Vol.2, No.5, 519-525 (2010) Natural Science
Copyright © 2010 SciRes. OPEN ACCESS
Genomic data provides simple evidence for a single
origin of life
Kenji Sorimachi
Educational Support Center, Dokkyo Medical University, Tochigi, Japan; kenjis@dokkyomed.ac.jp
Received 12 January 2010; revised 25 February 2010; accepted 20 March 2010.
One hundred and fifty years ago, Charles Darwin’s
on the Origin of Species explained the evolution
of species through evolution by natural selection.
To date, there is no simple piece of evidence
demonstrating this concept across species.
Chargaff’s first parity rule states that comple-
mentary base pairs are in equal proportion across
DNA strands. Chargaff’s second parity rule, in-
consistently followed across species, states that
the base pairs are in equal proportion within DNA
strands [G C, T A and (G + A) (C + T)]. Using
genomic libraries, we analyzed the extent to which
DNA samples followed Chargaff’s second parity
rule. In organelle DNA, nucleotide relationships
were heteroskedastic. After classifying organelles
into chloroplasts and mitochondria, and then into
plant, vertebrate, and invertebrate I and II mito-
chondria, nucleotide relationships were ex-
pressed by linear regression lines. All regres-
sion lines based on nuclear and organelle DNA
crossed at the same point. This is a simple dem-
onstration of a common ancestor across species.
Keywords: Evolution; Origin of Species; Darwin;
Genome; Chargaff’s Parity Rules; Organelle; DNA;
Linear Formula
On the Origin of Species was published in 1859, stem-
ming from observations Charles Darwin made during a
voyage on HMS Beagle. According to his theory, all
organisms have a common ancestor and a single origin.
Since publication, evidence for this theory has accumu-
lated. Although molecular clock researchusing amino
acid or nucleotide replacement rates [1]has enabled
scientists to draw a phylogenetic tree representing bio-
logical evolution [2-7], the “Origin of Life” has not yet
been drawn using these methods. During the past two
decades, advances in genomics have enabled the se-
quencing of entire genomes [8,9]; the first complete ge-
nome to be sequenced was that of Haemophilus influen-
zae [10]. The complete human genome was sequenced
early this century by two groups [11,12] and to date,
more than 2,000 species’ genomes have been completely
sequenced. Based on complete genome data, codon evo-
lution has been precisely analyzed [13], and organisms
have been consequently classified [14].
The double-stranded DNA structure is the principle
information-containing component of the genome [15].
Based on structural knowledge alone, Chargaff’s first
parity rule [16] [G = C, A = T and (G + A) = (T + C)]
makes intuitive sense. However, Chargaff’s second par-
ity rule [17], in which the same nucleotide relationships
are retained within single DNA strands, makes less intui-
tive sense. The biological significance of Chargaff’s
second parity rule has not been elucidated because of its
unclear logical foundation. In the 40 years since its pub-
lication, researchers have not known whether Chargaff’s
second parity rule is relevant to biological evolution.
However, a recent publication has solved this historic
puzzle [18]. The solution is based on the facts that ge-
nome structure is homogeneous regarding nucleotide
composition over the genome [19], and that both for-
ward and reverse strands are almost the same [20]. Using
the complementary relationship between the two strands,
both G and C contents are mathematically expressed by
the same G + C formula in a single strand, and eventu-
ally G C and T A [18]. Thus, the first parity rule
comes from the inherent characteristics of nucleotides,
and the second from the similarities of nucleotide com-
position between forward and reverse strands. These two
rules represent different phenomena. The former is
mathematically definitive and independent of biological
significance, and the latter is less definite, and may or
may not have biological significance.
Recently, Mitchell and Bridge examined a wide selec-
tion of biological DNA samples to determine whether
they fitted Chargaff’s second parity rule [21] (1,495 viral,
835 organelle, 231 bacterial and 20 archaeal genomes;
and 164 sequences from 15 eukaryotes). Only single
K. Sorimachi / Natural Science 2 (2010) 519-525
Copyright © 2010 SciRes. OPEN ACCESS
DNA strands that formed genomic double-stranded DNA
obeyed Chargaff’s second parity rule; organelle DNA
and single viral DNA strands did not [21]. Nikolaou and
Almirantis reported that mitochondrial DNA could be
classified into three groups based on the proportions of
G-C and A-T content [22]. They found that mitochon-
drial DNA deviated from Chargaff’s second parity rule,
and that chloroplasts shared the same relative nucleotide
compositions as bacterial genomes [22]. Similar devia-
tions from Chargaff’s second parity rule were reported
by Bell and Forsdyke [23]. My research group previ-
ously examined nuclear and organelle DNA nucleotide
correlations, and found that nucleotide contents are cor-
related with each other in coding, non-coding, and com-
plete nuclear DNA [20]; consistent results were obtained
from chloroplast and plant mitochondrial DNA, and only
homonucleotide contents are correlated with each other
between the coding or non-coding regions and the single
DNA strand in animal mitochondria [24]. These results
indicate that biological evolution can be expressed by
linear formulae [20]. If evolutionary processes are ex-
pressed by a single equation, it would suggest that evo-
lutionary processes proceeded under the same rule.
