Divergent mitochondrial lineages arose within a large, panmictic population of the Savannah Sparrow (Passerculus sandwichensis).

Unusual patterns of mtDNA diversity can reveal interesting aspects of a species’biology. However, making such inferences requires discerning among the many alternativescenarios that could underlie any given mtDNA pattern. Next-generation sequencing methodsprovide large, multi-locus datasets with increased power to resolve unusual mtDNA patterns. AmtDNA-based phylogeography of the Savannah sparrow previously identified two sympatric, butdivergent (~2%) clades within the nominate subspecies group and a third clade that consisted ofbirds sampled from northwest Mexico. We revisited the phylogeography of this species using apopulation genomic dataset to resolve the processes leading to the evolution of sympatric anddivergent mtDNA lineages. We identified two genetic clusters in the genomic datasetcorresponding to (1) the nominate subspecies group, and (2) Mexican birds. Followingdivergence, the nominate clade maintained a large, stable population, indicating that divergentmitochondrial lineages arose within a panmictic population. Simulations based on parameterestimates from this model further confirmed that this demographic history could produceobserved levels of mtDNA diversity. Patterns of divergent, sympatric mtDNA lineages arefrequently interpreted as admixture of historically isolated lineages. Our analyses reject thisinterpretation for Savannah sparrows and underscore the need for genomic datasets to resolve theevolutionary mechanisms behind anomalous, locus-specific patterns.