Partitioning of functional diversity reveals the scale and extent of trait convergence and divergence

Questions: Trait differentiation among species occurs at different spatial scales within a region. How does the partitioning of functional diversity help to identify different community assembly mechanisms? Location: Northeastern Spain. Methods: Functional diversity can be partitioned into within‐community (α) and among‐communities (β) components, in analogy to Whittaker's classical α and β species diversity concept. In light of ecological null models, we test and discuss two algorithms as a framework to measure α and β functional diversity (the Rao quadratic entropy index and the variance of trait values). Species and trait (specific leaf area) data from pastures under different climatic conditions in NE Spain are used as a case study. Results: The proposed indices show different mathematical properties but similarly account for the spatial components of functional diversity. For all vegetation types along the climatic gradient, the observed α functional diversity was lower than expected at random, an observation consistent with the hypothesis of trait convergence resulting from habitat filtering. On the other hand, our data exhibited a remarkably higher functional diversity within communities compared to among communities (α?β). In contrast to the high species turnover, there was a limited functional diversity turnover among communities, and a large part of the trait divergence occurred among coexisting species. Conclusions: Partitioning functional diversity within and among communities revealed that both trait convergence and divergence occur in the formation of assemblages from the local species pool. A considerable trait convergence exists at the regional scale in spite of changes in species composition, suggesting the existence of ecological redundancy among communities.     

Discriminating trait‐convergence and trait‐divergence assembly patterns in ecological community gradients

Question: Whereas similar ecological requirements lead to trait‐convergence assembly patterns (TCAP) of species in communities, the interactions controlling how species associate produce trait‐divergence assembly patterns (TDAP). Yet, the linking of the latter to community processes has so far only been suggested. We offer a method to elucidate TCAP and TDAP in ecological community gradients that will help fill this gap. Method: We evaluated the correlation between trait‐based described communities and ecological gradients, and using partial correlation, we separated the fractions reflecting TCAP and TDAP. The required input data matrices describe operational taxonomic units (OTUs) by traits, communities by the quantities or presence‐absence of these OTUs, and community sites by ecological variables. We defined plant functional types (PFTs) or species as community components after fuzzy weighting by the traits. The measured correlations for TCAP and TDAP were tested by permutation. The null model for TDAP preserves the trait convergence, the structure intrinsic in the fuzzy types, and community total abundances and autocorrelation. Results: We applied the method to trait‐based data from plant communities in south Brazil, one set in natural grassland experimental plots under different nitrogen and grazing levels, and another in sapling communities colonizing Araucaria forest patches of increasing size in a forest‐grassland mosaic. In these cases, depending on the traits considered, we found strong evidence of either TCAP or TDAP, or both, that was related to the environmental gradients. Conclusions: The method developed is able to reveal TCAP and TDAP that are more likely to be functional for specified ecological gradients, allowing establishment of objective hypotheses on their links to community processes.     

Cyclic nucleotide-gated ion channel gene family in rice,identification, characterization and experimental analysis of expression response to plant hormones,biotic and abiotic stresses

Background

Cyclic nucleotide-gated channels (CNGCs) are Ca²⁺-permeable cation transport channels, which are present in both animal and plant systems. They have been implicated in the uptake of both essential and toxic cations, Ca²⁺ signaling, pathogen defense, and thermotolerance in plants. To date there has not been a genome-wide overview of the CNGC gene family in any economically important crop, including rice (Oryza sativa L.). There is an urgent need for a thorough genome-wide analysis and experimental verification of this gene family in rice.

