Wednesday, January 11, 2017

Mark Lipson, David Reich , A working model of the deep relationships of diverse modern human genetic lineages outside of Africa, Molecular Biology and Evolution, is not a good model for the Out of Africa Exit

Mark Lipson, David Reich (2017), A working model of the deep relationship Humans genetic lineages outside of Africa  fails to live up to the hype associated with the new study. Articles about this study claim that it “the new model shows there was a major eastern-western population split once modern humans left Africa”. Read more: Here

In reality, the article does no such thing it fails to explain how Ust’-Ishim  can represent the western  ancestral Eurasian population, when this individual has no living descendants, and there appears to be two ancestral populations for the eastern Eurasians, since Tianyuan man is characterized by mtDNA B, while the Australasians mainly carry the mtDNA M clade.

As I pointed out elsewhere you can analyze genetic research papers via my  “ A PROTOCOL TO EVALUATE POPULATION GENETICS PAPERS”Here

The Protocol provide a framework for analyzing and int erpreting population genetics articles. Bayesian Statistics combines prior beliefs and sample DNA information to make inferences about the sample based on the researchers prior beliefs.

The authors claims that “Here, we report a model that provides a good statistical fit to allele-frequency correlation patterns among East Asians, Australasians, Native Americans, and ancient western and northern Eurasians, together with archaic human groups. The model features a primary eastern/western bifurcation dating to at least 45,000 years ago, with Australasians nested inside the eastern clade, and a parsimonious set of admixture events. “  These clades are represented by the Tianyuan individual (the eastern type) the  Malta individual (the western type) .The evidence in the paper does not support this conclusion.

The sample used in the study were the archaic humanoids: Altai Neanderthals, and the Denisova; the western Eurasian clade was represented by Mal’ta 1 and , Ust’-Ishim  individuals;  indigenous populations from , New Guinea, Australia,  Onge ( from the Andaman Islands), and the Ami (aboriginal Taiwanese) represented the eastern clade.

The basic error in this method is that the authors are comparing ancient and modern DNA, with the full knowledge that the ancient DNA, rarely corresponds to contemporary populations. In addition the authors use the date of the Ust’-Ishim individual as the terminal date for the separation of the eastern and western clades.

Granted, the authors acknowledge that the Ust’-Ishim individual shows no  admixture in Australasians . But this is not surprising , there are no living descendants of Ust’-Ishim. As a result, s/ he  can not represent the point when the eastern and western clades separated .

Interestingly, the Tianyuan DNA, belongs to the mtDNA R macrohaplogroup, namely haplogroup B, in addition a deletion of a 9-bp motif (5′-CCCCCTCTA-3′, revised Cambridge reference sequence positions 8,281–8,289). This haplogroup is not carried by the  indigenous populations from , New Guinea, Australia,  Onge ( from the Andaman Islands), and the Ami (aboriginal Taiwanese) that represented the eastern clade in this study.

The authors of this article failed to discuss the Tianyuan DNA which also dates to 40kya, while the eastern sample used in the study are all modern. The failure to adequately discuss the Tianyuan DNA, makes the conclusion of the paper suspect, since the authors are claiming that the Australasians, represent the eastern clade, eventhough the Tianyuan individual is 45ky old. Moreover, the presence of the 9-bp motif clearly indicates an African influence among the Tianyuan.


