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Jarausch A, von Thaden A, Sin T, Corradini A, Pop MI, Chiriac S, Gazzola A, Nowak C. Assessment of genetic diversity, population structure and wolf-dog hybridisation in the Eastern Romanian Carpathian wolf population. Sci Rep 2023; 13:22574. [PMID: 38114536 PMCID: PMC10730609 DOI: 10.1038/s41598-023-48741-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 11/29/2023] [Indexed: 12/21/2023] Open
Abstract
The Carpathian Mountains have been constantly inhabited by grey wolves and present one of the largest distribution areas in Europe, comprising between 2300 and 2700 individuals in Romania. To date, however, relatively little is known about the Romanian wolf population. We aimed to provide a first assessment of genetic diversity, population structure and wolf-dog hybridisation based on 444 mostly non-invasively collected samples in the Eastern Romanian Carpathians. Pack reconstruction and analysis of population genetic parameters were performed with mitochondrial DNA control-region sequencing and microsatellite genotyping. We found relatively high levels of genetic diversity, which is similar to values found in previous studies on Carpathian wolves from Poland and Slovakia, as well as to the long-lasting Dinaric-Balkan wolf population. We found no significant population structure in our study region, suggesting effective dispersal and admixture. Analysis of wolf-dog hybridisation using a Single Nucleotide Polymorphism panel optimised for hybrid detection revealed low rates of admixture between wolves and domestic dogs. Our results provide evidence for the existence of a genetically viable wolf population in the Romanian Carpathians. The genetic data obtained in this study may serve as valuable baseline information for the elaboration of monitoring standards and management plans for wolves in Romania.
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Affiliation(s)
- Anne Jarausch
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Clamecystraße 12, 63571, Gelnhausen, Germany.
- Department of Biological Sciences, Johann Wolfgang Goethe-University, Biologicum, Max-von-Laue-Straße 9, 60438, Frankfurt am Main, Germany.
| | - Alina von Thaden
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Clamecystraße 12, 63571, Gelnhausen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Teodora Sin
- Department of Systems Ecology and Sustainability, Faculty of Biology, University of Bucharest, Splaiul Independentei 91-95, 050095, Bucharest, Romania
- Association for the Conservation of Biological Diversity, Ion Creanga 12, 620083, Focsani, Romania
| | - Andrea Corradini
- Association for the Conservation of Biological Diversity, Ion Creanga 12, 620083, Focsani, Romania
- Animal Ecology Unit, Research and Innovation Centre, Fondazione Edmund Mach, Via Edmund Mach 1, 38098, San Michele all'Adige, TN, Italy
- NBFC, National Biodiversity Future Center, 90133, Palermo, PA, Italy
| | - Mihai I Pop
- Association for the Conservation of Biological Diversity, Ion Creanga 12, 620083, Focsani, Romania
| | - Silviu Chiriac
- Environmental Protection Agency, Vrancea County, Dinicu Golescu 2, 620106, Focsani, Romania
| | - Andrea Gazzola
- Association for the Conservation of Biological Diversity, Ion Creanga 12, 620083, Focsani, Romania
| | - Carsten Nowak
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Clamecystraße 12, 63571, Gelnhausen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
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Žunna A, Ruņģis DE, Ozoliņš J, Stepanova A, Done G. Genetic Monitoring of Grey Wolves in Latvia Shows Adverse Reproductive and Social Consequences of Hunting. BIOLOGY 2023; 12:1255. [PMID: 37759654 PMCID: PMC10525079 DOI: 10.3390/biology12091255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/17/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023]
Abstract
Nowadays, genetic research methods play an important role in animal population studies. Since 2009, genetic material from Latvian wolf specimens obtained through hunting has been systematically gathered. This study, spanning until 2021, scrutinizes the consequences of regulated wolf hunting on population genetic metrics, kinship dynamics, and social organization. We employed 16 autosomal microsatellites to investigate relationships between full siblings and parent-offspring pairs. Our analysis encompassed expected and observed heterozygosity, inbreeding coefficients, allelic diversity, genetic distance and differentiation, mean pairwise relatedness, and the number of migrants per generation. The Latvian wolf population demonstrated robust genetic diversity with minimal inbreeding, maintaining stable allelic diversity and high heterozygosity over time and it is not fragmented. Our findings reveal the persistence of conventional wolf pack structures and enduring kinship groups. However, the study also underscores the adverse effects of intensified hunting pressure, leading to breeder loss, pack disruption, territorial displacement, and the premature dispersal of juvenile wolves.
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Affiliation(s)
- Agrita Žunna
- Latvian State Forest Research Institute Silava, Rīgas Str. 111, LV-2169 Salaspils, Latvia; (D.E.R.)
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Hernández‐Alonso G, Ramos‐Madrigal J, Sun X, Scharff‐Olsen CH, Sinding MS, Martins NF, Ciucani MM, Mak SST, Lanigan LT, Clausen CG, Bhak J, Jeon S, Kim C, Eo KY, Cho S, Boldgiv B, Gantulga G, Unudbayasgalan Z, Kosintsev PA, Stenøien HK, Gilbert MTP, Gopalakrishnan S. Conservation implications of elucidating the Korean wolf taxonomic ambiguity through whole-genome sequencing. Ecol Evol 2023; 13:e10404. [PMID: 37546572 PMCID: PMC10401669 DOI: 10.1002/ece3.10404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/07/2023] [Accepted: 07/26/2023] [Indexed: 08/08/2023] Open
Abstract
The taxonomic status of the now likely extirpated Korean Peninsula wolf has been extensively debated, with some arguing it represents an independent wolf lineage, Canis coreanus. To investigate the Korean wolf's genetic affiliations and taxonomic status, we sequenced and analysed the genomes of a Korean wolf dated to the beginning of the 20th century, and a captive wolf originally from the Pyongyang Central Zoo. Our results indicated that the Korean wolf bears similar genetic ancestry to other regional East Asian populations, therefore suggesting it is not a distinct taxonomic lineage. We identified regional patterns of wolf population structure and admixture in East Asia with potential conservation consequences in the Korean Peninsula and on a regional scale. We find that the Korean wolf has similar genomic diversity and inbreeding to other East Asian wolves. Finally, we show that, in contrast to the historical sample, the captive wolf is genetically more similar to wolves from the Tibetan Plateau; hence, Korean wolf conservation programmes might not benefit from the inclusion of this specimen.
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Affiliation(s)
- Germán Hernández‐Alonso
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Jazmín Ramos‐Madrigal
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Xin Sun
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | | | | | - Nuno F. Martins
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Marta Maria Ciucani
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Sarah S. T. Mak
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Liam Thomas Lanigan
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Cecilie G. Clausen
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Jong Bhak
- Clinomics Inc.UlsanKorea
- Korean Genomics CenterUlsan National Institute of Science and TechnologyUlsanKorea
- Department of Biomedical Engineering, College of Information‐Bio Convergence EngineeringUlsan National Institute of Science and TechnologyUlsanKorea
- Personal Genomics InstituteGenome Research FoundationOsongKorea
| | - Sungwon Jeon
- Clinomics Inc.UlsanKorea
- Korean Genomics CenterUlsan National Institute of Science and TechnologyUlsanKorea
| | | | - Kyung Yeon Eo
- Department of Animal Health & WelfareSemyung UniversityJecheonKorea
| | - Seong‐Ho Cho
- Natural History MuseumKyungpook National UniversityGunwiKorea
| | - Bazartseren Boldgiv
- Laboratory of Ecological and Evolutionary SynthesisNational University of MongoliaUlaanbaatarMongolia
| | | | | | - Pavel A. Kosintsev
- Institute of Plant and Animal Ecology, Urals Branch of the Russian Academy of SciencesYekaterinburgRussia
- Ural Federal UniversityEkaterinburgRussia
| | - Hans K. Stenøien
- NTNU University MuseumNorwegian University of Science and TechnologyTrondheimNorway
| | - M. Thomas P. Gilbert
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- University MuseumNorwegian University of Science and TechnologyTrondheimNorway
| | - Shyam Gopalakrishnan
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Bioinformatics, Department of Health TechnologyTechnical University of DenmarkLyngbyDenmark
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Zhang C, Li J, Yang B, Dai Q. habCluster: identifying the geographical boundary among intraspecific units using community detection algorithms in R. FRONTIERS IN CONSERVATION SCIENCE 2022. [DOI: 10.3389/fcosc.2022.908012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Conservation management for a species generally rests on intraspecific units, while identification of their geographic boundaries is necessary for the implementation. Intraspecific units can be discriminated using population genetic methods, yet an analytical approach is still lacking for detecting their geographic boundaries. Here, based on landscape connectivity, we present a raster-based geographical boundary delineation method, habCluster, using community detection algorithms. Community detection is a technique in graph theory used to identify clusters of highly connected nodes within a network. We assume that the habitat raster cells with better connections tend to form a continuous habitat patch than the others, thus making the range of an intraspecific unit. The method was tested on the gray wolf (Canis lupus) habitat in Europe and the giant panda (Ailuropoda melanoleuca) habitat in China. The habitat suitability index (HSI) maps for gray wolves and giant pandas were evaluated using species distribution models. Each cell in the HSI raster is treated as a node and directly connected with its eight neighbor cells. The edge weight between nodes is the reciprocal of the relative distance between the centers of the nodes weighted by the average of their HSI values. We implement habCluster using the R programming language with the inline C++ code to speed up the computing. We found that the boundaries of the clusters delineated using habCluster could serve as a good indicator of habitat patches. In the giant panda case, the clusters match generally well with nature reserves. habCluster can provide a spatial analysis basis for conservation management plans such as monitoring, translocation and reintroduction, and population structure research.
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Plis K, Niedziałkowska M, Borowik T, Lang J, Heddergott M, Tiainen J, Bunevich A, Šprem N, Paule L, Danilkin A, Kholodova M, Zvychaynaya E, Kashinina N, Pokorny B, Flajšman K, Paulauskas A, Djan M, Ristić Z, Novák L, Kusza S, Miller C, Tsaparis D, Stoyanov S, Shkvyria M, Suchentrunk F, Kutal M, Lavadinović V, Šnjegota D, Krapal AM, Dănilă G, Veeroja R, Dulko E, Jędrzejewska B. Mitochondrial DNA diversity and the population genetic structure of contemporary roe deer (Capreolus capreolus) in Europe. Mamm Biol 2022. [DOI: 10.1007/s42991-022-00274-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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6
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Pacheco C, Stronen AV, Jędrzejewska B, Plis K, Okhlopkov IM, Mamaev NV, Drovetski SV, Godinho R. Demography and evolutionary history of grey wolf populations around the Bering Strait. Mol Ecol 2022; 31:4851-4865. [PMID: 35822863 PMCID: PMC9545117 DOI: 10.1111/mec.16613] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 06/16/2022] [Accepted: 07/04/2022] [Indexed: 11/28/2022]
Abstract
Glacial and interglacial periods throughout the Pleistocene have been substantial drivers of change in species distributions. Earlier analyses suggested that modern grey wolves (Canis lupus) trace their origin to a single Late Pleistocene Beringian population that expanded east and westwards, starting c. 25,000 years ago (ya). Here, we examined the demographic and phylogeographic histories of extant populations around the Bering Strait with wolves from two inland regions of the Russian Far East (RFE) and one coastal and two inland regions of North‐western North America (NNA), genotyped for 91,327 single nucleotide polymorphisms. Our results indicated that RFE and NNA wolves had a common ancestry until c. 34,400 ya, suggesting that these populations started to diverge before the previously proposed expansion out of Beringia. Coastal and inland NNA populations diverged c. 16,000 ya, concordant with the minimum proposed date for the ecological viability of the migration route along the Pacific Northwest coast. Demographic reconstructions for inland RFE and NNA populations reveal spatial and temporal synchrony, with large historical effective population sizes that declined throughout the Pleistocene, possibly reflecting the influence of broadscale climatic changes across continents. In contrast, coastal NNA wolves displayed a consistently lower effective population size than the inland populations. Differences between the demographic history of inland and coastal wolves may have been driven by multiple ecological factors, including historical gene flow patterns, natural landscape fragmentation, and more recent anthropogenic disturbance.
