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Moravčíková N, Kasarda R, Židek R, McEwan JC, Brauning R, Landete-Castillejos T, Chonco L, Ciberej J, Pokorádi J. Traces of Human-Mediated Selection in the Gene Pool of Red Deer Populations. Animals (Basel) 2023; 13:2525. [PMID: 37570333 PMCID: PMC10417186 DOI: 10.3390/ani13152525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/27/2023] [Accepted: 07/30/2023] [Indexed: 08/13/2023] Open
Abstract
In this study, we analysed the effect of human-mediated selection on the gene pool of wild and farmed red deer populations based on genotyping-by-sequencing data. The farmed red deer sample covered populations spread across seven countries and two continents (France, Germany, Hungary, Latvia, New Zealand, Poland, and Slovakia). The Slovak and Spain wild red deer populations (the latter one in a large game estate) were used as control outgroups. The gene flow intensity, relationship and admixture among populations were tested by the Bayesian approach and discriminant analysis of principal components (DAPC). The highest gene diversity (He = 0.19) and the lowest genomic inbreeding (FHOM = 0.04) found in Slovak wild population confirmed our hypothesis that artificial selection accompanied by bottlenecks has led to the increase in overall genomic homozygosity. The Bayesian approach and DAPC consistently identified three separate genetic groups. As expected, the farmed populations were clustered together, while the Slovak and Spanish populations formed two separate clusters. Identified traces of genetic admixture in the gene pool of farmed populations reflected a strong contemporary migration rate between them. This study suggests that even if the history of deer farming has been shorter than traditional livestock species, it may leave significant traces in the genome structure.
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Affiliation(s)
- Nina Moravčíková
- Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, 949 76 Nitra, Slovakia;
| | - Radovan Kasarda
- Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, 949 76 Nitra, Slovakia;
| | - Radoslav Židek
- Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, 949 76 Nitra, Slovakia;
| | - John Colin McEwan
- AgResearch, Invermay Agricultural Research Centre, Mosgiel 9024, New Zealand; (J.C.M.); (R.B.)
| | - Rudiger Brauning
- AgResearch, Invermay Agricultural Research Centre, Mosgiel 9024, New Zealand; (J.C.M.); (R.B.)
| | - Tomás Landete-Castillejos
- Instituto de Recursos Cinegéticos-Instituto de Desarrollo Regional, University of Castilla-La Mancha, 02071 Albacete, Spain; (T.L.-C.); (L.C.)
| | - Louis Chonco
- Instituto de Recursos Cinegéticos-Instituto de Desarrollo Regional, University of Castilla-La Mancha, 02071 Albacete, Spain; (T.L.-C.); (L.C.)
| | - Juraj Ciberej
- Department of Breeding and Diseases of Game, Fish and Bees, Ecology and Cynology, University of Veterinary Medicine and Pharmacy, 041 81 Košice, Slovakia
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Genetic Diversity of Wisent Bison bonasus Based on STR Loci Analyzed in a Large Set of Samples. DIVERSITY 2023. [DOI: 10.3390/d15030399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Wisent Bison bonasus is an example of a species saved from extinction and reintroduced into nature after a few decades of captive breeding. There were only twelve founders of the Lowland–Caucasian line (LC) and even fewer (seven out of twelve) of Lowland (LB) animals. The genetic diversity in studies based on pedigree or markers is very low. In this paper, we present a summary of the long-term genetic monitoring conducted for the worldwide population of European bison. We summarized the long-term genetic monitoring studies conducted on the worldwide population of wisents to date. We genotyped 2227 wisents from two genetic lines (LC and LB) and different populations at ten microsatellite loci. We found low polymorphism, with only 2.7 alleles per locus, and much lower values of observed heterozygosity (0.380 and 0.348 in the LC and LB lines, respectively) than expected heterozygosity. The difference between the lines is only noticeable in allele proportions, so the number of markers is not enough to distinguish the two genetic lines. We also present the genetic distance among four free-roaming populations that are geographically close to each other. We found that the genetic distance of one of them is larger than that of the others, which could be the effect of genetic drift.
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Milošević-Zlatanović S, Vukov T, Chovancová G, Anderwald P, Corlatti L, Tomašević Kolarov N. Cranial integration and modularity in chamois: The effects of subspecies and sex. J MAMM EVOL 2023. [DOI: 10.1007/s10914-022-09644-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
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Rezić A, Safner T, Iacolina L, Bužan E, Šprem N. Traces of past reintroduction in genetic diversity: The case of the Balkan chamois (Mammalia, Artiodactyla). Zookeys 2022; 1116:57-70. [PMID: 36760981 PMCID: PMC9848663 DOI: 10.3897/zookeys.1116.84577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/20/2022] [Indexed: 11/12/2022] Open
Abstract
The translocation of wild animal species became a common practice worldwide to re-establish local populations threatened with extinction. Archaeological data confirm that chamois once lived in the Biokovo Mountain but, prior to their reintroduction in the 1960s, there was no written evidence of their recent existence in the area. The population was reintroduced in the period 1964-1969, when 48 individuals of Balkan chamois from the neighbouring mountains in Bosnia and Herzegovina were released. The main objective of this study was to determine the accuracy of the existing historical data on the origin of the Balkan chamois population from the Biokovo Mountain and to assess the genetic diversity and population structure of the source and translocated populations 56 years after reintroduction. Sixteen microsatellite loci were used to analyse the genetic structure of three source chamois populations from Prenj, Čvrsnica and Čabulja Mountains and from Biokovo Mountain. Both STRUCTURE and GENELAND analyses showed a clear separation of the reintroduced population on Biokovo from Prenj's chamois and considerable genetic similarity between the Biokovo population and the Čvrsnica-Čabulja population. This suggests that the current genetic composition of the Biokovo population does not derive exclusively from Prenj, as suggested by the available literature and personal interviews, but also from Čvrsnica and Čabulja. GENELAND analysis recognised the Balkan chamois from Prenj as a separate cluster, distinct from the populations of Čvrsnica and Čabulja. Our results thus highlight the need to implement genetic monitoring of both reintroduced and source populations of endangered Balkan chamois to inform sustainable management and conservation strategies in order to maximise the chances of population persistence.
