沿海拔梯度变化的哀牢山亚热带森林群落系统发育结构

为揭示森林群落系统发育结构在海拔梯度上的变化及其驱动因素, 本研究以云南哀牢山西坡的亚热带森林群落为研究对象, 以APG III系统为基础框架, 结合DNA条形码序列信息解决末端分类单元亲缘关系的方法, 构建了哀牢山森林群落系统发育进化树, 采用净亲缘指数(net relatedness index, NRI)和最近亲缘指数(nearest taxon index, NTI), 探讨了不同植被类型的森林群落系统发育结构和沿海拔梯度的变化规律。结果表明, 从整体的海拔变化趋势上来看, 哀牢山森林群落系统发育结构随海拔上升由系统发育聚集(phylogenetic clustering)走向发散(phylogenetic overdispersion)或聚集程度降低。在低海拔地区, 群落表现为系统发育聚集, 表明生态位理论中的生境过滤作用在群落构建和生物多样性的维持中起着主导作用; 在中海拔地区, 出现了聚集与发散两种群落系统发育结构并存的现象, 推测可能是生境过滤和竞争排斥两种生态过程共同作用的结果; 在高海拔地区, 群落的系统发育结构因选择的指数不同而出现相反的结果, NRI表现出系统发育聚集, 而NTI却表现为随机或发散, 考虑到高海拔地区的环境胁迫可能促使植物发生趋同进化, 推测其群落构建的生态学过程需要更为综合的研究。本研究揭示群落系统发育结构沿海拔梯度确实存在显著的变化, 证明在生态群落的构建过程中非随机过程起到促进乃至关键作用。     

Species richness and phylogenetic diversity of seed plants across vegetation zones of Mount Kenya,East Africa

Mount Kenya is of ecological importance in tropical east Africa due to the dramatic gradient in vegetation types that can be observed from low to high elevation zones. However, species richness and phylogenetic diversity of this mountain have not been well studied. Here, we surveyed distribution patterns for a total of 1,335 seed plants of this mountain and calculated species richness and phylogenetic diversity across seven vegetation zones. We also measured phylogenetic structure using the net relatedness index (NRI) and the nearest species index (NTI). Our results show that lower montane wet forest has the highest level of species richness, density, and phylogenetic diversity of woody plants, while lower montane dry forest has the highest level of species richness, density, and phylogenetic diversity in herbaceous plants. In total plants, NRI and NTI of four forest zones were smaller than three alpine zones. In woody plants, lower montane wet forest and upper montane forest have overdispersed phylogenetic structures. In herbaceous plants, NRI of Afro‐alpine zone and nival zone are smaller than those of bamboo zone, upper montane forest, and heath zone. We suggest that compared to open dry forest, humid forest has fewer herbaceous plants because of the closed canopy of woody plants. Woody plants may have climate‐dominated niches, whereas herbaceous plants may have edaphic and microhabitat‐dominated niches. We also proposed lower and upper montane forests with high species richness or overdispersed phylogenetic structures as the priority areas in conservation of Mount Kenya and other high mountains in the Eastern Afro‐montane biodiversity hotspot regions.     

Multi-scale phylogenetic structure in coastal dune plant communities across the globe

Aims Studies integrating phylogenetic history and large-scale community assembly are few, and many questions remain unanswered. Here, we use a global coastal dune plant data set to uncover the important factors in community assembly across scales from the local filtering processes to the global long-term diversification and dispersal dynamics. Coastal dune plant communities occur worldwide under a wide range of climatic and geologic conditions as well as in all biogeographic regions. However, global patterns in the phylogenetic composition of coastal dune plant communities have not previously been studied.Methods The data set comprised vegetation data from 18463 plots in New Zealand, South Africa, South America, North America and Europe. The phylogenetic tree comprised 2241 plant species from 149 families. We calculated phylogenetic clustering (Net Relatedness Index, NRI, and Nearest Taxon Index, NTI) of regional dune floras to estimate the amount of in situ diversification relative to the global dune species pool and evaluated the relative importance of land and climate barriers for these diversification patterns by geographic analyses of phylogenetic similarity. We then tested whether dune plant communities exhibit similar patterns of phylogenetic structure within regions. Finally, we calculated NRI for local communities relative to the regional species pool and tested for an association with functional traits (plant height and seed mass) thought to vary along sea–inland gradients.Important findings Regional species pools were phylogenetically clustered relative to the global pool, indicating regional diversification. NTI showed stronger clustering than NRI pointing to the importance of especially recent diversifications within regions. The species pools grouped phylogenetically into two clusters on either side of the tropics suggesting greater dispersal rates within hemispheres than between hemispheres. Local NRI plot values confirmed that most communities were also phylogenetically clustered within regions. NRI values decreased with increasing plant height and seed mass, indicating greater phylogenetic clustering in communities with short maximum height and good dispersers prone to wind and tidal disturbance as well as salt spray, consistent with environmental filtering along sea–inland gradients. Height and seed mass both showed significant phylogenetic signal, and NRI tended to correlate negatively with both at the plot level. Low NRI plots tended to represent coastal scrub and forest, whereas high NRI plots tended to represent herb-dominated vegetation. We conclude that regional diversification processes play a role in dune plant community assembly, with convergence in local phylogenetic community structure and local variation in community structure probably reflecting consistent coastal-inland gradients. Our study contributes to a better understanding of the globally distributed dynamic coastal ecosystems and the structuring factors working on dune plant communities across spatial scales and regions.     

