Phylogenetic Diversity Metrics Research Articles

The curious case of small mammal community in a rice-Pantanal agroecosystem of Brazil: A tale of multiple diversity metrics

To understand how certain types of agroecosystem management provide resources for biodiversity and conservation opportunities beyond protected areas, it is necessary to consider the cumulative effects on a local scale. Our study focuses on a rice-Pantanal wetland agricultural system within Brazil, where our goals were: i) to quantify the impact of rice paddies on taxonomic, functional, and phylogenetic diversity metrics of small mammals as biodiversity indicators, ii) to compare diversity indices based on incidence and abundance data. We carried out a thorough assessment to sample small mammal species in both the rice paddy and the adjacent legal reserve by employing a multiple diversity metrics approach. We captured the small mammals until reaching saturation on the species accumulation curve over 12,774 trap nights, resulting in 447 individuals, 10 species, including seven rodents and three marsupial species. Abundance-based beta-diversity between rice-paddy and forest reserve were higher (0.95) than incidence-based estimate (0.33). The species composition differed between the legal reserve (8 spp.) and the rice paddy (7 spp.), with the reserve exhibiting higher taxonomic diversity values compared to the rice paddy. In terms of functional and phylogenetic diversity, overall, the rice paddy exhibited higher values for the incidence-based metrics and the abundance-based metrics indicated that the reserve was more diverse. We conclude that Neotropical Pantanal rice fields retain substantial functional and phylogenetic diversities, providing suitable habitats for species thriving in open and semi-aquatic environments. Simultaneously, the legal reserve retains an essential aspect of functional diversity, when considering abundance, needed to maintain ecosystem resilience and stability. Proper abundance estimation is thus a key parameter for accurately evaluating the role of agricultural landscapes as biodiversity conservation opportunities beyond protected areas. Abundance-based indices should be used to correctly evaluate the contribution of each habitat to agroecosystem sustainability, especially in seasonal or extreme event-prone environments.

Biodiversity and productivity in eastern US forests

Despite experimental and observational studies demonstrating that biodiversity enhances primary productivity, the best metric for predicting productivity at broad geographic extents-functional trait diversity, phylogenetic diversity, or species richness-remains unknown. Using >1.8 million tree measurements from across eastern US forests, we quantified relationships among functional trait diversity, phylogenetic diversity, species richness, and productivity. Surprisingly, functional trait and phylogenetic diversity explained little variation in productivity that could not be explained by tree species richness. This result was consistent across the entire eastern United States, within ecoprovinces, and within data subsets that controlled for biomass or stand age. Metrics of functional trait and phylogenetic diversity that were independent of species richness were negatively correlated with productivity. This last result suggests that processes that determine species sorting and packing are likely important for the relationships between productivity and biodiversity. This result also demonstrates the potential confusion that can arise when interdependencies among different diversity metrics are ignored. Our findings show the value of species richness as a predictive tool and highlight gaps in knowledge about linkages between functional diversity and ecosystem functioning.

Spatial phylogenetics of grasses in the Southern Cone provides insights into ecology and evolution of the family in South America

AbstractIn this study, we explored the distributions of grass genera in the Southern Cone (SC) of South America, applying several phylogenetic diversity (PD) metrics and randomization tests. Grasses appear to have been present in South America since their early evolution as tropical understory species more than 60 Ma. During the course of evolution, grasses have adapted to all terrestrial biomes and become one of the most successful plant families on earth. At present, the SC contains nearly all terrestrial biomes and a wide range of humid to arid ecoregions. Analyzing 126.514 point occurrences and four plastid markers for 148 genera (91% of the native grass genera), we found that tropical humid regions hold the highest PD, with no observed bias in branch lengths. These results indicate that niche conservatism dominates the diversity pattern of grasses in the SC. We found significantly low PD in the Dry Chaco and in the Patagonian Steppe, which suggest ecological filtering in both warm and cold arid regions. The Patagonian Steppe also holds significantly longer branches than expected by chance, as the native grass flora is mainly composed of distantly related Pooideae genera with a northern hemisphere origin. Short branches are found in the Uruguayan Savanna, suggesting that these grasslands could be a cradle for grass diversity within the SC. The dated phylogeny supported the current view of a relatively recent evolution of the family within the SC, with most diversification taking place from the middle Miocene and onwards.

