Walter Durka and Stefan G. Michalski. 2012. Daphne: a dated phylogeny of a large European flora for phylogenetically informed ecological analyses. Ecology 93:2297. http://dx.doi.org/10.1890/12-0743.1


Data Paper

Ecological Archives E093-214-D1.

Copyright


Authors
Data Files
Abstract
Metadata


Author(s)

Walter Durka
Helmholtz Centre for Environmental Research-UFZ
Department of Community Ecology (BZF)
Theodor-Lieser-Straße 4, D-06120 Halle, Germany
E-mail: walter.durka@ufz.de

Stefan G. Michalski
Helmholtz Centre for Environmental Research-UFZ
Department of Community Ecology (BZF)
Theodor-Lieser-Straße 4, D-06120 Halle, Germany


Data Files

DaPhnE_01.zip -- contains all four data files described below. [d93c96544d106a7ce37f99c7a631ecbc]

DaPhnE_01_Synonymy.txt -- tab-delimited ASCII file containing the list of the binomials used by the German, British, the Netherlands, and Swiss source databases and the respective binomials used in DaPhnE. [0785c354ec81a96b0453bcf36de29a65]

DaPhnE_01.tre -- ASCII file of the phylogeny in Newick format. [1ecfc21ba9c8a754ac8c784768cb1fb3]

DaPhnE_01_nodes_with_references.txt -- tab-delimited ASCII file containing 1212 lines listing nodes with either a reference for the partial phylogenies used to construct the supertree or to the node ages. [abcd006cd50353dcc3839f703c68401d]

DaPhnE_01_reference_list.txt -- tab-delimited ASCII file containing 738 references for phylogenies and node dates given in DaPhnE_01_nodes_with_references.txt. [01e130037c617d0f6e392497a9af4177]


Abstract

This data set represents a comprehensive, dated phylogeny of a large European flora comprising the vascular plants of the British Isles, Germany, the Netherlands, and Switzerland, totalling 4685 species. The phylogeny thus encompasses all species in the trait databases BIOLFLOR, PLANTATT, and BioBase 2003. The topology of the phylogenetic tree is based on a backbone family phylogeny of the Angiosperm Phylogeny Group III. Subsequently, partial phylogenetic subtrees derived from a total of 518 recent molecular studies were manually pruned onto the backbone tree, using multi-gene consensus topologies if possible. Similarly, 1103 internal nodes and the root node were dated based on 261 recent studies. Finally, an ultrametric tree was calculated by placing undated nodes evenly between dated nodes. The phylogeny provides a reference data set for comparative analyses of trait correlations, trait evolution, trait based ecological processes, community assembly, or other phylogenetically informed analyses across a large taxon of European plant species. It can readily be used in phylogenetic analysis tools like ape, phytools, picante, or MESQUITE.

BIOLFLOR; British flora; German flora; macroecology; Netherlands flora; phylogeny; PLANTATT; supertree; Swiss flora; vascular plants.