Understanding how the evolutionary dynamics of widespread species unfold in space and time is critical for uncovering the processes shaping biodiversity. We integrated mitochondrial DNA and genome-wide SNPs to investigate the diversification of the widespread Southern House Wren (Troglodytes musculus) in southern South America and its insular relative, Cobb’s Wren (T. cobbi) from the Malvinas/Falkland Islands (MFI). We aim to reveal processes shaping their evolutionary history and potentially that of other co-distributed taxa. Our analyses indicate a pattern of latitudinal divergence, with an initial split between northern populations (Bolivia, Northern and Central Argentina, Uruguay) and southern populations from Patagonia and the MFI. Shortly after, further diversification occurred, including the colonization of the MFI from Patagonia, where the insular population became isolated, and a split between an Andean lineage and a widespread lowland lineage. Both the timing of these splits and the mitochondrial and genomic patterns suggest a major role of glaciations, particularly the Great Patagonian Glaciation, in the diversification of these species in the southern Neotropics. The colonization of the MFI and negligible gene flow with the continent led to the formation of T. cobbi, contrasting with the notable post-glacial gene flow between the continental northern and southern lineages, although with reduced gene flow between Andean and lowland populations. These results underscore how historical divergence, ecological barriers, and secondary contact jointly shape population structure and genetic diversity, with implications for understanding diversification in widespread species.
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