View source for Human mitochondrial molecular clock

{{Short description|Archaeological record of human activity determined by rate of mutation in mitochondrial genome}}
The '''human mitochondrial molecular clock''' is the rate at which mutations have been accumulating in the [[mitochondrial genome]] of hominids during the course of [[human evolution]]. The archeological record of human activity from early periods in human prehistory is relatively limited and its interpretation has been controversial. Because of the uncertainties from the archeological record, scientists have turned to molecular dating techniques in order to refine the timeline of human evolution. A major goal of scientists in the field is to develop an accurate hominid mitochondrial [[molecular clock]] which could then be used to confidently date events that occurred during the course of human evolution.

Estimates of the mutation rate of human [[mitochondrial DNA]] (mtDNA) vary greatly depending on the available data and the method used for estimation. The two main methods of estimation, phylogeny-based methods and pedigree-based methods, have produced mutation rates that differ by almost an [[order of magnitude]]. Current research has been focused on resolving the high variability obtained from different rate estimates.

==Rate variability==
A major assumption of the molecular clock theory is that mutations within a particular genetic system occur at a statistically uniform rate and this uniform rate can be used for dating genetic events. In practice the assumption of a single uniform rate is an oversimplification. Though a single mutation rate is often applied, it is often a composite or an average of several different mutation rates.<ref name="loogvali2009"/> Many factors influence observed [[mutation rate]]s and these factors include the type of samples, the region of the genome studied and the time period covered.

===Actual vs. observed rates===
The rate at which mutations occur during reproduction, the [[germline mutation]] rate, is thought to be higher than all observed mutation rates, because not all mutations are successfully passed down to subsequent generations.<ref name="howell2003">{{Citation|last1=Howell|year=2003|title=The Pedigree Rate of Sequence Divergence in the Human Mitochondrial Genome: There Is a Difference Between Phylogenetic and Pedigree Rates|pmc=1180241|pmid=12571803|first1=N|last2=Smejkal|first2=CB|last3=MacKey|first3=DA|last4=Chinnery|first4=PF|last5=Turnbull|first5=DM|last6=Herrnstadt|first6=C|volume=72|issue=3|pages=659–70|doi=10.1086/368264|journal=American Journal of Human Genetics|postscript=.}}</ref> mtDNA is only passed down along the matrilineal line, and therefore mutations passed down to sons are lost. Random genetic drift may also cause the loss of mutations. For these reasons, the actual mutation rate will not be equivalent to the mutation rate observed from a population sample.<ref name="howell2003"/>

===Population size===
Population dynamics are believed to influence observed mutation rates. When a population is expanding, more [[germline mutation]]s are preserved in the population. As a result, observed mutation rates tend to increase in an expanding population. When populations contract, as in a [[population bottleneck]], more germline mutations are lost. Population bottlenecks thus tend to slow down observed mutation rates. Since the emergence of the species homo sapiens about 200,000 years ago, the human population has expanded from a few thousand individuals living in Africa to over 8 billion worldwide. However, the expansion has not been uniform, so the history of human populations may consist of both bottlenecks and expansions.<ref name="henn2009"/>

===Structural variability===
The mutation rate across the mitochondrial genome is not uniformly distributed. Certain regions of the genome are known to mutate more rapidly than others. The [[Hypervariable region]]s are known to be highly polymorphic relative to other parts of the genome.

The rate at which mutations accumulate in coding and [[non-coding region]]s of the genome also differs as mutations in the [[coding region]] are subject to [[natural selection|purifying selection]]. For this reason, some studies avoid coding region or [[nonsynonymous mutations]] when calibrating the molecular clock. {{Harvtxt|Loogvali|Kivisild|Margus|Villems|2009}} only consider synonymous mutations, they have recalibrated the molecular clock of human mtDNA as 7990 years per synonymous mutation over
the mitochondrial genome.<ref name="loogvali2009">{{Harvtxt|Loogvali|Kivisild|Margus|Villems|2009}}</ref>
{{Harvtxt |Soares|Ermini|Thomson|Mormina|2009}} consider both coding and non-coding region mutations to arrive at a single mutation rate, but apply a correction factor to account for selection in the coding region.

===Temporal variability===
The mutation rate has been observed to vary with time. Mutation rates within the human species are faster than those observed along the human-ape lineage. The mutation rate is also thought to be faster in recent times, since the beginning of the [[Holocene]] 11,000 years ago.<ref name="loogvali2009"/><ref name="henn2009">{{Harvtxt|Henn|Gignoux|Feldman|Mountain|2009}}</ref><ref name="ho2005">{{Citation|title=Time Dependency of Molecular Rate Estimates and Systematic Overestimation of Recent Divergence Times|url=http://mbe.oxfordjournals.org/cgi/content/full/22/7/1561|archive-url=https://archive.today/20130415154818/http://mbe.oxfordjournals.org/cgi/content/full/22/7/1561|url-status=dead|archive-date=2013-04-15|year=2005|doi=10.1093/molbev/msi145|pmid=15814826|volume=22|issue=7|pages=1561–8|vauthors=Ho SY, Phillips MJ, Cooper A, Drummond AJ |journal=Molecular Biology and Evolution|postscript=.|doi-access=free}}</ref>

===Parallel mutations and saturation===
Parallel mutation (sometimes referred to as Homoplasy) or [[convergent evolution]] occurs when separate lineages have the same mutation independently occur at the same site in the genome. 
[[Saturation (genetic)|Saturation]] occurs when a single site experiences multiple mutations. Parallel mutations and saturation result in the underestimation of the mutation rate because they are likely to be overlooked.<ref name="howell2003"/>

