Mean Nearest Taxon Distance Research Articles

Effects of urbanization on woody plant phylogenetic diversity and its associations with landscape features in the high latitude northern hemisphere region, Northeast China

Urbanization is one of the primary drivers of terrestrial modification, with marked biological homogenization worldwide but relatively poor knowledge of woody phylogenetic diversity. Here, we investigated 943 plots, about 93,000 woody plants from 130 species in Northeast China, and calculated six phylogenetic diversity indexes, and urbanization landscape metrics; the responses of phylogenetic diversity to urbanization and its coupling relationship with landscape features were explored at 25 km × 25 km, 50 km × 50 km and 75 km × 75 km grid scales. We found that urbanization had enhanced the evolutionary distinctiveness of woody plants, characterizing as increasing Faith phylogenetic diversity (FPD) and their mean pairwise distance (MPD) while decreasing the mean nearest taxon distance (MNTD); these trends were independent of landscape scales and gymnosperm inclusion or not. As indicated by increasing SesMPD (Standardized MPD), the dominant role of community assemblage changed from environmental filtering in low urbanization intensity (UI) to competitive exclusion in high UI regions. Artificial surface area (ASA) and its percentage, SHAPE_F (Shape index of forest), and PD_F (Patch density of forest) had a threshold effect on phylogenetic diversity. ASA%, GDP (gross domestic product), and population density were the most potent predictors for the variations of phylogenetic diversity, and GDP contributed the most (42.9%). A higher GDP accompanied a higher FPD, SesPD (Standardized FPD), and SesMNTD (Standardized MNTD); higher PD_F and lower SHAPE_F were associated with higher MNTD, MPD, and SesMPD. In conclusion, urbanization strongly modifies woody plant phylogenetic diversity. Identifying the threshold effects and significant factors for phylogenetic variations allows biodiversity assessment and conservation through proper landscape configuration under the urbanization context.

Assessing taxonomic and functional change in British breeding bird assemblages over time

AbstractAimThe aim was to identify the primary drivers of compositional change in breeding bird assemblages over a 40‐year period.LocationBritain.Time periodFrom 1970 to 2010.Major taxa studiedBirds.MethodsUsing morphological trait measurements and a dataset of presence–absence data for British breeding birds surveyed in 10 km × 10 km hectads during two time periods, we calculated temporal taxonomic and functional beta diversity for each hectad alongside the change in species richness, mean nearest taxon distance (MNTD) and mean pairwise distance (MPD). We also estimated potential drivers of beta diversity, including climatic and land‐use and land‐cover (LULC) change variables, elevation and assemblage species richness in 1970 (1970rich). We used random forest regressions to test which variables best explained compositional change in the assemblages. We also assessed spatial taxonomic and functional change by analysing multiple‐site beta diversity and pairwise dissimilarities between time periods.ResultsInitial (1970) species richness was the most important predictor (highest importance score) across all models, with areas characterized by higher initial richness experiencing less assemblage change overall. The coordinates included to capture spatial autocorrelation in the data were also important predictors of change. Most climate and LULC variables had relatively low explanatory power; elevation and average temperature were the most influential. All metrics increased slightly with increasing elevation, except for species richness change and MPD, which decreased.Main conclusionsThe composition of British breeding bird assemblages changed substantially between 1970 and 2010. Spatial heterogeneity increased, both taxonomically and functionally. We show evidence that hectads with larger assemblages have been buffered from temporal diversity change and that those at higher elevations changed more in composition than those at lower elevations. Overall, coarse‐resolution climate and LULC explained only small to moderate amounts of variation, suggesting that stochastic assembly change or finer‐scale drivers might be drivers of temporal changes in assemblage composition.

