Talk:Mitochondrial Eve

misconceptions section causes misconceptions

The misconceptions section implies that both mitochondrial eve and the MRCA are the same number of generations removed from every human. It's not just "do any of my 8 great grandparents overlap with any of your 8 great grandparents?" You need to compare all ancestors to find an MRCA. Things like, "do any of my 8 great grandparents overlap with any of your 32 great great great grandparents?" Similarly for ME, but you only need to compare the maternal line.

Sstrazdu (talk) 17:57, 8 April 2009 (UTC)

Parenthetical statement under misconceptions

I'm putting this here because I'm unsure of the meaning behind the above comment, but perhaps it pertains to this statement, in parentheses: "(albeit between any two individuals it may not be the same ancestor)." I do not think that is true. MRCA means the most recent discrete individual where, mathematically, it becomes certain that this individual is in every family tree at some point in time. I've heard different estimates--2,000 years, 5,000 years. But that's not important. The important thing is, it would, in fact, be the same individual--i.e., we could say with nth percent certainty that one individual was alive by this time who will show up in every family tree. I would move to omit the parenthetical qualifier, then, unless I misunderstand it, but I'm not an editor on this page, so I'll leave it alone, and instead raise the concern.65.117.234.99 (talk) 15:08, 22 September 2009 (UTC)

Technical detail

The level of technical detail in the current version appears to much too much for the general audience per Wikipedia:Make technical articles accessible. Pdeitiker, I believe has doubts about Mitochondrial Eve, but I don't see significant doubt among recent mainstream publications. Should this article therefore have significant portions devoted to doubts about the existence of an mtDNA MRCA. My impression was that many of these doubts were dealt with in the 1990s. Wapondaponda (talk) 06:44, 13 September 2009 (UTC)

Pdeitiker's general writing style far too obtuse and obscure. Article needs a serious cleanup. --Michael C. Price ^talk 18:29, 13 September 2009 (UTC)

I agree. I think it is great that this article is being enhanced. And I've watched changes over these past few weeks. But I think it is becoming a dissertation that is mostly inaccessible and unappealing to the general pubilc. Fred Hsu (talk) 21:25, 13 September 2009 (UTC). Look at the current version of the article.

Why are following sections even in this article at all? I am not saying they don't describe useful information. I am saying I can't see why this type of detail should be in this article.

Common approaches to interpreting Coalescence

Dependency of rate determinations of interspecific LCA anchoring

What is the second paragraph of the Establishing mutation rates trying to convey? It is completely unclear to me. Perhaps I am slow. Can someone explain to me what this paragraph is saying please? I see some facts, but what are the implications of these?

Does Both methods have major pitfalls mean mtDNA mutation analysis is useless?

Is On the other hand a code word for the second method? Or am I not searching hard enough for the description of second method's major pitfalls?

Certain sites on MtDNA... are not used ... by many researchers, and this implies what?

There are three approaches that have been used with mtDNA to calculated the TMRCA. What does this have to do with this paragraph?

Many questions here, I will address them one by one. First I am glad too see that there is interest in fixing this article, yes it is too technical, but I was going over some of the old literature there are a number of outstanding issues and I think I want to get this right.

1. . It is unfortunate that I undertook upgrading this article at the current time. White has weighed in offering that the chimp human LCA is probably greater than 7 mya, between 7 and 10 mya. There has been no contest of his logic, or the feasibility of pushing the orangutan/human LCA by at least 2 million years. The orangutan/Human LCA was one of the primary reasons the C/H LCA of 6 mya was favored (Gonder et al), as it was set at 14 million years for genomic DNA this result in a C/H LCA of about 6 million years. White claims it may be much older. 6 million years in an of itself is the outside range for Cann et al. and Vigilante et al. So that the movement of the C/H LCA from ~5 to >7 Ma is a significant movement. I probably should have left the large errors on this page alone until the dust is settled on two major outstanding issues.
2. . Presgrave and Ye have weighed into the arguement of Nuclear DNA evolution, they claim that nuclear DNA is evolving faster in Chimpanzee because of the rate of cell division in the chimpanzee testes places the evolution about 33% faster for Autosomes and ~90% faster for Y chromosome. I have gone over all the literature to examine to see if this finding can be supported, it can, which places the molecular clocking in Y chromosomal (times) used throughtout Wikipedia in trouble if the rate of Y is based on a Chimpanzee human anchor, this has to be compounded by the fact the LCA may be million(s) of years older than the LCA used to determine the mutation rate.
3. . If this finding proves to be true then the TMRCAs for X-linked will be slightly older than presented. The population size stipulated by Takahate and Shaffner will be slightly larger. Since mtDNA lineages spend all their time in females, they are uneffected by sperm cell divisions and as a consequence the mtDNA DNA TMRCA does not move. This places the mtDNA at the margin of significant different with regard to X-linked predicted effective female population size. This can be repaired if female:male ratio is dropped from 2:1 to 1.5:1 however this places Y chromosomal TMRCA at about 3 to 4 SD range unless it is reclocked.
4. . Certain sites are masked. Sites like 16129, 16183. This issue was brought up a decade ago when someone used these sites to suggest all humans evolved 6000 years ago, even though at the time many researchers were already masking these sites. Both Ingman and Gonder masked all the HVR sites, because of their tendency toward reticulations (star diagrams in which the peripheral branches merge back into each other). In addition some sites should be masked, these sites have shown no mutation in any sequenced genome within mammalian history (which branch lengths, cumulatively, is more than 1 billion years) IOW the rate at these sites is effectively zero, so that mutations that occur at these sites generally are retained for selective reasons or strong genetic drift as a result of isolation events.
5. . Usefulness is not a concern. If usefulness is the major issue then Y chromosomal clocking does not exist. The idea that is being bounced back and forth is how biasing various forces are in the determination of branch times. Let me refocuse the issue. The age of mitochondrial eve has no value in and of itself, it is stated correctly that mtDNA eve lived in a popultion with 1000s of other individuals. In addition it is not at the point that eve lived that is of interest, the point of interest is when the population went from one state (static) to a second state (expanding). If this is not stated clearly in the article the article has virtually no value. This occurred sometime after mtDNA even and is an issue of great debate. As the article states, Ingman looked at selection in 2000 and concluded that selection was not a predominant feature. Gonder looks at selection with a large sample size and sees evidence of selection everywhere. There are studies that argue that there has been no expansion within Africa (despite the fact Africa size is 6 magnitudes greater) and 4 papers of recent have been published that attempt to explain and deal with the issue of selection, the latest of which basically masks sites that exhibit in humans changes that have been extremely rare over evolutionary history. IOW, it through recognizing the errors in various methods, methods can be corrected, HVR alone gave a TMRCA of 161,000 (5my CH/LCA) (210 ka at 6.5 ma CH LCA) and compared to Gonders 194 ka only slightly older, again that variance is small compared to uncertainty about the C/H LCA, which has moved from 4 to 6 Ma to 6 to 10 Ma, and random factors that affect coalescence (namely the 50 or so most basal mutations in the mtDNA tree). However Ingman masked all HVR sites, some HVR sites do not show patterns of reticulation, Both Gonder and Ingman included sites that could not be effectively clocked because they have mutated 0,1, or 2 times in all of animal evolution. IOW there may be a compromize strategy for dealing with the problem areas of the two techniques. . . . . . Let me reiterate the point the TMRCA is not that important, what does it really matter if the population size was 4400 individuals or 2500 individuals for a period of 50,000 years, 150,000 years ago? The important point is when population size shifted, and within the selection data for various regions of Africa is buried what happened and when. The basic problem is if you can't clock the sites that define selection, and there is a reoccurrance of such similar sites, then how does one determine accurately branch times. That we see a difference between Ingman and Gonder indicates that our measures of selection and thus population growth are very sensitive to sampling parameters.
6. . The mtDNA evidence and these refined approaches are placing pressure on physical anthropologist to define events in Africa that explain the molecular phyletics, as we can see in the recent issue of PNAS on 'Out of Africa' however given the problem above in determing when people were limited to certain areas, it promises a period of contentious debate about the peopling of africa and the classification of fossil remains.PB666 ^yap 06:31, 18 October 2009 (UTC)
7. . I came across this article about 2 months ago while trying to find a references and it was top-loaded with inaccurate information, which for some reason at that time did not seem to bother anyone, but now that the article has a rather full coverage of the literature and the various points of view (balanced) a. The TMRCA stated by gonder was incorrectly placed here, someone wrote there was no bottleneck which is not clear at yet if there was or was not a constriction, someone offered up that the TMRCA was 6000 years ago, misrepresenting the article basically arguing that some sites are unclockable (and should be masked), and all kinds of wives tales, it is no wonder the article was removed from the GA list. I did ask that the article be fixed, and yet no-one wanted to fix it. So now are we going to be serious about fixing the article?PB666 ^yap 06:31, 18 October 2009 (UTC)
8. . I will go over the article tommorrow and try to condense and reword.

Couple of notes: The whole human genetic history project is a shamble, I have redone the Banner box for HGH which now includes a place where comments are to be made, if you are interested in making this page a GA or FA for wikipedia, please join the HGH and enter comments about what needs to be done to the article to bring it back to GA status. In addition I have created the Portal:Molecular Anthropology, the feature article is this page, we need to sit down and discus which articles we need to push to GA status so that the HGH project will at least have some representation in the Featured article list. A number of members of the HGH project are inactive and have been so for more than 1 year, and we have some new members who contribute to articles, but what we really need right now is contributers that can improve articles making allowing them to progress up the wiki totem-pole. Mitochondrial Eve is a core HGH article, it is our (plural) responsibility to get it back in shape.Talk:Mitochondrial_Eve/Comments

Removing the following

Homo sapiens is assumed to have speciated from Homo heidelbergensis in the period of 200–160 kya. The fact that Mitochondrial Eve happens to be dated to precisely this period has been taken as evidence of a population bottleneck (e.g. Toba catastrophe theory) giving rise to the human species. There are, however, many ways such family trees can be constructed. A tree can be constructed based on any gene, not just the mitochondrial DNA. When different such trees including the mtDNA tree are compared, no population bottleneck is found because different trees show different coalescent points. The inconsistencies between coalescent points indicate that there had been numerous gene interchanges between population groups around the world, even after the first exodus out of Africa. This idea forms the basis of Alan Templeton's 'Out of Africa Again and Again' theory.

The Mitochondrial DNA provides another support for the Out of Africa hypothesis in the form of gene diversity. One finding not subject to interpretation is that the greatest diversity of mitochondrial DNA sequences exists among Africans. This diversity is believed to have accumulated because humans have been living longer in Africa than anywhere. Family trees (or "phylogenies") constructed on the basis of mitochondrial DNA comparisons show that the living humans whose mitochondrial lineages branched earliest from the tree (L0) are prevalent among the San and the Mbuti people. The subsequent branches of L1, L2 and L3 are also largely confined to Africa, while only the macrogroups M and N, descended from L3, participated in the ancient migration(s) out of Africa.

