Mean Phylogenetic Distance Research Articles

Phylogenetic relatedness, not geographic origin, shapes traits across ontogenetic stages for common native and exotic plants in subtropical China

Abstract Functional traits, which shift as a plant develops from seed to adult and may be phylogenetically conserved, are widely acknowledged to be associated with exotic species invasion. However, existing studies comparing functional traits between native and invasive species often focus on a single ontogenetic stage, yielding mixed results. It remains unclear whether the functional trait differences and their relationship with invasiveness (e.g. range size) of exotic species remain consistent across ontogenetic stages. In this study, we experimentally compared 18 traits across the seed, early growth and adult stages of 127 native and exotic species from 19 families. These species are common and often co‐occur in the subtropical region of China. We also explored the linkage between these traits, alongside their phylogenetic relatedness with native species and exotic species' range size in China. Our results show that only seed mass differed between native and exotic species. Moreover, the compositions of traits across all stages and the entire lifespan were primarily influenced by phylogenetic relatedness rather than geographic origin. Further, the range size of exotic species in China positively correlated with their mean phylogenetic distance to native species, with no association with individual functional traits or functional distinctiveness. Synthesis. Our results emphasize the importance of comparing functional traits across ontogenetic stages between native and exotic species to improve our understanding of the role of functional traits in shaping plant invasion. Our findings also underscore the pivotal role of phylogenetic relatedness in shaping plant functional traits and the distribution of exotic species in their new ranges.

The Relationship between Trait-Based Functional Niche Hypervolume and Community Phylogenetic Structures of Typical Forests across Different Climatic Zones in China

Functional traits are pivotal for understanding the functional niche within plant communities. Yet, the relationship between the functional niches of typical forest plant communities across different climatic zones, as defined by functional traits, and their association with community and phylogenetic structures remains elusive. In this study, we examined 215 woody species, incorporating 11 functional traits spanning leaf economy, mechanical support, and reproductive phenology, gathered from forests in four climatic zones from tropical, subtropical, warm-temperate to cold-temperate zones in China and supplemented by the literature. We quantified the functional niche hypervolume (FNH), reflecting the multidimensional functional niche variability. We then probed into the correlation between the FNH and community and phylogenetic structures of forests. Our findings reveal that species richness significantly influences the geographic variance of functional niche space in forest vegetation across different climatic zones. Specifically, a community’s species richness correlates positively with the functional niche breadth occupied by the community species. The FNH of woody plants across diverse forest types shows significant associations with both the mean phylogenetic distance (MPD) and the mean nearest phylogenetic taxon distance (MNTD) of the communities. There is a progressive increase in tropical rainforest (TF), subtropical evergreen deciduous broad-leaved mixed forest (SF), and warm-temperate coniferous broad-leaved mixed forest (WF), followed by a decline in the cold-temperate coniferous forest (CF). This pattern suggests potential environmental filtering in CF, which may constrain the spatial extent of plant functional niches. Our research underscores the substantial variability in the FNH across China’s typical forest vegetation, highlighting the complex interplay between functional traits, community richness, and phylogenetic distance.

Release from aboveground enemies increases seedling survival in grasslands

Abstract Plant enemies can influence plant community assembly and structure. However, it is unclear how insect herbivores and fungal pathogens affect seedling recruitment. Complex interactions with competition and resource availability make it difficult to isolate the effect of enemies. This uncertainty can impede understanding of community assembly drivers, species coexistence and trophic interactions; and limits hypothesis testing such as of the enemy release hypothesis, a key hypothesis in invasion biology. Using a novel species‐specific approach, we examine how enemies affect seedling survival and recruitment of 16 grassland species. We planted seedlings of 16 native species from two functional groups (C4 grasses and non‐legume forbs) into two grassland sites (early and mid‐succession). We hand‐painted 1512 individual seedlings with pesticides (insecticide and fungicide) over the course of one growing season to enforce aboveground species‐specific release from enemies and tested whether it enhanced survival relative to untreated controls. Applying treatments to individuals allowed us to test for the effect of enemies on plant performance while controlling for contexts such as competition from the resident community and resource levels. Release from insects increased seedling survival by 56% on average, with no additional benefit of release from fungal pathogens. This effect was observed for both forbs and C4 grasses across both sites and was strongest in resource‐acquisitive species. There was no effect of the mean phylogenetic distance between our target species and the resident plant community, or of light availability or soil moisture. Synthesis. The significant positive effect of release from insect herbivores on survival early in colonisation—a trend that held across functional groups and types of resident community—suggests insects play an important regulatory role in community assembly, especially for resource‐acquisitive species. As variation between species could be explained by traits but not by phylogeny, we emphasise the importance of trait‐based approaches to plant community ecology. Our results also support the key mechanism (increased performance following release from enemies) underlying the enemy release hypothesis. Enemy release may therefore aid initial recruitment of plants during the invasion process.