Climatic correlates of phylogenetic relatedness of woody angiosperms in forest communities along a tropical elevational gradient in South America

Aims This study assesses the relationship between phylogenetic relatedness of angiosperm tree species and climatic variables in local forests distributed along a tropical elevational gradient in South America. In particular, this paper addresses two questions: Is phylogenetic relatedness of plant species in communities related to temperature variables more strongly than to water variables for tropical elevational gradients? Is phylogenetic relatedness of plant species in communities driven by extreme climatic conditions (e.g. minimum temperature (MT) and water deficit) more strongly than by climatic seasonal variability (e.g. temperature seasonality and precipitation seasonality)?Methods I used a set of 34 angiosperm woody plant assemblages along an elevational gradient in the Andes within less than 5 degrees of the equator. Phylogenetic relatedness was quantified as net relatedness index (NRI) and nearest taxon index (NTI) and was related to major climatic variables. Correlation analysis and structure equation modeling approach were used to assess the relationships between phylogenetic relatedness and climatic variables.Important findings Phylogenetic relatedness of angiosperm woody species in the local forest communities is more strongly associated with temperature-related variables than with water-related variables, is positively correlated with mean annual temperature (MAT) and MT, and is related with extreme cold temperature more strongly than with seasonal temperature variability. NTI was related with elevation, MAT and MT more strongly than was NRI. Niche convergence, rather than niche conservatism, has played a primary role in driving community assembly in local forests along the tropical elevational gradient examined. Negative correlations of phylogenetic relatedness with elevation and higher correlations of phylogenetic relatedness with elevation and temperature for NTI than for NRI indicate that evolution of cold tolerance at high elevations in tropical regions primarily occurred at recent (terminal) phylogenetic nodes widely distributed among major clades.     

不同空间尺度西藏色季拉山急尖长苞冷杉群落谱系结构特征

基于西藏色季拉山4 hm²亚高山暗针叶林固定样地调查数据,分析了急尖长苞冷杉群落内6个径级(1～2、2～4、4～7、7～11、11～16、>16 cm)的植物在5个空间尺度(5 m×5 m、10 m×10 m、20 m×20 m、50 m×50 m、100 m×100 m)上的谱系结构。结果表明: 不同空间尺度上,该群落的净谱系亲缘关系指数(NRI)和净最近种间亲缘关系指数(NTI)值均大于零,整体上表现为谱系聚集。在小空间尺度(5 m×5 m)上,谱系结构聚集强度最大。在所有空间尺度上,群落内小径级个体表现为谱系聚集,随着径级的增大(DBH>7 cm),逐渐表现为谱系发散,且发散程度随径级增加而增大。小径级个体的谱系聚集强度随空间尺度而增大;而大径级个体(DBH>7 cm)的谱系发散程度随空间尺度增加而增大。小径级群落的生境过滤和大径级群落的竞争排斥作用可能是驱动该区域急尖长苞冷杉群落构建的主要生态学过程。     

Altitudinal biodiversity patterns of seed plants along Gongga Mountain in the southeastern Qinghai–Tibetan Plateau

