Y-chromosome “Adam” was not necessarily human

phylogeny2This post is by Joe Pickrell

Metaphors in science play an important role in communicating results from one field to scientists in other fields and to the general public. In some cases, however, metaphors are so successful and so appealing that they actually obscure rather than enlighten.

In human population genetics, it is a simple fact that all of the Y chromosomes present in the world today can be traced back to a single common ancestor–if you follow my paternal line (my father’s father’s father’s father, and so on) and your paternal line back far enough, eventually they will overlap. At some point, a population geneticist had the clever idea of calling this common ancestor “Adam”. This is a biblical allusion, of course, and it probably was good for a bit of amusement a couple of decades ago. But it’s time to retire this metaphor–not only because it confuses the public (see a nice series of posts by Melissa Wilson Sayres on this topic here) or scientists in other fields–but because it confuses even practicing human population geneticists!

I was reminded of this when reading over a paper by Eran Elhaik, Dan Graur, and colleagues critiquing work on the human Y chromosome phylogeny by Mendez et al. The basic question being debated is: when did the most recent common ancestor (MRCA) of all Y chromosomes exist? Mendez et al. claimed that this Y chromosome was present around 300,000 years ago, and Elhaik et al. claim they arrived at this number incorrectly.

The details of these papers are not relevant for this post. The key thing I want to point out is an underlying assumption, perhaps most clearly expressed by Elhaik et al., who write:

[Mendez et al.] estimated the time to the most recent common ancestor (TMRCA) for the Y tree to be 338,000 years ago (95% CI=237,000–581,000). Such an extraordinarily early estimate contradicts all previous estimates in the literature and is over a 100,000 years older than the earliest fossils of anatomically modern humans. This estimate raises two astonishing possibilities

The implicit assumption here (the reason Elhaik et al. find the numbers “extraordinarily early” and “astonishing”) is that the individual carrying the most recent common ancestor of all human Y chromosomes (AKA “Adam”) should be an anatomically modern human. Amusingly, Elhaik et al. argue that to claim otherwise is analogous to claiming you have a unicorn in your backyard. But there is simply no reason that “Adam” must be a human. At the top of this post I’ve put a figure showing a hypothetical Y-chromosome genealogy superimposed on a hypothetical human phylogeny. In this (of course hypothetical) example, “Adam” existed well before the diversification of modern humans; this type of scenario is perfectly compatible with basic population genetic theory. From the point of view of population genetics, there is absolutely no reason that the common ancestor of all human Y chromosomes must have existed in an individual that we would identify as “human”.

So why would anyone make this assumption? Note that Elhaik et al. made a YouTube video describing their results; this video leads with a bit of religious iconography. It seems plausible that by calling the most recent common ancestor of all Y chromosomes “Adam”, population geneticists have confused themselves into thinking that “he” must have been human.

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30 comments

  1. Indeed, though of course this all depends on what you call human. Defining it as you are here (i.e. equivalent to ‘modern human’) then hardly any genetic loci have a ‘human’ common ancestor. Actually, thanks to a small number of loci under long-term balancing selection, not even all our common ancestors are _hominins_ (i.e. postdating the split from chimpanzees)..

  2. Joe, I am sorry to say that you are beating around the bush. The most prestigious journal in your field published the Mendez et al. paper and its implications were discussed all over the media 9 months back. I have not seen any argument from you challenging its claims or basic premise. Now that Dan Graur and colleagues came out to debunk their theory, you post this ‘know it all’ blog post to explain it all.

    Let us get a straight and honest answer –

    “From the point of view of population genetics, there is absolutely no reason that the common ancestor of all human Y chromosomes must have existed in an individual that we would identify as “human”.”

    Are you implying that Hammer, the leading researcher in your field, is clueless about what he is doing, and the most prestigious journal publishes garbage?

    1. Thanks for the response.

      Are you implying that Hammer, the leading researcher in your field, is clueless about what he is doing, and the most prestigious journal publishes garbage?

      No.

  3. Love the thinking. But considering that modern Africans are rather homogenous linguistically compared to “eastern non-Africans” (Amerindians, Papua New Guineans and some Asians) and language is a key sign of behavioral modernity, our “non-human Adam” is likely a “product” of admixture from extinct African archaics into modern humans that happened after modern humans colonized Africa.

