Christophe Dufresnes

École Pratique des Hautes Études

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Nicolas Perrin

Haute École Pédagogique du Canton de Vaud

Sylvain Dubey

University of Lausanne

Spartak N. Litvinchuk

Institute of Cytology

Pierre‐André Crochet

Centre d'Écologie Fonctionnelle et Évolutive

Matthias Stöck

Leibniz Institute of Freshwater Ecology and Inland Fisheries

ÍM

Íñigo Martínez‐Solano

Museo Nacional de Ciencias Naturales

Daniel Jablonski

Comenius University Bratislava

Alan Brelsford

University of California, Riverside

Johanna Ambu

Nanjing Forestry University

Miguel Vences

Technische Universität Braunschweig

Cooperative Institutions

Centre National de la Recherche Scientifique

104

University of Lausanne

Natural History Museum

American Museum of Natural History

École Pratique des Hautes Études

Consejo Superior de Investigaciones Científicas

Chinese Academy of Sciences

Real Jardín Botánico

Naturalis Biodiversity Center

Université de Montpellier

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Incognito in Ticino : a novel species of lizard for the swiss herpetofauna

Christophe Dufresnes Johanna Ambu Marco Nembrini Sylvain Dubey

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Using conventionalF-statistics to study unconventional sex-chromosome differentiation

PeerJ (2017)

Nicolas Rodrigues Christophe Dufresnes

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.

Heterogametic sex

Sexual Differentiation

10.7717/peerj.3207

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Citations (9)

Diversification and speciation in tree frogs from the Maghreb (Hyla meridionalis sensu lato), with description of a new African endemic

Molecular Phylogenetics and Evolution (2019)

Christophe Dufresnes Menad Beddek Dmitriy V. Skorinov Luca Fumagalli Nicolas Perrin

Sensu

Endemism

Introgression

Coalescent theory

10.1016/j.ympev.2019.02.009

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Citations (15)

Reaching the edge of the speciation continuum: hybridization between three sympatric species ofHylatree frogs

Biological Journal of the Linnean Society (2019)

Olivier Drillon Guillaume Dufresnes Nicolas Perrin Pierre‐André Crochet Christophe Dufresnes

Alloparapatric species meeting in secondary contact zones are evolutionary witnesses to how reproductive isolation progresses over time and space. Western Palearctic tree frogs of the genus Hyla are phenotypically similar and all the species pairs tested can hybridize and eventually admix at range margins, except one. The early-diverged Hyla meridionalis shows distinct phenotypic differences: a 'long' breeding call and the absence of a lateral stripe. In south-western Europe, this species co-occurs with the 'short-call' striped tree frogs H. arborea and H. molleri, two expanding lineages that admix at their parapatric margins. We estimated local gene flow between these three taxa at several syntopic breeding sites in western France. We congruently matched genotypes to phenotypes: the 'short-call' striped individuals were a nuclear mixture of H. arborea and H. molleri; the 'long-call' stripeless individuals all featured pure H. meridionalis nuclear ancestry and mitochondrial DNA, confirming complete genetic isolation from H. arborea/molleri. Yet, we documented an F1 hybrid between a female H. arborea/molleri and a male H. meridionalis: an incompletely striped male with an intermediate breeding call. These findings suggest H. meridionalis is still able to reproduce with parapatric congeners despite 20 Myr of divergence and strong phenotypic differentiation, but that intrinsic incompatibilities (sterility) prevent genetic introgression.

Parapatric speciation

Reproductive isolation

Introgression

Hybrid zone

Hyla

10.1093/biolinnean/bly198

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Citations (18)

Phylogeography of Aegean green toads (Bufo viridis subgroup): continental hybrid swarm vs. insular diversification with discovery of a new island endemic

BMC Evolutionary Biology (2018)

Christophe Dufresnes Petros Lymberakis Panagiotis Kornilios Romain Savary Nicolas Perrin

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.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.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.

Endemism

Entomology

10.1186/s12862-018-1179-0

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Citations (23)

Shedding light on taxonomic chaos: Diversity and distribution of South Asian skipper frogs (Anura, Dicroglossidae, Euphlyctis)

Figshare (2022)

Christophe Dufresnes Stephen Mahony Vishal Kumar Prasad Rachunliu G. Kamei Rafaqat Masroor

