Conserving extirpated sites: using habitat quality to manage unoccupied patches for metapopulation persistence

Conservation of metapopulations requires managing extirpated sites, particularly with current threats of increased fragmentation and displacement from global warming. Determining the habitat requirements of threatened species and how they relate to defining characteristics of occupied and unoccupied sites is key to managing suitable habitat in extirpated patches. Due to habitat destruction and degradation, the endangered Ohlone tiger beetle (Cicindela ohlone) is found in only five sites of a once more extensive metapopulation in Santa Cruz County, California. To determine the role of habitat quality in classifying sites, I measured vegetation and ground cover as well as plant and soil composition in sites in which C. ohlone are present, extirpated, and absent. I used conditional inference trees to determine what habitat factors significantly predicted the different sites types. I also analyzed habitat characteristics within present sites to determine factors that predicted egg-laying habitat. As isolation has been shown to be an important driver of metapopulation patch extirpation, I tested the spatial autocorrelation of C. ohlone occupancy to determine if extirpated patches were significantly isolated. Habitat characteristics successfully differentiated nearly 90 % of extirpated plots, which were not isolated from occupied sites. Sites in which C. ohlone are currently present were classified as having at least 10 % cover of bare ground, high forb cover, low litter cover and depth, and high soil bulk density, characteristics that extirpated sites lacked. I illustrate how the defining characteristics could be used to manage habitat in extirpated and absents sites for potential recolonization or translocation, which is vital for metapopulation persistence.     

Richness of ancient forest plant species indicates suitable habitats for macrofungi

Macrofungal species richness generally increases with forest continuity as does the richness of so-called ancient forest plant species (AFS). Based on this assumption, we examined the ability of AFS to indicate macrofungal diversity in six study areas covering a range of elevations and environments in the Czech Republic. In total, we used data from 106 sampling plots (2,500 m² each) distributed over six types of forest stands reflecting different intensities and temporal stages of forest management. Species composition of vascular plants and macrofungi was recorded by a single inventory and regular 2-year monitoring, respectively. In total, we found 71 AFS and 1,413 macrofungal species, of which 150 were red-listed macrofungal species. We documented that AFS show potential for being used in the prediction of macrofungi species richness, including endangered species, at the local scale (α-diversity). Additionally, we found significant differences in macrofungal species richness depending on study area and type of forest management, which did not, however, derogate the effect of AFS. Spatial congruence between species composition of AFS and macrofungi communities (β-diversity) increased with forest age and decreased with intensity of forest management. If we consider the simplicity of monitoring AFS in comparison to regular monitoring of macrofungi, we found a widely usable tool for estimating macrofungal diversity in all dominant types of managed forest in central Europe. However, we should be aware of the limited ability of AFS to capture macrofungal diversity across a broader spatial context (γ-diversity), especially in areas with a low diversity of AFS.     

The use of an unoccupied aerial vehicle to survey shark species over sand and rocky-reef habitats in a marine protected area

Cabo Pulmo National Park was established in 1995 and has since seen a large increase in fish biomass. An unoccupied aerial vehicle (UAV) was used to survey shallow coastal habitat in which lemon sharks (Negaprion brevirostris), bull sharks (Carcharhinus leucas) and Pacific nurse sharks (Ginglymostoma unami) were recorded. Sharks were more common in the afternoon, potentially using warmer shallow areas to behaviourally thermoregulate. This study highlights UAV surveying to be a viable tool for species identification, a limitation of previous terrestrial surveys conducted in the area.     

