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

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 normalρ > 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.

The phylogenetic diversity and structure of the seasonally dry forests in the Neotropics

“…This phylogenetic hypothesis comprised ~90% of our total pool of species, with ~45% of these species containing genetic data and the remaining species begin included according to their taxonomic arrangement (Smith & Brown, 2018). Such synthetic phylogenies have been recently shown to perform equally well as fully genetic phylogenies, particularly for community phylogenetic analyses as the one performed here (Li et al, 2019).…”

Biodiversity at the global scale: the synthesis continues

“…Smith et al, 2009) or as some type of aggregation of published phylogenetic results (“supertrees,” of which the most commonly used for plants are those of Webb and Donoghue, 2005; Hinchliff et al, 2015; Smith and Brown, 2018). Both methods, reviewed by Roquet et al (2013), have seen extensive use in recent large‐scale investigations (Li et al, 2015, 2019; Thornhill et al, 2017; Allen et al, 2019a).…”

FishPhyloMaker: An R package to generate phylogenies for ray-finned fishes

“…These limitations do not preclude the package applicability for studies in phylogenetic community ecology since synthesis phylogenies do not significantly impact phylogenetic diversity indices (Li et al, 2019). Moreover, this is the only automated tool able to provide a complete phylogenetic tree that can easily handle large datasets.…”