The loss of species in today’s environmental crisis not only threatens ecosystem function but also the evolutionary history these species embody. Understanding this history is imperative for developing sound conservation strategies, especially for declining iconic taxa like cockatoos of the genus Cacatua. The Triton Cockatoo (Cacatua triton) in particular, endemic to New Guinea and adjacent satellite islands in Melanesia, has remained taxonomically overlooked for nearly a century due to morphological conservatism across Cacatua species, sparse taxon sampling and limited genomic data. Using whole-genome resequencing of historical museum specimens, complemented by contemporary genomes, we reconstructed the evolutionary history and intraspecific structure of C. triton across its range. Genome-wide analyses affirm C. triton as a species deeply divergent from the largely Australian Sulphur-crested Cockatoo (Cacatua galerita) and reveals pronounced geographic structure across Melanesia. We identify two well-supported evolutionarily significant units corresponding to populations on either side of the Bird’s Neck, a biogeographic suture zone, consistent with isolation driven by the Pleistocene climatic cycles and regional orogenesis. These units align with the historically proposed subspecies C. triton triton and C. triton macrolophus. Populations from the Aru Islands, long considered to be Sulphur-crested Cockatoos (C. galerita eleonora), were nested within C. triton triton, suggesting historical connectivity across the Sahul Shelf. Despite evidence of gene flow among Cacatua lineages, introgression into C. triton appears limited. Our findings demonstrate the value of museomics in resolving cryptic diversity in under sampled regions and provide an updated systematic and conservation framework for Cacatua species.

Macroevolutionary forces, such as rare catastrophes, have repeatedly disrupted and reset the evolutionary trajectories of Earth's major organismal groups. The Cretaceous-Paleogene (K/Pg) extinction event, approximately 66 Ma, resulted in the demise of ∼75% of all species at the time, yet despite its magnitude, many major organismal lineages successfully passed through this mass extinction. The evolutionary origins of modern birds (crown-group Aves) remain a subject of substantial debate, as they are often thought to have undergone their primary diversification following the K/Pg boundary. In this review, we summarize the various approaches that have been applied to understanding the timing of avian diversification. We examine the inferred divergence times derived from modern phylogenomic studies based on datasets comprising 50 to over 300 whole genomes. Additionally, we evaluate the factors contributing to the continued discrepancies in divergence time estimates. Furthermore, we discuss significant new fossil discoveries from the Late Jurassic and Late Cretaceous periods that reshape our understanding of key evolutionary events in early avian diversification. Taken together, the paleontological evidence increasingly supports a Cretaceous origin for many extant bird lineages, with the major burst of ordinal diversification likely occurring prior to the K/Pg boundary-concurrent with the early radiations of flowering plants, pollinating insects, mammals, fishes and other groups that characterized the Cretaceous Angiosperm Terrestrial Revolution.

Universally recognized scientific names for organisms are necessary for accurate and efficient communication. Incongruence in taxonomic treatments results in situations where one name is used for different entities or one entity is known by different names, with negative consequences for conservation, science, trade, legislation, law enforcement, and education, leading to discord among stakeholders and confusion among users. Within the ornithological community taxonomic incongruence among four widely adopted global bird checklists has led to calls for the development of a single unified global avian taxonomy or checklist. Here we introduce AviList, a comprehensive, collaborative and evolving effort towards developing a unified global avian taxonomy, spearheaded by representatives of most current global checklists and many major regional authorities, and supported by the International Ornithologists’ Union (IOU), BirdLife International and the Cornell Lab of Ornithology. AviList version 2025, the first version, was officially launched on 11 June 2025 and is available online as a comprehensive, searchable public-access database. It recognizes 11,131 bird species in 2376 genera, 252 families and 46 orders. This global effort has resolved over 1000 species-level taxonomic incongruences among existing checklists. With AviList’s launch, the IOC World Bird List and the Clements Checklist of Birds of the World have ceased any independent taxonomic updates, while BirdLife International is in the process of total alignment, leading to a harmonization in the classification underpinning a number of major bird projects, including eBird, Macaulay Library, Merlin Bird ID and the IUCN Red List. Adoption of AviList will improve inter-operability across global biodiversity, molecular, ecological and spatial databases (e.g. GBIF). Strong governance of AviList will ensure it is a “living” document that is regularly updated by a global community of bird taxonomists as new scientific advances are made, with positive impacts for conservation, academia and human society. It is hoped that AviList will support and encourage taxonomic science by identifying areas where further research is most needed, and that it will provide a blueprint for taxonomic authorities in other organismic groups endeavoring to achieve taxonomic harmonization.

