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Smith CCR, Patterson G, Ralph PL, Kern AD. Estimation of spatial demographic maps from polymorphism data using a neural network. Mol Ecol Resour 2024:e14005. [PMID: 39152666 DOI: 10.1111/1755-0998.14005] [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: 03/26/2024] [Revised: 07/16/2024] [Accepted: 08/06/2024] [Indexed: 08/19/2024]
Abstract
A fundamental goal in population genetics is to understand how variation is arrayed over natural landscapes. From first principles we know that common features such as heterogeneous population densities and barriers to dispersal should shape genetic variation over space, however there are few tools currently available that can deal with these ubiquitous complexities. Geographically referenced single nucleotide polymorphism (SNP) data are increasingly accessible, presenting an opportunity to study genetic variation across geographic space in myriad species. We present a new inference method that uses geo-referenced SNPs and a deep neural network to estimate spatially heterogeneous maps of population density and dispersal rate. Our neural network trains on simulated input and output pairings, where the input consists of genotypes and sampling locations generated from a continuous space population genetic simulator, and the output is a map of the true demographic parameters. We benchmark our tool against existing methods and discuss qualitative differences between the different approaches; in particular, our program is unique because it infers the magnitude of both dispersal and density as well as their variation over the landscape, and it does so using SNP data. Similar methods are constrained to estimating relative migration rates, or require identity-by-descent blocks as input. We applied our tool to empirical data from North American grey wolves, for which it estimated mostly reasonable demographic parameters, but was affected by incomplete spatial sampling. Genetic based methods like ours complement other, direct methods for estimating past and present demography, and we believe will serve as valuable tools for applications in conservation, ecology and evolutionary biology. An open source software package implementing our method is available from https://github.com/kr-colab/mapNN.
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Affiliation(s)
- Chris C R Smith
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Gilia Patterson
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Peter L Ralph
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Andrew D Kern
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
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2
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Smith CCR, Patterson G, Ralph PL, Kern AD. Estimation of spatial demographic maps from polymorphism data using a neural network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.585300. [PMID: 38559192 PMCID: PMC10980082 DOI: 10.1101/2024.03.15.585300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
A fundamental goal in population genetics is to understand how variation is arrayed over natural landscapes. From first principles we know that common features such as heterogeneous population densities and barriers to dispersal should shape genetic variation over space, however there are few tools currently available that can deal with these ubiquitous complexities. Geographically referenced single nucleotide polymorphism (SNP) data are increasingly accessible, presenting an opportunity to study genetic variation across geographic space in myriad species. We present a new inference method that uses geo-referenced SNPs and a deep neural network to estimate spatially heterogeneous maps of population density and dispersal rate. Our neural network trains on simulated input and output pairings, where the input consists of genotypes and sampling locations generated from a continuous space population genetic simulator, and the output is a map of the true demographic parameters. We benchmark our tool against existing methods and discuss qualitative differences between the different approaches; in particular, our program is unique because it infers the magnitude of both dispersal and density as well as their variation over the landscape, and it does so using SNP data. Similar methods are constrained to estimating relative migration rates, or require identity by descent blocks as input. We applied our tool to empirical data from North American grey wolves, for which it estimated mostly reasonable demographic parameters, but was affected by incomplete spatial sampling. Genetic based methods like ours complement other, direct methods for estimating past and present demography, and we believe will serve as valuable tools for applications in conservation, ecology, and evolutionary biology. An open source software package implementing our method is available from https://github.com/kr-colab/mapNN .
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3
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Musiani M, Randi E. Conservation genomics of wolves: The global impact of RK Wayne's research. J Hered 2024; 115:458-469. [PMID: 38381553 DOI: 10.1093/jhered/esae007] [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] [Revised: 01/31/2024] [Accepted: 02/20/2024] [Indexed: 02/23/2024] Open
Abstract
RK Wayne has arguably been the most influential geneticist of canids, famously promoting the conservation of wolves in his homeland, the United States. His influence has been felt in other countries and regions outside the contiguous United States, where he inspired others, also including former graduate students and research fellows of his, to use modern molecular techniques to examine the evolutionary biology of canids to inform the conservation and management of wolves. In this review, we focus on the implications of Wayne's work on wolves outside the United States. He envisioned a clear future for wolf conservation research, involving the study of wolves' ecological and genetic diversity, and the description of ecotypes requiring conservation. He also documented widespread hybridization among canids and introgression of DNA from domestic dogs to wolves, a process that started dozens of thousands of years ago. His work therefore calls for innovative studies, such as examining the potential fitness benefits of introgression. Inspired by his results, for example, on the purging of deleterious alleles in small populations, wolf researchers should use novel molecular tools to challenge other conservation genetics paradigms. Overall, RK Wayne's work constitutes a call for answers, which as scientists or citizens concerned with conservation matters, we are obliged to address, as we contribute to monitoring and maintaining biodiversity during our period of dramatic transformations of the biosphere.
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Affiliation(s)
- Marco Musiani
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), University of Bologna, Bologna, Italy
| | - Ettore Randi
- Department of Chemistry and Bioscience, Aalborg University, Aalborg Øst, Denmark
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4
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vonHoldt BM, Stahler DR, Brzeski KE, Musiani M, Peterson R, Phillips M, Stephenson J, Laudon K, Meredith E, Vucetich JA, Leonard JA, Wayne RK. Demographic history shapes North American gray wolf genomic diversity and informs species' conservation. Mol Ecol 2024; 33:e17231. [PMID: 38054561 DOI: 10.1111/mec.17231] [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: 06/05/2023] [Revised: 11/19/2023] [Accepted: 11/21/2023] [Indexed: 12/07/2023]
Abstract
Effective population size estimates are critical information needed for evolutionary predictions and conservation decisions. This is particularly true for species with social factors that restrict access to breeding or experience repeated fluctuations in population size across generations. We investigated the genomic estimates of effective population size along with diversity, subdivision, and inbreeding from 162,109 minimally filtered and 81,595 statistically neutral and unlinked SNPs genotyped in 437 grey wolf samples from North America collected between 1986 and 2021. We found genetic structure across North America, represented by three distinct demographic histories of western, central, and eastern regions of the continent. Further, grey wolves in the northern Rocky Mountains have lower genomic diversity than wolves of the western Great Lakes and have declined over time. Effective population size estimates revealed the historical signatures of continental efforts of predator extermination, despite a quarter century of recovery efforts. We are the first to provide molecular estimates of effective population size across distinct grey wolf populations in North America, which ranged between Ne ~ 275 and 3050 since early 1980s. We provide data that inform managers regarding the status and importance of effective population size estimates for grey wolf conservation, which are on average 5.2-9.3% of census estimates for this species. We show that while grey wolves fall above minimum effective population sizes needed to avoid extinction due to inbreeding depression in the short term, they are below sizes predicted to be necessary to avoid long-term risk of extinction.
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Affiliation(s)
- Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Daniel R Stahler
- Yellowstone Center for Resources, Yellowstone National Park, Wyoming, USA
| | - Kristin E Brzeski
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | - Marco Musiani
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Università di Bologna, Bologna, Italy
| | - Rolf Peterson
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | | | | | - Kent Laudon
- California Department of Fish and Wildlife, Northern Region, Redding, California, USA
| | - Erin Meredith
- California Department of Fish and Wildlife, Wildlife Forensic Laboratory, Sacramento, California, USA
| | - John A Vucetich
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, USA
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5
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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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6
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Jan M, Stronen AV, Boljte B, Černe R, Huber Đ, Iosif R, Kljun F, Konec M, Kos I, Krofel M, Kusak J, Luštrik R, Majić Skrbinšek A, Promberger-Füerpass B, Potočnik H, Rigg R, Trontelj P, Skrbinšek T. Wolf genetic diversity compared across Europe using the yardstick method. Sci Rep 2023; 13:13727. [PMID: 37608038 PMCID: PMC10444868 DOI: 10.1038/s41598-023-40834-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 08/17/2023] [Indexed: 08/24/2023] Open
Abstract
Integrating data across studies with traditional microsatellite genetic markers requires careful calibration and represents an obstacle for investigation of wide-ranging species where populations require transboundary management. We used the "yardstick" method to compare results published across Europe since 2002 and new wolf (Canis lupus) genetic profiles from the Carpathian Mountains in Central Europe and the Dinaric Mountains in Southeastern Europe, with the latter as our reference population. We compared each population with Dinaric wolves, considering only shared markers (range 4-17). For each population, we calculated standard genetic diversity indices plus calibrated heterozygosity (Hec) and allelic richness (Ac). Hec and Ac in Dinaric (0.704 and 9.394) and Carpathian wolves (0.695 and 7.023) were comparable to those observed in other large and mid-sized European populations, but smaller than those of northeastern Europe. Major discrepancies in marker choices among some studies made comparisons more difficult. However, the yardstick method, including the new measures of Hec and Ac, provided a direct comparison of genetic diversity values among wolf populations and an intuitive interpretation of the results. The yardstick method thus permitted the integration of diverse sources of publicly available microsatellite data for spatiotemporal genetic monitoring of evolutionary potential.
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Affiliation(s)
- Maja Jan
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia.
| | - Astrid Vik Stronen
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
- DivjaLabs d.o.o., Aljaževa ulica 35a, 1000, Ljubljana, Slovenia
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Barbara Boljte
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
- DivjaLabs d.o.o., Aljaževa ulica 35a, 1000, Ljubljana, Slovenia
| | - Rok Černe
- Slovenia Forest Service, Večna pot 2, 1000, Ljubljana, Slovenia
| | - Đuro Huber
- Faculty of Veterinary Medicine, University of Zagreb, Vjekoslava Heinzelova 55, 10000, Zagreb, Croatia
| | - Ruben Iosif
- Foundation Conservation Carpathia, 27 Calea Feldioarei, 500471, Brașov, Romania
| | - Franc Kljun
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
| | - Marjeta Konec
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
- DivjaLabs d.o.o., Aljaževa ulica 35a, 1000, Ljubljana, Slovenia
| | - Ivan Kos
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
| | - Miha Krofel
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
| | - Josip Kusak
- Faculty of Veterinary Medicine, University of Zagreb, Vjekoslava Heinzelova 55, 10000, Zagreb, Croatia
| | - Roman Luštrik
- Genialis Inc, Vojkova cesta 63, 1000, Ljubljana, Slovenia
| | - Aleksandra Majić Skrbinšek
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
- DivjaLabs d.o.o., Aljaževa ulica 35a, 1000, Ljubljana, Slovenia
| | | | - Hubert Potočnik
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
| | - Robin Rigg
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
- Slovak Wildlife Society, Belanská 574/6, P.O. Box 72, Liptovský Hrádok, 033 01, Slovakia
| | - Peter Trontelj
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
| | - Tomaž Skrbinšek
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
- DivjaLabs d.o.o., Aljaževa ulica 35a, 1000, Ljubljana, Slovenia
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7
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Cavedon M, Neufeld L, Finnegan L, Hervieux D, Michalak A, Pelletier A, Polfus J, Schwantje H, Skinner G, Steenweg R, Thacker C, Poissant J, Musiani M. Genomics of founders for conservation breeding: the Jasper caribou case. CONSERV GENET 2023; 24:855-867. [PMID: 37969360 PMCID: PMC10638200 DOI: 10.1007/s10592-023-01540-3] [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: 12/05/2022] [Accepted: 06/07/2023] [Indexed: 11/17/2023]
Abstract
Conservation breeding programs are increasingly used as recovery actions for wild animals; bringing founders into captivity to rear captive populations for future reintroduction into the wild. The International Union for the Conservation of Nature recommends that founders should come from genetically close populations and should have sufficient genetic diversity to avoid mating among relatives. Genomic data are highly informative for evaluating founders due to their high resolution and ability to capture adaptive divergence, yet, their application in that context remains limited. Woodland caribou are federally listed as a Species at Risk in Canada, with several populations facing extirpation, such as those in the Rocky Mountains of Alberta and British Columbia (BC). To prevent local extirpation, Jasper National Park (JNP) is proposing a conservation breeding program. We examined single nucleotide polymorphisms for 144 caribou from 11 populations encompassing a 200,0002 km area surrounding JNP to provide information useful for identifying appropriate founders for this program. We found that this area likely hosts a caribou metapopulation historically characterized by high levels of gene flow, which indicates that multiple sources of founders would be appropriate for initiating a breeding program. However, population structure and adaptive divergence analyses indicate that JNP caribou are closest to populations in the BC Columbia range, which also have suitable genetic diversity for conservation breeding. We suggest that collaboration among jurisdictions would be beneficial to implement the program to promote recovery of JNP caribou and possibly other caribou populations in the surrounding area, which is strategically at the periphery of the distribution of this endangered species. Supplementary Information The online version contains supplementary material available at 10.1007/s10592-023-01540-3.