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Affiliation(s)
- Andrea Rezić
- University of Zagreb, Faculty of Agriculture, Department of Fisheries, Apiculture, Wildlife Management and Special Zoology, Svetošimunska c. 25, 10000, Zagreb, Croatia
| | - Toni Safner
- University of Zagreb, Faculty of Agriculture, Department of Fisheries, Apiculture, Wildlife Management and Special Zoology, Svetošimunska c. 25, 10000, Zagreb, Croatia,University of Zagreb, Faculty of Agriculture, Department of Plant Breeding, Genetics and Biometrics, Svetošimunska c. 25, 10000, Zagreb, Croatia
| | - Laura Iacolina
- University of Zagreb, Faculty of Agriculture, Department of Fisheries, Apiculture, Wildlife Management and Special Zoology, Svetošimunska c. 25, 10000, Zagreb, Croatia,Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska c. 25, 10000, Zagreb, Croatia,University of Primorska, Faculty of Mathematics, Natural Sciences and Information Technologies, Department of Biodiversity, Glagoljaška 8, 6000, Koper, Slovenia
| | - Elena Bužan
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska c. 25, 10000, Zagreb, Croatia,Aalborg University, Department of Chemistry and Bioscience, Section of Biology and Environmental Science, Fredrik Bajers Vej 7H, 9220 Aalborg East, Denmark
| | - Nikica Šprem
- University of Zagreb, Faculty of Agriculture, Department of Fisheries, Apiculture, Wildlife Management and Special Zoology, Svetošimunska c. 25, 10000, Zagreb, Croatia
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Phylogenetic Analysis of the Complete Mitochondrial Genomes in the Ten Rupicapra Subspecies and Implications for the Existence of Multiple Glacial Refugia in Europe. Animals (Basel) 2022; 12:ani12111430. [PMID: 35681894 PMCID: PMC9179332 DOI: 10.3390/ani12111430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 05/23/2022] [Accepted: 05/30/2022] [Indexed: 02/01/2023] Open
Abstract
Simple Summary The successive glaciations that took place during the Pleistocene shaped de distribution of temperate species in Europe, both plants and animals. Traditionally, it has been hypothesized that during the coldest periods, species took refuge in three areas of southern Europe (Iberian, Italian and Balkan peninsulas) and then recolonized the north when temperatures rose and conditions were more favorable. In the present work, the complete mitochondrial sequences of the ten described chamois populations have been analyzed to identify which areas of the continent have served as refuges for the species during the glaciations. The results of the present work are consistent with the existence of multiple glacial refugia across Europe, revealing a much more complex picture of the effect of glaciations on the genetics of temperate species than is commonly accepted, giving us a better understanding of how past events determine the present species. Abstract The current distribution of populations in Europe is marked by the effects of glaciations that occurred during the Pleistocene. Temperate species were isolated in glacial refugia that were the sources of postglacial recolonization. The traditional glacial refuge areas were the Iberian, the Italian and the Balkan peninsulas. Here we revisit the evolutionary history of chamois (Rupicapra genus) to evaluate other sites in continental Europe and Anatolia that have been suggested as potential refuges. We have obtained the complete mitochondrial sequence of seven chamois, including the subspecies parva, carpatica, caucasica, and asiatica whose mitochondrial genome had not been yet reported. These, together with the other fourteen sequences already in the GenBank, represent the different geographical populations of the Rupicapra genus. The phylogenetic analysis showed the three old clades, dating from the early Pleistocene, already reported: mtW in the Iberian Peninsula, mtC in the Appenines and the Massif of Chartreuse, and mtE comprising all the population from the Alps to the east. The genomes within each of the clades mtW and mtE, showed divergence times larger than 300 thousand years. From here, it can be argued that the present-day lineages across Europe are very old and their split dates back to the middle Pleistocene.
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Corlatti L, Iacolina L, Safner T, Apollonio M, Buzan E, Ferretti F, Hammer SE, Herrero J, Rossi L, Serrano E, Arnal MC, Brivio F, Chirichella R, Cotza A, Crestanello B, Espunyes J, Fernández de Luco D, Friedrich S, Gačić D, Grassi L, Grignolio S, Hauffe HC, Kavčić K, Kinser A, Lioce F, Malagnino A, Miller C, Peters W, Pokorny B, Reiner R, Rezić A, Stipoljev S, Tešija T, Yankov Y, Zwijacz‐Kozica T, Šprem N. Past, present and future of chamois science. WILDLIFE BIOLOGY 2022. [DOI: 10.1002/wlb3.01025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- L. Corlatti
- Chair of Wildlife Ecology and Management, Univ. of Freiburg Freiburg Germany
- Stelvio National Park Bormio Italy
| | - L. Iacolina
- Faculty of Mathematics, Natural Sciences and Information Technologies, Univ. of Primorska Koper Slovenia
- Aalborg Univ., Dept of Chemistry and Biosciences Aalborg Denmark
| | - T. Safner
- Faculty of Agriculture, Dept of Plant Breeding, Genetics and Biometrics, Univ. of Zagreb Zagreb Croatia
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP‐BioDiv) Zagreb Croatia
| | - M. Apollonio
- Dept of Veterinary Medicine, Univ. of Sassari Sassari Italy
| | - E. Buzan
- Faculty of Mathematics, Natural Sciences and Information Technologies, Univ. of Primorska Koper Slovenia
- Faculty of Environmental Protection Velenje Slovenia
| | - F. Ferretti
- Research Unit of Behavioural Ecology, Ethology and Wildlife Management, Dept of Life Sciences, Univ. of Siena Siena Italy
| | - S. E. Hammer
- Inst. of Immunology, Dept of Pathobiology, Univ. of Veterinary Medicine Vienna Austria
| | - J. Herrero
- Dept of Agrarian and Environmental Science, Univ. of Zaragoza Huesca Spain
| | - L. Rossi
- Dept of Veterinary Sciences, Univ. of Turin Grugliasco (TO) Italy
| | - E. Serrano
- Wildlife Ecology&Health Group (WE&H) and Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Dept de Medicina i Cirurgia Animals, Facultat de Veterinària, Univ. Autònoma de Barcelona Barcelona Spain
| | - M. C. Arnal
- Dept of Animal Pathology, Univ. of Zaragoza Zaragoza Spain
| | - F. Brivio
- Dept of Veterinary Medicine, Univ. of Sassari Sassari Italy
| | - R. Chirichella
- Dept of Veterinary Medicine, Univ. of Sassari Sassari Italy
| | - A. Cotza
- Research Unit of Behavioural Ecology, Ethology and Wildlife Management, Dept of Life Sciences, Univ. of Siena Siena Italy
| | - B. Crestanello
- Conservation Genomics Research Unit, Centre for Research and Innovation, Fondazione E. Mach S. Michele all'Adige (TN) Italy
| | - J. Espunyes
- Wildlife Conservation Medicine Research Group (WildCoM), Dept of Animal Medicine and Surgery, Univ. Autònoma de Barcelona Bellaterra Spain
| | | | - S. Friedrich
