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Genetic variation of different Peruvian populations using 23 autosomal STR markers

Published:October 19, 2022DOI:https://doi.org/10.1016/j.fsigss.2022.10.055

      Abstract

      In the present study the genetic variation of different Peruvian populations was investigated. The samples for this study were obtained from 669 individuals distributed among 11 populations from Peru. All samples were analyzed using 23 autosomal STR markers. The Arlequin v3.5.2.2 software was used to determine the genetic distances (Fst) of the studied populations. Notable population substructure was detected between some populations.

      Keywords

      1. Introduction

      Peru is an ethnically diverse country with different populations that are classified according to the region they reside (Coast, Sierra, Selva). However, there also are native populations that are distributed across the Coast, Sierra and Selva. The distances between different Peruvian populations have been studied previously using only 15 autosomal STRs [
      • Delgado E.
      • Neyra C.D.
      Frecuencias alélicas de 21 marcadores STR autosómicos en una población mestiza peruana aplicado a la práctica forense.
      ,
      • Neyra C.D.
      • Suarez M.
      • Cueva E.
      • Bailón H.
      • Gutierrez E.
      Identificación genética de recién nacidos en Perú: un estudio piloto.
      ,
      • Neyra C.D.
      • Delgado E.
      • Robles C.
      • Velasquez M.
      • Caceres O.
      • Budowle B.
      Population genetic study of a Peruvian population using human identification STRs.
      ,
      • Neyra-Rivera C.D.
      • Ticona A.
      • Delgado E.
      • Velasquez M.R.E.
      • Budowle B.
      Allelic frequencies with 23 autosomic STRS in the Aymara population of Peru.
      ,
      • Neyra-Rivera C.D.
      • Delgado E.
      • Diaz F.
      • Quispe J.S.
      • Ge J.
      • Budowle B.
      Genetic study with autosomal STR markers in people of the Peruvian jungle for human identification purposes.
      ,
      • Bermejo M.E.
      • Ge J.
      • Budowle B.
      • Infante C.
      • Neyra-Rivera C.D.
      Genetic study with 21 autosomal STRs in five Peruvian macro regions for human identification purposes.
      ] or Y-chromosome STRS [
      • Neyra-Rivera C.D.
      • Ticona A.
      • Delgado E.
      • Velasquez M.R.E.
      • Caceres O.
      • Budowle B.
      Population data of 27 Y-chromosome STRS in Aymara population from Peru.
      ]. To attempt to gain futher population resolution, this study studied the genetic variation in various Peruvian populations based on the 23 STRs included in the Verifiler Express kit.

      2. Materials and methods

      This study of genetic diversity was approved by the ethics committee of the Institute of Tropical Medicine “Daniel Alcides Carrion” from the Universidad Nacional Mayor de San Marcos (Certificate of Approval CIEI-2018–015) and all participants freely and voluntarily signed their informed consent. In the present investigation, 669 individuals distributed among 11 populations were genotyped: three mestizo samplings (n = 164 Costa, n = 30 Sierra and n = 7 Selva), and 8 population samplings of native individuals from the jungle and the sierra (people whose parents and grandparents were born in the area) were studied. The population of the jungle comprised 54 individuals from Amazonas, 187 from Loreto and 37 from Madre de Dios, individuals from Puno (10 from Chucuito, 35 from the floating islands, 60 from the border with Bolivia, 52 Yunguyo and 33 far from the border with Bolivia). A blood sample was taken by finger puncture from each donor and placed on Nucleid Cards (Copan). Then, a 1.2 mm punch was taken from each card, amplified by direct PCR using the Verifiler Express kit, and the amplified products were detected in the Applied Biosystem ™ 3500XL Genetic Analyzer (Life Technologies) following the manufacturer’s recommended protocols. After capillary electrophoresis, the data were imported into the GeneMapper® ID-X v1.5 software to generate the genetic profiles [
      • Dash H.R.
      • Shrivastava P.
      • Das S.
      Analysis of capillary electrophoresis results by GeneMapper® ID-X v 1.5 software.
      ]. The Arlequin v3.5.2.2 software was used to determine the genetic distances (Fst) of the studied populations [
      • Excoffier L.
      • Laval G.
      • Schneider S.
      Arlequin (version 3.0): an integrated software package for population genetics data analysis.
      ]. The genetic distances were used to generate a Multidimensional Scaling using the R software [
      • R Core Team
      R: A Language and Environment for Statistical Computing.
      ] and to generate a UPGMA tree using the MEGA 6.06 program [
      • Tamura K.
      • Stecher G.
      • Peterson D.
      • Filipski A.
      • Kumar S.
      MEGA6: molecular evolutionary genetics analysis version 6.0.
      ].

