Poor environmental tracking can make extinction risk insensitive to the colour of environmental noise

The relative importance of environmental colour for extinction risk compared with other aspects of environmental noise (mean and interannual variability) is poorly understood. Such knowledge is currently relevant, as climate change can cause the mean, variability and temporal autocorrelation of environmental variables to change. Here, we predict that the extinction risk of a shorebird population increases with the colour of a key environmental variable: winter temperature. However, the effect is weak compared with the impact of changes in the mean and interannual variability of temperature. Extinction risk was largely insensitive to noise colour, because demographic rates are poor in tracking the colour of the environment. We show that three mechanisms-which probably act in many species-can cause poor environmental tracking: (i) demographic rates that depend nonlinearly on environmental variables filter the noise colour, (ii) demographic rates typically depend on several environmental signals that do not change colour synchronously, and (iii) demographic stochasticity whitens the colour of demographic rates at low population size. We argue that the common practice of assuming perfect environmental tracking may result in overemphasizing the importance of noise colour for extinction risk. Consequently, ignoring environmental autocorrelation in population viability analysis could be less problematic than generally thought.     

Identification of the substrate specificity-conferring amino acid residues of 4-coumarate:coenzyme A ligase allows the rational design of mutant enzymes with new catalytic properties

4-Coumarate:coenzyme A ligases (4CLs) generally use, in addition to coumarate, caffeate and ferulate as their main substrates. However, the recently cloned Arabidopsis thaliana isoform At4CL2 is exceptional because it has no appreciable activity with ferulate. On the basis of information obtained from the crystal structure of the phenylalanine-activating domain of gramicidin S-synthetase, 10 amino acid residues were identified that may form the substrate binding pocket of 4CL. Among these amino acids, representing the putative "substrate specificity motif," only one residue, Met(293), was not conserved in At4CL2, compared with At4CL1 and At4CL3, two isoforms using ferulate. Substitution of Met(293) or Lys(320), another residue of the putative substrate specificity motif, which in the predicted three-dimensional structure is located in close proximity to Met(293), by smaller amino acids converted At4CL2 to an enzyme capable of using ferulate. The activity with caffeate was not or only moderately affected. Conversely, substitution of Met(293) by bulky aromatic amino acids increased the apparent affinity (K(m)) for caffeate up to 10-fold, whereas single substitutions of Val(294) did not affect substrate use. The results support our structural assumptions and suggest that the amino acid residues 293 and 320 of At4CL2 directly interact with the 3-methoxy group of the phenolic substrate and therefore allow a first insight into the structural principles determining substrate specificity of 4CL.     

Inferences on the population structure and colonization process of the invasive oriental fruit fly, Bactrocera dorsalis (Hendel)

The phytophagous insects of the Tephritidae family offer different case histories of successful invasions. An example is Bactrocera dorsalis sensu stricto, the oriental fruit fly which has been recognized as a key pest of Asia and the Pacific. It is known to have the potential to establish adventive populations in various tropical and subtropical areas. Despite the economic risk associated with a putative stable presence of this fly, the genetic aspects of its invasion process have remained relatively unexplored. Using microsatellite markers we have investigated the population structure and genetic variability in 14 geographical populations across the four areas of the actual species range: Far East Asia, South Asia, Southeast Asia and the Pacific Area. Results of clustering and admixture, associated with phylogenetic and migration analyses, were used to evaluate the changes in population genetic structure that this species underwent during its invasion process and establishment in the different areas. The colonization process of this fly is associated with a relatively stable population demographic structure, especially in an unfragmented habitat, rich in intensive cultivation such as in Southeast Asia. In this area, the results suggest a lively demographic history, characterized by evolutionary recent demographic expansions and no recent bottlenecks. Cases of genetic isolation attributable to geographical factors, fragmented habitats and/or fruit trade restrictions were observed in Bangladesh, Myanmar and Hawaii. Regarding the pattern of invasion, the overall genetic profile of the considered populations suggests a western orientated migration route from China to the West.     

Is optimal gene order impossible?

