The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

Abstract

We report the Simons Genome Diversity Project (SGDP) dataset: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioral modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that in other non-Africans.

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.…”

“…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). One difficulty in assessing the merits of these competing claims is that they are based on the output from complicated inference tools such as Fastsimcoal, 18 MSMC 19 or fineSTRUCTURE.…”

“…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).…”

The promise of discovering population-specific disease-associated genes in South Asia

“…We merged the South Asian and Ashkenazi Jewish data generated by the other Illumina arrays to create an "Illumina" dataset consisting of 172 individuals genotyped on 500,640 SNPs. We merged the data from the Affymetrix Human Origins arrays with the Ashkenazi Jewish data and data from the Simons Genome Diversity Project 19,20 to create a dataset with 4,402 individuals genotyped on 512,615 SNPs. We analyzed the four datasets separately due to the small intersection of SNPs between them.…”

Ancient DNA comes of age, but still has some teenage problems

“…8 This hive of African DNA analysis does not even include a wider range of research on the genetic lineages of living African peoples in search of the elusive point of divergence of our ancestors from the Neanderthals and other archaic populations and the subsequent divergence of populations in Africa. [9][10][11][12][13][14] But there are problems. This rush to extract the secrets of ancient DNA in Africa has presented the curators of the collections of archaeological skeletons with ethical issues because the research requires the destruction of human bone.…”