Supplementary material from "The right tool for the right question: contrasting biogeographic patterns in the notothenioid fish Harpagifer spp. along the Magellan province"

Molecular-based analysis has become a fundamental tool to understand the role of Quaternary glacial episodes. In the Magellan province in southern South America, ice covering during the last glacial maximum (20 Kya) radically altered the landscape/seascape, speciation rates and distribution of species. For the notothenioid fishes of the genus Harpagifer, in the area are described two nominal species. Nevertheless, this genus recently colonized South America from Antarctica, providing a short time for speciation processes. Combining DNA sequences and genotyping-by-sequencing SNPs, we evaluated the role of Quaternary glaciations over the patterns of genetic structure in Harpagifer across its distribution in Magellan Province. DNA sequences showed low phylogeographic structure, with shared and dominant haplotypes between nominal species, suggesting a single evolutionary unit. SNPs identified contrastingly two groups in Patagonia and a third well-differentiated group in the Falkland/Malvinas Islands with limited and asymmetric gene flow from. Linking the information of different markers allowed us to infer the relevance of postglacial colonization mediated by the general oceanographic circulation patterns. Contrasting rough- and fine-scale genetic patterns highlights the relevance combined methodologies for species delimitation, which, depending on the question to be addressed, allows discrimination among phylogeographic structure, discarding incipient speciation and contemporary spatial differentiation processes.