The merging of community ecology and phylogenetic biology

Geographic conditions impact the relationship between plant phenology and phylogeny

Plant phenology is influenced by a combined effect of phylogeny and climate, although it is yet unclear how these two variables work together to change phenology. We synthesized 107 previously published studies to examine whether phenological changes were impacted by both phylogeny and climate changes in various geographical settings globally. Phenological observation data from 52,463 plant species at 71 sites worldwide revealed that 90 % of phenological records showed phylogenetic conservation. i.e., closely related species exhibited similar phenology. To explore the significant and non-significant phylogenetic conservation between plant phenophases, our dataset comprises 5,47,000 observation records from the four main phenophases (leaf bud, leaf, flower, and fruit). Three-dimensional geographical distribution (altitude, latitude, and longitude) data analysis revealed that plant phenology may exhibit phylogenetic signals at finer special scales (optimal environmental conditions) that vanish in high altitude and latitude regions. Additionally, climatic sensitivity analysis suggested that phylogenetic signals were associated with plant phenophases and were stronger in the regions of ideal temperature (7-18 °C) and photoperiod (10-14 h) and weaker in harsh climatic conditions. These results show that phylogenetic conservation in plant phenological traits is frequently influenced by the interaction of harsh climatic conditions and geographical ranges. This meta-analysis enhances our knowledge of predicting species responses over geographic gradients under varied climatic conditions.

Time since fire as a driver of taxonomic and phylogenetic patterns of grassland plant communities

Fire plays a key role in grasslands, determining the distribution and evolution of species and boundaries with neighboring ecosystems. Evidence of community-wide responses to fire is largely based on taxonomic and functional descriptors, while the phylogenetic dimension is overlooked. Here we evaluated how the taxonomic and phylogenetic structure of grassland plant communities responded to a time since fire (TSF) gradient. We sampled 12 communities in Southern Brazil under varying TSF and calculated taxonomic species richness (S) and dominance (D), phylogenetic diversity (PD), and mean phylogenetic distances (MPD). We used Structural Equation Models to test the relationships between the environmental gradient and community descriptors. Communities with longer TSF presented higher PD and MPD but lower species richness and increased taxonomic dominance. These sites were dominated by monocots, specifically C4 grasses, but also presented exclusive clades, whereas recently-burned sites presented lower taxonomic dominance and more species distributed in a wider variety of clades. Our results indicate that these scenarios are interchangeable and dependent on fire management. Fire adaptation was not constrained by phylogenetic relatedness, contrasting with previous findings for tropical savannahs and indicating that temperate and tropical non-forest ecosystems from South America respond differently to fire, possibly due to different evolutionary histories.

Generalism in species interactions is more the consequence than the cause of ecological success

Generalism in resource use is commonly considered a critical driver of population success, species distribution and extinction risk. This idea can be questioned as generalism may be a result rather than the cause of species abundance and range size. We tested these contrasting causal hypotheses focusing on host use in three databases encompassing approximately 44,000 mutualistic (hummingbird-plant), commensalistic (lichen-plant) and parasitic (flea-mammal) interactions in 617 ecological communities across the Americas and Eurasia. Across all interaction types, our analyses indicated that range size and abundance influence the probability of encountering hosts and set the arena for species to express generalism potentials or adapt to new hosts. Hence, our findings support the hypothesis that generalism is a consequence of species ecological success. This highlights the importance of ecological opportunity in driving species characteristics considered key for their survival and conservation.

Examining the structure of plant-lemur interactions in the face of imperfect knowledge

Biotic interactions, such as plant-animal seed dispersal mutualisms, are essential for ecosystem function. Such interactions are threatened by the possible extinction of the animal partners. Using a data set that includes plant-lemur interactions across Madagascar, we studied the current state of knowledge of these interactions and their structure to determine which plant species are most at risk of losing dispersal services due to the loss of lemurs. We found substantial gaps in understanding of plant-lemur interactions; data were substantially skewed toward a few lemur species and locations. There was also a large gap in knowledge on the interactions of plants and small-bodied or nocturnal lemurs and lemurs outside a few highly studied locations. Of the recorded interactions, a significant portion occurred between lemurs and endemic plants, rather than native or introduced plants. We also found that lemur species tended to primarily consume closely related plant species. Such interaction patterns may indicate the threats to Malagasy endemic plants and highlight how lemur population loss or reductions could affect plant phylogenetic diversity. When examining the impacts of lemur extinction, losing critically endangered species left 164 plant species with no known lemur frugivore partners. Despite phylogenetic patterns in lemur diet, plants for which the only known lemur frugivore is critically endangered were not closely related. These results emphasize the need for further studies to complete our knowledge on these essential interactions and to inform conservation priorities.

Niche convergence and biogeographic history shape elevational tree community assembly in a subtropical mountain forest

Niche convergence or conservatism have been proposed as essential mechanisms underlying elevational plant community assembly in tropical mountain ecosystems. Subtropical mountains, compared to tropical mountains, are likely to be shaped by a mixing of different geographic affinities of species and remain somehow unclear. Here, we used 31 0.1-ha permanent plots distributed in subtropical forests on the eastern and western aspects of the Gaoligong Mountains, southwest China between 1498 m and 3204 m a.sl. to evaluate how niche-based and biogeographic processes shape tree community assembly along elevational gradients. We analyzed the elevational patterns of taxonomic, phylogenetic and functional diversity, as well as of individual traits, and assessed the relative importance of environmental effects on these diversity measures. We then classified tree species as being either tropical affiliated or temperate affiliated and estimated their contribution to the composition of biogeographic affinities. Species richness decreased with elevation, and species composition showed apparent turnover across the aspects and elevations. Most traits exhibited convergent patterns across the entire elevational gradient. Phylogenetic and functional diversity showed opposing patterns, with phylogenetic diversity increasing and functional diversity decreasing with elevation. Soil nutrients, especially phosphorus and nitrogen, appeared to be the main abiotic variables driving the elevational diversity patterns. Communities at lower elevations were occupied by tropical genera, while highlands contained species of tropical and temperate biogeographic affinities. Moreover, the high phylogenetic diversity at high elevations were likely due to differences in evolutionary history between temperate and tropical species. Our results highlight the importance of niche convergence of tropical species and the legacy of biogeographic history on the composition and structure of subtropical mountain forests. Furthermore, limited soil phosphorus caused traits divergence and the partitioning for different forms of phosphorus may explain the high biodiversity found in phosphorus-limited subtropical forests.

Variation in near-surface soil temperature drives plant assemblage differentiation across aspect

Quantifying assemblage variation across environmental gradients provides insight into the ecological and evolutionary mechanisms that differentiate assemblages locally within a larger climate regime. We assessed how vascular plant functional composition and diversity varied across microenvironment to identify ecological differences in assemblages in a mountainous fieldsite in northeastern Utah, USA. Then, we looked at how life-history strategies and information about phylogenetic differences affect the relationship between functional metrics and environment. We found less functionally dispersed assemblages that were shorter and more resource-conservative on south-facing slopes where intra-annual soil temperature was hotter and more variable. In contrast, we found more functionally dispersed assemblages, that were taller and more resource-acquisitive on north-facing slopes where intra-annual temperature was cooler and less variable. Herbaceous and woody perennials drove these trends. Additionally, including information about phylogenetic differences in a dispersion metric indicated that phylogeny accounts for traits we did not measure. At this fieldsite, soil temperature acts as an environmental filter across aspect. If soil temperature increases and becomes more variable, intra-annually, the function of north- versus south-facing assemblages may be at risk for contrasting reasons. On south-facing slopes, assemblages may not have the variance in functional diversity needed to respond to more intense, stressful conditions. Conversely, assemblages on north-facing slopes may not have the resource-conservative strategies needed to persist if temperatures become hotter and more variable intra-annually. Given these results, we advocate for the inclusion of aspect differentiation in studies seeking to understand species and assemblage shifts in response to changing climate conditions.

