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

Abstract

Unusual patterns of mtDNA diversity can reveal interesting aspects of a species’ biology. However, making such inferences requires discerning among the many alternative scenarios that could underlie any given mtDNA pattern. Next‐generation sequencing methods provide large, multilocus data sets with increased power to resolve unusual mtDNA patterns. A mtDNA‐based phylogeography of the Savannah sparrow (Passerculus sandwichensis) previously identified two sympatric, but divergent (~2%) clades within the nominate subspecies group and a third clade that consisted of birds sampled from northwest Mexico. We revisited the phylogeography of this species using a population genomic data set to resolve the processes leading to the evolution of sympatric and divergent mtDNA lineages. We identified two genetic clusters in the genomic data set corresponding to (a) the nominate subspecies group and (b) northwestern Mexico birds. Following divergence, the nominate clade maintained a large, stable population, indicating that divergent mitochondrial lineages arose within a panmictic population. Simulations based on parameter estimates from this model further confirmed that this demographic history could produce observed levels of mtDNA diversity. Patterns of divergent, sympatric mtDNA lineages are frequently interpreted as admixture of historically isolated lineages. Our analyses reject this interpretation for Savannah sparrows and underscore the need for genomic data sets to resolve the evolutionary mechanisms behind anomalous, locus‐specific patterns.

Genomic differentiation and local adaptation on a microgeographic scale in a resident songbird

“…The hypothesized role of selection in shaping patterns of differentiation is not unreasonable given the steep ecological gradients and adaptive challenges associated with freshwater‐saline ecotones (Greenberg et al, 2006; Walsh et al., 2019a). These patterns are notably different, however, from comparisons of tidal marsh Savannah Sparrows in San Francisco Bay, which exhibited low levels of genetic differentiation, even across ecological gradients (Benham & Cheviron, 2019). Pairwise comparisons resulted in the identification of 103 shared SNPs that exhibited elevated signals of differentiation ( F ST greater than 5 SD above the mean).…”

Ghost Introgression: Spooky Gene Flow in the Distant Past

“…Patterns of deep divergence in organellar DNA in combination with shallow nuclear divergence might be due to mitochondrial or plastid capture from an extinct species. [ 8–10 ] However, other demographic and evolutionary processes—including sex‐biased gene flow, [ 11 ] androgenesis, [ 12 ] genetic drift [ 13 ] or independent sorting of haplotypes in a large population [ 14 ] —can culminate in similar patterns. Therefore, it is advisable to rule out these alternative explanations and provide additional evidence for introgression from an extinct lineage, such as signatures of ghost introgression in the nuclear genome.…”

Two Divergent Genetic Lineages within the Horned Passalus Beetle, Odontotaenius disjunctus (Coleoptera: Passalidae): An Emerging Model for Insect Behavior, Physiology, and Microbiome Research

“…Notwithstanding our speculation that population-level processes (e.g., demographic history; see [56]) likely generated and maintain the two divergent, yet sympatric, mtDNA-based lineages reported here, there may, nonetheless, be consequential impacts on other fields of research for which O. disjunctus is used as model species (see Introduction, and Table 1). For example, deeply divergent intraspecific mtDNA clades can be indicative of corresponding differences in nuclear DNA regions (e.g., [57]).…”