These cell lines and DNA samples were prepared from blood samples collected from people living in the Lima-Callao, Peru metropolitan who identify themselves as having four grandparents who were born in Peru.
The samples were collected from people from many different parts of Peru. Also, many of their ancestors came from different regions of Europe and Africa.
Referring to Populations
It is important to refer to this community as "Peruvian in Lima, Peru (PEL)" when describing these samples in articles or presentations. These samples should not be referred to as “Hispanic” or “Latino” since these are cultural designators, encompassing diverse communities.
The full population descriptor is Peruvian in Lima, Peru (PEL) and the abbreviation is PEL.
Additional guidance about how to refer to the populations can be found at Guidelines for Referring to the Populations in Publications and Presentations.
- Carla Gallo - Universidad Peruana Cayetano Heredia, Peru
- Giovanni Poletti - Universidad Peruana Cayetano Heredia, Peru
- Mao X, Bigham AW, Mei R, Gutierrez G, Weiss KM, Brutsaert TD, Leon-Velarde F, Moore LG, Vargas E, McKeigue PM, Shriver MD, Parra EJ. (2007) A genomewide admixture mapping panel for Hispanic/Latino populations. Am J Hum Genet 80(6):1171-8.
- Price AL, Patterson N, Yu F, Cox DR, Waliszewska A, Mcdonald GJ, Tandon A, Schirmer C, Neubauer J, Bedoya G, Duque C, Villegas A, Bortolini M-C, Salzano Fm, Gallo C, Mazzotti G, Tello-Ruiz M, Riba L, Aguilar-Salinas CA, Canizales-Quinteros S, Menjivar M, Klitz W, Henderson B, Haiman CA, Winkler C, Tusie-Luna T, Ruiz-Linares A, Reich D. (2007) A genomewide admixture map for Latino populations. Am J Hum Gene 80(6):1024-1036.
- Wang S, Ray N, Rojas W, Parra Mv, Bedoya G, Gallo C, Poletti G, Mazzotti G, Hill K, Hurtado AM, Camrena B, Nicolini H, Klitz W, Barrantes R, Molina JA, Freimer N, Bortolini MC, Salzano FM, Petzl- Erler ML, Tsuneto LT, Dipierri JE, Alfaro EL, Bailliet G, Bianchi NO, Llop E, Rothhammer F, Excoffier L, Ruiz-Linares A. (2008) Geographic patterns of genome admixture in Latin American Mestizos. PLoS Genetics 4(3):e1000037.
Tracing the genomic ancestry of Peruvians reveals a major legacy of pre-Columbian ancestors
In order to investigate the underlying genetic structure and genomic ancestry proportions of Peruvian subpopulations, we analyzed 551 human samples of 25 localities from the Andean, Amazonian, and Coastal regions of Peru with a set of 40 ancestry informative insertion–deletion polymorphisms. Using genotypes of reference populations from different continents for comparison, our analysis indicated that populations from all 25 Peruvian locations had predominantly Amerindian genetic ancestry. Among populations from the Titicaca Lake islands of Taquile, Amantani, Anapia, and Uros, and the Yanque locality from the southern Peruvian Andes, there was no significant proportion of non-autochthonous genomes, indicating that their genetic background is effectively derived from the first settlers of South America. However, the Andean populations from San Marcos, Cajamarca, Characato and Chogo, and coastal populations from Lambayeque and Lima displayed a low but significant European ancestry proportion. Furthermore, Amazonian localities of Pucallpa, Lamas, Chachapoyas, and Andean localities of Ayacucho and Huancayo displayed intermediate levels of non-autochthonous ancestry, mostly from Europe. These results are in close agreement with the documented history of post-Columbian immigrations in Peru and with several reports suggesting a larger effective size of indigenous inhabitants during the formation of the current country’s population.
In recent years, some ancestry studies performed with Central and South American populations showed that ancestry proportions (in relation to aboriginal populations of continents) vary depending on their particular demographic dynamics and colonization history.1, 2, 3, 4
Like most Latin American populations,2, 4 current Peruvians were mainly formed during colonial times by three ancestral components: autochthonous Americans, Eurasians (mostly from Europe) and Africans. However, Peru is also known by the large numbers of indigenous populations reported when the Spaniards arrived in the region, particularly represented by the largest cities found in America and the vast Inca Empire at the time of European contact.5
In order to investigate the past dynamics of gene flow and continental roots of Latin American populations, ancestry components and admixture levels can be estimated with informative autosomal markers. A previous study with 642 690 randomly chosen autosomal single-nucleotide polymorphisms6 genotyped in reference continental populations from the HGDP-CEPH panel observed a remarkable structure according with their geographical distribution. Also, another preliminary study with a selected set of 40 autosomal insertion-deletion (INDELs) polymorphisms7 in the same panel of continental populations obtained virtually the same result, showing to be sufficiently informative for an adequate characterization of human population structure at the global level. Thus, a relatively increased resolution can be obtained with informative INDELs selected on the basis of alleles with divergent frequencies among continental populations, commonly known as ancestry informative markers. Recently, these 40 INDELs were successfully used to discriminate among autochthonous American, European and African ancestry in the admixture analysis of populations from different regions of Brazil.3
On the pre-Columbian settlement of Peru
The archeological, paleontological and human skeletal remains indicate that the first hunter-gatherers appeared in Peru at about 12 000 years ago (late Pleistocene), inhabiting Andean areas around the Guitarrero Cave, Ancash8 and Ayacucho complex.9 Along the Pacific coast, some traces of the earliest human groups were dated to about 7000 years ago,10 which later may have originated some ancient civilizations like Caral (north of Lima). The earliest evidences revealed the formation of emergent societies around the Titicaca Lake, dating about 4000 years ago.11 By about 3000 years ago,12, 13 other civilizations appeared, Chavín in the north and Paracas in the south, and soon after 2 100 years ago, others emerged such as Moche (north coast), Nazca (central coast), Wari (south-central Andes), Chimú (north coast) and Chachapoyas (current Amazonas Department). Finally, the Tawantin Suyu Empire (1432–1532), which was dominated by the Incas, controlled the Andean regions of Peru, Ecuador and Bolivia, and part of Argentina, Chile and Colombia.5
During the Tawantin Suyu, the Quechua language expanded throughout most of the Andes by means of the Inca road (Qhapaq Ñan), leading also to a concurrent admixture between northern and southern subpopulations, including Inca and non-Inca groups.14, 15, 16, 17
The migration flows and admixture in the post-Columbian Peru
The first Europeans that arrived in Peru in the XVI century were mainly from Spain, who also brought some Africans as slaves.5 In 1849 started an immigration from China to all regions of Peru to work in plantations and guano exploitation,18 and since 1899 there were also some Japanese immigrants. In 1853, some German families immigrated with the goal to colonize the Amazon region, but large numbers of Europeans from Italy and other countries came in the beginning of the XX century,5 particularly during the first world war and beginning of the second (1918–1938). During the first decade of the XX century, an important internal migration flow happened in the Peruvian Amazon, when many urban and indigenous communities were displaced from their homelands to profit or run away from the rubber industry boom.5 However, since 1940 a large migration movement took place inside of Peru, mainly to Lima coming from Junín, Ayacucho, La Libertad, Ica, Lambayeque, Cajamarca, Piura and in a lesser degree from other places.5 This late XX century internal migration was mostly composed by rural and indigenous people that moved to urbanized cities, thus we would expect a large impact on the genomic ancestry of the inhabitants of large urban centers like Lima.
Our present study is focused on uncovering the population structure due to possibly different ancestral backgrounds in the human genomes of contemporaneous subpopulations of Peru, based on the detailed analyses of 40 INDELs.7 We calculated the genomic ancestry proportions of 25 subpopulations from all major regions of Peru and inferred the admixture level to ascertain pre- and post-Columbian genetic influences in a historical perspective. We identified a predominant Amerindian genomic ancestry in all regions of Peru and a pattern of non-indigenous admixture that is concordant with the known post-Columbian history of immigration.
Materials and methods
The samples (blood or buccal swabs) were collected between 1998 and 2010 from unrelated volunteers, inhabitants from different regions of Peru. These participants were recruited with written informed consents approved by the USMP, Lima, Peru. For this study, 551 samples from 25 Peruvian localities were analyzed (Figure 1).
PCR and genotyping analysis
DNA was extracted and quantified according to the standard protocols19 in the laboratories from Peru (CGBM-USMP) and Brazil (LBEM-UFMG). The multiplex PCR reactions for 40 INDELs were performed following the previously standardized protocols.7, 20 Two microlitres of PCR products were added to 8 μl of Hi-Di formamide/GeneScan-500-LIZ solutions and subjected to capillary electrophoresis using the ABI 3130xl Genetic Analyzer (Life Technologies, Carlsbad, CA, USA). For allelic size scoring and visualization we used the GeneMapper ID v3.2 software (Life Technologies).
We used the same set of 40 INDELs (called MID#) that has been listed by Pena et al.,3 and the reference sequences (rs#) for each polymorphism are available in the NCBI Nucleotide Sequence Variation database (dbSNP) (http://www.ncbi.nlm.nih.gov/snp) and Marshfield Clinic Research Foundation (http://research.marshfieldclinic.org/genetics/home).
For comparisons we used published genotypic data7 for the 40 INDELs typed in 1064 individuals from 52 different worldwide populations (reference continental populations) of the HGDP-CEPH panel, which are distributed in seven geographical regions in all continents (http://www.cephb.fr/HGDP-CEPH-Panel).