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Affiliation(s)
- Maria Cavedon
- Deparment of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4 Canada
| | - Lalenia Neufeld
- Jasper National Park of Canada, Parks Canada, Jasper, Canada
| | - Laura Finnegan
- fRI Research, 1176 Switzer Drive, Hinton, AB T7V 1V3 Canada
| | - Dave Hervieux
- Fish and Wildlife Stewardship Branch, Alberta Environment and Protected Areas, Grande Prairie, AB T8V 6J4 Canada
| | - Anita Michalak
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 1N4 Canada
| | - Agnes Pelletier
- Ministry of Land, Water and Resource Stewardship Northeast Region, 400-10003-110Th Avenue, Fort St. John, BC V1J 6M7 Canada
| | - Jean Polfus
- Canadian Wildlife Service – Pacific Region, Environment and Climate Change Canada, 1238 Discovery Ave, Kelowna, BC V1V 1V9 Canada
| | - Helen Schwantje
- Wildlife and Habitat Branch, Ministry of Forests, Lands, Natural Resource Operations and Rural Development, Government of British Columbia, 2080 Labieux Road, Nanaimo, BC V9T 6J 9 Canada
| | - Geoff Skinner
- Jasper National Park of Canada, Parks Canada, Jasper, Canada
| | - Robin Steenweg
- Canadian Wildlife Service – Pacific Region, Environment and Climate Change Canada, 1238 Discovery Ave, Kelowna, BC V1V 1V9 Canada
| | - Caeley Thacker
- Wildlife and Habitat Branch, Ministry of Forests, Lands, Natural Resource Operations and Rural Development, Government of British Columbia, 2080 Labieux Road, Nanaimo, BC V9T 6J 9 Canada
| | - Jocelyn Poissant
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 1N4 Canada
| | - Marco Musiani
- Dipartimento Scienze Biologiche Geologiche Ambientali, Università Di Bologna, Via Zamboni, 33 - 40126 Bologna, Italia
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8
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Smith CCR, Tittes S, Ralph PL, Kern AD. Dispersal inference from population genetic variation using a convolutional neural network. Genetics 2023; 224:iyad068. [PMID: 37052957 PMCID: PMC10213498 DOI: 10.1093/genetics/iyad068] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/08/2023] [Accepted: 04/07/2023] [Indexed: 04/14/2023] Open
Abstract
The geographic nature of biological dispersal shapes patterns of genetic variation over landscapes, making it possible to infer properties of dispersal from genetic variation data. Here, we present an inference tool that uses geographically distributed genotype data in combination with a convolutional neural network to estimate a critical population parameter: the mean per-generation dispersal distance. Using extensive simulation, we show that our deep learning approach is competitive with or outperforms state-of-the-art methods, particularly at small sample sizes. In addition, we evaluate varying nuisance parameters during training-including population density, demographic history, habitat size, and sampling area-and show that this strategy is effective for estimating dispersal distance when other model parameters are unknown. Whereas competing methods depend on information about local population density or accurate inference of identity-by-descent tracts, our method uses only single-nucleotide-polymorphism data and the spatial scale of sampling as input. Strikingly, and unlike other methods, our method does not use the geographic coordinates of the genotyped individuals. These features make our method, which we call "disperseNN," a potentially valuable new tool for estimating dispersal distance in nonmodel systems with whole genome data or reduced representation data. We apply disperseNN to 12 different species with publicly available data, yielding reasonable estimates for most species. Importantly, our method estimated consistently larger dispersal distances than mark-recapture calculations in the same species, which may be due to the limited geographic sampling area covered by some mark-recapture studies. Thus genetic tools like ours complement direct methods for improving our understanding of dispersal.
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Affiliation(s)
- Chris C R Smith
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Silas Tittes
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Peter L Ralph
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Andrew D Kern
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
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9
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Judkins ME, Roemer GW, Millsap BA, Barnes JG, Bedrosian BE, Clarke SL, Domenech R, Herring G, Lamont M, Smith BW, Stahlecker DW, Stuber MJ, Warren WC, Van Den Bussche RA. A 37 K SNP array for the management and conservation of Golden Eagles (Aquila chrysaetos). CONSERV GENET 2023. [DOI: 10.1007/s10592-023-01508-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
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10
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Cubaynes S, Brandell EE, Stahler DR, Smith DW, Almberg ES, Schindler S, Wayne RK, Dobson AP, vonHoldt BM, MacNulty DR, Cross PC, Hudson PJ, Coulson T. Disease outbreaks select for mate choice and coat color in wolves. Science 2022; 378:300-303. [PMID: 36264784 DOI: 10.1126/science.abi8745] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
We know much about pathogen evolution and the emergence of new disease strains, but less about host resistance and how it is signaled to other individuals and subsequently maintained. The cline in frequency of black-coated wolves (Canis lupus) across North America is hypothesized to result from a relationship with canine distemper virus (CDV) outbreaks. We tested this hypothesis using cross-sectional data from wolf populations across North America that vary in the prevalence of CDV and the allele that makes coats black, longitudinal data from Yellowstone National Park, and modeling. We found that the frequency of CDV outbreaks generates fluctuating selection that results in heterozygote advantage that in turn affects the frequency of the black allele, optimal mating behavior, and black wolf cline across the continent.
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Affiliation(s)
- Sarah Cubaynes
- CEFE, University of Montpellier, CNRS, EPHE-PSL University, IRD, 34090 Montpellier, France
| | - Ellen E Brandell
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, State College, PA 16802, USA
| | - Daniel R Stahler
- Yellowstone Center for Resources, Yellowstone National Park, WY 82190, USA
| | - Douglas W Smith
- Yellowstone Center for Resources, Yellowstone National Park, WY 82190, USA
| | - Emily S Almberg
- Wildlife Division, Montana Fish Wildlife & Park, Bozeman, MT 59718, USA
| | - Susanne Schindler
- School of Biological Sciences, University of Bristol, Bristol BS8 1QU, UK
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Andrew P Dobson
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.,Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Daniel R MacNulty
- Department of Wildland Resources and Ecology Center, Utah State University, Logan, UT 84322, USA
| | - Paul C Cross
- US Geological Survey, Northern Rocky Mountain Science Center, Bozeman, MT 59715, USA
| | - Peter J Hudson
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, State College, PA 16802, USA
| | - Tim Coulson
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
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11
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Population structure of threatened caribou in western Canada inferred from genome-wide SNP data. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01475-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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12
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Bernard M, Dehaullon A, Gao G, Paul K, Lagarde H, Charles M, Prchal M, Danon J, Jaffrelo L, Poncet C, Patrice P, Haffray P, Quillet E, Dupont-Nivet M, Palti Y, Lallias D, Phocas F. Development of a High-Density 665 K SNP Array for Rainbow Trout Genome-Wide Genotyping. Front Genet 2022; 13:941340. [PMID: 35923696 PMCID: PMC9340366 DOI: 10.3389/fgene.2022.941340] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/24/2022] [Indexed: 12/02/2022] Open
Abstract
Single nucleotide polymorphism (SNP) arrays, also named « SNP chips », enable very large numbers of individuals to be genotyped at a targeted set of thousands of genome-wide identified markers. We used preexisting variant datasets from USDA, a French commercial line and 30X-coverage whole genome sequencing of INRAE isogenic lines to develop an Affymetrix 665 K SNP array (HD chip) for rainbow trout. In total, we identified 32,372,492 SNPs that were polymorphic in the USDA or INRAE databases. A subset of identified SNPs were selected for inclusion on the chip, prioritizing SNPs whose flanking sequence uniquely aligned to the Swanson reference genome, with homogenous repartition over the genome and the highest Minimum Allele Frequency in both USDA and French databases. Of the 664,531 SNPs which passed the Affymetrix quality filters and were manufactured on the HD chip, 65.3% and 60.9% passed filtering metrics and were polymorphic in two other distinct French commercial populations in which, respectively, 288 and 175 sampled fish were genotyped. Only 576,118 SNPs mapped uniquely on both Swanson and Arlee reference genomes, and 12,071 SNPs did not map at all on the Arlee reference genome. Among those 576,118 SNPs, 38,948 SNPs were kept from the commercially available medium-density 57 K SNP chip. We demonstrate the utility of the HD chip by describing the high rates of linkage disequilibrium at 2–10 kb in the rainbow trout genome in comparison to the linkage disequilibrium observed at 50–100 kb which are usual distances between markers of the medium-density chip.
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Affiliation(s)
- Maria Bernard
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
- INRAE, SIGENAE, Jouy-en-Josas, France
| | - Audrey Dehaullon
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
| | - Guangtu Gao
- USDA, REE, ARS, NEA, NCCCWA, Kearneysville, WV, United States
| | - Katy Paul
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
| | - Henri Lagarde
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
| | - Mathieu Charles
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
- INRAE, SIGENAE, Jouy-en-Josas, France
| | - Martin Prchal
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia, Vodňany, Czechia
| | - Jeanne Danon
- INRAE-UCA, Plateforme Gentyane, UMR GDEC, Clermont-Ferrand, France
| | - Lydia Jaffrelo
- INRAE-UCA, Plateforme Gentyane, UMR GDEC, Clermont-Ferrand, France
| | - Charles Poncet
- INRAE-UCA, Plateforme Gentyane, UMR GDEC, Clermont-Ferrand, France
| | | | | | - Edwige Quillet
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
| | | | - Yniv Palti
- USDA, REE, ARS, NEA, NCCCWA, Kearneysville, WV, United States
| | - Delphine Lallias
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
| | - Florence Phocas
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
- *Correspondence: Florence Phocas,
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13
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González-Bernal A, Rojas-Soto O, Martínez-Meyer E. Climatic comparison of the gray wolf ( Canis lupus) subspecies in North America using niche-based distribution models and its implications for conservation programs. J Mammal 2022. [DOI: 10.1093/jmammal/gyac066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
The gray wolf, Canis lupus, once inhabited much of the northern hemisphere worldwide; however, persecution drove its populations almost to extinction. In North America, diverse conservation programs have been implemented in the last decades to recover its populations in the wild, many of them guided by the historical distribution of the gray wolf subspecies. Over time, several authors have proposed different subspecies classifications. Nevertheless, most of them are mutually inconsistent regarding the number and distribution of subspecies, creating controversy when implementing conservation programs. This study used niche-based distribution models and cluster analysis to explore the bioclimatic profiles of C. lupus across North America and compare them with different subspecies classifications to identify environmental correlatives that support the proposed designations. Our cluster analysis results indicate that the optimal number of climatic groups was five, designated as Northern, Eastern, Western, Coastal, and Southern groups, with transitional overlap boundaries located at their peripheries, indicating climatic gradients between them and supporting the idea of intergrading zones. The geographic ranges of these groups mismatched to a different extent with all subspecies delimitations. In general, the boundaries of putative subspecies did not match the climatic patterns of North America. Our results may contribute to the recovery programs underway for this carnivore by identifying suitable areas for the release of individuals from specific lineages. New approaches to characterizing the intraspecific variation of the gray wolf should include all evidence available, including genetic, morphological, and ecological information.
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Affiliation(s)
- Alejandro González-Bernal
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de Mexico , Mexico City 04510 , Mexico
| | - Octavio Rojas-Soto
- Laboratorio de Bioclimatología, Instituto de Ecología A.C. , km 2.5 Carretera Antigua a Coatepec, Xalapa, Veracruz 91070 , Mexico
| | - Enrique Martínez-Meyer
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de Mexico , Mexico City 04510 , Mexico
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14
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Pacheco C, Stronen AV, Jędrzejewska B, Plis K, Okhlopkov IM, Mamaev NV, Drovetski SV, Godinho R. Demography and evolutionary history of grey wolf populations around the Bering Strait. Mol Ecol 2022; 31:4851-4865. [PMID: 35822863 PMCID: PMC9545117 DOI: 10.1111/mec.16613] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 06/16/2022] [Accepted: 07/04/2022] [Indexed: 11/28/2022]
Abstract
Glacial and interglacial periods throughout the Pleistocene have been substantial drivers of change in species distributions. Earlier analyses suggested that modern grey wolves (Canis lupus) trace their origin to a single Late Pleistocene Beringian population that expanded east and westwards, starting c. 25,000 years ago (ya). Here, we examined the demographic and phylogeographic histories of extant populations around the Bering Strait with wolves from two inland regions of the Russian Far East (RFE) and one coastal and two inland regions of North‐western North America (NNA), genotyped for 91,327 single nucleotide polymorphisms. Our results indicated that RFE and NNA wolves had a common ancestry until c. 34,400 ya, suggesting that these populations started to diverge before the previously proposed expansion out of Beringia. Coastal and inland NNA populations diverged c. 16,000 ya, concordant with the minimum proposed date for the ecological viability of the migration route along the Pacific Northwest coast. Demographic reconstructions for inland RFE and NNA populations reveal spatial and temporal synchrony, with large historical effective population sizes that declined throughout the Pleistocene, possibly reflecting the influence of broadscale climatic changes across continents. In contrast, coastal NNA wolves displayed a consistently lower effective population size than the inland populations. Differences between the demographic history of inland and coastal wolves may have been driven by multiple ecological factors, including historical gene flow patterns, natural landscape fragmentation, and more recent anthropogenic disturbance.
