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Measuring Phylogenetic Information of Incomplete Sequence Data

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Title
Measuring Phylogenetic Information of Incomplete Sequence Data
Other Titles
Gap이 포함된 DNA/아미노산 서열 데이터의 정보량 측정
Authors
Seo, Tae-Kun
Gascuel, Olivier
Thorne, Jeffrey L.
Subject
Evolutionary Biology
Keywords
MAXIMUM-LIKELIHOOD-ESTIMATIONNUCLEOTIDE SUBSTITUTIONEVOLUTIONARY INFERENCESTATISTICAL ALIGNMENTMODEL SELECTIONAMINO-ACIDDNATREEMITOCHONDRIALBLOCKS
Issue Date
2022-04-19
Citation
Seo, Tae-Kun, Gascuel, Olivier, Thorne, Jeffrey L.. 2022. "Measuring Phylogenetic Information of Incomplete Sequence Data". SYSTEMATIC BIOLOGY, 71(3): 630-648.
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.]
URI
https://repository.kopri.re.kr/handle/201206/13542
DOI
http://dx.doi.org/10.1093/sysbio/syab073
Type
Article
Station
기타()
Indexed
SCIE
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