I am removing because most is redundant in the article as currently rewritten. What is not redundant is obsolete. The TMRCAs that are published with X-linked and Autosomal are consistent with a population size of 11,000 individual over the last 700,000 years, however they are tolerant of oscillations. In addition Templeton argued from the perspective of MREH, which is all but a dead hypothesis. His theory is detailed and critiqued by Takahata in 1999, at which time Takahata concluded that less than 12% of human DNA could have been from early are repeated migrations from Africa. More recently the Neandertal genome sequencing project revealed that very little if any DNA was exchanged between neandertals and humans, two of the more closely related late hominid species.PB666 ^yap 21:58, 5 November 2009 (UTC)

Off-track

I haven't paid attention to what's been going on in this article, but it appears to have undergone a total transformation. The previous version was not necessarily great, but the current version also has numerous issues. Firstly it is laden with technical detail that I believe make the article inaccessible to the average reader. Secondly, a lot of the information contained in the article is not specifically about Mitochondrial Eve, but instead is related to the genomics of Mitochondrial DNA and is better placed in articles such as Mitochondrial DNA and Human mitochondrial DNA haplogroups rather than in the article about Mitochondrial Eve. Wapondaponda (talk) 04:35, 27 November 2009 (UTC)

Yes, this is a concern of a lot of editors. --Michael C. Price ^talk 05:12, 27 November 2009 (UTC)

Several areas are going to be moved off page. Starting tonight I am moving the CHLCA section to its page.PB666 ^yap 05:40, 1 December 2009 (UTC)

That is probably a good idea, though I have only heard of the term CHLCA on wikipedia. Maybe something like "the evolution of human mitochondrial DNA" would be a more appropriate article for much of the content in this article. Wapondaponda (talk) 19:21, 2 December 2009 (UTC)

Reverted to August version. I think Pdeitiker should seek consensus for his edits. They are either not directly related to mtEve or just plain original research. Wapondaponda (talk) 20:31, 5 December 2009 (UTC)

You reverted to a version with many false and inaccurate statements. If you want to propose a change of this nature WM you should at least make an effort to remove the dozen or so false or highly inaccurate statements. According to the GA review, this article was demoted because it contained too much population science and not enough facts. I completely agree with the reviewer, how do you feel about the review MW?PB666 ^yap 20:52, 5 December 2009 (UTC)

Muntawandi, for your point of view the article is off track now, but somehow it was not off-track when it was demoted. Here are some possible reasonse it was demoted. Not only did it loose FA status, but it also lost GA status in one fell swoop.

• "Mitochondrial Eve is believed to have lived about 170,000 years ago, or roughly 8,000 generations ago.

Misleading, age estimates of papers within the last 3 years range from 108,000 years ago to 198,000 years ago. for Gonder et al that would be 194,000 years + 2S.D. or 258,000 years.

• "This places her shortly after the speciation of Homo sapiens sapiens and the emergence of the first anatomically modern humans.

Speculation. It is unknown when Homo sapiens sapiens evolved.

• "Mitochondrial Eve lived significantly earlier than the out of Africa migration which occurred some 60,000 years ago.

Speculation. Some argue the out-africa migration occurred 45,000 years ago and some argue it occurred 95,000 years ago.

• “Gonder et al. (2007)[1] date the most ancient mtDNA lineage L0d to 106,000 BP. This is consistent with Ingman et al. (2000)[2], who date Mitochondrial Eve to 171,500 ± 50,000 BP. Ingman et al. sampled 53 persons, 32 of whom were Africans from different regions of sub-Saharan Africa. They sequenced the complete mtDNA but excluded the evolutionarily unpredictable D-loop in the analysis.”

False and irrelevant, The L0d branch point is significantly older and it is not the oldest lineage, the oldest lineages are L0 and 'L1', the basal lineages. Gonder specifically stated the age at 194.3 +/-32 ky.

• “Probabilistic studies[4], place her around 140,000 BP, in the lower range of the error margin given by both genetic studies mentioned above.”

False, it is not clearly when mtEve lived, the best and most comprehensive studies have a wide margin of error. For gonder et al. the 95%CI is 128,000 years in width. If we assume all possible ranges the TMRCA is from about 70,000 to 260,000 years.

• "Mitochondrial Eve is estimated to have lived around 120,000 years ago at the latest."

False. In the Review “evalaution the mitochondrial timescale of human evolution" Endicott et al placed favored MRCA for humans at 108,000 years. I don't believe this date but for a NPOV this is minimally a low date, not the lowest given variance.

• "The theoretical MRCA could have lived as recently as 3,000 years ago.[9]"

Theoretically pigs could grow wings and fly. No current publication is arguing that, that statement is based on the sole use of 5 or so sites on mtDNA that undergo hypermuation. This statement from the popular media (information we were supposed not to rely on) is based on the fact that these sites undergo saturation quickly.

• "The most recent common ancestor (MRCA) is the most recent person whom all of humanity can count as one of their ancestors."

False. That ancestor is unknown, but likely much more recent. Speculation on the last person for whom all humans have an ancestor is beyong the scope of Wikipedia.

• "'Adam' lived only 60,000 years ago.[4]"

False, there is much conflict over when Y-Adam lived, much more so than Eve. Early reported estimates were from 20,000 years ago, and several more recent attempts to correct for molecular clocking variation have estimated dates over 150,000 year. More than likely, if the new calibration techniques for Y based on Autosomes and X-linked comparions hold, on can expect this to be much, much older.

• "Using this new calibrated clock puts Mitochondrial Eve at a mere 6,000 years ago. [17]"

False and obsolete, it was a technique for examination of errors. Most current studies mask those sites because of the high rate of saturation. In Soares et al. (2009) 16182C, 16183C and 16194C were excluded in addition for site 16519 they were unable, with 2000 mitogenomes to estimate the rate. Gonder and Ingman excluded all HVR. Because of the high rate of saturation at these sites estimation of rates is difficult with out a large number of sequences. And it is only possible with a very large number of sequences to estimate TMRCA via parsimony analysis, would would be useless for analysis inside of Africa.

• "The fact that Mitochondrial Eve happens to be dated to precisely this period has been taken as evidence of a population bottleneck (e.g. Toba catastrophe theory) giving rise to the human species. There are, however, many ways such family trees can be constructed."

False. In fact several recent papers, including Endicott et al. and Atkinson are arguing for just that, there was a bottleneck. In fact Atkinson goes on to define how constrictive that it was. The modern idea of Bottleneck, as recently presented in PBS Nova series is that Africa underwent a drying period after 160,000 years ago, causing humans to become trapped around the few supportable pockets in South Africa. Toba volcano is generally considered too late to have caused a bottleneck. In addition Atkinson recently defines the size of the population, it was generally smaller than the X-linked and autosomal prediction.

Muntawandi, in your desire to correct this page how are you going to fix the hideous number of errors and remain within the guidelines of 'less popular science'? This page got to this point because it reflected the very worst in the Popular science presented, and intermingled within that some out an out false statements. Do you support keeping false statements on this page? Show me what your version is to correct these problems?

When I came across this page several months ago I was shocked that a FA on wikipedia could have so many errors, I brought this to the attention of Micheal, most of these errors that were obvious, some which I have since confirmed to mis represent the current literature, the statement was fix it yourself. Muntawandi you have had 4 months to fix these errors or come up with you own solution, are you saying now that you want to work on and improve the article. You have chosen to criticize what I have written, which means you either like the previous (flunked) version, or you simply don't mind pages with one contradition after another, and many false statements.?PB666 ^yap 21:42, 5 December 2009 (UTC)

World Map

There was a map added to this page, however it does not show L0.PB666 ^yap 06:03, 1 December 2009 (UTC)

Original research noticeboard

I have posted a thread that involves this article here. Wapondaponda (talk) 08:18, 6 December 2009 (UTC)

Muntawandi has criticized the range of 70,000 to 270000 years, I replaced this with a sentence, more difficult to read but is a dry rendition of two papers "The time of Mitochondrial Eve (TMRCA)is currently disputed, the early estimate by Gonder et al. (2007) places the at 194,000 +/- 32,000 years while Endicott & Ho (2008) place the estimate age between 82,000 and 134,000 years using a different method of calibration."PB666 ^yap 21:48, 6 December 2009 (UTC)

That sentence bears no resemblance to 70-270,000 years. Where did you get those numbers from? Fences&Windows 02:57, 7 December 2009 (UTC)

What is frequently quoted in the literature are point estimates that range from 150-200kya. Most of the recent dates have clustered around 200,000 years ago. These dates have remained remarkably consistent since the story was first published 22 years ago. Quoting a range of 270-70kya, gives a misimpression that there is a lot of uncertainty in the dating. Rather they are a few outliers. Endicott 2009 quote 108,000 years, but this is only mentioned in the images, and not in the text of the article. The aim of the Endicott article was not to determine the mtDNA MRCA, but rather to highlight the challenges in in dating mtDNA splits. As a result, I wouldn't give too much credence to Endicott's estimate, because it doesn't appear to have been a very detailed analysis( initial impression). Wapondaponda (talk) 07:01, 7 December 2009 (UTC)

OK, folks, this means that you have not been following the literature lately. Endicott and Ho has two sources of error, first, it is unlikely that the first modern humans to have left Africa left before 55,000 years ago, the problem is that even people like Tishkoff, the leading expert on African studies does not believe they migrated earlier than 93,000 (portraying this migration into the Levant as something that eventually retracted into Africa). The earliest evidence outside of Africa, it is contested at 68,000 years of age. Point estimates arguable have no meaning only confidence intervals have any meaning. The confidence interval range for all published studies from 2000 to Present excluding E&H is the exact same as the 96CI of Ingman 71,500 to 271,500 years (i.e. 175000 +/- 50000) this covers all the known confidence intervals of the last 10 years. I thought this was the best compromise but Muntawandi complained.

Before describing the second source of error, let me just state that the problem Endicott and Ho state is exactly in tune with my personal observation, that neither Soares et al. or Mishmar et al. have completely dealt with the issues of selection and adaptive evolution. As a consequence both are slighlty overestimating the temporal length of branches that are under the age ot 40,000 years.

Since Endicott and Ho Anchor fix the intermediate branch points at 50 ky they force the extended outer branches to contract, and this corrects the problem above, however by doing this the overcompensate for the because as Soares points out, the number of mutations that persist beyond 50,000 years persists.

How bad is the problem, I cannot give the details but lets just say that some branch times using an entirely external rate calibration are specifically lopsided in humans and present TMRCAs in the millions of years. The problem is more severe than what Soares et al and Mishmar et al. bring to the table, the is the reason that these authors sent me a copy of their paper, in one aspect it is rather easy to prove that Endicott and Ho are correct. The problem is that for both Soares and Mishmar we don't know what the CHLCA is. That is the key problem, if it is one million years older than what Soares used, and given that he has compensate for many of these mutations, and if we exclude some of the most problematic trees, then the Soares 192,000 is probably correct.

We can also look at this from the Endicott and Ho, if 108/50 * 80 = 172,500 years and considering they overcompensated the again its going to set right on 190,000 years. But again we can't do this. So here is the basic problem

• Endicott and Ho have identified a serious problem in the estimates that no other authors (except Cann et al 1987) have dealt with, however their method has its own problems.
• Soares et al have partially compensated for this serious problem, but they don't know what the CHLCA is and their method has not compensated for adaptive selection that is significantly evident in some parts of the world.
• Mishmar et al. have partially compenstate for the problem Endicott identified but they do not perform the type of compenstations that Soares have applied. They are using an even younger CHLCA, and their confidence interval is based on a fixed CHLCA.

Again we cannot perform WP:CRYSTAL. If the CHLCA is 7 or 6.5 million years in age then

• TMRCA is lower than Soares, since Soares gives no confidence interval, any level of difference is significantly lower.
• Mishmar gives a confidence range of 76,000 years (4 * 19 ka) Therefore if the TMCRA drops below 160,000 years then there is a significant error in their calculation
• White et al basically argues that CHLCA is open ended because of errors made in physical anthropology. IOW CHLACA is greater than 7 million years, greater than the CHLCA used by Ingman, Soares, Gonder, Mishmar, Kivilsid, etc.
• IOW all of the above appears to have serious errors in their premises. In this instance the best choice by WP standards is to apply the ranges that cover the most possible points of errors and reference them. So sorry folks but that is what Dweller stated and thats what its going to have to be for now.

