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.

Abstract Vagrant animals – individuals found far outside their normal range – offer powerful natural experiments for understanding migratory mechanisms. The yellow-browed warbler ( Phylloscopus inornatus ) provides perhaps the best-yet example, typically migrating from Siberia to South/Southeast Asia yet found in increasingly large numbers in Western Europe. This represents a strikingly unresolved evolutionary puzzle: why do so many migrants consistently move in almost the complete wrong direction? A critical first step toward solving this enigma is determining where these birds come from. If vagrants came from the proximal western range edge this would imply simple disorientation, whilst a more easterly origin could imply large-scale ‘reverse’ misorientation. Here, we develop a geolocation-by-genotype algorithm for low-coverage whole-genome resequencing data collected from feathers. Our method identifies spatially informative SNPs; clusters them to account for covariance in allele frequency through space; and employs a bootstrapped maximum-likelihood framework to estimate spatial origin with uncertainty. Applied to more than 80 European-caught birds, our results place their origin in central Siberia (118°E; 89–134°E [95% CI]); over 2000km east of the western range edge. These results suggest mass misorientation in a near-reverse direction, and highlight the yellow-browed warbler as an exceptional system for probing the mechanism, ontogeny and evolution of migration.

More than just a state, Alaska constitutes the entire northwestern extent of North America. Alaska is a vast area (586,412 mi2/1,518,800 km2 of land), spanning nearly 60 degrees of longitude and 20 degrees of latitude, with roughly ~45,000 mi/72,000 km of coastline. The area considered here includes surrounding waters within the U. S. 200-nautical-mile exclusive economic zone (see Gibson and Withrow 2015) and thus represents an area of over 2,000,000 mi2/~5,000,000 km2. It represents the eastern half of Beringia, a pivotally important area for the exchange of New and Old World avifaunas and for high-latitude avian endemism (Winker et al. 2023). Spanning a wide swath of the northern reaches of the Pacific Ocean, Alaska hosts breeding migrants from all seven continents, including tens of millions of birds from Asia (Winker and Gibson 2010). There are three main intrinsic drivers of Alaska’s avian diversity: Its geographic size and position on the globe, the diversity of its aquatic and terrestrial habitats, and its dynamic history of climatic and habitat fluctuations. This region’s high latitude causes extreme annual seasonality, making migration a predominant life-history strategy among the state’s birds. With migration, especially long-distance migration, comes enhanced dispersal, increasing the likelihood of vagrancy and colonization. Diverse contemporary habitat types occur in extensive expanses of nearshore and offshore marine waters; marine, brackish, and freshwater littoral zones; freshwater wetlands, rivers, lakes, and streams; the variety of heath and tundra types that dominate the Aleutian and Bering Sea islands, much of western and northern Alaska, and alpine areas; and meadows, shrubs, taiga (boreal forest), and temperate rainforests (e.g., Gabrielson and Lincoln 1959; Kessel 1979, 1998; Audubon Alaska 2014). Because of past glacial cycles, the availability and distribution of these habitats has changed throughout the Pleistocene, but the lack of major glaciation throughout much of Beringia caused the region as a whole to be a large glacial refugium within which smaller refugia also existed for some birds (Winker et al. 2023). This long-term history generated high levels of regional endemism (for this latitude) among species and subspecies of birds (ibid). In addition, southeast Alaska extends into the Pacific Northwest refugium complex, adding further to the state’s avian diversity (Shafer et al. 2010, Winker et al. 2023). The historic climatic dynamism of the Pleistocene continues today and into the future with global warming, which is occurring about four times faster in Arctic regions than elsewhere (Previdi et al. 2021, Rantanen et al. 2022). Alaska’s extensive Arctic environments (see U.S. Congress 1984) are thus undergoing rapid changes, affecting avian occurrences and distributions in multiple ways (e.g., Marcot et al. 2015, Smith et al. 2019, Renner et al. 2024). Importantly, many changes will not be due to habitat shifts. Among migratory birds in this region, extensive movements are made in eastern and western directions, such that the time available to reproduce, more than habitat, dictates range limits. As growing seasons lengthen, these range limits can change rapidly (see Benson and Winker 2015, Winker and Gibson 2018). Together, these drivers explain not only the current diversity of Alaska birds, but also why we expect this list to continue to grow over time. The starting point for this list is AOU (1998) and supplements through Chesser et al. (2023) for phylogenetic sequence and the limits of families, genera, and species. We no longer follow this list, because the American Ornithological Society decided to use avian nomenclature as a tool of social activism. This leaves us free to retain long-used names and to occasionally disagree over interpretations of the scientific evidence for some taxonomic changes. These differences