10.5061/DRYAD.CNP5HQC6W
Sanchez Reyes, Luna Luisa
0000-0001-7668-2528
University of California System
McTavish, Emily Jane
University of California System
O'Meara, Brian
University of Tennessee at Knoxville
DateLife: leveraging databases and analytical tools to reveal the dated
Tree of Life
Dryad
dataset
2022
tree
scaling
dating
ages
divergence times
Open science
congruification
supertree
secondary calibrations
FOS: Biological sciences
National Science Foundation
https://ror.org/021nxhr62
ABI-1458603
National Science Foundation
https://ror.org/021nxhr62
DBI-0905606
National Science Foundation
https://ror.org/021nxhr62
ABI-145872
National Science Foundation
https://ror.org/021nxhr62
ABI-1759846
2022-07-25T00:00:00Z
2022-07-25T00:00:00Z
en
https://doi.org/10.1101/782094
https://doi.org/10.5281/zenodo.6683665
https://doi.org/10.5281/zenodo.6683667
320047 bytes
3
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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 (Pheucticus tibialis, Rhodothraupis celaeno, Emberiza
citrinella, Emberiza leucocephalos, Emberiza elegans and Platyspiza
crassirostris); 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.
DateLife is a publlic and open source software
https://github.com/phylotastic/datelife#readme