Patterns and Predictors of Small Mammal Phylogenetic and Functional Diversity in Contrasting Elevational Gradients in Kenya

Mountains of the Afrotropics are global biodiversity hotspots and centers of speciation and endemism; however, very few studies have focused on the phylogenetic and functional dimensions of Afromontane small mammals. We investigated the patterns and mechanisms of small mammal phylogenetic and functional diversity and assembly along elevational gradients in Mount Kenya, the second highest mountain in Africa, and a contrasting low mountain range, Chyulu Hills. We sampled 24 200-m interval transects in both sites; 18 in Mt. Kenya (9 each in the windward side, Chogoria, and the leeward side, Sirimon) and 6 in Chyulu. We extracted the mitochondrialCytochrome bgene to reconstruct a time-calibrated species tree for estimating phylogenetic diversity indices [phylogenetic richness (PD), mean nearest taxon distance (PDMNTD), and nearest taxon index (PDNTI)]. A functional trait data set was compiled from the field-recorded measurements and published data sets for estimating functional diversity indices [functional richness (FD), mean nearest taxon distance (FDMNTD), and nearest taxon index (FDNTI)]. Several environmental variables representing water-energy availability, primary habitat productivity, and topographic heterogeneity were used to estimate the predictive power of abiotic conditions on diversity variances using generalized linear and generalized additive regression models. The PD and FD peaked around mid-elevations in Mt. Kenya, unimodally increased or decreased in Chogoria and Sirimon, and monotonically increased in Chyulu. The divergence and community structure indices—PDMNTD, FDMNTD, and PDNTIand FDNTI—were relatively weakly associated with elevation. Overall, the tendency of assemblages to be phylogenetically and functionally closely related than expected by chance decreased with elevation in Mt. Kenya but increased in Chyulu. Across the indices, the annual precipitation and topographic ruggedness were the strongest predictors in Mt. Kenya, evapotranspiration and temperature seasonality were the strongest predictors in Chyulu, while temperature seasonality and terrain ruggedness overlapped as the strongest predictors in Chogoria and Sirimon in addition to annual precipitation in the latter and normalized difference vegetation index in the former. The observed contrasting trends in diversity distribution and the strongest predictors between elevational gradients are integral to the sustainable management of the high faunal biodiversity in tropical Afromontane ecosystems.

Functional diversity loss and change in nocturnal behavior of mammals under anthropogenic disturbance.

In the Anthropocene, understanding the impacts of anthropogenic influence on biodiversity and behavior of vulnerable wildlife communities is increasingly relevant to effective conservation. However, comparative studies aimed at disentangling the concurrent effect of different types of human disturbance on multifaceted biodiversity and on activity patterns of mammals are surprisingly rare. We applied a multiregion community model to separately estimate the effects of cumulative human modification (e.g., settlement, agriculture, and transportation) and human presence (aggregated presence of dogs, people, and livestock) on species richness and functional composition of medium‐ and large‐bodied mammals based on camera trap data collected across 45 subtropical montane forests. We divided the detected mammal species into three trophic guilds–carnivores, herbivores, and omnivores–and assessed the nocturnal shifts of each guild in response to anthropogenic activities. Overall, species richness tended to increase (β coefficient = 0.954) as human modification increased but richness decreased as human presence increased (β = –1.054). Human modification was associated with significantly lower functional diversity (mean nearest taxon distance [MNTD], β = –0.134; standardized effect sizes of MNTD, β = –0.397), community average body mass (β = –0.240), and proportion of carnivores (β = –0.580). Human presence was associated with a strongly reduced proportion of herbivores (β = –0.522), whereas proportion of omnivores significantly increased as human presence (β = 0.378) and habitat modification (β = 0.419) increased. In terms of activity patterns, omnivores (β = 12.103) and carnivores (β = 9.368) became more nocturnal in response to human modification. Our results suggest that human modification and human presence have differing effects on mammals and demonstrate that anthropogenic disturbances can lead to drastic loss of functional diversity and result in a shift to nocturnal behavior of mammals. Conservation planning should consider concurrent effects of different types of human disturbance on species richness, functional diversity, and behavior of wildlife communities.

Phylogenetic diversity and community assembly in a naturally fragmented system.

