Environmental filtering is the main assembly rule of ground beetles in the forest and its edge but not in the adjacent grassland

In a fragmented landscape,transitional zones between neighboring habitats are common,and our understanding of community organizational forces across such habitats is important.Edge studies are numerous,but the majority of them utilize information on species richness and abundance.Abundance and taxonomic diversity,however,provide little information on the functioning and phylogeny of the co-existing species.Combining the evaluation of their functional and phylogenetic relationships,we aimed to assess whether ground beetle assemblages are deterministically or stochastically structured along grassland-forest gradients.Our results showed different community assembly rules on opposite sides of the forest edge.In the grassland,co-occurring species were functionally and phylogenetically not different from the random null model,indicating a random assembly process.Contrary to this,at the forest edge and the interior,co-occurring species showed functional and phylogenetic clustering,thus environmental filtering was the likely process structuring carabid assemblages.Community assembly in the grassland was considerably affected by asymmetrical species flows (spillover)across the forest edge:more forest species penetrated into the grassland than open-habitat and generalist species entered into the forest.This asymmetrical species flow underlines the importance of the filter function of forest edges.As unfavorable,human-induced changes to the structure,composition and characteristics of forest edges may alter their filter function,edges have to be specifically considered during conservation management.     

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.     

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。     

Examining differences in phylogenetic composition enhances understanding of the phylogenetic structure of the shrub community in the northeastern Qinghai‐Tibetan Plateau

Periodic climatic oscillations and species dispersal during the postglacial period are two important causes of plant assemblage and distribution on the Qinghai‐Tibet Plateau (QTP). To improve our understanding of the bio‐geological histories of shrub communities on the QTP, we tested two hypotheses. First, the intensity of climatic oscillations played a filtering role during community structuring. Second, species dispersal during the postglacial period contributed to the recovery of species and phylogenetic diversity and the emergence of phylogenetic overdispersion. To test these hypotheses, we investigated and compared the shrub communities in the alpine and desert habitats of the northeastern QTP. Notably, we observed higher levels of species and phylogenetic diversity in the alpine habitat than in the desert habitat, leading to phylogenetic overdispersion in the alpine shrub communities versus phylogenetic clustering in the desert shrub communities. This phylogenetic overdispersion increased with greater climate anomalies. These results suggest that (a) although climate anomalies strongly affect shrub communities, these phenomena do not act as a filter for shrub community structuring, and (b) species dispersal increases phylogenetic diversity and overdispersion in a community. Moreover, our investigation of the phylogenetic community composition revealed a larger number of plant clades in the alpine shrub communities than in the desert shrub communities, which provided insights into plant clade‐level differences in the phylogenetic structures of alpine and desert shrub communities in the northeastern QTP.     

Phylogenetic community structure metrics and null models: a review with new methods and software

Competitive exclusion and habitat filtering influence community assembly, but ecologists and evolutionary biologists have not reached consensus on how to quantify patterns that would reveal the action of these processes. Currently, at least 22 α‐diversity and 10 β‐diversity metrics of community phylogenetic structure can be combined with nine null models (eight for β‐diversity metrics), providing 278 potentially distinct approaches to test for phylogenetic clustering and overdispersion. Selecting the appropriate approach for a study is daunting. First, we describe similarities among metrics and null models across variance in phylogeny size and shape, species abundance, and species richness. Second, we develop spatially explicit, individual‐based simulations of neutral, competitive exclusion, or habitat filtering community assembly, and quantify the performance (type I and II error rates) of all 278 metric and null model combinations against each assembly process. Many α‐diversity metrics and null models are at least functionally equivalent, reducing the number of truly unique metrics to 12 and the number of unique metric + null model combinations to 72. An even smaller subset of metric and null model combinations showed robust statistical performance. For α‐diversity metrics, phylogenetic diversity and mean nearest taxon distance were best able to detect habitat filtering, while mean pairwise phylogenetic distance‐based metrics were best able to detect competitive exclusion. Overall, β‐diversity metrics tended to have greater power to detect habitat filtering and competitive exclusion than α‐diversity metrics, but had higher type 1 error in some cases. Across both α‐ and β‐diversity metrics, null model selection affected type I error rates more than metric selection. A null model that maintained species richness, and approximately maintained species occurrence frequency and abundance across sites, exhibited low type I and II error rates. This regional null model simulates neutral dispersal of individuals into local communities by sampling from a regional species pool. We introduce a flexible new R package, metricTester, to facilitate robust analyses of method performance.     

