Fig. 3: Fine-scale genetic relationships and admixture between global populations.
From: Population genomics of ancient and modern Trichuris trichiura
a Admixture plot depicting population ancestry proportions determined using NGSadmix (K = 3, variants = 484,914). See Supplementary Fig. 6 for a complete analysis of K from 2 to 10. Ancient (AN) and baboon samples are highlighted. b Treemix maximum likelihood tree of ancient and modern samples, including Colobus and Leaf monkey samples as outgroups, showing three migration edges. See Supplementary Fig. 8 for a complete analysis of migration edges from 0 to 5. c Outgroup f3 statistics were determined using qp3Pop in ADMIXTOOLS to compare allele frequency correlations between two source populations (indicated on the left side of the panel) relative to an outgroup population (right side of the panel). f3 values (f3 = [foutgroup-fsource1]*[foutgroup-fsource2], where f is the allele frequency, averaged over all variable sites) are indicated by a point and whiskers represent the standard error, calculated using a weighted block jackknife (2,575,411 SNPs; n = 3 blocks; default parameters). For all data presented, the Z score was significant (|Z| > 3). d The population demographic history of each population was determined using SMC++ to compare effective population size (Ne) over recent evolutionary history. The grey vertical box highlights the period between 50 and 60 thousand years ago, coinciding with the migration of modern humans out of Africa. Sample abbreviations: CHN = China; UGA = Uganda; HND = Honduras.
