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Biology subjects

Habib, B.

Publications and source records attributed to Habib, B..

11 recordsLinked to original sources

Population-specific drivers of reproductive phenology in a widespread large carnivore, the gray wolf

Animals often rely on cues from the environment to time reproduction with optimal conditions. However, for most species, which environmental cues are used and how their use varies across a species distribution remains poorly understood. The gray wolf (Canis lupus) is found across a broad latitudinal range (12{degrees}N to 83{degrees}N) and diverse natural habitats, making them an ideal study species to explore these questions. Using 1,261 estimated birth dates of wild and captive wolves across their global range, we investigated how environmental variables influence reproductive phenology in this widespread large carnivore. Birth dates for wild wolves ranged from November 22nd for Indian wolves (18{degrees}N) to June 15th for Arctic wolves (80{degrees}N). The best predictor of timing of birth was increasing daylength during the mating season, followed by precipitation variability during the year. The timing of birth in captive wolves was highly similar to wild wolves at same latitudes, suggesting they use similar environmental cues to time reproduction. Near the equator where photoperiod is more stable, wolves remained seasonal and likely use climatic cues to time reproduction. Our work reveals populations may use different environmental cues to time reproduction, a characteristic that likely facilitates adaptation to diverse environments.

ecology↗

Complex genomic ancestry in southern regions and drivers of continental-level genetic diversity in the wolves of Asia

Gray wolves (Canis lupus) in Asia encompass most of the species global genetic diversity and many endangered populations. However, a clear understanding of the evolutionary history of wolves from many parts of Asia, especially southern regions, is lacking. We used 98 whole genomes of wolves sampled across Eurasia to better resolve their evolutionary history by investigating phylogenetic and gene flow histories across the genome, and to characterize their demographic history and genetic diversity. The strongest barriers to gene flow coincided with boundaries separating the three major extant wolf lineages - Indian, Tibetan, and Holarctic. Wolves in the central Asian mountain ranges belonged to the Holarctic lineage, and despite their geographic adjacency only share minimal ancestry with the Tibetan lineage. In contrast, wolves from eastern Asia share population-wide ancestry with the Tibetan lineage, which may reflect an unsampled lineage similar, but not exactly to, the modern-day Tibetan lineage. Wolves from southwestern Asia also share population-wide ancestry with the Indian lineage, likely due to old (>6kya) admixture events. Long-term historical declines over the last 100,000 years, geographic isolation, and recent inbreeding have resulted in the Indian and Tibetan wolves having some of the lowest levels of genetic diversity and highest realized genetic loads. In contrast, adjacent populations exhibit some of the highest genetic diversity, due in part to admixture along contact zones. Our study illustrates how using multiple approaches that consider heterogenous signals across the genome can more fully resolve the historical and contemporary processes that have led to present-day species diversity.

evolutionary biology↗

Functional connectivity in northern swamp deer (Rucervus duvaucelii duvaucelii) population across a fragmented, human-dominated landscape along Gangetic Plains of north India: Implications for conservation in non-protected areas

The Indian subcontinent has witnessed disproportionate declines in large mammalian herbivore communities. The northern swamp deer (Rucervus duvaucelii duvaucelii) exemplifies the conservation challenges of typical non-protected area species, where apart from distribution status other ecological information is limited for the upper Gangetic basin population. We combined elements of radio-telemetry and conservation genetics to evaluate dispersal patterns, population connectivity and assess genetic variation and inbreeding status of this population living across a highly human-dominated area. We genetically identified 266 unique swamp deer and further analyses revealed presence of two spatially-admixed genetic lineages with moderate heterozygosity (Ho=0.51, SD= 0.10) and low inbreeding (FIS=0.133) status. Multi- disciplinary evidence suggests that the small, isolated grassland patches between Jhilmil Jheel Conservation Reserve (JJCR) and Hastinapur Wildlife Sanctuary (HWLS) are highly preferred by swamp deer during migrations and are genetically connected. The southern part of the area in HWLS showed early signatures of genetic discontinuity that require immediate conservation attention. We hypothesized that the human settlement history of this landscape, river dynamics and species ability to negotiate various pressures and disperse has helped to maintain such connectivity. While these signatures are encouraging for this small, isolated cervid population, careful management interventions are required to ensure the integrity and functionality of this landscape. We recommend a scientifically robust population estimation approach across this landscape and a multi-stakeholder-driven strategies to augment population and habitat recovery, plantation and riverscape management to ensure long-term survival of this species.

