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Liu A, Geraldes A, Taylor EB. Historical and contemporary processes driving the origin and structure of an admixed population within a contact zone between subspecies of a north temperate diadromous fish. Mol Ecol 2024; 33:e17459. [PMID: 38994921 DOI: 10.1111/mec.17459] [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: 11/30/2023] [Revised: 04/23/2024] [Accepted: 04/30/2024] [Indexed: 07/13/2024]
Abstract
Hybridization between divergent lineages can result in losses of distinct evolutionary taxa. Alternatively, hybridization can lead to increased genetic variability that may fuel local adaptation and the generation of novel traits and/or taxa. Here, we examined single-nucleotide polymorphisms generated using genotyping-by-sequencing in a population of Dolly Varden char (Pisces: Salmonidae) that is highly admixed within a contact zone between two subspecies (Salvelinus malma malma, Northern Dolly Varden [NDV] and S. m. lordi, Southern Dolly Varden [SDV]) in southwestern Alaska to assess the spatial distribution of hybrids and to test hypotheses on the origin of the admixed population. Ancestry analysis revealed that this admixed population is composed of advanced generation hybrids between NDV and SDV or advanced backcrosses to SDV; no F1 hybrids were detected. Coalescent-based demographic modelling supported the origin of this population about 55,000 years ago by secondary contact between NDV and SDV with low levels of contemporary gene flow. Ancestry in NDV and SDV varies within the watershed and ancestry in NDV was positively associated with distance upstream from the sea, contingent on habitat-type sampled, and negatively associated with the number of migrations that individual fish made to the sea. Our results suggest that divergence between subspecies over hundreds of thousands of years may not be associated with significant reproductive isolation, but that elevated diversity owing to hybridization may have contributed to adaptive divergence in habitat use and life history.
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Affiliation(s)
- Amy Liu
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Armando Geraldes
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Eric B Taylor
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Beaty Biodiversity Museum, University of British Columbia, Vancouver, British Columbia, Canada
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2
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Horníková M, Lanier HC, Marková S, Escalante MA, Searle JB, Kotlík P. Genetic admixture drives climate adaptation in the bank vole. Commun Biol 2024; 7:863. [PMID: 39009753 PMCID: PMC11251159 DOI: 10.1038/s42003-024-06549-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: 07/20/2023] [Accepted: 07/03/2024] [Indexed: 07/17/2024] Open
Abstract
Genetic admixture introduces new variants at relatively high frequencies, potentially aiding rapid responses to environmental changes. Here, we evaluate its role in adaptive variation related to climatic conditions in bank voles (Clethrionomys glareolus) in Britain, using whole-genome data. Our results reveal loci showing excess ancestry from one of the two postglacial colonist populations inconsistent with overall admixture patterns. Notably, loci associated with climate adaptation exhibit disproportionate amounts of excess ancestry, highlighting the impact of admixture between colonist populations on local adaptation. The results suggest strong and localized selection on climate-adaptive loci, as indicated by steep clines and/or shifted cline centres, during population replacement. A subset, including a haemoglobin gene, is associated with oxidative stress responses, underscoring a role of oxidative stress in local adaptation. Our study highlights the important contribution of admixture during secondary contact between populations from distinct climatic refugia enriching adaptive diversity. Understanding these dynamics is crucial for predicting future adaptive capacity to anthropogenic climate change.
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Affiliation(s)
- Michaela Horníková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Hayley C Lanier
- Department of Biology, Program in Ecology & Evolutionary Biology, University of Oklahoma, Norman, OK, USA
- Sam Noble Museum, University of Oklahoma, Norman, OK, USA
| | - Silvia Marková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Marco A Escalante
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Petr Kotlík
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic.
