Signs of continental ancestry in urban populations of Peru through autosomal STR loci and mitochondrial DNA typing

<div><p>The human genetic diversity around the world was studied through several high variable genetic markers. In South America the demic consequences of admixture events between Native people, European colonists and African slaves have been displayed by uniparental markers variability. The mitochondrial DNA (mtDNA) has been the most widely used genetic marker for studying American mixed populations, although nuclear markers, such as microsatellite loci (STRs) commonly used in forensic science, showed to be genetically and geographically structured. In this work, we analyzed DNA from buccal swab samples of 296 individuals across Peru: 156 Native Amazons (Ashaninka, Cashibo and Shipibo from Ucayali, Huambiza from Loreto and Moche from Lambayeque) and 140 urban Peruvians from Lima and other 33 urban areas. The aim was to evaluate, through STRs and mtDNA variability, recent migrations in urban Peruvian populations and to gain more information about their continental ancestry. STR data highlighted that most individuals (67%) of the urban Peruvian sample have a strong similarity to the Amazon Native population, whereas 22% have similarity to African populations and only ~1% to European populations. Also the maternally-transmitted mtDNA confirmed the strong Native contribution (~90% of Native American haplogroups) and the lower frequencies of African (~6%) and European (~3%) haplogroups. This study provides a detailed description of the urban Peruvian genetic structure and proposes forensic STRs as a useful tool for studying recent migrations, especially when coupled with mtDNA.</p></div

Absolute and relative (%) frequencies of mtDNA haplogroups in urban Peruvian sample.

<p>Absolute and relative (%) frequencies of mtDNA haplogroups in urban Peruvian sample.</p

Inter population diversity fixation index (Fst) values for each STR locus, calculated both for Native Amazon <i>vs</i> urban Peruvian populations and for Native Amazons, urban Peruvians, US Europeans and US Africans.

<p>Inter population diversity fixation index (Fst) values for each STR locus, calculated both for Native Amazon <i>vs</i> urban Peruvian populations and for Native Amazons, urban Peruvians, US Europeans and US Africans.</p

Signs of continental ancestry in urban populations of Peru through autosomal STR loci and mitochondrial DNA typing - Fig 3

<p><b>a) DAPC of STR genotype database.</b> DAPC of STR genotype database of urban and Amazon native Peruvian, US European and US African populations. Scatter plot showing the first two principal components. Dots represent individuals. <b>b) Loading plot of DAPC.</b> The main allele contributors to individual DAPC clustering are shown.</p

Genetic diversity values of STR loci in Native and urban Peruvians.

<p>Genetic diversity values of STR loci in Native and urban Peruvians.</p

Map of sampling areas.

<p>The map shows the birthplace of sampled Peruvian urban and native individuals. Gray dots are native communities, black dots are towns or small cities.</p

mtDNAs from urban Peruvian samplesbelonging to non-native mtDNA haplogroups.

<p>mtDNAs from urban Peruvian samplesbelonging to non-native mtDNA haplogroups.</p

Percentage of molecular variance amount among groups, among populations within groups and within populations.

<p>Percentage of molecular variance amount among groups, among populations within groups and within populations.</p

Composition of DAPC clusters for STR genotypes.

<p>Vertical bars represent the proportion (%) of each cluster in each population. In the table the absolute and relative (%) frequencies of each cluster for each population are reported.</p

Diversity indices of mtDNA sequences from South America belonging to Native American haplogroups A, B, C and D.

<p>Diversity indices of mtDNA sequences from South America belonging to Native American haplogroups A, B, C and D.</p