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Kuijt M, Oskam L, den Boer I, Dufresnes C, France J, Gilbert MJ, de Visser MC, Struijk RP, Wielstra B. The introduction of three cryptic tree frog species in the Dutch coastal dunes challenges conservation paradigms. AMPHIBIA-REPTILIA 2022. [DOI: 10.1163/15685381-bja10102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Abstract
Invasive species are considered one of the main drivers of the sixth mass extinction. Conservation solutions depend on whether a species is also indigenous to the country it invades (i.e., beyond its native range). In the case of invasive cryptic species, genetic tools are required to establish their identity. We illustrate these issues with the human-mediated colonization of the Dutch coastal dunes by Hyla tree frogs. Although previously assumed to concern the indigenous common tree frog H. arborea, European tree frogs comprise a complex of allopatric cryptic species, meaning the taxonomic identity of introduced Dutch populations warrants investigation. We sequence mtDNA for 173 individuals from native and introduced populations across the Netherlands and compare our dataset with hundreds of Hyla haplotypes previously barcoded in the Western Palearctic. Two of the dune populations carry an mtDNA haplotype of the native species H. arborea that occurs naturally elsewhere in the Netherlands. In contrast, mtDNA assigned to the eastern tree frog H. orientalis was detected in all three other dune populations. In one of these populations mtDNA of the Italian tree frog H. intermedia was also found. Not one, but three species of tree frogs have thus been introduced to the Dutch coastal dunes, only one of them being native to the Netherlands. This situation causes a conservation conundrum as some introduced populations are lawfully protected but could pose a threat to local biodiversity. Regarding the ‘true’ exotic tree frog species, all conservation options should be considered.
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Affiliation(s)
- Marit Kuijt
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands
| | - Liam Oskam
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands
| | | | - Christophe Dufresnes
- LASER, College of Biology and Environment, Nanjing Forestry University, Nanjing 210037, China
| | - James France
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands
| | - Maarten J. Gilbert
- Reptile, Amphibian and Fish Conservation Netherlands (RAVON), P.O. Box 1413, 6501 BK Nijmegen, The Netherlands
- Department Biomolecular Health Sciences – Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, P.O. Box 80.165, 3508 TD Utrecht, The Netherlands
| | - Manon C. de Visser
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands
| | - Richard P.J.H. Struijk
- Reptile, Amphibian and Fish Conservation Netherlands (RAVON), P.O. Box 1413, 6501 BK Nijmegen, The Netherlands
| | - Ben Wielstra
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands
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Majtyka T, Borczyk B, Ogielska M, Stöck M. Morphometry of two cryptic tree frog species at their hybrid zone reveals neither intermediate nor transgressive morphotypes. Ecol Evol 2022; 12:e8527. [PMID: 35127036 PMCID: PMC8794711 DOI: 10.1002/ece3.8527] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 12/17/2021] [Indexed: 11/20/2022] Open
Abstract
Under incomplete reproductive isolation, secondary contact of diverged allopatric lineages may lead to the formation of hybrid zones that allow to study recombinants over several generations as excellent systems of genomic interactions resulting from the evolutionary forces acting on certain genes and phenotypes. Hybrid phenotypes may either exhibit intermediacy or, alternatively, transgressive traits, which exceed the extremes of their parents due to epistasis and segregation of complementary alleles. While transgressive morphotypes have been examined in fish, reptiles, birds, and mammals, studies in amphibians are rare. Here, we associate microsatellite-based genotypes with morphometrics-based morphotypes of two tree frog species of the Hyla arborea group, sampled across a hybrid zone in Poland, to understand whether the genetically differentiated parental species also differ in morphology between each other and their hybrids and whether secondary contact leads to the evolution of intermediate or transgressive morphotypes. Using univariate approaches, explorative multivariate methods (principal component analyses) as well as techniques with prior grouping (discriminant function analyses), we find that morphotypes of both parental species and hybrids differ from each other. Importantly, hybrid morphotypes are neither intermediate nor transgressive but found to be more similar to H. orientalis than to H. arborea.
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Affiliation(s)
- Tomasz Majtyka
- Department of Evolutionary Biology and Conservation of VertebratesUniversity of WrocławWrocławPoland
| | - Bartosz Borczyk
- Department of Evolutionary Biology and Conservation of VertebratesUniversity of WrocławWrocławPoland
| | - Maria Ogielska
- Department of Evolutionary Biology and Conservation of VertebratesUniversity of WrocławWrocławPoland
| | - Matthias Stöck
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB)BerlinGermany
- Amphibian Research CenterHiroshima UniversityHigashi‐HiroshimaJapan
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3
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Podnar M, Grbac I, Tvrtković N, Hörweg C, Haring E. Hidden diversity, ancient divergences, and tentative Pleistocene microrefugia of European scorpions (Euscorpiidae: Euscorpiinae) in the eastern Adriatic region. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
| | - Irena Grbac
- Croatian Natural History Museum Zagreb Croatia
| | | | | | - Elisabeth Haring
- Natural History Museum Vienna Vienna Austria
- Faculty of Life Science Department of Evolutionary Biology University of Vienna Vienna Austria
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4
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Jin L, Liao WB, Merilä J. Genomic evidence for adaptive differentiation among
Microhyla fissipes
populations: Implications for conservation. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Long Jin
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
| | - Wen Bo Liao
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Programme Faculty of Biological and Environmental Sciences FI‐00014 University of Helsinki Helsinki Finland
- Research Division for Ecology and Biodiversity School Biological Sciences The University of Hong KongHong Kong SAR
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5
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Pröhl H, Auffarth J, Bergmann T, Buschmann H, Balkenhol N. Conservation genetics of the yellow-bellied toad (Bombina variegata): population structure, genetic diversity and landscape effects in an endangered amphibian. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01350-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractRevealing patterns of genetic diversity and barriers for gene flow are key points for successful conservation in endangered species. Methods based on molecular markers are also often used to delineate conservation units such as evolutionary significant units and management units. Here we combine phylo-geographic analyses (based on mtDNA) with population and landscape genetic analyses (based on microsatellites) for the endangered yellow-bellied toad Bombina variegata over a wide distribution range in Germany. Our analyses show that two genetic clusters are present in the study area, a northern and a southern/central one, but that these clusters are not deeply divergent. The genetic data suggest high fragmentation among toad occurrences and consequently low genetic diversity. Genetic diversity and genetic connectivity showed a negative relationship with road densities and urban areas surrounding toad occurrences, indicating that these landscape features act as barriers to gene flow. To preserve a maximum of genetic diversity, we recommend considering both genetic clusters as management units, and to increase gene flow among toad occurrences with the aim of restoring and protecting functional meta-populations within each of the clusters. Several isolated populations with especially low genetic diversity and signs of inbreeding need particular short-term conservation attention to avoid extinction. We also recommend to allow natural gene flow between both clusters but not to use individuals from one cluster for translocation or reintroduction into the other. Our results underscore the utility of molecular tools for species conservation, highlight outcomes of habitat fragmentation onto the genetic structure of an endangered amphibian and reveal particularly threatened populations in need for urgent conservation efforts.
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Jablonski D, Gkontas I, Poursanidis D, Lymberakis P, Poulakakis N. Stability in the Balkans: phylogeography of the endemic Greek stream frog, Rana graeca. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blaa224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
We still have little knowledge concerning the phylogeography of amphibians and reptiles from the Balkan Peninsula compared with the other two Mediterranean peninsulas. This raises concerns for endemic taxa from these peninsulas, because it might interfere with further conservation efforts. Here we focus on the endemic Greek stream frog (Rana graeca) and reconstruct its biogeography and evolutionary history. Using four genetic markers (Cytb, 16S, COI and BDNF) in > 350 sequences covering the whole distribution range, we conducted phylogenetic, demographic and ecological niche analyses, which revealed the phylogeography of this species. Surprisingly, this examination of R. graeca reveals a very shallow level of intraspecific genetic variability through the Balkans, with two main, statistically supported lineages having a partly sympatric distribution. The most variable marker was Cytb, which showed 19 haplotypes in 123 analysed sequences in the whole species distribution area. Here presented genetic data, together with the environmental niche projection and demographic analyses suggest that R. graeca was probably affected only marginally by climatic oscillations, with the Hellenides as the most suitable area for the occurrence of the species in different geological periods. This is consistent with the observed genetic diversity, which is mostly related to these mountains. Although the species shows a certain level of phenotypic variability and ecological preferences, this might be related to species plasticity affected by the micro-climatic conditions in small areas, which merits further research. Comparing phylogeography of other amphibian and reptile species in the Balkans, we showed that the observed pattern represents a new view on the phylogeography of the Balkan herpetofauna.
