What does the genetic evidence say?

29 Jul

A summary of the main points relating to the use of mitochondrial (and nuclear) DNA that I found very useful is given here in this link: http://www.digplanet.com/wiki/Mitochondrial_Eve. I will quote the relevant sections here for consideration: ‘By analysing descendants’ DNA, parts of ancestral genomes are estimated by scientists. The variation of mitochondrial DNA between different people can be used to estimate the time back to a common ancestor, such as Mitochondrial Eve. This works because, along any particular line of descent, mitochondrial DNA accumulates mutations at the rate of approximately one every 3,500 years. A certain number of these new variants will survive into modern times and be identifiable as distinct lineages. At the same time some branches, including even very old ones, co me to an end, when the last family in a distinct branch has no daughters.

Mitochondrial Eve is the most recent common matrilineal ancestor for all modern humans. Whenever one of the two most ancient branch lines dies out, the most recent common ancestor (MRCA) will move to a more recent female ancestor, always the most recent mother to have more than one daughter with living maternal line descendants alive today. The number of mutations that can be found distinguishing modern people is determined by two criteria: firstly and most obviously, the time back to her, but secondly and less obviously by the varying rates at which new branches have come into existence and old branches have become extinct. By looking at the number of mutations which have been accumulated in different branches of this family tree, and looking at which geographical regions have the widest range of least related branches, the region where Eve lived can be proposed.

The date when Mitochondrial Eve lived is estimated by determining the MRCA of a sample of mtDNA lineages. In 1980, Brown first proposed that modern humans possessed a mitochondrial common ancestor that may have lived as recently as 180,000 years ago. In 1987, Cann et al. suggested that mitochondrial Eve may have lived between 140-280 thousand years ago.’

My comments on the implications of the Eve hypothesis: The Eve hypothesis, which rules out all forms of multiregional hypotheses that date all current humanity to a common ancestral population of around 2 million years ago (thus excluding the suggestion of this blog that Han Chinese in particular descended from the East Asian Homo erectus that migrated there from Africa 1.5 million years ago), needs to be discussed in light of the following concerns that I have:

(1) We need to examine how it was determined that mtDNA only accumulates mutations at the rate of 1 every 3,500 years, so that the methodology needs to be analysed on the basis of this assumption upon which the rest of the calculations are made. Jokodo response: ”http://www.sciencedirect.com/science/article/pii/S0002929709001633 – short answer, they use colonisation events which can be dated from the archeological record, as well interspecific differences, as an anchor.”

(2) We need to know that the methodology ensures that the sample size for analysis represents the relevant global human populations.

(3) How do we know what branches emerged and became extinct in the past 1.5 million years to work out the ‘rates at which new branches have come into existence and old branches have become extinct’?

(4) We need an answer for why two different estimates of mitochondrial Eve were obtained by Brown and Cann et al, and why the latter generated a big range. I have modified this sentence on Jokodo’s response that they are both providing broadly the same estimate, which are ‘an order of magnitude off from what we need‘. This is strange because of Jokodo’s response of the empirical fact being that ‘genetic evidence strongly indicates that modern humans have emerged largely or entirely from a single ancestral population no longer than 100,000 years ago‘. This is between half to a third of figures that I cited above and Jokodo has not made any attempt to reconcile his figure with these estimates of an earlier divergence point. He merely queries my 1.5 million years ago figure.

(5) We need an answer for why the mitochondrial Eve results do not tally with the patrilineal ancestor as determined to be the Y-chormosomal Adam. Jokodo responds: ‘They’re not expected to align with each other. Why should they?’ I would like to ask him back: how could an Adam population have lived at a different time to an Eve population to be able to generate the humanity we see today?

