Editing Molecular clock (section)

==Calibration==
To use molecular clocks to estimate divergence times, molecular clocks need to be "calibrated". This is because molecular data alone does not contain any information on absolute times. For viral phylogenetics and [[ancient DNA]] studies—two areas of evolutionary biology where it is possible to sample sequences over an evolutionary timescale—the dates of the intermediate samples can be used to calibrate the molecular clock. However, most phylogenies require that the molecular clock be [[calibration|calibrated]] using independent evidence about dates, such as the [[fossil]] record.<ref name=Benton01>{{cite journal | vauthors = Benton MJ, Donoghue PC | title = Paleontological evidence to date the tree of life | journal = Molecular Biology and Evolution | volume = 24 | issue = 1 | pages = 26–53 | date = January 2007 | pmid = 17047029 | doi = 10.1093/molbev/msl150 | name-list-style = amp | doi-access = free }}</ref> There are two general methods for calibrating the molecular clock using fossils: node calibration and tip calibration.<ref name=Donoghue02>{{cite journal | vauthors = Donoghue PC, Yang Z | title = The evolution of methods for establishing evolutionary timescales | journal = Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences | volume = 371 | issue = 1699 | page = 20160020 | date = July 2016 | pmid = 27325838 | pmc = 4920342 | doi = 10.1098/rstb.2016.0020 | name-list-style = amp }}</ref>

===Node calibration===
Sometimes referred to as node dating, node calibration is a method for time-scaling [[phylogenetic tree]]s by specifying time constraints for one or more nodes in the tree. Early methods of clock calibration only used a single fossil constraint (e.g. non-parametric rate smoothing),<ref>{{Cite journal| vauthors = Sanderson M |date=1997|title=A nonparametric approach to estimating divergence times in the absence of rate constancy|journal=Molecular Biology and Evolution|volume=14|issue=12|pages=1218–1231|doi=10.1093/oxfordjournals.molbev.a025731|s2cid=17647010|doi-access=free}}</ref> but newer methods (BEAST<ref name="ReferenceA"/> and [[sourceforge:projects/r8s/|r8s]]<ref>{{cite journal | vauthors = Sanderson MJ | title = r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock | journal = Bioinformatics | volume = 19 | issue = 2 | pages = 301–302 | date = January 2003 | pmid = 12538260 | doi = 10.1093/bioinformatics/19.2.301 | doi-access = free }}</ref>) allow for the use of multiple fossils to calibrate molecular clocks. The oldest fossil of a [[clade]] is used to constrain the minimum possible age for the node representing the most recent common ancestor of the clade. However, due to incomplete fossil preservation and other factors, clades are typically older than their oldest fossils.<ref name="Donoghue02" /> In order to account for this, nodes are allowed to be older than the minimum constraint in node calibration analyses. However, determining how much older the node is allowed to be is challenging. There are a number of strategies for deriving the maximum bound for the age of a clade including those based on birth-death models, fossil [[stratigraphy|stratigraphic]] distribution analyses, or [[taphonomy|taphonomic]] controls.<ref name="O'Reilly03">{{cite journal | vauthors = O'Reilly JE, Dos Reis M, Donoghue PC | title = Dating Tips for Divergence-Time Estimation | journal = Trends in Genetics | volume = 31 | issue = 11 | pages = 637–650 | date = November 2015 | pmid = 26439502 | doi = 10.1016/j.tig.2015.08.001 | hdl-access = free | name-list-style = amp | hdl = 1983/ba7bbcf4-1d51-4b74-a800-9948edb3bbe6 | url = https://research-information.bris.ac.uk/en/publications/ba7bbcf4-1d51-4b74-a800-9948edb3bbe6 }}</ref> Alternatively, instead of a maximum and a minimum, a [[probability density]] can be used to represent the uncertainty about the age of the clade. These calibration densities can take the shape of standard probability densities (e.g. [[Normal distribution|normal]], [[Log-normal distribution|lognormal]], [[Exponential distribution|exponential]], [[Gamma distribution|gamma]]) that can be used to express the uncertainty associated with divergence time estimates. <ref name="ReferenceA">{{cite journal | vauthors = Drummond AJ, Suchard MA, Xie D, Rambaut A | title = Bayesian phylogenetics with BEAUti and the BEAST 1.7 | journal = Molecular Biology and Evolution | volume = 29 | issue = 8 | pages = 1969–1973 | date = August 2012 | pmid = 22367748 | pmc = 3408070 | doi = 10.1093/molbev/mss075 }}</ref> Determining the shape and parameters of the probability distribution is not trivial, but there are methods that use not only the oldest fossil but a larger sample of the fossil record of clades to estimate calibration densities empirically.<ref name="Claramunt2022">{{cite journal | last=Claramunt | first=S | title=CladeDate : Calibration information generator for divergence time estimation | journal=Methods in Ecology and Evolution | publisher=Wiley | volume=13 | issue=11 | date=2022 | issn=2041-210X | doi=10.1111/2041-210x.13977 | pages=2331–2338| s2cid=252353611 | doi-access=free | bibcode=2022MEcEv..13.2331C }}</ref> Studies have shown that increasing the number of fossil constraints increases the accuracy of divergence time estimation.<ref name=Zheng04>{{cite journal | vauthors = Zheng Y, Wiens JJ | title = Do missing data influence the accuracy of divergence-time estimation with BEAST? | journal = Molecular Phylogenetics and Evolution | volume = 85 | issue = 1 | pages = 41–49 | date = April 2015 | pmid = 25681677 | doi = 10.1016/j.ympev.2015.02.002 | bibcode = 2015MolPE..85...41Z | s2cid = 3895351 | name-list-style = amp }}</ref>

