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Uttam V, Vohra V, Chhotaray S, Santhosh A, Diwakar V, Patel V, Gahlyan RK. Exome-wide comparative analyses revealed differentiating genomic regions for performance traits in Indian native buffaloes. Anim Biotechnol 2024; 35:2277376. [PMID: 37934017 DOI: 10.1080/10495398.2023.2277376] [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] [Indexed: 11/08/2023]
Abstract
In India, 20 breeds of buffalo have been identified and registered, yet limited studies have been conducted to explore the performance potential of these breeds, especially in the Indian native breeds. This study is a maiden attempt to delineate the important variants and unique genes through exome sequencing for milk yield, milk composition, fertility, and adaptation traits in Indian local breeds of buffalo. In the present study, whole exome sequencing was performed on Chhattisgarhi (n = 3), Chilika (n = 4), Gojri (n = 3), and Murrah (n = 4) buffalo breeds and after stringent quality control, 4333, 6829, 4130, and 4854 InDels were revealed, respectively. Exome-wide FST along 100-kb sliding windows detected 27, 98, 38, and 35 outlier windows in Chhattisgarhi, Chilika, Gojri, and Murrah, respectively. The comparative exome analysis of InDels and subsequent gene ontology revealed unique breed specific genes for milk yield (CAMSAP3), milk composition (CLCN1, NUDT3), fertility (PTGER3) and adaptation (KCNA3, TH) traits. Study provides insight into mechanism of how these breeds have evolved under natural selection, the impact of these events on their respective genomes, and their importance in maintaining purity of these breeds for the traits under study. Additionally, this result will underwrite to the genetic acquaintance of these breeds for breeding application, and in understanding of evolution of these Indian local breeds.
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Affiliation(s)
- Vishakha Uttam
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Vikas Vohra
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Supriya Chhotaray
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Ameya Santhosh
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Vikas Diwakar
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Vaibhav Patel
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Rajesh Kumar Gahlyan
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
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2
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Sukhija N, Malik AA, Devadasan JM, Dash A, Bidyalaxmi K, Ravi Kumar D, Kousalaya Devi M, Choudhary A, Kanaka KK, Sharma R, Tripathi SB, Niranjan SK, Sivalingam J, Verma A. Genome-wide selection signatures address trait specific candidate genes in cattle indigenous to arid regions of India. Anim Biotechnol 2024; 35:2290521. [PMID: 38088885 DOI: 10.1080/10495398.2023.2290521] [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] [Indexed: 02/22/2024]
Abstract
The peculiarity of Indian cattle lies in milk quality, resistance to diseases and stressors as well as adaptability. The investigation addressed selection signatures in Gir and Tharparkar cattle, belonging to arid ecotypes of India. Double digest restriction-site associated DNA sequencing (ddRAD-seq) yielded nearly 26 million high-quality reads from unrelated seven Gir and seven Tharparkar cows. In all, 19,127 high-quality SNPs were processed for selection signature analysis. An approach involving within-population composite likelihood ratio (CLR) statistics and between-population FST statistics was used to capture selection signatures within and between the breeds, respectively. A total of 191 selection signatures were addressed using CLR and FST approaches. Selection signatures overlapping 86 and 73 genes were detected as Gir- and Tharparkar-specific, respectively. Notably, genes related to production (CACNA1D, GHRHR), reproduction (ESR1, RBMS3), immunity (NOSTRIN, IL12B) and adaptation (ADAM22, ASL) were annotated to selection signatures. Gene pathway analysis revealed genes in insulin/IGF pathway for milk production, gonadotropin releasing hormone pathway for reproduction, Wnt signalling pathway and chemokine and cytokine signalling pathway for adaptation. This is the first study where selection signatures are identified using ddRAD-seq in indicine cattle breeds. The study shall help in conservation and leveraging genetic improvements in Gir and Tharparkar cattle.
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Affiliation(s)
- Nidhi Sukhija
- ICAR-National Dairy Research Institute, Karnal, India
| | - Anoop Anand Malik
- TERI School of Advanced Studies, Delhi, India
- The Energy and Resources Institute, North Eastern Regional Centre, Guwahati, India
| | | | | | - Kangabam Bidyalaxmi
- ICAR-National Dairy Research Institute, Karnal, India
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - D Ravi Kumar
- ICAR-National Dairy Research Institute, Karnal, India
| | | | | | - K K Kanaka
- ICAR-National Dairy Research Institute, Karnal, India
- ICAR- Indian Institute of Agricultural Biotechnology, Ranchi, India
| | - Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | | | | | | | - Archana Verma
- ICAR-National Dairy Research Institute, Karnal, India
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3
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Bell KL, Noreuil A, Molloy EK, Fritz ML. Genetic and behavioral differences between above and below ground Culex pipiens bioforms. Heredity (Edinb) 2024; 132:221-231. [PMID: 38424351 DOI: 10.1038/s41437-024-00675-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 01/26/2024] [Accepted: 02/05/2024] [Indexed: 03/02/2024] Open
Abstract
Efficiency of mosquito-borne disease transmission is dependent upon both the preference and fidelity of mosquitoes as they seek the blood of vertebrate hosts. While mosquitoes select their blood hosts through multi-modal integration of sensory cues, host-seeking is primarily an odor-guided behavior. Differences in mosquito responses to hosts and their odors have been demonstrated to have a genetic component, but the underlying genomic architecture of these responses has yet to be fully resolved. Here, we provide the first characterization of the genomic architecture of host preference in the polymorphic mosquito species, Culex pipiens. The species exists as two morphologically identical bioforms, each with distinct avian and mammalian host preferences. Cx. pipiens females with empirically measured host responses were prepared into reduced representation DNA libraries and sequenced to identify genomic regions associated with host preference. Multiple genomic regions associated with host preference were identified on all 3 Culex chromosomes, and these genomic regions contained clusters of chemosensory genes, as expected based on work in Anopheles gambiae complex mosquitoes and in Aedes aegypti. One odorant receptor and one odorant binding protein gene showed one-to-one orthologous relationships to differentially expressed genes in A. gambiae complex members with divergent host preferences. Overall, our work identifies a distinct set of odorant receptors and odorant binding proteins that may enable Cx. pipiens females to distinguish between their vertebrate blood host species, and opens avenues for future functional studies that could measure the unique contributions of each gene to host preference phenotypes.
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Affiliation(s)
- Katherine L Bell
- Department of Biology, University of Nevada, Reno, NV, 89557, USA.
| | - Anna Noreuil
- Department of Entomology, University of Maryland, College Park, MD, 20742, USA
| | - Erin K Molloy
- Department of Computer Science, University of Maryland, College Park, MD, 20742, USA
| | - Megan L Fritz
- Department of Entomology, University of Maryland, College Park, MD, 20742, USA.
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4
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Dai JX, Cao LJ, Chen JC, Yang F, Shen XJ, Ma LJ, Hoffmann AA, Chen M, Wei SJ. Testing for adaptive changes linked to range expansion following a single introduction of the fall webworm. Mol Ecol 2024; 33:e17038. [PMID: 37277936 DOI: 10.1111/mec.17038] [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: 12/30/2022] [Accepted: 05/24/2023] [Indexed: 06/07/2023]
Abstract
Adaptive evolution following colonization can affect the impact of invasive species. The fall webworm (FWW) invaded China 40 years ago through a single introduction event involving a severe bottleneck and subsequently diverged into two genetic groups. The well-recorded invasion history of FWW, coupled with a clear pattern of genetic divergence, provides an opportunity to investigate whether there is any sign of adaptive evolution following the invasion. Based on genome-wide SNPs, we identified genetically separated western and eastern groups of FWW and correlated spatial variation in SNPs with geographical and climatic factors. Geographical factors explained a similar proportion of the genetic variation across all populations compared with climatic factors. However, when the two population groups were analysed separately, environmental factors explained more variation than geographical factors. SNP outliers in populations of the western group had relatively stronger response to precipitation than temperature-related variables. Functional annotation of SNP outliers identified genes associated with insect cuticle protein potentially related to desiccation adaptation in the western group and genes associated with lipase biosynthesis potentially related to temperature adaptation in the eastern group. Our study suggests that invasive species may maintain the evolutionary potential to adapt to heterogeneous environments despite a single invasion event. The molecular data suggest that quantitative trait comparisons across environments would be worthwhile.
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Affiliation(s)
- Jin-Xu Dai
- Beijing Key Laboratory for Forest Pests Control, Beijing Forestry University, Beijing, China
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Li-Jun Cao
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jin-Cui Chen
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Fangyuan Yang
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xiu-Jing Shen
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Li-Jun Ma
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ary Anthony Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Min Chen
- Beijing Key Laboratory for Forest Pests Control, Beijing Forestry University, Beijing, China
| | - Shu-Jun Wei
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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5
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Saubin M, Tellier A, Stoeckel S, Andrieux A, Halkett F. Approximate Bayesian Computation applied to time series of population genetic data disentangles rapid genetic changes and demographic variations in a pathogen population. Mol Ecol 2024; 33:e16965. [PMID: 37150947 DOI: 10.1111/mec.16965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 04/04/2023] [Accepted: 04/12/2023] [Indexed: 05/09/2023]
Abstract
Adaptation can occur at remarkably short timescales in natural populations, leading to drastic changes in phenotypes and genotype frequencies over a few generations only. The inference of demographic parameters can allow understanding how evolutionary forces interact and shape the genetic trajectories of populations during rapid adaptation. Here we propose a new Approximate Bayesian Computation (ABC) framework that couples a forward and individual-based model with temporal genetic data to disentangle genetic changes and demographic variations in a case of rapid adaptation. We test the accuracy of our inferential framework and evaluate the benefit of considering a dense versus sparse sampling. Theoretical investigations demonstrate high accuracy in both model and parameter estimations, even if a strong thinning is applied to time series data. Then, we apply our ABC inferential framework to empirical data describing the population genetic changes of the poplar rust pathogen following a major event of resistance overcoming. We successfully estimate key demographic and genetic parameters, including the proportion of resistant hosts deployed in the landscape and the level of standing genetic variation from which selection occurred. Inferred values are in accordance with our empirical knowledge of this biological system. This new inferential framework, which contrasts with coalescent-based ABC analyses, is promising for a better understanding of evolutionary trajectories of populations subjected to rapid adaptation.
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Affiliation(s)
- Méline Saubin
- Université de Lorraine, INRAE, IAM, Nancy, France
- Department for Life Science Systems, Technical University of Munich, Freising, Germany
| | - Aurélien Tellier
- Department for Life Science Systems, Technical University of Munich, Freising, Germany
| | - Solenn Stoeckel
- INRAE, Agrocampus Ouest, Université de Rennes, IGEPP, Le Rheu, France
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6
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Bohutínská M, Peichel CL. Divergence time shapes gene reuse during repeated adaptation. Trends Ecol Evol 2024; 39:396-407. [PMID: 38155043 DOI: 10.1016/j.tree.2023.11.007] [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: 08/10/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023]
Abstract
When diverse lineages repeatedly adapt to similar environmental challenges, the extent to which the same genes are involved (gene reuse) varies across systems. We propose that divergence time among lineages is a key factor driving this variability: as lineages diverge, the extent of gene reuse should decrease due to reductions in allele sharing, functional differentiation among genes, and restructuring of genome architecture. Indeed, we show that many genomic studies of repeated adaptation find that more recently diverged lineages exhibit higher gene reuse during repeated adaptation, but the relationship becomes less clear at older divergence time scales. Thus, future research should explore the factors shaping gene reuse and their interplay across broad divergence time scales for a deeper understanding of evolutionary repeatability.
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Affiliation(s)
- Magdalena Bohutínská
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, 3012, Switzerland; Department of Botany, Faculty of Science, Charles University, Prague, 12800, Czech Republic.
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, 3012, Switzerland
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7
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Sheppard EC, Martin CA, Armstrong C, González-Quevedo C, Illera JC, Suh A, Spurgin LG, Richardson DS. Genotype-environment associations reveal genes potentially linked to avian malaria infection in populations of an endemic island bird. Mol Ecol 2024; 33:e17329. [PMID: 38533805 DOI: 10.1111/mec.17329] [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: 03/07/2023] [Revised: 01/29/2024] [Accepted: 03/01/2024] [Indexed: 03/28/2024]
Abstract
Patterns of pathogen prevalence are, at least partially, the result of coevolutionary host-pathogen interactions. Thus, exploring the distribution of host genetic variation in relation to infection by a pathogen within and across populations can provide important insights into mechanisms of host defence and adaptation. Here, we use a landscape genomics approach (Bayenv) in conjunction with genome-wide data (ddRADseq) to test for associations between avian malaria (Plasmodium) prevalence and host genetic variation across 13 populations of the island endemic Berthelot's pipit (Anthus berthelotii). Considerable and consistent spatial heterogeneity in malaria prevalence was observed among populations over a period of 15 years. The prevalence of malaria infection was also strongly positively correlated with pox (Avipoxvirus) prevalence. Multiple host loci showed significant associations with malaria prevalence after controlling for genome-wide neutral genetic structure. These sites were located near to or within genes linked to metabolism, stress response, transcriptional regulation, complement activity and the inflammatory response, many previously implicated in vertebrate responses to malarial infection. Our findings identify diverse genes - not just limited to the immune system - that may be involved in host protection against malaria and suggest that spatially variable pathogen pressure may be an important evolutionary driver of genetic divergence among wild animal populations, such as Berthelot's pipit. Furthermore, our data indicate that spatio-temporal variation in multiple different pathogens (e.g. malaria and pox in this case) may have to be studied together to develop a more holistic understanding of host pathogen-mediated evolution.