- Wildlife Research Unit (WFS), Agricultural Center Baden‐Württemberg (LAZBW) Aulendorf Germany
- Wildlife Sciences, Faculty of Forest Sciences and Forest Ecology, Univ. of Goettingen Göttingen Germany
| | - D. Gačić
- Dept of Forest Resources Use, Faculty of Forestry, Univ. of Belgrade Belgrade Serbia
| | - L. Grassi
- Dept of Animal Medicine, Production and Health (MAPS), Univ. of Padua Legnaro Italy
| | - S. Grignolio
- Dept of Life Sciences and Biotechnology, Univ. of Ferrara Ferrara Italy
| | - H. C. Hauffe
- Conservation Genomics Research Unit, Centre for Research and Innovation, Fondazione E. Mach S. Michele all'Adige (TN) Italy
| | - K. Kavčić
- Faculty of Agriculture, Dept of Fisheries, Apiculture, Wildlife Management and Special Zoology, Univ. of Zagreb Zagreb Croatia
| | - A. Kinser
- Deutsche Wildtier Stiftung Hamburg Germany
| | - F. Lioce
- Conservation Genomics Research Unit, Centre for Research and Innovation, Fondazione E. Mach S. Michele all'Adige (TN) Italy
- Dept of Life Sciences and Biotechnology, Univ. of Ferrara Ferrara Italy
| | - A. Malagnino
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA Grenoble France
- Dept of Biosciences, College of Science, Swansea Univ. Swansea UK
| | - C. Miller
- Deutsche Wildtier Stiftung Hamburg Germany
| | - W. Peters
- Dept of Biodiversity, Conservation and Wildlife Management, Bavarian State Inst. of Forestry Freising Germany
| | - B. Pokorny
- Faculty of Environmental Protection Velenje Slovenia
- Slovenian Forestry Inst. Ljubljana Slovenia
| | - R. Reiner
- Inst. of Wildlife Biology and Game Management, Univ. of Natural Resources and Life Sciences Vienna Austria
- Berchtesgaden National Park Berchtesgaden Germany
| | - A. Rezić
- Faculty of Agriculture, Dept of Fisheries, Apiculture, Wildlife Management and Special Zoology, Univ. of Zagreb Zagreb Croatia
| | - S. Stipoljev
- Faculty of Agriculture, Dept of Fisheries, Apiculture, Wildlife Management and Special Zoology, Univ. of Zagreb Zagreb Croatia
| | - T. Tešija
- Faculty of Agriculture, Dept of Plant Breeding, Genetics and Biometrics, Univ. of Zagreb Zagreb Croatia
| | - Y. Yankov
- Faculty of Agriculture, Dept of Biology and Aquaculture, Trakia Univ. Stara Zagora Bulgaria
| | | | - N. Šprem
- Faculty of Agriculture, Dept of Fisheries, Apiculture, Wildlife Management and Special Zoology, Univ. of Zagreb Zagreb Croatia
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The Balkan chamois, an archipelago or a peninsula? Insights from nuclear and mitochondrial DNA. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01434-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Microsatellite based assignment reveals history of extirpated mountain ungulate. Genetica 2020; 148:41-46. [PMID: 31983008 DOI: 10.1007/s10709-020-00084-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/23/2019] [Accepted: 01/17/2020] [Indexed: 01/24/2023]
Abstract
During the early 1900s, Northern chamois (Rupicapra rupicapra) populations in the northern Dinaric Mountains were extirpated. During the 1960s and 1970s there were several reintroductions of individuals from two Northern chamois subspecies (Alpine chamois, R. r. rupicapra and Balkan chamois, R. r. balcanica) from neighbouring areas in the attempt to re-establish the population. Accurate taxonomic classification, at subspecies level, of the autochthonous extirpated population was not known. To clarify which subspecies was present before reintroduction, we genotyped four male chamois skulls originating from Velebit Mountain, collected around 25 years before the population local extinction. DNA was successfully extracted from middle layer and outer sheath of horns. Assignment based on microsatellite loci, using both Bayesian clustering in STRUCTURE (with q values between 0.55 and 0.73) and DAPC (with individual membership probabilities of 0.99 and 1.00) indicated higher assessed likelihood for the Alpine subspecies.
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Identification of genetic families based on mitochondrial D-loop sequence in population of the Tatra chamois (Rupicapra rupicapra tatrica). Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-019-00313-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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10
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Papaioannou H, Fernández M, Pérez T, Domínguez A. Genetic variability and population structure of chamois in Greece (Rupicapra rupicapra balcanica). CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01177-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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11
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Zecchin B, De Nardi M, Nouvellet P, Vernesi C, Babbucci M, Crestanello B, Bagó Z, Bedeković T, Hostnik P, Milani A, Donnelly CA, Bargelloni L, Lorenzetto M, Citterio C, Obber F, De Benedictis P, Cattoli G. Genetic and spatial characterization of the red fox (Vulpes vulpes) population in the area stretching between the Eastern and Dinaric Alps and its relationship with rabies and canine distemper dynamics. PLoS One 2019; 14:e0213515. [PMID: 30861028 PMCID: PMC6413928 DOI: 10.1371/journal.pone.0213515] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 02/24/2019] [Indexed: 01/02/2023] Open
Abstract
Information on the population dynamics of a reservoir species have been increasingly adopted to understand and eventually predict the dispersal patterns of infectious diseases throughout an area. Although potentially relevant, to date there are no studies which have investigated the genetic structure of the red fox population in relation to infectious disease dynamics. Therefore, we genetically and spatially characterised the red fox population in the area stretching between the Eastern and Dinaric Alps, which has been affected by both distemper and rabies at different time intervals. Red foxes collected from north-eastern Italy, Austria, Slovenia and Croatia between 2006–2012, were studied using a set of 21 microsatellite markers. We confirmed a weak genetic differentiation within the fox population using Bayesian clustering analyses, and we were able to differentiate the fox population into geographically segregated groups. Our finding might be due to the presence of geographical barriers that have likely influenced the distribution of the fox population, limiting in turn gene flow and spread of infectious diseases. Focusing on the Italian red fox population, we observed interesting variations in the prevalence of both diseases among distinct fox clusters, with the previously identified Italy 1 and Italy 2 rabies as well as distemper viruses preferentially affecting different sub-groups identified in the study. Knowledge of the regional-scale population structure can improve understanding of the epidemiology and spread of diseases. Our study paves the way for an integrated approach for disease control coupling pathogen, host and environmental data to inform targeted control programs in the future.
