1
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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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2
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Veilleux CC, Garrett EC, Pajic P, Saitou M, Ochieng J, Dagsaan LD, Dominy NJ, Perry GH, Gokcumen O, Melin AD. Human subsistence and signatures of selection on chemosensory genes. Commun Biol 2023; 6:683. [PMID: 37400713 DOI: 10.1038/s42003-023-05047-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/15/2023] [Indexed: 07/05/2023] Open
Abstract
Chemosensation (olfaction, taste) is essential for detecting and assessing foods, such that dietary shifts elicit evolutionary changes in vertebrate chemosensory genes. The transition from hunting and gathering to agriculture dramatically altered how humans acquire food. Recent genetic and linguistic studies suggest agriculture may have precipitated olfactory degeneration. Here, we explore the effects of subsistence behaviors on olfactory (OR) and taste (TASR) receptor genes among rainforest foragers and neighboring agriculturalists in Africa and Southeast Asia. We analyze 378 functional OR and 26 functional TASR genes in 133 individuals across populations in Uganda (Twa, Sua, BaKiga) and the Philippines (Agta, Mamanwa, Manobo) with differing subsistence histories. We find no evidence of relaxed selection on chemosensory genes in agricultural populations. However, we identify subsistence-related signatures of local adaptation on chemosensory genes within each geographic region. Our results highlight the importance of culture, subsistence economy, and drift in human chemosensory perception.
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Affiliation(s)
- Carrie C Veilleux
- Department of Anatomy, Midwestern University, 19555 N 59th Ave, Glendale, AZ, 85308, USA.
- Department of Anthropology & Archaeology, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada.
| | - Eva C Garrett
- Department of Anthropology & Archaeology, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada
- Department of Anthropology, Boston University, 232 Bay State Road, Boston, MA, 02215, USA
| | - Petar Pajic
- Department of Biological Sciences, University at Buffalo, 109 Cooke Hall, Buffalo, NY, 14260, USA
| | - Marie Saitou
- Department of Biological Sciences, University at Buffalo, 109 Cooke Hall, Buffalo, NY, 14260, USA
| | - Joseph Ochieng
- Department of Anatomy, Makerere University College of Health Sciences, Kampala, Uganda
| | - Lilia D Dagsaan
- National Commission for Indigenous Peoples, Botolan, Philippines
| | - Nathaniel J Dominy
- Department of Anthropology, Dartmouth College, 6047 Silsby Hall, Hanover, NH, 03755, USA
| | - George H Perry
- Departments of Anthropology and Biology, The Pennsylvania State University, 410 Carpenter Building, University Park, PA, 16802, USA
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, 109 Cooke Hall, Buffalo, NY, 14260, USA
| | - Amanda D Melin
- Department of Anthropology & Archaeology, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada.
- Department of Medical Genetics, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada.
- Alberta Children's Hospital Research Institute, 3330 Hospital Dr. NW, Calgary, AB, T2N 4N1, Canada.
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3
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Barash A, Preiss-Bloom S, Machluf Y, Fabbri E, Malkinson D, Velli E, Mucci N, Barash A, Caniglia R, Dayan T, Dekel Y. Possible origins and implications of atypical morphologies and domestication-like traits in wild golden jackals (Canis aureus). Sci Rep 2023; 13:7388. [PMID: 37149712 PMCID: PMC10164184 DOI: 10.1038/s41598-023-34533-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 05/03/2023] [Indexed: 05/08/2023] Open
Abstract
Deciphering the origins of phenotypic variations in natural animal populations is a challenging topic for evolutionary and conservation biologists. Atypical morphologies in mammals are usually attributed to interspecific hybridisation or de-novo mutations. Here we report the case of four golden jackals (Canis aureus), that were observed during a camera-trapping wildlife survey in Northern Israel, displaying anomalous morphological traits, such as white patches, an upturned tail, and long thick fur which resemble features of domesticated mammals. Another individual was culled under permit and was genetically and morphologically examined. Paternal and nuclear genetic profiles, as well as geometric morphometric data, identified this individual as a golden jackal rather than a recent dog/wolf-jackal hybrid. Its maternal haplotype suggested past introgression of African wolf (Canis lupaster) mitochondrial DNA, as previously documented in other jackals from Israel. When viewed in the context of the jackal as an overabundant species in Israel, the rural nature of the surveyed area, the abundance of anthropogenic waste, and molecular and morphological findings, the possibility of an individual presenting incipient stages of domestication should also be considered.
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Affiliation(s)
- Ayelet Barash
- School of Zoology and The Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv, Israel
- Unit of Agrigenomics, Shamir Research Institute, University of Haifa, 1290000, Kazerin, Israel
| | - Shlomo Preiss-Bloom
- School of Zoology and The Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv, Israel
| | - Yossy Machluf
- Unit of Agrigenomics, Shamir Research Institute, University of Haifa, 1290000, Kazerin, Israel
| | - Elena Fabbri
- Unit for Conservation Genetics (BIO‑CGE), Italian Institute for Environmental Protection and Research (ISPRA), Via Cà Fornacetta 9, Ozzano dell'Emilia, 40064, Bologna, Italy
| | - Dan Malkinson
- Department of Geography and Environmental Studies, University of Haifa, 3498838, Haifa, Israel
| | - Edoardo Velli
- Unit for Conservation Genetics (BIO‑CGE), Italian Institute for Environmental Protection and Research (ISPRA), Via Cà Fornacetta 9, Ozzano dell'Emilia, 40064, Bologna, Italy
| | - Nadia Mucci
- Unit for Conservation Genetics (BIO‑CGE), Italian Institute for Environmental Protection and Research (ISPRA), Via Cà Fornacetta 9, Ozzano dell'Emilia, 40064, Bologna, Italy
| | - Alon Barash
- The Azrieli Faculty of Medicine, Bar Ilan University, 8 Henrietta Szold St, Safed, Israel
| | - Romolo Caniglia
- Unit for Conservation Genetics (BIO‑CGE), Italian Institute for Environmental Protection and Research (ISPRA), Via Cà Fornacetta 9, Ozzano dell'Emilia, 40064, Bologna, Italy.
| | - Tamar Dayan
- School of Zoology and The Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv, Israel.
| | - Yaron Dekel
- Unit of Agrigenomics, Shamir Research Institute, University of Haifa, 1290000, Kazerin, Israel.
- The Cheryl Spencer Department of Nursing and The Cheryl Spencer Institute of Nursing Research, University of Haifa, 3498838, Haifa, Israel.
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4
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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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5
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Exposito-Alonso M, Booker TR, Czech L, Gillespie L, Hateley S, Kyriazis CC, Lang PLM, Leventhal L, Nogues-Bravo D, Pagowski V, Ruffley M, Spence JP, Toro Arana SE, Weiß CL, Zess E. Genetic diversity loss in the Anthropocene. Science 2022; 377:1431-1435. [PMID: 36137047 DOI: 10.1126/science.abn5642] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Anthropogenic habitat loss and climate change are reducing species' geographic ranges, increasing extinction risk and losses of species' genetic diversity. Although preserving genetic diversity is key to maintaining species' adaptability, we lack predictive tools and global estimates of genetic diversity loss across ecosystems. We introduce a mathematical framework that bridges biodiversity theory and population genetics to understand the loss of naturally occurring DNA mutations with decreasing habitat. By analyzing genomic variation of 10,095 georeferenced individuals from 20 plant and animal species, we show that genome-wide diversity follows a mutations-area relationship power law with geographic area, which can predict genetic diversity loss from local population extinctions. We estimate that more than 10% of genetic diversity may already be lost for many threatened and nonthreatened species, surpassing the United Nations' post-2020 targets for genetic preservation.
