A comprehensive multilocus phylogeny for the wood-warblers and a revised classification of the Parulidae (Aves)

DateLife: Leveraging Databases and Analytical Tools to Reveal the Dated Tree of Life

Chronograms-phylogenies with branch lengths proportional to time-represent key data on timing of evolutionary events, allowing us to study natural processes in many areas of biological research. Chronograms also provide valuable information that can be used for education, science communication, and conservation policy decisions. Yet, achieving a high-quality reconstruction of a chronogram is a difficult and resource-consuming task. Here we present DateLife, a phylogenetic software implemented as an R package and an R Shiny web application available at www.datelife.org, that provides services for efficient and easy discovery, summary, reuse, and reanalysis of node age data mined from a curated database of expert, peer-reviewed, and openly available chronograms. The main DateLife workflow starts with one or more scientific taxon names provided by a user. Names are processed and standardized to a unified taxonomy, allowing DateLife to run a name match across its local chronogram database that is curated from Open Tree of Life's phylogenetic repository, and extract all chronograms that contain at least two queried taxon names, along with their metadata. Finally, node ages from matching chronograms are mapped using the congruification algorithm to corresponding nodes on a tree topology, either extracted from Open Tree of Life's synthetic phylogeny or one provided by the user. Congruified node ages are used as secondary calibrations to date the chosen topology, with or without initial branch lengths, using different phylogenetic dating methods such as BLADJ, treePL, PATHd8, and MrBayes. We performed a cross-validation test to compare node ages resulting from a DateLife analysis (i.e, phylogenetic dating using secondary calibrations) to those from the original chronograms (i.e, obtained with primary calibrations), and found that DateLife's node age estimates are consistent with the age estimates from the original chronograms, with the largest variation in ages occurring around topologically deeper nodes. Because the results from any software for scientific analysis can only be as good as the data used as input, we highlight the importance of considering the results of a DateLife analysis in the context of the input chronograms. DateLife can help to increase awareness of the existing disparities among alternative hypotheses of dates for the same diversification events, and to support exploration of the effect of alternative chronogram hypotheses on downstream analyses, providing a framework for a more informed interpretation of evolutionary results.

Museum genomics provide insight into the extinction of a specialist North American warbler species

Museum genomics provide an opportunity to investigate population demographics of extinct species, especially valuable when research prior to extinction was minimal. The Bachman's warbler (Vermivora bachmanii) is hypothesized to have gone extinct due to loss of its specialized habitat. However, little is known about other potential contributing factors such as natural rarity or changes to connectivity following habitat fragmentation. We examined mitochondrial DNA (mtDNA) and genome-wide SNPs using specimens collected from breeding and migration sites across the range of the Bachman's warbler. We found no signals of strong population structuring across the breeding range of Bachman's warblers in both mtDNA and genome-wide SNPs. Thus, long-term population isolation did not appear to be a significant contributor to the extinction of the Bachman's warbler. Instead, our findings support the theory that Bachman's warblers underwent a rapid decline likely driven by habitat destruction, which may have been exacerbated by the natural rarity, habitat specificity and low genetic diversity of the species.

Niche position and niche breadth effects on population abundances: A case study of New World Warblers (Parulidae)

Species abundance patterns are influenced by a myriad of factors, including habitat availability and ecological niche characteristics. However, the evidence concerning the specific impact factors such as niche position and niche breadth on mean and maximum abundances in vertebrates at a broad geographical scale remains inconclusive. In this study, we investigated the influence of niche position and breadth on the abundance of 47 species of birds belonging to the Parulidae family, commonly known as New World Warblers. We obtained data on abundance and presence records spanning the reproductive distribution of these species and employed the outlying mean index analysis to calculate niche position and niche breadth. We assessed the relationship between abundance metrics and niche descriptors using phylogenetic regressions to account for the non-independence resulting from phylogenetic ancestry. Initially, we developed individual models for each predictor and subsequently formulated a multi-predictor model encompassing niche position, niche breadth, and their interaction. Our findings revealed a negative relationship between niche position and both mean and maximum abundance, while niche breadth exhibited a positive relationship with these niche characteristics. Notably, the results of the multi-predictor models indicated that niche position exerted the most substantial influence on both mean and maximum abundance. Additionally, the interaction between niche position and niche breadth had the most positive and significant contribution to mean population abundance. This study underscores the need for future research in other vertebrates to delve into the mechanisms underlying these patterns. Such endeavors will not only enhance our understanding of ecological dynamics but also equip us with predictive capabilities to anticipate population responses to environmental changes effectively.

An Elevational Phylogeographic Diversity Gradient in Neotropical Birds Is Decoupled from Speciation Rates

AbstractA key question about macroevolutionary speciation rates is whether they are controlled by microevolutionary processes operating at the population level. For example, does spatial variation in population genetic differentiation underlie geographical gradients in speciation rates? Previous work suggests that speciation rates increase with elevation in Neotropical birds, but underlying population-level gradients remain unexplored. Here, we characterize elevational phylogeographic diversity between montane and lowland birds in the megadiverse Andes-Amazonian system and assess its relationship to speciation rates to evaluate the link between population-level differentiation and species-level diversification. We aggregated and georeferenced nearly 7,000 mitochondrial DNA sequences across 103 species or species complexes in the Andes and Amazonia and used these sequences to describe phylogeographic differentiation across both regions. Our results show increased levels of both discrete and continuous metrics of population structure in the Andean mountains compared with the Amazonian lowlands. However, higher levels of population differentiation do not predict higher rates of speciation in our dataset. Multiple potential factors may lead to our observed decoupling of initial population divergence and speciation rates, including the ephemerality of incipient species and the multifaceted nature of the speciation process, as well as methodological challenges associated with estimating rates of population differentiation and speciation.

