Computational protocol: Dissecting the Within-Africa Ancestry of Populations of African Descent in the Americas

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[…] Arlequin 3.11 was used to estimate genetic distances utilizing the phylogenetic relationship defined by 429 FASTA-formatted mtDNA haplotypes, assuming Tamura and Nei's model for nucleotide substitution. Analysis of molecular variance (AMOVA) was used to assess the between group and within-population variation for each step. SAMOVA 1.0 software , combining AMOVA with geographical information, was used to explore the clustering of geographic regions or ethnic groups of the whole and W/WC Africa based on the genetic variation. [...] Multidimensional scaling (MDS) plots were constructed using SPSS with input data in the form of an Arlequin-generated matrix of Slatkin's linearized FST distances , incorporating the phylogenetic relationship among the 429 mtDNA haplotypes. For each MDS plot, we report the stress and RSQ statistics, which summarize the goodness of fit of multidimensional data in 2 dimensions. Additionally, AMOVA was reported for the parental populations (indicated in each MDS figure) showing the percentage of variation captured by defining the language/geography/ethnicity groups. For Figure S7 in , the coordinates for MDS plot capturing Senegalese and US African Americans with <5% of European ancestry based on 175 AIMs were calculated using PLINK and plotted using Excel. […]

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