posted                      

quote:

---

Originally posted by Oshun:
Okay so I heard it was from back migration, is that true? And if it is, are populations of men with ~95% v88 ~50% Eurasian? Or would you regard them as fully African? Also, if we know lineages from the Levant contained plenty of L lineages for example, how do we know those lineages similar to the Eurasian lineages in Chad, didn't mix throughout Africa?? Would those Africans be "African?" I'm just asking because I'm trying to sort at what point people think an African is "African."

---

quote:

---

‘‘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).

[...]

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).

[...]

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)
Haplogroup affiliation for 51 Y chromosomes
Table S1 analyzed in this study. (XLS)

---

Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010  |  IP: Logged | 

posted                      

quote:

---

Originally posted by xyyman:
R-V88 is not Eurasian because the mutation did NOT occur in Eurasia. The Mutation occurred in Africa. The oldest know R-V88 is Villabruna dated to about 14,000bc.

---

quote:

---

Originally posted by xyyman:
R-V88 is not Eurasian because the mutation did NOT occur in Eurasia. The Mutation occurred in Africa. The oldest know R-V88 is Villabruna dated to about 14,000bc.

---

Posts: 42919 | From: , | Registered: Jan 2010  |  IP: Logged | 

posted                      

quote:

---

Originally posted by xyyman:
Born in Italy, but had black complexion based upon SLC45A2 and SLC24A5.

---

quote:

---

Off course he was not born in Africa since his body was found in Italy dated 14,000BC. So let me ask YOU the question. Is he and African or European?


If a Nigerian born in Sweden 4 generations ago is still a Nigerian then Villabruna born in Italy 14000 years ago is still African since he is balck and had tropical body proportions. Right? Man this all twisted? Plasticity?

---

Posts: 42919 | From: , | Registered: Jan 2010  |  IP: Logged | 

posted                      

quote:

---

Originally posted by Fourty2Tribes:
[QB] Haplogroups have little to do with the bulk of one's genetic profile

---

Posts: 42919 | From: , | Registered: Jan 2010  |  IP: Logged | 

posted                      

quote:

---

Originally posted by the lioness,:

quote:

---

Originally posted by xyyman:
Born in Italy, but had black complexion based upon SLC45A2 and SLC24A5.

---

You are saying that a black complexion is based on SLC45A2 and SLC24A5 but a white complexion is not based on SLC45A2 and SLC24A5.

I am sorry to tell you. That is also silliness. The statement makes no sense. It's called talking loud and sayin' nothing

quote:

---

Off course he was not born in Africa since his body was found in Italy dated 14,000BC. So let me ask YOU the question. Is he and African or European?


If a Nigerian born in Sweden 4 generations ago is still a Nigerian then Villabruna born in Italy 14000 years ago is still African since he is balck and had tropical body proportions. Right? Man this all twisted? Plasticity?

---

Talking about 4 generations ago is a complete red herring. You just made that up.

Basal R* is found only in remains from 24,000 years BP at Mal'ta' in Siberia. That is before R1 even existed.

---

quote:

---

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

[...]

Indicate that La Bran ̃ a specimens (Figure 1) belong to the U5b haplotype (16192T-16270T).


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



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

---

Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010  |  IP: Logged | 

posted                      

quote:

---

Originally posted by the lioness,:


Basal R* is found only in remains from 24,000 years BP at Mal'ta' in Siberia. That is before R1 even existed.

---

Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010  |  IP: Logged | 

posted                      

quote:

---

Originally posted by Ish Gebor:

quote:

---

Originally posted by the lioness,:


Basal R* is found only in remains from 24,000 years BP at Mal'ta' in Siberia. That is before R1 even existed.

---

The above is not a basal.

Here is the basal of R:


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).


This was taken outside of Africa.

