Abstract
BackgroundRecently, various evolution-related journals adopted policies to encourage or require archiving of phylogenetic trees and associated data. Such attention to practices that promote sharing of data reflects rapidly improving information technology, and rapidly expanding potential to use this technology to aggregate and link data from previously published research. Nevertheless, little is known about current practices, or best practices, for publishing trees and associated data so as to promote re-use.FindingsHere we summarize results of an ongoing analysis of current practices for archiving phylogenetic trees and associated data, current practices of re-use, and current barriers to re-use. We find that the technical infrastructure is available to support rudimentary archiving, but the frequency of archiving is low. Currently, most phylogenetic knowledge is not easily re-used due to a lack of archiving, lack of awareness of best practices, and lack of community-wide standards for formatting data, naming entities, and annotating data. Most attempts at data re-use seem to end in disappointment. Nevertheless, we find many positive examples of data re-use, particularly those that involve customized species trees generated by grafting to, and pruning from, a much larger tree.ConclusionsThe technologies and practices that facilitate data re-use can catalyze synthetic and integrative research. However, success will require engagement from various stakeholders including individual scientists who produce or consume shareable data, publishers, policy-makers, technology developers and resource-providers. The critical challenges for facilitating re-use of phylogenetic trees and associated data, we suggest, include: a broader commitment to public archiving; more extensive use of globally meaningful identifiers; development of user-friendly technology for annotating, submitting, searching, and retrieving data and their metadata; and development of a minimum reporting standard (MIAPA) indicating which kinds of data and metadata are most important for a re-useable phylogenetic record.
Highlights
Various evolution-related journals adopted policies to encourage or require archiving of phylogenetic trees and associated data
The critical challenges for facilitating re-use of phylogenetic trees and associated data, we suggest, include: a broader commitment to public archiving; more extensive use of globally meaningful identifiers; development of user-friendly technology for annotating, submitting, searching, and retrieving data and their metadata; and development of a minimum reporting standard (MIAPA) indicating which kinds of data and metadata are most important for a re-useable phylogenetic record
Phylogenies Surprisingly, in the sample of 40 recent phylogenetic articles, we found that 5 studies rely on the same suite of phylogeny resources, namely the phylogeny of plant taxa maintained by the Angiosperm Phylogeny Group (APG; see Table 1) and available via Phylomatic [45]
Summary
The technologies and practices that facilitate data re-use can catalyze synthetic and integrative research. Journal web sites (1) fail to provide search interfaces that make supplementary data discoverable, (2) often require payments to access the data, (3) are not committed to ensuring the long-term preservation of the data, and (4) leave users confused about potential copyright restrictions on use of the data None of these conditions apply to public archives such as Dryad and TreeBASE. In the case in which data are obtained from a web site associated with a database or archive, the authors should cite a database publication where available, and provide, whenever possible, an identifier for the electronic record that is unique for that archive or database (e.g., accession number). Perhaps the most obviously remediable barrier to data re-use is the general ignorance (noted earlier) of the practices that facilitate sharing, and of the tools that support interoperability, e.g., producers of phylogenies frequently choose to archive images of trees, even though most tree-rendering tools u
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