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Affiliation(s)
- Bianca Zecchin
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
- * E-mail:
| | - Marco De Nardi
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Pierre Nouvellet
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Cristiano Vernesi
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro, Italy
| | - Barbara Crestanello
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Zoltán Bagó
- Austrian Agency for Health and Food Safety (AGES), Institute for Veterinary Disease Control, Mödling, Austria
| | | | - Peter Hostnik
- Virology Unit, Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Ljubljana, Slovenia
| | - Adelaide Milani
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Christl Ann Donnelly
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- National Institute for Health Research Health Protection Research Unit in Modelling Methodology, Imperial College London, London, United Kingdom
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro, Italy
| | - Monica Lorenzetto
- Department of Veterinary Epidemiology, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Carlo Citterio
- SCT2 Belluno, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Belluno, Italy
| | - Federica Obber
- SCT2 Belluno, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Belluno, Italy
| | - Paola De Benedictis
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Giovanni Cattoli
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
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Small-scale spatial genetic structure of Alpine chamois (Rupicapra rupicapra) in Northern Dinarides. EUR J WILDLIFE RES 2019. [DOI: 10.1007/s10344-019-1259-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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13
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Formenti N, Viganó R, Fraquelli C, Trogu T, Bonfanti M, Lanfranchi P, Palme R, Ferrari N. Increased hormonal stress response of Apennine chamois induced by interspecific interactions and anthropogenic disturbance. EUR J WILDLIFE RES 2018. [DOI: 10.1007/s10344-018-1228-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Kavčić K, Brivio F, Grignolio S, Ugarković D, Stankić I, Safner T, Apollonio M, Šprem N. Is chamois hybridization in the northern Dinaric Mountains an important factor for horn development? WILDLIFE BIOLOGY 2018. [DOI: 10.2981/wlb.00461] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Krešimir Kavčić
- K. Kavčić and N. Šprem, Dept of Fisheries, Beekeeping, Game Management and Special
| | - Francesca Brivio
- F. Brivio, S. Grignolio and M. Apollonio, Dept of Veterinary Medicine, Univ. of Sassari, Sassari, It
| | - Stefano Grignolio
- F. Brivio, S. Grignolio and M. Apollonio, Dept of Veterinary Medicine, Univ. of Sassari, Sassari, It
| | - Damir Ugarković
- D. Ugarković, Dept of Forest Ecology and Silviculture, Faculty of Forestry, Univ. of Zagreb, Zagreb,
| | - Igor Stankić
- I. Stankić, Energy and Environmental Protection Inst. (EKONERG), Zagreb, Croatia
| | - Toni Safner
- T. Safner, Dept of Plant Breeding, Genetics and Biometrics, Faculty of Agriculture, Univ. of Zagreb,
| | - Marco Apollonio
- F. Brivio, S. Grignolio and M. Apollonio, Dept of Veterinary Medicine, Univ. of Sassari, Sassari, It
| | - Nikica Šprem
- K. Kavčić and N. Šprem, Dept of Fisheries, Beekeeping, Game Management and Special
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Iacolina L, Corlatti L, Buzan E, Safner T, Šprem N. Hybridisation in European ungulates: an overview of the current status, causes, and consequences. Mamm Rev 2018. [DOI: 10.1111/mam.12140] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Laura Iacolina
- Department of Chemistry and Bioscience; Aalborg University; Frederik Bajers Vej 7H 9220 Aalborg Denmark
- Aalborg Zoo; Mølleparkvej 63 9000 Aalborg Denmark
| | - Luca Corlatti
- Wildlife Ecology and Management; University of Freiburg; Tennenbacher Straße 4 79106 Freiburg Germany
- Institute of Wildlife Biology and Game Management; University of Natural Resources and Life Sciences Vienna; Gregor-Mendel-Straße 33 1180 Vienna Austria
| | - Elena Buzan
- Department of Biodiversity; Faculty of Mathematics, Natural Sciences and Information Technologies; University of Primorska; Glagoljaška 8 6000 Koper Slovenia
| | - Toni Safner
- Faculty of Agriculture; Department of Plant Breeding, Genetics and Biometrics; University of Zagreb; Svetošimunska cesta 25 10000 Zagreb Croatia
| | - Nikica Šprem
- Faculty of Agriculture; Department of Fisheries, Beekeeping, Game Management and Special Zoology; University of Zagreb; Svetošimunska cesta 25 10000 Zagreb Croatia
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Ancient mitochondrial pseudogenes reveal hybridization between distant lineages in the evolution of the Rupicapra genus. Gene 2017; 628:63-71. [DOI: 10.1016/j.gene.2017.07.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 07/07/2017] [Accepted: 07/11/2017] [Indexed: 11/23/2022]
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17
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Affiliation(s)
- Marco Masseti
- Department of Evolutionary Biology; University of Florence; Via del Proconsolo 12 50122 Firenze Italy
| | - Leonardo Salari
- Department of Earth Sciences; Sapienza University of Rome (external collaborator); Piazzale Aldo Moro 5 00185 Roma Italy
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Pérez T, Fernández M, Hammer SE, Domínguez A. Multilocus Intron Trees Reveal Extensive Male-Biased Homogenization of Ancient Populations of Chamois (Rupicapra spp.) across Europe during Late Pleistocene. PLoS One 2017; 12:e0170392. [PMID: 28146581 PMCID: PMC5287467 DOI: 10.1371/journal.pone.0170392] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 01/04/2017] [Indexed: 11/19/2022] Open
Abstract
The inferred phylogenetic relationships between organisms often depend on the molecular marker studied due to the diverse evolutionary mode and unlike evolutionary histories of different parts of the genome. Previous studies have shown conflicting patterns of differentiation of mtDNA and several nuclear markers in chamois (genus Rupicapra) that indicate a complex evolutionary picture. Chamois are mountain caprine that inhabit most of the medium to high altitude mountain ranges of southern Eurasia. The most accepted taxonomical classification considers two species, R. pyrenaica (with the subspecies parva, pyrenaica and ornata) from southwestern Europe and R. rupicapra (with the subspecies cartusiana, rupicapra, tatrica, carpatica, balcanica, asiatica and caucasica) from northeastern Europe. Phylogenies of mtDNA revealed three very old clades (from the early Pleistocene, 1.9 Mya) with a clear geographical signal. Here we analyze a set of 23 autosomal introns, comprising 15,411 nucleotides, in 14 individuals covering the 10 chamois subspecies. Introns offered an evolutionary scenario that contrasts with mtDNA. The nucleotidic diversity was 0.0013± 0.0002, at the low range of what is found in other mammals even if a single species is considered. A coalescent multilocus analysis with *BEAST indicated that introns diversified 88 Kya, in the late Pleistocene, and the effective population size at the root was lower than 10,000 individuals. The dispersal of some few migrant males should have rapidly spread trough the populations of chamois, given the homogeneity of intron sequences. The striking differences between mitochondrial and nuclear markers can be attributed to strong female philopatry and extensive male dispersal. Our results highlight the need of analyzing multiple and varied genome components to capture the complex evolutionary history of organisms.
