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.

Synthesizing habitat connectivity analyses of a globally important human-dominated tiger-conservation landscape.

As ecological data and associated analyses become more widely available, synthesizing results for effective communication with stakeholders is essential. In the case of wildlife corridors, managers in human-dominated landscapes need to identify both the locations of corridors and multiple stakeholders for effective oversight. We synthesized 5 independent studies of tiger (Panthera tigris) connectivity in central India, a global priority landscape for tiger conservation, to quantify agreement on landscape permeability for tiger movement and potential movement pathways. We used the latter analysis to identify connectivity areas on which studies agreed and stakeholders associated with these areas to determine relevant participants in corridor management. Three or more of the 5 studies' resistance layers agreed in 63% of the study area. Areas in which all studies agree on resistance were of primarily low (66%, e.g., forest) and high (24%, e.g., urban) resistance. Agreement was lower in intermediate resistance areas (e.g., agriculture). Despite these differences, the studies largely agreed on areas with high levels of potential movement: >40% of high average (top 20%) current-flow pixels were also in the top 20% of current-flow agreement pixels (measured by low variation), indicating consensus connectivity areas (CCAs) as conservation priorities. Roughly 70% of the CCAs fell within village administrative boundaries, and 100% overlapped forest department management boundaries, suggesting that people live and use forests within these priority areas. Over 16% of total CCAs' area was within 1 km of linear infrastructure (437 road, 170 railway, 179 transmission line, and 339 canal crossings; 105 mines within 1 km of CCAs). In 2019, 78% of forest land diversions for infrastructure and mining in Madhya Pradesh (which comprises most of the study region) took place in districts with CCAs. Acute competition for land in this landscape with globally important wildlife corridors calls for an effective comanagement strategy involving local communities, forest departments, Appendix 1 and infrastructure planners. This article is protected by copyright. All rights reserved.

Ancient Hybridization with an Unknown Population Facilitated High-Altitude Adaptation of Canids.

Genetic introgression not only provides material for adaptive evolution but also confounds our understanding of evolutionary history. This is particularly true for canids, a species complex in which genome sequencing and analysis has revealed a complex history of admixture and introgression. Here, we sequence 19 new whole genomes from high-altitude Tibetan and Himalayan wolves and dogs and combine these into a larger data set of 166 whole canid genomes. Using these data, we explore the evolutionary history and adaptation of these and other canid lineages. We find that Tibetan and Himalayan wolves are closely related to each other, and that ∼39% of their nuclear genome is derived from an as-yet-unrecognized wolf-like lineage that is deeply diverged from living Holarctic wolves and dogs. The EPAS1 haplotype, which is present at high frequencies in Tibetan dog breeds and wolves and confers an adaptive advantage to animals living at high altitudes, was probably derived from this ancient lineage. Our study underscores the complexity of canid evolution and demonstrates how admixture and introgression can shape the evolutionary trajectories of species.

The population density of an urban raptor is inextricably tied to human cultural practices.

Human socio-cultural factors are recognized as fundamental drivers of urban ecological processes, but their effect on wildlife is still poorly known. In particular, human cultural aspects may differ substantially between the extensively studied urban settings of temperate regions and the poorly studied cities of the tropics, which may offer profoundly different niches for urban wildlife. Here, we report how the population levels of a scavenging raptor which breeds in the megacity of Delhi, the black kite Milvus migrans, depend on spatial variation in human subsidies, mainly in the form of philanthropic offerings of meat given for religious purposes. This tight connection with human culture, which generated the largest raptor concentration in the world, was modulated further by breeding-site availability. The latter constrained the level of resource-tracking by the kites and their potential ecosystem service, and could be used as a density-management tool. Similar ties between animal population densities, key anthropogenic resources and human beliefs may occur in thousands of cities all over the globe and may fit poorly with our current understanding of urban ecosystem functioning. For many urban animals, key resources are inextricably linked with human culture, an aspect that has been largely overlooked.

Schrodinger's scat: a critical review of the currently available tiger (Panthera Tigris) and leopard (Panthera pardus) specific primers in India, and a novel leopard specific primer.

