Representation of effective migration surfaces as obtained with EEMS on the reduced datasets derived from sPC 1 (A) and sPC2 (B).

<p>The coloured area covers only the user-defined polygon. The grid used by the program is shown in grey. Note that only 34 sampled demes appear (black dots, with size proportional to the n. of individuals), assigned to a grid vertex and not necessarily coinciding exactly with the original sampling location. Pooled locations were (numbered as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0167065#pone.0167065.s011" target="_blank">S1 Table</a>): 6+7, 9+10, 13+14+15+16, 25+26, 30+32. Note the different colour scales between the two maps. In both maps brown belts correspond to low migration values, i.e. barriers to gene flow.</p

Maps of: A) scores for the 41 locations in sPC1 obtained on the full dataset with adegenet; B) scores in sPC2 obtained as in A; C) posterior assignment probabilities of the 41 locations to either of two clusters obtained on the reduced dataset derived from sPC1 with Geneland; D) posterior assignment probabilities of the 41 locations to either of two clusters obtained on the reduced dataset derived from sPC2 with Geneland.

<p>In A and B white and black squares represent negative and positive scores, respectively, with square size proportional to the absolute value (inset in panel A). In each of panels C and D shades of grey indicate probabilities of assignment to one of two mutually exclusive clusters from 0 (dark grey) to 1 (white). Color versions of panels C and D are reported in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0167065#pone.0167065.s007" target="_blank">S7 Fig</a>.</p

Loci and alleles with the strongest impact on the SpatialPCA eigenvalues 1 and 2.

<p>Loci and alleles with the strongest impact on the SpatialPCA eigenvalues 1 and 2.</p

Fst analysis in the main geographic regions.

<p>Fst analysis in the main geographic regions.</p

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

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

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

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