Richness‐dependence of phylogenetic diversity indices

Phylogenetic diversity indices are widely used to characterize the structure and diversity of ecological communities. Most indices are based on a metric that is expected to vary with species richness, so they are standardized to remove this richness‐dependence. With this standardization, values of 0 are consistent with random phylogenetic structure, while phylogenetic clustering is associated with either negative or positive values (depending on the index). One common interpretation of phylogenetic clustering is that it indicates some combination of environmental and biological filtering that restricts the species that can be present in a community. Increasingly, studies are comparing phylogenetic indices along environmental gradients to infer differences in the factors structuring communities. This comparison implicitly assumes that index values are comparable among communities with different numbers of species. Using a set of simulations, I show here that this assumption is incorrect. Holding the strength of filtering constant, communities composed of more species show larger absolute index values. This problem is most pronounced when the environmental filter favors a moderate‐sized clade strongly over others and when using the net relatedness index (NRI) to measure clustering. This bias potentially casts doubt on studies studying phylogenetic index patterns along gradients where richness also varies. Fortunately, the arising generality that more stressful environments have lower species richness and stronger clustering is opposite to this bias and therefore robust. I also show that a simple rarefaction can remove the richness‐dependence of these indices, at the expense of increased error.     

The phylogenetic structure of primate communities: variation within and across continents

Aim Our goals are: (1) to examine the relative degree of phylogenetic overdispersion or clustering of species in communities relative to the entire species pool, (2) to test for across‐continent differences in community phylogenetic structure, and (3) to examine the relationship between species richness and community phylogenetic structure. Location Africa, Madagascar, Asia, and the Neotropics. Methods We collected species composition and phylogenetic data for over 100 primate communities. For each community, we calculated two measures of phylogenetic structure: (1) the net relatedness index (NRI), which provides a measure of the mean pairwise phylogenetic distance among all species in the community; and (2) the nearest taxon index (NTI), which measures the relative phylogenetic distance among the closest related species in a community. Both measures are relative to the phylogeny of the species in the entire species pool. The phylocom package uses a randomization procedure to test whether the NRI and NTI values are higher or lower than expected by chance alone. In addition, we used a Kruskal–Wallis test to examine differences in NRI and NTI across continents, and linear regressions to examine the relationship between species richness and NRI/NTI. Results We found that the majority of individual primate communities in Africa, Asia and the Neotropics consist of member species that are neither more nor less closely related than expected by chance alone. Yet 37% of Malagasy communities contain species that are more distantly related to each other compared with random species assemblages. Also, we found that the average degree of relatedness among species in communities differed significantly across continents, with African and Malagasy communities consisting of more distantly related taxa compared with communities in Asia and the Neotropics. Finally, we found a significant negative relationship between species richness and phylogenetic distance among species in African, Asian and Malagasy communities. The average relatedness among species in communities decreased as community size increased. Main conclusions The majority of individual primate communities exhibit a phylogenetic structure no different from random. Yet there are across‐continent differences in the phylogenetic structure of primate communities that probably result from the unique ecological and evolutionary characteristics exhibited by the endemic species found on each continent. In particular, the recent extinctions of numerous primates on Madagascar are likely responsible for the low levels of evolutionary relatedness among species in Malagasy communities.     

Phylogenetic plant community structure along elevation is lineage specific

The trend of closely related taxa to retain similar environmental preferences mediated by inherited traits suggests that several patterns observed at the community scale originate from longer evolutionary processes. While the effects of phylogenetic relatedness have been previously studied within a single genus or family, lineage‐specific effects on the ecological processes governing community assembly have rarely been studied for entire communities or flora. Here, we measured how community phylogenetic structure varies across a wide elevation gradient for plant lineages represented by 35 families, using a co‐occurrence index and net relatedness index (NRI). We propose a framework that analyses each lineage separately and reveals the trend of ecological assembly at tree nodes. We found prevailing phylogenetic clustering for more ancient nodes and overdispersion in more recent tree nodes. Closely related species may thus rapidly evolve new environmental tolerances to radiate into distinct communities, while older lineages likely retain inherent environmental tolerances to occupy communities in similar environments, either through efficient dispersal mechanisms or the exclusion of older lineages with more divergent environmental tolerances. Our study illustrates the importance of disentangling the patterns of community assembly among lineages to better interpret the ecological role of traits. It also sheds light on studies reporting absence of phylogenetic signal, and opens new perspectives on the analysis of niche and trait conservatism across lineages.     

