Phylogenetic diversity and nature conservation: where are we?

Advancing EDGE Zones to identify spatial conservation priorities of tetrapod evolutionary history

The biodiversity crisis is pruning the Tree of Life in a way that threatens billions of years of evolutionary history and there is a need to understand where the greatest losses are predicted to occur. We therefore present threatened evolutionary history mapped for all tetrapod groups and describe patterns of Evolutionarily Distinct and Globally Endangered (EDGE) species. Using a complementarity procedure with uncertainty incorporated for 33,628 species, we identify 25 priority tetrapod EDGE Zones, which are insufficiently protected and disproportionately exposed to high human pressure. Tetrapod EDGE Zones are spread over five continents, 33 countries, and 117 ecoregions. Together, they occupy 0.723% of the world's surface but harbour one-third of the world's threatened evolutionary history and EDGE tetrapod species, half of which is endemic. These EDGE Zones highlight areas of immediate concern for researchers, practitioners, policymakers, and communicators looking to safeguard the tetrapod Tree of Life.

Key innovations and niche variation promoted rapid diversification of the widespread Juniperus (Cupressaceae)

The processes of forming lineages undergoing widespread radiations remain a knowledge gap that is fundamental to our understanding of the geographic distributions of species. Although early studies emphasized the importance of dispersal ability and historical migration events, key innovations that promote rapid diversification and/or adaptation to new habitats may also strongly influence distribution ranges. Juniperus is the second largest genus of conifers and is widely distributed throughout the Northern Hemisphere. Here, we used phylogenetic, phenotypic, and climatic data to investigate the contributions of these processes to the wide distribution and rapid diversification of Juniperus. Combining a time-scaled phylogeny and macroevolutionary theory, we show that the key innovations of berry-like seed cones and dioecy promoted the rapid diversification of Juniperus and that increased dispersal ability promoted allopatric speciation. Ecological niches had significant divergence among different clades of Juniperus. Biogeographic results supported multiple long-distance dispersal events and niche variation that contributed to the modern range of Juniperus, while both phenotypic adaptation and ecological opportunity probably drove its distribution range. Our findings suggest that the current widespread distribution is likely the result of significant divergence driven by niche variation in which ecological opportunities from key innovation and phenotypic divergence.

PhyloNext: a pipeline for phylogenetic diversity analysis of GBIF-mediated data

BACKGROUND

Understanding biodiversity patterns is a central topic in biogeography and ecology, and it is essential for conservation planning and policy development. Diversity estimates that consider the evolutionary relationships among species, such as phylogenetic diversity and phylogenetic endemicity indices, provide valuable insights into the functional diversity and evolutionary uniqueness of biological communities. These estimates are crucial for informed decision-making and effective global biodiversity management. However, the current methodologies used to generate these metrics encounter challenges in terms of efficiency, accuracy, and data integration.

RESULTS

We introduce PhyloNext, a flexible and data-intensive computational pipeline designed for phylogenetic diversity and endemicity analysis. The pipeline integrates GBIF occurrence data and OpenTree phylogenies with the Biodiverse software. PhyloNext is free, open-source, and provided as Docker and Singularity containers for effortless setup. To enhance user accessibility, a user-friendly, web-based graphical user interface has been developed, facilitating easy and efficient navigation for exploring and executing the pipeline. PhyloNext streamlines the process of conducting phylogenetic diversity analyses, improving efficiency, accuracy, and reproducibility. The automated workflow allows for periodic reanalysis using updated input data, ensuring that conservation strategies remain relevant and informed by the latest available data.

CONCLUSIONS

PhyloNext provides researchers, conservationists, and policymakers with a powerful tool to facilitate a broader understanding of biodiversity patterns, supporting more effective conservation planning and policy development. This new pipeline simplifies the creation of reproducible and easily updatable phylogenetic diversity analyses. Additionally, it promotes increased interoperability and integration with other biodiversity databases and analytical tools.

Responses of multi-faceted benthic macroinvertebrates alpha and beta diversity to flooding in a highland floodplain

Flooding is an important process in natural fluvial floodplains. How the flood shapes aquatic community diversity in highland floodplains is still poorly understood. The aim of this study was to unravel the multi-faceted responses of benthic macroinvertebrate diversity to flooding and habitat environments in the Baihe River Basin from a taxonomic, phylogenetic, and functional perspective. We examined the alpha and beta diversity patterns of benthic macroinvertebrate communities in the mainstream, tributaries, and oxbow lakes during the normal water and flood periods. The results showed that the traditional alpha taxonomic diversity (TD) varied across habitats, despite minor changes after flood pulse. Alpha phylogenetic diversity (PD) decreased and alpha functional diversity (FD) markedly increased after flooding, with functional traits transiting toward risk avoidance. While all the three facets of beta diversity significantly responded to habitat differences, beta TD and PD shifted in response to flooding. Species turnover prominently increased in beta TD and PD after flood pulse, which contrasted with a weaker response of this process in FD. The explanatory power of significant environmental factors on both alpha and beta diversity was reduced by flooding. Compared with traditional TD, cooperating multi-faceted diversity could better depict the responses of benthic macroinvertebrate communities to flooding. The assessment and conservation of aquatic biodiversity in highland floodplains should take into account the three facets of alpha and beta diversity.

