Ancient mitochondrial diversity reveals population homogeneity in Neolithic Greece and identifies population dynamics along the Danubian expansion axis

Abstract

The aim of the study is to investigate mitochondrial diversity in Neolithic Greece and its relation to hunter-gatherers and farmers who populated the Danubian Neolithic expansion axis. We sequenced 42 mitochondrial palaeogenomes from Greece and analysed them together with European set of 328 mtDNA sequences dating from the Early to the Final Neolithic and 319 modern sequences. To test for population continuity through time in Greece, we use an original structured population continuity test that simulates DNA from different periods by explicitly considering the spatial and temporal dynamics of populations. We explore specific scenarios of the mode and tempo of the European Neolithic expansion along the Danubian axis applying spatially explicit simulations coupled with Approximate Bayesian Computation. We observe a striking genetic homogeneity for the maternal line throughout the Neolithic in Greece whereas population continuity is rejected between the Neolithic and present-day Greeks. Along the Danubian expansion axis, our best-fitting scenario supports a substantial decrease in mobility and an increasing local hunter-gatherer contribution to the gene-pool of farmers following the initial rapid Neolithic expansion. Οur original simulation approach models key demographic parameters rather than inferring them from fragmentary data leading to a better understanding of this important process in European prehistory.

Local increases in admixture with hunter-gatherers followed the initial expansion of Neolithic farmers across continental Europe

“…By dividing our estimated effective size (in number of chromosome copies) by two to get the number of effective individuals and then multiplying the result by three (53), we were able to roughly estimate a FA census size of approximately 0.27 individuals/km 2 (95 HDI = 0.19-0.35) within a deme of 100x100 km 2 . This estimate is close but lower than the estimate of Silva et al (30), based on ancient mitochondrial data (0.46 individuals/km 2 ) and in line with the upper range (0.6 individuals/km 2 ) estimated by Zimmermann et al (54) for the Linear Pottery culture (LBK).…”

“…This means that at each generation, when HGs and FAs coexist in a cell, a fraction γ of the contact between them results in admixture. This leads to the passage of HG genes into the FA population, and thus to gene flow from HG to FA, following previous simulation studies (29,30). Note that the model does not distinguish whether this gene flow is due to the adoption of agriculture by HGs, the assimilation of HGs into the agricultural population, or mixed encounters between individuals from the two populations resulting in the birth of a child in the FA population.…”

“…We then used an Approximate Bayesian Computations (ABC) framework to infer key demographic parameters by comparing the resulting simulated palaeogenomic data to recently published high quality genomic data from 67 individuals. Compared to previous demogenomic modeling of the Neolithic using ancient DNA, our simulation framework is able to manage more explicit spatial features than Marchi et al ( 11 ) and to handle the spatio-temporal variation of admixture between hunter-gatherers and farmers with more flexibility than Rasteiro & Chikhi ( 27 ) and Silva et al ( 30 ). The paleogenomic dataset we used is particularly well suited for demogenomic inferences as it is composed of genome-wide sequences selected from presumably neutral regions ( 31 ).…”

Past human expansions shaped the spatial pattern of Neanderthal ancestry

“…In Europe, a prominent genetic transition occurred during the spread of early Neolithic farmers, when they partially replaced Paleolithic/Mesolithic hunter-gatherers [i.e., the so-called Neolithic transition ( 33 , 34 , 35 )]. At least along the Danube route from Anatolia to Central Europe, paleogenetic analyses have revealed that the first stage of the Neolithic transition occurred through the migration of FAs, followed by admixture with local HGs in a second stage, e.g., ( 32 , 33 , 35 , 47 ). This transition began in the Fertile Crescent ~11,000 years BP ( 48 ), and its consequences on the distribution of NE ancestry have been weakly explored thus far ( 16 ).…”

RET Proto-Oncogene Variants in Patients with Medullary Thyroid Carcinoma from the Mediterranean Basin: A Brief Report

“…The present territory of modern Greece as a Mediterranean entity was unavoidably influenced during the Neolithic expansion era by the arrival of immigrant farmers from the Near East [ 46 ]. During this distinctive period, along with the obvious innovative stone-age technologies that were brought to the indigenous population, new genomic variations were also introduced, as a result of multi-phase mixing contributing in that way to their genetic distinctiveness [ 46 , 47 ].…”