PDA

View Full Version : Did modern humans come out of Africa?



Rathna
10-18-2013, 09:19 AM
Very interesting study - they found remains from 5 individuals dated at 1.8 million years (link) (http://www.nytimes.com/2013/10/18/science/fossil-skull-may-rewrite-humans-evolutionary-story.html?hp&_r=0).

A Greek friend interested in anthropology sent me a few minutes ago this link. I wrote this:

"The Dmanisi group is an example of the successful species that came out of that and then carried on to spread around the old world."
I thank you for posting this and am surprised of this your "anthropological" interests.
Then homo sapiens could be born also in Eurasia rather than in Africa!


P.S. The word "anthropological" is due to my suspicion that this Greek friend is actually "Dienekes Pontikos", even though he has always denied it.

Jean M
10-18-2013, 10:03 AM
Then homo sapiens could be born also in Eurasia rather than in Africa!

No, it does not mean that.

Rathna
10-18-2013, 10:19 AM
No, it does not mean that.
Jean Manco, beyond the positions of Anatole Klyosov, it is more and more clear that hg. E is in Africa like a back migration from Eurasia and probably the true Africans were those A00. We are waiting that next tests of Bonnie carry more information. Before that perhaps it would be more useful to practice the "epoché".

Jean M
10-18-2013, 11:50 AM
I see that hope springs eternal in the eurocentric breast, but we have a mountain of evidence that is not going to move any time soon that Homo sapiens arose in Africa. That is the view arrived at by experts who have weighed the evidence of physical anthropology, archaeology and genetics, which is not just a matter of Y-DNA. It was mtDNA that consolidated the Out-of-Africa story back in the 1980s, and this was supported much more recently by autosomal data (the highest variability in Koisan, etc.)

I would not be surprised to find that Y-DNA E arose in Eurasia and migrated back into Africa, but that would make absolutely no difference to the story of the origins of Homo sapiens itself, and the departure of a group of same from Africa c. 50,000 years ago. Nor does the discovery of A00. Both Y-DNA haplogroups A and B are found almost exclusively in Africa or those known to be of African descent.

The earliest Homo sapiens skulls and related artifacts are found in Africa.

http://www.sanger.ac.uk/research/projects/humanevolution/

http://upload.wikimedia.org/wikipedia/commons/c/ca/World_Map_of_Y-DNA_Haplogroups.png

The existence outside Africa of forms of Homo earlier than/different from Homo sapiens is not news. It has been known since the 19th century, and gave rise to the Multi-Regional theory of the origins of Homo sapiens, which was disproved in the 1980s by the combined evidence of physical anthropology and genetics.

Rathna
10-18-2013, 12:21 PM
I see that hope springs eternal in the eurocentric breast, but we have a mountain of evidence that is not going to move any time soon that Homo sapiens arose in Africa. That is the view arrived at by experts who have weighed the evidence of physical anthropology, archaeology and genetics, which is not just a matter of Y-DNA. It was mtDNA that consolidated the Out-of-Africa story back in the 1980s, and this was supported much more recently by autosomal data (the highest variability in Koisan, etc.)

I would not be surprised to find that Y-DNA E arose in Eurasia and migrated back into Africa, but that would make absolutely no difference to the story of the origins of Homo sapiens itself, and the departure of a group of same from Africa c. 50,000 years ago. Nor does the discovery of A00. Both Y-DNA haplogroups A and B are found almost exclusively in Africa or those known to be of African descent.

The earliest Homo sapiens skulls and related artifacts are found in Africa.

http://www.sanger.ac.uk/research/projects/humanevolution/

http://upload.wikimedia.org/wikipedia/commons/c/ca/World_Map_of_Y-DNA_Haplogroups.png

The existence outside Africa of forms of Homo earlier than/different from Homo sapiens is not news. It has been known since the 19th century, and gave rise to the Multi-Regional theory of the origins of Homo sapiens, which was disproved in the 1980s by the combined evidence of physical anthropology and genetics.

Yes, also this last paper of Chinese scholars, which strengthens the hypothesis that hg. E back migrated to Africa from Asia (Dienekes is saying that he said that so long ago, but probably I said that before him: we shall consult the fora of those years), don't deny the origin of mt and Y in Africa, and probably this will be the truth, but we don't know where lived the ancestress of L0 and the ancestor of A00. There were many hominins who lived in Europe (and also in Italy) who could be the ancestors of those people. Anyway I wouldn't want that someone is tempted to fight a prejudice with another prejudice. We stick to facts, whichever they will be.

Jean M
10-18-2013, 12:51 PM
There were many hominins who lived in Europe (and also in Italy) who could be the ancestors of those people.

Only in the dreams of those who don't like the evidence to the contrary. I recommend Chris Stringer, The Origin of Our Species (2011) as a clear, readable, up-to-date account.

Rathna
10-18-2013, 12:56 PM
Only in the dreams of those who don't like the evidence to the contrary. I recommend Chris Stringer, The Origin of Our Species (2011) as a clear, readable, up-to-date account.

In our field of research we are seeing more and more that R-M269 (that line survived) isn't the ancestor of R-L23, that L23 isn't the ancestor of L51, that L51 isn't the ancestor of L11 and so on. We have probably one line survived, one out many, etc. Probably Klyosov wanted to say the same about A00, A, B etc.
Certainly I have no interest to deny an origin in Africa if there are A00, A, B. It is the same argument that brought me to my theory of the Italian Refugium just for having Italy this "pathway" from R1b1* to R-M269* to R-L23* to R-L51*, but we are seeing that these paragroups are diffused in a vast territory more and more they are ancient and the "proof" lacks and I don't know whether the same aDNA will be able to give it.
But also in this case many (and I think you too) fought my prejudice with another prejudice.

Jean M
10-18-2013, 01:10 PM
Having evolved from something like the earlier species Homo habilis in Africa nearly 2 million years ago (Ma), Homo erectus dispersed from Africa about 1.7 Ma, in the event commonly known as Out of Africa 1. The species spread to the tropical and subtropical regions of eastern and southeastern Asia, where it may have lingered on, evolved into other forms, or died out. About 1.5 Ma, African erectus developed more advanced stone tools called handaxes, but these did not spread far from Africa until they turn up rather suddenly with the descendant species Homo heidelbergensis in places like southern Europe, and then in Britain, 500,000 to 600,000 years ago. So my view was that H. heidelbergensis subsequently underwent an evolutionary split around 300,000 to 400,000 years ago: it began to develop into the Neanderthals in western Eurasia, while the line in Africa had evolved into the ancestors of modern humans by about 130,000 years ago.

The origin of modern Homo sapiens must have been a relatively recent and restricted one in Africa, based on marked similarities between recent humans in both body form and DNA, and it may have been quite rapid, in one small favoured area such as East Africa. Some modern humans dispersed to the Middle East (Israel) about 100,000 years ago, and they had perhaps moved on as far as Australia by about 60,000 years. However, Homo sapiens did not enter Europe until about 35,000 years ago, following the rapid development of more advanced Later Stone Age tools and complex behaviours by African moderns about 50,000 years ago.

Chris Stringer, The Origin of Our Species.

GTC
10-18-2013, 01:20 PM
It is the same argument that brought me to my theory of the Italian Refugium

When will you be publishing this theory in a paper in (say) the Journal of Genetic Genealogy?

Rathna
10-18-2013, 01:21 PM
"However, Homo sapiens did not enter Europe until about 35,000 years ago".

This statement should be corrected now: it seems that homo sapiens sapiens was in Italy (Puglia) about 45,000YBP.

Jean M
10-18-2013, 01:26 PM
But also in this case many (and I think you too) fought my prejudice with another prejudice.

I am quite shockingly prejudiced in favour of science, it is true.

Jean M
10-18-2013, 01:29 PM
This statement should be corrected now: it seems that homo sapiens sapiens was in Italy (Puglia) about 45,000YBP.


In Ancestral Journeys, p. 49, I give the date c. 46,000 years asgo. That is based on papers that have come out since Chris Stringer was writing his book (which will have been a year or so before it came out.)

Rathna
10-18-2013, 01:31 PM
When will you be publishing this theory in a paper in (say) the Journal of Genetic Genealogy?

I am a literate, and not a genetist. I have written books of poetry and critics. I have worked 40 years like a teacher of Italian, Latin, History and Geoghraphy in the High School.
This last year I have nursed my mother 24h till her death. Now I am retired from 1st September, and I have time, but I am not so fluent in English. I have written my theory in thousands of letters and there it is. I deepen it day by day, and correct it. This last paper of Chinese scholars who says that hg. R1b migrated from Central Asia to Europe (and it seems that Italy and the Alpine zone was the core) between 19,000 and 8,000YBP seems in line with my theory of an Italian Refugium during the Younger Dryas. We will see.

Rathna
10-18-2013, 01:32 PM
In Ancestral Journeys, p. 49, I give the date c. 46,000 years ago. That is based on papers that have come out since Chris Stringer was writing his book (which will have been a year or so before it came out.)

I'll read your book.

GTC
10-18-2013, 01:35 PM
Now I am retired from 1st September, and I have time, but I am not so fluent in English.

I'm sure you will be able to find an editor to help you tidy up the final draft.

Rathna
10-19-2013, 03:30 AM
Wow, I expected John Hawks would have an interesting analysis, and he does not disappoint!

The new skull from Dmanisi (link) (http://johnhawks.net/weblog/fossils/lower/dmanisi/d4500-lordkipanidze-2013.html)

It seems that Hawks is opener than Jean Manco about human evolution:

"It implies some degree of continued dispersal and mixture. I expect that the dispersal and mixture were biased in direction, probably more moving out of Africa than back into Africa".

GailT
10-19-2013, 03:54 AM
I think Hawks and Jean are saying the same thing - your quote of Hawks above referred to early Homo evolution and the possibility of multi-regionalism in early Homo.

Quotes from Hawks on modern humans:



Modern humans have more than 90% of their genetic makeup from Africans of the late Middle Pleistocene, comprising one major layer of genetic similarity worldwide. This major layer (whether by massive gene flow or direct population movement) overlies a small contribution from earlier Neandertals, Denisovans, and one or more ancient African populations.

Humans today are a poor model for understanding early Homo, because the last major layer of shared ancestry has left us too genetically uniform. The last major out-of-Africa series of events do not provide a good model for the first out-of-Africa dispersal, but both may have been conditioned by population structure within Africa more than anything else.

GailT
10-19-2013, 04:03 AM
I think we all recognize that there have been extensive migrations in the last 20,000 years with back migrations of Europeans and southwest Asians back into Africa. We see traces of these back migrations in relatively young y-DNA and mtDNA haplogroups. But these people were mostly descended from the latest Out of Africa migration and were genetically very similar to modern Africans. We don't see evidence of migrations back to Africa at the beginning of the AMH era, say 200,000 to 100,000 years ago. So it's really not possible to argue that AMH originated in Europe or Asia, and then migrated into Africa.

Rathna
10-19-2013, 04:26 AM
I think we all recognize that there have been extensive migrations in the last 20,000 years with back migrations of Europeans and southwest Asians back into Africa. We see traces of these back migrations in relatively young y-DNA and mtDNA haplogroups. But these people were mostly descended from the latest Out of Africa migration and were genetically very similar to modern Africans. We don't see evidence of migrations back to Africa at the beginning of the AMH era, say 200,000 to 100,000 years ago. So it's really not possible to argue that AMH originated in Europe or Asia, and then migrated into Africa.

I was just speaking of those old times. About the most recent ones I wouldn't be so assertive: if hg. E migrated back to Africa and more hg. R-V88+, which would be the true African Y? Just that A00, perhaps some B (but many subclades of B are from very ancient times in Europe or Asia). Also in this case I ask only to examine the data without prejudice, in one direction or in another. Anyway the truth couldn't be falsified, the truth of the data. Your FG of the Y is shading some interesting light on hg. U152 and could confirm all my theories. We'll get soon the FG also of A00, A, B etc.

Jean M
10-19-2013, 08:53 AM
I was just speaking of those old times. About the most recent ones I wouldn't be so assertive: if hg. E migrated back to Africa and more hg. R-V88+, which would be the true African Y?

We get into a big mess when we start to talk about "true" this or that geographical category of person/animal as meaning "a line of descent from ancestors who have never moved from that geographical entity". How far back do you want to go? If you go back far enough, the continents as we now know them did not exist and our ancestors did not resemble primates. Homo sapiens arose in Africa, but that does not make us all Africans. That was 100,000 years ago! The past is not static. Things change. People, animals and even continents have moved around.

Jean M
10-19-2013, 09:01 AM
I think Hawks and Jean are saying the same thing

Hawks is more enthusiastic than I am about the possibility of inter-breeding between Homo sapiens and archaic Homo, but naturally we both accept the Out-of-Africa model which has decisively trumped the multiregional model in academia.

As you know, the current discussion on the skulls from Dmanisi is not a resurrection of the old debate about Out-of-Africa. It is a different discussion entirely.

Sein
10-21-2013, 06:43 AM
Hawks is more enthusiastic than I am about the possibility of inter-breeding between Homo sapiens and archaic Homo, but naturally we both accept the Out-of-Africa model which has decisively trumped the multiregional model in academia.

Hello Jean,

There is no serious contending with the fact that contemporary Homo sapiens sapiens share most of their ancestry, and that this overwhelmingly shared ancestry is ultimately traceable to the African continent. Living humans are genetically very uniform and homogenous, no question about that. But this was never really the bone of contention in the debate between multiregionalism and Out-of-Africa. It's really a question of paradigm, the conceptual scheme one is utilizing when examining human evolution. Out-of-Africa was always about conceptualizing human genetic variation as structured in a tree-like manner. The relative uniformity of our species was construed as being contingent on our comparatively recent origin from a very small number of African founders. Multiregionalism has always been about construing human genetic variation in terms of reticulation, seeing it as far more accurately pictured in terms of a rhizome, rather than a tree. Living human homogeneity really boils down to ever persistent gene flow-admixture, and isolation-by-distance dynamics. And it's obvious which paradigm is more feasible today. It is now quite clear that gene flow between populations is not some minor but annoying problem when modeling relationships between populations, but a very basic rule in the course of things, and one which has few exceptions. Another difference was that most proponents of Out-of-Africa believed that archaic hominins like Homo sapiens neanderthalensis were a completely separate species from AMHs. Just based on genetic differentiation, we now know that this is not the case. The amount of genetic differentiation that exists between living humans, Neanderthals, and Denisovans is equivalent to the amount of genetic differentiation found amongst Chimpanzee and Gorilla subspecies. Nobody has ever doubted that those taxon are only subspecies, and thus belong to a single species, so why think otherwise in the case of our lineage? But this is an absolutely moot point. The subspecific nature of these archaic hominins is demonstrated by the fact that we have some of their genes. Simple as that. Successful interbreeding is what being a single species is all about. And this brings us to the most important point. Archaic admixture which is specific to different parts of the world. All non-Sub-Saharan Africans have Neanderthal admixture, East Asians have more of this Neanderthal admixture than Europeans, Australasians have Denisovan admixture lacking in Eurasians, and it seems some Africans have Archaic admixture found only in the specific African populations in question. This was the biggest point in the whole debate, and it's been settled, to the satisfaction of most people, in favor of multiregionalism. Humans are like a braided river, as Hawks puts it aptly (I forgot the source for this metaphor), the confluence of many distinct streams fusing in a such a manner as to lose any distinctiveness. In short, the "main" idea behind multiregionalism, that Homo erectus was the only example of abrupt transformation in the history of our lineage, and that in a general sense, everything from Homo erectus and down has been a part of a single species united by gene flow, has been given an immense boast with the work on Dmanisi. Out-of-Africa was right in a very narrow sense, but the multiregional model was right about both process and product.

