Christophe Dufresnes

Verified

Christophe verified their affiliation via an institutional email.

Learn more

Verified

Christophe verified their affiliation via an institutional email.

Learn more

• PhD
• Associate Professor (Maître de Conférences) / Curator of Amphibians at Muséum National d'Histoire Naturelle

Characterizing the diversity and lability of the amphibian sex chromosomes holds key to understand what drives sex chromosome turnovers and assess the role of sex-linked genes in reproductive isolation and speciation. Here we show that the heterogametic transition previously reported between the hybridizing toads Bufo bufo (ZW) and B. spinosus (XY)...

The biodiversity of the Himalaya remains significantly understudied and, at the same time, is increasingly threatened by habitat loss due to rising anthropogenic pressures and climate change. Lazy Toads of the genus Scutiger are endemic to the Himalaya-Tibet orogen and form a diverse and characteristic component of the Himalayan montane zone. In ou...

While some biological invasions are well documented globally, others, more cryptic, are often underestimated despite multiple local warnings. This is the case of the marsh frog (Pelophylax ridibundus sensu lato), a Palearctic anuran amphibian distribured from Western Europe to Central Asia. Marsh frogs have been introduced into many European countr...

Speciation, i.e., the formation of new species, implies that diverging populations evolve genetic, phenotypic or ecological factors that promote reproductive isolation (RI), but the relative contributions of these factors remain elusive. Here we test which of genomic, bioacoustic, morphological, and environmental differences best predicts RI across...

la Stratégie nationale de gestion des amphibiens exotiques envahissants (SNG AEE) dont la rédaction, grâce à l’implication de nombreux experts, et coordonnée par la SHF, se concentre sur des problématiques émergentes connues en France hexagonale et concerne les quatre espèces les plus préoccupantes actuellement présentes sur ce territoire : la Gren...

The frog leg industry relies on a global, largely underregulated market with potentially important ecological impact such as the uncontrolled harvest of declining wild populations and the introduction of invasive species. Here, we inferred the taxonomic nature and geographic origins of frog legs imported to Switzerland by DNA barcoding. Out of 34 s...

Proper taxonomic and phylogeographic frameworks are a prerequisite in evolutionary, ecological, and conservation research, but many species still lack adequate assessments. Earlier studies on the northeast Asian treefrog, Dryophytes japonicus, identified a deep Mio-Pliocene diversification; however, phenotypic assessments were lacking, and the taxo...

Assessing how genetic diversity is spatially structured underlies many research questions in evolutionary ecology and contributes to understanding the factors implicated in population declines and extirpations, facilitating identification of conservation priorities and decision-making. In this study, we surveyed genomic diversity using genotyping b...

Syria has a broad range of natural landscapes, including mountains, forests, rivers, lakes, and arid landscapes that promoted the diversification of its amphibian fauna. Syrian amphibians presently consist of eight species belonging to five families. To map their occurrence, we reviewed available literature supplemented by new data obtained from ou...

The Balkan Peninsula hosts a great proportion of Europe’s biodiversity, and this is well illustrated by amphibian richness and endemism. Among them, the yellow-bellied toad Bombina variegata has been a model in ecology and evolution, but several aspects of its phylogeography and taxonomy remain surprisingly poorly understood. In this study, we comb...

Animal translocations provide striking examples of the human footprint on biodiversity. Combining continental-wide genomic and DNA-barcoding analyses, we reconstructed the historical biogeography of the Asian black-spined toad (Duttaphrynus melanostictus), a toxic commensal amphibian that currently threatens two biodiversity hotspots through biolog...

Snake-eyed, or ablepharine skinks, are common residents of the highest mountain ranges on Earth, including the Himalayas, the Tibetan Plateau, Karakoram, Pamir, and Tian Shan, colloquially known as the Roof of the World. Historically, these skinks were alternatively assigned to the genera Scincella, Ablepharus, Asymblepharus, and Hi-malblepharus, b...

Despite increased attention by molecular taxonomists, the herpetofauna of Southeast Asia still hides many undescribed species among far-ranging taxa. In this study, we reexamine the mitochondrial diversity of painted frogs of the microhylid genus Kaloula, based on ~2,455 bp of published and new 12S and 16S rRNA sequences, and describe two new speci...

Hybrid zones, i.e., geographic areas where diverging lineages meet, hybridize and eventually mix their genomes, offer opportunities to understand the mechanisms behind reproductive isolation and speciation. Hybrid zones are particularly well suited to study reinforcement, i.e., the process by which selection against hybridization increases reproduc...

