July 26, 2012

New evidence for archaic admixture in African hunter gatherers (Lachance et al. 2012)

At the end of last year I predicted that full genome sequencing would begin turning up evidence for more archaic admixture in Africa. Halfway into the year, it appears that my prediction has proven to be correct: a new study in Cell by Lachance et al. documents the existence of such admixture between an archaic hominin and Pygmies from Cameroon, and the East African Hadza and Sandawe.

Archaic admixture in Biaka and San was previously detected by Hammer et al. Hence, we now have evidence for archaic admixture from several regions that encompass all major regions within sub-Saharan Africa. It seems that my old idea about layers of Palaeoafricans being absorbed by early modern humans in Africa was basically correct, and that some of these layers correspond to archaic African populations.

But not all agree. The New York Times coverage of the paper suggests that there is a controversy surrounding the new study:
All human fossil remains in Africa for the last 100,000 years, and probably the last 200,000 years, are of modern humans, providing no support for a coexistent archaic species. 
... 
Paleoanthropologists like Dr. Klein consider it “irresponsible” of the geneticists to publish genetic findings about human origins without even trying to show how they may fit in with the existing fossil and archaeological evidence. Dr. Akey said he agreed that genetics can provide only part of the story. “But hopefully this is just a period when new discoveries are being made and there hasn’t been enough incubation time to synthesize all the disparities,” he said.
This is of course completely wrong; as Chris Stringer mentions in the NY Times piece, there is ample evidence for archaic Africans down to quite recent times in the form of Iwo Eleru and Ishango, and there is more evidence besides. Indeed, it does not appear at all that there was a punctuational event that replaced archaic hominins with a new Homo sapiens species. If anyone wants to criticize the new study, complaining about it being in disharmony with physical anthropology is not a good way to go about it. Nor is it, of course, "irresponsible" to report the new findings.  And, apparently, there is more on the way:

In a report still under review, a third group of geneticists says there are signs of Neanderthals having interbred with Asians and East Africans. But Neanderthals were a cold-adapted species that never reached East Africa.
Things are bound to become quite interesting.

From the paper:

A striking finding in our data set is that compelling evidence exists that extant hunter-gatherer genomes contain introgressed archaic sequence, consistent with previous studies (Hammer et al., 2011; Plagnol and Wall, 2006; Reich et al., 2010; Shimada et al., 2007; Wall et al., 2009). We note that unambiguous evidence of introgression is difficult to obtain in the absence of an archaic reference sequence, which currently does not exist and may never be feasible given the rapid decay of fossils in Africa. Although we carefully filtered our data set in an attempt to analyze only high-quality sequences (Supplementary Information), it is possible that unrecognized structural variants or other alignment errors could generate a spurious signature similar to introgression. Encouragingly, we did not see an enrichment of structural variation calls in our candidate introgression regions. Additionally, through extensive simulations and analysis of European whole-genome sequences (Supplementary Information), we have demonstrated that the signatures of introgression that we observed are unlikely to be entirely accounted for due to other aspects of population demographic history, natural selection, or sequencing errors. Moreover, we did not find strong evidence that introgressed regions were clustered in the genome more often than expected by chance (p > 0.05; Supplemental Information). Nor did we find significant evidence that introgressed regions were enriched in genic regions (p > 0.05); rather, genic regions were significantly depleted for introgression in several populations (Supplemental Information). Therefore, the simplest interpretation of these data is that introgressed regions in extant human populations represent neutrally evolving vestiges of archaic sequences. In short, we find that low levels of introgression from an unknown archaic population or populations occurred in the three African hunter-gatherer samples examined, consistent with findings of archaic admixture in non-Africans (Reich et al., 2010). 


What are the implications of the new research? Where did modern humans actually originate and how can their archaic admixture be explained?

One possible explanation, consistent with multi-regional evolution (MRE) theory, is that modern humans didn't originate anywhere in particular; they emerged out of Homo populations that lived everywhere. And, certainly, the discovery of archaic admixture of a local origin is quickly reducing the number of places where the common ancestors of modern humans could have begun their expansion. Western Eurasia is out due to Neandertals; East Eurasia and Oceania is out due to Denisovans; the entirety of Sub-Saharan Africa seems to also be out. North Africa and Southwest Asia appear to be the only remaining candidates.

I don't particularly agree with MRE; one of its predictions (about the relevance of archaic hominins to the human story) has proven to be correct: it increasingly seems that there never was a new Homo sapiens species that was in reproductive isolation from the rest of the Homo genus. On the other hand, the existence of local admixture with different sets of archaic hominins, together with the relative homogeneity of our species is indicative of a range expansion that largely replaced archaic humans -- but not completely.

There does seem to have been a Big Bang of modern humans which caused the demographical explosion of a particular subset of genetic variation. This Big Bang is often associated with Out-of-Africa, but there are good reasons to doubt the traditional 60,000-year old Out-of-Africa theory, according to which humans from South or East Africa crossed into Arabia and followed the coast to populate the world. We now have more reasons to doubt this: evidence of archaic admixture in both the postulated homelands: South Africa, often cited as the region where the first signs of behavioral modernity appear, and East Africa, where the earliest anatomically modern human fossils appear.

