Denisovan's strike again

[PB666]

What did I say?

http://blogs.discovermagazine.com/deadthings/2018/03/15/interbreeding-denisovans/#.WqsdGech2Ul

As I stated in the other threads, these outlier genes were noted years ago, people have kind of ignored them.

It was kind of odd also that Japan and Korea has such high Neanderthal contributions, this might explain at least some of that.

Of the particular genes that I questioned the highest frequencies were in the Orochon, so its would be interesting the see the gene contributions to this particular population.

Molecular genetics rules!

Expect more like this in Africa . . . .Extreme South Africa and West Africa.

Here's another paper reinforcing something I mentioned about 2 months ago concerning Europeans (and the general problem of publishing new molecular genetic ideas concerning Europeans because of the underlying bias in archeology and anthropology). Alot of the articles are old hat, Spanish molecular geneticist noted waves of migration from Africa direct to different regions of Europe, the conclusions did not suit well at all with archeologist.

The most profound was the highly apparent founder affect in the settlement of Sardinia, which archeaologist concluded was settled by the eastern mediterraneans. Nope, first colonized be NW Africans and that DNA compliment is still significant part of current population. 

 

[kerbiloid]

Spoiler

Those naughty sapienses.
Is there in the Earth village somebody not hm... contacted with them?

 

[PB666]

I think there were many attempts at interbreeding, most unsuccessful, so it was not particularly naughty.

Also I would point out, that on the north end of the range, given that most HSS traveled most of the time through the tropics and semitropics, that it was selectively beneficial to interbreed if you are moving into regions with less than tropical climate and risks. This has been expected for more than 30 years, and could have been predicted based upon the distributions 15 years ago (even though MPI claimed based on the original desinovan that there was no reason to believe other admixtures occurred).

From the south there are is one, maybe two immunological genes evident, from the northern part of the range there are potentially three from a single locus. One of these B48, carried over into the new-world (western populations).

The barrier between humans and other late hominims was sufficient to prevent productive hybrid formation, but it leaked, either on there side or hss side or both. It takes two genetic changes to form a barrier but it only takes lapse on one or the other side to negate that effect. If the formalizations are not fixed in one or the other population, then this can explain the general failure of admixture, but the occasional success.

I think a much better question is, with H.s.s. branching for H.s.n and H.s.n.d so recently why there was any impediment to admixture at all.

[YNM]

1 minute ago, PB666 said:

I think there were many attempts at interbreeding...

I don't get why they're even different. Are they as varied as the world's shortest person and the world's tallest person ?

[kerbiloid]

Spoiler

9 minutes ago, PB666 said:

there were many attempts at interbreeding

Not that they were treating that as attempts...
Not that their aim was the interbreeding...

 

[PB666]

22 hours ago, YNM said:

I don't get why they're even different. Are they as varied as the world's shortest person and the world's tallest person ?

 

Spoiler

 

That's a very old debate. To give an illustration way back several thousand years ago some folks from indonesia went to the region of what is now Taiwan and stole a bunch of females (there are telltale signs of this motion in the people of taiwan). They admixed and settled some of the pacific Islands. In that admixture we can tell by looking at the mtDNA the female and Y chromosome the male ancestries. We can also look at other sites and see about 1/3rd of the genetic contribution is from indonesia and 2/3rds from Taiwan.

When we look at all humans and all the myriad of branches, there is pretty much the assumption that the first permanent settlement out of africa were represented by their modern mtDNA descendants (M and N haplotypes) almost all the mtDNA haplotypes that exist in the world outside of africa are M and N derivatives. Those that are no are pretty much recent migrations from Africa (into the west and south asia) and more recent (colonial) into Europe and North America. Other than these there are no exceptions. Thus because the population was so large at the time when the various admixtures occurred, the number of human male/[x]-female admixtures are small.

There is convergence both in terms of time and place for the mtDNA. The place is along the southern African rift valley and the time was between 175 and 275 kya. The mitochondrial divergence times for N and human and Desinovan are about 3 to 6 times earlier than this, so this basically informs us that mtDNA contribution was not significant.

From the Y-chromosome, the previous Y-DNA convergence pointed to southern Africa, also, its MRCA was postulated to live about 130,000 years ago (the male center is postulated to be smaller because in pre-modern times the effective male to female breeding ratio was 2f:1m) [empahsized to prevent confusion with gender biased infant ratio]. However about a decade ago it was noted that a population of humans with more primative features existed near central Africa, this roughly coincided with a pocket of divergent HLA-B allelotypes that are found nowhere else in the world and are too divergent to be explained by recent evolution (no templates for recombination). Subsequently, after tracking a anomalous African American Y-chromosome back to Africa it was found the Y-chromosome existed in S. Africa that placed the Y-TMRCA much earlier than the mtDNA. This suggests admixture between a [euphemistic] Archaic homo sapeins (Probably North African Hominim)[We can call this homo sapiens idaltu if we like-but it muddles things up] and  Homo sapiens sapiens as the second expanded in the NW of their range in the direction of N. Africa. This was an exceptional event however. 'Since' that event it would appear there was no persistent introduction of non-Hss Y chromosome in the human population. This indicates, given an expanding population size as people migrated from Africa, settled india, and moved to other parts of the world that the number of male introgressions into the Hss population was also small.

Then the data which has been most thoroughly investigated by Tishkoff, but also elucidated by recent studies as the one mentioned above suggests that introgression did occur. This is notable previously by an anomolous alleles detected by Mark Stoneking but also evident as HLA-A*06:01 HLA-B*48, *67, *73 alleles in East Asia (HLA are mentioned because they are the most type genetic loci in humans because of the bone marrow databases). There was no such marker found in Europe however. Nonetheless from 1.5 to 3.0 percent of European genetic ancestry is shared with Neandertals during an entry admixture event somewhere in the vicinity of SW Asia and is shared by all exo-african populations. Based on the predicted number of individuals who initially left and remained Out of Africa this constituted a few (2 to 5) introgression events of undetermined gender. A second node was detected in indonesia that appears now to have been an individual of denisovan type that was an admixture with other Neandertals and appears to have settled across the Wallace line in Oceania. The haplotype studies indicate that this might be a single or plural event of less than few individuals. And of course there is the reference above, which has not been fully characterized. A note about the HLA that needs to be made, there is in contrast to Y and mtDNA, a strong heterozygous selection coefficient acting on HLA that acts to preserve and increase diversity in the human population. While Y and mtDNA act as haploid linkage groups, the HLA has an apparent ploidy >2 until the heterozygoous selection coefficient is factored in. Because of this we can see certain autosomal sources of variation much more readily than we can see Y and mtDNA variation, so basically HLA is like a more sensitive probe. None the less HLA contributions from Western Neandertals in Europeans is not evident, which is peculiar (and this may not be the end of the story given the diversity mode of some Ancient European haplotypes is in West and Central Africa).

So the consistencies are that few productive introgressions occurred. Others may have occurred, but the offspring, for whatever reason, did not survive. And consequently introgressions were the exception not the rule.

 

Summary: So what caused this leaky barrier.

It was unlikely between male and female reproductive biology per-say. We have to assume all the parts were compatible. A more likely area of problems is the receptivity of eggs with sperm. Given the evidence above it seems that male archaic sperm was compatible with Hss eggs, the vice-versa may not have been true. There could have been developmental abnormalities in the fetus that cause 9 or 16 week spontaneous abortions (possibly a false signal). Or there could be something about the offspring that did not allow them to survive the first generation without extended intervention of some form.

