Whole genome sequence data is an ideal tool for characterizing processes
in ecology and evolution. Despite the lowering in sequencing costs, it
can be challenging to produce a genome and high-coverage resequencing
data for a non-model species. New population genomics data analysis
pipelines based on genotype likelihoods allow for a significant
reduction in cost by efficiently extracting information from low
coverage sequence data. We demonstrate the robustness of such approaches
with a genomic data set consisting of two draft genomes of the European
sardine (Sardina pilchardus, Walbaum 1792), and resequencing data
(~1.5 X depth) for 78 individuals from 12 sampling
locations across the 5,000 Km of the species’ distribution range (from
the Eastern Mediterranean to the archipelagos of Madeira and Azores).
Our results clearly show at least three genetic clusters. One includes
individuals from Azores and Madeira (two archipelagos in the Atlantic),
the second corresponds to Iberia (the center of the sampling
distribution), and the third gathers the Mediterranean samples and those
from the Canary Islands. This suggests at least two important barriers
to gene flow, even though these do not seem complete, with individuals
from Iberia showing some degree of admixture. These results together
with the genetic resources generated for this commercially important
taxon provide a baseline for further studies aiming at identifying the
nature of these barriers between Sardine populations, and information
for transnational stock management of this highly exploited species
towards sustainable fisheries.