[genus]_[species]; Presenting phylogenies to facilitate synthesis

Area of Science:

• Evolutionary Biology
• Bioinformatics
• Computational Biology

Background:

• Published phylogenies are crucial for synthesizing the Tree of Life and supporting downstream research.
• However, a significant number of studies do not present phylogenetic data in a fully synthesizable format, hindering scientific progress.

Purpose of the Study:

• To review current phylogenetic presentation practices and identify barriers to data synthesis.
• To propose standardized guidelines for publishing phylogenetic data to enhance its usability and facilitate the creation of a comprehensive Tree of Life.

Main Methods:

• Review of phylogenetic presentation formats across published studies.
• Analysis of aspects hindering further computational and manual analysis of phylogenetic data.
• Proposal of a formal grammar for standardized phylogeny terminal formatting.

Main Results:

• Fewer than half of studies provide their primary phylogenetic results in a machine-readable tree format (e.g., Newick) in supplementary materials.
• Significant variation exists in the formatting of machine-readable trees, complicating parsing and data integration.
• Phylogenetic images also exhibit plotting style variations, necessitating automated transcription tools for data extraction.

Conclusions:

• Implementing standardized formats for machine-readable phylogenetic trees is essential for enabling large-scale data synthesis.
• Clear guidelines for file naming, terminal labels, and data delimiters will greatly improve the utility of published phylogenies.
• Developing automated tools to transcribe data from phylogenetic images is necessary to incorporate existing studies into the Tree of Life.