General population genetic tests and analysis of molecular variance (AMOVA) were performed using ARLEQUIN v184.108.40.206 (Bern, Switzerland)21 and GENEPOP 4.0 (Montpelier, France)22 packages. To estimate the genomic proportions of American, Eurasian and African ancestry in Peruvian subpopulations, we applied Bayesian MCMC clustering analyses using the software STRUCTURE v2.3 (Chicago, IL, USA).23, 24 We have processed and visualized STRUCTURE outputs in the software STRUCTURE HARVESTER,25 DISTRUCT,26 CLUMPP,27 and R project (http://www.r-project.org/main.shtml) packages SimCo and ade4. We also used a weighted-least-square method implemented in the ADMIX program (http://www.genetica.fmed.edu.uy/software.htm) to estimate admixture. Additionally, we analyzed the INDEL genotypic data with different methods based on the Bayesian admixture analysis available in BAPS (Bayesian Analysis of Population Structure)28 and clustering based on the principal component analysis available in PCAGEN (http://www2.unil.ch/popgen/softwares/pcagen.htm).
Ancestry proportions among peruvian subpopulations using structure
Population clustering and estimation of individual ancestry proportions were obtained with a model-based MCMC Bayesian algorithm implemented in the STRUCTURE software, which uses allelic frequencies for estimating a posterior distribution of the probability of membership to the predefined clusters (K), assuming that multiple loci are independent and are in Hardy-Weinberg equilibrium, as previously tested among 360 unrelated Brazilians.20
On the basis of historical records of Peru about the post-Columbian immigrations, we considered the admixture model and correlated allelic frequencies with parameters MCMC=200 000, burn-in=50 000 and MCMC=2 000 000, burn-in=100 000. The first analyses included only Peruvian samples, and they were performed without any information about the continental origin of Peruvians (PopFlag=0), and runs were made in 10 replicates with each K-value, ranging from K=1 to K=10. To identify substructuring among Peruvian subpopulations, the Q-membership (coefficient of ancestry proportion of membership to one of the K groups) results of STRUCTURE were processed by the Evanno method with STRUCTURE HARVESTER,25 which indicated ΔK=2 as the modal value and the best number of clusters fitting the data (Supplementary Figure 1). The second step of analyses (10 runs for each K, ranging from K=1 to K=10) were performed together with a selected set of data with 161 reference samples from Europe, 251 from East Asia and 105 from America, using the genetic data published in Bastos-Rodrigues et al.7 Reference continental samples were considered as known ‘parental’ populations (PopFlag=1), and Peruvian samples were labeled as unknown origin (PopFlag=0) in STRUCTURE input format. These two independent STRUCTURE analyses used the same parameters and showed the same partition of Peruvian subpopulations in two clusters (ΔK=2) by an Evanno method in STRUCTURE HARVESTER. The scores of averaged coefficients of Q-membership for partition K=2 generated by CLUMPP27 were plotted by a method of correspondence analysis implemented in ade4 package for visualization of the asymmetric clustering of Peruvian subpopulations (showed only without reference populations), indicating that there is a population substructure in Peru (Supplementary Figure 2).
The SimCo statistical package was used for comparisons of 10 STRUCTURE runs defining the clustering solution (ΔK=2) by similarity coefficients (SimCoef). Thus, in a population level, without reference populations (only 25 Peruvian subpopulations), the mean SimCoef was 0.978 (s.e.=0.002). When including selected reference populations (25 Peruvian and 3 reference populations), the mean SimCoef was 0.995 (s.e.=0.0004). In both cases, the SimCoef values indicate that the clustering performed (ΔK=2) using STRUCTURE was highly similar among the 10 compared runs (98% and 99% respectively). Using the same procedure, we determined the SimCoef value in an individual level. On the other hand, the average Q-membership values were obtained by using CLUMPP, and graphics were drawn with DISTRUCT to visualize the clustering pattern of individuals and populations. The results of analysis including the selected reference populations from Europe, East Asia and America, and using partition K=2, are displayed in Figure 2, where a clear admixture pattern can be also observed among Peruvian subpopulations.
We also used data of 1064 individuals from 52 reference HGDP-CEPH populations divided a priori in four regions (Africa, Eurasia (Europe, Middle East, Central Asia, East Asia), Oceania and America) to estimate the genomic ancestry proportions of Peruvians. The STRUCTURE results (only from K=3 to K=6) are shown in Supplementary Figure 3. For illustrative purposes, we also included a 3D plot with partition K=3 (Supplementary Figure 4), where the Peruvian subpopulations are distributed in a gradient pattern, dependent on the admixture level. The best overall partition obtained was K=5 (Figure 3), which fits to five geographic regions (East Asia, Eurasia – Europe, Middle East, Central Asia – Oceania, Africa and America), although Eurasia appears not to be regionally structured and highly intermixed with Oceania. Indeed, clustering in more than two population conglomerates is dependent on the level of relatedness, for example, the partitions K=3 or K=4 seem to be as valid as K=5, due often to the observation that Eurasians and Oceanians show similar genetic profiles in the admixture model (see Supplementary Figure 3). A likely explanation for this result is due to the fact that these 40 INDELs were initially selected as ancestry informative markers to discriminate among native Africans, Europeans and Americans, but not Oceanians.3, 7 However, when we used only Europeans (n=161, from eight subpopulations) and Native Americans (n=108, from five subpopulations) as ‘parental’ populations, we obtained very similar values of admixture proportions (Supplementary Table 1) using the weighted-least-square method implemented in the ADMIX program, which is based on gene identity probability.29
The analyses in STRUCTURE have also generated equivalent results with a model based on ‘no-admixture’ and ‘allele frequencies not-correlated’, using a priori K=5 (Supplementary Figure 5). It means that independently of assumed population model (admixture or not admixture), the clustering of samples by the Bayesian MCMC algorithm revealed a similar admixture profile of individuals or populations. However, the ‘admixture’ model explains better the results according to the scenario described by the known history of pre- and post-Columbian colonization of Peru.
The STRUCTURE results concerning the averaged proportions of membership (Q) are shown in Table 1. They were obtained in relation to the predefined reference populations of the HGDP-CEPH panel, and partitioned in K=2 (America and not-America) and in K=5 (Africa, Europe-Middle East (ME)-Central Asia (CA), East Asia, Oceania and America). In general, Peruvian subpopulations present a high proportion of autochthonous American ancestry (Q=0.538–0.965) and heterogeneous levels of non-autochthonous admixture. The values of Eurasian (Europe, ME, CA) ancestry proportions are displayed in Figure 4. In Table 1, the localities of San Marcos, Characato, Cajamarca, Chogo, Lambayeque and Lima presented the highest average proportions of membership (31.2%, 24.4%, 20.5%, 14.6%, 14.5% and 14.3%, respectively) to the Eurasian region (Europe, ME, CA). Intermediate levels of Eurasian ancestry were associated with the localities of Lamas, Ayacucho and Huancayo (8.7%, 8.1% and 6.1%, respectively). These Peruvian localities associated with a partial genomic ancestry derived from Europe, Middle East and Central Asia also present small genomic ancestry proportions from Africa (<3.4%). It is interesting to note that some ancestry proportions (Table 1) are more related to the East Asia region in Chachapoyas (8.2%), Mollebaya (8%) and Iquitos (6%), but Pucallpa presents 5.2% East Asian ancestry together with 9% from Oceania and 8% from Europe, Middle East, Central Asia. A large East Asian contribution is likely associated with recent post-Columbian migration into these areas, as indicated by recent historical reports.18 Because our sampling was anonymous and collected without genealogical information, East Asian ancestry for individual samples cannot be verified.
Bayesian clustering of peruvian subpopulations using BAPS
To compare with the results of the STRUCTURE clustering, we also performed a genetic admixture analysis using the BAPS28 with the 40 INDELs data of 25 Peruvian subpopulations at the individual and group levels. We used a priori upper bound value K=25, and 10 replicate runs of the stochastic estimation algorithm model using 10 000 iterations, which yielded the optimal posterior partition of the number of clusters of K=2 (Cluster 1: Cabanaconde, Chivay, Yanque, Mollebaya, Ocopon, Andahuaylas, Kaquiabamba, Huarochiri, Uros, Anapia, Amantani, Taquile, Andoas, Iquitos and Cluster 2: Ayacucho, Huancayo, Characato, Chogo, Cajamarca, San Marcos, Pucallpa, Chachapoyas, Lamas, Lambayeque, Lima), with a Log (marginal likelihood)=−24 471.48 and probability=0.986.
This independent analysis converged into the same partition for Peruvian subpopulations indicated using the STRUCTURE software (ΔK=2). Furthermore, a BAPS clustering approach using the HGDP-CEPH reference samples with a priori K=4 also showed a similar admixture pattern (Supplementary Figure 6) to the one obtained with STRUCTURE.
Clustering of peruvian subpopulations by principal components analysis
We performed a principal components analysis on 40 INDELs data to correlate allele frequencies and genotypes among all sampled individuals or populations. The computer package PCAGEN was used to estimate the percentage inertia of each PC axis and its associated P-value by 10 000 randomizations of genotypes. Next, two dimensional scatter plots of the first two principal components were produced. The analysis showed that the eigen values for the first two components (PC1=23.8%; PC2=11.3%) were highly significant (P-value=0), and also the PC1-Fst’s (1%) show a larger differentiation among populations than the PC2-Fst’s (0.5%). The global observed Fst was 4.4%, and the total heterozygosity was 37.3%.
In Supplementary Figure 7, the populations from CAsm (San Marcos), CA (Cajamarca), Char (Characato), LA (Lambayeque), LI (Lima) and Ch (Chogo) were distantly placed in comparison with populations from Taq (Taquile), Amt (Amantani), Ap (Anapia), Ur (Uros) and Yke (Yanque).
