Phylogenetic diversity–area curves

Helmus, Matthew R.; Ives, Anthony R.

doi:10.1890/11-0435.1

Cited by 54 publications

(63 citation statements)

References 75 publications

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“…For binomial samples from a power-law EAD, we observe a power-law increase in expected PD with sample size, consistent with the power-law increase in expected PD with sample size observed in other kinds of community [36], [37]. Poisson sampling produces an identical pattern up to very large sample sizes where replacement becomes important.…”

Section: Resultssupporting

confidence: 80%

Phylogenetic Diversity Theory Sheds Light on the Structure of Microbial Communities

2012

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Microbial communities are typically large, diverse, and complex, and identifying and understanding the processes driving their structure has implications ranging from ecosystem stability to human health and well-being. Phylogenetic data gives us a new insight into these processes, providing a more informative perspective on functional and trait diversity than taxonomic richness alone. But the sheer scale of high resolution phylogenetic data also presents a new challenge to ecological theory. We bring a sampling theory perspective to microbial communities, considering a local community of co-occuring organisms as a sample from a larger regional pool, and apply our framework to make analytical predictions for local phylogenetic diversity arising from a given metacommunity and community assembly process. We characterize community assembly in terms of quantitative descriptions of clustered, random and overdispersed sampling, which have been associated with hypotheses of environmental filtering and competition. Using our approach, we analyze large microbial communities from the human microbiome, uncovering significant variation in diversity across habitats relative to the null hypothesis of random sampling.

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Section: Resultssupporting

confidence: 80%

Phylogenetic Diversity Theory Sheds Light on the Structure of Microbial Communities

2012

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“…This axis could be envisioned in terms of a stress gradient assembly mechanism where low local dispersion and low turnover occurs in relatively harsh and spatially contiguous habitats, and high dispersion and high turnover occurs in more benign and potentially patchy habitats (Helmus and Ives 2012). The relative proportion of subplots falling on either end of this spectrum was generally equivalent.…”

Section: Phylogenetic and Functional Alpha And Beta Dispersion: Pairwmentioning

confidence: 99%

Phylogenetic and functional alpha and beta diversity in temperate and tropical tree communities

Swenson

Erickson

et al. 2012

Ecology

212

269

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Abstract. The study of biodiversity has tended to focus primarily on relatively information-poor measures of species diversity. Recently, many studies of local diversity (alpha diversity) have begun to use measures of functional and phylogenetic alpha diversity. Investigations into the phylogenetic and functional dissimilarity (beta diversity) of communities have been far less numerous, but these dissimilarity measures have the potential to infer the mechanisms underlying community assembly and dynamics. Here, we relate levels of phylogenetic and functional alpha diversity to levels of phylogenetic and functional beta diversity to infer the mechanism or mechanisms responsible for the assembly of tree communities in six forests located in tropical and temperate latitudes. The results show that abiotic filtering plays a role in structuring local assemblages and governing spatial turnover in community composition and that phylogenetic measures of alpha and beta diversity are not strong predictors of functional alpha and beta diversity in the forests studied.

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“…Ecologists now routinely apply such information to investigate the phylogenetic distribution of particular species and traits among communities in relation to abiotic and biotic factors at local and regional scales (e.g., Verdu´et al 2009, Fine and Kembel 2011, Swenson et al 2011, Cavender-Bares and Reich 2012, Helmus and Ives 2012, Knapp et al 2012). Our example is not the broadest synthesis of land plant relationships published to date (e.g., ca.…”

Section: Assembling a Literature-based Tree For Land Plantsmentioning

confidence: 99%

Synthesizing phylogenetic knowledge for ecological research

Beaulieu

Ree

Cavender‐Bares

et al. 2012

Ecology

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Abstract. The demand for knowledge about the tree of life is steadily rising in ecology and other fields, but bioinformatic resources designed to meet these needs remain poorly developed. Ecologists pursuing phylogenetic insights into the organization of communities have come to rely on relatively conservative reference trees that, in general, are poorly resolved and documented. New methods for inferring very large trees by mining data from DNA sequence repositories will undoubtedly be useful in community phylogenetics but are not without limitations. Here we argue that the collective phylogenetic knowledge embodied in the literature of systematics is a valuable resource that can be tapped in assembling synthetic trees. Assembling a composite ''literature-based'' tree by the judicious grafting of clades is one way to achieve a synthesis of current knowledge, and could, under some circumstances, better represent ''what we know'' about phylogenetic relationships than results obtained from automated pipelines. We describe an approach and new software for storing and annotating trees from published studies and grafting clades together in a documented and repeatable manner. Using this agglomerative approach, we are in the process of assembling a literaturebased tree for land plants, which presently contains 14 423 species from over 259 sources. For this strategy to be maximally effective, improvements in digital infrastructure are needed to capture and deploy advances in phylogenetic knowledge as they are published.

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Phylogenetic diversity–area curves

Cited by 54 publications

References 75 publications

Phylogenetic Diversity Theory Sheds Light on the Structure of Microbial Communities

Phylogenetic Diversity Theory Sheds Light on the Structure of Microbial Communities

Phylogenetic and functional alpha and beta diversity in temperate and tropical tree communities

Synthesizing phylogenetic knowledge for ecological research

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