Shared spatial effects on quantitative genetic parameters: accounting for spatial autocorrelation and home range overlap reduces estimates of heritability in wild red deer

Social structure, limited dispersal, and spatial heterogeneity in resources are ubiquitous in wild vertebrate populations. As a result, relatives share environments as well as genes, and environmental and genetic sources of similarity between individuals are potentially confounded. Quantitative genetic studies in the wild therefore typically account for easily captured shared environmental effects (e.g., parent, nest, or region). Fine-scale spatial effects are likely to be just as important in wild vertebrates, but have been largely ignored. We used data from wild red deer to build "animal models" to estimate additive genetic variance and heritability in four female traits (spring and rut home range size, offspring birth weight, and lifetime breeding success). We then, separately, incorporated spatial autocorrelation and a matrix of home range overlap into these models to estimate the effect of location or shared habitat on phenotypic variation. These terms explained a substantial amount of variation in all traits and their inclusion resulted in reductions in heritability estimates, up to an order of magnitude up for home range size. Our results highlight the potential of multiple covariance matrices to dissect environmental, social, and genetic contributions to phenotypic variation, and the importance of considering fine-scale spatial processes in quantitative genetic studies.     

Bachman's Sparrows at the northern periphery of their range: home range size and microhabitat selection

Populations of Bachman's Sparrows (Peucaea aestivalis) have declined range‐wide since the late 1960s. Populations at the periphery of their range have exhibited some of the steepest declines, and these sparrows are now rare or extirpated over much of the northern extent of their historical range. To better understand the spatial ecology of Bachman's Sparrows in this region of decline, we examined microhabitat selection and determined the home range sizes of radio‐tagged male Bachman's Sparrows (N = 37) in the Coastal Plain of North Carolina in 2014 and 2015. From April to July, we located males 1–2 times daily for 5–6 d per week. We measured vegetation structure in home ranges using 5‐m‐radius plots centered on a subset of 10 randomly selected telemetry locations as well as in available unused locations 50 m and in a random direction from each telemetry location. Mean size of home ranges (7.9 ha) was larger than estimates reported in most previous studies, with differences among studies possibly due, at least in part, to differences in the characteristics of habitats where studies were conducted. The home ranges of Bachman's Sparrows in our study had greater densities of woody and dead vegetation than unused areas. Although generally considered detrimental to the presence of Bachman's Sparrows, the presence of some woody vegetation in frequently burned (i.e., ≤ 3‐yr return interval) longleaf pine (Pinus palustris) communities like those in our study may be important in providing song perches for males and cover from attacking predators. Bachman's Sparrows in our study showed clear selection for several vegetation characteristics linked to frequent fire. Management strategies that approximate historical fire regimes in longleaf pine ecosystems should continue to be promoted as essential tools for the conservation of Bachman's Sparrows.     

Kernel density estimates of alongshore home range of Hector's dolphins at Banks Peninsula, New Zealand

Knowledge about home ranges is essential for understanding the resources required by a species, identifying critical habitats, and revealing the overlap with anthropogenic impacts. Ranging behavior of Hector's dolphins ( Cephalorhynchus hectori ) was studied via coastal photo-ID surveys in the Banks Peninsula Marine Mammal Sanctuary (BPMMS) between 1985 and 2006. Univariate kernel density estimates of alongshore home range were calculated for 20 individuals with 15 sightings or more. For each individual, sighting locations were transformed into a univariate data set by projecting sightings onto a line drawn 1 km from the coast and measuring the distance along this line relative to an origin. Sightings were weighted by survey effort. Ninety-five percent ( K ₉₅) of the density estimate was used as a measure of alongshore home range, and 50% of the estimate ( K ₅₀) was used to reveal core portions of coastline where dolphins concentrated their activity. The mean estimates of K ₉₅ and K ₅₀ were 49.69 km (SE = 5.29) and 17.13 km (SE = 1.89), respectively. Four distinct hubs were apparent where the core areas of different individuals coincided. Three of the dolphins' alongshore ranges extended beyond the current northern boundary of the BPMMS, raising fresh concerns that the sanctuary is not large enough. Proposed changes to gill netting regulations, if enacted, will result in the alongshore ranges of all the dolphins in our study being protected.     

