Forensic Science International: Genetics Supplement Series
Volume 1, Issue 1 , Pages 252-254, August 2008

Haplotype data for 12 Y-chromosome STR loci from Costa Rica

  • M. Villalta

      Affiliations

    • Unidad de Genética Forense, Sección de Bioquímica del Departamento de Ciencias Forenses, Poder Judicial, Costa Rica
    • Escuela de Biología, Instituto Tecnológico de Costa Rica, Costa Rica
    • ,
  • A. Rodriguez

      Affiliations

    • Unidad de Genética Forense, Sección de Bioquímica del Departamento de Ciencias Forenses, Poder Judicial, Costa Rica
    • ,
  • L. González

      Affiliations

    • Unidad de Genética Forense, Sección de Bioquímica del Departamento de Ciencias Forenses, Poder Judicial, Costa Rica
    • ,
  • V. Arce

      Affiliations

    • Unidad de Genética Forense, Sección de Bioquímica del Departamento de Ciencias Forenses, Poder Judicial, Costa Rica
    • ,
  • G. Arrieta

      Affiliations

    • Unidad de Genética Forense, Sección de Bioquímica del Departamento de Ciencias Forenses, Poder Judicial, Costa Rica
    • ,
  • A. Morales

      Affiliations

    • Unidad de Genética Forense, Sección de Bioquímica del Departamento de Ciencias Forenses, Poder Judicial, Costa Rica
    • ,
  • L. Gusmão

      Affiliations

    • IPATIMUP, Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
    • ,
  • M. Espinoza

      Affiliations

    • Unidad de Genética Forense, Sección de Bioquímica del Departamento de Ciencias Forenses, Poder Judicial, Costa Rica
    • Corresponding Author InformationCorresponding author. Tel.: +506 2277 4045; fax: +506 2277 4044.

Received 21 August 2007; accepted 10 October 2007.

Article Outline

Abstract 

Haplotype data were obtained from a sample of 100 unrelated male individuals from Costa Rica, for 12 Y-chromosome STRs. A total of 86 different haplotypes were identified, of which 76 were unique and the most frequent haplotype was found in 4 individuals. High haplotype diversity was found (99.6%), being DYS385, representing two loci, the most diverse marker, and DYS393 presented the lowest gene diversity value. Genetic distances were calculated between our results and previously published haplotype data for the same set of Y-STRs.

Keywords: Y-chromosome, Y-STR haplotypes, Population genetics, Forensics, Costa Rica

 

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1. Introduction 

Y-chromosome-specific short tandem repeats (Y-STRs) have proven to be valuable tools for criminal investigations and paternity testing. In this work, we analyzed 12 Y-STRs markers loci in 100 samples of unrelated male individuals from Costa Rica.

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2. Material and methods 

Blood samples were obtained from 100 unrelated males from different regions of Costa Rica. DNA extraction was carried out using Che lex [1] and samples were typed using the PowerPlex® Y System kit (Promega) in an ABI PRISM®310 Genetic Analyzer (AB Applied Biosystems) as described elsewhere [2]. Haplotype frequencies were estimated by counting. Haplotype diversity was calculated according to Nei [3]. Genetic distances were computed using ARLEQUIN Ver. 3.0 software [4], assuming the stepwise mutational model [5] and, therefore, DYS385 was not considered and the number of repeats in DYS389I was subtracted from DYS389II.

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3. Results and discussion 

Haplotype frequencies of the Costarrican 12 Y-STRs are shown in Table 1. The present haplotype data were compared with the previously published data for the same set of Y-STR loci in samples from Portugal [6], Spain [7], Rio de Janeiro [8], Cartagena [9], Equatorial Guinea [10] and Mozambique [11] (Table 2). The lowest pairwise genetic distance was obtained when compare with Rio de Janeiro. Although slightly higher, no significant genetic distances were observed with Cartagena, Portugal or Spain. Rst P values were lower than 5% in the comparisons with Portuga and Cartagena. Nevertheless, when Bonferroni correction is applied the significance level is 0.0083 and, therefore, both genetic distance values are not significant. The genetic distances between Costa Rica and African samples, although very high, are about 10% lower than those found between Iberian and African populations. The same was previously observed for Rio de Janeiro population [8] and, after analyzing SNP haplogroups’ composition, it was found to be due to the presence of 8.7% of male lineages of Sub-Saharan African origin in this sample [12]. Our results support a high proportion of European male lineages representing the background of Costa Rica. Because of the low genetic distance between Costa Rica and Rio de Janeiro, as well as the low distance values with African samples, Sub-Saharan haplotypes are expected to be present in Costa Rica, in a similar proportion that the one found in Rio de Janeiro.

