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The Y-chromosomal haplotype and haplogroup distribution of modern Switzerland still reflects the alpine divide as a geographical barrier for human migration

Open AccessPublished:June 21, 2020DOI:https://doi.org/10.1016/j.fsigen.2020.102345

      Highlights

      • This is the first detailed study on human Y-chromosomes from Switzerland.
      • 606 Swiss male individuals were typed for 27 Y-STRs and 34 Y-SNPs.
      • Significant intra-national differences in haplogroup distribution were revealed.
      • DYS533 allele 12.1 appears to be associated with haplogroup I2 (xM223, xP37.2).
      • Concordance between YFilerPlus® and PowerPlex® Y23 was checked.

      Abstract

      A sample of 606 Swiss individuals has been characterized for 27 Y-STR and 34 Y-SNPs, defining major European haplogroups. For the first time, a subsample from the southernmost part of Switzerland, the Italian speaking canton Ticino, has been included. The data reveals significant intra-national differences in the distribution of haplogroups R1b-U106, R1b-U152, I1 and J2a north and south of the alpine divide, with R1b-U152 being the most frequent haplogroup among all Swiss subpopulations, reaching 26 % in average and 53 % in the Ticino sample. In addition, a high percentage of haplogroup E1b1b-M35 in Eastern Switzerland corresponds well with data reported from Western Austria. In general, we detected a low level of differentiation between the subgroups north of the alpine divide. The dataset also revealed a variety of microvariants. Some of them were previously known to be associated with particular haplogroups. However, we discovered one microvariant in DYS533 that seems to be closely associated with haplogroup I2-P215 (xM223). This association had not yet been reported to date. The concordance study with two STR-kits suggests that the DYS533 microvariant is due to an InDel in the flanking regions of the marker. One individual carried a large deletion, frequently detected in people of East Asian ancestry, encompassing the amelogenin locus. To our knowledge, this is the first time that such a deletion has been observed within European haplogroup R1b-U152. This is the first comprehensive Y chromosomal dataset for Switzerland, demonstrating significant population substructure due to an intra-national geographical barrier.

      Keywords

      1. Introduction

      The utility of Y chromosome population genetics is twofold: First of all, Y-STR profiles are of tremendous value for forensic investigations. They are frequently used to separately interpret male components in biological traces recovered from victims of sexual abuse, where classical autosomal DNA profiles are not promising, because of excess female cell material. In addition, Y-chromosomal data from a crime scene can also be used to trace down a possible perpetrator by family links [
      • Kayser M.
      Forensic use of Y-chromosome DNA: a general overview.
      ]. For proper interpretation of DNA from crime scenes, numerous population genetic studies and a large and reliable database are necessary. Such a database exists with the Y Chromosome Haplotype Reference Database (YHRD) [
      • Willuweit S.
      • Roewer L.
      The new Y chromosome haplotype reference database.
      ], however needing continuous contributions. Second, because of the lack of recombination, the genetic data on the Y chromosome can be used to trace back historical events of human migration. The Y chromosome as lineage marker has contributed a good share to the revelation of the mechanisms underlying the geographical structuring of present day human genetic diversity [
      • Semino O.
      • Passarino G.
      • Oefner P.J.
      • Lin A.A.
      • Arbuzova S.
      • Beckman L.E.
      • De Benedictis G.
      • Francalacci P.
      • Kouvatsi A.
      • Limborska S.
      • Marcikiae M.
      • Mika A.
      • Mika B.
      • Primorac D.
      • Santachiara-Benerecetti A.S.
      • Cavalli-Sforza L.L.
      • Underhill P.A.
      The genetic legacy of Paleolithic Homo sapiens sapiens in extant Europeans: a Y chromosome perspective.
      ,
      • Underhill P.A.
      • Kivisild T.
      Use of y chromosome and mitochondrial DNA population structure in tracing human migrations.
      ,
      • Brandt G.
      • Szécsényi-Nagy A.
      • Roth C.
      • Alt K.W.
      • Haak W.
      Human paleogenetics of Europe – the known knowns and the known unknowns.
      ].
      With the present paper we would like to contribute to both fields of Y chromosome application. We characterized 606 Swiss male individuals for 27 Y-STRs, frequently used in forensic genetics, using two different multiplex PCR kits, YFiler Plus® and PowerPlex Y23®. Forensically relevant parameters were measured and the data was compared to data from neighboring countries. Furthermore, SNaPshot® assays, comprising 34 SNPs in total, were conducted for all samples to determine major European Y haplogroups. We compared the haplogroup distributions from different regional subpopulations among each other and revealed the associations of Y-STR microvariants with their respective haplogroup.
      Switzerland has for longtime been a missing piece in the European Y chromosome puzzle. With the present study we present the first comprehensive and systematically collected Y chromosomal population data for the three principal linguistic groups in Switzerland.

      2. Materials and methods

      2.1 Sample collection

      Samples from 606 male Swiss individuals were characterized for the present study. 435 individuals were German speaking, 118 French speaking and 51 Italian speaking. One person reported both, Italian and German as mother tongues, one person’s mother tongue was Romansh. Sizes of the defined regional subgroups were the following: WS (Western Switzerland) = 129, BE (canton of Bern) = 130, NW (Northwestern Switzerland) = 108, CS (Central Switzerland) = 79, TI (canton of Ticino) = 51, SG (canton of St. Gallen) = 109. For further details concerning the sampling procedure, check [
      • Zieger M.
      • Utz S.
      A "forensic biobank" to establish comprehensive genetic frequency data for Switzerland.
      ].

      2.2 STR typing

      For every sample, 1 μL of whole blood was extracted using the AutoMateExpress™ device with the PrepFiler Express™ kit (both ThermoFisher, USA). DNA extractions were not quantified by default. 0.5 μL of DNA extract was used in multiplex PCR. Quantification was only done for samples not leading to an interpretable profile and DNA input for multiplex PCR was adapted accordingly. We used a 7500 RT PCR System with the Quantifiler® HP Kit (both ThermoFisher, USA) for qPCR. Multiplex PCR was performed in a reduced reaction volume of 12.5 μL for both kits used in this study, PowerPlex® Y23 (Promega, USA) and YFiler™ Plus (ThermoFisher, USA). Capillary electrophoresis was run with a 3500xl genetic analyzer (ThermoFisher, USA) and data interpretation was carried out with Genemapper® ID-X, v1.4 (Thermo Fisher, US). All peaks above 300rfu were considered as true alleles.

