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Progress in phylogenetic community ecology is often limited by the availability of phylogenetic information and the lack of appropriate methods and solutions to deal with this problem. We estimate the effect of the lack of phylogenetic information on the relations among taxa measured by commonly used phylogenetic metrics in comparative studies and community ecology, namely: Blomberg's K phylogenetic signal, Faith's Phylogenetic Diversity (PD), Mean Phylogenetic Distance (MPD) and Mean Nearest Taxon Distance (MNTD). To overcome this problem, we tested two possible solutions: Polytomic trees and Operational trees. Our results show that the effects on K values strongly depended on the level of phylogenetic signal. In the case of the community metrics, the effects were insensitive to the patterns of species distribution in the communities. Community metrics tended to be overestimated with both Polytomic and Operational trees, but the overestimation was higher with Polytomic trees. PD and MPD metrics were less biased than MNTD metric. We show that the lack of phylogenetic resolution is not necessarily problematic for all analyses and that its effect will depend on the chosen metric and on the solutions used to deal with the problem. Based on our results, we suggest that ecologists should prefer the Operational tree solution to remove polytomies in the phylogenetic tree and take careful consideration while designing experiments, and analyzing and interpreting the results of phylogenetic metrics., (© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Background: A major challenge in biodiversity science is to understand the factors contributing to the variability of species richness -the number of different species in a community or region - among comparable taxonomic lineages. Multiple biotic and abiotic factors have been hypothesized to have an effect on species richness and have been used as its predictors, but identifying accurate predictors is not straightforward. Spiders are a highly diverse group, with some 48,000 species in 120 families; yet nearly 75% of all species are found within just the ten most speciose families. Here we use a Random Forest machine learning algorithm to test the predictive power of different variables hypothesized to affect species richness of spider genera., Results: We test the predictive power of 22 variables from spiders' morphological, genetic, geographic, ecological and behavioral landscapes on species richness of 45 genera selected to represent the phylogenetic and biological breath of Araneae. Among the variables, Random Forest analyses find body size (specifically, minimum male body size) to best predict species richness. Multiple Correspondence analysis confirms this outcome through a negative relationship between male body size and species richness. Multiple Correspondence analyses furthermore establish that geographic distribution of congeneric species is positively associated with genus diversity, and that genera from phylogenetically older lineages are species poorer. Of the spider-specific traits, neither the presence of ballooning behavior, nor sexual size dimorphism, can predict species richness., Conclusions: We show that machine learning analyses can be used in deciphering the factors associated with diversity patterns. Since no spider-specific biology could predict species richness, but the biologically universal body size did, we believe these conclusions are worthy of broader biological testing. Future work on other groups of organisms will establish whether the detected associations of species richness with small body size and wide geographic ranges hold more broadly.

Ecologists are increasingly making use of molecular phylogenies, especially in the fields of community ecology and conservation. However, these phylogenies are often used without full appreciation of their underlying assumptions and uncertainties. A frequent practice in ecological studies is inferring a phylogeny with molecular data from taxa only within the community of interest. These "inferred community phylogenies" are inherently biased in their taxon sampling. Despite the importance of comprehensive sampling in constructing phylogenies, the implications of using inferred community phylogenies in ecological studies have not been examined. Here, we evaluate how taxon sampling affects the quantification and comparison of community phylogenetic diversity using both simulated and empirical data sets. We demonstrate that inferred community trees greatly underestimate phylogenetic diversity and that the probability of incorrectly ranking community diversity can reach up to 25%, depending on the dating methods employed. We argue that to reach reliable conclusions, ecological studies must improve their taxon sampling and generate the best phylogeny possible., (© 2018 John Wiley & Sons Ltd.)

Premise of the Study: Many ecological and evolutionary processes shape the assembly of organisms into local communities from a regional pool of species. We analyzed phylogenetic and functional diversity to understand community assembly of the ferns of Florida at two spatial scales., Methods: We built a phylogeny for 125 of the 141 species of ferns in Florida using five chloroplast markers. We calculated mean pairwise dissimilarity (MPD) and mean nearest taxon distance (MNTD) from phylogenetic distances and functional trait data for both spatial scales and compared the results to null models to assess significance., Key Results: Our results for over vs. underdispersion in functional and phylogenetic diversity differed depending on spatial scale and metric considered. At the county scale, MPD revealed evidence for phylogenetic overdispersion, while MNTD revealed phylogenetic and functional underdispersion, and at the conservation area scale, MPD revealed phylogenetic and functional underdispersion while MNTD revealed evidence only of functional underdispersion., Conclusions: Our results are consistent with environmental filtering playing a larger role at the smaller, conservation area scale. The smaller spatial units are likely composed of fewer local habitat types that are selecting for closely related species, with the larger-scale units more likely to be composed of multiple habitat types that bring together a larger pool of species from across the phylogeny. Several aspects of fern biology, including their unique physiology and water relations and the importance of the independent gametophyte stage of the life cycle, make ferns highly sensitive to local, microhabitat conditions., (© 2018 The Authors. American Journal of Botany is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America.)

The increasing use of phylogenetic methods in community ecology recognizes that accumulated evolutionary differences among species mirror, to some extent, ecological processes. The scope of this work is thus to propose a new method for the measurement of community-level phylogenetic redundancy, which takes into account the branching pattern of the underlying phylogeny. Like for functional redundancy, a measure of phylogenetic redundancy can be described as a normalized measure in the range (0-1) that relates the observed community-level phylogenetic diversity to the value of a hypothetical assemblage with the same abundance distribution of the focal community in which all species had independent evolution. Therefore, phylogenetic redundancy can be interpreted as the diversity decrease that is obtained by taking into account the evolutionary relationships among species in the calculation of diversity. The behavior of the proposed method, for which we provide a simple R function called 'phyloredundancy', was evaluated with published data on Alpine plant communities along a primary succession on a glacier foreland in northern Italy. As shown by our results, the method accounts for the length of shared branches in the phylogeny, producing a coherent framework for describing the evolutionary relationships within a species assemblage. Being based on classical diversity measures, which have been used in ecology for decades, it also has a great potential for future research in phylogenetic community ecology.

The use of phylogenies in ecology is increasingly common and has broadened our understanding of biological diversity. Ecological sub-disciplines, particularly conservation, community ecology and macroecology, all recognize the value of evolutionary relationships but the resulting development of phylogenetic approaches has led to a proliferation of phylogenetic diversity metrics. The use of many metrics across the sub-disciplines hampers potential meta-analyses, syntheses, and generalizations of existing results. Further, there is no guide for selecting the appropriate metric for a given question, and different metrics are frequently used to address similar questions. To improve the choice, application, and interpretation of phylo-diversity metrics, we organize existing metrics by expanding on a unifying framework for phylogenetic information. Generally, questions about phylogenetic relationships within or between assemblages tend to ask three types of question: how much; how different; or how regular? We show that these questions reflect three dimensions of a phylogenetic tree: richness, divergence, and regularity. We classify 70 existing phylo-diversity metrics based on their mathematical form within these three dimensions and identify 'anchor' representatives: for α-diversity metrics these are PD (Faith's phylogenetic diversity), MPD (mean pairwise distance), and VPD (variation of pairwise distances). By analysing mathematical formulae and using simulations, we use this framework to identify metrics that mix dimensions, and we provide a guide to choosing and using the most appropriate metrics. We show that metric choice requires connecting the research question with the correct dimension of the framework and that there are logical approaches to selecting and interpreting metrics. The guide outlined herein will help researchers navigate the current jungle of indices., (© 2016 The Authors. Biological Reviews published by John Wiley © Sons Ltd on behalf of Cambridge Philosophical Society.)

Plant traits can be used to understand a range of ecological processes, including competition with invasive species. The extent to which native and invasive species are competing via limiting similarity or trait hierarchies has important implications for the management of invaded communities. We screened 47 native species that co-occur with Festuca perennis, a dominant invader in California serpentine grassland, for traits pertaining to resource use and acquisition. We then grew F. perennis with 10 species spanning a range of functional similarity in pairwise competition trials. Functionally similar species did not have a strong adverse effect on F. perennis performance as would be expected by limiting similarity theory. Phylogenetic relatedness, which may integrate a number of functional traits, was also a poor predictor of competitive outcome. Instead, species with high specific root length, low root-to-shoot biomass ratio, and low leaf nitrogen concentration were more effective at suppressing the growth of F. perennis. Our results suggest that fitness differences (i.e., trait hierarchies) may be more important than niche differences (i.e., limiting similarity) in structuring competitive outcomes in this system and may be a promising approach for the restoration of invaded systems., (© 2016 by the Ecological Society of America.)

