The components of biodiversity,with a particular focus on phylogenetic information

We present a framework for biodiversity metrics that organizes the growing panoply of metrics. Our framework distinguishes metrics based on the type of information–abundance, phylogeny, function–and two common properties–magnitude and variability. Our new metrics of phylogenetic diversity are based on a partition of the total branch lengths of a cladogram into the proportional share of each species, including: a measure of divergence which standardizes the amount of evolutionary divergence by species richness and time depth of the cladogram; a measure of regularity which is maximal when the tree is perfectly symmetrical so that all species have the same proportional branch lengths; a measure that combines information on the magnitude and variability of abundance with phylogenetic variability, and a measure of phylogenetically weighted effective mean abundance; and indicate how those metrics can be decomposed into α and β components. We illustrate the utility of these new metrics using empirical data on the bat fauna of Manu, Peru. Divergence was greatest in lowland rainforest and at the transition between cloud and elfin forests, and least in upper elfin forests and in cloud forests. In contrast, regularity was greatest in lowland rainforest, dipping to its smallest values in mid‐elevation cloud forests, and then increasing in high elevation elfin forests. These patterns indicate that the first species to drop out with increasing elevation are ones that are closely related to other species in the metacommunity. Measures of the effective number of phylogenetically independent or distinct species decreased very rapidly with elevation, and β‐diversity was larger. In contrast, a comparison of feeding guilds shows a different effect of phylogenetic patterning. Along the elevational gradient, each guild generally loses some species from each clade–rather than entire clades–explaining the maintenance of functional diversity as phylogenetic diversity decreases.     

Evaluation of an Integrated Framework for Biodiversity with a New Metric for Functional Dispersion

Growing interest in understanding ecological patterns from phylogenetic and functional perspectives has driven the development of metrics that capture variation in evolutionary histories or ecological functions of species. Recently, an integrated framework based on Hill numbers was developed that measures three dimensions of biodiversity based on abundance, phylogeny and function of species. This framework is highly flexible, allowing comparison of those diversity dimensions, including different aspects of a single dimension and their integration into a single measure. The behavior of those metrics with regard to variation in data structure has not been explored in detail, yet is critical for ensuring an appropriate match between the concept and its measurement. We evaluated how each metric responds to particular data structures and developed a new metric for functional biodiversity. The phylogenetic metric is sensitive to variation in the topology of phylogenetic trees, including variation in the relative lengths of basal, internal and terminal branches. In contrast, the functional metric exhibited multiple shortcomings: (1) species that are functionally redundant contribute nothing to functional diversity and (2) a single highly distinct species causes functional diversity to approach the minimum possible value. We introduced an alternative, improved metric based on functional dispersion that solves both of these problems. In addition, the new metric exhibited more desirable behavior when based on multiple traits.     

Phylogenetic diversity metrics for ecological communities: integrating species richness, abundance and evolutionary history

Phylogenetic information is increasingly being used to understand the assembly of biological communities and ecological processes. However, commonly used metrics of phylogenetic diversity (PD) do not incorporate information on the relative abundances of individuals within a community. In this study, we develop three indices of PD that explicitly consider species abundances. First, we present a metric of phylogenetic-abundance evenness that evaluates the relationship between the abundance and the distribution of terminal branch lengths. Second, we calculate an index of hierarchical imbalance of abundances at the clade level encapsulating the distribution of individuals across the nodes in the phylogeny. Third, we develop an index of abundance-weighted evolutionary distinctiveness and generate an entropic index of phylogenetic diversity that captures both information on evolutionary distances and phylogenetic tree topology, and also serves as a basis to evaluate species conservation value. These metrics offer measures of phylogenetic diversity incorporating different community attributes. We compare these new metrics to existing ones, and use them to explore diversity patterns in a typical California annual grassland plant community at the Jasper Ridge biological preserve.
Ecology Letters (2010) 13: 96–105     

Taxonomic,functional, and phylogenetic dimensions of rodent biodiversity along an extensive tropical elevational gradient