BACKGROUND: Non-invasive sampling has opened avenues for the genetic study of elusive species, which has contributed significantly to their conservation. Where field based identity of non-invasive sample is ambiguous (e.g. carnivore scats), it is essential to establish identity of the species through molecular approaches. A cost effective procedure to ascertain species identity is to use species specific primers (SSP) for PCR amplification and subsequent resolution through agarose gel electrophoresis. However, SSPs if ill designed can often cross amplify non-target sympatric species. Herein we report the problem of cross amplification with currently published SSPs, which have been used in several recent scientific articles on tigers (Panthera tigris) and leopards (Panthera pardus) in India. Since these papers form pioneering research on which future work will be based, an early rectification is required so as to not propagate this error further. RESULTS: We conclusively show cross amplification of three of the four SSPs, in sympatric non-target species like tiger SSP amplifying leopard and striped hyena (Hyaena hyaena), and leopard SSP amplifying tiger, lion (Panthera leo persica) and clouded leopard (Neofelis nebulosa), with the same product size. We develop and test a non-cross-amplifying leopard specific primer pair within the mitochondrial cytochrome b region. We also standardize a duplex PCR method to screen tiger and leopard samples simultaneously in one PCR reaction to reduce cost and time. CONCLUSIONS: These findings suggest the importance of an often overlooked preliminary protocol of conclusive identification of species from non-invasive samples. The cross amplification of published primers in conspecifics suggests the need to revisit inferences drawn by earlier work.

Adding constraints to predation through allometric relation of scats to consumption.

A thorough understanding of mechanisms of prey consumption by carnivores and the constraints on predation help us in evaluating the role of carnivores in an ecosystem. This is crucial in developing appropriate management strategies for their conservation and mitigating human-carnivore conflict. Current models on optimal foraging suggest that mammalian carnivores would profit most from killing the largest prey that they can subdue with minimal risk of injury to themselves. Wild carnivore diets are primarily estimated through analysis of their scats. Using extensive feeding experiments (n = 68) on a wide size range (4·5-130 kg) of obligate carnivores - lion, leopard, jungle cat and domestic cat, we parameterize biomass models that best relate consumption to scat production. We evaluate additional constraints of gut fill, prey digestibility and carcass utilization on carnivory that were hereto not considered in optimal foraging studies. Our results show that patterns of consumption to scat production against prey size are similar and asymptotic, contrary to established linear models, across these carnivores after accounting for the effect of carnivore size. This asymptotic, allometric relationship allowed us to develop a generalized model: biomass consumed per collectable scat/predator weight = 0·033-0·025exp(-4·284(prey weight/predator weight)) , which is applicable to all obligate carnivores to compute prey biomass consumed from scats. Our results also depict a relationship for prey digestibility which saturates at about 90% for prey larger than predator size. Carcass utilization declines exponentially with prey size. These mechanisms result in digestible biomass saturating at prey weights approximately equal to predator weight. Published literature on consumption by tropical carnivores that has relied on linear biomass models is substantially biased. We demonstrate the nature of these biases by correcting diets of tiger, lion and leopard in recent publications. Our analysis suggests that consumption of medium-sized prey was significantly underestimated, while large prey consumption was grossly overestimated in large carnivore diets to date. We highlight that additional constraints of prey digestibility and utilization combined with escalating handling time and risks of killing large prey make prey larger than the predator size unprofitable for obligate carnivores.

Megaherbivores provide biotic resistance against alien plant dominance.

While human-driven biological invasions are rapidly spreading, finding scalable and effective control methods poses an unresolved challenge. Here, we assess whether megaherbivores-herbivores reaching ≥1,000 kg of body mass-offer a nature-based solution to plant invasions. Invasive plants are generally adapted to maximize vegetative growth. Megaherbivores, with broad dietary tolerances, could remove large biomass of established plants, facilitating new plant growth. We used a massive dataset obtained from 26,838 camera stations and 158,979 vegetation plots to assess the relationships between megaherbivores, native plants and alien plants across India (~121,330 km2). We found a positive relationship between megaherbivore abundance and native plant richness and abundance, and a concomitant reduction in alien plant abundance. This relationship was strongest in protected areas with midproductive ecosystem and high megaherbivore density but it was lost in areas where thicket-forming alien plants predominated (>40% cover). By incorporating the role of ecosystem productivity, plants traits and densities of megaherbivores on megaherbivore-vegetation relationships, our study highlights a function of megaherbivores in controlling alien plant proliferation and facilitating diverse native plants in invaded ecosystems. The study shows great potential for megafauna-based trophic rewilding as a nature-based solution to counteract dominance of plant invasions.

Land cover and forest health indicator datasets for central India using very-high resolution satellite data.

