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Estimated ages of the introgressed haplotypes The majority of haplotypes shared between present-day humans and an archaic genome should result from incomplete lineage sorting in the population ancestral to them and, thus, be old and short.
HLA alleles and conserved extended haplotypes were analyzed by using high resolution HLA typing based on Sanger sequencing and next generation sequencing.
All haplotypes were submitted to Whit Athey’s Haplogroup Predictor (Athey, 2006) to obtain probabilities for the inferred haplogroups.
First, pairs of DNA-donors with a common documented ancestor in paternal lineage but with a different Y-chromosomal sub-haplogroup or Y-STR-haplotypes with more than six differences (out of 38 Y-STRs) were excluded from the dataset.
A haplogroup is really a large band of haplotypes, are often geographically oriented and are used to define genetic populations.
MVR haplotypes of aligned alleles in the group marked a are shown in Fig.
(2014) with minor modifications that are aimed to make the haplogroup nomenclature more amenable to the incorporation of novel haplotypes than it is now (Supplemental Information 6).