West Asian sources of the Eurasian component in Ethiopians: a reassessment

Abstract

Previous genome-scale studies of populations living today in Ethiopia have found evidence of 1 recent gene flow from an Eurasian source, dating to the last 3,000 years 1,2,3,4 . Haplotype 1 2 and genotype data based analyses of modern 2,4 and ancient data (aDNA) 3,5 have considered 3 Sardinia-like proxy 2 , broadly Levantine 1,4 or Neolithic Levantine 3 populations as a range of 4 possible sources for this gene flow. Given the ancient nature of this gene flow and the extent 5 of population movements and replacements that affected West Asia in the last 3000 years, 6 aDNA evidence would seem as the best proxy for determining the putative population source. 7 We demonstrate, however, that the deeply divergent, autochthonous African component which 8 accounts for ∼50% of most contemporary Ethiopian genomes, affects the overall allele frequency 9 spectrum to an extent that makes it hard to control for it and, at once, to discern between 10 subtly different, yet important, Eurasian sources (such as Anatolian or Levant Neolithic ones). 11Here we re-assess pattern of allele sharing between the Eurasian component of Ethiopians (here 12 called "NAF" for Non African) and ancient and modern proxies area after having extracted NAF 13 from Ethiopians through ancestry deconvolution, and unveil a genomic signature compatible 14 with population movements that affected the Mediterranean area and the Levant after the fall 15 of the Minoan civilization. 16 Results and Discussion 17To determine the most likely source of the Eurasian gene flow into the ancestral gene pool of 18 present-day Ethiopians we have used a combination of ancestry deconvolution (AD) and allele 19 sharing methods 6 . AD refers to analyses that determine the likeliest ancestry composition of 20 genomes of individuals with mixed ancestry at fine haplotype resolution. These methods have 21 1 allowed us to i) exploit high quality modern data and ii) harness the power of allele sharing 22 tools on genetic fractions with no or reduced African contributions. Such a strategy, while 23 potentially beneficial, introduce a novel source of bias which we aimed to explore here. Par-24 ticularly, after AD of 120 Ethiopian genomes 7 , we assigned each genomic SNP into one of the 25 following four categories based on the method likelihoods (see Methods for further details): 1) 26 confidently non African (NAF); 2) low confidence non African (X); 3) low confidence African 27 (Y) and 4) confidently African (AF, consistently filtered out from our analyses). While basing 28 our inference on the NAF component alone, we here demonstrate that the component X does 29 account for a minority of the genome and, when analysed together with NAF does not quali-30 tatively change the results. Furthermore, when joining together the NAF and AF confidently 31 assigned components (to create "Joint" components) we recapitulate the signals of the global 32 population (prior to ancestry deconvolution), showing that the X and Y components are not 33 holding a considerable or peculiar genetic signat...

The genetic origin of Daunians and the Pan-Mediterranean southern Italian Iron Age context

“…Southern Italy (Apulia) can be placed within a Pan-Mediterranean genetic continuum that stretches from Crete (Minoans 25 ) and the Levant (Sea People 22,24 ) to the Republican Rome and the Iberian The Daunians maintained strong commercial and political relations with the Illyrian people, controlling together the area spanning from the Dalmatia to the Gargano peninsula 10 and had many cultural affinities with them 26 . The material culture, involving peculiar anthropomorphic statue stelae, has provided some information on Daunian culture and may also help in unravelling their mysterious origin.…”

“…To better understand the putative contribution of more recent populations, we modelled our samples with base sources (WHG, AN, Steppe-related and CHG/IN) and, 9 alternatively, Minoans (Odigitria and Lasithi), Amhara_NAF and Roman Republicans (Figure 2C, Figure S5B-D, STAR Methods). Amhara_NAF can be used as a proxy for the Non-African component in modern Ethiopian individuals that was tentatively linked to the Sea People, a Bronze Age nomadic seafaring population 22,24 . Together with Minoans and Roman Republicans, this component can be broadly modelled as a Pan-Mediterranean population (constituted by AN and IN/CHG components) with the addition of WHG and Steppe-related ancestry in Roman Republicans.…”

“…We assembled a genome-wide dataset of ancient and modern samples by converting the following datasets, where needed, in PLINK format using convertf from the EIGENSOFT 8.0.0 52 and merging them together with PLINK 1.9 53 : i) the ancient individuals and the Mbuti Congolese individuals (HGDP 54 ) from the "1240K" dataset from Dr David Reich laboratory (https://reich.hms.harvard.edu/allen-ancient-dna-resource-aadr-downloadable-genotypes-presentday-and-ancient-dna-data, version 44.3 release), ii) the modern samples from "1240K+HO" of the same release, iii) the Italian Chalcolithic and Bronze Age samples produced by a recent study 11 , iv) the genotypes of an Italian hunter-gatherer from the Late Epigravettian site of Riparo Tagliente dated around 17kya 55 , v) additional genome-wide data of 129 modern-day Italian samples covering the entire country 56 , vi) genome-wide data of 217 present-day Apulian individuals (available at this link https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE44974) and 48 haploid genomes representing the Eurasian component of modern Ethiopians (here called Amhara_NAF for "Non African Fraction" 24 ). We excluded the ancient samples showing issues in their group assignment (i.e., "Ignore" in the "1240K" dataset) or in their DNA quality (e.g, those not containing the string "PASS", with the exception of the Iceman individual, or those with less than 5,000 SNPs) and one of a pair of related samples.…”

High Levels of Genetic Diversity within Nilo-Saharan Populations: Implications for Human Adaptation

“…The peoples who remained were more genetically diverse and have continued to diversify in response to changing environmental and disease pressures and admixture events. 1 , 2 , 3 , 4 , 5 , 6 African populations have also migrated and intermixed to create the rich mosaic of genetic and cultural variation that is found today. 7 The paucity of genetic, historical, and archaeological records has led to a heavy dependence on linguistic analysis for classification of African populations, and this strategy has identified four major African language families (Afro-Asiatic, Niger-Congo, Nilo-Saharan, and Khoisan) ( Figure 1 ) and provided evidence for the migration of Bantu speakers out of the Nigeria-Cameroon border region into South and East Africa.…”

Properties and unbiased estimation ofF- andD-statistics in samples containing related and inbred individuals

“…The recently introduced F -and D-statistics (Huson et al, 2005;Kulathinal et al, 2009;Reich et al, 2009;Green et al, 2010; have transformed the way geneticists measure population differentiation. These statistics have been instrumental in many major recent discoveries, including testing which Neanderthal populations are closest to the populations that admixed with modern humans (Hajdinjak et al, 2018), and detecting which population is likely the admixing source for European admixture in modern Ethiopian populations (Molinaro et al, 2019). Iterating through different combinations of populations using the F 4 -and D-statistics has allowed reconstruction of population histories in diverse groups such as Native Americans and South Asians Moorjani et al, 2013).…”