===Heteroplasmy===
Individuals affected by [[heteroplasmy]] have a mixture of mtDNA types, some with new mutations and some without. The new mutations may or may not be passed down to subsequent generations. Thus the presence of heteroplasmic individuals in a sample may complicate the calculation of mutation rates.<ref name="howell2003"/><ref name="sigrun2000">{{harvtxt|Sigurðardóttir|Helgason|Gulcher|Stefansson|2000}}</ref>

==Methods==

===Pedigree based===
Pedigree methods estimate the mutation rate by comparing the mtDNA sequences of a sample of parent/offspring pairs or analyzing mtDNA sequences of individuals from a deep-rooted genealogy. The number of new mutations in the sample is counted and divided by the total number of parent-to-child DNA transmission events to arrive at a mutation rate.<ref name="henn2009"/><ref name="sigrun2000"/>

===Phylogeny based===
Phylogeny based methods are estimated by first reconstructing the haplotype of the most recent common ancestor (MRCA) of a sample of two or more genetic lineages. A requirement is that the time to the most recent common ancestor ([[Most recent common ancestor#Time to MRCA estimates|TMRCA]]) of the sample of lineages must already be known from other independent sources, usually the archeological record. The average number of mutations that have accumulated since the [[Most recent common ancestor|MRCA]] is then computed and divided by the TMRCA to arrive at the mutation rate. The human mutation rate is usually estimated by comparing the sequences of modern humans and chimpanzees and then reconstructing the ancestral haplotype of the chimpanzee-human common ancestor. According to the paleontological record the last common ancestor of humans may have lived around 6 million years ago.<ref name="henn2009"/>

===Pedigree vs. phylogeny comparison===
Rates obtained by pedigree methods are about 10 times faster than those obtained by phylogenetic methods. Several factors acting together may be responsible for this difference. As pedigree methods record mutations in living subjects, the mutation rates from pedigree studies are closer to the germline mutation rate. Pedigree studies use genealogies that are only a few generations deep whereas phylogeny based methods use timescales that are thousands or millions of years deep. According to Henn et al. 2009, phylogeny based methods take into account events that occur over long time scales and are thus less affected by stochastic fluctuations. Howell et al. 2003 suggests that selection, saturation, parallel mutations and genetic drift are responsible for the differences observed between pedigree based methods and phylogeny based methods.

==Estimating based on AMH archaeology==
{|border="0" cellspacing="1" cellpadding="0" align="right" style="text-align:center; background:#cfcfcf; margin-leftt: 1em; margin-bottom: 1em; border:1px #3f3f3f solid;"
|+ style = "Color:#3f3f3f"| Methods/parameters for archaeologically estimated dates of mitochondrial Eve 
|-style="background:#e7e7e7"
| width = 130px | Study || width = 80px | Sequence<br>type || width = 120px | T<sub>Anchor</sub><br><small>(location)</small> || width = 150px | Referencing method<br><small>(correction method)</small>
|-style =  "background:#fcfcfc"
| style =  "background:#efefef" | {{Harvtxt  |Cann|Stoneking|Wilson|1987}} || Restriction fragments ||  40, 30, and 12 Ka<br><small>(Australia,<br> New Guinea<br> New World)</small>|| <small>archaeologically defined<br> migrations matched with<br> estimated sequence divergence rates</small>
|-style =  "background:#fcfcfc"
|  style =  "background:#efefef" |  {{Harvtxt |Endicott|Ho|2008}} || Genomic || 40 to 55 Ka<br><small>(Papua New Guinea)</small><br>14.5 to 21.5 Ka<br><small>(Haps H1 and H3)</small> || [[Papua New Guinea|PNG]] following<br> Haplogroup P  
|}
Anatomically modern humans (AMH) spread out of Africa and over a large area of Eurasia and left artifacts along the northern coast of the Southwest, South, Southeast and East Asia.  {{Harvtxt|Cann|Stoneking|Wilson|1987}} did not rely on a predicted T<sub>[[Chimpanzee–human last common ancestor|CHLCA]]</sub> to estimate [[single-nucleotide polymorphism]] (SNP) rates. Instead, they used evidence of colonization in Southeast Asia and Oceania to estimate mutation rates. In addition they used RFLP technology (''[[Restriction fragment length polymorphism]]'') to examine differences between DNA.  Using these techniques this group came up with a T<sub>MRCA</sub> of 140,000 to 290,000 years. Cann et al. (1987) estimated the TMRCA of humans to be approximately 210 ky and the most recent estimates Soares et al. 2009 (using 7 million year chimpanzee human mtDNA MRCA) differ by only 9%, which is relatively close considering the wide confidence range for both estimates and calls for more ancient T<sub>CHLCA</sub>.

{{Harvtxt |Endicott|Ho|2008}} have reevaluated the predicted migrations globally and compared those to the actual evidence. This group used the coding regions of sequences. They postulate that the molecular clock based on chimp-human comparisons is not reliable, particularly in predicting recent migrations, such as founding migrations into Europe, Australia, and the Americans. With this technique this group came up with a T<sub>MRCA</sub> of 82,000 to 134,000 years.

