Vulture Genomes Reveal Molecular Adaptations Underlying Obligate Scavenging and Low Levels of Genetic Diversity

Necrophages and necrophiles: a review of their antibacterial defenses and biotechnological potential

With antibiotic resistance on the rise, there is an urgent need for new antibacterial drugs and products to treat or prevent infection. Many such products in current use, for example human and veterinary antibiotics and antimicrobial food preservatives, were discovered and developed from nature. Natural selection acts on all living organisms and the presence of bacterial competitors or pathogens in an environment can favor the evolution of antibacterial adaptations. In this review, we ask if vultures, blow flies and other carrion users might be a good starting point for antibacterial discovery based on the selection pressure they are under from bacterial disease. Dietary details are catalogued for over 600 of these species, bacterial pathogens associated with the diets are described, and an overview of the antibacterial defenses contributing to disease protection is given. Biotechnological applications for these defenses are then discussed, together with challenges facing developers and possible solutions. Examples include use of (a) the antimicrobial peptide (AMP) gene sarcotoxin IA to improve crop resistance to bacterial disease, (b) peptide antibiotics such as serrawettin W2 as antibacterial drug leads, (c) lectins for targeted drug delivery, (d) bioconversion-generated chitin as an antibacterial biomaterial, (e) bacteriocins as antibacterial food preservatives and (f) mutualistic microbiota bacteria as alternatives to antibiotics in animal feed. We show that carrion users encounter a diverse range of bacterial pathogens through their diets and interactions, have evolved many antibacterial defenses, and are a promising source of genes, molecules, and microbes for medical, agricultural, and food industry product development.

Functional Decline of a Bitter Receptor Gene in New World Vultures

The bitter taste perception, crucial for avoiding harmful foods, is mediated by Tas2r taste receptors in vertebrates. Vultures are obligate scavengers of considerable conservation concern, consisting of Old World and New World vultures. While vultures primarily subsist on carrion, which contains various bitter secondary metabolites produced by microbes, their ability to sense bitterness remains unclear. In this work, we identified all Tas2r genes from the genomes of 6 vultures and 22 other Accipitriformes birds. Our analysis revealed that every species, except the osprey, possessed intact Tas2r1 and Tas2r2 genes. We observed the lack of genetic divergence in Tas2r1 among all species and relaxation of functional constraint in Tas2r2 in New World vultures. Molecular docking simulations revealed reduced binding affinity of Tas2r2 in New World vultures after testing 843 bitter compounds. Additionally, we conducted cell-based functional assays for Tas2r2 to assess its responsiveness to 24 natural bitter compounds with diverse chemical structures, and confirmed lower responsiveness in New World vultures compared to other birds. These findings suggest a functional decline of bitter taste perception in New World vultures, not observed in Old World vultures, aligning with functional relaxation and reduced binding affinity of Tas2r2 predicted in New World vultures. The functional decline of bitter taste may compromise their natural defense against synthetic bitter pesticides or veterinary drugs, highlighting the potential risks faced by New World vultures in contemporary environments.

Parallel Signatures of Diet Adaptation in the Invasive Common Myna Genome

Invasive species offer uniquely replicated model systems to study rapid adaptation. The common myna (Acridotheres tristis) has been introduced to over a dozen countries and is classified as one of the most invasive birds in the world. Their multiple invasions provide an opportunity to identify repeated adaptation, as invasive populations originated from multiple source populations. We compared whole-genome resequencing data from 80 individuals from four native and seven invasive populations, representing two independent introduction pathways. Results from two different selection scan methods were combined and identified a strongly selected region on chromosome 8 that spans two copies of AMY2A, part of the alpha-amylase gene family, a putative ncRNA and an insertion-deletion structural variant (SV) that contains an ERVK transposable element (TE). Outlier SNPs and the SV are polymorphic in native populations, but fixed or close-to-fixed in the two invasive pathways, with the fixation of the same alleles in two independent lineages providing evidence for parallel selection on standing variation. Intriguingly, the second copy of AMY2A has a non-conservative missense mutation at a phylogenetically conserved site. This mutation, alongside variation in the SV, TE and ncRNA, provide possible routes for changes to protein function or expression. AMY2A has been associated with human commensalism in house sparrows, and genes in this family have been linked to adaptation to high-starch diets in humans and dogs. This study illustrates the value of replicated analyses within and across species to understand rapid adaptation at the molecular level.

