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Velli E, Caniglia R, Mattucci F. Phylogenetic History and Phylogeographic Patterns of the European Wildcat ( Felis silvestris) Populations. Animals (Basel) 2023; 13:ani13050953. [PMID: 36899811 PMCID: PMC10000227 DOI: 10.3390/ani13050953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/27/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023] Open
Abstract
Disentangling phylogenetic and phylogeographic patterns is fundamental to reconstruct the evolutionary histories of taxa and assess their actual conservation status. Therefore, in this study, for the first time, the most exhaustive biogeographic history of European wildcat (Felis silvestris) populations was reconstructed by typing 430 European wildcats, 213 domestic cats, and 72 putative admixed individuals, collected across the entire species' distribution range, at a highly diagnostic portion of the mitochondrial ND5 gene. Phylogenetic and phylogeographic analyses identified two main ND5 lineages (D and W) roughly associated with domestic and wild polymorphisms. Lineage D included all domestic cats, 83.3% of putative admixed individuals, and also 41.4% of wildcats; these latter mostly showed haplotypes belonging to sub-clade Ia, that diverged about 37,700 years ago, long pre-dating any evidence for cat domestication. Lineage W included all the remaining wildcats and putative admixed individuals, spatially clustered into four main geographic groups, which started to diverge about 64,200 years ago, corresponding to (i) the isolated Scottish population, (ii) the Iberian population, (iii) a South-Eastern European cluster, and (iv) a Central European cluster. Our results suggest that the last Pleistocene glacial isolation and subsequent re-expansion from Mediterranean and extra-Mediterranean glacial refugia were pivotal drivers in shaping the extant European wildcat phylogenetic and phylogeographic patterns, which were further modeled by both historical natural gene flow among wild lineages and more recent wild x domestic anthropogenic hybridization, as confirmed by the finding of F. catus/lybica shared haplotypes. The reconstructed evolutionary histories and the wild ancestry contents detected in this study could be used to identify adequate Conservation Units within European wildcat populations and help to design appropriate long-term management actions.
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Colunga-Salas P, Marines-Macías T, Hernández-Canchola G, Barbosa S, Ramírez C, Searle JB, León-Paniagua L. Population genomics reveals differences in genetic structure between two endemic arboreal rodent species in threatened cloud forest habitat. MAMMAL RES 2023. [DOI: 10.1007/s13364-022-00667-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Abstract
Genomic tools are now commonly used to assess the genetic diversity and genetic structure of species and populations, and they provide the ability to describe and address the negative effects of population declines and fragmentation. However, such studies are lacking for arboreal mammals despite their contribution to various ecosystem services, especially in uncommon and critically endangered ecosystems such as cloud forests. The aim of this work was to evaluate and compare the genetic diversity and population structure of two endemic arboreal mice from Mexican cloud forests that are associated with areas with different levels of impacts from human activities. We performed genotyping-by-sequencing in 47 Habromys schmidlyi and 17 Reithrodontomys wagneri individuals to evaluate genetic diversity and differentiation. In both species, the genetic diversity was low compared to other cricetid species, and we observed different population structure patterns, potentially linked to the different ecological associations. We detected two genetic groups in H. schmidlyi, that is a territorial species present in areas of low incline, while a single genetic group was found in R. wagneri, which forms family groups in areas with steep slopes. Overall, these results highlight how species’ genetic diversity can be differentially impacted depending on differential ecological associations within the same ecosystem. This information is essential for the development of the adequate conservation and management of these species.