The type of Setophaga ruficoronata (Kaup 1851) is a hybrid: implications for the taxonomy of Myioborus warblers (Passeriformes: Parulidae)

Hybridization, rapid diversification, and uncertainties surrounding type specimens add complexity to the already intricate taxonomy of high Andean Myioborus warblers of northern South America. In this study, we propose a reassessment of species boundaries within M. ornatus and M. melanocephalus, drawing on comparisons of name-bearing types. We also consider insights from a recent study of a hybrid zone in southern Colombia and northern Ecuador. We present three species delimitation alternatives that offer improved clarity compared to the current taxonomy, and discuss the rationale behind recognizing chrysops and bairdi as distinct species while redefining the species ornatus and melanocephalus, given the available evidence.

Dispersal-Limited Symbionts Exhibit Unexpectedly Wide Variation in Host Specificity

A fundamental aspect of symbiotic relationships is host specificity, ranging from extreme specialists associated with only a single host species to generalists associated with many different species. Although symbionts with limited dispersal capabilities are expected to be host specialists, some are able to associate with multiple hosts. Understanding the micro- and macro-evolutionary causes of variations in host specificity is often hindered by sampling biases and the limited power of traditional evolutionary markers. Here, we studied feather mites to address the barriers associated with estimates of host specificity for dispersal-limited symbionts. We sampled feather mites (Proctophyllodidae) from a nearly comprehensive set of North American breeding warblers (Parulidae) to study mite phylogenetic relationships and host-symbiont codiversification. We used pooled-sequencing (Pool-Seq) and short-read Illumina technology to interpret results derived from a traditional barcoding gene (cytochrome c oxidase subunit 1) versus 11 protein-coding mitochondrial genes using concatenated and multispecies coalescent approaches. Despite the statistically significant congruence between mite and host phylogenies, mite-host specificity varies widely, and host switching is common regardless of the genetic marker resolution (i.e., barcode vs. multilocus). However, the multilocus approach was more effective than the single barcode in detecting the presence of a heterogeneous Pool-Seq sample. These results suggest that presumed symbiont dispersal capabilities are not always strong indicators of host specificity or of historical host-symbiont coevolutionary events. A comprehensive sampling at fine phylogenetic scales may help to better elucidate the microevolutionary filters that impact macroevolutionary processes regulating symbioses, particularly for dispersal-limited symbionts. [Codiversification; cophylogenetics; feather mites; host switching; pooled sequencing; species delineation; symbiosis, warblers.].

Genomes of the extinct Bachman's warbler show high divergence and no evidence of admixture with other extant Vermivora warblers

Bachman's warbler¹ (Vermivora bachmanii)-last sighted in 1988-is one of the only North American passerines to recently go extinct.^2,3,4 Given extensive ongoing hybridization of its two extant congeners-the blue-winged warbler (V. cyanoptera) and golden-winged warbler (V. chrysoptera)^5,6,7,8-and shared patterns of plumage variation between Bachman's warbler and hybrids between those extant species, it has been suggested that Bachman's warbler might have also had a component of hybrid ancestry. Here, we use historic DNA (hDNA) and whole genomes of Bachman's warblers collected at the turn of the 20^th century to address this. We combine these data with the two extant Vermivora species to examine patterns of population differentiation, inbreeding, and gene flow. In contrast to the admixture hypothesis, the genomic evidence is consistent with V. bachmanii having been a highly divergent, reproductively isolated species, with no evidence of introgression. We show that these three species have similar levels of runs of homozygosity (ROH), consistent with effects of a small long-term effective population size or population bottlenecks, with one V. bachmanii outlier showing numerous long ROH and a F_ROH greater than 5%. We also found-using population branch statistic estimates-previously undocumented evidence of lineage-specific evolution in V. chrysoptera near a pigmentation gene candidate, CORIN, which is a known modifier of ASIP, which is in turn involved in melanic throat and mask coloration in this family of birds. Together, these genomic results also highlight how natural history collections are such invaluable repositories of information about extant and extinct species.

Acoustic similarity of flight calls corresponds with the composition and structure of mixed-species flocks of migrating birds: evidence from a three-dimensional microphone array

Animals that migrate in mixed-species groups may communicate with both conspecific and heterospecific individuals, providing a low-cost mechanism for navigation whenever individuals share similar migratory routes or destinations. Many migratory birds produce calls while flying, but the function of these calls, and the forces contributing to their evolution, are poorly known. We studied flight calls in mixed-species groups of wood warblers (Parulidae), a biodiverse group of migratory songbirds. We used a spatial approach to examine whether acoustic similarity of flight calls varies with group composition, recording flight calls of mixed-species flocks with a wireless microphone array and triangulating the positions of birds in three dimensions. We found that the acoustic similarity of flight calls was correlated with spatial proximity: birds with similar calls fly closer together during migration. We also found relationships between acoustic similarity, flock size and mixed-species flock diversity: birds with similar calls fly in smaller flocks and in flocks with lower species diversity. Our results support the idea that migrating birds use flight calls to maintain contact with acoustically similar individuals in mixed-species flocks, with communication transcending species boundaries. These results suggest that acoustically similar flight calls are used as cues of group assembly for migratory animals. This article is part of the theme issue 'Mixed-species groups and aggregations: shaping ecological and behavioural patterns and processes'.