      3. Results and discussion

      The Peruvian population comparisons that have an Fst value less than 0.01 were the populations Cost-Mestizo with the Sierra-Meztizo, Jungle-mestizo, Puno no border Bolivia native, Puno-Chucuito-Native, Puno-Island-native, and Puno -Yunguyo-native; Sierra-mestizo with Puno-Chucuito-Native, Puno-Island-native, Puno-Border-Bolivia-Native, Puno-No-border-Bolivia-Native, Puno-Yunguyo-Native; Jungle-mestizo with Loreto-Native, Puno-Island-native and Puno-Border-Bolivia-Native. All Puno populations had a Fst value less than 0.01. The rest of the population comparisons showed Fst values greater than 0.01, which would indicate notable population substructure (Table 1 and Fig. 1).
      Table 1Average Fst values obtained between pairs of populations for 23 STR markers in common between 11 Peruvian populations.
      [1][2][3][4][5][6][7][8][9][10][11]
      [1]0.0000
      [2]0.00280.0000
      [3]0.00660.00860.0000
      [4]0.04000.04610.02990.0000
      [5]0.01370.01490.00760.03680.0000
      [6]0.08960.09300.12370.13050.10030.0000
      [7]0.00640.00910.01210.05300.01160.09950.0000
      [8]0.00750.00760.00990.04840.01640.08900.00000.0000
      [9]0.00750.00760.00990.04840.01640.08900.00000.00000.0000
      [10]0.00670.00440.02140.05460.01620.09150.00000.00240.00240.0000
      [11]0.00450.00290.01770.04730.01430.08710.00030.00190.00190.00000.0000
      [1]: Cost_Mestizo, [2]:Sierra_Mestizo, [3]: Jungle_Mestizo, [4]: Amazonas_native, [5]: Loreto_Native, [6]: Madre_de_Dios_Native, [7]: Puno_Chucuito_native; [8]: Puno_Island_native, [9]: Puno_locations_border_Bolivia_native, [10]: Puno_locations_not_border_Bolivia_native, [11]: Puno_Yunguyo_native.
      Fig. 1
      Fig. 1MDS plot showing distance (Fst) between the 11 Peruvian populations using 23 autosomal STR markers.
      In the UPGMA tree (Fig. 2) the Jungle Mestizo population is near to the Loreto native population, while Sierra mestizo population is near to the Costa Mestizo population. The Puno native populations are near native from Chucuito, native from Islands and native from localidades of border from Bolivia, but all of them are separated from native from Yunguyo and native from not near the border with Bolivia. Amazonas native population and Madre de Dios native population are separated of all other Peruvian populations.
      Fig. 2
      Fig. 2UPGMA tree based on 23 autosomal STR markers in common and Reynolds distances among the 11 populations.

      4. Conclusions

      These results support that studies demonstrate high genetic variation. Additionally, increasing these populations and characterizing other populations will provide a better understanding of genetic diversity and how it applies to identification and paternity cases in Peru.

      Funding

      None.

      Conflict of interest statement

      None.

      Acknowledgments

      To the Universidad Privada Peruano Alemana for supporting the publication of the research results.

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