复合种群动态研究进展

复合种群动态研究是当今保护生物学和生态学中最热门的课题之一。在此较为详细地介绍了复合种群动态的有关概念和术语、经验研究和理论探索的最新进展以及相关的预测模型 ,对我国开展相关研究有参考价值。     

Inferring species roles in metacommunity structure from species co-occurrence networks

A long-standing question in community ecology is what determines the identity of species that coexist across local communities or metacommunity assembly. To shed light upon this question, we used a network approach to analyse the drivers of species co-occurrence patterns. In particular, we focus on the potential roles of body size and trophic status as determinants of metacommunity cohesion because of their link to resource use and dispersal ability. Small-sized individuals at low-trophic levels, and with limited dispersal potential, are expected to form highly linked subgroups, whereas large-size individuals at higher trophic positions, and with good dispersal potential, will foster the spatial coupling of subgroups and the cohesion of the whole metacommunity. By using modularity analysis, we identified six modules of species with similar responses to ecological conditions and high co-occurrence across local communities. Most species either co-occur with species from a single module or are connectors of the whole network. Among the latter are carnivorous species of intermediate body size, which by virtue of their high incidence provide connectivity to otherwise isolated communities playing the role of spatial couplers. Our study also demonstrates that the incorporation of network tools to the analysis of metacommunity ecology can help unveil the mechanisms underlying patterns and processes in metacommunity assembly.     

Identification of suitable reference genes for expression profiling studies using qRT-PCR in an important insect pest,Maruca vitrata

Molecular Biology Reports - Maruca vitrata is one of the potential insect pests that cause devastating losses to legume cultivation worldwide. Gene functional studies facilitate dissecting the...     

A theory for species co-occurrence in interaction networks

The study of species co-occurrences has been central in community ecology since the foundation of the discipline. Co-occurrence data are, nevertheless, a neglected source of information to model species distributions and biogeographers are still debating about the impact of biotic interactions on species distributions across geographical scales. We argue that a theory of species co-occurrence in ecological networks is needed to better inform interpretation of co-occurrence data, to formulate hypotheses for different community assembly mechanisms, and to extend the analysis of species distributions currently focused on the relationship between occurrences and abiotic factors. The main objective of this paper is to provide the first building blocks of a general theory for species co-occurrences. We formalize the problem with definitions of the different probabilities that are studied in the context of co-occurrence analyses. We analyze three species interactions modules and conduct multi-species simulations in order to document five principles influencing the associations between species within an ecological network: (i) direct interactions impact pairwise co-occurrence, (ii) indirect interactions impact pairwise co-occurrence, (iii) pairwise co-occurrence rarely are symmetric, (iv) the strength of an association decreases with the length of the shortest path between two species, and (v) the strength of an association decreases with the number of interactions a species is experiencing. Our analyses reveal the difficulty of the interpretation of species interactions from co-occurrence data. We discuss whether the inference of the structure of interaction networks is feasible from co-occurrence data. We also argue that species distributions models could benefit from incorporating conditional probabilities of interactions within the models as an attempt to take into account the contribution of biotic interactions to shaping individual distributions of species.     

青藏高原高寒荒漠区藏羚适宜生境识别及其保护状况评估

藏羚作为青藏高原高寒荒漠区濒危有蹄类动物的典型代表,其生境保护对于维持其种群存续具有重要意义.本文考虑食物、地形、水系等藏羚关键生境因子及道路、居民点等人为干扰因子,基于生境适宜性模型,对青藏高原高寒荒漠区藏羚的潜在及有效生境适宜性进行了模拟分析.同时,基于保护比例及单位面积对适宜生境的捕获效率,评估了研究区内阿尔金山、可可西里和羌塘国家级自然保护区及其各功能分区的保护情况.结果表明： 青藏高原高寒荒漠区潜在和有效适宜生境面积分别为2.84×10⁵和2.08×10⁵ km²,人为干扰造成的生境退化达16.1%.其中,阿尔金山、可可西里和羌塘保护区所覆盖的潜在适宜生境面积分别为2.01×10⁴、3.13×10⁴和1.26×10⁵ km²;考虑道路、居民点等人为干扰因素,其有效适宜生境面积分别为1.75×10⁴、2.81×10⁴和9.95×10⁴ km²,上述干扰因素导致的生境减损率分别为12.9%、10.2%和21.1%,表明羌塘道路、居民点等人为干扰相对较严重.尽管目前该区域3大保护区保护了藏羚2/3以上的适宜生境,体现了良好的保护效率,但仍存在一定游离于保护体系之外的保护空缺.在保护区功能区划水平上,除核心区外,缓冲区和实验区的保护比例和保护效率也不容忽视.为强化对藏羚等濒危有蹄类的保护,有必要在保护区和功能分区水平上对现有保护体系进行优化调整,减少保护空缺、优化功能分区,提高保护体系对生境保护的有效性,并预先保护物种适应气候变化的潜在庇护所.     