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Affiliation(s)
- Moises Exposito-Alonso
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA.,Department of Biology, Stanford University, Stanford, CA 94305, USA.,Department of Global Ecology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Tom R Booker
- Department of Zoology, University of British Columbia, Vancouver, Canada.,Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Lucas Czech
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Lauren Gillespie
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA.,Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Shannon Hateley
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Christopher C Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | | | - Laura Leventhal
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA.,Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - David Nogues-Bravo
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Megan Ruffley
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Jeffrey P Spence
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Sebastian E Toro Arana
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA.,Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Clemens L Weiß
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Erin Zess
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
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6
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Hendricks SA, King JL, Duncan CL, Vickers W, Hohenlohe PA, Davis BW. Genomic Assessment of Cancer Susceptibility in the Threatened Catalina Island Fox ( Urocyon littoralis catalinae). Genes (Basel) 2022; 13:1496. [PMID: 36011407 PMCID: PMC9408614 DOI: 10.3390/genes13081496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/12/2022] [Accepted: 08/12/2022] [Indexed: 12/12/2022] Open
Abstract
Small effective population sizes raise the probability of extinction by increasing the frequency of potentially deleterious alleles and reducing fitness. However, the extent to which cancers play a role in the fitness reduction of genetically depauperate wildlife populations is unknown. Santa Catalina island foxes (Urocyon littoralis catalinae) sampled in 2007-2008 have a high prevalence of ceruminous gland tumors, which was not detected in the population prior to a recent bottleneck caused by a canine distemper epidemic. The disease appears to be associated with inflammation from chronic ear mite (Otodectes) infections and secondary elevated levels of Staphyloccus pseudointermedius bacterial infections. However, no other environmental factors to date have been found to be associated with elevated cancer risk in this population. Here, we used whole genome sequencing of the case and control individuals from two islands to identify candidate loci associated with cancer based on genetic divergence, nucleotide diversity, allele frequency spectrum, and runs of homozygosity. We identified several candidate loci based on genomic signatures and putative gene functions, suggesting that cancer susceptibility in this population may be polygenic. Due to the efforts of a recovery program and weak fitness effects of late-onset disease, the population size has increased, which may allow selection to be more effective in removing these presumably slightly deleterious alleles. Long-term monitoring of the disease alleles, as well as overall genetic diversity, will provide crucial information for the long-term persistence of this threatened population.
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Affiliation(s)
- Sarah A. Hendricks
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Julie L. King
- Catalina Island Conservancy, P.O. Box 2739, Avalon, CA 90704, USA
| | - Calvin L. Duncan
- Catalina Island Conservancy, P.O. Box 2739, Avalon, CA 90704, USA
| | - Winston Vickers
- Institute for Wildlife Studies, Arcata, CA 95521, USA
- Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Paul A. Hohenlohe
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID 83844, USA
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Brian W. Davis
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Science, Texas A&M University, College Station, TX 77840, USA
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Science, Texas A&M University, College Station, TX 77840, USA
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7
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AKHTAR MUHAMMADSHOAIB, ASHINO RYUICHI, OOTA HIROKI, ISHIDA HAJIME, NIIMURA YOSHIHITO, TOUHARA KAZUSHIGE, MELIN AMANDAD, KAWAMURA SHOJI. Genetic variation of olfactory receptor gene family in a Japanese population. ANTHROPOL SCI 2022. [DOI: 10.1537/ase.211024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- MUHAMMAD SHOAIB AKHTAR
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa
| | - RYUICHI ASHINO
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa
| | - HIROKI OOTA
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo
| | - HAJIME ISHIDA
- Department of Human Biology and Anatomy, Faculty of Medicine, University of the Ryukyus, Nishihara
| | - YOSHIHITO NIIMURA
- Department of Veterinary Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki
| | - KAZUSHIGE TOUHARA
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo
| | - AMANDA D. MELIN
- Department of Anthropology and Archaeology & Department of Medical Genetics, University of Calgary, Calgary
| | - SHOJI KAWAMURA
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa
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8
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Schweizer RM, Jones MR, Bradburd GS, Storz JF, Senner NR, Wolf C, Cheviron ZA. Broad Concordance in the Spatial Distribution of Adaptive and Neutral Genetic Variation across an Elevational Gradient in Deer Mice. Mol Biol Evol 2021; 38:4286-4300. [PMID: 34037784 PMCID: PMC8476156 DOI: 10.1093/molbev/msab161] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
When species are continuously distributed across environmental gradients, the relative strength of selection and gene flow shape spatial patterns of genetic variation, potentially leading to variable levels of differentiation across loci. Determining whether adaptive genetic variation tends to be structured differently than neutral variation along environmental gradients is an open and important question in evolutionary genetics. We performed exome-wide population genomic analysis on deer mice sampled along an elevational gradient of nearly 4,000 m of vertical relief. Using a combination of selection scans, genotype-environment associations, and geographic cline analyses, we found that a large proportion of the exome has experienced a history of altitude-related selection. Elevational clines for nearly 30% of these putatively adaptive loci were shifted significantly up- or downslope of clines for loci that did not bear similar signatures of selection. Many of these selection targets can be plausibly linked to known phenotypic differences between highland and lowland deer mice, although the vast majority of these candidates have not been reported in other studies of highland taxa. Together, these results suggest new hypotheses about the genetic basis of physiological adaptation to high altitude, and the spatial distribution of adaptive genetic variation along environmental gradients.
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Affiliation(s)
- Rena M Schweizer
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Matthew R Jones
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
- Southwest Biological Science Center, U.S. Geological Survey, Flagstaff, AZ, USA
| | - Gideon S Bradburd
- Ecology, Evolution, and Behavior Program, Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Nathan R Senner
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Cole Wolf
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Zachary A Cheviron
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
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9
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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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10
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Marcinek P, Haag F, Geithe C, Krautwurst D. An evolutionary conserved olfactory receptor for foodborne and semiochemical alkylpyrazines. FASEB J 2021; 35:e21638. [PMID: 34047404 DOI: 10.1096/fj.202100224r] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/09/2021] [Accepted: 04/15/2021] [Indexed: 12/11/2022]
Abstract
Molecular recognition is a fundamental principle in biological systems. The olfactory detection of both food and predators via ecological relevant odorant cues are abilities of eminent evolutionary significance for many species. Pyrazines are such volatile cues, some of which act as both human-centered key food odorants (KFOs) and semiochemicals. A pyrazine-selective odorant receptor has been elusive. Here we screened 2,3,5-trimethylpyrazine, a KFO and semiochemical, and 2,5-dihydro-2,4,5-trimethylthiazoline, an innate fear-associated non-KFO, against 616 human odorant receptor variants, in a cell-based luminescence assay. OR5K1 emerged as sole responding receptor. Tested against a comprehensive collection of 178 KFOs, we newly identified 18 pyrazines and (2R/2S)-4-methoxy-2,5-dimethylfuran-3(2H)-one as agonists. Notably, OR5K1 orthologs in mouse and domesticated species displayed a human-like, potency-ranked activation pattern of pyrazines, suggesting a domestication-led co-evolution of OR5K1 and its orthologs. In summary, OR5K1 is a specialized olfactory receptor across mammals for the detection of pyrazine-based key food odors and semiochemicals.
