Abstract
The South American country of Peru is composed by a highly admixed population, with Native American, European and African genetic contributions. Some Native American groups in Peru underwent low admixture with Europeans or Africans and they have kept much of their culture and their original language. In this work we have studied one of these groups called Ashaninka, for the 27 Y chromosome specific STR loci that were included in the recently released YFiler Plus kit. The samples have been collected from 58 unrelated males belonging to 41 different communities located in the margins of the Amazonian rivers Pichis and Palcazú, in the district of Puerto Bermúdez, Pasco region, Peru. A high Y-STR haplotype diversity was found (1.0000 ± 0.0022) with all haplotypes being unique in the studied sample. Two markers that usually present a high diversity in European populations showed very low values of diversity in the Ashaninka Native Americans, namely the DYS635 (Het = 0.2263) and DYS437 (Het = 0.1325). On the other hand, the DYS438 showed a much higher diversity in Ashaninka (Het = 0.6582) group than that usually found in European populations. Apart from the multi-loci markers DYS385 and DYF387S1, more than one allele was also observed in one sample for DYS518 locus. This study represents the first report of haplotype frequencies for the YFiler Plus markers’ set in a Native American population, showing a high diversity of haplotypes and, therefore, demonstrating their usefulness in forensic identification cases.
Keywords
1. Introduction
In Peru there are many native populations such as the Ashaninka, Awajún, Bora, Aymara, Jibaro, Matsigenka, Quechua, etc., which differ in their dialect, customs and phenotype. It is assumed that during the colonization of America these Native populations underwent low admixture with Europeans or Africans and they have kept much of their culture and their original language. In previous literature, Ashaninka people were also referred to as Andes, ATIS, redskins, kampas, cambas, tampas, thampas, komparias, kuruparias and campitis. The Ashaninka populations from Peru, are distributed in the departments of Ayacucho (province of Huanta, in the basins and tributaries of the Lower Apurimac river), Cusco (province of the Convention, in the basins of the Urubamba River), Huanuco (province of Puerto Inca, in the basin of the rivers Pachitea and Yorúa), Junin (Chanchamayo and Satipo provinces in the basin and tributaries of the Ene River, Tambo and Satipo), Pasco (province of Oxapampa district of Puerto Bermudez, in the basin and tributaries of the river Pichis and Palcazu), Lima (provinces of Atalaya and Coronel Portillo in the basin of the Upper Ucayali rivers) [
1
, 2
].The YFiler Plus kit was just recently released and no data is yet available for Native groups from South America. The aim of this study was to characterize the Y-STR haplotype variation of the Ashaninka in order to evaluate the discrimination power of the YFiler Plus kit when used to solve cases involving American Native groups.
2. Materials and methods
2.1 DNA samples
A total of 58 samples were selected from non-related individuals belonging to 41 different communities located in the margins of the Amazonian rivers Pichis and Palcazú, in the district of Puerto Bermúdez, Pasco region, Peru. Written informed consent was obtained from all participants for cooperation in this study under strictly confidential conditions.
DNA was extracted from bloodstains using a standard phenol–chloroform protocol.
2.2 Genotyping
The Yfiler™ Plus PCR Amplification kit (Applied Biosystems™) was used to analyze 27 Y-STR loci: DYS19, DYS385 a/b, DYS387S1 a/b, DYS389 I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS460, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635 (Y GATA C4) and YGATA H4. PCR was carried out following manufacturer’s recommendations. ABI 3130 and ABI 3500 Genetic Analysers (Applied Biosystems) were used for genotyping and analysis was performed with the GeneMapper® ID Software v4.0 (Applied Biosystems). The Y-STR alleles were designated according to the ISFG recommendations [
[3]
].Y haplotype data were included in the Y-STR Haplotype Reference Database (http://www.yhrd.org) and are available under the following accession number: Oxapampa, Peru [Ashaninka] YA004112.
