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vonHoldt BM, Stahler DR, Brzeski KE, Musiani M, Peterson R, Phillips M, Stephenson J, Laudon K, Meredith E, Vucetich JA, Leonard JA, Wayne RK. Demographic history shapes North American gray wolf genomic diversity and informs species' conservation. Mol Ecol 2024; 33:e17231. [PMID: 38054561 DOI: 10.1111/mec.17231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 11/19/2023] [Accepted: 11/21/2023] [Indexed: 12/07/2023]
Abstract
Effective population size estimates are critical information needed for evolutionary predictions and conservation decisions. This is particularly true for species with social factors that restrict access to breeding or experience repeated fluctuations in population size across generations. We investigated the genomic estimates of effective population size along with diversity, subdivision, and inbreeding from 162,109 minimally filtered and 81,595 statistically neutral and unlinked SNPs genotyped in 437 grey wolf samples from North America collected between 1986 and 2021. We found genetic structure across North America, represented by three distinct demographic histories of western, central, and eastern regions of the continent. Further, grey wolves in the northern Rocky Mountains have lower genomic diversity than wolves of the western Great Lakes and have declined over time. Effective population size estimates revealed the historical signatures of continental efforts of predator extermination, despite a quarter century of recovery efforts. We are the first to provide molecular estimates of effective population size across distinct grey wolf populations in North America, which ranged between Ne ~ 275 and 3050 since early 1980s. We provide data that inform managers regarding the status and importance of effective population size estimates for grey wolf conservation, which are on average 5.2-9.3% of census estimates for this species. We show that while grey wolves fall above minimum effective population sizes needed to avoid extinction due to inbreeding depression in the short term, they are below sizes predicted to be necessary to avoid long-term risk of extinction.
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Affiliation(s)
- Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Daniel R Stahler
- Yellowstone Center for Resources, Yellowstone National Park, Wyoming, USA
| | - Kristin E Brzeski
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | - Marco Musiani
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Università di Bologna, Bologna, Italy
| | - Rolf Peterson
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | | | | | - Kent Laudon
- California Department of Fish and Wildlife, Northern Region, Redding, California, USA
| | - Erin Meredith
- California Department of Fish and Wildlife, Wildlife Forensic Laboratory, Sacramento, California, USA
| | - John A Vucetich
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, USA
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2
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Tessler M, Neumann JS, Kamm K, Osigus HJ, Eshel G, Narechania A, Burns JA, DeSalle R, Schierwater B. Phylogenomics and the first higher taxonomy of Placozoa, an ancient and enigmatic animal phylum. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1016357] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Placozoa is an ancient phylum of extraordinarily unusual animals: miniscule, ameboid creatures that lack most fundamental animal features. Despite high genetic diversity, only recently have the second and third species been named. While prior genomic studies suffer from incomplete placozoan taxon sampling, we more than double the count with protein sequences from seven key genomes and produce the first nuclear phylogenomic reconstruction of all major placozoan lineages. This leads us to the first complete Linnaean taxonomic classification of Placozoa, over a century after its discovery: This may be the only time in the 21st century when an entire higher taxonomy for a whole animal phylum is formalized. Our classification establishes 2 new classes, 4 new orders, 3 new families, 1 new genus, and 1 new species, namely classes Polyplacotomia and Uniplacotomia; orders Polyplacotomea, Trichoplacea, Cladhexea, and Hoilungea; families Polyplacotomidae, Cladtertiidae, and Hoilungidae; and genus Cladtertia with species Cladtertia collaboinventa, nov. Our likelihood and gene content tree topologies refine the relationships determined in previous studies. Adding morphological data into our phylogenomic matrices suggests sponges (Porifera) as the sister to other animals, indicating that modest data addition shifts this node away from comb jellies (Ctenophora). Furthermore, by adding the first genomic protein data of the exceptionally distinct and branching Polyplacotoma mediterranea, we solidify its position as sister to all other placozoans; a divergence we estimate to be over 400 million years old. Yet even this deep split sits on a long branch to other animals, suggesting a bottleneck event followed by diversification. Ancestral state reconstructions indicate large shifts in gene content within Placozoa, with Hoilungia hongkongensis and its closest relatives having the most unique genetics.
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3
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Thomas NE, Hailer F, Bruford MW, Chadwick EA. Country‐wide genetic monitoring over 21 years reveals lag in genetic recovery despite spatial connectivity in an expanding carnivore (Eurasian otter,
Lutra lutra
) population. Evol Appl 2022; 15:2125-2141. [DOI: 10.1111/eva.13505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 08/05/2022] [Accepted: 10/06/2022] [Indexed: 11/16/2022] Open
Affiliation(s)
- Nia E. Thomas
- Organisms and Environment Research Division, School of Biosciences Cardiff University Cardiff Wales UK
| | - Frank Hailer
- Organisms and Environment Research Division, School of Biosciences Cardiff University Cardiff Wales UK
| | - Michael W. Bruford
- Organisms and Environment Research Division, School of Biosciences Cardiff University Cardiff Wales UK
| | - Elizabeth A. Chadwick
- Organisms and Environment Research Division, School of Biosciences Cardiff University Cardiff Wales UK
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4
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Buck R, Flores-Rentería L. The Syngameon Enigma. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11070895. [PMID: 35406874 PMCID: PMC9002738 DOI: 10.3390/plants11070895] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/21/2022] [Accepted: 03/25/2022] [Indexed: 05/17/2023]
Abstract
Despite their evolutionary relevance, multispecies networks or syngameons are rarely reported in the literature. Discovering how syngameons form and how they are maintained can give insight into processes such as adaptive radiations, island colonizations, and the creation of new hybrid lineages. Understanding these complex hybridization networks is even more pressing with anthropogenic climate change, as syngameons may have unique synergistic properties that will allow participating species to persist. The formation of a syngameon is not insurmountable, as several ways for a syngameon to form have been proposed, depending mostly on the magnitude and frequency of gene flow events, as well as the relatedness of its participants. Episodic hybridization with small amounts of introgression may keep syngameons stable and protect their participants from any detrimental effects of gene flow. As genomic sequencing becomes cheaper and more species are included in studies, the number of known syngameons is expected to increase. Syngameons must be considered in conservation efforts as the extinction of one participating species may have detrimental effects on the survival of all other species in the network.
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5
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Wilson PJ, Rutledge LY. Considering Pleistocene North American wolves and coyotes in the eastern Canis origin story. Ecol Evol 2021; 11:9137-9147. [PMID: 34257949 PMCID: PMC8258226 DOI: 10.1002/ece3.7757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 05/14/2021] [Accepted: 05/18/2021] [Indexed: 01/22/2023] Open
Abstract
The evolutionary origins and hybridization patterns of Canis species in North America have been hotly debated for the past 30 years. Disentangling ancestry and timing of hybridization in Great Lakes wolves, eastern Canadian wolves, red wolves, and eastern coyotes are most often partitioned into a 2-species model that assigns all ancestry to gray wolves and/or coyotes, and a 3-species model that includes a third, North American evolved eastern wolf genome. The proposed models address recent or sometimes late Holocene hybridization events but have largely ignored potential Pleistocene era progenitors and opportunities for hybridization that may have impacted the current mixed genomes in eastern Canada and the United States. Here, we re-analyze contemporary and ancient mitochondrial DNA genomes with Bayesian phylogenetic analyses to more accurately estimate divergence dates among lineages. We combine that with a review of the literature on Late Pleistocene Canis distributions to: (a) identify potential Pleistocene progenitors to southern North American gray wolves and eastern wolves; and (b) illuminate opportunities for ancient hybridization events. Specifically, we propose that Beringian gray wolves (C. lupus) and extinct large wolf-like coyotes (C. latrans orcutti) are likely progenitors to Mexican and Plains gray wolves and eastern wolves, respectively, and may represent a potentially unrecognized source of introgressed genomic variation within contemporary Canis genomes. These events speak to the potential origins of contemporary genomes and provide a new perspective on Canis ancestry, but do not negate current conservation priorities of dwindling wolf populations with unique genomic signatures and key ecologically critical roles.
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6
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vonHoldt BM, Aardema ML. Updating the Bibliography of Interbreeding among Canis in North America. J Hered 2021; 111:249-262. [PMID: 32034410 DOI: 10.1093/jhered/esaa004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 02/05/2020] [Indexed: 01/29/2023] Open
Abstract
This bibliography provides a collection of references that documents the evolution of studies evidencing interbreeding among Canis species in North America. Over the past several decades, advances in biology and genomic technology greatly improved our ability to detect and characterize species interbreeding, which has significance for understanding species in a changing landscape as well as for endangered species management. This bibliography includes a discussion within each category of interbreeding, the timeline of developing evidence, and includes a review of past research conducted on experimental crosses. Research conducted in the early 20th century is rich with detailed records and photographs of hybrid offspring development and behavior. With the progression of molecular methods, studies can estimate historical demographic parameters and detect chromosomal patterns of ancestry. As these methods continue to increase in accessibility, the field will gain a deeper and richer understanding of the evolutionary history of North American Canis.