While an increasing number of indices for estimating the functional trait diversity of biological communities are being proposed, there is a growing demand by ecologists to clarify their actual implications and simplify index selection. Several key indices relate to mean trait dissimilarity between species within biological communities. Among them, the most widely used include (a) the mean species pairwise dissimilarity (MPD) and (b) the Rao quadratic entropy (and related indices). These indices are often regarded as redundant and promote the unsubstantiated yet widely held view that Rao is a form of MPD. Worryingly, existing R functions also do not always simplify the use and differentiation of these indices. In this paper, we show various distinctions between these two indices that warrant mathematical and biological consideration. We start by showing an existing form of MPD that considers species abundances and is different from Rao both mathematically and conceptually. We then show that the mathematical relationship between MPD and Rao can be presented simply as Rao = MPD × Simpson, where the Simpson diversity index is defined as 1 - dominance. We further show that this relationship is maintained for both species abundances and presence/absence. This evidence dismantles the paradigm that the Rao diversity is an abundance-weighted form of MPD and indicates that both indices can differ substantially at low species diversities. We discuss the different interpretations of trait diversity patterns in biological communities provided by Rao and MPD and then provide a simple R function, called "melodic," which avoids the unintended results that arise from existing mainstream functions.

Species enter and persist in local communities because of their ecological fit to local conditions, and recently, ecologists have moved from measuring diversity as species richness and evenness, to using measures that reflect species ecological differences. There are two principal approaches for quantifying species ecological differences: functional (trait-based) and phylogenetic pairwise distances between species. Both approaches have produced new ecological insights, yet at the same time methodological issues and assumptions limit them. Traits and phylogeny may provide different, and perhaps complementary, information about species' differences. To adequately test assembly hypotheses, a framework integrating the information provided by traits and phylogenies is required. We propose an intuitive measure for combining functional and phylogenetic pairwise distances, which provides a useful way to assess how functional and phylogenetic distances contribute to understanding patterns of community assembly. Here, we show that both traits and phylogeny inform community assembly patterns in alpine plant communities across an elevation gradient, because they represent complementary information. Differences in historical selection pressures have produced variation in the strength of the trait-phylogeny correlation, and as such, integrating traits and phylogeny can enhance the ability to detect assembly patterns across habitats or environmental gradients., (© 2013 John Wiley & Sons Ltd/CNRS.)

Elucidating the functional and phylogenetic community structures is essential for understanding coexistence of plant species and biodiversity within ecosystems. Despite their significance, the manner in which these structures change along environmental gradients has not been explored extensively. We estimated the phylogenetic diversity (PD) and community-weighted mean (CWM) and functional diversity (FD) values of four key functional traits in 558 grassland plots across the Qinghai-Tibetan Plateau (QTP) and assessed their relationship to climate and soil factors. Our results demonstrate that climate has a more pronounced direct impact on community structures than soil properties. Moreover, the indirect effect of climate through soil conditions does not significantly contribute to the observed patterns in functional and phylogenetic diversity. Annual and seasonal temperature was a reliable predictor of functional structure of plant or organ size traits, especially CWM of leaf size and CWM and FD of plant height. CWM and FD of most leaf traits and PD were correlated positively with multiple precipitation factors and humidity but negatively with sunshine hours. We highlight the importance of temperature, local resource availability and environmental filtering in governing the functional and phylogenetic structures of the QTP grassland communities. These findings have the potential to improve our predictions of climate change impacts on plant community assembly.

Abstract We introduce a new “ecosystem‐scale” experiment at the Cedar Creek Ecosystem Science Reserve in central Minnesota, USA to test long‐term ecosystem consequences of tree diversity and composition. The experiment—the largest of its kind in North America—was designed to provide guidance on forest restoration efforts that will advance carbon sequestration goals and contribute to biodiversity conservation and sustainability. The new Forest and Biodiversity (FAB2) experiment uses native tree species in varying levels of species richness, phylogenetic diversity and functional diversity planted in 100 m2 and 400 m2 plots at 1 m spacing, appropriate for testing long‐term ecosystem consequences. FAB2 was designed and established in conjunction with a prior experiment (FAB1) in which the same set of 12 species was planted in 16 m2 plots at 0.5 m spacing. Both are adjacent to the BioDIV prairie‐grassland diversity experiment, enabling comparative investigations of diversity and ecosystem function relationships between experimental grasslands and forests at different planting densities and plot sizes. Within the first 6 years, mortality in 400 m2 monoculture plots was higher than in 100 m2 plots. The highest mortality occurred in Tilia americana and Acer negundo monocultures, but mortality for both species decreased with increasing plot diversity. These results demonstrate the importance of forest diversity in reducing mortality in some species and point to potential mechanisms, including light and drought stress, that cause tree mortality in vulnerable monocultures. The experiment highlights challenges to maintaining monoculture and low‐diversity treatments in tree mixture experiments of large extent. FAB2 provides a long‐term platform to test the mechanisms and processes that contribute to forest stability and ecosystem productivity in changing environments. Its ecosystem‐scale design, and accompanying R package, are designed to discern species and lineage effects and multiple dimensions of diversity to inform restoration of ecosystem functions and services from forests. It also provides a platform for improving remote sensing approaches, including Uncrewed Aerial Vehicles (UAVs) equipped with LiDAR, multispectral and hyperspectral sensors, to complement ground‐based monitoring. We aim for the experiment to contribute to international efforts to monitor and manage forests in the face of global change.

Incomplete elevational sampling in studies of biodiversity and community assembly along elevational gradients can result in inconsistent findings and potentially inaccurate conclusions about assembly mechanisms. In this study, we conducted extensive sampling of small mammals over a 3200 m elevational gradient on Xiling Snow Mountain, Southwestern China. We integrated functional and phylogenetic diversity to determine the mechanisms structuring small mammal assemblages. Our findings indicate that taxonomic, functional, and phylogenetic diversity, along with all species richness-corrected indices of functional and phylogenetic diversity, exhibit similar hump-shaped patterns. Our results suggest that environmental filtering plays a considerable role in structuring small mammal communities at low and high elevations, while competitive exclusion governs the assembly processes at middle elevations. Human footprint, Normalized Difference Vegetation Index, precipitation seasonality and potential evapotranspiration are key drivers of small mammal diversity and community structure along elevational gradients. In summary, our study provides evidence that phylogenetic diversity is a robust surrogate for functional diversity, and challenges the recent large-scale studies that advocate a linear relationship between small mammal assembly process and elevation. We emphasize the importance of continuously documenting general patterns of small mammal diversity across entire elevational gradients in future studies.

Dry rainforest communities are globally threatened by anthropogenic pressures and climatic change but are less well researched and more poorly conserved than mesic rainforests. In response to the increasing loss of biodiversity, the Australian Government joined other international signatory parties to adopt the Kunming-Montreal Global Biodiversity Framework (GBF). The GBF emphasises the maintenance of connectivity and genetic diversity of whole ecosystems via landscape-scale conservation initiatives. Rainforest plant diversity, distinctiveness, and the current level of conservation of seasonal rainforest regional ecosystems of the Central Queensland Coast region in Australia were evaluated. Our three-marker DNA barcode dated phylogeny of rainforest plant taxa together with community species lists were used to calculate phylogenetic diversity (PD) estimates and species composition. Levels of rainforest ecosystem protection were assessed using Queensland government data. This study found selection pressures for moisture and geology significantly influence rainforest distribution and species diversity and evidence of a high degree of variability in terms of conservation. While some phylogenetically distinctive rainforest community types were well conserved, restricted or endangered communities were very poorly protected. Additionally, we found smaller dry rainforests in the Central Queensland Coast represent regional plant migration but are inadequately protected, highlighting the need for a revision of conservation objectives within the region.

