Influence of tree shape and evolutionary time‐scale on phylogenetic diversity metrics

During the last decades, describing, analysing and understanding the phylogenetic structure of species assemblages has been a central theme in both community ecology and macro‐ecology. Among the wide variety of phylogenetic structure metrics, three have been predominant in the literature: Faith's phylogenetic diversity (PD_Faith), which represents the sum of the branch lengths of the phylogenetic tree linking all species of a particular assemblage, the mean pairwise distance between all species in an assemblage (MPD) and the pairwise distance between the closest relatives in an assemblage (MNTD). Comparisons between studies using one or several of these metrics are difficult because there has been no comprehensive evaluation of the phylogenetic properties each metric captures. In particular it is unknown how PD_Faith relates to MDP and MNTD. Consequently, it is possible that apparently opposing patterns in different studies might simply reflect differences in metric properties. Here, we aim to fill this gap by comparing these metrics using simulations and empirical data. We first used simulation experiments to test the influence of community structure and size on the mismatch between metrics whilst varying the shape and size of the phylogenetic tree of the species pool. Second we investigated the mismatch between metrics for two empirical datasets (gut microbes and global carnivoran assemblages). We show that MNTD and PD_Faith provide similar information on phylogenetic structure, and respond similarly to variation in species richness and assemblage structure. However, MPD demonstrate a very different behaviour, and is highly sensitive to deep branching structure. We suggest that by combining complementary metrics that are sensitive to processes operating at different phylogenetic depths (i.e. MPD and MNTD or PD_Faith) we can obtain a better understanding of assemblage structure.     

The influence of biogeographic history on the functional and phylogenetic diversity of passerine birds in savannas and forests of the Brazilian Amazon

Passeriformes is the largest and most diverse avian order in the world and comprises the Passeri and Tyranni suborders. These suborders constitute a monophyletic group, but differ in their ecology and history of occupation of South America. We investigated the influence of biogeographic history on functional and phylogenetic diversities of Passeri and Tyranni in forest and savanna habitats in the Brazilian Amazon. We compiled species composition data for 34 Passeriformes assemblages, 12 in savannas and 22 in forests. We calculated the functional (Rao's quadratic entropy, FD_Q) and phylogenetic diversities (mean pairwise distance, MPD, and mean nearest taxon distance, MNTD), and the functional beta diversity to investigate the potential role of biogeographic history in shaping ecological traits and species lineages of both suborders. The functional diversity of Passeri was higher than for Tyranni in both habitats. The MPD for Tyranni was higher than for Passeri in forests; however, there was no difference between the suborders in savannas. In savannas, Passeri presented higher MNTD than Tyranni, while in forest areas, Tyranni assemblages showed higher MNTD than Passeri. We found a high functional turnover (~75%) between Passeri and Tyranni in both habitats. The high functional diversity of Passeri in both habitats is due to the high diversity of ecological traits exhibited by species of this group, which enables the exploitation of a wide variety of resources and foraging strategies. The higher Tyranni MPD and MNTD in forests is likely due to Tyranni being older settlers in this habitat, resulting in the emergence and persistence of more lineages. The higher Passeri MNTD in savannas can be explained by the existence of a larger number of different Passeri lineages adapted to this severe habitat. The high functional turnover between the suborders in both habitats suggests an ecological strategy to avoid niche overlap.     

What factors potentially influence the ability of phylogenetic distance to predict trait dispersion in a temperate forest?

Although phylogenetic‐based approaches have been frequently used to infer ecological processes, they have been increasingly criticized in recent years. To date, the factors that affect phylogenetic signals and further the ability of phylogenetic distance to predict trait dispersion have been assumed but not empirically tested. Therefore, we investigate which factors potentially influence the ability of phylogenetic distance to predict trait dispersion. We quantified the phylogenetic and trait dispersions across size classes and spatial scales in a 9‐ha old‐growth temperate forest dynamics plot in northeastern China. Phylogenetic signals at the community level were generally lower than those at the species pool level, and phylogenetically clustered communities showed lower phylogenetic signals than did overdispersed communities. This pattern might explain the other three findings of our study. First, phylogenetically overdispersed communities performed better at predicting trait dispersion than did clustered communities. Second, the mean pairwise distance (MPD)‐based metric exhibited a stronger correlation with trait dispersion than did the mean nearest taxon distance (MNTD)‐based metric. Finally, the MNTD‐based metric showed that the prediction accuracy for trait dispersion decreased with increasing spatial scales, whereas its effects were weak on the MPD‐based metric. In addition, phylogeny could not determine the dispersions of all functional axes but was able to predict certain traits depending on whether they were evolutionarily conserved. These results were conserved when we removed the effects of space and environment. Our findings highlighted that using phylogenetic distance as a proxy of trait similarity might work in a temperate forest depending on the species in local communities sampled from total pool as well as the traits measured. Utilizing these rules, we should rethink the conclusions of previous studies that were based on phylogenetic‐based approaches.     

