Yes, it’s exactly correct. The L-haplotype is what you get as an outgroup when you do midpoint rooting. But it doesn’t make that the ancestral state. I do wonder what you would get if you rooted it on Neandertal, Denisovan, and/or chimps. I’m expecting that you would get the same midpoint root.
I am admittedly NOT an expert specifically in mitochondrial DNA and haplotypes, so there are far better people than me to go into the nitty gritty in detail on this one, but one thing I can do (and explain) is interpreting phylogenies, rooted and unrooted. And that unrooted phylogeny that Jeanson uses? Does not show what he says it shows. Of that, I am 100% sure.
Y haplotypes do not necessarily designate “lineages”. The tree of Y haplotypes and coalesce to trees of other parts of the genome will usually be different because recombination allows them to come from different ancestors.
Looks interesting. I don’t have the mental capacity to engage right now. I’ve just cracked Jeanson’s book. Anyway, I was hoping once I read it to read / watch all the criticisms. So I’ll bookmark for later. Thanks.
This is mtDNA? Do you have a typo in there? I’d like to understand your point but it’s not sinking in.
The trees will be, and are, different. If they are, why is it that people interested in descent from the time of Noah’s Ark decide that the mitochondrial lineages are the true ones? Note that they are not just descendants of the original mothers but had to stay in mothers all the way to the present.
The mitochondrial lineages from Europe and Asia coalesce with many different African lineages way back when. And of course there are a bunch of other African mtDNA lineages that don’t coalesce with any European or Asian mtDNA lineages. And of course all that occurs back about 100,000 years ago, not 4500 years ago.
You can root the tree anywhere. The only question is how much variation in evolutionary rate you’re willing to allow. Midpoint rooting, more or less, minimizes that variation. The more important point is that no matter where you put the root, Jeanson’s three groups are not clades. At least one of the three nodes (at least the “central” one) must be ancestral to another, and at least that node must be a polytomy. There is no 3-way split.
Because of drift, every piece of DNA eventually can be traced back to a single ancestral sequence; that is, one bit of sequence (“allele”) becomes fixed while others that once existed are lost. Because of recombination, the bits at different loci can take different paths, and the different bits that are eventually fixed can come from different ancestors. The mitochondrial genome and the Y chromosome are single units within which there is no recombination (ignoring the small part of the Y chromosome that recombines with part of the X), so each of them can be traced back to a single ancestor. But those ancestors can be widely separated in time and space.
Because creationists think we were created with differences, mtDNA and y chromosome data create the only data that can be used for a molecular clock or a phologeny, if I’m explaining it correctly, exactly as John says because there is no recombination. The differences can only be explained through mutation.
In an evolutionary paradigm. In a creationist one too, the mtDNA has to coalesce back to Eve and y chromosome to Noah. So they will be separated by time.
No, any data can be used for a molecular clock. mtDNA and Y chromosomes are unique in that their within-species descent is perfectly treelike, i.e. always branching but never joining.
In any paradigm that takes the actual data into account.
The data do not allow for such recent coalescence in either lineage, nor (back to the topic) do they allow for 3 mt lineages giving rise to all subsequent mitochondria. (Actually, they do, as would any tree in which the first two splits are dichotomous, but those three lineages can’t be the ones identified by Jeanson, and the most likely such three lineages are all within African populations.)
I don’t have time to redo my analysis to give a precise answer, but yes, when you use archaic humans or chimps as the outgroup and root the tree on the split, you get approximately the same root as the midpoint root - causing non-Africans to nest within African lineages.