Dataset Information

Gamma-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates.

ABSTRACT:

Background

Over the past two decades, there have been several approximate methods that adopt different mutation models and used for estimating nonsynonymous and synonymous substitution rates (Ka and Ks) based on protein-coding sequences across species or even different evolutionary lineages. Among them, MYN method (a Modified version of Yang-Nielsen method) considers three major dynamic features of evolving DNA sequences-bias in transition/transversion rate, nucleotide frequency, and unequal transitional substitution but leaves out another important feature: unequal substitution rates among different sites or nucleotide positions.

Results

We incorporated a new feature for analyzing evolving DNA sequences-unequal substitution rates among different sites-into MYN method, and proposed a modified version, namely gamma (gamma)-MYN, based on an assumption that the evolutionary rate at each site follows a mode of gamma-distribution. We applied gamma-MYN to analyze the key estimator of selective pressure omega (Ka/Ks) and other relevant parameters in comparison to two other related methods, YN and MYN, and found that neglecting the variation of substitution rates among different sites may lead to biased estimations of omega. Our new method appears to have minimal deviations when relevant parameters vary within normal ranges defined by empirical data.

Conclusion

Our results indicate that unequal substitution rates among different sites have variable influences on omega under different evolutionary rates while both transition/transversion rate ratio and unequal nucleotide frequencies affect Ka and Ks thus selective pressure omega.

SUBMITTER: Wang DP

PROVIDER: S-EPMC2702329 | biostudies-literature | 2009 Jun

REPOSITORIES: biostudies-literature

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Publications

Gamma-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates.

Wang Da-Peng DP Wan Hao-Lei HL Zhang Song S Yu Jun J

Biology direct 20090616

<h4>Background</h4>Over the past two decades, there have been several approximate methods that adopt different mutation models and used for estimating nonsynonymous and synonymous substitution rates (Ka and Ks) based on protein-coding sequences across species or even different evolutionary lineages. Among them, MYN method (a Modified version of Yang-Nielsen method) considers three major dynamic features of evolving DNA sequences-bias in transition/transversion rate, nucleotide frequency, and une ...[more]

PMID: 19531225

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Project description:An absolute timescale for evolution is essential if we are to associate evolutionary phenomena, such as adaptation or speciation, with potential causes, such as geological activity or climatic change. Timescales in most phylogenetic studies use geologically dated fossils or phylogeographic events as calibration points, but more recently, it has also become possible to use experimentally derived estimates of the mutation rate as a proxy for substitution rates. The large radiation of drosophilid taxa endemic to the Hawaiian islands has provided multiple calibration points for the Drosophila phylogeny, thanks to the "conveyor belt" process by which this archipelago forms and is colonized by species. However, published date estimates for key nodes in the Drosophila phylogeny vary widely, and many are based on simplistic models of colonization and coalescence or on estimates of island age that are not current. In this study, we use new sequence data from seven species of Hawaiian Drosophila to examine a range of explicit coalescent models and estimate substitution rates. We use these rates, along with a published experimentally determined mutation rate, to date key events in drosophilid evolution. Surprisingly, our estimate for the date for the most recent common ancestor of the genus Drosophila based on mutation rate (25-40 Ma) is closer to being compatible with independent fossil-derived dates (20-50 Ma) than are most of the Hawaiian-calibration models and also has smaller uncertainty. We find that Hawaiian-calibrated dates are extremely sensitive to model choice and give rise to point estimates that range between 26 and 192 Ma, depending on the details of the model. Potential problems with the Hawaiian calibration may arise from systematic variation in the molecular clock due to the long generation time of Hawaiian Drosophila compared with other Drosophila and/or uncertainty in linking island formation dates with colonization dates. As either source of error will bias estimates of divergence time, we suggest mutation rate estimates be used until better models are available.

Dataset Information

Gamma-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates.

Background

Results

Conclusion

Publications

Gamma-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates.

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