The exponential growth of molecular sequence data over the past decade has enabled the construction of numerous clade-specific phylogenies encompassing hundreds or thousands of taxa. These independent studies often include overlapping data, presenting a unique opportunity to build macrophylogenies (phylogenies sampling >1000 taxa) for entire classes across the Tree of Life. However, the inference of large trees remains constrained by logistical, computational, and methodological challenges. The Avian Tree of Life provides an ideal model for evaluating strategies to robustly infer macrophylogenies from intersecting data sets derived from smaller studies. In this study, we leveraged a comprehensive resource of sequence capture data sets to evaluate the phylogenetic accuracy and computational costs of four methodological approaches: (1) supermatrix approaches using concatenation, including the “fast” maximum likelihood (ML) methods, (2) filtering data sets to reduce heterogeneity, (3) supertree estimation based on published phylogenomic trees, and (4) a “divide-and-conquer” strategy, wherein smaller ML trees were estimated and subsequently combined using a supertree approach. Additionally, we examined the impact of these methods on divergence time estimation using a data set that includes newly vetted fossil calibrations for the Avian Tree of Life. Our findings highlight the advantages of recently developed fast tree search approaches initiated with parsimony starting trees, which offer a reasonable compromise between computational efficiency and phylogenetic accuracy, facilitating inference of macrophylogenies.

Mohoidae, the Hawaiian honeyeaters, are a group of extinct birds that once inhabited the Hawaiian Islands. Their genetic data are only available from historical museum specimens, so it is based on highly fragmented and damaged DNA. Sequences assembled from historical specimens can have large amounts of missing data and they often result in exceptionally long terminal branches in phylogenies. These long branches can distort estimates of phylogeny, an artifact known as long branch attraction. However, the best way to analyse this data is unclear because these long branches are typically artifactual, reflecting DNA quality. We investigated the position of Mohoidae within the superfamily Bombycilloidea using published alignments of ultraconserved elements (UCEs) and re-assembled UCEs from raw sequencing reads. The uncertainty involves two monotypic families (Hypocoliidae and Hylocitreidae). Re-aligning UCEs using a smaller taxon set closely related to Mohoidae, along with edge trimming and re-assembly, eliminated the long branches of Mohoidae and Hypocoliidae (also represented by a historical sample). The sister relationship of these two families in previous studies appears to be artifactual; our new analyses yielded congruent topologies that placed Mohoidae as sister to a clade comprising Hypocoliidae and Hylocitreidae. We also found that different assemblers (SPAdes vs. Trinity) yielded sequences with conflicts towards the ends of the UCEs, especially for the historical samples, although this did not alter the topology. Finally, combining the UCEs with traditional Sanger sequencing data allowed us to produce a strongly supported complete phylogeny of Bombycilloidea that included all extant species as well as the extinct Mohoidae.

Olfactory receptors (ORs), the largest vertebrate multigene family, exhibit wide copy number variation among taxa, ranging from ∼100 to 4000. The ecological importance of smell has been suggested to positively correlate with OR gene number, though debate exists on whether the number of total ORs, functional ORs, or the percentage of pseudogenes matters most. While olfaction has been poorly studied in most birds, Turkey Vultures (Cathartes aura) demonstrate keen olfactory ability, capable of foraging using smell alone. In contrast, Black Vultures (Coragyps atratus) have been thought to primarily use vision to locate food. Comparison of the OR genes in these two New World vultures presents an opportunity to examine the dynamics of OR evolution in related avian species that may differ in olfactory abilities. Using a PCR and cloning approach with degenerate primers, we sampled the OR subgenome in Turkey and Black Vultures, as well as Red-tailed Hawks (Buteo jamaicensis) and the distantly related Chicken (Gallus gallus), neither of which are thought to use olfaction extensively. Our results indicate that Turkey Vultures have many more OR genes than Red-tailed Hawks or chickens. Surprisingly, Black Vultures had an intermediate number of OR genes. The number of OR genes we estimated in the Turkey Vulture was much greater than previously reported in studies that used short-read sequencing. Additionally, we found that OR genes from New World vultures and Red-tailed Hawks form clades that were distinct from the clade that included most chicken OR genes, indicating that chickens share few OR orthologs with New World vultures or hawks. As previously observed in other animal groups, pseudogenes appeared throughout all clades and their percentage varied among taxa. These findings suggest the OR gene family is highly dynamic, changing rapidly over evolutionary time, and that taxa may have distinct suites of ORs in their genomes.

