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Aim: Myrcia is a plant genus exclusive of the Neotropical region and one of the most important components of the tree diversity in the Cerrado and Atlantic Forest domains. However, no mapping of its taxonomic diversity for this region exists. Our aim was to describe the spatial patterns of diversity and biogeographical history for Myrcia in the Neotropical region based on a phylogenetic regionalization. Location: Neotropics. Taxon: Genus Myrcia (Myrtaceae). Methods: We derived distributions for 307 species from occurrence records using buffering and species distribution modelling. We used stacked distributions to generate a richness map of the genus and its clades (sections). In addition, we used phylogenetic regionalization methods to define evolutionary regions (evoregions) and ancestral area reconstruction to reveal the biogeographical history across these evoregions. Results: We found high species richness in the Atlantic Forest and Cerrado, with some sections restricted to the East coast of South America, while others were widespread across the Neotropics. We defined five evoregions, named A–E; the ancestral reconstruction revealed that Myrcia originated in evoregion B, under a tropical climate, with further specialization of distant‐related lineages to the colder environmental condition in evoregion A. Main Conclusions: High species richness of Myrcia in South America eastern coast and in the Brazilian highlands coincides with the evoregions with most diversification. Our genus‐specific regionalization together with the ancestral area reconstruction showed that evoregions A and B were the main evolutionary regions where diversification took place. In addition, the biogeographical history of the group suggests that some lineages have adaptations to deal with colder environments, that probably evolved in response to cooling periods since the mid‐Miocene. [ABSTRACT FROM AUTHOR]

Aim: Speciation, extinction and historical dispersal are the ultimate factors generating and maintaining biodiversity. However, methods of macroevolution used to detect historical processes usually ignore the variation of macroevolutionary processes at scales finer than entire regions. Likewise, biogeography and community ecology often ignore deep‐time evolutionary processes. To overcome this problem, it is necessary to integrate data from ancestral state reconstructions, current species distributions and biogeographical regionalization. Herodotools is an R package designed to perform this integration. Location: Global application, with an example from Neotropics. Major taxa studied: Any taxa, with an example from small rodents (genus Akodon and subfamily Sigmodontinae). Methods: Herodotools streamline analyses of historical biogeography, including regionalization, calculation of assemblage age, lineage in situ diversification and community phylogenetic metrics, merging species occurrence with macroevolutionary methods of ancestral area and trait reconstruction. The main functions of our R package are presented with toy examples and by analysing the historical biogeography of small rodent assemblages in the Neotropics. Results: Our package can integrate methods from biogeography, macroevolution and community ecology, allowing us to downscale the effects of historical processes and calculate important historical variables (e.g., age of assemblages, in situ diversification, phylogenetic regionalization, phylogenetic transition zones, metrics of trait macroevolutionary dynamics and new metrics of phylogenetic diversity and endemism) in different scales, from entire regions to communities of co‐occurrent species. Main Conclusions: Herodotools is the first platform to streamline the analysis of historical biogeography, enabling a better understanding of historical processes at different levels of organization, from local assemblages to entire biogeographical regions and incorporating macroevolutionary models in commonly used community phylogenetic metrics. This integration bridges the gap between macroevolutionary, biogeography and community ecology methods. [ABSTRACT FROM AUTHOR]

The imprint left by niche evolution on the variation of biological diversity across spatial and environmental gradients is still debated among ecologists. Furthermore, understanding to what extent dispersal limitation may reinforce or blur such imprint is still a gap in the ecological knowledge. In this article we introduce a simulation approach coupled to approximate Bayesian computation (ABC) that parameterizes both the adaptation rate of species' niche positions over the evolution of a monophyletic lineage and the intensity of dispersal limitation associated with the variation of species alpha diversity among assemblages distributed across spatial and environmental gradients. The analytical tool was implemented in the R package 'mcfly' (www.r‐project.org). We evaluated the statistical performance of the analytical framework using simulated datasets, which confirmed the suitability of the analysis to estimate adaptation rate parameter but showed to be less precise in relation to the dispersal limitation parameter. Also, we found that increased dispersal limitation levels improved the parameterization of the adaptation rate of species' niche positions in simulated datasets. Further, we evaluated the role played by niche evolution and dispersal limitation on species alpha diversity variation of Phyllostomidae bats across the Neotropics. The framework proposed here shed light on the links between niche evolution, dispersal limitation and gradients of biological diversity, and thereby improved our understanding of evolutionary imprints on current biological diversity patterns. [ABSTRACT FROM AUTHOR]

We propose that a qualitative trait approach based on more detailed nuanced traits may reveal previously overlooked patterns, especially when combined with phylogenetic perspectives. By sampling epiphytic lichens and using a functional approach based on nuanced qualitative traits, such as a much greater resolution over photobiont identity, type of cortex, and chemical compounds, we evaluated the effects of environmental filtering and phylogenetic constraints on community assembly along a natural succession of Atlantic rainforest. We found changes in taxonomic, functional, and phylogenetic composition, structure, and diversity. Functional traits such as photobiont genera, type of cortex, reproductive structures, propagule size, and protection strategies showed strong responses to succession. Mature forests with a closed canopy impose strong environment filtering that is reflected in lichen species turnover, limiting diversity, but also holding different functional and phylogenetic composition. The use of a nuanced qualitative trait approach may overcome some of the limitations of using this type of traits and shows the importance of often‐overlooked key lichen functional traits, including the presence of carbon‐concentrating mechanisms in photobionts and cortex properties. Furthermore, this is the first study showing how patterns of phylogenetic assembly along forest succession structure lichen communities. [ABSTRACT FROM AUTHOR]

We evaluated whether evolution is faster at ecotones as niche shifts may be needed to persist under unstable environment. We mapped diet evolution along the evolutionary history of 350 sigmodontine species. Mapping was used in three new tip‐based metrics of trait evolution – Transition Rates, Stasis Time, and Last Transition Time – which were spatialized at the assemblage level (aTR, aST, aTL). Assemblages were obtained by superimposing range maps on points located at core and ecotone of the 93 South American ecoregions. Using Linear Mixed Models, we tested whether ecotones have species with more changes from the ancestral diet (higher aTR), have maintained the current diet for a shorter time (lower aST), and have more recent transitions to the current diet (lower aLT) than cores. We found lower aTR, and higher aST and aLT at ecotones than at cores. Although ecotones are more heterogeneous, both environmentally and in relation to selection pressures they exert on organisms, ecotone species change little from the ancestral diet as generalist habits are necessary toward feeding in ephemeral environments. The need to incorporate phylogenetic uncertainty in tip‐based metrics was evident from large uncertainty detected. Our study integrates ecology and evolution by analyzing how fast trait evolution is across space. [ABSTRACT FROM AUTHOR]

Studies on ecological communities often address patterns of species distribution and abundance, but few consider uncertainty in counts of both species and individuals when computing diversity measures.We evaluated the extent to which imperfect detection may influence patterns of taxonomic, functional, and phylogenetic diversity in ecological communities.We estimated the true abundance of fruit‐feeding butterflies sampled in canopy and understory strata in a subtropical forest. We compared the diversity values calculated by observed and estimated abundance data through the hidden diversity framework. This framework evaluates the deviation of observed diversity when compared with diversities derived from estimated true abundances and whether such deviation represents a bias or a noise in the observed diversity pattern.The hidden diversity values differed between strata for all diversity measures, except for functional richness. The taxonomic measure was the only one where we observed an inversion of the most diverse stratum when imperfect detection was included. Regarding phylogenetic and functional measures, the strata showed distinct responses to imperfect detection, despite the tendency to overestimate observed diversity. While the understory showed noise for the phylogenetic measure, since the observed pattern was maintained, the canopy had biased diversity for the functional metric. This bias occurred since no significant differences were found between strata for observed diversity, but rather for estimated diversity, with the canopy being more clustered.We demonstrate that ignore imperfect detection may lead to unrealistic estimates of diversity and hence to erroneous interpretations of patterns and processes that structure biological communities. For fruit‐feeding butterflies, according to their phylogenetic position or functional traits, the undetected individuals triggered different responses in the relationship of the diversity measures to the environmental factor. This highlights the importance to evaluate and include the uncertainty in species detectability before calculating biodiversity measures to describe communities. [ABSTRACT FROM AUTHOR]