Genetic diversity and interpopulation relationships
Several analyses were performed to characterize genetic diversity within and among Peruvian subpopulations from 25 localities. The AMOVA and Fst analyses done in ARLEQUIN followed three hierarchical groupings: (i) the localities were distributed in three different geographical regions (Amazon, Andes and Coast). In this case, the difference among groups was 0.33%, among populations within groups 2.18%. (ii) The localities from each region were analyzed independently. In this situation, the difference among subpopulations from the Amazon (n=122) was 0.99% (P-value =0.88), from the Andes (n=355) was 2.74% (P-value=0), and from the Coast (n=74) was 0.37% (P-value=0.86). (iii) The localities were considered belonging to a single macro region (Peru), without internal geographical division. Despite the difference among populations (Fst) was also relatively low (2.37%), it was significant (P-value=0). In the three AMOVA approaches, the results indicate little genetic differentiation among populations (< 2.74%), and most of differences were detected between individuals (>96%) (Supplementary Table 2). This low but significant interpopulation differentiation agrees with the known history of pre- and post-Columbian settlement of the country, composed by recurrent interchange of migrants from north to south, and between Coast, Andes and Amazon. The exact test of population differentiation was performed using the program GENEPOP with 100 000 permutations across all 40 INDELs, and it showed highly significant P-values (result not shown), particularly between subpopulations from the Titicaca Lake (Taquile, Amantani, Anapia, Uros) and subpopulations from San Marcos, Cajamarca, Characato, Lambayeque and Lima. Furthermore, MDS graphics generated using GenAlEx30 from pairwise Fst distances of Peruvian subpopulations only (figure not shown), or including also reference populations from continents (Figure 5), reveal a clustering pattern that is congruent with the analyses performed using STRUCTURE, BAPS and principal components analysis.
Among the 25 Peruvian subpopulations, the average observed heterozygosity (Ho=36%) for all 40 loci was similar to the expected heterozygosity (He=37%). Considering all subpopulations as one population group, the values were the same (Ho=36%; He=36%) and similar values were obtained using the PCAGEN package (Htotal=37.3%). However, the average heterozygosity over all loci among the 25 subpopulations showed a direct relationship with the admixture levels of subpopulations (Supplementary Figure 8). The highest expected heterozygosity was identified in Characato, followed by San Marcos, Cajamarca, Lambayeque, Lima and Chogo, and the lowest heterozygosity was found in Taquile, Anapia, Amantani, Yanque and Uros. Indeed, a correlation analysis (Supplementary Figure 8) between expected heterozygosities (He) and the gradient of admixture degree observed among Peruvian subpopulations in relation to non-autochthonous Americans (not-America) (Table 1) has shown a high and significant Pearson’s correlation index (r=0.975; P-value=2.20E−16).
Recently, different sets of AIMs were used to estimate ancestry proportions of Latin American populations in comparison with ‘parental’ or reference continental populations.2, 3, 31 The AIM set of 40 INDELs7 was used in this study to estimate the impact of pre- and post-Columbian colonization in the current Peruvian population.
Previously, the study of these 40 INDELs among Brazilian subpopulations from the political regions North, Northeast, Southeast and South (n=934) revealed that the level of admixture proportions is relatively uniform, with a predominant European ancestry (ranging 60.6–77.7%) in all regions.3 In contrast, our results on Peruvians using the same INDELs identified a predominant autochthonous American ancestry (ranging 53.8–96.5%). Those discrepant results agree with the known histories of colonization of Brazil and Peru, which indicate a much larger effective population size of indigenous Peruvians at the time of contact and during European colonization, particularly along the Andes.32
Some previous studies have indicated some level of structuration between regions of Peru. A study of dermatoglyphic patterns33 detected similar features between northern and central Peruvian subpopulations, but they were both differentiated from highlanders of the Puno region (Titicaca Lake). In a recent study using STR markers,34 Peruvians were suggested to be clustered in three main subgroups according to their geographical locations (north, central and south of Peru) and reported about 30% of admixture with non-autochthonous populations, a similar overall value compared with our results using K=2 (Table 1).
It is worth noting that for the inference of the genetic relationships of current worldwide populations, most studies assume that ‘native’ continental populations are geographically structured and not-admixed, which could result in a bias in recent admixture analyses. For example, the ‘native’ subpopulations of Middle East, Europe and north of Africa appear to be relatively admixed (Figure 3), as well as other regions of the world, which is fairly supported by a recent study using autosomal single-nucleotide polymorphisms arrays.35 In our STRUCTURE results, using an admixture model and partition K=2, the populations from Europe and East Asia were clustered in one macrogroup, whereas autochthonous Americans were found in another cluster (Figure 2). This evidence is in close agreement with the results obtained by Wang et al.,36 but in contrast with some previous studies where the East Asian populations were clustered with Native Americans.6, 7, 37 Nevertheless, our clustering results with partitions K=3 to K=6 including all 52 reference HGDP-CEPH subpopulations (Supplementary Figure 3) are similar to those obtained by all previous studies. In any case, the Q-membership proportions for each individual/population should be seen with caution, as ‘ad hoc approximations’, as they may change depending on number and type of markers, number of samples, the reference populations used and also the demographic history or degree of inter-population differentiation in the studied area.38
The population structure analyses of 25 Peruvian locations, using partition K=5, showed that in San Marcos, Cajamarca, Characato, Lima, Lambayeque, Chogo, Lamas, Huancayo and Ayacucho there is a high level of post-Columbian admixture (mainly with Europeans).5 It is in close agreement with the European colonization history of Peru. Also, we identified a significant admixture with East Asians in the localities of Mollebaya (Andes), Pucallpa, Chachapoyas and Iquitos (Amazon region), which is consistent with the historical records that report an immigration wave of Chinese, who occupied several parts of Peru since 1870, particularly the sampled Amazon locations.18
Among the inhabitants of the Titicaca Lake region (Taquile, Amantani, Uros, and Anapia) and Yanque (from Colca Canyon in Arequipa), there was no significant admixture with non-autochthonous Americans (in K=5). This could be explained by the relative isolation of this harsh Andean area, but could be also related with local mating practices and historical peculiarities. For example, in the Taquile Island there is an endogamous mating practice that excludes foreigners marrying local inhabitants to reside in the community (unpublished observations). Besides, the association between subpopulations from Titicaca Lake and the Yanque locality in Arequipa can be further supported by historical records before the Inca Empire, when the same Amerindian groups were occupying this southwestern region of Peru.39
The AMOVA results on Peruvians showed a low, but slightly higher level of genetic differentiation among Andean subpopulations when compared with Amazonian or Coastal. Indeed, previous studies of South American indigenous subpopulations14, 15, 16, 17 through the use of autosomal and uniparental markers (excluding admixture) have suggested a lower degree of genetic differentiation among the Andean communities than among the eastern Amerindian communities (Amazon and Brazilian plateau). Part of this pre-Columbian homogenization in the Andes was suggested to be due to the Mit’a system of forced movement of populations, which was a labor draft system used by the Inca Empire.32 These differences observed between genetic data on non-admixed indigenous populations, and INDEL markers on Peruvian subpopulations clearly support the impact of post-Columbian admixture in the population dynamics owing to the promotion of gene flow. Indeed, during the Spanish colonization a new reformulated Mit’a system was empowered by encomenderos,32 leading to relocation of many populations in the area as forced labor, which was especially documented for the colonial establishment of the silver mines in Potosí (in present-day Bolivia).32
Peruvian subpopulations from Taquile, Anapia and Amantani presented lower heterozygosity (<31.8%) and also an insignificant admixture, in contrast to the high heterozygosity and admixture observed in Cajamarca and Characato (Arequipa). The two latter populations form a compact cluster in MDS analyses with populations from San Marcos, Lima, Lambayeque and Chogo, suggesting a higher impact of post-Columbian admixture events, which is coherent with historical records.5, 32 Subpopulations from Ayacucho, Huancayo, Lamas, Chachapoyas and Pucallpa appeared closely related to each other, which could be explained by their similar level of admixture with Eurasians as well as by their shared autochthonous ancestry.40 Other associations found in the bidimensional analyses (MDS and principal components analysis) between subpopulations may have alternative explanations. Taquile and Amantani subpopulations appear very closely related in the MDS graphic, which agrees with their proximity (they are neighbors living in close islands in the Titicaca Lake) and also fit to local reports about their common origin, from Capachica peninsula (www.ogdpuno.org). Besides, these two subpopulations are near to Anapia (Aymara-speaking subpopulation), another island of the Titicaca Lake, but are located in the frontier between Peru and Bolivia. However, the Uros subpopulation (inhabitants of the floating islands of Titicaca) was shown to be more related with other far located subpopulations (Andoas, Chivay, and Cabanaconde), even though previous mitochondrial DNA analyses41 have shown a shared ancestry with their neighbors from Titicaca Lake region. The subpopulations from Cabanaconde and Chivay appear closely related in the MDS graphic, and both are located in the Colca Canyon as well as Yanque, but this latter subpopulation is separated from those by the observed pattern of non-admixture. Interestingly, Anapia, Taquile, Amantani and Yanque subpopulations present a closer affinity to an autochthonous group from the Brazilian Amazon (Karitiana), which also presents low levels of heterozygosity and admixture, thus it is likely due to their shared Amerindian ancestry. It is also interesting to observe that Peruvian Amazon subpopulations (Pucallpa, Iquitos, and Chachapoyas) appear closely related to other autochthonous American groups from the Amazon, such as Surui (Brazil) and Piapoco (Colombia). Although there is a long geographic distance between Mollebaya (Arequipa) and Ocopon (Ancash), they appear to be genetically close to each other in the bidimensional analyses. Their similarity is probably due to an equivalent admixture proportion estimated using STRUCTURE, like it also happens between Characato (south of Peru) and Cajamarca (north of Peru).
In summary, when clustering analyses are done with K=5 (coincident with five continental regions), the total genomic ancestry proportions in Peruvians are 83% for America and 17% are non-autochthonous, mainly from Europe. Using a partition in two main subgroups (K=2), the total average of non-autochthonous proportion among Peruvian genomes rises to about 20%, mainly due to European admixture, and autochthonous genomic heritage in Peru is about 80%, corresponding to a very high prevalence of pre-Columbian genes in the current population. These results indicate a clear effect of post-Columbian admixture in the population structure of Peru, portraying a gradient of autochthonous/non-autochthonous genomic background due to different degrees of admixture and shared ancestry among Peruvian subpopulations.
