Quantifying phylogenetic beta diversity: distinguishing between 'true' turnover of lineages and phylogenetic diversity gradients

Phylogenetic structure of moth communities (Geometridae, Lepidoptera) along a complete rainforest elevational gradient in Papua New Guinea

We use community phylogenetics to elucidate the community assembly mechanisms for Geometridae moths (Lepidoptera) collected along a complete rainforest elevational gradient (200-3700 m a.s.l) on Mount Wilhelm in Papua New Guinea. A constrained phylogeny based on COI barcodes for 604 species was used to analyse 1390 species x elevation occurrences at eight elevational sites separated by 500 m elevation increments. We obtained Nearest Relatedness Index (NRI), Nearest Taxon Index (NTI) and Standardised Effect Size of Faith's Phylogenetic Diversity (SES.PD) and regressed these on temperature, plant species richness and predator abundance as key abiotic and biotic predictors. We also quantified beta diversity in the moth communities between elevations using the Phylogenetic Sorensen index. Overall, geometrid communities exhibited phylogenetic clustering, suggesting environmental filters, particularly at higher elevations at and above 2200 m a.s.l and no evidence of overdispersion. NRI, NTI and SES.PD showed no consistent trends with elevation or the studied biotic and abiotic variables. Change in community structure was driven by turnover of phylogenetic beta-diversity, except for the highest 2700-3200 m elevations, which were characterised by nested subsets of lower elevation communities. Overall, the elevational signal of geometrid phylogeny was weak-moderate. Additional insect community phylogeny studies are needed to understand this pattern.

Deep biogeographic barriers explain divergent global vertebrate communities

Biogeographic history can lead to variation in biodiversity across regions, but it remains unclear how the degree of biogeographic isolation among communities may lead to differences in biodiversity. Biogeographic analyses generally treat regions as discrete units, but species assemblages differ in how much biogeographic history they share, just as species differ in how much evolutionary history they share. Here, we use a continuous measure of biogeographic distance, phylobetadiversity, to analyze the influence of biogeographic isolation on the taxonomic and functional diversity of global mammal and bird assemblages. On average, biodiversity is better predicted by environment than by isolation, especially for birds. However, mammals in deeply isolated regions are strongly influenced by isolation; mammal assemblages in Australia and Madagascar, for example, are much less diverse than predicted by environment alone and contain unique combinations of functional traits compared to other regions. Neotropical bat assemblages are far more functionally diverse than Paleotropical assemblages, reflecting the different trajectories of bat communities that have developed in isolation over tens of millions of years. Our results elucidate how long-lasting biogeographic barriers can lead to divergent diversity patterns, against the backdrop of environmental determinism that predominantly structures diversity across most of the world.

Stability and Assembly Mechanisms of Butterfly Communities across Environmental Gradients of a Subtropical Mountain

Mountain ecosystems harbor evolutionarily unique and exceptionally rich biodiversity, particularly in insects. In this study, we characterized the diversity, community stability, and assembly mechanisms of butterflies on a subtropical mountain in the Chebaling National Nature Reserve, Guangdong Province, China, using grid-based monitoring across the entire region for two years. The results showed that species richness, abundance, and Faith's phylogenetic diversity decreased with increasing elevation; taxonomic diversity played a considerable role in mediating the effects of environmental changes on stability. Moreover, our results showed that stochastic processes are dominant in governing the assembly of butterfly communities across all elevational gradients, with habitats at an elevation of 416-580 m subjected to the strongest stochastic processes, whereas heterogeneous selection processes displayed stronger effects on the assembly of butterfly communities at 744-908 m, 580-744 m, and 908-1072 m, with abiotic factors inferred as the main driving forces. In addition, significant differences were detected between the barcode tree and the placement tree for the calculated β-NTI values at 416-580 m. Overall, this study provides new insights into the effects of environmental change on the stability and assembly of butterflies in Chebaling, which will be beneficial for biodiversity conservation and policy development.

Urbanization drives biotic homogenization of the avian community in China

Urbanization-driven biotic homogenization has been recorded in various ecosystems on local and global scales; however, it is largely unexplored in developing countries. Empirical studies on different taxa and bioregions show conflicting results (i.e. biotic homogenization vs. biotic differentiation); the extent to which the community composition changes in response to anthropogenic disturbances and the factors governing this process, therefore, require elucidation. Here, we used a compiled database of 760 bird species in China to quantify the multiple-site β-diversity and fitted distance decay in pairwise β-diversities between natural and urban assemblages to assess whether urbanization had driven biotic homogenization. We used generalized dissimilarity models (GDM) to elucidate the roles of spatial and environmental factors in avian community dissimilarities before and after urbanization. The multiple-site β-diversities among urban assemblages were markedly lower than those among natural assemblages, and the distance decays in pairwise similarities in natural assemblages were more rapid. These results were consistent among taxonomic, phylogenetic, and functional aspects, supporting a general biotic homogenization driven by urbanization. The GDM results indicated that geographical distance and temperature were the dominant predictors of avian community dissimilarity. However, the contribution of geographical distance and climatic factors decreased in explaining compositional dissimilarities in urban assemblages. Geographical and environmental distances accounted for much lower variations in compositional dissimilarities in urban than in natural assemblages, implying a potential risk of uncertainty in model predictions under further climate change and anthropogenic disturbances. Our study concludes that taxonomic, phylogenetic, and functional dimensions elucidate urbanization-driven biotic homogenization in China.

Patterns and drivers of avian taxonomic and phylogenetic beta diversity in China vary across geographical backgrounds and dispersal abilities

Geographical background and dispersal ability may strongly influence assemblage dissimilarity; however, these aspects have generally been overlooked in previous large-scale beta diversity studies. Here, we examined whether the patterns and drivers of taxonomic beta diversity (TBD) and phylogenetic beta diversity (PBD) of breeding birds in China vary across (1) regions on both sides of the Hu Line, which demarcates China's topographical, climatic, economic, and social patterns, and (2) species with different dispersal ability. TBD and PBD were calculated and partitioned into turnover and nestedness components using a moving window approach. Variables representing climate, habitat heterogeneity, and habitat quality were employed to evaluate the effects of environmental filtering. Spatial distance was considered to assess the impact of dispersal limitation. Variance partitioning analysis was applied to assess the relative roles of these variables. In general, the values of TBD and PBD were high in mountainous areas and were largely determined by environmental filtering. However, different dominant environmental filters on either side of the Hu Line led to divergent beta diversity patterns. Specifically, climate-driven species turnover and habitat heterogeneity-related species nestedness dominated the regions east and west of the line, respectively. Additionally, bird species with stronger dispersal ability were more susceptible to environmental filtering, resulting in more homogeneous assemblages. Our results indicated that regions with distinctive geographical backgrounds may present different ecological factors that lead to divergent assemblage dissimilarity patterns, and dispersal ability determines the response of assemblages to these ecological factors. Identifying a single universal explanation for the observed pattern without considering these aspects may lead to simplistic or incomplete conclusions. Consequently, a comprehensive understanding of large-scale beta diversity patterns and effective planning of conservation strategies necessitate the consideration of both geographical background and species dispersal ability.