ABSTRACT Aim Location Taxon Methods Results Main Conclusions We address the relative importance of biogeographic regions (areas of endemism), regional climate and spatial factors on taxonomic, functional and phylogenetic beta diversity of bird assemblages in upland terra‐firme forests in the Amazon.Amazon biome.Birds.We gathered 27,498 occurrence records of 873 bird species for 115 bird assemblages distributed in all nine biogeographic regions delimited by the major Amazonian rivers. Only data from studies surveying whole communities with standard sampling methods and exhaustive sampling effort were included. We partitioned the fractions of taxonomic, functional and phylogenetic beta diversity explained by climate, biogeographic regions, spatial factors and the variation shared between them.Across the entire Amazon, we found higher total taxonomic (0.68 ± 0.10) than phylogenetic (0.46 ± 0.08) β‐diversity, and low functional β‐diversity (0.34 ± 0.08). Biogeographic regions showed the highest unique contributions explaining taxonomic and phylogenetic β‐total (7% and 5%, respectively) and turnover components (7% of β‐jtu taxonomic, 7% of β‐jtu phylogenetic), but accounted for only 2% of total functional β‐diversity and trait turnover. Climatic variables explained slightly more trait nestedness (5%) compared with species and lineage turnover (3% each). Species composition was clearly distinct between biogeographical regions limited by the Amazon River, but support for the effect of other rivers was mixed.Our study highlights the significant influence of biogeographic regions and climate on species composition in the Amazon. However, our findings also suggest that the Amazon River exerts a more pronounced impact on species distribution compared with other major Amazonian rivers. Species turnover across biogeographical regions is particularly evident at the species level, with minor effects observed in functional traits, suggesting that taxonomic turnover is driven mainly by functionally redundant species. In addition, recent diversification events, occurring predominantly at the tips of the phylogeny without substantial turnover at deeper nodes, are likely responsible for the patchy distribution of species across Amazonia. [ABSTRACT FROM AUTHOR]

Elevation gradients are drivers of species diversity, and, recently, studies have considered the evolutionary process in shaping community assembly patterns. Patterns of plant species richness across elevational gradients have been studied in different parts of the Atlantic Forest; however, little is known about plant phylogenetic diversity patterns. Thus, we aimed to analyse the phylogenetic diversity of angiosperm trees along an elevation gradient in southern Brazilian Plateau, in the subtropical portion of the Atlantic Forest. We expected a decrease in phylogenetic diversity along the elevation gradient, from lowlands towards to highlands, where species may be evolutionary closely related as many tropical lineages are not capable to inhabit colder conditions. We also investigated the distribution of phylogenetic clades along the elevation gradient through principal coordinates of phylogenetic structure. Data were obtained from 28 phytosociological surveys distributed across different elevation levels, ranging from 40 to 975 m. We found a negative association between phylogenetic diversity and the elevation gradient. The representativeness of families Myrtaceae and Lauraceae increased with elevation, while most of the families decreased in species richness and are replaced by temperate families such as Winteraceae (Drimys) in higher elevations. The decrease in phylogenetic diversity with increasing elevation may be linked to niche conservatism of tropical lineages that retain their historical climatic niches and thus many species are not capable to inhabit colder environments. Most tropical clades are restricted to lower elevations; however, Myrtaceae and Lauraceae probably evolved tolerance to colder temperatures during glacial cycles. Furthermore, the probably long‐term climate stability in lowlands than highland areas may have promoted the co‐occurrence of distantly related species, resulting in higher phylogenetic diversity. Finally, we observed how historical imprints and current environmental conditions shape the phylogenetic diversity of angiosperm tree species in subtropical Atlantic Forest. [ABSTRACT FROM AUTHOR]

Question: Habitat‐specific species pools are shaped by ecological and evolutionary processes such as speciation, extinction, and migration. However, their role is poorly known because of the lack of robust data on species pools across a large number of plant community types and large areas. Here, we analyse a unique dataset of species pools of diagnostic species for all European vegetation types, asking: (a) what are the patterns of phylogenetic structure and phylogenetic beta‐diversity across European vegetation types and biomes; (b) what are the drivers of these patterns; and (c) is there a signal of niche conservatism at the level of biomes and broad categories of vegetation types? Location: Europe, Canary Islands, Madeira, Azores, Cyprus, Caucasus, Iceland and Greenland. Methods: We built a dataset comprising 10,804 vascular plant species (almost 85% of the European flora) assigned to 106 vegetation types representing all European vegetated habitats, grouped into 11 biomes. This dataset represented habitat‐specific species pools. We analysed the phylogenetic structure of the species pools and related it to distribution range sizes of individual vegetation types, their successional status, levels of disturbance and environmental stress. Results: In European vegetation, phylogenetic overdispersion is associated with late‐successional habitats: several forest types, aquatic vegetation, and rock‐cliff vegetation serve as depositories of relict lineages. In contrast, phylogenetic clustering is typical of early successional and disturbed vegetation in anthropogenic, coastal and saline habitats, and in open‐canopy Mediterranean vegetation. The phylogenetic similarity of vegetation types is higher within than between broad categories of vegetation types and biomes. Conclusions: The variable phylogenetic structure of European vegetation types is a heritage of evolutionary processes in the Tertiary and Quaternary. Habitat‐specific species pools of different vegetation types and biomes have been formed by different evolutionary processes as indicated by the observation that certain clades are significantly associated with certain vegetation types or biomes, hence indicating the phylogenetic niche conservatism. [ABSTRACT FROM AUTHOR]

Biogeographic regionalization offers context to the geographical evolution of clades. The positions of bioregions inform both the spatial location of clusters in species distribution and where their most important boundaries are. Nevertheless, defining bioregions based on species distribution alone only incidentally recovers regions that are important during the evolution of the focal group. The extent to which bioregions correspond to centres of independent diversification depends on how clusters of species composition naturally reflect the radiation of single clades, which is not the case when mixed colonization occurred.Here, we show that using phylogenetic turnover based on fuzzy sets, instead of species composition, led to adequate detection of evolutionarily important bioregions, that is, regions that account for the independent diversification of lineages. Mapping those evoregions in the phylogenetic tree quickly reveals the timing and location of major shifts of biogeographic regions. Moreover, evolutionary transition zones are easily mapped, and permit the recognition of regions with high phylogenetic overlap.Our results using the global radiation of rats and mice (Muroidea) recovered four evoregions—three major evolutionary arenas corresponding to the Neotropics, a Nearctic‐Siberian, and a Paleotropical‐Australian evoregion and a fourth and fuzzy Afro‐Palearctic evoregion. Transition zones among evoregions were minimized when compared to other methods considering or not phylogenetic information, that is, the affiliation of cells to their assigned region was higher using evoregions than other approaches. Such higher affiliation values result from the lower phylogenetic overlap within evoregions, as expected when single radiations are accounted for as best as possible.Evoregions is a useful framework whenever the question is related to the identification of the most important centres of a group's diversification history and its evolutionary transitions zones. [ABSTRACT FROM AUTHOR]

Ecological literature offers a myriad of methods for quantifying β diversity. One such method is determining BDtotal (BD), which, unlike other methods, can be decomposed into meaningful components that indicate how unique a sampling unit is regarding its composition (local contribution) and how unique a species is regarding its occurrence in the community (species contribution). Despite this advantage, the original formulation of the BD metric only assesses taxonomic variation and neglects other important dimensions of biodiversity. We expanded the original formulation of BD to capture variation in the functional and phylogenetic dimensions of community data by computing two new metrics—BDFun and BDPhy—as well as their respective components that represent the local and species contribution. We tested the statistical performance of these new metrics for capturing variation in functional and phylogenetic composition through simulated communities and illustrated the potential use of these new metrics by analyzing β diversity of stream fish communities. Our results demonstrated that BDPhy and BDFun have acceptable type I error and great power to detect the effect of deep evolutionary relationships and attributes mediating patterns of β diversity. The empirical example illustrated how BDPhy and BDFun reveal complementary aspects of β diversity relative to the original BD metric. These new metrics can be used to identify local communities that are of conservation importance because they represent unique functional, phylogenetic, and taxonomic compositions. We conclude that BDPhy and BDFun are important tools for providing complementary information in the investigation of the structure of biological communities. [ABSTRACT FROM AUTHOR]

Questions: We asked: (a) whether the strength of conspecific and heterospecific neighborhood crowding effects on focal tree survival and growth vary with neighborhood radii; and (b) if the relative strength of the effect of neighborhood interactions on tree growth and survival varies with neighborhood scale. Location: Luquillo Forest Dynamics Plot, Puerto Rico. Methods: We used tree survival and growth data and included information on species‐mean trait values related to several leaf traits, maximum height, seed mass and wood density. We incorporated a tree neighborhood modeling approach that uses an area around a focal tree with a specified radius, to describe the interactions between a focal tree and its neighbors. We constructed survival and growth models for each functional trait using a Bayesian approach, and varied the size of the radius from 5 m to 30 m, at 5‐m intervals. Results: The results suggested that the estimated effects of conspecific and heterospecific neighbors on tree performance do not vary based on the size of the neighborhood (5–30 m), suggesting that the effects of conspecific and heterospecific neighbors on the performance of a focal tree likely do not vary substantially beyond a neighborhood radius of 5 m in the Luquillo forest. In contrast, the estimated strength of the functional neighborhood (effect of neighbors based on their functional trait values) on tree performance was dependent on the neighborhood range. Our results also suggested that the effects of trait distances and trait hierarchies on tree survival and growth are acting simultaneously and at the same spatial scales. Conclusion: Findings from this study highlight the importance of spatial scale in community assembly processes, and specifically, call for increased attention when selecting the radius that defines the neighborhood around a focal tree as the selected neighborhood radius influences the community patterns discovered, and affects the conclusions about the drivers that control community assembly. [ABSTRACT FROM AUTHOR]

