Mesozoic mitogenome rearrangements and freshwater mussel (Bivalvia: Unionoidea) macroevolution

© 2019, The Author(s), under exclusive licence to The Genetics Society. Using a new fossil-calibrated mitogenome-based approach, we identified macroevolutionary shifts in mitochondrial gene order among the freshwater mussels (Unionoidea). We show that the early Mesozoic divergence of the two Unionoidea clades, Margaritiferidae and Unionidae, was accompanied by a synchronous split in the gene arrangement in the female mitogenome (i.e., gene orders MF1 and UF1). Our results suggest that this macroevolutionary jump was completed within a relatively short time interval (95% HPD 201–226 Ma) that coincided with the Triassic–Jurassic mass extinction. Both gene orders have persisted within these clades for ~200 Ma. The monophyly of the so-called “problematic” Gonideinae taxa was supported by all the inferred phylogenies in this study using, for the first time, the M- and F-type mitogenomes either singly or combined. Within Gonideinae, two additional splits in the gene order (UF1 to UF2, UF2 to UF3) occurred in the Mesozoic and have persisted for ~150 and ~100 Ma, respectively. Finally, the mitogenomic results suggest ancient connections between freshwater basins of East Asia and Europe near the Cretaceous–Paleogene boundary, probably via a continuous paleo-river system or along the Tethys coastal line, which are well supported by at least three independent but almost synchronous divergence events

The complete mitochondrial genome of Thymallus thymallus (Linnaeus, 1758) (Actinopterygii, Salmonidae) obtained by long range PCRs and double multiplexing

International audienceLe génome mitochondrial complet du Thymallus thymallus (Linnaeus, 1758) (Actinopterygii, Salmonidae) obtenu par PCRs longues et double multiplexage. Le génome mitochondrial complet de Thymallus thymallus (Actinopterygii, Salmonidae) provenant d'un voucher enregistré en collection et capturé dans l'Ain (bassin du Rhône) a été séquencé. La séquence d'une longueur de 16 660 pb, contient 13 gènes codants, 22 ARN de transfert dont 2 ARNt-Leu et 2 ARNt-Ser, 2 gènes ARN ribosomiques et la région de contrôle. Un espace intergénique et des séquences se chevauchant ont été trouvés. La composition des bases du mitogénome est de 27,5% A, 27,9% T, 27,1% C et 17,5% G. Ce mitogénome a été séquencé pour moins de 20 euros

A third European species of grayling (Actinopterygii, Salmonidae), endemic to the Loire River basin (France), Thymallus ligericus n. sp

International audienceLoire grayling was already known to belong to a distinct lineage, compared to other European population, according to molecular data (enzymatic polymorphism, mtDNA sequencing and microsatellites). In this paper, we consider this lineage as a new species, Thymallus ligericus n. sp., which is endemic to the Loire drainage (France). Compared with the other species, T. ligericus n. sp. is characterized by a more elongated body, the presence of a pointed snout and a strait or convex snout profile, a more inferior mouth with a transversal aperture and a fleshier upper lip, usually more than 50 to several hundreds black dots on the flanks, a shorter head (20.0-23.7% SL), smaller occipital and orbital depths of the head (54.8-71.7% HL and 43.5-53.4% HL, respectively) and a shorter horizontal eye diameter (22.6-26.3% HL).L’ombre d’Auvergne est déjà connu pour appartenir à une lignée évolutive distincte par rapport aux autres populations d’ombre d’Europe d’après les données moléculaires (polymorphisme enzymatique, données mitochondriales et microsatellites). Dans cette étude, nous considérons cette lignée comme une nouvelle espèce, Thymallus ligericus n. sp., qui est endémique au bassin de la Loire (France). Cette espèce est caractérisée par un corps plus allongé, la présence d’un museau pointu lui conférant un profil droit ou convexe, une bouche plus infère avec une ouverture transverse et une lèvre supérieure plus charnue, généralement plus de 50 à plusieurs centaines de points noirs sur les flancs, une tête plus courte (20,0-23,7% SL), une hauteur occipitale et orbitale de la tête plus faible (respectivement 54,8-71,7% HL et 43,5-53,4 %HL) et un diamètre horizontal de l’œil plus petit (22,6-26,3% HL)

First Confirmed Record of the Smalltooth Sand Tiger, Odontapis Ferox, in Galicia (NW Spain)

5 pages, 3 figures.-- This article is licensed under a Creative Commons Attribution 4.0 International LicenseThe smalltooth sand tiger shark Odontaspis ferox (Risso, 1810) appears to have an extensive and fragmented distribution in tropical and warm-temperate worldwide oceans. One female of O. ferox was caught and released by a small-scale fishery vessel in Ría de Arousa (Northwest of Spain), subsequently stranded still alive on the coast (42°33’18.4"N 8°49’18.3"O) after a few hours. The individual (336 cm total length, weight ~ 300 kg) was identified based on a collection of features including the characteristic dentition, body morphology and by molecular assignment. This is the first confirmed record of O. ferox in Galician waters. This finding complements the knowledge of the geographic distribution and occurrence of this rare and sparse species in the Northeastern AtlanticThe Galician stranding network, coordinated by CEMMA, is funded by the Biodiversity Foundation, of the Spanish Ministry for Ecological Transition, through the REVARGAL project, and Xunta de Galicia. AL is funded by national funds (OE), through FCT – Fundação para a Ciência e a Tecnologia, This work was supported by the Foundation for Science and Technology to GS (SFRH/BD/139069/2018) and EF (CEECIND/00627/2017), by Strategic Funding UIDB/04423/2020 and UIDP/04423/2020. Open Access funding provided thanks to the CRUE-CSIC agreement with Springer NaturePeer reviewe

Evaluating a species phylogeny using ddRAD SNPs: cytonuclear discordance and introgression in the salmonid genus Thymallus (Salmonidae)

International audienceHybridization 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 all Thymallus (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

Global systematic diversity, range distributions, conservation and taxonomic assessments of graylings (Teleostei: Salmonidae; Thymallus spp.)

International audienceGraylings (Thymallus) are among the less well-studied groups of salmonid fishes, especially across their Asian distribution range. Here we perform a comprehensive global review of their phylogeography, systematic diversity and range distributions, including biogeographic reconstruction and assessment of both conservation and taxonomic status of each species. Based on a mitogenomic phylogenetic analysis, three approaches to the delineation of molecular operational units, and evaluation of 15 a-priori defined species, we provide biological support for the recognition of 13 grayling species, plus two additional species tentatively. Several instances of paraphyly and its potential effect on systematic inferences are discussed. Overall, the genus displays increasing species diversity and decreasing range size from higher to lower latitudes and ancestral trait reconstruction supports an East Asian origin for extant diversity, most likely centred in the Amur River drainage. Europe's colonization by Thymallus took place as early as the late Miocene, at least two colonisations of North America are supported, and multiple dispersal events likely took place into Western Siberia. The conservation status for the 15 taxa was estimated to be: 6 least concern, 1 near-threatened, 2 vulnerable, 3 endangered and 3 data deficient