Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers.

Increasing habitat fragmentation leads to wild populations becoming small, isolated, and threatened by inbreeding depression. However, small populations may be able to purge recessive deleterious alleles as they become expressed in homozygotes, thus reducing inbreeding depression and increasing population viability. We used whole-genome sequences from 57 tigers to estimate individual inbreeding and mutation load in a small-isolated and two large-connected populations in India. As expected, the small-isolated population had substantially higher average genomic inbreeding (FROH = 0.57) than the large-connected (FROH = 0.35 and FROH = 0.46) populations. The small-isolated population had the lowest loss-of-function mutation load, likely due to purging of highly deleterious recessive mutations. The large populations had lower missense mutation loads than the small-isolated population, but were not identical, possibly due to different demographic histories. While the number of the loss-of-function alleles in the small-isolated population was lower, these alleles were at higher frequencies and homozygosity than in the large populations. Together, our data and analyses provide evidence of 1) high mutation load, 2) purging, and 3) the highest predicted inbreeding depression, despite purging, in the small-isolated population. Frequency distributions of damaging and neutral alleles uncover genomic evidence that purifying selection has removed part of the mutation load across Indian tiger populations. These results provide genomic evidence for purifying selection in both small and large populations, but also suggest that the remaining deleterious alleles may have inbreeding-associated fitness costs. We suggest that genetic rescue from sources selected based on genome-wide differentiation could offset any possible impacts of inbreeding depression.

Recent Evolutionary History of Tigers Highlights Contrasting Roles of Genetic Drift and Selection.

Species conservation can be improved by knowledge of evolutionary and genetic history. Tigers are among the most charismatic of endangered species and garner significant conservation attention. However, their evolutionary history and genomic variation remain poorly known, especially for Indian tigers. With 70% of the world's wild tigers living in India, such knowledge is critical. We re-sequenced 65 individual tiger genomes representing most extant subspecies with a specific focus on tigers from India. As suggested by earlier studies, we found strong genetic differentiation between the putative tiger subspecies. Despite high total genomic diversity in India, individual tigers host longer runs of homozygosity, potentially suggesting recent inbreeding or founding events, possibly due to small and fragmented protected areas. We suggest the impacts of ongoing connectivity loss on inbreeding and persistence of Indian tigers be closely monitored. Surprisingly, demographic models suggest recent divergence (within the last 20,000 years) between subspecies and strong population bottlenecks. Amur tiger genomes revealed the strongest signals of selection related to metabolic adaptation to cold, whereas Sumatran tigers show evidence of weak selection for genes involved in body size regulation. We recommend detailed investigation of local adaptation in Amur and Sumatran tigers prior to initiating genetic rescue.

IDENTIFICATION OF TWO LETHAL CASES OF ELEPHANT ENDOTHELIOTROPIC HERPESVIRUS HEMORRHAGIC DISEASE IN SUMATRAN ELEPHANT CALVES IN INDONESIA.

As many as a dozen cases of lethal acute hemorrhagic disease (HD) in young captive-born Sumatran sub-species Asian elephant (Elephas maximus sumatranus roman) calves raised naturally in camps in Sumatra have been observed in recent years. To address whether these deaths, like many others documented worldwide, might be associated with acute systemic infection by elephant endotheliotropic herpesvirus (EEHV), diagnostic polymerase chain reaction (PCR) tests followed by subtype deoxyribonucleic acid (DNA) sequencing analysis were carried out on pathologic tissue samples from two lethal HD cases that occurred within 6 days of one another in calves at the same camp. Viral DNA from five selected PCR loci was found to be present at high levels in both calves and proved to be the same EEHV1A virus species that has been described most commonly previously in numerous lethal or surviving symptomatic cases in North America, Europe, India, and Thailand. Furthermore, the two cases were identical at all five PCR loci tested (covering a total of 3,050 base pairs) and were therefore likely to have been infected from the same epidemiologic source herdmate. However, the strain involved (which was subtype-D2 in the vGPCR1 locus) differed from all previously characterized EEHV1A strains. In conclusion, these two calves are the first two confirmed HD cases in Sumatra alongside several other suspected HD cases in Sumatra that have succumbed to the same devastating EEHV1A-HD that has afflicted young Asian elephants worldwide over the past 25 yr. Because the progeny of some of the 1,500 remaining red-listed critically endangered Sumatra subspecies elephants are bred naturally in camps from wild parents it seems very likely that the EEHV1A herpesvirus identified here in these HD camp cases is also present in the free-ranging Sumatran elephant population, and this will have to be taken into account in future wildlife management policies and decisions.