Identification of Lactobacillus species using tDNA-PCR

tDNA intergenic spacer PCR (tDNA-PCR) using consensus primers complementary to the conserved edges of the tRNA genes can amplify the intergenic spacers. Separation of the PCR products with capillary electrophoresis enables discrimination between fragments differing only one basepair in length. This method was applied to a collection of 82 Lactobacillus strains belonging to 37 species in order to evaluate the discriminatory power of this technique within this genus. Twenty-one species could be distinguished to species level on the basis of a unique tDNA fingerprint pattern. The other species grouped by two (e.g. L. fermentum and L. cellobiosus) or three (L. acidophilus, L. gallinarum and L. helveticus). Inclusion of the resulting fingerprints in a numerical database containing fingerprints of numerous other Gram-positive and Gram-negative species makes the identification of unknown strains possible.     

Disentangling community patterns of nestedness and species co-occurrence

Two opposing patterns of meta‐community organization are nestedness and negative species co‐occurrence. Both patterns can be quantified with metrics that are applied to presence‐absence matrices and tested with null model analysis. Previous meta‐analyses have given conflicting results, with the same set of matrices apparently showing high nestedness (Wright et al. 1998) and negative species co‐occurrence (Gotelli and McCabe 2002). We clarified the relationship between nestedness and co‐occurrence by creating random matrices, altering them systematically to increase or decrease the degree of nestedness or co‐occurrence, and then testing the resulting patterns with null models. Species co‐occurrence is related to the degree of nestedness, but the sign of the relationship depends on how the test matrices were created. Low‐fill matrices created by simple, uniform sampling generate negative correlations between nestedness and co‐occurrence: negative species co‐occurrence is associated with disordered matrices. However, high‐fill matrices created by passive sampling generate the opposite pattern: negative species co‐occurrence is associated with highly nested matrices. The patterns depend on which index of species co‐occurrence is used, and they are not symmetric: systematic changes in the co‐occurrence structure of a matrix are only weakly associated with changes in the pattern of nestedness. In all analyses, the fixed‐fixed null model that preserves matrix row and column totals has lower type I and type II error probabilities than an equiprobable null model that relaxes row and column totals. The latter model is part of the popular nestedness temperature calculator, which detects nestedness too frequently in random matrices (type I statistical error). When compared to a valid null model, a matrix with negative species co‐occurrence may be either highly nested or disordered, depending on the biological processes that determine row totals (number of species occurrences) and column totals (number of species per site).     

Identification of unoccupied but transformed nuclear estrogen receptor in cultured mouse Leydig cell

The molecular forms of estrogen receptor (ER) in estrogen-responsive mouse Leydig cell line (B-1) have been examined in relation to their biological activity. ER was predominantly recovered in the nuclear fraction upon homogenization even after cells were precultured in the absence of E2 and Phenol Red. This unoccupied nuclear ER (ERn) whose hormone binding ability was extremely thermostable could be extracted with 0.4 M KCl. This stability enabled us to determine hydrodynamic parameters in the ligand-free condition. The Stokes radius and sedimentation constant of this ERn in high salt condition were 5.5 nm and 6.0S, respectively, resulting in its molecular weight of 140,000. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of ER labeled with [3H]tamoxifen aziridine gave a single band of 65,000 Da, indicating that this ERn had a oligomer structure similar to that of transformed nuclear ER complexed with estrogen in the putative target cells. Therefore, we further examined the possibility that this ERn in B-1 cells can activate estrogen-responsive genes without any aid from estrogen. Estrogen responsive element-thymidine kinase promoter-chloramphenicol acetyltransferase fusion gene (ERE-tk-CAT) was transfected into B-1 cells. CAT activity was enhanced only in cells stimulated with estrogen. It may be concluded from these results that transformed ERn can be formed in the absence of estrogen but that binding to estrogen may be required in order to exert its biological activity.     

