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Serine codon usage bias in deep phylogenomics: pancrustacean relationships as a case study.
MedLine Citation:
PMID:  22962005     Owner:  NLM     Status:  Publisher    
Phylogenomic analyses of ancient relationships are usually performed using amino acid data, but it is unclear whether amino acids or nucleotides should be preferred. With the twofold aim of addressing this problem and clarifying pancrustacean relationships, we explored the signals in the 62 protein coding genes carefully assembled by Regier et al. (2010). With reference to the pancrustaceans, this dataset infers a highly supported nucleotide tree that is substantially different to the corresponding, but poorly supported, amino acid one. We show that the discrepancy between the nucleotide-based and the amino acids-based trees is caused by substitutions within synonymous codon families (especially those of serine - TCN and AGY). We show that different arthropod lineages are differentially biased in their usage of serine, arginine, and leucine synonymous codons, and that the serine bias is correlated with the topology derived from the nucleotides, but not the amino acids. We suggest that a parallel, partially compositionally driven, synonymous codon usage bias affects the nucleotide topology. As substitutions between serine codon families can proceed through threonine or cysteine intermediates, amino acid data sets might also be affected by the serine codon usage bias. We suggest that a Dayhoff recoding strategy would partially ameliorate the effects of such bias. Although amino acids provide an alternative hypothesis of pancrustacean relationships, neither the nucleotides nor the amino acids version of this data set seem to bring enough genuine phylogenetic information to robustly resolve the relationships within group, which should still be considered unresolved.
Omar Rota Stabelli; Nicolas Lartillot; Hervé Philippe; Davide Pisani
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Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2012-9-6
Journal Detail:
Title:  Systematic biology     Volume:  -     ISSN:  1076-836X     ISO Abbreviation:  Syst. Biol.     Publication Date:  2012 Sep 
Date Detail:
Created Date:  2012-9-10     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  9302532     Medline TA:  Syst Biol     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Department of Biology, The National University of Ireland, Maynooth, co. Kildare, Ireland.
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