Relationships among taxonomic, functional, and phylogenetic dimensions of biodiversity provide insight about the relative contributions of ecological and evolutionary processes in structuring local assemblages. We used data for rodent species distributions from an extensive tropical elevational gradient to 1) describe elevational gradients for each of three dimensions of biodiversity, 2) evaluate the sufficiency of species richness as a surrogate for other dimensions, and 3) quantify the relative support for mechanisms that increase or decrease phylogenetic or functional dispersion. Taxonomic biodiversity was quantified by species richness, as well as by richness, evenness, diversity, dominance, and rarity at generic and familial levels. Morphological and categorical traits were used to estimate functional biodiversity, and an ultrametric mammalian supertree was used as the basis for estimating phylogenetic biodiversity. Elevational gradients of each dimension of biodiversity were strong, with significant linear and non‐linear components based on orthogonal polynomial regression. Empirical linear and non‐linear regression components were consistently different than those expected based on species richness for generic, familial, and phylogenetic biodiversity, but not for functional biodiversity. Nevertheless, the congruence of dimensions of biodiversity based on correlation analyses indicated that any one dimension is a useful surrogate for the other dimensions for rodents at Manu. Given variation in species richness, assemblages from lowland rainforests comprised more biodiversity than expected, whereas assemblages from cloud and elfin forests represented less biodiversity than expected. Warm temperatures, vertical complexity of the vegetation, and high productivity likely facilitate niche differentiation in rainforests, whereas cricetid rodents are competitively superior to other clades in the less structurally complex, less productive, and colder, high elevation habitats.     

Phylogenetic Patterns of Extinction Risk in the Eastern Arc Ecosystems,an African Biodiversity Hotspot

There is an urgent need to reduce drastically the rate at which biodiversity is declining worldwide. Phylogenetic methods are increasingly being recognised as providing a useful framework for predicting future losses, and guiding efforts for pre-emptive conservation actions. In this study, we used a reconstructed phylogenetic tree of angiosperm species of the Eastern Arc Mountains – an important African biodiversity hotspot – and described the distribution of extinction risk across taxonomic ranks and phylogeny. We provide evidence for both taxonomic and phylogenetic selectivity in extinction risk. However, we found that selectivity varies with IUCN extinction risk category. Vulnerable species are more closely related than expected by chance, whereas endangered and critically endangered species are not significantly clustered on the phylogeny. We suggest that the general observation for taxonomic and phylogenetic selectivity (i.e. phylogenetic signal, the tendency of closely related species to share similar traits) in extinction risks is therefore largely driven by vulnerable species, and not necessarily the most highly threatened. We also used information on altitudinal distribution and climate to generate a predictive model of at-risk species richness, and found that greater threatened species richness is found at higher altitude, allowing for more informed conservation decision making. Our results indicate that evolutionary history can help predict plant susceptibility to extinction threats in the hyper-diverse but woefully-understudied Eastern Arc Mountains, and illustrate the contribution of phylogenetic approaches in conserving African floristic biodiversity where detailed ecological and evolutionary data are often lacking.     

Joint effect of phylogenetic relatedness and trait selection on the elevational distribution of Rhododendron species

Congeneric species may coexist at fine spatial scales through niche differentiation, however, the magnitude to which the effects of functional traits and phylogenetic relatedness contribute to their distribution along elevational gradients remains understudied. To test the hypothesis that trait and elevational range overlap can affect local speciesʼ coexistence, we first compared phylogenetic relatedness and trait (including morphological traits and leaf elements) divergence among closely related species of Rhododendron L. on Yulong Mountain, China. We then assessed relationships between the overlap of multiple functional traits and the degree of elevational range overlap among species pairs in a phylogenetic context. We found that phylogeny was a good predictor for most functional traits, where closely related species showed higher trait similarity and occupied different elevational niches at our study site. Species pairs of R. subgen. Hymenanthes (Blume) K. Koch showed low elevational range overlap and some species pairs of R. subgen. Rhododendron showed obvious niche differentiation. Trait divergence is greater for species in R. subgen. Rhododendron, and it plays an important role between species pairs with low elevational range overlap. Trait convergent selection takes place between co-occurring closely related species that have high elevational range overlap, which share more functional trait space due to environmental filtering or ecological adaptation in more extreme habitats. Our results highlight the importance of evolutionary history and trait selection for species coexistence at fine ecological scales along environmental gradients.     