      2.3 Haplogroup prediction

      Haplogroups were predicted to facilitate the selection of primer panels for subsequent SNaPshot® analysis. Next to Whit Atheys haplogroup predictor (HAPEST) [
      • Athey W.T.
      Haplogroup prediction from Y-STR values using an allele-frequency approach.
      ,
      • Athey W.T.
      Haplogroup prediction from Y-STR values using a Bayesian-allele-frequency approach.
      ] we used the information on Y-STR haplotype distributions within haplogroups provided by the YHRD under the feature “Ancestry information”. This program is not a prediction tool but assigns the 24,316 SNP-typed haplotypes within the YHRD [
      • Willuweit S.
      • Roewer L.
      The new Y chromosome haplotype reference database.
      ] (as of Release 61, June 24, 2019) to branches of the phylogenetic tree (haplogroups). This allows a prediction of the most probable haplogroup assignment of haplotypes by comparison of the new, yet unclassified STR haplotypes with the registered SNP-typed haplotypes from the YHRD. A reduction of loci in the panel increases the haplotype count in the database and the chance to receive a haplogroup frequency. The reduction of the haplotype however, may increase the chance to find haplotypes which are not “identical by descent” (IBD) but “identical by state” (IBS) and may therefore apparently fall in different branches of the phylogenetic tree. We followed a hierarchical approach by checking YHRD ancestry information in the following order, based on: YFiler haplotypes, minimal haplotypes, YFiler one-step neighbors and minimal one-step neighbors. To assess the overall prediction accuracy of the two approaches, the most probable predicted haplogroup was compared to the haplogroup revealed by SNP analysis. All predicted haplogroups not in conflict with a more specific haplogroup determined by SNP analysis, were counted as correct. If two different haplogroups were predicted equally probable and one of them was confirmed as correct, the prediction was counted as neither wrong nor right. If the clade predicted is less specific (e.g. J) than the clade determined (e.g. J1), this was counted as neither wrong nor right. According to the SNP typing, the following clades were defined to address the prediction accuracy for this Western European sample: D, E, G, I1, I2, J1, J2, R1b, R1a, R2, O, N, KLT (no Q, R, N, O), F (no G, I, J, KLT).

      2.4 SNP typing

      33 different haplogroup-defining SNPs and one recurrent SNP [
      • Niederstatter H.
      • Berger B.
      • Erhart D.
      • Willuweit S.
      • Geppert M.
      • Gassner C.
      • Schennach H.
      • Parson W.
      • Roewer L.
      Multiple recurrent mutations at four human Y-chromosomal single nucleotide polymorphism sites in a 37 bp sequence tract on the ARSDP1 pseudogene.
      ] were analyzed by SNaPshot® assay as described previously [
      • Geppert M.
      • Roewer L.
      SNaPshot® minisequencing analysis of multiple ancestry-informative Y-SNPs using capillary electrophoresis.
      ,
      • Haas C.
      • Shved N.
      • Ruhli F.J.
      • Papageorgopoulou C.
      • Purps J.
      • Geppert M.
      • Willuweit S.
      • Roewer L.
      • Krawczak M.
      Y-chromosomal analysis identifies the skeletal remains of Swiss national hero Jorg Jenatsch (1596–1639).
      ,
      • Nunez C.
      • Geppert M.
      • Baeta M.
      • Roewer L.
      • Martinez-Jarreta B.
      Y chromosome haplogroup diversity in a Mestizo population of Nicaragua.
      ], always accompanied by a blank negative control and 2800 M DNA as a positive control. Samples were run on an Applied Biosystems® 3130xl Genetic Analyzer with 36-cm capillaries and POP 4 polymer (Thermo Fisher, USA). Data interpretation was carried out with Genemapper® ID-X, v1.4 (Thermo Fisher, USA). Primers used in this study are listed in Supplementary Table 1. Supplementary Fig. 1 shows a schematic tree of the Y-SNPs analyzed in the present study. SNP information was gathered from YHRD [
      • Willuweit S.
      • Roewer L.
      The new Y chromosome haplotype reference database.
      ] and Phylotree Y [
      • van Oven M.
      • Van Geystelen A.
      • Kayser M.
      • Decorte R.
      • Larmuseau M.H.
      Seeing the wood for the trees: a minimal reference phylogeny for the human Y chromosome.
      ].

      2.5 Data analysis

      Haplotype diversity was calculated using Excel as n(1-∑pi2)/(n-1), with pi being the ith haplotype and n the total number of samples [
      • Nei M.
      • Tajima F.
      DNA polymorphism detectable by restriction endonucleases.
      ]. Haplotype frequencies, based on the YFiler marker subset, where estimated with the Discrete Laplace (DL) method [
      • Andersen M.M.
      • Eriksen P.S.
      • Morling N.
      The discrete Laplace exponential family and estimation of Y-STR haplotype frequencies.
      ] for the metapopulation "Western European" (YHRD release R61), as recommended for forensic case work [
      • Willuweit S.
      • Anslinger K.
      • Bäßler G.
      • Eckert M.
      • Fimmers R.
      • Hohoff C.
      • Kraft M.
      • Leuker C.
      • Molsberger G.
      • Pich U.
      • Razbin S.
      • Rothämel T.
      • Schneider H.
      • Schneider P.M.
      • Templin M.
      • Vennemann M.
      • Wächter A.
      • Weirich V.
      • Zierdt H.
      • Roewer L.
      Gemeinsame Empfehlungen der Projektgruppe „Biostatistische DNA-Berechnungen “und der Spurenkommission zur biostatistischen Bewertung von Y‑chromosomalen DNA-Befunden.
      ]. For 11 samples, no DL value could be estimated, due to duplicated, intermediate or null alleles in the YFiler marker subset. Interregional FST values were calculated using STRAF [
      • Gouy A.
      • Zieger M.
      STRAF-A convenient online tool for STR data evaluation in forensic genetics.
      ], excluding the markers DYS385a/b and DYF3871S1. For analysis with STRAF, DYS389I has been subtracted from DYS389II and intermediate or duplicated alleles were set as null. Principal component analysis of haplogroup I2 was also done with STRAF. The 12.1 allele in DYS533 was not used. Instead we used allele 12, as detected with PowerPlex® Y23. The multiple dimensional scaling (MDS) plot for national datasets was generated by the respective YHRD tool [
      • Willuweit S.
      • Roewer L.
      The new Y chromosome haplotype reference database.
      ], based on RST values for the PowerPlex® Y23 panel and 10,000 permutations. Information about the composition of the different national datasets can be retrieved from https://yhrd.org/pages/resources/national_databases. Sizes of PPY23 datasets from YHRD release 61 were the following: Austria (259 haplotypes), Belgium (728), Denmark (185), Germany (2821), Hungary (591), Ireland (823), Italy (1939), Spain (822). 17 haplotypes were removed for AMOVA and MDS, due to duplicated, triplicated, intermediate or null alleles. Fisher’s exact test for significance of the differences in haplogroup distribution was calculated using R [
      • R Core Team
      R: A Language and Environment for Statistical Computing.
      ]. Significance level was set to p < 0.05. Geographical representations were built by Heatmapper [
      • Babicki S.
      • Arndt D.
      • Marcu A.
      • Liang Y.
      • Grant J.R.
      • Maciejewski A.
      • Wishart D.S.
      Heatmapper: web-enabled heat mapping for all.
      ], using a Gaussian radius multiplier of 0.4 and 13 shades. The dataset was submitted to YHRD for quality control, as required by the ISFG guidelines [
      • Gusmao L.
      • Butler J.M.
      • Linacre A.
      • Parson W.
      • Roewer L.
      • Schneider P.M.
      • Carracedo A.
      Revised guidelines for the publication of genetic population data.
      ] and given the six accession numbers YA004658 to YA004663. The haplotypes are included in YHRD release R62. For all haplotypes with discordances between the two kits (e.g. 12.1 and 12 in DYS533), the full allele and not the intermediate allele has been registered on YHRD. The full dataset can be requested from the corresponding author of this paper, for academic research purpose only.