Choice of molecular marker influences spatial patterns of phylogenetic diversity.

Spatial patterns of phylogenetic diversity (PD) are increasingly becoming relevant for conservation decisions. PD measures are based on phylogenies estimated from molecular data. This paper addresses the question of how different molecular markers impact PD spatial patterns. We first conducted a simple simulation to explore the effect of deep and shallow changes in topology (simulating variations in molecular markers), using ultrametric and non-ultrametric trees, and then used a dataset of Chilean flora with four sets of markers to assess potential differences in spatial patterns of PD ranks using different markers and types of trees. The simulation consistently showed that the difference in PD rank was lower for ultrametric trees than for phylograms. A similar trend was observed using the Chilean flora dataset, with among-markers variability in spatial patterns of the PD metrics lower for ultrametric than for non-ultrametric trees, depicted as top 2.5 and 5% hotspots. Frequency distribution of PD values differed among markers as well, with this variation less apparent for ultrametric trees. We conclude that the choice of markers impacts spatial patterns of PD, and these results vary more strongly for phylograms, suggesting that ultrametric trees are more robust to the choice of marker.

Multiple dimensions of phylogenetic diversity are needed to explain the complex aboveground–belowground diversity relationships

The complex relationship between aboveground and belowground diversity and whether they act as surrogates for one another remains unresolved. Increasing evidence suggests that investigating phylogenetic diversity could provide valuable insights into the interplay between plants and soil microbes, but the proliferation of phylogenetic diversity metrics has hindered comparative studies and the identification of general patterns. To overcome this challenge, we implemented a multi‐dimensional framework that classifies phylogenetic diversity metrics into three dimensions: richness, divergence, and regularity, each of which captures different ecological aspects of species differences. Then we applied this framework to investigate the relationship between above and belowground diversity in a subtropical forest in eastern China. We found that phylogenetic diversity of plant and soil microbes, including bacteria and fungi, were more strongly correlated at the richness and regularity dimensions compared with divergence dimension. Further analyses revealed that these observed correlation patterns align with variations in soil total phosphorus content, a key factor influencing both plant and microbial phylogenetic diversity at richness and regularity dimensions. Together, our study demonstrated the necessity of using a multi‐dimensional approach to advance our understanding of the complex relationships between plant and soil microbial biodiversity.

Multiple facets of biodiversity are threatened by mining‐induced land‐use change in the Brazilian Amazon

AbstractAimMining is increasingly pressuring areas of critical importance for biodiversity conservation, such as the Brazilian Amazon. Biodiversity data are limited in the tropics, restricting the scope for risks to be appropriately estimated before mineral licensing decisions are made. As the distributions and range sizes of other taxa differ markedly from those of vertebrates—the common proxy for analysis of risk to biodiversity from mining—whether mining threatens lesser‐studied taxonomic groups differentially at a regional scale is unclear.LocationBrazilian Amazon.MethodsWe assess risks to several facets of biodiversity from industrial mining by comparing mining areas (within 70 km of an active mining lease) and areas unaffected by mining, employing species richness, species endemism, phylogenetic diversity and phylogenetic endemism metrics calculated for angiosperms, arthropods and vertebrates.ResultsMining areas contained higher densities of species occurrence records than the unaffected landscape, and we accounted for this sampling bias in our analyses. None of the four biodiversity metrics differed between mining and nonmining areas for vertebrates. For arthropods, species endemism was greater in mined areas. Mined areas also had greater angiosperm species richness, phylogenetic diversity and phylogenetic endemism, although less species endemism than unmined areas.Main ConclusionsUnlike for vertebrates, facets of angiosperm and arthropod diversity are relatively higher in areas of mining activity, underscoring the need to consider multiple taxonomic groups and biodiversity facets when assessing risk and evaluating management options for mining threats. Particularly concerning is the proximity of mining to areas supporting deep evolutionary history, which may be impossible to recover or replace. As pressures to expand mining in the Amazon grow, impact assessments with broader taxonomic reach and metric focus will be vital to conserving biodiversity in mining regions.