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Affiliation(s)
- Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Bratislava, Slovakia
| | - Ioannis Gkontas
- Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Irakleio, Greece
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, Irakleio, Greece
| | - Dimitris Poursanidis
- Foundation for Research and Technology Hellas, Institute of Applied and Computational Mathematics, The Remote Sensing Lab, Vassilika Vouton, Irakleio, Greece
| | - Petros Lymberakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, Irakleio, Greece
| | - Nikos Poulakakis
- Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Irakleio, Greece
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, Irakleio, Greece
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7
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Kirschner P, Arthofer W, Pfeifenberger S, Záveská E, Schönswetter P, Steiner FM, Schlick-Steiner BC. Performance comparison of two reduced-representation based genome-wide marker-discovery strategies in a multi-taxon phylogeographic framework. Sci Rep 2021; 11:3978. [PMID: 33597550 PMCID: PMC7889850 DOI: 10.1038/s41598-020-79778-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 12/09/2020] [Indexed: 01/31/2023] Open
Abstract
Multi-locus genetic data are pivotal in phylogenetics. Today, high-throughput sequencing (HTS) allows scientists to generate an unprecedented amount of such data from any organism. However, HTS is resource intense and may not be accessible to wide parts of the scientific community. In phylogeography, the use of HTS has concentrated on a few taxonomic groups, and the amount of data used to resolve a phylogeographic pattern often seems arbitrary. We explore the performance of two genetic marker sampling strategies and the effect of marker quantity in a comparative phylogeographic framework focusing on six species (arthropods and plants). The same analyses were applied to data inferred from amplified fragment length polymorphism fingerprinting (AFLP), a cheap, non-HTS based technique that is able to straightforwardly produce several hundred markers, and from restriction site associated DNA sequencing (RADseq), a more expensive, HTS-based technique that produces thousands of single nucleotide polymorphisms. We show that in four of six study species, AFLP leads to results comparable with those of RADseq. While we do not aim to contest the advantages of HTS techniques, we also show that AFLP is a robust technique to delimit evolutionary entities in both plants and animals. The demonstrated similarity of results from the two techniques also strengthens biological conclusions that were based on AFLP data in the past, an important finding given the wide utilization of AFLP over the last decades. We emphasize that whenever the delimitation of evolutionary entities is the central goal, as it is in many fields of biodiversity research, AFLP is still an adequate technique.
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Affiliation(s)
- Philipp Kirschner
- grid.5771.40000 0001 2151 8122Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria ,grid.5771.40000 0001 2151 8122Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - Wolfgang Arthofer
- grid.5771.40000 0001 2151 8122Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Stefanie Pfeifenberger
- grid.5771.40000 0001 2151 8122Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Eliška Záveská
- grid.5771.40000 0001 2151 8122Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - Peter Schönswetter
- grid.5771.40000 0001 2151 8122Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | | | - Florian M. Steiner
- grid.5771.40000 0001 2151 8122Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Birgit C. Schlick-Steiner
- grid.5771.40000 0001 2151 8122Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
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8
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Conservation genetics of yellow-bellied toads (Bombina variegata): a matter of geographical scale and isolation. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01320-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AbstractAmphibian populations world-wide are threatened by declines and extinctions mainly due to habitat loss and fragmentation. Habitat fragmentation threatens the yellow-bellied toad Bombina variegata in the northern and western regions of its distribution where it is strictly protected. We studied the genetic structure and diversity of populations at three geographical scales using microsatellite loci to detect potential threats for population persistence. At the local scale, we sampled four neighbouring localities at 1–2.6 km distance to detect effects of short-term (decades) fragmentation on connectivity. At the regional scale, five additional localities in the mountains of the Westerwald (Rhineland-Palatinate, Germany) were studied at up to 50.1 km distance to analyse genetic diversity and population structure. At the continental scale, we included data from regions in the northern distribution with fragmented populations (Hesse and Lower Saxony, Germany) and more continuous populations in the South (Alsace, France; Geneva, Switzerland; Trentino, Italy) to evaluate variation of genetic diversity. At the local scale, short-term fragmentation caused significant genetic differentiation between breeding assemblages only 1.4 km apart from each other. At the regional scale, we found notable genetic distance among localities. At the continental scale, we identified Alsace, Trentino and Geneva in the South as regions with low genetic structuring and high allelic richness, and the northern remaining regions in Germany as deeply structured with reduced allelic richness. We suggest that reduced genetic diversity and habitat fragmentation in northern regions makes these populations particularly vulnerable to decline. In conclusion, informed conservation management of B. variegata should focus on measures maintaining or improving connectivity among neighbouring populations.
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9
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Ben Chehida Y, Thumloup J, Schumacher C, Harkins T, Aguilar A, Borrell A, Ferreira M, Rojas-Bracho L, Robertson KM, Taylor BL, Víkingsson GA, Weyna A, Romiguier J, Morin PA, Fontaine MC. Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum. Sci Rep 2020; 10:15190. [PMID: 32938978 PMCID: PMC7494866 DOI: 10.1038/s41598-020-71603-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 08/17/2020] [Indexed: 01/30/2023] Open
Abstract
Historical variation in food resources is expected to be a major driver of cetacean evolution, especially for the smallest species like porpoises. Despite major conservation issues among porpoise species (e.g., vaquita and finless), their evolutionary history remains understudied. Here, we reconstructed their evolutionary history across the speciation continuum. Phylogenetic analyses of 63 mitochondrial genomes suggest that porpoises radiated during the deep environmental changes of the Pliocene. However, all intra-specific subdivisions were shaped during the Quaternary glaciations. We observed analogous evolutionary patterns in both hemispheres associated with convergent evolution to coastal versus oceanic environments. This suggests that similar mechanisms are driving species diversification in northern (harbor and Dall's) and southern species (spectacled and Burmeister's). In contrast to previous studies, spectacled and Burmeister's porpoises shared a more recent common ancestor than with the vaquita that diverged from southern species during the Pliocene. The low genetic diversity observed in the vaquita carried signatures of a very low population size since the last 5,000 years. Cryptic lineages within Dall's, spectacled and Pacific harbor porpoises suggest a richer evolutionary history than previously suspected. These results provide a new perspective on the mechanisms driving diversification in porpoises and an evolutionary framework for their conservation.
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Affiliation(s)
- Yacine Ben Chehida
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands
| | - Julie Thumloup
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands
| | - Cassie Schumacher
- Swift Biosciences, 674 S. Wagner Rd., Suite 100, Ann Arbor, MI, 48103, USA
| | - Timothy Harkins
- Swift Biosciences, 674 S. Wagner Rd., Suite 100, Ann Arbor, MI, 48103, USA
| | - Alex Aguilar
- IRBIO and Department of Evolutive Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Diagonal 643, 08071, Barcelona, Spain
| | - Asunción Borrell
- IRBIO and Department of Evolutive Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Diagonal 643, 08071, Barcelona, Spain
| | - Marisa Ferreira
- MATB-Sociedade Portuguesa de Vida Selvagem, Estação de Campo de Quiaios, Apartado EC Quiaios, 3080-530, Figueira da Foz, Portugal.,CPRAM-Ecomare, Estrada Do Porto de Pesca Costeira, 3830-565, Gafanha da Nazaré, Portugal
| | - Lorenzo Rojas-Bracho
- Comisión Nacional de Áreas Naturales Protegidas (CONANP), C/o Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana 3918, Fraccionamiento Zona Playitas, 22860, Ensenada, BC, Mexico
| | - Kelly M Robertson
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla, CA, 92037, USA
| | - Barbara L Taylor
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla, CA, 92037, USA
| | - Gísli A Víkingsson
- Marine and Freshwater Research Institute, Fornubúðum 5, 220, Hafnarfjörður, Iceland
| | - Arthur Weyna
- Institut Des Sciences de L'Évolution (Université de Montpellier, CNRS UMR 5554), Montpellier, France
| | - Jonathan Romiguier
- Institut Des Sciences de L'Évolution (Université de Montpellier, CNRS UMR 5554), Montpellier, France
| | - Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla, CA, 92037, USA
| | - Michael C Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands. .,Laboratoire MIVEGEC (Université de Montpellier, CNRS 5290, IRD 229) et Centre de Recherche en Écologie et Évolution de la Santé (CREES), Institut de Recherche Pour Le Développement (IRD), 911 Avenue Agropolis, BP 64501, 34394, Montpellier Cedex 5, France.
