Drivers of habitat availability for terrestrial mammals: Unravelling the role of livestock, land conversion and intrinsic traits in the past 50 years.

The global decline of terrestrial species is largely due to the degradation, loss and fragmentation of their habitats. The conversion of natural ecosystems for cropland, rangeland, forest products and human infrastructure are the primary causes of habitat deterioration. Due to the paucity of data on the past distribution of species and the scarcity of fine-scale habitat conversion maps, however, accurate assessment of the recent effects of habitat degradation, loss and fragmentation on the range of mammals has been near impossible. We aim to assess the proportions of available habitat within the lost and retained parts of mammals' distribution ranges, and to identify the drivers of habitat availability. We produced distribution maps for 475 terrestrial mammals for the range they occupied 50 years ago and compared them to current range maps. We then calculated the differences in the percentage of 'area of habitat' (habitat available to a species within its range) between the lost and retained range areas. Finally, we ran generalized linear mixed models to identify which variables were more influential in determining habitat availability in the lost and retained parts of the distribution ranges. We found that 59% of species had a lower proportion of available habitat in the lost range compared to the retained range, thus hypothesizing that habitat loss could have contributed to range declines. The most important factors negatively affecting habitat availability were the conversion of land to rangeland and high density of livestock. Significant intrinsic traits were those related to reproductive timing and output, habitat breadth and medium body size. Our findings emphasize the importance of implementing conservation strategies to mitigate the impacts caused by human activities on the habitats of mammals, and offer evidence indicating which species have the potential to reoccupy portions of their former range if other threats cease to occur.

Amine Induced Retardation of the Radical-Mediated Thiol-Ene Reaction via the Formation of Metastable Disulfide Radical Anions.

The effect of amines on the kinetics and efficacy of radical-mediated thiol-ene coupling (TEC) reactions was investigated. By varying the thiol reactant and amine additive, it was shown that amines retard thiyl radical-mediated reactions when the amine is adequately basic enough to deprotonate the thiol affording the thiolate anion, e.g., when the weakly basic amine tetramethylethylenediamine was incorporated in the TEC reaction between butyl 2-mercaptoacetate and an allyl ether at 5 mol %, the final conversion was reduced from quantitative to <40%. Alternatively, no effect is observed when the less acidic thiol butyl 3-mercaptopropionate is employed. The thiolate anion was established as the retarding species through the introduction of ammonium and thiolate salt additives into TEC formulations. The formation of a two-sulfur three-electron bonded disulfide radical anion (DRA) species by the reaction of a thiyl radical with a thiolate anion was determined as the cause for the reduction in catalytic radicals and the TEC rate. Thermodynamic and kinetic trends in DRA formations were computed using density functional theory and by modeling the reaction as an associative electron transfer process. These trends correlate well with the experimental retardation trends of various thiolate anions in TEC reactions.

Assessing the health risks of reintroduction: The example of the Amur leopard, Panthera pardus orientalis.

Translocation of wildlife as a means of reintroducing or reinforcing threatened populations is an important conservation tool but carries health risks for the translocated animals and their progeny, as well as wildlife, domestic animals and humans in the release area. Disease risk analyses (DRA) are used to identify, prioritize and design mitigation strategies to address these threats. Here, we use a DRA undertaken for Amur leopards (Panthera pardus orientalis) to illustrate how specific methodology can optimize mitigation strategy design. A literature review identified a total of 98 infectious hazards and 28 non-infectious hazards. Separate analyses were undertaken for disease risks in leopards from hazards of source origin (captive zoo collections and the transit pathway to the Russian Far East), or of destination origin (in breeding enclosures and wider release areas); and for disease risks in other wildlife, domesticated species or humans, similarly from hazards of source or destination origin. Hazards were assessed and ranked as priority 1, priority 2, priority 3 or low priority in each of the defined scenarios. In addition, we undertook a generic assessment of stress on individual leopards. We use three examples to illustrate the process: Chlamydophila felis, canine distemper virus (CDV) and feline immunodeficiency virus (FIV). We found that many potentially expensive screening procedures could be performed prior to export of leopards, putting the onus of responsibility onto the zoo sector, for which access to diagnostic testing facilities is likely to be optimal. We discuss how our methods highlighted significant data gaps relating to pathogen prevalence in the Russian Far East and likely future unpredictability, in particular with respect to CDV. There was emphasis at all stages on record keeping, meticulous planning, design, staff training and enclosure management, which are relatively financially inexpensive. Actions to minimize stress featured at all time points in the strategy and also focussed on planning, design and management.

