Examining Temporal Sample Scale and Model Choice with Spatial Capture-Recapture Models in the Common Leopard \u3ci\u3ePanthera pardus\u3c/i\u3e

Many large carnivores occupy a wide geographic distribution, and face treats from habitat loss and fragmentation, poaching, prey depletion, and human wildlife-conflicts. Conservation requires robust techniques for estimating population densities and trends, but the elusive nature and low densities of many large carnivores make them difficult to detect. Spatial capture-recapture (SCR) models provide a means for handling imperfect detectability, while linking population estimates to individual movement patterns to provide more accurate estimates than standard approaches. Within this framework, we investigate the effect of different sample interval lengths on density estimates, using simulations and a common leopard (Panthera pardus) model system. We apply Bayesian SCR methods to 89 simulated data sets and camera-trapping data from 22 leopards captured 82 times during winter 2010-2011 in Royal Manas National Park, Bhutan. We show that sample interval length from daily, weekly, monthly or quarterly periods did not appreciably affect median abundance or density, but did influence precision. We observed the largest gains in precision when moving from quarterly to shorter intervals. We therefore recommend daily sampling intervals for monitoring rare or elusive species where practicable, but note that monthly or quarterly sample periods can have similar informative value. We further develop a novel application of Bayes factors to select models where multiple ecological factors are integrated into density estimation. Our simulations demonstrate that these methods can help identify the true explanatory mechanisms underlying the data. Using this method, we found strong evidence for sex-specific movement distributions in leopards, suggesting that sexual patterns of space-use influence density. This model estimated a density of 10.0 leopards/100 km2 (95% credibility interval: 6.25-15.93), comparable to contemporary estimates in Asia. These SCR methods provide a guide to monitor and observe the effect of management interventions on leopards and other species of conservation interest

Royal Manas National Park, Bhutan: A Hot Spot for Wild Felids

The non-uniformity of the distribution of biodiversity makes allocation of the limited resources available for conservation of biodiversity a difficult task. Approaches such as biodiversity hotspot identification, endemic bird areas, crisis ecoregions, global 200 ecoregions, and the Last of the Wild are used by scientists and international conservation agencies to prioritize conservation efforts. As part of the biodiverse Eastern Himalayan region, Bhutan has been identified as a conservation priority area by all these different approaches, yet data validating these assessments are limited. To examine whether Bhutan is a biodiversity hot spot for a key taxonomic group, we conducted camera trapping in the lower foothills of Bhutan, in Royal Manas National Park, from November 2010 to February 2011. We recorded six species of wild felids of which five are listed on the IUCN Red List: tiger Panthera tigris, golden cat Pardofelis temminckii, marbled cat Pardofelis marmorata, leopard cat Prionailurus bengalensis, clouded leopard Neofelis nebulosa and common leopard Panthera pardus. Our study area of 74 km(2) has c. 16% of felid species, confirming Bhutan as a biodiversity hot spot for this group

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Partial Altitudinal Migration of a Himalayan Forest Pheasant : First Insights and Conservation Implications

