Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data

1. Coalescent-based species delimitation methods combine population genetic and phylogenetic theory to provide an objective means for delineating evolutionarily significant units of diversity. The Generalized Mixed Yule Coalescent (GMYC) and the Poisson Tree Process (PTP) are methods that use ultrametric (GMYC or PTP) or non-ultrametric (PTP) gene trees as input, intended for use mostly with single-locus data such as DNA barcodes. 2. Here we assess how robust the GMYC and PTP are to different phylogenetic reconstruction and branch smoothing methods. We reconstruct over 400 ultrametric trees using up to 30 different combinations of phylogenetic and smoothing methods and perform over 2,000 separate species delimitation analyses across 16 empirical datasets. We then assess how variable diversity estimates are, in terms of richness and identity, with respect to species delimitation, phylogenetic and smoothing methods. 3. The PTP method generally generates diversity estimates that are more robust to different phylogenetic methods. The GMYC is more sensitive, but provides consistent estimates for BEAST trees. The lower consistency of GMYC estimates is likely a result of differences among gene trees introduced by the smoothing step. Unresolved nodes (real anomalies or methodological artefacts) affect both GMYC and PTP estimates, but have a greater effect on GMYC estimates. Branch smoothing is a difficult step and perhaps an underappreciated source of bias that may be widespread among studies of diversity and diversification. 4. Nevertheless, careful choice of phylogenetic method does produce equivalent PTP and GMYC diversity estimates. We recommend simultaneous use of the PTP model with any model-based gene tree (e.g. RAxML) and GMYC approaches with BEAST trees for obtaining species hypotheses

Species traits and the form of individual species–energy relationships

Environmental energy availability explains much of the spatial variation in species richness at regional scales. While numerous mechanisms that may drive such total species–energy relationships have been identified, knowledge of their relative contributions is scant. Here, we adopt a novel approach to identify these drivers that exploits the composite nature of species richness, i.e. its summation from individual species distributions. We construct individual species–energy relationships (ISERs) for each species in the British breeding avifauna using both solar (temperature) and productive energy metrics (normalized difference vegetation index) as measures of environmental energy availability. We use the slopes of these relationships and the resultant change in deviance, relative to a null model, as measures of their strength and use them as response variables in multiple regressions that use ecological traits as predictors. The commonest species exhibit the strongest ISERs, which is counter to the prediction derived from the more individuals hypothesis. There is no evidence that predatory species have stronger ISERs, which is incompatible with the suggestion that high levels of energy availability increase the length of the food chain allowing larger numbers of predators to exist. We find some evidence that species with narrow niche breadths have stronger ISERs, thus providing one of the few pieces of supportive evidence that high-energy availability promotes species richness by increasing the occurrence of specialist species that use a narrow range of resources

PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data.

Microbial diversity is typically characterized by clustering ribosomal RNA (SSU-rRNA) sequences into operational taxonomic units (OTUs). Targeted sequencing of environmental SSU-rRNA markers via PCR may fail to detect OTUs due to biases in priming and amplification. Analysis of shotgun sequenced environmental DNA, known as metagenomics, avoids amplification bias but generates fragmentary, non-overlapping sequence reads that cannot be clustered by existing OTU-finding methods. To circumvent these limitations, we developed PhylOTU, a computational workflow that identifies OTUs from metagenomic SSU-rRNA sequence data through the use of phylogenetic principles and probabilistic sequence profiles. Using simulated metagenomic data, we quantified the accuracy with which PhylOTU clusters reads into OTUs. Comparisons of PCR and shotgun sequenced SSU-rRNA markers derived from the global open ocean revealed that while PCR libraries identify more OTUs per sequenced residue, metagenomic libraries recover a greater taxonomic diversity of OTUs. In addition, we discover novel species, genera and families in the metagenomic libraries, including OTUs from phyla missed by analysis of PCR sequences. Taken together, these results suggest that PhylOTU enables characterization of part of the biosphere currently hidden from PCR-based surveys of diversity

Understorey phylogenetic diversity in thermophilous deciduous forests : overstorey species identity can matter more than species richness

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Widespread correlations between climatic niche evolution and species diversification in birds

1. The adaptability of species’ climatic niches can influence the dynamics of colonization and gene flow across climatic gradients, potentially increasing the likelihood of speciation or reducing extinction in the face of environmental change. However, previous comparative studies have tested these ideas using geographically, taxonomically and ecologically restricted samples, yielding mixed results, and thus the processes linking climatic niche evolution with diversification remain poorly understood. 2. Focusing on birds, the largest and most widespread class of terrestrial vertebrates, we test whether variation in species diversification among clades is correlated with rates of climatic niche evolution and the extent to which these patterns are modified by underlying gradients in biogeography and species’ ecology. 3. We quantified climatic niches, latitudinal distribution and ecological traits for 7657 (~75%) bird species based on geographical range polygons and then used Bayesian phylogenetic analyses to test whether niche evolution was related to species richness and rates of diversification across genus- and family-level clades. 4. We found that the rate of climatic niche evolution has a positive linear relationship with both species richness and diversification rate at two different taxonomic levels (genus and family). Furthermore, this positive association between labile climatic niches and diversification was detected regardless of variation in clade latitude or key ecological traits. 5. Our findings suggest either that rapid adaptation to unoccupied areas of climatic niche space promotes avian diversification, or that diversification promotes adaptation. Either way, we propose that climatic niche evolution is a fundamental process regulating the link between climate and biodiversity at global scales, irrespective of the geographical and ecological context of speciation and extinction.</p