The speciose family Tyrannidae harbours numerous morphologically cryptic species that differ most notably in their innate vocalisations. Among these, five belong to the Neotropical genus Pseudocolopteryx, including a pair of cryptic sister species, P. flaviventris and P. citreola, which differ markedly in vocalisations and exhibit an extremely low mitochondrial divergence. Using genome-wide ddRADseq data, we reconstructed phylogenetic relationships and assessed population structure within the genus and evaluated four speciation scenarios for the sibling species pair using coalescent-based demographic simulations. Phylogenomic analyses found no mito-nuclear discordance in tree topologies and no disagreement between Z-linked and autosomal locus trees in the genus. P. citreola was monophyletic and embedded within a potentially paraphyletic P. flaviventris, whilst population structure analyses (PCA, ADMIXTURE) recovered both as different units. Coalescent-based demographic simulations estimated their divergence similar to 550,000 generations ago (similar to 0.55 to similar to 1.15 mya), with minor gene flow starting ca. similar to 935 generations ago (similar to 935 to similar to 1965 ya), without eroding their separate evolutionary trajectories. Therefore, the previously reported low mitochondrial differentiation could stem from past hybridization. Vocal differences are key traits of the specific mate recognition systems of P. flaviventris and P. citreola that evolved in the context of plumage stasis and were likely influenced by concomitant habitat switches, playing a fundamental role early in the speciation process. In non-learner species such as tyrant flycatchers, minimal genetic changes may suffice to produce acoustic innovations critical to species recognition. Exploring morphological differences and developmental processes underlying vocal tract anatomy could provide deeper insights into how vocal distinctions arise and lead to speciation in cryptic flycatchers.

Bats are known reservoirs for many viruses of zoonotic potential and can tolerate or clear infections efficiently. They are important hosts for multiple coronaviruses and harbour ancestral lineages of coronaviruses known to cause diseases in both humans and animals. In this study, we describe a high-quality hybrid genome assembly of the Blyth's horseshoe bat Rhinolophus lepidus. It is a widespread species and an important cell-line model system for studying virus entry and replication. We used a combination of short Illumina reads and long reads from Oxford Nanopore to assemble the genome, with N50 of 5.3 Mb and Benchmarking Universial Single-Copy Orthologs (BUSCO) score of ~94%. The Angiotensin-converting enzyme 2 receptor responsible for the entry of severe acute respiratory syndrome coronaviruses (SARS and SARS-CoV-2) was highly conserved within bats, especially the region responsible for virus entry into the cell. In total, 50% of the amino acids necessary for virus entry were conserved between humans and R. lepidus. We observed an effect of past climatic conditions on the effective population size with drastic population size reduction in the past 50,000 years. This study adds to the growing list of bat genomes which are important resources to understand the co-evolution of bats and viruses and the mechanism by which bats can tolerate and clear infections effectively.

ABSTRACT Horseshoe crabs are unique living fossils that have remained almost unaltered through 400 million years of global change. They face rapid worldwide declines under increasing anthropogenic pressure. Using comprehensive geographic and genomic sampling combined with approaches that integrate DNA with environmental and climatic datasets, we assessed the population genetic structure, demographic histories, and vulnerability to future climate change in three out of four extant horseshoe crab species, all centered in Asia. Our study highlights that the Sunda Shelf, a complex and dynamic shallow‐marine landscape, has been the sole repository of most genetic diversity among all three Asian species, and therefore crucial to the long‐term survival of horseshoe crabs. Our study not only provides the first genomic baseline data for the evaluation of Asian horseshoe crabs’ conservation status but also identifies core habitats that potentially act as refugia and corridors for Asian horseshoe crab populations with impending anthropogenic global warming.

