Phylogenetic Community Structure Research Articles

Response of Plant Phylogenetic Structure to Plateau Pika (Ochotona curzoniae) Disturbance on Alpine Meadow of Qinghai‐Tibetan Plateau

ABSTRACTPlant community construction is influenced by bottom‐up processes, such as environmental factors, and top‐down processes, such as herbivore disturbances. With climate change and overgrazing, the stability of plant community structure and function decreases, and more land at risk of degradation. However, the response of the plant community to interference from native herbivores under similar environmental conditions remains unclear. Plateau pika (Ochotona curzoniae) is an important small rodent inhabiting the alpine meadow of the Qinghai‐Tibetan Plateau, and its disturbance may accelerate the degradation of grassland ecosystems when its population experiences a burst. In this study, we investigated the plant communities, collected and analyzed the soil samples, to explore the effects of plateau pikas' disturbance intensity on species composition and phylogenetic structure of plant communities on the alpine meadow. We utilized the generalized additive model and structural equation model to explain and predict the response of plant phylogenetic structure and species competition to the disturbance of plateau pikas. Our results indicated that plateau pika disturbance altered the dominance of plant groups, increased species substitution, and facilitated coexistence among different species, and it affected deterministic processes, reduced interspecific competition intensity, and promoted the dispersion of phylogenetic structures. These findings suggested that plateau pika, as a small native herbivore, plays a significant role in fostering multi‐species plant communities. Therefore, it is essential to manage plateau pika disturbance intensity to maintain the stability of alpine meadow plant communities, as well as to influence the long‐term succession of grassland ecosystems. This study provides some new evidence for exploring the effects of native small herbivores on the changes in grassland plant communities.

Elevational patterns of bird alpha and beta diversity in Haba Snow Mountain, Southwestern China: Implication for conservation

Understanding environmental patterns of species diversity is essential for nature reserve planning and biodiversity conservation. In this study, we explored the birds’ alpha and beta diversity along the elevational gradients in Haba Snow Mountain Nature Reserve (hereafter, HBSM), a global biodiversity hotspot, and studied which environmental factor is the main driver in explaining alpha and beta diversity patterns. Our results indicated that taxonomic, functional, and phylogenetic alpha diversity consistently exhibited hump-shaped patterns with similar peaks. After controlling for species richness, both functional and phylogenetic alpha diversity increased with elevation, and the peaks at 3400–3700 m. Mean pairwise functional distance remained nearly constant along the elevation band, whereas mean pairwise phylogenetic distance shown hump-shaped pattern, and the predicted MPD peaked at the fifth band (3100–3400 m a.s.l). The functional and phylogenetic structure of bird communities in HBSM were more clustered along the elevation gradients, suggesting environmental filtering likely drove the assembly processes. Additionally, primary productivity (NDVI and/or habitat heterogeneity) and/or precipitation were robust predictors of variation in most diversity metrics. For multiple-site beta diversity, we observed that high turnover component in taxonomic, functional, and phylogenetic dimensions, indicating distinct bird assemblages across various elevational bands. In pairwise beta diversity, the spatial turnover of taxonomic and phylogenetic aspects was higher than nestedness, revealing species replacement occurs relatively frequently between evolutionarily related species with similar niche and functional traits. Overall, our findings highlight the importance of considering both different dimensions and multifaceted diversity when assessing elevational patterns of bird diversity. This study also provides valuable insights into the structuring mechanisms of bird communities and informs conservation planning along elevational gradients in HBSM, and offers a comprehensive case on species richness along elevational gradients.

Changes in the Phylogenetic Structure of Alpine Grassland Plant Communities on the Qinghai-Tibetan Plateau with Long-Term Nitrogen Deposition.

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.