In summary, is it not the case that in reality there is continuous divergent and convergent mutations that take place over long periods of time even in mtDNA thus giving such variable estimates and an unrepresentative picture of the total dispersal and extinction of humankind worldwide over 1.5 million years? Do not ‘colonisation events based on archaelogical’ and ‘interspecific differences’ alluded to by Jokodo constrict the time period over which humans existed in a biased way? If mutations in mitochondrial DNA cannot be predicted with the degree of certainty assumed by the researchers cited, can the conclusions of Eve-hypothesis that nothing now remains in humankind of human populations that preceded the species that is to be regarded as the Eve-generation worldwide, still be regarded as reliable?

What I find also of interest in the debate is that humans share as much as 95% or more of the DNA-sequence with its nearest evolutionary relative, the chimpanzees: http://www.ncbi.nlm.nih.gov/pubmed/12368483?dopt=Abstract. That leaves at most only 5 per cent of DNA-variation to account for all the phenotypic differences that is apparent between these two species of primates: so much gene-based differences contained in so little actual DNA does not seem plausible to me. Jokodo responds: ‘on what are you basing this? How did you quantify the differences?’ My reply: observations of the biological capacities of chimpanzees and humans. Humans are not a 5 per cent more improved species than chimpanzees but about 25 per cent more improved, would not Jokodo agree?

Finally, and as discussed earlier, whilst the real science should be based on an examination of the origins of actual genes in the human DNA (believed to range between 20,000 – 25,000) I am also not convinced that such an analysis will also yield direct modelling evidence of the origins of all current humans in terms of the first Homo ancestor, although it will establish real differences between populations across the world that science should endeavour to analyse. How can such studies inform us whether the Homo erectus of East Asia from 1.5 million years ago left any descendents that we can see today especially in China? If there were rates at which genes develop it might have some merit, but the reality is that there is no predicting the rates at which mutations take place in the genome and within genes. We therefore do not know how different genes develop through the apparently random process of DNA-mutations over time.

Jokodo’s conclusion: ‘It’s entirely conceivable (though very unlikely) that the argumentation for interpreting the data as evidence for a recent common origin is flawed, but you’re not giving us any reason to believe that this is so.’ Jokodo has not stated why he thinks it is very unlikely, has he?

Edited: 09.18 am, 31 July 2012 to incorporate Jokodo’s comments.

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22 Responses to “What does the genetic evidence say?”

  1. Jokodo July 31, 2012 at 9:08 am #

    “This is between half to a third of figures cited above and Jokodo has not made any attempt to reconcile his figures with these larger estimates.” What? “Mitochondrial Eve” is the most recent woman who was ancestor to all living humans through an uninterrupted maternal line. It does *not* indicate the last time when human ancestors formed one population, nor even the most recent common ancestor of all humans through any line – if anything, it provides a *very* generous upper bound to those. You can only expect the times of mitochondrial Eve and dispersal to coincide if you assume that, in the generation when humans started to disperse, all women alive were the daughters of one and the same mother. Sure you realise how unrealistic an assumption *that* is?

    “I would like to ask him back: how could an Adam population have lived at a different time to an Eve population to be able to generate the humanity we see today?” – What does this mean? Neither “mitochondrial Eve” nor “Y-chromosomal Adam” were the only woman/man alive at their times, nor even the only woman/man to leave descendants. They were the only humans alive at their respective times to leave descendents _through_a_female/male_only_line_ of intermediates. “Adam’s” contemporaries can have had as many daughters as you like, or they could have had sons or grandsons who in turn only had daughters, but because the Y-chromosome is passed on from male to male only, their variant of the chromosome went extinct.

    “My reply: observations of the biological capacities of chimpanzees and humans. Humans are not a 5 per cent more improved species than chimpanzees but about 25 per cent more improved, would not Jokodo agree?” – best as I can tell, this is a meaningless statement, so no, I don’t agree. I don’t even know what “more improved” means in the context, and how to determine whether chimpanzees are improved relative to humans or the other way around. We’re looking at genetic differences. Genes code for proteins. The biochemistry of humans and chimpanzees is very much the same. Human and chimp muscle tissue, or blood, or hair, is very much the same. Genes that influence *development* can have huge effects despite being a small part of the genome, but even restricting ourselves to these I don’t see how “humans are […] about 25 per cent more improved”, or what that would even mean.

