1
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Preckler-Quisquater S, Quinn CB, Sacks BN. Maintenance of a narrow hybrid zone between native and introduced red foxes (Vulpes vulpes) despite conspecificity and high dispersal capabilities. Mol Ecol 2024; 33:e17418. [PMID: 38847182 DOI: 10.1111/mec.17418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/04/2024] [Accepted: 05/13/2024] [Indexed: 06/27/2024]
Abstract
Human-facilitated introductions of nonnative populations can lead to secondary contact between allopatric lineages, resulting in lineage homogenisation or the formation of stable hybrid zones maintained by reproductive barriers. We investigated patterns of gene flow between the native Sacramento Valley red fox (Vulpes vulpes patwin) and introduced conspecifics of captive-bred origin in California's Central Valley. Considering their recent divergence (20-70 kya), we hypothesised that any observed barriers to gene flow were primarily driven by pre-zygotic (e.g. behavioural differences) rather than post-zygotic (e.g. reduced hybrid fitness) barriers. We also explored whether nonnative genes could confer higher fitness in the human-dominated landscape resulting in selective introgression into the native population. Genetic analysis of red foxes (n = 682) at both mitochondrial (cytochrome b + D-loop) and nuclear (19,051 SNPs) loci revealed narrower cline widths than expected under a simulated model of unrestricted gene flow, consistent with the existence of reproductive barriers. We identified several loci with reduced introgression that were previously linked to behavioural divergence in captive-bred and domestic canids, supporting pre-zygotic, yet possibly hereditary, barriers as a mechanism driving the narrowness and stability of the hybrid zone. Several loci with elevated gene flow from the nonnative into the native population were linked to genes associated with domestication and adaptation to human-dominated landscapes. This study contributes to our understanding of hybridisation dynamics in vertebrates, particularly in the context of species introductions and landscape changes, underscoring the importance of considering how multiple mechanisms may be maintaining lineages at the species and subspecies level.
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Affiliation(s)
- Sophie Preckler-Quisquater
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Cate B Quinn
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California, USA
- USDA Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish Conservation, Missoula, Montana, USA
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
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2
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Tensen L, Fischer K. Evaluating hybrid speciation and swamping in wild carnivores with a decision-tree approach. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2024; 38:e14197. [PMID: 37811741 DOI: 10.1111/cobi.14197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/12/2023] [Accepted: 06/28/2023] [Indexed: 10/10/2023]
Abstract
Hybridization is an important evolutionary force with a principal role in the origin of new species, known as hybrid speciation. However, ongoing hybridization can create hybrid swamping, in which parental genomes are completely lost. This can become a biodiversity threat if it involves species that have adapted to certain environmental conditions and occur nowhere else. Because conservation scientists commonly have a negative attitude toward hybrids, it is important to improve understanding of the influence of interspecific gene flow on the persistence of species. We reviewed the literature on species hybridization to build a list of all known cases in the order Carnivora. To examine the relative impact, we also noted level of introgression, whether fertile offspring were produced, and whether there was mention of negative or positive evolutionary effects (hybrid speciation and swamping). To evaluate the conservation implications of hybrids, we developed a decision-making tree with which to determine which actions should be taken to manage hybrid species. We found 53 hybrids involving 68 unique taxa, which is roughly 23% of all carnivore species. They mainly involved monophyletic (83%) and sympatric species (75%). For 2 species, the outcome of the assessment was to eliminate or restrict the hybrids: Ethiopian wolf (Canis simensis) and Scottish wildcat (Felis silvestris silvestris). Both species hybridize with their domestic conspecifics. For all other cases, we suggest hybrids be protected in the same manner as native species. We found no evidence of genomic extinction in Carnivora. To the contrary, some species appear to be of hybrid origin, such as the Asiatic black bear (Ursus thibetanus) and African golden wolf (Canis lupaster). Other positive outcomes of hybridization are novel genetic diversity, adaptation to extreme environments, and increased reproductive fitness. These outcomes are particularly valuable for counterbalancing genetic drift and enabling adaptive introgression in a human-dominated world.
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Affiliation(s)
- Laura Tensen
- Institute for Integrated Natural Sciences, Department of Zoology, University of Koblenz, Koblenz, Germany
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Johannesburg, South Africa
| | - Klaus Fischer
- Institute for Integrated Natural Sciences, Department of Zoology, University of Koblenz, Koblenz, Germany
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3
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Contrasting genetic trajectories of endangered and expanding red fox populations in the western U.S. Heredity (Edinb) 2022; 129:123-136. [PMID: 35314789 PMCID: PMC9338314 DOI: 10.1038/s41437-022-00522-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/24/2022] [Accepted: 02/25/2022] [Indexed: 12/04/2022] Open
Abstract
As anthropogenic disturbances continue to drive habitat loss and range contractions, the maintenance of evolutionary processes will increasingly require targeting measures to the population level, even for common and widespread species. Doing so requires detailed knowledge of population genetic structure, both to identify populations of conservation need and value, as well as to evaluate suitability of potential donor populations. We conducted a range-wide analysis of the genetic structure of red foxes in the contiguous western U.S., including a federally endangered distinct population segment of the Sierra Nevada subspecies, with the objectives of contextualizing field observations of relative scarcity in the Pacific mountains and increasing abundance in the cold desert basins of the Intermountain West. Using 31 autosomal microsatellites, along with mitochondrial and Y-chromosome markers, we found that populations of the Pacific mountains were isolated from one another and genetically depauperate (e.g., estimated Ne range = 3–9). In contrast, red foxes in the Intermountain regions showed relatively high connectivity and genetic diversity. Although most Intermountain red foxes carried indigenous western matrilines (78%) and patrilines (85%), the presence of nonindigenous haplotypes at lower elevations indicated admixture with fur-farm foxes and possibly expanding midcontinent populations as well. Our findings suggest that some Pacific mountain populations could likely benefit from increased connectivity (i.e., genetic rescue) but that nonnative admixture makes expanding populations in the Intermountain basins a non-ideal source. However, our results also suggest contact between Pacific mountain and Intermountain basin populations is likely to increase regardless, warranting consideration of risks and benefits of proactive measures to mitigate against unwanted effects of Intermountain gene flow.
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4
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Wierzbicki H, Zatoń-Dobrowolska M, Mucha A, Moska M. Insight into the Genetic Population Structure of Wild Red Foxes in Poland Reveals Low Risk of Genetic Introgression from Escaped Farm Red Foxes. Genes (Basel) 2021; 12:genes12050637. [PMID: 33922932 PMCID: PMC8146073 DOI: 10.3390/genes12050637] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/28/2021] [Accepted: 04/23/2021] [Indexed: 11/21/2022] Open
Abstract
In this study we assessed the level of genetic introgression between red foxes bred on fur farms in Poland and the native wild population. We also evaluated the impact of a geographic barrier and isolation by distance on gene flow between two isolated subpopulations of the native red fox and their genetic differentiation. Nuclear and mitochondrial DNA was collected from a total of 308 individuals (200 farm and 108 wild red foxes) to study non-native allele flow from farm into wild red fox populations. Genetic structure analyses performed using 24 autosomal microsatellites showed two genetic clusters as being the most probable number of distinct populations. No strong admixture signals between farm and wild red foxes were detected, and significant genetic differentiation was identified between the two groups. This was also apparent from the mtDNA analysis. None of the concatenated haplotypes detected in farm foxes was found in wild animals. The consequence of this was that the haplotype network displayed two genetically distinct groups: farm foxes were completely separated from native ones. Neither the River Vistula nor isolation by distance had a significant impact on gene flow between the separated wild red fox subpopulations. The results of our research indicate a low probability of genetic introgression between farm and native red foxes, and no threat to the genetic integrity of this species.
