Phylogenetic Diversity Research Articles

Phylogeny and bioprospecting: The diversity of medicinal plants used in cancer management

Societal Impact StatementAs the second‐leading cause of mortality worldwide, cancer is a major focus of drug discovery research. Traditional plant knowledge can guide the search for undiscovered compounds, but the efficacy of this approach for cancer, a highly complex disease affecting diverse tissues, is unknown. We investigated the patterns underlying plant selection for cancer treatment globally, finding certain lineages are repeatedly targeted. While this indicates therapeutic value, their relatedness with plants used for unrelated ethnobotanical uses suggests that plants are probably selected to treat cancer‐associated symptoms, rather than addressing tumour growth. Careful re‐examination and scoring of ethnobotanical reports may make the prediction of lineages for drug discovery more informative.Summary Cancer is a highly diverse disease and as the second‐leading cause of death worldwide is a focus of drug discovery research. Natural products have been shown to be a useful source of novel molecules for treating cancer. It is likely there are many plants with undiscovered molecules of therapeutic value, however identifying new leads from the vast diversity of plants is very challenging. Traditional knowledge might inform bioprospecting by predicting lineages of plants rich in therapeutically useful molecules. We characterise the phylogenetic diversity of plants used in traditional cancer management using a comprehensive genus‐level phylogeny of angiosperms, and a list of 597 genera used globally to treat different cancers. We phylogenetically predict which lineages may have elevated potential for drug discovery and assess the quality of the prediction. We demonstrate the independent and repeated targeting of specific lineages of plants by different peoples in different parts of the world. However, the lineages we report here as rich in plants used in traditional cancer management coincide with those for other ethnobotanical applications and contain few plants with proven anti‐cancer activity. That the same lineages are used to treat different cancers is suggestive of independent discovery of therapeutic value. However, it is likely that the traditional knowledge explored here is shaped by the selection of plants conferring milder effects for treating wider symptoms, such as tiredness or nausea, rather than for halting tumour growth. Accurate prediction of useful plant lineages for cancer management requires more nuanced information than is commonly provided in ethnobotanical records.

Competitive exclusion drives termite community assembly process on islands

ContextAbiotic filtering, including environmental and dispersal filtering, is frequently observed resulting in reduced diversity and more similar species assemblages following habitat fragmentation. Nonetheless, the significance of competitive exclusion is often underestimated.ObjectivesWe investigated the dominant assembly process among termite communities on land-bridge islands, focusing on species known for their high territoriality. We hypothesized that competitively superior species tend to dominate more favorable habitats, such as larger and less isolated islands. Consequently, we anticipated lower diversity and greater similarity in species assemblages than would be expected.MethodsTermite communities were surveyed using standardized transects on 24 islands. We quantified the standardized effects of island area and isolation on taxonomic, phylogenetic and functional diversity by comparing observed patterns with randomly generated communities (i.e., stochastic process). A phylogenetic generalized linear mixed model (PGLMM) was conducted to examine species-specific responses to environmental factors and competition intensity (i.e., heterospecific abundance).ResultsWe found that taxonomic, phylogenetic and functional diversity were lower than expected on larger and less isolated islands, suggesting that competitive exclusion was the dominant mechanism shaping termite communities in TIL. PGLMM showed that two fungus-growing species with larger body sizes increased with competition intensity, while other species exhibited negative responses. Notably, the abundance of fungus-growing species showed sharper increase with island area and decrease with isolation compared to other feeding groups. These findings demonstrate that competitively superior species prefer high-quality habitats and are more sensitive to habitat fragmentation.ConclusionsOur study highlights the significance of competitive exclusion in shaping termite communities and emphasizes the need to consider both competitive and niche difference among species or functional groups when predict changes in community structure and biodiversity loss resulting from habitat fragmentation.

Phylogenetic Diversity, Antibiotic Resistance, and Virulence of Escherichia coli Strains from Urinary Tract Infections in Algeria.