Results

In this study, a total of 16 full length rice CNGC genes distributed on chromosomes 1–6, 9 and 12, were identified by employing comprehensive bioinformatics analyses. Based on phylogeny, the family of OsCNGCs was classified into four major groups (I-IV) and two sub-groups (IV-A and IV- B). Likewise, the CNGCs from all plant lineages clustered into four groups (I-IV), where group II was conserved in all land plants. Gene duplication analysis revealed that both chromosomal segmentation (OsCNGC1 and 2, 10 and 11, 15 and 16) and tandem duplications (OsCNGC1 and 2) significantly contributed to the expansion of this gene family. Motif composition and protein sequence analysis revealed that the CNGC specific domain “cyclic nucleotide-binding domain (CNBD)” comprises a “phosphate binding cassette” (PBC) and a “hinge” region that is highly conserved among the OsCNGCs. In addition, OsCNGC proteins also contain various other functional motifs and post-translational modification sites. We successively built a stringent motif: (LI-X(2)-[GS]-X-[FV]-X-G-[1]-ELL-X-W-X(12,22)-SA-X(2)-T-X(7)-[EQ]-AF-X-L) that recognizes the rice CNGCs specifically. Prediction of cis-acting regulatory elements in 5′ upstream sequences and expression analyses through quantitative qPCR demonstrated that OsCNGC genes were highly responsive to multiple stimuli including hormonal (abscisic acid, indoleacetic acid, kinetin and ethylene), biotic (Pseudomonas fuscovaginae and Xanthomonas oryzae pv. oryzae) and abiotic (cold) stress.

Conclusions

There are 16 CNGC genes in rice, which were probably expanded through chromosomal segmentation and tandem duplications and comprise a PBC and a “hinge” region in the CNBD domain, featured by a stringent motif. The various cis-acting regulatory elements in the upstream sequences may be responsible for responding to multiple stimuli, including hormonal, biotic and abiotic stresses.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-853) contains supplementary material, which is available to authorized users.     

Plant functional traits and community assembly along interacting gradients of productivity and fragmentation

Quantifying the association of plant functional traits to environmental gradients is a promising approach for understanding and projecting community responses to land use and climatic changes. Although habitat fragmentation and climate are expected to affect plant communities interactively, there is a lack of empirical studies addressing trait associations to fragmentation in different climatic regimes.In this study, we analyse data on the key functional traits: specific leaf area (SLA), plant height, seed mass and seed number. First, we assess the evidence for the community assembly mechanisms habitat filtering and competition at different spatial scales, using several null-models and a comprehensive set of community-level trait convergence and divergence indices. Second, we analyse the association of community-mean traits with patch area and connectivity along a south–north productivity gradient.We found clear evidence for trait convergence due to habitat filtering. In contrast, the evidence for trait divergence due to competition fundamentally depended on the null-model used. When the null-model controlled for habitat filtering, there was only evidence for trait divergence at the smallest sampling scale (0.25 m × 0.25 m). All traits varied significantly along the S–N productivity gradient. While plant height and SLA were consistently associated with fragmentation, the association of seed mass and seed number with fragmentation changed along the S–N gradient.Our findings indicate trait convergence due to drought stress in the arid sites and due to higher productivity in the mesic sites. The association of plant traits to fragmentation is likely driven by increased colonization ability in small and/or isolated patches (plant height, seed number) or increased persistence ability in isolated patches (seed mass).Our study provides the first empirical test of trait associations with fragmentation along a productivity gradient. We conclude that it is crucial to study the interactive effects of different ecological drivers on plant functional traits.     

Phylogenetic turnover in tropical tree communities: impact of environmental filtering,biogeography and mesoclimatic niche conservatism