Rathna
10-21-2013, 07:51 AM
Hello Jean,

There is no serious contending with the fact that contemporary Homo sapiens sapiens share most of their ancestry, and that this overwhelmingly shared ancestry is ultimately traceable to the African continent. Living humans are genetically very uniform and homogenous, no question about that. But this was never really the bone of contention in the debate between multiregionalism and Out-of-Africa. It's really a question of paradigm, the conceptual scheme one is utilizing when examining human evolution. Out-of-Africa was always about conceptualizing human genetic variation as structured in a tree-like manner. The relative uniformity of our species was construed as being contingent on our comparatively recent origin from a very small number of African founders. Multiregionalism has always been about construing human genetic variation in terms of reticulation, seeing it as far more accurately pictured in terms of a rhizome, rather than a tree. Living human homogeneity really boils down to ever persistent gene flow-admixture, and isolation-by-distance dynamics. And it's obvious which paradigm is more feasible today. It is now quite clear that gene flow between populations is not some minor but annoying problem when modeling relationships between populations, but a very basic rule in the course of things, and one which has few exceptions. Another difference was that most proponents of Out-of-Africa believed that archaic hominins like Homo sapiens neanderthalensis were a completely separate species from AMHs. Just based on genetic differentiation, we now know that this is not the case. The amount of genetic differentiation that exists between living humans, Neanderthals, and Denisovans is equivalent to the amount of genetic differentiation found amongst Chimpanzee and Gorilla subspecies. Nobody has ever doubted that those taxon are only subspecies, and thus belong to a single species, so why think otherwise in the case of our lineage? But this is an absolutely moot point. The subspecific nature of these archaic hominins is demonstrated by the fact that we have some of their genes. Simple as that. Successful interbreeding is what being a single species is all about. And this brings us to the most important point. Archaic admixture which is specific to different parts of the world. All non-Sub-Saharan Africans have Neanderthal admixture, East Asians have more of this Neanderthal admixture than Europeans, Australasians have Denisovan admixture lacking in Eurasians, and it seems some Africans have Archaic admixture found only in the specific African populations in question. This was the biggest point in the whole debate, and it's been settled, to the satisfaction of most people, in favor of multiregionalism. Humans are like a braided river, as Hawks puts it aptly (I forgot the source for this metaphor), the confluence of many distinct streams fusing in a such a manner as to lose any distinctiveness. In short, the "main" idea behind multiregionalism, that Homo erectus was the only example of abrupt transformation in the history of our lineage, and that in a general sense, everything from Homo erectus and down has been a part of a single species united by gene flow, has been given an immense boast with the work on Dmanisi. Out-of-Africa was right in a very narrow sense, but the multiregional model was right about both process and product.

And I think not having said anything unscientific in saying that, if hg. E was a back migration from Eurasia, the true Africans were those A00 of about 320,000 years ago, as we have admixture with Neanderthals etc. Only that we haven't so far found any Y or mt of Neanderthals in Eurasians, whereas Africans are full of A00, A, B etc. and probably many L0 etc.
Like my ancestors Romans said : Absit iniuria verbi.

Jean M
10-21-2013, 09:36 AM
@ Sein

If you really want to debate Out-of-Africa, it should be on a separate thread. Perhaps a moderator will separate out this discussion for you.

I will merely say that Multi-regionalism has not "won" if the geneticists do end up agreeing that modern man has a bit of DNA acquired from archaic homo not of our own lineage. The tree-structure is intact and visible in Y-DNA and mtDNA.

See Chris Stringer, The Origin of Our Species (2011) for much more detailed discussion from all angles, not just DNA.

Sein
10-21-2013, 10:36 AM
I would actually really enjoy a discussion on human origins, if this could be separated into it's own topic. In regards to Y-DNA and mtDNA, you're dealing with two exceedingly small aspects of one's genetic ancestry, two markers that are often very uninformative of total genomic ancestry. It's a given you will see tree-like structure, but that's a statistical artifact. I mean, they don't even recombine. I don't think it's reasonable to fixate on these two rather aberrant and minor aspects of genomic ancestry, when we have data for millions of SNPs, and whole-genome sequencing isn't very far away. Also, separate species can't successfully interbreed, and if they can, then there not separate species. Not a radical idea, but a fairly mainstream, nay, fairly basic concept. In addition, genetic divergences between all three hominins are understood, and they are well within subspecific range for our closest living relatives. Anyway, Dmanisi is very relevant to the topic of multiregionalism and human origins, since many are now admitting that Taxonomic splitting was not a good idea, which has always been an important point of contention in all of this. Although, if your really not comfortable discussing this topic (don't know why, but to each his/her own), we can just can the whole thing. Forget I ever mentioned multiregionalism.

I enjoyed the book thoroughly, a lot of food for thought. I love his emphasis on complexity, and the dynamism he tries to portray. I think he adds much needed nuance.

Jean M
10-21-2013, 01:00 PM
@ Sein - Autosomal DNA tells the same story as Y-DNA and mtDNA on the origin in Africa. There have been a lot of studies, using various types of analysis. It is not possible to reproduce all of that discussion and data in a forum post and I have neither the time nor the interest in attempting to summarise. I'll point to a few papers, but that really is all from me on this topic. Other people might be interested in discussing it on a separate thread. If you cannot see the links below, just go to the drop-down menu bottom left of every forum page and change the style to default style.


Michael G.B. Blum and Mattias Jakobsson, Deep divergences of human gene trees and models of human origins (http://mbe.oxfordjournals.org/content/28/2/889), Molecular Biology and Evolution, (2011) 28 (2): 889-898.
Michael DeGiorgio, Mattias Jakobsson, and Noah A. Rosenberg, Explaining worldwide patterns of human genetic variation using a coalescent-based serial founder model of migration outward from Africa (http://www.pnas.org/content/early/2009/08/13/0903341106.abstract), Proceedings of the National Academy of Sciences of the USA, (Published online before print August 17, 2009)
Silvia Ghirotto, Luca Penso-Dolfin and Guido Barbujani, Genomic Evidence for an African Expansion of Anatomically Modern Humans by a Southern Route (http://www.ncbi.nlm.nih.gov/pubmed/21846205), Human Biology, vol. 83, no. 4 (August 2011), pp. 477-489.
Jun Z. Li et al. (including Luigi L. Cavalli-Sforza and Richard M. Myers), Worldwide human relationships inferred from genome-wide patterns of variation (http://www.sciencemag.org/content/319/5866/1100.abstract), Science, vol. 319 (22 February 2008), pp. 1100-1104.
Marta Melé, Asif Javed, Marc Pybus, Pierre Zalloua, Marc Haber, David Comas, Mihai G. Netea, Oleg Balanovsky, Elena Balanovska, Li Jin, Yajun Yang, R.M. Pitchappan, G. Arunkumar, Laxmi Parida, Francesc Calafell, Jaume Bertranpetit, and The Genographic Consortium, Recombination Gives a New Insight in the Effective Population Size and the History of the Old World Human Population (http://mbe.oxfordjournals.org/content/29/1/25), Molecular Biology and Evolution, vol. 29, no. 1 (January 2012), pp. 25-30.
Jinchuan Xing, W. Scott Watkins, Adam Shlien, Erin Walker, Chad D. Huff, David J. Witherspoon, Yuhua Zhang, Tatum S. Simonson, Robert B. Weiss, Joshua D. Schiffman, David Malkin, Scott R. Woodward and Lynn B. Jorde, Toward a more uniform sampling of human genetic diversity: A survey of worldwide populations by high-density genotyping (http://www.ncbi.nlm.nih.gov/pubmed/20643205), Genomics, 2010 Oct;96(4):199-210.

TigerMW
10-21-2013, 02:50 PM
The "Out of Africa" theory of expansion of human usually provides some controversy and can creep into other threads so I'll start up a new thread dedicated to it. I am taking this action based on requests from on bloggers on this forum and will move posts that belong here over here.

Sein
10-22-2013, 12:17 AM
@ Jean - Fascinating material, and I guess we'll leave it at that, but none are about explicit modeling or hypothesis testing. None really address what I'm saying, and most if not all precede the finding of archaic Homo sapiens admixture into Homo sapiens sapiens, but again, we'll just leave it at that. I have a feeling we won't be getting anywhere. Although, I would like to point to this old paper, very simple and concise, and I believe it might clear away quite a few misunderstandings http://u.math.biu.ac.il/~louzouy/courses/statgen/africa2.pdf. I always thought this paper was a good read http://141.213.232.243/bitstream/handle/2027.42/34270/11_ftp.pdf?sequence=1.

@ Mikewww - Thank you for creating a thread dedicated to human origins, it will be quite a lot of fun having some discussion on this topic. Nevertheless, I think the the thread title is somewhat problematic, since there is no question that modern humans are almost completely African. Admixture with archaic Homo sapiens constitutes only 10%, at most, of our genomic ancestry.

Jean M
10-24-2013, 03:02 PM
Another paper, which takes an interesting tack: Hitchhiking Virus Confirms Saga of Ancient Human Migration
http://www.sciencedaily.com/releases/2013/10/131021162657.htm


A study of the full genetic code of a common human virus offers a dramatic confirmation of the "out-of-Africa" pattern of human migration, which had previously been documented by anthropologists and studies of the human genome. The virus under study, herpes simplex virus type 1 (HSV-1), usually causes nothing more severe than cold sores around the mouth, says Curtis Brandt, a professor of medical microbiology and ophthalmology at UW-Madison. Brandt is senior author of the study, now online in the journal PLOS ONE.

Aaron W. Kolb, Cécile Ané, Curtis R. Brandt. Using HSV-1 Genome Phylogenetics to Track Past Human Migrations. PLoS ONE, 2013; 8 (10): e76267
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0076267


We compared 31 complete and nearly complete globally derived HSV-1 genomic sequences using HSV-2 HG52 as an outgroup to investigate their phylogenetic relationships and look for evidence of recombination. The sequences were retrieved from NCBI and were then aligned using Clustal W. The generation of a maximum likelihood tree resulted in a six clade structure that corresponded with the timing and routes of past human migration. The East African derived viruses contained the greatest amount of genetic diversity and formed four of the six clades. The East Asian and European/North American derived viruses formed separate clades. HSV-1 strains E07, E22 and E03 were highly divergent and may each represent an individual clade. Possible recombination was analyzed by partitioning the alignment into 5 kb segments, performing individual phylogenetic analysis on each partition and generating a.phylogenetic network from the results. However most evidence for recombination spread at the base of the tree suggesting that recombination did not significantly disrupt the clade structure. Examination of previous estimates of HSV-1 mutation rates in conjunction with the phylogenetic data presented here, suggests that the substitution rate for HSV-1 is approximately 1.38×10−7 subs/site/year. In conclusion, this study expands the previously described HSV-1 three clade phylogenetic structures to a minimum of six and shows that the clade structure also mirrors global human migrations. Given that HSV-1 has co-evolved with its host, sequencing HSV-1 isolated from various populations could serve as a surrogate biomarker to study human population structure and migration patterns.

parasar
10-24-2013, 05:12 PM
Another paper, which takes an interesting tack: Hitchhiking Virus Confirms Saga of Ancient Human Migration
http://www.sciencedaily.com/releases/2013/10/131021162657.htm

...

This looks reasonable,

Studies of human genomes have shown that our ancestors emerged from Africa roughly 150,000 to 200,000 years ago, and then spread eastward toward Asia, and westward toward Europeas long as they spread 150,000 to 200,000 ybp.

It the more recent exit date of 60000-50000ybp that is the problem. As we have discussed it before, I just can't see how almost instantaneously after that exit humans appear in Australia. That is the reason I believe that as far as the evidence from Y goes, most Africans are descended from intermediate non-Africans.

But if this figure is correct, then I would be wrong.
http://upload.wikimedia.org/wikipedia/commons/3/3d/Y-DNA_tree.GIF

I just think CT and DE should be in the pink area ie the common ancestor of CF and DE prior to CT migrated out of Africa, and E is a back-migration to Africa.

Ian B
10-25-2013, 02:28 AM
I can agree with what Parasar is saying. Australian Aborigines have been in Australia for ~50,000 to 60,000 years. That must make their exit date quite some years earlier. As times progress and more discoveries made, technology improves, it's quite probable that these views will change. I'd like to see a cultural comparison of the Australian Aborigines of say about five hundred years ago with African tribes prior to white settlement.

GailT
10-25-2013, 03:40 AM
This was the biggest point in the whole debate, and it's been settled, to the satisfaction of most people, in favor of multiregionalism. ... In short, the "main" idea behind multiregionalism, that Homo erectus was the only example of abrupt transformation in the history of our lineage, and that in a general sense, everything from Homo erectus and down has been a part of a single species united by gene flow, has been given an immense boast with the work on Dmanisi. Out-of-Africa was right in a very narrow sense, but the multiregional model was right about both process and product.

I think you've either misunderstood the main idea of multiregionalism or misunderstood the significance of the Dmanisi research. Multiregionalism argued that modern humans evolved concurrently on different continents from an early Homo erectus ancestor, and that significant gene flow between these distant populations resulted in genetic similarity among all modern humans. Analysis of modern and ancient DNA, both uniparental and autosomal, has shown convincingly that multiregionalism was wrong. At best, you can claim a very weak theory of mutiregionalism, with a minor degree of mixing with archaic humans. But this is better described as a modified, recent Out of Africa with very small (and relatively recent) contributions from archaic humans outside of Africa.

