Advanced formulation of base pair changes in the stem regions of ribosomal RNAs; its application to mitochondrial rRNAs for resolving the phylogeny of animals

Journal of Theoretical Biology
Jinya Otsuka, Nobuyoshi Sugaya

Abstract

The ribosomal RNAs (rRNAs) of animal mitochondria, especially those of arthropod mitochondria, have a higher content of G:U and U:G base pairs in their stem regions than the nuclear rRNAs. Thus, the theoretical formulation of base pair changes is extended to incorporate the faster base pair changes A:U<-->G:U<-->G:C and U:A<-->U:G<-->C:G into the previous formulation of the slower base pair changes between A:U, G:C, C:G and U:A. The relative base pair change probability containing the faster and slower base pair changes is theoretically derived to estimate the divergence time of rRNAs under the influence of selection for these base pairs. Using the cartilaginous fish-teleost fish divergence and the crustacean-insect divergence as calibration points, the present method successfully predicts the divergence times of the main branches of animals: Deuterostomia and Protostomia diverged 9.2 x 10(8) years ago, the divergence of Echinodermata, Hemichordata and Cephalochordata succeedingly occurred during the period from 8 x 10(8) to 6 x 10(8) years ago, while Arthropoda, Annelida and Mollusca diverged almost concomitantly about 7 x 10(8) years ago. The dating for the divergence of Platyhelminthes and Cnidaria is traced back to 1.2 x 10...Continue Reading

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Citations

Jan 19, 2008·Theory in Biosciences = Theorie in Den Biowissenschaften·Athanasius F BompfünewererChristina Witwer
Mar 19, 2011·Molecular Biology and Evolution·Dror Hilman, Uri Gat
Apr 17, 2012·BMC Evolutionary Biology·Sophie A O ArmitageIgnacio G Bravo
Feb 2, 2013·General and Comparative Endocrinology·Ravisankar ValsalanHelgi B Schiöth
Sep 29, 2011·Molecular Phylogenetics and Evolution·Peter RehmThorsten Burmester
Nov 11, 2015·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Gregory A Wray

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