Hi All,
Trying to consolidate L research in here focussing on India/Pakistan/Afghanistan as there seems to be a dearth of research due to low distribution frequencies of this haplogroup worldwide
Will update this post with new research as papers come out
Latest & Rumours: Davidski: The message we're all getting, one way or another, is that L-M20 is by far the dominant marker in these Harappan remains. No one seems to know anything about any R1a in them, but R2 is a possibility.
http://eurogenes.blogspot.com.au/201...ks-thread.html
Snippet from Khana in this forum:
So I don't know if this has been discussed, but I heard from somebody who knows an archeologist at the Rakhigarhi site.
They are going to release a paper later in the year and 80-90% of the samples were y-HG L-M20.
Distribution
The greatest diversity of Y-DNA haplogroup L is centered around the northwestern part of the subcontinent, especially Balochistan. Makranis (southern Baloch) exhibit L1a and L1b both at a frequency of 10%. Balochis exhibit L1a at 20% and L1c at 4%. Lastly, the Brahui exhibit both L1a and L1c at 4%. The diversity is thus highest in this area. In Pakistan, L1a is as frequent as L1c, although the northern areas of Pakistan very much lean towards L1c
Attachment 19632
FTdna
L1a1 (originally L1) occurs mainly in Western India and Southern Pakistan.
L1a2 (originally L3) occurs mainly in northern regions of Pakistan and India but is also found as far west as the Chechen Republic.
L1b (originally L2) occurs in Western Asia and Europe.
L2 (formerly L*) has to date been observed in a small number of Project members whose ancestry is from all over Europe. It may trace its origins back to the Middle East or the Caucasus.
Earliest known L1
Admixture
M536324 I1658 M182163 I1656 M930063 RISE423 M691697 RISE407 Modern
Armenia EBA Armenia MLBA Armenia MBA Armenia LBA Armenian
Run time 8.22 Run time 8.42 Run time 6.24 Run time 3.92 Run time
S-Indian 0.27 S-Indian - S-Indian - S-Indian - S-Indian 1
Baloch 25.53 Baloch 26.71 Baloch 23.13 Baloch 28.22 Baloch 18
Caucasian 56.75 Caucasian 42.8 Caucasian 38.66 Caucasian 30.75 Caucasian 57
NE-Euro 4.79 NE-Euro 16.99 NE-Euro 18.57 NE-Euro 24.77 NE-Euro 3
SE-Asian - SE-Asian - SE-Asian - SE-Asian - SE-Asian -
Siberian - Siberian - Siberian 0.54 Siberian - Siberian -
NE-Asian - NE-Asian - NE-Asian - NE-Asian - NE-Asian -
Papuan - Papuan - Papuan 0.92 Papuan - Papuan -
American - American 0.12 American 1.3 American 1.54 American
Beringian - Beringian - Beringian 0.59 Beringian - Beringian -
Mediterranean 5.88 Mediterranean 9.14 Mediterranean 9.34 Mediterranean 6.98 Mediterranean 8
SW-Asian 6.45 SW-Asian 4.23 SW-Asian 4.94 SW-Asian 6.38 SW-Asian 13
San - San - San - San - San -
E-African - E-African - E-African - E-African - E-African -
Pygmy - Pygmy - Pygmy - Pygmy - Pygmy -
W-African 0.33 W-African - W-African 1.99 W-African 1.36 W-African
The beginning of the Bronze Age in the southern Caucasus has been thought to coincide with theappearance of the Kura Araxes (KA) culture around 3500
CAL B.C.
KA artifacts are known not only from thesouthern Caucasus but also from sites in Anatolia, Iran, and the Levant. Recent discoveries from Areni-1Cave in the Vayots Dzor region of Armenia demonstrate that the origin of the distinctive KA artifactassemblage lies in the Late Chalcolithic of the late 5th to early 4th millennia
B.C
Data collected during the 2007 excavations of Areni-1 Cave enable the story of a Late Chalcolithic– Early Bronze Age population to be told in greaterdetail for the southern Caucasus,
Areni-1 is neither typical nor represen-tative of the Late Chalcolithic of the southernCaucasus as a whole, but it nevertheless provides anunusual and exciting opportunity to broaden ourunderstanding of the time period.
