Mitochondrial DNA (mtDNA) is inherited only through one's mother. As it does not recombine like chromosomes, it can be used in population genetics to trace back ancestry on the matrilineal side and to divide populations into haplogroups. The same can be done on the patrilineal side using the Y-chromosome (Y-DNA), which is inherited exclusively from father to son and does not recombine with the X chromosome. Only a few mutations distinguish the Y chromosome of a man and his father. These mutations are cumulative from generation to generation, so it is easy to trace the family tree of humanity by analyzing these mutations (SNPs) on the Y chromosome and mtDNA.
The majority of Iberian paternal lineages are of Indo-European (R1b, G2a3b1, J2b2 and a small amount of R1a), which can be attributed to the Proto-Celtic and Hallstatt Celtic invaders, and to a lower extent to later Roman and Germanic settlers. In total, these amount to 50-85% of Spanish Y-DNA and 60% of Portuguese Y-DNA. Maternal lineages, on the other hand, appear to have a mostly Neolithic and Mesolithic origin, notably haplogroups H1, H3, HV0, K1a, J1c, J2a1, J2b1a, T2, U5b, V and X, which make up over 80% of the mtDNA in regions like the Basque country or Asturias, and always over 50% of the population of any region.
Western Iberia, from Galicia and Asturias to southern Portugal and western Andalusia, have relatively high percentages of Southwest Asian Y-chromosomal haplogroups (E-M34, J1, J2a, T). Their historical origin is diverse, being the cumulative contributions of Levantine Neolithic herders, Phoenicians, Jews and Arabs, although their exact proportion remains difficult to assess and may vary a lot between regions. What can be ascertained is that northern regions such as Cantabria, Asturias and even Galicia have negligible medieval Arabic, Jewish and Phoenician ancestry, and therefore the presence of Southwest Asian haplogroups should be attributed to Neolithic herders. Maternal Southwest Asian lineages included especially HV, J1d, J2a2, U3, X1 as well as some K, T and X2 subclades. Autosomal data shows a maximum of 12% of Southwest Asian and Red Sea DNA in southern Portugal and western Andalusia, and a minimum of 0% in the Basque country.
Southwest Asian lineages are usually found side with North African lineages, like Y-haplogroup E-M81 and mt-haplogroups L, M1 and U6. The most likely explanation for the presence in Iberia is that they "hitchhiked" with Neolithic herders and medieval Arabic invaders passing through the Maghreb. Some North African lineages may even have come during the late Glacial period. The origin of mtDNA H1, H3 or HV0/V is unclear. They may have have been present in Iberia and/or the Maghreb in the Mesolithic period, since these three lineages are also found all over North Africa. Yet it can't be excluded that they integrated the Neolithic agricultural community in the Maghreb and moved into Iberia at that time. Autosomal data shows an average of 5% of North African DNA in the western half of Iberia, and 1 or 2% in the eastern half.
North-eastern Spain, from the Basque country to Catalonia, was colonised by Neolithic farmers from Italy and France, and consequently has the lowest incidence of Southwest Asian or North African DNA in the peninsula today.
Migrations and settlements in historical times had a smaller impact on the genetic structure of Iberian than Neolithic and Bronze Age events. Only Y-DNA can be used today to measure the contributions of other European populations in Iberia, and even Y-DNA can't yield accurate estimate without large quantities of high-resolution data. The Romans left perhaps between 1% and 15% of Y chromosomes behind them, with a higher proportion along the Mediterranean coast, in Andalusia and in Extremadura. Germanic male lineages now make up about 4% of the overall population, with the highest frequencies (6-10%) observed in the north-west and Catalonia.
Y-DNA frequencies by region
Total samples : Spain = 1798 ; Portugal = 1458 ; Sephardic Jews = 174. The Y-DNA frequencies for Lebanon are also indicated for the sake of comparison with the historical Phoenician homeland.