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Affiliation(s)
- Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ
| | - Matthew L Aardema
- Department of Biology, Montclair State University, Montclair, NJ.,Sackler Institute for Comparative Genomics, American Museum of Natural History, New York City, NY
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7
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Hervey SD, Rutledge LY, Patterson BR, Romanski MC, Vucetich JA, Belant JL, Beyer DE, Moore SA, Brzeski KE. A first genetic assessment of the newly introduced Isle Royale gray wolves (Canis lupus). CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01373-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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8
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Oliveira T, Benson JF, Thompson C, Patterson BR. Resource selection at homesites by wolves and eastern coyotes in a
Canis
hybrid zone. Ecosphere 2020. [DOI: 10.1002/ecs2.3320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Teresa Oliveira
- Department of Forestry and Renewable Forest Resources Biotechnical Faculty University of Ljubljana Večna pot 83 Ljubljana1000Slovenia
| | - John F. Benson
- School of Natural Resources University of Nebraska Lincoln Nebraska68583USA
| | - Connor Thompson
- Environmental and Life Sciences Graduate Program Trent University Peterborough OntarioK9L 0G2Canada
| | - Brent R. Patterson
- Environmental and Life Sciences Graduate Program Trent University Peterborough OntarioK9L 0G2Canada
- Wildlife Research and Monitoring Section Ontario Ministry of Natural Resources and Forestry Peterborough OntarioK9L 1Z8Canada
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9
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Genetic structure of tigers (Panthera tigris tigris) in India and its implications for conservation. Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2019.e00710] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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10
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Hinton JW, Heppenheimer E, West KM, Caudill D, Karlin ML, Kilgo JC, Mayer JJ, Miller KV, Walch M, vonHoldt B, Chamberlain MJ. Geographic patterns in morphometric and genetic variation for coyote populations with emphasis on southeastern coyotes. Ecol Evol 2019; 9:3389-3404. [PMID: 30962900 PMCID: PMC6434562 DOI: 10.1002/ece3.4966] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 12/02/2018] [Accepted: 12/20/2018] [Indexed: 12/31/2022] Open
Abstract
Prior to 1900, coyotes (Canis latrans) were restricted to the western and central regions of North America, but by the early 2000s, coyotes became ubiquitous throughout the eastern United States. Information regarding morphological and genetic structure of coyote populations in the southeastern United States is limited, and where data exist, they are rarely compared to those from other regions of North America. We assessed geographic patterns in morphology and genetics of coyotes with special consideration of coyotes in the southeastern United States. Mean body mass of coyote populations increased along a west-to-east gradient, with southeastern coyotes being intermediate to western and northeastern coyotes. Similarly, principal component analysis of body mass and linear body measurements suggested that southeastern coyotes were intermediate to western and northeastern coyotes in body size but exhibited shorter tails and ears from other populations. Genetic analyses indicated that southeastern coyotes represented a distinct genetic cluster that differentiated strongly from western and northeastern coyotes. We postulate that southeastern coyotes experienced lower immigration from western populations than did northeastern coyotes, and over time, genetically diverged from both western and northeastern populations. Coyotes colonizing eastern North America experienced different selective pressures than did stable populations in the core range, and we offer that the larger body size of eastern coyotes reflects an adaptation that improved dispersal capabilities of individuals in the expanding range.
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Affiliation(s)
- Joseph W. Hinton
- Warnell School of Forestry and Natural ResourcesUniversity of GeorgiaAthensGeorgia
| | | | | | - Danny Caudill
- Florida Fish and Wildlife Conservation CommissionGainesvilleFlorida
- Present address:
Alaska Department of Fish and GameFairbanksAlaska
| | - Melissa L. Karlin
- Department of Physics and Environmental SciencesSt. Mary's UniversitySan AntonioTexas
| | - John C. Kilgo
- United States Department of AgricultureForest Service Southern Research StationNew EllentonSouth Carolina
| | - John Joseph Mayer
- United States Department of Energy, Environmental Sciences, and BiotechnologySavannah River National LaboratoryAikenSouth Carolina
| | - Karl V. Miller
- Warnell School of Forestry and Natural ResourcesUniversity of GeorgiaAthensGeorgia
| | | | - Bridgett vonHoldt
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew Jersey
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11
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Heppenheimer E, Harrigan RJ, Rutledge LY, Koepfli KP, DeCandia AL, Brzeski KE, Benson JF, Wheeldon T, Patterson BR, Kays R, Hohenlohe PA, von Holdt BM. Population Genomic Analysis of North American Eastern Wolves (Canis lycaon) Supports Their Conservation Priority Status. Genes (Basel) 2018; 9:genes9120606. [PMID: 30518163 PMCID: PMC6316216 DOI: 10.3390/genes9120606] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 11/29/2018] [Accepted: 11/30/2018] [Indexed: 01/22/2023] Open
Abstract
The threatened eastern wolf is found predominantly in protected areas of central Ontario and has an evolutionary history obscured by interbreeding with coyotes and gray wolves, which challenges its conservation status and subsequent management. Here, we used a population genomics approach to uncover spatial patterns of variation in 281 canids in central Ontario and the Great Lakes region. This represents the first genome-wide single nucleotide polymorphism (SNP) dataset with substantial sample sizes of representative populations. Although they comprise their own genetic cluster, we found evidence of eastern wolf dispersal outside of the boundaries of protected areas, in that the frequency of eastern wolf genetic variation decreases with increasing distance from provincial parks. We detected eastern wolf alleles in admixed coyotes along the northeastern regions of Lake Huron and Lake Ontario. Our analyses confirm the unique genomic composition of eastern wolves, which are mostly restricted to small fragmented patches of protected habitat in central Ontario. We hope this work will encourage an innovative discussion regarding a plan for managed introgression, which could conserve eastern wolf genetic material in any genome regardless of their potential mosaic ancestry composition and the habitats that promote them.
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Affiliation(s)
- Elizabeth Heppenheimer
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.
| | - Ryan J Harrigan
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA.
| | - Linda Y Rutledge
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.
- Biology Department, Trent University, Peterborough, ON K9L 1Z8, Canada.
| | - Klaus-Peter Koepfli
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 20008, USA.
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, 199034 Saint Petersburg, Russia.
| | - Alexandra L DeCandia
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.
| | - Kristin E Brzeski
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA.
| | - John F Benson
- School of Natural Resources, University of Nebraska, Lincoln, NE 68583, USA.
| | - Tyler Wheeldon
- Environmental & Life Sciences, Trent University, Peterborough, ON K9L 0G2, Canada.
- Ontario Ministry of Natural Resources and Forestry, Trent University, Peterborough, ON K9L 0G2, Canada.
| | - Brent R Patterson
- Environmental & Life Sciences, Trent University, Peterborough, ON K9L 0G2, Canada.
- Ontario Ministry of Natural Resources and Forestry, Trent University, Peterborough, ON K9L 0G2, Canada.
| | - Roland Kays
- North Carolina Museum of Natural Sciences and Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27601, USA.
| | - Paul A Hohenlohe
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA.
| | - Bridgett M von Holdt
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.
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12
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Heppenheimer E, Brzeski KE, Hinton JW, Patterson BR, Rutledge LY, DeCandia AL, Wheeldon T, Fain SR, Hohenlohe PA, Kays R, White BN, Chamberlain MJ, vonHoldt BM. High genomic diversity and candidate genes under selection associated with range expansion in eastern coyote ( Canis latrans) populations. Ecol Evol 2018; 8:12641-12655. [PMID: 30619570 PMCID: PMC6309008 DOI: 10.1002/ece3.4688] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 10/10/2018] [Accepted: 10/15/2018] [Indexed: 12/29/2022] Open
Abstract
Range expansion is a widespread biological process, with well-described theoretical expectations associated with the colonization of novel ranges. However, comparatively few empirical studies address the genomic outcomes accompanying the genome-wide consequences associated with the range expansion process, particularly in recent or ongoing expansions. Here, we assess two recent and distinct eastward expansion fronts of a highly mobile carnivore, the coyote (Canis latrans), to investigate patterns of genomic diversity and identify variants that may have been under selection during range expansion. Using a restriction-associated DNA sequencing (RADseq), we genotyped 394 coyotes at 22,935 SNPs and found that overall population structure corresponded to their 19th century historical range and two distinct populations that expanded during the 20th century. Counter to theoretical expectations for populations to bottleneck during range expansions, we observed minimal evidence for decreased genomic diversity across coyotes sampled along either expansion front, which is likely due to hybridization with other Canis species. Furthermore, we identified 12 SNPs, located either within genes or putative regulatory regions, that were consistently associated with range expansion. Of these 12 genes, three (CACNA1C, ALK, and EPHA6) have putative functions related to dispersal, including habituation to novel environments and spatial learning, consistent with the expectations for traits under selection during range expansion. Although coyote colonization of eastern North America is well-publicized, this study provides novel insights by identifying genes associated with dispersal capabilities in coyotes on the two eastern expansion fronts.
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Affiliation(s)
| | - Kristin E. Brzeski
- Department of Ecology & Evolutionary BiologyPrinceton UniversityPrincetonNew Jersey
- School of Forest Resources and Environmental ScienceMichigan Technological UniversityHoughtonMichigan
| | - Joseph W. Hinton
- Warnell School of Forestry and Natural ResourcesUniversity of GeorgiaAthensGeorgia
| | - Brent R. Patterson
- Ontario Ministry of Natural Resources and ForestryPeterboroughOntarioCanada
- Trent UniversityPeterboroughOntario
| | - Linda Y. Rutledge
- Department of Ecology & Evolutionary BiologyPrinceton UniversityPrincetonNew Jersey
- Trent UniversityPeterboroughOntario
| | | | - Tyler Wheeldon
- Ontario Ministry of Natural Resources and ForestryPeterboroughOntarioCanada
- Trent UniversityPeterboroughOntario
| | | | - Paul A. Hohenlohe
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary StudiesUniversity of IdahoMoscowIdaho
| | - Roland Kays
- Department of Forestry and Environmental ResourcesNorth Carolina State UniversityRaleighNorth Carolina
- North Carolina Museum of Natural SciencesRaleighNorth Carolina
| | | | | | - Bridgett M. vonHoldt
- Department of Ecology & Evolutionary BiologyPrinceton UniversityPrincetonNew Jersey
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13
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Agung PP, Saputra F, Zein MSA, Wulandari AS, Putra WPB, Said S, Jakaria J. Genetic diversity of Indonesian cattle breeds based on microsatellite markers. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2018; 32:467-476. [PMID: 30145876 PMCID: PMC6409462 DOI: 10.5713/ajas.18.0283] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 07/31/2018] [Indexed: 12/02/2022]
Abstract
Objective This research was conducted to study the genetic diversity in several Indonesian cattle breeds using microsatellite markers to classify the Indonesian cattle breeds. Methods A total of 229 DNA samples from of 10 cattle breeds were used in this study. The polymerase chain reaction process was conducted using 12 labeled primers. The size of allele was generated using the multiplex DNA fragment analysis. The POPGEN and CERVUS programs were used to obtain the observed number of alleles, effective number of alleles, observed heterozygosity value, expected heterozygosity value, allele frequency, genetic differentiation, the global heterozygote deficit among breeds, and the heterozygote deficit within the breed, gene flow, Hardy-Weinberg equilibrium, and polymorphism information content values. The MEGA program was used to generate a dendrogram that illustrates the relationship among cattle population. Bayesian clustering assignments were analyzed using STRUCTURE program. The GENETIX program was used to perform the correspondence factorial analysis (CFA). The GENALEX program was used to perform the principal coordinates analysis (PCoA) and analysis of molecular variance. The principal component analysis (PCA) was performed using adegenet package of R program. Results A total of 862 alleles were detected in this study. The INRA23 allele 205 is a specific allele candidate for the Sumba Ongole cattle, while the allele 219 is a specific allele candidate for Ongole Grade. This study revealed a very close genetic relationship between the Ongole Grade and Sumba Ongole cattle and between the Madura and Pasundan cattle. The results from the CFA, PCoA, and PCA analysis in this study provide scientific evidence regarding the genetic relationship between Banteng and Bali cattle. According to the genetic relationship, the Pesisir cattle were classified as Bos indicus cattle. Conclusion All identified alleles in this study were able to classify the cattle population into three clusters i.e. Bos taurus cluster (Simmental Purebred, Simmental Crossbred, and Holstein Friesian cattle); Bos indicus cluster (Sumba Ongole, Ongole Grade, Madura, Pasundan, and Pesisir cattle); and Bos javanicus cluster (Banteng and Bali cattle).
