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.

Globally-distributed genera and species provide important opportunities to understand divergence and dispersal across and within continents. Butorides herons (Aves: Ardeidae), including the highly variable Striated Heron (B. striata) and Green Heron (B. virescens), are two species similar in their ecology and plumage. B. striata occurs world-wide, is concentrated in tropical regions, and has highly variable plumage that has led to the classification of at least 29 subspecies. One of the more distinctive is the dark-plumaged Lava Heron of the Galápagos archipelago (B. s. sundevalli). This taxon has been treated as either a full species or a subspecies, but its taxonomic status has been hindered by the lack of genetic assessments. Here, we present a genus-level phylogeny of Butorides herons based on thousands of ultraconserved elements (UCEs). We also investigate morphological variation collected from 308 live and preserved specimens across its broad geographic range. Our genetic results suggest a biogeographic split between Old and New World Butorides herons as well as significant phylogenetic and morphological structure within the Americas, requiring subsequent taxonomic reassessment. Contrary to earlier taxonomic assumptions, Old World Butorides herons are not the closest relative to South American Butorides, and Lava Herons were recovered as a monophyletic lineage sister to Green Herons. Morphological data also highlights the Lava Heron's evolutionary history as they possess unique bills that are possibly adapted to their insular diet behavior. Genetic and morphometric evidence adds to our understanding of Butorides and supports a reassessment of the B. striata label.

Seasonal migration is highly labile from an evolutionary perspective and known to rapidly evolve in response to selective pressures. However, long‐distance migratory birds rely partially on innate genetic programs and may be constrained in their ability to alter their migratory behavior. We take advantage of recent advances in our ability to genotype historical DNA samples to examine the temporal stability of migratory connections between breeding and nonbreeding populations (i.e. migratory connectivity) and population‐level nonbreeding distributions in the Wilson's warbler Cardellina pusilla, a long‐distance migratory songbird. By assigning historical and contemporary samples collected across the nonbreeding range to genetically distinct breeding clusters, we suggest that broad‐scale population‐level nonbreeding distributions within this species have remained largely consistent within Mexico from the mid‐1900s to the present day. These findings support the idea that the nonbreeding distributions of long‐distance migrants may remain stable over long time scales, even in the face of rapid environmental change.

We examined speciation in streamertail hummingbirds (Trochilus polytmus and Trochilus scitulus), Jamaican endemic taxa that challenge the rule that bird speciation cannot progress in situ on small islands. Our analysis shows that divergent selection acting on male bill color, a sexual ornament that is red in polytmus and black in scitulus, acts as a key reproductive barrier. We conducted a population-level analysis of genomic and phenotypic patterns to determine the traits that contribute the most to speciation despite ongoing gene flow across a narrow hybrid zone. We characterized genomic patterns using 6,451 single-nucleotide polymorphisms and a segment of the mitochondrial control region. Our analyses revealed high diversity within species, and low divergence between them, consistent with a recent speciation event or extensive gene flow following secondary contact. We observed narrow clines in two phenotypic traits and several SNP loci. The cline width for male bill color is only 2.3 km, marking it as one of the narrowest phenotypic clines documented in an avian hybrid zone. The coincidence of estimated cline centers with the Rio Grande Valley suggests that this landscape feature may contribute to hybrid zone stability. However, given that streamertails are highly mobile, it is unlikely that such a narrow river acts as a physical barrier to dispersal. The limited genomic divergence across scanned regions of the genome offers little support for postmating reproductive barriers. Instead, our findings point to strong premating selection acting on bill color as the primary driver of streamertail speciation.

We describe a new species of frog of the genus Sarcohyla from the Transvolcanic Belt of M & eacute;xico based on new specimens and individuals previously referred to S. hapsa. Adult males of the new species have nuptial excrescences on the prepollex and fingers I-III and a reddish-brown dorsum, the flanks of juveniles are uniformly dark with small round cream spots, and stages 26-28 tadpoles have black spots on the tail. The new species is the sister-species of S. hapsa and contained in the S. bistincta group.