Community Structure of Skipper Butterflies (Lepidoptera,Hesperiidae) along Elevational Gradients in Brazilian Atlantic Forest Reflects Vegetation Type Rather than Altitude

Species turnover across elevational gradients has matured into an important paradigm of community ecology. Here, we tested whether ecological and phylogenetic structure of skipper butterfly assemblages is more strongly structured according to altitude or vegetation type along three elevation gradients of moderate extent in Serra do Mar, Southern Brazil. Skippers were surveyed along three different mountain transects, and data on altitude and vegetation type of every collection site were recorded. NMDS ordination plots were used to assess community turnover and the influence of phylogenetic distance between species on apparent community patterns. Ordinations based on ecological similarity (Bray-Curtis index) were compared to those based on phylogenetic distance measures (MPD and MNTD) derived from a supertree. In the absence of a well-resolved phylogeny, various branch length transformation methods were applied together with four different null models, aiming to assess if results were confounded by low-resolution trees. Species composition as well as phylogenetic community structure of skipper butterflies were more prominently related to vegetation type instead of altitude per se. Phylogenetic distances reflected spatial community patterns less clearly than species composition, but revealed a more distinct fauna of monocot feeders associated with grassland habitats, implying that historical factors have played a fundamental role in shaping species composition across elevation gradients. Phylogenetic structure of community turned out to be a relevant additional tool which was even superior to identify faunal contrasts between forest and grassland habitats related to deep evolutionary splits. Since endemic skippers tend to occur in grassland habitats in the Serra do Mar, inclusion of phylogenetic diversity may also be important for conservation decisions.     

地理距离及环境差异对云南元江干热河谷植物群落beta多样性的影响

beta多样性反映了群落间物种组成的差异, 是生物多样性研究的热点之一。本研究通过对云南元江干热河谷41个植物群落样方进行调查, 用Jaccard相异系数表征物种beta多样性, 用样方之间的最近谱系距离(mean nearest taxon distance, MNTD)及平均谱系距离(mean pairwise distance, MPD)表征谱系beta多样性, 采用基于距离矩阵的多元回归和方差分解方法, 探讨了该区域干热河谷典型植物群落的物种beta多样性和谱系beta多样性与样方间环境差异(主要是气候)及地理距离之间的关系。结果表明: (1)群落间的地理距离和年平均温度差异对干热河谷植物群落的物种beta多样性和谱系beta多样性有显著影响; (2)地理距离对物种beta多样性和MNTD的影响最大; 地理距离和年平均温度差异对MPD的影响均较大; (3)样方间年平均温度与年平均降水量的差异和地理距离能够解释群落间beta多样性及谱系beta多样性11-13%的变异。以上结果表明, 生态位分化和扩散限制对该地区植物群落的beta多样性均有显著影响, 其中扩散限制的影响可能更大。此外, 人类活动等其他因素也很可能对元江干热河谷的群落组成具有非常重要的影响。     

The role of landscape in shaping bird community and implications for landscape management at Nanjing Lukou International Airport

Understanding the patterns of bird diversity and its driving force is necessary for bird strike prevention. In this study, we investigated the effects of landscape on phylogenetic and functional diversity of bird communities at Nanjing Lukou International Airport (NLIA). Bird identifications and counting of individuals were carried out from November 2017 to October 2019. Based on the land-cover data, the landscape was divided into four main types, including farmlands, woodlands, wetlands, and urban areas. Bird phylogenetic and functional diversity were strongly affected by landscape matrix types. Species richness and Faith's phylogenetic distance were highest in woodlands, while mean pairwise distance (MPD), mean nearest-taxon distance (MNTD), and functional dispersion (FDis) were highest in wetlands. Based on the feeding behavior, carnivorous birds had the lowest species richness but had the highest FDis, which implied that carnivorous birds occupied most niches at the NLIA. Moreover, bird assemblages exhibited phylogenetic and functional clustering in the four kinds of landscapes. A variety of landscape attributes had significant effects on species diversity, phylogenetic and functional diversity. Landscape-scale factors played an important role in the shaping of bird communities around NLIA. Our results suggest that landscape management surrounding airports can provide new approaches for policymakers to mitigate wildlife strikes.     

