Applications to models of nucleotide evolution, recombination, the Wright-Fisher process, coalescence, genetic mapping, sequence analysis.
The best-fit models of nucleotide evolution were estimated by MrModeltest v. 2.3 (Nylander, [2004]), with Akaike Information Criterion as a relative quality measure of the model (Posada and Buckley, [2004]).
The best models of nucleotide substitution were selected with MrModelTest v2.3 (available from www.abc.se/~nylander/) and PAUP v4.0b10 [21].
Optimal models of nucleotide substitution were assessed using the maximum likelihood approach implemented in Modeltest v3.7 [91].
In principle straightforward, in practice this is a computationally intensive procedure informed by complex models of nucleotide substitution [5].
Maximum likelihood phylogenetic trees were obtained with PHYML 2.4.4 [94] using the previously determined models of nucleotide substitution for each genome region and sample, and support for the nodes were evaluated by bootstrapping with 1000 pseudorreplicates.
As described for the mitochondrial analyses, the most appropriate models of nucleotide evolution for the ML and Bayesian analyses were determined to be HKY+I+G for Tub1 and TrN+I+G for Tub2.
Using the aligned sequences and the best-fit models of nucleotide substitution, we estimated a maximum likelihood phylogeny using the PHYML algorithm with a BIONJ starting tree [43], [44].
The alleles were also tested for positive and negative selection of individual codons using the single likelihood ancestor counting (SLAC) method [46] with both the General Reversible (REV) and HKY85 models of nucleotide substitution.
We used ModelTest Server running ModelTest 3.8 [68], [68] and MrModeltest 2.3 for the statistical selection of models of nucleotide substitution (confidence level for LRT's = 0.01 with branch lengths counted as parameters).
Supporting this hypothesis, Zeidner et al. (2005) [33] concluded that cyanophage psbA sequences evolve at an increased evolutionary rate compared to cyanobacterial sequences based on models of nucleotide and codon evolution.