Reference:
Qiaomei Fu et al. DNA analysis of an early modern human from Tianyuan Cave, China. PNAS, published online before print January 22, 2013. http://www.pnas.org/content/110/6/2223.full

Saturday, November 26, 2016

Review: Haber, Marc et al. (2016), Chad Genetic Diversity Reveals an African History Marked by Multiple Holocene Eurasian Migrations

 Haber, Marc et al. (2016), Chad Genetic Diversity Reveals an African History Marked by Multiple Holocene Eurasian Migrations, The American Journal of Human Genetics  , http://www.cell.com/ajhg/fulltext/S0002-9297(16)30448-7

Haber at al speculate that there were several migrations of Eurasians rom Arabia,  into Chad beginning around 7200 ya, which led to the origin of R1b-V88, a major y-Chromosome in much of Africa.. These authors wrote:
“We detected the earliest Eurasian migrations to Africa in the Laal-speaking people, an isolated language group of fewer than 800 speakers who inhabit southern Chad. We estimate that mixture occurred 4,750–7,200 ya, thus after the Neolithic transition in the Near East, a period characterized by exponential growth in human population size. Environmental changes during this period (which possibly triggered the Neolithic transition) also facilitated human migrations. The African Humid Period, for example, was a humid phase across North Africa that peaked 6,000–9,000 ya37 and biogeographically connected Africa to Eurasia, facilitating human movement across these regions.38 In Chad, we found a Y chromosome lineage (R1b-V88) that we estimate emerged during the same period 5,700–7,300 ya (Figure 3B). The closest related Y chromosome groups today are widespread in Eurasia and have been previously associated with human expansions to Europe.39, 40 We estimate that the Eurasian R1b lineages initially diverged 7,300–9,400 ya, at the time of the Neolithic expansions. However, we found that the African and Eurasian R1b lineages diverged 17,900–23,000 ya, suggesting that genetic structure was already established between the groups who expanded to Europe and Africa. R1b-V88 was previously found in Central and West Africa and was associated with a mid-Holocene migration of Afro-asiatic speakers through the central Sahara into the Lake Chad Basin.8 In the populations we examined, we found R1b in the Toubou and Sara, who speak Nilo-Saharan languages, and also in the Laal people, who speak an unclassified language. This suggests that R1b penetrated Africa independently of the Afro-asiatic language spread or passed to other groups through admixture.”

Thusly, according to Haber et al, “Chadian R1b emerged 5,700–7,300 ya, whereas most European R1b haplogroups emerged 7,300–9,400 ya. The African and Eurasian lineages coalesced 17,900–23,000 ya”. 

This statement is contradictory. How could Chadian R1b-V88 emerge 5,700 ya, and R1b-M269 emerge7,300 ya—but—“the African and Eurasian lineages coalesced 17,900–23,000 ya”.  The statement is contradictory because how could V-88 and M-269 coalesce 23,000 ya, when they did not  allegedly emerge  until 11-13,000 years after their proposed coalesce time.

In addition, to an incongruent coalesce time, there is no archaeological evidence for migration back into Africa 7,300 ya. we do see evidence of Africans migrating into the Levant. These Africans were Natufians.

By 13,000 BC, according to J.D. Clark said that the Natufians were collecting grasses which later became domesticated crops in Southwest Asia. In Palestine the Natufians established intensive grass collection. Ehret and  Wendorf,  have observed that  the Natufians used the Ibero-Maurusian tool industry and spread agriculture throughout Nubia into the Red Sea. 
   
The Natufians practiced evulsion of the incisors the same as Bantu people and inhabitants of the Saharan fringes. The modern civilizations of the Middle East were created by the Natufians. Since the Natufians came from Nubia, they can not be classified as Eurasians.
  
    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 Lavant, 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.
   
Holliday confirmed his hypothesis that the replacement of the Neanderthal people were Sub-Saharan Africans. This shows that there were no Eurasian types in the Middle East between 20,000-4,000ya, when Haber et al speculated Y-chromosomes R-V88 and R-M269  coalesced .




Moreover, we clearly see the continuity between African culture from Nubia to the Levant. This view is supported by the Natufians who originated in Africa, and took the Ibero-Maurusian tools into Europe, North Africa and the Middle East. 
Holliday wrote: "The current study demonstrates African-like affinities in the body shape of the Qafzeh-Skhul hominids. This finding is consistent with craniofacial evidence (Brace 1996) and with zooarchaeological data indicating the presence of African fauna at Qafzeh (Rabinovich and Tchernov 1995; Tchernov 1988, 1992)" (p.64). The continuity in the spread of Sub-Saharan fauna, flora and physical type in the Levant between 4000-23,000 ya, means that  R1 more than likely originated in Africa,  instead of Eurasia. Haber et al (2016) is invalid and lacks archaeogenetic evidence to support their conclusions.

