Computational protocol: Y Chromosome Lineages in Men of West African Descent

Similar protocols

Protocol publication

[…] To examine the Y chromosome diversity present in the African, Caribbean, and African American samples several diversity indices were estimated using Arlequin software . The following indices were estimated for each population: the number of haplotypes (k), haplotype diversity (H), allelic diversity (h), and mean pairwise differences (MPD). Here Y haplotypes are defined by the combination of tested alleles at each locus. In addition, Y chromosome average variance (based on the Y specific microsatellites) was estimated for each population. RST values using a stepwise mutation model and an analysis of molecular variance (AMOVA) were estimated to examine genetic distances between populations as well as test for the presence of population structure within the sampled groups. These analyses were also performed using Arlequin software . The genetic distances and the number of shared haplotypes were estimated between ethnic groups. The genetic distances were visualized using multidimensional scaling as implemented in the Statistica program.Expansion times for the West African Y chromosome lineage groups were estimated using the equation, t = −Ne ln(1−V/Neμ) and a mutation rate (μ) for Y chromosome microsatellites of 4.26×10−3 (95% CI, 2.38×10−3–7.26×10−3) as suggested from a recent examination of Y chromosome microsatellite mutation rates . The equation assumes a single-step mutation model for a haploid population and is robust for a population undergoing a strong bottleneck event followed by a rapid population expansion event . Among west African samples, we estimated the average variance (V) in microsatellite repeat numbers for each Y chromosome group denoted by the YAP and M89 polymorphisms. The effective population size (Ne) was assumed to be 1,000 and generation time of 25 years.Finally, proportions of European paternal ancestry were estimated using the weighted least squares method implemented in the ADMIX program (supplied by Dr. J.C. Long). […]

Pipeline specifications

Software tools Arlequin, Statistica
Applications Miscellaneous, Population genetic analysis
Organisms Homo sapiens, Oryza sativa