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Originally posted by capra:
Sorry Lioness don't know anything about pigmentation alleles.

Xyyman's interpretation of everything is of course that if it's found in Africa, that means it necessarily came from Africa, and therefore all evidence of back-migration from Eurasia is evidence against back-migration from Eurasia. Truly, he has a dizzying intellect.

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Posts: 949 | From: England | Registered: Oct 2015  |  IP: Logged | 

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Originally posted by the lioness,:

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Originally posted by Clyde Winters:

the Bell Beaker and Yamnaya people were Kushites

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EF share greater genetic affinity to populations from southern Europe than to those from northern Europe with an inverted pattern for WHG1,2,3,4,5. Surprisingly, we find that CHG influence is stronger in northern than Southern Europe (Fig. 4a and Supplementary Fig. 3A) despite the closer relationship between CHG and EF compared with WHG, suggesting an increase of CHG ancestry in Western Europeans subsequent to the early Neolithic period. We investigated this further using D-statistics of the form D(Yoruba, Kotias; EF, modern Western European population), which confirmed a significant introgression from CHG into modern northern European genomes after the early Neolithic period (Supplementary Fig. 4).

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We investigated the temporal stratigraphy of CHG influence by comparing these data to previously published ancient genomes. We find that CHG, or a population close to them, contributed to the genetic makeup of individuals from the Yamnaya culture, which have been implicated as vectors for the profound influx of Pontic steppe ancestry that spread westwards into Europe and east into central Asia with metallurgy, horseriding and probably Indo-European languages in the third millenium BC5,7. CHG ancestry in these groups is supported by ADMIXTURE analysis (Fig. 1b) and admixture f3-statistics14,25 (Fig. 5), which best describe the Yamnaya as a mix of CHG and Eastern European hunter-gatherers. The Yamnaya were semi-nomadic pastoralists, mainly dependent on stock-keeping but with some evidence for agriculture, including incorporation of a plow into one burial26

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• English Hattic Egyptian Malinke (Mande
  language)
  
  powerful ur wr'great,big' fara
  
  protect $uh swh solo-
  
  head tup tp tu 'strike the head'
  
  up,upper tufa tp dya, tu 'raising ground'
  
  to stretch put pd pe, bamba
  
  to prosper falfat -- find'ya
  
  pour duq --- du 'to
  dispense'
  
  child pin,pinu den
  
  Mother na-a -- na
  
  lord sa -- sa
  
  place -ka -ka

• Hurrian Sanscrit
  Mi-it-ra Mitra
  Aru-na Varuna
  In-da-ra Indra

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Given their geographic origin, it seems likely that CHG and EF are the descendants of early colonists from Africa who stopped south of the Caucasus, in an area stretching south to the Levant and possibly east towards Central and South Asia. WHG, on the other hand, are likely the descendants of a wave that expanded further into Europe. The separation of these populations is one that stretches back before the Holocene, as indicated by local continuity through the Late Palaeolithic/Mesolithic boundary and deep coalescence estimates, which date to around the LGM and earlier. Several analyses show that CHG are distinct from another inferred minor ancestral population, ANE, making them a divergent fourth strand of European ancestry that expands the model of the human colonization of that continent.


The separation between CHG and both EF and WHG ended during the Early Bronze Age when a major ancestral component linked to CHG was carried west by migrating herders from the Eurasian Steppe. The foundation group for this seismic change was the Yamnaya, who we estimate to owe half of their ancestry to CHG-linked sources. These sources may be linked to the Maikop culture, which predated the Yamnaya and was located further south, closer to the Southern Caucasus. Through the Yamanya, the CHG ancestral strand contributed to most modern European populations, especially in the northern part of the continent.

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Jones et al, make it clear that ”Given their geographic origin, it seems likely that CHG and EF are the descendants of early colonists from Africa who stopped south of the Caucasus, in an area stretching south to the Levant and possibly east towards Central and South Asia”. the African origin of these Levantines is supported by Holliday. Trenton W. Holliday, tested the hypothesis that if modern Africans had dispersed into the Levant from Africa, "tropically adapted hominids" would be represented in the archaeological history of the Levant, especially in relation to the Qafzeh-Skhul hominids. This researcher found that the Qafzeh-Skhul hominids (20,000-10,000),were assigned to the Sub-Saharan population, along with the Natufians samples (4000 BP). Holliday also found African fauna in the area. (See: Holiday, T. (2000). Evolution at the Crossroads: Modern Human Emergence in Western Asia, American Anthropologist,102(1)) .

As I have noted previously, the The Niger-Congo and Dravidian speakers were Kushites and belonged to the C-Group culture. The Kushites made corded ware and Red-and-black pottery.
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.

By 3500 BC the Dravidian and Mande tribes began to migrate out of Africa. Dr. Menges was the first archaeologist to argue that some Dravidians landed in Iran and migrated into India and the Indus Valley.
These Kushites were the ancestors of the Yamnaya or CHG culture bearers. They were the people who practiced horseback riding and etc.

The movement of the Kushite group is supported by the spread of BRW from Nubia to the Indus Valley and the South Indian megalithic.; and the Dravidian substratum in the prakrit, puranas and other languages in Eurasia.
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The Yamnaya and or CHG introduced the Agro-Pastoral traditions of the CHG. It was also the Kushites who introduced the R haplogroup carried by the CHG and the presence of V88 in early Europe.
The African origin of the CHG is supported by the following evidence:

1. The Kushites began to replace the Anu after the Great Flood, i.e., after 4000BC.

2. There is archaeological evidence of Kushites migrating into Eurasia from Middle Africa 6kya.The Kushites were the rounded headed cattle herders depicted in Saharan Rock art. They belonged to the C-Group . The C-Group was primarially composed of Niger-congo and Dravidian speakers.

'


'

3. there is no archaeological evidence for a back migration of Eurasians back into Africa.

4. Cattle domestication may have appeared first in the Neat East--but evidence for the first cattle herders appears in Middle African Rock art --not the Near East. These Africans took their Agro-Pastoral traditions into Eurasia.

5. Africans domesticated the horse before the I-E people as evident in the Saharan rock art.

6. Kushites introduced chariot riding and horseback riding to the world.

7. The Corded Ware pottery traditions began in Africa among the Kushites

8. The culture terms used by the I-E speakers are of Dravidian and Niger-Congo origin.

9. The I-E people were a bunch of nomads lacking any culture as supported by the so-called Proto- I.E., terms that are not of kushite origin. The I-E speakers remained isolated in Central Asia, until they attacked Kusite centers in Western Europe and Pakistan-India after 1400BC.

Posts: 13012 | From: Chicago | Registered: Jan 2006  |  IP: Logged | 

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Originally posted by Cass/:

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Originally posted by capra:
Sorry Lioness don't know anything about pigmentation alleles.

Xyyman's interpretation of everything is of course that if it's found in Africa, that means it necessarily came from Africa, and therefore all evidence of back-migration from Eurasia is evidence against back-migration from Eurasia. Truly, he has a dizzying intellect.

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But it doesn't really matter where they originated. For example SLC24A5's derived allele (rs1426654) is an extremely high frequency in Europeans (99%), but low to negligible in Sub-Saharan African populations, e.g. less than 1% of Yoruba. So if rs1426654 first appeared in a Sub-Saharan African population- it was carried by very few individuals. I couldn't really care where genotypic/phenotypic traits originated, what counts is their frequency.

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Frequencies display strong population differentiation, with the derived light skin pigmentation allele (A111T) fixed or nearly so in all European populations and the ancestral allele predominant in sub-Saharan Africa and East Asia (Lamason et al. 2005; Norton et al. 2007).

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Lalueza-Fox states: "However, the biggest surprise was to discover that this individual possessed African versions in the genes that determine the light pigmentation of the current Europeans, which indicates that he had dark skin, although we can not know the exact shade."

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This suggests a remarkable genetic uniformity and little phylogeographic structure over a large geographic area of the pre-Neolithic populations. Using Approximate Bayesian Computation, a model of genetic continuity from Mesolithic to Neolithic populations is poorly supported. Furthermore, analyses of 1.34% and 0.53% of their nuclear genomes, containing about 50,000 and 20,000 ancestry informative SNPs, respectively, show that these two Mesolithic individuals are not related to current populations from either the Iberian Peninsula or Southern Europe.

[...]


Figure 2 | Ancestral variants around the SLC45A2 (rs16891982, above) and SLC24A5 (rs1426654, below) pigmentation genes in the Mesolithic genome.



The SNPs around the two diagnostic variants (red arrows) in these two genes were analysed. The resulting haplotype comprises neighbouring SNPs that are also absent in modern Europeans (CEU) (n = 112) but present in Yorubans (YRI) (n = 113). This pattern confirms that the La Braña 1 sample is older than the positive-selection event in these regions. Blue, ancestral; red, derived.


[…]

The genotypic combination leading to a predicted phenotype of dark skin and non-brown eyes is unique and no longer present in contemporary European populations.

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Posts: 22246 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010  |  IP: Logged | 

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Originally posted by the lioness,:

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Originally posted by Ish Gebor:


Brenna Henn, in this 2014 interview on population genetics and population structure, considering African populations.

“African populations have the most genetic diversity in the world,” Henn said.“ If you compared people from the Kalahari Desert to people from Mali, they’d be as different from each other [genetically] as Italians and Chinese people.”

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So does this mean a West African is as different from an Egyptian as an Italian is from a Chinese person?

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Originally posted by Fourty2Tribes:

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Originally posted by the lioness,:

So does this mean a West African is as different from an Egyptian as an Italian is from a Chinese person?

