Phylogenetic structure of a palm community in the central Amazon: changes along a hydro-edaphic gradient

The concepts of phylogenetic community structure (PCS) and phylogenetic niche conservatism (PNC) allow ecologists to address the role of species’ evolutionary history in community assembly. It is important to test the role of historical legacies relative to environmental constraints at local scales, where communities are assembled. We studied phylogenetic structure and niche conservatism for palms (Arecaceae) in the 64-km² Ducke Reserve in the central Amazon, near Manaus. The 72 study plots, each covering 0.1 ha, were distributed regularly in a terra firme forest along a hydro-edaphic gradient. We compared the observed palm PCS with assemblages generated by null models. We also analyzed whether morphological and ecological traits are labile or conserved along the phylogeny and quantified the spatial structure of morphological traits in each plot. We found an overall neutral PCS in combination with low PNC (labile traits), suggesting that evolutionary history poses little constraint on palm community assembly in this Amazonian landscape. Still, there was a tendency towards phylogenetic overdispersion in bottomlands, suggesting competitive exclusion among close relatives or, more likely, environmental filtering acting on convergent traits that affect co-occurrence in flood-prone areas. We conclude that (1) PCS of local communities is random as a whole and morphological traits are overall labile, but that (2) the hydro-edaphic gradient within terra firme forests leads to differences in species co-occurrence so that closely related species occur less often than expected in bottomlands due to diffuse competition among close relatives or environmental filtering on convergent traits.     

COMPETITION FOR HUMMINGBIRD POLLINATION SHAPES FLOWER COLOR VARIATION IN ANDEAN SOLANACEAE

One classic explanation for the remarkable diversity of flower colors across angiosperms involves evolutionary shifts among different types of pollinators with different color preferences. However, the pollinator shift model fails to account for the many examples of color variation within clades that share the same pollination system. An alternate explanation is the competition model, which suggests that color divergence evolves in response to interspecific competition for pollinators, as a means to decrease interspecific pollinator movements. This model predicts color overdispersion within communities relative to null assemblages. Here, we combine morphometric analyses, field surveys, and models of pollinator vision with a species‐level phylogeny to test the competition model in the primarily hummingbird‐pollinated clade Iochrominae (Solanaceae). Results show that flower color as perceived by pollinators is significantly overdispersed within sites. This pattern is not simply due to phylogenetic history: phylogenetic community structure does not deviate from random expectations, and flower color lacks phylogenetic signal. Moreover, taxa that occur in sympatry occupy a significantly larger volume of color space than those in allopatry, supporting the hypothesis that competition in sympatry drove the evolution of novel colors. We suggest that competition among close relatives may commonly underlie floral divergence, especially in species‐rich habitats where congeners frequently co‐occur.     

Contrasting patterns of phylogenetic assemblage structure along the elevational gradient for major hummingbird clades

Aim We evaluated the hypothesis that, given niche conservatism, relatedness of co‐occurring hummingbird species of a given clade will increase at greater distances from the elevation where it originated. We also used prior knowledge of flight biomechanics and feeding specialization of hummingbird species (family Trochilidae) to evaluate which environmental variables were important predictors of changes in phylogenetic structure for each hummingbird clade. Location Ecuador. Methods We compiled species lists for 189 local hummingbird assemblages across major environmental gradients in Ecuador from a variety of published and non‐published sources. For the entire family and each of the major hummingbird clades (hermits, emeralds, mangoes, coquettes and brilliants) we quantified the phylogenetic structure of each assemblage using the net relatedness index (NRI). This index calculates the standardized mean of all possible pairwise phylogenetic distances between co‐occurring species. We related NRI for each clade to elevation, precipitation and vegetation‐related variables using generalized additive models. Results Our findings support the prediction of an increase in the co‐occurrence of close relatives away from the elevation of origin at the family level and for assemblages of mangoes and brilliants. The opposite pattern was found for assemblages of coquettes and emeralds. For the hermits, variation in phylogenetic structure was not explained by elevation. Clades with high levels of feeding specialization (hermits and brilliants) always included a vegetation‐related variable as an important predictor of change in phylogenetic structure. Main conclusions We found no overall support for the conservatism and zone of origin hypotheses. Knowledge of each clade’s natural history proved useful for predicting which environmental variables correlated with phylogenetic structure of local assemblages. Clades with the same elevation of origin appear to have radiated along the elevational gradient in association with different environmental factors.     