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Affiliation(s)
- Paskah Partogi Agung
- Research Center for Biotechnology-Indonesian Institute of Sciences, Cibinong 16911, West Java, Indonesia
| | - Ferdy Saputra
- Laboratory of Genetics Indonesia, Cikarang Technopark, Bekasi, West Java 17550, Indonesia
| | - Moch Syamsul Arifin Zein
- Research Center for Biology-Indonesian Institute of Sciences, Cibinong 16911, West Java, Indonesia
| | - Ari Sulistyo Wulandari
- Research Center for Biotechnology-Indonesian Institute of Sciences, Cibinong 16911, West Java, Indonesia
| | - Widya Pintaka Bayu Putra
- Research Center for Biotechnology-Indonesian Institute of Sciences, Cibinong 16911, West Java, Indonesia
| | - Syahruddin Said
- Research Center for Biotechnology-Indonesian Institute of Sciences, Cibinong 16911, West Java, Indonesia
| | - Jakaria Jakaria
- Faculty of Animal Science, Bogor Agricultural University, Darmaga Campus, Bogor 16680, Indonesia
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14
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Waples RS, Kays R, Fredrickson RJ, Pacifici K, Mills LS. Is the Red Wolf a Listable Unit Under the US Endangered Species Act? J Hered 2018; 109:585-597. [PMID: 29889268 PMCID: PMC6022562 DOI: 10.1093/jhered/esy020] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 05/08/2018] [Indexed: 11/12/2022] Open
Abstract
Defining units that can be afforded legal protection is a crucial, albeit challenging, step in conservation planning. As we illustrate with a case study of the red wolf (Canis rufus) from the southeastern United States, this step is especially complex when the evolutionary history of the focal taxon is uncertain. The US Endangered Species Act (ESA) allows listing of species, subspecies, or Distinct Population Segments (DPSs) of vertebrates. Red wolves were listed as an endangered species in 1973, and their status remains precarious. However, some recent genetic studies suggest that red wolves are part of a small wolf species (C. lycaon) specialized for heavily forested habitats of eastern North America, whereas other authors suggest that red wolves arose, perhaps within the last ~400 years, through hybridization between gray wolves (C. lupus) and coyotes (C. latrans). Using published genetic, morphological, behavioral, and ecological data, we evaluated whether each evolutionary hypothesis would lead to a listable unit for red wolves. Although the potential hybrid origin of red wolves, combined with abundant evidence for recent hybridization with coyotes, raises questions about status as a separate species or subspecies, we conclude that under any proposed evolutionary scenario red wolves meet both criteria to be considered a DPS: they are Discrete compared with other conspecific populations, and they are Significant to the taxon to which they belong. As population-level units can qualify for legal protection under endangered-species legislation in many countries throughout the world, this general approach could potentially be applied more broadly.
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Affiliation(s)
- Robin S Waples
- NOAA Fisheries, Northwest Fisheries Science Center, Seattle, WA
| | - Roland Kays
- Department of Forestry & Environmental Resources, North Carolina State University, Raleigh, NC
- North Carolina Museum of Natural Sciences, Raleigh, NC
| | | | - Krishna Pacifici
- Department of Forestry & Environmental Resources, North Carolina State University, Raleigh, NC
| | - L Scott Mills
- Wildlife Biology Program and the Office of Research and Creative Scholarship, University of Montana, Missoula, MT
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15
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Hinton JW, Gittleman JL, van Manen FT, Chamberlain MJ. Size-assortative choice and mate availability influences hybridization between red wolves ( Canis rufus) and coyotes ( Canis latrans). Ecol Evol 2018; 8:3927-3940. [PMID: 29721269 PMCID: PMC5916303 DOI: 10.1002/ece3.3950] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 01/09/2018] [Accepted: 01/27/2018] [Indexed: 01/30/2023] Open
Abstract
Anthropogenic hybridization of historically isolated taxa has become a primary conservation challenge for many imperiled species. Indeed, hybridization between red wolves (Canis rufus) and coyotes (Canis latrans) poses a significant challenge to red wolf recovery. We considered seven hypotheses to assess factors influencing hybridization between red wolves and coyotes via pair‐bonding between the two species. Because long‐term monogamy and defense of all‐purpose territories are core characteristics of both species, mate choice has long‐term consequences. Therefore, red wolves may choose similar‐sized mates to acquire partners that behave similarly to themselves in the use of space and diet. We observed multiple factors influencing breeding pair formation by red wolves and found that most wolves paired with similar‐sized conspecifics and wolves that formed congeneric pairs with nonwolves (coyotes and hybrids) were mostly female wolves, the smaller of the two sexes. Additionally, we observed that lower red wolf abundance relative to nonwolves and the absence of helpers increased the probability that wolves consorted with nonwolves. However, successful pairings between red wolves and nonwolves were associated with wolves that maintained small home ranges. Behaviors associated with territoriality are energetically demanding and behaviors (e.g., aggressive interactions, foraging, and space use) involved in maintaining territories are influenced by body size. Consequently, we propose the hypothesis that size disparities between consorting red wolves and coyotes influence positive assortative mating and may represent a reproductive barrier between the two species. We offer that it may be possible to maintain wild populations of red wolves in the presence of coyotes if management strategies increase red wolf abundance on the landscape by mitigating key threats, such as human‐caused mortality and hybridization with coyotes. Increasing red wolf abundance would likely restore selection pressures that increase mean body and home‐range sizes of red wolves and decrease hybridization rates via reduced occurrence of congeneric pairs.
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Affiliation(s)
- Joseph W Hinton
- Warnell School of Forestry and Natural Resources University of Georgia Athens GA USA
| | | | - Frank T van Manen
- U.S. Geological Survey Northern Rocky Mountain Science Center Interagency Grizzly Bear Study Team Bozeman MT USA
| | - Michael J Chamberlain
- Warnell School of Forestry and Natural Resources University of Georgia Athens GA USA
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Heppenheimer E, Cosio DS, Brzeski KE, Caudill D, Van Why K, Chamberlain MJ, Hinton JW, vonHoldt B. Demographic history influences spatial patterns of genetic diversityin recently expanded coyote (Canis latrans) populations. Heredity (Edinb) 2018; 120:183-195. [PMID: 29269931 PMCID: PMC5836586 DOI: 10.1038/s41437-017-0014-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/06/2017] [Accepted: 10/03/2017] [Indexed: 11/09/2022] Open
Abstract
Human-mediated range expansions have increased in recent decades and represent unique opportunities to evaluate genetic outcomes of establishing peripheral populations across broad expansion fronts. Over the past century, coyotes (Canis latrans) have undergone a pervasive range expansion and now inhabit every state in the continental United States. Coyote expansion into eastern North America was facilitated by anthropogenic landscape changes and followed two broad expansion fronts. The northern expansion extended through the Great Lakes region and southern Canada, where hybridization with remnant wolf populations was common. The southern and more recent expansion front occurred approximately 40 years later and across territory where gray wolves have been historically absent and remnant red wolves were extirpated in the 1970s. We conducted a genetic survey at 10 microsatellite loci of 482 coyotes originating from 11 eastern U.S. states to address how divergent demographic histories influence geographic patterns of genetic diversity. We found that population structure corresponded to a north-south divide, which is consistent with the two known expansion routes. Additionally, we observed extremely high genetic diversity, which is atypical of recently expanded populations and is likely the result of multiple complex demographic processes, in addition to hybridization with other Canis species. Finally, we considered the transition of allele frequencies across geographic space and suggest the mid-Atlantic states of North Carolina and Virginia as an emerging contact zone between these two distinct coyote expansion fronts.
