**Figure 10.**

*Nucleotide content differences in complete mitochondrial genomes (left side) and the three fragments of each mitochondrial genome (right side). Left to right: (G – C), (G – T), (G – A), (C – T), (C – A), and (T – A).*

Based on these results, these mitochondria are likely to be primitive. Consistent results were obtained from Ward's clustering analysis using amino acid compositions predicted from complete mitochondrial genomes as traits [59]. Thus, the *M. brevicollis* mitochondrion is the most primitive among the three. Although the *Reclinomonas americana* mtDNA (G: 0.148, C: 0.114) has previously been proposed as a mitochondrial ancestor [61], AT inversion was observed in the third fragment. In addition, differences in (G – C) and (T – A) values in *R. americana* mtDNA were smaller than those in the mtDNA of the previous three organisms. The unsymmetrical nucleotide content causes significant differences in nucleotide content

### *Cheminformatics and Its Applications*

patterns as a result of nucleotide content inversion. Judging from these results, the *R. americana* mitochondrion is probably more evolved than the former three mitochondria. In addition, AT inversion occurred in the following more highly evolved organisms: Mollusca species, squid (*Todarodes pacificus*), octopus (*Octopus vulgaris*), Echinodermata species, sea urchin (*Paracentrotus lividus*), water flea (*Daphnia pulex*), hermit crab (*Pagurus longicarpus*), and Humboldt squid (*Dosidicus gigas*) [53, 62]. In addition, large positive (G – A) values in the three fragments were observed in *Paragonimus westermani*, while large positive (G – C) and (A – T) values in the three fragments were observed for the mtDNA of representatives of the following phyla: Cnidaria (*Pavona clavus*), Platyhelminthes (*Schistosoma mansoni*), Porifera (*Geodia neptuni*), Arthropoda (*Tigriopus californicus*), and Chordata (*Branchiostoma belcheri*) [53]. Furthermore, the following invertebrate

**23**

*Visible Evolution from Primitive Organisms to* Homo sapiens

*carnosus*, and *Xenoturbella bocki* was examined [53].

mitochondria were also examined: *Acanthaster planci*, *Haliotis rubra*, *Lampsilis ornate,* and the mtDNA of hemichordates, *Saccoglossus kowalevskii, Balanoglossus* 

In the mtDNA of primate species *H. sapiens*, *P. troglodytes*, *G. gorilla*, *Macaca mulatta*, *Daubentonia madagascariensis*, *Nycticebus coucang*, and *Tupaia belangeri*, nucleotide content difference patterns were quite similar in the first four species, and large positive increases in (C – T) differences in the three fragments clearly indicated evolutionary divergence (**Figure 11**). The positive (C – T) differences in all three fragments were characteristic of these four primate mitochondria, while positive increases in (C – T) values were only observed in the third fragment of *N. coucang* and *T. belangeri* mtDNA. In contrast, nucleotide content difference patterns of the prosimian *Lemur catta* completely differed from those of the primates, although TA inversion was observed in the second fragment. The primate mtDNA nucleotide content patterns were also completely different from that of hemichordate *B. carnosus*, although their C contents were the highest among all organisms examined [59]. This finding indicates that mitochondrial structures respect epig-

In the normalization of nucleotide contents (G + C + A + T = 1), as (G = C) and (A = T) based on Chargaff's parity rules, (2G + 2A = 1) is obtained. This equation is altered to (A = 0.5 – G) and then (A – G = 0.5 – 2G). Finally, G – A = 2G – 0.5. The relationship between (G – A) and (G) is linear when both (G) and (A) are expressed by linear functions. In animal mitochondria, only the correlations between the two purines (A versus G) or the two pyrimidines (C versus T) are linear, while the correlations between purines and pyrimidines (A or G versus T or C) are weak or not correlated at all [62]. For example, when plotting (G – C), (G – T), (G – A), (C – T), (C – A), and (T – C) against G content, only (G – A) versus G content was linear in vertebrate mitochondria [59]. In invertebrate mitochondria, plotting nucleotide

