Single locus theory of admixture is insufficient for the study of complex traits in admixed populations

Admixed populations offer valuable insights into the genetic architecture of complex traits. Such an investigation demands a delicate theory that can handle the linkage disequilibrium structure of admixed genomes. With additional assumptions, we show that Pritchard-Stephens-Donnelly (PSD) can predict empirical GWAS findings. We call this the extended PSD (ePSD) model and evaluate the predictions using real data. When applied to real data of admixed genomes, the prediction of the ePSD model is very successful in explaining single-locus behaviors while falling short in predicting two-loci phenomena involving linkage disequilibrium. Our results show that a mosaic of independent single-continental segments is an insufficient approximation of contemporary admixed populations. A more advanced theory that better models linkage disequilibrium of admixed populations will be crucial to better understanding the genetic architecture of complex traits. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement MD-PhD/Medical Scientist Training Program through the Korea Health Industry Development (KHDI), funded by the Ministry of Health and Welfare, Republic of Korea. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present work are contained in the manuscript