IOW the reason why this was not common is more or less implicit in the molecular genetics observation, there is nothing about morphology separate from the Archaeology (e.g. Denisovan cave, Vdijna Cave) that gives us reason to believe that productive cross breeding could not be common. And herein lies the core of the debate between molecular genetics and paleoanthropology that started with this small paper  37 years ago,

https://www.ncbi.nlm.nih.gov/pubmed/6251473

But was noted that something weird about human population. . .

https://www.ncbi.nlm.nih.gov/pubmed/4120260

Its a good reason in science to postulate that good hypothesis are held up by several diverse legs, relying too heavily on one line of evidence can lead one down scientific dead ends.

 

 

 

Edited March 17, 2018 by PB666

[YNM]

1 hour ago, PB666 said:

There could have been developmental abnormalities in the fetus that cause 9 or 16 week spontaneous abortions (possibly a false signal). Or there could be something about the offspring that did not allow them to survive the first generation without extended intervention of some form.

Few questions :

- How do you even know that it was biologically "impossible" ? ie. Even if the result is a failed fetus, surely there are some chances that the bones would stay ? (I know erosion comes to play and smaller remains are a bit harder to identify and come by).

- Today there are still yet more simpler, subtler mixtures that means an intervention is needed. For instance, cross-blood type babies. I'm one of them (I'm AB, as with my father, yet my mom is B). Would such cases goes well down the road back in prehistory ?

- What if it's just geographical, like the Malagasy people ? True that they're mixed today, but there could be a time where entirely different "close" populations exists without mixing.

[PB666]

25 minutes ago, YNM said:

Few questions :

- How do you even know that it was biologically "impossible" ? ie. Even if the result is a failed fetus, surely there are some chances that the bones would stay ? (I know erosion comes to play and smaller remains are a bit harder to identify and come by).

- Today there are still yet more simpler, subtler mixtures that means an intervention is needed. For instance, cross-blood type babies. I'm one of them (I'm AB, as with my father, yet my mom is B). Would such cases goes well down the road back in prehistory ?

- What if it's just geographical, like the Malagasy people ? True that they're mixed today, but there could be a time where entirely different "close" populations exists without mixing.

The only instance were we can raise the question of impossibility is between Classic Neandertals (in the strictest sense) and AMH (~30 to 40 kya) and even that is tenuous.

There is almost no chance fetal remains from an admixture would persist. In essence if we assume for example there were say 30,000 HN in europe for the last say 200,000 years it means that 6 billion people, of those there is maybe representation in the fossil record of 10^-6 to 10^-7 most of the individuals were between 13 and 20 years of age, very few younger or older. The smaller a bone or set of remains are, the less likely it is to survive. Ancient DNA is particularly hard to obtain from non-hardened bones, the preference is the tooth or the hardened parts of the femur.

Erik Trinkaus is an expert on the evidence for admixture between Hss and Neandertals, however he is rather overconfident and some of his datings (like Oase1, https://www.ncbi.nlm.nih.gov/pubmed/14504393, https://www.ncbi.nlm.nih.gov/pubmed/14580595) are probably underdated and outside the window of admixture between HSS, but not betweeen HSI and HN (based on the lack of confident dating of the purified collagen). There are some that claim that widespread evidence of admixture within Europe itself, if so virtually all of these admixtures were eliminated from the population either by failure to produce offspring or some sort of population failure. One study of the Neandertal components in the human genome suggest that DNA around genes is removed more rapidly than expected, however this observations could be due to a improperly used time of admixture (admixture is older as many believed). There is lots of talk, I basically only adhere to what the molecular genetics allows, and when there is a death rely on accurately dated archaeology.

Indonesia is a tough example of human evolution, the country is divided by the Wallace line, which through the history of human evolution was crossed by multiple species on multiple occasions. The last and more recent of which was Hss ~50 kya (±15 ky). The problem of assessment here, for example Homo florisiensis appears to be an erectoid derivative with pre-erectine plesiomorphies and a few derived apomorphies. As far as we can tell Hf never contributed to the human population, there is reason to believe that all other versions of H. erectus died out before the arrival of Hss on the Sumatra, (all the continent was connected prior to the current interglacial). But as I made the comment in the post on PaloeAnth history, dating is a weak point in many studies, the older the study the weaker the point is. It is sufficient to say there were many calvara all indicative of a near classic erectine presence as late as 50 kya. (redating places these at 250 kya).

In American everyone is crossed, I have genetic ancestry going back 2000 years that covers the entire region from Mesoamerica to east Asia and in Europe from Ireland at least to the middle east, one parent carried a variant of a asian haplotype that probably introgressed into Europe as the glaciers declined, both parents carry a haplotype modal in the near East. Another haplotype appears according to one paper (its a disease allele unfortunately, I got a double dose of) evolved from the recombination of a iberian haplotype and one of the quintessential early European/Eastern European haplotypes. I don't have any recent African ancestry to speak of, but if I have iberian ancestry dating from the last ice-age, its a pretty good assumption that I also have NW African ancestry from just before the end of the last ice-age to about 8000 years ago. I can probably rule out ancestry from S. India, S.Africa, Australia, SE Asia. Doesn't leave much of the world.

The idea of race in the Victorian sense is an illusion, the barriers that we perceive don't exist, there is a certain sharpness between geographies but there are almost always gradients somewhere in between, this is a characteristic of the modern population. This is why it is conceptually hard for modern humans to understand that in the past much much sharper barriers exist.

But that is not the end of the story, Denisova child has mtDNA suggesting admixture between Eastern Neandertals of that type with Homo erectus (or some other species, the mtDNA is not informative since we have no mtDNA from erectus, all hope of that was lost with Zoukoudian samples during WWII). It is potentially true that Neandertals eliminated all H.erectus except Hf, meaning they eliminated all that they did not interbreed with.
Don't take this as stock, but the initial characterization of Denisovan and comparison with human suggests that humans got none of the erectine DNA, in Addition the denisovans that humans mixed with apparently had other Neandertal content that denisovans of the cave did not have. So very complex. Seems like Denisovans split one mixed with more modern Neandertals and went SE the other mixed with erectines and went north. In terms of the _new_ admixture in the N.china Sea/Amur river region (notable by HLA variants) the information is not yet descriptive enough to conclude.

Science at this level is an empirical process with theoretical implications, we try to ascertain what happened based on what is observed. The problem is that the process is in-determinant. It could be as simple as he liked this one and but no other hes liked any of the other shes. Who knows.  

There is but one thought process that we often fail to consider. We often treat modern homo sapiens as the core species, during the middle stone age and early part of the late stone age Subsaharan Africa may not have been a core area but a peripheral site of human evolution, other than N.Afr-ME hominims SSAs may have been a daughter species, capable only of admixing with the parent or those that also recently admixed with the parent. In that realm there are diminishing probabilities with added distance from the region, but as the human population grew in Africa, and appears to have absorbed part of the core and mostly eliminated the rest, this created nascent barriers in the human population that probably decreased probabilities. SW asia is complex and hard to explain why the percentage introduced is so low in this context. One model is demic diffusion, cycles of replacement (which is not evident in the mtDNA).

 

[Scotius]

Privately, i'm surprised the ratio of admixture is so high actually. Hunter-gatherer groups of both Homo neanderthaliensis and Homo sapiens were by necessity quite small. I'd say low tens for Neanderthals as medium\big game hunters, half a hundred or so for modern humans - because of their more generalist approach to food sources, allowing them to get more sustenance from numerous small sources ( small game, berries, fish, shellfish etc.). At the same time mortality rates for both adults and infants were quite high, and life expectancy was low. Today a woman can have viable offspring past forty years of age. Thousands of years ago it was unlikely she would even live that long - which meant she would have 10 to 15 years for childbearing tops. Yet, despite those factors "conspiring" to wipe out any "mixed race" individuals before they'd grow up and pass their genes along, those admixtures managed to persist. In my opinion it means: either interbreeding was actually quite widespread, resulting in so many hybrid individuals they still managed to propagate faster than they died. Or, hybridisation carried evolutionary advantages favoring the survival of people with Neanderthal\Denisovan genes. Or both.