Spatial analyses of intertidal assemblages on sheltered rocky shores

Abstract Understanding processes in complex assemblages depends on good understanding of spatial and temporal patterns of structure at various spatial scales. There has been little quantitative information about spatial patterns and natural temporal changes in intertidal assemblages on sheltered rocky shores in temperate Australia. Natural changes and responses to anthropogenic disturbances in these habitats cannot be accurately measured and assessed without quantitative data on patterns of natural variability in space and through time. This paper describes some suitable quantitative methods for examining spatial and temporal patterns of diversity and abundances of highshore, midshore and lowshore intertidal assemblages and the important component species for a number of shores in a bay that has not been severely altered by human disturbance. Despite a diverse flora and fauna on these shores, the midshore and lowshore assemblages on sheltered shores were characterized by a few species which were also the most important in discriminating among assemblages on a shore and, for each assemblage, among different shores. The same set of species was also important for measuring small-scale patchiness within each assemblage (i.e. between replicate sites on a shore). Therefore, these data provide a rationale for selecting species that are useful for measuring differences and changes in abundance among places and times at different scales and, hence, can be used in the more complex sampling designs necessary to detect environmental impacts. There was considerable spatial variability in all assemblages and all species (or taxa) examined at scales of metres, tens of metres and kilometres. There were no clear seasonal trends for most measures, with as much or more variability at intervals of 3 months as from year to year. Most interactions between spatial and temporal measures were at the smallest scale, with different sites on the same shore generally showing different changes from time to time. The cause(s) of this apparently idiosyncratic variability1 were not examined, but some potential causes are discussed. These data are appropriate for testing hypotheses about the applicability of these findings to other relatively undisturbed sheltered shores, about effects of different anthropogenic disturbances on sheltered intertidal assemblages and to test hypotheses about differences in intertidal assemblages on sheltered versus wave-exposed shores.     

Phylogenetic diversity and community assembly in a naturally fragmented system

We sought to assess effects of fragmentation and quantify the contribution of ecological processes to community assembly by measuring species richness, phylogenetic, and phenotypic diversity of species found in local and regional plant communities. Specifically, our fragmented system is Craters of the Moon National Monument and Preserve, Idaho, USA. CRMO is characterized by vegetated islands, kipukas, that are isolated in a matrix of lava. We used floristic surveys of vascular plants in 19 kipukas to create a local species list to compare traditional dispersion metrics, mean pairwise distance, and mean nearest taxon distance (MPD and MNTD), to a regional species list with phenotypic and phylogenetic data. We combined phylogenetic and functional trait data in a novel machine‐learning model selection approach, Community Assembly Model Inference (CAMI), to infer probability associated with different models of community assembly given the data. Finally, we used linear regression to explore whether the geography of kipukas explained estimated support for community assembly models. Using traditional metrics of MPD and MNTD neutral processes received the most support when comparing kipuka species to regional species. Individually no kipukas showed significant support for overdispersion. Rather, five kipukas showed significant support for phylogenetic clustering using MPD and two kipukas using MNTD. Using CAMI, we inferred neutral and filtering models structured the kipuka plant community for our trait of interest. Finally, we found as species richness in kipukas increases, model support for competition decreases and lower elevation kipukas show more support for habitat filtering models. While traditional phylogenetic community approaches suggest neutral assembly dynamics, recently developed approaches utilizing machine learning and model choice revealed joint influences of assembly processes to form the kipuka plant communities. Understanding ecological processes at play in naturally fragmented systems will aid in guiding our understanding of how fragmentation impacts future changes in landscapes.     