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10
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Dufresnes C, Alard B. An odyssey out of Africa: an integrative review of past and present invasions by the Mediterranean tree frog (Hyla meridionalis). Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
An illustration of the human footprint on biodiversity are the faunal movements that have accompanied commercial and cultural exchanges between civilizations throughout history. In this article, we provide an integrative review of biogeographical and archaeological knowledge to understand these processes for the Mediterranean tree frog (Hyla meridionalis), an African species that has reached several regions of south-western Europe and associated islands. By re-analysing molecular (multilocus mitochondrial and genome-wide markers) and bioclimatic (ecological niche modelling) data, we give a comprehensive picture of the genetic diversity, structure and environmental suitability of H. meridionalis across its natural and exotic ranges, which in turn offer specific clues to the putative routes of colonization and associated events. Long-term monitoring efforts suggest northwards shifts of local range margins, potentially due to global warming, and we further demonstrate that this species is the most frequent amphibian to travel via the food supply chain in Western Europe. High dispersal ability, ecological tolerance and proximity to human settlements have made H. meridionalis a recurrent witness to the complexity and diversity of the civilizations that ruled the Western Mediterranean.
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Affiliation(s)
- Christophe Dufresnes
- LASER, College of Biology and the Environment, Nanjing Forestry University, Nanjing, People’s Republic of China
| | - Bérénice Alard
- CIBIO – Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
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11
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The effect of phylogeographic history on species boundaries: a comparative framework in Hyla tree frogs. Sci Rep 2020; 10:5502. [PMID: 32218506 PMCID: PMC7099067 DOI: 10.1038/s41598-020-62382-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 03/11/2020] [Indexed: 01/13/2023] Open
Abstract
Because it is indicative of reproductive isolation, the amount of genetic introgression across secondary contact zones is increasingly considered in species delimitation. However, patterns of admixture at range margins can be skewed by the regional dynamics of hybrid zones. In this context, we posit an important role for phylogeographic history: hybrid zones located within glacial refugia (putatively formed during the Late-Pleistocene) should be better defined than those located in post-glacial or introduced ranges (putatively formed during the Holocene and the Anthropocene). We test this hypothesis in a speciation continuum of tree frogs from the Western Palearctic (Hyla), featuring ten identified contacts between species spanning Plio-Pleistocene to Miocene divergences. We review the rich phylogeographic literature of this group and examine the overlooked transition between H. arborea and H. molleri in Western France using a multilocus dataset. Our comparative analysis supports a trend that contacts zones resulting from post-glacial expansions and human translocations feature more extensive introgression than those established within refugial areas. Integrating the biogeographic history of incipient species, i.e. their age since first contact together with their genetic divergence, thus appears timely to draw sound evolutionary and taxonomic inferences from patterns of introgression across hybrid zones.
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12
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Dufresnes C, Mazepa G, Jablonski D, Oliveira RC, Wenseleers T, Shabanov DA, Auer M, Ernst R, Koch C, Ramírez-Chaves HE, Mulder KP, Simonov E, Tiutenko A, Kryvokhyzha D, Wennekes PL, Zinenko OI, Korshunov OV, Al-Johany AM, Peregontsev EA, Masroor R, Betto-Colliard C, Denoël M, Borkin LJ, Skorinov DV, Pasynkova RA, Mazanaeva LF, Rosanov JM, Dubey S, Litvinchuk S. Fifteen shades of green: The evolution of Bufotes toads revisited. Mol Phylogenet Evol 2019; 141:106615. [DOI: 10.1016/j.ympev.2019.106615] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/14/2019] [Accepted: 09/10/2019] [Indexed: 01/01/2023]
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13
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Lu RS, Chen Y, Tamaki I, Sakaguchi S, Ding YQ, Takahashi D, Li P, Isaji Y, Chen J, Qiu YX. Pre-quaternary diversification and glacial demographic expansions of Cardiocrinum (Liliaceae) in temperate forest biomes of Sino-Japanese Floristic Region. Mol Phylogenet Evol 2019; 143:106693. [PMID: 31778814 DOI: 10.1016/j.ympev.2019.106693] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 11/11/2019] [Accepted: 11/22/2019] [Indexed: 11/27/2022]
Abstract
The Sino-Japanese Floristic Region (SJFR) in East Asia is one of the most diverse temperate floras in the world. However, the relative influence of Neogene palaeogeographical changes and Quaternary climatic fluctuations as causal mechanisms on species diversification remains largely controversial, because most divergence time estimates were inferred from single-locus data and have limited geographic or taxonomic sampling. To evaluate these influences, we use SNP markers from restriction site-associated DNA sequencing (RAD-Seq) loci and expressed sequence tags-simple sequence repeat (EST-SSR) markers to investigate the levels of genetic variation, speciation and demographic history of the temperate-deciduous forest (TDF) endemic Cardiocrinum (Endlicher) Lindley (Liliaceae), a genus comprising three species in China (C. giganteum, C. cathayanum) and Japan (C. cordatum). Phylogenomic and population genomic coalescent-based analyses demonstrated that Late Neogene tectonic/climatic events triggered speciation of Cardiocrinum, and Pleistocene climatic fluctuations had limited influence on its divergence history. Population demographic inference using Approximate Bayesian Computation from EST-SSRs and palaeoclimatic niche models both indicated that all three Cardiocrinum species experienced population expansions during the transition from the LIG to the LGM. We also discussed the implications of these results on the conservation of montane TDF species in the SJFR under ongoing environmental change. Our results improve our understanding of how the constituents of montane TDF across the SJFR responded to previous periods of rapid climate and environmental change in terms of speciation and population demographic processes.
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Affiliation(s)
- Rui-Sen Lu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yang Chen
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ichiro Tamaki
- Gifu Academy of Forest Science and Culture, 88 Sodai, Mino, Gifu 501-3714, Japan
| | - Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yan-Qian Ding
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Daiki Takahashi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Pan Li
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yuji Isaji
- Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Jun Chen
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ying-Xiong Qiu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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14
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Dufresnes C, Strachinis I, Suriadna N, Mykytynets G, Cogălniceanu D, Székely P, Vukov T, Arntzen JW, Wielstra B, Lymberakis P, Geffen E, Gafny S, Kumlutaş Y, Ilgaz Ç, Candan K, Mizsei E, Szabolcs M, Kolenda K, Smirnov N, Géniez P, Lukanov S, Crochet PA, Dubey S, Perrin N, Litvinchuk SN, Denoël M. Phylogeography of a cryptic speciation continuum in Eurasian spadefoot toads (Pelobates). Mol Ecol 2019; 28:3257-3270. [PMID: 31254307 DOI: 10.1111/mec.15133] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 03/30/2019] [Accepted: 05/17/2019] [Indexed: 12/15/2022]
Abstract
Cryptic phylogeographic diversifications provide unique models to examine the role of phylogenetic divergence on the evolution of reproductive isolation, without extrinsic factors such as ecological and behavioural differentiation. Yet, to date very few comparative studies have been attempted within such radiations. Here, we characterize a new speciation continuum in a group of widespread Eurasian amphibians, the Pelobates spadefoot toads, by conducting multilocus (restriction site associated DNA sequencing and mitochondrial DNA) phylogenetic, phylogeographic and hybrid zone analyses. Within the P. syriacus complex, we discovered species-level cryptic divergences (>5 million years ago [My]) between populations distributed in the Near-East (hereafter P. syriacus sensu stricto [s.s.]) and southeastern Europe (hereafter P. balcanicus), each featuring deep intraspecific lineages. Altogether, we could scale hybridizability to divergence time along six different stages, spanning from sympatry without gene flow (P. fuscus and P. balcanicus, >10 My), parapatry with highly restricted hybridization (P. balcanicus and P. syriacus s.s., >5 My), narrow hybrid zones (~15 km) consistent with partial reproductive isolation (P. fuscus and P. vespertinus, ~3 My), to extensive admixture between Pleistocene and refugial lineages (≤2 My). This full spectrum empirically supports a gradual build up of reproductive barriers through time, reversible up until a threshold that we estimate at ~3 My. Hence, cryptic phylogeographic lineages may fade away or become reproductively isolated species simply depending on the time they persist in allopatry, and without definite ecomorphological divergence.
