Lost Branches on the Tree of Life

Authors

Bryan T. Drew, University of Florida
Romina Gazis, Clark University
Patricia Cabezas, Brigham Young University
Kristen S. Swithers, Smith College
Jiabin Deng, University of Florida
Roseana Rodriguez, University of Florida
Laura A. Katz, Smith College
Keith A. Crandall, The George Washington University
David S. Hibbett, Clark UniversityFollow
Douglas E. Soltis, University of Florida

Document Type

Article

Abstract

Until recently, uploading sequences to GenBank (or EMBL) was generally considered sufficient to ensure reproducibility of phylogenetic studies using DNA sequence data. Increasingly, however, the systematics community is realizing that archiving raw DNA sequences is not adequate, and that the underlying alignments of DNA sequences as well as the resulting phylogenetic trees are pivotal for reproducibility, comparative purposes, meta-analyses, and ultimately synthesis. Indeed, there has been a growing clamor for journals to adopt and enforce more rigorous data archiving practices across diverse disciplines [4]–[8]. As a result, about 35 evolutionary journals [5],[9] have adopted policies to encourage or require authors to upload alignments, phylogenetic trees, and other files requisite for study reproducibility [5] to TreeBASE (http://treebase.org/) and/or other public repositories such as Dryad (http://datadryad.org). Unfortunately, enforcement of such data deposition policies is generally lax, and most journals in systematics and evolution still do not require DNA sequence alignment or tree deposition. As a result, the alignments and trees underlying most published papers in systematics/phylogenetics and evolutionary biology remain inaccessible to the scientific community at large [8],[10].

Publication Title

PLoS Biology

Publication Date

9-2013

Volume

11

Issue

9

ISSN

1544-9173

DOI

10.1371/journal.pbio.1001636

Keywords

DNA sequencing, phylogeny, evolutionary biology

Repository Citation

Drew, Bryan T.; Gazis, Romina; Cabezas, Patricia; Swithers, Kristen S.; Deng, Jiabin; Rodriguez, Roseana; Katz, Laura A.; Crandall, Keith A.; Hibbett, David S.; and Soltis, Douglas E., "Lost Branches on the Tree of Life" (2013). Biology. 212.
https://commons.clarku.edu/faculty_biology/212

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 International License.

Copyright Conditions

Drew, B. T., Gazis, R., Cabezas, P., Swithers, K. S., Deng, J., Rodriguez, R., ... & Soltis, D. E. (2013). Lost branches on the tree of life. PLoS Biology, 11(9), e1001636. https://doi.org/10.1371/journal.pbio.1001636