The pollinator conservation approach “Farming with Alternative Pollinators”: Success and drivers

Global food security is heavily reliant on crop pollination. However, evidence on pollinator decline has been reported in all continents. Globally affordable conservation strategies need to be developed, as high-cost measures like European agri-environment schemes are not scalable in all countries. Here, we test, if a low-cost conservation approach named “Farming with Alternative Pollinators” (FAP) can benefit wild pollinator abundance and richness in agro-ecosystems and in crops, through establishment of marketable habitat enhancement plants (MHEP). The study was carried out in four Moroccan agro-climatic regions, during two years, using 6 main crops (pumpkin, zucchini, faba bean, tomato, eggplant and apple) and 201 sites. Additionally, we investigated how crop type, crop-MHEP composition (i.e. phylogenetic distances among crop and MHEP) and local climate can drive the success of the approach in comparison to monocultural fields. Based on 7097 recorded specimens, our results show that the wild pollinators of the entire FAP fields (i.e. 75% main crop and 25% MHEP) were significantly more abundant and species-rich than those of control fields (i.e. 100% main crop). Considering the main crop wild pollinators, FAP did not display any significant effect either on wild pollinator abundance or on pollinator richness. The mean phylogenetic distance between the main crop and MHEP, and climatic variables were not correlated with increase in wild pollinator abundance and richness in FAP fields. The crop type was found to influence the effect of the FAP approach. Our study provides strong evidence that FAP constitutes a relevant method for wild pollinator conservation in agro-ecosystems. Further research on additional environmental factors is necessary to outline the circumstances under which the FAP approach can positively affect wild pollinator communities.

Phylogenetic relatedness enhances the understanding of soil microbial coexistence in alpine wetlands of the Tibetan Plateau

Soil microorganisms, spanning diverse phylogenetic lineages, form complex ecological networks wherein various species coexist and contribute to multiple ecosystem services. While microbial networks facilitate the understanding of their coexistence and functions in soils, the influence of phylogenetic relatedness among soil microbes themselves on these networks remains largely unknown.To address this knowledge gap, we conducted a comprehensive survey of soil bacteria and archaea in twenty alpine wetlands on the Tibetan Plateau, characterized by wide edaphic and climatic heterogeneity. Through network and phylogenetic analyses, we evaluated the complexity of network associations and their dependence on phylogenetic relatedness.Our findings revealed consistencies and discrepancies between phylogenetic relatedness and network associations within soil bacterial and archaeal communities. Specifically, in bacterial networks, both positive and negative complexity were significantly associated with mean phylogenetic distance, whereas in archaeal networks, only negative complexity correlated with mean phylogenetic distance. Even after accounting for the effects of environmental factors, we observed that phylogenetic relatedness still explained variations in the complexities of bacterial and archaeal associations. Furthermore, a multi-threshold analysis indicated that network complexity exhibited phylogenetic signals in both bacterial and archaeal networks, albeit within different associated distance classes, suggesting distinct coexistence mechanisms of soil bacteria and archaea driven by niche and fitness trade-offs.Overall, our findings underscore the importance of incorporating phylogenetic information when studying microbial communities in complex soil habitats and demonstrate that phylogenetic relatedness crucially shapes coexistence outcomes among soil microbes.