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

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

Phylogenetic diversity,trait diversity and niches: species assembly of ferns along a tropical elevational gradient

Aim To analyse the structure of pteridophyte assemblages, based on phylogenetic relatedness and trait properties, along an elevational gradient. Ecological theory predicts that co‐occurring species may be: randomly selected from a regional pool; ecologically sorted so that they are functionally different hence resulting in reduced competition (overdispersion); or functionally similar as an adaptation to specific ecological conditions (clustering). Location Braulio Carrillo National Park and Cerro de la Muerte, Costa Rica, Central America. Methods We used an empirical dataset of the quantitative pattern of species occurrences and individual numbers of ferns within 156 plots along a tropical elevational gradient to test whether directed ecological sorting might cause deviations in patterns of trait and phylogenetic diversity. Mean pairwise distances of species based on phylogenetic and trait properties were compared with two different sets of null assemblages, one maintaining species frequency distributions (constrained) and one not (unconstrained). Results Applying different null models resulted in varying degrees of overdispersion and clustering, but overall patterns of deviation from random expectations remained the same. Contrary to theoretical predictions, phylogenetic and trait diversity were relatively independent from one another. Phylogenetic diversity showed no patterns along the elevational gradient, whereas trait diversity showed significant trends for epiphytes. Main conclusions Under stressful environmental conditions (drought at low elevations and frost at high elevations), epiphytic fern assemblages tended to be clustered with respect to trait characteristics, which suggests environmental filtering. Conversely, under less extreme environmental conditions (middle of the transect), the sorting was biased towards high differentiation (overdispersion), presumably because of interspecific competition and trait shifts among closely related species (character displacement).     

Phylogenies and traits provide distinct insights about the historical and contemporary assembly of aquatic insect communities

The assumption that traits and phylogenies can be used as proxies of species niche has faced criticisms. Evidence suggested that phylogenic relatedness is a weak proxy of trait similarity. Moreover, different processes can select different traits, giving opposing signals in null model analyses. To circumvent these criticisms, we separated traits of stream insects based on the concept of α and β niches, which should give clues about assembling pressures expected to act independently of each other. We investigated the congruence between the phylogenetic structure and trait structure of communities using all available traits and all possible combinations of traits (4095 combinations). To account for hierarchical assembling processes, we analyzed patterns on two spatial scales with three pools of genera. Beta niche traits selected a priori – i.e., traits related to environmental variation (e.g., respiration type) – were consistently clustered on the smaller scale, suggesting environmental filtering, while α niche traits – i.e., traits related to resource use (e.g., trophic position) – did not display the expected overdispersion, suggesting a weak role of competition. Using all traits together provided random patterns and the analysis of all possible combinations of traits provided scenarios ranging from strong clustering to overdispersion. Communities were phylogenetically overdispersed, a pattern previously interpreted as phylogenetic limiting similarity. However, our results likely reflect the co‐occurrence of ancient clades due to the stability of stream habitats along the evolutionary scale. We advise ecologists to avoid using combinations of all available traits but rather carefully traits based on the objective under consideration. Both trait and phylogenetic approaches should be kept in the ecologist toolbox, but phylogenetic distances should not be used as proxies of traits differences. Although the phylogenetic structure revealed processes operating at the evolutionary scale, only specific traits explained local processes operating in our communities.     

Phylogenetic relatedness limits co-occurrence at fine spatial scales: evidence from the schoenoid sedges (Cyperaceae: Schoeneae) of the Cape Floristic Region, South Africa

Species co-occurrence at fine spatial scales is expected to be nonrandom with respect to phylogeny because of the joint effects of evolutionary (trait convergence and conservatism) and ecological (competitive exclusion and habitat filtering) processes. We use data from 11 existing vegetation surveys to test whether co-occurrence in schoenoid sedge assemblages in the Cape Floristic Region shows significant phylogenetic structuring and to examine whether this changes with the phylogenetic scale of the analysis. We provide evidence for phylogenetic overdispersion in an alliance of closely related species (the reticulate-sheathed Tetraria clade) using both quantile regression analysis and a comparison between the mean observed and expected phylogenetic distances between co-occurring species. Similar patterns are not evident when the analyses are performed at a broader phylogenetic scale. Examination of six functional traits suggests a general pattern of trait conservatism within the reticulate-sheathed Tetraria clade, suggesting a potential role for interspecific competition in structuring co-occurrence within this group. We suggest that phylogenetic overdispersion of communities may be common throughout many of the Cape lineages, since interspecific interactions are likely intensified in lineages with large numbers of species restricted to a small geographic area, and we discuss the potential implications for patterns of diversity in the Cape.     

