The genetic male legacy from El Salvador

Allele frequencies and haplotype and haplogroup analysis have been performed for 16 Y-chromosome binary markers and 8 Y-chromosome STRs (DYS19, DYS385I and II, DYS389I and II, DYS390, DYS391, DYS392, DYS393). Data was obtained from a general sample of 93 unrelated individuals living in metropolitan areas from El Salvador, and 67 individuals from different historical ethnic groups, Conchagua, San Alejo, Panchimalco, Izalco and finally Nueva Concepción with white people. Levels of admixture among metropolitan and rural areas were evaluated and population substructure measured. A total of 13 haplogroups and 136 different haplotypes were found. The most frequent haplogroup in the general metropolitan population was the European R1b, while in the Indigenous samples considered as a whole the most frequent was the Amerindian haplogroup Q3.     

Y chromosome SNP analysis in a Portuguese population sample using a multiplex PCR and minisequencing strategy

The study of single nucleotide polymorphisms (SNPs) located on the Y chromosome specific region Y-SNPs (92R7, M70, M22, Tat, P25, SRY10831, M173, M213 and M9) was used to characterize a population sample from Central Portugal, in order to investigate the frequency distribution of the male lineages and to compare the observed results with those obtained in other Portuguese regions.The genotyping strategy was according to the described by Brion et al. [M. Brion, et al., Int. J. Legal Med. 119 (2004) 10-15].In this population sample from Central Portugal a typical Western European haplogroup composition was found. The majority of samples (almost 70%) were assigned inside haplogroup R. As for other Iberian populations, the most frequent haplogroup was R1b-P25 (52.2%), followed by F(xK)-M213 (15.2%), E-B-SRY10831.1, R1(xR1a,b)-M173 and R1a-SRY10831.2 (each of them with a 8.7% frequency), K2-M70 (4.3%) and L-M22 (2.2%). When comparing our sample with other samples from Portugal, no significant differences were found.     

Geographical heterogeneity of Y-chromosomal lineages in Norway

Y-chromosomal variation at five biallelic markers (Tat, YAP, 12f2, SRY(10831) and 92R7) and nine multiallelic short tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385I/II and DYS388) in a Norwegian population sample are presented. The material consists of 1766 unrelated males of Norwegian origin. The geographical distribution of the population sample reflects fairly well the population distribution around the year 1942, which is the median birth year of the index persons. Seven hundred and twenty-one different Y-STR haplotypes but 726 different lineages (Y-STRs plus biallelic markers) were encountered. We observed six known (P*(xR1a), BR(xDE, J, N3, P), R1a, N3, DE, J), and one previously undescribed haplogroup (probably a subgroup within haplogroup P*(xR1a)). Four of the haplogroups (P*(xR1a), BR(xDE, J, N3, P), R1a and N3) represented about 98% of the population sample. The analysis of population pairwise differences indicates that the Norwegian Y-chromosome distribution most closely resembles those observed in Iceland, Germany, the Netherlands and Denmark. Within Norway, geographical substructuring was observed between regions and counties. The substructuring reflects to some extent the European Y-chromosome gradients, with higher frequency of P*(xR1a) in the south-west and of R1a in the east. Heterogeneity in major founder groups, geographical isolation, severe epidemics, historical trading links and population movements may have led to population stratification and have most probably contributed to the observed regional differences in distribution of haplotypes within two of the major haplogroups.     

Results of a collaborative study of the EDNAP group regarding the reproducibility and robustness of the Y-chromosome STRs DYS19, DYS389 I and II, DYS390 and DYS393 in a PCR pentaplex format

A collaborative exercise was carried out by the European DNA Profiling Group (EDNAP) in the frame work of the STADNAP program, i.e. standardization of DNA profiling in Europe, in order to evaluate the performance of a Y-chromosome STR pentaplex, which includes the loci DYS19, DYS389 I and II, DYS390 and DYS393 and to determine whether uniformity of results could be achieved among different European laboratories.Laboratories were asked to analyze the five Y-STRs using singleplex and multiplex conditions in three bloodstains and one mixed stain (95% female and 5% male).All the laboratories reported the same results even for the mixed stain included in the exercise. This demonstrates the reproducibility and robustness of Y-chromosome STR typing even with multiplex formats and proves the usefulness of Y-STR systems for analyzing mixed stains with a male component.A total of 930 male samples from 10 different populations from Europe were also analysed for all the loci included in the pentaplex. Eight of these ten populations also included haplotype data.As for single gene analysis, haplotype diversity was higher in Germany and Italy and lower in Western European countries and Finland.Pairwise haplotype analysis shows the Finnish departure from the rest of the populations and a relatively homogeneity in the other European populations with F(ST) estimates lower than 0.05.UPGMA analysis shows an association of Western European population (Ireland, UK, Portugal and Galicia) on the one hand and central European populations on the other.     