Identifying global conservation priorities for terrestrial vertebrates based on multiple dimensions of biodiversity

The Kunming-Montreal Global Biodiversity Framework of the Convention on Biological Diversity calls for an expansion of the current protected areas (PAs) to cover at least 30% of global land and water areas by 2030 (i.e., the 30×30 target). Efficient spatial planning for PA expansion is an urgent need for global conservation practice. A spatial prioritization framework considering multiple dimensions of biodiversity is critical for improving the efficiency of the spatial planning of PAs, yet it remains a challenge. We developed an index for the identification of priority areas based on functionally rare, evolutionarily distinct, and globally endangered species (FREDGE) and applied it to 21,536 terrestrial vertebrates. We determined species distributions, conservation status (global endangerment), molecular phylogenies (evolutionary distinctiveness), and life-history traits (functional rarity). Madagascar, Central America, and the Andes were of high priority for the conservation of multiple dimensions of terrestrial vertebrate biodiversity. However, 68.8% of grid cells in these priority areas had <17% of their area covered by PAs, and these priority areas were under intense anthropogenic and climate change threats. These results highlight the difficulties of conserving multiple dimensions of biodiversity. Our global analyses of the geographical patterns of multiple dimensions of terrestrial vertebrate biodiversity demonstrate the insufficiency of the conservation of different biodiversity dimensions, and our index, based on multiple dimensions of biodiversity, provides a useful tool for guiding future spatial prioritization of PA expansion to achieve the 30×30 target under serious pressures.

Unravelling the functional and phylogenetic dimensions of novel ecosystem assemblages

Human activities are causing taxonomic rearrangements across ecosystems that often result in the emergence of novel communities (assemblies with no historical representative). It is commonly assumed that these changes in the taxonomic makeup of ecosystems also inevitably lead to changes in other aspects of biodiversity, namely functional and phylogenetic diversity. However, this assumption is not always valid, as the changes in functional and phylogenetic composition resulting from taxonomic shifts depend on the level of redundancy in the evaluated community. Therefore, we need improved theoretical frameworks to predict when we can expect coordinated or decoupled responses among these three facets of biodiversity. To advance this understanding, we discuss the conceptual and methodological issues that complicate establishing a link between taxonomic rearrangements driven by human activities and the associated functional and phylogenetic changes. Here, we show that is crucial to consider the expected changes in functional and phylogenetic composition as communities are reshaped owing to human drivers of biodiversity loss to forecast the impacts of novel assemblages on ecosystem functions and the services they provide to humanity. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.

Climate-driven shifts in the diversity of plants in the Neotropical seasonally dry forest: Evaluating the effectiveness of protected areas

Given the current environmental crisis, biodiversity protection is one of the most urgent socio-environmental priorities. However, the effectiveness of protected areas (PAs), the primary strategy for safeguarding ecosystems, is challenged by global climate change (GCC), with evidence showing that species are shifting their distributions into new areas, causing novel species assemblages. Therefore, there is a need to evaluate PAs' present and future effectiveness for biodiversity under the GCC. Here, we analyzed changes in the spatiotemporal patterns of taxonomic and phylogenetic diversity (PD) of plants associated with the Neotropical seasonally dry forest (NSDF) under GCC scenarios. We modeled the climatic niche of over 1000 plant species in five representative families (in terms of abundance, dominance, and endemism) of the NSDF. We predicted their potential distributions in the present and future years (2040, 2060, and 2080) based on an intermediate scenario of shared socio-economic pathways (SSP 3.70), allowing species to disperse to new sites or constrained to the current distribution. Then, we tested if the current PAs network represents the taxonomic and phylogenetic diversities. Our results suggest that GCC could promote novel species assemblages with local responses (communities' modifications) across the biome. In general, models predicted losses in the taxonomic and phylogenetic diversities of all the five plant families analyzed across the distribution of the NSDF. However, in the northern floristic groups (i.e., Antilles and Mesoamerica) of the NSDF, taxonomic and PD will be stable in GCC projections. In contrast, across the NSDF in South America, some cores will lose diversity while others will gain diversity under GCC scenarios. PAs in some NSDF regions appeared insufficient to protect the NSDF diversity. Thus, there is an urgent need to assess how the PA system could be better reconfigured to warrant the protection of the NSDF.

Global multifaceted biodiversity patterns, centers, and conservation needs in angiosperms

The Convention on Biological Diversity seeks to conserve at least 30% of global land and water areas by 2030, which is a challenge but also an opportunity to better preserve biodiversity, including flowering plants (angiosperms). Herein, we compiled a large database on distributions of over 300,000 angiosperm species and the key functional traits of 67,024 species. Using this database, we constructed biodiversity-environment models to predict global patterns of taxonomic, phylogenetic, and functional diversity in terrestrial angiosperms and provide a comprehensive mapping of the three diversity facets. We further evaluated the current protection status of the biodiversity centers of these diversity facets. Our results showed that geographical patterns of the three facets of plant diversity exhibited substantial spatial mismatches and nonoverlapping conservation priorities. Idiosyncratic centers of functional diversity, particularly of herbaceous species, were primarily distributed in temperate regions and under weaker protection compared with other biodiversity centers of taxonomic and phylogenetic facets. Our global assessment of multifaceted biodiversity patterns and centers highlights the insufficiency and unbalanced conservation among the three diversity facets and the two growth forms (woody vs. herbaceous), thus providing directions for guiding the future conservation of global plant diversity.

