Tables from Admixed Ancestry and Stratification of Quebec Regional Populations:
Population stratification results from unequal, nonrandom genetic contribution of ancestors and should be reflected in the underlying genealogies. In Quebec, the distribution of Mendelian diseases points to local founder effects suggesting stratification of the contemporary French Canadian gene pool. Here we characterize the population structure through the analysis of the genetic contribution of 7,798 immigrant founders identified in the genealogies of 2,221 subjects partitioned in eight regions. In all but one region, about 90% of gene pools were contributed by early French founders. In the eastern region where this contribution was 76%, we observed higher contributions of Acadians, British and American Loyalists. To detect population stratification from genealogical data, we propose an approach based on principal component analysis (PCA) of immigrant founders' genetic contributions. This analysis was compared with a multidimensional scaling of pairwise kinship coefficients. Both methods showed evidence of a distinct identity of the northeastern and eastern regions and stratification of the regional populations correlated with geographical location along the St-Lawrence River. In addition, we observed a West-East decreasing gradient of diversity. Analysis of PC-correlated founders illustrates the differential impact of early versus latter founders consistent with specific regional genetic patterns. These results highlight the importance of considering the geographic origin of samples in the design of genetic epidemiology studies conducted in Quebec. Moreover, our results demonstrate that the study of deep ascending genealogies can accurately reveal population structure. Am J Phys Anthropol, 2010. [. . .]
Time of arrival and origins of the founders
In the genealogies of the 2,221 subjects sampled, we identified a total of 7,798 immigrant founders (Table 1 and Fig. 2A). Among these founders, there were 2.6 times as many males as females (Fig. 2B), consistent with the skewed male-to-female ratio among the first settlers of Nouvelle-France (Charbonneau et al., 1993). Seventy-two percent of the immigrant founders settled during the French Regime (1608–1760) and 24% came in two major waves of immigration, the first between 1663 and 1673 and the second a hundred years later between 1755 and 1765 (Fig. 2B, Supporting Information Fig. S2 and Table S2). The first wave corresponds to the arrival of French women, the so-called ‘‘Filles du Roy’’ who were sent from France to encourage stable family-based settlement in Nouvelle-France (Charbonneau et al., 1993). The second wave coincides with the British Conquest. It included Acadians escaping deportation by the British from their original settlements in Acadia as well as French soldiers who stayed in Quebec once the war ended (Charbonneau et al., 2000).
Sixty-eight percent of the immigrant founders came from France. French founders represent the vast majority of Europeans who settled before the British Conquest (Fig. 2C - Supporting Information Table S3). Only 3% of the founders married before 1700 did not originate directly from France. The proportion of such founders increased to 35% in the period from 1700 to 1760. Acadians represent 14% of all the immigrant founders (Fig. 2C - Supporting Information Table S3). The remaining founders of known origin came from Great- Britain (4%), Germany (2%), Ireland (3%), other European countries (1%) and other American locations (besides Acadia) (4%) (Supporting Information Table S3). Amerindian origin was documented for one per cent of founders. Overall, the period of arrival and origins of the immigrant founders appearing in the genealogical ascendance of our contemporary sample well reflected those of the pioneer immigrants that settled in Quebec prior to the British Conquest (Charbonneau et al., 2000).
Partitioning of founders among regions
Not every founder contributed descendants to all regions of Quebec. One fifth of the founders (n 5 1,612; 20.7%) were common, that is, they contributed to all eight regions of Quebec (Fig. 2A). More than half of the founders (n 5 4,330; 55.5%) contributed to 2–7 regions and more than one fifth (n 5 1,856; 23.8%) were specific to only one region (Fig. 2A). All founders common to all eight regions married during the French rule and 97.2% of them before 1700. By contrast, 70% of the specific founders arrived after the installment of the British rule in 1760. We observed a negative correlation between founders’ arrival time and the number of regions where they have descendants (Pearson’s r 5 20.6, P-value \ 2.2 3 10216).
Mosaic origins of Quebec regional populations
Nearly 90% of the regional gene pools were contributed by French founders (Table 2) and 2–6% by Acadians, who are second in numerical importance. Other groups of immigrant founders each contributed 2% or less. These proportions were similar across regions except for the East where the genetic contribution of French founders was reduced (76%) to the advantage of Acadian (11%), British (3.4%), and American founders (3.5%). Despite the elevated contribution of French founders, the subjects from our sample were nearly all admixed: on average, each genealogies contained immigrant founders from 6.75 distinct origins. While virtually all genealogies (99.1%) had at least one founder originating from France (Table 3), founders of other origins also appeared in a large proportion of the genealogies: British in 93% of genealogies, Acadian in 79% and notably, Amerindian in 47%.
Differential contribution of early and late founders
[. . .] All regional populations of Quebec (except for the North of Montreal) had a minimum of a third of their gene pools descending from the earliest founders, defined as those founders who married before the first major immigration wave of 1660 (Supporting Information Table S4). These founders were mostly French, represented 9.3% of all founders (Supporting Information Table S2) and 93% of them were found in at least six out of eight regions (75% common to all regions). For the North-East and Quebec City ancestors, the contribution of the earliest founders was even higher, increasing over time up to 50% and 44%, respectively. This increase is not compatible with a simple model of population expansion (Supporting Information Fig. S5). Even if we assume that the rate of migration tends to zero, the contribution of the earliest founders is expected to stabilize and not to increase. For the North-East and Quebec City area, it suggests that the earliest founders had on average a higher number of descendants than expected under the assumption of uniform reproductive success of all founders. This points to a higher reproductive success of the earliest founders and their descendants throughout the period.
A substantial fraction of regional gene pools was also explained by founders married between 1660 and 1700 (Figs. 4A,B and Supporting Information Fig. S4). These founders represented 32% of all founders (Supporting Information Table S2), were mostly French (97%) and had a lower regional representation than the earliest founders with 74% appearing in at least six regions (40% common to all eight regions). However, the fraction of the gene pool explained by the 1660–1700 founders differed across regions as it decreased to the profit either of the earliest founders (in the Quebec City area and North- East) and/or of latecomers, arrived after 1700 (in all regions). Notably, the East region displayed the highest contribution of late founders (Supporting Information Fig. S4) who are more specific and have more diversified origins (Table 2).