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.     

EsD*5 gene frequency in Tuscany (Italy)

The distribution of the human red cell esterase D (EsD) "extended" polymorphism in a population sample from Tuscany (Italy) was studied using agarose gel isoelectric focusing. The estimated gene frequencies were: EsD*1 0.864, EsD*2 0.115, EsD*5 0.021. The EsD*5 allele frequency is very similar to those reported for other European populations. The "extension" of the EsD polymorphism may prove to be useful in paternity testing.     

A distinct Y-STR haplotype for Amelogenin negative males characterized by a large Y(p)11.2 (DYS458-MSY1-AMEL-Y) deletion

The use of STR multiplexes with the incorporated gender marker Amelogenin is common practice in forensic DNA analysis. However, when a known male sample shows a dropout of the Amelogenin Y-allele, the STR system falsely genotypes it as a female. To date, our laboratory has observed 18 such cases: 12 from our Y-STR database and six from casework. A study on 980 male individuals in the Malaysian population using the AmpFlSTR Y-filer has revealed a distinct Y-chromosome haplotype associated with the Amelogenin nulls. Our results showed that whilst the Amelogenin nulls were noticeably absent among the Chinese, both the Indians and Malays exhibited such mutations at 3.2 and 0.6%, respectively. It was also found that the Amelogenin negative individuals predominantly belonged to the J2e lineage, suggesting the possibility of a common ancestor for at least some of these chromosomes. The null frequencies showed concordance with the data published in Chang et al. [Higher failures of Amelogenin sex test in an Indian population group, J. Forensic Sci. 48 (2003) 1309-1313] on a smaller Malaysian population of 338 males which used a Y-STR triplex. In the current study, apart from the absence of the Amelogenin Y-locus, a complete absence of the DYS458 locus in all the nulls was also observed. This study together with the 2003 study has indicated a similar deletion region exists on the Y(p)11.2 band in all the 18 Y-chromosomes. Using bioinformatics, this deletion has been mapped to a region of at least 1.13 Mb on the Y(p)11.2 encompassing the Amelogenin, MSY1 minisatellite and DYS458 locus. Further, the Y-filer haplotypes revealed an additional null at Y-GATA H4 in two of the Indian males presented here.     

Spread and habitat selection of Chrysomya albiceps (Wiedemann) (Diptera Calliphoridae) in Northern Italy: forensic implications

Abstract: Habitat selection exploited by Chrysomya albiceps during its initial spread in Northern Italy was analyzed in relation to landscape structure. The results of two short studies and a case report are here discussed. C. albiceps was not found on experimental pig carcasses in the urban area of Pavia. It was missing in the woody mountains surrounding Lecco, but it was found in the same area, at a lower altitude, within the typical “urban sprawl” landscape. It was then recorded in a natural reserve, among a rich carrion‐fly population. Indications coming from habitat selection suggest that C. albiceps has not yet saturated its potential ecological niche in newly colonized areas of Northern Italy. Factors like temperature, altitude, and interspecific competition can act as limiting factors, affecting habitat selection and distribution in newly colonized areas; the influence of those factors has to be taken into account for forensic purposes.     

Population data of 8 X-STRs in South Italy (Calabria) using the Mentype Argus X-8 PCR Amplification Kit (Biotype)

X-STRs have been proven to be useful in case of deficiency paternity testing and in effective mother-son kinship and father-daughter testing.In the present study, we investigated the distribution of 8 X-STRs loci DXS8378, HPRTB, DXS7423, DXS7132, DXS10134, DXS10074, DXS10101, DXS10135 in an Italian population sample, using the Mentype^® Argus X-8 PCR Amplification Kit (Biotype).Samples for the study were obtained form 200 unrelated healthy individuals belonging to Calabria (South Italy) population since at least 3 generations.     

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.     

Genetic population data of 12 STR loci of the PowerPlex Y system in the state of São Paulo population (Southeast of Brazil)

Allele frequency distributions and population data for 12 Y-chromosomal short tandem repeats (STRs) included in the PowerPlex^®Y Systems (Promega) were obtained for a sample of 200 healthy unrelated males living in São Paulo State (Southeast of Brazil). A total of 192 haplotypes were identified, of which 184 were unique and 8 were found in 2 individuals. The average gene diversity of the 12 Y-STR was 0.6746 and the haplotype diversity was 0.9996. Pairwise analysis confirmed that our population is more similar with the Italy, North Portugal and Spain, being more distant of the Japan.     