Gut microbiome composition better reflects host phylogeny than diet diversity in breeding wood-warblers

Understanding the factors that shape microbiomes can provide insight into 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 faecal metabarcoding to characterize both the gut microbiome and diet of 15 wood-warbler species across a 4-year period and from two geographical 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.

A new species of Isospora (Apicomplexa: Eimeriidae) from the yellow warbler, Setophaga petechia (L.) (Passeriformes: Parulidae: Parulinae), in Oklahoma, USA

Isospora fitzpatricki n. sp. is described from a yellow warbler, Setophaga petechia (L.), from McCurtain County, Oklahoma, USA. Oöcysts of the new species are subspheroidal to ovoidal with a smooth bi-layered wall, measure (L × W) 24.2 × 20.4 μm, and have a length/width (L/W) ratio of 1.2; a micropyle and oöcyst residuum are both absent, but polar granule(s) are present. Sporocysts are ovoidal to ellipsoidal and measure 14.5 × 9.2 μm, L/W ratio of 1.6; a knob-like Stieda body is present as well as a distinct rounded sub-Stieda body. The sporocyst residuum is composed of various-sized granules in a compact rounded or irregular mass or dispersed between and across the sporozoite. The oöcysts of I. fitzpatricki n. sp. can be differentiated from five other congeners reported from members of the New World warbler family Parulidae from either Mexico, Costa Rica, or Brazil, by being larger on average as well as by possessing a prominent rounded sub-Stieda body, sporozoite striations, and an posterior refractile body. Information is also presented on an Isospora sp. being passed by S. petechia that we choose not to describe as a putative novel species of Isospora at this time. These two isosporans represent the first coccidians reported from S. petechia and, more importantly, the first known from the members of the Parulidae in the USA.

The evolution of wood warbler flight calls: Species with similar migrations produce acoustically similar calls

Diverse animal species engage in long-distance migrations. Many migrants travel in groups, and communication within these groups may be important to survival and successful migration. We examined migration and communication in 36 species of wood warblers (Parulidae), songbirds that breed in North America and migrate in mixed-species flocks to their wintering grounds. During migration, wood warblers produce short vocalizations called "flight calls." The function of flight calls and the patterns of acoustic similarity between species are poorly understood. We investigated whether acoustic similarity of flight calls of different species of warbler reflects the similarity in their migratory journeys or their phylogenetic relatedness. We found that phylogeny, similarity in breeding latitude, and overlap in the timing of migration predict acoustic flight call similarity across warbler species. Further, we found that phylogeny, similarity in migration distance, and overlap in wintering range predict acoustic flight call similarity in a subset of 12 species with highly similar calls, although this analysis has a small sample size. We conclude that migratory similarity may be an important force driving the evolution of acoustically similar calls in wood warblers, in addition to phylogenetic relatedness. Acoustic convergence in these species may facilitate communication between individuals with similar migrations.

Interspecific competition between resident and wintering birds: experimental evidence and consequences of coexistence

The contribution of interspecific competition to structuring population and community dynamics remains controversial and poorly tested. Interspecific competition has long been thought to influence the structure of migrant-resident bird communities in winter, yet experimental evidence remains elusive. The arrival of billions of songbirds into Neotropical habitats, where they co-exist with residents, provides a unique opportunity to assess interspecific competition and its consequences. Working in 15 ha of Jamaican black mangrove forest, we used removal experiments to test whether dominant resident Yellow Warblers compete interspecifically with subordinate wintering American Redstarts; we also used observational evidence (interspecific territorial overlap) to understand whether this coexistence influences physical condition, spring departure dates or annual return rates. Consistent with interspecific competition, after experimental removal of the resident, yearling male Redstarts (but not females or adult males) immediately moved into vacated Yellow Warbler territories, increasing their overlap with the space by 7.3%. Yearling Redstarts also appeared to adjust their territorial space use by actively avoiding Yellow Warblers; for example, Redstarts departing the wintering grounds as yearlings and returning the following winter shifted such that their territories overlapped 32% less with those of Yellow Warblers. Adult Redstarts showed no such territorial flexibility. Adult male Redstarts also showed evidence supporting the consequences of coexistence: territorial overlap with Yellow Warblers was negatively correlated with body condition and annual return rates. Adult male Redstarts with <25% territorial overlap with Yellow Warblers were more than three times as likely to return between seasons than those with 100% overlap. We propose that the territorial inflexibility of adult male Redstarts produces these consequences, which may be due to their years-long investment in that particular territory. More generally, the temporary nature of migrant-resident interspecific competition is likely what allows coexistence during winter, the most resource-poor time of year. Interspecific competition and the consequences of coexistence are likely age- and sex-specific and the product of intraspecific dominance hierarchy in Redstarts. Our observations suggest that interspecific coexistence has measurable consequences, and our experiments support the long-held, but previously untested belief that resident birds compete interspecifically with wintering migrants.

Sympatry drives colour and song evolution in wood-warblers (Parulidae)

Closely related species often exhibit similarities in appearance and behaviour, yet when related species exist in sympatry, signals may diverge to enhance species recognition. Prior comparative studies provided mixed support for this hypothesis, but the relationship between sympatry and signal divergence is likely nonlinear. Constraints on signal diversity may limit signal divergence, especially when large numbers of species are sympatric. We tested the effect of sympatric overlap on plumage colour and song divergence in wood-warblers (Parulidae), a speciose group with diverse visual and vocal signals. We also tested how number of sympatric species influences signal divergence. Allopatric species pairs had overall greater plumage and song divergence compared to sympatric species pairs. However, among sympatric species pairs, plumage divergence positively related to the degree of sympatric overlap in males and females, while male song bandwidth and syllable rate divergence negatively related to sympatric overlap. In addition, as the number of species in sympatry increased, average signal divergence among sympatric species decreased, which is likely due to constraints on warbler perceptual space and signal diversity. Our findings reveal that sympatry influences signal evolution in warblers, though not always as predicted, and that number of sympatric species can limit sympatry's influence on signal evolution.