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Depends on all four subjects.

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Posts: 22246 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010  |  IP: Logged | 

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Originally posted by Cass/:

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Originally posted by capra:
Man, Cass, your trolling here gets such predictable responses it's positively unsporting.

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Originally posted by Cass/:
No. I work with skulls/fossils. Isn't autosomal ancient DNA extraction limited to a certain time period? I mean where is the autosomal DNA for "AMH" 100,000 years ago? Obviously though ancient DNA will settle things for stuff like ancient Egypt, but this is a far more recent in time. How is ancient DNA going to help the human origins debate when there is none? We have to work with fossils.

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OK, I don't know much about fossils. So I'm not going to tell you your opinion is unjustified, or quote some unreviewed palaeontogy paper that says what I like. See how easy it is!

Actually we do have some relevant ancient DNA from northern Eurasia. It's Neanderthal and Denisovan. Hopefully we will get some aDNA from some of those interesting fossils in China.

It's not really political in the West, from what I can see. The evidence is straightforward. There's no political implications to these human origins theories in reality, people just use them for rhetorical purposes. If Multiregionalism had won out, people would be talking about how everyone is united by a million years of race-mixing. If you want to demonize Out-of-Africa, describe it as superior people from one continent conquering the world. No one's deciding whether the Negro is a man and a brother based on their common ancestry being 80 000 years ago with minimal gene flow and not a million years ago with lots of gene flow.

Anyway, we went over this before, so back to the topic. Whatever the topic was supposed to be.

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The Out-of-Africa (OOA) theory has creationist baggage, its pseudo-science. That's why I call it religious.


blah blah blah …

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Posts: 22246 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010  |  IP: Logged | 

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Originally posted by the lioness,:

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Originally posted by capra:
[QB] Sorry Lioness don't know anything about pigmentation alleles.

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well you already know more about genetics than most posters here, why not brush up on you pigmentation alleles?

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Originally posted by capra:


Xyyman's interpretation of everything is of course that if it's found in Africa, that means it necessarily came from Africa, and therefore all evidence of back-migration from Eurasia is evidence against back-migration from Eurasia. Truly, he has a dizzying intellect.

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that's more of an Ish Gegor/Clyde thing. If a Chinese person moves to Africa, bingo, all their DNA originated there

xyyman's thing is that if DNA is found in Africa it's evidence that Europeans are depigmented Africans whose ancestors live in Africa under 10,000 years ago, that's his thing
His second favorite theory is that the bantu migration never happened. He also says straight hair probably came before afro hair

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Posts: 22246 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010  |  IP: Logged | 

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The most surprising part of the project for Reich, however, was the discovery of the Basal Eurasians.

“This deep lineage of non-African ancestry branched off before all the other non-Africans branched off from one another,” he said. “Before Australian Aborigines and New Guineans and South Indians and Native Americans and other indigenous hunter-gatherers split, they split from Basal Eurasians. This reconciled some contradictory pieces of information for us.”

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We have identified the PM1 mitogenome as a basal haplogroup U6*, not previously found in any ancient or present-day humans. The derived U6 haplotypes are predominantly found in present-day North-Western African populations. Concomitantly, those found in Europe have been attributed to recent gene-flow from North Africa. The presence of the basal haplogroup U6* in South East Europe (Romania) at 35 ky BP confirms a Eurasian origin of the U6 mitochondrial lineage

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Given the presence of a basal U6 mitogenome in Romania 35 ky BP, the distance between Western Asia and Romania, and the estimated diffusion pace of hunter-gatherer populations30 suggest that the early populations carrying haplogroup U6 most likely started their spread to Eastern Europe before 40 ky BP.

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https://www.nature.com/articles/srep25501

Semantically calling them Eurasians makes absolutely no sense (because they would have looked unlike any modern Eurasian population today other than certain dark skinned Aboriginal populations or Africans.)

But nevertheless, because of this nonsensical model of ancient BASAL human lineages being claimed as "NON African" you get this idea that genetic populations within Africa can be divided up between "Africans" and "Eurasians".

So even more recently they have come with more papers reinforcing the concept of an ancient genetic and hereditary split between humans North of the Sahara vs those to the South. I don't intend to delve into that paper too much, but I want to use it as a reference for the actual means they use to main this historic distortion of African DNA history.

First a picture: (Reconstructing Prehistoric African Population Structure: Genome-wide analysis of 16 African individuals who lived up to 8,100 years ago)

https://www.ncbi.nlm.nih.gov/pubmed/27282030

The issue I want to point out here is that the image I captured here perfectly represents the underlying problem and the "model" by which all these papers operate. That model is based on using "reference populations" as proxies for regions in Africa and how they are labeled. If you look at the picture, they model "North Africa" as not being part of "African" prehistoric DNA history. No populations in the Sahara where numerous sites of ancient human settlement exist AND modern nomadic and semi-settled populations STILL exist. Therefore, they are modeling North Africans as being populations MOST SUBJECT to mixture from populations outside of Africa. Hence, by modeling North Africa this way and using labels like "Eurasian" for DNA lineages arising over 40,000 years ago, but are now found only in Africa, they have effectively AGREED on a model of African biological history where North Africans are no longer labeled as "indigenous African". And this is over and beyond the known historic events of conquest and mixture that has occurred within the last 2,000 years. We are talking about prehistory now.

On top of that this paper proposes that the only truly indigenous "African" lineages on the planet are those found far south of the Sahara. And again this reflects the idea that these populations, even though carrying lineages ANCESTRAL to all other human lineages, are isolated from that DNA history because of the labels and models being used for that history. More like putting the cart before the horse and child before the parent, which is how you wind up with ancient Eurasian settlement models in North Africa, meaning any genetic CHILDREN of Africans migrating out of Africa 40,000 or more years ago automatically get relabeled as something other than African. And by doing this it makes the lineages that likely arose in Africa appear to be something other than African.

But the issue here is that the papers that are written reinforce this model by picking reference populations within Africa that reinforce that ancient distortion of African DNA history. And therefore MOST papers that are published reinforce this ancient 'apartheid' segregation of African DNA. So populations in the Sahara across North Africa from East to West are not included, either in ancient samples of any remains or modern population samples. Populations along the Nile in the Sudan and Southern Egypt are not included even though these are populations directly along the path of migration out of Africa.... All of which means that most papers doing any kind of DNA studies in Africa are reinforcing this model of African genetic segregation in prehistory(nothing to do with race, there was no "white" race 30,000 years ago). This is all about labels and semantics and reinforcing a modern bias that has nothing to do with actual historical facts.

So to prove my point, if you look at many papers on African DNA you will see the same reference populations used over and over again following a similar pattern to the image shown in the recent paper above.... All the "African" lineages are called "Sub Saharan" because the reference populations are far south of the Sahara: Yoruba, Mbuti, Ethiopians, etc. But all the populations labeled as "North African" are exclusively from the extreme coasts of North Africa. None from within the Sahara, none from the Sahel, none from the Maghreb proper, none from Northern Sudan or Upper Egypt and Southern Libya. So of course that would make such populations "extremely distant" from each other because they ARE extremely distant from each other physically.

And to understand this you have to understand that when scientists write these papers they don't go out and collect their own DNA across the African continent. Most often they are simply using existing DNA sample sets from populations across Africa identified as "reference" populations for various regional and geographic characteristics. The problem is that in Africa there are only two primary regions: Sub Saharan and North African and it is based on the model I previously described of ancient Eurasian back migration and has nothing to do with understanding the regional diversity and history of DNA WITHIN indigenous African populations.... So because these reference DNA data sets are assigned to one of these two primary regions and because there are no DNA samples included from populations not along the coasts of North Africa, you get almost every paper that is published reinforcing the same historical model of African DNA and migration history.

It is no coincidence that the image of population samples for the recent paper almost matches (excluding North Africans) the samples used in the following paper from a few years back:

http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002397 (Genomic Ancestry of North Africans Supports Back-to-Africa Migrations)

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This is the new game being played. The assignment of geographic labels to DNA lineages. So if all humans came from Africa then by all logic all the founding lineages in Europe and Asia would have been African. Meaning if two Africans migrate out of Europe and have a child that child is still African even if born outside of Europe. But the way they created that nonsensical tree of "non African" vs "African" related to the spread of agriculture in Europe shows that agenda is at the root of almost everything they do. This is why you have so many ghost populations all over the place because the models they use for the genetic history of populations coming out of Africa and the labels associated with them are totally flawed.

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Posts: 13012 | From: Chicago | Registered: Jan 2006  |  IP: Logged | 

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Originally posted by Doug M:
long-winded rant

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Posts: 660 | From: Canada | Registered: Mar 2017  |  IP: Logged | 

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Originally posted by capra:

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Originally posted by Doug M:
long-winded rant

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So offer us a prediction. Once there is a more thorough sampling of Africa, with more ancient DNA, ancient Saharans, lots of present day Saharans, what do you expect the DNA picture to look like? How will it differ from the mainstream views now?

