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Tropical forest diversity is simultaneously threatened by habitat loss and exploitation for wildlife trade. Quantitative conservation assessments have previously considered these threats separately, yet their impacts frequently act together. We integrate forest extent maps in 2000 and 2015 with a method of quantifying exploitation pressure based upon a species’ commercial value and forest accessibility. We do so for 308 forest-dependent bird species, of which 77 are commercially traded, in the Southeast Asian biodiversity hotspot of Sundaland. We find 89% (274) of species experienced average habitat losses of 16% and estimate exploitation led to mean population declines of 37%. Assessing the combined impacts of deforestation and exploitation indicates the average losses of exploited species are much higher (54%), nearly doubling the regionally endemic species (from 27 to 51) threatened with extinction that should be IUCN Red Listed. Combined assessment of major threats is vital to accurately quantify biodiversity loss. Disentangling multiple drivers of species declines can be difficult yet is critical to species conservation. Here, the authors parse the relative contributions of deforestation and trapping to declines of native birds in Southeast Asia, finding that the extinction risk of trapped species may be underestimated.

In the absence of nuclear-genomic differentiation between two populations, deep mitochondrial divergence (DMD) is a form of mito-nuclear discordance. Such instances of DMD are rare and might variably be explained by unusual cases of female-linked selection, by male-biased dispersal, by “speciation reversal” or by mitochondrial capture through genetic introgression. Here, we analyze DMD in an Asian Phylloscopus leaf warbler (Aves: Phylloscopidae) complex. Bioacoustic, morphological, and genomic data demonstrate close similarity between the taxa affinis and occisinensis, even though DMD previously led to their classification as two distinct species. Using population genomic and comparative genomic methods on 45 whole genomes, including historical reconstructions of effective population size, genomic peaks of differentiation and genomic linkage, we infer that the form affinis is likely the product of a westward expansion in which it replaced a now-extinct congener that was the donor of its mtDNA and small portions of its nuclear genome. This study provides strong evidence of “ghost introgression” as the cause of DMD, and we suggest that “ghost introgression” may be a widely overlooked phenomenon in nature.

The evolutionary history of horseshoe crabs, spanning approximately 500 million years, is characterized by remarkable morphological stasis and a low species diversity with only four extant species. Here we report a chromosome-level genome assembly for the mangrove horseshoe crab ( Carcinoscorpius rotundicauda ) using PacBio reads and Hi-C data. The assembly spans 1.67 Gb with contig N50 of 7.8 Mb and 98% of the genome assigned to 16 chromosomes. The genome contains five Hox clusters with 34 Hox genes, the highest number reported in any invertebrate. Detailed analysis of the genome provides evidence that suggests three rounds of whole-genome duplication (WGD), raising questions about the relationship between WGD and species radiation. Several gene families, particularly those involved in innate immunity, have undergone extensive tandem duplication. These expanded gene families may be important components of the innate immune system of horseshoe crabs, whose amebocyte lysate is a sensitive agent for detecting endotoxin contamination. Horseshoe crabs have been morphologically stable across evolutionary time. Here, the authors generate a chromosome-level assembly for the mangrove horseshoe crab, with implications for innate immunity, and challenging assumptions about the role of genome duplication in adaptive radiation.

The timing of the diversification of placental mammals relative to the Cretaceous–Paleogene (KPg) boundary mass extinction remains highly controversial. In particular, there have been seemingly irreconcilable differences in the dating of the early placental radiation not only between fossil-based and molecular datasets but also among molecular datasets. To help resolve this discrepancy, we performed genome-scale analyses using 4,388 loci from 90 taxa, including representatives of all extant placental orders and transcriptome data from flying lemurs (Dermoptera) and pangolins (Pholidota). Depending on the gene partitioning scheme, molecular clock model, and genic deviation from molecular clock assumptions, extensive sensitivity analyses recovered widely varying diversification scenarios for placental mammals from a given gene set, ranging from a deep Cretaceous origin and diversification to a scenario spanning the KPg boundary, suggesting that the use of suboptimal molecular clock markers and methodologies is a major cause of controversies regarding placental diversification timing. We demonstrate that reconciliation between molecular and paleontological estimates of placental divergence times can be achieved using the appropriate clock model and gene partitioning scheme while accounting for the degree to which individual genes violate molecular clock assumptions. A birth-death-shift analysis suggests that placental mammals underwent a continuous radiation across the KPg boundary without apparent interruption by the mass extinction, paralleling a genus-level radiation of multituberculates and ecomorphological diversification of both multituberculates and therians. These findings suggest that the KPg catastrophe evidently played a limited role in placental diversification, which, instead, was likely a delayed response to the slightly earlier radiation of angiosperms.

Abstract Mountains are the world's most important centers of biodiversity. The Sino-Himalayan Mountains are global biodiversity hotspot due to their extremely high species richness and endemicity. Ample research investigated the impact of the Qinghai–Tibet Plateau uplift and Quaternary glaciations in driving species diversification in plants and animals across the Sino-Himalayan Mountains. However, little is known about the role of landscape heterogeneity and other environmental features in driving diversification in this region. We utilized whole genomes and phenotypic data in combination with landscape genetic approaches to investigate population structure, demography, and genetic diversity in a forest songbird species native to the Sino-Himalayan Mountains, the red-billed leiothrix (Leiothrix lutea). We identified 5 phylogeographic clades, including 1 in the East of China, 1 in Yunnan, and 3 in Tibet, roughly consistent with differences in song and plumage coloration but incongruent with traditional subspecies boundaries. Isolation-by-resistance model best explained population differentiation within L. lutea, with extensive secondary contact after allopatric isolation leading to admixture among clades. Ecological niche modeling indicated relative stability in the extent of suitable distribution areas of the species across Quaternary glacial cycles. Our results underscore the importance of mountains in the diversification of this species, given that most of the distinct genetic clades are concentrated in a relatively small area in the Sino-Himalayan Mountain region, while a single shallow clade populates vast lower-lying areas to the east. This study highlights the crucial role of landscape heterogeneity in promoting differentiation and provides a deep genomic perspective on the mechanisms through which diversity hotspots form.