Am i on right track of thought?

[PB666]

3 hours ago, Scotius said:

Privately, i'm surprised the ratio of admixture is so high actually. Hunter-gatherer groups of both Homo neanderthaliensis and Homo sapiens were by necessity quite small. I'd say low tens for Neanderthals as medium\big game hunters, half a hundred or so for modern humans - because of their more generalist approach to food sources, allowing them to get more sustenance from numerous small sources ( small game, berries, fish, shellfish etc.). At the same time mortality rates for both adults and infants were quite high, and life expectancy was low. Today a woman can have viable offspring past forty years of age. Thousands of years ago it was unlikely she would even live that long - which meant she would have 10 to 15 years for childbearing tops. Yet, despite those factors "conspiring" to wipe out any "mixed race" individuals before they'd grow up and pass their genes along, those admixtures managed to persist. In my opinion it means: either interbreeding was actually quite widespread, resulting in so many hybrid individuals they still managed to propagate faster than they died. Or, hybridisation carried evolutionary advantages favoring the survival of people with Neanderthal\Denisovan genes. Or both.

Am i on right track of thought?

Funny you should ask that question, at least for humans given temporal distances between parturition  and spread between children in paleolithic societies some women should have had children late just to keep the population going, but for Neandertals, no. The classic Neandertal would have had matured early had children early and pretty much been ancient by the time they reached what we call middle age. For paleolithic societies people were on the move limiting opportunities for childbirth, on sustenance diet breast feeding might last 2 or more years, limiting fertility. Given a 2:1 ration it means women neccesarily had to have 3 children on average, that does not represent loss for other reasons and infertility (about 15% of the population or so by a certain age). So on average an effective female was reproductive for 12 years. Assuming she matures at age 16 that means she is still reproductive at 28. . . .thats the average, the high-end was pushing 40, the low end dies in birth of first child. (Even hudreds of years ago women were having children into their early 40s, not recommended but occasionally happened). See how things spread out in a distribution. For men its somewhat different, many societies did and still do have rights of passage for males, if they fail to make it to adulthood or fail to pass the right or where killed in inter-tribal violence or intra-tribal violence . . . . . . So this gets to the problem. And the late age for childbearing is not a fixture either. For example if there was an abundance of food and time affords the processing of food (for examples mussles, clams and oysters can be processed into a kind of milk, the tuber and other cooked foods and decrease the time a child spend breastfeeding and increase fertility). The critical issue for women and childbirth is health, for example, teeth (can go 50 years on  a healthy diet, not near as long on a starchy or fruity diet), parasite load (again what foods are you eating, what are you cooking, what are the indigeonous zoonotic diseases . . .malaria, blindness, sleeping sickness, chaga's cardiomyopathy. Provided they are athletic, healthy eat well many problems we see today disappear, but parasite load eventually takes out most.

There's another thing. Although women in Neolithic and post Neolithic societies could have children closer together, they and their children were less healthy. The study of bones of mesolithic Europeans were compared with the bones of Neolithic Europeans of the same period (Cow farmers basically). The mesolithic societies were healthier, the ate more fish and nuts, their bone mass indicated they were more muscular . . . .So its likely they were loosing less children. The immune genes were in tune with their natural diet (which becomes problematic when those genes are subjected to todays processed diet) more so than people who came into Europe from SW Asia and the Near East. So things are not always as they appear, in fact in Neolithic Europe there is multiple evidence of population crashes, in Mesolithic Europeans simply moved in a seasonal manner and moved to different places when things got tough, but they did settle, seasonally, in particular spots and suspect based upon shell-fish consumption that these are places were they stopped gave birth took care of children and then when the weather got cold, they moved south again to s. France or  Iberia. Genetically the closest relatives are today the Basque, Irish, Scottish, Cornish, Welsh, Norwegians, Swedish,etc. Within the region of Paris the population is almost entirely derived from non-western-Europeans of the Mesolithic and Early Neolithic periods (Lots of italian, greek, anatolian, middle eastern genes).  

There is no particular immediate advantage to inter-specific interbreeding, but in Indonesia there was one. If you follow the immune genes from Africa to India into Malaysia, the diversity of immune genes falls and in certain regions of Indonesia the B*24:01 frequency is as high as it gets in the human population. As it turns out human females have a preference for males that don't carry the same immune genes that they have (in fact not only does being a homozygote increase risk of death from novel diseases, but also increases risk for autoimmune disease). So that once the males of the tribes are homogenous in HLA types females would basically be desirous to interlope with males dissimilar to the males from their tribe. If the fixation of immune genes was severe enough these females would be repeatedly pinging the barrier and eventually it leaked (as one hypothesis as too why it leaked). The extraordinary sexual selection coefficient cause by fixation of immune genes could have created a statistical force that tested the species barrier repeatedly until it failed and it onely did so once or twice.

In the sea of Japan region there is a different situation. First the problem, we don't really know when but we do know there were two major (formative) migrations into the region. The first largely represented by today's Japanese Ainu came from the west via a transiberian route with admixture from the south (similar groups are Nadine speakers, Orochon, Amur river, Tlinglet) , the second came from the south via the Chinese coast, there are genetic similarities between the Okinawans and Tiawanese and potentially the indigeonous people of the Shandong peninsula (Xixian). Who came first is unclear, but my bets are on the waves from indonesia (given the finds on Ryukyu dating to 28 kya). But soon there after people were all the way up on the northern coast of Siberia. The impetus for interbreeding here is both diversification and adaptation to the norther climate. Humans are basically gracile, we are lanky thin individuals that live in hot low lying areas (rivers, lakes, coastlines and in the tropics). African derivatives were not particularly well suited for living in the Ice-age Arctic. But the Denisovans were adapted to both cold weather and high altitude (one of the genes found in tibetian plateau is a denisovan gene likely from Sea of Japan region). Under circumstances where humans bring a suite of traits that are not particularly adapted to NE Asia, but advantageous none the less. The pressure in these instance is like such.

Suppose humans can go to point X, say 35'North but then they stop, if they admix then the admixture can travel to 45' north, and so at 45' north admixture frequency increases and the impetus to admix also goes up. Eventually the resource genes are all captured and over 100s of years can sort through the population, later humans can travel to the Arctic circle. Not only this but the assortment of potential mates might favor mates of a different species, once again the pressures for survival and adaptation might have been constantly pinging the species barrier and tested sufficiently it leaked. These are the types of pressures that encourage some admixture. BTW the examples is not so clear cut, apparently humans could travel well into the arctic along the coast following food ~30 kya, but traveling inland would have been more problematic for them.

There are more nefarious schemes. For example in some culture if a mans wife dies, rather than upset the balance in his tribe, he might set out to steal someone elses daughter or wife (called wife stealing) is a practice in some tribes in NE Asia in NW America. In these situations there is little choice, for example a female might have been taken and forced to mate with a male (as many times as it took) until she had offspring or died trying. I generally don't give stock to noble savage schemes, but often such things are often the result of some matter of choice on both sides. In the case of a declining population (like Neandertals were) the choice between no tribe or a declining tribe and a foreign tribe presents these types of choices.

 

 

[kerbiloid]

3 hours ago, PB666 said:

The classic Neandertal would have had matured early had children early

How much earlier? They are already humans, not apes.
https://news.nationalgeographic.com/news/2008/09/080908-neanderthal-brain.html

Quote

Neanderthals Grew Fast, but Sexual Maturity Came Late

"brutal face" != "playboy"

 

3 hours ago, PB666 said:

Assuming she matures at age 16 that means she is still reproductive at 28. . . .thats the average, the high-end was pushing 40

How long did they live? How late were their climacteric changes happened? Why would the late maturing mean the late finish? Maybe it means just a shorter career?