Gap Analysis and the Geographical Distribution of Parasites

Sampling biases can have enormous impacts on studies of parasite biogeography. While complete sampling is sometimes possible for local or regional patterns of parasitism, continental and global analyses often rely on data collected in a heterogeneous manner. At these larger scales, spatially-explicit methods to quantify and correct for geographic sampling biases are necessary. Approaches based on “gap analysis” can contribute to the development of corrective measures by identifying geographical variation in our knowledge of parasites and quantifying how sampling varies in relation to host characteristics and habitat features. In this chapter, we review these methods and describe how they have been applied to study gaps in our knowledge of primate parasites.Human Evolutionary Biolog

Local and regional ecological morphology of dung beetle assemblages across four biogeographic regions

Aim Niche partitioning within species assemblages is thought to influence species packing and/or total niche space occupied. The evolution of dung beetles (Scarabaeinae) is likely to have been strongly influenced by inter-specific competition, leading to niche partitioning. We consider whether local-scale processes leave a signature in regional patterns of functional diversity in dung beetle assemblages, and investigate the correlation between total exploited ecomorphological space and density of species packing with increased species richness. We test whether ecomorphological space occupied by local assemblages reflects that of their regional species pool, and the extent to which ecomorphological space is convergent or divergent within functional groups across regional pools. Location Neotropics, Africa, Australia and Madagascar. Methods Dung beetle assemblages were collected in a standardized manner from four biogeographic regions. Ecomorphological similarity among the assemblages was assessed by multivariate analysis of 19 linear measurements for 300 species and three functional nesting types (roller, tunneller or dweller), firstly on a local level within the Neotropics and Afrotropics, and then between the regional species pools. Results Key body measurements, in particular the hind tibia, separated rollers and tunnellers into largely non-overlapping entities along the first three axes of the shape analysis. Three Neotropical assemblages, which vary widely in species numbers, each harboured a similar amount of morphometric variation, resulting in increasingly dense species packing with greater species richness. Similar findings were obtained in two South African assemblages. Assemblages in the four biogeographic regions showed largely similar distributions of ecomorphological variation, including the separation of rollers and tunnellers, despite their distant phylogenetic relationships. Ecomorphological similarity among regions was particularly high in tunnellers, whilst the rollers exhibited greater regional differentiation. Main conclusions Local assemblages evidently represent the full diversity of functional groups available in the regional pool, even in species-poor assemblages. There is a strong trend towards convergence in morphology separating tunnellers and rollers in phylogenetically independent lineages. The ecomorphological similarity of regional assemblages suggests that morphological convergence is the result of common selective forces active within the assemblages themselves. This lends support to the widely hypothesized effect of inter-specific interactions and niche partitioning in determining assemblage composition and lineage evolution in the Scarabaeinae. © 2011 Blackwell Publishing Ltd

The mean and variance of phylogenetic diversity under rarefaction

Phylogenetic diversity (PD) depends on sampling intensity, which complicates the comparison of PD between samples of different depth. One approach to dealing with differing sample depth for a given diversity statistic is to rarefy, which means to take a random subset of a given size of the original sample. Exact analytical formulae for the mean and variance of species richness under rarefaction have existed for some time but no such solution exists for PD. We have derived exact formulae for the mean and variance of PD under rarefaction. We show that these formulae are correct by comparing exact solution mean and variance to that calculated by repeated random (Monte Carlo) subsampling of a dataset of stem counts of woody shrubs of Toohey Forest, Queensland, Australia. We also demonstrate the application of the method using two examples: identifying hotspots of mammalian diversity in Australasian ecoregions, and characterising the human vaginal microbiome. There is a very high degree of correspondence between the analytical and random subsampling methods for calculating mean and variance of PD under rarefaction, although the Monte Carlo method requires a large number of random draws to converge on the exact solution for the variance. Rarefaction of mammalian PD of ecoregions in Australasia to a common standard of 25 species reveals very different rank orderings of ecoregions, indicating quite different hotspots of diversity than those obtained for unrarefied PD. The application of these methods to the vaginal microbiome shows that a classical score used to quantify bacterial vaginosis is correlated with the shape of the rarefaction curve. The analytical formulae for the mean and variance of PD under rarefaction are both exact and more efficient than repeated subsampling. Rarefaction of PD allows for many applications where comparisons of samples of different depth is required.Comment: Final version to be published in Methods in Ecology and Evolutio