Evolution of breeding plumages in birds: A multiple-step pathway to seasonal dichromatism in New World warblers (Aves: Parulidae)

Many species of birds show distinctive seasonal breeding and nonbreeding plumages. A number of hypotheses have been proposed for the evolution of this seasonal dichromatism, specifically related to the idea that birds may experience variable levels of sexual selection relative to natural selection throughout the year. However, these hypotheses have not addressed the selective forces that have shaped molt, the underlying mechanism of plumage change. Here, we examined relationships between life-history variation, the evolution of a seasonal molt, and seasonal plumage dichromatism in the New World warblers (Aves: Parulidae), a family with a remarkable diversity of plumage, molt, and life-history strategies. We used phylogenetic comparative methods and path analysis to understand how and why distinctive breeding and nonbreeding plumages evolve in this family. We found that color change alone poorly explains the evolution of patterns of biannual molt evolution in warblers. Instead, molt evolution is better explained by a combination of other life-history factors, especially migration distance and foraging stratum. We found that the evolution of biannual molt and seasonal dichromatism is decoupled, with a biannual molt appearing earlier on the tree, more dispersed across taxa and body regions, and correlating with separate life-history factors than seasonal dichromatism. This result helps explain the apparent paradox of birds that molt biannually but show breeding plumages that are identical to the nonbreeding plumage. We find support for a two-step process for the evolution of distinctive breeding and nonbreeding plumages: That prealternate molt evolves primarily under selection for feather renewal, with seasonal color change sometimes following later. These results reveal how life-history strategies and a birds' environment act upon multiple and separate feather functions to drive the evolution of feather replacement patterns and bird coloration.

Genomic identification of intergeneric hybrids in New World wood-warblers (Aves: Parulidae)

The documentation of hybrids between distantly related taxa can illustrate an initial step to explain how genes might move between species that do not exhibit complete reproductive isolation. In birds, some of the most phylogenetically distant hybrid combinations occur between genera. Traditionally, morphological and plumage characters have been used to assign the identity of the parental species of a putative hybrid, although recently, nuclear introns also have been used. Here, we demonstrate how high-throughput short-read DNA sequence data can be used to identify the parentage of a putative intergeneric hybrid, in this case between a blue-winged warbler (Vermivora cyanoptera) and a cerulean warbler (Setophaga cerulea). This hybrid had mitochondrial DNA of a cerulean warbler, indicating the maternal parent. For hundreds of single nucleotide polymorphisms within six regions of the nuclear genome that differentiate blue-winged warblers and golden-winged warblers (Vermivora chrysoptera), the hybrid had roughly equal ancestry assignment to blue-winged and cerulean warblers, suggesting a blue-winged warbler as the paternal parent species and demonstrating that this was a first generation (F1) hybrid between these species. Unlike other recently characterized intergeneric warbler hybrids, this individual hybrid learned to song match its maternal parent species, suggesting that it might have been the result of an extra-pair mating and raised in a cerulean warbler nest.

Natural and sexual selection shape the evolution of colour and conspicuousness in North American wood-warblers (Parulidae)

Natural and sexual selection drive colour evolution in animals. However, these different selective forces are often studied independently or without considering environmental variation. We evaluated the roles of natural and sexual selection together on colour evolution in 15 sympatric wood-warbler species, while considering the influence of variation in the light environment and visual background. We tested the influence of each selective pressure on male and female coloration and contrast against the background using avian visual models in phylogenetically controlled analyses. We found natural and sexual selection simultaneously driving cryptic and conspicuous plumage in males by acting on different body regions. For example, we found that ground-nesting species had males with conspicuous under-body plumage and cryptic upper-body plumage, showing how natural and sexual selection can drive colour evolution concordantly. We also found interesting relationships with female plumage, such as nest predation positively covarying with female contrast against the background, suggesting a cost to female conspicuousness. Our findings here showcase the complexity of selection on coloration and illustrate the importance of: (1) accounting for environmental variation when assessing how natural and sexual selection drive colour evolution; and (2) testing how multiple selection pressures are shaping colour diversity among species.

Rates of ecomorphological trait evolution in passerine bird clades are independent of age

Although the links between species richness and diversification rates with clade age have been studied extensively, few studies have investigated the relationship between the rates of trait evolution and clade age. The rate of morphological trait evolution has repeatedly been shown to vary through time, as expected, for example, for adaptive radiations, but the strength and sources of this variation are not well understood. We compare the relationship between the rates of trait evolution and clade age across eight monophyletic clades of passerine birds by investigating ecomorphological traits, i.e. morphological traits that influence the ecology of the species directly. We study the ecomorphological divergence pattern using analyses of the disparity through time and determine the best-fitting model of evolution for each trait in each clade. We find no support for a consistent dependence of evolutionary rates on clade age across wing, tail, tarsus and beak shape in our eight clades and also show that early burst models of trait evolution are rarely the best-fitting models within these clades. These results suggest that key innovations or adaptive radiations might be less common evolutionary patterns and processes than generally thought or might depend on the taxonomic level investigated.