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Affiliation(s)
- Carolina Pacheco
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Astrid Vik Stronen
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.,Department of Biotechnology and Life Sciences, Insubria University, Varese, Italy.,Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | - Kamila Plis
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Innokentiy M Okhlopkov
- Institute of Biological Problems of Cryolithozone, Siberian Branch of Russian Academy of Sciences, Yakutsk, Russia
| | - Nikolay V Mamaev
- Institute of Biological Problems of Cryolithozone, Siberian Branch of Russian Academy of Sciences, Yakutsk, Russia
| | - Sergei V Drovetski
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Raquel Godinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
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7
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Plis K, Niedziałkowska M, Borowik T, Lang J, Heddergott M, Tiainen J, Bunevich A, Šprem N, Paule L, Danilkin A, Kholodova M, Zvychaynaya E, Kashinina N, Pokorny B, Flajšman K, Paulauskas A, Djan M, Ristić Z, Novák L, Kusza S, Miller C, Tsaparis D, Stoyanov S, Shkvyria M, Suchentrunk F, Kutal M, Lavadinović V, Šnjegota D, Krapal A, Dănilă G, Veeroja R, Dulko E, Jędrzejewska B. Pan‐European phylogeography of the European roe deer (
Capreolus capreolus
). Ecol Evol 2022; 12:e8931. [PMID: 35600675 PMCID: PMC9120558 DOI: 10.1002/ece3.8931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 04/13/2022] [Accepted: 04/25/2022] [Indexed: 11/18/2022] Open
Abstract
To provide the most comprehensive picture of species phylogeny and phylogeography of European roe deer (Capreolus capreolus), we analyzed mtDNA control region (610 bp) of 1469 samples of roe deer from Central and Eastern Europe and included into the analyses additional 1541 mtDNA sequences from GenBank from other regions of the continent. We detected two mtDNA lineages of the species: European and Siberian (an introgression of C. pygargus mtDNA into C. capreolus). The Siberian lineage was most frequent in the eastern part of the continent and declined toward Central Europe. The European lineage contained three clades (Central, Eastern, and Western) composed of several haplogroups, many of which were separated in space. The Western clade appeared to have a discontinuous range from Portugal to Russia. Most of the haplogroups in the Central and the Eastern clades were under expansion during the Weichselian glacial period before the Last Glacial Maximum (LGM), while the expansion time of the Western clade overlapped with the Eemian interglacial. The high genetic diversity of extant roe deer is the result of their survival during the LGM probably in a large, contiguous range spanning from the Iberian Peninsula to the Caucasus Mts and in two northern refugia.
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Affiliation(s)
- Kamila Plis
- Mammal Research Institute Polish Academy of Sciences Białowieża Poland
| | | | - Tomasz Borowik
- Mammal Research Institute Polish Academy of Sciences Białowieża Poland
| | - Johannes Lang
- Working Group for Wildlife Research at Clinic for Birds, Reptiles, Amphibians and Fish Justus‐Liebig‐University Giessen Gießen Germany
| | - Mike Heddergott
- Department of Zoology Musée National d’Histoire Naturelle Luxembourg City Luxembourg
| | - Juha Tiainen
- Lammi Biological Station University of Helsinki Lammi Finland
- Natural Resources Institute Finland (Luke) Helsinki Finland
| | - Aleksey Bunevich
- State National Park Belovezhskaya Pushcha Kamenyuki Republic of Belarus
| | - Nikica Šprem
- Department of Fisheries, Apiculture, Wildlife Management and Special Zoology Faculty of Agriculture University of Zagreb Zagreb Croatia
| | - Ladislav Paule
- Department of Phytology Technical University in Zvolen Zvolen Slovak Republic
| | - Aleksey Danilkin
- A.N. Severtsov Institute of Ecology and Evolution Russian Academy of Sciences Moscow Russia
| | - Marina Kholodova
- A.N. Severtsov Institute of Ecology and Evolution Russian Academy of Sciences Moscow Russia
| | - Elena Zvychaynaya
- A.N. Severtsov Institute of Ecology and Evolution Russian Academy of Sciences Moscow Russia
| | - Nadezhda Kashinina
- A.N. Severtsov Institute of Ecology and Evolution Russian Academy of Sciences Moscow Russia
| | - Boštjan Pokorny
- Faculty of Environmental Protection Velenje Slovenia
- Department of Forest Ecology Slovenian Forestry Institute Ljubljana Slovenia
| | - Katarina Flajšman
- Department of Forest Ecology Slovenian Forestry Institute Ljubljana Slovenia
| | | | - Mihajla Djan
- Department of Biology and Ecology Faculty of Sciences University of Novi Sad Novi Sad Republic of Serbia
| | - Zoran Ristić
- Department of Geography, Tourism and Hotel Management Faculty of Sciences University of Novi Sad Novi Sad Serbia
| | - Luboš Novák
- Department of Forest Protection and Wildlife Management Mendel University in Brno Brno Czech Republic
| | - Szilvia Kusza
- Centre for Agricultural Genomics and Biotechnology Faculty of Agricultural and Food Sciences and Environmental Management University of Debrecen Debrecen Hungary
| | | | - Dimitris Tsaparis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC) Hellenic Centre for Marine Research Heraklion, Crete Greece
| | - Stoyan Stoyanov
- Wildlife Management Department University of Forestry Sofia Bulgaria
| | | | - Franz Suchentrunk
- Research Institute of Wildlife Ecology University of Veterinary Medicine Vienna Vienna Austria
| | - Miroslav Kutal
- Department of Forest Ecology Faculty of Forestry and Wood Technology Mendel University in Brno Brno Czech Republic
| | | | - Dragana Šnjegota
- Faculty of Natural Sciences and Mathematics University of Banja Luka Banja Luka Bosnia and Herzegovina
| | - Ana‐Maria Krapal
- "Grigore Antipa" National Museum of Natural History Bucharest Romania
| | - Gabriel Dănilă
- Faculty of Forestry Stefan cel Mare University of Suceava Suceava Romania
| | - Rauno Veeroja
- Department of Wildlife Monitoring Estonian Environment Agency Tallin Estonia
| | - Elżbieta Dulko
- Department of Anesthesiology University of Virginia Health System Charlottesville Virginia USA
- Faculty of Biology University of Warsaw Warszawa Poland
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A reduced SNP panel to trace gene flow across southern European wolf populations and detect hybridization with other Canis taxa. Sci Rep 2022; 12:4195. [PMID: 35264717 PMCID: PMC8907317 DOI: 10.1038/s41598-022-08132-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 03/01/2022] [Indexed: 12/18/2022] Open
Abstract
Intra- and inter-specific gene flow are natural evolutionary processes. However, human-induced hybridization is a global conservation concern across taxa, and the development of discriminant genetic markers to differentiate among gene flow processes is essential. Wolves (Canis lupus) are affected by hybridization, particularly in southern Europe, where ongoing recolonization of historic ranges is augmenting gene flow among divergent populations. Our aim was to provide diagnostic canid markers focused on the long-divergent Iberian, Italian and Dinaric wolf populations, based on existing genomic resources. We used 158 canid samples to select a panel of highly informative single nucleotide polymorphisms (SNPs) to (i) distinguish wolves in the three regions from domestic dogs (C. l. familiaris) and golden jackals (C. aureus), and (ii) identify their first two hybrid generations. The resulting 192 SNPs correctly identified the five canid groups, all simulated first-generation (F1) hybrids (0.482 ≤ Qi ≤ 0.512 between their respective parental groups) and all first backcross (BC1) individuals (0.723 ≤ Qi ≤ 0.827 to parental groups). An assay design and test with invasive and non-invasive canid samples performed successfully for 178 SNPs. By separating natural population admixture from inter-specific hybridization, our reduced panel can help advance evolutionary research, monitoring, and timely conservation management.
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Viluma A, Flagstad Ø, Åkesson M, Wikenros C, Sand H, Wabakken P, Ellegren H. Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population. Genome Res 2022; 32:449-458. [PMID: 35135873 PMCID: PMC8896455 DOI: 10.1101/gr.276070.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 12/30/2021] [Indexed: 11/25/2022]
Abstract
Genetic drift can dramatically change allele frequencies in small populations and lead to reduced levels of genetic diversity, including loss of segregating variants. However, there is a shortage of quantitative studies of how genetic diversity changes over time in natural populations, especially on genome-wide scales. Here, we analyzed whole-genome sequences from 76 wolves of a highly inbred Scandinavian population, founded by only one female and two males, sampled over a period of 30 yr. We obtained chromosome-level haplotypes of all three founders and found that 10%–24% of their diploid genomes had become lost after about 20 yr of inbreeding (which approximately corresponds to five generations). Lost haplotypes spanned large genomic regions, as expected from the amount of recombination during this limited time period. Altogether, 160,000 SNP alleles became lost from the population, which may include adaptive variants as well as wild-type alleles masking recessively deleterious alleles. Although not sampled, we could indirectly infer that the two male founders had megabase-sized runs of homozygosity and that all three founders showed significant haplotype sharing, meaning that there were on average only 4.2 unique haplotypes in the six copies of each autosome that the founders brought into the population. This violates the assumption of unrelated founder haplotypes often made in conservation and management of endangered species. Our study provides a novel view of how whole-genome resequencing of temporally stratified samples can be used to visualize and directly quantify the consequences of genetic drift in a small inbred population.
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10
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Šnjegota D, Stronen AV, Boljte B, Ćirović D, Djan M, Huber D, Jelenčič M, Konec M, Kusak J, Skrbinšek T. Population genetic structure of wolves in the northwestern Dinaric-Balkan region. Ecol Evol 2021; 11:18492-18504. [PMID: 35003687 PMCID: PMC8717286 DOI: 10.1002/ece3.8444] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 11/29/2022] Open
Abstract
The Balkan Peninsula and the Dinaric Mountains possess extraordinary biodiversity and support one of the largest and most diverse wolf (Canis lupus) populations in Europe. Results obtained with diverse genetic markers show west-east substructure, also seen in various other species, despite the absence of obvious barriers to movement. However, the spatial extent of the genetic clusters remains unresolved, and our aim was to combine fine-scale sampling with population and spatial genetic analyses to improve resolution of wolf genetic clusters. We analyzed 16 autosomal microsatellites from 255 wolves sampled in Slovenia, Croatia, Bosnia and Herzegovina (BIH), and Serbia and documented three genetic clusters. These comprised (1) Slovenia and the regions of Gorski kotar and Lika in Croatia, (2) the region of Dalmatia in southern Croatia and BIH, and (3) Serbia. When we mapped the clusters geographically, we observed west-east genetic structure across the study area, together with some specific structure in BIH-Dalmatia. We observed that cluster 1 had a smaller effective population size, consistent with earlier reports of population recovery since the 1980s. Our results provide foundation for future genomic studies that would further resolve the observed west-east population structure and its evolutionary history in wolves and other taxa in the region and identify focal areas for habitat conservation. They also have immediate importance for conservation planning for the wolves in one of the most important parts of the species' European range.