3 hours ago, PB666 said:

The mesolithic societies were healthier, the ate more fish and nuts, their bone mass indicated they were more muscular . . . .So its likely they were loosing less children.

... or just were more muscular and could carry a heavier cargo on their head.
Modern people eat even better but need modern medicine to keep every 1:N baby alive.

Also Sapienses Sapienses were having the same diet, so this doesn't explain.

Spoiler

3 hours ago, PB666 said:

in Mesolithic Europeans simply moved in a seasonal manner

From one side of a glacier to another and back.

(Joking)

 

3 hours ago, PB666 said:

Genetically the closest relatives are today the Basque, Irish, Scottish, Cornish, Welsh, Norwegians, Swedish,etc.

Genetically how much of the listed are ancestors of much later invaders?

3 hours ago, PB666 said:

Within the region of Paris the population is almost entirely derived from non-western-Europeans of the Mesolithic and Early Neolithic periods (Lots of italian, greek, anatolian, middle eastern genes).  

They are still not Neanders. Even in Paris.

3 hours ago, PB666 said:

There is no particular immediate advantage to inter-specific interbreeding

Even if a Neander is 50% heavier than scawny ones of the tribe?

3 hours ago, PB666 said:

As it turns out human females have a preference for males that don't carry the same immune genes that they have

Proven fact or theoretical assumption?

4 boys vs 3 girls in a village. All of them are cousins. "19 year old and still not married" = "old maid and the shame of family"
What means "prefer"? Who is appointed by the parents, his/her immune genes are the best. So, the immune preferences are measured in heads of cattle or acres of plowland.

P.S.
https://en.wikipedia.org/wiki/Quest_for_Fire_(film)

depicts some aspects of how Neander genes could spread around a whole tribe.

Edited March 18, 2018 by kerbiloid

[Scotius]

Yes, genetic pressure is not everything. Across the history overwhelming majority of of societies had strong social taboos preventing incestuous relationships (marriages, basically). Families, clan systems, religious prohibitions etc. There must have been many instances, when individuals of both sexes were left with no other choice, than to look for a mate outside their clan or tribe. Given low population density in Ice Age, i wouldn't be surprised if for many of them, the only option in the range of several days of travel was members of that strange tribe of muscular hunters with weird language and customs. Or that strange tribe of thin, dark skinned clam eaters living near the sea shore. Voila! Numerous cases of intermarrying (voluntary... or not) of scandalous (but less scandalous than a brother marrying his sister) nature. And inevitable mixed race children. Rest was the population dynamics, which favored faster breeding generalists of the Homo sapiens sapiens species (race) in a dynamically changing environment of the ending Ice Age.

[YNM]

6 hours ago, PB666 said:

in fact not only does being a homozygote increase risk of death from novel diseases, but also increases risk for autoimmune disease

It's not too novel I think.

6 hours ago, PB666 said:

Suppose humans can go to point X, say 35'North but then they stop, if they admix then the admixture can travel to 45' north, and so at 45' north admixture frequency increases and the impetus to admix also goes up.

This sounds like Northeners and Southerners in England XD

 

But yeah, the large question is "how different they really are".

[PB666]

5 hours ago, YNM said:

But yeah, the large question is "how different they really are".

Two critical differences can form a species barrier. This is not to say they will appear first, but whenever or however they appear, it happens.

This was an old question of mine, it never particularly got answered in that how much isolation is bad, when does a population have to breed out to survive. The problem was that cliches in paleoanth believed what they wanted to believe irrespective of the facts and the questioned did not seem pertinent. Now we look at the molecular genetics and we really are not in a frame to ask where the ancestors of the 'admixed' parties lived. An example is Denisovan creates an exceptional conundrum. The sequence comes from a cave in central Asia and possibly SW Asia, the event occurred in Oceania and there is very little concern or debate as to how this came to be. Classic Neanderthals did not seem to be particularly interested in breeding-out, and its likely they're core would have gone extinct with or without humans. But the fringes of the population appear to have been buoyant, so in that regard it was human competition not some fantasy disease that resulted in the demise of most of the archaics (The term is pejorative since these almost certainly had their own suite of derived and adaptive traits). But if you think about it, currently for example with Denisovans, a few individuals (maybe 5) passed traits that are now present in 2 billion individuals at about a 1 to 2 percent level. That actually is pretty successful  (That's 40,000,000 people worth of ancestry). In particular these genes place people high up in the Tibetian plateau and are probably critical to the founding of the new world. When you compare that with the number of humans that entered Asia early on to go on and primarily represent Asia, thats reasonably successful. In the case of Neandertal contribution its not so clear cut. If the new studies prove to be correct, then some of the Eurasian percentage is going to be shaved down. But we are probably talking about this 'core' archaic population that lived in NAfr and SWAsia that humans bounced into and exchanged genes with over long periods. But in the push outwards in the direction of Asia proper, some sort of obvious introduction took place, some aspect of the archaic that SSAfr would not commonly had contact with (over the long periods of migrations in and out of SSAfr).

When we talk about Neanderthal we talk about whose Neanderthal and what Neanderthal. This is why I emphasized the paper by Woodworth, while he does define Homo rhodesiensis, he mentions on three occasions the strong affinity of the remains to Neanderthals and even paints a picture of this evolving through Neanderthals to humans. Homo rhodesiensis is obsolete terminology. And there is no widely agreed terminology to describe it. It is certainly not a predecessor of classic Neanderthals (at least in substance, because there are substantial remains in iberia that explain Hn evolution better) it may be a predecessor to human (although it could be an ancestor of a species living in S.Africa that recently went extinct).  There are several modern terminologies. Homo sapiens, Homo antecessor, Homo heidelbergensis. And so this gets into to the problem with NAfr and SW asian hominids, what are they?  They are very similar to humans, but evidence shows that humans arose in SSA, and these hominids contemporarily coexisted in NAfr and Middle east (as far back as 200 kya). The best answer is that they are derivatives of Archaic homo sapiens, which we are also derivatives of, IOW the same species. This may explain why no visible immune genes were passed, the human population in SSA already had captured these genes but we tended not to capture the fringe (or regionally adaptive genes). As a consequence when we move through the other edge of the core, we add Neanderthal contributions (And the core disappears), and what is left is homo sapiens sapiens and types of neanderthals.

So that the difference between Denisovans and SW Asian archaics is simply stepwise, they are a half to full step further away from humans than the SW Asians because of the isolation that distance affords. It also begs the question whether the barrier between the SW Asians was any greater than between denisovans, it does seem that there was insignificantly more of a barrier, but here again we don't know (can't see) the dynamics of the interactions. The interaction of humans leaving Africa with archaics may have been brief (doubtful), whereas the interaction with Denisovans may have been prolonged.

 

[PB666]

11 hours ago, kerbiloid said:

Neanderthals Grew Fast, but Sexual Maturity Came Late

The estimates given 8 years ago suggested females matured around the age of 9 o

 

r 10. When Neanderthals had calories, they probably had the richest source of calories one could imagine.
Neanderthals did not live long, European Neanderthals suffered from brutal injuries, such classified once as injuries expected from a rodeo rider.

 

11 hours ago, kerbiloid said:

Assuming she matures at age 16 that means she is still reproductive at 28. . . .thats the average, the high-end was pushing 40

Amoung the few remaining hunter gatherer societies, for example the !kung an adult can expect to have a life expectancy well into middle age, some take younger wives, so  . . .
!kung are exceptional however because they delay childbearing because of resource limitations. I don't think the life expectancy has markedly changed for the Namib dwellers in the last 150,000.

11 hours ago, kerbiloid said:

Genetically how much of the listed are ancestors of much later invaders?

