Genomic SNP data reveal allopatric divergence during pleistocene glaciations and fine-scale population structure in a southern South American silverside (Odontesthes nigricans)

Abstract

The silverside Odontesthes nigricans has the southernmost distribution in the genus, ranging from Buenos Aires (39° S) to Cape Horn (56° S), including the Islas Malvinas/Falkland Islands, and is the only species of the genus present in the BeagleChannel (BC). Previous evidence based on mitochondrial markers and phenotypic traits showed differentiation between BC and Atlantic coast groups, suggesting a putative contact zone along the Fuegian Atlantic coast (FAC). Here, we combinedmitochondrial control region (CR) sequencing and genome-wide SNPs (RAD-seq) to assess genetic diversity, population structure, and demographic history along a westeast gradient across the BC and adjacent Atlantic localities. We identified marked divergence between BC and FAC populations, with no evident admixture detected among individuals from the sampled sites. We also found recent fine-scale substructure within the BC, between Golondrina Bay (GB) and central Beagle Channel sites (CBC). Demographic modelling supported an initial allopatric divergence between BC and FAC lineages at ~253,000 years ago, followed by a more recent divergence within the BC at ~10,800 years ago. Recent demographic history indicated ancient population bottlenecks in GB and FAC, whereas CBC showed post-Last Glacial Maximum expansion. These results suggest that Quaternary glacial dynamics and shifts in spatial connectivity shaped population divergence in O. nigricans, contributing to our understanding of marine evolutionary processes in southern South America.