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

Matthew W. Pennell, Richard G. FitzJohn, William K. Cornwell
doi: https://doi.org/10.1101/024992
Matthew W. Pennell
1Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, U.S.A
2Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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  • For correspondence: mwpennell@gmail.com
Richard G. FitzJohn
3Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
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William K. Cornwell
4Ecology and Evolution Reaseach Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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Summary

  1. 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 is available. As a result, researchers are commonly forced to either drop species from analyses entirely or else impute the missing data.

  2. Here we outline a simple solution to increase the overlap while avoiding potential the biases introduced by imputing data. If some external topological or taxonomic information is available, this can be used to maximize the overlap between the data and the phylogeny. We develop an algorithm that replaces a species lacking data with a species that has data. This swap can be made because for those two species, all phylogenetic relationships are exactly equivalent.

  3. 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.

  4. Emerging online databases 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.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted August 20, 2015.
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A simple approach for maximizing the overlap of phylogenetic and comparative data
Matthew W. Pennell, Richard G. FitzJohn, William K. Cornwell
bioRxiv 024992; doi: https://doi.org/10.1101/024992
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A simple approach for maximizing the overlap of phylogenetic and comparative data
Matthew W. Pennell, Richard G. FitzJohn, William K. Cornwell
bioRxiv 024992; doi: https://doi.org/10.1101/024992

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