We sought to assess effects of fragmentation and quantify the contribution of ecological processes to community assembly by measuring species richness, phylogenetic, and phenotypic diversity of species found in local and regional plant communities. Specifically, our fragmented system is Craters of the Moon National Monument and Preserve, Idaho, USA. CRMO is characterized by vegetated islands, kipukas, that are isolated in a matrix of lava. We used floristic surveys of vascular plants in 19 kipukas to create a local species list to compare traditional dispersion metrics, mean pairwise distance, and mean nearest taxon distance (MPD and MNTD), to a regional species list with phenotypic and phylogenetic data. We combined phylogenetic and functional trait data in a novel machine‐learning model selection approach, Community Assembly Model Inference (CAMI), to infer probability associated with different models of community assembly given the data. Finally, we used linear regression to explore whether the geography of kipukas explained estimated support for community assembly models. Using traditional metrics of MPD and MNTD neutral processes received the most support when comparing kipuka species to regional species. Individually no kipukas showed significant support for overdispersion. Rather, five kipukas showed significant support for phylogenetic clustering using MPD and two kipukas using MNTD. Using CAMI, we inferred neutral and filtering models structured the kipuka plant community for our trait of interest. Finally, we found as species richness in kipukas increases, model support for competition decreases and lower elevation kipukas show more support for habitat filtering models. While traditional phylogenetic community approaches suggest neutral assembly dynamics, recently developed approaches utilizing machine learning and model choice revealed joint influences of assembly processes to form the kipuka plant communities. Understanding ecological processes at play in naturally fragmented systems will aid in guiding our understanding of how fragmentation impacts future changes in landscapes.

Evaluating the impact of roads on the diversity pattern and density of trees to improve the conservation of species.

Roadside trees alter biotic and abiotic factors of plants diversity in an ecosystem. Rows of plants grow along the roadside due to the interplay between the arrival of propagule and seedling establishment, which depends on the road's specifications, land pattern, and road administration and protection practices. A field study was conducted to measure the roadside tree diversity in the city of Karachi (Pakistan). A total of 180 plots, divided into three primary road groups, were surveyed. The highest quantity of tree biomass per unit area was found on wide roads, followed by medium roads. On narrow roads, the least biomass was detected. A single species or a limited number of species dominated the tree community. Conocarpus erectus was the most dominant non-native species on all types of sidewalks or roadsides, followed by Guaiacum officinale. A total of 76 species (32 non-natives and 44 natives) that were selectively spread along the roadsides of the city were studied. There was a significant difference in phylogenetic diversity (PD), phylogenetic mean pairwise distance (MPD), and phylogenetic mean nearest taxon distance (MNTD) among wide, medium, and narrow roads. Management practices have a significant positive correlation with diversity indices. Our study identified patterns of diversity in roadside trees in Karachi. It provides the basis for future planning for plant protection, such as the protection of plant species, the maintenance of plant habitats, and the coordination of plant management in Karachi.

Phylogenetic diversity of ferns reveals different patterns of niche conservatism and habitat filtering between epiphytic and terrestrial assemblages

Much attention has been directed to understanding species richness patterns, but adding an evolutionary perspective allows us to also consider the historical processes determining current diversity patterns. We analyzed phylogenetic patterns of fern species assemblages in 868 plots along a wide range of elevational (0-4000 m) and latitudinal (0°-23°N) gradients in the Neotropics to allow a deeper understanding of evolutionary processes underlying current patterns of diversity and community assembly. Overall, we found that phylogenetic mean pairwise distance (sMPD) and mean nearest taxon distance (sMNTD) decreased with increasing latitude and elevation, but that these geographical factors per se were weak explanatory variables. Incorporating environmental variables strongly enhanced the power of the predictive model, indicating that fern assemblages are phylogenetically more diverse under wet and warm to cool conditions at low latitudes and elevations. Further, whereas epiphytic fern assemblages were strongly influenced by climatic factors, this was not the case for terrestrial ones, suggesting that edaphic conditions and vegetation structure may have a stronger influence on the evolution and diversification of terrestrial ferns. We conclude that fern assemblages are strongly influenced by phylogenetic niche conservatism and environmental filtering. This has also been found for angiosperms, but the direction of the environment-phylogenetic relationship is often opposed in the two groups, suggesting that the older age of many fern lineages includes historical signals that are not evident in the more recent angiosperm radiation.

