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Genetic variation of high-altitude Ecuadorian population using autosomal STR markers

Published:September 23, 2019DOI:https://doi.org/10.1016/j.fsigss.2019.09.025

      Abstract

      Fifteen autosomal STRs were analyze in order to elucidate the differences between low and high land Ecuadorian population. Seven Ecuadorian geographic areas (Tisaleo-Mocha, Cañar, Quito, Rocafuerte, Santa Rosa, Guayaquil and Lago Agrio) from different altitude were selected for the study. After the analysis, little genetic distances were observed between all cities, the more distant cities (FST = 0.02354) were Rocafuerte at an elevation of 17 m.a.s.l. and Quito at 2850 m.a.s.l. and the similar cities (FST = 0.00033) were Rocafuerte (17 m.a.s.l.) and Santa Rosa (10 m.a.s.l). In conclusion, there is not a great genetic distance in the 15 STRs reported in high and low land Ecuadorian population, therefore previously reported frequencies could been used in identification and paternity cases under analysis.

      Keywords

      1. Introduction

      Ecuador, located in South America is bordering by the Pacific Ocean on the west, Colombia in the north and Peru in the east and south [
      • Instituto Oceanográfico de la Armada del Ecuador
      CAPÍTULO I: Información General de la República del Ecuador.
      ]. Ecuador is at an elevation between 4 m.a.s.l. in the coast and 3264 m.a.s.l. in the Andes region [
      • Instituto Oceanográfico de la Armada del Ecuador
      CAPÍTULO I: Información General de la República del Ecuador.
      ]. For these reason, the aim of the present study was to compare the genetic information of 15 STRs to visualize the genetic distances between low and high land population.

      2. Materials and methods

      2.1 Population

      The study included 328 unrelated individuals self – identified as mestizos from seven Ecuadorian provinces which are located in different high-altitude. From the highland the selected samples were: 49 samples from Tisaleo- Mocha (˜3200 m.a.s.l.) in Tungurahua province, 40 individuals from Cañar city (3125 m.a.s.l.) in Cañar province and 50 individuals from Quito (2850 m.a.s.l.) in Pichincha province. From the lowland the selected individuals were: 43 individuals from Rocafuerte (17 m.a.s.l.) in Manabí province, 47 samples from Santa Rosa (10 m.a.s.l.) in El Oro province, 50 individuals from Guayaquil (4masl) in Guayas province and 49 samples from Lago Agrio (418 m.a.s.l.) in Sucumbios province. The participants signed the informed consent in order to participate in the study.

      2.2 DNA extraction and amplification

      Blood samples on FTA card were extracted using FTA buffer (GE Healthcare), following the manufacture`s recommendation protocol [
      • GE Healthcare Life Sciences
      FTATM cards.
      ]. The amplification was done using PowerPlex 16 system (Promega) in a single multiplex following the protocol recommended by the manufacturer [
      • P. Corporation
      PowerPlex ® 16 System Instructions for Use of Products.
      ]. Positive (2800 M) and negative control was used in the amplification process. Capillary electrophoresis was performed on the 3130 and 3500 Genetic Analyzers (Applied Biosystems). Lastly, the results were analyzed by GeneMapper v3.2 and v5 (Applied Biosystems).

      2.3 Data analysis

      Data were analyzed using: Arlequin v 3.5.2.2 for population genetic differences, and SPSS Statistics v24 for visual representation.

      3. Results

      For population genetic comparison, the FST was computed between all population pairs of the seven Ecuadorian geographic provinces (Table 1).
      Table 1Genetic distances (FST) between Tisaleo-Mocha (Tungurahua), Santa Rosa (El Oro), Rocafuerte (Manabí), Lago Agrio (Sucumbios), Quito (Pichincha), Cañar (Cañar), Guayaquil (Guayas) (lower diagonal) and P-values (upper diagonal).
      Tisaleo -MochaSanta RosaRocafuerteLago AgrioQuitoCañarGuayaquil
      Tisaleo -

      Mocha
      ≤5e-5≤5e-5≤5e-50.01390.0350.0139
      Santa Rosa0.018060.03940.0121≤5e-5≤5e-5≤5e-5
      Rocafuerte0.023410.00033≤5e-5≤5e-5≤5e-5≤5e-5
      Lago Agrio0.020580.005350.01380≤5e-5≤5e-5≤5e-5
      Quito0.006070.022980.023540.009510.02780.0201
      Cañar0.002370.010900.017160.009730.002510.0433
      Guayaquil0.005610.012120.011900.012780.004920.00259
      All the p-values were statistically significant (p-value ≤ 0.05). In order to interpret the genetic distances obtained, we used the suggested values classification of Ballaux et al. [
      • Balloux F.
      • Lugon-Moulin N.
      The estimation of population differentiation with microsatellite markers.
      ]. Therefore, all the values were between 0–0.05 indicating little genetic distance between cities compared. The pairwise FST obtained is represented in a multidimensional scaling plot (Fig. 1) in order to visualize the similarities between the cities compared.
      Fig. 1
      Fig. 1Multidimensional scaling plot from the FST between the Ecuadorian cities (ROC: Rocafuerte, SRO: Santa Rosa, LAG: Lago Agrio, UIO: Quito, CAR: Cañar, GYE: Guayaquil, TMA: Tisaleo-Mocha).

      4. Discussion

      As it was expected low distant between low and high altitude cities was found due to its same origin [
      • Zambrano A.K.
      • et al.
      The three-hybrid genetic composition of an Ecuadorian population using AIMs-InDels compared with autosomes, mitochondrial DNA and Y chromosome data.
      ,
      • Séré M.
      • Thévenon S.
      • Belem A.M.G.
      • De Meeûs T.
      Comparison of different genetic distances to test isolation by distance between populations.
      ] and short geographic distances (the biggest distance is 796 km between Santa Rosa and Lago Agrio) that allow a constant migration inside the country [
      • Cuenca J.O.
      • Royuela V.
      Determinantes de la migración interna en Ecuador): un análisis de datos de panel.
      ]. Consequently, the 15 STRs could be used in the studied Ecuadorian population in forensic and kinship analysis, using the same frequencies reported [
      • Gaviria A.
      • et al.
      Twenty two autosomal microsatellite data from Ecuador (Powerplex Fusion).
      ].

      5. Conclusion

      In conclusion, there is not a genetic substructure evidence between low land and high land Ecuadorian population using 15 autosomal STR markers.

      Role of funding

      None.

      Declaration of Competing Interest

      None.

      Acknowledgments

      None.

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