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According to SNPS haplogroups which are the age of the first extinction event tend to be around 45–50 kya. Haplogroups of the second extinction event seemed to diverge 32–35 kya according to Mal'ta. The ground zero extinction event appears to be Toba during which haplogroup CDEF* appeared to diverge into C, DE and F. C and F have almost nothing in common while D and E have plenty in common. Extinction event #1 according to current estimates occurred after Toba, although older ancient DNA could push the ground zero extinction event to long before Toba, and push the first extinction event here back to Toba. Haplogroups with extinction event notes by them have a dubious origin and this is because extinction events lead to severe bottlenecks, so all notes by these groups are just guesses. Note that the SNP counting of ancient DNA can be highly variable meaning that even though all these groups diverged around the same time no one knows when

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North Africa is considered a distinct geographic and ethnic entity within Africa. Although modern humans originated in this Continent, studies of mitochondrial DNA (mtDNA) and Y-chromosome genealogical markers provide evidence that the North African gene pool has been shaped by the back-migration of several Eurasian lineages in Paleolithic and Neolithic times. More recent influences from sub-Saharan Africa and Mediterranean Europe are also evident. The presence of East-West and North-South haplogroup frequency gradients strongly reinforces the genetic complexity of this region. However, this genetic scenario is beset with a notable gap, which is the lack of consistent information for Algeria, the largest country in the Maghreb. To fill this gap, we analyzed a sample of 240 unrelated subjects from a northwest Algeria cosmopolitan population using mtDNA sequences and Y-chromosome biallelic polymorphisms, focusing on the fine dissection of haplogroups E and R, which are the most prevalent in North Africa and Europe respectively. The Eurasian component in Algeria reached 80% for mtDNA and 90% for Y-chromosome. However, within them, the North African genetic component for mtDNA (U6 and M1; 20%) is significantly smaller than the paternal (E-M81 and E-V65; 70%). The unexpected presence of the European-derived Y-chromosome lineages R-M412, R-S116, R-U152 and R-M529 in Algeria and the rest of the Maghreb could be the counterparts of the mtDNA H1, H3 and V subgroups, pointing to direct maritime contacts between the European and North African sides of the western Mediterranean. Female influx of sub-Saharan Africans into Algeria (20%) is also significantly greater than the male (10%). In spite of these sexual asymmetries, the Algerian uniparental profiles faithfully correlate between each other and with the geography.

The impressive genetic information gathered from North Africa is beset with a notable gap, the lack of consistent information for the Algerian populations. Algeria is the largest country of the Maghreb and, in fact, the largest country of the whole continent. Although at mtDNA sequencing level the first North African sample studied was from an Algerian Berber-speaking Mozabite population [43], it resulted to be a very isolated group not representative of the whole Algerian population. After that, only a small sample of miscellaneous Algerians has been analyzed [13]. Similarly, only small samples of Algerian Arabs and Berbers have been studied with Y-chromosome binary polymorphisms [26]. To fill in this gap we analyzed a representative cosmopolitan sample from the Oran area of northwestern Algeria. We chose an urban area because urban populations give more representative information than rural, often isolated, localities [15]. In addition, Oran is considered the second largest city in Algeria and lies near Siga, one of the main cities of the largest Algerian Berber kingdoms in classical times [3]. In this study we characterized 240 maternally unrelated Algerians from this area by mtDNA HVS-1 region sequencing and haplogroup diagnostic coding positions by RFLP and SNaPshot multiplexing in order to obtain their maternal profiles. The male sub-set of this sample (102 paternally unrelated males) was previously analyzed for Y-chromosomal binary markers and short tandem repeat haplotypes [44]. However, in the present study, this male sample was further genotyped for the recently described informative Y-chromosome polymorphisms within haplogroups E [41] and R [45] whose subdivision has increased the phylogeographic differentiation between Europe and North Africa. Furthermore, in order to obtain more accurate comparisons, we extended these Y-chromosome fine resolution analyses of haplogroups E1b (M78) and R1b (M343) to published samples of Iberians and Moroccans [46], Saharawi and Mauritanians [47] and Tunisians [15]. This uniparental genetic information has been used to integrate Algeria into the overall North African genetic landscape.

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Originally posted by Doug M:
If we believe the Saharan pump theory, then as populations "pulsed" in waves through the Sahara during various wet phases they may have had unique lineages that were spawned and then left Africa as a result of later dry phases.

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From the way it looks in the current distribution TO ME, U6 was much more wide spread at a very early point of time between Africa, the Near East and Europe. It could be that the populations carrying these lineages were part of a wave of Africans pushing out across North Africa into the Levant in Europe over 40,000 years ago.

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That said the more confusing part to me is why there aren't more 'downstream' lineages of L found in "sub saharan" Africa given that they are the oldest human lineages. Somehow it makes no sense that humans outside of Africa who are less than 100,000 years old have all the downstream lineages J,M,N, U R and so forth while populations in Africa are still carrying only L lineages.

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Dead end referring to populations who carried genetic branches or lineages that died out because the populations carrying them died out. And those dead end branches go back 300,000 years or more to include even older hominid types that we don't know about.

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According to SNPS haplogroups which are the age of the first extinction event tend to be around 45–50 kya. Haplogroups of the second extinction event seemed to diverge 32–35 kya according to Mal'ta. The ground zero extinction event appears to be Toba during which haplogroup CDEF* appeared to diverge into C, DE and F. C and F have almost nothing in common while D and E have plenty in common.

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Note that my theory surrounding the process of the spread of the U lineages also applies to M and N as well and many other lineages. All of these lineages arose in the same time frame: 40 - 50 KYA. Which is odd.

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But calling these wandering populations of Africans in Eurasia "Eurasians" is misleading. These were Africans genetically and physically.

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The problem is nobody has been able to find any remains from the populations in the time frame of 40,000 to 50,000 years ago. And certainly no DNA has been extracted from such remains.

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Posts: 660 | From: Canada | Registered: Mar 2017  |  IP: Logged | 

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Originally posted by capra:

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Originally posted by Doug M:
If we believe the Saharan pump theory, then as populations "pulsed" in waves through the Sahara during various wet phases they may have had unique lineages that were spawned and then left Africa as a result of later dry phases.

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Which waves of what are tied to which specific, actual wet phases, though?

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Originally posted by capra:

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From the way it looks in the current distribution TO ME, U6 was much more wide spread at a very early point of time between Africa, the Near East and Europe. It could be that the populations carrying these lineages were part of a wave of Africans pushing out across North Africa into the Levant in Europe over 40,000 years ago.

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It could, is there any archaeological evidence that indicates such a wave? Modern human populations were already well established outside Africa by then, and of course were still doing fine in Africa, so there is no reason to favour Africa -> Eurasia or Eurasia -> Africa a priori.

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Originally posted by capra:

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That said the more confusing part to me is why there aren't more 'downstream' lineages of L found in "sub saharan" Africa given that they are the oldest human lineages. Somehow it makes no sense that humans outside of Africa who are less than 100,000 years old have all the downstream lineages J,M,N, U R and so forth while populations in Africa are still carrying only L lineages.

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There is no 'only L', all those Eurasian lineages are sub-branches of L3 and no more or less 'downstream' than lineages in Africa which are labelled 'L'. There is no such thing as haplogroup L apart from all the others. The terminology originated when the phylogeny as still poorly understood. I suppose you will interpret this as a conspiracy, but in any case understand that, say, L4b2 is equivalent in age and phylogenetic position to R, and L3a to M.

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Originally posted by capra:

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Dead end referring to populations who carried genetic branches or lineages that died out because the populations carrying them died out. And those dead end branches go back 300,000 years or more to include even older hominid types that we don't know about.

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Yes, certainly.

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According to SNPS haplogroups which are the age of the first extinction event tend to be around 45–50 kya. Haplogroups of the second extinction event seemed to diverge 32–35 kya according to Mal'ta. The ground zero extinction event appears to be Toba during which haplogroup CDEF* appeared to diverge into C, DE and F. C and F have almost nothing in common while D and E have plenty in common.

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I'm not sure what you have in mind by the second extinction event, but I agree with you that the timing of Toba does match suspiciously well with the break-up of CDEF. This was followed by the severe cold and aridity of MIS 4/the Early Pleniglacial, so whatever population growth began after Toba (if that's really what we are seeing in the phylogeny) could have been arrested by the climate for some time, depending where they were actually located of course. I don't know why you say D and E have a lot in common and C and F don't? Seems like the opposite to me.

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Note that my theory surrounding the process of the spread of the U lineages also applies to M and N as well and many other lineages. All of these lineages arose in the same time frame: 40 - 50 KYA. Which is odd.

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The very rapid growth of M and N (and R), as well as C, D, and F (and K), ending with a great many basal branches spread out across most of the globe, can hardly be the result of anything but the population boom of modern humans expanding rapidly outside of Africa, so it makes perfect sense that they would all date to about the same time at the beginning of the Upper Palaeolithic. That E, and several basal branches of L3, are about the same age, likely means they were linked to the same cause, whatever exactly that was. Could be tied to the climate getting milder and wetter beginning about 60 000 years ago, though obviously that can't be the whole story.

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“This deep lineage of non-African ancestry branched off before all the other non-Africans branched off from one another,” he said. “Before Australian Aborigines and New Guineans and South Indians and Native Americans and other indigenous hunter-gatherers split, they split from Basal Eurasians. This reconciled some contradictory pieces of information for us.”

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Originally posted by capra:

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But calling these wandering populations of Africans in Eurasia "Eurasians" is misleading. These were Africans genetically and physically.

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They were genetically more related to modern Eurasians than to modern Africans, naturally, and physically there is no reason why they would be closer to modern Africans than to other tropical populations such as Papuans. They were the ancestors of Eurasians, they had undergone a bottleneck that made them genetically distinctive, they lived in Eurasia, and the whole point of names is to distinguish things - so we can call them ancestral Eurasians. Your complaining about it makes no sense to anyone else.

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Originally posted by capra:

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The problem is nobody has been able to find any remains from the populations in the time frame of 40,000 to 50,000 years ago. And certainly no DNA has been extracted from such remains.