My money continues to be on the "two deserts" theory I have proposed some time ago:

  • A green Sahara pumping the ancestors of modern humans pre-100 thousand years ago, and 
  • a deteriorating green Arabia pumping them post-70 thousand years ago, with some back-migration into Africa.
This would relate the two regions where no evidence (yet?) for archaic humans exist (North Africa and South West Asia), explain the causes of their dispersal (climate change), and harmonize with the evidence for archaic admixture, since the expanding wave of modern humans would partially absorb pre-existing hominins in both Sub-Saharan Africa and across Eurasia.


It must be noted that scientists have been rather conservative in their estimates of archaic admixture in the absence of ancient DNA sequence. Recombination obliterates traces of really old admixture, because introgressed segments become ever smaller, resulting in a pastiche of modern and archaic sequence that no longer looks statistically archaic. But, hopefully, the ever-solidifying case for archaic admixture in our species will finally deal the death blow to tree models, and reveal a much more interesting story of our origins.


Other coverage of the new paper: Nature, Science, ScienceDaily, EurekAlert, Washington Post, SciAm.


Cell doi:10.1016/j.cell.2012.07.009

Evolutionary History and Adaptation from High-Coverage Whole-Genome Sequences of Diverse African Hunter-Gatherers

Joseph Lachance et al.


To reconstruct modern human evolutionary history and identify loci that have shaped hunter-gatherer adaptation, we sequenced the whole genomes of five individuals in each of three different hunter-gatherer populations at >60x coverage: Pygmies from Cameroon and Khoesan-speaking Hadza and Sandawe from Tanzania. We identify 13.4 million variants, substantially increasing the set of known human variation. We found evidence of archaic introgression in all three populations, and the distribution of time to most recent common ancestors from these regions is similar to that observed for introgressed regions in Europeans. Additionally, we identify numerous loci that harbor signatures of local adaptation, including genes involved in immunity, metabolism, olfactory and taste perception, reproduction, and wound healing. Within the Pygmy population, we identify multiple highly differentiated loci that play a role in growth and anterior pituitary function and are associated with height.


Link

39 comments:

  1. "This would relate the two regions where no evidence (yet?) for archaic humans exist (North Africa and South West Asia).."

    Huh? What about Neandertals in the Levant who apparently replaced AMH there?

    "And, certainly, the discovery of archaic admixture of a local origin is quickly reducing the number of places where the common ancestors of modern humans could have begun their expansion. Western Eurasia is out due to Neandertals; East Eurasia and Oceania is out due to Denisovans; the entirety of Sub-Saharan Africa seems to also be out. North Africa and Southwest Asia appear to be the only remaining candidates."

    Don't forget America. The only place in which there were absolutely no archaic hominins for thousands of miles around.

    ReplyDelete
  2. Huh? What about Neandertals in the Levant who apparently replaced AMH there?

    There is no evidence for Neandertals south of Israel and Iran. That leaves a big chunk of South West Asia intact.

    Don't forget America. The only place in which there were absolutely no archaic hominins for thousands of miles around.

    As I told you before, Out of America is not welcome here.

    And, there is no evidence for archaic hominins in America, but there is no evidence for modern humans in America either: modern humans appear in America about ~15,000 years ago, when they appear in Europe ~45,000 years ago, and in the Levant >100,000 years ago.

    ReplyDelete
  3. "And, there is no evidence for archaic hominins in America, but there is no evidence for modern humans in America either: modern humans appear in America about ~15,000 years ago, when they appear in Europe ~45,000 years ago, and in the Levant >100,000 years ago."

    Your thinking is completely fossilized. We barely have any fossils of chimpanzees or gorillas and they've been around for millions of years.

    ReplyDelete
  4. Your thinking is completely fossilized. We barely have any fossils of chimpanzees or gorillas and they've been around for millions of years.

    There is absolutely no reason to think that the entirety of the Americas is less conducive to fossil preservation than the Old World. There are no human fossils, because humans weren't there.

    There's no archaeology, either.

    Don't waste any more comment space with your Out-of-America hallucinations.

    ReplyDelete
  5. This comment has been removed by a blog administrator.

    ReplyDelete
  6. Every day the OoA theory seems to get more and more ridiculous.

    Richard Fuerle has an interesting book on the subject, check it out here:
    http://erectuswalksamongst.us/
    Section III and IV

    ReplyDelete
  7. "There are no human fossils, because humans weren't there."

    How about South Asia? Humans are supposed to have gotten to Australia via South Asia - but where is the fossil evidence? (There are some tools - http://www.archaeology.org/0801/topten/paleolithic_tools.html - but that is not fossil evidence).

    ReplyDelete
  8. @German,

    But for OOAmerica, you would have to have the Native Americans arrive in Western Europe as Solutreans or something?!

