Genomic Insights into the Ancestry and Demographic History of South America
[['Our understanding of fine-scale patterns of population structure in humans has dramatically increased with the advent and deployment of fast , inexpensive , and accurate genome-wide technologies for assaying variation [1–3] .', 'However , our understanding of regional patterns of genomic variation is quite poor in many parts of the world particularly in populations that are currently underrepresented in GWAS studies , including those in Latin America [4] .', 'Understanding patterns of genomic variation is especially important for populations throughout the Americas , which have undergone multiple recent admixture events , making the reconstruction of their evolutionary past and the design of multi-ethnic medical genetic studies challenging .', 'Recently , studies in Mexico , the Caribbean , and throughout the Americas have shed light on the complex demographic processes that occurred in those regions and have illuminated how differences in the pre- and post-colonial history have shaped differences in genomic variation that ultimately impact variation in complex biomedical traits [5–7] .', 'The South American landmass features unique geographic , archaeological , and historical records that are distinct from other regions of the Americas [8] .', 'The contributions of these events to patterns of genomic variation remains to be laid out to a greater extent .', 'For example , in contrast to North America , South America’s indigenous population history derives from a single migration wave that rapidly expanded southwards throughout the Andean highlands and eastwards into the Amazon basin [9] .', 'Previous analyses of native South American variation based on microsatellites have reported a west-to-east difference in genetic diversity between Andean and eastern Brazilian tribes as one of the strongest signals of sub-continental genetic differentiation [10–12] .', 'The largest human settlements in South America , however , occurred throughout the Andean region and likely represent a major source of Native American variation in present day South American Latinos .', 'Characterizing the extent of substructure and differential contribution of these ancestral components is therefore crucial to understanding the genetic heterogeneity of the South American population .', 'Previous studies on South American Latino populations have either used a limited number of genetic markers to evaluate continental-level patterns of population structure or focused on particular geographic regions [13–18] .', 'Many of these studies and others have demonstrated a large amount of genetic diversity in Native American and mestizo populations , especially between different geographic regions [11–13 , 19] .', 'Wang et al . analyzed multiple mestizo populations throughout South America using 678 microsatellite markers [13] and found evidence of correlations between ancestry components and geography .', 'The Galanter et . al . and Ruiz-Linares et al . studies [15 , 16] used a limited set of ancestry informative markers to analyze the global ancestry proportions throughout Latin America .', 'However , due to the smaller numbers of markers , these studies were unable to perform analyses that rely upon dense genetic information such as local ancestry inference , ancestry specific principal components analysis , and demographic modeling based upon ancestry tract length .', 'Recent work in Brazil using dense genomic information has demonstrated that individuals differ markedly in ancestry proportions both within and between populations in metropolitan regions of South America [20] .', 'They also demonstrate significant variation within the European and African ancestry components .', 'Here , we expand upon previous work by focusing on admixed populations from five countries in Spanish speaking South America ( Argentina , Chile , Colombia , Ecuador , and Peru ) , spanning much of the Andean region of the continent .', 'Similar to other areas in Latin America , South America has experienced multiple migration and admixture events , including Native American settlement , European colonization , and the African slave trade .', 'However , the timing and magnitude of migration waves from a myriad of continental and subcontinental ancestral groups varies dramatically throughout the continent and affects the population genetic profile of the region at a local scale .', 'The earliest settlements in South America date back over 14 , 000 years ago [8] .', 'Native Americans developed multiple civilizations throughout the continent , including settlements in the Andes , the Amazon , and along the coasts .', 'In the 16th century , European colonization and conquest led to a dramatic population bottleneck in the Native American population as well as an increasing influx of European migrants , quickly followed by admixture with West Africans brought to the Americas through the slave trade .', 'During the following centuries , there was continuous admixture between European , Native Americans , and African individuals .', 'Early European migration into the Spanish South American