Interspecific territoriality is a prevalent form of interference competition among animals across environments. However, the connections between interspecific territorial aggression and other related aspects such as hybridization and climate remain unexplored. We investigated territorial aggression in two Neotropical wren species, Campylorhynchus zonatus brevirostris and C. fasciatus pallescens, along a precipitation gradient in western Ecuador using playback experiments. Campylorhynchus f. pallescens exhibits geographic variation: northern populations (C. f. pallescens north) are hybrids of C. z. brevirostris and C. f. fasciatus, while southern populations (C. f. pallescens south) show primary genetic admixture with C. f. fasciatus (from northeastern Peru). We pursued three objectives: 1) to compare intra‐ and inter‐territorial aggression of C. z. brevirostris and the admixed C. f. pallescens north and south; 2) to assess territorial aggression across these three genetic clusters; and 3) to examine direct and indirect (via primary productivity) associations between climate and territorial aggression. We simulated territory intrusion using playback experiments and quantified aggressive responses using principal component analysis (PCA) to integrate three behavioral measurements: minimum approach distance to the stimulus, latency to reach this distance, and the number of aggressive displays (fixed action patterns). Admixed C. f. pallescens north displayed no significant differences in aggression across treatments, supporting the established trend of high interspecific territoriality in hybrids. Campylorhynchus f. pallescens south was the only genetic cluster that showed significant differences among treatments, exhibiting more pronounced aggressive responses to intraspecific stimuli and higher aggression than C. z. brevirostris and C. f. pallescens north. This pattern of dominance in territorial aggression contrasts with the previously reported direction of genetic introgression from C. z. brevirostris towards C. f. pallescens. Precipitation is related to aggression, potentially through resource availability. We emphasize the importance of understanding the interactions among hybridization, territoriality, and environmental stressors in tropical birds.

The evolutionary histories of different genomic regions typically differ from each other and from the underlying species phylogeny. This makes species tree estimation challenging. Here, we examine the performance of phylogenomic methods using a well-resolved phylogeny that nevertheless contains many difficult nodes, the species tree of living birds. We compared trees generated by maximum likelihood (ML) analysis of concatenated data, gene tree summary methods, and SVDquartets. We also conduct the first empirical test of a “new” method called METAL (Metric algorithm for Estimation of Trees based on Aggregation of Loci), which is based on evolutionary distances calculated using concatenated data. We conducted this test using a novel dataset comprising more than 4,000 ultraconserved element (UCE) loci from almost all bird families and two existing UCE and intron datasets sampled from almost all avian orders. We identified “reliable clades” very likely to be present in the true avian species tree and used them to assess method performance. ML analyses of concatenated data recovered almost all reliable clades with less data and greater robustness to missing data than other methods. METAL recovered many reliable clades, but only performed well with the largest datasets. Gene tree summary methods (weighted ASTRAL and weighted ASTRID) performed well; they required less data than METAL but more data than ML concatenation. SVDquartets exhibited the worst performance of the methods tested. In addition to the methodological insights, this study provides a novel estimate of avian phylogeny with almost 99% of the currently recognized avian families. Only one of the 181 reliable clades we examined was consistently resolved differently by ML concatenation versus other methods, suggesting that it may be possible to achieve consensus on the deep phylogeny of extant birds.

Participants in mixed-species bird flocks (MSFs) have been shown to associate with species that are similar in body size, diet, and evolutionary history, suggesting that facilitation structures these assemblages. In addition, several studies have suggested that species in MSFs resemble each other in their plumage, but this question has not been systematically investigated for any MSF system. During the nonbreeding season of 2020 and 2021, we sampled 585 MSFs on 14 transects in 2 habitats of Tongbiguang Nature Reserve in western Yunnan Province, China. We performed social network analysis and the Multiple Regression Quadratic Assignment Procedure to evaluate the effect of 4 species traits (body size, overall plumage color, distinctive plumage patterns, and diet) and evolutionary history on species association strength at the whole-MSF and within-MSF levels. All 41 significant relationships showed that species with stronger associations were more similar in their various traits. Body size had the strongest effect on association strength, followed by phylogeny, plumage patterns, and plumage color; diet had the weakest effect. Our results are consistent with the hypotheses that the benefits of associating with phenotypically similar species outweigh the potential costs of interspecific competition, and that trait matching can occur in plumage characteristics, albeit more weakly than in other traits. Several explanations exist as to why similarities in plumage may occur in MSFs, including that they could reduce predators' ability to target phenotypically "odd" individuals. Whether trait matching in plumage occurs through assortative processes in ecological time or is influenced by co-evolution requires further study.

