posted
So. Did Busby lie when he said their is no North-South cline?
Being European my money is on he is a liar.
Help me out here.
It is always a good idea to go back to old papers. You will be surprise to know what you find.
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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posted
In fact if YOU understood what I posted it proves I am NOT a racist since there is no race.
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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posted
the new racism is done with code words, similar to when blacks enter an establishment and the workers start talking about "smurfs..." "hey I didn't use the N word, I'm not racist all I said was smurf"
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posted
lol! NICE!!! Right back at me. So what are you saying? From Kurdistan, to North Africa and back to Europe? Follow the trek of the young white male......
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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quote:Originally posted by xyyman: lol! NICE!!! Right back at me. So what are you saying? From Kurdistan, to North Africa and back to Europe? Follow the trek of the young white male......
there you go again with the racial element "young white male"
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posted
BTW. I am still trying to get my hands on the study where MA-1 was corrected from yDNA R to Q. Too many papers to read through. But I know it was corrected. On the other hand, I trying to get my hands of yDNA hg-O studies in Africa and came across this. Notice Q, R, P and O is found also in Africa. And the Islands off Africa.
Significance?!
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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posted
Crete, Sardinia, Sicily and Corsica are mixed in with main land Europeans. All Islands between Africa and Europe. Inhabitants of these islands are outliers within Europe. They know that. Their intent here is to mislead and mis-direct. In other words….cheat!
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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quote:Originally posted by xyyman: lol! NICE!!! Right back at me. So what are you saying? From Kurdistan, to North Africa and back to Europe? Follow the trek of the young white male......
there you go again with the racial element "young white male"
Ironically you seem to be bothered by this.
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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posted
Quick question, R1b or its predecessor emerged after the proposed intermixing between Neanderthals/etc. The majority if not all current OOA R1 carriers are + for N-Admixture... but V88 carriers are not? mind you the latter is most prevalent by far in SSA populations & can even be found in the Caribbean. ...dafuq is going on?
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See the similarities. He is trending R-M269 sub-clades to Northern Europe. I did the same thing. He left out Sardinia. (oH! you do realize he is messing with Torroni and Achilli with their Refugia nonsense?)
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Keep in mind Basal Eurasian do NOT carry Neanderthal ancestry (like Africans - which is a lie).
Modern Europeans are primarily "Basal Eurasian". They met an older population(Khoisan) which carried (Neanderthal ancestry ) as they migrated OUT from Africa. That is why Khoisan Carries the most Neanderthal ancestry than other SSAians. There was population "sub-structure" within Africa. Apparently Neolithic whose origin is in the Great Lakes area was a new and different population (maybe isolated) before they exploded on the scene bringing new technology.
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^ R-V88 carries highest diversity in INNER Africa as it radiates out. Frequency does not = diversity.
The diversity of R1b still has not been resolved. but RV-88 has been.
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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quote:Originally posted by xyyman: ^ R-V88 carries highest diversity in INNER Africa as it radiates out. Frequency does not = diversity.
The diversity of R1b still has not been resolved. but RV-88 has been.
Haplogroup R is more diverse outside of Africa.
R-V88 is merely one of it's branches, the clade that resides in Africa and is very rare outside of Africa. It's parent is M343 and the parent of M343 is the M207, both originating outside of Africa and M207 being the arcahic form of R before it split into R1 and R2.
The oldest human remains found carrying R, were found in Siberia.
So what does all this tell you?
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which region* is it most diverse? where in europe - Asia?
R-V88 is merely one of it's branches, the clade that resides in Africa and is very rare outside of Africa. It's parent is M343 and the parent of M343 is the M207, both originating outside of Africa and M207 being the arcahic form of R before it split into R1 and R2.
Were the locations resolved? And if so.. My initial question still remains unanswered... Whats going on with the lack of Neanderthal admixture in Afropopulations carrying R1b.
The oldest human remains found carrying R, were found in Siberia.
So what does all this tell you?
Nothing... Because you give no dates nor the clade the specimen belong too... wait, siberia? are you referring to pestera cu Oase? ... the 9% "neanderthal"?
@Xyzman Any other R1b clades discovered in Africa (whether estimated to be attributed to recent admixture/geneflow from EuA or not).?
EDIT: Just skimmed through the ESR thread, lol it made everything even more hilarious...(even my above questions) I hope that I'm just lacking on info on the topic, cuz the loose ends are just...lol
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. R1 originated in Africa and spread into Eurasia. As a result haplogroup R is very diverse in Africa.There is a great diversity of the macrohaplogroup R in Africa (See Figure 1). Ychromosome R is characterized by M207/V45. The V45 mutation is found among African populations ( Cruciani et al ,2010). ISOGG 2010 Y-DNA haplogroup tree makes it clear that V45 is phylogenetically equivalent to M207.The most common R haplogroup in Africa is R1 (M173). The predominant haplogroup is R1b (Berniell-Lee et al,2009; Coia et al, 2005; Winters, 2010b; Wood et al, 2009). Cruciani et al (2010) discovered new R1b mutations including V7, V8, V45, V69, and V88.
I specifically stated the frequency of R1 among African populations throughout my 2011 paper.
quote:
Y-chromosome R1 is found throghout Africa. The pristine form of R1-M173 is only found in Africa (Coia et al, 2005; Cruciani et al, 2002, 2010). The age of y chromosome R is 27ky. Most researchers believe that R(M173) is 18.5 ky.There is a great diversity of the macrohaplogroup R in Africa (See Figure 1). Ychromosome R is characterized by M207/V45. The V45 mutation is found among African populations ( Cruciani et al ,2010). ISOGG 2010 Y-DNA haplogroup tree makes it clear that V45 is phylogenetically equivalent to M207.The most common R haplogroup in Africa is R1 (M173). The predominant haplogroup is R1b (Berniell-Lee et al,2009; Coia et al, 2005; Winters, 2010b; Wood et al, 2009). Cruciani et al (2010) discovered new R1b mutations including V7, V8, V45, V69, and V88. Geography appears to play a significant role in the distribution of haplogroup R in Africa. Cruciani et al (2010) has renamed the R*- M173 (R P-25) in Africa V88. The TMRCA of V88 was 9200-5600 kya (Cruciani et al, 2010). Y-chromosome V88 (R1b1a) has its highest frequency among Chadic speakers, while the carriers of V88 among Niger-Congo speakers (predominately Bantu people) range between 2-66% ( Cruciani et al, 2010; Bernielle-Lee et al, 2009). Haplogroup V88 includes the mutations M18, V35 and V7. Cruciani et al (2010) revealed that R-V88 is also carried by Eurasians including the distinctive mutations M18, V35 and V7. R1b1-P25 is found in Western Eurasia. Haplogroup R1b1* is found in Africa at various frequencies. BerniellLee et al (2009) found in their study that 5.2% carried Rb1*. The frequency of R1b1* among the Bantu ranged from 2-20. The bearers of R1b1* among the Pygmy populations ranged from 1-25% (Berniell-Lee et al, 2009). The frequency of R1b1 among Guinea-Bissau populations was 12% (Carvalho et al,2010).
In relation to R-M269 in Africa I wrote:
quote: Around 0.1 of 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 archaeological and linguistic data indicate the successful colonization of Asia by SubSaharan Africans from Nubia 5-4kya (Winters, 2007,2008, 2010c). The archaeological evidence makes it clear that around 4kya intercultural style artifacts connected Africa and Eurasia (Winters, 2007,2010c).
As a result, I did not attempt to decieve anyone about the frequency of R1 in Africa as the author implies.
In fact recent research on y-haplogroups in Africa suggest that R1-M269 is also widespread in Africa.
Above is a figure from Gonzalez et al. 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.
The R1 haplogroup probably originated in Africa.
.
.