==Estimating based on CHLCA==
Because chimps and humans share a matrilineal ancestor, establishing the geological age of that last ancestor allows the estimation of the mutation rate. The [[chimp-human last common ancestor]] (CHLCA) is frequently applied as an anchor for mt-T<sub>MRCA</sub> studies with ranges between 4 and 13 million years cited in the literature.<ref name = "Soares09"/> This is one source of variation in the time estimates. The other weakness is the non-clocklike accumulation of SNPs, would tend to make more recent branches look older than they actually are.<ref name = "Endicott09">see:  {{Harvtxt |Endicott|Ho|Metspalu|Stringer|2009}}</ref>

{|border="0" cellspacing="1" cellpadding="0" align="right" style="text-align:center; background:#cfcfcf; margin-left: 2em; margin-bottom: 1em; border:1px #3f3f3f solid;" 
|+ SNP rates as described by Soares et al. (2009)
|-style =  "background:#e7e7e7"
| width = 75px| Regions(s) || width = 135px| Subregions<br>(or site within codon) || width = 105px | SNP rate<br>(per site * year) || 
|-style =  "background:#fcfcfc"
| style =  "background:#efefef" rowspan = 3 | Control<br>region ||style =  "background:#efefef" | [[hypervariable region|HVR]] I || 1.6 × 10<sup>−7</sup>||  
|- style =  "background:#fcfcfc"
|style =  "background:#efefef" | HVR II ||  2.3 × 10<sup>−7</sup>  || 
|- style =  "background:#fcfcfc"
| style =  "background:#efefef" | remaining  ||  1.5 × 10<sup>−8</sup> || 
|- style =  "background:#fcfcfc"
| style =  "background:#efefef" rowspan = 2 | Protein-<br>coding || style =  "background:#efefef" |([[Codon#Degeneracy of the genetic code|1st and 2nd]]) ||  8.8 × 10<sup>−9</sup> ||  
|- style =  "background:#fcfcfc" 
| style =  "background:#efefef" | ([[wobble base pair|3rd]]) || 1.9 × 10<sup>−8</sup> || 
|- style =  "background:#fcfcfc"
| style =  "background:#efefef" colspan = 2 | DNA encoding [[rRNA]] (rDNA) ||  8.2 × 10<sup>−9</sup> || 
|- style =  "background:#fcfcfc"
| style =  "background:#efefef" colspan = 2 | DNA encoding [[tRNA]] (tDNA) ||  6.9 × 10<sup>−9</sup> || 
|- style =  "background:#fcfcfc"
| style =  "background:#efefef" colspan = 2 | other ||  2.4 × 10<sup>−8</sup> ||
|- style =  "background:#fcfcfc"
|style =  "background:#dfdfdf" Colspan =  3 | T<sub>CHLCA</sub> assumed 6.5 Ma, relative rate to 1st & 2nd codons
|}
These two sources may balance each other or amplify each other depending on the direction of the T<sub>CHLCA</sub> error. There are two major reasons why this method is widely employed. First the pedigree based rates are inappropriate for estimates for very long periods of time. Second, while the archaeology anchored rates represent the intermediate range, archaeological evidence for human colonization often occurs well after colonization. For example, colonization of Eurasia from west to east is believed to have occurred along the Indian Ocean. However, the oldest archaeological sites that also demonstrate anatomically modern humans (AMH) are in China and Australia, greater than 42,000 years in age. However the oldest Indian site with AMH remains is from 34,000 years, and another site with AMH compatible archaeology is in excess of 76,000 years in age.<ref name = "Endicott09"/> Therefore, application of the anchor is a subjective interpretation of when humans were first present.

A simple measure the [[Genetic divergence|sequence divergence]] between humans and chimps can be bound by observing the SNPs. Given that the mitogenome is about 16553 base pairs in length (each base-pair which can be aligned with known references is called a site),<ref name = "Ingman00">{{Harvtxt |Ingman|Kaessmann|Pääbo|Gyllensten|2000}}</ref> the formula is:<br>
:::<math>rate = \frac{SNPs}{(2 T_{CHLCA}16553)}</math>
The '2' in the [[denominator]] is derived from the 2 lineages, human and chimpanzee, that split from the CHLCA. Ideally it represents the accumulation of mutations on both lineages but in different positions (SNPs). As long as the number of SNP observed approximates the number of mutations this formula works well. However, at rapidly evolving sites mutations are obscured by saturation affects. Sorting positions within the mitogenome by rate and compensating for saturation are alternative approaches.<ref>See: {{Harvtxt |Gonder|Mortensen|Reed|de Sousa|2007}},{{Harvtxt |Soares|Ermini|Thomson|Mormina|2009}}</ref>

Because the T<sub>CHLCA</sub> is subject to change with more paleontological information, the equation described above allows the comparison of TMRCA from different studies.

{|border="0" cellspacing="1" cellpadding="0" style="text-align:center; background:#cfcfcf; margin-right: 1em; margin-bottom: 1em; border:1px #3f3f3f solid;"
|+ style = "Color:#3f3f3f"| Methods/parameters for estimating date of mitochondrial Eve 
|-style="background:#e7e7e7"
| width = 130px | Study || width = 80px | Sequence<br>type || width = 100px | T<sub>CHLCA</sub><br><small>(sorting time)</small> || width = 150px | Referencing method<br><small>(correction method)</small>
|-style =  "background:#fcfcfc"
|  style =  "background:#efefef" |  {{Harvtxt |Vigilant|Stoneking|Harpending|Hawkes|1991}} || HVR || 4 to 6 Ma || CH transversions,<br><small>(15:1 transition:transversion)</small>  
|-style =  "background:#fcfcfc" 
|  style =  "background:#efefef" |  {{Harvtxt |Ingman|Kaessmann|Pääbo|Gyllensten|2000}} || genomic<br>(not HVR) ||5 Ma || CH genomic<br> comparison
|-style =  "background:#fcfcfc"
|  style =  "background:#efefef" |  {{Harvtxt |Endicott|Ho|2008}} || genomic<br>(not HVR) ||5 to 7.5 Ma || style="background:white" |CH <br> <small>(relaxed rate, rate-class defined)</small> 
|-style =  "background:#fcfcfc"
|  style =  "background:#efefef" |  {{Harvtxt |Gonder|Mortensen|Reed|de Sousa|2007}} || genomic<br>(not HVR) ||6.0 Ma<br><small>(+ 0.5 Ma)</small> || style="background:white" |CH <br> <small>(rate class defined)</small> 
|-style =  "background:#fcfcfc" 
|  style =  "background:#efefef" |  {{Harvtxt |Mishmar|Ruiz-Pesini|Golik|Macaulay|2003}} || genomic<br>(not HVR) ||6.5 Ma<br><small>(+ 0.5 Ma)</small> || style="background:white" |CH <br> <small>(rate class defined)</small> 
|-style =  "background:#fcfcfc"
|  style =  "background:#efefef" |  {{Harvtxt |Soares|Ermini|Thomson|Mormina|2009}} ||  genomic || 6.5Ma<br><small>(+ 0.5 Ma)</small> || CHLCA anchored, <small>(Examined selection by<br> Ka/(Ks + k))</small>  
|-
| style =  "background:#dfdfdf" colspan = 4 | <small>Chimpanzee to Human = CH, LCA = last common ancestor</small>  
|}