| Region/Haplogroup | I1 | I2*/I2a | I2b | R1a | R1b | G | J2 | J*/J1 | E1b1b | T | Q | N | Sample size |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Portugal | 2 | 1.5 | 3 | 1.5 | 56 | 6.5 | 9.5 | 3 | 14 | 2.5 | 0.5 | 0 |  |
| Spain | 1.5 | 4.5 | 1 | 2 | 69 | 3 | 8 | 1.5 | 7 | 2.5 | 0 | 0 | |
| 0 | 9.5 | 0 | 3.5 | 58.5 | 3 | 10.5 | 2 | 10 | 3 | 0 | 0 |  | |
| 2 | 14.5 | 1 | 2 | 60.5 | 1 | 10.5 | 0 | 5 | 4 | 0 | 0 |  | |
| 2 | 2 | 0 | 2.5 | 58.5 | 8 | 8 | 2 | 14 | 3 | 0 | 0 | | |
| 0.5 | 5 | 0 | 0 | 85 | 1.5 | 2.5 | 0.5 | 2.5 | 0 | 0.5 | 0 | | |
| 1 | 3 | 2 | 8.5 | 55 | 10.5 | 3 | 2.5 | 11 | 2.5 | 0 | 0 | | |
| 0.5 | 2 | 0.5 | 3 | 64 | 5 | 6 | 1 | 16 | 2 | 0 | 0 | | |
| 1.5 | 1.5 | 0.5 | 1.5 | 66 | 8 | 10 | 4 | 5 | 2 | 0 | 0 | | |
| 2 | 3.5 | 1.5 | 1.5 | 66.5 | 4.5 | 7.5 | 1.5 | 8.5 | 1 | 0 | 0 | | |
| 3.5 | 5 | 1 | 0 | 50 | 5 | 11.5 | 0 | 18.5 | 5 | 0 | 0 | | |
| 3 | 2.5 | 1.5 | 0 | 63 | 3 | 3.5 | 1 | 22 | 0.5 | 0 | 0 | | |
| 3 | 5.5 | 1 | 3 | 63.5 | 1 | 6 | 2 | 13.5 | 1.5 | 0 | 0 | | |
| Sephardic Jews | 0 | 1 | 0 | 5 | 13 | 15 | 25 | 22 | 9 | 6 | 2 | 0 | |
| (Lebanon) | 2 | 1.5 | 1.5 | 2.5 | 8 | 6.5 | 26 | 20 | 17.5 | 5 | 2 | 0 |  |
Sample sizes
: Under 100 samples : 100 to 250 samples : 250 to 500 samples : 500 to 1000 samples : Over 1000 samplesMtDNA frequencies by region
| Region/Haplogroup | L | HV | H | H1+H3 | H5 | HV0+V | J | T1 | T2 | U2 | U3 | U4 | U5 | U | K | I | W | X | Other | Size |
| Portugal | 6.4 | 0.1 | 43.9 | (26) | (2.1) | 4.8 | 6.8 | 3.3 | 6.3 | 1.2 | 0.9 | 1.7 | 6.5 | 3 | 6.1 | 2.2 | 1.8 | 2 | 2.9 | 1448 |
| Spain | 2.4 | 0.7 | 44.1 | (28) | (2.6) | 7.5 | 6.6 | 2.1 | 6.4 | 1.1 | 1.4 | 1.9 | 8.1 | 1.8 | 6.3 | 1.1 | 1.4 | 1.7 | 5.5 | 2506 |
| 7.4 | 0.8 | 44.3 | (29.5) | 4.8 | 8.9 | 2.3 | 2.6 | 1 | 1 | 1.6 | 5.7 | 1.2 | 6.8 | 1.3 | 1.6 | 3.2 | 3.1 | 310 | ||
| 1.2 | 1 | 39.3 | 5 | 15.8 | 0 | 10.9 | 0.8 | 0 | 1.7 | 9.6 | 0 | 4.2 | 1.7 | 0.8 | 0.8 | 7.2 | 119 | |||
| 0 | 1 | 54.1 | 5.6 | 9 | 0 | 1.1 | 0 | 2.2 | 0 | 12.3 | 2.2 | 7.9 | 1.1 | 1.1 | 0 | 2.4 | 89 | |||
| 0.3 | 0.8 | 49 | (44) | (2.8) | 7.9 | 7.6 | 1.5 | 6 | 1 | 0.3 | 0.8 | 11.7 | 1.9 | 5.3 | 0.6 | 1.1 | 2.3 | 1.8 | 618 | |
| 1.6 | 2.5 | 37.6 | (27) | 19 | 3.7 | 0.4 | 2.5 | 0.8 | 1.2 | 2.9 | 10.7 | 2.5 | 3.7 | 2.9 | 0 | 0 | 0.4 | 242 | ||
| 3.1 | 0.5 | 29.5 | 7.5 | 7 | 1.3 | 7.6 | 1.3 | 2.5 | 3.8 | 10.1 | 3.9 | 10 | 1.3 | 5 | 2.5 | 3.1 | 80 | |||
| 3.7 | 1 | 58.5 | (34) | 3.8 | 8.6 | 1.1 | 3.7 | 1.6 | 0 | 0.5 | 5.4 | 1.5 | 4.9 | 0.5 | 1.6 | 1.1 | 0.5 | 185 |
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