Editing Molecular clock (section)

=== Expansion calibration ===
Demographic changes in populations can be detected as fluctuations in historical coalescent [[effective population size]] from a sample of extant genetic variation in the population using coalescent theory.<ref>{{cite journal | vauthors = Rogers AR, Harpending H | title = Population growth makes waves in the distribution of pairwise genetic differences | journal = Molecular Biology and Evolution | volume = 9 | issue = 3 | pages = 552–569 | date = May 1992 | pmid = 1316531 | doi = 10.1093/oxfordjournals.molbev.a040727 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Shapiro B, Drummond AJ, Rambaut A, Wilson MC, Matheus PE, Sher AV, Pybus OG, Gilbert MT, Barnes I, Binladen J, Willerslev E, Hansen AJ, Baryshnikov GF, Burns JA, Davydov S, Driver JC, Froese DG, Harington CR, Keddie G, Kosintsev P, Kunz ML, Martin LD, Stephenson RO, Storer J, Tedford R, Zimov S, Cooper A | display-authors = 6 | title = Rise and fall of the Beringian steppe bison | journal = Science | volume = 306 | issue = 5701 | pages = 1561–1565 | date = November 2004 | pmid = 15567864 | doi = 10.1126/science.1101074 | bibcode = 2004Sci...306.1561S | s2cid = 27134675 | url = http://summit.sfu.ca/item/15088 }}</ref><ref>{{cite journal | vauthors = Li H, Durbin R | title = Inference of human population history from individual whole-genome sequences | journal = Nature | volume = 475 | issue = 7357 | pages = 493–496 | date = July 2011 | pmid = 21753753 | pmc = 3154645 | doi = 10.1038/nature10231 }}</ref> Ancient population expansions that are well documented and dated in the geological record can be used to calibrate a rate of molecular evolution in a manner similar to node calibration. However, instead of calibrating from the known age of a node, expansion calibration uses a two-epoch model of constant population size followed by population growth, with the time of transition between epochs being the parameter of interest for calibration.<ref name=":0">{{cite journal | vauthors = Crandall ED, Sbrocco EJ, Deboer TS, Barber PH, Carpenter KE | title = Expansion dating: calibrating molecular clocks in marine species from expansions onto the Sunda Shelf Following the Last Glacial Maximum | journal = Molecular Biology and Evolution | volume = 29 | issue = 2 | pages = 707–719 | date = February 2012 | pmid = 21926069 | doi = 10.1093/molbev/msr227 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Hoareau TB | title = Late Glacial Demographic Expansion Motivates a Clock Overhaul for Population Genetics | journal = Systematic Biology | volume = 65 | issue = 3 | pages = 449–464 | date = May 2016 | pmid = 26683588 | doi = 10.1093/sysbio/syv120 | doi-access = free | hdl = 2263/53371 | hdl-access = free }}</ref> Expansion calibration works at shorter, intraspecific timescales in comparison to node calibration, because expansions can only be detected after the [[most recent common ancestor]] of the species in question. Expansion dating has been used to show that molecular clock rates can be inflated at short timescales<ref name=":0" /> (< 1 MY) due to incomplete fixation of alleles, as discussed below<ref>{{cite journal | vauthors = Ho SY, Tong KJ, Foster CS, Ritchie AM, Lo N, Crisp MD | title = Biogeographic calibrations for the molecular clock | journal = Biology Letters | volume = 11 | issue = 9 | pages = 20150194 | date = September 2015 | pmid = 26333662 | pmc = 4614420 | doi = 10.1098/rsbl.2015.0194 }}</ref><ref name=":1" />