==Early, HVR, sequence-based methods==
To overcome the effects of [[saturation (genetic)|saturation]], HVR analysis relied on the [[transversion]]al distance between humans and chimpanzees.<ref name= "Vigilant87">{{Harvtxt |Vigilant|Pennington|Harpending |Kocher|1989}}</ref> A [[Transition (genetics)|transition]] to transversion ratio was applied to this distance to estimate sequence divergence in the HVR between chimpanzees and humans, and divided by an assumed T<sub>CHLCA</sub> of 4 to 6 million years.<ref name = "Vigilant91">{{Harvtxt |Vigilant|Stoneking|Harpending|Hawkes|1991}}</ref> Based on 26.4 substitutions between chimpanzee and human and 15:1 ratio, the estimated 396 transitions over 610 base-pairs demonstrated sequence divergence of 69.2% (rate * T<sub>CHLCA</sub> of 0.369), producing divergence rates of ''roughly 11.5% to 17.3% per million years''. [[File:SNP saturation.PNG|thumb|300px|right|HVR is exceptionally prone to saturation, leading to the underestimation of the SNP rate when comparing very distantly related lineages]]
{{Harvtxt |Vigilant|Stoneking|Harpending|Hawkes|1991}} also estimated the sequence divergence rate for the sites in the rapidly evolving HVR I and HVR II regions. As noted in the table above, the rate of evolution is so high that site saturation occurs in direct chimpanzee and human comparisons. Consequently, this study used transversions, which evolve at a slower rate than the more common transition polymorphisms. Comparing chimp and human mitogenomes, they noted 26.4 transversions within the HVR regions, however they made no correction for saturation. As more HVR sequence was obtained following this study, it was noted that the dinucleotide site CRS:16181-16182 experienced numerous transversions in parsimony analysis, many of these were considered to be sequencing errors. However the sequencing of [[Neanderthal genome project|Feldhofer I Neanderthal]] revealed that there was also a transversion between humans and Neanderthals at this site.<ref name = "Krings97">{{Harvtxt |Krings|Stone|Schmitz|Krainitzki|1997}}</ref> In addition, {{Harvtxt |Soares|Ermini|Thomson|Mormina|2009}} noted three sites in which recurrent transversions had occurred in human lineages, two of which are in HVR I, 16265 (12 occurrences) and 16318(8 occurrences).<ref group = "note">Soares et al excluded 16182 and 16183 from their analysis</ref> Therefore, 26.4 transversions was an underestimate of the likely number of transversion events. The year 1991 study also used a transition-to-transversion ratio from the study of old world monkeys of 15:1.{{Citation needed|date=October 2009}} However, examination of chimp and gorilla HVR reveals a rate that is lower, and the examination of humans places the rate at 34:1.<ref name = "Soares09">{{Harvtxt |Soares|Ermini|Thomson|Mormina|2009}}</ref> Therefore, this study underestimated that level of sequence divergence between chimpanzee and human. The estimated sequence divergence 0.738/site (includes transversions) is significantly lower than the ~2.5 per site suggested by Soares et al. (2009). These two errors would result in an overestimate of the human mitochondrial TMRCA. However, they failed to detect the basal L0 lineage in the analysis and also failed to detect recurrent transitions in many lineages, which also underestimate the TMRCA. Also, Vigilant et al. (1991) used a more recent CHLCA anchor of 4 to 6 million years.

==Coding region sequence based methods==
{{cladogram
  |title = African mtDNA haplogroups
  |clade = {{clade| thickness=2
    |label1=L0
    |1={{clade| thickness=2
      |1=L0d
      |2={{clade| thickness=2
        |1 = L0k
        |2 = {{clade| thickness=2
          |1 = L0f
          |2 = {{clade| thickness=2
            |1 = L0b
            |2 = L0a
          }} 
        }} 
      }} 
    }} 
    |2={{clade| thickness=2
      |1={{clade| thickness=2
        |label1 = L1
        |1 = {{clade| thickness=2
          |1 = L1b
          |2 = L1c
        }} 
        |2 = [[Haplogroup L5 (mtDNA)|L5]]
      }} 
      |2={{clade| thickness=2
        |1 = [[Haplogroup L2 (mtDNA)|L2]]
        |2 = {{clade| thickness=2
          |1 = [[Haplogroup L6 (mtDNA)|L6]]
          |2 = {{clade| thickness=2
            |1 = [[Haplogroup L3 (mtDNA)|L3]]
            |2 = [[Haplogroup L4 (mtDNA)|L4]]
          }} 
        }} 
      }} 
    }} 
   }}
}}

