Applications of Identity-By-Descent Analysis in Population Genetics Research: Methods for Demographic History Inference and Genetic Association Analysis

Abstract

The analysis of identity-by-descent (IBD) segments is an important tool in population genetics research and has led to important discoveries about human genetic history and population structures. While previous research has made significant progress in utilizing IBD segments to study population genetics, ongoing methodological advancements and increasing availability of genomic data create new opportunities for further exploration of the power of IBD segments in population genetics research. In this dissertation, we further explore the potential of IBD information in two key areas of genetics research: inferring demographic history and performing genetic association analysis (IBD mapping) for complex traits. First, we present a method to estimate the X chromosome effective population size using X chromosome IBD segments, and we demonstrate how the X chromosome effective population size can be combined with autosomal effective population size to inform sex-specific demographic history. Second, we introduce an IBD mapping approach for association analysis between genome-wide loci and complex traits, along with a novel multiple testing adjustment strategy that accounts for the correlation structure among test statistics in genome-wide IBD scans. Our research contributes new statistical and computational tools that enhance the use of IBD information in demographic inference and genetic association studies, improving our understanding of human evolutionary history and the genetic architecture of complex traits.