An enhanced calibration of a recently released megatree for the analysis of phylogenetic diversity

Abstract

Dated or calibrated phylogenetic trees, in which branch lengths correspond to evolutionary divergence times between nodes, are important requirements for computing measures of phylogenetic diversity or phylogenetic community structure. The increasing knowledge about the diversification and evolutionary divergence times of vascular plants requires a revision of the age estimates used for the calibration of phylogenetic trees by the bladj algorithm of the Phylocom 4.2 package. Comparing the recently released megatree R20120829.new with two calibrated vascular plant phylogenies provided in the literature, we found 242 corresponding nodes. We modified the megatree (R20120829mod. new), inserting names for all corresponding nodes. Furthermore, we provide files containing age estimates from both sources for the updated calibration of R20120829mod.new. Applying these files consistently in analyses of phylogenetic community structure or diversity serves to avoid erroneous measures and ecological misinterpretation.Keywords: R20120829.new, phylogenetic community analysis, ecological misinterpretation, phylogenetic diversity, evolutionary divergence times, phylogenetic dispersion, phylogeny of vascular plants.Calibração aperfeiçoada de uma megatree lançada recentemente para a análise da diversidade filogenética ResumoÁrvores filogenéticas datadas, ou calibradas, em que os comprimentos dos ramos correspondem ao tempo evolutivo de divergência entre os nós, são importantes requisitos para calcular medidas de diversidade filogenética ou de estrutura filogenética de comunidades. O conhecimento crescente sobre a diversificação e sobre o tempo de divergência evolutiva das plantas vasculares fez necessária uma revisão das estimativas de idades dos nós que são utilizadas para a calibração de árvores filogenéticas por meio do algoritmo bladj do pacote Phylocom 4.2. Comparando a mega-árvore R20120829.new, recentemente publicada, e outras duas filogenias calibradas de plantas vasculares, encontramos 242 nós correspondentes. Modificamos esta mega-árvore (R20120829mod.new), inserindo todos os nomes dos nós correspondentes. Além disso, providenciamos dois arquivos com todas as estimativas das idades para uma calibração mais atualizada. Utilizando esses arquivos de maneira consistente nas análises de diversidade ou de estrutura filogenética de comunidades, evita-se incorreções nas datações e imprecisões na interpretação de informações ecológicas.Palavras-chave: R20120829.new, análise filogenética de comunidades, má interpretação ecológica, diversidade filogenética, tempo de divergência evolutiva, dispersão filogenética, filogenia de plantas vasculares.

Are dominant plant species more susceptible to leaf‐mining insects? A case study at Saihanwula Nature Reserve, China

“…The plant phylogenetic trees, which were required for the above phylogenetic regression models, were constructed in the following way: The megatree R20120829mod.new and the corresponding ages of the main clades (Gastauer & Meira‐Neto, 2016) were updated to include all families of vascular plants. Therefore, lycophytes and their three extant families were added, and Athyriaceae was moved into the family Aspleniaceae (Christenhusz & Chase, 2014).…”

Effects of landscape configuration and composition on phylogenetic diversity of trees in a highly fragmented tropical forest

“…For the preparation of our phylogenetic tree, we constructed a list of all our family/genus/species according to APG III (). In the program phylocom version 4.2 (Webb, Ackerly & Kembel ), we then used the PHYLOMATIC function to return the phylogenetic hypothesis for the relationship between our 72 families, 273 genera and 604 species sampled in 6802 tree individuals, using the new modified megatree R20120829mod.new for vascular plants from Gastauer and Meira‐Neto (). In our phylogenetic hypothesis, more than two species per family or more than two genera of an unresolved family in R20120829mod.new were inserted as polytomies.…”

Updated angiosperm family tree for analyzing phylogenetic diversity and community structure

“…Differences to its precursor R20120829mod.new (Gastauer & Meira-Neto 2016) are the up-to-date placement of the newly recognized orders Dilleniales, Metteniusales, Icacinales, Boraginales and Vahliales and their subordered families (APG IV 2016). Furthermore, the recently described families Maundiaceae, Apodanthaceae, Peraceae, Ixonanthaceae, Francoaceae, Petenaeaceae, Macarthuriaceae, Microteaceae, Kewaceae, Petiveriaceae and Mazaceae are included, permitting the straightforward incorporation of species from these families within R20160415.new.…”

“…The younger node(s) are then distributed equally between the older, dated node and the subsequent node containing age estimates, thus distorting the calibrated trees. In order to avoid this, we altered the age of the descendant node by -0.01 Myr, because this will ensure the maintenance of a topology with less influence on measures of phylogenetic diversity or phylogenetic community structure than would distortions caused by equal node distribution (Gastauer & Meira-Neto 2016). When three subsequent nodes were estimated to be …”

“…For vascular plants, calibratable phylogenies (i.e., Gastauer & Meira-Neto 2016) are based on APG III (2009), nevertheless recent advances in angiosperm phylogeny (i.e., APG IV 2016) have made it necessary to update them.…”