Even as a highly urbanized city-state, Singapore has seen the recolonization of extirpated wildlife amidst habitat restoration efforts and ecological disruptions. This study investigates changes in greater mouse-deer (Tragulus napu) and wild pig (Sus scrofa) populations over 15 years in a human-modified forest before and after the 2023 African Swine Fever (ASF) outbreak. Using intensive transect and camera trap distance sampling, we estimated post-ASF population densities, validated a predictive model linking encounter rates to density, and compared the efficiency of both methods for long-term monitoring. Greater mouse-deer density quintupled to 293 individuals/ km(2), the highest recorded for the species, likely due to reduced competition after >98 % wild pig mortality, forest restoration, and low predation pressure. Despite their higher cost, camera traps allowed the concurrent detection of low-abundance species such as wild pigs. The re-establishment of wild pigs raises questions about future competition and forest dynamics. Long-term monitoring is essential to assess ecological consequences and inform conservation strategies for rapidly changing tropical landscapes.

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.

Ex situ conservation breeding programs can provide essential support for recovering endangered species. However, breeding recommendations and strategies may be suboptimal due to untested or incorrect assumptions about conservation units, hybrid ancestry, inbreeding history and family relationships. While genomic approaches have been used to address specific questions in ex situ programs, they are not yet routinely used to test and adjust assumptions, often due to limitations in sample availability and quality particularly at the start of a new program. Using a new conservation breeding program for the endangered red siskin (Spinus cucullatus) as an example, we demonstrate how genomic data from a relatively small number of samples, of uneven quality, may be employed to critically examine fundamental assumptions. Using genetic data from 72 individuals, we confirmed strong differentiation between birds from Venezuela and Guyana, supporting an assumption that they should not be mixed in a conservation breeding program. Molecular estimates of genetic diversity and inbreeding also aligned with assumptions that widespread historical illegal trade had introduced the species’ Venezuelan wild diversity into U.S. avicultural flocks. We found no evidence of hybrid ancestry with canaries, which would have resulted from intentional crosses to produce red-colored canaries. Finally, while observational pedigree data were generally reliable, molecular relationship assignments and kinship estimates had high accuracy only for first-degree relatives, limiting our ability to evaluate assumptions about relatedness. Our results highlight the utility of constrained but informative datasets for developing conservation breeding programs, supporting effective management for the long-term survival of endangered species.

To holistically understand the biology of animals, we must unravel the complexities and specificities of host-microbe interactions across animal taxa. Birds represent enigmatic and scientifically compelling hosts in which to understand these interactions. Here, we present a brief summary of a series of conversations among avian microbiome researchers regarding methodological challenges facing the avian microbiome field, where most research to date has focused on bacterial communities of the gut. Collectively, we acknowledged a commonly shared but underreported issue facing the avian microbiome field: that of difficulty in obtaining high-quality and high-yield microbial DNA from avian fecal samples. We discuss some of the potential reasons underlying low DNA yields, such as inhibitory compounds and rapid DNA degradation, and provide recommendations for how researchers in the avian microbiome field might cope with these methodological challenges. Collective and dedicated efforts to address these challenges will be required for a robust understanding of host-microbe interactions in avian systems.

Across diverse organisms, the strength and ecological drivers of sexual selection vary enormously. In birds, some of the families with the most elaborate plumage and display-such as birds of paradise, manakins, and cotingas-are also specialist frugivores, yet links between shifts in diet, changes in breeding system, and the evolution of elaborate traits are poorly understood. We focus on manakins, a radiation of frugivorous Neotropical birds well known for spectacular courtship rituals and colorful plumage, and present an integrative analysis of the transition in both diet and mating systems in this clade to examine the causes and consequences of strong sexual selection. In manakins, we find reduced genetic diversity on the Z sex chromosome relative to autosomes, a predicted signature of sexual selection. We also identify targets of positive selection across the manakin radiation, including genes related to muscle function, visual perception, and the transition to frugivory. Among these, we observe selection on sugar-sensing taste receptors, as well as on lactase-phlorizin hydrolase, implicated in the consumption of chemically defended fruits. For both, we confirm that selection signatures correspond to functional changes and infer the relative time of these changes, as well as of shifts in diet, breeding systems, and plumage coloration: elaborated traits evolved subsequent to changes in mating systems and after key physiological changes facilitating fruit-eating. Altogether, these results suggest that intensified frugivory set the stage for the radiation of one of the planet's most colorful and acrobatic avian lineages.

