haplogroup Q-M242

Haplogroup Q or Q-M242 is a Y-chromosome DNA haplogroup. It has one primary subclade, Haplogroup Q1 (L232/S432), which includes numerous subclades that have been sampled and identified in males among modern populations.

Q-M242 is the predominant Y-DNA haplogroup among Native Americans and several peoples of Central Asia and Northern Siberia.

Origins

Haplogroup Q-M242 is one of the two branches of P1-M45, the other being R-M207. P1, as well as R* and Q* were observed among Ancient North Eurasians, a deeply European hunter-gatherer related population.

Q-M242 is believed to have arisen around the Altai Mountains area (or South Central Siberia), approximately 17,000 to 31,700 years ago. However, the matter remains unclear due to limited sample sizes and changing definitions of Haplogroup Q: early definitions used a combination of the SNPs M242, P36.2, and MEH2 as defining mutations.

Technical specification of mutation

The polymorphism, “M242”, is a C→T transition residing in intron 1 (IVS-866) of the DBY gene and was discovered by Mark Seielstad et al. in 2003.
The technical details of M242 are:

:Nucleotide change: C to T
:Position (base pair): 180
:Total size (base pairs): 366
:Forward 5′→ 3′:
:Reverse 5′→ 3′:

Subclades

In Y chromosome phylogenetics, subclades are the branches of a haplogroup. These subclades are also defined by single-nucleotide polymorphisms (SNPs) or unique-event polymorphisms (UEPs). Haplogroup Q-M242, according to the most recent available phylogenetics has between 15 and 21 subclades. The scientific understanding of these subclades has changed rapidly. Many key SNPs and corresponding subclades were unknown to researchers at the time of publication are excluded from even recent research. This makes understanding the meaning of individual migration paths challenging.

Phylogenetic trees

There are several confirmed and proposed phylogenetic trees available for haplogroup Q-M242. The scientifically accepted one is the Y Chromosome Consortium (YCC) one published in Karafet 2008 and subsequently updated. A draft tree that shows emerging science is provided by Thomas Krahn at the Genomic Research Center in Houston, Texas. The International Society of Genetic Genealogy (ISOGG) also provides an amateur tree.

The 2015 ISOGG tree

The subclades of Haplogroup Q-M242 with their defining mutation (s), according to the 2015 ISOGG tree are provided below. The first three levels of subclades are shown. Additional detail is provided on the linked branch article pages.

*Q-M242 M242
**Q-P36.2 P36.2, L232, L273, L274 (Q1)
***Q-MEH2 MEH2 (Q1a)
****Q-F1096 F1096, F1215 (Q1a1)
***** Q-NWT01 NWT01 (Q1a1a)
****** Q-M120 M120, M265/N14 (Q1a1a1)
***** Q-M25 M25, M143 (Q1a1b)
****** Q-L712 L712 (Q1a1b1)
**** Q-M346 L56, L57, M346, L528 (Q1a2)
***** Q-L53 L53 (Q1a2a)
****** Q-L54 L54 (Q1a2a1)
******* Q-CTS11969 CTS11969, M930 (Q1a2a1a)
******** Q-M3 M3 (Q1a2a1a1)
********* Q-M19 M19 (Q1a2a1a1a)
******** Q-L804 L804 (Q1a2a1a2)
******* Q-CTS1780 CTS1780, M981, M971, Z780 (Q1a2a1b)
******* Q-L330 L330 (Q1a2a1c)
***** Q-F835 F835, L940 (Q1a2b)
***** Q-F1161 F1161
****** Q-L527 L527
*** Q-L275 L275, L314 (Q2)
**** Q-M378 M378/Page100, L214, L215/Page82 (Q2a)
***** Q-FGC1774 FGC1774, Y2016 (Q1b1a)
****** Q-245 L245 (Q1b1a1)
**** Q-Y1150 Y1150 (Q1b2) (Q1b-L68)

The Genomic Research Center draft tree

Below is a 2012 tree by Thomas Krahn of the Genomic Research Center. The first three levels of subclades are shown. Additional detail is provided on the linked branch article pages.

