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Phylogenetic diversity (PD) metrics estimate community diversity through evolutionary relationships, yet their potential in restoration ecology remains underutilized. This study reviews the literature on ecological restoration of terrestrial vegetation to evaluate the use of PD metrics, focusing on their application, global trends, and existing research gaps. Most studies were conducted in the United States, China, and Brazil, primarily in temperate broadleaf mixed forests (36.36%) and tropical and subtropical moist broadleaf forests (33.33%). Half of the papers were based on observational studies of restorations, and the other half were experimental studies. Plant PD was the primary focus in 90.09% of papers, with grasses and trees being the most studied life forms. Standardized effect size of the mean pairwise distance and mean nearest taxonomic distance metrics were the most commonly used metrics. The majority of studies used PD as a response variable and restoration indicators (e.g. age, initial seed/seedling mixture, and restoration impact) as explanatory variables. Research bias toward grassland and limited studies in Africa and Oceania were noted. Future studies should broaden geographic coverage in restoration to provide a more comprehensive understanding of PD dynamics globally. Also, efforts should be made to expand the taxonomic scope beyond to capture the full spectrum of biodiversity in restoration assessments. [ABSTRACT FROM AUTHOR]

ABSTRACT Aim Location Major Taxa Studied Methods Results Main Conclusions The Kunming‐Montreal Global Biodiversity Framework requires that evolutionary histories of species should be considered in conservation planning. The phylogenetic structure of species assemblages quantifies species evolutionary histories and increasingly becomes an endeavour for ecologists. Understanding the geographic patterns of phylogenetic structure of species assemblages and their drivers can provide a fundamental reference for conservation planning. Although several theoretical hypotheses based on the effects of contemporary environment, historical climate change and evolutionary niche conservatism had been widely discussed in previous studies, the relative contributions of these hypotheses on phylogenetic structure of angiosperms, especially herbaceous species, remain debated.East Eurasia.Angiosperms.We compiled distributions of 43,023 angiosperm species in east Eurasia at spatial resolution (100 × 100 km2). Using this newly compiled database and a species‐level phylogeny, we estimated the phylogenetic structure patterns for species with different growth forms. We explored the relationships of these patterns with contemporary environment and historical climate change to test predictions of the tropical niche conservatism hypothesis (TCH) and to compare the contribution of different hypotheses using generalised linear models and hierarchical partitioning.We found that phylogenetic structure of angiosperms displayed significant latitudinal gradients. Notably, phylogenetic structure patterns and their drivers differed between woody and herbaceous species. Actual evapotranspiration was the best predictor of phylogenetic structure patterns for all and herbaceous species, while the mean temperature of the coldest quarter was the best predictor for woody species. The effect of historical climate change on phylogenetic structure patterns was weak.Our results suggest that the TCH only explains the phylogenetic structure pattern of woody species, not herbaceous species. Moreover, contemporary climate influences the phylogenetic structure of angiosperms in east Eurasian by affecting herbaceous and woody species differently. [ABSTRACT FROM AUTHOR]

Introduction: Understanding how human activities affect biodiversity is needed to inform systemic policies and targets for achieving sustainable development goals. Shallow tillage to remove Artemisia ordosica is commonly conducted in the Mu Us Desert. However, the impacts of shallow tillage on plant community species diversity, phylogenetic structure, and community assembly processes remain poorly understood. Methods: This study explores the effects of shallow tillage on species diversity including three a-diversity and two b-diversity indicators, as well as phylogenetic structure [phylogenetic diversity (PD), net relatedness index (NRI), and nearest taxon index (NTI)]. Additionally, this research analyzes the effects of shallow tillage on the community assembly process. Results and discussion: The results showed that the a-diversity index, b-diversity index, and PD of the shallow tillage (ST) communities were significantly higher than those of the non-shallow tillage (NT) communities, and the phylogenetic structures of both the ST and NT communities tended to be differentiated, with competitive exclusion being the main mechanism of plant assembly. However, shallow tillage increased the relative importance of the stochastic processes dominated by dispersal limitation, mitigating plant competition in the communities. This conclusion was supported by the Raup-Crick difference index-based analysis. Conclusion: Therefore, for the ecological restoration of the Mu Us Desert, species with adaptability and low niche overlap should be selected to increase the utilization efficiency of the environmental resources. The results of this study provide a foundation for policy development for ecosystem management and restoration in the Mu Us Desert. [ABSTRACT FROM AUTHOR]

Mediterranean landscapes were drastically affected by high levels of abandonment of agricultural and other land practices during the last century. These changes in land use can have significant effects on diversity patterns by altering disturbance and competition equilibria within plant communities at the landscape level. Particularly, such changes have been found to affect the patterns of phylogenetic diversity and structure by causing nonrandom losses of species through filtering effects and landscape homogenization. By investigating diversity patterns across a region submitted to high levels of land use changes, located in a (sub‐) mountainous area of northwestern Greece (northern Pindus), we aimed at understanding the patterns of phylogenetic diversity and structure in relation to land abandonment and the subsequent recovery of natural vegetation. We sampled 250 vegetation plots equally divided in grasslands and forests, distributed across the different classes of land use occurring in the general study area based on the period since the last change in land use. Standardized metrics of Faith's phylogenetic diversity, mean phylogenetic distance, and mean nearest taxon distance were used to investigate phylogenetic diversity patterns across communities and different land‐use regimes. A Principal Coordinates of Phylogenetic Structure analysis was employed to evaluate the variation in lineage composition among communities, and boosted regression trees were used to identify the relative influence of community differentiation (as captured by the classification of sampling plots in ecologically and floristically distinct vegetation communities), plant life strategies (competition, stress tolerance, and disturbance), and climatic, topographic, and soil variables on phylogenetic diversity metrics. Community differentiation was identified as the main driver of phylogenetic patterns. Additionally, phylogenetic diversity and structure were observed as having a statistically significantly negative correlation with disturbance, a statistically significantly positive correlation with stress tolerance, and a weaker positive correlation with competition. Phylogenetic clustering was observed for the early successional grassland communities submitted to stronger effects of disturbance, while phylogenetic randomness (or rarely overdispersion) was observed in forest communities submitted to stronger effects of competition. Finally, phylogenetic clustering of grassland communities was more evident shortly after land abandonment. [ABSTRACT FROM AUTHOR]

Abstract Background The geographic patterns of plant diversity in the Qinghai-Tibet Plateau (QTP) have been widely studied, but few studies have focused on wetland plants. This study quantified the geographic patterns of wetland plant diversity in the QTP through a comprehensive analysis of taxonomic, phylogenetic and functional indices. Methods Based on a large number of floras, monographs, specimens and field survey data, we constructed a comprehensive dataset of 1,958 wetland plant species in the QTP. Species richness (SR), phylogenetic diversity (PD), functional diversity (FD), net relatedness index (NRI) and net functional relatedness index (NFRI) were used to assess the taxonomic, phylogenetic and functional diversity of wetland plants. We explored the relationships between the diversity indices and four categories of environmental variables (i.e. energy-water, climate seasonality, topography and human activities). We used four diversity indices, namely endemic species richness, weighted endemism, phylogenetic endemism and functional endemism, together with the categorical analysis of neo- and paleo-endemism (CANAPE), to identify the endemic centers of wetland plants in the QTP. Results SR, PD and FD were highly consistent and showed a decreasing trend from southeast to northwest, decreasing with increasing elevation. The phylogenetic structure of wetland plant assemblages in most parts of the plateau is mainly clustered. The functional structure of wetland plant assemblages in the southeast of the plateau is overdispersed, while the functional structure of wetland plant assemblages in other areas is clustered. Energy-water and climate seasonality were the two most important categories of variables affecting wetland plant diversity. Environmental variables had a greater effect on the functional structure of wetland plants than on the phylogenetic structure. This study identified seven endemic centres, mainly in the Himalayas and Hengduan Mountains. Conclusions Climate and topography are the main factors determining the geographic distribution of wetland plant diversity at large scales. The majority of grid cells in the QTP with significant phylogenetic endemism were mixed and super-endemism. At large scales, compared to climate and topography, human activities may not have a negative impact on wetland plant diversity in the QTP.