. The phylogeography of R1 in Africa makes it clear that this y-chromosome is spread globally across Africa and includes the genetic structure of diverse African populations including Berber, Chadic, Cushitic, Khoisan,Pygmy, Niger-Congo, Nilo-Saharan and Semitic speaking African populations (Berniell-Lee et al, 2009; Cruciani et al, 2010; Wood et al, 2009). The fact that Dravidians carry the R haplogroup illustrate the recent introduction of R y-chromosome to Eurasia.
Abu-Amero et al (20009) reveal the fact that Dravidians carry the R haplogroups illustrate the recent introduction of Ry-chromosomes to Eurasia. The frequency of haplotype M173 in Eurasia is as follows: Anatolia 0.19%, Iran 2.67%, Iraq 0.49% Oman 1.0%, Pakistan 0.57% and Oman 1.0% . This contrast sharply with the widespread distribution of R1 in Africa that ranges between 7- 95% in various parts of Africa, especially Cameroon (Coia et al, 2005). Coia et al (2005) has revealed that no maternal Eurasian lineages have been found among Sub-Saharan Africans with a R1- M173 profile. Haplogroup V88 has the greatest frequency in Africa. It is predominately carried by Chadic speakers, ranges between 2-60% among Central African Niger-Congo speakers (Cruciani et al, 2010). Researchers have found that the TMRCA of V88 was 9200-5600 kya (Cruciani et al, 2010).
The vast majority of Africans belong to the y-chromosome E macrohaplogroup. Phylogenetically haplogroup R1b is mainly found in West Africa and the Sahel.
In this region the frequency of R-M173 can range between 85-100% among some Niger Congo speakers in Cameroon (Cruciani et al, 2010). The paternal record of M173 on the African continent illustrates a greater distribution of this y-chromosome among varied African populations than, in Asia.
The greatest diversity of R1b in Africa is highly suggestive of an Africa origin for this male lineage because it is not isolated to just one part of Africa.
Archaeological (Lal, 1963), genetic (Winters, 2008;2010a), placenames (Balakrishnan, 2005) and linguistic data group (Aravanan,1979,1980; Upadhyaya, 1976,1979; Winters 1985a,1985b, 1989) linking Africans and Dravidian support the recent demic diffusion of SubSaharan Africans and gene flow from Africa to Eurasia. An early colonization of Eurasia 4kya by Sub-Saharan Africans and Dravidian carriers of R1-M173 is the best scenario to explain the high frequency and widespread geographical distribution of this y-chromosome on the African continent (Winters, 2010c). Given the greatest diversity of R1- M173, this is the most parsimonious model explaining the frequency of R-M173 in Africa.
Africans carry haplogroup R1a.
In India the Dravidian people carry the R1a haplogroup The Dravidian people of India originally lived in Middle Africa and belonged to the Proto-Saharan Civilization. The Proto-Saharan civilization was situated in the Proto-Sahara, which includes Cameroon. . . In Cameroon we find carriers of R1a. In addition to carriers of R1a in Cameroon; the Dravidian languages are still spoken today in Cameroon see:https://www.youtube.com/watch?v=vWyAYGlFZjkhttps://www.youtube.com/watch?v=vWyAYGlFZjk
In conclusion, the R macrohaplogroup probably originated in Africa. In my paper POSSIBLE AFRICAN ORIGIN OF Y-CHROMOSOME R1-M173 , I argue that the P clade originated in Africa because 1) the age of R-V88 and 2) the widespread nature of R1 in Africa.
Researchers have found that the TMRCA of V88 was 9200-5600 kya (Cruciani et al, 2010). Eurasians carry the M269 (R1b1b2) mutation. The subclades of R1b1b2 include Rh1b1b2g (U106) (TMRCA 8.3kya) and R1b1b2h (U152) (TMRCA 7.4kya). The most recent common ancestor for R1b1b2 is probably 8kya (Balaresque et al, 2010).
In Africa we find R-M269 and V88. Clearly, R-V88 is older than R-M269 there is no evidence of archaeological evidence of a back migration or haplogroup R into Africa, but there is evidence of the migration of the Kushites and Proto-Saharans into Eurasia from Middle Africa. This supports the proposition the R haplogroups originated in Africa, not Eurasia.
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which region* is it most diverse? where in europe - Asia?
R-V88 is merely one of it's branches, the clade that resides in Africa and is very rare outside of Africa. It's parent is M343 and the parent of M343 is the M207, both originating outside of Africa and M207 being the arcahic form of R before it split into R1 and R2.
Were the locations resolved? And if so.. My initial question still remains unanswered... Whats going on with the lack of Neanderthal admixture in Afropopulations carrying R1b.
The oldest human remains found carrying R, were found in Siberia.
So what does all this tell you?
Nothing... Because you give no dates nor the clade the specimen belong too... wait, siberia? are you referring to pestera cu Oase? ... the 9% "neanderthal"?
@Xyzman Any other R1b clades discovered in Africa (whether estimated to be attributed to recent admixture/geneflow from EuA or not).?
EDIT: Just skimmed through the ESR thread, lol it made everything even more hilarious...(even my above questions) I hope that I'm just lacking on info on the topic, cuz the loose ends are just...lol
I forgot to mention. the R found in Siberia is 24kya
so we have the highest diversity of R in Eurasia as well as the oldest evidence of it found
Posts: 42930 | From: , | Registered: Jan 2010
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which region* is it most diverse? where in europe - Asia?
R-V88 is merely one of it's branches, the clade that resides in Africa and is very rare outside of Africa. It's parent is M343 and the parent of M343 is the M207, both originating outside of Africa and M207 being the arcahic form of R before it split into R1 and R2.
Were the locations resolved? And if so.. My initial question still remains unanswered... Whats going on with the lack of Neanderthal admixture in Afropopulations carrying R1b.
The oldest human remains found carrying R, were found in Siberia.
So what does all this tell you?
Nothing... Because you give no dates nor the clade the specimen belong too... wait, siberia? are you referring to pestera cu Oase? ... the 9% "neanderthal"?
@Xyzman Any other R1b clades discovered in Africa (whether estimated to be attributed to recent admixture/geneflow from EuA or not).?
EDIT: Just skimmed through the ESR thread, lol it made everything even more hilarious...(even my above questions) I hope that I'm just lacking on info on the topic, cuz the loose ends are just...lol
I forgot to mention. the R found in Siberia is 24kya
so we have the highest diversity of R in Eurasia as well as the oldest evidence of it found
Are you talking about the frozen "neanderthal" finger? R1what.. elaborate or point me to a source please?
and Highest diversity? ...are you talking multiple sibling clades or downstream clades?
Where in Europe did the HG originate? & last but not least... Wheres the neanderthal admixture in the SSA's with the respective HG's
Posts: 1781 | From: New York | Registered: Jul 2016
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Y-DNA haplogroup R-M207 is believed to have arisen approximately 27,000 years ago in Asia. The two currently defined subclades are R1 and R2. R1-M173 is estimated to have arisen during the height of the Last Glacial Maximum (LGM), about 18,500 years ago, most likely in southwestern Asia. The two most common descendant clades of R1 are R1a and R1b. R1a-M420 is believed to have arisen on the Eurasian Steppe or the Indus Valley, and today is most frequently observed in eastern Europe and in western and central Asia. R1a-M458 is found at frequencies approaching or exceeding 30% in Eastern Europe. R1b-M343 is believed to have arisen in southwest Asia and today its sublcades are bound in various distributions across Eurasia and Africa. Paragroup R1b1* and R1b1a2-V88 are found most frequently in SW Asia and Africa. The African examples are almost entirely within R1b1a2 and are associated with the spread of Chadic languages. R1b1a1a-P297 is found throughout Eurasia. R1b-M73 is observed most frequently in Asia, with low frequency of observation in Europe. R1b-M269 is observed most frequently in Europe, especially western Europe, but with notable frequency in southwest Asia. R1b1a1a2-M269 is estimated to have arisen approximately 4,000 to 8,000 years ago in southwest Asia and to have spread into Europe from there. The Atlantic Modal Haplotype, or AMH, is the most common STR haplotype in R1b1a1a2a1a-L11/PF6539/S127 and most European R1b belongs to R1b1a1a2a1a1-M405/S21/U106 or R1b1a1a2a1a2-P312/PF6547/S116. R2-M479 is most often observed in Asia, especially on the Indian sub-continent and in central Asia. Additional Resources: (Projects arranged in the order that they appear on the tree.)