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Affiliation(s)
- Carolina Pacheco
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Astrid Vik Stronen
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.,Department of Biotechnology and Life Sciences, Insubria University, Varese, Italy.,Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | - Kamila Plis
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Innokentiy M Okhlopkov
- Institute of Biological Problems of Cryolithozone, Siberian Branch of Russian Academy of Sciences, Yakutsk, Russia
| | - Nikolay V Mamaev
- Institute of Biological Problems of Cryolithozone, Siberian Branch of Russian Academy of Sciences, Yakutsk, Russia
| | - Sergei V Drovetski
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Raquel Godinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
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15
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Stunz E, Fetcher N, Lavretsky P, Mohl JE, Tang J, Moody ML. Landscape Genomics Provides Evidence of Ecotypic Adaptation and a Barrier to Gene Flow at Treeline for the Arctic Foundation Species Eriophorum vaginatum. FRONTIERS IN PLANT SCIENCE 2022; 13:860439. [PMID: 35401613 PMCID: PMC8987161 DOI: 10.3389/fpls.2022.860439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Global climate change has resulted in geographic range shifts of flora and fauna at a global scale. Extreme environments, like the Arctic, are seeing some of the most pronounced changes. This region covers 14% of the Earth's land area, and while many arctic species are widespread, understanding ecotypic variation at the genomic level will be important for elucidating how range shifts will affect ecological processes. Tussock cottongrass (Eriophorum vaginatum L.) is a foundation species of the moist acidic tundra, whose potential decline due to competition from shrubs may affect ecosystem stability in the Arctic. We used double-digest Restriction Site-Associated DNA sequencing to identify genomic variation in 273 individuals of E. vaginatum from 17 sites along a latitudinal gradient in north central Alaska. These sites have been part of 30 + years of ecological research and are inclusive of a region that was part of the Beringian refugium. The data analyses included genomic population structure, demographic models, and genotype by environment association. Genome-wide SNP investigation revealed environmentally associated variation and population structure across the sampled range of E. vaginatum, including a genetic break between populations north and south of treeline. This structure is likely the result of subrefugial isolation, contemporary isolation by resistance, and adaptation. Forty-five candidate loci were identified with genotype-environment association (GEA) analyses, with most identified genes related to abiotic stress. Our results support a hypothesis of limited gene flow based on spatial and environmental factors for E. vaginatum, which in combination with life history traits could limit range expansion of southern ecotypes northward as the tundra warms. This has implications for lower competitive attributes of northern plants of this foundation species likely resulting in changes in ecosystem productivity.
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Affiliation(s)
- Elizabeth Stunz
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, United States
| | - Ned Fetcher
- Institute for Environmental Science and Sustainability, Wilkes University, Wilkes-Barre, PA, United States
| | - Philip Lavretsky
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, United States
| | - Jonathon E. Mohl
- Department of Mathematical Sciences, Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX, United States
| | - Jianwu Tang
- Marine Biological Laboratory, The Ecosystems Center, Woods Hole, MA, United States
| | - Michael L. Moody
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, United States
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16
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Cavedon M, vonHoldt B, Hebblewhite M, Hegel T, Heppenheimer E, Hervieux D, Mariani S, Schwantje H, Steenweg R, Theoret J, Watters M, Musiani M. Genomic legacy of migration in endangered caribou. PLoS Genet 2022; 18:e1009974. [PMID: 35143486 PMCID: PMC8830729 DOI: 10.1371/journal.pgen.1009974] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 12/01/2021] [Indexed: 11/18/2022] Open
Abstract
Wide-ranging animals, including migratory species, are significantly threatened by the effects of habitat fragmentation and habitat loss. In the case of terrestrial mammals, this results in nearly a quarter of species being at risk of extinction. Caribou are one such example of a wide-ranging, migratory, terrestrial, and endangered mammal. In populations of caribou, the proportion of individuals considered as "migrants" can vary dramatically. There is therefore a possibility that, under the condition that migratory behavior is genetically determined, those individuals or populations that are migratory will be further impacted by humans, and this impact could result in the permanent loss of the migratory trait in some populations. However, genetic determination of migration has not previously been studied in an endangered terrestrial mammal. We examined migratory behavior of 139 GPS-collared endangered caribou in western North America and carried out genomic scans for the same individuals. Here we determine a genetic subdivision of caribou into a Northern and a Southern genetic cluster. We also detect >50 SNPs associated with migratory behavior, which are in genes with hypothesized roles in determining migration in other organisms. Furthermore, we determine that propensity to migrate depends upon the proportion of ancestry in individual caribou, and thus on the evolutionary history of its migratory and sedentary subspecies. If, as we report, migratory behavior is influenced by genes, caribou could be further impacted by the loss of the migratory trait in some isolated populations already at low numbers. Our results indicating an ancestral genetic component also suggest that the migratory trait and their associated genetic mutations could not be easily re-established when lost in a population.
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Affiliation(s)
- Maria Cavedon
- Faculty of Environmental Design, University of Calgary, Calgary, Alberta, Canada
| | - Bridgett vonHoldt
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Mark Hebblewhite
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, College of Forestry and Conservation, University of Montana, Missoula, Montana, United States of America
| | - Troy Hegel
- Yukon Department of Environment, Whitehorse, Yukon, Canada
| | - Elizabeth Heppenheimer
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Dave Hervieux
- Fish and Wildlife Stewardship Branch, Alberta Environment and Parks, Grande Prairie, Alberta, Canada
| | - Stefano Mariani
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, United Kingdom
| | - Helen Schwantje
- Wildlife and Habitat Branch, Ministry of Forests, Lands, Natural Resource Operations and Rural Development, Government of British Columbia, Nanaimo, British Columbia, Canada
| | - Robin Steenweg
- Pacific Region, Canadian Wildlife Service, Environment and Climate Change Canada, Delta, British Columbia, Canada
| | - Jessica Theoret
- Faculty of Environmental Design, University of Calgary, Calgary, Alberta, Canada
| | - Megan Watters
- Land and Resource Specialist, Fort St. John, British Columbia, Canada
| | - Marco Musiani
- Department of Biological Sciences, Faculty of Science and Veterinary Medicine (Joint Appointment), University of Calgary, Calgary, Alberta, Canada
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17
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Stronen AV, Norman AJ, Vander Wal E, Paquet PC. The relevance of genetic structure in ecotype designation and conservation management. Evol Appl 2022; 15:185-202. [PMID: 35233242 PMCID: PMC8867706 DOI: 10.1111/eva.13339] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 12/02/2021] [Accepted: 12/20/2021] [Indexed: 11/28/2022] Open
Abstract
The concept of ecotypes is complex, partly because of its interdisciplinary nature, but the idea is intrinsically valuable for evolutionary biology and applied conservation. The complex nature of ecotypes has spurred some confusion and inconsistencies in the literature, thereby limiting broader theoretical development and practical application. We provide suggestions for how incorporating genetic analyses can ease confusion and help define ecotypes. We approach this by systematically reviewing 112 publications across taxa that simultaneously mention the terms ecotype, conservation and management, to examine the current use of the term in the context of conservation and management. We found that most ecotype studies involve fish, mammals and plants with a focus on habitat use, which at 60% was the most common criterion used for categorization of ecotypes. Only 53% of the studies incorporated genetic analyses, and major discrepancies in available genomic resources among taxa could have contributed to confusion about the role of genetic structure in delineating ecotypes. Our results show that the rapid advances in genetic methods, also for nonmodel organisms, can help clarify the spatiotemporal distribution of adaptive and neutral genetic variation and their relevance to ecotype designations. Genetic analyses can offer empirical support for the ecotype concept and provide a timely measure of evolutionary potential, especially in changing environmental conditions. Genetic variation that is often difficult to detect, including polygenic traits influenced by small contributions from several genes, can be vital for adaptation to rapidly changing environments. Emerging ecotypes may signal speciation in progress, and findings from genome-enabled organisms can help clarify important selective factors driving ecotype development and persistence, and thereby improve preservation of interspecific genetic diversity. Incorporation of genetic analyses in ecotype studies will help connect evolutionary biology and applied conservation, including that of problematic groups such as natural hybrid organisms and urban or anthropogenic ecotypes.
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Affiliation(s)
- Astrid V. Stronen
- Department of BiologyBiotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
- Department of Biotechnology and Life SciencesInsubria UniversityVareseItaly
- Department of Chemistry and BioscienceAalborg UniversityAalborgDenmark
| | - Anita J. Norman
- Department of Fish, Wildlife and Environmental StudiesSwedish University of Agricultural SciencesUmeåSweden
| | - Eric Vander Wal
- Department of BiologyMemorial University of NewfoundlandSt. John’sNLCanada
| | - Paul C. Paquet
- Department of GeographyUniversity of VictoriaVictoriaBCCanada
- Raincoast Conservation FoundationSidneyBCCanada
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18
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Prassack KA, Walkup LC. Maybe So, Maybe Not: Canis lepophagus at Hagerman Fossil Beds National Monument, Idaho, USA. J MAMM EVOL 2022. [DOI: 10.1007/s10914-021-09591-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AbstractA canid dentary is described from the Pliocene Glenns Ferry Formation at Hagerman Fossil Beds National Monument, south-central Idaho, USA. The specimen possesses traits in alliance with and measurements falling within or exceeding those of Canis lepophagus. The dentary, along with a tarsal IV (cuboid) and an exploded canine come from the base of the fossiliferous Sahara complex within the monument. Improved geochronologic control provided by new tephrochronologic mapping by the U.S. Geological Survey-National Park Service Hagerman Paleontology, Environments, and Tephrochronology Project supports an interpolated age of approximately 3.9 Ma, placing it in the early Blancan North American Land Mammal Age. It is conservatively referred to herein as Canis aff. C. lepophagus with the caveat that it is an early and robust example of that species. A smaller canid, initially assigned to Canis lepophagus and then to Canis ferox, is also known from Hagerman. Most specimens of Canis ferox, including the holotype, were recently reassigned to Eucyon ferox, but specimens from the Hagerman and Rexroad faunas were left as Canis sp. and possibly attributed to C. lepophagus. We agree that these smaller canids belong in Canis and not Eucyon but reject placing them within C. lepophagus; we refer to them here as Hagerman-Rexroad Canis. This study confirms the presence of two approximately coyote-sized canids at Hagerman and adds to the growing list of carnivorans now known from these fossil beds.
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19
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Šnjegota D, Stronen AV, Boljte B, Ćirović D, Djan M, Huber D, Jelenčič M, Konec M, Kusak J, Skrbinšek T. Population genetic structure of wolves in the northwestern Dinaric-Balkan region. Ecol Evol 2021; 11:18492-18504. [PMID: 35003687 PMCID: PMC8717286 DOI: 10.1002/ece3.8444] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 11/29/2022] Open
Abstract
The Balkan Peninsula and the Dinaric Mountains possess extraordinary biodiversity and support one of the largest and most diverse wolf (Canis lupus) populations in Europe. Results obtained with diverse genetic markers show west-east substructure, also seen in various other species, despite the absence of obvious barriers to movement. However, the spatial extent of the genetic clusters remains unresolved, and our aim was to combine fine-scale sampling with population and spatial genetic analyses to improve resolution of wolf genetic clusters. We analyzed 16 autosomal microsatellites from 255 wolves sampled in Slovenia, Croatia, Bosnia and Herzegovina (BIH), and Serbia and documented three genetic clusters. These comprised (1) Slovenia and the regions of Gorski kotar and Lika in Croatia, (2) the region of Dalmatia in southern Croatia and BIH, and (3) Serbia. When we mapped the clusters geographically, we observed west-east genetic structure across the study area, together with some specific structure in BIH-Dalmatia. We observed that cluster 1 had a smaller effective population size, consistent with earlier reports of population recovery since the 1980s. Our results provide foundation for future genomic studies that would further resolve the observed west-east population structure and its evolutionary history in wolves and other taxa in the region and identify focal areas for habitat conservation. They also have immediate importance for conservation planning for the wolves in one of the most important parts of the species' European range.
