For common community phylogenetic analyses, go ahead and use synthesis phylogenies.

Daijiang Li,Miao Sun,Pamela S Soltis,Julie M Allen,Benjamin Baiser,Douglas E Soltis,Robert P Guralnick,Hannah E Marx,Lauren Trotta

doi:10.1002/ecy.2788

Abstract

Should we build our own phylogenetic trees based on gene sequence data, or can we simply use available synthesis phylogenies? This is a fundamental question that any study involving a phylogenetic framework must face at the beginning of the project. Building a phylogeny from gene sequence data (purpose‐built phylogeny) requires more effort, expertise, and cost than subsetting an already available phylogeny (synthesis‐based phylogeny). However, we still lack a comparison of how these two approaches to building phylogenetic trees influence common community phylogenetic analyses such as comparing community phylogenetic diversity and estimating trait phylogenetic signal. Here, we generated three purpose‐built phylogenies and their corresponding synthesis‐based trees (two from Phylomatic and one from the Open Tree of Life, OTL). We simulated 1,000 communities and 12,000 continuous traits along each purpose‐built phylogeny. We then compared the effects of different trees on estimates of phylogenetic diversity (alpha and beta) and phylogenetic signal (Pagel's λ and Blomberg's K). Synthesis‐based phylogenies generally yielded higher estimates of phylogenetic diversity when compared to purpose‐built phylogenies. However, resulting measures of phylogenetic diversity from both types of phylogenies were highly correlated (Spearman's ρ > 0.8 in most cases). Mean pairwise distance (both alpha and beta) is the index that is most robust to the differences in tree construction that we tested. Measures of phylogenetic diversity based on the OTL showed the highest correlation with measures based on the purpose‐built phylogenies. Trait phylogenetic signal estimated with synthesis‐based phylogenies, especially from the OTL, was also highly correlated with estimates of Blomberg's K or close to Pagel's λ from purpose‐built phylogenies when traits were simulated under Brownian motion. For commonly employed community phylogenetic analyses, our results justify taking advantage of recently developed and continuously improving synthesis trees, especially the Open Tree of Life.

Highlights

Phylogenies describe the evolutionary history of species and provide important tools to study ecological and evolutionary questions (Baum and Smith 2012)
Community phylogenetics is rapidly becoming an important component of community ecology, macroecology, and biodiversity conservation (Webb et al 2002, Vamosi et al 2009)
For calculations and comparisons of community phylogenetic diversity and trait phylogenetic signal, an important question arises: can we derive phylogenies from already-available synthesis trees, or should we generate our own purpose-built phylogenies? Our results suggest that phylogenies derived from common synthesis trees yield higher estimates of phylogenetic diversity metrics when compared to purpose-built trees, but values of phylogenetic diversity are highly correlated with those of purpose-built trees

Summary

Introduction

Phylogenies describe the evolutionary history of species and provide important tools to study ecological and evolutionary questions (Baum and Smith 2012). Phylogenies have been used to understand patterns of community assembly better. The phylogenetic structure of ecological communities can lend insight into the processes by which local communities assemble from regional species pools (Webb et al 2002). If closely related species are more likely to co-occur in the same habitats, we might suspect that these species. Manuscript received 19 February 2019; revised 15 April 2019; accepted 29 May 2019.

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Conclusion