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Sunday, June 28, 2015

All Human beings have Two things in Common: Mitochondrial Eve and the LM3 Insertion

What is it that separates us all from archaic humans such as Neanderthal, Heidelberg and Denisovan?
Since the finding of archaic introgression and and a Y Chromosome lineage that split off 325 thousand years ago or longer, that question has become harder to answer.
Our anatomy is the most obvious answer, since everyone on the planet today shares an anatomy with homo sapien sapiens who lived 115 thousand years ago or longer in Africa, West Asia, and  Southern China. Descent from a common mother who lived in Africa 200k ago or whose earliest divergent lineage is now confined to Africa is another obvious answer.
But is there anything else?
Mitochondrial Eve was likely chinless but otherwise anatomically modern..
Y DNA Adam on the other hand is now a known archaic, since anatomical moderns are not known from 325k ago.
We can of course hypothesize that 325 thousand year old y haplogroup A00 is an example of introgression a population with it's suite of anatomical features already intact, so this is not necessarily cause to dismiss Y Adam as a needed component for modernity.
However, there is something else besides mito Eve that every population on earth has in common, and that is evidence of a past presence of mtDNA haplogroup LM3.

LM3 is a maternal haplogroup that split off from our own about the same time as Y haplogroup A00.
It was the haplogroup of Mungo Man, a fossil anatomically modern human (with a chin) from Australia that is dated to between 40k and 60k ago. Some have claimed that it is the fearliest indisputably modern fossil we have, though this idea has fallen out of favor. It is more gracile than later and even possible modern Australian aborigines with height estimates that range from 6'4 to 6'6.
Though it's maternal lineage is extinct, an erroneous insertion of it's mtDNA is widespread across the globe.
It's lowest frequency is in African pygmies, and it's highest in Japanese (Ainu?) and an isolated population of South American Indians.
So what does this all mean?
Looking at the chart above, since none of our ancestors really seem to match up with our nuclear DNA tree...could we have gotten our shared traits from a ghost population?

Joe Lyon Layden is a prehistoric fiction author and primitive musician. To receive a free copy of this entire novella "The Man from Parkho Khatune Bears Favor," as well as three free songs and monthly updates, freebies, and discounts on Joe's ongoing work, please sign up for the newsletter below.

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Thursday, June 25, 2015

First Peoples Starring John Hawks on PBS

Professor and famed blogger John Hawks was on PBS last night as a quest for the debut documentary series "First Peoples," and it did not disappoint- I've been waiting for it since he announced it on his blog a week or so ago;

The second part of the episode focuses on Africa and really might represent a milestone in our cultural understanding of human origins, being the best representation yet of a new hybrid theory of Hss evolution that has been emerging and being hinted at since the neanderthal genome was sequenced. It's a well presented model easily palatable for the public and I think they did a wonderful job.

Next week they will explore East Asia and I hope that the producers will have Hawks expound on what he wrote in this post from a while back:

One criticism I would have of last night's episode is that the model they presented again has Hss coming out of Africa only 55 thousand years ago and then assimilating neanderthal in the Middle East. They don't mention the problem of Hss already having been in Israel and South China by 115 thousand years ago.

However, the first episode made good use of presenting a theory and it's evidence, then providing an alternative and it's evidence, building on our understanding with each step. Perhaps they will continue this trend as they move across the continents.

In the next episode I think we'll be seeing something about Toba and it's effects on the new evolutionary model the show is building, as well as the problems of Denisovan introgression and maybe even the Red Deer Cave people and the hobbit. Can we hope for some talk about Microcephalin D introgression and the Mystery Hominid?

The shows talk about the neanderthals being driven down in to the Middle east by a cold spell before the OOA group gets to them 55 thousand years ago, but they don't mention how long the neanderthals had been in the Middle East previous to that meeting. It makes it seem like there were no hominid populations in between the two and the Middle East was abandoned, even drawing a line on a virtual map as they explain, showing neanderthal and Hss moving  into the Middle East at the same time only 55 thousand years in the past.

Actually the neanderthals had moved down into the Middle East by as early as 90 thousand years ago and therefore effectively blocked off Africans from the other half of the Hss population in China (and possibly northern India).
Was that "other" population of Hss in our genome, or did that part of our ancient genome go extinct? Was it assimilated along with the archaics in Africa, neanderthal, and Denisovan? Can we hope that Hawks will talk about Mungo Man and LM3 when we get to Australia?

