So, I was doing some writing, and made a realization:
Mitochondrial and Y-Chromosomal DNA are special parts of the human genome. These loci (i.e. locations) in the genome are special for two reasons. First, these two loci do not undergo recombination, which simplifies the analysis. Second, each loci is inherited exclusively from fathers or mothers.
The number of mitochondrial lineages active at different points in time puts a limit on the minimum number of women at that time. The number of active Y-Chromosome lineages does the same, placing a limit on the minimum number of men consistent with the genetic data.
We can use this minimum size estimate to rule out when single couple bottleneck could have occurred. Y-Chromosomal Adam (Y-Adam) is estimated to have lived, roughly, around 150,000 years ago. Likewise, Mitochondrial Eve (Mt-Eve) is estimated to have lived roughly the same time, though she did not likely live at the exact same time as Y-Adam. Presuming that Adam and Eve’s lineage does not interbreed with others, this data clearly rules out a single couple origin from Adam and Eve before about 150,000 years ago.
Lineage times estimate the minimum population size possible over time. So, we can also rule out larger bottlenecks, at least in principle, such as a Noahic bottleneck. The Noahic bottleneck is limited four Mitochondrial linages, one for Noah’s wife and the three wives of his sons. But this bottleneck is limited to just one Y-Chromosomal lineages, because all of his sons get their Y-Chromosomes from him. The lineage time for four Mitochondrial linages is not typically computed from the data, but it could be. Y-Adam is usually reported at around 150,000 or so years ago, very roughly. Unexpectedly, perhaps, the time of Y-Adam is the most recent time during which could have lived Noah, presuming that Noah’s lineage never interbred with others
What I want to know is whether or not Traced or Replacing Darwin make this observation at any point. I don’t recall from my reading of the two books, which was a while ago. It seems that Jeanson’s model should demand a Y-MRCA at just 4,000 years ago, and a Mt-MRCA at 6,000 years ago. So there should be a significant difference between the Y and Mt data. Does he realize this at any point? How does he report the data pertaining to this? I.e. what exactly are the dates he computes fro Mt-MRCA and Y-MRCA?
Even in this scenario, mtEve might not be biblical Eve. If the three wives came from the same town, as seems reasonable, their female lineages might coalesce considerably more recently. Then again, given that A&E lived for hundreds of years and had many children, there’s also a possibility that they would all be literally daughters of Eve. Then again, again, wouldn’t the mitochondria in Eve’s ovaries keep evolving at the rate needed for Jeanson’s scenario, actually diverging within her? The entire Genesis scenario quickly leads to weirdness.
I don’t know if I’ve seen him make this point explicitly, but he’s obviously aware that the timescales for Y-Adam and mt-Eve should be different in his model. His whole schtick is to use a (inflated) mutation rate in combination with the YEC timescale to calculate how many substitutions we’d expect to find in populations today, rather than using his mutation rates and the substitution counts to generate a specific prediction about the number of years ago Y-Adam or mt-Eve lived - after all, they are essentially fixed points in time in his model. When he does this, he uses 6000 years for mt-Eve (see here) and 4500 years for Y-Adam (see here).
We then applied the models-specific time of origin. Following Karmin et al. (2015), we adopted 250,000 years ago as the evolutionary time of origin for modern Homo sapiens . Conversely, for the YEC timescale, we adopted the post-Flood timescale. Because Genesis 9:18–19 indicates that all people alive today trace their ancestry back to the three sons of Noah, the Flood is a key time stamp for any genetic investigation. However, with respect to paternal inheritance of the Y chromosome, the Flood is the earliest time point accessible to us at present. Since Shem, Ham, and Japheth would have inherited their Y chromosomes from Noah, Noah’s Y chromosome is the earliest time point our studies could address, apart from pre-Flood fossil-derived Y chromosomes. Since no such fossil Y chromosome sequences are currently known, the earliest time point we can hope to model with our data is Noah’s birth.
I get that sometimes if you’re not engaged with a topic regularly, the details can go out of your head, but I was still amused that you did not know/had forgotten that he had y-chromosome Adam as Noah. After all the threads on the topic? So he’s also identified certain lineages as Shem, Ham, or Japheth, and even Joktan and Abraham once he decided on a root.
As has been pointed out ad nauseam, identification of those lineages is necessarily wrong, regardless of the root. If they were indeed the three sons of Noah, the three lineages should all proceed independently and directlly from the root. Instead, there is no way to root the tree so that at least one of the three is not directly ancestral to another. Jeanson doesn’t understand phylogenetic trees.
That’s because you, like Jeanson, don’t know how to read a tree. The actual Y-chromosome tree can’t be rooted so as to make those three groups come directly out of the root, as shown there.
I will be sure and tell you if you’re mischaracterizing anything from my perspective once your discussion comes out or even before publishing if you want. But it’s hard to get a big picture unless you’ve read the book. Also hard to remember the details unless you have the book to reference…
It would be helpful if you would show what you mean and give some more detail. I remember now we have discussed this already but you have mostly said it’s just wrong without giving detail IIRC.
I’m going to need a refresher. What data did Jeanson use to construct his tree? Is there a figure that shows the full, original, unrooted tree from the data? I seem to remember such a thing, and I was working from that memory. I’m afraid the figure caption doesn’t say, which it really ought to.
Thanks. It is indeed almost possible to root the tree on node 8 and end up with three immediate descendants. It was some previous tree he used, and a different identification of the three sons, that I was thinking of, and there the choice of sons resulted in absurdity. On this tree, if we assume node 9 as the root, there are three nodes immediately descending from it: nodes 10, 11, and 119. Are these in fact the nodes he identifies with Ham, Japheth, and Shem, respectively?
The big problem with this tree is that we have to assume a huge difference in evolutionary rates (or mutation rates if you prefer) between Ham’s lineage and the others (I’m assuming that Ham’s is the group containing all the Africans). And we’re talking about a factor of at least five. There’s no credible way to get such a difference.
Further, if Ham is node 10, all the Near-East sequences but one are in Ham’s lineage, including all the Jews and Arabs. The only other Near-East sequence is in Japheth’s (node 11) corner, leaving Shem (node 119) with none of them. Are you sure that works for you?
I notice that the tree in the figure you posted from Jeanson doesn’t match the one it’s supposedly taken from, Fig. S3. Both the supposed Ham and Shem lineages in Jeanson’s figure are not immediate descendants of node 9 in Fig. S3, and in fact they’re part of the same lineage, whereas the Japheth lineage in Jeanson’s figure combines two of node 9’s immediate descendants. Jeanson was very confused.
So he’s also identified certain lineages as Shem, Ham, or Japheth, and even Joktan and Abraham once he decided on a root.