Look at the map at top. The paragroup is M207
The only clade in Africa is R1b1a2 (R-V88) (aka R1b1c ) and small sub clades of it. This is after the split of R* into R1 and R2. The R-V88 coalescence time was estimated at 9200–5600 kya, in the early mid Holocene.
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Y-DNA haplogroup R-M207 is believed to have arisen approximately 27,000 years ago in Asia. The two currently defined subclades are R1 and R2. R1-M173 is estimated to have arisen during the height of the Last Glacial Maximum (LGM), about 18,500 years ago, most likely in southwestern Asia. The two most common descendant clades of R1 are R1a and R1b. R1a-M420 is believed to have arisen on the Eurasian Steppe or the Indus Valley, and today is most frequently observed in eastern Europe and in western and central Asia. R1a-M458 is found at frequencies approaching or exceeding 30% in Eastern Europe. R1b-M343 is believed to have arisen in southwest Asia and today its sublcades are bound in various distributions across Eurasia and Africa. Paragroup R1b1* and R1b1a2-V88 are found most frequently in SW Asia and Africa. The African examples are almost entirely within R1b1a2 and are associated with the spread of Chadic languages. R1b1a1a-P297 is found throughout Eurasia. R1b-M73 is observed most frequently in Asia, with low frequency of observation in Europe. R1b-M269 is observed most frequently in Europe, especially western Europe, but with notable frequency in southwest Asia. R1b1a1a2-M269 is estimated to have arisen approximately 4,000 to 8,000 years ago in southwest Asia and to have spread into Europe from there. The Atlantic Modal Haplotype, or AMH, is the most common STR haplotype in R1b1a1a2a1a-L11/PF6539/S127 and most European R1b belongs to R1b1a1a2a1a1-M405/S21/U106 or R1b1a1a2a1a2-P312/PF6547/S116. R2-M479 is most often observed in Asia, especially on the Indian sub-continent and in central Asia. Additional Resources: (Projects arranged in the order that they appear on the tree.)
Look at the map at top. The paragroup is M207
The only clade in Africa is R1b1a2 (R-V88) (aka R1b1c ) and small sub clades of it. This is after the split of R* into R1 and R2. The R-V88 coalescence time was estimated at 9200–5600 kya, in the early mid Holocene.
Yawn,
Statistically these African ('bantus') R* carriers should have had to carry high dosages of Neanderthal DNA. However, early reports said no Neanderthal DNA, according to your theory.
You can't have it both ways. lol
quote:
Table S1. Haplogroup Affiliation of the Seven Chromosomes that Were Re-sequenced
The deepest branching separates A1b from a monophyletic clade whose members (1a A2, A3, B, C, and R) all share seven mutually reinforcing derived mutations (five transitions and two transversions, all at non-CpG sites).
[...]
How does the present MSY tree compare with the backbone of the recently published “reference” MSY phylogeny?13 The phylogenetic relationships we observed among chromosomes belonging to haplogroups B, C, and R are reminiscent of those reported in the tree by Karafet et al.13 These chromosomes belong to a clade (haplogroup BT) in which chromosomes C and R share a common ancestor (Figure 2).
[...]
It is worth noting that this clade was previously detected in west Africa, although at low frequencies.10,30–32 Three chromosomes from the Bakola pygmy group from southern Cameroon (central Africa) were found to carry the derived allele at V164, V166, V196, and P114 and were classified as A1b. Interestingly, one chromosome from an Algerian Berber group (north- west Africa) was found to carry the derived allele at V164, V166, and V196 but carried the ancestral one at P114, implying a bipartite structure for A1b, where P114 defines an internal node.
Three features of our data are of particular interest. First, the branching order at the deepest points of the tree is different from that previously recognized. The root of the tree now falls between A1b and A1a-T, and the number of deep branchings leading to African-specific clades has doubled (Figure 2), providing further strong support for the MSY-based evidence of a modern human origin in the African continent.
Second, the MSY tree is deeper than previously believed. The present figure of about 140 KY for the inferred most recent common ancestor (MRCA) of the MSY phylogeny is older than previous estimates (about 100 KY or below)33–35 and easier to reconcile with plausible scenarios of modern human origin. 36 Clearly, calculation of the precise age of the tree largely depends on the accuracy of the assumed mutation rate. In any case, an antiquity of the root greater than that previously estimated is evident from the present tree structure. It is worth noting that A1b, long neglected in previous large-scale resequencing studies of the MSY, contributes to the older TMRCA and high nucleotide diversity values that we observe, highlighting the importance of targeted studies on rare haplogroups.
Third, contrary to previous phylogeny-based conclu- sions,15,16 the deepest clades of the revised MSY phylogeny are currently found in central and northwest Africa.
quote: The regional distribution of an ancient Y-chromosome haplogroup C-M130 (Hg C) in Asia provides an ideal tool of dissecting prehistoric migration events. We identified 465 Hg C individuals out of 4284 males from 140 East and Southeast Asian populations. We genotyped these Hg C individuals using 12 Y-chromosome biallelic markers and 8 commonly used Y-short tandem repeats (Y-STRs), and performed phylogeographic analysis in combination with the published data. The results show that most of the Hg C subhaplogroups have distinct geographical distribution and have undergone long-time isolation, although Hg C individuals are distributed widely across Eurasia. Furthermore, a general south-to-north and east-to-west cline of Y-STR diversity is observed with the highest diversity in Southeast Asia. The phylogeographic distribution pattern of Hg C supports a single coastal 'Out-of-Africa' route by way of the Indian subcontinent, which eventually led to the early settlement of modern humans in mainland Southeast Asia. The northward expansion of Hg C in East Asia started approximately 40 thousand of years ago (KYA) along the coastline of mainland China and reached Siberia approximately 15 KYA and finally made its way to the Americas.
--Zhong H1, Shi H, Qi XB, Xiao CJ, Jin L, Ma RZ, Su B.
Global distribution of Y-chromosome haplogroup C reveals the prehistoric migration routes of African exodus and early settlement in East Asia.
quote:But the first results were disappointing. The boy’s mitochondrial DNA belonged to the lineage known as U, which is commonly found among the modern humans who first entered Europe about 44,000 years ago. The lineages found among Native Americans are those designated A, B, C, D and X, so the U lineage pointed to contamination of the bone by the archaeologists or museum curators who had handled it, a common problem with ancient DNA projects. “The study was put on low speed for about a year because I thought it was all contamination,” Dr. Willerslev said.
quote:"haplogroup CF and DE molecular ancestors first evolved inside Africa and subsequently contributed as Y chromosome founders to pioneering migrations that successfully colonized Asia. While not proof, the DE and CF bifurcation (Figure 8d ) is consistent with independent colonization impulses possibly occurring in a short time interval."
Use of Y Chromosome and Mitochondrial DNA Population Structure in Tracing Human Migrations
--Peter A. Underhill , Toomas Kivisild - 2007
The Mal'ta boy didn't fell from the sky, onto Siberia near Lake Baikal?
quote:The population of AMH spreading in the eastern direction included “softened” Mongoloid elements. The “dialectal continuum” consisting of Proto-Uralic, Proto-Altaic and Palaeo-Siberian- related languages formed the principal communication media of Early Modern Humans in northern Eurasia.