Duplications of the Y-chromosome specific loci P25 and 92R7 and forensic implications

In the present study, we demonstrate that two commonly used Y-chromosome single nucleotide polymorphisms (SNPs), P25 and 92R7, are paralogous sequence variants (PSVs) originating from segmental duplications and that at least one of the sequence variants in each group of loci is polymorphic. Several methodologies were used in order to detect the SNP alleles and the PSVs of the loci. All results obtained with the various typing techniques supported the conclusion. The allele distributions of the binary markers were analysed in more than 600 males with seven different haplogroups. For P25, the ancestral allele C was found in several samples from different haplogroups. The derived allele A was always present with an additional C variant. Haplogroup P was defined by the derived allele A at the 92R7 locus. However, the ancestral allele G was always associated with an A variant due to the duplication.     

Duplications of the Y-chromosome specific loci P25 and 92R7 and forensic implications

In the present study, we demonstrate that two commonly used Y-chromosome single nucleotide polymorphisms (SNPs), P25 and 92R7, are paralogous sequence variants (PSVs) originating from segmental duplications and that at least one of the sequence variants in each group of loci is polymorphic. Several methodologies were used in order to detect the SNP alleles and the PSVs of the loci. All results obtained with the various typing techniques supported the conclusion. The allele distributions of the binary markers were analysed in more than 600 males with seven different haplogroups. For P25, the ancestral allele C was found in several samples from different haplogroups. The derived allele A was always present with an additional C variant. Haplogroup P was defined by the derived allele A at the 92R7 locus. However, the ancestral allele G was always associated with an A variant due to the duplication.     

Characterization of human control region sequences of the African American SWGDAM forensic mtDNA data set

The scientific working group on DNA analysis Methods (SWGDAM) mitochondrial DNA (mtDNA) population data set is used to infer the relative rarity of control region mtDNA profiles obtained from evidence samples and of profiles used for identification of missing persons. In this study, the African American haplogroup patterns in the SWGDAM data were analyzed in a phylogenetic context to determine relevant single nucleotide polymorphisms (SNPs) and to describe haplogroup distributions for Africans observed in these data sets. Over 200 SNPs (n=217) were observed in the African American data set (n=1148). These SNPs ranged from having 1-39 changes in the phylogenetic tree, with sites 152 and 16519 being the most variable. On average there were 5.8 changes for a character on the tree. The most variable sites (with 19 or more changes each) observed included 16093, 16129, 16189, 16311, 16362, 16519, 146, 150, 152, 189, and 195. These rapidly changing sites are consistent with other published analyses. Only 34 SNPs are needed to identify all clusters containing 10 or more individuals in the African American data set. The results show that the African American SWGDAM mtDNA data set contains variation consistent with that described in continental African populations. Thirteen of the 18 haplogroups previously observed in African populations were observed and include: L1a, L1b, L1c, L2a, L2b, L2c, L3b, L3d, L3e1, L3e2, L3e3, L3e4 and L3f. Haplogroup L2a is the most commonly observed cluster (18.8%) in the African American data set. The next most common haplogroups in the African American data set include the clusters L1c (11.0%), L1b (9.1%), L3e2 (9.0%) and L3b (8.1%). Approximately 8% of the haplogroups observed within African Americans were common in European Caucasians or East Asians; these were H (n=32), J (n=4), K (n=5), T (n=2), U5 (n=6), U6 (n=9 also known from North Africa), A (n=12), B (n=7), C (n=4), and M (n=16), respectively. The European Caucasian and East Asian haplogroups are expected due to admixture between individuals with recent ancestry in Western Eurasia and sub-Saharan Africa. The genetic characterization of these relevant data sets is fully consistent with other published mtDNA genetic variation. The sequence diversity observed in this data set makes it a valuable tool for forensic applications.     