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Affiliation(s)
- Elizabeth Heppenheimer
- Department of Ecology & Evolutionary Biology, Princeton University, 106 A Guyot Hall, Princeton, NJ, 08544, USA.
| | - Daniela S Cosio
- Department of Ecology & Evolutionary Biology, Princeton University, 106 A Guyot Hall, Princeton, NJ, 08544, USA
| | - Kristin E Brzeski
- Department of Ecology & Evolutionary Biology, Princeton University, 106 A Guyot Hall, Princeton, NJ, 08544, USA
| | - Danny Caudill
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, 1105 SW Williston Road, Gainesville, FL, 32601, USA
- Alaska Department of Fish Game, 1300 College Road, Fairbanks, AK, 99701, USA
| | - Kyle Van Why
- United States Department of Agriculture, Animal Plant Health Inspection Service, Wildlife Services, PO Box 60827, Harrisburg, PA, 17106, USA
| | - Michael J Chamberlain
- Warnell School of Forestry and Natural Resources, University of Georgia, 180 E Green Street, Athens, GA, 30621, USA
| | - Joseph W Hinton
- Warnell School of Forestry and Natural Resources, University of Georgia, 180 E Green Street, Athens, GA, 30621, USA
| | - Bridgett vonHoldt
- Department of Ecology & Evolutionary Biology, Princeton University, 106 A Guyot Hall, Princeton, NJ, 08544, USA
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17
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Bohling JH, Mastro LL, Adams JR, Gese EM, Owen SF, Waits LP. Panmixia and Limited Interspecific Introgression in Coyotes (Canis latrans) from West Virginia and Virginia, USA. J Hered 2017; 108:608-617. [PMID: 28821188 DOI: 10.1093/jhered/esx068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 07/25/2017] [Indexed: 02/04/2023] Open
Abstract
The expansion of coyotes (Canis latrans) into the eastern United States has had major consequences for ecological communities and wildlife managers. Despite this, there has been little investigation of the genetics of coyotes across much of this region, especially outside of the northeast. Understanding patterns of genetic structure and interspecific introgression would provide insights into the colonization history of the species, its response to the modern environment, and interactions with other canids. We examined the genetic characteristics of 121 coyotes from the mid-Atlantic states of West Virginia and Virginia by genotyping 17 polymorphic nuclear DNA microsatellite loci. These genotypes were compared with those from other canid populations to evaluate the extent of genetic introgression. We conducted spatial clustering analyses and spatial autocorrelation to assess genetic structure among sampled coyotes. Coyotes across the 2 states had high genetic diversity, and we found no evidence of genetic structure. Six to sixteen percent of individuals displayed some evidence of genetic introgression from other species depending on the method and criteria used, but the population possessed predominantly coyote ancestry. Our findings suggested introgression from other canid populations has played less of a role in shaping the genetic character of coyotes in these states compared with populations closer to the Canadian border. Coyotes appear to display a panmictic population structure despite high habitat heterogeneity and heavy human influence in the spatial environment, underscoring the adaptability of the species.
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Affiliation(s)
- Justin H Bohling
- U.S. Fish and Wildlife Service, Abernathy Fish Technology Center, Longview, WA 98632; U.S. Department of Agriculture-APHIS-Wildlife Services, Christiansburg, VA; Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID; U.S. Department of Agriculture-APHIS-Wildlife Services, National Wildlife Research Center, Utah State University, Logan, UT; West Virginia University Extension Service, Morgantown, WV
| | - Lauren L Mastro
- U.S. Fish and Wildlife Service, Abernathy Fish Technology Center, Longview, WA 98632; U.S. Department of Agriculture-APHIS-Wildlife Services, Christiansburg, VA; Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID; U.S. Department of Agriculture-APHIS-Wildlife Services, National Wildlife Research Center, Utah State University, Logan, UT; West Virginia University Extension Service, Morgantown, WV
| | - Jennifer R Adams
- U.S. Fish and Wildlife Service, Abernathy Fish Technology Center, Longview, WA 98632; U.S. Department of Agriculture-APHIS-Wildlife Services, Christiansburg, VA; Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID; U.S. Department of Agriculture-APHIS-Wildlife Services, National Wildlife Research Center, Utah State University, Logan, UT; West Virginia University Extension Service, Morgantown, WV
| | - Eric M Gese
- U.S. Fish and Wildlife Service, Abernathy Fish Technology Center, Longview, WA 98632; U.S. Department of Agriculture-APHIS-Wildlife Services, Christiansburg, VA; Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID; U.S. Department of Agriculture-APHIS-Wildlife Services, National Wildlife Research Center, Utah State University, Logan, UT; West Virginia University Extension Service, Morgantown, WV
| | - Sheldon F Owen
- U.S. Fish and Wildlife Service, Abernathy Fish Technology Center, Longview, WA 98632; U.S. Department of Agriculture-APHIS-Wildlife Services, Christiansburg, VA; Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID; U.S. Department of Agriculture-APHIS-Wildlife Services, National Wildlife Research Center, Utah State University, Logan, UT; West Virginia University Extension Service, Morgantown, WV
| | - Lisette P Waits
- U.S. Fish and Wildlife Service, Abernathy Fish Technology Center, Longview, WA 98632; U.S. Department of Agriculture-APHIS-Wildlife Services, Christiansburg, VA; Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID; U.S. Department of Agriculture-APHIS-Wildlife Services, National Wildlife Research Center, Utah State University, Logan, UT; West Virginia University Extension Service, Morgantown, WV
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18
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vonHoldt B, Heppenheimer E, Petrenko V, Croonquist P, Rutledge LY. Ancestry-Specific Methylation Patterns in Admixed Offspring from an Experimental Coyote and Gray Wolf Cross. J Hered 2017; 108:341-348. [PMID: 28182234 DOI: 10.1093/jhered/esx004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 01/19/2017] [Indexed: 12/18/2022] Open
Abstract
Reduced fitness of admixed individuals is typically attributed to genetic incompatibilities. Although mismatched genomes can lead to fitness changes, in some cases the reduction in hybrid fitness is subtle. The potential role of transcriptional regulation in admixed genomes could provide a mechanistic explanation for these discrepancies, but evidence is lacking for nonmodel organisms. Here, we explored the intersection of genetics and gene regulation in admixed genomes derived from an experimental cross between a western gray wolf and western coyote. We found a significant positive association between methylation and wolf ancestry, and identified outlier genes that have been previously implicated in inbreeding-related, or otherwise deleterious, phenotypes. We describe a pattern of site-specific, rather than genome-wide, methylation driven by inter-specific hybridization. Epigenetic variation is thus suggested to play a nontrivial role in both maintaining and combating mismatched genotypes through putative transcriptional mechanisms. We conclude that the regulation of gene expression is an underappreciated key component of hybrid genome functioning, but could also act as a potential source of novel and beneficial adaptive variation in hybrid offspring.
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Affiliation(s)
- Bridgett vonHoldt
- From the Ecology & Evolutionary Biology Department, Princeton University, 106A Guyot Hall, Princeton, NJ 08544 (vonHoldt, Heppenheimer, and Rutledge); and Biology Department, Anoka-Ramsey Community College, Coon Rapids, MN 55433 (Petrenko and Croonquist)
| | - Elizabeth Heppenheimer
- From the Ecology & Evolutionary Biology Department, Princeton University, 106A Guyot Hall, Princeton, NJ 08544 (vonHoldt, Heppenheimer, and Rutledge); and Biology Department, Anoka-Ramsey Community College, Coon Rapids, MN 55433 (Petrenko and Croonquist)
| | - Vladimir Petrenko
- From the Ecology & Evolutionary Biology Department, Princeton University, 106A Guyot Hall, Princeton, NJ 08544 (vonHoldt, Heppenheimer, and Rutledge); and Biology Department, Anoka-Ramsey Community College, Coon Rapids, MN 55433 (Petrenko and Croonquist)
| | - Paula Croonquist
- From the Ecology & Evolutionary Biology Department, Princeton University, 106A Guyot Hall, Princeton, NJ 08544 (vonHoldt, Heppenheimer, and Rutledge); and Biology Department, Anoka-Ramsey Community College, Coon Rapids, MN 55433 (Petrenko and Croonquist)
| | - Linda Y Rutledge
- From the Ecology & Evolutionary Biology Department, Princeton University, 106A Guyot Hall, Princeton, NJ 08544 (vonHoldt, Heppenheimer, and Rutledge); and Biology Department, Anoka-Ramsey Community College, Coon Rapids, MN 55433 (Petrenko and Croonquist)
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19
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Arbogast BS, Hodge AMC, Brenner-Coltrain J. Stable Isotope Analysis of Dietary Overlap between the Endangered Red Wolf and Sympatric Coyote in Northeastern North Carolina. SOUTHEAST NAT 2017. [DOI: 10.1656/058.016.0215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Brian S. Arbogast
- Department of Biology and Marine Biology, University of North Carolina-Wilmington, Wilmington, NC 28403
| | - Anne-Marie C. Hodge
- Department of Biology and Marine Biology, University of North Carolina-Wilmington, Wilmington, NC 28403
- Current address - Department of Zoology and Physiology, University of Wyoming, 1000 East University Avenue, Laramie, WY. 82070
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20
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Hohenlohe PA, Rutledge LY, Waits LP, Andrews KR, Adams JR, Hinton JW, Nowak RM, Patterson BR, Wydeven AP, Wilson PA, White BN. Comment on "Whole-genome sequence analysis shows two endemic species of North American wolf are admixtures of the coyote and gray wolf". SCIENCE ADVANCES 2017; 3:e1602250. [PMID: 28630899 PMCID: PMC5462499 DOI: 10.1126/sciadv.1602250] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 04/19/2017] [Indexed: 05/05/2023]
Abstract
Whole-genome data do not support a recent hybrid origin for red and eastern wolves.
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Affiliation(s)
- Paul A. Hohenlohe
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844-3051, USA
| | - Linda Y. Rutledge
- Biology Department, Trent University, Peterborough, Ontario K9L 0G2, Canada
| | - Lisette P. Waits
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID 83844-1136, USA
| | - Kimberly R. Andrews
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID 83844-1136, USA
| | - Jennifer R. Adams
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID 83844-1136, USA
| | - Joseph W. Hinton
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA 30602, USA
| | | | - Brent R. Patterson
- Ministry of Natural Resources and Forestry, Trent University, Peterborough, Ontario K9L 0G2, Canada
| | | | - Paul A. Wilson
- Biology Department, Trent University, Peterborough, Ontario K9L 0G2, Canada
| | - Brad N. White
- Biology Department, Trent University, Peterborough, Ontario K9L 0G2, Canada
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21
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Benson JF, Loveless KM, Rutledge LY, Patterson BR. Ungulate predation and ecological roles of wolves and coyotes in eastern North America. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2017; 27:718-733. [PMID: 28064464 DOI: 10.1002/eap.1499] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Revised: 11/29/2016] [Accepted: 12/21/2016] [Indexed: 06/06/2023]
Abstract
Understanding the ecological roles of species that influence ecosystem processes is a central goal of ecology and conservation biology. Eastern coyotes (Canis latrans) have ascended to the role of apex predator across much of eastern North America since the extirpation of wolves (Canis spp.) and there has been considerable confusion regarding their ability to prey on ungulates and their ecological niche relative to wolves. Eastern wolves (C. lycaon) are thought to have been the historical top predator in eastern deciduous forests and have previously been characterized as deer specialists that are inefficient predators of moose because of their smaller size relative to gray wolves (C. lupus). We investigated intrinsic and extrinsic influences on per capita kill rates of white-tailed deer (Odocoileus virginianus) and moose (Alces alces) during winter by sympatric packs of eastern coyotes, eastern wolves, and admixed canids in Ontario, Canada to clarify the predatory ability and ecological roles of the different canid top predators of eastern North America. Eastern coyote ancestry within packs negatively influenced per capita total ungulate (deer and moose combined) and moose kill rates. Furthermore, canids in packs dominated by eastern coyote ancestry consumed significantly less ungulate biomass and more anthropogenic food than packs dominated by wolf ancestry. Similar to gray wolves in previous studies, eastern wolves preyed on deer where they were available. However, in areas were deer were scarce, eastern wolves killed moose at rates similar to those previously documented for gray wolves at comparable moose densities across North America. Eastern coyotes are effective deer predators, but their dietary flexibility and low kill rates on moose suggest they have not replaced the ecological role of wolves in eastern North America.