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Lucati F, Miró A, Bosch J, Caner J, Jowers MJ, Rivera X, Donaire-Barroso D, Rebelo R, Ventura M. New insights on patterns of genetic admixture and phylogeographic history in Iberian high mountain populations of midwife toads. PLoS One 2022; 17:e0277298. [PMID: 36454960 PMCID: PMC9714896 DOI: 10.1371/journal.pone.0277298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 10/24/2022] [Indexed: 12/05/2022] Open
Abstract
Multiple Quaternary glacial refugia in the Iberian Peninsula, commonly known as "refugia within refugia", allowed diverging populations to come into contact and admix, potentially boosting substantial mito-nuclear discordances. In this study, we employ a comprehensive set of mitochondrial and nuclear markers to shed light onto the drivers of geographical differentiation in Iberian high mountain populations of the midwife toads Alytes obstetricans and A. almogavarii from the Pyrenees, Picos de Europa and Guadarrama Mountains. In the three analysed mountain regions, we detected evidence of extensive mito-nuclear discordances and/or admixture between taxa. Clustering analyses identified three major divergent lineages in the Pyrenees (corresponding to the eastern, central and central-western Pyrenees), which possibly recurrently expanded and admixed during the succession of glacial-interglacial periods that characterised the Late Pleistocene, and that currently follow a ring-shaped diversification pattern. On the other hand, populations from the Picos de Europa mountains (NW Iberian Peninsula) showed a mitochondrial affinity to central-western Pyrenean populations and a nuclear affinity to populations from the central Iberian Peninsula, suggesting a likely admixed origin for Picos de Europa populations. Finally, populations from the Guadarrama Mountain Range (central Iberian Peninsula) were depleted of genetic diversity, possibly as a consequence of a recent epidemic of chytridiomycosis. This work highlights the complex evolutionary history that shaped the current genetic composition of high mountain populations, and underscores the importance of using a multilocus approach to better infer the dynamics of population divergence.
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Affiliation(s)
- Federica Lucati
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & Global Change and Sustainability Institute (CHANGE), Faculty of Sciences, University of Lisbon, Lisbon, Portugal
- Centre for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Catalonia, Spain
- Sociodemography Research Group (DemoSoc), University Pompeu Fabra (UPF), Barcelona, Spain
| | - Alexandre Miró
- Centre for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Catalonia, Spain
| | - Jaime Bosch
- IMIB-Research Unit of Biodiversity (CSIC/UO/PA), Universidad de Oviedo, Mieres, Spain
- Centro de Investigación, Seguimiento y Evaluación, Parque Nacional Sierra de Guadarrama, Rascafría, Spain
| | - Jenny Caner
- Centre for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Catalonia, Spain
| | - Michael Joseph Jowers
- Departamento de Zoología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
- National Institute of Ecology (NIE), Maseo-myeon, Seocheon-gun, Republic of Korea
| | - Xavier Rivera
- Catalan Society of Herpetology, Museu Blau, Barcelona, Catalonia, Spain
| | | | - Rui Rebelo
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & Global Change and Sustainability Institute (CHANGE), Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Marc Ventura
- Centre for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Catalonia, Spain
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Carrier A, Prunier J, Poisson W, Trottier-Lavoie M, Gilbert I, Cavedon M, Pokharel K, Kantanen J, Musiani M, Côté SD, Albert V, Taillon J, Bourret V, Droit A, Robert C. Design and validation of a 63K genome-wide SNP-genotyping platform for caribou/reindeer (Rangifer tarandus). BMC Genomics 2022; 23:687. [PMID: 36199020 PMCID: PMC9533608 DOI: 10.1186/s12864-022-08899-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/15/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Development of large single nucleotide polymorphism (SNP) arrays can make genomic data promptly available for conservation problematic. Medium and high-density panels can be designed with sufficient coverage to offer a genome-wide perspective and the generated genotypes can be used to assess different genetic metrics related to population structure, relatedness, or inbreeding. SNP genotyping could also permit sexing samples with unknown associated metadata as it is often the case when using non-invasive sampling methods favored for endangered species. Genome sequencing of wild species provides the necessary information to design such SNP arrays. We report here the development of a SNP-array for endangered Rangifer tarandus using a multi-platform sequencing approach from animals found in diverse populations representing the entire circumpolar distribution of the species. RESULTS From a very large comprehensive catalog of SNPs detected over the entire sample set (N = 894), a total of 63,336 SNPs were selected. SNP selection accounted for SNPs evenly distributed across the entire genome (~ every 50Kb) with known minor alleles across populations world-wide. In addition, a subset of SNPs was selected to represent rare and local alleles found in Eastern Canada which could be used for ecotype and population assignments - information urgently needed for conservation planning. In addition, heterozygosity from SNPs located in the X-chromosome and genotyping call-rate of SNPs located into the SRY gene of the Y-chromosome yielded an accurate and robust sexing assessment. All SNPs were validated using a high-throughput SNP-genotyping chip. CONCLUSION This design is now integrated into the first genome-wide commercially available genotyping platform for Rangifer tarandus. This platform would pave the way to future genomic investigation of populations for this endangered species, including estimation of genetic diversity parameters, population assignments, as well as animal sexing from genetic SNP data for non-invasive samples.