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Affiliation(s)
- Trinidad Pérez
- Departamento de Biología Funcional, Universidad de Oviedo, Julián Clavería 6, Oviedo, Spain
| | - Margarita Fernández
- Departamento de Biología Funcional, Universidad de Oviedo, Julián Clavería 6, Oviedo, Spain
| | - Sabine E. Hammer
- Department of Pathobiology, Institute of Immunology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, Vienna, Austria
| | - Ana Domínguez
- Departamento de Biología Funcional, Universidad de Oviedo, Julián Clavería 6, Oviedo, Spain
- * E-mail:
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Mráz P, Ronikier M. Biogeography of the Carpathians: evolutionary and spatial facets of biodiversity. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12918] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Patrik Mráz
- Herbarium and Department of Botany; Charles University; Benátská 2 12801 Prague Czech Republic
| | - Michał Ronikier
- W. Szafer Institute of Botany; Polish Academy of Sciences; Lubicz 46 31-512 Kraków Poland
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Affiliation(s)
- Nikica Šprem
- Faculty of Agriculture; Department of Fisheries, Beekeeping, Game Management and Special Zoology; University of Zagreb; Svetošimunska cesta 25 Zagreb 10000 Croatia
| | - Elena Buzan
- Science and Research Centre; Institute for Biodiversity Studies; University of Primorska; Garibaldijeva 1 Koper 6000 Slovenia
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Vernesi C, Hoban SM, Pecchioli E, Crestanello B, Bertorelle G, Rosà R, Hauffe HC. Ecology, environment and evolutionary history influence genetic structure in five mammal species from the Italian Alps. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12651] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Cristiano Vernesi
- Department of Biodiversity and Molecular Ecology; Research and Innovation Centre; Fondazione Edmund Mach; 38010 S. Michele all'Adige (TN) Italy
| | - Sean M. Hoban
- National Institute for Mathematical and Biological Synthesis; University of Tennessee; 1122 Volunteer Blvd. Suite 106 Knoxville TN 37996-3410 USA
| | - Elena Pecchioli
- Department of Biodiversity and Molecular Ecology; Research and Innovation Centre; Fondazione Edmund Mach; 38010 S. Michele all'Adige (TN) Italy
| | - Barbara Crestanello
- Department of Biodiversity and Molecular Ecology; Research and Innovation Centre; Fondazione Edmund Mach; 38010 S. Michele all'Adige (TN) Italy
| | - Giorgio Bertorelle
- Department of Biology and Evolution; University of Ferrara; 44100 Ferrara Italy
| | - Roberto Rosà
- Department of Biodiversity and Molecular Ecology; Research and Innovation Centre; Fondazione Edmund Mach; 38010 S. Michele all'Adige (TN) Italy
| | - Heidi C. Hauffe
- Department of Biodiversity and Molecular Ecology; Research and Innovation Centre; Fondazione Edmund Mach; 38010 S. Michele all'Adige (TN) Italy
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Markov G, Zhelev P, Ben Slimen H, Suchentrunk F. Population genetic data pertinent to the conservation of Bulgarian chamois (Rupicapra rupicapra balcanica). CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0768-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Cornetti L, Ficetola GF, Hoban S, Vernesi C. Genetic and ecological data reveal species boundaries between viviparous and oviparous lizard lineages. Heredity (Edinb) 2015; 115:517-26. [PMID: 26126542 DOI: 10.1038/hdy.2015.54] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 05/18/2015] [Accepted: 05/18/2015] [Indexed: 11/09/2022] Open
Abstract
Identification of cryptic species is an essential aim for conservation biologists to avoid premature extinctions of 'unrecognized' species. Integrating different types of data can undoubtedly aid in resolving the issue of species delimitation. We studied here two lineages of the common lizard Zootoca vivipara that display different reproductive mode (the viviparous Z. v. vivipara and the oviparous Z. v. carniolica) and that overlap their distributional ranges in the European Alps. With the purpose of delimiting species' boundaries, we analyzed their ecological, genetic and natural history features. More than 300 samples were collected and analyzed at cytochrome b and 11 microsatellites loci for investigating genetic variation, population structure, individual relatedness and evolutionary histories of the two lineages. Additionally, we compared their ecological niches using eight ecological variables. Genetic data showed contrasting patterns of genetic structure between the two lineages, different demographic dynamics and no hybridization events. Also strong ecological differences (such as temperature) emerged between the two lineages, and niche overlap was limited. Taken together, these results indicate that Z. v. vivipara and Z. v. carniolica should be recognized as two separate species, and particular conservation consideration should be given to the oviparous lineage that tends to live in areas threatened by increasing impact of human activities. However, recent and rapid climate warming might determine an increasing risk for the persistence of the viviparous lineage, being adapted to cold environments.
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Affiliation(s)
- L Cornetti
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, San Michele all'Adige (TN), Italy.,Dipartimento di Scienze della Vita e Biotecnologie, University of Ferrara, via Borsari 46, Ferrara, Italy
| | - G F Ficetola
- Laboratoire d'Ecologie Alpine (LECA), Université Grenoble-Alpes, Grenoble, France.,LECA, CNRS, Grenoble, France
| | - S Hoban
- National Institute for Mathematical and Biological Synthesis, Knoxville, TN, USA
| | - C Vernesi
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, San Michele all'Adige (TN), Italy
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IMMOBILIZING THE VULNERABLE APENNINE CHAMOIS (RUPICAPRA PYRENAICA ORNATA) WITH A LOW-DOSE XYLAZINE-KETAMINE COMBINATION, REVERSED WITH IDAZOXAN OR ATIPAMEZOLE. J Zoo Wildl Med 2015; 46:213-23. [PMID: 26056871 DOI: 10.1638/2014-0079r.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Little information is available on chemical capture of the vulnerable subspecies within the genus Rupicapra. Low-dosage combinations of xylazine and ketamine were tested for immobilization of captive and free-ranging Apennine chamois, Rupicapra pyrenaica ornata (85 and 66 immobilizations, respectively) in a retrospective analysis. Of the six dosage groups, all of them providing an acceptable level of immobilization, the optimal trade-off between safety and efficacy was found following administration of a mean dosage of 0.24±0.03 mg/kg xylazine and 1.07±0.15 mg/kg ketamine, resulting in 7.50±3.31 min induction time, deep sedation with no or limited reaction to handling in 96% of the chamois, minimal deviation of physiologic parameters from previously reported physiologic values for anesthetized or physically restrained chamois, and no mortality. Intravenous injection of idazoxan (0.05±0.01 mg/kg) or atipamezole (0.38±0.37 mg/kg) resulted in faster reversal than intravenous injection of tolazoline (1.05±0.15 mg/kg) in 1.3 vs. 4.1 min. When free-ranging chamois were darted with similar xylazine and ketamine dosages, induction time was 8.49±5.48 min, 88% of the animals were deeply sedated, and a single animal died from respiratory arrest (1.5% mortality). Intramuscular atipamezole provided smoother reversal than intravenous idazoxan. The results of this study suggest that xylazine/ketamine combinations, at remarkably lower dosage than previously published in Caprinae, may be safely and effectively used in chemical capture protocols of Apennine chamois, to facilitate conservation-oriented relocation and research.
