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Bengal tigers (Panthera tigris tigris) serve a pivotal role as an apex predator in forest ecosystems. To increase our knowledge on factors impacting the viability and health of this endangered species, we studied the gut microbiota in 32 individual Bengal tigers from three geographically separated areas (Chitwan National Park (CNP), Bardia National Park (BNP) and Suklaphanta Wildlife Reserve (SWR)) in Nepal, using noninvasive genetic sampling methods. Gut microbiota influence the immune system, impact various physiological functions, and modulates metabolic reactions, that ultimately impact the host health, behavior and development. Across the tiger populations in Nepal, we found significant differences in the composition of microbial communities based on their geographic locations. Specifically, we detected significant differences between CNP and the other two protected areas (CNP vs BNP: pseudo t = 1.944, P = 0.006; CNP vs SWR: pseudo t = 1.9942, P = 0.0071), but no differences between BNP and SWR. This mirrors what has been found for tiger gene flow in the same populations, suggesting gut microbiota composition and host gene flow may be linked. Furthermore, predictive metagenome functional content analysis (PICRUSt) revealed a higher functional enrichment and diversity for significant gut microbiota in the Chitwan tiger population and the lowest enrichment and diversity in Suklaphanta. The CNP tiger population contained higher proportions of microbiota that are associated with predicted functions relevant for metabolism of amino acid, lipid, xenobiotics biodegradation, terpenoides and polyketides than the SWR population. We conclude the tiger population structure, gut microbiota profile and associated functional metabolic categories are correlated, with geographically most separated CNP and SWR tiger population having the most distinct and different host genotype and microbiota profiles. Our work dramatically expands the understanding of tiger microbiota in wild populations and provides a valuable case study on how to investigate genetic diversity at different hierarchical levels, including hosts as well as their microbial communities., Competing Interests: The authors have declared that no competing interests exist.

Riau Province in central Sumatra, with its peatland, lowland, and montane forest habitats, was once a stronghold for Sumatran tiger (Panthera tigris sumatrae) populations. Today, Riau may have one of the highest deforestation rates in the world and wildlife populations are dwindling, with natural forest now comprising approximately only 18% of the province, mostly contained within protected areas. Agriculture (acacia, rubber, and oil palm) makes up the majority of Riau's land cover and deforestation for the creation of new plantations is rampant. Natural forest and tigers still remain in Bukit Tigapuluh National Park and Rimbang Baling Wildlife Reserve, which remain connected to tiger populations in montane forest on the western edge of Sumatra. In this study, using freely available Landsat imagery and a maximum likelihood classification algorithm, we create land cover maps for central Sumatra from 2002 to 2016. We then use current land cover, elevation, and slope variables to predict changes from forest to plantation from 2016 to 2050 at five year intervals using a multilayer perceptron neural network. Finally, we compare connectivity based on a 100 km distance threshold (based on potential tiger dispersal) across the landscape and across years. Land cover maps had 80-90% accuracy, and we predict forest in Tesso Nilo and the western edge of the study area to be lost by 2050 given current rates of deforestation. Our connectivity analysis shows that Tesso Nilo and the area between Rimbang Baling and Bukit Tigapuluh are important components for maintaining connectivity throughout the study area. Focusing conservation and rehabilitation efforts on forests close to plantations in flat areas, including Tesso Nilo, is necessary to maintain forests and increase connectivity in Riau to ensure future habitat connectivity for survival of tigers and Sumatra's other diverse endemic species., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

Tiger (Panthera tigris) populations are in danger across their entire range due to habitat loss, poaching and the demand for tiger parts. The Bengal tiger (Panthera tigris tigris) is an endangered apex predator with a population size estimated to be less than 200 in Nepal. In spite of strict wildlife protection laws, illegal trade of tiger parts is increasing; and Nepal has become one of the major sources and transit routes for poached wildlife parts. Identification of wildlife parts is often challenging for law enforcement officials due to inadequate training and lack of available tools. Here, we describe a molecular forensic approach to gain insight into illegally trafficked tiger parts seized across Nepal. We created Nepal's first comprehensive reference genetic database of wild tigers through the Nepal Tiger Genome Project (2011-2013). This database has nuclear DNA microsatellite genotype and sex profiles, including geo-spatial information, of over 60% (n = 120) of the wild tigers of Nepal. We analyzed 15 putative cases of confiscated poached tiger parts and all were confirmed to be of tiger. Ten samples were identified as male and five were female. We determined probable geo-source location for 9 of the 14 samples with 6-8 nuclear DNA microsatellite loci using inferences from four different statistical assignment methods. Six samples were assigned to Bardia National Park and one of these was an exact match to a female tiger previously profiled in our fecal DNA reference database. Two tiger samples were assigned to Shuklaphanta Wildlife Reserve and one to Chitwan National Park. We are unable to definitively assign five tiger samples which could be offspring dispersers or might have come from tiger population outside of Nepal. Our study revealed that the western region, particularly Bardia National Park, is a poaching hotspot for illegal tiger trade in Nepal. We present feasibility of using molecular forensic based evidence to incriminate criminals in a court of law in the fight against wildlife crime., Competing Interests: The authors have declared that no competing interests exist.

