Molecular Clocks

DNA is not just the basic building block of life; it is also a data recorder. The genetic sequence of an individual tells the tale of their geographic ancestry and the genetic code of a species tells the tale of its evolution. By comparing the DNA sequences of different organisms, it is possible to determine how closely related those two organisms are, and it is also possible to estimate the time since they shared a common ancestor. Similarities in DNA decrease with the decrease in relatedness at the individual level, at the species level, and so on. Identical twins are born with identical genomes. Normal mammalian siblings share an average of 50 percent of their DNA, just like offspring share an average of 50 percent of their DNA with their parents. Grandchildren share 25 percent of their DNA with their grandparents. And so on. Whether two individuals shared a great-great-great-grandmother 100 years ago or whether they shared an ancestral root 100 million years ago, it is all spelled out in their DNA.

The method for comparing two sequences and then estimating the time since their common ancestry is based on the principle known as the "molecular clock." Late in the 1960s, Vincent Sarich and Allan Wilson were pioneers in applying the concept to human evolution. Their initial analysis comparing the African apes and humans resulted in a tree with humans and African apes grouped together, excluding Asian apes. This result along with corroboration from many other laboratories, contradicted the assumption based on anatomy and behavior held by many scientists for most of the first half of the 20th century. The long-standing view had grouped Asian and African apes together to the exclusion of humans, but these new genetic comparisons showed that humans were more closely related to gorillas and chimpanzees than African apes were to Asian apes.

The estimated splitting dates within the apes were also changed once molecular clocks were invented. Sarich and Wilson placed the chimpanzee-human split around 5 Mya and since then an abundance of molecular clock research has produced similar estimates between 8 and 4 Mya. Before molecular clocks, the split time was assumed to be much deeper in prehistory, between 30 and 20 Mya, which misled some prior paleoanthropologists into searching in much too old rocks for fossils of our bipedal ancestors.

Basically, the genetic distance between two samples is assessed by directly comparing the nucleotides in equivalent positions on each of the two sequences and counting up the number of times they differ. Molecular clock methods can be applied to genes, gene families, and, theoretically, to whole genomes. They are also commonly applied to the DNA sequences located in the mitochondria, the so-called "powerhouses" of the cell because they produce energy. Although DNA in a cell's nucleus can be used for molecular clock analysis, mitochondrial DNA (mtDNA) is often preferred because mutations in mtDNA accumulate randomly and often with little consequence to the fitness of the organism (unless they affect the proper functioning of the mitochondria, leading to muscle disorders). Neutral noncoding regions are preferred for use in molecular clocks since without selection acting on them, mutations in these regions accumulate at a steady, clock-like rate per generation.

Using molecular clocks, the splitting times of all the major groups of primates have been estimated and verified. The estimations generally span a range of time but they tend to average about the same. (Figure 2.2 shows the splitting dates for major primate lineages.) Variation in estimated splitting times can be influenced by the calibration method used, or as discussed above, whether or not neutral sequences are used.

The clock is calibrated using fossils and this helps determine the time of divergence at each branching event in the tree thereafter. A good calibration point for the molecular clock analysis of ape and human splitting times is the fossil evidence for the divergence of Old World monkeys and hominoids at the Oligocene-Miocene boundary, 23 Mya. --

Dna-Dna Hybridization

One way to compare genetic sequences is as follows. The DNA is heated up to break the bonds between the base pairs that hold the two strands together. The double-stranded DNA molecule splits into two separate strands in a process called "denaturing." Then the denatured DNA from the species to be compared is added to the mix and the entire sample is allowed to cool. During cooling, the DNA strands reassociate ("anneal" or "hybridize") to form new complete, double-stranded DNA molecules. The closer the species are, phylogenetically, the more similar their genetic sequences (base pairs) will be, the more likely their DNA strands will join together during this process, and the tighter their bonds will be. In order to evaluate how well the sequences fit together, they are reheated. If they denature faster than the original DNA molecule (from a single species), then there is a weaker bond because less base pairs are matched. If they require an equivalent amount of time to split as the original DNA, then the sequences are basically the same. --

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