Speciation, gene flow, and seasonal migration in Catharus thrushes (Aves:Turdidae)

Population genomics indicate three different modes of divergence and speciation with gene flow in the green-winged teal duck complex

The processes leading to divergence and speciation can differ broadly among taxa with different life histories. We examine these processes in a small clade of ducks with historically uncertain relationships and species limits. The green-winged teal (Anas crecca) complex is a Holarctic species of dabbling duck currently categorized as three subspecies (Anas crecca crecca, A. c. nimia, and A. c. carolinensis) with a close relative, the yellow-billed teal (Anas flavirostris) from South America. A. c. crecca and A. c. carolinensis are seasonal migrants, while the other taxa are sedentary. We examined divergence and speciation patterns in this group, determining their phylogenetic relationships and the presence and levels of gene flow among lineages using both mitochondrial and genome-wide nuclear DNA obtained from 1,393 ultraconserved element (UCE) loci. Phylogenetic relationships using nuclear DNA among these taxa showed A. c. crecca, A. c. nimia, and A. c. carolinensis clustering together to form one polytomous clade, with A. flavirostris sister to this clade. This relationship can be summarized as (crecca, nimia, carolinensis)(flavirostris). However, whole mitogenomes revealed a different phylogeny: (crecca, nimia)(carolinensis, flavirostris). The best demographic model for key pairwise comparisons supported divergence with gene flow as the probable speciation mechanism in all three contrasts (crecca-nimia, crecca-carolinensis, and carolinensis-flavirostris). Given prior work, gene flow was expected among the Holarctic taxa, but gene flow between North American carolinensis and South American flavirostris (M ∼0.1-0.4 individuals/generation), albeit low, was not expected. Three geographically oriented modes of divergence are likely involved in the diversification of this complex: heteropatric (crecca-nimia), parapatric (crecca-carolinensis), and (mostly) allopatric (carolinensis-flavirostris). Our study shows that ultraconserved elements are a powerful tool for simultaneously studying systematics and population genomics in systems with historically uncertain relationships and species limits.

Diversity patterns and speciation processes in a two-island system with continuous migration

Geographic isolation is a central mechanism of speciation, but perfect isolation of populations is rare. Although speciation can be hindered if gene flow is large, intermediate levels of migration can enhance speciation by introducing genetic novelty in the semi-isolated populations or founding small communities of migrants. Here, we consider a two-island neutral model of speciation with continuous migration and study diversity patterns as a function of the migration probability, population size, and number of genes involved in reproductive isolation (dubbed as genome size). For small genomes, low levels of migration induce speciation on the islands that otherwise would not occur. Diversity, however, drops sharply to a single species inhabiting both islands as the migration probability increases. For large genomes, sympatric speciation occurs even when the islands are strictly isolated. Then species richness per island increases with the probability of migration, but the total number of species decreases as they become cosmopolitan. For each genome size, there is an optimal migration intensity for each population size that maximizes the number of species. We discuss the observed modes of speciation induced by migration and how they increase species richness in the insular system while promoting asymmetry between the islands and hindering endemism.

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

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.

Estimating hybridization in the wild using citizen science data: a path forward

Genomic evidence of introgression in natural populations has reinvigorated the study of hybridization in recent years. Still, it is largely unknown how frequently individual organisms mate across species lines. Recently, Justyn et al. 2020 suggested that eBird, one of the world's largest citizen science databases, may supply adequate data for estimating hybridization rates. Here, we compare Justyn et al.'s estimates-and their conclusions that hybridization is rare-with estimates from museum and molecular data. We also estimate hybridization using eBird observations from areas and times when hybridization is possible, namely, in contact zones during the breeding season. These estimates are all considerably higher than those reported in Justyn et al., emphasizing that inferences from multiple datasets can differ radically. Finally, we demonstrate an approach for predicting the location of hybrid zones using eBird data, which can be done with high confidence and with unprecedented resolution. We show that citizen science data, far from settling the question of how frequently bird species hybridize, instead offer a promising step toward more focused study of hybrid zones. This article is protected by copyright. All rights reserved.

Drivers of community turnover differ between avian hemoparasite genera along a North American latitudinal gradient

The latitudinal diversity gradient (LDG) is an established macroecological pattern, but is poorly studied in microbial organisms, particularly parasites. In this study, we tested whether latitude, elevation, and host species predicted patterns of prevalence, alpha diversity, and community turnover of hemosporidian parasites. We expected parasite diversity to decrease with latitude, alongside the diversity of their hosts and vectors. Similarly, we expected infection prevalence to decrease with latitude as vector abundances decrease. Lastly, we expected parasite community turnover to increase with latitudinal distance and to be higher between rather than within host species. We tested these hypotheses by screening blood and tissue samples of three closely related avian species in a clade of North American songbirds (Turdidae: Catharus, n = 466) across 17.5° of latitude. We used a nested PCR approach to identify parasites in hemosporidian genera that are transmitted by different dipteran vectors. Then, we implemented linear-mixed effects and generalized dissimilarity models to evaluate the effects of latitude, elevation, and host species on parasite metrics. We found high diversity of hemosporidian parasites in Catharus thrushes (n = 44 lineages) but no evidence of latitudinal gradients in alpha diversity or prevalence. Parasites in the genus Leucocytozoon were most prevalent and lineage rich in this study system; however, there was limited turnover with latitude and host species. Contrastingly, Plasmodium parasites were less prevalent and diverse than Leucocytozoon parasites, yet communities turned over at a higher rate with latitude and host species. Leucocytozoon communities were skewed by the dominance of one or two highly prevalent lineages with broad latitudinal distributions. The few studies that evaluate the hemosporidian LDG do not find consistent patterns of prevalence and diversity, which makes it challenging to predict how they will respond to global climate change.