---

You don't understand

from the above article, the reference:

[34]

34. Cruciani F, Trombetta B, Sellitto D, Massaia A, Destro-Bisol G, et al. (2010) Human Y chromosome haplogroup R-V88: a paternal genetic record of early mid Holocene trans-Saharan connections and the spread of Chadic languages. Eur J Hum Genet 18: 800–807

The R-V88 coalescence time was estimated at 9200–5600 kya




Anything to the left on this chart is an ancestor M173 aka R1 is the oldest shown before mutations split into R1a and R1b.
Progressive subclades to the right.
The ancestor to M173, basal R* aka M207 is not shown because the article is about R1


_____________________________________



^ M207 that is basal R*
It has only been found in Siberia thus far

After this basal R* two mutations formed R1 and R2
R1 is M173 and R2 is M479

Then from each of these, like children, emerged sub clades R1a and R1b (M343)
and further downstream of R1 are sub clades V88 and P297, far from being basal R, the oldest original form of R, M207

Posts: 42919 | From: , | Registered: Jan 2010  |  IP: Logged | 

posted                      

quote:

---

Originally posted by beyoku:

Off the nutsack.

---

Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007  |  IP: Logged | 

posted                         

quote:

---

Originally posted by the lioness,:

The ancestor to M173, basal R* aka M207 is not shown because the article is about R1


_____________________________________



^ M207 that is basal R*
It has only been found in Siberia thus far

After this basal R* two mutations formed R1 and R2
R1 is M173 and R2 is M479

Then from each of these, like children, emerged sub clades R1a and R1b (M343)
and further downstream of R1 are sub clades V88 and P297, far from being basal R, the oldest original form of R, M207

---

SuperEuronut LIAR. M207 is the same as African V45. As a result, M207/V45 was not only found in Siberia.

.



.

The earliest offshoot of M343 was V88, not M269. So V88 is much older than M269 as noted by Kivisld et al 2017.

Stop making stuff up!

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

posted                         

quote:

---

Originally posted by Elmaestro:
V45 is 173, R1*.

Basal R is one step upstream from from V45.

---

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

posted                      

quote:

---

The V45 mutation is phylogenetically equivalent to M173. Among the other five mutations, V88 defines a new monophyletic clade (R-V88 or R1b1a), which includes haplogroups R-M18 (R1b1a1, formerly R1b1a), R-V8 (R1b1a2), R-V35 (R1b1a3, further subdivided by the V7 mutation to R1b1a3* and R1b1a3a), and R-V69 (R1b1a4)

---

Posts: 1781 | From: New York | Registered: Jul 2016  |  IP: Logged | 

posted                         

quote:

---

Originally posted by Elmaestro:
Uh V45 is unindexed in Isogg, can you give me a link to where it's placed phylogenetically?

Cruciani 2010

quote:

---

The V45 mutation is phylogenetically equivalent to M173. Among the other five mutations, V88 defines a new monophyletic clade (R-V88 or R1b1a), which includes haplogroups R-M18 (R1b1a1, formerly R1b1a), R-V8 (R1b1a2), R-V35 (R1b1a3, further subdivided by the V7 mutation to R1b1a3* and R1b1a3a), and R-V69 (R1b1a4)

---

10.1038/ejhg.2009.231

And would you mind posting a link to where basal V45/M173 being found in an extant population as well also???

I don't mind either way if R* is african or not, I just get excited when looking at this subclade because it has 'complex population history' written all over it, and to quote Xyyman, "not all Africans are Africans"

most African V88 carriers are considered SSA's lol and look there's obviously deep-rooted interactions between ancient Africans (both north and south of the Sahara) and Eurasians. A lot of factors point to there being minimal/neglegent Europe -> Africa migrations. R1 in africa could have came from the east and dispersed in multiple directions shaped by the geographic landscape.

Western european R1 could have very well came from north Africa, and bidrectional geneflow could have shaped North africa AND Southwest Europe during the dryphase via interactions over Gibraltar.

---

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

posted                      

quote:

---

Originally posted by Clyde Winters:
LOL. It is unindexed in ISOGG today, this was not the case in 2010. Now it is not indexed to allow researchers rewrite the genetic history of African R1. now that researchers are accepting the fact that V88 emerged first from 343, how long before they claim it is also the result of a back migration from Europe to Africa.

I was not relying on Cruciani 2010.My source was ISOGG 2010. As my Grandma used to say :Find a fool and Bump his head." In otherwords, if a person does no do adequate research you tell him any lie and he will believe it.

. [/QB]

---

LOL,
ISOGG source on V88 is based solely on Cruciani 2010,
Cruciani who discovered V88 in that same year!!

