Christophe Dufresnes

Nanjing Forestry University · College of Biology and the Environment

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...

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...

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...

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...

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...

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 hybri...

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)...

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...

Mediterranean tree frogs, Hyla gr. meridionalis Boettger, 1874 (Anura: Hylidae) are widespread around the Western Mediterranean Basin, where they naturally occur across the Maghreb (Morocco, Algeria, Tunisia). Individuals of diverse Moroccan origins have been introduced and have expanded throughout the Iberian Peninsula, southern France and norther...

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 tested...

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 are unique models to examine the role of phylogenetic divergence on the evolution of reproductive isolation, without extrinsic factors such as ecology. Yet, to date very few comparative studies were attempted within such radiations. Here, we characterize a new speciation continuum in a group of widespread Eu...

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...

Alloparapatric species meeting in secondary contact zones are evolutionary witnesses to how reproductive isolation progresses over time and space. Western Palearctic tree frogs (Hyla) are phenotypically similar and all the species pairs tested can hybridize and eventually admix at range margins. All except one. The early-diverged Hyla meridionalis...

Potential hybridization between wolves and dogs has fueled the sensitive conservation and political debate underlying the recovery of the grey wolf throughout Europe. Here we provide the first genetic analysis of wolf-dog admixture in an area entirely recolonized, the northwestern Alps. As part of a long-term monitoring program, we performed geneti...

The new photographic field guide for amphibians from the entire Western Palearctic region, based on an up-to-date taxonomy (139 species) incorporating the latest scientific advances, and featuring all key information on identification, life-history (incl. larvae/clutches), subspecies, distribution, etc., integrated together with stunning macro phot...

Biogeographic processes have led to different evolutionary taxa occurring in the northern and southern edges of the Alpine Mountains in Western Europe. The integrity of this diversity is being challenged by frequent human-mediated trans-alpine translocations, sometimes leading to biological invasions. Several alien terrestrial vertebrates of south...

Several lines of evidence support that north-Italian and Ticinese tree frogs, recently called Hyla perrini, represent a distinct species, formerly considered as Hyla intermedia. However, a nomenclatural clause for electronic publishing of species names according to the Code of International Nomenclature caused that the new name has been unavailable...

Divergence between incipient species remains an incompletely understood process. Hybrid zones provide great research potential, reflecting natural organismal genomic interactions and gene evolution in a variety of recombinants over generations. While sex chromosomes are known evolutionary drivers of reproductive isolation, empirical population gene...

The canonical model of sex-chromosome evolution predicts that, as recombination is suppressed along sex chromosomes, gametologs will progressively differentiate, eventually becoming heteromorphic. However, there are numerous examples of homomorphic sex chromosomes across the tree of life. This homomorphy has been suggested to result from frequent s...

The discovery of cryptic species by molecular tools is leading us to revisit our perception of amphibian diversity and distribution. Here an analysis is presented of amphibian diversity across the Western Palearctic based on an up-to-date taxonomic list accounting for recently discovered taxa. While glacial refugia locally host many species, the mo...

Shapefiles of amphibian species counts by 20x20 quadrats and by country

Despite increasing appreciation of the “speciation continuum”, delimiting and describing new species is a major yet necessary challenge of modern phylogeography to help optimize conservation efforts. In amphibians, the lack of phenotypic differences between closely-related taxa, their complex, sometimes unresolved phylogenetic relationships, and th...

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) makes 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...

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...

Dobzhansky‐Muller (DM) incompatibilities involving sex chromosomes have been proposed to account for Haldane's rule (lowered fitness among hybrid offspring of the heterogametic sex) as well as Darwin's corollary (asymmetric fitness costs with respect to the direction of the cross). We performed simulation studies of a hybrid zone to investigate the...

According to the canonical model of sex-chromosome evolution, the degeneration of Y or W chromosomes (as observed in mammals and birds respectively) results from an arrest of recombination in the heterogametic sex, driven by the fixation of sexually antagonistic mutations. However, sex chromosomes have remained homomorphic in many lineages of fishe...

The marsh frog (Pelophylax ridibundus sensu lato) is the number one amphibian invader in Western Europe. In Switzerland, marsh frogs were introduced in the 1950-1960s and progressively colonized most of the northern parts of the country. We investigated this invasion using molecular tools. We mapped the cryptic presence of three monophyletic mitoch...

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. hispa...

The genetic era has revolutionized our perception of biological invasions. Yet, it is usually too late to understand their genesis for efficient management. Here, we take the rare opportunity to reconstruct the scenario of an uprising invasion of the famous water frogs (Pelophylax) in southern France, through a fine-scale genetic survey. We identif...