The species diversity and phylogenetic structure patterns of desert plant communities in the Turpan-Hami region, Xinjiang

Desert plant communities play a crucial role in enhancing desert ecosystem productivity and stability but are highly susceptible to environmental changes owing to their limited resilience and resistance to disturbances, making it essential to understand the factors influencing their diversity patterns and community structure, particularly under the threat of climate change and intensifying droughts. This study focused on the Turpan-Hami desert region, a typical desert ecosystem in which diversity patterns and community structures remain unclear. We established 101 sampling sites ranging from elevations of -134 to 2056m and recorded community information, including species composition, height, coverage, and density, using the sample plot method. The diversity patterns were analyzed using regression analysis, and the phylogenetic structure was assessed. Additionally, Canonical Correspondence Analysis, Mantel tests, and General Linear Models were used to identify the key factors affecting community structure. Our results demonstrated that the species richness and phylogenetic diversity of plant communities exhibited a monotonic increase with elevation, and the phylogenetic structure exhibited low clustering and high dispersion along the elevational gradient. The annual mean temperature emerged as the most significant factor influencing diversity patterns, with soil nutrients, such as total potassium and available phosphorus, also affecting the spatial distribution of diversity. Notably, no significant correlations were found between community phylogenetic structure and abiotic factors, highlighting the complex interactions that drive diversity in the Turpan-Hami region. This study offers valuable insights into the mechanisms shaping desert plant community diversity and is essential for biodiversity conservation efforts in fragile desert ecosystems amid climate change.

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

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

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

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

Time since fire as a driver of taxonomic and phylogenetic patterns of grassland plant communities

Fire plays a key role in grasslands, determining the distribution and evolution of species and boundaries with neighboring ecosystems. Evidence of community-wide responses to fire is largely based on taxonomic and functional descriptors, while the phylogenetic dimension is overlooked. Here we evaluated how the taxonomic and phylogenetic structure of grassland plant communities responded to a time since fire (TSF) gradient. We sampled 12 communities in Southern Brazil under varying TSF and calculated taxonomic species richness (S) and dominance (D), phylogenetic diversity (PD), and mean phylogenetic distances (MPD). We used Structural Equation Models to test the relationships between the environmental gradient and community descriptors. Communities with longer TSF presented higher PD and MPD but lower species richness and increased taxonomic dominance. These sites were dominated by monocots, specifically C4 grasses, but also presented exclusive clades, whereas recently-burned sites presented lower taxonomic dominance and more species distributed in a wider variety of clades. Our results indicate that these scenarios are interchangeable and dependent on fire management. Fire adaptation was not constrained by phylogenetic relatedness, contrasting with previous findings for tropical savannahs and indicating that temperate and tropical non-forest ecosystems from South America respond differently to fire, possibly due to different evolutionary histories.

Two decades of increasing functional and phylogenetic richness in a mountaintop flora in central Norway

AbstractQuestionsAnalysing how multiple facets of biodiversity vary across space and time can help to predict the vulnerability of mountaintop floras to future environmental changes. Here we addressed the following questions: (a) Are elevational patterns of mountaintop plant diversity consistent across taxonomy, function and phylogeny? (b) How have the taxonomic, functional and phylogenetic dimensions of mountaintop plant communities changed over the past two decades? (c) Is the magnitude of these temporal trends dependent on elevation?LocationDovrefjell, central Norway.MethodsThe floristic composition of four mountaintops, spread across an elevational gradient from the tree line to the uppermost margins of vascular plant life, was surveyed every 7 years between 2001 and 2022. Six metrics of taxonomic, functional and phylogenetic richness and differentiation were calculated for each mountaintop and survey. Using these data, we assessed how richness and differentiation metrics varied over space (across the elevational gradient) and over time (between surveys).ResultsAll diversity metrics decreased towards higher elevations, except phylogenetic differentiation which increased significantly by 7% per 100 m elevational gain. Taxonomic richness remained virtually stable between 2001 and 2022, whereas phylogenetic richness increased by 7.5% per decade. Functional richness also increased, but mainly on the lowest mountaintop, by 17% per decade. No significant temporal trends in taxonomic, functional and phylogenetic differentiation were detected.ConclusionsOur findings underpin rearrangements in the functional and phylogenetic structure of mountain plant communities over the past two decades that cannot be predicted from trends in taxonomic richness alone. This highlights the necessity to look beyond species richness and consider multiple facets of biodiversity when studying environmental change impacts on mountain biodiversity and ecosystem functioning.