Recent evidence suggests that yeast genes encoding proteins that are present in the same protein complex tend to be linked and to be co-expressed. More generally, we found that genes that are close to each other in the protein interaction network tend to be linked more often than expected and are often co-expressed. Unexpectedly, we found that linked genes in network proximity have unusually high recombination rates. Because high recombination rates are associated with high rates of genome re-organization, our findings might explain why the clustering of genes in proximity in the network is such a weak effect: there could be a co-evolutionary cycle of physical linkage for co-expression, upwards modification of the recombination rate and concomitant break-up of a cluster. Under such a model an "optimal" gene order is never stable.     

Constrained clusters of gene expression profiles with pathological features

MOTIVATION: Gene expression profiles should be useful in distinguishing variations in disease, since they reflect accurately the status of cells. The primary clustering of gene expression reveals the genotypes that are responsible for the proximity of members within each cluster, while further clustering elucidates the pathological features of the individual members of each cluster. However, since the first clustering process and the second classification step, in which the features are associated with clusters, are performed independently, the initial set of clusters may omit genes that are associated with pathologically meaningful features. Therefore, it is important to devise a way of identifying gene expression clusters that are associated with pathological features. RESULTS: We present the novel technique of 'itemset constrained clustering' (IC-Clustering), which computes the optimal cluster that maximizes the interclass variance of gene expression between groups, which are divided according to the restriction that only divisions that can be expressed using common features are allowed. This constraint automatically labels each cluster with a set of pathological features which characterize that cluster. When applied to liver cancer datasets, IC-Clustering revealed informative gene expression clusters, which could be annotated with various pathological features, such as 'tumor' and 'man', or 'except tumor' and 'normal liver function'. In contrast, the k-means method overlooked these clusters.     

Risk factors for an outbreak of leptospirosis in California sea lions (Zalophus californianus) in California, 2004

Leptospirosis has been reported in California sea lions (Zalophus californianus) since 1970; however, the source of infection and mode of transmission remain unknown. To elucidate these features, demographic and environmental risk factors for leptospirosis were evaluated. California sea lion stranding records from northern California for 2004 were used to identify cases of leptospirosis (n = 316) and controls (n = 143). Demographic characteristics (age class, sex) and environmental factors, representing surrogates for exposure to dogs, cattle, rainfall, and freshwater sources, were compared between cases and controls with the use of a geographic information system (GIS) and logistic regression. Multivariate analyses revealed that summer and autumn seasons, juvenile age class, male sex, high dog-park density, and close proximity to dog parks were significantly associated with leptospirosis in sea lions, whereas county farmland cattle density, rainfall levels 30 days prior to stranding, human density, and proximity to freshwater sources were not associated. Thus, dogs and dog parks, or factors associated with them, might be further investigated to assess their relationship to leptospirosis in sea lions.     

The population genetic effects of ancestry and admixture in a subdivided cattle breed

The genetic structure of the Dexter, a minority cattle breed with complex demographic history, was investigated using microsatellite markers and a range of statistical approaches designed to detect both admixture and genetic drift. Modern representatives of two putative ancestral populations, the Devon and Kerry, together with the different populations of the Dexter, which have experienced different demographic histories, were analysed. Breed units showed comparatively high levels of genetic variability ( H _E = 0.63–0.68); however, distinct genetic subgroups were detected within the Dexter, which could be attributed to known demographic events. Much lower diversity was identified in three small, isolated Dexter populations ( H _E = 0.52–0.55) and higher differentiation ( F _ST > 0.13) was found. For one of these populations, where strong selection has taken place, we also found evidence of a demographic bottleneck. Three methods for quantifying breed admixture were applied and substantial method-based variation in estimates for the genetic contribution of the two proposed ancestral populations for each subdivision of the Dexter was found. Results were consistent only in the case of a group consisting of selected Traditional Dexter animals, where the ancestor of the modern Kerry breed was also determined as the greater parental contributor to the Dexter. The inconsistency of estimation of admixture proportions between the methods highlights the potentially confounding role of genetic drift in shaping small population structure, and the consequences of accurately describing population histories from contemporary genetic data.     