    So a reverse Solutrean hypothesis??

    I personally do not think OOAmerica can work.

    BTW, here are my father's (100% Native Irish AFAIK) results on the recent HarappaWorld Admix:


    HarappaOracle(c(0.07,10.85,3.80,51.09,0.00,0.12,0.00,0.41,0.50,0.00,33.10,0.00,0.06,0.00,0.00,0.00),k=20,mincount=4,mixedmode=T)
    [,1] [,2]
    [1,] "97.2% british_1000genomes_99 + 2.8% ukranian_yunusbayev_20" "0.5781"
    [2,] "89.4% british_1000genomes_99 + 10.6% n-european_xing_25" "0.588"
    [3,] "84.2% british_1000genomes_99 + 15.8% utahn-white_hapmap_18" "0.5908"
    [4,] "97.8% british_1000genomes_99 + 2.2% mordovian_yunusbayev_15" "0.596"
    [5,] "96.5% british_1000genomes_99 + 3.5% slovenian_xing_25" "0.597"
    [6,] "2.3% belorussian_behar_9 + 97.7% british_1000genomes_99" "0.6108"
    [7,] "96.5% british_1000genomes_99 + 3.5% hungarian_behar_19" "0.6198"
    [8,] "98.1% british_1000genomes_99 + 1.9% russian_hgdp_25" "0.6267"
    [9,] "77.1% british_1000genomes_99 + 22.9% utahn-white_1000genomes_100" "0.6388"
    [10,] "98.6% british_1000genomes_99 + 1.4% chuvash_behar_17" "0.66"
    [11,] "99.6% british_1000genomes_99 + 0.4% karitiana_hgdp_12" "0.6613"
    [12,] "99.6% british_1000genomes_99 + 0.4% surui_hgdp_6" "0.6613"
    [13,] "99.6% british_1000genomes_99 + 0.4% colombian_hgdp_7" "0.6614"
    [14,] "99.6% british_1000genomes_99 + 0.4% totonac_xing_23" "0.6628"
    [15,] "99.6% british_1000genomes_99 + 0.4% pima_hgdp_13" "0.6628"
    [16,] "0.4% bolivian_xing_22 + 99.6% british_1000genomes_99" "0.6651"
    [17,] "99.6% british_1000genomes_99 + 0.4% maya_hgdp_21" "0.666"
    [18,] "99.6% british_1000genomes_99 + 0.4% peruvian_1000genomes_69" "0.6731"
    [19,] "98.4% british_1000genomes_99 + 1.6% lithuanian_behar_10" "0.6781"
    [20,] "99% british_1000genomes_99 + 1% finnish_1000genomes_100" "0.6893"

    Notice he gets 0.4% admix with almost all South American ethnicities... probably a result of trying to force an un-admixed person into an admixture algorithm...

    ReplyDelete
  9. @pconroy

    But for OOAmerica, you would have to have the Native Americans arrive in Western Europe as Solutreans or something?!

    They would arrive to Europe at the time when we know modern humans arrived to Europe, around 40,000, so not the Solutreans. Solutrean-Clovis is technological convergence confirming how unrealiable toolkits are as signatures of population movements.

    ReplyDelete
  10. (Can you please post this in the Italy/Balkans C/P runs. I'm unable to post comments there.)

    Thanks for the runs.

    Are you sure the chunkcounts are normalized? My population assignment is ranked #4 in the individual counts.

    Are the Z-scores similar to iHS or XP-EHH?

    Cheers

    ReplyDelete
  11. "One possible explanation, consistent with multi-regional evolution (MRE) theory, is that modern humans didn't originate anywhere in particular; they emerged out of Homo populations that lived everywhere".

    That has long been my belief. Genetic change has occurred through what one of my friends call 'the wave theory of evolution'. Genes move in waves through the population of a species, changing it.

    "Huh? What about Neandertals in the Levant who apparently replaced AMH there?"

    The point is that they replaced them there. By the time Neanderthals replaced modern humans in the Levant those modern humans could have reached almost anywhere within Eurasia, except in Europe where it seems Neanderthals originated.

    "I personally do not think OOAmerica can work".

    I'm sorry German but I think most of us here agree with PConroy here.

    ReplyDelete
  12. "This would relate the two regions where no evidence (yet?) for archaic humans exist (North Africa and South West Asia).."

    Don't forget America. The only place in which there were absolutely no archaic hominins for thousands of miles around.

    .. and let's not overlook Australia.

    ReplyDelete
  13. The argument that all of "sub-Saharan Africa" is irrelevant to modern human origins does not hold any water. I could similarly argue that all of "Western Asia", including Arabia, is out because of Neanderthals found north of Arabia. East Africa, where the oldest modern human remains are found, lies outside the general scope of climatic variation in the continent. No archaic humans that aren't very ancient have been found in this region, and it is also the place with the richest variation of mtDNA L3 lineages.

