Sylvain Dubey

Mitochondrial and nuclear phylogeny of circum-Mediterranean tree frogs from the Hyla arborea group

Mitochondrial and nuclear phylogeny of circum-Mediterranean tree frogs from the Hyla arborea group

Origin of the parasites of an invading species, the Australian cane toad (Bufo marinus): are the lungworms Australian or American?

Phylogeographical analyses that identify the geographical origin of parasites in invading species can clarify the parasites’ potential for biological control of the invader and the risks posed by the parasite to native species. Our data on nuclear and mitochondrial genetic sequences show that the nematode lungworms (Rhabdias spp.) in invasive Australian populations of cane toads (Bufo marinus) are Rhabdias pseudosphaerocephala, a South American species. We did not find this lungworm species in any Australian frogs sympatric with cane toads, suggesting that the parasite does not attack Australian frogs and hence may offer potential as a biocontrol agent of the toad.

Landscape genetics of the Alpine newt (Mesotriton alpestris) inferred from a strip-based approach

Habitat destruction and fragmentation are known to strongly affect dispersal by altering the quality of the environment between populations. As a consequence, lower landscape connectivity is expected to enhance extinction risks through a decrease in gene flow and the resulting negative effects of genetic drift, accumulation of deleterious mutations and inbreeding depression. Such phenomena are particularly harmful for amphibian species, characterized by disjunct breeding habitats. The dispersal behaviour of amphibians being poorly understood, it is crucial to develop new tools, allowing us to determine the influence of landscape connectivity on the persistence of populations. In this study, we developed a new landscape genetics approach that aims at identifying land-uses affecting genetic differentiation, without a priori assumptions about associated ecological costs. We surveyed genetic variation at seven microsatellite loci for 19 Alpine newt (Mesotriton alpestris) populations in western Switzerland. Using strips of varying widths that define a dispersal corridor between pairs of populations, we were able to identify land-uses that act as dispersal barriers (i.e. urban areas) and corridors (i.e. forests). Our results suggest that habitat destruction and landscape fragmentation might in the near future affect common species such as M. alpestris. In addition, by identifying relevant landscape variables influencing population structure without unrealistic assumptions about dispersal, our method offers a simple and flexible tool of investigation as an alternative to least-cost models and other approaches.

Biogeographic origin and radiation of the Old World crocidurine shrews (Mammalia: Soricidae) inferred from mitochondrial and nuclear genes

The crocidurine shrews include the most speciose genus of mammals, Crocidura. The origin and evolution of their radiation is, however, poorly understood because of very scant fossil records and a rather conservative external morphology between species. Here, we use an alignment of 3560 base pairs of mitochondrial and nuclear DNA to generate a phylogenetic hypothesis for the evolution of Old World shrews of the subfamily Crocidurinae. These molecular data confirm the monophyly of the speciose African and Eurasian Crocidura, which also includes the fossorial, monotypic genus Diplomesodon. The phylogenetic reconstructions give further credit to a paraphyletic position of Suncus shrews, which are placed into at least two independent clades (one in Africa and sister to Sylvisorex and one in Eurasia), at the base of the Crocidura radiation. Therefore, we recommend restricting the genus Suncus to the Palaearctic and Oriental taxa, and to consider all the African Suncus as Sylvisorex. Using molecular dating and biogeographic reconstruction analyses, we suggest a Palaearctic-Oriental origin for Crocidura dating back to the Upper Miocene (6.8 million years ago) and several subsequent colonisations of the Afrotropical region by independent lineages of Crocidura.

Male-biased dispersal in a tropical Australian snake (Stegonotus cucullatus, Colubridae)

Sex‐based differences in dispersal distances can affect critical population parameters such as inbreeding rates and the spatial scale of local adaptation. Males tend to disperse further than females in mammals, whereas the reverse is true for birds; too few reptiles have been studied to reveal generalities for that group. Although reptiles are most diverse and abundant in the tropics, few tropical reptiles have been studied in this respect. We combine data from a long‐term (10‐year) mark–recapture study with genetic information (based on nine microsatellite markers) on slatey‐grey snakes (Stegonotus cucullatus, Colubridae) in the Australian wet‐dry tropics. Males attain larger body sizes than females, and both genetic and mark–recapture data show that males also disperse further than females. Recapture records show that hatchling males dispersed away from their release points whereas hatchling females did not, and adult males moved further than adult females. In the genetic analysis, males contributed less to overall FST and relatedness than did females (FSTm = 0.0025, FSTf = 0.0275, P < 0.001; rm = 0.0053; rf = 0.0550; P < 0.001). Spatial autocorrelation analyses within the largest population revealed a similar pattern, with spatial structuring stronger for females than males. Overall, our genetic analyses not only supported the mark–recapture data, but also extended our insights by revealing occasional long‐distance dispersal not detected by the mark–recapture study.