CANINE DISTEMPER VIRUS IN A WILD FAR EASTERN LEOPARD ( PANTHERA PARDUS ORIENTALIS).

The critically endangered population of Far Eastern leopards ( Panthera pardus orientalis) may number as few as 60 individuals and is at risk from stochastic processes such as infectious disease. During May 2015, a case of canine distemper virus (CDV) was diagnosed in a wild leopard exhibiting severe neurologic disease in the Russian territory of Primorskii Krai. Amplified sequences of the CDV hemagglutinin gene and phosphoprotein gene aligned within the Arctic-like clade of CDV, which includes viruses from elsewhere in Russia, China, Europe, and North America. Histologic examination of cerebral tissue revealed perivascular lymphoid cuffing and demyelination of the white matter consistent with CDV infection. Neutralizing antibodies against CDV were detected in archived serum from two wild Far Eastern leopards sampled during 1993-94, confirming previous exposure in the population. This leopard population is likely too small to maintain circulation of CDV, suggesting that infections arise from spillover from more-abundant domestic or wild carnivore reservoirs. Increasing the population size and establishment of additional populations of leopards would be important steps toward securing the future of this subspecies and reducing the risk posed by future outbreaks of CDV or other infectious diseases.

Phylogeography and genetic ancestry of tigers (Panthera tigris).

Eight traditional subspecies of tiger (Panthera tigris),of which three recently became extinct, are commonly recognized on the basis of geographic isolation and morphological characteristics. To investigate the species' evolutionary history and to establish objective methods for subspecies recognition, voucher specimens of blood, skin, hair, and/or skin biopsies from 134 tigers with verified geographic origins or heritage across the whole distribution range were examined for three molecular markers: (1) 4.0 kb of mitochondrial DNA (mtDNA) sequence; (2) allele variation in the nuclear major histocompatibility complex class II DRB gene; and (3) composite nuclear microsatellite genotypes based on 30 loci. Relatively low genetic variation with mtDNA,DRB,and microsatellite loci was found, but significant population subdivision was nonetheless apparent among five living subspecies. In addition, a distinct partition of the Indochinese subspecies P. t. corbetti in to northern Indochinese and Malayan Peninsula populations was discovered. Population genetic structure would suggest recognition of six taxonomic units or subspecies: (1) Amur tiger P. t. altaica; (2) northern Indochinese tiger P. t. corbetti; (3) South China tiger P. t. amoyensis; (4) Malayan tiger P. t. jacksoni, named for the tiger conservationist Peter Jackson; (5) Sumatran tiger P. t. sumatrae; and (6) Bengal tiger P. t. tigris. The proposed South China tiger lineage is tentative due to limited sampling. The age of the most recent common ancestor for tiger mtDNA was estimated to be 72,000-108,000 y, relatively younger than some other Panthera species. A combination of population expansions, reduced gene flow, and genetic drift following the last genetic diminution, and the recent anthropogenic range contraction, have led to the distinct genetic partitions. These results provide an explicit basis for subspecies recognition and will lead to the improved management and conservation of these recently isolated but distinct geographic populations of tigers.

Detection of Hepatozoon felis in Ticks Collected from Free-Ranging Amur Tigers ( Panthera tigris altaica), Russian Far East, 2002-12.

We collected 69 ticks from nine, free-ranging Amur tigers ( Panthera tigris altaica) between 2002 and 2011 and investigated them for tick-borne pathogens. DNA was extracted using alkaline digestion and PCR was performed to detect apicomplexan organisms. Partial 18S rDNA amplification products were obtained from 14 ticks from four tigers, of which 13 yielded unambiguous nucleotide sequence data. Comparative sequence analysis revealed all 13 partial 18S rDNA sequences were most similar to those belonging to strains of Hepatozoon felis (>564/572 base-pair identity, >99% sequence similarity). Although this tick-borne protozoon pathogen has been detected in wild felids from many parts of the world, this is the first record from the Russian Far East.

Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly.