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5
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Graham CF, Eberts RL, Goncin U, Somers CM. Spontaneous hybridization and introgression between walleye ( Sander vitreus) and sauger ( Sander canadensis) in two large reservoirs: Insights from genotyping by sequencing. Evol Appl 2021; 14:965-982. [PMID: 33897814 PMCID: PMC8061268 DOI: 10.1111/eva.13174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 11/09/2020] [Accepted: 11/11/2020] [Indexed: 12/22/2022] Open
Abstract
Anthropogenic activities may facilitate undesirable hybridization and genomic introgression between fish species. Walleye (Sander vitreus) and sauger (Sander canadensis) are economically valuable freshwater species that can spontaneously hybridize in areas of sympatry. Levels of genomic introgression between walleye and sauger may be increased by modifications to waterbodies (e.g., reservoir development) and inadvertent propagation of hybrids in stocking programs. We used genotyping by sequencing (GBS) to examine 217 fish from two large reservoirs with mixed populations of walleye and sauger in Saskatchewan, Canada (Lake Diefenbaker, Tobin Lake). Analyses with 20,038 (r90) and 478 (r100) single nucleotide polymorphisms clearly resolved walleye and sauger, and classified hybrids with high confidence. F1, F2, and multigeneration hybrids were detected in Lake Diefenbaker, indicating potentially high levels of genomic introgression. In contrast, only F1 hybrids were detected in Tobin Lake. Field classification of fish was unreliable; 7% of fish were misidentified based on broad species categories. Important for activities such as brood stock selection, 12 of 173 (7%) fish field identified as pure walleye, and one of 24 (4%) identified as pure sauger were actually hybrids. In addition, two of 15 (13%) field-identified hybrids were actually pure walleye or sauger. We conclude that hybridization and introgression are occurring in Saskatchewan reservoirs and that caution is warranted when using these populations in stocking programs. GBS offers a powerful and flexible tool for examining hybridization without preidentification of informative loci, eliminating some of the key challenges associated with other marker types.
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Affiliation(s)
| | - Rebecca L. Eberts
- Fish, Wildlife, and Lands Branch, Ministry of EnvironmentGovernment of SaskatchewanPrince AlbertSKCanada
| | - Una Goncin
- Department of BiologyUniversity of ReginaReginaSKCanada
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Tatler J, Prowse TA, Roshier DA, Cairns KM, Cassey P. Phenotypic variation and promiscuity in a wild population of pure dingoes (
Canis dingo
). J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12418] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Jack Tatler
- Centre for Applied Conservation Science and School of Biological Sciences University of Adelaide Adelaide South Australia Australia
| | - Thomas A.A. Prowse
- School of Mathematical Sciences University of Adelaide Adelaide South Australia Australia
| | - David A. Roshier
- Australian Wildlife Conservancy Subiaco East Western Australia Australia
- Centre for Ecosystem Science University of New South Wales Sydney New South Wales Australia
| | - Kylie M. Cairns
- Centre for Ecosystem Science University of New South Wales Sydney New South Wales Australia
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences University of New South Wales Sydney New South Wales Australia
| | - Phillip Cassey
- Centre for Applied Conservation Science and School of Biological Sciences University of Adelaide Adelaide South Australia Australia
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7
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Morris KY, Bowman J, Schulte‐Hostedde A, Wilson PJ. Functional genetic diversity of domestic and wild American mink ( Neovison vison). Evol Appl 2020; 13:2610-2629. [PMID: 33294012 PMCID: PMC7691469 DOI: 10.1111/eva.13061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/24/2020] [Accepted: 06/26/2020] [Indexed: 11/30/2022] Open
Abstract
The release of domestic organisms to the wild threatens biodiversity because the introduction of domestic genes through interbreeding can negatively impact wild conspecifics via outbreeding depression. In North America, farmed American mink (Neovison vison) frequently escape captivity, yet the impact of these events on functional genetic diversity of wild mink populations is unclear. We characterized domestic and wild mink in Ontario at 17 trinucleotide microsatellites located in functional genes thought to be associated with traits affected by domestication. We found low functional genetic diversity in both mink types, as only four of 17 genes were variable, yet allele frequencies varied widely between captive and wild populations. To determine whether allele frequencies of wild populations were affected by geographic location, we performed redundancy analysis and spatial analysis of principal components on three polymorphic loci (AR, ATN1 and IGF-1). We found evidence to suggest domestic release events are affecting the functional genetic diversity of wild mink, as sPCA showed clear distinctions between wild individuals near mink farms and those located in areas without mink farms. This is further substantiated through RDA, where spatial location was associated with genetic variation of AR, ATN1 and IGF1.
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Affiliation(s)
- Kimberley Y. Morris
- Environmental and Life Sciences Graduate ProgramTrent UniversityPeterboroughONCanada
| | - Jeff Bowman
- Environmental and Life Sciences Graduate ProgramTrent UniversityPeterboroughONCanada
- Wildlife Research and Monitoring SectionOntario Ministry of Natural Resources and ForestryPeterboroughONCanada
| | | | - Paul J. Wilson
- Environmental and Life Sciences Graduate ProgramTrent UniversityPeterboroughONCanada
- Department of BiologyTrent UniversityPeterboroughONCanada
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8
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Quinn CB, Alden PB, Sacks BN. Noninvasive Sampling Reveals Short-Term Genetic Rescue in an Insular Red Fox Population. J Hered 2020; 110:559-576. [PMID: 31002340 DOI: 10.1093/jhered/esz024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 04/15/2019] [Indexed: 11/12/2022] Open
Abstract
Genetic factors in the decline of small populations are extremely difficult to study in nature. We leveraged a natural experiment to investigate evidence of inbreeding depression and genetic rescue in a remnant population of subalpine-specialized Sierra Nevada red foxes (Vulpes vulpes necator) using noninvasive genetic monitoring during 2010-2017. Only 7 individuals were detected in the first 2 years. These individuals assigned genetically to the historical population and exhibited genetic hallmarks of inbreeding and no evidence of reproduction. Two years into the study, we detected 2 first-generation immigrant males from a recently expanding population of red foxes in the Great Basin Desert. Through annual resampling of individuals (634 red fox DNA samples, 41 individuals) and molecular reconstruction of pedigrees, we documented 1-3 litters/year for 5 years, all descended directly or indirectly from matings involving immigrant foxes. The observed heterozygosity and allelic richness of the population nearly doubled in 2 years. Abundance increased, indicative of a rapidly expanding population. Throughout the study, adult survival was high. Restoration of gene flow apparently improved the demographic trajectory of this population in the short term. Whether these benefits continue in the longer term could depend on numerous factors, such as maintenance of any locally adapted alleles. This study highlights the value of noninvasive genetic monitoring to assess rapidly shifting conditions in small populations. Uncertainties about the longer-term trajectory of this population underscore the need to continue monitoring and to research potential for both negative and positive aspects of continued genetic infusion.