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Huh? Do you mean in Africa? Ust' Ishim man from Siberia is ~45 000 years old.

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A key issue in the estimation of OoA dates using autosomal data is that the Yoruba of West Africa are commonly used as the reference point for AMH departure from East Africa, despite mtDNA and autosomal studies indicating a deep time separation of West and East African populations.98 Furthermore, many approaches assume that modern human groups are related via a simple bifurcating tree, which is likely an over simplistic view of human history. Another fundamental problem with many of the estimates used to date divergence times is that they are highly dependent on the choice of mutation rate, which can be estimated using a wide number of different approaches that often yield disparate values. The accumulation of heritable changes in the genome has traditionally been calculated from the divergence between humans and chimpanzees at pseudogenes, assuming a divergence time of around 6–7 million years ago (phylogenetic mutation rate 2.5 × 10−8/base/generation). With the advent of deep sequencing, it is now possible to directly calculate the mutation rate among present-day humans from parent-offspring trios. Using this method, the mutation rate has been estimated at 1.2 × 10−8/base/generation, half of the phylogenetic mutation rate, thus doubling the estimated divergence dates of Africans and suggesting that events in human evolution have occurred earlier than suggested previously.98–104 More recently, Harris reported that the rate of mutation has likely not been stable since the origin of modern humans, revealing higher mutation rates (particularly in the transition 5′-TCC-3′ to 5′-TTC-3′) in Europeans relative to African or Asian populations thus suggesting it may be too simplistic to assume the mutation rate is consistent across different populations.105 In addition to this, there is also considerable uncertainty in terms of the effect of paternal age at time of conception in the mutation rate with respect to ancestral populations.102 Recent work has attempted to mitigate some of these difficulties by instead calibrating estimates against fine-scale meiotic recombination maps. Using eight diploid genomes from modern non-Africans, Lipson et al calculated a mutation rate of 1.61 ± 0.13 × 10−8, which falls between phylogenetic and pedigree-based approaches.106

aDNA is becoming another major tool in appropriate calibration of mutation rate estimates and is likely to greatly refine our understanding of population divergence times, as it allows direct comparison of present-day and accurately dated ancient human DNA. For example, Fu et al used 10 whole mtDNA sequences from ancient AMHs spanning Europe and East Asia from 40 kya to directly estimate the mtDNA substitution rates based on a tip calibration approach. Using an amended mitochondrial substitution rate of 1.57 × 10−8, they dated the last major gene flow between Africans and non-Africans to 95 kya.107 Later work utilized high coverage aDNA from a 45,000-year-old western Siberian individual called Ust’-Ishim and a technique based on modeling the number of substitutions in relation to the PSMC inferred history, which led to slightly higher estimates of 1.3–1.8 × 10−8 per base per generation.108 It is likely that an increasing availability of ancient samples from different time periods will assist in further refining these estimates.

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The Way, Way Back Gene Machine

There is more genetic diversity among humans in Africa than in any other population, but until now, attempts to understand the different threads woven into that fabric have been limited almost entirely to studying modern African DNA.

“We have almost no human fossils from about 30,000 to 300,000 years ago,” says Thompson, acknowledging that despite advances in aDNA extraction, the chances of finding the same amount of it in Africa compared with cooler climes are slim. “We’re not going to have a 300,000 year old Homo heidelbergensis with preserved DNA like they had in Spain. I get that. But if we only look at modern genomics, what are we missing?”

Some researchers look to modern hunter-gatherers, such as the Hadza of Tanzania, and view them almost as frozen in time, representative of ancient populations. But Thompson points out that, despite their traditional lifestyles, the Hadza and other groups have had considerable interaction with populations around them over time.

Says Thompson: “To treat them as relics is tempting but not helpful. We’re able to step back to before them and see how people were actually interacting.”

By sequencing aDNA from the 15 prehistoric individuals and integrating the results with other African DNA and aDNA studies, the team was able to determine that people ancestral to the indigenous people of southern Africa were once distributed much more broadly, but that several of these populations were replaced over time by farmers moving in from western Africa.

The study also uncovered that herders who lived more than 3,000 years ago in what’s now Tanzania were partly ancestral to later individuals spread from Africa’s northeast to its southern edge.

A surprise find included relationships between some of the ancient African DNA with that of ancient DNA from early farmers of the Levant, or eastern Mediterranean, who lived roughly 10,000 years ago — but don’t assume that means there was a long-distance love connection. While it’s possible individuals from the two populations met, it’s also possible that the shared genetic material was inherited from an even older population ancestral to both.

The genetic makeup of the seven Malawi aDNA samples was particularly interesting: They indicate a long-standing population, distinctive to all others, that lasted for about 5,000 years but no longer exists.

What happened to the ancient Malawi people remains a mystery for now, but it’s a question that archaeologists and paleogeneticists may one day answer through further collaboration.

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Originally posted by Doug M:
Continuing the thought.

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Posts: 660 | From: Canada | Registered: Mar 2017  |  IP: Logged | 

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Originally posted by Doug M:
Continuing the thought. They have found 45,000 year old remains in Siberia and sequenced the DNA. They have found 35,000 year old remains in Romania and sequenced the DNA. But the "oldest" DNA they have sequenced in Africa is 8,000 years old and to hear them tell it, is the result of wandering Eurasians as if African DNA stems from Eurasians and not Africa. As if Africa is the child and Europe the parent. And people think this is logical.

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The Way, Way Back Gene Machine

There is more genetic diversity among humans in Africa than in any other population, but until now, attempts to understand the different threads woven into that fabric have been limited almost entirely to studying modern African DNA.

“We have almost no human fossils from about 30,000 to 300,000 years ago,” says Thompson, acknowledging that despite advances in aDNA extraction, the chances of finding the same amount of it in Africa compared with cooler climes are slim. “We’re not going to have a 300,000 year old Homo heidelbergensis with preserved DNA like they had in Spain. I get that. But if we only look at modern genomics, what are we missing?”

Some researchers look to modern hunter-gatherers, such as the Hadza of Tanzania, and view them almost as frozen in time, representative of ancient populations. But Thompson points out that, despite their traditional lifestyles, the Hadza and other groups have had considerable interaction with populations around them over time.

Says Thompson: “To treat them as relics is tempting but not helpful. We’re able to step back to before them and see how people were actually interacting.”

By sequencing aDNA from the 15 prehistoric individuals and integrating the results with other African DNA and aDNA studies, the team was able to determine that people ancestral to the indigenous people of southern Africa were once distributed much more broadly, but that several of these populations were replaced over time by farmers moving in from western Africa.

The study also uncovered that herders who lived more than 3,000 years ago in what’s now Tanzania were partly ancestral to later individuals spread from Africa’s northeast to its southern edge.

A surprise find included relationships between some of the ancient African DNA with that of ancient DNA from early farmers of the Levant, or eastern Mediterranean, who lived roughly 10,000 years ago — but don’t assume that means there was a long-distance love connection. While it’s possible individuals from the two populations met, it’s also possible that the shared genetic material was inherited from an even older population ancestral to both.

The genetic makeup of the seven Malawi aDNA samples was particularly interesting: They indicate a long-standing population, distinctive to all others, that lasted for about 5,000 years but no longer exists.

What happened to the ancient Malawi people remains a mystery for now, but it’s a question that archaeologists and paleogeneticists may one day answer through further collaboration.

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http://blogs.discovermagazine.com/deadthings/2017/09/21/oldest-african-dna-offers-rare-window-into-past/

But obviously you are missing a whole lot if you are modeling African DNA based on Eurasians that are only 50kya old whereas Africans have been around at least 3 to 4 times that long. How many times have Africans moved between East and West Africa over the last 250,000 years? How many times have Africans moved between Northern and Southern Africa over the same time period? Obviously there are many dead ends and branches that you won't find if you only look at modern DNA. Which means using modern DNA to model the past, especially modern DNA which is based on remains that are more recent than remains outside of Africa are going to produce misleading results.

So what they do is they use these populations like the Yoruba and other so-called "sub Saharan" populations as "proxies" for what African DNA was present 50,000 years ago, which is highly problematic. Which is why it seems like all these Africans are Eurasians as opposed to Eurasians being downstream descendants of Africans as they should be.

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Posts: 13012 | From: Chicago | Registered: Jan 2006  |  IP: Logged | 

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Originally posted by Doug M:

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Originally posted by capra:

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Originally posted by Doug M:
If we believe the Saharan pump theory, then as populations "pulsed" in waves through the Sahara during various wet phases they may have had unique lineages that were spawned and then left Africa as a result of later dry phases.

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Which waves of what are tied to which specific, actual wet phases, though?

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The only way to find out is more data from the Sahara, not just using the same reference populations along the coasts of North Africa. I guess what I am saying is ultimately a lot of the problem right now is the limited sample sets they use to model "North Africa" DNA. If most samples are from sites close to the coast then of course you are likely to see "mixture" with populations from outside Africa. But all populations in North Africa don't live close to the coasts. And during the various wet/dry phases it is not only likely that there are 'extinct' lineages representing populations that died out in the area, but also other "connector" lineages that are not represented in the DNA of modern "reference" populations along the coasts.

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Originally posted by capra:

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From the way it looks in the current distribution TO ME, U6 was much more wide spread at a very early point of time between Africa, the Near East and Europe. It could be that the populations carrying these lineages were part of a wave of Africans pushing out across North Africa into the Levant in Europe over 40,000 years ago.

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It could, is there any archaeological evidence that indicates such a wave? Modern human populations were already well established outside Africa by then, and of course were still doing fine in Africa, so there is no reason to favour Africa -> Eurasia or Eurasia -> Africa a priori.