can be found in the NOTES sections of the affected taxa and are summarized in the Appendix. For subspecies, the starting point is Gibson and Withrow (2015) and the two subsequent reports of the Alaska Checklist Committee (Gibson et al. 2018, 2023). The Alaska Checklist Committee (ACC) has been instrumental in collating, assessing, and publishing new records of Alaska birds. Designation of status (rare, casual, accidental; see Key to occurrence, below) at the species level follows this committee’s Checklist of Alaska Birds, 31st edition (Gibson et al. 2025). Changes from these starting points are based on published evidence and are referenced and explained (except for changes to status, which can generally be found in the ACC reports). The breeding status for all taxa is also given (see Key).We consider subspecies to be populations or groups of populations that breed in a portion of the species’ range that have a diagnosably different phenotype from other subspecies (in presumably heritable traits). Subspecies have the potential for gene flow between them, and diagnosability generally follows the 75% Rule (Patten and Unitt 2002, Winker and Haig 2010). We recognize that some of the subspecies recognized here might not meet stringent contemporary standards of diagnosability, but until they are examined in more detail and those results are published, we maintain the historical perspective as a working hypothesis. Subspecies in brackets are those not represented by an archived specimen and/or where the identity is an inference (usually geographic). Our ability to find differences among populations, especially in genetics, has grown immensely, but some traits (e.g., neutral genetic differences, vocalizations in taxa where they are learned) are not as indicative of the long-term, adaptive changes that subspecies nomenclature attempts to capture. For brevity, we do not give distributional statements, those being available elsewhere (e.g., AOU 1957, 1998; Vaurie 1959, 1965; Dickinson and Remsen 2013; Dickinson and Christidis 2014; del Hoyo and Collar 2014, 2016; Gibson and Withrow 2015; etc.). Full citations to the authorities for taxa listed here can be obtained, for example, from A. P. Peterson’s website (Zoonomen.net), D. Lepage’s and Birds Canada website Avibase (avibase.bsc-eoc.org), and in Lynx Edicions Handbook of the Birds of the World series.Alaska’s avian checklist has grown at a remarkably steady average of 3.5 species per year since the mid-1900s and shows no sign of reaching an asymptote. Gabrielson and Lincoln (1959) discussed 311 species of Alaska birds, and that number grew steadily through Kessel and Gibson (1978: 381), Gibson and Kessel (1992: 436), Gibson and Kessel (1997: 448), Gibson et al. (2003: 468), Gibson et al. (2008: 485), Gibson et al. (2013: 499), Gibson et al. (2018: 521), and Gibson et al. (2023: 541). This checklist of Alaska’s birds now includes 548 species and an additional 119 subspecies. Of these 548 species, 55 are rare, 159 are casual, and 85 are accidental; 234 species regularly breed within the state (“B”; with an additional 75 regularly breeding subspecies). An additional 38 species have at one time or another bred within the state (“b”), and 8 probably have (“?”), but are not here considered a normal part of the nesting avifauna.

Glacial cycles operating across Beringia have repeatedly exposed large swathes of the Bering Land Bridge, intermittently isolating and reuniting North American and Eurasian taxa. In high-latitude birds, these cycles are hypothesized to have been important in driving divergence and speciation. These repeated events have resulted in multiple trans-Beringian avian sister populations of varying degrees of taxonomic depth distributed across modern Beringia. We asked how these cyclic pulses have affected the temporal distribution and number of overall divergence events across Beringia. We sequenced full mitogenomes at high depth from 39 lineage pairs of varying levels of divergence, totaling 432 individuals of seven orders, 14 families, and 49 species from both Eurasia and North America. We then used a hierarchical approximate Bayesian comparative (hABC) approach to estimate the number and distribution of divergence events between the population pairs, using subsampled datasets. Net nucleotide divergence (DA) and Jukes-Cantor distance (JC-distance) were also calculated for each pairwise comparison to estimate divergence dates between taxa, using calibrated rates appropriate for shallow avian divergence events. Average divergence times were 200,000 ya for population-level taxa (n = 16), 720,000 ya for subspecies (n = 12), and 1 Mya for species (n = 11), although we consider these dating estimates conservative because of a lack of appropriate calibration for data of this quality. We found eighteen taxon pairs to be significantly differentiated (p < 0.05) by FST or substantially differentiated by haplotype clade, bounding the number of potential overall divergence events from 1 to 18, and two subsets of the full mitogenomic dataset analyzed in MTML-msBayes strongly supported simultaneous divergence of all Beringian lineages. However, this finding of simultaneous divergence is biologically unusual given the substantial variation in divergence dates among taxa and might indicate a relatively continuous spread of vicariance events, which is difficult to distinguish from a single, simultaneous vicariance event.