      3. Results

      3.1 STR haplotype diversity and DL frequency estimation results

      The haplotype diversity of the 606 Swiss male individuals for different marker subsets is shown in Table 1. Haplotype diversity was identical for the YFilerPlus® subset and the maximal marker set, additionally including the two markers DYS549 and DYS643 from PowerPlex Y23®. The distribution of haplotype frequencies, estimated with the Discrete Laplace method [
      • Andersen M.M.
      • Eriksen P.S.
      • Morling N.
      The discrete Laplace exponential family and estimation of Y-STR haplotype frequencies.
      ] in the YHRD metapopulation "Western European" based on YFiler haplotypes are depicted in the boxplot in Fig. 1a. The lowest frequency for this metapopulation has been capped to 1 in 73,136,090 haplotypes [
      • Roewer L.
      Y-chromosome short tandem repeats in forensics—sexing, profiling, and matching male DNA.
      ,
      • Roewer L.
      • Willuweit S.
      Y‑Chromosomale STR-analyse in der forensischen praxis.
      ]. The most common haplotype was estimated to 1 in 198. The median frequency is at 1 in 563,526. Fig. 1b illustrates the distribution of the ratios of the estimated haplotype frequencies in the global YHRD population and in the YHRD metapopulation "Western European". For explanation: a ratio of 6 means that the respective haplotype is estimated 6 times more frequent in the "Western European" metapopulation than in the global population. For 90 % of the haplotypes, this ratio is ≥1. For 95 % of the haplotypes the ratio is ≥0.5 and only 7 haplotypes (1.2 %) have a ratio less than 0.1, meaning that they are estimated more than 10 times less frequent in the "Western European" metapopulation than in the global population.
      Table 1Haplotype diversity for different marker sets.
      YFilerPlus / MaximalPowerPlex Y23YFiler
      Same haplotypes observed3 x double9 x double26 x double
      1 x triple9 x triple
      1 x quadruple
      Haplotype diversity0.9999510.9997870.999018
      Fig. 1
      Fig. 1A) Haplotype frequency distribution as estimated with DL for the YFiler marker set, displayed as reciprocal values. The median frequency is at 1 in 563‘526. B) Distribution of the ratios (pWE / pG) between the estimated haplotype frequency in the “Western European” metapopulation (pWE) and the estimated haplotype frequency in the global population (pG).
      Pairwise FST calculations based on the maximal STR marker set (YFilerPlus® + PowerPlex Y23®) show little intra-national differentiation among the 6 regional subpopulations (Table 2). In line with our previous observations [
      • Zieger M.
      • Utz S.
      A "forensic biobank" to establish comprehensive genetic frequency data for Switzerland.
      ], all subpopulations show the largest FST values in pairwise comparison with the southernmost Swiss canton Ticino subpopulation, with the largest difference being the one between Northwestern Switzerland and Ticino. We also compared our dataset to datasets from other countries, using the AMOVA tool from YHRD [
      • Willuweit S.
      • Roewer L.
      The new Y chromosome haplotype reference database.
      ]. The multiple dimensional scaling plot in Fig. 2a localizes the Swiss data between the datasets from neighboring countries. For one of the direct neighboring countries, no data was included, since there was no French dataset for PowerPlex® Y23 available on the YHRD. If we divide the sample into language subgroups, the German speaking subpopulation locates even closer to the Austrian sample, whereas the French speaking subpopulation is somewhat closer to the samples from Belgium and Spain. Surprisingly, the Italian speaking sample co-localizes with the sample from Spain and is significantly different from the Italian sample, registered on YHRD. As a control, we also checked the genetic distance of our regional subsamples to the four other Swiss YFiler datasets registered on YHRD. They show all a high degree of similarity, except for the sample from Basel that exhibits extremely large RST values towards all the other subpopulations, ranging from 0.084 to 0.173, even towards the sample from the same region of Northwestern Switzerland (0.101). All RST values and corresponding p-values generated with the YHRD AMOVA tool are available in Supplementary Table 2.
      Table 2Pairwise FST values among the different regional subgroups. NW = Northwestern Switzerland; CS = Central Switzerland; BE = Bern area; TI = Ticino; WS = Western Switzerland; SG = St. Gallen.
      NWCSBETIWSSG
      SG0.00680.00630.00640.01090.0049
      WS0.00430.00320.00360.0077
      TI0.01410.01020.0085
      BE0.00500.0044
      CS0.0063
      NW
      Fig. 2
      Fig. 2Multiple dimensional scaling blot based on RST values, generated for PowerPlex® Y23 datasets with the AMOVA tool from YHRD. A) Comparison of the whole sample ("Switzerland") to other national European datasets, registered on YHRD. B) Comparison of Swiss ("CH") subpopulations based on mother tongue to national datasets from neighboring countries. Spain was included as the next western country in mainland Europe, since no French sample for PowerPlex® Y23 was available on the YHRD. The data points for Spain and the Italian speaking Swiss subsample collapse into one.