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This isn't about what is greater or lesser in terms of geography. Firstly this is more an issue of semantics. Populations moving out of Africa 50 to 60 thousand years ago or even 40,000 years ago in Eurasia, were not closely similar in appearance to modern populations in the same areas. This is why calling them "Eurasian" is misleading. It would take a long time for "Eurasians" to diverge from Africans in terms of phenotype. But ultimately the point I am making is that they are guessing where these lineages arose because there are so many gaps. And that is what I mean by "waves". So if you set the clock back to 50,000 years ago, what I am saying is there would be a solid chunk of North Africa, the Near East and Europe with populations carrying U lineages, as part of an expansion or "wave" of populations carrying said lineage. Over time many of those populations moved or died out and other lineages became dominant in those areas. So what you see today is only a remnant of that ancient genetic expansion. It is hard to tell clearly where exactly a lineage like U arose in that scenario. The only thing they are doing is just assuming that any remains they find going back in time carrying a specific lineage represents the "origin point" of that lineage which does not have to be true. For example the example of U6 in Romania from the 35,000 year old remains there.

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Originally posted by capra:

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That said the more confusing part to me is why there aren't more 'downstream' lineages of L found in "sub saharan" Africa given that they are the oldest human lineages. Somehow it makes no sense that humans outside of Africa who are less than 100,000 years old have all the downstream lineages J,M,N, U R and so forth while populations in Africa are still carrying only L lineages.

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There is no 'only L', all those Eurasian lineages are sub-branches of L3 and no more or less 'downstream' than lineages in Africa which are labelled 'L'. There is no such thing as haplogroup L apart from all the others. The terminology originated when the phylogeny as still poorly understood. I suppose you will interpret this as a conspiracy, but in any case understand that, say, L4b2 is equivalent in age and phylogenetic position to R, and L3a to M.

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I am just saying the terminology as currently used to distiguish "African" (meaning L lineages) from (Non-African) (NON L or M and N derived lineages)is a bit misleading. Again note the topic of the thread and the way "African" DNA is seen as synonymous with "Sub Saharan" DNA as if the rest of Africa is "Non African" in terms of DNA. Such semantics only reinforces this idea of a "split" in the DNA tree going back to the tree found in the Laziridis papers which put OOA populations on a Non African branch. And to be clear, there is no "conspiracy" here. Many papers openly and bluntly suggest that the "Neanderthal interlude" is the reason for modeling the human DNA tree this way. Implying that "Eurasians" are separated from "Africans" by Neanderthal or Denisovan or whatever mixture. And the idea of North African DNA being "Eurasian" and not "African" is the subject of many other papers as well. Meaning it is hard to show the true genetic relationship and where various major branches arose with a model that claims a 'hard split' between African and Eurasian DNA and back migration into North Africa, which would effectively erase most direct evidence of any OOA lineages moving out of Africa. But again, they are using a limited set of "reference" samples for North Africa which produces this flawed model. They don't even have or use reference populations from Northern Sudan and Upper Egypt as reference populations in the "North African" data set.

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Originally posted by capra:

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Dead end referring to populations who carried genetic branches or lineages that died out because the populations carrying them died out. And those dead end branches go back 300,000 years or more to include even older hominid types that we don't know about.

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Yes, certainly.

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According to SNPS haplogroups which are the age of the first extinction event tend to be around 45–50 kya. Haplogroups of the second extinction event seemed to diverge 32–35 kya according to Mal'ta. The ground zero extinction event appears to be Toba during which haplogroup CDEF* appeared to diverge into C, DE and F. C and F have almost nothing in common while D and E have plenty in common.

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I'm not sure what you have in mind by the second extinction event, but I agree with you that the timing of Toba does match suspiciously well with the break-up of CDEF. This was followed by the severe cold and aridity of MIS 4/the Early Pleniglacial, so whatever population growth began after Toba (if that's really what we are seeing in the phylogeny) could have been arrested by the climate for some time, depending where they were actually located of course. I don't know why you say D and E have a lot in common and C and F don't? Seems like the opposite to me.

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Note that my theory surrounding the process of the spread of the U lineages also applies to M and N as well and many other lineages. All of these lineages arose in the same time frame: 40 - 50 KYA. Which is odd.

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The very rapid growth of M and N (and R), as well as C, D, and F (and K), ending with a great many basal branches spread out across most of the globe, can hardly be the result of anything but the population boom of modern humans expanding rapidly outside of Africa, so it makes perfect sense that they would all date to about the same time at the beginning of the Upper Palaeolithic. That E, and several basal branches of L3, are about the same age, likely means they were linked to the same cause, whatever exactly that was. Could be tied to the climate getting milder and wetter beginning about 60 000 years ago, though obviously that can't be the whole story.

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The question is where did this massive bottleneck occur? Did it occur in Syria? Iraq? Arabia? Central Asia? That is my point. If all these lineages spread from the same point and it was NOT in Africa then where was it? Because I assume it represents a bottlenecked population holed up in some refuge as a result of climate or other natural factors. Finding this site would be key to understanding what happened. But again all of these paths lead back to some major bottleneck population from which all these branches split. So they couldn't have been going in all directions if they were part of a large bottleneck after OOA. But it could be that this bottleneck was closer to Africa as well. We see evidence of it but nobody knows where it occurred. Hence the recent papers on "Basal Eurasian" which attempts to identify that bottlenecked population but in a very clumsy way IMO:

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“This deep lineage of non-African ancestry branched off before all the other non-Africans branched off from one another,” he said. “Before Australian Aborigines and New Guineans and South Indians and Native Americans and other indigenous hunter-gatherers split, they split from Basal Eurasians. This reconciled some contradictory pieces of information for us.”

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https://hms.harvard.edu/news/new-branch-added-european-family-tree

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Originally posted by capra:

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But calling these wandering populations of Africans in Eurasia "Eurasians" is misleading. These were Africans genetically and physically.

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They were genetically more related to modern Eurasians than to modern Africans, naturally, and physically there is no reason why they would be closer to modern Africans than to other tropical populations such as Papuans. They were the ancestors of Eurasians, they had undergone a bottleneck that made them genetically distinctive, they lived in Eurasia, and the whole point of names is to distinguish things - so we can call them ancestral Eurasians. Your complaining about it makes no sense to anyone else.

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This isn't about their relationship to modern populations. The point is that semantically the label makes no sense. Those populations and all their genes originated in Africa. We label populations and genetic lineages based on where they came from not where they wind up later. And obviously all these populations originated in Africa. That is why I am saying it is misleading. None of these populations would resemble "modern" Eurasians in most cases. And all "Eurasians" don't look the same today either. But ultimately my reading of the relevant papers says that the mixture with Neanderthals and other hominid species is the reason for this hard distinction between "Eurasian" and "African". So we have a bottleneck and during that major bottleneck a lot of mixture occurred with other hominids meaning the populations leaving from that point weren't "African" anymore, as they would have been before that which would have been the initial OOA population.

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Originally posted by capra:

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The problem is nobody has been able to find any remains from the populations in the time frame of 40,000 to 50,000 years ago. And certainly no DNA has been extracted from such remains.

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Huh? Do you mean in Africa? Ust' Ishim man from Siberia is ~45 000 years old.

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Of course, that is true but we can't depend on one man from Siberia to fully flesh out the DNA tree unfortunately. Not only that but the significance of this man was the amount of Neanderthal DNA found in him. Yes that is important for our knowledge of the past, but again modern science is trying to do a lot in terms of theoretical models of ancient DNA history with limited hard data. But ultimately at this point this DNA only reinforces the idea of OOA populations being bottle necked and then having a lot of admixture with other hominids as the distinguishing marker for "Eurasians" versus "Africans"...... "Basal Eurasian" only comes up much later as a result of less than expected Neanderthal mixture in Neolithic populations related to the spread of farming, which begs the question is this a result of later African gene flow or something else.

Also this bottleneck plus neanderthal mixture model kind of contradicts the Southern vs Northern migration route into Asia. Meaning if the Northern and Southern routes were separated by thousands of miles and involved different populations at different times, how could they all be related to a single "bottle necked" population outside of Africa somewhere? Sure it could have happened but depending on where this theoretical "bottle necked" refuge was it would be hard for the Southern route to have started in Africa or Arabia.