Extending trait dispersion across trophic levels: Predator assemblages act as top-down filters on prey communities

Studies of community assembly typically focus on the effects of abiotic environmental filters and stabilizing competition on functional trait dispersion within single trophic levels. Predation is a well-known driver of community diversity and composition, yet the role of functionally diverse predator communities in filtering prey community traits has received less attention. We examined functionally diverse communities of predators (fishes) and prey (epifaunal crustaceans) in eelgrass (Zostera marina) beds in two northern California estuaries to evaluate the filtering effects of predator traits on community assembly and how filters acting on predators influence their ability to mediate prey community assembly. Fish traits related to bottom orientation were correlated with more clustered epifauna communities, and epifauna were generally overdispersed while fishes were clustered, suggesting prey may be pushed to disparate areas of trait space to avoid capture by benthic sit-and-wait predators. We also found correlations between the trait dispersions of predator and prey communities that strengthened after accounting for the effects of habitat filters on predator dispersion, suggesting that habitat filtering effects on predator species pools may hinder their ability to affect prey community assembly. Our results present compelling observational evidence that specific predator traits have measurable impacts on the community assembly of prey, inviting experimental tests of predator trait means on community assembly and explicit comparisons of how the relative effects of habitat filters and intraguild competition on predators impact their ability to affect prey community assembly. Integrating our understanding of traits at multiple trophic levels can help us better predict the impacts of community composition on food web dynamics as regional species pools shift with climate change and anthropogenic introductions.

Phylogenetic conservatism and coordination in traits of Chinese woody endemic flora

Range-limited endemic species, often labeled as endangered due to their low adaptability to climate change, exhibit unclear evolutionary mechanisms influencing their distribution. This study explores the relationship between leaf length, maximum height, and seed diameter and their linkage to phylogeny and climate in the macroecology of 1,370 woody endemics. Using Bayesian analytical method that allows partitioning phylogenetic and environmental variances and covariance, we revealed moderate to high phylogenetic signals in these traits, indicating evolutionary constraints potentially impacting climate change adaptability. The study uncovered a phylogenetically conserved coordination between height and leaf length which showed to be independent of macroecological patterns of temperature and precipitation. These findings emphasize the role of phylogenetic ancestry in shaping the distribution of woody endemics, highlighting the need for prioritized in-situ conservation and providing insights for ex situ conservation strategies.

Large and non-spherical seeds are less likely to form a persistent soil seed bank

There is some evidence that seed traits can affect the long-term persistence of seeds in the soil. However, findings on this topic have differed between systems. Here, we brought together a worldwide database of seed persistence data for 1474 species to test the generality of seed mass-shape-persistence relationships. We found a significant trend for low seed persistence to be associated with larger and less spherical seeds. However, the relationship varied across different clades, growth forms and species ecological preferences. Specifically, relationships of seed mass-shape-persistence were more pronounced in Poales than in other order clades. Herbaceous species that tend to be found in sites with low soil sand content and precipitation have stronger relationships between seed shape and persistence than in sites with higher soil sand content and precipitation. For the woody plants, the relationship between persistence and seed morphology was stronger in sites with high soil sand content and low precipitation than in sites with low soil sand content and higher precipitation. Improving the ability to predict the soil seed bank formation process, including burial and persistence, could benefit the utilization of seed morphology-persistence relationships in management strategies for vegetation restoration and controlling species invasion across diverse vegetation types and environments.

Plant beta-turnover rather than nestedness shapes overall taxonomic and phylogenetic beta-diversity triggered by favorable spatial-environmental conditions in large-scale Chinese grasslands

Introduction

Although it is widely acknowledged that biodiversity maintains plant community assembly processes, exploring the patterns and drivers of beta-diversity (β-diversity; species variation among local plant communities) has received much less attention compared to alpha-diversity (α-diversity; species variation within a local plant community). Here, we aim to examine the patterns and spatial-environmental drivers of taxonomic and phylogenetic β-diversity, and their components such as species turnover and nestedness, in large-scale Leymus chinensis grassland communities.

Methods

We collected plant community data from 166 sites across widely distributed L. chinensis communities in northern China, and then calculated the taxonomic and phylogenetic β-diversity indices (overall, turnover and nestedness) using a pairwise dissimilarity approach. To assess the effects and to explain the variation in the patterns of β-diversity, we collected data on geospatial, climate and soil conditions. We applied descriptive statistics, Mental correlations, and multiple linear regression models to assess the patterns and spatial-environmental drivers of β-diversity.

Results

The β-turnover, as compared to β-nestedness, exhibited a predominant influence, constituting 92.6% of the taxonomic β-diversity and 80.4% of the phylogenetic β-diversity. Most of the spatial-environmental variables were significantly positively correlated with the overall taxonomic and phylogenetic β-diversity and β-turnover, but not with β-nestedness. Climatic factors such as MAP and MAT were the strongest predictors of both taxonomic and phylogenetic β-diversity and β-turnover. The variance partitioning analysis showed that the combined effects of spatial and environmental factors accounted for 19% and 16% of the variation in the taxonomic and phylogenetic β-diversity (overall), 17% and 12% of the variation in the β-turnover, and 7% and 1% of the variation in the β-nestedness, respectively, which were higher than independent effects of either spatial or environmental factors.

Discussion

At larger spatial scales, the turnover component of β-diversity may be associated with the species complementarity effect, but dominant or functionally important species can vary among communities due to the species selection effect. By incorporating β-diversity into grassland management strategies, we can enhance the provision of vital ecosystem services that bolster human welfare, serving as a resilient barrier against the adverse effects of climate change at regional and global scales.

Do phylogenetic community metrics reveal the South African quartz fields as terrestrial-habitat islands?

BACKGROUND AND AIMS

The quartz fields of the Greater Cape Floristic Region (GCFR) are arid and island-like special habitats, hosting ~142 habitat-specialized plant species, of which 81 % are local endemics, characterized by a rapid turnover of species between and among sites. We use several phylogenetic community metrics: (1) to examine species diversity and phylogenetic structure within and among quartz fields; (2) to investigate whether quartz field specialists are evolutionarily drawn from local species pools, whereas the alternative hypothesis posits that there is no significant evolutionary connection between quartz field specialists and the local species pools; and (3) to determine whether there is an association between certain traits and the presence of species in quartz fields.

METHODS

We sampled and developed dated phylogenies for six species-rich angiosperm families (Aizoaceae, Asteraceae, Crassulaceae, Cyperaceae, Fabaceae and Santalaceae) represented in the quartz field floras of southern Africa. Specifically, we focused on the flora of three quartz field regions in South Africa (Knersvlakte, Little Karoo and Overberg) and their surrounding species pools to address our research questions by scoring traits associated with harsh environments.

KEY RESULTS

We found that the Overberg and Little Karoo had the highest level of species overlap for families Aizoaceae and Fabaceae, whereas the Knersvlakte and the Overberg had the highest species overlap for families Asteraceae, Crassulaceae and Santalaceae. Although our phylogenetic community structure and trait analyses showed no clear patterns, relatively low pairwise phylogenetic distances between specialists and their local species pools for Aizoaceae suggest that quartz species could be drawn evolutionarily from their surrounding areas. We also found that families Aizoaceae and Crassulaceae in Knersvlakte and Little Karoo were phylogenetically even.

CONCLUSIONS

Despite their proximity to one another within the GCFR, the studied areas differ in their species pools and the phylogenetic structure of their specialists. Our work provides further justification for increased conservation focus on these unique habitats under future scenarios of global change.

Functional reorganization of North American wintering avifauna

Wintering birds serve as vital climate sentinels, yet they are often overlooked in studies of avian diversity change. Here, we provide a continental-scale characterization of change in multifaceted wintering avifauna and examine the effects of climate change on these dynamics. We reveal a strong functional reorganization of wintering bird communities marked by a north-south gradient in functional diversity change, along with a superimposed mild east-west gradient in trait composition change. Assemblages in the northern United States saw contractions of the functional space and increases in functional evenness and originality, while the southern United States saw smaller contractions of the functional space and stasis in evenness and originality. Shifts in functional diversity were underlined by significant reshuffling in trait composition, particularly pronounced in the western and northern United States. Finally, we find strong contributions of climate change to this functional reorganization, underscoring the importance of wintering birds in tracking climate change impacts on biodiversity.

