A New Topology of the Human Y Chromosome Haplogroup E1b1 (E-P2) Revealed through the Use of Newly Characterized Binary Polymorphisms
Beniamino Trombetta,1 Fulvio Cruciani,1 Daniele Sellitto,1,2 and Rosaria Scozzari1* 1Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Universitŕ di Roma, Rome, Italy 2Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Rome, Italy Vincent Macaulay, Editor University of Glasgow, United Kingdom
Conceived and designed the experiments: BT FC RS. Performed the experiments: BT DS. Analyzed the data: BT FC. Wrote the paper: BT FC RS.
Received November 17, 2010; Accepted December 6, 2010.
Abstract
Haplogroup E1b1, defined by the marker P2, is the most represented human Y chromosome haplogroup in Africa. A phylogenetic tree showing the internal structure of this haplogroup was published in 2008. A high degree of internal diversity characterizes this haplogroup, as well as the presence of a set of chromosomes undefined on the basis of a derived character. Here we make an effort to update the phylogeny of this highly diverse haplogroup by including seven mutations which have been newly discovered by direct resequencing. We also try to incorporate five previously-described markers which were not, however, reported in the 2008 tree. Additionally, during the process of mapping, we found that two previously reported SNPs required a new position on the tree. There are three key changes compared to the 2008 phylogeny. Firstly, haplogroup E-M2 (former E1b1a) and haplogroup E-M329 (former E1b1c) are now united by the mutations V38 and V100, reducing the number of E1b1 basal branches to two. The new topology of the tree has important implications concerning the origin of haplogroup E1b1. Secondly, within E1b1b1 (E-M35), two haplogroups (E-V68 and E-V257) show similar phylogenetic and geographic structure, pointing to a genetic bridge between southern European and northern African Y chromosomes. Thirdly, most of the E1b1b1* (E-M35*) paragroup chromosomes are now marked by defining mutations, thus increasing the discriminative power of the haplogroup for use in human evolution and forensics.
Introduction
Human Y chromosome haplogroups are defined by unique mutations within the male specific region of the Y chromosome (MSY). The lack of recombination in this portion of the genome makes it possible to reconstruct an unequivocal haplogroup phylogenetic tree, which can be related to the geographic distribution of the individual branches of the tree, by an approach known as “phylogeography” [1]. The high genealogical resolution of this system, established by recent advances in mutation-detection technology, and the phylogeographic method have together proven highly informative in tracing patterns of human prehistoric colonization and migrations.
A parsimonious phylogenetic tree for 20 major haplogroups (A-T) representing worldwide Y chromosomal variation was proposed in 2008 [2]. In the present work, we focused on the structure of haplogroup E1b1. Within haplogroup E, which represents the majority of the Y chromosomes found in Africa, E1b1 is the haplogroup which has the greatest geographic distribution. Three lineages, E1b1a (E-M2), E1b1b (E-M215) and E1b1c (E-M329) were included in the genealogy presented by Karafet et al. [2]. To gain a better understanding of the structure of this complicated haplogroup, we performed a high resolution analysis by sequencing, on the average, 45.4 kb in each of 13 E1b1 Y chromosomes (Table S1). Incorporating the information obtained from this analysis into the previously reported tree produced an extensively revised phylogeny for the haplogroup E1b1 resulting in 52 distinct haplogroups.
Results
A total of 7 new SNPs within the E1b1 clade were discovered and mapped on the Y chromosome tree. In addition, five mutations (M293, V68, V92, V95 and V100) that had been previously described [3]–[5] but not included in the tree reported by Karafet et al. [2], were phylogenetically characterized. Information regarding these 12 SNPs is given in Table 1. Finally, two previously reported mutations, M154 [6] and M281 [7], required changes to their position in the phylogenetic tree as reported by Karafet et al. [2]. Changes to the previous “by lineage” haplogroup names have come about as a result of the incorporation of the new SNPs into the tree. To avoid any confusion, we have referred to the names of previous haplogroups (uninformed by the SNPs here characterized) by adding the term “former” throughout the text.
List of the phylogenetically characterized polymorphisms in the present study.
The phylogeny of the haplogroup E1b1 without (A) and with (B) the newly characterized SNPs is shown in Figure 1. Two SNPs (V43 and V95) turned out to be phylogenetically equivalent to the previously characterized mutation defining haplogroup E1b1a1 (E-M2, former E1b1a). However, incorporating the remaining ten mutations into the tree resulted in important changes compared with the previously published phylogeny.
Phylogeny of the haplogroup E1b1 without (A) and with (B) the SNPs phylogenetically characterized in this study (in red). The tripartite structure of E1b1 has now been resolved by virtue of the new markers V38 and V100, which combined haplogroup E-M2 (former E1b1a) with E-M329 (former E1b1c) into the haplogroup E-V38 (E1b1a). Within this haplogroup, the M154 marker was repositioned to the E-U209 clade. Nine chromosomes out of 95 E-U209*(x U290, P59) turned out to carry the derived state at M154. In addition, a new lineage was found to be defined within the E-U209 clade by the newly discovered V39 mutation. Two among 86 E-U209*(xU290, P59, M154) sub-Saharan chromosomes were found to have this mutation. The V68 mutation was recently reported to be phylogenetically equivalent to M78 in a sample of 239 African chromosomes [4]. Here, undifferentiated paragroup E-V68*(xM78) chromosomes were observed in 3 among 9 E-M35* previously reported chromosomes from Europe [8]. A newly discovered mutation, V257, combined all the E-M81 and a subset (4/9 from Europe, 1/1 Marrakesh Berber and 1/1 Oromo from Kenya) of the E-M35* chromosomes reported by Cruciani et al. [8]. The V23 mutation was found to mark a new lineage within the E-M34 clade. Two out of 16 E-M34 Y chromosomes which had been previously observed in Africa [8] turned out to carry this mutation. The mutation M293 mutation [3] was shown to be positioned upstream of the P72 marker (Figure 1), which defines the E1b1b1f lineage in the tree by Karafet et al. [2]. All the sixteen Y chromosomes from southern Africa and 4/19 Y chromosomes from eastern Africa described by Cruciani et al. [8] as belonging to paragroup E-M35* turned out to carry the M293 mutation. The E-M35* undifferentiated state of two Jews and one Amhara from Ethiopia previously reported [8] has now been resolved by two mutations (V42 and V92, respectively), that identify two additional clades within the E-M35 haplogroup. Finally, we have found that M281 does not define a separate sub-lineage within E-M35; rather it is phylogenetically indistinct from the newly discovered V16 mutation and marks all the five E-M215* chromosomes reported by Cruciani et al. [4]. In conclusion, incorporating the newly characterized mutations into the E1b1 haplogroup, has led to a total of 52 lineages. This compares with the 44 lineages on the tree by Karafet et al. [2].
