Lazaridis et al Ver2- Basal Eurasian explained

[djoser-xyyman]

arxiv.org/abs/1312.6639 revised 2 Apr 2014 (version, v2)

[djoser-xyyman]

Just finished reading it. First Pass. Nothing really much different to the first version.

It looks like Lazaridis is reading my post and taking notes also, LOL! He is backing off the label “Baaal Eurasian”. Really?! Why call it “basal Eurasian”. It represent recent "African" genetic material plus it is not "Basal". WHG/ENE entered Europe first. That should be labeled “basal”.

1. As I said TREEMIX is the tool used to determine “direction”. But, ADMIXTURE is best used to determine relatedness or clustering. That is why “related” is a better word than admixed or “ancestry “ SNP. The layman reads the word "ancestry" and assumes it means eg North Africans are admixed with Europeans. Yes they do have some similar SNP make-up to Europeans but they are indigenous Africans because of their Haplogroups.

2. Of Europeans, Sardinians are closest to these older populations.


Why is that Beyoku? Tic! Toc!

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Quotes from the study.

As suggested previously for Basal Eurasians, we caution against a too literal reading of terminology, as the spatial and temporal distribution of the populations associated with the nodes of the model are still incompletely known

Conclusion
The TreeMix analyses on genotype and sequence data agree with each other and with ADMIXTUREGRAPH (SI14) and MixMapper (SI15) in inferring the major events discussed in this paper (Basal Eurasian admixture into early farmers, MA1 admixture into Native Americans, and Ancient North Eurasian admixture into Motala). The TreeMix analysis also raises additional possibilities about further gene flows. These should be possible to investigate further as UDG-treated data become available from southern European samples related to LaBrana and the Iceman.

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We used the TreeMix1 software to develop models of population relationships that also allow for multiple admixture events. TreeMix takes as input SNP genotype data from any number of populations, and then identifies a phylogenetic tree incorporating a specified number of admixture events that minimizes the difference between the observed and predicted f-statistics.

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We used the TreeMix1 software to develop models of population relationships that also allow for multiple admixture events. TreeMix takes as input SNP genotype data from any number of populations, and then identifies a phylogenetic tree incorporating a specified number of admixture events that minimizes the difference between the observed and predicted f-statistics. A limitation of TreeMix—along with the MixMapper method (SI15)—is that it does not allow users to explicitly specify models of population relationships and formally test the goodness of their fit to data. An advantage of TreeMix and MixMapper is that they are unsupervised procedures, and hence are ***less vulnerable*** to the concern that the **prior expectations about human history*** of the researchers using them will **bias** the results. Unsupervised methods can also be used to infer models of relationships for more populations than ADMIXTUREGRAPH, as ADMIXTUREGRAPH requires manual exploration of model space (SI14). Here we apply TreeMix both to Human Origins genotype data and to whole genome sequence data2.


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No present-day West Eurasians form a clade with either Loschbour or Stuttgart {/b]
We attempted to fit each individual West Eurasian population in turn as simple clades with Loschbour or Stuttgart. We did not expect this to be possible on the basis of Fig. 1B which shows that none of them cluster with the ancient samples, except possibly Sardinians. However f3-statistics indicate widespread admixture appear in nearly all West Eurasians (SI11) and we show in SI12 that at least 3 source populations are needed for present-day Europeans. Consistent with this evidence, we find that no West Eurasian populations form clades with either Loschbour or Stuttgart, suggesting that these ancient individuals belonged to populations that no longer exist in unadmixed form.

[djoser-xyyman]

Anyone who have read it. Checkout the supplemenatls with the TreeMix charts. Notice they used MButi as the base African group and NOT Yoruba as you would expect them to. Mbuti has a >50K year seperation from Yoruba.

However they were still surprised. Even the Mbuti shows genetic input to Stuttgart woman meaning...ancestry to "basal Eurasian". The Yoruban would showed markedly more input to basal Eurasian. LOL!

[djoser-xyyman]

At K3 is the “West Eurasian” component but ALL Africans carry it. Are these researchers idiots or just blind racist.
Do you now understand the color code Beyoku?

Quote:
For our main analyses, we identified a set of West Eurasian (European and Near Eastern) populations as those that had maximum membership of the West Eurasian ancestral population at K=3 (Fig. S9.4). Restricting to the 59 present-day populations (“simple” naming scheme), this is 777 individuals. This count differs from the 781 West Eurasian individuals reported in Table S9.3, as some populations that are geographically African (North African Jewish groups) cluster with West Eurasians in ADMIXTURE analysis, while some groups that are geographically West Eurasian have substantial African (e.g., Yemen) or East Eurasian (e.g., Nogai) ancestry. The list of 64 populations that are classified as West Eurasian in this way (include 5 ancient samples indicated in italics) is as follows:


Yeah. Yoruban have “West Eurasian” ancestry. LOL!
Quote:
Eliminating populations with any West Eurasian admixture whatsoever is DIFFICULT in view of recent results that even Sub-Saharan Africans6 possess a trace of such ancestry.

[djoser-xyyman]

Here is a thought! - if essentially ALL AFRICANs carry the genetic material then it is NOT Eurasian. LOL!