Posts: 42919 | From: , | Registered: Jan 2010  |  IP: Logged | 

posted                         

quote:

---

Originally posted by the lioness,:

quote:

---

Originally posted by Fourty2Tribes:
[QB] Haplogroups have little to do with the bulk of one's genetic profile

---

stop living in denial, thanks

Haplogroups have a lot to do with the bulk of one's genetic profile

---

Posts: 1254 | From: howdy | Registered: Mar 2014  |  IP: Logged | 

posted                      

quote:

---

Originally posted by Fourty2Tribes:

quote:

---

Originally posted by the lioness,:

quote:

---

Originally posted by Fourty2Tribes:
[QB] Haplogroups have little to do with the bulk of one's genetic profile

---

stop living in denial, thanks

Haplogroups have a lot to do with the bulk of one's genetic profile

---

I have nothing to deny. No denial here. So I will say it again. Haplogroups have little to do with your total ancestry.

Arent your charts missing the Fang thus giving west Africa a false 0%?

---

The Fang are a Central African group, estimated population 1.2 million




^ Map of Central Africa

The Fang people live in the tiny Equatorial Guinea as well as northern Gabon, and southern Cameroon.

.


,




https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2987365/

Published online 2010 Jan 6. doi: 10.1038/ejhg.2009.231
PMCID: PMC2987365
Human Y chromosome haplogroup R-V88: a paternal genetic record of early mid Holocene trans-Saharan connections and the spread of Chadic languages

Fulvio Cruciani,

Posts: 42919 | From: , | Registered: Jan 2010  |  IP: Logged | 

posted                      

Lioness can you explain why the title is "Molecular Dissection Basal Clades in the Human Y Chromosome Phylogenetic Tree"? since I don't understand.


The "from the above article, the reference" is not from this paper. It's from a different paper. smh

Can you explain why Cruciani places this R-M207 as the starting point, connect to seven mutations?
Can you explain the existence with these seven mutations?

quote:

---

‘‘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).

[...]

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).

[...]

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)
Haplogroup affiliation for 51 Y chromosomes
Table S1 analyzed in this study. (XLS)

---

Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010  |  IP: Logged | 

posted                      

quote:

---

Originally posted by Clyde Winters:


Moreover, the ISOGG page under Corrections/Additions since January 2010 mentions the addition of V45 and V88 yet only V88 is listed and not not V45 in the index. When I saw the index in 2010 it was stated that V45 was equivalent to M207. Clearly you removed it to support your lie.

---

Posts: 42919 | From: , | Registered: Jan 2010  |  IP: Logged | 

posted                      

quote:

---

Originally posted by Ish Gebor:
Lioness can you explain why the title is "Molecular Dissection Basal Clades in the Human Y Chromosome Phylogenetic Tree"? since I don't understand.


The "from the above article, the reference" is not from this paper. It's from a different paper. smh

Can you explain why Cruciani places this R-M207 as the starting point, connect to seven mutations?
Can you explain the existence with these seven mutations?

quote:

---

‘‘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).

[...]

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).

[...]

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)
Haplogroup affiliation for 51 Y chromosomes
Table S1 analyzed in this study. (XLS)

---

--Fulvio Cruciani et al.

Molecular Dissection of the Basal Clades in the Human Y Chromosome Phylogenetic Tree

---

quote:

---

Molecular Dissection of the Basal Clades in the Human Y Chromosome Phylogenetic Tree
Rosaria Scozzari, Andrea Massaia, Eugenia D’Atanasio, Natalie M. Myres, Ugo A. Perego, Beniamino Trombetta, Fulvio Cruciani
Published: November 7, 2012

Abstract

One hundred and forty-six previously detected mutations were more precisely positioned in the human Y chromosome phylogeny by the analysis of 51 representative Y chromosome haplogroups and the use of 59 mutations from literature. Twenty-two new mutations were also described and incorporated in the revised phylogeny. This analysis made it possible to identify new haplogroups and to resolve a deep trifurcation within haplogroup B2. Our data provide a highly resolved branching in the African-specific portion of the Y tree and support the hypothesis of an origin in the north-western quadrant of the African continent for the human MSY diversity.

---

Posts: 42919 | From: , | Registered: Jan 2010  |  IP: Logged | 

posted                      

quote:

---

Originally posted by Ish Gebor:
Clyde,

The chart from above by ISOGG is based on older data, not the younger data.