Contrasting impacts of non-native and threatened species on morphological, life history, and phylogenetic diversity in bird assemblages

Human activities have altered the species composition of assemblages through introductions and extinctions, but it remains unclear how those changes can affect the different facets of biodiversity. Here we assessed the impact of changes in species composition on taxonomic, functional, and phylogenetic diversity across 281 bird assemblages worldwide. To provide a more nuanced understanding of functional diversity, we distinguished morphological from life-history traits. We showed that shifts in species composition could trigger a global decline in avian biodiversity due to the high number of potential extinctions. Moreover, these extinctions were not random but unique in terms of function and phylogeny at the regional level. Our findings demonstrated that non-native species cannot compensate for these losses, as they are both morphologically and phylogenetically close to the native fauna. In the context of the ongoing biodiversity crisis, such alterations in the functional and phylogenetic structure of bird assemblages could heighten ecosystem vulnerability.

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.

Phylogenetic diversity and North Andean block conservation

Background

The Northern Andean Block (NAB) harbors high biodiversity; therefore, it is one of the most important areas in the Neotropics. Nevertheless, the settlement of several human populations has triggered the rapid transformation of ecosystems, leading to the extinction or endangerment of many species.

Methods

Because phylogenetic diversity indices quantify the historical distinctness between species, they are adequate tools for evaluating priority conservation areas. We reconstructed 93 phylogenies encompassing 1,252 species and, utilizing their occurrence data sourced from the Global Biodiversity Information Facility, computed the Average Taxonomic Distinctness Index (AvTD) for each grid cell with a spatial resolution of 0.25° within the NAB. The index values for each grid cell were categorized into quantiles, and grid cells displaying values within the upper quantile (Q5) were identified as the most significant in terms of phylogenetic diversity. We also calculated the contribution of endemic species to overall phylogenetic diversity within the NAB, specifically focusing on areas preserved within protected areas.

Results

The NAB Andean region exhibited the highest AvTD, with high AvTD values observed in the middle and southern areas of Cordilleras. Endemic species made a relatively modest contribution to the overall phylogenetic diversity of the NAB, accounting for only 1.2% of the total. Despite their relatively small geographical footprints, protected areas within the NAB have emerged as crucial repositories of biodiversity, encompassing 40% of the total phylogenetic diversity in the region.

Discussion

Although the NAB Andean region has been identified as the most crucial area in terms of AvTD, some regions in the Amazonian Piedemonte and Pacific lowlands have high AvTD levels. Interestingly, some protected areas have been found to harbor higher AvTDs than expected, given their smaller size. Although the delimitation of new PAs and species richness have been the primary factors driving the expansion of PAs, it is also essential to consider the evolutionary information of species to conserve all aspects of biodiversity, or at least cover most of them. Therefore, using phylogenetic diversity measures and the results of this study can contribute to expanding the PA network and improving the connectivity between PAs. This approach will help conserve different aspects of biodiversity and preserve evolutionary relationships between species.

A comprehensive evaluation of flowering plant diversity and conservation priority for national park planning in China

Establishment of a national park protection system in China, including the latest target proposed to protect at least 30% of the land area, calls for a comprehensive exploration of conservation priorities incorporating multiple diversity facets. We herein evaluate the spatial distribution of Chinese flowering plants from the perspectives of richness, uniqueness, vulnerability, and evolutionary history, by integrating three mega-phylogenies and comprehensive distribution data. We detect significantly high consistency among hotspots of different diversity measures for Chinese flowering plants, suggesting that multiple facets of evolutionary diversity are concentrically distributed in China. Affording legal protection to these areas is expected to maximize positive conservation outcomes. We propose two integrative diversity indices by incorporating three richness-based and three phylogeny-based measures, respectively. Both methods identify areas with high species richness, but the integrative phylogeny-based index also locates key areas with ancient and unique evolutionary histories (e.g., Ailao-Wuliang Mts, Dabie Mts, Hainan rainforest, Karst area of Yunnan-Guizhou-Guangxi, Nanling Mts, and southeast coastal regions). Of all the diversity indices explored, phylogenetic endemism maximizes the incidental protection of other indices in most cases, emphasizing its significance for conservation planning. Finally, 42 priority areas are identified by combining the 5%-criterion hotspots of two integrative indices and the minimum area to protect all threatened species analyzed. These priorities cover only 13.3% of China's land area, but host 97.1% of species richness (23,394/24,095), 96.5% of endemic species (11,841/12,274), 100% of threatened species (2,613/2,613), and 99.3% of phylogenetic diversity for flowering plants involved in this study. These frameworks provide a solid scientific basis for national park planning in China.