Recently introduced Y-SNPs improve the resolution within Y-chromosome haplogroup R1b in a central European population sample (Tyrol, Austria)

Three recently described Y-chromosome single nucleotide polymorphisms (Y-SNPs) were typed in a sample of 135 men from Tyrol (Austria). These SNPs define sub-clades of haplogroup (hg) R1b. The derived states of U152 (hg R1b3h) U106 (R1b3i) and U198 (R1b3i1) were found within the Austrian R1b population sub-sample (N = 42) in 9 (21.4%), 25 (59.5%), and 1 (2.4%) individuals, respectively. Only 8 (19.0%) of the hg R1b Y-chromosomes remained unresolved. These novel SNPs proved to be promising tools for distinguishing R1b lineages in the evolutionary as well as in the forensic context.     

Y-chromosome haplotype mismatch in different haplogroups: Coincidence or evidence of SNP mutation?

The analysis of 240 individuals from the populations of the Madeira and Azores archipelagos for both Y-chromosome STRs and SNPs allows the determination of a correlation between the haplotype and haplogroup for each individual.The variability within each haplogroup was analysed and coalescence age calculated. These results led to the detection of some founder effects in both populations.It was found that some individuals share the same haplotype but belong to different Y-chromosome haplogroup suggesting that SNP mutations may occur frequently. We propose using SNP and STR information together, which provides a more reliable characterization of an individual in terms of Y-chromosome origin, minimizing the risk of misassigment due to mutation.     

Report of a European collaborative exercise comparing DNA typing results using a single locus VNTR probe

A collaborative exercise was carried out in 1989 among 12 European forensic laboratories using the single locus VNTR probe pYNH24, the restriction enzyme HinfI, the same set of human genomic DNA samples, and a standardized DNA size marker. The objectives of the exercise were: (1) to study the degree of variation within and between laboratories, (2) to obtain information on requirements for technical standardization allowing the exchange of typing results and (3) to compare different approaches for the identification of allelic DNA fragments of unknown size. Each laboratory carried out up to 10 independent typing experiments using the same DNA samples. The results were analysed independently by two laboratories using three different methods. The results of the exercise demonstrate the correlation of typing that can be achieved within and between laboratories under conditions of minimal standardization.     

RNA/DNA co-analysis from blood stains—Results of a second collaborative EDNAP exercise

A second collaborative exercise on RNA/DNA co-analysis for body fluid identification and STR profiling was organized by the European DNA Profiling Group (EDNAP). Six human blood stains, two blood dilution series (5-0.001 μl blood) and, optionally, bona fide or mock casework samples of human or non-human origin were analyzed by the participating laboratories using a RNA/DNA co-extraction or solely RNA extraction method. Two novel mRNA multiplexes were used for the identification of blood: a highly sensitive duplex (HBA, HBB) and a moderately sensitive pentaplex (ALAS2, CD3G, ANK1, SPTB and PBGD). The laboratories used different chemistries and instrumentation. All of the 18 participating laboratories were able to successfully isolate and detect mRNA in dried blood stains. Thirteen laboratories simultaneously extracted RNA and DNA from individual stains and were able to utilize mRNA profiling to confirm the presence of blood and to obtain autosomal STR profiles from the blood stain donors. The positive identification of blood and good quality DNA profiles were also obtained from old and compromised casework samples. The method proved to be reproducible and sensitive using different analysis strategies. The results of this collaborative exercise involving a RNA/DNA co-extraction strategy support the potential use of an mRNA based system for the identification of blood in forensic casework that is compatible with current DNA analysis methodology.     

Results of collaborative study regarding the standardization of the Y-linked STR system DYS385 by the European DNA Profiling (EDNAP) group.

Y-chromosome linked short tandem repeat (STR) loci are inherited as a closely linked haplotype, which appears to remain stable in a given paternal lineage over many generations. In forensic cases, Y-linked STRs are particularly useful for the identification of human remains as well as in rape cases with mixed male/female stain samples. DYS385 is derived from tandemly duplicated segments of the Y chromosome thus giving rise to two fragments of variable length which do not behave like alleles but genotypes. The European DNA Profiling (EDNAP) group has carried out a collaborative exercise among 14 participating laboratories using DYS385 for typing of five unknown bloodstains and a control sample. Furthermore, population data from eight different European countries with samples sizes between 91 and 150 male individuals were collected. The results confirm previous observations that DYS385 is one of the most informative Y-linked STR loci. It could also be demonstrated that reproducible results can be obtained independently from the electrophoretic separation and detection methods used. Thus DYS385 may serve as a useful complementation to the routinely used autosomal STR systems in special cases.     

