Cryptic and extensive hybridization between ancient lineages of American crows

Abstract

Most species and therefore most hybrid zones have historically been defined using phenotypic characters. However, both speciation and hybridization can occur with negligible morphological differentiation. Recently developed genomic tools provide the means to better understand cryptic speciation and hybridization. The Northwestern Crow (Corvus caurinus) and American Crow (Corvus brachyrhynchos) are continuously distributed sister taxa that lack reliable traditional characters for identification. In this first population genomic study of Northwestern and American crows, we use genomic SNPs (nuDNA) and mtDNA to investigate the degree of genetic differentiation between these crows and the extent to which they may hybridize. Our results indicate that American and Northwestern crows have distinct evolutionary histories, supported by two nuDNA ancestry clusters and two 1.1%‐divergent mtDNA clades dating to the late Pleistocene, when glacial advances may have isolated crow populations in separate refugia. We document extensive hybridization, with geographic overlap of mtDNA clades and admixture of nuDNA across >900 km of western Washington and western British Columbia. This broad hybrid zone consists of late‐generation hybrids and backcrosses, but not recent (e.g., F1) hybrids. Nuclear DNA and mtDNA clines had concordant widths and were both centred in southwestern British Columbia, farther north than previously postulated. Overall, our results suggest a history of reticulate evolution in American and Northwestern crows, perhaps due to recurring neutral expansion(s) from Pleistocene glacial refugia followed by lineage fusion(s). However, we do not rule out a contributing role for more recent potential drivers of hybridization, such as expansion into human‐modified habitats.

Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex

“…At this stage of speciation, species boundaries are ephemeral and incipient species can continue to diverge and eventually form distinct species (complete reproductive isolation), or merge back into a single species (Feder et al., 2012; Harrison & Larson, 2014; Mallet, 2008). Therefore, it is critical for cryptic species delimitation to be scrutinized for evidence that lineages are on diverging trajectories of ancestor–descendant series of populations, among which independent lineage status has been achieved via cessation of gene flow (Chan et al., 2017), postzygotic incompatibilities (Pulido‐Santacruz et al., 2018), or prezygotic isolation mechanisms such as ecographic segregation (Dufresnes et al., 2020; Slager et al., 2020; Sobel & Streisfeld, 2015), environmental adaptation (Rundle & Nosil, 2005) and behavioural/mate recognition differentiation (Boake, Andreadis, & Witzel, 2000; Drillon et al, 2019; Köhler et al., 2017). These criteria are more robust, compatible with evolutionary theory and species concepts, and reflective of lineage separation; they should thus be included as part of a more informed, modern, multidisciplinary statistical species delimitation framework to avoid unnecessary taxonomic inflation.…”

How common is avian hybridization on an individual level?*

“…Moreover, some common hybrid combinations, such as American × Northwestern Crow (Slager et al. 2020), are unavailable for eBird data entry because it is not possible to identify them in the field.…”

Hybridization dynamics and extensive introgression in theDaphnia longispinaspecies complex: new insights from a high-qualityDaphnia galeatareference genome

“…(Figure 2C). We consider individuals with intermediate hybrid indices (>0.25 and <0.75) and lower heterozygosity (<0.5) to be later-generation hybrids (Slager, et al 2020) and individuals with a hybrid index of ≤0.25 or ≥0.75 to be backcrossed with the respective parental species.…”