colonies came mainly from the Iberian Peninsula .', 'Spanish conquistadors in the early 16th century conquered many of the indigenous populations in the Andean region of South America , establishing South American colonies throughout the continent [21] .', 'All five of the countries studied here were originally part of the Spanish viceroyalty of Peru .', 'These Spanish colonies followed separate but related developmental paths , eventually splitting into the viceroyalties of Peru , New Granada , and Rio de la Plata .', 'The Peruvian colony was a major source of silver for the Spanish Empire , while the colonies in Rio de la Plata ( including present day Argentina ) and New Granada ( including Colombia and Ecuador ) became important commercial centers [21 , 22] .', 'The Spanish colonies in South America continued to receive immigration from Europe concurrent with admixture with Native American populations .', 'In the 19th and 20th centuries , there is evidence of increased migration from many regions of Southern Europe , especially in Argentina [23 , 24] .', 'To explore the impact of this complex demographic history upon the current genetic structure of South American Latino populations , we analyze single nucleotide polymorphism ( SNP ) genotyping data from 436 unrelated admixed samples , including 175 Argentinians , 119 Peruvians , 27 Chileans , 19 Ecuadorians , and 96 Colombians .', 'We combined these data with reference panels of European and Native American populations , and applied admixture deconvolution methods to trace back the origin of each ancestry component within Europe and the Americas .', 'We also analyzed the length distribution of ancestral segments in admixed individuals to test hypotheses about past migration patterns and examine whether different countries have experienced different genetic histories .'], ['To characterize the ancestral components of South American Latino individuals from Colombia , Ecuador , Peru , Chile , and Argentina , we applied unsupervised clustering models and principal components analysis to genotype data from ancestral and admixed populations ( Fig 1 ) ( see Methods ) .', 'This data set contains 436 admixed South American individuals together with 204 European individuals from the POPRES study [1] , 50 Yoruban and 50 Han Chinese from the 1000 Genomes Project [3] , and 493 unmasked Native American individuals from Reich et al . 2012 [9] .', 'The South American individuals showed varying proportions of European , Native American and , to a lesser extent , West African ancestry in PCA space , supporting the notion of a broad range of global ancestry patterns throughout South America .', 'We observed some dispersion of Native American individuals away from the main ancestral cluster due to the presence of European admixture .', 'We then ran clustering models for K = 2 through K = 15 ancestral populations with ADMIXTURE [25] on a total of 1 , 233 individuals .', 'Cross validation errors for the ADMIXTURE analysis are shown in S2 Fig . The minimum CV error was observed at K = 13 .', 'When clustering is performed assuming K = 4 ancestral populations ( Fig 1C ) , the algorithm separates the individuals into four major continental clusters .', 'Average continental ancestry proportions for each of the admixed populations are shown in Table 1 .', 'As expected from historical records [21 , 22] and previous results from other Latino populations in the Caribbean [6] and Mexico [5] , South American Latino individuals show a mixture of European , Native American , and African ancestry .', 'However , some populations , especially those in Peru , Chile , and Argentina , tend to have a smaller proportion of African ancestry than seen in Latino populations in the Caribbean ( p < 2 . 2 x 10−16 , Wilcoxon test , S6 Fig ) , also observed in previous analyses [13 , 16–18] .', 'We find significant differences in global ancestry proportions between countries within South America .', 'The Peruvian individuals tend to have a higher proportion of Native American ancestry than individuals from any of the other South American populations ( Tukey HSD Test , p < 0 . 001 vs . Argentina , Chile , Colombia , Ecuador; S3 Fig ) .', 'We observed multiple Peruvian individuals with a >25% proportion of East Asian ancestry , which is not surprising given that there were large Asian migrations to Peru especially during the 19th and early 20th century where laborers from Guandong ( formerly Canton ) province in China were brought to the country [26] .', 'Peru opened its borders to Asian immigration in 1849 , and it is estimated that over 87 , 000 Chinese individuals entered Peru between 1859 and 1874 [22] .', 'This East Asian ancestry component is also seen in the Northern Amerindian individuals .', 'These individuals are from Eskimo , Aleut , and Na-Dene populations and the observed clustering is consistent with the hypothesis of multiple waves of gene flow from Asia to America suggested by a previous study [9] .', 'At higher values of K in ADMIXTURE , these individuals are assigned to their own ADMIXTURE component , indicating a unique ancestry component that is separate from the East Asian cluster ( Fig 1 and S5 Fig ) .', 'The Argentinian population has a significantly higher proportion of European ancestry than the Peruvian , Chilean , and Ecuadorian populations ( Tukey HSD Test , p = 0 . 