Application of Targeted Y-Chromosomal Capture Enrichment to Increase theResolution of Native American Haplogroup Q

Y-chromosomal haplogroups and the Y-SNPs defi ning them are relevant for the explorationof male lineages, inference of paternal ancestry, and reconstruction of migration pathways,to name a few. Currently, over 300,000 Y-SNPs have been reported, defi ning 20 mainhaplogroups. However, ascertainment bias in the investigations has led to somehaplogroups being overlooked, which hinders a representative depiction of certainpopulations and their migration events. For migration pattern analyses of the fi rst settlersof the Americas, the Native American main founding lineage Q-M3 needs to be furtherinvestigated to allow clear genetic diff erentiation of individuals of diff erent ethnogeographicorigins. To increase the resolution within this haplogroup, a total of 7.45 Mb of the Ychromosome of 59 admixed South Americans of haplogroup Q was targeted for sequencingusing hybridization capture enrichment. Data were combined with 218 publicly availablesequences of Central and South Americans of haplogroup Q. After rigorous data processing,variants not meeting the quality criteria were excluded and 4128 reliable Y-SNPs werereported. A total of 2224 Y-SNPs had previously unknown positions in the phylogenetic tree,and 1291 of these are novel. The phylogenetic relationships between the Y-SNPs wereestablished using the software SNPtotree in order to report a redesigned phylogenetic treecontaining 300 branches, defi ned by 3400 Y-SNPs. The new tree introduces 117 previouslyundescribed branches and is the most comprehensive phylogenetic tree of the NativeAmerican haplogroup Q lineages to date. The 214 sequences were assigned to 135 diff erentlow- to high-resolution branches, while in the previous phylogenetic tree, only 195sequences could be sorted into 14 low-resolution branches with the same quality criteria.