Elephant Endotheliotropic Herpesvirus Hemorrhagic Disease in Asian Elephant Calves in Logging Camps, Myanmar.

In recent years, an alarming number of cases of lethal acute hemorrhagic disease have occurred in Asian elephant calves raised in logging camps in Myanmar. To determine whether these deaths were associated with infection by elephant endotheliotropic herpesvirus (EEHV), we conducted diagnostic PCR subtype DNA sequencing analysis on necropsy tissue samples collected from 3 locations. We found that EEHV DNA from 7 PCR loci was present at high levels in all 3 calves and was the same EEHV1A virus type that has been described in North America, Europe, and other parts of Asia. However, when analyzed over 5,610 bp, the strains showed major differences from each other and from all previously characterized EEHV1A strains. We conclude that these 3 elephant calves in Myanmar died from the same herpesvirus disease that has afflicted young Asian elephants in other countries over the past 20 years.

CARNIVORE PROTOPARVOVIRUS 1 (PARVOVIRUSES) AT THE DOMESTIC-WILD CARNIVORE INTERFACE IN INDIA.

Carnivore protoparvovirus 1 (CP1, earlier called Feline panleukopenia virus) variants such as canine parvovirus (CPV) and feline parvovirus (FPV) are significant, emerging, multihost pathogens of domestic and wild carnivores. The diversity of CP1 variants was studied between 2008 and 2014 in Wayanad, India, where flagship wildlife species such as tigers (Panthera tigris) and leopards (Panthera pardus) coexist alongside domestic carnivores, including dogs (Canis lupus familiaris) and cats (Felis catus). Using polymerase chain reaction, FPV and CPV sequences were obtained from the heart blood of a necropsied leopard individual for the first time in the world and from rectal swabs of three sympatric and clinically ill domestic dogs. CP1 amplicons were also detected in a tiger. Cross-species transmission possibilities were identified, as the closest relatives to the leopard FPV sequence were found in domestic cats from a neighboring state.

Complete mitogenome reveals genetic divergence and phylogenetic relationships among Indian cattle (Bos indicus) breeds.

Indigenous cattle of India belong to the species, Bos indicus and they possess various adaptability and production traits. However, little is known about the genetic diversity and origin of these breeds. To investigate the status, we sequenced and analyzed the whole mitochondrial DNA (mtDNA) of seven Indian cattle breeds. In total, 49 single-nucleotide variants (SNVs) were identified among the seven breeds analyzed. We observed a common synonymous SNV in the COII gene (m.7583G > A) of all the breeds studied. The phylogenetic analysis and genetic distance estimation showed the close genetic relationship among the Indian cattle breeds, whereas distinct genetic differences were observed between Bos indicus and Bos taurus cattle. Our results indicate a common ancestor for European Zwergzebu breed and South Indian cattle. The estimated divergence time demonstrated that the Bos indicus and Bos taurus cattle lineages diverged 0.92 million years ago. Our study also demonstrates that ancestors of present zebu breeds originated in South and North India separately ∼30,000 to 20,000 years ago. In conclusion, the identified genetic variants and results of the phylogenetic analysis may provide baseline information to develop appropriate strategies for management and conservation of Indian cattle breeds.

Mycobacterium tuberculosis in Wild Asian Elephants, Southern India.

We tested 3 ild Asian elephants (Elephas maximus) in southern India and confirmed infection in 3 animals with Mycobacterium tuberculosis, an obligate human pathogen, by PCR and genetic sequencing. Our results indicate that tuberculosis may be spilling over from humans (reverse zoonosis) and emerging in wild elephants.

Lack of detection of SARS-CoV-2 in wildlife from Kerala, India in 2020-21.