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3
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McFarlane SE, Jahner JP, Lindtke D, Buerkle CA, Mandeville EG. Selection leads to remarkable variability in the outcomes of hybridisation across replicate hybrid zones. Mol Ecol 2024; 33:e17359. [PMID: 38699787 DOI: 10.1111/mec.17359] [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: 09/24/2022] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 05/05/2024]
Abstract
Hybrid zones have been viewed as an opportunity to see speciation in action. When hybrid zones are replicated, it is assumed that if the same genetic incompatibilities are maintaining reproductive isolation across all instances of secondary contact, those incompatibilities should be identifiable by consistent patterns in the genome. In contrast, changes in allele frequencies due to genetic drift should be idiosyncratic for each hybrid zone. To test this assumption, we simulated 20 replicates of each of 12 hybrid zone scenarios with varied genetic incompatibilities, rates of migration, selection and different starting population size ratios of parental species. We found remarkable variability in the outcomes of hybridisation in replicate hybrid zones, particularly with Bateson-Dobzhansky-Muller incompatibilities and strong selection. We found substantial differences among replicates in the overall genomic composition of individuals, including admixture proportions, inter-specific ancestry complement and number of ancestry junctions. Additionally, we found substantial variation in genomic clines among replicates at focal loci, regardless of locus-specific selection. We conclude that processes other than selection are responsible for some consistent outcomes of hybridisation, whereas selection on incompatibilities can lead to genomically widespread and highly variable outcomes. We highlight the challenge of mapping between pattern and process in hybrid zones and call attention to how selection against incompatibilities will commonly lead to variable outcomes. We hope that this study informs future research on replicate hybrid zones and encourages further development of statistical techniques, theoretical models and exploration of additional axes of variation to understand reproductive isolation.
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Affiliation(s)
- S Eryn McFarlane
- Department of Botany, University of Wyoming, Laramie, Wyoming, USA
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Joshua P Jahner
- Department of Botany, University of Wyoming, Laramie, Wyoming, USA
| | | | - C Alex Buerkle
- Department of Botany, University of Wyoming, Laramie, Wyoming, USA
| | - Elizabeth G Mandeville
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
- Biology Department, Northern Michigan University, Marquette, Michigan, USA
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4
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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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Sekino M, Hashimoto K, Nakamichi R, Yamamoto M, Fujinami Y, Sasaki T. Introgressive hybridization in the west Pacific pen shells (genus Atrina): Restricted interspecies gene flow within the genome. Mol Ecol 2023; 32:2945-2963. [PMID: 36855846 DOI: 10.1111/mec.16908] [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: 07/13/2022] [Revised: 02/03/2023] [Accepted: 02/14/2023] [Indexed: 03/02/2023]
Abstract
A compelling interest in marine biology is to elucidate how species boundaries between sympatric free-spawning marine invertebrates such as bivalve molluscs are maintained in the face of potential hybridization. Hybrid zones provide the natural resources for us to study the underlying genetic mechanisms of reproductive isolation between hybridizing species. Against this backdrop, we examined the occurrence of introgressive hybridization (introgression) between two bivalves distributed in the western Pacific margin, Atrina japonica and Atrina lischkeana, based on single-nucleotide polymorphisms (SNPs) derived from restriction site-associated DNA sequencing. Using 1066 ancestry-informative SNP sites, we also investigated the extent of introgression within the genome to search for SNP sites with reduced interspecies gene flow. A series of our individual-level clustering analyses including the principal component analysis, Bayesian model-based clustering, and triangle plotting based on ancestry-heterozygosity relationships for an admixed population sample from the Seto Inland Sea (Japan) consistently suggested the presence of specimens with varying degrees of genomic admixture, thereby implying that the two species are not completely isolated. The Bayesian genomic cline analysis identified 10 SNP sites with reduced introgression, each of which was located within a genic region or an intergenic region physically close to a functional gene. No, or very few, heterozygotes were observed at these sites in the hybrid zone, suggesting that selection acts against heterozygotes. Accordingly, we raised the possibility that the SNP sites are within genomic regions that are incompatible between the two species. Our finding of restricted interspecies gene flow at certain genomic regions gives new insight into the maintenance of species boundaries in hybridizing broadcast-spawning molluscs.
