Phylogenetic Diversity Measures Research Articles

Insight into the assembly process of angiosperms and arbuscular-mycorrhizal fungi in tropical wetland ecosystems

ABSTRACT Background The interaction between plants and mycorrhizal fungi is one of the most important and well-studied in ecology. However, the manner in which ecological communities of plants and arbuscular mycorrhizal (AM) fungi are structured by both deterministic and stochastic processes remains unclear. Aims To quantify the role of deterministic and stochastic assembly processes in both plant and arbuscular mycorrhizal (AM) fungal communities along with environmental filters in the assembly of communities in areas subject to flooding. Methods We studied phylogenetic relationships and diversity measures in plants and arbuscular mycorrhizal fungi in three tropical coastal wetland communities with contrasting landscapes and soil properties. Results We found that non-random processes were dominant in plant communities, while mycorrhizal communities appeared to be determined by stochastic processes. Clustering trends were predominant in plant communities in areas subject to flooding. Conclusion Environment filters and limiting similarity drive the plant community assembly, whereas ecological drift and/or dispersal limitations were determinants in the assembly of mycorrhizal communities. Environmental filters were found to be the main driver of plant community assembly in in areas subject to flooding.

Calculating functional diversity metrics using neighbor‐joining trees

The study of functional diversity (FD) provides ways to understand phenomena as complex as community assembly or the dynamics of biodiversity change under multiple pressures. Different frameworks are used to quantify FD, either based on dissimilarity matrices (e.g. Rao entropy, functional dendrograms) or multidimensional spaces (e.g. convex hulls, kernel‐density hypervolumes), each with their own strengths and limits. Frameworks based on dissimilarity matrices either do not enable the measurement of all components of FD (i.e. richness, divergence, and regularity), or result in the distortion of the functional space. Frameworks based on multidimensional spaces do not allow for comparisons with phylogenetic diversity (PD) measures and can be sensitive to outliers.We propose the use of neighbor‐joining trees (NJ) to represent and quantify FD in a way that combines the strengths of current frameworks without many of their weaknesses. Importantly, our approach is uniquely suited for studies that compare FD with PD, as both share the use of trees (NJ or others) and the same mathematical principles.We test the ability of this novel framework to represent the initial functional distances between species with minimal functional space distortion and sensitivity to outliers. The results using NJ are compared with conventional functional dendrograms, convex hulls, and kernel‐density hypervolumes using both simulated and empirical datasets.Using NJ, we demonstrate that it is possible to combine much of the flexibility provided by multidimensional spaces with the simplicity of tree‐based representations. Moreover, the method is directly comparable with taxonomic diversity (TD) and PD measures, and enables quantification of the richness, divergence and regularity of the functional space.

Weak phylogenetic effect on specialist plant assemblages and their persistence on habitat islands

AbstractAimThe influence of species phylogenetic relatedness on the formation of insular assemblages remains understudied in functional island biogeography, especially for terrestrial habitat islands (i.e. distinct habitat patches embedded in a matrix that differ in the prevailing environmental conditions). Here, we tested three eco‐evolutionary hypotheses: (1) functional specialization of species (i.e. specialism) is associated with phylogenetic clustering at the habitat archipelago scale, (2) such clustering increases with insularity at the habitat island scale and (3) traits indicative of effective local persistence strategies shape island specialism.LocationTerrestrial habitat islands, Europe (Fens in the Western Carpathians, Outcrops in Moravia and Mountaintops in the Cantabrian Range).TaxonAngiosperms.MethodsWe assessed the phylogenetic relatedness of habitat specialists in three different archipelagos composed of terrestrial habitat islands based on phylogenetic signals and phylogenetic diversity (PD) measures. We estimated the effect of insularity on PD using linear models and the effect of persistence traits on specialism using phylogenetic logistic regressions.ResultsOur hypotheses were largely not supported. Outcrop and mountaintop specialist assemblages did not exhibit any phylogenetic structuring, whereas fen specialists were clustered at the archipelago scale. Therefore, insularity seems not to act as a selective force for phylogenetic structure, and ecologically important persistence traits do not operate as precursors of specialism.Main ConclusionsOur results show that species phylogenetic relatedness plays a minor role in shaping habitat island specialist assemblages. Furthermore, the effects of phylogenetic relatedness on assemblages of island specialists are system and scale dependent. Finally, accounting for species' phylogenetic relatedness on persistence traits yielded results similar to previous studies, which corroborates the positive relationship between insularity and functional traits (indicative of enhanced plant persistence abilities with increasing within‐archipelago insularity).