The geography of evolutionary divergence in the highly endemic avifauna from the Sierra Madre del Sur, Mexico

Background

Mesoamerica is a remarkable region with a high geological and ecological complexity. Within northern Mesoamerica, the biotic province of the Sierra Madre del Sur (SMS) in southwestern Mexico harbors exceptionally high avian endemism and diversity. Herein, we searched for spatially and temporally concordant phylogeographic patterns, in four bird genera from three distinct avian orders co-distributed across Mesoamerica and investigated their causes through hypothesis testing regarding historical processes. Selected species include endemic and differentiated populations across the montane forests of Mesoamerica, and particularly within the SMS.

Results

We gathered mitochondrial DNA sequences for at least one locus from 177 individuals across all species. We assessed genetic structure, demographic history, and defined a framework for the coalescent simulations used in biogeographic hypothesis testing temporal and spatial co-variance. Our analyses suggested shared phylogeographic breaks in areas corresponding to the SMS populations, and between the main montane systems in Mesoamerica, with the Central Valley of Oaxaca and the Nicaragua Depression being the most frequently shared breaks among analyzed taxa. Nevertheless, dating analyses and divergence patterns observed were consistent with the hypothesis of broad vicariance across Mesoamerica derived from mechanisms operating at distinct times across taxa in the SMS.

Conclusions

Our study provides a framework for understanding the evolutionary origins and historical factors enhancing speciation in well-defined regions within Mesoamerica, indicating that the evolutionary history of extant biota inhabiting montane forests is complex and often idiosyncratic.

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 among 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 × cyanoptera × 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.

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_ST ), but there is much debate regarding the causes of this pattern. We briefly review the prominent models of genomic islands of differentiation and compare patterns of genomic differentiation in three closely related pairs of New World warblers with the goal of evaluating support for the four models. Each pair (MacGillivray's/mourning warblers; Townsend's/black-throated green warblers; and Audubon's/myrtle warblers) consists of forms that were likely separated in western and eastern North American refugia during cycles of Pleistocene glaciations and have now come into contact in western Canada, where each forms a narrow hybrid zone. We show strong differences between pairs in their patterns of genomic heterogeneity in F_ST , suggesting differing selective forces and/or differing genomic responses to similar selective forces among the three pairs. Across most of the genome, levels of within-group nucleotide diversity (π_Within ) are almost as large as levels of between-group nucleotide distance (π_Between ) within each pair, suggesting recent common ancestry and/or gene flow. In two pairs, a pattern of the F_ST peaks having low π_Between suggests that selective sweeps spread between geographically differentiated groups, followed by local differentiation. This "sweep-before-differentiation" model is consistent with signatures of gene flow within the yellow-rumped warbler species complex. These findings add to our growing understanding of speciation as a complex process that can involve phases of adaptive introgression among partially differentiated populations.

A Framework for Simultaneous Tests of Abiotic, Biotic, and Historical Drivers of Species Distributions: Empirical Tests for North American Wood Warblers Based on Climate and Pollen

Understanding how abiotic, biotic, and historical factors shape species distributions remains a central question in ecology, but studies linking biotic factors to continental-scale patterns remain scarce. Here, we present a novel framework for simultaneously testing patterns expected when abiotic, biotic, or historical factors drive species range limits. We use ecological niche models to produce empirical estimates of the "biotic, abiotic, and movement" paradigm (BAM diagrams), which previously has been used only theoretically. On the basis of climatic and pollen data as well as explicit consideration of dispersal limitations, we implement the framework for a group of North American birds (Oreothlypis warblers) with clear habitat associations. Because the pollen-based predictor variables characterize vegetation, they represent biotic factors needed by each bird species. Although continental-scale patterns of distribution are traditionally attributed to abiotic factors, only one species matched the hypothesis of solely abiotic drivers. In contrast, pollen-based models indicate biotic drivers for two species, correctly predicting their absence in climatically suitable areas. These results highlight the feasibility of considering and quantifying the potential effects of biotic interactions on species ranges, especially when interactions can be decoupled from abiotic factors. Furthermore, the availability of pollen data now and in the Holocene highlights the potential of these data to be used to predict range shifts of other organisms tightly dependent on particular vegetation types.

On geographic barriers and Pleistocene glaciations: Tracing the diversification of the Russet-crowned Warbler (Myiothlypis coronata) along the Andes

We studied the phylogeography and plumage variation of the Russet-crowned Warbler (Myiothlypis coronata), from Venezuela to Bolivia, with focus on populations from Ecuador and northern Peru. We analyzed sequences of mitochondrial and nuclear genes, geographic distributions, as well as photographs of specimens deposited at museum collections. Phylogenetic analyses identified three major lineages formed by populations from: Venezuela and Colombia (M. c. regulus), Ecuador and northern Peru (M. elata, M. castaneiceps, M. orientalis, M. c. chapmani), and central Peru and Bolivia (M. c. coronata). We found further population structure within M. c. regulus and M. c. coronata, and population structure and complexity of plumage variation within the Ecuador-northern Peru lineage. Time-calibrated trees estimated that most intraspecific variation originated during the Pleistocene; however, this pattern may not be attributed to an increase in diversification rate during that period. We discuss these results in the context of the importance of geographic-ecological barriers in promoting lineage diversification along the Andes and put forward a preliminary taxonomic proposal for major lineages identified in this study.

