Species-specific mitochondrial DNA markers for identification of non-invasive samples from sympatric carnivores in the Iberian Peninsula

Genetic species identification of non-invasively collected samples has become an important tool in ecological research, management and conservation and wildlife forensics. This is especially true for carnivores, due to their elusive nature, and is crucial when several ecologically and phylogenetically close species, with similar faeces, hairs, bones and/or pelts, occur in sympatry. This is the case of the Iberian Peninsula, a region with a carnivore community of 16 species—about two-thirds of the European carnivore fauna. Here we present a simple, efficient and reliable PCR-based protocol, using a novel set of species-specific primers, for the unambiguous identification to species of non-invasively collected samples or forensic materials from Iberian carnivores. For each species, from the consensus of all cytochrome b haplotypes, found here and previously reported, we designed species-specific primer pairs for short fragments, the most likely to persist in low-quantity and degraded DNA samples. The predicted specificity of each primer pair was assessed through PCR of positive DNA extracts from the carnivore species, from an exhaustive array of potential prey and from humans. The robustness of PCR amplification for non-invasively sampled DNA was tested with scat samples. The primers did not produce false positives and correctly identified all carnivore samples to the species level. In comparison with sequencing and PCR-RFLP assays, our method is, respectively, cost- and time-effective, and is especially suited for monitoring surveys targeting multiple populations/species. It also introduces an approach that works for a whole community of carnivores living sympatrically over a large geographic area.     

Identification of Regions with High Ozone Concentrations Aiming the Impact Assessment on Childhood Asthma

High concentrations of near-surface ozone are known to have negative impacts on human health, especially among risk groups such as persons with respiratory problems, children, and the elderly. The aim of this work was to identify regions with high ozone concentrations and very low concentrations of other pollutants, where further studies will be performed regarding the specific impact of ozone on childhood asthma. For that, the concentrations of ozone and of its precursors at remote areas were assessed and compared with those observed at an urban area influenced by traffic. Measurements using passive samplers were compared with those performed with continuous monitors and it was possible to conclude that measurements with passive samplers had satisfactory reproducibility and precision. For O₃, the comparison of both methods showed a maximum absolute difference of +4.10 μ g.m^?3 and relative differences lower than ?8.8%. The maximum absolute difference for NO₂ was +5.2 μ g.m^?3 and the relative differences were greater than 12% only for very low concentrations (2–3 μ g.m^?3). Comparing with one urban site, the results obtained at remote sites showed significantly lower concentrations of nitrogen dioxide (12 to 20 times) and volatile organic compounds (2 to 8 times) and greater ozone concentrations (2 to 3 times). It was inferred that the lower concentrations of nitrogen dioxide were the main reason for the greater ozone concentrations found at the remote sites. The remote areas studied showed very high ozone concentrations and very low concentrations of other pollutants, being an adequate zone to perform further studies regarding the specific impact of ozone on childhood asthma without the confounding effects of other pollutants.     

Incorporating uncertainty and prior information into stable isotope mixing models

Stable isotopes are a powerful tool for ecologists, often used to assess contributions of different sources to a mixture (e.g. prey to a consumer). Mixing models use stable isotope data to estimate the contribution of sources to a mixture. Uncertainty associated with mixing models is often substantial, but has not yet been fully incorporated in models. We developed a Bayesian-mixing model that estimates probability distributions of source contributions to a mixture while explicitly accounting for uncertainty associated with multiple sources, fractionation and isotope signatures. This model also allows for optional incorporation of informative prior information in analyses. We demonstrate our model using a predator–prey case study. Accounting for uncertainty in mixing model inputs can change the variability, magnitude and rank order of estimates of prey (source) contributions to the predator (mixture). Isotope mixing models need to fully account for uncertainty in order to accurately estimate source contributions.     

