Determining gene flow and the influence of selection across the equatorial barrier of the East Pacific Rise in the tube-dwelling polychaete Alvinella pompejana

International audienceBackground: Comparative phylogeography recently performed on the mitochondrial cytochrome oxidase I (mtCOI) gene from seven deep-sea vent species suggested that the East Pacific Rise fauna has undergone a vicariant event with the emergence of a north/south physical barrier at the Equator 1-2 Mya. Within this specialised fauna, the tube-dwelling polychaete Alvinella pompejana showed reciprocal monophyly at mtCOI on each side of the Equator (9 degrees 50'N/7 degrees 25'S), suggesting potential, ongoing allopatric speciation. However, the development of a barrier to gene flow is a long and complex process. Secondary contact between previously isolated populations can occur when physical isolation has not persisted long enough to result in reproductive isolation between genetically divergent lineages, potentially leading to hybridisation and subsequent allelic introgression. The present study evaluates the strength of the equatorial barrier to gene flow and tests for potential secondary contact zones between A. pompejana populations by comparing the mtCOI gene with nuclear genes. Results: Allozyme frequencies and the analysis of nucleotide polymorphisms at three nuclear loci confirmed the north/south genetic differentiation of Alvinella pompejana populations along the East Pacific Rise. Migration was oriented north-to-south with a moderate allelic introgression between the two geographic groups over a narrow geographic range just south of the barrier. Multilocus analysis also indicated that southern populations have undergone demographic expansion as previously suggested by a multispecies approach. A strong shift in allozyme frequencies together with a high level of divergence between alleles and a low number of `hybrid' individuals were observed between the northern and southern groups using the phosphoglucomutase gene. In contrast, the S-adenosylhomocysteine hydrolase gene exhibited reduced diversity and a lack of population differentiation possibly due to a selective sweep or hitch-hiking. Conclusions: The equatorial barrier leading to the separation of East Pacific Rise vent fauna into two distinct geographic groups is still permeable to migration, with a probable north-to-south migration route for A. pompejana. This separation also coincides with demographic expansion in the southern East Pacific Rise. Our results suggest that allopatry resulting from ridge offsetting is a common mechanism of speciation for deep-sea hydrothermal vent organisms

Amplicon sequencing of 42 nuclear loci supports directional gene flow between South Pacific populations of a hydrothermal vent limpet

In the past few decades, population genetics and phylogeographic studies have improved our knowledge of connectivity and population demography in marine environments. Studies of deep‐sea hydrothermal vent populations have identified barriers to gene flow, hybrid zones, and demographic events, such as historical population expansions and contractions. These deep‐sea studies, however, used few loci, which limit the amount of information they provided for coalescent analysis and thus our ability to confidently test complex population dynamics scenarios. In this study, we investigated population structure, demographic history, and gene flow directionality among four Western Pacific hydrothermal vent populations of the vent limpet Lepetodrilus aff. schrolli. These vent sites are located in the Manus and Lau back‐arc basins, currently of great interest for deep‐sea mineral extraction. A total of 42 loci were sequenced from each individual using high‐throughput amplicon sequencing. Amplicon sequences were analyzed using both genetic variant clustering methods and evolutionary coalescent approaches. Like most previously investigated vent species in the South Pacific, L. aff. schrolli showed no genetic structure within basins but significant differentiation between basins. We inferred significant directional gene flow from Manus Basin to Lau Basin, with low to no gene flow in the opposite direction. This study is one of the very few marine population studies using >10 loci for coalescent analysis and serves as a guide for future marine population studies

Panmixia in a fragmented and unstable environment: the hydrothermal shrimp Rimicaris exoculata disperses extensively along the Mid-Atlantic ridge

Dispersal plays a fundamental role in the evolution and persistence of species, and especially for species inhabiting extreme, ephemeral and highly fragmented habitats as hydrothermal vents. The Mid-Atlantic Ridge endemic shrimp species Rimicaris exoculata was studied using microsatellite markers to infer connectivity along the 7100-Km range encompassing the sampled sites. Astonishingly, no genetic differentiation was found between individuals from the different geographic origins, supporting a scenario of widespread large-scale dispersal despite the habitat distance and fragmentation. We hypothesize that delayed metamorphosis associated to temperature differences or even active directed migration dependent on physical and/or chemical stimuli could explain these results and warrant further studies on adaptation and dispersal mechanisms

Phylogéographie comparée des espèces hydrothermales de la dorsale du Pacifique oriental

