Disentangling Signatures of Selection Before and After European Colonization in Latin Americans

Area of Science:

• Human evolutionary genetics
• Population genetics
• Genomics

Background:

• Human evolutionary history is marked by large-scale migrations and admixture between distinct populations.
• While admixture offers historical insights, its role in human adaptation is underexplored.
• Identifying genetic selection in admixed groups requires specialized analytical approaches.

Purpose of the Study:

• To develop and validate a novel statistical model for detecting selection in admixed populations.
• To differentiate between selection that occurred prior to admixture versus post-admixture.
• To investigate genetic adaptations in admixed Latin American populations.

Main Methods:

• Development of a novel statistical model tailored for admixed populations to detect loci under selection.
• Extensive simulations to assess the model's accuracy in detecting selection and differentiating its timing (ancestral vs. admixed).
• Application of the model to genome-wide SNP data from approximately 4,000 individuals across five admixed Latin American cohorts.

Main Results:

• The method successfully detects selection in recently formed admixed populations and accurately distinguishes selection timing.
• Replication of known selection signals in the human leukocyte antigen (HLA) region, consistent with post-admixture selection.
• Identification of novel selection signals in 47 genes, including those related to immunity and energy metabolism, with many signals reinforced by an alternative local-ancestry-inference approach.

Conclusions:

• The developed statistical model is effective for identifying selection in admixed populations.
• Admixture has contributed to adaptive evolution in human populations, particularly in response to environmental factors like pathogens and diet.
• Novel genetic adaptations related to immunity and metabolism have been identified in Latin American admixed populations, reflecting their unique evolutionary history.