Using molecular (mitochondrial DNA, multilocus genomic loci) and phenotypic (morphology, coloration, osteology) analyses, we reveal a new cryptic species of crocodile newt of the Tylototriton asperrimus species group from Viet Bac Mountain Range, northern Vietnam. The new species was previously confounded with T. asperrimus, T. vietnamensis and mor...

Speciation, i.e., the formation of new species, implies that diverging populations evolve genetic and phenotypic factors that promote reproductive isolation (RI), but the adaptive vs. neutral origin of these factors and their relative contributions across the speciation continuum remain elusive. Here we test which of genomic, bioacoustic, morpholog...

Berdmore’s narrow-mouthed frog, Microhyla berdmorei (Blyth, 1856), is the largest member of the genus Microhyla and is distributed all over Southeast Asia, from Northeast India and southern China to Sumatra and Borneo in Indonesia. Here we demonstrate that M. berdmorei represents a complex of four species that are morphologically, acoustically, and...

Interspecific introgression is a potentially important source of novel variation of adaptive significance. Although multiple cases of adaptive introgression are well documented, broader generalizations about its targets and mechanisms are lacking. Multi-allelic balancing selection, particularly when acting through rare allele advantage, is an evolu...

A recent revision of the anacondas (Serpentes: Boidae: Eunectes), with the description of a new species of green anaconda, generated extensive publicity, but also provoked considerable controversy due to inadequacies of the evidence used and errors in nomenclature. We here use the case of this problematic publication to: (i) highlight common issues...

Despite decades of molecular research, phylogenetic relationships in Palearctic vipers (genus Vipera) still essentially rely on a few loci, such as mitochondrial barcoding genes. Here we examined the diversity and evolution of Vipera with ddRAD-seq data from 33 representative species and subspecies. Phylogenomic analyses of ∼ 1.1 Mb recovered nine...

The chytrid Batrachochytrium dendrobatidis (Bd) is a widespread fungus causing amphibian declines across the globe. Although data on Bd occurrence in Eastern Europe are scarce, a recent species distribution model (SDM) for Bd reported that western and north-western parts of Ukraine are highly suitable to the pathogen. We verified the SDM-predicted...

The fundamental value of universal nomenclatural systems in biology is that they enable unambiguous scientific communication. However, the stability of these systems is threatened by recent discussions asking for a fairer nomenclature, raising the possibility of bulk revision processes for "inappropriate" names. It is evident that such proposals co...

The plant-trade is among the main sources of accidental introduction of alien biodiversity. This includes amphibians, although effective colonization pathways have rarely been reported except from tropical areas. We document the discovery of an established breeding population of the Catalonian midwife toad, Alytes almogavarii almogavarii Arntzen an...

List of the 1543 additional coauthors. Co-authors who contributed revising translations are listed first. Then, the rest of the coauthors are listed according alphabetic order of countries/territories.

MtDNA barcoding is regularly applied to determine the provenance of invasive species. Variation in spatial genetic structuring across a species’ range, typically high within glacial refugia and low in postglacially colonized areas, influences the precision of this approach. The palmate newt (Lissotriton helveticus) has been introduced north of its...

Traditional methods of phylogenetic reconstruction and species delimitation may be impeded by frequent hybridization among lineages. In this study, we conducted phylogenetic and clustering analyses of ddRAD genomic data on the entire genus Salamandra, which includes six species and over 25 subspecies of terrestrial salamanders. We expanded previous...

The mapping, delimiting and naming of biodiversity forge the links between academic research, conservation efforts and communication about wildlife. Midwife toads from the subgenus Alytes are a group of high conservation concern widely popular among European naturalists, but for which the taxonomy remains unsettled. Six phylogeographic lineages tha...

The evolution of several orthopteran groups, especially within the grasshopper family Acrididae, remains poorly understood. This is particularly true for the subfamily Gomphocerinae, which comprises cryptic sympatric and syntopic species. Previous mitochondrial studies have highlighted major discrepancies between taxonomic and phylogenetic hypothes...

Water frogs (genus Pelophylax) are one of the most widespread and diverse, but also most invasive amphibians of the Western Palearctic region. As such, Pelophylax studies face the challenge of identifying similar taxa that hybridize in sympatry. For this purpose, the nuclear marker serum albumin intron 1 (SAI-1) has been used for over a decade in P...

Palearctic water frogs (genus Pelophylax) are an outstanding model in ecology and evolution, being widespread, speciose, either threatened or threatening to other species through biological invasions, and capable of siring hybrid offspring that escape the rules of sexual reproduction. Despite half a century of genetic research and hundreds of publi...

