MTDNA HAPLOGROUP U1A

In the literature, there is relatively little information about mtdna haplogroup U1a. While U is the second most common haplogroup in Europe (especially the subhaplogroup U5), U1a is instead more common in the Middle East. But I have not been able to find any good paper about it. Interestingly, I have found two other people who originate from Northern Tuscany (Garfagnana and Massa) and who are also U1a. Perhaps there is a cluster of U1a's in the region.

Haplogroup U is one of the many offshots of R. According to Achilli, U is estimated to be around 60,000 years old, that is, shortly after humans left Africa. Kiivisild (2006) gives a younger age for U, 45,000 year ago. U1 is a direct offshot of the U haplogroup, so it must have split from the other U subhaplogroups quite early. However, U1 and U1a are characterized by several mutations, which means that the common ancestor to all U1's must have been much later. The other U offshots are U5, U6, and the combined rest of U. U5 seems to have moved into Europe (possibly via Russia?), U6 went to North Africa, while U1 seems to have remained in the Middle East.

The small amount of data available clearly indicates that U1a has its highest frequencies in parts of the middle east. The haplogroup as a whole ranges from India (eg Kerala, Pakistan) to the Mediterranean and to the rest of Europe. It is extremely rare at the northern fringes of Europe (such as the UK of Scandinavia). Its sister clade U1b seems to mirror some of the distribution, though it is usually rarer: it doesn't seem to appear in India, and is clearly less common in the Mediterranean than U1a. However, there seems to be a little more U1b than U1a in certain parts of Eastern Europe.

Interestingly, including myself, mitosearch.org lists 3 U1a's from the northernmost part of Tuscany, with similarities in their HVR1. It is not clear how many Northern Tuscans there are on mitosearch, and no study exists on the mtdna of the area of Lucca and Massa (previous studies focused on Southern Tuscany, where the Etruscans lived. No U1a's so far, neither in the modern sample nor in the ancient skeletons studied). Presumably, there must be a larger number of U1a's around there. Also, in Italy, U1a seems to pop up especially in the South (though not only, I've seen people from a northern Alpine valley).

U1a is usually recognizable by the HVR motif (73-263-)285-16189-16249. Note that 16189-16249 are found also in other, totally unrelated, haplogroups (such as M1, F, B, L1, and others), which has occasionally generated incorrect haplogroup assignments when looking at HVR1 only. But as far as I know, 285T should confirm the assignment. (I have seen one possible case of no 285 mutation, whether a testing mistake or a backmutation I don't know.)

As shown by Achilli and Palanichamy (see below), the U1a tree includes:

• 11467, 12308, 12372 (at the root of the whole U)
• 285, 12879, 13104, 14070, 15148, 15594C, 16249 (at the root of both U1a and U1b)
• 2218,14364, 16183C (possibly), 16189.
• 4991, 6026, 7581 are present in most U1a's, except one sequence in Genbank. Therefore, these three mutations could identify a further subgroup of U1a. Phylotree.org uses the notation U1a'c for the whole group, and then U1a for those sequence with the three additional mutations.
• in addition, the usual mutations of the rCRS path, that is, 73, 263, 750, 1438, 2706, 4769, 7028, 8860, 15326.
• U1b, the sister clade, has instead some other mutations. In HVR1, in addition to 16249, it has usually 16311 and 16327 (though it seems to be absent in certain cases), in HVR2, in addition to 285, it has also 146. Unfortunately, there is only one full U1b sequence in Genbank, so it is not possible to characterize the group further.

• one characterized by 3591 and 13422 (which includes the Fraumene Sardinian sequences and the Palanichamy Indian ones. Phylotree.org calls it U1a1)
• one characterized by 15115 and 15217 (which Phylotree.org calls U1a3).

• My full mtdna, also available in Genbank, accession number EF692533. Note that I have done the test also with FTDNA. The results coincide except for 15671C, which FTDNA found and Argusbio did not.

Here is a list of references:

• Ian Logan has a collection of sequences, including many for haplogroup U. (At least 8 are U1a.) He also has extensive haplogroup trees.
• Ron Scott has some links to resources about haplogroup U (see under mtdna), including screen captures of Mitomap's trees and a list of full U sequences.
• Achilli et al.- Saami and Berbers: an unexpected mitochondrial DNA link - has a nice tree of haplogroup U, with U1a and U1b
• Phylogeny of Mitochondrial DNA Macrohaplogroup N in India by Palanichamy et al. has a (difficult to read) figure (figure 1) that characterizes the U1a people in her Indian sample. (She also includes a strange U1a sequence from another paper, which I believe has errors). Nothing particular is said about the group.
• Abu Amero et al. Eurasian and African mitochondrial dna influences in the Saudi Arabian population, BMC Evolutionary Biology 2007, and Abu Amero et al. Mitochondrial DNA structure of the Arabian peninsula (in particular the supplemental file) have tables summarizing the frequencies of many haplogroups, including U1a, in the Middle East. U1a reaches frequencies of 5% in certain parts of the Northern Middle East, such as Anatolia and Syria, and then seems to decrease from there.
• Where East meets West, by Quintana-Murci et al. shows frequencies of U1 in an India/Central Asian sample (may be most are U1a? who knows), around 5% or so in Turkey and the Caucasus.
• Tracing European Founder Lineages in the Near Eastern MTDNA pool by Richards et al. somehow connects U1 in Europe with a middle upper paleolithic expansion around 26K years ago. His sample (which uses also previous papers) shows a few U1a, mostly in the northern Middle East and the Mediterranean: among them, 7/218 in Turkey, 7/300 in Italy (but in a sample skewed towards the South), 7(/200?) in the Northern Caucasus, an 6/191 in Armenia.
• Richards et al. list some motifs to determine haplogroups.
• Unravelling migrations in the steppe by Lalueza-Fox et al. studies 30 or so ancient (3000 to 1500 years ago) skeletons from Kazakhstan and finds two belonging to U1, and most likely to U1a (they have 16189 16249 and 16183 16189 16249). The paper shows that Kazakhstan had only western Eurasian mtDNA in that period (which means that the eastern genetic imprint came later, with the Mongols and other similar groups).
• The Shen et al paper on the Samaritans mentioned above shows a few U1a's in the Middle East (e.g. 3/20 among Yemenite Jews, 2/20 among Palestinians).
• Ethiopian Mitochondrial DNA Heritage by Kivisild et al. apparently shows only two U1a (one one or two U1b) in a sample of Yemenites living in Kuwait, and none in Ethiopia, which suggests that U1a is more northern. (But as usual it is not clear if there is any particular selection in the Yemenite sample. Do they all come from one region?).
• Malyarchuk et al Mitochondrial DNA variability in Poles and Russians finds 2/200 U1a in Russians and none among the Poles.
• Helgason et al. (mtDNA and the Islands of the North Atlantic: Estimating the Proportions of Norse and Gaelic Ancestry) report fractions of U1 (ie including U1b) of .5 in Central Europe/Russia, 1.5 in France-Italy, and .2 in Spain.
• Fraumene et al. High Resolution Analysis and Phylogenetic Network Construction Using Complete mtDNA Sequences in Sardinian Genetic Isolates, Mol Biol Evol. 2006 Nov;23(11):2101-11 find two U1a in their Sardinian sample (out of 63).
• The data collected for the book Blood of the Isles by Sykes show only 5 or so (possible but unconfirmed) U1a's in the UK (in the Hebrides and Northern Isles), which confirms the lack of the haplogroup in the British isles, also noticeable from the tiny number of British (or in general NW Europeans) in mitosearch.org.
• Kivisild et al - Deep common ancestry of Indian and Western-Eurasian mitochondrial DNA lineages - is an early contribution about haplogroup U in India and Eurasia.
• Natural radioactivity and human mitochondrial DNA mutations by Forster et al. shows data from a Kerala sample. Although no haplogroups are assigned, many observations show the typical U1a motifs (and I have talked with a Keralan U1a myself).
• Watkins et al. Genetic variation in South Indian caste: evidence from Y chromosome, mitochondrial and autosomal polymorphisms (BMC Genetics 2008) finds about 12% U1a in a (40 people) sample of Tamil upper castes (much less in lower castes).
• Marchani et al: Culture creates genetic structure in the Caucasus. Dagestan. As a curiosity, the paper shows that the small Dagestani population of the Kubachi has almost 50% U1a.

My father belongs to mtdna haplogroup K1a* (full sequence). The lineage, as far as I know, is from the Massa area in Tuscany. I have not studied haplogroup K much. Bill Hurst placed the sequence in a group he defines pre-K1a10, based on 195C and the 524 insertions. I am not sure whether there is any additional branching structure in the pre-K1a10 group. (His K1a10 group has 16048, and is especially frequent in Ireland.) As far as I know, relative to the main K1a branch, the sequence shows the following additional coding region mutations: 5460A (this seems to appear independently somewhere else in K), 6182A, 7245G, 9148C, 12235C, 15930A; and the HVR1 mutation 16179T.

• Bill Hurst's K haplogroup page.

I'd like to know more about both haplogroups. Do you belong to haplogroup U1a (or K1a) as well? Do you have any information about it? I'd be happy to share. Send me an email to:

cacio 'at' cagetti . com
(type in the address with the @ in your mail program)

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