Hybrid de novo genome assembly of the sexually dimorphic Lady Amherst's pheasant.

Pheasants are an important group of birds, valued for their economic benefit as poultry birds, game birds, and as ornamental species for their plumage. Lady Amherst's pheasant Chrysolophus amherstiae is an ornamental species, valued for its elaborate and beautiful plumage. In this study, we present a high-quality de novo hybrid genome assembly of C. amherstiae. Previous attempts to sequence the genome of this species resulted in draft-level assemblies, which are not available in the public domain. Using a combination of Illumina short reads and Oxford Nanopore's long-reads, we assembled a high-quality genome of N50 ~3.9 Mb and near complete BUSCO assessment. We observed a correlation between effective population size and past climatic conditions, with an increase in population size during the warm interglacial periods. We further observed significant fluctuations in genes involved with the immune system and visual perception. C. amherstiae is a highly dimorphic species, and significant fluctuations in gene families involved in immune response, visual perception, among others, suggesting a role of mate choice and sexual selection in the evolution and maintenance of exaggerated traits in the males.

When colors mislead: Genomics and bioacoustics prompt re-classification of Asian flycatcher radiation (Aves: Niltavinae).

Traditional classification of many animals, including birds, has been highly dependent on external morphological characters like plumage coloration. However, both bioacoustics and genetic or genomic data have revolutionized our understanding of the relationships of certain lineages and led to sweeping taxonomic re-organizations. In this study, we present a case of erroneous delimitation of genus boundaries in the species-rich flycatcher subfamily Niltavinae. Genera within this subfamily have historically been delineated based on blue versus brown male body plumage until recent studies based on a few mitochondrial and nuclear loci unearthed several cases of generic misclassification. Here we use extensive bioacoustic data from 43 species and genomic data from 28 species for a fundamental reclassification of species in the Niltavinae. Our study reveals that song is an important trait to classify these birds even at the genus level, whereas plumage traits exhibit ample convergence and have led to numerous historic misattributions. Our taxonomic re-organization leads to new biogeographic limits of major genera, such that the genus Cyornis now only extends as far east as the islands of Sulawesi, Sula, and Banggai, whereas Eumyias is redefined to extend far beyond Wallace's Line to the islands of Seram and Timor. Our conclusions advise against an over-reliance on morphological traits and underscore the importance of integrative datasets.

Megafaunal extinctions, not climate change, may explain Holocene genetic diversity declines in Numenius shorebirds.

Understanding the relative contributions of historical and anthropogenic factors to declines in genetic diversity is important for informing conservation action. Using genome-wide DNA of fresh and historic specimens, including that of two species widely thought to be extinct, we investigated fluctuations in genetic diversity and present the first complete phylogenomic tree for all nine species of the threatened shorebird genus Numenius, known as whimbrels and curlews. Most species faced sharp declines in effective population size, a proxy for genetic diversity, soon after the Last Glacial Maximum (around 20,000 years ago). These declines occurred prior to the Anthropocene and in spite of an increase in the breeding area predicted by environmental niche modeling, suggesting that they were not caused by climatic or recent anthropogenic factors. Crucially, these genetic diversity declines coincide with mass extinctions of mammalian megafauna in the Northern Hemisphere. Among other factors, the demise of ecosystem-engineering megafauna which maintained open habitats may have been detrimental for grassland and tundra-breeding Numenius shorebirds. Our work suggests that the impact of historical factors such as megafaunal extinction may have had wider repercussions on present-day population dynamics of open habitat biota than previously appreciated.