Reference genome assemblies are essential infrastructure for investigating phylogeny and population/conservation genetics of wild organisms. Birds serve as model vertebrates in ecology and evolutionary biology due to their well-documented natural histories and extensive community science data. We release a set of 350 newly assembled avian genomes, which, when combined with 97 previously published genomes, represent 447 of the bird species recorded in Denmark, the Faroe Islands, and Greenland-the largest regional dataset of a vertebrate group to date. These genomes are published for various research activities. This data release advances the global effort to build comprehensive and accessible biodiversity genomic resources for the research community.

The application of high-throughput sequencing to phylogenetic analyses is allowing authors to reconstruct the true evolutionary history of species. This work can illuminate specific mechanisms underlying divergence when combined with analyses of gene flow, recombination and selection. We conducted a phylogenomic analysis of Catharus, a songbird genus with considerable potential for gene flow, variation in migratory behaviour and genomic resources. We documented discordance among trees constructed for mitochondrial, autosomal and sex (Z) chromosome partitions. Two trees were recovered on the Z. Both trees differed from the autosomes, one matched the mitochondria, and the other was unique to the Z. Gene flow with one species likely generated much of this discordance; substantial admixture between ustulatus and the remaining species was documented and linked to at least two historic events. The tree unique to the Z likely reflects the true history of Catharus; local genomic analyses recovered the same tree in autosomal regions with reduced admixture and recombination. Genes previously connected to migration were enriched in these regions suggesting transitions between migratory and non-migratory states helped generate divergence. Migratory (vs. nonmigratory) Catharus formed a monophyletic clade in a subset of genomic regions. Gene flow was elevated in some of these regions suggesting adaptive introgression may have occurred, but the dominant pattern was of balancing selection maintaining ancestral polymorphisms important for olfaction and perhaps, by extension, adaptation to temperate climates. This work illuminates the evolutionary history of an important model in speciation and demonstrates how differential resistance to gene flow can affect local genomic patterns.

Many North American species have diversified in response to past climate change, but the specific impacts of late Pleistocene glaciations on diversification and population structure in widespread North American species are uncertain. We tested drivers of continent-wide population genomic structure in North American great horned owls (Bubo virginianus). Using species distribution modeling and reduced representation genomic sequencing on 114 specimen-vouchered samples, we quantified genetic diversity, gene flow, and population divergence times to test the drivers of population structure. Specifically, we examined how contemporary and historical processes shaped this species' spatial patterns of genetic structure. We identified three populations corresponding to eastern, northwestern, and southwestern North America. Areas of relatively high effective genetic diversity corresponded to regions of high habitat suitability during the Last Glacial Maximum (LGM) and gene flow was low among recently diverged populations. Landscape genomic models accounting for least-cost path dispersal distances during the LGM and current landscape found support for both contemporary and historical geographic features driving genomic differentiation. Our results revealed how habitat fragmentation associated with historical and contemporary landscapes drove population structuring. Late Pleistocene glaciations, as recently as the LGM, seem to have driven population structure of this geographically widespread, charismatic, and large-bodied avian species.

