Secondary contact before the completion of reproductive isolation can alter speciation trajectories by impeding divergence through gene flow or accelerating it via reinforcement. Using genomic data, we investigated secondary contact between two pairs of Copsychus (Muscicapidae) lineages in Borneo: subspecies of magpie-robins (C. saularis) and two species of shamas (C. malabaricus and C. stricklandii). Although eastern and western lineages in both groups have similar divergence times, they show markedly different phenotypic and genomic outcomes following contact. Magpie-robins exhibit extensive genomic introgression and weak population structure across Borneo, consistent with shallow plumage clines. In contrast, eastern and western shama lineages remain genetically distinct, with little apparent evidence of late-generation hybrids or backcrosses, indicating strong postmating reproductive isolation. The genomic landscape of divergence in shamas contains pronounced peaks, including loci putatively associated with melanism and song learning and production. Mitogenomic data suggest repeated colonization of Borneo by western Sundaland magpie-robin lineages, displacing older Bornean lineages eastward, likely reflecting their greater ability to exploit open habitats that expanded across the Sunda Shelf during glacial periods. In magpie-robin, but not shama, absolute divergence (DXY) is positively associated with recombination rate at the chromosomal level, suggesting a greater role for within-population processes, such as reduced linked selection in high-recombination regions, in shaping genetic diversity, whereas divergence in shama reflects greater accumulation of differences between populations. Elevated introgression of the Z chromosome in magpie-robins suggests a role for sex-biased processes such as dispersal. Our study highlights Sundaland as a natural laboratory for understanding genomic and evolutionary outcomes of secondary contact.

Kalimantan comprises nearly three quarters of the island of Borneo and is the place where scientific study of Bornean birds began. We describe the history of bird research in Kalimantan from its beginning, highlighting the ornithologists who explored the region and how their interests and methods changed over time, from a concentration on specimen collection, to examinations of community ecology, to conservation in the face of habitat change and species depletion, to the latest investigations using satellite, genetic, and digital technology. We also highlight some future directions for research, especially the need for more work on basic ecology and biogeography. Following this historical review, we list in a gazetteer every site we could find where ornithologists and birdwatchers have conducted research or documented important records of bird occurrence. The gazetteer includes the latitude and longitude of each site and, in many cases, supplementary information on location, research history, specimen and vocal collections, and associated literature. It is followed by a bibliography of 693 references.

The Nanling Mountains, an important mountain range and watershed in south China, harbor a wealth of relictual plant species, and are considered a ‘museum' of subtropical biodiversity. With respect to birds, however, the roles of the Nanling Mountains in impeding the dispersal of the subtropical birds and, as a result, shaping their population and community structures have received little consideration. To examine these roles, we compiled and analyzed two datasets. 1) To test the mountains' influence on gene flow, we undertook a comparative phylogeographic study comparing mitochondrial COI and Cytb DNA sequences of five sylvioid resident bird species of the mountains (Huet's fulvetta Alcippe hueti , red‐billed leiothrix Leiothrix lutea , greater necklaced laughingthrush Pterorhinus pectoralis , Indochinese yuhina Staphida torqueola and mountain bulbul Ixos mcclellandii ). 2) To examine differential community development over the history of modern birds, we examined distributional data of all species of the Nanling region using public species occurrence records. For part 1), we sampled 327 individuals from 36 sites and conducted correlation analysis of genetic and geographic distances, taking into account the landscape of the mountains. We found that the mountains do not seriously impede gene flow among populations but influenced species differently. For part 2), comparative analysis of 446 species in 81 families indicated that family membership influenced the community composition of birds in Nanling region. Variation in family distributions is attributable to both environmental and evolutionary factors. Overall, we found that the Nanling Mountains are not currently a substantial barrier to gene flow among the species we studied but act as a corridor and refuge for these birds. However, analyses on higher ranked community data suggest the mountains acted as a barrier in older times, corresponding to the known diversification events in southeast Asian avifauna.