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Affiliation(s)
- Patrick Marcinek
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany.,Hamilton Germany GmbH, Gräfelfing, Germany
| | - Franziska Haag
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
| | - Christiane Geithe
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany.,Brandenburg University of Technology Cottbus - Senftenberg, Senftenberg, Germany
| | - Dietmar Krautwurst
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
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11
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Stahlke A, Bell D, Dhendup T, Kern B, Pannoni S, Robinson Z, Strait J, Smith S, Hand BK, Hohenlohe PA, Luikart G. Population Genomics Training for the Next Generation of Conservation Geneticists: ConGen 2018 Workshop. J Hered 2021; 111:227-236. [PMID: 32037446 PMCID: PMC7117792 DOI: 10.1093/jhered/esaa001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 01/06/2020] [Indexed: 12/30/2022] Open
Abstract
The increasing availability and complexity of next-generation sequencing (NGS) data sets make ongoing training an essential component of conservation and population genetics research. A workshop entitled “ConGen 2018” was recently held to train researchers in conceptual and practical aspects of NGS data production and analysis for conservation and ecological applications. Sixteen instructors provided helpful lectures, discussions, and hands-on exercises regarding how to plan, produce, and analyze data for many important research questions. Lecture topics ranged from understanding probabilistic (e.g., Bayesian) genotype calling to the detection of local adaptation signatures from genomic, transcriptomic, and epigenomic data. We report on progress in addressing central questions of conservation genomics, advances in NGS data analysis, the potential for genomic tools to assess adaptive capacity, and strategies for training the next generation of conservation genomicists.
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Affiliation(s)
- Amanda Stahlke
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
| | - Donavan Bell
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT
| | - Tashi Dhendup
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT.,Department of Forest and Park Services, Ugyen Wangchuck Institute for Conservation and Environmental Research, Bumthang, Bhutan
| | - Brooke Kern
- Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT.,Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN
| | - Samuel Pannoni
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT.,Flathead Lake Biological Station, Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT
| | - Zachary Robinson
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT
| | - Jeffrey Strait
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT
| | - Seth Smith
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT.,Flathead Lake Biological Station, Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT.,Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI
| | - Brian K Hand
- Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT.,Flathead Lake Biological Station, Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT
| | - Paul A Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
| | - Gordon Luikart
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT.,Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT.,Flathead Lake Biological Station, Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT
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12
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Schweizer RM, Saarman N, Ramstad KM, Forester BR, Kelley JL, Hand BK, Malison RL, Ackiss AS, Watsa M, Nelson TC, Beja-Pereira A, Waples RS, Funk WC, Luikart G. Big Data in Conservation Genomics: Boosting Skills, Hedging Bets, and Staying Current in the Field. J Hered 2021; 112:313-327. [PMID: 33860294 DOI: 10.1093/jhered/esab019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 04/13/2021] [Indexed: 02/07/2023] Open
Abstract
A current challenge in the fields of evolutionary, ecological, and conservation genomics is balancing production of large-scale datasets with additional training often required to handle such datasets. Thus, there is an increasing need for conservation geneticists to continually learn and train to stay up-to-date through avenues such as symposia, meetings, and workshops. The ConGen meeting is a near-annual workshop that strives to guide participants in understanding population genetics principles, study design, data processing, analysis, interpretation, and applications to real-world conservation issues. Each year of ConGen gathers a diverse set of instructors, students, and resulting lectures, hands-on sessions, and discussions. Here, we summarize key lessons learned from the 2019 meeting and more recent updates to the field with a focus on big data in conservation genomics. First, we highlight classical and contemporary issues in study design that are especially relevant to working with big datasets, including the intricacies of data filtering. We next emphasize the importance of building analytical skills and simulating data, and how these skills have applications within and outside of conservation genetics careers. We also highlight recent technological advances and novel applications to conservation of wild populations. Finally, we provide data and recommendations to support ongoing efforts by ConGen organizers and instructors-and beyond-to increase participation of underrepresented minorities in conservation and eco-evolutionary sciences. The future success of conservation genetics requires both continual training in handling big data and a diverse group of people and approaches to tackle key issues, including the global biodiversity-loss crisis.
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Affiliation(s)
- Rena M Schweizer
- Division of Biological Sciences, University of Montana, Missoula, MT
| | - Norah Saarman
- Department of Biology, Utah State University, Logan, UT
| | - Kristina M Ramstad
- Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC
| | | | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA
| | - Brian K Hand
- Division of Biological Sciences, University of Montana, Missoula, MT.,Flathead Lake Biological Station, University of Montana, Polson, MT
| | - Rachel L Malison
- Flathead Lake Biological Station, University of Montana, Polson, MT
| | - Amanda S Ackiss
- Wisconsin Cooperative Fishery Research Unit, University of Wisconsin Stevens Point, Stevens Point, WI
| | | | | | - Albano Beja-Pereira
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-UP), InBIO, Universidade do Porto, Vairão, Portugal.,DGAOT, Faculty of Sciences, University of Porto, Porto, Portugal.,Sustainable Agrifood Production Research Centre (GreenUPorto), Faculty of Sciences, University of Porto, Porto, Portugal
| | - Robin S Waples
- Northwest Fisheries Science Center, NOAA Fisheries, Seattle, WA
| | - W Chris Funk
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO
| | - Gordon Luikart
- Division of Biological Sciences, University of Montana, Missoula, MT.,Flathead Lake Biological Station, University of Montana, Polson, MT
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13
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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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14
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Hofmeister NR, Werner SJ, Lovette IJ. Environmental correlates of genetic variation in the invasive European starling in North America. Mol Ecol 2021; 30:1251-1263. [PMID: 33464634 DOI: 10.1111/mec.15806] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 12/17/2020] [Accepted: 01/04/2021] [Indexed: 12/31/2022]
Abstract
Populations of invasive species that colonize and spread in novel environments may differentiate both through demographic processes and local selection. European starlings (Sturnus vulgaris) were introduced to New York in 1890 and subsequently spread throughout North America, becoming one of the most widespread and numerous bird species on the continent. Genome-wide comparisons across starling individuals and populations can identify demographic and/or selective factors that facilitated this rapid and successful expansion. We investigated patterns of genomic diversity and differentiation using reduced-representation genome sequencing of 17 winter-season sampling sites. Consistent with this species' high dispersal rate and rapid expansion history, we found low geographical differentiation and few FST outliers even at a continental scale. Despite starting from a founding population of ~180 individuals, North American starlings show only a moderate genetic bottleneck, and models suggest a dramatic increase in effective population size since introduction. In genotype-environment associations we found that ~200 single-nucleotide polymorphisms are correlated with temperature and/or precipitation against a background of negligible genome- and range-wide divergence. Given this evidence, we suggest that local adaptation in North American starlings may have evolved rapidly even in this wide-ranging and evolutionarily young system. This survey of genomic signatures of expansion in North American starlings is the most comprehensive to date and complements ongoing studies of world-wide local adaptation in these highly dispersive and invasive birds.