There are only two current studies that produce TMRCA ranges that are credible, despite numerous internal errors. Ingman et al 2000 171+/- 50 ka= 71 to 271 ka at 96%CI (What was on the page) Gonder et al. 2007 194.3 +/-32.5 ka = 130 to 259 ka At the moment I would choose if I had to choose one Ingman et al 2000 as the range of highest confidence. Read the original sentence it spoke about confidence, not about point estimates, point estimates are meaningless.

Again there is an intense debate currently between different factions regarding the nature and extent of selection at the moment. I can tell you where I stand - by Nature of problem I stand with Endicott and Ho, by method of repair I stand between Soares and Mishmar, by time of CHLCA I stand between Soares and White.PB666 ^yap 15:29, 7 December 2009 (UTC)

tl;dr. However, "OK, folks, this means that you have not been following the literature lately." I shouldn't need to read the literature to read this article. That you want to put in statements you can't source directly to published articles shows the problem with your approach. Stop it. Leave synthesis of the literature to review articles. Fences&Windows 17:44, 7 December 2009 (UTC)

OK then the review article is Endicott, Ho, Metspale, and Stringer 2008. And is exactly the reason why I altered the lede estimate. There are four pertinent reviews at the moment, 2 by Tishkoff and one stated above, in additoin Atkinson et al on population size is a major consideration. EHM&S intercompare different estimates and they come to the conclusion that the archaeologically based estimates are the best because of the problem in the peripheral branches has dsitored CHLCA anchored estimates.

The problem was that this page started with Popular science which drifted into misrepresentations. WP:TLDR POV in editores of the page a problem on the previous page, literature was too long and technical and people did not read it and consequently this article was kicked from a FA to a C-class page. Now the page is too long and technical, so that issue needs now to be readability. I agree with most of the Wiki-guides, however with some aspects pertaining to the literature WP:OR is problematic because some papers either understate confidence or state no confidence (Soares et al. 2009) as a result following WP:OR creates problems of itself. The range I previously gave is a standard interprestation of the 95%CI for 171.5 +/-50. Since this is contested, then I think its better to present the full range of most recent dates.

PB666 ^yap 18:20, 7 December 2009 (UTC)

Problems with TMRCA and meaning of MtDNA Eve

The primary derivative result of the TMRCA is the population size estimates. We started out with HVR and population size estimates were given because the number of small HVR sequences propogated rapidly, by 1997 I had my hands on 2000 of these sequences. With these sequences there was the popular notion of a big-bang, an explosion of sequences about 90,000 years ago. With this there was a growing body of evidence for small population bottleneck somewhere in SSA dating to the period between 150 and 90 kya.

Constrasting evidence for big-bang'

When the big switch occurred in 2000 to genomic DNA the number of sequences people used dropped to 50 and then rose steadily to 100. Ingman et al observed no evidence of selection, which is frequently observed when populations expand rapidly. The problem was their sample size was too small to observe these things, and he did not detect the inadequacy. As a consequence the evidence for the big bang retracted and disappeared, and we began to see evidence of more recent exodus from Africa, before the exodus there was no expansion evident. The problem is basic to the rest of the discussion, evidence of selection and saturation is very difficult to detect, it is an ignorance is bliss situation. Saturation becomes more visible as the number of sequences increases. Selection in some lineages may be evident, but really becomes evident in contrast with older clades and branch points, particularly in comparisons between other species. As the number of lineages increases the number of positions that can be intercompared increases at different depths and the significance of the difference become more apparent.

Recent studies into populatin structure - Bottleneck

Since 2001 there is now about 2000 sequences and there has been a proliferation of evidence for an expansion of the L3 lineages about 80 to 100,000 years ago. (see Atkinson, Drummand, ...) Consequently after waning support for population bottleneck idea the support has returned. The loss of support for the population bottleneck was largely due to the failed recognition of inadequate sampling. As sampling increased so has the evidence for significant levels of selection acting all throughout the mtDNA tree, only one lineage L5 does not show signficant evidence of selection, and Tishkoff places the bearers, the Sandawe, very close to the epicenter of human evolution. In some of the most extreme examples shown in a recent critique of migrations to the new world (as discussed in Endicott, ....Stinger, we (i.e. many scientist) see profound regional selection for peoples who moved from the tropics to the Arctic and back to the american Artic within the last 50,000 years. For this reason some authors were stating that humans migrated to the Americas 40 and 60kya. However with close inspection the sites they were clocking were very rarely mutated in human, primate or therian evolution. This is the major point of Endicott and Ho and I absolutely agree with them on the extent of the problem at this level or 'depth' within the canopy of the mtDNA family tree.

Problems in the estimate of population size - current

So what is the problem - The problem is that when CHLCA increases and more selection is detected and compensated for in the peripheral branches then that length between the big-bang and the TMRCA increases. As the TMRCA increases the population size increases. This is important and pertains to theories regarding speciation of humans and the environment of sub-Saharan Africa, within the time frame between 70,000 and 190,000 years. In these theories MtMRCA provides a key understanding (its population size, its place(s) and its length).

In addition the time of the so-called 'Khoisan' branch ('L0k/L0d'/'Else' fissure detected by Tishkoff and Behar) will drop from 144,000 years. Remember that this fissure occurred before the big bang, and split two groups by geography and prevented the fixation of L1. So that we can expect in the very near future some discussion about the climate of Southeastern Africa that resulted in a fissure forming in the human population, these are going to be directed at the mtDNA and more than probably at the origin of Y-DNA.

Unfortunatley, these two aspects are the most important aspects regarding the calculation of the mtDNA eve. Negating issues of selection and calibration, the timing of mtDNA TMRCA is largely determined by the size of the population, the length of the population at that its early size (both the time estimate and in variance) within the bottleneck + the time since the bottleneck to the presence (provided that selection is compensated for and calibration is correct). The time since the bottleneck is more or less a spacer, a block of time that has little or no bearing on the fixed calender date in which Eve existed, and branching within that block should suffice for a near exact estimate of the block size. As a result, the variance of the TMRCA of Eve under these ideal circumstances should follow the evidence of branching within L2, L1, L0, L4, L5 trees back (See book intitled "The Coalescent") to the mtDNA MRCA should be a reflection of the variance in those subsets of estimates.

The Khoisan fissure of a rare component (L0) within the East Africa group effectively prevented fixation of L1 as population size was at a minimum, given that Tiskoff states that L0d and L0k were removed from the East African population, this leaves only the L0abf detected at very low levels in africa, L0 might have been excluded had it not been for this split and was on the brink of being excluded. Almost all the L0a and f lineages are extremely long and lack early ancient branch points, they have survived as a result of population expansion in Africa.

The tables I have added to the Main attempt to compensate for the broader aspects, however to go any further, to deal with selection within the context of a changing molecular clock, as indicated by Endicott,et al. and Soares et al. (I will provide quotes from these papers later) would be original research.

The major point however here is that the previous Main had made assumptions about things that were due to poor techniques, or poor usage of the popular or news literature. Recent work, although not perfect is now at the threshold of dealing with these various problems more effectively (Endicott an Ho are one of the groups trying to tackle this issue), it also demonstrates clearly the critique from the GA review, this page should not be using popular science as its backbone. Endicott and Ho are not so important in their estimates of CHLCA, but are important because they bring to the table a perspective that shines light on the trouble that is apparent in the canopy and younger branches of the mtDNA tree, this trouble indicate shifts in branch positions will occur in the future and so this page should stand by the current breadth of estimates so that we are not pandering to a 'popular' point of view, or views that are subject to rapid fluctuations in the mtDNA tree. In addition it is Endicott, Ho, Metspala and Stringer is a review, as with Tishkoffs two reviews should take priority on this page.

Conclusion

The most important aspect of the TMRCA of mtDNA Eve is the population size and geographic placement that facilitated 'fixation' of her descendant lineages (This issue was discussed in the lastest series of Human origins on PBS-Nova). More simply, structure that gave rise to our observed coalescent are important.

The TMRCA is not likely to change that much, however the population size growth, as a function of branching of certain L2 subclades (namely L3) may change. Nodes of branches are subject to considerable shift as positions of nodes approach the leaves of the mtDNA family tree canopy. If this shift does occur, based on Atkinson et al. the early population size estimates may change, probably increase, as the T L3-node pulls away from the TMRCA in the direction. The shift in the tree is a balance between two factors, errors in compensating for selection and errors in the estimate of the CHLCA or errors in entry times into Eurasia. Important to this page and core to the MtEve TMRCA is the period between the event, and the expansion (big-bang). This represents the core concept of the page, ergo information that reflects uncertainty in the population size estimate is a core aspect of the page. Things that within this time window are also important.

Less important or tangential to the page are issues dealing with M, N expansion or problems clocking migrations. Therefore Endicott and Ho should take a lessor importance since this paper is primarily designed with canopy topology issues. However E&H reflect on a core and currently unresolved problem, and this critique is important to the page. Again, I did not want to mention E&H or E,H,M&S review in the lede, I think a general time constraint is important, but MW feels that it is original research to display the full level of current uncertainty, in which case we abide by the strict rules, and unfortunately it is a representative. Becareful what you wish for MW because you may get it.PB666 ^yap 18:20, 7 December 2009 (UTC)

Issues brought up in recent reviews

I am going to go through these because they are considered 'premier' and some may not have access to reviews, since I have been accussed of creating walls of words, and because of fair-use limitations I am cutting these down to bare essentials.

CHLCA

From Endicott, Ho, Metspalu and Stringer, 2009 Chimpanzee human last common ancestor is the last common ancestor between humans and chimps.

The majority of published rate estimates for human mtDNA [....]have been claibrated with references to the human-chimpanzee divergence. In the simplest case, the genetic difference between humans and chipanzees is divided by the time since their divergence, to obtain and estimate of the rate per year. [See formula within Main]

Trying to stay within the fair use limitations.PB666 ^yap

..there is uncertainty over the exact timing of the human-chimpanzee divergence. A recent review of the molecular estimates suggest a possible age of 4-8 million years [Bradley 2008], whereas the fossil record suggests the split at least 6 million years ago [Benton and Donahue, 2007]

Note: White has revised this to 7 or more million years ago. Also see revised main page 6 studies rely on CHLCA, 2 on archaeological origins.PB666 ^yap Corroborating this critique from Soares et al. 2009

On the basis of the age of Sahelanthropus tchadensis, Benton and Donaghue have recommended that 7 mya be taken as the lower bound.(The discoverers of Orrorin tugenensis in fact claim an age for the split of considerably earlier than 7 mya, raising questions regarding estimate of 10.5 to 13.5 mya obtained when non-primate calibration points were used in molecular data but the wieght of moelcualr evidence argue against this.

These early dates are also supported by Pierolapithecus Conclusions three papers, Several papers have drawn into question the CHLCA time used to calibrate most major studies.

From Endicott, Ho, Metspalu and Stringer, 2009

Thus the first assumption [Those for CHLCA] can lead to the estimates of molecular rates that are inaccurate and artificially precise.

So this is from a review and they are cricizing one of the core problems with confidence intervals, artificially precise. I 100% agree with this statement and most of the literature since 2008 to present reflect this critique.

Muntawandi, what is your response to this?

