mtDNA Haplogroup U

The complete mitochondrial genome of the young man from Byrsa was identified as belonging to haplogroup U5b2c1 possessing all of the defining mutations with the exception of 16192T, one of the two mutations defining U5, which has shown to be unstable with frequent reversions [37]. He also had five additional, coding region mutations (Fig 4). None of the researchers who collected or processed the Phoenician sample have mitochondrial haplotypes belonging to Haplogroup U. All methods to avoid contamination were applied and the possibility of modern contamination in the sequence obtained was assessed using standard aDNA authenticity criteria and shown to be unlikely, thus we are confident that the haplotype identified is indeed that of the young man from Byrsa.



Given the reputed Lebanese origins of the founders of Carthage, we undertook full mitochondrial genome sequencing of 47 modern Lebanese samples that had previously been typed to Haplogroup U through analysis of the HVR-1 [12]. Haplogroups identified and haplogroup frequency are shown in Table 1. Only seven of the modern Lebanese samples belonged to Haplogroup U5 and of those, two were U5b, but neither belonged to U5b2c or derived haplotypes.


A phylogenetic analysis of all U5b2c sequences available in GenBank or from published supplementary data (Z2478) is shown in Fig 5.

Haplogroup U5 is considered to be one of the most ancient haplogroups in Europe and is believed to have arisen there [43]. The coalescence time estimate for U5 is 29.6 kya (22.7–37.2 kya) [25] and 20–24 kya for U5b [44]. It is not uncommon in Mesolithic European populations, particularly those from Central and Eastern Europe [45]. Haplogroup U5b2c1 has been identified in both La Braña 1 and 2, the 7000 year-old remains recovered from the La Braña-Arintero site in León in Northwestern Spain [42]. Our Phoenician differed from the La Braña 1 complete mitochondrial genome at eight sites (positions 3882, 5351, 5773, 6023, 9869, 16069, 16126, and 16192). The mutations at sites 16069 and 16126 appear to be private mutations for La Braña.

It appears that the U5b2c1 haplogroup is rare in modern populations, with only a few modern sequences published [33, 38, 46] or available in public databases (Family Tree DNA). All of the reported U5b2c1 carriers are of presumably (if not specifically stated) European ancestry, from Spain, Portugal, England, Ireland, Scotland, the United States and Germany. Three of the additional non-defining mutations found in our Phoenician, 5351G, 6023A, and 9869T, are shared with one “European” sample [46] and an individual from central Portugal [33]. Interestingly, Fig 5 shows that our Phoenician sample is most closely related to the modern sample from central Portugal. The unidentified “European” sequence (EF758625) which was deleted from the analysis due to missing data, also carries the three mutations which define the branch on which we find the Phoenician and the Portuguese sample. A separate branch within U5b2c1 contains five samples, from England and Germany or otherwise unidentified as to location of origin, with the La Braña Mesolithic sample (JX186998) on its own branch. Given the limited numbers of published full mitochondrial genomes, it is difficult to identify a likely origin for the mutations defining the Phoenician and Portuguese branch, but it is currently not inconsistent with a Southwest European origin. While the U5b2c2 sequences all originate in Central- and North-Western European or likely derived populations (e.g. US Caucasian), and the U5b2c sequences in GenBank (KC847158 and KU587510, which was excluded from the analysis due to missing data) originate in Germany and England respectively (both samples from Family Tree DNA), it is likely that U5b2c originated in Central/Northwestern Europe. Future complete mitochondrial genome sequencing of European populations, both ancient and modern, will undoubtedly provide more information regarding the distribution and frequency of the U5b2c1 haplogroup across the continent and thus will help us to reconstruct its evolutionary history.

It is generally argued that Mesolithic populations carrying high frequencies of U5 were replaced by Neolithic populations expanding into Western Europe during the Neolithic transition [47]. Recent analyses of ancient DNA suggest that there were two waves of Neolithic expansions that dramatically influenced the genetic makeup of Western Europe [48–51]. An early Neolithic expansion out of Anatolia, occurring some 7000–9000 years ago, moved into Western Europe and replaced many Mesolithic Hunter-Gatherer populations, resulting in an increase of Near Eastern mitochondrial lineages. After this initial invasion of Neolithic farmers, there appears to have been a resurgence in the Western Hunter-Gatherer genetic signatures, followed by a second migration and replacement in many locations from the Eurasian Steppes, associated with the spread of the Yamnaya culture, beginning some 4500 years ago [49]. Several other more regionally focused aDNA studies, however, have shown that there are different patterns of population replacements in various regions of Europe [52, 53]. Unlike the early Neolithic arrival in the Iberian peninsula, which likely arrived in coastal regions [54, 55], it is possible that the second, Eurasian Steppe derived, replacement occurred later or had less of an impact on the southern and western Iberian coast and other Mediterranean coastal regions than in more northern or eastern inland locations [49, 53] and thus the Western Hunter-Gatherer mtDNA lineages, including U5b2c1, may have been more common there at the time of Phoenician contact and settlement.