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We thank all volunteers who donated their samples to this project, M.Sc. Jaime Descailleaux and Margarita Velasquez (UNMSM, Lima, Peru), Cesar Ñique (USAT, Lambayeque, Peru) for providing storage of some samples, Dr. Daniela R. Lacerda (LBEM, Brazil) and Heloisa B. Pena (GENE-MG, Brazil) for technical support, PEC-PG CAPES/Brazil for the PhD scholarship to JRS, and FAPEMIG and CNPq from Brazil for financial support to the laboratory work.
Laboratório de Biodiversidade e Evolução Molecular (LBEM), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
Jose R Sandoval & Fabricio R Santos
Centro de Genética y Biología Molecular (CGBM), Facultad de Medicina Humana, Universidad de San Martin de Porres (USPM), Lima, Peru
Jose R Sandoval, Alberto Salazar-Granara, Oscar Acosta, Wilder Castillo-Herrera & Ricardo Fujita
GENE-Núcleo de Genética Médica, Belo Horizonte, MG, Brazil
Sergio DJ Pena
Laboratório de Genética Bioquímica (LGB), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
Sergio DJ Pena
Correspondence to Fabricio R Santos.
The authors declare no conflict of interest.
Supplementary Information accompanies the paper on Journal of Human Genetics website
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Sandoval, J., Salazar-Granara, A., Acosta, O. et al. Tracing the genomic ancestry of Peruvians reveals a major legacy of pre-Columbian ancestors. J Hum Genet58, 627–634 (2013). https://doi.org/10.1038/jhg.2013.73
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- colonization history
- genomic ancestry
- population structure
- pre-Columbian legacy
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Molecular Genetics and Genomics (2018)
Researchers in Peru believe they have traced the origins of the Incas —the largest pre-Hispanic civilization in the Americas—through the DNA of the modern-day descendants of their emperors.
From their ancient capital Cusco, the Incas controlled a vast empire called Tahuantinsuyo, which extended from the west of present-day Argentina to the south of Colombia.
They ruled for more than two hundred years before being conquered by the invading Spanish in the 16th century.
The empire included the mountain-top citadel of Machu Picchu in modern-day Peru—now a UNESCO World Heritage Site and a major tourist attraction.
After becoming fascinated by the Inca culture, their organizational skills and their mastery of engineering, researchers Ricardo Fujita and Jose Sandoval of Lima's University of San Martin de Porresit became interested in the genetic profile of their descendants.
They said the aim of the study, the first of its kind, was to reveal whether there was a unique Inca patriarch.
"It's like a paternity test, not between father and son but among peoples," Fujita told AFP.
The scientists wanted to verify two common legends about the origin of the Incas.
One attributes them to a couple from around Lake Titicaca, in Peru's Puno region. The other identifies the first Incas as the Ayar brothers from the Pacaritambo mountain in the Cusco region.
DNA samples were taken from inhabitants of both places.
"After three years of tracking the genetic fingerprints of the descendants, we confirm that the two legends explaining the origin of the Inca civilization could be related," said Fujita.
"They were compared with our genealogical base of more than 3,000 people to reconstruct the genealogical tree of all individuals," said Fujita.
"We finally reduced this base to almost 200 people sharing genetic similarities close to the Inca nobility."
The study released some preliminary results in April, in the review Molecular Genetics and Genomics.
"The conclusion we came to is that the Tahuantinsuyo nobility is descended from two lines, one in the region of Lake Titicaca, the other around the mountain of Pacaritambo in Cusco. That confirms the legends," said Sandoval.
But it also confirms that the two legends were linked.
"Probably the first migration came from the Puno region and was established in Pacaritambo for a few decades before heading to Cusco and founding Tahuantinsuyo," he said.
But the work of the researchers does not stop there. Now they want to go further back in time.
For that, they have to test the DNA of ancient relics, such as mummies, "to form the most complete picture of the origin of the most important pre-Hispanic civilization," said Fujita.
The task looks complicated because the Spanish Conquistadores, who arrived 1532, destroyed Inca mummies that families venerated, as they sought to convert people to Christianity.
The researchers are now looking for where the Incas' most direct descendants are buried in order to trace their history.
The DNA analysis would add to archeological and anthropological research to understand the exact origin of the people.
"In this case, we use ... genetics, the transmission of molecular features across the generations," said Fujita.
© 2018 AFP
Citation: Peruvian scientists use DNA to trace origins of Inca emperors (2018, May 26) retrieved 18 October 2021 from https://phys.org/news/2018-05-peruvian-scientists-dna-inca-emperors.html
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Andean ǀ South American
Photo: Peruvian woman in native attire (Pinterest)
Peru is a multiethnic country formed by the combination of different groups over five centuries, so people in Peru usually treat their nationality as a citizenship rather than an ethnicity. Amerindians inhabited Peruvian territory for several millennia before the Spanish Conquest in the 16th century; according to historian David N. Cook their population decreased from an estimated 5–9 million in the 1520s to around 600,000 in 1620 mainly because of infectious diseases. Spaniards and Africans arrived in large numbers under colonial rule, mixing widely with each other and with indigenous peoples. During the Republic, there has been a gradual immigration of European people (specially from Spain and Italy, and in a less extent from France, the Balkans, Portugal, Great Britain and Germany). Japanese and Chinese arrived in large numbers at the end of nineteenth century. Peru also is home to the renowned pyramids at Machu Picchu, built by the ancient Incan civilization, and the inexplicable Nazca lines that cover acres of land with elaborate drawings that are visible only from the air. Most Peruvians are either Spanish-speaking mestizos–a term that usually refers to a mixture of indigenous and European/Caucasian–or Amerindians, largely Quechua-speaking indigenous people. Peruvians of European descent make up about 15 percent of the population. There also are small numbers of persons of African, Japanese, and Chinese ancestry.
Mestizos compose about 47% to 59.5% of the total population. The term traditionally denotes Amerindian and European ancestry (mostly Spanish ancestry). This term was part of the caste classification used during colonial times, whereby people of exclusive Spanish descent who were born in the colonies were called criollos, people of mixed Amerindian and Spanish descent were called mestizos, those of African and Spanish descent were called mulattos, and those of Amerindian and African descent were called zambos.
Peruvian is an autosomal DNA population name within the metapopulation category of Andean and the megapopulation category of South American. The Peruvian population data represent DNA samples from 100 unrelated individuals living in the Republic of Peru. Individuals in all regions of Peru were represented by samples taken in the cities of
- Huancayo in the central highlands (Huancayo;
- Huaraz (Huaraz), in north-central Peru;
- Iquitos (Iquitos), the largest city in the Peruvian rainforest
- Lima (Lima), the nation’s capital — located along the nation’s central river valleys, and
- Piura, (Piura), Peru’s oldest Spanish-built city, located in the northwest.
Samples were obtained by the Molecular Biology Laboratory – DNA Forensics [Laboratoriode Biología Molecular –ADN Forense], in Peru, and by the Area Laboratory of the Ertzaintaza (Basque Police) [Area de Laboratorio Ertzaintaza], in Bilbao, Spain.
Source publication: Allele frequencies for the 13 CODIS STR loci in Peru, Forensic Science Int’l, 2003, 132, 164-165
Peruvian – Mesa Redonda Lima represents 151 relatives of missing persons of the fire on December 29th, 2001 at Mesa Redonda in the area of Lima, who were sampled in 2004 by the Instituto de Medicina Legal in Lima.
Source publication: Genetic Diversity of Sixteen STRs in the Peruvian Mesa Redonda Lima Population, JFS, 2004, p852-853.
Native American DNA Fingerprint Test Plus 18 Marker Ethnic Panel
People identified with the country of Peru
This article is about the ethnic group. For information on the population of Peru, see Demographics of Peru. For other uses, see Peruvian (disambiguation).
Flag of Peru
|c. 35.2 million|
Diaspora 2.1 million
| 33,105,273 |
|Peruvian Spanish • Quechua • Aymara|
5.09% Irreligion, 14.07% Evangelical, 1.64% Non-denominational Christian, 1.52% Adventist, 0.75% Jehovah's Witness, 0.49% Mormon and 0.41% Other
Peruvians (Spanish: peruanos) are the citizens of Peru. There were Andean and coastal ancient civilizations like Caral, which inhabited what is now Peruvian territory for several millennia before the Spanish conquest in the 16th century; Peruvian population decreased from an estimated 5–9 million in the 1520s to around 600,000 in 1620 mainly because of infectious diseases.Spaniards and Africans arrived in large numbers in 1532 under colonial rule, mixing widely with each other and with Native Peruvians. During the Republic, there has been a gradual immigration of European people (especially from Spain and Italy, and in a less extent from Germany, France, Croatia, and the British Isles). Chinese and Japanese arrived in large numbers at the end of the 19th century.
With 31.2 million inhabitants according to the 2017 census, Peru is the fifth most populous country in South America. Its demographic growth rate declined from 2.6% to 1.6% between 1950 and 2000; population is expected to reach approximately 46 - 51 million in 2050. As of 2017, 79.3% lived in urban areas and 20.7% in rural areas. Major cities include Lima, home to over 9.5 million people, Arequipa, Trujillo, Chiclayo, Piura, Iquitos, Huancayo, Cusco and Pucallpa, all of which reported more than 250,000 inhabitants. The largest expatriate Peruvian communities are in the United States, South America (Argentina, Chile, Venezuela and Brazil), Europe (Spain, Italy, France and the United Kingdom), Japan, Australia, and Canada.
Ethnic Peruvian Structure
In the 2017 census, those of 12 years old and above were asked what ancestral origin they belong to with 60.2% of Peruvians self-identified as mestizos, 22.3% as Quechuas, 5.9% as white, 3.6% as Afro-Peruvian, 2.4% as Aymaras, 0.3% as Amazonians, 0.16% as Asian. Indigenous people are found in the southern Andes, though a large portion, also to be found in the southern and central coast due to the massive internal labor migration from remote Andean regions to coastal cities, during the past four decades.