Inconsistent molecular clock and selection

From Endicott, Ho, Metspalu and Stringer, 2009

The second assumption is that the molecular evolutionary process along the human and chimpanzee lineages, as well as among humans, has been relatively homogeneous and neutral. In practice this assumption is reflection in the usage of methods based on a strict molecular clock [6,7]. There are two lines of evidence that cast doubt on the legitimacy of these assumptions

"What is the basis of the edits and the statements. This is derived from this critique. "In summary Pdeitiker has engaged in a pattern of original research in several articles. The original research is masked behind jargon, technical detail and verbosity. Overall it involves putting his own idiosyncratic spin on scientific information that is at odds with mainstream interpretations." Muntawand from WP:OR

Here is the basis of the spin (which I prefer to call neutrality and neutral presnetation) from the reviews:PB666 ^yap

First, human and mtDNA appears to be the subject to widespread purifying selection [7, 10 - 14]. Second, studies have shown that older calibrations tend to produce slower and older date estimates [15-18]. IN particular the disparity between the pedigree and phylogeny-based rate estimates is conspicuous [19-21]

From Soares et al. 2009

The mtDNA phylogeny seems to show a higher proportion of synonomous mutations in the anceitn thatn in the young branches - i.e. young branches present a higher proportion of non-synonomous mutations [Mutations that are strongest evidence of selection] in the protein coding genes and substitutions in the RNA genes.

From Mishmar et al. 2003

Our data suggest that regional variation in mtDNA sequence is likely to have been shaped by natural selection. MtDNA variation deviates from neutrality in European, Central Asian, and Siberian plus Native American mtDNA lineages but not African lineages.

From Gonder et al. 2007 Actually it deviates in African lineages, it deviates more in Asian lineages than African lineages as Gonder et al shows. PB666 ^yap

We detected significant departures from expectations (table 1), as measure be Tajima's D, int the global data set and the pooled African and non-African data setes, but not in Tanzanians. D* and F* statistics of Fu and Li revealed significant departure from neutrality in all populations.

From Endicott and Ho. 2008.

In contrast the 4 fold difference of PC1 + 2 [rates based on the first and second coding positions] can be at least partly attributed to the impact of negative selection

I concur with the severity of difference it is quite large. PB666 ^yap

From Subranmanian 2009

The average [omega, d_n/d_s, nonsynonomous divergence relative to synonomous divergence] observed for the young haplogroups <50 ky is 5.8 times higher than that estimated for human-chimpanzee pairs (0.23 vs 0.05). Within the human populations, the average omega of the young haplogroups is 28% higher than that of the groups aged between 50 and 100 ky (0.18) and 64% higher than that of the >100 ky-old African haplogroups. The omega for the human-Neandertal comparison is only slightly higher than that of the African haplogroups

I can provide more like this if desired. PB666 ^yap

So that here we have the five most recent papers on the topic and a review, Gonder and Mishmar present the least severe outcome and have the Highest TMRCAs, Soares and Endicott (Soares using the highest calibration) present Lower TMRCAs. The question is not whether selection has morphed the mtDNA TMRCA, the question now is how badly it has distorted the TMRCA. The data is overwhelming here, there is a clear lack of confidence in the rate estimates, that is why the rates change from Ingman's that is why the TMRCAs have tended to fall even though there have been large increases in the CHLCA.PB666 ^yap

OK, so next critique. Let me start how do we compress this information down and make it understandable.

So who is fabricating data or coming in with idiosyncratic theories, Muntawandi, you simply don't like what you are hearing and be honest about it.PB666 ^yap 05:37, 8 December 2009 (UTC)

Most of this article needs removal

The way this article has developed, it clearly is not sticking to the subject Mitochondrial Eve. Effectively it has become an essay about the problems associated with estimating time back to common ancestor. (Maybe there should be an article for that. But even then the style of writing currently being used would not be appropriate even for an article on quantum physics. So many acronyms. It is more the style you might see on a black board while someone is giving accompanying verbal explanation.) Anyway, this Wikipedia article only needs references to whatever the mainstream debates say. In the meantime, clear explanations about what Mitochondrial Eve really mean have actually become harder to find. From what I understand, most editors agree with what I am writing?--Andrew Lancaster (talk) 08:22, 8 December 2009 (UTC)

I agree, the article needs to be rewritten. Pdeitiker has gotten the wrong impression that some editors are "out to get him". In fact there is some useful information in Pdeitiker's wall of words version, but it is not directly relevant to the subject of mitochondrial eve and is better placed in other articles. Pdeitiker may have found himself in the unusual position where he has useful information, but at the same time he is harming the project with his somewhat idiosyncratic approach. He may turn out to be a net negative to the project if he doesn't alter his approach. It would be great to proceed reworking the article, but I am concerned about the walls of text that will follow. Wapondaponda (talk) 09:55, 8 December 2009 (UTC)

Agreed. I'm glad we seem to have a critical mass of concerned editors. Ultimately most of the material can find its way into new articles. But the style is awful -- far too idiosyncratic, hypothetical and jargony. --Michael C. Price ^talk 11:35, 8 December 2009 (UTC)

I have re-written the opening paragraphs in order to correct basic logic, wording and flow problems. I come to this section, and it is the first section I see where I can not see anything that is really about Mitochondrial Eve. It does not fit in any visible flow of discussion about her either? --Andrew Lancaster (talk) 10:12, 8 December 2009 (UTC) The passage as it stands is as follows:-

Paragraph 1. Humans are sexually reproducing organisms composed of two dimorphic sexes. Individuals within mammalian species cannot create exact duplicates of themselves. Instead, each individual passes ~1/2 of her or his genetic makeup to offspring with her or his mate contributing the other half. Through offspring production, individuals increase their genetic representation in the next generation, increasing the probability that more of their genes will be passed.

I see nothing here which is relevant?--Andrew Lancaster (talk) 10:12, 8 December 2009 (UTC)

Agreed. :-) --Michael C. Price ^talk 12:28, 8 December 2009 (UTC)

Paragraph 2. Mitochondria are overwhelmingly inherited from the female parent. Since female or male offspring are produced randomly at a ~1:1 ratios, when a mother passes a new mitochondrial mutation to her offspring, there is random risk that the new mutation will be lost in the first generation. Alternatively the mutation may be passed to one or more female offspring and survive. If a mutation survives in a population long enough, it may fix in that population (see figure:Most likely time in generations to fixation) as part of a forward-looking process. [note 1][4]

Paragraph 3. Estimating the time to the most recent common ancestor (TMRCA), however, requires the interpretation of a past process. The accumulation of genetic markers (single nucleotide polymorphisms; new mutations) lengthens and may creates new lineages. This process creates diversity and the larger the population, the more diversity can be accumulated. Alternatively, genetic drift prunes lineages from the mitochondrial family tree. As scientist measure diversity, they can estimate when lineages might have formed.

Paragraph 4. Mitochondria within the cell have identical DNA sequences. On rare occasion – about once every 4,000 years – a stable mutation occurs in a female and is passed to a female offspring and thus can be passed to subsequent generations.[5][note 2] The mutations that occurred in the lineages of Eve's descendants prevented her mitogenome from fixing. However, the markers that accumulated on each lineage allow scientists to estimate the time in which she lived. When scientists piece together the human mtDNA tree in order to describe the ancient population, the process is known as Coalescence analysis. This analysis involves complex computational formulas that determine the impact of the density of branches as time precedes from the MRCA to the present. The result is a glimpse of the ancient structure of the human population.

Most of what is relevant is being repeated. There are bits and pieces which might be able to be compressed into a simple extension of the opening paragraphs which immediately precede this section. But in any case I see no reason to keep a whole section for this? Comments?--Andrew Lancaster (talk) 10:12, 8 December 2009 (UTC)

I may suggest reverting back to the version before Pdeitiker's edits. It was not perfect version, but it was not obfuscated. We can then incorporate whatever useful information is in this version and merge the two. Wapondaponda (talk) 10:16, 8 December 2009 (UTC)

That is a bit nuclear. PB666 was certainly trying to fill in things he found missing. If we can keep any of that, then the article will be improved. I propose we go through section by section. You can certainly keep old versions in mind to keep asking yourself whether the new version of a section is better than the old one.--Andrew Lancaster (talk) 10:19, 8 December 2009 (UTC)

I agree with Muntuwandi that we should revert back to a pre-Pdeitiker version. Whereas previously I was prepared to accept that Pdeitiker knew what he was talking about and merely had poor editing skills, a series of non-sensical replies indicate I was being too generous. Given that we can't trust any of his statements total reversion seems prudent, before we start reincorporating his material. If he can't accept this then an RfC is in order requesting an article or topic ban. --Michael C. Price ^talk 03:54, 11 December 2009 (UTC)

Note this section says that mutations effectively appear and get passed on every 4000 years. The opening sections say every 3000 years. Which is right?--Andrew Lancaster (talk) 10:19, 8 December 2009 (UTC)

I replaced this with Soares actual statement, its based on a complex calculation. He excludes mutations from consideration that occur at 16182, 16183, 16194 because they occur to rapidly to clock, he also excludes site 16519 since it was detected over 200 times in his 2000 mitogenome analysis.PB666 ^yap 23:11, 8 December 2009 (UTC)

If I understand correctly the aim of this section is to go from explaining how mtDNA can show us a family tree to the next step which is that we can also try to estimate how old the tree and its branchings are. Is there anything else?--Andrew Lancaster (talk) 10:24, 8 December 2009 (UTC)

OK, I have merged the second third sub-sections, and I think it keeps everything important and now flows more easily. Then we hit a much bigger problem area: the middle of the article is dominated by two enormous sections: Mitochondrial Eve#Estimating time to MRCA and Mitochondrial Eve#Coalescent structure. These really appear to be articles in themselves? They divert all discussion into a tangent about problems in the TMRCA field, and divert all discussion away from many of the things which are most interesting about Mitochondrial Eve. They apparently replace a once small version called Clock. Going back to the old version is very tempting. Is there any way of compressing these to some reasonable level?--Andrew Lancaster (talk) 11:23, 8 December 2009 (UTC)

I ran into a problem in the lead. Even the estimate of when Eve lived is unncessarily verbose and illustrates some of the style problems here. We don't need to say, in the lead, "according to Gonder et al X" but "according to blah blah Y". Just say X-Y and cite the two refs inline. The footnotes and refs should be merged onto one coherent section, instead of the two level structure we have at the moment, which makes it very hard to verify anything, and is really just a lazy way to write. --Michael C. Price ^talk 12:00, 8 December 2009 (UTC)

Sounds correct to me. BTW the Harvtxt templates actually do not work in this article. I suspect, having worked with PB666 on other articles, that this is because he has an issue with "et al." referencing when there is a big list of authors. Citing with a full list of authors every time is something that will always go wrong eventually, and putting human error aside there seem to be errors in the way the cite templates have been used.--Andrew Lancaster (talk) 12:09, 8 December 2009 (UTC)

Can you clarify which sounds correct? My suggestion or the current method used in the article? (I have some sympathy with PB666's "et al" aversion you mention, but not sure why this leads to the present structure.) --Michael C. Price ^talk 12:26, 8 December 2009 (UTC)

This is a list of some of what could form the core of the article in no particular order. ::Much of this is from the old version

• Mitochondrial DNA in relation to Maternal inheritance and matrilineal descent
• The Common descent of Mitochondrial DNA
• Mitochondrial DNA and the molecular clock
• Genealogy of Eve( or of all humans back to Eve)
• Eve and theories of Human origins, ie possible speciation of Anatomically modern humans
• Eve in relation to Out of Africa vs Multiregional evolution
• Dating
• Misconceptions
• Controversies, uncertainties.