Avian raptors are indicator species and victims of high pathogenicity avian influenza virus HPAIV H5N1 (clade 2.3.4.4b) in Germany

Transition of highly pathogenic clade 2.3.4.4b H5 avian influenza virus (HPAIV) from epizootic to enzootic status in Northern European countries was associated with severe losses and even mass mortalities among various wild bird species. Both avian and mammalian raptors hunting infected debilitated birds or scavenging on virus-contaminated avian carcasses contracted HPAIV infection. This precarious pathogen-prey-predator relation further worsened when in 2021 and 2022 outbreaks in Germany overlapped with the hatching season of avian raptor species. Retro- and prospective surveillance revealed avian raptors as important indicators of HPAIV and its genetic diversity on the one hand. On the other hand, their role as victims of HPAIV is stipulated. The first case of an HPAIV H5N1-related death of a white-tailed sea eagle (Haliaeetus albicilla; WTSE) hatch in Germany, 2021, followed by several such cases in 2022, and a low overall seropositivity rate of 5.0-7.9% among WTSE nestlings, raised fears of a serious negative impact on reproduction rates of WTSEs and other birds of prey when HPAIV becomes enzootic in an ecosystem. However, comparably stable breeding success of WTSE in the study area in 2022 and a potentially evolving natural immunity raises hope for a less severe long-term impact.

The genetic architecture of repeated local adaptation to climate in distantly related plants

Closely related species often use the same genes to adapt to similar environments. However, we know little about why such genes possess increased adaptive potential and whether this is conserved across deeper evolutionary lineages. Adaptation to climate presents a natural laboratory to test these ideas, as even distantly related species must contend with similar stresses. Here, we re-analyse genomic data from thousands of individuals from 25 plant species as diverged as lodgepole pine and Arabidopsis (~300 Myr). We test for genetic repeatability based on within-species associations between allele frequencies in genes and variation in 21 climate variables. Our results demonstrate significant statistical evidence for genetic repeatability across deep time that is not expected under randomness, identifying a suite of 108 gene families (orthogroups) and gene functions that repeatedly drive local adaptation to climate. This set includes many orthogroups with well-known functions in abiotic stress response. Using gene co-expression networks to quantify pleiotropy, we find that orthogroups with stronger evidence for repeatability exhibit greater network centrality and broader expression across tissues (higher pleiotropy), contrary to the 'cost of complexity' theory. These gene families may be important in helping wild and crop species cope with future climate change, representing important candidates for future study.

Lead exposure and source attribution for a mammalian scavenger before and after a culling program

Lead-based ammunition is a significant source of environmental lead and threatens species that scavenge lead-shot carcasses, particularly in areas with intensive shooting. With the impacts of lead on avian scavengers well established, there is increasing focus on the effects of lead on mammalian scavengers. We investigated lead exposure in a morphologically specialized mammalian scavenger, the Tasmanian devil (Sarcophilus harrisii), by analyzing their blood lead levels (BLLs) before and after a marsupial culling program using linear mixed effects models. We compared lead isotope signatures in devil blood to those in the culling ammunition to inform potential source attributions. We sampled 23 devils before culling and 15 after culling, finding no significant difference in mean BLLs pre and post-culling. However, devils captured closer to forestry coupes where culling had occurred had higher BLLs, and a greater proportion of devils displayed elevated BLLs post-culling (33 % compared to 18 % pre-culling). The highest BLL (7.93 μg/dL) was found in a devil post-culling and this individual had lead isotope signatures that matched the ammunition samples analyzed, suggesting the individual was exposed to lead from scavenging on culled carcasses. While 18 % of the devil blood lead samples had isotope signatures consistent with the ammunition samples, most were measurably different, indicating other sources of lead in the landscape. BLLs in our study landscape were similar to published BLLs for wild devils across Tasmania. That said, lead isotope signatures in the blood of individual devils sampled both before and after culling shifted closer to those of ammunition samples post-culling. Our results indicate that while some individual devils may have been exposed to lead from culling, most devils in the landscape did not show evidence of recent exposure. However, even low lead levels can adversely impact wildlife health and immunity, a particular concern for devils, a species endangered by disease.