A morphological trait can have multiple functions shaped by varying selective forces. Bare parts in birds, such as wattles, casques and combs, are known to function in both signalling and thermoregulation. Studies have demonstrated such structures are targets of sexual selection via female choice in several species of Galliformes (junglefowl, turkeys and grouse), though other studies have shown some role in thermoregulation (guineafowl). Here, we tested fundamental hypotheses regarding the evolution and maintenance of bare parts in Galliformes. Using a phylogeny that included nearly 90% of species in the order, we evaluated the role of both sexual and natural selection in shaping the function of bare parts across different clades. We found a combination of both environmental and putative sexually selected traits strongly predicted the variation of bare parts for both males and females across Galliformes. When the analysis is restricted to the largest family, Phasianidae (pheasants, junglefowl and allies), sexually selected traits were the primary predictors of bare parts. Our results suggest that bare parts are important for both thermoregulation and sexual signalling across Galliformes but are primarily under strong sexual selection within the Phasianidae.

Environmental gradients have the potential to influence genetic differentiation among populations ultimately leading to allopatric speciation. However, environmental gradients can also facilitate hybridization between closely related taxa. We investigated a putative hybrid zone in western Ecuador, involving two polytypic wren species (Aves: Troglodytidae), Campylorhynchus zonatus and C. fasciatus. Our study addressed two primary questions: (1) Is there evidence of population structure and genetic admixture between these taxa in western Ecuador? and (2) What are the relative contributions of isolation by distance and isolation by the environment to the observed genetic differentiation along the environmental gradient in this region? We analyzed 4409 single-nucleotide polymorphisms (SNPs) from 112 blood samples sequenced using ddRadSeq and a de novo assembly. The optimum number of genetic clusters ranged from 2 to 4, aligning with geographic origins, known phylogenetics, and physical or ecological constraints. We observed notable transitions in admixture proportions along the environmental gradient in western Ecuador between C. z. brevirostris and the northern and southern genetic clusters of C. f. pallescens. Genetic differentiation between the two C. f. pallescens populations could be attributed to an unreported potential physical barrier in central western Ecuador, where the proximity of the Andes to the coastline restricts lowland habitats, limiting dispersal and gene flow, especially among dry-habitat specialists. The observed admixture in C. f. pallescens suggests that this subspecies may be a hybrid between C. z. brevirostris and C. fasciatus, with varying degrees of admixture in western Ecuador and northwestern Peru. We found evidence of isolation by distance, while isolation by the environment was less pronounced but still significant for annual mean precipitation and precipitation seasonality. This study enhances our understanding of avian population genomics in tropical regions.

Sexually selected weapons, such as the antlers of deer, claws of crabs, and tusks of beaked whales, are strikingly diverse across taxa and even within groups of closely related species. Phylogenetic comparative studies have typically taken a simplified approach to investigate the evolution of weapon diversity, examining the gains and losses of entire weapons, major shifts in size or type, or changes in location. Less understood is how individual weapon components evolve and assemble into a complete weapon. We addressed this question by examining weapon evolution in the diverse, multi-component hind-leg and body weapons of leaf-footed bugs, superfamily Coreoidea (Hemiptera: Heteroptera). Male leaf-footed bugs use their morphological weapons to fight for access to mating territories. We used a large multilocus dataset comprised of ultraconserved element loci for 248 species and inferred evolutionary transitions among component states using ancestral state estimation. Our results suggest that weapons added components over time with some evidence of a cyclical evolutionary pattern-gains of components followed by losses and then gains again. Furthermore, our best estimate indicated that certain trait combinations evolved repeatedly across the phylogeny, suggesting that they function together in battle or that they are genetically correlated. This work reveals the remarkable and dynamic evolution of weapon form in the leaf-footed bugs and provides insights into weapon assembly and disassembly over evolutionary time.

