Biology subjects

Toews, D. P. L.

Publications and source records attributed to Toews, D. P. L..

9 recordsLinked to original sources

bioRxiv2026

Repeated Transitions in Migratory Behavior Across a Songbird Radiation Are Not Driven by Selection on Shared Variation in Candidate Genes

Understanding the mechanisms facilitating the repeated evolution of traits is a core question in evolutionary biology. While repeated evolution has been observed across many systems, behavioral phenotypes have been less well studied than morphological traits. Migration is a behavioral adaptation to seasonality that has evolved independently in many animals, and repeated gains and losses of migratory behavior have been especially prevalent throughout the diversification of birds. While migratory traits are heritable in many taxa and candidate genes underlying intraspecific variation in migratory behavior have been identified, whether similar genetic changes are responsible for the repeated evolution of migration remains poorly understood. We used a phylogenomic approach to investigate the relationship between variation in candidate genes and migratory propensity across nearly all species in the parulid warbler radiation (n = 101), a group of songbirds in which migratory behavior has been lost and gained multiple times. Comparisons of candidate gene tree topologies to the parulid warbler species tree revealed cases of discordance, though these were explained by differences in the number of phylogenetically informative sites among genes rather than by elevated genetic similarity among species sharing migratory strategies. Testing models of coding sequence evolution identified sites with elevated dN/dS in five candidate genes, suggestive of positive selection; however, variation at these sites showed no clear association with migratory strategy, nor did we detect recurrent selection across lineages where transitions in migratory behavior most likely occurred. Together, these results contradict the hypothesis that selection on shared variation (ancestral polymorphisms or introgressed alleles) facilitated the repeated evolution of migration in this clade.

evolutionary biology↗

bioRxiv2026

Historically Small Population Size Limits Purging of Deleterious Mutations in a Conservation-Reliant Species, the Kirtlands Warbler

Strong population contractions can leave a persistent genomic legacy that can influence populations long after their demographic recovery. While bottlenecks facilitate the removal of strongly deleterious mutations, the effectiveness of purging may be limited in historically small populations. The Kirtlands warbler (Setophaga kirtlandii) is a rare North American songbird with an ancestrally small population. After narrowly evading extinction, they are one of few species that have been delisted from federal protections in the USA. Despite their recovery, a previous study showed evidence for recent inbreeding and a high burden of deleterious mutations that may have not been purged despite strong bottlenecks. Historical DNA offers a unique opportunity to understand the consequences of recent demographic declines on genetic diversity. Here, we use DNA from over 100-year-old museum specimens to estimate changes in genetic load in the Kirtlands warblers pre- and post-bottleneck. We validate our results with forward-in-time genetic simulations and explore how sample size and missing data can affect estimates. Both empirical data and simulations suggest a reduced ability to purge deleterious mutations in this historically small population. Our simulations also highlight that limited sampling design and data quality can constrain the ability to detect changes.

evolutionary biology↗

bioRxiv2025

Diversification and divergence in Myioborus warblers: insights into evolutionary relationships and plumage genetics

Genomic data can provide valuable insights into the evolutionary history of rapidly diversifying groups and the genetic basis of phenotypic differences among lineages. We used whole-genome sequencing of the warbler genus Myioborus to investigate dynamics of its recent diversification in Neotropical mountains. We found that mitochondrial and UCE phylogenies are mostly, but not fully, concordant, and we found phylogenetic support for a pattern of north-to-south and low-to-high elevation colonization in the genus. Within the ornatus-melanocephalus complex, which showed topological incongruence between our phylogenies, we found that genetic structure generally coincides with geographic variation in plumage, although three subspecies with striking plumage differences exhibit low mitochondrial divergence. The hybridizing taxa M. o. chrysops and M. m. bairdi show very shallow genomic differentiation, with marked peaks of divergence. Most of these are shared with other parulid warbler pairs, pointing to broad genomic features, like recombination rate, as the processes shaping these regions. However, other highly differentiated regions were unique to Myioborus, including one containing the gene CCDC91, which is associated with melanin-based plumage differences in several other birds. Lastly, we found higher levels of differentiation on the Z chromosome relative to autosomes, including two putative chromosomal inversions. Together, these results highlight the interplay of deep ancestral divergence, recent hybridization, and shared genomic architecture in shaping the evolution of phenotypic and genomic diversity within Myioborus.

