Genomic analyses inform on migration events during the peopling of Eurasia

Inferring Human Demographic Histories of Non-African Populations from Patterns of Allele Sharing

“…I started with the variant calls used in Pagani et al 16 (downloaded from the Estonian Biocenter website) and filtered them to consider only biallelic autosomal SNPs. I further considered only those variants where the reference allele was the ancestral allele and where the genotype was homozygous reference in 21 West and Central African (nine Yoruba, four Luhya, and eight Pygmy) genomes and in Neanderthal and Denisovan genomes.…”

“…For example, although enhanced D-statistics count sites that are homozygous ancestral in sub-Saharan Africans but derived in the Denisovan genome, the method introduced here counts variants that are homozygous ancestral in sub-Saharan Africans, Neanderthals, and Denisovans. 16 to simulate sequence data. I assumed (diploid) sample sizes of 21, 3, 3, and 3 for the West African, European, East Asian, and Australian populations.…”

“…I constructed five simple branching models (without migration) based on the split times described in Pagani et al 16 All models used a scaling of 2N generations ¼ 1 million years and, when possible, assumed that the median genetic split times as estimated from MSMC 19 are actual population split times. Models 1-3 are simple branching models ( Figure 3A) with a split time between Europeans and East Asians of 30 Kya, a split time between Eurasians and Papuans of 40 Kya, and a split time between Eurasians and West Africans of 75 Kya.…”

“…Specifically, Malaspinas et al 15 claimed that Melanesians are an outgroup in comparison to mainland Eurasians (i.e., Figure 1A), whereas Pagani et al 16 posited that Melanesians contain some ancestry from an older out-of-Africa migration (which we call ''ghost'' admixture) and implied (though did not state explicitly) that Figure 1A is the correct branching order (see, e.g., their Extended Data Figure 4A). In contrast Figures 1 and 3 in Mallick et al 14 suggested that Europeans are an outgroup in comparison to East Asians and Melanesians (i.e., Figure 1B).…”

“…More recently, several large whole-genome sequencing studies [14][15][16] have made conflicting claims regarding the historical branching order for the groups shown in Figure 1 (reviewed in Tucci and Akey, 2016 17 ). Specifically, Malaspinas et al 15 claimed that Melanesians are an outgroup in comparison to mainland Eurasians (i.e., Figure 1A), whereas Pagani et al 16 posited that Melanesians contain some ancestry from an older out-of-Africa migration (which we call ''ghost'' admixture) and implied (though did not state explicitly) that Figure 1A is the correct branching order (see, e.g., their Extended Data Figure 4A).…”