American journal of biological anthropology · 2026
Runs of Homozygosity and Signatures of Positive Selection in Colombian Native American Populations: Genetic Architecture and Demographic History.
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Criollo-Rayo Angel, Rubio-Vargas Catalina, Puentes Carlos, Molina-Campos Daniel, Bohórquez Mabel Elena, Carracedo Angel, Estrada-Flórez Ana, Díaz-Carmona Danna, Castro-Valencia Fabian, Carvajal-Carmona Luis, Echeverry María Magdalena
Аннотация
OBJECTIVES: Runs of homozygosity (ROHs) are suitable for studying population demographic history. This study analyzed whole-genome patterns of homozygosity and natural selection in Colombian indigenous populations to identify their role in population structure and demographic history.
MATERIALS AND METHODS: Individuals from four indigenous groups (Nasa, Pijao, Wayuu, and Emberá) were genotyped using an array of 758,740 SNPs. ROH distribution across the genome and signatures of selection were characterized and compared with reference populations.
RESULTS: Colombian Native Americans showed a population structure similar to that of Central and South American indigenous groups, with higher genome-wide homozygosity (mean = 179.40 Mb, median = 168.77 Mb, SD = 98.08 Mb), and the Emberá group showed the highest mean ROH size (2.46 Mb) and FROH (0.092). Admixture was negatively correlated with ROH content and length. We described 16 ROH islands and selection signatures, including EDAR, F13A1, SASH1, IYD, and FADS1, with the strongest ROH-selection co-occurrence at 2q24.2. These genomic regions showed larger haplotype blocks and reduced diversity compared with Europeans and Africans.
DISCUSSION: Frequent ROH islands in Colombian indigenous groups revealed homozygous chromosomal regions enriched for genes previously reported to be associated with cancer and metabolic and cardiovascular conditions. These islands harbor highly differentiated alleles in Native Americans, including signals of natural selection. However, the presence of these genes within ROH regions does not imply a direct association with disease in the populations analyzed here. Rather, these findings provide a foundational genomic resource for future phenotype-inclusive studies of complex disease architecture in Native American populations.
MATERIALS AND METHODS: Individuals from four indigenous groups (Nasa, Pijao, Wayuu, and Emberá) were genotyped using an array of 758,740 SNPs. ROH distribution across the genome and signatures of selection were characterized and compared with reference populations.
RESULTS: Colombian Native Americans showed a population structure similar to that of Central and South American indigenous groups, with higher genome-wide homozygosity (mean = 179.40 Mb, median = 168.77 Mb, SD = 98.08 Mb), and the Emberá group showed the highest mean ROH size (2.46 Mb) and FROH (0.092). Admixture was negatively correlated with ROH content and length. We described 16 ROH islands and selection signatures, including EDAR, F13A1, SASH1, IYD, and FADS1, with the strongest ROH-selection co-occurrence at 2q24.2. These genomic regions showed larger haplotype blocks and reduced diversity compared with Europeans and Africans.
DISCUSSION: Frequent ROH islands in Colombian indigenous groups revealed homozygous chromosomal regions enriched for genes previously reported to be associated with cancer and metabolic and cardiovascular conditions. These islands harbor highly differentiated alleles in Native Americans, including signals of natural selection. However, the presence of these genes within ROH regions does not imply a direct association with disease in the populations analyzed here. Rather, these findings provide a foundational genomic resource for future phenotype-inclusive studies of complex disease architecture in Native American populations.