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Allele frequency data for 15 autosomal strs and ancestral proportions using aims-indels in the shuar ethnic group from Ecuador

Published:September 23, 2019DOI:https://doi.org/10.1016/j.fsigss.2019.09.026

      Abstract

      The ethnic group Shuar is located in Ecuador. To identify their genetic composition, 46 ancestry-informative insertion deletion markers (AIM-INDELs) were used. Also, characterization of 15 tandem repeats (STRs) in the AmpFISTR Identifiler Kit were applied. Forensic parameters showed a matching probability of 0.1535, a power of discrimination of 0.8465, a polymorphism information content of 0.6584, probability of exclusion of 0.415 and a typical paternity index of 1.78. The Shuar are not influenced by admixture population events, being a Native American group 98.7%, along with a genetic diversity of 0.699346+/-0.356964.

      Keywords

      1. Introduction

      South America is home to several indigenous populations that show the less genetic diversity across the globe [
      • Paz-y-Miño C.
      • Guillen Sacoto M.J.
      • Leone P.E.
      Genetics and genomic medicine in Ecuador.
      ,
      • Ruíz-Linares A.
      • Adhikari K.
      • Acuña-Alonzo V.
      • Quinto-Sánchez M.
      • Jaramillo C.
      • Arias W.
      • González-José R.
      Admixture in Latin America: geographic structure, phenotypic diversity and self-perception of ancestry based on 7,342 individuals.
      ]. Ecuador, which was conquered by the Spanish, is inhabited by different ethnic groups such as the Shuar who are isolated and settled in the amazon region. Moreover, Ecuador is well known for its heterogeneous distribution and wide inter-population differentiation of three main ancestral contributions from Native Americans, Europeans and Africans [
      • Zambrano A.K.
      • Gaviria A.
      • Cobos-Navarrete S.
      • et al.
      The three-hybrid genetic composition of an Ecuadorian population using AIMs-InDels compared with autosomes, mitochondrial DNA and Y chromosome data.
      ]. The latest census showed, 71.9% of Ecuadorians self-identified as mestizos, 7.2% as Afro-Ecuadorians and 7% as indigenous []. There are few studies in indigenous populations about their genetic composition [
      • Geppert M.
      • Baeta M.
      • Núñez C.
      • Martínez-Jarreta B.
      • Zweynert S.
      • Cruz O.W.V.
      • Roewer L.
      Hierarchical Y-SNP assay to study the hidden diversity and phylogenetic relationship of native populations in South America.
      ]. We decided to characterize the Shuar ethnic group by determining the allele frequencies of 15 STRs, and by using 46 AIM-INDELs to determine their ancestral proportion.

      2. Materials and methods

      2.1 Population

      40 individuals from the Shuar community were randomly selected, 25 females and 15 males, whose blood samples were taken on FTA cards. All individuals signed an informed consent for population genetic studies. DNA was extracted following the manufacturer's recommendations (Whatman – GE Healthcare).

      2.2 Genetic markers and genotyping

      Amplification of the 46 AIM-Indels was performed according to Pereira [
      • Pereira R.
      • Phillips C.
      • Pinto N.
      • et al.
      Straightforward inference of ancestry and admixture proportions through ancestry-informative insertion deletion multiplexing.
      ], meanwhile, the 15 STRs were amplified in a multiplex reaction using the AmpFISTR Identifiler PCR Amplification Kit (Applied Biosystems, Foster City, CA, USA). DNA amplification was done according to manufacturer’s protocol, except that 30 cycles were used in a final volume of 5 ul. For genotyping, capillary electrophoresis separated the PCR products on an ABI PRISM 3130 Genetic analyzer (Applied Biosystems, Foster City, CA), and data were analyzed with the GeneMapper ID v3.2 (Applied Biosystems) [
      • Excoffier L.
      • Lischer H.
      Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows.
      ].

      2.3 Statistical analysis

      Allele frequencies, genetic diversity, Hardy-Weinberg equilibrium and linkage disequilibrium were calculated using the Arlequin v.3.5.1.3 software. Statistical parameters of forensic interest were obtained using the PowerStats v1.2 (Promega Corporation, USA) software [
      Promega, PowerStats A. Computer Program for the Analysis of Population Statistics.
      ]. The distribution of genetic ancestry was calculated using the STRUCTURE v.2.3.4 software.