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Affiliation(s)
| | - Claudia A Martin
- School of Biological Sciences, University of East Anglia, Norfolk, UK
- Terrestrial Ecology Unit, Biology Department, Ghent University, Ghent, Belgium
| | - Claire Armstrong
- School of Biological Sciences, University of East Anglia, Norfolk, UK
| | - Catalina González-Quevedo
- School of Biological Sciences, University of East Anglia, Norfolk, UK
- Grupo Ecología y Evolución de Vertebrados, Instituto de Biología, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Medellin, Colombia
| | - Juan Carlos Illera
- Biodiversity Research Institute (CSIC-Oviedo, University-Principality of Asturias), University of Oviedo, Mieres, Asturias, Spain
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norfolk, UK
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lewis G Spurgin
- School of Biological Sciences, University of East Anglia, Norfolk, UK
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McLaughlin CM, Li M, Perryman M, Heymans A, Schneider H, Lasky JR, Sawers RJH. Evidence that variation in root anatomy contributes to local adaptation in Mexican native maize. Evol Appl 2024; 17:e13673. [PMID: 38468714 PMCID: PMC10925829 DOI: 10.1111/eva.13673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/07/2024] [Accepted: 02/22/2024] [Indexed: 03/13/2024] Open
Abstract
Mexican native maize (Zea mays ssp. mays) is adapted to a wide range of climatic and edaphic conditions. Here, we focus specifically on the potential role of root anatomical variation in this adaptation. Given the investment required to characterize root anatomy, we present a machine-learning approach using environmental descriptors to project trait variation from a relatively small training panel onto a larger panel of genotyped and georeferenced Mexican maize accessions. The resulting models defined potential biologically relevant clines across a complex environment that we used subsequently for genotype-environment association. We found evidence of systematic variation in maize root anatomy across Mexico, notably a prevalence of trait combinations favoring a reduction in axial hydraulic conductance in varieties sourced from cooler, drier highland areas. We discuss our results in the context of previously described water-banking strategies and present candidate genes that are associated with both root anatomical and environmental variation. Our strategy is a refinement of standard environmental genome-wide association analysis that is applicable whenever a training set of georeferenced phenotypic data is available.
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Affiliation(s)
- Chloee M. McLaughlin
- Intercollege Graduate Degree Program in Plant BiologyThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Meng Li
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Melanie Perryman
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Adrien Heymans
- Umeå Plant Science Centre, Department of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeåSweden
- Earth and Life InstituteUC LouvainLouvain‐la‐NeuveBelgium
| | - Hannah Schneider
- Department of Physiology and Cell BiologyLeibniz Institute for Plant Genetics and Crop Plant Research (IPK)SeelandGermany
| | - Jesse R. Lasky
- Department of BiologyThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Ruairidh J. H. Sawers
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
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9
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Judson JM, Hoekstra LA, Janzen FJ. Demographic history and genomic signatures of selection in a widespread vertebrate ectotherm. Mol Ecol 2024; 33:e17269. [PMID: 38234254 PMCID: PMC10922411 DOI: 10.1111/mec.17269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/20/2023] [Accepted: 01/08/2024] [Indexed: 01/19/2024]
Abstract
Environmental conditions vary greatly across large geographic ranges, and yet certain species inhabit entire continents. In such species, genomic sequencing can inform our understanding of colonization history and the impact of selection on the genome as populations experience diverse local environments. As ectothermic vertebrates are among the most vulnerable to environmental change, it is critical to understand the contributions of local adaptation to population survival. Widespread ectotherms offer an opportunity to explore how species can successfully inhabit such differing environments and how future climatic shifts will impact species' survival. In this study, we investigated the widespread painted turtle (Chrysemys picta) to assess population genomic structure, demographic history, and genomic signatures of selection in the western extent of the range. We found support for a substantial role of serial founder effects in shaping population genomic structure: demographic analysis and runs of homozygosity were consistent with bottlenecks of increasing severity from eastern to western populations during and following the Last Glacial Maximum, and edge populations were more strongly diverged and had less genetic diversity than those from the centre of the range. We also detected outlier loci, but allelic patterns in many loci could be explained by either genetic surfing or selection. While range expansion complicates the identification of loci under selection, we provide candidates for future study of local adaptation in a long-lived, widespread ectotherm that faces an uncertain future as the global climate continues to rapidly change.
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Affiliation(s)
- Jessica M. Judson
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Current Address: W. K. Kellogg Biological Station, Departments of Fisheries and Wildlife & Integrative Biology, Michigan State University, Hickory Corners, MI 49060, USA
| | - Luke A. Hoekstra
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Current Address: Department of Integrative Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Fredric J. Janzen
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Current Address: W. K. Kellogg Biological Station, Departments of Fisheries and Wildlife & Integrative Biology, Michigan State University, Hickory Corners, MI 49060, USA
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10
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Bernatchez L, Ferchaud AL, Berger CS, Venney CJ, Xuereb A. Genomics for monitoring and understanding species responses to global climate change. Nat Rev Genet 2024; 25:165-183. [PMID: 37863940 DOI: 10.1038/s41576-023-00657-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2023] [Indexed: 10/22/2023]
Abstract
All life forms across the globe are experiencing drastic changes in environmental conditions as a result of global climate change. These environmental changes are happening rapidly, incur substantial socioeconomic costs, pose threats to biodiversity and diminish a species' potential to adapt to future environments. Understanding and monitoring how organisms respond to human-driven climate change is therefore a major priority for the conservation of biodiversity in a rapidly changing environment. Recent developments in genomic, transcriptomic and epigenomic technologies are enabling unprecedented insights into the evolutionary processes and molecular bases of adaptation. This Review summarizes methods that apply and integrate omics tools to experimentally investigate, monitor and predict how species and communities in the wild cope with global climate change, which is by genetically adapting to new environmental conditions, through range shifts or through phenotypic plasticity. We identify advantages and limitations of each method and discuss future research avenues that would improve our understanding of species' evolutionary responses to global climate change, highlighting the need for holistic, multi-omics approaches to ecosystem monitoring during global climate change.
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Affiliation(s)
- Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Anne-Laure Ferchaud
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada.
- Parks Canada, Office of the Chief Ecosystem Scientist, Protected Areas Establishment, Quebec City, Quebec, Canada.
| | - Chloé Suzanne Berger
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Clare J Venney
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Amanda Xuereb
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
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11
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Booker TR, Yeaman S, Whiting JR, Whitlock MC. The WZA: A window-based method for characterizing genotype-environment associations. Mol Ecol Resour 2024; 24:e13768. [PMID: 36785926 DOI: 10.1111/1755-0998.13768] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 01/17/2023] [Accepted: 01/23/2023] [Indexed: 02/15/2023]
Abstract
Genotype-environment association (GEA) studies have the potential to identify the genetic basis of local adaptation in natural populations. Specifically, GEA approaches look for a correlation between allele frequencies and putatively selective features of the environment. Genetic markers with extreme evidence of correlation with the environment are presumed to be tagging the location of alleles that contribute to local adaptation. In this study, we propose a new method for GEA studies called the Weighted-Z Analysis (WZA) that combines information from closely linked sites into analysis windows in a way that was inspired by methods for calculating FST . Performing GEA methods in analysis windows has the advantage that it takes advantage of the increased linkage disequilibrium expected surrounding sites subject to local adaptation. We analyse simulations modelling local adaptation to heterogeneous environments to compare the WZA with existing methods. In the majority of cases we tested, the WZA either outperformed single-SNP (single nucleotide polymorphism)-based approaches or performed similarly. In particular, the WZA outperformed individual SNP approaches when a small number of individuals or demes were sampled. Particularly troubling, we found that some GEA methods exhibit very high false positive rates. We applied the WZA to previously published data from lodgepole pine and identified candidate loci that were identified in the original study alongside numerous loci that were not found in the original study.
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Affiliation(s)
- Tom R Booker
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - James R Whiting
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Michael C Whitlock
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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12
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Howe NS, Hale MC, Waters CD, Schaal SM, Shedd KR, Larson WA. Genomic evidence for domestication selection in three hatchery populations of Chinook salmon, Oncorhynchus tshawytscha. Evol Appl 2024; 17:e13656. [PMID: 38357359 PMCID: PMC10866082 DOI: 10.1111/eva.13656] [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: 08/29/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/16/2024] Open
Abstract
Fish hatcheries are widely used to enhance fisheries and supplement declining wild populations. However, substantial evidence suggests that hatchery fish are subject to differential selection pressures compared to their wild counterparts. Domestication selection, or adaptation to the hatchery environment, poses a risk to wild populations if traits specific to success in the hatchery environment have a genetic component and there is subsequent introgression between hatchery and wild fish. Few studies have investigated domestication selection in hatcheries on a genomic level, and even fewer have done so in parallel across multiple hatchery-wild population pairs. In this study, we used low-coverage whole-genome sequencing to investigate signals of domestication selection in three separate hatchery populations of Chinook salmon, Oncorhynchus tshawytscha, after approximately seven generations of divergence from their corresponding wild progenitor populations. We sequenced 192 individuals from populations across Southeast Alaska and estimated genotype likelihoods at over six million loci. We discovered a total of 14 outlier peaks displaying high genetic differentiation (F ST) between hatchery-wild pairs, although no peaks were shared across the three comparisons. Peaks were small (53 kb on average) and often displayed elevated absolute genetic divergence (D xy) and linkage disequilibrium, suggesting some level of domestication selection has occurred. Our study provides evidence that domestication selection can lead to genetic differences between hatchery and wild populations in only a few generations. Additionally, our data suggest that population-specific adaptation to hatchery environments likely occurs through different genetic pathways, even for populations with similar standing genetic variation. These results highlight the need to collect paired genotype-phenotype data to understand how domestication may be affecting fitness and to identify potential management practices that may mitigate genetic risks despite multiple pathways of domestication.
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Affiliation(s)
- Natasha S. Howe
- Department of BiologyTexas Christian UniversityFort WorthTexasUSA
| | - Matthew C. Hale
- Department of BiologyTexas Christian UniversityFort WorthTexasUSA
| | - Charles D. Waters
- National Oceanographic and Atmospheric Administration, National Marine Fisheries ServiceAlaska Fisheries Science Center, Auke Bay LaboratoriesJuneauAlaskaUSA
| | - Sara M. Schaal
- National Oceanographic and Atmospheric Administration, National Marine Fisheries ServiceAlaska Fisheries Science Center, Auke Bay LaboratoriesJuneauAlaskaUSA
| | - Kyle R. Shedd
- Alaska Department of Fish and Game, Division of Commercial FisheriesGene Conservation LaboratoryAnchorageAlaskaUSA
| | - Wesley A. Larson
- National Oceanographic and Atmospheric Administration, National Marine Fisheries ServiceAlaska Fisheries Science Center, Auke Bay LaboratoriesJuneauAlaskaUSA
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13
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Goebl AM, Kane NC, Doak DF, Rieseberg LH, Ostevik KL. Adaptation to distinct habitats is maintained by contrasting selection at different life stages in sunflower ecotypes. Mol Ecol 2024; 33:e16785. [PMID: 36374153 DOI: 10.1111/mec.16785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/20/2022] [Accepted: 11/02/2022] [Indexed: 11/16/2022]
Abstract
Conspecific populations living in adjacent but contrasting microenvironments represent excellent systems for studying natural selection. These systems are valuable because gene flow is expected to force genetic homogeneity except at loci experiencing divergent selection. A history of reciprocal transplant and common garden studies in such systems, and a growing number of genomic studies, have contributed to understanding how selection operates in natural populations. While selection can vary across different fitness components and life stages, few studies have investigated how this ultimately affects allele frequencies and the maintenance of divergence between populations. Here, we study two sunflower ecotypes in distinct, adjacent habitats by combining demographic models with genome-wide sequence data to estimate fitness and allele frequency change at multiple life stages. This framework allows us to estimate that only local ecotypes are likely to experience positive population growth (λ > 1) and that the maintenance of divergent adaptation appears to be mediated via habitat- and life stage-specific selection. We identify genetic variation, significantly driven by loci in chromosomal inversions, associated with different life history strategies in neighbouring ecotypes that optimize different fitness components and may contribute to the maintenance of distinct ecotypes.
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Affiliation(s)
- April M Goebl
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Nolan C Kane
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Daniel F Doak
- Environmental Studies Programme, University of Colorado, Boulder, Colorado, USA
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kate L Ostevik
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Evolution, Ecology and Organismal Biology, University of California Riverside, Riverside, California, USA
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14
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Schiebelhut LM, Guillaume AS, Kuhn A, Schweizer RM, Armstrong EE, Beaumont MA, Byrne M, Cosart T, Hand BK, Howard L, Mussmann SM, Narum SR, Rasteiro R, Rivera-Colón AG, Saarman N, Sethuraman A, Taylor HR, Thomas GWC, Wellenreuther M, Luikart G. Genomics and conservation: Guidance from training to analyses and applications. Mol Ecol Resour 2024; 24:e13893. [PMID: 37966259 DOI: 10.1111/1755-0998.13893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/16/2023]
Abstract
Environmental change is intensifying the biodiversity crisis and threatening species across the tree of life. Conservation genomics can help inform conservation actions and slow biodiversity loss. However, more training, appropriate use of novel genomic methods and communication with managers are needed. Here, we review practical guidance to improve applied conservation genomics. We share insights aimed at ensuring effectiveness of conservation actions around three themes: (1) improving pedagogy and training in conservation genomics including for online global audiences, (2) conducting rigorous population genomic analyses properly considering theory, marker types and data interpretation and (3) facilitating communication and collaboration between managers and researchers. We aim to update students and professionals and expand their conservation toolkit with genomic principles and recent approaches for conserving and managing biodiversity. The biodiversity crisis is a global problem and, as such, requires international involvement, training, collaboration and frequent reviews of the literature and workshops as we do here.