Botanical and zoological nomenclatures provide some of the most stable pillars of modern science. These pillars are now being shaken by the proliferation of ideological concerns against eponymous taxa over ethical grounds. This includes thousands of amphibian species named after a person. We protest against recent initiatives aiming to subjectively...

European marbled newts come in two species that have abutting ranges. The northern species, Triturus marmoratus, is found in France and the northern part of the Iberian Peninsula, whereas the southern species, T. pygmaeus, is found in the southwestern corner of the Iberian Peninsula. We study the intraspecific genetic differentiation of the group b...

An accurate species‐level taxonomy is paramount for biogeographical research, and conversely, biogeographical data are of importance for species delimitation. We here review recent developments and future perspectives of taxonomy of direct relevance for biogeographers. The understanding that species are independently evolving segments of population...

Uncertainties on species taxonomy and distribution are major factors hampering efficient conservation planning in the current context of biodiversity erosion, even concerning widespread and abundant species in relatively well-studied regions. Species delimitation have long been based on phylogenetic analyses of a small number of standard markers, b...

The rich genetic and phenotypic diversity of species complexes is best recognized through formal taxonomic naming, but one must first assess the evolutionary history of phylogeographic lineages to identify and delimit candidate taxa. Using genomic markers, mitochondrial DNA barcoding and morphometric analyses, we examined lineage diversity and dist...

Delimiting and naming biodiversity is a vital step toward wildlife conservation and research. However, species delimitation must be consistent across biota so that the limited resources available for nature protection can be spent effectively and objectively. To date, newly discovered lineages typically are either left undescribed and thus remain u...

Many herpetofauna species have been introduced outside of their native range. MtDNA barcoding is regularly used to determine the provenance of such populations. The alpine newt has been introduced across the Netherlands, the United Kingdom and Ireland. However, geographical mtDNA structure across the natural range of the alpine newt is still incomp...

The advent of genomic methods allows us to revisit the evolutionary history of organismal groups for which robust phylogenies are still lacking, particularly in species complexes that frequently hybridize. In this study, we conduct RAD-sequencing (RAD-seq) analyses of midwife toads (genus Alytes), an iconic group of western Mediterranean amphibians...

Conservation genetics must find the balance between the technical challenges of DNA sampling while promoting animal welfare. In amphibians, buccal swabs offer a least intrusive source of DNA, but most herpetologists still refrain to use them, partly due to doubts regarding their effectiveness to provide enough material now that next-generation sequ...

Restriction site-Associated DNA sequencing (RADseq) has great potential for genome-wide systematics studies of non-model organisms. However, accurately assembling RADseq reads into orthologous loci remains a major challenge in the absence of a reference genome. Traditional assembly pipelines cluster putative orthologous sequences based on a user-de...

Crocodile newts (genera Echinotriton and Tylototriton) symbolize the outstanding biodiversity of Southeast Asia. In this study, we provide an exhaustive account of their evolution and diversity with an extensive phylogeography based on unprecedented mitochondrial (16.2kb) and nuclear sequence (3.2kb) alignments, combining barcoding information from...

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 hu...

Species that are threatened in their native range may actually prosper as introduced populations. To investigate how such introduced populations were established involves determining from where within the natural range the founder individuals originated. This can be accomplished through mtDNA barcoding. The common spadefoot toad (Pelobates fuscus)...

With five currently recognized species that form several secondary contact zones, slow worms (Anguidae: Anguis) offer a valuable model to study the fate of evolutionary lineages in the face of hybridization and genetic introgression. The relationships between the Western Slow Worm Anguis fragilis and the Italian Slow Worm Anguis veronensis are part...

Despite their paramount importance in molecular ecology and conservation, genetic diversity and structure remain challenging to quantify with traditional genotyping methods. Next-generation sequencing holds great promises, but this has not been properly tested in highly mobile species. In this article, we compared microsatellite and RAD-sequencing...

Linnaean and Wallacean shortfalls (Uncertainties on species taxonomy and distribution, respectively) are major factors hampering efficient conservation planning in the current context of biodiversity erosion. These shortfalls concern even widespread and abundant species in relatively well-studied regions such as the Mediterranean biodiversity hotsp...

Amphibians feature the highest rates of both new species discoveries and species declines among vertebrates worldwide. To characterize this diversity faster than it disappears, zoologists have been using molecular data to rapidly describe new frog and salamander lineages, from species to family levels. About a third of the approximately 8500 known...

Spatial overview of the levels of diversity and threats for the herpetofauna of France and neighboring countries - Exploiting recent advances in phylogeography, taxonomy, distribution and conservation, fine-scale levels of species diversity, as well as regional proportions of threatened species, were compiled for the amphibians and reptiles of Fran...