      3. Results

      The obtained genetic diversity was 0.699346+/-0.356964. Allelic frequencies and forensic parameters can be seen in Table 1. All markers were in Hardy-Weinberg equilibrium except for D7S820 and vWA, p < 0.05. An average matching probability of 0.1535, average discrimination power of 0.8465, average polymorphic information content of 0.6585, average power of exclusion of 0.415 and an average typical paternity index of 1.78 were obtained.
      Table 1Allele frequencies for the Shuar population sample and forensic parameters.
      AlleleD8S1179D21S11D7S820CSF1POD3S1358TH01D13S317D16S539D2S1338D19S433vWATPOXD18S51D5S818FGA
      5…..…..…..…..…..0.0125…..………..…..…..…..…..…..…..
      6…..…..…..…..…..0.3375…..………..…..…..…..…..…..…..
      7…..…..…..…..…..0.4875…..………..…..…..0.0125…..0.075…..
      8…..…..…..0.025…..…..…..………..…..…..0.4125…..…..…..
      9…..…..0.10.1375…..…..0.56250.1875…..…..…..…..…..0.225…..
      9,3…..…..…..…..…..0.1625…..………..…..…..…..…..…..…..
      100.2…..0.33750.1…..…..0.0750.3875…..…..…..0.0125…..0.025…..
      10,2…..…..…..…..…..…..…..………..0.0125…..…..…..…..…..
      110.0125…..0.21250.3…..…..…..0.025…..…..…..0.4625…..0.3125…..
      120.05…..0.33750.425…..…..0.0750.375…..…..…..0.10.0750.15…..
      130.5875…..0.01250.013…..…..0.16250.0125…..0.3375…..…..0.18750.2…..
      13,2…..…..…..…..…..…..…..………..0.0875…..…..…..…..…..
      140.1…..…..…..0.0125…..0.1250.0125…..0.08750.0375…..0.33750.0125…..
      14,2…..…..…..…..…..…..…..………..0.15…..…..…..…..…..
      150.05…..…..…..0,5625…..…..………..0.2250.2125…..0.1375…..…..
      15,2…..…..…..…..0.0375…..…..………..0.0125…..…..…..…..…..
      16…..…..…..…..0.2625…..…..………..0.01250.425…..0.0125…..…..
      16,2…..…..…..…..…..…..…..………..0.075…..…..…..…..…..
      17…..…..…..……0.125…..…..……0.0875…..0.175…..0.225…..…..
      18…..…..…..…..…..…..…..……0.0875…..0.1…..0.025…..…..
      19…..…..…..…..…..…..…..……0.3875…..0.05…..…..…..0.2625
      20…..…..…..…..…..…..…..……0.1625…..…..…..…..…..…..
      21…..…..…..…..…..…..…..……0.0125…..…..…..…..…..0.05
      22…..…..…..…..…..…..…..……0.025…..…..…..…..…..0.05
      23…..…..…..…..…..…..…..……0.2375…..…..…..…..…..0.1
      24…..…..…..…..…..…..…..……………………………………0.175
      25…..…..…..…..…..…..…..……………………………………0.2
      26…..…..…..…..…..…..…..……………………………………0.125
      27…..…..…..…..…..…..…..……………………………………0.0375
      28…..0.025…..…..…..…..…..………..…..…..…..…..…..…..
      29…..0.15…..…..…..…..…..………..…..…..…..…..…..…..
      30…..0.4…..…..…..…..…..………..…..…..…..…..…..…..
      30,2…..0.0375…..…..…..…..…..………..…..…..…..…..…..…..
      31…..0.05…..…..…..…..…..………..…..…..…..…..…..…..
      31,2…..0.25…..…..…..…..…..………..…..…..…..…..…..…..
      32,2…..0.0625…..…..…..…..…..………..…..…..…..…..…..…..
      33,2…..0.025…..…..…..…..…..………..…..…..…..…..…..…..
      MP0.21750.110.15380.16630.27630.2050.18130.17380.1050.0850.13250.2350.10250.09750.0613
      PD0.78250.890.84630.83380.72380.7950.81880.82630.8950.9150.86750.7650.89750.90250.9388
      PIC0.56030.71140.66480.65070.54060.5490.59480.60980.71540.76430.69230.52490.74150.74990.8066
      PE0.3220.3220.26190.55350.4680.26190.23510.35520.5990.3220.3220.26190.64620.69490.599
      TPI1.331.331.182.221.821.181.111.432,501.331.331.182.863.332.5
      Het Obs0.6250.6250.5750.7750.7250.5750.550.650.80.6250.6250.5750.8250.850.8
      PD: Power of Discrimination; PIC: Polymorphic Information Content; PE: Power of Exclusion; TPI: Typical Paternity Index; Het Obs: Heterozygosity Observed.
      Ancestry proportion was estimated from three reference populations: Africa, America and Europe (K = 3). The Shuar population consists of Native American 98.7%, European 0.5% and African 0.8% (Fig. 1).
      Fig. 1
      Fig. 1Ancestry component analysis result for the Shuar population. The bars with colour represent different ancestry origins from the analysis: red, Africa; green, Native American; blue, European. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article).

      4. Discussion

      The Ecuadorian ethnic group Shuar was characterized for its allelic frequencies for the first time. The observed genetic diversity value 0.699346 is lower than those seen in other studies for an indigenous population, which might be due to their culture and manners that include endogamy. However, it shows similar values when compared to the Waoranis, another Ecuadorian ethnic group [
      • Geppert M.
      • Baeta M.
      • Núñez C.
      • Martínez-Jarreta B.
      • Zweynert S.
      • Cruz O.W.V.
      • Roewer L.
      Hierarchical Y-SNP assay to study the hidden diversity and phylogenetic relationship of native populations in South America.
      ,
      • González-Andrade F.
      • Roewer L.
      • Willuweit S.
      • et al.
      Y-STR variation among ethnic groups from Ecuador: mestizos, kichwas, Afro-Ecuadorians and Waoranis.
      ]. Regarding the 15 analyzed STRs, the Shuar showed two new allelic variants 15.2 and 10.2 for D3S1358 and D19S433, respectively. Moreover, the genetic markers vWA and D7S820 are not in Hardy-Weinberg equilibrium which might be because the sample is too little to show a representative allelic distribution or the levels of endogamy were not revised [
      • Calisaya R.
      Creación De Una Base De Datos De Frecuencias Alélicas En Población Mestiza De La Región Andina Bolivariana, Tesis De Licenciatura En Bioquímica, Universidad Mayor De San Andrés [Online].
      ]. The AIM-INDELs showed that the Shuar is a Native American group 98.7%, hence not influenced by admixture population events. Isolation of this group has enabled to conserve their genetic material which should be considered for further studies.

      5. Conclusion

      The Shuar group is a conserved population with no influence from the European and African diaspora populations, allele frequencies of 15 STRs were obtained.

      Funding

      This research was founded by Centro de Investigación Genética y Genómica- Universidad UTE .

      Declaration of Competing Interest

      None.

      Acknowledgement

      None.

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