--Pavel M. DOLUKHANOV
Japan Review, 2003, 15:175-186 Archaeology and Languages in Prehistoric Northern Eurasia
School of Historical Studies, University of Newcastle upon Tyne, United Kingdom
Also from the paper, this chart of population clusters is quite interesting, because we can see which of these ancient samples share some heritage with today’s indigenous American populations, shown in grey. UPGH=Upper Paleolithic Hunter-Gatherer, MHG=Mesolithic Hunter Gatherer, which is later in time that Paleolithic, and NEOL=Neolithic indicating the farming population that arrived in Europe approximately 7,000-10,000 years ago from the Middle EastPosts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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posted
@ElMaestro - R-V88 in Afro Caribbean? Source? Lioness is BSing he/they know the difference between diversity within a haplogroups versus many para-clade. As usual they are muddying the water to confuse the readers. The diversity of R1b-269 has not been resolved between Africa and Europe. Within Europe, yes, it has been resolved. Busby et al and Hammer et al. Highest is in the South East per Hammer. Busby did NOT disclose his data. “Wheres the neanderthal admixture in the SSA's with the respective HG's”. It “appears” that SSA do not carry the supposed Neanderthal admixture. The reason it “appears “ that way has been explained in my thread on ESR on Neanderthals. Sources cited. Lazaridis recent paper explains that also with Basal Eurasian carry no Neanderthal ancestry.
@ Dr Winters – 1. “The pristine form of R1-M173 is only found in Africa (Coia et al, 2005; Cruciani et al, 2002, 2010). “ ???? 2. “R1b1* is found in Africa at various frequencies. Berniell Lee et al (2009) found in their study that 5.2% carried Rb1*.” - Are using the same nomenclature. R1b1* are we talking the UNDERIVED or are we referring to all sub-clades? 3. “Africans carry haplogroup R1a.” Source?? I have seen studies of R1a in Sardinia but never one of R1a in Africa. Although Berbers carry hg-Q. which would support your hypothesis. 4.
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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Statistically these African ('bantus') R* carriers should have had to carry high dosages of Neanderthal DNA. However, early reports said no Neanderthal DNA, according to your theory.
You can't have it both ways. lol
"We found evidence for historically complex and regionally distinct admixture with multiple HG and Eurasian populations across SSA (Fig. 2 and Supplementary Note 5). Specifically, ancient Eurasian admixture was observed in central West African populations (Yoruba; ~7,500–10,500 years ago), old admixture among Ethiopian populations (~2,400–3,200 years ago) consistent with previous reports10, 12, and more recent complex admixture in some East African populations (~150–1,500 years ago) (Fig. 2, Extended Data Fig. 7 and Supplementary Note 5). Our finding of ancient Eurasian admixture corroborates findings of non-zero Neanderthal ancestry in Yoruba, which is likely to have been introduced through Eurasian admixture and back migration, possibly facilitated by greening of the Sahara desert during this period13, 14."
The MA-1 mitochondrial genome belongs to haplogroup U, which has also been found at high frequency among Upper Palaeolithic and Mesolithic European hunter-gatherers10–12, and the Y chromosome of MA-1 is basal to modern-day western Eurasians and near the root of most Native American lineages
----
The Y chromosome of MA-1 was sequenced to an average depth of 1.5X, with coverage across 5.8 million bases. Acknowledging the low depth of coverage, we determined the most likely phylogenetic affiliation of the MA-1 Y chromosome to a basal lineage of haplogroup R (Supplementary Information, section 8 and Supplementary Fig. 5a). The extant sub-lineages of haplogroup R show regional spread patterns within western Eurasia, south Asia and also extend to the Altai region in southern Siberia (Supplementary Fig. 5b).
quote:Originally posted by the lioness,: "We found evidence for historically complex and regionally distinct admixture with multiple HG and Eurasian populations across SSA (Fig. 2 and Supplementary Note 5). Specifically, ancient Eurasian admixture was observed in central West African populations (Yoruba; ~7,500–10,500 years ago), old admixture among Ethiopian populations (~2,400–3,200 years ago) consistent with previous reports10, 12, and more recent complex admixture in some East African populations (~150–1,500 years ago) (Fig. 2, Extended Data Fig. 7 and Supplementary Note 5). Our finding of ancient Eurasian admixture corroborates findings of non-zero Neanderthal ancestry in Yoruba, which is likely to have been introduced through Eurasian admixture and back migration, possibly facilitated by greening of the Sahara desert during this period13, 14."
- The African Genome Variation Project shapes medical genetics in Africa
Deepti Gurdasani,
...Never forget.
@XYZman Y-chromosomal diversity in Haiti and Jamaica: Contrasting levels of sex-biased gene flow T. Simms 2012 Doi:10.1002/ajpa.22090
quote:To test this premise, 177 high-resolution Y-chromosome binary markers and 17 Y-STR loci were typed in Haiti (n 5 123) and Jamaica (n 5 159) and subsequently utilized for phylogenetic comparisons to available reference collections encompassing Africa, Europe, Asia (East and South), and the New World. Our results reveal that both studied populations exhibit a predominantly South Saharan paternal component, with haplogroups A1b-V152, A3-M32, B2-M182, E1a-M33, E1b1a-M2, E2b-M98, and R1b2-V88 comprising 77.2% and 66.7% of the Haitian and Jamaican paternal gene pools, respectively. Yet, European derived chromosomes (i.e., haplogroups G2a*- P15, I-M258, R1b1b-M269, and T-M184) were detected at commensurate levels in Haiti (20.3%) and Jamaica (18.9%), whereas Y-haplogroups indicative of Chinese [O-M175 (3.8%)] and Indian [H-M69 (0.6%) and L-M20 (0.6%)] ancestry were restricted to Jamaica.
...btw, Xyyman & Ish Gebor i see you, just wanted to know what lioness thinks... So Far it seems like she/he/it accepts that Bantus have this purported admixture, as well as khoisans and east Africans. YRI has Eurasian geneflow from 7-11 hundred years ago. I still don't know where she/he/it believes R1b emerged in Europe though her chart suggests western Europe ...is it safe to say western Europe Lioness?
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My bad!! I am so good I outdo myself. SMH and laughing. Yes. P,Q, R1, 207,173 is found in Africa significance?? Young White male found . .....
See the Supplemental Table above S6.
@ElMaestro. Thanks for the Haitian Jamaican study . Never came across that one.
Btw. YRI do not have Eurasian gene "flow". Pagani et al iirc dated Eurasian admixture in YRI in the Helocene. There are conflicting studies.
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Need to thank Dr winters for driving me to review Berniell-Lee et al 2009 again. I was a youngster when I first read this paper.
Indeed the young white male has been found……in inner Africa
Quote: A remarkable finding of our study is the substantial number of individuals belonging to haplogroup R1b1* (5.2%). Surprisingly, it has been previously observed in northern Cameroon (40%) at high frequencies (Cruciani et al. 2002) and at lower frequencies in southern Cameroon (1.12%) (Cruciani et al. 2002), Oman (1%), Egypt (2%), and Hutu from Rwanda (1%) (Luis et al. 2004). The presence of this lineage in Africa has been claimed to be a genetic signature of a possible backflow migration from west Asia into Africa (Cruciani et al. 2002). Here we observe R1b1* in 12 Bantu-agriculturalist populations (ranging from 2% to 20%) and in two Pygmy individuals. A network of R1b1* haplotypes performed using STR data (fig. 2) shows two main clusters, without any population structure. Interestingly, the estimated expansion time for these haplotypes— 7,000 years (SD 8,100)—precedes the time at which the Bantu expansion occurred.
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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Dr Winters is correct. R1b is found throughout Africa and has an African origin...may be as recent as within the last 8000years!!