Even if you accept the single species theory for Homo erectus, that does not imply that the early Out of Africa Homo erectus populations made any genetic contribution to modern humans. Perhaps Denisovans or Neandertals could have bred with remnants of those earlier populations, but I don't think we have any evidence that this actually occurred. Even if it did, their genetic contribution to modern humans (via Neandertals and Denisovans) would be extremely small, because the contribution from Neandertals and Denisovans to modern humans is small.

In the debate between Wolpoff and Stringer, Wolpoff's multiregionalism theory was clearly wrong, and the finding of early Homo erectus remains in Asia has no relevance in that debate because genetic evidence shows that all modern humans share (for the most part) the same set of recent African ancestors. For multiregionalism to be correct, you would have to show that the Dmanisi or other Homo erectus populations outside of Africa made a significant contribution to modern human genetic diversity. And this seems extremely unlikely. Quoting Hawks on the Dmanisi paper:



Modern humans have more than 90% of their genetic makeup from Africans of the late Middle Pleistocene, comprising one major layer of genetic similarity worldwide. This major layer (whether by massive gene flow or direct population movement) overlies a small contribution from earlier Neandertals, Denisovans, and one or more ancient African populations.

GailT
10-25-2013, 04:21 AM
I can agree with what Parasar is saying. Australian Aborigines have been in Australia for ~50,000 to 60,000 years. That must make their exit date quite some years earlier.

I can see this as support for an exit from Africa several thousand years earlier, assuming that the migration took that long, so perhaps that lends support to an exit between 55,000 to 65,000 ybp, which would be roughly consistent with Behar et al. age estimate for mtDNA haplogroup N, of about 60,000 years. I don't think we understand the precise details of when Out of Africa migrations occurred, or if there were multiple migrations over a period of many tens of thousands of years. But I don't think you can argue with any confidence that the migration to Australia required more than several thousand years.

GTC
10-25-2013, 04:54 AM
Folks interested in this question might also be interested in helping to fund a DNA project that promises to shine more light on the question.

If you can chip in some dollars/pounds/euros to help the project reach its funding goal, please do:

https://www.microryza.com/projects/which-of-cameroon-s-peoples-have-members-of-haplogroup-a00

Sein
10-27-2013, 07:52 AM
In the debate between Wolpoff and Stringer, Wolpoff's multiregionalism theory was clearly wrong, and the finding of early Homo erectus remains in Asia has no relevance in that debate because genetic evidence shows that all modern humans share (for the most part) the same set of recent African ancestors. For multiregionalism to be correct, you would have to show that the Dmanisi or other Homo erectus populations outside of Africa made a significant contribution to modern human genetic diversity. And this seems extremely unlikely.

Your understanding of multiregional theory is pretty common, but it still misses the point. Your focusing on a very narrow aspect of the theory (anyway, it's not really a single theory, but a family of theories). Nobody is arguing with the fact that modern humans share the overwhelming majority of their genomic ancestry. I've already recognized this indisputable fact at least twice on this thread. As was remarked a few years ago, modern humans could show a complete lack of archaic admixture, and the multiregional model could still be correct. Also, Dmanisi is crucial to the debate, because, as I assume you well know, the whole point of multiregionalism is that the only example of punctuated equilibrium in our lineage is Homo erectus. That's really the "big picture". This is the theoretical pivot, and some people may understate it. I don't.

I think people don't really "get" multiregionalism because it requires seeing more complexity when it comes to human evolution than Out-of-Africa, but things have changed, it's a very different academic atmosphere in comparison to 2007. I used to think Out-of-Africa was the only feasible explanation in accounting for the data, but things change fast in science. Also, the conditions you specify for multiregionalism to be correct are absolutely irrelevant. Besides, although this itself has no relevance, Hawks is still a multiregionalist.

Jean M
10-27-2013, 09:07 AM
Hawks is still a multiregionalist.

I see that you are right and I was wrong on that point. http://johnhawks.net/weblog/reviews/evolution/introgression/joyce-dalton-interbreeding-2010.html

Or let's say I had forgotten. I recalled his euphoria over the supposed evidence of interbreeding with Neanderthals very well. It was one of the factors that gradually made me suspicious of this concept. It was too readily - indeed joyously - accepted in some academic quarters and notably by the press. Alternative explanations of the data in that first paper did not get anything like the attention of the screaming headlines asserting interbreeding as fact. But the real cause of his joy - "Multiregional evolution lives!" - had slipped my mind.

Cochran and Harpending were unashamedly racist in The 10,000 Year Explosion (2009). They proposed that the first Homo sapiens to enter Europe had interbred with European big-brained Neanderthals and thereby gained some key intellectual advantage that explained their supposed superiority - that explosion of invention that produced cave paintings and amazing new tools and weapons. The flaws in that theory are :


Neanderthals had big brains, but were not using them to create improved tools, weapons or cave paintings.
Now that we can assess the Neanderthal and Denisovan genomes directly, the intellectual advantages of Homo Sapiens are starting to appear. See Meyer, A high-coverage genome sequence from an archaic Denisovan individual (http://www.sciencemag.org/content/338/6104/222), Science, vol. 338 (2012), pp. 222-6.
A separate line of inquiry suggests that Neanderthal brain size was probably completely unrelated to intelligence and simply reflects a large visual cortex: See http://www.anthrogenica.com/showthread.php?728-Neanderthals-not-as-bright-as-us
The incoming Homo sapiens had brought their superior tools and weapons with them into Europe, and had been engaged in modern behaviour such as jewellery-making before they ever left Africa. See Mellars et al. (eds.), Rethinking the Human Revolution (2007).
Europe has not been the hub of invention throughout human history. Pottery was invented in the Far East. Farming and writing within Eurasia were invented in the Near East - and separately in the Americas. And so on. There is a huge list of inventions which did not come from Europe. The Ancient Greeks had a much-admired burst of intellectual insight, but it was not enough to give Europe overall much of an edge at the time. It was only with the resurrection of science from the 18th century that Europe leaped ahead. Naturally that advantage looms large in thinking about Europe today, but it should not obscure the reality of European prehistory.

Sein
10-27-2013, 11:25 PM
Harpending and Cochran are both exceedingly marginal individuals, and The 10,000 Year Explosion was a pathetic attempt at scholarship. I don't see how any of this relates to multiregional theory. And I mean that honestly. What does that work have to do with multiregionalism? Anyway, there is no evidence that Neanderthal admixture has conferred any adaptive advantage on Eurasians. You have to divorce a lot of these notions from multiregionalism, because they have no connection to it, and are often held by scholars on the fringe (although Sean B. Carrol had his moment with this). I know Hawks still has a thing for "accelerating evolution", despite the lack of any evidence of recent signals of natural selection in our genome. But this is his own idiosyncratic hobby-horse.

Also, I really don't have any interest in any kind of ethnocentric project that would hail the non-existent glory of Europe. Reality can't be fought with, despite the Eurocentric desires and cravings of some scholars of European descent. The center of socio-political gravity throughout Eurasian history has always been in the area between Anatolia and the Indus, as well as in India, and most importantly, China. China was the "superpower" throughout the history of Eurasia, and Europe has always, with few exceptions, been peripheral (which makes geographic sense). It isn't surprising that Greece is where European civilization first had it's "burst", because Greece is the closest part of Europe to West Asia! In fact, many would argue that at that point in history Greece was far more organically connected to West Asia than Europe. A very fascinating piece of work, by one of the greatest anthropologists of the 20th century, that I would really recommend is Europe and the People Without History, by Eric Wolf. A beautiful example of what can be done when political economy is wedded to a richly holistic anthropology.

Ian B
10-28-2013, 01:46 AM
I can see this as support for an exit from Africa several thousand years earlier, assuming that the migration took that long, so perhaps that lends support to an exit between 55,000 to 65,000 ybp, which would be roughly consistent with Behar et al. age estimate for mtDNA haplogroup N, of about 60,000 years. I don't think we understand the precise details of when Out of Africa migrations occurred, or if there were multiple migrations over a period of many tens of thousands of years. But I don't think you can argue with any confidence that the migration to Australia required more than several thousand years.

@GailT: No, I agree with you. If it were possible to state with precision a single year in which Aborigines first set foot in Australia, that would be perfect. But we can't! All I'm saying is that it has been established that they arrived [I]between [I]50,000 and 60,000 ybp, so obviously the exit from Africa date was (probably) several thousand years before. We don't know the precise date of the African exit, how long it would have taken them to arrive in Australia, and so on. One day maybe........

parasar
10-28-2013, 03:27 AM
@GailT: No, I agree with you. If it were possible to state with precision a single year in which Aborigines first set foot in Australia, that would be perfect. But we can't! All I'm saying is that it has been established that they arrived [I]between [I]50,000 and 60,000 ybp, so obviously the exit from Africa date was (probably) several thousand years before. We don't know the precise date of the African exit, how long it would have taken them to arrive in Australia, and so on. One day maybe........

Ian,

Taking into account the new Denisovan evidence, it appears to me that the present Australians may not be carrying descending lines from the earliest Y and mtDNA lines of the first Australians. Pretty much as Neanderthal and Denisovan maternal and paternal identifying lines have died out but they themselves indeed have survived (autosomally, in a limited form).

As far back as 2000, it had been pointed out that LM3 possibly carried an mtDNA lineage with no known current descendants. "The LM3 Sequence Belongs to an Early Diverging mtDNA Lineage." http://www.pnas.org/content/98/2/537.full.pdf
To this claim there was much back and forth in academia, both on the dating and the analysis.

Now with the Denisovan evidence - showing admixture almost exclusively with Melanesians and Australians - I am persuaded that Adcock was correct.

Jean M
10-28-2013, 09:50 AM
Also, I really don't have any interest in any kind of ethnocentric project that would hail the non-existent glory of Europe.

I did not imagine for one moment that a Pashtun would. :) What I am pointing out is that Multiregionalism seems to bring joy to the lives of racists and causes the completely uncritical acceptance of a lot of rubbish. That is the sort of thing that gives me pause. In fact it is the sort of thing that makes me treat even a version of multiregionalism so watered-down as to take us into the realms of homeopathy with extreme caution. He who sups with the devil should have a long spoon.

Sein
10-28-2013, 10:38 AM
I think I understand your concerns much better now. I see where you're coming from on this. Nevertheless, I personally don't see any hint of racism in multiregionalism. I mean, the theoretical kernel of multiregionalism is contingent on gene-flow. The aim of most of it's mainstream proponents is providing an explanation for modern human genetic homogeneity. I'm sure Wolpoff is far from racist. I don't think I have the credibility to discuss the socio-cultural dynamics/issues involved in racism and other forms of callous stupidity, but I can discuss this from a biological perspective. There is geographic structure in our species, but geographic structure is not what "race" is biologically about. In biology, "race" is synonymous with "subspecies". And taking that as it is, there are no "races" today amongst living human populations. Living humans are just too uniform from a genetic perspective. All living people are equivalent to a single Chimpanzee or Gorilla subspecies. But even if we ignore modern human homogeneity, the biggest issue with subspecies would be the lack of monophyletic taxon amongst living people. Even if living human populations displayed deep divergences from each other (which they don't), this really puts a thorn in any attempt at arguing for biological "race" amongst living humans. You only see phenetic similarity, and even that is a function of geography. If someone wants to base their racism on biology, they're not in for a good time. But I have to agree with you, multiregionalism can attract idiots of various stripes who don't really understand the theory, but have a "candelabra" model in their heads. But doesn't this come with the territory? The whole subject of human origins has an unfortunate propensity to attract people with small minds, and unsavory views. People in domestic cat genomics don't have to deal with these issues :). A lot of scholars seem to have a hard time leaving their presumptions at the door when working on/thinking about human origins.

Jean M
11-13-2013, 09:30 PM
Just found an interesting video of Dr Michael Hammer: CARTA: The Origin of Us -- Michael Hammer: Interbreeding with Archaic Humans in Africa, from University of California Television (UCTV).


http://www.youtube.com/watch?v=GvoiPUHfOXI

lgmayka
11-14-2013, 12:43 AM
Just found an interesting video of Dr Michael Hammer: CARTA: The Origin of Us -- Michael Hammer: Interbreeding with Archaic Humans in Africa, from University of California Television (UCTV).
Unfortunately, Dr. Hammer makes a classic mistake: He occasionally refers to "behavioral modernity," but he actually presents absolutely zero evidence regarding that topic at all. Instead, his evidence consists of DNA fragments and skeletal fragments. He sometimes more correctly refers to "anatomical modernity," which is a reasonable term of art despite its rather shocking oversimplification. (Our anatomy consists of much more than just the skeleton!)

Jean M
11-14-2013, 01:07 AM
Dr Hammer's talk was one of several in an interesting series - all on YouTube:


One of the enduring questions of human origins is when, where and how we "Behaviorally Modern Humans" emerged and why and how we eventually replaced all the other human-like species. This series takes a fresh look at the situation today with a critical examination of the available evidence from multiple sources.

His focus was on interbreeding with archaic humans in Africa, and not on the evidence of behavioral modernity. That is a whole different subject.

Jean M
11-28-2013, 03:25 PM
On the topic of behavioral modernity, there is a new paper out which is making waves. I started a separate topic on it, as it belongs in archaeology. http://www.anthrogenica.com/showthread.php?1647-Stone-Tipped-Projectiles-from-the-Ethiopian-Rift

I'll just cross-post the gist here:

Yonatan Sahle, W. Karl Hutchings, David R. Braun, Judith C. Sealy, Leah E. Morgan, Agazi Negash, Balemwal Atnafu, Earliest Stone-Tipped Projectiles from the Ethiopian Rift Date to >279,000 Years Ago, PLoS ONE 8(11): e78092


Projectile weapons (i.e. those delivered from a distance) enhanced prehistoric hunting efficiency by enabling higher impact delivery and hunting of a broader range of animals while reducing confrontations with dangerous prey species. Projectiles therefore provided a significant advantage over thrusting spears. Composite projectile technologies are considered indicative of complex behavior and pivotal to the successful spread of Homo sapiens. Direct evidence for such projectiles is thus far unknown from >80,000 years ago. Data from velocity-dependent microfracture features, diagnostic damage patterns, and artifact shape reported here indicate that pointed stone artifacts from Ethiopia were used as projectile weapons (in the form of hafted javelin tips) as early as >279,000 years ago. In combination with the existing archaeological, fossil and genetic evidence, these data isolate eastern Africa as a source of modern cultures and biology.

