Literature Sample3: 100 randomly-selected 'phylogen*' articles published in 2010

The sole purpose of this survey was to estimate the frequency of reports of new trees among 2010 publications. We first searched Web of Science for 2010 papers that matched 'phylogen*' in any field. Many of the 11,664 matching publications might be false positives, i.e., papers that refer to 'phylogen*' in some way, but do not report a new tree. To estimate this fraction, we picked 100 papers at random. Each paper was assigned to BO, AS or RM for individual evaluation, with the result that 66 of the 100 papers reported a new tree.

The file "LitSample3_100RandomPhylogen2010.csv" contains results of the analysis of the sample of 100 publications. There is not much in this spreadsheet other than a determination of whether it has a new tree or not. This spreadsheet was populated by an online fillable form that is available from the authors on request (in case any reader would like to analyze their own literature sample).

We also considered false negatives due to papers that report a new phylogeny, but avoid the term 'phylogen*', using instead some term such as 'dendrogram', 'cladogram' or 'tree'. Because 'tree' has many non-phylogenetic uses, we used a restricted search methodology based on other terms associated with phylogenies, such as 'SSU' or 'cytb' and so on. By comparing matches to 'SSU + tree -phylogeny' to those for 'SSU + phylogeny', we can estimate how often authors use 'tree' as a synonym while avoiding 'phylogeny'. We got only about 1/100 as many hits, and many of these referred to "trees" that were not phylogenetic trees. Thus, the results suggest that phylogeny synonyms would increase the yield by less than 1 %.

We did not estimate false negatives due to poor indexing, or non-indexing, in Web of Science. Web of Science may contain information on articles that are indexed very incompletely, e.g., articles for which only the citation information is available, without keywords or abstract. A poorly indexed article that reports a phylogeny will only be found if 'phylogen*' appears in the title.

We also did not estimate the number of false negatives due to phylogeny reports that are not indexed at all in Web of Science. It is difficult to see how this could be done. However, one way to do it would be to take a very carefully researched review article, e.g., on phylogeny of major reptile groups, and then assess what fraction of cited phylogeny articles can be found in WoS. Apropos, TimeTree has nearly a thousand articles in its database, and a substantial fraction are not indexed in PubMed.