Spillover of SARS-CoV-2 into a variety of wild and domestic animals has been an ongoing feature of the human pandemic. The establishment of a new reservoir in white-tailed deer in North America and increasing divergence of the viruses circulating in them from those circulating in the human population has highlighted the ongoing risk this poses for global health. Some parts of the world have seen more intensive monitoring of wildlife species for SARS-CoV-2 and related coronaviruses but there are still very large gaps in geographical and species-specific information. This paper reports negative results for SARS-CoV-2 PCR based testing using a pan coronavirus end point RDRP PCR and a Sarbecovirus specific E gene qPCR on lung and or gut tissue from wildlife from the Indian State of Kerala. These animals included: 121 Rhinolophus rouxii (Rufous Horsehoe Bat), six Rhinolophus bedommei (Lesser Woolly Horseshoe Bat), 15 Rossettus leschenaultii (Fulvous Fruit Bat), 47 Macaca radiata (Bonnet macaques), 35 Paradoxurus hermaphroditus (Common Palm Civet), five Viverricula indica (Small Indian Civet), four Herpestes edwardsii (Common Mongoose), ten Panthera tigris (Bengal Tiger), eight Panthera pardus fusca (Indian Leopard), four Prionailurus bengalensis (Leopard cats), two Felis chaus (Jungle cats), two Cuon alpinus (Wild dogs) and one Melursus ursinus (sloth bear).

Two novel genera and one new species of treefrog (Anura: Rhacophoridae) highlight cryptic diversity in the Western Ghats of India.

Amphibian diversity in the Western Ghats-Sri Lanka biodiversity hotspot is extremely high, especially for such a geographically restricted area. Frogs in particular dominate these assemblages, and the family Rhacophoridae is chief among these, with hundreds of endemic species. These taxa continue to be described at a rapid pace, and several groups have recently been found to represent unique evolutionary clades at the genus level. Here, we report DNA sequences, larval and breeding data for two species of rhacophorid treefrog (Polypedates bijui and a new, hitherto undescribed species). Remarkably, they represent unique, independent clades which form successive sister groups to the Pseudophilautus (Sri Lanka) + Raorchestes (India, China & Indochina) clades. We place these species into two new genera (Beddomixalus gen. nov. and Mercurana gen. nov.). Both of these genera exhibit a distinct reproductive mode among Rhacophoridae of peninsular India and Sri Lanka, with explosive breeding and semiterrestrial, unprotected, non-pigmented eggs oviposited in seasonal swamp pools, which hatch into exotrophic, free-living aquatic tadpoles. Relationships and representation of reproductive modes in sister taxa within the larger clade into which these novel genera are placed, is also discussed. These results suggest that more undescribed taxa may remain to be discovered in South Asia, and the crucial importance of conserving remaining viable habitats.

Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex predation.

The tiger, a poster child for conservation, remains an endangered apex predator. Continued survival and recovery will require a comprehensive understanding of genetic diversity and the use of such information for population management. A high-quality tiger genome assembly will be an important tool for conservation genetics, especially for the Indian tiger, the most abundant subspecies in the wild. Here, we present high-quality near-chromosomal genome assemblies of a female and a male wild Indian tiger (Panthera tigris tigris). Our assemblies had a scaffold N50 of >140 Mb, with 19 scaffolds corresponding to the 19 numbered chromosomes, containing 95% of the genome. Our assemblies also enabled detection of longer stretches of runs of homozygosity compared to previous assemblies, which will help improve estimates of genomic inbreeding. Comprehensive genome annotation identified 26,068 protein-coding genes, including several gene families involved in key morphological features such as the teeth, claws, vision, olfaction, taste, and body stripes. We also identified 301 microRNAs, 365 small nucleolar RNAs, 632 transfer RNAs, and other noncoding RNA elements, several of which are predicted to regulate key biological pathways that likely contribute to the tiger's apex predatory traits. We identify signatures of positive selection in the tiger genome that are consistent with the Panthera lineage. Our high-quality genome will enable use of noninvasive samples for comprehensive assessment of genetic diversity, thus supporting effective conservation and management of wild tiger populations.

FoodKG: A Tool to Enrich Knowledge Graphs Using Machine Learning Techniques.