戴云山物种多样性与系统发育多样性海拔梯度分布格局及驱动因子

生物多样性的海拔分布格局是生态学研究的热点。海拔作为综合性因子驱动着植物群落的物种、系统发育与功能多样性的空间分布。以戴云山南坡900-1600 m森林植物群落为研究对象,探讨物种多样性、系统发育指数与环境驱动因子的相互关系以及环境因子在群落构建与多样性维持中的重要意义。结果表明：（1）森林植物群落的系统发育多样性与物种多样性沿海拔均呈现中间高度膨胀格局。（2）物种多样性Margalef指数、Shannon-Wiener指数与系统发育多样性指数呈显著正相关,表明物种多样性越高,系统发育多样性也越高。Shannon-Wiener指数与物种多样性指数（Margalef、Pielou、Simpson指数）、系统发育多样性及系统发育结构都存在显著相关性,一定程度上Shannon-Wiener指数可以代替其他指数。Pielou指数、Simpson指数、Shannon-Wiener指数与系统发育结构NRI （Net relatedness index）指数、NTI （Net nearest taxa index）指数存在显著正相关,表明群落优势度、均匀度与系统发育结构相关性较强。（3）土壤全磷含量是影响系统发育多样性和物种多样性的主要驱动因子,土壤含水量是影响Shannon-Wiener、Pielou、Simpson指数的最显著因子,海拔是影响群落系统发育结构的主要因素。海拔是影响系统发育结构变化的主要环境因子,而土壤因子是影响物种多样性与系统发育多样性的主要因素,进一步验证了物种多样性与系统发育多样性的高度相关,结果旨在揭示物种群落空间分布规律。     

Phylogenetic structure and phylogenetic diversity of angiosperm assemblages in forests along an elevational gradient in Changbaishan,China

Aims Understanding what drives the variation in species composition and diversity among local communities can provide insights into the mechanisms of community assembly. Because ecological traits are often thought to be phylogenetically conserved, there should be patterns in phylogenetic structure and phylogenetic diversity in local communities along ecological gradients. We investigate potential patterns in angiosperm assemblages along an elevational gradient with a steep ecological gradient in Changbaishan, China.Methods We used 13 angiosperm assemblages in forest plots (32×32 m) distributed along an elevational gradient from 720 to 1900 m above sea level. We used Faith's phylogenetic diversity metric to quantify the phylogenetic alpha diversity of each forest plot, used the net relatedness index to quantify the degree of phylogenetic relatedness among angiosperm species within each forest plot and used a phylogenetic dissimilarity index to quantify phylogenetic beta diversity among forest plots. We related the measures of phylogenetic structure and phylogenetic diversity to environmental (climatic and edaphic) factors.Important findings Our study showed that angiosperm assemblages tended to be more phylogenetically clustered at higher elevations in Changbaishan. This finding is consistent with the prediction of the phylogenetic niche conservatism hypothesis, which highlights the role of niche constraints in governing the phylogenetic structure of assemblages. Our study also showed that woody assemblages differ from herbaceous assemblages in several major aspects. First, phylogenetic clustering dominated in woody assemblages, whereas phylogenetic overdispersion dominated in herbaceous assemblages; second, patterns in phylogenetic relatedness along the elevational and temperature gradients of Changbaishan were stronger for woody assemblages than for herbaceous assemblages; third, environmental variables explained much more variations in phylogenetic relatedness, phylogenetic alpha diversity and phylogenetic beta diversity for woody assemblages than for herbaceous assemblages.     