Comparative genomics sheds new light on the convergent evolution of infrared vision in snakes

Infrared vision is a highly specialized sensory system that evolved independently in three clades of snakes. Apparently, convergent evolution occurred in the transient receptor potential ankyrin 1 (TRPA1) proteins of infrared-sensing snakes. However, this gene can only explain how infrared signals are received, and not the transduction and processing of those signals. We sequenced the genome of Xenopeltis unicolor, a key outgroup species of pythons, and performed a genome-wide analysis of convergence between two clades of infrared-sensing snakes. Our results revealed pervasive molecular adaptation in pathways associated with neural development and other functions, with parallel selection on loci associated with trigeminal nerve structural organization. In addition, we found evidence of convergent amino acid substitutions in a set of genes, including TRPA1 and TRPM2. The analysis also identified convergent accelerated evolution in non-coding elements near 12 genes involved in facial nerve structural organization and optic nerve development. Thus, convergent evolution occurred across multiple dimensions of infrared vision in vipers and pythons, as well as amino acid substitutions, non-coding elements, genes and functions. These changes enabled independent groups of snakes to develop and use infrared vision.

A comparison of antibiotic resistance genes and mobile genetic elements in wild and captive Himalayan vultures

As the most widely distributed scavenger birds on the Qinghai-Tibetan Plateau, Himalayan vultures (Gyps himalayensis) feed on the carcasses of various wild and domestic animals, facing the dual selection pressure of pathogens and antibiotics and are suitable biological sentinel species for monitoring antibiotic resistance genes (ARGs). This study used metagenomic sequencing to comparatively investigate the ARGs and mobile genetic elements (MGEs) of wild and captive Himalayan vultures. Overall, the resistome of Himalayan vultures contained 414 ARG subtypes resistant to 20 ARG types, with abundances ranging from 0.01 to 1,493.60 ppm. The most abundant resistance type was beta-lactam (175 subtypes), followed by multidrug resistance genes with 68 subtypes. Decreases in the abundance of macrolide-lincosamide-streptogramin (MLS) resistance genes were observed in the wild group compared with the zoo group. A total of 75 genera (five phyla) of bacteria were predicted to be the hosts of ARGs in Himalayan vultures, and the clinical (102 ARGs) and high-risk ARGs (35 Rank I and 56 Rank II ARGs) were also analyzed. Among these ARGs, twenty-two clinical ARGs, nine Rank I ARG subtypes, sixteen Rank II ARG subtypes were found to differ significantly between the two groups. Five types of MGEs (128 subtypes) were found in Himalayan vultures. Plasmids (62 subtypes) and transposases (44 subtypes) were found to be the main MGE types. Efflux pump and antibiotic deactivation were the main resistance mechanisms of ARGs in Himalayan vultures. Decreases in the abundance of cellular protection were identified in wild Himalayan vultures compared with the captive Himalayan vultures. Procrustes analysis and the co-occurrence networks analysis revealed different patterns of correlations among gut microbes, ARGs, and MGEs in wild and captive Himalayan vultures. This study is the first step in describing the characterization of the ARGs in the gut of Himalayan vultures and highlights the need to pay more attention to scavenging birds.

