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16 Ancient and Contemporary Mitochondrial DNA Variation in the Maya D. Andrew Merriwether, David M. Reed, and Robert E. Ferrell With the advent of the polymerase chain reaction (peR) (Saiki et al. 1988) it is now possible to extract DNA from ancient human bone, tissue , teeth, and hair and to amplify the number of copies of DNA to levels which enable molecular genetic analyses. Prior to the invention of peR, it was not possible to retrieve enough high molecular weight DNA from ancient remains to perform DNA sequencing or restriction fragment length polymorphism (RFLP) analyses . In addition, the advent of PCR has enabled researchers to amplify and analyze DNA from small amounts of blood or plasma from living individuals. In the past ten years these techniques have been applied to the study of the peopling of the New World through the analysis of mitochondrial DNA (mtDNA) variation in ancient and contemporary Native Americans . Wallace et al. (1985) showed that all Native Americans are closely related, and showed evidence for a bottleneck in Amerindian genetic variation compared with modern Asian varia208 tion. Schurr et al. (1990) demonstrated that all Native American mtDNA variation can be traced back to just four founding lineages, and that all contemporary Amerindians are descendants of one of these four lineages (termed A, B, C, and D). Merriwether et al. (1994, 1995) and Stone and Stoneking (1994) proved that variants of the four founding lineages were also present in ancient populations. It is first necessary to present some background about basic genetics, mtDNA, and the methods of data collection, before discussing the data and results. DNA consists of four different components (referred to as nucleotides or bases): adenosine (A), guanine (G), cytosine (C), and thymine (T). There are two primary locations for human genetic material in human cells. Nuclear DNA resides inside the nucleus of cells in the form of chromosomes (22 pairs of autosomes and a pair of sex chromosomes). An individual receives a complete set of 22 autosomes and one sex chromosome from each par- ent, for a total of 46 chromosomes. The maternally and paternally derived chromosomes exchange portions of their DNA during meiosis . This is called recombination, and leads to each chromosome in the nucleus of the progeny becoming a chimera of maternal and paternal genes. Mitochondrial DNA exists outside the nucleus in an organelle called the mitochondrion . Mitochondrial DNA is a circular molecule , some 16,569 nucleotides (nts) in length (Anderson et al. 1981). Mitochondrial DNA encodes genes which are involved in energy production for the cells, oxidative phosphorylation , and cellular respiration. There are 37 genes in the rntDNA molecule: 13 proteincoding genes, 2 ribosomal RNAs (rRNAs), and 22 transfer RNAs (tRNAs). The proteinencoding genes create subunits of Cytochrome oxidase, NADH dehydrogenase, ATPase, and Cytochrome B. The mtDNA has its own unique tRNAs, and some mtDNA tRNAs code for different amino acids than do the nuclear tRNAs. For example, in rntDNA both AGG and AGA code for protein chain termination, but in nuclear DNA they encode the amino acid arginine . There are approximately 1500 copies of mtDNA in every cell, as there are an average of 2.6 copies of mtDNA per mitochondrion, and an average of 750 mitochondria per cell. This means that there are many more copies of mtDNA than of nuclear DNA in each cell (an important consideration when trying to recover DNA from ancient or suboptimal sources). Mitochondrial DNA is maternally inherited in mammals, meaning that only females pass on their mtDNA to the next generation. Mitochondrial DNA does not undergo recombination , so it is transmitted intact from mother to daughter, generation after generation. The only changes that occur in mtDNA are due to point mutations, insertions, and deletions (with insertions and deletions being rare). Mitochondrial DNA has a mutation rate that is six to ten times higher than that of nuclear DNA, making it an excellent molecule to study when addressing questions involving relatively recently separated individuals, populations, or species. Lastly, the rntDNA from more than 100 individuals has heen completely sequenced, making it simple to design primers necessary for the peR technique, and making it relatively simple to assign the precise location to restriction site cuts. The data described here were collected by cutting the peR-amplified mtDNA with restriction enzymes. A restriction enzyme recognizes a specific sequence of four or more bases (nucleotides ) and cleaves the DNA strand whenever it detects this "recognition sequence." Restriction enzymes are produced by bacteria as a defense mechanism against...


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