Evaluating the informative power of Y-STRs: a comparative study using European and new African haplotype data

Male individuals from Maputo (Mozambique) were sampled and 18 Y-STRs were typed: the nine currently used to define the "minimal haplotype" employed in the European, American and Asian "Y-STR Haplotype Reference Databases", as well as the recently described DYS434, DYS437, DYS438, DYS439, DYS460, DYS461, GATA A10, GATA C4 and GATA H4. Allele and haplotype frequencies were estimated in a sample of 112 individuals, where it was possible to define 101 haplotypes, with an observed haplotype diversity (HD) of 0.9973. Allele diversity varied between 0.0179 and 0.9220, DYS385 showing the highest level of polymorphism and DYS392 the lowest. When considering only the most recent Y-STRs, the degree of diversity varied between 0.4011 (DYS438) and 0.6910 (GATA C4), except for DYS434 and DYS437 where a very low diversity was observed (0.0700 and 0.0526, respectively). When analysing the same 112 individuals for the nine Y-STRs included in the minimal haplotype, 78 haplotypes were distinguished with a corresponding observed diversity of 0.9884, a considerably lower value than those for Northern Portugal (n=208; HD: 0.9925) and Macao (n=63; HD: 0.9990). Concerning all 18 Y-STRs studied in this population, the observed diversity demonstrates their usefulness in forensic applications, with the exception of DYS434, DYS437 and DYS392. However, since the informative power of a marker has to be judged in haplotype context, a simple software, allowing the evaluation of the increase of HD through the addition of any combination of new markers to the minimum haplotype was designed. The statistical approach devised, demonstrates that an increment on HD is more rapidly obtained for the Mozambican database when adding GATA A10 or DYS439, DYS460, GATA C4, DYS461 or GATA H4, in this order, to the minimal haplotype. DYS434, DYS437 and DYS438, in conjunction with all the other 15 Y-STRs, do not contribute to an increment on HD. When applying the same approach to an European sample (Northern Portugal), the first three Y-STR choices coincide, but the next order of markers are GATA H4, then DYS437 and finally DYS461. In this sample, DYS434, DYS438 and GATA C4 do not increment HD any further.     

Y-chromosome STR haplotypes in two population samples: Azores Islands and Central Portugal

The Y-chromosome haplotypes defined by nine STRs (DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392 and DYS393) were studied in 207 unrelated individuals from Central Portugal and 63 from Azores Islands. The most common haplotype in Central Portugal was shared by 3.4% of the males, while 160 haplotypes were unique. In Azores Islands the most common haplotype was shared by 6.4% of the males, while 40 haplotypes were unique. The values of haplotype diversity were 0.993 for Central Portugal and 0.976 for Azores Islands.     

Population data for Y-chromosome haplotypes defined by 17 STRs (AmpFlSTR YFiler) in Portugal

The 17 Y-chromosomal short tandem repeats (STRs) included in the AmpFlSTR YFiler Amplification Kit (AB Applied Biosystems) (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4.1) were typed in 250 samples from Portugal. A total of 231 different haplotypes were found, where 17 haplotypes were shared by two individuals and one haplotype by three. The overall haplotype diversity (HD) was 0.9994. DYS458 non-consensus alleles found in 5 samples (out of 85) are all associated with paragroup J*(xJ1,2). Population comparisons with available Yfiler loci data in European samples were undertaken, namely with Northern Portuguese data (N=174) where no significant differences were observed with our sample (Rst=0.0000; P=0.8649+/-0.0310). Since both Portuguese databases can be joined (N=424; HD=0.9997; 394 distinct haplotypes), a study on the best loci for HD increment in this sample was also undertaken: by fixing the haplotypes generated from the minimal haplotype and SWGDAM core set (www.yhrd.org) and adding the other Yfiler loci one by one, the order in which the loci contribute more is DYS458, DYS456, GATA H4.1, DYS437 or DYS635, and finally DYS448. Therefore, at least in this population sample, all Yfiler loci are contributing for haplotype discrimination.     

Y-chromosome polymorphism data in Majorcan, Minorcan and Valencian populations (eastern Spain).