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Affiliation(s)
- Natalie R Hofmeister
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.,Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, USA
| | - Scott J Werner
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, CO, USA
| | - Irby J Lovette
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.,Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, USA
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15
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Heppenheimer E, Brzeski KE, Hinton JW, Chamberlain MJ, Robinson J, Wayne RK, vonHoldt BM. A Genome-Wide Perspective on the Persistence of Red Wolf Ancestry in Southeastern Canids. J Hered 2020; 111:277-286. [DOI: 10.1093/jhered/esaa006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 02/21/2020] [Indexed: 02/06/2023] Open
Abstract
Abstract
The red wolf (Canis rufus), a legally recognized and critically endangered wolf, is known to interbreed with coyotes (Canis latrans). Declared extirpated in the wild in 1980, red wolves were reintroduced to northeastern North Carolina nearly a decade later. Interbreeding with coyotes was thought to be restricted to a narrow geographic region adjacent to the reintroduced population and largely believed to threaten red wolf recovery. However, red wolf ancestry was recently discovered in canids along the American Gulf Coast, igniting a broader survey of ancestry in southeastern canid populations. Here, we examine geographic and temporal patterns of genome-wide red wolf ancestry in 260 canids across the southeastern United States at over 164 000 SNP loci. We found that red wolf ancestry was most prevalent in canids sampled from Texas in the mid-1970s, although non-trivial amounts of red wolf ancestry persist in this region today. Further, red wolf ancestry was also observed in a subset of coyotes inhabiting North Carolina, despite management efforts to limit the occurrence of hybridization events. Lastly, we found no evidence of substantial red wolf ancestry in southeastern canids outside of these 2 admixture zones. Overall, this study provides a genome-wide survey of red wolf ancestry in canids across the southeastern United States, which may ultimately inform future red wolf restoration efforts.
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Affiliation(s)
| | - Kristin E Brzeski
- Michigan Technological University, College of Forest Resources and Environmental Science, Houghton, MI
| | - Joseph W Hinton
- Department of Environmental and Forest Biology, College of Environmental Science and Forestry, State University of New York, Syracuse, NY
| | | | - Jacqueline Robinson
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA
| | - Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ
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16
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Haines ML, Luikart G, Amish SJ, Smith S, Latch EK. Evidence for adaptive introgression of exons across a hybrid swarm in deer. BMC Evol Biol 2019; 19:199. [PMID: 31684869 PMCID: PMC6827202 DOI: 10.1186/s12862-019-1497-x] [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: 04/04/2018] [Accepted: 08/22/2019] [Indexed: 12/21/2022] Open
Abstract
Background Secondary contact between closely related lineages can result in a variety of outcomes, including hybridization, depending upon the strength of reproductive barriers. By examining the extent to which different parts of the genome introgress, it is possible to infer the strength of selection and gain insight into the evolutionary trajectory of lineages. Following secondary contact approximately 8000 years ago in the Pacific Northwest, mule deer (Odocoileus hemionus hemionus) and black-tailed deer (O. h. columbianus) formed a hybrid swarm along the Cascade mountain range despite substantial differences in body size (up to two times) and habitat preference. In this study, we examined genetic population structure, extent of introgression, and selection pressures in freely interbreeding populations of mule deer and black-tailed deer using mitochondrial DNA sequences, 9 microsatellite loci, and 95 SNPs from protein-coding genes. Results We observed bi-directional hybridization and classified approximately one third of the 172 individuals as hybrids, almost all of which were beyond the F1 generation. High genetic differentiation between black-tailed deer and mule deer at protein-coding genes suggests that there is positive divergent selection, though selection on these loci is relatively weak. Contrary to predictions, there was not greater selection on protein-coding genes thought to be associated with immune function and mate choice. Geographic cline analyses were consistent across genetic markers, suggesting long-term stability (over hundreds of generations), and indicated that the center of the hybrid swarm is 20-30 km to the east of the Cascades ridgeline, where there is a steep ecological transition from wet, forested habitat to dry, scrub habitat. Conclusions Our data are consistent with a genetic boundary between mule deer and black-tailed deer that is porous but maintained by many loci under weak selection having a substantial cumulative effect. The absence of clear reproductive barriers and the consistent centering of geographic clines at a sharp ecotone suggests that ecology is a driver of hybrid swarm dynamics. Adaptive introgression in this study (and others) promotes gene flow and provides valuable insight into selection strength on specific genes and the evolutionary trajectory of hybridizing taxa. Electronic supplementary material The online version of this article (10.1186/s12862-019-1497-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Margaret L Haines
- Behavioral and Molecular Ecology Research Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53211, USA
| | - Gordon Luikart
- Montana Conservation Genomics Laboratory, Division of Biological Sciences, The University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA.,Montana Conservation Genomics Laboratory, Flathead Lake Biological Station, Division of Biological Sciences, The University of Montana, 32125 Bio Station Lane, Polson, MT, 59860, USA
| | - Stephen J Amish
- Montana Conservation Genomics Laboratory, Division of Biological Sciences, The University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA
| | - Seth Smith
- Montana Conservation Genomics Laboratory, Division of Biological Sciences, The University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA
| | - Emily K Latch
- Behavioral and Molecular Ecology Research Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53211, USA.
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17
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Larsen PA, Matocq MD. Emerging genomic applications in mammalian ecology, evolution, and conservation. J Mammal 2019. [DOI: 10.1093/jmammal/gyy184] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Peter A Larsen
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, USA
| | - Marjorie D Matocq
- Department of Natural Resources and Environmental Science; Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, USA
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18
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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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19
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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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20
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Digging for the spiny rat and hutia phylogeny using a gene capture approach, with the description of a new mammal subfamily. Mol Phylogenet Evol 2019; 136:241-253. [PMID: 30885830 DOI: 10.1016/j.ympev.2019.03.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 03/13/2019] [Accepted: 03/14/2019] [Indexed: 02/07/2023]
Abstract
Next generation sequencing (NGS) and genomic database mining allow biologists to gather and select large molecular datasets well suited to address phylogenomics and molecular evolution questions. Here we applied this approach to a mammal family, the Echimyidae, for which generic relationships have been difficult to recover and often referred to as a star phylogeny. These South-American spiny rats represent a family of caviomorph rodents exhibiting a striking diversity of species and life history traits. Using a NGS exon capture protocol, we isolated and sequenced ca. 500 nuclear DNA exons for 35 species belonging to all major echimyid and capromyid clades. Exons were carefully selected to encompass as much diversity as possible in terms of rate of evolution, heterogeneity in the distribution of site-variation and nucleotide composition. Supermatrix inferences and coalescence-based approaches were subsequently applied to infer this family's phylogeny. The inferred topologies were the same for both approaches, and support was maximal for each node, entirely resolving the ambiguous relationships of previous analyses. Fast-evolving nuclear exons tended to yield more reliable phylogenies, as slower-evolving sequences were not informative enough to disentangle the short branches of the Echimyidae radiation. Based on this resolved phylogeny and on molecular and morphological evidence, we confirm the rank of the Caribbean hutias - formerly placed in the Capromyidae family - as Capromyinae, a clade nested within Echimyidae. We also name and define Carterodontinae, a new subfamily of Echimyidae, comprising the extant monotypic genus Carterodon from Brazil, which is the closest living relative of West Indies Capromyinae.