This is by no means exhaustive, there is a lot of other information such as the history of study, popular culture/science, but I think it would be ideal to deal with the core issues first. The trouble with the current version is an emphasis only on dating mtEve. This is important, but it is not the only relevant aspect of the controversy. Wapondaponda (talk) 12:48, 8 December 2009 (UTC)

Just so it is clear, I also understand the problem with et al. It is purely a practical problem. I found by experience (as I have explained before to PD, that if you try to be too perfectionist with referencing, then your system will not survive when other editors come along. If the Harvard templates are used properly, then when you click on them they will take you to the references, meaning the end notes become more redundant. OTOH, I am not taking any strong position here. Any system that works is good.--Andrew Lancaster (talk) 16:01, 8 December 2009 (UTC)

I am going to work on the referencing, for odd reason some citations were converted to cite journal, I have repaired these back to citation, however the ultimate goal is to have them all citation style. Cite Journal will not work with the harvard referencing system only a properly constructed Citation will work. The Harvtext tag has to be packed ie. Harvtxt |Author1|Author2|Author3|Author4|YEAR. PB666 ^yap 20:13, 8 December 2009 (UTC)

Requesting we consider this deletion twice

I can see different arguments for and against this deletion. Michael obviously sees the argument for. On the other hand, won't many readers coming to this article want to be able to make just this type of link between key concepts? Isn't one of the "big things" that is said about "Eve" concerning the fact that she was African and recent? (Not just in Time, but also amongst scientists.)--Andrew Lancaster (talk) 21:02, 8 December 2009 (UTC)

Upon reflection perhaps a one sentence comment might be appropriate. Something like, "The recent date for mtEve was a blow to the multiregional hypothesis and a boost to the recent out of Africa hypothesis." But we can leave any further details to those articles. --Michael C. Price ^talk 05:43, 9 December 2009 (UTC)

I originally added it in some form; I cannot say whether this is my version or not but I think it can be reduced into more simple wording.PB666 ^yap 23:04, 8 December 2009 (UTC)

I think it belongs, it can be in both Out of africa page and here, just worded appropriately for a lede.PB666 ^yap 23:45, 8 December 2009 (UTC)

To include it here (especially in the lead) is wrong. The material should not be duplicated in both articles, and it does not clearly belong here. If multiregionalism was correct there would still be a mtEve. It is Out of Africa that demolishes multiregionalism. If it appears here it should also appear in Y-chromosomal Adam, and in every article about mtDNA, which is silly. The whole point of hyperlinking is to reduce duplication.--Michael C. Price ^talk 23:57, 8 December 2009 (UTC)

With all due respect Micheal mtDNA as a single entity was the weightiest evidence against MREH.PB666 ^yap 02:49, 9 December 2009 (UTC)

In which case a comment in mtDNA would be appropriate. --Michael C. Price ^talk 05:07, 9 December 2009 (UTC)

BTW it looks like we are mandated to change the date one more time. Endicott and Ho give to ranges that are HPD (95%CI) and the second is 213 Ka, in which case we do not violate WP:SYNTH and we only need one reference.

Michael, I see no reason to say that a subject can not be included in two article. I guess what you mean to say is that it should not be handled with the same level of detail in two articles? But this sentence you removed was quite a quick summary. There is I think a much bigger discussion somewhere in the body which can come into question, but removing all mention of this aspect of Mitochondrial Eve would not seem right to me?--Andrew Lancaster (talk) 06:48, 9 December 2009 (UTC)

Did you see my response above? I think we agree, a short summary is okay. I've suggested a one sentence form. --Michael C. Price ^talk 06:51, 9 December 2009 (UTC)

No problem with that. The words 'blow' and 'boost' might be substituted PB666 ^yap 10:59, 9 December 2009 (UTC)

Another candidate for deletion from the lead: "'Eve' would have been roughly contemporary with humans whose fossils have been found in Ethiopia near the Omo River and at Hertho." What is the relevance of this? Either it should be explained or deleted. --Michael C. Price ^talk 07:08, 9 December 2009 (UTC)

Don't you think this is the kind of people looking up the subject would want to know?--Andrew Lancaster (talk) 08:36, 9 December 2009 (UTC)

Obviously not, or I wouldn't have deleted it... :-) Seriously, I fail to see the relevance of this. We could also say that Eve was contemporaneous with Homo Erectus in Asia, but we don't. I just don't get what the sentence is trying to say (e.g. are they our ancestors or not?), and I don't think the general reader will get it either. --Michael C. Price ^talk 08:50, 9 December 2009 (UTC)

I see what the statement is getting at, but given the current state of the literature one could ask about the relevance of the statement. I would say delete.PB666 ^yap 11:02, 9 December 2009 (UTC)

OK--Andrew Lancaster (talk) 15:27, 9 December 2009 (UTC)

Moving forward

Much of the current article is PB's individual work that was done without much input from other editors. Many editors have expressed concern. Rather than get distracted with specifics, I would suggest a major rewrite of the article using information from this version and prior versions as well. A few things to consider

• The lead
• An outline of sub-headings
• The level of detail and complexity of the article, should it be at the popular science level or PHD level.
• Consider moving much of current content into an article such as Human mitochondrial DNA molecular clock.

Wapondaponda (talk) 05:01, 9 December 2009 (UTC)

Yes, let's move forward.

• The lead we can finish last, after defining the the headings and subheadings.
• I don't mind detail, in the appropriate subsections, but general accessiblility is most important. No reason why we can't have both, but the leads of each section and subsection must be written in general non-techie English. And we must remove material that is not directly relevant to mitochondrial Eve, as well as removing obfuscating jargon. The article is not a brain dump for every bit of associated material.
• Human mitochondrial DNA molecular clock looks a good idea. Possibly remove "DNA", since that is already implied? Or even split it between Human mitochondrial molecular clock and mitochondrial molecular clock?

--Michael C. Price ^talk 05:30, 9 December 2009 (UTC)

• The problem with that is that, because of the nature of the topic I avoided introducing material on rate variability. The majority of the rate variability material pertains to evolution after the exo-african migration. The material in this page is primarily focused on the pre-migration period.PB666 ^yap 11:06, 9 December 2009 (UTC)

• Why is that a problem? What has this to do moving inappropriate material to more appropriate articles? --Michael C. Price ^talk 12:04, 9 December 2009 (UTC)

• OK to rephrase, there is a problem with that; however, having considered the idea, and the fact that 80% of the references are already in place; so it sounds like a good idea. Lacking on entry the tables are already completed for the TMRCA material, except on small table, so that I can move the larger section of material off the page.PB666 ^yap 14:46, 9 December 2009 (UTC)

• This answer makes no sense whatsoever. --Michael C. Price ^talk 22:38, 9 December 2009 (UTC)

• Done! The lede for section:"Estimating time to MRCA" was not transfered to the new article, and the material in the article below "Calibrating the single nucleotide polymorphism rate" to "Estimated times of major mtDNA branchpoints".PB666 ^yap 14:58, 9 December 2009 (UTC)

• This answer makes no sense whatsoever. --Michael C. Price ^talk 22:38, 9 December 2009 (UTC)

New article, though no changes here. Possible subsections, if these are okay, we can get to work

• Intro, lead
• Mitochondria DNA

• Mitochondria-brief discussion of evolution and common descent of
• Maternal inheritance-brief discussion of mechanisms
• Molecular clock- brief summary of molecular clock

• Genealogy of Eve- L0-L6, M and N, coalescence theory
• Dates-Human mitochondrial molecular clock
• Eve and human origins-Speciation of AMH, OOA vs MREH
• Misconceptions
• Y-chromosomal Adam-Brief discussion of
• Popular science/culture

I believe this would essentially cover what mitochondrial eve is about. Any suggestions, comments? Wapondaponda (talk) 16:21, 9 December 2009 (UTC)

Not a bad start. Are the last 4 sections perhaps actually one big section with sub-sections?--Andrew Lancaster (talk) 17:49, 9 December 2009 (UTC)

Although completely lacking in the discussion of population size.PB666 ^yap 17:55, 9 December 2009 (UTC)

What would be an appropriate name for the four sub-sections. Wapondaponda (talk) 19:00, 9 December 2009 (UTC)

Yes population size is important. Current mtDNA diversity patterns have been used to infer prehistoric population size. My impression is that even when it is done, such estimates are still dependent on other assumptions. Prehistoric population sizes can still be determined, using non-genetic measures, typically archeological or computer simulations. In short, a lengthy discussion of population size in this article isn't necessary. However it is relevant to misconceptions, such as Eve was the only woman at the time. It is also connected to the speciation of AMH, since speciation events are sometimes marked by bottlenecks and there are some who suggest that existence of Eve coincides with the earliest fossils of AMH, implying a speciation bottleneck. I can see there is an article Pleistocene human population bottleneck in Africa that was recently created. Not a big fan of the title. Wapondaponda (talk) 19:00, 9 December 2009 (UTC)

Primary vs secondary sources

This is related to the policy at WP:PSTS which states, "Wikipedia articles should rely mainly on published reliable secondary sources and, to a lesser extent, on tertiary sources." Peer reviewed publications don't fit neatly into categories of primary or secondary sources. But for the purpose of this article I would consider them as primary sources, whereas books and news articles are secondary. Mitochondrial Eve is very much a popular science term, and her discovery played a major role in popularizing personal genetic genealogy. So I would suggest the use of some secondary sources. In fact many of the peer reviewed publications don't even use the term "mitochondrial eve" but simply refer to her as the MRCA (Gonder et al., Mishmar et al. and Behar et al.). Below are a two examples of how mitochondrial Eve would typically be covered in secondary sources.

• "Mitochondrial Eve-An Explanation". BBC.
• "Mitochondrial Eve: Notes". The University of North Carolina at Chapel Hill.

Of course none of these is perfect, some may say dumbed down, but the information is given in an accessible manner and is reasonably accurate. Wapondaponda (talk) 19:00, 9 December 2009 (UTC)

I notice that the BBC source contains the statement "There is no reason to suppose that she had more than one female child." Is that correct? I should have thought that we know that she had at least two daughters. (If she'd only had one daughter then that daughter would be a better candidate for being the mtEve.) --Michael C. Price ^talk 22:54, 9 December 2009 (UTC)

Well even the word candidate seems odd in this context. Isn't Eve defined in such a way that she MUST have at least 2 daughters? Or are there people out there using a different definition, such as the first person to have all the MRCA mutations?--Andrew Lancaster (talk) 23:38, 9 December 2009 (UTC)

Yes, it follows from definition: she must have had at least two daughters with their own matrilineal descendants alive today. The article should say this. --Michael C. Price ^talk 23:49, 9 December 2009 (UTC)

Not exactly, Forster L, Forster P, Gurney SM; et al. (2009). "Evaluating length heteroplasmy in the human mitochondrial DNA control region". Int. J. Legal Med. doi:10.1007/s00414-009-0385-0. PMID 19937256. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link) within a very small window that single mitochondria would have needed to produce its first defining mutation (within the L0-node to L1-node), within effectively 16 generations there would need to have been at least 2 females, probably many more.