The settlers came from many directions, about 8% of Irish is from W.Africa, there are a substantial smattering of ME, iberian (presumbably recent, of greece or East European), Italian, Greek proper, about 5% comes from East asia. There are two markers that I follow A2B7 and A1B8 and another, that hold at relative constant ratios in all these populations, they appear to have been diluted ~40 to 60% from the original makeup (the least are the NW Irish with pocket frequencies up in the 45% range. There maybe other particular haps that are also included so conservatively 40% dilution of the founder population. In the Parisian basin its more on the order of 90 to 95%.
 

11 hours ago, kerbiloid said:

.. or just were more muscular and could carry a heavier cargo on their head.
Modern people eat even better but need modern medicine to keep every 1:N baby alive.

Also Sapienses Sapienses were having the same diet, so this doesn't explain.

You are romanticizing the Neolithic, Neolithic tried to grow crops on the loess (Europe just coming out of the Arboreal phase) was not a nice meadows and decidous forest, lots of pesky conifer trees. Wheat types were monoploid with fiddly seed, and the problem here is that it was probably used as a fodder crop and only eaten in times of extreme scarcity. There is a hypothesis that Dolmans were placed at locations where Mesolithic Europeans (those living to the North and West) traded with Neoliths in order to get, so basically they lived off of some garden crops and herbs, milk and meat (and cheese as far north at the Isles). The mesoliths probably traded fish and shellfish bone tools and other implements for things like cheese, lemons, herbs, etc.  Its not until you have widescale replacement of the conifers with grassland and deciduous trees that the Neolithic begins to take hold.

Probably some dates you are unaware . .GB. first dairy > 8000 years ago (the Ilses early on where more suitable to cow cultures versus crop cultures).
Central Europe . . .7500 years ago LBK (thats the package, not the pottery . . .T1 taurids, pottery, monoploid wheat some diploid forms)
 England has just separated from continental culture, there is the Parisian culture, La hoguette, LBK, an Iberian version of corded ware pottery with some African influences, and of course settlement of Italy from the diffuse eastern mediterranean neolithic onset.

T1 Taurid means, essentially domesticated in NE greece, basically.
Monoploid wheat basically can be obtained anywhere is Europe, but the varieties grown were probably from the SW black sea region/greece. Emmers wheat was domesticated near the turkic syrian border, and Hexploid wheat (bread wheat) was domesticate about this time in what is now armenia and only much later spread to Europe. 

So basically when we talk about wheat cow pottery, think very primative, rather inept.

11 hours ago, kerbiloid said:

They are still not Neanders. Even in Paris.

Classic (European) Neandertals, as far as we can tell, went extinct. There are intermediates between Neandertals and Humans that were absorbed into the human population. These probably where best classified as Levantine Neandertals. Neither Iberia or the middle east are characterized (relative to other Eurasians) as having high Neandertal contributions. IOW, if you are investigating the Parisian population looking for evidence of Neanderthal introgression (as some have done in the past), you will have wasted the effort because there has been significant recent geneflow from Iberia and eastern Mediterranean. Currently the Eurasians considered to be most Neandertal like or the Central Asians/Mongolians. Those with the highest gene representation are the Koreans and Japanese (probably also includes the Orochon and people living n NE china/Manchuria) and now contested by recent finds. But the comparison between Neoliths and Mesoliths versue Late Stone Age and Neandertals is not lost, because in trying to survive an interior lifestyle (cave dwelling, basically joined to big game hunting) versus flexible humans that could afford to migrate to NW africa and back when those really harsh cold snaps hit Europe. What it takes for Neoliths to outcompete Mesoliths comes with multiple migrations into western Europe from the Mediterranean since the southern regions were prosperous. There are no comparables for Neanderthals, they had no prosperous rich uncles to the south quickly deliver new people after the last crash of the population. These migrataions afforded 3 or so thousand years to transform the landscape of Europe into one more hospitable for farming . . .Neandertals did not farm. I don't know if this proves anything, but it seems to indicate that humans had (after the LGM) a resource kit that allows them to changing circumstances and in fact cause a change in circumstances.

 

12 hours ago, kerbiloid said:

Proven fact or theoretical assumption?

4 boys vs 3 girls in a village. All of them are cousins. "19 year old and still not married" = "old maid and the shame of family"
What means "prefer"? Who is appointed by the parents, his/her immune genes are the best. So, the immune preferences are measured in heads of cattle or acres of plowland.

I used to participate in Y-VNTR analysis, despite what you think, false paternity is not as uncommon as you think. The idea of a sexual selection coefficient and interloper potential sort of skirts the idea of arranged marriages.
What I have found that the more conservative a culture pretends to be, the more productive interloping goes on. Again, some of the participants even deny having sexual relations with another man, even though the VNTR shows (after repeat analysis) that husband is not the father of the son (and you thought this only occurred on Maury Povich).  When a culture has open female selection of mates (not even marriages but temporary arrangements) there tends to be more rapid evolution (recombination) of immune genes versus constrained relationships were genes tend to flow from outside groups. If sexual selection is removed, a major component of balancing selection is lost, that sets up a situation where fixation of genes can occur, that only increases the sexual selection pressure for the next generation of females. This makes sense, because maintaining diversity also maintains the templates for recombination and thus introducing more diversity. But to give the paleolithic humans a break, isolation was often not enforced, the moved to a place with abundant food and a limited number of individuals, drift happens in small populations and fixation occurs quickly. If you repeat this process 10 or 20 times, no matter what the breeding system, diversity is lost, by the time humans cross the Wallace line, they are ripe for outbreeding.  Immune diversity may not be the only reason, healthy tribes also tend to have diversity in behaviors, these may also be under balancing selection. Effective leaders can also sometimes tend to have traits you might not want fixed in the population (such as bipolar personality disorders).

Interloping in chimpanzees and gorilla societies has also been observed, and for good reasons, if females permanently stay with the group. Once the dominant males have bred with all the older females, then the future of the tribe will be dominated by those males genes, so introduction of some variation, even if a subdominant male could be advantage to their offspring during the next major disease epidemic. Variable selection can take a dominant male and turn him into a subdominant male (i.e. dead) overnight, so . . . . Remember that generally all the females are either sisters, cousins or mothers of each other and a long standing male may have most of the progeny, this limits the number of combinations to around 8 for certain defensive loci. If a female mates with a male not exposed to the other females she can increase the number of combinations by two and make it more difficult for disease to spread and most important spread from the 8 bearers to her progeny. This is know as herd immunity. The number of effective breeding members in a sort of classic tribe of humans is maybe 20 or 30, if this splits to settle an island 10 to 15 or less. 

The bottom line here is that there are reasons to have all the females mate with the dominant males, but also there are a few reasons not to do this, this then gets balanced out in the behaviors.

Oh and female choice not to mate is not uncommon even in stone-age societies, these are sort of a reserve, in case a female parent dies. Prefer means that she marries the guy who kills the biggest monkeys, but when he is out killing monkeys she finds her own monkey to play with. But too the point, we don't know that this is female human and archaic male. The Y chromsomal studies from central Africa are suggestive that it did occur once, that it was possible in that direction.

 

[PB666]

Mesmiaskaya strikes again.

https://arstechnica.com/science/2018/03/five-new-ancient-genomes-tell-us-about-neanderthal-tribes/

Quote

 The finding implies that the population of Neanderthals in the Caucasus may have been wiped out at some point and replaced by an influx of Neanderthals from another region. The two events might not have been directly related, as that time window coincides precisely with “pronounced climatic fluctuations” in the region. -  Cathleen O'Grady - 3/22/2018, 3:14 PM - Five new ancient genomes tell us about Neanderthal tribes

Quote

The authors of the paper write. “no indications of recent gene flow from early modern humans to late Neanderthals,” Apparently Mateja Hajdinjak at MPI

Quote

The data also suggested that Neanderthal gene flow into humans happened before these five individuals were alive—between 70,000 and 150,000 years ago. -  Cathleen O'Grady - 3/22/2018, 3:14 PM - Five new ancient genomes tell us about Neanderthal tribes

So apparently they are going to reconstruct the European Neanderthal population.