* P-M45
**Q-M242 M242
*** P36.2, L232, L273.1, L274.1
**** MEH2, L472, L528
***** M120, N14/M265
***** M25, M143, L714, L716
***** M346, L56, L57, L474, L892, L942
***** P89.1
***** NWT01
**** L275, L314, L606, L612
***** M378, L214, L215

The Y Chromosome Consortium tree

This is the 2008 tree produced by the Y Chromosome Consortium (YCC). Subsequent updates have been quarterly and biannual. The current version is a revision of the 2010 update. The first three levels of subclades are shown. Additional detail is provided on the linked branch article pages.

* P-M45
**Q-M242 M242
***Q-P36.2 P36.2
**** Q-MEH2 MEH2
****** Q-M120 M120, N14, M265
****** Q-M25 M25, M143
***** Q-M346 L56, L57, M346
****** Q-P89.1 P89.1
**** Q-L275 L275
***** Q-M378 L214, L215, M378

Phylogenetic variants

The subclade (under Q-MEH2) proposed by Sharma (2007), which shows polymorphism (ss4bp, rs41352448) at 72,314 position of human arylsulfatase D pseudogene, is not represented in any current trees under Q-MEH2. The most plausible explanation for this could be an ancestral migration of individuals bearing Q-MEH2 to the Indian subcontinent followed by an autochthonous differentiation to Q-ss4bp.

Distribution

Americas

Several branches of haplogroup Q-M242 have been predominant pre-Columbian male lineages in indigenous peoples of the Americas. Most of them are descendants of the major founding groups who migrated from Asia into the Americas by crossing the Bering Strait. These small groups of founders must have included men from the Q-M346, Q-L54, Q-Z780, and Q-M3 lineages. In North America, two other Q-lineages also have been found. These are Q-P89.1 (under Q-MEH2) and Q-NWT01. They may have not been from the Beringia Crossings but instead come from later immigrants who traveled along the shoreline of Far East Asia and then the Americas using boats.

It is unclear whether the current frequency of Q-M242 lineages represents their frequency at the time of immigration or is the result of the shifts in a small founder population over time. Regardless, Q-M242 came to dominate the paternal lineages in the Americas.

North America

In the indigenous people of North America, Q-M242 is found in Na-Dené speakers at an average rate of 68%. The highest frequency is 92.3% in Navajo, followed by 78.1% in Apache, 87% in SC Apache, and about 80% in North American Eskimo (Inuit, Yupik)–Aleut populations. (Q-M3 occupies 46% among Q in North America)

On the other hand, a 4000-year-old Saqqaq individual belonging to Q1a-MEH2* has been found in Greenland. Surprisingly, he turned out to be genetically more closely related to Far East Siberians such as Koryaks and Chukchi people rather than Native Americans. Today, the frequency of Q runs at 53.7% (122/227: 70 Q-NWT01, 52 Q-M3) in Greenland, showing the highest in east Sermersooq at 82% and the lowest in Qeqqata at 30%.

Q-M242 is estimated to occupy 3.1% of the whole US population in 2010:

Mesoamerica & South America

Haplogroup Q-M242 has been found in approximately 94% of Indigenous peoples of Mesoamerica and South America.

The frequencies of Q among the whole male population of each country reach as follows:
* 61% in Bolivia.
* 51% in Guatemala,
* 40.1% (159/397) to 50% in Peru
* 37.6% in Ecuador,
* 37.3% (181/485) in Mexico (30.8% (203/659) among the specifically Mestizo segment)
* 31.2% (50/160) in El Salvador,
* 15.3% (37/242) to 21.8% (89/408) in Panama,
* 16.1% in Colombia,
* 15.2% (25/165) in Nicaragua,
* 9.7% (20/206) in Chile,
* 5.3% (13/246 in 8 provinces in northeastern, central, southern regions) to 23.4% (181/775 in 8 provinces in central-west, central, northwest regions) in Argentina,
* 5% in Costa Rica,
* 3.95% in Brazil, and so on.