    I would not completely disregard the importance of ancestral West Africans in this evolutionary history either. In terms of mtDNA, West Africans and their Bantu descendents lie in between East Africans and hunter-gatherers. However, they are not a simple admixture of the two, as they mainly belong to the L2'6 clade. They are transitional. Iwo Eleru was found in a region that was merely part of the Niger-Congo periphery, prior to the recent spread of Niger-Congo farmer across a massive portion of the African continent.

    The stone tool industry (Wilton) adopted by the Khoisan is associated with older stone tools found in East Africa. If the spread of these tools can be associated with the spread of hunter-gatherers from East Africa, who would also be the ancestors of the Hadza and Sandawe, then that would make a great deal of sense. The languages of East African hunter-gatherers (Hadza and Sandawe), although sometimes considered to be isolates, are probably very distantly related to the Southern African Khoisan languages.

    The presence of some of the most ancient mtDNA L0 branches (L0d, L0k) in the South African Khoisan, despite their absence in East African hunter-gatherers, may indicate the absorption of the previous inhabitants of South Africa by the Khoisan hunter-gatherers. Possibly tracing back to some of the first modern humans in Southern Africa (http://en.wikipedia.org/wiki/Klasies_River_Caves).

    I think it's important to emphasize that, so far, archaic admixture has been found in African hunter-gatherers living in Central-Southern-Eastern Africa, some of whom share relatively recent common ancestry. While I do not believe that archaic admixture is limited to these groups, a large part of their ancestors may trace back to the limited region of Central Africa and parts of Eastern Africa.

    However, in general, I think we need to start accepting the idea that prior to the Neolithic Revolution, it's highly possible that archaics may have persisted in many parts of the world.

    ReplyDelete
  14. The argument that all of "sub-Saharan Africa" is irrelevant to modern human origins does not hold any water. I could similarly argue that all of "Western Asia", including Arabia, is out because of Neanderthals found north of Arabia.

    Neandertals were a cold adapted species and have never been found in Arabia or South Asia.

    We now have evidence of archaic admixture of a deep nature in several places in Africa. Moreover, it does not appear that the two papers (Hammer and Lachance) refer to the same archaic population.

    If modern human populations lived in Sub-Saharan Africa for a long time (they evolved there), then they would have admixed with the archaic hominins, and would have carried the African archaic DNA into Eurasia. After all, they're supposed to have received Neandertal and Denisova DNA almost immediately after they left Africa, so why wouldn't they have exchanged genes with African archaics with whom they lived together for a much longer period of time?

    Moreover, if modern humans had been long established in Sub-Saharan Africa, why did it take them so long to replace local hominins (archaic forms persist down to the Holocene)? They would have had ample opportunity to do so, if they began their existence 200,000 years ago. It is not reasonable that they could not replace archaic humans in Africa over 190,000 years, but they did replace Neandertals and Denisovans in 10,000 years.

    it is also the place with the richest variation of mtDNA L3 lineages.

    L3 is irrelevant to the origin of modern humans, because modern humans existed before it. I will not repeat the arguments for the Asian origin of L3 (http://dienekes.blogspot.com/2011/11/age-of-mtdna-haplogroup-l3-about-70.html).

    The case is much more solid for DE-YAP which is almost certainly of Asian origin. According to recent Out of Africa theory, Eurasians' incredible reduction in genetic diversity is due to them having undergone a bottleneck of Biblical proportions. But, this doesn't square with the fact that within the CT clade, Eurasians possess both main subclades CF and DE, and indeed both subclades of DE (D and E), whereas Africans possess only the E twig.

    On the one hand, we are expected to believe that out of all the huge mtDNA tree only the N/M twigs made it Out of Africa due to the huge bottleneck, but the picture is completely different on the Y chromosome side.

    However, in general, I think we need to start accepting the idea that prior to the Neolithic Revolution, it's highly possible that archaics may have persisted in many parts of the world.

    I don't see what the Neolithic Revolution has to do with it. Archaic forms were replaced in some parts of the world long before it.

    ReplyDelete
  15. L3 is irrelevant to the origin of modern humans, because modern humans existed before it.

    That was in reference to the likely possibility of mtDNA L3 Out-of-Africans emanating from East Africa.

    But, this doesn't square with the fact that within the CT clade, Eurasians possess both main subclades CF and DE, and indeed both subclades of DE (D and E), whereas Africans possess only the E twig.
    Let's break that down a bit, shall we?

    Y-DNA DE is found in Africa and Tibet. D has a somewhat random distribution across the more easterly parts of Eurasia, and there's no indication it has anything to do with populations resembling modern West Eurasians.

    E is found in Africa and West Eurasia, with its West Eurasian representatives being overwhelmingly of the Y-DNA E1b1b1 clade, which is of recent African origin. So, E is basically African, D is basically Asian, and DE is found in both regions. The origin of DE is hence ambiguous, and I will not pretend to know where it originated. I personally suspect CT may have accompanied mtDNA L3 as it spread out of Africa, with DE either representing a subsequent migration out of Africa, or a migration back into Africa.