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Affiliation(s)
- John F Benson
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, K9J 7B8, Canada
| | - Karen M Loveless
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, K9J 7B8, Canada
| | - Linda Y Rutledge
- Ecology and Evolutionary Biology Department, Princeton University, Princeton, New Jersey, 08544, USA
| | - Brent R Patterson
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, K9J 7B8, Canada
- Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Peterborough, Ontario, K9J 7B8, Canada
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22
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Otis JA, Thornton D, Rutledge L, Murray DL. Ecological niche differentiation across a wolf-coyote hybrid zone in eastern North America. DIVERS DISTRIB 2017. [DOI: 10.1111/ddi.12543] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Josée-Anne Otis
- Department of Biology; Trent University; Peterborough ON Canada
| | - Dan Thornton
- School of the Environment; Washington State University; Pullman WA USA
| | - Linda Rutledge
- Department of Biology; Trent University; Peterborough ON Canada
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23
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Rutledge LY, Desy G, Fryxell JM, Middel K, White BN, Patterson BR. Patchy distribution and low effective population size raise concern for an at-risk top predator. DIVERS DISTRIB 2016. [DOI: 10.1111/ddi.12496] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Linda Y. Rutledge
- Biology Department; Trent University; 2140 East Bank Drive Peterborough ON K9J 7B8 Canada
| | - Glenn Desy
- Department of Integrative Biology; University of Guelph; Summerlee Science Complex Guelph ON N1G 2W1 Canada
| | - John M. Fryxell
- Department of Integrative Biology; University of Guelph; Summerlee Science Complex Guelph ON N1G 2W1 Canada
| | - Kevin Middel
- Ontario Ministry of Natural Resources & Forestry; Trent University; DNA Building 2140 East Bank Drive Peterborough ON K9L 0G2 Canada
| | - Bradley N. White
- Biology Department; Trent University; 2140 East Bank Drive Peterborough ON K9J 7B8 Canada
| | - Brent R. Patterson
- Ontario Ministry of Natural Resources & Forestry; Trent University; DNA Building 2140 East Bank Drive Peterborough ON K9L 0G2 Canada
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24
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vonHoldt BM, Cahill JA, Fan Z, Gronau I, Robinson J, Pollinger JP, Shapiro B, Wall J, Wayne RK. Whole-genome sequence analysis shows that two endemic species of North American wolf are admixtures of the coyote and gray wolf. SCIENCE ADVANCES 2016; 2:e1501714. [PMID: 29713682 PMCID: PMC5919777 DOI: 10.1126/sciadv.1501714] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 06/28/2016] [Indexed: 05/22/2023]
Abstract
Protection of populations comprising admixed genomes is a challenge under the Endangered Species Act (ESA), which is regarded as the most powerful species protection legislation ever passed in the United States but lacks specific provisions for hybrids. The eastern wolf is a newly recognized wolf-like species that is highly admixed and inhabits the Great Lakes and eastern United States, a region previously thought to be included in the geographic range of only the gray wolf. The U.S. Fish and Wildlife Service has argued that the presence of the eastern wolf, rather than the gray wolf, in this area is grounds for removing ESA protection (delisting) from the gray wolf across its geographic range. In contrast, the red wolf from the southeastern United States was one of the first species protected under the ESA and was protected despite admixture with coyotes. We use whole-genome sequence data to demonstrate a lack of unique ancestry in eastern and red wolves that would not be expected if they represented long divergent North American lineages. These results suggest that arguments for delisting the gray wolf are not valid. Our findings demonstrate how a strict designation of a species under the ESA that does not consider admixture can threaten the protection of endangered entities. We argue for a more balanced approach that focuses on the ecological context of admixture and allows for evolutionary processes to potentially restore historical patterns of genetic variation.
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Affiliation(s)
- Bridgett M. vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - James A. Cahill
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Zhenxin Fan
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, People’s Republic of China
| | - Ilan Gronau
- Efi Arazi School of Computer Science, Herzliya Interdisciplinary Center, Herzliya 46150, Israel
| | - Jacqueline Robinson
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095–1606, USA
| | - John P. Pollinger
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095–1606, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jeff Wall
- Department of Epidemiology and Biostatistics, School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095–1606, USA
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25
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Rutledge LY, Devillard S, Hohenlohe PA, White BN. Considering all the evidence: a reply to Sefc and Koblmüller (2016). Biol Lett 2016; 12:20151009. [PMID: 26843551 DOI: 10.1098/rsbl.2015.1009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- L Y Rutledge
- Department of Ecology and Evolutionary Biology, Princeton University, 106A Guyot Hall, Princeton, NJ 08544, USA
| | - S Devillard
- Université de Lyon, Lyon 69000, France; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, Villeurbanne 69622, France
| | - P A Hohenlohe
- Department of Biological Sciences and Institute of Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, USA
| | - B N White
- Department of Biology, Trent University, 2140 East Bank Drive, Peterborough, Ontario, Canada K9 J 7B9
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26
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Rutledge LY, Devillard S, Boone JQ, Hohenlohe PA, White BN. RAD sequencing and genomic simulations resolve hybrid origins within North American Canis. Biol Lett 2016; 11:rsbl.2015.0303. [PMID: 26156129 PMCID: PMC4528444 DOI: 10.1098/rsbl.2015.0303] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Top predators are disappearing worldwide, significantly changing ecosystems that depend on top-down regulation. Conflict with humans remains the primary roadblock for large carnivore conservation, but for the eastern wolf (Canis lycaon), disagreement over its evolutionary origins presents a significant barrier to conservation in Canada and has impeded protection for grey wolves (Canis lupus) in the USA. Here, we use 127 235 single-nucleotide polymorphisms (SNPs) identified from restriction-site associated DNA sequencing (RAD-seq) of wolves and coyotes, in combination with genomic simulations, to test hypotheses of hybrid origins of Canis types in eastern North America. A principal components analysis revealed no evidence to support eastern wolves, or any other Canis type, as the product of grey wolf × western coyote hybridization. In contrast, simulations that included eastern wolves as a distinct taxon clarified the hybrid origins of Great Lakes-boreal wolves and eastern coyotes. Our results support the eastern wolf as a distinct genomic cluster in North America and help resolve hybrid origins of Great Lakes wolves and eastern coyotes. The data provide timely information that will shed new light on the debate over wolf conservation in eastern North America.
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Affiliation(s)
- L. Y. Rutledge
- Biology Department, Trent University, 2140 East Bank Drive, Peterborough, Ontario, K9J 7B8Canada
- e-mail:
| | - S. Devillard
- Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622, Villeurbanne, France
| | | | - P. A. Hohenlohe
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - B. N. White
- Biology Department, Trent University, 2140 East Bank Drive, Peterborough, Ontario, K9J 7B8Canada
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27
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Bohling JH, Dellinger J, McVey JM, Cobb DT, Moorman CE, Waits LP. Describing a developing hybrid zone between red wolves and coyotes in eastern North Carolina, USA. Evol Appl 2016; 9:791-804. [PMID: 27330555 PMCID: PMC4908465 DOI: 10.1111/eva.12388] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 04/26/2016] [Indexed: 12/02/2022] Open
Abstract
When hybridizing species come into contact, understanding the processes that regulate their interactions can help predict the future outcome of the system. This is especially relevant in conservation situations where human activities can influence hybridization dynamics. We investigated a developing hybrid zone between red wolves and coyotes in North Carolina, USA to elucidate patterns of hybridization in a system heavily managed for preservation of the red wolf genome. Using noninvasive genetic sampling of scat, we surveyed a 2880 km2 region adjacent to the Red Wolf Experimental Population Area (RWEPA). We combined microsatellite genotypes collected from this survey with those from companion studies conducted both within and outside the RWEPA to describe the gradient of red wolf ancestry. A total of 311 individuals were genotyped at 17 loci and red wolf ancestry decreased along an east–west gradient across the RWEPA. No red wolves were found outside the RWEPA, yet half of individuals found within this area were coyotes. Hybrids composed only 4% of individuals within this landscape despite co‐occurrence of the two species throughout the RWEPA. The low proportion of hybrids suggests that a combination of active management and natural isolating mechanisms may be limiting intermixing within this hybrid system.
