Abstract Detail

Systematics Section/ASPT

Deng, Jiabin [1], Drew, Bryan T. [1], Gazis, Romina [2], Cabezas, Patricia [3], Swithers, Kristen S. [4], Rodriguez, Roseanna [5], Katz, Laura A. [4], Crandall, Keith A. [6], Hibbett, David S. [7], Soltis, Douglas [8].

Missing data lead to holes in the tree of life.

The fundamental importance of archiving scientific datasets has received increasing attention over the past several years, and failure to properly archive data can adversely affect study reproducibility. However, in plant systematics (or evolutionary biology) there has been no comprehensive review that examines the deposition practices of the underlying phylogenetic datasets and trees that are the foundation of the discipline. Furthermore, there is little understanding of how the deposition rate of DNA sequence alignments and phylogenetic trees has changed over time. In the process of gathering data to build the first tree of life for all ~1.9 million named species (the Open Tree of Life Project), we sifted through over 7200 peer-reviewed phylogenetic studies published between the years 2000 and 2012. Our survey covered over 100 journals and included publications focusing on green plants, animals, fungi, microbial eukaryotes, bacteria, and archaea. This broad survey included 1243 seed plant publications. Overall, we found that only 17% of examined studies made nucleotide alignment data and/or trees available in an accessible repository such as TreeBASE or Dryad. Within seed plants, only 24% of studies from the past 12 years have been archived. Furthermore, most corresponding authors (54% for seed plants) that we contacted for un-deposited datasets and trees did not respond to our repeated (2) requests for data. Thus, most of the trees and alignments produced during the past several decades is essentially lost forever. The plant systematics community needs to significantly improve data deposition practices to ensure that crucial data (trees, alignments) are archived and thus freely available to other interested scientists. Our results illustrate that voluntary data submission policies have not worked, and dictate the urgent need to adopt new policies requiring public archiving of DNA sequence alignments and trees in a routine manner as is done routinely with raw sequence data. These stark findings should encourage the systematic community as well as journal editorials to adopt data sharing policies that require deposition of alignments and resulting phylogenetic trees in established databases prior to publication.

Broader Impacts:

1 - University of Florida, Florida Museum of Natural History, Dickinson Hall-Museum Road- University of Florida, Gainesville, FL, Gainesville, FL, 32611, USA
2 - Clark University, Clark University, Worcester, Massachusetts, USA., USA
3 - Brigham Young University, Brigham Young University, Provo, Utah, USA, George Washington University, Washington DC, USA., USA
4 - Smith College, Smith College, Northampton, Massachusetts, USA, USA
5 - University of Florida, University of Florida, Gainesville, USA, Gainesville, FL, 32611, USA
6 - George Washington University, George Washington University, Washington DC, USA, Washington DC, USA
7 - Clark University, Clark University, Worcester, Massachusetts, USA, Massachusetts, USA
8 - University of Florida, Department of Botany, 220 BARTRAM HALL, Gainesville, FL, 32611, USA

Keywords:
seed plants
Dryad
TreeBASE
phylogeny
phylogenetic tree
public archives.

Presentation Type: Poster:Posters for Sections
Session: P
Location: Grand Salon A - D/Riverside Hilton
Date: Monday, July 29th, 2013
Time: 5:30 PM
Number: PSY009
Abstract ID:167
Candidate for Awards:None