Abstract Background Montane ecosystems play crucial roles as global biodiversity hotspots. However, climatic changes and anthropogenic pressure increasingly threaten the stability of montane community dynamics, such as diversity-elevation interactions, creating a challenge in understanding species biogeography and community ecology dynamics in these crucial conservation areas. We examined how varying sampling spatial grains influence small mammal diversity patterns within Kenya’s tallest montane ecosystems. Methods Employing a combination of multidimensional alpha diversity metrics and multisite beta diversity characteristics (species richness, phylogenetic and functional diversity and divergence, and multisite beta diversity) alongside spatial generalized additive multivariate regression analyses, we tested how spatial scaling influences elevational diversity gradient patterns and their associations with environmental and human activity variables. Results The diversity-elevation associations were generally homogeneous across spatial grains; however, idiosyncratic patterns emerged across mountains. The total (taxonomic, phylogenetic, and functional) beta diversity, nestedness, and turnover resultant components monotonically increased or decreased with varying spatial grains. The associations between the diversity patterns and the environmental and human footprint variables increased with spatial grain size but also presented variations across mountains and indices. Species richness and phylogenetic and functional richness indices were more strongly influenced by spatial scale variations than were the divergence and community structure indices in both the diversity distribution patterns and their associations with the environmental and human variables. Conclusions The diversity-elevation and diversity-environment (including human activity pressure) relationships across spatial grains suggest that montane small mammal diversity patterns portray subtle but systematic sensitivity to sampling spatial grain variation and underscore the importance of geographical context in shaping these elevational diversity gradients. For improved effectiveness, conservation efforts should consider these spatial effects and the unique geographical background of individual montane ecosystems.

The interplay of evolutionary, ecological, and anthropogenic processes is critical in shaping species distributions and biodiversity patterns. Recent studies highlight the importance of examining functional and phylogenetic traits to gain a more comprehensive understanding of these patterns. However, significant knowledge gaps remain regarding functional and phylogenetic diversity patterns among freshwater fish, particularly in the context of large-scale hydrological alterations such as the South-to-North Water Diversion Project (SNWDP). In this study, we investigated the spatial patterns of fish taxonomic, functional, and phylogenetic diversities and community assemblage, alongside their environmental drivers, within five impounded lakes of SNWDP. Our analysis sought to identify relationships between different aspects of diversity, assessing patterns of mismatch or congruence, and evaluating the efficacy of using one aspect as a proxy for another. Our results revealed that: 1) fish diversity and community assembly showed no longitudinal gradient, with spatial mismatches across diversity dimensions; 2) functional diversity was negatively correlated with both taxonomic and phylogenetic diversities, while the latter two showed no correlation; and 3) the SNWDP primarily affected taxonomic and functional diversities by altering water depth, nutrient status and promoting non-native species invasion, while phylogenetic diversity was mainly influenced by changes in water temperature and dissolved oxygen. These findings underscore the distinct contributions of various diversity measures and emphasize that no single measure can reliably predict another, highlighting the necessity of selecting diversity measures tailored to specific questions (e.g., for conservation or fisheries management).

ABSTRACT Understanding the mechanisms associated with community assembly can contribute to explaining the formation and maintenance of biodiversity patterns. In this study, we used the line transect method to survey breeding birds along the three major rivers of the Nandu River, Changhua River and Wanquan River on Hainan Island, south China. The patterns of community assembly were subsequently assessed by integrating functional and phylogenetic diversity, whereas environmental factors and interspecific competition intensity were incorporated to determine whether community assembly in these rivers is driven by environmental filtering or interspecific competition. Our findings revealed that bird communities within rivers were characterized by an overall slight clustering (i.e., more similar species), with the upper reaches of the Changhua River and the lower reaches of the Nandu River showing over‐dispersion, whereas the lower, middle, and upper reaches of the Wanquan River all showed clustering. Altitude and the human influence index were identified as the main factors driving bird community assembly within the three major rivers. Notably, for bird communities along different river reaches, the integration of functional and phylogenetic diversity prevented the mis‐classification of over‐dispersion or clustering in community structure caused by traits with weak phylogenetic signals, or the observation of traits unrelated to community assembly patterns. This empirical study demonstrates the importance of integrating functional and phylogenetic diversity, which not only contributes to gaining an understanding of the mechanisms underlying the development of community assemblies but also facilitates a determination of the extents to which function and phylogeny contribute to shaping the patterns of communities.

Abstract Animals perceive their ecosystems at multiple spatial scales such that the pattern–process relationships that determine their ecological and evolutionary opportunities are also spatially variable. Understanding how spatial scale impacts our observations of ecological and evolutionary patterns and processes is therefore crucial for effective biodiversity management. In this study, using a comprehensive dataset of small mammals from primary field surveys supplemented with literature data across Kenya, we investigated the effects of spatial scale on the distribution patterns of taxonomic, phylogenetic, and functional diversity indices. We also tested how relationships between taxonomic, phylogenetic, and functional diversity and various environmental and anthropogenic variables change across spatial scales. The results showed that with increasing spatial scale, species richness and phylogenetic and functional richness consistently increased. Community‐wide mean pairwise distance indices for phylogenetic and functional dimensions also increased, while fine‐scale mean nearest taxon distance indices decreased. Notably, community structure indices exhibited nonmonotonic patterns across spatial scales. The associations between diversity patterns and environmental and human covariates increased with scale but were more variable and complex across regions. These findings highlight a negative correlation between spatial scale and phylogenetic and functional divergence while reinforcing the species‐area hypotheses for richness‐dependent diversity indices. Identifying the optimal scales of field studies and conservational actions must factor in the species group of interest and the geographical context.

Understanding the spatial distribution characteristics and underling mechanisms of taxonomic, phylogenetic and functional diversity is crucial for advancing global biodiversity conservation. Here, we investigated the latitudinal and longitudinal patterns of multifaceted biodiversity of montane forest in a biodiversity hotspot, South-Central China. Multiple linear regression and hierarchical analysis were used to identify the critical factors affecting biodiversity. The results concluded that the latitudinal patterns of taxonomic, phylogenetic, and functional diversity were congruent with the latitudinal diversity gradient from the equator to the poles. Climatic and edaphic factors, particularly precipitation, played a crucial role in spatial patterns of biodiversity. Climatic and edaphic variables simultaneously explained 48%-66% of the spatial variation of multidimensional diversity, except Rao’s phylogenetic quadratic entropy. There were significant associations among multiple measures of diversity in subtropical montane forests. High water availability and low seasonal variation underlie the greater coexistence of tree species at low latitudes. These results present robust evidence for congruent latitudinal patterns of taxonomic, phylogenetic, and functional diversity, and provide a striking explanation that the same filtering effects of precipitation result in positive relationships among multifaceted diversity. Species richness might be a reliable indicator of taxonomic, phylogenetic, and functional diversity, and may be reasonably applied for conservation planning and forest management in subtropical montane regions.

Abstract Increases in the frequency, intensity, and duration of extreme climate events (ECEs) are already impacting ecosystems, with many of the strongest effects associated with high‐elevation areas. Most research on the ecological impacts of climate change has focused on climatic averages, which might differ from ECEs. Rhododendron, a diverse genus of alpine and subalpine woody plant, plays a crucial role in ecosystem stability and biodiversity in the biodiversity hotspots of the Himalayas and Hengduan Mountains. Here, we compared the predicted impacts of average climate with those including ECEs on 189 Rhododendron species in China for the historical period (1981–2010) and the future period (2071–2100) under two emissions scenarios (SSP2‐4.5 and SSP5‐8.5). We analyzed changes in suitable habitat and patterns of species richness, weighted endemism, and phylogenetic diversity, identifying areas of coinciding high‐risk as priority conservation areas. Inclusion of ECEs altered the projected areas of suitable habitat across all species from an increase of over 3% to a decrease exceeding 10%, with the distribution of most Rhododendron species strongly influenced by extremes of drought and high temperatures. We found fewer than 18% of high‐risk areas of diversity loss were currently protected, with priority conservation areas mainly located in the Daxue, Daliang, Wumeng, and Jade Dragon Snow Mountains, as well as in the Nyingchi. We suggest inclusion of ECEs is critical when projecting changes in alpine and subalpine species distributions for effective conservation planning for climate change.