    On the one hand, we are expected to believe that out of all the huge mtDNA tree only the N/M twigs made it Out of Africa due to the huge bottleneck, but the picture is completely different on the Y chromosome side.

    Y-DNA bottlenecks are not anything unusual in human populations, and probably nothing new. They still happen, and probably always have.

    As for mtDNA L3, I don't see what your objection is? The closest relatives of L3 did not make it out of Africa, and neither did most of its basal subclades. Looks like a bottleneck to me. Bottlenecks happen everywhere. The patterns of genetic diversity and linkage disequilibrium may or may not be related to this bottleneck.

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  16. Is there archaic admixture in West Africans?

    ReplyDelete
  17. I personally suspect CT may have accompanied mtDNA L3 as it spread out of Africa, with DE either representing a subsequent migration out of Africa, or a migration back into Africa.

    If CT was African, and Eurasians passed through a dramatic bottleneck, it is very strange (and improbable) that it would be Eurasians (the bottlenecked population) that would end up with two surviving lineages (DE and CF), and Africans that would end up with one (DE).

    It's more probable that CT originated in Asia, and one of its subclades (DE) back-migrated to Africa where it spawned E. This was probably the carrier of certain technological and/or cultural-behavioral innovations and was thus able to almost completely outcompete the pre-existing male population.

    Y-DNA bottlenecks are not anything unusual in human populations, and probably nothing new. They still happen, and probably always have.

    That is not really true. The massive decrease we see Out-of-Africa is not evident really evident for any other human migration (except perhaps the American one, for easy to understand reasons).

    There are differences in effective size between Eurasians, but these pale in comparison to the difference between Eurasians and Africans. We don't see "bottlenecks" of equivalent intensity associated with humans crossing from one region of Eurasian to another.

    Also, as I've said, an assumption of a bottleneck makes certain predictions, and one of them is that there will be a loss of diversity in the bottlenecked population; we observe the exact opposite in CT, where Eurasians are more diverse than Africans.

    The simplest explanation for the observed pattern is that modern humans originated in the Sahara or North Africa. The Sahara would have acted as a barrier to gene flow, which explains why archaic African DNA didn't leave Africa. Humans emanated from this primary homeland to both Asia and deeper into Africa. In neither case did they have the "tech" or behavioral adaptations necessary to replace pre-existing hominins, because for 150k years the earliest AMH co-inhabit the planet with other human types. Then, something drastic takes place, Neandertals are wiped off in Europe, "Denisovans" in East Asia, and eventually even the archaic humans in Africa die out, some of them absorbed by modern humans coming from Asia who absorb both the pre-existing AMH in Africa (the A's and B's), as well as the archaic forms that existed there and which had been incompletely assimilated by early AMHs who lacked the "killer package" that emerged near the UP boundary.

    ReplyDelete
  18. If CT was African, and Eurasians passed through a dramatic bottleneck, it is very strange (and improbable) that it would be Eurasians (the bottlenecked population) that would end up with two surviving lineages (DE and CF), and Africans that would end up with one (DE).

    Great. Now apply this same logic to mtDNA L3.

    It's more probable that CT originated in Asia, and one of its subclades (DE) back-migrated to Africa where it spawned E. This was probably the carrier of certain technological and/or cultural-behavioral innovations and was thus able to almost completely outcompete the pre-existing male population.

    It wouldn't be that strange at all. And I'm not opposed to DE back-migrating, it's just not clear that it did.

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  19. Great. Now apply this same logic to mtDNA L3.

    Not sure what you mean by that. There are Eurasian-specific and African-specific clades within L3; the bifurcating structure is unknown.

    Even if it turns out that L3 in Africa includes two of the descendant clades and Asia only one (which is uncertain, but let's assume it for the sake of argument), then there is a perfectly good explanation why that would be so, without recourse to any Out-of-Africa event: deterioration of living conditions in Arabia post-70ka.

    And, of course, the biggest argument for the Asian origin of L3 is the fact that there is absolutely no evidence for Out-of-Africa at the time of its emergence, while there are much earlier archaeological links with Africa, and numerous, populous settlements of humans in Arabia at the time of the supposed "extreme bottleneck".

    The situation is different in CT, because we actually know how it bifurcates and Eurasia has 2 and Africa has 1.

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  20. @Terry

    "I'm sorry German but I think most of us here agree with PConroy here."

    This makes me think that I'm onto something with out of America.

    @Tobus

    "and let's not overlook Australia."

    A more likely source for modern humans than Sahara, that's for sure.

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  21. @German Dziebel,

    What part of "Out of America discussion is not allowed here" don't you understand?

    You were banned recently, I let you post again anyway, but it seems that old habits die hard.

    ReplyDelete
  22. When you say 'pre-modern humans mixed with local archaic forms to make modern humans',
    what does it mean to be 'pre-modern' ?

