1
|
Domínguez JC, Alda F, Calero-Riestra M, Olea PP, Martínez-Padilla J, Herranz J, Oñate JJ, Santamaría A, Viñuela J, García JT. Genetic footprints of a rapid and large-scale range expansion: the case of cyclic common vole in Spain. Heredity (Edinb) 2023; 130:381-393. [PMID: 36966202 PMCID: PMC10238521 DOI: 10.1038/s41437-023-00613-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 03/27/2023] Open
Abstract
In the Anthropocene, many species are rapidly shifting their ranges in response to human-driven habitat modifications. Studying patterns and genetic signatures of range shifts helps to understand how species cope with environmental disturbances and predict future shifts in the face of global environmental change. We investigated the genetic signature of a contemporary wide-range expansion observed in the Iberian common vole Microtus arvalis asturianus shortly after a colonization event. We used mtDNA and microsatellite data to investigate patterns of genetic diversity, structure, demography, and gene flow across 57 localities covering the historical range of the species and the newly colonized area. The results showed a genetic footprint more compatible with a true range expansion (i.e. the colonization of previously unoccupied areas), than with a model of "colonization from within" (i.e. local expansions from small, unnoticed populations). Genetic diversity measures indicated that the source population was likely located at the NE of the historical range, with a declining gradient of genetic diversity towards the more recently invaded areas. At the expansion front, we observed the greatest gene flow and smallest pairwise differences between nearby localities. Both natural landscape features (rivers) and recent anthropogenic barriers (roads, railways) explained a large proportion of genetic variance among populations and had a significant impact on the colonization pathways used by voles.
Collapse
Affiliation(s)
- Julio C Domínguez
- IREC, Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM), Ronda de Toledo 12, 13071, Ciudad Real, Spain.
- IPE, Pyrenean Institute of Ecology (CSIC), 22700, Avda. Nuestra Señora de la Victoria 16, Jaca, Spain.
| | - Fernando Alda
- Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga, Chattanooga, TN, USA
| | - María Calero-Riestra
- IREC, Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM), Ronda de Toledo 12, 13071, Ciudad Real, Spain
- IPE, Pyrenean Institute of Ecology (CSIC), 22700, Avda. Nuestra Señora de la Victoria 16, Jaca, Spain
| | - Pedro P Olea
- Terrestrial Ecology Group (TEG)-Departamento de Ecología, and Centro de Investigación en Biodiversidad y Cambio Global, Universidad Autónoma de Madrid, c/ Darwin, 2, 28049, Madrid, Spain
| | - Jesús Martínez-Padilla
- IPE, Pyrenean Institute of Ecology (CSIC), 22700, Avda. Nuestra Señora de la Victoria 16, Jaca, Spain
| | - Jesús Herranz
- Terrestrial Ecology Group (TEG)-Departamento de Ecología, and Centro de Investigación en Biodiversidad y Cambio Global, Universidad Autónoma de Madrid, c/ Darwin, 2, 28049, Madrid, Spain
| | - Juan José Oñate
- Terrestrial Ecology Group (TEG)-Departamento de Ecología, and Centro de Investigación en Biodiversidad y Cambio Global, Universidad Autónoma de Madrid, c/ Darwin, 2, 28049, Madrid, Spain
| | - Ana Santamaría
- Terrestrial Ecology Group (TEG)-Departamento de Ecología, and Centro de Investigación en Biodiversidad y Cambio Global, Universidad Autónoma de Madrid, c/ Darwin, 2, 28049, Madrid, Spain
| | - Javier Viñuela
- IREC, Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM), Ronda de Toledo 12, 13071, Ciudad Real, Spain
| | - Jesús T García
- IREC, Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM), Ronda de Toledo 12, 13071, Ciudad Real, Spain
| |
Collapse
|
2
|
McDevitt AD, Coscia I, Browett SS, Ruiz-González A, Statham MJ, Ruczyńska I, Roberts L, Stojak J, Frantz AC, Norén K, Ågren EO, Learmount J, Basto M, Fernandes C, Stuart P, Tosh DG, Sindicic M, Andreanszky T, Isomursu M, Panek M, Korolev A, Okhlopkov IM, Saveljev AP, Pokorny B, Flajšman K, Harrison SWR, Lobkov V, Ćirović D, Mullins J, Pertoldi C, Randi E, Sacks BN, Kowalczyk R, Wójcik JM. Next-generation phylogeography resolves post-glacial colonization patterns in a widespread carnivore, the red fox (Vulpes vulpes), in Europe. Mol Ecol 2021; 31:993-1006. [PMID: 34775636 DOI: 10.1111/mec.16276] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 11/03/2021] [Accepted: 11/08/2021] [Indexed: 12/22/2022]