Effects of grazing on plant species and phylogenetic diversity in alpine grasslands, Northern Tibet

Plant diversity plays an important role in maintaining and upgrading ecosystem structure and functions, and there remain uncertainties on plant species and especially phylogenetic diversity to grazing in alpine grasslands. Therefore, this study compared the differences of plant species and phylogenetic α- and β-diversity between grazing and fencing conditions at three alpine grasslands (ASMWG: alpine steppe meadow for winter grazing; ASMSG: alpine steppe meadow for summer grazing; AMSG: alpine meadow for summer grazing), Northern Tibet. At the ASMSG site, grazing significantly decreased mean nearest taxon distance (MNTD) by 19.33%, and increased Pielou by 7.06%. Plant community compositions between fencing and grazing conditions were different (p = 0.021) at the ASMSG site. However, the Pielou, MNTD and plant community composition were not significantly different between the fencing and grazing conditions at the ASMWG and AMSG site. Grazing significantly increased the niche overlap at the ASMWG (levins: 51.36%, schooner: 28.97%, pianka: 28.11%, Czech: 28.97%; morisita: 28.75%) and ASMSG site (schooner: 35.19%, petraitis: 4.63%, pianka: 26.45%, czech: 35.19%; morisita: 30.86%), indicating that grazing may increase plant species competition and competitive exclusion at the ASMWG and ASMSG site. In contrast, grazing did not significantly affect niche overlap at the AMSG site. Therefore, the response of plant diversity to grazing can be different between species and phylogenetic diversity, and among alpine grasslands.

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.

Ability of Current Phylogenetic Clustering to Detect Speciation History

Phylogenetic diversity aims to quantify the evolutionary relatedness among the species comprising a community, using the phylogenetic tree as the metric of the evolutionary relationships. Could these measures unveil the evolutionary history of an area? For example, in a speciation hotspot (biodiversity cradle), we intuitively expect that the species in the community will be more phylogenetically clustered than randomly expected. Here, using a theoretical simulation model, we estimate the ability of phylogenetic metrics of current diversity to detect speciation history. We found that, in the absence of dispersal, if the incipient species do not coexist in the region of speciation (as expected under allopatric speciation), there was no clear phylogenetic clustering and phylogenetic diversity failed to detect speciation history. But if the incipient species coexisted (sympatric speciation), metrics such as standardized effect size of Faith’s Phylogenetic Diversity (PD) and of Mean Nearest Taxon Distance (MNTD) were able to identify areas of high speciation, while Mean Pairwise Distance (MPD) was a poor indicator. PD systematically outperformed MNTD. Dispersal was a game-changer. It allowed species to expand their range, colonize areas, and led to the coexistence of the incipient species originating from a common ancestor. If speciation gradient was spatially contiguous, dispersal strengthened the associations between phylogenetic clustering and speciation history. In the case of spatially random speciation, dispersal blurred the signal with phylogenetic clustering occurring in areas of low or no speciation. Our results imply that phylogenetic clustering is an indicator of speciation history only under certain conditions.