Partial coding region sequence originally supplemented HVR studies because complete coding region sequence was uncommon. There were suspicions that the HVR studies had missed major branches based on some earlier RFLP and coding region studies. {{Harvtxt |Ingman|Kaessmann|Pääbo|Gyllensten|2000}} was the first study to compare genomic sequences for coalescence analysis. Coding region sequence discriminated [[Haplogroup M (mtDNA)|M]] and [[Haplogroup N (mtDNA)|N]] haplogroups and [[Haplogroup L0|L0]] and [[Haplogroup L1|L1]] macrohaplogroups. Because the genomic DNA sequencing resolved the two deepest branches it improved some aspects estimating TMRCA over HVR  sequence alone. Excluding the [[D-loop]] and using a 5-million-year T<sub>CHLCA</sub>, {{Harvtxt |Ingman|Kaessmann|Pääbo|Gyllensten|2000}} estimated the mutation rate ''to be 1.70 × 10<sup>−8</sup> per site per year'' (rate * T<sub>CHLCA</sub> = 0.085, 15,435 sites).

However, coding region DNA has come under question because coding sequences are either under purifying selection to maintain structure and function, or under regional selection to evolve new capacities.<ref>see: {{Harvtxt|Suissa|Wang|Poole|Wittkopp|2009}}, {{Harvtxt|Balloux|Handley| Jombart|Liu|2009}}</ref>  The problem with mutations in the coding region has been described as such: mutations occurring in the coding region that are not [[Mutation#By effect on fitness|lethal]] to the mitochondria can persist but are negatively [[natural selection|selective]] to the host; over a few generations these will persist, but over thousands of generations these slowly are pruned from the population, leaving SNPs.<ref name="Soares09"/> However, over thousands of generations regionally selective mutations may not be discriminated from these transient coding region mutations. The problem with rare mutations in the human mitogenomes is significant enough to prompt a half-dozen recent studies on the matter.

{{Harvtxt |Ingman|Kaessmann|Pääbo|Gyllensten|2000}} estimated the ''non-D loop region'' evolution 1.7 × 10<sup>−8</sup> per year per site based on 53 non-identical genomic sequence overrepresenting Africa in a global sample. Despite this over-representation, the resolution of the L0 subbranches was lacking and one other deep L1 branches has been found. Despite these limitations that sampling was adequate for the hallmark study. Today, L0 is restricted to African populations, whereas L1 is the ancestral haplogroup of all non-Africans, as well as most Africans. Mitochondrial Eve's sequence can be approximated by comparing a sequence from L0 with a sequence from L1. By reconciling the mutations in L0 and L1. The mtDNA sequences of contemporary human populations will generally differ from Mitochondrial Eve's sequence by about 50 mutations.<ref name=Gonder07>{{Harvtxt |Gonder|Mortensen|Reed|de Sousa|2007}}</ref><ref name="Behar08">{{Cite journal |title=The dawn of human matrilineal diversity | journal = American Journal of Human Genetics | volume = 82 | issue = 5 | pages = 1130–40 |date=May 2008  |author1=Behar DM |author2=Villems R |author3=Soodyall H |author4=Blue-Smith J |author5=Pereira L |author6=Metspalu E |author7=Scozzari R |author8=Makkan H |author9=Tzur S |last10=Comas D |author11=Bertranpetit J |author12=Quintana-Murci L |author13=Tyler-Smith C |author14=Wells RS |author15=Rosset S |author16=Genographic Consortium  |pmid = 18439549 | pmc = 2427203 | doi = 10.1016/j.ajhg.2008.04.002 |first10=D}}</ref> Mutation rates were not classified according to site (other than excluding the HVR regions). The T<sub>CHLCA</sub> used in the year 2000 study of 5 Ma was also lower than values used in the most recent studies.

==Estimates from ancient DNA==
Since it has become possible to sequence large numbers of ancient mitogenomes, several studies have estimated the mitochondrial mutation rate by measuring how many more mutations on average have accumulated in modern (or later) genomes compared to ancient (or earlier) ones descending from the same phylogenetic node. These studies have obtained similar results: central estimates for the whole chromosome, in substitutions per site per year: 2.47 × 10<sup>−8</sup>;<ref>{{Citation |vauthors=Fu Q, Mittnick A et al. |title= A revised timescale for human evolution based on ancient mitochondrial genomes |journal=Curr. Biol. |volume=23 |issue=7 |pages=553–559 |date=April 2013 |doi= 10.1016/j.cub.2013.02.044 |url= |postscript=. |pmid=23523248 |pmc=5036973|bibcode= 2013CBio...23..553F |hdl= 11858/00-001M-0000-000E-F4B9-2 }}</ref> 2.14 × 10<sup>−8</sup>;<ref>{{Citation |vauthors=Rieux A, Eriksson A et al. |title=Improved calibration of the human mitochondrial clock using ancient genomes |journal=Mol. Biol. Evol. |volume=31 |issue=10 |pages=2780–2792 |date=August 2014 |doi=  10.1093/molbev/msu222 |url= |postscript=. |pmid=25100861 |pmc=4166928}}</ref> 2.53 × 10<sup>−8</sup>;<ref>{{Citation |vauthors=Fu Q, Li H et al. |title=Genome sequence of a 45,000-year-old modern human from western Siberia |journal=Nature |volume=514 |issue=7523 |pages=445–449 |date=October 2014 |doi=10.1038/nature13810 |postscript=. |pmid=25341783 |pmc=4753769|bibcode=2014Natur.514..445F |hdl=10550/42071 }}</ref> and 2.74 × 10<sup>−8</sup>.<ref>{{Citation |vauthors=Posth C, Renaud G et al. |title=Pleistocene mitochondrial genomes suggest a single major dispersal of non-Africans and a Late Glacial population turnover in Europe |journal=Curr. Biol. |volume=26 |issue=6 |pages=827–833 |date=March 2016 |doi=10.1016/j.cub.2016.01.037 |url=http://www.cell.com/current-biology/abstract/S0960-9822(16)00087-7 |postscript=. |pmid=26853362|bibcode=2016CBio...26..827P |hdl=2440/114930 |s2cid=140098861 |hdl-access=free }}</ref>