However, if this is the case, we cannot determine
whether evolution diverged from a single or multiple
origins, because all species are located on the same sin-
gle line. If multiple equations are required, the position
of the regression lines would either indicate a single or
multiple evolutionary origins.
Genome data were obtained from the National Center for Bio-
technology Information (http://www.ncbi.nlm.nih.gov/sites)
(NCBI). Chloroplast, plant mitochondria and animal
mitochondria were examined. The list of organelles ex-
amined has been described in our previous paper [24].
Using the same species, we examined newly collected
data alongside previous data [24]. For animal mitochon-
dria, classified species are as follows: Group I inverte-
brates contained echinodermata (starfish), mollusca (oc-
topus and squid) and arthropoda (insects); group II in-
vertebrates contained cnidaria (coral), porifera (sponge)
and protozoa (flagellate). All calculations were carried
out using Microsoft Excel 2003 (Microsoft, Redmond,
3.1. Chloroplasts
After normalization, the four nucleotide contents can be
expressed by the following equation: G + C + T + A = 1.
The nucleotide content of each species was expressed by
a linear formula, y = ax + b, where “y” and “x” are the
nucleotide contents, and “a” and “b” are constant values
(expressing the nucleotide alternation rate among species
and original nucleotide content at the vertical intercept).
In our previous study [20], this linear formula was
shown to be applicable across species. Nucleotide con-
tents based on the complete chloroplast genome were
plotted against C content (Figure 1, upper panel).
Two lines representing G/C content and C/C content
overlapped, as did lines representing T/C, and A/C con-
tent. These relationships obeyed Chargaff’s second par-
ity rule. Thus, in chloroplast evolution, the G/C content
alternations obey the same rule against C content, as
does T/A content. This shows that G C and T A, and
that the four kinds of nucleotide alternations occur syn-
chronously. The former (G and C) alternation is attrib-
uted to the latter (T and A) alternation in normalized
values. G and C exchanges or T and A exchanges do not
occur simultaneously under this rule. The equations,
represented by regression lines and regression coeffi-
cients, are shown in Table 1. Each regression coefficient
is close to 0.9 or more than 0.9. This demonstrates an
almost complete correlation between nucleotide content.
The slopes in the equations were close to 1 and –1, and
the constant values at the vertical intercept were close to
0 and 0.5, respectively.
Figure 1. Nucleotide relationships in normalized values. up-
per panel, chloroplast; lower panel, plant mitochondria. Blue
diamonds, G; pink squares, C; red triangles, T; and green
triangle, A. Each nucleotide was plotted against C content.
The vertical axis represents four nucleotide contents, the
horizontal axis represents C content.
K. Sorimachi / Natural Science 2 (2010) 519-525
Copyright © 2010 SciRes. OPEN ACCESS
3.2. Plant mitochondria
Plotting nucleotide contents against C content, the C/G
and A/T lines almost overlapped (Figure 1, lower panel).
This demonstrates that the alternations of the four nu-
cleotide contents occurred synchronously. G/C content
alternations obey the same rule in plant mitochondrial
evolution, as do T/A alternations.
The characteristics representing linear equations are
shown in Table 2. The absolute values of the slope were
close to 1 in many equations, whereas that of line T ex-
pressed by A was 0.576; line A expressed by T was 0.708.
In these two equations, the correlations were slightly
reduced and the regression coefficients were 0.67.
The characteristics representing linear equations are
shown in Table 2. The absolute values of the slope were
close to 1 in many equations, whereas that of line T ex-
pressed by A was 0.576; line A expressed by T was 0.708.
In these two equations, the correlations were slightly
reduced and the regression coefficients were 0.67.
