The molecular clock is a technique which estimates when two taxa diverged in evolution. It is based on comparing the detailed structure of key molecules. The method may be done for species, or any higher taxon, such as phyla. Adjustments are made by using what is known of the fossil record. The molecular data used for such calculations is often nucleotide sequences in genome analysis, or amino acid sequences for proteins such as haemoglobin. It is sometimes called a gene clock or evolutionary clock.
The key assumption behind the technique is that, in the long run, changes in molecular structure happen at a steady rate. Researchers such as Ayala have challenged this assumption. According to Ayala, these factors combine to limit the application of molecular clock models:
- Changing generation times: a mutation generally becomes fixed only from one generation to another. The shorter this timespan is, the more mutations can become fixed.
- Population size: apart from effects of small population size, genetic diversity will "bottom out" as populations become larger, and the fitness advantage of any one mutation becomes smaller.
- Species-specific differences due to differing metabolism, ecology, evolutionary history, etc.
- Ayala F.J. (1999). "Molecular clock mirages". BioEssays 21 (1): 71–75. doi:10.1002/(SICI)1521-1878(199901)21:1<71::AID-BIES9>3.0.CO;2-B. http://www3.interscience.wiley.com/cgi-bin/abstract/60000186/ABSTRACT?CRETRY=1&SRETRY=0.
- Schwartz J.H. and Maresc, B. (2006). "Do Molecular clocks run at all? A critique of molecular systematics". Biological Theory 1: 357–371. doi:10.1162/biot.2006.1.4.357. Lay summary – Science Daily.
- Jarmila Kukalová-Peck. 2008. Phylogeny of higher taxa in insecta: finding synapomorphies in the extant fauna and separating them from homoplasies. Evolutionary Biology 35, 4-51