Phylogenetic tests of community assembly across regional to continental scales in tropical and subtropical rain forests

Aim To measure and quantify community phylogenetic structure to evaluate how evolutionary, ecological and biogeographic processes have shaped the distributions and assemblage of tropical and subtropical rain forest tree species across local, regional and continental scales. Location Australia. Methods We used 596 assemblage‐level samples and 1137 woody species in rain forest vegetation sampled across two latitude regions (tropics and sub‐tropics) and five distinct areas. Based on this dataset, we obtained and analysed species‐level trait values (for leaf size, seed size, wood density and maximum height at maturity), measures of community phylogenetic structure and species turnover across space (beta) and evolutionary time (phylobeta). Results Phylobeta values showed that at continental scales (i.e. across the latitude regions combined) species replacement, as turnover in assemblages through time, was by more phylogenetically distant (i.e. less closely related) taxa. Within latitude regions replacement was by more closely related taxa. Assemblages of species were more phylogenetically clustered across the whole phylogeny (net relatedness index) and with respect to more recent divergences (nearest related taxon index) where the effects of historic disturbance (climatic oscillations) had been greater, and less clustered in long‐term stable (refugial) locations. Local species composition in the stable wet tropics showed significant phylogenetic evenness, but there was no corresponding evenness in distributions of the ecological traits measured. Main conclusions Despite a shared evolutionary and biogeographic history, the two regions diverged from each other before the development of internal divergences. Phylogenetic evenness is more evident in long‐term stable habitats (refugia) where species interact in conserved niches. Phylogenetic clustering is more evident where recolonization of more highly disturbed areas from historically reduced species pools reflects filtering of species into phylogenetically preferred habitats.     

芦芽山荷叶坪亚高山草甸生物多样性

以芦芽山荷叶坪亚高山草甸为研究对象,共设置150个5 m×5 m草本样方,进行群落生物学调查,对研究区36种草本植物重要值、α多样性指数、谱系多样性指数及其相关性进行研究.结果表明: 荷叶坪亚高山草甸物种多样性总体分布较均匀,边缘地区物种更丰富,呈现“边缘效应”;4个样地的群落谱系结构呈聚集模式,12个样地的群落谱系结构呈分散模式;谱系多样性指数(PD)与Petrick指数、Simpson指数和Shannon指数呈正相关,净亲缘关系指数(NRI)和最近种间亲缘关系指数(NTI)与α物种多样性指数无明显相关性.     

Phylogenetic community structure during succession: Evidence from three Neotropical forest sites

The phylogenetic structure of communities can reveal forces shaping community assembly, but the vast majority of work on phylogenetic community structure has been conducted in mature ecosystems. Here, we present an analysis of the phylogenetic structure of three Neotropical rain forest communities undergoing succession. In each site, the net relatedness of the community is initially high and consistently declines during succession. This pattern is evident both when comparing plots of different age classes and when comparing stem size classes within each plot: the oldest plots and the youngest stem cohorts, representing the most advanced stages of succession, have the lowest relatedness. Our results suggest that succession leaves a distinct signature in the phylogenetic structure of communities, which may reflect an increasing role of biotic interactions in community assembly during succession. We discuss theoretical explanations for the decline in community phylogenetic relatedness during succession, and suggest directions for future study.     

水淹干扰下水库水滨带植物群落谱系结构与物种多样性格局

群落谱系结构将物种系统发育信息整合到群落中,给生物多样性研究提供了全新视角。为探讨水淹干扰下水库水滨带植物群落物种多样性维持机制,以丹江口水库水滨带为研究区域,以南水北调中线一期工程运行前的原有水滨带植被为研究对象,分析不同水淹干扰强度下群落谱系结构和物种多样性及其与环境因素的关系。结果表明：(1)随着水淹干扰强度增加,群落物种丰富度、物种多样性和谱系多样性显著降低。谱系结构指数虽无显著差异,但随着水淹干扰强度增加呈现由发散到聚集的变化趋势。表明水滨带植物群落物种多样性维持机制是生境过滤和生态位分化共同驱动的结果,并且随着水淹干扰强度增加呈现生境过滤作用增加、物种间竞争排斥作用减弱的生态过程影响规律。(2)坡度、土壤质地、速效氮和全氮含量对整个水滨带植物群落物种丰富度、物种多样性和谱系多样性影响显著。此外,土层厚度和速效磷对物种丰富度和土层厚度对谱系多样性也影响显著。而仅有速效氮含量对谱系结构指数影响显著;轻度水淹干扰下坡向、速效磷含量与多样性指数显著相关;中度水淹干扰下坡度、土层厚度、土壤质地、土壤总氮含量与多样性指数显著相关,土壤pH、全氮和全磷含量与谱系结构指数显著相关;重度水淹...     