The home range of the Sonso community of chimpanzees from the Budongo Forest, Uganda

Early studies of chimpanzees in the Budongo Forest, Uganda, reported only rough estimates for home range size. This study aimed to quantify home range size and habitat composition for chimpanzees of the Sonso community in this forest. Home range is the habitually used portion of the total area over which an animal travels, and for chimpanzees the home range is shared by the community. From data collected in 1994 and 1995, the home range for this community was estimated to cover an area of 6.78 km² using the minimum convex polygon analysis technique and 6.89 km² using fixed kernel analysis. Habitat was highly heterogeneous. The small home range and consequent high local population density (approximately 6.8 individuals km^?1) suggests that the Sonso region is highly productive in chimpanzee foods, possibly in contrast to other parts of the forest. This estimate of home range size is among the smallest reported for habituated chimpanzees, but comparisons with other sites are confounded by methodological and analytical differences. Future studies of chimpanzee ranging patterns should endeavour to use precise locations and the latest analytical techniques to ensure accurate estimation of range size and structure, and intersite comparability.     

家域研究进展

家域是动物行为学和保护生物学的重要概念之一,它在动物对资源环境的适应与选择,种群密度及社会关系等生态学过程研究中有着重要的作用.对家域的内涵、特征、估算方法(包括取样方法,样本含量,位点数据自相关,模型评价等)等方面进行阐述,总结了家域估算模型的发展过程及发展方向,评述了3种主要家域估算模型的优势与不足,并结合最新的理论和应用,对未来的研究方向提出建议.     

Bayesian nonparametric quantile process regression and estimation of marginal quantile effects

Flexible estimation of multiple conditional quantiles is of interest in numerous applications, such as studying the effect of pregnancy-related factors on low and high birth weight. We propose a Bayesian nonparametric method to simultaneously estimate noncrossing, nonlinear quantile curves. We expand the conditional distribution function of the response in I-spline basis functions where the covariate-dependent coefficients are modeled using neural networks. By leveraging the approximation power of splines and neural networks, our model can approximate any continuous quantile function. Compared to existing models, our model estimates all rather than a finite subset of quantiles, scales well to high dimensions, and accounts for estimation uncertainty. While the model is arbitrarily flexible, interpretable marginal quantile effects are estimated using accumulative local effect plots and variable importance measures. A simulation study shows that our model can better recover quantiles of the response distribution when the data are sparse, and an analysis of birth weight data is presented.     

Temporal-method estimates of Ne from highly polymorphic loci

The temporal method is used widely to estimategenetic effective population size (N _e), a parameter of fundamental interestto studies of evolutionary and conservationbiology. The statistical properties oftemporal-method estimates have not beenexplored for highly polymorphic DNA markersthat often contain many alleles occurring invery low frequencies. We used a Monte Carlosimulation approach to assess accuracy andprecision of the temporal method whenimplemented with haplotypic/allelic data atmitochondrial (mt)DNA and nuclear-encodedmicrosatellite DNA loci. Estimates of N _e were between 2%–106% greater thantheir true values in 48 simulationsparameterized using different demographicscenarios, models of mutation, and samplesizes. Overestimation of N _e resultsfrom a bias in the approximation used by Waples(1989) to derive the relationship between theexpected temporal variance (F) and N _e when allele frequencies are very closeto 0 or 1. Our results show that one commonlyapplied solution to this problem, binning oflow-frequency alleles, results in a trade-offof accuracy and precision in some cases. Weshow that both chi-square and normalapproximations are appropriate for estimating95% confidence intervals of N _e andwe develop a power analysis based on thechi-square distribution to estimate samplesizes and allelic diversity required toevaluate specific hypotheses. For highlypolymorphic loci like mtDNA andmicrosatellites, the increased precisionafforded by the presence of rare allelesoutweighs the upward bias in temporal-methodestimates of N _e.     