      3.2 Kit concordance, dropouts, multi-allelic patterns and intermediate alleles

      All discordances between the two multiplex kits, deletions, copy number variants and intermediate alleles are listed in Table 3. The table also lists the haplogroup of the respective sample(s). Out of the 606 samples, 32 showed at least one particularity, leading to an event rate of 5.3 %. The two multiplex kits PowerPlex® Y23 and YFilerPlus® share 20 markers. Discordant allele values were detected for 8 samples, leading to a rate of discordant profiles of 1.3 %.
      Table 3Discordances, dropouts, multi-allelic patterns and intermediate alleles. Two samples, marked with */** are concerned by two events. R1b-M269 is equivalent to R1b-M269 (xU152, xU106), I2-P215 is equivalent to I2-P215 (xM223, xP37.2), with P37.2 being a recurrent mutation.
      YfilerPlusPowerPlex Y23Haplogroup
      Discordances
      DYS533 (5x)12.112I2-P215
      DYS4812525.1R2-M124
      DYS3921110.2G-M201
      Dropout, kit specific
      DYS390*22G-M201
      Dropout, both kits
      DYS448*G-M201
      Large deletionAMEL, DYS576, DYS627, DYS458, DYS570, DYS449, DYS481R1b-U152
      Copy number variants
      DYF387S1 (5x)3 allelesI1-M253, J2a-M410, R1a-M198, R1b-M269, R1b-U152
      DYS19 (5x)2 alleles (all 14/15)3x R1b M269, 2x G-M201
      DYS385a/b3 alleles (signal intensity 1:1:2)E1b1b-M35
      Intermediate alleles
      DYS385a/b (5x)12.2 (4x), 13.2R1b-U106; 13.2 = I1-M253
      DYS458 (3x)17.2, 18.2** (2x)J1-M267
      DYS627 (3x)20.1, 21.1, 22.1R1b-M269; 20.1 = R1b-U152
      DYS389II31.2I2-M223
      DYS44819.2**J1-M267
      The most frequent discordance is an intermediate allele 12.1 in DYS533, only detected with the YFilerPlus® kit. In the present dataset, this intermediate allele occurs exclusively in an I2-P215 background. In addition, all five samples show the ancestral version of M223 and the ancestral version of the recurrent SNP P37.2 [
      • Niederstatter H.
      • Berger B.
      • Erhart D.
      • Willuweit S.
      • Geppert M.
      • Gassner C.
      • Schennach H.
      • Parson W.
      • Roewer L.
      Multiple recurrent mutations at four human Y-chromosomal single nucleotide polymorphism sites in a 37 bp sequence tract on the ARSDP1 pseudogene.
      ]. All other individuals (n = 35) typed as I2-P215 show either a derived version of P37.2 or of M223. Principal component analysis of all samples belonging to haplogroup I2 shows a distinct cluster of those 5 samples, when the third component is included (Fig. 3).
      Fig. 3
      Fig. 3Principle component analysis of the 40 samples belonging to haplogroup I2, showing all correlations between the three first components (see titles on axes). The five samples with the 12.1 allele in DYS533, positive for I2-P215 but ancestral for M223 and the recurrent SNP P37.2, form a distinct cluster (orange), separate from the samples with derived SNPs for M223 (blue) and P37.2 (brown) (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article).
      One of the samples carries a larger chromosomal deletion, as shown by the simultaneous dropout of the six neighboring loci DYS576, DYS627, DYS458, DYS570, DYS449, DYS481 and Amelogenin, all located on the short arm of the Y chromosome.

      3.3 Success rates of haplogroup predictions

      To specifically target our SNaPshot analysis for Y haplogroups, we first predicted the haplogroups by two approaches: a search for the same or similar haplotypes, already typed for SNPs, on the YHRD [
      • Willuweit S.
      • Roewer L.
      The new Y chromosome haplotype reference database.
      ], and a classical prediction using With Athey’s haplogroup predictor [
      • Athey W.T.
      Haplogroup prediction from Y-STR values using an allele-frequency approach.
      ,
      • Athey W.T.
      Haplogroup prediction from Y-STR values using a Bayesian-allele-frequency approach.
      ]. Subsequent comparison with the SNaPshot data enables us to make a statement on the accuracies of the predictions. Overall the haplogroup predictions were quite reliable, as can be seen from Table 4. Whereas Whit Athey’s gives a prediction for every haplotype entered, the “prediction rate” based on YHRD data depends on whether any similar haplotype has already been registered and SNP typed or not. It has to be mentioned that all predictions concordant between YHRD and Whit Athey’s proofed to be right. Also, no wrong haplotypes were assigned when ancestry information could be retrieved from YHRD for the YFiler dataset. However, ancestry information from the YFiler dataset on YHRD could be retrieved for less than 50 % of the searched samples, due to a lack of registered SNP data.
      Table 4Haplogroup prediction rates and prediction accuracies for Whit Athey’s haplogroup predictor and the different YHRD ancestry information queries. Neighbors are 1-step neighbors, differing from the haplotype used for the query in one repeat, in one marker. The prediction rate is the percentage of all samples for which a prediction (meaning a retrieval of ancestry information) was possible. This rate is restricted by the available SNP data for comparison on the YHRD.
      hprg.comYHRD ancestry (YFiler)YHRD ancestry (minimal)YHRD ancestry (neighbors YFiler)YHRD ancestry (neighbors minimal)
      prediction rate100 %17.3 %68.2 %42.4 %89.4 %
      right95.4 %94.3 %96.6 %95.3 %95.6 %
      wrong4.6 %1.9 %3.5 %
      neutral5.7 %1.5 %4.7 %0.9 %

      3.4 Regional haplogroup distribution

      For the comparison of the haplogroup distributions among different regional subgroups, the regions defined in our previous work [
      • Zieger M.
      • Utz S.
      A "forensic biobank" to establish comprehensive genetic frequency data for Switzerland.
      ] were maintained. All haplogroup proportions are listed in Table 5. We detected five significant regional differences in haplogroup spread. Whereas the haplogroups I1-M253 and R1b-U106 are more or less evenly distributed north of the Alps, they are almost absent from the Ticino sample. In return, haplogroups J2a-M410 and R1b-U152 are far more abundant in the Ticino sample than in the rest of the country. Furthermore, we detected a significant enrichment of haplogroup E1b1b-M35 in the easternmost sample from St. Gallen. We could also detect a slightly larger proportion of E1b1b-M35 in the sample from Western Switzerland. However, this observation proofed not to be significant.
      Table 5Y Haplogroup distribution among regional subgroups (values given in %). Columns not summing up to 100 % are due to rounding errors. Significant differences in the Ticino and St. Gallen sample compared to the distribution over the rest of Switzerland are *p < 0.05, **p < 0.01 and ***p < 0.0001 (Fisher’s exact test). Abbreviations and absolute number of samples from the respective region: NW = Northwestern Switzerland (n=108); CS = Central Switzerland (n=79); WS = Western Switzerland (n=129); SG = St. Gallen (Eastern Switzerland; n=109); BE = Bern area (n=130); TI = Ticino (n=51); Hg (tot) = percentage of the respective haplogroup in the total Swiss sample of 606 individuals.
      NWCSWSSGBETIHg (tot)
      E1b1b (M35)44913**467
      G (M201)129661249
      I1 (M253)1391012112*10
      I2 (M223)753444
      I2 (P215)4421222
      J1 (M267)1110
      J2a (M410)114610*3
      J2b (M102)4331343
      N (M46)10
      O (M175)10
      QR (M45)20
      R1a (M198)7454424
      R1b (U106)12151213172*13
      R1b (U152)192924282053***26
      R1b (U198)110
      R1b (M269)14141913181616
      R1b (M343)10
      R2 (M124)10
      KLT (M9)21121
      F (M213)10