  4. When Michael F. Hammer published an article in which it is stated “Sex with Other Human Species Might Have Been Secret of Homo sapiens’s Success” and “DNA analyses find that early Homo sapiens mated with other human species and hint that such interbreeding played a key role in the triumph of our kind” (http://www.scientificamerican.com/article/sex-with-other-human-species-might-have-been-secret-homo-sapiens/) Dr. Joe Pickrell had nothing to say.
    Now, that we published a rebuttal, he screams! Unfortunately, his screams have the unmistakable odor of hypocrisy and brown nosing.
    Dear Dr. Pickerel, as the head of a statistics and genomics lab, how would you characterize Hammer’s article that was the subject of our rebuttal?
    Dan Graur

    1. Hi Dan,

      Thanks for reading. I would summarize the Mendez et al. article as follows:

      Mendez et al., in collaboration with members of the public and the FamilyTreeDNA company, have identified a novel Y haplotype that pushes back the estimate of the Y-specific TMRCA further than previous studies.

      (I hope you agree with this characterization; it’s a direct quote from your paper)

      1. Joe
        You should go into politics. You seem to be extremely good at not answering questions you do not wish to answer.
        So, let me ask you this time directly.
        How would you characterize Hammer’s article in Scientific American? In particular, what would be your characterization of the two sentences: (1)
        Sex with other human species might have been secret of Homo sapiens’s Success,” and “DNA analyses find that early Homo sapiens mated with other human species and hint that such interbreeding played a key role in the triumph of our kind.” Please note, that these are Hammer’s interpretations of his own article.
        Dan Graur

      2. Hi Dan,

        Thanks for clarifying (and for the reference to the SciAm article). I guess there are three questions you’re interested in:

        1. Did human and other hominids interbreed?

        Yes. At least two hominid groups–Neandertals and Denisovans–contributed to the genetics of humans living today. See Prufer et al. and references therein for details.

        2. Is the Y chromosome identified by Mendez et al. strong evidence of a third hominid group that contributed to the genetics humans today?

        No. The genealogy at a single locus is difficult to interpret, for the reasons I mention in this post. As Mendez et al. write, “the stochastic nature of the genealogical process can affect inference from a single locus and warrants caution during interpretation”.

        3. Did interbreeding with hominid groups play an important role in human adaptation to new environments?

        Unclear. There are reports that modern humans picked up adaptive alleles from mixture with Neandertals and Denisovans. See, for example, Abi-Rached et al., and the references in the SciAm article you linked. There are multiple interpretations of the evidence in these papers, so work is ongoing.

        Hope this helps.

        Best,

        Joe

      3. Here’s the text regarding archaic admixture from Mendez et al:

        ‘Although the stochastic nature of the evolutionary process can explain the aforementioned incongruences, the extreme age and rarity of the A00 lineage point to the possibility of a highly structured ancestral population, consistent with recent work on the autosomes. This could take the form of long-standing population structure among AMH populations or archaic introgression from an archaic form into the ancestors of AMHs.’

        No claims of strong evidence. Personally, while I don’t think it unlikely a priori that such introgression could have occurred, the genealogy at a single locus is actually very weak evidence for any particular demographic event, so I wouldn’t regard this as more than speculation. Nothing wrong with a bit of speculation between consenting adults.

      4. No claims of strong evidence. Personally, while I don’t think it unlikely a priori that such introgression could have occurred, the genealogy at a single locus is actually very weak evidence for any particular demographic event, so I wouldn’t regard this as more than speculation. Nothing wrong with a bit of speculation between consenting adults.

        I completely agree with this.

  5. @Joe

    “No. The genealogy at a single locus is difficult to interpret, for the reasons I mention in this post. As Mendez et al. write, “the stochastic nature of the genealogical process can affect inference from a single locus and warrants caution during interpretation”.

    If I may interject with a question: since the “genealogical process” “stochastic,” how do we know if Y-DNA A00, A and B (all the African-specific lineages) were not absorbed from an African archaic hominin by the incoming modern humans who carried hg E, which is a subset of non-African CDEF clade?

  6. Kate Wong here, from Scientific American. Regarding Dan Graur’s comment about Michael Hammer’s article in Scientific American, the lines in question are the title and subtitle of a popular article. The editors at Scientific American write the titles and subtitles for a general audience. They are necessarily more provocative than what one finds in technical papers, but they are supported by the content of the story itself. And the evidence for interbreeding–and the benefits it extended to anatomically modern humans–is mounting, as we’ve seen most recently in two papers published this week in Nature and Science:

    http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12961.html

    http://www.sciencemag.org/content/early/2014/01/28/science.1245938

  7. Or thinking that “he” was anything more than the most recent common male body hosting the MRCA of modern NRYs. Great post!

  8. If the individual, Albert Perry, has this ancient y-chromosome isn’t there a strong possibility that other equally ancient alleles could be present in a small fraction of his genome? What lab is doing the full genome with thorough coverage?

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