Assessing how metal reef restoration structures shape the functional and taxonomic profile of coral-associated bacterial communities

Significant threats to the long-term persistence of coral reefs have accelerated the adoption of coral propagation and out-planting approaches. However, how materials commonly used for propagation structures could potentially affect coral-associated bacterial communities remains untested. Here, we examined the impact of metal propagation structures on coral-associated bacterial communities. Fragments of the coral species Acropora millepora were grown on aluminium, sand/epoxy-coated steel (Reef Stars), and uncoated steel (rebar) structures. After 6 months, the functional and taxonomic profiles of coral-associated bacterial communities of propagated corals and reef colonies were characterised using amplicon (16S rRNA gene) and shotgun metagenomic sequencing. No differences in the phylogenetic structure or functional profile of coral-associated bacterial communities were observed between propagated corals and reef colonies. However, specific genes and pathways (e.g., lipid, nucleotide, and carbohydrate metabolism) were overrepresented in corals grown on different materials, and different taxa were indicative of the materials. These findings indicate that coral propagation on different materials may lead to differences in the individual bacterial taxa and functional potential of coral-associated bacterial communities, but how these contribute to changed holobiont fitness presents a key question to be addressed.

Environment and management jointly shape the spatial patterns of plant species diversity of moist grasslands in the mountains of Northeastern Yunnan

Grasslands account for about a quarter of the Earth’s land area and are one of the major terrestrial ecosystems, with significant ecological and economic value. The influence of environmental factors and management types on grassland biodiversity has garnered considerable attention. This study investigated how patterns of species richness are influenced by geographical distance, environmental gradients, and management type in the grasslands of northeastern Yunnan, China. We used structural equation modeling to disentangle the impacts of environment and management on phylogenetic community structure, and partial Mantel tests to estimate the roles of dispersal limitation and environmental filtering on taxonomic and phylogenetic beta diversity of three types of grasslands. Our results show that taxonomic alpha diversity increased in grazed grasslands and decreased in mowed grasslands, compared with protected grasslands. However, the phylogenetic structure of both grazed and mowed grassland communities was clustered, whereas that of protected communities was random. Moreover, both grazing and mowing significantly reduced the taxonomic and phylogenetic beta diversity of grasslands, with the lowest values observed in mowed grasslands. Both taxonomic and phylogenetic beta diversity were dominated by species turnover under different management types. The taxonomic and phylogenetic beta diversities of protected and grazed grasslands were simultaneously affected by environmental filtering and dispersal limitation, with the later playing a stronger role. In addition, mowing and related management measures had a stronger filtering effect on grassland community structure, as reflected by changes in community composition.

Reproducible responses of geochemical and microbial successional patterns in the subsurface to carbon source amendment

Carbon amendments designed to remediate environmental contamination lead to substantial perturbations when injected into the subsurface. For the remediation of uranium contamination, carbon amendments promote reducing conditions to allow microorganisms to reduce uranium to an insoluble, less mobile state. However, the reproducibility of these amendments and underlying microbial community assembly mechanisms have rarely been investigated in the field. In this study, two injections of emulsified vegetable oil were performed in 2009 and 2017 to immobilize uranium in the groundwater at Oak Ridge, TN, USA. Our objectives were to determine whether and how the injections resulted in similar abiotic and biotic responses and their underlying community assembly mechanisms. Both injections caused similar geochemical and microbial succession. Uranium, nitrate, and sulfate concentrations in the groundwater dropped following the injection, and specific microbial taxa responded at roughly the same time points in both injections, including Geobacter, Desulfovibrio, and members of the phylum Comamonadaceae, all of which are well established in uranium, nitrate, and sulfate reduction. Both injections induced a transition from relatively stochastic to more deterministic assembly of microbial taxonomic and phylogenetic community structures based on 16S rRNA gene analysis. We conclude that geochemical and microbial successions after biostimulation are reproducible, likely owing to the selection of similar phylogenetic groups in response to EVO injection.