Rivers constitute an important biogeographic divide in vast areas of tropical rainforest, such as the Amazon and Congo Basins. Southeast Asia's rainforests are currently fragmented across islands divided by sea, which has long obscured their extensive history of terrestrial connectivity as part of a vast (but now submerged) subcontinent - Sundaland - during most of the Quaternary. The role of paleo-rivers in determining population structure in Sundaic rainforests at a time when these forests were connected remains little understood. We examined the coloration of museum skins and used the genomic DNA of museum samples and freshly-collected blood tissue of a pair of Sundaic songbird species, the pin-striped and bold-striped tit-babblers (Mixornis gularis and M. bornensis, respectively), to assess the genetic affinity of populations on small Sundaic islands that have largely been ignored by modern research. Our genomic and morphological results place the populations from the Anambas and Natuna Islands firmly within M. gularis from the Malay Peninsula in western Sundaland, even though some of these islands are geographically much closer to Borneo, where M. bornensis resides. Our results reveal genetic structure consistent with the course of Sundaic paleo-rivers and the location of the interfluvia they formed, and add to a small but growing body of evidence that rivers would have been of equal biogeographic importance in Sundaland's former connected forest landscape as they are in Amazonia and the Congo Basin today.

Aim: Species occurrence patterns are typically analysed using data-randomisation approaches, which reveal when observed patterns deviate from random expectation, but give little insight why. Mechanistic models, such as neutral models, have been proposed as an alternative null model, but they are computationally expensive. Here, we develop an efficient method to simulate such models and use it to explore likely mechanisms governing the occurrence patterns of birds on islands. Location: Riau archipelago, Indonesia. Taxon: Birds. Methods: We used species richness and island area data to fit a niche--neutral model, where species obey neutral dynamics within non-overlapping discrete niches. We developed a sequential sampling algorithm that can efficiently generate randomised presence--absence matrices under the niche-neutral model and used mismatches to identify which mechanisms were potentially important to occurrence patterns. Results: Birds were more segregated and less nested than expected from both data randomisation and the niche--neutral model. The niche--neutral model reproduced the mean relationship between island size and species richness, but it could not produce sufficient variability to account for the richness data. The model was brought into closer agreement with the data by allowing niche diversity to vary across islands (increased segregation) and allowing the per-capita immigration rate to vary across islands (decreased nestedness). Main conclusion: While the species-area relationship could be explained by a model with constant per-capita immigration rates and number of niches across islands, inter-island heterogeneity was needed to explain higher-order metrics of nestedness and co-occurrence patterns. Our novel sequential sampling algorithm allowed us to explore different scenarios efficiently, and our approach may be useful for identifying the mechanisms structuring occurrence patterns in other systems. ### Competing Interest Statement The authors have declared no competing interest.

AbstractAimSpecies occurrence patterns are typically analysed using data-randomisation approaches, which reveal when observed patterns deviate from random expectation, but give little insight why. Mechanistic models, such as neutral models, have been proposed as an alternative null model, but they are computationally expensive. Here, we use an efficient method to simulate such models and to explore likely mechanisms governing the occurrence patterns of birds on islands.LocationRiau archipelago, Indonesia.TaxonBirds.MethodsWe used species richness and island area data to fit a niche–neutral model, where species obey neutral dynamics within non-overlapping discrete niches. We used a sequential sampling algorithm that can efficiently generate randomised presence– absence matrices under the niche-neutral model and used mismatches to identify which mechanisms were potentially important to occurrence patterns.ResultsBirds were more segregated and less nested than expected from both data randomisation and the niche–neutral model. The niche–neutral model reproduced the mean relationship between island size and species richness, but it could not produce sufficient variability to account for the richness data. The model was brought into closer agreement with the data by allowing niche diversity to vary across islands (increased segregation) and allowing the per-capita immigration rate to vary across islands (decreased nestedness).Main conclusionWhile the species-area relationship could be explained by a model with constant per-capita immigration rates and number of niches across islands, interisland heterogeneity was needed to explain higher-order metrics of nestedness and cooccurrence patterns. The sequential sampling algorithm allowed us to explore different scenarios efficiently, and our approach may be useful for identifying the mechanisms structuring occurrence patterns in other systems.

