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

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

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

International audienceWe 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

Les poissons d'eau douce de France

International audienc

An Overview of the French eDNA Data Landscape: Focus on a national technical repository of reference genetic sequences

Environmental DNA (eDNA) data enables biodiversity to be monitored at unprecedented resolution and scale. There is great potential in combining knowledge from traditional and innovative methods such as eDNA for biodiversity assessment. eDNA use cases are increasing in aquatic and marine environments, and studies on soils have been developed in recent years.PatriNat*1 (under the guardianship of the French Biodiversity Office (OFB), National Museum of Natural History (MNHN), National Center for Scientific Research (CNRS), and Research Institute for Development (IRD)) is a French data and expertise center working with environmental and research stakeholders to develop data exchanges at all levels. We discuss what eDNA data is (Fig. 1), the different types of data, and the importance of their storage and accessibility.As the amount of eDNA data increases, public agencies need to propose FAIR (Findable, Accessible, Interoperable, Reusable) tools and methods to facilitate their use and foster the development of relevant scientific expertise. We give an overview of the French eDNA data landscape and links with existing standards SINP*2 (National Heritage Inventory Information System), Darwin Core*3(Wieczorek et al. 2012) and workflows (Fig. 2).  A priority of eDNA data is to have reliable reference bases and FAIR metadata. PatriNat's new tool will provide access to expertly validated genetic sequence data on species present in France, and is urgently needed for research but also knowledge, monitoring, public policies, and potential law enforcement purposes. We therefore present this technical database built in conjunction with, among other initiatives, DiSSCo*4, iBOL*5 and TaxRef*6 (Gargominy et al. 2022). It will manage 3 data types:   Intrinsic sequence data (marker, sequencing methods, etc.).  Sequence management (organization, identifiers, URLs, etc.).   Voucher data   It will use the nomenclature of Chakrabarty et al. (2013) as well as:   The Global Genome Biodiversity Network (GGBN) standard*7 (Droege et al. 2016)The Minimum information about any sequence (MIxS) standard (Yilmaz et al. 2011)The Biological Collection Data (ABCD) standard*8 (Holetschek et al. 2012)The Collections Descriptions terms*9 (Woodburn et al. 2021)The DwC DNA extension*10 can be used for sharing parts of its contents to the Global Biodiversity Information Facility, but referencing sequences associated with specimens/vouchers will require other standards

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

Dna barcoding and molecular systematics of the benthic and demersal organisms of the ceamarc survey

The Dumont d\u27Urville Sea (East Antarctic region) has been less investigated for DNA barcoding and molecular taxonomy than other parts of the Southern Ocean, such as the Ross Sea and the Antarctic Peninsula. The Collaborative East Antarctic MARine Census (CEAMARC) took place in this area during the austral summer of 2007-2008. The Australian vessel RSV Aurora Australis collected very diverse samples of demersal and benthic organisms. The specimens were sorted centrally, and then distributed to taxonomic experts for molecular and morphological taxonomy and identification, especially barcoding. The COI sequences generated from CEAMARC material provide a sizeable proportion of the Census of Antarctic Marine Life barcodes although the studies are still ongoing, and represent the only source of sequences for a number of species. Barcoding appears to be a valuable method for identification within most groups, despite low divergences and haplotype sharing in a few species, and it is also useful as a preliminary taxonomic exploration method. Several new species are being described. CEAMARC samples have already provided new material for phylogeographic and phylogenetic studies in cephalopods, pycnogonids, teleost fish, crinoids and sea urchins, helping these studies to provide a better insight in the patterns of evolution in the Southern Ocean

Dna barcoding and molecular systematics of the benthic and demersal organisms of the ceamarc survey

The Dumont d'Urville Sea (East Antarctic region) has been less investigated for DNA barcoding and molecular taxonomy than other parts of the Southern Ocean, such as the Ross Sea and the Antarctic Peninsula. The Collaborative East Antarctic MARine Census (CEAMARC) took place in this area during the austral summer of 2007-2008. The Australian vessel RSV Aurora Australis collected very diverse samples of demersal and benthic organisms. The specimens were sorted centrally, and then distributed to taxonomic experts for molecular and morphological taxonomy and identification, especially barcoding. The COI sequences generated from CEAMARC material provide a sizeable proportion of the Census of Antarctic Marine Life barcodes although the studies are still ongoing, and represent the only source of sequences for a number of species. Barcoding appears to be a valuable method for identification within most groups, despite low divergences and haplotype sharing in a few species, and it is also useful as a preliminary taxonomic exploration method. Several new species are being described. CEAMARC samples have already provided new material for phylogeographic and phylogenetic studies in cephalopods, pycnogonids, teleost fish, crinoids and sea urchins, helping these studies to provide a better insight in the patterns of evolution in the Southern Ocean

Case 3 of Table 1.

<p>This situation is a mix of case 1 and case 2. A taxonomic decision would simply lead to case 2, where supplementary data about the tempo of diversification would then be required (see text).</p