Abstract Background Mountain ecosystems are critical hotspots of global biodiversity, yet the dynamics of community assembly along their elevational gradients are not well understood. This gap is primarily due to the complexity of environmental and biotic interactions that influence species distribution and community structure. Although extensive research has been conducted on certain taxa, such as small mammals and bats, comprehensive studies encompassing entire mammal assemblages are lacking. Our research aims to bridge this gap by examining the taxonomic, phylogenetic, and functional diversity, as well as the assemblage structures of mammal communities across elevational gradients in the Central and East Himalayas, exploring how diverse ecological and evolutionary processes impact community assembly. Methods We analyzed mammal elevational diversity patterns using species richness, functional diversity (FD), and phylogenetic diversity (PD). We compared the observed values of community structure, such as mean pairwise phylogenetic distance (MPD) and mean pairwise functional distance (MFD), with null-model corrected effect sizes to identify patterns and processes of community assembly. Using structural equation modeling and hierarchical partitioning, we investigated the relationships between climate, productivity, and various facets of diversity, describing the organization of each component across different elevations. Results Taxonomic, functional, and phylogenetic diversity generally decreased with elevation but showed varied patterns such as mid-elevation peaks, low-elevation plateaus, or monotonic declines across different regions. Richness-controlled functional diversity increased towards mid-low elevations and decreased at higher elevations in both regions, whereas richness-controlled phylogenetic diversity lacked consistent patterns. Phylogenetic structures tended to cluster from mid to high elevations, indicating closer relationships than those observed in random communities, likely due to significant environmental turnover near tree lines. Functional structure showed greater clustering at high elevations and increased over-dispersion at lower elevations, suggesting that species are more functionally similar than expected at higher elevations and more diverse at lower elevations. Our results revealed that environmental factors, evolutionary histories, and trait-driven ecological processes collectively shape species richness along these gradients. Conclusions Our results showed incongruent community structures across phylogenetic and functional diversity. Generally, functional traits are closely linked to environmental conditions, reducing the chance of observing traits that are misaligned with their surroundings. Species with similar ecological roles or distinct evolutionary lineages often show convergent adaptations to highland environments. Additionally, our findings emphasize that community assembly varies with the biogeography and diversification history of individual mountain ranges, complicating the development of a generalized theory. Using multiple measures is important for accurate community structure assessments and effective conservation planning, as variable elevational patterns exist across different diversity dimensions.

Topographic complexity supports the maintenance of a high diversity of microhabitats, which may act as important ‘safe havens’ – or microrefugia – for biodiversity. Microrefugia are sites with specific environmental conditions that facilitate the persistence of species during environmental changes and exhibit unique eco-evolutionary dynamics. However, our knowledge about how topographic complexity and related eco-evolutionary selective forces influence the functional and phylogenetic signatures of species assemblages in microrefugia is very limited. Although the conceptual framework on the systematic integration of plant functional traits into the study of refugia is well established, more empirical studies on functional trait composition and functional diversity in refugia are urgently needed for more effective conservation. Here we analyzed the distribution of various plant functional traits and phylogenetic patterns in microhabitats (south- and north-facing slopes, and bottoms) of 30 large topographic depressions (i.e. doline microrefugia) and microhabitats of the surrounding plateaus in two distant forested karst regions. We found that plant assemblages in the understory of dolines and their surroundings are characterized by unique functional values and combinations of traits. Doline bottoms had the highest functional diversity among doline microhabitats and supported plant assemblages with considerably different trait compositions from the plateaus. Bottoms also had the highest phylogenetic diversity. These results suggest that topographic complexity in forested dolines has a significant effect on the distribution of plant functional traits in the understory. High functional and phylogenetic diversity in doline bottoms can have important consequences for the long-term survival of plant populations, highlighting that these microhabitats may provide a higher resilience and support an adaptive community-level response to natural and anthropogenic stressors. Understanding mechanisms that drive the survival of species within microrefugia is required to determine the best conservation and management strategies.

ABSTRACT Interactions between plants and insects have long fascinated scientists. While some plants rely on insects for pollination and seed dispersal, insects rely on plants for food or as a habitat. Despite extensive research investigating pair‐wise species interactions, few studies have characterized plant and insect communities simultaneously, making it unclear if diverse plant communities are generally associated with diverse insect communities. This work aims to better understand the historical and evolutionary relationships between plant and insect phylogenetic diversity (PD) on islands. We hypothesized that phylogenetically diverse plant communities (i.e., high PD) support diverse insect communities, with the relationship varying with island isolation, area, age, and latitude. Species lists for plants and insects were compiled from the published literature, and plant PD was calculated using ´standardized mean pairwise distance´ (SES.MPD) and ´standardized mean nearest taxon distance´ (SES.MNTD). For insects, PD was estimated using the number of genera, families, and orders. We found that plant diversity in evolutionary recent times (SES.MNTD) is associated with recent insect diversity (number of genera), but no relationship was found between plant and insect diversity across whole phylogenies (plant SES.MPD vs. number of insect families). Distant islands generally support high PD of plants (high SES.MPD and SES.MNTD) and insects (low number of genera). Plant and insect PD was generally high on small islands, except for plant SES.MPD revealing no relationship with island size. Insect PD was somewhat higher on young islands (low number of families), whereas there was no relationship between island age and plant PD. Plant SES.MPD was higher on high latitude islands, yet we did not find significant relationships between the latitude and the metrics of insect PD or plant SES.MNTD. These findings suggest that protecting high plant PD may also help conserve high insect PD, with a focus on small and distant islands as potential hotspots of phylogenetic diversity across multiple taxa.

Cycas fairylakea is an endemic and Level-One National Key Protected Wild Plant in China. It is distributed in the Meilin Reservoir and Tanglangshan Country Park in Shenzhen. This study investigated two newly discovered wild populations in Taishan and Yangjiang, Guangdong Province. The forest community characteristics and population structure of these newly discovered populations remain unknown, and the sex ratio as well as the species’ responses to environmental factors have never been reported, despite their importance for the in-situ conservation of this Cycad. We conducted a comprehensive investigation of the ecological traits (soil properties, community characteristics, and phylogenetic diversity) and population characters (size, age structure, sex ratio, and spatial pattern) of C. fairylakea and determined the impact of environmental factors on the age structure and sex ratio. The results showed that the species number and composition of the two communities differed, yet no significant differences were observed in the plant diversity indices, with close phylogenetic affinities among species. Moreover, the sex ratio, determined by the MADS-Y marker, was relatively balanced. The age structure of the two populations exhibited a “reverse-J” shape, and the survival curves were of the Deevey’s type III, indicating low natural regeneration capacities with high mortality in the early stage. Redundancy analysis identified the soil properties as constraining factors of the C. fairylakea sex ratio, while climate factors and community species diversity and evenness indices positively impacted the sex ratio. The combined effects of soil, climate, topography, and shrub layer plant diversity were the main factors influencing the age structure and sex ratio of the C. fairylakea populations. A balanced sex ratio ensures reproductive capacity, which maintains population stability. However, the structural and numerical characteristics of C. fairylakea in the two regions are constrained by environmental pressures. The implementation of well-considered artificial conservation strategies and the safeguarding of the habitat are intended to bolster the survival rate of the seedlings, promote the healthy growth of middle-aged individuals, and maintain the sustained stability of the natural population of C. fairylakea.

Secondary forests represent an increasing proportion of global forest cover and offer a range of ecosystem services that are integral to environmental policy targets. Highly disturbed landscapes with temporal records of forest plant community composition offer key insights into the processes that shape plant communities as forests undergo secondary succession. We investigated patterns of plant community phylogenetic structure and phylogenetic beta diversity. Mean pairwise distance (MPD) and Mean Nearest Taxon Distance (MNTD) metrics were determined between co-occurring species within plant communities, in addition to phylogenetic beta diversity metrics relative to null models of random phylogenetic assembly. MPD and MNTD were compared between elevational and successional classes and modelled as products of intercommunity distance (metres) and forest community age (years). Phylogenetic nonmetric multidimensional scaling explored phylogenetic community structure between lowland and montane forest type in Hong Kong. We found that plant communities in secondary forests in Hong Kong exhibited patterns of increased basal phylogenetic clustering with increasing community elevation, while phylogenetic turnover was influenced by spatial and successional factors in lowland and montane forest. Our findings indicate differential community assembly in lowland compared to montane forest type in Hong Kong, as well as evidence for barriers to plant dispersal in secondary forest communities due to patterns of spatial phylogenetic clustering. Plant communities in montane forests were found to be phylogenetically distinct from lowland forest plant communities. Patterns of spatial phylogenetic clustering may suggest significant dispersal or post-dispersal processes causing the clustering of related species at fine spatial scales, while phylogenetic turnover with increasing successional age may indicate compositional changes during the process of passive forest regeneration. Collectively, these results emphasize the need to investigate active pathways for rewilding dispersal limited late successional forest tree species in Hong Kong.