Sulawesi is an important endemicity hotspot in Southeast Asia, with over 100 endemic species distributed on the island. Despite a long history of avian research on Sulawesi that has played a significant role in the development of evolutionary theory, many ornithological aspects remain unknown. The last few decades have seen novel discoveries, for example, in the form of new species range extensions and species discoveries in the face of ongoing habitat loss and conversion. We here report on a range extension and notes of morphological descriptions of the endemic Diabolical Nightjar and Indonesian Serin in Southeast Sulawesi, adding to our knowledge of the distribution of Sulawesi’s avifauna, especially in the southeastern part in which visits from ornithologists are less frequent. A review of recent museum collections adds another new locality for Diabolical Nightjar in South Sulawesi. Future taxonomic studies are needed to elucidate the status of both species, especially in the Indonesian Serin, as the subtle differences in the coloration of the forehead, rump, and upper tail covert may indicate more than one taxon exists in Sulawesi. In addition, we provide an annotated checklist of birds observed during the fieldwork encompassing areas around Kolaka and Makassar.

Bird-building collisions are responsible for a large number of bird deaths in cities around the world, yet they remain poorly studied outside of North America. This study presents one of the first city-wide fine-scale and landscape-scale analyses of bird-building collisions from Asia and represents a novel application of maximum entropy modeling (as commonly applied to species distribution modeling) to assess the drivers of bird-building collisions in the tropical city-state of Singapore. Our results show that the drivers of bird-building collisions often vary among taxa, with several migratory taxa having a higher relative collision risk linked to areas with high building densities and high levels of nocturnal blue light pollution. In contrast, non-migratory taxa had a higher collision risk in areas proximate to woodland cover. Projecting these models onto high-fidelity long-term government land-use plans, we demonstrate that our approach can be applied to predict future changes in bird-building collision risk stemming from future increases in blue light pollution and encroachment of buildings into forested areas. Our results suggest that bird-building collision mitigation measures need to account for the differential drivers of collision across both resident and migratory species, and show that combining community science and ecological modeling can be a powerful approach for analyzing bird-building collision data. Article impact statement Inferring the drivers and distribution patterns of bird-building collision hotspots in Singapore using community science and maximum entropy modeling

Accurate identification of evolutionarily significant units of rare and threatened organisms provides a foundation for effective management and conservation. Up to seven subspecies of the critically endangered Yellow-crested Cockatoo (Cacatua sulphurea) have been described, four of which were commonly recognised pre-2014. In the absence of genotypic data, C. sulphurea subspecies delimitation has been based on morphology, behaviour and biogeography. To clarify genetic relationships and shed light on the diversification of this parrot radiation, whole genomes were sequenced for 16 museum specimens, covering the geographic range of the proposed seven subspecies as well as one C. galerita galerita. Combined with four museum-derived wild Cacatua sequences from NCBI, the results indicate there are three distinct C. sulphurea subspecies clusters centred in different biogeographic subregions of Wallacea (Timor; Sumba; as well as the Sulawesi Region and the main Lesser Sunda chain), separated by shallow genetic distances (da < 0.148%). The results raise questions about the recent species-level elevation of the phenotypically most distinct subspecies, C. s. citrinocristata, and about the origins of C. s. abbotti, the only subspecies west of Wallace's Line. Our analyses suggest C. s. abbotti is unlikely to be embedded within C. sulphurea, suggesting its origin on the remote Masalembu islands may be due to human translocation via historical trade routes. These genomic results inform the prioritisation and streamlining of conservation measures for the critically endangered C. sulphurea by identifying and delimiting likely conservation units.