Identifying the Drivers of Spatial Taxonomic and Functional Beta-Diversity of British Breeding Birds

Spatial variation in community composition may be driven by a variety of processes, including environmental filtering and dispersal limitation. While work has been conducted on the relative importance of these processes on various taxa and at varying resolutions, tests using high-resolution empirical data across large spatial extents are sparse. Here, we use a dataset on the presence/absence of breeding bird species collected at the 10 km × 10 km scale across the whole of Britain. Pairwise spatial taxonomic and functional beta diversity, and the constituent components of each (turnover and nestedness/richness loss or gain), were calculated alongside two other measures of functional change (mean nearest taxon distance and mean pairwise distance). Predictor variables included climate and land use measures, as well as a measure of elevation, human influence, and habitat diversity. Generalized dissimilarity modeling was used to analyze the contribution of each predictor variable to variation in the different beta diversity metrics. Overall, we found that there was a moderate and unique proportion of the variance explained by geographical distance per se, which could highlight the role of dispersal limitation in community dissimilarity. Climate, land use, and human influence all also contributed to the observed patterns, but a large proportion of the explained variance in beta diversity was shared between these variables and geographical distance. However, both taxonomic nestedness and functional nestedness were uniquely predicted by a combination of land use, human influence, elevation, and climate variables, indicating a key role for environmental filtering. These findings may have important conservation implications in the face of a warming climate and future land use change.

Assessing the phylogenetic host breadth of millet pathogens and its implication for disease spillover

Abstract1. Increasing agriculture intensification has led to dramatically improved crop yields; however, this shift in agricultural practice has been accompanied by increasing threats from new and emerging plant pathogens. While the pathogens associated with crop species are often well studied, especially within North America and Europe, less is known about pathogen pressures on crops elsewhere, and our ability to predict the emergence of novel pathogens is limited. Here, we model phylogenetic constraints on the distribution of pathogens of millet – one of the most important crops in Africa.2. We conducted a literature review to compile a database of common millet pathogens and the non‐millet host crops associated with each. We then characterized the phylogenetic host range for each pathogen using measures of mean pairwise distance (MPD) and mean nearest taxon distance (MNTD) separating crop hosts.3. We detected robust phylogenetic clustering for both metrics of phylogenetic dispersion (MPD and MNTD). Evidence for phylogenetic clustering tended to be stronger (more negative standard effect sizes) and more variable for MPD than for MNTD.4. Although patterns for individual pathogens were variable, we did not find significant differences in phylogenetic dispersion of hosts among pathogen types (bacteria, viruses and fungi). However, in several cases, we observed evidence of phylogenetic clustering in evolutionarily distant host clades, a possible signal of occasional large phylogenetic host jumps.5. We show that pathogens cluster on closely related hosts, and it is thus likely that closely related millets also share similar pathogen communities. On average, the probability of a pathogen host shift may, therefore, be predicted by the phylogenetic relatedness between host species. However, host shifts between distantly related hosts are not infrequent. This finding has relevance not only for the design of agronomic systems to reduce disease spillover but also for biological control agents risk analysis, quarantine regulations in international trade and our understanding of the distribution and abundance of plants in natural systems.

Effects of disturbance and alien plants on the phylogenetic structure of riverine communities

AbstractQuestionsPhylogenetic analyses provide important insights in the study of biological invasions. Previous studies have shown contrasting effects of alien species on the phylogenetic structure of recipient communities. In this study, we focus on two riparian plant communities with contrasting natural disturbance regimes: riparian forests and river bar communities. We ask whether these communities differ in alpha diversity and degree of plant invasion. Further, are the phylogenetic diversity (PD) and structure of these habitats related to the level of plant invasion?LocationNorthern Spain.MethodsWe determined level of plant invasion in forest and river bar vegetation plots, and calculated PD using mean pairwise distance (MPD) and mean nearest taxon distance (MNTD). We applied null models to analyse the phylogenetic structure of plots, and we tested whether inclusion of alien plant species was associated with differences in observed phylogenetic structure.ResultsRiver bar plots experienced more invasion than forest plots, but the level of invasion was only related to the PD of native species in forests. Most plots had random phylogenetic structure, with a minority of plots tending to phylogenetic overdispersion in forests and to phylogenetic clustering in river bars. MPD increased with the inclusion of alien plant species in forest plots, suggesting phylogenetic overdispersion, while no such pattern was detected with MNTD. MPD increased slightly with increasing invasion in river bar plots, suggesting reduced clustering, while MNTD values decreased with increasing invasion, suggesting the opposite trend.ConclusionsInvasion by alien plants is differentially associated with phylogenetic structure in riparian habitats with different disturbance levels. Our results contrast with those of previous studies of plant invasion of riparian communities, which suggests geographic and ecological variation in the relationship between invasion and phylogenetic community structure in riparian systems. Research is needed to identify the causal factors underlying this variation.