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.

Taxonomic, functional, and phylogenetic diversity of primate communities in Ecuador

One of the fundamental objectives of ecology is to study the relative importance of ecological, evolutionary, and stochastic processes in determining local community structure. Many studies have focused on taxonomic diversity, paying relatively little attention to other dimensions of biological diversity, such as phylogenetic and functional diversity. Little is known about how these dimensions relate to each other, and the ecological processes that influence their variation. In this study, we characterize these three dimensions of biodiversity in 14 primate communities from different ecosystems in Ecuador to understand possible mechanisms responsible for their assembly. Results show that coastal communities are taxonomically less diverse than those from the Amazon and present different functional groups. On the other hand, phylogenetic diversity is higher in Amazonian communities, showing a tendency for overdispersion (high values of MPDPD = mean phylogenetic distance per pair and low PSC = degree to which coexisting species are related). This indicates a possible influence of biological factors, such as competition, on community assembly. For all three dimensions, climatic variables were the most significant predictors of community structure, while vertical forest structure contributed significantly to variation in the phylogenetic dimension. The high functional diversity reported in this study highlights the importance and vulnerability of this group and the ecosystems they inhabit. Macroecological studies, such as the one presented here, allow a better understanding of community structure and provide important information for the development of conservation strategies.

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.

Geographic patterns and environmental correlates of taxonomic and phylogenetic diversity of aquatic plants in China

AbstractStudies on large‐scale geographic patterns of aquatic plant diversity can promote research on the generality of macroecological patterns in different ecosystems. Here, we compiled a checklist of 889 aquatic angiosperms in China, including 738 helophytes (emergent and marshy plants) and 151 hydrophytes (submerged, free‐floating, and floating‐leaved plants). We explore the geographic patterns and environmental correlates of aquatic plant diversity based on six metrics including species richness (SR), weighted endemism (WE), phylogenetic diversity (PD), phylogenetic endemism (PE), the standardized effect size of phylogenetic diversity (PDses), and the standardized effect size of mean phylogenetic distance (MPDses). Our results show that the diversity of aquatic plants in China is extremely uneven, with high diversity in southeastern China and low diversity in northwestern China, and the geographic patterns of taxonomic and PD are generally consistent. The pattern of helophytes differs from that of hydrophytes. Notably, the wavy‐shaped pattern of aquatic plant diversity (especially SR and PD for hydrophytes) across the latitude observed in this study is not consistent with those previously observed for aquatic plants in other continents. Climatic variables and water environmental variables are the main drivers of aquatic plant diversity in China; however, the effects of individual variables differ between helophytes and hydrophytes. Water environmental variables have a greater impact on PDses and MPDses of hydrophytes than those of helophytes. Overall, our work provides insight into understanding the large‐scale patterns of aquatic plant diversity and is a critical addition to previous studies on the macroecological pattern of terrestrial organisms.

Phylogenetic structure of alien and native species in regional plant assemblages across China: Testing niche conservatism hypothesis versus niche convergence hypothesis