The mechanisms underlying elevation patterns in species and phylogenetic diversity remain a central issue in ecology and are vital for effective biodiversity conservation in the mountains. Gongga Mountain, located in the southeastern Qinghai–Tibetan Plateau, represents one of the longest elevational gradients (ca. 6,500 m, from ca. 1,000 to 7,556 m) in the world for studying species diversity patterns. However, the elevational gradient and conservation of plant species diversity and phylogenetic diversity in this mountain remain poorly studied. Here, we compiled the elevational distributions of 2,667 native seed plant species occurring in Gongga Mountain, and estimated the species diversity, phylogenetic diversity, species density, and phylogenetic relatedness across ten elevation belts and five vegetation zones. The results indicated that species diversity and phylogenetic diversity of all seed plants showed a hump‐shaped pattern, peaking at 1,800–2,200 m. Species diversity was significantly correlated with phylogenetic diversity and species density. The floras in temperate coniferous broad‐leaved mixed forests, subalpine coniferous forests, and alpine shrublands and meadows were significantly phylogenetically clustered, whereas the floras in evergreen broad‐leaved forests had phylogenetically random structure. Both climate and human pressure had strong correlation with species diversity, phylogenetic diversity, and phylogenetic structure of seed plants. Our results suggest that the evergreen broad‐leaved forests and coniferous broad‐leaved mixed forests at low to mid elevations deserve more conservation efforts. This study improves our understanding on the elevational gradients of species and phylogenetic diversity and their determinants and provides support for improvement of seed plant conservation in Gongga Mountain.     

Phylogenetic diversity of macromycetes and woody plants along an elevational gradient in Eastern Mexico

Phylogenetic information provides insight into the ecological and evolutionary processes that organize species assemblages. We compared patterns of phylogenetic diversity among macromycete and woody plant communities along a steep elevational gradient in eastern Mexico to better understand the evolutionary processes that structure their communities. Macrofungi and trees were counted and identified in eight sites from 100 to 3500 m asl, and sequence data retrieved from GenBank for the same or closely related species were used to reconstruct their phylogenies. Patterns of species richness and phylogenetic diversity were similar for both macrofungi and trees, but macromycete richness and diversity peaked at mid‐elevations, whereas woody plant richness and diversity did not show significant trends with elevation. Phylogenetic similarity among sites was low for both groups and decreased as elevational distance between sites increased. Macromycete communities displayed phylogenetic overdispersion at low elevations and phylogenetic clustering at high elevations; the latter is consistent with environmental filtering at high elevation sites. Woody plants generally exhibited phylogenetic clustering, consistent with the potential importance of environmental filtering throughout the elevational gradient.     

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.     

山西陵川南方红豆杉自然保护区鹅耳枥植物群落谱系结构特征

分析植物群落谱系结构,可以探究乔木层、灌木层和草本层物种对环境变化的响应情况。以山西陵川南方红豆杉自然保护区鹅耳枥群落为研究对象,采用样方法,分别从不同径级和不同坡向对鹅耳枥群落净谱系亲缘关系指数(Net relatedness index,NRI)和净最近种间亲缘关系指数(Nearest taxon index,NTI)进行研究,探讨了鹅耳枥群落沿着径级梯度形成群落谱系结构特征,进而分析了鹅耳枥群落构建的历史进程。结果表明:(1)该保护区鹅耳枥群落乔木层(26种)、灌木层(32种)和草本层(39种)谱系结构树可分为5个类群、5个类群和4个类群;乔木层(86.67%的样地,下同)和灌木层(73.33%)物种群落谱系结构呈谱系发散格局(NRI0,NTI0),但草本层(86.67%)物种群落谱系结构呈谱系聚集格局(NRI0,NTI0)。(2)鹅耳枥群落乔木层中,DBH在Ⅰ级至Ⅱ级间,NRI指数随着DBH的增大而减小,NTI指数随着DBH的增大而增大;在Ⅱ级至Ⅴ级之间,随着植物DBH增大NRI指数和NTI指数值均呈下降趋势;而且在不同DBH水平上群落NRI和NTI指数均差异显著(P0.05),说明随着径级的增大,群落谱系结构由谱系聚集变为谱系发散。(3)灌木层物种谱系结构在阴坡和阳坡均呈聚集型,乔木层阴坡物种的谱系结构呈发散型(NRI0,NTI0),乔木层阳坡和草本层阴阳坡群落均无法判定群落谱系结构是聚集还是发散。     