Scale dependence in the phylogenetic relatedness of alien and native taxa

AbstractAimsDarwin’s naturalization hypothesis proposes that successfully established alien species are less closely related to native species due to differences in their ecological niches. Studies have provided support both for and against this hypothesis. One reason for this is the tendency for phylogenetic clustering between aliens and natives at broad spatial scales with overdispersion at fine scales. However, little is known about how the phylogenetic relatedness of alien species alters the phylogenetic structure of the communities they invade, and at which spatial scales effects may manifest. Here, we examine if invaded understorey plant communities, i.e. containing both native and alien taxa, are phylogenetically clustered or overdispersed, how relatedness changes with spatial scale and how aliens affect phylogenetic patterns in understorey communities.MethodsField surveys were conducted in dry forest understorey communities in south-east Australia at five spatial scales (1, 20, 500, 1500 and 4500 m2). Standardized effect sizes of two metrics were used to quantify phylogenetic relatedness between communities and their alien and native subcommunities, and to examine how phylogenetic patterns change with spatial scale: (i) mean pairwise distance and (ii) mean nearest taxon distance (MNTD).Important FindingsAliens were closely related to each other, and this relatedness tended to increase with scale. Native species and the full community exhibited either no clear pattern of relatedness with increasing spatial scale or were no different from random. At intermediate spatial scales (20–500 m2), the whole community tended towards random whereas the natives were strongly overdispersed and the alien subcommunity strongly clustered. This suggests that invasion by closely related aliens shifts community phylogenetic structure from overdispersed towards random. Aliens and natives were distantly related across spatial scales, supporting Darwin’s naturalization hypothesis, but only when phylogenetic distance was quantified as MNTD. Phylogenetic dissimilarity between aliens and natives increased with spatial scale, counter to expected patterns. Our findings suggest that the strong phylogenetic clustering of aliens is driven by human-mediated introductions involving closely related taxa that can establish and spread successfully. Unexpected scale-dependent patterns of phylogenetic relatedness may result from stochastic processes such as fire and dispersal events and suggest that competition and habitat filtering do not exclusively dominate phylogenetic relationships at fine and coarse spatial scales, respectively. Distinguishing between metrics that focus on different evolutionary depths is important, as different metrics can exhibit different scale-dependent patterns.

Structure and Functional Diversity of Surface Bacterioplankton Communities in an Overwintering Habitat for Large Yellow Croaker, Pseudosciaena crocea, of the Southern East China Sea

Given the biogeochemical functions of marine microbes, the structure and functional diversity of bacterioplankton communities could be regarded as bioindicators that reflect environmental quality. The habitat of the large yellow croaker (Pseudosciaena crocea) is suffering from widespread degradation, but the study of croaker habitat is still insufficient. Here, we used 16S rRNA gene sequencing and functional prediction to investigate the surface bacterioplankton communities in an overwintering ground of P. crocea during the overwintering period (November 2018 to April 2019). Our results showed that the taxa and functions of the environmental bacterioplankton community exhibited obvious seasonality. Specifically, the bacterioplankton communities in autumn were characterized by animal parasites or symbionts, such as Acinetobacter baumannii and Moraxella, while organic substance-degrading bacteria, such as Rhodococcus, Stenotrophomonas and Alcanivorax, dominated in spring. Moreover, phylogenetic-based mean nearest taxon distance (MNTD) analyses indicated that dispersal limitation was the most important process governing the spatiotemporal assembly of the bacterioplankton communities. The distance decay of similarity also suggested the impact of dispersal limitation on the generation of biogeographical patterns. Furthermore, variation partitioning analysis and a partial Mantel test revealed that environmental filters, such as nutrients, temperature and salinity, had relatively weak deterministic effects on the bacterioplankton community assembly. Overall, these findings provide a basis for understanding the theory of surface microbial community assembly in the overwintering habitat of the large yellow croaker.