种群统计随机性和环境随机性对种群绝灭的影响

影响种群绝灭的随机干扰可分为种群统计随机性、环境随机性和随机灾害三大类。在相对稳定的环境条件下和相对较短的时间内,以前两类随机干扰对种群绝灭的影响为生态学家关注的焦点。但是,由于自然种群动态及其影响因子的复杂特征,进一步深入研究随机干扰对种群绝灭的作用在理论上和实践上都必须发展新的技术手段。本文回顾了种群统计随机性与环境随机性的概念起源与发展,系统阐述了其分析方法。归纳了两类随机性在种群绝灭研究中的应用范围、作用方式和特点的异同和区别方法。各类随机作用与种群动态之间关系的理论研究与对种群绝灭机理的实践研究紧密相关。根据理论模型模拟和自然种群实际分析两方面的研究现状,作者提出了进一步深入研究随机作用与种群非线性动态方法的策略。指出了随机干扰影响种群绝灭过程的研究的方向：更多的研究将从单纯的定性分析随机干扰对种群动力学简单性质的作用,转向结合特定的种群非线性动态特征和各类随机力作用特点具体分析绝灭极端动态的成因,以期做出精确的预测。     

Archaeology,demography and life history theory together can help us explain past and present population patterns

Population matters. Demographic patterns are both a cause and a consequence of human behaviour in other important domains, such as subsistence, cooperation, politics and culture. Demographers interested in contemporary and recent historical populations have rich data at their fingertips; the importance of demography means many interested parties have gathered demographic data, much of which is now readily available for all to explore. Those interested in the demography of the distant past are not so fortunate, given the lack of written records. Nevertheless, the emergence in recent years of a new interest in the demography of ancient populations has seen the development of a range of new methods for piecing together archaeological, skeletal and DNA evidence to reconstruct past population patterns. These efforts have found evidence in support of the view that the relatively low long-term population growth rates of prehistoric human populations, albeit ultimately conditioned by carrying capacities, may have been owing to ‘boom–bust’ cycles at the regional level; rapid population growth, followed by population decline. In fact, this archaeological research may have come to the same conclusion as some contemporary demographers: that demography can be remarkably hard to predict, at least in the short term. It also fits with evidence from biology that primates, and particularly humans, may be adapted to environmental variability, leading to associated demographic stochasticity. This evidence of the fluctuating nature of human demographic patterns may be of considerable significance in understanding our species'' evolution, and of understanding what our species future demographic trajectories might be.This article is part of the theme issue ‘Cross-disciplinary approaches to prehistoric demography’.     

A copula based topology preserving graph convolution network for clustering of single-cell RNA-seq data

Annotation of cells in single-cell clustering requires a homogeneous grouping of cell populations. There are various issues in single cell sequencing that effect homogeneous grouping (clustering) of cells, such as small amount of starting RNA, limited per-cell sequenced reads, cell-to-cell variability due to cell-cycle, cellular morphology, and variable reagent concentrations. Moreover, single cell data is susceptible to technical noise, which affects the quality of genes (or features) selected/extracted prior to clustering.Here we introduce sc-CGconv (copula based graph convolution network for single clustering), a stepwise robust unsupervised feature extraction and clustering approach that formulates and aggregates cell–cell relationships using copula correlation (Ccor), followed by a graph convolution network based clustering approach. sc-CGconv formulates a cell-cell graph using Ccor that is learned by a graph-based artificial intelligence model, graph convolution network. The learned representation (low dimensional embedding) is utilized for cell clustering. sc-CGconv features the following advantages. a. sc-CGconv works with substantially smaller sample sizes to identify homogeneous clusters. b. sc-CGconv can model the expression co-variability of a large number of genes, thereby outperforming state-of-the-art gene selection/extraction methods for clustering. c. sc-CGconv preserves the cell-to-cell variability within the selected gene set by constructing a cell-cell graph through copula correlation measure. d. sc-CGconv provides a topology-preserving embedding of cells in low dimensional space.     