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Affiliation(s)
- Dragana Šnjegota
- Department of Biology and EcologyFaculty of Natural Sciences and MathematicsUniversity of Banja LukaBanja LukaBosnia and Herzegovina
| | - Astrid Vik Stronen
- Department of BiologyBiotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
| | - Barbara Boljte
- Department of BiologyBiotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
| | - Duško Ćirović
- Faculty of BiologyUniversity of BelgradeBelgradeSerbia
| | - Mihajla Djan
- Department of Biology and EcologyFaculty of SciencesUniversity of Novi SadNovi SadSerbia
| | - Djuro Huber
- Department of BiologyFaculty of Veterinary MedicineUniversity of ZagrebZagrebCroatia
| | - Maja Jelenčič
- Department of BiologyBiotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
| | - Marjeta Konec
- Department of BiologyBiotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
| | - Josip Kusak
- Department of BiologyFaculty of Veterinary MedicineUniversity of ZagrebZagrebCroatia
| | - Tomaž Skrbinšek
- Department of BiologyBiotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
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11
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Metapopulation management of a critically endangered marsupial in the age of genomics. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01869] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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12
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Kloch A, Biedrzycka A, Szewczyk M, Nowak S, Niedźwiedzka N, Kłodawska M, Hájková A, Hulva P, Jędrzejewska B, Mysłajek R. High genetic diversity of immunity genes in an expanding population of a highly mobile carnivore, the grey wolf
Canis
lupus
, in Central Europe. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Agnieszka Kloch
- Department of Ecology, Institute of Functional Biology and Ecology, Faculty of Biology, Biological and Chemical Research Centre University of Warsaw Warszawa Poland
| | | | - Maciej Szewczyk
- Department of Vertebrate Ecology and Zoology Faculty of Biology University of Gdańsk Gdańsk Poland
| | - Sabina Nowak
- Association for Nature “Wolf” Twardorzeczka Poland
| | | | - Monika Kłodawska
- Department of Zoology Faculty of Science Charles University Prague Czech Republic
| | - Andrea Hájková
- State Nature Conservancy of the Slovak Republic Spišská Nová Ves Slovakia
| | - Pavel Hulva
- Department of Zoology Faculty of Science Charles University Prague Czech Republic
- Department of Biology and Ecology Faculty of Science University of Ostrava Ostrava Czech Republic
| | | | - Robert Mysłajek
- Department of Ecology, Institute of Functional Biology and Ecology, Faculty of Biology, Biological and Chemical Research Centre University of Warsaw Warszawa Poland
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13
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Szewczyk M, Nowak C, Hulva P, Mergeay J, Stronen AV, Bolfíková BČ, Czarnomska SD, Diserens TA, Fenchuk V, Figura M, Groot AD, Haidt A, Hansen MM, Jansman H, Kluth G, Kwiatkowska I, Lubińska K, Michaux JR, Niedźwiecka N, Nowak S, Olsen K, Reinhardt I, Romański M, Schley L, Smith S, Špinkytė-Bačkaitienė R, Stachyra P, Stępniak KM, Sunde P, Thomsen PF, Zwijacz-Kozica T, Mysłajek RW. Genetic support for the current discrete conservation unit of the Central European wolf population. WILDLIFE BIOLOGY 2021. [DOI: 10.2981/wlb.00809] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Maciej Szewczyk
- M. Szewczyk (https://orcid.org/0000-0001-7424-1120) ✉ , Dept of Vertebrate Ecology and Zoology, Faculty of Biology, Univ. of Gdańsk, Gdańsk, Poland
| | - Carsten Nowak
- C. Nowak (https://orcid.org/0000-0002-3139-1951), Senckenberg Research Inst. and Natural History Museum Frankfurt, Gelnhausen, Germany
| | - Pavel Hulva
- P. Hulva (https://orcid.org/0000-0002-4968-4859), Faculty of Science, Charles Univ. in Prague, Prague, Czech Republic, and: Faculty of Science, Univ. of Ostrava, Ostrava, Czech Republic
| | - Joachim Mergeay
- J. Mergeay (https://orcid.org/0000-0002-6504-0551), Research Inst. for Nature and Forest (INBO), Geraardsbergen, Belgium, and: Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
| | - Astrid V. Stronen
- A. V. Stronen (https://orcid.org/0000-0002-5169-6736), Dept of Biology, Biotechnical Faculty, Univ. of Ljubljana, Ljubljana, Slovenia
| | - Barbora Černá Bolfíková
- B. Černá Bolfíková (https://orcid.org/0000-0001-8059-4889), Dept of Animal Science and Food Processing, Faculty of Tropical AgriSciences, Czech Univ. of Life Sciences Prague, Prague 6, Czech Republic
| | - Sylwia D. Czarnomska
- S. D. Czarnomska (https://orcid.org/0000-0002-8081-0956), Museum and Inst. of Zoology, Polish Academy of Sciences, Gdańsk, Poland
| | - Tom A. Diserens
- T. A. Diserens (https://orcid.org/0000-0002-0693-4168), Mammal Research Inst., Polish Academy of Sciences, Białowieża, Poland, and: Faculty of Biology, Univ. of Warsaw, Warsaw, Poland
| | | | - Michał Figura
- M. Figura (https://orcid.org/0000-0001-8367-5828), N. Niedźwiecka (https://orcid.org/0000-0002-9352-8546) and S. Nowak (https://orcid.org/0000-0002-7771-8032), Association for Nature ‘Wolf’, Twardorzeczka, Lipowa, Poland
| | - Arjen de Groot
- A. de Groot (https://orcid.org/0000-0001-7308-9200) and H. Jansman, Wageningen Environmental Research, Wageningen Univ. and Research, Wageningen, Netherlands
| | - Andżelika Haidt
- A. Haidt (https://orcid.org/0000-0002-3570-8899), Dept of Forest Ecology, Forest Research Inst., Sekocin Stary, Raszyn, Poland
| | - Michael M. Hansen
- M. M. Hansen (https://orcid.org/0000-0001-5372-4828) and P. F. Thomsen (https://orcid.org/0000-0002-9867-4366), Dept of Biology, Aarhus Univ., Aarhus C, Denmark
| | - Hugh Jansman
- A. de Groot (https://orcid.org/0000-0001-7308-9200) and H. Jansman, Wageningen Environmental Research, Wageningen Univ. and Research, Wageningen, Netherlands
| | - Gesa Kluth
- G. Kluth and I. Reinhardt (https://orcid.org/0000-0003-4314-3362),LUPUS– German Inst. forWolfMonitoring andResearch, Spreewitz, Germany
| | - Iga Kwiatkowska
- I. Kwiatkowska (https://orcid.org/0000-0002-5618-6196) and R. W. Mysłajek (https://orcid.org/0000-0001-9619-2868), Dept of Ecology, Inst. of Functional Biology and Ecology, Faculty of Biology, Biological and Chemical Research Centre, Univ. of Warsaw,
| | | | - Johan R. Michaux
- J. Michaux (https://orcid.org/0000-0003-4644-9244), Conservation Genetics Laboratory, Univ. of Liège, Liège, Belgium
| | - Natalia Niedźwiecka
- M. Figura (https://orcid.org/0000-0001-8367-5828), N. Niedźwiecka (https://orcid.org/0000-0002-9352-8546) and S. Nowak (https://orcid.org/0000-0002-7771-8032), Association for Nature ‘Wolf’, Twardorzeczka, Lipowa, Poland
| | - Sabina Nowak
- M. Figura (https://orcid.org/0000-0001-8367-5828), N. Niedźwiecka (https://orcid.org/0000-0002-9352-8546) and S. Nowak (https://orcid.org/0000-0002-7771-8032), Association for Nature ‘Wolf’, Twardorzeczka, Lipowa, Poland
| | - Kent Olsen
- K. Olsen (https://orcid.org/0000-0002-5624-128X), Natural History Museum Aarhus, Aarhus C, Denmark
| | - Ilka Reinhardt
- G. Kluth and I. Reinhardt (https://orcid.org/0000-0003-4314-3362),LUPUS– German Inst. forWolfMonitoring andResearch, Spreewitz, Germany
| | | | - Laurent Schley
- L. Schley (https://orcid.org/0000-0001-7681-6143), Administration de la Nature et des Forêts, Diekirch, Luxembourg
| | - Steve Smith
- S. Smith (https://orcid.org/0000-0002-1318-0018), Konrad Lorenz Inst. of Ethology, Dept of Integrative Biology and Evolution, Univ. of Veterinary Medicine, Vienna, Austria
| | | | | | - Kinga M. Stępniak
- K. M. Stępniak (https://orcid.org/0000-0002-4506-2542), Inst. of Genetics and Biotechnology, Faculty of Biology, Univ. of Warsaw, Warszawa, Poland
| | - Peter Sunde
- P. Sunde (https://orcid.org/0000-0002-7485-037X), Dept of Bioscience, Aarhus Univ., Rønde, Denmark
| | - Philip F. Thomsen
- M. M. Hansen (https://orcid.org/0000-0001-5372-4828) and P. F. Thomsen (https://orcid.org/0000-0002-9867-4366), Dept of Biology, Aarhus Univ., Aarhus C, Denmark
| | - Tomasz Zwijacz-Kozica
- T. Zwijacz-Kozica(https://orcid.org/0000-0002-7488-975X), Tatra National Park, Zakopane, Poland
| | - Robert W. Mysłajek
- I. Kwiatkowska (https://orcid.org/0000-0002-5618-6196) and R. W. Mysłajek (https://orcid.org/0000-0001-9619-2868), Dept of Ecology, Inst. of Functional Biology and Ecology, Faculty of Biology, Biological and Chemical Research Centre, Univ. of Warsaw,
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14
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Abstract
Dogs and humans have coexisted together for thousands of years, but it was not until the Victorian Era that humans practiced selective breeding to produce the modern standards we see today. Strong artificial selection during the breed formation period has simplified the genetic architecture of complex traits and caused an enrichment of identity-by-descent (IBD) segments in the dog genome. This study demonstrates the value of IBD segments and utilizes them to infer the recent demography of canids, predict case-control status for complex traits, locate regions of the genome potentially linked to inbreeding depression, and to identify understudied breeds where there is potential to discover new disease-associated variants. Domestic dogs have experienced population bottlenecks, recent inbreeding, and strong artificial selection. These processes have simplified the genetic architecture of complex traits, allowed deleterious variation to persist, and increased both identity-by-descent (IBD) segments and runs of homozygosity (ROH). As such, dogs provide an excellent model for examining how these evolutionary processes influence disease. We assembled a dataset containing 4,414 breed dogs, 327 village dogs, and 380 wolves genotyped at 117,288 markers and data for clinical and morphological phenotypes. Breed dogs have an enrichment of IBD and ROH, relative to both village dogs and wolves, and we use these patterns to show that breed dogs have experienced differing severities of bottlenecks in their recent past. We then found that ROH burden is associated with phenotypes in breed dogs, such as lymphoma. We next test the prediction that breeds with greater ROH have more disease alleles reported in the Online Mendelian Inheritance in Animals (OMIA). Surprisingly, the number of causal variants identified correlates with the popularity of that breed rather than the ROH or IBD burden, suggesting an ascertainment bias in OMIA. Lastly, we use the distribution of ROH across the genome to identify genes with depletions of ROH as potential hotspots for inbreeding depression and find multiple exons where ROH are never observed. Our results suggest that inbreeding has played a large role in shaping genetic and phenotypic variation in dogs and that future work on understudied breeds may reveal new disease-causing variation.
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15
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Korablev MP, Korablev NP, Korablev PN. Genetic diversity and population structure of the grey wolf (Canis lupus Linnaeus, 1758) and evidence of wolf × dog hybridisation in the centre of European Russia. Mamm Biol 2020. [DOI: 10.1007/s42991-020-00074-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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16
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Shakarashvili M, Kopaliani N, Gurielidze Z, Dekanoidze D, Ninua L, Tarkhnishvili D. Population genetic structure and dispersal patterns of grey wolfs (
Canis lupus
) and golden jackals (
Canis aureus
) in Georgia, the Caucasus. J Zool (1987) 2020. [DOI: 10.1111/jzo.12831] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - N. Kopaliani
- Institute of Ecology Ilia State University Tbilisi Georgia
| | - Z. Gurielidze
- Institute of Ecology Ilia State University Tbilisi Georgia
- Tbilisi Zoo Tbilisi Georgia
| | - D. Dekanoidze
- Institute of Ecology Ilia State University Tbilisi Georgia
| | - L. Ninua
- Institute of Ecology Ilia State University Tbilisi Georgia
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17
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Silva P, Galaverni M, Ortega-Del Vecchyo D, Fan Z, Caniglia R, Fabbri E, Randi E, Wayne R, Godinho R. Genomic evidence for the Old divergence of Southern European wolf populations. Proc Biol Sci 2020; 287:20201206. [PMID: 32693716 PMCID: PMC7423677 DOI: 10.1098/rspb.2020.1206] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The grey wolf (Canis lupus) is one of the most widely distributed mammals in which a variety of distinct populations have been described. However, given their currently fragmented distribution and recent history of human-induced population decline, little is known about the events that led to their differentiation. Based on the analysis of whole canid genomes, we examined the divergence times between Southern European wolf populations and their ancient demographic history. We found that all present-day Eurasian wolves share a common ancestor ca 36 000 years ago, supporting the hypothesis that all extant wolves derive from a single population that subsequently expanded after the Last Glacial Maximum. We also estimated that the currently isolated European populations of the Iberian Peninsula, Italy and the Dinarics-Balkans diverged very closely in time, ca 10 500 years ago, and maintained negligible gene flow ever since. This indicates that the current genetic and morphological distinctiveness of Iberian and Italian wolves can be attributed to their isolation dating back to the end of the Pleistocene, predating the recent human-induced extinction of wolves in Central Europe by several millennia.