Discussion
Haplogroup E1b1 which is characterized by a high degree of internal diversity is the most represented Y chromosome haplogroup in Africa. Here we report on the characterization of 12 mutations within this haplogroup, eleven of which were discovered in the course of a resequencing and genotyping project performed in our laboratory. There are several changes compared to the most recently published Y chromosome tree [2]. Haplogroup E1b1 now contains two basal branches, E-V38 (E1b1a) and E-M215 (E1b1b), with V38/V100 joining the two previously separated lineages E-M2 (former E1b1a) and E-M329 (former E1b1c). Each of these two lineages has a peculiar geographic distribution. E-M2 is the most common haplogroup in sub-Saharan Africa, with frequency peaks in western (about 80%) and central Africa (about 60%). The same haplogroup is also present in North Africa, although at a lower frequency (usually below 10%) [9]–[11]. Haplogroup E-M329, on the other hand, was observed almost exclusively in eastern Africa [10], [12 and R.S. unpublished data], where E-M2 is virtually absent. The second basal branch of E1b1, E-M215, has a broad geographic distribution from southern Europe to northern and eastern Africa where it has been proposed to have originated [8]. The new topology here reported has important implications as to the origins of the haplogroup E1b1. Using the principle of the phylogeographic parsimony, the resolution of the E1b1b trifurcation in favor of a common ancestor of E-M2 and E-M329 strongly supports the hypothesis that haplogroup E1b1 originated in eastern Africa, as previously suggested [10], and that chromosomes E-M2, so frequently observed in sub-Saharan Africa, trace their descent to a common ancestor present in eastern Africa. Within E-M35, there are striking parallels between two haplogroups, E-V68 and E-V257. Both contain a lineage which has been frequently observed in Africa (E-M78 and E-M81, respectively) [6], [8], [10], [13]–[16] and a group of undifferentiated chromosomes that are mostly found in southern Europe (Table S2). An expansion of E-M35 carriers, possibly from the Middle East as proposed by other Authors [14], and split into two branches separated by the geographic barrier of the Mediterranean Sea, would explain this geographic pattern. However, the absence of E-V68* and E-V257* in the Middle East (Table S2) makes a maritime spread between northern Africa and southern Europe a more plausible hypothesis. A detailed analysis of the Y chromosomal microsatellite variation associated with E-V68 and E-V257 could help in gaining a better understanding of the likely timing and place of origin of these two haplogroups. Thanks to the newly characterized mutations, the large majority (34/45) of the chromosomes previously assigned to paragroup E-M35* [8] are now defined by unique mutations (Table S2). These findings will be of importance to those with research interests in human evolution [17]–[18] and forensic issues [19], [20].
Materials and Methods
This study was approved by the “Policlinico Umberto I, Sapienza Universitŕ di Roma” Ethical Committee (protocol number 1016/2010, according to the DM 15/7/1997 and following). The data were analyzed anonymously. DNA samples came from collections of the Authors, and haplogroup information is as reported [4], [8]. DNAs were obtained from a total of 174 individuals from each of the following haplogroups E-M2* (3), E-U209* (95), E-V39, E-M215* (5), E-M35* (45), E-M78, E-V257*, E-M34*(18), E-V23, E-M293*, E-V42, E-V92 and E-V16.
Amplification and Sequencing
Overall, 45,4 Kb were sequenced on the average for each of 13 unrelated Y chromosomes (Table S1). We designed polymerase chain reaction (PCR) and sequence primers on the basis of the Y-chromosome sequence reported in the February 2009 assembly of the UCSC Genome Browser (http://genome.ucsc.edu/) using Primer3 software (http://frodo.wi.mit.edu/primer3/). Sequencing templates were obtained through PCR in a 50-µl reaction containing 50 ng of genomic DNA, 200 µM each deoxyribonucleotide (dNTP), 2.5 mM MgCl2, 1 unit of Taq polymerase, and 10 pmoles of each primer. A touch-down PCR program was used with an annealing temperature decreasing from 62°C to 55°C over 14 cycles, followed by 30 cycles with an annealing temperature of 55°C. Following DNA amplification, PCR products were purified using theQIAquick PCR purification kit (Qiagen, Hilden, Germany). Cycle sequencing was performed using the BigDye Terminator Cycle Sequencing Kit with Amplitaq DNA polymerase (Applied Biosystems, Foster City, CA) and an internal or PCR primer. Cycle sequencing products were purified by ethanol precipitation and run on an ABI Prism 3730XL DNA sequencer (Applied Biosystems). Chromatograms were aligned and analyzed for mutations using Sequencher 4.8 (Gene Codes Corporation, Ann Arbor, MI).