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Affiliation(s)
- Lauren M Schiebelhut
- Life and Environmental Sciences, University of California, Merced, California, USA
| | - Annie S Guillaume
- Geospatial Molecular Epidemiology group (GEOME), Laboratory for Biological Geochemistry (LGB), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Arianna Kuhn
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
- Virginia Museum of Natural History, Martinsville, Virginia, USA
| | - Rena M Schweizer
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | | | - Mark A Beaumont
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Margaret Byrne
- Department of Biodiversity, Conservation and Attractions, Biodiversity and Conservation Science, Perth, Western Australia, Australia
| | - Ted Cosart
- Flathead Lake Biology Station, University of Montana, Missoula, Montana, USA
| | - Brian K Hand
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Leif Howard
- Flathead Lake Biology Station, University of Montana, Missoula, Montana, USA
| | - Steven M Mussmann
- Southwestern Native Aquatic Resources and Recovery Center, U.S. Fish & Wildlife Service, Dexter, New Mexico, USA
| | - Shawn R Narum
- Hagerman Genetics Lab, University of Idaho, Hagerman, Idaho, USA
| | - Rita Rasteiro
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Angel G Rivera-Colón
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - Norah Saarman
- Department of Biology and Ecology Center, Utah State University, Logan, Utah, USA
| | - Arun Sethuraman
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Helen R Taylor
- Royal Zoological Society of Scotland, Edinburgh, Scotland
| | - Gregg W C Thomas
- Informatics Group, Harvard University, Cambridge, Massachusetts, USA
| | - Maren Wellenreuther
- Plant and Food Research, Nelson, New Zealand
- University of Auckland, Auckland, New Zealand
| | - Gordon Luikart
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
- Flathead Lake Biology Station, University of Montana, Missoula, Montana, USA
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15
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McGaughran A, Dhami MK, Parvizi E, Vaughan AL, Gleeson DM, Hodgins KA, Rollins LA, Tepolt CK, Turner KG, Atsawawaranunt K, Battlay P, Congrains C, Crottini A, Dennis TPW, Lange C, Liu XP, Matheson P, North HL, Popovic I, Rius M, Santure AW, Stuart KC, Tan HZ, Wang C, Wilson J. Genomic Tools in Biological Invasions: Current State and Future Frontiers. Genome Biol Evol 2024; 16:evad230. [PMID: 38109935 PMCID: PMC10776249 DOI: 10.1093/gbe/evad230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/16/2023] [Accepted: 12/12/2023] [Indexed: 12/20/2023] Open
Abstract
Human activities are accelerating rates of biological invasions and climate-driven range expansions globally, yet we understand little of how genomic processes facilitate the invasion process. Although most of the literature has focused on underlying phenotypic correlates of invasiveness, advances in genomic technologies are showing a strong link between genomic variation and invasion success. Here, we consider the ability of genomic tools and technologies to (i) inform mechanistic understanding of biological invasions and (ii) solve real-world issues in predicting and managing biological invasions. For both, we examine the current state of the field and discuss how genomics can be leveraged in the future. In addition, we make recommendations pertinent to broader research issues, such as data sovereignty, metadata standards, collaboration, and science communication best practices that will require concerted efforts from the global invasion genomics community.
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Affiliation(s)
- Angela McGaughran
- Te Aka Mātuatua/School of Science, University of Waikato, Hamilton, New Zealand
| | - Manpreet K Dhami
- Biocontrol and Molecular Ecology, Manaaki Whenua Landcare Research, Lincoln, New Zealand
- School of Biological Sciences, Waipapa Taumata Rau/University of Auckland, Auckland, New Zealand
| | - Elahe Parvizi
- Te Aka Mātuatua/School of Science, University of Waikato, Hamilton, New Zealand
| | - Amy L Vaughan
- Biocontrol and Molecular Ecology, Manaaki Whenua Landcare Research, Lincoln, New Zealand
| | - Dianne M Gleeson
- Centre for Conservation Ecology and Genomics, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Lee A Rollins
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Carolyn K Tepolt
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Kathryn G Turner
- Department of Biological Sciences, Idaho State University, Pocatello, ID, USA
| | - Kamolphat Atsawawaranunt
- School of Biological Sciences, Waipapa Taumata Rau/University of Auckland, Auckland, New Zealand
| | - Paul Battlay
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Carlos Congrains
- Entomology Section, Department of Plant and Environmental Protection Sciences, University of Hawaiʻi at Mānoa, Honolulu, HI 96822, USA
- US Department of Agriculture-Agricultural Research Service, Daniel K. Inouye US Pacific Basin Agricultural Research Center, Hilo, HI 96720, USA
| | - Angelica Crottini
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto 4169–007, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão 4485-661, Portugal
| | - Tristan P W Dennis
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Claudia Lange
- Biocontrol and Molecular Ecology, Manaaki Whenua Landcare Research, Lincoln, New Zealand
| | - Xiaoyue P Liu
- Department of Marine Science, University of Otago, Dunedin, New Zealand
| | - Paige Matheson
- Te Aka Mātuatua/School of Science, University of Waikato, Hamilton, New Zealand
| | - Henry L North
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Iva Popovic
- School of the Environment, University of Queensland, Brisbane, QLD, Australia
| | - Marc Rius
- Centre for Advanced Studies of Blanes (CEAB, CSIC), Accés a la Cala Sant Francesc, Blanes, Spain
- Department of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg 2006, South Africa
| | - Anna W Santure
- School of Biological Sciences, Waipapa Taumata Rau/University of Auckland, Auckland, New Zealand
| | - Katarina C Stuart
- School of Biological Sciences, Waipapa Taumata Rau/University of Auckland, Auckland, New Zealand
| | - Hui Zhen Tan
- School of Biological Sciences, Waipapa Taumata Rau/University of Auckland, Auckland, New Zealand
| | - Cui Wang
- The Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Jonathan Wilson
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
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16
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Cheek RG, McLaughlin JF, Gamboa MP, Marshall CA, Johnson BM, Silver DB, Mauro AA, Ghalambor CK. A lack of genetic diversity and minimal adaptive evolutionary divergence in introduced Mysis shrimp after 50 years. Evol Appl 2024; 17:e13637. [PMID: 38283609 PMCID: PMC10818135 DOI: 10.1111/eva.13637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 11/17/2023] [Accepted: 12/07/2023] [Indexed: 01/30/2024] Open
Abstract
The successes of introduced populations in novel habitats often provide powerful examples of evolution and adaptation. In the 1950s, opossum shrimp (Mysis diluviana) individuals from Clearwater Lake in Minnesota, USA were transported and introduced to Twin Lakes in Colorado, USA by fisheries managers to supplement food sources for trout. Mysis were subsequently introduced from Twin Lakes into numerous lakes throughout Colorado. Because managers kept detailed records of the timing of the introductions, we had the opportunity to test for evolutionary divergence within a known time interval. Here, we used reduced representation genomic data to investigate patterns of genetic diversity, test for genetic divergence between populations, and for evidence of adaptive evolution within the introduced populations in Colorado. We found very low levels of genetic diversity across all populations, with evidence for some genetic divergence between the Minnesota source population and the introduced populations in Colorado. There was little differentiation among the Colorado populations, consistent with the known provenance of a single founding population, with the exception of the population from Gross Reservoir, Colorado. Demographic modeling suggests that at least one undocumented introduction from an unknown source population hybridized with the population in Gross Reservoir. Despite the overall low genetic diversity we observed, F ST outlier and environmental association analyses identified multiple loci exhibiting signatures of selection and adaptive variation related to elevation and lake depth. The success of introduced species is thought to be limited by genetic variation, but our results imply that populations with limited genetic variation can become established in a wide range of novel environments. From an applied perspective, the observed patterns of divergence between populations suggest that genetic analysis can be a useful forensic tool to determine likely sources of invasive species.
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Affiliation(s)
- Rebecca G. Cheek
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
- Graduate Degree Program in EcologyColorado State UniversityFort CollinsColoradoUSA
| | - Jessica F. McLaughlin
- Department of Environmental Science, Policy, and ManagementUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | - Maybellene P. Gamboa
- Department of Organismal Biology and EcologyColorado CollegeColorado SpringsColoradoUSA
| | - Craig A. Marshall
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
- Council on Science and TechnologyPrinceton UniversityPrincetonNew JerseyUSA
| | - Brett M. Johnson
- Department of Fish, Wildlife and Conservation BiologyColorado State UniversityFort CollinsColoradoUSA
| | - Douglas B. Silver
- Department of Fish, Wildlife and Conservation BiologyColorado State UniversityFort CollinsColoradoUSA
| | - Alexander A. Mauro
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
- Graduate Degree Program in EcologyColorado State UniversityFort CollinsColoradoUSA
- Department of Biology, Centre for Biodiversity Dynamics (CBD)Norwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Cameron K. Ghalambor
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
- Graduate Degree Program in EcologyColorado State UniversityFort CollinsColoradoUSA
- Department of Biology, Centre for Biodiversity Dynamics (CBD)Norwegian University of Science and Technology (NTNU)TrondheimNorway
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17
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Willis S, Coykendall DK, Campbell MR, Narum S. Contrasting patterns of sequence variation in steelhead populations reflect distinct evolutionary processes. Evol Appl 2024; 17:e13623. [PMID: 38283605 PMCID: PMC10810252 DOI: 10.1111/eva.13623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/24/2023] [Accepted: 11/10/2023] [Indexed: 01/30/2024] Open
Abstract
Multiple evolutionary processes influence genome-wide allele frequencies and quantifying effects of genetic drift, and multiple forms of selection remain challenging in natural populations. Here, we investigate variation at major effect loci in contrast to patterns of neutral drift across a wide collection of steelhead (Oncorhynchus mykiss) populations that have declined in abundance due to anthropogenic impacts. Whole-genome resequencing of 74 populations of steelhead revealed genome-wide patterns (~8 million SNPs) consistent with expected neutral population structure. However, allelic variation at major effect loci associated with adult migration timing (chromosome 28: GREB1L/ROCK1) and age at maturity (chromosome 25: SIX6) reflected how selection has acted on phenotypic variation in contrast with neutral structure. Variation at major effect loci was influenced by evolutionary processes with differing signals between the strongly divergent Coastal and Inland lineages, while allele frequencies within and among populations within the Inland lineage have been driven by local natural selection as well as recent anthropogenic influences. Recent anthropogenic effects appeared to have influenced the frequency of major effect alleles including artificial selection for specific traits in hatchery stocks with subsequent gene flow into natural populations. Selection from environmental factors at various scales has also likely influenced variation for major effect alleles. These results reveal evolutionary mechanisms that influence allele frequencies at major effect loci that are critical for conservation of phenotypic traits and life history variation of this protected species.
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Affiliation(s)
- Stuart Willis
- Hagerman Genetics LabColumbia River Inter‐Tribal Fish CommissionHagermanIdahoUSA
| | | | | | - Shawn Narum
- Hagerman Genetics LabColumbia River Inter‐Tribal Fish CommissionHagermanIdahoUSA
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18
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Kurland S, Saha A, Keehnen N, de la Paz Celorio-Mancera M, Díez-Del-Molino D, Ryman N, Laikre L. New indicators for monitoring genetic diversity applied to alpine brown trout populations using whole genome sequence data. Mol Ecol 2024; 33:e17213. [PMID: 38014725 DOI: 10.1111/mec.17213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/29/2023]
Abstract
International policy recently adopted commitments to maintain genetic diversity in wild populations to secure their adaptive potential, including metrics to monitor temporal trends in genetic diversity - so-called indicators. A national programme for assessing trends in genetic diversity was recently initiated in Sweden. Relating to this effort, we systematically assess contemporary genome-wide temporal trends (40 years) in wild populations using the newly adopted indicators and whole genome sequencing (WGS). We use pooled and individual WGS data from brown trout (Salmo trutta) in eight alpine lakes in protected areas. Observed temporal trends in diversity metrics (nucleotide diversity, Watterson's ϴ and heterozygosity) lie within proposed acceptable threshold values for six of the lakes, but with consistently low values in lakes above the tree line and declines observed in these northern-most lakes. Local effective population size is low in all lakes, highlighting the importance of continued protection of interconnected systems to allow genetic connectivity for long-term viability of these populations. Inbreeding (FROH ) spans 10%-30% and is mostly represented by ancient (<1 Mb) runs of homozygosity, with observations of little change in mutational load. We also investigate adaptive dynamics over evolutionarily short time frames (a few generations); identifying putative parallel selection across all lakes within a gene pertaining to skin pigmentation as well as candidates of selection unique to specific lakes and lake systems involved in reproduction and immunity. We demonstrate the utility of WGS for systematic monitoring of natural populations, a priority concern if genetic diversity is to be protected.
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Affiliation(s)
- Sara Kurland
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
- Department of Earth Sciences, Natural Resources and Sustainable Development, Uppsala University, Uppsala, Sweden
| | - Atal Saha
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
- Centre for Coastal Research, Department of Natural Sciences, University of Agder, Kristiansand, Norway
| | - Naomi Keehnen
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
- Department of Ecology, SLU, Uppsala, Sweden
| | | | - David Díez-Del-Molino
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Nils Ryman
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Linda Laikre
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
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19
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Soudi S, Jahani M, Todesco M, Owens GL, Bercovich N, Rieseberg LH, Yeaman S. Repeatability of adaptation in sunflowers reveals that genomic regions harbouring inversions also drive adaptation in species lacking an inversion. eLife 2023; 12:RP88604. [PMID: 38095362 PMCID: PMC10721221 DOI: 10.7554/elife.88604] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023] Open
Abstract
Local adaptation commonly involves alleles of large effect, which experience fitness advantages when in positive linkage disequilibrium (LD). Because segregating inversions suppress recombination and facilitate the maintenance of LD between locally adapted loci, they are also commonly found to be associated with adaptive divergence. However, it is unclear what fraction of an adaptive response can be attributed to inversions and alleles of large effect, and whether the loci within an inversion could still drive adaptation in the absence of its recombination-suppressing effect. Here, we use genome-wide association studies to explore patterns of local adaptation in three species of sunflower: Helianthus annuus, Helianthus argophyllus, and Helianthus petiolaris, which each harbour a large number of species-specific inversions. We find evidence of significant genome-wide repeatability in signatures of association to phenotypes and environments, which are particularly enriched within regions of the genome harbouring an inversion in one species. This shows that while inversions may facilitate local adaptation, at least some of the loci can still harbour mutations that make substantial contributions without the benefit of recombination suppression in species lacking a segregating inversion. While a large number of genomic regions show evidence of repeated adaptation, most of the strongest signatures of association still tend to be species-specific, indicating substantial genotypic redundancy for local adaptation in these species.
