Lost Branches on the Tree of Life

Failure to archive published data can impede reproducibility and inhibit downstream synthesis. Alarmingly, we estimate that ∼70% of existing DNA sequence alignments/phylogenetic trees, representing much of the underpinning of modern phylogenetic analysis, are no longer accessible. The evolutionary biology community needs to adopt policies ensuring that data are publicly archived upon publication.

[1]  Daphne J Fairbairn,et al.  THE ADVENT OF MANDATORY DATA ARCHIVING , 2011, Evolution; international journal of organic evolution.

[2]  J. Ioannidis,et al.  Public Availability of Published Research Data in High-Impact Journals , 2011, PloS one.

[3]  Nico Cellinese,et al.  Evolutionary informatics: unifying knowledge about the diversity of life. , 2012, Trends in ecology & evolution.

[4]  Richard Grenyer,et al.  Preserving the evolutionary potential of floras in biodiversity hotspots , 2007, Nature.

[5]  N. Schork,et al.  Kinase mutations in human disease: interpreting genotype–phenotype relationships , 2010, Nature Reviews Genetics.

[6]  C. Saslis-Lagoudakis,et al.  Phylogenies reveal predictive power of traditional medicine in bioprospecting , 2012, Proceedings of the National Academy of Sciences.

[7]  Arlin Stoltzfus,et al.  Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis , 2012, BMC Research Notes.

[8]  A. Vickers,et al.  Empirical Study of Data Sharing by Authors Publishing in PLoS Journals , 2009, PloS one.

[9]  C. Moritz,et al.  Variable responses of skinks to a common history of rainforest fluctuation: concordance between phylogeography and palaeo‐distribution models , 2009, Molecular ecology.

[10]  Simon J. Greenhill,et al.  Language Phylogenies Reveal Expansion Pulses and Pauses in Pacific Settlement , 2009, Science.

[11]  Heather A. Piwowar,et al.  Who Shares? Who Doesn't? Factors Associated with Openly Archiving Raw Research Data , 2011, PloS one.

[12]  Submission of data to GenBank. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[13]  M. Whitlock.  Data archiving in ecology and evolution: best practices. , 2011, Trends in ecology & evolution.

[14]  Katherine W. McCain,et al.  Mandating Sharing , 1995 .

[15]  James Regetz,et al.  Advances in global change research require open science by individual researchers , 2012 .

[16]  V. Roth,et al.  The Effects of Cenozoic Global Change on Squirrel Phylogeny , 2003, Science.

[17]  K. Pollard,et al.  Detection of nonneutral substitution rates on mammalian phylogenies. , 2010, Genome research.

[18]  D. Borsboom,et al.  The poor availability of psychological research data for reanalysis. , 2006, The American psychologist.

[19]  Heather A. Piwowar,et al.  Sharing Detailed Research Data Is Associated with Increased Citation Rate , 2007, PloS one.

[20]  Jennifer C Molloy,et al.  The Open Knowledge Foundation: Open Data Means Better Science , 2011, PLoS biology.

[21]  A. Rambaut,et al.  BEAST: Bayesian evolutionary analysis by sampling trees , 2007, BMC Evolutionary Biology.

[22]  M. Noor,et al.  Data Sharing: How Much Doesn't Get Submitted to GenBank? , 2006, PLoS biology.