Plant species coexistence in cliff habitats

An ecological analysis of the ledge and crevice vegetation of cliffs in north-east Ireland was carried out using a sampling programme based on multivariate land classification. The composition of the vegetation was shown to be determined primarily by distance from the sea, elevation and rock type. The chemical composition and physical structure of the cliffs, together with environmental gradients associated with aspect, elevation and nearness to the sea provide a wide range of habitats in which plants coexist. Certain types of cliff vegetation contained associations of species with a contrasting ecology, such as arctic–montane, maritime, woodland, calcicole and calcifuge plants. The positions of these species in ordination space were found to be unique but overlapping. A model is described to account for these observations. It proposes that species dominance in cliff habitats is prevented by factors such as physical disturbance and that plants are able to coexist in cliff habitats which meet their common environmental tolerances and preferences. The model predicts that cliff habitats with the greatest diversity of species are likely to be subject to less extremes of environmental variability. These habitats include inland sites with nutrient enrichment by sea spray, north-facing sites, seepage sites, base-rich sites, low elevation sites and sites with a heterogeneous physical structure.     

Identification and analysis of co-occurrence networks with NetCutter

Background

Co-occurrence analysis is a technique often applied in text mining, comparative genomics, and promoter analysis. The methodologies and statistical models used to evaluate the significance of association between co-occurring entities are quite diverse, however.

Methodology/Principal Findings

We present a general framework for co-occurrence analysis based on a bipartite graph representation of the data, a novel co-occurrence statistic, and software performing co-occurrence analysis as well as generation and analysis of co-occurrence networks. We show that the overall stringency of co-occurrence analysis depends critically on the choice of the null-model used to evaluate the significance of co-occurrence and find that random sampling from a complete permutation set of the bipartite graph permits co-occurrence analysis with optimal stringency. We show that the Poisson-binomial distribution is the most natural co-occurrence probability distribution when vertex degrees of the bipartite graph are variable, which is usually the case. Calculation of Poisson-binomial P-values is difficult, however. Therefore, we propose a fast bi-binomial approximation for calculation of P-values and show that this statistic is superior to other measures of association such as the Jaccard coefficient and the uncertainty coefficient. Furthermore, co-occurrence analysis of more than two entities can be performed using the same statistical model, which leads to increased signal-to-noise ratios, robustness towards noise, and the identification of implicit relationships between co-occurring entities. Using NetCutter, we identify a novel protein biosynthesis related set of genes that are frequently coordinately deregulated in human cancer related gene expression studies. NetCutter is available at http://bio.ifom-ieo-campus.it/NetCutter/).

Conclusion

Our approach can be applied to any set of categorical data where co-occurrence analysis might reveal functional relationships such as clinical parameters associated with cancer subtypes or SNPs associated with disease phenotypes. The stringency of our approach is expected to offer an advantage in a variety of applications.     

Identification of Bifidobacterium species using rep-PCR fingerprinting

The aim of the present study was to evaluate the use of repetitive DNA element PCR fingerprinting (rep-PCR) for the taxonomic discrimination among the currently described species within the genus Bifidobacterium. After evaluating several primer sets targeting the repetitive DNA elements BOX, ERIC, (GTG)s and REP, the BOXA1R primer was found to be the most optimal choice for the establishment of a taxonomical framework of 80 Bifidobacterium type and reference strains. Subsequently, the BOX-PCR protocol was tested for the identification of 48 unknown bifidobacterial isolates originating from human faecal samples and probiotic products. In conclusion, rep-PCR fingerprinting using the BOXA1R primer can be considered as a promising genotypic tool for the identification of a wide range of bifidobacteria at the species, subspecies and potentially up to the strain level.     

