A genomic history of Aboriginal Australia

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

“…So, although the ''true'' demographic history of non-African populations was certainly very complex, on average Melanesian and East Asian sequences are more genetically similar (and share a more recent common ancestor) than do European and East Asian or European and Melanesian sequences, and Figure 1B is likely to be the true population branching order. Note that the same conclusion was reached in the neighborjoining tree shown in Figure 1a of Mallick et al 14 and in the unrooted tree in Extended Data Figure 1 of Malaspinas et al 15 If we assume that sub-Saharan Africans are ancestral, then this branching order was proposed by Cavalli-Sforza and colleagues more than 50 years ago. 29 Next, I compared the expectations for P EA , P EM , and P AM under the demographic model proposed by Malaspinas and colleagues (cf.…”

“…The estimated split times for Aboriginal Australians (58 Kya) and ancestral Eurasians (57 Kya) are almost identical, and more importantly, these two ancestral populations are connected by high scaled migration rates (4Nm > 10, cf. Table S07.5 in Masaspinas et al 15 ) after the split. One consequence of the high Figure 2.…”

“…ms0ancient2 is a simple modification of Hudson's ms; 27 it changes branch lengths to allow for the past sampling of two archaic genomes. To sample non-African sequences roughly 42 Kya, I shifted the scaled times of events by 0.032324 (I used the same time scaling as in Malaspinas et al 15 ). Both sets of simulations included a total of 2.05 Gb of simulated sequence to roughly approximate the total length of the genome that was available after filtering.…”

“…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).…”

“…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).…”