      4. Discussion

      4.1 Population genetic parameters

      As expected, we observe a good correspondence of the dataset with the metapopulation “Western European”, what can be concluded from the distribution of the estimated haplotype frequencies. The fact that 90 % of the haplotypes are predicted to be more frequent in the Western European than in the global panel, can be seen as a successful quality control of the sampling scheme. The population sample also fits well in the context of the neighboring countries and shows no noteworthy differences compared to the Swiss datasets previously registered on the YHRD. The only exception concerns the sample from Basel. However, since the Basel sample on YHRD shows large genetic differences with all other Swiss samples, including our sample collected from the same region, we assume some kind of sampling error for this regional subsample and we would like to suggest that it should be used with caution for any interpretation and comparison. The fact that the Italian speaking subsample co-locates rather with the sample from Spain than with the sample from Italy (Fig. 2), might be attributed to the higher overall percentage of haplogroup R1b in Spain than in Italy [
      • Cruciani F.
      • Trombetta B.
      • Antonelli C.
      • Pascone R.
      • Valesini G.
      • Scalzi V.
      • Vona G.
      • Melegh B.
      • Zagradisnik B.
      • Assum G.
      • Efremov G.D.
      • Sellitto D.
      • Scozzari R.
      Strong intra- and inter-continental differentiation revealed by Y chromosome SNPs M269, U106 and U152.
      ]. The fraction of R1b in the Spanish population corresponds better to the 70 % R1b in the Ticino sample.