With fewer than 200 tigers (Panthera tigris tigris) left in Nepal, that are generally confined to five protected areas across the Terai Arc Landscape, genetic studies are needed to provide crucial information on diversity and connectivity for devising an effective country-wide tiger conservation strategy. As part of the Nepal Tiger Genome Project, we studied landscape change, genetic variation, population structure, and gene flow of tigers across the Terai Arc Landscape by conducting Nepal's first comprehensive and systematic scat-based, non-invasive genetic survey. Of the 770 scat samples collected opportunistically from five protected areas and six presumed corridors, 412 were tiger (57%). Out of ten microsatellite loci, we retain eight markers that were used in identifying 78 individual tigers. We used this dataset to examine population structure, genetic variation, contemporary gene flow, and potential population bottlenecks of tigers in Nepal. We detected three genetic clusters consistent with three demographic sub-populations and found moderate levels of genetic variation (He = 0.61, AR = 3.51) and genetic differentiation (FST = 0.14) across the landscape. We detected 3-7 migrants, confirming the potential for dispersal-mediated gene flow across the landscape. We found evidence of a bottleneck signature likely caused by large-scale land-use change documented in the last two centuries in the Terai forest. Securing tiger habitat including functional forest corridors is essential to enhance gene flow across the landscape and ensure long-term tiger survival. This requires cooperation among multiple stakeholders and careful conservation planning to prevent detrimental effects of anthropogenic activities on tigers.

While there are numerous wildlife ecology studies in lowland areas of Nepal, there are no in-depth studies of the hilly Churia habitat even though it comprises 7642 km 2 of potential wildlife habitat across the Terai Arc. We investigated tiger, leopard and prey densities across this understudied habitat. Our camera trapping survey covered 536 km 2 of Churia and surrounding areas within Chitwan National Park (CNP). We used 161 trapping locations and accumulated 2097 trap-nights in a 60-day survey period during the winter season of 2010-2011. In addition, we walked 136 km over 81 different line transects using distance sampling to estimate prey density. We photographed 31 individual tigers, 28 individual leopards and 25 other mammalian species. Spatial capture-recapture methods resulted in lower density estimates for tigers, ranging from 2.3 to 2.9 tigers per 100 km 2 , than for leopards, which ranged from 3.3 to 5.1 leopards per 100 km 2 . In addition, leopard densities were higher in the core of the Churia compared to surrounding areas. We estimated 62.7 prey animals per 100 km 2 with forest ungulate prey (sambar, chital, barking deer and wild pig), accounting for 47% of the total. Based on prey availability, Churia habitat within CNP could potentially support 5.86 tigers per 100 km 2 but our density estimates were lower, perhaps indicating that the tiger population is below carrying capacity. Our results demonstrate that Churia habitat should not be ignored in conservation initiatives, but rather management efforts should focus on reducing human disturbance to support higher predator numbers., (© 2016 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and John Wiley & Sons Australia, Ltd.)

The critically endangered Sumatran tiger (Panthera tigris sumatrae Pocock, 1929) is generally known as a forest-dependent animal. With large-scale conversion of forests into plantations, however, it is crucial for restoration efforts to understand to what extent tigers use modified habitats. We investigated tiger-habitat relationships at 2 spatial scales: occupancy across the landscape and habitat use within the home range. Across major landcover types in central Sumatra, we conducted systematic detection, non-detection sign surveys in 47, 17×17 km grid cells. Within each cell, we surveyed 40, 1-km transects and recorded tiger detections and habitat variables in 100 m segments totaling 1,857 km surveyed. We found that tigers strongly preferred forest and used plantations of acacia and oilpalm, far less than their availability. Tiger probability of occupancy covaried positively and strongly with altitude, positively with forest area, and negatively with distance-to-forest centroids. At the fine scale, probability of habitat use by tigers across landcover types covaried positively and strongly with understory cover and altitude, and negatively and strongly with human settlement. Within forest areas, tigers strongly preferred sites that are farther from water bodies, higher in altitude, farther from edge, and closer to centroid of large forest block; and strongly preferred sites with thicker understory cover, lower level of disturbance, higher altitude, and steeper slope. These results indicate that to thrive, tigers depend on the existence of large contiguous forest blocks, and that with adjustments in plantation management, tigers could use mosaics of plantations (as additional roaming zones), riparian forests (as corridors) and smaller forest patches (as stepping stones), potentially maintaining a metapopulation structure in fragmented landscapes. This study highlights the importance of a multi-spatial scale analysis and provides crucial information relevant to restoring tigers and other wildlife in forest and plantation landscapes through improvement in habitat extent, quality, and connectivity.