Phylogeny-based assignment of functional traits to DNA barcodes outperforms distance-based, in a comparison of approaches

The full potential for using DNA barcodes for profiling functional trait diversity has yet to be determined in plants and animals; thus, we outline a general framework for quantifying functional trait diversity of insect community DNA and propose and assess the accuracy of three methods for achieving this. We built a novel dataset of traits and DNA barcodes for wild bees in China. An informatics framework was developed for phylogeny-based integration of these data and prediction of traits for any subject barcodes, which was compared with two distance-based methods. For Phylogenetic Assignment, we additionally conducted a species-level analysis of publically available bee trait data. Under the specimen-level dataset, the rate of trait assignment was negatively correlated with distance between the query and the nearest trait-known reference, for all methods. Phylogenetic Assignment was found to perform best under several criteria; particularly, it had the lowest false-positive rate (rarely returning a state prediction where success was unlikely; where the distance from query to the nearest reference was high). For a wider range of compiled traits, conservative life-history traits showed the highest rates of assignment; for example, sociality was predicted with confidence at 53%, parasitism at 44% and nest location at 33%. As outlined herein, automated trait assignment might be applied at scale to either barcodes or metabarcodes. With further compilation and databasing of DNA barcode and trait data, the rate and accuracy of trait assignment is expected to increase to the point of being a widely viable and informative approach.

Conserving avian evolutionary history can effectively safeguard future benefits for people

Phylogenetic diversity (PD)-the evolutionary history of a set of species-is conceptually linked to the maintenance of yet-to-be-discovered benefits from biodiversity or "option value." We used global phylogenetic and utilization data for birds to test the PD option value link, under the assumption that the performance of sets of PD-maximizing species at capturing known benefits is analogous to selecting the same species at a point in human history before these benefits were realized. PD performed better than random at capturing utilized bird species across 60% of tests, with performance linked to the phylogenetic dispersion and prevalence of each utilization category. Prioritizing threatened species for conservation by the PD they encapsulate performs comparably to prioritizing by their functional distinctiveness. However, species selected by each metric show low overlap, indicating that we should conserve both components of biodiversity to effectively conserve a variety of uses. Our findings provide empirical support for the link between evolutionary history and benefits for future generations.

Phylogenetic Partitioning of Gansu Flora: Unveiling the Core Transitional Zone of Chinese Flora

Floristic regions, conventionally established using species distribution patterns, have often overlooked the phylogenetic relationships among taxa. However, how phylogenetic relationships influence the historical interconnections within and among biogeographic regions remains inadequately understood. In this research, we compiled distribution data for seed plants in Gansu, a region of significant biogeographic diversity located in northwestern China.We proposed a novel framework for floristic regions within Gansu, integrating distribution data and phylogenetic relationships of genera-level native seed plants, aiming to explore the relationship between phylogenetic relatedness, taxonomic composition, and regional phylogenetic delineation. We found that (1) phylogenetic relatedness was strongly correlated with the taxonomic composition among floras in Gansu. (2) The southeastern Gansu region showed the lowest level of spatial turnover in both phylogenetic relationships and the taxonomic composition of floristic assemblages across the Gansu region. (3) Null model analyses indicated nonrandom phylogenetic structure across the region, where most areas showed higher phylogenetic turnover than expected given the underlying taxonomic composition between sites. (4) Our results demonstrated a consistent pattern across various regionalization schemes and highlighted the preference for employing the phylogenetic dissimilarity approach in biogeographical regionalization investigations. (5) Employing the phylogenetic dissimilarity approach, we identified nine distinct floristic regions in Gansu that are categorized into two broader geographical units, namely the northwest and southeast. (6) Based on the phylogenetic graphic regions of China across this area.

Temperature drives elevational diversity patterns of different types of organisms in Qinghai-Tibetan Plateau wetlands

The spatial pattern and driving mechanism of biodiversity along elevational gradients are key topics in ecology. However, it is still unclear whether the multidimensional diversity of different types of organisms shows a similar response to elevation changes. Here, we measured the species and phylogenetic diversity of plants, bacteria, fungi, and microbial functional groups (nitrifiers, denitrifiers, methanogens, and methanotrophs) in 36 wetland sites on the Qinghai-Tibetan Plateau. The results showed that both species and phylogenetic diversity of plants, bacteria, and fungi exhibited a significant elevational gradient, in direct contrast to no significant diversity changes observed for denitrifiers, methanogens, and methanotrophs along the same altitude gradient. Our findings suggest that elevation and temperature were more likely to associate with the diversity of plants, bacteria, and fungi than the diversity of microbial functional groups, with important implications for assessing the effect of ongoing climate warming on biodiversity in Qinghai-Tibetan alpine wetlands.