The generation and maintenance of biodiversity are driven by population divergence and speciation. We investigated divergence, gene flow, and speciation in Beringia, a region at the top of the North Pacific Ocean with a history of dramatic landscape alteration through Pleistocene glacial cycles. These cycles repeatedly split and connected the Asian and North American continents, separating and reconnecting avian populations. Glacial refugia within Beringia also isolated some populations for a time before potentially enabling them to reunite during interglacial periods. Prior work suggests gene flow plays an important role in the divergence of Beringian birds. To improve our understanding of the generation of avian diversity in Beringia, we tested models of demographic history in 11 lineages from five avian orders (Anseriformes, Gaviiformes, Charadriiformes, Piciformes and Passeriformes) using population-, subspecies- and species-level pairwise comparisons. We sequenced an average of 3710 ultraconserved element (UCE) loci from the nuclear genomes of these taxa to examine genetic differentiation and test models of divergence through diffusion analysis for demographic inference (δaδi). All of the inferred best-fit models of divergence included gene flow. Together with prior work, this corroborates that divergence with gene flow is the predominant mode of divergence and speciation in Beringian birds.

Local adaptation occurs when populations evolve traits in response to local environmental challenges. Isolated island populations often experience different selection pressures than their mainland counterparts, which enables the study of how phenotypes and genotypes respond to differing selection regimes. We studied a group of five phenotypically differentiated subspecies of song sparrow (Melospiza melodia) in Alaska that demonstrate striking body size, color, and migratory behavioral differences to examine the effects of local adaptation on phenotypes and genotypes. We examined the phenotypic attributes of these populations and used whole-genome data to determine relationships and test candidate loci for evidence of selection. Phenotypic measurements of museum specimens (n = 227) quantified the dramatic size differences among these populations, with westernmost M. m. maxima being ~1.6 times larger than easternmost M. m. rufina. Using ultraconserved elements (UCEs) and McDonald-Kreitman tests, we showed that seven candidate genes associated with bill size, circadian rhythm regulation, plumage color, and salt tolerance exhibited signs of putative positive selection. Phylogenetic analysis of UCEs identified M. m. maxima as sister to the other Alaska M. melodia subspecies. This suggests M. m. maxima colonized earliest, perhaps before the last glacial maximum, and that Alaska was later recolonized by ancestors of the remaining four subspecies.

Modern genomic methods enable estimation of a lineage’s long-term effective population sizes back to its origins. This ability allows unprecedented opportunities to determine how the adoption of a major life-history trait affects lineages’ populations relative to those without the trait. We used this novel approach to study the population effects of the life-history trait of seasonal migration across evolutionary time. Seasonal migration is a common life-history strategy, but its effects on long-term population sizes relative to lineages that don’t migrate are largely unknown. Using whole-genome data, we estimated effective population sizes over millions of years in closely related seasonally migratory and resident lineages in a group of songbirds. Our main predictions were borne out: Seasonal migration is associated with larger effective population sizes (Ne), greater long-term variation in Ne, and a greater degree of initial population growth than among resident lineages. Initial growth periods were remarkably long (0.63–4.29 Myr), paralleling the expansion and adaptation phases of taxon cycles, a framework of lineage expansion and eventual contraction over time encompassing biogeography and evolutionary ecology. Heterogeneity among lineages is noteworthy, despite geographic proximity (including overlap) and close relatedness. Seasonal migration imbues these lineages with fundamentally different population size attributes through evolutionary time compared to closely related resident lineages.

Strong tropical cyclones directly devastate forest habitats and indirectly affect forest-dependent animals. Many forecast models suggest cyclone intensity and size will increase as a result of climate change, and cyclone frequency also may increase. Short-term effects of strong cyclones on vertebrate assemblages are well documented, but we know little about longer-term effects. From 1997 to 2013 we monitored avian assemblages at tropical forest in southern Belize, a forest that was largely destroyed by category 4 Hurricane Iris in October 2001. We found little change in recruitment or species richness, but evenness dropped markedly the first two sampling efforts after the hurricane and species turnover (beta diversity) did not stabilize until 6-9 years afterward. Body condition dropped immediately after the hurricane passed but recovered quickly. That population size of resident tropical, but not Neotropical migrant, bird species dropped across our 17-year study highlights the potential urgency of altered cyclonic activity: on average, a hurricane strikes Belize once per decade, yet an increase in frequency, to say nothing of destructive power, could serve to erode extant species associations, lead to local extirpation of forest-dependent species, and create novel, transitory assemblages whose chief characteristic is instability.