Metagenomic comparison of gut communities between wild and captive Himalayan griffons

Introduction

Himalayan griffons (Gyps himalayensis), known as the scavenger of nature, are large scavenging raptors widely distributed on the Qinghai-Tibetan Plateau and play an important role in maintaining the balance of the plateau ecosystem. The gut microbiome is essential for host health, helping to maintain homeostasis, improving digestive efficiency, and promoting the development of the immune system. Changes in environment and diet can affect the composition and function of gut microbiota, ultimately impacting the host health and adaptation. Captive rearing is considered to be a way to protect Himalayan griffons and increase their population size. However, the effects of captivity on the structure and function of the gut microbial communities of Himalayan griffons are poorly understood. Still, availability of sequenced metagenomes and functional information for most griffons gut microbes remains limited.

Methods

In this study, metagenome sequencing was used to analyze the composition and functional structures of the gut microbiota of Himalayan griffons under wild and captive conditions.

Results

Our results showed no significant differences in the alpha diversity between the two groups, but significant differences in beta diversity. Taxonomic classification revealed that the most abundant phyla in the gut of Himalayan griffons were Fusobacteriota, Proteobacteria, Firmicutes_A, Bacteroidota, Firmicutes, Actinobacteriota, and Campylobacterota. At the functional level, a series of Kyoto Encyclopedia of Genes and Genome (KEGG) functional pathways, carbohydrate-active enzymes (CAZymes) categories, virulence factor genes (VFGs), and pathogen-host interactions (PHI) were annotated and compared between the two groups. In addition, we recovered nearly 130 metagenome-assembled genomes (MAGs).

Discussion

In summary, the present study provided a first inventory of the microbial genes and metagenome-assembled genomes related to the Himalayan griffons, marking a crucial first step toward a wider investigation of the scavengers microbiomes with the ultimate goal to contribute to the conservation and management strategies for this near threatened bird.

Comprehensive genome assembly reveals genetic diversity and carcass consumption insights in critically endangered Asian king vultures

The Asian king vulture (AKV), a vital forest scavenger, is facing globally critical endangerment. This study aimed to construct a reference genome to unveil the mechanisms underlying its scavenger abilities and to assess the genetic relatedness of the captive population in Thailand. A reference genome of a female AKV was assembled from sequencing reads obtained from both PacBio long-read and MGI short-read sequencing platforms. Comparative genomics with New World vultures (NWVs) and other birds in the Family Accipitridae revealed unique gene families in AKV associated with retroviral genome integration and feather keratin, contrasting with NWVs' genes related to olfactory reception. Expanded gene families in AKV were linked to inflammatory response, iron regulation and spermatogenesis. Positively selected genes included those associated with anti-apoptosis, immune response and muscle cell development, shedding light on adaptations for carcass consumption and high-altitude soaring. Using restriction site-associated DNA sequencing (RADseq)-based genome-wide single nucleotide polymorphisms (SNPs), genetic relatedness and inbreeding status of five captive AKVs were determined, revealing high genomic inbreeding in two females. In conclusion, the AKV reference genome was established, providing insights into its unique characteristics. Additionally, the potential of RADseq-based genome-wide SNPs for selecting AKV breeders was demonstrated.

Convergent rates of protein evolution identify novel targets of sexual selection in primates

Sexual selection is the differential reproductive success of individuals, resulting from competition for mates, mate choice, or success in fertilization. In primates, this selective pressure often leads to the development of exaggerated traits which play a role in sexual competition and successful reproduction. In order to gain insight into the mechanisms driving the development of sexually selected traits, we used an unbiased genome-wide approach across 21 primate species to correlate individual rates of protein evolution to relative testes size and sexual dimorphism in body size, 2 anatomical hallmarks of sexual selection in mammals. Among species with presumed high levels of sperm competition, we detected strong conservation of testes-specific proteins responsible for spermatogenesis and ciliary form and function. In contrast, we identified accelerated evolution of female reproductive proteins expressed in the vagina, cervix, and fallopian tubes in these same species. Additionally, we found accelerated protein evolution in lymphoid tissue, indicating that adaptive immune functions may also be influenced by sexual selection. This study demonstrates the distinct complexity of sexual selection in primates revealing contrasting patterns of protein evolution between male and female reproductive tissues.