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21
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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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22
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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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23
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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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24
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Andrew SC, Jensen H, Hagen IJ, Lundregan S, Griffith SC. Signatures of genetic adaptation to extremely varied Australian environments in introduced European house sparrows. Mol Ecol 2018; 27:4542-4555. [DOI: 10.1111/mec.14897] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 09/24/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Samuel C. Andrew
- Department of Biological Sciences; Macquarie University; Sydney New South Wales Australia
| | - Henrik Jensen
- Centre for Biodiversity Dynamics; Department of Biology; Norwegian University of Science and Technology; Trondheim Norway
| | - Ingerid J. Hagen
- Centre for Biodiversity Dynamics; Department of Biology; Norwegian University of Science and Technology; Trondheim Norway
- Norwegian Institute for Nature Research; Trondheim Norway
| | - Sarah Lundregan
- Centre for Biodiversity Dynamics; Department of Biology; Norwegian University of Science and Technology; Trondheim Norway
| | - Simon C. Griffith
- Department of Biological Sciences; Macquarie University; Sydney New South Wales Australia
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25
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Muñoz-Fuentes V, Cacheiro P, Meehan TF, Aguilar-Pimentel JA, Brown SDM, Flenniken AM, Flicek P, Galli A, Mashhadi HH, Hrabě de Angelis M, Kim JK, Lloyd KCK, McKerlie C, Morgan H, Murray SA, Nutter LMJ, Reilly PT, Seavitt JR, Seong JK, Simon M, Wardle-Jones H, Mallon AM, Smedley D, Parkinson HE. The International Mouse Phenotyping Consortium (IMPC): a functional catalogue of the mammalian genome that informs conservation. CONSERV GENET 2018; 19:995-1005. [PMID: 30100824 PMCID: PMC6061128 DOI: 10.1007/s10592-018-1072-9] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 05/03/2018] [Indexed: 01/08/2023]
Abstract
The International Mouse Phenotyping Consortium (IMPC) is building a catalogue of mammalian gene function by producing and phenotyping a knockout mouse line for every protein-coding gene. To date, the IMPC has generated and characterised 5186 mutant lines. One-third of the lines have been found to be non-viable and over 300 new mouse models of human disease have been identified thus far. While current bioinformatics efforts are focused on translating results to better understand human disease processes, IMPC data also aids understanding genetic function and processes in other species. Here we show, using gorilla genomic data, how genes essential to development in mice can be used to help assess the potentially deleterious impact of gene variants in other species. This type of analyses could be used to select optimal breeders in endangered species to maintain or increase fitness and avoid variants associated to impaired-health phenotypes or loss-of-function mutations in genes of critical importance. We also show, using selected examples from various mammal species, how IMPC data can aid in the identification of candidate genes for studying a condition of interest, deliver information about the mechanisms involved, or support predictions for the function of genes that may play a role in adaptation. With genotyping costs decreasing and the continued improvements of bioinformatics tools, the analyses we demonstrate can be routinely applied.
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Affiliation(s)
- Violeta Muñoz-Fuentes
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Pilar Cacheiro
- Clinical Pharmacology, William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ UK
| | - Terrence F. Meehan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Juan Antonio Aguilar-Pimentel
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Steve D. M. Brown
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD UK
| | - Ann M. Flenniken
- The Centre for Phenogenomics, Toronto, ON M5T 3H7 Canada
- Mount Sinai Hospital, Toronto, ON M5G 1X5 Canada
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | | | - Hamed Haseli Mashhadi
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Martin Hrabě de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
- School of Life Science Weihenstephan, Technische Universität München, Alte Akademie 8, 85354 Freising, Germany
| | - Jong Kyoung Kim
- Department of New Biology, DGIST, Daegu, 42988 Republic of Korea
| | - K. C. Kent Lloyd
- Mouse Biology Program, University of California, Davis, CA 95618 USA
| | - Colin McKerlie
- The Centre for Phenogenomics, Toronto, ON M5T 3H7 Canada
- Mount Sinai Hospital, Toronto, ON M5G 1X5 Canada
- The Hospital for Sick Children, Toronto, ON M5G 1X84 Canada
| | - Hugh Morgan
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD UK
| | | | - Lauryl M. J. Nutter
- The Centre for Phenogenomics, Toronto, ON M5T 3H7 Canada
- The Hospital for Sick Children, Toronto, ON M5G 1X84 Canada
| | - Patrick T. Reilly
- PHENOMIN-iCS, 1 Rue Laurent Fries, 67404 Illkirch Cedex, Alsace France
| | - John R. Seavitt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Je Kyung Seong
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, Interdisciplinary Program for Bioinformatics and Program for Cancer Biology, Seoul National University, Seoul, Republic of Korea
| | - Michelle Simon
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD UK
| | | | - Ann-Marie Mallon
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD UK
| | - Damian Smedley
- Clinical Pharmacology, William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ UK
| | - Helen E. Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - the IMPC consortium
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
- Clinical Pharmacology, William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ UK
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD UK
- The Centre for Phenogenomics, Toronto, ON M5T 3H7 Canada
- Mount Sinai Hospital, Toronto, ON M5G 1X5 Canada
- Wellcome Trust Sanger Institute, Cambridge, CB10 1SA UK
- German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
- School of Life Science Weihenstephan, Technische Universität München, Alte Akademie 8, 85354 Freising, Germany
- Department of New Biology, DGIST, Daegu, 42988 Republic of Korea
- Mouse Biology Program, University of California, Davis, CA 95618 USA
- The Hospital for Sick Children, Toronto, ON M5G 1X84 Canada
- The Jackson Laboratory, Bar Harbor, ME 04609 USA
- PHENOMIN-iCS, 1 Rue Laurent Fries, 67404 Illkirch Cedex, Alsace France
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, Interdisciplinary Program for Bioinformatics and Program for Cancer Biology, Seoul National University, Seoul, Republic of Korea
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26
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Weigand H, Leese F. Detecting signatures of positive selection in non-model species using genomic data. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly007] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Hannah Weigand
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
| | - Florian Leese
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße, Essen, Germany
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27
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Doyle JM, Bell DA, Bloom PH, Emmons G, Fesnock A, Katzner TE, LaPré L, Leonard K, SanMiguel P, Westerman R, Andrew DeWoody J. New insights into the phylogenetics and population structure of the prairie falcon (Falco mexicanus). BMC Genomics 2018; 19:233. [PMID: 29618317 PMCID: PMC5885362 DOI: 10.1186/s12864-018-4615-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 03/22/2018] [Indexed: 12/30/2022] Open
Abstract
Background Management requires a robust understanding of between- and within-species genetic variability, however such data are still lacking in many species. For example, although multiple population genetics studies of the peregrine falcon (Falco peregrinus) have been conducted, no similar studies have been done of the closely-related prairie falcon (F. mexicanus) and it is unclear how much genetic variation and population structure exists across the species’ range. Furthermore, the phylogenetic relationship of F. mexicanus relative to other falcon species is contested. We utilized a genomics approach (i.e., genome sequencing and assembly followed by single nucleotide polymorphism genotyping) to rapidly address these gaps in knowledge. Results We sequenced the genome of a single female prairie falcon and generated a 1.17 Gb (gigabases) draft genome assembly. We generated maximum likelihood phylogenetic trees using complete mitochondrial genomes as well as nuclear protein-coding genes. This process provided evidence that F. mexicanus is an outgroup to the clade that includes the peregrine falcon and members of the subgenus Hierofalco. We annotated > 16,000 genes and almost 600,000 high-quality single nucleotide polymorphisms (SNPs) in the nuclear genome, providing the raw material for a SNP assay design featuring > 140 gene-associated markers and a molecular-sexing marker. We subsequently genotyped ~ 100 individuals from California (including the San Francisco East Bay Area, Pinnacles National Park and the Mojave Desert) and Idaho (Snake River Birds of Prey National Conservation Area). We tested for population structure and found evidence that individuals sampled in California and Idaho represent a single panmictic population. Conclusions Our study illustrates how genomic resources can rapidly shed light on genetic variability in understudied species and resolve phylogenetic relationships. Furthermore, we found evidence of a single, randomly mating population of prairie falcons across our sampling locations. Prairie falcons are highly mobile and relatively rare long-distance dispersal events may promote gene flow throughout the range. As such, California’s prairie falcons might be managed as a single population, indicating that management actions undertaken to benefit the species at the local level have the potential to influence the species as a whole. Electronic supplementary material The online version of this article (10.1186/s12864-018-4615-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jacqueline M Doyle
- Department of Biological Sciences, Towson University, 8000 York Rd, Baltimore, MD, 21212, USA. .,Department of Forestry and Natural Resources, Purdue University, 715 W. State Street, West Lafayette, IN, 47907, USA.