Are Mediterranean Island Mountains Hotspots of Taxonomic and Phylogenetic Biodiversity? The Case of the Endemic Flora of the Balearic Islands

The Mediterranean islands are exceptionally rich in endemism, most of which is narrowly distributed. Conservation measures, such as protected areas, have been prioritised, mainly on the basis of species richness and endemism, but phylogenetic information should also be taken into account. In this study, we calculated several taxonomic and phylogenetic metrics at a high resolution for the endemic flora of the Balearic Islands (154 taxa), in order to identify (i) the spatial patterns and environmental factors that explain this endemism, (ii) hotspots of species and phylogenetic endemism, and (iii) gaps in the protected areas. The taxonomic and phylogenetic metrics showed different distribution patterns, but the mountainous areas of Mallorca, and some coastal areas of the Balearic Islands, have the highest values. These values were positively related to elevation, precipitation, temperature, and slope, and negatively related to the distance from the coast, aspect, and the temperature of the wettest quarter. We identified top grid hotspots where all the metrics had the highest values, and we also identified nano-hotspots within these hotspots, in some of the highest peaks of Mallorca, where most of these metrics' maximum values coincided. This approach allowed us to identify some gaps in the conservation priority areas, and to highlight the need to review their boundaries and definition.

A network-based approach to identifying correlations between phylogeny, morphological traits and occurrence of fish species in US river basins

The complex network framework has been successfully used to model interactions between entities in Complex Systems in the Biological Sciences such as Proteomics, Genomics, Neuroscience, and Ecology. Networks of organisms at different spatial scales and in different ecosystems have provided insights into community assembly patterns and emergent properties of ecological systems. In the present work, we investigate two questions pertaining to fish species assembly rules in US river basins, a) if morphologically similar fish species also tend to be phylogenetically closer, and b) to what extent are co-occurring species that are phylogenetically close also morphologically similar? For the first question, we construct a network of Hydrologic Unit Code 8 (HUC8) regions as nodes with interaction strengths (edges) governed by the number of common species. For each of the modules of this network, which are found to be geographically separated, there is differential yet significant evidence that phylogenetic distance predicts morphological distance. For the second question, we construct and analyze nearest neighbor directed networks of species based on their morphological distances and phylogenetic distances. Through module detection on these networks and comparing the module-level mean phylogenetic distance and mean morphological distance with the number of basins of common occurrence of species in modules, we find that both phylogeny and morphology of species have significant roles in governing species co-occurrence, i.e. phylogenetically and morphologically distant species tend to co-exist more. In addition, between the two quantities (morphological distance and phylogentic distance), we find that morphological distance is a stronger determinant of species co-occurrences.

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.

An integrative bioinformatics pipeline shows that honeybee-associated microbiomes are driven primarily by pollen composition

The microbiomes associated with bee nests influence colony health through various mechanisms, although it is not yet clear how honeybee congeners differ in microbiome assembly processes, in particular the degrees to which floral visitations and the environment contribute to different aspects of diversity. We used DNA metabarcoding to sequence bacterial 16S rRNA from honey and stored pollen from nests of 4 honeybee species (Apis cerana, A. dorsata, A. florea, and A. laboriosa) sampled throughout Yunnan, China, a global biodiversity hotspot. We developed a computational pipeline integrating multiple databases for quantifying key facets of diversity, including compositional, taxonomic, phylogenetic, and functional ones. Further, we assessed candidate drivers of observed microbiome dissimilarity, particularly differences in floral visitations, habitat disturbance, and other key environmental variables. Analyses revealed that microbiome alpha diversity was broadly equivalent across the study sites and between bee species, apart from functional diversity which was very low in nests of the reclusive A. laboriosa. Turnover in microbiome composition across Yunnan was driven predominantly by pollen composition. Human disturbance negatively impacted both compositional and phylogenetic alpha diversity of nest microbiomes, but did not correlate with microbial turnover. We herein make progress in understanding microbiome diversity associated with key pollinators in a biodiversity hotspot, and provide a model for the use of a comprehensive informatics framework in assessing pattern and drivers of diversity, which enables the inclusion of explanatory variables both subtly and fundamentally different and enables elucidation of emergent or unexpected drivers.

Biodiversity patterns diverge along geographic temperature gradients

Models applying space-for-time substitution, including those projecting ecological responses to climate change, generally assume an elevational and latitudinal equivalence that is rarely tested. However, a mismatch may lead to different capacities for providing climatic refuge to dispersing species. We compiled community data on zooplankton, ectothermic animals that form the consumer basis of most aquatic food webs, from over 1200 mountain lakes and ponds across western North America to assess biodiversity along geographic temperature gradients spanning nearly 3750 m elevation and 30° latitude. Species richness, phylogenetic relationships, and functional diversity all showed contrasting responses across gradients, with richness metrics plateauing at low elevations but exhibiting intermediate latitudinal maxima. The nonmonotonic/hump-shaped diversity trends with latitude emerged from geographic interactions, including weaker latitudinal relationships at higher elevations (i.e. in alpine lakes) linked to different underlying drivers. Here, divergent patterns of phylogenetic and functional trait dispersion indicate shifting roles of environmental filters and limiting similarity in the assembly of communities with increasing elevation and latitude. We further tested whether gradients showed common responses to warmer temperatures and found that mean annual (but not seasonal) temperatures predicted elevational richness patterns but failed to capture consistent trends with latitude, meaning that predictions of how climate change will influence diversity also differ between gradients. Contrasting responses to elevation- and latitude-driven warming suggest different limits on climatic refugia and likely greater barriers to northward range expansion.

