Fig 1.
Graphical representations of the coancestry model, the standard admixture model, and the super admixture model.
(A) In the coancestry model, individuals in the present-day population are connected by a complex genealogy. (B) In the standard admixture model, the arrows connecting T with reflect that the antecedent populations evolved independently from T. Arrows connecting
with individuals in the present-day population reflect that these individuals were admixed from independent antecedent populations.(C) In the super admixture model, dashed lines connecting all pairs of antecedent populations reflect that antecedent populations have coancestry parameterized by
. Arrows connecting
with individuals in the present-day population reflect that these individuals were admixed from covarying antecedent populations.
Fig 2.
Heatmaps of individual-level coancestry estimates in the Human Origins (HO) data set.
Each cell represents the estimated coancestry between a pair of individuals, with warmer colors indicating higher values. (A)–(C) show estimates from the observed genotypes using the Ochoa–Storey (OS) method, the super admixture method, and the standard admixture method, respectively. (D) shows estimates from bootstrap re-sampled genotypes using the OS method, with antecedent allele frequencies simulated under a double-admixture approach. (E) shows estimates from bootstrapped re-sampled genotypes using the OS method, with antecedent allele frequencies simulated using the NORTA approach. See Results for full details.
Fig 3.
Visualization of population-level coancestry and admixture proportions in the Human Origins (HO) data set.
(A) Heatmap of antecedent population coancestry estimates. (B) Dendrogram representation of the antecedent population coancestry estimates. (C) Stacked bar plot of admixture proportions. See Results for full details.
Fig 4.
Heatmaps of individual-level coancestry estimates in admixed individuals (AMR) from the 1000 Genomes Project.
Each cell represents the estimated coancestry between a pair of individuals, with warmer colors indicating higher values. (A)–(C) show estimates from the observed genotypes using the Ochoa–Storey (OS) method, the super admixture method, and the standard admixture method, respectively. (D) shows estimates from bootstrap re-sampled genotypes using the OS method, with antecedent allele frequencies simulated under a double-admixture approach. (E) shows estimates from bootstrapped re-sampled genotypes using the OS method, with antecedent allele frequencies simulated using the NORTA approach.
Fig 5.
Visualization of population-level coancestry and admixture proportions in admixed individuals (AMR) from the 1000 Genomes Project.
(A) Heatmap of antecedent population coancestry estimates. (B) Dendrogram representation of the antecedent population coancestry estimates. (C) Stacked bar plot of admixture proportions.
Fig 6.
Heatmaps of individual-level coancestry estimates in the merged data set of mainland Indians from IND, and Central/South Asians and East Asians from HGDP.
Each cell represents the estimated coancestry between a pair of individuals, with warmer colors indicating higher values. (A)–(C) show estimates from the observed genotypes using the Ochoa–Storey (OS) method, the super admixture method, and the standard admixture method, respectively. (D) shows estimates from bootstrap re-sampled genotypes using the OS method, with antecedent allele frequencies simulated under a double-admixture approach. (E) shows estimates from bootstrapped re-sampled genotypes using the OS method, with antecedent allele frequencies simulated using the NORTA approach.
Fig 7.
Visualization of population-level coancestry and admixture proportions in the merged data set of mainland Indians from IND, and Central/South Asians and East Asians from HGDP.
(A) Heatmap of antecedent population coancestry estimates. (B) Dendrogram representation of the antecedent population coancestry estimates. (C) Stacked bar plot of admixture proportions.