Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified

Thomas M Keane, Christopher J Creevey, Melissa M Pentony, Thomas J Naughton, James O Mclnerney

Allbwn ymchwil: Cyfraniad at gyfnodolynErthygladolygiad gan gymheiriaid

939 Dyfyniadau(SciVal)
83 Wedi eu Llwytho i Lawr (Pure)

Crynodeb

Background
In recent years, model based approaches such as maximum likelihood have become the methods of choice for constructing phylogenies. A number of authors have shown the importance of using adequate substitution models in order to produce accurate phylogenies. In the past, many empirical models of amino acid substitution have been derived using a variety of different methods and protein datasets. These matrices are normally used as surrogates, rather than deriving the maximum likelihood model from the dataset being examined. With few exceptions, selection between alternative matrices has been carried out in an ad hoc manner.

Results
We start by highlighting the potential dangers of arbitrarily choosing protein models by demonstrating an empirical example where a single alignment can produce two topologically different and strongly supported phylogenies using two different arbitrarily-chosen amino acid substitution models. We demonstrate that in simple simulations, statistical methods of model selection are indeed robust and likely to be useful for protein model selection. We have investigated patterns of amino acid substitution among homologous sequences from the three Domains of life and our results show that no single amino acid matrix is optimal for any of the datasets. Perhaps most interestingly, we demonstrate that for two large datasets derived from the proteobacteria and archaea, one of the most favored models in both datasets is a model that was originally derived from retroviral Pol proteins.

Conclusion
This demonstrates that choosing protein models based on their source or method of construction may not be appropriate.
Iaith wreiddiolSaesneg
Rhif yr erthygl29
CyfnodolynBMC Evolutionary Biology
Cyfrol6
Dynodwyr Gwrthrych Digidol (DOIs)
StatwsCyhoeddwyd - 24 Maw 2006

Ôl bys

Gweld gwybodaeth am bynciau ymchwil 'Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified'. Gyda’i gilydd, maen nhw’n ffurfio ôl bys unigryw.

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