Assembling a fully-dated tree of life

Distributions of fully-dated complete trees of life Description of the data and file structure This dataset contains the distributions of trees described in the paper "Assembling a fully-dated complete tree of life". Files and variables This dataset contains six distributions of trees. Each archive file contains a distribution of Newick tree files. equal_splits_topo.tar.gz: 501 trees with varying topologies. Each tree has calibration dates set using the median of available date sources for a node, and missing dates interpolated using the EQS-LS method (see the paper). equal_splits_date.tar.gz: 501 trees with a single topology and varying dates. Each tree has calibration dates set using a randomly-selected date source for each node, and missing dates interpolated using the EQS-LS method. equal_splits_both.tar.gz: 1503 trees with a varying topologies and varying dates. Missing dates are interpolated using the EQS-LS method. birth_model_topo.tar.gz: 101 trees with varying topologies. Each tree has calibration dates set using the median of available date sources for a node, and missing dates interpolated using the birth model method (see the paper). birth_model_date.tar.gz: 101 trees with a single topology and varying dates. Each tree has calibration dates set using a randomly-selected date source for each node, and missing dates interpolated using the birth model method. birth_model_both.tar.gz: 303 trees with a varying topologies and varying dates. Missing dates are interpolated using the birth model method. In addition, we include a single "median" tree for each interpolation method. These are the trees that gave the median phylogenetic diversity estimate of all trees in the "topo" distributions above. Code/software The files are Newick tree files, readable with most phylogenetic software, for example the ape package in R or the DendroPy package in Python. For example usage see the Python notebooks in the accompanying Github repository. Access information Data was derived from the following sources: The Open Tree of Life: https://tree.opentreeoflife.org/opentree, whose data is available under CC0. The Open Tree of Life phylesystem: https://github.com/opentreeoflife/phylesystem, whose data is available under CC0. The 280 underlying date source trees are cited in the Supporting Information of the paper.