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Disturbance-mediated hybridization in black-capped and mountain chickadees


Grabenstein, Kathryn (2022), Disturbance-mediated hybridization in black-capped and mountain chickadees, Dryad, Dataset,


Human habitat disturbances can promote hybridization between closely related, but typically reproductively isolated, species. We explored whether human habitat disturbances are related to hybridization between two closely related songbirds, black-capped, and mountain chickadees, using both genomic and citizen science datasets. First, we genotyped 409 individuals from across both species’ ranges using reduced-representation genome sequencing and compared measures of genetic admixture to a composite measure of human landscape disturbance. Then, using eBird observations, we compared human landscape disturbance values for sites where phenotypically diagnosed hybrids were observed to locations where either parental species was observed to determine whether hybrid chickadees are reported in more disturbed areas. We found that hybridization between black-capped and mountain chickadees positively correlates with human habitat disturbances. From genomic data, we found that 1) hybrid index significantly increased with habitat disturbance, 2) more hybrids were sampled in disturbed habitats, 3) mean hybrid indexes were higher in disturbed habitats versus wild habitats, and 4) hybrids were detected in habitats with significantly higher disturbance values than parentals. Using eBird data, we found that both hybrid and black-capped chickadees were significantly more disturbance-associated than mountain chickadees. Surprisingly, we found that nearly every black-capped chickadee we sampled contained some proportion of hybrid ancestry, while we detected very few mountain chickadee backcrosses. Our results highlight that hybridization between black-capped and mountain chickadees is widespread, but initial hybridization is rare (few F1s were detected). We conclude that human habitat disturbances can erode pre-zygotic reproductive barriers between chickadees and that post-zygotic isolation is incomplete. Understanding what becomes of recently hybridizing species following large-scale habitat disturbances is a new, but pressing, consideration for successfully preserving genetic biodiversity in a rapidly changing world.


We sampled 196 phenotypic black-capped and 213 phenotypic mountain chickadees at 81 sites from across most of their contemporary North American distributions over ten years (2008-2018) during the May-August breeding season. To generate genomic sequence data, we used double-digest restriction site-associated DNA sequencing (ddRAD) following the protocol of Peterson, Weber, Kay, Fisher, & Hoekstra (2012) with modifications as described in Thrasher, Butcher, Campagna, Webster, & Lovette (2018).  After calculating FST for each SNP, we filtered SNPs to retain loci with FST > 0.80 (n = 443) to improve our estimation of population differentiation and hybrid indexes. To identify hybrids in our genomic dataset, we first calculated hybrid indexes and heterozygosity for all individuals using gghybrid (Bailey 2018) and a custom script (available on GitHub), respectively, then we used NewHybrids 1.1 Beta 3 (E. C. Anderson & Thompson, 2002) following the approach of Shurtliff et al. (2014) to assign individuals to one of eight genotypic classes (up to two generations of backcrosses). To measure human landscape disturbances across the continental scale, we used the Global Human Influence Index (Geographic) v2 dataset (1995-2004; WCS and Columbia University 2005). For both the genomic and phenotypic datasets, we plotted the capture location of individuals on the Global Human Influence Index map (Fig. 2a & Supplementary Fig. 5, respectively) and extracted Human Influence Index (HII) values for each chickadee sampling location using R v.4.2.0 (R Development Core Team 2018).


National Science Foundation, Award: DGE-1650115

National Science Foundation, Award: IOS-1754898

National Science Foundation, Award: DEB-1928891