    • shantanup July 31, 2012 at 9:27 am #

      Are you saying that the Mitochondrial Eve human population of say 200,000 years ago was dispersed worldwide (excluding the Americas and Australia) but including East Asia where it existed as the ancestors of who are now Han Chinese? – or was it located located entirely in East/North Africa comprising a few thousand people?

      • Jokodo July 31, 2012 at 9:49 am #

        Trying to parse your question, the timeframe in which “mitochondrial Eve” lived alone doesn’t tell us much – from those data alone, we could conclude that either all extant humans are derived from one population, or from different populations already dispersed over several continents but with high levels of gene flow between them such that one variant of the mitochondrial genome could have replaced all others despite the distances involved (what it is incompatible with, though, is the notion that the “Han Chinese” are more or less pure descendents of Asian homo erectus). Two decide between these two options, we need to take a closer look at the *patterns* of variation, both in mitochondrial and nuclear genomes. What we then find is that within-population variation gets smaller the further you move away from Africa, which is best explained through the founder effect – showing that non-African humans derive from a recent colonisation event.

        If that wasn’t your question, you may have to rephrase it. It’s not my job to try and make sense out of barely comprehensible remarks.

  2. shantanup July 31, 2012 at 9:57 am #

    Do you accept that there was a thriving unbroken lineage of human population in China between 100,000 and 500,000 years ago?

    • Jokodo July 31, 2012 at 11:21 am #

      What if? How’s this relevant? It doesn’t even bear on the genetic evidence showing that today’s population in China is descended largely or entirely from African ancestors.

      • shantanup July 31, 2012 at 11:33 am #

        If there was, does it not mean that the mitochondrial Eve population was present in large numbers in China and remained static genetically from 500,000 years ago to 100,000 years ago (your personal date of common origin dispersal) or 200,000 years ago as the corresponding date of the other researchers whose work I have cited above?

  3. Jokodo July 31, 2012 at 9:00 pm #

    No, it doesn’t mean that. Why should it, except by a leap of logic? Make your implicit assumptions explicit, and you’ll probably start to see yourself that they’re unreasonable.

    • shantanup July 31, 2012 at 9:25 pm #

      You had two options to choose from:
      (a) the mitochondrial Eve population with some fixed element in its mtDNA-constitution that researchers have traced maternally (through females only) came out of Ethiopia, Kenya or Tanzania, 100,000 years ago according to your model or around 210,000 according to the model of the other two workers cited earlier and spread to Asia only around 65,000-70,000 as Homo sapiens; or
      (b) the mitochondrial Eve population, as set out in (a), was already living in China 100,000/210,000 years ago.

      You seemed to have chosen the latter (b) option (correct me if I am wrong). If this is the case, how would you distinguish between the Chinese mitochondrial Eve population of 100,000/210,000 years ago from the lineages of the human population that we have fossils in China dating back to 500,000 years ago and earlier?

      • Jokodo August 1, 2012 at 9:21 am #

        False premise one: There’s no such thing as a “mitochondrial Eve population”. The concept of “mitochondrial Eve” refers to an individual. From the estimated *age* of mitochondrial Eve alone, the only thing we can conclude is that *if* archaic populations on different continents contributed to today’s humanity, there must have been extensive interbreeding in prehistoric times, so much so that one variant could entirely replace all others. We cannot, from these data alone, conclude *whether* archaic populations on continents other than Africa contributed at all, and I did not state so. What does give us a better idea is the global patterns of variation: For example, if we find (as we do) that variants that are exclusive to non-African populations are younger than ~70,000 years while as concerns older mutations, the variation in non-African populations is a proper subset of the variation found in Africa, we can conclude that mitochondrial Eve lived in Africa and that her version of the mitochondrial genome only started to spread to other continents less than 100,000 years ago.