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A key issue in the estimation of OoA dates using autosomal data is that the Yoruba of West Africa are commonly used as the reference point for AMH departure from East Africa, despite mtDNA and autosomal studies indicating a deep time separation of West and East African populations.98 Furthermore, many approaches assume that modern human groups are related via a simple bifurcating tree, which is likely an over simplistic view of human history. Another fundamental problem with many of the estimates used to date divergence times is that they are highly dependent on the choice of mutation rate, which can be estimated using a wide number of different approaches that often yield disparate values. The accumulation of heritable changes in the genome has traditionally been calculated from the divergence between humans and chimpanzees at pseudogenes, assuming a divergence time of around 6–7 million years ago (phylogenetic mutation rate 2.5 × 10−8/base/generation). With the advent of deep sequencing, it is now possible to directly calculate the mutation rate among present-day humans from parent-offspring trios. Using this method, the mutation rate has been estimated at 1.2 × 10−8/base/generation, half of the phylogenetic mutation rate, thus doubling the estimated divergence dates of Africans and suggesting that events in human evolution have occurred earlier than suggested previously.98–104 More recently, Harris reported that the rate of mutation has likely not been stable since the origin of modern humans, revealing higher mutation rates (particularly in the transition 5′-TCC-3′ to 5′-TTC-3′) in Europeans relative to African or Asian populations thus suggesting it may be too simplistic to assume the mutation rate is consistent across different populations.105 In addition to this, there is also considerable uncertainty in terms of the effect of paternal age at time of conception in the mutation rate with respect to ancestral populations.102 Recent work has attempted to mitigate some of these difficulties by instead calibrating estimates against fine-scale meiotic recombination maps. Using eight diploid genomes from modern non-Africans, Lipson et al calculated a mutation rate of 1.61 ± 0.13 × 10−8, which falls between phylogenetic and pedigree-based approaches.106

aDNA is becoming another major tool in appropriate calibration of mutation rate estimates and is likely to greatly refine our understanding of population divergence times, as it allows direct comparison of present-day and accurately dated ancient human DNA. For example, Fu et al used 10 whole mtDNA sequences from ancient AMHs spanning Europe and East Asia from 40 kya to directly estimate the mtDNA substitution rates based on a tip calibration approach. Using an amended mitochondrial substitution rate of 1.57 × 10−8, they dated the last major gene flow between Africans and non-Africans to 95 kya.107 Later work utilized high coverage aDNA from a 45,000-year-old western Siberian individual called Ust’-Ishim and a technique based on modeling the number of substitutions in relation to the PSMC inferred history, which led to slightly higher estimates of 1.3–1.8 × 10−8 per base per generation.108 It is likely that an increasing availability of ancient samples from different time periods will assist in further refining these estimates.

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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4844272/

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Posts: 13012 | From: Chicago | Registered: Jan 2006  |  IP: Logged | 

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Originally posted by capra:

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Originally posted by Doug M:
Continuing the thought.

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Someday you should try a new thought. And actually reading the paper. But why would you start now?

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Genetic studies have as yet been unable to settle the conflicting archeological evidence for these different dates, which can also be classified as pre-Toba (100–130 kya) or post-Toba (around 50–60 kya). Given the lack of ancient DNA (aDNA) data temporally and spatially, such genetic-based approaches have focused on inference using modern DNA. Studies based on reconstructing mtDNA phylogenies have suggested a date for modern humans leaving Africa between 60 and 40 kya,80 while dates inferred from STR analysis also fall within these estimates, positing an expansion date of around 50 kya for central African, European, and East Asian populations.82,93 Time estimates from whole-genome sequencing data have been more variable and depend largely on the choice of model used. For example, studies using the allele frequency spectrum, identity-by-state, or coalescent-based models suggest a divergence time of 60–50 kya,94–96 while analyses based on the pairwise sequencing Markovian coalescent (PSMC) model suggest that the divergence began 100–80 kya, with gene flow occurring until 20 kya.97

A key issue in the estimation of OoA dates using autosomal data is that the Yoruba of West Africa are commonly used as the reference point for AMH departure from East Africa, despite mtDNA and autosomal studies indicating a deep time separation of West and East African populations.98 Furthermore, many approaches assume that modern human groups are related via a simple bifurcating tree, which is likely an over simplistic view of human history. Another fundamental problem with many of the estimates used to date divergence times is that they are highly dependent on the choice of mutation rate, which can be estimated using a wide number of different approaches that often yield disparate values. The accumulation of heritable changes in the genome has traditionally been calculated from the divergence between humans and chimpanzees at pseudogenes, assuming a divergence time of around 6–7 million years ago (phylogenetic mutation rate 2.5 × 10-8/base/generation). With the advent of deep sequencing, it is now possible to directly calculate the mutation rate among present-day humans from parent-offspring trios. Using this method, the mutation rate has been estimated at 1.2 × 10-8/base/generation, half of the phylogenetic mutation rate, thus doubling the estimated divergence dates of Africans and suggesting that events in human evolution have occurred earlier than suggested previously.98–104 More recently, Harris reported that the rate of mutation has likely not been stable since the origin of modern humans, revealing higher mutation rates (particularly in the transition 5'-TCC-3' to 5'-TTC-3') in Europeans relative to African or Asian populations thus suggesting it may be too simplistic to assume the mutation rate is consistent across different populations.105 In addition to this, there is also considerable uncertainty in terms of the effect of paternal age at time of conception in the mutation rate with respect to ancestral populations.102 Recent work has attempted to mitigate some of these difficulties by instead calibrating estimates against fine-scale meiotic recombination maps. Using eight diploid genomes from modern non-Africans, Lipson et al calculated a mutation rate of 1.61 ± 0.13 × 10-8, which falls between phylogenetic and pedigree-based approaches.106

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Fossils discovered in Morocco are the oldest known remains of Homo sapiens, scientists reported on Wednesday, a finding that rewrites the story of mankind’s origins and suggests that our species evolved in multiple locations across the African continent.

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Posts: 8901 | Registered: May 2005  |  IP: Logged | 

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Originally posted by Doug M:
It says nothing about an African origin of EEF. It says nothing about an African origin of Eurasian DNA. It says the opposite.

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Posts: 43007 | From: , | Registered: Jan 2010  |  IP: Logged | 

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Originally posted by capra:
Only Luxmanda_3100BP and South_Africa_1200BP were modelled with PPNB ancestry. None of the ancient Malawians had anything of the kind.

Can't you ever discuss AFRICA without continually making it all about Eurasians? In this case the study used the Tanzanian Luxmanda_3100BP as their reference whenever possible and explicitly note that the ancestry they model as PPNB could be shared ancestry of African origin. So there is nothing in this paper that requires actual Eurasian ancestry in the ancient samples.

Now are you even capable of discussing Africa, do you know anything about it at all? All I ever see from you is vague wishful thinking full of errors.

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Posts: 1892 | From: NY | Registered: Sep 2014  |  IP: Logged | 

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Originally posted by capra:
Only Luxmanda_3100BP and South_Africa_1200BP were modelled with PPNB ancestry. None of the ancient Malawians had anything of the kind.

Indeed we don't have super-ancient DNA that would allows to draw any firm conclusions about the deep prehistory of Africa. Well, feel free to ignore everything that is said about it. But now we have recent DNA from Africa, so maybe now we can talk about the Bantu expansion, East-South Africa cline, Northeast African pastoralist migrations, which we now have data for?

Can't you ever discuss AFRICA without continually making it all about Eurasians? In this case the study used the Tanzanian Luxmanda_3100BP as their reference whenever possible and explicitly note that the ancestry they model as PPNB could be shared ancestry of African origin. So there is nothing in this paper that requires actual Eurasian ancestry in the ancient samples.

Now are you even capable of discussing Africa, do you know anything about it at all? All I ever see from you is vague wishful thinking full of errors.

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A great irony about Africa is that, even though it’s the birthplace of our species, we know almost nothing about the prehistoric populations who lived there: the bands of hunter gatherers who moved across the massive continent, interacting with and sometimes replacing other groups.

Today that changes.

Thanks to new research that includes the oldest African DNA ever successfully read, we’re seeing Africa’s prehistory like never before. Archaeologists and paleogeneticists are finally starting to fill in some crucial gaps about the human story.

Imagine you’re an archaeologist, specifically a paleolithic archaeologist who studies the earliest chapters of our story, before cities or iron or agriculture, and you’re focused on Africa, which is, after all, where all of us can trace back our ancestry. (Yes, all of us.)

Imagine what it’s like to sit through one conference after another as colleagues who work in Eurasia share one thrilling discovery after the next, all unearthed thanks to paleogenomic research, or the study of ancient DNA (aDNA). An entirely new ancient hominin, the Denisovans of Siberia, known only from fossil fragments that yielded aDNA! Awesome! Successful sequencing of a 430,000-year-old genome from Spain! Super cool!

Emory University’s Jessica Thompson doesn’t have to imagine. She is that paleolithic archaeologist, and she felt a mixture of awe and envy as colleagues working at Eurasian sites were able to extract and study aDNA, which needs cold, dry conditions to survive for any length of time.

The dearth of aDNA from Africa made it hard to understand the continent’s rich past, and it also fueled a centuries-old myth that Africa was less significant.

“The success of paleogenomic research in Eurasia feeds that narrative that Eurasia is somehow more important than Africa [and] that’s frustrating to me. We’re hungry to have more information,” says Thompson, echoing the feelings of other archaeologists working in Africa. “I know it’s because we don’t have these nice, cold environments.”

A lightbulb went off at one of those conferences for Thompson, however. She remembered a cave she’d visited as a tourist: it was in Malawi, on a high-plateau mountain called Hora where human skeletons had been excavated in the mid-20th century. And it was cold.

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Thompson found two ancient human samples in another lab, but analyzing them produced inconsistent results. So she decided to return to the Malawi sites where they were dug up to look for more clues. She ended up uncovering three more sets of human remains, which contained DNA dating back as far as 8,000 years ago; she collected other samples from scientific archives in Malawi.

Other researchers also sqeuenced eight more ancient samples from southern, which Thompson’s group included in a study published today in the journal Cell. Time had degraded the samples, says Pontus Skoglund, a geneticist at Harvard Medical School who led the study. However, with persistence and advancing genetic technology, researchers were able to obtain at least 30,000 DNA base pairs from each sample—“more than enough to do powerful statistical analyses,” Skoglund says.

The team compared these ancient sequences to hundreds of modern day genomes from Africa and around the world to place the ancestries of modern humans, and see who had moved around and who hadn’t. "What is most immediately obvious is this landscape of hunter-gatherer populations has now been changed quite radically," Skoglund says.

Before the widespread use of agriculture and livestock, humans survived through hunting and gathering. The adoption of agriculture by some groups of people is known to have driven great migrations among humans throughout ancient history, Thompson says, but this study made clear the scale of how much this disrupted the distribution of humans in southern Africa.