Plotting the ratios of C/G or T/A against the genome size
in plant mitochondria, deviations from 1 were observed in
the small genomes (less than 1 × 105 nucleotides), while
the ratios were fixed to 1 in the larger genome sizes (more
than 1 × 105 nucleotides); this rule was followed without
exception in the data we used (Figure 2).
3.3. Animal Mitochondria
Relationships between nucleotide contents were also ex-
amined in animal mitochondria including vertebrates and
invertebrates (Figure 3). The relationships were notably
heteroskedastic. The values obtained from plotting G con-
tent against C content was classified into two groups by
line C, which represents y(C) = x(C). The two groups
Figure 2. Ratios of nucleotide contents in plant mito-
chondrial genomes. The horizontal axis represents the
number of total nucleotides and the vertical axis
represents the ratios (G/C and A/T). Red squares, G/C;
and blue diamonds, A/T.
Figure 3. Nucleotide relationships in animal mito-
chondria. Nucleotide contents were normalized, and G
content was plotted against C content. Red squares
represent C content against C content. Vertical axis
represents G and C content and the horizontal axis
represents C content.
Table 1. Regression lines based on chloroplasts.
Sample Vs. pyrimidine R Vs. purine R
C = C
G = 0.902 C + 0.014
T = –0.889 C + 0.484
A = –1.013 C + 0.502
C = 1.024 G – 0.001
G = G
T = –0.972 G + 0.495
A = –1.052 G + 0.506
(97) C = –1.006 T + 0.506
G = –0.969 T + 0.487
T = T
A = 0.976 T + 0.004
C = –0.940 A + 0.481
G = –0.860 A+ 0.452
T = 0.800 A + 0.067
A = A
The numbers in parentheses represent the sample number examined. R represents the regression coefficient.
Table 2. Regression lines based on plant mitochondria.
Sample Vs. pyrimidine R Vs. purine R
C = C
G = 0.854 C + 0.037
T = –0.906 C + 0.481
A = –0.947 C + 0.482
C = 0.938 G – 0.003
G = G
T = –0.806 G + 0.476
A = –1.132 G + 0.527
(49) C = –0.988 T + 0.492
G = –0.799 T + 0.443
T = T
A = 0.708 T + 0.065
C = –0.755 A + 0.409
G = –0.821 A + 0.445
T = 0.576 A + 0.146
A = A
The numbers in parentheses represent the sample number examined. R represents the regression coefficient.
K. Sorimachi / Natural Science 2 (2010) 519-525
Copyright © 2010 SciRes. OPEN ACCESS
(invertebrates I and II) are located below and above
line C: this suggests that they diverged from this
crossing point. Regression lines representing nucleo-
tide content relationships in vertebrates, invertebrate I
and II are shown in Tables 3-5. Vertebrate mitochon-
dria belonged to the same group as invertebrate I mi-
tochondria, and the C content of vertebrate mitochon-
dria was relatively high.
Nucleotide contents in vertebrate mitochondria were
plotted against C content. T/C contents were correlated,
while G and A (purines) were not correlated against C
content (Figure 4). This finding may be due to the short
range of vertebrate distribution and their variations. Line
characteristics representing regression lines are shown in
Table 3. Even invertebrate mitochondria, when nucleo-
tide contents were plotted against G or A (purine) con-
tents, G/A contents were correlated, while C and T
(pyrimidines) were not correlated against G or A (purine)
content (Tables 4 and 5).
Group I invertebrate mitochondria were examined
and are plotted in Figure 5 (upper panel). Various nu-
cleotide content relationships are shown, plotted against
C content. The regression coefficients for the equations
expressing other nucleotide contents against C content
were 0.7-0.8 (Table 4). Extended lines representing G
and C content converged at 0.06, forming a clear cunei-
form. Similarly, A and T lines converged at around 0.05.
These results indicate that separations of G from C
started at around 0.05 C content, and around 0.45 for T
and A content. Regression values are shown in Table 4.
Group II invertebrate mitochondria were examined
using the same procedure as above. When G, A and T
content was plotted against C content, there was a corre-
lation between G and C content (Figure 4, middle panel).
A and T lines also converged when C content was 0.10,
although the extended C and G lines crossed when C
content was 0.02. When C content was plotted against G
content, C and G lines converged when G content was
0.16. Regression lines are shown in Table 5.
Table 3. Regression lines based on vertebrate mitochondria.
