Evaluating a species phylogeny using ddRAD SNPs: Cyto-nuclear discordance and introgression in the salmonid genus Thymallus (Salmonidae).

Hybridization and introgression are very common among freshwater fishes due to the dynamic nature of hydrological landscapes. Cyclic patterns of allopatry and secondary contact provide numerous opportunities for interspecific gene flow, which can lead to discordant paths of evolution for mitochondrial and nuclear genomes. Here, we used double digest restriction-site associated DNA sequencing (ddRADseq) to obtain a genome-wide single nucleotide polymorphism (SNP) dataset comprehensive for allThymallus (Salmonidae)species to infer phylogenetic relationships and evaluate potential recent and historical gene flow among species. The newly obtained nuclear phylogeny was largely concordant with a previously published mitogenome-based topology but revealed a few cyto-nuclear discordances. These incongruencies primarily involved the placement of internal nodes rather than the resolution of species, except for one European species where anthropogenic stock transfers are thought to be responsible for the observed pattern. The analysis of four contact zones where multiple species are found revealed a few cases of mitochondrial capture and limited signals of nuclear introgression. Interestingly, the mechanisms restricting interspecific gene flow might be distinct; while in zones of secondary contact, small-scale physical habitat separation appeared as a limiting factor, biologically based reinforcement mechanisms are presumed to be operative in areas where species presumably evolved in sympatry. Signals of historical introgression were largely congruent with the routes of species dispersal previously inferred from mitogenome data. Overall, the ddRADseq dataset provided a robust phylogenetic reconstruction of the genus Thymallus including new insights into historical hybridization and introgression, opening up new questions concerning their evolutionary history.

The rise and fall of the ancient northern pike master sex-determining gene.

The understanding of the evolution of variable sex determination mechanisms across taxa requires comparative studies among closely related species. Following the fate of a known master sex-determining gene, we traced the evolution of sex determination in an entire teleost order (Esociformes). We discovered that the northern pike (Esox lucius) master sex-determining gene originated from a 65 to 90 million-year-old gene duplication event and that it remained sex linked on undifferentiated sex chromosomes for at least 56 million years in multiple species. We identified several independent species- or population-specific sex determination transitions, including a recent loss of a Y chromosome. These findings highlight the diversity of evolutionary fates of master sex-determining genes and the importance of population demographic history in sex determination studies. We hypothesize that occasional sex reversals and genetic bottlenecks provide a non-adaptive explanation for sex determination transitions.

Morphological and molecular evidence of three species of pikes Esox spp. (Actinopterygii, Esocidae) in France, including the description of a new species.

This integrative taxonomy study of French pikes compares morphological characters and molecular sequence data (mitochondrial COI and nuclear Plagl2 genes). In addition to the expected E. lucius, DNA sequences and morphology both support a new species in France, E. aquitanicus sp. nov. from the Charente to the Adour drainages. It is characterized by a color pattern of sides with narrow 1-1.5-scale-wide oblique vertical bands, conferring it a marbled coat, a snout only 0.9 times larger than the postorbital length, an anal fin basis 1.1-1.2 times larger than the caudal peduncle length, 101 to 121 lateral scales, 53 to 57 vertebrae, as well as 24 diagnostic sites in the COI gene and 3 in the Plagl2 gene. Partial COI sequences (131 bp) from modern and historical specimens indicate also the presence of E. cisalpinus and E. lucius during the 19th century in Lake Geneva. Morphological and molecular data points to a possible hybridization between E. lucius with both other local pike species, representing a risk for them. Their endangerment status should be evaluated rapidly in order to take conservation measures.

Is the species flock concept operational? The Antarctic shelf case.