Swallows (Hirundinidae) are a globally distributed family of passerine birds that exhibit remarkable similarity in body shape but tremendous variation in plumage, sociality, nesting behavior, and migratory strategies. As a result, swallow species have become models for empirical behavioral ecology and evolutionary studies, and variation across the Hirundinidae presents an excellent opportunity for comparative analyses of trait evolution. Exploiting this potential requires a comprehensive and well -resolved phylogenetic tree of the family. To address this need, we estimated swallow phylogeny using genetic data from thousands of ultraconserved element (UCE) loci sampled from nearly all recognized swallow species. Maximum likelihood, coalescent -based, and Bayesian approaches yielded a well -resolved phylogenetic tree to the generic level, with minor disagreement among inferences at the species level, which likely reflect ongoing population genetic processes. The UCE data were particularly useful in helping to resolve deep nodes, which previously confounded phylogenetic reconstruction efforts. Divergence time estimates from the improved swallow tree support a Miocene origin of the family, roughly 13 million years ago, with subsequent diversification of major groups in the late Miocene and Pliocene. Our estimates of historical biogeography support the hypothesis that swallows originated in the Afrotropics and have subsequently expanded across the globe, with major in situ diversification in Africa and a secondary major radiation following colonization of the Neotropics. Initial examination of nesting and sociality indicates that the origin of mud nesting - a relatively rare nest construction phenotype in birds - was a major innovation coincident with the origin of a clade giving rise to over 40% of extant swallow diversity. In contrast, transitions between social and solitary nesting appear less important for explaining patterns of diversification among swallows.

Lay Summary center dot We use genetic data from across the genome and produce a robust family tree for herons, which clarifies the relationships among subfamilies and genera. center dot A comprehensive phylogeny of herons is lacking. As a result, their taxonomy is unstable and their evolutionary history is poorly known. center dot Several species were found to be incorrectly classified, and we recommend appropriate taxonomic revisions. center dot Comparisons of molecular evolution support previous studies. Bitterns have evolved comparatively faster, with some tiger herons and the Boat-billed Heron having evolved comparatively slower. Thoroughly sampled and well-supported phylogenetic trees are essential to taxonomy and to guide studies of evolution and ecology. Despite extensive prior inquiry, a comprehensive tree of heron relationships (Aves: Ardeidae) has not yet been published. As a result, the classification of this family remains unstable, and their evolutionary history remains poorly studied. Here, we sample genome-wide ultraconserved elements (UCEs) and mitochondrial DNA sequences (mtDNA) of >90% of extant species to estimate heron phylogeny using a combination of maximum likelihood, coalescent, and Bayesian inference methods. The UCE and mtDNA trees are mostly concordant with one another, providing a topology that resolves relationships among the 5 heron subfamilies and indicates that the genera Gorsachius, Botaurus, Ardea, and Ixobrychus are not monophyletic. We also present the first genetic data from the Forest Bittern Zonerodius heliosylus, an enigmatic species of New Guinea; our results suggest that it is a member of the genus Ardeola and not the Tigrisomatinae (tiger herons), as previously thought. Finally, we compare molecular rates between heron clades in the UCE tree with those in previously constructed mtDNA and DNA-DNA hybridization trees. We show that rate variation in the UCE tree corroborates rate patterns in the previously constructed trees-that bitterns (Ixobrychus and Botaurus) evolved comparatively faster, and some tiger herons (Tigrisoma) and the Boat-billed Heron (Cochlearius) more slowly, than other heron taxa.

The Oriental Dwarf Kingfisher species‐complex of South and Southeast Asia comprises two forms, the dark‐backed Ceyx erithaca of India and Indochina and the rufous‐backed Ceyx rufidorsa of Java and the Lesser Sunda Islands. Between these two extremes, the large area of Sundaland and the Philippines is occupied by individuals that have a rufous back, characteristic of C. rufidorsa, but exhibit a range of phenotypes that are intermediate between C. erithaca and C. rufidorsa. These potential intermediates have intrigued avian taxonomists for generations. To investigate the species dynamics of the two forms and understand the demographic history of the intermediates, we generated a genome‐scale dataset (ddRAD) representing multiple individuals across the entire range of the complex. Our findings support the distinctiveness of the two forms based on back colour. Demographic analysis suggests the two populations were isolated c. 820 000 years ago followed by secondary contact c. 140 000 years ago, with asymmetrical dispersal of C. rufidorsa into C. erithaca. Although some limited introgression appears to have occurred more recently between the two taxa in the northern parts of their range, we were unable to find any association of recent hybridization with the intermediate plumages of C. rufidorsa. We also found no support for the commonly recognized Borneo subspecies motleyi.

Sarawak is Malaysia’s largest state, covering most of northern Borneo. It has a remarkable history of scientific bird study, starting in the 1840s and growing ever since. To set the stage for the gazetteer, which is the core of this paper, we start with a review of this history and discuss various forces that have influenced the direction of bird research in the state. Following this introduction comes the gazetteer, which is an annotated list of c. 865 sites in Sarawak where birds have been collected, studied, or regularly observed. The gazetteer provides the latitude, longitude, and elevation of each site, and it lists publications, reports, and museum collections associated with each site. The purpose of the gazetteer is to help interested parties locate sites and investigate their research history. It is also intended to help museum curators geolocate specimens for various kinds of studies, including the assessment of bird distributions in relation to habitat change over time. A notable byproduct of the historical review and gazetteer is a bibliography of c. 750 references related to Sarawak ornithology. Another is the identification of areas in Sarawak where birds are better known and areas where they are not.

