The samples were genotyped for five Y‐SNPs found in the South American natives, M130, M242, M346, L54 and M3 (Karafet et al., 2008; Jota et al., 2011), using TaqMan assays (ABI) and a 7900HT Fast Real‐Time PCR System (ABI). Next, the Q‐M3 and Q‐M346* lineages were genotyped with 17 Y‐chromosome short tandem repeats (Y‐STRs) using Y‐filer Kit (ABI). The PCR reactions were performed following Sandoval et al. (2013b) and their products were subjected to capillary electrophoresis using the ABI 3130XL Genetic Analyzer (Applied Biosystems), with the alleles being visualised by the GeneMapper ID v3.2 software (Applied Biosystems, Foster City, California, USA). The DYS389b allele scoring was done by subtracting DYS389I from DYS389II (Zerjal et al., 1997) and the DYS385 marker was not included in the statistical analyses.
The complete mtDNA control region (1122 bp, 16024–576) according to the revised Cambridge Reference Sequence (rCRS; Andrews et al., 1999) was amplified and sequenced following Sandoval et al. (2013b), using a 3130XL Genetic Analyzer (ABI) and Big Dye Terminator v. 3.1. protocol. The sequence alignments were performed in relation to rCRS through SeqScape 2.6 software (Applied Biosystems), and major haplogroup assignment was obtained by MitoTool (Fan & Yao, 2011) or haplogroup prediction tool from the Genographic Project (Behar et al., 2007). Due to phylogenetic uncertainty and alignment controversy, the alignments at nucleotide positions 309.1C, 315.1C, indels at 515–522, 16182C, 16183C, 16193.1C and 16519 were not taken into account in the statistical analyses.
The complete mtDNA control region (1122 bp, 16024–576) according to the revised Cambridge Reference Sequence (rCRS; Andrews et al., 1999) was amplified and sequenced following Sandoval et al. (2013b), using a 3130XL Genetic Analyzer (ABI) and Big Dye Terminator v. 3.1. protocol. The sequence alignments were performed in relation to rCRS through SeqScape 2.6 software (Applied Biosystems), and major haplogroup assignment was obtained by MitoTool (Fan & Yao, 2011) or haplogroup prediction tool from the Genographic Project (Behar et al., 2007). Due to phylogenetic uncertainty and alignment controversy, the alignments at nucleotide positions 309.1C, 315.1C, indels at 515–522, 16182C, 16183C, 16193.1C and 16519 were not taken into account in the statistical analyses.