Populations genomics of deep-sea hydrothermal vent copepod Stygiopontius lauensis: from raw fasta files to filtered vcf file

Copepoda is the most abundant taxon in deep-sea hydrothermal vents, where
hard substrate is available. Despite the increasing interest in seafloor
massive sulphides exploitation, there have been no population genomic
studies conducted on vent meiofauna, which are known to contribute over
50% to metazoan biodiversity at vents. To bridge this knowledge gap,
restriction site-associated DNA sequencing, specifically 2b-RADseq, was
used to retrieve thousands of genome-wide single nucleotide polymorphisms
(SNPs) from abundant populations of the vent-obligate copepod
Stygiopontius lauensis from the Lau Basin. SNPs were used to investigate
population structure, demographic histories, genotype-environment
associations at a basin scale. Genetic analyses also helped to evaluate
the suitability of tailored larval dispersal models and the
parameterization of life history traits that better fit the population
patterns observed in the genomic dataset for the target organism. Highly
structured populations were observed on both spatial and temporal scales,
with divergence of populations between the north, mid, and south of the
basin estimated to have occurred after the creation of the major transform
fault dividing the Australian and the Niuafo’ou tectonic plate (350 kya),
with relatively recent secondary contact events (< 20 kya). Larval
dispersal models were able to predict the high levels of structure and the
highly asymmetric northward low-level gene flow observed in the genomic
data. These results differ from most studies conducted on megafauna in the
region, elucidating the need to incorporate smaller size when considering
site-prospecting for deep-sea exploitation of seafloor massive sulphides,
and the creation of area-based management tools to protect areas at risk
of local extinction, should mining occur.