Its apparent that Neandertals moved back and forth with the climate, and while humans and overlapped in Europe, the Neanderthals probably would have preferred the coldest areas, and was Europe was unusually cold, humans tended to move to the warmest areas. This may explain why AMH and European (classical) Neanderthals never intermixed. Lifestyles were incompatible.

[Green Baron]

8 hours ago, PB666 said:

https://arstechnica.com/science/2018/03/five-new-ancient-genomes-tell-us-about-neanderthal-tribes/

Its apparent that Neandertals moved back and forth with the climate, and while humans and overlapped in Europe, the Neanderthals probably would have preferred the coldest areas, and was Europe was unusually cold, humans tended to move to the warmest areas. This may explain why AMH and European (classical) Neanderthals never intermixed. Lifestyles were incompatible.

The article: https://www.nature.com/articles/nature26151

Though there are difficulties isolating the DNA due to poor preservation and contamination a special treatment allowed the isolation of 5 (39-47kyr) late Neandertals, from the Caucasus to western France.

The linked arstechnica article replicates the findings quite well but interprets a little more than the original paper. The "pronounced climatic fluctuation" persisted throughout OIS 3 (80.000 - 25.000 bp) and clearly did influence human occupation, be they Neandertal or modern human. It is another thing that Neandertals apparently did prefer warmer climates than modern humans, the latter being slightly more adaptable, as the article says, extreme cold might have driven some Neandertal groups out. The better adaptability of modern humans might be due to more sophisticated stone and bone tool technologies. This is a decades old discussion. (latest contribution i know of)

Neandertal and modern humans did intermix, as the article states. It only appears that these late specimen had little to no traces of modern human inflow. Most Neandertal inflow in modern humans happened from a population(s) that diverged from these Neandertal genomes here about 70.000y ago, so the conclusion. Together with a comparison of 2 geographically close but timewise apart Neandertals from Mesmayaska (1 and 2) this could mean that a "population turnover" happened in Neandertal populations between 70.000 and 45.000.

 

The study reflects the current state of ancient genome handling. It may be corrected or amended by future findings.

 

There is no "lifestyle incompatibility" between modern humans and Neandertals, nothing hints in that direction. If at all, then Neandertals retreated to warmer areas during cold phases, while modern humans stood the harsh conditions a little better. But that is another story.

 

Edited March 24, 2018 by Green Baron

[PB666]

3 hours ago, Green Baron said:

The article: https://www.nature.com/articles/nature26151

Though there are difficulties isolating the DNA due to poor preservation and contamination a special treatment allowed the isolation of 5 (39-47kyr) late Neandertals, from the Caucasus to western France.

The linked arstechnica article replicates the findings quite well but interprets a little more than the original paper. The "pronounced climatic fluctuation" persisted throughout OIS 3 (80.000 - 25.000 bp) and clearly did influence human occupation, be they Neandertal or modern human. It is another thing that Neandertals apparently did prefer warmer climates than modern humans, the latter being slightly more adaptable, as the article says, extreme cold might have driven some Neandertal groups out. The better adaptability of modern humans might be due to more sophisticated stone and bone tool technologies. This is a decades old discussion. (latest contribution i know of)

Neandertal and modern humans did intermix, as the article states. It only appears that these late specimen had little to no traces of modern human inflow. Most Neandertal inflow in modern humans happened from a population(s) that diverged from these Neandertal genomes here about 70.000y ago, so the conclusion. Together with a comparison of 2 geographically close but timewise apart Neandertals from Mesmayaska (1 and 2) this could mean that a "population turnover" happened in Neandertal populations between 70.000 and 45.000.

 

The study reflects the current state of ancient genome handling. It may be corrected or amended by future findings.

 

There is no "lifestyle incompatibility" between modern humans and Neandertals, nothing hints in that direction. If at all, then Neandertals retreated to warmer areas during cold phases, while modern humans stood the harsh conditions a little better. But that is another story.

 

Which is why i said classic Neandertal, the only mixture to date detected is in SW asia in a period and place best qualified as Levantine. The time period is not 70, but 70 to 150, it looks like MPI has finally been fixing thier clock. Most argue 75 to 100k. 

The study is likely to be refined with more findings. The statistics are begiining to build. 

Again my best calibrations of mtDNA, which unlike other clocks, accounted for adaptive evolution of mtDNA place African exit of N at 85,000 years ago. Since that estimated was made there have been essentially no improvements on the data. What this means is if gene flow happened before that time, then it occuurred in Africa and after in SW Asia. The model in Africa is indifferent as either it was or there was backflow. Tishkoff tends to think thats it backflow. 

Humans were not well adapted to the climate in Europe, despite what you think, the criiter data from the LGM to the Younger dryas, consistent with imm genes indicated that people bottled up in refuges when confronted with cold, even after the LGM ended. 

At the time moderns arrived in Europe Neadertals were better adapted. 

[Green Baron]

54 minutes ago, PB666 said:

Which is why i said classic Neandertal, the only mixture to date detected is in SW asia in a period and place best qualified as Levantine. The time period is not 70, but 70 to 150, it looks like MPI has finally been fixing thier clock. Most argue 75 to 100k. 

Source ? This study, published in Nature, does not place a date, but a population that derived from N before 70.000 from now which must be explained further because we have no modern humans in Europe before 45.000bp. And it concedes willingly that the dates can shift. It is based on 5 individuals spread all over Europe, i certainly expect further u-turns by genetics in the future as to when and where. If i just look at what they did to the poor chemistry to get any information at all ...

The mixture may have taken place much later, just not with people from these groups. It probably did.

Quote

Humans were not well adapted to the climate in Europe, despite what you think, the criiter data from the LGM to the Younger dryas, consistent with imm genes indicated that people bottled up in refuges when confronted with cold, even after the LGM ended. 

What i think is irrelevant, findings are relevant. All humans certainly were, from early erectus in Dmanisi on. Mapping find sites and reconstructed climate of Neandertal and modern human sites show a clear correlation between snow cover, temperature and occurrence in favor of modern humans, even if i don't like it (Excerpt). Genetics are NOT the only source of knowledge, indeed they are one that still needs a lot of work. But it can already contribute !

Quote

At the time moderns arrived in Europe Neadertals were better adapted. 

How do we know ?

It may well be that climate change actually played a role in Neandertal extinction, while modern humans, larger in number and with a better tool set, survived.

https://www.sciencedirect.com/science/article/pii/S1040618204002344

Edited March 24, 2018 by Green Baron

[PB666]

2 hours ago, Green Baron said:

Source ? This study, published in Nature, does not place a date, but a population that derived from N before 70.000 from now which must be explained further because we have no modern humans in Europe before 45.000bp. And it concedes willingly that the dates can shift. It is based on 5 individuals spread all over Europe, i certainly expect further u-turns by genetics in the future as to when and where. If i just look at what they did to the poor chemistry to get any information at all ...

The mixture may have taken place much later, just not with people from these groups. It probably did.

First, off MPI has typically used a late C/H LCA as a reference point, so when they say greater than 70 you have to keep that in mind. Yes, 150ky does sound a bit early, but the confidence range is rather encompassing (which is what confidence ranges should be, encompassing). My assessment works on a different basis than theirs. As to date is appears that all the evidence for admixture has been captured in 'form' if not in substance. There will be details on the substance forthcoming as these sequence of exo-specific genes are examined. The more recent study indicating admixture in NE completes the corroboration between my own estimates and what MPI now predicts. Prior to this MPI and my interpretations were a bit out-of-synch, including their interpretation of the spread of Denisovan traits. Over time the gap has closed and now, it appears to be closed. You should interpret to mean there is very little wiggle room for significant admixture elsewhere.  This is molecular genetics. Admixtures that underwent removal from the population are not a matter of concern because of the biases present in 20th century archaeology do not present a foundation for questioning and negating false hypothesis. You cannot know whether these are stable or unstable (as in persiste 1 or few generations before extreme negative selection, the barrier, takes its effect).