===Tip calibration===
Sometimes referred to as [[tip dating]], tip calibration is a method of molecular clock calibration in which fossils are treated as [[taxon|taxa]] and placed on the tips of the tree. This is achieved by creating a matrix that includes a [[molecular phylogenetics|molecular]] dataset for the [[neontology|extant taxa]] along with a [[morphology (biology)|morphological]] dataset for both the extinct and the extant taxa.<ref name="O'Reilly03" /> Unlike node calibration, this method reconstructs the tree topology and places the fossils simultaneously. Molecular and morphological models work together simultaneously, allowing morphology to inform the placement of fossils.<ref name="Donoghue02" /> Tip calibration makes use of all relevant fossil taxa during clock calibration, rather than relying on only the oldest fossil of each clade. This method does not rely on the interpretation of negative evidence to infer maximum clade ages.<ref name="O'Reilly03" />

=== 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" />

===Total evidence dating===
This approach to tip calibration goes a step further by simultaneously estimating fossil placement, topology, and the evolutionary timescale. In this method, the age of a fossil can inform its phylogenetic position in addition to morphology. By allowing all aspects of tree reconstruction to occur simultaneously, the risk of biased results is decreased.<ref name="Donoghue02" /> This approach has been improved upon by pairing it with different models. One current method of molecular clock calibration is total evidence dating paired with the fossilized birth-death (FBD) model and a model of morphological evolution.<ref name=Heath05>{{cite journal | vauthors = Heath TA, Huelsenbeck JP, Stadler T | title = The fossilized birth-death process for coherent calibration of divergence-time estimates | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 111 | issue = 29 | pages = E2957–E2966 | date = July 2014 | pmid = 25009181 | pmc = 4115571 | doi = 10.1073/pnas.1319091111 | name-list-style = amp | arxiv = 1310.2968 | doi-access = free | bibcode = 2014PNAS..111E2957H }}</ref> The FBD model is novel in that it allows for "sampled ancestors", which are fossil taxa that are the direct ancestor of a living taxon or [[lineage (evolution)|lineage]]. This allows fossils to be placed on a branch above an extant organism, rather than being confined to the tips.<ref name=Gavryushkina06>{{cite journal | vauthors = Gavryushkina A, Heath TA, Ksepka DT, Stadler T, Welch D, Drummond AJ | title = Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins | journal = Systematic Biology | volume = 66 | issue = 1 | pages = 57–73 | date = January 2017 | pmid = 28173531 | pmc = 5410945 | doi = 10.1093/sysbio/syw060 | name-list-style = amp | arxiv = 1506.04797 }}</ref>

===Methods===
Bayesian methods can provide more appropriate estimates of divergence times, especially if large datasets—such as those yielded by [[phylogenomics]]—are employed.<ref name="Dos Reis2012">{{cite journal | vauthors = dos Reis M, Inoue J, Hasegawa M, Asher RJ, Donoghue PC, Yang Z | title = Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny | journal = Proceedings. Biological Sciences | volume = 279 | issue = 1742 | pages = 3491–3500 | date = September 2012 | pmid = 22628470 | pmc = 3396900 | doi = 10.1098/rspb.2012.0683 }}</ref>