Asia

Q-M242 originated in Asia (Altai region), and is widely distributed across it. Q-M242 is found in Russia, Siberia ( Kets, Selkups, Siberian Yupik people, Nivkhs, Chukchi people, Yukaghirs, Tuvans, Altai people, Koryaks, etc.), Mongolia, China, Uyghurs, Tibet, Korea, Japan, Indonesia, Vietnam, Thailand, India, Pakistan, Afghanistan, Iran, Iraq, Saudi Arabia, Turkmenistan, Uzbekistan, and so on. (For details, see below.)

North Asia

In Siberia, the regions between Altai and Lake Baikal, which are famous for many prehistoric cultures and as the most likely birthplace of haplogroup Q, exhibit high frequencies of Q-M242. In a study (Dulik 2012), Q-M242 (mostly Q-M346 including some Q-M3) has been found in 24.3% (46/189: 45 Q-M346, 1 Q-M25) of all Altaian samples. Among them, Chelkans show the highest frequency at 60.0% (15/25: all Q-M346), followed by Tubalars at 41% (11/27: 1 Q-M25, 10 Q-M346) and Altaians-Kizhi at 17% (20/120).
In a former study, Q-M242 is found in 4.2% of southern Altaians and 32.0% of northern Altaians with the highest frequency of 63.6% in Kurmach-Baigol (Baygol). The frequency reaches 13.7% (20/146) in the whole samples. In another study, the frequency rises up to 25.8% (23/89: all Q-M346) in Altaians. Based on the results of these studies, the average frequency of Q-M242 in Altaians is about 21%.

Tuva, which is located on the east side of Altai Republic and west of Lake Baikal as well as on the north side of Mongolia, shows higher frequency of Q-M242. It is found in 14%KHARKOV, Vladimir Nikolaevich, "СТРУКТУРА И ФИЛОГЕОГРАФИЯ ГЕНОФОНДА КОРЕННОГО НАСЕЛЕНИЯ СИБИРИ ПО МАРКЕРАМ Y-ХРОМОСОМЫ," ''Genetika'' 03.02.07 and "АВТОРЕФЕРАТ диссертации на соискание учёной степени доктора биологических наук," Tomsk 2012
/ref>~38.0% (41/108) of Tuvans. Also, Todjins (Tozhu Tuvans) in eastern Tuva show the frequency at ≤22.2% (8/36 P(xR1))~38.5% (10/26, all Q-M346(xM3)). So, the average frequency of Q-M242 among Tuvans-Todjins in Tuva Republic is about 25%. Haplogroup Q-M242 has been found in 5.9% (3/51) of a sample of Tuvans from the village of Kanasi, 9.8% (5/51) of a sample of Tuvans from the village of Hemu, and 62.5% (30/48) of a sample of Tuvans from the village of Baihaba in northern Xinjiang near the international border with Altai Republic.

In Siberian Tatars, the Ishtyako-Tokuz sub-group of Tobol-Irtysh group has a frequency of Q-M242 at 38%.Пять генофондов пяти субэтносов сибирских татар
/ref>

The highest frequencies of Q-M242 in Eurasia are witnessed in Kets (central Siberia) at 93.8% (45/48) and in Selkups (north Siberia) at 66.4% (87/131). Russian ethnographers believe that their ancient places were farther south, in the area of the Altai and Sayan Mountains (Altai-Sayan region). Their populations are currently small in number, being just under 1,500 and 5,000 respectively. In linguistic anthropology, the Ket language is significant as it is currently the only surviving one in the Yeniseian language family which has been linked by some scholars to the Native American Na-Dené languages and, more controversially, the language of the Huns. (See: L. Lieti, E. Pulleybank, E. Vajda, A. Vovin, etc.)
Q-M346 is also found at lower rates in Sojots (7.1%, Q-M346), Khakassians (6.3%, Q-M346), Kalmyks (3.4%, Q-M25, Q-M346) and Khanty, and so on.

