INSIGHTS INTO PALEOGENETICS FROM NEXT-GENERATION SEQUENCING TECHNOLOGIES

February 9th, 2022

While ‘modern’ humans are the only hominin species existing on the planet today, in the past our species has overlapped both temporally and spatially with other archaic humans. A lot of archaeological research has been focused on determining the level of admixture between anatomically ‘modern’ humans and our sister species, the archaic humans – Neanderthals and Denisovans (Wolf and Akey, 2018). With the advancements in technology, the studies have stepped away from the comparison of the morphological features and focused on the prospect of obtaining and analysing ancient DNA (aDNA).

More than a decade has passed since the publications of not one, but two initial drafts of the genomes belonging to archaic human species. The research of ancient DNA has come to a turning point with the development of next-generation sequencing technologies, which allowed for a significant reduction in limitations in regards to the analysis of the aDNA (Hofreiter et al., 2015). For the first time, high-coverage nuclear and mitochondrial genomes were able to be obtained from aDNA, and DNA hybridization enrichment technique was used to provide a targeted approach to aDNA research and the retrieval of genomes from highly contaminated samples.

The results obtained suggested that non-African human populations shared 1-4% of their DNA with the Neanderthals, while some of the Southeast Asian populations (Melanesians) seemed to share 4-6% of the derived alleles with the Denisovans. Furthermore, it enabled a more precise estimate on when the population split had happened, estimated between 383 000 and 257 000 years ago for the anatomically modern humans and the population that evolved into Neanderthals and Denisovans, and between 236 000 to 190 000 years ago for Neanderthals and Denisovans (Sánchez-Quinto and Lalueza-Fox, 2015). An interesting finding in the comparison of the present-day human and Neanderthal genome sequence is the existence of areas of large depletions – ‘deserts of archaic ancestry (Wolf and Akey, 2018). This could allude to intense selection against Neanderthal haplotypes in the admixed populations, owing to the high probability of Neanderthals harbouring high frequencies of weakly deleterious alleles. On the other hand, the archaic alleles may have been useful to the adaptation of ‘modern’ humans to the unfriendly Eurasian environment – as certain populations were found to carry adaptive introgressed sequences from archaic hominins in their genomic sequences.

Recent developments in technology have greatly increased the accessibility of aDNA and provided the potential for novel research of humans’ evolutionary journey. The value of paleogenomic data has not yet reached its full potential, as researchers continue to optimise the techniques used to analyse and provide context for the aDNA in genomic research.

References:
Hofreiter, M. et al. (2015) ‘The future of ancient DNA: Technical advances and conceptual shifts’, BioEssays, 37(3), pp. 284–293. doi: 10.1002/bies.201400160.
Sánchez-Quinto, F. and Lalueza-Fox, C. (2015) ‘Almost 20 years of Neanderthal palaeogenetics: Adaptation, admixture, diversity, demography and extinction’, Philosophical Transactions of the Royal Society B: Biological Sciences, 370(1660). doi: 10.1098/rstb.2013.0374.
Wolf, A. B. and Akey, J. M. (2018) ‘Outstanding questions in the study of archaic hominin admixture’, PLoS Genetics, 14(5), pp. 1–14. doi: 10.1371/journal.pgen.1007349.

Nina Fajs, Edinburgh Genetics