The history of Ecuador was marked by the arrival of Europeans with Africans, resulting in the mixture of Native Americans with Africans and Europeans. The present study contributes to the knowledge of the Ecuadorian mestizo population by offering information about ancestry and ethnic heterogeneity. Forty-six AIM-InDels (Ancestry Informative Insertion/Deletion Markers) were used to obtain information on 240 Ecuadorian individuals from three regions (Amazonia, the Highlands, and the Coast). As a result, the population involved a significant contribution from Native Americans (values up to 51%), followed by Europeans (values up to 33%) and Africans (values up to 13%). Furthermore, we compared the data obtained with nine previously reported scientific articles on autosomal, mitochondrial DNA and Y chromosomes. The admixture results correspond to Ecuador’s historical background and vary slightly between regions.

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Fifteen autosomal STRs were analyze in order to elucidate the differences between low and high land Ecuadorian population. Seven Ecuadorian geographic areas

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The X-STR markers represent a powerful tool to complement the information provided by the autosomal and Y chromosome markers, particularly, in cases involving at least one woman. In the present study, allele frequencies, power of exclusion (PE), power of discrimination (PD) and polymorphism information content (PIC) were analyzed for 12 X chromosome loci. A total of 200 unrelated Ecuadorian individuals were selected for the population analysis. The data showed that DXS10135 locus had the highest power of discrimination value (PD = 0.9351), and polymorphism information content (PIC = 0.9313). The heterozygosity observed ranged from 0.9300 to 0.6400. The power of exclusion varied between 0.3417 to 0.8570 for DXS10135 and DXS8378 respectively. No significant departure from Hardy Weinberg equilibrium (HWE) was detected for any of the analyzed markers. The X-STR markers have demonstrated their potential to efficiently complement the analysis to solve complex kinship and forensic cases.