http://www.academia.edu/1462570/Aren...thern_Caucasus
Concerning haplogroup L, L1c-M357 is significantly higher in Burusho and Kalash (15% and 25%) than in other populations. L1a-M76 is most frequent in Balochi (20%), and is found at lower levels in Kyrgyz, Pashtun, Tajik, Uzbek and Turkmen populations.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3799995/
The Y-lineages observed in the present study may suggest two major episodes of migrations: One carried J2 and to some extent L and G with the Neolithic farmers (Underhill et al. 2001)
The synthesis of Y-genealogy and estimated diversity of several clades demonstrated that North Indians carry three Y-lineages, one derived from Central Asia or West Eurasia (R1a1★, R1b1b2★ and R2 haplogroups), one derived from the Middle East (J2★, Shia-specific E1b1b1, and to some extent G★ and L★ haplogroups), and the indigenous Indian Y-lineage marked by H1★, F★, O★ and C★ without the M217 transversion.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2755252/
This is the largest haplogroup in the Jat sample population. It is present in the Indian population at an overall frequency of about 7–15% (Basu et al., 2003; Cordaux et al., 2004). Genetic studies suggest that this may be one of the original haplogroups of the creators of Indus Valley Civilization (McElreavey and Quintana-Murci, 2005; Sengupta et al., 2006). It has a frequency of about 28% in western Pakistan and Baluchistan, from where the agricultural creators of this civilization emerged (Qamar et al., 2002). The origins of this haplogroup can be traced to the rugged and mountainous Pamir Knot region in Tajikistan (Wells, 2007).
Haplogroup India Pakistan Total Percent Marker Age (kya) Geographic origins
L 110 1 111 36.8% M11 ~25–30 Pamir Knot region (Hindu Kush, Tian Shan, Himalayas) in Tajikistan, Indus Valley
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5611447/
The major components (haplogroups E3b, G, J, I, L, N, K2, and R1; 94.1%) are shared with European and neighboring Near Eastern populations and contrast with only a minor share of haplogroups related to Central Asian (C, Q and O; 3.4%), Indian (H, R2; 1.5%) and African (A, E3*, E3a; 1%) affinity.
haplogroups G1 and L show affinities with south Caucasus populations in their geographic distribution as well as STR motifs
https://www.ncbi.nlm.nih.gov/pubmed/14586639
India
They are, in descending frequency order, HGs H and its subclades H1*, H1c, H1a, and H2 (26.4%); R1a1-M17 (15.8%); O2a-M95 (14.6%); R2-M124 (9.3%); J2-M172 (9.1%); O3e-M134 (8.0%); L1-M76 (6.3%); and F*-M89 (5.2%).
HGs L1-M76 and H1-M52 have peak variance distributions in the Maharashtra region in coastal western India.
Pakistan
In Pakistan, nine HGs exceed 5% frequency and account for 83.6% of the samples. They include HGs R1a1-M17 (24.4%), L*-M20 (13.1%), J2-M172 (11.9%), R2-M124 (7.4%), R1b-P25 (7.4%), G-M201 (6.3%), C3-M217 (6.8%), H-M69* (6.3%), and L1-M76 (5.1%).
The new L3-M357 subclade accounts for 86% of L-M20(xL1xL2) chromosomes in Pakistan but occurs only sporadically (3/728) in India.
The phylogeography and the similarity of microsatellite variation of HGs R1a1 and R2 to L1-M76 in South Asian tribes argues that they likely share a common demographic history.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1380230/
Hap 28 = Hap L in this study
haplogroup 28 was present in all except the Hazaras and the Kashmiris
The fifth haplogroup that is common in Pakistan, haplogroup 28, differs from all the others in its distribution. Within Pakistan, it made up 14% of our sample and was present in all but two populations (both of which had very small sample sizes), so it is both common and widespread. Outside Pakistan and the nearby countries, however, it is rare. It has been reported in India (30%; present in 3/3 populations), Tajikistan (10%; present in 5/6 populations), and Uzbekistan (3%; present in 10/13 populations), but it is rare in Russia (0.4%; present in 1/6 populations) and the Caucasus (1.4%; present in 1/6 populations (Wells et al. 2001) and has not been found at all in China or Mongolia (unpublished observations). BATWING estimates of the TMRCA of the Pakistani haplogroup 28 chromosomes were ∼7,000 (4,000–14,000) years (table 8). Thus, within this time period, the Pakistani populations have diverged from a common ancestral population or have experienced considerable male gene flow between themselves or from a common source. Since the estimated age corresponds to the early Neolithic period, the spread of this lineage might be associated with the local expansion of farmers.
Pakistan Parsi
Given the small effective population size of the Parsis, the closeness of their match to the Iranian data may be fortuitous, and the presence of haplogroup 28 chromosomes at 18% (4% in Iran; Wells et al. 2001) suggests some gene flow from the surrounding populations. The TMRCA for the Parsi-specific cluster in the haplogroup 28 networks was 1,800 (600–4,500) years (table 8), consistent with the migration of a small number of lineages from Iran.
Modern Greeks show a moderately high frequency of haplogroup 21 (28%; Rosser et al. 2000), but this haplogroup was not seen in either the Burusho or the Kalash sample and was found in only 2% of the Pathans, whereas the local haplogroup 28 was present at 17%, 25%, and 13%, respectively.
haplogroup 28 is present at 13% in the Pathans, so no support for a Jewish origin is found, and the admixture estimate was 0%
This difference and the high frequency of haplogroup 28 in the Baluch (29%) make a predominantly Syrian origin for their Y chromosome unlikely
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC447589/
Cordaux et al. (19) defined, heuristically, a package of haplogroups (J2, R1a, R2, and L) to be associated with the migration of IE people and the introduction of the caste system to India, again from Central Asia, because they had been observed at significantly lower proportions in South Indian tribal groups, with the high frequency of R1a among Chenchus of Andhra Pradesh (6) considered as an aberrant phenomenon (19).