Aim: Free‐living bacteria have long been assumed to have little biogeographic signature because of their high potential for passive dispersal. Raphidiopsis raciborskii and Microcystis aeruginosa are free‐living cosmopolitan cyanobacteria with a probable tropical origin, that frequently form toxic blooms and are considered invasive species in middle latitudes. Despite these similarities, their phylogeographic patterns have seldom been directly compared. Our aim was to reconstruct the phylogeographic histories of R. raciborskii and M. aeruginosa, in order to explore whether their current distributions could be attributed to the same biogeographic events. Location: Global. Taxa: Raphidiopsis raciborskii (Nostocales) and Microcystis aeruginosa (Chroococcales). Methods: The phylogeography of these species was studied based on global genetic diversity patterns from a dataset of worldwide 16S rRNA gene sequences. Genetic diversity indices were measured globally and by latitude. Analyses based on distance matrices were performed to evaluate the correlation between genetic divergence, geographic distance and climatic conditions. Demographic history was investigated through neutrality tests and Bayesian Skyline Plot analysis. Results: For both species, the genetic diversity is highest in tropical latitudes, and the data provided evidence of recent population expansions (in the last 2,500 years). R. raciborskii showed much lower genetic diversity than M. aeruginosa. A significant phylogeographic structure was found for R. raciborskii but not for M. aeruginosa. Climatic conditions had a significant influence on the genetic structure of both species, but this influence was stronger and varied according to latitude only for R. raciborskii. Main Conclusions: Supporting the hypothesis of a tropical origin and recent dispersal to temperate habitats, both species had higher genetic diversity in tropical latitudes and showed evidence of recent population expansions. R. raciborskii populations showed a significant decline in genetic similarity with increasing geographic distance, indicating an interaction between drift and some dispersal limitation on its phylogeography. In contrast, M. aeruginosa seemed to have a high frequency of intercontinental dispersal. Finally, the particularities of each species, such as the ability to form akinetes in R. raciborskii and high genome plasticity and niche specialization in M. aeruginosa, may be associated with the lower genetic diversity of R. raciborskii when compared to M. aeruginosa. [ABSTRACT FROM AUTHOR]

Biodiversity can be represented by different dimensions. While many diversity metrics try to capture the variation of these dimensions they also lead to a 'fragmentation' of the concept of biodiversity itself. Developing a unified measure that integrates all the dimensions of biodiversity is a theoretical solution for this problem, however, it remains operationally impossible. Alternatively, understanding which dimensions better represent the biodiversity of a set of communities can be a reliable way to integrate the different diversity metrics. Therefore, to achieve a holistic understand of biological diversity, we explore the concept of dimensionality. We define dimensionality of diversity as the number of complementary components of biodiversity, represented by diversity metrics, needed to describe biodiversity in an unambiguously and effective way. We provide a solution that joins two components of dimensionality – correlation and the variation – operationalized through two metrics, respectively: evenness of eigenvalues (EE) and importance values (IV). Through simulation we show that considering EE and IV together can provide information that is neglected when only EE is considered. We demonstrate how to apply this framework by investigating the dimensionality of South American small mammal communities. Our example evidenced that, for some representations of biological diversity, more attention is needed in the choice of diversity metrics necessary to effectively characterize biodiversity. We conclude by highlighting that this integrated framework provides a better understanding of dimensionality than considering only the correlation component. [ABSTRACT FROM AUTHOR]

Aim: To understand how variations in precipitation and topographic wetness influence tree community assembly at both regional and landscape scales in tropical forests. Location: New Caledonia (SW Pacific). Methods: We sampled 40 tree communities in 0.04‐ha plots laid along topographic gradients within two landscapes with contrasting precipitation. Within a dry (<1,400 mm/year) and a wet (>2,500 mm/year) landscape we used the Topographic Wetness Index (TWI) to sample communities in topographic position with low (e.g., ridges) and high (e.g., valleys) water accumulation. For each sampled species, we measured five functional traits involved in drought resistance and resource acquisition (wood density, leaf area, leaf specific area, leaf dry matter content, and leaf thickness). We first examined trait covariation across species. We then analysed how the functional composition of communities varied between landscapes (according to precipitation) and within landscapes (according to TWI), using trait‐based statistics and null models. Results: We identified two ecological trade‐offs driving trait variation across species: (i) one opposing high hydraulic efficiency to drought resistance, related to a wood economic spectrum; and (ii) the other opposing resource acquisition to resource conservation, related to a leaf economic spectrum. Across landscapes, species with drought resistance strategies were favoured at lower precipitation. Within landscapes, drought resistant species were selected under low TWI in the dry landscape, while low TWI increased the abundance of species with conservative strategies in the wet landscape. Conclusions: Precipitation and topography jointly shape the functional composition of tree communities. At low precipitation, hydric constraints prevailed on ridges and upslopes by filtering drought resistant strategies along the wood economic spectrum. Contrastingly, higher precipitation relaxed the hydric constraints and resource availability became a primary driver of changing strategies along the leaf economic spectrum. Thus, the landscape scale influence of topography on processes driving community assembly and functional composition critically depends on the regional climatic context. [ABSTRACT FROM AUTHOR]

Environmental gradients consist of sequential changes in the physical and structural characteristics of a region. These allow us to follow species responses and tolerances under different habitat conditions. Among them, forest fragmentation and succession comprise the most common examples of forest gradients, where organismal responses require distinct morphological, physiological, and behavioral adaptations. However, environmental changes can impose ecological and evolutionary constraints that act on species traits, as well as on local species assemblies through their phylogenetic history. In this study, we evaluated the differences in species distribution and composition on fruit-feeding butterfly assemblages along forest fragmentation and succession gradients. We combine functional and phylogenetic methods for determining butterfly assemblages, and inferred species resistance and resilience according to habitat changes in tropical forests. We used a database of 471 fruit-feeding butterflies of 60 species sampled from different environments in the central Amazon rainforest. A total of 13 functional traits were measured, and a phylogenetic tree was obtained for the sampled species. The trait–environment relationship was analyzed along both forest fragmentation and succession gradients, controlling for phylogenetic signal on species distribution and functional composition when necessary. Several traits presented phylogenetic signal, and phylogeny was also driving butterfly species distribution along the successional gradient. After controlling for phylogeny, individual characteristics related to flight speed (thoracic weight) and antipredatory strategies (camouflage) increased in early-successional forests, with large butterflies (body length) prevailing in primary forests. No clear functional and phylogenetic pattern was identified for the fragmentation gradient. Our results are consistent with the idea that butterflies may be employing distinct functional strategies to attenuate habitat change effects. Larger butterflies, with lower dispersal ability, are preferentially susceptible to local extinctions in the early-successional environments, mainly when forested habitat and its resources become spatially restricted. In addition, several anti-predatory strategies related to conspicuous colors may be losing their functionality in open areas, where not being distinctive against the background becomes the primary defense against predation. [ABSTRACT FROM AUTHOR]

Questions: What is the relative influence of: (a) traits related to dispersal (seed size) and growth (specific leaf area [SLA]), and; (b) regional species abundances, on the structure of local sapling communities? Which metacommunity models best explain the process of forest nucleation in grasslands? Location: Woody vegetation patches originating from nucleation and the continuous forest that neighbors native grasslands, in the southern Brazilian plateau (29°28′58.00″ S, 50°12′26.00″ W). Methods: We calculated community‐weighted trait means (CWM) and functional diversity for woody saplings, considering species occurrences (FD) and abundances (FDis) separately for both seed size and SLA, in woody vegetation patches of different sizes and in the continuous forest. We tested whether mean SLA and mean seed size differed between habitat types, and whether values of FD and FDis were lower than expected by chance. We also evaluated whether the relative abundances of species in woody vegetation patches were determined by their abundances in the continuous forest, using CATS models (Community Assembly by Trait Selection). The results were then compared to the expectations from each metacommunity model. Results: Functional diversity of SLA and seed size did not differ from what was expected by chance in most sites. Species in communities of different habitat types did not differ in their mean SLA values, but we observed differences in mean seed size, with large‐seeded species being typical of areas with more shade. Species abundances in the regional species pool were more important factors than species traits for determining species abundances in the local communities. Conclusions: The analytical framework employed in this study enables a straightforward test of different metacommunity structuring models. Mass effects were the metacommunity model that best explained the process of forest nucleation in the southern Brazilian plateau, which highlights the importance of dispersal for the structure of local communities. [ABSTRACT FROM AUTHOR]

