Extra‐pair paternity as a strategy to reduce the costs of heterospecific reproduction? Insights from the crow hybrid zone

Within hybrid zones of socially monogamous species, the number of mating opportunities with a conspecific can be limited. As a consequence, individuals may mate with a heterospecific (social) partner despite possible fitness costs to their hybrid offspring. Extra‐pair copulations with a conspecific may thus arise as a possible post hoc strategy to reduce the costs of hybridization. We here assessed the rate of extra‐pair paternity in the hybrid zone between all‐black carrion crows (Corvus (corone) corone ) and grey hooded crows (C. (c.) cornix ) and tested whether extra‐pair paternity (EPP) was more likely in broods where parents differed in plumage colour. The proportion of broods with at least one extra‐pair offspring and the proportion of extra‐pair offspring were low overall (6.98% and 2.90%, respectively) with no evidence of hybrid broods having higher EPP rates than purebred nests

Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex

Uncovering the genetic basis of species diversification is a central goal in evolutionary biology. Yet, the link between the accumulation of genomic changes during population divergence and the evolutionary forces promoting reproductive isolation is poorly understood. Here, we analysed 124 genomes of crow populations with various degrees of genome-wide differentiation, with parallelism of a sexually selected plumage phenotype, and ongoing hybridization. Overall, heterogeneity in genetic differentiation along the genome was best explained by linked selection exposed on a shared genome architecture. Superimposed on this common background, we identified genomic regions with signatures of selection specific to independent phenotypic contact zones. Candidate pigmentation genes with evidence for divergent selection were only partly shared, suggesting context-dependent selection on a multigenic trait architecture and parallelism by pathway rather than by repeated single-gene effects. This study provides insight into how various forms of selection shape genome-wide patterns of genomic differentiation as populations diverge

Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting

Closely related species may show similar levels of genetic diversity in homologous regions of the genome owing to shared ancestral variation still segregating in the extant species. However, after completion of lineage sorting, such covariation is not necessarily expected. On the other hand, if the processes that govern genetic diversity are conserved, diversity may potentially covary even among distantly related species. We mapped regions of conserved synteny between the genomes of two divergent bird speciescollared flycatcher and hooded crow-and identified more than 600 Mb of homologous regions (66% of the genome). From analyses of whole-genome resequencing data in large population samples of both species we found nucleotide diversity in 200 kb windows to be well correlated (Spearman's rho = 0.407). The correlation remained highly similar after excluding coding sequences. To explain this covariation, we suggest that a stable avian karyotype and a conserved landscape of recombination rate variation render the diversity-reducing effects of linked selection similar in divergent bird lineages. Principal component regression analysis of several potential explanatory variables driving heterogeneity in flycatcher diversity levels revealed the strongest effects from recombination rate variation and density of coding sequence targets for selection, consistent with linked selection. It is also possible that a stable karyotype is associated with a conserved genomic mutation environment contributing to covariation in diversity levels between lineages. Our observations imply that genetic diversity is to some extent predictable

Genetic and Environmental Drivers of Migratory Behavior in Western Burrowing Owls and Implications for Conservation and Management

Migration is driven by a combination of environmental and genetic factors, but many questions remain about those drivers. Potential interactions between genetic and environmental variants associated with different migratory phenotypes are rarely the focus of study. We pair low coverage whole genome resequencing with a de novo genome assembly to examine population structure, inbreeding, and the environmental factors associated with genetic differentiation between migratory and resident breeding phenotypes in a species of conservation concern, the western burrowing owl (Athene cunicularia hypugaea). Our analyses reveal a dichotomy in gene flow depending on whether the population is resident or migratory, with the former being genetically structured and the latter exhibiting no signs of structure. Among resident populations, we observed significantly higher genetic differentiation, significant isolation-by-distance, and significantly elevated inbreeding. Among migratory breeding groups, on the other hand, we observed lower genetic differentiation, no isolation-by-distance, and substantially lower inbreeding. Using genotype–environment association analysis, we find significant evidence for relationships between migratory phenotypes (i.e., migrant versus resident) and environmental variation associated with cold temperatures during the winter and barren, open habitats. In the regions of the genome most differentiated between migrants and residents, we find significant enrichment for genes associated with the metabolism of fats. This may be linked to the increased pressure on migrants to process and store fats more efficiently in preparation for and during migration. Our results provide a significant contribution toward understanding the evolution of migratory behavior and vital insight into ongoing conservation and management efforts for the western burrowing owl