When we talk about aDNA sequencing is you get these huge files (The denisovan sequence was 48 gb) of sequences that are aligned to create a genomic sequence. Many many passes. The first genome was actually the worst, since then marked improvements have been made in isolating good DNA and getting good aDNA sequence. Once you have a Neanderthal sequence that aligns well with others then its a matter of classifying the potential errors. In the world of a DNA sequence there are two primary errors, given the pairing of (C:G)(A:T) cytosine deamination is the predominant error that results is the conversion of deoxy cytosine with uracil, and uracil then binds deoxythymidine instead of deoxyguanine. As a result you get C->T and G->A posthumous changes in the DNA. These appeared rampantly in the first mtDNA and the first genome (which did not have that many passes). Techniques now have cleaned all that up. If you have enough sequence to derive a genome, then you probably have enough passes to root out the errors and they will be few and far between.

 

5 hours ago, Green Baron said:

What i think is irrelevant, findings are relevant. All humans certainly were, from early erectus in Dmanisi on. Mapping find sites and reconstructed climate of Neandertal and modern human sites show a clear correlation between snow cover, temperature and occurrence in favor of modern humans, even if i don't like it (Excerpt). Genetics are NOT the only source of knowledge, indeed they are one that still needs a lot of work. But it can already contribute !

Quote

Modern humans were not protoErectines. We DID evolve and erectines evolved, more or less separately after a given period of time ~800,000 years ago. And on top of that we have relatively precise timing telling us when modern humans left Africa and spread northward into Asia, As stated above the window was much less than 100,000 years. In the case of Homo georgiensis they have no fathom how much longer this protoErectine lineage first left Africa or how long it took for them via adaptive evolution to reach the Caucasus region, and even that is not near as severe as central European climate during a cold spat. So that is one clear logical flaw in the argument. The proto evolution of erectines is a mess, many assumptions that cannot be demonstrated. Modern humans evolved in Africa, if we had the ability to enter Europe 70-85 ky we certainly would have, as we moved into India and many points Eastward before the presence of AMH in Europe. Even if I use an extremely late timeline, say 60ky, it still takes 20ky humans to move 500 miles to the NW into Europe. Whereas within that 60 to 42kya period they would have had to have travel 6000 miles from SW asia to the Solomon islands. Thats an appreciable bias in the rate of migration and its indicative of selective preferences, simple as that. 

The mtDNA evidence and the evidence regarding central African admixture suggests a rather slow initial progression from E/SE Africa north and northwest in Africa. The L2/L3 mt DNA are more or less like layers on a a cake, as humans spread north they introduced another layer. Sometime shortly after L3 evolved (probably 2 or 3 thousand years) humans permanently left Africa, admixed with other archaic derivatives while dispersing in parts of SW Asia. While it is clear to others that this admixture did not occur in Africa, I have reasons to believe it might have. The evidence I draw upon are a set of human haplotypes that have been poorly studied in N.Africa. From these studies they detailed an area extending from SSA to N. Mediterranean coast.  WIthin these a pattern appears that the common ancestral population of the haplotypes no longer exists (what I like to call the rosette). The by products are spread into areas to the North and West (iberia where N concentrations are lower than expected) and to the NE (where N concentrations are higher than expected). This suggests that there is at least the potential as early as human occupation of superequitorial Africa that events occurred followed by near complete dispersion. Most of the dispersed admixtures ended up in Asia, some in Africa, and non-admixed displaced the population of whatever was in NW africa. I consider just as likely as admixture in SW asia.  

The primary issue is relational, not chemical, that's where you need to clear your mind. We do not have a map reference for every late archaic derivative, we have only the mapped references for those whose DNA survived. So that when we do a search and ask who is the closest, its going to give an answer that is better than no answer at all but that may not be the best answer (and this part of the problem created a bias that blinded MPI for almost a decade from seeing other possibilities). That is the problem. If we ask a different question, the question I asked, what highly evolved genes do not belong in SSA-derived humans, you get a different set of answers. The first clear example comes from the region just southwest of lake Chad in Africa (verified in several steps) multiple, possible 10 admixtures and recent (<70 ky), the second comes from the region of NE Yellow sea region and sea of Japan (verified 2018). This region indicates a minimum of 3 admixture events (3 offspring introduced). The third comes from Indonesia (Verified 2012) and a minimum of 1 event. There is nothing to suggest anything in Europeans that did not come from SSA. 6-loci, 5000 variants, nothing.

SO if this admixture occurred Levant or Arabia where did it go.

To see how this falls out, a more detailed look at Denisovans indicated that the D content to Indonesians was not simple, but complex, that content itself appeared to be an admixture of traits not found in the Altai - Denisovan sequence (where as Altai has evidence of erectine? no present in Indonesian admix-Denisovan sequence). There is a base assumption that humans were a species, and any reasonable doubt places a barrier between classic N and modern H. That says nothing about the between. It is apparent from the d-admixture that something in between N/D/H was capable of mxing with D, probably capable on repeat exposure of admixing with H and likely admixed with N. Of the three D appears the most distantly evolved, which means that if it could so, could have admixed with SSA-derived humans. So it appears there was a barrier between H and N living in Europe. If we type what was going on in the Levant 50,000 years prior what you probably find is an intermediate, not modern human in its content not really Neandertal and trace amounts of Denisovan. In the N. part of the range it was more Neanderthal. In the Eastern part of the range it was more Denisovan. In Africa it was more human like and forth-party-like. When human travel into NE Africa they admix, but the human content in that intermediate is invisible to us (its not subtractable), we only see that part that is different within its componentsfrom the African human population. If you move further east, finally into SW asia, more mixture, more chance at capturning N, but also more chance of hitting the barrier.

In that light, we look at trait evolution in N. Africa and the Levant, and compare, based upon what we know about were modern humans (SSA primarily of origin) came most recently from we see the potential collison of two gradients, genes migrating from one direction with some admixture over time (thus these immune genes already exist in humans) and a pre-existing gradient from Europe which collide in the middle east or Arabia. So that genes, even variable genes get filtered out over time by local selection. So what is SW Arabia and the Levant more like, is it more like Europe or more like the Horn of Africa, that will determine the most likely persistent of the immune genes. Yes, there are candidate genes that might have infiltrated with this particular group, I have these genes identified and they were later successful in Europe, but they also exist in the far reaches of Africa, just much less commonly, its wishy washy. The point about Europe has been made many times in diverse papers. The immune genes of Europe have very tiny amounts of variation relative to other non-african populations, this is not something one expects on admixture. Take for instance the HLA A*02 gene, The gene is part of one of three haplotype cluster that is common to the most isolated Western Europeans the A2C5B44 hap. And yet, oddly this very old European haplotype has 3 loci-alleles that show very little variation that might be expected from a gene that persisted for a long period of time (say 200,000 years). In the Baloch part of Iran and Pakistan, there are a magnitude more A2 variants per a given sample size. This is not simply an affair of one locus or one allelegroup of one locus. Its all European loci and all variant groups at those loci look as if they recently arrived from elsewhere.

 

 

5 hours ago, Green Baron said:

t may well be that climate change actually played a role in Neandertal extinction, while modern humans, larger in number and with a better tool set, survived.

Yep, but then again during very cold period Neanderthals would have needed a larger range because less biomass production (That is why I refered to the critter data, only the very most hardy critters could surive at the LGM outside of the refuges, these are animals that survive in places were even recent moderns find it very difficult to survive). [I have a ton of reviews on this stuff, I just have to dig it out of my very dusty files].