References:

J.D. Clark , "The origins of domestication in Ethiopia", Fifth Panafrican Congress of prehistory and quaternary Studies, Nairobi,1977

Christopher Ehret ( "On the antiquity of agriculture in Ethiopia", Jour. Of African History 20, [1979], p.161)

Trenton W. Holliday. (2000) "Evolution at the Crossroads: Modern Human Emergence in Western Asia, American Anthropologist,102(1).

F. Wendorf, The History of Nubia, Dallas,1968, pp.941-46). 






Thursday, November 24, 2016

Bantu in Mozambique carry R1 M269


Rowold , Perez-Benedico , Stojkovic , Garcia-Bertrand , Herrera . On the Bantu expansion. Gene. 2016 Nov 15;593(1):48-57. http://www.sciencedirect.com/science/article/pii/S0378111916305704 , report the discovery of Southeast African Bantu carriers of R1-M269

In West and Central Africa populations exhibit extremely high frequencies (61% to 95%) of R1b1-P25, or V88.  In contrast, two of the three Southeast African Bantu populations genotyped in this study, display  polymorphic levels of M269  in Central Mozambique 9% and Maputo 1%.
Rowold et al, speculate that M269 was introduced into Southeast Africa by Arabs or Western Europeans.

R1 originated in Africa and spread into Eurasia. I specifically stated the frequency of R1 among African populations throughout my 2011 paper.



Many Sub Saharan Africans carry R1b1b2. Wood et al (2009) found that Khoisan (2.2%) and Niger-Congo (0.4%) speakers carried the R-M269 y-chromosome. The Khoisan also carry RM343 (R1b) and M 198 (R1a1) (Naidoo et al., 2010) The Gonzalez et al article  found that 10 out of 19 subjects in the study carried R1b1-P25 or M269. This is highly significant because it indicates that 53% of the R1 carriers in this study were M269, this finding is further proof of the widespread nature of this so-called Eurasian genes in Africa among populations that have not mated with Europeans.

Friday, August 26, 2016

The Whiteout of Blacks in Ancient History

The white race is not monolithic. Often white populations that recently migrated into a region are passed off in history text as the original historic population that in reality were Blacks or Negroes.

History as written today is nothing but falsehood. For example, here is a Sumerian:
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But instead of showing Sumerians in textbooks scholars provide pictures of Gutians from Lagash:

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Without the concept of race the lie being taught that the Sumerians were non-Blacks--Gutians-- will exist forever, since text book publishers only publish what they want us to believe.You can continue to follow the Eurocentrists propaganda that erases Blacks from ancient history--I would rather stick to reality.

The Gutians were Southern whites. They did not look like the Sumerians, who were Blacks.
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Gutians
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To understand whites you have to realize that there are a number of white populations. The European whites can be divided into at least two groups the Northern and Southern Europeans. The Northern Europeans mated with the Black Europeans, but for the most part they were able to maintain a much lighter complexion.

The Southern Euopeans were less numerous so they retain a much darker complexions than the Northern Europeans. The Nordic whites, although they may have blond hair, retain big lips and wide noses and may represent some sort of Albino origin.


The second Sub- group of whites are the Syrians, Turks and Indo-Aryan speakers. The ancestors of these whites are the Gutians. They are Mountain people that originated in the Highlands of Central Asia and Mesopotamia. First mention of these whites go back to Sumerian and Akkadian times.

