Thrushes in Love: Extensive Gene Flow, With Differential Resistance and Selection, Obscures and Reveals the Evolutionary History of a Songbird Clade.

The application of high-throughput sequencing to phylogenetic analyses is allowing authors to reconstruct the true evolutionary history of species. This work can illuminate specific mechanisms underlying divergence when combined with analyses of gene flow, recombination and selection. We conducted a phylogenomic analysis of Catharus, a songbird genus with considerable potential for gene flow, variation in migratory behaviour and genomic resources.

Mapping seasonal migration in a songbird hybrid zone -- heritability, genetic correlations, and genomic patterns linked to speciation.

Seasonal migration is a widespread behavior relevant for adaptation and speciation, yet knowledge of its genetic basis is limited. We leveraged advances in tracking and sequencing technologies to bridge this gap in a well-characterized hybrid zone between songbirds that differ in migratory behavior. Migration requires the coordinated action of many traits, including orientation, timing, and wing morphology.

Night-time neuronal activation of Cluster N in a North American songbird.

Night-migrating songbirds utilize the Earth's magnetic field to help navigate to and from their breeding sites each year. A region of the avian forebrain called Cluster N has been shown to be activated during night migratory behavior and it has been implicated in processing geomagnetic information. Previous studies with night-migratory European songbirds have shown that neuronal activity at Cluster N is higher at night than during the day.

Gene regulation and speciation in a migratory divide between songbirds.

Behavioral variation abounds in nature. This variation is important for adaptation and speciation, but its molecular basis remains elusive. Here, we use a hybrid zone between two subspecies of songbirds that differ in migration - an ecologically important and taxonomically widespread behavior---to gain insight into this topic.

Structural genomic variation and migratory behavior in a wild songbird.

Structural variants (SVs) are a major source of genetic variation; and descriptions in natural populations and connections with phenotypic traits are beginning to accumulate in the literature. We integrated advances in genomic sequencing and animal tracking to begin filling this knowledge gap in the Eurasian blackcap. Specifically, we (a) characterized the genome-wide distribution, frequency, and overall fitness effects of SVs using haplotype-resolved assemblies for 79 birds, and (b) used these SVs to study the genetics of seasonal migration.

Learning and memory in hybrid migratory songbirds: cognition as a reproductive isolating barrier across seasons.

Hybrid zones can be used to identify traits that maintain reproductive isolation and contribute to speciation. Cognitive traits may serve as post-mating reproductive isolating barriers, reducing the fitness of hybrids if, for example, misexpression occurs in hybrids and disrupts important neurological mechanisms. We tested this hypothesis in a hybrid zone between two subspecies of Swainson's thrushes (Catharus ustulatus) using two cognitive tests-an associative learning spatial test and neophobia test.

Genomic architecture of migration timing in a long-distance migratory songbird.

The impact of climate change on spring phenology poses risks to migratory birds, as migration timing is controlled predominantly by endogenous mechanisms. Despite recent advances in our understanding of the underlying genetic basis of migration timing, the ways that migration timing phenotypes in wild individuals may map to specific genomic regions requires further investigation. We examined the genetic architecture of migration timing in a long-distance migratory songbird (purple martin, Progne subis subis) by integrating genomic data with an extensive dataset of direct migratory tracks.

The genetics of bird migration.

Bird migration is one of the most amazing biological phenomena exhibited by organisms today, with birds as small as three grams travelling thousands of kilometers twice each year. Most people are familiar with this behaviour; they likely recognize the seasonal movements of birds each year and may have even witnessed specific migratory events (e.g.

Population-specific association of Clock gene polymorphism with annual cycle timing in stonechats.

Timing is essential for survival and reproduction of organisms across the tree of life. The core circadian clock gene Clk is involved in the regulation of annual timing events and shows highly conserved sequence homology across vertebrates except for one variable region of poly-glutamine repeats. Clk genotype varies in some species with latitude, seasonal timing and migration.

Individual variability and versatility in an eco-evolutionary model of avian migration.

Seasonal migration is a complex and variable behaviour with the potential to promote reproductive isolation. In Eurasian blackcaps (), a migratory divide in central Europe separating populations with southwest (SW) and southeast (SE) autumn routes may facilitate isolation, and individuals using new wintering areas in Britain show divergence from Mediterranean winterers. We tracked 100 blackcaps in the wild to characterize these strategies.

Estimating hybridization rates in the wild: Easier said than done?

Hybridization has important effects on the evolutionary trajectories of natural populations but estimates of this process in the wild and at the individual-level are lacking. Justyn et al. attempted to fill this gap using the citizen science database eBird but there are limitations to this approach.

Shared Patterns of Genome-Wide Differentiation Are More Strongly Predicted by Geography Than by Ecology.