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Affiliation(s)
- Cate B Quinn
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, Davis, CA
| | - Preston B Alden
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, Davis, CA.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, Davis, CA.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA
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9
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Telcİoğlu M, İbİş O, Aksöyek E, Özcan S, Moradİ M, Gürkan ÖFİ, Tez C. Genetic analysis of Iranian and Turkish red foxes ( Vulpes vulpes) based on mitochondrial DNA (D-loop) sequences. ETHOL ECOL EVOL 2019. [DOI: 10.1080/03949370.2019.1639079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Murat Telcİoğlu
- Graduate School of Natural and Applied Sciences, Erciyes University, Kayseri, Turkey
| | - Osman İbİş
- Department of Agricultural Biotechnology, Faculty of Agriculture, Erciyes University, Kayseri, Turkey
- Genome and Stem Cell Center (GENKOK), Erciyes University, Kayseri, Turkey
| | - Eren Aksöyek
- Graduate School of Natural and Applied Sciences, Erciyes University, Kayseri, Turkey
| | - Servet Özcan
- Genome and Stem Cell Center (GENKOK), Erciyes University, Kayseri, Turkey
- Department of Biology, Faculty of Sciences, Erciyes University, Kayseri, Turkey
| | - Mohammad Moradİ
- Department of Biology, Faculty of Science, University of Zanjan, Zanjan, Iran
| | - Ömer Fİkret Gürkan
- Graduate School of Natural and Applied Sciences, Erciyes University, Kayseri, Turkey
| | - Coşkun Tez
- Genome and Stem Cell Center (GENKOK), Erciyes University, Kayseri, Turkey
- Department of Biology, Faculty of Sciences, Erciyes University, Kayseri, Turkey
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10
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Statham MJ, (Smith) Woollett DA, Fresquez S, Pfeiffer J, Richmond J, Whitelaw A, Richards NL, Westphal MF, Sacks BN. Noninvasive Identification of Herpetofauna: Pairing Conservation Dogs and Genetic Analysis. J Wildl Manage 2019. [DOI: 10.1002/jwmg.21772] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Mark J. Statham
- Department of Population Health and Reproduction, School of Veterinary Medicine, Mammalian Ecology and Conservation Unit, Veterinary Genetics LaboratoryUniversity of California One Shields Avenue Davis CA 95616‐8744 USA
| | | | - Susan Fresquez
- Mammalian Ecology and Conservation Unit, Veterinary Genetics LaboratoryUniversity of California One Shields Avenue Davis CA 95616‐8744 USA
| | - Jerene Pfeiffer
- Mammalian Ecology and Conservation Unit, Veterinary Genetics LaboratoryUniversity of California One Shields Avenue/Old Davis Road Davis CA 95616‐8744 USA
| | - Jonathan Richmond
- U.S. Geological Survey 4165 Spruance Rd. Suite 200 San Diego CA 92101 USA
| | - Alice Whitelaw
- Working Dogs for Conservation P.O. Box 280 Bozeman MT 59771 USA
| | | | - Michael F. Westphal
- U.S. Bureau of Land Management Central Coast Field Office Marina CA 93933 USA
| | - Benjamin N. Sacks
- Department of Population Health and Reproduction, School of Veterinary Medicine, Mammalian Ecology and Conservation Unit, Veterinary Genetics LaboratoryUniversity of California One Shields Avenue Davis CA 95616‐8744 USA
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11
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Sacks BN, Lounsberry ZT, Statham MJ. Nuclear Genetic Analysis of the Red Fox Across its Trans-Pacific Range. J Hered 2019; 109:573-584. [PMID: 29889225 DOI: 10.1093/jhered/esy028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 06/05/2018] [Indexed: 11/14/2022] Open
Abstract
The red fox (Vulpes vulpes) occurs on multiple continents in diverse habitats, making it an informative system for evolutionary genomic research. However, its phylogeography remains unclear. Previously, mitochondrial DNA and small numbers of nuclear loci provided discordant views. Both markers indicated deep divergence (~ 0.5 million years [MY]) between Eurasian and southern North American populations but differed in the apparent continental affinity of Alaskan red foxes, implying some degree of gene exchange during secondary contact (~0.1 MY). We assayed >173000 nuclear genomic sites in 52 red foxes, along with 2 Rueppell's foxes (Vulpes rueppellii) and a gray wolf (Canis lupus) using the Illumina CanineHD BeadChip. We obtained 5107 single nucleotide polymorphisms (SNPs) in the foxes. Consistent with the Afro-Eurasian origins of red foxes, genetic diversity was higher in Eurasian than North American samples. Phylogenetic trees indicated that Alaskan and southern North American red foxes formed a monophyletic group nested within the Eurasian clade. However, admixture models suggested Alaskan red foxes contained up to 40% Eurasian ancestry. We hypothesize that North American red foxes either hybridized with Eurasian foxes in Beringia at the start of the last glaciation or merged with a Beringian population after the last glaciation. Future work is needed to test between these scenarios and assess speciation.
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Affiliation(s)
- Benjamin N Sacks
- Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, University of California, Davis, Davis, CA.,Department of Population Health and Reproduction, University of California, Davis, Davis, CA
| | - Zachary T Lounsberry
- Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, University of California, Davis, Davis, CA
| | - Mark J Statham
- Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, University of California, Davis, Davis, CA.,Department of Population Health and Reproduction, University of California, Davis, Davis, CA
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12
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Zecchin B, De Nardi M, Nouvellet P, Vernesi C, Babbucci M, Crestanello B, Bagó Z, Bedeković T, Hostnik P, Milani A, Donnelly CA, Bargelloni L, Lorenzetto M, Citterio C, Obber F, De Benedictis P, Cattoli G. Genetic and spatial characterization of the red fox (Vulpes vulpes) population in the area stretching between the Eastern and Dinaric Alps and its relationship with rabies and canine distemper dynamics. PLoS One 2019; 14:e0213515. [PMID: 30861028 PMCID: PMC6413928 DOI: 10.1371/journal.pone.0213515] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 02/24/2019] [Indexed: 01/02/2023] Open
Abstract
Information on the population dynamics of a reservoir species have been increasingly adopted to understand and eventually predict the dispersal patterns of infectious diseases throughout an area. Although potentially relevant, to date there are no studies which have investigated the genetic structure of the red fox population in relation to infectious disease dynamics. Therefore, we genetically and spatially characterised the red fox population in the area stretching between the Eastern and Dinaric Alps, which has been affected by both distemper and rabies at different time intervals. Red foxes collected from north-eastern Italy, Austria, Slovenia and Croatia between 2006–2012, were studied using a set of 21 microsatellite markers. We confirmed a weak genetic differentiation within the fox population using Bayesian clustering analyses, and we were able to differentiate the fox population into geographically segregated groups. Our finding might be due to the presence of geographical barriers that have likely influenced the distribution of the fox population, limiting in turn gene flow and spread of infectious diseases. Focusing on the Italian red fox population, we observed interesting variations in the prevalence of both diseases among distinct fox clusters, with the previously identified Italy 1 and Italy 2 rabies as well as distemper viruses preferentially affecting different sub-groups identified in the study. Knowledge of the regional-scale population structure can improve understanding of the epidemiology and spread of diseases. Our study paves the way for an integrated approach for disease control coupling pathogen, host and environmental data to inform targeted control programs in the future.