        False premise two: There is no conflict between the ~200,000 years figure for mitochondrial Eve and the <100,000 years figure for modern human dispersal out of Africa, since there is no reason to assume that the parent population of the colonisers was entirely homogeneous.

        Mitochondrial data alone may not show that Asian homo erectus went extinct. What they do show is that Asian homo erectus has not contributed any living human's mitochondrial DNA. This can in principle be explained in two ways: (1) the African variant of mitochondrial DNA has come to dominate all populations in a selective sweep during the last <100,000 years despite low levels of intercontinental gene flow (you still need *some*), or (2) modern humans globally are derived largely or entirely from an African population of <100,000 years ago. (1) seems implausible since mitochondria are functionally very conserved (i.e., our mitochondria work very much exactly the same as those of a flatworm), thus selection has largely a conservative function here; if you do find any evidence that modern human mitochondria are significantly improved relative to our closest relatives, that would be a Nobel-prize worthy discovery because of how surprising and revolutionary it would be, and it's definitely not something you can assume for convenience; the only way I see you could save hypothesis (1) is by modifying it: (1b) in the Asian homo erectus population, a deleterous mutation had reached fixation, and upon contact the African variant swept the population not because it was superior to the ancestral version but merely because it was unaffected by the deleterous mutation; but in order for a deleterous mutation to reach fixation, what is needed is extreme inbreeding, with expected deleterous consequences not only for the mitochondrial but even more so the nuclear genome. If that's so, African mt-DNA wouldn't be the only thing to conquer the Asian population in a selective sweep, but so would nuclear DNA – in effect, we're thus back to (a weak version of) (2): Despite interbreeding, modern Asians are largely derived from Africans of <100,000 years ago.

  4. shantanup August 1, 2012 at 10:14 am #

    First, my term ‘mitochondrial Eve population’ refers to the entire population of humans in the world at this date of Eve that is established as 200,000 years ago. You have not spelt out whether you think that any of that population lived in East Asia (China) at that time. Why?

    Secondly, mitochondrial DNA is also subject to mutational variation and is not as ‘conserved’ as you have written. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1762815/

    Thirdly, you indicate that the ‘founder effect’ is crucial to the alternative ‘Recent Out of Afica’ hypothesis. As I understand you you are saying that the African continent has more DNA sequence-variation per unit of the population than there is in China and elsewhere, so that the Chinese population and other populations must have migrated from Africa. This theory is also based on mtDNA analyses rather than nuclear DNA analysis, can you confirm? And why are you not showing us what this founder effect tells us about when the migration started to take place?

    • Jokodo August 1, 2012 at 10:45 am #

      “First, my term ‘mitochondrial Eve population’ refers to the entire population of humans in the world at this date of Eve that is established as 200,000 years ago. ” – That’s a useless concept then. That there were humans in other places at any given time does not imply that they’re also the ancestors of anyone alive today, much less that they’re more or less the sole, or at least the primary, ancestors of entire modern populations.

      “You have not spelt out whether you think that any of that population lived in East Asia (China) at that time. Why?” – What is this question supposed to mean? Did members of the genus homo live in East Asia 200k years ago? Yeah, sure. Whoever said otherwise? The relevant question you have to ask is rather this: Is there any evidence that modern East Asians are largely or entirely derived from archaic Asian populations? And the answer to *that* question is a clear “no”.