Angiosperm phylogenetic diversity is lower in Africa than South America

Although originating from a common Gondwanan flora, the diversity and composition of the floras of Africa and South America have greatly diverged since continental breakup of Africa from South America now having much higher plant species richness. However, the phylogenetic diversity of the floras and what this tells us about their evolution remained unexplored. We show that for a given species richness and considering land surface area, topography, and present-day climate, angiosperm phylogenetic diversity in South America is higher than in Africa. This relationship holds regardless of whether all climatically matched areas or only matched areas in tropical climates are considered. Phylogenetic diversity is high relative to species richness in refugial areas in Africa and in northwestern South America, once the gateway for immigration from the north. While species richness is strongly influenced by massive plant radiations in South America, we detect a pervasive influence of historical processes on the phylogenetic diversity of both the South American and African floras.

Multidimensional beta-diversity across local and regional scales in a Chinese subtropical forest: The role of forest structure

Beta-diversity, or the spatio-temporal variation in community composition, can be partitioned into turnover and nestedness components in a multidimensional framework. Forest structure, including comprehensive characteristics of vertical and horizontal complexity, strongly affects species composition and its spatial variation. However, the effects of forest structure on beta-diversity patterns in multidimensional and multiple-scale contexts are poorly understood. Here, we assessed beta-diversity at local (a 20-ha forest dynamics plot) and regional (a plot network composed of 19 1-ha plots) scales in a Chinese subtropical evergreen broad-leaved forest. We then evaluated the relative importance of forest structure, topography, and spatial structure on beta-diversity and its turnover and nestedness components in taxonomic, functional, and phylogenetic dimensions at local and regional scales. We derived forest structural parameters from both unmanned aerial vehicle light detection and ranging (UAV LiDAR) data and plot inventory data. Turnover component dominated total beta-diversity for all dimensions at the two scales. With the exception of some components (taxonomic and functional turnover at the local scale; functional nestedness at the regional scale), environmental factors (i.e., topography and forest structure) contributed more than pure spatial variation. Explanations of forest structure for beta-diversity and its component patterns at the local scale were higher than those at the regional scale. The joint effects of spatial structure and forest structure influenced component patterns in all dimensions (except for functional turnover) to some extent at the local scale, while pure forest structure influenced taxonomic and phylogenetic nestedness patterns to some extent at the regional scale. Our results highlight the importance and scale dependence of forest structure in shaping multidimensional beta-diversity and its component patterns. Clearly, further studies need to link forest structure directly to ecological processes (e.g., asymmetric light competition and disturbance dynamics) and explore its roles in biodiversity maintenance.

Wild and cultivated comestible plant species in the Gulf of Mexico: phylogenetic patterns and convergence of type of use

Cross-cultural research on edible plants might include ecological and evolutionary perspectives to understand processes behind species selection and management. With a database of approximately 500 comestible plants of the Province of the Gulf of Mexico in Mesoamerica, phylogenetic analyses are conducted to identify convergence and phylogenetic signal of type of use and significant clustering in the resulting phylogenetic trees. Analyses considered type of management (wild/managed vs. cultivated), type of use (edible, condiment, for wrapping food) and organ utilized. Elevated phylogenetic diversity and signal are expected for wild comestible taxa, indicating that people are using lineages across the angiosperm tree for food, resulting in broadness in diet and use of their regional resources. Main results are: (i) condiment species were identified in groups with an elevated phylogenetic signal; (ii) hot nodes for lineages utilized for wrapping food were found in many monocot groups as well as in epiphytes of cloud forests with leathery leaves; (iii) edible taxa were identified with the highest significant clustering restricted to certain branches in the phylogeny; (iv) wild and cultivated edible plants belong to identical lineages with replacement of species, implying that same plant groups known for their comestible benefits are substituted by species distributed in the Province and (v) wild versus cultivated lineages for condiment are different. Most food species in the Province belong to four families, namely Fabaceae, Cactaceae, Solanaceae and Asparagaceae. Analyses discovered underutilized wild species in identical clades to managed/cultivated taxa that can be studied further to identify cultivation practices. Results suggest that people are utilizing different lineages in the angiosperm tree available locally, for particular uses, like condiment or for wrapping food. Evidence can be used to study further undervalued edible species closely related to the most common food taxa as well as for bioprospection of their nutritional content.

Long-term subtropical grassland plots take a long time to change: Replacement is more important than richness differences for beta diversity

We studied β diversity of grasses in a subtropical grassland over 60 years in South Africa. We examined the effects of burning and mowing on 132 large plots. We sought to determine the effects of burning and mowing, and mowing frequency, on the replacement of species and the species richness. We conducted the study at Ukulinga, research farm of the University of KwaZulu-Natal, Pietermaritzburg, South Africa (29°24'E, 30°24'S) from 1950-2010. Plots were burned annually, biennially, triennially, and a control (unburned). Plots were mowed in spring, late summer, spring plus late summer, and a control (unmowed). We calculated β diversity, with a focus on replacement and richness differences. We also used distance-based redundancy analyses to examine the relative effects of replacement and richness differences on mowing and burning. We used beta regressions to test for the effect of soil depth and its interactions with mowing and burning. There was no significant change in grass beta diversity until 1995. Thereafter, there were changes in β diversity that demonstrated the primary effects of summer mowing frequency. There was no significant effect of richness differences but a strong effect of replacement post-1995. There was a significant interaction between mowing frequency and soil depth in one of the analyses. Changes in grassland composition took a long time to manifest themselves and were unapparent prior to 1988. However, there was a change in sampling strategy prior to 1988, from point hits to nearest plants, that may also have influenced the rates of changes in replacement and richness differences. Using β-diversity indices, we found that mowing was more important than burning that burning frequency was unimportant, and there was a significant interaction effect between mowing and soil depth in one of the analyses.

Species assemblages of insular Caribbean Sticta (lichenized Ascomycota: Peltigerales) over ecological and evolutionary time scales

Phylogenetic approaches to macroevolution have provided unique insight into evolutionary relationships, ancestral ranges, and diversification patterns for many taxa. Similar frameworks have also been developed to assess how environmental and/or spatial variables shape species diversity and distribution patterns at different spatial/temporal scales, but studies implementing these are still scarce for many groups, including lichens. Here, we combine phylogeny-based ancestral range reconstruction and diversification analysis with community phylogenetics to reconstruct evolutionary origins and assess patterns of taxonomic and phylogenetic relatedness between island communities of the lichenized fungal genus Sticta in the Caribbean. Sampling was carried out in the Greater Antilles (Cuba, Jamaica, Dominican Republic, and Puerto Rico) and Lesser Antilles (Dominica, Guadeloupe, and Martinique). Data for six molecular loci were obtained for 64 candidate Caribbean species and used to perform both macroevolutionary phylogenetics, which also included worldwide taxa, and phylobetadiversity analyses, which emphasized island-level communities. Our work uncovered high levels of island endemism (∼59%) in Caribbean Sticta. We estimate initial colonization of the region occurred about 19 Mya from a South American ancestor. Reverse migration events by Caribbean lineages to South America were also inferred. We found no evidence for increased diversification rates associated with range expansion into the Caribbean. Taxonomic and phylogenetic turnover between island-level communities was most strongly correlated with environmental variation rather than with geographic distance. We observed less dissimilarity among communities from the Dominican Republic and Jamaica than between these islands and the Lesser Antilles/Puerto Rico. High levels of hidden diversity and endemism in Caribbean Sticta reaffirm that islands are crucial for the maintenance of global biodiversity of lichenized fungi. Altogether, our findings suggest that strong evolutionary links exist between Caribbean and South American biotas but at regional scales, species assemblages exhibit complex taxonomic and phylogenetic relationships that are determined by local environments and shared evolutionary histories.

