Interactive phylogenetic trees in online journal articles
About the interactive tree viewer
Displayed in the middle article pane below abstract, this application allows the reader to interactively explore phylogenetic trees on ScienceDirect. To support this functionality, authors of relevant articles are invited to submit their tree data in Newick and NexML formats.
Figure 1. Representation of how the interactive tree viewer will appear on ScienceDirect.
Using the viewer, it is possible to export tree data, zoom in/out of certain tree areas, change the tree layout, search in the tree, collapse / expand tree nodes and branches.
Benefits for authors and readers
The interactive tree viewer functionality enables authors to enrich their relevant online articles by displaying interactive phylogenetic trees directly within the article. This allows readers to get quick and intuitive access to the phylogenetic data and hence understand better the outcome of scientific experiments described in the article.
Innovating & enriching content
For almost 350 years, academic articles have been published in a similar layout – a format which starts with an abstract and ends with a conclusion and a list of references. Articles were presented in this way with the reader of the printed version in mind. However most researchers now access articles online, which means that readership styles and how information is gathered have changed.
We are adapting to these changes because we want to help authors improve how their research is presented online and readers to gain deeper insights faster. Offering the interactive tree viewer functionality in our journals is just one of the ways we are doing this.
Tree data formats
The interactive tree viewer developed by Elsevier supports the following tree data formats: Newick and NeXML. Tree data submitted in other formats will not be processed.
Newick is a commonly used data format for representing phylogenetic trees. It is used by many phylogenetics software packages, e.g. PAUP*, GARLI, MrBayes, PHYLIP, TREE-PUZZLE, etc. Software packages like PAUP* and FigTree allow other tree file formats to be converted to Newick.
NeXML is a new exchange standard for representing phyloinformatic data. NeXML read and write abilities are implemented in a number of software applications, e.g. Mesquite, phylobase package for R, DAMBE, etc. It is also possible to convert other tree file formats to NeXML using conversion utilities available at: http://www.nexml.org.
Preparation of taxon labels (as also recommended by TreeBase)
- Make sure that taxon names in the tree file match the corresponding figure in the article
- Avoid using quotation marks, brackets, parentheses, commas, colons and semicolons
- Do not abbreviate taxon names (e.g. write "Homo sapiens" not "H. sapiens")
- Avoid using codes for non-redundant names (e.g. write "Drosophila melanogaster" not "DMelan45GRX”)
Each tree must be contained in an individual data file before being uploaded separately to the online submission system, via the "phylogenetic tree data" submission category or as a supplementary file, depending on the journal (for details please refer to Guide for Authors). Newick files must have the extension .new or .nwk (note that a semicolon is needed to end the tree). Please do not enclose comments in Newick files and also delete any artificial line breaks within the tree data because these will stop the tree from showing. For NeXML, the file extension should be .xml. Please do not enclose comments in the file. Tree data submitted with other file extensions will not be processed.
Normally the trees should be limited to those that were published as figures in the manuscript. However, a set of trees that were used to produce a published consensus tree is also acceptable.
It is strongly recommended to validate Newick and NeXML files prior to submission using the validation tool that we provide. For optimal performance, please use Internet Explorer 9 or Mozilla Firefox 4 and higher. You will have to copy the entire content of your Newick/NeXML file and paste the data you copied in the space provided by the validation tool. Once this is done, click on the "Display tree" button to see how the tree will look like. Please only upload your tree data to the online submission system if you are satisfied with the phylogenetic tree rendering provided by the tool.
Interactive Phylogenetic Trees will be provided in the online version of the article. The PDF/printed version of the article will feature static figures only (if those figures are included in the article manuscript). In the online version, it will also be possible to download the original tree files using the interactive tree viewer. Authors are encouraged to upload their tree data to relevant data repositories such as TreeBase and Dryad.
The Interactive Tree Viewer was developed using the jsPhyloSVG library.
If you wish to provide feedback on the interactive tree viewer or have a suggestion for another innovation that would further enhance the online article please get in touch.