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Affiliation(s)
- Dragana Šnjegota
- Department of Biology and EcologyFaculty of Natural Sciences and MathematicsUniversity of Banja LukaBanja LukaBosnia and Herzegovina
| | - Astrid Vik Stronen
- Department of BiologyBiotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
| | - Barbara Boljte
- Department of BiologyBiotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
| | - Duško Ćirović
- Faculty of BiologyUniversity of BelgradeBelgradeSerbia
| | - Mihajla Djan
- Department of Biology and EcologyFaculty of SciencesUniversity of Novi SadNovi SadSerbia
| | - Djuro Huber
- Department of BiologyFaculty of Veterinary MedicineUniversity of ZagrebZagrebCroatia
| | - Maja Jelenčič
- Department of BiologyBiotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
| | - Marjeta Konec
- Department of BiologyBiotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
| | - Josip Kusak
- Department of BiologyFaculty of Veterinary MedicineUniversity of ZagrebZagrebCroatia
| | - Tomaž Skrbinšek
- Department of BiologyBiotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
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20
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McDevitt AD, Coscia I, Browett SS, Ruiz-González A, Statham MJ, Ruczyńska I, Roberts L, Stojak J, Frantz AC, Norén K, Ågren EO, Learmount J, Basto M, Fernandes C, Stuart P, Tosh DG, Sindicic M, Andreanszky T, Isomursu M, Panek M, Korolev A, Okhlopkov IM, Saveljev AP, Pokorny B, Flajšman K, Harrison SWR, Lobkov V, Ćirović D, Mullins J, Pertoldi C, Randi E, Sacks BN, Kowalczyk R, Wójcik JM. Next-generation phylogeography resolves post-glacial colonization patterns in a widespread carnivore, the red fox (Vulpes vulpes), in Europe. Mol Ecol 2021; 31:993-1006. [PMID: 34775636 DOI: 10.1111/mec.16276] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 11/03/2021] [Accepted: 11/08/2021] [Indexed: 12/22/2022]
Abstract
Carnivores tend to exhibit a lack of (or less pronounced) genetic structure at continental scales in both a geographic and temporal sense and this can confound the identification of post-glacial colonization patterns in this group. In this study we used genome-wide data (using genotyping by sequencing [GBS]) to reconstruct the phylogeographic history of a widespread carnivore, the red fox (Vulpes vulpes), by investigating broad-scale patterns of genomic variation, differentiation and admixture amongst contemporary populations in Europe. Using 15,003 single nucleotide polymorphisms (SNPs) from 524 individuals allowed us to identify the importance of refugial regions for the red fox in terms of endemism (e.g., Iberia). In addition, we tested multiple post-glacial recolonization scenarios of previously glaciated regions during the Last Glacial Maximum using an Approximate Bayesian Computation (ABC) approach that were unresolved from previous studies. This allowed us to identify the role of admixture from multiple source population post-Younger Dryas in the case of Scandinavia and ancient land-bridges in the colonization of the British Isles. A natural colonization of Ireland was deemed more likely than an ancient human-mediated introduction as has previously been proposed and potentially points to a larger mammalian community on the island in the early post-glacial period. Using genome-wide data has allowed us to tease apart broad-scale patterns of structure and diversity in a widespread carnivore in Europe that was not evident from using more limited marker sets and provides a foundation for next-generation phylogeographic studies in other non-model species.
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Affiliation(s)
- Allan D McDevitt
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Ilaria Coscia
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Samuel S Browett
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Aritz Ruiz-González
- Department of Zoology and Animal Cell Biology, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
| | - Mark J Statham
- Department of Population Health and Reproduction, School of Veterinary Medicine, Mammalian Ecology and Conservation Unit, Center for Veterinary Genetics, University of California, Davis, California, USA
| | - Iwona Ruczyńska
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Liam Roberts
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Joanna Stojak
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Alain C Frantz
- Musée National d'Histoire Naturelle, Luxembourg, Luxembourg
| | - Karin Norén
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Erik O Ågren
- Department of Pathology and Wildlife Diseases, National Veterinary Institute, Uppsala, Sweden
| | - Jane Learmount
- National Wildlife Management Centre, Animal and Plant Health Agency, Sand Hutton, UK
| | - Mafalda Basto
- Department of Animal Biology, Faculty of Sciences, CE3C - Centre for Ecology, Evolution and Environmental Changes, University of Lisbon, Lisbon, Portugal
| | - Carlos Fernandes
- Department of Animal Biology, Faculty of Sciences, CE3C - Centre for Ecology, Evolution and Environmental Changes, University of Lisbon, Lisbon, Portugal
| | - Peter Stuart
- Biological and Pharmaceutical Sciences Department, Institute of Technology Tralee, Kerry, Ireland
| | - David G Tosh
- National Museums of Northern Ireland, Hollywood, UK
| | - Magda Sindicic
- Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | | | - Marja Isomursu
- Finnish Food Authority, Veterinary Bacteriology and Pathology Research Unit, Oulu, Finland
| | | | - Andrey Korolev
- Institute of Biology of Komi Science, Remote Centre of the Ural Branch of the Russian Academy of Sciences, Syktyvkar, Russia
| | - Innokentiy M Okhlopkov
- Institute of Biological Problems of Cryolithozone, Siberian Branch of Russian Academy of Sciences, Yakutsk, Russia
| | - Alexander P Saveljev
- Department of Animal Ecology, Russian Research Institute of Game Management and Fur Farming, Kirov, Russia
| | | | | | - Stephen W R Harrison
- School of Animal Rural & Environmental Sciences, Nottingham Trent University, Southwell, UK
| | - Vladimir Lobkov
- Faculty of Biology, Odessa I.I. Mechnykov National University, Odessa, Ukraine
| | - Duško Ćirović
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Jacinta Mullins
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Cino Pertoldi
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Ettore Randi
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.,Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Benjamin N Sacks
- Department of Population Health and Reproduction, School of Veterinary Medicine, Mammalian Ecology and Conservation Unit, Center for Veterinary Genetics, University of California, Davis, California, USA
| | - Rafał Kowalczyk
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Jan M Wójcik
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
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21
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Baecklund TM, Donaldson ME, Hueffer K, Kyle CJ. Genetic structure of immunologically associated candidate genes suggests arctic rabies variants exert differential selection in arctic fox populations. PLoS One 2021; 16:e0258975. [PMID: 34714859 PMCID: PMC8555846 DOI: 10.1371/journal.pone.0258975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 10/10/2021] [Indexed: 11/24/2022] Open
Abstract
Patterns of local adaptation can emerge in response to the selective pressures diseases exert on host populations as reflected in increased frequencies of respective, advantageous genotypes. Elucidating patterns of local adaptation enhance our understanding of mechanisms of disease spread and the capacity for species to adapt in context of rapidly changing environments such as the Arctic. Arctic rabies is a lethal disease that largely persists in northern climates and overlaps with the distribution of its natural host, arctic fox. Arctic fox populations display little neutral genetic structure across their North American range, whereas phylogenetically unique arctic rabies variants are restricted in their geographic distributions. It remains unknown if arctic rabies variants impose differential selection upon host populations, nor what role different rabies variants play in the maintenance and spread of this disease. Using a targeted, genotyping-by-sequencing assay, we assessed correlations of arctic fox immunogenetic variation with arctic rabies variants to gain further insight into the epidemiology of this disease. Corroborating past research, we found no neutral genetic structure between sampled regions, but did find moderate immunogenetic structuring between foxes predominated by different arctic rabies variants. FST outliers associated with host immunogenetic structure included SNPs within interleukin and Toll-like receptor coding regions (IL12B, IL5, TLR3 and NFKB1); genes known to mediate host responses to rabies. While these data do not necessarily reflect causation, nor a direct link to arctic rabies, the contrasting genetic structure of immunologically associated candidate genes with neutral loci is suggestive of differential selection and patterns of local adaptation in this system. These data are somewhat unexpected given the long-lived nature and dispersal capacities of arctic fox; traits expected to undermine local adaptation. Overall, these data contribute to our understanding of the co-evolutionary relationships between arctic rabies and their primary host and provide data relevant to the management of this disease.
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Affiliation(s)
- Tristan M. Baecklund
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada
- * E-mail:
| | - Michael E. Donaldson
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada
| | - Karsten Hueffer
- Department of Veterinary Medicine, University of Alaska Fairbanks, Fairbanks, AK, United States of America
| | - Christopher J. Kyle
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada
- Forensic Science Department, Trent University, Peterborough, ON, Canada
- Natural Resources DNA Profiling & Forensic Centre, Trent University, Peterborough, ON, Canada
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22
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Upadhyay M, Kunz E, Sandoval-Castellanos E, Hauser A, Krebs S, Graf A, Blum H, Dotsev A, Okhlopkov I, Shakhin A, Bagirov V, Brem G, Fries R, Zinovieva N, Medugorac I. Whole genome sequencing reveals a complex introgression history and the basis of adaptation to subarctic climate in wild sheep. Mol Ecol 2021; 30:6701-6717. [PMID: 34534381 DOI: 10.1111/mec.16184] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 09/01/2021] [Accepted: 09/07/2021] [Indexed: 11/29/2022]
Abstract
To predict species responses to anthropogenic disturbances and climate change, it is reasonable to use species with high sensitivity to such factors. Snow sheep (Ovis nivicola) could represent a good candidate for this; as the only large herbivore species adapted to the cold and alpine habitats of northeastern Siberia, it plays a crucial role in its ecosystem. Despite having an extensive geographical distribution among all ovine species, it is one of the least studied. In this study, we sequenced and analysed six genomes of snow sheep in combination with all other wild sheep species to infer key aspects of their evolutionary history and unveil the genetic basis of their adaptation to subarctic environments. Despite their large census population size, snow sheep genomes showed remarkably low heterozygosity, which could reflect the effect of isolation and historical bottlenecks that we inferred using the pairwise sequential Markovian coalescent and runs of homozygosity. F4 -statistics indicated instances of introgression involving snow sheep with argali (Ovis ammon) and Dall (Ovis dalli) sheep, suggesting that these species might have been more widespread during the Pleistocene. Furthermore, the introgressed segments, which were identified using mainly minimum relative node depth, covered genes associated with immunity, adipogenesis and morphology-related traits, representing potential targets of adaptive introgression. Genes related to mitochondrial functions and thermogenesis associated with adipose tissue were identified to be under selection. Overall, our data suggest introgression as a mechanism facilitating adaptation in wild sheep species and provide insights into the genetic mechanisms underlying cold adaptation in snow sheep.
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Affiliation(s)
- Maulik Upadhyay
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Munich, Germany
| | - Elisabeth Kunz
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Munich, Germany
| | | | - Andreas Hauser
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Arsen Dotsev
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, Russia
| | | | - Alexey Shakhin
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, Russia
| | - Vugar Bagirov
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, Russia
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, VMU, Vienna, Austria
| | - Ruedi Fries
- Lehrstuhl für Tierzucht, Technische Universität München, Freising, Germany
| | - Natalia Zinovieva
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, Russia
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Munich, Germany
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23
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Johnston RA, Rheinwald JG, vonHoldt BM, Stahler DR, Lowry W, Tung J, Wayne RK. K Locus Effects in Gray Wolves: Experimental Assessment of TLR3 Signaling and the Gene Expression Response to Canine Distemper Virus. J Hered 2021; 112:458-468. [PMID: 34132805 PMCID: PMC8567826 DOI: 10.1093/jhered/esab029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/04/2021] [Accepted: 05/06/2021] [Indexed: 12/21/2022] Open
Abstract
In North American gray wolves, black coat color is dominantly inherited via a 3 base pair coding deletion in the canine beta defensin 3 (CBD103) gene. This 3 base pair deletion, called the KB allele, was introduced through hybridization with dogs and subsequently underwent a selective sweep that increased its frequency in wild wolves. Despite apparent positive selection, KBB wolves have lower fitness than wolves with the KyB genotype, even though the 2 genotypes show no observable differences in black coat color. Thus, the KB allele is thought to have pleiotropic effects on as-yet unknown phenotypes. Given the role of skin-expressed CBD103 in innate immunity, we hypothesized that the KB allele influences the keratinocyte gene expression response to TLR3 pathway stimulation and/or infection by canine distemper virus (CDV). To test this hypothesis, we developed a panel of primary epidermal keratinocyte cell cultures from 24 wild North American gray wolves of both Kyy and KyB genotypes. In addition, we generated an immortalized Kyy line and used CRISPR/Cas9 editing to produce a KyB line on the same genetic background. We assessed the transcriptome-wide responses of wolf keratinocytes to the TLR3 agonist polyinosinic:polycytidylic acid (polyI:C), and to live CDV. K locus genotype did not predict the transcriptional response to either challenge, suggesting that variation in the gene expression response does not explain pleiotropic effects of the KB allele on fitness. This study supports the feasibility of using cell culture methods to investigate the phenotypic effects of naturally occurring genetic variation in wild mammals.