Simultaneous competition and environmental filtering in woody communities of the understory of Eucalyptus plantations in the Cerrado

Dense and species-rich understory communities have been commonly found in old or abandoned stands of Eucalyptus plantations in the Cerrado domain presenting plant species and ecological niches that suggest a repository of the original biodiversity. This repository depends on the largely unknown effect of Eucalyptus plantations on their understories. We addressed this issue by testing if the effect of Eucalyptus trees on the assembly of Cerrado communities causes environmental filtering or competitive exclusion. For the test, 40 plots (20 inside stands and 20 outside) were allocated and all woody plants with a circumference at the ground level equal to or greater than 10 cm were sampled. Species richness, diversity indexes and species turnover were determined. The phylogenetic structure was evaluated at different scales using the values of Mean Pairwise Distance (MPD), the Mean Nearest Taxon Distance (MNTD), the Net Relatedness Index (NRI) and the Nearest Taxon Index (NTI), as well as phylobetadiversity indices. The metrics of alpha and beta phylogenetic diversity (NTI, MNTD, NRI and MPD, betaMPD and betaMNTD) fell within the random expectation in each plant community, suggesting a phylogenetic uniformity, but fewer plants of the Fabaceae family than expected by chance were detected outside Eucalyptus stands suggesting that this family is filtered in inside Eucalyptus stands. Species richness is lower inside than outside Eucalyptus stands. The pattern is congruent with simultaneous environmental filtering and competitive exclusion in a context of niche conservatism which means that functional traits are conserved within phylogenetic lineages.

Effect of sampling design on estimation of phylogenetic diversity metrics of fish community.

Phylogenetic diversity has been widely used to explore diversity patterns and assess processes governing the species composition in community. The estimates of many metrics depend on high-quality data collected from well-designed sampling surveys. However, knowledge of impacts of sampling design on estimation of phylogenetic diversity metrics remains unclear. This study is aim to evaluate the influence of sampling design on phylogenetic diversity metrics estimation of fish community. Simple random sampling (SRS), systematic sampling (SS) and stratified random sampling (StRS) with different sampling intensities were chosen and mean pairwise distances (MPD), mean nearest taxon distance (MNTD), phylogenetic diversity (PD), phylogenetic species variability (PSV), phylogenetic species evenness (PSE) and phylogenetic species richness (PSR) were selected. SRS and StRS showed similar impact on phylogenetic diversity indices estimation and performed relatively well for collecting data to estimate phylogenetic diversity. The accuracy and precision of the estimation increased with sampling intensity under SRS and StRS except SS. MNTD was the only metric not underestimated in four seasons. Metrics strongly influenced by species richness were underestimated when sampling intensity was insufficient. MPD, PSV and PSE showed an obvious seasonal change, which was due to the seasonal differences in fish species composition. In cases where under-sampling is suspected or logistically unavoidable, phylogenetic diversity metrics that are relatively insensitive to sampling design (e.g., MPD and PSV) should be prioritized, especially for exploring the temporal variation infish community. This study reveals it is indispensable to evaluate sampling design when estimating phylogenetic diversity metrics, especially those indices susceptible to species richness.

Spatial‐ and lineage‐dependent processes underpin floristic assembly in the megadiverse Eastern South American mountains