Animal migration is a complex phenomenon exhibited across many taxonomic groups and occurs in every major ecosystem on our planet. Given the sheer number of animals on the move, migration profoundly shapes, alters and regulates our environment. Though animal migration has been a subject of study for decades, the ultimate drivers and consequences of migration are still not clearly established. Bird migration in particular has received a great deal of attention from biologists. Till date, most studies have focused on long distance, cross continental latitudinal migrants. However, a significant proportion of birds undertake annual migrations along elevational gradients across mountain regions of the world. So far, only a few studies have examined altitudinal migration systems due to which altitudinal migrations remain poorly understood. This thesis therefore is the first documentation of an altitudinal migration system in the high altitude Himalayas of Bhutan with state-of-the-art accelerometer enabled GPS telemetry.I present the first detailed patterns for a complex partial altitudinal migration system for the Satyr Tragopans (Tragopan satyra) in the Bhutan Himalayas. Contrary to current perceptions, I found that altitudinal migration is not a simple up-and-down slope movement of individuals by documenting 3 main patterns of migration: 1) crossing multiple mountains; 2) descending/ascending longitudinally; 3) moving higher up in winter and lower down in summer. Migrants departed consistently across the years and much ahead of snowfall suggesting that altitudinal migrations do not occur as a response to extreme weather events. I also found that although females are more likely to migrate, no consistent patterns can be established to explain who migrates and who remains resident within sexes and therefore suggest that extant hypotheses consider both inter as well as intra-sexual differences while explaining partial migration systems. And I provide anecdotal evidence that individuals can switch strategy from being a migrant to becoming a resident.Within partial migration systems, proximate tradeoffs associated with the decision to either migrate or to remain a resident are not clearly understood. I therefore examined the possible tradeoffs related to migratory decisions in terms of energy expenditure and home range sizes. I found that winter home ranges for residents overlapped with conspecifics and were significantly larger than migrants whose home ranges occurred at discrete non-overlapping sites. Over the course of a migratory season, I did not find any significant differences between migrants and residents in energy expenditure as measured by dynamic body acceleration (DBA). Nevertheless, for migrants, I noted higher DBA scores and activity states associated with running/flying and walking during migration. Given that an individual’s migratory status does not significantly affect its overall energy expenditure despite manifesting differently in terms of space use, I suggest that fluctuating micro-habitat conditions across time may enable the maintenance of a partial migration system.Having assessed the patterns of migration and the possible proximate tradeoffs involved in such a system, I next considered the conservation requirements for partial altitudinal migrants. Both migrants and residents occupied forests all year round. Using accelerometer data, I found that migrants walk to-and-fro between summer breeding and non-breeding winter grounds taking multiple days and halting along mountain slopes across forested landscapes. I also found that females migrated in a south easterly direction while males migrated in random directions and that migrants occupied south-east facing slopes, while residents chose to remain on south-west facing slopes. I therefore suggest corridors in ideal situations would need to run in random directions and recommend that protected areas in mountainous regions include different habitat configurations (aspects) in addition to having a representation of all habitat types.The findings from my PhD thesis challenge many of the assumptions associated with altitudinal migrants and offer new perspectives to our understanding of both altitudinal and partial migration systems. In addition, by demonstrating habitat associations, migratory modes and pathways, the thesis contributes towards helping conserve such magnificent migrations which occur across the mountain regions of our planet. Taking advantage of the advances in accelerometer enabled GPS telemetry, my thesis has demonstrated that it is possible to track individuals and illustrate previously unknown patterns of migration over annual cycles. I recommend that future studies collate data across multiple years measuring explanatory variables associated with habitat quality, fecundity, mortality rates, individual condition and predation pressure, while simultaneously tracking both migrants and residents. Such a study will contribute significantly in helping understand and uncover both the proximate and ultimate causes and consequences of migrations

Good fences are key to sustainable pasture management and harmonious pastoral society of Merak and Sakteng in Bhutan

Abstract There is limited knowledge about the traditional tsamdro management practice, particularly the building of walls and fences by the pastoral nomads of Merak and Sakteng. Conflicts related to tsamdro resource access are not a new phenomenon in Bhutanese pastoral communities. In the recent past, as an adaptive response to external economic, political, social and ecological changes, the tsamdro was nationalized. This change in policies brought a host of challenges specifically in managing the existing and building new tsamdro border structures. The objective of the study was to elucidate the motives and purposes behind the building of tsamdro structures, and to explore the historical development, significance and future of yak farming by Brokpas. We used a semi-structured questionnaire and face-to-face interview for collecting both quantitative and qualitative data from 40 yak herders opportunistically selected from both Merak and Sakteng gewogs, village block, refers to a group of villages in Bhutan Trashigang district. The study revealed that tsamdro border structures were primarily built to ensure harmony within the Brokpa society by reducing conflicts caused by livestock trespassing, but structures indirectly assisted in tsamdro management. The structures were one of the encashable family assets passed across generations and played a critical role in shaping the socio-economic developments of Brokpas. Though the tsamdro was nationalized, the Brokpas still continue to hold tsamdro ownership rights and build new tsamdro border structures to protect their livelihood. The contradiction between the government’s policy and Brokpas’ livelihood pattern will have a detrimental effect on both the social harmony of nomadic herders and the traditional tsamdro management practice. We suggest the government develop nomadic-centered policies that encourage tsamdro resource sharing within the Brokpa communities. Socio-economic development incentives are required to address the trespassing conflicts

New distribution record of the Bhutan Takin Budorcas taxicolor whitei Hodgson, 1850 (Cetartiodactyla: Bovidae) in Bhutan

A camera trapping survey in eastern Bhutan in 2015 has yielded a picture of the Bhutan Takin in the uplands of Kurichu River watersheds in east of Wangchuck Centennial National Park, and is the easternmost documented  distribution of the species in Bhutan. The photograph was taken on 30th June 2015 at 9:24 AM in the site located on 27056’03.8’’E &amp; 91004’53.7”N at 3,898m. The habitat is dominated by Fir and Rhododendron.</p

Partial altitudinal migration of the Near Threatened satyr tragopan Tragopan satyra in the Bhutan Himalayas : implications for conservation in mountainous environments