Seasonal and habitat dependence of plant species, functional and phylogenetic diversity in agricultural landscapes

The biodiversity of agricultural landscapes is under significant threat, while non-agricultural habitats within these landscapes play a crucial role in biodiversity conservation. There has been limited investigation into how plant species, functional and phylogenetic diversity varies across different seasons and habitats in agricultural landscapes. Thus, we carried out a survey of the plant communities in non-agricultural habitats in China's lower Yellow River plain. We investigated the diversity features of plant functionality, phylogeny, and plant species. We compared differences in plant community structure using non-metric multidimensional scaling analysis and tested phylogenetic signal using phylogenetic methods. Our analysis of plant community and diversity characteristics revealed significant differences in plant community structure between seasons and habitats, with the season having a more significant impact. The levels of plant species, functional, and phylogenetic diversity followed a seasonal pattern, with spring seeing the highest values and autumn seeing the lowest. Woodland and hedgerow habitats had the highest levels of diversity, while field roads had the lowest. The community phylogenetic structure of non-agricultural habitats was relatively concentrated and mainly influenced by human interference and environmental filtering. These findings offer scientific support for the preservation of ecosystem services and biodiversity in agricultural landscapes.

Do phylogenetic community metrics reveal the South African quartz fields as terrestrial-habitat islands?

The quartz fields of the Greater Cape Floristic Region (GCFR) are arid and island-like special habitats, hosting ~142 habitat-specialized plant species, of which 81 % are local endemics, characterized by a rapid turnover of species between and among sites. We use several phylogenetic community metrics: (1) to examine species diversity and phylogenetic structure within and among quartz fields; (2) to investigate whether quartz field specialists are evolutionarily drawn from local species pools, whereas the alternative hypothesis posits that there is no significant evolutionary connection between quartz field specialists and the local species pools; and (3) to determine whether there is an association between certain traits and the presence of species in quartz fields. We sampled and developed dated phylogenies for six species-rich angiosperm families (Aizoaceae, Asteraceae, Crassulaceae, Cyperaceae, Fabaceae and Santalaceae) represented in the quartz field floras of southern Africa. Specifically, we focused on the flora of three quartz field regions in South Africa (Knersvlakte, Little Karoo and Overberg) and their surrounding species pools to address our research questions by scoring traits associated with harsh environments. We found that the Overberg and Little Karoo had the highest level of species overlap for families Aizoaceae and Fabaceae, whereas the Knersvlakte and the Overberg had the highest species overlap for families Asteraceae, Crassulaceae and Santalaceae. Although our phylogenetic community structure and trait analyses showed no clear patterns, relatively low pairwise phylogenetic distances between specialists and their local species pools for Aizoaceae suggest that quartz species could be drawn evolutionarily from their surrounding areas. We also found that families Aizoaceae and Crassulaceae in Knersvlakte and Little Karoo were phylogenetically even. Despite their proximity to one another within the GCFR, the studied areas differ in their species pools and the phylogenetic structure of their specialists. Our work provides further justification for increased conservation focus on these unique habitats under future scenarios of global change.

Elevational patterns of fish functional and phylogenetic community structure in a monsoon climate river basin

AbstractAimUnderstanding 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.LocationThe Chishui River basin, China.MethodsWe 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.ResultsFish 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.ConclusionsAt 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.

Phylogenetic diversity patterns of woody species across different tree sizes and spatial scales in a tropical forest community on Con Dao Islands

