Estimating the Population Size and Genetic Diversity of Amur Tigers in Northeast China

Over the past century, the endangered Amur tiger (Panthera tigris altaica) has experienced a severe contraction in demography and geographic range because of habitat loss, poaching, and prey depletion. In its historical home in Northeast China, there appears to be a single tiger population that includes tigers in Southwest Primorye and Northeast China; however, the current demographic status of this population is uncertain. Information on the abundance, distribution and genetic diversity of this population for assessing the efficacy of conservation interventions are scarce. We used noninvasive genetic detection data from scats, capture-recapture models and an accumulation curve method to estimate the abundance of Amur tigers in Northeast China. We identified 11 individual tigers (6 females and 5 males) using 10 microsatellite loci in three nature reserves between April 2013 and May 2015. These tigers are confined primarily to a Hunchun Nature Reserve along the border with Russia, with an estimated population abundance of 9–11 tigers during the winter of 2014–2015. They showed a low level of genetic diversity. The mean number of alleles per locus was 2.60 and expected and observed heterozygosity were 0.42 and 0.49, respectively. We also documented long-distance dispersal (~270 km) of a male Amur tiger to Huangnihe Nature Reserve from the border, suggesting that the expansion of neighboring Russian populations may eventually help sustain Chinese populations. However, the small and isolated population recorded by this study demonstrate that there is an urgent need for more intensive regional management to create a tiger-permeable landscape and increased genetic connectivity with other populations.     

Estimating Minimum Area of Suitable Habitat and Viable Population Size for the Northern Muriqui (Brachyteles hypoxanthus)

A population viability analysis (PVA) using the computer package VORTEX was conducted to assess the minimum viable population (MVP) of the Atlantic Forest endemic primate Brachyteles hypoxanthus. The objectives were: (1) to estimate demographic and genetic MVPs that could be used as quasi-extinction thresholds for future modeling, and (2) to estimate the minimum area of suitable habitat (MASH). The model predicted that populations of 40 and 700 individuals were necessary to achieve demographic and genetic stability, respectively. The model was more sensitive to changes in inbreeding depression, sex ratio and reproduction (percentage of breeding females). MASH estimated to contain genetically viable populations reached 11,570 ha. Muriquis have managed to persist despite severe habitat disturbance, but the results suggest that although most of the extant populations are not threatened by extinction, they are too small to be genetically viable in the long-run, and will loose most of their heterozygosity.     

A Comparison of Social Organization in Asian Elephants and African Savannah Elephants

Asian and African elephant species have diverged by ca. 6 million years, but as large, generalist herbivores they occupy similar niches in their respective environments. Although the multilevel, hierarchical nature of African savannah elephant societies is well established, it has been unclear whether Asian elephants behave similarly. Here we quantitatively compare the structure of both species’ societies using association data collected using the same protocol over similar time periods. Sociality in both species demonstrates well-defined structure, but in contrast to the African elephants of Samburu the Uda Walawe Asian elephants are found in smaller groups, do not maintain coherent core groups, demonstrate markedly less social connectivity at the population level, and are socially less influenced by seasonal differences in ecological conditions. The Uda Walawe Asian elephants, however, do maintain a complex, well-networked society consisting of ≥2 differentiated types of associates we term ephemeral and long-term affiliates. These findings imply we must broaden our recognition of multilevel social organization to encompass societies that fall along a gradient of nestedness, and not merely those that exhibit hierarchical nesting. This in turn suggests that multilevel structures may be more diverse and widespread than generally thought, and that phylogenetic comparisons within species-rich clades, such as that of primates, using the methods presented can provide fresh insights into their socioecological basis.     

Estimating Population Size and Density Using Line Transect Sampling

ANDERSON and POSPAHALA (1970) investigated the estimation of wildlife population size using the belt or line transect sampling method and devised a correction for bias, thus leading to a class of estimators with desirable characteristics. This work was given a basic and rigorous mathematica framework by BURNHAM and ANDERSON (1976). In the present article we use this mathematical framework to develop an estimator of population size and density using weighted least squares. The approach is a two-stage Method.     

Evaluating Habitat Suitability for the Establishment of Monochamus spp. through Climate-Based Niche Modeling

Pine sawyer beetle species of the genus Monochamus are vectors of the nematode pest Bursaphelenchus xylophilus. The introduction of these species into new habitats is a constant threat for those regions where the forestry industry depends on conifers, and especially on species of Pinus. To obtain information about the potential risk of establishment of these insects in Chile, we performed climate-based niche modeling using data for five North American and four Eurasian Monochamus species using a Maxent approach. The most important variables that account for current distribution of these species are total annual precipitation and annual and seasonal average temperatures, with some differences between North American and Eurasian species. Projections of potential geographic distribution in Chile show that all species could occupy at least 37% of the area between 30° and 53°S, where industrial plantations of P. radiata are concentrated. Our results indicated that Chile seems more suitable for Eurasian than for North American species.     