The role of environmental gradients and microclimates in structuring communities and functional groups of lizards in a rainforest-savanna transition area

Environmental heterogeneity poses a significant influence on the functional characteristics of species and communities at local scales. Environmental transition zones, such as at the savanna-forest borders, can act as regions of ecological tension when subjected to sharp variations in the microclimate. For ectothermic organisms, such as lizards, environmental temperatures directly influence physiological capabilities, and some species use different thermoregulation strategies that produce varied responses to local climatic conditions, which in turn affect species occurrence and community dynamics. In the context of global warming, these various strategies confer different types of vulnerability as well as risks of extinction. To assess the vulnerability of a species and understand the relationships between environmental variations, thermal tolerance of a species and community structure, lizard communities in forest-savanna transition areas of two national parks in the southwestern Amazon were sampled and their thermal functional traits were characterized. Then, we investigated how community structure and functional thermal variation were shaped by two environmental predictors (i.e., microclimates estimated locally and vegetation structure estimated from remote sensing). It was found that the community structure was more strongly predicted by the canopy surface reflectance values obtained via remote sensing than by microclimate variables. Environmental temperatures were not the most important factor affecting the occurrence of species, and the variations in ecothermal traits demonstrated a pattern within the taxonomic hierarchy at the family level. This pattern may indicate a tendency for evolutionary history to indirectly influence these functional features. Considering the estimates of the thermal tolerance range and warming tolerance, thermoconformer lizards are likely to be more vulnerable and at greater risk of extinction due to global warming than thermoregulators. The latter, more associated with open environments, seem to take advantage of their lower vulnerability and occur in both habitat types across the transition, potentially out-competing and further increasing the risk of extinction and vulnerability of forest-adapted thermoconformer lizards in these transitional areas.

Phylogenetic conservation in plant phenological traits varies between temperate and subtropical climates in China

Phenological traits, such as leaf and flowering dates, are proven to be phylogenetically conserved. The relationship between phylogenetic conservation, plant phenology, and climatic factors remains unknown. Here, we assessed phenological features among flowering plants as evidence for phylogenetic conservatism, the tendency for closely related species to share similar ecological and biological attributes. We use spring phenological traits data from 1968-2018 of 65 trees and 49 shrubs in Xi'an (temperate climate) and Guiyang (subtropical climate) to understand plant phenological traits' relationship with phylogeny. Molecular datasets are employed in evolutionary models to test the phylogenetic conservatism in spring phenological characteristics in response to climate-sensitive phenological features. Significant phylogenetic conservation was found in the Xi'an plant's phenological traits, while there was a non-significant conservation in the Guiyang plant species. Phylogenetic generalized least squares (PGLS) models correlate with phenological features significantly in Xi'an while non-significantly in Guiyang. Based on the findings of molecular dating, it was suggested that the Guiyang species split off from their relatives around 46.0 mya during the middle Eocene of the Tertiary Cenozoic Era, while Xi'an species showed a long evolutionary history and diverged from their relatives around 95 mya during the late Cretaceous Mesozoic Era. First leaf dates (FLD) indicative of spring phenology, show that Xi'an adjourned the case later than Guiyang. Unlike FLD, first flower dates (FFD) yield different results as Guiyang flowers appear later than Xi'an's. Our research revealed that various factors, including phylogeny, growth form, and functional features, influenced the diversity of flowering phenology within species in conjunction with local climate circumstances. These results are conducive to understanding evolutionary conservation mechanisms in plant phenology concerning evolutionary processes in different geographical and climate zones.

Relationships between functional alpha and beta diversities of flea parasites and their small mammalian hosts

We studied the relationships between functional alpha and beta diversities of fleas and their small mammalian hosts in 4 biogeographic realms (the Afrotropics, the Nearctic, the Neotropics and the Palearctic), considering 3 components of alpha diversity (functional richness, divergence and regularity). We asked whether (a) flea alpha and beta diversities are driven by host alpha and beta diversities; (b) the variation in the off-host environment affects variation in flea alpha and beta diversities; and (c) the pattern of the relationship between flea and host alpha or beta diversities differs between geographic realms. We analysed alpha diversity using modified phylogenetic generalized least squares and beta diversity using modified phylogenetic generalized dissimilarity modelling. In all realms, flea functional richness and regularity increased with an increase in host functional richness and regularity, respectively, whereas flea functional divergence correlated positively with host functional divergence in the Nearctic only. Environmental effects on the components of flea alpha diversity were found only in the Holarctic realms. Host functional beta diversity was invariantly the best predictor of flea functional beta diversity in all realms, whereas the effects of environmental variables on flea functional beta diversity were much weaker and differed between realms. We conclude that flea functional diversity is mostly driven by host functional diversity, whereas the environmental effects on flea functional diversity vary (a) geographically and (b) between components of functional alpha diversity.

Forest disturbance increases functional diversity but decreases phylogenetic diversity of an arboreal tropical ant community

Tropical rainforest trees host a diverse arthropod fauna that can be characterised by their functional diversity (FD) and phylogenetic diversity (PD). Human disturbance degrades tropical forests, often coinciding with species invasion and altered assembly that leads to a decrease in FD and PD. Tree canopies are thought to be particularly vulnerable, but rarely investigated. Here, we studied the effects of forest disturbance on an ecologically important invertebrate group, the ants, in a lowland rainforest in New Guinea. We compared an early successional disturbed plot (secondary forest) to an old-growth plot (primary forest) by exhaustively sampling their ant communities in a total of 852 trees. We expected that for each tree community (1) disturbance would decrease FD and PD in tree-dwelling ants, mediated through species invasion. (2) Disturbance would decrease ant trait variation due to a more homogeneous environment. (3) The main drivers behind these changes would be different contributions of true tree-nesting species and visiting species. We calculated FD and PD based on a species-level phylogeny and 10 ecomorphological traits. Furthermore, we assessed by data exclusion the influence of species, which were not nesting in individual trees (visitors) or only nesting species (nesters), and of non-native species on FD and PD. Primary forests had higher ant species richness and PD than secondary forest. However, we consistently found increased FD in secondary forest. This pattern was robust even if we decoupled functional and phylogenetic signals, or if non-native ant species were excluded from the data. Visitors did not contribute strongly to FD, but they increased PD and their community weighted trait means often varied from nesters. Moreover, all community-weighted trait means changed after forest disturbance. Our finding of contradictory FD and PD patterns highlights the importance of integrative measures of diversity. Our results indicate that the tree community trait diversity is not negatively affected, but possibly even enhanced by disturbance. Therefore, the functional diversity of arboreal ants is relatively robust when compared between old-growth and young trees. However, further study with higher plot-replication is necessary to solidify and generalise our findings.

Temperate woody species across the angiosperm phylogeny acquire tolerance to water deficit stress during the growing season

Understanding the capacity of temperate trees to acclimate to limited soil water has become essential in the face of increasing drought risk due to climate change. We documented seasonal - or phenological - patterns in acclimation to water deficit stress in stems and leaves of tree species spanning the angiosperm phylogeny. Over 3 yr of field observations carried out in two US arboreta, we measured stem vulnerability to embolism (36 individuals of 7 Species) and turgor loss point (119 individuals of 27 species) over the growing season. We also conducted a growth chamber experiment on 20 individuals of one species to assess the mechanistic relationship between soil water restriction and acclimation. In three-quarters of species measured, plants became less vulnerable to embolism and/or loss of turgor over the growing season. We were able to stimulate this acclimatory effect by withholding water in the growth chamber experiment. Temperate angiosperms are capable of acclimation to soil water deficit stress, showing maximum vulnerability to soil water deficits following budbreak and becoming more resilient to damage over the course of the growing season or in response to simulated drought. The species-specific tempo and extent of this acclimatory potential constitutes preadaptive climate change resilience.