Feather mite abundance varies but symbiotic nature of mite-host relationship does not differ between two ecologically dissimilar warblers

Feather mites are obligatory ectosymbionts of birds that primarily feed on the oily secretions from the uropygial gland. Feather mite abundance varies within and among host species and has various effects on host condition and fitness, but there is little consensus on factors that drive variation of this symbiotic system. We tested hypotheses regarding how within-species and among-species traits explain variation in both (1) mite abundance and (2) relationships between mite abundance and host body condition and components of host fitness (reproductive performance and apparent annual survival). We focused on two closely related (Parulidae), but ecologically distinct, species: Setophaga cerulea (Cerulean Warbler), a canopy dwelling open-cup nester, and Protonotaria citrea (Prothonotary Warbler), an understory dwelling, cavity nester. We predicted that feather mites would be more abundant on and have a more parasitic relationship with P. citrea, and within P. citrea, females and older individuals would harbor greater mite abundances. We captured, took body measurements, quantified feather mite abundance on individuals' primaries and rectrices, and monitored individuals and their nests to estimate fitness. Feather mite abundance differed by species, but in the opposite direction of our prediction. There was no relationship between mite abundance and any measure of body condition or fitness for either species or sex (also contrary to our predictions). Our results suggest that species biology and ecological context may influence mite abundance on hosts. However, this pattern does not extend to differential effects of mites on measures of host body condition or fitness.

Evolution and plasticity: Divergence of song discrimination is faster in birds with innate song than in song learners in Neotropical passerine birds

Plasticity is often thought to accelerate trait evolution and speciation. For example, plasticity in birdsong may partially explain why clades of song learners are more diverse than related clades with innate song. This "song learning" hypothesis predicts that (1) differences in song traits evolve faster in song learners, and (2) behavioral discrimination against allopatric song (a proxy for premating reproductive isolation) evolves faster in song learners. We tested these predictions by analyzing acoustic traits and conducting playback experiments in allopatric Central American sister pairs of song learning oscines (N = 42) and nonlearning suboscines (N = 27). We found that nonlearners evolved mean acoustic differences slightly faster than did leaners, and that the mean evolutionary rate of song discrimination was 4.3 times faster in nonlearners than in learners. These unexpected results may be a consequence of significantly greater variability in song traits in song learners (by 54-79%) that requires song-learning oscines to evolve greater absolute differences in song before achieving the same level of behavioral song discrimination as nonlearning suboscines. This points to "a downside of learning" for the evolution of species discrimination, and represents an important example of plasticity reducing the rate of evolution and diversification by increasing variability.

The conquering of North America: dated phylogenetic and biogeographic inference of migratory behavior in bee hummingbirds

BACKGROUND

Geographical and temporal patterns of diversification in bee hummingbirds (Mellisugini) were assessed with respect to the evolution of migration, critical for colonization of North America. We generated a dated multilocus phylogeny of the Mellisugini based on a dense sampling using Bayesian inference, maximum-likelihood and maximum parsimony methods, and reconstructed the ancestral states of distributional areas in a Bayesian framework and migratory behavior using maximum parsimony, maximum-likelihood and re-rooting methods.

RESULTS

All phylogenetic analyses confirmed monophyly of the Mellisugini and the inclusion of Atthis, Calothorax, Doricha, Eulidia, Mellisuga, Microstilbon, Myrmia, Tilmatura, and Thaumastura. Mellisugini consists of two clades: (1) South American species (including Tilmatura dupontii), and (2) species distributed in North and Central America and the Caribbean islands. The second clade consists of four subclades: Mexican (Calothorax, Doricha) and Caribbean (Archilochus, Calliphlox, Mellisuga) sheartails, Calypte, and Selasphorus (incl. Atthis). Coalescent-based dating places the origin of the Mellisugini in the mid-to-late Miocene, with crown ages of most subclades in the early Pliocene, and subsequent species splits in the Pleistocene. Bee hummingbirds reached western North America by the end of the Miocene and the ancestral mellisuginid (bee hummingbirds) was reconstructed as sedentary, with four independent gains of migratory behavior during the evolution of the Mellisugini.

CONCLUSIONS

Early colonization of North America and subsequent evolution of migration best explained biogeographic and diversification patterns within the Mellisugini. The repeated evolution of long-distance migration by different lineages was critical for the colonization of North America, contributing to the radiation of bee hummingbirds. Comparative phylogeography is needed to test whether the repeated evolution of migration resulted from northward expansion of southern sedentary populations.

Rapid postglacial diversification and long-term stasis within the songbird genus Junco: phylogeographic and phylogenomic evidence

Natural systems composed of closely related taxa that vary in the degree of phenotypic divergence and geographic isolation provide an opportunity to investigate the rate of phenotypic diversification and the relative roles of selection and drift in driving lineage formation. The genus Junco (Aves: Emberizidae) of North America includes parapatric northern forms that are markedly divergent in plumage pattern and colour, in contrast to geographically isolated southern populations in remote areas that show moderate phenotypic divergence. Here, we quantify patterns of phenotypic divergence in morphology and plumage colour and use mitochondrial DNA genes, a nuclear intron, and genomewide SNPs to reconstruct the demographic and evolutionary history of the genus to infer relative rates of evolutionary divergence among lineages. We found that geographically isolated populations have evolved independently for hundreds of thousands of years despite little differentiation in phenotype, in sharp contrast to phenotypically diverse northern forms, which have diversified within the last few thousand years as a result of the rapid postglacial recolonization of North America. SNP data resolved young northern lineages into reciprocally monophyletic lineages, indicating low rates of gene flow even among closely related parapatric forms, and suggesting a role for strong genetic drift or multifarious selection acting on multiple loci in driving lineage divergence. Juncos represent a compelling example of speciation in action, where the combined effects of historical and selective factors have produced one of the fastest cases of speciation known in vertebrates.