Environment and evolutionary history depict phylogenetic alpha and beta diversity in the Atlantic coastal white‐sand woodlands

AbstractQuestionsHow do ecological and evolutionary processes affect the phylogenetic alpha and beta diversity of angiosperm tree assemblages in an evolutionarily young coastal environment?LocationCoastal vegetation of the Brazilian Atlantic Forest Domain (restingas), spanning 20° of latitude.MethodsWe calculated phylogenetic alpha and beta diversity at deep and shallow levels for angiosperm tree species in 136 circular sites of 10 km diameter (hereafter assemblages). The metrics we used for alpha diversity were the mean pairwise distance (MPD) and mean nearest taxon distance (MNTD), and mean pairwise distance separating species in two assemblages (Dpw) and mean nearest taxon distance separating species in two assemblages (Dnn) for beta diversity. We then investigated the relationship between phylogenetic diversity, historical (Quaternary) and current climatic variables, and edaphic conditions along the latitudinal gradient.ResultsWe found that MPD increased with precipitation and latitude. MNTD increased with modern‐day temperature, historical temperature instability and precipitation, and it was higher in more fertile and less saline soils. Dpw did not correlate either with geographic or environmental distances between assemblages. However, Dnn was strongly correlated with both geographic and environmental distances between assemblages.ConclusionsThe increase in MPD with precipitation and latitude suggests the presence of old Gondwanan lineages colonising restingas from refugia at higher latitudes. The increase in MNTD with modern‐day temperature, historical temperature instability, precipitation, and it being higher in more fertile and less saline soils indicates that the distance between phylogenetic closest relatives tends to increase in assemblages less affected by environmental filtering. Low Dpw suggests the presence of widespread lineages across restingas, whereas high Dnn may indicate niche conservatism and dispersal limitation of more derived lineages. Our results offer insights into how ecological and evolutionary processes act to shape current patterns of biodiversity in geologically young environments.

Phylogenetic and phenotypic filtering in hummingbirds from urban environments in Central Mexico

Cities act as biological filters on native biodiversity, selecting for traits allowing species to use urban resources, which may modify the phylogenetic structure and composition of biotic assemblages. Although many studies about urban filtering have included bird communities, few have focused on diverse and specialized groups, such as hummingbirds. Here, we investigate if: (1) the urbanization process may have modified the phylogenetic and phenotypic structure of regional hummingbird assemblages in five cities along the Trans-Mexican Volcanic Belt in central Mexico, and (2) hummingbird species in urban environments have been filtered through the selection of particular morphological traits. We measured eight morphological traits related to the ability of hummingbird species to use resources, three of which (wing chord, culmen and bill curvature) were retained for phenotypic analyses. We estimated phylogenetic (MPD, mean pairwise distance, and MNTD, mean nearest taxon distance) and phenotypic structure values (pMPD and pMNTD) in regional and urban hummingbird assemblages, which allowed us to assess significant phylogenetic structure and phenotypic similarity among coexisting species, respectively. We also calculated phylogenetic signal to determine if traits are labile or conserved. We performed generalized linear mixed-effect models and a classification and regression tree analysis to determine which traits explained species’ presence in urban environments. Our results showed that urbanization modified the phylogenetic structure from a random pattern in regional assemblages towards more overdispersed values in urban assemblages, while phenotypic structure values changed either towards clustering or overdispersion in the different cities. Regression tree analyses showed that traits related to body-size and bill culmen may influence the presence of different hummingbird species in cities. Our results show that the urbanization process may change the phylogenetic and phenotypic structure of hummingbird assemblages, favoring species with generalist morphologies (intermediate body-sizes and relatively longer bills).