Increased competition does not lead to increased phylogenetic overdispersion in a native grassland

That competition is stronger among closely related species and leads to phylogenetic overdispersion is a common assumption in community ecology. However, tests of this assumption are rare and field‐based experiments lacking. We tested the relationship between competition, the degree of relatedness, and overdispersion among plants experimentally and using a field survey in a native grassland. Relatedness did not affect competition, nor was competition associated with phylogenetic overdispersion. Further, there was only weak evidence for increased overdispersion at spatial scales where plants are likely to compete. These results challenge traditional theory, but are consistent with recent theories regarding the mechanisms of plant competition and its potential effect on phylogenetic structure. We suggest that specific conditions related to the form of competition and trait conservatism must be met for competition to cause phylogenetic overdispersion. Consequently, overdispersion as a result of competition is likely to be rare in natural communities.     

What factors shape rates of phenotypic evolution? A comparative study of cranial morphology of four mammalian clades

Understanding why rates of morphological evolution vary is a major goal in evolutionary biology. Classical work suggests that body size, interspecific competition, geographic range size and specialization may all be important, and each may increase or decrease rates of evolution. Here, we investigate correlates of proportional evolutionary rates in phalangeriform possums, phyllostomid bats, platyrrhine monkeys and marmotine squirrels, using phylogenetic comparative methods. We find that the most important correlate is body size. Large species evolve the fastest in all four clades, and there is a nonlinear relationship in platyrrhines and phalangeriformes, with the slowest evolution in species of intermediate size. We also find significant increases in rate with high environmental temperature in phyllostomids, and low mass-specific metabolic rate in marmotine squirrels. The mechanisms underlying these correlations are uncertain and appear to be size specific. We conclude that there is significant variation in rates of evolution, but that its meaning is not yet clear.     

Phylogenetic and functional relationships in pastures and meadows from the North Adriatic Karst

Probably due to its phytogeographic position, the grasslands in the North Adriatic Karst are among the richest grasslands in the world and harbour the highest small-scale density of plant species found in terrestrial habitats. Different moisture and soil conditions determine distinct vegetation types, such as meadows, composed by mesophyllous plants and on mesic conditions, and semi-natural pastures, composed by sclerophyllous plants and on oligotrophic conditions. Even though plants in these two vegetation types differ in some of their attributes, their functional and phylogenetic relationships remain to be tested. We used a dataset comprising 180 species, in which 48 plots in the meadows and 52 plots in the pastures had been sampled, and tested the phylogenetic and functional relationships between the two vegetation types. The pastures contained more original species, but both the pastures and the meadows are expected to be important to increase biodiversity at landscape level. Different community assembly processes occurred in the two vegetation types, with limiting similarity leading to functional overdispersion in the meadows and environmental filtering leading to functional clustering in the pastures. Overall, traits were convergent, leading to a clustered phylogenetic structure in the meadows, probably due to pair-wise competition, and an overdispersed phylogenetic structure in the pastures, where species from different clades were filtered by the oligotrophic conditions. Transhumance may have contributed to the random pattern of trait diversity we found across the nodes of the phylogenetic tree.     

Functional and phylogenetic approaches reveal the evolution of diversity in a hyper diverse biota

Ant communities in tropical forests may be governed by varying assembly mechanisms, depending on the particular habitat investigated. We compared phylogenetic diversity and structure across two forest biomes (dry and humid) and two vertical layers (arboreal and terricolous) in ant communities in Madagascar, and assessed the influence of invasive species on this community structure. We estimated phylogenetic signal and correlated evolution for habitat and several functional traits and tested for conservatism in relevant functional and habitat traits. Ancestral states were reconstructed to illuminate the evolution of habitat traits. All analyses utilized phylogenies estimated from newly generated data from three nuclear markers for 290 Malagasy ant taxa. Dry forests, although lower in species richness, were found to support equally high lineage diversity as humid forests. In contrast, phylogenetic diversity was much lower in arboreal than in terricolous communities. We observed significant phylogenetic clustering in the combined humid forest and in the arboreal–humid, arboreal–dry and terricolous–humid communities, whereas the combined dry forest community was overdispersed. Among ant communities in Madagascar, overdispersion and competition therefore may be more prevalent in dry forest, and habitat filtering may be more dominant in humid forest. Excluding invasive ant species had little overall effect on community structure. All investigated traits showed low to intermediate conservatism; strong support for correlated evolution was found for increased eye size and an arboreal lifestyle. Habitat transitions from humid to dry and from terricolous to arboreal occurred more frequently, and ancestors of most lineages were predicted to be terricolous or humid‐forest adapted. We conclude that most Malagasy ant clades first colonized humid forests and subsequently transitioned into dry forests, indicating that previous hypotheses on the evolution of Madagascar's hyperdiverse biota may not apply to ants and other arthropods.     