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Affiliation(s)
- Alexandra Carrier
- Département de sciences animales, Faculté de l'agriculture et d'alimentation, Université Laval, Quebec City, Québec, Canada.,Centre de recherche en reproduction, développement et santé intergénérationnelle (CRDSI), Quebec City, Québec, Canada.,Réseau Québécois en reproduction (RQR), Saint-Hyacinthe, Québec, Canada
| | - Julien Prunier
- Département de médecine moléculaire, Faculté de médecine, Université Laval, Quebec City, Québec, Canada
| | - William Poisson
- Département de sciences animales, Faculté de l'agriculture et d'alimentation, Université Laval, Quebec City, Québec, Canada.,Centre de recherche en reproduction, développement et santé intergénérationnelle (CRDSI), Quebec City, Québec, Canada.,Réseau Québécois en reproduction (RQR), Saint-Hyacinthe, Québec, Canada
| | - Mallorie Trottier-Lavoie
- Département de sciences animales, Faculté de l'agriculture et d'alimentation, Université Laval, Quebec City, Québec, Canada.,Centre de recherche en reproduction, développement et santé intergénérationnelle (CRDSI), Quebec City, Québec, Canada.,Réseau Québécois en reproduction (RQR), Saint-Hyacinthe, Québec, Canada
| | - Isabelle Gilbert
- Département de sciences animales, Faculté de l'agriculture et d'alimentation, Université Laval, Quebec City, Québec, Canada.,Centre de recherche en reproduction, développement et santé intergénérationnelle (CRDSI), Quebec City, Québec, Canada.,Réseau Québécois en reproduction (RQR), Saint-Hyacinthe, Québec, Canada
| | - Maria Cavedon
- Department of biological sciences, Faculty of Science, University of Calgary, Calgary, Canada
| | | | - Juha Kantanen
- Natural Resources Institute Finland, Jokioinen, Finland
| | - Marco Musiani
- Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
| | - Steeve D Côté
- Département de biologie - Faculté de sciences et génie, Caribou Ungava, Université Laval, Quebec City, Québec, Canada
| | - Vicky Albert
- Ministère des Forêts, de la Faune et des Parcs du Québec (MFFP), Quebec City, Québec, Canada
| | - Joëlle Taillon
- Ministère des Forêts, de la Faune et des Parcs du Québec (MFFP), Quebec City, Québec, Canada
| | - Vincent Bourret
- Ministère des Forêts, de la Faune et des Parcs du Québec (MFFP), Quebec City, Québec, Canada
| | - Arnaud Droit
- Département de médecine moléculaire, Faculté de médecine, Université Laval, Quebec City, Québec, Canada
| | - Claude Robert
- Département de sciences animales, Faculté de l'agriculture et d'alimentation, Université Laval, Quebec City, Québec, Canada. .,Centre de recherche en reproduction, développement et santé intergénérationnelle (CRDSI), Quebec City, Québec, Canada. .,Réseau Québécois en reproduction (RQR), Saint-Hyacinthe, Québec, Canada.