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Zemanová B, Hájková P, Hájek B, Martínková N, Mikulíček P, Zima J, Bryja J. Extremely low genetic variation in endangered Tatra chamois and evidence for hybridization with an introduced Alpine population. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0696-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Pérez T, González I, Essler SE, Fernández M, Domínguez A. The shared mitochondrial genome of Rupicapra pyrenaica ornata and Rupicapra rupicapra cartusiana: old remains of a common past. Mol Phylogenet Evol 2014; 79:375-9. [PMID: 25047552 DOI: 10.1016/j.ympev.2014.07.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 07/01/2014] [Accepted: 07/07/2014] [Indexed: 11/30/2022]
Abstract
Mitochondrial DNA (mtDNA) has largely been used for species delimitation. However, mtDNA introgression across species boundaries can lead to inconsistent phylogenies. Partial sequences of the mitochondrial genome in the chamois, genus Rupicapra, show the presence of three well differentiated clades, West (mtW), Central (mtC) and East (mtE), each with a geographically restricted distribution. The complete mtDNAs of the clades mtW and mtE (main representatives of the two currently considered species R. pyrenaica and R. rupicapra respectively) have been reported. In the present study, we sequenced the clade mtC present in populations from both species inhabiting the central area of Europe: the Apennines (R. pyrenaica ornata) and the Chartreuse Mountains (R. rupicapra cartusiana). The phylogenetic comparison with the genomes of Caprini highlights the ancient presence of chamois in Europe relative to the fossil record, and the old age of the chamois clade mtC that was split from the clade mtW in the early Pleistocene. The separation of R. pyrenaica ornata and R. rupicapra cartusiana female lineages was recent, dating of the late Pleistocene. Our data represent an example of mtDNA introgression of resident females of Chartreuse Mountains into immigrant males of R. rupicapra due to male-biased migration and female phylopatry.
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Affiliation(s)
- Trinidad Pérez
- Universidad de Oviedo, Biología Funcional (Genética), Julián Clavería 6, 33071 Oviedo, Spain
| | - Iago González
- Universidad de Oviedo, Biología Funcional (Genética), Julián Clavería 6, 33071 Oviedo, Spain
| | - Sabine E Essler
- University of Veterinary Medicine Vienna, Department of Pathobiology, Institute of Immunology, Veterinaerplatz 1, A-1210 Vienna, Austria
| | - Margarita Fernández
- Universidad de Oviedo, Biología Funcional (Genética), Julián Clavería 6, 33071 Oviedo, Spain
| | - Ana Domínguez
- Universidad de Oviedo, Biología Funcional (Genética), Julián Clavería 6, 33071 Oviedo, Spain.
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Roffler GH, Talbot SL, Luikart G, Sage GK, Pilgrim KL, Adams LG, Schwartz MK. Lack of sex-biased dispersal promotes fine-scale genetic structure in alpine ungulates. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0583-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Pérez T, Essler S, Palacios B, Albornoz J, Domínguez A. Evolution of the melanocortin-1 receptor gene (MC1R) in chamois (Rupicapra spp.). Mol Phylogenet Evol 2013; 67:621-5. [PMID: 23499612 DOI: 10.1016/j.ympev.2013.02.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Revised: 02/27/2013] [Accepted: 02/28/2013] [Indexed: 10/27/2022]
Abstract
The taxonomy of chamois and the effects of historical and evolutionary events on its diversification are still under discussion given that different morphological and genetic features presented partially discordant views. One of the morphological features that differentiate the two currently considered species, Rupicapra pyrenaica (southern chamois) and R. rupicapra (northern chamois) is coat color pattern. The melanocortin-1 receptor gene (MC1R) is related with differences in coloration in different mammals and was analyzed here in a sample of 25 chamois covering the 10 subspecies recognized, three in R. pyrenaica, (parva, pyrenaica and ornata) and seven in R. rupicapra (cartusiana, rupicapra, tatrica, carpatica, balcanica, asiatica and caucasica). Comparison with other caprinae showed that the MC1R gene has evolved under strong purifying selection. Three well differentiated haplotypes were identified: one shared by the seven subspecies of R. rupicapra, other common to the two Iberian chamois, both of the species R. pyrenaica, and a third haplotype, basal in the phylogenetic tree, unique to the subspecies from the Apennines, R. pyrenaica ornata. This pattern of variation, with three conspicuous clades, concurs with previous findings on microsatellites and mtDNA and argues in favor of the old classifications that distinguished the species R. ornata.
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Affiliation(s)
- Trinidad Pérez
- Universidad de Oviedo, Biología Funcional, Genética, Julián Clavería 6, 33071 Oviedo, Spain
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Buzan EV, Bryja J, Zemanová B, Kryštufek B. Population genetics of chamois in the contact zone between the Alps and the Dinaric Mountains: uncovering the role of habitat fragmentation and past management. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0469-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Martínková N, Zemanová B, Kranz A, Giménez MD, Hájková P. Chamois introductions to Central Europe and New Zealand. FOLIA ZOOLOGICA 2012. [DOI: 10.25225/fozo.v61.i3.a8.2012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Natália Martínková
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, v.v.i., Květná 8, 603 65 Brno, Czech Republic;, ,
- Institute of Biostatistics and Analyses, Masaryk University, Kamenice 3, 625 00 Brno, Czech Republic
| | - Barbora Zemanová
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, v.v.i., Květná 8, 603 65 Brno, Czech Republic;, ,
| | | | - Mabel D. Giménez
- Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Posadas, Argentina
| | - Petra Hájková
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, v.v.i., Květná 8, 603 65 Brno, Czech Republic;, ,
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Cavallero S, Marco I, Lavín S, D'Amelio S, López-Olvera JR. Polymorphisms at MHC class II DRB1 exon 2 locus in Pyrenean chamois (Rupicapra pyrenaica pyrenaica). INFECTION GENETICS AND EVOLUTION 2012; 12:1020-6. [PMID: 22425496 DOI: 10.1016/j.meegid.2012.02.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 02/19/2012] [Accepted: 02/28/2012] [Indexed: 11/12/2022]
Abstract
Chamois (Rupicapra spp.) are mountain ungulates from Southern and Central Europe and the Near East. A newly reported border disease virus (BDV) has affected the easternmost populations of Pyrenean chamois, leading to a dramatic population decrease that may drive to genetic variability loss. The Major Histocompatibility Complex (MHC) is a sensitive marker for genetic variation of populations: polymorphism on the MHC genes is affected both by pathogens and population dynamics and it is ecologically relevant, as depending on host-pathogen relationships and life history features. In the present study MHC class II DRB1 exon 2 variation was investigated in 81 Pyrenean chamois (Rupicapra pyrenaica pyrenaica) belonging to four populations. Haplotype analysis, population genetics statistics and network analysis were carried out, in order to analyze variability, phylogeography and genealogy, and the effects of geography and demographic trend. Twenty-nine haplotypes were identified, 26 of them newly described, with high Gene diversity (Gd). The variability observed in the easternmost populations of Pyrenean chamois showed a higher genetic diversity than that previously reported for other populations of Pyrenean and Cantabrian chamois (Rupicapra pyrenaica parva). The most frequent allele was RupyDRB*15, previously undetected, which seems to play a significant role in genotyping the variability, suggesting a possible effect of positive selection.