Mapping and genotyping of the new mutations were performed by using a total of 174 DNA samples classified as indicated above.
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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I missed this one. Glad you reposted. Basically it reaffirms an East African connection noted in other studies like Tishkoff etc. I wonder though when we will hear Haplogroup E generally referred to as an "African Haplogroup" based on its most frequent occurrence in Africa. Some scholars seem to have no problem referring to say Haplogroup K as "Eurasian" due to distribution, but on their same websites when it comes to Haplogroup E the consistency disappears. There is a lot of qualification and detailed separation. See for example: http://www.drpeterjdadamo.com/wiki/wiki.pl/
Above writer also refers to Haplogroup H as "European" again, on the strength of its frequency distribution, but curiously does not apply the same consistency when in comes to Haplogroup E and its predominant frequency distribution in Africa. Interesting double standard...
"Using the principle of the phylogeographic parsimony, the resolution of the E1b1b trifurcation in favor of a common ancestor of E-M2 and E-M329 strongly supports the hypothesis that haplogroup E1b1 originated in eastern Africa, as previously suggested [10], and that chromosomes E-M2, so frequently observed in sub-Saharan Africa, trace their descent to a common ancestor present in eastern Africa. -- Trombetta et al. 2011. A New Topology of the Human Y Chromosome Haplogroup E1b1. PLoS ONE 6(1)
-------------------- Note: I am not an "Egyptologist" as claimed by some still bitter, defeated, trolls creating fake profiles and posts elsewhere. Hapless losers, you still fail. My output of hard data debunking racist nonsense has actually INCREASED since you began.. Posts: 5905 | From: The Hammer | Registered: Aug 2008
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Haplogroup T (K) actually has its highest frequencies in eastern Africa.
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Haplogroup T has intermediate frequencies in the Near East and East Africa. It originated in the Near East though
Posts: 1502 | From: Dies Irae | Registered: Oct 2010
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And you are basing the area of origin on what?
-------------------- The Complete Picture of the Past tells Us what Not to Repeat Posts: 7516 | From: Somewhere on Earth | Registered: Jan 2008
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quote:Originally posted by The Explorer: And you are basing the area of origin on what?
General consensus among scientists is that haplogroup T originated in the northern parts of the Middle East.
T branches off from LT and y-DNA L is virtually absent in Africa.
Posts: 695 | From: وكان المصريون القدماء القوقازين | Registered: Jan 2011
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I didn't ask for "general consensus". I asked for specifics of the underlying premise for the whereabouts of the clade's origins.
L was reportedly also located in northern Africa.
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Origin and Dispersal of Haplogroup T in the Near East.
Three lines of evidence support the hypothesis that haplogroup T originated in the Near East and subsequently expanded from there. First, the geographic distribution of the two sister clades, haplogroup L and haplogroup T, overlap in the Near East, although L has a more easterly epicenter in India and Pakistan (Sengupta et al. 2006). Second, almost all of M70* chromosomes surveyed here are found in the Near East, and the two main subclades (T1a and T1b) also predominate in this area. Finally, the internal structure of the T clade, with the single T* sample coming from Syria, provides evidence that the most basal haplogroup T branch is present in the Near East.
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I suspected that you were relying on this study, as it had been posted here earlier. The idea that hgs L and T exist in the "Near East" doesn't really amount to much in of itself. The relative diversity of M70 here doesn't say much either, considering that only a few African populations have been analyzed; hg T (K2) had been located in quite a number of African territories from Somalia, Egypt, Ethiopia, Tanzania, Zambia to as far west as Nigeria. I highly doubt that all of these regions have the exact same clusters of K2. In fact, if anything, the results posted in the study cited above indicates that African T chromosomes are reasonably diverse. The T haplotypes found in the Lemba for example, are markedly different from those of the Ethiopian, Egyptians and Moroccans, and the Ethiopian structure for this haplogroup in turn differs from those of Morocco and Egypt. This haplogroup has even been identified in relatively isolated groups like the Omo groups of Ethiopia. The point here being that Africa was severely under-sampled against the so-called "Near East", considering that the highest reported incidences of K2 had traditionally been in Africa than anywhere else.
The only strong point mentioned above for a possible "Near Eastern" origin, is the location of a single Syrian T* clade. Previous studies on hg T don't exactly have that much of a high resolution, and so, it is hard to gauge the specifics of the clusters involved. It is possible that the singular Syrian T* represents a basal T clade, but it is also possible that it another yet unidentified sub-clade of hg T. It should be pointed out that the authors' hg T resolution wasn't very high, as they did not account for all the basic clades of T1a, which means that some of their M70* chromosomes could be amongst the untested M70 sub-clades.
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Besides a Syrian T* (M184*) sample in Mendez et al. (2011) there were also two Near Eastern T1* (M70*) samples (one Iranian Jew and an Iraqi Jew respectively).
Egyptian and Ethiopian T samples belonged to the derived T1a subclade, this subclade is most frequent in Assyrians.
The T1b* lineage that became prevalent in the Lemba (a Bantu speaking group claiming Near Eastern ancestry) looks like a clear-cut case of founder effect. T1b* haplotypes were also found in European Jews, as well as in a Turk and a Jordanian.
No basal lineages were found in Africa. Somali T1 is estimated to have an expansion time of 3.3 kya, which also looks like a case of founder effect and low diversity.
Posts: 695 | From: وكان المصريون القدماء القوقازين | Registered: Jan 2011
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Did you read what I just said about the M70* chromosomes?
"Looks like" is not a substitute for "is". However, it "looks like" my point about the diversity of the fairly limited African samples of your cited work had escaped your attention. As a matter of fact, your post actually talks right past the message being conveyed in mine.