---

Posts: 42919 | From: , | Registered: Jan 2010  |  IP: Logged | 

posted                         

quote:

---

Originally posted by the lioness,:

quote:

---

Originally posted by Ish Gebor:
Clyde,

The chart from above by ISOGG is based on older data, not the younger data.

---

What Clyde likes to do is if he doesn't like current information he goes digging in outdated data, articles when the data was brand new and not well understood. That way he can add the "Winter's Spin"

However as you point out this is 2017 not 2010 and genetic discoveries have been made since 2010 and they have to update the phylogenetic sequence to reflect reality.

---

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

posted                         

quote:

---

Originally posted by Fourty2Tribes:
The Fang are like 80% of Guinea and they were reported to have the highest frequency of R1. They are a west African tribe. Meh I see only 4 west African groups were sampled. Sample size issues.

---

quote:

---

• (i) Motivation
  There were a number of populations for which we did not have access to unadmixed samples. To learn about the history of such populations, we needed to adjust for the presence of non-Native ancestry. We used three complementary approaches to do this. The concordance of results from all these approaches increases our confidence in the key findings of this study.
  
  (1) Restricting to unadmixed samples: We restricted some analyses to 163 Native American samples (34 populations) without any evidence of recent European or African admixture (Note S2). A limitation of these studies, however, is that we could not analyze 16 populations in which all individuals were inferred to have some degree of recent admixture.
  
  (2) Local ancestry masking: We identified segments of the genome in each individual that had an appreciable probability of harboring non-Native American or Siberian ancestry. We then created a “masked” dataset that treated genetic data in these sections as missing (Note S4).
  
  (3) Ancestry Subtraction: We explicitly corrected for the effect of the estimated proportion of European and African in each sample by adjusting the value of f4-statistics by the amount that is expected from this admixture. This is discussed in what follows.
  
  (ii) Details of Ancestry Subtraction
  Assume that we have an accurate estimate of African and European ancestry for each sample (whether it is an individual or a pool of individuals). In practice, we used the ADMIXTURE k=4 estimates, because as described below, they appear to be accurate for Native American populations (with the possible exception of Aleuts as we discuss below). We can then define:
  
  a = % African ancestry in a test sample
  e = % European ancestry in a test sample
  1-a-e = % Native ancestry
  
  For many of our analyses, we are computing f4 statistics, whose values are affected in a known way by European and African admixture. Thus, we can algebraically correct for the effect of recent European or African admixture on the test statistics, obtaining an “Ancestry Subtracted” statistic that is what is expected for the sample if it had no recent European or African ancestry.
  
  The main context in which we compute f4 statistics is in our implementation of the 4 Population Test, to evaluate whether the allele frequency correlation patterns in the data are consistent with the proposed tree ((Unadmixed, Test),(Outgroup1, Outgroup2)), where the Unadmixed population is a set of Native American samples assumed to derive all of their ancestry from the initial population that peopled America, the Test population is another Native American population, and the two outgroups are Asian populations. An f4 statistic consistent with zero suggests that the Unadmixed and Test populations form a clade with no evidence of ancestry from more recent streams of gene flow from Asia. If the Test population harbors recent European or African ancestry, however, a significant deviation of this statistic from zero would be expected, making it difficult to interpret the results. We thus compute a linear combination of f4 statistics that is expected to equal what we would obtain if we had access to the Native American ancestors of the Test population without recent European or African admixture:
  
  S_1=(f_4 (Unadmixed,Test;Out1,Out2)-(a) f_4 (Unadmixed,Yoruba;Out1,Out2)-(e) f_4 (Unadmixed,French;Out1,Out2))/(1-a-e) (S3.1)
  
  Intuitively, this statistic is subtracting the contribution to the f4 statistic that is expected from their proportion a of West African-like ancestry (Yoruba), and their proportion e of West Eurasian-like ancestry (French). We then renormalize by 1/(1-a-e) to obtain the statistic that would be expected if the sample was unadmixed.
  