ecology↗

Waning grasslands: a quantitative temporal evaluation of the grassland habitats across human-dominated upper Gangetic Plains, north India

Grassland habitats currently face severe anthropogenic exploitations leading to cascading effects on the survival of grassland-dependent biodiversity globally, particularly in non-protected areas. Significant amount of such biodiversity-rich grasslands in India are found outside protected areas but lack quantitative information on their status. We evaluated the current and historical (30 years) status of the grasslands using a combination of intensive field surveys and GIS tools across one of the most fertile, human-dominated region: the upper Gangetic Plains of north India. On-ground mapping and visual classifications revealed 57% decline in grassland habitats between 1985 (418 km2) and 2015 (178km2), mostly driven by conversion to croplands (74% contribution). Radio-telemetry data from the largest endemic cervid swamp deer (n=2) showed grassland-dominated average home range (50% BBMM) size of 1.02 km2. The animals highly preferred these patches (average Ivlevs index- 0.85) and showed highest temporal continuity (88%) compared to other LULC classes. Camera trapping within the core habitats suggests critical use of these patches as fawning/breeding grounds. Habitat suitability analysis indicates only [~]18% of the entire area along Ganges is suitable for swamp deer. Accurate mapping (86% accuracy) and characterization of four major grass species revealed a total 144.04 km{superscript 2} vegetation area, dominted by Saccharum sp. (35%). We recommend protection and recovery of these critical grassland patches to maintain dynamic corridors and other appropriate management strategies involving multiple stakeholders to ensure survival of this critical ecosystem. Such evaluations, if spatially expanded, would be critical to restore this rapidly vanishing ecosystem worldwide.

ecology↗

Predation by Himalayan Wolves: Understanding conflict, culture and co-existence amongst Indo-Tibetan community and large carnivores in High Himalaya

The wolves in the Hindukush-Himalayan region belong to one the most basal lineages within Canis lupus, yet little is known about its ecology, distribution, and behavior. To understand ecological aspects of wolves in this landscape, we predict wolf distribution, diet patterns and conflict perception in Spiti, India using field and remotely sensed information. We collected scats (n = 283) of canid species namely, Wolves, and other predators over a period of 3 years (2014-17) [66]. Wolf diet constituted mostly of domestic prey (79.02 %) while wild prey constituted to 17.80% of wolf diet over the three years. Village surveys recorded only 4% of the respondents confirmed wolf presence and perceived them as a possible threat to various livestock. Over, 98% of the respondents claimed that wolves were not safe for livestock and were averse to its presence. Marginal response curves depicted the model to have positive responses to animal location, LULC, village population, village density and wolf depredation. We found perceived presence/threat distribution wolves in the area significantly differed from actual ecological presence and distribution of wolves. The Himalayan wolf is an apex flagship predator in this fragile high altitude system, whose role is intricately linked with the ecology of the region. The use of such methods can aid in understanding such aspects as well as designing effective long-term conservation strategies for the species.

ecology↗

Characterising the vocal repertoire of the Indian wolf (Canis lupus pallipes)