Urinary tract infections (UTIs) caused by Escherichia coli represent a significant public health concern due to the high virulence and antimicrobial resistance exhibited by these pathogens. This study aimed to analyze the phylogenetic diversity and antibiotic resistance profiles of Uropathogenic E. coli (UPEC) strains isolated from UTI patients in Algeria, focusing on virulence factors such as extended β-lactamase (ESBL) production, biofilm formation, and hemolytic activity. Phylogenetic grouping of 86 clinical imipenem resistant E. coli isolates showed the prevalence of group B2 (48.9%), followed by groups E (22.1%), unknown (12.8%), A (8.1%), and B1 (4.7%), and Clade I, D, Clade I, or Clade II (1.2%). The highest resistance rates were observed towards amoxicillin (86.04%), ticarcillin (82.55%), piperacillin (73.25%), nitrofurantoin (84.88%), and trimethoprim-sulfamethoxazole (51.16%). Notably, 69.8% of UPEC strains were multidrug-resistant (MDR) and 23.2% were extensively drug-resistant (XDR). Additionally, 48.9%, 42%, and 71% of strains demonstrated ESBL production, hemolytic activity, and weak biofilm production, respectively. Continuous monitoring and characterization of UPEC strains are essential to track the spread of the most resistant and virulent phylogenetic groups over time, facilitating rapid therapeutic decisions to treat infections and prevent the emergence of new resistant organisms, helping choose the most effective antibiotics and reducing treatment failure.

Do linear clearings in boreal peatlands recover? Comparing taxonomic, phylogenetic, and functional plant diversity

Land-use changes and anthropogenic disturbances are major threats to biodiversity, affecting ecosystem function and recovery. In boreal Alberta, Canada, petroleum development has led to extensive landscape fragmentation, notably through linear clearings created for seismic exploration that remove surface vegetation and microtopography. Despite partial recovery on forested seismic lines, peatland recovery is often arrested, impacting wildlife and carbon dynamics. Restoration efforts employ silviculture techniques to create microtopography and foster tree growth, but the efficacy of restoration treatments in restoring peatland plant diversity remains uncertain. We compared taxonomic, phylogenetic, and functional diversity of understory plant communities across treated and untreated seismic lines, alongside reference sites in treed bogs and fens. Treated lines generally had a twofold increase in plant height, leaf dry matter content, and foliar nitrogen and phosphorus contents compared to reference sites. In bogs, treated lines differed from reference conditions driven by increases in herbaceous taxa, while fens displayed disparities mainly in taxonomic and phylogenetic diversity. Differential responses of bogs and fens underline the necessity for tailored management strategies. Changes in plant diversity away from restoration targets have implications for ecosystem recovery, emphasizing the importance of long-term monitoring to evaluate the effectiveness of silviculture techniques in restoring boreal peatland plant communities.

Phylogenetic diversity and interspecies competition shaped species diversity in adaptive radiated Ligustrum (Oleaceae)

Phylogenetic diversity and interspecies competition shaped species diversity in adaptive radiated <i>Ligustrum</i> (Oleaceae)

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.

Predicting undetected native vascular plant diversity at a global scale

Vascular plants are diverse and a major component of terrestrial ecosystems, yet their geographic distributions remain incomplete. Here, I present a global database of vascular plant distributions by integrating species distribution models calibrated to species' dispersal ability and natural habitats to predict native range maps for 201,681 vascular plant species into unsurveyed areas. Using these maps, I uncover unique patterns of native vascular plant diversity, endemism, and phylogenetic diversity revealing hotspots in underdocumented biodiversity-rich regions. These hotspots, based on detailed species-level maps, show a pronounced latitudinal gradient, strongly supporting the theory of increasing diversity toward the equator. I trained random forest models to extrapolate diversity patterns under unbiased global sampling and identify overlaps with modeled estimations but unveiled cryptic hotspots that were not captured by modeled estimations. Only 29% to 36% of extrapolated plant hotspots are inside protected areas, leaving more than 60% outside and vulnerable. However, the unprotected hotspots harbor species with unique attributes that make them good candidates for conservation prioritization.

Soundscapes and airborne laser scanning identify vegetation density and its interaction with elevation as main driver of bird diversity and community composition