Evolutionary history of <Emphasis Type="Italic">campo rupestre</Emphasis>: an approach for conservation of woody plant communities

The campo rupestre sensu lato is among the most species-rich vegetation in the world, harbouring a high proportion of endemic species. We aimed to identify the processes that could generate a high level of phylogenetic diversity (PD) in campo rupestre for woody species and point out biodiversity hotspot areas which may provide additional information for conservation planning. We compiled a database of 2049 woody species from 185 community inventories. We calculated the evolutionary history using species richness (SR), PD, mean pairwise phylogenetic distance between species (MPD), the mean nearest taxon distance (MNTD) and their equivalents standardised (ses.PDss, ses.MPD, ses.MNTD), evolutionary distinctiveness (ED), and biogeographically weighted evolutionary distinctiveness (BED). Cloud dwarf-forests had the highest SR, PD, MPD and ses.MPD and lowest MNTD, while rupestrian cerrado presented the highest ses.PD and ses.MNTD. All areas are important for conservation, but the intersections between the hotspots should receive special attention in future conservation actions. The grids identified as hotspots by three or more metrics were localized mainly in Espinhaço Range in Minas Gerais State and a further expansion of protected areas is required. Moreover, the intersections between the hotspots obtained by mean ED and ses.PD are concentrated in the rocky dwarf forest and rupestrian cerrado, with considerable conservation gaps. The degree of protection of campo rupestre was low with unprotected areas comprising 56% of the species. Our results show an urgent need for increasing protected areas of campo rupestre in order to avoid the loss of valuable, endemic species with unique evolutionary history.     

Small-scale spatial variability in intertidal and subtidal turfing algal assemblages and the temporal generality of these patterns

Spatial and temporal variation in patterns of distribution and abundance of algal assemblages is large and often occurs at extremely small spatial and temporal scales. Despite this, few studies investigate interactions between these scales, that is, how patterns of spatial variation change through time. This study investigated a number of scales of spatial variation (from tens of centimetres to kilometres) in assemblages of intertidal and subtidal turfing algae. Significant differences were found in the composition and abundances of species in assemblages of turf at all spatial scales tested. Much of the variation among assemblages could, however, be explained at the scale of quadrats (tens of centimetres apart) (27±1.4 (SE)% of dissimilarity) with an additional 7±1.2% explained at the scale of sites (tens of metres apart) and 10±1.5% at the scale of locations (kilometres apart). Although the greatest dissimilarity in assemblages occurred at the scale of habitats, this accounted for a relatively small proportion of the overall variation in assemblages. These patterns were consistent through time, that is, at each sampling time the spatial scale explaining the greatest proportion of variation in assemblages was replicate quadrats separated by tens of centimetres. These patterns appear to be due to small-scale variation in patterns of distribution and abundances of the individual species that comprise turfing algal assemblages. The results of this experiment suggest that large scale processes have less effect on patterns of variability of algal assemblages than those occurring on relatively smaller spatial scales and that small-scale spatial variation should not be considered as simply “noise”.     

The hypothesis of sympatric speciation as the dominant generator of endemism in a global hotspot of biodiversity

Allopatric or sympatric speciation influence the degree to which closely related species coexist in different manners, altering the patterns of phylogenetic structure and turnover among and between communities. The objective of this study was to examine whether phylogenetic community structure and turnover in the Brazilian Atlantic Forest permit conclusions about the dominant process for the formation of extant angiosperm richness of tree species. Therefore, we analyzed phylogenetic community structure (MPD, MNTD) as well as taxonomic (Jaccard similarity) and phylogenetic turnover (betaMPD, betaMNTD) among and between 49 tree communities distributed among three different habitat types. Mean annual precipitation and mean annual temperature in each survey area were estimated. Phylogenetic community structure does not differ between habitat types, although MPD reduces with mean annual temperature. Jaccard similarity decreases and betaMNTD increases with spatial distance and environmental differences between study sites. Spatial distance explains the largest portions of variance in the data, indicating dispersal limitation and the spatial aggregation of recently formed taxa, as betaMNTD is related to more recent evolutionary events. betaMPD, that is related to deep evolutionary splits, shows no spatial or environmental pattern, indicating that older clades are equally distributed across the Brazilian Atlantic Forest. While similarity pattern indicates dispersal limitations, the spatial turnover of betaMNTD is consistent with a high degree of sympatric speciation generating extant diversity and endemism in the Brazilian Atlantic Forest. More comprehensive approaches are necessary to reduce spatial sampling bias, uncertainties regarding angiosperm diversification patterns and confirm sympatric speciation as the dominant generator for the formation of extant species diversity in the Brazilian Atlantic Forest.     