BACKGROUND: There are three main dietary groups in mammals: carnivores, omnivores, and herbivores. Currently, there is limited comparative genomics insight into the evolution of dietary specializations in mammals. Due to recent advances in sequencing technologies, we were able to perform in-depth whole genome analyses of representatives of these three dietary groups. RESULTS: We investigated the evolution of carnivory by comparing 18 representative genomes from across Mammalia with carnivorous, omnivorous, and herbivorous dietary specializations, focusing on Felidae (domestic cat, tiger, lion, cheetah, and leopard), Hominidae, and Bovidae genomes. We generated a new high-quality leopard genome assembly, as well as two wild Amur leopard whole genomes. In addition to a clear contraction in gene families for starch and sucrose metabolism, the carnivore genomes showed evidence of shared evolutionary adaptations in genes associated with diet, muscle strength, agility, and other traits responsible for successful hunting and meat consumption. Additionally, an analysis of highly conserved regions at the family level revealed molecular signatures of dietary adaptation in each of Felidae, Hominidae, and Bovidae. However, unlike carnivores, omnivores and herbivores showed fewer shared adaptive signatures, indicating that carnivores are under strong selective pressure related to diet. Finally, felids showed recent reductions in genetic diversity associated with decreased population sizes, which may be due to the inflexible nature of their strict diet, highlighting their vulnerability and critical conservation status. CONCLUSIONS: Our study provides a large-scale family level comparative genomic analysis to address genomic changes associated with dietary specialization. Our genomic analyses also provide useful resources for diet-related genetic and health research.

Mortality of Amur tigers: The more things change, the more they stay the same.

Poaching as well as loss of habitat and prey are identified as causes of tiger population declines. Although some studies have examined habitat requirements and prey availability, few studies have quantified cause-specific mortality of tigers. We used cumulative incidence functions (CIFs) to quantify cause-specific mortality rates of tigers, expanding and refining earlier studies to assess the potential impact of a newly emerging disease. To quantify changes in tiger mortality over time, we re-examined data first collected by Goodrich et al. (; study period 1: 1992-2004) as well as new telemetry data collected since January 2005 (study period 2: 2005-2012) using a total of 57 tigers (27 males and 30 females) monitored for an average of 747 days (range 26-4718 days). Across the entire study period (1992 to 2012) we found an estimated average annual survival rate of 0.75 for all tigers combined. Poaching was the primary cause of mortality during both study periods, followed by suspected poaching, distemper and natural/unknown causes. Since 2005, poaching mortality has remained relatively constant and, if combined with suspected poaching, may account for a loss of 17-19% of the population each year. Canine distemper virus (CDV) may be an additive form of mortality to the population, currently accounting for an additional 5%. Despite this relatively new source of mortality, poaching remains the main threat to Amur tiger survival and, therefore, population growth.

Effects of Roads and Human Disturbance on Amur Tigers.

Understanding the effects of human disturbance on endangered wildlife populations is critical to their conservation. We examined the effects of roads and human disturbance on the survivorship and foraging efficiency of Amur tigers ( Panthera tigris altaica) on and near Sikhote-Alin State Biosphere Zapovednik, Primorye Krai ( province), Russia. To evaluate the effects of roads, we estimated survivorship of radiocollared tigers and their cubs living in three types of areas: (1) areas with primary roads, (2) areas containing secondary roads, and (3) areas with minimal or no road access. We classified a tiger into one of these three treatments based on which types of roads bisected their 50% minimum convex polygon home ranges. Over a 9-year period (1991-2000), adult female survival was greatest (χ 2 = 12.2, df = 2, p = 0.002) for radiocollared tigers in roadless areas. All adult female tigers in roadless areas survived their tenure in those locations (n = 2), whereas all died or disappeared prematurely from areas with primary roads (n = 6). Cub survival was lower in areas with primary and secondary roads than in roadless areas (χ 2 = 10.9, df = 1, p < 0.009). We evaluated the effects of human disturbance at kill sites by examining 86 kills made by 15 tigers determining whether human disturbance had occurred at the kill site, and examining prey carcasses after tigers left, to estimate the percent meat eaten and whether the tiger abandoned the kill following human disturbance. Tigers undisturbed at kills consumed more meat ( Z = 3.71, p = 0.0002) from each kill than disturbed tigers did. Undisturbed tigers also spent more time at each kill site than disturbed tigers did ( Z = 2.3; p = 0.02). Abandonment of kills occurred in 63% of 24 instances when tigers were disturbed by people. Because roads decrease the survivorship and reproductive success of tigers, we recommend that in habitats managed for tigers, construction of new roads should be prohibited wherever possible and access to secondary roads (e.g., logging roads) should be reduced or prevented wherever possible. Protected areas seem to cease functioning as source populations where road access exists, and unprotected areas-the majority of Amur tiger range-cannot sustain stable populations with the increasing threat of human access to tiger habitat.

