Biological macromolecules, like organismal phenotypes, evolve at highly variable tempos and modes within and across organismal lineages. In other words, molecular evolution was thought to be an erratic or idiosyncratic process.
molecular clocks; DNA sequence
Biological macromolecules, like organismal phenotypes, evolve at highly variable tempos and modes within and across organismal lineages. In other words, molecular evolution was thought to be an erratic or idiosyncratic process.
The new paradigm was that at least some molecules evolve with sufficient regularity as to provide molecular timepieces. Emile Zuckerkandl and Linus Pauling were the first to propose the concept of a “molecular clock”. The idea fits well with the neutrality theory of molecular evolution (see Chapter 40) because the rate of neutral evolution in DNA sequences is in principle equal to the mutation rate to neutral alleles. However, molecular clocks need not be incompatible with natural selection, because if large numbers of DNA sequences are acted upon by multifarious selection pressures over long periods of evolutionary time, then short-term fluctuations in selection could cancel out such that genetic distances between taxa might correlate well with times elapsed since common ancestry.
Two aspects of the molecular clock concept should not be misconstrued. First, the proposal is not that the clock is metronomic, but rather that it might tick at a stochastically constant rate, like radioactive decay. Second, molecular clocks may be helpful but they are not prerequisite for the use of DNA sequences in molecular systematics (see Chapter 31), either because many tree-building algorithms relax assumptions of rate homogeneity among genes and lineages, or because they deal with raw sequence characters before the latter are converted into estimates of inter-taxon genetic distance (see Chapter 35).
In countless empirical studies conducted during the past half-century, various DNA sequences have proved to evolve at heterogeneous rates at several levels: across nucleotide positions within a codon; among non-homologous genes within a lineage; among different classes of DNA within a genome; and among different genomes within an organismal lineage. Thus, there is no single molecular clock but rather a large ensemble of clocks ticking at different rates. This may seem disconcerting, but it also means that researchers can choose molecular clocks that are tailored to the approximate evolutionary timescale of each exercise in phylogenetic dating. For example, ribosomal RNA sequences have been extremely informative in reconstructing ancient events in the history of life (see Chapter 50), whereas rapidly evolving mitochondrial DNA sequences have revolutionized phylogenetic appraisals at the far more recent timescales of intraspecific differentiation (see Chapter 51).
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