Choice of molecular marker influences spatial patterns of phylogenetic diversity.

Spatial patterns of phylogenetic diversity (PD) are increasingly becoming relevant for conservation decisions. PD measures are based on phylogenies estimated from molecular data. This paper addresses the question of how different molecular markers impact PD spatial patterns. We first conducted a simple simulation to explore the effect of deep and shallow changes in topology (simulating variations in molecular markers), using ultrametric and non-ultrametric trees, and then used a dataset of Chilean flora with four sets of markers to assess potential differences in spatial patterns of PD ranks using different markers and types of trees. The simulation consistently showed that the difference in PD rank was lower for ultrametric trees than for phylograms. A similar trend was observed using the Chilean flora dataset, with among-markers variability in spatial patterns of the PD metrics lower for ultrametric than for non-ultrametric trees, depicted as top 2.5 and 5% hotspots. Frequency distribution of PD values differed among markers as well, with this variation less apparent for ultrametric trees. We conclude that the choice of markers impacts spatial patterns of PD, and these results vary more strongly for phylograms, suggesting that ultrametric trees are more robust to the choice of marker.

Phylogenetic Biodiversity Metrics Should Account for Both Accumulation and Attrition of Evolutionary Heritage.

Phylogenetic metrics are essential tools used in the study of ecology, evolution and conservation. Phylogenetic diversity (PD) in particular is one of the most prominent measures of biodiversity and is based on the idea that biological features accumulate along the edges of phylogenetic trees that are summed. We argue that PD and many other phylogenetic biodiversity metrics fail to capture an essential process that we term attrition. Attrition is the gradual loss of features through causes other than extinction. Here we introduce "EvoHeritage", a generalization of PD that is founded on the joint processes of accumulation and attrition of features. We argue that while PD measures evolutionary history, EvoHeritage is required to capture a more pertinent subset of evolutionary history including only components that have survived attrition. We show that EvoHeritage is not the same as PD on a tree with scaled edges; instead, accumulation and attrition interact in a more complex non-monophyletic way that cannot be captured by edge lengths alone. This leads us to speculate that the one-dimensional edge lengths of classic trees may be insufficiently flexible to capture the nuances of evolutionary processes. We derive a measure of EvoHeritage and show that it elegantly reproduces species richness and PD at opposite ends of a continuum based on the intensity of attrition. We demonstrate the utility of EvoHeritage in ecology as a predictor of community productivity compared with species richness and PD. We also show how EvoHeritage can quantify living fossils and resolve their associated controversy. We suggest how the existing calculus of PD-based metrics and other phylogenetic biodiversity metrics can and should be recast in terms of EvoHeritage accumulation and attrition.

Low-level pathogen infection and geographic location correlate with the skin microbiomes of Columbia spotted frogs (Rana luteiventris) in a montane landscape

