The first reported case of the rare mitochondrial haplotype H4a1 in ancient Egypt

Abstract

Takabuti, was a female who lived in ancient Egypt during the 25th Dynasty, c.660 BCE. Her mummified remains were brought to Belfast, Northern Ireland, in 1834 and are currently displayed in the Ulster Museum. To gain insight into Takabuti's ancestry, we used deep sampling of vertebral bone, under X-ray control, to obtain non-contaminated bone tissue from which we extracted ancient DNA (aDNA) using established protocols. We targeted the maternally inherited mitochondrial DNA (mtDNA), known to be highly informative for human ancestry, and identified 38 single nucleotide variants using next generation sequencing. The specific combination of these SNVs suggests that Takabuti belonged to mitochondrial haplogroup H4a1. Neither H4 nor H4a1 have been reported in ancient Egyptian samples, prior to this study. The modern distribution of H4a1 is rare and sporadic and has been identified in areas including the Canary Islands, southern Iberia and the Lebanon. H4a1 has also been reported in ancient samples from Bell Beaker and Unetice contexts in Germany, as well as Bronze Age Bulgaria. We believe that this is an important finding because first, it adds to the depth of knowledge about the distribution of the H4a1 haplogroup in existing mtDNA, thus creating a baseline for future occurrences of this haplogroup in ancient Egyptian remains. Second, it is of great importance for archaeological sciences, since a predominantly European haplogroup has been identified in an Egyptian individual in Southern Egypt, prior to the Roman and Greek influx (332BCE).

Figure 1

Fragmentation and misincorporation patterns for the dual enriched sequence read dataset: Data generated with MapDamage v.2.0. The upper four panels show the frequency of each of the four nucleotides at positions –10 to + 10 relative to the 5´and 3´ends of the sequence reads, and the lower two panels show the C > T (red) and G > A (blue) misincorporation patterns within the initial 25 and final 25 nucleotides of each read. The patterns are consistent with the fragmentation and misincorporation models typical for ancient DNA.

Figure 2

Haplogroup assignment based on Haplogrep2.

Figure 3

Mitochondrial haplotypes in ancient Egypt through time, from 2000BCE to 400CE. Light grey areas show where individual cases (4 out of 7) have influenced understanding of mitochondrial haplogroups. Copyright: Tony Freemont.

Figure 4

Sampling in situ. Ulster Museum, Belfast, Northern Ireland. Takabuti is positioned on the fibreboard and the X-ray imaging intensifier is positioned next to her. Copyright: Konstantina Drosou.

Figure 5

X-ray of the L3 vertebra. Biopsy needle is shown entering the body of L3 at two different angles. Copyright: Robert Loynes, Mark Regan.