In far eastern Siberia, Q-M242 is found in 35.3% of Nivkhs (Gilyaks) in the lower Amur River, and 33.3% of Chukchi people and 39.2% of Siberian Yupik people in Chukotka (Chukchi Peninsula). The SNPs used in the paper are P-M45, R1a1-M17, Q1a2-M3, and other xP-M45 SNPs. And the author mentions that, among ethnic groups in the paper, R1-M173 is harbored only in some eastern Siberian Udegeys and Koryaks and Native Americans. Also, R2 (distributed in India and its neighbours) cannot be found in far east Siberia. Thus, P-M45 except some samples mentioned above virtually means Q-M242 (xM3). In the paper, 35.3% of Nivkhs and 20.8% of Chukchi people and 18.2% of Siberian Eskimos are shown in P-M45, and 12.5% of Chukchis and 21.2% of Siberian Eskimos are in Q-M3. All of them can be estimated to be in haplogroup Q. It is found in 30.8% of Yukaghirs who live in the basin of the Kolyma River, which is located northwest of Kamchatka. It is also found in 15% (Q1a* 9%, Q-M3 6%) of Koryaks in Kamchatka.

East Asia

In some studies, various subgroups of Q-M242 are observed in Mongolia. Q1a2-M346 (mostly Q-L330) occupies 1.4~3.1% of Mongols (1/2~2/3 among Q samples), followed by Q1a1a1-M120 (0.25~1.25%), Q1a1b-M25 (0.25~0.63%), Q1b-M378. In another study, Q is found in 4% of Mongols. Karafet ''et al.'' (2018) found Q-L54(xM3) in 2.7% (2/75) and Q-M25 in another 2.7% (2/75) for a total of 5.3% (4/75) haplogroup Q Y-DNA in a sample of Khalkha Mongols from Ulaanbaatar, Mongolia. Based on these studies, the average frequency of Q-M242 in Mongols is estimated to be about 4~5%.

However, most of Q-M242 people in East Asia belong to subclade Q-M120, which distributes most intensively across northern China (the provinces of which the capitals locate northern to Huai River-Qin Mountains line). Q-M242 ranged from 4~8% in northwest China (Xinjiang, Gansu, Shaanxi), north China (Shanxi, Hebei), central China (Henan), and upper east China (Shandong) to 3~4% in northeast China. The average frequency of Q-M242 in northern China is around 4.5%. However, it decreases to about 2% in southern China. In a study published in 2011, researchers have found Q-M242 in 3.3% (12/361) of the samples of unrelated Han-Chinese male volunteers at Fudan University in Shanghai with the origins from all over China, though with the majority coming from east China. In another study published in 2011, Hua Zhong ''et al.'' found haplogroup Q-M242 in 3.99% (34/853, including 30/853 Q-M120, 3/853 Q-M346, and 1/853 Q-M25) of a pool of samples of Han Chinese from northern China and 1.71% (15/876, including 14/876 Q-M120 and 1/876 Q-M346) of a pool of samples of Han Chinese from southern China. Q1a1-M120 is unique to East Asians. It is not found in South east Asia except with low diversity in Y-STR among southern Han Chinese indicating it spread during the Neolithic with Han Chinese culture to southern China from northern China. Q1a3*-M346 is only found among Hui and southern Han Chinese in South East Asia in southern China but not found in non-Han indigenous peoples at all. It came from northern China (north east Asia) with the Han. Only Native Americans have Q1a3a-M3, which is a descendant haplogroup of Q1a3*-M346. The Americas was populated by migrants from Central Asia in prehistoric times. Q1a1 is attested in over 3,000 year old Han Chinese ancestral remains in the Shang and Zhou dynasties from the Hengbei archeological site. Modern northern Han Chinese Y haplogroups and mtdna match those of ancient northern Han Chinese ancestors 3,000 years ago from the Hengbei archeological site. 89 ancient samples were taken. Y haplogroups O3a, O3a3, M, O2a, Q1a1, and O* were all found in Hengbei samples.

