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Intl. J. of Mol. Evol. and Biodivers. 2012, Vol. 2, No.1, 1-7
http://ijmeb.sophiapublisher.com
Markov Chain Method, we obtained the
oligonucleotide transition probability matrix of each
organism, which contain whole genome’s information
and can be used for the inference of evolutionary
relationship, then took advantage of image registration
to evaluate the diversity between transition probability
matrixes by mapping their joint histogram. Here, the
joint histogram divergence was used as a parameter to
measure the evolutionary distance of organisms
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. Our results illustrated that this new
method could cover the shortages of the
above-mentioned traditional methods and take more
accurate phylogenetic analysis, which is not only for
the closely related organisms, but also for the distantly
related organisms.
1 Results and Analysis
2
1.1 The joint histogram divergence can truly reflect
the evolutionary relationship of organisms
For the 100 bacterial genomes (Supplement 1), the
joint histogram divergence (JHD) of any two genomes
was calculated. And the results suggested that the
higher rank of taxon was the larger joint histogram
divergence it has. Take
Streptococcus pneumoniae
TIGR4 (abbreviated as
S. pneu
_TI) for example, the
JHD of
S. pneu
_TI and
Streptococcus pneumonia
D39
that belonged to the same species was 49.0273, while
that of
S. pneu
_TI and
Streptococcus gordonii
str.
Challis substr.
CH1, which belonged to the same
genus, was 375.7789. Meanwhile, the JHD between
S.
pneu
_TI and
Lactococcus lactis
subsp. Cremoris
MG1363 belonged to the same family,
S. pneu_
TI and
Lactococcus salivarius
UCC118 belonged to the same
order,
S. pneu
_TI and Staphylococcus epidermidis
ATCC RP62A belonged to the same class,
S. pneu
TI
and
Clostridium botulinum
F str.
Langeland belonged
to the same phylum and,
S. pneu
_TI and
Aster
yellows withches’-broom phytoplasma
AYWB
belonged to the same kingdom were 1488.7139,
2015.58, 2339.584, 3054.2965 and 4088.1014,
respectively, and JHD exhibited monotonically raising
trend with increasing of the phylogenetic distance. In
order to investigate the general trend of JHD with the
rank of taxon, all the JHD data were divided into 7
groups according to taxonomic level, such as
“different strains within the same species”, “different
species within the same genus”, “different genus
within the same family”, “different families within the
same order”, “different orders within the same class”,
“different classes within the same phylum” and
“different phylum within the same kingdom”. The
calculated result demonstrated that the relation
between the JHD’s average values of each group and
its corresponding taxonomic level is positive
correlation, and the Pearson correlation coefficient is
0.987 (p<0.01). Also via T-test, the difference of JHD
between any two of these groups was significantly
different (Figure 1). Our result suggested that the JHD
was a reliable parameter for identification of
evolutionary relationship because it could truly reflect
the evolutionary distance of organisms.
Figure 1 The distribution of the average joint histogram
divergence (HD) according the rank of taxon
Note: The horizontal axis and the longitudinal axis represent
the rank of taxon and the average of joint histogram divergence
respectively; the differences between taxon groups are
statistically significant by t-test (P < 0.01)
1.2 The novel method based on image registration
has higher discrimination
Because the lineage of
Lactococcus lactis
and other
organisms is clearer, the discrimination of this novel
method was evaluated on the basis of
Lactococcus
lactis
. For example,
Lactococcus lactis
subsp.
cremoris
MG1363,
Lactococcus lactis subsp. cremoris
SK11 and
Lactococcus lactis subsp. lactis
I11403
(abbreviated as
L. lac
_MG,
L. lac
_SK and
L. lac
_I1
respectively) belonged to the same species