Ian B
11-29-2013, 01:29 AM
@Jean M. I read an article only this week which proposed that modern man came out of Australia, rather than Africa. Now that I want to refer to it I can't find it again. Have you seen this article? If so, is there any credibility to it.

Ian B
11-29-2013, 03:12 AM
@Jean M. I read an article only this week which proposed that modern man came out of Australia, rather than Africa. Now that I want to refer to it I can't find it again. Have you seen this article? If so, is there any credibility to it.

@Jean M: I've just found the article, it's in Ancient Origins, http://ancient-origins.net/opinion-guest-authors-human-origins-science/out-africa-yesterday-australia-today-and-pleiades (http://ancient-origins.net/opinion-guest-authors-human-origins-science/out-africa-yesterday-australia-today-and-pleiades) . It's a three piece article . Like your opinion on it. "

Jean M
11-29-2013, 12:59 PM
Ian - this looks like the type of website that would appeal to you and appall me. So it is a bit unfair to ask me to comment. You know that I don't like to spoil your enjoyment of the weird and wonderful. Not that I don't enjoy fantasy for entertainment. I just prefer it written by Terry Pratchett. ;)

Ian B
11-30-2013, 01:05 AM
Ian - this looks like the type of website that would appeal to you and appall me. So it is a bit unfair to ask me to comment. You know that I don't like to spoil your enjoyment of the weird and wonderful. Not that I don't enjoy fantasy for entertainment. I just prefer it written by Terry Pratchett. ;)

So I take it that this site isn't the most credible source of information, I haven't the experience to know. As you know, I'm a novice in this field, and searching for sources of credible information and discussion, I'm on a very steep learning curve. I guess I'll have to keep on searching. Thanks anyway

Jean M
11-30-2013, 10:37 AM
So I take it that this site isn't the most credible source of information, I haven't the experience to know.

Sorry Ian. I thought you were having fun with me. The website in question makes no secret of the fact that it is presenting alternative views. Anything that has a feel of aliens-ate-my-granny about it is a no-no if you want the serious stuff. University or research institute sites are a safer bet. Some individual academics can go out on a limb, and need to be balanced against their peers. But usually you get some sort of consensus view on the website of the actual university. For Australia, I would recommend the Australian Centre for Ancient DNA at the University of Adelaide: http://www.adelaide.edu.au/acad/ . They do the ancient DNA research for the Genographic Project. The latter has a map of human migration, which may not be exactly right in all particulars, but reflects one strand in current thinking (two routes out of Africa): https://genographic.nationalgeographic.com/human-journey/

The first Aboriginal genome was sequenced in 2011. http://www.nature.com/news/2011/110922/full/news.2011.551.html


A 90-year-old tuft of hair has yielded the first complete genome of an Aboriginal Australian, a young man who lived in southwest Australia. He, and perhaps all Aboriginal Australians, the genome indicates, descend from the first humans to venture far beyond Africa more than 60,000 years ago, and thousands of years before the ancestors of most modern Asians trekked east in a second migration out of Africa. "Aboriginal Australians are descendents of the first human explorers. These are the guys who expanded to unknown territory into an unknown world, eventually reaching Australia," says Eske Willerslev, a palaeogeneticist at the University of Copenhagen, Denmark, who led the study. It appears online today in Science.

GailT
12-10-2013, 05:01 AM
Again, this is a dogmatic statement. Y-DNA can easily be interpreted as showing a major back migration into Africa marked by a pan-African hg E. The low-frequency, African specific clades such as Y-DNA A, B and mtDNA L0, L1, L2, L4, L5 can be seen as archaic admixture. And this is without even subjecting mtDNA trees to the kind of critique I've launched.

It is a theory strongly supported by genetic and physical evidence, but it is not accurate to call it "dogmatic". Dogma is impervious to counter evidence. The problem with your claim is that no data has been provided that would challenge this theory or support an alternate theory that is consistent with the DNA evidence.

I find it remarkable that you suggest that most of the mtDNA and y-DNA variation found in Africa today represents archaic humans. All of the mtDNA L nodes date to long after the origin of modern humans around 200,000 years ago. If you are claiming that the L nodes predate the origin of modern humans, this would then imply an extremely large amount of archaic autosomal DNA in modern Africans, which is very clearly not the case. The same is true of y-DNA, with the exception of A00, which could extend past the widely accepted date for the origin of anatomically modern humans, but which represent an extremely small percentage of modern human y-DNA, and which also confirms the origin of the root of the y-DNA tree in Africa. None of these arguments make any sense in terms of basic cladistic analysis for uniparental DNA.



This is an assumption created during the times when only modern human DNA was available. Now that we have actual historical data, let's just look at human mtDNA variation from the point of view of Neandertal, Denisovan and, now, Sima de los Huesos sequences and "play" with different versions of the tree.

Neandertal mtDNA: extinct
Denisovan mtDNA: extinct
Sima de los Huesos mtDNA: extinct

You can't pull a few individual mutations out of any of these archaic mtDNA sequences and then argue that these extinct mtDNA lineages survive in or are ancestral to modern humans.

With more than 30,000 modern human mtDNA full sequences tested, no archaic mtDNA sequences have been found. If they do survive in modern humans, they represent an extremely tiny, undiscovered percentage, and it is simply not possible to construct a phylotree in which any modern human mtDNA descends from the archaic branches. If you think you can do it, then please share your phylotree, with each branch labeled with the specific mutations that show your proposed line of descent, accounting for all of the mutations in each sequence.

Many different people have done this over the last 25 years, and each has found that the mtDNA tree of living people has a root that dates to the era of modern humans. This analysis is independent of other types of evidence - you can't use evidence based on linguistic or cultural diversity to redraw the phylotree because the tree is independently and uniquely determined by molecular evolutionary processes. This is why the DNA is evidence is so compelling and has transformed our understanding of human origins.

German Dziebel
12-11-2013, 06:36 PM
It is a theory strongly supported by genetic and physical evidence, but it is not accurate to call it "dogmatic". Dogma is impervious to counter evidence. The problem with your claim is that no data has been provided that would challenge this theory or support an alternate theory that is consistent with the DNA evidence... All of the mtDNA L nodes date to long after the origin of modern humans around 200,000 years ago.

How can you call your thinking non-dogmatic if you reference a date that came from fossils to justify phylogenies that are not derived from the DNA obtained from those fossils? We don't know if AMH fossils in Africa represent our species. We need to prove it. Paleobiology is pretty definitive about the watershed horizon of 40,000 years ago. After 40K and before 12K all modern human skulls derived from populations of behaviorally modern humans living in all continents form one clear cut cluster. The African member of this cluster, the Hofmeyr skull, doesn't show any special affinity with the 200-100,000 YO AMH fossils from Africa but instead clusters with UP Eurasians. This is consistent with linguistic evidence showing reduced level of stock diversity in Africa. The easiest way to reconcile this picture with genetic evidence is to assume that African-specific haploid lineages derive from African archaics and got into modern human gene pool through admixture. Evidence of archaic admixture in Africa comes from fossils (Iwo Eleru) and autosomal DNA. The dates of the admixture event(s) derived from the autosomal evidence is consistent with the 40,000 year old horizon. Y-DNA provides further support for this interpretation: hg E is a subset of Eurasian CT clade and it's found all over Africa including such remote populations as Khoisans and Pygmies that have high frequencies of the "basal" lineages A and B.


The same is true of y-DNA, with the exception of A00, which could extend past the widely accepted date for the origin of anatomically modern humans

Same mistake here. You assume that the "widely accepted date" that comes from fossils has any bearing on genetic phylogenies. This is non-sequitur because the phylogenies are not built with the ancient DNA from those fossils.


None of these arguments make any sense in terms of basic cladistic analysis for uniparental DNA.

Another dogmatic statement. You need to provide specific reasons for why not. Earlier, I randomly picked a couple of nodes of the mtDNA phylogeny and showed that hg L3 is defined by an ancestral retention (as ascertained in Denisovans) and a derived base. Same for M, N, U, M29'Q and a host of other nodes. You need to prove that those ancestral retentions are in fact homoplasies. Also, hundreds of substitutions on mtDNA lineages are recurrent and back mutations within modern humans, so the premise that a "unique combination of mutations" (haplotype) guarantees common descent is questionable. You need to first shed off all recurrent mutations and then see the pattern of distribution of uniquely derived states vs. ancestral retentions.


You can't pull a few individual mutations out of any of these archaic mtDNA sequences and then argue that these extinct mtDNA lineages survive in or are ancestral to modern humans.

There are a lot of those mutations. I recently scanned the M29'Q node and it contains some 30% of "ancestral retentions" only in the stems of M29'Q and M29.


With more than 30,000 modern human mtDNA full sequences tested, no archaic mtDNA sequences have been found. If they do survive in modern humans, they represent an extremely tiny, undiscovered percentage, and it is simply not possible to construct a phylotree in which any modern human mtDNA descends from the archaic branches. If you think you can do it, then please share your phylotree, with each branch labeled with the specific mutations that show your proposed line of descent, accounting for all of the mutations in each sequence.

It's really not my job to do it. It's the job of people who are closer to mtDNA research to actually include ancient DNA evidence into consideration, remove recurrent derived mutations from the tree and supply several alternate typologies to see which one works best. It'll be a shame if it ends up that one man had to do the job of dozens of people. I'm happy to assist in whatever way I can but it's unfair to ask it from me. In addition to actually ploughing my way through 2500 languages and building a phylogeny there, I've already provided enough critique for someone like you to go back to the drawing board.


Many different people have done this over the last 25 years, and each has found that the mtDNA tree of living people has a root that dates to the era of modern humans.

We need quality, not quantity. By this I mean we need different people with different expertise, ideally well-rounded in both molecular and cultural phylogenies, to peer review those trees in order to avoid a single-discipline bias.


This analysis is independent of other types of evidence - you can't use evidence based on linguistic or cultural diversity to redraw the phylotree because the tree is independently and uniquely determined by molecular evolutionary processes.

As I've already pointed out, I use a holistic approach to modern human origins. But when it comes to molecular phylogenies I don't directly use inferences from linguistic diversity.


This is why the DNA is evidence is so compelling and has transformed our understanding of human origins.

Do you write for New York Times?

GailT
12-12-2013, 03:26 AM
It's really not my job to do it. It's the job of people who are closer to mtDNA research to actually include ancient DNA evidence into consideration, remove recurrent derived mutations from the tree and supply several alternate typologies to see which one works best.


They have done it, and they explained how they did it in the peer reviewed literature. The basic mtDNA phylotree of modern humans is well understood. You are the one who is claiming that the entire community of researchers who specialize in the field have fundamentally misunderstood and misinterpreted the data. Yet you haven't provided any data that challenge that research in any way. If you spend any time at all analyzing mtDNA trees, a very superficial look at the data shows that there is absolutely no possible tree in which modern human mtDNA descends from any of the known extinct archaic human mtDNA sequences.

It is not dogmatic to claim that the current evidence strongly supports a particular theory. It is dogmatic to constantly claim that the theory is wrong without providing any evidence or analysis to support the claim.

German Dziebel
12-12-2013, 02:43 PM
This is the worst thing I've ever seen anyone write on a public forum,are you just waiting to be banned or what?

It's a factually accurate statement. There's a rich historiography of images of primitive people in European imagination. The belief that Pygmies and Khoisan lineages are somehow "basal" to the human tree (often rooted in a chimp sequence), which is one of out-of-Africa claims, is the very same Eurocentric idea as having these populations described as "primitive," "ape-like" people. The style of the argument has changed over the years but the content has not. And I don't care if you "ban" me. I don't even know who you are.

German Dziebel
12-12-2013, 03:05 PM
They have done it, and they explained how they did it in the peer reviewed literature. The basic mtDNA phylotree of modern humans is well understood. You are the one who is claiming that the entire community of researchers who specialize in the field have fundamentally misunderstood and misinterpreted the data. Yet you haven't provided any data that challenge that research in any way. If you spend any time at all analyzing mtDNA trees, a very superficial look at the data shows that there is absolutely no possible tree in which modern human mtDNA descends from any of the known extinct archaic human mtDNA sequences. ... It is dogmatic to constantly claim that the theory is wrong without providing any evidence or analysis to support the claim.

It's plain obvious that you haven't responded to any specific observations and objections I've made about mtDNA phylogeny or phylogeography. Instead, you continue to hide behind appeal-to-authority statements. But with two doctorates from two world class universities, I'm an authority, too, so what I need from you are facts, logic and smart interpretations.

Here's another specific volley for you to react to. Molecular clock has been shown to be problematic on a number of occasions. Why should it come as a surprise that someone questions the phylogeny itself?


a very superficial look at the data shows that there is absolutely no possible tree in which modern human mtDNA descends from any of the known extinct archaic human mtDNA sequences."

This is just ridiculous. Modern human mtDNA got to descend from some archaic sequence. All archaic hominins are extinct. You don't believe we need ancient DNA from Africa to test our phylogenies and you reject the available archaic sequences as casting any light on the evolution of modern human mtDNA. So who did we descend from, in your opinion? An African deity?


It is not dogmatic to claim that the current evidence strongly supports a particular theory.

You were writing as if human origins at 200,000 years is a fact. In the absence of ancient DNA, it's not a fact. But you've been using this pseudo-fact as the reason to dismiss alternative interpretations. And you did it in a repeated fashion. This is dogmatic.

parasar
12-12-2013, 04:56 PM
... Multiregionalism has been tested, and it has failed. The gene flow between archaic hominids and Homo Sapiens Sapiens was not extensive.
...

And how do you know that.

1. Just a few short years back multi-regionalism was totally dead. Now it is being considered seriously again due to the evidence from ancient DNA.

2. We do not have ancient DNA from Africa to confirm, so if go by the assumption that all of current African DNA is AMH, then sure the archaic admixture will look small in comparison.

To understand German's point, first we have to define what is AMH, what is Early AMH, and what is Archaic. German thinks that AMH is about 40-50000 years old. This is quite possible.

parasar
12-12-2013, 05:11 PM
...


a very superficial look at the data shows that there is absolutely no possible tree in which modern human mtDNA descends from any of the known extinct archaic human mtDNA sequences."
This is just ridiculous. Modern human mtDNA got to descend from some archaic sequence. All archaic hominins are extinct. You don't believe we need ancient DNA from Africa to test our phylogenies and you reject the available archaic sequences as casting any light on the evolution of modern human mtDNA.

...