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Affiliation(s)
- Bianca Zecchin
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
- * E-mail:
| | - Marco De Nardi
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Pierre Nouvellet
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Cristiano Vernesi
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro, Italy
| | - Barbara Crestanello
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Zoltán Bagó
- Austrian Agency for Health and Food Safety (AGES), Institute for Veterinary Disease Control, Mödling, Austria
| | | | - Peter Hostnik
- Virology Unit, Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Ljubljana, Slovenia
| | - Adelaide Milani
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Christl Ann Donnelly
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- National Institute for Health Research Health Protection Research Unit in Modelling Methodology, Imperial College London, London, United Kingdom
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro, Italy
| | - Monica Lorenzetto
- Department of Veterinary Epidemiology, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Carlo Citterio
- SCT2 Belluno, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Belluno, Italy
| | - Federica Obber
- SCT2 Belluno, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Belluno, Italy
| | - Paola De Benedictis
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Giovanni Cattoli
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
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13
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Santos JL, Žagar A, Drašler K, Rato C, Ayres C, Harris DJ, Carretero MA, Salvi D. Phylogeographic evidence for multiple long-distance introductions of the common wall lizard associated with human trade and transport. AMPHIBIA-REPTILIA 2019. [DOI: 10.1163/15685381-20181040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
The common wall lizard has been widely introduced across Europe and overseas. We investigated the origin of putatively introduced Podarcis muralis populations from two southern Europe localities: (i) Ljubljana (Slovenia), where uncommon phenotypes were observed near the railway tracks and (ii) the port of Vigo (Spain), where the species was recently found 150 km far from its previously known range. We compared cytochrome-b mtDNA sequences of lizards from these populations with published sequences across the native range. Our results support the allochthonous status and multiple, long-distance origins in both populations. In Ljubljana, results support two different origins, Serbia and Italy. In Vigo, at least two separate origins are inferred, from western and eastern France. Such results confirm that human-mediated transport is promoting biological invasion and lineage admixture in this species. Solid knowledge of the origin and invasion pathways, as well as population monitoring, is crucial for management strategies to be successful.
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Affiliation(s)
- Joana L. Santos
- 1CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, N° 7, 4485-661 Vairão, Vila do Conde, Portugal
| | - Anamarija Žagar
- 1CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, N° 7, 4485-661 Vairão, Vila do Conde, Portugal
- 2National insitute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
- 3Herpetological society – Societas herpetological slovenica, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Katarina Drašler
- 3Herpetological society – Societas herpetological slovenica, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Catarina Rato
- 1CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, N° 7, 4485-661 Vairão, Vila do Conde, Portugal
| | - César Ayres
- 4Asociación Herpetológica Española, Museo Nacional de Ciencias Naturales, C/ José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - D. James Harris
- 1CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, N° 7, 4485-661 Vairão, Vila do Conde, Portugal
| | - Miguel A. Carretero
- 1CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, N° 7, 4485-661 Vairão, Vila do Conde, Portugal
| | - Daniele Salvi
- 1CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, N° 7, 4485-661 Vairão, Vila do Conde, Portugal
- 5Department of Health, Life and Environmental Sciences, University of L’Aquila, Via Vetoio, 67100 Coppito, L’Aquila, Italy
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Black KM, Preckler-Quisquater S, Batter TJ, Anderson S, Sacks BN. Occupancy, habitat, and abundance of the Sacramento Valley red fox. J Wildl Manage 2019. [DOI: 10.1002/jwmg.21556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Kathleen M. Black
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory; University of California, Davis; One Shields Avenue/Old Davis Road Davis CA 95616 USA
| | - Sophie Preckler-Quisquater
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory; University of California, Davis; One Shields Avenue/Old Davis Road Davis CA 95616 USA
| | - Tom J. Batter
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory; University of California, Davis; One Shields Avenue/Old Davis Road Davis CA 95616 USA
| | - Stacy Anderson
- California Department of Fish and Wildlife; North Central Region; 1701 Nimbus Road Rancho Cordova CA 95670 USA
| | - Benjamin N. Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, Department of Population Health and Reproduction; University of California, Davis; One Shields Avenue/Old Davis Road Davis CA 95616 USA
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Sacks BN, Milburn PJ. Genetic characterization of kit foxes at their northern range extent and monitoring recommendations. WILDLIFE SOC B 2018. [DOI: 10.1002/wsb.933] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Benjamin N. Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory and Department of Population Health and Reproduction; School of Veterinary Medicine, University of California, Davis, One Shields Avenue/Old Davis Road; Davis CA 95616 USA
| | - Philip J. Milburn
- Oregon Department of Fish and Wildlife; 3814 Clark Boulevard Ontario OR 97914 USA
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Castañeda I, Bellard C, Jarić I, Pisanu B, Chapuis J, Bonnaud E. Trophic patterns and home‐range size of two generalist urban carnivores: a review. J Zool (1987) 2018. [DOI: 10.1111/jzo.12623] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- I. Castañeda
- Centre d'Ecologie et des Sciences de la Conservation (CESCO UMR 7204) Sorbonne Universités MNHN CNRS UPMC Paris France
- Ecologie, Systématique et Evolution (UMR CNRS 8079) Université Paris‐Sud XI Orsay Cedex France
| | - C. Bellard
- Unité Biologie des Organismes et Écosystèmes Aquatiques (BOREA UMR 7208) Sorbonne Universités Muséum National d'Histoire Naturelle Université Pierre et Marie Curie Université de Caen Normandie CNRS, IRD Université des Antilles Paris France
| | - I. Jarić
- Biology Centre of the Czech Academy of Sciences Institute of Hydrobiology České Budějovice Czech Republic
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries Berlin Germany
- Institute for Multidisciplinary Research University of Belgrade Belgrade Serbia
| | - B. Pisanu
- Centre d'Ecologie et des Sciences de la Conservation (CESCO UMR 7204) Sorbonne Universités MNHN CNRS UPMC Paris France
- UMS 2006 Patrimoine Naturel AFB, MNHN CNRS Paris France
| | - J.‐L. Chapuis
- Centre d'Ecologie et des Sciences de la Conservation (CESCO UMR 7204) Sorbonne Universités MNHN CNRS UPMC Paris France
| | - E. Bonnaud
- Ecologie, Systématique et Evolution (UMR CNRS 8079) Université Paris‐Sud XI Orsay Cedex France
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Red Fox Ancestry and Connectivity Assessments Reveal Minimal Fur Farm Introgression in Greater Yellowstone Ecosystem. JOURNAL OF FISH AND WILDLIFE MANAGEMENT 2018. [DOI: 10.3996/092017-jfwm-073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Abstract
Rocky Mountain red foxes Vulpes vulpes macroura potentially encounter other red fox Vulpes vulpes lineages at lower elevations, which may include nonindigenous red foxes derived from fur farms. Introgression from nonindigenous red foxes could have negative evolutionary consequences for the rare Rocky Mountain red fox subspecies. Red foxes at high elevations in the Greater Yellowstone Ecosystem exhibit lighter coat colors than those at lower elevations, potentially indicating that they represent the indigenous subspecies and that gene flow across the elevational gradient is restricted. We collected tissue samples across a 1,750-m elevation range and examined mitochondrial DNA sequences and nuclear DNA microsatellite genotypes to assess the ancestry and genetic population structure of red foxes in the northern Greater Yellowstone Ecosystem. We also used reference samples from fur farm red foxes and indigenous red foxes of the western United States to assess the extent of nonindigenous introgression across the ecosystem. We found little overlap in the elevational distribution of maternally inherited mitochondrial DNA haplotypes: above 1,600 m, we only found indigenous Rocky Mountain haplotypes (n = 4), whereas below 1,600 m, we found haplotypes not indigenous to the Rocky Mountains (n = 5) that were associated with fur farms or indigenous to the Great Plains. In contrast, biparentally inherited microsatellite variation showed little population structure across the elevational gradient. Despite this evidence of nuclear gene flow across the elevational gradient, we found little fur farm introgression in the microsatellite genotypes. It is possible that long-standing nuclear (but apparently not mitochondrial) gene flow between Rocky Mountain red foxes and indigenous red foxes on the Great Plains explained the low nuclear differentiation of these populations. Importantly, our results suggested that high elevations of the northern Greater Yellowstone Ecosystem remained free of significant fur farm introgression. Mitonuclear discordance could reflect sex-biased dispersal, which we hypothesize could be the effect of elevational differences in reproductive phenology.