Estimating Population Size for Continuous-Time Capture-Recapture Models Via Sample Coverage

An estimation procedure using the idea of sample coverage is proposed to estimate population size for capture-recapture experiments in continuous time. The capture rates (intensity) are allowed to vary by time and individuals (heterogeneity). Only capture frequency history are sufficient for estimating population size while capture times and sequential orders of animals caught are irrelevant for the analysis. An example is given for illustration. The performance of the proposed estimation procedure is also investigated by simulation.     

Methods for Estimating Population Density in Data-Limited Areas: Evaluating Regression and Tree-Based Models in Peru

Obtaining accurate small area estimates of population is essential for policy and health planning but is often difficult in countries with limited data. In lieu of available population data, small area estimate models draw information from previous time periods or from similar areas. This study focuses on model-based methods for estimating population when no direct samples are available in the area of interest. To explore the efficacy of tree-based models for estimating population density, we compare six different model structures including Random Forest and Bayesian Additive Regression Trees. Results demonstrate that without information from prior time periods, non-parametric tree-based models produced more accurate predictions than did conventional regression methods. Improving estimates of population density in non-sampled areas is important for regions with incomplete census data and has implications for economic, health and development policies.     

Habitat Suitability and Population Size Estimates for the Mongoose Lemurs (Eulemur mongoz) of Madagascar and the Comoro Islands,and Implications for Their Conservation

International Journal of Primatology - Tropical forests face an alarming rate of loss driven by anthropogenic pressures, exposing forest-dwelling species such as primates to extinction risks....     

Evaluating Methods to Correct for Population Stratification when Estimating Paternity Indexes

The statistical interpretation of the forensic genetic evidence requires the use of allelic frequency estimates in the reference population for the studied markers. Differences in the genetic make up of the populations can be reflected in statistically different allelic frequency distributions. One can easily figure out that collecting such information for any given population is not always possible. Therefore, alternative approaches are needed in these cases in order to compensate for the lack of information. A number of statistics have been proposed to control for population stratification in paternity testing and forensic casework, Fst correction being the only one recommended by the forensic community. In this study we aimed to evaluate the performance of Fst to correct for population stratification in forensics. By way of simulations, we first tested the dependence of Fst on the relative sizes of the sub-populations, and second, we measured the effect of the Fst corrections on the Paternity Index (PI) values compared to the ones obtained when using the local reference database. The results provide clear-cut evidence that (i) Fst values are strongly dependent on the sampling scheme, and therefore, for most situations it would be almost impossible to estimate real values of Fst; and (ii) Fst corrections might unfairly correct PI values for stratification, suggesting the use of local databases whenever possible to estimate the frequencies of genetic profiles and PI values.     

Estimating Competition in Cladocerans Using Data on Dynamics of Clutch Size and Population Density

Negative correlations between clutch size and population density are proposed to be considered as indices of intra- and interspecific competition in cladocerans if they are revealed while analyzing population dynamics and clutch size and time lags are taken into account. The proper correlation analysis of summer populations of Diaphanosoma brachyurum, Bosmina coregoni, Daphnia cucullata and D. galeata from mesotrophic Lake Glubokoye (Moscow Region) in 1975, 1978, and 1979 indicates the important role of competition of both types for the community studied. High niche overlap in food and space in the four populations was also observed.     

圈养亚洲象的刻板行为初探

2011年1月、7月、10～12月,采用事件记录法记录并分析了成都动物园圈养的2只(1♀1 ♂)亚洲象的刻板行为发生频次(次·h-1)和持续时间.结果表明,在刻板行为类型及其时间分配格局中,雌象以摇头最多,占73.93％,而雄象则以刻板踱步最多,占69.58％.雌象和雄象的刻板行为的发生频次和持续时间均是下午(12:00～17:00)多于上午(9:00～11:00);刻板行为持续时间最长的时间段均是16:00～17:00,雌象和雄象的刻板行为发生频次和持续时间还存在个体差异性.     