AbstractAimMountain ecosystems are hotspots of biodiversity due to their high variation in climate and habitats. Yet, above average rates of climate change and enhanced forest disturbance regimes alter local climatic conditions and vegetation structure, which should impact biodiversity. We here investigated the impact of vegetation and elevation as well as their interactions on bird communities to improve our ability to predict climate change effects on bird communities.LocationEuropean Alps, Germany.MethodsWe studied patterns and drivers of bird communities at 213 plots along gradients in vegetation density and elevation using autonomous sound recorders. Bird species were identified from soundscapes by Convolutional Neural Networks (BirdNET) and taxonomists.ResultsBird diversity and community metrics were moderately to strongly correlated for data based on either identification by BirdNET or taxonomists (Pearson's r = .47–.94), and ecological findings were overall similar for both datasets. Vegetation density 1–2 m and &gt;2 m above ground strongly affected bird diversity and community composition and mediated effects of elevation. Community composition changed with elevation more strongly in habitats with low than high vegetation density &gt;2 m. Species numbers decreased with elevation in habitats with low vegetation density 1–2 m and &gt;2 m above ground, but increased in habitats with high vegetation density. Overall, functional and phylogenetic diversity increased with elevation indicating lower habitat filtering, but patterns were also mediated by vegetation density.Main ConclusionsOur results indicate that bird communities in the German Alps are determined by strong interactive effects of elevation and vegetation, underlining the importance to consider variation in vegetation in studies of biodiversity patterns along elevational gradients and under climate change. Combining remote sensing data and biodiversity monitoring based on autonomous sampling and AI‐based species identification opens new avenues for bird monitoring and research in remote areas.

Contrasting luxury effect on urban plant phylogenetic and taxonomic diversity in West African cities

ABSTRACT Urbanization is a driving factor for biodiversity loss and potential climate change by reducing carbon stocks. Understanding how urban development, as mitigated by socio-economic factors alters urban biodiversity is crucial for effective urban planning that maintains or improves environmental resilience. The luxury effect hypothesis predicts that wealthier parts of a city will have higher levels of biodiversity. This effect has been tested widely but we still have limited understanding of how wealth influences urban biodiversity in tropical regions of developing countries where plant species play profound sociocultural roles beyond aesthetics. This study investigates links between household income and the diversity of cultivated plants distribution within neighborhoods of two growing cities in Benin. We conducted a survey of 936 randomly selected households to record their socioeconomic characteristics and survey the cultivated plant species found in household gardens’. This enabled us to estimate household-level diversity metrics including taxonomic diversity and phylogenetic diversity. We found no global support for the luxury effect on phylogenetic diversity but rented properties had lower plant taxonomic diversity along with less phylogenetic diversity than privately owned houses. Taxonomic diversity is higher in the less urbanized areas while phylogenetic diversity is weakened. Household’s cultural connection to plants has a negative effect on both diversity indices. Our results highlight the complex relationships between socioeconomic traits and urban plant diversity distribution in two tropical African cities, which only partly confirmed the luxury effect hypothesis. Disentangling these complex relationships can help city planners and policymakers to take informed decisions to promote sustainable cities.

Characteristics and assembly mechanisms of bacterial and fungal communities in soils from Chinese forests across different climatic zones

Forest soils are intricate ecosystems that harbor a diverse array of microorganisms, yet our current understanding of the characteristics and environmental implications of forest soil microbiomes remains limited. Here we present a continental-scale study on soil microbiomes of ten forests in China, spanning latitudes from 18°54′N to 50°48′N, resulting in a comprehensive catalog of bacterial and fungal operational taxonomic units (OTUs). Both bacterial and fungal communities exhibited discernible spatial variations in taxonomic and phylogenetic diversity. The composition of bacterial communities varied distinctively due to climatic zones—cold temperate, temperate, subtropical, and tropical—whereas fungal communities did not exhibit such pronounced distinctions. The co-occurrence network complexity of bacterial communities displayed a decremental trend along the cold temperate, temperate, subtropical, and tropical zones, whereas that of fungal communities displayed an incremental pattern. These results may be attributed to the facts that low temperatures sustain a high biomass of bacteria and foster increased interactions, while high temperatures and precipitation stimulate fungi-plant interactions. Furthermore, community assembly modeling revealed that forest soil microbial communities were dominated by stochastic processes. The bacterial community structure was mainly driven by homogeneous selection (26–41%) and dispersal limitation (35–44%), whereas dispersal limitation (51–56%) had the greatest impact on fungal community structure. Notably, bacterial functional genes associated with carbon fixation were more abundant in cold temperate soils compared to tropical soils. This study sheds light on spatial variations of forest soil microbiomes in China, enhancing further understanding of their response to global changes and implications for soil organic carbon cycles.

Epidemiological, Phylogenetic, and Resistance Heterogeneity Among Acinetobacter baumannii in a Large U.S. Deep South Healthcare system.