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Affiliation(s)
- Christophe Dufresnes
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,Hintermann & Weber SA, Montreux, Switzerland.,Laboratory for Conservation Biology, University of Lausanne, Lausanne, Switzerland
| | - Ilias Strachinis
- School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Nataliia Suriadna
- Melitopol Insitute of Ecology and Social Technologies of University "Ukraine", Melitopol, Zaporizhia, Ukraine
| | | | - Dan Cogălniceanu
- Faculty of Natural Sciences and Agricultural Sciences, University Ovidius Constanţa, Constanţa, Romania
| | - Paul Székely
- Departamento de Ciencias Biológicas, EcoSs Lab, Universidad Técnica Particular de Loja, Loja, Ecuador
| | - Tanja Vukov
- Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković", National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Jan W Arntzen
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Ben Wielstra
- Naturalis Biodiversity Center, Leiden, The Netherlands.,Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Petros Lymberakis
- Natural History Museum of Crete, University of Crete, Irakleio, Crete, Greece
| | - Eli Geffen
- School of Zoology, Tel Aviv University, Tel Aviv, Israel
| | - Sarig Gafny
- School of Marine Sciences, Ruppin Academic Center, Michmoret, Israel
| | - Yusuf Kumlutaş
- Department of Biology, Faculty of Science, Dokuz Eylül University, Buca, İzmir, Turkey.,Research and Application Center for Fauna and Flora, Dokuz Eylül University, Buca, İzmir, Turkey
| | - Çetin Ilgaz
- Department of Biology, Faculty of Science, Dokuz Eylül University, Buca, İzmir, Turkey.,Research and Application Center for Fauna and Flora, Dokuz Eylül University, Buca, İzmir, Turkey
| | - Kamil Candan
- Department of Biology, Faculty of Science, Dokuz Eylül University, Buca, İzmir, Turkey.,Research and Application Center for Fauna and Flora, Dokuz Eylül University, Buca, İzmir, Turkey
| | - Edvárd Mizsei
- Department of Tisza River Research, Danube Research Institute, Centre for Ecological Research, Hungarian Academy of Sciences, Debrecen, Hungary
| | - Márton Szabolcs
- Department of Tisza River Research, Danube Research Institute, Centre for Ecological Research, Hungarian Academy of Sciences, Debrecen, Hungary
| | - Krzysztof Kolenda
- Department of Evolutionary Biology and Conservation of Vertebrates, Institute of Environmental Biology, University of Wrocław, Wrocław, Poland
| | - Nazar Smirnov
- Department of Nature, Chernivtsi Regional Museum, Chernivtsi, Ukraine
| | - Philippe Géniez
- CEFE, EPHE-PSL, CNRS, University of Montpellier, University Paul Valéry Montpellier 3, IRD, Montpellier, France
| | - Simeon Lukanov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Pierre-André Crochet
- CEFE, CNRS, University of Montpellier, University Paul Valéry Montpellier 3, EPHE, IRD, Montpellier, France
| | - Sylvain Dubey
- Hintermann & Weber SA, Montreux, Switzerland.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Agrosustain SA, Nyon, Switzerland
| | - Nicolas Perrin
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Spartak N Litvinchuk
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia.,Department of Zoology and Physiology, Dagestan State University, Makhachkala, Russia
| | - Mathieu Denoël
- Laboratory of Fish and Amphibian Ethology, Behavioural Biology Group, Freshwater and OCeanic science Unit of reSearch (FOCUS), University of Liège, Liège, Belgium
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15
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Drillon O, Dufresnes G, Perrin N, Crochet PA, Dufresnes C. Reaching the edge of the speciation continuum: hybridization between three sympatric species of Hyla tree frogs. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/bly198] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Olivier Drillon
- Agence Française pour la Biodiversité, Service Départemental de la Charente, Champniers, France
| | | | - Nicolas Perrin
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Pierre-André Crochet
- CEFE, CNRS, University of Montpellier, University Paul Valéry Montpellier, EPHE, IRD, Montpellier, France
| | - Christophe Dufresnes
- Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Sheffield, UK
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16
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Dufresnes C, Mazepa G, Rodrigues N, Brelsford A, Litvinchuk SN, Sermier R, Lavanchy G, Betto-Colliard C, Blaser O, Borzée A, Cavoto E, Fabre G, Ghali K, Grossen C, Horn A, Leuenberger J, Phillips BC, Saunders PA, Savary R, Maddalena T, Stöck M, Dubey S, Canestrelli D, Jeffries DL. Genomic Evidence for Cryptic Speciation in Tree Frogs From the Apennine Peninsula, With Description of Hyla perrini sp. nov. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00144] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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17
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Dufresnes C, Lymberakis P, Kornilios P, Savary R, Perrin N, Stöck M. Phylogeography of Aegean green toads (Bufo viridis subgroup): continental hybrid swarm vs. insular diversification with discovery of a new island endemic. BMC Evol Biol 2018; 18:67. [PMID: 29720079 PMCID: PMC5930823 DOI: 10.1186/s12862-018-1179-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 04/16/2018] [Indexed: 11/18/2022] Open
Abstract
Background Debated aspects in speciation research concern the amount of gene flow between incipient species under secondary contact and the modes by which post-zygotic isolation accumulates. Secondary contact zones of allopatric lineages, involving varying levels of divergence, provide natural settings for comparative studies, for which the Aegean (Eastern Mediterranean) geography offers unique scenarios. In Palearctic green toads (Bufo viridis subgroup or Bufotes), Plio-Pleistocene (~ 2.6 Mya) diverged species show a sharp transition without contemporary gene flow, while younger lineages, diverged in the Lower-Pleistocene (~ 1.9 Mya), admix over tens of kilometers. Here, we conducted a fine-scale multilocus phylogeographic analysis of continental and insular green toads from the Aegean, where a third pair of taxa, involving Mid-Pleistocene diverged (~ 1.5 Mya) mitochondrial lineages, earlier tentatively named viridis and variabilis, (co-)occurs. Results We discovered a new lineage, endemic to Naxos (Central Cyclades), while coastal islands and Crete feature weak genetic differentiation from the continent. In continental Greece, both lineages, viridis and variabilis, form a hybrid swarm, involving massive mitochondrial and nuclear admixture over hundreds of kilometers, without obvious selection against hybrids. Conclusions The genetic signatures of insular Aegean toads appear governed by bathymetry and Quaternary sea level changes, resulting in long-term isolation (Central Cyclades: Naxos) and recent land-bridges (coastal islands). Conversely, Crete has been isolated since the end of the Messinian salinity crisis (5.3 My) and Cretan populations thus likely result from human-mediated colonization, at least since Antiquity, from Peloponnese and Anatolia. Comparisons of green toad hybrid zones support the idea that post-zygotic hybrid incompatibilities accumulate gradually over the genome. In this radiation, only one million years of divergence separate a scenario of complete reproductive isolation, from a secondary contact resulting in near panmixia. Electronic supplementary material The online version of this article (10.1186/s12862-018-1179-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christophe Dufresnes
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland.,Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield, S10 2TN, UK
| | - Petros Lymberakis
- Natural History Museum of Crete, University of Crete, Knosos Av, P.O. Box 2208, 71409, Irakleio, Crete, Greece
| | - Panagiotis Kornilios
- Section of Animal Biology, Department of Biology, School of Natural Sciences, University of Patras, GR-26500, Patras, Greece.,Department of Biology, University of Washington, Box 351800, Seattle, WA, 98195-1800, USA
| | - Romain Savary
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland
| | - Nicolas Perrin
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, D-12587, Berlin, Germany.
