Sylvain Dubey

Sylvain Dubey
University of Lausanne | UNIL · Department of Ecology and Evolution

PhD and Privat-docent

About

239
Publications
78,233
Reads
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2,798
Citations
Citations since 2016
35 Research Items
1715 Citations
2016201720182019202020212022050100150200250300
2016201720182019202020212022050100150200250300
2016201720182019202020212022050100150200250300
2016201720182019202020212022050100150200250300
Additional affiliations
December 2015 - present
Hintermann & Weber SA
Position
  • Project Manager
August 2013 - present
University of Lausanne
Position
  • Privat-Docent
October 2011 - November 2015
University of Lausanne
Position
  • Group Leader

Publications

Publications (239)
Article
The first commercial use of synthetic pesticides for crop protection dates back to the 1940s, followed by a fast spreading of their use and the development of a large number of compounds. In contrast to synthetic pesticides that are nowadays designed with the help of artificial intelligence that includes computational science and combinatorial chem...
Article
Emerging infectious fungal diseases such as chytridiomycosis, caused by Batrachochytrium dendrobatidis and B. salamandrivorans in amphibians, or ophidiomycosis in reptiles (Ophidiomyces ophiodiicola), are major threats that can drive species or entire populations to extinction over a short period of time. Besides these well-documented pathogens, su...
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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...
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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...
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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-...
Article
Sex-biased dispersal is common among vertebrates and numerous studies have documented a tendency towards male-biased dispersal in mammals and female-biased dispersal in birds. A few studies have demonstrated that male-biased dispersal seems to be prevalent in reptiles. However, most of these studies considered only a single study site without takin...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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The bicolored shrew Crocidura leucodon consists of two phylogeographic lineages which diverged during the Middle Pleistocene and are roughly separated by the Bosporus Strait at the contact point of Europe and Asia Minor. In this study we analysed mitochondrial cytochrome b genes (1137 bp) of nine shrews from the Caspian region in Iran. Phylogenetic...
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A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
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Parasites profoundly influence the lives of their hosts, yet the dynamics of host–parasite interactions are poorly understood – especially in reptiles. We examined the ecological correlates of parasitism by ixodid ticks in an assemblage of 10 snake species in tropical Australia. In total, we recorded 3803 ticks on 1841 individual snakes of six spec...
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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...
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The medium-sized vipers of the genus Vipera are mainly parapatric in Europe and only a few contact zones (syntopies) are known between two species. The partial syntopy of three viper species (V. ammodytes, V. aspis, and V. berus) is exceptional and has become known only from two neighbouring valleys in the southern Julian Pre-Alps along the Italian...
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The challenge of identifying the proximate causes and ecological consequences of phenotypic variation can be facilitated by studying traits that are usually but not always bilaterally symmetrical; deviations from symmetry likely reflect disrupted embryogenesis. Based on a 19-year mark-recapture study of >1300 slatey-grey snakes (Stegonotus cucullat...
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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...
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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...
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Human introductions of exotic amphibians can have catastrophic effects on native species. However, they usually remain unnoticed without genetic tools when species are difficult to distinguish morphologically. In Western Europe, pool frogs (Pelophylax sp.) make a worrisome case: recent genetic data showed the presence of Italian (Pelophylax bergeri...
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We report the occurrence of alien grass snakes (Natrix natrix ssp.) in Western Switzerland (Lausanne), at a locality where striped grass snakes, presumably from Croatia (N. n. persa), escaped from outdoor enclosures of a reptile park in the 1970s, within the natural range of the threatened barred grass snake (N. n. helvetica). Three gravid females...
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Artificial stocking practices are widely used by resource managers worldwide, in order to sustain fish populations exploited by both recreational and commercial activities, but their benefits are controversial. Former practices involved exotic strains, although current programs rather consider artificial breeding of local fishes (supportive breedin...
Article