Satellite imagery has been used to provide global and regional estimates of forest cover. Despite increased availability and accessibility of satellite data, approaches for detecting forest degradation have been limited. We produce a very-high resolution 3-meter (m) land cover dataset and develop a normalized index, the Bare Ground Index (BGI), to detect and map exposed bare ground within forests at 90 m resolution in central India. Tree cover and bare ground was identified from Planet Labs Very High-Resolution satellite data using a Random Forest classifier, resulting in a thematic land cover map with 83.00% overall accuracy (95% confidence interval: 61.25%-90.29%). The BGI is a ratio of bare ground to tree cover and was derived by aggregating the land cover. Results from field data indicate that the BGI serves as a proxy for intensity of forest use although open areas occur naturally. The BGI is an indicator of forest health and a baseline to monitor future changes to a tropical dry forest landscape at an unprecedented spatial scale.

Genome Sequencing of a Gray Wolf from Peninsular India Provides New Insights into the Evolution and Hybridization of Gray Wolves.

The gray wolf (Canis lupus) is among the few large carnivores that survived the Late Pleistocene megafaunal extinctions. Thanks to their complex history of admixture and extensive geographic range, the number of gray wolf subspecies and their phylogenetic relationships remain poorly understood. Here, we perform whole-genome sequencing of a gray wolf collected from peninsular India that was phenotypically distinct from gray wolves outside India. Genomic analyses reveal that the Indian gray wolf is an evolutionarily distinct lineage that diverged from other extant gray wolf lineages ∼110 thousand years ago. Demographic analyses suggest that the Indian wolf population declined continuously decline since separating from other gray wolves and, today, has exceptionally low genetic diversity. We also find evidence for pervasive and mosaic gene flow between the Indian wolf and African canids including African wolf, Ethiopian wolf, and African wild dog despite their current geographical separation. Our results support the hypothesis that the Indian subcontinent was a Pleistocene refugium and center of diversification and further highlight the complex history of gene flow that characterized the evolution of gray wolves.

Morphometric variation in wolves and golden jackal in India (Mammalia, Carnivora).

Species of Canis (Carnivora, Canidae) have similar morphology and distinguishing sympatric species is challenging. We present data on morphometry of skull, body and hair of three wild Canis species that occur in India, which include two wolves (Indian wolf, Canislupuspallipes; and Himalayan wolf, Canishimalayensis) and the golden jackal (Canisaureus). A total of 20 cranial and six body measurements and microscopic characteristics of guard hair were analysed, using multivariate ordination to differentiate between species. Cranial measures of the Himalayan wolves were found to be the largest followed by Indian wolves and golden jackals. However, many measures overlapped amongst the three species. Two Principal Components each, for body measures and cranial measures, explained 86 and 91% of the variation in the data, respectively. These Components discriminated the two wolves from golden jackals, but could not distinguish between wolves. Hair medullary patterns were simple and wide type, whereas hair cuticular patterns showed crenate scale margins, near scale distance and irregular wavey scale patterns for all Canis taxa and were not useful to distinguish species. Data reported in this study further contribute to the existing global data on wild canids for a holistic understanding of the variation within the genus and show that distinguishing between all sympatric species from morphology alone may not be possible.

Camera trap placement for evaluating species richness, abundance, and activity.

Information from camera traps is used for inferences on species presence, richness, abundance, demography, and activity. Camera trap placement design is likely to influence these parameter estimates. Herein we simultaneously generate and compare estimates obtained from camera traps (a) placed to optimize large carnivore captures and (b) random placement, to infer accuracy and biases for parameter estimates. Both setups recorded 25 species when same number of trail and random cameras (n = 31) were compared. However, species accumulation rate was faster with trail cameras. Relative abundance indices (RAI) from random cameras surrogated abundance estimated from capture-mark-recapture and distance sampling, while RAI were biased higher for carnivores from trail cameras. Group size of wild-ungulates obtained from both camera setups were comparable. Random cameras detected nocturnal activities of wild ungulates in contrast to mostly diurnal activities observed from trail cameras. Our results show that trail and random camera setup give similar estimates of species richness and group size, but differ for estimates of relative abundance and activity patterns. Therefore, inferences made from each of these camera trap designs on the above parameters need to be viewed within this context.

Contrasting levels of social distancing between the sexes in lions.