Demographic consequences of climate change and land cover help explain a history of extirpations and range contraction in a declining snake species

Developing conservation strategies for threatened species increasingly requires understanding vulnerabilities to climate change, in terms of both demographic sensitivities to climatic and other environmental factors, and exposure to variability in those factors over time and space. We conducted a range‐wide, spatially explicit climate change vulnerability assessment for Eastern Massasauga (Sistrurus catenatus), a declining endemic species in a region showing strong environmental change. Using active season and winter adult survival estimates derived from 17 data sets throughout the species' range, we identified demographic sensitivities to winter drought, maximum precipitation during the summer, and the proportion of the surrounding landscape dominated by agricultural and urban land cover. Each of these factors was negatively associated with active season adult survival rates in binomial generalized linear models. We then used these relationships to back‐cast adult survival with dynamic climate variables from 1950 to 2008 using spatially explicit demographic models. Demographic models for 189 population locations predicted known extant and extirpated populations well (AUC = 0.75), and models based on climate and land cover variables were superior to models incorporating either of those effects independently. These results suggest that increasing frequencies and severities of extreme events, including drought and flooding, have been important drivers of the long‐term spatiotemporal variation in a demographic rate. We provide evidence that this variation reflects nonadaptive sensitivity to climatic stressors, which are contributing to long‐term demographic decline and range contraction for a species of high‐conservation concern. Range‐wide demographic modeling facilitated an understanding of spatial shifts in climatic suitability and exposure, allowing the identification of important climate refugia for a dispersal‐limited species. Climate change vulnerability assessment provides a framework for linking demographic and distributional dynamics to environmental change, and can thereby provide unique information for conservation planning and management.     

Evaluating the demographic buffering hypothesis with vital rates estimated for Weddell seals from 30 years of mark-recapture data

1. Life-history theory predicts that those vital rates that make larger contributions to population growth rate ought to be more strongly buffered against environmental variability than are those that are less important. Despite the importance of the theory for predicting demographic responses to changes in the environment, it is not yet known how pervasive demographic buffering is in animal populations because the validity of most existing studies has been called into question because of methodological deficiencies. 2. We tested for demographic buffering in the southern-most breeding mammal population in the world using data collected from 5558 known-age female Weddell seals over 30 years. We first estimated all vital rates simultaneously with mark-recapture analysis and then estimated process variance and covariance in those rates using a hierarchical Bayesian approach. We next calculated the population growth rate's sensitivity to changes in each of the vital rates and tested for evidence of demographic buffering by comparing properly scaled values of sensitivity and process variance in vital rates. 3. We found evidence of positive process covariance between vital rates, which indicates that all vital rates are affected in the same direction by changes in annual environment. Despite the positive correlations, we found strong evidence that demographic buffering occurred through reductions in variation in the vital rates to which population growth rate was most sensitive. Process variation in vital rates was inversely related to sensitivity measures such that variation was greatest in breeding probabilities, intermediate for survival rates of young animals and lowest for survival rates of older animals. 4. Our work contributes to a small but growing set of studies that have used rigorous methods on long-term, detailed data to investigate demographic responses to environmental variation. The information from these studies improves our understanding of life-history evolution in stochastic environments and provides useful information for predicting population responses to future environmental change. Our results for an Antarctic apex predator also provide useful baselines from a marine ecosystem when its top- and middle-trophic levels were not substantially impacted by human activity.     

Food‐web structure varies along environmental gradients in a high‐latitude marine ecosystem

Large‐scale patterns in species diversity and community composition are associated with environmental gradients, but the implications of these patterns for food‐web structure are still unclear. Here, we investigated how spatial patterns in food‐web structure are associated with environmental gradients in the Barents Sea, a highly productive shelf sea of the Arctic Ocean. We compared food webs from 25 subregions in the Barents Sea and examined spatial correlations among food‐web metrics, and between metrics and spatial variability in seawater temperature, bottom depth and number of days with ice cover. Several food‐web metrics were positively associated with seawater temperature: connectance, level of omnivory, clustering, cannibalism, and high variability in generalism, while other food‐web metrics such as modularity and vulnerability were positively associated with sea ice and negatively with temperature. Food‐web metrics positively associated with habitat heterogeneity were: number of species, link density, omnivory, path length, and trophic level. This finding suggests that habitat heterogeneity promotes food‐web complexity in terms of number of species and link density. Our analyses reveal that spatial variation in food‐web structure along the environmental gradients is partly related to species turnover. However, the higher interaction turnover compared to species turnover along these gradients indicates a consistent modification of food‐web structure, implying that interacting species may co‐vary in space. In conclusion, our study shows how environmental heterogeneity, via environmental filtering, influences not only turnover in species composition, but also the structure of food webs over large spatial scales.     