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Affiliation(s)
- Rachel A Johnston
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
| | - James G Rheinwald
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Daniel R Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, WY, USA
| | - William Lowry
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Jenny Tung
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
- Department of Biology, Duke University, Durham, NC, USA
- Duke Population Research Institute, Duke University, Durham, NC, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
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24
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Stronen AV, Konec M, Boljte B, Bošković I, Gačić D, Galov A, Heltai M, Jelenčič M, Kljun F, Kos I, Kovačič T, Lanszki J, Pintur K, Pokorny B, Skrbinšek T, Suchentrunk F, Szabó L, Šprem N, Tomljanović K, Potočnik H. Population genetic structure in a rapidly expanding mesocarnivore: golden jackals in the Dinaric-Pannonian region. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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25
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Marcus J, Ha W, Barber RF, Novembre J. Fast and flexible estimation of effective migration surfaces. eLife 2021; 10:61927. [PMID: 34328078 PMCID: PMC8324296 DOI: 10.7554/elife.61927] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 06/07/2021] [Indexed: 12/12/2022] Open
Abstract
Spatial population genetic data often exhibits ‘isolation-by-distance,’ where genetic similarity tends to decrease as individuals become more geographically distant. The rate at which genetic similarity decays with distance is often spatially heterogeneous due to variable population processes like genetic drift, gene flow, and natural selection. Petkova et al., 2016 developed a statistical method called Estimating Effective Migration Surfaces (EEMS) for visualizing spatially heterogeneous isolation-by-distance on a geographic map. While EEMS is a powerful tool for depicting spatial population structure, it can suffer from slow runtimes. Here, we develop a related method called Fast Estimation of Effective Migration Surfaces (FEEMS). FEEMS uses a Gaussian Markov Random Field model in a penalized likelihood framework that allows for efficient optimization and output of effective migration surfaces. Further, the efficient optimization facilitates the inference of migration parameters per edge in the graph, rather than per node (as in EEMS). With simulations, we show conditions under which FEEMS can accurately recover effective migration surfaces with complex gene-flow histories, including those with anisotropy. We apply FEEMS to population genetic data from North American gray wolves and show it performs favorably in comparison to EEMS, with solutions obtained orders of magnitude faster. Overall, FEEMS expands the ability of users to quickly visualize and interpret spatial structure in their data.
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Affiliation(s)
- Joseph Marcus
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Wooseok Ha
- Department of Statistics, University of California, Berkeley, Berkeley, United States
| | | | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, United States.,Department of Ecology and Evolution, University of Chicago, Chicago, United States
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26
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Lee KD, Millar CD, Brekke P, Whibley A, Ewen JG, Hingston M, Zhu A, Santure AW. The design and application of a 50 K SNP chip for a threatened Aotearoa New Zealand passerine, the hihi. Mol Ecol Resour 2021; 22:415-429. [PMID: 34323011 DOI: 10.1111/1755-0998.13480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 11/30/2022]
Abstract
Next-generation sequencing has transformed the fields of ecological and evolutionary genetics by allowing for cost-effective identification of genome-wide variation. Single nucleotide polymorphism (SNP) arrays, or "SNP chips", enable very large numbers of individuals to be consistently genotyped at a selected set of these identified markers, and also offer the advantage of being able to analyse samples of variable DNA quality. We used reduced representation restriction-aided digest sequencing (RAD-seq) of 31 birds of the threatened hihi (Notiomystis cincta; stitchbird) and low-coverage whole genome sequencing (WGS) of 10 of these birds to develop an Affymetrix 50 K SNP chip. We overcame the limitations of having no hihi reference genome and a low quantity of sequence data by separate and pooled de novo assembly of each of the 10 WGS birds. Reads from all individuals were mapped back to these de novo assemblies to identify SNPs. A subset of RAD-seq and WGS SNPs were selected for inclusion on the chip, prioritising SNPs with the highest quality scores whose flanking sequence uniquely aligned to the zebra finch (Taeniopygia guttata) genome. Of the 58,466 SNPs manufactured on the chip, 72% passed filtering metrics and were polymorphic. By genotyping 1,536 hihi on the array, we found that SNPs detected in multiple assemblies were more likely to successfully genotype, representing a cost-effective approach to identify SNPs for genotyping. Here, we demonstrate the utility of the SNP chip by describing the high rates of linkage disequilibrium in the hihi genome, reflecting the history of population bottlenecks in the species.
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Affiliation(s)
- Kate D Lee
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Craig D Millar
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Patricia Brekke
- Institute of Zoology, Zoological Society of London, Regent's Park, London, UK
| | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - John G Ewen
- Institute of Zoology, Zoological Society of London, Regent's Park, London, UK
| | - Melanie Hingston
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Amy Zhu
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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27
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Taron UH, Salado I, Escobar-Rodríguez M, Westbury MV, Butschkau S, Paijmans JLA, vonHoldt BM, Hofreiter M, Leonard JA. A sliver of the past: The decimation of the genetic diversity of the Mexican wolf. Mol Ecol 2021; 30:6340-6354. [PMID: 34161633 DOI: 10.1111/mec.16037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 06/21/2021] [Indexed: 01/07/2023]
Abstract
The endangered Mexican wolf (Canis lupus baileyi) is known to carry exceedingly low levels of genetic diversity. This could be (i) the result of long-term evolutionary patterns as they exist at the southernmost limit of the species distribution at a relatively reduced effective size, or (ii) due to rapid population decline caused by human persecution over the last century. If the former, purifying selection is expected to have minimized the impact of inbreeding. If the latter, rapid and recent declines in genetic diversity may have resulted in severe fitness consequences. To differentiate these hypotheses, we conducted comparative whole-genome analyses of five historical Mexican wolves (1907-1917) and 18 contemporary Mexican and grey wolves from North America and Eurasia. Based on whole-genome data, historical and modern Mexican wolves together form a discrete unit. Moreover, we found that modern Mexican wolves have reduced genetic diversity and increased inbreeding relative to the historical population, which was widespread across the southwestern United States and not restricted to Mexico as previously assumed. Finally, although Mexican wolves have evolved in sympatry with coyotes (C. latrans), we observed lower introgression between historical Mexican wolves and coyotes than with modern Mexican wolves, despite similarities in body size. Taken together, our data show that recent population declines probably caused the reduced level of genetic diversity, but not the observed differentiation of the Mexican wolves from other North American wolves.
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Affiliation(s)
- Ulrike H Taron
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Isabel Salado
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | | | - Michael V Westbury
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Susanne Butschkau
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | - Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
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28
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vonHoldt BM, Aardema ML. Updating the Bibliography of Interbreeding among Canis in North America. J Hered 2021; 111:249-262. [PMID: 32034410 DOI: 10.1093/jhered/esaa004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 02/05/2020] [Indexed: 01/29/2023] Open
Abstract
This bibliography provides a collection of references that documents the evolution of studies evidencing interbreeding among Canis species in North America. Over the past several decades, advances in biology and genomic technology greatly improved our ability to detect and characterize species interbreeding, which has significance for understanding species in a changing landscape as well as for endangered species management. This bibliography includes a discussion within each category of interbreeding, the timeline of developing evidence, and includes a review of past research conducted on experimental crosses. Research conducted in the early 20th century is rich with detailed records and photographs of hybrid offspring development and behavior. With the progression of molecular methods, studies can estimate historical demographic parameters and detect chromosomal patterns of ancestry. As these methods continue to increase in accessibility, the field will gain a deeper and richer understanding of the evolutionary history of North American Canis.
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Affiliation(s)
- Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ
| | - Matthew L Aardema
- Department of Biology, Montclair State University, Montclair, NJ.,Sackler Institute for Comparative Genomics, American Museum of Natural History, New York City, NY
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29
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Baecklund TM, Morrison J, Donaldson ME, Hueffer K, Kyle CJ. The role of a mechanistic host in maintaining arctic rabies variant distributions: Assessment of functional genetic diversity in Alaskan red fox (Vulpes vulpes). PLoS One 2021; 16:e0249176. [PMID: 33831031 PMCID: PMC8031376 DOI: 10.1371/journal.pone.0249176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 03/12/2021] [Indexed: 11/18/2022] Open
Abstract
Populations are exposed to different types and strains of pathogens across heterogeneous landscapes, where local interactions between host and pathogen may present reciprocal selective forces leading to correlated patterns of spatial genetic structure. Understanding these coevolutionary patterns provides insight into mechanisms of disease spread and maintenance. Arctic rabies (AR) is a lethal disease with viral variants that occupy distinct geographic distributions across North America and Europe. Red fox (Vulpes vulpes) are a highly susceptible AR host, whose range overlaps both geographically distinct AR strains and regions where AR is absent. It is unclear if genetic structure exists among red fox populations relative to the presence/absence of AR or the spatial distribution of AR variants. Acquiring these data may enhance our understanding of the role of red fox in AR maintenance/spread and inform disease control strategies. Using a genotyping-by-sequencing assay targeting 116 genomic regions of immunogenetic relevance, we screened for sequence variation among red fox populations from Alaska and an outgroup from Ontario, including areas with different AR variants, and regions where the disease was absent. Presumed neutral SNP data from the assay found negligible levels of neutral genetic structure among Alaskan populations. The immunogenetically-associated data identified 30 outlier SNPs supporting weak to moderate genetic structure between regions with and without AR in Alaska. The outliers included SNPs with the potential to cause missense mutations within several toll-like receptor genes that have been associated with AR outcome. In contrast, there was a lack of genetic structure between regions with different AR variants. Combined, we interpret these data to suggest red fox populations respond differently to the presence of AR, but not AR variants. This research increases our understanding of AR dynamics in the Arctic, where host/disease patterns are undergoing flux in a rapidly changing Arctic landscape, including the continued northward expansion of red fox into regions previously predominated by the arctic fox (Vulpes lagopus).
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Affiliation(s)
- Tristan M. Baecklund
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
- * E-mail:
| | - Jaycee Morrison
- Forensic Science Undergraduate Program, Trent University, Peterborough, Ontario, Canada
| | - Michael E. Donaldson
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
| | - Karsten Hueffer
- Department of Veterinary Medicine, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
| | - Christopher J. Kyle
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
- Forensic Science Department, Trent University, Peterborough, Ontario, Canada
- Natural Resources DNA Profiling & Forensic Centre, Trent University, Peterborough, Ontario, Canada
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30
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Carroll C, Rohlf DJ, vonHoldt BM, Treves A, Hendricks SA. Wolf Delisting Challenges Demonstrate Need for an Improved Framework for Conserving Intraspecific Variation under the Endangered Species Act. Bioscience 2021; 71:73-84. [PMID: 33442329 PMCID: PMC7791361 DOI: 10.1093/biosci/biaa125] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Recent advances in genomics have increased our understanding of geographic patterns of intraspecific variation and the importance of this variation in enhancing species’ potential to adapt to novel threats. However, as part of an effort to limit the scope of the Endangered Species Act (ESA), the US government has proposed the removal of the gray wolf from the list of protected species on the basis of a claim that the statute permits a species to be declared recovered given the existence of a single presently secure population. We rebut this interpretation and propose a framework for the conservation of adaptive potential that builds on current agency practice in delineating subspecific recovery units and reconciles the definition of significance in the statute's “distinct population segment” and “significant portion of range” clauses. Such a coordinated policy would enhance the ESA's effectiveness in stemming loss of biodiversity in the face of climate change and other factors altering Earth's ecosystems.
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Affiliation(s)
- Carlos Carroll
- Klamath Center for Conservation Research, Orleans, California
| | - Daniel J Rohlf
- Earthrise Law Center, in the Lewis and Clark Law School, Portland, Oregon
| | - Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey
| | - Adrian Treves
- Nelson Institute for Environmental Studies, University of Wisconsin, Madison, Wisconsin
| | - Sarah A Hendricks
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho
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31
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Muir AP, Dubois SF, Ross RE, Firth LB, Knights AM, Lima FP, Seabra R, Corre E, Le Corguillé G, Nunes FLD. Seascape genomics reveals population isolation in the reef-building honeycomb worm, Sabellaria alveolata (L.). BMC Evol Biol 2020; 20:100. [PMID: 32778052 PMCID: PMC7418442 DOI: 10.1186/s12862-020-01658-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 07/17/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Under the threat of climate change populations can disperse, acclimatise or evolve in order to avoid fitness loss. In light of this, it is important to understand neutral gene flow patterns as a measure of dispersal potential, but also adaptive genetic variation as a measure of evolutionary potential. In order to assess genetic variation and how this relates to environment in the honeycomb worm (Sabellaria alveolata (L.)), a reef-building polychaete that supports high biodiversity, we carried out RAD sequencing using individuals from along its complete latitudinal range. Patterns of neutral population genetic structure were compared to larval dispersal as predicted by ocean circulation modelling, and outlier analyses and genotype-environment association tests were used to attempt to identify loci under selection in relation to local temperature data. RESULTS We genotyped 482 filtered SNPs, from 68 individuals across nine sites, 27 of which were identified as outliers using BAYESCAN and ARLEQUIN. All outlier loci were potentially under balancing selection, despite previous evidence of local adaptation in the system. Limited gene flow was observed among reef-sites (FST = 0.28 ± 0.10), in line with the low dispersal potential identified by the larval dispersal models. The North Atlantic reef emerged as a distinct population and this was linked to high local larval retention and the effect of the North Atlantic Current on dispersal. CONCLUSIONS As an isolated population, with limited potential for natural genetic or demographic augmentation from other reefs, the North Atlantic site warrants conservation attention in order to preserve not only this species, but above all the crucial functional ecological roles that are associated with their bioconstructions. Our study highlights the utility of using seascape genomics to identify populations of conservation concern.