018 vs . Chile , p = 0 . 129 vs . Colombia , p<0 . 001 vs . Peru and Ecuador ) with some individuals having close to 100% European ancestry ( S3 Fig ) .', 'Even so , there is a large range of ancestry proportions within individuals from Argentina , consistent with previous results based on a small number of ancestry informative markers and blood group antigens [17 , 27 , 28] .', 'This variance is most likely a result of the contrasting histories of different Argentinean regions .', 'For example , the original Spanish settlers of Argentina came through the Pacific/Andean region [21] .', 'However , as Argentina developed , individuals from Spain and Southern Europe settled throughout the coastal regions on the Atlantic [23] .', 'We also observed a small number of Argentinian individuals with relatively high amounts of African ancestry , whereas the rest of the individuals have a very low African ancestry component .', 'This diversity is reflected in the large range in ancestry proportions seen within Argentina and is consistent with previous studies [17 , 28 , 29] .', 'At higher order Ks ( K = 13 in Fig 1 ) , we observed significant substructure in both the Native American and European populations .', 'The North-South gradient among European populations is strongly correlated with the latitude of each country’s capital ( p < 2 . 2 X 10−16 , linear regression ) , with a southern European component ( light blue ) most prominent in Spain , Portugal , Italy , and Greece .', 'Most of the admixed Latino individuals in the sample have a high proportion of this southern European component , suggesting that the Europeans involved in admixture events in South America are from the Iberian Peninsula and Mediterranean Europe .', 'This observation is consistent with historical migration patterns and maintained cultural influence [19] .', 'On the other hand , the primary cluster of Native ancestry is reflective of the local indigenous diversity .', 'We find that a component of the Native American ancestry in the Peruvian samples is shared with local Andean native groups , such as Quechua and Aymara , and that of Colombians is more closely shared with the Southern and Central Amerindian groups ( Fig 1 , K = 13 ) .', 'In contrast , we see that the Native American component in Argentina and Chile is shared between components from Central/Southern Native American and Andean Native American groups , showing a wider range of ancestral origins that we explore below in further analyses ( Fig 1C , K = 13 ) .', 'Sex biased ancestry is an important feature of many Latin American populations , and has been observed and described thoroughly in many previous research articles [6 , 18] .', 'European migrants to the Americas were mainly male , especially during the earlier years of colonization .', 'This has resulted in increased Amerindian ancestry on the X-chromosome when compared to the autosomes .', 'After excluding admixed males from the analysis , we had admixed individuals from only four populations: Argentina , Chile , Colombia , and Peru .', 'We compared ADMIXTURE estimates at K = 3 of autosomal and X-chromosomal ancestry ( S7 Fig ) .', 'We find an increase in Native American ancestry on the X-chromosome compared to the autosomes ( S8 Fig , Wilcoxon p < 0 . 001 ) .', 'This is suggestive of the fact that there was an overabundance of European males and Amerindian females that participated in the admixture process .', 'To identify the admixed individuals’ subcontinental lineages rooted within Europe and South America , we performed ancestry-specific PCA analysis .', 'ASPCA is a technique developed to perform principal components analysis on the fraction of an individual’s ancestry from a specific continental origin .', 'In contrast to PCA , which is performed on individual ( unphased ) diploid genotype calls , ASPCA is performed on phased haploid genomes conditional on ancestry calls ( see Methods for details ) .', 'To explore their European origins , we combined our admixed individuals with the POPRES European data set [1] and performed ASPCA on the merged data set ( Fig 2 ) .', 'Due to the limited overlap between the POPRES data set and our samples , we performed ASPCA on the Argentinian , Chilean , and Peruvian haplotypes separately from the Colombian and Ecuadorian haplotypes .', 'The European reference samples cluster according to geography [30] .', 'We find that the majority of the European haplotypes of the admixed samples cluster with Iberian and Southern Europeans , consistent with historical records and previous reports [6 , 31] .', 'However , we observed interesting differences between countries in South America .', 'For example , Argentina showed the highest number of European haplotypes that cluster in the Italian peninsula .', 'This is consistent with recent migration events from Italy to Argentina in the late 19th and early 20th centuries [22] .', 'Between 1880 and 1930 , 2 . 3 million of the 4 . 