Vocal communication in social animals plays a crucial role in mate choice, maintaining social structure, and foraging strategy. The Indian grey wolf, among the less studied subspecies, is a social carnivore that lives in groups called packs and has many types of vocal communication. In this study, we characterise harmonic vocalisation types in the Indian wolf using howl survey responses and opportunistic recordings from captive and nine packs (each pack contains 2-9 individuals) of free-ranging Indian wolves. Using principal component analysis, hierarchical clustering, and discriminant function analysis, we found four vocal types using 270 recorded vocalisations (Average Silhouette width Si = 0.598) which include howls and howl-bark (N=238), whimper (N=2), social squeak (N=28), and whine (N=2). Although having a smaller body size, Indian wolf howls have an average mean fundamental frequency of 0.422KHz ({+/-}0.126), which is similar to other Holarctic clade subspecies. The whimper showed the highest frequency modulation (37.296{+/-}4.601 KHz) and the highest mean fundamental frequency (1.708{+/-}0.524 KHz) compared to other call types. Less information is available on the third vocalisation type, i.e. Social squeak or talking (Mean fundamental frequency =0.461{+/-}0.083 KHz), which is highly variable (coefficient of frequency variation = 18.778{+/-}3.587 KHz). Our studys characterisation of the Indian wolfs harmonic vocal repertoire provides a first step in understanding the function and contextual use of vocalisations in this social mammal.

animal behavior and cognition↗

A practive faeces collection protocol for multidisciplinary research in wildlife science

Faecal samples have become important non-invasive source of information in wildlife biology and ecological research. Despite regular use of faeces, there is no universal protocol available for faeces collection and storage to answer various questions in wildlife biology. We collected 1408 faeces from ten different species using a dry sampling approach, and achieved 94.87% and 86.02% success rate in mitochondrial and nuclear marker amplifications. We also suggest a universal framework to use the same samples for different use. This protocol provides an easy, quick and cheap option to collect non-invasive samples from species living at different environmental conditions to answer multidisciplinary questions in wildlife biology.

ecology↗

Catch me if you can: Species interactions and moon illumination effect on mammals of tropical semi-evergreen forest of Manas National Park, Assam, India

Species interaction plays a vital role in structuring communities by stimulating behavioral responses in temporal niche affecting the sympatric associations and prey-predator relationships. We studied relative abundance indices (RAI) and activity patterns of each species, temporal overlap between sympatric species, and effects of moon cycle on predator-prey relationships, through camera-trapping in tropical semi-evergreen forests of Manas National Park. A total of 35 species were photo-captured with 16214 independent records over 7337 trap nights. Overall, relatively high number of photographs was obtained for large herbivores (11 species, n=13669), and low number of photographs were recorded for large carnivores (five species, n=657). Activity periods were classified into four categories: diurnal (day-time), nocturnal (night-time), crepuscular (twilight), and cathemeral (day and night time) of which 52% records were found in diurnal period followed by 37% in nocturnal phase whereas only 11% photographs during twilight. Small carnivores were strictly nocturnal (leopard cat and civets) or diurnal (yellow-throated marten and mongooses); whereas large carnivores were cathemeral (tiger, leopard, clouded leopard and Asiatic black bear). Analysis of activity patterns throughout the 24-h cycle revealed a high degree of temporal overlap (>60%) among most of the sympatric species; however, differences in the activity peaks were found between most of the species pairs. Moon phase was classified according to the percentage of visible moon surface as new (0-25%), waxing (25-50%), waning (50-75%) and full moon (75-100%). Moon phase did not have any correlation with activity of large carnivore and large prey. The large carnivore followed the feed and starve pattern of cyclic activity. The activity of small carnivore was influenced negatively by moonlight (partial correlation r = -0.221, p<0.01). The result suggests that large carnivores were active non-differentially across moon phases; however, small carnivores showed significantly high activity in darker nights. These patterns indicate that small predators may differ their activity temporally as an anti-predator strategy or otherwise to increase their foraging efficiency.

animal behavior and cognition↗

Standardization and validation of a panel of cross-species microsatellites to individually identify the Asiatic wild dog (Cuon alpinus): implications in population estimation and dynamics