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Affiliation(s)
- Masashi Sekino
- Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Kazumasa Hashimoto
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Nagasaki, Japan
| | - Reiichiro Nakamichi
- Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Masayuki Yamamoto
- Fisheries Division, Kagawa Prefectural Government, Takamatsu, Kagawa, Japan
| | - Yuichiro Fujinami
- Goto Field Station, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Nagasaki, Japan
| | - Takenori Sasaki
- The University Museum, The University of Tokyo, Tokyo, Japan
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6
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DeVos TB, Bock DG, Kolbe JJ. Rapid introgression of non-native alleles following hybridization between a native Anolis lizard species and a cryptic invader across an urban landscape. Mol Ecol 2023; 32:2930-2944. [PMID: 36811388 DOI: 10.1111/mec.16897] [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: 03/08/2022] [Revised: 02/14/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023]
Abstract
Invasive species can impact native populations through competition, predation, habitat alteration, and disease transmission, but also genetically through hybridization. Potential outcomes of hybridization span the continuum from extinction to hybrid speciation and can be further complicated by anthropogenic habitat disturbance. Hybridization between the native green anole lizard (Anolis carolinensis) and a morphologically similar invader (A. porcatus) in south Florida provides an ideal opportunity to study interspecific admixture across a heterogeneous landscape. We used reduced-representation sequencing to describe introgression in this hybrid system and to test for a relationship between urbanization and non-native ancestry. Our findings indicate that hybridization between green anole lineages was probably a limited, historic event, producing a hybrid population characterized by a diverse continuum of ancestry proportions. Genomic cline analyses revealed rapid introgression and disproportionate representation of non-native alleles at many loci and no evidence for reproductive isolation between parental species. Three loci were associated with urban habitat characteristics; urbanization and non-native ancestry were positively correlated, although this relationship did not remain significant when accounting for spatial nonindependence. Ultimately, our study demonstrates the persistence of non-native genetic material even in the absence of ongoing immigration, indicating that selection favouring non-native alleles can override the demographic limitation of low propagule pressure. We also note that not all outcomes of admixture between native and non-native species should be considered intrinsically negative. Hybridization with ecologically robust invaders can lead to adaptive introgression, which may facilitate the long-term survival of native populations otherwise unable to adapt to anthropogenically mediated global change.
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Affiliation(s)
- Tyler B DeVos
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Dan G Bock
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | - Jason J Kolbe
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
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7
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Frayer ME, Payseur BA. Demographic history shapes genomic ancestry in hybrid zones. Ecol Evol 2021; 11:10290-10302. [PMID: 34367575 PMCID: PMC8328415 DOI: 10.1002/ece3.7833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/03/2021] [Accepted: 06/08/2021] [Indexed: 12/26/2022] Open
Abstract
Demographic factors such as migration rate and population size can impede or facilitate speciation. In hybrid zones, reproductive boundaries between species are tested and demography mediates the opportunity for admixture between lineages that are partially isolated. Genomic ancestry is a powerful tool for revealing the history of admixed populations, but models and methods based on local ancestry are rarely applied to structured hybrid zones. To understand the effects of demography on ancestry in hybrids zones, we performed individual-based simulations under a stepping-stone model, treating migration rate, deme size, and hybrid zone age as parameters. We find that the number of ancestry junctions (the transition points between genomic regions with different ancestries) and heterogenicity (the genomic proportion heterozygous for ancestry) are often closely connected to demographic history. Reducing deme size reduces junction number and heterogenicity. Elevating migration rate increases heterogenicity, but migration affects junction number in more complex ways. We highlight the junction frequency spectrum as a novel and informative summary of ancestry that responds to demographic history. A substantial proportion of junctions are expected to fix when migration is limited or deme size is small, changing the shape of the spectrum. Our findings suggest that genomic patterns of ancestry could be used to infer demographic history in hybrid zones.