That is absolutely correct.
So the issue is where you demarcate archaic from modern.

German Dziebel
12-12-2013, 05:25 PM
To understand German's point, first we have to define what is AMH, what is Early AMH, and what is Archaic. German thinks that AMH is about 40-50000 years old. This is quite possible.

Yes, that's accurate. The misnomer "anatomically modern humans" (Herto, Omo, Skhul/Qafzeh, etc.) emerged prior to the realization that the fossils dating to between 40,000 and 12,000 years globally form a cluster of their own, they are found on every continent including America, and the African representative of that cluster, Hofmeyr dated at 36,000 YBP, is not closer to the so-called AMH cluster than the other fossils from the 40,000 YBP cluster. Properly speaking, the 40,000YBP cluster should be called "anatomically (and behaviorally) modern humans" (ABMH) with Neandertals in Eurasia, the Herto-Omo-etc. in Africa, as well as other groups as altogether different Archaic clusters. The model that I have in my mind is that ABMH expanded from a TBD-location and admixed with Neandertals in Eurasia and with the Herto-Omo-etc. populations in Africa.

German Dziebel
12-12-2013, 06:17 PM
So the issue is where you demarcate archaic from modern.

Precisely. And then how do you distinguish later archaic introgressions and the original descent from an archaic antecedent. Out-of-Africa makes modern Africans into an archaic antecedent of modern non-Africans who presumably went through a bottleneck. IMO, this is not likely for the many reasons I've already presented. The divergence of modern Africans from non-Africans should be explained by other models such as the one that postulates greater extent of genetic introgression from Africa-specific archaics into modern Africans compared to the contribution of Eurasian archaics to modern Eurasian populations.

ZephyrousMandaru
12-13-2013, 02:58 AM
And how do you know that.

1. Just a few short years back multi-regionalism was totally dead. Now it is being considered seriously again due to the evidence from ancient DNA.

Because the nuclear DNA of Homo Sapiens Sapiens only exhibits minimal affinities to only two archaic species that we know of. Even then, this isn't definitive, because it could very well just indicate shared ancestry and not necessarily gene flow in either direction. Multiregionalism is not being revived, at least not within the science community and you're being dishonest by suggesting that it is.


2. We do not have ancient DNA from Africa to confirm, so if go by the assumption that all of current African DNA is AMH, then sure the archaic admixture will look small in comparison.

The DNA evidence we have tracing our origin to Africa is not an assumption, it has been corroborated through uniparental data and the oldest haplogroups, with the highest genetic variances are located in Africa.

parasar
12-13-2013, 03:53 AM
...
The DNA evidence we have tracing our origin to Africa is not an assumption, it has been corroborated through uniparental data and the oldest haplogroups, with the highest genetic variances are located in Africa.

Yes it is as far as AMH is concerned.
Corroborations from modern distributions strongly support that assumption, but they do not confirm. For confirmation we will need ancient DNA.
Plus those oldest haplogroups may be from archaic or early AMH living in Africa with whom derived but returning AMH admixed resulting in greater apparent diversity. We may never know for sure, but recent advances in testing ancient DNA give us hope if there is sufficient endogenous material remaining (say at the Iwo Eleru site).

lgmayka
12-13-2013, 04:00 AM
German thinks that AMH is about 40-50000 years old. This is quite possible.
What basis do you have to say that? The archaeological consensus is apparently that anatomically modern humans (AMH) are roughly 200,000 years old (http://en.wikipedia.org/wiki/Anatomically_modern_humans).

Perhaps I need to repeat what I must periodically post: The definition of AMH is based entirely on skeletal structure, and so its age can only be determined by archaeologists. Moreover, both its definition and its application to specific cases (e.g., Flores (http://en.wikipedia.org/wiki/Homo_floresiensis#Hypotheses_of_origin)) continue to be hotly disputed.

Several fields throw around an even vaguer, more disputable, and less supportable/refutable term, behavioral modernity (http://en.wikipedia.org/wiki/Behavioral_modernity); but since it includes religion, art, music, storytelling, cooking, games, and jokes (religion, art, music, myth, cooking, games, and jokes), it is questionable whether any single human living today fully meets the definition. (Perhaps Danny Kaye (http://en.wikipedia.org/wiki/Danny_Kaye)? But he died in 1987.)

Geneticists can invent some new term such as Genetically Modern Human (GMH) if they wish, but then they must define it precisely.

parasar
12-13-2013, 04:57 AM
What basis do you have to say that? The archaeological consensus is apparently that anatomically modern humans (AMH) are roughly 200,000 years old (http://en.wikipedia.org/wiki/Anatomically_modern_humans).

Perhaps I need to repeat what I must periodically post: The definition of AMH is based entirely on skeletal structure, and so its age can only be determined by archaeologists. Moreover, both its definition and its application to specific cases (e.g., Flores (http://en.wikipedia.org/wiki/Homo_floresiensis#Hypotheses_of_origin)) continue to be hotly disputed.

Several fields throw around an even vaguer, more disputable, and less supportable/refutable term, behavioral modernity (http://en.wikipedia.org/wiki/Behavioral_modernity); but since it includes religion, art, music, storytelling, cooking, games, and jokes (religion, art, music, myth, cooking, games, and jokes), it is questionable whether any single human living today fully meets the definition. (Perhaps Danny Kaye (http://en.wikipedia.org/wiki/Danny_Kaye)? But he died in 1987.)

Geneticists can invent some new term such as Genetically Modern Human (GMH) if they wish, but then they must define it precisely.

German clarified:

the 40,000YBP cluster should be called "anatomically (and behaviorally) modern humans" (ABMH) with Neandertals in Eurasia, the Herto-Omo-etc. in Africa, as well as other groups as altogether different Archaic clusters. The model that I have in my mind is that ABMH expanded from a TBD-location and admixed with Neandertals in Eurasia and with the Herto-Omo-etc. populations in Africa.
http://www.anthrogenica.com/showthread.php?1486-Did-modern-humans-come-out-of-Africa&p=22890&viewfull=1#post22890

I have not seen a clear enough definition (is there somewhere I could find a precise definition?), for example when we say gracile - the next question would be the level of bone density; and the same issue with the light built, degree of forehead slant, prominence of jaw, brow ridge etc. etc.


Based on fossil evidence, eastern Africa has often been considered the most likely location for the emergence of AMH. The Omo 1 cranium found in south-western Ethiopia and dating to ~190–200 ka (thousand years ago) is the oldest known fossil agreed to display AMH features [3] and alongside crania from Herto (in northern Ethiopia), dating to ~154–160 ka [4,5], and remains from Sudan and Tanzania [6], provide the palaeoanthropological case for an eastern African origin. Other early modern Homo sapiens remains include the Jebel Irhoud fossils in Morocco, also dating to ~160 ka [7], albeit with wide confidence intervals and some disagreement about their status [2], and the Skhul/Qafzeh remains in Israel, usually dated to ~90–135 ka [8] although the dates for Skhul are much less certain than those from Qafzeh (~85–95 ka) [9]. The oldest agreed AMH fossil known in southern Africa is from the Klasies River caves and dates to ~65–105 ka [9], although again its status as AMH has been contested [10]; although there are more archaic remains (notably from Florisbad, South Africa) dating to 190–330 ka [9], indicating that a southern origin is a possibility. Thus the fossil record is extremely patchy, but tends to point to a northern rather than southern, and in particular an eastern African, origin for AMH.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3827445/
Hardly confidence inspiring, especially if you read the actual papers referenced within.

GailT
12-13-2013, 05:41 AM
1. Just a few short years back multi-regionalism was totally dead. Now it is being considered seriously again due to the evidence from ancient DNA.


Multi-regionalism in the form that Milford Wolpoff proposed it is still dead. He argued that humans co-evolved from Homo erectus, with gene exchange at the edges of the distinct populations. DNA evidence, both uniparental and autosomal, shows that this theory was incorrect. What we have left is a an weak form of multi-regionalism, with minor mixing of modern humans outside of Africa with archaic humans, and possibly within Africa, although that remains uncertain.

GailT
12-13-2013, 05:58 AM
It's plain obvious that you haven't responded to any specific observations and objections I've made about mtDNA phylogeny or phylogeography.

I have pointed the out flaws in your thinking several times, but you seem unwilling to process that information, as you continue to repeat the same flawed arguments. Let me try it another way. mtDNA haplogroups R0 and U are sister clades that share a common ancestor in R around 55,000 years ago. If we look at individual subclades within R0 and U, we will find some samples and some subclades in each branch that share some of the same mutations, and yet the most parsimonious tree is readily apparent. So this does not mean that some U subclades descend from R0 or that some R0 subclades descend from U. The fact that you continue to make these same arguments shows that you simply don't understand mtDNA or cladistic analysis.

And your use of this very obviously flawed analysis to argue that Africans at the time of the OoA migration were "archaic" is just plain offensive.

parasar
12-13-2013, 03:52 PM
Multi-regionalism in the form that Milford Wolpoff proposed it is still dead. He argued that humans co-evolved from Homo erectus, with gene exchange at the edges of the distinct populations. DNA evidence, both uniparental and autosomal, shows that this theory was incorrect. What we have left is a an weak form of multi-regionalism, with minor mixing of modern humans outside of Africa with archaic humans, and possibly within Africa, although that remains uncertain.

We do not have ancient DNA as yet from Africa to confirm, so if go by the assumption that all of current African DNA is AMH, then sure the non-African archaic admixture will look small in comparison, and Africans will appear to have little if any of non-African archaic admixture. Almost all of our DNA is archaic, the provenance of the portion that makes us AMH is not confirmed.


...

And your use of this very obviously flawed analysis to argue that Africans at the time of the OoA migration were "archaic" is just plain offensive.

While I will not go into German's analysis and will let him explain (that is if he is given the chance), IMO, it is very likely that OoA migrants were "archaic." I do not see any evidence for a 50-60000ybp OoA, and the ones about 100000ybp or earlier (incld. Skhul and Qafzeh hominids at best early modern humans) have not been conclusively shown to be AMH.
I definitely do not find it offensive that we are likely ~95% African "archaic" and most of the balance non-African "archaic."

BMG
12-13-2013, 05:26 PM
We do not have ancient DNA as yet from Africa to confirm, so if go by the assumption that all of current African DNA is AMH, then sure the non-African archaic admixture will look small in comparison, and Africans will appear to have little if any of non-African archaic admixture. Almost all of our DNA is archaic, the provenance of the portion that makes us AMH is not confirmed.

"
While we know the recent common y ancestor of AMH is from africa can we say that that person is anatomically AMH ? Couldn't it be like while evolving into AMH two or more distinct lines survived while the common ancestor of these distinct lines may not be even AMH .
Another possibility is that AMH went through bottlenecks that surviving lineage happened to be of african origins .
Anyway we know that hominids wasnt restricted to africa and one line of the hominids evolved to become AMH and it doesnt necessarily should have happened in Africa itself

parasar
12-13-2013, 05:42 PM
While we know the recent common y ancestor of AMH is from africa can we say that that person is anatomically AMH ? Couldn't it be like while evolving into AMH two or more distinct lines survived while the common ancestor of these distinct lines may not be even AMH .
Another possibility is that AMH went through bottlenecks that surviving lineage happened to be of african origins .
Anyway we know that hominids wasnt restricted to africa and one line of the hominids evolved to become AMH and it doesnt necessarily should have happened in Africa itself


My main problem is not with OoA itself since even if Neanderthals and Denisovans and perhaps other non-Africans were involved with our makeup we are quite African or Africans are quite us.

The issue I have is with the 50-60000ybp time-frame which cannot be confirmed by any archaeological evidence in South or Inner Asia. Just subsequent to this time-frame we see an explosion of Upper-Paleolithic finds all over.

To explain this, I have proposed two scenarios: 1. The African exodus though Asia is much older (~100000ybp) and the Upper Paleolithic people descend from a later node of expansion. 2. There was a migration across the ocean to SE Asia and E Asia directly from Africa which would explain why there is a lack of AMH remains in South and Inner Asia.

Since the second scenario looks quite unlikely, but not impossible, I think #1 is what happened.

Sein
12-18-2013, 11:46 PM
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12886.html

This is what Dienekes had to say:
"There seems to have been a lot of inter-"species" sex during the Paleolithic, and that's just from a handful of Eurasian hominins sequenced so far....My guess is that once all is said and done, the tree of Homo will fill up with "red" admixture edges, and those who argued for a single Homo lineage evolving over hundreds of thousands of years, with gene flow between regional populations, will have the upper hand."
http://dienekes.blogspot.com/2013/12/a-neandertal-from-altai-mountains.html

:biggrin1:

But on a more serious note, this is merely a finishing touch, just like the Dmanisi work. The only viable intellectual options: a very weak Out-of-Africa with assimilation, or Multiregionalism, and both of these are basically two sides of a single coin. On a paradigmatic level, we are all multiregionalists now, whether we like to admit it, or not.

BMG
12-19-2013, 02:26 AM
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12886.html

This is what Dienekes had to say:
"There seems to have been a lot of inter-"species" sex during the Paleolithic, and that's just from a handful of Eurasian hominins sequenced so far....My guess is that once all is said and done, the tree of Homo will fill up with "red" admixture edges, and those who argued for a single Homo lineage evolving over hundreds of thousands of years, with gene flow between regional populations, will have the upper hand."
http://dienekes.blogspot.com/2013/12/a-neandertal-from-altai-mountains.html

:biggrin1:

But on a more serious note, this is merely a finishing touch, just like the Dmanisi work. The only viable intellectual options: a very weak Out-of-Africa with assimilation, or Multiregionalism, and both of these are basically two sides of a single coin. On a paradigmatic level, we are all multiregionalists now, whether we like to admit it, or not.
What do you mean by a weak out of africa migrations ?
Multiregionalists believe we evolved into homo sapiens at different regions and then mixed with each other .Also the inter-species sex with other hominds into humans always seems a bit exaggerated to me .It wouldnt have much of a difference .

Sein
12-19-2013, 03:14 AM
What do you mean by a weak out of africa migrations ?
Multiregionalists believe we evolved into homo sapiens at different regions and then mixed with each other .Also the inter-species sex with other hominds into humans always seems a bit exaggerated to me .It wouldnt have much of a difference .

By weak Out-of-Africa, I mean Out-of-Africa with assimilation. And from a conceptual angle, that's basically a variation on the multiregional model. For people who would deny this, frankly, they just aren't familiar with multiregionalism.