Closely related populations often display similar patterns of genomic differentiation, yet it remains an open question which ecological and evolutionary forces generate these patterns. The leading hypothesis is that this similarity in divergence is driven by parallel natural selection. However, several recent studies have suggested that these patterns may instead be a product of the depletion of genetic variation that occurs as result of background selection (i.

Avian Population Genomics Taking Off: Latest Findings and Future Prospects.

Birds are one of the most recognizable and diverse groups of organisms on earth. This group has played an important role in many fields, including the development of methods in behavioral ecology and evolutionary theory. The use of population genomics took off following the advent of high-throughput sequencing in various taxa.

Comparative analysis examining patterns of genomic differentiation across multiple episodes of population divergence in birds.

Heterogeneous patterns of genomic differentiation are commonly documented between closely related populations and there is considerable interest in identifying factors that contribute to their formation. These factors could include genomic features (e.g.

A comparison of genomic islands of differentiation across three young avian species pairs.

Detailed evaluations of genomic variation between sister species often reveal distinct chromosomal regions of high relative differentiation (i.e., "islands of differentiation" in F ), but there is much debate regarding the causes of this pattern.

Gene flow and selection interact to promote adaptive divergence in regions of low recombination.

Adaptation to new environments often occurs in the face of gene flow. Under these conditions, gene flow and recombination can impede adaptation by breaking down linkage disequilibrium between locally adapted alleles. Theory predicts that this decay can be halted or slowed if adaptive alleles are tightly linked in regions of low recombination, potentially favouring divergence and adaptive evolution in these regions over others.

Candidate genes for migration do not distinguish migratory and non-migratory birds.

Migratory traits in birds have been shown to have a strong heritable component and several candidate genes have been suggested to control these migratory traits. To investigate if the genetic makeup of one or a set of these candidate genes can be used to identify a general pattern between migratory and non-migratory birds, we extracted genomic sequence data for 25 hypothesised candidate genes for migration from 70 available genomes across all orders of Aves and characterised sequence divergence between migratory and non-migratory phenotypes. When examining each gene separately across all species, we did not identify any genetic variants in candidate genes that distinguished migrants from non-migrants; any resulting pattern was driven by the phylogenetic signal.

Migratory orientation in a narrow avian hybrid zone.

Background: Zones of contact between closely related taxa with divergent migratory routes, termed migratory divides, have been suggested as areas where hybrid offspring may have intermediate and inferior migratory routes, resulting in low fitness of hybrids and thereby promoting speciation. In the Rocky Mountains of Canada there is a narrow hybrid zone between Audubon's and myrtle warblers that is likely maintained by selection against hybrids. Band recoveries and isotopic studies indicate that this hybrid zone broadly corresponds to the location of a possible migratory divide, with Audubon's warblers migrating south-southwest and myrtle warblers migrating southeast.

Recurrent selection explains parallel evolution of genomic regions of high relative but low absolute differentiation in a ring species.

Recent technological developments allow investigation of the repeatability of evolution at the genomic level. Such investigation is particularly powerful when applied to a ring species, in which spatial variation represents changes during the evolution of two species from one. We examined genomic variation among three subspecies of the greenish warbler ring species, using genotypes at 13 013 950 nucleotide sites along a new greenish warbler consensus genome assembly.

Investigating Factors that Generate and Maintain Variation in Migratory Orientation: A Primer for Recent and Future Work.

The amazing accuracy of migratory orientation performance across the animal kingdom is facilitated by the use of magnetic and celestial compass systems that provide individuals with both directional and positional information. Quantitative genetics analyses in several animal systems suggests that migratory orientation has a strong genetic component. Nevertheless, the exact identity of genes controlling orientation remains largely unknown, making it difficult to obtain an accurate understanding of this fascinating behavior on the molecular level.

Phenotypic divergence during speciation is inversely associated with differences in seasonal migration.

Differences in seasonal migration might promote reproductive isolation and differentiation by causing populations in migratory divides to arrive on the breeding grounds at different times and/or produce hybrids that take inferior migratory routes. We examined this question by quantifying divergence in song, colour, and morphology between sister pairs of North American migratory birds. We predicted that apparent rates of phenotypic differentiation would differ between pairs that do and do not form migratory divides.

Genomic analysis of a migratory divide reveals candidate genes for migration and implicates selective sweeps in generating islands of differentiation.

Differential gene flow, reductions in diversity following linked selection and/or features of the genome can structure patterns of genomic differentiation during the process of speciation. Possible sources of reproductive isolation are well studied between coastal and inland subspecies groups of Swainson's thrushes, with differences in seasonal migratory behaviour likely playing a key role in reducing hybrid fitness. We assembled and annotated a draft reference genome for this species and generated whole-genome shotgun sequence data for populations adjacent to the hybrid zone between these groups.