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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My interpretation is the R1b1 is undefined meaning the resolution did not determine R1b-V88 or R1b-M269. So it is NOT R1b-undefined. The * is indicative undetermined and not undefined. Another main point in the study is a sub-set of R1b were discovered and., yes, R1b-M269 may be present. Not enough data has been obtained.
There are some interesting parts …
---------- quote: Nevertheless, the non negligible presence of theR1b1* lineage in west Central African samples (with a frequency over 5%) might point toward additional demographic expansions within the area besides the ‘‘Bantu expansion.’’ The presence of this haplogroup has also been reported by Cruciani et al. (2002) in Cameroon, as well as in Oman, Egypt, Rwanda (Luis et al. 2004), and Sudan (Hassan et al. 2008), although slightly different genetic markers were analyzed. The presence of this haplogroup in the region is especially puzzling given that, according to the known Y-chromosome phylogeny (Underhill et al. 2000), the geographic origin of the R1b lineage is situated Eurasia and not in Africa.
The internal STR diversity of this lineage in west Central Africa points toward a putative expansion occurring 7,000 years ago, ****before**** the ‘‘Bantu expansion.’’ However, this estimated expansion time could represent an underestimation and may simply show the expansion of a subset of the diversity within haplogroup R1b1* to west Central Africa through the Bantu expansion, having been shown to be especially frequent in northern Cameroon, near the putative Bantu expansion origin (Cruciani et al. 2002). Surprisingly, no traces of non-African maternal lineages (i.e., mtDNA) have been observed in west Central Africa (Coia et al. 2005; Quintana-Murci et al. 2008), pointing to a putative sexual asymmetrical demographic expansion in Central Africa. Further analyses in an extended group of Central African populations (including Nigeria, Niger, Chad, and Sudan) might be pivotal to shed light on this poorly known demographic event in the region. It is noteworthy that the Fang population is the Bantu-agriculturalist group presenting the highest frequency of R1b1*. The presence of the Fang in west Central Africa appears to be recent, and they are thought to have entered the region from the north-eastern open grassland plateau during the 17th and 18th centuries (Perrois 2006).
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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Curious, does that guy have the mutated OCA2, TYR, TYRP1, SLC24A5 genes? If so, then he is a white/albino person.....
Maybe this does some sort prove the whole idea about Albinos being forced out of Africa and Southern Asia to find cooler temperatures relatively recent.
I know you don't always subscribe to my ideas xyyman but I thought you might want to check this out:
Did the emergence of the European type R1b found in Africa, and white males like this, be attributable to cosmic planetary events as suggested in the article?
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quote:Originally posted by Elmaestro: ...btw, Xyyman & Ish Gebor i see you, just wanted to know what lioness thinks... So Far it seems like she/he/it accepts that Bantus have this purported admixture, as well as khoisans and east Africans. YRI has Eurasian geneflow from 7-11 hundred years ago. I still don't know where she/he/it believes R1b emerged in Europe though her chart suggests western Europe ...is it safe to say western Europe Lioness? [/QB]
go back and read my post of ISOGG 2016
Posts: 42930 | From: , | Registered: Jan 2010
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Statistically these African ('bantus') R* carriers should have had to carry high dosages of Neanderthal DNA. However, early reports said no Neanderthal DNA, according to your theory.
You can't have it both ways. lol
"We found evidence for historically complex and regionally distinct admixture with multiple HG and Eurasian populations across SSA (Fig. 2 and Supplementary Note 5). Specifically, ancient Eurasian admixture was observed in central West African populations (Yoruba; ~7,500–10,500 years ago), old admixture among Ethiopian populations (~2,400–3,200 years ago) consistent with previous reports10, 12, and more recent complex admixture in some East African populations (~150–1,500 years ago) (Fig. 2, Extended Data Fig. 7 and Supplementary Note 5). Our finding of ancient Eurasian admixture corroborates findings of non-zero Neanderthal ancestry in Yoruba, which is likely to have been introduced through Eurasian admixture and back migration, possibly facilitated by greening of the Sahara desert during this period13, 14."
- The African Genome Variation Project shapes medical genetics in Africa
Deepti Gurdasani,
LOL So now the Yoruba are the main R* carriers? LOL
BTW I WROTE. However, early reports said no.... DO YOU NOT UNDERSTAND THOSE WORDS? You respond with a supposed found (likeliness) in 23 October 2014. LOL
You are predictable. LOL you are not just any kind of dumb box of rocks, you are a special kind of dumb box of rocks. You try hard everytime, but you skew up the whole process.
Than again, we do know the Neanderthal originated from Africa. So I don't understand that likeliness they are talking about? Perhaps they pulled it out of their asses?
You also need to explain why Ethiopians don't carry Hg R*, for that same back migration? LOL
Ironic is that paragroup DE* was found in Nigerians. And ironic is that DE* has similar mutations in the root as R does, BEFORE IT LEFT THE AFRICAN CONTINENT. But I guess you didn't know that yet.
The root of Hg R* is in Africa, not outside of Africa. Admitting to this is like the biggest nightmare ever!
Let's get to, the nitty gritty!
quote: An independent high resolution MSY phylogeny has been recently obtained from 2,870 Y-SNPs discovered (or re- discovered) in the course of a large whole-genome re-sequencing study, but the observed variable sites all belong to the recent ‘‘out of Africa’’ CT clade [15]. Recently, in a re-sequencing study of the Y chromosome, the root of the tree moved to a new position and several changes at the basal nodes of the phylogeny were introduced [16]
[..]
Phylogenetic Mapping
Most of the mutations here analyzed belong to the African portion of the MSY phylogeny, which is comprised of haplogroups A1b, A1a, A2, A3 and B [16]. Through phylogenetic mapping it was possible to identify 15 new African haplogroups and to resolve one basal trifurcation (Figure 1). A new deep branch within the ‘‘out of Africa’’ haplogroup C was also identified (Figure S1).
Haplogroup A1b. The P114 mutation, which defines hap- logroup A1b according to Karafet et al. [14], had been detected in central-western Africa at very low frequencies (in total, three chromosomes from Cameroon) [16,19].
[...]
‘‘Out of Africa’’ haplogroups. All Y-clades that are not exclusively African belong to the macro-haplogroup CT, which is defined by mutations M168, M294 and P9.1 [14,31] and is subdivided into two major clades, DE and CF [1,14]. In a recent study [16], sequencing of two chromosomes belonging to haplogroups C and R, led to the identification of 25 new mutations, eleven of which were in the C-chromosome and seven in the R-chromosome. Here, the seven mutations which were found to be shared by chromosomes of haplogroups C and R [16], were also found to be present in one DE sample (sample 33 in Table S1), and positioned at the root of macro-haplogroup CT (Figure 1 and Figure S1). Six haplogroup C chromosomes (samples 34–39 in Table S1) were analyzed for the eleven haplogroup C- specific mutations [16] and for SNPs defining branches C1 to C6 in the tree by Karafet et al. [14] (Figure S1). Through this analysis we identified a chromosome from southern Europe as a new deep branch within haplogroup C (C-V20 or C7, Figure S1). Previously, only a few examples of C chromosomes (only defined by the marker RPS4Y711) had been found in southern Europe [32,33]. To improve our knowledge regarding the distribution of haplogroup C in Europe, we surveyed 1965 European subjects for the mutation RPS4Y711 and identified one additional haplogroup C chromosome from southern Europe, which has also been classified as C7 (data not shown). Further studies are needed to establish whether C7 chromosomes are the relics of an ancient European gene pool or the signal of a recent geographical spread from Asia. Two mutations, V248 and V87, which had never been previously described, were found to be specific to haplogroups C2 and C3, respectively (Figure S1). Three of the seven R-specific mutations (V45, V69 and V88) were previously mapped within haplogroup R [34], whereas the remaining four mutations have been here positioned at the root of haplogroups F (V186 and V205), K (V104) and P (V231) (Figure S1) through the analysis of 12 haplogroup F samples (samples 40–51, in Table S1).