Functional and phylogenetic structure of forest and savanna bird assemblages across spatial scales

Ecological and evolutionary mechanisms that drive community assembly vary in space and time. However, little is known about how such mechanisms act in contrasting habitats. Here, we estimated the functional and phylogenetic structure of forest and savanna bird assemblages across different spatial scales to understand: 1) the mechanisms that govern the structure of assemblages in these habitats; 2) the relationship between phylogenetic and functional structure; and 3) the influence of species richness on the functional and phylogenetic structure of assemblages. We used a null model where forest and savanna bird species were allowed to occur in the same null assemblages and other where species were separated based on their habitats. According to the first null model, forest bird assemblages were functionally and phylogenetically clustered at all spatial scales, whereas savanna bird assemblages generally showed random functional and phylogenetic structure. These results can be explained by the low dispersal rate of forest species across of the patchy habitats and the widespread distribution of savanna species. However, in the second null model, both forest and savanna bird assemblages showed random functional and phylogenetic structure at regional and local scales. This suggests that trait‐based assembly might not play an important role in both habitats and across different spatial scales. In addition, the phylogenetic and functional structure of assemblages were not correlated, evidencing that caution is necessary when using phylogenetic relationships as a surrogate to functional distances among species. Finally, the relationships between species richness and functional and phylogenetic structure indicated that an increase in the number of species can promote both clustering and overdispersion, depending on the studied habitat and scale. Our study shows that integrating different types of habitat, spatial scales and biodiversity components in a single framework can shed light on the mechanisms that determine the community assembly.     

海南尖峰岭热带山地雨林林冠层树种功能多样性特征

以海南尖峰岭热带山地雨林3块1 hm²样地为研究对象,利用11个林冠功能性状结合样地地形及林冠乔木树种样地清查数据,分别基于单维性状和多维性状比较物种多度加权对群落功能离散度指数——平均成对距离(MPD)和平均最近类群距离(MNTD)的影响;同时分析林冠层功能丰富度(FRic)与物种丰富度之间的关系,最后利用零模型探讨不同生境类型下标准化效应MPD和MNTD(经过物种多度加权且剔除群落物种丰富度差异影响)的变化,进而评价林冠层群落水平功能多样性格局及其对局域生境异质性的响应.结果表明: 功能性状维度和物种多度对MPD的影响强烈,不同维度功能性状多度加权前后MPD相关性较弱(R=0.359～0.628);但对MNTD的影响相对较弱,不同维度功能性状多度加权前后MNTD相关性较强(R=0.746～0.820);未经物种多度加权的MPD和MNTD均普遍高估了林冠层的功能离散度.林冠层功能丰富度与物种丰富度基本呈指数相关关系(F=128.20;R²=0.632;AIC=97.72;P＜0.001),且功能丰富度很有可能存在一定的物种丰富度阈值.基于不同维度功能性状的林冠层功能多样性格局及其生境响应存在一定的差异性.在生物竞争激烈的低沟生境中,林冠层功能多样性倾向于比预期零模型随机产生的功能多样性高,林冠树种功能性状表现出离散分布;而在其他生境类型中,林冠层功能多样性倾向于接近或低于随机产生的功能多样性,林冠树种功能性状随机或聚集分布.     

Niche evolution in Australian terrestrial mammals? Clarifying scale-dependencies in phylogenetic and functional drivers of co-occurrence