Pervasive Local-Scale Tree-Soil Habitat Association in a Tropical Forest Community

We examined tree-soil habitat associations in lowland forest communities at Paracou, French Guiana. We analyzed a large dataset assembling six permanent plots totaling 37.5 ha, in which extensive LIDAR-derived topographical data and soil chemical and physical data have been integrated with precise botanical determinations. Map of relative elevation from the nearest stream summarized both soil fertility and hydromorphic characteristics, with seasonally inundated bottomlands having higher soil phosphate content and base saturation, and plateaus having higher soil carbon, nitrogen and aluminum contents. We employed a statistical test of correlations between tree species density and environmental maps, by generating Monte Carlo simulations of random raster images that preserve autocorrelation of the original maps. Nearly three fourths of the 94 taxa with at least one stem per ha showed a significant correlation between tree density and relative elevation, revealing contrasted species-habitat associations in term of abundance, with seasonally inundated bottomlands (24.5% of species) and well-drained plateaus (48.9% of species). We also observed species preferences for environments with or without steep slopes (13.8% and 10.6%, respectively). We observed that closely-related species were frequently associated with different soil habitats in this region (70% of the 14 genera with congeneric species that have a significant association test) suggesting species-habitat associations have arisen multiple times in this tree community. We also tested if species with similar habitat preferences shared functional strategies. We found that seasonally inundated forest specialists tended to have smaller stature (maximum diameter) than species found on plateaus. Our results underline the importance of tree-soil habitat associations in structuring diverse communities at fine spatial scales and suggest that additional studies are needed to disentangle community assembly mechanisms related to dispersal limitation, biotic interactions and environmental filtering from species-habitat associations. Moreover, they provide a framework to generalize across tropical forest sites.     

Dispersal process driving subtropical forest reassembly: evidence from functional and phylogenetic analysis

Understanding the mechanisms of secondary succession related to forest management practices is receiving increasing attention in community ecology and biodiversity conservation. Abiotic and biotic filtering are deterministic processes driving community reassembly. A functional trait or phylogeny-based approach predicts that environmental filtering induced by clearcut-logging results in functional/phylogenetic clustering in younger forests, while biotic filtering (competitive exclusion) promotes functional/phylogenetic overdispersion in old-growth forests. From this perspective, we examined the patterns of functional/phylogenetic structures using tree community data (147 species × 170 plots). These data were chronosequenced from clearcut secondary forests to old-growth subtropical forests in the Ryukyu Archipelago, with species’ trait data (leaf and stem) and species level phylogeny. To detect clustering or overdispersion in the functional and phylogenetic structures, we calculated the standardized effect size of mean nearest trait distance and mean nearest phylogenetic distance within the plots. Functional or phylogenetic clustering was relatively weak in secondary forests, and their directional change with increasing forest age was not generally detected. Mean nearest trait/phylogenetic distance for most plots fell within the range of random expectation. The results suggest that abiotic/biotic filtering related to functional traits or phylogenetic relatedness plays a diminished role in shaping species assembly during secondary succession in the subtropical forest. Our findings of functional and phylogenetic properties might shed light on the importance of dispersal (stochastic) processes in the regional species pool during community reassembly after anthropogenic disturbance. It will also contribute to the development of coordinated schemes that maintain potential species assembly processes in the subtropical forest.     

Phylogenetic turnover during subtropical forest succession across environmental and phylogenetic scales

Although spatial and temporal patterns of phylogenetic community structure during succession are inherently interlinked and assembly processes vary with environmental and phylogenetic scales, successional studies of community assembly have yet to integrate spatial and temporal components of community structure, while accounting for scaling issues. To gain insight into the processes that generate biodiversity after disturbance, we combine analyses of spatial and temporal phylogenetic turnover across phylogenetic scales, accounting for covariation with environmental differences. We compared phylogenetic turnover, at the species‐ and individual‐level, within and between five successional stages, representing woody plant communities in a subtropical forest chronosequence. We decomposed turnover at different phylogenetic depths and assessed its covariation with between‐plot abiotic differences. Phylogenetic turnover between stages was low relative to species turnover and was not explained by abiotic differences. However, within the late‐successional stages, there was high presence‐/absence‐based turnover (clustering) that occurred deep in the phylogeny and covaried with environmental differentiation. Our results support a deterministic model of community assembly where (i) phylogenetic composition is constrained through successional time, but (ii) toward late succession, species sorting into preferred habitats according to niche traits that are conserved deep in phylogeny, becomes increasingly important.     

