The molecular clock

In addition to permitting reconstruction of relationships among species to generate a phylogenetic tree, molecular genetics can also yield valuable information with respect to the timescale for that tree. With the very first reconstructions conducted using molecular data, it was observed that the rate of change in amino acid sequences of particular proteins (and hence in the DNA sequences of the genes responsible) seemed to be relatively constant along different lineages. This led on to the notion of the "molecular clock", according to which the degree of difference between DNA sequences or amino acid sequences in any two species can provide an indication of the time elapsed since their separation. However, it should be noted that accumulating evidence has indicated that the rate of molecular change is in fact quite variable. In the first place, it was obvious from the outset that some genes evolve faster than others, and it was then shown that the overall rate of change in mtDNA is considerably greater than that in nDNA. Moreover, it also became clear that rates of change differ markedly even within individual genes. Some of this variation in rate of change within genes is to be expected. For

The Euarchontoglires grouping of placental mammals is represented by mammals such as the woodchuck (Marmota monax). (Photo by © John Conrad/Corbis. Reproduced by permission.)

whale dolphin hippo ruminant pig llama rhino tapir horse cat caniform pangolin flying fox rousette fruit bat rhinolophoid bat phyllostomid microbat free-tailed bat hedgehog shrew mole mouse rat hystricid caviomorph sciurid rabbit pika flying lemur tree shrew strepsirrhine human sloth anteater armadillo tenrec golden mole s.e.elephant shrew l.e.elephant shrew aardvark sirenian hyrax elephant opossum diprotodontian

Cetartiodactyla

Perissodactyla

Carnivora Pholidota

Chiroptera

Eulipotyphla

Rodentia

Lagomorpha

Dermoptera Scandentia

Primates

Pilosa Cingulata

Afrosoricida

Macroscelidea

Tubulidentata Sirenia Hyracoidea Proboscidea

Xenarthra

Afrotheria

Marsupialia

Phylogeny of living placental mammals, based on a large molecular data set (16,397 base pairs) including 19 nuclear genes and 3 mitochondrial genes. Based on Murphy et al. 2001. (Illustration by GGS. Courtesy of Gale.)

example, "silent mutations" (notably in third base positions) and mutations within non-coding regions of genes (introns) are inherently likely to accumulate faster because they do not lead to changes in amino acid sequences and are hence not subject to natural selection. In sum, it is now widely recognized that the concept of the "molecular clock" must be used with caution and that there may be quite marked differences between lineages in the rates of molecular change. Methods have therefore been developed to identify differences in rates of change between lineages and to apply the notion of "local clocks".

It should be noted that molecular data cannot directly yield information on elapsed time and that phylogenetic trees produced with such data always require calibration using information from the fossil record. Once a tree that is characterized by relatively uniform rates of change has been calibrated with at least one date from the fossil record, it is possible to convert genetic distances into time differences. However, conversion of genetic distances into time differences requires that genetic change should be linearly related to time. This generally seems to be the case once a global correction has been made for repeated mutation at a given site. Unfortunately, even if rates of molecular change along lineages are approximately linear (as is required for reliable application of a clock model), calibration dates derived from paleontological evidence introduce an additional source of error. The problem is that the fossil record can only yield a minimum date for the time of emergence of a particular lineage, by taking the age of the earliest known member of that lineage. The lineage may have existed for some considerable period of time prior to the earliest known fossil representative. Clearly, the size of the gap between the actual date of emergence of a lineage and the age of the earliest known representative of that lineage will vary according to the quality of the fossil record. If the fossil record is relatively well documented, as is probably the case with large-bodied hoofed mammals, the earliest known fossil representative may be quite close to the time of origin. In other cases, however, use of the age of the earliest known fossil to calibrate a phylogenetic tree may lead to considerable underestimation of dates of divergence. For instance, the earliest known undoubted primates are about 55 million years old, but statistical modeling indicates that we have so far discovered less than 5% of extinct fossil primate species. Correction for the numerous gaps in the primate fossil record indicates that the common ancestor of living primates existed about 85 million years ago (mya), rather than 60-65 mya as is commonly assumed. Molecular evolutionary phylogenetic trees have also been accurately determined for the common chimpanzee, pygmy chimpanzee, gorilla, and orangutan.

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