Mestizos compose 60.2% of the total population. The term traditionally denotes Peruvians of mixed indigenous and European ancestry (mostly Spanish ancestry). This term was part of the caste classification used during colonial times, whereby people of exclusive Spanish descent who were born in the colonies were called criollos, people of mixed Indigenous and Spanish descent were called mestizos, those of African and Spanish descent were called mulatos, and those of Indigenous and African descent were called zambos. Genetic analysis indicates that Peruvian Mestizos are of predominantly indigenous ancestry. Most mestizos are urban dwellers and show stronger European inheritance in regions like Lima Region, La Libertad Region, Callao Region, Cajamarca Region, San Martin Region, Piura Region, Lambayeque Region, and Arequipa Region.
Main article: Indigenous peoples of Peru
Ethnic groups of Peruvian origin constitute 25.8% of the total population. The two major ethnic groups are the Quechuas (belonging to various cultural subgroups), followed by the Aymara, mostly found in the extreme southern Andes. A large proportion of the ethnic groups who live in the Andean highlands still speak Quechua and have vibrant cultural traditions, some of which were part of the Inca Empire.
Dozens of Peruvian cultures are also dispersed throughout the country beyond the Andes Mountains in the Amazon basin. This region is rapidly becoming urbanized. Important urban centers include Iquitos, Nauta, Puerto Maldonado, Pucallpa and Yurimaguas. This region is home to numerous ethnic groups, though they do not constitute a large proportion of the total population. Examples of ethnic groups residing in eastern Peru include the Shipibo, Urarina, Cocama, and Aguaruna. There is no special law for ethnic groups or reserves; they are Peruvians and legally treated as such. There are some tribal communities especially in the Amazon but it is their own choice of lifestyle; they have the right to choose their place of residence, they have the freedom to live and travel, to enter and leave the country, with few limitations due to health issues or by order of a judge or international migration laws, supported by the Peruvian Constitutions and International Human Rights, they do have representation in the Congress as any other Peruvian community.
White or European
Main article: Peruvians of European descent
European descendants total 5.9% of the total population. Most of them are descendants of Spanish settlers that came to the country during the colonial era, while others are descendants of other Europeans ethnic groups that arrived in the 19th and 20th centuries like Italians, Germans, British, French, Irish, Dutch, Portuguese, Polish, and Croats . Most of them also live in the largest cities, generally in the northern cities of Peru: Trujillo, Chiclayo and Piura, and also in the capital Lima.
The city of Arequipa in the south of Peru displays the majority of Spanish descendants in the south. Cajamarca in the highlands, parts of San Martin in the Rupa-Rupa or Amazonian Andes Area; Oxapampa and Pozuzo were populated by German and Austrian settlers also in the Rupa-Rupa or Amazonian Andes area. A considerable European population migrated to Peru, they came for oil, mining, fishing, sugar, cotton, guano, rubber, and other booming industries in the mid-1800. Recently,[when?] Peru has seen an immigration of American senior citizens and businessmen looking for permanent residency to settle in the country, due to inexpensive living, tasty fresh food, gastronomy, friendly people, excellent mild weather, beautiful ocean views, Amazon forest environment, freedom in many aspects compared with other countries, and how easy it is to do business in Peru due to economic booms from 2000 to the present. Also, people from other Latin American countries like Venezuela migrated Peru due to socio-economical issues.
Main article: Afro-Peruvians
Afro-Peruvians constitute a 3.6% of the population. Peru as a Spanish colony in the Conquista has a history of slave trading, from Ghana, Angola, Nigeria, Republic of Congo, Democratic Republic of Congo, Mozambique, and Madagascar. During the colonial period to perform labor work in sugar cane, cotton fields and vineyards, very few of them in gold mines in Cuzco. The Spaniards brought 500 Africans from Guinea as part of the troops for the Conquista by 1531. Slavery in Peru was abolished in 1854 by President Ramon Castilla. Today also mulatos (mixed African and European) and zambos (mixed African and Indigenous) constitute an important part of the population as well, especially in Piura, Tumbes, Lambayeque, Lima and Ica regions. The Afro-Peruvian population is concentrated mostly in coastal cities south of Lima, such as those found in the Ica Region, in cities like Cañete, Chincha, Ica, Nazca and Acarí in the border with the Arequipa Region. The African descendants brought their own dances and drumming music style, creating some instruments like the "Cajon" and some culinary art characterized by their delicious taste. Some of the best soccer players in Peru are Afro-descendants. One of the most untouchable unmixed African population is still today El Carmen en Chincha Alta Ica, Peru.
Another large but less promoted segment of Afro-Peruvian presence is in the Yunga regions (west and just below the Andean chain of northern Peru), (i.e., Piura and Lambayeque), where sugarcane, lemon, and mango production are still of importance. Important communities are found all over the Morropón Province, such as in the city of Chulucanas. One of them is Yapatera, a community in the same city, as well as smaller farming communities like Pabur or La Matanza and even in the mountainous region near Canchaque. Further south, the colonial city of Zaña or farming towns like Capote and Tuman in Lambayeque are also important regions with Afro-Peruvian presence.
Main article: Asian Peruvians
Asian Peruvians constitute a 0.16% of the population. Peru has the largest population of Chinese descendants in Latin America since Peru became independent from Spain in 1821 and banned the imports of slaves. The first group of Asians came in 1849 in the Danish ship named Federico Guillermo to replace slavery as part of the plan to abolished slavery in 1854 by replacing it with Asian labor force. During the next 25 years, 100,000 Chinese arrived to Peru, hired in eight-year contracts from Macao, Hong Kong, Canton, and Fujian, including some Sangley people. They were hired for sugar cane fields, rice fields, extracting guano and constructing the railroads in the Andes in semi-slavery working conditions.
Geographically Chinese descendants communities are found throughout the Peruvian upper Amazon, including cities such as Yurimaguas, Nauta, Iquitos and the north-central coast (Lambayeque and Trujillo) and the capital Lima.
In contrast to the Japanese community in Peru, the Chinese appear to have intermarried much more since they came to work in the rice fields during the Viceroyalty and to replace the African slaves, as laborers during the abolition of slavery itself. Despite the presence of Peruvians of Asian heritage being quite recent, in the past decade, they have made significant advancements in business and political fields; a past president (Alberto Fujimori), several past cabinet members, and one member of the Peruvian congress are of Chinese or Japanese origin. There are also large numbers of Arab Peruvians, mostly Palestinians, Lebanese, Syrians, Iraqis.
Immigration after independence
Main article: Immigration to Peru
After independence, there has been a gradual European immigration from Spain, Italy, Croatia, France, Germany, and Austria.Chinese arrived in the 1850s as a replacement for slave workers in the sugar plantations of the north coast and have since become a major influence in Peruvian society. Other immigrant groups include Japanese, Arabs, South Asians, and Americans from the United States.
See also: Peruvian Spanish
Peruvian Spanish, is the main language of 82.6% majorly spoken in the Coastal cities, It is the primary language of the country used for the public media, television, radio, newspapers, internet in general with very minimal exceptions. It coexists with several Indigenous languages, the most common Quechua,13.9% and Aymara 1.6%, both spoken mostly in the Andes, Ashaninka 0.3% in the Rainforest. Other Native and foreign languages were spoken at that time by 0.8% and 0.2% of Peruvians, respectively. Literacy was estimated at 94.2% in 2017; this rate is lower in rural areas (83%) than in urban areas (96.8%).
According to 2017 census, Christianity is the largest religion in Peru, with Roman Catholics having the most adherents (76%), other Christians 18.6%, Other 0.5%, non-religious 5%.Lord of Miracles is a mural painted by an Angolan slave in the 17th century of Jesus Christ that is venerated in Lima and the main Catholic festivity in Peru and one of the biggest processions around the world. Every year, in October, hundreds of thousands of pilgrims from all walks of life, dress in purple to celebrate the also known "Black Christ" in a religious procession through the streets of Lima. The story tells that some earthquakes in Lima during the 17th and 18th Centuries destroyed most of the city leaving only that mural that was painted by the Angolan slave in 1651 was the only standing wall after the quakes in 1655,1687 and 1746 8.6 magnitude earthquake. These facts contributed to the growth and the solidification of devoted veneration to the mural known as "Christ of Pachacamilla"
Main article: Culture of Peru
Peruvian culture is primarily rooted in amerindian traditions, mainly Inca, and Hispanic heritage. It has also been influenced by various European, African, and Asian ethnic groups. Peruvian artistic traditions date back to the elaborate pottery, textiles, jewelry, and sculpture of Pre-Inca cultures. The Incas maintained these crafts and made architectural achievements including the construction of Machu Picchu. Baroque dominated colonial art, though modified by Native traditions. During this period, most arts focused on religious subjects; the numerous churches of the era and the paintings of the Cuzco School are representative. Arts stagnated after independence until the emergence of Indigenismo in the early 20th century. Since the 1950s, Peruvian art has been eclectic and shaped by both foreign and local art currents. The Peruvian culture today is modern with global influences, always open to new trends and is constantly moving and changing in Music, Art, Literature. Peruvians are expressive, using hand gestures when talking and are tactile, expecting a kiss on the cheek for hi and bye. It is not uncommon to see couples showing affection in public places. Peruvians also have respect for elders, people of higher positions at work, skilled professionals and educated people.
Peruvian literature has its roots in the oral traditions of pre-Columbian civilizations. Spaniards introduced writing in the 16th century; colonial literary expression included chronicles and religious literature. After independence, Costumbrism and Romanticism became the most common literary genres, as exemplified in the works of Ricardo Palma. In the early 20th century, the Indigenismo movement produced such writers as Ciro Alegría,José María Arguedas, and César Vallejo. During the second half of the century, Peruvian literature became more widely known because of authors such as Nobel laureateMario Vargas Llosa, a leading member of the Latin American Boom.María Jesús Alvarado Rivera was a Peruvian rebel feminist, educator, journalist, writer and social activist who was noted by the National Council of Women of Peru in 1969 as the "first modern champion of women's rights in Peru".