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We'll just have to be patient and wait for further investigation on T sub-clades within Africa (which weren't featured in Mendez et al.), but I am strongly leaning towards a Near Eastern origin for the time being.
Posts: 695 | From: وكان المصريون القدماء القوقازين | Registered: Jan 2011
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What you wish to lean on is your choice. My point is straightforward:
1) The highest incidences of K2 (now labelled as being part of hg T) has traditionally been reported in Africa.
2) The study cited above only concerned a few African samples against a more geographically comprehensive "Near Eastern" sampling. This makes little sense, considering point #1.
3) Even the fairly limited African samples provide a quick snapshot of African hg T diversity.
If the Lemba T haplotypes are different from those of the other African samples, and likewise, the Ethiopian hg T genetic structure is different from the other African samples, then there is no reason to jump the gun that hg T gene pool from Zambia all the way to Algeria are of the same gene pool either.
[Ps: Just because other samples reported T-L131*, for which the highest incidence was reported in the Lemba, that doesn't mean the different samples implicated share the same STR clusters or even potential downstream EUPs]
4) Only a single Syrian haplotype has the potential of being a basal T haplotype. Finding this rare Syrian haplotype was obviously contingent on the relative geographical comprehensiveness of the "Near Eastern" sampling.
On the other hand, the rare single Syrian haplotype could just as well turn out to be a rare T sub-clade that is yet to be fully established.
5) T-M70* of the cited work is not all that finely resolute, because a number of basic nodes within the T1a clade had not even been tested!
6) Both L and T have been reportedly located in northern Africa. So the mere argument that these two clades exist in the "Near East" goes out the window.
And adding something new to the list,
7) The fact that the authors couldn't even geographically get Ethiopia correct, placing it in "north Africa" while singling the Lemba out as the lone "sub-Saharan" sample, has got be cause to cast suspicion on the judgement of the authors.
Posts: 7516 | From: Somewhere on Earth | Registered: Jan 2008
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Forget T, L, or even LT, let's go straight to the root K*. Paragroup K (haplogroups K*, K1, K2, K3 and K4) are found in Oceania, and Australia and at low frequency in South Asia and the Malay Archipelago.
The are no known African K(xLT and K(xLT))samples. Ultimately any haplogroup besides A/B/DE trace back to Eurasia.
Posts: 695 | From: وكان المصريون القدماء القوقازين | Registered: Jan 2011
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What is K(xLT and K (xLT)) supposed to mean?
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I take it that you don't know what you wrote says, and hence, I have to look for its meaning in the link?
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quote:1) The highest incidences of K2 (now labelled as being part of hg T) has traditionally been reported in Africa.
They say that it appears at at intermediate frequencies in the Near East and East Africa.
quote:The study cited above only concerned a few African samples against a more geographically comprehensive "Near Eastern" sampling. This makes little sense, considering point #1.
I suppose it doesn't. I agree with Perahu that it has to be further investigated in Africa.
quote:If the Lemba T haplotypes are different from those of the other African samples, and likewise, the Ethiopian hg T genetic structure is different from the other African samples, then there is no reason to jump the gun that hg T gene pool from Zambia all the way to Algeria are of the same gene pool either.
[Ps: Just because other samples reported T-L131*, for which the highest incidence was reported in the Lemba, that doesn't mean the different samples implicated share the same STR clusters or even potential downstream EUPs]
I agree.
quote:T-M70* of the cited work is not all that finely resolute, because a number of basic nodes within the T1a clade had not even been tested!
6) Both L and T have been reportedly located in northern Africa. So the mere argument that these two clades exist in the "Near East" goes out the window.
It's not that the appear in the Near East alone, but because haplogroup L and haplogroup T, overlap in the Near East.
quote:7) The fact that the authors couldn't even geographically get Ethiopia correct, placing it in "north Africa" while singling the Lemba out as the lone "sub-Saharan" sample, has got be cause to cast suspicion on the judgement of the authors.
They actually explain why they do that.
-------------------- L Writes: Posts: 1502 | From: Dies Irae | Registered: Oct 2010
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Now that it's been established that the guy (Perahu) doesn't know what he is writing, e.g. K(xLT and K(xLT)), it's time to confront this:
Forget T, L, or even LT, let's go straight to the root K*. Paragroup K (haplogroups K*, K1, K2, K3 and K4) are found in Oceania, and Australia and at low frequency in South Asia and the Malay Archipelago. - Perahu
K* is more than likely a reference to rare K clades that don't fall into either the LT sub-family or the K(xLT) sub-family. That doesn't necessarily mean they are basal to either sub-family; take for instance from the ISOGG link:
The 50f2/C deletion in the AZFc region of the human Y chromosome has been observed in several different haplogroups and is not a unique event polymorphism. It is notable, however, that it has been detected at relatively high levels in subgroups of K in Melanesia - K* (21%), and K3 (14%).
quote:Originally posted by L':
It's not that the appear in the Near East alone, but because haplogroup L and haplogroup T, overlap in the Near East.
Elaborate.
quote: They say that it appears at at intermediate frequencies in the Near East and East Africa.
Apparently, I'm not going by what "they say".
quote:
quote:7) The fact that the authors couldn't even geographically get Ethiopia correct, placing it in "north Africa" while singling the Lemba out as the lone "sub-Saharan" sample, has got be cause to cast suspicion on the judgement of the authors.
They actually explain why they do that.
Oh, there is a justification for getting basic geography wrong. I'd love to hear this one.
