The Diversity Present in 5140 Human Mitochondrial Genomes

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The Diversity Present in 5140 Human Mitochondrial Genomes Luísa Pereira, Fernando Freitas, Verónica Fernandes, Joana B. Pereira, Marta D. Costa, Stephanie Costa, Valdemar Máximo, Vincent Macaulay, Ricardo Rocha, David C. Samuels The American Journal of Human Genetics Volume 84, Issue 5, Pages 628-640 (May 2009) DOI: 10.1016/j.ajhg.2009.04.013 Copyright © 2009 The American Society of Human Genetics Terms and Conditions

Figure 1 The Geographical Origin of the 5140 mtDNA Sequences Deposited in GenBank, as of the End of August 2008 African-American descendants were included in sub-Saharan Africa and European-American descendants were included in Eurasians given that they were homogeneous groups, bearing haplogroups belonging to these regions, whereas USA “Hispanics” constituted a mixed sample, with most lineages belonging to East Asian haplogroups observed in Native Americans. The American Journal of Human Genetics 2009 84, 628-640DOI: (10.1016/j.ajhg.2009.04.013) Copyright © 2009 The American Society of Human Genetics Terms and Conditions

Figure 2 Protein Diversity Correlation between the observed polymorphic positions and the gene size (bp) in the 13 protein-coding genes (A) and distributions of types of amino acids before and after the substitution (B). The American Journal of Human Genetics 2009 84, 628-640DOI: (10.1016/j.ajhg.2009.04.013) Copyright © 2009 The American Society of Human Genetics Terms and Conditions

Figure 3 Transitions and Transversions Correlation between the observed and maximum possible variations for (A) transitions and (B) transversions in the 13 protein-coding genes. The American Journal of Human Genetics 2009 84, 628-640DOI: (10.1016/j.ajhg.2009.04.013) Copyright © 2009 The American Society of Human Genetics Terms and Conditions

Figure 4 Synonymous and Nonsynonymous Sequence Changes Correlation between observed and maximum possible variations for (A) synonymous and (B) nonsynonymous substitutions in the 13 protein-coding genes. The American Journal of Human Genetics 2009 84, 628-640DOI: (10.1016/j.ajhg.2009.04.013) Copyright © 2009 The American Society of Human Genetics Terms and Conditions

Figure 5 Correlation between Observed and Maximum Possible Variations for Amino Acids Originated from Nonsynonymous Mutations The amino acids from group (VIAMT) are represented by red squares and the ones from group (FLPS) are represented by blue circles; the remaining amino acids are represented by black diamonds. The American Journal of Human Genetics 2009 84, 628-640DOI: (10.1016/j.ajhg.2009.04.013) Copyright © 2009 The American Society of Human Genetics Terms and Conditions

Figure 6 Distribution of Polymorphic Positions in the Various Structural Regions of the tRNA Genes The American Journal of Human Genetics 2009 84, 628-640DOI: (10.1016/j.ajhg.2009.04.013) Copyright © 2009 The American Society of Human Genetics Terms and Conditions

Figure 7 Variability in the Region of the Origin of the Light Strand Related to the Inferred DNA Secondary Structure Secondary structure of the OL region inferred in mfold28 with the observed polymorphic positions 5741, 5742, 5744, 5746, and 5747 indicated. The American Journal of Human Genetics 2009 84, 628-640DOI: (10.1016/j.ajhg.2009.04.013) Copyright © 2009 The American Society of Human Genetics Terms and Conditions

Figure 8 Variability in a tRNA Gene Related to the RNA Secondary Structure The secondary structure of the threonine tRNA and the observed polymorphic positions in the human database (gray hexagons), and positions that are 100% (square) and >90% (circle) conserved in mammalian species.30 The American Journal of Human Genetics 2009 84, 628-640DOI: (10.1016/j.ajhg.2009.04.013) Copyright © 2009 The American Society of Human Genetics Terms and Conditions