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Affiliation(s)
- Anna P Muir
- Conservation Biology Research Group, Department of Biological Sciences, University of Chester, Parkgate Road, Chester, CH1 4BJ, UK.
- Laboratoire des Sciences de l'Environnement Marin, LEMAR UMR 6539 CNRS/UBO/IRD/Ifremer, Université de Brest (UBO), Université Européenne de Bretagne (UEB), Institut Universitaire Européen de la Mer (IUEM), 29280, Plouzané, France.
| | - Stanislas F Dubois
- Ifremer, DYNECO, Laboratory of Coastal Benthic Ecology, F-29280, Plouzané, France
| | - Rebecca E Ross
- Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, University of Plymouth, Plymouth, PL4 8AA, UK
- Institute of Marine Research, 1870 Nordnes, 5817, Bergen, Norway
| | - Louise B Firth
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, PL4 8AA, UK
| | - Antony M Knights
- Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, University of Plymouth, Plymouth, PL4 8AA, UK
| | - Fernando P Lima
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Rui Seabra
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Erwan Corre
- CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique de Roscoff, 29680, Roscoff, France
| | - Gildas Le Corguillé
- CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique de Roscoff, 29680, Roscoff, France
| | - Flavia L D Nunes
- Laboratoire des Sciences de l'Environnement Marin, LEMAR UMR 6539 CNRS/UBO/IRD/Ifremer, Université de Brest (UBO), Université Européenne de Bretagne (UEB), Institut Universitaire Européen de la Mer (IUEM), 29280, Plouzané, France
- Ifremer, DYNECO, Laboratory of Coastal Benthic Ecology, F-29280, Plouzané, France
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32
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Individual-based population genomics reveal different drivers of adaptation in sympatric fish. Sci Rep 2020; 10:12683. [PMID: 32728037 PMCID: PMC7391720 DOI: 10.1038/s41598-020-69160-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 07/03/2020] [Indexed: 01/08/2023] Open
Abstract
Connectivity and local adaptation are two contrasting evolutionary forces highly influencing population structure. To evaluate the impact of early-life traits and environmental conditions on genetic structuring and adaptation, we studied two sympatric fish species in the Western Mediterranean Sea: Symphodus tinca and S. ocellatus. We followed an individual-based approach and measured early-life history traits from otolith readings, gathered information on environmental variables and obtained genome-wide markers from genotyping-by-sequencing (GBS). The two species presented contrasting population structure across the same geographic gradient, with high and significant population differentiation in S. ocellatus, mostly determined by oceanographic fronts, and low differentiation and no front effect in S. tinca. Despite their different levels of genetic differentiation, we identified in both species candidate regions for local adaptation by combining outlier analysis with environmental and phenotypic association analyses. Most candidate loci were associated to temperature and productivity in S. ocellatus and to temperature and turbulence in S. tinca suggesting that different drivers may determine genomic diversity and differentiation in each species. Globally, our study highlights that individual-based approach combining genomic, environmental and phenotypic information is key to identify signals of selection and the processes mediating them.
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Fraik AK, Margres MJ, Epstein B, Barbosa S, Jones M, Hendricks S, Schönfeld B, Stahlke AR, Veillet A, Hamede R, McCallum H, Lopez-Contreras E, Kallinen SJ, Hohenlohe PA, Kelley JL, Storfer A. Disease swamps molecular signatures of genetic-environmental associations to abiotic factors in Tasmanian devil (Sarcophilus harrisii) populations. Evolution 2020; 74:1392-1408. [PMID: 32445281 DOI: 10.1111/evo.14023] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 05/14/2020] [Indexed: 12/11/2022]
Abstract
Landscape genomics studies focus on identifying candidate genes under selection via spatial variation in abiotic environmental variables, but rarely by biotic factors (i.e., disease). The Tasmanian devil (Sarcophilus harrisii) is found only on the environmentally heterogeneous island of Tasmania and is threatened with extinction by a transmissible cancer, devil facial tumor disease (DFTD). Devils persist in regions of long-term infection despite epidemiological model predictions of species' extinction, suggesting possible adaptation to DFTD. Here, we test the extent to which spatial variation and genetic diversity are associated with the abiotic environment (i.e., climatic variables, elevation, vegetation cover) and/or DFTD. We employ genetic-environment association analyses using 6886 SNPs from 3287 individuals sampled pre- and post-disease arrival across the devil's geographic range. Pre-disease, we find significant correlations of allele frequencies with environmental variables, including 365 unique loci linked to 71 genes, suggesting local adaptation to abiotic environment. The majority of candidate loci detected pre-DFTD are not detected post-DFTD arrival. Several post-DFTD candidate loci are associated with disease prevalence and were in linkage disequilibrium with genes involved in tumor suppression and immune response. Loss of apparent signal of abiotic local adaptation post-disease suggests swamping by strong selection resulting from the rapid onset of DFTD.
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Affiliation(s)
- Alexandra K Fraik
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
| | - Mark J Margres
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
| | - Brendan Epstein
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164.,Plant Biology, University of Minnesota, Minneapolis, Minnesota, 55455
| | - Soraia Barbosa
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive, Moscow, Idaho, 83844
| | - Menna Jones
- School of Biological Sciences, University of Tasmania, Hobart, TAS, 7004, Australia
| | - Sarah Hendricks
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive, Moscow, Idaho, 83844
| | - Barbara Schönfeld
- School of Biological Sciences, University of Tasmania, Hobart, TAS, 7004, Australia
| | - Amanda R Stahlke
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive, Moscow, Idaho, 83844
| | - Anne Veillet
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive, Moscow, Idaho, 83844
| | - Rodrigo Hamede
- School of Biological Sciences, University of Tasmania, Hobart, TAS, 7004, Australia
| | - Hamish McCallum
- School of Environment, Griffith University Nathan, Nathan, QLD, 4111, Australia
| | - Elisa Lopez-Contreras
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
| | - Samantha J Kallinen
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
| | - Paul A Hohenlohe
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive, Moscow, Idaho, 83844
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
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34
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Fuller J, Ferchaud A, Laporte M, Le Luyer J, Davis TB, Côté SD, Bernatchez L. Absence of founder effect and evidence for adaptive divergence in a recently introduced insular population of white‐tailed deer (
Odocoileus virginianus
). Mol Ecol 2019; 29:86-104. [DOI: 10.1111/mec.15317] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 10/25/2019] [Accepted: 10/29/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Jérémie Fuller
- Département de Biologie Université Laval Québec QC Canada
- Natural Sciences and Engineering Research Council of Canada (NSERC) Research Chair in Integrated Management of the Resources of Anticosti Island and Centre d'Études Nordiques (CEN) Québec QC Canada
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Anne‐Laure Ferchaud
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Martin Laporte
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Jérémy Le Luyer
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | | | - Steeve D. Côté
- Département de Biologie Université Laval Québec QC Canada
- Natural Sciences and Engineering Research Council of Canada (NSERC) Research Chair in Integrated Management of the Resources of Anticosti Island and Centre d'Études Nordiques (CEN) Québec QC Canada
| | - Louis Bernatchez
- Département de Biologie Université Laval Québec QC Canada
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
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35
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Chavarria‐Pizarro T, Gomez JP, Ungvari‐Martin J, Bay R, Miyamoto MM, Kimball R. Strong phenotypic divergence in spite of low genetic structure in the endemic Mangrove Warbler subspecies ( Setophaga petechia xanthotera) of Costa Rica. Ecol Evol 2019; 9:13902-13918. [PMID: 31938490 PMCID: PMC6953683 DOI: 10.1002/ece3.5826] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 10/18/2019] [Indexed: 12/13/2022] Open
Abstract
Despite the enormous advances in genetics, links between phenotypes and genotypes have been made for only a few nonmodel organisms. However, such links can be essential to understand mechanisms of ecological speciation. The Costa Rican endemic Mangrove Warbler subspecies provides an excellent subject to study differentiation with gene flow, as it is distributed along a strong precipitation gradient on the Pacific coast with no strong geographic barriers to isolate populations. Mangrove Warbler populations could be subject to divergent selection driven by precipitation, which influences soil salinity levels, which in turn influences forest structure and food resources. We used single nucleotide polymorphisms (SNPs) and morphological traits to examine the balance between neutral genetic and phenotypic divergence to determine whether selection has acted on traits and genes with functions related to specific environmental variables. We present evidence showing: (a) associations between environmental variables and SNPs, identifying candidate genes related to bill morphology (BMP) and osmoregulation, (b) absence of population genetic structure in neutrally evolving markers, (c) divergence in bill size across the precipitation gradient, and (d) strong phenotypic differentiation (P ST) which largely exceeds neutral genetic differentiation (F ST) in bill size. Our results indicate an important role for salinity, forest structure, and resource availability in maintaining phenotypic divergence of Mangrove Warblers through natural selection. Our findings add to the growing body of literature identifying the processes involved in phenotypic differentiation along environmental gradients in the face of gene flow.
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Affiliation(s)
- Tania Chavarria‐Pizarro
- Department of BiologyUniversity of FloridaGainesvilleFLUSA
- Department of BiologyLudwig Maximilian University of MunichMunichGermany
| | - Juan Pablo Gomez
- Department of BiologyUniversity of FloridaGainesvilleFLUSA
- Departamento de Química y BiologíaUniversidad del NorteBarranquillaColombia
| | | | - Rachael Bay
- Department of Evolution and EcologyUniversity of CaliforniaDavisCAUSA
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36
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Arostegui MC, Quinn TP. Ontogenetic and ecotypic variation in the coloration and morphology of rainbow trout (Oncorhynchus mykiss) in a stream–lake system. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Alternative ecotypes of diverse animal taxa exhibit distinct, habitat-specific phenotypes. Rainbow trout (Oncorhynchus mykiss), a salmonid fish, exhibits stream-resident (fluvial), lake-migrant (adfluvial) and ocean-migrant (anadromous) ecotypes throughout its range. We investigated the coloration, and morphology associated with swimming performance of wild, native non-anadromous rainbow trout in connected stream and lake habitats of a south-west Alaskan watershed to assess if they exhibited phenotypic diversity consistent with the presence of alternative fluvial and adfluvial ecotypes. Colour differences among rainbow trout of different size classes and habitats (stream or lake) indicated ecotype-specific pathways, diverging at the same point in ontogeny and resulting in different terminal coloration patterns. Specifically, lake-caught fish exhibited distinct silvering of the body, whereas stream-caught fish displayed banded coloration when small and bronze colour when larger. The morphology of lake-caught rainbow trout also differed from that of stream-caught fish in features associated with swimming performance, and they exhibited both shared and unique morphological patterns compared to sympatric Salvelinus species in those habitats [Dolly Varden (S. malma) in streams, and Arctic char (S. alpinus) in the lake]. Greater morphological variation within stream- than lake-caught rainbow trout, and their limited overlap in morphology, suggested population-specific partial migration. This study highlights the intraspecific diversity of migratory behaviour and how conservation of particular phenotypes depends on managing both for genotypes and for habitats.
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Affiliation(s)
- M C Arostegui
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - T P Quinn
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
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37
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Looking for Local Adaptation: Convergent Microevolution in Aleppo Pine ( Pinus halepensis). Genes (Basel) 2019; 10:genes10090673. [PMID: 31487909 PMCID: PMC6771008 DOI: 10.3390/genes10090673] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 08/29/2019] [Accepted: 09/03/2019] [Indexed: 01/15/2023] Open
Abstract
Finding outlier loci underlying local adaptation is challenging and is best approached by suitable sampling design and rigorous method selection. In this study, we aimed to detect outlier loci (single nucleotide polymorphisms, SNPs) at the local scale by using Aleppo pine (Pinus halepensis), a drought resistant conifer that has colonized many habitats in the Mediterranean Basin, as the model species. We used a nested sampling approach that considered replicated altitudinal gradients for three contrasting sites. We genotyped samples at 294 SNPs located in genomic regions selected to maximize outlier detection. We then applied three different statistical methodologies-Two Bayesian outlier methods and one latent factor principal component method-To identify outlier loci. No SNP was an outlier for all three methods, while eight SNPs were detected by at least two methods and 17 were detected only by one method. From the intersection of outlier SNPs, only one presented an allelic frequency pattern associated with the elevational gradient across the three sites. In a context of multiple populations under similar selective pressures, our results underline the need for careful examination of outliers detected in genomic scans before considering them as candidates for convergent adaptation.