Acinetobacter baumannii (Ab) disease in the United States is commonly attributed to outbreaks of 1 or 2 monophyletic carbapenem resistance (CR) Ab lineages that vary by region. However, there is limited knowledge regarding CRAb epidemiology and population structures in the U.S. Deep South, and few studies compare contemporary CR and carbapenem-susceptible (Cs) Ab, despite relative prevalence of the latter. We performed a multiyear analysis of 2462 Ab cases in a large healthcare system in Birmingham, AL, and 89 post-2021 Ab isolates were sequenced and phenotyped by antibiotic susceptibility tests. Although the cumulative CR rate was 17.7% in our cohort, rates regularly increased in winter months as result of seasonal changes in case incidence of CsAb, specifically. Genotyped CRAb belonged to clonal group (CG) 1, CG2, CG108, CG250, or CG499, with local clones of CG108, CG250, and CG499 persisting over multiple months. There was no clonal expansion of any CsAb lineage. Among CRAb isolates, levels of β-lactam antibiotic resistance and the repertoire of related genetic resistance determinants, which included the novel CR-conferring FtsI A515V polymorphism, differed according to CG. CG108 and CG499 isolates displayed specific heteroresistance to sulbactam and trimethoprim/sulfamethoxazole, respectively, which resulted in discrepant susceptibility results in microbroth versus agar-based antibiotic susceptibility tests modalities. We report an unusually high degree of CRAb phylogenetic diversity principally driven by emergent U.S. lineages harboring novel resistance elements that must be incorporated into diagnostic, surveillance, and preclinical research efforts.

Environmental Filters Structure Cushion Bogs' Floristic Composition along the Southern South American Latitudinal Gradient.

The environmental filtering hypothesis predicts that abiotic factors restrict communities by selecting species capable of survival and persistence under specific conditions, resulting in variations in beta diversity, phylogenetic clustering, and niche differentiation among communities when studying environmental gradients. Cushion bogs and high-altitude wetlands along the Andes display homogeneous flora contrasting with zonal vegetation. Despite being influenced by microclimatic conditions, these ecosystems are subject to diverse environmental effects. Here, we test the environmental filtering hypothesis on the structure of cushion bog communities along a broad-scale latitudinal gradient from 15° S to 42° S. We analyzed 421 bogs and 293 species across three macroclimatic regions with distinct summer, winter, and transitional arid rainfall regimes. Using variance partitioning and membership-based regionalization models, we examined the impacts of climatic, edaphic, and spatial variables on beta diversity. We also assessed species' niche overlap and the influence of environmental filters on the communities' phylogenetic diversity. Results show that species turnover and niche overlap vary with macroclimatic differences, delineating three distinct regions. Notably, phylogenetic clustering in the driest part of the gradient (23° S-24° S) highlights the impact of environmental filtering. Aridity and temperature variations at a broad scale serve as environmental filters shaping the composition of bog communities across southern South America.

Identifying areas of conservation importance based on spatial patterns of evolutionary diversity for non-volant small mammals in the Andean Puna

Ecosystems around the world face a variety of threats from anthropogenic activities and drylands are among the most affected due to their unique environmental characteristics. To maintain phylogenetic history and ecological functionality in these areas, it is imperative to preserve community structure and composition by identifying and protecting key conservation areas. Various methods have been used to define these areas in need of protection; in this study, we used patterns of taxonomic and phylogenetic diversity in the arid lands of the Altiplano-Puna Bioregion of South America, using non-volant small mammal communities as a model system. Based on detailed records of species presence in the study area we estimated indices of species richness and phylogenetic redundancy. The geographic distribution of these indices was then compared to the distribution of protected areas in the region. These analyses identified areas around Lake Titicaca as being of exceptional conservation importance and in need of protection efforts. We propose a network of interconnected areas that together would provide high conservation value while allowing genetic exchange and facilitating ecological processes across landscapes.

Avian phylogenetic and functional diversity are better conserved by land‐sparing than land‐sharing farming in lowland tropical forests

