DOI: 10.5061/dryad.cnp5hqc6w
title: DateLife: leveraging databases and analytical tools to reveal the dated Tree of Life

description: Achieving a high-quality reconstruction of a phylogenetic tree with branch
 lengths proportional to absolute time (chronogram) is a difficult and
 time-consuming task. But the increased availability of fossil and
 molecular data, and time-efficient analytical techniques has resulted in
 many recent publications of large chronograms for a large number and wide
 diversity of organisms. Knowledge of the evolutionary time frame of
 organisms is key for research in the natural sciences. It also represent
 valuable information for education, science communication, and policy
 decisions. When chronograms are shared in public, open databases, this
 wealth of expertly-curated and peer-reviewed data on evolutionary
 timeframe is exposed in a programatic and reusable way, as intensive and
 localized efforts have improved data sharing practices, as well as
 incentivizited open science in biology. Here we present DateLife, a
 service implemented as an R package and an R Shiny website application
 available at www.datelife.org, that provides functionalities for efficient
 and easy finding, summary, reuse, and reanalysis of expert, peer-reviewed,
 public data on time frame of evolution. The main DateLife workflow
 constructs a chronogram for any given combination of taxon names by
 searching a local chronogram database constructed and curated from the
 Open Tree of Life Phylesystem phylogenetic database, which incorporates
 phylogenetic data from the TreeBASE database as well. We implement and
 test methods for summarizing time data from multiple source chronograms
 using supertree and congruification algorithms, and using age data
 extracted from source chronograms as secondary calibration points to add
 branch lengths proportional to absolute time to a tree topology. DateLife
 will be useful to increase awareness of the existing variation in
 alternative hypothesis of evolutionary time for the same organisms, and
 can foster exploration of the effect of alternative evolutionary timing
 hypotheses on the results of downstream analyses, providing a framework
 for a more informed interpretation of evolutionary results.
description: This dataset contains files, figures and tables from the two
 examples shown in the manuscript (small example and fringillidae example),
 as well as from the cross validation analysis performed.
 Small example of the Datelife workflow. 1. Processed an input of
 6 bird species within the Passeriformes (<em>Pheucticus tibialis,
 Rhodothraupis celaeno, Emberiza citrinella, Emberiza leucocephalos,
 Emberiza elegans and Platyspiza crassirostris</em>); 2. Used process
 names to search DateLife's chronogram database; 3. Summarized results
 from matching chronograms. Fringillidae example:
 http://phylotastic.org/datelife/articles/fringiliidae.html
 Cross validation: We performed a cross validation analysis of the
 DateLife workflow using 19 Fringillidae chronograms found in
 datelife's database. We used the individual tree topologies from each
 of the 19 source chronograms as inputs, treating their node ages as
 unknown. We then estimated dates for these topologies using node ages of
 chronograms belonging t o the remaining 12 studies as secondary
 calibrations, smoothingwith BLADJ.
description: DateLife is a publlic and open source software
 https://github.com/phylotastic/datelife#readme