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Stratakis M, Koutmanis I, Ilgaz Ç, Jablonski D, Kukushkin OV, Crnobrnja‐Isailovic J, Carretero MA, Liuzzi C, Kumlutaş Y, Lymberakis P, Poulakakis N. Evolutionary divergence of the smooth snake (Serpentes, Colubridae): The role of the Balkans and Anatolia. ZOOL SCR 2022. [DOI: 10.1111/zsc.12533] [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]
Affiliation(s)
- Manos Stratakis
- Department of Biology School of Sciences and Engineering University of Crete Irakleio Greece
- Natural History Museum of Crete School of Sciences and Engineering University of Crete Irakleio Greece
| | - Iraklis Koutmanis
- Department of Biology School of Sciences and Engineering University of Crete Irakleio Greece
- Natural History Museum of Crete School of Sciences and Engineering University of Crete Irakleio Greece
| | - Çetin Ilgaz
- Department of Biology Faculty of Science Dokuz Eylül University Buca‐İzmir Turkey
- Research and Application Center for Fauna and Flora Dokuz Eylul University Buca‐İzmir Turkey
| | - Daniel Jablonski
- Department of Zoology Comenius University in Bratislava Bratislava Slovakia
| | - Oleg V. Kukushkin
- Department of Biodiversity Studies and Ecological Monitoring T.I. Vyazemski Karadag Research Station – Nature Reserve of Russian Academy of Sciences Theodosia Crimea
- Department of Herpetology Institute of Zoology of Russian Academy of Sciences Saint Petersburg Russia
| | - Jelka Crnobrnja‐Isailovic
- Department of Biology and Ecology Faculty of Sciences and Mathematics University of Niš Niš Serbia
- Department of Evolutionary Biology Institute for Biological Research “Siniša Stanković” ‐ National Institute of Republic of Serbia University of Belgrade Beograd Serbia
| | - Miguel A. Carretero
- CIBIO Research Centre in Biodiversity and Genetic Resources InBIO Universidade do Porto Vila do Conde Portugal
- Departamento de Biologia Faculdade de Ciências da Universidade do Porto Porto Portugal
- BIOPOLIS Program in Genomics Biodiversity and Land Planning CIBIO Vairão Portugal
| | | | - Yusuf Kumlutaş
- Department of Biology Faculty of Science Dokuz Eylül University Buca‐İzmir Turkey
- Research and Application Center for Fauna and Flora Dokuz Eylul University Buca‐İzmir Turkey
| | - Petros Lymberakis
- Natural History Museum of Crete School of Sciences and Engineering University of Crete Irakleio Greece
| | - Nikos Poulakakis
- Department of Biology School of Sciences and Engineering University of Crete Irakleio Greece
- Natural History Museum of Crete School of Sciences and Engineering University of Crete Irakleio Greece
- Institute of Molecular Biology and Biotechnology (IMBB) Foundation for Research and Technology ‐ Hellas (FORTH) Irakleio Greece
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6
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Strachinis I, Poulakakis N, Karaiskou N, Patronidis P, Patramanis I, Poursanidis D, Jablonski D, Triantafyllidis A. Phylogeography and systematics of
Algyroides
(Sauria: Lacertidae) of the Balkan Peninsula. ZOOL SCR 2021. [DOI: 10.1111/zsc.12471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Ilias Strachinis
- Department of Genetics, Development and Molecular Biology School of Biology Faculty of Natural Sciences Aristotle University of Thessaloniki Greece
| | - Nikos Poulakakis
- Department of Biology University of Crete Irakleio Greece
- Natural History Museum of CreteUniversity of Crete Irakleio Greece
| | - Nikoleta Karaiskou
- Department of Genetics, Development and Molecular Biology School of Biology Faculty of Natural Sciences Aristotle University of Thessaloniki Greece
| | - Politis Patronidis
- Department of Genetics, Development and Molecular Biology School of Biology Faculty of Natural Sciences Aristotle University of Thessaloniki Greece
| | | | - Dimitris Poursanidis
- Foundation for Research and Technology – Hellas (FORTH) Institute of Applied and Computational Mathematics Iraklion Greece
| | | | - Alexandros Triantafyllidis
- Department of Genetics, Development and Molecular Biology School of Biology Faculty of Natural Sciences Aristotle University of Thessaloniki Greece
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7
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Spadavecchia G, Chiocchio A, Bisconti R, Canestrelli D. Paso doble: A two-step Late Pleistocene range expansion in the Tyrrhenian tree frog Hyla sarda. Gene 2021; 780:145489. [PMID: 33588038 DOI: 10.1016/j.gene.2021.145489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 01/30/2021] [Accepted: 02/02/2021] [Indexed: 10/22/2022]
Abstract
The Tyrrhenian tree frog, Hyla sarda, is an amphibian endemic to the Tyrrhenian islands (Western Mediterranean). Previous investigations of its Pleistocene evolutionary history suggested that it colonised the northern portion of its current range, through a spatial diffusion process from the Sardinia island, during the last glaciation. However, southern and northern portions of the species' range experienced markedly different climatic conditions during the Late Pleistocene, suggesting the possibility of an unusual two-step process of demographic expansion. Here, we use Bayesian phylogeographic approaches to locate the ancestral area in Sardinia and to characterise better the demographic component of this expansion event. These analyses located the ancestral area for H. sarda populations along the central-eastern coast of the Sardinia island, within an area previously shown to host suitable bioclimatic conditions for H. sarda populations throughout the Late Pleistocene. Historical demographic reconstructions clearly showed that a two-step process of demographic growth fits well the data, with northern populations expanding later than Sardinia populations. The harsher climatic conditions occurred in northern islands during the glacial epoch, as compared to Sardinia, likely delayed tree frog colonisation of northern territories, and the associated demographic growth.