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38
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Zimmerman SJ, Aldridge CL, Oh KP, Cornman RS, Oyler‐McCance SJ. Signatures of adaptive divergence among populations of an avian species of conservation concern. Evol Appl 2019; 12:1661-1677. [PMID: 31462921 PMCID: PMC6708427 DOI: 10.1111/eva.12825] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 05/23/2019] [Accepted: 05/24/2019] [Indexed: 12/16/2022] Open
Abstract
Understanding the genetic underpinning of adaptive divergence among populations is a key goal of evolutionary biology and conservation. Gunnison sage-grouse (Centrocercus minimus) is a sagebrush obligate species with a constricted range consisting of seven discrete populations, each with distinctly different habitat and climatic conditions. Though geographically close, populations have low levels of natural gene flow resulting in relatively high levels of differentiation. Here, we use 15,033 SNP loci in genomic outlier analyses, genotype-environment association analyses, and gene ontology enrichment tests to examine patterns of putatively adaptive genetic differentiation in an avian species of conservation concern. We found 411 loci within 5 kbp of 289 putative genes associated with biological functions or pathways that were overrepresented in the assemblage of outlier SNPs. The identified gene set was enriched for cytochrome P450 gene family members (CYP4V2, CYP2R1, CYP2C23B, CYP4B1) and could impact metabolism of plant secondary metabolites, a critical challenge for sagebrush obligates. Additionally, the gene set was also enriched with members potentially involved in antiviral response (DEAD box helicase gene family and SETX). Our results provide a first look at local adaption for isolated populations of a single species and suggest adaptive divergence in multiple metabolic and biochemical pathways may be occurring. This information can be useful in managing this species of conservation concern, for example, to identify unique populations to conserve, avoid translocation or release of individuals that may swamp locally adapted genetic diversity, or guide habitat restoration efforts.
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Affiliation(s)
- Shawna J. Zimmerman
- Department of Ecosystem Science and Sustainability and Natural Resource Ecology Laboratory, Colorado State University in Cooperation with U.S. Geological SurveyFort Collins Science CenterFort CollinsColorado
| | - Cameron L. Aldridge
- Department of Ecosystem Science and Sustainability and Natural Resource Ecology Laboratory, Colorado State University in Cooperation with U.S. Geological SurveyFort Collins Science CenterFort CollinsColorado
| | - Kevin P. Oh
- U.S. Geological SurveyFort Collins Science CenterFort CollinsColorado
| | - Robert S. Cornman
- U.S. Geological SurveyFort Collins Science CenterFort CollinsColorado
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39
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Ribeiro ÂM, Puetz L, Pattinson NB, Dalén L, Deng Y, Zhang G, da Fonseca RR, Smit B, Gilbert MTP. 31° South: The physiology of adaptation to arid conditions in a passerine bird. Mol Ecol 2019; 28:3709-3721. [PMID: 31291502 DOI: 10.1111/mec.15176] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 06/21/2019] [Accepted: 06/24/2019] [Indexed: 12/17/2022]
Abstract
Arid environments provide ideal ground for investigating the mechanisms of adaptive evolution. High temperatures and low water availability are relentless stressors for many endotherms, including birds; yet birds persist in deserts. While physiological adaptation probably involves metabolic phenotypes, the underlying mechanisms (plasticity, genetics) are largely uncharacterized. To explore this, we took an intraspecific approach that focused on a species that is resident over a mesic to arid gradient, the Karoo scrub-robin (Cercotrichas coryphaeus). Specifically, we integrated environmental (climatic and primary productivity), physiological (metabolic rates: a measure of energy expenditure), genotypic (genetic variation underlying the machinery of energy production) and microbiome (involved in processing food from where energy is retrieved) data, to infer the mechanism of physiological adaptation. We that found the variation in energetic physiology phenotypes and gut microbiome composition are associated with environmental features as well as with variation in genes underlying energy metabolic pathways. Specifically, we identified a small list of candidate adaptive genes, some of them with known ties to relevant physiology phenotypes. Together our results suggest that selective pressures on energetic physiology mediated by genes related to energy homeostasis and possibly microbiota composition may facilitate adaptation to local conditions and provide an explanation to the high avian intraspecific divergence observed in harsh environments.
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Affiliation(s)
- Ângela M Ribeiro
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Lara Puetz
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Yuan Deng
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen, China.,Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Rute R da Fonseca
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ben Smit
- Department of Zoology, Nelson Mandela University, Port Elizabeth, South Africa.,Department of Zoology and Entomology, Rhodes University, Grahamstown, South Africa
| | - M Thomas P Gilbert
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Norwegian University of Science and Technology, University Museum, Trondheim, Norway
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40
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Smith SP, Phillips JB, Johnson ML, Abbot P, Capra JA, Rokas A. Genome-wide association analysis uncovers variants for reproductive variation across dog breeds and links to domestication. Evol Med Public Health 2019; 2019:93-103. [PMID: 31263560 PMCID: PMC6592264 DOI: 10.1093/emph/eoz015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 05/09/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND AND OBJECTIVES The diversity of eutherian reproductive strategies has led to variation in many traits, such as number of offspring, age of reproductive maturity and gestation length. While reproductive trait variation has been extensively investigated and is well established in mammals, the genetic loci contributing to this variation remain largely unknown. The domestic dog, Canis lupus familiaris is a powerful model for studies of the genetics of inherited disease due to its unique history of domestication. To gain insight into the genetic basis of reproductive traits across domestic dog breeds, we collected phenotypic data for four traits, cesarean section rate, litter size, stillbirth rate and gestation length, from primary literature and breeders' handbooks. METHODOLOGY By matching our phenotypic data to genomic data from the Cornell Veterinary Biobank, we performed genome-wide association analyses for these four reproductive traits, using body mass and kinship among breeds as covariates. RESULTS We identified 12 genome-wide significant associations between these traits and genetic loci, including variants near CACNA2D3 with gestation length, MSRB3 and MSANTD1 with litter size, SMOC2 with cesarean section rate and UFM1 with stillbirth rate. A few of these loci, such as CACNA2D3 and MSRB3, have been previously implicated in human reproductive pathologies, whereas others have been associated with domestication-related traits, including brachycephaly (SMOC2) and coat curl (KRT71). CONCLUSIONS AND IMPLICATIONS We hypothesize that the artificial selection that gave rise to dog breeds also influenced the observed variation in their reproductive traits. Overall, our work establishes the domestic dog as a system for studying the genetics of reproductive biology and disease. LAY SUMMARY The genetic contributors to variation in mammalian reproductive traits remain largely unknown. We took advantage of the domestic dog, a powerful model system, to test for associations between genome-wide variants and four reproductive traits (cesarean section rate, litter size, stillbirth rate and gestation length) that vary extensively across breeds. We identified associations at a dozen loci, including ones previously associated with domestication-related traits, suggesting that selection on dog breeds also influenced their reproductive traits.
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Affiliation(s)
- Samuel P Smith
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37203, USA
- Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA
| | - Julie B Phillips
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37203, USA
- Department of Biological Sciences, Cumberland University, Lebanon, TN 37087, USA
| | - Maddison L Johnson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37203, USA
| | - Patrick Abbot
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37203, USA
| | - John A Capra
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37203, USA
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37203, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37203, USA
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37203, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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41
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Robinson JA, Räikkönen J, Vucetich LM, Vucetich JA, Peterson RO, Lohmueller KE, Wayne RK. Genomic signatures of extensive inbreeding in Isle Royale wolves, a population on the threshold of extinction. SCIENCE ADVANCES 2019; 5:eaau0757. [PMID: 31149628 PMCID: PMC6541468 DOI: 10.1126/sciadv.aau0757] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 04/23/2019] [Indexed: 05/08/2023]
Abstract
The observation that small isolated populations often suffer reduced fitness from inbreeding depression has guided conservation theory and practice for decades. However, investigating the genome-wide dynamics associated with inbreeding depression in natural populations is only now feasible with relatively inexpensive sequencing technology and annotated reference genomes. To characterize the genome-wide effects of intense inbreeding and isolation, we performed whole-genome sequencing and morphological analysis of an iconic inbred population, the gray wolves (Canis lupus) of Isle Royale. Through population genetic simulations and comparison with wolf genomes from a variety of demographic histories, we find evidence that severe inbreeding depression in this population is due to increased homozygosity of strongly deleterious recessive mutations. Our results have particular relevance in light of the recent translocation of wolves from the mainland to Isle Royale, as well as broader implications for management of genetic variation in the fragmented landscape of the modern world.
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Affiliation(s)
- Jacqueline A. Robinson
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
- Corresponding author.
| | - Jannikke Räikkönen
- Department of Environmental Research and Monitoring, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden
| | - Leah M. Vucetich
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - John A. Vucetich
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Rolf O. Peterson
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
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42
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Cavedon M, Gubili C, Heppenheimer E, vonHoldt B, Mariani S, Hebblewhite M, Hegel T, Hervieux D, Serrouya R, Steenweg R, Weckworth BV, Musiani M. Genomics, environment and balancing selection in behaviourally bimodal populations: The caribou case. Mol Ecol 2019; 28:1946-1963. [PMID: 30714247 DOI: 10.1111/mec.15039] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 01/09/2019] [Accepted: 01/23/2019] [Indexed: 02/03/2023]
Abstract
Selection forces that favour different phenotypes in different environments can change frequencies of genes between populations along environmental clines. Clines are also compatible with balancing forces, such as negative frequency-dependent selection (NFDS), which maintains phenotypic polymorphisms within populations. For example, NFDS is hypothesized to maintain partial migration, a dimorphic behavioural trait prominent in species where only a fraction of the population seasonally migrates. Overall, NFDS is believed to be a common phenomenon in nature, yet a scarcity of studies were published linking naturally occurring allelic variation with bimodal or multimodal phenotypes and balancing selection. We applied a Pool-seq approach and detected selection on alleles associated with environmental variables along a North-South gradient in western North American caribou, a species displaying partially migratory behaviour. On 51 loci, we found a signature of balancing selection, which could be related to NFDS and ultimately the maintenance of the phenotypic polymorphisms known within these populations. Yet, remarkably, we detected directional selection on a locus when our sample was divided into two behaviourally distinctive groups regardless of geographic provenance (a subset of GPS-collared migratory or sedentary individuals), indicating that, within populations, phenotypically homogeneous groups were genetically distinctive. Loci under selection were linked to functional genes involved in oxidative stress response, body development and taste perception. Overall, results indicated genetic differentiation along an environmental gradient of caribou populations, which we found characterized by genes potentially undergoing balancing selection. We suggest that the underlining balancing force, NFDS, plays a strong role within populations harbouring multiple haplotypes and phenotypes, as it is the norm in animals, plants and humans too.
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Affiliation(s)
- Maria Cavedon
- Faculty of Environmental Design, University of Calgary, Calgary, Alberta, Canada
| | - Chrysoula Gubili
- Faculty of Environmental Design, University of Calgary, Calgary, Alberta, Canada.,School of Environment and Life Sciences, University of Salford, Salford, UK.,Hellenic Agricultural Organisation, Fisheries Research Institute, Kavala, Greece
| | - Elizabeth Heppenheimer
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, New Jersey
| | - Bridgett vonHoldt
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, New Jersey
| | - Stefano Mariani
- School of Environment and Life Sciences, University of Salford, Salford, UK
| | - Mark Hebblewhite
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, College of Forestry and Conservation, University of Montana, Missoula, Montana
| | - Troy Hegel
- Yukon Department of Environment, Whitehorse, Yukon, Canada
| | - Dave Hervieux
- Resource Management - Operations Division, Alberta Environment and Sustainable Resource Development, Grande Prairie, Alberta, Canada
| | - Robert Serrouya
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Robin Steenweg
- Resource Management - Operations Division, Alberta Environment and Sustainable Resource Development, Grande Prairie, Alberta, Canada
| | | | - Marco Musiani
- Department of Biological Sciences, Faculty of Science and Veterinary Medicine (Joint Appointment), University of Calgary, Calgary, Alberta, Canada
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43
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Smeds L, Kojola I, Ellegren H. The evolutionary history of grey wolf Y chromosomes. Mol Ecol 2019; 28:2173-2191. [PMID: 30788868 PMCID: PMC6850511 DOI: 10.1111/mec.15054] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 02/11/2019] [Accepted: 02/13/2019] [Indexed: 12/30/2022]
Abstract
Analyses of Y chromosome haplotypes uniquely provide a paternal picture of evolutionary histories and offer a very useful contrast to studies based on maternally inherited mitochondrial DNA (mtDNA). Here we used a bioinformatic approach based on comparison of male and female sequence coverage to identify 4.7 Mb from the grey wolf (Canis lupis) Y chromosome, probably representing most of the male-specific, nonampliconic sequence from the euchromatic part of the chromosome. We characterized this sequence and then identified ≈1,500 Y-linked single nucleotide polymorphisms in a sample of 145 resequenced male wolves, including 75 Finnish wolf genomes newly sequenced in this study, and in 24 dogs and eight other canids. We found 53 Y chromosome haplotypes, of which 26 were seen in grey wolves, that clustered in four major haplogroups. All four haplogroups were represented in samples of Finnish wolves, showing that haplogroup lineages were not partitioned on a continental scale. However, regional population structure was indicated because individual haplotypes were never shared between geographically distant areas, and genetically similar haplotypes were only found within the same geographical region. The deepest split between grey wolf haplogroups was estimated to have occurred 125,000 years ago, which is considerably older than recent estimates of the time of divergence of wolf populations. The distribution of dogs in a phylogenetic tree of Y chromosome haplotypes supports multiple domestication events, or wolf paternal introgression, starting 29,000 years ago. We also addressed the disputed origin of a recently founded population of Scandinavian wolves and observed that founding as well as most recent immigrant haplotypes were present in the neighbouring Finnish population, but not in sequenced wolves from elsewhere in the world, or in dogs.