Competition for time: Evidence for an overlooked, diversity-maintaining competitive mechanism

Understanding how diversity is maintained in plant communities requires that we first understand the mechanisms of competition for limiting resources. In ecology, there is an underappreciated but fundamental distinction between systems in which the depletion of limiting resources reduces the growth rates of competitors and systems in which resource depletion reduces the time available for competitors to grow, a mechanism we call 'competition for time'. Importantly, modern community ecology and our framing of the coexistence problem are built on the implicit assumption that competition reduces the growth rate. However, recent theoretical work suggests competition for time may be the predominant competitive mechanism in a broad array of natural communities, a significant advance given that when species compete for time, diversity-maintaining trade-offs emerge organically. In this study, we first introduce competition for time conceptually using a simple model of interacting species. Then, we perform an experiment in a Mediterranean annual grassland to determine whether competition for time is an important competitive mechanism in a field system. Indeed, we find that species respond to increased competition through reductions in their lifespan rather than their rate of growth. In total, our study suggests competition for time may be overlooked as a mechanism of biodiversity maintenance.

Different sets of traits determine transition of alien species along the invasion continuum

Invasive alien species are currently considered as one of the dominant drivers of global environmental change. Till now, the majority of studies have focused on single or a few traits of alien species that facilitate their invasion. Also inclusion of all the traits which determine the transition of aliens along the different stages of invasion continuum (casual, naturalised and invasive) has remained largely overlooked. In this study, we collected a comprehensive trait dataset on 144 alien plant species of Kashmir Himalaya - a global biodiversity hotspot region. To test which traits of alien species, individually or in combination along with anthropogenic factors, determine their transition along the invasion continuum, we employed chi-square tests, boosted regression trees and phylogenetic methods. We found the perennial life span, longer residence time, greater number of introduced regions, and better seed dispersal mechanism were critical in determining the transition from casual to naturalised. The herbaceous growth form, therophyte Raunkiaer life-form, annual life span, achene fruit, longer residence time and broader introduced range were the species' traits determining transition from naturalised to invasive. Aliens introduced as ornamentals have more propensity to become naturalised; whereas aliens introduced unintentionally show overrepresentation at the invasive stage. Phylogeny alone showed mixed results indicating both clustering and dispersion; however, in combination with other traits, it plays a significant role in determining the stage of invasion. Overall, our study disentangles the individual and interactive roles of multiple traits that determine the transition of alien species' along the invasion continuum. Further, we foresee the potential applicability of our findings in designing robust invasion risk analysis protocols and stage-specific invasion management strategies in this Himalayan region, with learnings for elsewhere in the world.

A Community-Based Framework Integrates Interspecific Interactions into Forest Genetic Conservation

Forest genetic conservation is typically species-specific and does not integrate interspecific interaction and community structure. It mainly focuses on the theories of population and quantitative genetics. This approach depicts the intraspecific patterns of population genetic structure derived from genetic markers and the genetic differentiation of adaptive quantitative traits in provenance trials. However, it neglects possible interspecific interaction in natural forests and overlooks natural hybridization or subspeciation. We propose that the genetic diversity of a given species in a forest community is shaped by both intraspecific population and interspecific community evolutionary processes, and expand the traditional forest genetic conservation concept under the community ecology framework. We show that a community-specific phylogeny derived from molecular markers would allow us to explore the genetic mechanisms of a tree species interacting with other resident species. It would also facilitate the exploration of a species' ecological role in forest community assembly and the taxonomic relationship of the species with other species specific to its resident forest community. Phylogenetic β-diversity would assess the similarities and differences of a tree species across communities regarding ecological function, the strength of selection pressure, and the nature and extent of its interaction with other species. Our forest genetic conservation proposal that integrates intraspecific population and interspecific community genetic variations is suitable for conserving a taxonomic species complex and maintaining its evolutionary potential in natural forests. This provides complementary information to conventional population and quantitative genetics-based conservation strategies.

A phylogenomic perspective on interspecific competition

Evolutionary processes may have substantial impacts on community assembly, but evidence for phylogenetic relatedness as a determinant of interspecific interaction strength remains mixed. In this perspective, we consider a possible role for discordance between gene trees and species trees in the interpretation of phylogenetic signal in studies of community ecology. Modern genomic data show that the evolutionary histories of many taxa are better described by a patchwork of histories that vary along the genome rather than a single species tree. If a subset of genomic loci harbour trait-related genetic variation, then the phylogeny at these loci may be more informative of interspecific trait differences than the genome background. We develop a simple method to detect loci harbouring phylogenetic signal and demonstrate its application through a proof-of-principle analysis of Penicillium genomes and pairwise interaction strength. Our results show that phylogenetic signal that may be masked genome-wide could be detectable using phylogenomic techniques and may provide a window into the genetic basis for interspecific interactions.

Variation of floristic diversity, community composition, endemism, and conservation status of tree species in tropical rainforests of Sri Lanka across a wide altitudinal gradient

Tropical rainforests in Sri Lanka are biodiversity hotspots, which are sensitive to anthropogenic disturbance and long-term climate change. We assessed the diversity, endemism and conservation status of these rainforests across a wide altitudinal range (100-2200 m above sea level) via a complete census of all trees having ≥ 10 cm diameter at breast height in ten one-hectare permanent sampling plots. The numbers of tree families, genera and species and community-scale tree diversity decreased with increasing altitude. Tree diversity, species richness and total basal area per ha across the altitudinal range were positively associated with long-term means of maximum temperature, annual rainfall and solar irradiance. Percentage of endangered species increased with increasing altitude and was positively associated with cumulative maximum soil water deficit, day-night temperature difference and high anthropogenic disturbance. Percentage of endemic species was greater in the lowland rainforests than in high-altitude montane forests. Nearly 85% of the species were recorded in three or less plots, which indicated substantial altitudinal differentiation in their distributions. Less than 10 individuals were recorded in 41% of the endemic species and 45% of the native species, which underlined the need for urgent conservation efforts across the whole altitudinal range.

Assembly mechanisms of microbial communities in plastisphere related to species taxonomic types and habitat niches

A lot of plastic floats are presented in the kelp cultivation zone, enabling us to effectively evaluate the differences between surface water (SW) and plastic-attached (PA) microbial communities. In this study, we explored the microbial communities (both bacteria and protists) in SW and PA niches during the kelp cultivation activities. Effects of habitat niches on the diversity and composition of microbial communities were found. Beta partitioning and core taxa analyses showed species turnover and local species pool governed the microbial community assembly, and they contributed more to bacteria and protists, respectively. Based on the results of null model, bacterial communities presented a more deterministic and homogeneous assembly compared to protistan communities. Moreover, microbial communities in PA niche had higher species turnover and homogenizing assembly compared to the SW niche. The results of this study supplemented the theory of microbial community assembly and expanded our understanding of protists in plastisphere.

Influence of Ecological Multiparameters on Facets of β-Diversity of Freshwater Plankton Ciliates

Understanding the relative importance of the factors that drive global patterns of biodiversity is among the major topics of ecological and biogeographic research. In freshwater bodies, spatial, temporal, abiotic, and biotic factors are important structurers of these ecosystems and can trigger distinct responses according to the facet of biodiversity considered. The objective was to evaluate how different facets of β-diversity (taxonomic, functional, and phylogenetic) based on data from the planktonic ciliate community of a Neotropical floodplain, are influenced by temporal, spatial, abiotic, and biotic factors. The research was conducted in the upper Paraná River floodplain between the years 2010 and 2020 in different water bodies. All predictors showed significant importance on the facets of β-diversity, except the abiotic predictors on species composition data, for the taxonomic facet. The functional and phylogenetic facets were mostly influenced by abiotic, biotic, and spatial factors. For temporal predictors, results showed influence on taxonomic (structure and composition data) and functional (structure data) facets. Also, a fraction of shared explanation between the temporal and abiotic components was observed for the distinct facets. Significant declines in β-diversity in continental ecosystems have been evidenced, especially those with drastic implications for ecosystemic services. Therefore, the preservation of a high level of diversity in water bodies, also involving phylogenetic and functional facets, should be a priority in conservation plans and goals, to ensure the maintenance of important ecological processes involving ciliates.