For simplicities sake lets say yes.PB666 ^yap 02:14, 10 December 2009 (UTC)

In this unusual situation, still 2 daughters are needed to form 2 lineages, it does stretch Eve across several generations. No biblical analogies for the daughters of Eve, only Cain and Abel for sons. The BBC got that one wrong, but their point was that just because she is the MRCA doesn't mean that she had plenty of children, but she must have had daughters. Wapondaponda (talk) 04:09, 10 December 2009 (UTC)

.PB666, it is not a matter of simplicity, it is a matter of definitions. Your response makes no sense to me. Eve would still have to have had two or more daughters. How does that study you cited change anything? --Michael C. Price ^talk 08:40, 10 December 2009 (UTC)

OK, A new mutation that appears in a population of mtDNA can be passed as follows. First it can be in a family with two female offspring, one with the mutation and one without and this would explain the result. Second, it could appear in the sole female offspring, however the sister, aunt, great aunt, great aunt of the MtMRCA type may sustain the Nodal type (without mutation). As with everything in molecular evolution the argument is statistical. In practicality you are right, if a line does not duplicate quickly it dies out. The random risk of a single occurance mtDNA type is ~37% per generation. Therefore if the line does not duplicate itself rapidly then it dies (Markov chain is ~ 0.36, 0.23, 0.15, 0.09, 0.06, 0.04, 0.02, 0.02, 0.01, 0.01, 0.004, 0.003, 0.002 for 1,2,3,4,5,6,7,8....13th generation). The probability of an allele fixing is equal to 1 over population size. The rate of exclusion is highest in the first few generations (I have a graph for that but I never added it to the page, but see chain) for alleles that go onto fixation the probability of fixation for each successive generation without two female decreases. While Eve hereself did not need to have two daughters, statistically speaking if she, or her daughter or at least a granddaughter did not have multiple female progeny then the probability that Eves mtDNA would fix drops markedly.

The MRCA is defined by sequence, MRCA is the first female with that sequence.

1. 1 Eve-(d1Eve, d2Eve*) * = first mutation d=daughter = g=grand
2. 2 Eve-dEve-(gd1Eve, gd2Eve*)
3. 3 Eve-dEve-gdEve-(gd1Eve, gd2Eve*) * = first mutation
4. 4 Eve-dEve-gdEve-ggdEve-gggdEve-(gggggd1Eve, ggggd2Eve*) * = first mutation
5. 5 Eve-(d1Eve, d2Eve)-d(d1Eve),d(d2Eve*) and so on. You get the point.

Micheal I don't necessarily advocate changing the page, because given uncertainty about the rapidly mutating sites and the risk of exclusion, for all intents and purposes the risk the Eve did not have two daughter or two maternal lines granddaughter is relatively low, two problems (risk of not having a recurrent mutation, risk of being excluded) squeeze the MRCA within a small number of generations of the first defining mutation.

For the sake of not being tentitious lets avoid this issue for now.PB666 ^yap 17:14, 10 December 2009 (UTC)

Eve is defined as the most recent common mt ancestor, i.e. whether everybody has inherited their mtDNA from her. It has nothing to do with how much the mtDNA has mutated since then. My father is still my father, even if my Y-chromosome has picked up a mutation en route.--Michael C. Price ^talk 20:15, 10 December 2009 (UTC)

Let's not get sidetrack but I agree with Michael. If an aunt of grandmother of Eve is an independent ancestor of surviving lines, then Eve would not be Eve by definition, if the definition is MRCA. The only question is whether that is the only definition and I have certainly never heard of any other.--Andrew Lancaster (talk) 21:28, 10 December 2009 (UTC)

Think Heisenberg uncertainty principle.PB666 ^yap 22:39, 10 December 2009 (UTC)

Another non-sensical reply by PB666; ancestory is not subject to Heisenberg. I take it that this means that he is unable to simply agree about something, even when he is undisputedly wrong? --Michael C. Price ^talk 03:19, 11 December 2009 (UTC)

L1) or the first bearer of the haplotype

If this is what you want to believe, remember I rewrote the section on Eve having 2 daughters which essentially contains the argument that you are making. Uncertainty principle applies to quanta that have statistically definable behaviors. The mutations propagate forward on matter but can also be thought of as waves. The important point is this, it does not matter, given a constant mutation rate, definition of branch times declines as one converges in the direction of the MRCA, however the basal-most branches have a rather large statistical variance. Then we add in uncertainty concerning anchors, rate variation in different parts of the tree. There is no importance to arguing what where within a 200 year bracket the MRCA existed when the 200 year bracket is anywhere within a 100,000 year bracket. In fact we can consider that statement trivia. If you insist I can prove the point.PB666 ^yap 14:38, 11 December 2009 (UTC)

As one can see at least one woman in that population before the last MRCA defining mutation occurred and the first branch mutation occurred, at least one female between those two points, had 2 daughters, there is no doubt about that, but the way it is described on the Main is not correct. Mutations either preceding or following in terms of single generations maybe independent. Uncertainty principle applies here because according to theory and the Markov chain patterns the 2N rules has a flip side, haplotypes that go onto to fix tend to expand at the average rate of 1/2 of a female per generation. As a consequence the highest probabilities for MRCA are within a very few generations of the MRCA haplotype. However when we attempt to define the TMRCA we do so by looking at branch mutations and using these we tend to equate the MRCA with the female as the point in generations when the MRCA is more probable than L0 and/or L1.PB666 ^yap 15:59, 11 December 2009 (UTC)

In the way that the BBC states this "She didn't live alone – she would have lived within a community. She didn't just pump babies out, either. There is no reason to suppose that she had more than one female child. But there is reason to suppose that whatever female children she had, they contained specific advantages for survival over the rest of the population." This statement is incorrect, since they did not mention mutations or haplotypes, simply the female.PB666 ^yap 16:02, 11 December 2009 (UTC)

(deindent) AFAICS PB666 has taken on board not a single word of my earlier reply. Where is the evidence for the statement However when we attempt to define the TMRCA we do so by looking at branch mutations and using these we tend to equate the MRCA with the female as the point in generations when the MRCA is more probable than L0 and/or L1. This is just pure obfuscation to the point of lunacy. Digest this: There was single individual who was mtEve, and she had at least two daughters, by definition. Estimating when she lived is an entirely different and unrelated issue.--Michael C. Price ^talk 16:09, 11 December 2009 (UTC)

I didn't realize that you were focused on a BBC article that had nothing to do with the page, I was focused, as we are supposed to be about what was written on the main page and improve it. "Mitochondrial Eve's sequence is typically represented as the top root node of the human mitochondrial phylogenetic tree. The first split in the tree is found between macrohaplogroup L0 and macrohaplogroup L1. From this it can be inferred that Mitochondrial Eve had at least two daughters who survived to have their own children[5]." as it was originally written and I had rewritten it was not-necessarily true. That was what I am referring, and I am pointing out that within the two basal lineages and from the origin of the haplotype there are going to be females that only have one female offspring. Based on statistics alone we can infer there was a woman with two daughters but we cannot infer whether her mother or her children had multiple children. All that we can argue is that from the first defining mutation (L0 or L1) the average rate of MRCA bearers is on average +0.5/generation. From a molecular point of view the MRCA is the female that had the MRCA haplotype and a child that had a mutation, but that is immaterial because of uncertainty. Case in point, Klyosov 2009s (for Y chromosome) gives an excellent example the MRCA of two individuals with a single defining mutation separating them is 0 to 1200 years for certain mutations. What that means is that we don't know whether that first mutation occurred last year or 4000 years ago. In addition there is the remote possibility that a male passed ever so rarely the mtDNA to his/her offspring, in addition females and their germlines are not neccesarily clonal.

This is not a place to focus these argument, the place to focus the argument is writing the overwhelming agreement here in a way that can be understood, that's really the only point. What else can I tell, the version you gave is the version that belongs on the page, do I have to repeat this again?PB666 ^yap 19:52, 11 December 2009 (UTC)

You just don't get it, do you? Buried that mass of pseudoscience is a half truth.

Based on statistics alone we can infer there was a woman with two daughters but we cannot infer whether her mother or her children had multiple children.

It is not based on statistics, but follows from the simple definition of mtEve as the mtMRCA. Since you have nowhere responded to the points I've raised I can't take this dialogue any further. This article will not improve until you are topic banned. --Michael C. Price ^talk 21:46, 11 December 2009 (UTC)

Grandstanding.PB666 ^yap 21:30, 14 December 2009 (UTC)

Micheal, I have a question for you? This article was in disrepair for 6 months, stated exactly why it was removed from GA status, and you have been tending that page for an appreciable time. I pointed out to you multiple misfactual statement, you could have very well said, yes, I will inspect the literature and I would have checked back in 6 months or so, instead you blew it off. Now you make comments like the above, wqhen I wrote "OK to rephrase, there is a problem with that; however, having considered the idea, and the fact that 80% of the references are already in place; so it sounds like a good idea. Lacking on entry the tables are already completed for the TMRCA material, except on small table, so that I can move the larger section of material off the page.PB666 yap 14:46, 9 December 2009 (UTC)"; "This answer makes no sense whatsoever. --Michael C. Price talk 22:38, 9 December 2009 (UTC)"Done! The lede for section:"Estimating time to MRCA" was not transfered to the new article, and the material in the article below "Calibrating the single nucleotide polymorphism rate" to "Estimated times of major mtDNA branchpoints".PB666 yap 14:58, 9 December 2009 (UTC). " This answer makes no sense whatsoever. --Michael C. Price talk 22:38, 9 December 20. And then you talk on your talk page about going Nuclear. You were here on this page on the day the article was demoted, you where here in the weeks before when it underwent review when it could have been correct to maintain GA status, over that six months did you lift a finger to fix the problem with the article? As you state on your talk page, let me ask you a question, why should I actually take anything you say seriously? At least there is considerable referenced material on the page and the popular science now plays a diminutive position. As some point we need a critical mass of people, a mass of people within the realm of molecular anthropology who want to actually improve, not just gripe and whine.PB666 ^yap 06:17, 15 December 2009 (UTC)

Ask yourself this question, for someone who has read all of this literature, why should I care what you think? Give me a sign or reason to believe that you want at some point to actually improve the article according to the recommendations.PB666 ^yap 06:17, 15 December 2009 (UTC)

PB666 this is a nonsense and ad hominem reply, nothing to do with the points at hand. Mt Eve, or indeed the Eve at any particular point in time, is DEFINED ONLY by her relationship to her descendants. There is simply no way to argue that she might have had a different number of daughters than her DEFINITION requires. You are once again arguing with a tautology.--Andrew Lancaster (talk) 00:29, 16 December 2009 (UTC)

Exactly. And her definition requires 2 or more daughters. --Michael C. Price ^talk 00:33, 16 December 2009 (UTC)

Exactly, if you mean >99% of the time. Andrew, go back an look and DNA Anthro, there is a paper I presented 2 years ago that basically states that paternal passage cannot be discriminated by current tests, some studies suggested it could other suggested it could not. In addition there is a recent paper for December that claims that mtDNA are not passed clonally, and new mutations may not fix within the first individual that possesses them. Again this is all immaterial, since what is on the page is not addressing either of these issues. I repeat the uncertainty principles apply here, at least until it can be defined how often anomolous passage occurs. Tautology is not important here either, and after dealing with the Zhirovosky/UNderhill issue and relevant timeframes you should be more than aware that DNA based estimates are more of estimates than calculation. There may be (most probably) a female defined as mtDNA eve who however theoretically she exists cannot be defined. For example look at the MRCA sequence from Kivilsild, Soares, etc. These are all different, L0 and L1 branches have different mutations in different studies, Gonder stated correctly that it is impossible to resolve which are L0 or L1, however Soares, who used Neanderthal outgroup maybe the closest. Within the 20 or so mutations between L0 and L1 is 'Heisenberg' cloud of probabilities (times, sequences, and population sizes) that result in L0 and L1. So the individual does not really matter, because everything converges into this 'cloud' and everything we know about the cloud is an estimate.

