Nathaniel Jeanson’s Traced

I was thinking more about all the possible rooted topologies for N taxa. Could there be some topologies out there that fit better than the one he’s testing. If you think of all possible rooted topologies or all rooted trees for any given topology (based on neighbor joining or whatever else) Jeanson is still only looking at a handful of possibilities and doing so in the most ridiculous of ways.

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Jeanson originally had 3 possible roots, so he eliminated one before his original paper, then? The final rooting in the book is just based separating the deep lineages of Ham and Japheth and where the Bible says they end up, as well as some statistical analysis of to narrow down the lineage of Abraham as T to get the grouping for Shem.

Well, both these questions relate to what I was trying to ask about in the earlier first thread on Jeanson’s book for a week or more. I felt like I was getting stonewalled on making sure I understood it correctly. So now I really hope I can get this answered. And I also kept trying to picture what drift looks like in a tree with rare mutations, so I really appreciate your explanation about bifurcation.

As far as I understand it, if there are multiple mutations per generation, each node of the y-chromosome tree represents an individual. If we had the y-chromosome of every man alive, we’d have one giant patrilineal genealogy.

And then as far as I understand it now, if there are not multiple mutations per generation, each branch is a mutation that represents a population with that mutation. The tree will bifurcate to indicate the population with and without the mutation.

Basically, my assumption is that if there are multiple mutations per generation, Jeanson’s hypothesis should work as it combines genealogy with the y-chromosome tree, but if there are not, it won’t work in a population of constant size or may not be reliable.

If anyone could explain where my thinking on this is wrong and/or right, I would be extremely grateful. It’s definitely a pet peeve of mine not to understand something and here especially to have little way of discovering the answer except through this forum, so I’ve just tried to be patient. :slightly_smiling_face:

As I understand it, the tree isn’t Jeanson’s analysis at all, just taken from a published paper. So his only concern is rooting. No?

I actually think the book will be successful in terms of sales in the YEC market, tapping into the level of interest which attends both origins and the connection to genealogy. After all, Ken Ham’s son in law has traced his family tree back to Adam through Noah; others will wish to do the same.

Does not pedigree mutation demands that branching will continual to the last baby regardless of population growth? Forensic genetics does not cease to work in a declining population.

Would it not be the exception that only one branch be left in a given population at any time period? There has always been some degree of intermingling. You have made this case yourself. So even a static population would carry forward branching due to mutation as well as representation from the prior existing diversity. In principle, given a population of a million with a hundred identifiable lineages, that could reduce to a hundred male souls, all representative of those distinct lineages. It could grow again, then shrink again, become isolated, become assimilated, and diversity would not be proportional to population throughout. This is not the same as drift and founder effects.

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No. I have.no clue where you got that idea. Again: there is no way to root that tree so it will give you the three sons of Noah. At best, one of those sons will be ancestral to another. You and Jeanson are hopelessly confused.

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Interesting. Lol, I or anyone else with European heritage could probably claim that ancestry except for the last 500-1000 years.

Sorry I wasn’t clear there. The lineage up to the last baby would continue to accumulate mutations but wouldn’t branch. So the child’s mutations would be different than his father but you’d see no branching on the tree unless the child had back mutations (or brothers obviously but we’re talking about a population that’s not growing).

Yes, true, but in small populations I’d think you’d still only end up with 1 left.

No, there would be no branching in a genealogical sense, you’d only see a number of lineages continuing to accumulate mutations. It would like like flatlining. Example from the book:

Diversity is obviously not by default
proportional to population size changes because of drift. But branch diversity is going to be proportional to population growth . Genealogically the branches need to grow as the population does.

Sorry, when I’m thinking of the lineages that survive during a population downturn and “trim” the tree, I have no idea if that fits under the definition of drift, but I’ve been using it that way.

Just to show you how wrong Jeanson is in how he interprets virtually any bifurcating tree in terms of population growth consider this figure from Hein et al 2005 Gene Genealogies, Variation and Evolution: A Primer on Coalescent Theory.