Understanding sexual segregation is crucial to comprehend sociality. A comparative analysis of long-term lion data from Serengeti and Ngorongoro in Tanzania, and Gir in India, reveals that male-female associations are contingent upon male and female group size, prey-size and availability, and the number of prides that each male coalition currently resides. Males maintain proximity with females, whereas females are responsible for segregation except at large kills. Lions feed on the largest prey in Ngorongoro and the smallest in Gir, and females spend the most time with males in Ngorongoro and the least in Gir. Females roar less often in prey-scarce circumstances in Serengeti and throughout the year in Gir possibly to prevent being tracked by males that parasitize on female kills. However, females readily associate with males when available prey is large and abundant. Contrasting availability of resources between Gir and Serengeti/Ngorongoro helps explain the varying degrees of sexual segregation and appears to drive differences in mating systems between these lion populations.

Feasibility of reintroducing grassland megaherbivores, the greater one-horned rhinoceros, and swamp buffalo within their historic global range.

Reintroduction of endangered species is an effective and increasingly important conservation strategy once threats have been addressed. The greater one-horned rhinoceros and swamp buffalo have declined through historic hunting and habitat loss. We identify and evaluate available habitat across their historic range (India, Nepal, and Bhutan) for reintroducing viable populations. We used Species Distribution Models in Maxent to identify potential habitats and evaluated model-identified sites through field visits, interviews of wildlife managers, literature, and population-habitat viability analysis. We prioritize sites based on size, quality, protection, management effectiveness, biotic pressures, and potential of conflict with communities. Our results suggest that populations greater than 50 for rhinoceros and 100 for buffalo were less susceptible to extinction, and could withstand some poaching, especially if supplemented or managed as a metapopulation. We note some reluctance by managers to reintroduce rhinoceros due to high costs associated with subsequent protection. Our analysis subsequently prioritised Corbett and Valmiki, for rhino reintroduction and transboundary complexes of Chitwan-Parsa-Valmiki and Dudhwa-Pilibhit-Shuklaphanta-Bardia for buffalo reintroductions. Establishing new safety-nets and supplementing existing populations of these megaherbivores would ensure their continued survival and harness their beneficial effect on ecosystems and conspecifics like pygmy hog, hispid hare, swamp deer, hog deer, and Bengal florican.

The role of kinship and demography in shaping cooperation amongst male lions.

The influence of kinship on animal cooperation is often unclear. Cooperating Asiatic lion coalitions are linearly hierarchical; male partners appropriate resources disproportionately. To investigate how kinship affect coalitionary dynamics, we combined microsatellite based genetic inferences with long-term genealogical records to measure relatedness between coalition partners of free-ranging lions in Gir, India. Large coalitions had higher likelihood of having sibling partners, while pairs were primarily unrelated. Fitness computations incorporating genetic relatedness revealed that low-ranking males in large coalitions were typically related to the dominant males and had fitness indices higher than single males, contrary to the previous understanding of this system based on indices derived from behavioural metrics alone. This demonstrates the indirect benefits to (related) males in large coalitions. Dominant males were found to 'lose less' if they lost mating opportunities to related partners versus unrelated males. From observations on territorial conflicts we show that while unrelated males cooperate, kin-selected benefits are ultimately essential for the maintenance of large coalitions. Although large coalitions maximised fitness as a group, demographic parameters limited their prevalence by restricting kin availability. Such demographic and behavioural constraints condition two-male coalitions to be the most attainable compromise for Gir lions.

Spatially explicit density and its determinants for Asiatic lions in the Gir forests.

Asiatic lions (Panthera leo persica) are an icon of conservation success, yet their status is inferred from total counts that cannot account for detection bias and double counts. With an effort of 4,797 km in 725 km2 of western Gir Protected Area, India, we used polygon search based spatially explicit capture recapture framework to estimate lion density. Using vibrissae patterns and permanent body marks we identified 67 lions from 368 lion sightings. We conducted distance sampling on 35 transects with an effort of 101.5 km to estimate spatial prey density using generalized additive modeling (GAM). Subsequently, we modeled lion spatial density with prey, habitat characteristics, anthropogenic factors and distance to baiting sites. Lion density (>1-year-old lions) was estimated at 8.53 (SE 1.05) /100 km2 with lionesses having smaller movement parameter (σ = 2.55 km; SE 0.12) compared to males (σ = 5.32 km; SE 0.33). Detection corrected sex ratio (female:male lions) was 1.14 (SE 0.02). Chital (Axis axis) was the most abundant ungulate with a density of 63.29 (SE 10.14) as determined by conventional distance sampling (CDS) and 58.17 (SE 22.17)/km2 with density surface modeling (DSM), followed by sambar (Rusa unicolor) at 3.84 (SE 1.07) and 4.73 (SE 1.48)/km2 estimated by CDS and DSM respectively. Spatial lion density was best explained by proximity to baiting sites and flat valley habitat but not as much by prey density. We demonstrate a scientifically robust approach to estimate lion abundance, that due to its spatial context, can be useful for management of habitat and human-lion interface. We recommend this method for lion population assessment across their range. High lion densities in western Gir were correlated with baiting. The management practice of attracting lions for tourism can perturb natural lion densities, disrupt behavior, lion social dynamics and have detrimental effects on local prey densities.