Habitat filtering influences the phylogenetic structure of avian communities across a coastal gradient in southern Brazil

The evolution of a particular trait or combination of traits within lineages may affect subsequent evolutionary outcomes, leading closely related species to exhibit higher phenotypic similarity than expected under a simple Brownian‐motion evolutionary model. Niche theory postulates that phenotypes determine species distribution across environmental gradients, leading to a phylogenetic signature in the community assembly. Thus, the incorporation of species phylogeny in the analysis of community ecology structure allows one to link broader environmental, spatial and temporal factors to local, small‐scale ecological processes, thus enabling understanding of community assembly patterns in a broader context. We used the net relatedness index to assess phylogenetic structure within avian communities across a harshness gradient in coastal habitats in southern Brazil. We also evaluated phylogenetic beta diversity, to test whether closely related species exploit habitats with similar environmental conditions. In order to do so, we scaled up phylogenetic information from the species to site level using phylogenetic fuzzy weighting. We found a pattern of phylogenetic clustering in less‐vegetated habitats, namely sandy beach and dunes, which are subject to harsher conditions because of proximity to the ocean. Basal lineages were associated with the more structurally homogeneous sandy beach, while late‐divergence clades occurred in more complex habitats, which were positively related to vegetation cover and height. The observed pattern of phylogenetic clustering suggested the importance of harsh conditions in constraining the distribution of avian lineages. Furthermore, contrasting environmental features between habitats influenced phylogenetic variation, demonstrating the prevalence of phylogenetic habitat filtering. From an applied point of view, such as planning and management of biological reserves, we showed that the full array of habitat patches embedded within coastal ecological gradients must be included in order to preserve distinct evolutionary lineages.     

Habitat choice in Phylloscopus warblers: the role of morphology, phylogeny and competition

We studied ecological and evolutionary aspects of habitat choice in a group of closely related bird species to gain insight into factors influencing bird community structure. Seven species of Phylloscopus warblers breed sympatrically in the middle taiga subzone of Central Siberia. We examine how the distribution of species among habitats is related to morphology, phylogeny and competition, and we compare our results with an earlier study on the ecomorphology of Phylloscopus warblers in Kashmir. We found that in Siberia, large warbler species prefer productive habitats with mostly deciduous vegetation, whereas small species occupy poor coniferous forests. Possible explanations for this finding remain to be tested in the future. Moreover, we found a tendency for species with large feet, small bills and short wings to occupy habitats with an abundance of bush thickets near the ground. In the Kashmir study, competition was considered a major factor in structuring the Phylloscopus community, and patterns of habitat choice were not influenced by phylogenetic relationships. In strong contrast, we found that in the Siberian community, closely related species occupy similar habitats. We discuss whether this conservative evolution of habitat preferences in Siberia may be due to low intensity of interspecific competition or to other ecological factors.     

Functional traits of tree species with phylogenetic signal co-vary with environmental niches in two large forest dynamics plots

Aims While using phylogenetic and functional approaches to test the mechanisms of community assembly, functional traits often act as the proxy of niches. However, there is little detailed knowledge regarding the correlation between functional traits of tree species and their niches in local communities. We suggest that the co-varying correlation between functional traits and niches should be the premise for using phylogenetic and functional approaches to test mechanisms of community assembly. Using functional traits, phylogenetic and environmental data, this study aims to answer the questions: (i) within local communities, do functional traits of co-occurring species co-vary with their environmental niches at the species level? and (ii) what is the key ecological process underlying community assembly in Xishuangbanna and Ailaoshan forest dynamic plots (FDPs)?Methods We measured seven functional traits of 229 and 36 common species in Xishuangbanna and Ailaoshan FDPs in tropical and subtropical China, respectively. We also quantified the environmental niches for these species based on conditional probability. We then analyzed the correlations between functional traits and environmental niches using phylogenetic independent contrasts. After examining phylogenetic signals of functional traits using Pagel's λ, we quantified the phylogenetic and functional dispersion along environmental gradients within local tree communities.Important findings For target species, functional traits do co-vary with environmental niches at the species level in both of the FDPs, supporting that functional traits can be used as a proxy for local-scale environmental niches. Functional traits show significant phylogenetic signals in both of the FDPs. We found that the phylogenetic and functional dispersion were significantly clustered along topographical gradients in the Ailaoshan FDP but overdispersion in the Xishuangbanna FDP. These patterns of phylogenetic and functional dispersion suggest that environmental filtering plays a key role in structuring local tree assemblages in Ailaoshan FDP, while competition exclusion plays a key role in Xishuangbanna FDP.     