Abstract The transformation of natural habitats for farming is a major driver of tropical biodiversity loss. To mitigate impacts, two alternatives are promoted: intensifying agriculture to offset protected areas (land sparing) or integrating wildlife‐friendly habitats within farmland (land sharing). In the montane and dry tropics, phylogenetic and functional diversity, which underpin evolutionary values and the provision of ecosystem functioning and services, are best protected by land sparing. A key question is how these components of biodiversity are best conserved in the more stable environments of lowland moist tropical forests. Focusing on cattle farming within the Colombian Amazon, we investigated how the occupancy of 280 bird species varies between forest and pasture spanning gradients of wildlife‐friendly features. We then simulated scenarios of land‐sparing and land‐sharing farming to predict impacts on phylogenetic and functional diversity metrics. Predicted metrics differed marginally between forest and pasture. However, community assembly varied significantly. Wildlife‐friendly pastures were inadequate for most forest‐dependent species, while phylogenetic and functional diversity indices showed minimal variation across gradients of wildlife‐friendly features. Land sparing consistently retained higher levels of Faith's phylogenetic diversity (~30%), functional richness (~20%) and evolutionarily distinct lineages (~40%) than land sharing, and did so across a range of landscape sizes. Securing forest protection through land‐sparing practices remains superior for conserving overall community phylogenetic and functional diversity than land sharing. Synthesis and applications: To minimise the loss of avian phylogenetic diversity and functional traits from farming in the Amazon, it is imperative to protect large blocks of undisturbed and regenerating forests. The intensification required within existing farmlands to make space for spared lands while meeting agricultural demand needs to be sustainable, avoiding long‐term negative impacts on soil quality and other ecosystem services. Policies need to secure the delivery of both actions simultaneously.

Shallow tillage mitigates plant competition by increasing diversity and altering plant community assembly process.

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. 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. 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. 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.

Identification and functional characterization of a novel cystatin in amphioxus, ancient origin of vertebrate type-2 cystatin homologues

Cystatins are well known as a vast superfamily of functional proteins participated in the reversible competitive inhibition of cysteine proteases. Currently, increasing evidences point to the extensive phylogenetic diversity and crucial immune roles of type-2 cystatins in the vertebrate species. However, no information is available regarding the homologue in cephalochordate amphioxus, the representative of most basal living chordates, whose immune regulation are still ambiguous. Here, we clearly identified the presence of type-2 cystatin gene in amphioxus Branchiostoma japonicum, termed Bjcystatin-2, which was structurally characterized by typical wedge-shaped cystatin feature. Evolutionary analyses revealed that Bjcystatin-2 is the putative ancestral type-2 cystatin for chordates, with gene diversity emerging through duplication events. The expression of Bjcystatin-2 showed tissue-specific profile and was inducible upon invasive pathogens. Significantly, the recombinant Bjcystatin-2 exhibited not merely cathepsin L inhibitory activity, but also the ability to bind with bacteria and their characteristic molecules. Furthermore, Bjcystatin-2 also showed the capacity to enhance the macrophage-driven bacterial phagocytosis and to attenuate the generation of pro-inflammatory cytokines within macrophages. In summary, these findings demonstrate that Bjcystatin-2 exhibits dual role acting as both a protease inhibitor and an immunoactive molecule, greatly enriching our understanding of immune defense mechanisms of type-2 cystatin within the amphioxus.

Where are the provincial-level new records in China from the past 20 years, and which traits determine their shift directions?

Birds are sensitive to environmental changes and can drive range shifts rapidly due to their high mobility. Though previous studies have examined the associations between species traits and range shifts, whether species traits could still explain heterogeneity in shift directions remains poorly explored. Here, we compiled new bird records of China from 2000 to 2019 and analyzed species traits associated with apparent shift directions. We collected 350 provincial-level new records of birds belonging to 67 families of 22 orders. Of these, 32 are threatened, with 3 critically endangered, 11 endangered, and 18 vulnerable. Provinces in western China (i.e., Yunnan and Xizang) had relatively higher species richness of new recorded birds; this pattern was also reflected in the phylogenetic diversity we observed. In addition, provinces in northern China (i.e., Tianjin, Shandong, and Beijing) had relatively higher richness-controlled phylogenetic diversity. Phylogenetic overdispersion of new recorded bird communities was observed in 61.29% of provinces (19 of 31). The main shift directions indicated by new bird records were northward (with nearly 50% of birds moving NW, N and NE). Migration, hand-wing index (HWI), body mass, and range size are the four key factors that most significantly influence the shift directions in bird species, suggesting that bird movement toward newly suitable areas varies with species-specific traits. Together, these results demonstrate the importance of considering species ecological traits when predicting shift directions of birds.