Metagenomic analysis of ecological niche overlap and community collapse in microbiome dynamics

Species utilizing the same resources often fail to coexist for extended periods of time. Such competitive exclusion mechanisms potentially underly microbiome dynamics, causing breakdowns of communities composed of species with similar genetic backgrounds of resource utilization. Although genes responsible for competitive exclusion among a small number of species have been investigated in pioneering studies, it remains a major challenge to integrate genomics and ecology for understanding stable coexistence in species-rich communities. Here, we examine whether community-scale analyses of functional gene redundancy can provide a useful platform for interpreting and predicting collapse of bacterial communities. Through 110-day time-series of experimental microbiome dynamics, we analyzed the metagenome-assembled genomes of co-occurring bacterial species. We then inferred ecological niche space based on the multivariate analysis of the genome compositions. The analysis allowed us to evaluate potential shifts in the level of niche overlap between species through time. We hypothesized that community-scale pressure of competitive exclusion could be evaluated by quantifying overlap of genetically determined resource-use profiles (metabolic pathway profiles) among coexisting species. We found that the degree of community compositional changes observed in the experimental microbiome was correlated with the magnitude of gene-repertoire overlaps among bacterial species, although the causation between the two variables deserves future extensive research. The metagenome-based analysis of genetic potential for competitive exclusion will help us forecast major events in microbiome dynamics such as sudden community collapse (i.e., dysbiosis).

Preliminary species diversity and community phylogenetics of wood-inhabiting basidiomycetous fungi in the Dabie Mountains, Central China reveal unexpected richness

Wood-inhabiting fungi have important economic values as well as playing a major ecological role in forest ecosystem cycles. The Dabie Mountains, at the junction of Henan, Hubei, and Anhui Provinces, Central China, provide an ideal climate and favorable niches for the speciation and diversification of various forms of life including fungi. We studied the species diversity and community phylogenetics of wood-inhabiting basidiomycetous fungi that revealed 175 wood-inhabiting basidiomycetous species, of which 20 represented unidentified species, based on morphological and phylogenetic analyses of 575 specimens collected from ten sampling sites. These species belonged to two classes, 11 orders, 42 families, and 106 genera of Basidiomycota, and included 12 edible species, 28 medicinal species, four poisonous species, and seven forest pathogens. Four types of fungal distribution pattern at the genus level were recognized for 65 genera, while another 41 genera could not be placed in any known distribution pattern. The five sampling sites in the eastern part of the Dabie Mountains had significantly higher species diversity and phylogenetic diversity of wood-inhabiting basidiomycetous fungi than those in the western part, and thus deserve priority in terms of conservation. The community of wood-inhabiting basidiomycetous fungi in the Dabie Mountains is generally affected by a combination of habitat filtering and competitive exclusion. This study provides a basis on which to build actions for the comprehensive recognition, utilization, and conservation of wood-inhabiting basidiomycetous fungi in the region.

Global biogeography of the smallest plankton across ocean depths

Tiny ocean plankton (picoplankton) are fundamental for the functioning of the biosphere, but the ecological mechanisms shaping their biogeography were partially understood. Comprehending whether these microorganisms are structured by niche versus neutral processes is relevant in the context of global change. We investigate the ecological processes (selection, dispersal, and drift) structuring global-ocean picoplanktonic communities inhabiting the epipelagic (0 to 200 meters), mesopelagic (200 to 1000 meters), and bathypelagic (1000 to 4000 meters) zones. We found that selection decreased, while dispersal limitation increased with depth, possibly due to differences in habitat heterogeneity and dispersal barriers such as water masses and bottom topography. Picoplankton β-diversity positively correlated with environmental heterogeneity and water mass variability, but this relationship tended to be weaker for eukaryotes than for prokaryotes. Community patterns were more pronounced in the Mediterranean Sea, probably because of its cross-basin environmental heterogeneity and deep-water isolation. We conclude that different combinations of ecological mechanisms shape the biogeography of the ocean microbiome across depths.

What Can Evolutionary History Tell Us about the Functioning of Ecological Communities? The ASN Presidential Debate

AbstractIn January 2018, Sharon Strauss, then president of the American Society of Naturalists, organized a debate on the following topic: does evolutionary history inform the current functioning of ecological communities? The debaters-Ives, Lau, Mayfield, and Tobias-presented pro and con arguments, caricatured in standard debating format. Numerous examples show that both recent microevolutionary and longer-term macroevolutionary history are important to the ecological functioning of communities. On the other hand, many other examples illustrate that the evolutionary history of communities or community members does not influence ecological function, or at least not very much. This article aims to provide a provocative discussion of the consistent and conflicting patterns that emerge in the study of contemporary and historical evolutionary influences on community function, as well as to identify questions for further study. It is intended as a thought-provoking exercise to explore this complex field, specifically addressing (1) key assumptions and how they can lead us astray and (2) issues that need additional study. The debaters all agree that evolutionary history can inform us about at least some aspects of community function. The underlying question at the root of the debate, however, is how the fields of ecology and evolution can most profitably collaborate to provide a deeper and broader understanding of ecological communities.

Phylogenetic diversity and structure in moist and dry upland forests in the semi-arid region of Brazil

Understanding the factors influencing variation in the diversity and structure of rich biological communities (e.g., Neotropical upland forests) is essential in the context of climate change. In this study, we examine how environmental filters (temperature, precipitation, and elevation) and distinct habitats (moist upland forests - MUF and dry upland forests - DHF) influence the phylogenetic diversity and structure of 54 tree communities (28 MHF and 26 DHF). We used the standardized effect size (ses) of the metrics phylogenetic diversity (ses.PD), mean pairwise distance (ses.MPD), and mean nearest neighbor distance (ses.MNTD) to quantify changes in tree community diversity and structure. Then, we assessed the relationships of the phylogenetic metrics with the environmental filters as predictors using generalized linear models (GLMs). Our results indicate that increasing temperature negatively affects the phylogenetic indices analyzed, leading to less diverse and more clustered communities. In contrast, increasing precipitation and elevation showed a significant positive relationship with the analyzed indices, directing communities towards greater phylogenetic diversity and random or overdispersed structure. Our findings also reveal that phylogenetic diversity and structure vary with habitat type. For example, while MUFs exhibit higher phylogenetic diversity and random structure, DUFs display lower phylogenetic diversity and clustered structure. In conclusion, our results suggest that the phylogenetic patterns exhibited by upland communities in the semiarid region are strongly related to climatic conditions and the habitat in which they are found. Therefore, if the predicted temperature increases and precipitation decreases in climate change scenarios for the semi-arid region materialize, these communities may face significant biodiversity loss.

Forest habitats and plant communities strongly predicts Megachilidae bee biodiversity

Megachilidae is one of the United States' most diverse bee families, with 667 described species in 19 genera. Unlike other bee families, which are primarily ground nesters, most megachilid bees require biotic cavities for nesting (i.e., wood, pithy stems, etc.). For this group, the availability of woody-plant species may be as important as nectar/pollen resources in maintaining populations. We studied Megachilidae biodiversity in the continental United States. We confirmed that the highest species richness of Megachilidae was in the southwestern United States. We examined the relationship between species richness and climate, land cover, tree species richness, and flowering plant diversity. When examining environmental predictors across the conterminous United States, we found that forested habitats, but not tree diversity, strongly predicted Megachilidae richness. Additionally, Megachilidae richness was highest in areas with high temperature and low precipitation, however this was not linearly correlated and strongly positively correlated with flowering plant diversity. Our research suggests that the availability of nesting substrate (forested habitats), and not only flowering plants, is particularly important for these cavity-nesting species. Since trees and forested areas are particularly susceptible to climate change, including effects of drought, fire, and infestations, nesting substrates could become a potential limiting resource for Megachilidae populations.

The landscape ecological view of vertebrate species richness in urban areas across biogeographic realms

Understanding how the spatial arrangement of remnant green spaces in cities complements biodiversity provides an opportunity for synergy between urban development and biological conservation. However, the geography of urbanization is shifting from Europe and North America to Asia and Africa, and more research is needed for fast-growing regions. To understand how shifting urbanization shapes biodiversity patterns, we analyzed the contribution of landscape factors in explaining vertebrate species richness in urban areas across biogeographic realms. We used variation partitioning to quantify and compare the relative importance of landscape factors (composition and configuration) and environmental factors (climate, elevation, and latitude) in explaining vertebrate species richness in landscapes with at least a million inhabitants across biogeographic realms. Our results pointed out that in the Indo-Malayan, the Afrotropical, and the Neotropical realm (on average of 16.46%) and China and India (11.88%), the influence of landscape factors on vertebrate species richness are significantly higher than that of the Palearctic and Nearctic realms (6.48%). Our findings outline the importance of landscape composition and configuration in shaping biodiversity patterns in regions with fast urban growth during the next two decades, such as Africa, Latin America, and Southeastern Asia. We suggest improving land governance and urban planning to construct eco-friendly landscape structures to mitigate biodiversity loss due to urbanization.