We describe two new bird species from the Meratus Mountains of southeastern Borneo, Indonesia: a jungle-flycatcher (genus Cyornis) and a white-eye (genus Zosterops). Our descriptions are based on comparisons of plumage, mitochondrial ND2 DNA sequences, and vocalizations of the new species and their congeners. The new Meratus jungle-flycatcher is most closely related to Cyornis montanus but morphologically distinguished by lighter blue on the upperparts and more whitish and less reddish on the underparts. The new Meratus white-eye is most closely related to Zosterops chloris but distinguished by olive upperparts and darker underparts. Vocalizations and genetic divergence values also corroborate species status for both new taxa. Both new species are probably confined to the Meratus Mountains, which are currently surrounded by degraded lower elevation secondary woodland or converted agricultural landscape. They appear to have diverged from their sister species through geographic isolation in this remote mountain range compounded by altered population dynamics in a depauperate montane bird community. Although both species are relatively common in the restricted area of the Meratus Mountains, continued habitat alteration and the imminent threat of poaching may be in the process of endangering them. Therefore, we recommend the IUCN Red List status of " Vulnerable" for the new species based on criteria B1 and B2.

Intraspecific polymorphism in birds, especially plumage colour polymorphism, and the mechanisms that control it are an area of active research in evolutionary biology. The black-headed bulbul (Brachypodius atriceps) is a polymorphic species with two distinct morphs, yellow and grey. This species inhabits the mainland and virtually all continental islands of Southeast Asia where yellow morphs predominate, but on two islands in the Sunda region, Bawean and Maratua, grey morphs are common or exclusive. Here, we generated a high-quality reference genome of a yellow individual and resequenced genomes of multiple individuals of both yellow and grey morphs to study the genetic basis of coloration and population history of the species. Using PCA and STRUCTURE analysis, we found the Maratua Island population (which is exclusively grey) to be distinct from all other B. atriceps populations, having been isolated c. 1.9 million years ago (Ma). In contrast, Bawean grey individuals (a subset of yellow and grey individuals on that island) are embedded within an almost panmictic Sundaic clade of yellow birds. Using FST and dxy to compare variable genomic segments between Maratua and yellow individuals, we located peaks of divergence and identified candidate loci involved in the colour polymorphism. Tests of selection among coding-proteins in high FST regions, however, did not indicate selection on the candidate genes. Overall, we report on some loci that are potentially responsible for the grey/yellow polymorphism in a species that otherwise shows little genetic diversification across most of its range.

A Correction to this paper has been published: https://doi.org/10.1038/s41586-021-03473-8.

Abstract Indochina and Sundaland are biologically diverse, interconnected regions of Southeast Asia with complex geographic histories. Few studies have examined phylogeography of bird species that span the two regions because of inadequate population sampling. To determine how geographic barriers/events and disparate dispersal potential have influenced the population structure, gene flow, and demographics of species that occupy the entire area, we studied five largely codistributed rainforest bird species: Arachnothera longirostra, Irena puella, Brachypodius atriceps, Niltava grandis, and Stachyris nigriceps. We accomplished relatively thorough sampling and data collection by sequencing ultraconserved elements (UCEs) using DNA extracted from modern and older (historical) specimens. We obtained a genome‐wide set of 753–4,501 variable loci and 3,919–18,472 single nucleotide polymorphisms. The formation of major within‐species lineages occurred within a similar span of time (0.5–1.5 mya). Major patterns in population genetic structure are largely consistent with the dispersal potential and habitat requirements of the study species. A population break across the Isthmus of Kra was shared only by the two hill/submontane insectivores (N. grandis and S. nigriceps). Across Sundaland, there is little structure in B. atriceps, which is a eurytopic and partially frugivorous species that often utilizes forest edges. Two other eurytopic species, A. longirostra and I. puella, possess highly divergent populations in peripheral Sunda Islands (Java and/or Palawan) and India. These species probably possess intermediate dispersal abilities that allowed them to colonize new areas, and then remained largely isolated subsequently. We also observed an east–west break in Indochina that was shared by B. atriceps and S. nigriceps, species with very different habitat requirements and dispersal potential. By analyzing high‐throughput DNA data, our study provides an unprecedented comparative perspective on the process of avian population divergence across Southeast Asia, a process that is determined by geography, species characteristics, and the stochastic nature of dispersal and vicariance events.

