Friday, September 30, 2016

Y-chromosome Adam

Two statements by Jerry Coyne, back-to-back:

...genes on the Y chromosome trace back to one male who lived about 60,000-90,000 years ago 
Since sequencing of human genomes became possible on a large scale, we can back-calculate from the observed genetic diversity in our species to find out roughly when different forms of human genes diverged from one another, and how many forms of a given gene existed at a given time…We can, for example, trace all the Y chromosomes of existing males back to a single man who lived between 120,000 and 340,000 years ago. This individual is often called "Y-chromosome Adam"…all the Y chromosomes of modern humans descend from this one individual… J. Coyne, Faith Versus Fact (Viking, 2015), 127.

i) I find it striking that even though he's talking about the very same thing in both cases, the upper estimate in the first quote is 30K years below the lower estimate in the second quote. In the first quote there's a 30K spread. In the second quote, there's a 220K spread. So where are these figures coming from?

ii) In addition, there were, presumably, thousands of other human males (or protohumans) contemporaneous with Y-chromosome Adam. Just as he had descendants, many or most of them had descendants. Given the extent of human interbreeding, how could all modern humans derive their Y chromosomes exclusively from a single common ancestor? Surely Coyne doesn't think all the descendants of Y-chromosome Adam's contemporaries died out. I don't see how the argument goes through even on his own assumptions. 

iii) There's the additional question of whether human males would even be male without the Y chromosome. Perhaps, though, the precise function of the Y chromosome is in dispute.


  1. 1. My best guess about Coyne's widely divergent figures is the different scientists who are doing different studies are using different genetic parameters. For example, take mutation rates. A study has to assume some kind of mutation rate (e.g. low or high, variable or constant). If one study assumes a different mutation rate than another study, then that could significantly change the results. Different input, different output (potentially).

    I think there's a more fundamental problem with mutation rates though: how are mutation rates calibrated in the first place? It's not as if there's a universal mutation rate by which to compare all other mutation rates, is there? As far as I can tell, it's relative. There are better and worse arguments for assuming this or that mutation rate, but ultimately it all seems quite debatable from what I gather.

    As such, why couldn't, say, a YEC assume variable mutation rates in order to come up with a Y chromosome Adam around, say, 10,000 years old?

    Of course, mutation rates is just one parameter among several others.

    2. I suppose it's always possible Coyne's huge discrepancies are simply because he changed his mind between 2011 and 2015 due to more recent or persuasive research in his mind.

    If so, I assume the main reason he'd give is the typical rigmarole about scientific figures always being open to revision, "self-correcting" science, and so on.

    Of course, if this is his reply, then it'd apply to his most recent figures too. He can't say Y chromosome Adam is 340k years old (or whatever). At best, such figures are always provisional figures.

    3. It looks like Coyne has this citation in his book: "Y chromosome data from Francalacci et al. 2013; Poznik et al. 2013; Mendez et al. 2013".

    I looked up each of these three papers:
    * Francalacci estimates Y chromosome Adam to be 180-200k years ago based on a population of 1,204 men in Sardinia.
    * Poznik estimates Y chromosome Adam to be 120-156k years ago based on 69 men in Africa.
    * Mendez estimates Y chromosome Adam to be 338k years ago based on a single African American men from South Carolina (presumably this is Albert Perry).

    A couple of interesting takeaways, at least based on the abstract (I didn't read beyond the abstracts):

    a. Some evolutionists argue Y chromosome Adam and Mitochondrial Eve couldn't have lived at the same time with one another. However, in two of the very studies Coyne cites, it looks like there's significant overlap between the dates for Y chromosome Adam and Mitochondrial Eve. So, even on evolutionary grounds, it seems possible argue for a biblical Adam and Eve. (I presume this is what many theistic evolutionists would do.)

    b. The Mendez study notes its conclusions are tentative: "This underscores how the stochastic nature of the genealogical process can affect inference from a single locus and warrants caution during the interpretation of the geographic location of divergent branches of the Y chromosome phylogenetic tree for the elucidation of human origins".

    This is a much weaker claim than Coyne's stronger claim about Y chromosome Adam in his book.

    Although Coyne doesn't exactly strike me as the type of person who is ever faulted for a lack of confidence in anything he says. Right or wrong, but never unsure! :-)

  2. "There's the additional question of whether human males would even be male without the Y chromosome. Perhaps, though, the precise function of the Y chromosome is in dispute."

    It's true we wouldn't be male humans without a Y chromosome. Not in the way we now know anyway. Unless for example another chromosome somehow took over the Y chromosome's functions, etc.

    Genetically speaking, males aren't solely our Y chromosomes, but we likewise have another X chromosome (i.e. we're XY) as well as 22 non-sex chromosomes (i.e. autosomes).

    That's another consideration in all this stuff about Y chromosome Adam (and Mitochondrial Eve): we are only looking at essentially 0.5 chromosomes, not the other 22.5 chromosomes.

  3. By the way, in case anyone is interested, here are the studies Coyne cites: