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The first model is the null model without adaptive evolution and the second model is the alternative model with adaptive evolution, so a significant improvement in maximum likelihood supports positive selection.
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All results obtained were supported by high Bayesian and Maximum likelihood support values.
The phylogenetic analyses using parsimony and maximum likelihood supported the results from Bayesian inference on the combined five-locus dataset.
For Groups 2, 3 and 5 maximum likelihood support values were similar to Bayesian support values.
Maximum-likelihood support for the Bayesian maximum-clade-credibility trees was estimated using 1,000 bootstrap replicates.
Maximum-likelihood support was calculated for the trees inferred from the three data supermatrices.
For a small number of nodes, notably within Pitheciidae, there was no maximum-likelihood support for the nodes estimated using Bayesian analysis.
Maximum-likelihood support for the inferred topology was generated from 100 bootstrap replicates of the data with PhyML3.0 (63) (LG matrix; GTR+Γ+I, as described above).
As larger amounts of data were incorporated into the analyses, however, this picture was modified – using complete 12S rRNA and cytochrome b sequences, Tougard et al. [ 8] found high support (maximum likelihood bootstrap support of 97%) for the phylogeny as outlined by geography (although they could not, using a Kishino-Hasegawa test, reject outright the horn topology).
Indeed, phylogenetic analysis of the EF1 family with bacterial SelB and other long branches subgroups excluded shows a relationship of EF-Tu with a/eEF1A to the exclusion of aIF2g and aSelB, albeit with low statistical support (maximum likelihood bootstrap support of 51%, Additional file 4).
The resulting maximum likelihood tree supports the grouping of Mfav-SCRiP2 and Mfav-SCRiP5, Mfav-SCRiP4 and Mfav-SCRiP6, and Mcap-SCRiP1 and Amil-SCRiP3, while the relationship between the remaining SCRiPs, i.e. Mfav-SCRiP1, 8 and Amil-SCRiP2 could not be resolved (Figure 2).
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