evolutionary biology↗

bioRxiv2024

Migration strategies of a high-latitude breeding songbird (Setophaga coronata coronata) revealed using multi-sensor geolocators and stable isotopes

Seasonal migration allows animals to use habitat where conditions are unfavorable for part of the year but may constrain breeding ranges due to the costs of longer migrations as ranges expand poleward. In species with large ranges, high latitude breeding populations may employ different migratory strategies allowing them to persist far from other core non-breeding areas. The myrtle warbler (Setophaga coronata coronata) has two disjunct non-breeding ranges in North and Central America-one along the Gulf Coast and the other on the Pacific. Previous work indirectly linked birds breeding in Alaska with the Pacific non-breeding area, suggesting that high latitude populations evolved a shorter migration route. We directly tested this hypothesis using geolocators measuring both light and atmospheric pressure to track Alaskan myrtle warbler migration in fine detail and inferred non-breeding areas using hydrogen isotopes for a larger sample of birds breeding in Alaska, British Columbia, and Alberta. We found, contrary to expectations, that all geolocator-tracked birds and most birds with stable isotope data migrated to the southeastern United States, while only a small subset of birds ([~]5%) likely wintered on the Pacific Coast. We additionally demonstrate the advantages of pressure geolocation for characterizing migratory behavior at a fine scale.

animal behavior and cognition↗

bioRxiv2022

Host phylogeny, but not diet diversity, influences gut microbiome composition in breeding wood-warblers

Understanding the factors that shape microbiomes can provide insight on the importance of host-symbiont interactions and on co-evolutionary dynamics. Unlike for mammals, previous studies have found little or no support for an influence of host evolutionary history on avian gut microbiome diversity and instead have suggested a greater influence of the environment or diet due to fast gut turnover. Because effects of different factors may be conflated by captivity and sampling design, examining natural variation using large sample sizes is important. Our goal was to overcome these limitations by sampling wild birds to compare environmental, dietary, and evolutionary influences on gut microbiome structure. We performed fecal metabarcoding to characterize both the gut microbiome and diet of fifteen wood-warbler species across a four-year period and from two geographic localities. We find host taxonomy generally explained [~]10% of the variation between individuals, which is [~]6-fold more variation of any other factor considered, including diet diversity. Further, gut microbiome similarity was more congruent with the host phylogeny than with host diet similarity and we found little association between diet diversity and microbiome diversity. Together, our results suggest evolutionary history is the strongest predictor of gut microbiome differentiation among wood-warblers. Although the phylogenetic signal of the warbler gut microbiome is not very strong, our data suggest that a stronger influence of diet (as measured by diet diversity) does not account for this pattern. The mechanism underlying this phylogenetic signal is not clear, but we argue host traits may filter colonization and maintenance of microbes.

evolutionary biology↗

bioRxiv2020

Quantitative Amplicon Sequencing for Meta-DNA Analysis Reveals Patterns inPollen Use by Bees

Determining how pollinators visit plants versus how they carry and transfer pollen is an ongoing project in pollination ecology. The differences between how pollinators visit flowers versus how they carry pollen can be appreciable, but the current tools for identifying the pollens that bees carry have different strengths and weaknesses when used for ecological inference. In this study we use three methods to better understand a system of congeneric, co-flowering plants in the genus Clarkia and their bee pollinators: observations of plant-pollinator contact in the field, and two different molecular methods to estimate the relative abundance of each Clarkia pollen in samples collected from pollinators. We use these methods to investigate if observations of plant-pollinator contact in the field correspond to the pollen bees carry; if individual bees carry Clarkia pollens in predictable ways, based on previous knowledge of their foraging behaviors; and how the three approaches differ for understanding plant-pollinator interactions. We find that observations of plant-pollinator contact are generally predictive of the pollens that bees carry while foraging, and network topologies using the three different methods are statistically indistinguishable from each other. Results from molecular pollen analysis also show that while bees can carry multiple species of Clarkia at the same time, they often carry one species of pollen. Our work contributes to the growing body of literature aimed at resolving how pollinators use floral resources. We suggest our novel relative amplicon quantification method as another tool in the developing molecular ecology and pollination biology toolbox.