Structural variants (SVs) are widespread in vertebrate genomes, yet their evolutionary dynamics remain poorly understood. Using 45 long-read de novo genome assemblies and pangenome tools, we analyze SVs within three closely related species of North American jays (Aphelocoma, scrub-jays) displaying a 60-fold range in effective population size. We find rapid evolution of genome architecture, including ~100 Mb variation in genome size driven by dynamic satellite landscapes with unexpectedly long (> 10 kb) repeat units and widespread variation in gene content, influencing gene expression. SVs exhibit slightly deleterious dynamics modulated by variant length and population size, with strong evidence of adaptive fixation only in large populations. Our results demonstrate how population size shapes the distribution of SVs and the importance of pangenomes to characterizing genomic diversity.

Introduced species often encounter novel environments that test their capacity for ecological flexibility and adaptation. We investigated ecological niche dynamics in Nanday Parakeets (Aratinga nenday), a naturalized parrot species in Los Angeles, to assess whether their introduced range reflects a shift from their native range in South America. Using principal components analysis and niche overlap tests, we found that the introduced population occupies a distinct environmental space—cooler, drier, and with less tree cover—with no measurable niche overlap. Habitat suitability modeling in Los Angeles suggests that their current habitat is narrowly concentrated in south-facing coastal canyons and not in more arid inland or high-elevation areas. Data from iNaturalist show that Nanday Parakeets roost and feed mainly in sycamore trees. The 2025 Palisades Fire impacted only 3

The Yellow Warbler (Setophaga petechia) is a small songbird in the wood-warbler family (Parulidae) that exhibits phenotypic and ecological differences across a widespread distribution and is important to California's riparian habitat conservation. Here, we present a high-quality de novo genome assembly of a vouchered female Yellow Warbler from southern California. Using HiFi long-read and Omni-C proximity sequencing technologies, we generated a 1.22 Gb assembly including 687 scaffolds with a contig N50 of 6.80 Mb, scaffold N50 of 21.18 Mb, and a BUSCO completeness score of 96.0%. This highly contiguous genome assembly provides an essential resource for understanding the history of gene flow, divergence, and local adaptation in Yellow Warblers and can inform conservation management of this charismatic bird species.

Understanding the source of non-native introduced populations is crucial for forecasting geographic invasion potential and understanding the ecological consequences of potential establishment. Here we use genomics to identify the source populations and invasion dynamics of two non-native introduced populations from the iconic avian lineage of ‘great speciators’ known as white-eyes (genus Zosterops ). We established confidently for the first time that introduced Zosterops populations in Hawaii and southern California are completely unrelated and derived from independent introductions of the species Z. japonicus and Z. simplex , respectively. We used descriptive population genetic statistics to identify a reduction in genetic diversity and increase in private alleles in the southern California population supporting a recent, potentially ongoing, genetic bottleneck in this population. In contrast, the introduced population in Hawaii showed no such characteristics, likely due to a larger founding population size and repeated introductions in this intentionally introduced population. Ecological niche modeling indicated that there is little environmentally suitable habitat for Z. simplex across the continent of North America, suggesting limited invasion potential, assuming niche conservatism. Yet, portions of the introduced Z. simplex population have already surpassed areas projected as suitable, likely because the urbanized environment of southern California offers biotic resources and microhabitats not captured by our model. Because Z. simplex appears to have overcome both the ‘invasion paradox’ of low founding genetic diversity and relatively unfamiliar environmental conditions in southern California, we suggest that this population may continue expanding beyond our environmental niche model projections in other temperate, urban regions.

Hummingbirds are often sexually dimorphic, the males of many species showing an ornamental gorget that females lack. Males use this ornamental plumage to attract mates and establish a territory, while females build nests and care for the young alone. In Los Angeles, California, we observed a nesting Anna’s Hummingbird with male-like plumage on the crown and gorget but the rectrix morphology of a female—and it reared chicks. The extent of gorget development on this individual likely represents one of the most extreme examples of a male-plumaged female hummingbird yet documented.