Phylogenetic diversity offers critical insights into the ecological dynamics shaping species composition and ecosystem function, thereby informing conservation strategies. Despite its recognized importance in ecosystem management, the assessment of phylogenetic diversity in endangered habitats, such as vernal pools, remains limited. Vernal pools, characterized by cyclical inundation and unique plant communities, present an ideal system for investigating the interplay between ecological factors and phylogenetic structure. This study aims to characterize the phylogenetic patterns of vernal pools and their associated vegetation zones, addressing questions about taxonomic and phylogenetic community discreteness, the role of flooding as a habitat filter, the influence of invasive species on phylogenetic structure, and the impact of seasonal variation on phylogenetic diversity. I find that zones‐of‐vegetation exhibit high between zone taxonomic and phylogenetic beta diversity whereas each zone forms a unique cluster, suggesting that zones are taxonomically and phylogenetically discrete units. Regions of high‐inundation pressure exhibit phylogenetic clustering, indicating that flooding is a habitat filter in vernal pool habitats. Competition between native species conform to the 'competitive relatedness hypothesis' and, conversely, communities dominated by invasive Eurasian grass species are phylogenetically clustered. In addition, I find that phylogenetic diversity within zones fluctuates across the spring season in response to changing water levels, precipitation, and temperature. By analyzing three pools within the Merced Vernal Pool and Grassland Reserve, this research elucidates the phylogenetic dynamics of vernal pools. The findings underscore the need for tailored conservation strategies that account for the unique ecological characteristics of each vegetation zone within vernal pool habitats. [ABSTRACT FROM AUTHOR]

Insertion/Deletion (InDel) polymorphisms, characterized by their smaller amplicons, reduced mutation rates, and compatibility with the prevalent capillary electrophoresis (CE) platforms in forensic laboratories, significantly contribute to the advancement and application of genetic analysis. Guizhou province in China serves as an important region for investigating the genetic structure, ethnic group origins, and human evolution. However, DNA data and the sampling of present-day populations are lacking, especially about the InDel markers. Here, we reported data on 47 autosomal InDels from 592 individuals from four populations in Guizhou (Han, Dong, Yi, and Chuanqing). Genotyping was performed with the AGCU InDel 50 kit to evaluate their utility for forensic purposes and to explore the population genetic structure. Our findings showed no significant deviations from Hardy-Weinberg and linkage equilibriums. The combined power of discrimination (CPD) and the combined power of exclusion (CPE) for each population demonstrated that the kit could be applied to forensic individual identification and was an effective supplement for parentage testing. Genetic structure analyses, including principal component analysis, multidimensional scaling, genetic distance calculation, STRUCTURE, and phylogenetic analysis, highlighted that the genetic proximity of the studied populations correlates with linguistic, geographical, and cultural factors. The observed genetic variances within four research populations were less pronounced than those discerned between populations across different regions. Notably, the Guizhou Han, Dong, and Chuanqing populations showed closer genetic affiliations with linguistically similar groups than the Guizhou Yi. These results underscore the potential of InDel markers in forensic science and provide insights into the genetic landscape and human evolution in multi-ethnic regions like Guizhou. Key points InDel markers show promise for forensic individual identification and parentage testing via the AGCU InDel 50 kit. Genetic analysis of Guizhou populations reveals correlations with linguistic, geographical, and cultural factors. Guizhou Han, Dong, and Chuanqing populations showed closer genetic affiliations with linguistically similar groups than the Guizhou Yi. [ABSTRACT FROM AUTHOR]

Urbanization is a major cause of biotic homogenization and evolutionary poverty. Urban remnant forests are biodiversity hotspots in cities but are prone to phylogenetic homogenization. However, how urbanization‐driven changes in patch attributes and landscape heterogeneity levels of the surrounding matrix affect plant phylogenetic diversity in urban remnant forests remains unclear. We quantified tree phylogenetic diversity and structure in 30 remnant forest patches in Guiyang, China, using chloroplast genome data and analyzed the effects of patch attributes and the surrounding matrix on tree phylogenetic diversity and structure in the forests while considering tree species stage. The phylogenetic diversity of saplings/seedlings was lower than that of adult trees. Small patches contributed more than large patches to the overall phylogenetic diversity of remnant forest ecosystems. Additionally, tree phylogenetic diversity was positively associated with configurational heterogeneity of the surrounding matrix, while phylogenetic diversity and relatedness were negatively related to the percentage of surrounding impervious surfaces and patch size. Accordingly, we suggest maintaining configurational heterogeneity and controlling the speed of urban expansion in the surrounding matrix to better conserve urban remnant forests. Furthermore, the preservation of small forest remnants and tree species in the sapling/seedling stage should be prioritized. [ABSTRACT FROM AUTHOR]

This study examines the woody plant community in the Sygera Mountains to reveal the diversity changes and phylogenetic structure of woody plants in different vertical zones. Three plots of 400 m2 and two plots of 900 m2 are set up in each zone. The line transect method is used to supplement the woody plant species list. Meteorological data are adopted to analyze the composition of woody plant flora, the characteristics of the phylogenetic structure, and their relationship with annual average temperature. Results showed that (1) temperate woody plants account for a large proportion (65.6%) in the woody plant community of the Sygera Mountains, and widespread woody genera account for a small proportion (12.6%). The composition of families and genera is rich in the mountainous warm temperate zone, and the species composition is rich in the mountainous temperate zone. (2) The Gleason index and phylogenetic diversity of the woody plant communities in the five vertical zones are significantly positively correlated with the annual average temperature (P < 0.01), whereas the net relatedness and nearest taxon indices are not correlated with the annual average temperature. (3) The woody plant communities in the alpine frigid and alpine desert zones of the Sygera Mountains exhibit phylogenetic clustering, which suggests that habitat filtering plays an important role in the construction of woody plant communities in these vertical zones. However, the other vertical zones show either phylogenetic clustering or phylogenetic overdispersion, indicating that the results might be the combined effects of habitat filtering and competitive exclusion. This study provides new insights into the diversity composition and construction mechanisms of woody plant communities in the Sygera Mountains. [ABSTRACT FROM AUTHOR]

Aim: Understanding the patterns and drivers of biodiversity across space and time is commonly based on species diversity, which may ignore species' functional role and evolutionary history and result in an incomplete understanding of community assembly. It is suggested that integrating species, functional, and phylogenetic diversity could provide a more holistic assessment of community assembly in natural ecosystems. This study aimed to explore the elevational patterns and environmental drivers of multiple facets of fish diversity and community structure in a subtropical river during the wet and dry seasons. Location: The Chishui River basin, China. Methods: We investigated the responses of fish species richness, functional richness, and phylogenetic diversity to elevation in different seasons. Moreover, we compared functional dispersion and mean pairwise distance with those obtained from null models to infer assembly mechanisms shaping community structure. Additionally, we examined the environmental drivers (e.g. water chemistry, temperature, and river size) of fish diversity and community structure. Results: Fish species richness, functional richness, and phylogenetic diversity showed a negative relationship with elevation in the Chishui River basin. Fish communities tended to be on average functionally random but phylogenetically clustered. Furthermore, phylogenetic structure exhibited a decreasing pattern along the elevational gradient. Despite no significant seasonal changes for fish diversity (except for phylogenetic diversity), fish communities became more phylogenetically overdispersed and clustered at low and high elevations in the dry season. Additionally, the responses of fish diversity and community structure to environmental variables were not synchronous. Conclusions: At the basin scale, environmental filtering was prevalent in shaping fish phylogenetic structure, whereas stochasticity was likely more important for functional structure. Moreover, the ecological mechanisms shaping individual fish communities switched from limiting similarity to environmental filtering as elevation increased, and the underlying forces at two ends of the elevational gradient became more prominent in the dry season. [ABSTRACT FROM AUTHOR]

Both human populations and marine biodiversity are concentrated along coastlines, with growing conservation interest in how these ecosystems can survive intense anthropogenic impacts. Tropical urban centres provide valuable research opportunities because these megacities are often adjacent to mega‐diverse coral reef systems. The Pearl River Delta is a prime exemplar, as it encompasses one of the most densely populated and impacted regions in the world and is located just northwest of the Coral Triangle. However, the spatial and taxonomic complexity of this biodiversity, most of which is small, cryptic in habitat and poorly known, make comparative analyses challenging. We deployed standardized settlement structures at seven sites differing in the intensity of human impacts and used COI metabarcoding to characterize benthic biodiversity, with a focus on metazoans. We found a total of 7184 OTUs, with an average of 665 OTUs per sampling unit; these numbers exceed those observed in many previous studies using comparable methods, despite the location of our study in an urbanized environment. Beta diversity was also high, with 52% of the OTUs found at just one site. As expected, we found that the sites close to point sources of pollution had substantially lower diversity (44% less) relative to sites bathed in less polluted oceanic waters. However, the polluted sites contributed substantially to the total animal diversity of the region, with 25% of all OTUs occurring only within polluted sites. Further analysis of Arthropoda, Annelida and Mollusca showed that phylogenetic clustering within a site was common, suggesting that environmental filtering reduced biodiversity to a subset of lineages present within the region, a pattern that was most pronounced in polluted sites and for the Arthropoda. The water quality gradients surrounding the PRD highlight the unique role of in situ studies for understanding the impacts of complex urbanization pressures on biodiversity. [ABSTRACT FROM AUTHOR]