Anthony Hemingway “Tony” Bledsoe died at the age of 62 on September 14, 2019. Tony was an outstanding ornithologist, life-long birdwatcher, and most of all an inspirational teacher of ecology and evolution. He was an Elective Member (1990) of the American Ornithologists’ Union (AOU), Director of the Ornithological Societies of North America (1998–2000), Assistant to the AOU Treasurer (1996–2000), a key organizer of the AOU’s annual meeting in Pittsburgh (1989), and a founding member of the Connecticut Ornithological Association (1983). Tony was born to Carter and Phyllis Bledsoe in Washington, D.C., on October 10, 1956, but grew up on the Main Line of Philadelphia, graduating from Lower Merion High School. As a young natural history enthusiast, he volunteered to work in the collections at the Academy of Natural Sciences of Philadelphia, where he was inspired to “think clearly” about evolutionary issues by Frank Gill and herpetologist Tom Uzzell. Following high school, Tony attended the University of California, Santa Cruz, where he honed his birdwatching and natural history skills. In 1978, he started his PhD studies in the laboratory of Charles Sibley at Yale University. At the time molecular systematics was a small field, and studies using DNA were rare. With huge intellectual curiosity and boyish naiveté, Tony jumped into the program and soon became an expert in all aspects of phylogenetics. At the time, cladistic morphology was in its full glory, and antipathy toward Sibley’s DNA hybridization, which was viewed (inaccurately) as phenetic and thus hopelessly flawed, led to epic philosophical battles. Tony threw his substantial intellectual powers into those battles and helped guide the Sibley school through much of the fray. Tony’s graduate studies were focused on the adaptive radiation of 9-primaried oscines. It seems quaint today, but he spent many years obtaining DNA-hybridization comparisons of just 27 bird species. Nevertheless, literally everything he discovered about the relationships of those birds (e.g., the radical observation that South American “emberizids” clustered with tanagers rather than sparrows) has endured the test of time and been confirmed by modern DNA sequencing studies. In the process of his PhD studies, Tony became an expert in what we now call genomics. DNA hybridization compared large segments of bird DNA (the “single-copy” genome) and required a substantial understanding of genomic structure and data analysis. In 1984, Tony finished his PhD and began a series of postdocs, first as a Guyer Fellow at the University of Wisconsin (1985–1986), then as a Rea Fellow at the Carnegie

To help resolve phylogenetic and phylogeographic relationships of Southeast Asian birds, we have collected specimens in Borneo, Sumatra, and Java for phylogenetic and morphological study. Here, we compare mitochondrial ND2 gene sequences from some of these new specimens to sequences obtained in previous studies to shed light on genealogical relationships in nine passerine clades: Erythropitta venusta/granatina/ussheri (pittas); Dicrurus hottentottus (drongos); Alophoixus bulbuls; Napothera, Turdinus and Pellorneum babblers; Anthipes flycatchers; Brachypteryx shortwings; and Myophonus whistling thrushes. These comparisons resolve or shed substantial light on taxonomic problems in pittas, Alophoixus, Napothera, Dicrurus, Brachypteryx, and Myophonus, and they confirm assumed (but previously unquantified) genetic relationships within Turdinus and Anthipes. The resulting trees also allow us to (1) suggest improved taxonomic arrangements in several groups, (2) confirm the rediscovery of a “lost” species within Napothera, and (3) provide the basis for the description of a new subspecies of Alophoixus.

Disjunct, pantropical distributions are a common pattern among avian lineages, but disentangling multiple scenarios that can produce them requires accurate estimates of historical relationships and timescales. Here, we clarify the biogeographical history of the pantropical avian family of trogons (Trogonidae) by re‐examining their phylogenetic relationships and divergence times with genome‐scale data. We estimated trogon phylogeny by analysing thousands of ultraconserved element (UCE) loci from all extant trogon genera with concatenation and coalescent approaches. We then estimated a time frame for trogon diversification using MCMCTree and fossil calibrations, after which we performed ancestral area estimation using BioGeoBEARS. We recovered the first well‐resolved hypothesis of relationships among trogon genera. Trogons comprise three clades, each confined to one of three biogeographical regions: Africa, Asia and the Neotropics, with the African clade sister to the others. These clades diverged rapidly during the Oligocene‐Miocene transition. Our biogeographical analyses identify a Eurasian origin for stem trogons and a crown clade arising from ancestors broadly distributed across Laurasia and Africa. The pantropical ranges of trogons are relicts of a broader Afro‐Laurasian distribution that was fragmented across Africa, Asia and the New World in near coincident fashion during the Oligocene‐Miocene transition by global cooling and changing habitats along the Beringian land bridge and North Africa.