| | - Douglas A Bell
- East Bay Regional Park District, 2950 Peralta Oaks Court, Oakland, CA, 94605, USA.,Department of Ornithology and Mammalogy, California Academy of Sciences, 55 Concourse Drive, Golden Gate Park, San Francisco, CA, 94118, USA
| | - Peter H Bloom
- Bloom Research Inc., 1820 S. Dunsmuir, Los Angeles, CA, 90019, USA
| | - Gavin Emmons
- National Park Service, Pinnacles National Park, 5000 Highway 146, Paicines, CA, 95043, USA
| | - Amy Fesnock
- California State Office, Bureau of Land Management, 2800 Cottage Way, Suite W-1928, Sacramento, CA, 95825, USA
| | - Todd E Katzner
- U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center, 970 Lusk Street, Boise, ID, 83706, USA
| | - Larry LaPré
- Bureau of Land Management, California Desert District, 22835 Calle San Juan De Los Lagos, Moreno Valley, CA, 92553, USA
| | - Kolbe Leonard
- Department of Computer and Information Sciences, Towson University, 8000 York Rd, Baltimore, MD, 21212, USA
| | - Phillip SanMiguel
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
| | - Rick Westerman
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
| | - J Andrew DeWoody
- Department of Forestry and Natural Resources, Purdue University, 715 W. State Street, West Lafayette, IN, 47907, USA.,Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN, 47907, USA
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28
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Elbers JP, Brown MB, Taylor SS. Identifying genome-wide immune gene variation underlying infectious disease in wildlife populations - a next generation sequencing approach in the gopher tortoise. BMC Genomics 2018; 19:64. [PMID: 29351737 PMCID: PMC5775545 DOI: 10.1186/s12864-018-4452-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 01/15/2018] [Indexed: 11/25/2022] Open
Abstract
Background Infectious disease is the single greatest threat to taxa such as amphibians (chytrid fungus), bats (white nose syndrome), Tasmanian devils (devil facial tumor disease), and black-footed ferrets (canine distemper virus, plague). Although understanding the genetic basis to disease susceptibility is important for the long-term persistence of these groups, most research has been limited to major-histocompatibility and Toll-like receptor genes. To better understand the genetic basis of infectious disease susceptibility in a species of conservation concern, we sequenced all known/predicted immune response genes (i.e., the immunomes) in 16 Florida gopher tortoises, Gopherus polyphemus. All tortoises produced antibodies against Mycoplasma agassizii (an etiologic agent of infectious upper respiratory tract disease; URTD) and, at the time of sampling, either had (n = 10) or lacked (n = 6) clinical signs. Results We found several variants associated with URTD clinical status in complement and lectin genes, which may play a role in Mycoplasma immunity. Thirty-five genes deviated from neutrality according to Tajima’s D. These genes were enriched in functions relating to macromolecule and protein modifications, which are vital to immune system functioning. Conclusions These results are suggestive of genetic differences that might contribute to disease severity, a finding that is consistent with other mycoplasmal diseases. This has implications for management because tortoises across their range may possess genetic variation associated with a more severe response to URTD. More generally: 1) this approach demonstrates that a broader consideration of immune genes is better able to identify important variants, and; 2) this data pipeline can be adopted to identify alleles associated with disease susceptibility or resistance in other taxa, and therefore provide information on a population’s risk of succumbing to disease, inform translocations to increase genetic variation for disease resistance, and help to identify potential treatments. Electronic supplementary material The online version of this article (10.1186/s12864-018-4452-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jean P Elbers
- School of Renewable Natural Resources, 227 RNR Bldg., Louisiana State University and AgCenter, Baton Rouge, LA, 70803, USA.
| | - Mary B Brown
- Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Sabrina S Taylor
- School of Renewable Natural Resources, 227 RNR Bldg., Louisiana State University and AgCenter, Baton Rouge, LA, 70803, USA
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29
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Donaldson ME, Rico Y, Hueffer K, Rando HM, Kukekova AV, Kyle CJ. Development of a genotype-by-sequencing immunogenetic assay as exemplified by screening for variation in red fox with and without endemic rabies exposure. Ecol Evol 2017; 8:572-583. [PMID: 29321894 PMCID: PMC5756825 DOI: 10.1002/ece3.3583] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 09/28/2017] [Accepted: 10/02/2017] [Indexed: 12/30/2022] Open
Abstract
Pathogens are recognized as major drivers of local adaptation in wildlife systems. By determining which gene variants are favored in local interactions among populations with and without disease, spatially explicit adaptive responses to pathogens can be elucidated. Much of our current understanding of host responses to disease comes from a small number of genes associated with an immune response. High‐throughput sequencing (HTS) technologies, such as genotype‐by‐sequencing (GBS), facilitate expanded explorations of genomic variation among populations. Hybridization‐based GBS techniques can be leveraged in systems not well characterized for specific variants associated with disease outcome to “capture” specific genes and regulatory regions known to influence expression and disease outcome. We developed a multiplexed, sequence capture assay for red foxes to simultaneously assess ~300‐kbp of genomic sequence from 116 adaptive, intrinsic, and innate immunity genes of predicted adaptive significance and their putative upstream regulatory regions along with 23 neutral microsatellite regions to control for demographic effects. The assay was applied to 45 fox DNA samples from Alaska, where three arctic rabies strains are geographically restricted and endemic to coastal tundra regions, yet absent from the boreal interior. The assay provided 61.5% on‐target enrichment with relatively even sequence coverage across all targeted loci and samples (mean = 50×), which allowed us to elucidate genetic variation across introns, exons, and potential regulatory regions (4,819 SNPs). Challenges remained in accurately describing microsatellite variation using this technique; however, longer‐read HTS technologies should overcome these issues. We used these data to conduct preliminary analyses and detected genetic structure in a subset of red fox immune‐related genes between regions with and without endemic arctic rabies. This assay provides a template to assess immunogenetic variation in wildlife disease systems.