      4.2 Microvariants and concordance

      We observed a variety of intermediate alleles among the 606 individuals (Table 3). Some of the detected variant alleles have previously been described as being associated with particular haplogroups. The .2 alleles in DYS458 are usually associated with haplogroup J1 [
      • Iacovacci G.
      • D’Atanasio E.
      • Marini O.
      • Coppa A.
      • Sellitto D.
      • Trombetta B.
      • Berti A.
      • Cruciani F.
      Forensic data and microvariant sequence characterization of 27 Y-STR loci analyzed in four Eastern African countries.
      ,
      • Serin A.
      • Canan H.
      • Alper B.
      • Kotan D.
      Molecular structure and genealogical characterization of the DYS458.2 allelic variants founded in Turkey population samples.
      ], as it is the case for our Swiss population sample. The kit-dependent variant allele 25.1 in DYS481, being caused by a SNP in the flanking region of the marker, has been shown to be associated with haplogroup R2 [
      • Lee E.Y.
      • Shin K.-J.
      • Rakha A.
      • Sim J.E.
      • Park M.J.
      • Kim N.Y.
      • Yang W.I.
      • Lee H.Y.
      Analysis of 22 Y chromosomal STR haplotypes and Y haplogroup distribution in Pathans of Pakistan.
      ,
      • Lee E.Y.
      • Lee H.Y.
      • Shin K.-J.
      Off-ladder alleles due to a single nucleotide polymorphism in the flanking region at DYS481 detected by the PowerPlex® Y23 System.
      ], just like the one we could observe. Intermediate alleles in DYS385a/b occur within various haplogroups [
      • Myres N.M.
      • Ritchie K.H.
      • Lin A.A.
      • Hughes R.H.
      • Woodward S.R.
      • Underhill P.A.
      Y-chromosome short tandem repeat intermediate variant alleles DYS392.2, DYS449.2, and DYS385.2 delineate new phylogenetic substructure in human Y-chromosome haplogroup tree.
      ]. The same tri-allelic pattern for DYS385a/b as we could observe here has been previously reported in a sample from Eastern Africa, also within a haplogroup E background [
      • Iacovacci G.
      • D’Atanasio E.
      • Marini O.
      • Coppa A.
      • Sellitto D.
      • Trombetta B.
      • Berti A.
      • Cruciani F.
      Forensic data and microvariant sequence characterization of 27 Y-STR loci analyzed in four Eastern African countries.
      ].
      We observed one kit dependent dropout in DYS390 and a null allele for DYS448 in the same individual. Whereas we could not find a reported case for the DYS390 dropout, deletion or dropout due to primer binding site mutations of DYS448 has been described previously [
      • Budowle B.
      • Aranda X.G.
      • Lagace R.E.
      • Hennessy L.K.
      • Planz J.V.
      • Rodriguez M.
      • Eisenberg A.J.
      Null allele sequence structure at the DYS448 locus and implications for profile interpretation.
      ,
      • Sánchez C.
      • Barrot C.
      • Xifró A.
      • Ortega M.
      • de Aranda I.G.
      • Huguet E.
      • Corbella J.
      • Gené M.
      Haplotype frequencies of 16 Y-chromosome STR loci in the Barcelona metropolitan area population using Y-Filer™ kit.
      ]. We assume that the signal dropout for DYS448 is rather due to a deletion than to a primer binding site mutation, since we observe strictly no CE signal with both multiplex kits. The locus DYS448 is located in an area of the Y-chromosome prone to deletions and recombination due to repeat structures [
      • Park M.J.
      • Shin K.-J.
      • Kim N.Y.
      • Yang W.I.
      • Cho S.-H.
      • Lee H.Y.
      Characterization of deletions in the DYS385 flanking region and null alleles associated with AZFc microdeletions in Koreans.
      ,
      • Kuroda-Kawaguchi T.
      • Skaletsky H.
      • Brown L.G.
      • Minx P.J.
      • Cordum H.S.
      • Waterston R.H.
      • Wilson R.K.
      • Silber S.
      • Oates R.
      • Rozen S.
      • Page D.C.
      The AZFc region of the Y chromosome features massive palindromes and uniform recurrent deletions in infertile men.
      ]. Deletions of DYS448 appear to have a higher rate of occurrence in Asians [
      • Mizuno N.
      • Nakahara H.
      • Sekiguchi K.
      • Yoshida K.
      • Nakano M.
      • Kasai K.
      16 Y chromosomal STR haplotypes in Japanese.
      ,
      • Parkin E.J.
      • Kraayenbrink T.
      • Opgenort J.R.M.L.
      • van Driem G.L.
      • Tuladhar N.M.
      • de Knijff P.
      • Jobling M.A.
      Diversity of 26-locus Y-STR haplotypes in a Nepalese population sample: isolation and drift in the Himalayas.
      ,
      • Chang Y.M.
      • Perumal R.
      • Keat P.Y.
      • Kuehn D.L.C.
      Haplotype diversity of 16 Y-chromosomal STRs in three main ethnic populations (Malays, Chinese and Indians) in Malaysia.
      ,
      • Ye Y.
      • Gao J.
      • Fan G.
      • Liao L.
      • Hou Y.
      Population genetics for 23 Y-STR loci in Tibetan in China and confirmation of DYS448 null allele.
      ,
      • Yang Y.
      • Wang W.
      • Cheng F.
      • Chen M.
      • Chen T.
      • Zhao J.
      • Chen C.
      • Shi Y.
      • Li C.
      • Chen C.
      • Liu Y.
      • Yan J.
      Haplotypic polymorphisms and mutation rate estimates of 22 Y-chromosome STRs in the Northern Chinese Han father–son pairs.
      ] and are mostly associated with haplogroup C [
      • Roewer L.
      • Krüger C.
      • Willuweit S.
      • Nagy M.
      • Rodig H.
      • Kokshunova L.
      • Rothämel T.
      • Kravchenko S.
      • Jobling M.A.
      • Stoneking M.
      • Nasidze I.
      Y-chromosomal STR haplotypes in Kalmyk population samples.
      ,
      • Balaresque P.
      • Bowden G.R.
      • Parkin E.J.
      • Omran G.A.
      • Heyer E.
      • Quintana-Murci L.
      • Roewer L.
      • Stoneking M.
      • Nasidze I.
      • Carvalho-Silva D.R.
      • Tyler-Smith C.
      • de Knijff P.
      • Jobling M.A.
      Dynamic nature of the proximal AZFc region of the human Y chromosome: multiple independent deletion and duplication events revealed by microsatellite analysis.
      ]. However, one case from Egypt has been reported, where the deletion occurs also within a haplogroup G background [
      • Balaresque P.
      • Bowden G.R.
      • Parkin E.J.
      • Omran G.A.
      • Heyer E.
      • Quintana-Murci L.
      • Roewer L.
      • Stoneking M.
      • Nasidze I.
      • Carvalho-Silva D.R.
      • Tyler-Smith C.
      • de Knijff P.
      • Jobling M.A.
      Dynamic nature of the proximal AZFc region of the human Y chromosome: multiple independent deletion and duplication events revealed by microsatellite analysis.
      ], as is the case in our study.
      One individual from our study displayed a large Y-chromosomal deletion (Table 3), previously described in people of Asian ancestry [
      • Purps J.
      • Siegert S.
      • Willuweit S.
      • Nagy M.
      • Alves C.
      • Salazar R.
      • Angustia S.M.
      • Santos L.H.
      • Anslinger K.
      • Bayer B.
      • Ayub Q.
      • Wei W.
      • Xue Y.
      • Tyler-Smith C.
      • Bafalluy M.B.
      • Martinez-Jarreta B.
      • Egyed B.
      • Balitzki B.
      • Tschumi S.
      • Ballard D.
      • Court D.S.
      • Barrantes X.
      • Bassler G.
      • Wiest T.
      • Berger B.
      • Niederstatter H.
      • Parson W.
      • Davis C.
      • Budowle B.
      • Burri H.
      • Borer U.
      • Koller C.
      • Carvalho E.F.
      • Domingues P.M.
      • Chamoun W.T.
      • Coble M.D.
      • Hill C.R.
      • Corach D.
      • Caputo M.
      • D'Amato M.E.
      • Davison S.
      • Decorte R.
      • Larmuseau M.H.
      • Ottoni C.
      • Rickards O.
      • Lu D.
      • Jiang C.
      • Dobosz T.
      • Jonkisz A.
      • Frank W.E.
      • Furac I.
      • Gehrig C.
      • Castella V.
      • Grskovic B.
      • Haas C.
      • Wobst J.
      • Hadzic G.
      • Drobnic K.
      • Honda K.
      • Hou Y.
      • Zhou D.
      • Li Y.
      • Hu S.
      • Chen S.
      • Immel U.D.
      • Lessig R.
      • Jakovski Z.
      • Ilievska T.
      • Klann A.E.
      • Garcia C.C.
      • de Knijff P.
      • Kraaijenbrink T.
      • Kondili A.
      • Miniati P.
      • Vouropoulou M.
      • Kovacevic L.
      • Marjanovic D.
      • Lindner I.
      • Mansour I.
      • Al-Azem M.
      • Andari A.E.
      • Marino M.
      • Furfuro S.
      • Locarno L.
      • Martin P.
      • Luque G.M.
      • Alonso A.
      • Miranda L.S.
      • Moreira H.
      • Mizuno N.
      • Iwashima Y.
      • Neto R.S.
      • Nogueira T.L.
      • Silva R.
      • Nastainczyk-Wulf M.
      • Edelmann J.
      • Kohl M.
      • Nie S.
      • Wang X.
      • Cheng B.
      • Nunez C.
      • Pancorbo M.M.
      • Olofsson J.K.
      • Morling N.
      • Onofri V.
      • Tagliabracci A.
      • Pamjav H.
      • Volgyi A.
      • Barany G.
      • Pawlowski R.
      • Maciejewska A.
      • Pelotti S.
      • Pepinski W.
      • Abreu-Glowacka M.
      • Phillips C.
      • Cardenas J.
      • Rey-Gonzalez D.
      • Salas A.
      • Brisighelli F.
      • Capelli C.
      • Toscanini U.
      • Piccinini A.
      • Piglionica M.
      • Baldassarra S.L.
      • Ploski R.
      • Konarzewska M.
      • Jastrzebska E.
      • Robino C.
      • Sajantila A.
      • Palo J.U.
      • Guevara E.
      • Salvador J.
      • Ungria M.C.
      • Rodriguez J.J.
      • Schmidt U.
      • Schlauderer N.
      • Saukko P.
      • Schneider P.M.
      • Sirker M.
      • Shin K.J.
      • Oh Y.N.
      • Skitsa I.
      • Ampati A.
      • Smith T.G.
      • Calvit L.S.
      • Stenzl V.
      • Capal T.
      • Tillmar A.
      • Nilsson H.
      • Turrina S.
      • De Leo D.
      • Verzeletti A.
      • Cortellini V.
      • Wetton J.H.
      • Gwynne G.M.
      • Jobling M.A.
      • Whittle M.R.
      • Sumita D.R.
      • Wolanska-Nowak P.
      • Yong R.Y.
      • Krawczak M.
      • Nothnagel M.
      • Roewer L.
      A global analysis of Y-chromosomal haplotype diversity for 23 STR loci.
      ,
      • Aliferi A.
      • Thomson J.
      • McDonald A.
      • Paynter V.M.
      • Ferguson S.
      • Vanhinsbergh D.
      • Syndercombe Court D.
      • Ballard D.
      UK and Irish Y-STR population data-A catalogue of variant alleles.
      ]. In our study, this large deletion surprisingly occurred within an R1b-U152 haplogroup background, a haplogroup that is thought to have a relatively recent origin in Europe [
      • Valverde L.
      • Illescas M.J.
      • Villaescusa P.
      • Gotor A.M.
      • García A.
      • Cardoso S.
      • Algorta J.
      • Catarino S.
      • Rouault K.
      • Férec C.
      • Hardiman O.
      • Zarrabeitia M.
      • Jiménez S.
      • Pinheiro M.F.
      • Jarreta B.M.
      • Olofsson J.
      • Morling N.
      • de Pancorbo M.M.
      New clues to the evolutionary history of the main European paternal lineage M269: dissection of the Y-SNP S116 in Atlantic Europe and Iberia.
      ,
      • Olalde I.
      • Brace S.
      • Allentoft M.E.
      • Armit I.
      • Kristiansen K.
      • Booth T.
      • Rohland N.
      • Mallick S.
      • Szecsenyi-Nagy A.
      • Mittnik A.
      • Altena E.
      • Lipson M.
      • Lazaridis I.
      • Harper T.K.
      • Patterson N.
      • Broomandkhoshbacht N.
      • Diekmann Y.
      • Faltyskova Z.
      • Fernandes D.
      • Ferry M.
      • Harney E.
      • de Knijff P.
      • Michel M.
      • Oppenheimer J.
      • Stewardson K.
      • Barclay A.
      • Alt K.W.
      • Liesau C.
      • Rios P.
      • Blasco C.
      • Miguel J.V.
      • Garcia R.M.
      • Fernandez A.A.
      • Banffy E.
      • Bernabo-Brea M.
      • Billoin D.
      • Bonsall C.
      • Bonsall L.
      • Allen T.
      • Buster L.
      • Carver S.
      • Navarro L.C.
      • Craig O.E.
      • Cook G.T.
      • Cunliffe B.
      • Denaire A.
      • Dinwiddy K.E.
      • Dodwell N.
      • Ernee M.
      • Evans C.
      • Kucharik M.
      • Farre J.F.
      • Fowler C.
      • Gazenbeek M.
      • Pena R.G.
      • Haber-Uriarte M.
      • Haduch E.
      • Hey G.
      • Jowett N.
      • Knowles T.
      • Massy K.
      • Pfrengle S.
      • Lefranc P.
      • Lemercier O.
      • Lefebvre A.
      • Martinez C.H.
      • Olmo V.G.
      • Ramirez A.B.
      • Maurandi J.L.
      • Majo T.
      • McKinley J.I.
      • McSweeney K.
      • Mende B.G.
      • Modi A.
      • Kulcsar G.
      • Kiss V.
      • Czene A.
      • Patay R.
      • Endrodi A.
      • Kohler K.
      • Hajdu T.
      • Szeniczey T.
      • Dani J.
      • Bernert Z.
      • Hoole M.
      • Cheronet O.
      • Keating D.
      • Veleminsky P.
      • Dobes M.
      • Candilio F.
      • Brown F.
      • Fernandez R.F.
      • Herrero-Corral A.M.
      • Tusa S.
      • Carnieri E.
      • Lentini L.
      • Valenti A.
      • Zanini A.
      • Waddington C.
      • Delibes G.
      • Guerra-Doce E.
      • Neil B.
      • Brittain M.
      • Luke M.
      • Mortimer R.
      • Desideri J.
      • Besse M.
      • Brucken G.
      • Furmanek M.
      • Haluszko A.
      • Mackiewicz M.
      • Rapinski A.
      • Leach S.
      • Soriano I.
      • Lillios K.T.
      • Cardoso J.L.
      • Pearson M.P.
      • Wlodarczak P.
      • Price T.D.
      • Prieto P.
      • Rey P.J.
      • Risch R.
      • Rojo Guerra M.A.
      • Schmitt A.
      • Serralongue J.
      • Silva A.M.
      • Smrcka V.
      • Vergnaud L.
      • Zilhao J.
      • Caramelli D.
      • Higham T.
      • Thomas M.G.
      • Kennett D.J.
      • Fokkens H.
      • Heyd V.
      • Sheridan A.
      • Sjogren K.G.
      • Stockhammer P.W.
      • Krause J.
      • Pinhasi R.
      • Haak W.
      • Barnes I.
      • Lalueza-Fox C.
      • Reich D.
      The Beaker phenomenon and the genomic transformation of northwest Europe.
      ]. To our knowledge, this is the first time that such a deletion is reported for an individual of European paternal ancestry.
      Concordance of multiplex kits is crucial, whenever profiles are generated by different labs for comparison. PowerPlex® Y23 and YFilerPlus® are two Y-STR kits that are probably the most widely used in the field. In our study, the two kits exhibit a good concordance rate. Of the 8 samples, showing different allele values between the two kits, 5 displayed the same .1 allele with YFilerPlus® in DYS533. This allele could be due to an InDel in the flanking regions of the marker. Such an InDel has been previously described by Huszar et al. [
      • Huszar T.I.
      • Jobling M.A.
      • Wetton J.H.
      A phylogenetic framework facilitates Y-STR variant discovery and classification via massively parallel sequencing.
      ], yet in another Y haplogroup background (C1a). All five samples from our study occurred in an I2-P215 (xM223, xP37.2) background, what has not yet been reported to date. The discordant DYS533 allele 12.1 might therefore carry valuable phylogenetic information. However, the allele occurred at a relatively high frequency in our sample and might be problematic for Y-STR databases, since it remains undetected with the widely used kit PowerPlex® Y23. A quick search on the YHRD returned a total of 24 intermediate .1 alleles for DYS533, spanning the allelic range from 11.1 to 14.1.