Understanding the maintenance of diversity and the assembly of communities is a primary concern in community ecology. This study explored the phylogenetic structure of an evergreen broadleaved tree community in Con Dao National Park, Vietnam. The survey, conducted in December 2023, encompassed all tree individuals with a diameter at breast height (DBH) ≥ 2.5 cm within a 4-ha study plot. These individuals were identified by species name, and their DBH was measured. Subsequently, a community phylogenetic tree was constructed using the Phylomatic online platform. The 4-ha study plot was subdivided into there different subplots based on three spatial scales (25 m × 25 m, 50 m × 50 m, and 100 m × 100 m) and all trees were classified into three different DBH classes (2.5 cm ≤ DBH < 10 cm representing small trees; 10 cm ≤ DBH < 20 cm as medium trees; and DBH ≥ 20 cm as large trees). The net relatedness index (NRI) and net nearest taxon index (NTI) were utilized to evaluate the phylogenetic structure and infer ecological processes. Our findings revealed a consistent decrease in both NRI and NTI with increasing spatial scales and tree sizes. These results suggest an overdispersed phylogenetic structure within the community across different spatial scales and tree sizes. Additionally, negative density dependence was found to have a pronounced effect on the phylogenetic structure, with a more significant impact on tree individuals from small and medium DBH classes than large ones. This study underscores the significance of phylogenetic density dependence as a primary mechanism governing species diversity and shaping the community structure of evergreen broadleaved forests in Vietnam.

Antibiotic resistance profiles of gut microbiota across various primate species in Guangxi.

Understanding the gut microbiota and antibiotic resistance gene (ARG) profiles in non-human primates (NHPs) is crucial for evaluating their potential impact on human health and the environment. In this study, we performed metagenomic analysis of 203 primate fecal samples, including nine NHP species and humans, to comprehensively characterize their gut microbiota and ARGs. Our study reveals the prevailing phyla in primates as Firmicutes, Bacteroidetes, Euryarchaeota, and Proteobacteria. The captive NHPs exhibited higher ARG abundance compared to their wild counterparts, with tetracycline and beta-lactam resistance genes prevailing. Notably, ARG subtypes in Trachypithecus leucocephalus (T. leucocephalus) residing in karst limestone habitats displayed a more dispersed distribution compared to other species. Interestingly, ARG profiles of NHPs clustered based on geographic location and captivity status. Co-occurrence network analysis revealed intricate correlations between ARG subtypes and bacterial taxa. Procrustes analysis unveiled a significant correlation between ARGs and microbial phylogenetic community structure. Taxonomic composition analysis further highlighted differences in microbial abundance among NHPs and humans. Our study underscores the impact of lifestyle and geographical location on NHP gut microbiota and ARGs, providing essential insights into the potential risks posed by NHPs to antibiotic resistance dissemination. This comprehensive analysis enhances our understanding of the interplay between NHPs and the gut resistome, offering a critical reference for future research on antibiotic resistance and host-microbe interactions.

Non‐linear thresholds in the effect of area on three dimensions of diversity of herpetofauna in the West Indies

AbstractAimThe small‐island effect (SIE) describes an anomalous feature of the species–area relationship (SAR) on smaller compared to larger islands. However, previous studies on SIEs mainly focused on taxonomic diversity and overlooked phylogenetic and functional diversity. In this study, we explored SIEs in three dimensions of diversity. We expect to see the non‐linear thresholds in the effect of area on three dimensions of diversity as well as on community structures, because the dominant assembly processes vary across spatial scales.LocationThe West Indies.TaxonHerpetofauna.MethodsWe derived data on the presence/absence of 199 amphibian species on 163 islands and 614 reptile species on 748 islands in the West Indies. We built a species‐level phylogenetic tree and a species‐level functional tree to estimate six taxonomic, phylogenetic and functional diversity indices. Four community metrics on behalf of the phylogenetic and functional community structure of each island were calculated using a null modelling framework and was quantified using the standardized effect size (SES). We explored the non‐linear thresholds in the effect of area for each of the diversity indices and SES values of community metrics by comparing six piecewise regression models with a linear regression model and a null model.ResultsWe found evidence of SIEs in four diversity indices representing all three dimensions of diversity. Besides, area thresholds were also found in the phylogenetic and functional community structure for both amphibians and reptiles. Random extinction, competitive exclusion and adaptive radiation are the dominant processes structuring reptile communities on small, intermediate and large islands respectively.Main ConclusionsTo conduct a comprehensive biodiversity conservation plan concerning taxonomic, phylogenetic and functional diversity, we suggest it is necessary to explore the SIEs in various diversity indices representing all three dimensions of diversity and apply the lowest threshold value to make management strategies.

