The influence of ignoring secondary structure on divergence time estimates from ribosomal RNA genes

Molecular Phylogenetics and Evolution
Martin Dohrmann

Abstract

Genes coding for ribosomal RNA molecules (rDNA) are among the most popular markers in molecular phylogenetics and evolution. However, coevolution of sites that code for pairing regions (stems) in the RNA secondary structure can make it challenging to obtain accurate results from such loci. While the influence of ignoring secondary structure on multiple sequence alignment and tree topology has been investigated in numerous studies, its effect on molecular divergence time estimates is still poorly known. Here, I investigate this issue in Bayesian Markov Chain Monte Carlo (BMCMC) and penalized likelihood (PL) frameworks, using empirical datasets from dragonflies (Odonata: Anisoptera) and glass sponges (Porifera: Hexactinellida). My results indicate that highly biased inferences under substitution models that ignore secondary structure only occur if maximum-likelihood estimates of branch lengths are used as input to PL dating, whereas in a BMCMC framework and in PL dating based on Bayesian consensus branch lengths, the effect is far less severe. I conclude that accounting for coevolution of paired sites in molecular dating studies is not as important as previously suggested, as long as the estimates are based on Bayesian consensus ...Continue Reading

References

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Sep 1, 1994·Molecular Phylogenetics and Evolution·M Schöniger, A von Haeseler
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Jun 19, 2009·Bioinformatics·Nicolas LartillotSamuel Blanquart

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Citations

Nov 13, 2014·Molecular Biology and Evolution·Thomas BourguignonTheodore A Evans

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