Aim We addressed the roles of environmental filtering, historical biogeography and evolutionary niche conservatism on the phylogenetic structure of tropical tree communities with the following questions. (1) What is the impact of mesoclimatic gradients and dispersal limitation on phylogenetic turnover and species turnover? (2) How does phylogenetic turnover between continents compare in intensity with the turnover driven by climatic gradients at a regional scale? (3) Are independent phylogenetic reconstructions of the mesoclimatic niche of clades congruent between continents? Location Panama Canal Watershed and Western Ghats (India), two anciently divergent biogeographic contexts but with comparable rainfall gradients. Methods Using floristic data for 50 1‐ha plots in each region, independent measures of phylogenetic turnover (Π_ST) and species turnover (Jaccard) between plots were regressed on geographic and ecological distances. Mesoclimatic niches were reconstructed for each node of the phylogeny and compared between the two continents. Results (1) The phylogenetic turnover within each region is best explained by mesoclimatic differences (environmental filtering), while species turnover depends both on mesoclimatic differences and geographic distances (dispersal limitation). (2) The phylogenetic turnover between continents (Π_ST = 0.009) is comparable to that caused by mesoclimatic gradients within regions (Π_ST = 0.010) and both effects seem cumulative. (3) Independent phylogenetic reconstructions of the mesoclimatic niches were strongly correlated between the two continents (r = 0.61), despite the absence of shared species. Main conclusions Our results demonstrate a world‐wide deep phylogenetic signal for mesoclimatic niche within a biome, indicating that positive phylogenetic turnover at a regional scale reflects environmental filtering in plant communities.     

Univariate Community Assembly Analysis (UniCAA): Combining hierarchical models with null models to test the influence of spatially restricted dispersal,environmental filtering,and stochasticity on community assembly

Identifying the influence of stochastic processes and of deterministic processes, such as dispersal of individuals of different species and trait‐based environmental filtering, has long been a challenge in studies of community assembly. Here, we present the Univariate Community Assembly Analysis (UniCAA) and test its ability to address three hypotheses: species occurrences within communities are (a) limited by spatially restricted dispersal; (b) environmentally filtered; or (c) the outcome of stochasticity—so that as community size decreases—species that are common outside a local community have a disproportionately higher probability of occurrence than rare species. The comparison with a null model allows assessing if the influence of each of the three processes differs from what one would expect under a purely stochastic distribution of species. We tested the framework by simulating “empirical” metacommunities under 15 scenarios that differed with respect to the strengths of spatially restricted dispersal (restricted vs. not restricted); habitat isolation (low, intermediate, and high immigration rates); and environmental filtering (strong, intermediate, and no filtering). Through these tests, we found that UniCAA rarely produced false positives for the influence of the three processes, yielding a type‐I error rate ≤5%. The type‐II error rate, that is, production of false negatives, was also acceptable and within the typical cutoff (20%). We demonstrate that the UniCAA provides a flexible framework for retrieving the processes behind community assembly and propose avenues for future developments of the framework.     

环境筛选和扩散限制在地表和地下螨群落物种共存中的调控作用

识别扩散限制和环境筛选在群落物种共存中的相对作用,是土壤动物群落物种共存机制研究的重要内容,然而少有针对地表和地下土壤动物群落的探讨。在三江平原农田生态系统,设置一个50 m×50 m的空间尺度,探讨环境筛选和扩散限制对地表和地下土壤螨群落物种共存的调控作用。基于Moran特征向量图(MEMs)和变差分解的方法来区分环境筛选和扩散限制的调控作用;采用偏Mantel检验进一步分析环境距离和空间距离的相对贡献;使用RDA分析环境因子对螨群落物种组成的解释能力。变差分解结果表明,空间变量对地表、地下和地表-地下土壤螨群落具有较大的显著方差解释量,而环境变量和空间环境结构的解释量相对较小且不显著;偏Mantel检验没有发现环境距离或空间距离的显著贡献;RDA分析表明土壤p H值、大豆株高和土壤含水量对土壤螨群落具有显著的解释能力,说明环境变量对螨群落物种组成的重要作用。研究表明,在三江平原农田生态系统,地表和地下土壤螨群落物种共存主要受到扩散限制的调控作用,同时环境筛选的调控作用也不容忽视。     

Habitat diversity associated to island size and environmental filtering control the species richness of rock‐savanna plants in neotropical inselbergs