Complex patterns of genome evolution associated with the end-Cretaceous [Cretaceous-Paleogene (K–Pg)] mass extinction limit our understanding of the early evolutionary history of modern birds. Here, we analyzed patterns of avian molecular evolution and identified distinct macroevolutionary regimes across exons, introns, untranslated regions, and mitochondrial genomes. Bird clades originating near the K–Pg boundary exhibited numerous shifts in the mode of molecular evolution, suggesting a burst of genomic heterogeneity at this point in Earth’s history. These inferred shifts in substitution patterns were closely related to evolutionary shifts in developmental mode, adult body mass, and patterns of metabolic scaling. Our results suggest that the end-Cretaceous mass extinction triggered integrated patterns of evolution across avian genomes, physiology, and life history near the dawn of the modern bird radiation.

Sexual selection is often studied with a focus on female mate choice, wherein females evaluate male signals to select an optimal mate. However, in some systems, males should also make careful decisions about the females they choose to court, particularly when faced with the risk of precopulatory sexual cannibalism. Here, we explore the idea that male jumping spiders (Habronattus brunneus) may mitigate this risk by responding to female cues probably associated with female aggression and/or receptivity. We tested mature male spiders’ ability to discriminate between substrate-borne cues (i.e. silk and excreta) produced by conspecific females of different ages and mating statuses. We found that males spent more time exploring cues produced by mature, non-mated females compared with either immature females or mated females. Heightened interest in cues produced by females that are sexually mature but not yet mated may allow males to reduce cannibalism risk, reduce wasted courtship effort and increase their reproductive success. The use of chemical and/or tactile cues in jumping spider courtship behaviour has been vastly understudied compared with the ways they use vision; this study provides the groundwork for understanding how these sensory modalities interact.

The phytophagous insect superfamily Coreoidea (Heteroptera) is a diverse group of similar to 3100 species in five extant families, with many of agricultural importance and model organisms in behavioural studies. Most species (similar to 2800 species) are classified in the family Coreidae (four subfamilies, 37 tribes). While previous phylogenetic studies have primarily focused on the larger and more diverse subfamilies and tribes of Coreidae, several smaller tribes remain poorly studied in a phylogenetic context. Here, we investigated the phylogenetic positions of three less diverse tribes using ultraconserved elements: Agriopocorini, Amorbini, and Manocoreini. Our study is the first to test phylogenetic hypotheses for the Agriopocorini and Amorbini in a cladistic analysis. All three tribes were recovered within the subfamily Coreinae with robust support. The monophyletic Agriopocorini were supported as the sister-group of Colpurini, the monophyletic Amorbini as sister to Mictini, and the monogeneric Manocoreini as sister to Dasynini + Homoeocerini. We briefly discuss the evolution of wing development in Coreidae, putative synapomorphies for clades of interest, and taxonomic considerations. Our study emphasizes the importance of including smaller, less diverse groups in phylogenetic analyses. By doing so, we gain valuable insights into evolutionary relationships, identify future investigations of trait evolution, and resolve systematic controversies.

The New World warblers (Parulidae) are a model group for ecological and evolutionary analyses. However, current phylogenetic relationships across this family are based upon few loci. Here we use ultraconserved elements (UCEs) to estimate a rigorous species-level phylogeny for the family. As is true for many groups, high-quality tissues were unavailable for some taxa. Thus, we explored methods for incorporating sequences derived from historical (toe pad) samples to expand the phylogenetic datasets. We recovered an average of 4,186 UCE loci and mitochondrial bycatch data (supplemented with published mitochondrial data) from 96% of all currently recognized species. We found that the UCE phylogeny built with alignments with less than 70% of gaps and ambiguities recovered the most robust phylogenetic relationships for this family, representing 101 species. Using this phylogeny as a topological backbone and adding ten fair quality "bad" samples effectively generated an overall well supported phylogeny, representing 108 species (∼90% of all species). Based on this tree, we then added in seven poor quality "ugly" samples and six of those were placed within their expected genera. We also explored the phylogenetic positions of the likely extinct Leucopeza semperi and the endangered Catharopeza bishopi where limited data was obtained. Overall, taxonomic placements in our UCE trees largely correspond to previously published studies with the recovery of all currently recognized genera as monophyletic except for Basileuterus which was rendered paraphyletic by B. lachrymosus. Our study provides insights in understanding the phylogenetic relationships of a model Passeriformes family and outlines effective practices for managing sparse genomic data sourced from historical museum specimens. Variable topological arrangements across datasets and analyses reflect the evolutionary complexity of this group and provide future topics for in-depth studies.