Impacts of selective logging on avian phylogenetic and functional diversity in the Amazon

AbstractSelective logging is the most extensive land use threatening tropical forests worldwide, making our understanding of its impacts on biodiversity vital for the conservation of these hyperdiverse ecosystems. We investigated the effects of selective logging on the phylogenetic and functional diversity (FD) of Amazonian forest avifauna. We sampled the overall and the understorey bird community using point counts and mist‐netting, respectively, in logged and unlogged forests. The overall bird community showed significantly lower phylogenetic diversity (PD) and FD in logged than unlogged forests, but significantly higher standard effect size (ses) of PD, ses mean pairwise distance (MPD), mean nearest taxon distance (MNTD), ses functional MPD (sesfMPD) and functional MNTD (fMNTD) in logged sites. Evolutionary distinctiveness, sesMPD, sesFD, fMNTD and sesfMNTD of understorey birds were significantly higher in logged forests. Higher logging intensity affected some metrics negatively and others positively, although the relatively small changes in phylogenetic and FD suggest limited overall effects from logging at lower intensity. In combination, selective logging brings deleterious effects for some components of phylogenetic and FD of the overall Amazonian bird community. Nonetheless, selectively logged forests retain important avian diversity, underscoring their high conservation value. Relatively, low impacts of selective logging may be due to the reduced‐impact logging (RIL) techniques used, high connectivity with well‐preserved unlogged forests or focus on short‐term logging impacts. Because even low‐intensity RIL causes some losses in evolutionary history and functional traits, an optimal approach for conserving phylogenetic and FD requires incorporating some land‐sparing logging to protect more old‐growth patches within the logged matrix.

Dramatic impact of metric choice on biogeographical regionalization

For a quantitative biogeographical regionalization, the choice of an appropriate dissimilarity index to measure pairwise distances is crucial. Several different metrics have been used, but there is no specific study to test the impact of metric choice on biogeographical regionalization. We herein applied a hierarchical cluster analysis on the mean nearest taxon distance (MNTD) and the phylogenetic turnover component of the Sørensen dissimilarity index (pβsim) pairwise distances to generate two schemes of phylogenetic regionalization of the Chinese flora, and then evaluated the effect of metric choice. Floristic regionalization based on MNTD was influenced by richness differences, but regionalization based on pβsim can clearly reflect the evolutionary history of the Chinese flora. We provided a brief description of the five regions identified by pβsim, and the regionalization can help develop strategies to effectively conserve the taxa and floristic regions with different origins and evolutionary histories.

Climate and evolutionary history define the phylogenetic diversity of vegetation types in the central region of South America.

In South America the biogeographic history has produced different biomes with different vegetation types and distinct floras. As these vegetation types may diverge in evolutionary histories, we analysed how alpha and beta phylogenetic diversity vary across them and determine the main drivers of variation in phylogenetic diversity. To this end, we compiled a list of 205 sites and 1222 tree species spread over four biomes and eight vegetation types in central South America. For each site we evaluated six measures of evolutionary alpha diversity (species richness, phylogenetic diversity sensu stricto and the standardized effect size of phylogenetic diversity, mean phylogenetic distance and mean nearest taxon distance) and beta diversity (phylogenetic Sorensen's similarity). We checked the influence of spatial and environmental variables using generalized least squares models. The greatest phylogenetic differentiation was found between west and east of central South America, mainly between the Chaco communities and the other vegetation types, suggesting that species found in this biome come from different lineages, comparing with the others vegetation types. Our results also showed a clustered phylogenetic structure for the Dry Chaco woodlands, which may be associated with harsh environmental conditions. In addition to historical process, climatic conditions are the main drivers shaping phylogenetic patterns among the distinct vegetation types. Understanding patterns of phylogenetic diversity and distribution can greatly improve conservation planning and management since it allows the conservation of unique biome characteristics.