AbstractAimThe astonishing diversity of ancient mountains was likely shaped by multiple evolutionary processes. However, there is an ongoing debate on what were the main processes driving the assembly of campos rupestres, the mega‐diverse flora of Eastern South American mountains. Although the ancient nature of these mountains suggests their flora should be composed by relatively older lineages, they harbour a number of recently diverged clades. To better understand the evolution of ancient mountains' floras, we tested if the campos rupestres are mainly composed by relatively old or recent communities and if angiosperm diversity is geographically structured using analyses of diversity and endemism.LocationEastern South America.Time PeriodOligocene/Miocene to the present.TaxonFlowering plants.MethodsWe used analyses of diversity and endemism for 10% of the campos rupestres flora. We obtained distribution data from online databases, and phylogenetic hypotheses from the literature. With these datasets, we estimated alpha and beta metrics of taxonomic and phylogenetic diversity, and conducted categorical analyses of neo‐ and palaeo‐endemism.ResultsPhylogenetic overdispersion predominates in the campos rupestres. However, this general pattern is permeated by both lineage‐ and site‐specific phylogenetic clustering, suggesting that recent diversification events depend on particular regional conditions and on the overall maintenance of old lineages. Although endemism patterns vary among different campos rupestres sites, palaeo‐endemism is widespread and particularly prominent where phylogenetic overdispersion is evident. Moreover, while phylogenetic composition indicates variable past spatial connections across different sites, taxonomic composition is highly geographically structured and seems to be influenced by the vegetation surrounding the campos rupestres and/or by abiotic conditions.Main ConclusionsOur results reinforce the idiosyncratic nature of diversification patterns in ancient mountains and suggest that old, climatically buffered, infertile montane ecosystems not only include both relatively old and recent lineages, but that recent diversification is lineage‐ and spatially‐dependent.

Ecotourist trail-use affects the taxonomic, functional and phylogenetic diversity of mammals in a protected area: lessons for conservation management.

Ecotourism, by definition, aims to engage peoples' interest in wildlife and the environment. The use of tourist roads and trails to access sites within protected areas (PAs) can detrimentally affect the behavior and distribution of species. The way mammals respond to anthropogenic pressures may differ across taxonomic, functional, and phylogenetic groups; nevertheless, how ecotourist trail-use affects these different diversity remains under-investigated. Here, we assessed 6 metrics of taxonomic, phylogenetic, and functional diversity for a mammal community in a PA in central China, recording how Trail use (using Trail type as a proxy) and habitat variables affected sightings and signs of mammals across 60 replicate 0.5 km transects. We then examined how Trail use affected the taxonomic, functional, and phylogenetic diversity indices of species (>1 kg). Using generalized liner mixed modeling, we identified that more used trail types had a greater adverse effect on all diversity richness indices than did less used trail types. Consequently, tourist pressure was associated with a general tendency to homogenize the site's mammal community. In contrast, the effects of Trail Types on all diversity evenness indices were non-significant. Furthermore, more developed and more heavily used trail types had a greater, significant negative effect on taxonomic, functional, and phylogenetic richness, whereas these richness indices were unaffected by minor trail types, used less intensively. As a general principle, lower biodiversity indices reduce ecosystem resilience, and so it is vital to better understand these responses to balance public access against biodiversity management in PAs.

Species pool size and rainfall account for the relationship between biodiversity and biomass production in natural forests of China.

The strength of biodiversity–biomass production relationships increases with increasing environmental stress and time. However, we know little about the effects of abiotic (e.g., climate) and biotic (e.g., species pool and community composition) factors on this trend. Whether variation in biomass production is best explained by phylogenetic diversity metrics or traditional measures of species richness also remains elusive. We compiled estimates of community composition and biomass production for tree species in 111 permanent quadrats spanning three natural forests (tropical, subtropical, and temperate) in China. Based on ~10 years of data, we compared temperature, rainfall, species pool size, and community composition in each forest each year. We estimated species richness and phylogenetic diversity in each quadrat each year; the latter metric was based on the sum of branch lengths of a phylogeny that connects species in each quadrat each year. Using generalized linear mixed‐effect models, we found that top‐ranked models included the interaction between forest and biodiversity and the interaction between forest and year for both biodiversity metrics. Variation in biomass production was best explained by phylogenetic diversity; biomass production generally increased with phylogenetic diversity, and the relationship was stronger in subtropical and temperate forests. Increasing species pool size, temperature, and rainfall and decreasing inter‐quadrat dissimilarity range shifted the relationship between biomass production and phylogenetic diversity from positive to neutral. When considered alone, species pool size had the strongest influence on biomass production, while species pool size, rainfall, and their interaction with phylogenetic diversity constituted the top‐ranked model. Our study highlights the importance of species pool size and rainfall on the relationship between phylogenetic diversity and biomass production in natural forest ecosystems.