Q-M242 has been found with notable frequency in some samples of Uyghurs: 15.38% (22/143, including 6/143 Q-M378, 5/143 Q-P36.2*, 4/143 Q-M120, 4/143 Q-M346, 1/143 Q-M25) of a sample of Uyghurs from the Turpan area (吐鲁番地区),Lu Yan (2011), "Genetic Mixture of Populations in Western China." Shanghai: Fudan University, 2011: 1-84. (Doctoral dissertation in Chinese: 陆艳, “中国西部人群的遗传混合”, 上海：复旦大学，2011: 1-84.) 7.9% (6/76, including 2/76 Q1b1-L215/Page82/S325, 1/76 Q1a2-M346*, 1/76 Q1a1a1-M120, 1/76 Q1a2a1c-L330*, 1/76 Q1a2a1c1-L332) of a sample of Dolan Uyghurs (刀郎人) from Horiqol Township of Awat County, and 7.74% (37/478, including 24/478 Q-M346, 7/478 Q-P36.2*, 5/478 Q-M120) of a sample of Uyghurs from the Hotan area (和田地区). However, other studies have found haplogroup Q in much smaller percentages of Uyghur samples: 3.0% (2/67) Q-P36 Uygur, 1.6% (1/64) Q-M120 Lop Uyghur (罗布人). Haplogroup Q was not observed in a sample of 39 Keriyan Uyghurs (克里雅人) from the village of Darya Boyi, located on the Keriya River deep in the Taklamakan Desert.

Haplogroup Q was observed in 3.2% (5/156 : 2 Q-M120, 3 Q-M346) of males in Tibet in one study and in 1.23% (29/2354) of males in Tibet in another study, but this haplogroup was not observed in a sample of males from Tibet (''n''=105) in a third study.

It is found in about 1.9% of South Koreans, showing the highest frequency in Seoul and Gyeonggi Province at 2.7% and decreasing ones to the south (Kim 2010). It has been found in about 0.3% of JapanesePeter A. Underhill, Peidong Shen, Alice A. Lin, ''et al.'' (2000), "Y chromosome sequence variation and the history of human populations." ''Nature Genetics'', Volume 26, November 2000. (with known examples from Shizuoka and Saitama) and in 0.3%~1.2% of Taiwanese.

Subclade Q1b-M378 is also found in China and its neighboring countries at very low frequencies. It exists throughout all Mongolia, with rare examples in Japan.

Southeast Asia

Haplogroup Q shows low frequencies in Southeast Asia. In a study, the frequencies of haplogroup Q is 5.4% (2/37) in Indonesia, 3.1% (2/64) in the Philippines, 2.5% (1/40) in Thailand. However, other studies show 0% or near 0% frequencies in those countries.

In the case of Vietnam, the frequency is 7.1% in one study of a sample of Vietnamese reported to be from southern Vietnam and 4.3% in a sample of Kinh people from Ho Chi Minh City in southern Vietnam, but 0% or under 1% in other studies in which samples have been collected in Hanoi in northern Vietnam. So, it is hard to define average frequencies. However, Macholdt ''et al.'' (2020) have tested a sample of fifty Kinh people from northern Vietnam (all but one of whom are from the Red River Delta region, and 42 of whom are from Hanoi) and found that two of them (4%) belong to Q-M120.Enrico Macholdt, Leonardo Arias, Nguyen Thuy Duong, ''et al.'', "The paternal and maternal genetic history of Vietnamese populations." ''European Journal of Human Genetics'' (2020) 28:636–645. https://doi.org/10.1038/s41431-019-0557-4

Only some regions and ethnic groups in the continent show high frequencies. Q-M242 is found in 2.8% (3/106, all Q-M346) in Myanmar, and all the Q samples are concentrated in 18.8% in Ayeyarwady (2/11) and 7.1% Bago (1/14) regions in southwest Myanmar. And, Q-M242 is found in 55.6% (15/27) in the Akha tribe in northern Thailand.

Central Asia

In Central Asia, the southern regions show higher frequencies of Q than the northern ones.

In the northern regions, Q-M242 is found in about 2%~6% (average 4%) of Kazakhs. A study published in 2017 found haplogroup Q Y-DNA in 3.17% (41/1294) of a large pool of samples of Kazakh tribes; however, haplogroup Q was concentrated in the members of the Qangly