Analysis of 13 tetrameric short tandem repeat loci in a population of Tuscany (Central Italy) performed by means of an automated infrared sequencer

Allele frequencies for the 13 STRs of the Combined DNA Index System (CODIS) core were obtained from a sample of 188 unrelated individuals living in the area of Florence, Prato and Pistoia (Tuscany, Central Italy).     

Population data for 8 X-chromosome STR loci in a population sample from Northern Italy and from the Sardinia island

To establish a database for DXS8378, HPRTB, DXS7423, DXS7132, DXS10134, DXS10074, DXS10101, DXS10135 loci in an Italian population sample from Brescia (Northern Italy) and from the Sardinia island, 131 unrelated individuals were typed. DNA was amplified in a multiplex reaction with subsequent automatic detection using capillary electrophoresis. The obtained data give a contribution to the definition of Italian population STR allele frequencies for the eight analysed loci.     

Population data for 12 Y-chromosome STRs in a sample from Brescia (northern Italy)

Twelve Y-chromosome STRs--DYS19, DYS389-I, DYS389-II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438, DYS439--were typed in a population sample (n=104) of unrelated males from Brescia (northern Italy). A total of 91 haplotypes were identified by the 12 Y-STR loci. The haplotype diversity (98.68%), discrimination capacity (87.50%) and gene diversity were calculated.     

Genetic STRs variation in a large population from Tuscany (Italy)

Allele frequencies for 17 STRs, together with some parameters of forensic interest, were estimated in a sample of 835 unrelated individuals born in Tuscany, an Italian region. These data were compared with Italian, Chinese, Kosovo Albanian, Romanian and Tunisian populations, strongly represented in this area. No significant differences in single loci were detected, except for Chinese in comparison with all the other populations.     

Species identification of some common necrophagous flies in Guangdong province, southern China based on the rDNA internal transcribed spacer 2 (ITS2)

Despite the fact that the differences in epidermal ridge density between men and women have been accepted for some time, they have only been thoroughly demonstrated in a small number of populations. The aim of this study is to determine whether such differences exist in a sample of the Spanish population by counting epidermal ridges within three well-defined fingerprint areas. If significant gender differences do exist, then the likelihood of inferring gender from given ridge densities will be explored. The data used in this study was obtained from all 10 fingerprints of 200 individuals of the Spanish Caucasian population (100 males and 100 females) between the ages of 20 and 30. Results show that women tend to have a significantly higher ridge density than men in the distal region of all 10 fingers (radial and ulnar count areas), but not in the proximal region (lower count area). The application of Bayes' theorem, assuming that prior probabilities known for each sex, indicate a threshold for discrimination of sexes.     

Allele frequency distribution of the STR loci HUMTPOX, HUMTH01 and HUMVWA in Asturias (north Spain)

In order to use genetic loci in forensic identity testing, some population data are needed. This paper presents a report of allele frequency data for the loci HUMTH01, HUMTPOX and HUMVWA in a population sample from Northern Spain. No deviation from the Hardy-Weinberg equilibrium was detected in any of the three markers investigated and there was no evidence of association between the alleles of these loci. Statistical analysis was also carried out to obtain some parameters of medicolegal interest and comparative studies were carried out with other populations studied to date for these five loci. The Asturian sample does not differ substantially from other Caucasian and Spanish populations.     

Polymorphism of plasminogen in Tuscany (Italy)

The distribution of PLG phenotypes in the population of Tuscany (Central Italy) has been investigated by means of isoelectric focusing followed by immunofixation of desialyzed sera. In a random sample of 383 unrelated healthy blood donors registered at the Hospital of Pisa, three common phenotypes, PLG A, A-B, and B, and two rare variants were found. The allele frequencies calculated in our study were: PLG*A = 0.6749, PLG*B = 0.3225, and PLG*rare = 0.0026. The theoretical exclusion rate in cases of disputed paternity is 17.42%.     