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, w...

Biodiversity analyses can greatly benefit from coherent species delimitation schemes and up-to-date distribution data. In this article, we have made the daring attempt to delimit and map described and undescribed lineages of anuran amphibians in the Eastern Palaearctic (EP) region in its broad sense. Through a literature review, we have evaluated t...

Written in french, Le Petit Guide Herpéto combines the latest knowledge in herpetology to showcase the diversity of amphibians and reptiles of France and neighboring countries (Switzerland, Belgium, Luxemburg). It is designed for a family audience accessible to kids, based on naturalist drawings, stunning photography, up-to-date distribution maps,...

As reflected by the two rules of speciation (Haldane’s rule and the large X-/Z-effect), sex chromosomes are expected to behave like supergenes of speciation: they recombine only in one sex (XX females or ZZ males), supposedly recruit sexually antagonistic genes and evolve faster than autosomes, which can all contribute to pre-zygotic and post-zygot...

We report on the discovery of a population related to the Blunt-headed Salamander (Ambystoma amblycephalum), a micro-endemic axolotl from Mexico scientifically confirmed only once since its original description in 1940, and now presumably extinct. In 2018, paedomorphic and metamorphosed adults, as well as clutches and larvae, were found in a cattle...

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...

A deeper phylogeographic structure is expected for slow‐dispersing habitat specialists compared to widespread adaptable species, especially in topographically complex regions. We tested this classic assumption by comparing the genomic (RAD‐sequencing) phylogeographies of two amphibians inhabiting the Swiss Alps: the mobile, cosmopolitan common frog...

Old World tree frogs from the family Rhacophoridae, one of the most species-rich groups of amphibians worldwide, are becoming a model in ecological and evolutionary research, notably for their tremendous diversity of breeding systems. In this study, we provide the most comprehensive temporally and spatially explicit phylogeographical framework for...

National species lists, especially red lists, must account for the latest taxonomic updates in order to best protect newly discovered biodiversity. Here we demonstrate the cryptic presence of a new species for the Swiss herpetofauna : Carnie’s lizard Zootoca carniolica, an oviparous form of the viviparous common lizard Z. vivipara, which was recent...

Although necessary to promote conservation, defining evolutionary units and naming biodiversity remain a difficult task, especially in problematic species groups that experienced a dynamic biogeographic history. In this article, we undertake such task for midwife toads of the Alytes obstetricans complex by integrating recent molecular studies altog...

Reproductive isolation is instrumental to the formation of new species (speciation), but it remains largely enigmatic how many incompatibilities are required to prevent hybridization and where they lie across the genome. By studying patterns of admixture in amphibian hybrid zones, we found that reproductive isolation is initiated by numerous small-...

The dynamic biogeography of glacial refugia may cause complex patterns of genetic admixture between parapatric taxa, which in turn can mislead their systematics, diversity, and distributions. We investigated this issue for green toads (Bufotes) inhabiting the circum-Aegean region, a biodiversity hotspot of the Eastern Mediterranean. A previous phyl...

Sex chromosomes are classically predicted to stop recombining in the heterogametic sex, thereby enforcing linkage between sex-determining (SD) and sex-antagonistic (SA) genes. With the same rationale, a pre-existing sex asymmetry in recombination is expected to affect the evolution of heterogamety, e. g. a low rate of male recombination might favor...

The Czech edition of Amphibians of Europe, North Africa and the Middle East: A Photographic Guide (Bloomsbury, 2019), translated by Zdeněk Kymla. https://www.knizniklub.cz/knihy/457742-obojzivelnici.html

Several water frogs from the genus Pelophylax have a hybrid origin and perpetuate by hybridogenesis, a peculiar mode of reproduction ruled by complex phenomena such as clonality and polyploidy, and which can constitute a transient stage towards the formation of novel species. Different kinds of hybridogenetic complexes have been documented througho...

Least intrusive sampling should be prioritized for wildlife conservation and bioethics. In birds, DNA samples are typically obtained from blood. Here we emphasized buccal swabs as an alternative source. We tested swabs in adults and nestlings representative of 17 European species (n = 189), ranging from small passerines to large Strigiformes (owls)...

Aim The amount of gene flow between parapatric species can be greatly variable depending on how species boundaries are maintained in respect to numerous genetic and ecological factors that affect the strength of reproductive isolation. We quantified this variability to understand its effect on the genetic integrity of a well‐studied pair of hybridi...

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 meridi...

The growing interest in the lability of sex determination in non-model vertebrates such as amphibians and fishes has revealed high rates of sex chromosome turnovers among closely related species of the same clade. Can such lineages hybridize and admix with different sex-determining systems, or could the changes have precipitated their speciation? W...