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Affiliation(s)
- Giada Spadavecchia
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia. Viale dell'Università s.n.c., I-01100 Viterbo, Italy
| | - Andrea Chiocchio
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia. Viale dell'Università s.n.c., I-01100 Viterbo, Italy; Department of Biology, Lunds Universitet, Sölvegatan 37, 223 62 Lund, Sweden
| | - Roberta Bisconti
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia. Viale dell'Università s.n.c., I-01100 Viterbo, Italy.
| | - Daniele Canestrelli
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia. Viale dell'Università s.n.c., I-01100 Viterbo, Italy
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8
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Liu Y, Dietrich CH, Wei C. Genetic divergence, population differentiation and phylogeography of the cicada Subpsaltria yangi based on molecular and acoustic data: an example of the early stage of speciation? BMC Evol Biol 2019; 19:5. [PMID: 30621591 PMCID: PMC6323834 DOI: 10.1186/s12862-018-1317-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 12/04/2018] [Indexed: 11/17/2022] Open
Abstract
Background Geographical isolation combined with historical climatic fluctuations have been identified as two major factors that contribute to the formation of new species. On the other hand, biotic factors such as competition and predation are also able to drive the evolution and diversification of organisms. To determine whether geographical barriers contributed to population divergence or speciation in the rare endemic cicada Subpsaltria yangi the population differentiation, genetic structure and phylogeography of the species were investigated in the Loess Plateau and adjacent areas of northwestern China by analysing mitochondrial and nuclear DNA and comparing the calling song structure of 161 male individuals. Results The results reveal a low level of genetic differentiation and relatively simple phylogeographic structure for this species, but two independent clades corresponding to geographically isolated populations were recognised. Genetic and geographical distances were significantly correlated among lineages. Results of divergence-time estimation are consistent with a scenario of isolation due to glacial refugia and interglacial climate oscillation in northwestern China. Significant genetic divergence was found between the population occurring in the Helan Mountains and other populations, and recent population expansion has occurred in the Helan Mountains and/or adjacent areas. This population is also significantly different in calling song structure from other populations. Conclusions Geographical barriers (i.e., the deserts and semi-deserts surrounding the Helan Mountains), possibly coupled with related ecological differences, may have driven population divergence and allopatric speciation. This provides a possible example of incipient speciation in Cicadidae, improves understanding of population differentiation, acoustic signal diversification and phylogeographic relationships of this rare cicada species of conservation concern, and informs future studies on population differentiation, speciation and phylogeography of other insects with a high degree of endemism in the Helan Mountains and adjacent areas. Electronic supplementary material The online version of this article (10.1186/s12862-018-1317-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yunxiang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, and Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Christopher H Dietrich
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, 61820, USA
| | - Cong Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, and Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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9
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Queirós J, Acevedo P, Santos JPV, Barasona J, Beltran-Beck B, González-Barrio D, Armenteros JA, Diez-Delgado I, Boadella M, Fernandéz de Mera I, Ruiz-Fons JF, Vicente J, de la Fuente J, Gortázar C, Searle JB, Alves PC. Red deer in Iberia: Molecular ecological studies in a southern refugium and inferences on European postglacial colonization history. PLoS One 2019; 14:e0210282. [PMID: 30620758 PMCID: PMC6324796 DOI: 10.1371/journal.pone.0210282] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 12/19/2018] [Indexed: 01/31/2023] Open
Abstract
