DOI: 10.5061/dryad.ffbg79cwq
title: Subtle limits to connectivity revealed by outlier loci within two divergent metapopulations of the deep-sea hydrothermal gastropod Ifremeria nautilei

description: Hydrothermal vents form archipelagos of ephemeral deep-sea habitats that
 raise interesting questions about the evolution and dynamics of the
 associated endemic fauna, constantly subject to extinction-recolonization
 processes. These metal-rich environments are coveted for the mineral
 resources they harbor, thus raising recent conservation concerns. The
 evolutionary fate and demographic resilience of hydrothermal species
 strongly depend on the degree of connectivity among and within their
 fragmented metapopulations. In the deep sea, however, assessing
 connectivity is difficult and usually requires indirect genetic
 approaches. Improved detection of fine-scale genetic connectivity is now
 possible based on genome-wide screening for genetic differentiation. Here,
 we explored population connectivity in the hydrothermal vent snail
 Ifremeria nautilei across its species range encompassing five distinct
 back-arc basins in the Southwest Pacific. The global analysis, based on 10
 570 single nucleotide polymorphism (SNP) markers derived from double
 digest restriction-site associated DNA sequencing (ddRAD-seq), depicted
 two semi-isolated and homogeneous genetic clusters. Demo-genetic modeling
 suggests that these two groups began to diverge about 70 000 generations
 ago, but continue to exhibit weak and slightly asymmetrical gene flow.
 Furthermore, a careful analysis of outlier loci showed subtle limitations
 to connectivity between neighboring basins within both groups. This
 finding indicates that migration is not strong enough to totally
 counterbalance drift or local selection, hence questioning the potential
 for demographic resilience at this latter geographical scale. These
 results illustrate the potential of large genomic datasets to understand
 fine-scale connectivity patterns in hydrothermal vents and the deep sea.
description: VCF datasets were generated “de novo” with Stacks V.2.52 from
 reads produce by the protocols used and provided in the
 manuscript.<br><br>Sample associated metadata were collected
 during field sampling.<br><br>
description: <strong># Usage note</strong><br>VCF datasets
 were generated “<em>de novo</em>” with Stacks V.2.52 from
 reads produce by the protocols used and provided in the
 manuscript.<br><br>Sample associated metadata were collected
 during field sampling.<br><br><strong># File
 description</strong><br><br><strong>Metadata
 file</strong><br><br>Metadata csv file about samples
 information.<br>This contains information about the 486 samples
 during the field work. (cruise part, basin, locality, sample site ,depth
 and the associated name used in the analyses)<br>-
 <strong>SampleID</strong> : Sample ID of all
 individual<br>- <strong>Cruise_part</strong> : part of
 the sampling cruise <br>-<strong> Individual </strong>:
 Individual name of the sample<br>-
 <strong>Sample_name</strong> : Sample name used in the
 ddRad-seq libraries<br>- <strong>Sample_site</strong> :
 ID of the sampling site (within the locality)<br>-
 <strong>Locality</strong> : Name of the locality or
 hydrothermal field for all samples <br>-
 <strong>Locality2</strong>    : Name of the locality or
 hydrothermal for only Chubacarc sample<br>-
 <strong>Basin</strong> : Name of the basin <br>-
 <strong>Depth(m)</strong> : Depth of the sampling sites in
 meter<br>- <strong>Cruise</strong> : Origin (cruise or
 collection) of the sample  (SH: Stephane Hourdez collection &
 C_LVD : Cindy Lee Van Dover collection) missing data
 are mentionned by an
 "n/a"<br><br><strong>ddRad-seq VCF
 files</strong><br><br>VCF files of the ddRad-seq
 dataset.<br>the VCF file
 *“<em>Ifremeria_VCF_global_analysis_1SNP_loci.vcf</em>”*
 contains all the 10 570 Radtag with 1 SNP per Radtag loci used in the
 global analysis. the second VCF file
 *“<em>Ifremeria_VCF_global_analysis_1SNP_loci.vcf</em>“*
 contains all the 17 365 Radtag with 1 SNP per Radtag loci used in
 <em>dadi</em> inferences.