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Affiliation(s)
- Pedro Silva
- CIBIO/InBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Marco Galaverni
- Conservation Unit, WWF Italia, Via Po 25/c - 00198 Roma, Italy
| | - Diego Ortega-Del Vecchyo
- International Laboratory for Human Genome Research, National Autonomous University of Mexico, Santiago de Querétaro, Querétaro 76230, Mexico
| | - Zhenxin Fan
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, People's Republic of China
| | - Romolo Caniglia
- Unit for Conservation Genetics (BIO-CGE), Department for the Monitoring and Protection of the Environment and for Biodiversity Conservation, Italian Institute for Environmental Protection and Research (ISPRA), Via Cà Fornacetta 9, 40064 Ozzano dell'Emilia (Bo), Italy
| | - Elena Fabbri
- Unit for Conservation Genetics (BIO-CGE), Department for the Monitoring and Protection of the Environment and for Biodiversity Conservation, Italian Institute for Environmental Protection and Research (ISPRA), Via Cà Fornacetta 9, 40064 Ozzano dell'Emilia (Bo), Italy
| | - Ettore Randi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Selmi 3, Bologna 40126, Italy.,Department of Chemistry and Bioscience, Faculty of Engineering and Science, University of Aalborg, Aalborg, Denmark
| | - Robert Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Raquel Godinho
- CIBIO/InBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal.,Department of Zoology, Faculty of Sciences, University of Johannesburg, Auckland Park 2006, South Africa
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18
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Gula R, Bojarska K, Theuerkauf J, Król W, Okarma H. Re-evaluation of the wolf population management units in central Europe. WILDLIFE BIOLOGY 2020. [DOI: 10.2981/wlb.00505] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Roman Gula
- R. Gula (https://orcid.org/000-0002-0619-5123) and J. Theuerkauf (https://orcid.org/0000-0002-7273-3073), Museum and Inst. of Zoology, Polish Academy of Sciences, Warszawa, Poland
| | | | - Jörn Theuerkauf
- R. Gula (https://orcid.org/000-0002-0619-5123) and J. Theuerkauf (https://orcid.org/0000-0002-7273-3073), Museum and Inst. of Zoology, Polish Academy of Sciences, Warszawa, Poland
| | - Wiesław Król
- W. Król and H. Okarma, Inst. of Nature Conservation, Polish Academy of Sciences, Mickiewicza 33, PL-31-120 Kraków, Poland
| | - Henryk Okarma
- W. Król and H. Okarma, Inst. of Nature Conservation, Polish Academy of Sciences, Mickiewicza 33, PL-31-120 Kraków, Poland
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19
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Dondina O, Orioli V, Torretta E, Merli F, Bani L, Meriggi A. Combining ensemble models and connectivity analyses to predict wolf expected dispersal routes through a lowland corridor. PLoS One 2020; 15:e0229261. [PMID: 32092115 PMCID: PMC7039448 DOI: 10.1371/journal.pone.0229261] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 02/02/2020] [Indexed: 01/07/2023] Open
Abstract
The Italian wolf (Canis lupus italicus) population has remained isolated South of the Alps for the last few thousand years. After a strong decline, the species has recolonized the Apennines and the Western Alps, while it is currently struggling to colonize the Eastern Alps. Recently, the species was detected in a lowland park connecting the Northern Apennines to the Central Alps. If the park was able to sustain a net wolf dispersal flow, this could significantly boost the connection with the Eastern Alps and the Dinaric-Balkan population. We investigated the suitability of the park as a functional ecological corridor for the wolf through the unhospitable lowland of Northern Italy. We collected wolf occurrence data in two study areas. We modeled species distribution running a separate ensemble model for each study area and then merging the output of the models to obtain an integrated suitability map. We used this map to identify corridors for the wolf adopting a factorial least-cost path and a cumulative resistant kernel approach. The connectivity models showed that only two corridors exist in the lowland areas between the Northern Apennines and the Central Alps. The Western corridor is a blind route, while the eastern corridor passes through the park and has a continuous course. However, the models also revealed a scarce resilience of corridor connectivity in the passageways between the park and the Apennines and the Prealps, which suggests that urgent management actions are necessary to ensure the future functionality of this important corridor.
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Affiliation(s)
- Olivia Dondina
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milano, Italy
- * E-mail:
| | - Valerio Orioli
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milano, Italy
| | - Elisa Torretta
- Department of Earth and Environmental Sciences, University of Pavia, Pavia, Italy
| | - Federico Merli
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milano, Italy
| | - Luciano Bani
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milano, Italy
| | - Alberto Meriggi
- Department of Earth and Environmental Sciences, University of Pavia, Pavia, Italy
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20
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Ericson HS, Fedorca A, Toderas I, Hegyeli Z, Plis K, Dykyy I, Jędrzejewska B, Ionescu G, Fedorca M, Iacolina L, Stronen AV. Genome-wide profiles indicate wolf population connectivity within the eastern Carpathian Mountains. Genetica 2019; 148:33-39. [PMID: 31873826 DOI: 10.1007/s10709-019-00083-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 12/17/2019] [Indexed: 11/26/2022]
Abstract
The Carpathian Mountains provide critical wildlife habitat in central Europe, and previous genome-wide studies have found western Carpathian Mountain wolves (Canis lupus) to be a separate population. Whereas differentiation to the north may be explained by a lowland-mountain transition and habitat fragmentation, the eastern Carpathian Mountains extending through Romania appear to offer continuous wildlife habitat southward. Our objective was to assess gene flow patterns and population connectivity among wolves in Romania, western Ukraine, and the Republic of Moldova. We sought to determine if the Carpathian Mountain region is best described by a north-south gradient in genetic profiles, or whether Romanian wolves show population structure with northern individuals clustering with western Ukraine. We genotyped 48 individuals with 170 000 single nucleotide polymorphism markers, and successful profiles from Romania (n = 27) and Moldova (n = 2) were merged with existing data from western Ukraine (n = 10). Expected heterozygosity was 0.234 (SE 0.001) for Romania and 0.229 (SE 0.001) for western Ukraine, whereas observed heterozygosity values were 0.230 (SE 0.001) versus 0.231 (SE 0.001). Population structure analyses with a maximum likelihood method supported K = 1 population, followed by K = 2 where Romania formed one cluster, and western Ukraine and Moldova formed another. Principal component analysis results were broadly consistent with K = 2. Pairwise FST between western Ukraine and Romania was 0.042 (p = 0.001). Our findings indicated weak population differentiation, and future research may clarify whether the spatial distribution of genetic diversity in the region is associated with environmental and ecological factors such as terrain ruggedness and the distribution of prey species.
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Affiliation(s)
- H S Ericson
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - A Fedorca
- National Institute for Research and Development in Forestry "Marin Dracea", Brasov, Romania
- Transilvania University of Brasov, Brasov, Romania
| | - I Toderas
- Institute of Zoology, Moldova Academy of Sciences, Chisinau, Republic of Moldova
| | - Z Hegyeli
- "Milvus Group" Bird and Nature Protection Association, Târgu Mureș, Romania
| | - K Plis
- Mammal Research Institute Polish Academy of Sciences, Białowieża, Poland
| | - I Dykyy
- Department of Zoology, Biological Faculty, Ivan Franko National University of Lviv, Lviv, Ukraine
| | - B Jędrzejewska
- Mammal Research Institute Polish Academy of Sciences, Białowieża, Poland
| | - G Ionescu
- National Institute for Research and Development in Forestry "Marin Dracea", Brasov, Romania
- Transilvania University of Brasov, Brasov, Romania
| | - M Fedorca
- National Institute for Research and Development in Forestry "Marin Dracea", Brasov, Romania
- Transilvania University of Brasov, Brasov, Romania
| | - L Iacolina
- Department of Fisheries, Apiculture, Wildlife Management and Special Zoology, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000, Zagreb, Croatia
| | - A V Stronen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
- Department of Biotechnology and Life Sciences, Insubria University, Varese, Italy.
- Biology Department, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000, Ljubljana, Slovenia.
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21
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Szewczyk M, Nowak S, Niedźwiecka N, Hulva P, Špinkytė-Bačkaitienė R, Demjanovičová K, Bolfíková BČ, Antal V, Fenchuk V, Figura M, Tomczak P, Stachyra P, Stępniak KM, Zwijacz-Kozica T, Mysłajek RW. Dynamic range expansion leads to establishment of a new, genetically distinct wolf population in Central Europe. Sci Rep 2019; 9:19003. [PMID: 31831858 PMCID: PMC6908625 DOI: 10.1038/s41598-019-55273-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 11/06/2019] [Indexed: 11/12/2022] Open
Abstract
Local extinction and recolonization events can shape genetic structure of subdivided animal populations. The gray wolf (Canis lupus) was extirpated from most of Europe, but recently recolonized big part of its historical range. An exceptionally dynamic expansion of wolf population is observed in the western part of the Great European Plain. Nonetheless, genetic consequences of this process have not yet been fully understood. We aimed to assess genetic diversity of this recently established wolf population in Western Poland (WPL), determine its origin and provide novel data regarding the population genetic structure of the grey wolf in Central Europe. We utilized both spatially explicit and non-explicit Bayesian clustering approaches, as well as a model-independent, multivariate method DAPC, to infer genetic structure in large dataset (881 identified individuals) of wolf microsatellite genotypes. To put the patterns observed in studied population into a broader biogeographic context we also analyzed a mtDNA control region fragment widely used in previous studies. In comparison to a source population, we found slightly reduced allelic richness and heterozygosity in the newly recolonized areas west of the Vistula river. We discovered relatively strong west-east structuring in lowland wolves, probably reflecting founder-flush and allele surfing during range expansion, resulting in clear distinction of WPL, eastern lowland and Carpathian genetic groups. Interestingly, wolves from recently recolonized mountainous areas (Sudetes Mts, SW Poland) clustered together with lowland, but not Carpathian wolf populations. We also identified an area in Central Poland that seems to be a melting pot of western, lowland eastern and Carpathian wolves. We conclude that the process of dynamic recolonization of Central European lowlands lead to the formation of a new, genetically distinct wolf population. Together with the settlement and establishment of packs in mountains by lowland wolves and vice versa, it suggests that demographic dynamics and possibly anthropogenic barriers rather than ecological factors (e.g. natal habitat-biased dispersal patterns) shape the current wolf genetic structure in Central Europe.
