janice E K Cooke
- Department of Biological Sciences, University of Alberta, 5-108 Centennial Centre for Interdisciplinary Science, Edmonton, AB T6G2E9, Canada
| | - Bruno Fady
- Mediterranean Forest Ecology (URFM), Institut National de la Recherche Agronomique (INRA), Domaine St Paul, Site Agroparc, 84914 Avignon, France
| | | | - Myriam Heuertz
- BIOGECO, INRA, Universite de Bordeaux, 69 Route d'Arcachon, 33612 Cestas, France
| | - Juan-Pablo Jaramillo-Correa
- Institute of Ecology, Universidad Nacional Autonoma de Mexico (UNAM) Circuito Exterior s/n, Apartado Postal 70-275, 04510 Ciudad de México, Mexico City, Mexico
| | - Christian Lexer
- Department of Botany and Biodiversity Research, University of Vienna Faculty of Life SciencesRennweg 14, Room 217, A-1030, Vienna, Austria
| | - Margaret Staton
- Department of Entomology and Plant Pathology, University of Tennessee, 370 Plant Biotechnology Building, 2505 EJ Chapman Drive, Knoxville, TN 37996, USA
| | - Ross W Whetten
- Department of Forestry and Environmental Resources, North Carolina State University Jordan Hall Addition 5231, Raleigh, NC 27695, USA
| | - Christophe Plomion
- BIOGECO, INRA, Universite de Bordeaux, 69 Route d'Arcachon, 33612 Cestas, France
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