      4.3 Haplogroup prediction

      Given the dubious reputation of the prediction tools [
      • Muzzio M.
      • Ramallo V.
      • Motti J.M.B.
      • Santos M.R.
      • López Camelo J.S.
      • Bailliet G.
      Software for Y-haplogroup predictions: a word of caution.
      ,
      • Athey W.
      Comments on the article, "Software for Y haplogroup predictions, a word of caution.
      ], we were surprised how well the haplogroup predictions corresponded to the haplogroups determined by SNaPshot assay. So, even though we would agree that for reliable results, every SNP should be finally determined in the wet lab, we cannot deny that for samples of Western European ancestry, predictors seem to deliver good preliminary results. The HAPEST predictor we used here has already been shown to deliver accurate predictions for typical European haplogroups [
      • Emmerova B.
      • Ehler E.
      • Comas D.
      • Votrubova J.
      • Vanek D.
      Comparison of Y-chromosomal haplogroup predictors.
      ,
      • Petrejcikova E.
      • Carnogurska J.
      • Hronska D.
      • Bernasovska J.
      • Boronova I.
      • Gabrikova D.
      • Bozikova A.
      • Macekova S.
      Y-SNP analysis versus Y-haplogroup predictor in the Slovak population.
      ]. We assume that such a high accuracy of haplogroup prediction of 95 % could be achieved only because we have very good data coverage for Western Europe. For most reliable predictions, we recommend combining an YHRD search with the haplogroup prediction tool. All haplogroups that were concordant between YHRD ancestry information and HAPEST haplogroup prediction turned out to be correct.