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Affiliation(s)
- Justin H Bohling
- Department of Fish and Wildlife Resources University of Idaho Moscow ID USA
| | - Justin Dellinger
- School of Environmental and Forest Sciences University of Washington Seattle WA USA
| | - Justin M McVey
- Department of Forestry and Environmental Resources North Carolina State University Raleigh NC USA
| | - David T Cobb
- North Carolina Wildlife Resources Commission Raleigh NC USA
| | - Christopher E Moorman
- Department of Forestry and Environmental Resources North Carolina State University Raleigh NC USA
| | - Lisette P Waits
- Department of Fish and Wildlife Resources University of Idaho Moscow ID USA
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vonHoldt BM, Kays R, Pollinger JP, Wayne RK. Admixture mapping identifies introgressed genomic regions in North American canids. Mol Ecol 2016; 25:2443-53. [PMID: 27106273 DOI: 10.1111/mec.13667] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 04/12/2016] [Accepted: 04/15/2016] [Indexed: 12/21/2022]
Abstract
Hybrid zones typically contain novel gene combinations that can be tested by natural selection in a unique genetic context. Parental haplotypes that increase fitness can introgress beyond the hybrid zone, into the range of parental species. We used the Affymetrix canine SNP genotyping array to identify genomic regions tagged by multiple ancestry informative markers that are more frequent in an admixed population than expected. We surveyed a hybrid zone formed in the last 100 years as coyotes expanded their range into eastern North America. Concomitant with expansion, coyotes hybridized with wolves and some populations became more wolflike, such that coyotes in the northeast have the largest body size of any coyote population. Using a set of 3102 ancestry informative markers, we identified 60 differentially introgressed regions in 44 canines across this admixture zone. These regions are characterized by an excess of exogenous ancestry and, in northeastern coyotes, are enriched for genes affecting body size and skeletal proportions. Further, introgressed wolf-derived alleles have penetrated into Southern US coyote populations. Because no wolves currently exist in this area, these alleles are unlikely to have originated from recent hybridization. Instead, they probably originated from intraspecific gene flow or ancient admixture. We show that grey wolf and coyote admixture has far-reaching effects and, in addition to phenotypically transforming admixed populations, allows for the differential movement of alleles from different parental species to be tested in new genomic backgrounds.
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Affiliation(s)
- Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Roland Kays
- North Carolina Museum of Natural Science and NC State University, Raleigh, NC, 27612, USA
| | - John P Pollinger
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
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Wayne RK, Shaffer HB. Hybridization and endangered species protection in the molecular era. Mol Ecol 2016; 25:2680-9. [DOI: 10.1111/mec.13642] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 04/03/2016] [Accepted: 04/08/2016] [Indexed: 01/05/2023]
Affiliation(s)
- Robert K. Wayne
- Department of Ecology and Evolutionary Biology 610 Charles E. Young Dr. South University of California Los Angeles CA 90095 USA
| | - H. Bradley Shaffer
- Department of Ecology and Evolutionary Biology 610 Charles E. Young Dr. South University of California Los Angeles CA 90095 USA
- La Kretz Center for California Conservation Science Institute of the Environment and Sustainability 619 Charles E. Young Dr. South University of California Los Angeles CA 90095 USA
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Agung PP, Saputra F, Septian WA, Lusiana, Zein MSA, Sulandari S, Anwar S, Wulandari AS, Said S, Tappa B. Study of Genetic Diversity among Simmental Cross Cattle in West Sumatra Based on Microsatellite Markers. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 29:176-83. [PMID: 26732442 PMCID: PMC4698697 DOI: 10.5713/ajas.15.0155] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 05/11/2015] [Accepted: 07/17/2015] [Indexed: 11/27/2022]
Abstract
A study was conducted to assess the genetic diversity among Simmental Cross cattle in West Sumatra using microsatellite DNA markers. A total of 176 individual cattle blood samples was used for obtaining DNA samples. Twelve primers of microsatellite loci as recommended by FAO were used to identify the genetic diversity of the Simmental Cross cattle population. Multiplex DNA fragment analysis method was used for allele identification. All the microsatellite loci in this study were highly polymorphic and all of the identified alleles were able to classify the cattle population into several groups based on their genetic distance. The heterozygosity values of microsatellite loci in this study ranged from 0.556 to 0.782. The polymorphism information content (PIC) value of the 12 observed loci is high (PIC>0.5). The highest PIC value in the Simmental cattle population was 0.893 (locus TGLA53), while the lowest value was 0.529 (locus BM1818). Based on the genetic distance value, the subpopulation of the Simmental Cross-Agam and the Simmental Cross-Limapuluh Kota was exceptionally close to the Simmental Purebred thus indicating that a grading-up process has taken place with the Simmental Purebred. In view of the advantages possessed by the Simmental Cross cattle and the evaluation of the genetic diversity results, a number of subpopulations in this study can be considered as the initial (base) population for the Simmental Cross cattle breeding programs in West Sumatra, Indonesia.
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Affiliation(s)
- Paskah Partogi Agung
- Research Center for Biology-Indonesian Institute of Sciences, Cibinong 16911, West Java, Indonesia
| | - Ferdy Saputra
- Research Center for Biology-Indonesian Institute of Sciences, Cibinong 16911, West Java, Indonesia
| | - Wike Andre Septian
- Research Center for Biology-Indonesian Institute of Sciences, Cibinong 16911, West Java, Indonesia
| | - Lusiana
- Research Center for Biology-Indonesian Institute of Sciences, Cibinong 16911, West Java, Indonesia
| | - Moch Syamsul Arifin Zein
- Research Center for Biology-Indonesian Institute of Sciences, Cibinong 16911, West Java, Indonesia
| | - Sri Sulandari
- Research Center for Biology-Indonesian Institute of Sciences, Cibinong 16911, West Java, Indonesia
| | - Saiful Anwar
- Research Center for Biology-Indonesian Institute of Sciences, Cibinong 16911, West Java, Indonesia
| | - Ari Sulistyo Wulandari
- Research Center for Biology-Indonesian Institute of Sciences, Cibinong 16911, West Java, Indonesia
| | - Syahruddin Said
- Research Center for Biology-Indonesian Institute of Sciences, Cibinong 16911, West Java, Indonesia
| | - Baharuddin Tappa
- Research Center for Biology-Indonesian Institute of Sciences, Cibinong 16911, West Java, Indonesia
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31
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Basto MP, Santos-Reis M, Simões L, Grilo C, Cardoso L, Cortes H, Bruford MW, Fernandes C. Assessing Genetic Structure in Common but Ecologically Distinct Carnivores: The Stone Marten and Red Fox. PLoS One 2016; 11:e0145165. [PMID: 26727497 PMCID: PMC4699814 DOI: 10.1371/journal.pone.0145165] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 11/30/2015] [Indexed: 11/23/2022] Open
Abstract
The identification of populations and spatial genetic patterns is important for ecological and conservation research, and spatially explicit individual-based methods have been recognised as powerful tools in this context. Mammalian carnivores are intrinsically vulnerable to habitat fragmentation but not much is known about the genetic consequences of fragmentation in common species. Stone martens (Martes foina) and red foxes (Vulpes vulpes) share a widespread Palearctic distribution and are considered habitat generalists, but in the Iberian Peninsula stone martens tend to occur in higher quality habitats. We compared their genetic structure in Portugal to see if they are consistent with their differences in ecological plasticity, and also to illustrate an approach to explicitly delineate the spatial boundaries of consistently identified genetic units. We analysed microsatellite data using spatial Bayesian clustering methods (implemented in the software BAPS, GENELAND and TESS), a progressive partitioning approach and a multivariate technique (Spatial Principal Components Analysis-sPCA). Three consensus Bayesian clusters were identified for the stone marten. No consensus was achieved for the red fox, but one cluster was the most probable clustering solution. Progressive partitioning and sPCA suggested additional clusters in the stone marten but they were not consistent among methods and were geographically incoherent. The contrasting results between the two species are consistent with the literature reporting stricter ecological requirements of the stone marten in the Iberian Peninsula. The observed genetic structure in the stone marten may have been influenced by landscape features, particularly rivers, and fragmentation. We suggest that an approach based on a consensus clustering solution of multiple different algorithms may provide an objective and effective means to delineate potential boundaries of inferred subpopulations. sPCA and progressive partitioning offer further verification of possible population structure and may be useful for revealing cryptic spatial genetic patterns worth further investigation.
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Affiliation(s)
- Mafalda P. Basto
- Ce3C – Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Cardiff School of Biosciences, Cardiff University, Cardiff, United Kingdom
- * E-mail:
| | - Margarida Santos-Reis
- Ce3C – Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Luciana Simões
- Ce3C – Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Clara Grilo
- Centro Brasileiro de Estudos em Ecologia de Estradas/Programa de Pós-graduação em Ecologia Aplicada, Universidade Federal de Lavras, Lavras, Minas Gerais, Brasil
| | - Luís Cardoso
- Departamento de Ciências Veterinárias, Escola de Ciências Agrárias e Veterinárias, Universidade de Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
| | - Helder Cortes
- Laboratório de Parasitologia Victor Caeiro, Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Évora, Portugal
| | - Michael W. Bruford
- Cardiff School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Carlos Fernandes
- Ce3C – Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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Power JW, LeBlanc N, Bondrup-Nielsen S, Boudreau MJ, O'Brien MS, Stewart DT. Spatial Genetic and Body-Size Trends in Atlantic CanadaCanis latrans(Coyote) Populations. Northeast Nat (Steuben) 2015. [DOI: 10.1656/045.022.0314] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Vergara M, Basto MP, Madeira MJ, Gómez-Moliner BJ, Santos-Reis M, Fernandes C, Ruiz-González A. Inferring Population Genetic Structure in Widely and Continuously Distributed Carnivores: The Stone Marten (Martes foina) as a Case Study. PLoS One 2015; 10:e0134257. [PMID: 26222680 PMCID: PMC4519273 DOI: 10.1371/journal.pone.0134257] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 07/07/2015] [Indexed: 11/20/2022] Open
Abstract
The stone marten is a widely distributed mustelid in the Palaearctic region that exhibits variable habitat preferences in different parts of its range. The species is a Holocene immigrant from southwest Asia which, according to fossil remains, followed the expansion of the Neolithic farming cultures into Europe and possibly colonized the Iberian Peninsula during the Early Neolithic (ca. 7,000 years BP). However, the population genetic structure and historical biogeography of this generalist carnivore remains essentially unknown. In this study we have combined mitochondrial DNA (mtDNA) sequencing (621 bp) and microsatellite genotyping (23 polymorphic markers) to infer the population genetic structure of the stone marten within the Iberian Peninsula. The mtDNA data revealed low haplotype and nucleotide diversities and a lack of phylogeographic structure, most likely due to a recent colonization of the Iberian Peninsula by a few mtDNA lineages during the Early Neolithic. The microsatellite data set was analysed with a) spatial and non-spatial Bayesian individual-based clustering (IBC) approaches (STRUCTURE, TESS, BAPS and GENELAND), and b) multivariate methods [discriminant analysis of principal components (DAPC) and spatial principal component analysis (sPCA)]. Additionally, because isolation by distance (IBD) is a common spatial genetic pattern in mobile and continuously distributed species and it may represent a challenge to the performance of the above methods, the microsatellite data set was tested for its presence. Overall, the genetic structure of the stone marten in the Iberian Peninsula was characterized by a NE-SW spatial pattern of IBD, and this may explain the observed disagreement between clustering solutions obtained by the different IBC methods. However, there was significant indication for contemporary genetic structuring, albeit weak, into at least three different subpopulations. The detected subdivision could be attributed to the influence of the rivers Ebro, Tagus and Guadiana, suggesting that main watercourses in the Iberian Peninsula may act as semi-permeable barriers to gene flow in stone martens. To our knowledge, this is the first phylogeographic and population genetic study of the species at a broad regional scale. We also wanted to make the case for the importance and benefits of using and comparing multiple different clustering and multivariate methods in spatial genetic analyses of mobile and continuously distributed species.
