Evolution of base frequency gradients in primate mitochondrial genomes

Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, LA 70803, USA.
Genome Research (Impact Factor: 14.63). 05/2005; 15(5):665-73. DOI: 10.1101/gr.3128605
Source: PubMed


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.

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Available from: Herve Seligmann,
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    • "Vertebrate mitogenomes almost universally break Chargaff's second parity rule (Albrecht-Buehler, 2006) that in single stranded DNA, complementary nucleotides have almost equal frequencies. This mitochondrial exception is probably due to asymmetrical, directional replication (Lee and Clayton, 1998; Clayton, 2000a, 2000b; Brown and Clayton, 2006), which produces directional mutation gradients (Reyes et al., 1998; Krishnan et al., 2004a, 2004b; Raina et al., 2005), biasing differently nucleotide contents of different mitogenome Q2 regions (Seligmann et al., 2006; Seligmann, 2008, 2010, 2011, 2012a, 2013a). Mitochondrial genomes are usually short. "

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    • "This provided us with the opportunity to compare the strand asymmetry of genes coded on different strands. Contrastingly, in mammal mitochondrial genomes, which are frequently used models for studies of strand asymmetry, only one protein-coding gene is coded on the minority strand, and this gene has been excluded from many [23], [45] but not all [25] studies. Here, we analyzed strand asymmetry for individual protein-coding genes in 120 insect mitochondrial genomes with special reference to the relationship between strand asymmetry and gene direction/genome replication orientation. "
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    ABSTRACT: Strand asymmetry in nucleotide composition is a remarkable feature of animal mitochondrial genomes. Understanding the mutation processes that shape strand asymmetry is essential for comprehensive knowledge of genome evolution, demographical population history and accurate phylogenetic inference. Previous studies found that the relative contributions of different substitution types to strand asymmetry are associated with replication alone or both replication and transcription. However, the relative contributions of replication and transcription to strand asymmetry remain unclear. Here we conducted a broad survey of strand asymmetry across 120 insect mitochondrial genomes, with special reference to the correlation between the signs of skew values and replication orientation/gene direction. The results show that the sign of GC skew on entire mitochondrial genomes is reversed in all species of three distantly related families of insects, Philopteridae (Phthiraptera), Aleyrodidae (Hemiptera) and Braconidae (Hymenoptera); the replication-related elements in the A+T-rich regions of these species are inverted, confirming that reversal of strand asymmetry (GC skew) was caused by inversion of replication origin; and finally, the sign of GC skew value is associated with replication orientation but not with gene direction, while that of AT skew value varies with gene direction, replication and codon positions used in analyses. These findings show that deaminations during replication and other mutations contribute more than selection on amino acid sequences to strand compositions of G and C, and that the replication process has a stronger affect on A and T content than does transcription. Our results may contribute to genome-wide studies of replication and transcription mechanisms.
    PLoS ONE 09/2010; 5(9):e12708. DOI:10.1371/journal.pone.0012708 · 3.23 Impact Factor
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    • "Mitochondrial transition substitution rates and substitution gradients across the genome may also evolve substantially across lineages (Raina et al. 2005b). Because transversion (TV; purinepyrimidine) substitution dynamics in mtDNA are slower and far more consistent than transitions (Raina et al. 2005b), they are much less prone to saturation, the use of exclusively transversions for relative rate comparisons (e.g., dN/dS) can eliminate many potential errors (Raina et al. 2005a; Yang et al. 2000). Thus, the transversion component of dN/dS was estimated by averaging over all 3 rd codon positions in the mtDNA with conserved four-fold redundancy (dS TV4X ), while the non-synonymous transversion rate was measured at first and second codon positions (dN TV12 ) for each gene under consideration. "
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    ABSTRACT: This chapter contains sections titled: Introduction Overview of Considerations in Studying Protein Evolution Function and Evolutionary Genomics Integrating Inferences to Detect and Interpret Adaptation: An Example with Snake Metabolic Proteins Conclusion References
    Evolutionary Genomics and Systems Biology, 07/2010: pages 183-202; , ISBN: 9780470195147
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