The macroevolutionary impact of recent and imminent mammal extinctions on Madagascar

Many of Madagascar's unique species are threatened with extinction. However, the severity of recent and potential extinctions in a global evolutionary context is unquantified. Here, we compile a phylogenetic dataset for the complete non-marine mammalian biota of Madagascar and estimate natural rates of extinction, colonization, and speciation. We measure how long it would take to restore Madagascar's mammalian biodiversity under these rates, the "evolutionary return time" (ERT). At the time of human arrival there were approximately 250 species of mammals on Madagascar, resulting from 33 colonisation events (28 by bats), but at least 30 of these species have gone extinct since then. We show that the loss of currently threatened species would have a much deeper long-term impact than all the extinctions since human arrival. A return from current to pre-human diversity would take 1.6 million years (Myr) for bats, and 2.9 Myr for non-volant mammals. However, if species currently classified as threatened go extinct, the ERT rises to 2.9 Myr for bats and 23 Myr for non-volant mammals. Our results suggest that an extinction wave with deep evolutionary impact is imminent on Madagascar unless immediate conservation actions are taken.

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

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

Environmental DNA metabarcoding reveals the impacts of anthropogenic pollution on multitrophic aquatic communities across an urban river of western China

Anthropogenic activities are intensively affecting the structure and function of biological communities in river ecosystems. The effects of anthropogenic pollution on single-trophic community have been widely explored, but their effects on the structures and co-occurrence patterns of multitrophic communities remain largely unknown. In this study, we collected 13 water samples from the Neijiang River in Chengdu City of China, and identified totally 2352 bacterial, 207 algal, 204 macroinvertebrate, and 33 fish species based on the eDNA metabarcoding to systematically investigate the responses of multitrophic communities to environmental stressors. We observed significant variations in bacterial, algal, and macroinvertebrate community structures (except fish) with the pollution levels in the river. Network analyses indicated a more intensive interspecific co-occurrence pattern at high pollution level. Although taxonomic diversity of the multitrophic communities varied insignificantly, phylogenetic diversities of fish and algae showed significantly positive and negative associations with the pollution levels, respectively. We demonstrated the primary role of environmental filtering in driving the structures of bacteria, algae, and macroinvertebrates, while the fish was more controlled by dispersal limitation. Nitrogen was identified as the most important factor impacting the multitrophic community, where bacterial composition was mostly associated with NO₃^--N, algal spatial differentiation with TN, and macroinvertebrate and fish with NH₄⁺-N. Further partial least-squares path model confirmed more important effect of environmental variables on the relative abundance of bacteria and algae, while macroinvertebrate and fish communities were directly driven by the algae-mediated pathway in the food web. Our study highlighted the necessity of integrated consideration of multitrophic biodiversity for riverine pollution management, and emphasized the importance of controlling nitrogen inputs targeting a healthy ecosystem.

Preserving the woody plant tree of life in China under future climate and land-cover changes

The tree of life (TOL) is severely threatened by climate and land-cover changes. Preserving the TOL is urgent, but has not been included in the post-2020 global biodiversity framework. Protected areas (PAs) are fundamental for biological conservation. However, we know little about the effectiveness of existing PAs in preserving the TOL of plants and how to prioritize PA expansion for better TOL preservation under future climate and land-cover changes. Here, using high-resolution distribution maps of 8732 woody species in China and phylogeny-based Zonation, we find that current PAs perform poorly in preserving the TOL both at present and in 2070s. The geographical coverage of TOL branches by current PAs is approx. 9%, and less than 3% of the identified priority areas for preserving the TOL are currently protected. Interestingly, the geographical coverage of TOL branches by PAs will be improved from 9% to 52-79% by the identified priority areas for PA expansion. Human pressures in the identified priority areas are high, leading to high cost for future PA expansion. We thus suggest that besides nature reserves and national parks, other effective area-based conservation measures should be considered. Our study argues for the inclusion of preserving the TOL in the post-2020 conservation framework, and provides references for decision-makers to preserve the Earth's evolutionary history.

Grassland Degradation Has Stronger Effects on Soil Fungal Community Than Bacterial Community across the Semi-Arid Region of Northern China

Soil microbes play crucial roles in grassland ecosystem functions, such as soil carbon (C) pool and nutrient cycle. Soil microbes in grasslands are susceptible to the degradation mediated by climate change and anthropogenic disturbance. However, research on how the degradation influences the diversity and community structure of different soil microbial taxa is relatively scarce. We conducted a large-scale field survey to describe the effects of four degradation levels (PD: potential degradation, LD: light degradation, MD: moderate degradation, and SD: severe degradation) on soil bacterial and fungal community in the semi-arid grasslands of northern China. We found that soil moisture, nutrients, and clay content decreased, but soil sand content increased along the increasing degradation gradient. However, the degradation had no effects on soil pH and the C:N ratio. Grassland degradation had non-significant effect on soil bacterial diversity, but it significantly affected soil bacterial community structure. The degradation decreased soil fungal diversity and had a relatively larger influence on the community structure of soil fungi than that of bacteria. The community composition and structure of soil fungi were mainly affected by soil nutrients and texture, while those of soil bacteria were mainly affected by soil pH. These results indicate that changes in soil properties induced by grassland degradation mainly drive the variation in the soil fungal community and have less effect on the soil bacterial community. This study reveals the sensitivity of soil fungal community to grassland degradation, highlighting the priority of soil fungal community for the management and restoration of degraded grasslands.