Global beta-diversity of angiosperm trees is shaped by Quaternary climate change

As Earth's climate has varied strongly through geological time, studying the impacts of past climate change on biodiversity helps to understand the risks from future climate change. However, it remains unclear how paleoclimate shapes spatial variation in biodiversity. Here, we assessed the influence of Quaternary climate change on spatial dissimilarity in taxonomic, phylogenetic, and functional composition among neighboring 200-kilometer cells (beta-diversity) for angiosperm trees worldwide. We found that larger glacial-interglacial temperature change was strongly associated with lower spatial turnover (species replacements) and higher nestedness (richness changes) components of beta-diversity across all three biodiversity facets. Moreover, phylogenetic and functional turnover was lower and nestedness higher than random expectations based on taxonomic beta-diversity in regions that experienced large temperature change, reflecting phylogenetically and functionally selective processes in species replacement, extinction, and colonization during glacial-interglacial oscillations. Our results suggest that future human-driven climate change could cause local homogenization and reduction in taxonomic, phylogenetic, and functional diversity of angiosperm trees worldwide.

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

BACKGROUND AND AIMS

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.

METHODS

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.

KEY RESULTS

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.

CONCLUSIONS

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.

Geographic patterns of taxonomic and phylogenetic β-diversity of aquatic angiosperms in China

China covers a vast territory harbouring a large number of aquatic plants. Although there are many studies on the β-diversity of total, herbaceous or woody plants in China and elsewhere, few studies have focused on aquatic plants. Here, we analyse a comprehensive data set of 889 aquatic angiosperm species in China, and explore the geographic patterns and climatic correlates of total taxonomic and phylogenetic β-diversity as well as their turnover and nestedness components. Our results show that geographic patterns of taxonomic and phylogenetic β-diversity are highly congruent for aquatic angiosperms, and taxonomic β-diversity is consistently higher than phylogenetic β-diversity. The ratio between the nestedness component and total β-diversity is high in northwestern China and low in southeastern China. The geographic patterns of taxonomic and phylogenetic β-diversity of aquatic angiosperms in China are obviously affected by geographic and climatic distances, respectively. In conclusion, the geographic patterns of taxonomic and phylogenetic β-diversity of aquatic angiosperms are consistent across China. Climatic and geographic distances jointly affect the geographic patterns of β-diversity of aquatic angiosperms. Overall, our work provides insight into understanding the large-scale patterns of aquatic angiosperm β-diversity, and is a critical addition to previous studies on the macroecological patterns of terrestrial organisms.

Spatial and phylogenetic structure of Alpine stonefly assemblages across seven habitats using DNA-species

Stream ecosystems are spatially heterogeneous, with many different habitat patches distributed within a small area. The influence of this heterogeneity on the biodiversity of benthic insect communities is well documented; however, studies of the role of habitat heterogeneity in species coexistence and assembly remain limited. Here, we investigated how habitat heterogeneity influences spatial structure (beta biodiversity) and phylogenetic structure (evolutionary processes) of benthic stonefly (Plecoptera, Insecta) communities. We sampled 20 sites along two Alpine rivers, including seven habitats in four different reaches (headwaters, meandering, bar-braided floodplain, and lowland spring-fed). We identified 21 morphological species and delineated 52 DNA-species based on sequences from mitochondrial cox1 and nuclear ITS markers. Using DNA-species, we first analysed the patterns of variation in richness, diversity, and assemblage composition by quantifing the contribution of each reach and habitat to the overall DNA-species diversity using an additive partition analysis and distance-based redundancy analysis. Using gene-tree phylogenies, we assessed whether environmental filtering could lead to the co-occurrence of DNA-species using a two-step analysis to detect a phylogenetic signal. All four reaches significantly contributed to DNA-species richness, with the meandering reach having the highest contribution. Habitats had an effect on DNA-species diversity, where glide, riffle and, pool influenced the spatial structure of stonefly assemblage possibly due to the high habitat heterogeneity. Among the habitats, the pool showed significant phylogenetic clustering, suggesting high levels of evolutionary adaptation and strong habitat filtering. This assemblage structure may be caused by long-term stability of the habitat and the similar requirements for co-occurring species. Our study shows the importance of different habitats for the spatial and phylogenetic structure of stonefly assemblage and sheds light on the habitat-specific diversity that may help improve conservation practices.

The interactive effects of environmental gradient and dispersal shape spatial phylogenetic patterns

Introduction

The emergence and maintenance of biodiversity include interacting environmental conditions, organismal adaptation to such conditions, and dispersal. To understand and quantify such ecological, evolutionary, and spatial processes, observation and interpretation of phylogenetic relatedness across space (e.g., phylogenetic beta diversity) is arguably a way forward as such patterns contain signals from all the processes listed above. However, it remains challenging to extract information about complex eco-evolutionary and spatial processes from phylogenetic patterns.

Methods

We link environmental gradients and organismal dispersal with phylogenetic beta diversity using a trait-based and eco-evolutionary model of diversification along environmental gradients. The combined effect of the environment and dispersal leads to distinct phylogenetic patterns between subsets of species and across geographical distances.

Results and discussion

Steep environmental gradients combined with low dispersal lead to asymmetric phylogenies, a high phylogenetic beta diversity, and the phylogenetic diversity between communities increases linearly along the environmental gradient. High dispersal combined with a less steep environmental gradient leads to symmetric phylogenies, low phylogenetic beta diversity, and the phylogenetic diversity between communities along the gradient increases in a sigmoidal form. By disentangling the eco-evolutionary mechanisms that link such interacting environment and dispersal effects and community phylogenetic patterns, our results improve understanding of biodiversity in general and help interpretation of observed phylogenetic beta diversity.

Understanding the relative roles of local environmental, geo-climatic and spatial factors for taxonomic, functional and phylogenetic β-diversity of stream fishes in a large basin, Northeast China

The primary objective of this study was to determine the relative roles of local environmental (Local), geo-climatic (Geo), and spatial (Spatial) factors to taxonomic, functional, and phylogenetic β-diversity of stream fish in a large basin in Northeast China. We quantified the current biodiversity patterns of fish communities in the Hun-Tai River using β-diversity. We assessed (i) corresponding contributions of turnover and nestedness within the taxonomic, functional, and phylogenetic β-diversity of fishes; (ii) correlations among β-diversity facets (i.e., taxonomic, functional, and phylogenetic facets); (iii) relative contributions of Local, Geo, and Spatial factors to β-diversity. We collected fish communities from 171 sampling sites. Mantel tests were used to examine the correlation of three facets of β-diversity and their components (i.e., total, nestedness, and turnover). Distance-based redundancy analysis and variation partitioning assess the relative contributions of Local, Geo, and Spatial factors to β-diversity. We found that turnover is the main driving mechanism for β-diversity in fish. Among the facets of β-diversity, taxonomic and phylogenetic facets have strong ecological information association. Spatial factors have a general contribution to various facets of β-diversity and its components. From aspects of fish β-diversity conservation, connectivity and habitat heterogeneity need to be maintained in the entire aquatic environment. In addition, protecting taxonomic β-diversity is helpful for maintaining phylogenetic β-diversity.

