**11. Organelle evolution**

In Chargaff's first parity rule [12], G = C and A = T in a double DNA strand, while in the second parity rule [14], G ≈ C and A ≈ T in a complete single DNA strand. Based on Chargaff's second parity rule, nucleotide content differences such as (G – C) and (A – T) reflect biological evolution. In addition, the other nucleotide content differences, (G – A, G – T, C – A, and C – T), also reflect biological evolution [34, 53].

Six nucleotide content differences among the complete mitochondria of the four species (*M. brevicollis, P. pallidum, D. discoideum*, and *R. Americana*) were examined (**Figure 10**, left panel). The GC and AT skew are expressed by the ratios of (G – C)/ (G + C) and (A – T)/(A + T), respectively [54]. The skew seems to be due to differences in replication processes between the leading and lagging strands [55]. In the replication of the lagging strand, the deamination of cytosine increases the probability of mutations, and the inversion of nucleotide content differences reflects biological divergence. Similarly, these phenomena are observed in mitochondria, consisting of heavy (H) and light (L) chains [56–58]. When the GC skew was plotted against G content, animal mitochondria were classified into two groups: high and low C/G [59].

To allow simple comparison of inter- and intraspecies genome structures, genomes were divided into three fragments throughout subsequent analyses, from which three separate patterns emerged. There is no inversion of nucleotide content differences that was observed in the mtDNA of *M. brevicollis* (G: 0.081, C: 0.059), the mycetozoan *Polysphondylium pallidum* (G: 0.143, C: 0.085), or *Dictyostelium discoideum* (G: 0.171, C: 0.104) (**Figure 10**), whereas differences in (G – C) and (T – A) values for *M. brevicollis* mtDNA were the lowest among these species. Choanoflagellates are most closely related to animals based on genome sequencing [60]. The fact that the nucleotide content difference patterns of the three fragments were almost identical for these three species indicates that their nucleotide distributions were homogeneous, and that the nucleotide content was symmetrical.

**21**

**Figure 10.**

*Visible Evolution from Primitive Organisms to* Homo sapiens

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

*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).*

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

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

*Cheminformatics and Its Applications*

obtained, but with some additional exceptions [50].

were classified into vertebrates not into invertebrates [49].

**11. Organelle evolution**

hagfish (*E. burgeri*) with the terrestrial vertebrates may reflect the controversy over the classification of this fish [52]. If the hagfish truly belongs to the terrestrial group, it suggests that hagfish still possesses some primitive mitochondrial characteristics that were present before its evolution. The frog (*R. nigromaculata*) was consistently grouped with the aquatic vertebrates which may reflect the conservation of tadpole characteristics after metamorphosis. The coelacanth (*Latimeria chalumnae*), the Queensland lungfish (*Neoceratodus forsteri*), which is a living fossil and one of the oldest living vertebrate genera, and the American paddlefish (*Polyodon spathula*), which is the oldest living animal species in North America, all belonged to an additional small cluster. Using the G, C, A, and T content of the coding regions, non-coding regions, and complete mitochondrial genomes as the traits in cluster analyses, similar results were

Single genes have been used to construct phylogenetic trees [7–11], and 16S rRNA has been frequently examined [27, 29]. The phylogenetic tree based on 16S rRNA sequences of various vertebrates is shown in **Figure 9**. The tree is consistent with that based on nucleotide contents. The hagfish (*E. burgeri*) fell into the terrestrial vertebrates, while the black spotted frog (*R. nigromaculata*) belonged to the terrestrial vertebrates. These results indicate that vertebrate evolution is controlled by natural selection under both an internal bias resulting nucleotide replacement rules and by an external bias caused by environmental biospheric conditions. In addition, based on amino acid composition or nucleotide content of complete mitochondrial genomes, Hemichordates (*Balanoglossus carnosus* and *Saccoglossus kowalevskii*) and Xenoturbella

In Chargaff's first parity rule [12], G = C and A = T in a double DNA strand, while

in the second parity rule [14], G ≈ C and A ≈ T in a complete single DNA strand. Based on Chargaff's second parity rule, nucleotide content differences such as (G – C) and (A – T) reflect biological evolution. In addition, the other nucleotide content differences, (G – A, G – T, C – A, and C – T), also reflect biological evolution [34, 53]. Six nucleotide content differences among the complete mitochondria of the four species (*M. brevicollis, P. pallidum, D. discoideum*, and *R. Americana*) were examined (**Figure 10**, left panel). The GC and AT skew are expressed by the ratios of (G – C)/ (G + C) and (A – T)/(A + T), respectively [54]. The skew seems to be due to differences in replication processes between the leading and lagging strands [55]. In the replication of the lagging strand, the deamination of cytosine increases the probability of mutations, and the inversion of nucleotide content differences reflects biological divergence. Similarly, these phenomena are observed in mitochondria, consisting of heavy (H) and light (L) chains [56–58]. When the GC skew was plotted against G content, animal mitochondria were classified into two groups: high and low C/G [59]. To allow simple comparison of inter- and intraspecies genome structures, genomes were divided into three fragments throughout subsequent analyses, from which three separate patterns emerged. There is no inversion of nucleotide content differences that was observed in the mtDNA of *M. brevicollis* (G: 0.081, C: 0.059), the mycetozoan *Polysphondylium pallidum* (G: 0.143, C: 0.085), or *Dictyostelium discoideum* (G: 0.171, C: 0.104) (**Figure 10**), whereas differences in (G – C) and (T – A) values for *M. brevicollis* mtDNA were the lowest among these species. Choanoflagellates are most closely related to animals based on genome sequencing [60]. The fact that the nucleotide content difference patterns of the three fragments were almost identical for these three species indicates that their nucleotide distributions were homogeneous, and that the nucleotide content was symmetrical.

**20**