Questions: Do neighbourhood interactions in trees result in discernible spatial and phylogenetic signals among their nearest neighbours in a montane evergreen and deciduous forest? Are neighbourhood patterns of different species associated with their abundances and traits? Location: Badagongshan National Nature Reserve, Hunan, China. Methods: We used four nearest‐neighbour indices: average spatial distance to the nearest conspecific cohort‐mate (SNCC), average spatial distance to the nearest conspecific adult (SNCA), average phylogenetic distance to the nearest heterospecific cohort‐mate (PNHC), and average phylogenetic distance to the nearest heterospecific adult (PNHA). We focused on 77 abundant species in a 25‐ha plot. We evaluated whether the changes in SNCC, PNHC, SNCA and PNHA deviated significantly from expected values of spatially random mortality during two life stage transitions. Results: For more than one‐fourth of the tested species, the changes in SNCC and PNHC deviated significantly from the expectations of random mortality. Nearly one‐third of the tested species showed greater SNCC at the juvenile stage than expected of random mortality, which may be mainly explained by conspecific tree competition for space and resources. Approximately 60% and 40% of the tested species showed significantly smaller SNCA and PNHA than expected by random mortality, respectively, which suggests the effects of facilitation and habitat filtering. In addition, abundant and taller species were suppressed by conspecific cohorts to a greater degree than locally rarer and shorter species. Deciduous species were more negatively influenced by conspecifics and closely related heterospecifics than evergreen species. Conclusions: Our study focused on long‐term responses of individual species to their conspecific and phylogenetic neighbourhoods and revealed the associations between species traits and neighbourhood patterns. Such trait–neighbourhood interactions provide support for stabilizing mechanisms driving species coexistence in this species‐rich subtropical forest. [ABSTRACT FROM AUTHOR]

Questions: All else being equal, populations of dioecious species with a 50:50 sex ratio have only half the effective reproductive population size of bisexual species of equal abundance. Consequently, there is a need to explain how dioecious and bisexual species coexist. Increased mean individual seed mass, fecundity, and population density have all been proposed as attributes of unisexual individuals or populations that may contribute to the persistence or resilience of dioecious species. To date, no studies have compared sympatric dioecious and cosexual species with respect to all three components of fitness. In this study, we sought evidence for these compensatory advantages (higher seed mass, greater seed production per unit basal area, and higher population density) in dioecious species. Location: Five 20–25 ha forest dynamic plots spanning a latitudinal gradient in China, including two temperate, two subtropical, and one tropical forest. Methods: We used a phylogenetically corrected generalized linear modelling approach to assess the phylogenetic dependence and joint evolution of sexual system, seed mass and production, and ecological abundances among 48–333 species and 32,568–136,237 individuals per forest. Results: Across all five forests, we detected no consistent advantage for dioecious relative to sympatric cosexual species with respect to mean individual seed mass, seed production or the density of stems in any size class. Conclusions: Our study suggests that seed traits may provide compensatory mechanisms in some forests, but most often the coexistence of sexual systems cannot be explained by advantages of dioecy related to seed quality and demographic parameters. Future investigations of the factors that promote coexistence may increase our understanding by expanding the search to include attributes such as lifespan and tolerance or resistance to herbivores. [ABSTRACT FROM AUTHOR]

Aim: The Theory of Island Biogeography posits that ecological and evolutionary processes regulate species richness of isolated areas. We assessed the influences of an island area and distance from the mainland on species richness, phylogenetic diversity, and phylogenetic composition of snakes on coastal islands. Location: Coastal islands of the megadiverse Atlantic Forest in southeastern Brazil. Methods: We compiled the species composition of 17 coastal islands in southeastern Brazil. Species richness and phylogenetic diversity were calculated for each island. Phylogenetic composition was measured using principal coordinates of phylogenetic structure. We then employed generalized linear models to test the influence of area and distance from the mainland on the diversity metrics. Results: We found a prominent influence of area on species richness, whereas phylogenetic diversity was more affected by distance from the mainland. Snake clades were distinctly associated with area and distance. The Boidae family was associated with nearer and larger islands, whereas Elapidae was broadly distributed. Distance from the mainland was associated with the distribution of Dipsadidae, whereas Colubridae was influenced by both the area and distance. The Viperidae family attained higher values of phylogenetic diversity in smaller and more remote islands. Main conclusions: This island system conserved a considerable piece of snake richness from southeastern Brazil, including island endemic species. Area and distance from the mainland were important drivers of snake diversity in the Atlantic Forest coastal islands. However, these predictors affected the different components of diversity in different ways. Phylogenetic composition analysis enables us to understand how basal nodes contributed to high levels of phylogenetic diversity on smaller and farther islands regardless of the decrease in species richness. [ABSTRACT FROM AUTHOR]

Multiple factors drive species interactions in ecological networks, such as morphological barriers, spatio–temporal distribution, abundances and evolutionary histories of species. Novel methods are making it possible to evaluate the relative importance of each of these drivers. However, the lack of appropriate methods has prevented evaluating the extent to which interaction networks are shaped by species’ evolutionary histories. This study includes the evolutionary histories of species among the potential drivers of interactions, allowing the comparative analysis of its importance in structuring ecological networks. We hypothesized different possible phylogenetic scenarios to predict frequencies of interactions between species by combining concepts from the fields of ecological networks and ecophylogenetics. The usage of these scenarios is illustrated in a plant–hummingbird interaction network database from the Atlantic Forest, southeastern Brazil. We first evaluated which phylogenetic hypotheses better predict the observed network; subsequently, we evaluated the relative importance of species evolutionary histories, abundances, and matching on species morphologies and phenologies as drivers of their frequencies of interactions. The results suggest that the evolutionary histories of hummingbirds are more important than the species abundances in structuring the studied plant–hummingbird network but less important than the morphological and phenological matching among species. The approach developed here offers the potential to advance our understanding of the multiple factors structuring ecological networks. [ABSTRACT FROM AUTHOR]

Abstract: Functional traits mediate ecological responses of organisms to the environment, determining community structure. Community‐weighted trait means (CWM) are often used to characterize communities by combining information on species traits and distribution. Relating CWM variation to environmental gradients allows for evaluating species sorting across the metacommunity, either based on correlation tests or ordinary least squares (OLS) models. Yet, it is not clear if phylogenetic signal in both traits and species distribution affect those analyses. On one hand, phylogenetic signal might indicate niche conservatism along clade evolution, reinforcing the environmental signal in trait assembly patterns. On the other hand, it might introduce phylogenetic autocorrelation to mean trait variation among communities. Under this latter scenario, phylogenetic signal might inflate type I error in analysis relating CWM variation to environmental gradients. We explore multiple ways phylogenetic history may influence analysis relating CWM to environmental gradients. We propose the concept of neutral trait diffusion, which predicts that for a functional trait x, CWM variation among local communities does not deviate from the expectation that x evolved according to a neutral evolutionary process. Based on this framework we introduce a graphical tool called neutral trait diffusion representation (NTDR) that allows for the evaluation of whether it is necessary to carry out phylogenetic correction in the trait prior to analyzing the association between CWM and environmental gradients. We illustrate the NTDR approach using simulated traits, phylogenies and metacommunities. We show that even under moderate phylogenetic signal in both the trait used to define CWM and species distribution across communities, OLS models relating CWM variation to environmental gradients lead to inflated type I error when testing the null hypothesis of no association between CWM and environmental gradient. To overcome this issue, we propose a phylogenetic correction for OLS models and evaluate its statistical performance (type I error and power). Phylogeny‐corrected OLS models successfully control for type I error in analysis relating CWM variation to environmental gradients but may show decreased power. Combining the exploratory tool of NTDR and phylogenetic correction in traits, when necessary, guarantees more precise inferences about the environmental forces driving trait‐mediated species sorting across metacommunities. [ABSTRACT FROM AUTHOR]

Question Analysing taxonomic, phylogenetic and functional species distribution across a metacommunity allows understanding of how landscape dynamics may influence forest expansion over grassland. In this context, climbing plants are particularly interesting vegetation components, since they actively prospect the best sunlight position, altering forest structure. We investigated if forest structure differentiation along a patch size/isolation gradient would determine the distribution of phylogenetic clades, dispersal and/or establishment-related traits in climbing plant assemblages. We hypothesized that taxonomic, phylogenetic and functional species diversities would show a nested pattern along the gradient of increasing vegetation complexity. Furthermore, less mobile diaspores, as well as climbing mechanisms independent of support limitations, and deeper phylogenetic clades characterized by shade-tolerant species would be associated with more developed and less isolated patches. Location Subtropical grassland surrounded by Araucaria forest, southern Brazil. Method We recorded the composition and abundance of climbing plant species along a gradient of forest patches increasing in size and isolation from the surrounding continuous forest. We performed an analysis of principal coordinates of phylogenetic structure ( PCPS) to investigate the distribution of phylogenetic clades across sites, tested its relationship with patch area and isolation using linear models, and for the correlation to species dispersal traits and climbing mechanisms. We employed the tree NODF (Nestedness based on Overlap and Decreasing Fill) method to estimate if there was a phylogenetic, compositional and/or functional nested pattern of the metacommunity structure during forest expansion over grassland. Results We found that species composition distribution was explained by patch size and isolation, but not by phylogeny. Dispersal traits were more structured along the gradient compared to climbing mechanisms. We also found a nested pattern of combined species and phylogenetic/functional diversities, where smaller patches are subsets of larger patches and of continuous forest sites. Conclusion Patch area, isolation and dispersal traits play significant roles in the distribution of climbing plants during the process of forest advance over grassland, independently of phylogenetic relatedness among species. The nested pattern indicated that continuous forest and larger patches provide all the diaspores that colonize the smaller patches in this process, making them important targets for conservation. [ABSTRACT FROM AUTHOR]