  A potential concern is that the African and European ancestry in any real Native American test sample is not likely to be from Yoruba and French exactly; instead, it will be from related populations. However, S1 is still expected to have the value we wish to compute if we choose the outgroups to be East Asians or Siberians. The reason is that genetic differences between Yoruba and the true African ancestors, and French and the true European ancestors, are not expected to be correlated to the frequency differences between two East Asian or Siberian outgroups. Specifically, the allele frequency differences are due to history within Africa or Europe, which is not expected to be correlated to allele frequency differences within East Asia and within Siberia.
  
  (iii) Ancestry Subtraction gives results concordant with those on unadmixed samples
  To compare the performance of our three approaches to address the confounder of recent European and African admixture, we computed 48 = 8×6 statistics of the form f4(Unadmixed, Test; Han, San). We choose “Unadmixed” to be one of 8 Native American groups from Meso-America southward that have sample sizes of at least two and for which all samples are inferred to be unadmixed by ADMIXTURE k=4 (Chane, Embera, Guahibo, Guaymi, Karitiana, Kogi, Surui and Waunana). We choose “Test” to be one of 8 Native American populations from Meso-America southward with at least two samples that are entirely unadmixed, and that also have at least two samples that have >5% non-Native admixture according to the ADMIXTURE k=4 analysis (Aymara, Cabecar, Pima, Tepehuano, Wayuu and Zapotec1). This allows us to compare results on admixed and unadmixed samples from the same population.
  
  If the Test population harbors European or West African admixture that we have not corrected, we expect to see a significant deviation of the statistic from zero. For example, f4(Karitiana, French; Han, San), corresponding to the statistic expected for an entirely European-admixed Native American population, is significant at Z = 45 standard errors from zero, and f4(Karitiana, Yoruba; Han, San), which gives the f4-value we would expect for an entirely West African-admixed Native American population, is significant at Z = 101.
  
  Figure S3.1 shows the scatterplots of Z-scores we obtain without Ancestry Subtraction, with Ancestry Subtraction, and with local ancestry masking (Note S4). The x-axis shows data for the unadmixed samples from each Test population, while the y-axis shows the results for the >5% admixed samples from the same populations. We find that:
  • Without Ancestry Subtraction there are significant deviations from zero (|Z|>3) (Fig. S3.1A)
  • With Ancestry Subtraction, there are no residual |Z|-scores >3 (Figure S3.1B)
  • With local ancestry masking (Note S4), there are again no residual |Z|-scores >3 (Figure S3.1C), showing that this method also appears to be appropriately correcting for the admixture.

---

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

posted                         

quote:

---

Originally posted by the lioness,:

quote:

---

Originally posted by Clyde Winters:


Moreover, the ISOGG page under Corrections/Additions since January 2010 mentions the addition of V45 and V88 yet only V88 is listed and not not V45 in the index. When I saw the index in 2010 it was stated that V45 was equivalent to M207. Clearly you removed it to support your lie.

---

I out up an image of the summary, not the whole indexing of all the numerous clades and alleles as per 2010.
ISOGG doesn't do the primary research. They compile informations from researchers, in this case Cruciani. He is the one who mapped these clades. "V45" is not even current terminology. The current terminology is R173

Only one confirmed example of basal R* has been found, in 24,000 year old remains, known as MA1, found at Mal'ta near Lake Baikal in Siberia.

That is M207 and the DNA analysis on those remains was only published in 2014

That's in Siberia and it far predates any form of R in Africa or elsewhere, so stop the nonsense

Also notice the very scant occurrence of M269 in Africa as I have shown in the charts

---

Malta Man was not M207, he was just R1.

.

.

The researchers characterized Malta man as M207 to make it appear that he was ancestral to the R haplogroup to make it appear haplogroup R originated in Europe.

The Figure SI 5a, is interesting because if you notice while there were 8 mutations for haplogroup R, there were 11 mutations for haplogroup E. The researchers could have claimed that Malta man was any Y-chromosome haplogroup that supported the assumptions they already held about this hominid.

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

posted                      

quote:

---

Originally posted by the lioness,:

quote:

---

Originally posted by Ish Gebor:
Lioness can you explain why the title is "Molecular Dissection Basal Clades in the Human Y Chromosome Phylogenetic Tree"? since I don't understand.


The "from the above article, the reference" is not from this paper. It's from a different paper. smh

Can you explain why Cruciani places this R-M207 as the starting point, connect to seven mutations?
Can you explain the existence with these seven mutations?

quote:

---

‘‘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).