Demographic history and past gene flow between populations of deep-sea hydrothermal vent species along the East Pacific Rise (EPR) were assessed using a phylogeographic approach combining a classical allele-frequency-based analysis and more sophisticated coalescence-based methods. A comparative phylogeographic COI-based analysis of seven species (one bivalve, three gastropods, three polychaetes) showed the occurrence of a vicariant event associated with the raise of a physical barrier between the Northern and Southern EPR, 1,3 Mya probably due to the formation of transform faults in the equatorial region (0°-7°25S). This fauna separation was then followed by a more recent (< 0.5 Myr) population expansion in the South for all species. A multilocus approach was then performed on three targeted taxa with different life trait histories (the polychaete: A. pompejana, the bivalve: B. thermophilus, and two cryptic species of the gastropod L. elevatus). This study confirmed results obtained from the previous multi-species approach. Hybridization between divergent lineages from each of the three taxa suggested that the barrier is semi-permeable. The range of the secondary contact zone was however variable depending on life-history traits of each species and selective processes acting at a given gene. Phylogeographic and biogeographical patterns derived from species and assemblages are in agreement with the hypothesis of two biogeographical EPR provinces across the Equator.L’histoire démographique des espèces hydrothermales profondes et leurs échanges génétiques le long de la dorsale du Pacifique oriental ont été analysés en combinant des approches classiques d’analyses de fréquences alléliques entre populations avec des méthodes d’analyse plus récentes basées sur la théorie de la coalescence. Une approche de phylogéographie comparée sur sept espèces (un bivalve, trois gastéropodes, trois polychètes), réalisée sur le gène mitochondrial Cytochrome Oxydase I, a permis de révéler une barrière aux flux de gènes, commune à toutes les espèces entre le Nord et le Sud EPR datant d’environ 1,3 Ma et probablement liée à la formation de failles transformantes entre 0°-7°25’N. Cette séparation de faune s’est accompagnée d’une expansion démographique généralisée plus récente (< 0,5 Ma) au Sud. Une approche multi-locus a ensuite été effectuée sur trois taxons cibles aux traits d’histoire de vie contrastés : le polychète A. pompejana, le bivalve B. thermophilus et le gastéropode L. elevatus (comprenant deux espèces cryptiques). Cette approche a permis de confirmer les résultats obtenus par l’approche multi-spécifique. L’hybridation entre lignées divergentes, détectée chez ces trois taxons, suggère une semi-perméabilité de la barrière aux flux de gènes. L’étendue de la zone de contact secondaire dépend du taxon considéré selon ses traits d’histoire de vie, et des forces de sélection agissant au locus considéré. Les patrons de distributions phylogéographique et biogéographique mis en évidence sur les espèces et les communautés s’accordent pour séparer la dorsale du Pacifique oriental en deux provinces biogéographiques différentes de part et d’autre de l’Equateur

The world's deepest known vent shrimp: a new species of Alvinocarididae from hydrothermal vents on the Mid-Cayman Spreading Centre

We report initial observations of the morphology, phylogeny and ecology of a new species of Alvinocaridid shrimp that dominates the near-vent fauna at hydrothermal vents on the Mid-Cayman Spreading Centre in the Caribbean Sea. Specimens were collected from the world's deepest known vent field at a depth of 4960 m, and an off-axis vent field at a depth of 2300 m. Molecular phylogenetic data confirm that the specimens from these two sites are monospecific. Morphologically, the new species is consistent with the genus Rimicaris, but also has some features previously considered diagnostic for Chorocaris. Based on morphological and phylogenetic evidence, it is provisionally assigned to the genus Rimicaris. Its discovery extends the known geographic range of the Alvinocarididae in the Caribbean Sea and represents their deepest known occurrence. The two known populations of the species occur at sites that differ in depth by 2660 m and exhibit contrasting vent geochemistry, but are only 30 km apart within an isothermal water column. These features will allow future investigation of the influence of depth and local hydrography on population connectivity and gene flow.<br/

Phylogéographie comparée des espèces hydrothermales de la dorsale du Pacifique oriental

L histoire démographique des espèces hydrothermales profondes et leurs échanges génétiques le long de la dorsale du Pacifique oriental ont été analysés en combinant des approches classiques d analyses de fréquences alléliques entre populations avec des méthodes d analyse plus récentes basées sur la théorie de la coalescence. Une approche de phylogéographie comparée sur sept espèces (un bivalve, trois gastéropodes, trois polychètes), réalisée sur le gène mitochondrial Cytochrome Oxydase I, a permis de révéler une barrière aux flux de gènes, commune à toutes les espèces entre le Nord et le Sud EPR datant d environ 1,3 Ma et probablement liée à la formation de failles transformantes entre 0-725 N. Cette séparation de faune s est accompagnée d une expansion démographique généralisée plus récente (< 0,5 Ma) au Sud. Une approche multi-locus a ensuite été effectuée sur trois taxons cibles aux traits d histoire de vie contrastés : le polychète A. pompejana, le bivalve B. thermophilus et le gastéropode L. elevatus (comprenant deux espèces cryptiques). Cette approche a permis de confirmer les résultats obtenus par l approche multi-spécifique. L hybridation entre lignées divergentes, détectée chez ces trois taxons, suggère une semi-perméabilité de la barrière aux flux de gènes. L étendue de la zone de contact secondaire dépend du taxon considéré selon ses traits d histoire de vie, et des forces de sélection agissant au locus considéré. Les patrons de distributions phylogéographique et biogéographique mis en évidence sur les espèces et les communautés s accordent pour séparer la dorsale du Pacifique oriental en deux provinces biogéographiques différentes de part et d autre de l EquateurPARIS-BIUSJ-Physique recherche (751052113) / SudocROSCOFF-Observ.Océanol. (292393008) / SudocSudocFranceF