A Generalized Approach for Estimating Effective Population Size from Temporal Changes in Allele Frequency

The temporal method for estimating effective population size (Ne) from the standardized variance in allele frequency change (F) is presented in a generalized form. Whereas previous treatments of this method have adopted rather limiting assumptions, the present analysis shows that the temporal method is generally applicable to a wide variety of organisms. Use of a revised model of gene sampling permits a more generalized interpretation of Ne than that used by some other authors studying this method. It is shown that two sampling plans (individuals for genetic analysis taken before or after reproduction) whose differences have been stressed by previous authors can be treated in a uniform way. Computer simulations using a wide variety of initial conditions show that different formulas for computing F have much less effect on Ne than do sample size (S), number of generations between samples (t), or the number of loci studied (L). Simulation results also indicate that (1) bias of F is small unless alleles with very low frequency are used; (2) precision is typically increased by about the same amount with a doubling of S, t, or L; (3) confidence intervals for Ne computed using a chi 2 approximation are accurate and unbiased under most conditions; (4) the temporal method is best suited for use with organisms having high juvenile mortality and, perhaps, a limited effective population size.     

Exposure of Asian Elephants and Other Exotic Ungulates to Schmallenberg Virus

Schmallenberg virus (SBV) is an emerging Orthobunyavirus, first described in 2011 in cattle in Germany and subsequently spread throughout Europe, affecting mainly ruminant livestock through the induction of foetal malformations. To gain a better understanding of the spectrum of susceptible species and to assess the value of current SBV serological assays, screening of serum samples from exotic artiodactyls and perissodactyls collected at the Living Collections from the Zoological Society of London (Whipsnade and London Zoos) and Chester Zoo was carried out. There was compelling evidence of SBV infection in both zoological collections. The competitive ELISA has proved to be applicable for the detection of SBV in exotic Bovidae, Cervidae, Suidae, Giraffidae and most notably in endangered Asian elephants (Elephas maximus), but unreliable for the screening of Camelidae, for which the plaque reduction neutralisation test was considered the assay of choice.     

Some Statistical Improvements for Estimating Population Size and Mutation Rate from Segregating Sites in DNA Sequences

In population genetics, under a neutral Wright-Fisher model, the scaling parameter straight theta=4Nmu represents twice the average number of new mutants per generation. The effective population size is N and mu is the mutation rate per sequence per generation. Watterson proposed a consistent estimator of this parameter based on the number of segregating sites in a sample of nucleotide sequences. We study the distribution of the Watterson estimator. Enlarging the size of the sample, we asymptotically set a Central Limit Theorem for the Watterson estimator. This exhibits asymptotic normality with a slow rate of convergence. We then prove the asymptotic efficiency of this estimator. In the second part, we illustrate the slow rate of convergence found in the Central Limit Theorem. To this end, by studying the confidence intervals, we show that the asymptotic Gaussian distribution is not a good approximation for the Watterson estimator.     

Development of a Model For Estimating the Size and Dynamics of the Pet Dog Population

Abstract

A conceptual model was developed to describe the dynamics of the pet dog population. The model synthesizes existing data collected for a variety of purposes to estimate the size of the various components of the pet dog population in Washington and Iowa during 1991. The total population mortality rate was estimated as 12.4% per year. Animal shelters in Washington and Iowa handled 7.6% and euthanized 4.0% of the dog population in those two states. When these estimates were extrapolated to the entire U.S. dog population, the model predicted that the total annual turnover in owned dogs was 14.7%, or 7.71 million dogs, that 4 million dogs were handled by animal shelters, and that 2.1 million were euthanized. It was also estimated that 79% of all female dogs were spayed, that household breeding could be attributed to less than one-fifth (18.7%) of the female dogs in the reproductive pool, and that the number of owners contributing to total dog population turnover through failure to retain their dog (103,453) was approximately three times the number of owners who allowed their female dogs to be bred (32,513).     

四川小寨子沟国家级自然保护区绿尾虹雉种群密度调查与栖息地评价

2015年6—8月和2016年3—8月,在四川小寨子沟国家级自然保护区及周边地区,采用绝对密度调查法,对繁殖期绿尾虹雉Lophophorus lhuysii的密度进行了调查,并基于Max Ent对繁殖期绿尾虹雉的栖息地质量进行了评价。结果显示:在保护区及其周边区域内,绿尾虹雉繁殖期常活动于海拔3 500~4 100 m靠近阳坡的草甸、灌丛生境。在整个评价区域内适宜栖息地120.05 km~2,次适宜栖息地141.67 km~2;在保护区内繁殖期绿尾虹雉的平均密度为4.99只/km~2,适宜栖息地49.17 km~2,次适宜栖息地48.27 km~2,推测其种群数量为245只。放牧、资源采集等人类活动是影响绿尾虹雉种群密度的主要因子,因此在本区域的保护区网络间需要加强对人类活动的控制,限制放牧活动,以保护高海拔区域的生物多样性。     