Co-infections of haemosporidian and trypanosome parasites in a North American songbird

Hosts frequently harbour multiple parasite infections, yet patterns of parasite co-occurrence are poorly documented in nature. In this study, we asked whether two common avian blood parasites, one haemosporidian and one trypanosome, affect each other's occurrence in individuals of a single host species. We used molecular genotyping to survey protozoan parasites in the peripheral blood of yellow-breasted chats (Aves: Passeriformes [Parulidae]: Icteria virens) from the Ozarks of Southern Missouri. We also determined whether single and co-infections differently influence white blood cell and polychromatic erythrocyte counts, the latter being a measure of regenerative anaemia. We found a positive association between the haemosporidian and trypanosome parasites, such that infection by one increases the probability that an individual host is infected by the other. Adult individuals were more likely than juveniles to exhibit haemosporidian infection, but co-infections and single trypanosome infections were not age-related. We found evidence of pathogenicity of trypanosomes in that infected individuals exhibited similar levels of regenerative anaemia as birds infected with haemosporidian parasites of the genus Plasmodium. Counts of white blood cells did not differ with respect to infection status.

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. Consistent with this prediction, results from mixed effects models and Ornstein-Uhlenbeck models of evolution showed different rates of divergence between these groups; surprisingly, differentiation was greater among non-divide pairs. We interpret this finding as a result of variable rates of population blending and fusion between partially diverged forms. Ancient pairs of populations that subsequently fused are now observed as a single form, whereas those that did not fuse are observable as pairs and included in our study. We propose that fusion of two populations is more likely to occur when they have similar migratory routes and little other phenotypic differentiation that would cause reproductive isolation. By contrast, pairs with migratory divides are more likely to remain reproductively isolated, even when differing little in other phenotypic traits. These findings suggest that migratory differences may be one among several isolating barriers that prevent divergent populations from fusing and thereby increase the likelihood that they will continue differentiating as distinct species.

Migration and the evolution of sexual dichromatism: evolutionary loss of female coloration with migration among wood-warblers

The mechanisms underlying evolutionary changes in sexual dimorphism have long been of interest to biologists. A striking gradient in sexual dichromatism exists among songbirds in North America, including the wood-warblers (Parulidae): males are generally more colourful than females at northern latitudes, while the sexes are similarly ornamented at lower latitudes. We use phylogenetically controlled comparative analysis to test three non-mutually exclusive hypotheses for the evolution of sexual dichromatism among wood-warblers. The first two hypotheses focus on the loss of female coloration with the evolution of migration, either owing to the costs imposed by visual predators during migration, or owing to the relaxation of selection for female social signalling at higher latitudes. The third hypothesis focuses on whether sexual dichromatism evolved owing to changes in male ornamentation as the strength of sexual selection increases with breeding latitude. To test these hypotheses, we compared sexual dichromatism to three variables: the presence of migration, migration distance, and breeding latitude. We found that the presence of migration and migration distance were both positively correlated with sexual dichromatism, but models including breeding latitude alone were not strongly supported. Ancestral state reconstruction supports the hypothesis that the ancestral wood-warblers were monochromatic, with both colourful males and females. Combined, these results are consistent with the hypotheses that the evolution of migration is associated with the relaxation of selection for social signalling among females and that there are increased predatory costs along longer migratory routes for colourful females. These results suggest that loss of female ornamentation can be a driver of sexual dichromatism and that social or natural selection may be a stronger contributor to variation in dichromatism than sexual selection.

Niche-tracking migrants and niche-switching residents: evolution of climatic niches in New World warblers (Parulidae)

Differences in life-history traits between tropical and temperate lineages are often attributed to differences in their climatic niche dynamics. For example, the more frequent appearance of migratory behaviour in temperate-breeding species than in species originally breeding in the tropics is believed to have resulted partly from tropical climatic stability and niche conservatism constraining tropical species from shifting their ranges. However, little is known about the patterns and processes underlying climatic niche evolution in migrant and resident animals. We evaluated the evolution of overlap in climatic niches between seasons and its relationship to migratory behaviour in the Parulidae, a family of New World passerine birds. We used ordination methods to measure seasonal niche overlap and niche breadth of 54 resident and 49 migrant species and used phylogenetic comparative methods to assess patterns of climatic niche evolution. We found that despite travelling thousands of kilometres, migrants tracked climatic conditions across the year to a greater extent than tropical residents. Migrant species had wider niches than resident species, although residents as a group occupied a wider climatic space and niches of migrants and residents overlapped extensively. Neither breeding latitude nor migratory distance explained variation among species in climatic niche overlap between seasons. Our findings support the notion that tropical species have narrower niches than temperate-breeders, but does not necessarily constrain their ability to shift or expand their geographical ranges and become migratory. Overall, the tropics may have been historically less likely to experience the suite of components that generate strong selection pressures for the evolution of migratory behaviour.

Evolution of opsin expression in birds driven by sexual selection and habitat

Theories of sexual and natural selection predict coevolution of visual perception with conspecific colour and/or the light environment animals occupy. One way to test these theories is to focus on the visual system, which can be achieved by studying the opsin-based visual pigments that mediate vision. Birds vary greatly in colour, but opsin gene coding sequences and associated visual pigment spectral sensitivities are known to be rather invariant across birds. Here, I studied expression of the four cone opsin genes (Lws, Rh2, Sws2 and Sws1) in 16 species of New World warblers (Parulidae). I found levels of opsin expression vary both across species and between the sexes. Across species, female, but not male Sws2 expression is associated with an index of sexual selection, plumage dichromatism. This fits predictions of classic sexual selection models, in which the sensory system changes in females, presumably impacting female preference, and co-evolves with male plumage. Expression of the opsins at the extremes of the light spectrum, Lws and Uvs, correlates with the inferred light environment occupied by the different species. Unlike opsin spectral tuning, regulation of opsin gene expression allows for fast adaptive evolution of the visual system in response to natural and sexual selection, and in particular, sex-specific selection pressures.

