Genetic profile of the Madeira Archipelago population using the new PowerPlex16 System kit

Allele and haplotype frequencies of 17 chromosome STR loci, 15 of them included in the kit PowerPlex 16 System from Promega, were determined in a sample of unrelated males from Madeira and Porto Santo Islands. PowerPlex 16 includes STRs not studied before in the Madeira population. The-kit includes two new allele markers (Penta D and Penta E), which proved to be extremely useful for paternity testing (PD = 0.952 and 0.977, respectively). The study revealed that the Madeira population does not differ from that of the north Portugal. Nevertheless, some loci presented alleles found in sub-Saharan and North European populations which were not reported so far in Portugal.     

Distribution of Y-chromosome STR defined haplotypes in Iberia

Seven Y-specific STR loci (DYS19, DYS389I, DY5389II, DYS390, DYS391, DYS392 and DYS393) were studied in five populations from the Iberian Peninsula: Andalusia, Valencia, Basque Country, Galicia and Northern Portugal. Haplotype and allele frequencies of these seven Y-chromosome STRs were estimated. Observed haplotype diversities are in a range between 0.96 (Basque Country) and 0.99 (Valencia and Andalusia). Significant population differentiation was registered between Basques and all the other Iberian populations and also between Valencia and Northern Portugal.     

Y-chromosome STR haplotypes in the Madeira archipelago population.

Allele and haplotype frequencies of seven Y-chromosome STR loci were determined from a sample of 95 and 16 unrelated males from Madeira and Porto Santo Islands, respectively.     

STR data (AmpFlSTR profiler plus) from north Portugal

Allele frequencies for the nine STRs included in the AmpFlSTR Profiler Plus kit (D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317 and D7S820) were estimated from a sample of 365-427 unrelated individuals born in north Portugal.     

Mismatch distribution analysis of Y-STR haplotypes as a tool for the evaluation of identity-by-state proportions and significance of matches—the European picture

We suggest the use of the mismatch distribution methodology as an easy way to estimate the distance between all pairs of haplotypes present in a sample. This approach allows the evaluation of the proportion of pairs of Y-STR haplotypes that are prone to become identical by state (IBS), in one generation, by recurrent mutation, a statistic of major importance in the forensic field. The mismatch approach presents some advantages alternatively to the empirical one, since it is not necessary to have simultaneous information on STRs and SNPs, and it allows the evaluation of IBS also within-haplogroups. The estimation of IBS at an European scale showed that there is a high population substructuring for this parameter, increasing from southern-central European countries towards west and north, in accordance to what was found for Y-biallelic markers. This result seems to imply a more careful use of large databases for matching evaluation, even in the absence of population structure for general Y-STR diversity. Furthermore, mismatch distribution can be used to measure the distance between a particular haplotype and all the haplotypes in a sample. When applied to the most frequent haplotypes in Europe it revealed that the opportunity for IBS is not directly related to the frequency of a haplotype, but highly dependent on the proportion of neighbouring haplotypes—so, that reporting on the haplotype frequency for evaluating the significance of a match can be misleading.     

Human Identification by Oral Prosthesis Analysis with Probability Rates Higher than DNA Analysis

Several techniques are used to perform an appropriate and reliable human identification. Forensic dentistry has achieved great relevance over the past years. The aim of this article is to report the method used for the identification of a male body found in the colliquative stage of putrefaction. The identification of the victim was succeeded confronting the dental findings found in the corpse with the data present on dental records provided by his dentist. The major elements for the identity′s recognition were a metal core and a prosthetic crown that were being fabricated. These elements associated with the dental records were compelling for the elucidation of the case, and a positive body identification was achieved with high levels of probability. In the present case, cadaveric analysis of stomatognathic system structures achieved a probability value higher than DNA identification techniques, emphasizing the importance of forensic dentistry.     

The Karimojong from Uganda: Genetic characterization using an X-STR decaplex system

The Karimojong, an African group from the Karamoja region of Northeast Uganda, were genetically analysed using a decaplex system for X chromosome short tandem repeats (X-STRs). A total of 255 individuals (117 males and 138 females) were genotyped for the following loci: DXS8378, DXS9898, DXS7133, GATA31E08, GATA172D05, DXS7423, DXS6809, DXS7132, DXS9902 and DXS6789. Allele frequencies and parameters for forensic evaluation were calculated for each STR. No association was found between any pairs of loci studied. DXS6789 was the most polymorphic marker in this sample, followed by DXS6809, with gene diversities of 84.79% and 83.94%, respectively. The less discriminating locus observed was DXS7133, with a gene diversity of 39.79%. High overall values of power of discrimination were obtained for female (1 in 1.8 × 10¹⁰) and male samples (1 in 1.6 × 10⁶), as well as high power of exclusion in father/mother/daughter trios (99.9997%), in father daughter duos (99.9862%) and in half sisters with same father (99.0331%). These results confirm the potential of this 10-plex in parentage testing and in human identification.     

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.     

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.     

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.