[...]

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).

[...]

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)
Haplogroup affiliation for 51 Y chromosomes
Table S1 analyzed in this study. (XLS)

---

--Fulvio Cruciani et al.

Molecular Dissection of the Basal Clades in the Human Y Chromosome Phylogenetic Tree

---

Your assumption is that in an article entitled Molecular Dissection of the Basal Clades in the Human Y Chromosome Phylogenetic Tree that any clade discussed is the earliest form of a haplogroup. That is not the case.

quote:

---

Molecular Dissection of the Basal Clades in the Human Y Chromosome Phylogenetic Tree
Rosaria Scozzari, Andrea Massaia, Eugenia D’Atanasio, Natalie M. Myres, Ugo A. Perego, Beniamino Trombetta, Fulvio Cruciani
Published: November 7, 2012

Abstract

One hundred and forty-six previously detected mutations were more precisely positioned in the human Y chromosome phylogeny by the analysis of 51 representative Y chromosome haplogroups and the use of 59 mutations from literature. Twenty-two new mutations were also described and incorporated in the revised phylogeny. This analysis made it possible to identify new haplogroups and to resolve a deep trifurcation within haplogroup B2. Our data provide a highly resolved branching in the African-specific portion of the Y tree and support the hypothesis of an origin in the north-western quadrant of the African continent for the human MSY diversity.

---

^ They are discussing mutations stemming out of CT, they are not all basal clades

---

quote:

---

Abstract

Our data provide a highly resolved branching in the African-specific portion of the Y tree and support the hypothesis of an origin in the north-western quadrant of the African continent for the human MSY diversity.

[…]


A new deep branch within the “out of Africa” haplogroup C was also identified

---

Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010  |  IP: Logged | 

posted                      

quote:

---

Originally posted by the lioness,:

quote:

---

Originally posted by Ish Gebor:
Clyde,

The chart from above by ISOGG is based on older data, not the younger data.

---

What Clyde likes to do is if he doesn't like current information he goes digging in outdated data, articles when the data was brand new and not well understood. That way he can add the "Winter's Spin"

However as you point out this is 2017 not 2010 and genetic discoveries have been made since 2010 and they have to update the phylogenetic sequence to reflect reality.

---

Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010  |  IP: Logged | 

posted                         

quote:

---

Originally posted by Ish Gebor:

quote:

---

Originally posted by the lioness,:

quote:

---

Originally posted by Ish Gebor:
Clyde,

The chart from above by ISOGG is based on older data, not the younger data.

---

What Clyde likes to do is if he doesn't like current information he goes digging in outdated data, articles when the data was brand new and not well understood. That way he can add the "Winter's Spin"

However as you point out this is 2017 not 2010 and genetic discoveries have been made since 2010 and they have to update the phylogenetic sequence to reflect reality.

---

I think what Clyde is doing is comparison of old and new data. How it sometimes contradicts, changes or expands.

---

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

posted                      

quote:

---

Originally posted by Clyde Winters:

quote:

---

Originally posted by Ish Gebor:

quote:

---

Originally posted by the lioness,:

quote:

---

Originally posted by Ish Gebor:
Clyde,

The chart from above by ISOGG is based on older data, not the younger data.

---

What Clyde likes to do is if he doesn't like current information he goes digging in outdated data, articles when the data was brand new and not well understood. That way he can add the "Winter's Spin"

However as you point out this is 2017 not 2010 and genetic discoveries have been made since 2010 and they have to update the phylogenetic sequence to reflect reality.

---

I think what Clyde is doing is comparison of old and new data. How it sometimes contradicts, changes or expands.

---

You are correct. For example R-M207 in Africa is given new nomenclatures every time you see new studies, to make it appear that R-M207 is only found in Europe. We have already noted how ISOGG 2010, listed V45 as the same as M207. Interestingly, Scozzari, R., Massaia, A., D’Atanasio, E., Myres, N. M., Perego, U. A., Trombetta, B., & Cruciani, F. (2012). Molecular Dissection of the Basal Clades in the Human Y Chromosome Phylogenetic Tree. PLoS ONE, 7(11), e49170, http://doi.org/10.1371/journal.pone.0049170, notes that another former M207 clade in Cameroon is now named V69 or R1b1a4, as noted in Table S1 (SUPPLEMENT).