The skin microbiome of amphibians can influence host susceptibility towards the fungal pathogen Batrachochytrium dendrobatidis (Bd), while simultaneously having the potential to be altered by Bd. Severe Bd infections are known to alter the amphibian skin microbiome; however, little is known about microbiome interactions in amphibians with low infection intensity. In addition to disease dynamics, environmental factors may influence the microbiome. To test for patterns in bacterial diversity based on pathogen infection and environmental factors, 399 Columbia spotted frogs (Rana luteiventris) were sampled throughout northern Idaho and northeastern Washington across two years. Bd prevalence and intensity were measured in 376 frogs, revealing a prevalence of 69%, but generally low infection intensity (Mean = 127 Bd zoospore equivalents among infected frogs). Skin bacterial communities were characterized in 92 frogs using 16S rRNA gene amplicon sequencing. Our results indicated correlations of decreasing Shannon diversity and evenness as infection intensity increased. Latitude was correlated with bacterial richness and Faith's Phylogenetic Diversity measures, indicating increased diversity in northern locations. Beta diversity (UniFrac) analyses revealed that skin microbiomes were distinct between infected and uninfected frogs, and infection intensity had a significant effect on microbiome composition. Site explained the majority of microbiome variation (weighted UniFrac: 57.5%), suggesting a combination of local habitat conditions explain variation, as only small proportions of variation could be explained by year, month, temperature, elevation, and latitude individually. Bacterial genera with potential for Bd-inhibitory properties were found with differential relative abundance in infected and uninfected frogs, with higher Stenotrophomonas and lower Pseudomonas relative abundance observed in infected frogs. Further study may indicate if Bd inhibition by members of the skin microbiome is an influence behind the low infection intensities observed and whether low Bd infection intensities are capable of altering skin microbiome composition.

Numbers of fish species, higher taxa, and phylogenetic similarity decrease with latitude and depth, and deep-sea assemblages are unique.

Species richness has been found to increase from the poles to the tropics but with a small dip near the equator over all marine fishes. Phylogenetic diversity measures offer an alternative perspective on biodiversity linked to evolutionary history. If phylogenetic diversity is standardized for species richness, then it may indicate places with relatively high genetic diversity. Latitudes and depths with both high species and phylogenetic diversity would be a priority for conservation. We compared latitudinal and depth gradients of species richness, and three measures of phylogenetic diversity, namely average phylogenetic diversity (AvPD), the sum of the higher taxonomic levels (STL) and the sum of the higher taxonomic levels divided by the number of species (STL/spp) for modelled ranges of 5,619 marine fish species. We distinguished all, bony and cartilaginous fish groups and four depth zones namely: whole water column; 0 -200 m; 201-1,000 m; and 1,001-6,000 m; at 5° latitudinal intervals from 75°S to 75°N, and at 100 m depth intervals from 0 m to 3,500 m. Species richness and higher taxonomic richness (STL) were higher in the tropics and subtropics with a small dip at the equator, and were significantly correlated among fish groups and depth zones. Species assemblages had closer phylogenetic relationships (lower AvPD and STL/spp) in warmer (low latitudes and shallow water) than colder environments (high latitudes and deep sea). This supports the hypothesis that warmer shallow latitudes and depths have had higher rates of evolution across a range of higher taxa. We also found distinct assemblages of species in different depth zones such that deeper sea species are not simply a subset of shallow assemblages. Thus, conservation needs to be representative of all latitudes and depth zones to encompass global biodiversity.

Spaces of Phylogenetic Diversity Indices: Combinatorial and Geometric Properties

Biodiversity is a concept most naturally quantified and measured across sets of species. However, for some applications, such as prioritising species for conservation efforts, a species-by-species approach is desirable. Phylogenetic diversity indices are functions that apportion the total biodiversity value of a set of species across its constituent members. As such, they aim to measure each species’ individual contribution to, and embodiment of, the diversity present in that set. However, no clear definition exists that encompasses the diversity indices in current use. This paper presents conditions that define diversity indices arising from the phylogenetic diversity measure on rooted phylogenetic trees. In this context, the diversity index ‘score’ given to a species represents a measure of its unique and shared evolutionary history as displayed in the underlying phylogenetic tree. Our definition generalises the diversity index notion beyond the popular Fair Proportion and Equal-Splits indices. These particular indices may now be seen as two points in a convex space of possible diversity indices, for which the boundary conditions are determined by the underlying shape of each phylogenetic tree. We calculated the dimension of the convex space associated with each tree shape and described the extremal points.

