What DNA Sequence Should I Use?
WHAT HAPPENS TO A DNA SEQUENCE WHEN TWO POPULATIONS ARE SEPARATED FROM EACH OTHER?
When two populations are separated and cannot interbreed, there is no gene exchange between them. If a random mutation occurs in the first population, it is unlikely that the same mutation will occur in the second population. Over time, genetic differences (DNA sequence differences) between the two populations accumulate. When these differences become large enough, the two isolated populations are called new species. The exact point at which two populations should be called new species is a matter of considerable debate.
If you want to ask questions about the genetic relatedness of two populations, you can begin to answer that question by comparing a DNA sequence from individuals in each population. But, which DNA sequence should you use? Different DNA sequences accumulate mutations at different rates. You will need a sequence that has accumulated several different mutations but not so many that you have mutations on top of mutations (the same base mutates twice or three times).
THE RIBOSOMAL RNA GENES
A good segment for DNA sequence comparisons is the DNA that produces ribosomal RNAs. This is one of the few genes that does not produce a protein. The ribosomal segment has regions that accumulate mutations fairly rapidly and regions that change very slowly over evolutionary time. The ribosomal gene products (ribosomal RNAs) are needed in great quantities by the cell so these genes are repeated genes (thousands of copies placed side by side).
The ribosomal repeat is shown to the left. The 18S gene product (an RNA, not a protein) combines with proteins to form the small ribosomal subunit. The 5.8S RNA gene product, the 5S gene product and the Large Subunit RNA gene product (shown here as a 27S RNA) combine with proteins to form the large ribosomal subunit.
The 18S gene changes very slowly and is used for "deep" phylogenies. The ITS 1 region between the 18S and 5.8S genes and the ITS2 region between the 5.8S gene and the Large Subunit Gene (27S in the diagram) are not part of the ribosomes and accumulate mutations faster. These regions have been used to compare species within a genus. The 3' end of the Large Subunit genes accumulates mutations at a rate between the ITS regions and the 18S gene and is being used to examine family and order-level relationships.
HOW CAN DNA SEQUENCES BE COMPARED
DNA sequence differences can be obtained directly by sequencing a segment of DNA. This is an expensive process and often beyond the means of a researcher who wants to compare many different individuals or populations. DNA differences can also be estimated by sampling just a part of the sequence indirectly. The way to do that is to use restriction enzymes to digest DNA. Restriction digests can tell you if a small sequence in two different individuals is the same or different. By using many different restriction enzymes, you can sample several different small pieces of a sequence, often as much as 10% of the sequence and for significantly less money.