Mean Nearest Taxon Distance Research Articles

Hot node limitations and impact of taxonomic resolution on phylogenetic divergence patterns: A case study on Ecuadorian ethnomedicinal flora

SummarySocietal Impact StatementNovel phylogenetic approaches have emerged in recent years to study traditional medicinal plants, aiming to identify potential sources of new drugs. This line of research holds considerable promise yet remains in its early stages. Here, we examine the prevalent methods employed in the field, revealing the impact of methodological choices that have often been made arbitrarily. We also highlight a widespread misconception regarding ‘hot node analysis’, a tool gaining popularity for identifying plants with high bioactive potential. Our findings should advance future research aimed at guiding the selection of promising candidates for bioprospection.Summary Advances in phylogenetics offer a ground‐breaking approach to analysing ethnobotanical data. This line of research typically involves calculating the degree of phylogenetic clustering (i.e. phylogenetic divergence) of a set of medicinal plants and identifying clades with a significant overabundance of these plants, known as hot nodes, which are purportedly responsible for the clustering patterns. However, despite showing great promise, the adequacy of this procedure remains to be tested, and the results have so far been inconclusive and, at times, contradictory. Here, we examine two key elements through a case study of Ecuadorian medicinal flora: the impact of taxonomic resolution (species‐ and genus‐level data) on phylogenetic divergence metrics (Mean Pairwise Distance; MPD, and Mean Nearest Taxon Distance; MNTD), and the efficacy of the hot node analysis in identifying clades that significantly influence these metrics. To identify clades with a significant impact on MPD and MNTD, we implemented a jackknifing procedure and compared outcomes with the hot nodes. Phylogenetic divergence was strongly dependent on the taxonomic resolution, with clustering mainly revealed by MPD at the genus level. Further, the hot nodes incompletely matched those with significant influence on MPD and MNTD according to the jackknifing analysis. We highlight the impact of taxonomic resolution on commonly used phylogenetic divergence metrics and the limitations of hot nodes in identifying influential clades, stressing the potential of alternative jackknifing techniques. We recommend the use of the most resolved tree possible and combining jackknifing with hot node analyses as complementary sources to pinpoint clades for bioprospection.

Phylogenetic structure and turnover between lowland and montane subtropical forests indicate differential community assembly processes, affected by successional stage and spatial gradients

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

Latitudinal gradients in the phylogenetic assembly of angiosperms in Asia during the Holocene

Spatio-temporal assessment of phylogenetic diversity gradients during the Holocene (past 12,000 years) provides an opportunity for a deeper understanding of the dynamics of species co-occurrence patterns under environmental fluctuations. Using two robust metrics of phylogenetic dispersion (PD) and 99 fossil pollen sequences containing 6557 samples/assemblages, we analyse spatio-temporal variation in PD of angiosperms and its relationship with Holocene climate in central Asia. Overall, PD throughout the Holocene decreases linearly with increasing latitude, except for a rise in mean nearest taxon distance from ca. 25 to 35° N. This indicates that phylogenetically divergent taxa decrease progressively with increasing latitude, leaving more phylogenetically closely related taxa in the assemblages, thereby increasing phylogenetic relatedness among the co-occurring taxa. The latitudinal gradient of PD has not been consistent during the Holocene, and this temporal variation is concordant with the Holocene climate dynamics. In general, profound temporal changes in the latitudinal PD toward higher latitudes implies that the major environmental changes during the Holocene have driven considerable spatio-temporal changes in the phylogenetic assembly of high-latitude angiosperm assemblages. Our results suggest that environmental filtering and the tendency of taxa and lineages to retain ancestral ecological features and geographic distributions (phylogenetic niche conservatism) are the main mechanisms underlying the phylogenetic assembly of angiosperms along the climate-latitudinal gradient. Ongoing environmental changes may pose future profound phylogenetic changes in high-latitude plant assemblages, which are adapted to harsh environmental conditions, and therefore are phylogenetically less dispersed (more conservative or clustered).

Dynamic restoration mechanism of plant community in the burned area of northeastern margin of Qinghai-Tibet Plateau.