The genetic diversity of indigenous chickens, which comprise over 80% of the chicken resources in Uganda, is largely not well-characterized for their genetic contribution. This study assessed the genetic diversity and population structure of the indigenous chicken population in Uganda to serve as an essential component for improvement and conservation strategies. A set of 344 mitochondrial DNA (mtDNA) D-loop sequences among 12 Ugandan chicken populations was evaluated. Twenty-eight polymorphic sites, accounting for 4.26% of the total analyzed loci of 658 bp, defined 32 haplotypes. The haplotype diversity (Hd) was 0.437, with a nucleotide diversity (π) of 0.0169, while the average number of nucleotide differences (k) was 0.576, indicating a population that is moderately genetically diverse. Analysis of molecular variance found 98.39% (ρ < 0.01) of the total sequence variation among the chicken haplotypes within populations, 1.08% (ρ < 0.05) among populations, and 0.75% (ρ > 0.05) among populations within regions. This revealed subtle genetic differentiation among the populations, which appeared to be influenced by population fragmentation, probably due to neutral mutation, random genetic drift, and/or balancing selection. All the haplotypes showed affinity exclusively to the haplogroup-E mtDNA phylogeny, with haplotype UGA01 signaling an ancestral haplotype in Uganda. Neutrality tests Tajima’sD(−2.320) and Fu’s Fs (−51.369), augmented with mismatch distribution to measure signatures of recent historical demographic events, supported a population expansion across the chicken populations. The results show one matrilineal ancestry of Ugandan chickens from a lineage widespread throughout the world that began in the Indian subcontinent. The lack of phylogeographic signals is consistent with recent expansion events with extensive within-country genetic intermixing among haplotypes. Thus, the findings in this study hold the potential to guide conservation strategies and breeding programs in Uganda, given that higher genetic diversity comes from within the chicken population. [ABSTRACT FROM AUTHOR]

The composition of microbial communities on leaf surface is closely related to plant foliar diseases. However, the response in fungal community on plant leaves to the severity of pant diseases are still unknown. In this study, we used high-throughput ITS amplicon sequencing technology to investigate the differences in the composition and diversity of fungal community on plant leaves with different disease severities of powdery mildew disease in Solanaceae crops. We analyzed the changes in the topological properties of molecular ecological networks of fungal community and explored the ecological processes of community phylogenetic assembly. Diversity analysis showed that as the severity of powdery mildew disease increased, the richness and diversity of fungal communities gradually decreased. Network analysis revealed that compared to plants with moderate and severe infection, plants with mild disease symptoms had more nodes and connections in the ecological network, with higher network density, clustering coefficient, and average connectivity. Among the plants with different disease severities, the ecological processes of phylogenetic assembly in fungal communities were dominated by stochastic processes, whereas the fungal communities tended to have phylogenetic dispersion with increasing severity of powdery mildew. In conclusion, invasive pathogens alter the existing community structure, disrupt the interactions between fungal communities, and influence the ecological processes of community phylogenetic assembly. These findings provide a deep insight into the association between powdery mildew disease and the fungal community on plant leaves. [ABSTRACT FROM AUTHOR]

Abstract Phylogenetic diversity offers critical insights into the ecological dynamics shaping species composition and ecosystem function, thereby informing conservation strategies. Despite its recognized importance in ecosystem management, the assessment of phylogenetic diversity in endangered habitats, such as vernal pools, remains limited. Vernal pools, characterized by cyclical inundation and unique plant communities, present an ideal system for investigating the interplay between ecological factors and phylogenetic structure. This study aims to characterize the phylogenetic patterns of vernal pools and their associated vegetation zones, addressing questions about taxonomic and phylogenetic community discreteness, the role of flooding as a habitat filter, the influence of invasive species on phylogenetic structure, and the impact of seasonal variation on phylogenetic diversity. I find that zones‐of‐vegetation exhibit high between zone taxonomic and phylogenetic beta diversity whereas each zone forms a unique cluster, suggesting that zones are taxonomically and phylogenetically discrete units. Regions of high‐inundation pressure exhibit phylogenetic clustering, indicating that flooding is a habitat filter in vernal pool habitats. Competition between native species conform to the ‘competitive relatedness hypothesis’ and, conversely, communities dominated by invasive Eurasian grass species are phylogenetically clustered. In addition, I find that phylogenetic diversity within zones fluctuates across the spring season in response to changing water levels, precipitation, and temperature. By analyzing three pools within the Merced Vernal Pool and Grassland Reserve, this research elucidates the phylogenetic dynamics of vernal pools. The findings underscore the need for tailored conservation strategies that account for the unique ecological characteristics of each vegetation zone within vernal pool habitats.

Nitrogen (N) deposition rates have notably increased around the world, especially in high-altitude regions like the Qinghai–Tibetan Plateau (QTP). We conducted a six-year comprehensive experiment to simulate nitrogen deposition in an alpine grassland area near Qinghai Lake. Four levels of nitrogen depositions, i.e., 0 (CK), 8 kg N ha−1year−1 (N1), 40 kg N ha−1year−1 (N2), and 72 kg N ha−1year−1 (N3), with three replicates for each N treatment, were tested annually in early May and early July, with the meticulous collection of plant and soil samples during the peak growth period from 15 July to 15 August. We used the null model to evaluate the impact of environmental filtration and interspecific competition on the dynamics of the plant community was assessed based on the level of discrete species affinities within the plant community by constructing a phylogenetic tree. The results showed that the environmental filter was the predominant driver for the change of community’s genealogical fabric. The N2 and N3 treatments increased the influence of soil factors on the change of plant community structure. Climatic factors played a crucial role on the change of plant community in the CK grassland area, while soil factors were dominant in the N1- and N3-treated grasslands.

Disentangling the distribution patterns of biodiversity along altitudinal gradients and their drivers has been a hot topic in ecological research. Different forest strata show multiple distribution patterns influenced by different community assembly mechanisms. Here, we measure the dominant ecological processes affecting three forest strata (tree, shrub, and herb layers) along altitudinal gradients. We sampled plants with different forest strata in 21 plots located from 2500 to 3700 m in Lasha Mountain, northwestern Yunnan. The taxonomic alpha diversity of the herb layer showed a monotonic decreasing trend with increasing altitude, while the shrub layer was characterized by a single peak, and the tree layer showed no significant change with increasing altitude. We observed a decreasing pattern of phylogenetic diversity with increasing altitude in the herb layer, whereas phylogenetic diversity did not change in the tree and shrub layers. The phylogenetic structure of these three layers showed the same pattern: phylogenetic clustering at low altitudes and overdispersion at middle and high altitudes. The diversity and phylogenetic structure of the herb layer were driven by climate (average dry season precipitation) and topographic (slope and aspect) factors, while shrub layer diversity was mainly influenced by tree layer richness. Overall, the phylogenetic structure pattern of the three forest strata changed from clustered to overdispersed with increasing altitude, indicating that environmental filtering was the main driver at low altitudes, while interspecific competition dominated at middle and high altitudes. [ABSTRACT FROM AUTHOR]

BRCA1 gene plays an important role in DNA damage repair, cell cycle, and transcription process regulation; hence it's called gate keeper. The current research aims to perform bioinformatics analyzes of the BRCA1 gene of different breeds of domestic and wild sheep from 49 breeds in 14 countries using the NCBI genome database. The desired sequences were aligned using MEGA11 software and a phylogenetic tree was drawn by Neighbor-Joining method. The number of mutations, nucleotide diversity, and haploid diversity were also analyzed using Dnaspv5 software. The analyses showed 296 polymorphisms, which led to the creation of 45 different haplotypes with a haplotype diversity of 0.035. Nucleotide diversity and average nucleotide differences among breeds were estimated as 0.259 and 0.052, respectively. The average genetic distance within the population of countries was calculated as 0.052. The amount of sequence conservation in this research was 0.313 on average, which indicates the high polymorphism of this gene and the emergence of new proteins. Tajima's D value in Tajima's neutrality test was −2.421, which was significant (p < 0.05). One of the reasons for the high genetic diversity in Iran's wild sheep population is the existence of forests and open environments, which prevent genetic drift and reduce inbreeding. [ABSTRACT FROM AUTHOR]