Urbanization is resulting in habitat loss and fragmentation around the world, but its effects on biodiversity remain poorly understood. We investigated how the increase of urban cover surrounding nine Brazilian Atlantic forest reserves (14 ha - 1058 ha) affects the taxonomic, functional and phylogenetic diversity of bird communities, considering forest and non-forest species separately. Using a multi-scale local landscape approach, we estimated the percentage of urban cover in circular buffers of varying radii (200–1000 m). We calculated 10 complementary metrics of bird diversity and modelled them against the percentage of urban cover using generalized additive models. Urbanization had a negative, non-linear impact on the taxonomic diversity of bird communities, with a sharp decrease of up to 50 % in the effective number of rare, typical and dominant species in landscapes with 20–40 % of urbanization. This decrease was not restricted to forest species (urban avoiders), but also affected non-forest ones (urban utilizers and dwellers). The impact of urbanization on functional and phylogenetic diversity were less evident, suggesting that the vulnerability to urbanization has a weak phylogenetic and phenotypic signal. We conclude that urbanization impacts a broad spectrum of bird clades and traits and drastically reduce the taxonomic diversity of bird communities.

ABSTRACT While the link between plant species diversity and biomass has been well‐studied, the impact of evolutionary diversity on community biomass across long timescales or ongoing change remains a subject of debate. We elucidated the association between evolutionary diversity and community aboveground biomass (AGB) using an ideal experimental system with over 150‐year history of natural vegetation regeneration. Higher phylogenetic diversity facilitated the sampling effect under the influence of environmental filtering, and caused an increase in AGB. Phylogenetic structure varied from aggregation to dispersion during the later period of vegetation recovery (70–150 years), which was correlated with increases in niche complementarity and increasing AGB. Woody plant evolutionary diversity was used as a key to predict the relationship between vegetation recovery and AGB, with a total explanatory power of ~84.7%. Mixed forests composed of evergreen conifers and deciduous broadleaf forests had higher carbon sequestration potential than that of pure forests, which is advantageous for increasing top‐stage AGB. This research expands our knowledge of the causes and effects of biodiversity and ecosystem function dynamics over time and space, which is important for accurately predicting future climate change effects.

Understanding the dynamics and spatial patterns of forest biodiversity and functioning is vital for effective conservation and management. This study introduces a new framework for estimating the spatio-temporal dynamics of biodiversity and ecosystem functions in northeastern China. Our novel approach evaluates 96 future scenarios, including four points in time, four socio-economic pathways, and six global climate models based on an extensive network of permanent field plots with specific bioclimatic, topographic, and soil data. Our findings indicate a future trend of diminishing biodiversity and forest biomass productivity and increasing biomass density and carbon storage. The relationship between biodiversity and ecosystem functionality indicates a non-linear response to changes in temperature and precipitation, and a stable correlation between biodiversity and ecosystem stability across most of the socio-economic pathways. Unravelling the complex relationship between biodiversity, ecosystem functions, and stability of production, in the face of global change, requires new methods of analysis that were used in this study, including machine learning and other advanced methods.

Marine protected areas are set up across the globe to safeguard biodiversity and support coastal ecosystem functioning. In Hong Kong, partially protected marine parks and a no-take marine reserve have been managed under legislation for years, yet a comprehensive evaluation of their conservation impact is still pending despite the region’s reputation for high marine diversity. Most studies assess conservation effectiveness solely in terms of taxonomic diversity, without delving into the contributions of functional and phylogenetic diversity. In this study, we used environmental DNA combined with multifaceted diversity indicators to assess the impact of the level of protection on the fish community in Hong Kong waters. Our results indicated that the marine protected areas significantly contributed to fish community conservation. The no-take marine reserve exhibited the highest taxonomic and phylogenetic diversity, while partially protected marine parks showed the most balanced community composition. No significant increase in fish functional diversity was found in the protected areas. Water quality, hydrological condition, and protection level were the primary factors affecting community variation for taxonomic, functional, and phylogenetic diversity, respectively. Fish species composition significantly varied with different protection levels, and species turnover was the main component of the dissimilarity. Future management of marine protected areas should assess multifaceted biological indicators and establish a rational conservation scheme.

Unraveling the complexity of the diversity-productivity relationship (DPR) is a pivotal task in ecology, necessitating extensive long-term research. Regrettably, the scarcity of long-term permanent plots poses a significant obstacle to our comprehension of how DPR evolves over time. To bridge this gap, we conducted a thorough analysis utilizing data from 110 permanent plots in natural mixed forests in northeastern China, spanning seven periods from 1987 to 2017. We employed Random Forest (RF) and composite structural equation models (SEMs) to delve into the intricate relationships among diversity, topography, climate, and productivity. Our primary objective was to assess the relative contributions of species diversity, structural diversity, and phylogenetic diversity.Our findings revealed a notable negative correlation between species diversity and productivity, whereas phylogenetic diversity exhibited a positive influence on productivity. It is noteworthy that the impact of structural diversity did not prove to be significantly influential. Furthermore, we emphasize the paramount importance of phylogenetic diversity, highlighting its crucial role in shaping DPRs and underscoring its significance in sustainable forest management.

Acoustic indices are cost-efficient tools for monitoring acoustically active taxa. Despite their increasing popularity, their suitability as biodiversity proxies remains debated due to theoretical and practical issues. Existing research has predominantly focused on assessing their capacity to capture species richness and abundance of sounds, with limited attention given to other biodiversity facets like phylogenetic and functional diversity. Yet, phylogenetic distance and trait diversity may influence acoustic communication, so acoustic indices may be better suited to capture their changes than changes in the mere number of species. Here, we investigated the ability of acoustic indices to represent the species, phylogenetic, and functional diversity of acoustically active avian species across three habitat types in Italy: urban, riparian forest and deciduous woodland.Recordings were collected at dawn by a trained ornithologist, who also identified acoustically active species captured, first in the field and secondarily from recordings. We then applied eleven widely used acoustic indices for each recording and tested their ability to capture differences in species, functional and phylogenetic diversity across sites (i.e., listening points) within each habitat type using a linear mixed effect model. We then reduced the acoustic indices dimensionality to a few axes and repeated the analysis to test if compound indices delivered comparable information.Species richness and phylogenetic diversity correlated with at least one acoustic index across the three habitat types, while functional diversity correlated with an index only in the urban habitat. However, the nature of the relationships identified was often opposite to what expected by the indices’ formulation. Furthermore, across the three habitat types the interrelations among indices varied, as well as the observed relationships with diversity indices. Compound indices also exhibited inconsistent relationships across sites and contrary to what expected based on their correlation with acoustic indices.Our results cast doubts on the suitability of acoustic indices as proxies for biodiversity for biodiversity monitoring. Additionally, the inconsistent relationship among indices across the three areas suggests they are unsuitable for geographic comparisons. Temporal comparisons are possible but require local validation and may need adjustments over time of the community composition changes. Despite the attractiveness of acoustic indices as easy and cheap tools for biodiversity monitoring, we urge caution on their application.

Birds are sensitive to environmental changes and can drive range shifts rapidly due to their high mobility. Though previous studies have examined the associations between species traits and range shifts, whether species traits could still explain heterogeneity in shift directions remains poorly explored. Here, we compiled new bird records of China from 2000 to 2019 and analyzed species traits associated with apparent shift directions. We collected 350 provincial-level new records of birds belonging to 67 families of 22 orders. Of these, 32 are threatened, with 3 critically endangered, 11 endangered, and 18 vulnerable. Provinces in western China (i.e., Yunnan and Xizang) had relatively higher species richness of new recorded birds; this pattern was also reflected in the phylogenetic diversity we observed. In addition, provinces in northern China (i.e., Tianjin, Shandong, and Beijing) had relatively higher richness-controlled phylogenetic diversity. Phylogenetic overdispersion of new recorded bird communities was observed in 61.29% of provinces (19 of 31). The main shift directions indicated by new bird records were northward (with nearly 50% of birds moving NW, N and NE). Migration, hand-wing index (HWI), body mass, and range size are the four key factors that most significantly influence the shift directions in bird species, suggesting that bird movement toward newly suitable areas varies with species-specific traits. Together, these results demonstrate the importance of considering species ecological traits when predicting shift directions of birds.