Abstract
Carnivores tend to exhibit a lack of (or less pronounced) genetic structure at continental scales in both a geographic and temporal sense and this can confound the identification of post-glacial colonization patterns in this group. In this study we used genome-wide data (using genotyping by sequencing [GBS]) to reconstruct the phylogeographic history of a widespread carnivore, the red fox (Vulpes vulpes), by investigating broad-scale patterns of genomic variation, differentiation and admixture amongst contemporary populations in Europe. Using 15,003 single nucleotide polymorphisms (SNPs) from 524 individuals allowed us to identify the importance of refugial regions for the red fox in terms of endemism (e.g., Iberia). In addition, we tested multiple post-glacial recolonization scenarios of previously glaciated regions during the Last Glacial Maximum using an Approximate Bayesian Computation (ABC) approach that were unresolved from previous studies. This allowed us to identify the role of admixture from multiple source population post-Younger Dryas in the case of Scandinavia and ancient land-bridges in the colonization of the British Isles. A natural colonization of Ireland was deemed more likely than an ancient human-mediated introduction as has previously been proposed and potentially points to a larger mammalian community on the island in the early post-glacial period. Using genome-wide data has allowed us to tease apart broad-scale patterns of structure and diversity in a widespread carnivore in Europe that was not evident from using more limited marker sets and provides a foundation for next-generation phylogeographic studies in other non-model species.
Collapse
Affiliation(s)
- Allan D McDevitt
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Ilaria Coscia
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Samuel S Browett
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Aritz Ruiz-González
- Department of Zoology and Animal Cell Biology, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
| | - Mark J Statham
- Department of Population Health and Reproduction, School of Veterinary Medicine, Mammalian Ecology and Conservation Unit, Center for Veterinary Genetics, University of California, Davis, California, USA
| | - Iwona Ruczyńska
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Liam Roberts
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Joanna Stojak
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Alain C Frantz
- Musée National d'Histoire Naturelle, Luxembourg, Luxembourg
| | - Karin Norén
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Erik O Ågren
- Department of Pathology and Wildlife Diseases, National Veterinary Institute, Uppsala, Sweden
| | - Jane Learmount
- National Wildlife Management Centre, Animal and Plant Health Agency, Sand Hutton, UK
| | - Mafalda Basto
- Department of Animal Biology, Faculty of Sciences, CE3C - Centre for Ecology, Evolution and Environmental Changes, University of Lisbon, Lisbon, Portugal
| | - Carlos Fernandes
- Department of Animal Biology, Faculty of Sciences, CE3C - Centre for Ecology, Evolution and Environmental Changes, University of Lisbon, Lisbon, Portugal
| | - Peter Stuart
- Biological and Pharmaceutical Sciences Department, Institute of Technology Tralee, Kerry, Ireland
| | - David G Tosh
- National Museums of Northern Ireland, Hollywood, UK
| | - Magda Sindicic
- Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | | | - Marja Isomursu
- Finnish Food Authority, Veterinary Bacteriology and Pathology Research Unit, Oulu, Finland
| | | | - Andrey Korolev
- Institute of Biology of Komi Science, Remote Centre of the Ural Branch of the Russian Academy of Sciences, Syktyvkar, Russia
| | - Innokentiy M Okhlopkov
- Institute of Biological Problems of Cryolithozone, Siberian Branch of Russian Academy of Sciences, Yakutsk, Russia
| | - Alexander P Saveljev
- Department of Animal Ecology, Russian Research Institute of Game Management and Fur Farming, Kirov, Russia
| | | | | | - Stephen W R Harrison
- School of Animal Rural & Environmental Sciences, Nottingham Trent University, Southwell, UK
| | - Vladimir Lobkov
- Faculty of Biology, Odessa I.I. Mechnykov National University, Odessa, Ukraine
| | - Duško Ćirović
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Jacinta Mullins
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Cino Pertoldi