RESUMEN: Entender los efectos de la perturbación humana sobre poblaciones de vida silvestre en peligro es crítico para su conservación. Examinamos los efectos de caminos y perturbación humana sobre la supervivencia y eficiencia de forrajeo de tigres Amur ( Panthera tigris altaica) en y cerca de Biosfera Estatal Zapovednik Sikhote-Alin, Primorye Krai ( provincia), Rusia. Para evaluar los efectos de los caminos, estimamos la supervivencia de tigres con radio-collares y sus crías en áreas de tres tipos: 1) áreas con caminos primarios, 2) áreas con caminos secundarios y 3) áreas con mínimo o sin acceso de caminos. Clasificamos un tigre en uno de estos tres tratamientos con base en cuales tipos de caminos dividen el 50 % mínimo del polígono convexo de sus rangos de hogar. En un período de 9 años (1991-2000), la supervivencia de hembras adultas fue mayor (χ 2 = 12.2, g.l. = 2, p = 0.002) en tigres con radio-collar en áreas sin caminos. Todas las hembras adultas en áreas sin caminos sobrevivieron su dominio en esas localidades (n = 2), mientras que todas murieron o desaparecieron prematuramente en las áreas con caminos primarios (n = 6). La supervivencia de crías fue menor en áreas con caminos primarios y secundarios que en áreas sin caminos (χ 2 = 10.9, g.l. = 1, p < 0.009). Evaluamos los efectos de la perturbación humana en sitios de depredación mediante el examen de 86 muertes causadas por 15 tigres, determinando si había ocurrido perturbación humana en el sitio, y mediante el examen de restos de las presas después de que se alejaron los tigres, para estimar el porcentaje de carne consumida y si el tigre abandonó su presa después de una perturbación humana. Los tigres no perturbados consumieron más carne ( Z = 3.71, p = 0.0002) de cada presa que los tigres perturbados. Tigres no perturbados pasaron más tiempo con su presa que tigres perturbados ( Z = 2.3, p = 0.02). El abandono de presas ocurrió en 63 % de 24 eventos cuando los tigres fueron perturbados por humanos. Debido a que los caminos reducen la supervivencia y el éxito reproductivo de los tigres, recomendamos que en los hábitats bajo manejo para tigres, se debe prohibir la construcción de caminos donde sea posible y se debe reducir o prevenir el acceso a caminos secundarios (e. g. caminos madereros) donde sea posible. Las áreas protegidas dejan de funcionar como poblaciones fuente donde existe acceso a caminos, y las áreas no protegidas ( la mayor parte del rango de tigre Amur) no pueden sostener poblaciones estables con la incremento en la amenaza del acceso humano al hábitat de los tigres.

Estimating the potential impact of canine distemper virus on the Amur tiger population (Panthera tigris altaica) in Russia.

Lethal infections with canine distemper virus (CDV) have recently been diagnosed in Amur tigers (Panthera tigris altaica), but long-term implications for the population are unknown. This study evaluates the potential impact of CDV on a key tiger population in Sikhote-Alin Biosphere Zapovednik (SABZ), and assesses how CDV might influence the extinction potential of other tiger populations of varying sizes. An individual-based stochastic, SIRD (susceptible-infected-recovered/dead) model was used to simulate infection through predation of infected domestic dogs, and/or wild carnivores, and direct tiger-to-tiger transmission. CDV prevalence and effective contact based on published and observed data was used to define plausible low- and high-risk infection scenarios. CDV infection increased the 50-year extinction probability of tigers in SABZ by 6.3% to 55.8% compared to a control population, depending on risk scenario. The most significant factors influencing model outcome were virus prevalence in the reservoir population(s) and its effective contact rate with tigers. Adjustment of the mortality rate had a proportional impact, while inclusion of epizootic infection waves had negligible additional impact. Small populations were found to be disproportionately vulnerable to extinction through CDV infection. The 50-year extinction risk in populations consisting of 25 individuals was 1.65 times greater when CDV was present than that of control populations. The effects of density dependence do not protect an endangered population from the impacts of a multi-host pathogen, such as CDV, where they coexist with an abundant reservoir presenting a persistent threat. Awareness of CDV is a critical component of a successful tiger conservation management policy.

Human-carnivore conflict in China: a review of current approaches with recommendations for improved management.