Does anthropogenic fragmentation selectively filter avian phylogenetic diversity in a critically endangered forest system?

SummaryDocumenting phylogenetic diversity for conservation practice allows elucidation of ecosystem functioning and processes by highlighting the commonality and divergence of species’ functional traits within their evolutionary context. Conserving distinct evolutionary histories has intrinsic value, and the conservation of phylogenetically diverse communities is more likely to preserve distinct or relic evolutionary lineages. We explored the potential for anthropogenic forest fragmentation to act as a selective filter of avian phylogenetic diversity within the community of forest-dependent birds of the critically endangered Indian Ocean Coastal Belt Forest (IOCBF), South Africa. We conducted avian point count surveys during the austral breeding season, and calculated fragmentation metrics of forest structural complexity, patch size and isolation. We constructed a maximum likelihood phylogeny using the combined analysis of two mitochondrial genes and three nuclear markers and measured the influence of the fragmentation metrics on six measures of phylogenetic diversity. Our results indicated that the avian community was variously affected by anthropogenic forest fragmentation, with the different metrics of phylogenetic diversity responding with no definitive overall pattern. However, forest structural complexity emerged as an important metric explaining phylogenetic structuring. While the avian community’s phylogenetic diversity displayed resilience to anthropogenic fragmentation, previous research showed a reduction in functional diversity along the fragmentation gradient. Therefore, we recommend studies that especially aim to guide conservation management, incorporate both phylogenetic and functional diversity measures to sufficiently interrogate communities’ resilience to the threats under investigation.

Central and Northern European caterpillar assemblages show strong phylogenetic structure

AbstractPhylogenetic diversity metrics have been used to tackle an increasing number of questions in ecology and evolutionary biology. Here we present a novel use of phylogenetic diversity metrics namely the investigation of insect herbivore assemblages on select plant species in order to investigate possible drivers shaping the phylogenetic structure of those assemblages.We investigated the phylogenetic structure of lepidopteran herbivore assemblages on 208 species of central European vascular plants. A dataset of 2,553 species of Lepidoptera from 68 families, comprising 8,584 individual herbivore‐host associations, was analysed for patterns of phylogenetic α‐ and β‐diversity in relation to plant growth form, plant phylogeny and the accumulation of some characteristic major classes of secondary plant metabolites.Distinct patterns of phylogenetic β‐diversity were detected when plants were partitioned into three growth form categories (graminoid, herbaceous and woody). In contrast, groupings of plants according to higher taxa or key secondary metabolites did not yield similarly clear patterns. Notable exceptions were assemblages on graminoid plants, especially those containing silica, which could be distinguished by both plant phylogeny and their phytochemical characteristics. Additionally plants containing highly toxic glucosinolates (all of the family Brassicaceae) harbour highly distinct lepidopteran assemblages. Phylogenetic α‐diversity of associated caterpillars differed greatly between graminoid, herbaceous and woody plants. Assemblages on graminoid plants were found to be the most phylogenetically clustered, followed by herbs and woody plants which showed the least degree of phylogenetic clustering. In conclusion, our results indicate that the phylogenetic structure of the investigated herbivore assemblages in the nemoral and boreal zones of the Western Palaearctic region is most heavily influenced by plant growth form while categories derived from higher plant systematics or classifications reflecting secondary metabolites leave far less signal at this macroecological scale.The approach taken in this study proved to be very successful in identifying patterns in the phylogenetic structure of herbivore assemblages. Our findings are in line with the ‘classical’ plant apparency hypothesis. Plant secondary compounds were found to have only limited explanatory power on our scale of analysis.A freePlain Language Summarycan be found within the Supporting Information of this article.