[...]
Supporting Information
Figure S1 Structure of the macro-haplogroup CT. For details on mutations see legend to Figure 1. Dashed lines indicate putative branchings (no positive control available). The position of V248 (haplogroup C2) and V87 (haplogroup C3) compared to mutations that define internal branches was not determined. Note that mutations V45, V69 and V88 have been previously mapped (Cruciani et al. 2010; Eur J Hum Genet 18:800–807). (TIF)
--Fulvio Cruciani et al.
Molecular Dissection of the Basal Clades in the Human Y Chromosome Phylogenetic Tree
quote: deepest branching separates A1b from a monophyletic clade whose members (A1a, A2, A3, B, C, and R) all share seven mutually reinforcing derived mutations (five transitions and two transversions, all at non-CpG sites).
[...]
The first branching in the MSY tree has been reported to be the one that separates the African-specific clade A (called clade I in 10) from clade BT (clade II-X in 10), whereas the second branching determines the subdivision of BT in clades B, mostly African, and CT, which comprises the majority of African and all non-African chromosomes.13,14 This branching pattern, along with the geographical distribu- tion of the major clades A, B, and CT, has been interpreted as supporting an African origin for anatomically modern humans,10 with Khoisan from south Africa and Ethiopians from east Africa sharing the deepest lineages of the phylogeny.15,16
[...]
To test the robustness of the backbone and the root of current Y chromosome phylogeny, we searched for SNPs that might be informative in this respect. To this aim, a resequencing analysis of a 205.9 kb MSY portion (183.5 kb in the X-degenerate and 22.4 kb in the X-transposed region) was performed for each of seven chromosomes that are representative of clade A (four chromosomes belonging to haplogroups A1a, A1b, A2, and A3), clade B, and clade CT (two chromosomes belonging to haplogroups C and R) (Table S1 available online).
The phylogenetic relationships we observed among chromosomes belonging to haplogroups B, C, and R are reminiscent of those reported in the tree by Karafet et al.13 These chromosomes belong to a clade (haplogroup BT) in which chromosomes C and R share a common ancestor (Figure 2).
--Fulvio Cruciani
A Revised Root for the Human Y Chromosomal Phylogenetic Tree: The Origin of Patrilineal Diversity in Africa
Karafet was already posted.
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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Statistically these African ('bantus') R* carriers should have had to carry high dosages of Neanderthal DNA. However, early reports said no Neanderthal DNA, according to your theory.
You can't have it both ways. lol
quote:
The MA-1 mitochondrial genome belongs to haplogroup U, which has also been found at high frequency among Upper Palaeolithic and Mesolithic European hunter-gatherers10–12, and the Y chromosome of MA-1 is basal to modern-day western Eurasians and near the root of most Native American lineages
----
The Y chromosome of MA-1 was sequenced to an average depth of 1.5X, with coverage across 5.8 million bases. Acknowledging the low depth of coverage, we determined the most likely phylogenetic affiliation of the MA-1 Y chromosome to a basal lineage of haplogroup R (Supplementary Information, section 8 and Supplementary Fig. 5a). The extant sub-lineages of haplogroup R show regional spread patterns within western Eurasia, south Asia and also extend to the Altai region in southern Siberia (Supplementary Fig. 5b).
quote:Figure 1: Sample locations and MA-1 genetic affinities.
From Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans
Maanasa Raghavan, Pontus Skoglund, Kelly E. Graf, Mait Metspalu, Anders Albrechtsen, Ida Moltke, Simon Rasmussen, Thomas W. Stafford Jr, Ludovic Orlando, Ene Metspalu, Monika Karmin, Kristiina Tambets, Siiri Rootsi, Reedik Mägi, Paula F. Campos, Elena Balanovska, Oleg Balanovsky, Elza Khusnutdinova, Sergey Litvinov, Ludmila P. Osipova, Sardana A. Fedorova, Mikhail I. Voevoda, Michael DeGiorgio, Thomas Sicheritz-Ponten, Søren Brunak et al. Nature (2013) doi:10.1038/nature12736
Sample locations and MA-1 genetic affinities.
a, Geographical locations of Mal’ta and Afontova Gora-2 in south-central Siberia.
For reference, Palaeolithic sites with individuals belonging to mtDNA haplogroup U are shown (red and black triangles): 1, Oberkassel; 2, Hohle Fels; 3, Dolni Vestonice; 4, Kostenki-14. A Palaeolithic site with an individual belonging to mtDNA haplogroup B is represented by the square: 5, Tianyuan Cave. Notable Palaeolithic sites with Venus figurines are marked by brown circles: 6, Laussel; 7, Lespugue; 8, Grimaldi; 9, Willendorf; 10, Gargarino.
Other notable Palaeolithic sites are shown by grey circles: 11, Sungir; 12, Yana RHS. b, PCA (PC1 versus PC2) of MA-1 and worldwide human populations for which genomic tracts from recent European admixture in American and Siberian populations have been excluded19. c, Heat map of the statistic f3(Yoruba; MA-1, X) where X is one of 147 worldwide non-African populations (standard errors shown in Supplementary Fig. 21). The graded heat key represents the magnitude of the computed f3 statistics.
quote:Figure 2: Admixture graph for MA-1 and 16 complete genomes.
From Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans
Maanasa Raghavan, Pontus Skoglund, Kelly E. Graf, Mait Metspalu, Anders Albrechtsen, Ida Moltke, Simon Rasmussen, Thomas W. Stafford Jr, Ludovic Orlando, Ene Metspalu, Monika Karmin, Kristiina Tambets, Siiri Rootsi, Reedik Mägi, Paula F. Campos, Elena Balanovska, Oleg Balanovsky, Elza Khusnutdinova, Sergey Litvinov, Ludmila P. Osipova, Sardana A. Fedorova, Mikhail I. Voevoda, Michael DeGiorgio, Thomas Sicheritz-Ponten, Søren Brunak et al.
Nature (2013) doi:10.1038/nature12736
Admixture graph for MA-1 and 16 complete genomes.
An admixture graph with two migration edges (depicted by arrows) was fitted using TreeMix21 to relate MA-1 to 11 modern genomes from worldwide populations22, 4 modern genomes produced in this study (Avar, Mari, Indian and Tajik), and the Denisova genome22. Trees without migration, graphs with different number of migration edges, and residual matrices are shown in Supplementary Information, section 11. The drift parameter is proportional to 2Ne generations, where Ne is the effective population size. The migration weight represents the fraction of ancestry derived from the migration edge. The scale bar shows ten times the average standard error (s.e.) of the entries in the sample covariance matrix. Note that the length of the branch leading to MA-1 is affected by this ancient genome being represented by haploid genotypes.
quote:Figure 3: Evidence of gene flow from a population related to MA-1 and western Eurasians into Native American ancestors.
From Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans
Maanasa Raghavan, Pontus Skoglund, Kelly E. Graf, Mait Metspalu, Anders Albrechtsen, Ida Moltke, Simon Rasmussen, Thomas W. Stafford Jr, Ludovic Orlando, Ene Metspalu, Monika Karmin, Kristiina Tambets, Siiri Rootsi, Reedik Mägi, Paula F. Campos, Elena Balanovska, Oleg Balanovsky, Elza Khusnutdinova, Sergey Litvinov, Ludmila P. Osipova, Sardana A. Fedorova, Mikhail I. Voevoda, Michael DeGiorgio, Thomas Sicheritz-Ponten, Søren Brunak et al.