ecology↗

bioRxiv2019

Selection on a pleiotropic color gene block underpins early differentiation between two warbler species

When one species gradually splits into two, divergent selection on specific traits can cause peaks of differentiation in the genomic regions encoding those traits. Whether speciation is initiated by strong selection on a few genomic regions with large effects or by more diffused selection on many regions with small effects remains controversial. Differentiated phenotypes between differentiating lineages are commonly involved in reproductive isolation, thus their genetic underpinnings are key to the genomics architecture of speciation. When two species hybridize, recombination over multiple generations can help reveal the genetic regions responsible for the differentiated phenotypes against a genomic background that has been homogenized via backcrossing and introgression. We used admixture mapping to investigate genomic differentiation and the genetic basis of differentiated plumage features (relative melanin and carotenoid pigment) between hybridizing sister species in the early stage of speciation: Townsends (Setophaga townsendi) and Hermit warblers (S. occidentalis). We found a few narrow and dispersed divergent regions between allopatric parental populations, consistent with the divergence with gene flow model of speciation. One of the divergent peaks involves three genes known to affect pigmentation: ASIP, EIF2S2, and RALY (the ASIP-RALY gene block). After controlling for population substructure, we found that a single nucleotide polymorphism (SNP) inside the intron of RALY displays a strong pleiotropic association with cheek, crown, and breast coloration. In addition, we detect selection on the ASIP-RALY gene block, as the geographic cline of the RALY marker of this gene block has remained narrower than the plumage cline, which remained narrower than expected under neutral diffusion over two decades. Despite extensive gene flow between these species across much of the genome, the selection on ASIP-RALY gene block maintains stable genotypic and plumage difference between species allowing further differentiation to accumulate via linkage to its flanking genetic region or linkage-disequilibrium genome-wide.

evolutionary biology↗

bioRxiv2019

Selection on VPS13A linked to long-distance migratory behavior in a songbird

Animal migration demands an interconnected suite of physiological, behavioral, and neurological adaptations for individuals to successfully navigate and travel over long distances1-3. This trait complex is especially crucial for small songbirds whose migratory behaviors--like directionality and orientation--are innate4,5, rather than being learned as in many large, longer-lived birds. Identifying causal genes involved in these traits has been a central goal of migration ecology, and this endeavor has been furthered by genome-scale comparisons6. However, even the most successful studies of migration genetics have only achieved low resolution associations, identifying large chromosomal regions, across multiple haplotype blocks, that encompass hundreds of putatively causal genes7,8. Here we leverage the extreme genomic similarity among golden-winged (Vermivora chrysoptera) and blue-winged warblers (Vermivora cyanoptera)9 to identify a single gene--Vacuolar Protein Sorting 13 Homolog A (VPS13A)--that is associated with distinct differences in migration directionality to Central American (CA) versus South American (SA) wintering areas10. Moreover, we find significantly reduced sequence variation in this gene-region for SA wintering birds, and show this is the result of strong natural selection on this gene. In humans, VPS13A codes for chorein, and variants of this gene are associated with the neurodegenerative disorder chorea-acanthocytosis11. This new association provides the strongest gene-level linkage for avian migration directionality, and further interrogation of this gene will allow for a better understanding of its role in neuro-muscular processes across vertebrates.

evolutionary biology↗

bioRxiv2018

Black or red: A sex-linked colour polymorphism in a songbird is maintained by balancing selection

Colour polymorphisms play a key role in sexual selection and speciation, yet the mechanisms that generate and maintain them are not fully understood. We therefore used genomic and transcriptomic tools to identify the precise genetic architecture and evolutionary history of a sex-linked colour polymorphism in the Gouldian finch Erythrura gouldiae that is also accompanied by remarkable differences in behaviour and physiology. We found that differences in colour are associated with an ~72-kbp region of the Z chromosome in a putative regulatory region for follistatin, an antagonist of the TGF-{beta} superfamily genes. The region is highly differentiated between morphs, unlike the rest of the genome, yet we found no evidence that an inversion is involved in maintaining the distinct haplotypes. Coalescent simulations confirm that that there is elevated nucleotide diversity and an excess of intermediate frequency alleles at this locus. We conclude that this pleiotropic colour polymorphism is most probably maintained by balancing selection.

evolutionary biology↗