Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: a mega-phylogeny approach.

David L Erickson,W John Kress,Stuart J Davies,Dingliang Xing,Robert W Howe,W Ye,Nathan G Swenson,John D Parker,Keping Ma,Jess K Zimmerman,Zhanqing Hao,Wenna Chen,Norman A Bourg,Xiangcheng Mi,Nancai Pei,James A Lutz,Madhava Meegaskumbura,Andrew J Larson,I Fang-Sun,S Joseph Wright,F Andrew Jones ,Amy Wolf ,Xue‐Jun Ge ,Ching-Hua Huang ,Shawn Lum

doi:10.3389/fgene.2014.00358

Abstract

Forest dynamics plots, which now span longitudes, latitudes, and habitat types across the globe, offer unparalleled insights into the ecological and evolutionary processes that determine how species are assembled into communities. Understanding phylogenetic relationships among species in a community has become an important component of assessing assembly processes. However, the application of evolutionary information to questions in community ecology has been limited in large part by the lack of accurate estimates of phylogenetic relationships among individual species found within communities, and is particularly limiting in comparisons between communities. Therefore, streamlining and maximizing the information content of these community phylogenies is a priority. To test the viability and advantage of a multi-community phylogeny, we constructed a multi-plot mega-phylogeny of 1347 species of trees across 15 forest dynamics plots in the ForestGEO network using DNA barcode sequence data (rbcL, matK, and psbA-trnH) and compared community phylogenies for each individual plot with respect to support for topology and branch lengths, which affect evolutionary inference of community processes. The levels of taxonomic differentiation across the phylogeny were examined by quantifying the frequency of resolved nodes throughout. In addition, three phylogenetic distance (PD) metrics that are commonly used to infer assembly processes were estimated for each plot [PD, Mean Phylogenetic Distance (MPD), and Mean Nearest Taxon Distance (MNTD)]. Lastly, we examine the partitioning of phylogenetic diversity among community plots through quantification of inter-community MPD and MNTD. Overall, evolutionary relationships were highly resolved across the DNA barcode-based mega-phylogeny, and phylogenetic resolution for each community plot was improved when estimated within the context of the mega-phylogeny. Likewise, when compared with phylogenies for individual plots, estimates of phylogenetic diversity in the mega-phylogeny were more consistent, thereby removing a potential source of bias at the plot-level, and demonstrating the value of assessing phylogenetic relationships simultaneously within a mega-phylogeny. An unexpected result of the comparisons among plots based on the mega-phylogeny was that the communities in the ForestGEO plots in general appear to be assemblages of more closely related species than expected by chance, and that differentiation among communities is very low, suggesting deep floristic connections among communities and new avenues for future analyses in community ecology.

Highlights

Phylogenetic hypotheses have played an increasingly important role in ecology over the last decade and their use in understanding community processes has been well reviewed (Webb et al, 2002; Cavender-Bares et al, 2009; Swenson, 2013)
The application of evolutionary information to questions in community ecology has been limited in large part by the lack of accurate estimates of phylogenetic relationships among individual species found within communities
Phylogenetic information has been applied to the identification of specific environments critical for conservation (Faith, 1992; Forest et al, 2007; Morlon et al, 2011)

Summary

Introduction

Phylogenetic hypotheses have played an increasingly important role in ecology over the last decade and their use in understanding community processes has been well reviewed (Webb et al, 2002; Cavender-Bares et al, 2009; Swenson, 2013). The application of evolutionary information to questions in community ecology has been limited in large part by the lack of accurate estimates of phylogenetic relationships among individual species found within communities. This dearth of information has been true for the most species- and ecologically-diverse communities in the tropics where existing phylogenetic data are most limiting (Webb and Donoghue, 2005; Kress et al, 2009). In communities where diverse sets of species are present, the very large evolutionary divergences among co-occurring taxa and more sparse taxonomic sampling have been thought to hinder accurate reconstructions of phylogenetic relationships (Poe and Swofford, 1999)

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