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The genetic diversity of indigenous chickens, which comprise over 80% of the chicken resources in Uganda, is largely not well-characterized for their genetic contribution. This study assessed the genetic diversity and population structure of the indigenous chicken population in Uganda to serve as an essential component for improvement and conservation strategies. A set of 344 mitochondrial DNA (mtDNA) D-loop sequences among 12 Ugandan chicken populations was evaluated. Twenty-eight polymorphic sites, accounting for 4.26% of the total analyzed loci of 658 bp, defined 32 haplotypes. The haplotype diversity (Hd) was 0.437, with a nucleotide diversity (π) of 0.0169, while the average number of nucleotide differences (k) was 0.576, indicating a population that is moderately genetically diverse. Analysis of molecular variance found 98.39% (ρ < 0.01) of the total sequence variation among the chicken haplotypes within populations, 1.08% (ρ < 0.05) among populations, and 0.75% (ρ > 0.05) among populations within regions. This revealed subtle genetic differentiation among the populations, which appeared to be influenced by population fragmentation, probably due to neutral mutation, random genetic drift, and/or balancing selection. All the haplotypes showed affinity exclusively to the haplogroup-E mtDNA phylogeny, with haplotype UGA01 signaling an ancestral haplotype in Uganda. Neutrality tests Tajima’s D (−2.320) and Fu’s Fs (−51.369), augmented with mismatch distribution to measure signatures of recent historical demographic events, supported a population expansion across the chicken populations. The results show one matrilineal ancestry of Ugandan chickens from a lineage widespread throughout the world that began in the Indian subcontinent. The lack of phylogeographic signals is consistent with recent expansion events with extensive within-country genetic intermixing among haplotypes. Thus, the findings in this study hold the potential to guide conservation strategies and breeding programs in Uganda, given that higher genetic diversity comes from within the chicken population.

Habitat filtering and dispersal limitation are the main ecological processes affecting species composition variation (β diversity) in forest communities, but their relative importance in subtropical Masson pine (Pinus massoniana) forests remains unclear. Jointly analysis of how phylogenetic and species β diversity varies with habitat factors and geographic distance is critical to understand the roles played by historical and current ecological processes in shaping the regional biodiversity. In this study, 37 Masson pine forest plots in Suichang County, Zhejiang Province were selected to analyze the species and phylogenetic β diversities, and the main ecological mechanisms driving the differences of species composition among communities were explored. Species β diversity index (Bray-Curtis) and phylogenetic β diversity index (the mean phylogenetic dissimilarity, Dnn; the mean nearest taxon distance, Dpw) were calculated, and their correlation with habitat factors including soil and topography, as well as geographical distance were analyzed. The relative importance of habitat factors and geographical distance on species and phylogenetic β diversity was analyzed by variance partitioning. In addition, two life stages (divided by diameter class) and growth form were for the same analyses. The results were as follows: (1) Bray-Curtis index significantly correlated with soil factors, topographic factors and geographical distance. Dnn correlated with geographical distance only. Dpw correlated with soil factors and geographical distance. (2) The explanatory degree of habitat factors to Bray-Curtis and Dpw was higher than that of geographical distance. (3) For species diversity, habitat factors could better explain Bray-Curtis of both life stages than geographical distance. For phylogenetic diversity, geographical distance could better explain Dnn and Dpw of sapling stage, while habitat factors were more likely to explain Dpw of adult stage. To conclude, The results show that habitat filtering is the main ecological mechanism driving species and phylogenetic β diversity of Masson pine forests in this region. Dispersal limitation plays a dominant role in the β diversity of Masson pine forests only at the sapling stage. The most important finding of this research is that the main mechanism drives for species and phylogenetic β diversity in Masson pine forests are different, which highlights the necessity of joint analysis of species and phylogenetic β diversity. This research also suggests that the main ecological mechanism drives β diversity may change as plants shift across different growth stages.

Species diversity of angiosperms (flowering plants) varies greatly among regions. Geographic patterns of variation in species diversity are shaped by the interplay of ecological and evolutionary processes. Here, using a comprehensive data set for regional angiosperm floras across the world, we show geographic patterns of taxonomic (species) diversity, phylogenetic diversity, phylogenetic dispersion, and phylogenetic deviation (i.e., phylogenetic diversity after accounting for taxonomic diversity) across the world. Phylogenetic diversity is strongly and positively correlated with taxonomic diversity; as a result, geographic patterns of taxonomic and phylogenetic diversity across the world are highly similar. Areas with high taxonomic and phylogenetic diversity are located in tropical regions whereas areas with low taxonomic and phylogenetic diversity are located in temperate regions, particularly in Eurasia and North America, and in northern Africa. Similarly, phylogenetic dispersion is, in general, higher in tropical regions and lower in temperate regions. However, the geographic pattern of phylogenetic deviation differs substantially from those of taxonomic and phylogenetic diversity and phylogenetic dispersion. As a result, hotspots and coldspots of angiosperm diversity identified based on taxonomic and phylogenetic diversity and phylogenetic dispersion are incongruent with those identified based on phylogenetic deviations. Each of these metrics may be considered when selecting areas to be protected for their biodiversity.

Interpreting biodiversity patterns and the underlying processes is crucial for evaluating the mechanisms of community assembly, but the view of multifaceted diversity patterns spanning broad spatial extents is less strengthened. We implemented an inventory of 1260 vegetation plots from shrublands across China with standardized methods and analyzed patterns of taxonomic and phylogenetic diversity with differential weighting of common and rare species, as well as phylogenetic co-occurrence structures. Taxonomic and phylogenetic diversity were linearly correlated when common and rare species were weighted equally, but had a logarithmic correlation when species were weighted with their relative abundances. While most shrubland communities were phylogenetically unstructured, the correlation between taxonomic and phylogenetic diversity covaried with phylogenetic relatedness when incorporating relative abundance, but only weakly so in phylogenetically over-dispersed communities. When we correlated patterns of taxonomic and phylogenetic diversity with different weightings for common versus rare species, we found an important role for geographic (e.g., longitude, altitude), climatic (temperature, precipitation) and soil factors. The importance of underlying variables varied between facets of diversity. We found a strong role for altitude in taxonomic, but less so for phylogenetic diversity. Furthermore, the importance of several environmental drivers varied depending on whether diversity metrics were strongly influenced by rare species or put more weight on common and/or dominant species. Overall, our assessment highlights the importance of synthetic analyses of patterns and processes of different facets of biodiversity to capture the full complexity of diversity in conservation studies.

ABSTRACT The emerging infectious agent Elizabethkingia meningoseptica is associated with life-threatening infections in immunocompromised individuals. However, there are limited data on its geographic distribution, phylogenetic evolution, pathogenesis, and transmission. In this study, we comprehensively analyze and compare the genomic features, evolutionary history, emergence date, and transmission networks of global E. meningoseptica. Geographical distribution reveals the presence of the emerging bacteria in Asia, Europe, and North America, three continents with similar latitudes. Phylogenetic analyses show no relationship between the strain’s evolutionary history and its location, origin, or source, despite the presence of genetic diversity. Analysis of the emergence timeline suggests that America is the most likely source of E. meningoseptica with the common ancestor of this pathogen dating back 90 years. Putative transmission networks indicate that E. meningoseptica bacteria can spread within the same hospital and even across borders. Minor variations in resistance genotypes and virulence genes are observed, supporting existing evidence of inherent resistance and pathogenicity in E. meningoseptica. Additionally, minocycline and doxycycline demonstrate potent antimicrobial activity against this pathogen, making them promising candidates for treating E. meningoseptica infections. Our research highlights the potential for severe nosocomial outbreaks caused by E. meningoseptica with horizontal transmission occurring between countries worldwide. To prevent future outbreak infections, increased genomic surveillance of global E. meningoseptica populations is necessary. IMPORTANCE Elizabethkingia meningoseptica is an emerging infectious agent associated with life-threatening infections in immunocompromised individuals. However, there are limited data available on the genomic features of E. meningoseptica. This study aims to characterize the geographical distribution, phylogenetic evolution, pathogenesis, and transmission of this bacterium. A systematic analysis of the E. meningoseptica genome revealed that a common ancestor of this bacterium existed 90 years ago. The evolutionary history showed no significant relationship with the sample source, origin, or region, despite the presence of genetic diversity. Whole genome sequencing data also demonstrated that E. meningoseptica bacteria possess inherent resistance and pathogenicity, enabling them to spread within the same hospital and even across borders. This study highlights the potential for E. meningoseptica to cause severe nosocomial outbreaks and horizontal transmission between countries worldwide. The available evidence is crucial for the development of evidence-based public health policies to prevent global outbreaks caused by emerging pathogens.