7 million migrants to Argentina had Italian nationality [24] .', 'We also find that Argentina has the largest range in the European ancestry components and even includes two haploid genomes that cluster near individuals from Germany , Poland , and Hungary in the top right of the ASPCA plot ( Fig 2 ) .', 'No other South American population showed samples with such distant ancestry from the Iberian cluster , nor other Latino samples from previous studies in the Caribbean and Mexico [5 , 6] .', 'To further our investigation of the European component beyond the Spanish ancestry found in the Iberian Peninsula , we combined masked samples from the Canary Islands with South American individuals from Colombia and Ecuador .', 'The Canary Islands were colonized by the Spanish in the early 15th century and became a stopping point for Spanish on their way to the Americas .', 'Here , we find undifferentiated patterns of ancestry between the European component of these three populations ( S9 Fig ) , suggesting that the European ancestry of these groups either originated from a similar source on the Iberian peninsula or that methods of increased resolution are needed to untangle more subtle differences .', 'To investigate the Native American component of the South American individuals’ ancestry , we combined our samples with those from 49 Native American populations previously genotyped [9] .', 'We removed Native American samples that appeared as outliers in ASPCA space and that were geographically distant from South America ( see Methods and S10 Fig ) .', 'We also excluded Native American individuals with greater than 10% estimated European ancestry , as we found these individuals were biasing the principal components analysis towards a European/Native American axis ( S11 , S12 and S13 Figs ) .', 'For visualization purposes , Native American populations were grouped corresponding to the labels used in Reich et al . [9] and are referenced geographically ( see S1 Table for mapping ) .', 'We find that the Native American component of the South American haplotypes clusters along a gradient between the Andean Amerindian populations and the Southern Amerindian populations along ASPC1 and ASPC2 ( Fig 3 ) .', 'Notably , the Native American ancestry in the admixed South American individuals is drastically different from the genetic components observed among Central and Northern Native American groups , such as Kaqchikel in Guatemala and Zapotec or Tepehuano in Mexico .', 'None of these groups showed close affinities with Latino-derived South American haplotypes , supporting the notion of a highly substructured architecture of the Native American component among Latinos from different regions across Latin America .', 'Our ASPCA analysis revealed that South American native haplotypes cluster primarily into two groups: one represented by central Andean individuals , such as Quechua and Aymara , and another group that includes most of the remaining native populations from South America .', 'The differentiation between the Andean Amerindians and other South Amerindians is consistent with previous results using Y chromosome and mtDNA analyses [11 , 12] , and suggests that the mountain range of the Andes acted as a major geographic barrier to gene flow during Native American evolution .', 'This created further population structure among South Native American groups separating populations in the Amazon and east coastal regions from highland populations in the Andes .', 'Interestingly , a number of the populations classified as Andean such as the Hulliche , Inga , and Yahgan clustered close to the Southern/Amazonian Native Americans and far from the other Andean Native Americans such as the Quechua and Aymara .', 'Reich et al . in 2012 [9] suggested that , based on linguistic affinities , these populations would be expected to cluster with the Aymara and Quechua populations .', 'Indeed , among the samples from the main Amazonian cluster in Fig 3 , these are the only ones spreading towards the Quechua/Aymara cluster , supporting the idea of pre-Columbian admixture events giving rise to populations like the Inga , Huilliche , and Yahgan along the Andes .', 'The separation between the Andean and other South American populations is consistent with the hypotheses of either multiple migration routes into South America , with an early split soon after crossing the Isthmus of Panama , or restricted levels of gene flow shortly after establishment of Native American settlements in the continent [8 , 11 , 12 , 32] .', 'Likewise , the clustering of northern Argentinian Wichi and Paraguayan Guarani and Toba with lowland groups from Brazil and Colombia , suggests an Amazonian origin of Native American migration into the Gran Chaco and Pampas areas rather than strong evidence of a trans-Andean route .', 'The branching pattern of these ancestral migrations have directly impacted the genetic profile of present day South American Latino populations , even between neighboring countries such as Argentina and Chile .', 'We detail these patterns in what follows .', 'The clustering of the masked haploid genomes from the admixed individuals tended