Abstract Vegetation characteristics are an important proxy to measure the outcome of ecological restoration and monitor vegetation changes. Similarly, the classification of remotely sensed images is a prerequisite for many field ecological studies. We have a limited understanding of how the remote sensing approach can be utilized to classify spontaneous vegetation in post‐industrial spoil heaps that dominate urban areas. We aimed to assess whether an objective a priori classification of vegetation using remotely sensed data allows for ecologically interpretable division. We hypothesized that remote sensing‐based vegetation clusters will differ in alpha diversity, species, and functional composition; thereby providing ecologically interpretable division of study sites for further analyses. We acquired remote‐sensing data from Sentinel 2A for each studied heap from July to September 2020. We recorded vascular plant species and their abundance across 400 plots on a post‐coal mine in Upper Silesia, Poland. We assessed differences in alpha diversity indices and community‐weighted means (CWMs) among remote sensing‐based vegetation units. Analysis of remotely sensed characteristics revealed five clusters that reflected transition in vegetation across successional gradients. Analysis of species composition showed that the 1st (early‐succession), 3rd (late‐succession), and 5th (mid‐succession) clusters had 13, 10, and 12 exclusive indicator species, respectively, however, the 2nd and 4th clusters had only one species. While the 1st, 2nd, and 4th can be combined into a single cluster (early‐succession), we found the lowest species richness in the 3rd cluster (late‐succession) and the highest in the 5th cluster (mid‐succession). Shannon's diversity index revealed a similar trend. In contrast, the 3rd cluster (late‐succession) had significantly higher phylogenetic diversity. The 3rd cluster (late‐succession) had the lowest functional richness and the highest functional dispersion. Our approach underscored the significance of a priori classification of vegetation using remote sensing for vegetation surveys. It also highlighted differences between vegetation types along a successional gradient in post‐mining spoil heaps.

Abstract Mediterranean landscapes were drastically affected by high levels of abandonment of agricultural and other land practices during the last century. These changes in land use can have significant effects on diversity patterns by altering disturbance and competition equilibria within plant communities at the landscape level. Particularly, such changes have been found to affect the patterns of phylogenetic diversity and structure by causing nonrandom losses of species through filtering effects and landscape homogenization. By investigating diversity patterns across a region submitted to high levels of land use changes, located in a (sub‐) mountainous area of northwestern Greece (northern Pindus), we aimed at understanding the patterns of phylogenetic diversity and structure in relation to land abandonment and the subsequent recovery of natural vegetation. We sampled 250 vegetation plots equally divided in grasslands and forests, distributed across the different classes of land use occurring in the general study area based on the period since the last change in land use. Standardized metrics of Faith's phylogenetic diversity, mean phylogenetic distance, and mean nearest taxon distance were used to investigate phylogenetic diversity patterns across communities and different land‐use regimes. A Principal Coordinates of Phylogenetic Structure analysis was employed to evaluate the variation in lineage composition among communities, and boosted regression trees were used to identify the relative influence of community differentiation (as captured by the classification of sampling plots in ecologically and floristically distinct vegetation communities), plant life strategies (competition, stress tolerance, and disturbance), and climatic, topographic, and soil variables on phylogenetic diversity metrics. Community differentiation was identified as the main driver of phylogenetic patterns. Additionally, phylogenetic diversity and structure were observed as having a statistically significantly negative correlation with disturbance, a statistically significantly positive correlation with stress tolerance, and a weaker positive correlation with competition. Phylogenetic clustering was observed for the early successional grassland communities submitted to stronger effects of disturbance, while phylogenetic randomness (or rarely overdispersion) was observed in forest communities submitted to stronger effects of competition. Finally, phylogenetic clustering of grassland communities was more evident shortly after land abandonment.

Abstract Inundations in Amazonian black‐water river floodplain result in the selection of different tree lineages, thus promoting coexistence between species. We investigated whether Amazonian tree communities are phylogenetically structured and distributed along a flooding gradient from irregularly flooded forests along streams embedded within upland (terra‐firme) forest to seasonally flooded floodplains of large rivers (igapós). Floristic inventories and hydrological monitoring were performed along the Falsino River, a black‐water river in the eastern Amazon within the Amapá National Forest. We constructed a presence‐and‐absence matrix and generated a phylogeny using the vascular plant database available in GenBank. We calculated the standardized values of the metrics of phylogenetic diversity (ses.PD), average phylogenetic distance (ses.MPD), and average nearest‐neighbor distance (ses.MNTD) to test whether the history of relationships between species in the community is influenced by inundation. We used the phylogenetic endemism (PE) metric to verify the existence of taxa with restricted distribution. Linear regressions were used to test whether phylogenetic metrics have a significant relationship with the variables: maximum flood height, maximum water table depth, and maximum flood amplitude. The results show that forests subject to prolonged seasonal flooding have reduced taxon richness, low phylogenetic diversity, and random distribution of lineages within communities. On the other hand, terra‐firme riparian forests showed higher rates of taxon richness, diversity, and phylogenetic dispersion, in addition to greater phylogenetic endemism. These results indicate that seasonal and predictable soil flooding filters tree lineages along the hydrographic gradient. Different adaptations to root waterlogging are likely requirements for colonization in these environments and may represent an important factor in the diversification of tree lineages in the Amazon biome.

An adequate description of biodiversity patterns requires an integration of different biological dimensions, including phylogenetic, functional, and taxonomic patterns. In this sense, dimensionality is defined as the number of complementary dimensions represented by metrics necessary to describe diversity in a non-redundant and effective way, with a correlation component (Evenness of Eigenvalues- EE) and the variation component (Importance Values- IV). Here we describe the dimensionality of global diversity patterns for sharks, based on several metrics of taxonomic, functional, and phylogenetic dimensions and the spatial patterns in dimensionality across marine biogeographic realms. We also investigated the relationship between dimensionality and emergent characteristics of each realm, including total richness, body size, area, latitude, and environmental dimensionality. Realm area and latitude were important ecological predictors of the dimensionality correlation component in realms. Phylogenetic diversity was the metric that contributed most to variation in the fundamental space of biodiversity, globally and within realms, highlighting the importance of evolutionary history in structuring shark communities. This is the first work on the diversity dimensionality of sharks, revealing important diversity patterns of the taxon and potential biological and ecological mechanisms related to the phenomenon of dimensionality.

Research on understory plant diversity and its response to environmental factors helps in the sustainable development of plantation forests. We investigated the characteristics of understory plant diversity in Eucalyptus plantation forests located in Dongfang, Ding'an, Tunchang, and Lingao on Hainan Island by leveraging the plot survey method, and analyzing how the understory plant diversity in these Eucalyptus plantation forests responds to environmental factors. The results showed that a total of 124 plant species belonging to 62 families and 112 genera were recorded in the sampled plots of the Dongfang, Ding’an, Tunchang, and Lingao regional sites on Hainan Island, among which species of Fabaceae and Poaceae comprised the largest number of plants. The number of species and plant diversity indices of the shrub layer and herb layer in Eucalyptus plantation forests varied at different sites, The richest understory vegetation in Tunchang, located in the center of Hainan Island, and the highest α-diversity whether gauged by species or phylogenetically. The similarity of the understory plant community species was greatest between Ding’an and Tunchang, whereas the difference in composition was largest between Dongfang and the other three sites. Phylogenetically, the understory plant community at Ding’an had the most distant affinities among species, whereas that at Tunchang had the closest affinities among species. The results of the Mantel test and redundancy analysis revealed differing correlations between plant diversity in the shrub layer versus herb layer and various environmental factors. In particular, elevation and annual average temperature are the two main factors influencing plant diversity in the shrub layer, and soil available nitrogen and annual average sunshine duration are the two main factors influencing plant diversity in the herb layer. Variance decomposition showed that the combined effect of soil, climate, and topography factors is the main driver shaping plant diversity in the shrub layer of the understory in Eucalyptus plantation forests, while the combined effect of climate and soil factors is the main one determining plant diversity in their herb layer.

Abstract Forest soils are a critical component of terrestrial ecosystems and host a large number of animal decomposer species. One diverse and abundant decomposer taxon is oribatid mites (Acari: Oribatida), whose species composition varies with forest type and tree species composition. We used functional traits that indicate different niche dimensions, to infer assembly processes of oribatid mite communities in monocultures and mixed forests of native and introduced tree species. We found that coexisting species differed more in the resource‐related niche dimension, i.e., reproductive mode and trophic guild, than in the morphological dimension, e.g., body length and width, sclerotization and concealability. These results suggest that both filtering and partitioning processes structure oribatid mite communities. In native European beech forests, but not in non‐native Douglas fir forests, oribatid mites were mainly structured by filtering processes acting via traits related both to environmental tolerance and to resources. Furthermore, oribatid mite trait diversity, but not phylogenetic diversity, differed significantly between monocultures and mixed forests, demonstrating that multidimensional diversity indices provide additional information on soil biodiversity. Overall, the study provides evidence that traits representing different niche dimensions need to be considered for understanding assembly processes in soil animal communities and thereby soil biodiversity.