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Ettore Randi
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.,Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Benjamin N Sacks
- Department of Population Health and Reproduction, School of Veterinary Medicine, Mammalian Ecology and Conservation Unit, Center for Veterinary Genetics, University of California, Davis, California, USA
| | - Rafał Kowalczyk
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Jan M Wójcik
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| |
Collapse
|
3
|
Klauder K, Borg BL, Prugh LR. Living on the edge: spatial response of coyotes (Canis latrans) to wolves (Canis lupus) in the subarctic. CAN J ZOOL 2021. [DOI: 10.1139/cjz-2020-0050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Understanding how mesopredators manage the risks associated with apex predators is key to explaining impacts of apex predators on mesopredator populations and patterns of mesopredator space use. Here we examine the spatial response of coyotes (Canis latrans Say, 1823) to risk posed by wolves (Canis lupus Linnaeus, 1758) using data from sympatric individuals fitted with GPS collars in subarctic Alaska, USA, near the northern range limit for coyotes. We show that coyotes do not universally avoid wolves, but instead demonstrate season-specific responses to both wolf proximity and long-term use of the landscape by wolves. Specifically, coyotes switched from avoiding wolves in summer to preferring areas with wolves in winter, and this selection was consistent across short-term and longer term temporal scales. In the summer, coyotes responded less strongly to risk of wolves when in open areas than when in closed vegetation. We also demonstrate that coyotes maintain extremely large territories averaging 291 km2, and experience low annual survival (0.50) with large carnivores being the largest source of mortality. This combination of attraction and avoidance predicated on season and landcover suggests that mesopredators use complex behavioral strategies to mediate the effects of apex predators.
Collapse
Affiliation(s)
- Kaija Klauder
- University of Washington, College of the Environment, School of Environmental and Forest Sciences, Box 352100, Seattle, WA 98195-2100, USA
| | - Bridget L. Borg
- National Park Service, Denali National Park and Preserve, P.O. Box 9, Denali Park, AK 99755, USA
| | - Laura R. Prugh
- University of Washington, College of the Environment, School of Environmental and Forest Sciences, Box 352100, Seattle, WA 98195-2100, USA
| |
Collapse
|
4
|
Walton Z, Hagenlund M, Østbye K, Samelius G, Odden M, Norman A, Willebrand T, Spong G. Moving far, staying close: red fox dispersal patterns revealed by SNP genotyping. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01332-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
AbstractThe genetic structure of a population can provide important insights into animal movements at varying geographical scales. Individual and social behaviors, such as philopatry and dispersal, affect patterns of relatedness, age and sex structure, shaping the local genetic structure of populations. However, these fine scale patterns may not be detected within broader population genetic structure. Using SNP genotyping for pairwise relatedness estimates, we investigated the spatial and genetic structuring of 141 red foxes within south-central Sweden at two scales. First, we looked at broad scale population structuring among red foxes at the regional level. We then estimated pairwise relatedness values to evaluate the spatial and genetic structure of male, female and mixed sex pairs for patterns of philopatry and dispersal at a more localized scale. We found limited genetic differentiation at the regional scale. However, local investigations revealed patterns of female philopatry and male biased dispersal. There were significant differences in pairwise geographic distances between highly related same sex pairs with the average distance between related males, 37.8 km, being six times farther than that of related females, averaging 6.3 km. In summary, the low levels of genetic differentiation found in this study illustrates the mobility and dispersal ability of red foxes across scales. However, relatedness plays a strong role in the spatial organization of red foxes locally, ultimately contributing to male biased dispersal patterns.
