DOI: 10.5061/dryad.573n5tbb8
title: Disturbance-mediated hybridization in black-capped and mountain chickadees

description: 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.
description: 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 F<sub>ST</sub> for each SNP, we
 filtered SNPs to retain loci with FST &gt; 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).