Disentangling the multiple factors controlling species diversity is a major challenge in ecology. Island biogeography and environmental filtering are two influential theories emphasizing respectively island size and isolation, and the abiotic environment, as key drivers of species richness. However, few attempts have been made to quantify their relative importance and investigate their mechanistic basis. Here, we applied structural equation modelling, a powerful method allowing test of complex hypotheses involving multiple and indirect effects, on an island‐like system of 22 French Guianan neotropical inselbergs covered with rock‐savanna. We separated the effects of size (rock‐savanna area), isolation (density of surrounding inselbergs), environmental filtering (rainfall, altitude) and dispersal filtering (forest‐matrix openness) on the species richness of all plants and of various ecological groups (terrestrial versus epiphytic, small‐scale versus large‐scale dispersal species). We showed that the species richness of all plants and terrestrial species was mainly explained by the size of rock‐savanna vegetation patches, with increasing richness associated with higher rock‐savanna area, while inselberg isolation and forest‐matrix openness had no measurable effect. This size effect was mediated by an increase in terrestrial‐habitat diversity, even after accounting for increased sampling effort. The richness of epiphytic species was mainly explained by environmental filtering, with a positive effect of rainfall and altitude, but also by a positive size effect mediated by enhanced woody‐plant species richness. Inselberg size and environmental filtering both explained the richness of small‐scale and large‐scale dispersal species, but these ecological groups responded in opposite directions to altitude and rainfall, that is positively for large‐scale and negatively for small‐scale dispersal species. Our study revealed both habitat diversity associated with island size and environmental filtering as major drivers of neotropical inselberg plant diversity and showed the importance of plant species growth form and dispersal ability to explain the relative importance of each driver.     

Trends in single trait dispersion between early-mid successional stages: the importance of species pool extension and habitat scale

Aims Are there trends of increasing/decreasing dispersion of single, categorical traits related to early/late-successional species between stages of community development? If yes, are these trends dependent on species pool extension and habitat scale? Is there a consistent reduction in single trait convergence or divergence in any seral stage when scaling down from ecological to local species pool?Methods Presence of all vascular species rooted within plots of 5 × 5 m was recorded in assemblages of exposed mining spoils (EMS) and heathlands (HTL), which form a chronosequence on two abandoned ore tailing heaps located close to each other in the south-eastern Carpathians (Romania). Fifteen nominal, trait attributes of plant species co-occurring in the two seral assemblages were collected from available databases and subsequently classified as either successionally 'pioneer' or 'mature'. The strength of single trait convergence or divergence was estimated by comparison with null plant assemblages at patch type (meta-community) level by reference to the ecological or local species pool, and at community level.Important findings At patch type level, all pioneer and mature trait attributes (apart from short life span), with significant variation between the two seral stages, increased and, respectively, decreased in dispersion irrespective of species pool extension. However, these trends were more conspicuous when using the ecological species pool, very likely due to relaxation in abiotic filtering and dispersal limitation. At community level, no consistent trends were observed between EMS and HTL assemblages, probably because most trait attributes were sorted by microenvironmental filters displaying high variation, like topography or habitat patch geometry. In both seral stages, there was a general weakening of trait convergence or divergence at patch type level when scaling down from the ecological to the local species pool, which was due to niche space contraction. At community level, there was a trend of rise in dispersion of pioneer attributes along the observed chronosequence, presumably imputable to increasing competition for light and underground water, but an opposite trend of dispersion drop in mature attributes was not so evident. Based on these findings, we proposed two rules of thumb concerning the expected changes in dispersion of trait attributes at patch level along successions and between levels of species pool extension. In conclusion, trends in the successional dynamics of pioneer and mature trait dispersion are clearly detectable at meta-community level, especially by reference to the ecological species pool. Habitat scale and species pool extension are key factors to consider and report when estimating the magnitude of single trait dispersion.     