The Importance of Biologically Relevant Microclimates in Habitat Suitability Assessments

Predicting habitat suitability under climate change is vital to conserving biodiversity. However, current species distribution models rely on coarse scale climate data, whereas fine scale microclimate data may be necessary to assess habitat suitability and generate predictive models. Here, we evaluate disparities between temperature data at the coarse scale from weather stations versus fine-scale data measured in microhabitats required for a climate-sensitive mammal, the American pika (Ochotona princeps). We collected two years of temperature data in occupied talus habitats predicted to be suitable (high elevation) and unsuitable (low elevation) by the bioclimatic envelope approach. At low elevations, talus surface and interstitial microclimates drastically differed from ambient temperatures measured on-site and at a nearby weather station. Interstitial talus temperatures were frequently decoupled from high ambient temperatures, resulting in instantaneous disparities of over 30°C between these two measurements. Microhabitat temperatures were also highly heterogeneous, such that temperature measurements within the same patch of talus were not more correlated than measurements at distant patches. An experimental manipulation revealed that vegetation cover may cool the talus surface by up to 10°C during the summer, which may contribute to this spatial heterogeneity. Finally, low elevation microclimates were milder and less variable than typical alpine habitat, suggesting that, counter to species distribution model predictions, these seemingly unsuitable habitats may actually be better refugia for this species under climate change. These results highlight the importance of fine-scale microhabitat data in habitat assessments and underscore the notion that some critical refugia may be counterintuitive.     

Estimating Effective Population Size from Linkage Disequilibrium between Unlinked Loci: Theory and Application to Fruit Fly Outbreak Populations

There is a substantial literature on the use of linkage disequilibrium (LD) to estimate effective population size using unlinked loci. The estimates are extremely sensitive to the sampling process, and there is currently no theory to cope with the possible biases. We derive formulae for the analysis of idealised populations mating at random with multi-allelic (microsatellite) loci. The ‘Burrows composite index’ is introduced in a novel way with a ‘composite haplotype table’. We show that in a sample of diploid size , the mean value of or from the composite haplotype table is biased by a factor of , rather than the usual factor for a conventional haplotype table. But analysis of population data using these formulae leads to estimates that are unrealistically low. We provide theory and simulation to show that this bias towards low estimates is due to null alleles, and introduce a randomised permutation correction to compensate for the bias. We also consider the effect of introducing a within-locus disequilibrium factor to , and find that this factor leads to a bias in the estimate. However this bias can be overcome using the same randomised permutation correction, to yield an altered with lower variance than the original , and one that is also insensitive to null alleles. The resulting formulae are used to provide estimates on 40 samples of the Queensland fruit fly, Bactrocera tryoni, from populations with widely divergent expectations. Linkage relationships are known for most of the microsatellite loci in this species. We find that there is little difference in the estimated values from using known unlinked loci as compared to using all loci, which is important for conservation studies where linkage relationships are unknown.     

Comparing Habitat Suitability and Connectivity Modeling Methods for Conserving Pronghorn Migrations

Terrestrial long-distance migrations are declining globally: in North America, nearly 75% have been lost. Yet there has been limited research comparing habitat suitability and connectivity models to identify migration corridors across increasingly fragmented landscapes. Here we use pronghorn (Antilocapra americana) migrations in prairie habitat to compare two types of models that identify habitat suitability: maximum entropy (Maxent) and expert-based (Analytic Hierarchy Process). We used distance to wells, distance to water, NDVI, land cover, distance to roads, terrain shape and fence presence to parameterize the models. We then used the output of these models as cost surfaces to compare two common connectivity models, least-cost modeling (LCM) and circuit theory. Using pronghorn movement data from spring and fall migrations, we identified potential migration corridors by combining each habitat suitability model with each connectivity model. The best performing model combination was Maxent with LCM corridors across both seasons. Maxent out-performed expert-based habitat suitability models for both spring and fall migrations. However, expert-based corridors can perform relatively well and are a cost-effective alternative if species location data are unavailable. Corridors created using LCM out-performed circuit theory, as measured by the number of pronghorn GPS locations present within the corridors. We suggest the use of a tiered approach using different corridor widths for prioritizing conservation and mitigation actions, such as fence removal or conservation easements.