Alpha and beta phylogenetic diversities jointly reveal ant community assembly mechanisms along a tropical elevational gradient

Despite the long-standing interest in the organization of ant communities across elevational gradients, few studies have incorporated the evolutionary information to understand the historical processes that underlay such patterns. Through the evaluation of phylogenetic α and β-diversity, we analyzed the structure of leaf-litter ant communities along the Cofre de Perote mountain in Mexico and evaluated whether deterministic- (i.e., habitat filtering, interspecific competition) or stochastic-driven processes (i.e., dispersal limitation) were driving the observed patterns. Lowland and some highland sites showed phylogenetic clustering, whereas intermediate elevations and the highest site presented phylogenetic overdispersion. We infer that strong environmental constraints found at the bottom and the top elevations are favoring closely-related species to prevail at those elevations. Conversely, less stressful climatic conditions at intermediate elevations suggest interspecific interactions are more important in these environments. Total phylogenetic dissimilarity was driven by the turnover component, indicating that the turnover of ant species along the mountain is actually shifts of lineages adapted to particular locations resembling their ancestral niche. The greater phylogenetic dissimilarity between communities was related to greater temperature differences probably due to narrow thermal tolerances inherent to several ant lineages that evolved in more stable conditions. Our results suggest that the interplay between environmental filtering, interspecific competition and habitat specialization plays an important role in the assembly of leaf-litter ant communities along elevational gradients.

Historical connectivity and environmental filtering jointly determine the freshwater fish assemblages on Taiwan and Hainan Islands of China

The biotas of Taiwan and Hainan Islands are of continental origin, but the manner with which historical and ecological factors shaped these insular species is still unclear. Here, we used freshwater fish as a model to fill this gap by quantifying the phylogenetic structure of the insular faunas and disentangling the relative contribution of potential drivers. Firstly, we used clustering and ordination analyses to identify regional species pools. To test whether the insular freshwater fish faunas were phylogenetically clustered or overdispersed, we calculated the net relatedness index (NRI) and the nearest taxon index (NTI). Finally, we implemented logistic regressions to disentangle the relative importance of species attributes (i.e. maximum body length, climatic niche dissimilarity, and diversification) and historical connectivity in explaining the insular faunas. Our results showed that the most possible species pools of Taiwan are Zhejiang and Fujian provinces, and those of Hainan are Guangdong and Guangxi provinces. These insular faunas showed random phylogenetic structures in terms of NRI values. According to the NTI values, however, the Taiwanese fauna displayed more phylogenetic clustering, while the Hainanese one was more overdispersed. Both the standard and phylogenetic logistic regressions identified historical connectivity and climatic niche dissimilarity as the two top explanatory variables for species assemblages on these islands. Our reconstruction of the paleo-connected drainage basins provides insight into how historical processes and ecological factors interact to shape the freshwater fish fauna of the East Asian islands.

Influence of phylogenetic scale on the relationships of taxonomic and phylogenetic turnovers with environment for angiosperms in China

We aim to assess the influence of phylogenetic scale on the relationships of taxonomic and phylogenetic turnovers with environment for angiosperms in China. Specifically, we quantify the effects of contemporary climate on β-diversity at different phylogenetic scales representing different evolutionary depths of angiosperms. We sampled a latitudinal gradient and a longitudinal gradient of angiosperm assemblages across China (each ≥3400 km). Species composition in each assemblage was documented. Three metrics of β-diversity (βsim.tax measuring taxonomic β-diversity; βsim.phy and Dpw measuring tip- and basal-weighted phylogenetic β-diversity, respectively) were quantified among assemblages at sequential depths in the evolutionary history of angiosperms from the tips to deeper branches. This was done by slicing the angiosperm phylogenetic tree at six evolutionary depths (0, 15, 30, 45, 60, and 75 million years ago). β-diversity at each evolutionary depth was related to geographic and climatic distances between assemblages. In general, the relationship between β-diversity and climatic distance decreased from shallow to deep evolutionary time slice for all the three metrics. The slopes of the decreasing trends for βsim.tax and βsim.phy were much steeper for the latitudinal gradient than for the longitudinal gradient. The decreasing trend of the strength of the relationship was monotonic in all cases except for Dpw across the longitudinal gradient. Geographic distance between assemblages explained little variation in β-diversity that was not explained by climatic distance. Our study shows that the strength of the relationship between β-diversity and climatic distance decreases conspicuously from shallow to deep evolutionary depth for the latitudinal gradient, but this decreasing trend is less steep for the longitudinal gradient than for the latitudinal gradient, which likely reflects the influence of historical processes (e.g., the collision of the Indian plate with the Eurasian plate) on β-diversity.

Niche Conservatism Drives the Elevational Diversity Gradient in Major Groups of Free-Living Soil Unicellular Eukaryotes

Ancestral adaptations to tropical-like climates drive most multicellular biogeography and macroecology. Observational studies suggest that this niche conservatism could also be shaping unicellular biogeography and macroecology, although evidence is limited to Acidobacteria and testate amoebae. We tracked the phylogenetic signal of this niche conservatism in far related and functionally contrasted groups of common soil protists (Bacillariophyta, Cercomonadida, Ciliophora, Euglyphida and Kinetoplastida) along a humid but increasingly cold elevational gradient in Switzerland. Protist diversity decreased, and the size of the geographic ranges of taxa increased with elevation and associated decreasing temperature (climate), which is consistent with a macroecological pattern known as the Rapoport effect. Bacillariophyta exhibited phylogenetically overdispersed communities assembled by competitive exclusion of closely related taxa with shared (conserved) niches. By contrast, Cercomonadida, Ciliophora, Euglyphida and Kinetoplastida exhibited phylogenetically clustered communities assembled by habitat filtering, revealing the coexistence of closely related taxa with shared (conserved) adaptations to cope with the humid but temperate to cold climate of the study site. Phylobetadiversity revealed that soil protists exhibit a strong phylogenetic turnover among elevational sites, suggesting that most taxa have evolutionary constraints that prevent them from colonizing the colder and higher sites of the elevation gradient. Our results suggest that evolutionary constraints determine how soil protists colonize climates departing from warm and humid conditions. We posit that these evolutionary constraints are linked to an ancestral adaptation to tropical-like climates, which limits their survival in exceedingly cold sites. This niche conservatism possibly drives their biogeography and macroecology along latitudinal and altitudinal climatic gradients.