Modern advances in DNA sequencing hold the promise of facilitating descriptions of new organisms at ever finer precision but have come with challenges as the major Codes of bionomenclature contain poorly defined requirements for species and subspecies diagnoses (henceforth, species diagnoses), which is particularly problematic for DNA-based taxonomy. We, the commissioners of the International Commission on Zoological Nomenclature, advocate a tightening of the definition of “species diagnosis” in future editions of Codes of bionomenclature, for example, through the introduction of requirements for specific information on the character states of differentiating traits in comparison with similar species. Such new provisions would enhance taxonomic standards and ensure that all diagnoses, including DNA-based ones, contain adequate taxonomic context. Our recommendations are intended to spur discussion among biologists, as broad community consensus is critical ahead of the implementation of new editions of the International Code of Zoological Nomenclature and other Codes of bionomenclature.

Human activities have precipitated a rise in the levels of introgressive gene flow among animals. The investigation of conspecific populations at different time points may shed light on the magnitude of human-mediated introgression. We used the red junglefowl Gallus gallus , the wild ancestral form of the chicken, as our study system. As wild junglefowl and domestic chickens readily admix, conservationists fear that domestic introgression into junglefowl may compromise their wild genotype. By contrasting the whole genomes of 51 chickens with 63 junglefowl from across their natural range, we found evidence of a loss of the wild genotype across the Anthropocene. When comparing against the genomes of junglefowl from approximately a century ago using rigorous ancient-DNA protocols, we discovered that levels of domestic introgression are not equal among and within modern wild populations, with the percentage of domestic ancestry around 20–50%. We identified a number of domestication markers in which chickens are deeply differentiated from historic junglefowl regardless of breed and/or geographic provenance, with eight genes under selection. The latter are involved in pathways dealing with development, reproduction and vision. The wild genotype is an allelic reservoir that holds most of the genetic diversity of G . gallus , a species which is immensely important to human society. Our study provides fundamental genomic infrastructure to assist in efforts to prevent a further loss of the wild genotype through introgression of domestic alleles.

Parasite host switches may trigger disease emergence, but prehistoric host ranges are often unknowable. Lymphatic filariasis and loiasis are major human diseases caused by the insect-borne filarial nematodes Brugia , Wuchereria and Loa . Here we show that the genomes of these nematodes and seven tropical bird lineages exclusively share a novel retrotransposon, AviRTE, resulting from horizontal transfer (HT). AviRTE subfamilies exhibit 83–99% nucleotide identity between genomes, and their phylogenetic distribution, paleobiogeography and invasion times suggest that HTs involved filarial nematodes. The HTs between bird and nematode genomes took place in two pantropical waves, >25–22 million years ago (Myr ago) involving the Brugia / Wuchereria lineage and >20–17 Myr ago involving the Loa lineage. Contrary to the expectation from the mammal-dominated host range of filarial nematodes, we hypothesize that these major human pathogens may have independently evolved from bird endoparasites that formerly infected the global breadth of avian biodiversity. Lymphatic filariasis and loiasis are diseases caused by insect-borne filarial nematodes. Here, Suh et al . identify a retrotransposon that is present in the genomes of these nematodes and seven tropical bird lineages, indicating two waves of horizontal gene transfer around 17–25 million years ago.

Non‐native species can be introduced to novel environments such as cities via wildlife trade. These populations may have conservation value—particularly if they are of a species threatened in its native range. Genetic tools can help assess the fitness of introduced populations by indicating if they are (1) suffering the consequences typically associated with small, isolated populations derived from few founders (e.g., inbreeding, low genetic diversity) or (2) they demonstrate gene flow indicative of mixed‐origin founders, successful breeding, and/or continual introductions of conspecifics. Such data can inform management interventions in the ex‐situ environment and highlight potential contributions of introduced populations to native‐range conservation. We examined multiple metrics of genetic health of a non‐native population of ca. 200 critically endangered Yellow‐crested Cockatoos (Cacatua sulphurea)—native to the eastern Indonesian archipelago—introduced to Hong Kong (HK) from the 1960s. We sequenced whole genomes and mitochondrial DNA of HK cockatoos and compared them to native‐range C. sulphurea, Sulphur‐crested Cockatoos (C. galerita) from Australia, and representatives from five additional wild parrot populations. Results indicate HK's cockatoos may have as yet evaded the severe negative genetic consequences of small, isolated populations, and currently have Ne and nucleotide diversity comparable to other wild parrot populations. Their genetic characteristics conform to those of young, mixed‐origin, non‐native populations: high individual‐level variance in relatedness and inbreeding/outbreeding, and influences of admixture. Given that C. sulphurea subspecies exhibit very low genetic distances, HK's city cockatoos are worthy of further examination as a potential genetic reservoir and rescue source for C. sulphurea.