Phylogeny and co‐occurrence of mammal species on Southeast Asian islands

Aim Islands have often been used as model systems in community ecology. The incorporation of information on phylogenetic relatedness of species in studies of island assemblage structure is still uncommon, but could provide valuable insights into the processes of island community assembly. We propose six models of island community assembly that make different predictions about the associations between co‐occurrences of species pairs on islands, phylogenetic relatedness and ecological similarity. We then test these models using data on mammals of Southeast Asian islands. Location Two hundred and forty islands of the Sundaland region of Southeast Asia. Methods We quantified the co‐occurrence of species pairs on islands, and identified pairs that co‐occur more frequently (positive co‐occurrence) or less frequently (negative co‐occurrence) than expected under null models. We then examined the distributions of these significantly deviating pairs with respect to phylogenetic relatedness and ecological differentiation, and compared these patterns with those predicted by the six community assembly models. We used permutation regression to test whether co‐occurrence patterns are predicted by relatedness, body size difference or difference in diet quality. Separate co‐occurrence matrices were analysed in this way for seven mammal families and four smaller subsets of the islands of Sundaland. Results In many matrices, average numbers of negative co‐occurrences were higher than expected under null models. This is consistent with assemblage structuring by competition, but may also result from low geographic overlap of species pairs, which contributes to negative co‐occurrences at the archipelago‐wide level. Distributions of species pairs within plots of phylogenetic distance × ecological differentiation were consistent with competition, habitat filtering or within‐island speciation models, depending on the taxon. Regressions indicated that co‐occurrence was more likely among closely related species pairs within the Viverridae and Sciuridae, but in most matrices phylogenetic distance was unrelated to co‐occurrence. Main conclusions Simple deterministic models linking co‐occurrence with phylogeny and ecology are a useful framework for interpreting distributions and assemblage structure of island species. However, island assemblages in Sundaland have probably been shaped by a complex idiosyncratic set of interacting ecological and evolutionary processes, limiting the predictive power of such models.     

Landscape-driven effects on taxonomic,functional, and phylogenetic diversity of vegetation developing on sand-gravel pits of early successional stages

Among the key drivers of the progressive transformation of biomes are mining activities, usually leading to the establishment of novel ecosystems, characterized by new species assemblages, combinations of habitats, and unprecedented functioning. It remains unknown how the composition of surrounding land cover may influence species composition, community assembly processes, and the phylogenetic relatedness structure of vegetation developing spontaneously on these de novo established biological systems. In this study, I investigated the influence of different landscape types in the proximity of 31 sand-gravel pits of pioneer successional stages on vegetation's taxonomical, functional, and phylogenetic diversity. Further, I accounted for the effects of the surrounding landscape on ten ecological groups of plant species, and biotic novelty indices as a supporting explanation of mechanisms shaping the species' co-occurrence patterns. I explored that plants' functional and phylogenetic diversity was higher in pits surrounded by riverine landscape, and lower if the contribution of settlements in the surrounding landscape was higher. Both landscape features promoted the occurrence of exotic species on sand-gravel pits, but only the settlements' proportion exerted a positive effect on biotic novelty indices. On the other hand, pits with a prevalence of forests in the surroundings were dominated by phylogenetically diverse, but functionally more homogenous native taxa, reflected, inter alia, in negative effects of forests on biotic novelty indices. Comprehensive assessment of the impacts of the surrounding landscape on different components of plant diversity may be used as a useful predictor in the exploration of successional trajectories, as well as a helpful tool in the formulation of strategies for mining-transformed ecosystems management.     