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Affiliation(s)
- Maciej Szewczyk
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawińskiego 5a, 02-106, Warsaw, Poland.,Association for Nature "Wolf", Twardorzeczka, Cynkowa 4, 34-324, Lipowa, Poland.,Department of Vertebrate Ecology and Zoology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308, Gdańsk, Poland
| | - Sabina Nowak
- Association for Nature "Wolf", Twardorzeczka, Cynkowa 4, 34-324, Lipowa, Poland
| | - Natalia Niedźwiecka
- Association for Nature "Wolf", Twardorzeczka, Cynkowa 4, 34-324, Lipowa, Poland
| | - Pavel Hulva
- Faculty of Science, Charles University in Prague, Viničná 7, 128 43, Prague, Czech Republic.,Faculty of Science, University of Ostrava, Chittussiho 10, 170 00, Ostrava, Czech Republic
| | | | - Klára Demjanovičová
- Faculty of Science, University of Ostrava, Chittussiho 10, 170 00, Ostrava, Czech Republic
| | - Barbora Černá Bolfíková
- Department of Animal Science and Food Processing, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, Prague 6, 165 00, Czech Republic
| | - Vladimír Antal
- State Nature Conservancy of Slovak Republic, Tajovského 28B, 974 01, Banská Bystrica, Slovakia
| | - Viktar Fenchuk
- APB-BirdLife Belarus, Engelsa 34A - 1, 220030, Minsk, Belarus
| | - Michał Figura
- Association for Nature "Wolf", Twardorzeczka, Cynkowa 4, 34-324, Lipowa, Poland
| | - Patrycja Tomczak
- Association for Nature "Wolf", Twardorzeczka, Cynkowa 4, 34-324, Lipowa, Poland.,Institute of Romance Studies, Faculty of Modern Languages and Literature, Adam Mickiewicz University in Poznań, Al. Niepodległości 4, 61-874, Poznań, Poland
| | | | - Kinga M Stępniak
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawińskiego 5a, 02-106, Warsaw, Poland.,Association for Nature "Wolf", Twardorzeczka, Cynkowa 4, 34-324, Lipowa, Poland
| | | | - Robert W Mysłajek
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawińskiego 5a, 02-106, Warsaw, Poland.
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22
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Fitak RR, Rinkevich SE, Culver M. Genome-Wide Analysis of SNPs Is Consistent with No Domestic Dog Ancestry in the Endangered Mexican Wolf (Canis lupus baileyi). J Hered 2019; 109:372-383. [PMID: 29757430 DOI: 10.1093/jhered/esy009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 02/28/2018] [Indexed: 11/13/2022] Open
Abstract
The Mexican gray wolf (Canis lupus baileyi) was historically distributed throughout the southwestern United States and northern Mexico. Extensive predator removal campaigns during the early 20th century, however, resulted in its eventual extirpation by the mid 1980s. At this time, the Mexican wolf existed only in 3 separate captive lineages (McBride, Ghost Ranch, and Aragón) descended from 3, 2, and 2 founders, respectively. These lineages were merged in 1995 to increase the available genetic variation, and Mexican wolves were reintroduced into Arizona and New Mexico in 1998. Despite the ongoing management of the Mexican wolf population, it has been suggested that a proportion of the Mexican wolf ancestry may be recently derived from hybridization with domestic dogs. In this study, we genotyped 87 Mexican wolves, including individuals from all 3 captive lineages and cross-lineage wolves, for more than 172000 single nucleotide polymorphisms. We identified levels of genetic variation consistent with the pedigree record and effects of genetic rescue. To identify the potential to detect hybridization with domestic dogs, we compared our Mexican wolf genotypes with those from studies of domestic dogs and other gray wolves. The proportion of Mexican wolf ancestry assigned to domestic dogs was only between 0.06% (SD 0.23%) and 7.8% (SD 1.0%) for global and local ancestry estimates, respectively; and was consistent with simulated levels of incomplete lineage sorting. Overall, our results suggested that Mexican wolves lack biologically significant ancestry with dogs and have useful implications for the conservation and management of this endangered wolf subspecies.
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Affiliation(s)
| | | | - Melanie Culver
- US Geological Survey Arizona Cooperative Fish and Wildlife Research Unit, School of Natural Resources and the Environment, University of Arizona, Tucson, AZ
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23
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McLennan EA, Wright BR, Belov K, Hogg CJ, Grueber CE. Too much of a good thing? Finding the most informative genetic data set to answer conservation questions. Mol Ecol Resour 2019; 19:659-671. [DOI: 10.1111/1755-0998.12997] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 01/10/2019] [Accepted: 01/14/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Elspeth A. McLennan
- School of Life and Environmental Sciences University of Sydney Sydney New South Wales Australia
| | - Belinda R. Wright
- School of Life and Environmental Sciences University of Sydney Sydney New South Wales Australia
| | - Katherine Belov
- School of Life and Environmental Sciences University of Sydney Sydney New South Wales Australia
| | - Carolyn J. Hogg
- School of Life and Environmental Sciences University of Sydney Sydney New South Wales Australia
| | - Catherine E. Grueber
- School of Life and Environmental Sciences University of Sydney Sydney New South Wales Australia
- San Diego Zoo Global San Diego California
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24
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Ekblom R, Brechlin B, Persson J, Smeds L, Johansson M, Magnusson J, Flagstad Ø, Ellegren H. Genome sequencing and conservation genomics in the Scandinavian wolverine population. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2018; 32:1301-1312. [PMID: 29935028 DOI: 10.1111/cobi.13157] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 06/01/2018] [Accepted: 06/06/2018] [Indexed: 06/08/2023]
Abstract
Genetic approaches have proved valuable to the study and conservation of endangered populations, especially for monitoring programs, and there is potential for further developments in this direction by extending analyses to the genomic level. We assembled the genome of the wolverine (Gulo gulo), a mustelid that in Scandinavia has recently recovered from a significant population decline, and obtained a 2.42 Gb draft sequence representing >85% of the genome and including >21,000 protein-coding genes. We then performed whole-genome resequencing of 10 Scandinavian wolverines for population genomic and demographic analyses. Genetic diversity was among the lowest detected in a red-listed population (mean genome-wide nucleotide diversity of 0.05%). Results of the demographic analyses indicated a long-term decline of the effective population size (Ne ) from 10,000 well before the last glaciation to <500 after this period. Current Ne appeared even lower. The genome-wide FIS level was 0.089 (possibly signaling inbreeding), but this effect was not observed when analyzing a set of highly variable SNP markers, illustrating that such markers can give a biased picture of the overall character of genetic diversity. We found significant population structure, which has implications for population connectivity and conservation. We used an integrated microfluidic circuit chip technology to develop an SNP-array consisting of 96 highly informative markers that, together with a multiplex pre-amplification step, was successfully applied to low-quality DNA from scat samples. Our findings will inform management, conservation, and genetic monitoring of wolverines and serve as a genomic roadmap that can be applied to other endangered species. The approach used here can be generally utilized in other systems, but we acknowledge the trade-off between investing in genomic resources and direct conservation actions.
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Affiliation(s)
- Robert Ekblom
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Birte Brechlin
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Jens Persson
- Grimsö Wildlife Research Station, Department of Ecology, Swedish University of Agricultural Sciences, Riddarhyttan, Sweden
| | - Linnéa Smeds
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Malin Johansson
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Jessica Magnusson
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | | | - Hans Ellegren
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
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25
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Cryptic population structure reveals low dispersal in Iberian wolves. Sci Rep 2018; 8:14108. [PMID: 30237419 PMCID: PMC6147861 DOI: 10.1038/s41598-018-32369-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 09/04/2018] [Indexed: 01/07/2023] Open
Abstract
Highly mobile mammalian carnivores are expected to have the capability to maintain high levels of gene flow across large geographic scales. Nonetheless, surprising levels of genetic structure have been found in many such populations. We combined genetic and spatial behavioural information from wolves (Canis lupus) in the Iberian Peninsula (Western Europe) during the last two decades to present a particular case of low dispersal levels in a large carnivore population persisting in human-dominated landscapes. We found an exceptionally reticulated pattern of cryptic population structure emerging at two hierarchical levels, in which four or eleven meaningful genetic clusters can be recognized, respectively. These clusters were characterized by moderate-high levels of differentiation (average pairwise FST = 0.09–0.19), low levels of admixture and varying degrees of genetic diversity. The number of dispersers identified among the 11 clusters was very low (<4% out of 218 wolves). Spatial information of tracked wolves further confirmed the geographical genetic patterns (only 2 out of 85 collared wolves overlapped with more than one genetic cluster). The high levels of genetic structure in this population may be determined by the recent demographic history of this population, among other factors. The identification of meaningful genetic clusters has implications for the delineation of conservation units and, consequently, on the conservation and management actions for Iberian wolves.
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26
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Czarnomska SD, Niedziałkowska M, Borowik T, Jędrzejewska B. Regional and local patterns of genetic variation and structure in yellow-necked mice - the roles of geographic distance, population abundance, and winter severity. Ecol Evol 2018; 8:8171-8186. [PMID: 30250693 PMCID: PMC6145024 DOI: 10.1002/ece3.4291] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 05/01/2018] [Accepted: 05/29/2018] [Indexed: 02/03/2023] Open
Abstract
The goal of this study, conducted in seven large woodlands and three areas with small woodlots in northeastern Poland in 2004-2008, was to infer genetic structure in yellow-necked mouse Apodemus flavicollis population and to evaluate the roles of environmental and population ecology variables in shaping the spatial pattern of genetic variation using 768 samples genotyped at 13 microsatellite loci. Genetic variation was very high in all studied regions. The primal genetic subdivision was observed between the northern and the southern parts of the study area, which harbored two major clusters and the intermediate area of highly admixed individuals. The probability of assignment of individual mice to the northern cluster increased significantly with lower temperatures of January and July and declined in regions with higher proportion of deciduous and mixed forests. Despite the detected structure, genetic differentiation among regions was very low. Fine-scale structure was shaped by the population density, whereas higher level structure was mainly shaped by geographic distance. Genetic similarity indices were highly influenced by mouse abundance (which positively correlated with the share of deciduous forests in the studied regions) and exhibited the greatest change between 0 and 1 km in the forests, 0 and 5 km in small woodlots. Isolation by distance pattern, calculated among regions, was highly significant but such relationship between genetic and geographic distance was much weaker, and held the linearity at very fine scale (~1.5 km), when analyses were conducted at individual level.
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Affiliation(s)
- Sylwia D. Czarnomska
- Mammal Research InstitutePolish Academy of SciencesBiałowieżaPoland
- Present address:
Institute of Biochemistry and Biophysics of the Polish Academy of Sciences (IBB PAS)WarszawaPoland
| | | | - Tomasz Borowik
- Mammal Research InstitutePolish Academy of SciencesBiałowieżaPoland
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Caniglia R, Fabbri E, Hulva P, Bolfíková BČ, Jindřichová M, Stronen AV, Dykyy I, Camatta A, Carnier P, Randi E, Galaverni M. Wolf outside, dog inside? The genomic make-up of the Czechoslovakian Wolfdog. BMC Genomics 2018; 19:533. [PMID: 30005602 PMCID: PMC6043967 DOI: 10.1186/s12864-018-4916-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 07/02/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Genomic methods can provide extraordinary tools to explore the genetic background of wild species and domestic breeds, optimize breeding practices, monitor and limit the spread of recessive diseases, and discourage illegal crossings. In this study we analysed a panel of 170k Single Nucleotide Polymorphisms with a combination of multivariate, Bayesian and outlier gene approaches to examine the genome-wide diversity and inbreeding levels in a recent wolf x dog cross-breed, the Czechoslovakian Wolfdog, which is becoming increasingly popular across Europe. RESULTS Pairwise FST values, multivariate and assignment procedures indicated that the Czechoslovakian Wolfdog was significantly differentiated from all the other analysed breeds and also well-distinguished from both parental populations (Carpathian wolves and German Shepherds). Coherently with the low number of founders involved in the breed selection, the individual inbreeding levels calculated from homozygosity regions were relatively high and comparable with those derived from the pedigree data. In contrast, the coefficient of relatedness between individuals estimated from the pedigrees often underestimated the identity-by-descent scores determined using genetic profiles. The timing of the admixture and the effective population size trends estimated from the LD patterns reflected the documented history of the breed. Ancestry reconstruction methods identified more than 300 genes with excess of wolf ancestry compared to random expectations, mainly related to key morphological features, and more than 2000 genes with excess of dog ancestry, playing important roles in lipid metabolism, in the regulation of circadian rhythms, in learning and memory processes, and in sociability, such as the COMT gene, which has been described as a candidate gene for the latter trait in dogs. CONCLUSIONS In this study we successfully applied genome-wide procedures to reconstruct the history of the Czechoslovakian Wolfdog, assess individual wolf ancestry proportions and, thanks to the availability of a well-annotated reference genome, identify possible candidate genes for wolf-like and dog-like phenotypic traits typical of this breed, including commonly inherited disorders. Moreover, through the identification of ancestry-informative markers, these genomic approaches could provide tools for forensic applications to unmask illegal crossings with wolves and uncontrolled trades of recent and undeclared wolfdog hybrids.