2.3 Data analysis
Haplotype frequencies and genetic diversities according to Nei [
[4]
] were estimated with the software Arlequin 3.5.1.2 [[5]
]. Genetic distances (RST) were calculated between our sample and 12 other population samples from Peru that are available in Roewer et al. [[6]
] (data submitted to the YHRD). Among these populations, pairwise genetic distances were calculated with the online tool implemented in YHRD [[7]
]. For the calculation of genetic distances with the YHRD tool, haplotypes presenting null, intermediate, duplicated are removed, and the number of repeats in DYS389I are subtracted from DYS389II. RST p-values were calculated for 10,000 permutations.3. Results and discussion
A high Y-STR haplotype diversity was found (1.0000 ± 0.0022) with all haplotypes being unique in the studied sample. Two markers that usually present a high diversity in European populations showed very low values of diversity in the Ashaninka Native Americans, namely the DYS635 (Het = 0.2263) and DYS437 (Het = 0.1325). On the other hand, the DYS438 showed a much higher diversity in Ashaninka (Het = 0.6582) group than that usually found in European populations. Apart from the multi-loci markers DYS385 and DYF387S1, more than one allele was also observed in one sample for DYS518 locus.
The full haplotype data can be obtained upon request to first author, Dean Herman Tineo ([email protected]).
In order to infer the most likely origin of the male lineages present in our sample, we have used an online available tool (http://www.hprg.com/hapest5/) to predict Y-chromosome haplogroups from Y-STR genotypes. All Y-STR profiles were predicted (with a probability of 99–100%) as belonging to the Q haplogroup, which is the most frequent in Native Americans. Genetic distance analysis revealed significant differences between Ashaninka and most population groups of Peru (Table 1). However, no-significant differences were observed among samples from Oxapampa, Peru [Ashaninka], Puno, Peru [Aymara] and Loreto, Peru [Iquito], which cluster together.
Table 1Matrix showing the pairwise RST values (below diagonal) among sample from different population groups in Peru. The corresponding non-differentiation p-values are indicated in the above diagonal.
| Population | Ashaninka, Peru | Puno, Peru [Aymara] | Amazonas, Peru [Cajamarca] | Amazonas, Peru [Chachapoya] | Cuzco, Peru [Chumbivilca] | Arequipa, Peru [Chuquibamba] | Amazonas, Peru [Huanca] | Junín, Peru [Huanca] | Loreto, Peru [Iquito] | Amazonas, Peru [Jivaro] | Peru [Mestizo] | Lima, Peru [Quechua] | Ucayali, Peru [Shipibo-Conibo] |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Ashaninka | – | 0.6298 | <5E-05 | 0.0000 | 0.0000 | 0.0002 | 0.0136 | 0.0000 | 0.8619 | 0.0053 | 0.0000 | 0.0006 | 0.0000 |
| Puno [Aymara] | −0.0617 | – | 0.2261 | 0.3420 | 0.0292 | 0.1435 | 0.3228 | 0.0882 | 0.9755 | 0.3541 | 0.5267 | 0.2211 | 0.0712 |
| Amazonas [Cajamarca] | 0.1493 | 0.0590 | – | 0.1997 | 0.0003 | 0.0000 | 0.0286 | 0.0001 | 0.2293 | 0.0026 | 0.5343 | 0.2402 | 0.0000 |
| Amazonas [Chachapoya] | 0.1000 | 0.0109 | 0.0098 | – | 0.0000 | 0.0000 | 0.0425 | 0.0003 | 0.2058 | 0.0012 | 0.3720 | 0.3566 | 0.0001 |
| Cuzco [Chumbivilca] | 0.1894 | 0.3023 | 0.3444 | 0.2871 | – | 0.8154 | 0.0008 | 0.2478 | 0.0858 | 0.0002 | 0.0000 | 0.0018 | 0.0000 |
