Hierarchical analysis of 30 Y-chromosome SNPs in European populations

Abstract

Analysis of Y-chromosome haplogroups defined by binary polymorphisms, has became a standard approach for studying the origin of modern human populations and for measuring the variability between them. Furthermore, the simplicity and population specificity of binary polymorphisms allows inferences to be drawn about the population origin of any male sample of interest for forensic purposes. From the 245 binary polymorphisms that can be analysed by PCR described in the Y Chromosome Consortium tree, we have selected 30 markers. The set of 30 has been grouped into 4 multiplexes in order to determine the most frequent haplogroups in Europe, using only 1 or 2 multiplexes. In this way, we avoid typing unnecessary SNPs to define the final haplogroup saving effort and cost, since we only need to type 9 SNPs in the best case and in the worst case, no more than 17 SNPs to define the haplogroup. The selected method for allele discrimination was a single base extension reaction using the SNaPshot multiplex kit. A total of 292 samples from 8 different districts of Galicia (northwest Spain) were analysed with this strategy. No significant differences were detected among the different districts, except for the population from Marina Lucense, which showed a distant haplogroup frequency but not higher Phi(st) values.

Admixture and population structure in Mexican-Mestizos based on paternal lineages

“…Finally, in anthropology, these results contribute to historical research, providing an overview of male migration effects after European contact in Mexican territory. 33 European and Native American paternal ancestry The frequency of European haplogroups R1b1*, R*, R1a*, I* and E1b1b1* (49.9%) plus Eurasian haplogroups G*, J* and K* (14.7%) defined the total European ancestry of Mexican-Mestizos in 64.6% Eurasian lineages; that is, those found both in Asia and in Europe, were considered European rather than Asian based on the following: (1) historical records on Mexican population that largely involve Spanish conquerors; 3,34 (2) the elevated frequency of the cited Eurasian lineages in Europe, particularly in the Iberian Peninsula, where Spain is located, 22,[35][36][37][38] and (3) the scarce frequency of Asian ancestry (range, 1-1.4%) detected in Mexican-Mestizos according to genome-wide SNP results. 5 A higher frequency of European ancestry was observed in the north and west and vice versa; Native American ancestry increased toward Center-South and southeast (Table 2) (Figure 3).…”

The relationship between surname frequency and Y chromosome variation in Spain

“…Further information on the loci can be found on the YHRD and NIST webpages (www.yhrd.org; www.cstl.nist.gov/strbase/y_strs.htm). Twentytwo slowly mutating SNP markers (SRY-1532, M213, M9, M70, 92R7, M22, TAT, M173, P25, M269, M62, M172, M170, M26, M304, M201, M34, M81, M78, M35, M96 and M123) were grouped in three different multiplex sets, as previously described, 11 and SNP results were used to assign Y chromosome haplogroups. Multiplex PCR amplification of DNA samples was performed using the Type-it Microsatellite PCR kit (QIAGEN, Dusseldorf, Germany).…”

Between Andes and Amazon: The genetic profile of the Arawak‐speaking Yanesha

“…Sixteen SNPs were tested with a SNaPshot TM Multiplex kit (Applied Biosystems) as described in Brion et al (2005). The first multiplex identified major European clades which were subsequently confirmed through their Y-STR profiles (Bayesian inference by THE GENETIC PROFILE OF ARAWAK-SPEAKING YANESHA http://www.hprg.com/hapest5/).…”