Interactions,Environmental Sorting and Chance: Phylostructure of a Tropical Forest Assembly

Density dependence, environmental sorting and chance have been discussed for the purpose of understanding, predicting and explaining the species richness, composition and structural parameters of living communities. Different ecological mechanisms occur individually in an overlapping manner, so the structure of each local community is influenced by an independent mixture of these factors. To identify which of these factors prevails in organizing the species-rich tree community from 100 plots of 10 × 10 m in a primary forest patch (the Forest of Seu Nico – FSN, from the Atlantic Forest domain), we analyzed species-environment correlations via canonical correspondence analysis and identified two different pedo-environments. We analyzed the community’s phylogenetic structure using Phylocom 4.2 software to calculate the net relatedness index (NRI) and the nearest taxon index (NTI). Furthermore, we partitioned the total phylogenetic diversity into independent α and β components (Π_ST). To reveal the overlap of ecological mechanisms such as neutrality, environmental filtering and density-dependent factors, we analyzed the phylogenetic structure in both pedo-environments. The species-environment correlations observed in the FSN are weak in comparison with those found in other studies, although the permanent plot presents a short environmental gradient, dividing the plot into an upper, more acidic hillside and a lower, more fertile bottom. The overall phylogenetic structure of the FSN community shows strong and significant phylogenetic overdispersion. This overdispersion indicates that density-dependent factors, such as interspecific competition, play an important role in maintaining the species richness and community structure in megadiverse ecosystems such as the FSN when we assume traits to be conserved within evolutionary lineages. The NRI and NTI are correlated positively with the soil pH and negatively with the soil’s aluminum concentration, so the bottom plots show higher phylogenetic overdispersion and lower Π_ST values than the hillside plots. This pattern can be explained by the greater importance of environmental filters in more acidic soils that form less favorable habitats, while the influence of competition and therefore also the rate of competitive exclusion are higher in the more favorable, less acidic plots.     

Phylogenetic patterns of colonization and extinction in experimentally assembled plant communities

Background

Evolutionary history has provided insights into the assembly and functioning of plant communities, yet patterns of phylogenetic community structure have largely been based on non-dynamic observations of natural communities. We examined phylogenetic patterns of natural colonization, extinction and biomass production in experimentally assembled communities.

Methodology/Principal Findings

We used plant community phylogenetic patterns two years after experimental diversity treatments (1, 2, 4, 8 or 32 species) were discontinued. We constructed a 5-gene molecular phylogeny and statistically compared relatedness of species that colonized or went extinct to remaining community members and patterns of aboveground productivity. Phylogenetic relatedness converged as species-poor plots were colonized and speciose plots experienced extinctions, but plots maintained more differences in composition than in phylogenetic diversity. Successful colonists tended to either be closely or distantly related to community residents. Extinctions did not exhibit any strong relatedness patterns. Finally, plots that increased in phylogenetic diversity also increased in community productivity, though this effect was inseparable from legume colonization, since these colonists tended to be phylogenetically distantly related.

Conclusions

We found that successful non-legume colonists were typically found where close relatives already existed in the sown community; in contrast, successful legume colonists (on their own long branch in the phylogeny) resulted in plots that were colonized by distant relatives. While extinctions exhibited no pattern with respect to relatedness to sown plotmates, extinction plus colonization resulted in communities that converged to similar phylogenetic diversity values, while maintaining differences in species composition.     

The equivalence of two phylogenetic biodiversity measures: the Shapley value and Fair Proportion index

Most biodiversity conservation programs are forced to prioritise species in order to allocate their funding. This paper contains a mathematical proof that provides biological support for one common approach based on phylogenetic indices. Phylogenetic trees describe the evolutionary relationships between a group of taxa. Two indices for computing the distinctiveness of each taxon in a phylogenetic tree are considered here—the Shapley value and the Fair Proportion index. These indices provide a measure of the importance of each taxon for overall biodiversity and have been used to prioritise taxa for conservation. The Shapley value is the biodiversity contribution a taxon is expected to make if all taxa are equally likely to become extinct. This interpretation makes it appealing to use the Shapley value in biodiversity conservation applications. The Fair Proportion index lacks a convenient interpretation, however it is significantly easier to calculate and understand. It has been empirically observed that there is a high correlation between the two indices. This paper shows the mathematical basis for this correlation and proves that as the number of taxa increases, the indices become equivalent. Consequently in biodiversity prioritisation the simpler Fair Proportion index can be used whilst retaining the appealing interpretation of the Shapley value.     