My own theory is that the neanderthal incursion into the Middle East created just the type of "hybrid zones" the show talks about in the context of baboons. Likely hybrid zones would have been East Africa/Arabia (Y haplogroup E?), the southern coasts of Arabia/Asia Minor (Y Haplogroup G?), Pakistan/India (Y haplogroup F?), and Central Asia or NE Asia(Y Haplogroup D and/oror C?).
I think Y Haplogroup H might have assimilated archaics in southern South Asia to produce Balangoda Man, providing some non neanderthal tainted lineages to explain the lower admixture in South Asia.
Similarly, there were plenty of populations in Africa to dilute the neanderthal genes carried by populations containing y haplogroup E (the dominant haplogroup in Africa today). These included the various lineages of A and B, at least one of which assimilated still ANOTHER archaic(as revealed in last nights episode and elsewhere).
  A population containing haplogroup F must have spawned haplogroup K, and t K assimilated some more archaics in SE Asia...likely one that carried Microcephalin D.

I have a related theory that the reason we only find trace amounts of Denisovan in Chinese, but have recently learned that the ancestors of the Chinese got a second dose of neanderthal genes when they moved into China, is because neanderthal had pushed east and mostly assimilated the hominids in East Asia before Hss ever got there. By 70k, neanderthal may have assimilated most mainland hominids outside of Africa just as we were later destined to do. His species may have been dominate since then, on a path to assimilate us as well...and we were only saved by the Toba eruption. Or Toba and limited reproductivity, since the lack of assimilated neanderthal reproductive genes is a hint that our hybrids may have not been entirely fertile
I wonder if something akin to this idea might be put forth on this series as well?
The program states that it is likely that it takes 2 million years of sexual separation for a primate to lose the ability to mate with a closely related sister species, so maybe they have some evidence contrary to the missing neanderthal testes or maybe they will address that in a later episode.

I was a tad disappointed with the way the show presented the controversial Kennewick Man, however.
Finding y haplogroup Q and mtDNA X in Kennewick Man doesn't prove that there weren't several waves of migrations into the New World, and in fact the diet of seals they examine might mean that Q and X didn't use the ice corridor to get into North America. In fact Q and/or X may have been the most recent arrivals.Neither does John Hawks' explanation that Native Americans crania have evolved from a Polynesian form in the past 10,000 years due to "settling down" provide a satisfactory explanation of why they used to have crania most like Ainu and Polynesians.
For one thing, Y haplogroup Q is  descended from Y haplogroup P. which has it's most ancient and dominate presence in the Aeta of the Phillipines- it's possible that Q travelled up from Indonesia along the coast to get to the Berring Sea and Siberia as well as America, and hence would be more akin to Polynesian and Sundadonty.
 Or Kennewick Man could could have been a recent conquerer, with Y haplogroup D matched with mtDNA X before his arrival on the West Coat of America, only to be wiped out by the invaders like so many other Y lineages in the past. This would explain why he had a body made for the throwing spear- this is a technology that is known to big game hunters that descended from Y haplogroup K (Australian Aborigines, Mongolians, late paleolithic Europeans, and late Native Americans) but was not known to the Ainu or Jomon.
 They didn't bother mentioning the Topper excavations which may be turning up lithics from 50 thousand years ago along the Savannah River in the discussion of the Americas, and they didn't extract DNA from Eva or mention the Australoid morphology of Luzia on the program. When you put all the facts together, it seems pretty impossible that America was settled in one wave or that Q and C are the only haplogroups that  had ever made to the New World in prehistoric times.
To me, it seems like y haplogroup D is no longer present in many areas of Asia that it must have been present in the past, and the same goes for y haplogroup C, and there's no reason why the same thing couldn't have happened in large parts of America. Indeed, even in America recent studies have shown an extinction of Y lineages that spikes at the time of their neolithic Revolution. Haplogroup C is so rare in Europe it's gone undetected for decades, but seems to have been fairly ubiquitous there before the agricultural revolution. The high levels of the LM3 insertion in Japanese and South Americans even implies a connection there, and probably means there were several ghost populations of that our genome assimilated as we moved east in the paleolithic, and they may have even made it to America before us.
Maybe the descendents of Kennewick Man lost their Polynesian features through admixture with Mungo Man's kin,. the population that carried y haplogroup C to America, and the other mtDNA haplogroups other than X. Just a tad disappointed that they didn't address this, and instead acted like the morphological and dietary evidence had been trumped by the DNA.. I had a feeling that they may have taken John's explanation out of context in that segment, as he may have been speaking about the Neolithic in general rather than specifically about Kennewick Man.

Overall  this was an excellent update of our understanding of human evolution, and I was very glad to see hybridization between closely related species and subspecies presented as as a driving force, and possibly the MAIN driving force, of our heritage.

Tuesday, June 16, 2015

Ned Stark's Mother Was a White Walker

I just wanted to be the first to say it. I don't have a lot to back this up except that she's the only matriarch in all the houses that isn't mentioned or even named as some other bloggers have pointed out.
I'll expand on this in a bit but feel free to comment and let's figure out if this could be true and what it might mean....