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Affiliation(s)
- Megan E. Frayer
- Laboratory of GeneticsUniversity of Wisconsin MadisonMadisonWIUSA
| | - Bret A. Payseur
- Laboratory of GeneticsUniversity of Wisconsin MadisonMadisonWIUSA
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8
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Jahner JP, Parchman TL, Matocq MD. Multigenerational backcrossing and introgression between two woodrat species at an abrupt ecological transition. Mol Ecol 2021; 30:4245-4258. [PMID: 34219316 DOI: 10.1111/mec.16056] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/28/2021] [Indexed: 12/27/2022]
Abstract
When organisms experience secondary contact after allopatric divergence, genomic regions can introgress differentially depending on their relationships with adaptation, reproductive isolation, recombination, and drift. Analyses of genome-wide patterns of divergence and introgression could provide insight into the outcomes of hybridization and the potential relationship between allopatric divergence and reproductive isolation. Here, we generate population genetic data (26,262 SNPs; 353 individuals) using a reduced-representation sequencing approach to quantify patterns of ancestry, differentiation, and introgression between a pair of ecologically distinct mammals-the desert woodrat (N. lepida) and Bryant's woodrat (N. bryanti)-that hybridize at a sharp ecotone in southern California. Individual ancestry estimates confirmed that hybrids were rare in this bimodal hybrid zone, and entirely consisted of a few F1 individuals and a broad range of multigenerational backcrosses. Genomic cline analyses indicated more than half of loci had elevated introgression from one genomic background into the other. However, introgression was not associated with relative or absolute measures of divergence, and loci with extreme values for both were not typically found near detoxification enzymes previously implicated in dietary specialization for woodrats. The decoupling of differentiation and introgression suggests that processes other than adaptation, such as drift, may underlie the extreme clines at this contact zone.
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Affiliation(s)
- Joshua P Jahner
- Department of Biology, University of Nevada, Reno, Nevada, USA.,Department of Botany, University of Wyoming, Laramie, Wyoming, USA
| | - Thomas L Parchman
- Department of Biology, University of Nevada, Reno, Nevada, USA.,Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, Nevada, USA
| | - Marjorie D Matocq
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, Nevada, USA.,Department of Natural Resources and Environmental Science, University of Nevada, Reno, Nevada, USA
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Howard-McCombe J, Ward D, Kitchener AC, Lawson D, Senn HV, Beaumont M. On the use of genome-wide data to model and date the time of anthropogenic hybridisation: An example from the Scottish wildcat. Mol Ecol 2021; 30:3688-3702. [PMID: 34042240 DOI: 10.1111/mec.16000] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 11/28/2022]
Abstract
While hybridisation has long been recognised as an important natural phenomenon in evolution, the conservation of taxa subject to introgressive hybridisation from domesticated forms is a subject of intense debate. Hybridisation of Scottish wildcats and domestic cats is a good example in this regard. Here, we developed a modelling framework to determine the timescale of introgression using approximate Bayesian computation (ABC). Applying the model to ddRAD-seq data from 129 individuals, genotyped at 6546 loci, we show that a population of wildcats genetically distant from domestic cats is still present in Scotland. These individuals were found almost exclusively within the captive breeding programme. Most wild-living cats sampled were introgressed to some extent. The demographic model predicts high levels of gene-flow between domestic cats and Scottish wildcats (13% migrants per generation) over a short timeframe, the posterior mean for the onset of hybridisation (T1 ) was 3.3 generations (~10 years) before present. Although the model had limited power to detect signals of ancient admixture, we found evidence that significant recent hybridisation may have occurred subsequent to the founding of the captive breeding population (T2 ). The model consistently predicts T1 after T2 , estimated here to be 19.3 generations (~60 years) ago, highlighting the importance of this population as a resource for conservation management. Additionally, we evaluate the effectiveness of current methods to classify hybrids. We show that an optimised 35 SNP panel is a better predictor of the ddRAD-based hybrid score in comparison with a morphological method.
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Affiliation(s)
| | - Daniel Ward
- School of Mathematics, University of Bristol, Bristol, UK
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Edinburgh, UK
| | - Daniel Lawson
- School of Mathematics, University of Bristol, Bristol, UK
| | - Helen V Senn
- RZSS WildGenes Laboratory, Royal Zoological Society of Scotland, Edinburgh, UK
| | - Mark Beaumont
- School of Biological Sciences, University of Bristol, Bristol, UK
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