Questions (1) Which disturbances (harvesting, browsing, drought and fire) are important for tree mortality in a tropical dry forest ( TDF), and do these change with size class (juvenile, sapling, adult)? (2) How is mortality and recruitment in a TDF related to soil moisture content ( SMC) and does the relationship change for different size classes? (3) Is disturbance-related mortality selectively removing particular species from the TDF? Location Sonebhadra and Mirzapur districts, Uttar Pradesh, India. Methods We analysed the structure of a TDF in central India in terms of the tree composition of juveniles, saplings and adults at five distinct sites located along a gradient of SMC, and recorded the numbers of individuals in each size class killed by the four disturbance types over 2 yr. We also recorded total stem density and recruitment at each site. We compared annual mortality index ( AMI) and its four disturbance components (harvesting, browsing, drought and fire) and annual recruitment index ( ARI) against the mean SMC of each site using GLMM. Results The impact of all disturbances on total AMI decreased as SMC increased whereas ARI increased as SMC increased. Mortality due to harvesting was substantially higher than other disturbances for adult and sapling trees, whereas both harvesting and browsing were important drivers of mortality for juveniles. There was little evidence that particular species were being deliberately selected for harvesting across sites. Conclusions Tree saplings and adults in this TDF were mainly killed by harvesting, indicating that anthropogenic impacts on tree mortality are more important than non-anthropogenic impacts in the TDF, and impacts of all disturbances become more severe with increasing water stress. Thus changes in TDF structure due to harvesting are likely to be more rapid in more arid environments. [ABSTRACT FROM AUTHOR]

Questions Mosaics of evergreen and deciduous trees that are characteristic of evergreen broad-leaved forests ( EBLF) are thought to arise from habitat heterogeneity, but empirical evidence for this is limited. We test this assertion asking: (1) whether environmental heterogeneity explains the distribution of deciduous and evergreen trees; (2) which are the most important environmental variables; and (3) does their importance change with scale? Location Tiantong National Forest Park, Ningbo, Zhejiang, China. Methods We used data from a 20-ha individual-mapped EBLF in spatial point-pattern analyses testing the scale of aggregation within, and segregation between, the two life forms. We used a heterogeneous Poisson process model to remove the effects of environmental heterogeneity, predicting segregation would disappear if the mosaic was due to habitat heterogeneity alone. Finally, we tested the relative importance of theoretically important environmental variables using multivariate regression trees at three spatial scales (10, 20 and 50 m grid cells). Results We found evergreen and deciduous trees were aggregated at scales below 125 m and 60 m, respectively, and mutually exclusive at scales <120 m. Evidence of any spatial segregation between the life forms was removed at all scales after controlling for environmental heterogeneity. Only soil phosphorus concentrations contributed to spatial patterns at all scales, with values >0.27-0.30 g·kg−1 favouring deciduous species. Conclusions Our study is consistent with habitat heterogeneity creating the observed mosaics of evergreen and deciduous tree species, but micro-habitat heterogeneity contributed even at scales <20 m. Soil phosphorus availability appears to be the major environmental variable maintaining these mosaic patterns at hillslope scales in EBLF. [ABSTRACT FROM AUTHOR]

Question It is often assumed, but poorly tested, that patterns of phylogenetic diversity reflect functional diversity in plant communities. Here we test whether phylogeny can be used as a proxy for functional diversity in general and specifically for diversity in plant niche preferences, dispersal strategies and competitiveness-related traits. Location Central Europe, Belgium and the Netherlands. Methods We used a species composition data set from seven urban habitats, each sampled in 32 large cities of ten countries, and combined this with information about species phylogeny and functional traits, the latter divided into categories representing niche preferences, dispersal strategies and competitiveness. Results We found positive significant, yet very weak, relationships between phylogenetic diversity and overall functional diversity, and between phylogenetic diversity and diversity in both species dispersal strategies and competitiveness. The relationship between phylogenetic diversity and diversity in species niche preferences was not significant. Conclusions We suggest that the combination of multiple trait states that co-exist in urban plant communities and even within the same lineages weakens the phylogeny-function relationship. Phylogenetic diversity is a weak proxy for functional diversity of urban plant communities. For some facets of functional diversity, the phylogeny-function relationship may not apply at all. [ABSTRACT FROM AUTHOR]

Arthropods and land plants are the major macroscopic sources of biodiversity on the planet. Knowledge of the organization and specialization of plant-herbivore interactions, such as their roles in food webs is important for understanding the processes for maintaining biodiversity. A limited number of studies have examined herbivory through geological time. The most have analyzed localities from one restricted interval within a geological period, or a time transition such as the Paleocene-Eocene boundary interval. In the present study, we analyzed the frequency of herbivory and density of damage type ( DT) from the Middle Devonian to the early Miocene. The data were compiled from literature sources and focused on studies that describe occurrences of leaves with DTs indicating herbivore consumption as a proportion of the total number of leaves analyzed. The data were standardized based on the DT categories in the Damage Type Guide, and the age of each locality was updated based on the most recent geochronological standard and expressed in millions of years. Temperature and geological age were the best descriptors of the variation in herbivory frequency, which tended to increase at higher temperatures. Two models were equivalent to explain DT density: the interaction between CO2 levels and geological age, and O2 levels and geological age had the same predictive power. The density of DT tended to increase with higher content of atmospheric CO2 and O2 compared to modern values. The frequency of herbivory and the density of DTs appear to be influenced by long-term atmospheric variables. [ABSTRACT FROM AUTHOR]

Metacommunity phylogenetics aims at evaluating environmental and/or historical factors driving clade distribution. Phylogenetic fuzzy weighting ( PFW) describes clade distribution across metacommunities based on fuzzy sets defined by phylogenetic relatedness among species. The method enables analysing environmental and/or biogeographic determinants of clade distribution. PFW also offers an exploratory tool for visualizing clade distribution via Principal Coordinates of Phylogenetic Structure ( PCPS). In this article, we describe the theoretical properties and biological backgrounds of PFW and evaluate its statistical performance (type I error and statistical power) in assessing environmental and phylogenetic determinants of species distribution in comparison with other phylobetadiversity methods ( COMDIST, COMDISTNT, Rao's H and UniFrac)., The statistical performance of PFW and the other phylobetadiversity metrics was tested by (i) simulating metacommunities under different species assembly scenarios (species distribution influenced or not by environment and/or phylogeny), niche breadth tolerance and species pool sizes; (ii) submitting community matrices to PFW and deriving pairwise phylogenetic dissimilarities between communities ( D P) and PCPS; (iii) submitting these metrics and the other phylobetadiversity methods to different analytical approaches (Mantel test, regression on dissimilarity matrices - ADONIS, and GLM) to evaluate the influence of environment and phylogeny on metacommunity phylogenetic structure; and (iv) estimating type I error and power estimates via alternative permutation procedures., Results demonstrated that PFW provides robust assessment of environmental and phylogenetic drivers of species distribution across metacommunities. Although all methods had acceptable type I error for both Mantel test and ADONIS, only PFW showed acceptable power for both tests. Rao's H had acceptable power only for Mantel test, while COMDIST had acceptable power only for ADONIS. COMDISTNT and UniFrac showed poor statistical performance for both tests. Conversely, GLM had acceptable power only for the first PCPS., Performing ADONIS on DP provides a robust overall assessment of environmental and phylogenetic drivers of species distribution. On the other hand, performing PCPS analysis after rejecting the null hypotheses via ADONIS allows identifying the phylogenetic nodes mostly associated with environmental gradients. PFW enables synthesizing and analysing phylogenetic patterns in metacommunities, allowing attaining a more complete portrait of ecological and evolutionary drivers of species distribution. [ABSTRACT FROM AUTHOR]

Aim Body size variation in animal assemblages is a widely addressed pattern in biogeographical studies, and is affected by both environmental gradients and phylogenetic constraints. However, no study has yet explored to what extent the association between body size variation and environmental gradients across broad spatial scales is influenced by the biogeographical distribution of different phylogenetic lineages. In this study, we discriminate the influences of environmental variables and phylogenetic community composition on body size variation in South American sigmodontine rodents. Location South America. Methods We computed the mean body mass of sigmodontine species co-occurring in 1 × 1° cells across South America. For each cell we recorded mean values for three environmental variables. We characterized the phylogenetic composition of sigmodontine assemblages within each cell using phylogenetic fuzzy-weighting and principal coordinates of phylogenetic structure ( PCPS). We then partitioned out the influence of environmental factors and the phylogenetic community composition on mean body size. Results Mean body size variation was mostly explained by shared influence of phylogenetic community composition ( PCPS) and environmental factors (68%), while exclusive influence of PCPS was low (19%), and of environment was even lower (0.47%). Increases in body size were related to increases in annual mean temperature, and the influence of environment on body size was mediated by the distribution of sigmodontine lineages across South America. Main conclusions Environment alone was not sufficient to explain body size variation in sigmodontine assemblages. Rather, environmental gradients interacted with historical processes to determine body size variation in the Neotropical assemblages. These results have implications for the way we think of body size gradients across species assemblages, because any gradient in a trait may be a result of differences in the biogeographical distribution of lineages across space, which should be considered in an explicit context. [ABSTRACT FROM AUTHOR]