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Rando HM, Stutchman JT, Bastounes ER, Johnson JL, Driscoll CA, Barr CS, Trut LN, Sacks BN, Kukekova AV. Y-Chromosome Markers for the Red Fox. J Hered 2017; 108:678-685. [PMID: 28821189 DOI: 10.1093/jhered/esx066] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 07/11/2017] [Indexed: 01/17/2023] Open
Abstract
The de novo assembly of the red fox (Vulpes vulpes) genome has facilitated the development of genomic tools for the species. Efforts to identify the population history of red foxes in North America have previously been limited by a lack of information about the red fox Y-chromosome sequence. However, a megabase of red fox Y-chromosome sequence was recently identified over 2 scaffolds in the reference genome. Here, these scaffolds were scanned for repeated motifs, revealing 194 likely microsatellites. Twenty-three of these loci were selected for primer development and, after testing, produced a panel of 11 novel markers that were analyzed alongside 2 markers previously developed for the red fox from dog Y-chromosome sequence. The markers were genotyped in 76 male red foxes from 4 populations: 7 foxes from Newfoundland (eastern Canada), 12 from Maryland (eastern United States), and 9 from the island of Great Britain, as well as 48 foxes of known North American origin maintained on an experimental farm in Novosibirsk, Russia. The full marker panel revealed 22 haplotypes among these red foxes, whereas the 2 previously known markers alone would have identified only 10 haplotypes. The haplotypes from the 4 populations clustered primarily by continent, but unidirectional gene flow from Great Britain and farm populations may influence haplotype diversity in the Maryland population. The development of new markers has increased the resolution at which red fox Y-chromosome diversity can be analyzed and provides insight into the contribution of males to red fox population diversity and patterns of phylogeography.
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Affiliation(s)
- Halie M Rando
- Department of Animal Science, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Laboratory of Comparative Behavioral Genomics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20892-9412; Institute of Cytology and Genetics of the Russian Academy of Sciences, Novosibirsk 630090, Russia; Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616; Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616
| | - Jeremy T Stutchman
- Department of Animal Science, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Laboratory of Comparative Behavioral Genomics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20892-9412; Institute of Cytology and Genetics of the Russian Academy of Sciences, Novosibirsk 630090, Russia; Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616; Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616
| | - Estelle R Bastounes
- Department of Animal Science, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Laboratory of Comparative Behavioral Genomics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20892-9412; Institute of Cytology and Genetics of the Russian Academy of Sciences, Novosibirsk 630090, Russia; Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616; Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616
| | - Jennifer L Johnson
- Department of Animal Science, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Laboratory of Comparative Behavioral Genomics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20892-9412; Institute of Cytology and Genetics of the Russian Academy of Sciences, Novosibirsk 630090, Russia; Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616; Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616
| | - Carlos A Driscoll
- Department of Animal Science, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Laboratory of Comparative Behavioral Genomics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20892-9412; Institute of Cytology and Genetics of the Russian Academy of Sciences, Novosibirsk 630090, Russia; Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616; Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616
| | - Christina S Barr
- Department of Animal Science, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Laboratory of Comparative Behavioral Genomics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20892-9412; Institute of Cytology and Genetics of the Russian Academy of Sciences, Novosibirsk 630090, Russia; Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616; Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616
| | - Lyudmila N Trut
- Department of Animal Science, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Laboratory of Comparative Behavioral Genomics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20892-9412; Institute of Cytology and Genetics of the Russian Academy of Sciences, Novosibirsk 630090, Russia; Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616; Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616
| | - Benjamin N Sacks
- Department of Animal Science, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Laboratory of Comparative Behavioral Genomics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20892-9412; Institute of Cytology and Genetics of the Russian Academy of Sciences, Novosibirsk 630090, Russia; Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616; Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616
| | - Anna V Kukekova
- Department of Animal Science, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Laboratory of Comparative Behavioral Genomics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20892-9412; Institute of Cytology and Genetics of the Russian Academy of Sciences, Novosibirsk 630090, Russia; Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616; Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616
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Merson C, Statham MJ, Janecka JE, Lopez RR, Silvy NJ, Sacks BN. Distribution of native and nonnative ancestry in red foxes along an elevational gradient in central Colorado. J Mammal 2017. [DOI: 10.1093/jmammal/gyx004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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21
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A Preliminary Range-Wide Distribution Model for the Sacramento Valley Red Fox. JOURNAL OF FISH AND WILDLIFE MANAGEMENT 2016. [DOI: 10.3996/072016-jfwm-057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Abstract
The Sacramento Valley red fox Vulpes vulpes patwin of California is a newly named subspecies recently found to be distinct both from other native red foxes and nearby introduced populations. The Sacramento Valley red fox experienced a historical demographic bottleneck resulting in a critically small genetic effective population size, causing concern over its current status and management requirements, yet little is known about its contemporary abundance, demographic trajectory, or habitat use. The hot, arid Sacramento Valley contrasts starkly in climate and physiography with the boreal habitats of other indigenous red foxes in western North America, indicating the need to obtain information specifically on the habitat requirements of this subspecies. A 3-y effort to locate reproductive den sites throughout the Sacramento Valley resulted in 42 independent dens, which we used to obtain preliminary information on habitat use and to develop a distribution model for this subspecies, and 28 Sacramento Valley red foxes killed by vehicles, which we used as independent data to test the models. Foxes were present significantly more than expected in grasslands and less than expected in wetlands and flooded agriculture and also tended to occur in proximity to human development, potentially as refuges from coyotes Canis latrans. We used Maxent to build predictive models. The best model, which incorporated vegetation/land-use classes and proximity to human development, identified 24% of the study area as predicted-presence habitat, which contained 76% of the den sites used to construct the model and 89% of independent locations used to test the model. Our model greatly narrowed the area over which foxes are predicted to occur and will facilitate future surveys to assess occupancy and ultimately abundance and population trends.