The nest-founding stage represents an especially vulnerable period of the bumble bee (Bombus) life cycle, during which solitary queens must locate and collect sufficient foraging resources to sustain themselves and their brood. Yet, we lack contemporary information about floral foraging resources used by queens in early spring. Here, we use next-generation sequencing to characterize the floral species used by queens for pollen provisions during early nest establishment. We collected pollen loads from over 100 wild bumble bee queens at working farms, rural and city parks, and nature preserves across the Piedmont region of Virginia, USA. Using metabarcoding of two universal DNA barcodes for plants, ITS2 and rbcL, we determined the taxonomic composition of pollen used by queens. Pollen loads contained native and non-native woody (e.g., Cercis: Fabaceae, Prunus: Rosaceae, Salix: Salicaceae), herbaceous (e.g., Lamium: Lamiaceae, Viola: Violaceae), and vine (e.g., Lonicera: Caprifoliaceae) taxa. The non-native Lamium and Elaeagnus (Elaeagnaceae) most frequently hosted foraging queens, owing in part to their abundance across sites and the season. Pollen composition varied more over time than among bumble bee species or across sites, but land cover predicted a small amount of variation in pollen composition. Specifically, the percentage of crop land within 1 km increased the representation of Lamium in queen pollen loads, likely reflecting the abundance of the disturbance-adapted flower in fallow cornfields. Finally, the pollen communities detected by rbcL were twice as diverse as those by ITS2, perhaps owing to the better taxonomic resolution afforded by the fast-evolving rbcL marker. This study demonstrates that queens are flexible foragers and that among the most common Bombus species, plant phenology drives pollen use more than species identity. Further, this study highlights the importance of monitoring pollen diets to inform regional management strategies and considerations about metabarcoding techniques.

The Mountain bongo (Tragelaphus eurycerus isaaci), a critically endangered tragelaphine antelope native to the montane forests of Kenya, faces significant threats from habitat loss and hunting. Although the Mountain bongo is a flagship species in Kenya, the majority are found in small, isolated populations of less than 100 animals total, making it a species of high conservation concern. In this report, we present a chromosome-length draft genome assembly for the Mountain bongo, generated using a combination of linked-read and proximity ligation (Hi-C) sequencing techniques. The assembly resulted in a 2.96 Gb sized genome with a contig N50 of 79.5 kb and a scaffold N50 of 192 Mb. Assembly completeness was 95.1% based on 12,234 Benchmarking Universal Single-Copy Orthologs (BUSCO) and annotation revealed 29,820 protein-coding genes, of which 27,761 were functionally annotated, and a repetitive content of 47.31%. Synteny analysis against the domestic cattle (Bos taurus) genome assembly revealed numerous chromosomal rearrangements between the 2 species. Our analysis also revealed insights into the evolutionary and demographic history of the Mountain bongo, offering valuable information for conservation management. We also assembled and annotated the mitochondrial genome which showed <1% differences from the Lowland bongo subspecies, T. e. eurycerus. By integrating genomic data with traditional conservation methods, this reference lays the foundation to evaluate and preserve genetic diversity of both in situ and ex situ populations of the Mountain bongo amidst growing environmental pressures.

In a hybrid zone between two tropical lekking birds, yellow male plumage of one species has introgressed asymmetrically replacing white plumage of another via sexual selection. Here, we present a detailed analysis of the plumage trait to uncover its physical and genetic bases and trace its evolutionary history. We determine that the carotenoid lutein underlies the yellow phenotype and describe microstructural feather features likely to enhance color appearance. These same features reduce predicted water shedding capacity of feathers, a potential liability in the tropics. Through genome-scale DNA sequencing of hybrids and each species in the genus, we identify BCO2 as the major gene responsible for the color polymorphism. The BCO2 gene tree and genome-wide allele frequency patterns suggest that carotenoid-pigmented collars initially arose in a third species and reached the hybrid zone through historical gene flow. Complex interplay between sexual selection and hybridization has thus shaped phenotypes of these species, where conspicuous sexual traits are key to male reproductive success.