| Arequipa [Chuquibamba] | 0.1092 | 0.1018 | 0.2856 | 0.2189 | −0.0415 | – | 0.0166 | 0.7861 | 0.2752 | 0.0005 | 0.0000 | 0.0015 | 0.0000 |
| Amazonas [Huanca] | 0.0788 | 0.0301 | 0.1009 | 0.0561 | 0.2584 | 0.1292 | – | 0.0409 | 0.4140 | 0.0092 | 0.0889 | 0.0475 | 0.0000 |
| Junín [Huanca] | 0.1253 | 0.1458 | 0.2548 | 0.1975 | 0.0225 | −0.0343 | 0.0920 | – | 0.2096 | 0.0012 | 0.0003 | 0.0039 | 0.0000 |
| Loreto [Iquito] | −0.0806 | −0.2126 | 0.0434 | 0.0401 | 0.1255 | 0.0290 | 0.0092 | 0.0540 | – | 0.1949 | 0.4197 | 0.1919 | 0.0553 |
| Amazonas [Jivaro] | 0.0540 | 0.0309 | 0.1276 | 0.0863 | 0.2601 | 0.1652 | 0.1363 | 0.1725 | 0.0635 | – | 0.0057 | 0.0335 | 0.0014 |
| Peru [Mestizo] | 0.0650 | −0.0296 | −0.0047 | 0.0002 | 0.2313 | 0.1761 | 0.0375 | 0.1619 | −0.0031 | 0.0584 | – | 0.3586 | 0.0000 |
| Lima [Quechua] | 0.1518 | 0.0803 | 0.0189 | 0.0033 | 0.3275 | 0.2450 | 0.0923 | 0.2043 | 0.0656 | 0.0905 | 0.0024 | – | 0.0000 |
| Ucayali [Shipibo-Conibo] | 0.1587 | 0.1337 | 0.1755 | 0.1347 | 0.3928 | 0.3082 | 0.2480 | 0.3215 | 0.1587 | 0.1260 | 0.1061 | 0.2086 | – |
Note: When using a RST threshold of 0.01 two clusters were obtained: cluster 1 (pink): Puno, Peru [Aymara]; Ashaninka_Peru; Loreto, Peru [Iquito]; and cluster 2 (light green): Amazonas, Peru [Chachapoya]; Amazonas, Peru [Cajamarca]; Peru [Mestizo]. For threshold of 0.02 another population was included on cluster 2 (dark Green): Lima [Quechua].
4. Conclusions
Data on allele/haplotype frequencies are crucial to evaluate the strength of forensic genetic evidences. Therefore, the use of new markers or kits requires studies concerning their behaviour in different populations. This is especially relevant in what concerns Y-chromosomal markers since they do not recombine and haplotype frequencies must be considered instead of single locus allele frequencies. Moreover, due to a higher susceptibility for genetic drift, Y chromosome specific markers tend to show more differences among population. Most countries in South America underwent recent admixture, retaining, at the same time, small isolated Native groups that are highly differentiated from the surrounding population.
This study represents the first report of haplotype frequencies for the YFiler Plus markers’ set in a Native American population, showing a high diversity of haplotypes and, therefore, demonstrating their usefulness in forensic identification cases. At the same time, comparisons between the current population and other populations from Peru showed a high heterogeneity.
Financial support
We would like to acknowledge Life Technologies Corporation for providing the YFiler Plus Kit and analysis support. Financial support was also granted by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) and DNA Program—State University and Justice Court of Rio de Janeiro, Brazil. IPATIMUP integrates the i3S Research Unit, which is partially supported by FCT, the Portuguese Foundation for Science and Technology.
Conflict of interest
None.
References
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Article info
Publication history
Published online: September 19, 2015
Accepted:
September 16,
2015
Received:
August 30,
2015
Identification
Copyright
© 2015 Elsevier Ireland Ltd. Published by Elsevier Inc. All rights reserved.