Frequency data of the six STRs: (1) DYS19; (2) DYS389I; (3) DYS389II; (4) DYS390; (5) DYS391 and (6) DYS393, and the DYS287 polymorphism (YAP) were determined in a sample of 117 unrelated males from three eastern Spanish populations: 53 from Majorca, 40 from Minorca and 24 from Valencia.     

Population data for Y-chromosome haplotypes defined by 17 STRs (AmpFlSTR YFiler) in Central Portugal

The 17 Y-chromosome STR loci (DYS19, DYS389I, DYS389II, DYS390, DYS456, DYS391, DYS392, DYS393 and DYS385 a/b, DYS458, DYS439, DYS635, GATA H4.1, DYS437, DYS438 and DYS448) were determined for 100 unrelated males, living in Central Portugal, using the AmpFlSTR YFiler PCR Amplification kit (Applied Biosystems).A total of 99 different haplotypes were found, with only two individuals sharing the same haplotype. The overall haplotype diversity (HD) was determined as 0.9998, a value similar to other Y Filer data sets.Y-STR polymorphisms in Central Portugal population, using YFiler, provide a powerful discrimination tool for routine forensic applications.     

Results of the GEP-ISFG collaborative study on the Y chromosome STRs GATA A10, GATA C4, GATA H4, DYS437, DYS438, DYS439, DYS460 and DYS461: population data

The Spanish and Portuguese ISFG Working Group (GEP-ISFG) carried out a collaborative exercise in order to asses the performance of two Y chromosome STR tetraplexes, which include the loci DYS461, GATA C4, DYS437 and DYS438 (GEPY I), and DYS460, GATA A10, GATA H4 and DYS439 (GEPY II). The groups that reported correct results in all the systems were also asked to analyse a population sample in order to evaluate the informative content of these STRs in different populations. A total of 1020 males out of 13 population samples from Argentina, Brazil, Costa Rica, Macao, Mozambique, Portugal and Spain were analysed for all the loci included in the present study. Haplotype and allele frequencies of these eight Y-STRs were estimated in all samples. The lowest haplotype diversity was found in the Lara (Argentina) population (95.44%) and the highest (99.90%) in Macao (China). Pairwise haplotype analysis showed the relative homogeneity of the Iberian origin samples, in accordance with what was previously found in the European populations for other Y-STR haplotypes (http://www.ystr.org). As expected, the four non-Caucasian samples, Macao (Chinese), Mozambique (Africans), Costa Rica (Africans) and Argentina (Lara, Amerindians), show highly significant Phist values in the pairwise comparisons with all the Caucasian samples.     

Y chromosome microsatellite genetic variation in two Native American populations from Argentina: Population stratification and mutation data

Two Native American populations from North and northwest regions of Argentina (Toba and Colla) were analyzed for 17 Y chromosome short tandem repeat loci (Y-STRs), namely, DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4.1. Over 357 allele transfers, two one-step mutations could be detected at DYS456 and GATA H4.1 loci. A new 16.1 ‘micro-variant’ allele was observed for DYS385, characterized by an insertion at the fifth GAAA repeat. We also observed two alleles at the DYS448 locus in three samples (two from Toba and one from Colla). A total of 34 and 16 different haplotypes were detected for Toba and Colla, respectively, the former with a haplotype diversity value of 0.9769 ± 0.01, whereas 0.9497 ± 0.02 for the latter. Significant population differences were observed between Colla and Toba, at least in part, due to a more prevalent European input in the Colla. In agreement with this observation is the fact that the genetic distances between Colla and Iberian populations are lower than those observed between Iberian and any other Native American population. The results of multiscaling dimensional analysis and genetic distances (Rst) among Native American population samples also reflect this fact. The data show the existence of clear population stratification in the Argentina, a fact that should be taken into account in forensic casework.     

Y-miniSTR: New application for compromised samples (population data)

In this work 127 unrelated individuals living in the North of Portugal were typed for 8 Y-miniSTRs (DYS504, DYS508, DYS522, DYS540, DYS556, DYS570, DYS576 and DYS632). One hundred and one different haplotypes were detected and 88 of them were found to be unique. Haplotype diversity (0.9936) and discrimination capacity (69.29%) were calculated.     

Population frequency distribution of HumF13A01, HumFXIIIB, and HumLIPOL loci in the Basque Country (Northern Spain)

A population study of unrelated individuals from the Basque Country (Northern Spain) was carried out using the GenePrint STR System. The PCR products were separated on denaturing polyacrylamide gels and visualized by silver staining. Three tetrameric loci were evaluated: HumF13A01, HumFXIIIB, and HumLIPOL. All loci fit Hardy-Weinberg expectations, and independence of alleles was found between these STR loci. A comparison with other population groups indicated allele frequencies are well conserved in Caucasians, but differ from other racial groups. The calculated parameters a priori probability of exclusion (Pex) and "power of discrimination" (PD) show how informative these loci are for the determination of identity and relatedness of individuals.     

Y chromosome STR haplotypes in the Caribbean city of Cartagena (Colombia)

Haplotype data were obtained from a sample of 173 unrelated male individuals from Cartagena (Colombia), for 16 Y-chromosome STRs (DYS19, DYS385, DYS389 I, DYS389 II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS460, DYS461, DYS635, GATA H4 and GATA A10). No shared haplotypes were observed, demonstrating the usefulness and informative power of these Y-STRs in male lineage identification in Cartagena. Genetic distances were calculated using previously published haplotype data and the lowest values were found for the comparisons with samples of Iberian origin.     

A Spanish population study of 17 Y-chromosome STR loci

Haplotype, allele frequencies and population data of 17 Y-chromosome STR loci DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS460 (GATA A7.1), DYS461 (GATA A7.2), GATA A10, GATA C4 and GATA H4 were determined from a sample of 148 unrelated male individuals from Spain. A total of 144 haplotypes were identified by the 17 Y-STR markers, of which 141 were unique, two were found in two individuals and one was found in three individuals. The haplotype diversity (99.95%) and discrimination capacity (97.30%) were calculated. Comparisons were made with previously published haplotype data on other Iberian population samples and no significant differences were found.     

Y-chromosome STR haplotypes from a Western Mediterranean population sample

Nine Y-chromosome STRs were investigated in a male population sample from the Western Mediterranean region of Valencia (Eastern Spain). Complete nine Y-chromosomal STRs haplotypes were obtained in 140 individuals, among which 113 different haplotypes were observed. The most common haplotype was shared by 5% of the sample, while 99 haplotypes were unique. The gene diversity was 0.9892 and the discrimination capacity was 0.8071. Significant population differences were observed with respect to other Iberian populations, such as the Basques and Northern Portugueses.     

High resolution Y chromosome typing: 19 STRs amplified in three multiplex reactions

Nineteen Y-specific short tandem repeat (STR) loci have been amplified in 768 samples from the Iberian Peninsula in order to evaluate their usefulness in forensic casework. Two previously published multiplex reactions by Thomas et al. [Hum. Genet. 6 (1999) 577] (MS1, modified here: DYS19, DYS388, DYS390, DYS391, DYS392 and DYS393) and by Ayub et al. [Nucl. Acids Res. 28 (2000) e8] (CTS: DYS434, DYS435, DYS436, DYS437, DYS438 and DYS439) plus a novel one reported here (EBF: DYS385, DYS389, DYS460, DYS461, DYS462 and amelogenin) have been used. DYS385, DYS439 and DYS391 were the most informative loci with allele diversities of 0.7997, 0.6683 and 0.5940, respectively. A total of 635 different haplotypes were observed, of which 573 (90.24%) were found in single individuals. The overall haplotype diversity was 0.9988 and that obtained by each multiplex system was 0.9812 for EBF, 0.9292 for MS1 and 0.9089 for CTS.     

Allele frequencies and population data for 17 Y-STR loci (AmpFlSTR Y-filer) in a Northern Portuguese population sample

Allele frequencies and population data for 17 Y-STR loci included in a new commercial kit that has recently been available, the AmpFlSTR Y-filer PCR amplification kit (Applied Biosystems), that permits the simultaneous amplification of all the markers included in the actually used European "extended haplotype", DYS19, DYS189I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385I/II, DYS438, DYS439 and also DYS437, DYS448, DYS456, DYS458, DYS635 and Y GATA H4, were obtained from a sample of 175 healthy unrelated males and 45 father-son pairs from the North of Portugal. A total of 171 haplotypes were identified, of which 167 were unique and 4 were found in 2 individuals. The haplotype diversity (99.97%) and discrimination capacity (95.43%) were calculated. We report some non-standard situations, such as allele duplications and mutations. We also report a case of disputed paternity in which duplicated alleles plus an inconsistency of the transmitted alleles appeared.     