Conserving evolutionarily distinct species is critical to safeguard human well-being

Although there is growing interest in safeguarding the Tree of Life to preserve the human benefits that are directly provided by biodiversity, their evolutionary distribution remains unknown, which has hampered our understanding of the potential of phylodiversity indicators to evince them. Here, I drew on a global review of plant benefits and comprehensive phylogenetic information to breakdown their evolutionary distribution and thereby show why the commonly used Phylogenetic Diversity and Evolutionary Distinctiveness indicators can unequivocally help to preserve these natural services. Beneficial species clumped within phylogenetically overdispersed genera and closely related species often contributed very few and redundant benefits, suggesting that multiple plant lineages are required to maintain a wide variety of services. Yet, a reduced number of species stood out as multi-beneficial and evolutionarily distinct plants relative to both the entire phylogeny and the subset of beneficial species, and they collectively contributed a higher-than-expected number of records for most types of benefits. In addition to providing a clear mechanistic understanding for the recently proved success of Phylogenetic Diversity in capturing plant benefits, these findings stress the decisive role that conservation programmes aimed at protecting evolutionarily distinct taxa will play in safeguarding the beneficial potential of biodiversity for the future.

The global loss of floristic uniqueness

Regional species assemblages have been shaped by colonization, speciation and extinction over millions of years. Humans have altered biogeography by introducing species to new ranges. However, an analysis of how strongly naturalized plant species (i.e. alien plants that have established self-sustaining populations) affect the taxonomic and phylogenetic uniqueness of regional floras globally is still missing. Here, we present such an analysis with data from native and naturalized alien floras in 658 regions around the world. We find strong taxonomic and phylogenetic floristic homogenization overall, and that the natural decline in floristic similarity with increasing geographic distance is weakened by naturalized species. Floristic homogenization increases with climatic similarity, which emphasizes the importance of climate matching in plant naturalization. Moreover, floristic homogenization is greater between regions with current or past administrative relationships, indicating that being part of the same country as well as historical colonial ties facilitate floristic exchange, most likely due to more intensive trade and transport between such regions. Our findings show that naturalization of alien plants threatens taxonomic and phylogenetic uniqueness of regional floras globally. Unless more effective biosecurity measures are implemented, it is likely that with ongoing globalization, even the most distant regions will lose their floristic uniqueness.

Opposing community assembly patterns for dominant and nondominant plant species in herbaceous ecosystems globally

Biotic and abiotic factors interact with dominant plants-the locally most frequent or with the largest coverage-and nondominant plants differently, partially because dominant plants modify the environment where nondominant plants grow. For instance, if dominant plants compete strongly, they will deplete most resources, forcing nondominant plants into a narrower niche space. Conversely, if dominant plants are constrained by the environment, they might not exhaust available resources but instead may ameliorate environmental stressors that usually limit nondominants. Hence, the nature of interactions among nondominant species could be modified by dominant species. Furthermore, these differences could translate into a disparity in the phylogenetic relatedness among dominants compared to the relatedness among nondominants. By estimating phylogenetic dispersion in 78 grasslands across five continents, we found that dominant species were clustered (e.g., co-dominant grasses), suggesting dominant species are likely organized by environmental filtering, and that nondominant species were either randomly assembled or overdispersed. Traits showed similar trends for those sites (<50%) with sufficient trait data. Furthermore, several lineages scattered in the phylogeny had more nondominant species than expected at random, suggesting that traits common in nondominants are phylogenetically conserved and have evolved multiple times. We also explored environmental drivers of the dominant/nondominant disparity. We found different assembly patterns for dominants and nondominants, consistent with asymmetries in assembly mechanisms. Among the different postulated mechanisms, our results suggest two complementary hypotheses seldom explored: (1) Nondominant species include lineages adapted to thrive in the environment generated by dominant species. (2) Even when dominant species reduce resources to nondominant ones, dominant species could have a stronger positive effect on some nondominants by ameliorating environmental stressors affecting them, than by depleting resources and increasing the environmental stress to those nondominants. These results show that the dominant/nondominant asymmetry has ecological and evolutionary consequences fundamental to understand plant communities.

Spatial patterns of phylogenetic diversity and endemism in the Western Ghats, India: A case study using ancient predatory arthropods

The Western Ghats (WG) mountain chain in peninsular India is a global biodiversity hotspot, one in which patterns of phylogenetic diversity and endemism remain to be documented across taxa. We used a well-characterized community of ancient soil predatory arthropods from the WG to understand diversity gradients, identify hotspots of endemism and conservation importance, and highlight poorly studied areas with unique biodiversity. We compiled an occurrence dataset for 19 species of scolopendrid centipedes, which was used to predict areas of habitat suitability using bioclimatic and geomorphological variables in Maxent. We used predicted distributions and a time-calibrated species phylogeny to calculate taxonomic and phylogenetic indices of diversity, endemism, and turnover. We observed a decreasing latitudinal gradient in taxonomic and phylogenetic diversity in the WG, which supports expectations from the latitudinal diversity gradient. The southern WG had the highest phylogenetic diversity and endemism, and was represented by lineages with long branch lengths as observed from relative phylogenetic diversity/endemism. These results indicate the persistence of lineages over evolutionary time in the southern WG and are consistent with predictions from the southern WG refuge hypothesis. The northern WG, despite having low phylogenetic diversity, had high values of phylogenetic endemism represented by distinct lineages as inferred from relative phylogenetic endemism. The distinct endemic lineages in this subregion might be adapted to life in lateritic plateaus characterized by poor soil conditions and high seasonality. Sites across an important biogeographic break, the Palghat Gap, broadly grouped separately in comparisons of species turnover along the WG. The southern WG and Nilgiris, adjoining the Palghat Gap, harbor unique centipede communities, where the causal role of climate or dispersal barriers in shaping diversity remains to be investigated. Our results highlight the need to use phylogeny and distribution data while assessing diversity and endemism patterns in the WG.

Trait similarity in reef fish faunas across the world's oceans

Species' traits, rather than taxonomic identities, determine community assembly and ecosystem functioning, yet biogeographic patterns have been far less studied for traits. While both environmental conditions and evolutionary history shape trait biogeography, their relative contributions are largely unknown for most organisms. Here, we explore the global biogeography of reef fish traits for 2,786 species from 89 ecoregions spanning eight marine realms with contrasting environmental conditions and evolutionary histories. Across realms, we found a common structure in the distribution of species traits despite a 10-fold gradient in species richness, with a defined "backbone" of 21 trait combinations shared by all realms globally, both temperate and tropical. Across ecoregions, assemblages under similar environmental conditions had similar trait compositions despite hosting drastically different species pools from separate evolutionary lineages. Thus, despite being separated by thousands of kilometers and millions of years of evolution, similar environments host similar trait compositions in reef fish assemblages worldwide. Our findings suggest that similar trait-based management strategies can be applied among regions with distinct species pools, potentially improving conservation outcomes across diverse jurisdictions.