Y-chromosome variation in a Norwegian population sample

Y-chromosome DNA profiles are promising tools in population genetics and forensic science. Here we present DNA profiles of 300 unrelated Y-chromosomes of Norwegian origin. The profile is composed of eight short tandem repeats (STRs) and one single nucleotide polymorphism (SNP). In more than 2/3 of the haplotypes the modular structure in the 5' end of the minisatellite locus DYF155S1 was revealed by minisatellite variant repeat PCR (MVR-PCR) These haplotypes were also typed for deletions of fragment 50f2C (DYF155S2). Allele distribution and paternity exclusion parameters are given for each marker. The degree of haplotype diversity and its implication for statistics are evaluated. In the 300 samples 177 different haplotypes were encountered, of which 137 were observed once only. Analysis showed that the main source of variation is within the population. The Fst values were less than 0.015 in general. Haplotype grouping by the SNP demonstrated two haplogroups (Tat/T and Tat/C). Haplogroup Tat/C--found in 5.7% of the present material - is the same haplogroup as encountered in 60% of Finnish males [Am. J. Hum. Genet. 62 (1998) 1171]. Mutation analysis in 150 father/son pairs (a total of 1200 meiotic events) revealed an average mutation frequency of 0.0042 (95% CI 0.0014-0.0097).     

Male amelogenin dropouts: phylogenetic context, origins and implications

Several commercial PCR multiplex kits incorporate the amelogenin locus for the purpose of human gender identification. Consequently, erroneous results in the electropherogram profile of this locus can carry important forensic implications. In this study, dropout of the amelogenin Y allele was detected in 5 out of 77 phenotypically normal Kathmandu males using the AmpFlSTR Identifiler kit. A battery of male-specific markers including SNPs, STRs, STSs, and a minisatellite were amplified for the five amelogenin null samples in order to delineate the breakpoints of the deletions as well as assess the overall integrity of the Y-chromosome. This study represents the first to examine the haplogroup affiliation of the AMGY deletions. The analyses performed suggest a single origin for the five deletions as indicated by their allocation to a specific Y-haplogroup (J2b2-M241), related Y-STR haplotypes and identical regional localization of breakpoints. The age estimated from the microsatellite variation for the amelogenin deletions (if they are associated by descent) is approximately 6.5+/-3.3 ky, younger than the previously reported related age of the M241 haplogroup representatives (13-14 ky). Our data in combination with previous publications suggest a concentration of afflicted individuals in the Indian subcontinent, possibly as a result of common ancestry. The elevated incidence of the amelogenin dropout in these populations accentuates the need to utilize other loci for gender determination in order to obtain an accurate set of inclusion criteria in forensic casework.     

Development of multiplex PCRs for evolutionary and forensic applications of 37 human Y chromosome SNPs

This work describes an efficient and rapid test for typing 37 single nucleotide polymorphisms (SNPs) of the non-recombining region of Y chromosome (NRY) from a minimal amount of DNA using six PCR multiplexes. Markers were drawn following a hierarchical strategy based on the phylogenetic tree of Y chromosome proposed by the Y Chromosome Consortium [The Y Chromosome Consortium, A nomenclature system for the tree of human Y-chromosomal binary haplogroups, Genome Res. 12 (2002) 339-348]. Two multiplexes--arbitrarily named MY1 and MY2--were developed to explore the basal branches of the tree encompassing all the major clades A-R: MY1 for markers M35, M89, M172, M170, M9, M173, M45 and MY2 for markers M52, M216, M174, M181, M201, M91, M96, M214. Four multiplexes able of typing the more superficial branches typical of most frequent European haplogroups E3b, J2, R1 and I, were also developed and named MY-E3b (M78, M107, M224, M165, M148, M81), MY-J2 (M158, M68, M47, M102, M137, M67), MY-R1 (M17, M269, M18, P25, SRY10831.2) and MY-I (M72, M223, M26, M21, M161). SNP genotyping was carried out by hot-start PCR amplification with primers yielding fragments between 63 and 210 nucleotides, followed by minisequencing reaction based on dideoxy single-base extension and capillary electrophoresis of extension products. The sequential application of these multiplexes is a robust and effective resource for typing the most frequent European Y-SNP haplogroups, and appears to be suitable for forensic purposes and evolutionary studies.     