Forest fires play a pivotal role in influencing ecosystem evolution, exerting a profound impact on plant diversity and community stability. Understanding post-fire recovery strategies holds significant scientific importance for the ecological succession and restoration of forest ecosystems. This study utilized Partial Least Squares Path Modeling (PLS-PM) to investigate dynamic relationships among plant species diversity, phylogenetic diversity, soil properties, and community stability during various recovery stages (5-year, 15-year, and 23-year) following wildfires on the northeastern margin of the Qinghai-Tibet Plateau. The findings revealed: (1) Over time, species richness significantly decreased (p< 0.05 or p< 0.01), while species diversity and dominance increased, resulting in uniform species distribution. Community stability progressively improved, with increased species compositional similarity. (2) Throughout succession, phylogenetic diversity (PD) significantly decreased (p< 0.01), accompanied by rising Mean Pairwise Distance (MPD) and Mean Nearest Taxon Distance (MNTD). Net Relatedness Index (NRI) shifted from positive to negative, indicating an increasing aggregation and dominance of plants with similar evolutionary traits in burned areas. Early succession witnessed simultaneous environmental filtering and competitive exclusion, shifting predominantly to competitive exclusion in later stages. (3) PLS-PM revealed that in the early recovery stage, soil properties mainly affected community stability, while species diversity metamorphosed into the primary factor in the mid-to-late stages. In summary, this study showed that plant diversity and phylogenetic variation were successful in revealing changes in community structure during the succession process. Soil characteristics functioned as selective barriers for plant communities during succession, and community stability underwent a multi-faceted and dynamic process. The soil-plant dynamic feedback continuously enhanced soil conditions and community vegetation structure thereby augmenting stability. Post-fire vegetation gradually transitioned towards the original native state, demonstrating inherent ecological self-recovery capabilities in the absence of secondary disturbances.

Phylogenetic diversity and community wide-trait means offer different insights into mechanisms regulating aboveground carbon storage

Both attributes of functional traits and phylogenetic diversity influence ecosystem functions, but which of these factors is most important is still poorly understood in natural systems. Using data from West African forests and tree savannas, we analyse how (i) phylogenetic diversity complements attributes of functional traits in explaining aboveground carbon (AGC); (ii) phylogenetic diversity relates with attributes of functional traits along gradients of phylogenetic signal; and (iii) pathways between phylogenetic diversity and attributes of functional traits relate AGC to soil and climate. Phylogenetic diversity was measured as standardised effect size of Mean Pairwise Distance (sesMPD) and Mean Nearest Taxon Distance (sesMNTD). Functional dispersion (FDis) and community weighted mean (CWM) were calculated for four traits related to leaf economics spectrum and plant life-history.Functional traits-based models explained 11 % of AGC variability. With two out of the four traits being phylogenetically conserved, incorporating phylogenetic diversity in the models increased the explained variance in AGC by 15 %. The slope of phylogenetic diversity-trait relationship was more responsive to trait conservatism for FDis than CWM. AGC was positively influenced by sesMPD and CWM of plant maximum height. In turn, CWM of plant maximum height increased with higher soil nitrogen and climate moisture, whereas sesMPD was negatively related with climate moisture. Although FDis was positively associated with sesMPD, it was not as important as sesMPD and CWM of plant maximum height in influencing and relating AGC to soil nitrogen and climate moisture.Our results suggest that phylogenetic diversity is important for AGC but does not fully reflect the functional mechanisms pertaining to community-wide trait means. The study also demonstrates the role of environment in regulating AGC, which operates through differences in community fitness driven by tall plant stature, and evolutionary processes whereby closely related species are maintained in less arid environments.

Response of Aboveground Net Primary Production, Species and Phylogenetic Diversity to Warming and Increased Precipitation in an Alpine Meadow.