Simulations on the Primitive Electrolyte Environment of a High Charge-density Polyelectrolyte. A Sampling Problem and its Solution

Abstract

We show that the classical Metropolis Monte Carlo (MMC) algorithm converges very slowly when applied to the primitive electrolyte environment for a high charge-density polyelectrolyte. This slowness of convergence, which is due to the large density inhomogeneity around the polyelectrolyte, produces noticeable errors in the ion distribution functions for MMC runs of 1.3 × 10⁶ trial steps started from nonequilibrium distributions. We report that an algorithm which we call DSMC (for density-scaled Monte Carlo) overcomes this problem and provides relatively rapid convergence in this application. We suggest that DSMC should be well-suited for other Monte Carlo simulations on physical systems where large density inhomogeneities occur.     

Choice of analytical method can have dramatic effects on primate home range estimates

Primate home range sizes can vary tremendously as a consequence of the analytical technique chosen to estimate home range. This is exemplified by a recent dataset on free ranging snub-nosed monkeys (Rhinopithecus bieti) in Northwest Yunnan, China. Our findings show that the grid cell method cannot substitute for the minimum convex polygon (MCP) method and vice versa. MCP-based estimates are far too large, especially when the form of the home range is irregular due to forays into peripheral areas. Here, we propose an adjusted polygon method, whereby unsuitable and never visited areas are clipped out from the polygon, thus producing more accurate results. Compared to the grid cell method, the adjusted MCP is much more robust when the number of group relocations is limited; MCP turned out to be the method of choice for calculation of monthly and seasonal home ranges. The grid cell method on the other hand yielded the most precise estimates for total or annual home ranges. The style of ranging exhibited by a given primate taxon or population determines which analytical procedures should be applied to estimate home range size, and we would stress the need for thorough evaluation of the pros and cons of home range estimators before conducting field work and analysing data.     

Adsorption into the MFI zeolite of aromatic molecule of biological relevance. Investigations by Monte Carlo simulations

Adsorption of paracresol and water into the silicalite-1 (MFI) zeolite has been investigated using canonical and grand-canonical Monte Carlo simulations. The most stable sites of adsorption of paracresol are found to be located at the channel intersections. Grand-canonical simulations have shown that at low loading, water molecules adsorb preferably at the vicinity of paracresol molecules, whereas they are also located in the sinusoidal channels as the loading increases. In order to explain the experimental adsorption isotherm observed for the coadsorption of water and paracresol in the MFI zeolite we propose a new concept of apparent adsorption enthalpy that varies with the concentration of the solution. The mathematical expression for the apparent enthalpy is introduced in an adsorption isotherm model. We shall refer to this theoretical isotherm as a non-langmuirian isotherm. The non-linear expression for the apparent adsorption enthalpy accounts for a variable accessibility of the sites of adsorption with respect to the concentration of the solution. Figure Co-adsorption of paracresol and water in silicalite-1 zeolite and comparison between experimental and modelled adsorption isotherms.     

A density estimation model of plateau pika (Ochotona curzoniae) supporting camera‐monitoring programs

As an important species in the Qinghai‐Tibet Plateau, the roles played by plateau pikas in grassland degradation and protection are controversial. The behavior characteristics and population density of this species are important in answering this question, but these traits have not been fully elucidated to date. Camera‐capture methods have been used widely in recent years to characterize or calculate population density with the advantage of simple operation and nonintrusive investigation. However, establishing the relationship between actual population density and monitoring data with the condition that individual identification is not possible is a major challenge for this method. In this study, a model composed of a behavioral module and a burrow system module is proposed and applied to simulate the moving path of each individual pika. Based on Monte Carlo method, the model is used to develop the relationship between population density and recorded capture number, which is compared with the results derived from the random encounter model (REM) based on field observations. The simulated results mixed with the calculated density based on observation data could reach R ² = 0.98 using linear fitting, with proper parameter settings. A novel index named activity intensity of pikas per population density is also proposed, providing information on both the ecological physical characteristics and monitoring space. The influence of different parameters on this index, mainly the pika number per burrow system, pika activity time outside the burrow, and activity intensity, is discussed. The proposed methodology can be applied to different scenarios in further studies when behavioral characteristics of pikas change for such reasons as climate change and vegetation degradation.     

