Comparing population structure as inferred from genealogical versus genetic information

Abstract

Algorithms for inferring population structure from genetic data (ie, population assignment methods) have shown to effectively recognize genetic clusters in human populations. However, their performance in identifying groups of genealogically related individuals, especially in scanty-differentiated populations, has not been tested empirically thus far. For this study, we had access to both genealogical and genetic data from two closely related, isolated villages in southern Italy. We found that nearly all living individuals were included in a single pedigree, with multiple inbreeding loops. Despite F st between villages being a low 0.008, genetic clustering analysis identified two clusters roughly corresponding to the two villages. Average kinship between individuals (estimated from genealogies) increased at increasing values of group membership (estimated from the genetic data), showing that the observed genetic clusters represent individuals who are more closely related to each other than to random members of the population. Further, average kinship within clusters and F st between clusters increases with increasingly stringent membership threshold requirements. We conclude that a limited number of genetic markers is sufficient to detect structuring, and that the results of genetic analyses faithfully mirror the structuring inferred from detailed analyses of population genealogies, even when F st values are low, as in the case of the two villages. We then estimate the impact of observed levels of population structure on association studies using simulated data.

Genetic genealogy comes of age: Perspectives on the use of deep‐rooted pedigrees in human population genetics

“…One study revealed strong genetic inbreeding in two isolated villages in Italy six km apart from each other. Extensive genealogical data of all participants from those villages confirmed the observed inbreeding patterns based on full genome data and could give more insights in the effect of inbreeding on the genome (Colonna et al, 2009). Another genomic study in Quebec (Canada) by Roy- showed significant population structure that corroborated the genealogical analysis that was performed previously (Gagnon and Heyer, 2001;Bherer et al, 2011).…”

Small effective population size and genetic homogeneity in the Val Borbera isolate

“…Despite clustering analysis of the villages showing no significant stratification (P-value 40.05 for both first and second principal components, Supplementary Figure 8), F ST values indicate some extent of structuring, which has already been observed in isolates, 43,44 even for populations with recent shared genealogy. 45 We speculate that the slight observed stratification can be related to the high proportion of marriages occurring between inhabitants of the same village, as demonstrated by analysis of marriage acts and surnames (data not shown). Further, we observe a more rapid decay of LD in the valley with respect to villages and opposite trend of LD-based estimates of nN e consistently with metapopulation dynamics.…”

Fine-scale human genetic structure in Western France

“…[10][11][12] Evidence of population structure accumulates at the scale of European countries [13][14][15][16][17][18] and even at a finer scale. 19,20 Fine-scale genetic structure can result from different processes including founder effect, endogamy, historical migration, cultural barriers to gene flow or selection processes. 11,21,22 Our study focuses on genetic variation in Western France as defined by Historical Geography literature.…”