The uncertain responses of aboveground net primary productivity (ANPP) and plant diversity to climate warming and increased precipitation will limit our ability to predict changes in vegetation productivity and plant diversity under future climate change and further constrain our ability to protect biodiversity and ecosystems. A long-term experiment was conducted to explore the responses of ANPP, plant species, phylogenetic α-diversity, and community composition to warming and increased precipitation in an alpine meadow of the Northern Tibet from 2014 to 2019. Coverage, height, and species name were obtained by conventional community investigation methods, and ANPP was obtained using observed height and coverage. Open-top chambers with two different heights were used to simulate low- and high-level climate warming. The low- and high-level increased precipitation treatments were achieved by using two kinds of surface area funnel devices. The high-level warming reduced sedge ANPP (ANPPsedge) by 62.81%, species richness (SR) by 21.05%, Shannon by 13.06%, and phylogenetic diversity (PD) by 14.48%, but increased forb ANPP (ANPPforb) by 56.65% and mean nearest taxon distance (MNTD) by 33.88%. Species richness, Shannon, and PD of the high-level warming were 19.64%, 9.67%, and 14.66% lower than those of the low-level warming, respectively. The high-level warming-induced dissimilarity magnitudes of species and phylogenetic composition were greater than those caused by low-level warming. The low- rather than high-level increased precipitation altered species and phylogenetic composition. There were significant inter-annual variations of ANPP, plant species, phylogenetic α-diversity and community composition. Therefore, climate warming and increased precipitation had non-linear effects on ANPP and plant diversity, which were due to non-linear changes in temperature, water availability, and/or soil nutrition caused by warming and increased precipitation. The inter-annual variations of ANPP and plant diversity were stronger than the effects of warming and especially increased precipitation on ANPP and plant diversity. In terms of plant diversity conservation and related policy formulation, we should pay more attention to regions with greater warming, at least for the northern Tibet grasslands. Besides paying attention to the responses of ANPP and plant diversity to climate change, the large inter-annual changes of ANPP and plant diversity should be given great attention because the large inter-annual variation indicates the low temporal stability of ANPP and plant diversity and thus produces great uncertainty for the development of animal husbandry.

Seasonal and spatial dynamics of phylogenetic structure of fish communities in coastal waters

Understanding community assembly has long attracted the attention of ecologists. There are a lot of studies on how community assembly mechanisms work through phylogenetic analysis. Nevertheless, phylogenetic structures have generally been assumed to be stable over time in most studies, and little attention has been paid to seasonal shifts in phylogenetic structure, which is important to mobile animals. In this study, phylogenetic distance was measured as the mean pairwise distance (MPD) and as mean nearest taxon distance (MNTD). The phylogenetic structures of fish communities in different regions, subregions and at sampling stations were examined using the standardized effect sizes of MPD and MNTD (SES.MPD and SES.MNTD) under null model independent swap over four seasons in the coastal waters of Shandong Province, China. Generalized additive model (GAM) was used to detect which environmental factors have an important impact on phylogenetic structure indices at each sampling station. The fish communities were phylogenetically clustered in most seasons in the whole survey waters, indicating environmental filtering tended to shape the whole fish assemblage. Two phylogenetic indices indicated that the phylogenetic structure (phylogenetic over-dispersion or phylogenetic clustering) was inconsistent on the different regions and subregions. For fish assemblages at each sampling station, the phylogenetic structure of fish communities presented patchy distribution patterns in different seasons. GAM analysis showed that phylogenetic structure responded differently to different environmental factors over four seasons, and the change in phylogenetic structure indices was significantly associated with environmental factors, especially in autumn and winter. SES.MPD can better respond to environmental changes than SES.MNTD. Spatial factors (longitude and latitude) were important factors influencing fish community assembly, indicating that fish communities at offshore stations with low latitude exhibit a relatively high degree of phylogenetic overdispersion. It was difficult to draw consistent conclusions about seasonal changes in phylogenetic structure of fish communities on different temporal and spatial scales. It is possible that seasonal variations and spatial scales in assembly mechanisms contribute to maintaining marine fish diversity in temperate waters, resulting in different phylogenetic structures in fish community.

Structural and functional diversity of the microbiome during the Phaeocystis globosa winter bloom in the southern Yellow Sea of China