A new species of Rimicaris (Crustacea: Decapoda: Caridea: Alvinocarididae) from hydrothermal vent fields on the Mid-Cayman Spreading Centre, Caribbean

Rimicaris hybisae sp. nov. is described from hydrothermal vent fields on the world's deepest seafloor spreading centre, the Mid-Cayman Spreading Centre (MCSC), Caribbean, at depths of 2300-4960 m. The new species is described and illustrated on the basis of 17 specimens. Brief notes on the distribution and habitat of the new species are provided. Molecular phylogenetic data from mitochondrial COI (460 base pair (bp)), 16S ribosomal RNA (549 bp) and nuclear 18S ribosomal RNA (576 bp) regions is used to complement the description. Morphological variation within R. hybisae sp. nov. and morphological affinities with previously described species are discussed. Based on morphological and molecular evidence, the new species is provisionally assigned to the genus Rimicaris, and differs from all known species in the genus by a distinctive pair of 'pores' on the posterior lobes of its four-lobed dorsal organ. An emended diagnosis for Rimicaris is provided. Rimicaris hybisae sp. nov. is the first taxon to be described from MCSC vent fields. This record extends the known geographical range of Rimicaris into the Caribbean Sea and constitutes the deepest documented occurrence of alvinocaridid shrimp

Iheyaspira bathycodon new species (Vetigastropoda: Trochoidea: Turbinidae: Skeneinae) from the Von Damm Vent Field, Mid-Cayman Spreading Centre, Caribbean

Iheyaspira bathycodon sp. nov. is described from the Von Damm Vent Field on the world's deepest spreading centre, the Mid-Cayman Spreading Centre (MCSC), Caribbean, at 2300 m depth. The new species is defined and illustrated from 11 specimens, with brief notes on habitat and known distribution. Molecular phylogenetic data from partial COI mDNA, 16S rDNA and nuclear 18S rDNA regions are used to analyse the species’ phylogenetic position and its morphology is compared with previously described skeneid and vent taxa. The new species is distinguished from the most closely allied vent species, Iheyaspira lequios Okutani, Sasaki & Tsuchida, 2000 by morphological differences in radula diagnosis and appendage structure of the head-foot. Iheyaspira bathycodon sp. nov. is the tenth turbinid to be described from a hydrothermal-vent environment and the second species to be named from recently discovered hydrothermal vents on the MCSC. Determining the faunal composition of assemblages at the vent fields of the MCSC will help to elucidate the vent biogeography of the region

TREE2FASTA: a flexible Perl script for batch extraction of FASTA sequences from exploratory phylogenetic trees

Abstract Objective The body of DNA sequence data lacking taxonomically informative sequence headers is rapidly growing in user and public databases (e.g. sequences lacking identification and contaminants). In the context of systematics studies, sorting such sequence data for taxonomic curation and/or molecular diversity characterization (e.g. crypticism) often requires the building of exploratory phylogenetic trees with reference taxa. The subsequent step of segregating DNA sequences of interest based on observed topological relationships can represent a challenging task, especially for large datasets. Results We have written TREE2FASTA, a Perl script that enables and expedites the sorting of FASTA-formatted sequence data from exploratory phylogenetic trees. TREE2FASTA takes advantage of the interactive, rapid point-and-click color selection and/or annotations of tree leaves in the popular Java tree-viewer FigTree to segregate groups of FASTA sequences of interest to separate files. TREE2FASTA allows for both simple and nested segregation designs to facilitate the simultaneous preparation of multiple data sets that may overlap in sequence content

The complete mitochondrial genome of the symbiotic infaunal snapping shrimp Leptalpheus forceps (Decapoda, Alpheidae)

The snapping shrimp Leptalpheus forceps (family Alpheidae) has a unique natural history as an infaunal symbiont of larger burrowing crustaceans. The mitogenome of L. forceps was sequenced, the first for a symbiotic representative of the family and the first for a species outside of the genus Alpheus. The complete mitogenome was 15,463 bp in length and included 13 protein-coding genes, 12 tRNAs, and 2 rRNAs. The gene order matched all known alpheid mitogenomes. Similar to other caridean mitogenomes, the nucleotide composition was A + T biased (62%). A maximum-likelihood phylogenetic analysis of caridean mitogenomes strongly supported monophyly of the family Alpheidae