What you've stated is a simple, cardboard caricature. To give an idea of what a multiregional perspective implies, there is no question of inter-species sex, since this is all happening within a single lineage. That's why Dienekes put "species" in quotation marks. But you don't have to be a blatant multiregionalist to admit that. It's pretty standard and well accepted. If a set of populations can interbreed successfully, and the offspring can successfully interbreed, you're not dealing with separate species. The fact that you and I have Neanderthal ancestry is enough to demonstrate this. Also, if you read the supplements, Sub-Saharan Africans also have Neanderthal ancestry, due to Eurasian admixture. This is in addition to the minor Archaic admixture Sub-Saharan Africans already have. No living population is free from Archaic admixture. It's no longer tenable to speak in terms of "us vs them", since "they" are an unambiguous part of our genetic heritage. The Dmanisi work is also implicated in this, since a single lineage is much more parsimonious now.

GailT
12-19-2013, 03:26 AM
But on a more serious note, this is merely a finishing touch, just like the Dmanisi work. The only viable intellectual options: a very weak Out-of-Africa with assimilation, or Multiregionalism, and both of these are basically two sides of a single coin. On a paradigmatic level, we are all multiregionalists now, whether we like to admit it, or not.


A multiregional theory based on a very small degree of admixture between modern and archaic humans is not the same multiregionalism advocated by Wolpoff (http://en.wikipedia.org/wiki/Multiregional_origin_of_modern_humans). Wolpoff's multiregionalism is a dead theory. It has been proved to be incorrect. So no, we are not all multiregionalists now. I'd be interested to know specifically what you mean by "multiregionalism".

More than 90% of the genome of people outside of Africa is from the recent Out of Africa migration, so this very obviously suggests a primarily out of Africa migration. It is much more accurate to describe this as a strong Out-of-Africa migration with a small amount of archaic admixture. If this is what you mean by multiregionalism, I think you have used the term incorrectly.

GailT
12-19-2013, 03:33 AM
By weak Out-of-Africa, I mean Out-of-Africa with assimilation. And from a conceptual angle, that's basically a variation on the multiregional model. For people who would deny this, frankly, they just aren't familiar with multiregionalism.


I'm eager to hear how you define mutiregionalism, as you seem not to be familiar with the way the theory has traditionally been described.

Sein
12-19-2013, 03:59 AM
Why does it feel like we've discussed this before? Probably because we have, only a few pages back. You have a very narrow understanding of what multiregionalism entails. You seem to be heavily struck by "labels". The "labels" are consistently determinative for you, while the deeper theoretical stakes don't seem to really interest you. In so far as multiregional theory implies reticulation, admixture, and genetic dynamism between Pleistocene humans, we are all multiregionalists. In so far as it implies a single Homo lineage, we are all multiregionalists. To claim otherwise is dull at best, and disingenuous at worst. Since you seem to be a bright person, the latter looks to be the case.

GailT
12-19-2013, 04:11 AM
Why does it feel like we've discussed this before? Probably because we have, only a few pages back. You have a very narrow understanding of what multiregionalism entails. You seem to be heavily struck by "labels". The "labels" are consistently determinative for you, while the deeper theoretical stakes don't seem to really interest you. In so far as multiregional theory implies reticulation, admixture, and genetic dynamism between Pleistocene humans, we are all multiregionalists. In so far as it implies a single Homo lineage, we are all multiregionalists. To claim otherwise is dull at best, and disingenuous at worst. Since you seem to be a bright person, the latter looks to be the case.

I'm simply asking how you define multiregionalism. Do you think the evidence supports Wolpoff's multiregionalism, or does it mean something else to you? I think it is important to use terms accurately, as multiregionalism has a very specific meaning for most people familiar with the history of theories on human origins. If you mean primarily Out of Africa with weak admixture with archaics, then multiregionalism is not an accurate term.

Sein
12-19-2013, 04:36 AM
I'm sorry if I was a bit rude.

For Wolpoff, Pleistocene human history involved subspecies, rather than actual species. I think that is undeniable now. It seems human populations have always been linked by gene flow. To me, this is basically the crux of multiregionalism, and all of the recent genetic evidence supports it. Multiregionalism also predicted an irreducible archaic contribution to living human populations. That is also strongly supported by recent data. Wolpoff did overstate the contribution, but he always recognized that the amount of "archaic" admixture isn't necessarily relevant. What really matters is how we all share most of our ancestry, rather than just the fact that we do. Clinal dynamics between neighboring populations could also explain the fact that we all share around 90% of our ancestry, rather than a single migration out of Africa. In fact, the latter seems more plausible. We have no evidence of a recent expansion from Africa, yet we all share some very substantial recent ancestry. To me, this just bespeaks of a kaleidoscope of expansions, isolation-by-distance, population turnovers, and huge episodes of admixture. This would have seemed far from parsimonious not too long ago, but recent genetic data has turned the tables. The closer we look, the more admixture we find. Non-admixed populations just don't exist, and trees don't describe human genetic variation, not by a long shot. Our species is African, but this is due to the direction of gene-flow. The African continent has been more of a source than a sink. But even this isn't absolute. Africa has clearly seen Eurasian back migration. All Sub-Saharan Africans have Eurasian admixture, as demonstrated by the Reich lab, even hunter gatherers in Southern Africa.

GailT
12-19-2013, 05:07 AM
John Hawks has a very helpful and nuanced discussion of the fossil and the DNA evidence. (link) (http://johnhawks.net/weblog/fossils/lower/dmanisi/d4500-lordkipanidze-2013.html). Human origins, beginning with Homo erectus around 2 millions years ago, were complex and are poorly understood. It is reasonable to think in terms of multiregional evolution on the scale of 2 million to several hundred thousand years ago. There might have been multiple migrations out of Africa during that time. It is uncertain if there were different species or different sub-species of Homo at that time, and it is uncertain to what degree they interbred. We are just beginning to understand the complexity of that period and it will likely take many decades of research before we understand it, or it may be that not enough evidence survives to fully understand the population dynamics of that period.

We have a somewhat better understanding of recent human origins, within the last 100,000 years, largely because of the DNA evidence. It is still a complex history, including admixture with archaics and uncertainty in the specific timing of migrations. I think that the timing and path of the most recent OoA migration is especially interesting - was it a migration out of Africa around 60,000 years ago, or perhaps an earlier migration from Africa to Arabia, followed by expansion from Arabia to Eurasia? No one can claim to know for certain how and precisely when these population migrations and expansions occurred.

But we do have strong evidence based on the genetic similarity of all living people, and especially based on uniparental DNA, that we primarily descend from recent African ancestors, with a small degree of admixture with archaic humans. There are many people who are ideologically uncomfortable with that conclusion, not so much in the academic community, but very much so in the online and hobbyist community. If you participate in certain online forums, it's very obvious that some of the discomfort is based on racism. I definitely do not ascribe that motive to people in this forum, but when we do not describe the data accurately, it provides ammunition for people who refuse to accept a recent African origin because of their prejudice against Africans. So I think it is important to describe accurately what we do know.

We know that modern humans do not descend from distinct regional populations originating in a common Homo erectus ancestor dating to around 2 million years ago, as Wolpoff suggested in his theory of multiregional evolution. The genetic evidence very clearly shows that we primarily descend from a recent African ancestor. I believe that this is almost universally understood and accepted as the strongest theory by academic researchers. (If you disagree, please share your sources.) So it is primarily in the non-academic community where we have this failure to understand or to accept the implications of the genetic data. I think that this is a problem, so when I believe that people inaccurately describe the science, it is important to comment on this.

Sein
12-19-2013, 05:52 AM
It is relevant to mention, as I did previously, that Hawks is still a multiregionalist. He always has been. And the link is pretty unambiguous about this.

But your description of multiregional theory is still off the mark, even for Wolpoff. I think we're at different frequencies here, and we're just not registering information in a like manner. Also, I've read Wolpoff's work, not secondary descriptions of his work. Perhaps this explains why your understanding of multiregional theory seems so inaccurate to me? I mean, read what you wrote about distinct regional populations again.

Anyway, the uniparental genetics literature is very weak tea in such a discussion. We've reached a point where we can just ignore all of it. The immense discordance between uniparental data, and data from the autosome, is just incredible.

Also, we cannot let our science be hijacked by random individuals at the fringe. The online-hobbyist community doesn't really matter in this context. People will project emotional idiosyncrasies onto solid science. Racism was not alien to Out-of-Africa. Dimwits like Nicholas Wade would describe the "exodus" from Africa in celebratory terms, as if there was something fundamentally wrong about the continent, and about those "who stayed behind". Then you had the genocidal scenarios, with Homo sapiens sapiens annihilating the feeble-minded Neanderthal, in a classic veni, vidi, vici narrative. Creating affective and irrational associations is something some people can't avoid, and multiregionalism is not unique or distinctive in this respect. The only people who can see racism here are those who assume a candelabra model, which is absolutely alien to multiregional thought. To be frank, I think you're idea of multiregionalism is still just a caricature that strongly resembles a candelabra model.

GailT
12-19-2013, 06:31 AM
Hawks is certainly not a Multiregionalist in the Wolpoff school. Quoting from the link above:


Modern humans have more than 90% of their genetic makeup from Africans of the late Middle Pleistocene, comprising one major layer of genetic similarity worldwide.
... The "out of Africa" layer of genetic similarity is the last global one.


If you read Hawks, it is clear that he refers to the possibility of multiregionalism in the period from about 2 million to a few hundred thousand years ago, and only as a possibility. He does not believe that archaic humans contributed significantly to modern humans, and he very clearly states that modern humans originated in and migrated from Africa.

Contrary to your claim, I have accurately described Wolpoff's theory of Multiregionalism. Here is Wolpoff himself describing it in exactly the same way (link). (http://www-personal.umich.edu/~wolpoff/Papers/Case%20against%20Eve.pdf) Quoting Wolpoff:



Some consider a migration of conquering humans from Africa to be at odds with the fossil record. ... For the past 12 years we have been working on the problem of human origins with colleagues in the United States, Australia and China. Recently we have uncovered new fossil evidence which challenges the existence of Eve. We have discovered some important similarities between the skulls of ancient humans and their modern counterparts, similarities that are hard to square with a theory based on African migration and mass replacement. We back a completely different theory: that Homo sapiens evolved from ancient humans gradually in many parts of the world.





Anyway, the uniparental genetics literature is very weak tea in such a discussion. We've reached a point where we can just ignore all of it. The immense discordance between uniparental data, and data from the autosome, is just incredible.


Where exactly do you see discordance between uniparental and autosomal DNA? Please cite some papers. I believe that both are consistent in showing primarily a recent origin of modern humans in Africa. Even if they were discordant, which I dispute, it is remarkably careless to claim that we can simply ignore uniparental DNA. Any theory of human origins must also account for the recent African origin of uniparental DNA.

Sein
12-19-2013, 07:08 AM
Gail, Hawks is a multiregionalist. He still considers himself as such. Whatever you say in this regard, that's how he describes his thinking. Also, here is something I said earlier in this thread:

"...there is no question that modern humans are almost completely African. Admixture with archaic Homo sapiens constitutes only 10%, at most, of our genomic ancestry."

If you read through the thread, you'll find that we're beginning to get strongly redundant. We seem to be running over the same points over and over again, and the quality of our discussion seems to be deteriorating. This goes for me as much as it goes for you, in fact, more so for me.

No one is arguing for Wolpoff here, you brought him up. You've restricted the discussion to him. I'm not a multiregionalist in the manner of Wolpoff. I've always gravitated towards Alan R. Templeton. Multiregionalism is a class of theories. Anyway, a 4 page piece written for a science magazine is not what I had in mind.

Also, going by uniparental DNA, living Homo sapiens sapiens should have no archaic ancestry. That's obviously wrong. That's the discordance. Things will get more complicated and fun as we start seeing work on whole genomes. There is a paper in the works which argues for a Neanderthal contribution of 4%-8% to Eurasians. Besides, genetic divergences between uniparental lineages are much more substantial than genetic divergences on the autosome. Compare Denisovan atDNA with Denisovan mtDNA.

BMG
12-19-2013, 02:24 PM
Two questions
1)Are the available neanderthal/denisovan genomes good enough for comparisons with human genome?
2)Is there a reliable method to estimate the archaic admixture in humans?

GailT
12-19-2013, 03:34 PM
Also, here is something I said earlier in this thread:

"...there is no question that modern humans are almost completely African. Admixture with archaic Homo sapiens constitutes only 10%, at most, of our genomic ancestry."


I agree that we can use the term multiregionalism in different ways, it might apply to archaic humans, and it also can be used to describe the small amount of genetic contribution of archaics to modern humans. But I think it is important to clarify what one means by the term, as there are many people who still interpret it to mean that modern humans did not originate in Africa. So I do think this has been a helpful discussion.

And I also agree that uniparental DNA only provides evidence of a recent African origin, and that it is not able to detect the small amount of archaic contribution, and therefore is not sufficient for completely describing human origins. This is not surprising given the very low probability of a continuous direct male or female archaic DNA line surviving for tens of thousands of years in a primarily Out of Africa population. But this does not mean that we should ignore the uniparental evidence. The fact that Neandertal and Denisovan mtDNA and y-DNA do not survive is important evidence that is consistent with autosomal DNA, which shows small contributions from archaics. If you spend any time at all on this and other discussion forums, you will see that there are many people who continue to deny the interpretation and/or the significance of uniparental DNA. So it is helpful to state explicitly how one interprets this evidence.

Jean M
12-19-2013, 03:55 PM
The fact that Neandertal and Denisovan mtDNA and y-DNA do not survive is important evidence that is consistent with autosomal DNA, which shows small contributions from archaics.

Razib Khan just posted something similar.


...it does seem that the human phylogeny is more properly defined as a graph than a tree. But don’t forget that it doesn’t seem like all the edges were weighted the same. We’re a whole lot more Neo-African than we are Neanderthal or Denisovan.

http://www.unz.com/gnxp/not-separate-but-not-equal/

GailT
12-20-2013, 12:19 AM
And now we hear from the "Out of Australia" camp (link). (http://www.riseearth.com/2013/12/dna-evidence-debunks-out-of-africa.html#more)

The link above demonstrate an astonishing ignorance of the data and a deep suspicion of the scientific process.

Ian B
12-20-2013, 05:41 AM
And now we hear from the "Out of Australia" camp (link). (http://www.riseearth.com/2013/12/dna-evidence-debunks-out-of-africa.html#more)

The link above demonstrate an astonishing ignorance of the data and a deep suspicion of the scientific process.