Human-wildlife conflict (HWC) is a conservation concern that increasingly threatens the continued existence of some of the world's most endangered species. With an increase in human population, urban sprawl and subsequent encroachment on wild land, human and wildlife interaction has become inevitable. In the majority of cases, this interaction results in a negative outcome for humans, wildlife or both. In China, these key elements, along with a decrease in wild prey species, have resulted in the expansion of HWC encounters, and the need for alleviating this conflict has become a conservation priority. Loss of human life, livestock and/or crops is most often the catalysts that fuel HWC. Techniques to alleviate conflict around the world have included preventative measures and mitigation techniques, such as financial compensation and other incentive programs. Both types of measures have had variable success. We review the current status of human-carnivore conflict management in China, and, drawing lessons from around the globe, we make recommendations for improving conservation management in China. For example, an increase in law enforcement in nature reserves is vital to reducing human disturbance in prime carnivore habitat, thereby reducing conflict encounters. Also, modifications to current wildlife compensation programs, so that they are linked with preventative measures, will ensure that moral hazards are avoided. Furthermore, investigating the potential for a community self-financed insurance scheme to fund compensation and increasing efforts to restore wild prey populations will improve the outcome for wildlife conservation. Ultimately, HWC management in China will greatly benefit from an integrative approach.

Serosurvey of free-ranging Amur tigers in the Russian Far East.

Wild Amur tigers (Panthera tigris altaica, n=44) from the Russian Far East were tested for antibodies to feline leukemia virus, feline corona virus (FCoV), feline immunodeficiency virus, feline parvovirus (FPV), canine distemper virus (CDV), Toxoplasma gondii, and Bartonella henselae. Antibodies to FCoV, CDV, FPV, and T. gondii were detected in 43, 15, 68, and 42% of tigers, respectively. No differences were detected in antibody prevalence estimates between tigers captured as part of a research program and those captured to mitigate human-tiger conflicts. Domestic dogs (Canis familiaris) were tested as a potential source for CDV; 16% were vaccinated against CDV and 58% of unvaccinated dogs were antibody positive for CDV. A high percentage of tigers were exposed to potential pathogens that could affect the survival of this species. We recommend continued monitoring of wild tigers throughout Asia, development of standardized sampling and postmortem examination procedures, and additional research to better understand potential domestic and wild animal sources for these pathogens.

Human-tiger conflict: a review and call for comprehensive plans.

Human-tiger (Panthera tigris Linnaeus, 1758) conflicts (HTC), manifested primarily as attacks on people and domestic animals, exacerbate at least 2 major threats to tigers: (i) conflicts often result in mortality or removal of tigers from the wild; and (ii) they result in negative attitudes towards tigers by local people, thereby reducing support for tiger conservation. Although HTC has decreased over the past century, it will likely increase if current and proposed conservation initiatives to double tiger populations are successful. Increased HTC could undermine successful conservation initiatives if proactive steps are not taken to reduce HTC. The present paper provides a review of the impacts of HTC and the measures taken to reduce it in ways that reduce negative impacts on both humans and tigers, and stresses the need for development and implementation of comprehensive plans to reduce HTC.

Review of research methodologies for tigers: telemetry.

Over the past half century, wildlife research has relied on technological advances to gain additional insight into the secretive lives of animals. This revolution started in the 1960s with the development of radio telemetry and continues today with the use of Global Positioning System (GPS)-based research techniques. In the present paper we review the history of radio telemetry from its origins with grizzly bears in Yellowstone to its early applications in tiger research and conservation in Asia. We address the different types of data that are available using radio telemetry as opposed to using other research techniques, such as behavioral observations, camera trapping, DNA analysis and scat analysis. In the late 1990s, the rapid development of GPS collar technology revolutionized wildlife research. This new technology has enabled researchers to dramatically improve their ability to gather data on animal movements and ecology. Despite the ecological and conservation benefits of radio telemetry, there have been few telemetry studies of tigers in the wild, and most have been on the Bengal or Amur subspecies. We close with an assessment of the current tiger conservation efforts using GPS technology and discuss how this new information can help to preserve tigers for future generations.

Morbillivirus infection in a wild siberian tiger in the Russian Far East.

We report the first documented case of morbillivirus infection in a wild, free-ranging Siberian tiger (Panthera tigris altaica). The tigress entered a small village in the Russian Far East in an ambulatory but stuporous state with no apparent recognition or fear of humans. Her condition progressed rapidly with neurological signs, anorexia, and ultimately death. Histologic lesions included vacuolated to malacic white matter in the brain stem, cerebellum, and thalamus, with associated lymphocytic meningoencephalitis. Large, intranuclear, eosinophilic inclusions were within regional astrocytes, and the brain lesions were immunohistochemically positive when stained for canine distemper viral antigen. Hematologic and blood chemistry results were consistent with overwhelming systemic infection and starvation. The animal also was antibody-positive for canine distemper virus, feline panleukopenia, and feline coronavirus.