Functional diversity regulates the effects of habitat degradation on biocrust phylogenetic and taxonomic diversities

Biocrusts are major contributors to dryland diversity, functioning, and services. However, little is known about how habitat degradation will impact multiple facets of biocrust diversity and measurable functional traits. We evaluated changes in taxonomic, functional, and phylogenetic diversity of biocrust-forming lichens along a habitat degradation gradient related to the presence of linear infrastructure (i.e., a road) and a profound agricultural driven transformation. To do so, we selected 50 remnants of a Mediterranean shrubland. We considered several surrogates of habitat quality and causal disturbance on the various diversity facets of biocrusts by using structural equation modeling, hypothesizing that habitat degradation primarily affects functional diversity, which in turn regulates changes in taxonomic and phylogenetic diversities, and also that taxonomic and phylogenetic diversities are coupled. Fragment connectivity, distance to linear infrastructure (i.e., a road) and, particularly, soil fertility (i.e., soil P concentration), had mostly negative effects on biocrust functional diversity, which in turn affected both taxonomic and phylogenetic diversities. However, we found no direct effects of habitat degradation variables on the taxonomic and phylogenetic diversities. We also found that increases in phylogenetic diversity had a positive effect on taxonomic diversity along the habitat degradation gradient. Our results indicate that functional diversity of biocrusts is strongly affected by habitat degradation, which may profoundly alter their contribution to ecosystem functioning and services. Furthermore, functional diversity regulates the response of biocrust taxonomic and phylogenetic diversity to habitat degradation. These findings indicate that habitat degradation alters and simplifies the diversity of functional traits of biocrust-forming lichens, leading to biodiversity loss, with important consequences for the conservation of global drylands biodiversity.

The contribution of mutualistic interactions to functional and phylogenetic diversity

Reduction of functional diversity (FD) and phylogenetic diversity (PD) likely affects ecosystem functions and reduces the potential of communities to respond to changes, such as climate change. Mutualistic interactions are essential for maintaining diversity, but their role has largely been ignored in conservation planning. We propose using a species' interaction niche - the diversity of its interaction partners - to measure a species' contribution to the maintenance of FD and PD via mutualistic interactions, and thus identify species and interspecific interactions that are particularly important for the conservation of ecosystem functions and evolutionary lineages in ecological communities. Our approach represents a switch in perspective that allows a direct assessment of the importance of mutualistic interactions for the maintenance of biodiversity and ecosystem functioning.

Discriminating ecological processes affecting different dimensions of α- and β-diversity in desert plant communities

Understanding the spatial distribution of plant diversity and its drivers are major challenges in biogeography and conservation biology. Integrating multiple facets of biodiversity (e.g., taxonomic, phylogenetic, and functional biodiversity) may advance our understanding on how community assembly processes drive the distribution of biodiversity. In this study, plant communities in 60 sampling plots in desert ecosystems were investigated. The effects of local environment and spatial factors on the species, functional, and phylogenetic α- and β-diversity (including turnover and nestedness components) of desert plant communities were investigated. The results showed that functional and phylogenetic α-diversity were negatively correlated with species richness, and were significantly positively correlated with each other. Environmental filtering mainly influenced species richness and Rao quadratic entropy; phylogenetic α-diversity was mainly influenced by dispersal limitation. Species and phylogenetic β-diversity were mainly consisted of turnover component. The functional β-diversity and its turnover component were mainly influenced by environmental factors, while dispersal limitation dominantly effected species and phylogenetic β-diversity and their turnover component of species and phylogenetic β-diversity. Soil organic carbon and soil pH significantly influenced different dimensions of α-diversity, and soil moisture, salinity, organic carbon, and total nitrogen significantly influenced different dimensions of α- and β-diversity and their components. Overall, it appeared that the relative influence of environmental and spatial factors on taxonomic, functional, and phylogenetic diversity differed at the α and β scales. Quantifying α- and β-diversity at different biodiversity dimensions can help researchers to more accurately assess patterns of diversity and community assembly.

The Edaphic and Vegetational Properties Controlling Soil Aggregate Stability Vary with Plant Communities in an Arid Desert Region of Northwest China