Phylogenetic diversity statistics for all clades in a phylogeny.

The classic quantitative measure of phylogenetic diversity (PD) has been used to address problems in conservation biology, microbial ecology, and evolutionary biology. PD is the minimum total length of the branches in a phylogeny required to cover a specified set of taxa on the phylogeny. A general goal in the application of PD has been identifying a set of taxa of size k that maximize PD on a given phylogeny; this has been mirrored in active research to develop efficient algorithms for the problem. Other descriptive statistics, such as the minimum PD, average PD, and standard deviation of PD, can provide invaluable insight into the distribution of PD across a phylogeny (relative to a fixed value of k). However, there has been limited or no research on computing these statistics, especially when required for each clade in a phylogeny, enabling direct comparisons of PD between clades. We introduce efficient algorithms for computing PD and the associated descriptive statistics for a given phylogeny and each of its clades. In simulation studies, we demonstrate the ability of our algorithms to analyze large-scale phylogenies with applications in ecology and evolutionary biology. The software is available at https://github.com/flu-crew/PD_stats.

Range restricted old and young lineages show the southern Western Ghats to be both a museum and a cradle of diversity for woody plants.

The Western Ghats (WG) mountain chain is a global biodiversity hotspot with high diversity and endemicity of woody plants. The latitudinal breadth of the WG offers an opportunity to determine the evolutionary drivers of latitudinal diversity patterns. We examined the spatial patterns of evolutionary diversity using complementary phylogenetic diversity and endemism measures. To examine if different regions of the WG serve as a museum or cradle of evolutionary diversity, we examined the distribution of 470 species based on distribution modelling and occurrence locations across the entire region. In accordance with the expectation, we found that the southern WG is both a museum and cradle of woody plant evolutionary diversity, as a higher proportion of both old and young evolutionary lineages are restricted to the southern WG. The diversity gradient is likely driven by high geo-climatic stability in the south and phylogenetic niche conservatism for moist and aseasonal sites. This is corroborated by persistent lineage nestedness at almost all evolutionary depths (10-135 million years), and a strong correlation of evolutionary diversity with drought seasonality, precipitation and topographic heterogeneity. Our results highlight the global value of the WG, demonstrating, in particular, the importance of protecting the southern WG-an engine of plant diversification and persistence.

Assessing taxonomic, functional and phylogenetic diversity of giant clams across the Indo‐Pacific for conservation prioritization

AbstractAimGiant clams are iconic bivalves known to serve numerous ecological roles contributing to the functioning of coral reef ecosystems. In the next decade, giant clams will continue to face critical anthropogenic pressures from over‐exploitation for their meat and shells, the aquarium trade and global warming that threaten the persistence of their species. Here, we assess the relationships between different biodiversity components to inform conservation prioritization and management.LocationIndo‐Pacific marine realm.MethodsWe quantified taxonomic, functional and phylogenetic diversity measures throughout 25 marine provinces and assessed their relationships for all 12 giant clam species in the subfamily Tridacninae. These biodiversity measures were used to identify potentially threatened species that contribute disproportionately to trait and evolutionary diversity and to highlight areas for global conservation prioritization of giant clam species.ResultsAnalyses show positive correlations among species richness (SR), functional diversity (FD) and phylogenetic diversity (PD), with the strongest relationship between FD and PD. However, spatial patterns of higher‐than‐expected FD and PD are incongruent with SR patterns, indicating that SR omits information associated with functional and phylogenetic diversity. Among the giant clam species, Tridacna gigas and Hippopus spp. have the greatest functional and evolutionary diversity contributions within assemblies, respectively. Spatial analyses reveal that the Bay of Bengal, Andaman and numerous parts of the eastern Indo‐Pacific potentially hold higher‐than‐expected FD and PD levels relative to their SR and thus warrant more attention with respect to conserving the diversity of giant clams.ConclusionsOur findings underscore the importance of integrating functional trait contributions and evolutionary diversity into conservation planning to better differentiate giant clam assemblages, as it remains challenging to implement dedicated conservation given the limited resources. This study provides comprehensive biodiversity information for managers to initiate measures that holistically capture species' ecological and evolutionary standings across global reef ecosystems.

Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig.

Intensive farming practices can increase exposure of animals to infectious agents against which antibiotics are used. Orally administered antibiotics are well known to cause dysbiosis. To counteract dysbiotic effects, numerous studies in the past two decades sought to understand whether probiotics are a valid tool to help re-establish a healthy gut microbial community after antibiotic treatment. Although dysbiotic effects of antibiotics are well investigated, little is known about the effects of intramuscular antibiotic treatment on the gut microbiome and a few studies attempted to study treatment effects using phylogenetic diversity analysis techniques. In this study we sought to determine the effects of two probiotic- and one intramuscularly administered antibiotic treatment on the developing gut microbiome of post-weaning piglets between their 3rd and 9th week of life. Shotgun metagenomic sequences from over 800 faecal time-series samples derived from 126 post-weaning piglets and 42 sows were analysed in a phylogenetic framework. Differences between individual hosts such as breed, litter, and age, were found to be important contributors to variation in the community composition. Host age was the dominant factor in shaping the gut microbiota of piglets after weaning. The post-weaning pig gut microbiome appeared to follow a highly structured developmental program with characteristic post-weaning changes that can distinguish hosts that were born as little as two days apart in the second month of life. Treatment effects of the antibiotic and probiotic treatments were found but were subtle and included a higher representation of Mollicutes associated with intramuscular antibiotic treatment, and an increase of Lactobacillus associated with probiotic treatment. The discovery of correlations between experimental factors and microbial community composition is more commonly addressed with OTU-based methods and rarely analysed via phylogenetic diversity measures. The latter method, although less intuitive than the former, suffers less from library size normalization biases, and it proved to be instrumental in this study for the discovery of correlations between microbiome composition and host-, and treatment factors.

Phylogenetic clustering of tree communities decreases with stand age and environmental quality along a mineland rehabilitation chronosequence

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.

RecPD: A Recombination-aware measure of phylogenetic diversity.

A critical step in studying biological features (e.g., genetic variants, gene families, metabolic capabilities, or taxa) is assessing their diversity and distribution among a sample of individuals. Accurate assessments of these patterns are essential for linking features to traits or outcomes of interest and understanding their functional impact. Consequently, it is of crucial importance that the measures employed for quantifying feature diversity can perform robustly under any evolutionary scenario. However, the standard measures used for quantifying and comparing the distribution of features, such as prevalence, phylogenetic diversity, and related approaches, either do not take into consideration evolutionary history, or assume strictly vertical patterns of inheritance. Consequently, these approaches cannot accurately assess diversity for features that have undergone recombination or horizontal transfer. To address this issue, we have devised RecPD, a novel recombination-aware phylogenetic-diversity statistic for measuring the distribution and diversity of features under all evolutionary scenarios. RecPD utilizes ancestral-state reconstruction to map the presence / absence of features onto ancestral nodes in a species tree, and then identifies potential recombination events in the evolutionary history of the feature. We also derive several related measures from RecPD that can be used to assess and quantify evolutionary dynamics and correlation of feature evolutionary histories. We used simulation studies to show that RecPD reliably reconstructs feature evolutionary histories under diverse recombination and loss scenarios. We then applied RecPD in two diverse real-world scenarios including a preliminary study type III effector protein families secreted by the plant pathogenic bacterium Pseudomonas syringae and growth phenotypes of the Pseudomonas genus and demonstrate that prevalence is an inadequate measure that obscures the potential impact of recombination. We believe RecPD will have broad utility for revealing and quantifying complex evolutionary processes for features at any biological level.