The near absence of L lineages within the IE speakers from Bihar (0%), Orissa (0%), and West Bengal (1.5%) further suggests that the current distribution of Y haplogroups in India is associated primarily with geographic rather than linguistic or cultural determinants.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347984/
Haplogroup L-M20 is found predominantly in India and Pakistan (15%) and has tentatively been associated with the expansion of farming, thus implying a nonIndian origin
These estimates are based on the frequencies of seven haplogroups (which account for >80% of Indian Y chromosomes), assuming that haplogroups H-M52, O-M95, and F-M89 have indigenous origins, whereas J-M172, L-M20, R-M17 and R-M124 have nonindigenous origins given their putative phylogeography (see text).
http://www.sciencedirect.com/science...60982204000405
The spread of clade L is confined mostly to southern, central, and western Asia (table 3). Being virtually absent in Europe, it is also found irregularly and at low frequencies in populations of the Middle East and southern Caucasus (Nebel et al. 2001; Scozzari et al. 2001; Weale et al. 2001; Wilson et al. 2001). It occurs in Pakistan at a frequency of 13.5% (Qamar et al. 2002). In Indians, all Y chromosomes that had the derived allele at M11, M20, and M61 also shared M27 specific to its subclade L1.
Interestingly, mtDNA haplogroup U7 (Richards et al. 2000), like Y-chromosomal clade L (Underhill et al. 2000), is also found, though at low frequencies, in western Asia and occasionally in Mediterranean Europe. The differences in STR modal haplotypes of the L clade between the Caucasus (Weale et al. 2001) and India point to their independent expansions from two distinct founder populations.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC379225/
Frequency of haplogroup L- (M11/M20), which is also proposed to be associated with the expansion of farming, was 13.7%, with the highest occurrences in caste populations. A similar frequency of L lineage has previously been reported from Pakistan [21]. An M27 mutation that defined the subclad L1 was found in all the L-M11 samples in the present study. This is in accordance with the previous studies that M27 characterizes the Indian and Pakistani lineages, which is absent in their Turkish counterparts [22]. This result, together with the differences in STR nodal haplotypes of the L clad between the Caucasus and Indian populations [4], and matches in the six STR loci typed between Turkish and Armenians [22], lead to the assumption that the Indian and Pakistani L lineages might have originated from a distinct founder population. This view is supported by the much lower STR variance of the L haplogroups compared with the other Indian Y-lineages, observed in the present study.
https://bmcgenet.biomedcentral.com/a...1471-2156-7-42
The spread of haplogroup L-M11 lineages is largely re-stricted to populations of the south Caucasus (Weale et al.2001), Middle East (Nebel et al. 2001b), Pakistan (Qamar et al. 2002) and India (Kivisild et al. 2003). InterestinglyTurkish L lineages lack the M27 mutation that character-izes Indian and Pakistani L lineages.
http://www.academia.edu/5557321/Exca...ta_in_Anatolia
From Rukha
Sayyid Ajjal is the ancestor of many Muslims in areas all across China. And one of his descendants is the famous Navigator of Ming Dynasty, Zheng He, who led the largest armada in the world of 15th century. The origin of Sayyid Ajjal's family remains unclear although many studies have been done on this topic of Muslim history. In this paper, we studied the Y chromosomes of his present descendants, and found they all have haplogroup L1a-M76, proving a southern Persian origin.
http://dienekes.blogspot.com.au/2013...mosome-of.html
Bosch et al. [14] studied Y chromosome variation in the Balkans, including a sample of 41 Greeks. Greeks belonged to the major Caucasoid haplogroups. The identity of the K*(xP) chromosomes is not clear, but they could belong to the minor Caucasoid haplogroups K2 and L which have been previously observed in Greeks, or to other K-related lineages.
http://carswell.com.au/wp-content/do...n-analysis.pdf
L-M20 was found in 51% of Syrians from Raqqa, a northern Syrian city in which its previous inhabitants have been wiped out by the Mongol genocides and repopulated in recent times by local Bedouin populations and Chechen war refugees from Russia (El-Sibai 2009)
Y-chromosome haplogroup (L-M20) has a high mean frequency of 14% in Pakistan and so differs from all other haplogroups in its frequency distribution. L-M20 is also observed, although at lower frequencies, in neighbouring countries, such as India, Tajikistan, Uzbekistan and Russia. Both the frequency distribution and estimated expansion time (7000 YBP) of this lineage suggest that its spread in the Indus Valley may be associated with the expansion of local farming groups during the Neolithic period (Qamar et al. 2002).
http://dienekes.blogspot.com.au/2005...us-valley.html
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Originally Posted by BMG