About 20,000 years ago, the Earth was a much colder world roamed by giant mastodons, gigantic elks, woolly mammoths and sabre-tooth tigers. Yet these imposing creatures were living on borrowed time: by the start of the Holocene, around 10,000 years later, many animals over 45kg had vanished across the Northern Hemisphere, closing the book on what is known as the Quaternary extinction event. As large grazers disappeared, the landscape likely changed too. Where open tundra and grasslands may have once dominated, woodlands and shrubs probably took over, creating ripple effects for surviving species. These extinction events took place in a changing world, with glaciers starting to retreat about 20,000 years ago and human populations colonizing an increasing share of this planet's land area. In fact, since the end of this last glacial maximum, ecosystems have been reshaped by a succession and a combination of climatic, historical and human-driven forces. This makes it difficult for scientists to disentangle the relative contribution of these factors on the lives of animals. Tan et al. decided to explore this question by reconstructing how effective population sizes changed over the past 20,000 years for nine species of curlews and whimbrels. These shorebirds, which together comprise the genus Numenius, breed slowly and nest in open environments such as moorlands or tundra. Many are currently under threat. Fluctuations in the numbers of breeding individuals affect the genetic diversity of a species, and these events leave tell-tale genetic signatures that can be uncovered through DNA analyses. Tan et al. had enough fresh and museum samples to infer these changes for five Numenius species, revealing that genetic diversity brutally dropped soon after the last glacial period ended. At the time, humans were yet to make significant changes on their environment and a warming world should have supported population growth. Tan et al. suggest that, instead, this sharp decline is linked to the late Quaternary extinctions of large mammals: with the demise of grazing animals which could keep woodlands at bay, the shorebirds lost their open nesting grounds. This event has left its mark in the genome of existing species, with these birds still exhibiting a low level of genetic diversity that may put them at further risk for extinction.

Genomic Insights Into the Evolution and Demographic History of the SARS-CoV-2 Omicron Variant: Population Genomics Approach.

Background: A thorough understanding of the patterns of genetic subdivision in a pathogen can provide crucial information that is necessary to prevent disease spread. For SARS-CoV-2, the availability of millions of genomes makes this task analytically challenging, and traditional methods for understanding genetic subdivision often fail. Objective: The aim of our study was to use population genomics methods to identify the subtle subdivisions and demographic history of the Omicron variant, in addition to those captured by the Pango lineage. Methods: We used a combination of an evolutionary network approach and multivariate statistical protocols to understand the subdivision and spread of the Omicron variant. We identified subdivisions within the BA.1 and BA.2 lineages and further identified the mutations associated with each cluster. We further characterized the overall genomic diversity of the Omicron variant and assessed the selection pressure for each of the genetic clusters identified. Results: We observed concordant results, using two different methods to understand genetic subdivision. The overall pattern of subdivision in the Omicron variant was in broad agreement with the Pango lineage definition. Further, 1 cluster of the BA.1 lineage and 3 clusters of the BA.2 lineage revealed statistically significant signatures of selection or demographic expansion (Tajima's D<-2), suggesting the role of microevolutionary processes in the spread of the virus. Conclusions: We provide an easy framework for assessing the genetic structure and demographic history of SARS-CoV-2, which can be particularly useful for understanding the local history of the virus. We identified important mutations that are advantageous to some lineages of Omicron and aid in the transmission of the virus. This is crucial information for policy makers, as preventive measures can be designed to mitigate further spread based on a holistic understanding of the variability of the virus and the evolutionary processes aiding its spread.

Next Generation Sequencing Revolutionizes Organismal Biology Research in Bats.

The advent of next generation sequencing technologies (NGS) has greatly accelerated our understanding of critical aspects of organismal biology from non-model organisms. Bats form a particularly interesting group in this regard, as genomic data have helped unearth a vast spectrum of idiosyncrasies in bat genomes associated with bat biology, physiology, and evolution. Bats are important bioindicators and are keystone species to many eco-systems. They often live in proximity to humans and are frequently associated with emerging infectious diseases, including the COVID-19 pandemic. Nearly four dozen bat genomes have been published to date, ranging from drafts to chromosomal level assemblies. Genomic investigations in bats have also become critical towards our understanding of disease biology and host-pathogen coevolution. In addition to whole genome sequencing, low coverage genomic data like reduced representation libraries, resequencing data, etc. have contributed significantly towards our understanding of the evolution of natural populations, and their responses to climatic and anthropogenic perturbations. In this review, we discuss how genomic data have enhanced our understanding of physiological adaptations in bats (particularly related to ageing, immunity, diet, etc.), pathogen discovery, and host pathogen co-evolution. In comparison, the application of NGS towards population genomics, conservation, biodiversity assessment, and functional genomics has been appreciably slower. We reviewed the current areas of focus, identifying emerging topical research directions and providing a roadmap for future genomic studies in bats.