Context The cane toad (Rhinella marina), a native species of central and southern America, was introduced to Australia in 1935 as a biocontrol agent after a complex history of prior introductions. The population rapidly expanded and has since spread through much of the Australian landmass, with severe impacts on the endemic wildlife, primarily via...
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Background Strong variations are observed between and within taxonomic groups in the age of extant species and these differences can clarify factors that render species more vulnerable to extinction. Understanding the factors that influence the resilience of species is thus a key component of evolutionary biology, but it is also of prime importance...
Article
In ectotherms, thermoregulation strongly depends on environmental conditions, as well as on intrinsic factors, such as skin colour. Indeed, due to its physical properties, melanin pigments allow melanistic morphs to benefit of a more efficient thermoregulation compared to non-melanistic ones. Despite thermal benefits of melanism have often been hig...
Data
1) Supplementary material Table S1: Mitochondrial diversity for the three species 2) Supplementary material: Table S2: Microsatellite diversity and Hardy-Weinberg equilibrium 3) Supplementary material: Figure S1: Results of the Structure analyses
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Contact zones of closely related and ecologically similar species constitute rare opportunities to study the evolutionary consequences of past speciation processes. They represent natural laboratories in which strong competition could lead to the exclusion of one species, or the various species may switch into distinct ecological niches. Alternativ...
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Hybridization by introduced taxa is a major threat to native species. Characterizing human introductions is thus one of the missions of conservation geneticists. Here we survey a declining population of the regionally endangered European tree frog (Hyla arborea) in the Grangettes natural reserve (Rhone valley, Western Switzerland), where previous e...
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The presence of intraspecific color polymorphism can have multiple impacts on the ecology of a species; as a consequence, particular color morphs may be strongly selected for in a given habitat type. For example, the asp viper (Vipera aspis) shows a high level of color polymorphism. A blotched morph (cryptic) is common throughout its range (central...
Article
Wood mice of the genus Apodemus are widely distributed in Eurasia, with the Eastern Mediterranean being considered as a hotspot. Indeed, numerous species have been documented in Iran, including A. witherbyi, A. hyrcanicus, A. uralensis, A. avicennicus, A. hermonensis, and A. arianus. In this study, 129 specimens were collected from different Irania...
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Biological invasions can bring both the invader and native taxa into contact with novel parasites. As cane toads (Rhinella marina) have spread through Australia, they have encountered lungworms (Rhabdias hylae) that occur in native frogs. Field surveys suggest that these lungworms have not host-switched to toads. In our laboratory studies, R. hylae...
Article
Non-indigenous species can have strong impacts on biodiversity by affecting trophic relationships in their new environments. The piscivorous dice snake (Natrix tessellata) has been introduced to Geneva Lake, western Switzerland, where the endangered viperine snake (Natrix maura) is native. Local, dramatic declines in the viperine snake population m...
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Influence of climate on the presence of colour polymorphism in two montane reptile species. Biol. Lett. 10: The coloration of ectotherms plays an important role in thermoregulation pro-cesses. Dark individuals should heat up faster and be able to reach a higher body temperature than light individuals and should therefore have benefits in cool areas...
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Because an individual's investment into the immune system may modify its dispersal rate, immune function may evolve rapidly in an invader. We collected cane toads (Rhinella marina) from sites spanning their 75-year invasion history in Australia, bred them, and raised their progeny in standard conditions. Evolved shifts in immune function should man...
Article
The marsh frog (Pelophylax ridibundus) has been introduced in many areas in Central and Western Europe as a result of commercial trade with Eastern Europe, and is rapidly replacing the native pool frog (P. lessonae). A large number of Pelophylax species are distributed in Eastern Europe and the strong phenotypic similarity between these species is...
Article
The adaptive function of melanin located in the integument is well known. Although pigments are also deposited in various internal organs, their function is unclear. A review of the literature revealed that “internal melanin” protects against parasites, pollutants, low temperature, oxidative stress, hypoxemia and UV-light, and is involved in the de...
Article
Coastal primary rainforests have suffered damage in Côte d'Ivoire as a result of a lack of protection and urban pressures. Consequently, the highly endemic and critically endangered Wimmer's shrew, Crocidura wimmeri, known only from its type locality, Adiopodoumé, near Abidjan, was considered to have been extinct since 1976. Shrew species assignmen...
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In polyandrous species females produce successive clutches with several males. Female barn owls (Tyto alba) often desert their offspring and mate to produce a 2(nd) annual brood with a second male. We tested whether copulating during chick rearing at the 1(st) annual brood increases the male's likelihood to obtain paternity at the 2(nd) annual bree...