渭河底栖动物性状和功能对空间尺度环境变量响应的生态区差异性

以我国中部渭河南部流域山区和平原生态区的底栖动物为研究对象,通过计算29个生物性状类别和7个功能多样性指数,比较了不同生态区的生物性状组成和功能与性状多样性指数差异性;应用综合RLQ和fourth-corner方法探索底栖动物生物性状组成与土地利用和理化变量的关系;通过广义线性模型(GLM)比较不同空间尺度环境变量对底栖动物功能与性状多样性指数影响的生态区差异性。研究发现,共18个底栖动物性状组成在山区和平原间存在显著差异性,其中具有无庇护所和以叶片为庇护所材料、外骨骼轻微骨化和骨化良好、草食性、捕食性等生物性状的底栖动物栖息于栖境状况较好的山区,体壁呼吸、虫体柔软、集食者等生物性状更多的集中在人类活动较严重的平原区。除了功能均匀度指数外,山区的性状和功能多样性指数均显著高于平原,说明平原环境干扰显著降低了底栖动物性状和功能多样性。综合RLQ和fourth-corner方法表明底栖动物生物性状对环境胁迫的响应存在可预测性。GLM模型结果表明,山区和平原生物性状和功能多样性指数受到不同空间尺度土地利用和理化环境变量的影响:流域尺度城镇用地、水温和TN含量是影响山区功能和性状多样性指数模型的重要环境变量,但平原区河段尺度农业用地面积百分比和平均水深是影响功能和性状多样性的主要因子。     

A review on Monte Carlo simulation methods as they apply to mutation and selection as formulated in Wright-Fisher models of evolutionary genetics

A case has made for the use of Monte Carlo simulation methods when the incorporation of mutation and natural selection into Wright-Fisher gametic sampling models renders then intractable from the standpoint of classical mathematical analysis. The paper has been organized around five themes. Among these themes was that of scientific openness and a clear documentation of the mathematics underlying the software so that the results of any Monte Carlo simulation experiment may be duplicated by any interested investigator in a programming language of his choice. A second theme was the disclosure of the random number generator used in the experiments to provide critical insights as to whether the generated uniform random variables met the criterion of independence satisfactorily. A third theme was that of a review of recent literature in genetics on attempts to find signatures of evolutionary processes such as natural selection, among the millions of segments of DNA in the human genome, that may help guide the search for new drugs to treat diseases. A fourth theme involved formalization of Wright-Fisher processes in a simple form that expedited the writing of software to run Monte Carlo simulation experiments. Also included in this theme was the reporting of several illustrative Monte Carlo simulation experiments for the cases of two and three alleles at some autosomal locus, in which attempts were to made to apply the theory of Wright-Fisher models to gain some understanding as to how evolutionary signatures may have developed in the human genome and those of other diploid species. A fifth theme was centered on recommendations that more demographic factors, such as non-constant population size, be included in future attempts to develop computer models dealing with signatures of evolutionary process in genomes of various species. A brief review of literature on the incorporation of demographic factors into genetic evolutionary models was also included to expedite and stimulate further development on this theme.     

Identification of a conserved 8 aa insert in the PIP5K protein in the Saccharomycetaceae family of fungi and the molecular dynamics simulations and structural analysis to investigate its potential functional role

Homologs of the phosphatidylinositol‐4‐phosphate‐5‐kinase (PIP5K), which controls a multitude of essential cellular functions, contain a 8 aa insert in a conserved region that is specific for the Saccharomycetaceae family of fungi. Using structures of human PIP4K proteins as templates, structural models were generated of the Saccharomyces cerevisiae and human PIP5K proteins. In the modeled S. cerevisiae PIP5K, the 8 aa insert forms a surface exposed loop, present on the same face of the protein as the activation loop of the kinase domain. Electrostatic potential analysis indicates that the residues from 8 aa conserved loop form a highly positively charged surface patch, which through electrostatic interaction with the anionic portions of phospholipid head groups, is expected to play a role in the membrane interaction of the yeast PIP5K. To unravel this prediction, molecular dynamics (MD) simulations were carried out to examine the binding interaction of PIP5K, either containing or lacking the conserved signature insert, with two different membrane lipid bilayers. The results from MD studies provide insights concerning the mechanistic of interaction of PIP5K with lipid bilayer, and support the contention that the identified 8 aa conserved insert in fungal PIP5K plays an important role in the binding of this protein with membrane surface. Proteins 2017; 85:1454–1467. © 2017 Wiley Periodicals, Inc.