Guide to Patagonia's Monsters & Mysterious beings

I have written a book on this intriguing subject which has just been published.
In this blog I will post excerpts and other interesting texts on this fascinating subject.

Austin Whittall

Wednesday, July 30, 2014

A special Y chromosome marker

The Y chromosome has a "male-specific region" or MSY; it is the sector of the Y chromosome that differentiates sexes (females and males). It spans roughly 95% of the chromosome's length and is is made up of different sequences, one of which is known as "X-degenerate".

Despite its name, its sequences are the relicts of the ancient autosomes which later evolved into our current X and Y human sexual chromosomes.

A paper (Rozen et al., 2009)[1] analysed the human MSY region and reached some interesting conclusions.

An interesting mutation

The researchers sequenced a global sample of Y chromomes (belonging to haplogroups: A, B, C, D, E, G, H, I, J, T, L, M, N, O, P, Q and R) and found that they were all extremely similar in the X-degenerate protein sequences: any two chromosomes selected in a random draw only differ in one aminoacid; and in 50% of the cases, the differences are due to one particular mutation.

This special mutation switched Aspartic Acid for Glutamic Acid at a certain spot of the MSY region ( mim400005). It happened quite some time ago: the authors calculate that this mutation took place roughly 50 kya - 95% CI 37.7 - 55.7 kya (my comments on this date can be seen below).

They also found out that natural selection seems to be operating as a factor that preserves amino acid sequences in this part of the Y chromosome therefore raising doubts about the assumed "neutrality" of mutations taking place in the Y chromosome: they are assumed to be random but apparently are not.

The image below, (from [1]) shows the Y chromosome's haplogroups that were tested. The red dots mark nonsynonymous nucleotide substitutions, the other dots (blue and gray) mark other kinds of substitutions. The arrow indicates the particular mutation mentioned in the text above. I added a red sector indicating those haplogroups that do not carry this mutation, the "oldest" haplogroups A, B, C, D and E.

Y chromosome tree hgs. and mutations.. From [1]

Its location, at the root of branches leading to all the other haplogroups from G to R, makes it the oldest of the twelve mutations that the study found, as well as the closest one to the root of MSY genealogy.

The African haplogroups A and B, plus the most ancient Eurasian ones C and D as well as the East African E hg., do not carry this mutation, all other sampled haplogroups do. So this suggests that it originated in Asia After the Out of Africa migration of modern Humans.

The issue of the dates

The date assigned to this ancient mutation (37.7 to 55.7 ky) was not calculated directly. Instead the paper is based on another study (Karafet et al., 2008) [2], which provides the usual mainstream accepted dates for an OoA event of 50 to 60 kya.

I have already given my critical opinion on these dates and the assumptions on which they are based on, so I will not repeat them again here, but one of the objections is that mutations used to time the "molecular clocks" used to date human events (either using mtDNA or Y chromosome substitutions) may not be random, due to pure chance (or neutral), but may be selected for by evolutionary forces.

And, as mentioned above, this very paper [1] includes a comment which impacts directly on one of the basic assumptions of the "genetic clock": since Natural Selection is acting, then "the assumption that all MSY SNPs—as well as any structural polymorphisms in the Y chromosomes marked by these SNPs— are selectively neutral." is false. The paper adds (bold mine):

" [our] data contradict this simplifying assumption. The MSY does not undergo sexual recombination with a homologous chromosome, so it is subject to natural selection as an indivisible unit. Even if the particular MSY SNPs employed in a population study are functionally inconsequential, they may have been coupled to detrimental or beneficial SNPs or structural variants elsewhere in the MSY... Taken together, these studies of structural polymorphism and coding sequence variation in the MSY highlight the role of natural selection in human MSY lineages. This new awareness means that we can no longer assume selective neutrality in the MSY when drawing conclusions from population genetic studies." [1]

This mutation is selected for in a positive manner, it appeared and was conserved intact in the MSY region. It may have appeared a long time ago, 80 ky or 100 ky or even 300 ky ago. Which brings me to the reason for my post.

An ancient Eurasian mutation

If it appeared and was not obliterated by natural selection and it is not neutral, then it must provide an advantage to its carriers. The paper [1] points out that the substitution of Asp. for Glu. "may be of little functional consequence", and that 11 out of 12 mammals and birds studied have glutamic acid in this locus like men belonging to hgs. G to R.

The only one with aspartic acid instead of glutamic acid is the mouse and of course the "ancestral sequence of humans" found only among those men belonging to haplogroups A to D.

In other words it is absent among contemporary Africans (hg. A, B) and the oldest haplogroups (C, D, E), so it evidently originated in Eurasia. Since I distrust the 50 ky age, and believe the mutation to be much older, I ask: Was it a Neanderthal Trait? Did it admix back into H. sapiens from the Neanderthal?

Or if the date is correct, it may even be a Homo sapiens mutation that is not found in older Y chromosome lineages that, as I have suggested in other posts, date back even further than Neanderthals.

A closer look at the tree above shows that the mutation took place just after the split of C and the ancestor of all the other groups G to R. Perhaps the mutation marks the spread of Modern Humans out of Africa and even more interestingly, it spreads overlying the more ancient non-mutated haplogroups, which in turn reflect those of archaic humans. Which as I have suggested in previous posts (i.e. C hg.) mark the presence of H. erectus in Eurasia.


[1] Steve Rozen, Janet D. Marszalek, Raaji K. Alagappan, Helen Skaletsky, David C. Page, (2009). Remarkably Little Variation in Proteins Encoded by the Y Chromosome's Single-Copy Genes, Implying Effective Purifying Selection. Am J Hum Genet. 2009 December 11; 85(6): 923–928. doi: 10.1016/j.ajhg.2009.11.011
[2] Karafet TM1, Mendez FL, Meilerman MB, Underhill PA, Zegura SL, Hammer MF, (2008). New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree. Genome Res. 2008 May;18(5):830-8. doi: 10.1101/gr.7172008. Epub 2008 Apr 2.

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