Using Environmental Sampling to Enable Zoonotic Pandemic Preparedness.

The current pandemic caused by the SARS CoV-2, tracing back its origin possibly to a coronavirus associated with bats, has ignited renewed interest in understanding zoonotic spillovers across the globe. While research is more directed towards solving the problem at hand by finding therapeutic strategies and novel vaccine techniques, it is important to address the environmental drivers of pathogen spillover and the complex biotic and abiotic drivers of zoonoses. The availability of cutting-edge genomic technologies has contributed enormously to preempt viral emergence from wildlife. However, there is still a dearth of studies from species-rich South Asian countries, especially from India. In this review, we outline the importance of studying disease dynamics through environmental sampling from wildlife in India and how ecological parameters of both the virus and the host community may play a role in mediating cross-species spillovers. Non-invasive sampling using feces, urine, shed hair, saliva, shed skin, and feathers has been instrumental in providing genetic information for both the host and their associated pathogens. Here, we discuss the advances made in environmental sampling protocols and strategies to generate genetic data from such samples towards the surveillance and characterization of potentially zoonotic pathogens. We primarily focus on bat-borne or small mammal-borne zoonoses and propose a conceptual framework for non-invasive strategies to tackle the threat of emerging zoonotic infections.

Island Biogeography Revisited: Museomics Reveals Affinities of Shelf Island Birds Determined by Bathymetry and Paleo-Rivers, Not by Distance to Mainland.

Island biogeography is one of the most powerful subdisciplines of ecology: its mathematical predictions that island size and distance to mainland determine diversity have withstood the test of time. A key question is whether these predictions follow at a population-genomic level. Using rigorous ancient-DNA protocols, we retrieved approximately 1,000 genomic markers from approximately 100 historic specimens of two Southeast Asian songbird complexes from across the Sunda Shelf archipelago collected 1893-1957. We show that the genetic affinities of populations on small shelf islands defy the predictions of geographic distance and appear governed by Earth-historic factors including the position of terrestrial barriers (paleo-rivers) and persistence of corridors (Quaternary land bridges). Our analyses suggest that classic island-biogeographic predictors may not hold well for population-genomic dynamics on the thousands of shelf islands across the globe, which are exposed to dynamic changes in land distribution during Quaternary climate change.

Novel genome reveals susceptibility of popular gamebird, the red-legged partridge (Alectoris rufa, Phasianidae), to climate change.

We produced a high-quality de novo genome assembly of the red-legged partridge A. rufa, the first reference genome of its genus, by utilising novel 10× Chromium technology. The estimated genome size was 1.19 Gb with an overall genome heterozygosity of 0.0022; no runs of homozygosity were observed. In total, 21,589 protein coding genes were identified and assigned to 16,772 orthologs. Of these, 201 emerged as unique to Alectoris and were enriched for positive regulation of epithelial cell migration, viral genome integration and maturation. Using PSMC analysis, we inferred a major demographic decline commencing ~140,000 years ago, consistent with forest expansion and reduction of open habitats during the Eemian interglacial. Present-day populations exhibit the historically lowest genetic diversity. Besides implications for management and conservation, this genome also promises key insights into the physiology of these birds with a view to improving poultry husbandry practices.

Gene Flow in Volant Vertebrates: Species Biology, Ecology and Climate Change.

Gene flow, the exchange of genetic material between populations is an important biological process, which shapes and maintains biodiversity. The successful movement of individuals between populations depends on multiple factors determined by species biology and the environment. One of the most important factors regulating gene flow is the ability to move, and flight allows individuals to easily move across geographical barriers. Volant vertebrates are found on some of the remotest islands and contribute significantly to the biodiversity and ecosystem. The availability of next-generation sequencing data for non-model animals has substantially improved our understanding of gene flow and its consequences, allowing us to look at fine-scale patterns. However, most of our understanding regarding gene flow comes from the temperate regions and the Neotropics. The lack of studies from species-rich Asia is striking. In this review, we outline the importance of gene flow and the factors affecting gene flow, especially for volant vertebrates. We especially discuss research studies from tropical biomes of South and Southeast Asia, highlight the lacuna in literature and provide an outline for future studies in this species-rich region.