Stream noise,habitat filtering,and the phenotypic and phylogenetic structure of Neotropical anuran assemblages

The structure of assemblages may be determined by interspecific interactions or environmental factors (e.g. competition and habitat filtering). Since communication between conspecific and heterospecific affects fitness of individuals, habitat characteristics that prevent communication could determine habitat use and co-occurrence of species. However, at present there are few studies, most with birds, testing the relationship between sensory ecology and community ecology. Abiotic noise on streams could impede the detection and decoding of auditory signals by receivers through a process named auditory masking. Therefore, we tested the role of abiotic noise on streams as a habitat characteristic influencing the phenotypic and phylogenetic structure of Neotropical anuran assemblages. We tested this hypothesis using data of male body size, call frequency, calling place (alongside and away from streams), and phylogenetic relationship of 110 and 38 anuran species at regional and local scale, respectively. After we found quantitative evidence suggesting that call frequency and body size are conserved phenotypic traits, we found that assemblages alongside streams exhibit both phenotypic and phylogenetic clustering, while assemblages away from streams exhibit both phenotypic and phylogenetic overdispersion. These results offer quantitative evidence suggesting a role of noise on streams promoting a process of habitat filtering and affecting the structure of anuran assemblages alongside streams both at Neotropical and local scale. This is the first study using modern phylogenetic comparative metrics for covering potential causes of phenotypic and phylogenetic structure of anuran assemblages, and one of the few testing a link between community ecology and the evolutionary biology of acoustic communication to understand the processes mediating species co-occurrence in vertebrates.     

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

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

Species matter: the role of competition in the assembly of congeneric bacteria

Interspecific competition is an important driver of community assembly in plants and animals, but phylogenetic evidence for interspecific competition in bacterial communities has been elusive. This could indicate that other processes such as habitat filtering or neutral processes are more important in bacterial community assembly. Alternatively, this could be a consequence of the lack of a consistent and meaningful species definition in bacteria. We hypothesize that competition in bacterial community assembly has gone undetected at least partly because overly broad measures of bacterial diversity units were used in previous studies. First, we tested our hypothesis in a simulation where we showed that how species are defined can dramatically affect whether phylogenetic overdispersion (a signal consistent with competitive exclusion) will be detected. Second, we demonstrated that using finer-scale Operational Taxonomic Units (OTUs) (with more stringent 16S rRNA sequence identity cutoffs or based on fast-evolving protein coding genes) in natural populations revealed previously undetected overdispersion. Finally, we argue that bacterial ecotypes, diversity units incorporating ecological and evolutionary theory, are superior to OTUs for the purpose of studying community assembly.     

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

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

Abiotic stress tolerance and competition‐related traits underlie phylogenetic clustering in soil bacterial communities

Soil bacteria typically coexist with close relatives generating widespread phylogenetic clustering. This has been ascribed to the abiotic filtering of organisms with shared ecological tolerances. Recent theoretical developments suggest that competition can also explain the phylogenetic similarity of coexisting organisms by excluding large low‐competitive clades. We propose that combining the environmental patterns of traits associated with abiotic stress tolerances or competitive abilities with phylogeny and abundance data, can help discern between abiotic and biotic mechanisms underlying the coexistence of phylogenetically related bacteria. We applied this framework in a model system composed of interspersed habitats of highly contrasted productivity and comparatively dominated by biotic and abiotic processes, i.e. the plant patch‐gap mosaic typical of drylands. We examined the distribution of 15 traits and 3290 bacterial taxa in 28 plots. Communities showed a marked functional response to the environment. Conserved traits related to environmental stress tolerance (e.g. desiccation, formation of resistant structures) were differentially selected in either habitat, while competition related traits (e.g. organic C consumption, formation of nutrient‐scavenging structures) prevailed under high resource availability. Phylogenetic clustering was stronger in habitats dominated by biotic filtering, suggesting that competitive exclusion of large clades might underlie the ecological similarity of co‐occurring soil bacteria.     