放牧干扰梯度下川西亚高山植物群落的组合机理

为了阐明放牧干扰对川西亚高山区域植物群落的组合过程以及群落结构的影响, 研究了放牧干扰梯度下的功能群均匀度和群落谱系结构的变化趋势。结果显示: 在干扰较轻的阔叶林与针叶林样地, 部分样方的功能群均匀度显著高于无效模型, 随着干扰梯度的增强, 功能群均匀度呈线性下降, 样方平均值从0.930降至0.840, 其高于无效模型的次数也逐渐降低, 干扰程度较大的草甸中出现部分样方的功能群均匀度显著低于无效模型。随着干扰程度的增强, 群落的谱系结构指数也呈逐渐上升趋势, 净关联指数平均值由-0.634逐渐增加至2.360, 邻近类群指数由-0.158上升至2.179。草甸与低矮灌丛受干扰较为严重, 其大部分样方的谱系结构指数显著高于随机群落, 表明干扰群落的谱系结构呈聚集分布。功能群均匀度与谱系结构的变化趋势一致, 表明生境筛滤效应与种间竞争作用的平衡决定着群落的组合过程。干扰降低了竞争作用, 促进了少数耐干扰功能群的优势地位, 造成功能群均匀度下降, 同时通过生境筛滤作用, 使群落的谱系结构呈现出聚集分布; 而未干扰的群落中由于竞争作用的效应, 功能群均匀度较高, 谱系结构也更加分散。研究区域植物群落的功能群均匀度与物种丰富度呈负相关, 表明物种间特别是相似物种间的竞争限制了群落的物种多样性。研究结果说明, 生态位分化和物种间的相互竞争在物种共存与群落组合中具有重要作用。     

The ecology of differences: assessing community assembly with trait and evolutionary distances

Species enter and persist in local communities because of their ecological fit to local conditions, and recently, ecologists have moved from measuring diversity as species richness and evenness, to using measures that reflect species ecological differences. There are two principal approaches for quantifying species ecological differences: functional (trait‐based) and phylogenetic pairwise distances between species. Both approaches have produced new ecological insights, yet at the same time methodological issues and assumptions limit them. Traits and phylogeny may provide different, and perhaps complementary, information about species' differences. To adequately test assembly hypotheses, a framework integrating the information provided by traits and phylogenies is required. We propose an intuitive measure for combining functional and phylogenetic pairwise distances, which provides a useful way to assess how functional and phylogenetic distances contribute to understanding patterns of community assembly. Here, we show that both traits and phylogeny inform community assembly patterns in alpine plant communities across an elevation gradient, because they represent complementary information. Differences in historical selection pressures have produced variation in the strength of the trait‐phylogeny correlation, and as such, integrating traits and phylogeny can enhance the ability to detect assembly patterns across habitats or environmental gradients.     

Phylogenetic relatedness explains highly interconnected and nested symbiotic networks of woody plants and arbuscular mycorrhizal fungi in a Chinese subtropical forest

Elucidating symbiotic relationships between arbuscular mycorrhizal fungi (AMF) and plants contributes to a better understanding of their reciprocally dependent coexistence and community assembly. However, the main drivers of plant and AMF community assembly remain unclear. In this study, we examined AMF communities from 166 root samples of 17 woody plant species from 10 quadrats in a Chinese subtropical forest using 454 pyrosequencing of 18S rRNA gene to describe symbiotic AMF–plant association. Our results show the woody plant–AMF networks to be highly interconnected and nested, but in antimodular and antispecialized manners. The nonrandom pattern in the woody plant–AMF network was explained by plant and AMF phylogenies, with a tendency for a stronger phylogenetic signal by plant than AMF phylogeny. This study suggests that the phylogenetic niche conservatism in woody plants and their AMF symbionts could contribute to interdependent AMF and plant community assembly in this subtropical forest ecosystem.     

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.     