Question Understanding how the relative importance of different community assembly processes changes during secondary succession of diverse systems remains elusive. Functional and phylogenetic approaches that place species along continuous axes of niche differentiation and evolutionary relatedness, however, are deepening our understanding of the mechanisms that drive successional dynamics. We ask whether successional shifts in the functional and phylogenetic composition of post-agricultural tropical forests provide evidence for niche partitioning or competitive dominance hierarchies as drivers of successional change. Location Subtropical wet forests, Puerto Rico. Methods We combined data on four functional traits [leaf dry mass per area ( LMA), wood density ( WD), maximum height ( Hmax), seed dry mass] and a well-resolved molecular phylogeny to characterize taxonomic, functional and phylogenetic composition of sapling and adult tree communities along a regionally replicated chronosequence. We used a null model approach to assess how functional and phylogenetic diversity change with forest age. Results Corresponding increases of community-weighted mean LMA, Hmax and seed mass with forest age reflected a shift in dominance of species with acquisitive resource-use strategies and small seeds towards species with more conservative resource use and larger seeds. A negative relationship between forest age and local diversity of Hmax and seed mass suggested increased importance of competitive hierarchies for light capture and shade-tolerant regeneration in older forests. In contrast, the colonization of palms in older forest plots led to a positive relationship between forest age and local phylogenetic diversity, suggesting functional convergence of distantly related lineages on traits that confer competitive dominance under low resource conditions. Conclusions We linked both functional and phylogenetic dimensions of community diversity with successional trajectories of post-agricultural tropical forests. Contrasting patterns of these dimensions of diversity shed light on the underlying community assembly processes. We argue that integrating traits and phylogeny with specific hypotheses about physiological and historical mechanisms is essential for advancing our understanding of the drivers of community change during succession. [ABSTRACT FROM AUTHOR]

Questions: We analysed trait convergence and trait divergence assembly patterns across a metacommunity of grassland types (dry, wet and rocky) occurring along an edaphic gradient. We asked whether (1) floristics and phylogenetic structures vary among grassland types; (2) there is convergence and/or divergence in plant traits along the gradient; (3) the functional structure is influenced by phylogeny; and (4) abiotic or biotic filters generate the assembly patterns. Location: Campos Gerais region, Paraná State, southern Brazil (ca. 25°15002" S, 49°59059" W). Methods: We sampled plant functional traits and soil variables at 81.1-m2 quadrats in three natural grassland vegetation types across three different sites. We analysed the relationship between species composition (abundance), phylogenetic relationships, functional traits and soil characteristics using matrix correlations, where soil characteristics were the predictors of functional and phylogenetic assembly patterns. Results: A total of 168 plant specieswere sampled on the three vegetation types. Wet grassland quadrats were more similar to each other in species composition and phylogeny than with those on dry and rocky grasslands. We found trait convergence (not phylogenetically constrained) and trait divergence (phylogenetically constrained) assembly patterns in the three vegetation types along the edaphic gradient. Traits that generated convergence and divergence are related to strategies for survival in dry and low nutrient availability soils; nutritional soil gradient determined trait differences at small scales. Conclusion: Species composition and phylogenetic structure of communities occurring in different grassland types are related to edaphic gradient. The occurrence of both trait convergence and trait divergence patterns suggests, respectively, that environmental filters and biotic filters (competition) are structuring the plant assemblages. [ABSTRACT FROM AUTHOR]

Recent studies have shown that accounting for intraspecific trait variation ( ITV) may better address major questions in community ecology. However, a general picture of the relative extent of ITV compared to interspecific trait variation in plant communities is still missing. Here, we conducted a meta-analysis of the relative extent of ITV within and among plant communities worldwide, using a data set encompassing 629 communities (plots) and 36 functional traits. Overall, ITV accounted for 25% of the total trait variation within communities and 32% of the total trait variation among communities on average. The relative extent of ITV tended to be greater for whole-plant (e.g. plant height) vs. organ-level traits and for leaf chemical (e.g. leaf N and P concentration) vs. leaf morphological (e.g. leaf area and thickness) traits. The relative amount of ITV decreased with increasing species richness and spatial extent, but did not vary with plant growth form or climate. These results highlight global patterns in the relative importance of ITV in plant communities, providing practical guidelines for when researchers should include ITV in trait-based community and ecosystem studies. [ABSTRACT FROM AUTHOR]

Question What is the effect of past land use and environmental gradients on plant functional traits within coastal marsh plant communities? Location Mediterranean microtidal marshes in the Llobregat Delta, NE Spain. Methods We used a data set collected previously comprising 45 vegetation plots with associated soil parameters, water table conditions and past land use. For each species we obtained the values or states for a set of plant functional traits: plant height, leaf dry matter content, specific leaf area, seed production, seed weight, life form and lateral expansion. To account for the effect of phylogeny, we evaluated trait diversity skewness by means of an ultrametric phylogenetic tree specifically constructed for the species studied. The association between both environmental gradients and past disturbance, and plant functional traits was tested by means of RLQ analysis. Results Of all the traits, only seed weight showed a phylogenetic signal; consequently, phylogeny was not included in the RLQ analysis. Conductivity was negatively correlated with seed weight, whereas water table conditions and soil ionic balance were negatively correlated with specific leaf area. Past disturbance was negatively correlated with leaf dry matter content and with lateral expansion. Conclusions Plant traits of Llobregat Delta coastal marsh communities are conditioned by environmental gradients and by past land use. Soil ionic balance and water table conditions determine key plant functional traits such as specific leaf area. This finding also corroborates the importance of soil ionic balance as a plant life driver in microtidal Mediterranean marshes. The effect of past land use on species traits might, however, be partially indirect and mediated by associated environmental changes. [ABSTRACT FROM AUTHOR]

Aims In agro-ecosystems, crop types, i.e., the crop species and its associated agricultural practices, have been shown to influence the taxonomic as well as functional composition of weed communities. However, the processes underlying weed community assembly within a crop type are poorly understood, especially regarding the contributions of local factors and stochastic processes. In this study, we investigate the effects of the crop type in shaping local weed communities. Location LTER Zone Atelier Plaine et Val de Sèvre, an intensive cereal system in western France. Methods We selected 105 fields of five crop types and investigated the functional structure of weed communities for those traits that define the Leaf-Height-Seed (L-H-S) strategy as well as phenological traits. We compared the observed trait distribution to trait distributions expected under random assembly. The trait distributions were described by the range, the community-weighted mean and the dispersion of each trait, and simulated communities were generated with a null model approach that randomizes the 'species × traits' matrix to maintain equiprobable the occurrence of each trait combination. The relationship between trait values and species abundance within each community was investigated using Kendall rank correlation tests. Results Our results showed that, in ca. 90% of the fields, the functional diversity of weed communities did not differ from what would be expected under random assembly. Departures from random expectations essentially resulted from shifts in weighted mean values for phenological traits. Weed communities of sunflower, maize and spring pea had later onsets of emergence and flowering than randomly expected. Communities of winter wheat had smaller species and earlier onset of flowering, and communities from oilseed rape had a larger duration of the emergence period and earlier onset of flowering. In addition, we found a positive significant relationship between species abundance and trait values for phenology for spring pea, sunflower and maize, suggesting that species with a later onset of emergence and flowering period have higher performance in these weed communities. Conclusions At landscape scale, weed communities generally showed patterns of functional diversity in accordance with those expected under random community assembly, except for phenological traits in spring and summer crops, where patterns were rather consistent with environmental filtering. [ABSTRACT FROM AUTHOR]

Questions What is the magnitude of between-species trait variability ( BSV) and within-species trait variability ( WSV) of specific leaf area ( SLA) in a sapling meta-community? To what extent do species turnover and WSV influence community-level mean trait responses to an environmental gradient and trait spread patterns across this gradient? What is the role of WSV for mean plant responses to environmental variation and niche partitioning in structuring sapling communities? Location Forest patches within a native grassland matrix in southern Brazil. Methods We recorded saplings in community plots across a canopy openness gradient in forest patches and described each of the 1129 individuals using SLA. First, we partitioned trait variation into BSV and WSV irrespective of co-occurrence in plots. Then, using the community data, we partitioned the total variation of community-weighted trait means ( CWM) and Rao's functional diversity ( FD) into components explained by canopy openness, species turnover and WSV. We also partitioned the effects of WSV between and within plots on FD. Finally, we explored the responses of CWM and FD to the gradient using the whole trait variability, only BSV or only WSV. Results Specific leaf area presented a substantial proportion of variation within species (37%), although it varied more between species (63%). Species turnover and WSV explained 48% and 19% of the variation in CWM across the gradient, respectively. Species turnover and WSV explained 51% and 45% of the variation in FD across the gradient, respectively. SLA varied within species more along the gradient than within communities. Within-species variability enhanced shifts in CWM and FD across the gradient. Canopy openness significantly predicted CWM at all levels, and FD at all but the within-species level. Conclusions Plastic responses of species mirrored the average response of communities to the environmental gradient. Within-species trait variability enhanced the mean plant responses to environmental variation as well as niche partitioning, and was especially important in enabling species to establish in a wider portion of the environmental gradient. Our study provides new evidence that population-level phenomena matter for community assembly. [ABSTRACT FROM AUTHOR]

