Compared with Europe, palaeogenetics in Africa is poorly studied, in part because DNA degrades faster in tropical and dry environments. Chapter 4 aims to unveil population movements in Egypt and Sudan from the Neolithic onward. DNA was extracted from 94 samples from Armant (Egypt), Nuerat (Egypt) and Ghaba (Sudan) dated from the Early Neolithic to the historic period. Genome-wide data were successfully recovered from one sample from Nuerat sequenced to 0.22X coverage, dated to 2,868-2,492 cal BCE (95.4% probability) - consistent with the 3rd-4th Dynasties of the Old Kingdom. Allele frequency-based analyses (PCA, ADMIXTURE, f-statistics, qpAdm) show a strong genetic affinity of this sample to Levantine Natufians. Compared with genomes dated from the end of the Dynastic period (Third Intermediate Period) and present-day Egyptians, the Nuerat sample did not carry the Caucasus Hunter-Gatherer genetic component that started to spread across West Asia ~4,000 years ago and is widely spread in present-day populations. The presence of this component in Egypt is likely associated with admixture between local Egyptian populations and Bronze Age-related populations from West Asia. This admixture pattern might result from the dominance of Lower Egypt by Canaanite (Levantine) rulers during the Second Intermediate Period (ca. 1,650-1,550 BCE).
Even though optimised wet-laboratory techniques improved retrieval of aDNA, it is still a challenging technique, with a higher proportion of failure than success, especially for samples from tropical and sub-tropical regions. Alternative methods are required. Tooth crown and root traits, like those in the Arizona State University Dental Anthropology System (ASUDAS), are seemingly useful as genetic proxies. Chapter 5 investigates whether such traits can approximate genetic relatedness in the absence of aDNA, among continental and global samples. For 12 African and 32 global populations, Mantel correlations were calculated between the mean measure of divergence (MMD) distances from up to 36 ASUDAS traits, and FST distances from >350,000 single nucleotide polymorphisms (SNPs) among matched dental and genetic samples. A close ASUDAS/SNP association, based on MMD and FST correlations, is evident, with rm-values between 0.84 in Africa and 0.72 globally. Partial MMD/FST correlations controlling for geographic distances are strong for Africa (0.78) and moderate globally (0.4). Relative to prior studies, MMD/FST correlations imply greater dental and genetic correspondence. The implication is that ASUDAS traits can be used instead of genomic markers when the latter are unavailable.
Even though optimised wet-laboratory techniques improved retrieval of aDNA, it is still a challenging technique, with a higher proportion of failure than success, especially for samples from tropical and sub-tropical regions. Alternative methods are required. Tooth crown and root traits, like those in the Arizona State University Dental Anthropology System (ASUDAS), are seemingly useful as genetic proxies. Chapter 5 investigates whether such traits can approximate genetic relatedness in the absence of aDNA, among continental and global samples. For 12 African and 32 global populations, Mantel correlations were calculated between the mean measure of divergence (MMD) distances from up to 36 ASUDAS traits, and FST distances from >350,000 single nucleotide polymorphisms (SNPs) among matched dental and genetic samples. A close ASUDAS/SNP association, based on MMD and FST correlations, is evident, with rm-values between 0.84 in Africa and 0.72 globally. Partial MMD/FST correlations controlling for geographic distances are strong for Africa (0.78) and moderate globally (0.4). Relative to prior studies, MMD/FST correlations imply greater dental and genetic correspondence. The implication is that ASUDAS traits can be used instead of genomic markers when the latter are unavailable.
