Population: One hundred thirty male individuals, strictly selected for typical regional surnames and for the geographical origin based on their place of birth and that of relatives two generations back, were submitted to the analysis. Males with non-typical region surnames were omitted. Personal inquiries were made to each individual in order to avoid close kinship. Appropriate informed consent was obtained from all participants in this study. The geographical location of the population is shown in SupplementaryFig. 1.
Modena is a city and municipality located on the south side of the Po valley, in the Emilia-Romagna region of Northern Italy. The estimated population of Modena is close to 200,000 residents, divided among 75,000 families. It is an ancient town, with the University founded in 1175 and now best known as “the capital of engines” because of the factories of the famous Italian sports car makers Ferrari, Lamborghini, Maserati, Pagani, and more.
Briefly, the territory around Modena (Roman Mutina) was inhabited by the Villanovans in the Iron Age, and later by Ligurian tribes, Etruscans, and the Gallic Boii (Roman name of an ancient celtic tribe). Although the exact date of its foundation is unknown, it was already in existence in the 3rd century BC. The city was likely abandoned after Hannibal's invasion of Italy, nonetheless it was rebuilt and quickly became an important centre in Cisalpine Gaul for its strategic importance and because it was on a main crossroads between north and south Italy. The Este family controlled the city from the Middle to Modern Age, and in 1859 the representative of Modena declared their territory part of the Kingdom of Italy, after a short time of Austrian domination.
Extraction: DNA was purified from blood and saliva samples using either the Chelex method [1] or by QIAGEN micro Kit extraction (Qiagen, Chatsworth, CA) according to manufacturer's instructions.
PCR: The kit AmpFLSTR Y-Filer was used for amplification according to manufacturers (Applied Biosystem, Foster City, CA).
A total of 15 binary markers in two multiplex PCR (MY1 and MY2) were typed for all the samples according to Onofri et al. [2] (with lower minor modifications). Supplementary four SNPs from Brion et al. [3] were also typed (M78, M70, P25, SRY10831.2).
Typing: Typing of Y-STRs was achieved using an ABI 3130 Genetic Analyzer (Applied Biosystems) by comparison to reference sequenced ladders provided by the manufacturers. Samples were analyzed by GeneMapper ID v. 3.2 software (Applied Biosystems).
Y-SNPs typing were carried out as described by the original papers [2], [3].
Results: See Supplementary Tables S1–S6.
Quality control: In house proficiency testing with control DNA, proficiency testing of the GeFI-ISFG working group in 2006, quality control test with blind haplotyping of five DNA samples with Y-Filer for Y-STR haplotype reference database (http://www.yhrd.org).
Analysis of data: Haplotype and haplogroup frequencies were estimated by gene counting. Gene diversity and haplotype diversity were calculated according to Nei [4] using Arlequin software ver 3.01 [5]. AMOVA analysis and pairwise genetic distances (Rst, for STR-haplotypes and Fst for SNP-haplogroups) were also performed using the Arlequin package.
Access to the data: The complete dataset is available upon request to the corresponding author via e-mail at gianmarco.ferri@unimore.it:
Other remarks: The neutral genetic diversity observed today can be a mixture of ancient and past recent population movements that can be recognized by MSY analysis of two kind of markers with different mutation rates [6], [7]. The combined use of SNPs and STRs, also called lineages, is indeed essential to reconstruct the genetic history of the populations.
Nevertheless, in forensic genetics, Y-chromosome variations have been validated and found to be a valuable tool in caseworks applications. The need for information about the distribution of Y-STRs haplotypes and Y-SNPs haplogroups in selected population samples leads to the production of hundreds of population data useful in the forensic field, but up to now, only few papers typed both markers on the same samples. Complementing haplotypes data with binary markers will help to better understand the prediction of ethnic or geographic origin of unknown samples, useful when no suspect is available.
To investigate the genetic legacy and population substructure for Modena, we analyzed MSY diversity using seventeen Y-STRs and nineteen Y-SNPs in 130 selected males for typical regional surnames and for the pedigree.