to be population specific ( Fig 3 ) .', 'We find that the Peruvian individuals cluster more closely with the Andean Native American individuals than with any other Native American group , suggesting that the Native American component of the Peruvian population is mainly from the Andean region .', 'While the Andean Native Americans and Peruvian individuals cluster closely , many of them do not overlap .', 'Both the Quechua and Aymara individuals are from the Central Andes , while the admixed individuals are from Lima .', 'Mitochondrial and Y-chromosomal studies of Andean ancestry have indicated that there is relatively low geographically-correlated genetic diversity in the Andean region , likely due to the historically higher gene flow and population size in the Andean region [11 , 12] .', 'While there seems to be less geographic correlation in ancestry in the Andean Native Americans than in other Native American populations , some geographic stratification may be detected through high-density genotyping that was not detected using mitochondrial or Y-chromosomal analysis .', 'In other populations with lower levels of genetic differentiation , such as Europeans , high density genotyping data revealed correlations between geography and ancestry [30] .', 'Also , our reference panel has little representation from coastal Peruvian Native Americans , and these groups may also have contributed to the admixture process in cosmopolitan areas .', 'Argentinian individuals show a broader range of indigenous ancestry: some cluster closer to the Southern/Amazonian Native Americans , while others cluster with the Latino Peruvians and the Andean group , reflecting a rich diversity of pre-Columbian roots in Argentina , whose geography spans the breadth of the continent from the Andes to the Atlantic , thus absorbing haplotypes from both major streams of Native American migration .', 'We find only a marginal relationship between clustering and sampling location within Argentina .', 'We find that sampling latitude is marginally associated with ASPC1 in a linear regression ( p = 0 . 025 , S14 Fig ) , and not significantly associated with ASPC2 ( p = 0 . 3387 , S15 Fig ) .', 'We find no significant linear relationship between longitude and ASPCs ( p = 0 . 322 vs . ASPC1 and p = 0 . 844 vs . ASPC2; S16 and S17 Figs ) .', 'However , we do not expect the sampling locations in our current sample to be indicative of an individual’s history to this degree of resolution .', 'Most individuals were sampled at hospitals in major cities throughout Argentina , with the largest number of individuals sampled in Buenos Aires .', 'Because of recent major migrations of individuals , especially from rural to urban areas , current location may not be indicative of the location of an individual’s ancestors .', 'There has also been recent intraregional migration throughout South America , especially in urban regions such as Buenos Aires [33 , 34] .', 'This could be contributing to the genetic diversity we observe within the Argentinian individuals’ Native American ancestry .', 'A sampling scheme based upon the “four grandparent” ancestry principle , such as the one used in the European POPRES [1] study , along with more representation for different regions throughout Argentina may better elucidate finer scale structure in the country , although this is also known to be imperfect [17] .', 'In contrast , the Colombian and Ecuadorian Latino haplotypes tend to cluster with geographically nearby Southern Native Americans , such as the Wayuu , Piapoco , and Ticuna from Colombia .', 'The Ecuadorian individuals cluster farther away from this ancestral group than the Colombians , which could be due to the lack of Ecuadorian Native American groups in the reference panel or be the result of admixture with Andean Native American lineages .', 'The Chilean individuals cluster towards the middle of the admixed group , between the Andean cluster and the Chilean Huilliche and Yaghan samples .', 'The Native American reference panel used here does not include many Native Americans from Southern Chile .', 'Only two haploid genomes from one Hulliche individual are in the subset of the reference panel used for analysis due to the high proportion of European ancestry in the remaining Hulliche individuals .', 'The lack of representation of Hulliche and other Chilean Native Americans could explain why we do not see a strong differentiation of the admixed Chilean haploid genomes .', 'A deeper sampling effort is needed to assess fine-scale genetic patterns within Chile .', 'We find that the Native American ancestry of admixed Latinos is associated with population of origin ( ANOVA p < 2 x 10−16 for both ASPC1 and ASPC2 ) .', 'This is consistent with many previous results in population history analysis , which have also shown strong correlation between geographic features and ancestry .', 'To further investigate the differences between the European and Native American ancestry components of South American individuals , we used GERMLINE [35] to identify genomic regions of identity by descent ( IBD ) in the admixed individuals and compared the patterns of IBD matching within and among populations to the local ancestry calls inferred throughout each IBD match .', 'We find 12 , 348 segments of IBD shared within populations compared with only 4 , 941 segments of IBD shared between populations .', 'On average , the individuals from Colombia share the most IBD within the population ( 15 . 