Experimental design in phylogenetics: testing predictions from expected information

Systematic Biology
Diego San MauroTim Massingham

Abstract

Taxon and character sampling are central to phylogenetic experimental design; yet, we lack general rules. Goldman introduced a method to construct efficient sampling designs in phylogenetics, based on the calculation of expected Fisher information given a probabilistic model of sequence evolution. The considerable potential of this approach remains largely unexplored. In an earlier study, we applied Goldman's method to a problem in the phylogenetics of caecilian amphibians and made an a priori evaluation and testable predictions of which taxon additions would increase information about a particular weakly supported branch of the caecilian phylogeny by the greatest amount. We have now gathered mitogenomic and rag1 sequences (some newly determined for this study) from additional caecilian species and studied how information (both expected and observed) and bootstrap support vary as each new taxon is individually added to our previous data set. This provides the first empirical test of specific predictions made using Goldman's method for phylogenetic experimental design. Our results empirically validate the top 3 (more intuitive) taxon addition predictions made in our previous study, but only information results validate unambiguo...Continue Reading

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Citations

Feb 1, 2014·Molecular Phylogenetics and Evolution·Diego San MauroMark Wilkinson
Jun 9, 2017·Systematic Biology·Seraina KlopfsteinNick Goldman
Mar 25, 2019·Molecular Biology and Evolution·Karen Siu-TingChristopher J Creevey
Feb 11, 2021·BMC Ecology and Evolution·Jifeng ZhangLiuwang Nie

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