Evolution of base-substitution gradients in primate mitochondrial genomes

Abstract

Inferences of phylogenies and dates of divergence rely on accurate modeling of evolutionary processes; they may be confounded by variation in substitution rates among sites and changes in evolutionary processes over time. In vertebrate mitochondrial genomes, substitution rates are affected by a gradient along the genome of the time spent being single-stranded during replication, and different types of substitutions respond differently to this gradient. The gradient is controlled by biological factors including the rate of replication and functionality of repair mechanisms; little is known, however, about the consistency of the gradient over evolutionary time, or about how evolution of this gradient might affect phylogenetic analysis. Here, we evaluate the evolution of response to this gradient in complete primate mitochondrial genomes, focusing particularly on A-->G substitutions, which increase linearly with the gradient. We developed a methodology to evaluate the posterior probability densities of the response parameter space, and used likelihood ratio tests and mixture models with different numbers of classes to determine whether groups of genomes have evolved in a similar fashion. Substitution gradients usually evolve slowly in primates, but there have been at least two large evolutionary jumps: on the lineage leading to the great apes, and a convergent change on the lineage leading to baboons (Papio). There have also been possible convergences at deeper taxonomic levels, and different types of substitutions appear to evolve independently. The placements of the tarsier and the tree shrew within and in relation to primates may be incorrect because of convergence in these factors.

Figure 1.

G/A ratios for complete primate mitochondrial genomes and two near outgroups. Third codon positions containing G/A were grouped into 20 equal-size bins for each genome, and the ratio of G/A in each bin is graphed versus the average DssH for that bin.

Figure 2.

Graph of MLE slopes versus MLE intercepts along with major clusters in ratio cluster analyses. We performed mixture (A) and hierarchical analyses (B) of G/A ratios, and hierarchical analyses of (C) C/T and (D) Y/R ratios. Groups are labeled by their order of clustering.

Figure 3.

Posterior probabilities for each species to belong to each model for the five-model mixture. The posterior probabilities are averaged across 10 independent chains. The models in descending order of magnitude of intercept are black (Group S), gray (Group T), white (Group U), diagonal lines (Group V), and gray hatch (Group W). Group identifications are the same as in Figure 2B.

Figure 4.

G/A mixture model groups mapped onto a phylogenetic tree of the primate species used in this study. This is the primate phylogeny most compatible with the mitochondrial sequences, but is probably inaccurate in some topological details (see Methods). Arrows indicate possible locations of large changes in the response curve, and are labeled to match the mixture model clusters in Figure 2B. A double-headed arrow is used between the flying lemur and the rest of the species to indicate the slight ambiguity in its outgroup status, as discussed in the text. Clusters shown are for the model with five clusters, except that clusters V and W have similar slopes and intercepts, and are grouped into cluster Z as in the three-cluster analysis.

Figure 5.

Graph of MLE slopes versus MLE intercepts along with major groups showing a summary interpretation of G/A evolution. Arrows indicate possible changes in response curves, and are discussed in the text.

Figure 6.

Regression of slope plus intercept for different codon positions. The MLE estimators of slope plus intercept response curves for each species in the analysis for first codon positions (diamonds) and second codon positions (circles) versus third codon positions. The regression line is shown, and the slope, intercept, and R² values are shown adjacent to each line.

Figure 7.

Comparison of the most likely trees relating the deeply diverging primate groups and outgroups. Bootstrap values for the DNA-based NJ analysis are shown on (A) when <100%. Posterior probabilities for the nucleotide Bayesian analysis were 100%, and the one branch <100% in the amino acid analysis is shown in (B). The likelihood is shown for (A), the most likely topology under the DNA-based analysis, and differences from the most likely tree are shown underneath topologies (B–E).

Figure 8.

Linear regression of (A) G/A intercept and (B) R/Y slope versus gestation time. The slope, intercept, and R² values are shown next to the regression lines.