Genomic data provides simple evidence for a single origin of life

doi:10.4236/ns.2010.25065

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Vol.2, No.5, 519-525 (2010) Natural Science

http://dx.doi.org/10.4236/ns.2010.25065

Genomic data provides simple evidence for a single

origin of life

Kenji Sorimachi

Educational Support Center, Dokkyo Medical University, Tochigi, Japan; [email protected]

Received 12 January 2010; revised 25 February 2010; accepted 20 March 2010.

ABSTRACT

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

1. INTRODUCTION

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 research—using 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

520

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.

2. MATERIALS AND METHODS

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,

WA, USA).

3. RESULTS

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

521

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

0.96

0.95

0.98

C = 1.024 G – 0.001

G = G

T = –0.972 G + 0.495

A = –1.052 G + 0.506

0.96

0.97

0.95

Chloroplasts

(97) C = –1.006 T + 0.506

G = –0.969 T + 0.487

T = T

A = 0.976 T + 0.004

0.95

0.97

0.88

C = –0.940 A + 0.481

G = –0.860 A+ 0.452

T = 0.800 A + 0.067

A = A

0.98

0.95

0.88

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

0.90

0.95

0.84

C = 0.938 G – 0.003

G = G

T = –0.806 G + 0.476

A = –1.132 G + 0.527

0.90

0.80

0.96

Plant

Mitochondria

(49) C = –0.988 T + 0.492

G = –0.799 T + 0.443

T = T

A = 0.708 T + 0.065

0.95

0.80

0.67

C = –0.755 A + 0.409

G = –0.821 A + 0.445

T = 0.576 A + 0.146

A = A

0.85

0.96

0.67

The numbers in parentheses represent the sample number examined. R represents the regression coefficient.

K. Sorimachi / Natural Science 2 (2010) 519-525

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(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

0.25

0.78

0.37

C = 0.340 G + 0.223

G = G

T = –0.119 G + 0.286

A = –1.221 G + 0.491

0.08

0.09

0.82

Ve rtebrate

Mitochondria

(39) C = –0.782 T + 0.482

G = –0.068 T + 0.163

T = T

A = –0.150 T + 0.355

0.78

0.09

0.67

C = –0.333 A + 0.377

G = –0.549 A + 0.317

T = –0.118 A + 0.306

A = A

0.37

0.82

0.13

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

0.83

0.84

0.72

C = 1.804 G – 0.012

G = G

T = –1.383 G + 0.482

A = –1.422 G + 0.553

0.83

0.68

0.78

Invertebrate I

Mitochondria

(30) C = –0.897 T + 0.485

G = –0.339 T + 0.224

T = T

A = 0.236 T + 0.292

0.84

0.68

0.26

C = –0.860 A + 0.511

G = –0.433 A + 0.273

T = 0.293 A + 0.216

A = A

0.72

0.78

0.26

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

0.71

0.22

0.75

C = 0.342 G + 0.066

G = G

T = –0.102 G + 0.383

A = –1.239 G + 0.551

0.71

0.16

0.88

Invertebrate II

Mitochondria

(24) C = –0.160 T + 0.186

G = –0.244 T + 0.270

T = T

A = –0.596 T + 0.544

0.22

0.16

0.27

C = –0.253 A + 0.211

G = –0.622 A + 0.384

T = –0.125 A + 0.406

A = A

0.75

0.88

0.27

The numbers in parentheses represent the sample number examined. R represents the regression coefficient.

K. Sorimachi / Natural Science 2 (2010) 519-525

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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 square、C; 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.

4. DISCUSSION

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

524

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].

5. CONCLUSIONS

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.

6. ACKNOWLEDGMENTS

The author would like to thank David Bann of Edanz Writing for edi-

torial support.

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