In addition, we compared the lineages data between Modena and neighbouring populations, including two populations of the same region but located near the Adriatic sea, Rimini and Val Marecchia [8], [9], [10], [11], [12], [13], [14]. Populations were compared for differences in the distribution of haplotype frequencies using Rst and for differences of haplogroup frequencies using Fst, both estimated from Analysis of Molecular Variance.
The relative frequencies of Y-filer alleles are shown in Table S1 with respective loci diversity values. In Table S2 the list of haplotypes and haplogroups identified in Modena sample.
DYS385 multi copy locus and DYS458 locus emerged for the highest diversity values that exceeding of 80 and 70%, respectively, while the lowest were observed at DYS393locus with value under the 50%.
In 130 subjects, 129 haplotypes were observed, 128 of which were unique, but if we consider only eleven loci a total of 118 haplotypes were found (Tables S2 and S3). We also analyzed the sample by considering the minimal YHRD haplotype (with or without DYS385) in order to evaluate the diversity values of the Y-STR core set [15]. A total of 88 and 108 haplotypes were found, respectively without and with the DYS385. The most frequent minimal haplotype with and without the DYS385 was found in 8 and 19 Modena males in that order (14-13-29-24-11-13-13, 11-14). These haplotypes recurred as the most frequent in several papers [8], [9], [16], and were found respectively in about 2.4 and 4.4% of European males (YHRD). This haplotype is also frequent in the whole world, with 1955 matches on 54,863 samples or by adding the DYS385, with 1066 matches on 53,075 samples.
The database search showed that this haplotype is also present in the Asian metapopulation (12 and 3 matches, in Africa population sample with 53 and 33 matches, in Latin America with 482 and 278 matches, and North America with 193 and 96 matches respectively if DYS385 was added). Curiously, this frequent minimal haplotype was also found one time in the newly added Artic population (n
=70) (www.yhrd.org). No. of haplotypes, gene diversity, mean number of pairwise differences and average gene diversity over loci for minimal YHRD haplotype, extended haplotype (plus DYS437) and Y-Filer are shown in Table S3 where the specific informativeness of DYS385 multi-copy locus emerged, resulting in a high level of differentiation.
A total number of nine Y-haplogroups were found with a haplogroup diversity of 0.5252±0.0505. Relative haplogroups frequencies are shown in Table S4, where R1b was found as the most frequent, with a frequency of 67.7%.
In order to detect possible genetic structure among populations, or among groups divided for geographic area, an analysis of the molecular variance was performed using the Arlequin package ver 3.01 [5].
No significant level of genetic structure was found for both kind of markers (SNPs and 11 STRs or 17 STRs haplotype composition) neither considering all populations as a single group nor grouping populations according to geographic location (Table S5).
We remark just a slight increase of values among groups if the three populations of Emilia-Romagna were divided considering Modena in the Northern area (as always, for geographic affiliation) and Rimini and Val Marecchia (south of the same region, near the sea) were grouped with population samples from central Italy. The level of differentiation among groups rises from −0.04 and 1.89% to 1.54 and 2.89%, respectively, for 11 STRs haplotype and SNPs haplogroup composition (Table S5). In this case the population movement could have occurred by the sea, avoiding the Apennine mountains, a low natural barrier from North to Central-Southern Italy.
The analysis shows that the main source of variation, as usually observed in humans, is within the population, even if a little percentage of differences resulted among Modena and the Adriatic samples by haplogroups’ frequencies comparisons. Table S6 shows the haplogroups frequencies analyzed in different Italian samples with a characteristic distribution of the main R1 (xR1a) haplogroup. The former was the main type in the North-North-West, decreasing in frequency moving South. The E3b seems to have an inverse similar distribution, even if the frequency differences and the gradient were less marked [8], [9], [10], [11], [12].
The genetic structure of a population is a mosaic of past and recent migration patterns that can be useful in forensic genetic to infer the provenience of the subject implicated in criminal caseworks. Detailed information about joint distribution of MSY polymorphisms on selected population samples can provide useful assistance to forensic scientists.
This paper follows the guidelines for publication of population data requested by the journal [17].
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