Early modern human dispersal from Africa: genomic evidence for multiple waves of migration

Abstract

[...]modern populations might differ in the amount of archaic genes incorporated in their gene pool, which are eventually expressed and may result in phenotypic differences affecting, for example, the immune response [8] or lipid catabolism [9]. To obtain insight into the past history of Eurasian populations, we analyzed genome-wide autosomal single nucleotide polymorphisms (SNPs) from 71 worldwide populations (Additional files 1 and 2). When merging data from different SNP chip versions, strand identification can be ambiguous, possibly leading to mistakes in identifying the right alleles for A/T and G/C SNPs (as also reported in the PLINK tool documentation [37]). [...]to preserve as much genetic information as possible, we selected from each dataset only these ambiguous SNPs and we used the information contained in the Affymetrix Annotation file to evaluate the strand polarity used to define each allele.