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Lounsberry ZT, Quinn CB, Statham MJ, Angulo CL, Kalani TJ, Tiller E, Sacks BN. Investigating genetic introgression from farmed red foxes into the wild population in Newfoundland, Canada. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0914-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Sacks BN, Brazeal JL, Lewis JC. Landscape genetics of the nonnative red fox of California. Ecol Evol 2016; 6:4775-91. [PMID: 27547312 PMCID: PMC4979706 DOI: 10.1002/ece3.2229] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 05/06/2016] [Accepted: 05/16/2016] [Indexed: 01/18/2023] Open
Abstract
Invasive mammalian carnivores contribute disproportionately to declines in global biodiversity. In California, nonnative red foxes (Vulpes vulpes) have significantly impacted endangered ground‐nesting birds and native canids. These foxes derive primarily from captive‐reared animals associated with the fur‐farming industry. Over the past five decades, the cumulative area occupied by nonnative red fox increased to cover much of central and southern California. We used a landscape‐genetic approach involving mitochondrial DNA (mtDNA) sequences and 13 microsatellites of 402 nonnative red foxes removed in predator control programs to investigate source populations, contemporary connectivity, and metapopulation dynamics. Both markers indicated high population structuring consistent with origins from multiple introductions and low subsequent gene flow. Landscape‐genetic modeling indicated that population connectivity was especially low among coastal sampling sites surrounded by mountainous wildlands but somewhat higher through topographically flat, urban and agricultural landscapes. The genetic composition of populations tended to be stable for multiple generations, indicating a degree of demographic resilience to predator removal programs. However, in two sites where intensive predator control reduced fox abundance, we observed increases in immigration, suggesting potential for recolonization to counter eradication attempts. These findings, along with continued genetic monitoring, can help guide localized management of foxes by identifying points of introductions and routes of spread and evaluating the relative importance of reproduction and immigration in maintaining populations. More generally, the study illustrates the utility of a landscape‐genetic approach for understanding invasion dynamics and metapopulation structure of one of the world's most destructive invasive mammals, the red fox.
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Affiliation(s)
- Benjamin N Sacks
- Mammalian Ecology and Conservation Unit Veterinary Genetics Laboratory University of California, Davis One Shields Avenue/Old Davis Road Davis California 95616-8744; Department of Population Health and Reproduction University of California, Davis One Shields Avenue Davis California 95616
| | - Jennifer L Brazeal
- Mammalian Ecology and Conservation Unit Veterinary Genetics Laboratory University of California, Davis One Shields Avenue/Old Davis Road Davis California 95616-8744
| | - Jeffrey C Lewis
- Washington Department of Fish and Wildlife 600 Capitol Way N Olympia Washington 98501-1091
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Efficient Genome-Wide Sequencing and Low-Coverage Pedigree Analysis from Noninvasively Collected Samples. Genetics 2016; 203:699-714. [PMID: 27098910 PMCID: PMC4896188 DOI: 10.1534/genetics.116.187492] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 04/18/2016] [Indexed: 12/31/2022] Open
Abstract
Research on the genetics of natural populations was revolutionized in the 1990s by methods for genotyping noninvasively collected samples. However, these methods have remained largely unchanged for the past 20 years and lag far behind the genomics era. To close this gap, here we report an optimized laboratory protocol for genome-wide capture of endogenous DNA from noninvasively collected samples, coupled with a novel computational approach to reconstruct pedigree links from the resulting low-coverage data. We validated both methods using fecal samples from 62 wild baboons, including 48 from an independently constructed extended pedigree. We enriched fecal-derived DNA samples up to 40-fold for endogenous baboon DNA and reconstructed near-perfect pedigree relationships even with extremely low-coverage sequencing. We anticipate that these methods will be broadly applicable to the many research systems for which only noninvasive samples are available. The lab protocol and software (“WHODAD”) are freely available at www.tung-lab.org/protocols-and-software.html and www.xzlab.org/software.html, respectively.
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Kasprowicz AE, Statham MJ, Sacks BN. Fate of the other redcoat: remnants of colonial British foxes in the eastern United States. J Mammal 2015. [DOI: 10.1093/jmammal/gyv179] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Red foxes were absent or rare in the southeastern United States until the late 1800s. Their origins potentially include natural population increase/expansion, translocations from Europe, and, eventually, 20th century fur farming. Previous studies have found no European haplotypes in North America, but few samples were sourced from the Atlantic coastal plain, closer to the source of putative introductions. Through analysis of mitochondrial DNA in 584 red foxes from this region, we identified indigenous haplotypes in ≥ 35% of foxes, 1 of 2 European haplotypes in 17% of foxes and fur farm haplotypes in ≥ 13% of foxes; another 35% of foxes had haplotypes potentially indigenous or native. In contrast, only 3 of 135 (2%) male foxes carried a single European Y chromosome haplotype. Most European and fur farm haplotypes were found near the densely human-populated coastal plain and Hudson River lowlands; most red foxes of the Appalachians and Piedmont had native eastern haplotypes. Our findings suggest that the more remote, upland populations primarily reflect indigenous red fox matrilines, whereas urban-associated populations in and around the mid-Atlantic coastal plain and Hudson lowlands reflect an admixture of native and nonnative maternal sources. Autosomal markers are needed to further elucidate the extent of European and fur farm introgression in the Appalachians and further west.
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Miles KA, Holtz MN, Lounsberry ZT, Sacks BN. A paired comparison of scat-collecting versus scat-swabbing methods for noninvasive recovery of mesocarnivore DNA from an arid environment. WILDLIFE SOC B 2015. [DOI: 10.1002/wsb.600] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Kathleen A. Miles
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory; University of California, Davis; 1 Shields Avenue Davis CA 95616 USA
| | - Michelle N. Holtz
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory; University of California, Davis; 1 Shields Avenue Davis CA 95616 USA
| | - Zachary T. Lounsberry
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory; University of California, Davis; 1 Shields Avenue Davis CA 95616 USA
| | - Benjamin N. Sacks
- Department of Population Health and Reproduction and Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory; University of California, Davis; 1 Shields Avenue Davis CA 95616 USA
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Hiller TL, McFadden-Hiller JE, Sacks BN. Genetic and Photographic Detections Document Sierra Nevada Red Fox in the Northern Cascades of Oregon. NORTHWEST SCIENCE 2015. [DOI: 10.3955/046.089.0410] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Goddard NS, Statham MJ, Sacks BN. Mitochondrial Analysis of the Most Basal Canid Reveals Deep Divergence between Eastern and Western North American Gray Foxes (Urocyon spp.) and Ancient Roots in Pleistocene California. PLoS One 2015; 10:e0136329. [PMID: 26288066 PMCID: PMC4546004 DOI: 10.1371/journal.pone.0136329] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 07/10/2015] [Indexed: 01/22/2023] Open
Abstract
Pleistocene aridification in central North America caused many temperate forest-associated vertebrates to split into eastern and western lineages. Such divisions can be cryptic when Holocene expansions have closed the gaps between once-disjunct ranges or when local morphological variation obscures deeper regional divergences. We investigated such cryptic divergence in the gray fox (Urocyon cinereoargenteus), the most basal extant canid in the world. We also investigated the phylogeography of this species and its diminutive relative, the island fox (U. littoralis), in California. The California Floristic Province was a significant source of Pleistocene diversification for a wide range of taxa and, we hypothesized, for the gray fox as well. Alternatively, gray foxes in California potentially reflected a recent Holocene expansion from further south. We sequenced mitochondrial DNA from 169 gray foxes from the southeastern and southwestern United States and 11 island foxes from three of the Channel Islands. We estimated a 1.3% sequence divergence in the cytochrome b gene between eastern and western foxes and used coalescent simulations to date the divergence to approximately 500,000 years before present (YBP), which is comparable to that between recognized sister species within the Canidae. Gray fox samples collected from throughout California exhibited high haplotype diversity, phylogeographic structure, and genetic signatures of a late-Holocene population decline. Bayesian skyline analysis also indicated an earlier population increase dating to the early Wisconsin glaciation (~70,000 YBP) and a root height extending back to the previous interglacial (~100,000 YBP). Together these findings support California's role as a long-term Pleistocene refugium for western Urocyon. Lastly, based both on our results and re-interpretation of those of another study, we conclude that island foxes of the Channel Islands trace their origins to at least 3 distinct female founders from the mainland rather than to a single matriline, as previously suggested.