There has been a significant body of literature on species flock definition but not so much about practical means to appraise them. We here apply the five criteria of Eastman and McCune for detecting species flocks in four taxonomic components of the benthic fauna of the Antarctic shelf: teleost fishes, crinoids (feather stars), echinoids (sea urchins) and crustacean arthropods. Practical limitations led us to prioritize the three historical criteria (endemicity, monophyly, species richness) over the two ecological ones (ecological diversity and habitat dominance). We propose a new protocol which includes an iterative fine-tuning of the monophyly and endemicity criteria in order to discover unsuspected flocks. As a result nine « full ¼ species flocks (fulfilling the five criteria) are briefly described. Eight other flocks fit the three historical criteria but need to be further investigated from the ecological point of view (here called "core flocks"). The approach also shows that some candidate taxonomic components are no species flocks at all. The present study contradicts the paradigm that marine species flocks are rare. The hypothesis according to which the Antarctic shelf acts as a species flocks generator is supported, and the approach indicates paths for further ecological studies and may serve as a starting point to investigate the processes leading to flock-like patterning of biodiversity.

Genus-level supertree of Cyprinidae (Actinopterygii: Cypriniformes), partitioned qualitative clade support and test of macro-evolutionary scenarios.

We used the supertree approach of matrix representation with parsimony to reconstruct to date the most exhaustive (genus-level) phylogeny of Cyprinidae. The supertree of Cyprinidae, representing 397 taxa (237 nominal genera) and 990 pseudocharacters, was well resolved (96%) through extended consensus majority rule, although 36 nodes (9.4%) were unsupported. The proportion of shared taxa among source trees was very low after calculation of the taxonomic coverage index (TCI = 0.059), which is proposed here as a more accurate alternative to the usual ratios calculated from the number of pseudo-characters or source trees per taxon. We define a new index for the calculation of partitioned qualitative clade support, the partitioned rQS ((p)rQS), which offers a straightforward visualization of the relative supports of source tree partitions at supertree nodes.The use of (p)rQS showed that the molecular source tree partition contributed to most node supports within the supertree of Cyprinidae (73%, contra 21% for the morphological partition) and evidenced a fair proportion of conflict at nodes between the two partitions (21%), notably reflecting (i) the greater number and resolution of molecular source trees, and (ii) potential morphological convergences. Most of the higher-level relationships within Cyprinidae were supported by both morphological and molecular source tree partitions. Our supertree showed a well-supported dichotomy between a clade consisting of a 'barbine' + 'rasborine' lineage, sister group to (Barbinae [paraphyletic], (Cyprininae, Labeoninae)), and a clade consisting of other rasborines (large polytomy) and the two monophyletic groups ((Tincinae, Tanichthys), (Ecocarpia, (Acheilognathinae, (Gobioninae, Leuciscinae)))) and (Squaliobarbinae, (Xenocyprinae, Cultrinae)). Through the non-monophyly of almost all the traditional subfamilies of Cyprinidae and 34 genera, our supertree exemplified the taxonomic chaos that reigns in the classification of the family. It also highlighted that further efforts should aim at increasing taxonomic sampling and generating alternative phylogenetic signals, notably for the still poorly apprehended Tincinae, Squaliobarbinae, Acheilognathinae, Gobioninae, and Rasborinae, the latter representing a key taxon for the understanding of early cyprinid evolution. Our supertree also proved useful for testing macro-evolutionary scenarios at a wide taxonomic scale. Ancestral reconstructions using linear parsimony confirmed that the Oriental tropical region was the centre of origin of Cyprinidae, and identified three Oriental-to-Palaearctic, two Palaearctic-to-Nearctic, and one Oriental-to-Afrotropical major migration events. On the other hand, we almost completely rejected the hypothesis of presence of barbels as a plesiomorphic condition within Cyprinidae (although ambiguous for maxillary barbels of the Barbinae-Cyprininae type). The supertree of Cyprinidae serves as a basis to discuss the applications and bias of the newly proposed (p)rQS, to provide future guidelines for a better achievement of cyprinid phylogeny, and to elaborate further on inter-continental migrations and the adaptive value of barbels.