Breaking the reproductive barrier of divergent species to explore the genomic landscape.

Background: Climate change will have significant consequences for species. Species range shifts induce the emergence of new hybrid zones or the spatial displacement of pre-existing ones. These hybrid zones may become more porous as alleles are passed from one species to another. Currently, hybridization between highly divergent species living in sympatry seems extremely limited. Indeed, this phenomenon involves breaking two barriers. The first is the pre-mating barrier, related to the reproductive phenology of the two species. The second is the post-zygotic barrier, related to the genetic divergence between these species. Here, we were interested in identifying new hybridization patterns and potential implications, especially in the context of environmental modifications. Methods: We sampled Telestes souffia and Parachondrostoma toxostoma wild specimens from different locations across France and genotyped them for SNP markers. We identified discriminant loci using F1-hybrid specimens and parental species and performed principal component analysis and Bayesian model-based clustering to analyze phylogenetic information. Furthermore, we assessed deviation in allele frequency from F1 to F2 and for Hardy-Weinberg equilibrium for F2 and assessed gene function associated with two F2 cohorts. Results: We demonstrate that by breaking the ecological barrier, massive introgressive hybridization is possible between two endemic lineages of Cyprinidae belonging to two distinct genera. For both cohorts studied (=2 cm and >2 cm), a large majority of loci (>88%) presented no deviation in allele frequency and no departure from the Hardy-Weinberg equilibrium. For individuals beyond the 2 cm stage, two phenomena were observed. The first was an allelic imbalance in favor of P. toxostoma, for some genomic regions, with genes involved in developmental regulatory processes, cytoskeletal organization, and chromosome organization. The second was an excess of heterozygous loci coupled with an equilibrium of allelic frequencies for genes involved in immune response and kidney/liver development. Moreover, the 2 cm-sized specimens with high mortality yielded a particular genomic signature. Conclusion: Our study displayed important results for understanding the early stages of hybridization between divergent lineages and predicting the emergence of future hybrid zones in the wild. Moreover, this hybridization generates a wide spectrum of hybrids that are a potential source of important evolutionary novelties.

Twenty-four hours in the life of Zingel asper.

For the first time, radio-tracking observations were made over 24 h cycles during the growing season to quantify the habitat use and home range of Zingel asper, a critically endangered fish species, endemic to the Rhône River with a high risk of extinction (IUCN). New advances in radio telemetry with regard to the size of tags provided an opportunity to collect behavioural and habitat use information while remaining non-lethal. Zingel asper was characterized by small ranges of habitat use and, contrary to previous assumptions, the species was diurnal as illustrated by a smaller home range during the night than during daytime.

Heterogeneous colonization pattern of European Cyprinids, as highlighted by the dace complex (Teleostei: Cyprinidae).

The dace (Leuciscus leuciscus), with a very large geographic distribution all over Europe, represents an interesting species model for studies of the global mechanisms underlying aquatic system biodiversity. To assess the congruence with the past colonization process hypothesis of the freshwater fauna in Western Europe, we investigated the evolutionary history of this species, by integrating morphological variation (eight meristic characters), mitochondrial (cytochrome b, 16S rDNA and control region, over a total of 2169 bp) and nuclear (12 allozymes loci) phylogenetic relationships, and investigating population dynamics via expansion, migration, bottleneck, and divergence time analyses. We carried out nested clade phylogeographic analysis for a total of 663 specimens from 31 populations taken from all over the distribution area. Unlike previous studies, we found that L. leuciscus is currently constituted by five lineages belonging to two clades (yielding 6.3% of pairwise divergence). The relationships between these lineages were accounted for by complex biogeographical patterns due to Pliocene and Pleistocene paleoclimatic events, validating the identification of new glacial refuges for freshwater fish in Western Europe. Finally, we demonstrated hybridization between L. leuciscus and Leuciscus idus.