Each is a simulation of a coalescent process involving five replicate simulations of ten genes in THE SAME POPULATION. Figure 4.2 are five simulations of ten genes in a CONSTANT population. Figure 4.3 are five simulations of ten genes in an exponentially growing population. Jeanson would count up the branches and treat this as a proxy for population growth and in doing so be wildly wrong about both of those populations.

Try it yourself. Count up the branches along a series of time slices for each tree as Jeanson does and see what you would conclude.

Lots of things affect tree branch length including population dynamics, size, selection, and population subdivision. None of these things does Jeanson consider. All he did was make up some very naive methods that made intuitive sense to him and could be used to rationalize what he wanted to believe.

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Jeanson’s trees are just distance-based trees. You basically create a table with the individual sequences listed on either axis of the table and in the cells of this table are pairwise distances. Pairs of sequences with fewer differences will be placed closer together on a tree. Pairs of sequences with more differences will be placed farther apart. That’s all it is. It is a graphical illustration of the pairwise diversity of the sequences. Each branch is not a population with a mutation or an individual. It is just a graphical way to illustrate the differences between two sequences. That is it. There are other ways to make trees that are more explicit regarding models of how genes change over time (maximum likelihood or Bayesian approaches). But Jeanson never employs those approaches. I suspect this is because he doesn’t have the understanding or resources to do so.

Imagine you had a population that was steady over time. It neither decreased nor increased. On average every breeding individual just in effect replaced themselves in the population. Each generation there is that possibility for mutation to be passed from parent to offspring. Lets say over four generations one mutation occurred in one generation, one in the next, another in the next, and another in the next. That is four different sequences. You then look at those sequences place them on a table calculate their pairwise differences and build a tree. Depending on how those mutations occur you will get some sort of branching diagram of their diversity. Notice that this branching diagram exists completely independent of the whether the population is growing or not. In this case it is completely steady but still you have this bifurcating pattern that displays the diversity among these different copies of this gene.

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So here is how he justified the rooting scheme and this article is cited in Traced.

He used three different roots.

One what he calls the “evo” root. Just the root using Neanderthal as an outgroup as any normal person would do.

Then he used other rooting schemes in accordance with his Biblical beliefs.

“For alternate root positions, I used two types of mutually exclusive criteria to identify a range of candidates. The first criterion attempted to optimize the detection of triad-like structures near the root, as well as ethnically diverse lineages near the root. The pursuit of triad-like structures arose from the hypothesis that all three sons of Noah—Shem, Ham, and Japheth—would have left male descendants that would be easily identified today by a small but global sampling of male Y chromosome lineages.”

and…

“The second criterion attempted to mathematically optimize the orientation of the population growth curve. Biblically, the male post-Flood population began with just 4 men (Noah, Shem, Ham, Japheth), yet by 1975 (i.e., the final date given in McEvedy and Jones (1978)), the population had grown to nearly 2 billion. Practically, mathematical optimization would produce a tree orientation that put the fewest number of lineages near the root and the largest number of lineages at the tips. Thus, almost by definition, this mathematical optimization method avoided the pursuit of triad-like structures and the pursuit of a maximum of early, ethnically diverse lineages—since both pursuits would have inflated the number of early lineages and skewed the early-versus-late math ratios.”

So how many rooted trees can you have for ANY topology for this many tips. Many billions.

How many rooted trees can you have for the specific topology in this particular neighbor joining tree? Hundreds.

He tested three or four. And he did so in the most ridiculous of methods by assuming the branches represent population growth and lining up the progression of branches with a curve for population growth within his Biblical time scale.

It’s one of the dumbest things I’ve ever seen.