==Inter-comparing rates and studies==
Molecular clocking of mitochondrial DNA has been criticized because of its inconsistent molecular clock.<ref>{{Citation |vauthors=Ho SY, Larson G |title=Molecular clocks: when times are a-changin' |journal=Trends Genet. |volume=22 |issue=2 |pages=79–83 |date=February 2006 |pmid=16356585 |doi=10.1016/j.tig.2005.11.006 |postscript=.}}</ref><ref name = "pmid9441404">{{Citation |author=Gibbons A |title=Calibrating the mitochondrial clock |journal=Science |volume=279 |issue=5347 |pages=28–9 |date=January 1998 |pmid=9441404 |doi=10.1126/science.279.5347.28 |bibcode=1998Sci...279...28G |s2cid=29855766 |postscript=.}}</ref><ref name = "pmid18618067">{{Citation|journal =J Mol Evol|year = 2008 |volume =67|issue =2|pages =191–200|title = Frequency and pattern of heteroplasmy in the control region of human mitochondrial DNA|vauthors=Santos C, Sierra B, Alvarez L, Ramos A, Fernández E, Nogués R, Aluja MP |doi =10.1007/s00239-008-9138-9|pmid =18618067|bibcode = 2008JMolE..67..191S |s2cid = 1143395 |postscript =.}}</ref> A retrospective analysis of any pioneering process will reveal inadequacies. With mitochondrial the inadequacies are the [[argument from ignorance]] of rate variation and overconfidence concerning the T<sub>CHLCA</sub> of 5 Ma. Lack of historical perspective might explain the second issue, the problem of rate variation is something that could only be resolved by the massive study of mitochondria that followed. The number of HVR sequences that have accumulated from 1987 to 2000 increased by magnitudes. {{Harvtxt |Soares|Ermini|Thomson|Mormina|2009}} used 2196 mitogenomic sequences and uncovered 10,683 substitution events within these sequences. Eleven of 16560 sites in the mitogenome produced greater than 11% of all the substitutions with statistically significant rate variation within the 11 sites.<ref group = "note">(CRS sites 16519, 152, 16311, 145, 195, 16189, 16129, 16083, 16362, 160, 709, 16129, 16083, 16362, 150, and 709)</ref> They argue that there is a neutral-site mutation rate which is a magnitude slower than rate observed for the fastest site, CRS 16519. Consequently, purifying selection aside, the rate of mutation itself varies between sites, with a few sites much more likely to undergo new mutations relative to others.<ref name="pmid10563016">{{Citation |vauthors=Excoffier L, Yang Z |title=Substitution rate variation among sites in mitochondrial hypervariable region I of humans and chimpanzees |journal=Mol. Biol. Evol.|volume= 16| issue= 10|pages=1357–68 |date=October 1999 |pmid=10563016 |doi= 10.1093/oxfordjournals.molbev.a026046|postscript=.|doi-access=free}}</ref> Soares et al. (2009) noted two spans of DNA, CRS 2651-2700 and 3028-3082, that had no SNPs within the 2196 mitogenomic sequences.