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Affiliation(s)
- Shaghayegh Soudi
- Department of Biological Sciences, University of CalgaryCalgaryCanada
| | - Mojtaba Jahani
- Department of Biological Sciences, University of CalgaryCalgaryCanada
- Department of Botany, University of British ColumbiaVancouverCanada
| | - Marco Todesco
- Department of Botany, University of British ColumbiaVancouverCanada
- Michael Smith Laboratories, University of British ColumbiaVancouverCanada
- Irving K. Barber Faculty of Science, University of British Columbia OkanaganKelownaCanada
| | | | | | | | - Sam Yeaman
- Department of Biological Sciences, University of CalgaryCalgaryCanada
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20
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Berdan EL, Barton NH, Butlin R, Charlesworth B, Faria R, Fragata I, Gilbert KJ, Jay P, Kapun M, Lotterhos KE, Mérot C, Durmaz Mitchell E, Pascual M, Peichel CL, Rafajlović M, Westram AM, Schaeffer SW, Johannesson K, Flatt T. How chromosomal inversions reorient the evolutionary process. J Evol Biol 2023; 36:1761-1782. [PMID: 37942504 DOI: 10.1111/jeb.14242] [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: 05/05/2023] [Revised: 09/13/2023] [Accepted: 10/05/2023] [Indexed: 11/10/2023]
Abstract
Inversions are structural mutations that reverse the sequence of a chromosome segment and reduce the effective rate of recombination in the heterozygous state. They play a major role in adaptation, as well as in other evolutionary processes such as speciation. Although inversions have been studied since the 1920s, they remain difficult to investigate because the reduced recombination conferred by them strengthens the effects of drift and hitchhiking, which in turn can obscure signatures of selection. Nonetheless, numerous inversions have been found to be under selection. Given recent advances in population genetic theory and empirical study, here we review how different mechanisms of selection affect the evolution of inversions. A key difference between inversions and other mutations, such as single nucleotide variants, is that the fitness of an inversion may be affected by a larger number of frequently interacting processes. This considerably complicates the analysis of the causes underlying the evolution of inversions. We discuss the extent to which these mechanisms can be disentangled, and by which approach.
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Affiliation(s)
- Emma L Berdan
- Bioinformatics Core, Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Nicholas H Barton
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Roger Butlin
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
- Ecology and Evolutionary Biology, School of Bioscience, The University of Sheffield, Sheffield, UK
| | - Brian Charlesworth
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Rui Faria
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Inês Fragata
- CHANGE - Global Change and Sustainability Institute/Animal Biology Department, cE3c - Center for Ecology, Evolution and Environmental Changes, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | | | - Paul Jay
- Center for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
| | - Martin Kapun
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
- Central Research Laboratories, Natural History Museum of Vienna, Vienna, Austria
| | - Katie E Lotterhos
- Department of Marine and Environmental Sciences, Northeastern University, Boston, Massachusetts, USA
| | - Claire Mérot
- UMR 6553 Ecobio, Université de Rennes, OSUR, CNRS, Rennes, France
| | - Esra Durmaz Mitchell
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Functional Genomics & Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Marta Pascual
- Departament de Genètica, Microbiologia i Estadística, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Marina Rafajlović
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
- Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
| | - Anja M Westram
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Stephen W Schaeffer
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Kerstin Johannesson
- Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
- Tjärnö Marine Laboratory, Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
| | - Thomas Flatt
- Department of Biology, University of Fribourg, Fribourg, Switzerland
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21
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Lovell RSL, Collins S, Martin SH, Pigot AL, Phillimore AB. Space-for-time substitutions in climate change ecology and evolution. Biol Rev Camb Philos Soc 2023; 98:2243-2270. [PMID: 37558208 DOI: 10.1111/brv.13004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 07/20/2023] [Accepted: 07/24/2023] [Indexed: 08/11/2023]
Abstract
In an epoch of rapid environmental change, understanding and predicting how biodiversity will respond to a changing climate is an urgent challenge. Since we seldom have sufficient long-term biological data to use the past to anticipate the future, spatial climate-biotic relationships are often used as a proxy for predicting biotic responses to climate change over time. These 'space-for-time substitutions' (SFTS) have become near ubiquitous in global change biology, but with different subfields largely developing methods in isolation. We review how climate-focussed SFTS are used in four subfields of ecology and evolution, each focussed on a different type of biotic variable - population phenotypes, population genotypes, species' distributions, and ecological communities. We then examine the similarities and differences between subfields in terms of methods, limitations and opportunities. While SFTS are used for a wide range of applications, two main approaches are applied across the four subfields: spatial in situ gradient methods and transplant experiments. We find that SFTS methods share common limitations relating to (i) the causality of identified spatial climate-biotic relationships and (ii) the transferability of these relationships, i.e. whether climate-biotic relationships observed over space are equivalent to those occurring over time. Moreover, despite widespread application of SFTS in climate change research, key assumptions remain largely untested. We highlight opportunities to enhance the robustness of SFTS by addressing key assumptions and limitations, with a particular emphasis on where approaches could be shared between the four subfields.
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Affiliation(s)
- Rebecca S L Lovell
- Ashworth Laboratories, Institute of Ecology and Evolution, The University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
| | - Sinead Collins
- Ashworth Laboratories, Institute of Ecology and Evolution, The University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
| | - Simon H Martin
- Ashworth Laboratories, Institute of Ecology and Evolution, The University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
| | - Alex L Pigot
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
| | - Albert B Phillimore
- Ashworth Laboratories, Institute of Ecology and Evolution, The University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
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22
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Marková S, Lanier HC, Escalante MA, da Cruz MOR, Horníková M, Konczal M, Weider LJ, Searle JB, Kotlík P. Local adaptation and future climate vulnerability in a wild rodent. Nat Commun 2023; 14:7840. [PMID: 38030627 PMCID: PMC10686993 DOI: 10.1038/s41467-023-43383-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: 06/02/2023] [Accepted: 11/08/2023] [Indexed: 12/01/2023] Open
Abstract
As climate change continues, species pushed outside their physiological tolerance limits must adapt or face extinction. When change is rapid, adaptation will largely harness ancestral variation, making the availability and characteristics of that variation of critical importance. Here, we used whole-genome sequencing and genetic-environment association analyses to identify adaptive variation and its significance in the context of future climates in a small Palearctic mammal, the bank vole (Clethrionomys glareolus). We found that peripheral populations of bank vole in Britain are already at the extreme bounds of potential genetic adaptation and may require an influx of adaptive variation in order to respond. Analyses of adaptive loci suggest regional differences in climate variables select for variants that influence patterns of population adaptive resilience, including genes associated with antioxidant defense, and support a pattern of thermal/hypoxic cross-adaptation. Our findings indicate that understanding potential shifts in genomic composition in response to climate change may be key to predicting species' fate under future climates.
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Affiliation(s)
- Silvia Marková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburská 89, 277 21, Liběchov, Czech Republic
| | - Hayley C Lanier
- School of Biological Sciences, University of Oklahoma, 730 Van Vleet Oval, Norman, OK, 73019, USA
- Sam Noble Museum, University of Oklahoma, 2401 Chautauqua Ave, Norman, OK, 73072, USA
| | - Marco A Escalante
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburská 89, 277 21, Liběchov, Czech Republic
| | - Marcos O R da Cruz
- School of Biological Sciences, University of Oklahoma, 730 Van Vleet Oval, Norman, OK, 73019, USA
- Sam Noble Museum, University of Oklahoma, 2401 Chautauqua Ave, Norman, OK, 73072, USA
| | - Michaela Horníková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburská 89, 277 21, Liběchov, Czech Republic
| | - Mateusz Konczal
- Faculty of Biology, Evolutionary Biology Group, Adam Mickiewicz University, Poznań, Poland
| | - Lawrence J Weider
- School of Biological Sciences, University of Oklahoma, 730 Van Vleet Oval, Norman, OK, 73019, USA
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Corson Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Petr Kotlík
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburská 89, 277 21, Liběchov, Czech Republic.
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23
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Carbeck K, Arcese P, Lovette I, Pruett C, Winker K, Walsh J. Candidate genes under selection in song sparrows co-vary with climate and body mass in support of Bergmann's Rule. Nat Commun 2023; 14:6974. [PMID: 37935683 PMCID: PMC10630373 DOI: 10.1038/s41467-023-42786-2] [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: 01/10/2023] [Accepted: 10/19/2023] [Indexed: 11/09/2023] Open
Abstract
Ecogeographic rules denote spatial patterns in phenotype and environment that may reflect local adaptation as well as a species' capacity to adapt to change. To identify genes underlying Bergmann's Rule, which posits that spatial correlations of body mass and temperature reflect natural selection and local adaptation in endotherms, we compare 79 genomes from nine song sparrow (Melospiza melodia) subspecies that vary ~300% in body mass (17 - 50 g). Comparing large- and smaller-bodied subspecies revealed 9 candidate genes in three genomic regions associated with body mass. Further comparisons to the five smallest subspecies endemic to California revealed eight SNPs within four of the candidate genes (GARNL3, RALGPS1, ANGPTL2, and COL15A1) associated with body mass and varying as predicted by Bergmann's Rule. Our results support the hypothesis that co-variation in environment, body mass and genotype reflect the influence of natural selection on local adaptation and a capacity for contemporary evolution in this diverse species.
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Affiliation(s)
- Katherine Carbeck
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, T6T 1Z4, Canada.
| | - Peter Arcese
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, T6T 1Z4, Canada
| | - Irby Lovette
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14850, USA
| | - Christin Pruett
- Department of Biology, Ouachita Baptist University, Arkadelphia, AR, 71998, USA
| | - Kevin Winker
- University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
| | - Jennifer Walsh
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, USA
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24
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Willis S, Micheletti S, Andrews KR, Narum S. PoolParty2: An integrated pipeline for analysing pooled or indexed low-coverage whole-genome sequencing data to discover the genetic basis of diversity. Mol Ecol Resour 2023. [PMID: 37921673 DOI: 10.1111/1755-0998.13888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 09/29/2023] [Accepted: 10/19/2023] [Indexed: 11/04/2023]
Abstract
Whole-genome sequencing data allow survey of variation from across the genome, reducing the constraint of balancing genome sub-sampling with estimating recombination rates and linkage between sampled markers and target loci. As sequencing costs decrease, low-coverage whole-genome sequencing of pooled or indexed-individual samples is commonly utilized to identify loci associated with phenotypes or environmental axes in non-model organisms. There are, however, relatively few publicly available bioinformatic pipelines designed explicitly to analyse these types of data, and fewer still that process the raw sequencing data, provide useful metrics of quality control and then execute analyses. Here, we present an updated version of a bioinformatics pipeline called PoolParty2 that can effectively handle either pooled or indexed DNA samples and includes new features to improve computational efficiency. Using simulated data, we demonstrate the ability of our pipeline to recover segregating variants, estimate their allele frequencies accurately, and identify genomic regions harbouring loci under selection. Based on the simulated data set, we benchmark the efficacy of our pipeline with another bioinformatic suite, angsd, and illustrate the compatibility and complementarity of these suites using angsd to generate genotype likelihoods as input for identifying linkage outlier regions using alignment files and variants provided by PoolParty2. Finally, we apply our updated pipeline to an empirical dataset of low-coverage whole genomic data from population samples of Columbia River steelhead trout (Oncorhynchus mykiss), results from which demonstrate the genomic impacts of decades of artificial selection in a prominent hatchery stock. Thus, we not only demonstrate the utility of PoolParty2 for genomic studies that combine sequencing data from multiple individuals, but also illustrate how it compliments other bioinformatics resources such as angsd.
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Affiliation(s)
- Stuart Willis
- Hagerman Genetics Lab, Columbia River Inter-Tribal Fish Commission, Hagerman, Idaho, USA
| | - Steven Micheletti
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kimberly R Andrews
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, Idaho, USA
| | - Shawn Narum
- Hagerman Genetics Lab, Columbia River Inter-Tribal Fish Commission, Hagerman, Idaho, USA
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25
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Sherpa S, Paris JR, Silva‐Rocha I, Di Canio V, Carretero MA, Ficetola GF, Salvi D. Genetic depletion does not prevent rapid evolution in island-introduced lizards. Ecol Evol 2023; 13:e10721. [PMID: 38034325 PMCID: PMC10682264 DOI: 10.1002/ece3.10721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/02/2023] [Accepted: 10/23/2023] [Indexed: 12/02/2023] Open
Abstract
Experimental introductions of species have provided some of the most tractable examples of rapid phenotypic changes, which may reflect plasticity, the impact of stochastic processes, or the action of natural selection. Yet to date, very few studies have investigated the neutral and potentially adaptive genetic impacts of experimental introductions. We dissect the role of these processes in shaping the population differentiation of wall lizards in three Croatian islands (Sušac, Pod Kopište, and Pod Mrčaru), including the islet of Pod Mrčaru, where experimentally introduced lizards underwent rapid (~30 generations) phenotypic changes associated with a shift from an insectivorous to a plant-based diet. Using a genomic approach (~82,000 ddRAD loci), we confirmed a founder effect during introduction and very low neutral genetic differentiation between the introduced population and its source. However, genetic depletion did not prevent rapid population growth, as the introduced lizards exhibited population genetic signals of expansion and are known to have reached a high density. Our genome-scan analysis identified just a handful of loci showing large allelic shifts between ecologically divergent populations. This low overall signal of selection suggests that the extreme phenotypic differences observed among populations are determined by a small number of large-effect loci and/or that phenotypic plasticity plays a major role in phenotypic changes. Nonetheless, functional annotation of the outlier loci revealed some candidate genes relevant to diet-induced adaptation, in agreement with the hypothesis of directional selection. Our study provides important insights on the evolutionary potential of bottlenecked populations in response to new selective pressures on short ecological timescales.