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

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

Phylogenetic structure of mammal assemblages at large geographical scales: linking phylogenetic community ecology with macroecology

Phylogenetic community ecology seeks to explain the processes involved in the formation of species assemblages by analysing their phylogenetic structure, and to date has focused primarily on local-scale communities. Macroecology, on the other hand, is concerned with the structure of assemblages at large geographical scales, but has remained largely non-phylogenetic. Analysing the phylogenetic structure of large-scale assemblages provides a link between these two research programmes. In this paper, I ask whether we should expect large-scale assemblages to show significant phylogenetic structure, by outlining some of the ecological and macroevolutionary processes that may play a role in assemblage formation. As a case study, I then explore the phylogenetic structure of carnivore assemblages within the terrestrial ecoregions of Africa. Many assemblages at these scales are indeed phylogenetically non-random (either clustered or overdispersed). One interpretation of the observed patterns of phylogenetic structure is that many clades underwent rapid biome-filling radiations, followed by diversification slowdown and competitive sorting as niche space became saturated.     

Intercontinental trends in functional and phylogenetic structure of stream fish assemblages

Understanding of community assembly has been improved by phylogenetic and trait‐based approaches, yet there is little consensus regarding the relative importance of alternative mechanisms and few studies have been done at large geographic and phylogenetic scales. Here, we use phylogenetic and trait dispersion approaches to determine the relative contribution of limiting similarity and environmental filtering to community assembly of stream fishes at an intercontinental scale. We sampled stream fishes from five zoogeographic regions. Analysis of traits associated with habitat use, feeding, or both resulted in more occurrences of trait underdispersion than overdispersion regardless of spatial scale or species pool. Our results suggest that environmental filtering and, to a lesser extent, species interactions were important mechanisms of community assembly for fishes inhabiting small, low‐gradient streams in all five regions. However, a large proportion of the trait dispersion values were no different from random. This suggests that stochastic factors or opposing assembly mechanisms also influenced stream fish assemblages and their trait dispersion patterns. Local assemblages tended to have lower functional diversity in microhabitats with high water velocity, shallow water depth, and homogeneous substrates lacking structural complexity, lending support for the stress‐dominance hypothesis. A high prevalence of functional underdispersion coupled with phylogenetic underdispersion could reflect phylogenetic niche conservatism and/or stabilizing selection. These findings imply that environmental filtering of stream fish assemblages is not only deterministic, but also influences assemblage structure in a fairly consistent manner worldwide.     

Sensitivity of metrics of phylogenetic structure to scale, source of data and species pool of hummingbird assemblages along elevational gradients

Patterns of phylogenetic structure of assemblages are increasingly used to gain insight into the ecological and evolutionary processes involved in the assembly of co-occurring species. Metrics of phylogenetic structure can be sensitive to scaling issues and data availability. Here we empirically assess the sensitivity of four metrics of phylogenetic structure of assemblages to changes in (i) the source of data, (ii) the spatial grain at which assemblages are defined, and (iii) the definition of species pools using hummingbird (Trochilidae) assemblages along an elevational gradient in Colombia. We also discuss some of the implications in terms of the potential mechanisms driving these patterns. To explore how source of data influence phylogenetic structure we defined assemblages using three sources of data: field inventories, museum specimens, and range maps. Assemblages were defined at two spatial grains: coarse-grained (elevational bands of 800-m width) and fine-grained (1-km(2) plots). We used three different species pools: all species contained in assemblages, all species within half-degree quadrats, and all species either above or below 2000 m elevation. Metrics considering phylogenetic relationships among all species within assemblages showed phylogenetic clustering at high elevations and phylogenetic evenness in the lowlands, whereas those metrics considering only the closest co-occurring relatives showed the opposite trend. This result suggests that using multiple metrics of phylogenetic structure should provide greater insight into the mechanisms shaping assemblage structure. The source and spatial grain of data had important influences on estimates of both richness and phylogenetic structure. Metrics considering the co-occurrence of close relatives were particularly sensitive to changes in the spatial grain. Assemblages based on range maps included more species and showed less phylogenetic structure than assemblages based on museum or field inventories. Coarse-grained assemblages included more distantly related species and thus showed a more even phylogenetic structure than fine-grained assemblages. Our results emphasize the importance of carefully selecting the scale, source of data and metric used in analysis of the phylogenetic structure of assemblages.