Web sites such as this serve to confuse people like me who are newcomers to the field of Genetics, and should either make it very clear that their information is unconfirmed by science or is pure speculation. I read the article you referred to and was advised by JeanM that it wasn't really credible. I accept her advice without reservation.

Sein
12-20-2013, 07:06 AM
I think someone's even argued for Out-of-America!

Muircheartaigh
12-20-2013, 10:55 AM
Razib Khan just posted something similar.



http://www.unz.com/gnxp/not-separate-but-not-equal/

Bearing in mind the recent discoveries of Haplogroups A0 and A00, and who can say that there aren't people, surviving today with X or Y chromosomes of Neanderthal or Denisovan, albeit they may be Modern Human in all other respects?

GailT
12-20-2013, 03:36 PM
Web sites such as this serve to confuse people like me who are newcomers to the field of Genetics, and should either make it very clear that their information is unconfirmed by science or is pure speculation.

The intention of this person is to confuse people, and to attract attention. He is also selling a book claiming that Australians came from ancient aliens, so he is very obviously a charlatan trying to deceive people and make a buck. But unfortunately, he is also very successful. The genealogy-DNA list is moderated by a person who denies an African origins (it was actually the list moderator who posted the link there). The same list as also been an active forum for bigfoot DNA. There is an amazing level of scientific illiteracy and outright distrust of science among a large number of people in the genetic genealogy community. I don't know how much of this should be attributed to prejudice or to simple ignorance, but it is disturbing either way.

GailT
12-20-2013, 03:51 PM
Bearing in mind the recent discoveries of Haplogroups A0 and A00, and who can say that there aren't people, surviving today with X or Y chromosomes of Neanderthal or Denisovan, albeit they may be Modern Human in all other respects?

Although it seems very unlikely, I don't think we can rule out the possibility that Neanderthal or Denisovan uniparental DNA might survive. If they do survive, it would be at extremely low frequency, given that they have not yet been detected in a very large sample size. Given current estimates that Neandertals might have contributed around 2% of modern European DNA, from an admixture that occurred more than 40,000 years ago, what would be the probability of a direct maternal or paternal line surviving from that time? Probably very close to zero. If we do find a surviving Neandertal line, it would be very interesting, but I don't think it would tell us anything new about the contribution of those archaic humans to the modern gene pool, as this is best estimated using autosomal DNA. A00 is a good example, it is possible that it could date to before the emergence of modern humans, and it could be evidence of archaic admixture in Africa, but it represents a tiny fraction of modern human y-DNA. So studies of autosomal DNA are needed to assess archaic human contributions to modern humans within Africa.

parasar
12-21-2013, 05:40 AM
Bearing in mind the recent discoveries of Haplogroups A0 and A00, and who can say that there aren't people, surviving today with X or Y chromosomes of Neanderthal or Denisovan, albeit they may be Modern Human in all other respects?

With the admixture we are seeing, we know for sure that that had to have happened at some point in time. Plus the Denisovan Y line is unknown.

Muircheartaigh
12-21-2013, 10:59 AM
Given current estimates that Neandertals might have contributed around 2% of modern European DNA, from an admixture that occurred more than 40,000 years ago, what would be the probability of a direct maternal or paternal line surviving from that time? Probably very close to zero..

I agree, all of the Neanderthal and Denisovan lines are probably now extinct but the discovery of A00 revealed a previously unknown Haplogroup in people of African decent who's Y chromosome indicates branching maybe 400,000 years ago. Is this considered to be in the era of Modern Humans or is their Y DNA from an earlier sub-species?

The percentage of people that have been Y DNA tested is small compared to the world population, and there are areas of the world more remote than Africa where isolated groups with different Haplogroups to our own may have survived.

lgmayka
12-22-2013, 01:33 AM
I agree, all of the Neanderthal and Denisovan lines are probably now extinct but the discovery of A00 revealed a previously unknown Haplogroup in people of African decent who's Y chromosome indicates branching maybe 400,000 years ago.
The published estimate was 338,000 ybp (http://www.cell.com/AJHG/retrieve/pii/S0002929713000736), with a very large confidence interval; and IMHO that figure was somewhat inflated (which is easy to do since it is based on so many assumptions). I would simply round to the nearest hundred-thousand, and say "roughly 300,000 years ago."

GailT
12-22-2013, 06:04 AM
The published estimate was 338,000 ybp (http://www.cell.com/AJHG/retrieve/pii/S0002929713000736), with a very large confidence interval; and IMHO that figure was somewhat inflated (which is easy to do since it is based on so many assumptions). I would simply round to the nearest hundred-thousand, and say "roughly 300,000 years ago."

Given the uncertainty in the age of A00 and uncertainty when AMH originated (usually assumed to be around 200,000 years ago) it seems possible that A00 might have represented archaic admixture in Africa, but I don't think that we can be certain of this. In any case, it does not seem to be very archaic, especially when compared to archaic admixture with Neandertals and Denisovans. At most, it seems like one might argue that A00 was "slightly" archaic, or perhaps not archaic at all.

There is some autsomal DNA evidence for archaic mixture in Africa, so if it is not A00, there may be another source, although there is no mtDNA or y-DNA evidence, yet, of admixture older than A00.

Jean M
01-07-2014, 01:28 PM
A new paper from Cruciani's team has appeared online before print:

Rosaria Scozzari, Andrea Massaia, Beniamino Trombetta, Giovanna Bellusci, Natalie M. Myres, Andrea Novelletto, Fulvio Cruciani, An unbiased resource of novel SNP markers provides a new chronology for the human Y chromosome and reveals a deep phylogenetic structure in Africa, Genome Research, online 4 January 2014.
http://genome.cshlp.org/content/early/2014/01/06/gr.160788.113.abstract

Abstract


The phylogeography of the paternally-inherited MSY has been the subject of intense research. However, sequence diversity and the ages of the deepest nodes of the phylogeny remain largely unexplored due to the severely biased collection of SNPs available for study. We characterized 68 worldwide Y chromosomes by high-coverage next generation sequencing, including 18 deep-rooting ones, and identified 2,386 SNPs, 80% of which were novel. Many aspects of this pool of variants resembled the pattern observed among genome-wide de novo events, suggesting that in the MSY a large proportion of newly arisen alleles have survived in the phylogeny. Some degree of purifying selection emerged in the form of an excess of private missense variants. Our MSY tree recapitulated the previously known topology, but the relative lengths of major branches were drastically modified and the associated node ages were remarkably older. We found significantly different branch lengths when comparing the rare deep-rooted A1b African lineage with the rest of the tree. Our dating results and phylogeography led to the following main conclusions: 1) patrilineal lineages with ages approaching those of early AMH fossils survive today only in central-western Africa; 2) only a few evolutionarily successful MSY lineages survived between 160 and 115 kya; 3) an early exit out of Africa (before 70 kya), which fits recent western Asian archaeological evidence, should be considered. Our experimental design produced an unbiased resource of new MSY markers informative for the initial formation of the anatomically modern human gene pool, i.e. a period of our evolution which had been previously considered to be poorly accessible with paternally-inherited markers.


New Y-DNA Tree

1173

Thanks to JaG for posting this news in New DNA Papers. http://www.anthrogenica.com/showthread.php?709-New-DNA-Papers&p=26102&viewfull=1#post26102

parasar
01-07-2014, 04:14 PM
My main problem is not with OoA itself since even if Neanderthals and Denisovans and perhaps other non-Africans were involved with our makeup we are quite African or Africans are quite us.

The issue I have is with the 50-60000ybp time-frame which cannot be confirmed by any archaeological evidence in South or Inner Asia. Just subsequent to this time-frame we see an explosion of Upper-Paleolithic finds all over.

To explain this, I have proposed two scenarios: 1. The African exodus though Asia is much older (~100000ybp) and the Upper Paleolithic people descend from a later node of expansion. 2. There was a migration across the ocean to SE Asia and E Asia directly from Africa which would explain why there is a lack of AMH remains in South and Inner Asia.

Since the second scenario looks quite unlikely, but not impossible, I think #1 is what happened.

Based on what Jean has posted above from the Cruciani team, the window of exodus from Africa is approximately 30000 years from 120200ybp.
The lower limit for the exodus is 82500ybp. This 82500ybp lower limit would consider E to be African. From the phylogeny this looks extremely unlikely as E has immense separation from B, and there is essentially no daylight between (D)E's split from CF, so much so that upper boundaries reverse (88.7 vs 87.9) in age! E is therefore most likely Eurasian implying E in Africa is a back-migration.

Diverclic
01-11-2014, 12:50 AM
Anatole Klyosov is the only author of a paper to come out soon entitled : " Reconsideration of the “Out of Africa” Concept as Not Having Enough Proof " . I had a chance to read a draft of this article. Basically, the good point is a sharp criticism on how people have repeated the "out of Africa" idea and with little knowledge on the timing. Only A00 and A0 branch are African. Even some A-M13 were found in Europe (see the Francalacci paper, for example), making it hard to justify an African position for the A1 branch.
The finding of B-M60 haplogroups in Iran on the persian gulf coast (on Iran side - facing Arabian peninsula) is suggesting to me a possible origin of spread in the peninsula but I know that even so will be contested by A. Klyosov, as the spli between B and [C-T] is large (si last Scozzari paper - 2014). More than 30000 years is a long time to imagine that early branch confined in the peninsula all that time. Also, some Hazaras were B-M60. So, the first point for the scientific community is to go back and stop always thinking of "Out of Africa" as a paradigm.

GailT
01-11-2014, 04:24 AM
Anatole Klyosov is the only author of a paper to come out soon entitled : " Reconsideration of the “Out of Africa” Concept as Not Having Enough Proof".

In Anatole's 2013 self-published paper he badly misinterpreted the y-DNA tree by using STR analysis and ignoring SNPs. He claimed that CT did not descend from A, and instead, that A and CT shared a common ancestor who probably lived outside of Africa. If he now recognizes that CT descends from A, that will be progress.

Diverclic
01-12-2014, 01:30 AM
I think you are mistakingly interpreting the present tree. Let me be clear : if you belong to the CT branch (most probably) then you share no SNP with A0 or A00 guys. This is what is called the polyphyletic nature of haplogroup A. Read the Scozzari et al. paper (2014) and you'll find the same reading of the tree : the monophyletic tree is mainly that of the B - CT branch and some upstream SNPs (leading also to some A branches). May be it was a bad idea to use the same letter "A" when the polyphyletic nature was recognized. I also think Klyosov is right not to have stopped STR just because Busby et al. said it. His work with slow mutating STRs (22 markers haplotype) found the tree described by Scozzari, earlier. i mean, he was, as far as I can know the first one to insist that the A- B node was very ancient and that only B haplogroup was close to the CT branch. He also contested the "demonstration" that B was "African" and he insisted that there was no prove for that : B might have been elsewhere and then migrated to Africa. Several scientists are now thinking this way.

GailT
01-12-2014, 02:10 AM
I think you are mistakingly interpreting the present tree. Let me be clear : if you belong to the CT branch (most probably) then you share no SNP with A0 or A00 guys.

No, I did not say that CT descends from A00 or A0, these are parallel branches on the Y tree. But CT does descend from A0'1'2'3'4. Here is the line of descent, using the branch names from the Y phylotree (http://www.phylotree.org/Y/tree/):

Y-MRCA
A0'1'2'3'4
A1'2'3'4
A2'3'4
A4=BCDEF
CDEF
CF

All of the branches older than CDEF are found primarily in Africa or in people of recent African descent. Anatole claims that the non-African branch, which he called "beta", does not descend from or share ancestry with African branches. Instead, he claims that beta descends directly from Y-MRCA, which he called "alpha". For his claim to be correct, you would have to show that CF does not share the SNPs in the descent from Y-MRCA to CDEF. This is inconsistent with every major study of Y phylogeny since the 1990s. Anatole claims that the authors of all these studies have misinterpreted their data.

Which scientists are now thinking that B originated outside of Africa and then migrated to Africa? From the new Scozzari paper, it looks like they have an age estimate for B of about 110 kya, while CF and E diverge around 86 kya. I have not looked at distributions of Y haplogroups, apart from looking at the FTDNA B project, which suggests that men in B are primarily found in Africa today, or men of African descent. If that is correct, it would suggest that B originated in Africa.

lgmayka
01-12-2014, 03:21 AM
Which scientists are now thinking that B originated outside of Africa and then migrated to Africa? From the new Scozzari paper, it looks like they have an age estimate for B of about 110 kya, while CF and E diverge around 86 kya. I have not looked at distributions of Y haplogroups, apart from looking at the FTDNA B project, which suggests that men in B are primarily found in Africa today, or men of African descent. If that is correct, it would suggest that B originated in Africa.
According to the B Y-DNA Project (http://www.familytreedna.com/public/BYDNA/default.aspx?section=yresults), B has a significant presence on the Arabian Peninsula. For some time, Dienekes has championed his "Out of Arabia" hypothesis (http://dienekes.blogspot.com/2012/01/arabian-cradle-fernandes-et-al-2012.html), according to which modern humans--after leaving Africa--spent thousands of years in Arabia before expanding into the Levant and beyond. Archaeological support for this concept (http://dienekes.blogspot.com/2013/12/arabian-origin-of-upper-paleolithic-in.html) may be increasing. One possible implication of this is that Y-DNA B may actually be Arabian, not African, in origin, although B mostly went westward back into Africa while CT expanded toward the north and east.

Diverclic
01-12-2014, 08:38 AM
I agree with Lawrence (above) ; this is what I had in mind and it's true that this was championed first (as far as I know) by Dienekes.

For GailT : I also agree with this description ; now is A0'1'2'3'4 ; A1'2'3'4 ; A2'3'4 , in this order, "haplogroup A" ? The saying by A. Klyosov was "extreme" but I think it did participate in the modern view on the tree. What I mean, basically, is that I am finding rather unfair what I can read on A. Klyosov. He isn't my champion but I remember that his tree with "alpha" (I have no greek symbols) and "beta" was clearly early when it was published. I find it unfair not to find a single reference to these publications in recent articles on the subject.

Let's go back to the "out of Africa" theory. If the idea that the moment of the way out might have been at B - T stage, then it makes it much earlier and may be much much earlier. Finally, one extreme view (that Klyosov likes) is that the geographical origin might be consubstantial with homo sapiens arising. If B could be in arabian peninsula, why not A4 branching with B-T ? According to Scozzari et al. (2014) that would be some 160 000 years ago and not so long ago it was thought that this was, about, the extreme dates for modern homo sapiens.