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Affiliation(s)
- Michael E Donaldson
- Environmental and Life Sciences Graduate Program Trent University Peterborough ON Canada
| | - Yessica Rico
- CONACYT Instituto de Ecología A.C.Centro Regional del Bajio Pátzcuaro Michoacán Mexico
| | - Karsten Hueffer
- Department of Veterinary Medicine University of Alaska Fairbanks Fairbanks AK USA
| | - Halie M Rando
- Department of Animal Sciences College of ACES University of Illinois at Urbana-Champaign Urbana IL USA
| | - Anna V Kukekova
- Department of Animal Sciences College of ACES University of Illinois at Urbana-Champaign Urbana IL USA
| | - Christopher J Kyle
- Environmental and Life Sciences Graduate Program Trent University Peterborough ON Canada.,Forensic Science Department Trent University Peterborough ON Canada
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30
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Hulva P, Černá Bolfíková B, Woznicová V, Jindřichová M, Benešová M, Mysłajek RW, Nowak S, Szewczyk M, Niedźwiecka N, Figura M, Hájková A, Sándor AD, Zyka V, Romportl D, Kutal M, Finďo S, Antal V. Wolves at the crossroad: Fission-fusion range biogeography in the Western Carpathians and Central Europe. DIVERS DISTRIB 2017. [DOI: 10.1111/ddi.12676] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Pavel Hulva
- Department of Zoology, Faculty of Science; Charles University; Prague Czech Republic
- Department of Biology and Ecology, Faculty of Science; University of Ostrava; Ostrava Czech Republic
| | - Barbora Černá Bolfíková
- Department of Animal Science and Food Processing, Faculty of Tropical AgriSciences; Czech University of Life Sciences Prague; Prague Czech Republic
| | - Vendula Woznicová
- Department of Biology and Ecology, Faculty of Science; University of Ostrava; Ostrava Czech Republic
| | - Milena Jindřichová
- Department of Animal Science and Food Processing, Faculty of Tropical AgriSciences; Czech University of Life Sciences Prague; Prague Czech Republic
| | - Markéta Benešová
- Department of Zoology, Faculty of Science; Charles University; Prague Czech Republic
| | - Robert W. Mysłajek
- Institute of Genetics and Biotechnology, Faculty of Biology; University of Warsaw; Warszaw Poland
| | | | - Maciej Szewczyk
- Institute of Genetics and Biotechnology, Faculty of Biology; University of Warsaw; Warszaw Poland
| | - Natalia Niedźwiecka
- Institute of Genetics and Biotechnology, Faculty of Biology; University of Warsaw; Warszaw Poland
- Association for Nature “Wolf”; Lipowa Poland
| | | | - Andrea Hájková
- State Nature Conservancy of Slovak Republic; Banská Bystrica Slovakia
| | - Atilla D. Sándor
- Department of Parasitology and Parasitic Diseases, Faculty of Veterinary Medicine; University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca; Cluj-Napoca Romania
| | - Vladimír Zyka
- Department of Zoology, Faculty of Science; Charles University; Prague Czech Republic
| | - Dušan Romportl
- Department of Zoology, Faculty of Science; Charles University; Prague Czech Republic
| | - Miroslav Kutal
- Friends of the Earth Czech Republic; Olomouc Branch; Olomouc Czech Republic
- Institute of Forest Ecology, Faculty of Forestry and Wood Technology; Mendel University in Brno; Brno Czech Republic
| | - Slavomír Finďo
- Forest Protection and Wildlife Management; National Forest Centre; Zvolen Slovakia
| | - Vladimír Antal
- State Nature Conservancy of Slovak Republic; Banská Bystrica Slovakia
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31
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Donaldson ME, Davy CM, Willis CKR, McBurney S, Park A, Kyle CJ. Profiling the immunome of little brown myotis provides a yardstick for measuring the genetic response to white-nose syndrome. Evol Appl 2017; 10:1076-1090. [PMID: 29151862 PMCID: PMC5680615 DOI: 10.1111/eva.12514] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 06/26/2017] [Indexed: 12/19/2022] Open
Abstract
White‐nose syndrome (WNS) has devastated populations of hibernating bats in eastern North America, leading to emergency conservation listings for several species including the previously ubiquitous little brown myotis (Myotis lucifugus). However, some bat populations near the epicenter of the WNS panzootic appear to be stabilizing after initial precipitous declines, which could reflect a selective immunogenetic sweep. To investigate the hypothesis that WNS exerts significant selection on the immunome of affected bat populations, we developed a novel, high‐throughput sequence capture assay targeting 138 adaptive, intrinsic, and innate immunity genes of putative adaptive significance, as well as their respective regulatory regions (~370 kbp of genomic sequence/individual). We used the assay to explore baseline immunogenetic variation in M. lucifugus and to investigate whether particular immune genes/variants are associated with WNS susceptibility. We also used our assay to detect 1,038 putatively neutral single nucleotide polymorphisms and characterize contemporary population structure, providing context for the identification of local immunogenetic adaptation. Sequence capture provided a cost‐effective, “all‐in‐one” assay to test for neutral genetic and immunogenetic structure and revealed fine‐scale, baseline immunogenetic differentiation between sampling sites <600 km apart. We identified functional immunogenetic variants in M. lucifugus associated with WNS susceptibility. This study lays the foundations for future investigations of rangewide immunogenetic adaptation to WNS in M. lucifugus and provides a blueprint for studies of evolutionary rescue in other host–pathogen systems.
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Affiliation(s)
- Michael E Donaldson
- Environmental and Life Sciences Graduate Program Trent University Peterborough ON Canada
| | - Christina M Davy
- Environmental and Life Sciences Graduate Program Trent University Peterborough ON Canada.,Wildlife Research and Monitoring Section Ontario Ministry of Natural Resources and Forestry Peterborough ON Canada
| | - Craig K R Willis
- Department of Biology and Centre for Forest Interdisciplinary Research (C-FIR) University of Winnipeg Winnipeg MB Canada
| | - Scott McBurney
- Canadian Wildlife Health Cooperative Atlantic Region Atlantic Veterinary College University of Prince Edward Island Charlottetown PEI Canada
| | - Allysia Park
- Canadian Wildlife Health Cooperative Atlantic Region Atlantic Veterinary College University of Prince Edward Island Charlottetown PEI Canada
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32
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vonHoldt B, Fan Z, Ortega-Del Vecchyo D, Wayne RK. EPAS1 variants in high altitude Tibetan wolves were selectively introgressed into highland dogs. PeerJ 2017; 5:e3522. [PMID: 28717592 PMCID: PMC5510585 DOI: 10.7717/peerj.3522] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 06/08/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Admixture can facilitate adaptation. For example, black wolves have obtained the variant causing black coat color through past hybridization with domestic dogs and have higher fitness than gray colored wolves. Another recent example of the transfer of adaptive variation between the two species has been suggested by the similarity between high altitude Tibetan mastiffs and wolves at the EPAS1 gene, a transcription factor induced in low oxygen environments. METHODS Here, we investigate the directionality of admixture in EPAS1 between 28 reference highland gray wolves, 15 reference domestic dogs, and 21 putatively admixed highland wolves. This experimental design represents an expanded sample of Asian dogs and wolves from previous studies. Admixture was inferred using 17,709 publicly available SNP genotypes on canine chromosome 10. We additionally conducted a scan for positive selection in the highland dog genome. RESULTS We find an excess of highland gray wolf ancestry at the EPAS1 locus in highland domestic dogs, suggesting adaptive introgression from wolves to dogs. The signal of admixture is limited in genomic extent to a small region on chromosome 10, indicating that it is the focus of selection in an oxygen-limited environment. DISCUSSION Our results suggest that an adaptive variant of EPAS1 in highland wolves was transferred to highland dogs, carrying linked variants that potentially function in hypoxia response at high elevation. The intertwined history of dogs and wolves ensures a unique evolutionary dynamic where variants that have appeared in the history of either species can be tested for their effects on fitness under natural and artificial selection. Such coupled evolutionary histories may be key to the persistence of wild canines and their domesticated kin given the increasing anthropogenic modifications that characterize the future of both species.