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Affiliation(s)
- Natalie S. Goddard
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
| | - Mark J. Statham
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
| | - Benjamin N. Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
- * E-mail:
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Leite JV, Álvares F, Velo-Antón G, Brito JC, Godinho R. Differentiation of North African foxes and population genetic dynamics in the desert—insights into the evolutionary history of two sister taxa, Vulpes rueppellii and Vulpes vulpes. ORG DIVERS EVOL 2015. [DOI: 10.1007/s13127-015-0232-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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30
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Volkmann LA, Statham MJ, Mooers AØ, Sacks BN. Genetic distinctiveness of red foxes in the Intermountain West as revealed through expanded mitochondrial sequencing. J Mammal 2015. [DOI: 10.1093/jmammal/gyv007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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31
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Statham MJ, Murdoch J, Janecka J, Aubry KB, Edwards CJ, Soulsbury CD, Berry O, Wang Z, Harrison D, Pearch M, Tomsett L, Chupasko J, Sacks BN. Range-wide multilocus phylogeography of the red fox reveals ancient continental divergence, minimal genomic exchange and distinct demographic histories. Mol Ecol 2014; 23:4813-30. [DOI: 10.1111/mec.12898] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 08/19/2014] [Accepted: 08/20/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Mark J. Statham
- Mammalian Ecology and Conservation Unit; Veterinary Genetics Laboratory; University of California; One Shields Avenue/Old Davis Road Davis CA 95616-8744 USA
| | - James Murdoch
- Rubenstein School of Environment and Natural Resources; 303A Aiken Center; University of Vermont; 81 Carrigan Drive Burlington VT 05405 USA
| | - Jan Janecka
- Department of Biological Sciences; Duquesne University; 600 Forbes Avenue Pittsburgh PA 15282 USA
| | - Keith B. Aubry
- U.S. Forest Service; Pacific Northwest Research Station; Olympia WA 98512 USA
| | - Ceiridwen J. Edwards
- Research Laboratory for Archaeology; University of Oxford; Dyson Perrins Building; South Parks Road Oxford OX1 3QY UK
| | - Carl D. Soulsbury
- School of Life Sciences; University of Lincoln; Brayford Pool Lincoln LN6 7TS UK
| | - Oliver Berry
- CSIRO Marine and Atmospheric Research; Centre for Environment and Life Sciences; Floreat WA 6014 Australia
- Invasive Animals Cooperative Research Centre; School of Animal Biology (M092); The University of Western Australia; Crawley WA 6009 Australia
| | - Zhenghuan Wang
- School of Life Sciences; East China Normal University; No. 3663 North Zhongshan Road 200062 Shanghai China
| | - David Harrison
- Harrison Institute; Bowerwood House; 15 St. Botolph's Road Sevenoaks Kent TN13 3AQ UK
| | - Malcolm Pearch
- Harrison Institute; Bowerwood House; 15 St. Botolph's Road Sevenoaks Kent TN13 3AQ UK
| | - Louise Tomsett
- Mammal Section; Department of Life Sciences; The Natural History Museum; Cromwell Road London SW7 5BD UK
| | - Judith Chupasko
- Mammalogy Department; Harvard Museum of Comparative Zoology; 52 Oxford Street Cambridge MA 02138 USA
| | - Benjamin N. Sacks
- Mammalian Ecology and Conservation Unit; Veterinary Genetics Laboratory; University of California; One Shields Avenue/Old Davis Road Davis CA 95616-8744 USA
- Department of Population Health and Reproduction; University of California; One Shields Avenue/Old Davis Road Davis CA 95616-8744 USA
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Ancient DNA reveals prehistoric habitat fragmentation and recent domestic introgression into native wild reindeer. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0606-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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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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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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Reponen SEM, Brown SK, Barnett BD, Sacks BN. Genetic and morphometric evidence on a Galápagos Island exposes founder effects and diversification in the first-known (truly) feral western dog population. Mol Ecol 2013; 23:269-83. [PMID: 24261528 DOI: 10.1111/mec.12595] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 11/14/2013] [Accepted: 11/15/2013] [Indexed: 11/29/2022]
Abstract
Domesticated animals that revert to a wild state can become invasive and significantly impact native biodiversity. Although dogs can be problematic locally, only the Australasian dingo is known to occur in isolation from humans. Western dogs have experienced more intense artificial selection, which potentially limits their invasiveness. However, feral dogs eradicated from Isabela Island, Galápagos in the 1980s could be the first-known exception. We used DNA and morphometric data from 92 of these dogs to test the hypotheses that (i) these dogs persisted independently of humans for up to a century and a half since descending from a handful of dogs introduced in the early 1800s, vs. (ii) similarly to other western feral dog populations, they reflected continuous recruitment of strays from human settlements on a portion of the Island. We detected one dominant maternal lineage and one dominant paternal lineage shared by the three subpopulations, along with low autosomal genetic diversity, consistent with the hypothesized common origins from a small founder population. Genetic diversity patterns among the three island subpopulations were consistent with stepping-stone founder effects, while morphometric differentiation suggested rapid phenotypic divergence, possibly due to drift and reinforced by selection corresponding to distinct microclimates and habitats on Isabela. Despite the continued presence of free-ranging dogs in the vicinity of settlements on Isabela and other Galápagos Islands, feral populations have not reestablished in remote areas since the 1980s, emphasizing the rarity of conditions necessary for feralization of modern western dogs.