The red deer (Cervus elaphus) is a widespread wild ungulate in Europe that has suffered strong anthropogenic impacts over their distribution during the last centuries, but also at the present time, due its economic importance as a game species. Here we focus on the evolutionary history of the red deer in Iberia, one of the three main southern refugial areas for temperate species in Europe, and addressed the hypothesis of a cryptic refugia at higher latitudes during the Last Glacial Maximum (LGM). A total of 911 individuals were sampled, genotyped for 34 microsatellites specifically developed for red deer and sequenced for a fragment of 670 bp of the mitochondrial (mtDNA) D-loop. The results were combined with published mtDNA sequences, and integrated with species distribution models and historical European paleo-distribution data, in order to further examine the alternative glacial refugial models and the influence of cryptic refugia on European postglacial colonization history. Clear genetic differentiation between Iberian and European contemporary populations was observed at nuclear and mtDNA levels, despite the mtDNA haplotypes central to the phylogenetic network are present across western Europe (including Iberia) suggesting a panmictic population in the past. Species distribution models, fossil records and genetic data support a timing of divergence between Iberian and European populations that overlap with the LGM. A notable population structure was also found within the Iberian Peninsula, although several populations displayed high levels of admixture as a consequence of recent red deer translocations. Five D-loop sub-lineages were found in Iberia that belong to the Western European mtDNA lineage, while there were four main clusters based on analysis of nuclear markers. Regarding glacial refugial models, our findings provide detailed support for the hypothesis that red deer may have persisted in cryptic northern refugia in western Europe during the LGM, most likely in southern France, southern Ireland, or in a region between them (continental shelf), and these regions were the source of individuals during the European re-colonization. This evidence heightens the importance of conserving the high mitochondrial and nuclear diversity currently observed in Iberian populations.
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Affiliation(s)
- João Queirós
- Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO)/InBio Laboratório Associado, Universidade do Porto, R. Monte-Crasto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Porto, Portugal
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
- * E-mail:
| | - Pelayo Acevedo
- Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO)/InBio Laboratório Associado, Universidade do Porto, R. Monte-Crasto, Vairão, Portugal
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - João P. V. Santos
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
- Departamento de Biologia & CESAM, Universidade de Aveiro, Aveiro, Portugal
| | - Jose Barasona
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Beatriz Beltran-Beck
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - David González-Barrio
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Jose A. Armenteros
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Iratxe Diez-Delgado
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Mariana Boadella
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
- SABIOtec. Ed. Polivalente UCLM, Ciudad Real, Spain
| | - Isabel Fernandéz de Mera
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Jose F. Ruiz-Fons
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Joaquin Vicente
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Jose de la Fuente
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, United States of America
| | - Christian Gortázar
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Jeremy B. Searle
- Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO)/InBio Laboratório Associado, Universidade do Porto, R. Monte-Crasto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Porto, Portugal
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States of America
| | - Paulo C. Alves
- Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO)/InBio Laboratório Associado, Universidade do Porto, R. Monte-Crasto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Porto, Portugal
- Wildlife Biology Program, University of Montana, Missoula, MT, United States of America
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10