The origin of the German cockroach,Blattella germanica, is enigmatic, in part because it is ubiquitous worldwide in human-built structures but absent from any natural habitats. The first historical records of this species are from ca. 250 years ago (ya) from central Europe (hence its name). However, recent research suggests that the center of diversity of the genus is Asian, where its closest relatives are found. To solve this paradox, we sampled genome-wide markers of 281 cockroaches from 17 countries across six continents. We confirm thatB. germanicaevolved from the Asian cockroachBlattella asahinaiapproximately 2,100 ya, probably by adapting to human settlements in India or Myanmar. Our genomic analyses reconstructed two primary global spread routes, one older, westward route to the Middle East coinciding with various Islamic dynasties (~1,200 ya), and another younger eastward route coinciding with the European colonial period (~390 ya). While Europe was not central to the early domestication and spread of the German cockroach, European advances in long-distance transportation and temperature-controlled housing were likely important for the more recent global spread, increasing chances of successful dispersal to and establishment in new regions. The global genetic structure of German cockroaches further supports our model, as it generally aligns with geopolitical boundaries, suggesting regional bridgehead populations established following the advent of international commerce.

Most birds are characterized by a seasonal phenology closely adapted to local climatic conditions, even in tropical habitats where climatic seasonality is slight. In order to better understand the phenologies of resident tropical birds, and how phenology may differ among species at the same site, we used ~70 000 hours of audio recordings collected continuously for two years at four recording stations in Singapore and nine custom‐made machine learning classifiers to determine the vocal phenology of a panel of nine resident bird species. We detected distinct seasonality in vocal activity in some species but not others. Native forest species sang seasonally. In contrast, species which have had breeding populations in Singapore only for the last few decades exhibited seemingly aseasonal or unpredictable song activity throughout the year. Urbanization and habitat modification over the last 100 years have altered the composition of species in Singapore, which appears to have influenced phenological dynamics in the avian community. It is unclear what is driving the differences in phenology between these two groups of species, but it may be due to either differences in seasonal availability of preferred foods, or because newly established populations may require decades to adjust to local environmental conditions. Our results highlight the ways that anthropogenic habitat modification may disrupt phenological cycles in tropical regions in addition to altering the species community.

We investigated the population genetic trajectory and genetic diversity of a wintering population of Common Redshanks (Tringa totanus) in Southeast Asia. Using 23,000 genome-wide single nucleotide polymorphisms (SNPs) harvested by double-digest restriction-site associated DNA sequencing (ddRADseq) of Common Redshanks collected in Singapore across 28 years, we uncovered evidence for long-term genetic homogeneity that points to sustained migratory connectivity of individuals found in Singapore. Our population genetic analyses also revealed that Singapore’s Common Redshanks have harboured persistently low levels of genetic diversity throughout the temporal sampling regime. We further furnish, for the first time in shorebirds, genomic evidence for migratory site fidelity within closely related familial pairs across multiple seasons. Our findings are consistent with population genetic stability and support past results on the species’ exceptional site fidelity, with ramifications for the population’s conservation status and management strategy. Our work highlights the utility of genome-wide DNA techniques in combination with robust longitudinal sampling regimes for effective genetic monitoring programs targeted at highly mobile avian taxa, with broad applicability and relevance to highly dispersive taxa in general. We recommend that future studies expand the current sampling regime to achieve a comprehensive phylogeographic overview for insights into the genetic and migratory connectivity of the species.

Acoustic signaling among birds is central to intra-species communication, courtship, and reproductive success, and so habitat suitability is partially dependent upon the availability of a suitable acoustic niche. It is well documented that birds may modify their vocal behavior to avoid overlap with anthropogenic noise pollution, but responses to biotic signal making are less well understood. This study uses more than 50,000 h of audio recorded in tropical forest, and machine learning methods for the detection of the vocalizations of nine species of bird and tymbalizations of three species of cicada to examine patterns of signal masking and co-chorusing avoidance among species pairs. Among these focal species, no bird avoided co-chorusing with any other bird. Birds avoided co-chorusing with cicadas only and always when (1) the bird vocalized in a frequency band completely overlapped by the cicada tymbalization, and (2) the cicada tymbalization saturated the majority of that frequency band. These results indicate that avian behavioral modifications in response to biotic noise in longstanding species communities is similar to behavioral modifications observed in populations subjected to high levels of anthropogenic noise pollution—in all cases overlap avoidance is species-specific and dependent upon both frequency and intensity.

