which may be used in defining a genetic group. Y-DNA is transmitted only through
the paternal line, while mtDNA is passed on only through the maternal line. This
also means that a haplotype is a collection of statistically related single nucleotide
polymorphisms (SNPs) on a single chromosome. By examining these relationships
and the allelomorphic character of the haplogroup block, it is possible to see other
polymorphism regions in the area, information that is highly used in researching the
background of various diseases.
Because mitochondrial DNA has a higher rate of mutation than nuclear DNA
(around ten times as large), some individuals may have a sequence of recurring,
independently arising mutations at the same site, which can cause some difficulties
in analysis. In other words, if there is a probability that one base in a sequence of
Y-DNA within the nucleus will mutate is one in 100,000 years, then for mtDNA
such a mutation may occur around once in 10,000 years. This means that quite a
few recurring mutations may have occurred independently in the same mtDNA base
locus in various continents over the past few dozen millennia. Because mtDNA
does not cross like the Y chromosome, however, it is possibility to classify old
sequences by analyzing lines according to haplotype.
The degree of polymorphism in a restriction enzyme fragment at a substitution
region in mtDNA amplified through PCR may be obtained through nucleon
diversity, the extent of RFLP mixing ratio through haplo diversity using the
equation h ¼ 2n 1 À
P X
2
i
À
Á = 2n À 1
ð
Þ. In this case, X i refers to the frequency of
nucleons or haplos in the same, while n is the number of individual in the sample.
Number of base substitutions and net base substitutions: Serving as indicators of
genetic specialization between groups, the number of base substitutions and net
base substitutions may be obtained through the following formulas. The number of
base substitutions between two haplos in the same population is shown by
d x ¼ n x =n x À 1
ð
Þ
P X i X j d ij . Here, n x is the number of samples, while d ij represents
the number of base substitutions per site for haplos i and j. The number of base
substitutions arising between the DNA haplo and Y-DNA haplo from populations
X and Y and its average is shown by d xy ¼
P X i yj dij . Here, dij is the number of
base substitutions between haplo i taken from population X and haplo j taken from
population Y.
Net base substitutions between the two populations can be found through the
equation d A ¼ d xy À d x þ d y
À
Á =2. The time since the two groups’ division can be
found by substituting d A = 2kT into the equation d A = d xy − (d x + d y )/2 (Taniguchi
2000).
5.5 Genetic Analysis Through DNA Markers
119
the paternal line, while mtDNA is passed on only through the maternal line. This
also means that a haplotype is a collection of statistically related single nucleotide
polymorphisms (SNPs) on a single chromosome. By examining these relationships
and the allelomorphic character of the haplogroup block, it is possible to see other
polymorphism regions in the area, information that is highly used in researching the
background of various diseases.
Because mitochondrial DNA has a higher rate of mutation than nuclear DNA
(around ten times as large), some individuals may have a sequence of recurring,
independently arising mutations at the same site, which can cause some difficulties
in analysis. In other words, if there is a probability that one base in a sequence of
Y-DNA within the nucleus will mutate is one in 100,000 years, then for mtDNA
such a mutation may occur around once in 10,000 years. This means that quite a
few recurring mutations may have occurred independently in the same mtDNA base
locus in various continents over the past few dozen millennia. Because mtDNA
does not cross like the Y chromosome, however, it is possibility to classify old
sequences by analyzing lines according to haplotype.
The degree of polymorphism in a restriction enzyme fragment at a substitution
region in mtDNA amplified through PCR may be obtained through nucleon
diversity, the extent of RFLP mixing ratio through haplo diversity using the
equation h ¼ 2n 1 À
P X
2
i
À
Á = 2n À 1
ð
Þ. In this case, X i refers to the frequency of
nucleons or haplos in the same, while n is the number of individual in the sample.
Number of base substitutions and net base substitutions: Serving as indicators of
genetic specialization between groups, the number of base substitutions and net
base substitutions may be obtained through the following formulas. The number of
base substitutions between two haplos in the same population is shown by
d x ¼ n x =n x À 1
ð
Þ
P X i X j d ij . Here, n x is the number of samples, while d ij represents
the number of base substitutions per site for haplos i and j. The number of base
substitutions arising between the DNA haplo and Y-DNA haplo from populations
X and Y and its average is shown by d xy ¼
P X i yj dij . Here, dij is the number of
base substitutions between haplo i taken from population X and haplo j taken from
population Y.
Net base substitutions between the two populations can be found through the
equation d A ¼ d xy À d x þ d y
À
Á =2. The time since the two groups’ division can be
found by substituting d A = 2kT into the equation d A = d xy − (d x + d y )/2 (Taniguchi
2000).
5.5 Genetic Analysis Through DNA Markers
119