Phytoplankton blooms affect the microbial community seriously in marine ecosystems. Here, we used 16 S rRNA gene high-throughput sequencing and functional prediction to reveal the microbiome communities in different stages of the Phaeocystis globosa bloom in the southern Yellow Sea in December 2021. The total microbial abundance and diversity increased from the middle to the late stage of the bloom, but the dominant taxa remained the same, including Alphaproteobacteria, Bacteroidia, and Gammaproteobacteria. In terms of temporal changes, the abundance of Alphaproteobacteria decreased significantly over time (p < 0.05). The dominant families in both periods were Rhodobacteraceae and Flavobacteriaceae, but their abundance varied significantly over time (p < 0.05), for the proportion of Rhodobacteraceae decreased from 51.05% to 43.55%, while the Flavobacteriaceae increased from 16.60% to 20.91%. Other less abundant but important functional groups also varied significantly over time, with the percentage of Comamonadaceae decreased (p < 0.001), while Methylophagaceae and Microbacteriaceae increased dramatically (p < 0.01). The predicted functions of the microbial communities were characterized by chemoheterotrophy, oxidation of sulfur, sulfur compounds and sulfite, and reduction of nitrate, and significant differences were also observed between stages and fractions. Multiple environmental factors (temperature, phosphate, silicate, and colony density) showed significant effects on the microbial community, and phylogenetic-based mean nearest taxon distance (MNTD) analyses indicated that stochastic processes were more important in governing the spatiotemporal assembly of the microbiome during the bloom. Overall, the microbial responses to the P. globosa bloom suggested a substrate-controlled succession in the microbiome communities.

Asymmetric warming among elevations may homogenize plant α-diversity and aboveground net primary production of alpine grasslands

It is well known that asymmetric warming among elevations (i.e., warming magnitude increases with increasing elevation) will weaken the difference of air temperature among elevations. However, it remains controversial on whether asymmetric warming among elevations can homogenize plant α-diversity and above-ground net primary production (ANPP) in alpine regions. In the present study, we conducted an experiment of asymmetric warming among elevations in alpine grasslands, Northern Tibet since 2010. There were four experiment treatments, including a treatment under natural conditions at elevation 4,313 m (C4313), a treatment under natural conditions at elevation 4,513 m (C4513), a treatment under warming conditions at elevation 4,513 m (W4513) and a treatment under warming conditions at elevation 4,693 m (W4693). We investigated ANPP, taxonomic α-diversity (i.e., species richness, Shannon, Simpson and Pielou) and phylogenetic α-diversity (mean nearest taxon distance, MNTD; phylogenetic diversity, PD) in 2011–2019. There were no significant differences of mean air temperature between C4313 and W4513, or between C4513 and W4693 in 2011–2019, indicating the differences of air temperature were eliminated among elevations. Then we found that the differences of plant α-diversity and ANPP were also eliminated among elevations: (1) there were no significant differences of ANPP, Pielou and MNTD between C4313 and W4513, or between C4513 and W4693 in 2011–2019. (2) There were also no significant differences of mean species richness, Shannon and Simpson between C4513 and W4693 in 2011–2019. (3) There were also no significant differences of ANPP, species richness, Shannon, Simpson, Pielou, PD and MNTD between C4313 and W4513, or C4513 and W4693 in 2019. Therefore, asymmetric warming among elevations may homogenize plant α-diversity and aboveground net primary production in alpine grasslands, at least in Northern Tibet.

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.

Latitudinal gradients in the skull shape and assemblage structure of delphinoid cetaceans

AbstractWithin delphinoid cetaceans, snout shape is significantly correlated to diet, with long-snouted raptorial-feeding predators preying on smaller and more agile prey than shorter-snouted species. Although there have been several studies into longirostry from a functional perspective there have been no quantitative analyses of spatial variation in skull shape or how the pattern in skull shape morphospace occupation varies between assemblages. Here we analyse the cranial morphological variation of Delphinoidea assemblages. Firstly, we calculate mean and Gi* hotspot statistics of skull shape across the world’s oceans. We find that tropical and subtropical assemblages exhibit higher average measures of longirostry. This pattern is likely caused by differences in the availability of certain prey types in warmer and cooler environments. Secondly, we calculate mean pairwise distance as well as mean nearest taxon distance in functional traits between the members of 119 unique delphinoid assemblages. There was a trend for low latitude assemblages to exhibit greater overdispersion in PC1 (snout length) compared those from high latitudes. Our results suggest that ocean temperature is influential in determining the diversity, range limits and assemblage structure of delphinoid cetaceans.