The how and why of the spatial variation in biodiversity is one of the fundamental topics in biogeography research, but accurate insights require the incorporation of phylogenetic information. Here, to provide a better understanding of the origin and mechanism of biodiversity in montane ecosystems and thus support conservation planning, we explored the elevational patterns of phylogenetic diversity and structure of seed plants in the Gyirong Valley, the longest valley in China’s central Himalayas. The observed patterns were related to climatic, historical, geographical, and disturbance-related factors, and the relative contributions of these factors in explaining them were assessed. Our results showed that phylogenetic diversity of seed plants in the central Himalayas were described by a strongly hump-shaped pattern, peaking at 2700 m around. The phylogenetic structure of the plants was characterized by overdispersion at lower elevations and clustering at higher elevations, reflecting the cooperation between interspecies competition and environmental filtering in community assembly. Among the examined environmental factors, climatic factors showed the highest explanatory power, suggesting environmental filtering was largely driven by climatic rather than other factors. In summary, our finding indicating that mild climate at lower elevations presumably encourage phylogenetic differentiation by promoting interspecies competition, whereas increasingly harsh climatic condition with elevation may lead to closer phylogenetic relatedness through environmental filtering. Overall, our findings improve our knowledge about the elevational gradient of biodiversity in the Himalayas, and highlight the need for intensified conservation efforts at middle elevations as well as greater scientific concern regarding the impact of climate change on the biodiversity.

Background and aims: Insight for vegetation restoration in karst mountains could come from understanding the methods by which communities are built along a successional chronosequence. We integrated species diversity, phylogenetic structure, and functional trait diversity to investigate the mechanisms governing community assembly along a successional chronosequence in the northern tropical karst mountains, South China. Methods: Five successional sequences, including grassland, shrubland, young forest, middle-aged forest, and primary forest, were selected in the northern tropical karst mountains using the space-for-time substitution method. The relationships between species diversity and environmental variables (elevation, slope degree and rock exposed rate) were investigated using redundancy analysis and variance partitioning methods. Results and discussion: Our results showed that as succession progressed, species and phylogenetic diversity showed an increasing trend, then a decreasing trend, with the maximum value occurring in young forests, which displayed the optimum curves over the successional gradient. In terms of functional diversity, shrubland, and young forest had significantly higher functional richness than grassland and middle-aged forest, and grassland and young forest had significantly higher quadratic entropy coefficients than primary forest. The vegetative community changed in phylogenetic structure from clustering in the early stages of succession to diverging in the late stages.In contrast, the leaf thickness density decreased as succession progressed, suggesting that the young forest vegetation had the highest resource acquisition ability and utilization rate as the successional progressed. Additionally, the chlorophyll content, leaf thickness, and leaf area showed a first increased then decreased trend as successional progressed. Conclusions: Our results suggest that due to harsher soil conditions, the vegetation in early successional stage was dominated by environmental filtering (i.e., limitation of environmental resources), whereas the vegetation in late successional stage was governed by competitive exclusion (i.e., species competition). Our findings can guide plants conservation and ecological restoration in the tropical karst regions. [ABSTRACT FROM AUTHOR]

Understanding how community phylogenetic and functional structures change over succession has gained increasing attention during the last decades, but the lack of long-term time-series data has limited our understanding of the patterns and mechanisms of these changes. This is especially the case for forest communities. Here, we used an exceptionally long-term data over 68 years to analyze the secondary succession dynamics of a subtropical forest in Southeast China. We found that community phylogenetic and functional structures showed opposite temporal trends. The mean pairwise phylogenetic distance between species increased, but the mean nearest taxon distance decreased over succession, indicating both phylogenetically distantly related and sister species co-occurred in late-successional communities. In contrast, both the mean pairwise functional distance and mean nearest functional distance between species decreased over time, and community functional structure switched from overdispersion to clustering. We further distinguished the contributions of species colonization and extinction to community structural changes. We found that the new colonists were generally more distantly related to each other and to the residents than the local extinct species, resulting in increased phylogenetic overdispersion over succession. In contrast, from a functional perspective, we found that species with more similar traits to the resident species had a greater chance to colonize but a lower chance to go locally extinct, which shifted community functional structure toward clustering. Together, our study highlights the critical role of species colonization and extinction in disentangling assembly mechanisms underlying community phylogenetic and functional structures over long-term succession. [ABSTRACT FROM AUTHOR]

Introduction: Phylogenetic relatedness is one of the important factors in the community assembly process. Here, we aimed to understand the large-scale phylogenetic relationship between alien plant species at different stages of the invasion process and how these relationships change in response to the environmental filtering process at multiple spatial scales and different phylogenetic extents. Methods: We identified the alien species in three invasion stages, namely invasive, naturalized, and introduced, in China. The occurrence records of the species were used to quantify two abundance-based phylogenetic metrics [the net relatedness index (NRI) and the nearest taxon index (NTI)] from a highly resolved phylogenetic tree. The metrics were compared between the three categories of alien species. Generalized linear models were used to test the effect of climate on the phylogenetic pattern. All analyses were conducted at four spatial scales and for three major angiosperm families. Results: We observed significantly higher NRI and NTI values at finer spatial scales, indicating the formation of more clustered assemblages of phylogenetically closely related species in response to the environmental filtering process. Positive NTI values for the invasive and naturalized aliens suggested that the presence of a close relative in the community may help the successful naturalization and invasion of the introduced alien species. In the twodimensional phylogenetic space, the invasive species communities significantly differed from the naturalized and introduced species, indicating that established alien species need to be phylogenetically different to become invasive. Positive phylogenetic measures for the invasive aliens across the spatial scales suggested that the presence of invasive aliens could facilitate the establishment of other invasive species. Phylogenetic relatedness was more influenced by temperature than precipitation, especially at a finer spatial scale. With decreased temperature, the invasive species showed a more clustered assemblage, indicating conservatism of their phylogenetic niche. The phylogenetic pattern was different at the family level, although there was a consistent tendency across families to form more clustered assemblages. Discussion: Overall, our study showed that the community assemblage became more clustered with the progression of the invasion process. The phylogenetic measures varied at spatial and taxonomic scales, thereby highlighting the importance of assessing phylogenetic patterns at different gradients of the community assembly process. [ABSTRACT FROM AUTHOR]

Introduced plants can have long-lasting and irreversible effects on the communities and ecosystems they invade. A critical step towards understanding the legacy of plant introductions is the characterisation of changes in the invaded plant communities and how these changes are related to biogeochemical modifications. Here, we addressed this issue by comparing the impacts of two large invasive herbs, Gunnera tinctoria and Impatiens glandulifera, on the compositional, functional, and phylogenetic structure of the standing vegetation (above-ground communities) and the soil seed bank (below-ground communities). The introduction of both invasive species was associated with a significant decrease in above-ground species richness, with subsequent changes in the functional diversity and phylogenetic dispersion of the vegetation. Yet, these invaders differed in their long-term impacts and the reversibility of any modifications they caused. While G. tinctoria invasions resulted in phylogenetically clustered communities (both above and below-ground) that were clearly distinct from uninvaded ones, seed bank communities invaded by I. glandulifera were indistinguishable from uninvaded ones, despite major compositional changes above-ground. Further, we found alterations in nutrient cycling associated with G. tinctoria invasions that could facilitate its local persistence and exacerbate any negative effects on native diversity. Our findings suggest a high susceptibility of pre-invasion above-ground communities to colonisation by distantly related herbs. However, the seed banks showed a degree of resilience against both invaders, with no major differences in species richness. Ultimately, differences in the impacts of these large invasive herbs suggest that dominance in the vegetation and a large stature are poor predictors of long-term plant community changes, including regeneration potential from seed, which are associated with plant introductions. [ABSTRACT FROM AUTHOR]