物种谱系不确定性对群落谱系格局指标的影响

物种谱系关系常被用于衡量群落谱系格局及推断格局背后的生态过程,但多数研究往往忽视谱系关系的不确定性及其可能对群落谱系格局造成的影响.为此,本文以浙江天童20 hm^2样地内150个树种为研究对象,采用这些物种叶绿体DNA的rbcL和matK碱基序列构建1棵一致系统发育树和反映谱系不确定性的999棵系统发育树,然后结合样地物种分布数据计算标准化净亲缘指数(NRI)和最近亲缘指数(NTI),最后运用独立置换零模型衡量样地群落谱系格局.结果表明:物种系统发育树在拓扑结构和物种谱系分支节点年龄上均存在较大的不确定性,谱系不确定性随着谱系分支节点年龄的减小而增大,也随物种间平均谱系距离的增加而增加;在样方尺度上,物种谱系的不确定性增加了标准化NRI和NTI指数的变异,但对两个指数的影响几乎独立;其对两指数的空间分布影响不同,且程度不一,其中标准化NRI受到的影响相对更大;在群落尺度上,物种谱系的不确定性增加了标准化NRI和NTI的变异,平均变异系数分别为0.37和0.077,表明群落水平的标准化NRI更易受到谱系不确定性的影响.这说明物种谱系不确定性会传递到常用的群落谱系格局指标中,且不同指标受影响的程度不同,进而影响对群落谱系格局的衡量及相关生态过程的推断.该结论也暗示以往不考虑谱系不确定性的研究中,非随机的群落谱系格局比例可能被高估.     

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。     

Historical and contemporary determinants of global phylogenetic structure in tropical reef fish faunas

Identifying the main determinants of tropical marine biodiversity is essential for devising appropriate conservation measures mitigating the ongoing degradation of coral reef habitats. Based on a gridded distribution database and phylogenetic information, we compared the phylogenetic structure of assemblages for three tropical reef fish families (Labridae: wrasses, Pomacentridae: damselfishes and Chaetodontidae: butterflyfishes) using the net relatedness (NRI) and nearest taxon (NTI) indices. We then related these indices to contemporary and historical environmental conditions of coral reefs using spatial regression analyses. Higher levels of phylogenetic clustering were found for fish assemblages in the Indo‐Australian Archipelago (IAA), and more particularly when considering the NTI index. The phylogenetic structure of the Pomacentridae, and to a lower extent of the Chaeotodontidae and Labridae, was primarily associated with the location of refugia during the Quaternary period. Phylogenetic clustering in the IAA may partly result from vicariance events associated with coral reef fragmentation during the glacial periods of the Quaternary. Variation in the patterns among fish families further suggest that dispersal abilities may have interacted with past habitat availability in shaping the phylogenetic structure of tropical reef fish assemblages.     

基于系统发育的燕山东麓植物群落的构建机制

群落构建机制对解释植物物种共存、多样性的维持与发展至关重要。本文以燕山山脉东麓的植物群落为研究对象,野外调查了374个植物样方（20 m×30 m）。通过多元回归树、植物群落亲缘关系指数、高斯核函数密度估计等研究,重点探究了植物群落构建的机制。研究结果表明,燕山东麓的植物群落可划分为以荆条（Vitex negundo var.heterophylla）、槲栎（Quercus aliena）、蒙古栎（Quercus mongolica）、栓皮栎（Quercus variabilis）和白蜡树（Fraxinus chinensis）为优势的5个群系。植物最大树高这一功能性状表现出了较强的系统发育信号,此区域植物功能性状保守性较强。荆条灌丛、槲栎、蒙古栎群系的群落构建过程以环境过滤为主导,栓皮栎群系的群落构建过程以负密度制约为主导,白蜡树群落的构建机制有由环境过滤向负密度制约过渡的趋势。另外,本文引用高斯核密度分布估计对亲缘关系指数的分布进行估计,直观、真实地反映了亲缘关系指数的个体值及整体趋势,为探讨群落构建的生态位机制和中性理论间的争论提供更直接的证据。     

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.     

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.     

Exploring the community phylogenetic structure along the slope aspect of subalpine meadows in the eastern Qinghai–Tibetan Plateau,China

Exploring the community assembly has been important for explaining the maintenance mechanisms of biodiversity and species coexistence, in that it is a central issue in community ecology. Here, we examined patterns of the community phylogenetic structure of the subalpine meadow plant community along the slope gradient in the Qinghai–Tibetan Plateau of China. We surveyed all species and constructed the phylogenetic tree of the plant community based on data from the Angiosperm Phylogeny Group III. We selected the net relative index (NRI) and evaluated the community phylogenetic structure along the five slope plants communities. We found that the phylogenetic structure varied from phylogenetic clustering to phylogenetic overdispersion with the slope aspect from north to south. In the north slope, the community phylogenetically cluster indicated that the limiting similarity played a leading role in the community assembly and the maintenance of biodiversity. Community phylogenetic overdispersion in the east, southeast, and south slopes indicated that habitat filtration was the driving force for community assembly. The NRI index of the northeast slope was close to zero, implying random dispersion. But it may be driven by the neutral process or limiting similarity, in that the community assembly process was the result of a combination of several ecological factors and thus required further study.     