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Affiliation(s)
- María Vergara
- Department of Zoology and Animal Cell Biology, Zoology Laboratory, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
- Systematics, Biogeography and Population Dynamics Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Mafalda P. Basto
- CE3C—Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - María José Madeira
- Department of Zoology and Animal Cell Biology, Zoology Laboratory, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
- Systematics, Biogeography and Population Dynamics Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Benjamín J. Gómez-Moliner
- Department of Zoology and Animal Cell Biology, Zoology Laboratory, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
- Systematics, Biogeography and Population Dynamics Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Margarida Santos-Reis
- CE3C—Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Carlos Fernandes
- CE3C—Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Aritz Ruiz-González
- Department of Zoology and Animal Cell Biology, Zoology Laboratory, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
- Systematics, Biogeography and Population Dynamics Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
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34
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Ellington EH, Murray DL. Influence of hybridization on animal space use: a case study using coyote range expansion. OIKOS 2015. [DOI: 10.1111/oik.01824] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- E. Hance Ellington
- Environmental and Life Sciences, Trent Univ.; 2140 East Bank Drive Peterborough, ON K9J 7B8 Canada
| | - Dennis L. Murray
- Biology Dept; Trent Univ.; 2140 East Bank Drive Peterborough, ON K9J 7B8 Canada
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35
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A genetic discontinuity in moose (Alces alces) in Alaska corresponds with fenced transportation infrastructure. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0700-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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36
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Benson JF, Patterson BR. Spatial overlap, proximity, and habitat use of individual wolves within the same packs. WILDLIFE SOC B 2014. [DOI: 10.1002/wsb.506] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- John F. Benson
- Environmental and Life Sciences Graduate Program; Trent University; Peterborough ON K9J 7B8 Canada
| | - Brent R. Patterson
- Wildlife Research and Monitoring Section; Ontario Ministry of Natural Resources and Forestry; Peterborough ON K9J 7B8 Canada
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37
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Multivariate analysis of polyploid data reveals the role of railways in the spread of the invasive South African Ragwort (Senecio inaequidens). CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0676-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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38
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Aghbolaghi MA, Rezaei HR, Scandura M, Kaboli M. Low gene flow between Iranian Grey Wolves(Canis lupus)and dogs documented using uniparental genetic markers. ZOOLOGY IN THE MIDDLE EAST 2014. [DOI: 10.1080/09397140.2014.914708] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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39
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Benson JF, Patterson BR, Mahoney PJ. A protected area influences genotype-specific survival and the structure of a Canis hybrid zone. Ecology 2014; 95:254-64. [PMID: 24669720 DOI: 10.1890/13-0698.1] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
It is widely recognized that protected areas can strongly influence ecological systems and that hybridization is an important conservation issue. However, previous studies have not explicitly considered the influence of protected areas on hybridization dynamics. Eastern wolves are a species of special concern and their distribution is largely restricted to a protected population in Algonquin Provincial Park (APP), Ontario, Canada, where they are the numerically dominant canid. We studied intrinsic and extrinsic factors influencing survival and cause-specific mortality of hybrid and parental canids in the three-species hybrid zone between eastern wolves, eastern coyotes, and gray wolves in and adjacent to APP. Mortality risk for eastern wolves in areas adjacent to APP was significantly higher than for other sympatric Canis types outside of APP, and for eastern wolves and other canids within APP. Outside of APP, the annual mortality rate of all canids by harvest (24%) was higher than for other causes of death (4-7%). Furthermore, eastern wolves (hazard ratio = 3.5) and nonresidents (transients and dispersing animals, hazard ratio = 2.7) were more likely to die from harvest relative to other Canis types and residents, respectively. Thus, eastern wolves dispersing from APP were especially vulnerable to harvest mortality. For residents, eastern wolf survival was more negatively influenced by increased road density than for other Canis types, further highlighting the sensitivity of eastern wolves to human disturbance. A cycle of dispersal from APP followed by high rates of mortality and hybridization appears to maintain eastern wolves at low density adjacent to APP, limiting the potential for expansion beyond the protected area. However, high survival and numerical dominance of eastern wolves within APP suggest that protected areas can allow rare hybridizing species to persist even if their demographic performance is compromised and barriers to hybridization are largely absent in the adjacent matrix.
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Monzón J. First regional evaluation of nuclear genetic diversity and population structure in northeastern coyotes ( Canis latrans). F1000Res 2014; 3:66. [PMID: 25075291 PMCID: PMC4097358 DOI: 10.12688/f1000research.3567.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/03/2014] [Indexed: 12/15/2022] Open
Abstract
Previous genetic studies of eastern coyotes ( Canis latrans) are based on one of two strategies: sampling many individuals using one or very few molecular markers, or sampling very few individuals using many genomic markers. Thus, a regional analysis of genetic diversity and population structure in eastern coyotes using many samples and several molecular markers is lacking. I evaluated genetic diversity and population structure in 385 northeastern coyotes using 16 common single nucleotide polymorphisms (SNPs). A region-wide analysis of population structure revealed three primary genetic populations, but these do not correspond to the same three subdivisions inferred in a previous analysis of mitochondrial DNA sequences. More focused geographic analyses of population structure indicated that ample genetic structure occurs in coyotes from an intermediate contact zone where two range expansion fronts meet. These results demonstrate that genotyping several highly heterozygous SNPs in a large, geographically dense sample is an effective way to detect cryptic population genetic structure. The importance of SNPs in studies of population and wildlife genomics is rapidly increasing; this study adds to the growing body of recent literature that demonstrates the utility of SNPs ascertained from a model organism for evolutionary inference in closely related species.
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Affiliation(s)
- Javier Monzón
- Departments of Ecology & Evolution and Molecular Genetics & Microbiology, Stony Brook University, Stony Brook, NY, 11794, USA
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41
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Galov A, Sindičić M, Gomerčić T, Arbanasić H, Baburić M, Bošković I, Florijančić T. PCR-based Y chromosome marker for discriminating between golden jackal (Canis aureus) and domestic dog (Canis lupus familiaris) paternal ancestry. CONSERV GENET RESOUR 2013. [DOI: 10.1007/s12686-013-0110-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Monzón J, Kays R, Dykhuizen DE. Assessment of coyote-wolf-dog admixture using ancestry-informative diagnostic SNPs. Mol Ecol 2013; 23:182-97. [PMID: 24148003 DOI: 10.1111/mec.12570] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 10/11/2013] [Accepted: 10/17/2013] [Indexed: 01/27/2023]
Abstract
The evolutionary importance of hybridization as a source of new adaptive genetic variation is rapidly gaining recognition. Hybridization between coyotes and wolves may have introduced adaptive alleles into the coyote gene pool that facilitated an expansion in their geographic range and dietary niche. Furthermore, hybridization between coyotes and domestic dogs may facilitate adaptation to human-dominated environments. We genotyped 63 ancestry-informative single-nucleotide polymorphisms in 427 canids to examine the prevalence, spatial distribution and the ecology of admixture in eastern coyotes. Using multivariate methods and Bayesian clustering analyses, we estimated the relative contributions of western coyotes, western and eastern wolves, and domestic dogs to the admixed ancestry of Ohio and eastern coyotes. We found that eastern coyotes form an extensive hybrid swarm, with all our samples having varying levels of admixture. Ohio coyotes, previously thought to be free of admixture, are also highly admixed with wolves and dogs. Coyotes in areas of high deer density are genetically more wolf-like, suggesting that natural selection for wolf-like traits may result in local adaptation at a fine geographic scale. Our results, in light of other previously published studies of admixture in Canis, revealed a pattern of sex-biased hybridization, presumably generated by male wolves and dogs mating with female coyotes. This study is the most comprehensive genetic survey of admixture in eastern coyotes and demonstrates that the frequency and scope of hybridization can be quantified with relatively few ancestry-informative markers.
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Affiliation(s)
- J Monzón
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, 11794, USA; Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11794, USA
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Wheeldon TJ, Rutledge LY, Patterson BR, White BN, Wilson PJ. Y-chromosome evidence supports asymmetric dog introgression into eastern coyotes. Ecol Evol 2013; 3:3005-20. [PMID: 24101990 PMCID: PMC3790547 DOI: 10.1002/ece3.693] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 06/20/2013] [Accepted: 06/23/2013] [Indexed: 11/20/2022] Open
Abstract
Hybridization has played an important role in the evolutionary history of Canis species in eastern North America. Genetic evidence of coyote–dog hybridization based on mitochondrial DNA (mtDNA) is lacking compared to that based on autosomal markers. This discordance suggests dog introgression into coyotes has potentially been male biased, but this hypothesis has not been formally tested. Therefore, we investigated biparentally, maternally, and paternally inherited genetic markers in a sample of coyotes and dogs from southeastern Ontario to assess potential asymmetric dog introgression into coyotes. Analysis of autosomal microsatellite genotypes revealed minimal historical and contemporary admixture between coyotes and dogs. We observed only mutually exclusive mtDNA haplotypes in coyotes and dogs, but we observed Y-chromosome haplotypes (Y-haplotypes) in both historical and contemporary coyotes that were also common in dogs. Species-specific Zfy intron sequences of Y-haplotypes shared between coyotes and dogs confirmed their homology and indicated a putative origin from dogs. We compared Y-haplotypes observed in coyotes, wolves, and dogs profiled in multiple studies, and observed that the Y-haplotypes shared between coyotes and dogs were either absent or rare in North American wolves, present in eastern coyotes, but absent in western coyotes. We suggest the eastern coyote has experienced asymmetric genetic introgression from dogs, resulting from predominantly historical hybridization with male dogs and subsequent backcrossing of hybrid offspring with coyotes. We discuss the temporal and spatial dynamics of coyote–dog hybridization and the conditions that may have facilitated the introgression of dog Y-chromosomes into coyotes. Our findings clarify the evolutionary history of the eastern coyote.
