Biology subjects

Vezina, H.

Publications and source records attributed to Vezina, H..

4 recordsLinked to original sources

bioRxiv2022

GENLIB: new function to simulate haplotype transmission in large complex genealogies

SummaryFounder populations with deep genealogical data are well suited for investigating genetic variants contributing to diseases. Here, we present a new function added to the genealogical analysis R package GENLIB, which can simulate the transmission of haplotypes from founders to probands along very large and complex user-specified genealogies. Availability and implementationThe new function is available in the latest version of the GENLIB package (v1.1.6), available on the CRAN repository and from https://github.com/R-GENLIB/GENLIB. Stand-alone scripts for analyzing the output of the function can be accessed at https://github.com/R-GENLIB/simuhaplo_scripts.

bioinformatics↗

bioRxiv2022

Deciphering the genetic structure of the Quebec founder population using genealogies

Using genealogy to study the demographic history of a population makes it possible to overcome the models and assumptions often used in population genetics. The Quebec founder population is one of the few populations in the World having access to the complete genealogy of the last 400 years. The goal of this paper is to follow the evolution of the Quebec population structure generation per generation from the beginning of European colonization until the present day. To do so, we calculated the kinship coefficients of all ancestors pairs in the ascending genealogy of 665 individuals from eight regional and ethnocultural groups per 25-year period. We show that the Quebec population structure appeared in the St. Lawrence valley as early as 1750. At that time, the ancestors of two groups, the Sagueneans and the Acadians from the Gaspe Peninsula, experienced a marked increase in kinship and inbreeding levels which have shaped the contemporary population structure. Interestingly, this structure arose before the colonization of the Saguenay region and at the very beginning of the Gaspe Peninsula settlement. The resulting regional founder effects in these two groups, but also in the other regional groups, led to differences in the present-day identity-by-descent sharing and are directly linked to the number of most recent common ancestors and their genetic contribution to the studied subjects.

genetics↗

bioRxiv2022

On the Genes, Genealogies, and Geographies of Quebec

Population genetic models only provide coarse representations of real-world ancestry. We use a pedigree compiled from four million parish records and genotype data from 2,276 French and 20,451 French Canadian (FC) individuals, to finely model and trace FC ancestry through space and time. The loss of ancestral French population structure and the appearance of spatial and regional structure highlights a wide range of population expansion models. Geographic features shaped migrations throughout, and we find enrichments for migration, genetic and genealogical relatedness patterns within river networks across Quebec regions. Finally, we provide a freely accessible simulated whole-genome sequence dataset with spatiotemporal metadata for 1,426,749 individuals reflecting intricate FC population structure. Such realistic populations-scale simulations provide new opportunities to investigate population genetics at an unprecedented resolution. Lay SummaryWe all share common ancestors ranging from a couple generations ago to hundreds of thousands of years ago. The genetic differences between individuals today mostly depends on how closely related they are. The only problem is that the actual genealogies that relate all of us are often forgotten over time. Some geneticists have tried to come up with simple models of our shared ancestry but they dont really explain the full, rich history of humanity. Our study uses a multi-institutional project in Quebec that has digitized parish records into a single unified genealogical database that dates back to the arrival of the first French settlers four hundred years ago. This genealogy traces the ancestry of millions of French-Canadian and we have used it to build a very high resolution genetic map. We used this genetic map to study in detail how certain historical events, and landscapes have influenced the genomes of French-Canadians today. One-Sentence SummaryWe present an accurate and high resolution spatiotemporal model of genetic variation in a founder population.

genomics↗

bioRxiv2021

The effective family size of immigrant founders predicts their long-term demographic outcome: from Quebec settlers to their 20th-century descendants

Human evolution involves population splits, size fluctuations, founder effects, and admixture. Population history reconstruction based on genetic diversity data routinely relies on simple demographic models while projecting the past. No specific demographic assumptions are needed to understand the genetic structure of the founder population of Quebec. Because genealogy and genetics are intimately related, we used descending genealogies of this population to pursue the fate of its founder lineages. Maternal and paternal lines reflect the transmission of mtDNA and the Y-chromosome, respectively. We followed their transmission in real-time, from the 17th century down to its 20th-century population. We counted the number of married children of immigrants (i.e., their effective family size, EFS), estimated the proportion of successful immigrants in terms of their survival ratio, and assessed net growth rates and extinction. Likewise, we evaluated the same parameters for their Quebec-born descendants. The survival ratio of the first immigrants was the highest and declined over time in association with the decreasing immigrants EFS. Parents with high EFS left plentiful married progeny, putting EFS as the most important variable determining the parental demographic success throughout time for generations ahead. The 17th and 18th-century immigrants bear the most remarkable demographic and genetic impact on the 20th-century population of Quebec. Lessons learned from Quebec genealogies can teach us about the consequences of founder effects and migrations through real peoples history. The effective family size of immigrant founders predicts their long-term demographic outcome.

evolutionary biology↗