    Coelacanths, for example, can be described as living fossils anatomically but genetically there is little chance that their modern DNA sequences doesn't show up as very different from the old forms. And inversely, the 200 000 years old modern humans from Africa might have been modern anatomically (more or less) but still completely archaic genetically. Therefore could that mean that archaic admixture in genetic terms was indistinguishable from a persistence of archaic sequences present in the so-called 'modern humans' in 200 000 years old Africa?
    These archaic sequences would have been lost by the time European and Asian O-O-Africa invaders mixed with their own local archaics.

    Great blog by the way.

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  23. @ brwntrd

    According to these two recent studies addressing archaic admixture in Africa, the genetictsts only detected archaic admixture among Africa's divergent hunter-gatherer populations, i.e. Central African pygmies (Biaka and Mbuti), the South African Khoisan (Khoe and San), and the distantly related Hadze and Sandawe in Tanzania. Traces of this admixture were detected among other African populations with known admixture from these groups, for example the Xhosa of South Africa. West Africans lacked such admixture, most notably the Mandenka of the Senegambian region.

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  24. Admixture here, admixture there, but no archaic mitochondria anywhere. A mystery, no?

    It seems that the archaic lineages have been selectively lost from admixed populations again and again and again.

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  25. Proofs of admixture arise from everywhere: Europe (Neanderthal), Asia (Denisova) and Africa (unknown). At this point, Dienekes is right to point the end of Out Of Africa. I'm alos agree to consider Arabia (or around) the most plausible region to the point of origin of modern humans'colonization of the world.
    But lots of questions don't have answer and lead to other questions: how many different homo species existed at the time of emergence of modern humans? which ones have contributed to our genes? how admixture happened (rape, birthrate,....) and so on.
    An answer could be with the way modern human dealed with neanderthal, the only well-documented archaic homo. If the level of admixture of ancient modern human of Europe is higher then the present one, and perhaps with specific Y or Mt haplotypes (or absence of), we will have some answers. But we lack studies of premium dna analysis from +30ky modern human from Europe. A new model is needed, but history of admiwture could be different from continent to continent. The future will tell.

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  26. "L3 is irrelevant to the origin of modern humans, because modern humans existed before it. I will not repeat the arguments for the Asian origin of L3"

    In spite of what you say I find it very difficult to make a case that L3 originated outside Africa, even though some other L haplogroups are found just beyond Africa. These latter appear to be downstream members of the various African haplogroups, presumably originating and emerging from Africa after M and N had already formed. L3 is very relevant 'to the origin of modern humans' as both the haplogroups widespread outside Africa belong to it. I agree that mt-DNA is far from the only consideration though.

    "I personally suspect CT may have accompanied mtDNA L3 as it spread out of Africa, with DE either representing a subsequent migration out of Africa, or a migration back into Africa".

    That is the most likely explanation as I see it, but I agree with Dienekes:

    "It's more probable that CT originated in Asia, and one of its subclades (DE) back-migrated to Africa where it spawned E".

    Certainly the most likely scenario. DE is most likely a migration back into Africa. So just one Y-DNA and two mt-DNAs managed to emerge from Africa at that time. Previously many other lineages had obviously left Africa several times since H. erectus evolved though.

    "We don't see 'bottlenecks' of equivalent intensity associated with humans crossing from one region of Eurasian to another".

    But that huge bottleneck during the OoA (whatever that was) is perhaps evidence of a very narrow 'gateway'. More evidence against a sea crossing and evidence in favour of a Sinai Peninsula exit?

    "Then, something drastic takes place, Neandertals are wiped off in Europe, 'Denisovans' in East Asia, and eventually even the archaic humans in Africa die out, some of them absorbed by modern humans coming from Asia who absorb both the pre-existing AMH in Africa"

    I strongly suspect some 'cultural package', perhaps the development of wider social connections allowing improved survival during adverse conditions. In fact the evidence is mounting that the haplogroups expanded much more widely, and more completely, than many of the other genes. That argues against some sudden 'genetic' improvement as explanation.

    "Admixture here, admixture there, but no archaic mitochondria anywhere. A mystery, no?"

    Not if the haplogroups' spread was the product of a newly developed social structure, which did pull in a number of humans from other groups. Such certainly takes place today.

    "how many different homo species existed at the time of emergence of modern humans?"

    Personally I would prefer to use the term 'subspecies' as they obviously were capable of producing fertile hybrid offspring.

    "But we lack studies of premium dna analysis from +30ky modern human from Europe. A new model is needed, but history of admiwture could be different from continent to continent. The future will tell".

    Yes. I'm sure we would all agree with that. However we have to work with the information we have.

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  27. TerryT, I don't follow. You wrote: "Not if the haplogroups' spread was the product of a newly developed social structure, which did pull in a number of humans from other groups. Such certainly takes place today."