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Affiliation(s)
- Romolo Caniglia
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell’Emilia, Bologna, Italy
| | - Elena Fabbri
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell’Emilia, Bologna, Italy
| | - Pavel Hulva
- Department of Zoology, Charles University in Prague, Prague, Czech Republic
- Department of Biology and Ecology, Ostrava University, Ostrava, Czech Republic
| | - Barbora Černá Bolfíková
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Milena Jindřichová
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Astrid Vik Stronen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg Øst, Denmark
| | - Ihor Dykyy
- Department of Zoology, Ivan Franko National University of Lviv, Lviv, Ukraine
| | | | - Paolo Carnier
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy
| | - Ettore Randi
- Dipartimento BIGEA, Università di Bologna, Bologna, Italy
- Department 18/ Section of Environmental Engineering, Aalborg University, Aalborg Øst, Denmark
| | - Marco Galaverni
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell’Emilia, Bologna, Italy
- Area Conservazione, WWF Italia, Rome, Italy
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28
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The use of museum skins for genomic analyses of temporal genetic diversity in wild species. CONSERV GENET RESOUR 2018. [DOI: 10.1007/s12686-018-1036-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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29
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Kopatz A, Eiken HG, Schregel J, Aspi J, Kojola I, Hagen SB. Genetic substructure and admixture as important factors in linkage disequilibrium-based estimation of effective number of breeders in recovering wildlife populations. Ecol Evol 2017; 7:10721-10732. [PMID: 29299252 PMCID: PMC5743533 DOI: 10.1002/ece3.3577] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 10/03/2017] [Accepted: 10/04/2017] [Indexed: 01/18/2023] Open
Abstract
The number of effective breeders (Nb ) and effective population size (Ne ) are population parameters reflective of evolutionary potential, susceptibility to stochasticity, and viability. We have estimated these parameters using the linkage disequilibrium-based approach with LDNE through the latest phase of population recovery of the brown bears (Ursus arctos) in Finland (1993-2010; N = 621). This phase of the recovery was recently documented to be associated with major changes in genetic composition. In particular, differentiation between the northern and the southern genetic cluster declined rapidly within 1.5 generations. Based on this, we have studied effects of the changing genetic structure on Nb and Ne , by comparing estimates for whole Finland with the estimates for the two genetic clusters. We expected a potentially strong relationship between estimate sizes and genetic differentiation, which should disappear as the population recovers and clusters merge. Consistent with this, our estimates for whole Finland were lower than the sum of the estimates of the two genetic clusters and both approaches produced similar estimates in the end. Notably, we also found that admixed genotypes strongly increased the estimates. In all analyses, our estimates for Ne were larger than Nb and likely reflective for brown bears of the larger region of Finland and northwestern Russia. Conclusively, we find that neglecting genetic substructure may lead to a massive underestimation of Nb and Ne . Our results also suggest the need for further empirical analysis focusing on individuals with admixed genotypes and their potential high influence on Nb and Ne .
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Affiliation(s)
| | - Hans Geir Eiken
- NIBIO—Norwegian Institute of Bioeconomy ResearchSvanvikNorway
| | - Julia Schregel
- NIBIO—Norwegian Institute of Bioeconomy ResearchSvanvikNorway
| | - Jouni Aspi
- Department of BiologyUniversity of OuluOuluFinland
| | - Ilpo Kojola
- Natural Resources Institute Finland (Luke)RovaniemiFinland
| | - Snorre B. Hagen
- NIBIO—Norwegian Institute of Bioeconomy ResearchSvanvikNorway
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30
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Subotić S, Višnjić-Jeftić Ž, Penezić A, Ćirović D. Concentrations of Selected Elements in Liver Tissue of Grey Wolves (Canis lupus) from Serbia. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2017; 99:701-705. [PMID: 29119216 DOI: 10.1007/s00128-017-2209-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/02/2017] [Indexed: 06/07/2023]
Abstract
The grey wolf (Canis lupus) is a large carnivore species and a top predator in the ecosystems that it inhabits. Considering its role in food webs, wolves may be exposed to high concentrations of potentially harmful elements. Therefore liver samples from 28 legally hunted wolves were analyzed for concentrations of 16 elements using inductively coupled plasma optical emission spectrometry. The Mann-Whitney U test showed a significant difference between the genders only for Li, and there were no differences between individuals caught in different years. The majority of statistically significant correlations between element levels were positive, except for three cases. Compliance with several criteria for suitable bioindicator organisms imply that wolves may serve for monitoring environmental contamination.
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Affiliation(s)
- Srđan Subotić
- Faculty of Biology, University of Belgrade, Studentski trg 16, 11000, Belgrade, Serbia.
| | - Željka Višnjić-Jeftić
- Institute for Multidisciplinary Research, University of Belgrade, Kneza Višeslava 1, 11000, Belgrade, Serbia
| | - Aleksandra Penezić
- Faculty of Biology, University of Belgrade, Studentski trg 16, 11000, Belgrade, Serbia
| | - Duško Ćirović
- Faculty of Biology, University of Belgrade, Studentski trg 16, 11000, Belgrade, Serbia
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31
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Hulva P, Černá Bolfíková B, Woznicová V, Jindřichová M, Benešová M, Mysłajek RW, Nowak S, Szewczyk M, Niedźwiecka N, Figura M, Hájková A, Sándor AD, Zyka V, Romportl D, Kutal M, Finďo S, Antal V. Wolves at the crossroad: Fission-fusion range biogeography in the Western Carpathians and Central Europe. DIVERS DISTRIB 2017. [DOI: 10.1111/ddi.12676] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Pavel Hulva
- Department of Zoology, Faculty of Science; Charles University; Prague Czech Republic
- Department of Biology and Ecology, Faculty of Science; University of Ostrava; Ostrava Czech Republic
| | - Barbora Černá Bolfíková
- Department of Animal Science and Food Processing, Faculty of Tropical AgriSciences; Czech University of Life Sciences Prague; Prague Czech Republic
| | - Vendula Woznicová
- Department of Biology and Ecology, Faculty of Science; University of Ostrava; Ostrava Czech Republic
| | - Milena Jindřichová
- Department of Animal Science and Food Processing, Faculty of Tropical AgriSciences; Czech University of Life Sciences Prague; Prague Czech Republic
| | - Markéta Benešová
- Department of Zoology, Faculty of Science; Charles University; Prague Czech Republic
| | - Robert W. Mysłajek
- Institute of Genetics and Biotechnology, Faculty of Biology; University of Warsaw; Warszaw Poland
| | | | - Maciej Szewczyk
- Institute of Genetics and Biotechnology, Faculty of Biology; University of Warsaw; Warszaw Poland
| | - Natalia Niedźwiecka
- Institute of Genetics and Biotechnology, Faculty of Biology; University of Warsaw; Warszaw Poland
- Association for Nature “Wolf”; Lipowa Poland
| | | | - Andrea Hájková
- State Nature Conservancy of Slovak Republic; Banská Bystrica Slovakia
| | - Atilla D. Sándor
- Department of Parasitology and Parasitic Diseases, Faculty of Veterinary Medicine; University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca; Cluj-Napoca Romania
| | - Vladimír Zyka
- Department of Zoology, Faculty of Science; Charles University; Prague Czech Republic
| | - Dušan Romportl
- Department of Zoology, Faculty of Science; Charles University; Prague Czech Republic
| | - Miroslav Kutal
- Friends of the Earth Czech Republic; Olomouc Branch; Olomouc Czech Republic
- Institute of Forest Ecology, Faculty of Forestry and Wood Technology; Mendel University in Brno; Brno Czech Republic
| | - Slavomír Finďo
- Forest Protection and Wildlife Management; National Forest Centre; Zvolen Slovakia
| | - Vladimír Antal
- State Nature Conservancy of Slovak Republic; Banská Bystrica Slovakia
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32
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Montana L, Caniglia R, Galaverni M, Fabbri E, Ahmed A, Bolfíková BČ, Czarnomska SD, Galov A, Godinho R, Hindrikson M, Hulva P, Jędrzejewska B, Jelenčič M, Kutal M, Saarma U, Skrbinšek T, Randi E. Combining phylogenetic and demographic inferences to assess the origin of the genetic diversity in an isolated wolf population. PLoS One 2017; 12:e0176560. [PMID: 28489863 PMCID: PMC5425034 DOI: 10.1371/journal.pone.0176560] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 04/12/2017] [Indexed: 11/18/2022] Open
Abstract
The survival of isolated small populations is threatened by both demographic and genetic factors. Large carnivores declined for centuries in most of Europe due to habitat changes, overhunting of their natural prey and direct persecution. However, the current rewilding trends are driving many carnivore populations to expand again, possibly reverting the erosion of their genetic diversity. In this study we reassessed the extent and origin of the genetic variation of the Italian wolf population, which is expanding after centuries of decline and isolation. We genotyped wolves from Italy and other nine populations at four mtDNA regions (control-region, ATP6, COIII and ND4) and 39 autosomal microsatellites. Results of phylogenetic analyses and assignment procedures confirmed in the Italian wolves a second private mtDNA haplotype, which belongs to a haplogroup distributed mostly in southern Europe. Coalescent analyses showed that the unique mtDNA haplotypes in the Italian wolves likely originated during the late Pleistocene. ABC simulations concordantly showed that the extant wolf populations in Italy and in south-western Europe started to be isolated and declined right after the last glacial maximum. Thus, the standing genetic variation in the Italian wolves principally results from the historical isolation south of the Alps.
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Affiliation(s)
- Luca Montana
- Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell’Emilia, Bologna, Italy
- * E-mail:
| | - Romolo Caniglia
- Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell’Emilia, Bologna, Italy
| | - Marco Galaverni
- Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell’Emilia, Bologna, Italy
| | - Elena Fabbri
- Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell’Emilia, Bologna, Italy
| | - Atidje Ahmed
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Barbora Černá Bolfíková
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | | | - Ana Galov
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Raquel Godinho
- CIBIO/InBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Maris Hindrikson
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Pavel Hulva
- Department of Zoology, Charles University in Prague, Prague, Czech Republic
- Department of Biology and Ecology, Ostrava University, Ostrava, Czech Republic
| | | | - Maja Jelenčič
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Miroslav Kutal
- Department of Forest Ecology, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno, Czech Republic
- Friends of the Earth Czech Republic, Olomouc Branch, Olomouc, Czech Republic
| | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Tomaž Skrbinšek
- Department of Forest Ecology, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno, Czech Republic
| | - Ettore Randi
- Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell’Emilia, Bologna, Italy
- Department 18/ Section of Environmental Engineering, Aalborg University, Aalborg, Denmark
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33
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Montana L, Caniglia R, Galaverni M, Fabbri E, Randi E. A new mitochondrial haplotype confirms the distinctiveness of the Italian wolf (Canis lupus) population. Mamm Biol 2017. [DOI: 10.1016/j.mambio.2017.01.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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34
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Ersmark E, Klütsch CFC, Chan YL, Sinding MHS, Fain SR, Illarionova NA, Oskarsson M, Uhlén M, Zhang YP, Dalén L, Savolainen P. From the Past to the Present: Wolf Phylogeography and Demographic History Based on the Mitochondrial Control Region. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2016.00134] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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35
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Hermosilla C, Kleinertz S, Silva LMR, Hirzmann J, Huber D, Kusak J, Taubert A. Protozoan and helminth parasite fauna of free-living Croatian wild wolves (Canis lupus) analyzed by scat collection. Vet Parasitol 2016; 233:14-19. [PMID: 28043382 DOI: 10.1016/j.vetpar.2016.11.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 11/08/2016] [Accepted: 11/10/2016] [Indexed: 10/20/2022]
Abstract
The European wolf (Canis lupus) is a large carnivore species present in limited areas of Europe with several small populations still being considered as endangered. Wolves can be infected by a wide range of protozoan and metazoan parasites with some of them affecting free-living wolf health condition. On this account, an epidemiological survey was conducted to analyze the actual parasite fauna in Croatian wild wolves. In total, 400 individual faecal samples were collected during field studies on wolf ecology in the years 2002-2011. Parasite stages were identified by the sodium acetate acetic acid formalin (SAF)-technique, carbolfuchsin-stained faecal smears and Giardia/Cryptosporidium coproantigen-ELISAs. A subset of taeniid eggs-positive wolf samples was additionally analyzed by PCR and subsequent sequencing to identify eggs on Echinococcus granulosus/E. multilocularis species level. In total 18 taxa of parasites were here detected. Sarcocystis spp. (19.1%) occurred most frequently in faecal samples, being followed by Capillaria spp. (16%), ancylostomatids (13.1%), Crenosoma vulpis (4.6%), Angiostrongylus vasorum (3.1%), Toxocara canis (2.8%), Hammondia/Neospora spp. (2.6 %), Cystoisospora ohioensis (2.1%), Giardia spp. (2.1%), Cystoisospora canis (1.8%), Cryptosporidium spp. (1.8%), Trichuris vulpis (1.5%), Taenia spp. (1.5%), Diphyllobothrium latum (1.5%), Strongyloides spp. (0.5%), Opisthorchis felineus (0.5%), Toxascaris leonina (0.3%), Mesocestoides litteratus (0.3%) and Alaria alata (0.3%). Some of the here identified parasites represent relevant pathogens for wolves, circulating between these carnivorous definitive hosts and a variety of mammalian intermediate hosts, e. g. Taenia spp. and Sarcocystis spp., while others are considered exclusively pathogenic for canids (e.g. A. vasorum, C. vulpis, T. vulpis, Cystoisospora spp.). This study provides first records on the occurrence of the two relevant anthropozoonotic parasites, Giardia spp. and Cryptosporidium spp., in wild wolves from Croatia.
