PopAffiliator: online calculator for individual affiliation to a major population group based on 17 autosomal short tandem repeat genotype profile.

Because of their sensitivity and high level of discrimination, short tandem repeat (STR) maker systems are currently the method of choice in routine forensic casework and data banking, usually in multiplexes up to 15-17 loci. Constraints related to sample amount and quality, frequently encountered in forensic casework, will not allow to change this picture in the near future, notwithstanding the technological developments. In this study, we present a free online calculator named PopAffiliator ( http://cracs.fc.up.pt/popaffiliator ) for individual population affiliation in the three main population groups, Eurasian, East Asian and sub-Saharan African, based on genotype profiles for the common set of STRs used in forensics. This calculator performs affiliation based on a model constructed using machine learning techniques. The model was constructed using a data set of approximately fifteen thousand individuals collected for this work. The accuracy of individual population affiliation is approximately 86%, showing that the common set of STRs routinely used in forensics provide a considerable amount of information for population assignment, in addition to being excellent for individual identification.

Y-STR genetic diversity in Moroccans from the Figuig oasis.

Seventeen Y-chromosomal short tandem repeats (STRs) (DYS392, DYS437, DYS448, GATAH4.1, DYS389II, DYS439, DYS635, DYS393, DYS438, DYS391, DYS389I, DYS390, DYS19, DYS458, DYS456 and DYS385a,b) were typed in DNA samples from 96 unrelated Moroccan men from the Figuig oasis. Fifty-two haplotypes were identified, of which 36 were unique. The overall haplotype diversity was 0.966, and the discrimination capacity was 0.542. Population comparisons with previously published data revealed significant genetic heterogeneity between the Figuig Moroccans and other North African populations. Results also showed that the minimal haplotype 11-30-13-10-13-25-15 (DYS392-DYS389II-DYS393-DYS391-DYS389I-DYS390-DYS19) was the most frequent haplotype observed in Figuig men.

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.

Allele frequencies of 15 short tandem repeats (STRs) in three Egyptian populations of different ethnic groups.

DNA typing of 15 short tandem repeat (STR) loci included in the AmpFlSTR Identifiler PCR amplification kit (Applied Biosystems), was carried out in three Egyptian populations of different ethnic groups: the Berbers from the Siwa oasis (in the North-Western Egyptian desert), the Muslims and the Copts from Adaima (Upper Egypt). A total of 297 individuals were typed. 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 and population differentiation tests showed that 7, 10 and 8 out of 15 loci have significant differences between the Berbers and the Muslim samples, between the Berbers and the Copts, and between the two samples from Adaima, respectively. Comparative analyses between our population data and other geographically related populations gathered from the literature were performed.

Population genetic data of 15 tetrameric short tandem repeats (STRs) in Berbers from Morocco.

The allele frequency distribution of 15 short tandem repeats (STR) loci contained in the AmpFlSTR Identifiler PCR Amplification Kit (Applied Biosystems), was determined in two Berber populations from Asni and Bouhria, in Central and Eastern Morocco, respectively. A total of 209 individuals were typed. No deviations from the Hardy-Weinberg equilibrium were observed for Asni at the 15 STRs loci whereas for the Bouhria samples, two loci (D5S818 and TH01) showed significant departures from Hardy-Weinberg expectations (after Bonferroni's correction). All loci are highly polymorphic and population differentiation tests showed that the Moroccan samples from Asni and Bouhria have significant differences in 4 out of 15 loci (D21S11, D7S820, D16S539 and TPOX). The aim of the study was to obtain accurate allele frequencies relevant for forensic applications. Comparative analyses between our population data and other population samples gathered from the literature are also presented.

The mtDNA legacy of the Levantine early Upper Palaeolithic in Africa.

Sequencing of 81 entire human mitochondrial DNAs (mtDNAs) belonging to haplogroups M1 and U6 reveals that these predominantly North African clades arose in southwestern Asia and moved together to Africa about 40,000 to 45,000 years ago. Their arrival temporally overlaps with the event(s) that led to the peopling of Europe by modern humans and was most likely the result of the same change in climate conditions that allowed humans to enter the Levant, opening the way to the colonization of both Europe and North Africa. Thus, the early Upper Palaeolithic population(s) carrying M1 and U6 did not return to Africa along the southern coastal route of the "out of Africa" exit, but from the Mediterranean area; and the North African Dabban and European Aurignacian industries derived from a common Levantine source.