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18
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Marchesini A, Ficetola GF, Cornetti L, Battisti A, Vernesi C. Fine-scale phylogeography of Rana temporaria (Anura: Ranidae) in a putative secondary contact zone in the southern Alps. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx114] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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19
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Rodrigues N, Dufresnes C. Using conventional F-statistics to study unconventional sex-chromosome differentiation. PeerJ 2017; 5:e3207. [PMID: 28462023 PMCID: PMC5410149 DOI: 10.7717/peerj.3207] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 03/20/2017] [Indexed: 01/23/2023] Open
Abstract
Species with undifferentiated sex chromosomes emerge as key organisms to understand the astonishing diversity of sex-determination systems. Whereas new genomic methods are widening opportunities to study these systems, the difficulty to separately characterize their X and Y homologous chromosomes poses limitations. Here we demonstrate that two simple F-statistics calculated from sex-linked genotypes, namely the genetic distance (Fst) between sexes and the inbreeding coefficient (Fis) in the heterogametic sex, can be used as reliable proxies to compare sex-chromosome differentiation between populations. We correlated these metrics using published microsatellite data from two frog species (Hyla arboreaand Rana temporaria), and show that they intimately relate to the overall amount of X–Y differentiation in populations. However, the fits for individual loci appear highly variable, suggesting that a dense genetic coverage will be needed for inferring fine-scale patterns of differentiation along sex-chromosomes. The applications of these F-statistics, which implies little sampling requirement, significantly facilitate population analyses of sex-chromosomes.
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Affiliation(s)
- Nicolas Rodrigues
- Department of Ecology & Evolution, University of Lausanne, Lausanne, Switzerland
| | - Christophe Dufresnes
- Department of Ecology & Evolution, University of Lausanne, Lausanne, Switzerland
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20
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Hu ZM, Li JJ, Sun ZM, Gao X, Yao JT, Choi HG, Endo H, Duan DL. Hidden diversity and phylogeographic history provide conservation insights for the edible seaweed Sargassum fusiforme in the Northwest Pacific. Evol Appl 2017; 10:366-378. [PMID: 28352296 PMCID: PMC5367075 DOI: 10.1111/eva.12455] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 12/13/2016] [Indexed: 02/03/2023] Open
Abstract
Understanding the evolutionary processes that have created diversity and the genetic potential of species to adapt to environmental change is an important premise for biodiversity conservation. Herein, we used mitochondrial trnW‐L and cox3 and plastid rbcL‐S data sets to analyze population genetic variation and phylogeographic history of the brown alga Sargassum fusiforme, whose natural resource has been largely exterminated in the Asia–Northwest Pacific in the past decades. Phylogenetic trees and network analysis consistently revealed three major haplotype groups (A, B, and C) in S. fusiforme, with A and B distributed in the Japan‐Pacific coast. Group C consisted of three subgroups (C1, C2, and C3) which were distributed in the Sea of Japan, the Yellow–Bohai Sea, and East China Sea, respectively. Isolation‐with‐migration (IMa) analysis revealed that the three groups diverged approximately during the mid‐Pleistocene (c. 756–1,224 ka). Extended Bayesian skyline plots (EBSP) showed that groups A and B underwent relatively long‐term stable population size despite a subsequent rapid demographic expansion, while subgroups C2 and C3 underwent a sudden expansion at c. 260 ka. FST and AMOVA detected low population‐level genetic variation and high degrees of divergence between groups. The cryptic diversity and phylogeographic patterns found in S. fusiforme not only are essential to understand how environmental shifts and evolutionary processes shaped diversity and distribution of coastal seaweeds but also provide additional insights for conserving and managing seaweed resources and facilitate predictions of their responses to future climate change and habitat loss.
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Affiliation(s)
- Zi-Min Hu
- Key Laboratory of Experimental Marine Biology Institute of Oceanology Chinese Academy of Sciences Qingdao China; Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology Qingdao China
| | - Jing-Jing Li
- Key Laboratory of Experimental Marine Biology Institute of Oceanology Chinese Academy of Sciences Qingdao China; Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology Qingdao China; College of Earth Science University of Chinese Academy of Sciences Beijing China; Present address: Institute of Marine Biology College of Oceanography Hohai University Nanjing 210098 China
| | - Zhong-Min Sun
- Laboratory of Marine Organism Taxonomy & Phylogeny Institute of Oceanology Chinese Academy of Sciences Qingdao China
| | - Xu Gao
- Research Centre for Inland Seas Kobe University Rokkodai Kobe Japan
| | - Jian-Ting Yao
- Key Laboratory of Experimental Marine Biology Institute of Oceanology Chinese Academy of Sciences Qingdao China; Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology Qingdao China
| | - Han-Gil Choi
- Faculty of Biological Science and Research Institute for Basic Science Wonkwang University Iksan Korea
| | - Hikaru Endo
- Faculty of Fisheries Kagoshima University Kagoshima Japan
| | - De-Lin Duan
- Key Laboratory of Experimental Marine Biology Institute of Oceanology Chinese Academy of Sciences Qingdao China; Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology Qingdao China
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21
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Jablonski D, Najbar B, Grochowalska R, Gvoždík V, Strzała T. Phylogeography and postglacial colonization of Central Europe by Anguis fragilis and Anguis colchica. AMPHIBIA-REPTILIA 2017. [DOI: 10.1163/15685381-00003133] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Five slow-worm species are distributed in the Palearctic region. Two species, Anguis fragilis and A. colchica, are native to Central Europe, where only limited information on the phylogeography of the genus exists. Here, we examined the situation in Poland and surrounding regions, where a mitochondrial contact zone between the species is expected. We used new mitochondrial DNA sequences and available published data from Central Europe and the northern Balkans. Haplotypes of both species were recorded in the study area. Anguis fragilis is represented by a single haplogroup, while A. colchica by three haplogroups. This suggests four independent sources/refugia for postglacial colonization of northern Central Europe. The mitochondrial contact zone seems to mirror the borders between lowlands of the North European Plain and East European Plain, and the south-eastern Poland uplands, while the Vistula River does not constitute a barrier. The presence of both species, A. fragilis and A. colchica, in Poland should also be considered for protection by the Polish conservation legislation.