Long-Term Clonal Dynamics upon Allogeneic Haematopoietic Stem Cell Transplantation Revealed Using Somatic Mutations As Clonal Tracking Marks in HSC Donor and Recipient Pairs

▪Allogeneic haematopoietic stem cell transplantation (HSCT) is a potentially curative treatment for over 40,000 patients/year in Europe and the US alone. However, substantial treatment-related mortality and morbidity, as well as risks of disease relapse give a survival rate of about 50% and leave considerable room for improvement. Despite being an established treatment for over 50 years, fundamental questions remain regarding its biology. For example, how many of the frequently >100 million transplanted CD34+ cells are true haematopoietic stem cells (HSCs), determined by long-term engraftment and contribution to multi-lineage hematopoiesis (long-term engrafting HSCs [LTE-HSCs])? What are the mutational consequences for transplanted HSCs given their proliferation and potential mutagenic insults in the post-transplant period? Most recently, the discovery of clonal haematopoiesis (CH) has raised interest in the interaction between this and HSCT. Do such clones further expand during HSCT? This may potentially lead to the devastating complication of donor-cell leukemia or other CH-related risks, e.g. cardiovascular disease. Recently, some studies have addressed this using targeted sequencing panels for myeloid cancer genes. However, many clonal expansions in normal blood are not driven by mutations in such genes, with evidence suggesting that the set of potential ‘driver’ genes is much larger than currently recognized (Poon et al, bioRXiv 2020).Advances in HSC tracking methodologies - using naturally-occurring somatic mutations as clonal markers (Lee-Six et al, Nature 2018) - provide a powerful tool to simultaneously address these questions. Whole-genome sequencing of hundreds of single-cell derived haematopoietic stem and progenitor cell (HSPC) colonies from a single individual is used to compile a complete set of somatic mutations in each colony founder cell, and the pattern of shared mutations amongst cells used to infer their phylogeny or ‘family tree’. The constant rate of mutation acquisition during post-development life allows estimation of the timing of mutation acquisition. Using phylodynamic approaches borrowed from pathogen biology, patterns of branching points can be used to infer important parameters such as the size of population ‘bottlenecks’ (in this context the number of LTE-HSCs), and the growth dynamics of expanded clones.We selected 7 donor/ recipient (D/ R) pairs who had undergone HSCT 9-31 years previously. For each individual (D and R), peripheral blood CD34+ HSPC-derived colonies were grown on methylcellulose medium. Whole-genome sequencing (WGS) was performed on 100-300 colonies per individual - a total of 2,278 genomes. Mutations were called using established pipelines, then filtered to remove artefacts, germline variants, and in vitro mutations leaving only somatically-acquired mutations. Phylogenies for each D/R pair were inferred, using a maximum parsimony algorithm. Mutational signatures were extracted using a hierarchical dirichlet process. D/R phylogenies were compared using metrics of phylogenetic diversity. Clonal fractions of expanded clones in D/R were compared. Approximate Bayesian computation was used to estimate numbers of LTE-HSCs.Our results reveal that HSCT engraftment is remarkably polyclonal, with thousands of transplanted HSCs (in most cases >5,000) actively contributing to haematopoiesis decades after transplant. HSCs suffer little consequence in terms of their somatic mutation burden. Recipient haematopoiesis showed decreased clonal diversity compared to their donors with a mean 20% decrease of the Shannon's Diversity Index. This may partly result from increased selective pressures during HSCT. Intriguingly, several DNMT3A-driven expansions seen in donors had lower clonal fractions in recipients. Conversely, clones with >1 driver mutation (e.g. DNMT3A/CHEK2) showed larger expansions in recipients compared to donors, despite originating in the donor. DNMT3A mutations frequently originated in early development - in one case occurring in utero.We demonstrate the power of applying a novel clonal tracking approach to HSCT, for the first time giving a detailed picture of the clonal dynamics of engraftment. Overall, our findings are reassuring from a safety perspective, but the different clonal composition in recipients merits further investigation to better understand the factors involved. DisclosuresManz: University of Zurich: Patents & Royalties: CD117xCD3 TEA; CDR-Life Inc: Consultancy, Current holder of stock options in a privately-held company. Campbell: Mu Genomics: Current holder of individual stocks in a privately-held company, Membership on an entity's Board of Directors or advisory committees.