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Affiliation(s)
- Stéphanie Sherpa
- Dipartimento di Scienze e Politiche AmbientaliUniversità degli Studi di MilanoMilanoItaly
| | - Josephine R. Paris
- Dipartimento di Medicina Clinica, Sanità Pubblica, Scienze della Vita e dell'AmbienteUniversità degli Studi dell'AquilaL'Aquila‐CoppitoItaly
| | - Iolanda Silva‐Rocha
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), InBIO Laboratório AssociadoUniversidade do PortoVairãoPortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land PlanningCIBIOVairãoPortugal
| | - Viola Di Canio
- Dipartimento di Scienze e Politiche AmbientaliUniversità degli Studi di MilanoMilanoItaly
| | - Miguel Angel Carretero
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), InBIO Laboratório AssociadoUniversidade do PortoVairãoPortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land PlanningCIBIOVairãoPortugal
- Departamento de Biologia, Faculdade de CiênciasUniversidade do PortoPortoPortugal
| | | | - Daniele Salvi
- Dipartimento di Medicina Clinica, Sanità Pubblica, Scienze della Vita e dell'AmbienteUniversità degli Studi dell'AquilaL'Aquila‐CoppitoItaly
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26
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Pratt EAL, Beheregaray LB, Fruet P, Tezanos-Pinto G, Bilgmann K, Zanardo N, Diaz-Aguirre F, Secchi ER, Freitas TRO, Möller LM. Genomic Divergence and the Evolution of Ecotypes in Bottlenose Dolphins (Genus Tursiops). Genome Biol Evol 2023; 15:evad199. [PMID: 37935115 PMCID: PMC10655200 DOI: 10.1093/gbe/evad199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 10/03/2023] [Accepted: 10/14/2023] [Indexed: 11/09/2023] Open
Abstract
Climatic changes have caused major environmental restructuring throughout the world's oceans. Marine organisms have responded to novel conditions through various biological systems, including genomic adaptation. Growing accessibility of next-generation DNA sequencing methods to study nonmodel species has recently allowed genomic changes underlying environmental adaptations to be investigated. This study used double-digest restriction-site associated DNA (ddRAD) sequence data to investigate the genomic basis of ecotype formation across currently recognized species and subspecies of bottlenose dolphins (genus Tursiops) in the Southern Hemisphere. Subspecies-level genomic divergence was confirmed between the offshore common bottlenose dolphin (T. truncatus truncatus) and the inshore Lahille's bottlenose dolphin (T. t. gephyreus) from the southwestern Atlantic Ocean (SWAO). Similarly, subspecies-level divergence is suggested between inshore (eastern Australia) Indo-Pacific bottlenose dolphin (T. aduncus) and the proposed Burrunan dolphin (T. australis) from southern Australia. Inshore bottlenose dolphin lineages generally had lower genomic diversity than offshore lineages, a pattern particularly evident for T. t. gephyreus, which showed exceptionally low diversity. Genomic regions associated with cardiovascular, musculoskeletal, and energy production systems appear to have undergone repeated adaptive evolution in inshore lineages across the Southern Hemisphere. We hypothesize that comparable selective pressures in the inshore environment drove similar adaptive responses in each lineage, supporting parallel evolution of inshore bottlenose dolphins. With climate change altering marine ecosystems worldwide, it is crucial to gain an understanding of the adaptive capacity of local species and populations. Our study provides insights into key adaptive pathways that may be important for the long-term survival of cetaceans and other organisms in a changing marine environment.
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Affiliation(s)
- Eleanor A L Pratt
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
- Cetacean Ecology, Behaviour and Evolution Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Pedro Fruet
- Laboratório de Ecologia e Conservação da Megafauna Marinha (ECOMEGA), Universidade Federal do Rio Grande-FURG, Rio Grande, Brazil
- Museu Oceanográfico Prof. Eliézer de C. Rios, Universidade Federal do Rio Grande-FURG, Rio Grande, Brazil
- Kaosa, Rio Grande, Brazil
| | | | - Kerstin Bilgmann
- Department of Biological Sciences, Macquarie University, North Ryde, New South Wales, Australia
| | - Nikki Zanardo
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
- Cetacean Ecology, Behaviour and Evolution Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
- Department of Environment and Water, Adelaide, South Australia, Australia
| | - Fernando Diaz-Aguirre
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
- Cetacean Ecology, Behaviour and Evolution Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Eduardo R Secchi
- Laboratório de Ecologia e Conservação da Megafauna Marinha (ECOMEGA), Universidade Federal do Rio Grande-FURG, Rio Grande, Brazil
- Museu Oceanográfico Prof. Eliézer de C. Rios, Universidade Federal do Rio Grande-FURG, Rio Grande, Brazil
| | - Thales R O Freitas
- Laboratório de Citogenética e Evolução, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Luciana M Möller
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
- Cetacean Ecology, Behaviour and Evolution Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
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27
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Bazzicalupo E, Ratkiewicz M, Seryodkin IV, Okhlopkov I, Galsandorj N, Yarovenko YA, Ozolins J, Saveljev AP, Melovski D, Gavashelishvili A, Schmidt K, Godoy JA. Genome-environment association analyses reveal geographically restricted adaptive divergence across the range of the widespread Eurasian carnivore Lynx lynx (Linnaeus, 1758). Evol Appl 2023; 16:1773-1788. [PMID: 38029067 PMCID: PMC10681490 DOI: 10.1111/eva.13570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 05/18/2023] [Accepted: 06/06/2023] [Indexed: 12/01/2023] Open
Abstract
Local adaptations to the environment are an important aspect of the diversity of a species and their discovery, description and quantification has important implications for the fields of taxonomy, evolutionary and conservation biology. In this study, we scan genomes from several populations across the distributional range of the Eurasian lynx, with the objective of finding genomic windows under positive selection which may underlie local adaptations to different environments. A total of 394 genomic windows are found to be associated to local environmental conditions, and they are enriched for genes involved in metabolism, behaviour, synaptic organization and neural development. Adaptive genetic structure, reconstructed from SNPs in candidate windows, is considerably different than the neutral genetic structure of the species. A widespread adaptively homogeneous group is recovered occupying areas of harsher snow and temperature climatic conditions in the north-western, central and eastern parts of the distribution. Adaptively divergent populations are recovered in the westernmost part of the range, especially within the Baltic population, but also predicted for different patches in the western and southern part of the range, associated with different snow and temperature regimes. Adaptive differentiation driven by climate does not correlate much with the subspecies taxonomic delimitations, suggesting that subspecific divergences are mostly driven by neutral processes of genetic drift and gene flow. Our results will aid the selection of source populations for assisted gene flow or genetic rescue programs by identifying what climatic patterns to look for as predictors of pre-adaptation of individuals. Particularly, the Carpathian population is confirmed as the best source of individuals for the genetic rescue of the endangered, isolated and genetically eroded Balkan population. Additionally, reintroductions in central and western Europe, currently based mostly on Carpathian lynxes, could consider the Baltic population as an additional source to increase adaptive variation and likely improve adaptation to their milder climate.
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Affiliation(s)
- Enrico Bazzicalupo
- Department of Ecology and EvolutionEstación Biológica de Doñana (CSIC)SevilleSpain
| | | | - Ivan V. Seryodkin
- Laboratory of Ecology and Conservation of AnimalsPacific Institute of Geography of Far East Branch of Russian Academy of SciencesVladivostokRussia
| | - Innokentiy Okhlopkov
- Institute for Biological Problems of CryolithozoneSiberian Branch of the Russian Academy of SciencesYakutskRussia
| | | | - Yuriy A. Yarovenko
- Pre‐Caspian Institute of Biological ResourcesDagestan Federal Scientific Centre of RASMakhachkalaRussia
| | - Janis Ozolins
- Department of Hunting and Wildlife ManagementLatvijas Valsts mežzinātnes institūts "Silava"SalaspilsLatvia
| | - Alexander P. Saveljev
- Department of Animal EcologyRussian Research Institute of Game Management and Fur FarmingKirovRussia
| | - Dime Melovski
- Macedonian Ecological Society (MES)SkopjeNorth Macedonia
| | | | | | - José A. Godoy
- Department of Ecology and EvolutionEstación Biológica de Doñana (CSIC)SevilleSpain
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28
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Diniz FDA, Moura JDO, Bajay MM, Branco LC, Bezerra RD, de Araújo AM. Capra hircus outliers markers in Brazil: Searching for genomic regions under the action of natural selection. Genet Mol Biol 2023; 46:e20230084. [PMID: 37882366 PMCID: PMC10594045 DOI: 10.1590/1678-4685-gmb-2023-0084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 08/21/2023] [Indexed: 10/27/2023] Open
Abstract
Identifying genome regions subject to selection in local breeds of Brazil is an opportunity to elucidate the C. hircus genome plasticity, flowing the colonization history of the country. Using SNP Bead Chip Illumina 50K genotyping of Brazilian Anglo-Nubian (standardized breed) and Marota (local endangered population from the semiarid area of Brazil) to show outliers loci in genome regions subject to selection. After applying data quality control, 45,600 SNPs were included in this investigation. Principal component analysis (PCAdapt) and FDIST2 analysis signalized 14 genomic regions more affected by selection in the Brazilian dry zone environment. The genome study signalized regions that are close to the sequences of genes related to growth and embryonic skeletal development (FGF12, AMPD2, OSTN). In addition, flagged regions close to the genes UTSB2 and SLC5A2 contribute to research on functional adaptation with low water needs and poor nutritive diet to survive. Both genes encode proteins that act on osmotic pathways and avoid cell flooding on stress cell responses. Further studies on the genetic role and involvement of these outliers' genomic regions, building a robust conceptual high-resolution map of natural selection drives, help to achieve hardiness candidate genes linked to the evolutionary history of Capra hircus in the semiarid area of Brazil.
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Affiliation(s)
- Francisco de A. Diniz
- Universidade Federal do Piauí, Teresina, PI, Brazil
- Instituto Federal do Piauí, Teresina, PI, Brazil
| | | | - Miklos M. Bajay
- Universidade do Estado de Santa Catarina, Laguna, SC, Brazil
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29
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Márquez-Corro JI, Martín-Bravo S, Blanco-Pastor JL, Luceño M, Escudero M. The holocentric chromosome microevolution: From phylogeographic patterns to genomic associations with environmental gradients. Mol Ecol 2023. [PMID: 37795678 DOI: 10.1111/mec.17156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/06/2023]
Abstract
Geographic isolation and chromosome evolution are two of the major drivers of diversification in eukaryotes in general, and specifically, in plants. On one hand, range shifts induced by Pleistocene glacial oscillations deeply shaped the evolutionary trajectories of species in the Northern Hemisphere. On the other hand, karyotype variability within species or species complexes may have adaptive potential as different karyotypes may represent different recombination rates and linkage groups that may be associated with locally adapted genes or supergenes. Organisms with holocentric chromosomes are ideal to study the link between local adaptation and chromosome evolution, due to their high cytogenetic variability, especially when it seems to be related to environmental variation. Here, we integrate the study of the phylogeography, chromosomal evolution and ecological requirements of a plant species complex distributed in the Western Euro-Mediterranean region (Carex gr. laevigata, Cyperaceae). We aim to clarify the relative influence of these factors on population differentiation and ultimately on speciation. We obtained a well-resolved RADseq phylogeny that sheds light on the phylogeographic patterns of molecular and chromosome number variation, which are compatible with south-to-north postglacial migration. In addition, landscape genomics analyses identified candidate loci for local adaptation, and also strong significant associations between the karyotype and the environment. We conclude that karyotype distribution in C. gr. laevigata has been constrained by both range shift dynamics and local adaptation. Our study demonstrates that chromosome evolution may be responsible, at least partially, for microevolutionary patterns of population differentiation and adaptation in Carex.
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Affiliation(s)
- José Ignacio Márquez-Corro
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Seville, Spain
- Jodrell Laboratory, Department of Trait Diversity and Function, Royal Botanic Gardens, Kew, Richmond, UK
| | - Santiago Martín-Bravo
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Seville, Spain
| | - José Luis Blanco-Pastor
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Seville, Spain
- Departamento de Biología, IVAGRO, Universidad de Cádiz, Campus de Excelencia Internacional Agroalimentario (CeiA3), Cádiz, Spain
| | - Modesto Luceño
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Seville, Spain
| | - Marcial Escudero
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Seville, Spain
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30
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Petak C, Frati L, Brennan RS, Pespeni MH. Whole-Genome Sequencing Reveals That Regulatory and Low Pleiotropy Variants Underlie Local Adaptation to Environmental Variability in Purple Sea Urchins. Am Nat 2023; 202:571-586. [PMID: 37792925 DOI: 10.1086/726013] [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] [Indexed: 10/06/2023]
Abstract
AbstractOrganisms experience environments that vary across both space and time. Such environmental heterogeneity shapes standing genetic variation and may influence species' capacity to adapt to rapid environmental change. However, we know little about the kind of genetic variation that is involved in local adaptation to environmental variability. To address this gap, we sequenced the whole genomes of 140 purple sea urchins (Strongylocentrotus purpuratus) from seven populations that vary in their degree of pH variability. Despite no evidence of global population structure, we found a suite of single-nucleotide polymorphisms (SNPs) tightly correlated with local pH variability (outlier SNPs), which were overrepresented in regions putatively involved in gene regulation (long noncoding RNA and enhancers), supporting the idea that variation in regulatory regions is important for local adaptation to variability. In addition, outliers in genes were found to be (i) enriched for biomineralization and ion homeostasis functions related to low pH response, (ii) less central to the protein-protein interaction network, and (iii) underrepresented among genes highly expressed during early development. Taken together, these results suggest that loci that underlie local adaptation to pH variability in purple sea urchins fall in regions with potentially low pleiotropic effects (based on analyses involving regulatory regions, network centrality, and expression time) involved in low pH response (based on functional enrichment).
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31
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Mascarenhas R, Meirelles PM, Batalha-Filho H. Urbanization drives adaptive evolution in a Neotropical bird. Curr Zool 2023; 69:607-619. [PMID: 37637315 PMCID: PMC10449428 DOI: 10.1093/cz/zoac066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 08/16/2022] [Indexed: 08/29/2023] Open
Abstract
Urbanization has dramatic impacts on natural habitats and such changes may potentially drive local adaptation of urban populations. Behavioral change has been specifically shown to facilitate the fast adaptation of birds to changing environments, but few studies have investigated the genetic mechanisms of this process. Such investigations could provide insights into questions about both evolutionary theory and management of urban populations. In this study, we investigated whether local adaptation has occurred in urban populations of a Neotropical bird species, Coereba flaveola, specifically addressing whether observed behavioral adaptations are correlated to genetic signatures of natural selection. To answer this question, we sampled 24 individuals in urban and rural environments, and searched for selected loci through a genome-scan approach based on RADseq genomic data, generated and assembled using a reference genome for the species. We recovered 46 loci as putative selection outliers, and 30 of them were identified as associated with biological processes possibly related to urban adaptation, such as the regulation of energetic metabolism, regulation of genetic expression, and changes in the immunological system. Moreover, genes involved in the development of the nervous system showed signatures of selection, suggesting a link between behavioral and genetic adaptations. Our findings, in conjunction with similar results in previous studies, support the idea that cities provide a similar selective pressure on urban populations and that behavioral plasticity may be enhanced through genetic changes in urban populations.
