Molecular evolutionMolecular evolution refers to incremental changes in the nucleotide sequence of DNA--usually to changes in the DNA of the chromosomes--which take place over the history of a species and distinguish the species from its forebears. Because biologists and geneticists view every heritable change in trait or phenotype as necessarily a result of DNA changes, the evolution of molecular sequences relates to evolution more generally. But the two do not relate in a simple way, and exactly how is a subject of more than one scientific controversy. One obvious inequivalence is that molecular evolution takes place not only in the gene sequences which code for structural, enzymatic or other gene products, but in DNA with no known function (so-called "junk DNA"), so that in principle the DNA of a lineage might "evolve molecularly," even while the phenotype of descendants remains constant.
One of the central questions surrounding molecular evolution is what proportion of mutations are neutral with respect to natural selection, meaning mutations that do not convey a selective advantage or disadvantage to the individual that inherits them. Answering such questions is an aim of population genetics.
Rare spontaneous errors in DNA replication cause the mutations that drive molecular evolution. The molecular clock technique, which researchers use to date when two species diverged by comparing their DNA, deduces elapsed time from the number of differences. The technique was inspired by the once common assumption that the DNA error rate is constant--not just over time, but across all species and every part of a genome that you might want to compare. Because the enzymes that replicate DNA differ only very slightly between species, the assumption seemed reasonable a priori. But as molecular evidence has accumulated, the constant-rate assumption has proven false--or at least overly general. Molecular clock users are developing workaround solutions.
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