{{clear}}

{{MtDNA}}

==Notes==
{{Reflist|group="note"}}

== Footnotes ==
{{reflist|3}}

==References==
{{refbegin}}
<!------{{Citation |year= |title= |journal= |volume= |issue= |pages= |url= |doi= }} Please copy this first and the past names, ----> 
*{{Citation |last1= Atkinson|first1=QD |last2= Gray|first2=RD |last3=Drummond |first3=AJ| title = Bayesian coalescent inference of major human mitochondrial DNA haplogroup expansions in Africa | journal = Proceedings of the Royal Society B: Biological Sciences | volume = 276 | issue = 1655 | pages = 367–73 |date= 2009 | pmid = 18826938 | doi = 10.1098/rspb.2008.0785|pmc= 2674340}}
*{{Citation| last1= Balloux | first1= F | last2= Handley | first2= LJ | last3= Jombart | first3= T | last4= Liu | first4=H | last5= Manica | first5= A|title = Climate shaped the worldwide distribution of human mitochondrial DNA sequence variation|journal =   Proceedings of the Royal Society B: Biological Sciences|year = 2009 |volume =276 |issue = 1672|pages =3447–55 |pmid = 19586946|doi = 10.1098/rspb.2009.0752 | pmc=2817182}}
*{{Cite journal |title=The dawn of human matrilineal diversity | journal = American Journal of Human Genetics | volume = 82 | issue = 5 | pages = 1130–40 |date= 2008  |author1=Behar DM |author2=Villems R |author3=Soodyall H |author4=Blue-Smith J |author5=Pereira L |author6=Metspalu E |author7=Scozzari R |author8=Makkan H |author9=Tzur S |last10=Comas D |author11=Bertranpetit J |author12=Quintana-Murci L |author13=Tyler-Smith C |author14=Wells RS |author15=Rosset S |author16=Genographic Consortium  |pmid = 18439549 | pmc = 2427203 | doi = 10.1016/j.ajhg.2008.04.002 |first10=D}}
*{{Citation|last1= Cann|first1= RL|last2= Stoneking|first2= M|last3=Wilson |first3=AC|title=Mitochondrial DNA and human evolution |journal=Nature |volume=325 |issue=6099 |pages=31–6 |year=1987 |pmid=3025745 |doi=10.1038/325031a0 |bibcode= 1987Natur.325...31C|s2cid= 4285418}}
*{{Citation |last1=Cox | first1 = MP |title=Accuracy of molecular dating with the rho statistic: deviations from coalescent expectations under a range of demographic models |journal=Human Biology |volume=80 |issue=4 |pages=335–57 |date= 2008 |pmid=19317593 |doi=10.3378/1534-6617-80.4.335 | s2cid = 207701422 }}
*{{Citation|last1 =Endicott | first1 = P | last2 = Ho | first2 = SY |title=A Bayesian evaluation of human mitochondrial substitution rates |journal=American Journal of Human Genetics |volume=82 |issue=4 |pages=895–902 |date=2008 |pmid=18371929 |pmc=2427281 |doi=10.1016/j.ajhg.2008.01.019 }}
*{{citation|last1=Endicott | first1=P |last2=Ho | first2=SY | last3=Metspalu | first3=M | last4=Stringer | first4=C |title=Evaluating the mitochondrial timescale of human evolution |journal=Trends in Ecology and Evolution |volume=24 |issue=9 |pages=515–21 |date=2009 |pmid=19682765 |doi=10.1016/j.tree.2009.04.006 | bibcode=2009TEcoE..24..515E }}
*{{Citation |last1=Gonder |first1=MK |last2=Mortensen |first2=HM |last3=Reed |first3=FA |last4=de Sousa |first4=A |last5=Tishkoff |first5=SA |title=Whole-mtDNA genome sequence analysis of ancient African lineages |journal=Molecular Biology and Evolution |volume= 24| issue=3 |pages=757–68 |date=2007 |pmid=17194802 |doi=10.1093/molbev/msl209|doi-access=free }}
*{{Citation|url=http://mbe.oxfordjournals.org/cgi/content/full/26/3/713-a|title=Characterizing the time dependency of human mitochondrial DNA mutation rate estimates|year=2009|last1=Henn|last2=Gignoux|last3=Feldman|last4=Mountain|doi=10.1093/molbev/msn244|first1=B. M.|first2=C. R.|first3=M. W.|first4=J. L.|journal=Molecular Biology and Evolution|volume=26|pages=217–230|pmid=18984905|issue=1|access-date=2010-01-03|archive-url=https://web.archive.org/web/20090221030800/http://mbe.oxfordjournals.org/cgi/content/full/26/3/713-a|archive-date=2009-02-21|url-status=dead|doi-access=free}}
*{{Cite book | editor = Ho, S.Y.W. | year = 2020 | title = The Molecular Evolutionary Clock | publisher = Cham: Springer | doi=10.1007/978-3-030-60181-2 | isbn = 978-3-030-60180-5 | s2cid = 231672167 }}
*{{Citation |last1=Ingman |first1=M |last2= Kaessmann|first2= H|last3= Pääbo|first3=S |last4=Gyllensten |first4= U|title=Mitochondrial genome variation and the origin of modern humans |journal=Nature |volume=408 |issue=6813 |pages=708–13 |date=2000 |pmid=11130070 |doi=10.1038/35047064 |bibcode=2000Natur.408..708I |s2cid=52850476 }}
*{{Citation | last1=Krings | first1=M. | last2=Stone | first2=A. | last3=Schmitz | first3=R.W. | last4=Krainitzki | first4=H. | last5=Stoneking | first5=M. | last6=Pääbo | first6=S. | date=1997 | title=Neandertal DNA sequences and the origin of modern humans | journal=Cell | volume=90 | issue=1 | pages=19–30 | doi=10.1016/s0092-8674(00)80310-4 | pmid=9230299 | doi-access=free| hdl=11858/00-001M-0000-0025-0960-8 | hdl-access=free }}
*{{Citation|last1=Loogvali|last2=Kivisild|last3=Margus|last4=Villems|year=2009|title=Explaining the imperfection of the molecular clock of hominid mitochondria|doi=10.1371/journal.pone.0008260|pmid=20041137|pmc=2794369|editor1-last=O'Rourke|editor1-first=Dennis|first1=Eva-Liis|first2=Toomas|first3=Tõnu|first4=Richard|journal=PLOS ONE|volume=4|issue=12|pages=e8260|bibcode=2009PLoSO...4.8260L|doi-access=free}}