Climate factors can impact the multifunctionality of steppe ecosystem by altering plant diversity. The pivotal role of diversity in mediating these effects is of paramount importance. Given that various facets of plant diversity exhibit diverse responses to climate change and impart distinct impacts on steppe ecosystem multifunctionality, the elucidation of how different dimensions of diversity mediate the effects of climate factors on steppe ecosystem multifunctionality assumes significance. The study area of this research was the typical steppe in Hulun Buir. Its main objective was to examine the direct and indirect impacts of climate factors on plant diversity and ecosystem multifunctionality. The findings showed that, in terms of the role played by climatic factors, precipitation had a greater effect on species diversity, while functional diversity and phylogenetic diversity were mainly influenced by temperature. The impact of climatic factors on below-ground ecosystem multifunctionality was notably substantial. With regard to the mediating role of plant diversity, species diversity played a greater role in moderating the effects of climatic factors on above- and below-ground ecosystem multifunctionality, while functional and phylogenetic diversity were important in mediating the effects of above- and below-ground ecosystem multifunctionality, respectively. To summarize, this study elucidates the correlation between multiple plant community diversities and ecosystem multifunctionality in a typical steppe under climate change, along with the potential mechanisms through which plant diversity moderates the influence of climate factors on ecosystem multifunctionality. Overall, species diversity and functional diversity take precedence over phylogenetic diversity, which can better predict the ecosystem multifunctionality of steppe and provide guidance for the conservation and sustainability of steppe plant diversity.

Climate refugia, where local populations of species can persist through periods of unfavorable regional climate, play a key role in the maintenance of regional biodiversity during times of environmental change. However, the ability of refugia to buffer biodiversity change may be mediated by the landscape context of refugial habitats. Here, we examined how plant communities restricted to refugial sky islands of alpine tundra in the Colorado Rockies are changing in response to rapid climate change in the region (increased temperature, declining snowpack, and earlier snow melt-out) and if these biodiversity changes are mediated by the area or geographic isolation of the sky island. We resampled plant communities in 153 plots at seven sky islands distributed across the Colorado Rockies at two time points separated by 12 years (2007/2008–2019/2020) and found changes in taxonomic, phylogenetic, and functional diversity over time. Specifically, we found an increase in species richness, a trend toward increased phylogenetic diversity, a shift toward leaf traits associated with the stress-tolerant end of leaf economics spectrum (e.g., lower specific leaf area, higher leaf dry matter content), and a decrease in the functional dispersion of specific leaf area. Importantly, these changes were partially mediated by refugial area but not by geographic isolation, suggesting that dispersal from nearby areas of tundra does not play a strong role in mediating these changes, while site characteristics associated with a larger area (e.g., environmental heterogeneity, larger community size) may be relatively more important. Taken together, these results suggest that considering the landscape context (area and geographic isolation) of refugia may be critical for prioritizing the conservation of specific refugial sites that provide the most conservation value.

Community assembly theory hypothesizes that two main niche-based processes act to shape composition and organization of biological assemblages: abiotic filtering and biological interactions. Here, we conducted repeated surveys of bird abundance along an undisturbed elevational gradient in the tropical Andes to investigate 1) signals of deterministic processes driving community assembly and 2) potential mechanisms by which these forces operate (temperature, habitat complexity, fruit and insect availability), while correcting for imperfect detection and modeling species abundances with N-mixture models. We observed strong signals of abiotic filtering driving functionally and phylogenetically clustered assemblages towards higher elevations, and a weaker signal of limiting similarity resulting in few overdispersed assemblages at lower elevations. Whereas the decay in species richness with increasing elevation was explained by temperature, trait and phylogenetic dispersion were explained by both temperature and vegetation structure, implying that an interplay of abiotic and biotic mechanisms determines abundance-based community structure in our montane assemblages. Interestingly, trait and phylogenetic dispersion consistently decreased until ~3000 m but increased above this elevation, highlighting a potential role of competition in resource-scarce habitats. Combined, our findings suggest abiotic filters are still the main process shaping montane biotas across elevations, whereas resource availability might act locally upon assemblages further modifying them. Our study challenges recent studies in tropical mountains that suggest that biotic filters are a stronger force than abiotic filters in shaping tropical montane assemblages, and exemplifies how accounting for imperfect detection might overcome potential biases in detecting environmental filtering signals in community assembly studies.

The biodiversity of agricultural landscapes is under significant threat, while non-agricultural habitats within these landscapes play a crucial role in biodiversity conservation. There has been limited investigation into how plant species, functional and phylogenetic diversity varies across different seasons and habitats in agricultural landscapes. Thus, we carried out a survey of the plant communities in non-agricultural habitats in China's lower Yellow River plain. We investigated the diversity features of plant functionality, phylogeny, and plant species. We compared differences in plant community structure using non-metric multidimensional scaling analysis and tested phylogenetic signal using phylogenetic methods. Our analysis of plant community and diversity characteristics revealed significant differences in plant community structure between seasons and habitats, with the season having a more significant impact. The levels of plant species, functional, and phylogenetic diversity followed a seasonal pattern, with spring seeing the highest values and autumn seeing the lowest. Woodland and hedgerow habitats had the highest levels of diversity, while field roads had the lowest. The community phylogenetic structure of non-agricultural habitats was relatively concentrated and mainly influenced by human interference and environmental filtering. These findings offer scientific support for the preservation of ecosystem services and biodiversity in agricultural landscapes.

Habitat loss is among one of the main causes of biodiversity decline worldwide. Therefore, assessing different dimensions of diversity such taxonomic, phylogenetic, and functional is important for more effective conservation strategies. Also, important but scarce, is the comparison of different life-stages which can bring insights due to different time delay on species responses to anthropogenic changes. Herein we assessed the influence of landscape-scale forest cover loss on different diversity dimensions of adult and juvenile tree assemblages. Our results showed that richness, phylogenetic and functional diversity were highly correlated for both life-stages. Forest cover loss leads to a decline in species richness more sharply in juveniles than adults, but in general, it did not affect phylogenetic and functional diversity. The responses among life-stages differed only for richness and phylogenetic mean pairwise distance. The negative impacts of forest cover loss on richness were not mirrored by phylogenetic and functional diversity, although there are some differences among life-stages. Our findings suggest that for practical purposes species richness is a primary and effective biodiversity measure at the landscape-scale. Furthermore, the stronger effects on juvenile assemblages indicate recruitment limitation and an impoverished future plant community, highlighting the importance to include different life-stages into conservation actions.

Understanding the process underlying the spatial gradients in biodiversity is a fundamental issue in ecology. Altitudinal gradients are ideal systems for examining the community assembly process because they represent rapid changes in environmental conditions over relatively short distances. The functional and phylogenetic approaches allow a deeper mechanistic understanding of the underlying assembly process. However, whether community assembly from montane to alpine zones is driven more by ecological constraints or human settlement patterns is not fully resolved and may vary by system. Here, we examined the phylogenetic and trait-based functional structures from the montane to alpine zones and clarified the effects of natural environmental factors and human-induced landscape transformation on the breeding bird assemblage on Mount Norikura, central Japan. Breeding birds from 700 to 3026 m a.s.l. were surveyed in 2016–2017. Bird community structures were examined based on species richness, functional and phylogenetic structures. A null modelling approach was performed to examine functional and phylogenetic cluster/overdispersion structures; clustering and overdispersion imply species elimination by environmental filters and limiting similarity as a corollary of competitive exclusion of species, respectively. Furthermore, we examined the relative effect of natural environments and human disturbance. Bird species richness was high in the mountain base to mid-elevation, then decreased with elevation. We found a contrasting pattern in the phylogenetic and functional structures in the alpine zone: phylogenetic overdispersion and functional clustering. In contrast, the functional and phylogenetic structures were clustered in the upper parts of the subalpine zone. The functional and phylogenetic clusterings in the lower parts of the subalpine and montane zones were negligible with the weak effects of the environmental filtering. Single-trait analysis showed that the high abiotic tolerance and foraging or nesting capabilities in treeless environments were clustered in the alpine zone, and mobility was clustered in the subalpine zones. Natural environments strongly affected bird community structures, but human disturbance added species to assemblages in the mountain base to mid-elevation and changed the functional and phylogenetic structures. Our findings highlight that filtering by severe natural environments is a fundamental community assembly process in high mountain regions, whereas filtering effects can be weaker at lower elevations. Furthermore, the filtering effect should differ between the alpine and the upper parts of the subalpine zones because of different combinations of clustered traits. Climate change and landscape transformation pressures may strongly impact biodiversity in the alpine and subalpine zones, respectively.

