Genomic approaches to understanding population divergence and speciation in birds

© 2016 American Ornithologists\u27 Union. The widespread application of high-throughput sequencing in studying evolutionary processes and patterns of diversification has led to many important discoveries. However, the barriers to utilizing these technologies and interpreting the resulting data can be daunting for first-time users. We provide an overview and a brief primer of relevant methods (e.g., whole-genome sequencing, reduced-representation sequencing, sequence-capture methods, and RNA sequencing), as well as important steps in the analysis pipelines (e.g., loci clustering, variant calling, whole-genome and transcriptome assembly). We also review a number of applications in which researchers have used these technologies to address questions related to avian systems. We highlight how genomic tools are advancing research by discussing their contributions to 3 important facets of avian evolutionary history. We focus on (1) general inferences about biogeography and biogeographic history, (2) patterns of gene flow and isolation upon secondary contact and hybridization, and (3) quantifying levels of genomic divergence between closely related taxa. We find that in many cases, high-throughput sequencing data confirms previous work from traditional molecular markers, although there are examples in which genome-wide genetic markers provide a different biological interpretation. We also discuss how these new data allow researchers to address entirely novel questions, and conclude by outlining a number of intellectual and methodological challenges as the genomics era moves forward

Data from: A wood-warbler produced through both interspecific and intergeneric hybridization

Hybridization between divergent taxa can provide insight into the breakdown of characters used in mate choice, as well as reproductive compatibility across deep evolutionary timescales. Hybridization can also occur more frequently in declining populations, as there is a smaller pool of conspecific mates from which to choose. Here we report an unusual combination of factors that has resulted in a rare, three-species hybridization event amongst two genera of warblers, one of which is experiencing significant population declines. We use bioacoustic, morphometric, and genetic data, to demonstrate that an early generation female hybrid between a golden-winged warbler (Vermivora chrysoptera) and a blue-winged warbler (V. cyanoptera) went on to mate and successfully reproduce with a chestnut-sided warbler (Setophaga pensylvanica). We studied the product of this event—a putative chrysoptera x cyanoptera x pensylvanica hybrid—and show that this male offspring sang songs like S. pensylvanica, but had morphometric traits similar to Vermivora warblers. The hybrid’s maternal parent had V. chrysoptera mitochondrial DNA and, with six plumage-associated loci, we predicted the maternal parent’s phenotype to show that it was likely an early generation Vermivora hybrid. That this hybridization event occurred within a population of Vermivora warblers in significant decline suggests that females may be making the best of a bad situation, and that wood-warblers in general have remained genetically compatible long after they evolved major phenotypic differences

Data from: Admixture mapping in a hybrid zone reveals loci associated with avian feather coloration

Identifying the genetic bases for color patterns has provided important insights into the control and expression of pigmentation and how these characteristics influence fitness. However, much more is known about the genetic bases for traits based on melanin pigments than for traits based on another major class of pigments, carotenoids. Here we use natural admixture in a hybrid zone between Audubon’s and myrtle warblers (Setophaga coronata auduboni / S. c. coronata) to identify genomic regions associated with both types of pigmentation. Warblers are known for rapid speciation and dramatic differences in plumage. For each of five plumage coloration traits, we found highly significant associations with multiple SNPs across the genome and these were clustered in discrete regions. Regions near significantly associated SNPs were enriched for genes associated with keratin filaments, fibrils that makeup feathers. A carotenoid-based trait that differs between the taxa—throat color—had more than a dozen genomic regions of association. One cluster of SNPs for this trait overlaps the Scavenger Receptor Class F Member 2 (SCARF2) gene. Other scavenger receptors are presumed to be expressed at target tissues and involved in the selective movement of carotenoids into the target cells, making SCARF2 a plausible new candidate for carotenoid processing. In addition, two melanin-based plumage traits—colors of the eye line and eye spot—show very strong associations with a single genomic region mapping to chromosome 20 in the zebra finch. These findings indicate that only a subset of the genomic regions differentiated between these two warblers are associated with the plumage differences between them and demonstrate the utility of reduced-representation genomic scans in hybrid zones

Data from: Cultural isolation is greater than genetic isolation across an avian hybrid zone