The tropics are the source of most biodiversity yet inadequate sampling obscures answers to fundamental questions about how this diversity evolves. We leveraged samples assembled over decades of fieldwork to study diversification of the largest tropical bird radiation, the suboscine passerines. Our phylogeny, estimated using data from 2389 genomic regions in 1940 individuals of 1283 species, reveals that peak suboscine species diversity in the Neotropics is not associated with high recent speciation rates but rather with the gradual accumulation of species over time. Paradoxically, the highest speciation rates are in lineages from regions with low species diversity, which are generally cold, dry, unstable environments. Our results reveal a model in which species are forming faster in environmental extremes but have accumulated in moderate environments to form tropical biodiversity hotspots.

Aim Physiological tolerances and biotic interactions along habitat gradients are thought to influence species occurrence. Distributional differences caused by such forces are particularly noticeable on tropical mountains, where high species turnover along elevational gradients occurs over relatively short distances and elevational distributions of particular species can shift among mountains. Such shifts are interpreted as evidence of the importance of spatial variation in interspecific competition and habitat or climatic gradients. To assess the relative importance of competition and compression of habitat and climatic zones in setting range limits, we examined differences in elevational ranges of forest bird species among four Bornean mountains with distinct features. Location Bornean mountains Kinabalu, Mulu, Pueh and Topap Oso. Taxon Rain forest bird communities along elevational gradients. Methods We surveyed the elevational ranges of rain forest birds on four mountains in Borneo to test which environmental variables-habitat zone compression or presence of likely competitors-best predicted differences in elevational ranges of species among mountains. For this purpose, we used two complementary tests: a comparison of elevational range limits between pairs of mountains, and linear mixed models with naive occupancy as the response variable. Results We found that lowland species occur higher in elevation on two small mountains compared to Mt. Mulu. This result is inconsistent with the expectation that distributions of habitats are elevationally compressed on small mountains, but is consistent with the hypothesis that a reduction in competition (likely diffuse) on short mountains, which largely lack montane specialist species, allows lowland species to occur higher in elevation. The relative influence of competition changes with elevation, and the correlation between lower range limits of montane species and the distribution of their competitors was weaker than in lowland species. Main conclusions These findings provide support for the importance of biotic interactions in setting elevational range limits of tropical bird species, although abiotic gradients explain the majority of distribution patterns. Thus, models predicting range shifts under climate change scenarios must include not only climatic variables, as is currently most common, but also information on potentially resulting changes in species interactions, especially for lowland species.

Siberut Island, Mt. Talamau, Rimbo Panti Nature Reserve, and intervening locations in West Sumatra Province were visited during two expeditions in 2018-2019 by ornithologists from the Museum Zoologicum Bogoriense (MZB) - Indonesian Institute of Sciences (LIPI), Louisiana State University Museum of Natural Science (LSUMNS), and Andalas University. The main objective of these expeditions was to obtain data and tissue-subsample rich museum specimens for morphological and genetic studies of phylogeny and population genetics of Southeast Asian birds aimed at understanding the causes of avian diversification in the region. We also observed, photographed, and audio-recorded numerous bird species during the expeditions and archived these data. In total, 285 species were identified, and specimen material was collected from 13 species and 26 subspecies not previously represented in tissue resource collections. Here, we provide complete lists of birds found at each location, highlight distributional discoveries, and note cases of potential taxonomic, ecological, and conservation interest.

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1–4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families—including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.

Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyperdiverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships among all passerine families. Then, we calibrated this phylogeny using 13 fossils to examine the effects of different events in Earth history on the timing and rate of passerine diversification. Our analyses reconcile passerine diversification with the fossil and geological records; suggest that passerines originated on the Australian landmass ∼47 Ma; and show that subsequent dispersal and diversification of passerines was affected by a number of climatological and geological events, such as Oligocene glaciation and inundation of the New Zealand landmass. Although passerine diversification rates fluctuated throughout the Cenozoic, we find no link between the rate of passerine diversification and Cenozoic global temperature, and our analyses show that the increases in passerine diversification rate we observe are disconnected from the colonization of new continents. Taken together, these results suggest more complex mechanisms than temperature change or ecological opportunity have controlled macroscale patterns of passerine speciation.