The contribution of environmental and dispersal filters on phylogenetic and taxonomic beta diversity patterns in Amazonian tree communities

Environmental and dispersal filters are key determinants of species distributions of Amazonian tree communities. However, a comprehensive analysis of the role of environmental and dispersal filters is needed to understand the ecological and evolutionary processes that drive phylogenetic and taxonomic turnover of Amazonian tree communities. We compare measures of taxonomic and phylogenetic beta diversity in 41 one-hectare plots to test the relative importance of climate, soils, geology, geomorphology, pure spatial variables and the spatial variation of environmental drivers of phylogenetic and taxonomic turnover in Ecuadorian Amazon tree communities. We found low phylogenetic and high taxonomic turnover with respect to environmental and dispersal filters. In addition, our results suggest that climate is a significantly better predictor of phylogenetic turnover and taxonomic turnover than geomorphology and soils at all spatial scales. The influence of climate as a predictor of phylogenetic turnover was stronger at broader spatial scales (50 km2) whereas geomorphology and soils appear to be better predictors of taxonomic turnover at mid (5 km2) and fine spatial scales (0.5 km2) but a weak predictor of phylogenetic turnover at broad spatial scales. We also found that the combined effect of geomorphology and soils was significantly higher for taxonomic turnover at all spatial scales but not for phylogenetic turnover at large spatial scales. Geographic distances as proxy of dispersal limitation was a better predictor of phylogenetic turnover at distances of 50 < 500 km. Our findings suggest that climatic variation at regional scales can better predict phylogenetic and taxonomic turnover than geomorphology and soils.

Fish taxonomic, functional, and phylogenetic diversity and their vulnerabilities in the largest river in southeastern China

Freshwater biodiversity is currently under multiple threats. Conservation of freshwater fish biodiversity needs to be prioritized because natural conservation resources are always limited.Samples were collected at 24 sites in the Min River, the largest basin in southeastern China. Taxonomic, functional, and phylogenetic diversity were analyzed. Biodiversity vulnerability was measured by removing one species each time out of the community with replacement.Results suggested that hotspots for taxonomic and phylogenetic diversity were located at two impounded sites, while for functional diversity were those sites with no upstream dams. Little congruence was observed between taxonomic, functional, and phylogenetic diversity. Fragmentation of river network connectivity caused by dams was a significant factor affecting the biodiversity patterns. Beta turnover was the driving component for beta diversity, indicating that biodiversity dissimilarity along the river was mostly explained by environmental sorting. Fifteen out of 16 species that contributed the most to different facets of biodiversity were mostly endemic, either they had distinctive functional traits or they were the most prevalent species. Sites with the highest diversity vulnerability were characterized by these distinctive species. Functional diversity was more vulnerable to species loss comparing with the other two biodiversity facets.Prioritizing those biodiversity hotspots, sites with extreme functional vulnerability, and those distinctive endemic species which contributed the most to biodiversity vulnerability is suggested in the Min River. The study found evidence that congruence among different facets of biodiversity is hard to achieve, and functional diversity is the most vulnerable in a freshwater system fragmented by intensive dam constructions. This work will help to develop systematic conservation planning from the perspective of different biodiversity facets.

Heavy Grazing Altered the Biodiversity–Productivity Relationship of Alpine Grasslands in Lhasa River Valley, Tibet

Grazing is a crucial anthropogenic disturbance on grasslands. However, it is unknown how livestock grazing affects the relationship between biodiversity and productivity of alpine grasslands in Tibet. We carried out a grazing-manipulated experiment from 2016 to 2019 with grazing intensity levels of null (control, grazing exclusion, C.K.), moderate grazing [1.65 standardized sheep unit (SSU) per hectare, M.G.], and heavy grazing (2.47 SSU per hectare, H.G.) on a typical alpine grassland in the Lhasa River Basin, central Tibet. We measured aboveground biomass (AGB), species assembly (alpha and beta diversity indices), and soil nutrients’ availability. The results showed that grazing differently affected plant community in different treatments. Notably, the total dissimilarity value between C.K. and H.G. is 0.334. Grazing decreased the Shannon–Wiener index, increased the Berger–Parker index from 2016 to 2018 significantly, and decreased AGB and total soil nitrogen (STN) significantly. Our results also showed that the grazing affected the relationship between AGB and diversity indices and soil nutrients, including soil organic carbon (SOC) and total soil phosphorus (STP). Specifically, AGB decreased with increasing SOC and STP in all treatments, and heavy grazing changed the positive relationships between AGB, STP, and Shannon–Wiener index to negative correlations significantly compared with grazing exclusion. There was a significant negative correlation between Berger–Parker and Shannon–Wiener indices under each treatment. The general linear models showed that H.G. altered the relationship between diversity and productivity of grassland in central Tibet, and AGB and Shannon–Wiener index positively correlated in C.K. but negatively correlated in H.G. Our study suggests that H.G. caused a negative relationship between plant diversity and productivity. Therefore, sustainable grazing management calls for a need of better understanding the relationship between biodiversity and productivity of alpine grassland in central Tibet.

Assessing the equilibrium between assemblage composition and climate: A directional distance-decay approach

The variation of assemblage composition in space is characterised by the decrease in assemblage similarity with spatial distance. Climatic constraint and dispersal limitation are major drivers of distance-decay of similarity. Distance-decay of similarity is usually conceptualised and modelled as an isotropic pattern, that is, assuming that similarity decays with the same rate in all directions. Because climatic gradients are markedly anisotropic, that is, they have different strength in different directions, if species distributions were in equilibrium with climate, the decay of assemblage similarity should be anisotropic in the same direction as the climatic gradient, that is, faster turnover in the direction that maximises the climatic gradient. Thus, deviations from equilibrium between assemblage composition and climatic conditions would result in differences in anisotropy between distance-decay of similarity and climatic gradients. We assessed anisotropy in distance-decay patterns in marine plankton assemblages, terrestrial vertebrates and European beetles, using two procedures: (a) measuring the correlation between the residuals of a distance-decay model and the angle in which pairs of sites are separated and (b) computing two separate distance-decay models for each dataset, one using only pairwise cases that are separated on North-South direction and another one using pairwise cases separated on East-West direction. We also analysed whether the degree of anisotropy in distance-decay is related to dispersal ability (proportion of wingless species and body size) and ecological niche characteristics (main habitat and trophic position) by assessing these relationships among beetle taxonomic groups (n = 21). Anisotropy varied markedly across realms and biological groups. Despite climatic gradients being steeper in North-South direction than in East-West direction in all datasets, North-South distance-decays tended to be steeper than East-West distance-decays in plankton and most vertebrate assemblages, but flatter in European amphibians and most beetle groups. Anisotropy also markedly varied across beetle groups depending on their dispersal ability, as the proportion of wingless species explained 60% of the variance in the difference between North-South and East-West distance-decay slopes. Our results suggest that the degree of equilibrium decreases from marine to terrestrial realms, and is markedly different between vertebrates and beetles. This has profound implications on the expected ability of different groups to track their suitable climates, and thus on the impact of climate change on biodiversity.