Visual mimicry is less understood in birds than in other taxa. The interspecific social dominance mimicry (ISDM) hypothesis asserts that subordinate species resemble dominant ones to reduce aggression. Plumage mimicry has also been consistently noted in mixed-species flocks (MSFs), suggesting a connection to grouping behaviour, although it is unclear whether this is linked to ISDM. We studied greater necklaced laughingthrush (GNLT, Pterorhinus pectoralis) and lesser necklaced laughingthrush (LNLT, Garrulax monileger), which were recently placed in different genera. Measurements of 162 museum specimens showed LNLT converging in sympatry with GNLT in necklace colour, but diverging in necklace to body ratio, with proportionally smaller necklaces. The species were closely associated in six of seven MSF systems from Nepal to China. In a study of foraging behaviour in Nepal, aggression was rare between the species, LNLT followed GNLT and had lower foraging rates when further from GNLT. Our data suggest a link between this MSF-associated mimicry and ISDM, and that the subordinate LNLT may be the mimic and gain more from the resemblance. The species spend much time together in dense and poorly lit vegetation, where the LNLTs resemblance to GNLTs potentially allows them to forage closer to GNLTs than would be otherwise possible.

Climate variability can cause genetic and phenotypic diversity within species, which affects the evolution of biodiversity. A balance between gene flow and selection maintains changes in the frequency of genetic and phenotypic variants along an environmental gradient. In this study, we investigated a hybrid zone in western Ecuador involving two species of wrens (Aves: Troglodytidae), Campylorhynchus zonatus and C. fasciatus, and their admixed populations. We hypothesized that isolation by distance (IBD) and different ecological preferences, isolation by environment (IBE), result in limited dispersal between populations along the precipitation gradient in western Ecuador. We asked two main questions: (1) What is the relative contribution of IBD and IBE to patterns of genetic differentiation of these species along the environmental gradient in western Ecuador? And (2) Is there evidence of genetic admixture and introgression between these taxa in western Ecuador? We analyzed 4,409 SNPs from the blood of 112 individuals sequenced using ddRadSeq. The most likely clusters ranged from K=2-4, corresponding to categories defined by geographic origins, known phylogenetics, and physical or ecological constraints. Evidence for IBD was strong across all models, and evidence for IBE was less strong but still significant for annual mean precipitation and precipitation seasonality. We observed gradual changes in genetic admixture between C. f. pallescens and C. zonatus along the environmental gradient. Genetic differentiation of the two populations of C. f. pallescens could be driven by a previously undescribed potential physical barrier near the center of western Ecuador. Lowland habitats in this region may be limited due to the proximity of the Andes to the coastline, limiting dispersal and gene flow, particularly among dry-habitat specialists. We do not propose taxonomic changes, but the admixture observed in C. f. pallescens suggests that this described subspecies could be a hybrid between C. z. brevirostris and C. fasciatus, with different degrees of admixture along western Ecuador and northwestern Peru. This study contributes to the knowledge of avian population genomics in the tropics.