Effects of land‐use change on avian taxonomic, functional and phylogenetic diversity in a tropical montane rainforest

AbstractAimAlthough land use change is a leading cause of biodiversity loss worldwide, there is scant information on the extent to which it has affected the structure and composition of bird communities in the Afrotropical region. This study aimed to quantify the effects of habitat transformation on taxonomic, functional and phylogenetic diversity in Afrotropical bird communities.LocationNyungwe landscape, a montane rainforest with adjoining farmland in south‐west Rwanda.MethodsData on bird occurrence, abundance and functional traits were collected in 2017/18 using point counts. We also collected data on habitat and morphological traits for all bird species recorded. We quantified bird diversity using a range of metrics, including the inverse Simpson index, functional dispersion and the standardized effect size of mean nearest taxon distance.ResultsIn comparison with primary forest areas, even low levels of land use change altered species composition and reduced species diversity. Although overall functional diversity and phylogenetic diversity were similar across land use types, we found a significant contraction of trophic and locomotory trait structures of bird communities in restored areas and cultivated areas, respectively. Soil moisture, elevation and lower vegetation height were major factors influencing taxonomic, functional and phylogenetic dimensions of bird communities, although their effects varied across these dimensions.Main conclusionsThe sensitivity of forest species to minor habitat disturbance emphasizes the value of conserving primary vegetation. Long‐term conservation of bird communities in Afromontane ecosystems requires halting wide‐scale destruction of primary forest, promoting vegetation heterogeneity in the ecological restoration of degraded habitats and adopting wildlife‐friendly agricultural practices. Our results suggest that monitoring and conservation in these landscapes can be refined using taxonomic, functional and phylogenetic diversity metrics to provide complementary information about the current and likely future impacts of land use change.

Phylogenetic uncertainty and the inference of patterns in community ecology and comparative studies.

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.

Taxonomic, phylogenetic and functional diversity of understorey plants respond differently to environmental conditions in European forest edges

Abstract Forest biodiversity world‐wide is affected by climate change, habitat loss and fragmentation, and today 20% of the forest area is located within 100 m of a forest edge. Still, forest edges harbour a substantial amount of terrestrial biodiversity, especially in the understorey. The functional and phylogenetic diversity of forest edges have never been studied simultaneously at a continental scale, in spite of their importance for the forests' functioning and for communities' resilience to future change. We assessed nine metrics of taxonomic, phylogenetic and functional diversity of understorey plant communities in 225 plots spread along edge‐to‐interior gradients in deciduous forests across Europe. We then derived the relative effects and importance of edaphic, stand and landscape conditions on the diversity metrics. Here, we show that taxonomic, phylogenetic and functional diversity metrics respond differently to environmental conditions. We report an increase in functional diversity in plots with stronger microclimatic buffering, in spite of their lower taxonomic species richness. Additionally, we found increased taxonomic species richness at the forest edge, but in forests with intermediate and high openness, these communities had decreased phylogenetic diversity. Functional and phylogenetic diversity revealed complementary and important insights in community assembly mechanisms. Several environmental filters were identified as potential drivers of the patterns, such as a colder macroclimate and less buffered microclimate for functional diversity. For phylogenetic diversity, edaphic conditions were more important. Interestingly, plots with lower soil pH had decreased taxonomic species richness, but led to increased phylogenetic diversity, challenging the phylogenetic niche conservatism concept. Synthesis. Taxonomic, phylogenetic and functional diversity of understorey communities in forest edges respond differently to environmental conditions, providing insight into different community assembly mechanisms and their interactions. Therefore, it is important to look beyond species richness with phylogenetic and functional diversity approaches when focusing on forest understorey biodiversity.

