Abstract
ABSTRACT The computation of phylogenetic diversity and phylogenetic community structure demands an accurately calibrated, high-resolution phylogeny, which reflects current knowledge regarding diversification within the group of interest. Herein we present the angiosperm phylogeny R20160415.new, which is based on the topology proposed by the Angiosperm Phylogeny Group IV, a recently released compilation of angiosperm diversification. R20160415.new is calibratable by different sets of recently published estimates of mean node ages. Its application for the computation of phylogenetic diversity and/or phylogenetic community structure is straightforward and ensures the inclusion of up-to-date information in user specific applications, as long as users are familiar with the pitfalls of such hand-made supertrees.
Highlights
The phylogenetic structure of a biological community determines whether species that coexist within a given community are more closely related than expected by chance, and is essential information for investigating community assembly rules (Kembel & Hubbell 2006; Gastauer & Meira-Neto 2014a; Miazaki et al 2015; Lamare et al 2016) as well as determining the evolutionary processes that generated extant biodiversity (Fine & Kembel 2011; Gastauer et al 2015a)
The inclusion of recently described angiosperm families and orders within R20160415.new justifies the relevance of this phylogeny in the analysis of phylogenetic community structure and phylogenetic diversity
Case studies have shown that using R20160415. new to analyze phylogenetic community structure or to compute phylogenetic diversity is straightforward
Summary
The phylogenetic structure of a biological community determines whether species that coexist within a given community are more closely related than expected by chance, and is essential information for investigating community assembly rules (Kembel & Hubbell 2006; Gastauer & Meira-Neto 2014a; Miazaki et al 2015; Lamare et al 2016) as well as determining the evolutionary processes that generated extant biodiversity (Fine & Kembel 2011; Gastauer et al 2015a). Calibratable phylogenies (i.e., Gastauer & Meira-Neto 2016) are based on APG III (2009), recent advances in angiosperm phylogeny (i.e., APG IV 2016) have made it necessary to update them. The aim of this study is to provide a fully resolved, up-to-date angiosperm family tree based on APG IV (2016) and Stevens (2016) including features necessary for its accurate calibration. Such a tree will permit the inclusion of recent advances regarding angiosperm phylogeny in userspecific analyses of phylogenetic diversity and phylogenetic community structure
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