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Affiliation(s)
- Rilquer Mascarenhas
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Instituto de Biologia, Universidade Federal da Bahia, 40170-115 Salvador, Bahia, Brazil
| | - Pedro Milet Meirelles
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Instituto de Biologia, Universidade Federal da Bahia, 40170-115 Salvador, Bahia, Brazil
| | - Henrique Batalha-Filho
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Instituto de Biologia, Universidade Federal da Bahia, 40170-115 Salvador, Bahia, Brazil
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32
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James ME, Allsopp RN, Groh JS, Kaur A, Wilkinson MJ, Ortiz-Barrientos D. Uncovering the genetic architecture of parallel evolution. Mol Ecol 2023; 32:5575-5589. [PMID: 37740681 DOI: 10.1111/mec.17134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 07/31/2023] [Accepted: 08/07/2023] [Indexed: 09/25/2023]
Abstract
Identifying the genetic architecture underlying adaptive traits is exceptionally challenging in natural populations. This is because associations between traits not only mask the targets of selection but also create correlated patterns of genomic divergence that hinder our ability to isolate causal genetic effects. Here, we examine the repeated evolution of components of the auxin pathway that have contributed to the replicated loss of gravitropism (i.e. the ability of a plant to bend in response to gravity) in multiple populations of the Senecio lautus species complex in Australia. We use a powerful approach which combines parallel population genomics with association mapping in a Multiparent Advanced Generation Inter-Cross (MAGIC) population to break down genetic and trait correlations to reveal how adaptive traits evolve during replicated evolution. We sequenced auxin and shoot gravitropism-related gene regions in 80 individuals from six natural populations (three parallel divergence events) and 133 individuals from a MAGIC population derived from two of the recently diverged natural populations. We show that artificial tail selection on gravitropism in the MAGIC population recreates patterns of parallel divergence in the auxin pathway in the natural populations. We reveal a set of 55 auxin gene regions that have evolved repeatedly during the evolution of the species, of which 50 are directly associated with gravitropism divergence in the MAGIC population. Our work creates a strong link between patterns of genomic divergence and trait variation contributing to replicated evolution by natural selection, paving the way to understand the origin and maintenance of adaptations in natural populations.
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Affiliation(s)
- Maddie E James
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, Queensland, Australia
| | - Robin N Allsopp
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Jeffrey S Groh
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Avneet Kaur
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, Queensland, Australia
| | - Melanie J Wilkinson
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, Queensland, Australia
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, Queensland, Australia
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33
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Heraghty SD, Jackson JM, Lozier JD. Whole genome analyses reveal weak signatures of population structure and environmentally associated local adaptation in an important North American pollinator, the bumble bee Bombus vosnesenskii. Mol Ecol 2023; 32:5479-5497. [PMID: 37702957 DOI: 10.1111/mec.17125] [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] [Received: 03/08/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 09/14/2023]
Abstract
Studies of species that experience environmental heterogeneity across their distributions have become an important tool for understanding mechanisms of adaptation and predicting responses to climate change. We examine population structure, demographic history and environmentally associated genomic variation in Bombus vosnesenskii, a common bumble bee in the western USA, using whole genome resequencing of populations distributed across a broad range of latitudes and elevations. We find that B. vosnesenskii exhibits minimal population structure and weak isolation by distance, confirming results from previous studies using other molecular marker types. Similarly, demographic analyses with Sequentially Markovian Coalescent models suggest that minimal population structure may have persisted since the last interglacial period, with genomes from different parts of the species range showing similar historical effective population size trajectories and relatively small fluctuations through time. Redundancy analysis revealed a small amount of genomic variation explained by bioclimatic variables. Environmental association analysis with latent factor mixed modelling (LFMM2) identified few outlier loci that were sparsely distributed throughout the genome and although a few putative signatures of selective sweeps were identified, none encompassed particularly large numbers of loci. Some outlier loci were in genes with known regulatory relationships, suggesting the possibility of weak selection, although compared with other species examined with similar approaches, evidence for extensive local adaptation signatures in the genome was relatively weak. Overall, results indicate B. vosnesenskii is an example of a generalist with a high degree of flexibility in its environmental requirements that may ultimately benefit the species under periods of climate change.
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Affiliation(s)
- Sam D Heraghty
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, USA
| | - Jason M Jackson
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, USA
| | - Jeffrey D Lozier
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, USA
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Bedford JA, Carine M, Chapman MA. Detection of locally adapted genomic regions in wild rice (Oryza rufipogon) using environmental association analysis. G3 (BETHESDA, MD.) 2023; 13:jkad194. [PMID: 37619981 PMCID: PMC10542315 DOI: 10.1093/g3journal/jkad194] [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: 07/19/2023] [Revised: 08/14/2023] [Accepted: 08/17/2023] [Indexed: 08/26/2023]
Abstract
Oryza rufipogon is the wild progenitor of cultivated rice Oryza sativa and exhibits high levels of genetic diversity across its distribution, making it a useful resource for the identification of abiotic stress-tolerant varieties and genes that could limit future climate-changed-induced yield losses. To investigate local adaptation in O. rufipogon, we analyzed single nucleotide polymorphism (SNP) data from a panel of 286 samples located across a diverse range of climates. Environmental association analysis (EAA), a genome-wide association study (GWAS)-based method, was used and revealed 15 regions of the genome significantly associated with various climate factors. Genes within these environmentally associated regions have putative functions in abiotic stress response, phytohormone signaling, and the control of flowering time. This provides an insight into potential local adaptation in O. rufipogon and reveals possible locally adaptive genes that may provide opportunities for breeding novel rice varieties with climate change-resilient phenotypes.
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Affiliation(s)
- James A Bedford
- Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
- Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Mark Carine
- Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
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35
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Bock DG, Cai Z, Elphinstone C, González-Segovia E, Hirabayashi K, Huang K, Keais GL, Kim A, Owens GL, Rieseberg LH. Genomics of plant speciation. PLANT COMMUNICATIONS 2023; 4:100599. [PMID: 37050879 PMCID: PMC10504567 DOI: 10.1016/j.xplc.2023.100599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/21/2023] [Accepted: 04/06/2023] [Indexed: 06/19/2023]
Abstract
Studies of plants have been instrumental for revealing how new species originate. For several decades, botanical research has complemented and, in some cases, challenged concepts on speciation developed via the study of other organisms while also revealing additional ways in which species can form. Now, the ability to sequence genomes at an unprecedented pace and scale has allowed biologists to settle decades-long debates and tackle other emerging challenges in speciation research. Here, we review these recent genome-enabled developments in plant speciation. We discuss complications related to identification of reproductive isolation (RI) loci using analyses of the landscape of genomic divergence and highlight the important role that structural variants have in speciation, as increasingly revealed by new sequencing technologies. Further, we review how genomics has advanced what we know of some routes to new species formation, like hybridization or whole-genome duplication, while casting doubt on others, like population bottlenecks and genetic drift. While genomics can fast-track identification of genes and mutations that confer RI, we emphasize that follow-up molecular and field experiments remain critical. Nonetheless, genomics has clarified the outsized role of ancient variants rather than new mutations, particularly early during speciation. We conclude by highlighting promising avenues of future study. These include expanding what we know so far about the role of epigenetic and structural changes during speciation, broadening the scope and taxonomic breadth of plant speciation genomics studies, and synthesizing information from extensive genomic data that have already been generated by the plant speciation community.
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Affiliation(s)
- Dan G Bock
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Zhe Cai
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Cassandra Elphinstone
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Eric González-Segovia
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | | | - Kaichi Huang
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Graeme L Keais
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Amy Kim
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Gregory L Owens
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.
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Rahman SR, Lozier JD. Genome-wide DNA methylation patterns in bumble bee (Bombus vosnesenskii) populations from spatial-environmental range extremes. Sci Rep 2023; 13:14901. [PMID: 37689750 PMCID: PMC10492822 DOI: 10.1038/s41598-023-41896-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 09/01/2023] [Indexed: 09/11/2023] Open
Abstract
Unraveling molecular mechanisms of adaptation to complex environments is crucial to understanding tolerance of abiotic pressures and responses to climatic change. Epigenetic variation is increasingly recognized as a mechanism that can facilitate rapid responses to changing environmental cues. To investigate variation in genetic and epigenetic diversity at spatial and thermal extremes, we use whole genome and methylome sequencing to generate a high-resolution map of DNA methylation in the bumble bee Bombus vosnesenskii. We sample two populations representing spatial and environmental range extremes (a warm southern low-elevation site and a cold northern high-elevation site) previously shown to exhibit differences in thermal tolerance and determine positions in the genome that are consistently and variably methylated across samples. Bisulfite sequencing reveals methylation characteristics similar to other arthropods, with low global CpG methylation but high methylation concentrated in gene bodies and in genome regions with low nucleotide diversity. Differentially methylated sites (n = 2066) were largely hypomethylated in the northern high-elevation population but not related to local sequence differentiation. The concentration of methylated and differentially methylated sites in exons and putative promoter regions suggests a possible role in gene regulation, and this high-resolution analysis of intraspecific epigenetic variation in wild Bombus suggests that the function of methylation in niche adaptation would be worth further investigation.
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Affiliation(s)
| | - Jeffrey D Lozier
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, USA
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37
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Recuerda M, Palacios M, Frías O, Hobson K, Nabholz B, Blanco G, Milá B. Adaptive phenotypic and genomic divergence in the common chaffinch (Fringilla coelebs) following niche expansion within a small oceanic island. J Evol Biol 2023; 36:1226-1241. [PMID: 37485603 DOI: 10.1111/jeb.14200] [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: 12/14/2022] [Revised: 06/06/2023] [Accepted: 06/09/2023] [Indexed: 07/25/2023]
Abstract
According to models of ecological speciation, adaptation to adjacent, contrasting habitat types can lead to population divergence given strong enough environment-driven selection to counteract the homogenizing effect of gene flow. We tested this hypothesis in the common chaffinch (Fringilla coelebs) on the small island of La Palma, Canary Islands, where it occupies two markedly different habitats. Isotopic (δ13 C, δ15 N) analysis of feathers indicated that birds in the two habitats differed in ecosystem and/or diet, and analysis of phenotypic traits revealed significant differences in morphology and plumage colouration that are consistent with ecomorphological and ecogeographical predictions respectively. A genome-wide survey of single-nucleotide polymorphism revealed marked neutral structure that was consistent with geography and isolation by distance, suggesting low dispersal. In contrast, loci putatively under selection identified through genome-wide association and genotype-environment association analyses, revealed amarked adaptive divergence between birds in both habitats. Loci associated with phenotypic and environmental differences among habitats were distributed across the genome, as expected for polygenic traits involved in local adaptation. Our results suggest a strong role for habitat-driven local adaptation in population divergence in the chaffinches of La Palma, a process that appears to be facilitated by a strong reduction in effective dispersal distances despite the birds' high dispersal capacity.
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Affiliation(s)
- María Recuerda
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Mercè Palacios
- Department of Biodiversity, Ecology and Evolution, Universidad Complutense de Madrid, Madrid, Spain
| | - Oscar Frías
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Keith Hobson
- Biology Department, Western University, London, Ontario, Canada
| | - Benoit Nabholz
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France
- Institut Universitaire de France (IUF), Paris, France
| | - Guillermo Blanco
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
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38
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Swift DG, O'Leary SJ, Grubbs RD, Frazier BS, Fields AT, Gardiner JM, Drymon JM, Bethea DM, Wiley TR, Portnoy DS. Philopatry influences the genetic population structure of the blacktip shark (Carcharhinus limbatus) at multiple spatial scales. Mol Ecol 2023; 32:4953-4970. [PMID: 37566208 DOI: 10.1111/mec.17096] [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: 04/04/2022] [Revised: 07/22/2023] [Accepted: 07/28/2023] [Indexed: 08/12/2023]
Abstract
Understanding how interactions among microevolutionary forces generate genetic population structure of exploited species is vital to the implementation of management policies that facilitate persistence. Philopatry displayed by many coastal shark species can impact gene flow and facilitate selection, and has direct implications for the spatial scales of management. Here, genetic structure of the blacktip shark (Carcharhinus limbatus) was examined using a mixed-marker approach employing mitochondrial control region sequences and 4339 SNP-containing loci generated using ddRAD-Seq. Genetic variation was assessed among young-of-the-year sampled in 11 sites in waters of the United States in the western North Atlantic Ocean, including the Gulf of Mexico. Spatial and environmental analyses detected 68 nuclear loci putatively under selection, enabling separate assessments of neutral and adaptive genetic structure. Both mitochondrial and neutral SNP data indicated three genetically distinct units-the Atlantic, eastern Gulf, and western Gulf-that align with regional stocks and suggest regional philopatry by males and females. Heterogeneity at loci putatively under selection, associated with temperature and salinity, was observed among sites within Gulf units, suggesting local adaptation. Furthermore, five pairs of siblings were identified in the same site across timescales corresponding with female reproductive cycles. This indicates that females re-used a site for parturition, which has the potential to facilitate the sorting of adaptive variation among neighbouring sites. The results demonstrate differential impacts of microevolutionary forces at varying spatial scales and highlight the importance of conserving essential habitats to maintain sources of adaptive variation that may buffer species against environmental change.
