The Dawn of Open Access to Phylogenetic Data

Abstract

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 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.

Navigating the unfolding open data landscape in ecology and evolution

“…Although an ideally described data set (how and where the data were collected, processed and analysed) should minimize any room for data misinterpretation, many ecological data sets still lack the complete information to enable a full understanding 12,29,30 . Furthermore, ecological data are often context specific, and their interpretation and informed use can only take place if this context is properly described (which is sometimes difficult to achieve, and it fully relies on whether the data owners had reuse in mind).…”

How and Why to Build a Unified Tree of Life

“…[35] However, since the above publications, there has been an increased push in the scientific community to make published data more available via publicly available archives. [34,[38][39][40][41][42] Nonetheless, deposition rates have not improved (see Box 2). The result of evolutionary estimates not being readily available is that taxonomy is often used as a proxy for evolutionary relatedness (e.g., Tree of Sex Consortium [43] ).…”

A machine-compiled microbial supertree from figure-mining thousands of papers

“…Methods for synthesising larger trees ('supertrees') from a collection of smaller trees exist, but supertrees are rarely created because of the scarcity of published trees in semantic, reusable forms , Drew et al 2013, Magee et al 2014. Although formats and ontologies exist (e.g.…”

“…The data underlying articles are often not published in the first place (Wicherts et al 2006,Drew et al 2013,Magee et al 2014,Caetano and Aisenberg 2014 • Some journals allow data to be "embargoed" and not made available for up to 10 years after the publication of an associated article (Roche et al 2014) • When data are published, it can be in a manner that is not machine-readable. Data are frequently obfuscated in pixel-based figures, and even where data are tabulated the formatting is often esoteric.…”