Sample Vs. pyrimidine R Vs. purine R
C = C
G = 0.192 C + 0.093
T = –0.772 C + 0.479
A = –0.420 C + 0.429
C = 0.340 G + 0.223
G = G
T = –0.119 G + 0.286
A = –1.221 G + 0.491
Ve rtebrate
(39) C = –0.782 T + 0.482
G = –0.068 T + 0.163
T = T
A = –0.150 T + 0.355
C = –0.333 A + 0.377
G = –0.549 A + 0.317
T = –0.118 A + 0.306
A = A
The numbers in parentheses represent the sample number examined. R represents the regression coefficient.
Table 4. Regression lines based on invertebrate I mitochondria.
Sample Vs. pyrimidine R Vs. purine R
C = C
G = 0.386 C + 0.039
T = –0.782 C + 0.476
A = –0.604 C + 0.485
C = 1.804 G – 0.012
G = G
T = –1.383 G + 0.482
A = –1.422 G + 0.553
Invertebrate I
(30) C = –0.897 T + 0.485
G = –0.339 T + 0.224
T = T
A = 0.236 T + 0.292
C = –0.860 A + 0.511
G = –0.433 A + 0.273
T = 0.293 A + 0.216
A = A
The numbers in parentheses represent the sample number examined. R represents the regression coefficient.
Table 5. Regression lines based on invertebrate II mitochondria
Sample Vs. pyrimidine R Vs. purine R
C = C
G = 1.488 C + 0.009
T = –0.291 C + 0.402
A = –2.197 C + 0.607
C = 0.342 G + 0.066
G = G
T = –0.102 G + 0.383
A = –1.239 G + 0.551
Invertebrate II
(24) C = –0.160 T + 0.186
G = –0.244 T + 0.270
T = T
A = –0.596 T + 0.544
C = –0.253 A + 0.211
G = –0.622 A + 0.384
T = –0.125 A + 0.406
A = A
The numbers in parentheses represent the sample number examined. R represents the regression coefficient.
K. Sorimachi / Natural Science 2 (2010) 519-525
Copyright © 2010 SciRes. OPEN ACCESS
Figure 4. Nucleotide relationships in vertebrate mito-
chondria. Nucleotide contents were normalized, and nu-
cleotide contents were plotted against C content. The
horizontal axis represents C content, and the vertical axis
represents four nucleotide contents. Pink square, C; blue
diamond, G; green triangle, T; and red triangle, A.
Figure 5. Regression lines representing nucleotide al-
ternations in various organelles. Upper panel, inverte-
brate I mitochondria; middle panel, invertebrate II mi-
tochondria; and lower panel, invertebrate I plus verte-
brate mitochondria. The vertical axis represents four nu-
cleotide contents and the horizontal axis represents C
content. Blue diamond, G; pink squareC; green dia-
mond, T; red triangle, A; dark red squares, chloroplasts;
and large black square, vertebrates.
3.4. Origin of Life
When G/C contents were plotted for various organelles
and nuclei, all extended regression lines converged
when C content was 0.03 0.02 (mean value s. d.)
(Figure 6). Vertebrate mitochondria (a relatively re-
cent group) are located towards the right of the slope.
This confirms the evolutionary direction (left to right),
and confirms that all organisms diverged from the
same origin. In fact, Ureaplasma urealyticum, which
has the smallest genome size [25], is located towards
the left of the slope, though this position is not abso-
lute because of reversible nucleotide alternations on
the genome.
This study used recent genomic data and knowledge of
Chargaff’s second parity rule to demonstrate common
ancestry across species.
Although evolution by natural selection applies to all
organelles, animal mitochondrial evolution seems to
differ from both nuclei evolution and plant organelle
evolution. Brown et al. previously reported the rapid
evolution of animal mitochondrial DNA [26]. Animal
mitochondria do not follow Chargaff’s second parity rule,
but this study revealed that they evolved from a common
ancestor. We previously showed that plasmids (not com-
partmentalized from the nucleus) have codon frequen-
cies that resemble those of the parent organism, although
there is no evidence that plasmids pass nuclear genomic
material across generations [27]. Thus, the compartmen-
talization of cellular organelles strongly influences
characteristically organelle evolution.
