Demographic history differences between Hispanics and Brazilians imprint haplotype features

Area of Science:

• Population Genetics
• Human Genomics
• Complex Trait Genetics

Background:

• Genetic admixture profoundly impacts population genetic landscapes.
• Human phenotype-related genetic variation differs across populations, yet admixed groups remain understudied.
• Latin American populations exhibit complex demographic histories, including admixture, bottlenecks, expansions, and continental adaptations.

Purpose of the Study:

• To investigate the impact of demographic history on the genetic structure of Latino populations.
• To analyze haplotype features like linkage disequilibrium, identity by descent, and homozygosity patterns.
• To identify genetic markers under selection in admixed populations.

Main Methods:

• Analysis of haplotype features: linkage disequilibrium, identity by descent segments, runs of homozygosity, and integrated haplotype score.
• Utilized data from Latinos in the 1000 Genome Project and Brazilian samples.
• Employed simulations to filter positive selection signals, accounting for random sampling and linkage disequilibrium.

Main Results:

• Linkage disequilibrium decay correlates with American and African ancestry proportions.
• Identity by descent sharing positively correlates with historical effective population sizes, generally steady or increasing, except in Puerto Ricans and Colombians.
• Runs of homozygosity were enriched only in Peruvians and Native Americans.
• Identified 244 unique markers under selection, with 26 common across multiple populations, some consistent with adaptation to the Americas.

Conclusions:

• Latino populations display highly divergent haplotype characteristics.
• These divergent features influence overall genetic architecture.
• Haplotype variations contribute to the basis of complex phenotypes in these admixed groups.