Abstract In the Galápagos Islands, much attention has been devoted to the radiation of iconic species like Darwin’s finches, yet the Galápagos Islands offer an overlooked but equally remarkable opportunity for investigating plant radiations. Using a combination of genomic and phenotypic data, we present evidence of the early stages of a radiation in prickly pear cactus (Opuntia), a lineage widespread across the archipelago. We show that despite extensive ecophenotypic variation, there is limited genomic differentiation, consistent with the hypothesis that Opuntia is in the early stages of the diversification process. Phylogenomic and population genomic analyses show that notwithstanding low genetic differentiation across islands, there is marked geographical structure that is broadly consistent with the palaeogeography of the Galápagos. Because low genetic differentiation stands in stark contrast to the exceptional eco-phenotypic diversity displayed by cacti, it is plausible that the genetic architecture of phenotypic divergence mismatches our genomic sequencing, that phenotypic plasticity precedes genetic divergence and is the source of adaptive evolution, or that introgression influences local adaptation. Models of population relationships including admixture indicate that gene flow is common, probably facilitated by dispersal via animals known to feed on Opuntia flowers, fruits, and seeds. Because the prickly pear cacti of the Galápagos are a radiation in the making, they provide an exciting opportunity to investigate the interplay between ecological and genomic mechanisms promoting diversification.

The impact of preserved museum specimens is transforming and increasing by three-dimensional (3D) imaging that creates high-fidelity online digital specimens. Through examples from the openVertebrate (oVert) Thematic Collections Network, we describe how we created a digitization community dedicated to the shared vision of making 3D data of specimens available and the impact of these data on a broad audience of scientists, students, teachers, artists, and more. High-fidelity digital 3D models allow people from multiple communities to simultaneously access and use scientific specimens. Based on our multiyear, multi-institution project, we identify significant technological and social hurdles that remain for fully realizing the potential impact of digital 3D specimens.

Aim Introduced species offer insight on whether and how organisms can shift their ecological niches during translocation. The genus Amazona offers a clear test case, where sister species Red-crowned (A. viridigenalis) and Lilac-crowned Parrots (A. finschi) have established breeding populations in southern California following introduction via the pet trade from Mexico where they do not coexist. After establishment in the 1980s, introduced population sizes have increased, with mixed species flocks found throughout urban Los Angeles. Here, we investigate the differences between the environmental conditions of the native and introduced ranges of these now co-occurring species. Location Southern California and Mexico. Methods Using environmental data on climate and habitat from their native and introduced ranges, we tested whether Red-crowned and Lilac-crowned Parrots have divergent realized niches between their native ranges, and whether each species has significantly shifted its realized niche to inhabit urban southern California. We also analysed data from Texas and Florida introductions of Red-crowned Parrots for comparative analysis. Results There are significant differences in the native-range niches of both parrot species, but a convergence into a novel, shared environmental niche into urban southern California, characterized by colder temperatures, less tree cover and lower rainfall. Texas and Florida Red-crowned Parrots also show evidence for niche shifts with varying levels of niche conservatism through the establishment of somewhat different realized niches. Main Conclusions Despite significant niche shifts, introduced parrots are thriving, suggesting a broad fundamental niche and an ability to exploit urban resources. Unique niche shifts in different U.S. introductions indicate that Amazona parrots can adapt to diverse environmental conditions, with cities offering a resource niche and the timing of introduction playing a crucial role. Cities can potentially serve as refugia for threatened parrot species, but the risk of hybridization between species emphasizes the need for ongoing monitoring and genetic investigations.