Environmental and organismal predictors of intraspecific variation in the stoichiometry of a neotropical freshwater fish

The elemental composition of animals, or their organismal stoichiometry, is thought to constrain their contribution to nutrient recycling, their interactions with other animals, and their demographic rates. Factors that affect organismal stoichiometry are generally poorly understood, but likely reflect elemental investments in morphological features and life history traits, acting in concert with the environmental availability of elements. We assessed the relative contribution of organismal traits and environmental variability to the stoichiometry of an insectivorous Neotropical stream fish, Rivulus hartii. We characterized the influence of body size, life history phenotype, stage of maturity, and environmental variability on organismal stoichiometry in 6 streams that differ in a broad suite of environmental variables. The elemental composition of R. hartii was variable, and overlapped with the wide range of elemental composition documented across freshwater fish taxa. Average %P composition was ～3.2%(±0.6), average %N～10.7%(±0.9), and average %C～41.7%(±3.1). Streams were the strongest predictor of organismal stoichiometry, and explained up to 18% of the overall variance. This effect appeared to be largely explained by variability in quality of basal resources such as epilithon N:P and benthic organic matter C:N, along with variability in invertebrate standing stocks, an important food source for R. hartii. Organismal traits were weak predictors of organismal stoichiometry in this species, explaining when combined up to 7% of the overall variance in stoichiometry. Body size was significantly and positively correlated with %P, and negatively with N:P, and C:P, and life history phenotype was significantly correlated with %C, %P, C:P and C:N. Our study suggests that spatial variability in elemental availability is more strongly correlated with organismal stoichiometry than organismal traits, and suggests that the stoichiometry of carnivores may not be completely buffered from environmental variability. We discuss the relevance of these findings to ecological stoichiometry theory.     

Ecological and demographic correlates of cooperation from individual to budding dispersal

Identifying the ecological and demographic factors that promote the evolution of cooperation is a major challenge for evolutionary biologists. Explanations for the adaptive evolution of cooperation seek to determine which factors make reproduction in cooperative groups more favourable than independent breeding or other selfish strategies. A vast majority of the hypotheses posit that cooperative groups emerge in the context of philopatry, high costs of dispersal, high population density and environmental stability. This route to cooperation, however, fails to explain a growing body of empirical evidence in which cooperation is not associated with one or more of these predictors. We propose an alternative evolutionary path towards the emergence of cooperation that accounts for the disparities observed in the current literature. We find that when dispersal is mediated by a group mode of dispersal, commonly termed budding dispersal, our mathematical model reveals an association between cooperation and immigration, lower costs of dispersal, low population density and environmental variability. Furthermore, by studying the continuum from the individual to the partial and full budding mode of dispersal, we can explicitly explain why the correlates of cooperation change under budding. This enables us to outline a general model for the evolution of cooperation that accounts for a substantial amount of empirical evidence. Our results suggest that natural selection may have favoured two major contrasting pathways for the evolution of cooperation depending on a set of key ecological and demographic factors.     

Analysis of candidate genes on chromosome 2 in oral cleft case-parent trios from three populations

Isolated oral clefts, including cleft lip with/without cleft palate (CL/P) and cleft palate (CP), have a complex and heterogeneous etiology. Case-parent trios from three populations were used to study genes spanning chromosome 2, where single nucleotide polymorphic (SNP) markers were analyzed individually and as haplotypes. Case-parent trios from three populations (74 from Maryland, 64 from Singapore and 95 from Taiwan) were genotyped for 962 SNPs in 104 genes on chromosome 2, including two well-recognized candidate genes: TGFA and SATB2. Individual SNPs and haplotypes (in sliding windows of 2–5 SNPs) were used to test for linkage and disequilibrium separately in CL/P and CP trios. A novel candidate gene (ZNF533) showed consistent evidence of linkage and disequilibrium in all three populations for both CL/P and CP. SNPs in key regions of ZNF533 showed considerable variability in estimated genotypic odds ratios and their significance, suggesting allelic heterogeneity. Haplotype frequencies for regions of ZNF533 were estimated and used to partition genetic variance into among-and within-population components. Wright’s fixation index, a measure of genetic diversity, showed little difference between Singapore and Taiwan compared with Maryland. The tensin-1 gene (TNS1) also showed evidence of linkage and disequilibrium among both CL/P and CP trios in all three populations, albeit at a lower level of significance. Additional genes (VAX2, GLI2, ZHFX1B on 2p; WNT6–WNT10A and COL4A3–COL4A4 on 2q) showed consistent evidence of linkage and disequilibrium only among CL/P trios in all three populations, and TGFA showed significant evidence in two of three populations.Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Population trends of Adélie penguin (<Emphasis Type="Italic">Pygoscelis adeliae</Emphasis>) breeding colonies: a spatial analysis of the effects of snow accumulation and human activities