Relative to long-distance migrants, altitudinal migrants have been understudied, perhaps because of a perception that their migrations are less complex and therefore easier to protect. Nonetheless, altitudinal migrants may be at risk as they are subject to ongoing anthropogenic pressure from land use and climate change. We used global positioning system/accelerometer telemetry to track the partial altitudinal migration of the satyr tragopan Tragopan satyra in central Bhutan. The birds displayed a surprising diversity of migratory strategies: some individuals did not migrate, others crossed multiple mountains to their winter ranges, others descended particular mountains, and others ascended higher up into the mountains in winter. In all cases migration between summer breeding and winter non-breeding grounds was accomplished largely by walking, not by flying. Females migrated in a south-easterly direction whereas males migrated in random directions. During winter, migrants occupied south-east facing slopes whereas residents remained on south-west facing slopes. Migratory and resident tragopans utilized a range of forest types, with migratory individuals preferring cool broadleaved forests during winter. These complex patterns of migration suggest that conservation measures should extend across multiple mountains, protect the full range of forest types and encompass multiple landscape configurations to protect aspect diversity. Given the diversity of migratory strategies employed by this single species it seems clear that more research on altitudinal migrants is needed to understand what must be done to ensure their future in an era of widespread land-use and climate change.publishe

Data from: Examining temporal sample scale and model choice with spatial capture-recapture models in the common leopard Panthera pardus

Many large carnivores occupy a wide geographic distribution, and face threats from habitat loss and fragmentation, poaching, prey depletion, and human wildlife-conflicts. Conservation requires robust techniques for estimating population densities and trends, but the elusive nature and low densities of many large carnivores make them difficult to detect. Spatial capture-recapture (SCR) models provide a means for handling imperfect detectability, while linking population estimates to individual movement patterns to provide more accurate estimates than standard approaches. Within this framework, we investigate the effect of different sample interval lengths on density estimates, using simulations and a common leopard (Panthera pardus) model system. We apply Bayesian SCR methods to 89 simulated datasets and camera-trapping data from 22 leopards captured 82 times during winter 2010–2011 in Royal Manas National Park, Bhutan. We show that sample interval length from daily, weekly, monthly or quarterly periods did not appreciably affect median abundance or density, but did influence precision. We observed the largest gains in precision when moving from quarterly to shorter intervals. We therefore recommend daily sampling intervals for monitoring rare or elusive species where practicable, but note that monthly or quarterly sample periods can have similar informative value. We further develop a novel application of Bayes factors to select models where multiple ecological factors are integrated into density estimation. Our simulations demonstrate that these methods can help identify the “true” explanatory mechanisms underlying the data. Using this method, we found strong evidence for sex-specific movement distributions in leopards, suggesting that sexual patterns of space-use influence density. This model estimated a density of 10.0 leopards/100 km2 (95% credibility interval: 6.25–15.93), comparable to contemporary estimates in Asia. These SCR methods provide a guide to monitor and observe the effect of management interventions on leopards and other species of conservation interest

Indirect remote sensing of a cryptic forest understorey invasive species

Remote sensing has successfully been applied to map the distribution of canopy dominating invasive species. Many invaders however, do not dominate the canopy, and remote sensing has so far not been applied to map such species. In this study, an indirect method was used to map the seed production of Chromolaena odorata , one of the world's 100 worst invasive species. The study was executed in lowland Shorea robusta forest in Nepal, where Chromolaena invaded the understorey of a degraded forest. A Landsat ETM+ image processed through a neural network predicted 89 and 81% of forest canopy density and light intensity reaching the understorey, respectively. We inverted these models to predict Chromolaena seed productivity. Light intensity determined 93% of the variation in log10 seed production per plant. Chromolaena failed to produce seed below a light intensity of 6.5 mJ m- 2 day-1. Further analysis revealed that Chromolaena was absent above this light intensity in case of a high biomass of other shrub and herb species, a situation occurring in the absence of grazing. We therefore suggest that other species control Chromolaena through competitive exclusion in the absence of grazing, whereas grazing breaks the dominance of these other species thus creating the conditions for Chromolaena attain canopy dominance. The presence of grazing was related to distance from the forest edge, a variable that together with light intensity allowed us to map 64% of variation in Chromolaena cover. Predicted Chromolaena cover and seed production per plant were combined into a map displaying the total seed production per unit area. Such map displaying seed producing sites could be used to significantly reduce the costs of controlling Chromolaena infestation by providing information on the spatial segregation of source and sink populations, which will support efficient habitat ranking to restore invaded areas and protect non-invaded ecosystems. This may prove particularly valuable when implementing control measures under circumstances of limited capital and manpower