While there exist a plethora of datasets on the Internet related to Food, Energy, and Water (FEW), there is a real lack of reliable methods and tools that can consume these resources. This hinders the development of novel decision-making applications utilizing knowledge graphs. In this paper, we introduce a novel software tool, called FoodKG, that enriches FEW knowledge graphs using advanced machine learning techniques. Our overarching goal is to improve decision-making and knowledge discovery as well as to provide improved search results for data scientists in the FEW domains. Given an input knowledge graph (constructed on raw FEW datasets), FoodKG enriches it with semantically related triples, relations, and images based on the original dataset terms and classes. FoodKG employs an existing graph embedding technique trained on a controlled vocabulary called AGROVOC, which is published by the Food and Agriculture Organization of the United Nations. AGROVOC includes terms and classes in the agriculture and food domains. As a result, FoodKG can enhance knowledge graphs with semantic similarity scores and relations between different classes, classify the existing entities, and allow FEW experts and researchers to use scientific terms for describing FEW concepts. The resulting model obtained after training on AGROVOC was evaluated against the state-of-the-art word embedding and knowledge graph embedding models that were trained on the same dataset. We observed that this model outperformed its competitors based on the Spearman Correlation Coefficient score.

Corrigendum: FoodKG: A Tool to Enrich Knowledge Graphs Using Machine Learning Techniques.

[This corrects the article DOI: 10.3389/fdata.2020.00012.].

The Indian cobra reference genome and transcriptome enables comprehensive identification of venom toxins.

Snakebite envenoming is a serious and neglected tropical disease that kills ~100,000 people annually. High-quality, genome-enabled comprehensive characterization of toxin genes will facilitate development of effective humanized recombinant antivenom. We report a de novo near-chromosomal genome assembly of Naja naja, the Indian cobra, a highly venomous, medically important snake. Our assembly has a scaffold N50 of 223.35 Mb, with 19 scaffolds containing 95% of the genome. Of the 23,248 predicted protein-coding genes, 12,346 venom-gland-expressed genes constitute the 'venom-ome' and this included 139 genes from 33 toxin families. Among the 139 toxin genes were 19 'venom-ome-specific toxins' (VSTs) that showed venom-gland-specific expression, and these probably encode the minimal core venom effector proteins. Synthetic venom reconstituted through recombinant VST expression will aid in the rapid development of safe and effective synthetic antivenom. Additionally, our genome could serve as a reference for snake genomes, support evolutionary studies and enable venom-driven drug discovery.

Reinvestigating the status of malaria parasite (Plasmodium sp.) in Indian non-human primates.

Many human parasites and pathogens have closely related counterparts among non-human primates. For example, non-human primates harbour several species of malaria causing parasites of the genus Plasmodium. Studies suggest that for a better understanding of the origin and evolution of human malaria parasites it is important to know the diversity and evolutionary relationships of these parasites in non-human primates. Much work has been undertaken on malaria parasites in wild great Apes of Africa as well as wild monkeys of Southeast Asia however studies are lacking from South Asia, particularly India. India is one of the major malaria prone regions in the world and exhibits high primate diversity which in turn provides ideal setting for both zoonoses and anthropozoonoses. In this study we report the molecular data for malaria parasites from wild populations of Indian non-human primates. We surveyed 349 fecal samples from five different Indian non-human primates, while 94 blood and tissue samples from one of the Indian non-human primate species (Macaca radiata) and one blood sample from M. mulatta. Our results confirm the presence of P. fragile, P. inui and P. cynomolgi in Macaca radiata. Additionally, we report for the first time the presence of human malarial parasite, P. falciparum, in M. mulatta and M. radiata. Additionally, our results indicate that M. radiata does not exhibit population structure probably due to human mediated translocation of problem monkeys. Human mediated transport of macaques adds an additional level of complexity to tacking malaria in human. This issue has implications for both the spread of primate as well as human specific malarias.

Next-generation sequencing analysis reveals high bacterial diversity in wild venomous and non-venomous snakes from India.