Plant community assembly of alpine meadow at different altitudes in NortheastQinghai‐TibetPlateau

AbstractThe mechanism of community assembly is the core of ecological research. Using phylogenetic‐based and functional trait‐based methods jointly to explore the processes is a useful way to explain the change in assembly mechanisms. The present study combined these methods to explore the mechanism of plant community assembly in alpine meadows at different altitudes on the northeast Qinghai‐Tibet Plateau. We established a permanent study plot of 1.85 × 105 m2and investigated 162 quadrats of 50 × 50 cm. We calculated the species richness, phylogenetic diversity (PD), standardized effect sizes PD (SES·PD), mean pairwise distance (SES·MPD), mean nearest taxon distance (SES·MNTD), and analyzed plant functional traits and phylogenetic signals. We found that the species richness and PD of plant community showed a “hump‐shaped” pattern, SES·PD showed a decreasing trend, and the phylogenetic structure changed from overdispersion (SES·MPD &gt; 0, SES·MNTD &gt; 0) to clustering (SES·MPD &lt; 0, SES·MNTD &lt; 0) with increasing altitude. The functional structure changed from overdispersion (nearest function index [NFI] &lt; 0) to clustering (NFI &gt; 0) with increasing altitude. Specific leaf area, leaf carbon content, and leaf phosphorus content had weak phylogenetic signals (K &lt; 1,p &lt; 0.05), and the other functional traits (plant height, leaf nitrogen content, leaf dry matter content, and relative chlorophyll content) did not show phylogenetic signals (K &lt; 1,p &gt; 0.05). The above results showed that competitive exclusion was the main driving force of community assembly at low altitudes (3000 and 3250 m), and habitat filtration was the main driving force of community assembly at high altitudes (4000 and 4500 m). For medium altitudes (3500 and 3750 m), the habitat was more complex because it was in the transition area between high and low altitudes, so the process of community construction may be random, habitat filtering, or competitive exclusion. On the whole, the niche process (deterministic process) was more important in driving for plant community assembly in the alpine meadow of the Qinghai‐Tibetan Plateau.

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.

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.

Taxonomic, functional, and phylogenetic diversity of communities hosting Ionopsidium savianum (Brassicaceae) growing on serpentine and limestone substrates

We analysed two different plant communities hosting Ionopsidium savianum (Brassicaceae), a species of EU interest included in the Habitats Directive 92/43/CEE annexes, for which specific studies on the ecology of communities where the species grows are lacking and more in-depth knowledge is needed. We examined two important sites of occurrence of this species in Tuscany with different soil types, namely limestone (Mt. Calvi) and serpentine (Mt. Pelato), to determine the structural and functional profile of the communities hosting this species in such different contexts. At each site, we surveyed the plant communities with I. savianum in ten 1 m2 quadrats to determine information on communities' species composition and total plant cover, as well as taxonomic (species richness, and Shannon H’ index), phylogenetic (phylogenetic diversity, mean nearest taxon distance and mean pairwise distance) and functional diversity (focusing on Rao’s Q, leaf functional traits and adaptive strategies community weighted mean). We took into account site location, soil type, slope aspect and microrelief as plot-level environmental factors. The two communities were highly diverging from multiple points of view. Differences were in species composition, richness and diversity, with Mt. Calvi hosting higher diversity. The indices of phylogenetic diversity were influenced significantly by site and microrelief, allowing the presence of peculiar niches occupied by the fern Asplenium ceterach. From the functional point of view, communities at Mt. Calvi showed a higher functional diversity and a higher specific leaf area. Plant height was influenced by the slope aspect and was higher on north-facing slopes. In terms of Grime’s adaptive strategies, the Mt. Pelato communities resulted to be more stress tolerant than those surveyed at Mt. Calvi. Here, a decrease in stress-tolerant strategy associated with an increase in ruderal strategy was detected in communities on north-facing slopes.

