Phylogenetic representativeness: a new method for evaluating taxon sampling in evolutionary studies

Background: Taxon sampling is a major concern in phylogenetic studies. Incomplete, biased, or improper taxon sampling can lead to misleading results in reconstructing evolutionary relationships. Several theoretical methods are available to optimize taxon choice in phylogenetic analyses. However, most involve some knowledge about the genetic relationships of the group of interest (i.e., the ingroup), or even a well-established phylogeny itself; these data are not always available in general phylogenetic applications. Results: We propose a new method to assess taxon sampling developing Clarke and Warwick statistics. This method aims to measure the "phylogenetic representativeness" of a given sample or set of samples and it is based entirely on the pre-existing available taxonomy of the ingroup, which is commonly known to investigators. Moreover, our method also accounts for instability and discordance in taxonomies. A Python-based script suite, called PhyRe, has been developed...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Federico Plazzi, Ronald R. Ferrucci, Marco Passamonti
• Keywords: BMCBI 2010, Phylogenetic, Phylogenetic Studies, Taxon