BACKGROUND: The oral cavities of snakes are replete with various types of bacterial flora. Culture-dependent studies suggest that some of the bacterial species are responsible for secondary bacterial infection associated with snakebite. A complete profile of the ophidian oral bacterial community has been unreported until now. Therefore, in the present study, we determined the complete bacterial compositions in the oral cavity of some snakes from India. METHODS: Total DNA was isolated from oral swabs collected from three wild snake species (Indian Cobra, King Cobra and Indian Python). Next, the DNA was subjected to PCR amplification of microbial 16S rRNA gene using V3-region-specific primers. The amplicons were used for preparation of DNA libraries that were sequenced on an Illumina MiSeq platform. RESULTS: The cluster-based taxonomy analysis revealed that Proteobacteria and Actinobacteria were the most predominant phyla present in the oral cavities of snakes. This result indicates that snakes show more similarities to birds than mammals as to their oral bacterial communities. Furthermore, our study reports all the unique and common bacterial species (total: 147) found among the oral microbes of snakes studied, while the majority of commonly abundant species were pathogens or opportunistic pathogens to humans. A wide difference in ophidian oral bacterial flora suggests variation by individual, species and geographical region. CONCLUSION: The present study would provide a foundation for further research on snakes to recognize the potential drugs/antibiotics for the different infectious diseases.

The complete mitochondrial genome of Indian cattle (Bos indicus).

India has 40 distinct zebuine cattle breeds with different adaptability and production traits. In the present study, we report the complete mitochondrial genome sequence of Indian cattle for the first time. The mitogenome contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and a control region (D-loop region). The phylogenetic analysis showed close genetic relationship among the Indian cattle breeds studied, where as, distinct genetic differences were observed between Bos indicus and Bos taurus cattle. Our results will expand genomic information for further studies on evolution, domestication and conservation of indigenous cattle breeds in India.

Conservation priorities for endangered Indian tigers through a genomic lens.

Tigers have lost 93% of their historical range worldwide. India plays a vital role in the conservation of tigers since nearly 60% of all wild tigers are currently found here. However, as protected areas are small (<300 km2 on average), with only a few individuals in each, many of them may not be independently viable. It is thus important to identify and conserve genetically connected populations, as well as to maintain connectivity within them. We collected samples from wild tigers (Panthera tigris tigris) across India and used genome-wide SNPs to infer genetic connectivity. We genotyped 10,184 SNPs from 38 individuals across 17 protected areas and identified three genetically distinct clusters (corresponding to northwest, southern and central India). The northwest cluster was isolated with low variation and high relatedness. The geographically large central cluster included tigers from central, northeastern and northern India, and had the highest variation. Most genetic diversity (62%) was shared among clusters, while unique variation was highest in the central cluster (8.5%) and lowest in the northwestern one (2%). We did not detect signatures of differential selection or local adaptation. We highlight that the northwest population requires conservation attention to ensure persistence of these tigers.

A novel third species of the Western Ghats endemic genus Ghatixalus (Anura: Rhacophoridae), with description of its tadpole.

The Western Ghats biodiversity hotspot is a recognized center of rhacophorid diversity as demonstrated by several recent studies. The endemic genus Ghatixalus is represented by two species from two separate high-elevation regions within the Ghats. Here, we describe a third species that can be distinguished by morphological and larval characters, as well as by its phylogenetic placement.

Detection of elephant endotheliotropic herpesvirus infection among healthy Asian elephants (Elephas maximus) in South India.

Elephant endotheliotropic herpesviruses (EEHVs) can cause fatal hemorrhagic disease in Asian (Elephas maximus) and African (Loxodonta africana) elephants. Of the seven known EEHV species, EEHV1 is recognized as the most common cause of hemorrhagic disease among Asian elephants in human care worldwide. Recent data collected from ex situ Asian elephants located in multiple North American and European institutions suggest that subclinical EEHV1 infection is common in this population of elephants. Although fatal EEHV1-associated hemorrhagic disease has been reported in range countries, data are lacking regarding the prevalence of subclinical EEHV infections among in situ Asian elephants. We used previously validated EEHV-specific quantitative real-time PCR assays to detect subclinical EEHV infection in three regionally distinct Asian elephant cohorts, totaling 46 in situ elephants in South India, during October and November 2011. Using DNA prepared from trunk washes, we detected EEHV1, EEHV3/4, and EEHV5 at frequencies of 7, 9, and 20% respectively. None of the trunk washes was positive for EEHV2 or 6. At least one EEHV species was detectable in 35% (16/46) of the samples that were screened. These data suggest that subclinical EEHV infection among in situ Asian elephants occurs and that Asian elephants may be natural hosts for EEHV1, EEHV3 or 4, and EEHV5, but not EEHV2 and EEHV6. The methodology described in this study provides a foundation for further studies to determine prevalences of EEHV infection in Asian elephants throughout the world.