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Affiliation(s)
- Carlos Hermosilla
- Institute of Parasitology, Justus Liebig University Giessen, 35392 Giessen, Germany.
| | - Sonja Kleinertz
- Institute of Parasitology, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Liliana M R Silva
- Institute of Parasitology, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Jörg Hirzmann
- Institute of Parasitology, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Djuro Huber
- Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Josip Kusak
- Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Anja Taubert
- Institute of Parasitology, Justus Liebig University Giessen, 35392 Giessen, Germany
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36
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Hindrikson M, Remm J, Pilot M, Godinho R, Stronen AV, Baltrūnaité L, Czarnomska SD, Leonard JA, Randi E, Nowak C, Åkesson M, López-Bao JV, Álvares F, Llaneza L, Echegaray J, Vilà C, Ozolins J, Rungis D, Aspi J, Paule L, Skrbinšek T, Saarma U. Wolf population genetics in Europe: a systematic review, meta-analysis and suggestions for conservation and management. Biol Rev Camb Philos Soc 2016; 92:1601-1629. [PMID: 27682639 DOI: 10.1111/brv.12298] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 08/01/2016] [Accepted: 08/26/2016] [Indexed: 01/04/2023]
Abstract
The grey wolf (Canis lupus) is an iconic large carnivore that has increasingly been recognized as an apex predator with intrinsic value and a keystone species. However, wolves have also long represented a primary source of human-carnivore conflict, which has led to long-term persecution of wolves, resulting in a significant decrease in their numbers, genetic diversity and gene flow between populations. For more effective protection and management of wolf populations in Europe, robust scientific evidence is crucial. This review serves as an analytical summary of the main findings from wolf population genetic studies in Europe, covering major studies from the 'pre-genomic era' and the first insights of the 'genomics era'. We analyse, summarize and discuss findings derived from analyses of three compartments of the mammalian genome with different inheritance modes: maternal (mitochondrial DNA), paternal (Y chromosome) and biparental [autosomal microsatellites and single nucleotide polymorphisms (SNPs)]. To describe large-scale trends and patterns of genetic variation in European wolf populations, we conducted a meta-analysis based on the results of previous microsatellite studies and also included new data, covering all 19 European countries for which wolf genetic information is available: Norway, Sweden, Finland, Estonia, Latvia, Lithuania, Poland, Czech Republic, Slovakia, Germany, Belarus, Russia, Italy, Croatia, Bulgaria, Bosnia and Herzegovina, Greece, Spain and Portugal. We compared different indices of genetic diversity in wolf populations and found a significant spatial trend in heterozygosity across Europe from south-west (lowest genetic diversity) to north-east (highest). The range of spatial autocorrelation calculated on the basis of three characteristics of genetic diversity was 650-850 km, suggesting that the genetic diversity of a given wolf population can be influenced by populations up to 850 km away. As an important outcome of this synthesis, we discuss the most pressing issues threatening wolf populations in Europe, highlight important gaps in current knowledge, suggest solutions to overcome these limitations, and provide recommendations for science-based wolf conservation and management at regional and Europe-wide scales.
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Affiliation(s)
- Maris Hindrikson
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51014, Tartu, Estonia
| | - Jaanus Remm
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51014, Tartu, Estonia
| | - Malgorzata Pilot
- School of Life Sciences, University of Lincoln, Green Lane, LN6 7DL, Lincoln, UK
| | - Raquel Godinho
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Astrid Vik Stronen
- Department of Chemistry and Bioscience, Section of Biology and Environmental Science, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg Øst, Denmark
| | - Laima Baltrūnaité
- Laboratory of Mammalian Biology, Nature Research Centre, Akademijos 2, 08412, Vilnius, Lithuania
| | - Sylwia D Czarnomska
- Mammal Research Institute Polish Academy of Sciences, Waszkiewicza 1, 17-230, Białowieża, Poland
| | - Jennifer A Leonard
- Department of Integrative Ecology, Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Avd. Americo Vespucio s/n, 41092, Seville, Spain
| | - Ettore Randi
- Department of Chemistry and Bioscience, Section of Biology and Environmental Science, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg Øst, Denmark
- Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), 40064, Ozzano dell'Emilia, Bologna, Italy
| | - Carsten Nowak
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Clamecystrasse 12, 63571, Gelnhausen, Germany
| | - Mikael Åkesson
- Department of Ecology, Grimsö Wildlife Research Station, Swedish University of Agricultural Sciences, SE-730 91, Riddarhyttan, Sweden
| | | | - Francisco Álvares
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - Luis Llaneza
- ARENA Asesores en Recursos Naturales S.L. c/Perpetuo Socorro, n° 12 Entlo 2B, 27003, Lugo, Spain
| | - Jorge Echegaray
- Department of Integrative Ecology, Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Avd. Americo Vespucio s/n, 41092, Seville, Spain
| | - Carles Vilà
- Department of Integrative Ecology, Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Avd. Americo Vespucio s/n, 41092, Seville, Spain
| | - Janis Ozolins
- Latvian State Forest Research Institute "Silava", Rigas iela 111, LV-2169, Salaspils, Latvia
| | - Dainis Rungis
- Latvian State Forest Research Institute "Silava", Rigas iela 111, LV-2169, Salaspils, Latvia
| | - Jouni Aspi
- Department of Genetics and Physiology, University of Oulu, 90014, Oulu, Finland
| | - Ladislav Paule
- Department of Phytology, Faculty of Forestry, Technical University, T.G. Masaryk str. 24, SK-96053, Zvolen, Slovakia
| | - Tomaž Skrbinšek
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Vecna pot 111, 1000, Ljubljana, Slovenia
| | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51014, Tartu, Estonia
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Karamanlidis AA, Czarnomska SD, Kopatz A, Georgiadis L, Jędrzejewska B. Wolf population genetics at the south-eastern edge of their European range. Mamm Biol 2016. [DOI: 10.1016/j.mambio.2016.06.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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38
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de Groot GA, Nowak C, Skrbinšek T, Andersen LW, Aspi J, Fumagalli L, Godinho R, Harms V, Jansman HA, Liberg O, Marucco F, Mysłajek RW, Nowak S, Pilot M, Randi E, Reinhardt I, Śmietana W, Szewczyk M, Taberlet P, Vilà C, Muñoz-Fuentes V. Decades of population genetic research reveal the need for harmonization of molecular markers: the grey wolf C
anis lupus
as a case study. Mamm Rev 2015. [DOI: 10.1111/mam.12052] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- G. Arjen de Groot
- Animal Ecology; Alterra, Wageningen UR; P.O. Box 47 6700 AA Wageningen The Netherlands
| | - Carsten Nowak
- Conservation Genetics Group; Senckenberg Research Institute and Natural History Museum Frankfurt; Clamecystrasse 12 63571 Gelnhausen Germany
| | - Tomaž Skrbinšek
- Department of Biology; Biotechnical Faculty; University of Ljubljana; Večna pot 111 Ljubljana 1000 Slovenia
| | | | - Jouni Aspi
- Department of Biology, Genetics and Physiology; University of Oulu; P.O. Box 3000 90014 Oulu Finland
| | - Luca Fumagalli
- Department of Ecology and Evolution; Laboratory for Conservation Biology; Biophore Building; University of Lausanne; 1015 Lausanne Switzerland
| | - Raquel Godinho
- Research Center in Biodiversity and Genetic Resources; CIBIO/InBio; Campus Agrário de Vairão 4485-661 Vairão Portugal
- Department of Biology; Faculty of Sciences; University of Porto; Rua do Campo Alegre s/n 4169-007 Porto Portugal
- Department of Zoology; Faculty of Sciences; University of Johannesburg; Auckland Park 2006 Johannesburg South Africa
| | - Verena Harms
- Conservation Genetics Group; Senckenberg Research Institute and Natural History Museum Frankfurt; Clamecystrasse 12 63571 Gelnhausen Germany
| | - Hugh A.H. Jansman
- Animal Ecology; Alterra, Wageningen UR; P.O. Box 47 6700 AA Wageningen The Netherlands
| | - Olof Liberg
- Swedish University of Agricultural Sciences (SLU); Grimsö Wildlife Research Station SE-730 91 Riddarhyttan Sweden
| | - Francesca Marucco
- Parco Naturale Alpi Marittime; Centro Gestione e Conservazione Grandi Carnivori; Piazza Regina Elena 30 12010 Valdieri Italy
| | - Robert W. Mysłajek
- Institute of Genetics and Biotechnology; Faculty of Biology; University of Warsaw; Pawińskiego 5a 02-106 Warszawa Poland
| | - Sabina Nowak
- Association for Nature ‘Wolf’; Twardorzeczka 229 34-324 Lipowa Poland
| | - Małgorzata Pilot
- School of Life Sciences; University of Lincoln; Green Lane Lincoln LN6 7DL UK
| | - Ettore Randi
- Laboratorio di Genetica; Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA); Via Cà Fornacetta 9 40064 Ozzano dell'Emilia (BO) Italy
- Aalborg University; Department 18/Section of Environmental Engineering; Sohngårdsholmsvej 57 9000 Aalborg Denmark
| | - Ilka Reinhardt
- LUPUS - German Institute for Wolf Monitoring and Research; Dorfstraße 20 02979 Spreewitz Germany
| | - Wojciech Śmietana
- Polish Academy of Sciences; Institute of Nature Conservation; Mickiewicza 33 31-120 Kraków Poland
| | - Maciej Szewczyk
- Institute of Genetics and Biotechnology; Faculty of Biology; University of Warsaw; Pawińskiego 5a 02-106 Warszawa Poland
| | - Pierre Taberlet
- Centre National de la Recherche Scientifique; Laboratoire d'Ecologie Alpine (LECA); F-38000 Grenoble France
- Université Grenoble Alpes; Laboratoire d'Ecologie Alpine (LECA); F-38000 Grenoble France
| | - Carles Vilà
- Doñana Biological Station (EBD-CSIC); Avenida Americo Vespucio s/n 41092 Sevilla Spain
| | - Violeta Muñoz-Fuentes
- Conservation Genetics Group; Senckenberg Research Institute and Natural History Museum Frankfurt; Clamecystrasse 12 63571 Gelnhausen Germany
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39
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Stronen AV, Jędrzejewska B, Pertoldi C, Demontis D, Randi E, Niedziałkowska M, Borowik T, Sidorovich VE, Kusak J, Kojola I, Karamanlidis AA, Ozolins J, Dumenko V, Czarnomska SD. Genome-wide analyses suggest parallel selection for universal traits may eclipse local environmental selection in a highly mobile carnivore. Ecol Evol 2015; 5:4410-25. [PMID: 26664688 PMCID: PMC4667828 DOI: 10.1002/ece3.1695] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 08/18/2015] [Indexed: 01/03/2023] Open
Abstract
Ecological and environmental heterogeneity can produce genetic differentiation in highly mobile species. Accordingly, local adaptation may be expected across comparatively short distances in the presence of marked environmental gradients. Within the European continent, wolves (Canis lupus) exhibit distinct north–south population differentiation. We investigated more than 67‐K single nucleotide polymorphism (SNP) loci for signatures of local adaptation in 59 unrelated wolves from four previously identified population clusters (northcentral Europe n = 32, Carpathian Mountains n = 7, Dinaric‐Balkan n = 9, Ukrainian Steppe n = 11). Our analyses combined identification of outlier loci with findings from genome‐wide association study of individual genomic profiles and 12 environmental variables. We identified 353 candidate SNP loci. We examined the SNP position and neighboring megabase (1 Mb, one million bases) regions in the dog (C. lupus familiaris) genome for genes potentially under selection, including homologue genes in other vertebrates. These regions included functional genes for, for example, temperature regulation that may indicate local adaptation and genes controlling for functions universally important for wolves, including olfaction, hearing, vision, and cognitive functions. We also observed strong outliers not associated with any of the investigated variables, which could suggest selective pressures associated with other unmeasured environmental variables and/or demographic factors. These patterns are further supported by the examination of spatial distributions of the SNPs associated with universally important traits, which typically show marked differences in allele frequencies among population clusters. Accordingly, parallel selection for features important to all wolves may eclipse local environmental selection and implies long‐term separation among population clusters.