ABSTRACT Interspecific territoriality is a prevalent form of interference competition among animals. However, the connections between hybridization, climate, and interspecies territorial aggression in tropical regions remain largely unexplored. Here, we investigated territorial aggression in two hybridizing tropical bird species, C. z. brevirostris and C. f. pallescens , in western Ecuador using playback experiments. We tested three hypotheses: 1) hybridizing species exhibit comparable intra- and inter-specific territorial aggression; 2) asymmetrical aggression driven by C. z. brevirostris dominance determines gene flow patterns; and 3) precipitation influences territorial aggression. Supporting hypothesis 1, the admixed C. f. pallescens North showed no difference in intra-vs inter-specific aggression. However, the non-admixed C. f. pallescens South exhibited greater inter-specific aggression, providing partial support for hypothesis 1. Contrary to hypothesis 2, C. f. pallescens South displayed significantly higher aggression than C. z. brevirostris and C. f. pallescens North . Furthermore, precipitation models outperformed null models, supporting hypothesis 3 that precipitation influences Campylorhynchus territorial aggression. Collectively, these findings suggest hybridization can stabilize coexistence via territoriality, and precipitation strongly affects aggression, potentially through resource availability. Unexpectedly, C. z. brevirostris dominance did not appear to drive asymmetric introgression between species, warranting further investigation into the underlying mechanisms. Complex factors shape territorial aggression in tropical birds, including genetic admixture, group size, latitude, and climate. This study highlights the need for additional research elucidating the relationships between hybridization, territoriality, and environmental stressors in tropical avian communities. We discuss possible mechanisms explaining the detected effects of precipitation on aggression and the lack of C. z. brevirostris dominance in determining introgression patterns.

Elongated tails are elaborate plumage traits possessed by a variety of bird species. Sexual selection has long been the dominant hypothesis for explaining why certain species possess such long tails. During the past three decades, however, alternative hypotheses have been proposed and tested. Here, we review evidence, and the lack thereof, for four hypothesised functions of elongated tails in birds: sexual selection, aerodynamic enhancement, anti-predation signalling and perch balancing. Sexual selection has received the most attention, though with inconsistent support. The other three hypothesised functions, in contrast, have gained less attention, with perch balancing remaining largely speculative. After reviewing and synthesizing information about these functions, we show that our current knowledge of avian elongated tails is not comprehensive. To advance our understanding of this topic, we suggest (1) devising a uniform definition of elongated tails that can be applied to a wide variety of bird species, (2) further investigation of less-studied functions of such tails, (3) conducting meta-analyses to discover the origins and trait correlates of elongated tails, (4) considering the possibility that elongated tails serve multiple functions simultaneously, and (5) testing unexplored functions of elongated tails.

Despite the increasing feasibility of sequencing whole genomes from diverse taxa, a persistent problem in phylogenomics is the selection of appropriate genetic markers or loci for a given taxonomic group or research question. In this review, we aim to streamline the decision-making process when selecting specific markers to use in phylogenomic studies by introducing commonly used types of genomic markers, their evolutionary characteristics, and their associated uses in phylogenomics. Specifically, we review the utilities of ultraconserved elements (including flanking regions), anchored hybrid enrichment loci, conserved nonexonic elements, untranslated regions, introns, exons, mitochondrial DNA, single nucleotide polymorphisms, and anonymous regions (nonspecific regions that are evenly or randomly distributed across the genome). These various genomic elements and regions differ in their substitution rates, likelihood of neutrality or of being strongly linked to loci under selection, and mode of inheritance, each of which are important considerations in phylogenomic reconstruction. These features may give each type of marker important advantages and disadvantages depending on the biological question, number of taxa sampled, evolutionary timescale, cost effectiveness, and analytical methods used. We provide a concise outline as a resource to efficiently consider key aspects of each type of genetic marker. There are many factors to consider when designing phylogenomic studies, and this review may serve as a primer when weighing options between multiple potential phylogenomic markers.

A morphological trait can have multiple functions shaped by varying selective forces. Bare parts in birds, such as wattles, casques and combs, are known to function in both signalling and thermoregulation. Studies have demonstrated such structures are targets of sexual selection via female choice in several species of Galliformes (junglefowl, turkeys and grouse), though other studies have shown some role in thermoregulation (guineafowl). Here, we tested fundamental hypotheses regarding the evolution and maintenance of bare parts in Galliformes. Using a phylogeny that included nearly 90% of species in the order, we evaluated the role of both sexual and natural selection in shaping the function of bare parts across different clades. We found a combination of both environmental and putative sexually selected traits strongly predicted the variation of bare parts for both males and females across Galliformes. When the analysis is restricted to the largest family, Phasianidae (pheasants, junglefowl and allies), sexually selected traits were the primary predictors of bare parts. Our results suggest that bare parts are important for both thermoregulation and sexual signalling across Galliformes but are primarily under strong sexual selection within the Phasianidae.