Posts: 7516 | From: Somewhere on Earth | Registered: Jan 2008
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They never make the claim that the two clades support a Near Eastern origin just because they appear in the Near East, they state that the geographic distribution of these clades overlap the Near East:
"Three lines of evidence support the hypothesis that haplogroup T originated in the Near East and subsequently expanded from there. First, the geographic distribution of the two sister clades, haplogroup L and haplogroup T, overlap in the Near East, although L has a more easterly epicenter in India and Pakistan (Sengupta et al. 2006)."-Mendez et al
quote:Oh, there is a justification for getting basic geography wrong. I'd love to hear this one.
"Given the low frequency of T chromosomes, individuals from several populations were pooled under the assumption that they could be treated as coming from a single population."-Mendez et al
If they did think Ethiopians were in north Africa I would be highly concerned, lol.
Posts: 1502 | From: Dies Irae | Registered: Oct 2010
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They never make the claim that the two clades support a Near Eastern origin just because they appear in the Near East, they state that the geographic distribution of these clades overlap the Near East:
"Three lines of evidence support the hypothesis that haplogroup T originated in the Near East and subsequently expanded from there. First, the geographic distribution of the two sister clades, haplogroup L and haplogroup T, overlap in the Near East, although L has a more easterly epicenter in India and Pakistan (Sengupta et al. 2006)."-Mendez et al
What do you understand by "overlap in the Near East"? I already know what they said; I'd like to know what you understand by it.
quote:"Given the low frequency of T chromosomes, individuals from several populations were pooled under the assumption that they could be treated as coming from a single population."Mendez et al
If they did think Ethiopians were in north Africa I would be highly concerned, lol.
First of all, I don't see "Ethiopia" in your cited piece. Secondly, they couldn't have treated "Ethiopia" as coming from a single population in Northern Africa, because Ethiopia has been treated as a standalone sample, just as Lemba and the other samples were treated, in the table showing frequencies. Thirdly, it wouldn't have made sense to treat Ethiopia as a part of a single "North African" sample, since the Ethiopian T genetic structure, as I noted, is different from the "north African" samples reported.
Posts: 7516 | From: Somewhere on Earth | Registered: Jan 2008
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quote:What do you understand by "overlap in the Near East"? I already know what they said; I'd like to know what you understand by it.
According to them it supports the hypothesis. Not sure what to think of it now. I just pointed out that they weren't saying that a Near Eastern origin was supported solely because L and T are in the Near East. What are your opinions on the new SNP uniting L and T?
quote:First of all, I don't see "Ethiopia" in your cited piece. Secondly, they couldn't have treated "Ethiopia" as coming from a single population in Northern Africa, because Ethiopia has been treated as a standalone sample, just as Lemba and the other samples were treated, in the table showing frequencies. Thirdly, it wouldn't have made sense to treat Ethiopia as a part of a single "North African" sample, since the Ethiopian T genetic structure, as I noted, is different from the "north African" samples reported.
You're right. That is weird.
Posts: 1502 | From: Dies Irae | Registered: Oct 2010
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According to them it supports the hypothesis. Not sure what to think of it now. I just pointed out that they weren't saying that a Near Eastern origin was supported solely because L and T are in the Near East. What are your opinions on the new SNP uniting L and T?
I never said they were relying solely on the occurrence of hgs L and T in the so-called "Near East" either. I did however, confront the reasons they laid out to make a case for a "Near Eastern" origin on a point by point basis.
And the SNP uniting L and T? It strikes me as an inference from the occurrence of the said SNP on sub-clades spanning hg L and hg T chromosomes, rather than a discovering of a chromosome just bearing the said SNP without additional downstream mutations.
quote:
quote:First of all, I don't see "Ethiopia" in your cited piece. Secondly, they couldn't have treated "Ethiopia" as coming from a single population in Northern Africa, because Ethiopia has been treated as a standalone sample, just as Lemba and the other samples were treated, in the table showing frequencies. Thirdly, it wouldn't have made sense to treat Ethiopia as a part of a single "North African" sample, since the Ethiopian T genetic structure, as I noted, is different from the "north African" samples reported.
You're right. That is weird.
I knew that the only scenario under which the authors would pool samples is when they were attempting to estimate the coalescence or TMRCA ages, and so, I jumped straight to the section dealing with that, and sure enough, I located the piece you cited earlier. A passage under the section in question does go onto reinforce what I was saying about the "genetic structuring" factor anyway; quote:
The populations originally considered were Egyptians, Tunisians, Ethiopians, Lemba, Turks, Assyrians, Druze, Bedouins, Palestinians, Syrians, Jordanians, Lebanese, Iraqis, Iranians, Saudi Arabians, Yemenis, Bulgarians, Bulgarian Jews, Turkish Jews, Moroccan Jews, Tunisian Jews, Yemenite Jews, Kurdish Jews, Iraqi Jews, Iranian Jews, Uzbeki Jews, Ashkenazi Jews, and Roman Jews. Ethiopian Jews were not successfully genotyped for the 10 Y-STRs and were excluded from this analysis. To comply with the assumptions of the coalescence analysis, samples were included regardless of their haplogroup affiliation. We sought to reduce the effect of population structure by sequentially performing a Principal Component Decomposition (PCD) on the population haplogroup frequencies and then excluding the population that appeared isolated in a plot of the first two principal components. After the sequential removal of Ethiopians, Iranian Jews, Uzbeki Jews, Lemba, and Tunisians, no further outliers could be seen in the PCD plot (Supplemental Figure 1). The samples successfully genotyped in these populations (n 1279) were chosen for BATWING analysis. - Mendez et al. (2011).
Ps: I also couldn't help but notice that the likes of "Assyrians" and "Roman Jews" were included above. When one hears these names, one thinks of the ancient kingdoms associated with them. Should the Assyrian sample, for example, be from the historic complex, then one also has to wonder how the DNA samples of the series were collected without any contamination or degradation complications in the process.