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Affiliation(s)
- Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Bartłomiej Najbar
- Faculty of Biological Sciences, University of Zielona Góra, Prof. Z. Szafrana 1, 65-516 Zielona Góra, Poland
| | - Renata Grochowalska
- Department of Biochemistry and Bioinformatics, Faculty of Biological Sciences, University of Zielona Góra, Prof. Z. Szafrana 1, 65-001 Zielona Góra, Poland
| | - Václav Gvoždík
- Institute of Vertebrate Biology, Czech Academy of Sciences, 603 65 Brno, Czech Republic
- Department of Zoology, National Museum, 193 00 Prague, Czech Republic
| | - Tomasz Strzała
- Faculty of Biology and Animal Science, Department of Genetics, Wrocław University of Environmental and Life Sciences, Kożuchowska 7, 51-631 Wrocław, Poland
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22
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Cryptic invasion of Italian pool frogs (Pelophylax bergeri) across Western Europe unraveled by multilocus phylogeography. Biol Invasions 2016. [DOI: 10.1007/s10530-016-1359-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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23
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Dufresnes C, Litvinchuk SN, Borzée A, Jang Y, Li JT, Miura I, Perrin N, Stöck M. Phylogeography reveals an ancient cryptic radiation in East-Asian tree frogs (Hyla japonica group) and complex relationships between continental and island lineages. BMC Evol Biol 2016; 16:253. [PMID: 27884104 PMCID: PMC5121986 DOI: 10.1186/s12862-016-0814-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 10/28/2016] [Indexed: 11/21/2022] Open
Abstract
Background In contrast to the Western Palearctic and Nearctic biogeographic regions, the phylogeography of Eastern-Palearctic terrestrial vertebrates has received relatively little attention. In East Asia, tectonic events, along with Pleistocene climatic conditions, likely affected species distribution and diversity, especially through their impact on sea levels and the consequent opening and closing of land-bridges between Eurasia and the Japanese Archipelago. To better understand these effects, we sequenced mitochondrial and nuclear markers to determine phylogeographic patterns in East-Asian tree frogs, with a particular focus on the widespread H. japonica. Results We document several cryptic lineages within the currently recognized H. japonica populations, including two main clades of Late Miocene divergence (~5 Mya). One occurs on the northeastern Japanese Archipelago (Honshu and Hokkaido) and the Russian Far-East islands (Kunashir and Sakhalin), and the second one inhabits the remaining range, comprising southwestern Japan, the Korean Peninsula, Transiberian China, Russia and Mongolia. Each clade further features strong allopatric Plio-Pleistocene subdivisions (~2-3 Mya), especially among continental and southwestern Japanese tree frog populations. Combined with paleo-climate-based distribution models, the molecular data allowed the identification of Pleistocene glacial refugia and continental routes of postglacial recolonization. Phylogenetic reconstructions further supported genetic homogeneity between the Korean H. suweonensis and Chinese H. immaculata, suggesting the former to be a relic population of the latter that arose when the Yellow Sea formed, at the end of the last glaciation. Conclusions Patterns of divergence and diversity were likely triggered by Miocene tectonic activities and Quaternary climatic fluctuations (including glaciations), causing the formation and disappearance of land-bridges between the Japanese islands and the continent. Overall, this resulted in a ring-like diversification of H. japonica around the Sea of Japan. Our findings urge for important taxonomic revisions in East-Asian tree frogs. First, they support the synonymy of H. suweonensis (Kuramoto, 1980) and H. immaculata (Boettger, 1888). Second, the nominal H. japonica (Günther, 1859) represents at least two species: an eastern (new taxon A) on the northern Japanese and Russian Far East islands, and a southwestern species (n. t. B) on southern Japanese islands and possibly also forming continental populations. Third, these continental tree frogs may also represent an additional entity, previously described as H. stepheni Boulenger, 1888 (senior synonym of H. ussuriensis Nikolskii, 1918). A complete revision of this group requires further taxonomic and nomenclatural analyses, especially since it remains unclear to which taxon the species-epitheton japonica corresponds to. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0814-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christophe Dufresnes
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, 1015, Lausanne, Switzerland
| | - Spartak N Litvinchuk
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky pr. 4, 194064, St. Petersburg, Russia
| | - Amaël Borzée
- Laboratory of Behavioral Ecology and Evolution, School of Biological Sciences, Seoul National University, 151-747, Seoul, Republic of Korea.,Division of EcoScience, Ewha Womans University, Seoul, 120-750, Republic of Korea
| | - Yikweon Jang
- Division of EcoScience, Ewha Womans University, Seoul, 120-750, Republic of Korea
| | - Jia-Tang Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Ikuo Miura
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashihiroshima, 739-8526, Japan
| | - Nicolas Perrin
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, 1015, Lausanne, Switzerland
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, D-12587, Berlin, Germany. .,Visiting Research Fellow at the Graduate School of Science, Hiroshima University, Hiroshima, Japan.
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24
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Dufresnes C, Litvinchuk SN, Leuenberger J, Ghali K, Zinenko O, Stöck M, Perrin N. Evolutionary melting pots: a biodiversity hotspot shaped by ring diversifications around the Black Sea in the Eastern tree frog (Hyla orientalis). Mol Ecol 2016; 25:4285-300. [PMID: 27220555 DOI: 10.1111/mec.13706] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 04/26/2016] [Accepted: 05/11/2016] [Indexed: 11/30/2022]
Abstract
Hotspots of intraspecific genetic diversity, which are of primary importance for the conservation of species, have been associated with glacial refugia, that is areas where species survived the Quaternary climatic oscillations. However, the proximate mechanisms generating these hotspots remain an open issue. Hotspots may reflect the long-term persistence of large refugial populations; alternatively, they may result from allopatric differentiation between small and isolated populations, that later admixed. Here, we test these two scenarios in a widely distributed species of tree frog, Hyla orientalis, which inhabits Asia Minor and southeastern Europe. We apply a fine-scale phylogeographic survey, combining fast-evolving mitochondrial and nuclear markers, with a dense sampling throughout the range, as well as ecological niche modelling, to understand what shaped the genetic variation of this species. We documented an important diversity centre around the Black Sea, composed of multiple allopatric and/or parapatric diversifications, likely driven by a combination of Pleistocene climatic fluctuations and complex regional topography. Remarkably, this diversification forms a ring around the Black Sea, from the Caucasus through Anatolia and eastern Europe, with terminal forms coming into contact and partially admixing in Crimea. Our results support the view that glacial refugia generate rather than host genetic diversity and can also function as evolutionary melting pots of biodiversity. Moreover, we report a new case of ring diversification, triggered by a large, yet cohesive dispersal barrier, a very rare situation in nature. Finally, we emphasize the Black Sea region as an important centre of intraspecific diversity in the Palearctic with implications for conservation.
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Affiliation(s)
- Christophe Dufresnes
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, Lausanne, 1015, Switzerland
| | - Spartak N Litvinchuk
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky pr. 4, St. Petersburg, 194064, Russia
| | - Julien Leuenberger
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, Lausanne, 1015, Switzerland
| | - Karim Ghali
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, Lausanne, 1015, Switzerland
| | - Oleksandr Zinenko
- The Museum of Nature, V. N. Karazin Kharkiv National University, Trinkler st. 8, Kharkiv, 61058, Ukraine
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, Berlin, D-12587, Germany
| | - Nicolas Perrin
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, Lausanne, 1015, Switzerland
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Dowie NJ, Grubisha LC, Trowbridge SM, Klooster MR, Miller SL. Variability of ecological and autotrophic host specificity in a mycoheterotrophic system: Pterospora andromedea and associated fungal and conifer hosts. FUNGAL ECOL 2016. [DOI: 10.1016/j.funeco.2015.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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McCartney-Melstad E, Shaffer HB. Amphibian molecular ecology and how it has informed conservation. Mol Ecol 2015; 24:5084-109. [PMID: 26437125 DOI: 10.1111/mec.13391] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 09/15/2015] [Accepted: 09/16/2015] [Indexed: 02/02/2023]
Abstract
Molecular ecology has become one of the key tools in the modern conservationist's kit. Here we review three areas where molecular ecology has been applied to amphibian conservation: genes on landscapes, within-population processes, and genes that matter. We summarize relevant analytical methods, recent important studies from the amphibian literature, and conservation implications for each section. Finally, we include five in-depth examples of how molecular ecology has been successfully applied to specific amphibian systems.