Influence of phylogenetic diversity of plant communities on tri-trophic interactions

Phylogenetic diversity of plant communities can influence the interaction between plants, herbivores, and their natural enemies. Plant communities with phylogenetically distant species tend to present a wide variety of functional traits and ecological niches, which in turn can influence competitive interactions among plants as well as food and habitat quality for herbivores and their natural enemies. To assess some different mechanisms by which phylogenetic diversity of plant communities can influence herbivores and their natural enemies, we established 12 experimental plots of tropical trees with two treatments: high and low phylogenetic diversity. We measured plant growth and anti-herbivore defenses, herbivore foliar damage, and predator activity in seven species that were present in both treatments. We found significant differences in the expression of plant traits as a function of species identity and their life history, but also depending on the phylogenetic context in which they grew. Pioneer species had higher growth and produced more phenolics in plots with high phylogenetic diversity versus plants in plots with low phylogenetic diversity. Accordingly, herbivore damage in these species was greater in plots with low phylogenetic diversity. Finally, predator activity on caterpillar clay models placed on plants was greater within the low phylogenetic diversity treatment, but only for non-myrmecophytic species. These results suggest that plant phylogenetic diversity can influence the expression of growth and defensive traits and further modify the interaction between plants, herbivores, and their natural enemies. However, such effects depend on plant life history and the presence of mutualistic interaction with ants.

Can we meaningfully estimate the impacts of climate on zooplankton biodiversity? A review on uses and limitations of marine time series

Climate events compromise ecosystems functioning and services. Marine zooplankton play a key role linking primary producers and higher consumers, in the carbon export to deeper regions, and respond quickly to environmental change. We conducted a systematic review to assess the effects of climate on marine zooplankton diversity. We describe the major findings, uses and limitations raised in the literature from worldwide time series ≥5 years. Thirty-five studies were included and only 6 presented extractable data (i.e., those that could be extracted from images) for the most studied group (i.e., copepods). Responses to climate were conflicting, and studies were mostly restricted to the global north, applied richness, alpha- and beta-diversity equally, and had a large number of unresolved taxonomic identification. Standardized open long-term data would meaningfully help unveiling assemblage reorganization and allow meta-analyses to improve our understanding of the effects of climate change and variability on zooplankton biodiversity.

Salinization and sedimentation drive contrasting assembly mechanisms of planktonic and sediment-bound bacterial communities in agricultural streams

Agriculture is the most dominant land use globally and is projected to increase in the future to support a growing human population but also threatens ecosystem structure and services. Bacteria mediate numerous biogeochemical pathways within ecosystems. Therefore, identifying linkages between stressors associated with agricultural land use and responses of bacterial diversity is an important step in understanding and improving resource management. Here, we use the Mississippi Alluvial Plain (MAP) ecoregion, a highly modified agroecosystem, as a case study to better understand agriculturally associated drivers of stream bacterial diversity and assembly mechanisms. In the MAP, we found that planktonic bacterial communities were strongly influenced by salinity. Tolerant taxa increased with increasing ion concentrations, likely driving homogenous selection which accounted for ~90% of assembly processes. Sediment bacterial phylogenetic diversity increased with increasing agricultural land use and was influenced by sediment particle size, with assembly mechanisms shifting from homogenous to variable selection as differences in median particle size increased. Within individual streams, sediment heterogeneity was correlated with bacterial diversity and a subsidy-stress relationship along the particle size gradient was observed. Planktonic and sediment communities within the same stream also diverged as sediment particle size decreased. Nutrients including carbon, nitrogen, and phosphorus, which tend to be elevated in agroecosystems, were also associated with detectable shifts in bacterial community structure. Collectively, our results establish that two understudied variables, salinity and sediment texture, are the primary drivers of bacterial diversity within the studied agroecosystem, whereas nutrients are secondary drivers. Although numerous macrobiological communities respond negatively, we observed increasing bacterial diversity in response to agricultural stressors including salinization and sedimentation. Elevated taxonomic and phylogenetic bacterial diversity likely increases the probability of detecting community responses to stressors. Thus, bacteria community responses may be more reliable for establishing water quality goals within highly modified agroecosystems that have experienced shifting baselines.

Tree communities and functional traits determine herbivore compositional turnover

There are many factors known to drive species turnover, although the mechanisms by which these operate are less clear. Based on comprehensive datasets from the largest tree diversity experiment worldwide (BEF-China), we used shared herbivore species (zeta diversity) and multi-site generalized dissimilarity modelling to investigate the patterns and determinants of species turnover of Lepidoptera herbivores among study plots across a gradient in tree species richness. We found that zeta diversity declined sharply with an increasing number of study plots, with complete changes in caterpillar species composition observed even at the fine spatial scale of our study. Plant community characteristics rather than abiotic factors were found to play key roles in driving caterpillar compositional turnover, although these effects varied with an increasing number of study plots considered, due to the varying contributions of rare and common species to compositional turnover. Our study reveals details of the impact of phylogeny- and trait-mediated processes of trees on herbivore compositional turnover, which has implications for forest management and conservation and shows potential avenues for maintenance of heterogeneity in herbivore communities.

Evolutionary history shapes grassland productivity through opposing effects on complementarity and selection

Phylogenetic diversity (PD), the evolutionary history of the organisms comprising a community, is increasingly recognized as an important driver of ecosystem function. However, biodiversity-ecosystem function experiments have rarely included PD as an a priori treatment. Thus, PD's effects in existing experiments are often confounded by covarying differences in species richness and functional trait diversity (FD). Here we report an experimental demonstration of strong PD effects on grassland primary productivity that are independent of FD, which was separately manipulated, and species richness, which was planted uniformly high to mimic diverse natural grasslands. Partitioning diversity effects demonstrated that higher PD increased complementarity (niche partitioning and/or facilitation) but lowered selection effects (probability of sampling highly productive species). Specifically, for every 5% increase in PD, complementarity increased by 26% on average (±8% SE), while selection effects decreased more modestly (8 ± 16%). PD also shaped productivity through clade-level effects on functional traits, that is, trait values associated with particular plant families. This clade effect was most pronounced in the Asteraceae (sunflower family), which, in tallgrass prairies, generally comprises tall, high-biomass species with low phylogenetic distinctiveness. FD also reduced selection effects but did not alter complementarity. Our results show that PD, independent of richness and FD, mediates ecosystem function through contrasting effects on complementarity and selection. This adds to growing evidence that consideration of phylogenetic dimensions of biodiversity can advance ecological understanding and inform conservation and restoration.

Cryptic functional diversity within a grass mycobiome

Eukaryotic hosts harbor tremendously diverse microbiomes that affect host fitness and response to environmental challenges. Fungal endophytes are prominent members of plant microbiomes, but we lack information on the diversity in functional traits affecting their interactions with their host and environment. We used two culturing approaches to isolate fungal endophytes associated with the widespread, dominant prairie grass Andropogon gerardii and characterized their taxonomic diversity using rDNA barcode sequencing. A randomly chosen subset of fungi representing the diversity of each leaf was then evaluated for their use of different carbon compound resources and growth on those resources. Applying community phylogenetic analyses, we discovered that these fungal endophyte communities are comprised of phylogenetically distinct assemblages of slow- and fast-growing fungi that differ in their use and growth on differing carbon substrates. Our results demonstrate previously undescribed and cryptic functional diversity in carbon resource use and growth in fungal endophyte communities of A. gerardii.