The Niger-Congo speakers introduced R1a and R1b to Europe during the Kushite expansion.
The Semitic speaking Africans followed the Kushites into Europe. First mention of these Semites are in Egyptian and Sumerian documents as Puntites and Meluhites. Another Semite tribe was the Akkadians of Mesopotamia. The Ethiopian Semites spread haplogroups G, I and J to Eurasia. 

I am beginning to believe that after the Hittites defeated the Hatti and Kaska and other
peoples belonging to the Hurrian and Mitanni kingdoms, these people were uprooted and forced into Iran.The lost of Anatolia to the Hittites, probably forced these people to become nomads.

In Iran they probably formed a significant portion of the Proto-Arya population. Here they may have met Indo-Iranian speaking people,who may have practiced a hunter-gatherer existence, that adopted aspects of their culture especially the religion and use of Mitanni religious terms and chariot culture.

Joining forces with the Mitannian-Hurrian exiles they probably attacked Dravidian and Austronesian speaking people who probably lived in walled cities. The Austronesian and Dravidian people probably came in intimate contact during the Xia and Shang periods of China.

I have to reject the Afghanistan origin for the Indo-Iranian speaking people because the cultures there in ancient times show no affinity to Indo-European civilization. Given the Austronesian and Dravidian elements in Sanskrit and etc., I would have to date the expansion of the Indo-Aryan people sometime after 800 BC, across Iran, India down into Afghanistan, since the Austronesia people probably did not begin to enter India until after the fall of the Anyang Shang Dynasty sometime after 1000 BC. 

This would explain why "the Vedic and Avestan mantras are not carbon copies of each other",they may have had a similar genesis, but they were nativised by different groups of Indic and Iranian speakers after the settlement of nomadic Hurrian and Mitanni people in Iran. 

Friday, August 19, 2016

PaleoAmericans lived first at the Serra da Capivara National Park



Dr. Guidon says the first PaleoAmericans lived at Pedra Furada in Brazil.


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The first Americans lived in the Serra da Capivara National Park. Dr. Guidon claims that people from Africa had established settlements at this site 100kya.


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The Cerra de Capivarains probably landed on the Coast of Brazil and made their way to Serra da Capivara National Park. Sailing down the South American rivers or overland the Cerra de Capivarains made their way to Monte Verde in Chile 33kya.

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PaleoAmericans were at Arroyo del Vizcaino by 30kya.

Wednesday, August 10, 2016

Khoisan Introduced haplogroup R1 among the First Europeans

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Myres et al argues that the neolithic European gene pool was probably influenced most, by events in Western Europe, rather than intrusive pioneer farmers from the Near East(1). They argue that R1b  lineage , phylogeographic and temperal patterns support a Central European origin for this clade and not a recent genetic heritage from Anatolia.

The archaeogenetic evidence fails to support this conclusion. The genetic, craniometric and archaeological evidence all support a Khoisan , rather than Southwest Asian or Central European origin for R1b, just like the Khoisan origin of hg N among the Aurignacians and Salutreans.
The presence of R1 among the ancient Europeans also supports their Khoisan origin . C. M Schlebusch, in her PhD Dissertation Genetic Variation in Khoisan-Speaking populations from Southern Africa , found R1b widespread among the Khoisan. She noted that the percentage of Khoisan carrying Rb1 was:
Karretjie  0.105
Khomani  0.182
Nama    0.071
Naro      0.500
Herero  0.067


Among the Herero 0.067% carried R1a1.

The Khoisan first crossed into Europe from Africa, landing in Iberia 44kya.

Sunday, August 7, 2016

Can Color Terms be Used to Describe Racial Groups: "Yes".

Races exist. The terms black and white to identify a particular race  are legitimate trms to classify members of a particular race. The precise scientific definition of Black is what ever  people agree on.

In ordinary language--colloquial talk--the above also holds true. But , we must remember that in  ordinary  language  words have  meaning  only when  they are  reducible to  their  definitions  and the  class  boundaries  of these  definitions. As a result, the definition of  of a word may often fail to reflect the meaning of a particular word used colloquially .