---

quote:

---

The R-V88 coalescence time was estimated at 9200–5600 kya, in the early mid Holocene.

--Human Y chromosome haplogroup R-V88: a paternal genetic record of early mid Holocene trans-Saharan connections and the spread of Chadic languages.
Fulvio Cruciani

---

Posts: 42919 | From: , | Registered: Jan 2010  |  IP: Logged | 

posted                      

quote:

---

Originally posted by Ish Gebor:
Since you mentioned Cruciani as the prime source.

I am still waiting for you to explain why, 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 are positioned at the root of macro-haplogroup CT (Figure 1 and Figure S1), before leaving Africa. Why is that? lol


Explain why are the four remainder mutations of R positioned at the root of haplogroups F (V186 and V205)? Why is that? lol


Further more do C, CT, CF, F and DE have an African origin? lol

---

Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010  |  IP: Logged | 

posted                      

quote:

---

Besides the haplogroup C lineages that are atypical to present-day populations living in the area the Y chromosome pool of the early Holocene hunter-gatherer and farmer populations of Europe and Middle East was characterised by a diverse set of haplogroups, such as G, H, I, J and R, which are restricted in their present-day distribution by and large to Europe, Middle East, North Africa, South and Central Asia.

---

Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010  |  IP: Logged | 

posted                      

quote:

---

Originally posted by Ish Gebor:
Since you mentioned Cruciani as the prime source.

I am still waiting for you to explain why, 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 are positioned at the root of macro-haplogroup CT (Figure 1 and Figure S1), before leaving Africa. Why is that? lol


Explain why are the four remainder mutations of R positioned at the root of haplogroups F (V186 and V205)? Why is that? lol


C, CT, CF, F and DE have an African origin, the chromosomes that make up R cluster with the aforementioned Hg's before leaving Africa! lol

---

quote:

---

We estimated the TMRCA of human Y chromosomes as 338 kya (95% CI = 237–581 kya). Using a joint likelihood20 and the same mutation rate, we also estimated a divergence time between A0 chromosomes and the human reference as 202 kya (95% CI = 125–382 kya), a time that is older than that previously obtained by Cruciani et al. (142 kya).6 This discrepancy in the age of A0 is due to the fact that the earlier study did not utilize mutation rates based on recently obtained whole-genome sequence data.14; 15; 16; 17 ; 18 If we were to use the higher mutation rate (1.0 × 10−9 per base per year6) rather than a realistic range derived from whole-genome sequencing (4.39 × 10−10 − 7.07 × 10−10), the estimated TMRCA for the tree incorporating A00 as the basal lineage would be 209 kya, which is only slightly older than current estimates of the TMRCA of mtDNA and the age of the oldest AMH fossil remains. We note, however, that the higher mutation rate produces an estimate for the common ancestor of all non-African Y chromosome haplogroups (C through T) of ∼39 kya6 (i.e., versus ∼63 kya for the mutation rate used here). It is difficult to reconcile the younger estimate with the timing of the out-of-Africa dispersal on the basis of the analyses of autosomal DNA21 and the fossil record outside of Africa.22; 23; 24 ; 25 Regardless of which mutation rate is applied, the analysis of relative ages of nodes26 shows that the TMRCA of the A00-rooted tree is 67% older (95% CI = 35%–126%) than that of the A0-rooted tree.


Genotyping of a DNA sample that was submitted to a commercial genetic-testing facility demonstrated that the Y chromosome of this African American individual carried the ancestral state of all known Y chromosome SNPs. To further characterize this lineage, which we dubbed A00 (see Figure S1, available online, for proposed nomenclature), we sequenced multiple regions (totaling ∼240 kb) of the X-degenerate portion of this chromosome, as well as a subset of these regions (∼180 kb) on a chromosome belonging to the previously known basal lineage A1b (which we rename here as A0).

---

quote:

---

The 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). To retain the information from the reference MSY tree13 as much as possible, we named this clade A1a-T (Figure 1). Within A1a-T, the transversion V221 separates A1a from a monophyletic clade (called A2-T) consisting of three branches: A2, A3, and BT, the latter being supported by ten mutations (Figure 1)


.

---

Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010  |  IP: Logged |