      “Secondly, mitochondrial DNA is also subject to mutational variation and is not as ‘conserved’ as you have written. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1762815/” – Learn to read, for goodness’ sake! Selection playing a conservative role does not imply there is no mutational variation. If anything the opposite – without mutational variation, there wouldn’t be any selection whatsoever, conservative or otherwise. It only implies that mutations that don’t produce a functionally equivalent outcome will be selected against. Human mitochondria work the same way mitochondria in chimpanzees work, or those in our last common ancestor with chimpanzees worked, or those in the LCA with sharks, for that matter – they have a limited function which they fulfill perfectly, as nearly as as is possible within the constraints given by the overall architecture of the cell (barring deleterous mutations that are selected against and thus will only ever reach fixation in tiny populations). Do mutations occur? Of course, even at higher rates than in nuclear DNA. Do novel mutations reach fixation? Of course, otherwise mtDNA would be useless as a genetic clock. Do those novel variants bestow their carriers with novel *functions*, giving them a selective advantage? Extremely unlikely, and therefore a selective sweep is an extremely unlikely explanation for the recent date of “mitochondrial Eve”.

      ” This theory is also based on mtDNA analyses rather than nuclear DNA analysis, can you confirm? ” – It was first observed with mtDNA as as far as I know, but it was reconfirmed with nuclear DNA.

      I’m out of here. You need to do some reading and come back with *relevant* questions, and try to stop putting things in people’s mouths.

      • shantanup August 1, 2012 at 10:49 am #

        Is this a promise now that we will not have to any longer put up with more of your rubbish in this blogsite?

  5. Jokodo August 1, 2012 at 12:38 pm #

    It’s more than anything else a promise to myself that I’ll stop wasting my time with you as long as your resistence to learning, and your habit of ignoring everything that has been said while not bothering to do any reading yourself, isn’t wearing off.

    • Jokodo August 1, 2012 at 12:43 pm #

      Also, remember the last time you started to call my contributions “rubbish” because you were unable to answer them? A day or so later, you came back begging me to continue. Make your mind up, will you?

      • shantanup August 1, 2012 at 1:15 pm #

        Since you did not reply to my post of 10.49 am immediately, I knew I had to put in a new post to summarise my view. I do not suppress truth, so despite the critical content I have approved all your three posts again. I practice a religion known as satya-advaita as a truth-seeker who strives oneness with truth. I leave the readers to judge each one of our comments and my posts in the way that will serve humanity best.

  6. Jokodo August 1, 2012 at 1:23 pm #

    Are you fucking serious? “Since I did not reply to your post of 10.49 am immediately …” – you think you have a god-given right to receive immediate replies to everything you write on this post? I don’t know about you, but I have other things to do. If you want me to be your private lecturer, available at all times, we’re going to have to talk about my salary.

    Also, your post of 10.49 am was content-free. You’re the one who still hasn’t addressed the content of my post of 10.45, which I spent considerable time writing. If and when you’ve addressed that, I may find it worthwhile to engage you more. If you keep ignoring everything that has been said, thanks but no thanks.

    • shantanup August 1, 2012 at 1:35 pm #

      I am very serious: when you wrote ‘I am out of here’, it meant to me that you had stopped commenting in my blog, which you should have confirmed but you wanted to keep open your option to post further comments as it suited your objectives, as events clearly show.

      • Jokodo August 1, 2012 at 1:55 pm #

        “My objectives”? Pray tell me what my objectives are. I’m trying to help you make a coherent argument by showing where the “arguments” presented so far break down. Obviously you’re not even reading my posts, so I’m inclined to give up unless you start to actually address objections.

  7. shantanup August 1, 2012 at 2:17 pm #

    Your objectives are between you and your conscience.

    • Jokodo August 1, 2012 at 2:45 pm #

      Instead of trying to be witty, could you formulate your claims in a way that amounts to more than “but, my gut feeling”, and/or address objections?

      That would be so nice.

      • shantanup August 1, 2012 at 3:19 pm #

        Why, have you not been finding this blog ‘revelatory’ enough so far the way it has been progressing?

  8. Jokodo August 1, 2012 at 3:43 pm #

    Revelatory? No. We’re at 17 posts and you haven’t made an argument for your core claim yet. Instructive maybe since I had to look up a few points – but really you should have been the one to do so before posting.

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