Diving animals must sustain high activity with limited O2 stores to successfully capture prey. Studies suggest that increasing body O2 stores supports breath-hold diving, but less is known about metabolic specializations that underlie underwater locomotion. We measured maximal activities of 10 key enzymes in locomotory muscles (gastrocnemius and pectoralis) to identify biochemical changes associated with diving in pathways of oxidative and substrate-level phosphorylation and compared them across three groups of ducks-the longest diving sea ducks (eight spp.), the mid-tier diving pochards (three spp.) and the non-diving dabblers (five spp.). Relative to dabblers, both diving groups had increased activities of succinate dehydrogenase and cytochrome c oxidase, and sea ducks further showed increases in citrate synthase (CS) and hydroxyacyl-CoA dehydrogenase (HOAD). Both diving groups had relative decreases in capacity for anaerobic metabolism (lower ratio of lactate dehydrogenase to CS), with sea ducks also showing a greater capacity for oxidative phosphorylation and lipid oxidation (lower ratio of pyruvate kinase to CS, higher ratio of HOAD to hexokinase). These data suggest that the locomotory muscles of diving ducks are specialized for sustaining high rates of aerobic metabolism, emphasizing the importance of body O2 stores for dive performance in these species.

In high-latitude species with high dispersal ability, such as long-distance migratory birds, populations are often assumed to exhibit little genetic structure due to high gene flow or recent postglacial expansion. We sequenced over 120 low-coverage whole genomes from across the breeding range of a long-distance migratory bird, the Veery (Catharus fuscescens), revealing strong evidence for isolation by distance. Additionally, we found distinct genetic structure between boreal, western montane U.S., and southern Appalachian sampling regions. We suggest that population genetic structure in this highly migratory species is detectable with the high resolution afforded by whole-genomic data because, similar to many migratory birds, the Veery exhibits high breeding-site fidelity, which likely limits gene flow. Resolution of isolation by distance across the breeding range was sufficient to assign likely breeding origins of individuals sampled in this species’ poorly understood South American nonbreeding range, demonstrating the potential to assess migratory connectivity in this species using genomic data. As the Veery’s breeding range extends across both historically glaciated and unglaciated regions in North America, we also evaluated whether contemporary patterns of structure and genetic diversity are consistent with historical population isolation in glacial refugia. We found that patterns of genetic diversity did not support southern montane regions (southern Appalachians or western U.S. mountains) as glacial refugia. Overall, our findings suggest that isolation by distance yields subtle associations between genetic structure and geography across the breeding range of this highly vagile species even in the absence of obvious historical vicariance or contemporary barriers to dispersal.

A proposal by Foley & Rutter (2020) to eliminate all eponymous English bird names was published in the Washington Post, a Washington D.C. newspaper. Fears (2021) reported in this same newspaper that a racist and colonialist history is perpetuated in some English bird names, especially eponyms, and that a social movement is working to change those names. These articles generated hundreds of online comments. I used sentiment analysis on these comments to quantify public reaction to this proposal and topic. Among the 340 scored comments to Foley & Rutter (2020), negative opinions outnumbered positive ones by 3.36:1. Scoring comments by relative magnitude of their sentiment (-3, -2, -1, 0, 1, 2, 3) yielded an average score of -1.18. These results indicate this proposed action is very unpopular among these readers and causes pronounced divisiveness. The 570 scored comments to the Fears (2021) article were also negatively skewed (2.3:1), though less so (average score -0.58). Politicization and the left-right nature of the issue were rampant in the comments on both articles, indicating that the subject was immediately brought into the culture wars (i.e., conflict between liberal and conservative groups over cultural issues). The divisive nature of the topic was also evident within self-identified left-leaning respondents. These results likely underestimate public negativity to this proposal, because the Washington Post is a left-leaning newspaper. Similarly, Guedes et al. (2023) called for eliminating all eponymous organismal names, and a sentiment analysis of comments about that article was even more starkly negative, showing 90 % of commenters opposed. More data like these are needed. There is considerable risk that broadly de-commemorating eponymous organismal names will create more negative than positive outcomes (e.g., through asymmetric polarization and the culture wars). We must also ask: does excluding people who do not share our views achieve our objective of inclusiveness? When is it acceptable to take away someone’s hard-won knowledge by changing key terms in our shared biodiversity linguistic infrastructure? There are more constructive ways to address diversity, equity and inclusion.