AbstractAimThe introduction of alien species may be influenced by the phylogenetic structure of the native assemblage, while at the same time altering that structure. Understanding these effects sheds light on both the factors influencing naturalization of introduced species and their impacts. Considering regional angiosperm assemblages across China, we ask the following questions: (a) Do geographic patterns and climate relationships of alien species richness and phylogenetic structure mirror those of natives? (b) Has the addition of alien species resulted in stronger phylogenetic clustering as predicted by Darwin's preadaptation hypothesis? (c) To what degree does the answer to these questions depend on phylogenetic scale?LocationChina.Time periodCurrent.TaxonAngiosperms (flowering plants).MethodsWe divided China into 28 province‐level regions and collated native and naturalized alien species lists of angiosperms for each region. For each region, we computed two types of phylogenetic structure metrics [mean phylogenetic distance (MPD) and mean nearest neighbour distance (MNND), and their standardized effect sizes] for the native, alien and combined assemblages, and for angiosperms as a whole, 5 major clades and 10 well‐represented families. We then related these to climatic factors using correlation analyses.ResultsRichness of alien angiosperms is highest in regions with species rich and phylogenetically dispersed native assemblages. The standardized effect size of mean phylogenetic distance (MPDses) for aliens was positively correlated with that for natives. The introduction of alien species generally increased phylogenetic clustering of the combined assemblage compared to the natives for large phylogenetic extents, but effects within plant families were mixed. The MPDses was positively correlated with temperature and precipitation for both natives and aliens.Main conclusionsThe phylogenetic relationships at a lower level of phylogenetic scale may differ substantially from those at a higher level of phylogenetic scale. At the broadest phylogenetic extents, alien species tend to recapitulate the biogeographic patterns of natives, showing similar spatial patterns of species richness and phylogenetic structure, and tending to represent the same major angiosperm clades. This is highly consistent with Darwin's preadaptation hypothesis. Across narrower swaths of the phylogeny, these patterns are less clear, with a substantial number of plant families showing support for the biogeographic barrier hypothesis.

Phylogenetic Distance Metrics for Studies of Focal Species in Communities: Quantiles and Cumulative Curves

The phylogenetic distance between species often predicts differences in ecologically important traits. The phylogenetic diversity and structure of biological communities can inform our understanding of the processes that shape those communities, and there is a well-developed framework for comparing phylogenetic structures of communities. However, particularly in studies of phylogenetic distances from one focal species to other members of its assemblage (a one-to-many framework), the standard metrics of community-wide studies encounter significant limitations due to the left-skewed distribution of pairwise phylogenetic distances in most biological communities. For studies that require estimating the degree of phylogenetic isolation of a focal taxon, the mean phylogenetic distance (MPD) usually provides little power to distinguish among taxa because it is heavily weighted by the many ways to be distantly related, whereas the nearest taxon distance (NTD) is highly idiosyncratic and ignores cases where multiple close relatives may contribute equally strongly to influence the focal species. Here we highlight the value of examining the cumulative distribution of phylogenetic distances in studies that take a focal-species approach. We describe and discuss the benefits of two new metrics. An integrated metric of phylogenetic distances (AUPhyDC) uses information from the whole cumulative distribution, whereas the tenth quantile (PD10) is an extremely simple metric that improves on NTD by capturing the influence of multiple close relatives on ecological interactions. Several recent examples found that PD10 did a better job of revealing ecological patterns than NTD or MPD. We provide R code to facilitate the use of these approaches and advocate for the inclusion of PD10 along with NTD and MPD in statistical packages for phylogenetic ecology.

Dung beetles maintain phylogenetic divergence but functional convergence across a highly fragmented tropical landscape

Abstract Understanding how human‐modified landscapes affect the phylogenetic composition and assembly mechanisms of biological communities is critical for effectively managing and restoring tropical ecosystems. We evaluated how forest coverage loss, fragmentation and landscape heterogeneity affect the phylogenetic diversity of dung beetles and their assembly mechanisms in Los Tuxtlas Biosphere Reserve, a protected but highly fragmented tropical landscape. We calculated Faith's phylogenetic diversity, mean pairwise phylogenetic distance and mean nearest taxon distance for 5,388 individuals in 36 species. The standardised effect sizes of these metrics were estimated to control their correlation with species richness. Phylogenetic diversity was also assessed separately for each dung beetle functional group. Finally, we compared the mean functional and phylogenetic pairwise distance and mean nearest taxon distance and measured the phylogenetic signal among dung beetle functional traits to determine the influence of niche conservatism on the phylogenetic structure of species assemblages. Faith's phylogenetic diversity of dung beetles was positively correlated with forest coverage, while their mean phylogenetic and nearest taxon distance values decreased with increasing landscape fragmentation. Necrophagous beetles and forest specialists responded most negatively to forest coverage loss and fragmentation. Alpha and beta diversity values showed phylogenetic overdispersion but functional convergence and weak phylogenetic signals in their functional traits, suggesting low niche conservatism. Landscapes with moderate forest coverage (≥40%) favoured higher phylogenetic beta diversity, whereas phylogenetic and functional beta diversity decreased significantly in landscapes with low forest coverage (<30%). Synthesis and applications. Forest habitats in fragmented landscapes are essential for safeguarding the evolutionary history of dung beetles, reducing biotic homogenisation processes by favouring phylogenetic overdispersion and complementarity between sites. Therefore, to secure the phylogenetic diversity of dung beetles within fragmented tropical reserves, we recommend protecting the existing forests, preventing further fragmentation of continuous forest areas and increasing matrix quality by implementing biodiversity‐friendly production systems. Finally, managers should consider assessing different functional groups in other species, as their response to landscape disturbance may not be phylogenetically similar. The above will allow more effective management practices to protect the species most susceptible to disturbances.