Nature (2013) doi:10.1038/nature12736
Allele frequency-based D-statistic tests20 of the forms. a, D(Yoruba, MA-1; Han, X), where X represents modern-day populations from North and South America. The D-statistic is significantly positive for all the tests, providing evidence for gene flow between Native American ancestors and the MA-1 population lineage; however, it is not informative with respect to the direction of gene flow. b, D(Yoruba, X; Han, Karitiana), where X represents non-African populations. Since all of the 17 tested western Eurasian populations are closer to Karitiana than to Han Chinese, the most parsimonious explanation is that Native Americans have western Eurasian-related ancestry. c, D(Sardinian, X; Papuan, Han), where X represents non-African populations. MA-1 is not significantly closer to Han Chinese than to Papuans, which is compatible with MA-1 having no Native American-related admixture in its ancestry. Thick and thin error bars correspond to 1 and 3 standard errors of the D-statistic, respectively.
quote: The Y chromosome Alu polymorphism (YAP, also called M1) defines the deep-rooted haplogroup D/E of the global Y-chromosome phylogeny [1]. This D/E haplogroup is further branched into three sub-haplogroups DE*, D and E (Figure 1). The distribution of the D/E haplogroup is highly regional, and the three subgroups are geographically restricted to certain areas, therefore informative in tracing human prehistory (Table 1). The sub-haplogroup DE*, presumably the most ancient lineage of the D/E haplogroup was only found in Africans from Nigeria [2], supporting the "Out of Africa" hypothesis about modern human origin. The sub-haplogroup E (E-M40), defined by M40/SRY4064 and M96, was also suggested originated in Africa [3-6], and later dispersed to Middle East and Europe about 20,000 years ago [3,4]. Interestingly, the sub-haplogroup D defined by M174 (D-M174) is East Asian specific with abundant appearance in Tibetan and Japanese (30–40%), but rare in most of other East Asian populations and populations from regions bordering East Asia (Central Asia, North Asia and Middle East) (usually less than 5%) [5-7]. Under D-M174, Japanese belongs to a separate sub-lineage defined by several mutations (e.g. M55, M57 and M64 etc.), which is different from those in Tibetans implicating relatively deep divergence between them [1]. The fragmented distribution of D-M174 in East Asia seems not consistent with the pattern of other East Asian specific lineages, i.e. O3-M122, O1-M119 and O2-M95 under haplogroup O [8,9].
--Hong Shi et al. 2008:
Y chromosome evidence of earliest modern human settlement in East Asia and multiple origins of Tibetan and Japanese populations
quote: Further refinement awaits the finding of new markers especially within paragroup E3a*-M2. The microsatellite profile of the DE* individual is one mutational step away from the allelic state described for Nigerians (DYS390*21, DYS388 not tested; [37], therefore suggesting a common ancestry but not elucidating the phylogenetics.
Haplogroup DE* in Guinea-Bissau:
Y-chromosomal diversity in the population of Guinea-Bissau: a multiethnic perspective
quote: There has been considerable debate on the geographic origin of the human Y chromosome Alu polymor- phism (YAP). Here we report a new, very rare deep-rooting haplogroup within the YAP clade, together with data on other deep-rooting YAP clades. The new haplogroup, found so far in only five Nigerians, is the least-derived YAP haplogroup according to currently known binary markers. However, because the interior branching order of the Y chromosome genealogical tree remains unknown, it is impossible to impute the origin of the YAP clade with certainty. We discuss the problems presented by rare deep-rooting lineages for Y chromosome phylogeography.
Haplogroup DE* in Nigerians:
Rare Deep-Rooting Y Chromosome Lineages in Humans: Lessons for Phylogeography
SI 1. The archaeological sites of Mal’ta and Afontova Gora-2 S1 1.1 Mal’ta Mal’ta is a multi-component site located along the Belaya River, tributary of the Angara River in the Pre-Baikal region of southern Siberia, about 86 km northwest of Irkutsk (Figure 1a). It is most noted for its rich middle Upper Palaeolithic (MUP) archaeological materials, including the famous double-child burial and “Venus” figurines. The site was originally excavated during the early 20th century (1928-1958) by Gerasimov1,2, and later during the 1990s by Medvedev and colleagues3. Original excavations were extensive, covering 1348 m2, where Gerasimov reported a single cultural layer for the Upper Palaeolithic found 1.5 m below the surface1.
SI 8. Y chromosome haplogroup of MA-1
Due to low depth-of-coverage of the MA-1 individual (1.5X on 5.8 million bases), genotyping at each site on the Y chromosome was performed by selecting the allele with the highest frequency of bases with a base quality of 13 or higher. Additionally, a multi-fasta file was generated from the variable positions on the Y chromosomes available from 24 Complete Genomics public genomes1. SNPs were filtered for quality (using VQHIGH as the threshold, as defined by Complete Genomics), with tri-allelic positions excluded and only those Y chromosome regions determined as being phylogenetically informative being used2. This yielded a final dataset of 22492 positions. MA-1 Y chromosome data was then included, and MEGA phylogenetic software3 was used to construct a Neighbor Joining (NJ) tree with default parameters (Figure SI 5a). MA-1 is placed as a basal lineage to hg R2,4. Phylogenetically informative positions and their state in MA-1 were then determined to confirm the placement of MA-1 on the tree. In the course of this analysis, the original dataset was severely pruned. Non-informative positions, including those with more than four Ns in the public dataset, were excluded (633 positions). Moreover, the following positions were also excluded which were 1) in reference state in all individuals including MA-1 (7172 positions); 2) N in MA-1 and either N or reference state among the rest of the individuals (9682 positions); 3) ‘N-ref’ – those with only N or reference state among all individuals (586 positions) and ‘N-alt’ - positions with alternative alleles, but difficult to classify (11 positions); 4) reference specific (79 positions); and, 5) recurrent (28 positions). This resulted in 4301 positions being retained that were classified according to their hg affiliations. Among those phylogenetically informative positions, 1889 non-N positions were retrieved from MA-1. When counting from the split of hg DE on the unrooted phylogenetic tree, MA-1 is determined to be carrying the derived allele in 183 sites and the ancestral allele in 1706 sites. The position of MA-1 on the phylogenetic tree is established by the state of the 313 basal mutations separating hgs DE and R, where MA-1 has 143 informative positions. Of these, 138 are in the derived and 5 in the ancestral state, placing MA-1 as a lineage basal to hg R. With only a few exceptions characterized below, all other informative positions in MA-1 are in the ancestral state, further supporting the phylogenetic positioning of MA-1 on the tree.
Among the derived markers in the final dataset only a few (11) mutations were detected that are likely to be false positives based on the phylogenetic analysis, where it is assumed that recurrent mutation is less likely than a sequencing error. One position among the 35 private to MA-1 is characteristic of a distant hg – namely C3c14.
Based on current data, 10 additional phylogenetically non-concordant positions in MA-1 were found – 1 position for hgs E, G, Q, R1b, R1 each, 2 defining positions for hg I and 3 private mutations for R1b individuals (shown in red on Figure SI 5a). Additionally, among the mutations originally excluded (the reference-private mutations), two positions were found where MA-1 is in derived state.
quote:Originally posted by the lioness,: go back ...
You can't have it both ways. lol
quote: SI 12. MixMapper analysis
Admixture graphs were constructed relating MA-1 to modern groups using MixMapper v1.01, a recently developed approach that utilizes f2 distances between populations to fit admixture graphs of population history. MixMapper is based on an approach where a scaffold tree is constructed from populations that are assumed to be unadmixed, upon which other populations can then be fitted as either simple branches off the scaffold, two-way admixtures between populations in the scaffold tree, or alternatively three-way admixtures between an unadmixed population, and a two-way admixed population.