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Affiliation(s)
- Serena Cavallero
- Department of Public Health and Infectious Diseases, Section of Parasitology, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
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Y-chromosome phylogeny in the evolutionary net of chamois (genus Rupicapra). BMC Evol Biol 2011; 11:272. [PMID: 21943106 PMCID: PMC3198967 DOI: 10.1186/1471-2148-11-272] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Accepted: 09/26/2011] [Indexed: 11/10/2022] Open
Abstract
Background The chamois, distributed over most of the medium to high altitude mountain ranges of southern Eurasia, provides an excellent model for exploring the effects of historical and evolutionary events on diversification. Populations have been grouped into two species, Rupicapra pyrenaica from southwestern Europe and R. rupicapra from eastern Europe. The study of matrilineal mitochondrial DNA (mtDNA) and biparentally inherited microsatellites showed that the two species are paraphyletic and indicated alternate events of population contraction and dispersal-hybridization in the diversification of chamois. Here we investigate the pattern of variation of the Y-chromosome to obtain information on the patrilineal phylogenetic position of the genus Rupicapra and on the male-specific dispersal of chamois across Europe. Results We analyzed the Y-chromosome of 87 males covering the distribution range of the Rupicapra genus. We sequenced a fragment of the SRY gene promoter and characterized the male specific microsatellites UMN2303 and SRYM18. The SRY promoter sequences of two samples of Barbary sheep (Ammotragus lervia) were also determined and compared with the sequences of Bovidae available in the GenBank. Phylogenetic analysis of the alignment showed the clustering of Rupicapra with Capra and the Ammotragus sequence obtained in this study, different from the previously reported sequence of Ammotragus which groups with Ovis. Within Rupicapra, the combined data define 10 Y-chromosome haplotypes forming two haplogroups, which concur with taxonomic classification, instead of the three clades formed for mtDNA and nuclear microsatellites. The variation shows a west-to-east geographical cline of ancestral to derived alleles. Conclusions The phylogeny of the SRY-promoter shows an association between Rupicapra and Capra. The position of Ammotragus needs a reinvestigation. The study of ancestral and derived characters in the Y-chromosome suggests that, contrary to the presumed Asian origin, the paternal lineage of chamois originated in the Mediterranean, most probably in the Iberian Peninsula, and dispersed eastwards through serial funding events during the glacial-interglacial cycles of the Quaternary. The diversity of Y-chromosomes in chamois is very low. The differences in patterns of variation among Y-chromosome, mtDNA and biparental microsatellites reflect the evolutionary characteristics of the different markers as well as the effects of sex-biased dispersal and species phylogeography.
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Demontis D, Czarnomska SD, Hájková P, Zemanová B, Bryja J, Loeschcke V, Pertoldi C. Characterization of 151 SNPs for population structure analysis of the endangered Tatra chamois (Rupicapra rupicapra tatrica) and its relative, the Alpine chamois (R. r. rupicapra). Mamm Biol 2011. [DOI: 10.1016/j.mambio.2010.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Zemanová B, Hájková P, Bryja J, Zima J, Hájková A, Zima J. Development of multiplex microsatellite sets for noninvasive population genetic study of the endangered Tatra chamois. FOLIA ZOOLOGICA 2011. [DOI: 10.25225/fozo.v60.i1.a11.2011] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Barbora Zemanová
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, v.v.i., Department of Population Biology, Květná 8, 603 65 Brno, Czech Republic; e-mails: , , , , ,
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Petra Hájková
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, v.v.i., Department of Population Biology, Květná 8, 603 65 Brno, Czech Republic; e-mails: , , , , ,
| | - Josef Bryja
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, v.v.i., Department of Population Biology, Květná 8, 603 65 Brno, Czech Republic; e-mails: , , , , ,
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Jan Zima
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, v.v.i., Department of Population Biology, Květná 8, 603 65 Brno, Czech Republic; e-mails: , , , , ,
- Department of Zoology, Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Andrea Hájková
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, v.v.i., Department of Population Biology, Květná 8, 603 65 Brno, Czech Republic; e-mails: , , , , ,
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague, Czech Republic
| | - Jan Zima
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, v.v.i., Department of Population Biology, Květná 8, 603 65 Brno, Czech Republic; e-mails: , , , , ,
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Scandura M, Iacolina L, Cossu A, Apollonio M. Effects of human perturbation on the genetic make-up of an island population: the case of the Sardinian wild boar. Heredity (Edinb) 2010; 106:1012-20. [PMID: 21179064 DOI: 10.1038/hdy.2010.155] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Game species are often manipulated by human beings, whose activities can deeply affect their genetic make-up and population structure. We focused on a geographically isolated wild boar population (Sardinia, Italy), which is classified, together with the Corsican population, as a separate subspecies (Sus scrofa meridionalis). Two hundred and ten wild boars collected across Sardinia were analysed with a set of 10 microsatellites and compared with 296 reference genotypes from continental wild populations and to a sample of domestic pigs. The Sardinian population showed remarkable diversity and a high proportion of private alleles, and strongly deviated from the equilibrium. A Bayesian cluster analysis of only the Sardinian sample revealed a partition into five subpopulations. However, two different Bayesian approaches to the assignment of individuals, accounting for different possible source populations, produced consistent results and proved the admixed nature of the Sardinian population. Indeed, introgressive hybridization with boars from multiple sources (Italian peninsula, central Europe, domestic stocks) was detected, although poor evidence of crossbreeding with free-ranging domestic pigs was unexpectedly found. After excluding individuals who carried exotic genes, the population re-entered Hardy-Weinberg proportions and a clear population structure with three subpopulations emerged. Therefore, the inclusion of introgressed animals in the Bayesian analysis implied an overestimation of the number of clusters. Nonetheless, two of them were consistent between analyses and corresponded to highly pure stocks, located, respectively, in north-west and south-west Sardinia. This work shows the critical importance of including adequate reference samples when studying the genetic structure of managed wild populations.