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Affiliation(s)
- Dominic G Swift
- Marine Genomics Laboratory, Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, Texas, USA
| | - Shannon J O'Leary
- Marine Genomics Laboratory, Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, Texas, USA
- Department of Biology, Saint Anselm College, Manchester, New Hampshire, USA
| | - R Dean Grubbs
- Florida State University Coastal and Marine Laboratory, St. Teresa, Florida, USA
| | - Bryan S Frazier
- South Carolina Department of Natural Resources, Marine Resources Research Institute, Charleston, South Carolina, USA
| | - Andrew T Fields
- Marine Genomics Laboratory, Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, Texas, USA
| | - Jayne M Gardiner
- Division of Natural Sciences, New College of Florida, Sarasota, Florida, USA
| | - J Marcus Drymon
- Coastal Research and Extension Center, Mississippi State University, Biloxi, Mississippi, USA
- Mississippi-Alabama Sea Grant Consortium, Ocean Springs, Mississippi, USA
| | - Dana M Bethea
- NOAA Fisheries, U.S. Department of Commerce, Southeast Regional Office, Interagency Cooperation Branch, Protected Resources Division, St. Petersburg, Florida, USA
| | - Tonya R Wiley
- Havenworth Coastal Conservation, Palmetto, Florida, USA
| | - David S Portnoy
- Marine Genomics Laboratory, Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, Texas, USA
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Leites L, Benito Garzón M. Forest tree species adaptation to climate across biomes: Building on the legacy of ecological genetics to anticipate responses to climate change. GLOBAL CHANGE BIOLOGY 2023; 29:4711-4730. [PMID: 37029765 DOI: 10.1111/gcb.16711] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/30/2023] [Accepted: 03/17/2023] [Indexed: 06/19/2023]
Abstract
Intraspecific variation plays a critical role in extant and future forest responses to climate change. Forest tree species with wide climatic niches rely on the intraspecific variation resulting from genetic adaptation and phenotypic plasticity to accommodate spatial and temporal climate variability. A centuries-old legacy of forest ecological genetics and provenance trials has provided a strong foundation upon which to continue building on this knowledge, which is critical to maintain climate-adapted forests. Our overall objective is to understand forest trees intraspecific responses to climate across species and biomes, while our specific objectives are to describe ecological genetics models used to build our foundational knowledge, summarize modeling approaches that have expanded the traditional toolset, and extensively review the literature from 1994 to 2021 to highlight the main contributions of this legacy and the new analyzes of provenance trials. We reviewed 103 studies comprising at least three common gardens, which covered 58 forest tree species, 28 of them with range-wide studies. Although studies using provenance trial data cover mostly commercially important forest tree species from temperate and boreal biomes, this synthesis provides a global overview of forest tree species adaptation to climate. We found that evidence for genetic adaptation to local climate is commonly present in the species studied (79%), being more common in conifers (87.5%) than in broadleaf species (67%). In 57% of the species, clines in fitness-related traits were associated with temperature variables, in 14% of the species with precipitation, and in 25% of the species with both. Evidence of adaptation lags was found in 50% of the species with range-wide studies. We conclude that ecological genetics models and analysis of provenance trial data provide excellent insights on intraspecific genetic variation, whereas the role and limits of phenotypic plasticity, which will likely determine the fate of extant forests, is vastly understudied.
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Affiliation(s)
- Laura Leites
- Department of Ecosystem Science and Management, Penn State University, University Park, Pennsylvania, USA
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40
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Teterina AA, Willis JH, Lukac M, Jovelin R, Cutter AD, Phillips PC. Genomic diversity landscapes in outcrossing and selfing Caenorhabditis nematodes. PLoS Genet 2023; 19:e1010879. [PMID: 37585484 PMCID: PMC10461856 DOI: 10.1371/journal.pgen.1010879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 08/28/2023] [Accepted: 07/21/2023] [Indexed: 08/18/2023] Open
Abstract
Caenorhabditis nematodes form an excellent model for studying how the mode of reproduction affects genetic diversity, as some species reproduce via outcrossing whereas others can self-fertilize. Currently, chromosome-level patterns of diversity and recombination are only available for self-reproducing Caenorhabditis, making the generality of genomic patterns across the genus unclear given the profound potential influence of reproductive mode. Here we present a whole-genome diversity landscape, coupled with a new genetic map, for the outcrossing nematode C. remanei. We demonstrate that the genomic distribution of recombination in C. remanei, like the model nematode C. elegans, shows high recombination rates on chromosome arms and low rates toward the central regions. Patterns of genetic variation across the genome are also similar between these species, but differ dramatically in scale, being tenfold greater for C. remanei. Historical reconstructions of variation in effective population size over the past million generations echo this difference in polymorphism. Evolutionary simulations demonstrate how selection, recombination, mutation, and selfing shape variation along the genome, and that multiple drivers can produce patterns similar to those observed in natural populations. The results illustrate how genome organization and selection play a crucial role in shaping the genomic pattern of diversity whereas demographic processes scale the level of diversity across the genome as a whole.
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Affiliation(s)
- Anastasia A. Teterina
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
- Center of Parasitology, Severtsov Institute of Ecology and Evolution RAS, Moscow, Russia
| | - John H. Willis
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Matt Lukac
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Richard Jovelin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Asher D. Cutter
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Patrick C. Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
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Ropp AJ, Reece KS, Snyder RA, Song J, Biesack EE, McDowell JR. Fine-scale population structure of the northern hard clam ( Mercenaria mercenaria) revealed by genome-wide SNP markers. Evol Appl 2023; 16:1422-1437. [PMID: 37622097 PMCID: PMC10445094 DOI: 10.1111/eva.13577] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 06/07/2023] [Accepted: 06/16/2023] [Indexed: 08/26/2023] Open
Abstract
Aquaculture is growing rapidly worldwide, and sustainability is dependent on an understanding of current genetic variation and levels of connectivity among populations. Genetic data are essential to mitigate the genetic and ecological impacts of aquaculture on wild populations and guard against unintended human-induced loss of intraspecific diversity in aquacultured lines. Impacts of disregarding genetics can include loss of diversity within and between populations and disruption of local adaptation patterns, which can lead to a decrease in fitness. The northern hard clam, Mercenaria mercenaria (Linnaeus, 1758), is an economically valuable aquaculture species along the North American Atlantic and Gulf coasts. Hard clams have a pelagic larval phase that allows for dispersal, but the level of genetic connectivity among geographic areas is not well understood. To better inform the establishment of site-appropriate aquaculture brood stocks, this study used DArTseq™ genotyping by sequencing to characterize the genetic stock structure of wild clams sampled along the east coast of North America and document genetic diversity within populations. Samples were collected from 15 locations from Prince Edward Island, Canada, to South Carolina, USA. Stringent data filtering resulted in 4960 single nucleotide polymorphisms from 448 individuals. Five genetic breaks separating six genetically distinct populations were identified: Canada, Maine, Massachusetts, Mid-Atlantic, Chesapeake Bay, and the Carolinas (F ST 0.003-0.046; p < 0.0001). This is the first study to assess population genetic structure of this economically important hard clam along a large portion of its native range with high-resolution genomic markers, enabling identification of previously unrecognized population structure. Results of this study not only broaden insight into the factors shaping the current distribution of M. mercenaria but also reveal the genetic population dynamics of a species with a long pelagic larval dispersal period along the North American Atlantic and Gulf coasts.
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Affiliation(s)
- Ann J. Ropp
- Virginia Institute of Marine Science, William & MaryGloucester PointVirginiaUSA
| | - Kimberly S. Reece
- Virginia Institute of Marine Science, William & MaryGloucester PointVirginiaUSA
| | - Richard A. Snyder
- Virginia Institute of Marine Science, William & MaryGloucester PointVirginiaUSA
| | - Jingwei Song
- Virginia Institute of Marine Science, William & MaryGloucester PointVirginiaUSA
| | - Ellen E. Biesack
- Virginia Institute of Marine Science, William & MaryGloucester PointVirginiaUSA
| | - Jan R. McDowell
- Virginia Institute of Marine Science, William & MaryGloucester PointVirginiaUSA
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42
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Mendoza-Portillo V, García-De León FJ, von der Heyden S. Responses of population structure and genomic diversity to climate change and fishing pressure in a pelagic fish. GLOBAL CHANGE BIOLOGY 2023; 29:4107-4125. [PMID: 37078996 DOI: 10.1111/gcb.16732] [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: 01/04/2022] [Revised: 03/28/2023] [Accepted: 04/16/2023] [Indexed: 05/03/2023]
Abstract
The responses of marine species to environmental changes and anthropogenic pressures (e.g., fishing) interact with ecological and evolutionary processes that are not well understood. Knowledge of changes in the distribution range and genetic diversity of species and their populations into the future is essential for the conservation and sustainable management of resources. Almaco jack (Seriola rivoliana) is a pelagic fish with high importance to fisheries and aquaculture in the Pacific Ocean. In this study, we assessed contemporary genomic diversity and structure in loci that are putatively under selection (outlier loci) and determined their potential functions. Using a combination of genotype-environment association, spatial distribution models, and demogenetic simulations, we modeled the effects of climate change (under three different RCP scenarios) and fishing pressure on the species' geographic distribution and genomic diversity and structure to 2050 and 2100. Our results show that most of the outlier loci identified were related to biological and metabolic processes that may be associated with temperature and salinity. The contemporary genomic structure showed three populations-two in the Eastern Pacific (Cabo San Lucas and Eastern Pacific) and one in the Central Pacific (Hawaii). Future projections suggest a loss of suitable habitat and potential range contractions for most scenarios, while fishing pressure decreased population connectivity. Our results suggest that future climate change scenarios and fishing pressure will affect the genomic structure and genotypic composition of S. rivoliana and lead to loss of genomic diversity in populations distributed in the eastern-central Pacific Ocean, which could have profound effects on fisheries that depend on this resource.
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Affiliation(s)
- Verónica Mendoza-Portillo
- Laboratorio de Genética para la Conservación, Centro de Investigaciones Biológicas del Noroeste, La Paz, Mexico
| | - Francisco J García-De León
- Laboratorio de Genética para la Conservación, Centro de Investigaciones Biológicas del Noroeste, La Paz, Mexico
| | - Sophie von der Heyden
- Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Matieland, South Africa
- School of Climate Studies, Stellenbosch University, Matieland, South Africa
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43
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Tóth EG, Cseke K, Benke A, Lados BB, Tomov VT, Zhelev P, Kámpel JD, Borovics A, Köbölkuti ZA. Key triggers of adaptive genetic variability of sessile oak [Q. petraea (Matt.) Liebl.] from the Balkan refugia: outlier detection and association of SNP loci from ddRAD-seq data. Heredity (Edinb) 2023:10.1038/s41437-023-00629-2. [PMID: 37316726 PMCID: PMC10382515 DOI: 10.1038/s41437-023-00629-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/22/2023] [Accepted: 05/22/2023] [Indexed: 06/16/2023] Open
Abstract
Knowledge on the genetic composition of Quercus petraea in south-eastern Europe is limited despite the species' significant role in the re-colonisation of Europe during the Holocene, and the diverse climate and physical geography of the region. Therefore, it is imperative to conduct research on adaptation in sessile oak to better understand its ecological significance in the region. While large sets of SNPs have been developed for the species, there is a continued need for smaller sets of SNPs that are highly informative about the possible adaptation to this varied landscape. By using double digest restriction site associated DNA sequencing data from our previous study, we mapped RAD-seq loci to the Quercus robur reference genome and identified a set of SNPs putatively related to drought stress-response. A total of 179 individuals from eighteen natural populations at sites covering heterogeneous climatic conditions in the southeastern natural distribution range of Q. petraea were genotyped. The detected highly polymorphic variant sites revealed three genetic clusters with a generally low level of genetic differentiation and balanced diversity among them but showed a north-southeast gradient. Selection tests showed nine outlier SNPs positioned in different functional regions. Genotype-environment association analysis of these markers yielded a total of 53 significant associations, explaining 2.4-16.6% of the total genetic variation. Our work exemplifies that adaptation to drought may be under natural selection in the examined Q. petraea populations.
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Affiliation(s)
- Endre Gy Tóth
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary.
| | - Klára Cseke
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary
| | - Attila Benke
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary
| | - Botond B Lados
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary
| | - Vladimir T Tomov
- Department of Landscape Architecture, Faculty of Ecology and Landscape Architecture, University of Forestry (UF), Kliment Ohridsky 10, Sofia, 1797, Bulgaria
| | - Petar Zhelev
- Department of Dendrology, Faculty of Forestry, University of Forestry (UF), Kliment Ohridsky 10, Sofia, 1797, Bulgaria
| | - József D Kámpel
- Ottó Herman Environmental and Agricultural Technical School, Vocational School and College (Agricultural Vocational Centre of the Kisalföld Region), Ernuszt Kelemen 1, Szombathely, 9700, Hungary
| | - Attila Borovics
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary
| | - Zoltán A Köbölkuti
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary
- Departement of Applied Forest Genetics Research, Bavarian Office for Forest Genetics (AWG), Forstamtsplatz 1, Teisendorf, 83317, Germany
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Soudi S, Crepeau M, Collier TC, Lee Y, Cornel AJ, Lanzaro GC. Genomic signatures of local adaptation in recent invasive Aedes aegypti populations in California. BMC Genomics 2023; 24:311. [PMID: 37301847 DOI: 10.1186/s12864-023-09402-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
BACKGROUND Rapid adaptation to new environments can facilitate species invasions and range expansions. Understanding the mechanisms of adaptation used by invasive disease vectors in new regions has key implications for mitigating the prevalence and spread of vector-borne disease, although they remain relatively unexplored. RESULTS Here, we integrate whole-genome sequencing data from 96 Aedes aegypti mosquitoes collected from various sites in southern and central California with 25 annual topo-climate variables to investigate genome-wide signals of local adaptation among populations. Patterns of population structure, as inferred using principal components and admixture analysis, were consistent with three genetic clusters. Using various landscape genomics approaches, which all remove the confounding effects of shared ancestry on correlations between genetic and environmental variation, we identified 112 genes showing strong signals of local environmental adaptation associated with one or more topo-climate factors. Some of them have known effects in climate adaptation, such as heat-shock proteins, which shows selective sweep and recent positive selection acting on these genomic regions. CONCLUSIONS Our results provide a genome wide perspective on the distribution of adaptive loci and lay the foundation for future work to understand how environmental adaptation in Ae. aegypti impacts the arboviral disease landscape and how such adaptation could help or hinder efforts at population control.
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Affiliation(s)
- Shaghayegh Soudi
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, University of California Davis, Davis, CA, USA
| | - Marc Crepeau
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, University of California Davis, Davis, CA, USA
| | - Travis C Collier
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, University of California Davis, Davis, CA, USA
| | - Yoosook Lee
- Florida Medical Entomology Laboratory, University of Florida, Vero Beach, FL, USA
| | - Anthony J Cornel
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, University of California Davis, Davis, CA, USA
- Mosquito Control Research Laboratory, Department of Entomology and Nematology, University of California, Parlier, CA, USA
| | - Gregory C Lanzaro
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, University of California Davis, Davis, CA, USA.