But the Neanderthals could persistently survive in Europe, the last Neanderthals were found in Europe and there was extensive overlap.

https://www.smithsonianmag.com/science-nature/the-rock-of-gibraltar-neanderthals-last-refuge-42545293/

If we assume that Homo heidelbergensis is protoNeanderthal and given this and given the climate extremes of 500,000 years we cannot have a sustained presence of N in Europe and Western Asia without region specific adaptations, that's just plain silliness, human mtDNA underwent regional evolutionary adaptation traveling 10,000 years through Siberia to S.America. While their ancestors may have originated, classic Neanderthals are a West Eurasian hominid, not a equatorial African hominid.

From my point of view, what I studied, is that Iberia was critical, not just as the last place of the Neanderthals, but also as a place were African immune genes were directly introduced to Europe and evolved to a unique state with a molecular clock on that state as late as 20kya. So this means that humans probably crosses the very same point where Neanderthals last existed, more or less about the same time, but there is no evidence of admixture, not in the immune genes, not in specific to the time in the genome. Again, it is very incredibly unlikely that these Gibraltar Neanderthals were the very last, that they were the only ones, and certainly other humans made it to Iberia earlier, and we know that Iberia was an Ice-age and pre YD refuge. So that both humans and Neandertals are weathering out an Ice-age end in the same place. So how exactly are they cohabitation in a confined area and not mixing. 

One potential explanation lies in the genes that arrived from Africa. This particular gene is maladaptive in modern times, but _seems_ (this is a guess that immunologist I know have thrown around) to have been protective for people engaging in maritime foraging activities. Humans possible traveled over, fished in Iberia, harvested clams and seaweed, other shellfish, lived near a coastline long buried by the current stand, from the paleolithic a high C-13 content in the bones and comparison between N and H suggest humans stayed near the coast, probably moved on the water to avoid bad weather and simply avoided Neanderthals who liked to hunt inland. The people in Western Eurasia who have the highest ratio of West African:East African genes typically have the lowest content of Neanderthal admix contribution, so basically these markers mark something else, a relative genetic aversion to Neanderthals. Neanderthal genes were probably most adaptive for people who hunted the interior of continents, just as Denisovan genes benefit modern Tibetans. Likewise the Eurasians that have the highest East African ratios also tend to have the Highest Admixture ratios (not necessarily Neanderthal, again a new debate has opened up in NE Asia).

Time will tell, molecular genetics marches, if you find the molecular genetics troubling, and have difficult explaining cro-magnon remains, you might also consider dating problems and other issues of poor archaeology.

 

 

[Green Baron]

18 minutes ago, PB666 said:

... you might also consider dating problems and other issues of poor archaeology.

I certainly do. Poor archaeology usually doesn't find a way in the journals and if it does it won't take long until people start to frown. And normally difficulties and uncertainties are discussed. If not, that may be a hint that something has not been taken into consideration.

Otoh poor genetics did find a way into the journals in its yet short history, and ancient genetics is a hype right now. It'll level off again. What i criticise is not the working principle but the absolutism of the presentation, unproved claims and misinterpretations. An extreme case was Woodward's definition of Homo rhodesiensis in distinction of Neandertals, gladly the case is closed. I don't want to add more bad vibes by tearing apart some of the claims in the OP.

So, let's keep it civil, stay away from false claims and respect each other. In case of different opinions these can be underlain by links other than pop science. I can read and understand most of it ;-) (not all)

[PB666]

6 hours ago, Green Baron said:

Otoh poor genetics did find a way into the journals in its yet short history, and ancient genetics is a hype right now. It'll level off again. What i criticise is not the working principle but the absolutism of the presentation, unproved claims and misinterpretations. An extreme case was Woodward's definition of Homo rhodesiensis in distinction of Neandertals, gladly the case is closed. I don't want to add more bad vibes by tearing apart some of the claims in the OP.

So, let's keep it civil, stay away from false claims and respect each other. In case of different opinions these can be underlain by links other than pop science. I can read and understand most of it ;-) (not all)

Early on, yeah, alot, but since then things have markedly improved, namely if you publish crap people will call you out and fast for it. Most of MPI sequence data is online, I have a fair amount of the early stuff. Now a days, if you publish 5 genomes, there is so much data that these types of errors that might lead to marked misinterpretation are rare.

But lets compare the two, molecular anthropology started in 1975, the first credible paper in 1980, lots of crap in the 90s alot of reform at the turn of the millennium. And just to point, these were not errors it took 10 years to find, we found the errors immediately, reported them immediately. Top dog published a paper in 1995 and you did something not kosher, in a month the bbs were hopping with critiques. Paleoanthropology started out with immense bias, fraud, frauds that persisted for almost a half a century, bias based upon fraud, assumptive dating techniques . . . . . . Its no wonder that molecular genetics turned it upside down. There is almost no comparison between the two fields.

Anyway suit yourself, the molecular genetics is only going to strengthen its case, as it is doing.

 

 

Edited March 25, 2018 by PB666

[PB666]

http://www.ox.ac.uk/news/2018-03-21-oldest-dna-africa-offers-clues-ancient-cultures

Late stone age of Morocco, ancient DNA sequence.

[Green Baron]

[snip]

22 hours ago, PB666 said:

Paleoanthropology started out with immense bias, fraud, frauds that persisted for almost a half a century, bias based upon fraud, assumptive dating techniques . . . . . . Its no wonder that molecular genetics turned it upside down. There is almost no comparison between the two fields.

[snip] Nothing is turned upside down, this is only your grumpy attitude. Science is not about fighting. When there are contradictions these must be resolved and maybe they will.

I introduced myself to you via PM and asked who you are as you always mention your work, research and pretend to be a studied guy. But you ignored it and instead turned the info i gave you against me in the OP by generalized barking against archaeology.

On 3/15/2018 at 6:40 PM, PB666 said:

What did I say?

Year, what did you say ?

Quote

http://blogs.discovermagazine.com/deadthings/2018/03/15/interbreeding-denisovans/#.WqsdGech2Ul

Here's another paper reinforcing something I mentioned about 2 months ago concerning Europeans (and the general problem of publishing new molecular genetic ideas concerning Europeans because of the underlying bias in archeology and anthropology). Alot of the articles are old hat,

There is no underlying bias, only what you accept to include in work or what you refuse. Classic archaeology without genetics can and does say only little about Denisovans because there is almost nothing. You cannot accuse them for anything. One or two potentially other find places from last year in China still wait for proper publications. So, this is a highlight for genetics.

Quote

Spanish molecular geneticist noted waves of migration from Africa direct to different regions of Europe, the conclusions did not suit well at all with archeologist.

Archaeology has always discussed several probabilities and left the actual ways open. Different probabilities for different human species and times, climates, sea level stand, palynological data, faunal or floral stages. Really, do you know at all howarchaeology works ? I doubt it ...

Quote

The most profound was the highly apparent founder affect in the settlement of Sardinia, which archeaologist concluded was settled by the eastern mediterraneans. Nope, first colonized be NW Africans and that DNA compliment is still significant part of current population.

And as usual a claim without a source and embedded in generalized scoffing. Is this all you have ? Afaik Sardinia got its first people in the epipalaelothic from Iberia and or Italy. But this is speculative. Even genetics point to Europe as the source for the first settlement, not Africa. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5400395/

Or have you something newer on this ?

Manmanman, you are tedious ...

--------------------------

The work you linked above is a good piece (http://science.sciencemag.org/content/early/2018/03/14/science.aar8380.full). Contradictions will be resolved one day, where is the problem ?

 

Edited March 25, 2018 by Vanamonde

[PB666]

[snipping rambling retort to last weeks topic]

As i said suit yourself. The molecular genetics will inevitably win the day and peal backs decades of false assumptions, some will still refuse to accept the conclusion, due to their past allegiances, but then isnt the cycle of life and death the way humans evolve.