物种多度和径级尺度对于评价群落系统发育结构的影响: 以尖峰岭热带山地雨林为例

研究不同径级尺度群落系统发育多样性有助于了解不同年龄模式下物种的亲缘关系及其群落系统发育结构; 但是关于物种多度对群落系统发育结构影响的研究较少。以海南尖峰岭热带山地雨林群落为例, 首先在不同径级尺度比较物种多度加权与否分别对4个广泛采用的系统发育指数的影响, 继而利用其中2个经过标准化处理的系统发育多样性指数: 净种间亲缘关系指数(net relatedness index, NRI)和净最近种间亲缘关系指数(nearest taxon index, NTI), 结合群落的生境类型来量度不同局域生境条件下不同径级尺度木本植物系统发育关系。结果发现: (1)未考虑物种多度加权的系统发育平均成对距离(mean pairwise distance, MPD)指数比考虑物种多度加权的MPD指数显著地高估了群落整体系统发育多样性, 且这种现象在小径级尺度(1 cm≤DBH<5 cm)最为明显。因此, 在森林监测样地中对于中、小径级群落系统发育结构研究中建议考虑物种多度信息。(2) 从群落组成整体系统发育结构来看, 尖峰岭热带山地雨林在几乎所有径级尺度和生境下均倾向于系统发育发散, 且随着径级的递增发散程度趋于明显(NRI<0)。(3)从群落组成局部系统发育结构来看, 尖峰岭热带山地雨林在中、小径级倾向于系统发育聚集(NTI>0), 而在大径级(DBH≥15 cm)则倾向于系统发育发散(NTI<0)。总之, 研究群落系统发育结构时应考虑物种多度的影响以及径级尺度效应。     

Directional biases in phylogenetic structure quantification: a Mediterranean case study

Recent years have seen an increasing effort to incorporate phylogenetic hypotheses to the study of community assembly processes. The incorporation of such evolutionary information has been eased by the emergence of specialized software for the automatic estimation of partially resolved supertrees based on published phylogenies. Despite this growing interest in the use of phylogenies in ecological research, very few studies have attempted to quantify the potential biases related to the use of partially resolved phylogenies and to branch length accuracy, and no work has examined how tree shape may affect inference of community phylogenetic metrics. In this study, we tested the influence of phylogenetic resolution and branch length information on the quantification of phylogenetic structure, and also explored the impact of tree shape (stemminess) on the loss of accuracy in phylogenetic structure quantification due to phylogenetic resolution. For this purpose, we used 9 sets of phylogenetic hypotheses of varying resolution and branch lengths to calculate three indices of phylogenetic structure: the mean phylogenetic distance (NRI), the mean nearest taxon distance (NTI) and phylogenetic diversity (stdPD) metrics. The NRI metric was the less sensitive to phylogenetic resolution, stdPD showed an intermediate sensitivity, and NTI was the most sensitive one; NRI was also less sensitive to branch length accuracy than NTI and stdPD, the degree of sensitivity being strongly dependent on the dating method and the sample size. Directional biases were generally towards type II errors. Interestingly, we detected that tree shape influenced the accuracy loss derived from the lack of phylogenetic resolution, particularly for NRI and stdPD. We conclude that well‐resolved molecular phylogenies with accurate branch length information are needed to identify the underlying phylogenetic structure of communities, and also that sensitivity of phylogenetic structure measures to low phylogenetic resolution can strongly vary depending on phylogenetic tree shape.     

Phylogenetic habitat filtering influences forest nucleation in grasslands

Because species–environment interactions are mediated by phenotypic tradeoffs, the maintenance of ancestral traits in some phylogenetic clades and the emergence of evolutionary novelties in others are likely to limit the types of habitats that species occupy, generating phylogenetic habitat filtering. To test for phylogenetic habitat filtering in woody sapling communities in vegetation patches scattered in southern Brazilian grasslands, I estimated if patches of different sizes encompassed species of different phylogenetic groups. I analyzed patch composition with principal coordinates of phylogenetic structure (PCPS), extracted from a matrix of phylogeny‐weighted species composition, and compared these results against net relatedness index (NRI) analyses. NRI analysis revealed that most communities were phylogenetically random, and that patches of different sizes did not differ from each other with respect to NRI. The first four PCPS contained ? 91% of total variation in phylogeny‐weighted species composition. In the first two PCPS, scores of large patches differed from those of small and medium patches, which did not differ from each other. Large patches were associated with basal plant clades, whereas small patches were mostly related to asterids, and medium patches were phylogenetically diverse. Phylogenetic habitat filtering was detected only by PCPS analysis, possibly because NRI analysis does not take into account the habitat specificity of species. Taking phylogenetic habitat filtering into account in comparative studies likely enhances our capability to understand the ways that plants interact with their environment.