Reduced diversity in human mitogenomes from Eivissa (Balearic Islands)

The Balearic Islands, off the NE coast of the Iberian Peninsula, have a rich and diverse history. We had previously reported that genomic diversity in one of the Balearics, Eivissa, shows the signs of a reduced effective population size and founder effect when compared not only to populations of the mainland but also to Menorca, another Balearic Island of comparable area and population size but with a more open historic trajectory. In the current work, we investigate whether the same pattern can be observed in the mitogenomes, and leverage the rich phylogeographic information contained in mitochondrial DNA (mtDNA) to detect the sources of the maternal lineages in Eivissa and Menorca. Indeed, Eivissa shows a reduced mtDNA haplotype diversity compared to Menorca and mainland populations, but similar to that in islands in other archipelagos (Canaries, Orkney, Shetland). However, other measures of diversity, such as number of segregating sites or nucleotide diversity do not show this reduction, probably because one of the founder lineages in Eivissa belongs to the deeply divergent L2c haplogroup, which is of Sub-Saharan origin and with a time to the most recent common ancestor that suggests that it was introduced during the Punic colonization of the island. Still, direct comparison with ancient DNA samples of various periods did not yield any sequence match that could indicate continuity with the population present in the islands before the Catalan-Aragonese conquest of the 13th century.