Our final task is to develop an algorithm to reconstruct phylogenetic relationships based on sequence data. In the final homework problem, the source sequences are mitochondrial DNA from a number of modern human individuals, as well as from several fossils, including a Neanderthal. Let us begin by saying something about these sequences and how they are used to create input for our algorithm.
The cells of eukaryotes, such as humans, contain two types of DNA. The largest type is the nuclear DNA which is found in sets of chromosomes that are inherited sexually, with one copy of each chromosome coming from either parent. A second type of DNA can be found in the mitochondria, organelles specializing in energy metabolism. Mitochondria contain their own circular DNA molecule. As it turns out, mitochondria are inherited maternally – individual humans get their mitochondria from their mother’s egg rather than their father’s sperm. Thus, mitochondrial DNA is passed along the maternal line only.
Mitochondrial DNA has frequently been used in studies of human evolution. One advantage is the fact that it’s inherited from a single parent, and thus is not subject to recombination. Another advantage is the fact that mutations arise comparatively quickly in mammalian mitochondrial DNA. If we are comparing closely related samples, such as human individuals, a higher rate of mutation is good because it produces more differences with which to distinguish the samples.
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