Leveraging genomics to understand threats in a migratory waterbird

Understanding how risk factors affect populations across their annual cycle is a major challenge for conserving migratory birds. For example, disease outbreaks may happen on the breeding grounds, the wintering grounds, or during migration and are expected to accelerate under climate change. The ability to identify the geographic origins of impacted individuals, especially outside of breeding areas, might make it possible to predict demographic trends and inform conservation decision-making. However, such an effort is made more challenging by the degraded state of carcasses and resulting low quality of DNA available. Here, we describe a rapid and low-cost approach for identifying the origins of birds sampled across their annual cycle that is robust even when DNA quality is poor. We illustrate the approach in the common loon (Gavia immer), an iconic migratory aquatic bird that is under increasing threat on both its breeding and wintering areas. Using 300 samples collected from across the breeding range, we develop a panel of 158 single-nucleotide polymorphisms (SNP) loci with divergent allele frequencies across six genetic subpopulations. We use this SNP panel to identify the breeding grounds for 142 live nonbreeding individuals and carcasses. For example, genetic assignment of loons sampled during botulism outbreaks in parts of the Great Lakes provides evidence for the significant role the lakes play as migratory stopover areas for loons that breed across wide swaths of Canada, and highlights the vulnerability of a large segment of the breeding population to botulism outbreaks that are occurring in the Great Lakes with increasing frequency. Our results illustrate that the use of SNP panels to identify breeding origins of carcasses collected during the nonbreeding season can improve our understanding of the population-specific impacts of mortality from disease and anthropogenic stressors, ultimately allowing more effective management.Published versio

Insights into the \u3cem\u3eEtheostoma spectabile\u3c/em\u3e species complex: Incongruence between mitochondrial and nuclear gene sequence data

Hybridization is recognized as an evolutionary process that can provide a significant source of genetic variation and whose genetic consequences have been investigated across a wide taxonomic range of plants and animals. Darters (Percidae: Etheostomatinae) are a clade with documented interspecific hybridization and many species with a recent evolutionary origin, yet most molecular phylogenetic analyses of darters to date have relied primarily on mitochondrial DNA (mtDNA) sequences. Inferring relationships within and between closely related species using a single locus gene tree is potentially confounded by introgression as well as retention of ancestral polymorphisms. This can lead to incongruence between the gene tree and the species tree, and confound interpretations of phylogeography and species relationships. Considering these limitations, I utilized both mtDNA and six nuclear genes to reconstruct the phylogeny of the E. spectabile species complex, a hypothesized reciprocally monophyletic group with known instances of intergradation and hybridization. My objectives were twofold: 1) to determine if the molecular evidence supported the recent species delimitations based on meristics and breeding male coloration and 2) to determine the phylogenetic utility and congruence of mtDNA and nuclear DNA data to address possible hybridization in the species complex. I found concordance between distinct genetic signals, meristics and geographic distributions that supported many, but not all of the recognized species. I also found that introgression is prevalent throughout the history of the E. spectabile species complex, and confounds the monophyly of the complex, specifically with E. fragi and E. uniporum mtDNA haplotypes grouping outside of the complex. Understanding the prevalence of introgression is crucial for future investigation of the evolution of these fishes

Data from: Explicit tests of paleodrainage connections of southeastern North America and the historical biogeography of Orangethroat Darters (Percidae: Etheostoma: Ceasia)