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Affiliation(s)
- Evan McCartney-Melstad
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, 610 Charles E Young Drive South, Los Angeles, CA, USA
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, 610 Charles E Young Drive South, Los Angeles, CA, USA
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27
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Barrow LN, Bigelow AT, Phillips CA, Lemmon EM. Phylogeographic inference using Bayesian model comparison across a fragmented chorus frog species complex. Mol Ecol 2015; 24:4739-58. [DOI: 10.1111/mec.13343] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 07/24/2015] [Accepted: 08/08/2015] [Indexed: 01/17/2023]
Affiliation(s)
- Lisa N. Barrow
- Department of Biological Science Florida State University 319 Stadium Drive, P.O. Box 3064340 Tallahassee FL 32306‐4340 USA
| | - Alyssa T. Bigelow
- Department of Biological Science Florida State University 319 Stadium Drive, P.O. Box 3064340 Tallahassee FL 32306‐4340 USA
| | - Christopher A. Phillips
- Illinois Natural History Survey Prairie Research Institute University of Illinois 185 Natural Resources Bldg, 607 E. Peabody Drive Champaign IL 61820 USA
| | - Emily Moriarty Lemmon
- Department of Biological Science Florida State University 319 Stadium Drive, P.O. Box 3064340 Tallahassee FL 32306‐4340 USA
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Gonçalves H, Maia-Carvalho B, Sousa-Neves T, García-París M, Sequeira F, Ferrand N, Martínez-Solano I. Multilocus phylogeography of the common midwife toad, Alytes obstetricans (Anura, Alytidae): Contrasting patterns of lineage diversification and genetic structure in the Iberian refugium. Mol Phylogenet Evol 2015; 93:363-79. [PMID: 26282950 DOI: 10.1016/j.ympev.2015.08.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 08/07/2015] [Accepted: 08/07/2015] [Indexed: 10/23/2022]
Abstract
Recent investigations on the evolutionary history of the common midwife toad (Alytes obstetricans) revealed high levels of geographically structured genetic diversity but also a situation where delineation of major historical lineages and resolution of their relationships are much more complex than previously thought. We studied sequence variation in one mitochondrial and four nuclear genes throughout the entire distribution range of all recognized A. obstetricans subspecies to infer the evolutionary processes that shaped current patterns of genetic diversity and population subdivision. We found six divergent, geographically structured mtDNA haplogroups diagnosing population lineages, and varying levels of admixture in nuclear markers. Given the timeframe inferred for the splits between major lineages, the climatic and environmental changes that occurred during the Pleistocene seem to have shaped the diversification history of A. obstetricans. Survival of populations in allopatric refugia through the Ice Ages supports the generality of the "refugia-within-refugia" scenario for the Iberian Peninsula. However, lineages corresponding to subspecies A. o. almogavarii, A. o. pertinax, A. o. obstetricans, and A. o. boscai responded differently to Pleistocene climatic oscillations after diverging from a common ancestor. Alytes o. obstetricans expanded northward from a northern Iberian refugium through the western Pyrenees, leaving a signal of contrasting patterns of genetic diversity, with a single mtDNA haplotype north of the Pyrenees from SW France to Germany. Both A. o. pertinax and A. o. boscai are widespread and genetically diverse in Iberia, the latter comprising two divergent lineages with a long independent history. Finally, A. o. almogavarii is mostly restricted to the north-eastern corner of Iberia north of the Ebro river, with additional populations in a small region in south-eastern France. This taxon exhibits unparalleled levels of genetic diversity and little haplotype sharing with other lineages, suggesting a process of incipient speciation.
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Affiliation(s)
- H Gonçalves
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal.
| | - B Maia-Carvalho
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4099-002 Porto, Portugal
| | - T Sousa-Neves
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Museu Paraense Emílio Goeldi, Caixa Postal 399, Belém, PA 66040-170, Brazil
| | - M García-París
- Museo Nacional de Ciencias Naturales, MNCN-CSIC, c/José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - F Sequeira
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - N Ferrand
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4099-002 Porto, Portugal; Department of Zoology, University of Johannesburg, Johannesburg, South Africa
| | - I Martínez-Solano
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM), Ronda de Toledo, s/n, 13005 Ciudad Real, Spain; Ecology, Evolution and Development Group, Department of Wetland Ecology, Estación Biológica de Doñana (EBD-CSIC), Avenida Américo Vespucio, s/n, 41092 Sevilla, Spain
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Timeframe of speciation inferred from secondary contact zones in the European tree frog radiation (Hyla arborea group). BMC Evol Biol 2015; 15:155. [PMID: 26253600 PMCID: PMC4528686 DOI: 10.1186/s12862-015-0385-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 05/20/2015] [Indexed: 12/02/2022] Open
Abstract
Background Hybridization between incipient species is expected to become progressively limited as their genetic divergence increases and reproductive isolation proceeds. Amphibian radiations and their secondary contact zones are useful models to infer the timeframes of speciation, but empirical data from natural systems remains extremely scarce. Here we follow this approach in the European radiation of tree frogs (Hyla arborea group). We investigated a natural hybrid zone between two lineages (Hyla arborea and Hyla orientalis) of Mio-Pliocene divergence (~5 My) for comparison with other hybrid systems from this group. Results We found concordant geographic distributions of nuclear and mitochondrial gene pools, and replicated narrow transitions (~30 km) across two independent transects, indicating an advanced state of reproductive isolation and potential local barriers to dispersal. This result parallels the situation between H. arborea and H. intermedia, which share the same amount of divergence with H. orientalis. In contrast, younger lineages show much stronger admixture at secondary contacts. Conclusions Our findings corroborate the negative relationship between hybridizability and divergence time in European tree frogs, where 5 My are necessary to achieve almost complete reproductive isolation. Speciation seems to progress homogeneously in this radiation, and might thus be driven by gradual genome-wide changes rather than single speciation genes. However, the timescale differs greatly from that of other well-studied amphibians. General assumptions on the time necessary for speciation based on evidence from unrelated taxa may thus be unreliable. In contrast, comparative hybrid zone analyses within single radiations such as our case study are useful to appreciate the advance of speciation in space and time. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0385-2) contains supplementary material, which is available to authorized users.
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Dufresnes C, Perrin N. Effect of biogeographic history on population vulnerability in European amphibians. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2015; 29:1235-1241. [PMID: 25833793 DOI: 10.1111/cobi.12490] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 12/23/2014] [Indexed: 06/04/2023]
Abstract
The genetic diversity of populations, which contributes greatly to their adaptive potential, is negatively affected by anthropogenic habitat fragmentation and destruction. However, continental-scale losses of genetic diversity also resulted from the population expansions that followed the end of the last glaciation, an element that is rarely considered in a conservation context. We addressed this issue in a meta-analysis in which we compared the spatial patterns of vulnerability of 18 widespread European amphibians in light of phylogeographic histories (glacial refugia and postglacial routes) and anthropogenic disturbances. Conservation statuses significantly worsened with distances from refugia, particularly in the context of industrial agriculture; human population density also had a negative effect. These findings suggest that features associated with the loss of genetic diversity in post-glacial amphibian populations (such as enhanced fixation load or depressed adaptive potential) may increase their susceptibility to current threats (e.g., habitat fragmentation and pesticide use). We propose that the phylogeographic status of populations (i.e., refugial vs. post-glacial) should be considered in conservation assessments for regional and national red lists.
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Affiliation(s)
- Christophe Dufresnes
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, CH-1015, Lausanne, Switzerland
| | - Nicolas Perrin
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, CH-1015, Lausanne, Switzerland
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31
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Introgressive hybridization of threatened European tree frogs (Hyla arborea) by introduced H. intermedia in Western Switzerland. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0745-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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32
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Stoffel C, Dufresnes C, Okello JBA, Noirard C, Joly P, Nyakaana S, Muwanika VB, Alcala N, Vuilleumier S, Siegismund HR, Fumagalli L. Genetic consequences of population expansions and contractions in the common hippopotamus (Hippopotamus amphibius) since the Late Pleistocene. Mol Ecol 2015; 24:2507-20. [PMID: 25827243 DOI: 10.1111/mec.13179] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 03/11/2015] [Accepted: 03/18/2015] [Indexed: 11/30/2022]
Abstract
Over the past two decades, an increasing amount of phylogeographic work has substantially improved our understanding of African biogeography, in particular the role played by Pleistocene pluvial-drought cycles on terrestrial vertebrates. However, still little is known on the evolutionary history of semi-aquatic animals, which faced tremendous challenges imposed by unpredictable availability of water resources. In this study, we investigate the Late Pleistocene history of the common hippopotamus (Hippopotamus amphibius), using mitochondrial and nuclear DNA sequence variation and range-wide sampling. We documented a global demographic and spatial expansion approximately 0.1-0.3 Myr ago, most likely associated with an episode of massive drainage overflow. These events presumably enabled a historical continent-wide gene flow among hippopotamus populations, and hence, no clear continental-scale genetic structuring remains. Nevertheless, present-day hippopotamus populations are genetically disconnected, probably as a result of the mid-Holocene aridification and contemporary anthropogenic pressures. This unique pattern contrasts with the biogeographic paradigms established for savannah-adapted ungulate mammals and should be further investigated in other water-associated taxa. Our study has important consequences for the conservation of the hippo, an emblematic but threatened species that requires specific protection to curtail its long-term decline.
