The modern classification of plants was introduced over 250 years ago by Carl Linnaeus. A century later, Charles Darwin suggested that all species descended from a common ancestor and established the “tree of life” – a unique hierarchical model of relationships among all organisms based on their similarities and differences. Since then, taxonomists in the world of botany and ecology have attempted to map classifications from plants to tree to trace evolutionary links.
In the case of vascular plants, which have tissues that conduct water, sap and nutrients, only about 20% of the 357,000 species worldwide have 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.
In 2015, Dr. Hong Qian, who is affiliated with the Research and Collections Center of the Illinois State Museum in the United States, came up with the idea of creating two freely available software packages to solve this problem – one for seed plants (S. PhyloMaker) and one for vascular plants (V.PhyloMaker). R packages, which are based on open source software widely used in the circle of researchers, rely on 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 that researchers find them useful.
However, according to Dr. Qian, the packages had a downside: “Plant names in the evolutionary trees implemented in both packages have been standardized according to The Plant List (a working list of all known plant species), which has been static since 2013. and is now obsolete. Considering that several global plant databases have been recently developed, we felt it was time to update V.PhyloMaker, especially,” says he.
In an article published in the journal KeAi Plant diversity, Dr. Qian and his colleague introduce the new version of V.PhyloMaker – V.PhyloMaker2. This update retains the botanical nomenclature from The Plant List, but also includes two new botanical nomenclatures: the Leipzig Vascular Plant Catalog Database and the World Plant Database.
Dr. Qian notes, “As a result, V.PhyloMaker2 can generate more robust evolutionary trees that help researchers obtain more reliable results and conclusions.
Contact the author: Hong Qian, [email protected]
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The title of the article
V.PhyloMaker2: An updated and expanded R package that can generate very large phylogenies for vascular plants
Conflict of Interest Statement
The authors declare that they have no known competing financial interests or personal relationships which might appear to influence the work reported in this article.
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