Collapse
|
5
|
Rød‐Eriksen L, Skrutvold J, Herfindal I, Jensen H, Eide NE. Highways associated with expansion of boreal scavengers into the alpine tundra of Fennoscandia. J Appl Ecol 2020. [DOI: 10.1111/1365-2664.13668] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lars Rød‐Eriksen
- Norwegian Institute for Nature Research (NINA) Trondheim Norway
- Department of Biology Centre for Biodiversity Dynamics (CBD) Norwegian University of Science and Technology (NTNU) Trondheim Norway
| | | | - Ivar Herfindal
- Department of Biology Centre for Biodiversity Dynamics (CBD) Norwegian University of Science and Technology (NTNU) Trondheim Norway
| | - Henrik Jensen
- Department of Biology Centre for Biodiversity Dynamics (CBD) Norwegian University of Science and Technology (NTNU) Trondheim Norway
| | - Nina E. Eide
- Norwegian Institute for Nature Research (NINA) Trondheim Norway
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Unique genetic features of canine adenovirus type 1 (CAdV-1) infecting red foxes (Vulpes vulpes) in northern Norway and arctic foxes (Vulpes lagopus) in Svalbard. Vet Res Commun 2019; 43:67-76. [DOI: 10.1007/s11259-019-09746-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 02/15/2019] [Indexed: 10/27/2022]
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
|
10
|
Wallén J, Statham MJ, Ågren E, Isomursu M, Flagstad Ø, Bjørneboe-Berg T, Sacks BN, Norén K. Multiple recolonization routes towards the north: population history of the Fennoscandian red fox (Vulpes vulpes). Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Johan Wallén
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Mark J Statham
- Mammalian Ecology and Conservation Unit, Center for Veterinary Genetics, University of California Davis, Davis, CA, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Erik Ågren
- National Veterinary Institute, Department of Pathology and Wildlife Diseases, Uppsala, Sweden
| | - Marja Isomursu
- Finnish Food Safety Authority Evira, Production Animal and Wildlife Health Research Unit, Elektroniikkatie, Oulu, Finland
| | | | | | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Center for Veterinary Genetics, University of California Davis, Davis, CA, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Karin Norén
- Department of Zoology, Stockholm University, Stockholm, Sweden
- Mammalian Ecology and Conservation Unit, Center for Veterinary Genetics, University of California Davis, Davis, CA, USA
| |
Collapse
|
11
|
Norén K, Angerbjörn A, Wallén J, Meijer T, Sacks BN. Red foxes colonizing the tundra: genetic analysis as a tool for population management. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0910-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
12
|
Polymorphisms in ERAP1 and ERAP2 are shared by Caninae and segregate within and between random- and pure-breeds of dogs. Vet Immunol Immunopathol 2016; 179:46-57. [PMID: 27590425 DOI: 10.1016/j.vetimm.2016.08.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 08/03/2016] [Accepted: 08/04/2016] [Indexed: 01/01/2023]
Abstract
Specific polymorphisms in the endoplasmic reticulum amino peptidase genes ERAP1 and ERAP2, when present with certain MHC class receptor types, have been associated with increased risk for specific cancers, infectious diseases and autoimmune disorders in humans. This increased risk has been linked to distinct polymorphisms in both ERAPs and MHC class I receptors that affect the way cell-generated peptides are screened for antigenicity. The incidence of cancer, infectious disease and autoimmune disorders differ greatly among pure breeds of dogs as it does in humans and it is possible that this heightened susceptibility is also due to specific polymorphisms in ERAP1 and ERAP2. In order to determine if such polymorphisms exist, the ERAP1 and ERAP2 genes of 10 dogs of nine diverse breeds were sequenced and SNPs causing synonymous or non-synonymous amino acid changes, deletions or insertions were identified. Eight ERAP1 and 10 ERAP2 SNPs were used to create a Sequenom MassARRAY iPLEX based test panel which defined 24 ERAP1, 36 ERAP2 and 128 ERAP1/2 haplotypes. The prevalence of these haplotypes was then measured among dog, wolf, coyote, jackal and red fox populations. Some haplotypes were species specific, while others were shared across species, especially between dog, wolf, coyote and jackal. The prevalence of these haplotypes was then compared among various canid populations, and in particular between various populations of random- and pure-bred dogs. Human-directed positive selection has led to loss of ERAP diversity and segregation of certain haplotypes among various dog breeds. A phylogenetic tree generated from 45 of the most common ERAP1/2 haplotypes demonstrated three distinct clades, all of which were rooted with haplotypes either shared among species or specific to contemporary dogs, coyote and wolf.
Collapse
|