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Title: Measuring Phylogenetic Information of Incomplete Sequence Data
Abstract Widely used approaches for extracting phylogenetic information from aligned sets of molecular sequences rely upon probabilistic models of nucleotide substitution or amino-acid replacement. The phylogenetic information that can be extracted depends on the number of columns in the sequence alignment and will be decreased when the alignment contains gaps due to insertion or deletion events. Motivated by the measurement of information loss, we suggest assessment of the effective sequence length (ESL) of an aligned data set. The ESL can differ from the actual number of columns in a sequence alignment because of the presence of alignment gaps. Furthermore, the estimation of phylogenetic information is affected by model misspecification. Inevitably, the actual process of molecular evolution differs from the probabilistic models employed to describe this process. This disparity means the amount of phylogenetic information in an actual sequence alignment will differ from the amount in a simulated data set of equal size, which motivated us to develop a new test for model adequacy. Via theory and empirical data analysis, we show how to disentangle the effects of gaps and model misspecification. By comparing the Fisher information of actual and simulated sequences, we identify which alignment sites and tree branches are most affected by gaps and model misspecification. [Fisher information; gaps; insertion; deletion; indel; model adequacy; goodness-of-fit test; sequence alignment.]  more » « less
Award ID(s):
1754142
PAR ID:
10339446
Author(s) / Creator(s):
; ;
Editor(s):
Ho, Simon
Date Published:
Journal Name:
Systematic Biology
Volume:
71
Issue:
3
ISSN:
1063-5157
Page Range / eLocation ID:
630 to 648
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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