HOMOLOGOUS SEX CHROMOSOMES IN THREE DEEPLY DIVERGENT ANURAN SPECIES

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 chromosome pairs might be more likely than others to be co‐opted as sex chromosomes. Empirical support, however, is still very limited. Here we show that sex‐linked markers from three highly divergent groups of anurans map to Xenopus tropicalis scaffold 1, a large part of which is homologous to the avian sex chromosome. Accordingly, the bird sex determination gene DMRT1, known to play a key role in sex differentiation across many animal lineages, is sex linked in all three groups. Our data provide strong support for the idea that some chromosome pairs are more likely than others to be co‐opted as sex chromosomes because they harbor key genes from the sex determination pathway.

Molecular cophylogenetic relationships between European bats and their ectoparasitic mites (Acari, Spinturnicidae)

Cospeciation between host-parasite species is generally thought to result in mirror-image congruent phylogenies. Incongruence can be explained by mechanisms such as host switching, duplication, failure to speciate and sorting events. To investigate the level of association in the host-parasite relationship between Spinturnicid mites and their bat hosts, we constructed the phylogenetic tree of the genus Spinturnix (Acari, Mesostigmata) and compared it to the host phylogeny. We sequenced 938bp of the mitochondrial 16S rDNA and Cytochrome Oxydase subunit I (COI) genes among eleven morphospecies of Spinturnix collected on 20 European Vespertilionid and Rhinolophid bat species. Phylogenetic reconstruction of hosts and parasites showed statistical evidence for cospeciation and suggested that their evolutionary history involved also failure to speciate events and host switches. The latter seem to be mainly promoted by similar roosting habits of the host. As currently understood, host associations of Spinturnicid mites likely results from a complex interaction between the phylogenetic history of the host and the behaviour and the ecology of both parasite and host.

Mediterranean populations of the lesser white‐toothed shrew (Crocidura suaveolens group): an unexpected puzzle of Pleistocene survivors and prehistoric introductions

An earlier study revealed the strong phylogeographical structure of the lesser white‐toothed shrew (Crocidura suaveolens group) within the northern Palaearctic. Here, we aim to reconstruct the colonization history of Mediterranean islands and to clarify the biogeography and phylogeographical relationships of the poorly documented Middle East region with the northern Palaearctic. We performed analyses on 998‐bp‐long haplotypes of the mitochondrial cytochrome b gene of 143 samples collected around the Mediterranean basin, including islands and the Middle East. The analyses suggest that the Cypriot shrew belongs to the rare group of relict insular Pleistocene mammal taxa that have survived to the present day. In contrast, the Cretan, Corsican and Menorcan populations were independently introduced from the Middle East during the Holocene. The phylogeographical structure of this temperate Palaearctic species within the Middle East appears to be complex and rich in diversity, probably reflecting fragmentation of the area by numerous mountain chains. Four deeply divergent clades of the C. suaveolens group occur in the area, meaning that a hypothetical contact zone remains to be located in central western Iran.

Restricted dispersal and genetic diversity in populations of an endangered montane lizard (Eulamprus leuraensis, Scincidae).

Many alpine species are under threat from global climate change, as their geographic ranges become increasingly fragmented and unsuitable. Understanding rates and determinants of gene flow among such fragmented populations, over historical as well as recent timescales, can help to identify populations under threat. It is also important to clarify the degree to which loss of local populations reduces overall genetic diversity within the taxon. The endangered Blue Mountains Water Skink (Eulamprus leuraensis) is restricted to <40 small swamps in montane south‐eastern Australia. Our analyses of seven microsatellite loci of 241 animals from 13 populations show strong geographic structure, with major genetic divergence even between populations separated by <0.5 km. Dispersal between populations is scarce, and appears to involve mostly males. Our analyses suggest potential recent bottleneck events in all the identified populations, and lower genetic diversity and population size parameter at lower‐elevation sites than at higher‐elevation sites. Management of this endangered taxon thus needs to treat most populations separately, because of their genetic distinctiveness and low rates of genetic exchange.

False phylogenies on wood mice due to cryptic cytochrome-b pseudogene

The phylogeny and phylogeography of the Old World wood mice (subgenus Sylvaemus, genus Apodemus, Muridae) are well-documented. Nevertheless, the distributions of species, such as A. fulvipectus and A. ponticus remain dubious, as well as their phylogenetic relationships with A. sylvaticus. We analysed samples of Apodemus spp. across Europe using the mitochondrial cytochrome-b gene (cyt-b) and compared the DNA and amino-acid compositions of previously published sequences. The main result stemming from this study is the presence of a well-differentiated lineage of Sylvaemus including samples of various species (A. sylvaticus, A. fulvipectus, A. ponticus) from distant locations, which were revealed to be nuclear copies of the mitochondrial cyt-b. The presence of this cryptic pseudogene in published sequences is supported by different pathways. This has led to important errors in previous molecular trees and hence to partial misinterpretations in the phylogeny of Apodemus.