Results of the GEP-ISFG collaborative study on two Y-STRs tetraplexes: GEPY I (DYS461, GATA C4, DYS437 and DYS438) and GEPY II (DYS460, GATA A10, GATA H4 and DYS439)

A collaborative exercise was carried out by the Spanish and Portuguese ISFG Working Group (GEP-ISFG) in order to evaluate the performance of two Y-chromosome STR PCR tetraplexes, which include the loci DYS461, GATA C4, DYS437 and DYS438 (GEPY I), and DYS460, GATA A10, GATA H4 and DYS439 (GEPY II). The participating laboratories were asked to type three samples for the eight markers, using a specific amplification protocol. In addition, two control samples, with known haplotypes, were provided. The results obtained by the 13 different participating laboratories were identical, except for two laboratories that failed to type correctly the same two samples for GATA C4. By sequence analyses, two different GATA C4 allele structures were found. One control sample (allele 21) and two questioned samples (allele 22, correctly typed by all the laboratories, and allele 25) presented the following repeat structure: (TCTA)4(TGTA)2(TCTA)2(TGTA)2(TCTA)n, but different from the one found for allele 26 in one sample included in this exercise, as well as in the second control sample (allele 23), namely (TCTA)4(TGTA)2(TCTA)2(TGTA)2(TCTA)2(TGTA)2(TCTA)n. The collaborative exercise results proved that both Y-tetraplexes produce good amplification results, with the advantage of being efficiently typed using different separation and detection methodologies. However, since GATA C4 repeat presents a complex structure, with alleles differing in sequence structure, efficient denaturing conditions should be followed in order to avoid typing errors due to sizing problems.     

Y-chromosome lineages in São Tomé e Príncipe and Cabo Verde islands: Different input of European influence

The Y-chromosome haplogroup composition of the population of São Tomé e Príncipe and Cabo Verde Archipelagos was profiled by using 24 biallelic markers, and compared with populations from Europe, Africa and the Middle East. According to the traditional view, these archipelagos colonized by the Portuguese in the 15th century were settled mainly by West African slaves, with the addition of a minor fraction of male colonizers from Europe. Although the major proportion of the founding population of São Tomé e Príncipe cluster in haplogroup E3a (84.2%), very common among sub-Saharans, this lineage was observed at a frequency of only 15.9% in Cabo Verde. Haplogroups I, J and R1, characterized of populations of Europe and the Middle East account for more than half of the paternal lineages of Cabo Verdeans (53.5%). These West Eurasian haplogroups are found at a frequency of only 12.5% in the population of São Tomé e Príncipe. Our findings suggest that despite the sub-Saharan genetic background of these archipelagos, a relevant contribution of European paternal lineages is present in nowadays populations indicating that gene flow from multiple sources have been important in the formation of the diversity of the islanders, nevertheless with a different degree of admixture.     

Microgeographic genetic variation of Y chromosome in a population sample of Ravenna's area in the Emilia-Romagna region (North of Italy)

The analysis of the genetic structure of regions with a complex demographic history shed light on the various topographic, linguistic and historical influences which form the present genetic landscape of Europe. In the Emilia-Romagna region (North of Italy) Ravenna is a geographical area with a historical complex background: it was an important seaport on the Mediterranean sea, the capital of the Ostrogothic kingdom of Italy and the seat of the Byzantine governor of Italy. The purpose of this study was to investigate the microgeographic variation of Y chromosome haplotypes of the area of Ravenna by analyzing 17 Y-chromosome short tandem repeats (Y-STRs) in 122 unrelated males. 100% of all haplotypes were different. A comparison with neighbouring Italian as well as with European and Levante root populations was done by AMOVA and visualized by a phylogenetic tree. The two main haplogroups found in this area were R1b and E3b1. The results of the present study add to the data for the forensic databases and can be useful also for anthropological studies.     

Finnish mitochondrial DNA HVS-I and HVS-II population data

We have analyzed the two hypervariable regions HVS-I and HVS-II of 200 Finnish male individuals for forensic purposes. The distribution of the haplotypes within Finland was determined by the geographical knowledge of the donors' maternal ancestors. In our population sample, we identified 135 different mtDNA haplotypes. Different mtDNA sequences were further divided to haplogroups using the EMPOP software. The most common haplogroups were H (40.0%) and U (27.5%). Subgroup U5b, which contains earlier described "Saami motif", consisted majority (65.5%) of the sample in the U haplogroup. Analysis of the mtDNA sequence hypervariable regions I and II showed that the mtDNA diversity within the Finnish population sample was comparable to other European populations and uniformly distributed. This is contrary to the Y-STR "minimal haplotype" diversity, which in Finland is lower than in any of the other European populations studied so far.