Data for: Sampling affects population genetic inference: a case study of the Allen's (Selasphorus sasin) and rufous hummingbird (Selasphorus rufus) (Part 2/2)

Gene flow can affect evolutionary inference when species are undersampled. Here, we evaluate the effects of gene flow and geographic sampling on demographic inference of two hummingbirds that hybridize, Allen's hummingbird (Selasphorus sasin), and the rufous hummingbird (S. rufus). Using whole-genome data and extensive geographic sampling, we find widespread connectivity, with introgression far beyond the Allen's × rufous hybrid zone, although the Z chromosome resists introgression beyond the hybrid zone. We test alternative hypotheses of speciation history of Allen's, rufous, and Calliope (S. calliope) hummingbirds and find that the rufous hummingbird is the sister taxon to Allen's hummingbird, and the Calliope hummingbird is the outgroup. A model treating the two subspecies of Allen's hummingbird as a single panmictic population fit observed genetic data better than models treating the subspecies as distinct populations, in contrast to morphological and behavioral differences and ..., Fastq files that were aligned to the Anna's Hummingbird reference genome., , # Sampling affects population genetic inference: a case study of the Allen's (Selasphorus sasin) and rufous hummingbird (Selasphorus rufus)

[https://doi.org/10.5061/dryad.d2547d876](https://doi.org/10.5061/dryad.d2547d876)

## Description of the data and file structure

Fastq files that were aligned to the Anna's Hummingbird reference genome.

Names of individuals are named as they are described in the supplemental material tables.