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.

The gut microbiome of bees is vital for the health of their hosts.Given the ecosystem functions performed by bees, and the declines faced by many species, it is important to improve our understanding of the amount of natural variation in the gut microbiome, the level of sharing of bacteria among co-occurring species (including between native and non-native species), and how gut communities respond to infections.We conducted 16S rRNA metabarcoding to discern the level of microbiome similarity between honey bees (Apis mellifera, N = 49) and bumble bees (Bombus spp., N = 66) in a suburban-rural landscape.We identified a total of 233 amplicon sequence variants (ASVs) and found simple gut microbiomes dominated by bacterial taxa belonging to Gilliamella, Snodgrassella, and Lactobacillus.The average number of ASVs per species ranged from 4.00 -15.00 (8.79 + 3.84, mean + SD).Amplicon sequence variant of one bacterial species, G. apicola (ASV 1), was widely shared across honey bees and bumble bees.However, we detected another ASV of G. apicola that was either exclusive to honey bees, or represented an intra-genomic 16S rRNA haplotype variant in honey bees.Other than ASV 1, honey bees and bumble bees rarely share gut bacteria, even ones likely derived from outside environments (e.g., Rhizobium spp., Fructobacillus spp.).Honey bee bacterial microbiomes exhibited higher alpha diversity but lower beta and gamma diversities than those of bumble bees, likely a result of the former possessing larger, perennial hives.Finally, we identified pathogenic or symbiotic bacteria (G.apicola, Acinetobacter sp. and Pluralibacter sp.) that associate with Trypanosome and/or Vairimorpha infections in bees.Such insights help to determine bees' susceptibility to infections should gut microbiomes become disrupted by chemical pollutants and contribute to our understanding of what constitutes a state of dysbiosis.

We document gut parasites in co-occurring Apis, Bombus, and Osmia spp. in the Northern Virginia region, USA. Trypanosomatidea occurred in sixty percent of specimens and 13% carried Nosematidae. We found strong host partitioning: Lotmaria passim and Vairimorpha (Nosema) ceranae predominated in Apis, and Crithidia bombi and V. bombi in Bombus. We did not detect pathogen spread from Apis to Bombus but did detect sharing of C. bombi between Bombus and Osmia, higher parasite levels in Apis at sites with apiaries, and clustering of Vairimopha infection. Given the presence of C. bombi in Osmia, we suggest disease sharing across taxa be monitored.

Adaptation to local environments is common in widespread species and the basis of ecological speciation. The song sparrow (Melospiza melodia) is a widespread, polytypic passerine that occurs in shrubland habitats throughout North America. We examined the population structure of two parapatric subspecies that inhabit different environments: the Atlantic song sparrow (M. m. atlantica), a coastal specialist, and the eastern song sparrow (M. m. melodia), a shrubland generalist. These populations lacked clear mitochondrial population structure, yet coastal birds formed a distinct nuclear genetic cluster. We found weak overall genomic differentiation between these subspecies, suggesting either recent divergence, extensive gene flow, or a combination thereof. There was a steep genetic cline at the transition to coastal habitats, consistent with isolation by environment, not isolation by distance. A phenotype under divergent selection, bill size, varied with the amount of coastal ancestry in transitional areas, but larger bill size was maintained in coastal habitats regardless of ancestry, further supporting a role for selection in the maintenance of these subspecies. Demographic modeling suggested a divergence history of limited gene flow followed by secondary contact, which has emerged as a common theme in adaptive divergence across taxa.