Pardiñas, Valenzuela, and Salazar-Bravo (2017) are concerned that eventual differences in species mean body masses and in the phylogenetic hypothesis used in Maestri et al. (2016)-compared with those available on other potential sources-could affect the results of our original article. Here, we used a new phylogenetic hypothesis to conduct the same analyses of the original article, and we randomly sampled 1000 values of body mass within approximately 35% upper and lower intervals around the mean body mass for each species included in our database. We show that our previous results and conclusions are robust and valid, and they persist despite uncertainty in mean body mass estimation. We argue that sampling variation and uncertainty in both species mean body mass estimation and phylogenetic hypothesis are to be expected and should not always be confused with inaccuracies. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The rapid global decline of amphibian population is alarming because many occur for apparently unknown or enigmatic reasons, even inside protected areas (PAs). Some studies have predicted the effects of climate change on amphibians' distribution and extinction, but the relationship and consequences of climate change to the phylogenetic structure of amphibian assemblages remain obscure. By applying robust techniques for ecological niche modeling and a cutting-edge approach on community phylogenetics, here, we evaluate how climate change affects the geographical pattern of amphibian species richness and phylogenetic diversity in the Atlantic Forest Biodiversity Hotspot, Brazil, as well as how the phylogenetic composition of amphibian assemblages respond to climate change. We found that most species contracted their ranges and that such responses are clade specific. Basal amphibian clades (e.g. Gymnophiona and Pipidae) were positively affected by climate change, whereas late-divergent clades (e.g. Cycloramphidae, Centrolenidae, Eleutherodactylidae, Microhylidae) were severely impacted. Identifying major changes in the phylogenetic pool represents a first step towards a better understanding of how assembly processes related to climate change will affect ecological communities. A deep analysis of the impacts of climate change not only on species, but also on the evolutionary relationships among species might foster the discussion on clade-level conservation priorities for this imperiled fauna. [ABSTRACT FROM AUTHOR]

Questions Functional redundancy in assemblages may insure ecosystem processes after perturbation, potentially causing temporary or permanent local species extinctions. Yet, functional redundancy has only been inferred by indirect evidence or measured by methods that may not be the most appropriate. Here, we apply an existing method to measure functional redundancy, which is the fraction of species diversity not expressed by functional diversity, to assess whether functional redundancy affects community resilience after disturbance. Location Subtropical grassland, south Brazil (30°05′46″S, 51°40′37″W). Method Species traits and community composition were assessed in quadrats before grazing and after community recovery. Grazing intensity ( G) was measured in each quadrat. We used traits linked to grazing intensity to define functional redundancy ( FR) as the difference of Gini- Simpson index of species diversity ( D) and Rao's quadratic entropy ( Q). Also, with the same traits, we defined community functional stability ( S) as the similarity between trait-based community composition before grazing and 47 and 180 d after grazing ending. Using path analysis we assessed different postulated causal models linking functional diversity ( Q), functional redundancy ( FR), grazing intensity ( G) and community-weighted mean traits to community stability ( S) under grazing. Results Path analysis revealed the most valid causal model FR → S ← G, with a significant positive path coefficient for FR → S and a marginally significant negative one for S ← G. Since FR and G were independent in their covariation and in their effects on S, the model discriminated community resistance to grazing (the effect of G on S) from community resilience after grazing caused by functional redundancy (indicated by the effect of FR on S). Conclusion We show that expressing functional redundancy mathematically is a useful tool for testing causal models linking diversity to community stability. The results support the conclusion that functional redundancy enhanced community resilience, therefore corroborating the insurance hypothesis. [ABSTRACT FROM AUTHOR]

Evidence of phylogenetic conservatism in plant ecological traits has accumulated over the past few years, suggesting an interplay between the distribution of phylogenetic clades and major environmental gradients. Nonetheless, determining what environmental factors underlie the distribution of phylogenetic lineages remains a challenge because environmental factors are correlated with spatial gradients where the latter might indicate some degree of dispersal limitation in phylogenetic pools. We analyzed the phylogenetic structure of plant assemblages across the Brazilian Araucaria forests and assessed how phylogenetic structure responds to environmental and spatial gradients. We compiled data on plant occurrence in 45 plots across the Araucaria forest biome. The phylogenetic structure of the plots was characterized using phylogenetic fuzzy-weighting followed by principal coordinates of phylogenetic structure (PCPS). We used distance-based redundancy analysis (db-RDA) to analyze the relationships between phylogenetic clades and environmental and spatial factors. Variation partitioning showed that the phylogenetic structure of Brazilian Araucaria forests was better explained by environment factors (altitude and annual mean temperature) than by space. Yet, spatially-structured environmental variation explained about one-third of total variation in the phylogenetic structure. Thus, the influence of spatial filters on the phylogenetic structure was more related to environmental gradients across the Brazilian Araucaria forest biome than to dispersal limitation of phylogenetic lineages. Furthermore, the influence of explanatory factors on the phylogenetic structure was concentrated in few nodes, the one splitting tree ferns from seed plants, and a second splitting malvids from other eurosids. Assessing the functional links between species distribution patterns and environmental gradients is not an easy task when we have to deal with large species pools. Identifying major phylogenetic gradients across an environmental and/or geographical range of interest can represent a first step towards a better understanding of general assembly processes in ecological communities. [ABSTRACT FROM AUTHOR]

We aimed to verify if frugivory in Tyrannidae birds (tyrants flycatchers) is influenced by environmental conditions, spatial filters, phylogenetic structure and food availability in Brazilian Araucaria forests. We used range maps to describe Tyrannidae species composition of 33 cells (0.25°× 0.25°) distributed along the Araucaria forest distribution range. Araucaria forests occur in southern and southeastern Brazil and northeastern Argentina, from 30°S to 20°S and at elevations above 500 m a.s.l. We compiled the feeding habits of each species from literature to calculate the proportion of frugivorous Tyrannidae in each cell. After that, we evaluated separately the influence of environmental descriptors, spatial filters (PCNM), phylogenetic structure (PCPS) and resource availability (proportion of zoochorous species) on the proportion of frugivorous birds using model selection based on AIC. Then we built a path model to evaluate the direct and indirect influences of different set of variables on frugivory. The path model showed that phylogenetic structure and spatial filters were the main factors determining the variation in frugivory in Araucaria forest sites. The environmental variable had no direct effect on frugivory, but presented an indirect effect via phylogenetic structure. Furthermore, zoochory was not selected as an important variable determining any other and was not included in the model. Our results showed that the influence of environment on frugivory by Tyrannidae birds was indirect via spatial and phylogenetic structure, that zoochory was not an important factor determining frugivory and that phylogenetic niche conservatism in feeding habits plays a role in determining the structure of Tyrannidae bird communities in Brazilian Araucaria forests. [ABSTRACT FROM AUTHOR]

Question Do regional differences in latitude, and local factors of disturbance and distance from mature forest, influence dispersal syndromes, rate of accumulation of species and total richness in a recovering temperate, subtropical and tropical forest? Location Temperate old-growth red pine forest, Canada; subtropical Araucaria Atlantic forest, southern Brazil; tropical Gallery forest, central Brazil. Methods We used path analysis to determine causal relationships of regional (latitude) and local (disturbance intensity, distance of recovering site from forest) factors on percentage zoochory, exponent z from species-area relationships and total richness. Results Path results showed linear decreases in percentage zoochory, z and richness with increasing latitude. Disturbance and distance from mature forest each reduced richness by similar amounts; however responses of percentage zoochory and z were inconsistent between the two local factors. A second path model, using only the subtropical and tropical forest, greatly increased model significance, yielded insignificant regional effects and strengthened effects of local factors on the three richness responses. Important results from this path model were linear decreases of z (0.1) and percentage zoochory (10%) and a log-decrease of richness (five-fold) 100 m from the mature subtropical and tropical forest. Conclusions Regional differences in latitude and local effects of dispersal limitation can influence forest richness as strongly as disturbance alone. Isolated, recovering subtropical and tropical forest fragments of southern and central Brazil may therefore be recovering at much slower rates than estimates made from those adjacent to mature forest stands. [ABSTRACT FROM AUTHOR]

Question Are trait-convergence assembly patterns ( TCAP) and/or trait-divergence assembly patterns ( TDAP) of tree sapling communities related to microhabitat gradients in forest patches? If so, which traits are related to such patterns? What are the niche mechanisms potentially responsible for community assembly? Location Grassland-forest mosaic in Serra do Sudeste region, southern Brazil (ca. 30.8°S, 53.1°W). Methods We used individual-based trait information of 1132 tree saplings in 40 plots along gradients of canopy openness and grazing intensity in forest patches in southern Brazil. We used a trait-based approach, bypassing taxonomic identification, as a first assessment of sapling community assembly in forest patches. Results Both TCAP and TDAP indicate niche mechanisms underlying assembly of tree sapling communities. Specific leaf area ( SLA), mean leaf area ( LA) and relative abundance of toothed leaf margin ( TLM) maximized TCAP. SLA and TLM tended to increase under more closed canopies, whereas LA had higher values at intermediate canopy openness. SLA and LA maximized TDAP and tended to vary more in more closed canopies, whereas SLA and presence of spines, which also maximized TDAP, showed higher variation under lower grazing intensity. Conclusion The taxon-free approach was very useful to infer niche mechanisms of tree sapling assembly in forest patches. By adopting an individual-based trait approach, we assumed that both intra-specific and intra-population trait variability were relevant for revealing assembly patterns. We highlight that the use of individual-based trait data in a metacommunity framework is an excellent way to evaluate TCAP and TDAP at the metacommunity scale, since it takes into account the entire variation of traits throughout communities. [ABSTRACT FROM AUTHOR]