Temporal dynamics of bacterial communities during seed development and maturation

Seed microbiota acts as a starting point for the assembly of the plant microbiota and contributes to successful plant establishment. To date, the order and timing of microbial taxa immigration during seed development and maturation remained unknown. We investigated the temporal dynamics of seed bacterial communities in bean and radish. A high phylogenetic turnover was observed for both plant species with few taxa associated with all seed developmental stages. Greater heterogeneity in communities structure within each stage was observed for radish. While, about one-third of radish seed bacterial taxa were detected in buds, flowers and fruits, very few taxa seem to be transmitted by the floral route in bean. In the latter species, bacterial populations belonging to the P. fluorescens species complex were found either in buds, flowers and fruits or in seeds. The relative phylogenetic proximity of these bacterial populations combined with their habitat specificity led us to explore the genetic determinants involved in successful seed transmission in bean. Comparative genomic analyses of representatives bacterial strains revealed dozens of coding sequences specifically associated with seed-transmitted strains. This study provided a first glimpse on processes involved in seed microbiota assembly, which could be used for designing plant-beneficial microbial consortia.

Two ways to be endemic. Alps and Apennines are different functional refugia during climatic cycles

Endemics co-occur because they evolved in situ and persist regionally or because they evolved ex situ and later dispersed to shared habitats, generating evolutionary or ecological endemicity centres, respectively. We investigate whether different endemicity centres can intertwine in the region ranging from Alps to Sicily, by studying their butterfly fauna. We gathered an extensive occurrence data set for butterflies of the study area (27,123 records, 269 species, in cells of 0.5 × 0.5 degrees of latitude-longitude). We applied molecular-based delimitation methods (GMYC model) to 26,557 cytochrome c oxidase subunit 1 (COI) sequences of Western Palearctic butterflies. We identified entities based on molecular delimitations and/or the checklist of European butterflies and objectively attributed occurrences to their most probable entity. We obtained a zoogeographic regionalisation based on the 69 endemics of the area. Using phylogenetic ANOVA we tested if endemics from different centres differ from each other and from nonendemics for key ecological traits and divergence time. Endemicity showed high incidence in the Alps and Southern Italy. The regionalisation separated the Alps from the Italian Peninsula and Sicily. The endemics of different centres showed a high turnover and differed in phylogenetic distances, phenology and distribution traits. Endemics are on average younger than nonendemics and the Peninsula-Sicily endemics also have lower variance in divergence than those from the Alps. The observed variation identifies Alpine endemics as paleoendemics, now occupying an ecological centre, and the Peninsula-Sicily ones as neoendemics, that diverged in the region since the Pleistocene. The results challenge the common view of the Alpine-Apennine area as a single "Italian refugium".

Taxonomic and phylogenetic beta diversity of cricetid rodents in Oaxaca, southern Mexico

Understanding the ecological and historical causes and processes that shape biodiversity distribution patterns remains a challenging and fundamental task in biogeography, ecology, and evolution. To address this issue, taxonomic and phylogenetic β diversity can help us to assess the importance of ecological and historical factors that structure these biotic patterns. To make inferences about the processes underlying current spatial patterns in communities of Cricetidae across the state of Oaxaca, Mexico, their taxonomic and phylogenetic β diversity were assessed jointly. Our aims were: 1) to examine taxonomic and phylogenetic β diversity and their turnover and nestedness components among physiographic subprovinces; 2) to test for statistical significance of observed phylogenetic β diversity against the expected values of a null model; and 3) to evaluate if these metrics were correlated with geographical distance. We obtained the species composition for 12 subprovinces based on distribution models for 49 cricetid species present in Oaxaca, then carried out a maximum likelihood analysis to estimate their phylogenetic relationships. Our results show that the taxonomic and phylogenetic dissimilarities mainly were explained by the turnover component of species and lineages. In almost all pairwise comparisons, the null model approach revealed random patterns for phylogenetic β diversity values and its components. Mantel correlation models showed that the values of total taxonomic and phylogenetic diversity and their components are correlated with the geographical distances between subprovinces. Our results suggest that both taxonomic and phylogenetic β diversity are explained by the interplay between biogeographical history from southern Mexico, and the recent speciation processes in cricetid rodents. Given that speciation processes are allopatric for most cricetid taxa, the high values of spatial turnover can be explained by the small ranges of species, coupled with current abiotic conditions that act as filters, promoting specialization of species on particular conditions. Our results show the importance of the phylogenetic approach to unravel the multidimensional spatial patterns of biodiversity.

Higher evolutionary rates in life-history traits in insular than in mainland palms

Isolated islands, due to the reduced interspecific competition compared to mainland habitats, present ecological opportunities for colonizing lineages. As a consequence, island lineages may be expected to experience higher rates of trait evolution than mainland lineages. However, island effects on key life-history traits of vascular plants remain underexplored at broad spatiotemporal scales, even for emblematic island clades such as palms. Here, we used phylogenetic comparative methods to evaluate potential differences in size and macroevolutionary patterns of height and fruit diameter among mainland, continental, and volcanic island palms. Further, phylogenetic beta-diversity was used to determine if lineage turnover supported an adaptive radiation scenario on volcanic islands. Volcanic island palms were taller than their continental island and mainland counterparts, whereas continental island palms exhibited smaller fruit size. Height and fruit size of palms evolved under evolutionary constraints towards an optimal value. However, scenarios of adaptive radiation and niche conservatism were not supported for the height and fruit size of volcanic and mainland palm clades, respectively, as expected. Instead, continental island palms exhibited higher evolutionary rates for height and fruit size. Insular palm assemblages (continental and volcanic) are composed of unique lineages. Beyond representing evolutionary sources of new palm lineages, our results demonstrate that insular habitats are important in shaping palm trait diversity. Also, the higher phenotypic evolutionary rates of continental island palms suggest disparate selection pressures on this habitat type, which can be an important driver of trait diversification over time. Taken together, these results stress the importance of insular habitats for conservation of functional, phylogenetic, and taxonomic diversity of palms.

Macroevolutionary and macroecological approaches to understanding the evolution of stress tolerance in plants

Environmental stress response in plants has been studied using a wide range of approaches, from lab-based investigation of biochemistry and genetics, to glasshouse studies of physiology and growth rates, to field-based trials and ecological surveys. It is also possible to investigate the evolution of environmental stress responses using macroevolutionary and macroecological analyses, analysing data from many different species, providing a new perspective on the way that environmental stress shapes the evolution and distribution of biodiversity. "Macroevoeco" approaches can produce intriguing results and new ways of looking at old problems. In this review, we focus on studies using phylogenetic analysis to illuminate macroevolutionary patterns in the evolution of environmental stress tolerance in plants. We follow a particular thread from our own research-evolution of salt tolerance-as a case study that illustrates a macroevolutionary way of thinking that opens up a range of broader questions on the evolution of environmental stress tolerances. We consider some potential future applications of macroevolutionary and macroecological analyses to understanding how diverse groups of plants evolve in response to environmental stress, which may allow better prediction of current stress tolerance and a way of predicting the capacity of species to adapt to changing environmental stresses over time.

Rapid climate change results in long-lasting spatial homogenization of phylogenetic diversity

Scientific understanding of biodiversity dynamics, resulting from past climate oscillations and projections of future changes in biodiversity, has advanced over the past decade. Little is known about how these responses, past or future, are spatially connected. Analyzing the spatial variability in biodiversity provides insight into how climate change affects the accumulation of diversity across space. Here, we evaluate the spatial variation of phylogenetic diversity of European seed plants among neighboring sites and assess the effects of past rapid climate changes during the Quaternary on these patterns. Our work shows a marked homogenization in phylogenetic diversity across Central and Northern Europe linked to high climate change velocity and large distances to refugia. Our results suggest that the future projected loss in evolutionary heritage may be even more dramatic, as homogenization in response to rapid climate change has occurred among sites across large landscapes, leaving a legacy that has lasted for millennia.