2 cM ) , followed by Chile ( 3 . 42 cM ) , Ecuador ( 2 . 58 cM ) , Peru ( 2 . 06 cM ) , and Argentina ( 0 . 84 cM ) .', 'We find that segments shared between populations are shorter than those shared within populations ( Wilcox p < 2 . 2e-16 ) .', 'For IBD segments that could be identified using a haploid comparison , we calculated for each segment the proportion of European , Native American , and African local ancestry .', 'We find that in both within and between populations , longer IBD segments have a higher proportion of European ancestry ( linear regression , p = 4 . 04 x 10−16 ) .', 'The effect size based upon linear regression is greater in IBD segments shared between populations ( β = 0 . 050 ± 0 . 0084 s . e . , p = 3 . 7 x 10−9 ) than in IBD segments shared within populations ( β = 0 . 0076 ± 0 . 0011 s . e . , p = 4 . 4 x 10−11 ) ( S18 , S19 and S20 Figs ) .', 'To test if a single admixed population primarily drove the observed effect , we also analyzed the shared IBD segments within each admixed South American population on its own .', 'We observed a significant association in a linear regression model between IBD segment length and ancestry in the Peruvian and Argentinian populations ( Peru p = 6 . 01 x 10−8 , Argentina p = 0 . 0088 , S21 Fig ) , a suggestive association in the Colombian populations ( p = 0 . 0955 , S21 Fig ) , and found no evidence for the association in Chilean or Ecuadorian populations ( Chile p = 0 . 132 , Ecuador p = 0 . 903 , S21 Fig ) .', 'However , the difference in significance may be a function of the differential power to detect this effect within populations due to sample sizes differences , since we have the lowest number of admixed individuals from Chile and Ecuador .', 'We also find that the majority of the long IBD segments ( greater than 10 cM ) shared between populations are of European ancestry ( 20 European vs . 2 Native American ) .', 'IBD tracts shared between populations tend to consist of only a single continental ancestry , while those shared within populations often contain multiple ancestry switch points .', 'These patterns are consistent with previous studies of IBD sharing in Latino populations [36] and suggest that the most recent common ancestors shared between Latino populations in South America are much more likely to be European than Native American , and that these trace back to a reduced source of founders .', 'These results are also supported by the ASPCA analyses , where we find remarkable substructure among the different Native American components of each Latino population , but similar patterns of Southern European ancestry across Latino populations in ASPCA space .', 'To further confirm the results of the ASPCA analysis , we looked for diploid IBD matches between admixed and reference populations ( S22 Fig and S23 Fig ) .', 'We find that consistent with the ASPCA , the most IBD sharing with European populations occurs between admixed populations and Iberian populations .', 'The Peruvian individuals also share a much higher amount of IBD with the Andean Native Americans such as the Quechua and Aymara , as suggested by the ASPCA plots .', 'Taken together , the ASPCA and IBD results suggest that admixture between Europeans and Native Americans occurred in multiple locations throughout the colonization of the Americas and involved many different Native American populations .', 'Individuals in our study were collected from major metropolitan regions in South American countries ( Argentina , Peru , Chile , Colombia ) or are recent US immigrants ( Ecuador , Colombia ) .', 'Our sample is thus an important reflection of the admixture patterns in cosmopolitan areas of these South American countries .', 'While not fully representing the breadth of diversity across South America , the unique signatures of each of these populations gives deeper insight into regions that have historically been understudied .', 'Important insights into population structure have been discovered using similar sampling schemes in previous work [6 , 18] .', 'A more comprehensive sampling scheme throughout South American countries will help to reveal finer population structure patterns [17] .', 'Analyzing the length of contiguous tracts of the same ancestry in an admixed population can help to determine the timing of admixture events and subsequent migrations .', 'We used the program Tracts [37] to fit multiple models of admixture to the observed data .', 'Tracts uses an optimization function to fit the ancestry tract length distribution under a given population history model to the observed tract length distribution .', 'It also estimates the timing of major admixture and migration events within the model .', 'Multiple models can be compared based upon their observed likelihoods given the data .', 'To infer the genetic migration history of