Adaptations to a cold climate promoted social evolution in Asian colobine primates

The biological mechanisms that underpin primate social evolution remain poorly understood. Asian colobines display a range of social organizations, which makes them good models for investigating social evolution. By integrating ecological, geological, fossil, behavioral, and genomic analyses, we found that colobine primates that inhabit colder environments tend to live in larger, more complex groups. Specifically, glacial periods during the past 6 million years promoted the selection of genes involved in cold-related energy metabolism and neurohormonal regulation. More-efficient dopamine and oxytocin pathways developed in odd-nosed monkeys, which may have favored the prolongation of maternal care and lactation, increasing infant survival in cold environments. These adaptive changes appear to have strengthened interindividual affiliation, increased male-male tolerance, and facilitated the stepwise aggregation from independent one-male groups to large multilevel societies.

Similar adaptative mechanism but divergent demographic history of four sympatric desert rodents in Eurasian inland

Phenotypes associated with metabolism and water retention are thought to be key to the adaptation of desert species. However, knowledge on the genetic changes and selective regimes on the similar and divergent ways to desert adaptation in sympatric and phylogenetically close desert organisms remains limited. Here, we generate a chromosome level genome assembly for Northern three-toed jerboa (Dipus sagitta) and three other high-quality genome assemblies for Siberian jerboa (Orientallactaga sibirica), Midday jird (Meriones meridianus), and Desert hamster (Phodopus roborovskii). Genomic analyses unveil that desert adaptation of the four species mainly result from similar metabolic pathways, such as arachidonic acid metabolism, thermogenesis, oxidative phosphorylation, insulin related pathway, DNA repair and protein synthesis and degradation. However, the specific evolved genes in the same adaptative molecular pathway often differ in the four species. We also reveal similar niche selection but different demographic histories and sensitivity to climate changes, which may be related to the diversified genomic adaptative features. In addition, our study suggests that nocturnal rodents have evolved some specific adaptative mechanism to desert environments compared to large desert animals. Our genomic resources will provide an important foundation for further research on desert genetic adaptations.

Comparative transcriptome analysis reveals molecular adaptations underlying distinct immunity and inverted resting posture in bats

Understanding how natural selection shapes unique traits in mammals is a central topic in evolutionary biology. The mammalian order Chiroptera (bats) is attractive for biologists as well as the general public due to their specific traits of extraordinary immunity and inverted resting posture. However, genomic resources for bats that occupy key phylogenetic positions are not sufficient, which hinders comprehensive investigation of the molecular mechanisms underpinning the origin of specific traits in bats. Here, we sequenced the transcriptomes of five bats that are phylogenetically divergent and occupy key positions in the phylogenetic tree of bats. In combination with the available genomes of 19 bats and 21 other mammals, we built a database consisting of 10,918 one-to-one ortholog genes and reconstructed phylogenetic relationships of these mammals. We found that genes related to immunity, bone remodeling and cardiovascular system are targets of natural selection along the ancestral branch of bats. Further analyses revealed that the T cell receptor signaling pathway involved in immune adaptation is specifically enriched in bats. Moreover, molecular adaptations of bone remodeling, cardiovascular system, and balance sensing may help to explain the reverted resting posture in bats. Our study provides valuable transcriptome resources, enabling us to tentatively identify genetic changes associated with bat-specific traits. This work is among the first to advance our understanding of molecular underpinnings of inverted resting posture in bats, which could provide insight into healthcare applications such as hypertension in humans. This article is protected by copyright. All rights reserved.