Posts: 7516 | From: Somewhere on Earth | Registered: Jan 2008
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quote:I never said they were relying solely on the occurrence of hgs L and T in the so-called "Near East" either. I did however, confront the reasons they laid out to make a case for a "Near Eastern" origin on a point by point basis.
Yeah you did. I was confused, I guess, by the following:
"Both L and T have been reportedly located in northern Africa. So the mere argument that these two clades exist in the "Near East" goes out the window."
quote:Ps: I also couldn't help but notice that the likes of "Assyrians" and "Roman Jews" were included above. When one hears these names, one thinks of the ancient kingdoms associated with them. Should the Assyrian sample, for example, be from the historic complex, then one also has to wonder how the DNA samples of the series were collected without any contamination or degradation complications in the process.
They just have some serious labeling problems
-------------------- L Writes: Posts: 1502 | From: Dies Irae | Registered: Oct 2010
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Patrol, what do you have on Haplogroup T (Ydna) having its highest frequency inside Africa?
-------------------- Note: I am not an "Egyptologist" as claimed by some still bitter, defeated, trolls creating fake profiles and posts elsewhere. Hapless losers, you still fail. My output of hard data debunking racist nonsense has actually INCREASED since you began.. Posts: 5905 | From: The Hammer | Registered: Aug 2008
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quote:I never said they were relying solely on the occurrence of hgs L and T in the so-called "Near East" either. I did however, confront the reasons they laid out to make a case for a "Near Eastern" origin on a point by point basis.
Yeah you did. I was confused, I guess, by the following:
"Both L and T have been reportedly located in northern Africa. So the mere argument that these two clades exist in the "Near East" goes out the window."
Yeah, the cited piece was taken from my notes, but what you failed to see, which is puzzling really, is that it was just one of the several points addressing the positions of the author(s) of the extract you cited, as it relates to the origin of hg T. You'd be advised to stop cherry-picking only what you want to see in the given post, and avail yourself the opportunity to actually learn.
Posts: 7516 | From: Somewhere on Earth | Registered: Jan 2008
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While your post cites pieces with regards to hg L both in terms of the Y-DNA and mtDNA, Trollpatrol, it strikes me that you are not necessarily making such a distinction. In fact, your posts suggest that you are focusing on the mtDNA L markers, whereas the focus of the topic was on the Y-DNA. If I'm missing something here, let me know.
Posts: 7516 | From: Somewhere on Earth | Registered: Jan 2008
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quote:Originally posted by The Explorer: While your post cites pieces with regards to hg L both in terms of the Y-DNA and mtDNA, Trollpatrol, it strikes me that you are not necessarily making such a distinction. In fact, your posts suggest that you are focusing on the mtDNA L markers, whereas the focus of the topic was on the Y-DNA. If I'm missing something here, let me know.
Yes, you are right. I overlooked that part.
Here is info pertaining Y-DNA Hg L. But here they state that people in these populations carry sub-groups of Hg L.
Y-DNA haplogroup L is found primarily as sub-group L1a (former L1) in India, Southern Pakistan and Sri Lanka. Paragroups L1b* and L1b1* (former L2*) and sub-group L1b1a (former L2a) are found at low frequencies in the Middle East and Europe. Sub-group L1c (former L3) is found mainly in northern Pakistan, northern India and west-central Asia.
Increasing phylogenetic resolution of the Y chromosome haplogroup tree has led to finer temporal and spatial resolution for studies of human migration. Haplogroup T, initially known as K2 and defined by mutation M70, is found at variable frequencies across West Asia, Africa, and Europe. While several SNPs were recently discovered that extended the length of the branch leading to haplogroup T, only two SNPs are known to mark internal branches of haplogroup T. This low level of phylogenetic resolution has hindered studies of the origin and dispersal of this interesting haplogroup, which is found in Near Eastern non-Jewish populations, Jewish populations from several communities, and in the patrilineage of President Thomas Jefferson. Here we map 10 new SNPs that, together with the previously known SNPs, mark 11 lineages and two large subclades (T1a and T1b) of haplogroup T. We also report a new SNP that links haplogroups T and L within the major framework of Y chromosome evolution. Estimates of the timing of the branching events within haplogroup T, along with a comprehensive geographic survey of the major T subclades, suggest that this haplogroup began to diversify in the Near East -25 kya. Our survey also points to a complex history of dispersal of this rare and informative haplogroup within the Near East and from the Near East to Europe and sub-Saharan Africa. The presence of T1a2 chromosomes in Near Eastern Jewish and non-Jewish populations may reflect early exiles between the ancient lands of Israel and Babylon. The presence of different subclades of T chromosomes in Europe may be explained by both the spread of Neolithic farmers and the later dispersal of Jews from the Near East. Finally, the moderately high frequency (-18%) of T1b* chromosomes in the Lemba of southern Africa supports the hypothesis of a Near Eastern, but not necessarily a Jewish, origin for their paternal line.
High Resolution Phylogeographic Map of Y-Chromosomes Reveal the Genetic Signatures of Pleistocene Origin of Indian Populations
R. Trivedi, Sanghamitra Sahoo, Anamika Singh, G. Hima Bindu, Jheelam Banerjee, Manuj Tandon, Sonali Gaikwad, Revathi Rajkumar, T Sitalaximi, Richa Ashma, G. B. N. Chainy and V. K. Kashyap
Here is info pertaining Y-DNA Hg L. But here they state that people in these populations carry sub-groups of Hg L.