The Spanish edition of Amphibians of Europe, North Africa and the Middle East: A Photographic Guide (Bloomsbury, 2019), translated by Manuel Pijoan Rotgé. http://www.ediciones-omega.es/1716-anfibios-de-europa-norte-de-africa-y-oriente-proximo-978-84-282-1733-0.html

The original diversity of Pelophylax water frogs has been compromised by multiple biological invasions all over Western Europe. For the European pool frog (P. lessonae), the Joux Valley – a 30km highland depression in northwestern Switzerland – stands as the last stronghold spared by exotic lineages. In order to manage P. lessonae in the valley, we...

The last species list of the European herpetofauna was published by Speybroeck, Beukema and Crochet (2010). In the meantime, ongoing research led to numerous taxonomic changes, including the discovery of new species-level lineages as well as reclassifications at genus level, requiring significant changes to this list. As of 2019, a new Taxonomic Co...

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: hy...

Molecular ecologists often rely on phylogenetic evidence for assessing the species-level systematics of newly-discovered lineages. Alternatively, the extent of introgression at phylogeographic transitions can provide a more direct test to assign candidate taxa into subspecies or species categories. Here we compared phylogenetic versus hybrid zone a...

Subdivided Pleistocene glacial refugia, best known as “refugia within refugia”, provided opportunities for diverging populations to evolve into incipient species and/or to hybridize and merge following range shifts tracking the climatic fluctuations, potentially promoting extensive cytonuclear discordances and “ghost” mtDNA lineages. Here, we teste...

Genomic tools like RAD-sequencing can provide the resolution to understand the complex genetic patterns underlying cryptic biological invasions. Here we use this method to clarify the genetic consequences of a rampant invasion by the Italian pool frog (Pelophylax bergeri) north of the Alps, threatening the native P. lessonae and its hybridogenetic...

While estimates of genetic divergence are increasingly used in molecular taxonomy, hybrid zone analyses can provide decisive evidence for evaluating candidate species. Applying a population genomic approach (RAD-sequencing) to a fine-scale transect sampling, we analyzed the transition between two Iberian subspecies of the common midwife toad (Alyte...

Despite generally conserved phenotypes across radiations, Hylid frogs exhibit substantial intraspecific variation in size and coloration, especially the background color and the lateral black and white stripe patterns (linea marginalis). We examined these traits in a phylogeographic context across 14 populations (276 adults) representative of the t...

The sociopolitical acceptance necessary for the conservation of controversial species requires scientific knowledge that disentangles empirical facts from myth and misinformation. An epitome of such, the grey wolf (Canis lupus), had been eradicated from most of Western Europe by the early 20th century. However, a few mysteriously re-appeared in the...

The French edition of Amphibians of Europe, North Africa and the Middle East: A Photographic Guide (Bloomsbury, 2019), translated by the author. In December 2020, the book was awarded the Bernard Fiocre Award by the French Veterinary Academy. http://www.delachauxetniestle.com/ouvrage/guide-photographique-des-amphibiens-d-europe-d-afrique-du-nord-...

Phylogeographic breaks can be viewed as regional hotspots of diversity where the genetic integrity of incipient species is put to the test. We focus on an understudied species transition from the Middle-East: the Dead Sea Rift in the Levant region, which presumably divided the tree frogs Hyla savignyi and H. felixarabica. Combining multilocus genet...

Background – Hybridogenesis can represent the first stage towards hybrid speciation where the hybrid taxon eventually weans off its parental species. In hybridogenetic water frogs, the hybrid Pelophylax kl. esculentus (genomes RL) usually eliminates one genome from its germline and relies on its parental species P. lessonae (genomes LL) or P. ridib...

Rapid management responses against invasive species soon after their establishment is the most efficient way to limit their biological and economic impacts. Early-detection and reliable monitoring is however challenging when cryptic taxa are involved. Here we show how environmental DNA (eDNA) metabarcoding of water samples efficiently unveiled an e...

The genomic era contributes to update the taxonomy of many debated terrestrial vertebrates. In an accompanying work, we provided a comprehensive molecular assessment of spadefoot toads (Pelobates) using genomic data. Our results call for taxonomic updates in this group. First, nuclear phylogenomics confirmed the species-level divergence between the...

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 spec...

Comparative molecular studies emphasized a new biogeographic paradigm for the terrestrial fauna of North Africa, one of the last uncharted ecoregions of the Western Palearctic: two independent east-west divisions across the Maghreb. Through a comprehensive phylogeography, we assessed how this model suits the genetic diversification documented for t...