 Consequently, precision in language is sometmes lacking –often the colloquial form has little in common with the actual definition of a particular word—yet people accept the usage of a particular word, as the valid definition of a word.

For example, in the applied linguistic course I teach, I often begin the class by asking my students the question “what does the word love mean”.

They respond with various words based on their own interpretation of the word ‘love’ especially my female students.The definitions they give for ‘love’, include, love is respect, love is understanding your mate, and etc.  After I place the words on the board I have someone read a dictionary definition of the word. This definition is: affection and sex.

My students are often surprised that their definitions have nothing to do with the actual meaning of the word ‘love’. I use this to illustrate that the word meanings we subscribe too, based on popular usage may have little validity with the dictionary meaning of words.

This illustrates that in ordinary language words have meanings different from there dictionary meanings and they are not reducible to their book definitions and the class boundaries of these definitions since people may agree on a colloquial definition not included in the book definition. This means that the definitions of words are dynamic and can not be restricted to definitions listed in a dictionary.

Granted the populations associated with the words: negro, blanco etc. are not exact descriptions of the ‘races’ they are used to represent, yet people accept them as adequate descriptors for diverse “races”. This is why based on the color lexemes associated with a particular cultural group there can be more than the three races we find associated with western culture, based on the color a group may use to identify a racial group. No matter the colors associated with diverse races---population groups use to define a racial group—the race and the color people use to describe that race are valid ‘scientific terms’ since they reflect the agreed upon definition/descriptor of a particular racial group by that particular population.

Since people say races exist—there are various races agreed upon by members of a particular society based on their world view. These races are also represented by color lexemes agreed upon by populations who have defined a particular race, by a particular color term. Racial categorizations are therefore based on a groups agreed upon descriptor for a particular population/racial group. Since the term applied to a race is accepted by members of the community that term is real, scientific and valid.

This results from the fact that science is ‘knowledge gained by observation and experimentation’. People observe that other human beings in a particular geographical region share physical features which they group as a race. This agrees with the definition of race:  “any of the major groups into which human beings are divided based on some physical features such as color of hair and skin”.


This makes any population defined by a particular “color” a legitimate racial group for that particular population.



Thusly the ancient Blacks when they came in contact with Caucasians and Mongoloid people they used color terms to describe themselves: Black, as opposed to the new population they came in contact with e.g., the term ‘white’ for Caucasians.

By the rise of the River Valley civilizations we see caucasoids in Mesopotamia/Anatolia. I have seen no iconographic evidence of whites in Africa before 1200 BC. After 1200 BC we see the Hua invading China,and the Peoples of the Sea invading Egypt and Mesopotamia.

First mention of whites is by the Sumerians who note invasions by the Gutians, who they referred to as 'wild men', coming down from the mountains into Sumer.

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Gutian..Sumerian


By Akkadian times, the Mesopotamians began to call themselves sag gi ga 'black people' to differentiate between themselves and the Gutians.

The white group to appear in Mesopotamia which represents the European white type was the Hittites. The Black tribe in Mesopotamia was called Hattic-- not  Hittite.

In China, the Hua tribes came down from the mountains and began to attack the Black people. The black Chinese began to refer to themselves as 'li min'='black people'.

The textual evidence indicates to me that there were no whites in Africa. It also shows that when Blacks came in contact with non-Blacks they used terms to describe themselves as 'dark or black' in comparison to to new folk they encountered in their migrations out of Africa.

Interestingly, these non- Blacks invade the Black nations from montainous areas e.g., Gutians, Caucasus Mountains (caucasians), Huangshan mountains (Hua/Contemporary Chinese people).


The use of sag gi ga in Mesopotania, and li min in China make it clear that Blacks recognized different racial groups. They would have been familiar with albinos in Africa, so they probably would have never referred to themselves by racial terms--unless the Gutians and Hua were recognized as racially different from themselves.