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Affiliation(s)
- Tyler J Wheeldon
- Environmental and Life Sciences Graduate Program, Trent University Peterborough, ON, Canada, K9J 7B8
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44
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Khosravi R, Rezaei HR, Kaboli M. Detecting hybridization between Iranian wild wolf (Canis lupus pallipes) and free-ranging domestic dog (Canis familiaris) by analysis of microsatellite markers. Zoolog Sci 2013; 30:27-34. [PMID: 23317363 DOI: 10.2108/zsj.30.27] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The genetic threat due to hybridization with free-ranging dogs is one major concern in wolf conservation. The identification of hybrids and extent of hybridization is important in the conservation and management of wolf populations. Genetic variation was analyzed at 15 unlinked loci in 28 dogs, 28 wolves, four known hybrids, two black wolves, and one dog with abnormal traits in Iran. Pritchard's model, multivariate ordination by principal component analysis and neighbor joining clustering were used for population clustering and individual assignment. Analysis of genetic variation showed that genetic variability is high in both wolf and dog populations in Iran. Values of H(E) in dog and wolf samples ranged from 0.75-0.92 and 0.77-0.92, respectively. The results of AMOVA showed that the two groups of dog and wolf were significantly different (F(ST) = 0.05 and R(ST) = 0.36; P < 0.001). In each of the three methods, wolf and dog samples were separated into two distinct clusters. Two dark wolves were assigned to the wolf cluster. Also these models detected D32 (dog with abnormal traits) and some other samples, which were assigned to more than one cluster and could be a hybrid. This study is the beginning of a genetic study in wolf populations in Iran, and our results reveal that as in other countries, hybridization between wolves and dogs is sporadic in Iran and can be a threat to wolf populations if human perturbations increase.
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Affiliation(s)
- Rasoul Khosravi
- Department of Environmental Sciences, Faculty of Natural Resources, University of Tehran, Karaj 4111, Iran
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45
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Tessier N, Stronen AV, Lapointe FJ. A technique to discriminateCanismitochondrial DNA of New World and Old World origins using specific primers. WILDLIFE SOC B 2012. [DOI: 10.1002/wsb.230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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46
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Genetic diversity and population structure in wild Sichuan rhesus macaques. Mol Biol Rep 2012; 40:3033-41. [PMID: 23269618 DOI: 10.1007/s11033-012-2377-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 12/17/2012] [Indexed: 10/27/2022]
Abstract
Because wild rhesus macaque (Macaca mulatta) populations have suffered major declines, there is a growing need to characterize their genetic and population structure in order to protect the genetic integrity of this species. In this study, we genotyped a sample comprising 120 wild rhesus macaques from six sites in Sichuan Province for 30 nuclear microsatellite (STR) loci using an ABI 3130xl genetic analyzer. Bayesian analyses and PCA clearly differentiated monkeys from Heishui from those at other sites. The samples from all six sites exhibited high gene diversity suggesting that the Sichuan wild rhesus macaque populations are not threatened by a lack of genetic diversity. Deviation from Hardy-Weinberg equilibrium was more frequent in the Danba and Heishui populations. This may be due to the more fragmented habitat and less disturbance by humans in this area that foster greater subpopulation structuring than occurs in eastern China. We suggest that this population subdivision is the result of both long-term geographic barriers and human activity.
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Benson JF, Patterson BR, Wheeldon TJ. Spatial genetic and morphologic structure of wolves and coyotes in relation to environmental heterogeneity in aCanishybrid zone. Mol Ecol 2012; 21:5934-54. [DOI: 10.1111/mec.12045] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 08/16/2012] [Accepted: 08/22/2012] [Indexed: 11/29/2022]
Affiliation(s)
- John F. Benson
- Environmental and Life Sciences Graduate Program; Trent University; Peterborough ON Canada K9J 7B8
| | - Brent R. Patterson
- Wildlife Research and Development Section; Ontario Ministry of Natural Resources; Peterborough ON Canada K9J 7B8
| | - Tyler J. Wheeldon
- Environmental and Life Sciences Graduate Program; Trent University; Peterborough ON Canada K9J 7B8
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Hindrikson M, Männil P, Ozolins J, Krzywinski A, Saarma U. Bucking the trend in wolf-dog hybridization: first evidence from europe of hybridization between female dogs and male wolves. PLoS One 2012; 7:e46465. [PMID: 23056315 PMCID: PMC3463576 DOI: 10.1371/journal.pone.0046465] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Accepted: 09/03/2012] [Indexed: 11/21/2022] Open
Abstract
Studies on hybridization have proved critical for understanding key evolutionary processes such as speciation and adaptation. However, from the perspective of conservation, hybridization poses a concern, as it can threaten the integrity and fitness of many wild species, including canids. As a result of habitat fragmentation and extensive hunting pressure, gray wolf (Canis lupus) populations have declined dramatically in Europe and elsewhere during recent centuries. Small and fragmented populations have persisted, but often only in the presence of large numbers of dogs, which increase the potential for hybridization and introgression to deleteriously affect wolf populations. Here, we demonstrate hybridization between wolf and dog populations in Estonia and Latvia, and the role of both genders in the hybridization process, using combined analysis of maternal, paternal and biparental genetic markers. Eight animals exhibiting unusual external characteristics for wolves - six from Estonia and two from Latvia - proved to be wolf-dog hybrids. However, one of the hybridization events was extraordinary. Previous field observations and genetic studies have indicated that mating between wolves and dogs is sexually asymmetrical, occurring predominantly between female wolves and male dogs. While this was also the case among the Estonian hybrids, our data revealed the existence of dog mitochondrial genomes in the Latvian hybrids and, together with Y chromosome and autosomal microsatellite data, thus provided the first evidence from Europe of mating between male wolves and female dogs. We discuss patterns of sexual asymmetry in wolf-dog hybridization.
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Affiliation(s)
- Maris Hindrikson
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Peep Männil
- Estonian Environment Information Centre, Tartu, Estonia
| | - Janis Ozolins
- State Forest Research Institute “Silava”, Salaspils, Latvia
| | | | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
- * E-mail:
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Wheeldon TJ, Patterson BR. Genetic and morphological differentiation of wolves (Canis lupus) and coyotes (Canis latrans) in northeastern Ontario. CAN J ZOOL 2012. [DOI: 10.1139/z2012-090] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Gray wolves ( Canis lupus L., 1758), eastern wolves ( Canis lycaon Schreber, 1775), and coyotes ( Canis latrans Say, 1823) are presently managed as a single biological population in primary wolf range in Ontario with the intent of minimizing incidental harvest of wolves. This management strategy is based on the assumption that wolves and coyotes cannot be reliably distinguished because of hybridization, and the resulting restrictions on coyote harvest are unpopular with hunters and farmers. We genetically and morphologically characterized a sample of sympatric wolves and coyotes harvested in the Lesser Clay Belt area of northeastern Ontario in 2006–2009 to test the hypothesis that these species cannot be reliably distinguished. We found that wolves and coyotes were genetically and morphologically distinct, with minimal hybridization between them. Our findings suggest that wolves and coyotes in the sampled area can be reliably distinguished, but further sampling is required to determine the full extent of areas in Ontario where wolves and coyotes are reliably distinguishable. We discuss unresolved issues regarding the feasibility of separate management for these species. We also discuss implications of our findings regarding wolf recovery in the northeastern United States.
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Affiliation(s)
- Tyler J. Wheeldon
- Ontario Ministry of Natural Resources, DNA Building, Trent University, 2140 East Bank Drive, Peterborough, ON K9J 7B8, Canada
| | - Brent R. Patterson
- Ontario Ministry of Natural Resources, DNA Building, Trent University, 2140 East Bank Drive, Peterborough, ON K9J 7B8, Canada
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An Account of the Taxonomy of North American Wolves From Morphological and Genetic Analyses. ACTA ACUST UNITED AC 2012. [DOI: 10.3996/nafa.77.0001] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Abstract
The available scientific literature was reviewed to assess the taxonomic standing of North American wolves, including subspecies of the gray wolf, Canis lupus. The recent scientific proposal that the eastern wolf, C. l. lycaon, is not a subspecies of gray wolf, but a full species, Canis lycaon, is well-supported by both morphological and genetic data. This species' range extends westward to Minnesota, and it hybridizes with gray wolves where the two species are in contact in eastern Canada and the Upper Peninsula of Michigan, Wisconsin, and Minnesota. Genetic data support a close relationship between eastern wolf and red wolf Canis rufus, but do not support the proposal that they are the same species; it is more likely that they evolved independently from different lineages of a common ancestor with coyotes. The genetic distinctiveness of the Mexican wolf Canis lupus baileyi supports its recognition as a subspecies. The available genetic and morphometric data do not provide clear support for the recognition of the Arctic wolf Canis lupus arctos, but the available genetic data are almost entirely limited to one group of genetic markers (microsatellite DNA) and are not definitive on this question. Recognition of the northern timber wolf Canis lupus occidentalis and the plains wolf Canis lupus nubilus as subspecies is supported by morphological data and extensive studies of microsatellite DNA variation where both subspecies are in contact in Canada. The wolves of coastal areas in southeastern Alaska and British Columbia should be assigned to C. lupus nubilus. There is scientific support for the taxa recognized here, but delineation of exact geographic boundaries presents challenges. Rather than sharp boundaries between taxa, boundaries should generally be thought of as intergrade zones of variable width.
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