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Affiliation(s)
- Astrid Vik Stronen
- Section of Biology and Environmental Science Department of Chemistry and Bioscience Aalborg University Fredrik Bajers Vej 7H DK-9220 Aalborg Øst Denmark ; Mammal Research Institute Polish Academy of Sciences ul. Waszkiewicza 1 PL 17-230 Bialowieza Poland
| | - Bogumiła Jędrzejewska
- Mammal Research Institute Polish Academy of Sciences ul. Waszkiewicza 1 PL 17-230 Bialowieza Poland
| | - Cino Pertoldi
- Section of Biology and Environmental Science Department of Chemistry and Bioscience Aalborg University Fredrik Bajers Vej 7H DK-9220 Aalborg Øst Denmark ; Aalborg Zoo Mølleparkvej 63 DK-9000 Aalborg Denmark
| | - Ditte Demontis
- Department of Human Genetics University of Aarhus Wilhelm Meyers Allé DK-8000 Aarhus Denmark
| | - Ettore Randi
- Section of Biology and Environmental Science Department of Chemistry and Bioscience Aalborg University Fredrik Bajers Vej 7H DK-9220 Aalborg Øst Denmark ; Laboratorio di Genetica ISPRA via Cà Fornacetta 9 I-40064 Ozzano Emilia (BO) Italy
| | - Magdalena Niedziałkowska
- Mammal Research Institute Polish Academy of Sciences ul. Waszkiewicza 1 PL 17-230 Bialowieza Poland
| | - Tomasz Borowik
- Mammal Research Institute Polish Academy of Sciences ul. Waszkiewicza 1 PL 17-230 Bialowieza Poland
| | - Vadim E Sidorovich
- Institute of Zoology Scientific and Practical Centre for Biological Resources National Academy of Science of Belarus Akademicheskaya Str 27 220072 Minsk Belarus
| | - Josip Kusak
- Department of Biology Faculty of Veterinary Medicine University of Zagreb Zagreb Croatia
| | - Ilpo Kojola
- Natural Resources Institute Finland Box 16 FI-96500 Rovaniemi Finland
| | - Alexandros A Karamanlidis
- ARCTUROS Civil Society for the Protection and Management of Wildlife and the Natural Environment GR-53075 Aetos Greece ; Department of Ecology and Natural Resources Management Norwegian University of Life Sciences NO-1432 Ås Norway
| | - Janis Ozolins
- Latvian State Forest Research Institute "Silava" Rīgas 111 LV-2169 Salaspils Latvia
| | - Vitalii Dumenko
- Biosphere Reserve Askania Nova Frunze Str. 13 Askania-Nova Chaplynka District Kherson Region 75230 Ukraine
| | - Sylwia D Czarnomska
- Mammal Research Institute Polish Academy of Sciences ul. Waszkiewicza 1 PL 17-230 Bialowieza Poland
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41
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Ratkiewicz M, Matosiuk M, Saveljev AP, Sidorovich V, Ozolins J, Männil P, Balciauskas L, Kojola I, Okarma H, Kowalczyk R, Schmidt K. Long-range gene flow and the effects of climatic and ecological factors on genetic structuring in a large, solitary carnivore: the Eurasian lynx. PLoS One 2014; 9:e115160. [PMID: 25551216 PMCID: PMC4281111 DOI: 10.1371/journal.pone.0115160] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 11/19/2014] [Indexed: 11/26/2022] Open
Abstract
Due to their high mobility, large terrestrial predators are potentially capable of maintaining high connectivity, and therefore low genetic differentiation among populations. However, previous molecular studies have provided contradictory findings in relation to this. To elucidate patterns of genetic structure in large carnivores, we studied the genetic variability of the Eurasian lynx, Lynx lynx throughout north-eastern Europe using microsatellite, mitochondrial DNA control region and Y chromosome-linked markers. Using SAMOVA we found analogous patterns of genetic structure based on both mtDNA and microsatellites, which coincided with a relatively little evidence for male-biased dispersal. No polymorphism for the cytochrome b and ATP6 mtDNA genes and Y chromosome-linked markers were found. Lynx inhabiting a large area encompassing Finland, the Baltic countries and western Russia formed a single genetic unit, while some marginal populations were clearly divergent from others. The existence of a migration corridor was suggested to correspond with distribution of continuous forest cover. The lowest variability (in both markers) was found in lynx from Norway and Białowieża Primeval Forest (BPF), which coincided with a recent demographic bottleneck (Norway) or high habitat fragmentation (BPF). The Carpathian population, being monomorphic for the control region, showed relatively high microsatellite diversity, suggesting the effect of a past bottleneck (e.g. during Last Glacial Maximum) on its present genetic composition. Genetic structuring for the mtDNA control region was best explained by latitude and snow cover depth. Microsatellite structuring correlated with the lynx's main prey, especially the proportion of red deer (Cervus elaphus) in its diet. Eurasian lynx are capable of maintaining panmictic populations across eastern Europe unless they are severely limited by habitat continuity or a reduction in numbers. Different correlations of mtDNA and microsatellite population divergence patterns with climatic and ecological factors may suggest separate selective pressures acting on males and females in this solitary carnivore.
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Affiliation(s)
| | - Maciej Matosiuk
- Institute of Biology, University of Białystok, Białystok, Poland
| | - Alexander P. Saveljev
- B. M. Zhitkov Russian Research Institute of Game Management and Fur Farming, Russian Academy of Sciences, Kirov, Russia
| | - Vadim Sidorovich
- Centre for Biological Resources (former Institute of Zoology) of National Academy of Sciences, Minsk, Belarus
| | - Janis Ozolins
- Latvian State Forest Research Institute “Silava”, Salaspils, Latvia
| | | | | | - Ilpo Kojola
- Finnish Game and Fisheries Research Institute, Oulu Game and Fisheries Research, University of Oulu, Finland
| | - Henryk Okarma
- Institute of Nature Conservation, Polish Academy of Sciences, Kraków, Poland
| | - Rafał Kowalczyk
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Krzysztof Schmidt
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
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42
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Djan M, Maletić V, Trbojević I, Popović D, Veličković N, Burazerović J, Ćirović D. Genetic diversity and structuring of the grey wolf population from the Central Balkans based on mitochondrial DNA variation. Mamm Biol 2014. [DOI: 10.1016/j.mambio.2014.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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43
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Genetic variability of the grey wolf Canis lupus in the Caucasus in comparison with Europe and the Middle East: distinct or intermediary population? PLoS One 2014; 9:e93828. [PMID: 24714198 PMCID: PMC3979716 DOI: 10.1371/journal.pone.0093828] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 03/07/2014] [Indexed: 01/17/2023] Open
Abstract
Despite continuous historical distribution of the grey wolf (Canis lupus) throughout Eurasia, the species displays considerable morphological differentiation that resulted in delimitation of a number of subspecies. However, these morphological discontinuities are not always consistent with patterns of genetic differentiation. Here we assess genetic distinctiveness of grey wolves from the Caucasus (a region at the border between Europe and West Asia) that have been classified as a distinct subspecies C. l. cubanensis. We analysed their genetic variability based on mtDNA control region, microsatellite loci and genome-wide SNP genotypes (obtained for a subset of the samples), and found similar or higher levels of genetic diversity at all these types of loci as compared with other Eurasian populations. Although we found no evidence for a recent genetic bottleneck, genome-wide linkage disequilibrium patterns suggest a long-term demographic decline in the Caucasian population--a trend consistent with other Eurasian populations. Caucasian wolves share mtDNA haplotypes with both Eastern European and West Asian wolves, suggesting past or ongoing gene flow. Microsatellite data also suggest gene flow between the Caucasus and Eastern Europe. We found evidence for moderate admixture between the Caucasian wolves and domestic dogs, at a level comparable with other Eurasian populations. Taken together, our results show that Caucasian wolves are not genetically isolated from other Eurasian populations, share with them the same demographic trends, and are affected by similar conservation problems.
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44
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Pilot M, Greco C, vonHoldt BM, Jędrzejewska B, Randi E, Jędrzejewski W, Sidorovich VE, Ostrander EA, Wayne RK. Genome-wide signatures of population bottlenecks and diversifying selection in European wolves. Heredity (Edinb) 2013; 112:428-42. [PMID: 24346500 DOI: 10.1038/hdy.2013.122] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 10/14/2013] [Accepted: 10/16/2013] [Indexed: 12/21/2022] Open
Abstract
Genomic resources developed for domesticated species provide powerful tools for studying the evolutionary history of their wild relatives. Here we use 61K single-nucleotide polymorphisms (SNPs) evenly spaced throughout the canine nuclear genome to analyse evolutionary relationships among the three largest European populations of grey wolves in comparison with other populations worldwide, and investigate genome-wide effects of demographic bottlenecks and signatures of selection. European wolves have a discontinuous range, with large and connected populations in Eastern Europe and relatively smaller, isolated populations in Italy and the Iberian Peninsula. Our results suggest a continuous decline in wolf numbers in Europe since the Late Pleistocene, and long-term isolation and bottlenecks in the Italian and Iberian populations following their divergence from the Eastern European population. The Italian and Iberian populations have low genetic variability and high linkage disequilibrium, but relatively few autozygous segments across the genome. This last characteristic clearly distinguishes them from populations that underwent recent drastic demographic declines or founder events, and implies long-term bottlenecks in these two populations. Although genetic drift due to spatial isolation and bottlenecks seems to be a major evolutionary force diversifying the European populations, we detected 35 loci that are putatively under diversifying selection. Two of these loci flank the canine platelet-derived growth factor gene, which affects bone growth and may influence differences in body size between wolf populations. This study demonstrates the power of population genomics for identifying genetic signals of demographic bottlenecks and detecting signatures of directional selection in bottlenecked populations, despite their low background variability.
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Affiliation(s)
- M Pilot
- 1] School of Life Sciences, University of Lincoln, Lincoln, UK [2] Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland
| | - C Greco
- Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Rome and Ozzano Emilia (BO), Italy
| | - B M vonHoldt
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - B Jędrzejewska
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - E Randi
- 1] Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Rome and Ozzano Emilia (BO), Italy [2] Aalborg University, Department 18, Section of Environmental Engineering, Aalborg, Denmark
| | - W Jędrzejewski
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - V E Sidorovich
- Institute of Zoology, National Academy of Sciences of Belarus, Minsk, Belarus
| | - E A Ostrander
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - R K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
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