Understanding the spatiotemporal distribution of species diversity in response to climatic change is essential for the conservation and management of species resources. Spring ephemeral plants (SEs) have played a crucial role in sustaining the desert and woodland ecosystems of northern China. However, our knowledge regarding the spatiotemporal variation of species diversity in SEs is limited. In this study, we employed occurrence and phylogenetic data for 200 SEs, alongside 19 environmental variables, to model their geographical distribution during the Last Glacial Maximum (LGM), Current, and the year 2070 (considering two representative concentration pathway scenarios, SSP2–4.5 and SSP5–8.5). We also visualized the phylogenetic diversity patterns in the Current. Our findings revealed that more than half of the SEs notably expanded their range and continuously shifted northeastward from LGM to 2070. From LGM to Current and from Current to SSP2–4.5_2070, 64% and 54% of SEs shifted from higher to lower elevations, and 53% of them will slightly shift to higher elevations from Current to SSP5–8.5_2070. We identified three distinct bioregions corresponding to the core ranges of desert SEs and understory SE ecotypes. The Ili Valley, Tacheng Basin, northern and southern Junggar Basin, and Changbai Mountains were identified as hotspots for species richness, phylogenetic diversity, and endemism for the two SE ecotypes. Notably, these hotspots had limited overlap with existing nature reserves. Additionally, the suitable habitat of desert SEs was primarily determined by precipitation seasonality and precipitation of driest month, whereas the distribution of forest understory SEs was mainly influenced by annual precipitation and temperature seasonality. This study significantly contributes to a comprehensive understanding of the modern diversity distribution patterns and conservation priorities for SEs within a species distribution and phylogenetic framework.

Monitoring and evaluating river ecosystems are of paramount importance in addressing ecological and environmental challenges. While eDNA (environmental deoxyribonucleic acid)-based method has emerged as a valuable tool for understanding these issues, its application in assessing phylogenetic diversity, community stability, and the identification of key species within river systems has been limited. In this study, we conducted eDNA metabarcoding to assess fish community phylogenetic diversity, species composition, assembly variations, and their relationship with hydrologic characteristics. We also explored ecological stability and the roles of key species in a river system comprising a mainstem (MS) and a tributary (TB) with distinct hydrologic features. Our findings uncovered previously unknown endemic fish species diversity, exemplified by the discovery of Triplophysa. We identified disparities in diversity, community composition, and assembly between the MS and TB. Furthermore, we established significant associations between water-level variations, water flow, and changes in community composition. Triplophysa, with its high diversity, played a pivotal role in the ecological network, contributing significantly to community stability. The loss of Triplophysa increased fragility in co-occurrence patterns. Comparing the ecological network of fish communities between the MS and TB, we found that the MS displayed greater robustness and lower vulnerability, with increased species competition likely promoting network stability. Overall, this study highlights the potential of integrating eDNA metabarcoding data for monitoring phylogenetic diversity, community structure, and variations in stability within fish communities.

The metric called phylogenetic diversity (PD) has been employed over the last 30 years to add an evolutionary dimension to the exploration of biodiversity. However, the application of PD was until recently limited by both technology and methodology. Newly available distributional data from global museum databasing efforts, rapidly increasing coverage of DNA sequence data and improvements to computer hardware and software have enabled a new 'big data' approach to the application of PD‐based metrics and randomization‐based hypothesis tests called 'spatial phylogenetics'. It can be defined most simply as turning a phylogeny into a GIS layer, which can then be used with other GIS layers to understand drivers of phylodiversity patterns and for conservation prioritization. Alpha and beta phylodiversity can be measured using different ways of representing branch lengths on a given topology (called 'facets'), each yielding a different, interesting perspective that are best viewed in combination. Challenges posed by available data need to be addressed through careful cleaning and gathering further data in a targeted manner. Spatial phylogenetics is only in its infancy, showing much promise but with many elements awaiting expansion to address further questions. [ABSTRACT FROM AUTHOR]

Understanding the interactions between abiotic (environmental and anthropogenic) factors and species diversity and distribution patterns is fundamental to improving the ecological representativeness of biodiversity management tools such as protected areas (PAs). However, significant knowledge gaps remain about how species’ ecological and evolutionary opportunities are associated with abiotic factors, especially in biodiversity-rich but economically ill-equipped countries such as Kenya. Here, we explored the interactions of terrestrial mammal diversity patterns and abiotic factors across species groups and ecoregions in Kenya. We coupled data on terrestrial mammal occurrences, phylogeny, functional traits, and environmental predictors in Kenya to derive multiple diversity indices, encompassing species richness and phylogenetic and functional richness, and mean pairwise and nearest taxon distances. We explored the interactions of these indices with several abiotic factors using multivariate regression analyses while adjusting for spatial autocorrelation. The results showed weak correlations between species richness versus the phylogenetic and functional diversity indices. The best-fit models explained variable proportions of diversity indices between species groups and ecoregions and consistently retained annual temperature and precipitation averages and seasonality and human footprint as the strongest predictors. Compared to the species-poor xeric northern and eastern Kenya regions, the predictors had weak associations with diversity variances in the species-rich mesic western and central Kenya regions, similar to focal species groups compared to ordinal classifications and the combined species pool. These findings illustrate that climate and human footprint interplay determine multiple facets of terrestrial mammal diversity patterns in Kenya. Accordingly, curbing human activities degrading long-term climatic regimes is vital to ensuring the ecological integrity of terrestrial mammal communities and should be integrated into biodiversity management frameworks. For a holistic representation of critical conservation areas, biodiversity managements should also prioritize terrestrial mammal phylogenetic and functional attributes besides species richness.

Regions and localities may lose many species to extinction under rapid climate change and may gain other species that colonize from nearby warmer environments. Here, it is argued that warming-induced species losses will generally exceed gains and there will be more net declines than net increases in plant community richness. Declines in richness are especially likely in water-limited climates where intensifying aridity will increasingly exceed plant tolerances, but also in colder temperature-limited climates where steep climatic gradients are lacking, and therefore, large pools of appropriate species are not immediately adjacent. The selectivity of warming-induced losses may lead to declines in functional and phylogenetic diversity as well as in species richness, especially in water-limited climates. Our current understanding of climate-caused diversity trends may be overly influenced by numerous studies coming from north-temperate alpine mountaintops, where conditions are unusually favourable for increases-possibly temporary-in local species richness. This article is part of the theme issue 'Climate change and ecosystems: threats, opportunities and solutions'.

Studies of the factors governing global patterns of biodiversity are key to predicting community responses to ongoing and future abiotic and biotic changes. Although most research has focused on present-day climate, a growing body of evidence indicates that modern ecological communities may be significantly shaped by paleoclimatic change and past anthropogenic factors. However, the generality of this pattern is unknown, as global analyses are lacking. Here we quantify the phylogenetic and functional trait structure of 515 tropical and subtropical large mammal communities and predict their structure from past and present climatic and anthropogenic factors. We find that the effects of Quaternary paleoclimatic change are strongest in the Afrotropics, with communities in the Indomalayan realm showing mixed effects of modern climate and paleoclimate. Malagasy communities are poorly predicted by any single factor, likely due to the atypical history of the island compared with continental regions. Neotropical communities are mainly codetermined by modern climate and prehistoric and historical human impacts. Overall, our results indicate that the factors governing tropical and subtropical mammalian biodiversity are complex, with the importance of past and present factors varying based on the divergent histories of the worlds biogeographic realms and their native biotas. Consideration of the evolutionary and ecological legacies of both the recent and ancient past are key to understanding the forces shaping global patterns of present-day biodiversity and its response to ongoing and future abiotic and biotic changes in the 21st century.

Speciation is thought to be predominantly driven by the geographical separation of populations of the ancestral species. Yet, in the marine realm, there is substantial biological diversity despite a lack of pronounced geographical barriers. Here, we investigate this paradox by considering the biogeography of marine mammals: cetaceans (whales and dolphins) and pinnipeds (seals and sea lions). We test for associations between past evolutionary diversification and current geographical distributions, after accounting for the potential effects of current environmental conditions. In general, cetacean lineages are widely dispersed and show few signs of geographically driven speciation, albeit with some notable exceptions. Pinnipeds, by contrast, show a more mixed pattern, with true seals (phocids) tending to be dispersed, whereas eared seals (otariids) are more geographically clustered. Both cetaceans and pinnipeds show strong evidence for environmental clustering of their phylogenetic lineages in relation to factors such as sea temperature, the extent of sea ice, and nitrate concentrations. Overall, current marine mammal biogeography is not indicative of geographical speciation mechanisms, with environmental factors being more important determinants of current species distributions. However, geographical isolation appears to have played a role in some important taxa, with evidence from the fossil record showing good support for these cases.