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Wang L, Yeo S, Lee M, Endah S, Alhuda NA, Yue GH. Combination of GWAS and F ST-based approaches identified loci associated with economic traits in sugarcane. Mol Genet Genomics 2023:10.1007/s00438-023-02040-2. [PMID: 37289230 DOI: 10.1007/s00438-023-02040-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 05/28/2023] [Indexed: 06/09/2023]
Abstract
Sugarcane is a globally important plant for both sugar and biofuel production. Although conventional breeding has played an important role in increasing the productivity of sugarcane, it takes a long time to achieve breeding goals such as high yield and resistant to diseases. Molecular breeding, including marker-assisted breeding and genomic selection, can accelerate genetic improvement by selecting elites at the seedling stage with DNA markers. However, only a few DNA markers associated with important traits were identified in sugarcane. The purpose of this study was to identify DNA markers associated with sugar content, stalk diameter, and sugarcane top borer resistance. The sugarcane samples with trait records were genotyped using the restriction site-associated DNA sequencing (RADseq) technology. Using FST analysis and genome-wide association study (GWAS), a total of 9, 23 and 9 DNA variants (single nucleotide polymorphisms (SNPs)/insertions and deletions (indels)) were associated with sugar content, stalk diameter, and sugarcane top borer resistance, respectively. The identified genetic variants were on different chromosomes, suggesting that these traits are complex and determined by multiple genetic factors. These DNA markers identified by both approaches have the potential to be used in selecting elite clones at the seeding stage in our sugarcane breeding program to accelerate genetic improvement. Certainly, it is essential to verify the reliability of the identified DNA markers associated with traits before they are used in molecular breeding in other populations.
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Affiliation(s)
- Le Wang
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
| | - Shadame Yeo
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
| | - May Lee
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
| | - S Endah
- Research and Development, PT Gunung Madu Plantations, KM 90 Terusan Nunyai, Central Lampung, Lampung, 34167, Indonesia
| | - N A Alhuda
- Research and Development, PT Gunung Madu Plantations, KM 90 Terusan Nunyai, Central Lampung, Lampung, 34167, Indonesia
| | - G H Yue
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore.
- Department of Biological Sciences, National University of Singapore, 14 Science Drive, Singapore, 117543, Singapore.
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Ortiz V, Chang HX, Sang H, Jacobs J, Malvick DK, Baird R, Mathew FM, Estévez de Jensen C, Wise KA, Mosquera GM, Chilvers MI. Population genomic analysis reveals geographic structure and climatic diversification for Macrophomina phaseolina isolated from soybean and dry bean across the United States, Puerto Rico, and Colombia. Front Genet 2023; 14:1103969. [PMID: 37351341 PMCID: PMC10282554 DOI: 10.3389/fgene.2023.1103969] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 04/20/2023] [Indexed: 06/24/2023] Open
Abstract
Macrophomina phaseolina causes charcoal rot, which can significantly reduce yield and seed quality of soybean and dry bean resulting from primarily environmental stressors. Although charcoal rot has been recognized as a warm climate-driven disease of increasing concern under global climate change, knowledge regarding population genetics and climatic variables contributing to the genetic diversity of M. phaseolina is limited. This study conducted genome sequencing for 95 M. phaseolina isolates from soybean and dry bean across the continental United States, Puerto Rico, and Colombia. Inference on the population structure using 76,981 single nucleotide polymorphisms (SNPs) revealed that the isolates exhibited a discrete genetic clustering at the continental level and a continuous genetic differentiation regionally. A majority of isolates from the United States (96%) grouped in a clade with a predominantly clonal genetic structure, while 88% of Puerto Rican and Colombian isolates from dry bean were assigned to a separate clade with higher genetic diversity. A redundancy analysis (RDA) was used to estimate the contributions of climate and spatial structure to genomic variation (11,421 unlinked SNPs). Climate significantly contributed to genomic variation at a continental level with temperature seasonality explaining the most variation while precipitation of warmest quarter explaining the most when spatial structure was accounted for. The loci significantly associated with multivariate climate were found closely to the genes related to fungal stress responses, including transmembrane transport, glycoside hydrolase activity and a heat-shock protein, which may mediate climatic adaptation for M. phaseolina. On the contrary, limited genome-wide differentiation among populations by hosts was observed. These findings highlight the importance of population genetics and identify candidate genes of M. phaseolina that can be used to elucidate the molecular mechanisms that underly climatic adaptation to the changing climate.
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Affiliation(s)
- Viviana Ortiz
- Department of Plant, Soil and Microbial Sciences, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, United States
- Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, MI, United States
| | - Hao-Xun Chang
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
| | - Hyunkyu Sang
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, Republic of Korea
| | - Janette Jacobs
- Department of Plant, Soil and Microbial Sciences, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, United States
| | - Dean K. Malvick
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Richard Baird
- BCH-EPP Department, Mississippi State University, Mississippi State, MS, United States
| | - Febina M. Mathew
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| | | | - Kiersten A. Wise
- Department of Plant Pathology, College of Agriculture, Food and Environment, University of Kentucky, Princeton, KY, United States
| | - Gloria M. Mosquera
- Plant Pathology, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), The Americas Hub, Palmira, Colombia
| | - Martin I. Chilvers
- Department of Plant, Soil and Microbial Sciences, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, United States
- Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, MI, United States
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Moreira LR, Smith BT. Convergent genomic signatures of local adaptation across a continental-scale environmental gradient. SCIENCE ADVANCES 2023; 9:eadd0560. [PMID: 37205757 PMCID: PMC10198635 DOI: 10.1126/sciadv.add0560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 04/17/2023] [Indexed: 05/21/2023]
Abstract
Convergent local adaptation offers a glimpse into the role of constraint and stochasticity in adaptive evolution, in particular the extent to which similar genetic mechanisms drive adaptation to common selective forces. Here, we investigated the genomics of local adaptation in two nonsister woodpeckers that are codistributed across an entire continent and exhibit remarkably convergent patterns of geographic variation. We sequenced the genomes of 140 individuals of Downy (Dryobates pubescens) and Hairy (Dryobates villosus) woodpeckers and used a suite of genomic approaches to identify loci under selection. We showed evidence that convergent genes have been targeted by selection in response to shared environmental pressures, such as temperature and precipitation. Among candidates, we found multiple genes putatively linked to key phenotypic adaptations to climate, including differences in body size (e.g., IGFPB) and plumage (e.g., MREG). These results are consistent with genetic constraints limiting the pathways of adaptation to broad climatic gradients, even after genetic backgrounds diverge.
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Affiliation(s)
- Lucas R. Moreira
- Department of Ecology, Evolution and Environmental Biology, Columbia University, NY, USA
- Department of Ornithology, American Museum of Natural History, New York City, NY, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, New York City, NY, USA
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Wos G, Palomar G, Marszałek M, Babik W, Sniegula S. The effect of temperature and invasive alien predator on genetic and phenotypic variation in the damselfly Ischnura elegans: cross-latitude comparison. Front Zool 2023; 20:13. [PMID: 37032330 PMCID: PMC10084621 DOI: 10.1186/s12983-023-00494-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 04/04/2023] [Indexed: 04/11/2023] Open
Abstract
BACKGROUND Understanding and predicting how organisms respond to human-caused environmental changes has become a major concern in conservation biology. Here, we linked gene expression and phenotypic data to identify candidate genes underlying existing phenotypic trait differentiation under individual and combined environmental variables. For this purpose, we used the damselfly Ischnura elegans. Egg clutches from replicated high- (southern Sweden) and central-latitude (southern Poland) populations facing different degrees of seasonal time constraints were collected. Damselfly larvae were exposed to experimental treatments: current and mild warming temperatures crossed with the presence or absence of an invasive alien predator cue released by the spiny-cheek crayfish, Faxonius limosus, which is only present in Poland to date. We measured the following traits: larval development time, body size, mass and growth rate, and used the larvae for gene expression analysis by RNA-seq. Data were analysed using a multivariate approach. RESULTS We showed latitudinal differences in coping with mild warming and predator cues. When exposed to an increased temperature and a predator cue, central-latitude individuals had the shortest development and the fastest growth compared to high-latitude individuals. There was a general effect of predator cues regarding mass and growth rate reduction independent of latitude. Transcriptome analysis revealed that metabolic pathways related to larval anatomy and development tended to be upregulated in response to mild warming but only in fast-growing central-latitude individuals. Metabolic pathways linked to oxidative stress tended to be downregulated in response to a predator cue, especially in central-latitude individuals. CONCLUSION Different phenotypic and transcriptomic responses to environmental factors might be attributed to the variability in I. elegans life history strategies between the two latitudes caused by seasonal time constraints and to its coexistence with the invasive alien predator in nature. By providing insights into how organisms may respond to future anthropogenic changes, our results may be of particular interest in conservation biology.
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Affiliation(s)
- Guillaume Wos
- Institute of Nature Conservation Polish Academy of Sciences, al. Adama Mickiewicza 33, 31-120, Kraków, Poland.
| | - Gemma Palomar
- Institute of Nature Conservation Polish Academy of Sciences, al. Adama Mickiewicza 33, 31-120, Kraków, Poland
- Department of Genetics, Physiology, and Microbiology, Complutense University of Madrid, C/Jose Antonio Novais 12, 28040, Madrid, Spain
| | - Marzena Marszałek
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Wiesław Babik
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Szymon Sniegula
- Institute of Nature Conservation Polish Academy of Sciences, al. Adama Mickiewicza 33, 31-120, Kraków, Poland.
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Lotterhos KE. The paradox of adaptive trait clines with nonclinal patterns in the underlying genes. Proc Natl Acad Sci U S A 2023; 120:e2220313120. [PMID: 36917658 PMCID: PMC10041142 DOI: 10.1073/pnas.2220313120] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/03/2023] [Indexed: 03/16/2023] Open
Abstract
Multivariate climate change presents an urgent need to understand how species adapt to complex environments. Population genetic theory predicts that loci under selection will form monotonic allele frequency clines with their selective environment, which has led to the wide use of genotype-environment associations (GEAs). This study used a set of simulations to elucidate the conditions under which allele frequency clines are more or less likely to evolve as multiple quantitative traits adapt to multivariate environments. Phenotypic clines evolved with nonmonotonic (i.e., nonclinal) patterns in allele frequencies under conditions that promoted unique combinations of mutations to achieve the multivariate optimum in different parts of the landscape. Such conditions resulted from interactions among landscape, demography, pleiotropy, and genetic architecture. GEA methods failed to accurately infer the genetic basis of adaptation under a range of scenarios due to first principles (clinal patterns did not evolve) or statistical issues (clinal patterns evolved but were not detected due to overcorrection for structure). Despite the limitations of GEAs, this study shows that a back-transformation of multivariate ordination can accurately predict individual multivariate traits from genotype and environmental data regardless of whether inference from GEAs was accurate. In addition, frameworks are introduced that can be used by empiricists to quantify the importance of clinal alleles in adaptation. This research highlights that multivariate trait prediction from genotype and environmental data can lead to accurate inference regardless of whether the underlying loci display clinal or nonmonotonic patterns.
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Affiliation(s)
- Katie E. Lotterhos
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA01908
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50
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Binaghi M, Esfeld K, Mandel T, Freitas LB, Roesti M, Kuhlemeier C. Genetic architecture of a pollinator shift and its fate in secondary hybrid zones of two Petunia species. BMC Biol 2023; 21:58. [PMID: 36941631 PMCID: PMC10029178 DOI: 10.1186/s12915-023-01561-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 03/10/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Theory suggests that the genetic architecture of traits under divergent natural selection influences how easily reproductive barriers evolve and are maintained between species. Divergently selected traits with a simple genetic architecture (few loci with major phenotypic effects) should facilitate the establishment and maintenance of reproductive isolation between species that are still connected by some gene flow. While empirical support for this idea appears to be mixed, most studies test the influence of trait architectures on reproductive isolation only indirectly. Petunia plant species are, in part, reproductively isolated by their different pollinators. To investigate the genetic causes and consequences of this ecological isolation, we deciphered the genetic architecture of three floral pollination syndrome traits in naturally occurring hybrids between the widespread Petunia axillaris and the highly endemic and endangered P. exserta. RESULTS Using population genetics, Bayesian linear mixed modelling and genome-wide association studies, we found that the three pollination syndrome traits vary in genetic architecture. Few genome regions explain a majority of the variation in flavonol content (defining UV floral colour) and strongly predict the trait value in hybrids irrespective of interspecific admixture in the rest of their genomes. In contrast, variation in pistil exsertion and anthocyanin content (defining visible floral colour) is controlled by many genome-wide loci. Opposite to flavonol content, the genome-wide proportion of admixture between the two species predicts trait values in their hybrids. Finally, the genome regions strongly associated with the traits do not show extreme divergence between individuals representing the two species, suggesting that divergent selection on these genome regions is relatively weak within their contact zones. CONCLUSIONS Among the traits analysed, those with a more complex genetic architecture are best maintained in association with the species upon their secondary contact. We propose that this maintained genotype-phenotype association is a coincidental consequence of the complex genetic architectures of these traits: some of their many underlying small-effect loci are likely to be coincidentally linked with the actual barrier loci keeping these species partially isolated upon secondary contact. Hence, the genetic architecture of a trait seems to matter for the outcome of hybridization not only then when the trait itself is under selection.
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Affiliation(s)
- Marta Binaghi
- Institute of Plant Sciences, University of Bern, 3013, Bern, Switzerland
| | - Korinna Esfeld
- Institute of Plant Sciences, University of Bern, 3013, Bern, Switzerland
| | - Therese Mandel
- Institute of Plant Sciences, University of Bern, 3013, Bern, Switzerland
| | - Loreta B Freitas
- Department of Genetics, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, RS, 91501-970, Brazil
| | - Marius Roesti
- Institute of Ecology and Evolution, University of Bern, 3012, Bern, Switzerland
| | - Cris Kuhlemeier
- Institute of Plant Sciences, University of Bern, 3013, Bern, Switzerland.
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