A global analysis of mosses reveals low phylogenetic endemism and highlights the importance of long‐distance dispersal

AbstractAimDigitization of herbarium specimens and DNA sequencing efforts in the past decade have enabled integrative analyses of patterns of diversity and endemism in a phylogenetic context. Here, we compare the best available floristic databases to a comprehensive specimen database to examine spatial patterns of moss phylogenetic assembly. We test the hypotheses that (1) mosses exhibit phylogenetic regionalization, (2) islands contain significantly high phylogenetic diversity and (3) that moss phylogenetic endemism is low on a global scale.LocationGlobal.TaxonMosses.MethodsWe developed a phylogeny of 3654 moss species using 25 markers and compiled a global specimen database from online repositories. We calculated floristic and phylogenetic measures of diversity and endemism and performed randomizations to test for significant deviations from expectations. We use rarefaction and extrapolation to alleviate substantial differences in sampling effort across the globe. We used both phylogenetic and floristic methods to test for spatial regionalization. We compare our specimen‐based results to those obtained using a floristic dataset.ResultsPhylogenetic diversity is more robust to missing data than species richness. Mean phylogenetic distance was significantly higher than expected in areas with high species richness, indicating that reported richness in these areas is likely a product of repeated colonization. Phylogenetic endemism is low globally. Phylogenetic regionalizations cluster into a Holarctic/Holantarctic temperate region, a pantropical region, and a region composed of Australia, New Zealand and South Africa.Main ConclusionsFuture efforts for collecting, sequencing and databasing moss species should focus on the tropics, particularly Africa and Southeast Asia. We provide further evidence to support several important theories developed in moss biogeography, including the role of long‐distance dispersal in shaping floristic patterns, the dominance of anagenesis in driving patterns of island diversity, and the role of climatic instability in driving patterns of assembly in the Holarctic.

Anthropogenic factors are stronger drivers of patterns of endemic plant diversity on Hainan Island of China than natural environmental factors.

The roles of natural and anthropogenic factors in contributing to the organization of biodiversity at large and small scales have long been challenging to disentangle, and doing so has never been attempted for the island province of Hainan in China based on patterns of taxonomic and phylogenetic diversity. Therefore, in this study, we evaluated the taxonomic and phylogenetic diversity of endemic plants on the island as a function of anthropogenic and natural variables based on non-metric multi-dimensional scaling (NMDS) ordination and generated generalized linear models (GLMs). We found that the highest phylogenetic diversity (1006) and the lowest mean phylogenetic distance (515.5) was in the provincial capital, Haikou. The NMDS analyses indicated that taxonomic diversity was significantly correlated with industrial revenue (p = 0.006) and population (p = 0.004). Furthermore, most phylogenetic diversity indices were strongly correlated with population and agricultural revenue, while the sampled natural environmental variables were not significantly correlated with plant diversity indices. These findings indicate that anthropogenic factors are the main present-day driving forces of plant diversity in Hainan, though we did detect a significant latitudinal diversity gradient of richness that likely reflects the historical roles of natural environmental factors in the organization of biodiversity on the island. Overall, our results are alarming for biodiversity of the island and indicate that conservation and sustainable use of endemic plant species must be made a critical priority.

