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.     

Suitability Modeling of Lake Sturgeon Habitat in Five Northern Lake Michigan Tributaries: Implications for Population Rehabilitation

The availability of lotic spawning, staging, and nursery habitats is considered a major factor limiting the recovery of Lake sturgeon ( Acipenser fulvescens ) in Lake Michigan. Despite efforts to better understand the population biology and habitat use of remnant Lake sturgeon stocks, little information exists on the quantity, quality, and spatial distribution of habitats for riverine life stages. We applied georeferenced habitat information on substrate, water depth, and stream gradient to a Lake sturgeon habitat suitability index in a geographic information system to produce spatially explicit models of life stage–specific habitat characteristics in the Menominee River, Michigan–Wisconsin; the Peshtigo, Oconto, and lower Fox rivers, Wisconsin; and the Manistique River, Michigan. High-quality Lake sturgeon spawning habitat associated with coarse substrates (≥2.1 mm) and moderate- to high-stream gradients (≥0.6 m/km) comprised 1–6% of the available habitat in each system. Staging habitat characterized by water depths greater that 2 m located near potential spawning habitat comprised an additional 17–41%. However, access to a majority of these habitat types (range 30–100%) by Lake sturgeon from Lake Michigan is currently impeded by dams. High-quality juvenile Lake sturgeon habitat associated with finer substrates, lower stream gradients, and a broad range of water depths (i.e., 0.5–8 m) was relatively ubiquitous throughout each system and comprised 69–100% of the available habitat. Our study suggests that efforts to rehabilitate Lake sturgeon populations should consider providing fish passage and creating supplemental spawning habitat to increase reproductive and recruitment potential.     

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....     

新疆哈密山区天山马鹿种群数量和冬季生境选择

2010年12月至2011年2月,在新疆哈密山区,采用截线抽样法和遥感技术,对野生天山马鹿（Cervus elaphus songaricus）种群现状和冬季生境选择进行了研究。在不同区域和不同类型栖息地共布设了28条样线,样线总长度达60.1 km。其中,16条样线上发现马鹿共233头,调查区域平均种群密度（2.83±1.01）头/km²,种群数量（1 684.56±379.71）头,与1993年的调查结果相比有所上升。雌雄性比为2.24：1,幼体和亚成体总数多于成体和老体总数,种群数量呈增长趋势。根据野外考察GPS数据并解译天山马鹿分布生境2006秋季的LANDSAT TM/ETM+遥感影像,将生境要素分为山地针叶林、草甸、灌木丛、农田和戈壁5种类型,其中,草甸与山地针叶林为天山马鹿冬季适宜生境。     

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.     

Estimating Effective Population Size and Mutation Rate from Sequence Data Using Metropolis-Hastings Sampling

We present a new way to make a maximum likelihood estimate of the parameter 4N(e)μ (effective population size times mutation rate per site, or θ) based on a population sample of molecular sequences. We use a Metropolis-Hastings Markov chain Monte Carlo method to sample genealogies in proportion to the product of their likelihood with respect to the data and their prior probability with respect to a coalescent distribution. A specific value of θ must be chosen to generate the coalescent distribution, but the resulting trees can be used to evaluate the likelihood at other values of θ, generating a likelihood curve. This procedure concentrates sampling on those genealogies that contribute most of the likelihood, allowing estimation of meaningful likelihood curves based on relatively small samples. The method can potentially be extended to cases involving varying population size, recombination, and migration.     

甘肃省大熊猫数量及栖息地现状

20 0 0～ 2 0 0 3年的调查表明 ,甘肃省野生大熊猫 (Ailuropodmelanoleuca)现有 1 1 7只 ,分布在文县 1 0 3只、迭部县 1 1只、舟曲县 1只和武都县 2只。栖息地呈互不相连的 5块 ,总面积 1 82 7 .3 5km2 ,其中白水江保护区 1 1 65 .1 6km2 、迭部县 5 1 8. 91km2 ,为 2块面积较大的稳定栖息地 ,其余 3块为面积很小、不稳定的栖息地。     

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.     

利用微卫星研究普洱亚洲象种群的遗传多样性

本文采用非损伤性取样法获得普洱地区亚洲象粪便样品113份,试剂盒法提取粪便基因组总DNA,利用9对微卫星引物对DNA进行特异性扩增,CERVUS 3.0软件基因分型得到49个独特的基因型。利用GenAlEx v6.5与Arlequin v3.5进行位点遗传信息检测和种群遗传多样性分析,结果表明：研究采用的所有微卫星位点均未偏离哈迪温伯格平衡,位点的平均等位基因数为3.111,平均香农信息指数为0.804,平均期望杂合度为0.468,平均观测杂合度为0.476。比较相同位点上不同地区亚洲象的遗传杂合度,表明普洱地区亚洲象的种群遗传多样性较低。     

Effects of Small Habitat Size and Isolation on the Population Structure of Common Wetland Species

Abstract: Habitat fragmentation may cause plant species to suffer from inbreeding and genetic drift, which affects population viability negatively. Less viable populations may contain an altered population structure, i.e., they have a smaller proportion of seedlings and a larger proportion of vegetative adults, when compared to large extensive populations. We applied a hierarchical-spatial field design, consisting of large habitat islands with surrounding near and distant small habitat islands to distinguish between the two components of habitat fragmentation, i.e., the effect of small habitat size and the effect of isolation. We studied two common habitat-specific species: Carex davalliana (Cyperaceae) and Succisa pratensis (Dipsacaceae). We identified a decrease in the proportion of C. davalliana seedlings and an increase in the proportion of vegetative tillers in response to isolation. In S. pratensis, we identified a decrease in the proportion of seedlings and an increase in the proportion of vegetative rosettes that were attributable to small habitat size. Hence, we confirmed alterations in the population structure of those common species, although both species were affected by a different component of habitat fragmentation. The observed discrepancy between species could be related their life history. We conclude that habitat fragmentation adversely affects not only rare but also common species. Their loss of viability can inevitably lead to alterations in vegetation structure and consequently lead to the further loss of this species-rich and threatened ecosystem type.     

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.