Main article: Architecture of Peru
Macchu Picchu, one of the seven wonders of the world, Sacsayhuaman, Chan chan, the architecture was constructed to congregate hundreds if no thousands of peoples for ceremonies and to cohabit in harmony with others and with nature. Some of the highlights were the development in acoustics, aqueducts, silos to preserve grains, the terraces, the perfection fitting the giant's boulders of 20 tons perfectly, astronomical observatories, the perfection with the solstice, the construction of entrances for the sunlight denoting meaning for every season, some of these constructions until today do not have logical human explanation, on how they were constructed.
Peruvian cuisine shows influences from Andean, Spanish, Chinese, Italian, Arab, African, and Japanese cooking. Common dishes include anticuchos, ceviche and pachamanca. Because of the variety of climates within Peru, a wide range of plants and animals are available for cooking. Peruvian cuisine has an especial ingredient that gives the flavor to the majority of dishes "aji seco" if the same dish is prepared in another part of the world it might look the same, but the raw vegetables, potatoes, ingredients have a different taste in other parts of the world. Examples of these are the eggs, quinoa, Lima beans, the fish, the lime more acidic, they taste totally different in other countries. Peru gave to the world the potatoes with more than 3000 species, introduced to Europe by the Spaniards in 1532 after the Conquista the Quinoa, both from the highlands. Ancient Peruvians were harvesting potatoes between 8000–5000 years according to scientific research.
Peruvian music has Andean, Spanish, and African roots. In pre-Hispanic times, musical expressions varied widely from region to region; the quena and the tinya were two common instruments. Spanish conquest brought the introduction of new instruments such as the guitar and the harp, as well as the development of crossbred instruments like the charango. African contributions to Peruvian music include its rhythms and the cajón, a percussion instrument.Peruvian folk dances include marinera, tondero and huayno.
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- Francesco Messina ,
- Tullia Di Corcia,
- Michele Ragazzo,
- Cesar Sanchez Mellado,
- Irene Contini,
- Patrizia Malaspina,
- Bianca Maria Ciminelli,
- Olga Rickards,
- Carla Jodice
- Francesco Messina,
- Tullia Di Corcia,
- Michele Ragazzo,
- Cesar Sanchez Mellado,
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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.
Citation: Messina F, Di Corcia T, Ragazzo M, Sanchez Mellado C, Contini I, Malaspina P, et al. (2018) Signs of continental ancestry in urban populations of Peru through autosomal STR loci and mitochondrial DNA typing. PLoS ONE 13(7): e0200796. https://doi.org/10.1371/journal.pone.0200796
Editor: Alessandro Achilli, Universita degli Studi di Pavia, ITALY
Received: March 20, 2018; Accepted: July 3, 2018; Published: July 18, 2018
Copyright: © 2018 Messina et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Availability: All relevant data are within the paper and its Supporting Information files.
Funding: This work was supported by grants of the Italian Ministry of Justice (grant number CUP E81J10001270005) to C.J., P.M. and B.M.C. F.M. was supported by a fellowship from the Italian Ministry of Justice. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
The rapid advancements in genotyping techniques and the growing availability of genetic data in open databases have greatly improved our view of human population structure. Many regions of the human genome can be analyzed to investigate admixture events among populations from different continents, as those associated with the European colonization and the African slave trade in the Americas. New methods for analysis of genome wide SNPs data contributed to determine the continental ancestry in admixed populations from urban Brazilian people, showing their high degree of admixture along with a strong European contribution [1, 2]. In addition, tetranucleotide microsatellite loci (STRs) showed to be geographically more structured than other nuclear markers, with a good power of discrimination on inter-continental scale [3–7].
Many STRs, having an observed heterozygosity >70%, show a high individual discriminating power. Therefore, these markers are widely used in human individual identification for resolving forensic cases [8–10]. Although autosomal STRs of forensic panels show high heterozygosity and low random match probability values, i.e. the probability of obtaining a match between genotypes of two distinct and unrelated individuals, they are also associated to a good capability of ancestry identification . Therefore, these markers can provide valuable information to evaluate nature and extent of transcontinental admixture in South American populations.
The complex historical origin of urban populations in South America was mainly investigated through uniparental and non-recombining genetic markers (mitochondrial DNA and Y chromosome), by means of region-specific haplotypes or haplogroups [12, 13]. Studies on mtDNA composition in Natives from Peru and Ecuador allowed to reconstruct genetic similarity and to clarify early peopling of these areas [14–17]. However, the geographical structuring of mtDNA haplotypes and haplogroups is not able to clearly assign geographical ancestry of individuals as much as thousands autosomal SNPs can do. The mtDNA captures information on the ancestral maternal contribution, but autosomal markers can reveal different scenarios concerning continental origins: i.e. individuals carrying A, B, C and D mtDNA haplogroups, which are predominantly associated to East Asian or Native American ancestry, can turn out to harbor a different ancestry when studied at the level of autosomal markers . Combined analyses of autosomal SNPs and mtDNA data in South American mixed populations have indeed highlighted clear signals of sex-biased genetic inputs from the different continental components [18–20].
In this work, we analyzed 16 STR loci, commonly used in forensic science, in Native Amazon Peruvians from Ucayali, Loreto and Lambayeque regions and in Peruvians from Lima's urban area and other urban areas of Peru (Fig 1). Moreover, we sequenced the D-loop non-coding region and several SNPs in the coding region of mtDNA to estimate external maternal contributions to the urban Peruvian population. The aim of this work was to quantify, through statistical methods of cluster analysis, the extent of recent migrations in the urban Peruvian population. The results increased our knowledge on Peruvian continental ancestry highlighting effective signs of admixture also in high variable loci of the genome.
Materials and methods
Buccal swabs of a total of 296 individuals were sampled across the entire territory of Peru during three sampling campaigns along the years 2012–2015. Of these, 156 were Native Amazonian Peruvians belonging to Ashaninka, Cashibo and Shipibo people from Ucayali, Huambiza from Loreto and Moche from Lambayeque, while 140 were individuals from the urban area of Lima and other 33 Peruvian towns (S1 Table and Fig 1). The indigenous individuals of the present study were sampled in their own communities settled in the Amazon rainforest or in the desert of Morrope, while urban Peruvian people were sampled in urban areas and the close countryside. The project was also approved by the Ethics Committee of the University of Rome Tor Vergata (June 22nd 2011). Each subject was also asked to report the origin of his/her parents in order to exclude recent immigrants from other continents, and to sign a written informed consent according to the guidelines of the Ethics Committee of University of Rome Tor Vergata. The buccal swab samples were then sent to the Centre of Molecular Anthropology of University of Rome Tor Vergata. The essential information about the samples are given in S1 Table: based on sampling location, for each individual the area of origin (urban area of Lima, North, South and Centre of Peru) and the ecoregion (Rainforest or "Selva", Mountain or "Sierra", Coast or "Costa" and Lima’s urban area) were reported. Sample information on the linguistic group were unknown and samples from urban areas were referred to as "urban", because of the lack of information on ethnicity.
Genomic DNA was extracted using standard procedures  and amplified with the commercial kit commonly used for forensic analyses AmpFLSTR® NGM SElect™ PCR Amplification Kit (Applied Biosystems, Foster City, CA) for the D10S1248, vWA, D16S539, D2S1338, Amelogenin, D8S1179, D21S11, D18S51, D22S1045, D19S433, TH01, FGA, D2S441, D3S1358, D1S1656, D12S391 and SE33 loci [22, 23]. After the amplification, all PCR products were separated with the same ABI PRISM 3500 XL Genetic Analyzer, polymer and capillary types, and constant run conditions across the plate set (Life Technologies, Foster City, CA), while the analysis of DNA profiles was carried out using the software GeneMapper® ID-X (Life Technologies, Foster City, CA). All runs included a negative (water) control, 6 replicates of the reference allelic ladder included in the kit, as well as the positive control provided by the manufacturer (Control DNA 007). Profiles were inspected by two independent operators. Independent spreadsheets were produced and compared. Profiles with missing amplification at one or more loci were discarded.
To detect hidden relatedness, we also ran the program Familias 3. 2. 1  using allele frequencies obtained in the whole series. For comparisons, allele frequency databases of US Hispanics  and North American Native Americans  were employed. Thresholds for the likelihood ratio took into account the number of pairwise comparisons within each population sample . This step led to the exclusion of 64 subjects, since they were identified as Parent/Offspring or Full Sibs (8 urban Peruvians, 5 Ashaninka, 36 Cashibo, 15 Shipibo) (S1 Table) leading to a total sample size of 100 Native Amazon and 132 urban Peruvian individuals.
The mtDNA of 132 urban Peruvian samples and 10 Native Amazon individuals belonging to Moche population were analyzed by sequencing, while mtDNA haplotypes of the other Native individuals were already published . The amplification of the first and second hypervariable segments (HVS-I and HVS-II) of the mtDNA control region was carried out in a 25 μl reaction volume under standard conditions . The primers in the amplification reactions allowed sequences to be read from nucleotide position np 15996 to np 16401 and from np 00029 to np 00408 for HVS-I and HVS-II, respectively [14, 27, 28]. Sequence data were obtained using fluorescent dye labeling and the ABI PRISM 3130 AVANT DNA Sequencer (Applied Biosystems, Foster City, CA) following the manufacturer’s protocols. HVS-I and HVS-II sequences were compared with the revised Cambridge reference sequence [29, 30]. After alignment, control-region haplotypes were analyzed via the HaploGrep website, obtaining phylogenetically classification with a high confidence percentage (>85%) . Moreover, to improve the haplogroup classification, several selected diagnostic SNPs in the mtDNA coding region (8281-8289d, 489C, 493G, 10400T) were assayed by PCR amplification and sequencing .