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Querejeta M, Castresana J. Evolutionary history of the endemic water shrew Neomys anomalus: Recurrent phylogeographic patterns in semi-aquatic mammals of the Iberian Peninsula. Ecol Evol 2018; 8:10138-10146. [PMID: 30397453 PMCID: PMC6206195 DOI: 10.1002/ece3.4487] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 07/27/2018] [Accepted: 08/08/2018] [Indexed: 11/10/2022] Open
Abstract
The Cabrera's water shrew (Neomys anomalus) is a small semi-aquatic mammal whose taxonomic status was recently elevated from subspecies to species; as a consequence of this change, this species is now endemic to the Iberian Peninsula. In this study, we looked at its evolutionary history by combining phylogeography, the spatial distribution of genetic diversity, and species distribution modeling. To perform these analyses, we used noninvasive samples collected across the species distribution range and sequenced partial mitochondrial cytochrome b and D-loop genes. Maximum-likelihood and Bayesian phylogenetic trees derived from these sequences indicated that N. anomalus is divided into two main phylogroups that correlate strongly with geography, with two contact zones between the groups that showed limited spatial mixing between them. River basins were responsible for only a small percentage of the structure of the genetic diversity of this species despite its riparian habitat. The nucleotide diversity variation map showed the highest genetic diversity to be in the north of the Iberian Peninsula. Finally, species distribution modeling allowed the inference of an optimal area during the Last Interglacial in the north of the Iberian Peninsula, and multiple glacial refugia during the Last Glacial Maximum. The phylogeographic pattern of N. anomalus is strikingly similar to that of another semi-aquatic Iberian mammal, the Pyrenean desman (Galemys pyrenaicus), revealing how Pleistocene glaciations could have had equivalent effects on species of similar ecology and distribution. This phylogeographic structure is consistent with N. anomalus having been isolated for long periods in multiple glacial refugia within the Iberian Peninsula, in agreement with the "refugia-within-refugia" hypothesis, and further supporting its status as a distinct species.
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Affiliation(s)
- Marina Querejeta
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
- Bavarian State Collection of ZoologyMünchenGermany
| | - Jose Castresana
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
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11
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Barbosa S, Mestre F, White TA, Paupério J, Alves PC, Searle JB. Integrative approaches to guide conservation decisions: Using genomics to define conservation units and functional corridors. Mol Ecol 2018; 27:3452-3465. [PMID: 30030869 DOI: 10.1111/mec.14806] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 07/01/2018] [Accepted: 07/05/2018] [Indexed: 01/13/2023]
Abstract
Climate change and increasing habitat loss greatly impact species survival, requiring range shifts, phenotypic plasticity and/or evolutionary change for long-term persistence, which may not readily occur unaided in threatened species. Therefore, defining conservation actions requires a detailed assessment of evolutionary factors. Existing genetic diversity needs to be thoroughly evaluated and spatially mapped to define conservation units (CUs) in an evolutionary context, and we address that here. We also propose a multidisciplinary approach to determine corridors and functional connectivity between CUs by including genetic diversity in the modelling while controlling for isolation by distance and phylogeographic history. We evaluate our approach on a Near Threatened Iberian endemic rodent by analysing genotyping-by-sequencing (GBS) genomic data from 107 Cabrera voles (Microtus cabrerae), screening the entire species distribution to define categories of CUs and their connectivity: We defined six management units (MUs) which can be grouped into four evolutionarily significant units (ESUs) and three (putatively) adaptive units (AUs). We demonstrate that the three different categories of CU can be objectively defined using genomic data, and their characteristics and connectivity can inform conservation decision-making. In particular, we show that connectivity of the Cabrera vole is very limited in eastern Iberia and that the pre-Pyrenean and part of the Betic geographic nuclei contribute the most to the species genetic diversity. We argue that a multidisciplinary framework for CU definition is essential and that this framework needs a strong evolutionary basis.