In order to place the MA-1 genome in the context of modern day variation, a scaffold tree was constructed using 4 African genomes (San, Yoruba, Mandenka, Dinka), Sardinian and Han3. The Mbuti genome was excluded for the main analyses since the Mbuti are known to have substantial amounts of recent Bantu-speaker-related ancestry, and are difficult to fit using admixture graphs1,2, but similar results were obtained by us when the Mbuti was also included (see below). Sardinian and Han were chosen as representatives of the western and eastern extremes of modern-day Eurasian genetic differentiation. All transitions were excluded, and standard errors of the f-statistics were estimated using 500 bootstrap replicates over 50 blocks of the autosomal genome
When adding the Karitiana genome to this scaffold tree, 422 of 500 bootstrap pseudoreplicates were found to fit Karitiana as a mix between the Sardinian and Han lineages, with 73.7% (95% CI: 61.8-85.7%) of its ancestry being derived from the Han lineage and the remainder 26.3% (14.3-38.2%) from the Sardinian lineage (Figure SI 18; Table SI 12). When the Mbuti was included, the bootstrap support was 432 of 500 and the Sardinian-related ancestry in MA-1 was 13.4-35.4%. Fitting MA-1 to the scaffold with Sardinian, the best fit (496 of 500 bootstraps) suggested that MA- 1 is a mixture of the Sardinian and Han lineages, with 22.1-75.0% of its ancestry being derived from the Han lineage (Figure SI 18; Table SI 12).
Subsequently, Karitiana was fitted as a three-way mixture between MA-1 (modeled as a mixture as above, see SI 14) and Han, since it is likely that populations related to MA-1 mediated the mixture event between western Eurasians and Native Americans. Here, 496 bootstrap replicates supported Karitiana as having 26.1% (7.7-44.4%) ancestry from the MA-1 lineage and the remainder from Han, consistent with the previous analysis.
A previous study1 used MixMapper and data ascertained in a San individual, and subsequently genotyped in a large number of human populations, to fit Sardinians as a mixture of a western Eurasian lineage and Karitiana, which would suggest that it is inappropriate to use Sardinians in the scaffold tree. If the Sardinian is replaced with Karitiana in the scaffold tree, the highest number of bootstrap pseudoreplicates for any one combination (231 of 500) fitted Sardinians as a mix between Dinka and Karitiana (with 27.7-33.4% ancestry from the Dinka lineage). Lipson et al. (2013) 1 chose the set of populations to be included in the scaffold based on observed f3 tests and additivity of f2-distances in the scaffold tree. However, as discussed later on in SI 14, the reason for Native Americans not displaying negative f3-statstics when tested for having dual ancestry from eastern and western Eurasians could be the extensive amount of genetic drift that has occurred since their divergence. We found that the scaffold tree with Sardinian was more additive than the scaffold tree with Karitiana, suggesting that Karitiana are better fitted as admixed than Sardinians are (Figure SI 19). This was also consistent when Han was replaced by Dai in the scaffold tree and when both East Asians were included (Figure SI 19). It was also consistent when Mbuti was included in the scaffold tree for either (or both) East Asian genomes.
Sardinians also do not display any significant f3-tests, or evidence of admixture linkage disequilibrium with Native Americans4,5. However, we note that if Sardinians themselves have admixture from a Native American source as suggested by Lipson et al. (2013)1, or some other type of complex ancestry (they have evidence of 0.6±0.2% African ancestry5,6 but that is likely negligible for our estimates), the estimates of western Eurasian ancestry in Karitiana are likely to be affected.
Current admixture graph models are not suitable for dealing with possible bidirectional gene flow, and so a future line of study would be to simultaneously infer gene flow between genomic samples from Native American and western Eurasian populations.
Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans
Nature 505, 87–91 (02 January 2014) doi:10.1038/nature12736
Received 14 July 2013 Accepted 04 October 2013 Published online 20 November 2013
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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quote:The lack of Late Pleistocene human fossils from sub-Saharan Africa has limited paleontological testing of competing models of recent human evolution. We have dated a skull from Hofmeyr, South Africa, to 36.2 ± 3.3 thousand years ago through a combination of optically stimulated luminescence and uranium-series dating methods. The skull is morphologically modern overall but displays some archaic features. Its strongest morphometric affinities are with Upper Paleolithic (UP) Eurasians rather than recent, geographically proximate people. The Hofmeyr cranium is consistent with the hypothesis that UP Eurasians descended from a population that emigrated from sub-Saharan Africa in the Late Pleistocene.
--F. E. Grine et al.
Late Pleistocene Human Skull from Hofmeyr, South Africa, and Modern Human Origins
Science 12 Jan 2007: Vol. 315, Issue 5809, pp. 226-229 DOI: 10.1126/science.1136294
quote:"It is often claimed that “AMHs” date from up to 200 ka ago, yet no such specimens exist. The skulls from Omo Kibish offer some relatively modern features as well as substantially archaic ones; especially Omo 2 is very robust indeed (McDougall et al., 2005). Their dating, also, is not secure, and Omo 2 is a surface find. The much more complete and better dated Herto skull, BOU-VP- 16/1, is outside the range of all recent humans in several cranial measurements (White et al., 2003)—and is just as archaic as other specimens of the late Middle Pleistocene, in Africa or elsewhere. The lack of “anatomically modern” humans from sub-Saharan Africa prior to the supposed Exodus is glaring: the Border Cave specimens have no stratigraphic context; Dar es Soltan is undated; and the mandibles of Klasies River Mouth lack cranial and post-cranial remains. The Hofmeyr skull from South Africa, about 36 ka old, features 'intermediate' morphology (Grine et al., 2007, 2010)."
--Bednarik, (2013)
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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posted
wow! Ish. Take your hands off the Nuke button. lol!
"MA-1 is ancestral to haplogroup R"
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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quote:Originally posted by xyyman: wow! Ish. Take your hands off the Nuke button. lol!
"MA-1 is ancestral to haplogroup R"
In order to place the MA-1 genome in the context of modern day variation, a scaffold tree was constructed using 4 African genomes (San, Yoruba, Mandenka, Dinka),
quote:*According to the current data East Africa is home to nearly 2/3 of the world genetic diversity independent of sampling effect. Similar figure have been suggested for sub-Saharan Africa populations [1].* The antiquity of the east African gene pool could be viewed not only from the perspective of the amount of genetic diversity endowed within it but also by signals of uni-modal distribution in their mitochondrial DNA (Hassan et al., unpublished) usually taken as an indication of populations that have passed through *‘‘recent’’ demographic expansion [33], although in this case, may in fact be considered a sign of extended shared history of in situ evolution where alleles are exchanged between neighboring demes [34].*
--Jibril Hirbo, Sara Tishkoff et al.
The Episode of Genetic Drift Defining the Migration of Humans out of Africa Is Derived from a Large East African Population Size
PLoS One. 2014; 9(5): e97674. Published online 2014 May 20. doi: 10.1371/journal.pone.0097674
quote:Originally posted by xyyman: Great information. Blasting trolls into smithereens. Lol! I was trying to relocate that study on DE* in Nigeria. Ta!
quote:Originally posted by xyyman: wow! Ish. Take your hands off the Nuke button. lol!
"MA-1 is ancestral to haplogroup R"
I am trying to warp my head around this one here?
quote: Bedouins, Jordanians, Palestinians and Saudi Arabians are located in close proximity to each other, which is consistent with a common origin in the Arabian Peninsula25, whereas the Egyptian, Moroccan, Mozabite Berber, and Yemenite samples are located closer to sub- Saharan populations (Fig. 1a and Supplementary Fig. 2a).
--Bayazit Yunusbayev, Oleg Balanovsky et al.
The genome-wide structure of the Jewish people
Vol 466|8 July 2010|doi:10.1038/nature09103
Received 9 December 2009; accepted 21 April 2010. Published online 9 June 2010.
Busby et al said based upon STR diversity . There is no longitudinal Cline. Therefore no migration from the Eastern Steppes
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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