Climate and Species Richness Predict the Phylogenetic Structure of African Mammal Communities

We have little knowledge of how climatic variation (and by proxy, habitat variation) influences the phylogenetic structure of tropical communities. Here, we quantified the phylogenetic structure of mammal communities in Africa to investigate how community structure varies with respect to climate and species richness variation across the continent. In addition, we investigated how phylogenetic patterns vary across carnivores, primates, and ungulates. We predicted that climate would differentially affect the structure of communities from different clades due to between-clade biological variation. We examined 203 communities using two metrics, the net relatedness (NRI) and nearest taxon (NTI) indices. We used simultaneous autoregressive models to predict community phylogenetic structure from climate variables and species richness. We found that most individual communities exhibited a phylogenetic structure consistent with a null model, but both climate and species richness significantly predicted variation in community phylogenetic metrics. Using NTI, species rich communities were composed of more distantly related taxa for all mammal communities, as well as for communities of carnivorans or ungulates. Temperature seasonality predicted the phylogenetic structure of mammal, carnivoran, and ungulate communities, and annual rainfall predicted primate community structure. Additional climate variables related to temperature and rainfall also predicted the phylogenetic structure of ungulate communities. We suggest that both past interspecific competition and habitat filtering have shaped variation in tropical mammal communities. The significant effect of climatic factors on community structure has important implications for the diversity of mammal communities given current models of future climate change.     

Disentangling niche and neutral influences on community assembly: assessing the performance of community phylogenetic structure tests

Patterns of phylogenetic relatedness within communities have been widely used to infer the importance of different ecological and evolutionary processes during community assembly, but little is known about the relative ability of community phylogenetics methods and null models to detect the signature of processes such as dispersal, competition and filtering under different models of trait evolution. Using a metacommunity simulation incorporating quantitative models of trait evolution and community assembly, I assessed the performance of different tests that have been used to measure community phylogenetic structure. All tests were sensitive to the relative phylogenetic signal in species metacommunity abundances and traits; methods that were most sensitive to the effects of niche-based processes on community structure were also more likely to find non-random patterns of community phylogenetic structure under dispersal assembly. When used with a null model that maintained species occurrence frequency in random communities, several metrics could detect niche-based assembly when there was strong phylogenetic signal in species traits, when multiple traits were involved in community assembly, and in the presence of environmental heterogeneity. Interpretations of the causes of community phylogenetic structure should be modified to account for the influence of dispersal.     

The influence of historical dispersal on the phylogenetic structure of tree communities in the tropical Andes

We test for evidence of the Tropical Niche Conservatism or the Out of The Tropics hypotheses in structuring patterns of tree community composition along a 2000 + meter elevational gradient in the northern tropical Andes. By collecting and integrating data on the presence–absence of tree species within plots with phylogenetic information, we analyzed the following: (a) patterns of phylogenetic dispersion and species diversity along the elevational gradient based on indexes of net relatedness, nearest taxon relatedness, and species richness (α‐diversity); and (b) the replacement of lineages along the gradient using the PhyloSorensen metric (β‐diversity). More specifically, we established 20 0.25‐ha permanent tree inventory plots between 750 and 2,802 m asl where all individuals with diameter at breast height (DBH) ≥ 10 cm were measured and identified. We then used a series of linear models to test for changes in α and β diversity between plots in relation to elevation. Neither the net relatedness index nor the nearest taxon index showed a significant relationship with elevation. However, there was greater phylogenetic overdispersion at intermediate elevations; this likely reflects the mixing of species with contrasting origins from tropical and temperate lineages. β‐diversity between plots was negatively related to the corresponding difference in elevation, indicating that closely related lineages occupy similar ranges of elevation and temperature. We conclude that the immigration of lineages from extra‐tropical regions has significant effects in determining the phylogenetic structure of tree communities in tropical Andean forests. Abstract in Spanish is available with online material.     