Partial combination applied to phylogeny of European cyprinids using the mitochondrial control region.

Previous molecular phylogenies of European cyprinids led to some solid facts and some uncertainties. This study is based on a stretch of more than 1 kb in the mitochondrial control region newly sequenced for 35 European cyprinids and on previous cytochrome b and 16S rDNA data. The trees based on the control region are more accurate and robust than those obtained from the two other genes. Character incongruence among the three genes was tested using the incongruence length difference (ILD) test. Iterative removals of individual sequences followed by new ILD tests identified two sequences responsible for statistically significant incongruence. A partial combination was conducted, that is, a combination of the three data sets, removing the two sequences previously identified. The phylogenetic analysis of this partial combination gives a more robust and resolved picture of subfamilial interrelationships. The Rasborinae are the sister group of all other cyprinids. The monophyletic Cyprininae emerges next. Tinca tinca first and then Rhodeus are the sister groups of all the remaining nonrasborine and noncyprinine species. Gobio is the sister group of the Leuciscinae, in which the Phoxinini are the sister group of the Leuciscini. Within the Leuciscini, the genus Leuciscus and the subfamily Alburninae are both paraphyletic. The Rasborinae are the most basal cyprinid subfamily and the Tincinae are not the sister group of the Cyprininae. These two results challenge only two anatomical characters, which need to be reinterpreted or considered as homoplastic in cyprinid evolution: the modification of the first pleural rib and its parapophysis and the bony composition of the interorbital septum.

Mitochondrial phylogeny of the European cyprinids: implications for their systematics, reticulate evolution, and colonization time.

Two different mitochondrial genes, the cytochrome b and the 16S rDNA, support the same European cyprinid molecular phylogeny: the most basal subfamily is the paraphyletic Rasborinae, the Cyprininae are monophyletic, the Tincinae and Gobioninae are close to the Cyprininae or more basal lineages but not close to Leuciscinae or Alburninae, and the Leuciscinae are paraphyletic but can become monophyletic if we include the biphyletic alburninae and exclude the Phoxinini. The relationship of the Acheilognathinae remains obscure. Natural intergeneric and interspecific hybridizations are clearly demonstrated within the Leuciscinae, both from high bootstrap proportions and intermediate morphological features: Chondrostoma toxostoma and Rutilus rutilus, Scardinius erythrophthalmus and R. rutilus, and Leuciscus multicellus and Leuciscus soufia. Finally, the use of the nonsaturated and clockwise 16S mtDNA sequences have been used to infer from nonintrogressive taxa the time of the first European cyprinid cladogeneses. The estimation confirms the hypothesis of Almaça and Banarescu that European cyprinid subfamilies started to diversify 35 mya and confirms the hypothesis of Bianco on the diversification of European leuciscines in the Mediterranean area during the late Messinian (6.5 to 5.3 mya).

[Study of the variability of Leuciscus soufia, cyprinidae fish, by analysis of enzyme polymorphism and meristic characteres]. / Etude de la variabilité de Leuciscus soufia, poisson cyprinidé, par analyse du polymorphisme enzymatique et de caractères méristiques.

An analysis of 30 presumptive enzyme loci and 7 meristic characters has been used to study different populations of the cyprinid Leuciscus (Telestes) soufia. This fish is considered autochthonous in south-eastern France, with 3 described sub-species. The estimates of gene diversity were similar to results from studies on Cyprinidae from North America. The sample from the upper reaches of the river Durance showed higher levels of gene diversity; heterozygosity and percentage of polymorphic loci than all other samples. Furthermore, the samples from the Durance, as a whole, seem to embrace a population with little or no subdivision. Six of the 7 measured meristic characters yielded no significant differences between samples. The population sample of the sub-species soufia from the river Var differs from the other samples only by allele frequencies, low level of heterozygosity and the number of gill rakers. It is argued that these characters are quite insufficient and may cast doubt as to the validity of the subspecies rank of this population.