Fine-scale genomic analyses of admixed individuals reveal unrecognized genetic ancestry components in Argentina - PubMed (original) (raw)

. 2020 Jul 16;15(7):e0233808.

doi: 10.1371/journal.pone.0233808. eCollection 2020.

Angelina García 1 2 3, Juan Manuel Berros 4, Josefina M B Motti 5, Darío A Demarchi 1 2 3, Emma Alfaro 6 7, Eliana Aquilano 8, Carina Argüelles 9 10, Sergio Avena 11 12, Graciela Bailliet 8, Julieta Beltramo 8 13, Claudio M Bravi 8, Mariela Cuello 8, Cristina Dejean 11 12, José Edgardo Dipierri 7, Laura S Jurado Medina 8, José Luis Lanata 14, Marina Muzzio 8, María Laura Parolin 15, Maia Pauro 1 2 3, Paula B Paz Sepúlveda 8, Daniela Rodríguez Golpe 8, María Rita Santos 8, Marisol Schwab 8, Natalia Silvero 8, Jeremias Zubrzycki 16, Virginia Ramallo 17, Hernán Dopazo 18 19

Affiliations

Fine-scale genomic analyses of admixed individuals reveal unrecognized genetic ancestry components in Argentina

Pierre Luisi et al. PLoS One. 2020.

Abstract

Similarly to other populations across the Americas, Argentinean populations trace back their genetic ancestry into African, European and Native American ancestors, reflecting a complex demographic history with multiple migration and admixture events in pre- and post-colonial times. However, little is known about the sub-continental origins of these three main ancestries. We present new high-throughput genotyping data for 87 admixed individuals across Argentina. This data was combined to previously published data for admixed individuals in the region and then compared to different reference panels specifically built to perform population structure analyses at a sub-continental level. Concerning the Native American ancestry, we could identify four Native American components segregating in modern Argentinean populations. Three of them are also found in modern South American populations and are specifically represented in Central Andes, Central Chile/Patagonia, and Subtropical and Tropical Forests geographic areas. The fourth component might be specific to the Central Western region of Argentina, and it is not well represented in any genomic data from the literature. As for the European and African ancestries, we confirmed previous results about origins from Southern Europe, Western and Central Western Africa, and we provide evidences for the presence of Northern European and Eastern African ancestries.

PubMed Disclaimer

Conflict of interest statement

I have read the journal's policy and the authors of this manuscript have the following competing interests: PL provides consulting services to myDNAmap S.L. JMB and JZ are employed by Biocódices S.A. HD is the scientific director of Biocódices S.A. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

Figures

Fig 1

Fig 1. Sample locations from the present study.

The samples are divided according to regions for visualization only. N: The number of samples that passed genotyping Quality Controls.

Fig 2

Fig 2. Admixture analyses in a worldwide context.

Admixture for K = 8. 1 st row: 1000 Genomes Samples from Europe, Africa and South America [42]. 2 nd row: Modern Native American samples grouped following [38]. 3 rd row: Chilean, Peruvian and Argentinean admixed samples from [31]. 4 th row: Argentinean admixed samples from the present study. Samples are grouped according to regions (Fig 1); CYA: Cuyo Region in Argentina; NEA: Northeastern Region, NWA: Northwestern Region; PPA: Pampean Region; PTA: Patagonia Region. CLM: Colombians from Medellin; PEL: Peruvians from Lima.

Fig 3

Fig 3. European ancestry specific principal component analysis.

(A) Multidimensional scaling scatterplot (MDS) from Euclidian distances calculated from weighted 5-first European-specific Principal Components performed using the European reference samples, and admixed samples masked for African ancestry. Individuals from the European reference panel are colored according to main European geographic regions as shown in (B) while South American individuals are represented as shown in the legend. Elbow method to choose the best number of PCs to compute MDS is shown in S6 Fig.

Fig 4

Fig 4. African ancestry-specific admixture analysis.

Admixture for K = 5. 1 st row: 1,685 reference samples with >99% of African ancestry. Populations are grouped following [48]. 2 nd and 3 rd rows: Peruvian and Argentinean admixed samples from [31] and from the present study. Samples are grouped according to region. CYA: Cuyo Region; NEA: Northeastern Region, NWA: Northwestern Region; PPA: Pampean Region; PTA: Patagonia Region. Genotype data for admixed samples were masked for African ancestry.