Haplotypes for 12 Y-chromosomal STR loci in a Korean population (the central region)

Haplotypes and allele frequencies of 12 STR loci included in the PowerPlex Y system (DYS391, DYS389I, DYS439, DYS389II, DYS438, DYS437, DYS19, DYS392, DYS393, DYS390, and DYS385a/b) were obtained from a sample of 569 unrelated individuals living in the central region of Korea. A total of 473 haplotypes were observed in the 569 individuals studied, of which 426 (90.06%) were unique. The overall haplotype diversity for the 12 Y-STR loci was 0.9985, and the discrimination capacity was 0.8313. In DYS439, we found a new intermediate-sized allele that added an A at base 3 upstream from the repeat region's first GATA motif. The allele was named 11 (U3Ains) according to its sequence structure.     

Powerplex® Y 23 System: Molecular characterization of a null allele at locus DYS549

We observed a null allele pattern at locus DYS549 in a male subject from North-East Italy typed with the PowerPlex^® Y 23 System (Promega). To investigate whether this pattern was due to the presence of a microdeletion/mutation in primer binding sites or in the locus target region, the sample was amplified with our designed DYS549 primers obtained from GenBank sequence (GDB: 515022). After amplification, a normal hemizygous genotype at this locus was generated, thus indicating the presence of a point mutation in the binding site of the original primer set of PowerPlex^® Y 23 System (Promega). This was further confirmed by sequence analysis, carried out with the Big Dye Terminator v3.1 Cycle Sequencing kit (Applied Biosystems), according to the manufacturer's instructions. Sequences were run on the ABI Prism 3130 Genetic Analyzer (Applied Biosystems) and analyzed using the Sequencing Analysis v.5.3.1 and the SeqScape v2.6 softwares (Applied Biosystems). Ascertainment of the frequency of null alleles generated from variations at primer binding sites of short tandem repeats loci is of great importance in forensic genetics.     

Belgian canine population and purebred study for forensics by improved mitochondrial DNA sequencing

In canine population studies for forensics, the mitochondrial DNA is profiled by sequencing the two hyper variable regions, HV1 and HV2 of the control region.In a first effort to create a Belgian population database some samples showed partially poor sequence quality. We demonstrated that a nuclear pseudogene was co-amplified with the mtDNA control region. Using a new combination of primers this adverse result was no longer observed and sequencing quality was improved. All former samples with poor sequence data were reanalyzed. Furthermore, the forensic canine population study was extended to 208 breed and mixed dogs. In total, 58 haplotypes were identified, resulting in an exclusion capacity of 0.92. The profile distribution of the Belgian population sample was not significantly different from those observed in population studies of three other countries.In addition to the total population study 107 Belgian registered pedigree dogs of six breeds were profiled. Per breed, the obtained haplotypes were supplemented with those from population and purebred studies. The combined data revealed that some haplotypes were more or less prominent present in particular dog breeds. The statistically significant differences in haplotype distribution between breeds and population sample can have consequences on mtDNA databasing and matching probabilities in forensics.     

Northeast Italy population data using multiplex PCR (HUMCD4, HUMTH01, HUMTPOX, and HUMCSF1P0) loci

Allele and genotype frequencies for four short tandem repeat (STR) loci (HUMCD4, HUMTH01, HUMTPOX, and HUMCSF1P0) were determined in 100 unrelated individuals from Veneto (Northeast Italy). After a multiplex polymerase chain reaction (PCR)-amplification, semi-automatic DNA profiling was performed using an A.L.F.express DNA Sequencer. Conditions were optimized for the PCR co-amplification of these four STR loci and the quadruplex PCR was performed on various forensic DNA samples such as whole blood, blood-stains, teeth, and saliva from Caucasians living in the Northeast Italy. The distribution of the genotype frequencies showed no significant deviation from Hardy-Weinberg expectations in the sampled population. The combined Power of Discrimination (PD) of the quadruplex was 0.9999.     

Y-chromosomal STR haplotype in Toscany (central Italy)

Here we show the Y-haplotype database consisting in the loci DYS19, DYS388, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385, YCAII and DXYS156Y of 107 males living in Toscany (central Italy).     

Y-chromosomal STR haplotype in Toscany (central Italy)

Here we show the Y-haplotype database consisting in the loci DYS19, DYS388, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385, YCAII and DXYS156Y of 107 males living in Toscany (central Italy).