Plotting (X – Y)/(X + Y) against (X – Y), the following linear relationship was obtained in mitochondria, chloroplasts, and chromosomes (**Figure 12**): (X – Y)/ (X + Y) = a (X – Y) + b, where X and Y are nucleotide contents, and (a) and (b) are constants. As (b) was almost null and (a) was ~2.0, (X – Y)/(X + Y) ≈ 2.0 (X – Y). In these genome analyses, which are independent of Chargaff's parity rules, the values of (a) for (G, C), (G, A), (G, T), (C, T), (C, A), and (A, T) were 2.5858, 1.85558, 1.9908, 1.9771, 1.9968, and 1.5689, respectively, in our previous results [53, 54]. Based on these results, (G + C), (G + A), (G + T), (C + A), (C + T), and (A + T) were 0.39, 0.54, 0.50, 0.51, 0.50, and 0.64, respectively. In virus genome analyses [53, 54], the constant values for (a) were 1.9–2.1, and the values for (X + Y) were 0.47–0.53. In contrast, in the normalization of nucleotide contents (G + C + A + T = 1), as (G = C) and (A = T) based on Chargaff's parity rules, (2G + 2A = 1) is obtained. This equation is altered to (G + A = 0.5). This value is consistent with the value obtained above from genome analyses. Similarly, (G + T = 0.5), (C + A = 0.5), and (C + T = 0.5), although (G + C) and (A + T) cannot be determined. Therefore, the four nucleotide contents are expressed by the following regression lines, plotted against G content: A = 0.5 – G, T = 0.5 – G, C = G, and G = G. Lines G and C overlap, as do lines A and T, and the former line is symmetrical to the latter against line (y = 0.25). The intercepts of lines G and C are close to the origin, while those of lines A and T are close to 0.5 at the vertical and horizontal axes. All organisms from bacteria to *H. sapiens* are located on the

*DOI: http://dx.doi.org/10.5772/intechopen.91170*

enomic evolutionary functions.

**12. Definitive universal equations**

content differences against G content was weakly linear.

#### **Figure 11.**

*Nucleotide differences in the three fragments of each primate mitochondrial genome. Left to right: (G – C), (G – T), (G – A), (C – T), (C – A), and (T – A).*

*Visible Evolution from Primitive Organisms to* Homo sapiens *DOI: http://dx.doi.org/10.5772/intechopen.91170*

*Cheminformatics and Its Applications*

patterns as a result of nucleotide content inversion. Judging from these results, the *R. americana* mitochondrion is probably more evolved than the former three mitochondria. In addition, AT inversion occurred in the following more highly evolved organisms: Mollusca species, squid (*Todarodes pacificus*), octopus (*Octopus vulgaris*), Echinodermata species, sea urchin (*Paracentrotus lividus*), water flea (*Daphnia pulex*), hermit crab (*Pagurus longicarpus*), and Humboldt squid (*Dosidicus gigas*) [53, 62]. In addition, large positive (G – A) values in the three fragments were observed in *Paragonimus westermani*, while large positive (G – C) and (A – T) values in the three fragments were observed for the mtDNA of representatives of the following phyla: Cnidaria (*Pavona clavus*), Platyhelminthes (*Schistosoma mansoni*), Porifera (*Geodia neptuni*), Arthropoda (*Tigriopus californicus*), and Chordata (*Branchiostoma belcheri*) [53]. Furthermore, the following invertebrate

*Nucleotide differences in the three fragments of each primate mitochondrial genome. Left to right: (G – C),* 

**22**

**Figure 11.**

*(G – T), (G – A), (C – T), (C – A), and (T – A).*

mitochondria were also examined: *Acanthaster planci*, *Haliotis rubra*, *Lampsilis ornate,* and the mtDNA of hemichordates, *Saccoglossus kowalevskii, Balanoglossus carnosus*, and *Xenoturbella bocki* was examined [53].

In the mtDNA of primate species *H. sapiens*, *P. troglodytes*, *G. gorilla*, *Macaca mulatta*, *Daubentonia madagascariensis*, *Nycticebus coucang*, and *Tupaia belangeri*, nucleotide content difference patterns were quite similar in the first four species, and large positive increases in (C – T) differences in the three fragments clearly indicated evolutionary divergence (**Figure 11**). The positive (C – T) differences in all three fragments were characteristic of these four primate mitochondria, while positive increases in (C – T) values were only observed in the third fragment of *N. coucang* and *T. belangeri* mtDNA. In contrast, nucleotide content difference patterns of the prosimian *Lemur catta* completely differed from those of the primates, although TA inversion was observed in the second fragment. The primate mtDNA nucleotide content patterns were also completely different from that of hemichordate *B. carnosus*, although their C contents were the highest among all organisms examined [59]. This finding indicates that mitochondrial structures respect epigenomic evolutionary functions.
