Data from: The dawn of open access to phylogenetic data

The scientific enterprise depends critically on the preservation of and
open access to published data. This basic tenet applies acutely to
phylogenies (estimates of evolutionary relationships among species).
Increasingly, phylogenies are estimated from increasingly large,
genome-scale datasets using increasingly complex statistical methods that
require increasing levels of expertise and computational investment.
Moreover, the resulting phylogenetic data provide an explicit historical
perspective that critically informs research in a vast and growing number
of scientific disciplines. One such use is the study of changes in rates
of lineage diversification (speciation – extinction) through time. As part
of a meta-analysis in this area, we sought to collect phylogenetic data
(comprising nucleotide sequence alignment and tree files) from 217 studies
published in 46 journals over a 13-year period. We document our attempts
to procure those data (from online archives and by direct request to
corresponding authors), and report results of analyses (using Bayesian
logistic regression) to assess the impact of various factors on the
success of our efforts. Overall, complete phylogenetic data for ~ 60% of
these studies are effectively lost to science. Our study indicates that
phylogenetic data are more likely to be deposited in online archives
and/or shared upon request when: (1) the publishing journal has a strong
data-sharing policy; (2) the publishing journal has a higher impact
factor, and; (3) the data are requested from faculty rather than students.
Importantly, our survey spans recent policy initiatives and
infrastructural changes; our analyses indicate that the positive impact of
these community initiatives has been both dramatic and immediate. Although
the results of our study indicate that the situation is dire, our findings
also reveal tremendous recent progress in the sharing and preservation of
phylogenetic data.