Partial NADH dehydrogenase subunit 2 (ND2) gene sequences for Trochilidae hummingbirds

Anthropogenic changes have altered the historical distributions of many North American taxa.  As environments shift, ecological and evolutionary processes can combine in complex ways to either stimulate or inhibit range expansion. Here we examine the role of evolution in a rapid range expansion whose ecological context has been well-documented, Anna’s Hummingbird (Calypte anna). Previous work suggests that the C. anna range expansion is the result of an ecological release facilitated by human-mediated environmental changes, where access to new food sources has allowed further filling of the abiotic niche. We examine the role of gene flow and adaptation during range expansion from their native California breeding range, north into Canada and east into New Mexico and Texas, USA. Using low-coverage whole genome sequencing, we found high genetic diversity, low divergence, and little evidence of selection on the northern and eastern expansion fronts. Additionally, there are no clear barriers to gene flow across the native and expanded range. The lack of selective signals between core and expanded ranges could reflect i) an absence of novel selection pressure in the expanded range (supporting the ecological release hypothesis), ii) swamping of adaptive variation due to high gene flow, or iii) limitations of genome scans for detecting small shifts in allele frequencies across many loci. Nevertheless, our results provide an example where strong selection is not apparent during a rapid, contemporary range shift.

Methods
To identify potential Anna’s Hummingbird (Calypte anna) samples, we sequenced nestlings and fledglings of unknown hummingbird species and samples that had been identified as Anna’s Hummingbird (C. anna) and other hummingbird species likely to be collected in the region: Costa’s (C. costae), Allen’s (Selasphorus sasin), Calliope (S. calliope), and Rufous (S. rufus) Hummingbirds. Tissue samples were provided by Dr. Lisa Tell at UC Davis and we extracted genomic DNA using DNeasy Blood & Tissue Kit (Qiagen). We amplified part of the NADH dehydrogenase subunit 2 (ND2) gene using H6313, H6316, and L5219 primers (Sorenson et al., 1999), cleaned the products using an ExoSAP protocol, then sequenced them at UCDNA Sequencing Facility at the University of California, Davis.

For more information, see Adams et al. 2023. Widespread gene flow following range expansion in Anna's Hummingbird. Molecular Ecology. Accepted. DOI:10.1111/mec.16928.