Data sets and analyses for genomics of cryptic speciation in Catharus thrushes

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 ~120 - 420 thousand 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 re-sequenced genomes from population samples of C.
bicknelli, C. minimus, and two individuals of the Swainson’s Thrush (C.
ustulatus). The genome of C. bicknelli exhibits markedly higher abundances
of transposable elements compared to 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.