*{{Citation |last1 =Maca-Meyer |first1 =  N |last2 = González |first2 =  AM |last3 = Larruga |first3 = JM |last4 = Flores |first4 = C |last5 =  Cabrera |first5 = VM |title=Major genomic mitochondrial lineages delineate early human expansions |journal=BMC Genet. |volume=2|pages=13 |year=2001 |pmid=11553319 |pmc=55343 |doi=10.1186/1471-2156-2-13 |doi-access = free }}
*{{Citation  | last1=Mishmar | first1=D. | last2=Ruiz-Pesini | first2=E. | last3=Golik | first3=P. | last4=Macaulay | first4=V. | last5=Clark | first5=A.G. | last6=Hosseini | first6=S. | last7=Brandon | first7=M. | last8=Easley | first8=K. | last9=Chen | first9=E. | last10=Brown | first10=M.D. | last11=Sukernik | first11=R.I. | last12=Olckers | first12=A. | last13=Wallace | first13=D.C. | date=2003 | title=Natural selection shaped regional mtDNA variation in humans | journal=Proceedings of the National Academy of Sciences of the United States of America | volume=100 | issue=1 | pages=171–176 | doi=10.1073/pnas.0136972100 | pmid=12509511 | pmc=140917 | bibcode=2003PNAS..100..171M | doi-access=free }}
*{{Citation |last1=Nielsen |first1 =R |last2= Beaumont |first2= MA |title=Statistical inferences in phylogeography |journal=Molecular Ecology |volume=18 |issue=6 |pages=1034–47 |date= 2009 |pmid=19207258 |doi=10.1111/j.1365-294X.2008.04059.x |s2cid =13613087 |doi-access=free |bibcode =2009MolEc..18.1034N }}
*{{Citation |author=Oppenheimer, Stephen |title=The Real Eve: Modern Man's Journey Out of Africa |publisher=Carroll & Graf |location=New York, NY |year=2004 |isbn=978-0-7867-1334-9 }}
*{{Citation |title=A high observed substitution rate in the human mitochondrial DNA control region |journal=Nat. Genet. |volume=15 |issue=4 |pages=363–8 |date= 1997 |pmid=9090380 |doi=10.1038/ng0497-363 |last1=Parsons |first1=TJ |last2=Muniec |first2=DS |last3=Sullivan |first3=K  |last4=Woodyatt |first4=N |last5=Alliston-Greiner |first5=R |last6=Wilson |first6=MR |last7=Berry |first7=DL |last8=Holland |first8=KA |last9=Weedn |first9=VW  |last10=Holland |first10=MM |s2cid=32812244 }}
*{{Citation|last1=Sigurðardóttir|last2=Helgason|last3=Gulcher|last4=Stefansson|last5=Donnelly|title=The Mutation Rate in the Human mtDNA Control Region|year=2000|pmc=1378010|pmid=10756141|first1=S|first2=A|first3=JR|first4=K|first5=P|volume=66|issue=5|pages=1599–609|journal=American Journal of Human Genetics|doi=10.1086/302902}}
*{{Citation |last1=Soares |first1=P |last2=Ermini |first2=L |last3=Thomson |first3=N |last4=Mormina  |first4=M |last5=Rito |first5=T |last6=Röhl |first6=A |last7=Salas |first7= A |last8=Oppenheimer |first8=S |last9=Macaulay |first9=V |last10=Richards |first10=MB  |title=Correcting for purifying selection: an improved human mitochondrial molecular clock |journal=[[American Journal of Human Genetics]] |volume=84 |issue=6 |pages=740–59 |date=2009 |pmid=19500773 |doi=10.1016/j.ajhg.2009.05.001 |pmc=2694979}}
*{{citation |last1=Suissa |first1=S |last2=Wang |first2=Z |last3=Poole |first3=J |last4=Wittkopp |first4=S |last5=Feder |first5=J |last6=Shutt |first6=TE |last7=Wallace |first7=DC |last8=Shadel |first8=GS |last9=Mishmar |first9=D  |title=Ancient mtDNA genetic variants modulate mtDNA transcription and replication |journal=PLOS Genetics |year=2009 |volume=5 |issue=5 |pmid=19424428 |doi=10.1371/journal.pgen.1000474 |pages=e1000474 |pmc=2673036 |editor1-last=Desalle |editor1-first=R |doi-access=free }}
*{{Citation |last1=Takahata |first1=  N |title=Allelic genealogy and human evolution |journal=Molecular Biology and Evolution |volume=10 |issue=1 |pages=2–22 |date=1993 |pmid=8450756 |doi= 10.1093/oxfordjournals.molbev.a039995|url=http://mbe.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=8450756 |archive-url=https://archive.today/20121205105223/http://mbe.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=8450756 |url-status=dead |archive-date=2012-12-05 |doi-access=free }}
*{{Citation | last1 =Vigilant| first1=L| last2 =Pennington| first2 =R| last3 =Harpending| first3 =H | last4 =Kocher| first4 =TD| last5 =Wilson| first5 =AC| title =Mitochondrial DNA sequences in single hairs from a southern African population |journal=Proceedings of the National Academy of Sciences of the USA |volume=86 |issue=23 |pages=9350–4 |date=1989 |pmid=2594772 |pmc=298493 | doi=10.1073/pnas.86.23.9350| bibcode=1989PNAS...86.9350V| doi-access=free}}
*{{Citation |last1=Vigilant|first1 =L| last2 =Stoneking |first2 =M |last3= Harpending |first3= H |last4=Hawkes |first4 =K|last5 =Wilson|first5 =AC|title=African populations and the evolution of human mitochondrial DNA |journal=Science |volume=253 |issue=5027 |pages=1503–7 |date=1991 |pmid=1840702 |doi=10.1126/science.1840702|bibcode =1991Sci...253.1503V|s2cid =23260602}}
*{{citation |vauthors=Watson E, Forster P, Richards M, Bandelt HJ |title=Mitochondrial footprints of human expansions in Africa |journal=American Journal of Human Genetics |volume=61 |issue=3 |pages=691–704 |date= 1997 |pmid=9326335 |pmc=1715955 |doi=10.1086/515503 }}
{{refend}}

[[Category:Biology timelines]]
[[Category:DNA]]
[[Category:Evolutionary biology]]
[[Category:Genetic genealogy]]
[[Category:Human evolution]]
[[Category:Human mitochondrial genetics]]
[[Category:Human mtDNA haplogroups|*]]
[[Category:Phylogenetics]]
[[Category:Prehistoric Africa]]