Figure 3.

IBD network community detection

We infer the community structure using the Infomap algorithm based on a matrix of IBD segments >5 cM.

(A) Top 20 IBD network communities. Only individuals with connections >30 are included in the layout calculation for visualization purposes. The community labels, such as CA1 and CA2, are named according to the IBD version used and the rank of the community sizes, with CA1 representing the largest community when using all IBD segments, including short (5–9.3 cM) and long (>9.3 cM) segments.

(B) Average IBD sharing among the top 30 inferred communities (ordered by agglomerative clustering; the same order is followed in C and D).

(C) Distribution of IBD shared among individuals in each community.

(D) Enrichment of IBD community membership in the country of origin (i.e., proportions of community labels for individuals born in a given country). Note that for individuals without exact birth country information, broader geographic labels were used when available, such as Central America and South America. To visualize the dynamics before and after the Spanish colonization of the Americas, two different IBD networks were built based on IBD short (Figure S15) and long segments (Figure S16), respectively, which revealed distinct patterns of detected communities.