Editing Molecular clock (section)

==Non-constant rate of molecular clock==
Sometimes only a single divergence date can be estimated from fossils, with all other dates inferred from that. Other sets of species have abundant fossils available, allowing the hypothesis of constant divergence rates to be tested. DNA sequences experiencing low levels of [[negative selection (natural selection)|negative selection]] showed divergence rates of 0.7–0.8% per&nbsp;[[Myr]] in bacteria, mammals, invertebrates, and plants.<ref name=Ochman87>{{cite journal | vauthors = Ochman H, Wilson AC | title = Evolution in bacteria: evidence for a universal substitution rate in cellular genomes | journal = Journal of Molecular Evolution | volume = 26 | issue = 1–2 | pages = 74–86 | year = 1987 | pmid = 3125340 | doi = 10.1007/BF02111283 | s2cid = 8260277 | bibcode = 1987JMolE..26...74O }}</ref>  In the same study, genomic regions experiencing very high negative or purifying selection (encoding rRNA) were considerably slower (1% per 50&nbsp;Myr).

In addition to such variation in rate with genomic position, since the early 1990s variation among taxa has proven fertile ground for research too,<ref name=Douzery03>{{cite journal | vauthors = Douzery EJ, Delsuc F, Stanhope MJ, Huchon D | title = Local molecular clocks in three nuclear genes: divergence times for rodents and other mammals and incompatibility among fossil calibrations | journal = Journal of Molecular Evolution | volume = 57 | issue = Suppl 1 | pages = S201–S213 | year = 2003 | pmid = 15008417 | doi = 10.1007/s00239-003-0028-x | s2cid = 23887665 | citeseerx = 10.1.1.535.897 | bibcode = 2003JMolE..57S.201D }}</ref> even over comparatively short periods of evolutionary time (for example [[mockingbird]]s<ref name=Hunt01>{{cite journal | vauthors = Hunt JS, Bermingham E, Ricklefs RE |year=2001 |title=Molecular systematics and biogeography of Antillean thrashers, tremblers, and mockingbirds (Aves: Mimidae) |journal=[[Auk (journal)|Auk]] |volume=118 |issue=1 |pages=35–55|doi=10.1642/0004-8038(2001)118[0035:MSABOA]2.0.CO;2 |s2cid=51797284 |issn=0004-8038|doi-access=free }}</ref>). [[Procellariiformes|Tube-nosed seabirds]] have molecular clocks that on average run at half speed of many other birds,<ref name=Rheindt05>{{cite journal |author1=Rheindt, F. E.  |author2=Austin, J.  |name-list-style=amp |year=2005 |title=Major analytical and conceptual shortcomings in a recent taxonomic revision of the Procellariiformes – A reply to Penhallurick and Wink (2004) |journal=[[Emu (journal)|Emu]] |volume=105 |issue=2 |pages=181–186|url=http://www.publish.csiro.au/?act=view_file&file_id=MU04039.pdf |doi=10.1071/MU04039|bibcode=2005EmuAO.105..181R |s2cid=20390465 }}</ref> possibly due to long [[generation]] times, and many turtles have a molecular clock running at one-eighth the speed it does in small mammals, or even slower.<ref name=Avise92>{{cite journal | vauthors = Avise JC, Bowen BW, Lamb T, Meylan AB, Bermingham E | title = Mitochondrial DNA evolution at a turtle's pace: evidence for low genetic variability and reduced microevolutionary rate in the Testudines | journal = Molecular Biology and Evolution | volume = 9 | issue = 3 | pages = 457–473 | date = May 1992 | pmid = 1584014 | doi = 10.1093/oxfordjournals.molbev.a040735 | doi-access = free }}</ref> Effects of [[small population size]] are also likely to confound molecular clock analyses. Researchers such as [[Francisco J. Ayala]] have more fundamentally challenged the molecular clock hypothesis.<ref name=Ayala99>{{cite journal | vauthors = Ayala FJ | title = Molecular clock mirages | journal = BioEssays | volume = 21 | issue = 1 | pages = 71–75 | date = January 1999 | pmid = 10070256 | doi = 10.1002/(SICI)1521-1878(199901)21:1<71::AID-BIES9>3.0.CO;2-B | url = http://www3.interscience.wiley.com/cgi-bin/abstract/60000186/ABSTRACT?CRETRY=1&SRETRY=0 | url-status = dead | archive-url = https://archive.today/20121216135641/http://www3.interscience.wiley.com/cgi-bin/abstract/60000186/ABSTRACT?CRETRY=1&SRETRY=0 | archive-date = 16 December 2012 | url-access = subscription }}</ref><ref name=Schwartz06>{{cite journal |author1=Schwartz, J. H.  |author2=Maresca, B.  |name-list-style=amp |year=2006 |title=Do Molecular Clocks Run at All? A Critique of Molecular Systematics |journal=Biological Theory |volume=1 |pages=357–371|doi=10.1162/biot.2006.1.4.357 |issue=4|citeseerx=10.1.1.534.4502  |s2cid=28166727}}
*{{cite press release |date=February 12, 2007 |title=No Missing Link? Evolutionary Changes Occur Suddenly, Professor Says |website=[[ScienceDaily]] |url=https://www.sciencedaily.com/releases/2007/02/070210170623.htm}}</ref><ref name=Pascual2019>{{cite journal | vauthors = Pascual-García A, Arenas M, Bastolla U | title = The Molecular Clock in the Evolution of Protein Structures | journal = Systematic Biology | volume = 68 | issue = 6 | pages = 987–1002 | date = November 2019 | pmid = 31111152 | doi = 10.1093/sysbio/syz022 |doi-access= | name-list-style = amp | hdl = 20.500.11850/373053 | hdl-access = free }}</ref> According to Ayala's 1999 study, five factors combine to limit the application of molecular clock models:

* Changing generation times (If the rate of new mutations depends at least partly on the number of generations rather than the number of years)
* Population size ([[Genetic drift]] is stronger in small populations, and so more mutations are effectively neutral)
* Species-specific differences (due to differing metabolism, ecology, evolutionary history,&nbsp;...)
* Change in function of the protein studied (can be avoided in closely related species by utilizing [[non-coding DNA]] sequences or emphasizing [[silent mutation]]s)
* Changes in the intensity of natural selection.

[[File:Molecular evolution bamboos.svg|thumb|300px|left|alt=Phylogram showing three groups, one of which has strikingly longer branches than the two others|Woody bamboos (tribes [[Arundinarieae]] and [[Bambuseae]]) have long generation times and lower mutation rates, as expressed by short branches in the [[phylogenetic tree]], than the fast-evolving herbaceous bamboos ([[Olyreae]]).]]

Molecular clock users have developed workaround solutions using a number of statistical approaches including [[maximum likelihood]] techniques and later [[Bayesian statistics|Bayesian modeling]]. In particular, models that take into account rate variation across lineages have been proposed in order to obtain better estimates of divergence times. These models are called '''relaxed molecular clocks'''<ref name=Drummond06>{{cite journal | vauthors = Drummond AJ, Ho SY, Phillips MJ, Rambaut A | title = Relaxed phylogenetics and dating with confidence | journal = PLOS Biology | volume = 4 | issue = 5 | pages = e88 | date = May 2006 | pmid = 16683862 | pmc = 1395354 | doi = 10.1371/journal.pbio.0040088 | doi-access = free }}</ref> because they represent an intermediate position between the 'strict' molecular clock hypothesis and [[Joseph Felsenstein]]'s many-rates model<ref name=Felsenstein01>{{cite journal | vauthors = Felsenstein J | title = Taking variation of evolutionary rates between sites into account in inferring phylogenies | journal = Journal of Molecular Evolution | volume = 53 | issue = 4–5 | pages = 447–455 | year = 2001 | pmid = 11675604 | doi = 10.1007/s002390010234 | s2cid = 9791493 | bibcode = 2001JMolE..53..447F }}</ref> and are made possible through [[Markov chain Monte Carlo|MCMC]] techniques that explore a weighted range of tree topologies and simultaneously estimate parameters of the chosen substitution model. It must be remembered that divergence dates inferred using a molecular clock are based on statistical [[inference]] and not on direct [[evidence]].

The molecular clock runs into particular challenges at very short and very long timescales. At long timescales, the problem is [[Saturation (genetic)|saturation]]. When enough time has passed, many sites have undergone more than one change, but it is impossible to detect more than one. This means that the observed number of changes is no longer [[Linear function|linear]] with time, but instead flattens out.  Even at intermediate genetic distances, with phylogenetic data still sufficient to estimate topology, signal for the overall scale of the tree can be weak under complex likelihood models, leading to highly uncertain molecular clock estimates.<ref>Marshall, D. C., et al. 2016. Inflation of molecular clock rates and dates: molecular phylogenetics, biogeography, and diversification of a global cicada radiation from Australasia (Hemiptera: Cicadidae: Cicadettini). [https://academic.oup.com/sysbio/article/65/1/16/2461540/Inflation-of-Molecular-Clock-Rates-and-Dates Systematic Biology 65(1):16–34].</ref>

At very short time scales, many differences between samples do not represent [[Fixation (population genetics)|fixation]] of different sequences in the different populations. Instead, they represent alternative [[alleles]] that were both present as part of a polymorphism in the common ancestor. The inclusion of differences that have not yet become [[Fixation (population genetics)|fixed]]
leads to a potentially dramatic inflation of the apparent rate of the molecular clock at very short timescales.<ref name=":1">{{cite journal | vauthors = Ho SY, Phillips MJ, Cooper A, Drummond AJ | title = Time dependency of molecular rate estimates and systematic overestimation of recent divergence times | journal = Molecular Biology and Evolution | volume = 22 | issue = 7 | pages = 1561–1568 | date = July 2005 | pmid = 15814826 | doi = 10.1093/molbev/msi145 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Peterson GI, Masel J | title = Quantitative prediction of molecular clock and ka/ks at short timescales | journal = Molecular Biology and Evolution | volume = 26 | issue = 11 | pages = 2595–2603 | date = November 2009 | pmid = 19661199 | pmc = 2912466 | doi = 10.1093/molbev/msp175 }}</ref>