Supplemental Material

Supplemental material, including descriptions and results from supplemental simulation studies

CoMET data archive

This data archive contains the scripts used to generate and analyze all the data in the accompanying manuscript (May et al., MEE), as well as the simulated data that were analyzed for that work. The archive is broken into five subdirectores, each corresponding to one set of simulations/analyses performed in the manuscript. The descriptions of each subdirectory are provided in the README.txt file

Availability of phylogenetic data as a function of impact factor.

<p>We estimated the effect of the impact factor of the publishing journal on our ability to procure partial (top panels) and complete (bottom panels) phylogenetic datasets from online archives (left panels) or by direct solicitation (right panels). Generally, studies published in journals with a higher impact factor are more likely to both deposit the corresponding (partial or complete) datasets in online archives and to provide those data upon direct request. The shaded areas reflect the credible intervals of the estimates.</p

Dawn_of_Open_Access_Data_files

Data table analyzed in the paper and data files gathered. Includes ReadMe

Flowchart of data acquisition.

<p>We identified a total of articles exploring temporal variation in rates of lineage diversification. Data for of these studies were archived in online repositories; data for the remaining studies were solicited by direct requests to the corresponding author by an undergraduate student ( studies), a graduate student (), or a professor (). A maximum of three requests were made at weekly intervals. Recovered phylogenetic data comprised tree files (green), alignment files (orange), or both (blue). Datasets not obtained after the third request were deemed unavailable (gray).</p

Availability of solicited phylogenetic data as a function of age.

<p>We estimated the effect of publication age on our ability to procure partial (top panels) and complete (bottom panels) phylogenetic datasets by direct solicitation. Overall, the probability of successfully recovering phylogenetic data decreases over time (left panel). Paradoxically, the probability of soliciting data from studies with NSF funding and/or published in JDAP journals is <i>lower</i> than that for studies without NSF funding and/or published in non-JDAP journals. However, this likely reflects the fact that the data from these studies are so often available in online archives that there is essentially no <i>need</i> for direct solicitation. Shaded areas reflect the credible intervals.</p

Relative probability of procuring phylogenetic data by solicitation.

<p>Relative probability of procuring phylogenetic data by solicitation.</p

Summary of logistic model parameters and their interpretation.

<p>Summary of logistic model parameters and their interpretation.</p

Detailed breakdown of data availability.

<p>The number of studies with available phylogenetic data—as tree files (green), alignments files (orange) or both (blue), procured either from online archives or by direct request—organized by year of publication (barplot). Phylogenetic data of some kind (tree and/or alignment files) were available from an online archive for approximately of the studies, and additional data were successfully solicited by direct request for of the studies. Complete datasets were unavailable for of published studies, and data of any kind were unavailable for of studies (gray). The ‘policy’ arrow indicates the onset of several community initiatives to improve the sharing and preservation of evolutionary (including phylogenetic) data, which coincides with a marked increase in the deposition of phylogenetic data to online archives. For each pair of barplots, the left/right bars correspond to archived/solicited data, respectively. Grayscale image available at <a href="http://dx.doi.org/10.6084/m9.figshare.1148872" target="_blank">http://dx.doi.org/10.6084/m9.figshare.1148872</a>.</p

Availability of archived phylogenetic data as a function of age.

<p>We estimated the effect of publication age on our ability to procure partial (top panels) and complete (bottom panels) phylogenetic datasets from online archives. Overall, the probability of recovering archived phylogenetic data increases toward the present, with a conspicuous recent increase for partial datasets (left panels). The recent surge of archived phylogenetic data likely reflects recent policy changes (middle panels): studies with NSF funding are more likely to archive alignment (but not tree) files (<i>c.f.</i>, Table S15); whereas studies published in journals with JDAP membership are dramatically more likely to archive both partial and complete phylogenetic datasets. The effects of these policy initiatives are not strictly additive (right panels): the correlation of these predictor variables suggests that studies published in JDAP journals are likely to have NSF funding. Shaded areas reflect the credible intervals.</p