Phylogenetic analysis suggests that habitat filtering is structuring marine bacterial communities across the globe

The phylogenetic structure and community composition were analysed in an existing data set of marine bacterioplankton communities to elucidate the evolutionary and ecological processes dictating the assembly. The communities were sampled from coastal waters at nine locations distributed worldwide and were examined through the use of comprehensive clone libraries of 16S ribosomal RNA genes. The analyses show that the local communities are phylogenetically different from each other and that a majority of them are phylogenetically clustered, i.e. the species (operational taxonomic units) were more related to each other than expected by chance. Accordingly, the local communities were assembled non-randomly from the global pool of available bacterioplankton. Further, the phylogenetic structures of the communities were related to the water temperature at the locations. In agreement with similar studies, including both macroorganisms and bacteria, these results suggest that marine bacterial communities are structured by “habitat filtering”, i.e. through non-random colonization and invasion determined by environmental characteristics. Different bacterial types seem to have different ecological niches that dictate their survival in different habitats. Other eco-evolutionary processes that may contribute to the observed phylogenetic patterns are discussed. The results also imply a mapping between phenotype and phylogenetic relatedness which facilitates the use of community phylogenetic structure analysis to infer ecological and evolutionary assembly processes.     

The Interplay between Environmental Filtering and Spatial Processes in Structuring Communities: The Case of Neotropical Snake Communities

Both habitat filters and spatial processes can influence community structure. Space alone affects species immigration from the regional species pool, whereas habitat filters affect species distribution and inter-specific interactions. This study aimed to understand how the interplay between environmental and geographical processes influenced the structure of Neotropical snake communities in different habitat types. We selected six studies that sampled snakes in forests, four conducted in savannas and two in grasslands (the latter two are grouped in a non-forest category). We used the net relatedness and nearest taxon indices to assess phylogenetic structure within forest and non-forest areas. We also used the phylogenetic fuzzy-weighting algorithm to characterize phylogenetic structure across communities and the relation of phylogenetic composition patterns to habitat type, structure, and latitude. Finally, we tested for morphological trait convergence and phylogenetic niche conservatism using four forest and four non-forest areas for which morphological data were available. Community phylogenetic composition changed across forest and non-forest areas suggesting that environmental filtering influences community structure. Species traits were affected by habitat type, indicating convergence at the metacommunity level. Tail length, robustness, and number of ventral scales maximized community convergence among forest and non-forest areas. The observed patterns suggested environmental filtering, indicating that less vertically structured habitats represent a strong filter. Despite the fact that phylogenetic structure was not detected individually for each community, we observed a trend towards communities composed by more closely related species in higher latitudes and more overdispersed compositions in lower latitudes. Such pattern suggests that the limited distribution of major snake lineages constrained species distributions. Structure indices for each community were also related to habitat type, showing that communities from non-forest areas tend to be more clustered. Our study showed that both environmental filtering and spatial gradients play important roles in shaping the composition of Neotropical snake communities.     

A ‘fast-food approach’ to the standardization of quadratic diversity

Abstract

Intuitively, a community composed of ecologically dissimilar taxa is more diverse than a community composed of more similar taxa. However, since traditional diversity indices such as Shannon's entropy or Simpson's diversity are computed solely from the relative abundances of a given species assemblage, they cannot account for ecological differences between species. There have been recent developments regarding the use of quadratic entropy, a diversity index that incorporates both species relative abundances and a measure of the pairwise ecological differences between species. In this paper we firstly show that under some specific circumstances quadratic entropy can be additively decomposed into α- β- and γ-diversities, a property that renders it a desirable measure of diversity in the ecological practice. Next, we suggest a quick and simple method for obtaining a standardized version of quadratic entropy that may allow an easier interpretation of the resulting diversity values.