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Subtle limits to connectivity revealed by outlier loci within two divergent metapopulations of the deep-sea hydrothermal gastropod Ifremeria nautilei

Citation

Tran Lu Y, Adrien et al. (2022), Subtle limits to connectivity revealed by outlier loci within two divergent metapopulations of the deep-sea hydrothermal gastropod Ifremeria nautilei, Dryad, Dataset, https://doi.org/10.5061/dryad.ffbg79cwq

Abstract

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.

Methods

VCF datasets were generated “de novo” with Stacks V.2.52 from reads produce by the protocols used and provided in the manuscript.

Sample associated metadata were collected during field sampling.

Usage Notes

# Usage note
VCF datasets were generated “de novo” with Stacks V.2.52 from reads produce by the protocols used and provided in the manuscript.

Sample associated metadata were collected during field sampling.

# File description

Metadata file

Metadata csv file about samples information.
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)
- SampleID : Sample ID of all individual
- Cruise_part : part of the sampling cruise
- Individual : Individual name of the sample
- Sample_name : Sample name used in the ddRad-seq libraries
- Sample_site : ID of the sampling site (within the locality)
- Locality : Name of the locality or hydrothermal field for all samples
- Locality2    : Name of the locality or hydrothermal for only Chubacarc sample
- Basin : Name of the basin
- Depth(m) : Depth of the sampling sites in meter
- Cruise : 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"

ddRad-seq VCF files

VCF files of the ddRad-seq dataset.
the VCF file *“Ifremeria_VCF_global_analysis_1SNP_loci.vcf”* contains all the 10 570 Radtag with 1 SNP per Radtag loci used in the global analysis.

the second VCF file *“Ifremeria_VCF_global_analysis_1SNP_loci.vcf“* contains all the 17 365 Radtag with 1 SNP per Radtag loci used in dadi inferences.