Acoustic indices fail to represent different facets of biodiversity

Acoustic indices are cost-efficient tools for monitoring acoustically active taxa. Despite their increasing popularity, their suitability as biodiversity proxies remains debated due to theoretical and practical issues. Existing research has predominantly focused on assessing their capacity to capture species richness and abundance of sounds, with limited attention given to other biodiversity facets like phylogenetic and functional diversity. Yet, phylogenetic distance and trait diversity may influence acoustic communication, so acoustic indices may be better suited to capture their changes than changes in the mere number of species. Here, we investigated the ability of acoustic indices to represent the species, phylogenetic, and functional diversity of acoustically active avian species across three habitat types in Italy: urban, riparian forest and deciduous woodland.Recordings were collected at dawn by a trained ornithologist, who also identified acoustically active species captured, first in the field and secondarily from recordings. We then applied eleven widely used acoustic indices for each recording and tested their ability to capture differences in species, functional and phylogenetic diversity across sites (i.e., listening points) within each habitat type using a linear mixed effect model. We then reduced the acoustic indices dimensionality to a few axes and repeated the analysis to test if compound indices delivered comparable information.Species richness and phylogenetic diversity correlated with at least one acoustic index across the three habitat types, while functional diversity correlated with an index only in the urban habitat. However, the nature of the relationships identified was often opposite to what expected by the indices’ formulation. Furthermore, across the three habitat types the interrelations among indices varied, as well as the observed relationships with diversity indices. Compound indices also exhibited inconsistent relationships across sites and contrary to what expected based on their correlation with acoustic indices.Our results cast doubts on the suitability of acoustic indices as proxies for biodiversity for biodiversity monitoring. Additionally, the inconsistent relationship among indices across the three areas suggests they are unsuitable for geographic comparisons. Temporal comparisons are possible but require local validation and may need adjustments over time of the community composition changes. Despite the attractiveness of acoustic indices as easy and cheap tools for biodiversity monitoring, we urge caution on their application.

Lessons from Extremophiles: Functional Adaptations and Genomic Innovations across the Eukaryotic Tree of Life.

From hydrothermal vents, to glaciers, to deserts, research in extreme environments has reshaped our understanding of how and where life can persist. Contained within the genomes of extremophilic organisms are the blueprints for a toolkit to tackle the multitude of challenges of survival in inhospitable environments. As new sequencing technologies have rapidly developed, so too has our understanding of the molecular and genomic mechanisms that have facilitated the success of extremophiles. Although eukaryotic extremophiles remain relatively understudied compared to bacteria and archaea, an increasing number of studies have begun to leverage 'omics tools to shed light on eukaryotic life in harsh conditions. In this perspective paper, we highlight a diverse breadth of research on extremophilic lineages across the eukaryotic tree of life, from microbes to macrobes, that are collectively reshaping our understanding of molecular innovations at life's extremes. These studies are not only advancing our understanding of evolution and biological processes but are also offering a valuable roadmap on how emerging technologies can be applied to identify cellular mechanisms of adaptation to cope with life in stressful conditions, including high and low temperatures, limited water availability, and heavy metal habitats. We shed light on patterns of molecular and organismal adaptation across the eukaryotic tree of life and discuss a few promising research directions, including investigations into the role of horizontal gene transfer in eukaryotic extremophiles and the importance of increasing phylogenetic diversity of model systems.

Water temperature and salt ions respectively drive the community assembly of bacterial generalists and specialists in diverse plateau lakes

Plateau lakes (e.g., freshwater and saltwater lakes) are formed through intricate processes and harbor diverse microorganisms that mediate aquatic ecosystem functions. The adaptive mechanisms of lake microbiota to environmental changes and the ecological impacts of such changes on microbial community assembly are still poorly understood in plateau regions. This study investigated the structure and assembly of planktonic bacterial communities in 24 lakes across the Qinghai-Tibetan and Inner Mongolia Plateaus, with particular focus on habitat generalists, opportunists, and specialists. High-throughput sequencing of the 16S ribosomal RNA genes revealed that bacterial generalists had a lower species number (2196) but higher alpha diversity than the specialist and opportunist counterparts. Taxonomic dissimilarity and phylogenetic diversity analyses unraveled less pronounced difference in the community composition of bacterial generalists compared to the specialist and opportunist counterparts. Geographical scale (14.4 %) and water quality (12.6 %) emerged as major ecological variables structuring bacterial communities. Selection by water temperature and related variables, including mean annual temperature, elevation, longitude, and latitude, mainly shaped the assembly of bacterial generalists. Ecological drift coupled with selection by salt ions and related variables, including total phosphorus, chlorophyll a, and salinity, predominantly drove the assembly of bacterial specialists and opportunists. This study uncovers distinct bacterial responses to interacting ecological variables in diverse plateau lakes and the ecological processes structuring bacterial communities across various lake habitats under anthropogenic disturbance or climate change.