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Affiliation(s)
- M Scandura
- Department of Zoology and Evolutionary Genetics, University of Sassari, Sassari, Italy.
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BRYJA J, SMITH C, KONEČNÝ A, REICHARD M. Range‐wide population genetic structure of the European bitterling (
Rhodeus amarus
) based on microsatellite and mitochondrial DNA analysis. Mol Ecol 2010; 19:4708-22. [DOI: 10.1111/j.1365-294x.2010.04844.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- J. BRYJA
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Květná 8, 603 65 Brno, Czech Republic
| | - C. SMITH
- School of Biology, University of St Andrews, St Andrews, Fife KY16 8LB, UK
| | - A. KONEČNÝ
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Květná 8, 603 65 Brno, Czech Republic
| | - M. REICHARD
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Květná 8, 603 65 Brno, Czech Republic
- School of Biology, University of St Andrews, St Andrews, Fife KY16 8LB, UK
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Miller JM, Poissant J, Kijas JW, Coltman DW. A genome-wide set of SNPs detects population substructure and long range linkage disequilibrium in wild sheep. Mol Ecol Resour 2010; 11:314-22. [PMID: 21429138 DOI: 10.1111/j.1755-0998.2010.02918.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The development of genomic resources for wild species is still in its infancy. However, cross-species utilization of technologies developed for their domestic counterparts has the potential to unlock the genomes of organisms that currently lack genomic resources. Here, we apply the OvineSNP50 BeadChip, developed for domestic sheep, to two related wild ungulate species: the bighorn sheep (Ovis canadensis) and the thinhorn sheep (Ovis dalli). Over 95% of the domestic sheep markers were successfully genotyped in a sample of fifty-two bighorn sheep while over 90% were genotyped in two thinhorn sheep. Pooling the results from both species identified 868 single-nucleotide polymorphisms (SNPs), 570 were detected in bighorn sheep, while 330 SNPs were identified in thinhorn sheep. The total panel of SNPs was able to discriminate between the two species, assign population of origin for bighorn sheep and detect known relationship classes within one population of bighorn sheep. Using an informative subset of these SNPs (n=308), we examined the extent of genome-wide linkage disequilibrium (LD) within one population of bighorn sheep and found that high levels of LD persist over 4 Mb.
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Affiliation(s)
- J M Miller
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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Rodríguez F, Pérez T, Hammer SE, Albornoz J, Domínguez A. Integrating phylogeographic patterns of microsatellite and mtDNA divergence to infer the evolutionary history of chamois (genus Rupicapra). BMC Evol Biol 2010; 10:222. [PMID: 20649956 PMCID: PMC2923631 DOI: 10.1186/1471-2148-10-222] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2009] [Accepted: 07/22/2010] [Indexed: 01/24/2023] Open
Abstract
Background The chamois, distributed over most of the medium to high altitude mountain ranges of southern Eurasia, provides an excellent model for exploring the effects of historical and evolutionary events on diversification. Populations have been grouped into two species, Rupicapra pyrenaica from southwestern Europe and R. rupicapra from eastern Europe. However, a previous study of cytochrome b revealed that the two proposed species were non-monophyletic. The reconstruction of phylogenetic relationships between animal species often depends on the markers studied. To further elucidate the evolutionary history of chamois, we extended earlier studies by analysing DNA sequences of four mitochondrial regions (ND1, 12S, tRNApro and Control Region) and microsatellites (20 loci) to include all subspecies and cover its entire distribution range. Results We found discordant microsatellite (μsat) and mitochondrial (mt) DNA phylogenies. Mitochondrial phylogenies form three clades, West, Central and East (mtW, mtC and mtE), at variance with taxonomic classification. Our divergence age estimates indicate an initial separation into branches mtW-mtC and mtE 1.7 million years ago (mya), in the late Pliocene-early Pleistocene, quickly followed by the split of clades mtW and mtC. Clade mtW contains haplotypes from the Iberian peninsula and the western Alps, Clade mtC includes haplotypes from the Apennines and the Massif of Chartreuse and Clade mtE comprises populations to the east of the Alps. Divergence among populations within these three major clades is recent (< 0.5 mya). New microsatellite multilocus genotypes added to previously published data revealed differences between every pair of subspecies, forming three well defined groups (μsatW, μsatC and μsatE) also with a strong geographic signature. Grouping does not correspond with the mitochondrial lineages but is closer to morphology and taxonomic classification. Recent drastic reductions in population size can be noted for the subspecies ornata as an extremely low diversity. Conclusions The phylogeographic patterns for mtDNA and microsatellites suggest an evolutionary history with limited range contractions and expansions during the Quaternary period and reflect a major effect of the Alpine barrier on west-east differentiation. The contrasting phylogenies for mtDNA and microsatellites indicate events of hybridization among highly divergent lineages in the central area of distribution. Our study points to the importance of reticulate evolution, with periods of isolation and reduction of population size followed by expansions and hybridizations, in the diversification at the level of close species or subspecies.
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Affiliation(s)
- Fernando Rodríguez
- Departamento de Biología Funcional, Universidad de Oviedo, Genética, Julián Clavería 6, 33071 Oviedo, Spain
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Bertorelle G, Benazzo A, Mona S. ABC as a flexible framework to estimate demography over space and time: some cons, many pros. Mol Ecol 2010; 19:2609-25. [PMID: 20561199 DOI: 10.1111/j.1365-294x.2010.04690.x] [Citation(s) in RCA: 290] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The analysis of genetic variation to estimate demographic and historical parameters and to quantitatively compare alternative scenarios recently gained a powerful and flexible approach: the Approximate Bayesian Computation (ABC). The likelihood functions does not need to be theoretically specified, but posterior distributions can be approximated by simulation even assuming very complex population models including both natural and human-induced processes. Prior information can be easily incorporated and the quality of the results can be analysed with rather limited additional effort. ABC is not a statistical analysis per se, but rather a statistical framework and any specific application is a sort of hybrid between a simulation and a data-analysis study. Complete software packages performing the necessary steps under a set of models and for specific genetic markers are already available, but the flexibility of the method is better exploited combining different programs. Many questions relevant in ecology can be addressed using ABC, but adequate amount of time should be dedicated to decide among alternative options and to evaluate the results. In this paper we will describe and critically comment on the different steps of an ABC analysis, analyse some of the published applications of ABC and provide user guidelines.
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Affiliation(s)
- G Bertorelle
- Department of Biology and Evolution, University of Ferrara, Via Borsari 46, 44100 Ferrara, Italy.
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Population genetic structure of Alpine chamois (Rupicapra r. rupicapra) in the Italian Alps. EUR J WILDLIFE RES 2010. [DOI: 10.1007/s10344-010-0382-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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