DOI: 10.5061/dryad.83p1130j
title: Data from: Experimental design in phylogenetics: testing predictions from expected information

description: Taxon and character sampling is 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. Using mitogenomic and rag1
 sequences (some newly determined for this study) from additional caecilian
 species we studied how information (both expected and observed) and
 bootstrap support varies as each new taxon is individually added,
 providing the first empirical test of specific predictions made using
 Goldman’s method for phylogenetic experimental design. Our results
 empirically validate the top three (more intuitive) taxon addition
 predictions made in our previous study, but only information results
 validate unambiguously the fourth (less intuitive) prediction. This
 highlights a complex relationship between information and support,
 reflecting that each measures different things: information is related to
 the ability to estimate branch length accurately, and support to the
 ability to estimate the tree topology accurately. Thus, an increase in
 information may be correlated with but does not necessitate an increase in
 support Our results also provide the first empirical validation of the
 widely held intuition that additional taxa that join the tree proximal to
 poorly supported internal branches are more informative and enhance
 support more than additional taxa that join the tree more distally. Our
 work supports the view that adding more data for a single (well chosen)
 taxon may increase phylogenetic resolution and support in weakly supported
 parts of the tree without adding more characters/genes while illustrating
 that less well chosen taxon additions can have the opposite effect.
 Altogether our results corroborate that, although still underexplored,
 Goldman’s method offers a powerful tool for experimental design in
 molecular phylogenetic studies. However, there are still several drawbacks
 to overcome, and further assessment of the method is needed in order to
 make it better understood, more accessible, and able to assess additions
 of multiple taxa.
description: Master
 AlignmentMaster alingment of
 mitochondrial genome and nuclear rag1 data in nexus format. The matrix
 includes a tree block with the maximum likelihood tree obtained with RAxML
 v7.2.6. This data file has also been deposited in TreeBASE under accession
 number S11625.ML_Combined.nxsSupplementary MaterialDistinct structural features of the mitochondrial genome of Crotaphatrema lamottei.Supplementary_Material.pdfSupplementary TableComparison of geometric means of boostrap proportions including and not including the controversial branch.Supplementary_Table.pdf