Interactive forces between competition and habitat filtering drive many biogeographic patterns over evolutionary time scales. However, the responsiveness of assemblages to these two forces is highly influenced by spatial scale, forming complex patterns of niche separation. We explored these spatial dependencies by quantifying the influence of phylogeny and functional traits in shaping present day native terrestrial mammal assemblages at multiple scales, principally by identifying the spatial scales at which niche evolution operates. We modelled the distribution of 53 native terrestrial mammal species across New South Wales, Australia. Using predicted distributions, we estimated the range overlap between each pair of species at increasing grain sizes (~0.8, 5.1, 20, 81, 506, 2,025, 8,100 km²). We employed a decision tree to identify how interactions among functional traits and phylogenetic relatedness translated to levels of sympatry at increasing spatial scales. We found that Australian terrestrial mammals displayed phylogenetic over-dispersion that was inversely related to spatial scale, suggesting that ecological processes were more influential than biogeographic sympatry patterns in defining assemblages of species. While the contribution of phylogenetic relatedness to patterns of co-occurrence decreased as spatial scale increased, the reverse was true for habitat preferences. At the same time, functional traits also operated at different scales, as dietary preferences dominated at local spatial scales (<10 km²) while body mass has a stronger effect at larger spatial scales. Our findings show that ecological and evolutionary processes operate at different scales and that Australian terrestrial mammals diverged slower along their micro-scale niche compared to their macro-scale niche. By combining phylogenetic and niche methods through the modelling of species distributions, we assessed whether specific traits were related to a particular niche. More importantly, conducting multi-scale spatial analysis avoids categorical assignment of traits-to-niches, providing a clearer relationship between traits and a species ecological niche and a more precise scaling for the axes of niche evolution.     

The phylogenetic properties of native‐ and exotic‐dominated plant communities

Phylogenetic properties of communities (phylogenetic diversity and phylogenetic structure) allow for the characterisation of phylogenetic patterns and provide the information necessary to infer mechanisms of species assembly. Because humans have introduced exotic species and modified the physical conditions of landscapes, the phylogenetic properties of communities should change according to the proportion of natives to exotics hosted by sites and to the strength of the conditions that act as habitat filters in human‐disturbed habitats. To assess the effects of the introduction of exotic plant species, we characterized the phylogenetic properties of 67 plant communities with different degrees of exotic species dominance in a region of central Chile with a Mediterranean climate. Five indices were used to estimate the phylogenetic properties. The Faith index (FPD), the mean pairwise distance (MPD) and the mean nearest neighbour distance (MNND) were used to estimate phylogenetic diversity, and the nearest relative index (NRI) and the nearest taxon index (NTI) were used as estimators of the phylogenetic structure (the phylogenetic distribution of taxa in a community) of species assemblages. We observed greater phylogenetic diversity of natives versus exotic plants despite the fact that natives accounted for a fewer number of taxa among the studied communities. Second, assemblages exhibited a phylogenetically clustered structure, which is attributable to an over‐representation of some families of exotic flora (Asteraceae, Brassicaceae, Fabaceae, Papaveraceae, Poaceae) and suggests habitat filtering processes that could have acted by selecting species with traits that permit adaptation to the harsh conditions of human‐disturbed sites.     

Phylogenetic scale in ecology and evolution

Aim

Many important patterns and processes vary across the phylogeny and depend on phylogenetic scale. Nonetheless, phylogenetic scale has never been formally conceptualized, and its potential remains largely unexplored. Here, we formalize the concept of phylogenetic scale, review how phylogenetic scale has been considered across multiple fields and provide practical guidelines for the use of phylogenetic scale to address a range of biological questions.

Innovation

We summarize how phylogenetic scale has been treated in macroevolution, community ecology, biogeography and macroecology, illustrating how it can inform, and possibly resolve, some of the longstanding controversies in these fields. To promote the concept empirically, we define phylogenetic grain and extent, scale dependence, scaling and the domains of phylogenetic scale. We illustrate how existing phylogenetic data and statistical tools can be used to investigate the effects of scale on a variety of well‐known patterns and processes, including diversification rates, community structure, niche conservatism or species‐abundance distributions.

Main conclusions

Explicit consideration of phylogenetic scale can provide new and more complete insight into many longstanding questions across multiple fields (macroevolution, community ecology, biogeography and macroecology). Building on the existing resources and isolated efforts across fields, future research centred on phylogenetic scale might enrich our understanding of the processes that together, but over different scales, shape the diversity of life.     