While the U5b frequency in modern populations in Western Europe is less than 2% it is much rarer in today’s Near Eastern populations [12]. In our full mitogenome sequencing results of 47 modern Lebanese U samples, we found only two individuals who carried haplotypes belonging to U5b2 and neither of these belonged to the U5b2c1 subgroup. It has been demonstrated, however, that modern Levantine populations do not reliably represent the haplogroups present in the Neolithic period, though haplogroup U5 was only found at low frequencies in pre-pottery Neolithic (PPNB) samples from the Levant [54]. U5b is found in only 0.4% of the modern populations from the Iberian peninsula, and only 0.18% Europe-wide [42], which provides us with further confidence of the authenticity of our ancient DNA result. Only the Saami, in northern Scandinavia, retain high levels of U5, and U5b1b in particular, with frequencies over 50% in some Saami populations [56].

Interestingly, haplogroup U5 and U5b have been identified in modern populations from North and Northwest Africa [57–59]. It must be noted, however, that there are few North African complete mitogenomes publicly available and HVR sequencing alone cannot identify beyond the U5b haplogroup (with the C150T HVR mutation) since the seven derived defining mutations (C1721T and A13637G, which define U5b2; A723G, 960XC and A13017G, which define U5b2c; and C6920a and A13484G, which define U5b2c1) are all in the coding regions. Achilli, et al. [59], using full mitochondrial genome sequencing identified a U5b1b1 cluster that grouped Amazigh (North African Berbers) and Saami populations. This cluster is based on the control region motif (16270–150) which is present at low frequencies in Amazigh, North African and nearly all European populations with the exception of the Scandinavian Saami where it is at about 48%. The divergence time of this cluster is around 8600 years ago (+/- 2400) consistent with an expansion from Franco-Cantabrian refuge which is believed to have been a major refuge for the European hunter-gatherers prior to their post LGM expansion [44]. It is suggested that European haplogroup U5 and the more prevalent U6 “Berber cluster” diverged from a common ancestor in the Near East and spread along the north and south coasts, respectively, of the Mediterranean, as far as Iberia to the north and Cyrenaica to the south [60]. It is very plausible that descendants of the Mesolithic hunter-gatherers carried U5b1b1 and sister lineages across the Straits of Gibraltar into North Africa [59], but there is no indication of when this migration may have happened. While it is possible that U5b2 haplogroups were also carried across the Straits of Gibraltar prior to Phoenician arrival in North Africa, our result now provides a minimum date of arrival. We can now say that U5b2c1 was present by the late 6th century BCE.

So how did a young Phoenician man, with a European mitochondrial lineage end up in Carthage, North Africa? The earliest Phoenician site in Iberia is believed to be Gadir or Cadiz as it is known today, established in 1110 BCE [1]. Phoenician colonies were also established in Ibiza, southern Sardinia, western Sicily and along the southern shores of the Iberian Peninsula [1, 61, 62] and, later, these were also major Carthagenian trade ports. It has been suggested that the Phoenician east-west trade route from Tyre and Sidon across the Mediterranean and through the Straits of Gibraltar departed following a northerly route, travelling with the prevailing winds and tides westwards, stopping in Cyprus, Sicily, Ibiza and several locations along the southern coast of Spain, reaching Cadiz and beyond. Return trips back to the Levant took a southerly Mediterranean route, again, with the prevailing currents, sailing along the North African coast [1]. While early Phoenician occupation of and trade in the western Mediterranean would have been from the Levant, Carthage, once established, came to dominate the western Mediterranean trade networks, but would most likely have continued with this well travelled, counterclockwise circular route.

Matisoo-Smith EA, Gosling AL, Boocock J, Kardailsky O, Kurumilian Y, Roudesli-Chebbi S, et al. (2016) A European Mitochondrial Haplotype Identified in Ancient Phoenician Remains from Carthage, North Africa.