Testing support for the northern and southern dispersal routes out of Africa: an analysis of Levantine and southern Arabian populations

Abstract

Our results are consistent with a history of gene flow between the Levant and southern Arabia. Consideration of genetic, archaeological, and paleoclimate data provide a slight edge for the SDR but, ultimately, more data are needed to definitively identify which dispersal route out of Africa was used.

Analyses of Neanderthal introgression suggest that Levantine and southern Arabian populations have a shared population history

“…We analyzed genotyping data from the Affymetrix Human Origins array (Patterson et al, 2012) from three Yemeni populations (n=90) and three Eritrean individuals generated by Vyas, Al-Meeri, & Mulligan (2017a) along with populations from around the world selected from the “fully public” and “restrictive” datasets from Lazaridis et al (2014) to yield a total modern human dataset of 2058 individuals from 165 populations. The data from Vyas et al (2017a) are available on the Dryad Digital Repository (https://doi.org/10.5061/dryad.1pm3r) (Vyas, Al-Meeri, & Mulligan, 2017b). Data from the Altai Neanderthal, composite Vindija Neanderthal, and Denisovan genomes were also obtained from the “fully public” dataset from Lazaridis et al (2014) (Green et al, 2010; Meyer et al, 2012; Prüfer et al, 2014; Reich et al, 2010).…”

“…Data from the Altai Neanderthal, composite Vindija Neanderthal, and Denisovan genomes were also obtained from the “fully public” dataset from Lazaridis et al (2014) (Green et al, 2010; Meyer et al, 2012; Prüfer et al, 2014; Reich et al, 2010). Data from Lazaridis et al (2014) were converted to Plink format using EIGENSOFT and then merged with the data from Vyas et al (2017a) using Plink v1.07 (Patterson, Price, & Reich, 2006; Price et al, 2006; Purcell et al, 2007). To avoid the effects of sex-biased demographic events, we only analyzed data from autosomal SNPs.…”

“…Throughout this study, the BedouinA, BedouinB, Druze, Jordanian, Lebanese, Palestinian, and Syrian populations from Lazaridis et al (2014) were considered as representative Levantine populations, and the Yemen Desert, Yemen Highlands, and Yemen Northwest from Vyas et al (2017a) as well as the Saudi and Yemenite Jewish populations from Lazaridis et al (2014) were considered as representative southern Arabian populations; a map of these populations is depicted in Figure 1. Consistent with Vyas et al (2017a), we labeled the Yemeni population from Lazaridis et al (2014) as “Kuwaiti Yemeni” and did not include them as a southern Arabian population.…”

“…All populations analyzed in this study are listed in Table S1 along with their sample sizes, geographic region identifiers, and the analyses in which they were used. Populations were grouped into regions based on geography (e.g., Oceania, Siberia, West Africa), and some regions were also grouped into larger regions (e.g., eastern Europe, western Europe, northern Europe, and southern Europe were grouped into Europe); groupings were assigned based on groupings from Vyas et al (2017a), which were derived from Lazaridis et al (2014). In many analyses, populations were also pooled based on regions or larger regions (e.g., Europe, South Asia, Oceania) in order to provider clearer comparisons between different parts of the world; these pooled populations are listed in Table S1.…”

“…Finally, to confirm that a SNP was due to Neanderthal introgression and not due to an ancient polymorphism shared between Neanderthals and modern humans, SNPs were removed if the Neanderthal alleles were present in sub-Saharan African populations (since Neanderthal introgression is not thought to have occurred in Africa). Since many sub-Saharan African populations have low levels of Neanderthal introgression due to admixture from back-migrations and gene flow with Eurasia (e.g., Hodgson, Mulligan, Al-Meeri, & Raaum, 2014; Llorente et al, 2015; Pagani et al, 2012; Pagani et al, 2015; Skoglund et al, 2017; S. Wang, Lachance, Tishkoff, Hey, & Xing, 2013), we only filtered using African populations that were non-admixed per the ADMIXTURE results from Vyas et al (2017a) (i.e., BantuKenya, Biaka, Dinka, Esan, Hadza, Luhya, Luo, Mende, Mbuti, and Yoruba). These ten sub-Saharan African populations have a total of 167 genotyped individuals and all of the SNPs with a non-zero frequency in this set of individuals were removed (i.e., if even one of these individuals had an allele matching the Neanderthal, the SNP was removed).…”