Analysis of the phylogenetic structure of a community based on the phylogenetic relationships among species in the community can reflect the ecological process of community composition and determine the mechanism of plant community construction. In this study, we analyzed the characteristics of the phylogenetic structure and diversity of plant communities in the Gurbantunggut Desert and their interactions with soil factors and explored the mechanisms of species maintenance in the communities. The results showed that the ecological traits of plants were conserved, habitat filtering was the primary process affecting plant communities, and the diversity of phylogeny was ranked as fixed dunes > semifixed dunes > mobile dunes. At different slope positions within the dune, there is greater phylogenetic diversity at the bottom and lower slope, and habitat filtering dominates community construction, with the dominant role of habitat filtering in the community diminishing as the slope position rises. The phylogenetic diversity of plant communities of different life types is ranked as short-lived plants > small trees and shrubs > annual and perennial herbs. On the bottom and lower slopes, short-lived plants and annual and perennial herbaceous communities are mainly influenced by habitat filtering. Habitat filterability decreased with increasing slope position. On the upper slopes and at the top, competitive exclusion effects between small trees and shrubs dominated. Our analysis shows that soil water content and organic carbon affect phylogenetic diversity mainly by influencing community species richness and that the interaction between soil water content, grain size and plant diversity leads to clustering of species with similar soil preferences, which in turn affects the phylogenetic structure of the community. In addition, the change from habitat filtering to intraspecific competition in plant community construction from the bottom to the top of the slope is mainly influenced by short-lived plant communities, and this type of plant needs to be given priority consideration in the conservation and restoration of desert plant communities.

IntroductionPhylogenetic relatedness is one of the important factors in the community assembly process. Here, we aimed to understand the large-scale phylogenetic relationship between alien plant species at different stages of the invasion process and how these relationships change in response to the environmental filtering process at multiple spatial scales and different phylogenetic extents.MethodsWe identified the alien species in three invasion stages, namely invasive, naturalized, and introduced, in China. The occurrence records of the species were used to quantify two abundance-based phylogenetic metrics [the net relatedness index (NRI) and the nearest taxon index (NTI)] from a highly resolved phylogenetic tree. The metrics were compared between the three categories of alien species. Generalized linear models were used to test the effect of climate on the phylogenetic pattern. All analyses were conducted at four spatial scales and for three major angiosperm families.ResultsWe observed significantly higher NRI and NTI values at finer spatial scales, indicating the formation of more clustered assemblages of phylogenetically closely related species in response to the environmental filtering process. Positive NTI values for the invasive and naturalized aliens suggested that the presence of a close relative in the community may help the successful naturalization and invasion of the introduced alien species. In the two-dimensional phylogenetic space, the invasive species communities significantly differed from the naturalized and introduced species, indicating that established alien species need to be phylogenetically different to become invasive. Positive phylogenetic measures for the invasive aliens across the spatial scales suggested that the presence of invasive aliens could facilitate the establishment of other invasive species. Phylogenetic relatedness was more influenced by temperature than precipitation, especially at a finer spatial scale. With decreased temperature, the invasive species showed a more clustered assemblage, indicating conservatism of their phylogenetic niche. The phylogenetic pattern was different at the family level, although there was a consistent tendency across families to form more clustered assemblages.DiscussionOverall, our study showed that the community assemblage became more clustered with the progression of the invasion process. The phylogenetic measures varied at spatial and taxonomic scales, thereby highlighting the importance of assessing phylogenetic patterns at different gradients of the community assembly process.

Aim: We used an eco‐phylogenetic approach to investigate the diversity and assembly patterns of tropical dry forests (TDFs) in Central India. We aimed at informing conservation and restoration practices in these anthropogenically disturbed forests by identifying potential habitats of conservation significance and elements of regional biodiversity most vulnerable to human impact and climate change. Location: Tropical dry forests of Madhya Pradesh, Central India. Methods: We analysed the species richness, stem density, basal area and phylogenetic structure (standardized effect size of MNTD, MPD, PD and community evolutionary distinctiveness cED) of 117 tree species assemblages distributed across a ~230 to ~940 m elevational gradient. We examined how these community measures and taxonomic (Sørensen) and phylogenetic (UniFrac) beta diversity varied with elevation, precipitation, temperature and climatic stress. Results: Species richness, phylogenetic diversity, stem density and basal area were positively correlated with elevation, with high‐elevation plots exhibiting cooler temperatures, higher precipitation and lower stress. High‐elevation assemblages also trended towards greater phylogenetic dispersion, which diminished at lower elevations and in drier, more stressful plots. Phylogenetic turnover was observed across the elevation gradient, and species evolutionary distinctiveness increased at lower elevations and under harsher abiotic conditions. Main Conclusions: Harsher abiotic conditions at low elevations may act as a selective filter on plant lineages, leading to phylogenetically clustered low‐diversity assemblages. These assemblages contained more evolutionarily distinct species that may contribute disproportionately to biodiversity. Conversely, milder abiotic conditions at high elevations may serve as refuges for drought‐sensitive species, resulting in more diverse assemblages. Conservation practices that prioritize both high‐ and low‐elevation habitats could promote the persistence of evolutionarily distinct species and areas of high biodiversity within the Central Indian landscape. Establishing connectivity between these habitats may provide a range of climatic conditions for species to retreat to or persist within as climates change. [ABSTRACT FROM AUTHOR]

Habitat filtering and dispersal limitation are the main ecological processes affecting species composition variation (β diversity) in forest communities, but their relative importance in subtropical Masson pine (Pinus massoniana) forests remains unclear. Jointly analysis of how phylogenetic and species β diversity varies with habitat factors and geographic distance is critical to understand the roles played by historical and current ecological processes in shaping the regional biodiversity. In this study, 37 Masson pine forest plots in Suichang County, Zhejiang Province were selected to analyze the species and phylogenetic β diversities, and the main ecological mechanisms driving the differences of species composition among communities were explored. Species β diversity index (Bray-Curtis) and phylogenetic β diversity index (the mean phylogenetic dissimilarity, Dnn; the mean nearest taxon distance, Dpw) were calculated, and their correlation with habitat factors including soil and topography, as well as geographical distance were analyzed. The relative importance of habitat factors and geographical distance on species and phylogenetic β diversity was analyzed by variance partitioning. In addition, two life stages (divided by diameter class) and growth form were for the same analyses. The results were as follows: (1) Bray-Curtis index significantly correlated with soil factors, topographic factors and geographical distance. Dnn correlated with geographical distance only. Dpw correlated with soil factors and geographical distance. (2) The explanatory degree of habitat factors to Bray-Curtis and Dpw was higher than that of geographical distance. (3) For species diversity, habitat factors could better explain Bray-Curtis of both life stages than geographical distance. For phylogenetic diversity, geographical distance could better explain Dnn and Dpw of seedling stage, while habitat factors were more likely to explain Dpw of adult stage. To conclude, The results show that habitat filtering is the main ecological mechanism driving species and phylogenetic β diversity of Masson pine forests in this region. Dispersal limitation plays a dominant role in the β diversity of Masson pine forests only at the sapling stage. The most important finding of this research is that the main mechanism drives species and phylogenetic β diversity in Masson pine forests is different, which highlights the necessity of joint analysis of species and phylogenetic β diversity. This research also suggests that the main ecological mechanism drives β diversity may change as plants shift across different growth stages. [ABSTRACT FROM AUTHOR]

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Elizabethkingia anophelis is an emerging species and has increasingly been reported to cause life-threatening infections and even outbreaks in humans. Nevertheless, there is little data regarding the E. anophelis geographical distribution, phylogenetic structure, and transmission across the globe, especially in Asia. We utilize whole-genome sequencing (WGS) data to define a global population framework, phylogenetic structure, geographical distribution, and transmission evaluation of E. anophelis pathogens. The geographical distribution diagram revealed the emerging pathogenic bacteria already distributed in various countries worldwide, especially in the USA and China. Strikingly, phylogenetic analysis showed a part of our China original E. anophelis shared the same ancestor with the USA outbreak strain, which implies the possibility of localized outbreaks and global spread. These closer related strains also contained ICEEaI, which might insert into a disrupted DNA repair mutY gene and made the strain more liable to mutation and outbreak infection. BEAST analysis showed that the most recent common ancestor for ICEEaI E. anophelis was dated twelve years ago, and China might be the most likely recent source of this bacteria. Our study sheds light on the potential possibility of E. anophelis causing the large-scale outbreak and rapid global dissemination. Continued genomic surveillance of the dynamics of E. anophelis populations will generate further knowledge for optimizing future prevent global outbreak infections.