    Still, shouldn't these other groups have left behind a MtDNA legacy in modern populations? They certainly left behind a legacy in the autosomes. To me, it's still a mystery that needs solved. When population replacement takes place today, you see lots of MtDNA evidence for it. What percentage of the Brazilian population carries native American MtDNA? Lots. There is still hunter/gatherer MtDNA banging around Europe. But nothing from the archaics that modern humans interbred with. That MtDNA is missing. As is the MtDNA of ALL the archaics whose autosomal DNA we find in modern genomes.

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  28. This is a fascinating paper. I strongly suspect that we are getting even the Big Bang idea wrong, because so much of the maths in human genetics has been built around assumptions made when OOA was king. I'm betting several small bangs with gene flow inbetween is a more accurate description of what actually happened.

    A word of caution re making assumption about "archaics" (time to ditch that word) in East Africa.

    The Hadza are genrally supposed to be related to the Khoisan for linguistic reasons, and the Sangawe are supposed to be related to the Hadza for geographical and cultural reasons. Given this relationship, there is no evidence to suppose they were even in East Africa 60k-1050k years ago. Their ancestors (on the distinctive line)could have been in South Africa, or at a point intermediate between their and the Khoisan's present territories.

    They could have been anywhere in Africa, or even outside it (although the last option is least probable).

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  29. 'TerryT, I don't follow".

    Sorry. I'll try to explain.

    "Still, shouldn't these other groups have left behind a MtDNA legacy in modern populations?"

    If the spread was simply genetic we would expect to find 'ancient' mt-DNA. But if the spread was 'familial', spread by social group or 'tribe', only the direct family would leave either Y-DNA or mt-DNA. I strongly suspect that mt-DNA spread is associated with cultural innovation and Y-DNA with technological. In the first culture is largely spread from mother to daughter and in the second technology is largely spread from father to son.

    "They certainly left behind a legacy in the autosomes".

    Yes, but the legacy is not as great as if we were dealing with a simple hybrid situation. People who were not actually direct members of the tribe must have been accepted in as spouses to members. But the incoming 'tribal group' with complex social organisation came to dominate, and even eliminate previous less complexly organised populations.

    "To me, it's still a mystery that needs solved".

    I'm certainly prepared to accept any alternative explanation but to me the above seems to explain the end result adequately.

    "When population replacement takes place today, you see lots of MtDNA evidence for it. What percentage of the Brazilian population carries native American MtDNA?"

    True, but we are dealing with larger well-organised populations and the process is only a few hundred years old. What will the situation be like in 20,000 or 40,000 years time? Haplogroup lines are eliminated over time in a population of constant size.

    "There is still hunter/gatherer MtDNA banging around Europe. But nothing from the archaics that modern humans interbred with".

    Those hunter-gatherer genes are a minority though, and are more recent than are Neanderthal lines.

    " I strongly suspect that we are getting even the Big Bang idea wrong, because so much of the maths in human genetics has been built around assumptions made when OOA was king. I'm betting several small bangs with gene flow inbetween is a more accurate description of what actually happened".

    I accept both ideas. My brother says that humans are obsessed with finding single origins or single explanations for everything, but reality is much more complicated.

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  30. TerryT, I may be dim, but it feels like we're still talking past each other. I'm not sure what you mean by: "the legacy is not as great as if we were dealing with a simple hybrid situation. People who were not actually direct members of the tribe must have been accepted in as spouses to members. But the incoming 'tribal group' with complex social organisation came to dominate"

    --That may well be true, but the fact remains that modern humans carry a significant amount of archaic admixture--regardless of social organisation, tribal acceptance, or whatever else-- and yet no archaic mitochondria. I could buy into the chance loss of archaic lineages if it happened just once, or twice, in one or two of the discreet populations where we find specific evidence for admixture. But now we're looking at admixture from Neanderthals, Denisovans, and whatever this archaic lineage in Africa was… and according to this paper, the list will go on.

    Yet, every single time, in every population in which mixture has happened, the archaic MtDNA lineage appears to have been lost. That, to me, is still a mystery.

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  31. "the fact remains that modern humans carry a significant amount of archaic admixture--regardless of social organisation, tribal acceptance, or whatever else-- and yet no archaic mitochondria".

    Those mt-DNA haplogroups would have been lost because the 'parent' tribes to which they belonged have become extinct. The archaic admixture present in modern humans is from members of those lost tribes who joined the incoming groups. Remember that once a new haplogroup enters a region and has children with residents half their offsprings' autosomal DNA will be from the 'indigenous' tribe. So there is an immediate mismatch between the offsprings' autosomal DNA and their haplogroup. In the case of non-human hybridisation the survival of haplogroup and autosomal DNA is more balanced. But even in that case you will find John Hawks has a post at his blog claiming introgression and replacement of mt-DNA and Y-DNA is widespread amoung animals and birds.

    "Yet, every single time, in every population in which mixture has happened, the archaic MtDNA lineage appears to have been lost. That, to me, is still a mystery".

    The carriers of that mt-DNA must have had some advantage. And I think it unlikely that the advantage lay in the mt-DNA itself. The advantage has to be something non-genetic carried by those women who emerged from Africa.