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This study investigated the small mammal community of the periurban Banco National Park (34 km(2)), Abidjan, Cote d'Ivoire, using identical numbers of Sherman and Longworth traps. We aimed to determine the diversity and distribution of rodents and shrews in three different habitats: primary forest, secondary forest and swamp. Using 5014 trap-nights...
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Comparative genomic studies are revealing that, in sharp contrast with the strong stability found in birds and mammals, sex determination mechanisms are surprisingly labile in cold-blooded vertebrates, with frequent transitions between different pairs of sex chromosomes. It was recently suggested that, in context of this high turnover, some chromos...
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Alternative morphotypes can confer important selective advantages in different habitats, whereas they can be penalized in other circumstances. In ectotherms, such as reptiles, the body colour can have direct effects on numerous aspects of their existence, such as thermoregulation or prey–predator interactions. Darker melanic individuals show lower...
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In terrestrial snakes, many cases of intraspecific shifts in dietary habits as a function of predator sex and body size are driven by gape limitation and hence are most common in species that feed on relatively large prey and exhibit a wide body-size range. Our data on sea snakes reveal an alternative mechanism for intraspecific niche partitioning,...
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The Zarudny’s rock shrew, Crocidura zarudnyi Ognev, 1928, is found in very few localities in Afghanistan, Pakistan and Iran. Therefore, a record of the occurrence of additional populations of this species is very interesting. During surveys in Zabol (Iran), we caught three adult males of Crocidura sp. Based on external, dental and cranial measureme...
Article
Capsule: We present a review of the propensity to eat amphibians in the Barn Owl Tyto alba in Europe. Based on the analysis of 596 published studies reporting 3.32 million prey items identified in pellets, 17 869 amphibians (0.54%) were found. An analysis of 9036 amphibians identified to the species level showed that Barn Owls avoid consuming toxic...
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Background Information on the age structure within populations of an endangered species can facilitate effective management. The Blue Mountains Water Skink (Eulamprus leuraensis) is a viviparous scincid lizard that is restricted to < 40 isolated montane swamps in south-eastern Australia. We used skeletochronology of phalanges (corroborated by mark-...
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Colour polymorphism is widespread among vertebrates and plays important roles in prey–predator interactions, thermoregulation, social competition, and sexual selection. However, the genetic mechanisms involved in colour variation have been studied mainly in domestic mammals and birds, whereas information on wild animals remains scarce. Interestingl...
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Background Climatic oscillations throughout the Quaternary had profound effects on temperate biodiversity, but the extent of Quaternary climate change was more severe in temperate regions of the northern hemisphere than in the southern hemisphere. We sought to determine whether this geographic disparity differentially influenced the timing of intra...
Data
Appendix S1. Raw data on the age of species, based on oldest intraspecific diversification events as revealed by molecular phylogenies. The Table shows Species, Hemisphere (N: northern, S: southern), Latitude (below 40°, above 40°, or in both areas), Age (millions of years), and corresponding references.
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Expressing parental care after oviposition or parturition is usually an obligate (evolved) trait within a species, despite evolutionary theory predicting that widespread species should vary in whether or not they express parental care according to local selection pressures. The lizard Eutropis longicaudata expresses maternal care only in a single p...
Article
Capsule We present a review of the propensity to eat reptiles in the Barn Owl Tyto alba in Europe. Based on the analysis of 591 published studies reporting 3.07 million prey items identified in pellets, only 2402 reptiles (0.08%) were found. Reptiles were most often captured in southern parts of the European continent and on islands. A large propor...
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Invasive species may carry with them parasites from their native range, differing from parasite taxa found in the invaded range. Host switching by parasites (either from the invader to native fauna or from native fauna to the invader) may have important consequences for the viability of either type of host (e.g., their survivorship, fecundity, disp...
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Many characteristics, for example life‐history traits, physiological tolerance to heat and cold, and energy requirements, contribute to a population's ability to persist in the face of climatic variation. Recent studies have suggested that the presence of intraspecific colour polymorphism could be another potential contributor to population resilie...