Modern-day people native to Malawi appear to be completely unrelated to the ancient humans who lived in their country a few thousand years ago—reflecting a much more dramatic migration than Thompson and others would have expected. Other samples confirmed how much movement within Africa has occurred in the last few thousand years, and included a Tanzanian herder who was found to have descendants spread from north to south on the continent.

These movements mean that the lineage of modern humans in Africa appears to have mixed much more than previously thought, according to Thompson. "It appears to be one of the most complete population replacements ever documented," she says.

"Human genetic history was complex, and ancient DNA studies from Africa are needed to understand the history there, and are eagerly awaited," said Chris Tyler-Smith, a geneticist at the Wellcome Trust Sanger Institute, via email. "This is the first substantial study of ancient African DNA."

Tyler-Smith, who wasn't involved in the research, said some of the conclusions were expected, such as the fact that populations of hunter-gatherers were replaced by agricultural populations. But other insights, such as how branched the tree of ancestry for modern-day west Africans is, surprised him.

The completion of this sequencing, he says, opens the door to more and better sequencing down the road, and raises more questions about our ancestors.

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Originally posted by capra:
OK, if you are done complaining about the title, why not discuss what the new findings suggest to you about the recent prehistory of Africa?

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Summary

We assembled genome-wide data from 16 prehistoric Africans. We show that the anciently divergent lineage that comprises the primary ancestry of the southern African San had a wider distribution in the past, contributing approximately two-thirds of the ancestry of Malawi hunter-gatherers ∼8,100–2,500 years ago and approximately one-third of the ancestry of Tanzanian hunter-gatherers ∼1,400 years ago. We document how the spread of farmers from western Africa involved complete replacement of local hunter-gatherers in some regions, and we track the spread of herders by showing that the population of a ∼3,100-year-old pastoralist from Tanzania contributed ancestry to people from northeastern to southern Africa, including a ∼1,200-year-old southern African pastoralist. The deepest diversifications of African lineages were complex, involving either repeated gene flow among geographically disparate groups or a lineage more deeply diverging than that of the San contributing more to some western African populations than to others. We finally leverage ancient genomes to document episodes of natural selection in southern African populations.

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Originally posted by capra:
ah fuck it waste of time

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Originally posted by Elmaestro:
What if the same studies you are criticizing provides evidence that what people considered OOA, Eurasian or Back-migration is actually African and you just haven't realized yet cuz your head's so far up your ass?

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Originally posted by Elmaestro:

..yeah, tell us who actually read and keep up with where the data leads us, that we're wasting our time when you still show signs of a lack of comprehension of the African genetic landscape mapped out by aDNA since Lazaradis 2016.

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First ancient African genome reveals vast Eurasian migration

DNA from Ethiopian man pre-dates the movement of Eurasian farmers 'back to Africa'.

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Originally posted by Elmaestro:

you need to keep it simple.
What story does the aDNA we have sample tells you?
Who do you want sampled or sequenced?
^What do you expect to see when they are researched?

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Originally posted by Elmaestro:

Prove that you aren't a waste of time and answer those questions... otherwise just admit that you have nothing meaningful to contribute, and that your rants are just dmg control for your lack of understanding and previous failures for predicting the outcome what aDNA revealed.

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Originally posted by Elmaestro:
The problem isn't that you're criticizing the paper... almost Everyone one here criticize these papers lmao, the problem is that you're posts are a waste of time.

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Originally posted by Elmaestro:

I asked you 3 questions,
What story does the aDNA we have sample tells you?

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Originally posted by Elmaestro:

Who do you want sampled or sequenced?
^What do you expect to see when they are researched?

Can you finish answering them?

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The human past on many timescales is of broad intrinsic interest, and genetics contributes to our understanding of it, as do paleontology, archaeology, linguistics and other disciplines. Geneticists have long studied present-day populations to glean information about their past, using models to infer past population events such as migrations or replacements, generally invoking Occam’s razor to favor the simplest model consistent with the data. But this is not the most straightforward approach to understanding such events: the obvious way to study any aspect of human genetic history is to analyze population samples from before, during and after the period of interest, and to simply catalogue the changes. Advances in ancient DNA (aDNA) technology are now beginning to make this more direct approach possible, facilitated by new sequencing technologies that are now capable of generating gigabases of data at moderate cost (Box 1). This abundance of data, combined with an understanding of the damage patterns indicative of authentic aDNA, greatly simplify the recognition and avoidance of the bugbear of the field: contamination.

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Neanderthal ancestry in all present-day non-Africans is estimated to be 1.5–2.1 % [14]. The broad geographical distribution, together with the size of the DNA segments contributed by Neanderthals, suggests that the gene flow most likely occurred at an early stage of the out-of-Africa expansion: around 47,000–65,000 ya [12], before the divergence of Eurasian groups from each other. Sequences from the genomes of ancient Eurasians show that they carried longer archaic segments that have been affected by less recombination than those in present-day humans, consistent with the ancient individuals being closer to the time of the admixture event with Neanderthals. For example, a genome sequence from Kostenki 14 who lived in Russia 38,700–36,200 ya had a segment of Neanderthal ancestry of ~3 Mb on chromosome 6 [15], whereas present-day humans carry, on average, introgressed haplotypes of ~57 kb in length [16]. The genome sequence of a 45,000-year-old modern human male named Ust’-Ishim (after the region in Siberia where he was discovered), shows genomic segments of Neanderthal ancestry that are ~1.8–4.2 times longer than those observed in present-day individuals, suggesting that the Neanderthal gene flow occurred 232–430 generations before Ust’-Ishim lived, or approximately 50,000–60,000 ya [17], narrowing the previous range.[ Moreover, the Neanderthal-derived DNA in all non-Africans is more closely related to a Neanderthal from the Caucasus than it is to either the Neanderthal from Siberia or the Neanderthal from Croatia [14], providing more evidence that archaic admixture occurred in West Asia early during modern humans’ exit from Africa.

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aDNA evidence has thus supported the replacement model as an explanation for most human variation, but has transformed and enriched this model in ways not anticipated in the earlier debate: first by discovering Denisovans, whose fossil record currently remains unrecognized, and second by revealing the multiplicity of admixture events, which include at least one that cannot be detected in present-day DNA.

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Recent aDNA studies reveal, however, that populating Europe has been a much more complex process, and that the Neolithic transition (Box 3) was not even the event that most influenced the present-day genetic landscape.

The first aDNA complete genome sequence from Europe came from the Tyrolean Iceman; a 5300-year-old (Late Neolithic or ‘Copper Age’) natural mummy discovered in 1991 in the Ötztal Alps. Surprisingly, the Iceman had more genetic affinity to present-day Sardinians than to the present-day populations inhabiting the region where he probably lived [28], showing that major demographic changes have occurred in Europe after the Neolithic era. A more substantial revision of the demic diffusion model was introduced when several 7000–8000-year-old individuals from Western Europe [29] and a 24,000-year-old individual from Siberia [30] were sequenced. Analysis showed that at least three different ancient populations contributed to the genetics of present-day Europeans: (1) West European hunter-gatherers, (2) ancient north Eurasians related to Upper Paleolithic Siberians, and (3) early European farmers, who were mainly of Near Eastern origin [29]. The contributions of these three populations to modern European ancestry were not necessarily direct, and the demic diffusion model was further refined by analyzing 69 additional Europeans who lived between 3000 and 8000 ya (Fig. 1).

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Adaptation to non-African environments was also believed to be the cause of human variation in skin color. It was thought that the light skin of Europeans was a Paleolithic adaptation to facilitate vitamin D production in reduced sunlight regions [43]. Consistent with this hypothesis, aDNA analyses show that Scandinavian hunter-gatherers and Early European farmers indeed carried derived alleles contributing to light skin [44]. However, western hunter-gatherers of central and southern European populations survived in Palaeolithic Europe with dark skin pigmentation [44, 45]; thus, light skin has not been an essential adaptation for survival in this environment, and perhaps has resulted instead from sexual selection.

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Findings from aDNA research are currently transforming our understanding of human history at an ever-increasing pace. When evolution was parsimonious, aDNA may support the prevailing model, as with the initial peopling of the Americas; but more often, evolution was not parsimonious, and aDNA reveals a much richer history, as in the other examples considered here. In either situation, human evolutionary genetics is moving to a paradigm where we first look for evidence from aDNA and interpret present-day genetic variation in its light.

What are the limits to how far this can go? Very ancient samples more than 100,000 years old and some geographical regions of great interest, such as the Near East and Africa, remain challenging for aDNA research. Both time and poor DNA preservation in hot wet climates may impose insurmountable limits to resolving many questions related to the origin and genetic diversity of our species. Identifying favorable locations within these regions [46], or relevant relict populations and migrant individuals, offers some ways around such limitations. Improvements in aDNA extraction and library construction will push the limits, but sequences below 25 base pairs in length often do not map uniquely to the human genome, and so provide little useful information. There is room for methodological improvements in repair and perhaps reconstruction of ancient molecules within the fossils.

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Originally posted by Doug M:
As I said earlier it tells us nothing about what most of us really want to know which is key splits in human DNA related to OOA and whether they happened IN Africa or outside Africa. This is the issue and has been the underlying issue for quite a while now.

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Of course Africa is of no interest beyond its relationship to Eurasia.