GPS-telemetry unveils the regular high-elevation crossing of the Himalayas by a migratory raptor: implications for definition of a "Central Asian Flyway".

Remote technologies are producing leapfrog advances in identifying the routes and connectivity of migratory species, which are still unknown for hundreds of taxa, especially Asian ones. Here, we used GPS-telemetry to uncover the migration routes and breeding areas of the massive population of migratory Black-eared kites wintering around the megacity of Delhi-India, which hosts the largest raptor concentration of the world. Kites migrated for 3300-4800 km along a narrow corridor, crossing the Himalayas at extremely high elevations (up to > 6500 m a.s.l.) by the K2 of the Karakoram Range and travelled long periods at elevations above 3500 m. They then crossed/circumvented the Taklamakan Desert and Tian Shan Range to reach their unknown breeding quarters at the intersection between Kazakhstan, Russia, China and Mongolia. Route configuration seemed to be shaped by dominant wind support and barrier avoidance. Wintering ranges were smaller than breeding ranges and concentrated around Delhi, likely in response to massive human food-subsidies. Our results illustrate that high-elevation crossings by soaring migrants may be more common than previously appreciated and suggest the delineation of a hitherto poorly-appreciated "Central Asian Flyway", which must funnel hundreds of thousands of migrants from central Asia into the Indian subcontinent via multiple modes of the Himalayan crossing.

Twisted tale of the tiger: the case of inappropriate data and deficient science.

Publications in peer-reviewed journals are often looked upon as tenets on which future scientific thought is built. Published information is not always flawless and errors in published research should be expediently reported, preferably by a peer-review process. We review a recent publication by Gopalaswamy et al. (10.1111/2041-210X.12351) that challenges the use of "double sampling" in large-scale animal surveys. Double sampling is often resorted to as an established economical and practical approach for large-scale surveys since it calibrates abundance indices against absolute abundance, thereby potentially addressing the statistical shortfalls of indices. Empirical data used by Gopalaswamy et al. (10.1111/2041-210X.12351) to test their theoretical model, relate to tiger sign and tiger abundance referred to as an Index-Calibration experiment (IC-Karanth). These data on tiger abundance and signs should be paired in time and space to qualify as a calibration experiment for double sampling, but original data of IC-Karanth show lags of (up to) several years. Further, data points used in the paper do not match the original sources. We show that by use of inappropriate and incorrect data collected through a faulty experimental design, poor parameterization of their theoretical model, and selectively picked estimates from literature on detection probability, the inferences of this paper are highly questionable. We highlight how the results of Gopalaswamy et al. were further distorted in popular media. If left unaddressed, the paper of Gopalaswamy et al. could have serious implications on statistical design of large-scale animal surveys by propagating unreliable inferences.

Do conservation strategies that increase tiger populations have consequences for other wild carnivores like leopards?

Most large carnivore populations are declining across their global range except in some well managed protected areas (PA's). Investments for conserving charismatic apex carnivores are often justified due to their umbrella effect on biodiversity. We evaluate population trends of two large sympatric carnivores, the tiger and leopard through spatially-explicit-capture-recapture models from camera trap data in Kanha PA, India, from 2011 to 2016. Our results show that the overall density (100 km-2) of tigers ranged between 4.82 ± 0.33 to 5.21 ± 0.55SE and of leopards between 6.63 ± 0.71 to 8.64 ± 0.75SE, with no detectable trends at the PA scale. When evaluated at the catchment scale, Banjar catchment that had higher prey density and higher conservation investments, recorded significant growth of both carnivores. While Halon catchment, that had lower prey and conservation investments, populations of both carnivores remained stable. Sex ratio of both carnivores was female biased. As is typical with large carnivores, movement parameter sigma (an index for range size), was larger for males than for females. However, sigma was surprisingly similar for the same genders in both carnivores. At home-range scale, leopards achieved high densities and positive growth rates in areas that had low, medium or declining tiger density. Our results suggest that umbrella-species conservation value of tigers is likely to be compromised at very high densities and therefore should not be artificially inflated through targeted management.