Host abundance,durability, basidiome form and phylogenetic isolation determine fungivore species richness

Species with close associations to a specific host species, such as parasites and phytophages, make immense contributions to biodiversity. Hence, factors determining the variation in species richness among hosts are a main focus of ecological research. Investigations of determining factors of fungivorous species among host species are still scarce. Based on ecological patterns of parasites and phytophages, we hypothesized that the species richness of tree‐fungus beetles of the family Ciidae (Coleoptera) would increase with increasing basidiome size, niche diversity of the growth form, durability, increasing abundance and decreasing phylogenetic isolation of the host fungus. Our generalized least‐squares model, controlled by host phylogeny, revealed that Ciidae species richness increases with host abundance, but decreases with host phylogenetic isolation. In contrast with our prediction, Ciidae species richness was higher in annual basidiomes than in perennials. Pileate basidiomes revealed higher species richness than resupinate and stipitate basidiomes, which may be interpreted as being a result of their higher host niche diversity. The importance of host abundance, measured on the landscape scale, corroborates that fungivore species richness among macrofungal hosts is determined by factors similar to those that determine parasite and phytophage species richness among their hosts. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 699–708.     

生态学的多样性指数:功能与系统发育

生物多样性是生态学的核心问题。传统的多样性指数仅包含物种数和相对多度的信息,这类基于分类学的多样性指数并不能很好地帮助理解群落构建和生态系统功能。不同物种对群落构建和生态系统功能所起到的作用类型和贡献也不完全相同,且物种在生态过程中的作用和贡献往往与性状密切相关,因此功能多样性已经成为反映物种群落构建、干扰以及环境因素对群落影响的重要指标。同时,由于亲缘关系相近的物种往往具有相似的性状,系统发育多样性也可以作为功能多样性的一个替代。功能多样性和系统发育多样性各自具有优缺点,但二者均比分类多样性更能揭示群落和生态系统的构建、维持与功能。     

The spatial structure of phylogenetic and functional diversity in the United States and Canada: An example using the sedge family (Cyperaceae)

Systematically quantifying diversity across landscapes is necessary to understand how clade history and ecological heterogeneity contribute to the origin, distribution, and maintenance of biodiversity. Here, we chart the spatial structure of diversity among all species in the sedge family (Cyperaceae) throughout the USA and Canada. We first identify areas of remarkable species richness, phylogenetic diversity, and functional trait diversity, and highlight regions of conservation priority. We then test predictions about the spatial structure of this diversity based on the historical biogeography of the family. Incorporating a phylogeny, over 400 000 herbarium records, and a database of functional traits mined from online floras, we find that species richness and functional trait diversity peak in the Northeastern USA, while phylogenetic diversity peaks along the Gulf of Mexico. Floristic turnover among assemblages increases significantly with distance, but phylogenetic turnover is twice as rapid along latitudinal gradients as along longitudinal gradients. These patterns reflect the expected distribution of Cyperaceae, which originated in the tropics but radiated in temperate regions. We identify assemblages with an abundance of rare, range‐restricted lineages, and assemblages composed of species generally lacking from diverse regions. We argue that both of these metrics are useful for developing targeted conservation strategies. We use the data generated here to establish future research priorities, including the testing of a series of hypotheses regarding the distribution of chromosome numbers, photosynthetic pathways, and resource partitioning in sedges.     