Habitat features and long-distance dispersal modify the use of social information by a long-distance migratory bird

The processes by which individuals select breeding sites have important consequences for individual tness as well as population- and community-dynamics. Although there is increasing evidence that many animal species use information acquired from conspecics to assess the suitability of potential breeding sites, little is known about how the use of this social information is modified by biotic and abiotic conditions. We used an automated playback experiment to simulate two types of social information, post-breeding public information and pre-breeding location cues, to determine the relative importance of these cues for breeding site selection by a migratory songbird, the American redstart (Setophaga ruticilla). In addition, we used stable hydrogen isotopes to determine the dispersal status of individuals that responded to our experimental treatments and quantify whether long-distance dispersers use different social cues to select breeding sites compared to philopatric individuals. We found that points that received pre-breeding location cue treatments were signi cantly more likely to be settled by redstarts than control points that received no playback. However, we found no evidence the redstarts used post-breeding public information gathered during one season to select breeding sites the following year. Breeding site habitat structure was also a strong predictor of settlement probability, indicating that redstarts modi ed the use of social information based on habitat cues. Furthermore, stable hydrogen isotope signatures from individuals that responded to location cue treatments suggest that long-distance dispersers may rely more heavily on these cues than local recruits. Collectively, these results indicate that redstarts use multiple sources of information to select breeding sites, which could buffer individuals from selecting suboptimal sites when they breed in unfamiliar locations or when habitat quality becomes decoupled from social cues.

Life history as a constraint on plasticity: developmental timing is correlated with phenotypic variation in birds

Understanding why organisms vary in developmental plasticity has implications for predicting population responses to changing environments and the maintenance of intraspecific variation. The epiphenotype hypothesis posits that the timing of development can constrain plasticity-the earlier alternate phenotypes begin to develop, the greater the difference that can result amongst the final traits. This research extends this idea by considering how life history timing shapes the opportunity for the environment to influence trait development. We test the prediction that the earlier an individual begins to actively interact with and explore their environment, the greater the opportunity for plasticity and thus variation in foraging traits. This research focuses on life history variation across four groups of birds using museum specimens and measurements from the literature. We reasoned that greater phenotypic plasticity, through either environmental effects or genotype-by-environment interactions in development, would be manifest in larger trait ranges (bills and tarsi) within species. Among shorebirds and ducks, we found that species with relatively shorter incubation times tended to show greater phenotypic variation. Across warblers and sparrows, we found little support linking timing of flight and trait variation. Overall, our results also suggest a pattern between body size and trait variation, consistent with constraints on egg size that might result in larger species having more environmental influences on development. Taken together, our results provide some support for the hypothesis that variation in life histories affects how the environment shapes development, through either the expression of plasticity or the release of cryptic genetic variation.

Evolutionary dynamics of Rh2 opsins in birds demonstrate an episode of accelerated evolution in the New World warblers (Setophaga)

Low rates of sequence evolution associated with purifying selection can be interrupted by episodic changes in selective regimes. Visual pigments are a unique system in which we can investigate the functional consequences of genetic changes, therefore connecting genotype to phenotype in the context of natural and sexual selection pressures. We study the RH2 and RH1 visual pigments (opsins) across 22 bird species belonging to two ecologically convergent clades, the New World warblers (Parulidae) and Old World warblers (Phylloscopidae) and evaluate rates of evolution in these clades along with data from 21 additional species. We demonstrate generally slow evolution of these opsins: both Rh1 and Rh2 are highly conserved across Old World and New World warblers. However, Rh2 underwent a burst of evolution within the New World genus Setophaga, where it accumulated substitutions at 6 amino acid sites across the species we studied. Evolutionary analyses revealed a significant increase in dN /dS in Setophaga, implying relatively strong selective pressures to overcome long-standing purifying selection. We studied the effects of each substitution on spectral tuning and found they do not cause large spectral shifts. Thus, substitutions may reflect other aspects of opsin function, such as those affecting photosensitivity and/or dark-light adaptation. Although it is unclear what these alterations mean for colour perception, we suggest that rapid evolution is linked to sexual selection, given the exceptional plumage colour diversification in Setophaga.

SWS2 visual pigment evolution as a test of historically contingent patterns of plumage color evolution in warblers

Distantly related clades that occupy similar environments may differ due to the lasting imprint of their ancestors-historical contingency. The New World warblers (Parulidae) and Old World warblers (Phylloscopidae) are ecologically similar clades that differ strikingly in plumage coloration. We studied genetic and functional evolution of the short-wavelength-sensitive visual pigments (SWS2 and SWS1) to ask if altered color perception could contribute to the plumage color differences between clades. We show SWS2 is short-wavelength shifted in birds that occupy open environments, such as finches, compared to those in closed environments, including warblers. Phylogenetic reconstructions indicate New World warblers were derived from a finch-like form that colonized from the Old World 15-20 Ma. During this process, the SWS2 gene accumulated six substitutions in branches leading to New World warblers, inviting the hypothesis that passage through a finch-like ancestor resulted in SWS2 evolution. In fact, we show spectral tuning remained similar across warblers as well as the finch ancestor. Results reject the hypothesis of historical contingency based on opsin spectral tuning, but point to evolution of other aspects of visual pigment function. Using the approach outlined here, historical contingency becomes a generally testable theory in systems where genotype and phenotype can be connected.