Global patterns and drivers of raptor phylogenetic and functional diversity

AbstractAimRaptors, a highly threatened but ecologically important group of birds, have been recognized as a good proxy for overall biodiversity in conservation planning. However, previous work on raptor diversity focused predominantly on taxonomic diversity. Here, we assess the global patterns of raptor taxonomic, phylogenetic and functional diversity and their association with current and historical environmental factors.LocationGlobal.Time periodPresent day.Major taxa studiedRaptors.MethodsWe compiled information from distribution maps, global trait datasets and avian phylogenies for all extant raptors. We used generalized least squares (GLS) to assess the relationship between historical and contemporary environmental predictors and species richness, phylogenetic diversity [Faith's phylogenetic diversity index (Faith's PD), mean pairwise distance (MPD) and mean nearest taxon distance (MNTD)] and functional diversity of traits related to raptor morphology, lifestyles, diet, foraging and vagility, while controlling for spatial autocorrelation.ResultsRaptor taxonomic diversity peaked in tropical regions and nearby mountain ranges. After controlling for species richness, species‐poor assemblages in high latitudes and deserts were more phylogenetically and functionally diverse than expected by chance. In species‐rich assemblages, diet and foraging traits had greater variation, whereas morphological traits had less variation than expected, suggesting that species packing promoted adaptive radiation in these assemblages. Historical climate influenced phylogenetic diversity and functional diversity of morphological, foraging and diet traits, leaving a signal of evolutionary history on modern assemblages. Human footprint was also an important driver of MPD and of niche and vagility trait functional diversity, with higher phylogenetic diversity in disturbed areas and with higher functional diversity in regions with intermediate levels of disturbance.Main conclusionsBoth palaeoclimate and contemporary environmental conditions are important drivers of raptor phylogenetic and functional diversity. We found large mismatches among taxonomic, functional and phylogenetic diversity, demonstrating how different processes filter lineages and species traits shaping raptor assemblages. Our results highlight the need to consider multiple dimensions of diversity to inform conservation planning better when using raptors as umbrella species.

Variation in plant traits and phylogenetic structure associated with native and nonnative species in an industrialized flora

Industrialized sites are hotspots for nonnative species because of continuous anthropogenic disturbance and nonnative propagule rain resulting from hitchhikers exchanged through global trade. Investigating plant traits and the phylogenetic structure of species at initial ports of entry can contribute to our understanding of how species are introduced to, assembled into, and survive at industrialized sites, which can also inform how susceptible these sites are to nonnative plant invasions. To compare native and nonnative species, we asked three questions: 1) Are plant traits differentially associated with species nativity (native versus nonnative)? (2) Do these traits have phylogenetic signals? and (3) What is the phylogenetic structure of each trait for native and nonnative species? We collected, identified, and vouchered 170 angiosperm species within the Garden City Terminal at the Port of Savannah, Georgia, USA, the largest container terminal in North America. Species nativity was derived from the literature, as were traits of pollination syndrome, dispersal syndrome, duration, and growth habit. Pearson’s Chi-squared tests were used to determine if traits were differentially associated with species nativity. Phylogenetic signal, along with mean pairwise distance (MPD) and mean nearest taxon distance (MNTD), were used to assess the degree of phylogenetic relatedness of native and nonnative species with each trait. Nonnative species showed a significant association with multiple pollination syndromes. Native species were significantly associated with perennial duration and zoophily pollination syndrome. All traits possessed a phylogenetic signal, and the anemophily pollination syndrome was significantly clustered for both native and nonnative species. Still, most other traits differed in their phylogenetic structure pattern based on the nativity. Overall, findings suggest that the environment is filtering for native and nonnative species that possess traits promoting introduction and survival at this industrialized point-of-entry. They also suggest that nonnative species trait differences partition available niches that promote their introduction to the site. More research is needed at industrialized sites to inventory and monitor the floristic community, investigate the establishment and spread probabilities of nonnative species, and prevent and mitigate nonnative species risks and impacts.

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

The Atlantic Forest biodiversity hotspot is a complex mosaic of habitat types. However, the diversity of the rain forest at the core of this complex has received far more attention than that of its marginal habitats, such as cloud forest, semi-deciduous forest or restinga. Here, we investigate broad-scale angiosperm tree diversity patterns along elevation gradients in the south-east Atlantic Forest and test if the diversity of marginal habitats is shaped from the neighbouring rain forest, as commonly thought. We calculated phylogenetic indices that capture basal [mean pairwise phylogenetic distance (MPD)] and terminal [mean nearest taxon distance (MNTD)] phylogenetic variation, phylogenetic endemism (PE) and taxonomic and phylogenetic beta diversity (BD and PBD) for 2074 angiosperm tree species distributed in 108 circular sites of 10 km diameter across four habitat types i.e. rain forest, cloud forest, semi-deciduous forest and coastal vegetation known as restinga. We then related these metrics to elevation and environmental variables. Communities in wetter and colder forests show basal phylogenetic overdispersion and short phylogenetic distances towards the tips, respectively. In contrast, communities associated with water deficit and salinity show basal phylogenetic clustering and no phylogenetic structure toward the tips. Unexpectedly, rain forest shows low PE given its species richness, whereas cloud and semi-deciduous forests show unusually high PE. The BD and PBD between most habitat types are driven by the turnover of species and lineages, except for restinga. Our results contradict the idea that all marginal habitat types of the Atlantic Forest are sub-sets of the rain forest. We show that marginal habitat types have different evolutionary histories and may act as 'equilibrium zones for biodiversity' in the Atlantic Forest, generating new species or conserving others. Overall, our results add evolutionary insights that reinforce the urgency of encompassing all habitat types in the Atlantic Forest concept.