Taxonomic,functional, and phylogenetic β‐diversity patterns of stream fish assemblages in tropical agroecosystems

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Evolutionary diversity gradients in neotropical tree assemblages: New insights from Non-Flooded Evergreen forests

We investigated spatial patterns of evolutionary diversity along Neotropical Non-Flooded Evergreen Forests (NEF). We addressed the following questions: (i) What are the main NEF evolutionary groups? (ii) How evolutionary diversity varies across NEF environmental gradients? Based on a phylogeny of 1248 tree genera distributed over 1824 NEF assemblages, we examined the evolutionary differentiation using UPGMA and evopca. We measured lineage diversity (ses.PD) and structure (ses.MPD and ses.MNTD) and tested their response to environmental gradients using linear models. Phylogenetic dissimilarity segregated NEF into 12 evolutionary groups that largely confirm groups obtained in our previous work based on floristic similarity. However, one discrepancy was the amalgamation of Amazon and northern Atlantic Forest assemblages, while the southern Atlantic Forest remained an isolated group. Furthermore, Mesoamerica, which had been recognized as a single group, here split into six evolutionary groups. We found greater lineage diversity as altitude and latitude increased and temperature decreased. Evolutionary groups with the highest mean values of lineage diversity were those composed of Mesoamerican cloud forests, which harbor a mixture of tropical and temperate lineages representing a confluence of South and North American floras. We found that variations in phylogenetic diversity in NEF are primarily related to the coexistence of lineages of temperate and tropical climates in the mountain and nebular environments of NEF, indicating the strong contribution of extratropical niche conservatism in structuring evolutionary diversity.     

Spatial and Temporal Patterns in Assemblages of Temperate Reef Fish

SYNOPSIS. For reef fish in temperate marine regions, such componentsof local assemblage diversity (i.e., within a reef) as speciesrichness, total fish density, and rank order of abundance canremain relatively constantthrough time. Long-term data (17 years)for assemblages on 2 reefs in Southern California revealed that,despite high turnover in rare species, overall species richnesswas affected only moderately by major oceanographicdisturbances.This resilience of the assemblage is in marked contrast to hightemporal variation in densities exhibited by many local populationsof individual species, and it suggests that measurements ofdiversity to indicate status of an assemblage should be usedwith caution. Here we consider various processes and factors,together with the spatial and temporal scales over which theyoperate, that can influence local diversity (and its estimation)of reef fishes. Mechanisms that can "buffer" local diversityof reef fishes include dispersal of young that inter-connectssubpopulations, high "inertia" in relative abundance and populationstructures (especially for long-lived species), and broad ecologicalrequirements of many species. These considerations suggest thatthe effect of disturbances on local diversity of reef fisheswill depend in part on the magnitude, duration, frequency andspatial scale of the perturbation. While long-term data arefew, available information suggests that, due to life historycharacteristics of the fish and the spatial and temporal scalesat which disturbances are likely to occur, assemblages of temperatemarine reef fish might be relatively resilient to environmentalperturbations     

Phylogenetic and morphological relationships between nonvolant small mammals reveal assembly processes at different spatial scales

The relative roles of historical processes, environmental filtering, and ecological interactions in the organization of species assemblages vary depending on the spatial scale. We evaluated the phylogenetic and morphological relationships between species and individuals (i.e., inter‐ and intraspecific variability) of Neotropical nonvolant small mammals coexisting in grassland‐forest ecotones, in landscapes and in regions, that is, three different scales. We used a phylogenetic tree to infer evolutionary relationships, and morphological traits as indicators of performance and niche similarities between species and individuals. Subsequently, we applied phylogenetic and morphologic indexes of diversity and distance between species to evaluate small mammal assemblage structures on the three scales. The results indicated a repulsion pattern near forest edges, showing that phylogenetically similar species coexisted less often than expected by chance. The strategies for niche differentiation might explain the phylogenetic repulsion observed at the edge. Phylogenetic and morphological clustering in the grassland and at the forest interior indicated the coexistence of closely related and ecologically similar species and individuals. Coexistence patterns were similar whether species‐trait values or individual values were used. At the landscape and regional scales, assemblages showed a predominant pattern of phylogenetic and morphological clustering. Environmental filters influenced the coexistence patterns at three scales, showing the importance of phylogenetically conserved ecological tolerances in enabling taxa co‐occurrence. Evidence of phylogenetic repulsion in one region indicated that other processes beyond environmental filtering are important for community assembly at broad scales. Finally, ecological interactions and environmental filtering seemed important at the local scale, while environmental filtering and historical colonization seemed important for community assembly at broader scales.