To those who are missing the salient point. Lazaridis just agreed with DNATribes.

[djoser-xyyman]

And now the pictures for those who learn through them.

[djoser-xyyman]

As one can see how rediculous these labels are. All African groups carry "basal Eurasian" and "non-African" DNA material with the exception of Taa and Ju Hoan. They created the illusion that more Africans do NOT carry non-African DNA by splitting these two groups creating 6 sub-populations. The games these people play.

Even the isolated such as the Hadza, Sandawe, Mbuti and Biaka carry both "non-african" and "basal Eurasian" DNA material,


"Basal Eurasian"...Really???!!

[djoser-xyyman]

Africans even carry the "East Asian" components at K3. Ha! Ha! Ha!

[zarahan]

Why call it "basal Eurasian"? Something like "African transitional"
is just as good if the idea is a group or pattern pointing to
an OOA mutation or change. But of course the idea is usually to
downplay anything that seems "too African." How often have assorted
labels such as "Oriental", "Mediterranean", "Middle Eastern" etc
been used to denote indigenous Africans...

[djoser-xyyman]

What is really fascinating is that the Sandawe and Hadza carry more "non-African" genetic material than AFRAMS!!!! Which proves even further that ALL these genetic material is African origin.

DNATribes got the African origin correct but the population may not be the Nilo-Saharans. The Hadza and Sandawe and far south.

[djoser-xyyman]

Taa /ˈtɑː/, also known as ǃXoon (!Khong, !Xóõ) /ˈkoʊ/[2] or Tsasi, is a Khoisan language known for its large number of phonemes, perhaps the largest in the world. Most speakers live in Botswana, but a few hundred live in Namibia. The people call themselves ǃXoon (pl. ǃXooŋake) or ʼNǀohan (pl. Nǀumde), depending on the dialect they speak.
Taa is the word for 'human being'; the local name of the language is Taa ǂaan, from ǂaan 'language'. ǃXoon is an ethnonym used at opposite ends of the Taa-speaking area, but not by Taa speakers in between.[3] Most living Taa speakers are ethnic ǃXoon (plural ǃXooŋake) or 'Nǀohan (plural Nǀumde).[4]

1.0 Relatives[edit]
Until the rediscovery of a few elderly speakers of Nǁng in the 1990s, Taa was thought to be the last surviving member of the Tuu language family.

1.0 Dialects[edit]
There is sufficient dialectal variation in Taa that it might be better described as a dialect continuum than as a single language. Taa dialects fall into two groups, suggesting a historical spread from west to east:[5]
• West Taa: Traill's West ǃXoon and Dorothea Bleek's Nǀuǁʼen
• East Taa
o !Ama (Western)
o (Eastern)
 East ǃXoon (Lone Tree)
 Tsaasi–ǂHuan
 Tsaasi
 ǂHuan
Traill worked primarily with East ǃXoon, and the DoBeS project is working with ’Nǀohan (in East Taa) and West ǃXoon.
ǀ’Auni and Kiǀhazi, previously considered dialects of Taa, were more divergent than the dialects here, and are now classified as a distinct language, Lower Nossob.

Taa has at least 58 consonants, 31 vowels, and four tones (Traill 1985, 1994 on East ǃXoon), or at least 87 consonants, 20 vowels, and two tones (DoBeS 2008 on West ǃXoon), by many counts the most of any known language. These include 20 (Traill) or 43 (DoBeS) click consonants and several vowel phonations, though opinions vary as to which of the 130 (Traill) or 164 (DoBeS) consonant sounds are single segments and which are consonant clusters.

Westphal also studied ǂHuan (ǂhũa) dialect (or ǂHũa-ʘwani), and used this name for the entire language. However, the term is ambiguous between Taa (Western ǂHũa) and ǂ’Amkoe (Eastern ǂHũa), and for this reason Traill chose to call the language ǃXóõ.
Tsaasi dialect is quite similar to ǂHuan, and like ǂHuan, the name is used ambiguously for a dialect of ǂ’Amkoe. This is a Tswana name, variously rendered Tshasi, Tshase, Tʃase, Tsase, and Sase.
The Tswana term for Bushmen, Masarwa, is frequently encountered. More specific to the Taa are Magon (Magong) and the Tshasi mentioned above.

[djoser-xyyman]

[djoser-xyyman]

History of Click-Speaking Populations of Africa Inferred from mtDNA and Y Chromosome Genetic Variation

Sarah A. Tishkoff

[djoser-xyyman]

Use the Cluster chart above. It is clear the Taa, Ju Huoan and Naro has no "basal Eurasian". ALL other African groups carry "basal Eurasian" including Yorubas. Obviously the basal Eurasian "split" occured amounts the Khoisan click speakers. Their mtDNA lineage is L0*. It seems like the Samdawe is ancestral to ALL AMH groups that carry "basal Eurasian" including indigenous Africans.

Here ar ethe pictures...

[djoser-xyyman]

Jun 16, 2014 20:00:04 GMT -5 djoser-xyyman said:

And now the pictures for those who learn through them.