Upgrade for popular free software tool that builds evolutionary trees for vascular plants

The modern classification of plants was introduced more than 250 years ago by Carl Linnaeus. A century later, Charles Darwin suggested that all species are descended from a common ancestor, and established ‘the tree of life’ - a unique hierarchical pattern of relationships between all organisms based on their similarities and differences. Since then, taxonomists in the world of botany and ecology have been trying to map plant classifications to the tree to trace evolutionary links.

In the case of vascular plants, which have tissues that conduct water, sap and nutrients, only around 20% of the 357,000 species in the world have ever been sequenced. This has led many botanists and ecologists to rely on mega-tree approaches, which use taxonomic information to infer evolutionary relationships between species.

Back in 2015, Dr. Hong Qian, who is affiliated to the Research and Collections Center at the US’ Illinois State Museum, conceived the idea of creating two freely-available software packages to address this problem – one for seed plants (S.PhyloMaker) and one for vascular plants (V.PhyloMaker). The R packages, which are based on open-source software widely used in the circle of researchers, draw on the mega-tree approaches to build plant evolutionary trees for research use. He says: “Since their launch, they have been widely used in published studies, suggesting researchers find them useful.” 

However, according to Dr. Qian, the packages had a drawback: “Plant names in the evolutionary trees implemented in the two packages were standardised according to The Plant List (a working list of all known plant species), which has been static since 2013 and is now outdated. Considering that several global plant databases have recently been developed, we felt it was time to update V.PhyloMaker, in particular,” he explains.

In an article published in the KeAi journal Plant Diversity, Dr. Qian and his colleague present the new version of V.PhyloMaker - V.PhyloMaker2. This upgrade retains the botanical nomenclature of The Plant List, but also includes two new botanical nomenclatures: the Leipzig Catalogue of Vascular Plants database and the World Plants database.

Dr. Qian notes: “As a result, V.PhyloMaker2 can generate more robust evolutionary trees that help researchers achieve more reliable results and conclusions.”

Image: The number of publications that have used either S.PhyloMaker or V.PhyloMaker in each year, based on Clarivate’S ISI Web of Science (accessed on April 21, 2022). CREDIT: Jin and Qian, 2022, Plant Diversity https://doi.org/10.1016/j.pld.2022.05.005

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Contact the author: Hong Qian, hong.qian@illinoisstatemuseum.org