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Affiliation(s)
- Linnéa Smeds
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Ilpo Kojola
- Natural Resources Institute Finland (Luke), Rovaniemi, Finland
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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44
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Schweizer RM, Durvasula A, Smith J, Vohr SH, Stahler DR, Galaverni M, Thalmann O, Smith DW, Randi E, Ostrander EA, Green RE, Lohmueller KE, Novembre J, Wayne RK. Natural Selection and Origin of a Melanistic Allele in North American Gray Wolves. Mol Biol Evol 2019; 35:1190-1209. [PMID: 29688543 DOI: 10.1093/molbev/msy031] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Pigmentation is often used to understand how natural selection affects genetic variation in wild populations since it can have a simple genetic basis, and can affect a variety of fitness-related traits (e.g., camouflage, thermoregulation, and sexual display). In gray wolves, the K locus, a β-defensin gene, causes black coat color via a dominantly inherited KB allele. The allele is derived from dog-wolf hybridization and is at high frequency in North American wolf populations. We designed a DNA capture array to probe the geographic origin, age, and number of introgression events of the KB allele in a panel of 331 wolves and 20 dogs. We found low diversity in KB, but not ancestral ky, wolf haplotypes consistent with a selective sweep of the black haplotype across North America. Further, North American wolf KB haplotypes are monophyletic, suggesting that a single adaptive introgression from dogs to wolves most likely occurred in the Northwest Territories or Yukon. We use a new analytical approach to date the origin of the KB allele in Yukon wolves to between 1,598 and 7,248 years ago, suggesting that introgression with early Native American dogs was the source. Using population genetic simulations, we show that the K locus is undergoing natural selection in four wolf populations. We find evidence for balancing selection, specifically in Yellowstone wolves, which could be a result of selection for enhanced immunity in response to distemper. With these data, we demonstrate how the spread of an adaptive variant may have occurred across a species' geographic range.
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Affiliation(s)
- Rena M Schweizer
- Division of Biological Sciences, University of Montana, Missoula, MT.,Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA
| | - Arun Durvasula
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA
| | - Joel Smith
- Department of Ecology and Evolution, University of Chicago, Chicago, IL
| | - Samuel H Vohr
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA
| | - Daniel R Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, WY
| | | | - Olaf Thalmann
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Douglas W Smith
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, WY
| | - Ettore Randi
- Department of Biology, University of Bologna, Bologna, Italy.,Department of Chemistry and Bioscience, Faculty of Engineering and Science, University of Aalborg, Aalborg, Denmark
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA
| | - John Novembre
- Department of Ecology and Evolution, University of Chicago, Chicago, IL.,Department of Human Genetics, University of Chicago, IL
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA
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45
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Hendricks SA, Schweizer RM, Harrigan RJ, Pollinger JP, Paquet PC, Darimont CT, Adams JR, Waits LP, vonHoldt BM, Hohenlohe PA, Wayne RK. Natural re-colonization and admixture of wolves (Canis lupus) in the US Pacific Northwest: challenges for the protection and management of rare and endangered taxa. Heredity (Edinb) 2019; 122:133-149. [PMID: 29880893 PMCID: PMC6327037 DOI: 10.1038/s41437-018-0094-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 04/20/2018] [Accepted: 04/22/2018] [Indexed: 12/30/2022] Open
Abstract
Admixture resulting from natural dispersal processes can potentially generate novel phenotypic variation that may facilitate persistence in changing environments or result in the loss of population-specific adaptations. Yet, under the US Endangered Species Act, policy is limited for management of individuals whose ancestry includes a protected taxon; therefore, they are generally not protected under the Act. This issue is exemplified by the recently re-established grey wolves of the Pacific Northwest states of Washington and Oregon, USA. This population was likely founded by two phenotypically and genetically distinct wolf ecotypes: Northern Rocky Mountain (NRM) forest and coastal rainforest. The latter is considered potentially threatened in southeast Alaska and thus the source of migrants may affect plans for their protection. To assess the genetic source of the re-established population, we sequenced a ~ 300 bp portion of the mitochondrial control region and ~ 5 Mbp of the nuclear genome. Genetic analysis revealed that the Washington wolves share ancestry with both wolf ecotypes, whereas the Oregon population shares ancestry with NRM forest wolves only. Using ecological niche modelling, we found that the Pacific Northwest states contain environments suitable for each ecotype, with wolf packs established in both environmental types. Continued migration from coastal rainforest and NRM forest source populations may increase the genetic diversity of the Pacific Northwest population. However, this admixed population challenges traditional management regimes given that admixture occurs between an adaptively distinct ecotype and a more abundant reintroduced interior form. Our results emphasize the need for a more precise US policy to address the general problem of admixture in the management of endangered species, subspecies, and distinct population segments.
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Affiliation(s)
- Sarah A Hendricks
- Department of Biological Sciences and Institute of Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive, Moscow, ID, 83844, USA.
| | - Rena M Schweizer
- Division of Biological Sciences, University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA
| | - Ryan J Harrigan
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, 300 LaKretz Hall, Los Angeles, CA, 90095, USA
| | - John P Pollinger
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, 300 LaKretz Hall, Los Angeles, CA, 90095, USA
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA, 90095, USA
| | - Paul C Paquet
- Raincoast Conservation Foundation, Sidney, BC, V8L 3Y3, Canada
- Department of Geography, University of Victoria, Box 1700, Stn CSC, Victoria, BC, V8W 2Y2, Canada
| | - Chris T Darimont
- Raincoast Conservation Foundation, Sidney, BC, V8L 3Y3, Canada
- Department of Geography, University of Victoria, Box 1700, Stn CSC, Victoria, BC, V8W 2Y2, Canada
| | - Jennifer R Adams
- Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive, Moscow, ID, 83844, USA
| | - Lisette P Waits
- Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive, Moscow, ID, 83844, USA
| | - Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, M151 Guyot Hall, Princeton, NJ, 08544, USA
| | - Paul A Hohenlohe
- Department of Biological Sciences and Institute of Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive, Moscow, ID, 83844, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA, 90095, USA
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46
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Stronen AV, Iacolina L, Ruiz-Gonzalez A. Rewilding and conservation genomics: How developments in (re)colonization ecology and genomics can offer mutual benefits for understanding contemporary evolution. Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2018.e00502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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47
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Population genomics of grey wolves and wolf-like canids in North America. PLoS Genet 2018; 14:e1007745. [PMID: 30419012 PMCID: PMC6231604 DOI: 10.1371/journal.pgen.1007745] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 10/06/2018] [Indexed: 12/30/2022] Open
Abstract
North America is currently home to a number of grey wolf (Canis lupus) and wolf-like canid populations, including the coyote (Canis latrans) and the taxonomically controversial red, Eastern timber and Great Lakes wolves. We explored their population structure and regional gene flow using a dataset of 40 full genome sequences that represent the extant diversity of North American wolves and wolf-like canid populations. This included 15 new genomes (13 North American grey wolves, 1 red wolf and 1 Eastern timber/Great Lakes wolf), ranging from 0.4 to 15x coverage. In addition to providing full genome support for the previously proposed coyote-wolf admixture origin for the taxonomically controversial red, Eastern timber and Great Lakes wolves, the discriminatory power offered by our dataset suggests all North American grey wolves, including the Mexican form, are monophyletic, and thus share a common ancestor to the exclusion of all other wolves. Furthermore, we identify three distinct populations in the high arctic, one being a previously unidentified "Polar wolf" population endemic to Ellesmere Island and Greenland. Genetic diversity analyses reveal particularly high inbreeding and low heterozygosity in these Polar wolves, consistent with long-term isolation from the other North American wolves.
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48
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Hendricks SA, Schweizer RM, Wayne RK. Conservation genomics illuminates the adaptive uniqueness of North American gray wolves. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1118-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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49
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Caniglia R, Fabbri E, Hulva P, Bolfíková BČ, Jindřichová M, Stronen AV, Dykyy I, Camatta A, Carnier P, Randi E, Galaverni M. Wolf outside, dog inside? The genomic make-up of the Czechoslovakian Wolfdog. BMC Genomics 2018; 19:533. [PMID: 30005602 PMCID: PMC6043967 DOI: 10.1186/s12864-018-4916-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 07/02/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Genomic methods can provide extraordinary tools to explore the genetic background of wild species and domestic breeds, optimize breeding practices, monitor and limit the spread of recessive diseases, and discourage illegal crossings. In this study we analysed a panel of 170k Single Nucleotide Polymorphisms with a combination of multivariate, Bayesian and outlier gene approaches to examine the genome-wide diversity and inbreeding levels in a recent wolf x dog cross-breed, the Czechoslovakian Wolfdog, which is becoming increasingly popular across Europe. RESULTS Pairwise FST values, multivariate and assignment procedures indicated that the Czechoslovakian Wolfdog was significantly differentiated from all the other analysed breeds and also well-distinguished from both parental populations (Carpathian wolves and German Shepherds). Coherently with the low number of founders involved in the breed selection, the individual inbreeding levels calculated from homozygosity regions were relatively high and comparable with those derived from the pedigree data. In contrast, the coefficient of relatedness between individuals estimated from the pedigrees often underestimated the identity-by-descent scores determined using genetic profiles. The timing of the admixture and the effective population size trends estimated from the LD patterns reflected the documented history of the breed. Ancestry reconstruction methods identified more than 300 genes with excess of wolf ancestry compared to random expectations, mainly related to key morphological features, and more than 2000 genes with excess of dog ancestry, playing important roles in lipid metabolism, in the regulation of circadian rhythms, in learning and memory processes, and in sociability, such as the COMT gene, which has been described as a candidate gene for the latter trait in dogs. CONCLUSIONS In this study we successfully applied genome-wide procedures to reconstruct the history of the Czechoslovakian Wolfdog, assess individual wolf ancestry proportions and, thanks to the availability of a well-annotated reference genome, identify possible candidate genes for wolf-like and dog-like phenotypic traits typical of this breed, including commonly inherited disorders. Moreover, through the identification of ancestry-informative markers, these genomic approaches could provide tools for forensic applications to unmask illegal crossings with wolves and uncontrolled trades of recent and undeclared wolfdog hybrids.
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Affiliation(s)
- Romolo Caniglia
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell’Emilia, Bologna, Italy
| | - Elena Fabbri
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell’Emilia, Bologna, Italy
| | - Pavel Hulva
- Department of Zoology, Charles University in Prague, Prague, Czech Republic
- Department of Biology and Ecology, Ostrava University, Ostrava, Czech Republic
| | - Barbora Černá Bolfíková
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Milena Jindřichová
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Astrid Vik Stronen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg Øst, Denmark
| | - Ihor Dykyy
- Department of Zoology, Ivan Franko National University of Lviv, Lviv, Ukraine
| | | | - Paolo Carnier
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy
| | - Ettore Randi
- Dipartimento BIGEA, Università di Bologna, Bologna, Italy
- Department 18/ Section of Environmental Engineering, Aalborg University, Aalborg Øst, Denmark
| | - Marco Galaverni
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell’Emilia, Bologna, Italy
- Area Conservazione, WWF Italia, Rome, Italy
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50
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Nigenda‐Morales SF, Hu Y, Beasley JC, Ruiz‐Piña HA, Valenzuela‐Galván D, Wayne RK. Transcriptomic analysis of skin pigmentation variation in the Virginia opossum (
Didelphis virginiana
). Mol Ecol 2018; 27:2680-2697. [DOI: 10.1111/mec.14712] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 04/05/2018] [Accepted: 04/17/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Sergio F. Nigenda‐Morales
- Department of Ecology and Evolutionary Biology University of California, Los Angeles Los Angeles California
| | - Yibo Hu
- Key Lab of Animal Ecology and Conservation Biology Institute of Zoology Chinese Academy of Sciences Chaoyang, Beijing China
| | - James C. Beasley
- Savannah River Ecology Lab Warnell School of Forestry and Natural Resources University of Georgia Aiken South Carolina
| | - Hugo A. Ruiz‐Piña
- Centro de Investigaciones Regionales “Dr. Hideyo Noguchi” Universidad Autónoma de Yucatán Mérida Yucatán Mexico
| | - David Valenzuela‐Galván
- Departamento de Ecología Evolutiva Centro de Investigación en Biodiversidad y Conservación Universidad Autónoma del Estado de Morelos Cuernavaca Morelos Mexico
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology University of California, Los Angeles Los Angeles California
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