Statistical analysis on microsatellites and mitochondrial DNA data
Allele frequencies, observed and expected heterozygosity, Fis and Fst values, and the exact test for the Hardy-Weinberg equilibrium (HWE) were calculated using Arlequin v. 3. 5. 2. 2 and 1 million steps in Markov chain .
To estimate possible contribution of non-Native American source populations to the urban Peruvian gene pool, we added to our data set genetic profilesfrom two different population samples both from USA : one of European ancestry (US Europeans) and one of African ancestry (US Africans). First, we applied the program STRUCTURE 2. 3. 2  using the admixture model with correlation between allele frequencies. The number of clusters (K) investigated ranged from 2 to 6, and for each K, a burn-in of 50,000 iterations, followed by 50,000 iterations of MCMC (Markov Chain Monte Carlo method) was applied for estimates of clustering.
Principal Component Analysis (PCA), based on individual STR profiles, was carried out by R package factoextra to graphically represent affinities among all genotypes and to ascertain which alleles mainly contributed to between-individuals diversity.
To assess the relationships between different possible population sources (US Africans, US Europeans and Native Amazon Peruvians) and urban populations, an independent evaluation of membership probabilities for each individual in each population was obtained by means of Discriminant Analysis of Principal Components (DAPC). This multivariate method defines a model in which the component of genetic variation between groups is maximized by minimizing the within-group component . Analyses were performed using the R package adegenet . Then, allele frequencies were submitted to a centered PCA, and the best fitting model in the wide STR database was identified by the function find. cluster. The retained PCs (100) were passed to a Linear Discriminant Analysis and the first two components were shown on Scatterplots of the DAPC.
For maternal ancestry identification, each mtDNA was phylogenetically classified and standard diversity molecular indices and Tajima's D test of neutrality were calculated for all populations in our database on the basis of the HVS-I haplotype using the software Arlequin v. 3. 5. 2. 2 [33, 37]. Using HVS-I data for each population as output, computation of pairwise genetic Fst matrix and AMOVA was done with Arlequin v. 3. 5. 2. 2 [33, 37] and the significance tested through 10,000 permutations (p<0.05). To represent Fst matrix, a non-metric multidimensional scaling analysis (nmMDS) was performed using PAST version 2. 16 software [38, 39]. The stress values related to the goodness of fit in two-dimensional space yielded results that were acceptable for the plots . The 3D representation of nmMDS was made by R package plot3D, while Mantel test was calculated by Passage 2 software, using 10,000 permutations . Geographic distances in kilometers were calculated on the Great Circle, using appropriate R script, while altitude distances were calculated on Euclidean distance by Passage 2 software.
After relationship filtering, the final dataset comprised 232 subjects (100 Native Amazon and 132 urban Peruvian individuals), all typed at 16 STR loci (S1 Table). The number of alleles per locus varied between 6 (locus D10S1248) and 28 (SE33). Overall, 183 alleles were recorded and the exact test for the Hardy-Weinberg equilibrium (HWE) for all loci did not show departures from the expectation (S2 Table).
To check for a decrease of heterozygosity, Fis indices were calculated for all Native Amazon and urban Peruvian populations. They were quite symmetrical around 0, with no significant values (Table 1). However, it is notable that most of the urban Peruvian samples showed slightly positive Fis values, whereas most of the Amazon samples had slightly negative Fis values. We compared the inbreeding Fis values with those obtained in comparable Native Amazon and mixed American populations typed for 645 STRs . Karitiana, the only Native American population from Brazilian Amazon reported in , showed a Fis value of -0.0126079, which was in agreement with excess of heterozygosity in all here studied Amazon samples from Peru. On the other hand, Fis values in admixed populations from Mexico, Brazil, Colombia and Argentina displayed reduced heterozygosity (Fis values >0), as shown also in our urban Peruvian samples.
Continental ancestral information from microsatellite database
We performed an exploratory analysis to highlight genetic structure caused by different continental ancestries. The best clustering model was identified by STRUCTURE 2. 3. 2 software , evaluating the maximal value of lnP(D) for each cluster (K) . A 3 K model (lnP(D) = -58263) was chosen as the best clustering model, because all other tested K had lower lnP(D) values. However, we plotted also a 2 K model (lnP(D) = -59135) (S1 Fig). In the 3 K model, the Native Amazon individuals were characterized by only one main component shared with urban Peruvian populations, which was very rare or absent in the two source populations (US Europeans and US Africans). On the other hand, urban Peruvians showed a strong heterogeneity; in fact, on the Native American background an African component was also present, especially in the Lima sample. The strength of the Native component was already evident in the 2 K model.
PCA based on STR genotypes mainly confirmed admixed structure of urban Peruvians contributed by Native Amazon and African populations (Fig 2A). The total variance percentage of PC1 and PC2, was 3% (PC1 1.7% and PC2 1.3%). The position of both Native Amazon people and urban Peruvians was sharply influenced by the contribution of the D2S441-10 allele, the most frequent in our populations (Native Amazon 0.56439 and urban Peruvians 0.675) (Fig 2B). The overlapping centroids for Lima and other Peruvian urban regions suggested the same degree of admixture.
a) PCA plot based on STR genotypes of urban and Amazon natives Peruvian, US European and US African populations. Dots represent individuals and the colors are associated with geographic origin. The first principal component accounts for 1. 7% of the total variability, while the second principal component accounts for 1. 3%. b) Contributions of each STR allele to PCA plot. The main allele contributors to the first and second PCs are shown.
A comparable degree of admixture for Lima and other Peruvian urban regions was confirmed not only by a null Fst value (-0.00138; not significant) of Lima vs. pooled data of the other Peruvian regions, but also by null Fst values between the single population samples (S3A Table). Considering whole dataset as only 4 populations (Native Amazon, Urban Peruvians, US Europeans and US Africans), the lowest Fst value was obviously observed between urban Peruvians vs. Native Amazon (Fst = 0. 0144; p = 0. 000). The Fst urban Peruvians vs. US Africans (Fst = 0. 0276; p = 0. 000) was lower than that urban Peruvians vs. US Europeans (Fst = 0. 0368; p = 0. 000),thus allowing us to further confirm the African contribution in urban Peruvians (S3B Table). Table 2 reports Fst values for each STR locus, calculated both for Native Amazon vs urban Peruvian populations and for Native Amazons, urban Peruvians, US Europeans and US Africans.
Table 2. Inter population diversity fixation index (Fst) values for each STR locus, calculated both for Native Amazon vs urban Peruvian populations and for Native Amazons, urban Peruvians, US Europeans and US Africans.
We used DAPC to define clusters of genetically related individuals. The best fitting model in the wide STR database was 5 K (BIC = 1755.36). After a Linear Discriminant Analysis, the first two components were represented on Scatterplots of the DAPC (Fig 3A), which showed the same trend of the STR genotypes PCA. Clusters 1 and 5 were strongly defined and located respectively in first and second quarters, while clusters 2, 3 and 4 resulted widely overlapping and undistinguished. The TH01-7 allele was underlined as the main contributor to individual clustering, posing threshold 0.07 loadings (TH01-7 = 0. 13380305 loading value) (Fig 3B). The height of each bar is proportional to the contribution of each allele (loading). When threshold loading was set to 0.05, also D1S1656-14 exceed it (loading value = 0.05763481). The strong contribution of the TH01-7 allele was not a surprise: the amount of genetic diversity, preserved in the TH01 locus, was described by high Fst value (Fst TH01 entire STR dataset = 0.06916; Table 2). The TH01-7 allele showed high frequencies in both urban (33% - 45%) and Amazon (35% - 68%) populations. In US Europeans its frequency was 19%, while in the US Africans was 40%. The strongly different allele frequencies in the dataset contributed to the scattered distribution of genotypes on the plot.
a) DAPC of STR genotype database. 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) Loading plot of DAPC. The main allele contributors to individual DAPC clustering are shown.
The model highlighted an association between some clusters and the populations under study (Fig 4). Specifically, Native Amazon individuals were found typically within cluster 5, US Africans within clusters 2 and 3, while US Europeans in cluster 1. Cluster 4 seems not to be associated with specific populations. Cluster 5 contains most Native Amazon (77.2% - 100%) and urban Peruvian individuals (33.3% - 72%), while individuals of the source populations were almost absent. Clusters 2 and 3 clearly marked individuals belonging to the US African sample (27% for cluster 2 and 42.1% for cluster 3). It is worth noticing that many urban and few Native Peruvian individuals fall into African clusters 2 and 3. Instead, cluster 1 is almost exclusive of US Europeans, and only one individual from Lima was found in this cluster. At last, the origin of cluster 4 remained unknown and probably it could be attributed to mixed individuals between source populations.
Fig 4. Composition of DAPC clusters for STR genotypes.
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.
Mitochondrial genetic diversity
The results of clustering of STR profiles obtained by DAPC were compared with those from mtDNA analysis. mtDNAs of 132 urban Peruvian and 10 Moche individuals were newly genotyped, while the haplotypes of the remaining 90 Native Amazons were already available . In S1 Table, for each subject, the variants of mtDNA HVS-I, HVS-II and coding regions are listed, along with the haplogroup and STR cluster affiliations.
Table 3 reports the haplogroup frequencies for the urban Peruvian sample. Most of the mtDNA haplogroups were of Native American origin (6. 1% A, 51.5% B, 15.2% C, 17.4% D), while 3.2%, 7.1% and 0.8% were of European, African and Asian origin, respectively.
To accurately estimate the native contribution, a dataset reporting only mtDNA haplotypes belonging to the Native American haplogroups A, B, C and D was created for urban Peruvian sample, and it was then compared with the mtDNA Native haplotype dataset of admixed and Native people from Peru, Bolivia, Chile and Amazon region of Brazil (Table 4). The genetic diversity parameters in urban Peruvian samples did not differ from those of other South American populations. All Tajima’s D values were negative indicating no selection on mtDNA, nevertheless, after applying Bonferroni correction (p<0. 004),only two p values were significant (Table 4). In Table 3 the haplogroup frequencies for urban Peruvian sample are reported. Most of the mtDNA haplogroups were of Native American origin (6.1% A, 51.5% B, 15.2% C, 17.4% D), but European (3.2%), African (7.1%) and Asian (0.8%) matrilineal inputs were also found.