Shotgun mitogenomics across body size classes in a local assemblage of tropical Diptera: Phylogeny,species diversity and mitochondrial abundance spectrum

Mitochondrial genomes can be assembled readily from shotgun‐sequenced DNA mixtures of mass‐trapped arthropods (“mitochondrial metagenomics”), speeding up the taxonomic characterization. Bulk sequencing was conducted on some 800 individuals of Diptera obtained by canopy fogging of a single tree in Borneo dominated by small (<1.5 mm) individuals. Specimens were split into five body size classes for DNA extraction, to equalize read numbers across specimens and to study how body size, a key ecological trait, interacts with species and phylogenetic diversity. Genome assembly produced 304 orthologous mitochondrial contigs presumed to each represent a different species. The small‐bodied fraction was the by far most species‐rich (187 contigs). Identification of contigs was through phylogenetic analysis together with 56 reference mitogenomes, which placed most of the Bornean community into seven clades of small‐bodied species, indicating phylogenetic conservation of body size. Mapping of shotgun reads against the mitogenomes showed wide ranges of read abundances within each size class. Ranked read abundance plots were largely log‐linear, indicating a uniformly filled abundance spectrum, especially for small‐bodied species. Small‐bodied species differed greatly from other size classes in neutral metacommunity parameters, exhibiting greater levels of immigration, besides greater total community size. We suggest that the established uses of mitochondrial metagenomics for analysis of species and phylogenetic diversity can be extended to parameterize recent theories of community ecology and biodiversity, and by focusing on the number mitochondria, rather than individuals, a new theoretical framework for analysis of mitochondrial abundance spectra can be developed that incorporates metabolic activity approximated by the count of mitochondria.     

High evolutionary and functional distinctiveness of endemic monocots in world islands

Functionally and evolutionarily distinct species have traits or an evolutionary history that are shared by few others in a given set, which make them priority species for biodiversity conservation. On islands, life in isolation has led to the evolution of many distinct forms and functions as well as to a high level of endemism. The aim of this study is to assess the evolutionary and functional distinctiveness of insular monocotyledons and their distribution across 126 islands worldwide. We show that evolutionary and functional distinctiveness are decoupled but that both are higher on islands than on continental areas. Anagenesis on islands followed by extinctions and/or diversification on the mainland may have led to highly evolutionarily distinct species while functionally distinct species may have arisen from ecological niche shift or niche expansion. Insular endemic species with high evolutionary distinctiveness but not with high functional distinctiveness are significantly range-restricted compared to less distinct species, possibly indicating differences in dispersal potential. By showing that distinctiveness is high on islands and that the most distinct species are range-restricted, our study has important conservation implications. Indeed, islands are among the most threatened systems of the world, and extinctions of the most distinct species could lead to significant loss of phylogenetic and functional diversity.

     

Phylogenetic generalised dissimilarity modelling: a new approach to analysing and predicting spatial turnover in the phylogenetic composition of communities

Compared to species turnover, patterns of phylogenetic turnover provide extra information about the spatial structure of biodiversity, for example providing more informative comparisons between the biota of sites which share no species. To harness this information for broad‐scale spatial analysis, we present phylo‐GDM, a technique for interpolating the spatial structure of phylogenetic turnover between sampled locations in relation to environment, based on generalised dissimilarity modelling (GDM). Using a database of over 150 000 location records for 114 myobatrachid frog species in Australia, linked to a species‐level phylogeny inferred from 2467 base pairs of mitochondrial DNA, we calculated species and phylogenetic turnover between pairs of sites. We show how phylogenetic turnover extended the range of informative comparison of compositional turnover to more biologically and environmentally dissimilar sites. We generated GDM models which predict species and phylogenetic turnover across Australia, and tested the fit of models for different ages within the phylogeny to find the phylogenetic tree depth at which the relationship to current day environment is greatest. We also incorporated explanatory variables based on biogeographic patterns, to represent broad‐scale turnover resulting from divergent evolutionary histories. We found that while the predictive power of our models was lower for full phylogenetic turnover than for species turnover, models based on the more recent components of the phylogeny (closer to the tips) outperformed species models and full phylogenetic models. Phylo‐GDM has considerable potential as a method for incorporating phylogenetic relationships into biodiversity analyses in ways not previously possible. Because phylogenies do not require named taxa, phylo‐GDM may also provide a means of including lineages with poorly resolved taxonomy (e.g. from metagenomic sequencing) into biodiversity planning and phylogeographic analysis.     