Environmental filtering along a bathymetric gradient: A metabarcoding meta-analysis of free-living nematodes.

Identifying and understanding patterns of biological diversity is crucial at a time when even the most remote and pristine marine ecosystems are threatened by resource exploitation such as deep-seabed mining. Metabarcoding provides the means through which one can perform comprehensive investigations of diversity by examining entire assemblages simultaneously. Nematodes commonly represent the most abundant infaunal metazoan group in marine soft sediments. In this meta-analysis, we compiled all publicly available metabarcoding datasets targeting the 18S rRNA v1-v2 region from sediment samples to conduct a global-scale examination of nematode amplicon sequence variant (ASV) alpha diversity patterns and phylogenetic community structure at different depths and habitats. We found that nematode ASV richness followed a parabolic trend, increasing from the intertidal to the shelf, reaching a maximum in the bathyal and decreasing in the abyssal zone. No depth- or habitat-specific assemblages were identified as a large fraction of genera were shared. Contrastingly, the vast majority of ASVs were unique to each habitat and/or depth zone; genetic diversity was thus highly localized. Overwhelmingly, nematode ASVs in all habitats exhibited phylogenetic clustering, pointing to environmental filtering as the primary force defining community assembly rather than competitive interactions. This finding stresses the importance of habitat preservation for the maintenance of marine nematode diversity.

Assessing riverine fish community diversity and stability by eDNA metabarcoding

Monitoring and evaluating river ecosystems are of paramount importance in addressing ecological and environmental challenges. While eDNA (environmental deoxyribonucleic acid)-based method has emerged as a valuable tool for understanding these issues, its application in assessing phylogenetic diversity, community stability, and the identification of key species within river systems has been limited. In this study, we conducted eDNA metabarcoding to assess fish community phylogenetic diversity, species composition, assembly variations, and their relationship with hydrologic characteristics. We also explored ecological stability and the roles of key species in a river system comprising a mainstem (MS) and a tributary (TB) with distinct hydrologic features. Our findings uncovered previously unknown endemic fish species diversity, exemplified by the discovery of Triplophysa. We identified disparities in diversity, community composition, and assembly between the MS and TB. Furthermore, we established significant associations between water-level variations, water flow, and changes in community composition. Triplophysa, with its high diversity, played a pivotal role in the ecological network, contributing significantly to community stability. The loss of Triplophysa increased fragility in co-occurrence patterns. Comparing the ecological network of fish communities between the MS and TB, we found that the MS displayed greater robustness and lower vulnerability, with increased species competition likely promoting network stability. Overall, this study highlights the potential of integrating eDNA metabarcoding data for monitoring phylogenetic diversity, community structure, and variations in stability within fish communities.

Seasonal Variations in Plant Species Diversity and Phylogenetic Diversity in Abandoned Farmland of China’s Huang–Huai Plain

Amidst urbanization and industrialization in China, abandoned farmland plays a crucial role in safeguarding plant diversity within agricultural landscapes. This study aimed to examine the patterns of seasonal variation in plant diversity within abandoned farmland habitats in the Huang–Huai Plain region. Nonparametric tests were employed to analyze plant species diversity and phylogenetic diversity across seasons. Redundancy analysis and linear regression were conducted to examine the associations between plant species composition, species diversity, phylogenetic diversity, and soil environmental factors. Our results showed that plant species diversity, richness, and phylogenetic diversity were highest in spring, followed by summer, and lowest in autumn. The phylogenetic structure of plant communities demonstrated a tendency to diverge in spring, become random in summer, and cluster in autumn. Soil available potassium and soil organic matter emerged as important factors influencing plant species composition. The content of soil organic matter and ammonium nitrogen level exhibited a significantly positive correlation with the species diversity and phylogenetic diversity of plants. This study underscores the significance of considering seasonal and temporal scales when investigating plant diversity and provides a theoretical basis for biodiversity conservation in agricultural landscapes.