Taxon sampling is a key point in phylogenetic studies. Incomplete, biased, or improper taxon sampling can lead to misleading results in reconstructing phylogenies. Several methods are available to optimize taxon choice, involving genetic distance evaluations, interruption of long branches, etc. However, all are conceived as a posteriori tests, i. e. they can only be carried out after data collection, when most of the experimental work is already done. We think it would be very useful to have an a priori test, allowing to compute and predict goodness of taxon sampling before the phylogenetic work starts. The established taxonomy of the group under study (although not necessary the “true” one), which is usually available from literature, may help in this: given a master list of organisms, it is possible to measure to which degree different subsamples do represent the whole assemblage. For this reason, we proposed a new method to assess the representativeness of a given taxon sampling, by developing the Clarke and Warwick statistics on taxonomic distinctness. Our 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. Moreover, our method also accounts for instability and discordance in systematics: we conceived a randomization algorithm on master lists, mimicking taxonomic revisions, therefore addressing test reliability. A Python-based script suite, called PhyRe, was developed to implement all analyses, and it is available for free download at www.mozoolab.net. We showed that this method is sensitive and allows direct discrimination between representative and unrepresentative samples. It is also informative about the addition of taxa to improve taxonomic coverage of the ingroup. Provided that the investigators’ expertise is mandatory in this field, phylogenetic representativeness makes up an objective touchstone in planning phylogenetic studies.
PHYLOGENETIC REPRESENTATIVENESS: A NEW METHOD FOR EVALUATING TAXON SAMPLING IN EVOLUTIONARY STUDIES
PLAZZI, FEDERICO;PASSAMONTI, MARCO
2010
Abstract
Taxon sampling is a key point in phylogenetic studies. Incomplete, biased, or improper taxon sampling can lead to misleading results in reconstructing phylogenies. Several methods are available to optimize taxon choice, involving genetic distance evaluations, interruption of long branches, etc. However, all are conceived as a posteriori tests, i. e. they can only be carried out after data collection, when most of the experimental work is already done. We think it would be very useful to have an a priori test, allowing to compute and predict goodness of taxon sampling before the phylogenetic work starts. The established taxonomy of the group under study (although not necessary the “true” one), which is usually available from literature, may help in this: given a master list of organisms, it is possible to measure to which degree different subsamples do represent the whole assemblage. For this reason, we proposed a new method to assess the representativeness of a given taxon sampling, by developing the Clarke and Warwick statistics on taxonomic distinctness. Our 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. Moreover, our method also accounts for instability and discordance in systematics: we conceived a randomization algorithm on master lists, mimicking taxonomic revisions, therefore addressing test reliability. A Python-based script suite, called PhyRe, was developed to implement all analyses, and it is available for free download at www.mozoolab.net. We showed that this method is sensitive and allows direct discrimination between representative and unrepresentative samples. It is also informative about the addition of taxa to improve taxonomic coverage of the ingroup. Provided that the investigators’ expertise is mandatory in this field, phylogenetic representativeness makes up an objective touchstone in planning phylogenetic studies.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