Phylogenetic Diversity of Urban Floras in the Central Urals

Modern cities harbor a high diversity of plants, and urban floras are significantly different from non-urban floras especially when considering the proportion of alien species found in cities. However, it is not clear whether urban areas disproportionately select for species from relatively few evolutionary lineages or provide opportunities for species across the full spectrum of plant lineages. Here, we examined the taxonomic and phylogenetic diversity of the floras in four cities (Yekaterinburg, Kamensk-Uralsky, Krasnoufimsk, and Turinsk) in the understudied region of Central Urals (Russian Federation). We classified native species into indigenous and apophytic species, namely, those that are sensitive to anthropogenic disturbance and those that have expanded their range with human activity, respectively. Alien species were classified into archaeophytes and neophytes according to when they were introduced (i.e., before or after than 1800). Phylogenetic diversity was quantified using Faith’s index to reflect total evolutionary history in urban areas and mean phylogenetic distance (MPD) to reflect species dissimilarity. Phylogenetic diversity of native species was higher than that for alien species, and the standardized effect size (SES) of MPD for natives was positive, reflecting their general dissimilarity from one another, while it was very negative for aliens, showing that they were phylogenetically clustered. However, among natives, apophytes were significantly clustered, while indigenous species were overdispersed. For the aliens, MPD was higher for archaeophytes compared to neophytes, though both groups were significantly clustered. These results show that urbanization leads to a non-random selection of plants. Apophytes and alien plants were composed of closely related species, reflecting similar ecological traits and are likely to be pre-adapted to the environmentally altered and highly disturbed urban environment.

Ecological and evolutionary distances from neighbouring plants do not influence leaf herbivory by chewing insects in a Neotropical savanna

ABSTRACT Background Coexisting plant species frequently exhibit marked differences in leaf damage caused by chewing insects. Such variation in leaf herbivory has often been attributed to interspecific differences in leaf defensive traits, leaf nutritional quality and leaf abundance. Aims We aimed to investigate the hypothesis that plants surrounded by more similar neighbours tend to exhibit higher levels of herbivory than plants surrounded by less similar neighbours. Methods We sampled 27 tree and shrub species in 49 plots of 10 m2 located in a Neotropical savanna. For each of the 815 plants sampled, we quantified leaf damage, specific leaf area, leaf toughness, height, and conspecific abundance. We analysed the relationship between herbivory levels and plant traits comparing each individual with its neighbouring plants. The effect of phylogenetic similarity was addressed using the mean phylogenetic distance between a focal plant individual and its neighbours (i.e., the phylogenetic isolation). Results Leaf herbivory damage ranged from zero to 29.6%. We found that phylogenetic isolation, specific leaf area, plant height, and plant abundance were not related to differences in leaf herbivory at the individual level in a neighbourhood. Conclusions Our findings show that leaf herbivory damage of individual plants was not consistently influenced either by phylogenetic or by trait similarity with neighbours.

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.

Phylogenetic Community and Nearest Neighbor Structure of Disturbed Tropical Rain Forests Encroached by Streblus macrophyllus

Although woody plant encroachment of tropical forest ecosystems has been related to altered disturbance regimes, its impacts on the nearest neighborhood structures and community phylogenetics are still poorly understood. Streblus macrophyllus is a light-demanding species during its early life stages and is shade-tolerant as a mature tree. S. macrophyllus can be found in tropical karst evergreen forests in northern Vietnam. It often regenerates at high densities in anthropogenic disturbed forest stands. To understand the structural patterns of disturbed forests encroached by S. macrophyllus at different abundance levels, three fully mapped 1-ha plots were established in Cuc Phuong National Park. Methods considering the phylogenetic community and nearest neighbor statistics were applied to identify how community structure changes during S. macrophyllus encroachment. Results showed that phylogenetic distance, phylogenetic diversity, and mean phylogenetic distance increased when species diversity increased and the abundance of S. macrophyllus decreased in forest communities. Net related index values were positive, which indicates a clustered phylogenetic structure among all sampled forest communities. S. macrophyllus trees were mixed well with heterospecifics and had regular to aggregated distributions, whereas the species showed evidence of being a strong competitor with its neighbors. Competition could be a major ecological process regulating forest communities encroached by S. macrophyllus. According to the forest disturbance effects, phylogenetic community properties showed the loss of phylogenetic relatedness when S. macrophyllus increased in abundance. To our knowledge, S. macrophyllus encroaches tropical rain forest communities as a disturbance-adapted species.