Anastatus orientalis, native to northern China, is an egg parasitoid wasp of the spotted lanternfly (Lycorma delicatula) and is being tested as a potential biological control agent for invasive L. delicatula in the United States. As a component of these evaluations, live A. orientalis collected from Beijing and Yantai in China were reared in containment in the U.S. These specimens showed different responses in diapause behaviors to rearing conditions used previously by other researchers. To understand the primary mechanism potentially driving discrepancies in important life history traits, we used molecular tools to examine the genetic composition of A. orientalis from China and from South Korea, where the parasitoid has been introduced to aid in the population management of invasive L. delicatula. Molecular analysis of mitochondrial DNA recovered six haplotype groups, which exhibit biased frequency of abundance between collection sites. Some haplotypes are widespread, and others only occur in certain locations. No apparent pattern is observed between wasps collected from different years or emergence seasons. Uncorrected genetic distances between haplotype groups range from 0.44% to 1.44% after controlling for within-group variation. Genetic variance of A. orientalis is characterized by high levels of local diversity that contrasts with a lack of a broad-scale population structure. The introduced Korean population exhibits lower genetic diversity compared to native populations. Additionally, we created iso-female lines for major haplotype groups through laboratory rearing. Differences in diapause behavior were correlated with mitochondrial haplotype. Our results indicate that the observed life history traits in A. orientalis have a genetic base.

Hybrid zones are natural experiments for the study of avian evolution. Hybrid zones can be dynamic, moving as species adjust to new climates and habitats, with unknown implications for species and speciation. There are relatively few studies that have comparable modern and historic sampling to assess change in hybrid zone location and width over time, and those studies have generally found mixed results, with many hybrid zones showing change over time, but others showing stability. The white-throated magpie-jay (Calocitta formosa) and black-throated magpie-jay (Calocitta colliei) occur along the western coast of Mexico and Central America. The two species differ markedly in throat color and tail length, and prior observation suggests a narrow hybrid zone in southern Jalisco where individuals have mixed throat color. This study aims to assess the existence and temporal stability of this putative hybrid zone by comparing throat color between georeferenced historical museum specimens and modern photos from iNaturalist with precise locality information. Our results confirm the existence of a narrow hybrid zone in Jalisco, with modern throat scores gradually increasing from the parental ends of the cline toward the cline center in a sigmoidal curve characteristic of hybrid zones. Our temporal comparison suggests that the hybrid zone has not shifted its position between historical (pre-1973) and modern (post-2005) time periods-a surprising result given the grand scale of habitat change to the western Mexican lowlands during this time. An anomalous pocket of white-throated individuals in the northern range of the black-throated magpie-jay hints at the possibility of prehistorical long-distance introduction. Future genomic data will help disentangle the evolutionary history of these lineages and better characterize how secondary contact is affecting both the DNA and the phenotype of these species.

We announce the assembly of the first de novo reference genome for the California Scrub-Jay (Aphelocoma californica). The genus Aphelocoma comprises four currently recognized species including many locally adapted populations across Mesoamerica and North America. Intensive study of Aphelocoma has revealed novel insights into the evolutionary mechanisms driving diversification in natural systems. Additional insights into the evolutionary history of this group will require continued development of high-quality, publicly available genomic resources. We extracted high molecular weight genomic DNA from a female California Scrub-Jay from northern California and generated PacBio HiFi long-read data and Omni-C chromatin conformation capture data. We used these data to generate a de novo partially phased diploid genome assembly, consisting of two pseudo-haplotypes, and scaffolded them using inferred physical proximity information from the Omni-C data. The more complete pseudo-haplotype assembly (arbitrarily designated "Haplotype 1") is 1.35 Gb in total length, highly contiguous (contig N50 = 11.53 Mb), and highly complete (BUSCO completeness score = 97%), with comparable scaffold sizes to chromosome-level avian reference genomes (scaffold N50 = 66.14 Mb). Our California Scrub-Jay assembly is highly syntenic with the New Caledonian Crow reference genome despite ~10 million years of divergence, highlighting the temporal stability of the avian genome. This high-quality reference genome represents a leap forward in publicly available genomic resources for Aphelocoma, and the family Corvidae more broadly. Future work using Aphelocoma as a model for understanding the evolutionary forces generating and maintaining biodiversity across phylogenetic scales can now benefit from a highly contiguous, in-group reference genome.