未来气候变化对不同国家茶适宜分布区的影响

茶是对气候变化敏感的重要经济作物, 评价全球气候变化对茶分布和生产的影响对相关国家经济发展和茶农的生计至关重要。本研究基于全球858个茶分布点和6个气候因子数据, 利用物种分布模型预测全球茶的潜在适宜分布区及其在2070年的不同温室气体排放情景(RCP2.6和RCP8.5)下的变化。结果表明: 当前茶在五大洲均有适宜分布区, 主要集中在亚洲、非洲和南美洲, 并且最冷季平均温和最暖季降水量主导了茶的分布。预计2070年, 茶的适宜分布区变化在不同的大洲、国家和气候情景间将存在差异。具体来说, 茶的适宜分布区总面积将会减少, 减少的区域主要位于低纬度地区, 而中高纬度地区的适宜分布区将扩张, 由此可能导致茶的适宜分布区向北移动; 重要的产茶国中, 阿根廷、缅甸、越南等茶适宜分布区面积会减少57.8%-95.8%, 而中国和日本的适宜分布面积则会增加2.7%-31.5%。未来全球新增的适宜分布区中, 约有68%的地区土地覆盖类型为自然植被, 因此可能导致新茶树种植园的开垦和自然植被及生物多样性保护产生冲突。     

Short-term studies underestimate 30-generation changes in a butterfly metapopulation

Most studies of rare and endangered species are based on work carried out within one generation, or over one to a few generations of the study organism. We report the results of a study that spans 30 generations (years) of the entire natural range of a butterfly race that is endemic to 35 km(2) of north Wales, UK. Short-term studies (surveys in single years and dynamics over 4 years) of this system led to the prediction that the regional distribution would be quite stable, and that colonization and extinction dynamics would be relatively unimportant. However, a longer-term study revealed unexpectedly high levels of population turnover (local extinction and colonization), affecting 18 out of the 20 patches that were occupied at any time during the period. Modelling the system (using the 'incidence function model' (IFM) for metapopulations) also showed higher levels of colonization and extinction with increasing duration of the study. The longer-term dynamics observed in this system can be compared, at a metapopulation level, with the increased levels of variation observed with increasing time that have been observed in single populations. Long-term changes may arise from local changes in the environment that make individual patches more or less suitable for the butterfly, or from unusual colonization or extinction events that take metapopulations into alternative states. One implication is that metapopulation and population viability analyses based on studies that cover only a few animal or plant generations may underestimate extinction threats.     

桫椤的潜在适生区及其变化

桫椤是极为珍贵的孑遗木本蕨类植物.本研究利用Maxent生态位模型研究其全球潜在适生区及其变化,并运用受试者工作特征曲线(ROC)验证了精度,以为其资源的保护、搜寻和引种栽培提供参考.结果表明:桫椤的潜在适生区主要位于亚洲,少量分布于北美洲、中美洲和香草四岛、新西兰、新喀里多尼亚、斐济.当前气候条件下,桫椤的全球适生区...     

Non-random co-occurrence of native and exotic plant species in Mediterranean grasslands

Invasion by exotic species in Mediterranean grasslands has determined assembly patterns of native and introduced species, knowledge of which provides information on the ecological processes underlying these novel communities. We considered grasslands from Spain and Chile. For each country we considered the whole grassland community and we split species into two subsets: in Chile, species were classified as natives or colonizers (i.e. exotics); in Spain, species were classified as exclusives (present in Spain but not in Chile) or colonizers (Spanish natives and exotics into Chile). We used null models and co-occurrence indices calculated in each country for each one of 15 sites distributed along a precipitation gradient and subjected to similar silvopastoral exploitation. We compared values of species co-occurrence between countries and between species subsets (natives/colonizers in Chile; exclusives/colonizers in Spain) within each country and we characterised them according to climatic variables. We hypothesized that: a) the different coexistence time of the species in both regions should give rise to communities presenting a spatial pattern further from random in Spain than in Chile, b) the co-occurrence patterns in the grasslands are affected by mesoclimatic factors in both regions. The patterns of co-occurrence are similar in Spain and Chile, mostly showing a spatial pattern more segregated than expected by random. The colonizer species are more segregated in Spain than in Chile, possibly determined by the longer residence time of the species in the source area than in the invaded one. The segregation of species in Chile is related to water availability, being species less segregated in habitat with greater water deficit; in Spain no relationship with climatic variables was found. After an invasion process, our results suggest that the possible process of alteration of the original Chilean communities has not prevented the assembly between the native and colonizer species together.