BackgroundThe Asiatic wild dog or dhole (Cuon alpinus) is a highly elusive, monophyletic, forest dwelling, social canid distributed across south and Southeast Asia. Severe pressures from habitat loss, prey depletion, disease, human persecution and interspecific competition resulted in global population decline in dholes. Despite a declining population trend, detailed information on population size, ecology, demography and genetics is lacking. Generating reliable information and landscape level for dholes is challenging due to their secretive behaviour and monomorphic physical features. Recent advances in non-invasive DNA-based tools can be used to monitor populations and individuals across large landscapes. In this paper, we describe standardization and validation of faecal DNA-based methods for individual identification of dholes. We tested this method on field-collected dhole faeces in four tiger reserves of the central Indian landscape in the state of Maharashtra, India. Further, we conducted preliminary analyses of dhole population structure and demography in the study area.\n\nResultsWe tested a total of 18 cross-species markers and developed a panel of 12 markers for unambiguous individual identification of dholes. This marker panel identified 101 unique individuals from faecal samples collected across our pilot field study area. These loci showed varied level of amplification success (57-88%), polymorphism (3-9 alleles), heterozygosity (0.23-0.63) and produced a cumulative probability of identity (unbiased) and probability of identity (sibs) value of 4.7x10-10 and 1.5x10-4, respectively. Our preliminary analyses of population structure indicated four genetic subpopulations in dholes. Qualitative analyses of population demography show signal of population decline.\n\nConclusionOur results demonstrated that the selected panel of 12 microsatellite loci can conclusively identify dholes from poor quality, non-invasive biological samples and help in exploring various population parameters. Our methods can be used to estimate dhole populations and assess population trends for this elusive, social carnivore.

genetics↗

The Cuon Enigma: Genome survey and comparative genomics of the endangered Dhole (Cuon alpinus)

The Asiatic wild dog is an endangered monophyletic canid restricted to Asia; facing threats from habitat fragmentation and other anthropogenic factors. Dholes have unique adaptations as compared to other wolf-like canids for large litter size (larger number of mammae) and hypercarnivory making it evolutionarily notable. Over evolutionary time, dhole and the subsequent divergent wild canids have lost coat patterns found in African wild dog. Here we report the first high coverage genome survey of Asiatic wild dog and mapped it with African wild dog, dingo and domestic dog to assess the structural variants. We generated a total of 124.8 Gb data from 416140921 raw read pairs and retained 398659457 reads with 52X coverage and mapped 99.16% of the clean reads to the three reference genomes. We identified ~13553269 SNVs, ~2858184 InDels, ~41000 SVs, ~1854109 SSRs and about 1000 CNVs. We compared the annotated genome of dingo and domestic dog with dhole genome sequence to understand the role of genes responsible in pelage pattern, dentition and mammary glands. Positively selected genes for these phenotypes were looked for SNP variants and top ranked genes for coat pattern, dentition and mammary glands were found to play a role in signalling and developmental pathways. Mitochondrial genome assembly predicted 35 genes, 11 CDS and 24 tRNA. This genome information will help in understanding the divergence of two monophlyletic canids, Cuon and Lycaon, and the evolutionary adaptations of dholes with respect to other canids.

genomics↗

Risky home with easy food: Denning of a generalistic and widely distributed carnivore red fox

Dens are crucial for the survival of all canids, however, for a meso-carnivore like red fox, denning is of greater importance as they utilize dens all throughout the year for protection, resting and breeding. The red fox known for its generalist and opportunistic behavior and extremely good adaptability to the dynamic anthropogenic changes is the most widespread and successful wild land carnivore. With an ever-growing human population the choice of space for wild animals is limited and such adaptability is important for species survival. In this study we examined the denning preferences and den characteristics of red fox. Intensive surveys were conducted across two study sites Chiktan and Changthang. Foxes preferred to den on mountain slopes (43.70 {+/-} 3.38 SE) where human disturbances were minimal. The red fox chose den sites closer to human settlements, water and road as compared to random points (Pillais trace = .487, F= 31.014 and P = 3.497e-14), which are risky and may expose the pups to humans but also provide the advantage of procuring anthropogenic food subsidies. In Changthang, foxes preferred to den at a greater distance (936 {+/-} 223 meters) from human settlements as compared to Chiktan (403 {+/-} 50 meters). The present research is of broad significance, given the increasing presence of human settlements within original animal ranges, even in remote harsh environments like the Trans-Himalaya.

ecology↗