GailT
01-12-2014, 10:11 AM
Yes, I agree it is a very interesting theory, but also very speculative. Quoting from Dienekes comments on the Fenandez et al. 2012 paper:


However, if the second hypothesis is true, there is a problem: haplogroup L3 is dated to 70ka, so if the expansion associated with it started in Asia, that means that there must have been substantial back-migration of L3-related lineages back to Africa. I don't see any major problem with that hypothesis, but it is true that many scientists are reluctant to feature extensive back-migration to Africa into their models. At present it has not been possible to determine to what extent genetic diversity in Africa is due to great antiquity vs. admixture of divergent human populations, which I have called Afrasian (related to Eurasians) and Palaeoafrican. If L3 did originate in Africa, then the concusion of a recent African exodus is inescapable.

The major contribution of the current paper is that it fixes a major human expansion Out-of-Arabia at very close to 60ka. Whether this expansion originated from transient Out-of-Africans who had recently exited Africa, or from long settled populations of Asia (prior to 100ka) remains to be seen.


First, I think that scientists are right to be very cautious in proposing models that depend on extensive back migrations. The simplest explanation is that early branches of haplogroups found primarily throughout Africa today probably originated in Africa. You would need strong evidence to argue that they migrated from Africa to Asia, lived in Asia for thousands of years, and then migrated back to Africa without leaving a significant component in Asia. It is possible, but it is not the most likely scenario, and it remains highly speculative until there is other evidence (perhaps autosomal DNA?) that supports it.

Another possibility is that mtDNA age estimates are biased low. It doesn't seem likely that they could be biased low enough to place mtDNA M and N in Arabia around 100 kya. But suppose L3 is 80 kya, and that a group of L3 women arrived in Arabia around 80 kya, lived there for 10 ky giving rise to M and N, which then expanded from Arabia to Asia around 70 kya. This is also highly speculative and depends on large age underestimates of mtDNA haplogroups. There are all sorts of plausible scenarios that one can construct, but I don't think there is enough data yet to test the details of any of those complex scenarios.

We can be very confident that modern mtDNA and yDNA haplgroups originated in Africa roughly around 200 kya, consistent with the theory that anatomically modern humans originated in Africa around that time. It is simply not possible to argue that the mtDNA or yDNA phylogeny shows that AMH originated in Asia, as Anatole claims, because you have more than 100 ky of evolution of branches of A in Africa before you get to a branch (perhaps CDEF) that could have plausibly expanded into Eurasia.

I can't see giving credit to Anatole when he ignores the SNP data and fundamentally distorts the Y phylotree to support his belief that AMH originated in Asia. Even if he did predict some haplogroup age estimates accurately based on STR analysis, he reaches conclusions that are very obviously incorrect and unsupported by his analysis. For example, look at Figure 1 in "DNA Genealogy and Linguistics. Ancient Europe", his self-published paper in 2013. To get credit in the scientific community, one must publish a coherent theory in a peer reviewed journal.

Diverclic
01-12-2014, 11:38 AM
OK, I have been thinking on how to reconcile the data and the different theories. That Figure 1 is precisely a good result, with possibly a (small) bias, from STR data. To bad I don't know how to extract it from the pdf and compare it to other trees. The point is that STR are reflecting strongly any bottleneck while SNP do NOT, even though a large SNP accumulation on 1 node can be indicative of a bottleneck. So, if instead of 60 000 Klyosov had a 70 000 (in rough figures) for the "beta" stage then a "Toba" effect would appear as the best explanation : the long line from "alpha" to "beta" might just reflect the disappearance of many lineages and a founder effect. A limitation explained by a bottleneck wouldn't be that bad as it would tell something on the "story".

Now, about the "back to Africa" theory. You miss part of the point. So, what's following isn't really my best scenario but I want to depict a scenario where the link to Africa becomes weaker for AMH. First point, I am not sure at all there were AMH before 170 000 years ago as dating of bones and skulls of this age is not that precise (C14 is short) . Say there was a geographical split some 170 000 years ago and part of the ancient homo population (from Africa) became "trapped" in arabian peninsula, while the rest was in Africa. Why trapped ? The way out by the north might have been uneasy because of Neandertal groups (just an idea to explain a group linked to the peninsula). I am saying that the evolution to modern homo sapiens (real AMH) might have been limited to the arabian peninsula. We lack good fossiles records from there but Israel is just north of it. So, there would have been an evolution in situ leading to the ONLY AMH that ever occurred. For mitochondrial DNA this would be the L3 stage and for Y it would be the B-A split with some A haplogroup belonging to that group. Why so many "come back" to Africa ? probably a change in climate and a maximum in population led to different waves. Those A haplogroup with modern traits went back first ; cross mating between "archaîc" (african) resident population and incoming "modern" A group allowed a spread of the new traits and this the way I explain the polyphyletic state of haplogroup A. The selection for modern traits must have been strong. A second wave back to Africa would have been B haplogroup (with a few trying going east) ; the last wave was DE, evolving in situ (africa) as E while those DE migrating toward east moved to D haplogroup.
In the scenario above a Toba effect is still to be positioned. The main step toward AMH is NOT in Africa (though close to it). I forgot to say that the present Y tree in the last Scozzari paper is similar to the mitochondrial tree as presented (for example) in the Mishmar et al. paper (2002) ; each main branch has a fit in the other tree. This is one reason why I believe that the very old branches of the Y tree such as A00 are the product of some late introgression.

GailT
01-12-2014, 08:54 PM
The point is that STR are reflecting strongly any bottleneck while SNP do NOT, even though a large SNP accumulation on 1 node can be indicative of a bottleneck.


With full Y sequencing I think we will soon have much more precise SNP estimates of haplogroup ages and lengths of bottlenecks than is possible with STR data, so many of these questions might be resolved in the next few years. I was disappointed that the new Scozzari paper did not do a full Y sequence for A00, but hopefully those results will be available soon.

But a key point is that, for the more ancient branching in the Y tree, SNP data provide a more certain approach to construct a Y phylogenetic tree, and if an analysis of the tree structure based on STR data is in conflict with a tree based on SNP data, as in Figure 1, it is almost certain that the STR based conclusions are wrong.



Now, about the "back to Africa" theory. You miss part of the point. So, what's following isn't really my best scenario but I want to depict a scenario where the link to Africa becomes weaker for AMH. First point, I am not sure at all there were AMH before 170 000 years ago as dating of bones and skulls of this age is not that precise (C14 is short) . Say there was a geographical split some 170 000 years ago and part of the ancient homo population (from Africa) became "trapped" in arabian peninsula, while the rest was in Africa.

I agree with you that there are a wide variety of hypothetical scenarios one can construct. I don't think we can test these more complex migration theories with modern mtDNA and yDNA data, for several reasons: It is difficult to infer ancient origins from present day distributions; there is uncertainty in the age estimates; there may be large gaps in the present day data as results of extinction of certain mtDNA and yDNA lineages. Perhaps autosomal DNA will provide better evidence to test different theories about complex migrations, but ultimately I think we will need much more physical anthropology evidence.

So I think that mtDNA and yDNA only provide a coarse level characterization of ancient migrations. But I might be wrong - perhaps with larger datasets of full Y and mtDNA, and better age estimates, we might be able to tease out more information from yDNA and mtDNA.

Diverclic
01-13-2014, 04:23 PM
I think Cruciani (and co-authors) do not see A00 as part of AMH. I tried to communicate with him on the possibility of introgression for that case, with no answer until now. Cruciani is discussing dates of AMH and dates for bones and known skulls ; obviously he doesn't believe anything beyong 300000 years ago can be modern homo sapiens. You didn't comment (GailT) but the similarity between Y tree and mtDNA tree is for trees like those published by Cruciani et al. (and the timing is similar in the cases I mentioned)
I am not so optimistic for SNP timing as Cruciani demonstrated (in my view) that special care must be taken to find ALL SNPs in any given segments, with no errors (false positives are a great problem). Next work by others will have to respect this criteria for any chance on timing. For example I think that the date for american conquest by Q haplogroup was a good idea but what was missing was a good Q branch estimate relative to (all) other branches of the tree.

GailT
01-14-2014, 04:34 AM
Perhaps Cruciani doesn't have access to an A00 sample to test? With 50x coverage on full Y sequencing, I hope we will get a good count of the number of SNPs that define each branch in the Y tree. There are several people who did both the Full Y and BigY, so the comparison of those results might help estimate how many SNPs are being missed in the full Y sequencing.

Diverclic
01-14-2014, 09:56 AM
I am expecting much more than a number of SNPs from a full Y sequencing of A00 with high coverage : see the differences between human Y and the Chimp Y ? I am expecting many many changes in the organization of the Y chromosome. Large rearrangements will be the main information at this stage.

Sein
02-20-2014, 11:28 PM
http://www.genetics.org/content/early/2014/02/10/genetics.114.162396.abstract

"Although there has been much interest in estimating histories of divergence and admixture from genomic data, it has proven difficult to distinguish recent admixture from long-term structure in the ancestral population. Thus, recent genome-wide analyses based on summary statistics have sparked controversy about the possibility of interbreeding between Neandertals and modern humans in Eurasia. Here we derive the probability of full mutational configurations in non-recombining sequence blocks under both admixture and ancestral structure scenarios. Dividing the genome into short blocks gives an efficient way to compute maximum likelihood estimates of parameters. We apply this likelihood scheme to triplets of human and Neandertal genomes and compare the relative support for a model of admixture from Neandertals into Eurasian populations after their expansion out of Africa against a history of persistent structure in their common ancestral population in Africa. Our analysis allows us to conclusively reject a model of ancestral structure in Africa and instead reveals strong support for Neandertal admixture in Eurasia at a higher rate (3.4%-7.3%) than suggested previously. Using analysis and simulations we show that our inference is more powerful than previous summary statistics and robust to realistic levels of recombination."

This is pretty important.

parasar
09-21-2016, 07:37 PM
xOoA

"Proposed xOoA model"
http://www.nature.com/nature/journal/vaop/ncurrent/fig_tab/nature19792_SF10.html

http://www.nature.com/nature/journal/vaop/ncurrent/images/nature19792-sf10.jpg

parasar
09-21-2016, 08:06 PM
From the Reich group.
http://www.nature.com/nature/journal/vaop/ncurrent/fig_tab/nature18964_F3.html
http://www.nature.com/nature/journal/vaop/ncurrent/images/nature18964-f3.jpg

GailT
09-21-2016, 08:36 PM
From the Pagani et al. paper: "We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa."

Fairly definitive results (along with the other two Nature papers published today) that the recent OoA expansion mostly replaced any remnants of earlier OoA expansions of AMH. It will be interesting to know if Denisovans first interbred with the early OoA to form a hybrid population that later interbred with the more recent OoA. (as opposed to separate interbreeding events of recent OoA with Denisovans and with early OoA).

parasar
09-21-2016, 10:01 PM
From the Pagani et al. paper: "We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa."

Fairly definitive results (along with the other two Nature papers published today) that the recent OoA expansion mostly replaced any remnants of earlier OoA expansions of AMH. It will be interesting to know if Denisovans first interbred with the early OoA to form a hybrid population that later interbred with the more recent OoA. (as opposed to separate interbreeding events of recent OoA with Denisovans and with early OoA).

Maybe, maybe not, as that earlier split is prior to all modern Africans.

GailT
09-22-2016, 04:05 AM
Maybe, maybe not, as that earlier split is prior to all modern Africans.

Pagani et al. refer to an earlier OoA expansion after the origin of AMH, so more recent than 200,000 years ago.

parasar
09-22-2016, 04:10 PM
Pagani et al. refer to an earlier OoA expansion after the origin of AMH, so more recent than 200,000 years ago.

Maybe. My point was to indicate that it not necessarily an earlier OoA, just xOoA, since it is separate from modern Africans who are also on the OoA branch. http://www.nature.com/nature/journal/vaop/ncurrent/fig_tab/nature19792_SF10.html
We will need ancient DNA to resolve whether or not this xOoA was indeed from Africa.

GailT
09-22-2016, 09:11 PM
Maybe. My point was to indicate that it not necessarily an earlier OoA, just xOoA,
xOoA is an earlier OoA. Pagani defines xOoA as "an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa"

parasar
09-22-2016, 09:37 PM
xOoA is an earlier OoA. Pagani defines xOoA as "an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa"

We don't know that it was African despite what the paper may assume.
We don't even know if this largely extinct xOoA line was AMH or not.

parasar
09-22-2016, 09:58 PM
I can agree with what Parasar is saying. Australian Aborigines have been in Australia for ~50,000 to 60,000 years. That must make their exit date quite some years earlier. As times progress and more discoveries made, technology improves, it's quite probable that these views will change. I'd like to see a cultural comparison of the Australian Aborigines of say about five hundred years ago with African tribes prior to white settlement.

That is about the period it appears.
The diversity is immense in Australia.
"After an exodus some 72,000 years ago, they split away from the larger genetic group (along with their future neighbors in Papua New Guinea) 58,000 years ago and arrived on the Australian continent around 8,000 years later ....
There's other genetic evidence for Aboriginal people's long relationship with their homeland: Since reaching the continent 50,000 years ago, the group has continued to divide into distinct ethnic lineages. Willerslev and his colleagues found that individual Aboriginals from different parts of Australia could be as genetically distinct from one another as Europeans are from East Asians. This points to a long, long period of separation - tens of thousands of years living on opposite sides of massive deserts."
http://www.chicagotribune.com/news/nationworld/ct-native-australians-origin-20160922-story.html

parasar
11-20-2017, 09:15 PM
A multivariate assessment of the Dali hominin cranium from China: Morphological affinities and implications for Pleistocene evolution in East Asia
Athreya et al.
http://onlinelibrary.wiley.com/doi/10.1002/ajpa.23305/abstract

"Dali aligns with Middle Paleolithic H. sapiens and is clearly more derived than African or Eurasian Middle Pleistocene Homo. When just the neurocranium is considered, Dali is most similar to African and Eastern Eurasian but not Western European Middle Pleistocene Homo. When both sets of variables are considered together, Dali exhibits a unique morphology that is most closely aligned with the earliest H. sapiens from North Africa and the Levant ...
Dali a “transitional” form between Chinese H. erectus and H. sapiens. Athough no taxonomic allocation is appropriate at this time for Dali, it appears to represent a population that played a more central role in the origin of Chinese H. sapiens ...
we propose that Pleistocene populations in China were shaped by periods of isolated evolutionary change within local lineages at certain times, and gene flow between local lineages or between Eastern and Western Eurasia, and Africa at other times, resulting in contributions being made in different capacities to different regions at different times."