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Affiliation(s)
- Bridgett vonHoldt
- Ecology & Evolutionary Biology, Princeton University, Princeton, NJ, United States of America
| | - Zhenxin Fan
- College of Life Sciences, Sichuan University, Chengdu, China
| | - Diego Ortega-Del Vecchyo
- Department of Integrative Biology, University of California, Berkeley, CA, United States of America
| | - Robert K Wayne
- Ecology & Evolutionary Biology, University of California, Los Angeles, CA, United States of America
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33
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McLean CA, Lutz A, Rankin KJ, Stuart-Fox D, Moussalli A. Revealing the Biochemical and Genetic Basis of Color Variation in a Polymorphic Lizard. Mol Biol Evol 2017; 34:1924-1935. [DOI: 10.1093/molbev/msx136] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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34
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Christmas MJ, Biffin E, Breed MF, Lowe AJ. Targeted capture to assess neutral genomic variation in the narrow-leaf hopbush across a continental biodiversity refugium. Sci Rep 2017; 7:41367. [PMID: 28145488 PMCID: PMC5286450 DOI: 10.1038/srep41367] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 12/20/2016] [Indexed: 11/09/2022] Open
Abstract
The Adelaide geosyncline, a mountainous region in central southern Australia, is purported to be an important continental refugium for Mediterranean and semi-arid Australian biota, yet few population genetic studies have been conducted to test this theory. Here, we focus on a plant species distributed widely throughout the region, the narrow-leaf hopbush, Dodonaea viscosa ssp. angustissima, and examine its genetic diversity and population structure. We used a hybrid-capture target enrichment technique to selectively sequence over 700 genes from 89 individuals across 17 sampling locations. We compared 815 single nucleotide polymorphisms among individuals and populations to investigate population genetic structure. Three distinct genetic clusters were identified; a Flinders/Gammon ranges cluster, an Eastern cluster, and a Kangaroo Island cluster. Higher genetic diversity was identified in the Flinders/Gammon Ranges cluster, indicating that this area is likely to have acted as a refugium during past climate oscillations. We discuss these findings and consider the historical range dynamics of these populations. We also provide methodological considerations for population genomics studies that aim to use novel genomic approaches (such as target capture methods) on non-model systems. The application of our findings to restoration of this species across the region are also considered.
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Affiliation(s)
- Matthew J. Christmas
- Environment Institute and School of Biological Sciences, The University of Adelaide, North Terrace, SA 5005, Australia
| | - Ed Biffin
- State Herbarium of South Australia, Hackney Road, Adelaide, SA 5000, Australia
| | - Martin F. Breed
- Environment Institute and School of Biological Sciences, The University of Adelaide, North Terrace, SA 5005, Australia
| | - Andrew J. Lowe
- Environment Institute and School of Biological Sciences, The University of Adelaide, North Terrace, SA 5005, Australia
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Rico Y, Ethier DM, Davy CM, Sayers J, Weir RD, Swanson BJ, Nocera JJ, Kyle CJ. Spatial patterns of immunogenetic and neutral variation underscore the conservation value of small, isolated American badger populations. Evol Appl 2016; 9:1271-1284. [PMID: 27877205 PMCID: PMC5108218 DOI: 10.1111/eva.12410] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 07/14/2016] [Indexed: 12/29/2022] Open
Abstract
Small and isolated populations often exhibit low genetic diversity due to drift and inbreeding, but may simultaneously harbour adaptive variation. We investigate spatial distributions of immunogenetic variation in American badger subspecies (Taxidea taxus), as a proxy for evaluating their evolutionary potential across the northern extent of the species' range. We compared genetic structure of 20 microsatellites and the major histocompatibility complex (MHC DRB exon 2) to evaluate whether small, isolated populations show low adaptive polymorphism relative to large and well-connected populations. Our results suggest that gene flow plays a prominent role in shaping MHC polymorphism across large spatial scales, while the interplay between gene flow and selection was stronger towards the northern peripheries. The similarity of MHC alleles within subspecies relative to their neutral genetic differentiation suggests that adaptive divergence among subspecies can be maintained despite ongoing gene flow along subspecies boundaries. Neutral genetic diversity was low in small relative to large populations, but MHC diversity within individuals was high in small populations. Despite reduced neutral genetic variation, small and isolated populations harbour functional variation that likely contribute to the species evolutionary potential at the northern range. Our findings suggest that conservation approaches should focus on managing adaptive variation across the species range rather than protecting subspecies per se.
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Affiliation(s)
- Yessica Rico
- Forensic Science DepartmentTrent UniversityPeterboroughONCanada
- Natural Resources DNA Profiling and Forensics CentreTrent UniversityPeterboroughONCanada
- Present address: CONACYTInstituto de Ecología A.C.Centro Regional del BajíoAvenida Lázaro Cárdenas 253PátzcuaroMichoacán61600México
| | - Danielle M. Ethier
- Ontario Badger ProjectGuelphONCanada
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
| | - Christina M. Davy
- Forensic Science DepartmentTrent UniversityPeterboroughONCanada
- Natural Resources DNA Profiling and Forensics CentreTrent UniversityPeterboroughONCanada
| | | | - Richard D. Weir
- Ecosystems Protection & Sustainability BranchMinistry of EnvironmentVictoriaBCCanada
| | | | - Joseph J. Nocera
- Wildlife Research and Monitoring SectionMinistry of Natural Resources & ForestryPeterboroughONCanada
| | - Christopher J. Kyle
- Forensic Science DepartmentTrent UniversityPeterboroughONCanada
- Natural Resources DNA Profiling and Forensics CentreTrent UniversityPeterboroughONCanada
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Christmas MJ, Biffin E, Breed MF, Lowe AJ. Finding needles in a genomic haystack: targeted capture identifies clear signatures of selection in a nonmodel plant species. Mol Ecol 2016; 25:4216-33. [DOI: 10.1111/mec.13750] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 06/27/2016] [Accepted: 07/06/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Matthew J. Christmas
- Environment Institute and School of Biological Sciences The University of Adelaide North Terrace SA 5005 Australia
| | - Ed Biffin
- State Herbarium of South Australia Hackney Road Adelaide SA 5000 Australia
| | - Martin F. Breed
- Environment Institute and School of Biological Sciences The University of Adelaide North Terrace SA 5005 Australia
| | - Andrew J. Lowe
- Environment Institute and School of Biological Sciences The University of Adelaide North Terrace SA 5005 Australia
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Jensen JD, Foll M, Bernatchez L. The past, present and future of genomic scans for selection. Mol Ecol 2016; 25:1-4. [PMID: 26745554 DOI: 10.1111/mec.13493] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 11/16/2015] [Indexed: 12/18/2022]
Affiliation(s)
- Jeffrey D Jensen
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Matthieu Foll
- Genetic Cancer Susceptibility, International Agency for Research on Cancer, Lyon, France
| | - Louis Bernatchez
- IBIS (Institut de Biologie Intégrative et des Systèmes), Université Laval, Québec, Québec, Canada
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