So what I did was ignoring all of this in that paragraph and painting an encyclopedic pretty picture that may are may not be true, and immaterial either way. IOW we don't care about WP:TRUTH we only care about what is encyclopedic. That which is not encyclopedic should not be placed, that includes speculation about the male mtDNA inclusion rate, clonality, or other uncertainties. PB666 ^yap 06:11, 19 December 2009 (UTC)

I mean that the probability that Eve had 2 or more daughters is more like somewhere between >99.999% and 100% (inclusive), since we don't know that paternal inheritance leads to viable offerspring (the only known example of human paternal inheritance was in a sterile male with other "evidence" being false positives [1][2]). See also the archives. --Michael C. Price ^talk 07:39, 19 December 2009 (UTC)

"The L0 and L1 haplogroups evolved from one of these possible haplotypes. Therefore, based on this convergence of lineages and matrilineality one female had at least two female children. This female would be the mitochondrial MRCA, 'Eve'." as the article states if anyone has any objection to this otherwise the conversation is over.PB666 ^yap 06:11, 19 December 2009 (UTC)

I see you are still trying to cloud the issue by talking about mutatons and waffling on about Heisenberg clouds and such crap. This is completely irrelevant to the question of how many daughters mtEve had, as has been repeatedly pointed out to, and ignored by, you. --Michael C. Price ^talk 07:39, 19 December 2009 (UTC)

Reminder to everyone

This article was demoted because of the following Talk:Mitochondrial_Eve/GA1, so instead of trying to draft new, potentially popular media factoids into the article, lets stick to secondary literature (preferred) or primary literature. What the Beeb said on "Date: 28 February 2002" is not of any value here, arguing over it is of less value.PB666 ^yap 20:03, 11 December 2009 (UTC) I know there is one individual who is trying to promote a popular science revamp of the page, I can only say that this will be frowned upon. While we can introduce some popular science and media to the article, if the backbone of the article is popular science driven the this page will have future problems. At the same time I should mention that the maps that have appeared in the top box of this page and many other mtDNA pages has many errors on it and in some cases not appropriate for those pages, I removed the map from this page. PB666 ^yap 20:03, 11 December 2009 (UTC)

Every improvement is an improvement. Incremental improvements are good. If aiming too high means we do not get incremental improvements, it would not be a good aim. Just improve, and do not make things more complicated?--Andrew Lancaster (talk) 21:17, 12 December 2009 (UTC)

Is the the kind of incremental improvements you wanted merging 7 haplogroups into 1, that kind of incremental improvement? The basic problem here is by and large no-one has any idea what an improvement is, if they did, during the 6 mos after february they would have improved, from what I can tell the article got worse. The reason they have stuck with the popular literature is, from what I can tell, that is the reading level here. The way to turn this process around is for folks to start reading the primary literature, instead of trying to guess which editor has or has not read that literature.PB666 ^yap 12:10, 15 December 2009 (UTC)

As usual your response has nothing to do with what it is responding to. My point stands as a simple statement of fact.--Andrew Lancaster (talk) 00:24, 16 December 2009 (UTC)

Its hard for me to believe, after the R1a page and E1b1b page that you understand what improvement is. If you did, Haplogroup_E1b1b_(Y-DNA)#E1b1b1b_.28E-M81.29 to Haplogroup_E1b1b_(Y-DNA)#E1b1b1g_.28E-M293.29 would have improved, and in case you have looked recently R1b is getting worse not better. This is very simple, these pages need to become encyclopedic, I don't understand why this is so difficult to understand.PB666 ^yap 03:33, 25 December 2009 (UTC)

And once again, your response ad hominem and not responding to anything of relevance about this article. I am not working on R1b. My biggest efforts on E1b1b and R1a have always corresponded with the publication of new articles, giving better sources. My main is to give a basic readable and neutral summary of what has been published. If we get better sourcing for R1b then this would allow better editing on that article. You have yourself many times recognized my efforts on E1b1b and R1a as major improvements, and so your insinuations above make you look a little dishonest. Sourcing is a key issue on Wikipedia, and a particular challenge on Y haplogroup articles, at least for those of us who follow the neutrality and NOR policies. Much of what is in the R1b article right now could be argued about in circles forever, between deleting all mention of newer findings, making the article extremely wrong, and being strict about Wikipedia sourcing norms. Therefore for the time being it is my choice not to waste too much time on it. You have no right to assign jobs to others, and I would ask you to cease doing it. Anyway, coming back to my point, improvements are improvements and improvements are good. When someone disagrees with you about are particular proposal for improvement, then this can be discussed case by case. --Andrew Lancaster (talk) 13:47, 28 December 2009 (UTC)

Any wiki page can be improved with the information at hand, and R1b can be improved, E1b1b can be improved. There is more information on R1b than just about any other Y-DNA, therefore your excuse is not legitimate. The critical problem is there is no will among the various editors to make the page encyclopedic. The clear reason is they misunderstand the goals of Wikipedia. If there is a will, no matter what, the page would become encyclopedic. Simply stated the goal as it currently appears regarding several editors within the project is to make articles less accessible and more technical rather than increased their interest and readability. It is not dishonest to recommend making things more encyclopedic, but giving good advice. Nor is it an ad-hominim attack.PB666 ^yap 17:09, 28 December 2009 (UTC)

Sourcing is indeed a problem, what did I tell you, for these types of articles is may take hours to come up with one or two good sentences. However R1b page has alot of sources, it is a matter of will, not sources that determines whether the page becomes encyclopedic. If you want a good example of how not to write a page see: Y-chromosomal Adam, where sources are thrown willy-nilly on the page.PB666 ^yap 17:09, 28 December 2009 (UTC)

Yes of course all problems in Wikipedia are caused by everyone else, and you are a lonesome knight on a crusade, trying to bring people back to the true path. This is the normal speech of many disruptive editors.--Andrew Lancaster (talk) 19:39, 28 December 2009 (UTC)

TMRCA section

My general dissatisfaction with the size and verbosity of this section has been greatly reduced, of course with a good night's sleep and a fresh view tomorrow I will find more to trim back. I think the WP:OR issues have been solved in the tables while essentially displaying the same confidence, just a matter of thinking through how to inter-compare different presentation styles. The 'stray' tag has been placed on a couple of more sections, any recommendations?PB666 ^yap 17:54, 9 December 2009 (UTC)

A lot has been made of the dates. I have an opinion on this. The very first date proposed was from Cann et al. which was 140-280kya, mean 210kya. A google books search reveals

• [3]
• [4]
• [5]

This is a quick and unscientific poll, but it shows that the most popular date cited in secondary sources is 200,000 years ago. Others cite 100-200kya, 170kya, 150kya and less than 300kya but the majority use approximately 200kya. Unless someone invents time travel, we may never know the exact date when mtDNA eve lived. Its a futile effort to shoot for accuracy. The TMRCA is a statistical quantity and represents probability, not certainty. Of course several dates have been proposed by peer reviewed studies, most cluster around 200kya(Soares, Behar, Gonder etc). There are some outliers (Endicott and Ho) at 108kya. To summarize, my suggestion is to mention the "mainstream view" in the lead, which is either "approximately 200kya" or "approximately 150-200kya" and ignore confidence intervals for simplicity's sake. A slightly more detailed discussion of dates can take place in the subsection devoted to dates and this can include a brief discussion of CIs. Wapondaponda (talk) 19:53, 9 December 2009 (UTC)

Are there secondary sources which are recent? Is there any agreement between them?--Andrew Lancaster (talk) 21:47, 9 December 2009 (UTC)

Endicott, Ho, Metspalu and Stringer is a secondary source. See above. They use in their review Endicott and Ho (2007), Mishmar et al. (2003) and Kivilsid. If one goes by the review and stick to WP:SYNTH to the exact letter the range is 108,000 to 198,000 (These are TMRCA not confidence ranges) if one includes the confidence ranges is 82,000 to 217,000 years.PB666 ^yap 23:35, 9 December 2009 (UTC)

Didn't we just get finished with the WP:SYNTH, we have to use only those values provided.

The question is whether you want to break from popular science or go back to what got this article flunked last year.

Cann el. 1987 140 to 290 Ka.

Tamura and Nie 1993 is 80 to 480 Ka, mean = 160 Ka

Nie also produced a 96%CI for Vigilant 1991 of 110,000 to 504,000 Ka.PB666 ^yap 23:23, 9 December 2009 (UTC)

Whatever numbers we quote, 228,000 just looks silly given the uncertainties. c 200,000 would be preferable. --Michael C. Price ^talk 23:26, 9 December 2009 (UTC)

We need to use 227,000, I just got the OK from WP:OR that we can use standard deviation ranges. ::In which case you can stick with the value.PB666 ^yap 23:35, 9 December 2009 (UTC)

I see no one arguing against taking confidence intervals into account where they exist in a meaningful form. But Michael's suggestion to approximate more also has no "technical" problem (synth etc) as far as I can see?--Andrew Lancaster (talk) 23:41, 9 December 2009 (UTC)

Somewhere there is a policy about false precision, which we should abide by. --Michael C. Price ^talk 23:51, 9 December 2009 (UTC)

See above, its quoted, not policy. Endicott, Ho, Metspala, Stringer, the TRMCAs based on CHLCA have a false precision. I really thought that 70 to 270 range covered all possible confidence scenarios based on 2007-2009 studies.PB666 ^yap 00:00, 10 December 2009 (UTC)

The 70-270kya range may cover all CI scenarios, however it misrepresents the dates most commonly cited in secondary sources. Is there a mainstream date or range of dates?. If there is, that is what we should cite, at least in the lead. A date of 70kya does not have a probability equal to a date of 150kya or 200kya. A date of 70kya creates a lot of problems, for example some suggest that the OOA migration had already taken place by 70kya which makes this date for the MRCA impractical with the OOA hypothesis. According to the tree at http://phylotree.org, at least 35 mutations separate haplogroups L3, M and N from Mitochondrial Eve. Haplogroups M and N, which are the signature haplogroups for the OOA migration, have since accumulated 20-30 mutations. With simple arithmetic it means that the time from mitochondrial Eve to the time of the OOA migration is longer than the time from the OOA till today. If OOA migration took place 50-80kya, then we know that Eve lived significantly more than 100-160kya. This simple arithmetic ignores population size, but if it were considered it would push TMRCA further back in time. But most importantly, I haven't seen any publication that cites 70kya. Wapondaponda (talk) 07:13, 10 December 2009 (UTC)

Muntawandi, I don't think you realize the depth of the problem. I will try to explain this in as few words as possible. Variation in the rate of certain substitutions at the canopy of the mtDNA tree has been found to be profoundly different from the rates observed at same sites in longer branches. There are 5 references above that confirm this. I did not create this problem. This observations is the consequence of going from 50 mitogenomes (Ingman: no evidence of selection) to 100s of mitogenomes. If you want a basic paper on sampling effects read Tamura and Nei, 1994 and Wakely, 1994. As a consequence the compression of the canopy of the mtDNA tree is something that is currently an educated guess. Or should I state otherwise many people have observed this 'effect' in the last 4 years, however no-one is greatly sure how to compensate for it. E&H do exact a method, but that method itself is based on to controversial assumptions.PB666 ^yap 14:44, 10 December 2009 (UTC)

Personally, I strongly suspect its not as bad as Endicott and Ho present, I think 42 Ka is way too late for exoafrican migration, and even if it is some the canopy variation issue has much less effect on early african variance. Ergo the Soares estimates for differences between MRCA (192.3) and L3 (71.6) delta = 120.7 and given Endicotts et al. minimum ages for archaeology one can be somewhat comfortable with dates above 150 Ka, however some of the studies done in the 1990s are still relevant today, and the conclusion of a couple of papers would argue if the CHLCA is between 7 and 10 million years, then the human MRCA is between 200,000 and 300,000 years, on paper in particular, Tamura and Nei is roughly immune to the Canopy issue, they argue that the TMRCA can fall between 80 and 480Ka. Nie basically said, if the CHCLA is 9 million years in age, then the MtMRCA can be 760,000 years in age. The top side variation is what I have the most concern about, not bottom side. Since it still appears understanding issues remain I am going to go ahead and add T&N to the table. Remember, NPOV.PB666 ^yap 14:44, 10 December 2009 (UTC)

I think it is correct that just counting the mutations does not work Muntuwandi. How many mutations have died out and left no trace? And more importantly, does the rate of dieing out stay constant over long epochs? No it does not.--Andrew Lancaster (talk) 12:13, 19 December 2009 (UTC)

Though methods for dating seem complex, it really comes down to counting mutations. For example, the article

• Henn; et al. (2009). "Characterizing the Time Dependency of Human Mitochondrial DNA Mutation Rate Estimates". {{cite journal}}: Cite journal requires |journal= (help); Explicit use of et al. in: |last= (help)

states

Phylogeny-based mutation rates are estimated by first constructing either a gene genealogy or a species phylogeny. In the latter case, one then calibrates the species split with external paleontological evidence. The number of mutations between two groups is subsequently computed, either by averaging the number of differences between species or by taking two sequences with the greatest number of differences. The number of mutations between two species lineages is then divided by the externally derived divergence date.