Standardized taxonomies and lists of birds were created to improve communication. They are linguistic infrastructure―biodiversity indices and dictionaries―that have been painstakingly built and maintained and that have enhanced regional and global participation in the study and enjoyment of birds. Inclusion of people has been a core objective in creating and maintaining these standardized lists, and dissatisfaction and desires to overwrite objectionable names have been associated with them for nearly two centuries. Suggestions that bird names should be changed are continuous. Today, these suggestions include the view that some bird names must be changed to make them more accurate, inoffensive, and culturally appropriate to further increase diversity and inclusion among ornithologists and bird watchers. The latter, meritorious goal has been largely successful thus far despite many ongoing objections. Historic examples indicate that large-scale name changes, however, are not needed to accomplish major societal goals of inclusion. Some barriers to inclusion likely remain, and some changes are likely needed for English names. Often overlooked or underappreciated in name change discussions are that: 1) standardized names lists have had numerically staggering success in fostering inclusion of diverse participants globally; 2) stability is vital in such systems, and destabilization has exclusionary effects; 3) dissatisfaction with such lists and the names they include has been ongoing since these naming systems began; 4) important flexibilities exist in conjunction with these communication systems that enhance local and regional communication (e.g., alternative names in English and other languages); and 5) cultural values, important as they are, are neither universally shared nor constant, and thus risk bringing divisiveness and instability when used as a central reason for change. Consideration of standardized lists of bird names as communication systems in the fuller context of history, language, and culture will improve our management of these systems and their continued utility in fostering inclusion. With standardized, stable naming systems acting as a skeleton, proactively building outwards, both within and among languages and cultures, offers a positive and productive way to increase inclusion and to improve cultural and biodiversity conservation.

Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying whether it will ever be possible to completely do away with whole animal specimen collection.

The processes leading to divergence and speciation can differ broadly among taxa with different life histories. We examine these processes in a small clade of ducks with historically uncertain relationships and species limits. The green-winged teal ( Anas crecca ) complex is a Holarctic species of dabbling duck currently categorized as three subspecies ( Anas crecca crecca , A. c. nimia , and A. c. carolinensis ) with a close relative, the yellow-billed teal ( Anas flavirostris ) from South America. We examined divergence and speciation patterns in this group, determining their phylogenetic relationships and the presence and levels of gene flow among lineages using both mitochondrial and genome-wide nuclear DNA obtained from 1,393 ultraconserved element (UCE) loci. Phylogenetic relationships using nuclear DNA among these taxa showed A. c. crecca , A. c. nimia , and A. c. carolinensis clustering together to form one polytomous clade, with A.flavirostris sister to this clade. This relationship can be summarized as ( crecca , nimia , carolinensis )( flavirostris ). However, whole mitogenomes revealed a different phylogeny: ( crecca , nimia)(carolinensis , flavirostris ). The best demographic model for key pairwise comparisons supported divergence with gene flow as the probable speciation mechanism in all three contrasts ( crecca − nimia , crecca − carolinensis , and carolinensis − flavirostris ). Given prior work, gene flow was expected among the Holarctic taxa, but gene flow between North American carolinensis and South American flavirostris ( M ∼0.1 - 0.4 individuals/generation), albeit low, was not expected. Three geographically oriented modes of divergence are likely involved in the diversification of this complex: heteropatric ( crecca − nimia ), parapatric ( crecca − carolinensis ), and (mostly) allopatric ( carolinensis − flavirostris ). Ultraconserved elements are a powerful tool for simultaneously studying systematics and population genomics in systems like this. Graphical Abstract

AbstractEcogeographic rules denote spatial patterns in phenotype and environment that may reflect local adaptation as well as a species’ capacity to adapt to change. To identify genes underlying Bergmann’s Rule, which posits that spatial correlations of body mass and temperature reflect natural selection and local adaptation in endotherms, we compare 79 genomes from nine song sparrow (Melospiza melodia) subspecies that vary ~300% in body mass (17 − 50 g). Comparing large- and smaller-bodied subspecies revealed 9 candidate genes in three genomic regions associated with body mass. Further comparisons to the five smallest subspecies endemic to California revealed eight SNPs within four of the candidate genes (GARNL3, RALGPS1, ANGPTL2, and COL15A1) associated with body mass and varying as predicted by Bergmann’s Rule. Our results support the hypothesis that co-variation in environment, body mass and genotype reflect the influence of natural selection on local adaptation and a capacity for contemporary evolution in this diverse species.