Worldwide, roads are a main driver of deforestation and degradation as they increase forest access along the forest edge. In many tropical areas, unofficial roads go unreported and unrecorded, resulting in inaccurate estimates of intact forested areas. This is the case in central Sumatra, which boasts populations of critically endangered Sumatran elephants (Elephas maximus sumatrensis), tigers (Panthera tigris sumatrae) and other endemic flora and fauna that make the area globally unique. However, maps do not reflect the reality of forest loss in the area. Here we present new maps from 2002 and 2016 of digitized and ground-truthed roads in one of Sumatra’s unique lowland tropical protected areas, Tesso Nilo National Park. Using our newly created roads dataset, we examine the distribution of forest with respect to distance to roads. Our data show >2,400 km of roads within the national park in 2016 –nearly a 10-fold increase from roads known in 2002. Most forest (82–99%) within Tesso Nilo falls within 100 m, 500 m, and 1000 m of road edges. Length of road increased 157% and road density increased from 1.06 km/km2 to 2.63 km/km2 from 2002–2016. Our results suggest that this endemic ecosystem is facing substantial threat from roads and their associated impacts. Without swift management action, such as road closures and increased enforcements by park management, this ecosystem, and its endemic wildlife, could be lost. It is imperative that protected areas worldwide more rigorously consider roads and road effects on ecosystem fragmentation in their conservation plans. [ABSTRACT FROM AUTHOR]

Understanding spatial distribution, habitat use, and temporal activity patterns is important for species conservation planning. This information especially is crucial for mega herbivores like elephants as their ranging patterns encompass a myriad of habitats types. Churia habitat is geological fragile yet important for wildlife in Nepal and India. We used camera trapping and sign surveys covering 536 km2 of Churia and surrounding areas within Chitwan National Park. Across 152 trapping locations, we accumulated 2,097 trap nights in a 60-day survey during the winter season of 2010–11. We used a non-parametric kernel density function to analyze winter activity patterns of elephants detected in camera-traps. Additionally, we walked 643 km over 76 grid cells in two surveys (winter and summer) to estimate elephant distribution and intensity of habitat use using an occupancy framework. Multi-season models allowed us to make seasonal (winter versus summer) inferences regarding changes in habitat use based on covariates influencing use and detection. We photographed 25 mammalian species including elephants with calves with a trapping rate of 2.72 elephant photos events per 100 trap nights. Elephant winter activity pattern was found to be mainly nocturnal, with crepuscular peaks. Covariates such as normalized differential vegetation index and terrain ruggedness positively influenced elephant spatial distribution and habitat use patterns within the Churia habitat. We also found lower elephant habitat use () of Churia in winter 0.51 (0.02) than in summer 0.57 (0.02). Elephants heavily used the eastern portion of Churia in both seasons (67–69%). Overall, Churia habitat, which is often ignored, clearly is used by elephants, with increases in summer use in the west and high use year-round in the east, and thus should no longer be neglected or forgotten in species conservation planning. [ABSTRACT FROM AUTHOR]

In this study, we estimate life history parameters and abundance for a protected jaguar population using camera-trap data from a 14-year monitoring program (2002–2015) in Belize, Central America. We investigated the dynamics of this jaguar population using 3,075 detection events of 105 individual adult jaguars. Using robust design open population models, we estimated apparent survival and temporary emigration and investigated individual heterogeneity in detection rates across years. Survival probability was high and constant among the years for both sexes (φ = 0.78), and the maximum (conservative) age recorded was 14 years. Temporary emigration rate for the population was random, but constant through time at 0.20 per year. Detection probability varied between sexes, and among years and individuals. Heterogeneity in detection took the form of a dichotomy for males: those with consistently high detection rates, and those with low, sporadic detection rates, suggesting a relatively stable population of ‘residents’ consistently present and a fluctuating layer of ‘transients’. Female detection was always low and sporadic. On average, twice as many males than females were detected per survey, and individual detection rates were significantly higher for males. We attribute sex-based differences in detection to biases resulting from social variation in trail-walking behaviour. The number of individual females detected increased when the survey period was extended from 3 months to a full year. Due to the low detection rates of females and the variable ‘transient’ male subpopulation, annual abundance estimates based on 3-month surveys had low precision. To estimate survival and monitor population changes in elusive, wide-ranging, low-density species, we recommend repeated surveys over multiple years; and suggest that continuous monitoring over multiple years yields even further insight into population dynamics of elusive predator populations. [ABSTRACT FROM AUTHOR]