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  32. The relevant John Hawks link is here:

    http://johnhawks.net/weblog/reviews/genomics/non-primate/polar-bears-coyne-2012.html

    This is what he starts with (in capital letters):

    "DO NOT MAKE EVOLUTIONARY TREES OF ANIMALS AND PLANTS BASED ENTIRELY ON MITOCHONDRIAL DNA (mtDNA): PLEASE USE NUCLEAR DNA WHENEVER YOU CAN. THIS IS BECAUSE mtDNA APPEARS TO MOVE MORE READILY BETWEEN SPECIES THAN DOES NUCLEAR DNA (nDNA), CAUSING A DISCORDANCE BETWEEN EVOLUTIONARY TREES BASED ON MITOCHONDRIAL GENES (‘GENE TREES’) AND THOSE BASED ON POPULATION AND SPECIES HISTORY THAT ARE DISCERNED FROM ANALYSES OF MANY NUCLEAR GENES (‘SPECIES TREES’)".

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  33. Terryt, I can see now that we're singing the same tune. It's precisely the logical requirement that "carriers of that mt-DNA must have had some advantage" that I was talking about. To me, the scenario where archaic autosomal DNA is retained while MtDNA is mysteriously lost, repeatedly, again and again, requires we invoke selection. But invoking selection in MtDNA lineages is its own can of worms with far reaching implications for the calibration of the mitochondrial clock. We invoke selection at our peril. It is also a bit of mathematical fudgery, if we're honest, like using imaginary "lethals" to make complex Punnet squares fit the phenotypes you see with your eyes. It's a black box cheat-- but it is sometimes also the right answer. The larger question is this: if strong selection for certain MtDNA lineages is taking place, can we trust the ages that the mitochondrial clock gives us for when populations split? I'm not qualified to give an answer to that, but I suspect that the answer is no. Also, it's late here, and I can't sleep, so I'll go ahead and throw this out there, too, and risk undermining everything I've said by going too far (always a risk in science) because I haven't thought about it deeply... but it seems to me that everything we're talking about with MtDNA would probably also apply to the Y-chromosome, wouldn't it? There is a distinct lack of archaic Y's floating around the modern gene pool.

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  34. "The larger question is this: if strong selection for certain MtDNA lineages is taking place, can we trust the ages that the mitochondrial clock gives us for when populations split? I'm not qualified to give an answer to that, but I suspect that the answer is no".

    We also seem to be in agreement here. I have very strong doubts about the molecular clock, whether for mt-DNA or Y-DNA. However it is very interesting to accept such dates presented literally and then try to draw some conclusions. Dienekes blog on Y-DNA falls into this category.

    "but it seems to me that everything we're talking about with MtDNA would probably also apply to the Y-chromosome, wouldn't it?"

    Yes. But with a subtle difference. I've been suggesting for years that mt-DNA represents selection for culture and Y-DNA represents selection for technology. So far I have had little agreement with that idea.

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  35. I'm quite new at this subject, but would like to ask some questions. Is the mutation of Genes from lets say A to B not in a very short time not caused by mixture of two subspecies ? If it is, could the different Haplogroups not count as the amount of times interbreeding took place between subspecies ? For me reading through the discussions, I get the distinct feeling that DNA of Homo Heidelbergensis or Ergaster is needed to clarify a great many maybees.

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  36. Another question or two.

    If you have 10 brothers from the same mother and father, would their DNA and Haplogroups be mostly the same ?

    And if they are would't it be reasonable that most would inherit the same potential for a specific mutation to happen under certain circumstances ?

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  37. Another thing that may help in pinpointing the original area from which most of "modern man" came, might be looking at diseases.

    Amerindians were almost wiped out by Pox which Europeans introduced. Seeing that Amerindians and Europeans are not so distantly related according to DNA shows that Pox immunity of Europeans must have come from a later stage after the split in Central Asia. This could indicate a purely European origin of Pox. Eg.

    The sickle cell found in Africa and the middle East is not present outside that areas as far as I know. If all modern humans came from central Africa there must have been some kind of Malaria resistance in all of us or the sickle cell trait must have been more widespread. Eg.

    If we could look at all diseases and find the ones that most of us have immunity against it might pinpoint an area of origin.....

    ReplyDelete
  38. Another thing that may help in pinpointing the original area from which most of "modern man" came, might be looking at diseases.

    Amerindians were almost wiped out by Pox which Europeans introduced. Seeing that Amerindians and Europeans are not so distantly related according to DNA shows that Pox immunity of Europeans must have come from a later stage after the split in Central Asia. This could indicate a purely European origin of Pox. Eg.

    The sickle cell found in Africa and the middle East is not present outside that areas as far as I know. If all modern humans came from central Africa there must have been some kind of Malaria resistance in all of us or the sickle cell trait must have been more widespread. Eg.

    If we could look at all diseases and find the ones that most of us have immunity against it might pinpoint an area of origin.....

    ReplyDelete

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