Many highly recognizable species lack genetic data important for conservation due to neglect over their hyperabundance. This likely applies to the Sulfur-crested Cockatoo ( Cacatua galerita), one of the world's most iconic parrots. The species is native to Australia, New Guinea, and some surrounding Melanesian islands of the latter. Four subspecies are currently recognised based on morphology. Australian subspecies and populations are abundant, but several factors threaten those in New Guinea and Melanesia. Genetic data from natural populations are scarce-information that is vital to identifying evolutionarily significant units (ESUs) important for modern conservation planning. We used whole-genome resequencing to investigate patterns of differentiation, evolutionary affinities, and demographic history across C. galerita's distribution range to assess whether currently recognised subspecies represent ESUs. We complement this with an assessment of bioacoustic variation across the species' distribution landscape. Our results point to C. galerita sensu lato ( s.l. ) comprising two species. We restrict C. galerita sensu stricto (s.s.) to populations in Australia and the Trans-Fly ecodomain of southern New Guinea. The second species, recognised here as Cacatua triton, likely occurs over much of the rest of New Guinea. Restricting further discussion of intraspecific diversity in C. triton, we show that within C. galerita s.s. two ESUs exist, which align to Cacatua galerita galerita in eastern Australia and southern New Guinea and Cacatua galerita fitzroyi in northern and north-western Australia. We suggest that the evolution of these species and ESUs are linked to Middle and Late Pleistocene glacial cycles and their effects on sea level and preferential habitats. We argue that conservation assessments need updating, protection of preferential forest and woodland habitats are important and reintroductions require careful management to avoid possible negative hybridization effects of non-complementary lineages.

Surveillance programs focused on bird ticks are often challenging owing to the difficulty in capturing and screening birds as well as the fact that ticks on avian hosts frequently occur at a low prevalence. Nonetheless, elucidating the diversity and host preferences of avian ticks is critical for understanding public health risks posed by both migratory and resident birds. The first nation-wide surveillance program of avian ticks was initiated to examine bird-tick interactions in Singapore, a key juncture along the East Asian-Australasian flyway. Two tick species were detected, namely Haemaphysalis wellingtoni and Rhipicephalus linnaei, while five bird species were found to host ticks in Singapore, namely Columba livia, Gallus gallus, Ixobrychus flavicollis, Lanius cristatus, and Pitta moluccensis. The threats posed to public health by the human-biting tick H. wellingtoni are discussed along with the potential for migratory birds and ticks to transport tick-borne pathogens into, and through, Singapore.

Habitat loss is one of the greatest threats to biodiversity, but there is considerable debate over the interplay between the total amount of habitat lost versus the degree of habitat fragmentation. Previous studies on this topic focused on the effects of habitat loss on species richness or genetic diversity over long timescales, while neglecting shorter timescales that are of immediate conservation concern. To address this knowledge gap, we examined the rate and extent of genetic diversity loss under different non-equilibrium scenarios of habitat loss, by performing analytical calculations for a non-spatial setting and individual-based simulations for spatially explicit settings, including a real-world case study of malleefowl (Leipoa ocellata, Galliformes) populations in Australia. Our work revealed that the total amount of habitat lost had the biggest negative effect on genetic diversity via reductions in population abundance and associated genetic drift, with the degree of fragmentation having smaller but nonetheless substantial negative effects. The latter result suggested that to optimize the conservation of genetic diversity, it is better to preserve a single large reserve over several small ones. Furthermore, reductions in population abundance led to loss of genetic diversity in the population only after long time-lags, which highlights the potential for genetic rescue shortly after habitat loss. The malleefowl case study revealed how sampling uncertainty due to low sample sizes can blur the effects of habitat loss on genetic diversity, underscoring the limitations of conservation genetic studies based on small sample size and uneven spatial distribution.