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Thank you for the explanation and the time it took to provide it, as it helps me see where I may not be understanding things correctly. I’ll think on it. I might still be a bit stuck though because none of your examples refer to what happens in a tree with multiple mutations per generation, which is what I really want someone to critique. I think that based on everything you shared and what I just briefly read in the last week about distance-based trees (I’m trying @John_Harshman :slightly_smiling_face:) I will just have to create sequences with various scenarios, build a tree and see what happens.

I believe in Jeanson 2019 where he explained this crazy rationale for choosing which rooted tree he would use he also says he recreated the Y tree using neighbor joining. Always neighbor joining. Ham is too cheap to buy him a computer with enough memory and processing speed to do a ML tree with that much data.

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OK so they are accumulating mutations. So that means there are different sequences in the population, even though it’s not growing, but staying a constant size. So now take all those sequences that are different because of mutation and do what? Measure the differences between them and display those differences as what? A bifurcating tree!

You are acting as if the entire population would get the same mutation all at the same time and all of the ancestral sequences would disappear. That’s just silly.

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Makes no sense even in its own terms. Noah is not one of 4 ancestors; he’s the root. “Triad-like structure” is a meaningless buzzphrase. And he has no clue about how coalescence works.

It’s a reasonable hypothesis that this is indeed a scam for people like @thoughtful.

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A quick check finds that Ken Ham’s son-in-law has just copied the names from the Anglo-Saxon chronicle (see here), but for some reason has chosen to call Scef a variant of Japheth, while the ASC explains that Scef was Noah’s fourth son, born on the ark.

Perhaps AiG consider Scef to be non-biblical, but that’s no excuse for misrepresentation of their source.

The whole genealogy is as fishy as a barrel of herrings.

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That he certainly does not.

He’s thinking Noah’s sons would all have different Y chromosomes because of mutation. But yes they all would have got their Y from Noah. Again the only people any of this makes sense to are people who know absolutely nothing about population genetics and can’t read a genetic tree.

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There are any number of mutations taking place in those examples. That’s how you get different sequences.

All this is not easy to understand, especially in an online forum, so look for very basic red flags. When the only people saying Jeanson absolutely knows what he’s doing are Jeanson himself and people with no expertise in the subject that should be a red flag. You have multiple professional people with experience in this field telling you what Jeanson is doing here is bonkers. To take that and completely ignore it and say that people with no experience are right and people with experience are wrong is a leap.

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I get what you’re saying, and your scenario of tree building makes sense to me if the tree was describing a population of constant size in the recent past - the tips of the tree.

But…that’s not what’s true of world population. We have exponential growth. So in ancient and past downturns the tree gets “trimmed” and then the population does inherit those mutations “all at once” as it pertains to how the tree looks, as far as I can tell. The population with exponential growth will share a long flat line of mutations during the period of population decrease as well as a period before it.

That is not what is going on. At all. Read what I posted above.

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We are dealing with someone who treats St. George slaying the dragon as history, so I am beyond surprise when it comes to Bodie Hodge.

Here is his explanation for the Sceaf identification:

Most believe the name Sceaf is a variant name of Japheth after the event that occurred at Babel in Genesis 11:1–9. Name changes were very common after the confusion; by this, his son Bedwig is merely another son after the split occurred at Babel. Other rare proposals are that (1) Bedwig was Magog or that (2) Sceaf is Ashkenaz, where Sceaf is not Japheth but Ashkenaz, the son of Japheth with a variant name. Though these possibilities are not as common, I made the main connection that Sceaf is Japheth.

Well, if “most believe”, I guess that settles it. I mean, who am I to dispute with “most”? So pervasive is the common knowledge that good ol’ Sceaf is Japheth’s nickname, there is no need for any sort of reference. >>> I would suggest that the same degree of rigor is on display here as attends most claims which emanate from AiG. I could trace my ancestry to Aragorn of middle earth with as much credibility.

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I had a nice chat with @Herman_Mays earlier today and he did a nice job laying out the bananas methods Jeanson uses throughout Traced.

Nobody should be taking any of this seriously. Really. Just amateur hour at AiG.

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