Community phylogenetic structure and diversity analysis are useful complements to species-centric approaches in biodiversity studies by providing new insights into the processes that drive community assembly. In this study, we aimed to understand the differences in the relative importance of abiotic filtering, biotic interactions, and dispersal limitation on community assembly of trees at different vegetation growth stages. We also examined the influence of geographical distance, elevation, terrain, and soil. Thus, we examined the phylogenetic structures and β-diversities of saplings and adults along different abiotic gradients. The results of the net relatedness index (NRI) showed that, instead of being random, the phylogenetic structure of saplings tended to be convergent, whereas that of adults tended to be divergent. This result implies that the relative forces of abiotic filtering and biotic interactions change throughout vegetation growth. The results of generalized dissimilarity modelling (GDM) showed that dispersal limitation (geographical distance) and abiotic filtering influenced the community assembly of both adults and saplings. This result confirmed our hypothesis that both deterministic and stochastic processes were prevalent. The explanatory rates of geographic distance and environmental factor distance to phylogenetic β-diversity were quite different between adults and saplings, which meant that the relative force of dispersal limitation and abiotic filtering had also changed. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Continuous systematic monitoring is necessary to measure the success or failure of mineland rehabilitation. Here, we aimed to outline how measures of phylogenetic diversity and phylogenetic community structure complement existing monitoring frameworks along a waste pile rehabilitation chronosequence in Carajás National Forest, Brazil, including primary rainforest as the desired outcome. We pruned the megatree R20160415.new to tree species found in this study and computed the phylogenetic diversity (PD), mean pairwise distance (MPD) among taxa and individuals and their standard effect sizes (ses.PD and ses.MPD) via the 'phylogeny pool' null model. PD and MPD increased with rehabilitation progress. Dominance of Fabales species caused phylogenetic clustering during early rehabilitation stages. This clustering disappeared in older stands and switched to phylogenetic overdispersion at reference sites, indicating that mechanisms impeding the recruitment of species from certain phylogenetic lineages during initial stages, such as environmental filtering, tend to decrease with rehabilitation advancement. Furthermore, this pattern indicates the recovery of coexistence-stabilizing interactions with rehabilitation time, even if a constrained number of species was used to launch rehabilitation. Positive associations between all phylogenetic variables and previously determined measures of environmental quality indicate the importance of community assembly processes and niche diversification for ecosystem performance in rehabilitating minelands.

Understanding community assembly process could enhance forest conservation and restoration, while which dominant ecological process drives the community assembly during forest succession is still controversial. In this study, the phylogeny-based and functional trait-based indicators were used to investigate the community assembly processes during forest succession in southern China. 30 dominant species and 33 functional trait indicators related to plant competition, reproduction, and defense strategies, 7 environmental factors related to light availability and soil nutrients, and species richness were selected to explore the dominant ecological processes during succession via Monte Carlo method, structural equation model, multiple linear regression, and one-way ANOVA analysis. Results showed that both the community phylogenetic and functional trait structures changed during succession. Phylogenetic structure clustering and functional trait clustering were evident in early succession. In middle succession, the phylogenetic structure and functional trait structure were randomly dispersed. In middle and later succession, the phylogenetic structure clustering, functional trait clustering, and functional trait evenly dispersed were found. The environmental factors, especially the soil P content, and species richness were found to have significant effects on the community assembly processes during succession. Dominant species in early succession always occupied acquisitive strategies and had high light-use ability and low investment in defense, but dominant species in later succession showed more conservative strategies and exhibited diverse defense strategy, reproductive strategy, and light and nutrient resource-use strategy, apparently in order to adapt changing and more complex environments. The results demonstrate that the relative importance of ecological processes changed during succession. Environmental filtering mainly dominated in early succession, and its strength gradually decreased as succession progressed. Both environmental filtering and competitive exclusion had important effects on community assembly in later succession. The assessment of the relative importance of ecological processes during succession could be biased if only based on one plant functional strategy.

Understanding the spatial patterns and the maintenance of biodiversity is a central target in ecology and biogeography, which provide important insights into community assembly processes. Mountain ecosystems provide informative systems for examining how biodiversity is distributed and identifying the mechanisms underlying those patterns. However, most of the existed studies only focused on plants, birds, and microbes, while little attention has been paid on amphibians, especially tadpoles. In the present study, we explored the elevational patterns of multiple facets of tadpole diversity and the community assembly mechanisms in temperate montane streams of Mount Emei, China. The taxonomic, functional, and phylogenetic diversity of tadpole assemblages in montane streams were quantified. Their elevational patterns were investigated using first and second-order polynomial regression analyses. The microhabitat determinants of these patterns were assessed by ordinary least squares models and hierarchical partitioning analyses. The phylogenetic tree of tadpoles and the Eucliden distance of traits between tadpoles were constructed. They were subsequently used to calculate the standardized effect size of mean pairwise phylogenetic and functional distances, and to speculate the tadpole assembly rules. Our results indicated that the Faith’s PD and the standardized effect size of Faith’s PD had hump-shaped responses to elevation, while the relationships between elevation and observed taxonomic diversity, observed functional diversity, and the standardized effect size of functional diversity were not significant. Interestingly, these patterns were determined by microhabitat variables, such as water conductivity, river width, water depth, and substrate type. Mean pairwise phylogenetic distance also showed hump-shaped correlations with the elevational gradient. Tadpole functional and phylogenetic structures were more clustered in low and high elevational streams, suggesting that environmental filtering was the main driver. At mid-elevations, functional and phylogenetic structures were overdispersal, indicating that limiting similarity plays a dominant role in shaping the tadpole assemblages.

East Yunnan‐Kweichow Plateau is rich in biodiversity in China. Complex geographical and climatic conditions and rich bird resources made this area an ideal system for studying the spatial distribution mechanism and influencing factors of birds, which were still unknown. Bird community data from 37 sites in this region were collected, including 505 bird species and 164 species of resident passerine bird, were extracted for analysis. The taxonomic diversity, phylogenetic diversity, functional diversity (FD), and community structure index were calculated. Ordinary least square (OLS), spatial autoregressive models (SAR), and structural equation model (SEM) were used to explore the relationship between bird diversity index and environmental factors which were used to describe the habitat conditions of birds. Results indicated that species richness (SR), phylogenetic diversity (PD), and FD have similar distribution patterns and are mainly affected by vascular plant species richness, habitat area, and vertical altitude difference. The phylogenetic and functional structure of bird community changed in both longitude and latitude direction, and the phylogenetic structure of community was dispersed in the west and clustered in the east, significantly related to habitat area, and vertical altitude difference, the functional structure was dispersed in all sites, significantly related to average annual precipitation. The community in the west and south of the East Yunnan‐Kweichow Plateau is mainly driven by interspecific competitive, while the process in the east and north is mainly driven by environmental filtration. Distribution pattern of bird diversity was caused by the comprehensive action of various habitat factors which were mainly related to food availability and habitat heterogeneity. For maintaining the living space of birds, the protection of urban parks, wetland parks, campuses, and other urban green spaces is as important as national and provincial nature reserves. Revealing the construction mechanism and main influencing factors of bird communities in different areas is conducive to targeted protection work. [ABSTRACT FROM AUTHOR]

Aim: Most studies focusing on terrestrial ecosystems have shown that non‐native species are more likely to invade phylogenetically clustered communities, that the introduction of non‐native species increases phylogenetic clustering in the recipient communities, and that the latter is more conspicuous for recipient communities at a larger spatial scale. However, whether these patterns hold for aquatic ecosystems is rarely tested. Here, we investigate the phylogenetic structure of native and non‐native freshwater fish assemblages at a continental spatial extent. Location: The continental United States and Canada. Time period: Current. Methods: We collated native and naturalized non‐native species lists of freshwater fishes for each watershed at local and regional spatial scales. Two phylogenetic metrics (MPDses and MNNDses) representing different evolutionary depths were used to quantify the phylogenetic dispersion of each watershed fish assemblage and were related to temperature and precipitation using correlation and regression analyses. Values of the metrics were compared between the two spatial scales. Results: Our study found that (1) phylogenetically more diverse fish communities tended to be invaded by fewer non‐native fish species, and that non‐native species more frequently invaded communities with lower phylogenetic dispersion (i.e. higher phylogenetic clustering), (2) introduction of non‐native fishes reduced phylogenetic clustering in some watershed but increased clustering in others, (3) introduction of non‐native species caused phylogenetic dispersion to increase in watersheds with low phylogenetic diversity and to decrease in watersheds with high phylogenetic diversity and (4) phylogenetic clustering for fish assemblages at the larger spatial scale was smaller than that at the smaller spatial scale. Main conclusions: Support for Darwin's naturalization and preadaptation hypotheses in freshwater fish assemblages depends on the phylogenetic diversity of assemblages within the invaded watersheds. Our results are contrary to previous studies that found that the introduction of non‐native species increases phylogenetic clustering in the recipient communities more strongly at a larger spatial scale. [ABSTRACT FROM AUTHOR]

Societal Impact Statement: The plants sold in nurseries directly influence urban landscapes by providing habitat that supports humans and other organisms and indirectly influence the natural landscape by acting as a major source of invasive species. We analyzed the ornamental plants sold in US nurseries from 1719 to 1946 and found broad patterns of increasing diversity occurring in step with an increase in species relatedness, a switch from native to alien species, and a decrease in regional distinctness. Patterns like these, which have been observed recently in urban areas, thus have a basis in cultivation/horticultural history. Summary: Cultivated plants are foundational species in urban areas, where they simultaneously provide essential ecosystem services while posing a risk of invasion into natural communities. We sought to characterize the spatial and temporal patterns of taxonomic and phylogenetic diversity of cultivated plants using historical data to better understand the origins of the patterns of diversity observed in present‐day human‐dominated landscapes.Using records of 5098 ornamental vascular plant species available in 319 US nursery catalogs published from 1719 to 1946, we quantified the taxonomic and phylogenetic α‐diversity, phylogenetic structure, and β‐diversity of the historical US nursery flora in cultural regions, biomes, latitudinal bands, and longitudinal zones.We showed a peaked increase in taxonomic and phylogenetic diversity of the US nursery flora over time, concurrent with the proliferation of nurseries and the addition of new species to nursery offerings. However, standardized phylogenetic diversity showed a convex pattern, with a trough during a time of peak growth and connectivity in the nursery industry, and diversity actually decreased at the end of the time series. We also showed a pattern of increasing homogenization of regional nursery floras, as well as a shift from offering predominately native to predominately alien species.Echos of the history of the US nursery industry can be found today in patterns with great ecological relevance. Previous reports of high alien plant diversity in urban areas, phylogenetic clustering and overdispersion among naturalized alien plants, and homogenization of urban plant communities are all consistent with the historical availability of these plants in the nursery flora. [ABSTRACT FROM AUTHOR]

The scientific work of Alexander von Humboldt was influenced by his interaction with the diversity and natural wealth of the Neotropics. He proposed that climate determines plant diversity along elevational gradients based on his observations. Here, we evaluated the most prominent climate-based hypotheses in explaining plant diversity along an elevational gradient that Humboldt himself visited during his journey across Mexico. Specifically, we examined how climatic variables and forest-use intensity affected species richness and phylogenetic structure of major angiosperm life forms (trees, shrubs, epiphytes, herbs and lianas) along the Cofre de Perote mountain, Veracruz, Mexico. We analysed species richness and phylogenetic structure of angiosperms at eight sites between 30 to 3500 m a.s.l. We estimated the phylogenetic structure using a mega-phylogeny of angiosperms and the abundance-weighted net relatedness index. We considered multiple environmental factors' direct and indirect effects by applying a piecewise structural equation modelling approach. Each life form responds differently to the environmental variables included in our model; however, it is observed that temperature is the main predictor of the taxonomic and phylogenetic diversity of the angiosperms studied, both when the different life forms are grouped and separated. Potential evapotranspiration and precipitation are variables that also influence some life forms' diversity, especially taxonomic diversity. The forest-use intensity negatively affected only the taxonomic diversity of trees. These results highlight the influence of studying the different life forms of angiosperms in diversity gradient models and show the great influence that temperature has in conjunction with other environmental variables to promote the taxonomic and phylogenetic diversity of plant communities. Given the current global environmental crisis, an integrative biogeographically oriented vision based on Humboldt's method is necessary. Honouring the work of Humboldt and continuing his legacy demands more research to understand the causes behind elevational diversity gradients. [ABSTRACT FROM AUTHOR]

Aim: This study aimed to investigate the distribution patterns of plant diversity in Kenya, how climatic fluctuations and orogeny shaped them, and the formation of its β‐diversity. Location: Kenya, East Africa. Taxon: Angiosperms. Methods: We quantified patterns of turnover and nestedness components of phylogenetic β‐diversity for angiosperm species among neighbouring sites using a well‐resolved phylogenetic tree and extensive distribution records from public databases and other published sources. We applied clustering methods to delineate biota based on pairwise similarities among multiple sites and used a random assembly null model to assess the effects of species abundance distribution on phylogenetic β‐diversity. Results: The phylogenetic turnover of the Kenyan flora, intersecting with the biodiversity hotspots Eastern Afromontane, Coastal Forests of Eastern Africa, and Horn of Africa, shows a non‐monotonic pattern along a latitudinal gradient that is strongly structured into volcanic and coastal areas. The other areas are mainly dominated by phylogenetic nestedness, even in the eastern part of the equatorial region parallel to the volcanic area. Phylogenetic diversity and phylogenetic structure analyses explain the mechanism of the observed phylogenetic turnover and nestedness patterns. We identified five phytogeographical regions in Kenya: the Mandera, Turkana, Volcanic, Pan Coastal and West Highland Regions. Conclusions: Variations in turnover gradient and coexistence are highly dependent on the regional biogeographical history resulting from climatic fluctuations and long‐lasting orogeny, which jointly shaped the biodiversity patterns of the Kenyan flora. The nestedness component dominated climatically unstable regions and is presumed to have been caused by heavy local species extinction and recolonization from the Volcanic Region. The high turnover component in climatically stable regions may have preserved old lineages and the prevalence of endemic species within narrow ranges. [ABSTRACT FROM AUTHOR]

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

Large-scale patterns of biodiversity and the underlying mechanisms that regulate these patterns are central topics in biogeography and macroecology. The Qinghai-Tibet Plateau serves as a natural laboratory for studying these issues. However, most previous studies have focused on the entire Qinghai-Tibet Plateau, leaving independent physical geographic subunits in the region less well understood. We studied the current plant diversity of the Kunlun Mountains, an independent physical geographic subunit located in northwestern China on the northern edge of the Qinghai-Tibet Plateau. We integrated measures of species distribution, geological history, and phylogeography, and analyzed the taxonomic richness, phylogenetic diversity, and community phylogenetic structure of the current plant diversity in the area. The distribution patterns of 1911 seed plants showed that species were distributed mainly in the eastern regions of the Kunlun Mountains. The taxonomic richness, phylogenetic diversity, and genera richness showed that the eastern regions of the Kunlun Mountains should be the priority area of biodiversity conservation, particularly the southeastern regions. The proportion of Chinese endemic species inhabiting the Kunlun Mountains and their floristic similarity may indicate that the current patterns of species diversity were favored via species colonization. The Hengduan Mountains, a biodiversity hotspot, is likely the largest source of species colonization of the Kunlun Mountains after the Quaternary. The net relatedness index indicated that 20 of the 28 communities examined were phylogenetically dispersed, while the remaining communities were phylogenetically clustered. The nearest taxon index indicated that 27 of the 28 communities were phylogenetically clustered. These results suggest that species colonization and habitat filtering may have contributed to the current plant diversity of the Kunlun Mountains via ecological and evolutionary processes, and habitat filtering may play an important role in this ecological process.

Contemporary biodiversity patterns are shaped by not only modern climate but also factors such as past climate fluctuations. Investigating the relative degree of paleoclimate legacy could help us understand the formation of current biodiversity patterns. However, an assessment of this issue in China is lacking. Here, we investigated the phylogenetic structure and functional diversity patterns of Chinese terrestrial vertebrates. We found that Southern China harbored higher functional richness, while Northern and Western China were more phylogenetically clustered with higher functional divergence and evenness, indicating environmental filtering effects. Moreover, we found that drastic Last Glacial Maximum climate changes were positively related to phylogenetic clustering, lower functional richness, and higher functional divergence and evenness, although this effect varied among different taxonomic groups. We further found that mammal communities experiencing more drastic Last Glacial Maximum temperature changes were characterized by “faster” life-history trait values. Our findings provide new evidence of the paleoclimate change legacies influencing contemporary biodiversity patterns that will help guide national-level conservation plans.