Spatial evolutionary and ecological vicariance analysis (SEEVA), a novel approach to biogeography and speciation research,with an example from Brazilian Gentianaceae

Aim Spatial evolutionary and ecological vicariance analysis (SEEVA) is a simple analytical method that evaluates environmental or ecological divergence associated with evolutionary splits. It integrates evolutionary hypotheses, phylogenetic data, and spatial, temporal, environmental and geographical information to elucidate patterns. Using a phylogeny of Prepusa Mart. and Senaea Taub. (Angiospermae: Gentianaceae), SEEVA is used to describe the radiation and ecological patterns of this basal gentian group across south‐eastern Brazil. Location Latin America, global. Methods Environmental data for 151 geolocated botanical collections, associated with specimens from seven species, were compiled with Arc GIS, and were matched with geolocated base layers of eight climatological variables, as well as one each of geological, soil type, elevational and vegetation variables. Sister groups were defined on the basis of the six nested nodes that defined the phylogenetic tree of these two genera. A (0, 1)‐scaled divergence index (D) was defined and tested for each of 12 environmental and for each of the six phylogenetic nodes, by means of contingency analyses. We contrast divergence indices of nested clades, allopatric and sympatric sister clades. Results The level of ecological divergence between sister clades/species, defined in terms of D measures, was substantial for five of six nodes, with 21 of 72 environmental comparisons having D > 0.75. Soil types and geological age of bedrock were strongly divergent only for basal nodes in the phylogeny, by contrast with temperature and precipitation, which exhibited strong divergence at all nodes. There has been strong divergence and progressive occupation of wetter and colder habitats throughout the history of Prepusa. Nodes separating allopatric sister clades exhibited larger niche divergence than did those separating sympatric sister clades. Main conclusions SEEVA provides a multi‐source, direct analysis method for correlating field collections, phylogenetic hypotheses, species distributions and georeferenced environmental data. Using SEEVA, it was possible to quantify and test the divergence between sister lineages, illustrating both niche conservatism and ecological specialization. SEEVA permits elucidation of historical and ecological vicariance for evolutionary lineages, and is amenable to wide application, taxonomically, geographically and ecologically.     

The need for the incorporation of phylogeny in the measurement of biological diversity,with special reference to ecosystem functioning research

Defining and measuring biodiversity is an important research area in biology, with very interesting theoretical and applied aspects. Numerous definitions have been proposed, and these definitions of biodiversity influence how it is measured. From the still commonly used measure of species diversity, through higher taxon diversity, molecular measures, ecological measures and indicator taxa, these measures have as their fundamental shortcoming the lack of an explicit consideration of the evolutionary context represented by phylogenies. Attempts have been made to incorporate phylogenetic considerations into measuring biodiversity, but more hypothesis‐driven research needs to be done. A specific case study is presented of how this added emphasis on phylogeny‐based biodiversity measurement can influence the way in which research is directed and hypotheses are generated. The elucidation of the relationship of biodiversity to ecosystem functioning is a very timely concern with the unarguable loss of biodiversity this planet is experiencing, whichever way biodiversity is measured.     

Disentangling phylogenetic from non‐phylogenetic functional structure of bird assemblages in a tropical dry forest

Understanding the factors driving assembling structure of ecological communities remains a fundamental problem in ecology, especially when focusing on ecological and evolutionary relatedness among species rather than on their taxonomic identity. It remains critical though to separate the patterns and drivers of phylogenetic and functional structures, because traits are phylogenetically constrained, but phylogeny alone does not fully reflect trait variability among species. Using birds from the Brazilian dry forest as a study case, we employed two different approaches to decompose functional structure into its components that are shared and non‐shared with the phylogenetic structure. We investigated the spatial pattern and environmental hypotheses for these phylogenetically constrained and unconstrained aspects of functional structure, including climate‐induced physiological constraints, historical climatic stability, resource availability and habitat partitioning. We found only partial congruence between the two methods of structure decomposition. Still, we found a differential effect of factors on specific components of functional structure of bird assemblages. While climate affects phylogenetically constrained traits through endurance, habitat partitioning (especially forest cover) affects the functional structure that is independent of phylogeny. With this strategy, we were able to decompose the patterns and drivers of the functional structure of birds along a semiarid gradient and showed that the decomposition of the functional structure into its phylogenetic and non‐phylogenetic counterparts can offer a more complete portrait of the assembling rules in ecological communities. We claim for a further development and use of this sort of strategy to investigate assembling rules in ecological communities.     