When dealing with large amounts of data, it may not be appropriate to call it "counting" but that is basically what it is. The Henn article has some useful information about mutation rates, and it does have some bearing on the dates for mitochondrial eve, but it is a general controversy that is related to human mitochondrial molecular clock and not specifically to the existence of a mitochondrial eve. Wapondaponda (talk) 08:07, 20 December 2009 (UTC)

You are headed off into an area you do not want to go into. Interspecies comparisons results in pairwise comparisons that are simply counted or rate classed. Almost all current studies rate class sites. Fast evolving sites saturate, for example in vigilant et al the CH pairwise difference estimated was close to 100%, that is why they counted 15 fold slower transversions. As some sites would have changed several times and some sites did not change. As two lines grow apart a collection of unstable mutations appear.PB666 ^yap

• Slightly deleterious mutations
• Adaptive mutations
• Rapidly evolving sites

Over a period of 500,000 years the slightly deleterious mutations are removed, the adaptive mutations will persist only if the selective force remains constant and more refined mutations do not appear. The rapidly evolving sites will saturate quickly meaning, in essence at any point as the lines diverge if you stop evolution the site will be in either state (all but randomly).

If one ignores the third set of sites, comparisons between species of 500,000 to roughly 20,000,000 years produce nearly linear correlation and minor corrections need to be applied past 10,000,000 years for saturation at slowly evolving sites. Therefore the molecular clock has the most trouble in the shorter time frames, under 100,000 years. The way rapidly evolving sites are handled is with parsimonious analysis, it works well when there are lots of branches, over deeper time depths large corrections need to be made and this increases variance. Reversions and homoplasies will be common in deep branches. The interspecies comparisons generate a stable SNP rate for most stable sites. This rate is useful at the base of a species tree, however as one moves toward the outer branches the rate needs to be increased, the so-called soft, of depth dependent mutation rate corrects for selection at some sites and saturation at others. However the method is not entirely objective.PB666 ^yap

Muntuwandi, there are two things, not one: counting mutations, and then also making assumptions about the rates at which lineages (carrying those mutations) have died out or come into being over time. If we were just to count mutations, and not to consider rates dieing out and coming into being for lineages, then I suppose an approach might be to treat every lineage as having undergone a random walk from Eve, as follows:

• look at every individual tested so far, and count mutations from proposed ancestral haplotype
• you will have a very wide range of mutation counts I think
• calculate implied age for all of these, and you will have a very wide range of age estimations I think

If you try it let me know what happens BTW. I think you will get an extremely wide range of estimates, but it will also be very strongly effected by what samples you have?--Andrew Lancaster (talk) 13:56, 28 December 2009 (UTC)

(Outdent)I believe the assumption of a constant molecular clock means that even lineages that have died out, would have statistically the same number of mutations with extant lineages, if they hadn't died out. IOW extinct lineages may only increase the variation in the number of mutations, but under the assumption of a constant molecular clock, they will not change the average number of mutations from the MRCA. If the sample size for existing lineages is large enough and diverse enough, then extinct lineages can be ignored, which might be the case for homo sapiens. As for lineages that come into being, every new mutation is potentially a new lineage. I have done some counting from http://phylotree.org. Though there is variation, for a few lineages I have counted so far, range from 39-65 mutations from Mitochondrial Eve. So we are still looking at an average of about 50 mutations on any given lineage from Mitochondrial Eve. The rho statistic is used to determine the average number of mutations from a sample of lineages. This rho is then multiplied by the substitution rate to determine the TMRCA. Wapondaponda (talk) 17:16, 28 December 2009 (UTC)

Yes, that is kind of what I was explaining. If you just take every individual line and ignore all others you can get a very wide range of estimations, right? This could at least give a min-max range. But (a) it might not be as big as it should be, if we consider that many consider that databases will tend to be a bit biased against the deepest rooting branches, not only overall but also within every clade, and (b) this still gives us not uncontroversial way of estimating a most likely age WITHIN that min-max range.--Andrew Lancaster (talk) 19:36, 28 December 2009 (UTC)

Simplification

I have done one partial version, that is significantly "dumbed down". It is by no means definitive, but I decided to have a go. If others have the time, you can have a whack at it as well. Did it in hurry as I have to disappear for a few days, so its a bit scrappy, but I'll take a look again when I get back. Wapondaponda (talk) 23:39, 10 December 2009 (UTC)

Yes I can tell, moved it here for now Talk:Mitochondrial_Eve/MW_Version.PB666 ^yap 00:50, 11 December 2009 (UTC)

I see no reason to "dumb down" this or any other article, and I have great difficulty in figuring out just what it is Muntuwandi is trying to achieve (not for the first time, either). --dab (𒁳) 22:56, 11 December 2009 (UTC)

"Dumbed down" is not literal. The article simply doesn't need excess complexity to explain the concept of mtEve. PB666 has exaggerated the problems of dating, and has made the article about mtEve largely about dating the problems associated. Wapondaponda (talk) 18:21, 18 December 2009 (UTC)

dab, I wrote most of the 'technical' version, it does need to be simplified, I am currently going over what MW wrote to see if there are any good ideas.PB666 ^yap 15:45, 13 December 2009 (UTC)

In addressing several complaints about the state of the Article on December 1.

• Female and mitochondrial ancestry
• Estimating time to MRCA

• Time estimates based on archaeological methods
• Time estimates based on chimpanzee-human last common ancestor
• Estimated times of major mtDNA branchpoints
• Inter-comparing rates and studies

• Early modern human population structure

• Solitary female Eve as a misconception
• Proposals of a flat population structure
• Proposals for a population bottleneck

• Implications of dating and placement of Eve

• Geographic and Temporal constraints of early modern humans
• Mitochondrial MRCA and the MRCA of all humans

• In popular science and culture
• See also
• Footnotes
• References
• External links

There were 46 sections, there are now 18.

The article was at its largest about 95 kb, it is now about 60 kb. And there are still some reductions to be had in the Female and mitochondrial ancestry section. Although I think 60 Kb for an article of this importance is appropriate and reduction of material is no longer a concern.

The reference section has been converted to citation style with full author representation. Removal of redundant referecnes in the text or reference section.PB666 ^yap 06:19, 15 December 2009 (UTC)

a bold proposal

Here is a bold proposal. Section 3.1 can be moved to section 4, and the rest of sections 3 and 4 can be deleted. Maybe there are a couple of sentences worth saving. What do others think?--Andrew Lancaster (talk) 19:44, 28 December 2009 (UTC)

I would support that, but I would suggest going further and deleting much of section 2 as well. The material in section 2 is already covered in human mitochondrial molecular clock. Wapondaponda (talk) 21:37, 28 December 2009 (UTC)

Support. Delete all of sections 2, 3 & 4 except 3.1. --Michael C. Price ^talk 06:24, 29 December 2009 (UTC)

I can agree with that about section 2 also. Is there anything else in these sections needing saving in summarized form? Perhaps links need to at least be carefully placed in order to make sure people can get to more specialized articles?--Andrew Lancaster (talk) 11:24, 29 December 2009 (UTC)

new source

http://www.plosone.org/article/info:doi/10.1371/journal.pone.0008260 --Andrew Lancaster (talk) 21:28, 29 December 2009 (UTC)

The dates for mtEve from this study is 186kya. The dating is quite consistent, around 200kya for most studies. To avoid information overload, I suggest including information from only the most recent studies in this article. I have chosen 2007 as a cutoff date for the studies. Wapondaponda (talk) 17:13, 30 December 2009 (UTC)

I am not sure a strict cut off is what is called for.--Andrew Lancaster (talk) 21:05, 30 December 2009 (UTC)

I agree - no cut off is required. --Michael C. Price ^talk 21:52, 30 December 2009 (UTC)

It would be great to have all the information, but since there is quite a lot of information, just as a practical matter to make editing and reading easier, it might be a good idea to not use all the information. For example we had Kivisild et al. 2006 publishing a date of 160kya, and then Kivislid is a co-author in the above study(Loogvali et al. 2009), which is said to be more accurate, publishing a date of 186kya. Would it therefore be necessary to include an older study by the same author. Another problem, is the excessive amount of formatting in the article. Wapondaponda (talk) 04:25, 31 December 2009 (UTC)

Does an author putting his name to 2 different estimations necessarily mean that he favors which ever is newest? I think in an uncertain field like this it does not necessarily mean so?--Andrew Lancaster (talk) 11:11, 31 December 2009 (UTC)

Newest is not always best, but I think some of the recent studies are quite comprehensive. Furthermore the newest studies have used the most updated phylogenetic trees which includes newly discovered lineages and previously undiscovered mutations. The study Loogvali et al. 2009 cites Kivisild 2006 extensively, so they have taken into account many of the previous studies. There are a studies throughout the 1990s and now the last decade, that all have published dates for the TMRCA. Whats great about this field is that published dates for TMRCA over the last 30 years have not varied much, such that quoting a just few studies doesn't result in the loss of a lot of information . Much of the controversy isn't so much about Mitochondrial Eve, but about lineages that arose after mtEve, and more specifically lineages that arose during and after the OOA migration. I believe the controversial subjects that could really benefit from an accurate molecular clock are

• Dating the OOA migration by determing the coalescence of haplogroups L3, M and N.
• Dating the settlement of Australasia, which should correspond with the OOA
• Dating the settlement of the Americas

In short all these studies may have some useful information, but I don't see much value from citing Ingman et al. 2001, or Tamura and Nei 1993, we are in 2010 now and we have numerous studies from 2007-2010. Wapondaponda (talk) 16:21, 1 January 2010 (UTC)

misconceptions need more discussion

I believe in earlier versions of this article several common misconceptions were discussed in a whole section. To me it seems a good idea. Apart form the one already specifically mentioned, I can think of several potential confusions, some of which are touched upon in a passing way...

• That Mitochondrial Eve must be contemporary with Y DNA Adam
• That Mitochondrial Eve is the MRCA of all humans (along all lines of descent)
• That Mitchondrial Eve is somehow a fixed concept signifying something to do with the start of humanity (as opposed to just a formal concept which can be embodied by different people depending upon what happens in modern populations)

Do others agree with me on this?--Andrew Lancaster (talk) 14:30, 30 December 2009 (UTC)

I agree, we can simply restore the old information and clean it up. The misconceptions arise because of the biblical analogy of "Eve". It should be clarified that the biblical analogy is not strict. Wapondaponda (talk) 17:13, 30 December 2009 (UTC)

I do not think all the misconceptions arise from Biblical confusion -- but I agree we should put them all in one section. --Michael C. Price ^talk 21:57, 30 December 2009 (UTC)