How do altitude and soil properties influence the taxonomic and phylogenetic structure and diversity of Brazilian páramo vegetation?

Altitude and environmental variables such as edaphic properties are considered determinants of species distribution and community composition in mountain ecosystems. Here, we aimed to outline the effects of distinct mountain peaks, altitude and soil properties on community composition, species density, phylogenetic structure and diversity of angiosperm paramo communities from the Serra do Brigadeiro State Park, Minas Gerais, southeastern Brazil. For that, we identified all angiosperm species found in 300 plots (1 m × 1 m) from three mountain peaks, measured soil depth and analyzed soil fertility and texture in each plot. To reduce the number of soil variables and species composition, we computed principal coordinates based on soil properties and principal coordinates based on species-plot matrix for each plot. Furthermore, we computed the standard effect sizes of the mean phylogenetic pairwise distance and the mean nearest phylogenetic taxon distance for each plot to investigate differences in the degree of relatedness among coexisting species. We compared differences in response variables between peaks and modelled them in function of altitude and principle components of soil properties using mixed effect models. Species density and phylogenetic diversity differed between peaks, but, contrary to the previous findings, no relationships between species richness or phylogenetic diversity and altitude or soil properties were found, indicating that further investigations are necessary to understand the altitude-biodiversity relationship in Brazilian paramo vegetation. Community composition differed between peaks and depended on altitude, soil properties and interactions between them, indicating that upward shifting of bioclimatic conditions due to climate changes may alter communities of this ecosystem. Phylogenetic structure differed between peaks and was influenced by altitude and soil properties. As phylogenetic clustering increased with altitude, eventual upward movements of species in Brazilian paramo vegetation due to climate change may alter community composition and the degree of relatedness among coexisting species, increasing the risk of species from higher altitudes to disappear. Therefore, conservation priorities arise for higher landscape portions, where these high altitude species may find refuges.

Richness, phylogenetic diversity, and abundance all have positive effects on invader performance in an arid ecosystem

AbstractIn search of generalities in biological invasions, it is sometimes forgotten that invader success can be a function of both the diversity of the invaded community and the relatedness of the invader relative to community residents. Both qualities are likely to be especially important in stressful ecosystems, and identifying the species and community attributes that influence biological invasions can help direct management efforts in a sensitive ecosystem like those in arid regions. Pink Morning Glory, Ipomoea carnea Jaq. (Family: Convolvulaceae), is an annual vine native to Central and South America and is invasive in Egypt. We examined the performance of I. carnea at different densities in assembled communities of Egyptian annual native species. The native plant communities were manipulated to represent gradients of species richness and phylogenetic diversity and relatedness to I. carnea. We quantified the performance of I. carnea in these communities and examined the contribution of resident species richness, phylogenetic diversity, and phylogenetic relatedness to invader resistance. Our findings revealed that there was a positive relationship between invader performance and its mean phylogenetic distance to the resident species. Furthermore, species‐rich communities with more distantly related species positively contributed to invader performance in contrast to the classic biotic resistance hypothesis. Beyond these positive relationships, a positive density‐dependent effect of I. carnea on its performance was observed. We conclude that facilitative interactions are potentially important drivers promoting the successful invasion of the nonnative species I. carnea in water‐limited and harsh ecosystems. These results suggest that perhaps contrary to understanding from temperate systems, communities with a higher diversity of species could be more likely to be invaded by arid‐adapted species that are distantly related to natives. Thus, policy and management in arid regions should carefully consider reviewing the importation of nonnative species that are phylogenetically distinct and adapted to arid conditions and prioritizing their control once they are established.