The alteration of paleodrainage river connections has shaped patterns of speciation, genetic diversity, and the geographic distribution of the species-rich freshwater fauna of North America. The integration of ancestral range reconstruction methods and divergence time estimates provides an opportunity to infer paleodrainage connectivity and test alternative paleodrainage hypotheses. Members of the Orangethroat Darter clade, Ceasia, are endemic to southeastern North America and occur north and south of the Pleistocene glacial front, a distributional pattern that makes this clade of closely related species an ideal system to investigate the number and location of glacial refugia and compare alternative hypotheses regarding the proposed evolution of the Teays-Mahomet paleodrainage. This study utilized time-calibrated mitochondrial and nuclear gene phylogenies and present-day geographic distributions to investigate hypothesized Teays-Mahomet River connections through time using a dispersal-extinction cladogenesis framework (DEC). Results of DEC ancestral area reconstructions indicate that the Teays-Mahomet River was a key dispersal route between disjunct highland regions connecting the Mississippi River tributaries to the Old-Ohio Drainage minimally at two separate occasions during the Pleistocene. There was a dynamic interplay between paleodrainage connections through time and postglacial range expansion from three glacial refugia that shaped the current genetic structure and geographic distributions of the species that comprise Ceasia

BEAST and *BEAST analyses

We utilized a Bayesian strategy that relied on external fossil calibrations in the perciform fish clade Centrarchidae to time-calibrate the mtDNA phylogeny, individual gene trees inferred from each of the ten nuclear genes and a phylogeny inferred from the concatenation of ten nuclear genes, and a phylogeny inferred from the concatenation of ten nuclear and two mitochondrial genes in BEAST. We also calibrated divergence times on a nuclear species tree using *BEAST, excluding the mitochondrial genes to avoid incongruence among gene trees resulting from mitochondrial replacement via introgressive hybridization that is common among species of Ceasia. The xml files were generated in BEAUti, however the species tree divergence time xml file were also changed by hand. All samples were collected in the field and accession numbers for each gene accompany this dryad submissio

Genetic and ecological drivers of molt in a migratory bird

Abstract The ability of animals to sync the timing and location of molting (the replacement of hair, skin, exoskeletons or feathers) with peaks in resource availability has important implications for their ecology and evolution. In migratory birds, the timing and location of pre-migratory feather molting, a period when feathers are shed and replaced with newer, more aerodynamic feathers, can vary within and between species. While hypotheses to explain the evolution of intraspecific variation in the timing and location of molt have been proposed, little is known about the genetic basis of this trait or the specific environmental drivers that may result in natural selection for distinct molting phenotypes. Here we take advantage of intraspecific variation in the timing and location of molt in the iconic songbird, the Painted Bunting (Passerina ciris) to investigate the genetic and ecological drivers of distinct molting phenotypes. Specifically, we use genome-wide genetic sequencing in combination with stable isotope analysis to determine population genetic structure and molting phenotype across thirteen breeding sites. We then use genome-wide association analysis (GWAS) to identify a suite of genes associated with molting and pair this with gene-environment association analysis (GEA) to investigate potential environmental drivers of genetic variation in this trait. Associations between genetic variation in molt-linked genes and the environment are further tested via targeted SNP genotyping in 25 additional breeding populations across the range. Together, our integrative analysis suggests that molting is in part regulated by genes linked to feather development and structure (GLI2 and CSPG4) and that genetic variation in these genes is associated with seasonal variation in precipitation and aridity. Overall, this work provides important insights into the genetic basis and potential selective forces behind phenotypic variation in what is arguably one of the most important fitness-linked traits in a migratory bird

lagrange_analysis_files

We applied the DEC model implemented in lagrange (Ree & Smith 2008) to obtain reconstructed ancestral areas at all internal nodes and infer probable dispersal scenarios over a distribution of dated mitonuclear phylogenies and dated nuclear species trees. The files implemented in lagrange include the geographic data for the mitonuclear data set and the nuclear species tree data set (.data files), the rate matrices for each time period within each paleodrainage hypothesis (.rm files), the distribution of mitonuclear phylogenies and species trees (.trees files) and the scripts to call each (.lg files)