Functional diversity of Himalayan bat communities declines at high elevation without the loss of phylogenetic diversity

Species richness exhibits well-known patterns across elevational gradients in various taxa, but represents only one aspect of quantifying biodiversity patterns. Functional and phylogenetic diversity have received much less attention, particularly for vertebrate taxa. There is still a limited understanding of how functional, phylogenetic and taxonomic diversity change in concert across large gradients of elevation. Here, we focused on the Himalaya—representing the largest elevational gradients in the world—to investigate the patterns of taxonomic, functional and phylogenetic diversity in a bat assemblage. Combining field data on species occurrence, relative abundance, and functional traits with measures of phylogenetic diversity, we found that bat species richness and functional diversity declined at high elevation but phylogenetic diversity remained unchanged. At the lowest elevation, we observed low functional dispersion despite high species and functional richness, suggesting a niche packing mechanism. The decline in functional richness, dispersion, and divergence at the highest elevation is consistent with patterns observed due to environmental filtering. These patterns are driven by the absence of rhinolophid bats, four congeners with extreme trait values. Our data, some of the first on mammals from the Himalayan region, suggest that in bat assemblages with relatively high species diversity, phylogenetic diversity may not be a substitute to measure functional diversity.

Does anthropogenic fragmentation selectively filter avian phylogenetic diversity in a critically endangered forest system?

SummaryDocumenting phylogenetic diversity for conservation practice allows elucidation of ecosystem functioning and processes by highlighting the commonality and divergence of species’ functional traits within their evolutionary context. Conserving distinct evolutionary histories has intrinsic value, and the conservation of phylogenetically diverse communities is more likely to preserve distinct or relic evolutionary lineages. We explored the potential for anthropogenic forest fragmentation to act as a selective filter of avian phylogenetic diversity within the community of forest-dependent birds of the critically endangered Indian Ocean Coastal Belt Forest (IOCBF), South Africa. We conducted avian point count surveys during the austral breeding season, and calculated fragmentation metrics of forest structural complexity, patch size and isolation. We constructed a maximum likelihood phylogeny using the combined analysis of two mitochondrial genes and three nuclear markers and measured the influence of the fragmentation metrics on six measures of phylogenetic diversity. Our results indicated that the avian community was variously affected by anthropogenic forest fragmentation, with the different metrics of phylogenetic diversity responding with no definitive overall pattern. However, forest structural complexity emerged as an important metric explaining phylogenetic structuring. While the avian community’s phylogenetic diversity displayed resilience to anthropogenic fragmentation, previous research showed a reduction in functional diversity along the fragmentation gradient. Therefore, we recommend studies that especially aim to guide conservation management, incorporate both phylogenetic and functional diversity measures to sufficiently interrogate communities’ resilience to the threats under investigation.

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

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

Effects of dam construction and fish invasion on the species, functional and phylogenetic diversity of fish assemblages in the Yellow River Basin

An understanding of the consequences of human-mediated disturbances from multi-facet diversity (i.e. species, functional and phylogenetic) perspectives is of great significance in biodiversity assessment and conservation planning. Most previous studies have concentrated on anthropogenic effects on species diversity in the Yellow River Basin (YRB) in China, but information on anthropogenic effects on phylogenetic and functional facets is still pending. Here, we identified the temporal changes in species, functional, and phylogenetic alpha diversity of fish assemblages in 18 reaches (i.e. 15 mainstream reaches and 3 tributaries) of the YRB under the background of long-term cascade hydropower construction and widespread introduction of non-native fish species. The results showed that native fishes experienced a sharp decline through time, with an average of 25.6 (extirpation rate 46.7%) native species extirpated per sub-region, and 89 of 182 (48.9%) native species extirpated across the whole basin during the period considered. However, the number of non-native fish species substantially increased, with an average increase of 8.6 species (invasion rate 26.9%) per sub-region. Furthermore, the percentage of non-native species showed a significant unimodal relationship with average altitude, with highest invasion rates (ca. 70%) in upstream reaches. The extirpation rate was negatively related to altitude, increasing from upstream to downstream reaches. Interestingly, the functional diversity indices (FEve, FDiv, FDis, RaoQ) and phylogenetic diversity indices (Δ+ and Λ+) of the entire fish fauna significantly increased through time, whereas these indices based on native fish fauna only did not change. Such increases in functional and phylogenetic diversities were mainly triggered by introductions of non-native species, which were functionally distinct and phylogenetically distant from native species, and extirpation of congeneric endemic species. In general, the present study revealed anthropogenic impacts on the multi-faceted diversity of fish assemblages in a large river and highlighted the negative effects of cascaded hydropower developments and non-native fish invasions on native fish. Moreover, evaluating the responses of multi-faceted diversity to anthropogenic disturbances is a suitable means to understand assemblage reorganization and to assess how such impacts lead to the decline of biodiversity. The complementary information derived from using the multi-faceted diversity approach indicate functional and phylogenetic diversity measures could be implemented in biodiversity planning in the sediment-laden and ecologically important Yellow River Basin.