Intercontinental comparison of phylogenetic relatedness in introduced plants at the transition from naturalization to invasion: A case study on the floras of South Africa and China

Invasive species may pose significant threats to biodiversity and ecosystem structure and functioning. The number of introduced species that have become invasive is substantial and is rapidly increasing. Identifying potentially invasive species and preventing their expansion are of critical importance in invasion ecology. Phylogenetic relatedness between invasive and native species has been used in predicting invasion success. Previous studies on the phylogenetic relatedness of plants at the transition from naturalization to invasion have shown mixed results, which may be because different methods were used in different studies. Here, I use the same method to analyze two comprehensive data sets from South Africa and China, using two phylogenetic metrics reflecting deep and shallow evolutionary histories, to address the question whether the probability of becoming invasive is higher for naturalized species distantly related to the native flora. My study suggests that the probability of becoming invasive is higher for naturalized species closely related to the native flora. The finding of my study is consistent with Darwin's preadaptation hypothesis.

Sex differences in the skin microbiome of burn scars

Sex differences are observed in various spectrums of skin diseases, and there are differences in wound healing rate. Herein, sex differences were identified for the newly healed skin microbiome of burn patients. Fifty-two skin samples (26 normal skin, 26 burn scars) were collected from 26 burn patients (12 male, 14 female) and microbiota analysis was performed. The correlation between skin microbiota and biomechanical properties of burn scars was also investigated. There were no significant differences in clinical characteristics between male and female patients. Considering the biomechanical properties of burn scars and normal skin around it performed before sample collection, the mean erythema level of men's normal skin was significantly higher than that of women, whereas the mean levels of melanin, transepidermal water loss and skin hydration showed no significant sex differences. The erythrocyte sedimentation rate was significantly higher in females than that in males. Alpha diversity showed no significant differences between normal skin and burn scars in the male group. However, the scar was significantly higher than that of normal skin in the female group. Microbial network analysis revealed that the male group had more complex microbial network than the female group. Additionally, in the male group, the edge density and clustering coefficient were higher in burn scars when compared to normal skin, than the female group. There were sex differences in the results of microbiome of normal skin and burn scars. Some of the altered microbiota have been correlated with the biomechanical properties of burn scars. In conclusion, sex difference in the burn scar microbiome was confirmed. These results suggest that burn treatment strategies should vary with sex.

Capturing patterns of evolutionary relatedness with reflectance spectra to model and monitor biodiversity

Biogeographic history can set initial conditions for vegetation community assemblages that determine their climate responses at broad extents that land surface models attempt to forecast. Numerous studies have indicated that evolutionarily conserved biochemical, structural, and other functional attributes of plant species are captured in visible-to-short wavelength infrared, 400 to 2,500 nm, reflectance properties of vegetation. Here, we present a remotely sensed phylogenetic clustering and an evolutionary framework to accommodate spectra, distributions, and traits. Spectral properties evolutionarily conserved in plants provide the opportunity to spatially aggregate species into lineages (interpreted as "lineage functional types" or LFT) with improved classification accuracy. In this study, we use Airborne Visible/Infrared Imaging Spectrometer data from the 2013 Hyperspectral Infrared Imager campaign over the southern Sierra Nevada, California flight box, to investigate the potential for incorporating evolutionary thinking into landcover classification. We link the airborne hyperspectral data with vegetation plot data from 1372 surveys and a phylogeny representing 1,572 species. Despite temporal and spatial differences in our training data, we classified plant lineages with moderate reliability (Kappa = 0.76) and overall classification accuracy of 80.9%. We present an assessment of classification error and detail study limitations to facilitate future LFT development. This work demonstrates that lineage-based methods may be a promising way to leverage the new-generation high-resolution and high return-interval hyperspectral data planned for the forthcoming satellite missions with sparsely sampled existing ground-based ecological data.

Interspecific sociality alters the colonization and extinction rates of birds on subtropical reservoir islands

Island biogeography theory has proved a robust approach to predicting island biodiversity on the assumption of species equivalency. However, species differ in their grouping behaviour and are entangled by complex interactions in island communities, such as competition and mutualism. We here investigated whether intra- and/or interspecific sociality may influence biogeographic patterns, by affecting movement between islands or persistence on them. We classified bird species in a subtropical reservoir island system into subcommunities based on their propensity to join monospecific and mixed-species flocks. We found that subcommunities which had high propensity to flock interspecifically had higher colonization rates and lower extinction rates over a 10-year period. Intraspecific sociality increased colonization in the same analysis. A phylogenetically corrected analysis confirmed the importance of interspecific sociality, but not intraspecific sociality. Group-living could enable higher risk crossings, with greater vigilance also linked to higher foraging efficiency, enabling colonization or long-term persistence on islands. Further, if group members are other species, competition can be minimized. Future studies should investigate different kinds of island systems, considering positive species interactions driven by social behaviour as potential drivers of community assembly on islands. This article is part of the theme issue 'Mixed-species groups and aggregations: shaping ecological and behavioural patterns and processes'.

Neotropical mixed-species bird flocks in a community context

Mixed-species flocks are an important component of bird communities, particularly in the Neotropics, where flocks reach their highest diversity. The extent to which mixed-species flocks represent unique functional or ecological roles within communities, and how these attributes change over environmental gradients, however, is not well understood. We use a trait-based approach to examine functional aspects of flocking assemblages as they relate to those observed in the larger avian community across a 3000 m elevational gradient. Our results reveal similar ecological strategies among flocking species and the communities in which they occur, at the scale of the regional pool and across elevations. Trait variation in flocking and non-flocking assemblages is structured along two major axes defined by size- and resource-related traits. The trait space occupied by flocking species, however, represents only half (51%) that of the larger community. Similarly, the trait space of flocks across elevations is restricted compared to non-flocking species. The shared trait space across flock types represents small-bodied invertivores foraging in lower forest strata, traits associated with increased vulnerability to predation. The concentration of flocking species in functional trait space suggests high niche packing and either more overlap in ecological strategies or more finely divided niches relative to non-flocking species. This article is part of the theme issue 'Mixed-species groups and aggregations: shaping ecological and behavioural patterns and processes'.

The Elevational Gradient of Bird Beta Diversity in the Meili Snow Mountains, Yunnan Province, China

Understanding the elevational patterns of beta diversity in mountain regions is a long-standing problem in biogeography and ecology. Previous research has generally focused on the taxonomy facet on a large scale, but was limited with regard to multi-facet beta diversity. Accordingly, we constructed a multi-dimensional (taxonomic/phylogenetic/functional) framework to analyze the underlying mechanisms of beta diversity. Within an approximately 2000 m altitudinal range (from 2027 m to 3944 m) along the eastern slope of the Meili Snow Mountains in Deqin County, Yunnan Province, China, we performed field surveys of breeding and non-breeding birds in September/2011 and May/2012, respectively. In total, 132 bird species were recorded during the fieldwork. The results indicated that taxonomic beta diversity contributed 56% of the bird species diversity, and its turnover process dominated the altitudinal pattern of taxon beta diversity; beta phylogenetic diversity contributed 42% of the bird phylogenetic diversity, and its turnover process also appeared to be stronger than the nestedness. For both taxonomy and phylogeny, the null models standardized measures (SES.β_sim/SES.β_sne/SES.β_sor) of paired dissimilarities between elevation zones all showed statistically significant differences (p ≤ 0.05) and were higher than expected (SES.β > 0). However, standardized functional beta diversity showed convergence along the elevational gradient with no significant change. Moreover, the functional beta diversity contributed 50% of the bird functional diversity; there was no significant difference between the turnover and the nestedness-resultant component. Based on these results, we discerned that taxonomic and phylogenetic beta diversity patterns among the elevational zone were overdispersed, which indicated that limiting similarity dominated the turnover process among the bird species and phylogenetic communities in the Meili Snow Mountains.