Y-DNA haplogroup L is found primarily as sub-group L1a (former L1) in India, Southern Pakistan and Sri Lanka. Paragroups L1b* and L1b1* (former L2*) and sub-group L1b1a (former L2a) are found at low frequencies in the Middle East and Europe. Sub-group L1c (former L3) is found mainly in northern Pakistan, northern India and west-central Asia.
Yes, I was aware that Y-DNA hg L was present in parts of Asia. Just wanted to make sure you were aware that the hg L we were discussing here was the Y-DNA one, since it seemed that you were under the impression the mtDNA version was subject of the debate.
Posts: 7516 | From: Somewhere on Earth | Registered: Jan 2008
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quote:Originally posted by zarahan- aka Enrique Cardova: Patrol, what do you have on Haplogroup T (Ydna) having its highest frequency inside Africa?
All you have to do is view reports of distribution and concentration of the haplogroup across global samples.
If something contradicts my earlier claim that the haplogroup has its highest concentration within Africa, I'm open to examining it.
Posts: 7516 | From: Somewhere on Earth | Registered: Jan 2008
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This argument I found, what do you think of it? I understand some of it was captured already. But anyway...
quote:Haplogroup T
K2-M70 is believed to have originated in Asia after the emergence of the K-M9 polymorphism (45–30 ky) (Underhill et al. 2001a). As deduced from the collective data (Underhill et al. 2000; Cruciani et al. 2002; Semino et al. 2002; present study), K2-M70 individuals, at some later point, proceeded south to Africa. While these chromosomes are seen in relatively high frequencies in Egypt, Oman, Tanzania, Ethiopia, they are especially prominent in the Fulbe 18%( [Scozzari et al. 1997, 1999])"
Haplogroup T (M70, M184, M193, M272) is found in an insignificant majority of Kurru, Bauris & Lodha in South Asia; and in a significant minority of Rajus and Mahli in South Asia; Somalis, southern Egyptians and Fulbe in north Cameroon; Chian Greeks, Saccensi/Sicilians, Eivissencs / Ibizans and Northeastern Portuguese Jews in Europe; and Zoroastrians, Bakhtiaris in the Middle East.
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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Do you know of a well working SNP database? None of those I have found works properly or gives the requested criteria.
You are making this too complicated. You simply have to be mindful of various studies that claim to do world-wide sampling, observe trends in frequency estimations, and extrapolate geographical distribution from that; some apply maps of continents to aid in this.
Y-search databases are more useful for locating information for STR profiles, for which you'll have to be familiar with standard nomenclature applied to various Y segments/loci.
quote:This argument I found, what do you think of it? I understand some of it was captured already. But anyway...
quote:Haplogroup T
K2-M70 is believed to have originated in Asia after the emergence of the K-M9 polymorphism (45–30 ky) (Underhill et al. 2001a). As deduced from the collective data (Underhill et al. 2000; Cruciani et al. 2002; Semino et al. 2002; present study), K2-M70 individuals, at some later point, proceeded south to Africa. While these chromosomes are seen in relatively high frequencies in Egypt, Oman, Tanzania, Ethiopia, they are especially prominent in the Fulbe 18%( [Scozzari et al. 1997, 1999])"
Haplogroup T (M70, M184, M193, M272) is found in an insignificant majority of Kurru, Bauris & Lodha in South Asia; and in a significant minority of Rajus and Mahli in South Asia; Somalis, southern Egyptians and Fulbe in north Cameroon; Chian Greeks, Saccensi/Sicilians, Eivissencs / Ibizans and Northeastern Portuguese Jews in Europe; and Zoroastrians, Bakhtiaris in the Middle East.
More of a summary than an argument. It doesn't really challenge any of the specifics I laid out earlier for the haplogroup (T, formerly K2), in response to allegations made in Mendez et al.'s (2011) analysis. I observe data, not merely what some researcher "believes" could have happened. That data suggests that the jury is still out, and does not rule out an African origin.
Posts: 7516 | From: Somewhere on Earth | Registered: Jan 2008
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quote:Evolutionary history of mtDNA haplogroup structure in African populations inferred from mtDNA d-loop and RFLP analysis.
(A) Relationships among different mtDNA haplogroup lineages inferred from mtDNA d-loop sequences and mtDNA coding region SNPs from previous studies (Kivisild, Metspalu, et al. 2006). Dashed lines indicate previously unresolved relationships.
(B) Relative frequencies of haplogroups L0, L1, L5, L2, L3, M, and N in different regions of Africa from mtDNA d-loop and mtDNA coding region SNPs from previous studies.
(C) Relative frequencies of haplogroups L0, L1, and L5 subhaplogroups (excluding L2 and L3) in different regions of Africa from mtDNA d-loop and mtDNA coding region SNPs from previous studies. Haplogroup frequencies from previously published studies include East Africans (Ethiopia [Rosa et al. 2004], Kenya and Sudan [Watson et al. 1997; Rosa et al. 2004]), Mozambique (Pereira et al. 2001; Salas et al. 2002), Hadza (Vigilant et al. 1991), and Sukuma (Knight et al. 2003); South Africans (Botswana !Kung [Vigilant et al. 1991]); Central Africans (Mbenzele Pygmies [Destro-Bisol et al. 2004], Biaka Pygmies [Vigilant et al. 1991], and Mbuti Pygmies [Vigilant et al. 1991]); West Africans (Niger, Nigeria [Vigilant et al. 1991; Watson et al. 1997]; and Guinea [Rosa et al. 2004]). L1*, L2*, and L3* from previous studies indicate samples that were not further subdivided into subhaplogroups.