Long-term observation of a pollination network: fluctuation in species and interactions, relative invariance of network structure and implications for estimates of specialization

We analysed the dynamics of a plant-pollinator interaction network of a scrub community surveyed over four consecutive years. Species composition within the annual networks showed high temporal variation. Temporal dynamics were also evident in the topology of the network, as interactions among plants and pollinators did not remain constant through time. This change involved both the number and the identity of interacting partners. Strikingly, few species and interactions were consistently present in all four annual plant-pollinator networks (53% of the plant species, 21% of the pollinator species and 4.9% of the interactions). The high turnover in species-to-species interactions was mainly the effect of species turnover (c. 70% in pairwise comparisons among years), and less the effect of species flexibility to interact with new partners (c. 30%). We conclude that specialization in plant-pollinator interactions might be highly overestimated when measured over short periods of time. This is because many plant or pollinator species appear as specialists in 1 year, but tend to be generalists or to interact with different partner species when observed in other years. The high temporal plasticity in species composition and interaction identity coupled with the low variation in network structure properties (e.g. degree centralization, connectance, nestedness, average distance and network diameter) imply (i) that tight and specialized coevolution might not be as important as previously suggested and (ii) that plant-pollinator interaction networks might be less prone to detrimental effects of disturbance than previously thought. We suggest that this may be due to the opportunistic nature of plant and animal species regarding the available partner resources they depend upon at any particular time.     

The IBD process along four chromosomes

In this note, we present the continuous-time Markov rate matrix that models identity by descent (ibd) patterns among four chromosomes in a population. The equilibrium distribution of this Markov process along a chromosome is the set of 4-gene state probabilities given by the Ewens sampling formula. This model will facilitate inference of identity by descent among the four chromosomes of a pair of individuals, using data at dense SNP loci among which there may be linkage disequilibrium.     

Application of universally amplifying plastid primers to environmental sampling of a stream periphyton community

To demonstrate the utility of universal plastid primers for probing of environmental samples, we extracted DNA from a tropical stream periphyton community and created two environmental clone libraries. We demonstrate the recovery of DNA sequences corresponding to the major groups of algae observed microscopically in the sample, illustrating the utility of these primers for analysis of environmental samples. Using a touchdown polymerase chain reaction technique, almost 99% of recovered sequences correspond to plastid-containing or cyanobacterial taxa, which allows algae to be targeted to the almost complete exclusion of noncyanobacterial prokaryotes and nonplastid-containing eukaryotes.     

Point pattern analysis under conditions of replicated sampling

Aims The analysis of point patterns, which deals with data sets consisting of mapped locations of organisms in a study region, is especially important to plant ecological studies because the locations of plants can often be approximated as points. However, few studies used point pattern analysis with data collected by replicated sampling a principle procedure of acquiring data in ecological research. Therefore, we explore the applicability of point pattern analysis under conditions of replicated sampling in this studyMethodsThree replicated 5 m × 5 m plots of homogenous communities were established on a site with eight years of restoration in Nei Mongol steppe. In each plot, the locations of individuals in Leymus chinensis and Stipa grandis populations were mapped. O-Ring function was used to describe the population patterns and species association between L. chinensis and S. grandis for each plot as well as the integrative data of the three replicates.Important findings Population patterns and species associations differed among the three replicated plots. This illustrates that if point pattern analysis was applied to describe the population patterns and species associations only by using data from a single plot sampling, the results could be misleading. Whereas it would be more reliable to integrate the data of replicated plots in the point pattern analysis because in this way the resulting O-Ring function is a weighted average, where the weight is the number of points in the replicate i divided by the total number of points in all replicated plots.     

鄱阳湖湿地典型草洲植物群落种-面积关系

为了解鄱阳湖湿地草洲植物群落的结构,对其3种典型草洲植物群落种-面积关系进行了研究。采用巢式样方法调查植物物种数量,并用3种非饱和曲线拟合种-面积方程。结果表明,基于实测数据,3个草洲物种数随着取样面积的增加先快速增加后趋于平稳;群落最小取样面积均为30 m~2。幂函数模型对3个草洲群落的种-面积关系拟合效果均为最佳,3个草洲群落的RSE分别为0.35、0.35和0.56,AAD分别为0.23、0.17和0.35,AARD分别为0.06、0.02和0.07,而指数模型、Fisher模型的拟合效果一般。指数模型计算得到的不同比例因子下3个草洲最小取样面积与实际情况最为吻合。这为鄱阳湖区进行植物群落数据采集的样方设置提供了理论参考。