Phylogenetic and functional trait-based community assembly within Pacific Cyrtandra (Gesneriaceae): Evidence for clustering at multiple spatial scales

Tropical rainforest communities are often characterized by a small number of species-rich genera that contribute disproportionately to the alpha diversity in these habitats. In the Pacific Basin, there are nearly 200 species of Cyrtandra, most of which are white-flowered woody shrubs that are single-island endemics. Within these island communities, multiple Cyrtandra species are commonly observed to occur sympatrically in wet forest understories, forming swarms of what appear to be ecologically similar taxa. The aim of this study was to determine whether species of these plants are randomly assembled with respect to phylogenetic relatedness and traits that are ecologically relevant. I examined assembly patterns across three Pacific archipelagoes using a combination of 10 functional traits and a well-resolved phylogeny comprising 34 species of Cyrtandra. Coexisting species were found to be more closely related and more phenotypically similar than would be expected by chance. This pattern was observed at both regional (island) and local (site) spatial scales. The retention of phylogenetic signal in floral traits and the strong influence of these traits on the observed degree of phylogenetic clustering may indicate that generalist insect pollinators act as a biotic filter on oceanic islands, driving selection for similar floral morphology among closely related species of Pacific Cyrtandra. Phylogenetic signal was also detected in leaf size, which contributed to niche clustering at both spatial scales. Coupled with a propensity for long-distance dispersal, and the restricted distribution of Cyrtandra to rainforest understories, this finding suggests that environmental filtering along this trait axis may be more important than dispersal limitation in determining species assemblages. This study supports the theory that plant species are not randomly assembled, and instead, that niche-based processes structure biodiversity at regional and local spatial scales in diverse congeneric species assemblages.

Partitioning and integrating of plant traits and phylogeny in assessing diversity along secondary forest succession in Loess Plateau of China

Assessing plant diversity during community succession based on plant trait and phylogenetic features within a community (alpha scale) and among communities (beta scale) could improve our understanding of community succession mechanism. However, whether changes of community functional diversity at alpha and beta scale are structured by different traits and whether integrating plant traits and phylogeny can enhance the ability in detecting diversity pattern have not been studied in detail. Thirty plots representing different successional stages were established on the Loess Plateau of China and 15 functional traits were measured for all coexisting species. We first analyzed the functional alpha and beta diversity along succession by decomposing species trait into alpha and beta components and then integrated key traits with phylogenetic information to explore their roles in shaping species turnover during community succession. We found that functional alpha diversity increased along successional stages and was structured by morphological traits, while beta diversity decreased during succession and was more structured by stoichiometry traits. Phylogenetic alpha diversity showed congruent pattern with functional alpha diversity because of phylogenetic conservation of trait alpha components (variation within community), while beta diversity showed incongruent pattern due to phylogenetic randomness of trait beta components (variation among communities). Furthermore, only integrating relatively conserved traits (plant height and seed mass) and phylogenetic information can raise the detecting ability in assessing diversity change. Overall, our results reveal the increasing niche differentiation within community and functional convergence among communities with succession process, indicating the importance of matching traits with scale in studying community functional diversity and the asymmetry of traits and phylogeny in reflecting species ecological differences under long-term selection pressures.

U.PhyloMaker: An R package that can generate large phylogenetic trees for plants and animals

The previously released packages of the PhyloMaker series (i.e. S.PhyloMaker, V.PhyloMaker, and V.PhyloMaker2) have been broadly used to generate phylogenetic trees for ecological and biogeographical studies. Although these packages can be used to generate phylogenetic trees for any groups of plants and animals for which megatrees are available, they focus on generating phylogenetic trees for plants based on the megatrees provided by the packages. How to use these packages to generate phylogenetic trees based on other megatrees is not straightforward. Here, we present a new tool, which is called 'U.PhyloMaker', and a simple R script that can be used to easily generate large phylogenetic trees for both plants and animals at a relatively fast speed.

Effect of environmental and spatial factors on the phylogenetic and functional diversity of the Mediterranean tree communities of Europe

The tree flora of the Mediterranean Basin contains an outstanding taxonomic richness and a high proportion of endemic taxa. Contrary to other regions of the Mediterranean biome, a comprehensive phylogenetic analysis of the relationship between phylogenetic diversity, trait diversity and environmental factors in a spatial ecological context is lacking. We inferred the first calibrated phylogeny of 203 native tree species occurring in the European Mediterranean Basin based on 12 DNA regions. Using a set of four functional traits, we computed phylogenetic diversity for all 10,042 grid cells of 10 × 10 km spatial resolution to completely cover Mediterranean Europe. Then, we tested the spatial influence of environmental factors on tree diversity. Our results suggest that the nature of the relationship between traits and phylogeny varies among the different studied traits and according to the evolutionary distance considered. Phylogenetic diversity and functional diversity of European Mediterranean trees correlated strongly with species richness. High values of these diversity indices were located in the north of the study area, at high altitude, and minimum temperature of the coldest month. In contrast, the two phylogenetic indices that were not correlated with species richness (Mean Phylogenetic Distance, Phylogenetic Species Variability) were located in the south of the study area and were positively correlated with high altitude, soil organic carbon stock and sand soil texture. Our study provides support for the use of phylogenies in conservation biology to assess ecosystem functioning, and provides insights for the implementation of sustainable forest ecosystem management.

Plant community phylogeny responses to protections and its main drivers in boreal forests, China: General pattern and implications

Patterns of the phylogenetic structure have been broadly applied to predict community assembly processes. However, the distribution pattern of evolutionary diversity and its drivers under nature conservation are still poorly understood in boreal forests. Here, we investigated 1738 sampling plots and subplots from distinct protection intensities (PIs) zones in five representative National Nature Reserves (NNRs). Multiple comparisons, redundancy analysis, and linear mixed model were performed to identify the changes in community phylogeny across different PIs and NNRs and the drivers for these variations. Our results showed considerable plant community phylogeny variations in different NNRs. As indicated by SesMPD (standardized mean pairwise distance) and SesMNTD (standardized the mean nearest taxon distance), trees, shrubs, and herbs presented overdispersed, clustered, and random distribution patterns, respectively, in different PIs. Protection resulted in the phylogenetic structure between the nearest species of trees showing a more overdispersed pattern (p < 0.05). Protection decreased the phylogenetically clustered degree between the nearest species of shrubs (p > 0.05), while the herbs still maintained a random pattern. Community traits explained the most to phylogeny variation of different communities (24 %-71 %, p < 0.01), followed by geoclimatic factors (2 %-24 %) and conservation processes (1 %-21 %). The higher mean annual precipitation and under branch height at the lower latitude area accompanied the higher SesMPD and SesMNTD. The higher PIs attended with higher tree SesMPD, and the longer protection time resulted in higher shrub PSR (phylogenetic species richness) and PSV (phylogenetic species variability). Including the location of NNRs, community traits, and years of protection, rather than only emphasizing PI itself, could optimize community phylogenetic structure and preserve the evolutionary potential of biodiversity.

Evolutionary history of marginal habitats regulates the diversity of tree communities in the Atlantic Forest

BACKGROUND AND AIMS

The Atlantic Forest biodiversity hotspot is a complex mosaic of habitat types. However, the diversity of the rain forest at the core of this complex has received far more attention than that of its marginal habitats, such as cloud forest, semi-deciduous forest or restinga. Here, we investigate broad-scale angiosperm tree diversity patterns along elevation gradients in the south-east Atlantic Forest and test if the diversity of marginal habitats is shaped from the neighbouring rain forest, as commonly thought.

METHODS

We calculated phylogenetic indices that capture basal [mean pairwise phylogenetic distance (MPD)] and terminal [mean nearest taxon distance (MNTD)] phylogenetic variation, phylogenetic endemism (PE) and taxonomic and phylogenetic beta diversity (BD and PBD) for 2074 angiosperm tree species distributed in 108 circular sites of 10 km diameter across four habitat types i.e. rain forest, cloud forest, semi-deciduous forest and coastal vegetation known as restinga. We then related these metrics to elevation and environmental variables.

KEY RESULTS

Communities in wetter and colder forests show basal phylogenetic overdispersion and short phylogenetic distances towards the tips, respectively. In contrast, communities associated with water deficit and salinity show basal phylogenetic clustering and no phylogenetic structure toward the tips. Unexpectedly, rain forest shows low PE given its species richness, whereas cloud and semi-deciduous forests show unusually high PE. The BD and PBD between most habitat types are driven by the turnover of species and lineages, except for restinga.

CONCLUSIONS

Our results contradict the idea that all marginal habitat types of the Atlantic Forest are sub-sets of the rain forest. We show that marginal habitat types have different evolutionary histories and may act as 'equilibrium zones for biodiversity' in the Atlantic Forest, generating new species or conserving others. Overall, our results add evolutionary insights that reinforce the urgency of encompassing all habitat types in the Atlantic Forest concept.