Fitting nonstationary general-time-reversible models to obtain edge-lengths and frequencies for the barry-hartigan model.

Abstract:

:Among models of nucleotide evolution, the Barry and Hartigan (BH) model (also known as the General Markov Model) is very flexible as it allows separate arbitrary substitution matrices along edges. For a given tree, the estimates of the BH model are a set of joint probability matrices, each giving the pairwise frequencies of nucleotides at the ends of the edge. We have previously shown that, due to an identifiability problem, these cannot be expected to consistently estimate the actual pairwise frequencies. A further consequence is that internal node frequency estimates are likely to be incorrect. Here we define a nonstationary GTR model for each edge that we refer to as the NSGTR model. We fit the NSGTR model by minimizing the sums of squares between the estimates of transition probabilities under the NSGTR model and the estimates provided by a fitted BH model. This NSGTR model provides estimates that avoid the identifiability difficulties of the BH model while closely fitting it. With the best-fitting NSGTR estimates, we are able to get interpretable frequency vectors at internal nodes as well as edge length estimates that are otherwise not yielded by the BH model. These edge lengths are interpretable as the expected number of substitutions along an edge for the model. We also show that for a nonstationary continuous-time model these are not the same as the edge length parameters for conventional substitution matrices that are output by nonstationary model phylogenetic estimation programs such as nhPhyML.

journal_name

Syst Biol

journal_title

Systematic biology

authors

Zou L,Susko E,Field C,Roger AJ

doi

10.1093/sysbio/sys046

subject

Has Abstract

pub_date

2012-12-01 00:00:00

pages

927-40

issue

6

eissn

1063-5157

issn

1076-836X

pii

sys046

journal_volume

61

pub_type

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