Comparative Population Genomics of Cryptic Speciation and Adaptive Divergence in Bicknell’s and Gray-Cheeked Thrushes (Aves:Catharus bicknelliandCatharus minimus)

Abstract

Cryptic speciation may occur when reproductive isolation is recent or the accumulation of morphological differences between sister lineages is slowed by stabilizing selection preventing phenotypic differentiation. In North America, Bicknell’s Thrush (Catharus bicknelli) and its sister species, the Gray-cheeked Thrush (Catharus minimus), are parapatrically breeding migratory songbirds, distinguishable in nature only by subtle differences in song and coloration, and were recognized as distinct species only in the 1990s. Previous molecular studies have estimated that the species diverged approximately 120,000–420,000 YBP and found very low levels of introgression despite their similarity and sympatry in the spring (prebreeding) migration. To further clarify the history, genetic divergence, genomic structure, and adaptive processes in C. bicknelli and C. minimus, we sequenced and assembled high-coverage reference genomes of both species and resequenced genomes from population samples of C. bicknelli, C. minimus, and two individuals of the Swainson’s Thrush (Catharus ustulatus). The genome of C. bicknelli exhibits markedly higher abundances of transposable elements compared with other Catharus and chicken. Demographic and admixture analyses confirm moderate genome-wide differentiation (Fst ≈ 0.10) and limited gene flow between C. bicknelli and C. minimus, but suggest a more recent divergence than estimates based on mtDNA. We find evidence of rapid evolution of the Z-chromosome and elevated divergence consistent with natural selection on genomic regions near genes involved with neuronal processes in C. bicknelli. These genomes are a useful resource for future investigations of speciation, migration, and adaptation in Catharus thrushes.

Genetic architecture of behavioural resilience to ocean acidification

“…2, see Methods for details on window definition and filtering). Similar analyses with comparable number of samples have been used previously to identify genomic regions associated with tame behaviour in farm-bred red foxes (Kukekova et al 2018), genomic signatures of speciation for in Lake Victoria cichlids (Nakamura et al 2021) and North American songbirds (Termignoni-Garcia et al 2022) amongst others. This analysis yielded three genomic outlier regions with consistently strong signal for all three measures (Table S9, Fig.…”

Coinfection rates of avian blood parasites increase with latitude in parapatric host species

“…Closely related host species that exist across parapatric boundaries are useful for this purpose, as it is possible to assess how the dynamics of coinfection change (or do not) from 1 species to the next despite relatively small geographic distances. There is evidence to suggest that parasites could help maintain parapatric boundaries among species if there is differential susceptibility to the co-evolved parasites of each host species (Thornhill and Fincher, 2013;Theodosopoulos et al, 2019), or increased susceptibility of hybrid offspring to parasite infection (Sage et al, 1986;Wolinska et al, 2004). If coinfections have greater virulence and fitness costs than single infections, a higher prevalence of coinfections could accentuate this 'wedge effect' and help to maintain species boundaries.…”

“…1 ) and were likely more geographically disparate during the Pleistocene (FitzGerald et al ., 2020 ). These species were elevated from sub-species to full species due to recognition of significant differences in morphology, vocalizations and habitats (Ouellet, 1993 ), and confirmed genetically more recently (FitzGerald et al ., 2020 ; Termignoni-Garcia et al ., 2022 ). These 2 species are similar in their high rates and diversity of haemosporidian infections, with especially high prevalence of parasites in the understudied genus Leucocytozoon (Starkloff et al ., 2020 ).…”

Seasonally migratory songbirds have different historic population size characteristics than resident relatives

“…2015Delmore et al,. , 2016Outlaw et al, 2003 ;Ruegg et al, 2014 ;Termignoni-Garcia et al, 2022 ;Voelker et al, 2013 ;Winker, 2000Winker, , 2010Winker and Pruett, 2006 ). These animals are relatively small, omnivorous or insectivorous, forest-related birds with lineages that are long-distance seasonal migrants in North America and others that are resident in tropical North and South America (Collar, 2005 ).…”