Elucidating the relationship between genetic and cultural evolution is important in understanding speciation, as learned premating barriers might be involved in maintaining species differences. Here we test this relationship by examining a widely recognized premating barrier, bird song, in a hybrid zone between black-throated green (Setophaga virens) and Townsend's warblers (S. townsendi). We use song analysis, genomic techniques and playback experiments to characterize the cultural and genetic backgrounds of individuals in this region, expecting that if song is an important reproductive barrier between these species, there should be a strong relationship between song and genotype. We show that songs in the hybrid zone correspond to the distinctly different songs found in allopatry but that song and genotype are not tightly coupled in sympatry. Allopatric individuals responded only to local songs, indicating that individuals may have learned to respond to songs they commonly hear. We observed discordance between song and genotype clines; a narrower cline suggests that cultural selection on song is stronger than natural selection on genotype. These findings indicate that song is unlikely to play a role in reproductive isolation between these species, and we suggest that spatial variation in song may nonetheless be maintained by frequency-dependent cultural selection. This decoupling of genes and culture may contribute to hybridization in this region

Data from: Prevalence and diversity of haemosporidian parasites in the yellow-rumped warbler hybrid zone

Parasites can play a role in speciation, by exerting different selection pressures on different host lineages, leading to reproductive barriers in regions of possible interbreeding. Hybrid zones therefore offer an ideal system to study the effect of parasites on speciation. Here we study a hybrid zone in the foothills of the Rocky Mountains where two yellow-rumped warbler subspecies, Setophaga coronata coronata and S. c. auduboni, interbreed. There is partial reproductive isolation between them, but no evidence of strong assortative mating within the hybrid zone, suggesting the existence of a postzygotic selection against hybrids. Here, we test whether haemosporidian parasites might play a role in selecting against hybrids between S. c. coronata and S. c. auduboni. We screened birds from 5 transects across the hybrid zone for three phylogenetic groupings of avian haemosporidians Plasmodium, Haemoproteus and Leucocytozoon parasites and quantified intensity of infection. Contrary to our prediction, hybrids did not have higher haemosporidian parasite prevalence. Variation in Haemoproteus prevalence was best explained by an interaction between a birds’ hybrid index and elevation, while the probability of infection with Leucocytozoon parasites was only influenced by elevation. We also found no significant difference in the diversity of haemosporidian lineages between the warbler subspecies and their hybrids. Finally, intensity of infection by Haemoproteus increased significantly with elevation, but was not significantly linked to birds’ hybrid index. In conclusion, our data suggest that haemosporidian parasites do not seem to play a major role in selecting against hybrids in this system

Dunlin_HighSeq_2014_R1_001.fastq

Genomic data from Illumina sequencing for Dunli

Dunlin_HighSeq_2014_R2_001.fastq

Genomic data from Illumina sequencing for Dunli

A robust new metric of phenotypic distance to estimate and compare multiple trait differences among populations

Whereas a rich literature exists for estimating population genetic divergence, metrics of phenotypic trait divergence are lacking, particularly for comparing multiple traits among three or more populations. Here, we review and analyze via simulation Hedges’ g, a widely used parametric estimate of effect size. Our analyses indicate that g is sensitive to a combination of unequal trait variances and unequal sample sizes among populations and to changes in the scale of measurement. We then go on to derive and explain a new, non-parametric distance measure, “Δp”, which is calculated based upon a joint cumulative distribution function (CDF) from all populations under study. More precisely, distances are measured in terms of the percentiles in this CDF at which each population’s median lies. Δp combines many desirable features of other distance metrics into a single metric; namely, compared to other metrics, p is relatively insensitive to unequal variances and sample sizes among the populations sampled. Furthermore, a key feature of Δp—and our main motivation for developing it—is that it easily accommodates simultaneous comparisons of any number of traits across any number of populations. To exemplify its utility, we employ Δp to address a question related to the role of sexual selection in speciation: are sexual signals more divergent than ecological traits in closely related taxa? Using traits of known function in closely related populations, we show that traits predictive of reproductive performance are, indeed, more divergent and more sexually dimorphic than traits related to ecological adaptation

Current methods and future directions in avian diet analysis

Identifying the composition of avian diets is a critical step in characterizing the roles of birds within ecosystems. However, because birds are a diverse taxonomic group with equally diverse dietary habits, gaining an accurate and thorough understanding of avian diet can be difficult. In addition to overcoming the inherent difficulties of studying birds, the field is advancing rapidly, and researchers are challenged with a myriad of methods to study avian diet, a task that has only become more difficult with the introduction of laboratory techniques to dietary studies. Because methodology drives inference, it is important that researchers are aware of the capabilities and limitations of each method to ensure the results of their study are interpreted correctly. However, few reviews exist which detail each of the traditional and laboratory techniques used in dietary studies, with even fewer framing these methods through a bird-specific lens. Here, we discuss the strengths and limitations of morphological prey identification, DNA-based techniques, stable isotope analysis, and the tracing of dietary biomolecules throughout food webs. We identify areas of improvement for each method, provide instances in which the combination of techniques can yield the most comprehensive findings, introduce potential avenues for combining results from each technique within a unified framework, and present recommendations for the future focus of avian dietary research