Many of the Adélie penguin colonies used for long-term demographic studies are located near research stations, and there is a need to disentangle the effects of human activities and environmental variability on Adélie penguin population trends. This study used Geographic Information Systems and decision trees to examine whether potential changes in snow cover and/or proximity to human activities were able to explain the varying population trends of colonies at two breeding localities near Casey, East Antarctica. At the less visited site, Whitney Pt, wind exposure and snow accumulation correctly predicted the broad trends of colonies in most (84%) instances, whereas at Shirley I their predictive accuracy fell to 58%. At Shirley I, proximity to human activity correctly predicted the broad trends for 84% of colonies. While snow accumulation patterns are a primary driver of variation in population trends among colonies, the effect of snow accumulation is outweighed by proximity to human activities near Casey.     

Birth of a hotspot of intraspecific genetic diversity: notes from the underground

Hotspots of intraspecific diversity have been observed in most species, often within areas of putative Pleistocene refugia. They have thus mostly been viewed as the outcome of prolonged stability of large populations within the refugia. However, recent evidence has suggested that several other microevolutionary processes could also be involved in their formation. Here, we investigate the contribution of these processes to current range-wide patterns of genetic diversity in the Italian endemic mole Talpa romana, using both nuclear (30 allozyme loci) and mitochondrial markers (cytochrome b sequences). Southern populations of this species showed an allozyme variation that is amongst the highest observed in small mammals (most populations had an expected heterozygosity of 0.10 or above), which was particularly unexpected for a subterranean species. Population genetic, phylogeographic and historical demographic analyses indicated that T. romana populations repeatedly underwent allopatric differentiations followed by secondary admixture within the refugial range in southern Italy. A prolonged demographic stability was reliably inferred from the mitochondrial DNA data only for a population group located north and east of the Calabrian peninsula, showing comparatively lower levels of allozyme variability, and lacking evidence of secondary admixture with other groups. Thus, our results point to the admixture between differentiated lineages as the main cause of the higher levels of diversity of refugial populations. When compared with the Pleistocene evolutionary history recently inferred for species from both the same and other geographic regions, these results suggest the need for a reappraisal of the role of gene exchange in the formation of intraspecific hotspots of genetic diversity.     

Evaluation of alternate harvesting strategies using experimental microcosms

Experimental evidence to evaluate alternate conservation policies for harvested populations is currently meager. We used populations of the ciliate Tetrahymena thermophila growing in test tube microcosms to experimentally evaluate the effects of alternate harvesting policies in a controlled, replicable setting. Simple density-dependent models were effective in predicting patterns of ciliate population growth in the microcosms. We evaluated several univariate models, finding that a Ricker logistic model was a better predictor of ciliate population dynamics than Gompertz logistic, non-linear logistic, or random walk models. Using the Ricker logistic model as a demographic skeleton, we modeled ciliate population dynamics with respect to three alternate harvesting policies (fixed quota, fixed proportion, and fixed escapement), each conducted at four comparable levels of harvest intensity. The parameterized demographic models predicted that fixed quota harvesting would lead to lower mean ciliate abundance and higher temporal variability in ciliate abundance than fixed proportion or fixed escapement policies, with an appreciable risk of extinction, even under the controlled environmental conditions of our experimental system. For each harvesting policy, the intensity of harvest had demonstrable effects on population density. Population variability was higher for fixed quota harvesting than the other policies. The stochastic demographic model successfully predicted heightened extinction risk in the fixed quota system, relative to the other management treatments. Our experimental evidence lends support to the theoretical prediction that fixed quota harvesting is riskier than fixed proportion or fixed escapement policies.