The stability of soil aggregates is the basis for supporting ecosystem functions and related services provided by the soil. In order to explore the mechanism of the influence of soil and vegetation properties on the stability of soil aggregates in desert communities, the particle size distribution and aggregate in different communities were compared, and the contribution of soil physical and chemical properties (soil salinity, soil water content, soil pH, soil organic carbon, soil total phosphorus, soil total nitrogen, etc.) and vegetation properties (species richness, phylogenetic richness, plant height and coverage, etc.) to the stability of soil aggregates was determined by using a structural equation model. The results show the following: Soil water content, organic carbon, and salt in river bank plant communities have significant direct positive effects on the mean weight diameter of soil, with path coefficients of 0.50, 0.11, and 0.24, respectively (p < 0.01). Water also indirectly affects soil stability by affecting plant height, soil salt, and soil organic carbon; species richness and vegetation coverage have significant direct positive effects on the soil stability index, with path coefficients of 0.13 and 0.11, respectively (p < 0.01). In the desert marginal plant community, the plant coverage and species richness have significant positive effects on soil stability, with path coefficients of 0.43 (p < 0.001) and 0.35 (p < 0.001), respectively. Phylogenetic richness has a significant direct negative effect on soil stability (p < 0.05), with an effect value of −0.27. Phylogenetic richness indirectly affects soil stability by adjusting the coverage, with an indirect effect value of 0.23. Moisture, ammonium nitrogen, and nitrate nitrogen have significant direct positive effects on soil stability, with effect values of 0.12, 0.09, and 0.15, respectively. Our research shows that the process of soil stabilization is mainly controlled by soil factors and vegetation characteristics, but its importance varies with different community types.

Use of environmental DNA in assessment of fish functional and phylogenetic diversity

Assessing the impact of global changes and protection effectiveness is a key step in monitoring marine fishes. Most traditional census methods are demanding or destructive. Nondisturbing and nonlethal approaches based on video and environmental DNA are alternatives to underwater visual census or fishing. However, their ability to detect multiple biodiversity factors beyond traditional taxonomic diversity is still unknown. For bony fishes and elasmobranchs, we compared the performance of eDNA metabarcoding and long-term remote video to assess species' phylogenetic and functional diversity. We used 10 eDNA samples from 30 L of water each and 25 hr of underwater videos over 4 days on Malpelo Island (pacific coast of Colombia), a remote marine protected area. Metabarcoding of eDNA detected 66% more molecular operational taxonomic units (MOTUs) than species on video. We found 66 and 43 functional entities with a single eDNA marker and videos, respectively, and higher functional richness for eDNA than videos. Despite gaps in genetic reference databases, eDNA also detected a higher fish phylogenetic diversity than videos; accumulation curves showed how 1 eDNA transect detected as much phylogenetic diversity as 25 hr of video. Environmental DNA metabarcoding can be used to affordably, efficiently, and accurately census biodiversity factors in marine systems. Although taxonomic assignments are still limited by species coverage in genetic reference databases, use of MOTUs highlights the potential of eDNA metabarcoding once reference databases have expanded.

Effects of urbanization on taxonomic, functional and phylogenetic avian diversity in Europe

Europe is an urbanized continent characterized by a long history of human-wildlife interactions. This study aimed to assess the effects of specific elements of urbanization and urban pollution on complementary avian diversity metrics, to provide new insights on the conservation of urban birds. Our study recorded 133 bird species at 1624 point counts uniformly distributed in seventeen different European cities. Our results thus covered a large spatial scale, confirming both effects of geographical and local attributes of the cities on avian diversity. However, we found contrasting effects for the different diversity components analyzed. Overall, taxonomic diversity (bird species richness), phylogenetic diversity and relatedness were significantly and negatively associated with latitude, while functional dispersion of communities showed no association whatsoever. At the local level (within the city), we found that urban greenery (grass, bush, and trees) is positively correlated with the number of breeding bird species, while the building cover showed a detrimental effect. Functional dispersion was the less affected diversity metric, while grass and trees and water (rivers or urban streams) positively affected the phylogenetic diversity of avian communities. Finally, the phylogenetic relatedness of species increased with all the main indicators of urbanization (building surface, floors, pedestrian's density and level of light pollution) and was only mitigated by the presence of bushes. We argue that maintaining adequate levels of avian diversity within the urban settlements can help to increase the potential resilience of urban ecosystems exposed to the stress provoked by rapid and continuous changes. We listed some characteristics of the cities providing positive and negative effects on each facet of urban avian diversity.

Phylogenetic diversity and conservation of crop wild relatives in Colombia

Crop wild relatives (CWR) are an important agricultural resource as they contain genetic traits not found in cultivated species due to localized adaptation to unique environmental and climatic conditions. Phylogenetic diversity (PD) measures the evolutionary relationship of species using the tree of life. Our knowledge of CWR PD in neotropical regions is in its infancy. We analysed the distribution of CWR PD across Colombia and assessed its conservation status. The areas with the largest concentration of PD were identified as being in the northern part of the central and western Andean mountain ranges and the Pacific region. These centres of high PD were comprised of predominantly short and closely related branches, mostly of species of wild tomatoes and black peppers. In contrast, the CWR PD in the lowland ecosystems of the Amazon and Orinoquia regions had deeply diverging clades predominantly represented by long and distantly related branches (i.e. tuberous roots, grains and cacao). We categorized 50 (52.6%) of the CWR species as 'high priority', 36 as 'medium priority' and nine as 'low priority' for further ex-situ and in situ conservation actions. New areas of high PD and richness with large ex-situ gap collections were identified mainly in the northern part of the Andes of Colombia. We found that 56% of the grid cells with the highest PD values were unprotected. These baseline data could be used to create a comprehensive national strategy of CWR conservation in Colombia.