Despite the establishment of a national protected area system at the beginning of the 20th century to protect some of the world's most biodiverse forests, Indonesia has one of the highest deforestation rates in the world, due in part to the expansion of the global palm oil industry. The unique ecosystems of Sumatra, Indonesia provide habitat for critically endangered Sumatran tigers (Panthera tigris sumatrae), Sumatran elephants (Elephas maximus sumatrensis), and two species of orangutans (Pongo abelii and Pongo tapanuliensis). In this study, we use a matching method with generalized boosted models to determine the effectiveness of three nationally protected areas in preventing deforestation from 2002 to 2016. We also examine leakage – an increase in deforestation directly outside of protected areas relative to the wider landscape – to provide a clearer picture of the effects of agricultural expansion in this landscape. We found that Tesso Nilo National Park, with its lowland rain forest and conditions suitable for oil palm, offered the least protection from deforestation (avoided deforestation rate = 4.18%, p < 0.05 95% CI [1.97% - 6.45%]). Bukit Tigapuluh National Park, which may experience some de facto protection (i.e. protection due to factors independent of policy) with its mountainous terrain and difficult access, had the highest avoided deforestation rate (26.36%, p < 0.05 95% CI [24.17–28.55]), but had relatively high leakage (10.21%, p < 0.05 95% CI [7.51–12.98]). The low avoided deforestation rate in Tesso Nilo could be due to high localized human population and/or other socio-economic factors we were unable to control for in this study. The quantitative evidence of deforestation and effectiveness of protected areas in this heavily modified landscape supports the need for increased enforcement around protected areas locally, and globally in other oil palm production regions. These actions are critical in the preservation of global, tropical endemic flora and fauna. Meskipun telah membangun sistem kawasan konservasi sejak awal abad ke 20 untuk melindungi hutan dengan keanekaragaman hayati yang sangat tinggi, Indonesia masih merupakan negara yang memiliki laju deforestasi yang tertinggi di dunia, akibat penkembangan industri sawit di dunia. Ekosistem-ekosistem endemic di Sumatera-Indonesia merupakan habitat bagi spesies-spesies yang memiliki status konservasi kritis yaitu harimau Sumatera (Panthera tigris sumatrae), gajah Sumatera (Elephas maximus sumatrensis), dan dua species orangutan (Pongo abelii dan Pongo tapanuliensis). Dalam penelitian ini, kami menggunakan metode matching dengan model generalized boosted untuk menentukan efektivitas dari tiga kawasan konservasi dalam mencegah terjadinya deforestasi dari tahun 2002–2016. Kami juga menilai leakage (kebocoran) – yang merupakan kenaikan laju deforestasi pada area yang berdekatan dengan kawasan konservasi– untuk memberikan gambaran yang utuh atas dampak industri sawit dunia. Kami menemukan bahwa Taman Nasional Tesso Nilo, dengan habitat dan kondisi hutan tropis dataran rendah, yang juga sesuai untuk tanaman sawit, merupakan kawasan konservasi yang memiliki kemampuan paling rendah dalam melindungi dari deforestasi (laju pencegahan deforestasi = 4.18%, p < 0.05 95% CI [1.97% - 6.45%]). Sedangkan Taman Nasional Bukit Tigapuluh yang merupakan kawasan pegunungan memiliki laju pencegahan deforestasi tertinggi (26.36%, p < 0.05 95% CI [24.17–28.55]), namun memilki nilai kebocoran yang relatif tinggi (10.21%, p < 0.05 95% CI [7.51–12.98]). Fakta kuantitatif dari deforestasi dan efektivitas kawasan konservasi pada landskap yang termodifikasi sangat berat ini mengkonfirmasi adanya kebutuhan yang mendesak untuk melakukan penguatan di sekitar kawasan konservasi baik di tingkat lokal maupun global pada wilayah yang ditujukan untuk produksi sawit. Aksi-aksi tersebut sangat dibutuhkan untuk mendukung perlindungan flora dan fauna endemik di dunia. [ABSTRACT FROM AUTHOR]