Data from: Continental diversification and insular speciation in a widespread passerine (Troglodytes musculus/cobbi species complex) in southern South America

This dataset supports a population genomic and phylogeographic study of the Southern Wren (Troglodytes musculus) and Cobb's Wren (Troglodytes cobbi) across southern South America. We integrated mitochondrial DNA sequences and genome-wide SNP data to investigate patterns of genetic structure, gene flow, and historical demography. The data reveal a pronounced latitudinal split between northern (T. musculus populations from Bolivia, Northern/Central Argentina, and Uruguay) and southern populations (Patagonia and T. cobbi from the Malvinas/Falkland Islands). Genetically distinct populations were identified in Highland Bolivia and the Malvinas/Falkland Islands, while Central Argentina exhibited high diversity and admixture, indicating a potential zone of secondary contact. The dataset includes VCF files and mitochondrial alignments. These data contribute to understanding how historical isolation, ecological barriers, and secondary contact shape genetic diversity in widely distributed bird species.