Phylogenetic composition of native island floras influences naturalized alien species richness

Islands are hotspots of plant endemism and are particularly vulnerable to the establishment (naturalization) of alien plant species. Naturalized species richness on islands depends on several biogeographical and socioeconomic factors, but especially on remoteness. One potential explanation for this is that the phylogenetically imbalanced composition of native floras on remote islands leaves unoccupied niche space for alien species to colonize. Here, we tested whether the species richness of naturalized seed plants on 249 islands worldwide is related to the phylogenetic composition of their native floras. To this end, we calculated standardized effect size (ses) accounting for species richness for three phylogenetic assemblage metrics (Faith's phylogenetic diversity (PD), PDses; mean pairwise distance (MPD), MPDses; and mean nearest taxon distance (MNTD), MNTDses) based on a phylogeny of 42 135 native island plant species and related them to naturalized species richness. As covariates in generalized linear mixed models, we included native species richness and biogeographical, climatic and socioeconomic island characteristics known to affect naturalized species richness. Our analysis showed an increase in naturalized species richness with increasing phylogenetic clustering of the native assemblages (i.e. native species more closely related than expected by chance), most prominently with MPDses. This effect, however, was smaller than the influence of native species richness and biogeographical factors, e.g. remoteness. Further, the effect of native phylogenetic structure (MPDses) on naturalized species richness was stronger for smaller islands, but this pattern was not consistent across all phylogenetic assemblage metrics. This finding suggests that the phylogenetic composition of native island floras may affect naturalized species richness, particularly on small islands where species are more likely to co‐occur locally. Overall, we conclude that the composition of native island assemblages affects their susceptibility to plant naturalizations in addition to other socioeconomic and biogeographical factors, and should be considered when assessing invasion risks on islands.

Effects of land use and climate change on functional and phylogenetic diversity of terrestrial vertebrates in a Himalayan biodiversity hotspot

AbstractAimThe synergy between human land use and climate change is accelerating the global decline of biodiversity. In the fragile Himalayas, this trend has a strong ecological impact on wildlife communities, and a better understanding is needed to discern changes in the mechanisms. This study aims to understand the effects of land use and climate change on the functional (FD) and phylogenetic diversity (PD) of mammal and bird communities across the land use gradient.LocationEastern Himalayan biodiversity hotspot, Bhutan.MethodsMammal data were gathered from a camera trap survey and bird data from point counts. We used morphological and ecological traits of 45 mammal species and 336 bird species to construct functional trait space. We quantified FD and PD using standardized effect size of functional richness, functional dispersion, mean pairwise distance and mean nearest taxon distance. We used linear regression to evaluate the relationship between FD and PD and land use/climate variables.ResultsThe functional space of mammals was structured by body mass (small–large) and diet (herbivore–carnivore) as one major axis, and habitat breadth (generalist‐specialist) as the other, whereas bird functional space was structured by beak shape and size (large and long–small and short), body mass (small–large), foraging strata (canopy–ground) and diet (ectotherm–scavenge) along four axes. Land use (agriculture and road) negatively affected mammal FD, whereas both land use (tree cover and built‐up area) and climate (temperature and precipitation) affected PD, although the effects were highly variable. Climate (temperature) had a pronounced negative effect on bird FD while land use (agriculture, built‐up area and settlement) on PD.Main conclusionsThe realized functional space of the vertebrate groups can be represented by different planes on which species are clumped around a small number of functional strategies. The loss of species at the edge of functional space is non‐random and could result in the loss of irreplaceable traits impacting long‐term ecological and evolutionary processes. Our study demonstrates the filtering effect of anthropogenic pressure and climate change on vertebrate FD and PD. However, the association with land use suggests the potential for ecosystem services (particularly by birds). Our findings reveal nuances of dimensions of biodiversity and provide novel insights into the structure and drivers of vertebrate assemblages in the eastern Himalayas.