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Originally posted by Doug M:

You need far more ancient DNA from Africa across multiple parts of Africa, but most especially North Africa

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Here's some ancient North African DNA, two different areas


On the origin of Iberomaurusians: new data based on ancient mitochondrial DNA and phylogenetic
analysis of Afalou and Taforalt populations. Forsenic Sciences Research 2016.
Rym Kefi, Meriem Hechmi, Chokri Naouali, Haifa Jmel, Sana Hsouna, Eric Bouzaid, show all
Pages 1-11 | Received 17 Sep 2016, Accepted 04 Nov 2016, Published online: 30 Dec 2016


Morocco, 23,000–10,800 YBP
and
Algeria 15,000–11,000 YBP

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Originally posted by Doug M:
So what is your reason for responding to me as if there is something INVALID behind what I am saying then? I made my point clear numerous times on this thread? Otherwise if the papers are flawed then why on earth are you responding to me as if there is something "not right" about HOW I say the papers are flawed? Or do you not see that?

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Originally posted by Elmaestro:

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Originally posted by Doug M:
So what is your reason for responding to me as if there is something INVALID behind what I am saying then? I made my point clear numerous times on this thread? Otherwise if the papers are flawed then why on earth are you responding to me as if there is something "not right" about HOW I say the papers are flawed? Or do you not see that?

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..wanna know my reason?
Read your answers to my simple questions... You haven't even gotten to the point to where your criticisms can be "Invalid."

1.You basically say the data we do have paints no picture for Africans...OK

2.You want ADNA from north Africa (which we now have), the Sahel and an upper Egypt, east Africa... which is fine I guess, but don't you think I'd be extremely important to get some west African aDNA over 6kya? at least explain why not

3.What do you think these genomes will tell you when you get them!! Stop dancing around the question..
For example... Which Uniparental haplogroups will you expect from Ancient Sahelians? Which modern populations will they draw affinity towards? Will their DNA correspond to archeological findings and patterns mapped out from (...guess who), aDNA and modern samples that we CURRENTLY HAVE?

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Originally posted by capra:

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Originally posted by Doug M:
As I said earlier it tells us nothing about what most of us really want to know which is key splits in human DNA related to OOA and whether they happened IN Africa or outside Africa. This is the issue and has been the underlying issue for quite a while now.

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Of course Africa is of no interest beyond its relationship to Eurasia.

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On the origin of Iberomaurusians: new data based on ancient mitochondrial DNA and phylogenetic
analysis of Afalou and Taforalt populations.
Abstract

The Western North African population was characterized by the presence of Iberomaurusian civilization at the Epiplaeolithic period (around 20,000 years before present (YBP) to 10,000 YBP). The origin of this population is still not clear: they may come from Europe, Near East, sub-Saharan Africa or they could have evolved in situ in North Africa. With the aim to contribute to a better knowledge of the settlement of North Africa we analysed the mitochondrial DNA extracted from Iberomaurusian skeletons exhumed from the archaeological site of Afalou (AFA) (15,000-11,000 YBP) in Algeria and from the archaeological site of Taforalt (TAF) (23,000-10,800 YBP) in Morocco. Then, we carried out a phylogenetic analysis relating these Iberomaurusians to 61 current Mediterranean populations. The genetic structure of TAF and AFA specimens contains only North African and Eurasian maternal lineages. These finding demonstrate the presence of these haplotypes in North Africa from at least 20,000 YBP. The very low contribution of a Sub-Saharan African haplotype in the Iberomaurusian samples is confirmed. We also highlighted the existence of genetic flows between Southern and Northern coast of the Mediterranean.

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Originally posted by Elmaestro:
holy fuck, just answer the questions ...what do you believe you will see when you get your desired samples? There is absolutely nothing complex about that.

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Modern-day people native to Malawi appear to be completely unrelated to the ancient humans who lived in their country a few thousand years ago—reflecting a much more dramatic migration than Thompson and others would have expected. Other samples confirmed how much movement within Africa has occurred in the last few thousand years, and included a Tanzanian herder who was found to have descendants spread from north to south on the continent.

These movements mean that the lineage of modern humans in Africa appears to have mixed much more than previously thought, according to Thompson. "It appears to be one of the most complete population replacements ever documented," she says.

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In archaeology, this debate has played out around the issue of whether sudden changes in material culture apparent in the archaeological record can be attributed to the spread of culture or to population movements: “pots versus people” [1]. In physical anthropology, the debate has played out around the issue of whether changes in morphological characters over time are due to in situ evolution or to the arrival of new populations (e.g., [2]).

The same debate has also played out in genetics. On the side of population replacements, there are the “wave of advance” and “demic diffusion” models, first proposed to describe the spread of agriculture through Europe. In these models, the Neolithic transition was accompanied by the spread of farmers from the Near East across Europe, who partially or completely replaced resident hunter-gatherers [3–6]. On the side of stasis, there are the “serial founder effect” models [7,8], which proposed that populations have remained in the locations they first colonized after the out-of-Africa expansion, exchanging migrants only at a low rate with their immediate neighbors until the long-range migrations of the last 500 years [9–12].

These genetic models – the wave-of-advance models on the one hand, and the serial founder effect models on the other – were proposed prior to the availability of large-scale genomic data. The great synthesis of genetic data with historical, archaeological and linguistic information, “The History and Geography of Human Genes” [13], was written based on data from around one hundred protein polymorphisms, and the papers that popularized the notion of a serial founder effect model were written based on data from around 1,000 microsatellites. However, it is now possible to genotype millions of polymorphisms in thousands of individuals using high-throughput sequencing. Because of these technological advances, the last few years have seen a dramatic increase in the quantity of data available for learning about human history. Equally important has been rapid innovation in methods for making inferences from these data. Here, we argue that the technological breakthroughs of the past few years motivate a systematic re-evaluation of human history using modern genomic tools—a new “History and Geography of Human Genes” that exploits many orders of magnitude more data than the original synthesis.

In the first section of the paper, we summarize what we see as major lessons from the recent literature. In particular, it is now clear that the data contradict any model in which the genetic structure of the world today is approximately the same as it was immediately following the out-of-Africa expansion. Instead, the last 50,000 years of human history have witnessed major upheavals, such that much of the geographic information about the first human migrations has been overwritten by subsequent population movements. However, the data also often contradict models of population replacement: when two distinct population groups come together during demographic expansions, the result is often genetic admixture rather than complete replacement. This suggests that new types of models—with admixture at their center—are necessary for describing key aspects of human history (for early examples of admixture models, see [14–16]).

In the second section of the paper, we sketch out a way forward for data-driven construction of these models. We specifically highlight the potential of ancient DNA studies of individuals from archaeologically-important cultures. Such studies in principle provide a source of information about history that bypasses some fundamental ambiguities in the interpretation of genetic, archaeological, or anthropological evidence alone. We discuss a number of potential applications of this technology to outstanding questions in human history.


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These simulations show that the main observation that has been marshaled in support of the serial founder effect model is also consistent with very different histories (see also [29,38,39,41]). Specifically, in the absence of additional data, the smooth linear decline in heterozygosity away from Africa could represent a signal of many population bottlenecks during the initial out-of-Africa expansion tens of thousands of years ago, or it could represent a signal of extensive population mixture within the last few thousand years (or, of course, a combination of these or many other models that we have not considered). Because the data are compatible with both, arguing for one over the other involves a subjective determination of which class of model is more likely a priori. Perhaps the most important issue affecting this determination is how important migration has been over the last 50,000 years of human history. How representative are populations today of the populations that lived in the same locations after the out-of-Africa expansion?

The answer to the question posed above has been the subject of considerable research over the past several years. In our opinion one finding is already clear: long-range migration and concomitant population replacement or admixture have occurred often enough in recent human history that the present-day inhabitants of many places in the world are rarely related in a simple manner to the more ancient peoples of the same region

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Figure 3 shows the geographic locations of all the populations, along with the locations of the best present-day proxies of their ancestral populations. Admixture between populations related to ones that are now geographically distant is evident in most populations of the world. For example, Native American-related ancestry is present throughout Europe [54], likely reflecting the genetic input from the Ancient Northern Eurasian population related to Upper Paleolithic Siberians [53,54] both into the Americas (most likely prior to 15,000 years ago) and into Europe [52,53]. Also, ancestry from a population related to those living in the Near East is found in Cambodia [30], likely due to mixture from an ancestral South Asian population that was itself an admixed population containing ancestry related to present-day Near Easterners [65]. The test we use as the basis for Figure 3 detects only one signal of admixture per population, and cannot detect complete population replacement. The true population history is thus likely to have been even more complex.

These examples show that the populations in a given region today are rarely descended in a simple manner from the inhabitants in the distant past. This provides further evidence that the serial founder effect model is no longer a reasonable null model for the relationship between present-day populations and their ancestors. Instead, clines in genetic diversity observed in data may often be better modeled as outcomes of admixture (as in Figures 1B and 1C) rather than a series of bottlenecks.

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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4163019/

Ultimately all of this is just basically saying that the best way to understand ancient movements and changes in populations as well as the movement and changes of DNA lineages is to get as much ancient DNA from various regions as possible. Just using existing populations as proxies for ancient ones wont work. And that especially applies to Africa which would benefit most greatly from more aDNA to answer many long standing questions about how DNA evolved there before and after OOA.

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Originally posted by Elmaestro:
If the data wasn't skewed what would it look like?

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In the first section of the paper, we summarize what we see as major lessons from the recent literature. In particular, it is now clear that the data contradict any model in which the genetic structure of the world today is approximately the same as it was immediately following the out-of-Africa expansion. Instead, the last 50,000 years of human history have witnessed major upheavals, such that much of the geographic information about the first human migrations has been overwritten by subsequent population movements.

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