The Archaeogenetics of European Ancestry


The archaeogenetics of Europe remains deeply controversial. Advances in ancient deoxyribonucleic acid (DNA) analysis have suggested gene flow between Neanderthals and modern humans, who arrived in Europe <50 000 years ago, but have so far failed to support evolution of Neanderthals from a population of Homo heidelbergensis represented by remains in northern Spain. The extent to which European Mesolithic forager populations versus Neolithic pioneers from the Near East contributed to the extant gene pool of Europeans also continues to be contested. Whilst analyses of extant mitochondrial lineages have emphasised late Palaeolithic and Mesolithic expansions, ancient DNA (aDNA) results suggest significant Neolithic dispersals from the southern ‘refugial’ zone into the northern ‘bio‐tidal’ zone. However, whether these had a primarily Near Eastern or North Mediterranean source remains a matter for debate. Meanwhile, aDNA has also begun to highlight an important role for later dispersals, especially during the late Neolithic, in shaping the European gene pool.

Key Concepts:

  • The archaeogenetics of Europe has been intensively studied but remains in flux and deeply controversial, with no universally accepted methodological approach.

  • Hominins, including Homo antecessor, Homo heidelbergensis, Neanderthals and modern humans, have been present in Europe for more than 1 million years (My).

  • Neanderthals and modern humans are thought to have a common ancestor, Homo heidelbergensis, approximately half a million years ago, and to have interbred at low levels as modern humans dispersed into Eurasia from Africa approximately 60 000 years ago.

  • However, the status of hominin remains from northern Spain as representing a step from this ancestor towards the Neanderthals has recently been questioned by mtDNA evidence.

  • The importance of the phylogeographic approach can be seen in the elucidation of the relationships between the north European, Finnic‐speaking Saami people, who traditionally lacked agriculture, and farming‐based Europeans.

  • Analyses of contemporary mtDNAs suggest that most arose within the pre‐Neolithic foraging communities of Europe >10 000 years ago, rather than being introduced with farming from the Near East approximately 9000 years ago, but ancient DNA evidence from central and northern Europe has questioned this view.

  • The solution may lie in the distinction between ‘bio‐tidal’ sink and ‘refugium’ source areas, north and south of the continental divide respectively – there may have been significant dispersals from the latter into the former regions in the Neolithic as well as in the Late Glacial and immediate postglacial periods.

  • With increasing success in the recovery of ancient DNA, archaeogenetics is finally also beginning to shed light on post‐Neolithic dispersals – as illustrated by the recent demonstration that most Ashkenazi maternal lineages have a European, rather than Levantine, source.

  • An integrated combination of both ancient and contemporary DNA studies and an eclectic variety of approaches to data analysis may be the best way forward for archaeogenetics.

Keywords: archaeogenetics; phylogeography; founder analysis; STRUCTURE‐like analyses; principal components analysis; genealogy; whole‐mtDNA genomes; Y‐chromosome variation; genome‐wide autosomal variation; ancient DNA

Figure 1.

Phylogenetic tree of whole‐mtDNA genome sequences from two modern humans (within haplogroups L0 and R0: the latter is the revised Cambridge Reference sequence), nine Neanderthals, three ‘Denisovans’ and a H. heidelbergensis from Atapuerca, estimated by hand and rooted with chimpanzee and bonobo sequences. Ambiguous nucleotides are emboldened when the missing base is inferred for the tree reconstruction. Approximate ages of the remains in ka are given below the GenBank accession codes. Age estimates of the major nodes calculated using BEAST software and a phylogenetic tree containing 5 Pan troglodytes, 5 Pan paniscus, 139 human mtDNA genomes (representing all the oldest nodes in the human mtDNA tree) and the 11 archaic Homo sequences and 4 Pleistocene human sequences (FN600416, KC521459, KC521458 and KC417443), using a relaxed molecular‐clock (uncorrelated lognormal with γ‐distributed rates) and incorporating estimates of the ages of the samples.

Figure 2.

Principal components analysis (PCA) of genome‐wide autosomal single‐nucleotide polymorphism (SNP) data of individuals from Europe including several ‘outliers’, the Caucasus and the Near East. Analysis carried out using the smartpca program (with default settings) of the EIGENSOFT package, and data thinned by removing one SNP from all pairs in strong linkage disequilibrium (LD). The fraction of variance explained by each component is given in parentheses: note the extremely low values for these high‐resolution data. All data from Illumina 610 K to 650 K chip with 544 193 SNPs; after LD pruning the total number of SNPs was 234 699.

Figure 3.

Genome‐wide SNP ADMIXTURE analysis of populations from Europe, the Near East, the Caucasus and North and Eastern Africa. Analysis conducted on global populations with random seed number generator on the LD pruned data set at K=2–16. K=14, which had the lowest cross‐validation scores, is shown. Data source as above.



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Further Reading

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Pala, Maria, Chaubey, Gyaneshwer, Soares, Pedro, and Richards, Martin B(Jul 2014) The Archaeogenetics of European Ancestry. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0024624]