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Affiliation(s)
- Soraia Barbosa
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto/InBIO Laboratório Associado, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York
| | - Frederico Mestre
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade de Évora/InBIO Laboratório Associado, Évora, Portugal
| | - Thomas A White
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Joana Paupério
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto/InBIO Laboratório Associado, Vairão, Portugal
| | - Paulo C Alves
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto/InBIO Laboratório Associado, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Jeremy B Searle
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto/InBIO Laboratório Associado, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York
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12
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Psonis N, Antoniou A, Karameta E, Leaché AD, Kotsakiozi P, Darriba D, Kozlov A, Stamatakis A, Poursanidis D, Kukushkin O, Jablonski D, Crnobrnja–Isailović J, Gherghel I, Lymberakis P, Poulakakis N. Resolving complex phylogeographic patterns in the Balkan Peninsula using closely related wall-lizard species as a model system. Mol Phylogenet Evol 2018; 125:100-115. [DOI: 10.1016/j.ympev.2018.03.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 03/08/2018] [Accepted: 03/14/2018] [Indexed: 10/17/2022]
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13
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Ferreira CM, Sabino-Marques H, Barbosa S, Costa P, Encarnação C, Alpizar-Jara R, Pita R, Beja P, Mira A, Searle JB, Paupério J, Alves PC. Genetic non-invasive sampling (gNIS) as a cost-effective tool for monitoring elusive small mammals. EUR J WILDLIFE RES 2018. [DOI: 10.1007/s10344-018-1188-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Lin D, Bi K, Conroy CJ, Lacey EA, Schraiber JG, Bowie RCK. Mito-nuclear discordance across a recent contact zone for California voles. Ecol Evol 2018; 8:6226-6241. [PMID: 29988439 PMCID: PMC6024151 DOI: 10.1002/ece3.4129] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 03/16/2018] [Accepted: 03/29/2018] [Indexed: 11/17/2022] Open
Abstract
To examine the processes that maintain genetic diversity among closely related taxa, we investigated the dynamics of introgression across a contact zone between two lineages of California voles (Microtus californicus). We tested the prediction that introgression of nuclear loci would be greater than that for mitochondrial loci, assuming ongoing gene flow across the contact zone. We also predicted that genomic markers would show a mosaic pattern of differentiation across this zone, consistent with genomes that are semi-permeable. Using mitochondrial cytochrome b sequences and genome-wide loci developed via ddRAD-seq, we analyzed genetic variation for 10 vole populations distributed along the central California coast; this transect included populations from within the distributions of both parental lineages as well as the putative contact zone. Our analyses revealed that (1) the two lineages examined are relatively young, having diverged ca. 8.5-54 kya, (2) voles from the contact zone in Santa Barbara County did not include F1 or early generation backcrossed individuals, and (3) there appeared to be little to no recurrent gene flow across the contact zone. Introgression patterns for mitochondrial and nuclear markers were not concordant; only mitochondrial markers revealed evidence of introgression, putatively due to historical hybridization. These differences in genetic signatures are intriguing given that the contact zone occurs in a region of continuous vole habitat, with no evidence of past or present physical barriers. Future studies that examine specific isolating mechanisms, such as microhabitat use and mate choice, will facilitate our understanding of how genetic boundaries are maintained in this system.
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Affiliation(s)
- Dana Lin
- Museum of Vertebrate ZoologyUniversity of California, BerkeleyBerkeleyCalifornia
- Department of Integrative BiologyUniversity of California, BerkeleyBerkeleyCalifornia
| | - Ke Bi
- Computational Genomics Resource LaboratoryCalifornia Institute for Quantitative BiosciencesUniversity of California, BerkeleyBerkeleyCalifornia
| | - Christopher J. Conroy
- Department of Integrative BiologyUniversity of California, BerkeleyBerkeleyCalifornia
| | - Eileen A. Lacey
- Museum of Vertebrate ZoologyUniversity of California, BerkeleyBerkeleyCalifornia
- Department of Integrative BiologyUniversity of California, BerkeleyBerkeleyCalifornia
| | - Joshua G. Schraiber
- Department of BiologyCenter for Computational Genetics and GenomicsTemple UniversityPhiladelphiaPennsylvania
- Institute for Genomics and Evolutionary MedicineTemple UniversityPhiladelphiaPennsylvania
| | - Rauri C. K. Bowie
- Museum of Vertebrate ZoologyUniversity of California, BerkeleyBerkeleyCalifornia
- Department of Integrative BiologyUniversity of California, BerkeleyBerkeleyCalifornia
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15
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Biedma L, Román J, Calzada J, Friis G, Godoy JA. Phylogeography of Crocidura suaveolens (Mammalia: Soricidae) in Iberia has been shaped by competitive exclusion by C. russula. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx126] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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16
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Mestre F, Risk BB, Mira A, Beja P, Pita R. A metapopulation approach to predict species range shifts under different climate change and landscape connectivity scenarios. Ecol Modell 2017. [DOI: 10.1016/j.ecolmodel.2017.06.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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