Only 13 mtDNAs (10%) out of the 132 genotyped in urban Peruvians belonged to non-Native American haplogroups (Table 5): 8 belonged to Sub-Saharan haplogroups (6%), 4 to European haplogroups (3%) and 1 to an Asian haplogroup (1%). With the exception of two mtDNAs belonging to the African haplogroup L2a1 found in the Lima population, all the others differed from each other. Among the 13 non-Native mtDNAs, 7 were carried by individuals belonging to STR cluster 5 (Native American), the remaining 6 (5% of the overall mtDNA dataset) belonged to individuals of non-Native STR clusters, but none of them was associated to STR cluster 1 (only European) (Table 5). Moreover, all these 13 mtDNAs were from the Lima’s urban area and other urban Coast regions (S2 Fig), suggesting a sex-biased geographical distribution of admixture events.
Pairwise genetic Fst matrix was built on the mtDNA HVS-I haplotype data obtained from the present research and other populations from urban, Amazon and Andean places of the South American West Coast. They were plotted through 3D nmMDS to identify maternal genetic relationships with 0.02 Stress value (S3 Fig). The lines under each point highlight the distance on Third Dimension, while different colors (black-to-red) help to visualize the Second Dimension. This plot showed four main population groups: "Amazon" group (including AmazonPeru, AmazonBrazil and LlandosBolivia), "Lake Titicaca" group (LaPazBolivia, SubAndesBolivia, TiticacaPeru and also TemucoChile), "Andes Peru" group (NCAndePeru and UrbanPeru) and "Chile" group (NativesSArgentinaChile, SantiagoChile, IquiqueChile, ConceptionChileand Punta Arenas near Tierra del Fuego).
The same populations were grouped according to a geopolitical or ecoregional criterion and for each grouping we performed AMOVA. Grouping described by 3D nmMDS showed greater amount of variance among groups than geopolitical and ecoregional grouping (Table 6). Moreover, the Native mtDNA component of the Temuco sample seems to have a contribution from Lake Titicaca group, as showed also by Fst values between Temuco and La Paz, Bolivian, sub Andes and Lake Titicaca Peru (0.03468, 0.03608 and 0.03929, respectively).
Finally, to test possible associations between geography and genetics, the Fst matrix was correlated with both altitudinal and geographical distance matrices among populations. This test showed a light correlation index between altitude and genetics (r = 0.31285, p = 0.014 by Mantel test), while no correlation between genetics and geographical distances (r = 0.102, not significant) was found.
In this work, we tried to shed light on the transcontinental contributions to the gene pool of admixed urban Peruvian populations, using recently developed multivariate methods for clustering analysis on STR loci commonly used in individual identification. Moreover, we also took advantage of the geographic origin information provided by the maternally-transmitted mtDNA.
The slightly reduced heterozygosity (slightly positive not significant Fis values) showed by urban Peruvians, may be due to a low level of endogamy in these populations. Inbreeding of urban people in Peru was also confirmed  by positive Fis values based on different STR loci of urban populations: Chiclayo, Lima, Piura and Huancayo showed Fis positive values (0.012, 0.010, 0.007 and 0.015, respectively). Similar trends were described for the STR gene pools of Peruvians and other admixed South American populations also in .
The clustering and multivariate methods applied on STR genotype database allowed to highlight admixed origin of urban Peruvian populations, in which the African component was evident on the most abundant Native background, especially in the Lima sample (Figs 2A and S1). These findings are in contrast with the STR genotype dataset of admixed populations from the rest of South America, in which a large European component and a considerable Native American component, followed by a small and residual African contribution, seem to constitute a genetic leitmotiv. Such a structure was commonly described in admixed urban populations from Venezuela, Colombia, Brazil and US Hispanics [44, 45]. In urban admixed populations from all over South America, commonly called "Mestizos", typing of autosomal and X chromosome STR loci showed variable Native contribution, ranging from 70% in Andean regions and Meso-America to 20% in Colombia and Central America, while European ancestry resulted the highest external component (from 25% in Chilean Andean region to 70% in Southern Brazilian people). African ancestry in the entire dataset is low (<10%) .
As regarding Peru, the genomic ancestry proportions based on autosomal STRs showed 30% of admixture with non-Native American populations , while proportions provided by INDEL polymorphisms in Peruvians from Coast, Andes and Amazon were identified as 83% Native American and 17% non-autochthonous, mainly from Europe . These proportions allowed us to consider the results obtained by DAPC reliable (Fig 4). In fact, very many urban Peruvian individuals belonged to the Native cluster (33.3% - 72%), that is the cluster made up of a high percentage of Native Amazon individuals (77.2% - 100%). The low number of individuals in African and European clusters (clusters 2 and 3, and cluster 1, respectively) was strongly consistent with the history of other populations from this part of South America. Moreover, in autosomal SNPs, mtDNA and Y chromosome of Bolivian admixed people, the continental ancestry of Native Americans was the most abundant, followed by European and African ones [49, 50].
The identification of STR alleles with geographic variation on global scale was the other main point of this work. In the present study, the main contributor to individual clustering provided by DAPC was the TH01-7 allele (Fig 3B). High frequencies of this allele, similar to those here observed, were already described in the Andean and coastal population from Peru (43% - 51%) and Native Amazon people from Ecuador (40%) [3, 43]. In Afro-Caribbean people and in African ancestry Colombians this allele showed a 40% frequency [51–54], while in all other South American populations (Brazil, Argentina and Chile) it ranged between 24% and 26%, consistent with European-Native American admixture [55–59]. However, a strong diversity of TH01 allele frequencies on geographic scale was already well known. As described in previous works, the TH01-6 allele showed an increasing West-East cline in Europe, whereas the TH01-9.3 allele displayed a marked latitudinal gradient with high frequencies in Northern Europe [4, 60]. This wide diversity of TH01 allele frequencies could be due to selection or demic events.
The second part of our study extends this discussion through the study of mtDNA background. mtDNA haplotypes belonging to non-Native haplogroups were concentrated only in Lima and on the urban Coast region. In particular, in the here studied urban Peruvians, the African maternal contribution (6%) was slightly more represented than the European maternal contribution (3%) (S2 Fig and Table 5). Indeed, the African component was higher (6%) than in Bolivian and Chilean populations (~1%) [61, 62], whereas the European component (3%) is comparable with that reported in Bolivia (~1%), and less than that found in Chile (~11%), which was strongly involved in a recent migration from Europe . Furthermore, no maternal Old World contributions were identified in Ecuadorians [14, 63].
These data fitted with STR cluster proportions: 13% and 9% of urban Peruvian samples resulted to belong to African clusters 2 and 3, whereas only 1% belonged to the European cluster. These data could suggest past slavery, which especially involved Lima and towns on the Coast region and influenced heavily the population composition of this area: by XVIII century more than a third of the Lima's population included slaves, mainly Africans . These results demonstrate that it is possible to detect signs of admixture events in autosomal STR and mtDNA gene pool on population scale [11, 18].
Finally, the Native mitochondrial component showed a strong similarity in urban Peruvian and Andean populations, indicating Andean people as the most probable Native source population of urban Peruvians. This scenario is plausible, because, unlike Native Amazon populations, Andeans maintained larger population sizes also after European colonization and greater mobility . The analysis of Native mtDNA gene pool revealed that the diversity of the urban Peruvian sample is an integral part of South America mtDNA variability.
In this work, we tried to shed light on the presumed admixed origin of urban Peruvian populations through clustering and multivariate methods. In the STR genotype database strong signs of continental ancestry were highlighted, also supported by mtDNA composition. Finally, this work confirmed the important role of autosomal STRs and mtDNA for historical reconstructions, underlining the advantage of a combined use of the autosomal and uniparental markers usually employed in forensic applications.
S1 Fig. STRUCTURE analysis at Ks 2 and 3 for urban and Native Amazon Peruvian, US European and US African samples.
The colors are as follows: dark grey for European, grey for African and light grey for Native Amazon ancestry component. The presence of more than one component in US European and US African samples was due to the multiethnic origin of United States populations.
S3 Fig. 3D nmMDS of pairwise Fst matrix.
3DnmMDS on the first three axes based on the matrix of pairwise Fst values of HVS-I mtDNA after grouping into 14 geographic samples. Color shades from bright red to black refer to position on dimension 2. The references of all samples were reported: UrbanPeru (this paper); NCAndePeru  (this paper); AmazonPeru [15, 17]; LaPazBolivia ; LlandosBolivia ; SubAndeBolivia ; TiticacaPeru [16, 48]; AmazonBrazil ; TemucoChile ; SantiagoChile , PuntaArenas , IquiqueChile , ConceptionChile , NativesSArgentinaChile [66, 67].
S1 Table. List of sampled individuals.
List of sampled individuals with birthplace and geographic information, geographic coordinates, response after filtering with Familias 3 software, STR DAPC cluster, mtDNA haplotypes and haplogroups.
S3 Table. Pairwise Fixation Indices (Fst) in all STR loci.
Pairwise Fixation Indices (Fst) in all STR loci: a) using all single population samples. b) considering whole dataset as only 4 populations. All values were significant (p < 0.05). Above diagonal P-values; below diagonal pairwise Fst value. In bold: not significant P values.
We thank all anonymous donors for their voluntary participation in this study as well as: Carlos Obando Peralta, Consul of Peru in Rome, and the overall staff of the Consulate of Peru in Rome, for the logistic and institutional support during the sampling and the help to divulgate this research; Maria Carmelita Cardinale for the important work and assistance with the sample collection; Andrea Novelletto for support and useful discussions about statistical applications.
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