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Affiliation(s)
- Céline Stoffel
- Department of Ecology and Evolution, Laboratory for Conservation Biology, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland
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Speciation history and widespread introgression in the European short-call tree frogs (Hyla arborea sensu lato, H. intermedia and H. sarda). Mol Phylogenet Evol 2015; 83:143-55. [DOI: 10.1016/j.ympev.2014.11.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 11/10/2014] [Accepted: 11/22/2014] [Indexed: 11/21/2022]
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Dufresnes C, Brelsford A, Perrin N. First-generation linkage map for the European tree frog (Hyla arborea) with utility in congeneric species. BMC Res Notes 2014; 7:850. [PMID: 25430653 PMCID: PMC4258042 DOI: 10.1186/1756-0500-7-850] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 11/12/2014] [Indexed: 11/10/2022] Open
Abstract
Background Western Palearctic tree frogs (Hyla arborea group) represent a strong potential for evolutionary and conservation genetic research, so far underexploited due to limited molecular resources. New microsatellite markers have recently been developed for Hyla arborea, with high cross-species utility across the entire circum-Mediterranean radiation. Here we conduct sibship analyses to map available markers for use in future population genetic applications. Findings We characterized eight linkage groups, including one sex-linked, all showing drastically reduced recombination in males compared to females, as previously documented in this species. Mapping of the new 15 markers to the ~200 My diverged Xenopus tropicalis genome suggests a generally conserved synteny with only one confirmed major chromosome rearrangement. Conclusions The new microsatellites are representative of several chromosomes of H. arborea that are likely to be conserved across closely-related species. Our linkage map provides an important resource for genetic research in European Hylids, notably for studies of speciation, genome evolution and conservation. Electronic supplementary material The online version of this article (doi:10.1186/1756-0500-7-850) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christophe Dufresnes
- Department of Ecology and Evolution, Biophore building, University of Lausanne, 1015 Lausanne, Switzerland.
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Dufresnes C, Bertholet Y, Wassef J, Ghali K, Savary R, Pasteur B, Brelsford A, Rozenblut-Kościsty B, Ogielska M, Stöck M, Perrin N. Sex-chromosome differentiation parallels postglacial range expansion in European tree frogs (Hyla arborea). Evolution 2014; 68:3445-56. [PMID: 25209463 DOI: 10.1111/evo.12525] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 08/25/2014] [Indexed: 11/28/2022]
Abstract
Occasional XY recombination is a proposed explanation for the sex-chromosome homomorphy in European tree frogs. Numerous laboratory crosses, however, failed to detect any event of male recombination, and a detailed survey of NW-European Hyla arborea populations identified male-specific alleles at sex-linked loci, pointing to the absence of XY recombination in their recent history. Here, we address this paradox in a phylogeographic framework by genotyping sex-linked microsatellite markers in populations and sibships from the entire species range. Contrasting with postglacial populations of NW Europe, which display complete absence of XY recombination and strong sex-chromosome differentiation, refugial populations of the southern Balkans and Adriatic coast show limited XY recombination and large overlaps in allele frequencies. Geographically and historically intermediate populations of the Pannonian Basin show intermediate patterns of XY differentiation. Even in populations where X and Y occasionally recombine, the genetic diversity of Y haplotypes is reduced below the levels expected from the fourfold drop in copy numbers. This study is the first in which X and Y haplotypes could be phased over the distribution range in a species with homomorphic sex chromosomes; it shows that XY-recombination patterns may differ strikingly between conspecific populations, and that recombination arrest may evolve rapidly (<5000 generations).
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Affiliation(s)
- Christophe Dufresnes
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015, Lausanne
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Dufresnes C, Stöck M, Brelsford A, Perrin N. Range-wide sex-chromosome sequence similarity supports occasional XY recombination in European tree frogs (Hyla arborea). PLoS One 2014; 9:e97959. [PMID: 24892652 PMCID: PMC4043726 DOI: 10.1371/journal.pone.0097959] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 04/27/2014] [Indexed: 11/18/2022] Open
Abstract
In contrast with mammals and birds, most poikilothermic vertebrates feature structurally undifferentiated sex chromosomes, which may result either from frequent turnovers, or from occasional events of XY recombination. The latter mechanism was recently suggested to be responsible for sex-chromosome homomorphy in European tree frogs (Hyla arborea). However, no single case of male recombination has been identified in large-scale laboratory crosses, and populations from NW Europe consistently display sex-specific allelic frequencies with male-diagnostic alleles, suggesting the absence of recombination in their recent history. To address this apparent paradox, we extended the phylogeographic scope of investigations, by analyzing the sequences of three sex-linked markers throughout the whole species distribution. Refugial populations (southern Balkans and Adriatic coast) show a mix of X and Y alleles in haplotypic networks, and no more within-individual pairwise nucleotide differences in males than in females, testifying to recurrent XY recombination. In contrast, populations of NW Europe, which originated from a recent postglacial expansion, show a clear pattern of XY differentiation; the X and Y gametologs of the sex-linked gene Med15 present different alleles, likely fixed by drift on the front wave of expansions, and kept differentiated since. Our results support the view that sex-chromosome homomorphy in H. arborea is maintained by occasional or historical events of recombination; whether the frequency of these events indeed differs between populations remains to be clarified.
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Affiliation(s)
- Christophe Dufresnes
- Department of Ecology and evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
- * E-mail:
| | - Alan Brelsford
- Department of Ecology and evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
| | - Nicolas Perrin
- Department of Ecology and evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
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Dufresnes C, Brelsford A, Béziers P, Perrin N. Stronger transferability but lower variability in transcriptomic- than in anonymous microsatellites: evidence from Hylid frogs. Mol Ecol Resour 2014; 14:716-25. [PMID: 24345298 DOI: 10.1111/1755-0998.12215] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 12/03/2013] [Accepted: 12/11/2013] [Indexed: 11/28/2022]
Abstract
A simple way to quickly optimize microsatellites in nonmodel organisms is to reuse loci available in closely related taxa; however, this approach can be limited by the stochastic and low cross-amplification success experienced in some groups (e.g. amphibians). An efficient alternative is to develop loci from transcriptome sequences. Transcriptomic microsatellites have been found to vary in their levels of cross-species amplification and variability, but this has to date never been tested in amphibians. Here, we compare the patterns of cross-amplification and levels of polymorphism of 18 published anonymous microsatellites isolated from genomic DNA vs. 17 loci derived from a transcriptome, across nine species of tree frogs (Hyla arborea and Hyla cinerea group). We established a clear negative relationship between divergence time and amplification success, which was much steeper for anonymous than transcriptomic markers, with half-lives (time at which 50% of the markers still amplify) of 1.1 and 37 My, respectively. Transcriptomic markers are significantly less polymorphic than anonymous loci, but remain variable across diverged taxa. We conclude that the exploitation of amphibian transcriptomes for developing microsatellites seems an optimal approach for multispecies surveys (e.g. analyses of hybrid zones, comparative linkage mapping), whereas anonymous microsatellites may be more informative for fine-scale analyses of intraspecific variation. Moreover, our results confirm the pattern that microsatellite cross-amplification is greatly variable among amphibians and should be assessed independently within target lineages. Finally, we provide a bank of microsatellites for Palaearctic tree frogs (so far only available for H. arborea), which will be useful for conservation and evolutionary studies in this radiation.
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Affiliation(s)
- Christophe Dufresnes
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, Lausanne , 1015, Switzerland
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