Insect biomass is not a consistent proxy for biodiversity metrics in wild bees

Recent studies have reported on dramatic cases of aerial insect population declines by focusing on the measure of the total biomass of caught insects. However, there is currently no consensus about how biomass patterns among sites and habitats might consistently capture the subtleties of changes in aerial insect community structure. Here, we investigated the relationship between the total biomass of wild bees collected using pan traps in urban, agricultural, and semi-natural habitats on one hand, and a spectrum of biodiversity metrics on the other hand, particularly species richness (SR), alpha diversity, functional diversity (FD) and three different forms of phylogenetic diversity (PD). Our results indicate that although biomass is significantly and highly correlated with the abundance of wild bees, it is generally significantly but only moderately and non-linearly correlated to the various facets of wild bee diversity among habitats. By contrast, we also found that all three measures of PD used are consistent across habitats, suggesting that a taxonomic hierarchy based on Linnaean classification could be used as a proxy for the measurement of PD in wild bees, particularly in other well-studied areas such as Western Europe where a multi-gene molecular phylogeny is unavailable as yet. Collectively, our results illustrate the clear limitations of biodiversity monitoring through measures of trapped insects biomass. We advocate for more robust measures of biodiversity trends in wild bees, requiring both standardized surveys, and the identification of caught specimens down to the species level to capture the subtleties of species, traits-based and phylogeny-based community changes across habitats or time. Scaling out this approach is an essential prerequisite for more global conservation planning tailored to the ecological requirements of the targeted insect species.

Phylogenetic diversity metrics from molecular phylogenies: modelling expected degree of error under realistic rate variation

AbstractAimPhylogenetic diversity or phylo‐diversity measures use information about evolutionary history and relationships to inform conservation priorities. These metrics are usually derived from the branches of molecular phylogenies. But inferring phylogenetic timescale from molecular data relies on many assumptions about the evolutionary process, most of which are based on statistical convenience rather than biological information. Here we ask whether known patterns of variation in rate of molecular evolution can lead to errors in phylo‐diversity measures.LocationGlobal.MethodsWe generated sequences with biologically realistic rate variation, parameterized by empirically well‐supported relationships between species traits, macroevolutionary patterns and rate of molecular evolution. We then tested how well commonly used phylo‐diversity measures from these phylogenies reflected the true evolutionary history.ResultsWe show that reconstructed Faith’s phylogenetic diversity (FPD) measures differ from true values by an average of about 10% and up to 38%. Species rankings based on evolutionary distinctness (ED) are also affected by rate variation, with the ranks of taxa changing by up to 10‐11 positions after estimation.Main conclusionsWe have shown that realistic levels of rate variation can generate error in FPD and ED measures that could potentially influence prioritization ranking. Studies using metrics based on molecular phylogenetic branch lengths should consider the likely effect of uncertainty in phylogenetic reconstruction on their conclusions.