Phylogenetic density dependence and environmental filtering predict seedling mortality in a tropical forest

Negative density dependence (NDD) and environmental filtering (EF) shape community assembly, but their relative importance is poorly understood. Recent studies have shown that seedling's mortality risk is positively related to the phylogenetic relatedness of neighbours. However, natural enemies, whose depredations often cause NDD, respond to functional traits of hosts rather than phylogenetic relatedness per se. To understand the roles of NDD and EF in community assembly, we assessed the effects on seedling mortality of functional similarity, phylogenetic relatedness and stem density of neighbouring seedlings and adults in a species-rich tropical forest. Mortality risks increased for common species when their functional traits departed substantially from the neighbourhood mean, and for all species when surrounded by close relatives. This indicates that NDD affects community assembly more broadly than does EF, and leads to the tentative conclusion that natural enemies respond to phylogenetically correlated traits. Our results affirm the prominence of NDD in structuring species-rich communities.     

A phylogenetic community approach for studying termite communities in a West African savannah

Termites play fundamental roles in tropical ecosystems, and mound-building species in particular are crucial in enhancing species diversity, from plants to mammals. However, it is still unclear which factors govern the occurrence and assembly of termite communities. A phylogenetic community approach and null models of species assembly were used to examine structuring processes associated with termite community assembly in a pristine savannah. Overall, we did not find evidence for a strong influence of interspecific competition or environmental filtering in structuring these communities. However, the presence of a single species, the mound-building termite Macrotermes bellicosus, left a strong signal on structuring and led to clustered communities of more closely related species. Hence, this species changes the assembly rules for a whole community. Our results show the fundamental importance of a single insect species for community processes, suggesting that more attention to insect species is warranted when developing conservation strategies.     

Point process models,the dimensions of biodiversity and the importance of small-scale biotic interactions

Aims Recent mechanistic explanations for community assembly focus on the debates surrounding niche-based deterministic and dispersal-based stochastic models. This body of work has emphasized the importance of both habitat filtering and dispersal limitation, and many of these works have utilized the assumption of species spatial independence to simplify the complexity of the spatial modeling in natural communities when given dispersal limitation and/or habitat filtering. One potential drawback of this simplification is that it does not consider species interactions and how they may influence the spatial distribution of species, phylogenetic and functional diversity. Here, we assess the validity of the assumption of species spatial independence using data from a subtropical forest plot in southeastern China.Methods We use the four most commonly employed spatial statistical models—the homogeneous Poisson process representing pure random effect, the heterogeneous Poisson process for the effect of habitat heterogeneity, the homogenous Thomas process for sole dispersal limitation and the heterogeneous Thomas process for joint effect of habitat heterogeneity and dispersal limitation—to investigate the contribution of different mechanisms in shaping the species, phylogenetic and functional structures of communities.Important findings Our evidence from species, phylogenetic and functional diversity demonstrates that the habitat filtering and/or dispersal-based models perform well and the assumption of species spatial independence is relatively valid at larger scales (50×50 m). Conversely, at local scales (10×10 and 20×20 m), the models often fail to predict the species, phylogenetic and functional diversity, suggesting that the assumption of species spatial independence is invalid and that biotic interactions are increasingly important at these spatial scales.     

Phylogenetic similarity and structure of Agaricomycotina communities across a forested landscape

The Agaricomycotina are a phylogenetically diverse group of fungi that includes both saprotrophic and mycorrhizal species, and that form species – rich communities in forest ecosystems. Most species are infrequently observed, and this hampers assessment of the role that environmental heterogeneity plays in determining local community composition and in driving β‐diversity. We used a combination of phenetic (TRFLP) and phylogenetic approaches [Unifrac and Net Relatedness Index (NRI)] to examine the compositional and phylogenetic similarity of Agaricomycotina communities in forest floor and surface soil of three widely distributed temperate upland forest ecosystems (one, xeric oak – dominated and two, mesic sugar maple dominated). Generally, forest floor and soil communities had similar phylogenetic diversity, but there was little overlap of species or evolutionary lineages between these two horizons. Forest floor communities were dominated by saprotrophic species, and were compositionally and phylogenetically similar in all three ecosystems. Mycorrhizal species represented 30% to 90% of soil community diversity, and these communities differed compositionally and phylogenetically between ecosystems. Estimates of NRI revealed significant phylogenetic clustering in both the forest floor and soil communities of only the xeric oak‐dominated forest ecosystem, and may indicate that this ecosystem acts as a habitat filter. Our results suggest that environmental heterogeneity strongly influences the phylogenetic β‐diversity of soil inhabiting Agaricomycotina communities, but has only a small influence on forest floor β‐diversity. Moreover, our results suggest that the strength of community assembly processes, such as habitat filtering, may differ between temperate forest ecosystems.