Fig 5

Fig 5. Native American ancestry-specific principal component analysis.

(A) Localization map of the studied samples. Color and point coding matches sample groups: ancient populations are grouped following [35], modern Native American populations are grouped following [38] while Argentinean admixed sample locations are grouped according to Regions (Fig 1). For clarity, some geographic coordinates have been slightly changed. (B) Multidimensional scaling scatterplot from Euclidian distance calculated from weighted Native American ancestry specific Principal Components. Elbow method to choose the best number of PCs to compute MDS is shown in S12 Fig.

Fig 6

Fig 6. Native American ancestry-specific admixture analysis.

Admixture for K = 3. 1 st row: Ancient samples grouped following [35]. 2 nd row: Modern Native American samples grouped following [38]. 3 rd row: Chilean, Peruvian and Argentinean admixed samples from [31]. 4 th row: Argentinean admixed samples from the present study; sample locations are grouped according to Regions (Fig 1); CYA: Cuyo Region; NEA: Northeastern Region, NWA: Northwestern Region; PPA: Pampean Region; PTA: Patagonia Region. Genotype data for all modern samples were masked for Native American ancestry.

Fig 7

Fig 7. Relationship among the four Native American groups identified.

(A) f 3(Target; S1, S2) to test for treeness. (B) FST between pairs of Native American groups. (C) f 4 (YRI, Target; S1, S2) to test whether Target shares more ancestry with S1 or S2. Since f 4 is symmetrical when switching S1 and S2, only positive comparisons are shown. (D) Neighbor-joining tree estimated from distance matrix of the form 1/ f 3(YRI; X, Y). The tree was estimated using ancient sample from Upward Sun River site in Beringia (USR1) as outgroup. CAN: Central Andes; STF: Subtropical and Tropical Forests; CCP: Central Chile / Patagonia; CWA: Central Western Argentina; YRI: Yoruba from 1KGP. Vertical segments are the +/- 3 standard errors intervals in A and B.

Fig 8

Fig 8. Changes across time of genetic affinity of the four Native American with ancient samples.

Each point represents a f _3_-Outgroup score of the form f 3 (YRI; X, Ancient) vs the age of ancient samples, where X is one of the four identified modern Native American components, and Ancient is an ancient group. X is represented by the color of the square while the symbol inside the square represents Ancient. The legend for plotted symbols is shown in Fig 5**. (A)** f 3 vs age of ancient samples from Southern Cone. (B) f 3 vs age of ancient samples from the Andes. (C) f 3 vs age of ancient samples from Southern Cone considering correction for both f 3 and age. (D) f 3 vs age of ancient samples from the Andes considering correction for both f 3 and age correction. Linear regression slopes and the associated _P-_values are shown. CAN: Central Andes; STF: Subtropical and Tropical Forests; CCP: Central Chile / Patagonia; CWA: Central Western Argentina; YRI: Yoruba from 1KGP.

References

    1. Bravi CM, Sans M, Bailliet G, Martínez-Marignac V, Portas M, Barreto I, et al. Characterization of mitochondrial DNA and Y-chromosome haplotypes in a Uruguayan population of African ancestry. Hum Biol. 1997;69: 641–652. -PubMed
    1. Sala A, Penacino G, Corach D. Comparison of allele frequencies of eight STR loci from Argentinean Amerindian and European populations. Hum Biol. 1998;70: 937–947. -PubMed
    1. Goicoechea A., Carnese FR, Dejean C, Avena SA, Weimer TA, Franco MHLP, et al. Genetic Relationships Between Amerindian Populations of Argentina. Am J Phys Anthropol. 2001;115: 133–143. 10.1002/ajpa.1063 -DOI -PubMed
    1. Dejean CB, Crouau-Roy B, Goicoechea AS, Avena SA, Carnese FR. Genetic variability in Amerindian populations of northern Argentina. Genet Mol Biol. 2004;27: 489–495.
    1. Fejerman L, Carnese F, Goicoechea A, Avena S, Dejean C, Ward R. African ancestry of the population of Buenos Aires. Am J Phys Anthropol. 2005;128: 164–70. 10.1002/ajpa.20083 -DOI -PubMed

Publication types

MeSH terms

Substances

LinkOut - more resources