Extrinsic environmental factors,not resident diversity itself,lead to invasion of <Emphasis Type="Italic">Ageratum conyzoides</Emphasis> L. in diverse communities

The relationship between diversity and invasibility might be confounded by extrinsic environmental factors and the evolutionary structure of the resident community. To examine the role of extrinsic environmental factors, species and phylogenetic diversity in regulating community susceptibility to invasion, we established 109 plots either with or without Ageratum conyzoides L. in Liandu, China. We identified all the species in our samples, weighed the aboveground biomass of each species, and measured environmental variables. For all species recorded in our survey, we constructed a community phylogeny using PhytoPhylo mega-phylogeny as a backbone. We selected the best-fit environment model based on the minimum corrected Akaike information criteria score to examine the effect of extrinsic environmental variables on the relative abundance of A. conyzoides. Relationship between biodiversity and invasion of A. conyzoides was examined by a multiple regression, in which extrinsic ecological factors and biodiversity were combined to predict the relative abundance of A. conyzoides. To reduce the number of extrinsic variables, the first six components produced by a principal component analysis of environmental variables were used as predictive variables in the multiple regression. The best-fit environment model indicated that the relative abundance of A. conyzoides was higher in summer and in communities with lower total organic matter and higher total nitrogen in the soil. The multiple regression indicated that only the positive relationship between the Shannon–Wiener diversity of exotics and the relative abundance of A. conyzoides was significant. This result challenges the importance of diversity–resistance to plant invasion. Generalist facilitation might exist between A. conyzoides and other exotic species, although mechanisms for such facilitation are unclear. Overall, our finding suggests the extrinsic factors covarying with diversity are more important than diversity itself in regulating community susceptibility to invasion.     

Hidden patterns of phylogenetic non‐stationarity overwhelm comparative analyses of niche conservatism and divergence

Aim Despite the importance of the niche concept in ecological and evolutionary theory, there are still many discussions about its definition and operational evaluation, especially when dealing with niche divergence and conservatism in an explicit phylogenetic context. Here we evaluate patterns of niche evolution in 67 New World Carnivora species, measured using Hellinger distances based on MAXENT models of species distribution. We show how inferences on niche conservatism or divergence depend on the way phylogenetic patterns are analysed using matrix comparison techniques. Innovation Initially we used the simplest approach of Mantel tests to compare Hellinger distances ( N ) derived from MAXENT and phylogenetic distances ( P ) among species. Then we extended the Mantel test to generate a multivariate correlogram, in which phylogenetic patterns are analysed at multiple levels in the phylogeny and can reveal nonlinearity in the relationship between divergence and time. Finally, we proposed a new approach to generate ‘local’ (or ‘specific’) leverages of components for Mantel correlation, evaluating the non‐stationarity in the relationship between N and P for each species. This new approach was used to show if some lineages are more prone to niche shift or conservatism than others. Main conclusions Standard Mantel tests indicated a poor correspondence between N and P matrices, discarding the idea of niche conservatism for Carnivora, but the correlogram supports that closely related species tend to be more similar than expected by chance. Moreover, the variance among Hellinger distances between pairs of closely phylogenetically related species is much larger than for the entire clade. Phylogenetic non‐stationarity analysis shows that in some Carnivora families the niche tends to divergence (Mustelidae and Canidae), whereas in others it tends to conservatism (Procyonidae and Mustelidae) at short phylogenetic distances. Our analyses clearly show that misleading results may appear if niche divergence is analysed only by simple matrix correlations not taking into account complex patterns of phylogenetic nonlinearity and non‐stationarity.