Table 1. Haplotype frequencies for 12 Y-STR loci of unrelated males from Costa Rica (N=100)
DYS391DYS389 IDYS439DYS389 IIDYS438DYS437DYS19DYS392DYS393DYS390DYS385 a/bNo.
1015133012151413132411–141
914103010141311132413–142
1014123012151513132411–141
1013113111141511132116–161
1013122912151413122411–141
912122810161411142113–151
1013122911141315132414–171
1114113012141413132411–141
1013132912151413132411–141
1113122912151413132211–152
1113122912141413132311–151
1113122911151413132411–141
1013132912141413132411–141
1012122910161610142215–151
1016122813161411132212–131
1113113010141511132317–181
1014113110141512142315–151
1014123012141414132411–141
1112122811161611142214–151
1114132912151513122411–141
813123110141311132212–161
1113122912151413132412–141
1113122913151413132412–142
1013153210141411132416–171
1114132912151413122511–141
914103010141311132413–154
111212289161511122414–171
1113112912151413122412–141
912132810161511142313–151
1013133010141311132314–161
1012132910161510132215–151
1112112811161611142214–153
1113112912151413132511–141
1114123012151413132411–141
101314309151411122314–161
1113132911151414122511–141
111311291215141313249–141
1113133012151513132411–142
1113112912151513132411–141
1113133011141414142414–171
1113122910151512142315–151
1113122912151513132311–141
1014123012141413132411–141
1012112811161611142214–142
914103110141411122313–141
1113132912151413132411–142
1113123012151413132413–151
1112122812141414132411–141
913123111141314142413–171
1114123012151513132411–131
1112142912161411132411–141
1213112912151413132411–151
1114133012141414132411–151
914123012151413122511–141
1114123012171113132411–141
1013113013151513132411–142
1012142910161511152113–162
1113132912151313132411–151
1115132712151413132311–141
1113132912171413132414–151
1013122912151414132511–142
1013142912151413132411–141
101313317161511122513–151
1114123010161511142213–131
1112122912141413132411–151
914103010141311132514–141
1113112912151413132411–151
1113122912151413132311–141
1013122810151711132312–121
1113122912141413132411–141
1013113010161511142214–151
1013133112141614132414–171
1012112812161314132415–161
101311299141513132314–161
1014123011141315142414–181
1114123210151511132411–111
1013113010151512152414–151
1114113110141511132416–171
1013143210141411132416–171
1213122912141413132411–151
101311309161611122313–171
1013123011141511142115–191
1114123212141413132411–141
1114123012141414132411–151
1011122710171511132213–161
1012112810161411142313–131

Haplotypes found more than once are indicated in bold.

Table 2. Genetic distances obtained from comparison between Costa Rica and other populations
Costa Rica vs.RstRst P-value±S.E.
Portugal0.013910.01871±0.0013
Cartagena (Colombia)0.010850.03079±0.0018
Rio de Janeiro (Brazil)0.003030.22404±0.0047
Spain0.008950.06108±0.0023
Mozambique0.332050.00000±0.0000
Equatorial Guinea0.305640.00000±0.0000

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Conflict of interest 

None.

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Acknowledgement 

IPATIMUP is partially supported by Fundação para a Ciência e a Tecnologia, through POCI.

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References 

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PII: S1875-1768(08)00138-8

doi:10.1016/j.fsigss.2007.10.101

Forensic Science International: Genetics Supplement Series
Volume 1, Issue 1 , Pages 252-254, August 2008

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