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Data from: A simple approach for maximizing the overlap of phylogenetic and comparative data

posted on 2022-06-11, 04:23 authored by Matthew W. Pennell, Richard G. FitzJohn, William K. Cornwell
Biologists are increasingly using curated, public data sets to conduct phylogenetic comparative analyses. Unfortunately, there is often a mismatch between species for which there is phylogenetic data and those for which other data are available. As a result, researchers are commonly forced to either drop species from analyses entirely or else impute the missing data. A simple strategy to improve the overlap of phylogenetic and comparative data is to swap species in the tree that lack data with ‘phylogenetically equivalent’ species that have data. While this procedure is logically straightforward, it quickly becomes very challenging to do by hand. Here, we present algorithms that use topological and taxonomic information to maximize the number of swaps without altering the structure of the phylogeny. We have implemented our method in a new R package phyndr, which will allow researchers to apply our algorithm to empirical data sets. It is relatively efficient such that taxon swaps can be quickly computed, even for large trees. To facilitate the use of taxonomic knowledge, we created a separate data package taxonlookup; it contains a curated, versioned taxonomic lookup for land plants and is interoperable with phyndr. Emerging online data bases and statistical advances are making it possible for researchers to investigate evolutionary questions at unprecedented scales. However, in this effort species mismatch among data sources will increasingly be a problem; evolutionary informatics tools, such as phyndr and taxonlookup, can help alleviate this issue.

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Land plant taxonomic lookup tableThis dataset is a stable version (version 1.0.1) of the dataset contained in the taxonlookup R package (see for the most recent version). It contains a taxonomic reference table for 16,913 genera of land plants along with the number of recognized species in each genus.plant_lookup.csv


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