Although deviations from Chargaff’s second parity
rule have been previously discussed [22,23], the results
obtained here either demonstrate evolutionary phenom-
ena or are caused by other confounding factors. In the
Figure 6. C content (horizontal axis) and G content (ver-
tical axis) in nuclei and various organelles. Blue dia-
monds, invertebrate I and vertebrate mitochondria; pink
diamonds, invertebrate II mitochondria; red squares,
plant mitochondria; green triangles, chloroplasts; and
black squares, nuclei.
K. Sorimachi / Natural Science 2 (2010) 519-525
Copyright © 2010 SciRes. OPEN ACCESS
present study, deviations from Chargaff’s second parity
rule in plant mitochondria depended on the genome size
and disappeared in the larger genome size (Figure 2).
Thus, differences in gene density between the cyto-
sine-rich light and guanine-rich heavy strands affect
Chargaff’s second parity rule in the relatively small
animal mitochondria, while they were cancelled out in
the larger plant mitochondria. In fact, the ratios (C/G and
T/A) were extremely close to 1 in the chloroplast DNA
where genome sizes were more than 5 × 105 nucleotides;
no exceptions were observed in the samples examined
(unpublished data). This fact clearly shows that genome
size is an important factor in Chargaff’s second parity
rule [22]. In the Treponema pallidum genome, although
the gene density differs between the forward and reverse
strands [28], this organism obeys Chargaff’s second par-
ity rule [21]. The nuclear genome of Ureaplasma urea-
lyticum, which also obeys Chargaff’s second parity rule,
consists of 7.5 × 105 nucleotides [25]. This reflects the
fact that plant mitochondrial genome sizes are much
smaller than plant nuclear genomes.
Animal mitochondria did not obey Chargaff’s second
parity rule, even after classification into vertebrate, in-
vertebrate I and II mitochondrial genes. This suggests
that nuclear, chloroplast and plant mitochondrial evolu-
tion is governed under the same rule, while animal mi-
tochondrial evolution is governed under different rules.
The fact that evolution is expressed by linear formulas
suggests that it proceeded linearly. The crossing of two
regression lines suggests two evolutionary distinct proc-
esses, and a crossing point suggests either divergence or
convergence at a single origin. The degree of difference
in two evolutionary processes is expressed by the dif-
ference in linear regression slopes: small and large dif-
ferences are expressed by sharp and dull angles, respec-
tively. A single evolutionary process is expressed by a
single regression line. The appearance of many regres-
sion lines which have the same slope but different inter-
cept values would indicate multiple evolutionary origins.
A previous study found that regression lines representing
nucleotide relationships in the coding region were al-
most identical in chromosomal DNA among bacteria,
archaea and eukaryotes [20]. In our previous study [24],
two regression lines representing homonucleotide con-
tents in chloroplasts and plant mitochondria converged
at the top of the cuneiform in both coding and
non-coding regions. This suggests that chloroplasts and
plant mitochondria diverged from the same origin. As
research suggests that the former are derived from
cyanobacteria [29] and the latter are derived from pro-
teobacteria [30], both organelles are likely to be derived
from the same origin. In addition, the formation of the
cuneiform is obtained naturally in the comparison be-
tween coding and non-coding regions, because both
fragments belong to the same strand [24].
When evolutionary direction is discovered, elucidating
whether it occurs by divergence or convergence is not
straightforward. In invertebrate mitochondria, as more
recently evolved (and more advanced) vertebrates were
located on the end of invertebrate I data, results indi-
cated that invertebrate I and II evolution diverged from
the opposite side of vertebrates. Nuclear, chloroplast and
plant mitochondrial evolution is expressed by the same
regression line based on Chargaff’s second parity rule
(Figure 6). In nuclei, chloroplasts and mitochondria
from plants, amino acid compositions deduced from
complete genome data were very similar, although they
differed from animal mitochondria [24]. In the present
study, regression lines based on plant chloroplasts, mi-
tochondria and nuclei overlapped, while animal mito-
chondrial regression lines converged at the same single
point. Finally, all extended regression lines representing
chromosomes, chloroplasts, plant mitochondria, verte-
brates and invertebrates I and II converged at the same
point (Figure 6). Therefore, I conclude that there is one
single origin of life from which all organisms derived.
This is consistent with the chemical conditions during
prebiotic evolution, in which primitive replicators such
as ribosomes would have formed [31], and in which
primitive life forms would have similar cellular amino
acid compositions presumed from those of present or-
ganisms [32,33]. Thus all advanced forms of life, as de-
duced using genomic data in this study, descended from
a single origin.
The author would like to thank David Bann of Edanz Writing for edi-
torial support.
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