--Norman A. Johnson (2007) Darwinian Detectives: Revealing the Natural History of Genes and Genomes pg100
quote:Genetic evidence of an early exit of Homo sapiens sapiens from Africa through eastern Africa
The mitochondrial haplogroup M, first regarded as an ancient marker of East-Asian origin4, 5, has been found at high frequency in India6 and Ethiopia7, raising the question of its origin.(A haplogroup is a group of haplotypes that share some sequence variations.) Its variation and geographical distribution suggest that Asian haplogroup M separated from eastern-African haplogroup M more than 50,000 years ago.
Two other variants (489C and 10873C) also support a single origin of haplogroup M in Africa.
These findings, together with the virtual absence of haplogroup M in the Levant and its high frequency in the South-Arabian peninsula, render M the first genetic indicator for the hypothesized exit route from Africa through eastern Africa/western India. This was possibly the only successful early dispersal event of modern humans out of Africa.
quote:In modern humans, this elongation is a pattern characteristic of warm-adapted populations, and this physique may be an early Cro-Magnon retention from African ancestors. Similar retentions may be observed in certain indices of facial shape ...
--Encyclopedia of Human Evolution and Prehistory: Second Edition by Eric Delson
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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Do you know of a well working SNP database? None of those I have found works properly or gives the requested criteria.
You are making this too complicated. You simply have to be mindful of various studies that claim to do world-wide sampling, observe trends in frequency estimations, and extrapolate geographical distribution from that; some apply maps of continents to aid in this.
Y-search databases are more useful for locating information for STR profiles, for which you'll have to be familiar with standard nomenclature applied to various Y segments/loci.
quote:This argument I found, what do you think of it? I understand some of it was captured already. But anyway...
quote:Haplogroup T
K2-M70 is believed to have originated in Asia after the emergence of the K-M9 polymorphism (45–30 ky) (Underhill et al. 2001a). As deduced from the collective data (Underhill et al. 2000; Cruciani et al. 2002; Semino et al. 2002; present study), K2-M70 individuals, at some later point, proceeded south to Africa. While these chromosomes are seen in relatively high frequencies in Egypt, Oman, Tanzania, Ethiopia, they are especially prominent in the Fulbe 18%( [Scozzari et al. 1997, 1999])"
Haplogroup T (M70, M184, M193, M272) is found in an insignificant majority of Kurru, Bauris & Lodha in South Asia; and in a significant minority of Rajus and Mahli in South Asia; Somalis, southern Egyptians and Fulbe in north Cameroon; Chian Greeks, Saccensi/Sicilians, Eivissencs / Ibizans and Northeastern Portuguese Jews in Europe; and Zoroastrians, Bakhtiaris in the Middle East.
More of a summary than an argument. It doesn't really challenge any of the specifics I laid out earlier for the haplogroup (T, formerly K2), in response to allegations made in Mendez et al.'s (2011) analysis. I observe data, not merely what some researcher "believes" could have happened. That data suggests that the jury is still out, and does not rule out an African origin.
quote: The estimates of their dates overlap (around fifth thousand years ago) and they both probably lived in northeast Africa. Africa? Yes, Africa. Although nearly all EUrasian mtDNA and Y chromosomes currently existing can be traced back to L3 and M168 respectively, M168 and L3 also had African descendants."
--Norman A. Johnson (2007) Darwinian Detectives: Revealing the Natural History of Genes and Genomes pg100
quote:Y-DNA haplogroup A contains lineages deriving from the earliest branching in the human Y chromosome tree. The oldest branching event, separating A0-P305 and A1-V161, is thought to have occurred about 140,000 years ago. Haplogroups A0-P305, A1a-M31 and A1b1a-M14 are restricted to Africa and A1b1b-M32 is nearly restricted to Africa. The haplogroup that would be named A1b2 is composed of haplogroups B through T. The internal branching of haplogroup A1-V161 into A1a-M31, A1b1, and BT (A1b2) may have occurred about 110,000 years ago. A0-P305 is found at low frequency in Central and West Africa. A1a-M31 is observed in northwestern Africans; A1b1a-M14 is seen among click language-speaking Khoisan populations. A1b1b-M32 has a wide distribution including Khoisan speaking and East African populations, and scattered members on the Arabian Peninsula.
Y-DNA haplogroup B, like Y-DNA haplogroup A, is seen only in Africa and is scattered widely, but thinly across the continent. B is thought to have arisen approximately 50,000 years ago. These haplogroups have higher frequencies among hunter-gather groups in Ethiopia and Sudan, and are also seen among click language-speaking populations. The patchy, widespread distribution of these haplogroups may mean that they are remnants of ancient lineages that once had a much wider range but have been largely displaced by more recent population events.
quote:Some geographic structuring is seen between the sub-groups B2a (B-M150) and B2b (B-M112). Sub-group B2b is seen among Central African Pygmies and South African Khoisan. Sub-group B2a is seen among Cameroonians, East Africans, and among South African Bantu speakers. B2a1a (B-M109) is the most commonly seen sub-group of B2a. About 2.3% of African-Americans belong to haplogroup B - with 1.5% of them belonging to the sub-group B2a1a.
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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posted
[QUOTE who="big mike M"]<quoted text> I don't even know what that is! O_o Have you really given up? LOL![/QUOTE]
According to Barros, now I am lying to say:
Yes, 5 U6 samples have been found in modern Egypt.
And 8 U6 samples have been found in modern Guinea-Bissau.
However, the attempt is still pathetic. Since:
No southwest Asian specific clades for M1 or U6 were discovered. U6 and M1 frequencies in North Africa, the Middle East and Europe do not follow similar patterns, and their sub-clade divisions do not appear to be compatible with their shared history reaching back to the Early Upper Palaeolithic. --Toomas Kivisild Divorcing the Late Upper Palaeolithic demographic histories of mtDNA haplogroups M1 and U6 in Africa
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