Questions: Do small rocky outcrops favor forest plant colonization and establishment in grasslands? If so, what are the potential mechanisms involved in this process? Location: Araucaria forest and Campos grassland mosaic in southern Brazilian highlands (29°29′S, 50°12′W). Methods: We collected data on the density of forest woody species in plots located on rocky outcrops and in open fields subject to different management regimes. We evaluated the influence of outcrops on the density of forest plants ≤60-cm tall, and the effects of other environmental variables and of site on plant density; we also used information on diaspore traits of the species to discuss the way in which plants disperse to the outcrops. Results: Rocky outcrops harbored a significantly higher density of forest plants than open fields, irrespective of site effect, and rock height was the best predictor for plant density on outcrops. Diaspores of all recorded species possess characteristics associated with dispersal by birds or mammals or by both. Conclusions: Small rocky outcrops markedly influence forest expansion by acting as perches for vertebrate dispersers and as nurse objects and safe sites for plants. Forest expansion starting in small outcrops possibly occurs as follows: perching of dispersers and increase of seed rain on rocks, promotion of better conditions of establishment for forest plants by nurse rocks, protection of plants sensitive to grazing and fire, and nucleation of forest vegetation. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Questions: Perching and nursing effects drive initial steps of forest expansion over grasslands. Nursing effect is obviously related to niche mechanisms, while perching effect is likely to result both from neutral and niche factors. This study assessed the effect of neutral and niche factors on species composition in sapling communities developing beneath isolated trees/shrubs (ITS) in grassland. Location: A mosaic of Campos grassland and Araucaria forest in São Francisco de Paula, southern Brazil (29°28′S, 50°13′W). Methods: We described sapling communities beneath 32 ITS using mean number of forest woody saplings of different species. We performed a stepwise canonical correspondence analysis (CCA) to select ITS traits that maximized the association with species composition. Then we evaluated the contribution of distance from seed source, ITS traits and distance-structured ITS traits on sapling community assembly using a variation partitioning method based on CCA and partial CCA. Results: Sapling species composition was significantly explained by ITS traits (ITS dispersal mode, ITS growth form, crown area:ITS height ratio, crown area, ITS height and crown area:volume ratio). Distance from seed sources explained only a minor, non-significant fraction of sapling species composition. Distance-structured trait variation was negligible. Conclusions: Sapling community assembly beneath ITS was mostly explained by niche factors related to both nursing and perching effects. Dispersal limitation explained only a small fraction of variation in species composition beneath ITS, suggesting that neutral-based perching effect had a minor role in community assembly. [ABSTRACT FROM AUTHOR]

Ecology Letters (2010) 13: 587–596 It is well known that species evolutionary history plays a crucial role in community assembly. Here, we offer a formal analytical framework to integrate in metacommunity analysis the species’ phylogeny with their functional traits and abundances. We define phylogenetic structure of a community as phylogenetically weighted species composition. This is used to reveal patterns of phylogenetic community variation and to measure and test by specified null models the phylogenetic signal at the metacommunity level, which we distinguish from phylogenetic signal at the species pool level. The former indicates that communities more similar in their phylogenetic structure are also similar in their average trait values, which may indicate species’ niche conservation for the given traits. We apply this framework to an example from grassland communities and find that traits with significant phylogenetic signal at the metacommunity level exhibit ecological filtering along the resource gradient, but since both mechanisms act independently on traits, niche conservatism is not supported. [ABSTRACT FROM AUTHOR]

Aim Our objective was to evaluate the influence of distinct macroecological factors (space, floristics and environment) on the variation in seed dispersal strategies of shrubs and trees in the Araucaria forest biome in the southern and south-eastern Brazilian highlands. We hypothesize that history-related factors (space, floristics) are major determinants of the proportion of endo- and syn-zoochorous species in Araucaria forests, despite the current gradients in environmental conditions. Location Araucaria forest is the main forest biome in southern Brazil, at altitudes above 500 m a.s.l. (latitude ≤ 30° S). Their northern limit in Brazil is at latitude 20° S, where forests occur at elevations above 1000 m a.s.l. Methods We compiled information from 27 floristic checklists comprising shrub and tree species distributed along the geographical range of the Brazilian Araucaria forest biome. We classified species as zoochorous and non-zoochorous, based on morphological attributes of their diaspores. Sites were described by geographical coordinates (latitude, longitude) and five environmental variables. We evaluated separately the influence of floristic, spatial and environmental variables on zoochory using correspondence analysis and linear regressions. Further, we evaluated causal connections between these variable groups using Mantel tests and path analysis. Results Zoochory increased with both latitude and longitude. Regression analysis showed that rainfall seasonality was the only environmental variable explaining the variation in the proportion of zoochorous species. All pairwise Mantel correlations between space, rainfall seasonality, floristics and zoochory were significant. Path analysis showed that rainfall seasonality was strongly determined by spatial distances between sites, and floristics was directly determined by rainfall seasonality. Further zoochory was mostly determined by floristics. Main conclusions Taking into account historical factors in the interpretation of macroecological patterns improves our understanding of biodiversity gradients. Hypotheses based on long-term dynamics of distinct floristic groups provide some useful insights into patterns shown by studies elsewhere. Here we offer an analytical solution to incorporate history-related factors into macroecological analyses. While history-based hypotheses do not replace any other ideas concerning macroecological patterns, they are likely to improve our understanding on factors determining present-day ecological patterns. [ABSTRACT FROM AUTHOR]

Questions: In a natural grassland-forest mosaic: What is the influence of phylogeny and diaspore traits related to disperser attraction (DAT) on (1) seed size/number trade-off (SSNT) in woody species colonizing forest patches; (2) on the frequency of the species? 3. What is the influence of forest patch area on mean seed size and number. 4. Do phylogeny and DAT expressed at the species level affect this relationship? Location: Campos grassland and Araucaria forest in São Francisco de Paula, RS, Brazil, at ca. 29°28′ S; 50° 3′ W. Methods: Forest patches of different sizes in a grassland site recovering for ten years since human disturbances were surveyed by the relative abundance of vertebrate-dispersed woody saplings. We described colonizer species according to taxonomic phylogenetic relationships and diaspore type, size and color. We analyzed with a variation partitioning method their influence on SSNT and on species frequency in the patches. At the community level we regressed mean seed size and number on forest patch area and evaluated how these relationships were affected by phylogeny and DAT at the species level. Results: 1. Phylogeny and DAT mostly explained seed size and seed number per diaspore variation. 2. By controlling phylogeny and DAT influence the frequency of species in forest patches was positively associated with their seed number in the diaspores, and negatively associated with their seed size. 3. Mean seed size and seed number at the community level were positively associated with patch area. 4. When phylogeny and DAT influences on seed size were removed this relationship was stronger for seed size and weaker for seed number. Conclusions: 1. Energy allocation to dispersal in detriment of offspring survival increased the successful establishment of colonizer species in forest patches, despite phylogenetic relationships and DAT variation in their diaspores. 2. Although patch area exerted a selective pressure on seed size, habitat preferences of dispersers may also influence patch colonization. [ABSTRACT FROM AUTHOR]

Questions: 1. Do the species composition, richness and diversity of sapling communities vary significantly in differently sized patches? 2. Do forest patches of different sizes differ in woody plant colonization patterns? Location: São Francisco de Paula, Rio Grande do Sul, Brazil, 29°28′ S, 50°13′ W. Methods: Three woody vegetation types, differing in structural development (patch size) and recovering for 10 years from cattle and burning disturbances, were sampled on grassland. We analysed the composition and complexity of the woody sapling communities, through relative abundance, richness and diversity patterns. We also evaluated recruitment status (residents vs. colonizers) of species in communities occurring in different forest patch size classes. Results: 1. There is a compositional gradient in sapling communities strongly associated with forest patch area. 2. Richness and diversity are positively correlated to patch area, but only in poorly structured patches; large patches present richness and diversity values similar to small patches. 3. Resident to colonizer abundance ratio increases from nurse plants to large patches. The species number proportion between residents and colonizers is similar in small and large patches and did not differ between these patch types. 4. Large patches presented a high number of exclusive species, while nurse plants and small patches did not. Conclusions: Woody plant communities in Araucaria forest patches are associated with patch structure development. Richness and diversity patterns are linked to patch colonization patterns. Generalist species colonize the understorey of nurse plants and small patches; resident species cannot recruit many new individuals. In large patches, sapling recruitment by resident adults precludes the immigration of new species into the patches, limiting richness and diversity. [ABSTRACT FROM AUTHOR]