Detection of Single-Nucleotide Polymorphisms (SNPs)

    Differences between the DNA sequences of individuals and species are due to alterations of the four-letter ACGT code. Most such observed differences are not newly-arisen "mutations" between the previous and present generations, but rather persistent variation already present in populations. These are called single-nucleotide polymorphisms or SNPs.  The image is a portion of an Applied Biosystems Automated DNA sequencer chromatogram.The top window shows an 80-nucleotide stretch of DNA from a group of eight Atlantic Cod.  Black dots in the upper window flag positions with at least one SNP variant.  The grey bracket frames an eight-base region with two SNPs, for which the chromatogram data are shown in the lower window.  Most individuals have the sequence CACATAGG: individuals BS02 & BS11 share a CT SNP variant at the third position (CATATAGG), and individual BS03 has a unique AG SNP at the sixth position (CACATGGG).  Identification of such genetic differences among individuals or species permits inferences about relationships among individuals in time (genealogy) and space (phylogeography), and the evolutionary history (phylogeny) of species. For example, reconstruction of the pattern of SNP variation shows that individuals BS02 and BS03 are less closely related to each other than either is to individual BS01.

          BS02,11   T|C   BS01,04,07,09,10   A|G   BS03                 

CATATAGG   T|C         CACATAGG       A|G   CACATGGG