Regional Technology Policy and the Emergence of an R&D System in the Basque Country

The political changes of the late 1970s early 1980s opened up a process of devolution and decentralization in Spain which reached very important levels in historical regions such as the Basque Country and Catalonia. In the R&D policy realm, Basque government policies had an important impact in the emergence of a regional R&D system from stratch in a short period of time. The industry-oriented Basque model was also rather innovative in the Spanish context of the 1980s, which was dominated by public, basic science-oriented national research councils. In this paper we analyze the process of configuration of regional R&D policies in the Basque Country by looking at the interplay between structural factors, actors, interests, ideas, and institutions. We also look at the main achievements and shortcomings of those policies.     

Grouping of Y-STR haplotypes discloses European geographic clines

Y-STR haplotypes are widely studied in Europe and an extensive databasing effort has been conducted (http://www.ystr.org). The distribution of these haplotypes has been considered to present no evidence for substructure at central and southern European level. This picture contrasts with the one that results from Y haplogroups defined by binary markers. This paradox has been solved by admitting that the high STR mutation rate and corresponding recurrence has erased geographic structuration. This explanation prompted us to reanalyse Y-STR haplotypes distribution bearing in mind the commonly admitted model for the generation of diversity in these markers, namely the stepwise mutation model (SMM) and, thus, taking the molecular distance between haplotypes into consideration. Accordingly, we have studied the European distribution of the two most frequent haplotypes in the Iberian Peninsula and their one step neighbours using the European samples deposited in the Y STR database (http://www.ystr.org). For the first group we found a clear-cut decreasing W-E gradient, while for the second the highest frequencies were found in the Iberian Peninsula (3.98% in Portugal and 3.85% in Spain), dropping to 2.88% in France and showing a less well defined SW-NW gradient. Furthermore, we have tested the agreement between haplotype groups and binary markers haplogroups in a random sample of 292 individuals from Northern Portugal. Our results demonstrate that (a) Y-STR haplotype data can be used for wide-scale anthropological approaches disclosing information that has been considered only available through binary markers and (b) forensic use of continental databases needs careful refinement, due to the macro-geographic pattern now evidenced.     

Allele frequencies of 15 tetrameric short tandem repeats (STRs) in Andalusians from Huelva (Spain)

The allele frequency distribution of 15 short tandem repeat (STR) loci contained in the AmpFlSTR Identifiler PCR Amplification Kit (Applied Biosystems), was determined in 114 individuals from Andalusia (province of Huelva), in the southernmost part of the Iberian Peninsula. After Bonferroni's correction, no deviations from the Hardy-Weinberg equilibrium were observed for all samples at the 15 STR loci. All loci are highly polymorphic. The aim of the study was to obtain accurate allele frequencies relevant for applications in forensics and population genetics. Comparative analyses between our population data and other population samples gathered from the literature are also presented.     

Data for nine autosomal STRs markers from Valencia (East Mediterranean coast of the Iberian Peninsula)

Nine STRs loci have been typed in a sample from Valencia, a population from the East Mediterranean coast of the Iberian Peninsula.     

X-linked microsatellites in two Northern Spain populations

The X-chromosomal microsatellites HPRTB, DXS101, ARA, DXS7423, and DXS8377 were analysed by a pentaplex PCR in an expanded population sample from Cantabria and an independent sample of unrelated individuals from the Basque Country. Allele frequencies showed similar distributions, but minor variations were found for some loci.     

Y-chromosome STR haplotype diversity in three ethnic populations in Singapore

In this study, 12 Y-STR loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a/b, DYS437, DYS438 and DYS439) were genotyped in the three major ethnic populations in Singapore, namely the Chinese, Malay and Indian. Allele frequency distribution, locus diversity, haplotype diversity and discrimination capacity were estimated. Analysis of molecular variance between the three ethnic populations indicated that 87.71% of the haplotypic variation is found within population and 12.29% is between populations (Fixation Index FST=0.123, p=0.000). Population pairwise comparisons showed significant Phist values between all population pairs, with the lowest (RST=0.05) for Chinese-Malay and the highest (RST=0.19) for Chinese-Indian.