固定核空间法和最小凸多边形法估计藏狐家域的比较

最小凸多边形法(MCP)和固定核空间法(FKE)是目前最常用的家域计算方法,但受空间自相关性、偏远位点等问题的影响,两种方法均存在明显的局限性。本文根据2006 年和2007 年在四川省石渠县和青海省都兰县的7 只藏狐352 个活动位点数据,分析MCP 和FKE 家域估计的效果和存在的问题。结果显示:(1)利用概率百分比≤95% 时,MCP 计算结果和FKE 没有显著差异;(2)极端点对高百分比(85% ～ 100% ) 下MCP影响显著,而FKE 对极端点影响控制较好;(3)FKE 家域外形复杂,计算结果受平滑度系数设置影响显著。因此,研究领域行为时,应同时使用FKE 和95% MCP 两种方法。当数据分布较理想时,FKE 能够给出更为准确的面积估计,而MCP 则因其通用性,使得研究数据与其他研究的结果更具可比性。
     

Population densities and home range sizes of the Chestnut Wood-quail

ABSTRACT.   We present the first report of population density and home range estimates for the Chestnut Wood-quail ( Odontophorus hyperythrus ), an endemic and nearly threatened species of the Colombian Andes. Density estimates were obtained using playbacks and spot mapping and point transect methods. Home range sizes were estimated by radio tracking five wood-quail. Estimated densities varied from 0.3 to 0.4 groups per hectare. These densities are similar to those reported for other mountain wood-quail, but higher than those for lowland wood-quail and other species in the family Odontophoridae. Estimates of home range size varied from 2.6 to 9.0 hectares per group, and seemed to be correlated with group size. We also found evidence of overlap in the home ranges of neighboring groups. Population densities may vary with factors such as habitat type, but our estimates allow a first approximation of the population sizes of Chestnut Wood-quail in forest fragments.     

Application of GPS occurrence data to understand African white‐backed vultures Gyps africanus spatial home range overlaps

Understanding key overlap zones and habitats which are intensively shared by species in space and time is crucial as it provides vital information to inform spatial conservation with maximum benefits. The advent of high‐resolution GPS technologies associated with new analytical algorithms is revolutionizing studies underpinning species spatial and social interaction patterns within ecosystems. Here, using a robust home range estimation algorithm, the autocorrelated kernel density estimator (AKDE) equipped with an equally powerful home range overlap metric, the Bhattacharyya''s coefficient (BC), we provide one of the first attempts to estimate and delineate spatial home range overlap zones for critically endangered African white‐backed vultures to inform conservation planning. Six vultures were captured in Hwange National Park using a modified cannon net system after which they were tagged and tracked with high‐resolution GPS backpacks. Overall, results suggested weaker average home range overlaps based on both the pooled data (0.38 ± 0.26), wet non‐breeding seasonal data (0.32 ± 0.23), and dry breeding season data (0.34 ± 0.28). Vultures 4, 5, and 6 consistently revealed higher home range overlaps across all the scales with values ranging between 0.60 and 0.99. Individual vultures showed consistence in space use patterns as suggested by high between‐season home range overlaps, an indication that they may be largely resident within the Hwange ecosystem. Importantly, we also demonstrate that home range overlapping geographic zones are all concentrated within the protected area of Hwange National Park. Our study provides some of the first results on African vulture home range overlaps and segregation patterns in the savanna ecosystem based on unbiased telemetry data and rigorous analytical algorithms. Such knowledge may provide vital insights for prioritizing conservation efforts of key geographic overlap zones to derive maximum conservation benefits especially when targeting wide‐ranging and critically endangered African white‐backed vultures. To this end, spatial overlap zones estimated here, although based on a small sample size, could provide a strong foundation upon which other downstream social and ecological questions can be explored further to expand our understanding on shared space use mechanisms among African vulture species.     