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Affiliation(s)
- Sini E M Reponen
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, One Shields Avenue/Old Davis Road, Davis, CA, 95616, USA
| | - Sarah K Brown
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, One Shields Avenue/Old Davis Road, Davis, CA, 95616, USA.,Department of Anthropology, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Bruce D Barnett
- Barnett Environmental, 5214 El Cemonte Ave., Davis, CA, 95618, USA
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, One Shields Avenue/Old Davis Road, Davis, CA, 95616, USA.,Department of Population Health and Reproduction, University of California, One Shields Avenue/Old Davis Road, Davis, CA, 95616, USA
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Devillard S, Jombart T, Léger F, Pontier D, Say L, Ruette S. How reliable are morphological and anatomical characters to distinguish European wildcats, domestic cats and their hybrids in France? J ZOOL SYST EVOL RES 2013. [DOI: 10.1111/jzs.12049] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sébastien Devillard
- Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR5558; Laboratoire de Biométrie et Biologie Evolutive; F-69622; Villeurbanne France
| | - Thibaut Jombart
- MRC Centre for Outbreak Analysis and Modelling; Department of Infectious Disease Epidemiology; Imperial College - School of Public Health; London UK
| | - François Léger
- Office National de la Chasse et de la Faune Sauvage; Montfort Birieux France
| | - Dominique Pontier
- Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR5558; Laboratoire de Biométrie et Biologie Evolutive; F-69622; Villeurbanne France
| | - Ludovic Say
- Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR5558; Laboratoire de Biométrie et Biologie Evolutive; F-69622; Villeurbanne France
| | - Sandrine Ruette
- Office National de la Chasse et de la Faune Sauvage; Montfort Birieux France
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Costa M, Fernandes C, Birks JDS, Kitchener AC, Santos-Reis M, Bruford MW. The genetic legacy of the 19th-century decline of the British polecat: evidence for extensive introgression from feral ferrets. Mol Ecol 2013; 22:5130-47. [PMID: 24050727 DOI: 10.1111/mec.12456] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2013] [Revised: 05/28/2013] [Accepted: 06/13/2013] [Indexed: 12/01/2022]
Abstract
In the 19th century, the British polecat suffered a demographic contraction, as a consequence of direct persecution, reaching its lowest population in the years that preceded the First World War. The polecat is now recovering and expanding throughout Britain, but introgressive hybridization with feral ferrets has been reported, which could be masking the true range of the polecat and introducing domestic genes into the species. We used a fragment of the mitochondrial DNA control region and 11 microsatellite loci to characterize the frequency and extent of hybridization and introgression between the two species and assess whether the 19th-century decline corresponded to a genetic bottleneck in the polecat. The proportion of admixture detected in the wild was high (31%) and hybrids were more frequently found outside Wales, suggesting that hybridization is more likely to occur along the eastern edge of the polecat's range expansion. The patterns observed in the mitochondrial and nuclear DNA data show that introgression was mediated by crosses between male polecats and female ferrets, whose offspring backcrossed with polecats. No first-generation (F1 ) hybrids were identified, and the broad range of observed admixture proportions agrees with a scenario of past extensive hybridization between the two species. Using several different methods to investigate demographic history, we did not find consistent evidence for a genetic bottleneck in the British polecat, a result that could be interpreted as a consequence of hybridization with ferrets. Our results highlight the importance of the Welsh polecat population for the conservation and restoration of the genetic identity of the British polecat.
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Affiliation(s)
- M Costa
- Centro de Biologia Ambiental, Faculdade de Ciências da Universidade de Lisboa, Edifício C2, 5º Piso, Campo Grande, 1749-016, Lisboa, Portugal; OnE - Organisms and Environment Division, School of Biosciences, Cardiff University, Sir Martin Evans Building, Cardiff, CF10 3AX, UK
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Strong genetic differentiation due to multiple founder events during a recent range expansion of an introduced wall lizard population. Biol Invasions 2013. [DOI: 10.1007/s10530-013-0480-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Bohling JH, Adams JR, Waits LP. Evaluating the ability of Bayesian clustering methods to detect hybridization and introgression using an empirical red wolf data set. Mol Ecol 2012; 22:74-86. [DOI: 10.1111/mec.12109] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2011] [Revised: 09/25/2012] [Accepted: 10/03/2012] [Indexed: 11/27/2022]
Affiliation(s)
- Justin H. Bohling
- Department of Ecosystem Science and Management; Penn State University; University Park; PA; 16802; USA
| | - Jennifer R. Adams
- Department of Fish and Wildlife Sciences; University of Idaho; Moscow; ID; 83844-1136; USA
| | - Lisette P. Waits
- Department of Fish and Wildlife Sciences; University of Idaho; Moscow; ID; 83844-1136; USA
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40
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Champagnon J, Crochet PA, Kreisinger J, Čížková D, Gauthier-Clerc M, Massez G, Söderquist P, Albrecht T, Guillemain M. Assessing the genetic impact of massive restocking on wild mallard. Anim Conserv 2012. [DOI: 10.1111/j.1469-1795.2012.00600.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
| | - P-A. Crochet
- Centre d'Ecologie Fonctionnelle et Evolutive; UMR 5175 - CNRS; Montpellier Cedex 5; France
| | - J. Kreisinger
- Department of Zoology; Faculty of Science; Charles University in Prague; Praha 2; Czech Republic
| | - D. Čížková
- Department of Population Biology; Institute of Vertebrate Biology; Academy of Sciences of the Czech Republic; Brno; Czech Republic
| | | | - G. Massez
- Les Marais du Vigueirat; Arles; France
| | | | | | - M. Guillemain
- Office National de la Chasse et de la Faune Sauvage; CNERA Avifaune Migratrice; Arles; France
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Kraus RHS, van Hooft P, Megens HJ, Tsvey A, Fokin SY, Ydenberg RC, Prins HHT. Global lack of flyway structure in a cosmopolitan bird revealed by a genome wide survey of single nucleotide polymorphisms. Mol Ecol 2012; 22:41-55. [PMID: 23110616 DOI: 10.1111/mec.12098] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 09/19/2012] [Accepted: 09/20/2012] [Indexed: 01/13/2023]
Abstract
Knowledge about population structure and connectivity of waterfowl species, especially mallards (Anas platyrhynchos), is a priority because of recent outbreaks of avian influenza. Ringing studies that trace large-scale movement patterns have to date been unable to detect clearly delineated mallard populations. We employed 363 single nucleotide polymorphism markers in combination with population genetics and phylogeographical approaches to conduct a population genomic test of panmixia in 801 mallards from 45 locations worldwide. Basic population genetic and phylogenetic methods suggest no or very little population structure on continental scales. Nor could individual-based structuring algorithms discern geographical structuring. Model-based coalescent analyses for testing models of population structure pointed to strong genetic connectivity among the world's mallard population. These diverse approaches all support the conclusion that there is a lack of clear population structure, suggesting that the world's mallards, perhaps with minor exceptions, form a single large, mainly interbreeding population.
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Affiliation(s)
- Robert H S Kraus
- Resource Ecology Group, Wageningen University, PO Box 47, 6700 AA, Wageningen, The Netherlands.
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SCHULTE ULRICH, VEITH MICHAEL, HOCHKIRCH AXEL. Rapid genetic assimilation of native wall lizard populations (Podarcis muralis) through extensive hybridization with introduced lineages. Mol Ecol 2012; 21:4313-26. [DOI: 10.1111/j.1365-294x.2012.05693.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Statham MJ, Sacks BN, Aubry KB, Perrine JD, Wisely SM. The origin of recently established red fox populations in the United States: translocations or natural range expansions? J Mammal 2012. [DOI: 10.1644/11-mamm-a-033.1] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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