South American Latinos , we compared three potential hypotheses ( S24 Fig ) .', 'First , we fit a model with a single admixture event between Europeans and Native Americans followed by a migration of Africans .', 'We considered this model our base model , reflecting the initial colonial-era contact followed by slave importation .', 'Next , we fit a second model with an additional European migration event .', 'A third model consisted of the base model with an additional African migration event .', 'We compared the fits of the models using the observed likelihoods .', 'The tracts model makes an assumption about independence of the tract length distributions that may not necessarily be true and can cause likelihood based methods to falsely reject a model in favor of a model with more ancestry pulses [38] .', 'In order to ensure we were correctly rejecting the single pulse model , we compared our observed changes in likelihood to the changes in likelihood seen in 1000 simulations of the single pulse model ( see Methods ) .', 'We find that for all of the admixed populations studied , the model with the extra pulse of European migration was preferred ( P < 0 . 001 for Argentina and Colombia , P = 0 . 002 for Peru , P = 0 . 003 for Ecuador , and P = 0 . 027 for Chile , S28 Fig ) .', 'The best fitting models for each population are shown in Fig 4 .', 'This result suggests a demographic history of continued European migration to Latin South America .', 'This is in contrast to many countries within the Caribbean , where Tracts models estimated multiple pulses of African migration [6] .', 'This contrast reflects historical differences in the slave trade among regions of the Americas
['Introduction', 'Results and Discussion', 'Materials and Methods']
['South America has a complex demographic history shaped by multiple migration and admixture events in pre- and post-colonial times .', 'Settled over 14 , 000 years ago by Native Americans , South America has experienced migrations of European and African individuals , similar to other regions in the Americas .', 'However , the timing and magnitude of these events resulted in markedly different patterns of admixture throughout Latin America .', 'We use genome-wide SNP data for 437 admixed individuals from 5 countries ( Colombia , Ecuador , Peru , Chile , and Argentina ) to explore the population structure and demographic history of South American Latinos .', 'We combined these data with population reference panels from Africa , Asia , Europe and the Americas to perform global ancestry analysis and infer the subcontinental origin of the European and Native American ancestry components of the admixed individuals .', 'By applying ancestry-specific PCA analyses we find that most of the European ancestry in South American Latinos is from the Iberian Peninsula; however , many individuals trace their ancestry back to Italy , especially within Argentina .', 'We find a strong gradient in the Native American ancestry component of South American Latinos associated with country of origin and the geography of local indigenous populations .', 'For example , Native American genomic segments in Peruvians show greater affinities with Andean indigenous peoples like Quechua and Aymara , whereas Native American haplotypes from Colombians tend to cluster with Amazonian and coastal tribes from northern South America .', 'Using ancestry tract length analysis we modeled post-colonial South American migration history as the youngest in Latin America during European colonization ( 9–14 generations ago ) , with an additional strong pulse of European migration occurring between 3 and 9 generations ago .', 'These genetic footprints can impact our understanding of population-level differences in biomedical traits and , thus , inform future medical genetic studies in the region .']
['South America is home to over 400 million people who share a rich demographic history , including settlement by Native Americans , European colonization , and the African slave trade .', 'We use genomic data to infer which populations from Europe and the Americas contributed to these admixture events .', 'We provide evidence for multiple origins of the Native American ancestry of admixed South American Latinos .', 'The Native American ancestral component correlates strongly with geography , indicating that admixture occurred between European colonists and local Native American populations throughout South America .', 'We also show that the European ancestry of South American Latinos comes mainly from the Iberian peninsula , however , a significant number of Argentinians have European ancestry from other Southern European regions .', 'The genetic signal of European admixture in South American populations is younger than the signal observed in Mexico and the Caribbean .', 'We find evidence for a second pulse of European migration to many regions of South America subsequent to the original colonization .', 'These results demonstrate the heterogeneous nature of the Latino population in South America and help elucidate the complex genetic and admixture events that shaped the population structure of the region .']
[]