A known haven of amphibian diversity, South Asia is also a hotspot of taxonomic confusions. Vastly distributed from Saudi Arabia to Myanmar, the dicroglossid genus Euphlyctis (“skittering” or “skipper” frogs) is a representative example. Combining phylogenetic analyses with 16S barcoding and genome size variation of 403 frogs from 136 localities, we examined genetic diversity and distributions across the whole range of Euphlyctis, with a particular focus on taxonomic and nomenclatural issues. We recovered two deeply divergent mitochondrial clades totalling ten lineages that we considered as species, and eight could be attributed valid taxonomic names and junior synonyms. The first clade (subgenus Phrynoderma) is confirmed in South India, Bangladesh and Sri Lanka, and comprises six species: E. karaavali, E. hexadactyla, E. aloysii, E. kerala and two undescribed taxa. Five are endemic to the Western Ghats biodiversity hotspot and four of them form the E. aloysii species complex. The second clade (subgenus Euphlyctis) extends across South Asia and neighbouring regions, and comprises four species: E. ehrenbergii, E. jaladhara, and two widespread lineages erroneously called “E. mudigere” and “E. kalasgramensis” in recent literature, while their oldest valid names appear to be E. cyanophlyctis and E. adolfi, respectively. Additional analyses on this pair of taxa highlighted strong phenotypic resemblance, notable intraspecific phylogeographic structure, and an extensive contact zone along the southern slopes of the Himalaya, with putative signs of genetic introgression. Through an independent investigation of the historical literature, we identified overlooked issues and misconceptions regarding the status of many old and recent taxa, and proposed solutions, such as transferring “E. ghoshi” to the genus Limnonectes. Our study illustrates how range-wide genetic barcoding can clarify taxonomic confusions, and we call to solve remaining issues prior to the description of new taxa.

10.6084/m9.figshare.20731674

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Howling from the past: historical phylogeography and diversity losses in European grey wolves

Proceedings of the Royal Society B Biological Sciences (2018)

Christophe Dufresnes Christian Miquel Nadège Remollino François Biollaz Nicolas Salamin

Genetic bottlenecks resulting from human-induced population declines make alarming symbols for the irreversible loss of our natural legacy worldwide. The grey wolf (Canis lupus) is an iconic example of extreme declines driven by anthropogenic factors. Here, we assessed the genetic signatures of 150 years of wolf persecution throughout the Western Palaearctic by high-throughput mitochondrial DNA sequencing of historical specimens in an unprecedented spatio-temporal framework. Despite Late Pleistocene bottlenecks, we show that historical genetic variation had remained high throughout Europe until the last several hundred years. In Western Europe, where wolves nearly got fully exterminated, diversity dramatically collapsed at the turn of the twentieth century and recolonization from few homogeneous relict populations induced drastic shifts of genetic composition. By contrast, little genetic displacement and steady levels of diversity were maintained in Eastern European regions, where human persecution had lesser effects on wolf demography. By comparing prehistoric, historic and modern patterns of genetic diversity, our study hence traces the timeframe and the active human role in the decline of the grey wolf, an emblematic yet controversial animal which symbolizes the complex relationship between human societies and nature conservation.

Ancient DNA

Gray wolf

Demographic history

10.1098/rspb.2018.1148

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Citations (48)

An extinct vertebrate preserved by its living hybridogenetic descendant

Scientific Reports (2017)

Sylvain Dubey Christophe Dufresnes

Abstract Hybridogenesis is a special mode of hybrid reproduction where one parental genome is eliminated and the other is transmitted clonally. We propose that this mechanism can perpetuate the genome of extinct species, based on new genetic data from Pelophylax water frogs. We characterized the genetic makeup of Italian hybridogenetic hybrids ( P . kl. hispanicus and esculentus ) and identified a new endemic lineage of Eastern-Mediterranean origin as one parental ancestor of P . kl. hispanicus . This taxon is nowadays extinct in the wild but its germline subsists through its hybridogenetic descendant, which can thus be considered as a “semi living fossil”. Such rare situation calls for realistic efforts of de-extinction through selective breeding without genetic engineering, and fuels the topical controversy of reviving long extinct species. “Ghost” species hidden by taxa of hybrid origin may be more frequent than suspected in vertebrate groups that experienced a strong history of hybridization and semi-sexual reproduction.

Extinction (optical mineralogy)

Descendant

Lineage (genetic)

10.1038/s41598-017-12942-y

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Low neutral and immunogenetic diversity in northern fringe populations of the green toad Bufotes viridis: implications for conservation

Conservation Genetics (2021)

‎Jacob Höglund Lucas Bolender María Cortázar-Chinarro Sara Meurling Anssi Laurila

Abstract Genetic variation is often lower at high latitudes, which may compromise the adaptability and hence survival of organisms. Here we show that genetic variability is negatively correlated with northern latitude in European green toads ( Bufotes viridis ). The result holds true for both putatively neutral microsatellite variation and supposedly adaptive MHC Class IIB variation. In particular, our findings have bearing on the conservation status of this species in Sweden, on the northern limit of its distribution where local populations are small and fragmented. These genetically impoverished populations are closely related to other populations found around the Baltic Sea basin. The low neutral and adaptive variation in these fringe populations compared to population at central ranges confirms a pattern shared across all other amphibians so far studied. In Sweden, the situation of green toads is of concern as the remaining populations may not have the evolutionary potential to cope with present and future environmental challenges.

Adaptability

10.1007/s10592-021-01407-5

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Integrating hybrid zone analyses in species delimitation: lessons from two anuran radiations of the Western Mediterranean

Heredity (2020)

Christophe Dufresnes Manon Pribille Bérénice Alard Helena Gonçalves Fèlix Amat

Introgression

Coalescent theory

Reproductive isolation

Hybrid zone

Phylogenomics

Genetic algorithm

10.1038/s41437-020-0294-z

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Citations (62)