Fruit trees and herbaceous plants increase functional and phylogenetic diversity of birds in smallholder rubber plantations

Rubber plantations are widespread in mainland South-east Asia. Intensive monocultural rubber cultivation practices predominate, which negatively impact biodiversity. Some plantations are managed as high-yielding agroforests, where the integration of fruit trees and other plant species marginally enhances crop diversity relative to monocultures, providing benefits for species richness of some taxa without compromising yields. A key question is whether these high-yielding agroforestry systems also support enhanced functional and phylogenetic diversity relative to monoculture. Focusing on birds in rubber monocultures and agroforests in two provinces of Southern Thailand, we study plantation habitat structure and wider landscape characteristics to identify effects on functional and phylogenetic diversity metrics. Functional diversity, phylogenetic diversity and evolutionary distinctiveness of birds were comparable between rubber monocultures and intensive agroforests. The density of fruit stems and taller herbaceous plants within agroforests positively influenced functional and phylogenetic diversity, and evolutionary distinctiveness. Functional and phylogenetic diversity was higher in landscapes with a greater proportion of fruit orchards, but was lower in landscapes with a greater proportion of degraded natural forest patches. Our study suggests that the integration of fruit trees and maintaining taller herbaceous plants within rubber plantations could help support bird diversity at evolutionary and functional levels. Small patches of degraded forest in areas dominated by agriculture may need time to generate positive spillover effects on the functional and phylogenetic diversity of birds within rubber plantations. Better management of existing rubber plantations could sustain higher diversity, while offering food security and alternative revenue streams.

Recent changes in mountain hay meadows of high conservation value in eastern France

AbstractAimTo assess vegetation changes in mountain hay meadows of high conservation value over 15 years.LocationJura Mountains and Vosges Mountains (France).MethodsIn 2019, we resampled old phytosociological relevés (made from 2005 to 2009) in extensive mountain hay meadows. To detect shifts in composition from old to recent relevés, we performed a permutational multivariate analysis of variance, and visualized observed patterns using non‐metric multidimensional scaling on the Bray–Curtis dissimilarity matrix of the vegetation data. We tested for differences in taxonomic, functional and phylogenetic diversity metrics, CSR strategies and ecological indicator values using paired Wilcoxon–Mann–Whitney tests.ResultsNon‐metric multidimensional scaling paired with a permutational multivariate analysis of variance showed that, overall, old and recent plant communities were not different in the Vosges Mountains, contrary to the situation in the Jura Mountains. Wilcoxon–Mann–Whitney paired tests revealed that, in the Jura Mountains, plant communities underwent a significant decrease in taxonomic, functional and phylogenetic diversity, associated with an increase of ruderal and competitive strategies. Ecological indicator values for nutrient availability and defoliation tolerance both increased, suggesting an intensification of agricultural practices. In the Vosges Mountains, only species richness increased while the inverse Simpson index and Pielou evenness decreased.ConclusionsOur results show that plant diversity is not currently threatened in the studied grasslands in the Vosges Mountains. By contrast, in the studied grasslands in the Jura Mountains, plant diversity is declining. The situation in the Vosges shows that agricultural activities and biodiversity conservation can be reconciled. This situation should be further investigated to help resolve conflicts between agriculture and biodiversity conservation in semi‐natural grasslands.

Using phylogenetic diversity to explore the socioeconomic and ecological drivers of a tropical, coastal urban forest

Relatively little is known about the dynamics of tropical urban forests, their phylogenetic diversity, as well as the socioeconomic and ecological factors that influence overall diversity across the urban landscape. However, permanent forest inventory and monitoring plot networks are increasingly being established across forests and cities of the world to monitor structural and functional attributes of urban forests, as well as ecosystem services. We analyzed a tropical, coastal urban forest in San Juan, Puerto Rico using metrics of phylogenetic diversity (PD), plant diversity, and available permanent plot data from an urban forest inventory and monitoring system. In total, we found 152 species belonging to 119 genera and 44 families in San Juan. PD tended to be highest in forest remnant areas. We also explored correlations between socioeconomic factors and taxonomic diversity and found that plant species richness was correlated with population density and housing price. We found marginally significant relationships between housing price, population density, and several PD metrics. Our results further suggest mixed evidence of luxury and legacy effects, two factors that have been linked to the plant diversity of anthropogenic ecosystems in other research. Overall, despite centuries of human influence, the existing urban forest diversity in San Juan - although perhaps not the particular species composition - is likely to be primarily the result of climate, biome, and multi-scale socioeconomic contexts and not legacy effects. The approach used and findings from this study could be used to better understand the application of PD metrics for assessing urban biodiversity and other beneficial attributes and traits of urban forests.