Mitochondrial DNA analysis has proven to be a powerful tool to study maternal inheritance among populations. It is also useful to infer geographical origin and relationships between individuals and population samples. In this study, mtDNA control region was sequenced from 54 self-declared Ecuadorian mestizos. Haplotype diversity (0.9986 +/-0.0039) and mean number of pairwise differences (17.586303 +/-7.933894) were high, in accordance to previous studies. Around 96% of the analyzed individuals had Native American maternal lineages. Based on genetic distances, Ecuador showed significant differences with other South American populations, except in the comparison with another sample from Ecuadorian mestizos, as expected.

Objectives According to demographic history, Ecuador has experienced shifts in its Native American populations caused by European colonization and the African slave trade. The continuous admixture events among Europeans, Native Americans, and Africans occurred differently in each region of the country, producing a stratified population. Thus, the aim of this study was to investigate the level of genetic substructure in the Ecuadorian Mestizo population. Materials and methods A total of 377 male and 209 female samples were genotyped for two sets of X‐chromosomal markers (32 X‐Indels and 12 X‐STRs). Population analyses performed included Hardy–Weinberg equilibrium tests, LD analysis, PCA, pairwise FSTs, and AMOVA. Results Significant levels of LD were observed between markers separated by distances of less than 1 cM, as well as between markers separated by distances varying from 10.891 to 163.53 cM. Among Ecuadorian regions, Amazonia showed the highest average R2 value. Discussion When X‐chromosomal and autosomal differentiation values were compared, a sex‐biased admixture between European men and Native American and African women was revealed, as well as between African men and Native American women. Moreover, a distinct Native American ancestry was discernible in the Amazonian population, in addition to sex‐biased gene flow between Amazonia and the Andes and Pacific coast regions. Overall, these results underline the importance of integrating X chromosome information to achieve a more comprehensive view of the genetic and demographic histories of South American admixed populations.

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