Hybrid zones offer a window into the processes and outcomes of evolution, from species formation or fusion to genomic underpinnings of specific traits and isolating mechanisms. Sexual selection is believed to be an important factor in speciation processes, and hybrid zones present special opportunities to probe its impact. The manakins (Aves, Pipridae) are a promising group in which to study the interplay of sexual selection and natural hybridization: they show substantial variation across the family in the strength of sexual selection they experience, they readily hybridize within and between genera, and they appear to have formed hybrid species, a rare event in birds. A hybrid zone between two manakins in the genus Manacus is unusual in that plumage and behavioral traits of one species have introgressed asymmetrically into populations of the second species through positive sexual selection, then apparently stalled at a river barrier. This is one of a handful of documented examples of asymmetric sexual trait introgression with a known selective mechanism. It offers opportunities to examine reproductive isolation, introgression, plumage color evolution, and natural factors enhancing or constraining the effects of sexual selection in real time. Here, we review previous work in this system, propose new hypotheses for observed patterns, and recommend approaches to test them.

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.

With the advent of high-resolution and cost-effective genomics and bioinformatics tools and methods contributing to a large database of both human (HAdV) and simian (SAdV) adenoviruses, a genomics-based re-evaluation of their taxonomy is warranted. Interest in these particular adenoviruses is growing in part due to the applications of both in gene transfer protocols, including gene therapy and vaccines, as well in oncolytic protocols. In particular, the re-evaluation of SAdVs as appropriate vectors in humans is important as zoonosis precludes the assumption that human immune system may be naïve to these vectors. Additionally, as important pathogens, adenoviruses are a model organism system for understanding viral pathogen emergence through zoonosis and anthroponosis, particularly among the primate species, along with recombination, host adaptation, and selection, as evidenced by one long-standing human respiratory pathogen HAdV-4 and a recent re-evaluation of another, HAdV-76. The latter reflects the insights on amphizoonosis, defined as infections in both directions among host species including "other than human", that are possible with the growing database of nonhuman adenovirus genomes. HAdV-76 is a recombinant that has been isolated from human, chimpanzee, and bonobo hosts. On-going and potential impacts of adenoviruses on public health and translational medicine drive this evaluation of 174 whole genome sequences from HAdVs and SAdVs archived in GenBank. The conclusion is that rather than separate HAdV and SAdV phylogenetic lineages, a single, intertwined tree is observed with all HAdVs and SAdVs forming mixed clades. Therefore, a single designation of "primate adenovirus" (PrAdV) superseding either HAdV and SAdV is proposed, or alternatively, keeping HAdV for human adenovirus but expanding the SAdV nomenclature officially to include host species identification as in ChAdV for chimpanzee adenovirus, GoAdV for gorilla adenovirus, BoAdV for bonobo adenovirus, and ad libitum.

Captive management of many wildlife species can be challenging, with individuals displaying health disorders that are not generally described in the wild population. Retrospective studies have identified gastrointestinal (GI) diseases, in particular inflammatory bowel disease (IBD), as the second leading cause of captive adult red wolf (Canis rufus) mortality. Recent molecular studies show that imbalanced gut microbial composition is tightly linked to IBD in the domestic dog. The goal of the present study was to address two main questions: (1) how do red wolf gut microbiomes differ between animals with loose stool consistency, indicative of GI issues, and those with normal stool consistency and (2) how does dietary type relate to stool consistency and red wolf gut microbiomes? Fresh fecal samples were collected from 48 captive wolves housed in eight facilities in the United States and from two wild wolves living in Alligator River National Wildlife Refuge, NC, United States. For each individual, the stool consistency was categorized as loose or normal using a standardized protocol and their diet was categorized as either wild, whole meat, a mix of whole meat and kibble or kibble. We characterized gut microbiome structure using 16S rRNA gene amplicon sequencing. We found that red wolves with a loose stool consistency differed in composition than wolves with normal stool consistency, suggesting a link between GI health and microbiome composition. Diet was not related to stool consistency but did significantly impact gut microbiome composition; gut microbiome composition of wolves fed a kibble diet were significantly different than the gut microbiome composition of wolves fed a mixed, whole meat and wild diet. Findings from this study increase the understanding of the interplay between diet and GI health in the red wolf, a critical piece of information needed to maintain a healthy red wolf population ex situ.

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.