5.5.5 Computer Software Use in Population Analysis
As described above, high-sensitivity DNA polymorphs markers also have large
numbers of alleles or genotypes at a single gene locus, which severely complicates
calculations of Hardy-Weinberg equilibrium of population heterogeneity testing in
population genetics analysis. Due to low allele frequency, it may also be necessary
to prepare a large number of samples per sample group to use these markers
effectively. Given this use, use of population analysis computer software is
essential. Fortunately, such software may be downloaded online (Nishita 1998).
5.6 Research Applying DNA Markers
5.6.1 DNA Polymorph Marker Sensitivity and Use
When a marker is described as sensitive, this typically means a high level of polymorphism in the marker gene. Among the DNA polymorphs serving as new genetic
markers, some allow for differentiation of organisms; these are known as DNA
fingerprints. In studies involving the release of fish and shellfish, some of the
organisms released are marked through attachment of a label or clipping of a fin.
DNA fingerprinting offers the convenience of allowing all artificial seedlings to be
marked automatically at the stage of parent genotype determination (Saunders 2005).
In some cases, even these high-sensitivity markers cannot be called necessarily
appropriate in distinguishing different species or making determinations of relatedness among multiple species, as they are subject to influence from non-statistical
similarities in allele frequency.
When protein and DNA polymorphs are compared for usefulness as gene
markers for population analysis, isoenzymes are still seen as highly trustworthy in
terms of gene identification accuracy and data stability, and highly useful for certain
organisms (such as freshwater organisms) where small populations can be segregated easily. It is not rare for sibling species that cannot be distinguished by
outward form to be identified through isozyme markers.
In contrast, mitochondrial DNA D-loop region polymorphs exhibit great
diversity and are highly useful in making determinations on genetic differentiation
in a population and relatedness between populations and in estimating evolution
periods. At the same time, DNA D-loop region polymorphs have disadvantages in
terms of the characteristic rises in inbreeding and homozygosity in sexually
reproducing populations and are unable to provide effective information in distinguishing simple population mixing from genetic mixing.
The single locus method for minisatellites and microsatellites (VNTR) is sure to
play a major role in analysis of fish population structure going ahead, as it shows
both outstanding reproducibility and a high degree of sensitivity. In particular, the
high degree of usability in microsatellite DNA polymorphs, which have a far higher
5.5 Genetic Analysis Through DNA Markers
125
As described above, high-sensitivity DNA polymorphs markers also have large
numbers of alleles or genotypes at a single gene locus, which severely complicates
calculations of Hardy-Weinberg equilibrium of population heterogeneity testing in
population genetics analysis. Due to low allele frequency, it may also be necessary
to prepare a large number of samples per sample group to use these markers
effectively. Given this use, use of population analysis computer software is
essential. Fortunately, such software may be downloaded online (Nishita 1998).
5.6 Research Applying DNA Markers
5.6.1 DNA Polymorph Marker Sensitivity and Use
When a marker is described as sensitive, this typically means a high level of polymorphism in the marker gene. Among the DNA polymorphs serving as new genetic
markers, some allow for differentiation of organisms; these are known as DNA
fingerprints. In studies involving the release of fish and shellfish, some of the
organisms released are marked through attachment of a label or clipping of a fin.
DNA fingerprinting offers the convenience of allowing all artificial seedlings to be
marked automatically at the stage of parent genotype determination (Saunders 2005).
In some cases, even these high-sensitivity markers cannot be called necessarily
appropriate in distinguishing different species or making determinations of relatedness among multiple species, as they are subject to influence from non-statistical
similarities in allele frequency.
When protein and DNA polymorphs are compared for usefulness as gene
markers for population analysis, isoenzymes are still seen as highly trustworthy in
terms of gene identification accuracy and data stability, and highly useful for certain
organisms (such as freshwater organisms) where small populations can be segregated easily. It is not rare for sibling species that cannot be distinguished by
outward form to be identified through isozyme markers.
In contrast, mitochondrial DNA D-loop region polymorphs exhibit great
diversity and are highly useful in making determinations on genetic differentiation
in a population and relatedness between populations and in estimating evolution
periods. At the same time, DNA D-loop region polymorphs have disadvantages in
terms of the characteristic rises in inbreeding and homozygosity in sexually
reproducing populations and are unable to provide effective information in distinguishing simple population mixing from genetic mixing.
The single locus method for minisatellites and microsatellites (VNTR) is sure to
play a major role in analysis of fish population structure going ahead, as it shows
both outstanding reproducibility and a high degree of sensitivity. In particular, the
high degree of usability in microsatellite DNA polymorphs, which have a far higher
5.5 Genetic Analysis Through DNA Markers
125