两种核域估算方法在野生藏狐家域研究中的比较

核域是野生动物重点利用、含有更多居所、隐蔽场所及依赖性食物资源的区域。关于核域的确定和划分一直存在争议,且很难找到客观的并能准确展示动物生物学信息的数理统计方法。2006 年4 月,2006 年9 ～10月和2007 年1 ～4 月,我们共记录青海省都兰县沟里乡3 只藏狐的199 个活动位点,通过固定核空间(Fixed kernel)和调和平均值(Harmonic mean)模型,结合独立区域法的计算原理,估算藏狐的核域,并对两种估算方法进行比较分析,以确定更理想的核域数学模型。研究结果表明:(1)两种估算方法中核域面积均受到家域总面积的影响,固定核空间法的核域面积受家域总面积影响较大,而且变量系数不稳定; (2) 随着样本量的增加,固定核空间法估算的核域面积逐渐减小,而调和平均值法则增大,前者从数理统计上更好地描述了藏狐对家域资源的利用分布,后者更符合客观实际;(3)调和平均值法在划定家域边界时容易包括不属于家域范围的区域,而在估算核域时可以在一定程度上克服该缺陷;(4)调和平均值法能够真实地反应动物的活动中心,估算的核域中包含有更多的活动位点。因此,尽管在估算藏狐核域时固定核空间法有稳定的计算结果等优点,调和平均值法为更理想的核域估算模型。     

呼中林区森林景观的历史变域模拟及评价

在大兴安岭地区呼中区,将物种的年龄和分布信息进行随机化处理后,应用空间直观景观模型LANDIS对森林景观进行长时间(2500a)模拟,取物种演替稳定时间段作为模拟历史变域的数据来源.分别在景观水平和年龄类型水平上利用景观指数空间分析、主成分分析和核密度估计方法分析景观格局历史变域的模拟结果,并在二维空间坐标内,将研究区1990年、2000年森林景观特征与之比较.结果表明,各树种面积比例在模拟900a后都达到稳定状态,可作为无干扰条件下森林景观特征的历史变域;由于长期采伐,研究区1990年景观的斑块面积和破碎化程度都偏离了该历史变域,其中,过熟林偏离最明显,其斑块面积远小于历史变域,破碎化程度非常严重;虽然1990年后的采伐管理方案比之前的更为合理,但2000年的森林景观仍旧继续偏离历史变域.     

On computational efficiency of the hybrid Monte Carlo method applied to the multicanonical ensemble

Abstract

In the present paper, computational efficiency of the hybrid Monte Carlo (HMC) method applied to the multicanonical ensemble is studied; the HMC is an equation of motion guided Monte Carlo method. As in the standard HMC for the canonical ensemble, the multicanonical HMC calculations with high acceptance ratio show better efficiency; about 60% acceptance yields the best performance for the system examined.     

Bayesian Estimation of Positively Selected Sites

In protein-coding DNA sequences, historical patterns of selection can be inferred from amino acid substitution patterns. High relative rates of nonsynonymous to synonymous changes (=d _N /d _S ) are a clear indicator of positive, or directional, selection, and several recently developed methods attempt to distinguish these sites from those under neutral or purifying selection. One method uses an empirical Bayesian framework that accounts for varying selective pressures across sites while conditioning on the parameters of the model of DNA evolution and on the phylogenetic history. We describe a method that identifies sites under diversifying selection using a fully Bayesian framework. Similar to earlier work, the method presented here allows the rate of nonsynonymous to synonymous changes to vary among sites. The significant difference in using a fully Bayesian approach lies in our ability to account for uncertainty in parameters including the tree topology, branch lengths, and the codon model of DNA substitution. We demonstrate the utility of the fully Bayesian approach by applying our method to a data set of the vertebrate -globin gene. Compared to a previous analysis of this data set, the hierarchical model found most of the same sites to be in the positive selection class, but with a few striking exceptions.