The Long-tailed Wood-Partridge (Dendrortyx macroura) is distributed in the temperate forests of the TransMexican Volcanic Belt, Sierra Norte de Oaxaca, and Sierra Madre del Sur. Populations are geographically isolated throughout their distribution range, which has led to the historical description of 7 subspecies based on morphological differences. Our work analyses the geographic variation of D. macroura based on its morphology and plumage patterns. We measured 121 specimens for morphological traits and assessed differences between sexes. We separated the specimens into Operational Geographical Units (OGUs) and applied multivariate statistical analyses, including principal components analysis, and a clustering method. Then, we carried out a classification analysis of the color and pattern of the chest and belly stripes to determine if there is a relationship between plumage patterns and geography. We found significant differences between males and females in 3 morphological variables. Plumage patterns were similar between the sexes. Our results do not strongly support the distinctiveness of all existing subspecies, but morphological data suggest a distinct group in central Mexico (D. m. macroura and D. m. griseipectus). Our results do not concur with the currently recognized subspecific divisions within this complex, but further genetic data are needed to assess their taxonomic status.

Hybrid zones can be studied by modeling clines of trait variation (e.g., morphology, genetics) over a linear transect. Yet, hybrid zones can also be spatially complex, can shift over time, and can even lead to the formation of hybrid lineages with the right combination of dispersal and vicariance. We reassessed Sibley's (1950) gradient between Collared Towhee (Pipilo ocai) and Spotted Towhee (Pipilo maculatus) in Central Mexico to test whether it conformed to a typical tension-zone cline model. By comparing historical and modern data, we found that cline centers for genetic and phenotypic traits have not shifted over the course of 70 years. This equilibrium suggests that secondary contact between these species, which originally diverged over 2 million years ago, likely dates to the Pleistocene. Given the amount of mtDNA divergence, parental ends of the cline have very low autosomal nuclear differentiation (FST = 0.12). Dramatic and coincident cline shifts in mtDNA and throat color suggest the possibility of sexual selection as a factor in differential introgression, while a contrasting cline shift in green back color hints at a role for natural selection. Supporting the idea of a continuum between clinal variation and hybrid lineage formation, the towhee gradient can be analyzed as one population under isolation-by-distance, as a two-population cline, and as three lineages experiencing divergence with gene flow. In the middle of the gradient, a hybrid lineage has become partly isolated, likely due to forested habitat shrinking and fragmenting as it moved upslope after the last glacial maximum and a stark environmental transition. This towhee system offers a window into the potential outcomes of hybridization across a dynamic landscape including the creation of novel genomic and phenotypic combinations and incipient hybrid lineages.

The Steller’s jay is a familiar bird of western forests from Alaska south to Nicaragua. Here, we report a draft reference assembly for the species generated from PacBio HiFi long-read and Omni-C chromatin-proximity sequencing data as part of the California Conservation Genomics Project (CCGP). Sequenced reads were assembled into 352 scaffolds totaling 1.16 Gb in length. Assembly metrics indicate a highly contiguous and complete assembly with a contig N50 of 7.8 Mb, scaffold N50 of 25.8 Mb, and BUSCO completeness score of 97.2%. Repetitive elements span 16.6% of the genome including nearly 90% of the W chromosome. Compared with high-quality assemblies from other members of the family Corvidae, the Steller’s jay genome contains a larger proportion of repetitive elements than 4 crow species (Corvus), but a lower proportion of repetitive elements than the California scrub-jay (Aphelocoma californica). This reference genome will serve as an essential resource for future studies on speciation, local adaptation, phylogeography, and conservation genetics in this species of significant biological interest.