How past climate change has affected biodiversity over large spatial scales remains underexplored. Here, the authors find marked homogenization in flowering plant phylogenetic diversity across Central and Northern Europe linked to rapid climate change and large distances to glacial refugia.

An Overview of Bioinformatics Tools for DNA Meta-Barcoding Analysis of Microbial Communities of Bioaerosols: Digest for Microbiologists

High-throughput DNA sequencing (HTS) has changed our understanding of the microbial composition present in a wide range of environments. Applying HTS methods to air samples from different environments allows the identification and quantification (relative abundance) of the microorganisms present and gives a better understanding of human exposure to indoor and outdoor bioaerosols. To make full use of the avalanche of information made available by these sequences, repeated measurements must be taken, community composition described, error estimates made, correlations of microbiota with covariates (variables) must be examined, and increasingly sophisticated statistical tests must be conducted, all by using bioinformatics tools. Knowing which analysis to conduct and which tools to apply remains confusing for bioaerosol scientists, as a litany of tools and data resources are now available for characterizing microbial communities. The goal of this review paper is to offer a guided tour through the bioinformatics tools that are useful in studying the microbial ecology of bioaerosols. This work explains microbial ecology features like alpha and beta diversity, multivariate analyses, differential abundances, taxonomic analyses, visualization tools and statistical tests using bioinformatics tools for bioaerosol scientists new to the field. It illustrates and promotes the use of selected bioinformatic tools in the study of bioaerosols and serves as a good source for learning the “dos and don’ts” involved in conducting a precise microbial ecology study.

Exploring the potential of metabarcoding to disentangle macroinvertebrate community dynamics in intermittent streams

Taxonomic sufficiency represents the level of taxonomic detail needed to detect ecological patterns to a level that match the requirement of a study. Most bioassessments apply the taxonomic sufficiency concept and assign specimens to the family or genus level given time constraints and the difficulty to correctly identify species. This holds particularly true for stream invertebrates because small and morphologically similar larvae are hard to distinguish. Low taxonomic resolution may hinder detecting true community dynamics, which thus leads to incorrect inferences about community assembly processes. DNA metabarcoding is a new, affordable and cost-effective tool for the identification of multiple species from bulk samples of organisms. As it provides high taxonomic resolution, it can be used to compare results obtained from different identification levels. Measuring the effect of taxonomic resolution on the detection of community dynamics is especially interesting in extreme ecosystems like intermittent streams to test if species at intermittent sites are subsets of those from perennial sources or if independently recruiting taxa exist. Here we aimed to compare the performance of morphological identification and metabarcoding to detect macroinvertebrate community dynamics in the Trebbia River (Italy). Macroinvertebrates were collected from four perennial and two intermittent sites two months after flow resumption and before the next dry phase. The identification level ranged from family to haplotype. Metabarcoding and morphological identifications found similar alpha diversity patterns when looking at family and mixed taxonomic levels. Increasing taxonomic resolution with metabarcoding revealed a strong partitioning of beta diversity in nestedness and turnover components. At flow resumption, beta diversity at intermittent sites was dominated by nestedness when family-level information was employed, while turnover was evidenced as the most important component when using Operational Taxonomic Units (OTUs) or haplotypes. The increased taxonomic resolution with metabarcoding allowed us to detect species adapted to deal with intermittency, like the chironomid Cricotopus bicinctus and the ephemeropteran Cloeon dipterum. Our study thus shows that family and mixed taxonomic level are not sufficient to detect all aspects of macroinvertebrate community dynamics. High taxonomic resolution is especially important for intermittent streams where accurate information about species-specific habitat preference is needed to interpret diversity patterns induced by drying and the nestedness/turnover components of beta diversity are of interest to understand community assembly processes.

Patterns of change in α and β taxonomic and phylogenetic diversity in the secondary succession of semi-natural grasslands in the Northern Apennines

We studied the secondary succession in semi-natural grasslands (dry grasslands and hay meadows) located in the eastern side of the Tuscan Apennines (Tuscany, Central Italy). We compared these habitats, investigating: (i) the changes in species richness, composition and phylogenetic diversity during the succession; (ii) whether the trends in species loss and species turnover in taxonomic diversity matched those in phylogenetic diversity. We performed a stratified random sampling, in a full factorial design between habitat type and succession stage (60 sampled plots, 10 × 2 types of habitat × 3 stages of succession). We constructed a phylogenetic tree of the plant communities and compared the differences in taxonomic/phylogenetic α- and β-diversity between these two habitats and during their succession. We identified indicator species for each succession stage and habitat. Looking at α-diversity, both habitats displayed a decrease in species richness, with a random process of species selection in the earlier succession stages from the species regional pool. Nevertheless, in the latter stage of dry grasslands we recorded a shift towards phylogenetic overdispersion at the higher-level groups in the phylogenetic tree. In both habitats, while the richness decreased with succession stage, most species were replaced during the succession. However, the hay meadows were characterized by a higher rate of new species’ ingression whereas the dry grasslands became dominated with Juniperus communis. Accordingly, the two habitats showed similar features in phylogenetic β-diversity. The main component was true phylogenetic turnover, due to replacement of unique lineages along the succession. Nevertheless, in dry grasslands this trend is slightly higher than expected considering the major importance of difference in species richness of dry grasslands sites and this is due to the presence of a phylogenetically very distant species (J. communis).

Passive rewilding may (also) restore phylogenetically rich and functionally resilient forest plant communities

Passive rewilding is increasingly seen as a promising tool to counterbalance biodiversity losses and recover native forest ecosystems. One key question, crucial to understanding assembly processes and conservation issues underlying land-use change, is the extent to which functional and phylogenetic diversity may recover in spontaneous recent woodlands. Here, we compared understorey plant communities of recent woodlands (which result from afforestation on agricultural lands during the 20th century) with those of ancient forests (uninterrupted for several centuries) in a hotspot of farmland abandonment in western Europe. We combined taxonomic, functional, and phylogenetic diversity metrics to detect potential differences in community composition, structure (richness, divergence), conservation importance (functional originality and specialization, evolutionary distinctiveness) and resilience (functional redundancy, response diversity). The recent and ancient forests harbored clearly distinct compositions, especially regarding the taxonomic and phylogenetic facets. Recent woodlands had higher taxonomic, functional and phylogenetic richness and a higher evolutionary distinctiveness, whereas functional divergence and phylogenetic divergence were higher in ancient forests. On another hand, we did not find any significant differences in functional specialization, originality, redundancy, or response diversity between recent and ancient forests. Our study constitutes one of the first empirical pieces of evidence that recent woodlands may spontaneously regain plant communities phylogenetically rich and functionally resilient, at least as much as those of ancient relict forests. As passive rewilding is the cheapest restoration method, we suggest that it should be a very useful tool to restore and conserve native forest biodiversity and functions, especially when forest areas are restricted and fragmented.