      4.4 Haplogroup distributions

      SNP typing for common European haplogroups revealed some expected patterns, demonstrating that the modern Swiss population still reflects the Alps as geographical barrier for human migration. We detected significantly less haplogroup I1-M253 south of the alpine divide than in the German and French speaking parts of Switzerland (Table 5, Fig. 4a). This was expected, since I1 is most common in Northern Europe and can only be found in small proportions south of the Alps. It has been suggested, that haplogroup I1 has been spread in Scandinavia by migration from Western Europe after the last glacial maximum [
      • Rootsi S.
      • Magri C.
      • Kivisild T.
      • Benuzzi G.
      • Help H.
      • Bermisheva M.
      • Kutuev I.
      • Barac L.
      • Pericic M.
      • Balanovsky O.
      • Pshenichnov A.
      • Dion D.
      • Grobei M.
      • Zhivotovsky L.A.
      • Battaglia V.
      • Achilli A.
      • Al-Zahery N.
      • Parik J.
      • King R.
      • Cinnioglu C.
      • Khusnutdinova E.
      • Rudan P.
      • Balanovska E.
      • Scheffrahn W.
      • Simonescu M.
      • Brehm A.
      • Goncalves R.
      • Rosa A.
      • Moisan J.P.
      • Chaventre A.
      • Ferak V.
      • Furedi S.
      • Oefner P.J.
      • Shen P.
      • Beckman L.
      • Mikerezi I.
      • Terzic R.
      • Primorac D.
      • Cambon-Thomsen A.
      • Krumina A.
      • Torroni A.
      • Underhill P.A.
      • Santachiara-Benerecetti A.S.
      • Villems R.
      • Semino O.
      Phylogeography of Y-chromosome haplogroup I reveals distinct domains of prehistoric gene flow in europe.
      ].
      Fig. 4
      Fig. 4Maps of Switzerland with geographical representations of five haplogroups, showing significant differences in geographical spread: (a) I1-M253, (b) J2a-M410, (c) R1b-U106, (d) R1b-U152, (e) E1b1b-M35.
      Also not surprising is the significant enrichment of haplogroup J2a-M410 in the Ticino sample (Table 5, Fig. 4b). J2 probably originates from the Near East [
      • Cinnioğlu C.
      • King R.
      • Kivisild T.
      • Kalfoğlu E.
      • Atasoy S.
      • Cavalleri G.L.
      • Lillie A.S.
      • Roseman C.C.
      • Lin A.A.
      • Prince K.
      • Oefner P.J.
      • Shen P.
      • Semino O.
      • Cavalli-Sforza L.L.
      • Underhill P.A.
      Excavating Y-chromosome haplotype strata in Anatolia.
      ] and subclades of J2a-M410 are frequently detected in Italy and the Mediterranean in general, but more rarely north of the Alps [
      • Semino O.
      • Magri C.
      • Benuzzi G.
      • Lin A.A.
      • Al-Zahery N.
      • Battaglia V.
      • Maccioni L.
      • Triantaphyllidis C.
      • Shen P.
      • Oefner P.J.
      • Zhivotovsky L.A.
      • King R.
      • Torroni A.
      • Cavalli-Sforza L.L.
      • Underhill P.A.
      • Santachiara-Benerecetti A.S.
      Origin, diffusion, and differentiation of Y-chromosome haplogroups E and J: inferences on the neolithization of Europe and later migratory events in the Mediterranean area.
      ].
      We also detected significant differences for the Ticino sample compared to the rest of Switzerland for two sub-lineages of R1b-M267. R1b-M267 is the most frequent haplogroup in Western Europe, with increasing proportions from east to west [
      • Cruciani F.
      • Trombetta B.
      • Antonelli C.
      • Pascone R.
      • Valesini G.
      • Scalzi V.
      • Vona G.
      • Melegh B.
      • Zagradisnik B.
      • Assum G.
      • Efremov G.D.
      • Sellitto D.
      • Scozzari R.
      Strong intra- and inter-continental differentiation revealed by Y chromosome SNPs M269, U106 and U152.
      ,
      • Balaresque P.
      • Bowden G.R.
      • Adams S.M.
      • Leung H.Y.
      • King T.E.
      • Rosser Z.H.
      • Goodwin J.
      • Moisan J.P.
      • Richard C.
      • Millward A.
      • Demaine A.G.
      • Barbujani G.
      • Previdere C.
      • Wilson I.J.
      • Tyler-Smith C.
      • Jobling M.A.
      A predominantly neolithic origin for European paternal lineages.
      ,
      • Myres N.M.
      • Rootsi S.
      • Lin A.A.
      • Järve M.
      • King R.J.
      • Kutuev I.
      • Cabrera V.M.
      • Khusnutdinova E.K.
      • Pshenichnov A.
      • Yunusbayev B.
      • Balanovsky O.
      • Balanovska E.
      • Rudan P.
      • Baldovic M.
      • Herrera R.J.
      • Chiaroni J.
      • Di Cristofaro J.
      • Villems R.
      • Kivisild T.
      • Underhill P.A.
      A major Y-chromosome haplogroup R1b holocene era founder effect in central and Western Europe.
      ]. It has probably been brought to Central and Western Europe by migration from the Eurasian steppe around 3000 BCE [
      • Haak W.
      • Lazaridis I.
      • Patterson N.
      • Rohland N.
      • Mallick S.
      • Llamas B.
      • Brandt G.
      • Nordenfelt S.
      • Harney E.
      • Stewardson K.
      • Fu Q.
      • Mittnik A.
      • Banffy E.
      • Economou C.
      • Francken M.
      • Friederich S.
      • Pena R.G.
      • Hallgren F.
      • Khartanovich V.
      • Khokhlov A.
      • Kunst M.
      • Kuznetsov P.
      • Meller H.
      • Mochalov O.
      • Moiseyev V.
      • Nicklisch N.
      • Pichler S.L.
      • Risch R.
      • Rojo Guerra M.A.
      • Roth C.
      • Szecsenyi-Nagy A.
      • Wahl J.
      • Meyer M.
      • Krause J.
      • Brown D.
      • Anthony D.
      • Cooper A.
      • Alt K.W.
      • Reich D.
      Massive migration from the steppe was a source for Indo-European languages in Europe.
      ,
      • Allentoft M.E.
      • Sikora M.
      • Sjogren K.G.
      • Rasmussen S.
      • Rasmussen M.
      • Stenderup J.
      • Damgaard P.B.
      • Schroeder H.
      • Ahlstrom T.
      • Vinner L.
      • Malaspinas A.S.
      • Margaryan A.
      • Higham T.
      • Chivall D.
      • Lynnerup N.
      • Harvig L.
      • Baron J.
      • Della Casa P.
      • Dabrowski P.
      • Duffy P.R.
      • Ebel A.V.
      • Epimakhov A.
      • Frei K.
      • Furmanek M.
      • Gralak T.
      • Gromov A.
      • Gronkiewicz S.
      • Grupe G.
      • Hajdu T.
      • Jarysz R.
      • Khartanovich V.
      • Khokhlov A.
      • Kiss V.
      • Kolar J.
      • Kriiska A.
      • Lasak I.
      • Longhi C.
      • McGlynn G.
      • Merkevicius A.
      • Merkyte I.
      • Metspalu M.
      • Mkrtchyan R.
      • Moiseyev V.
      • Paja L.
      • Palfi G.
      • Pokutta D.
      • Pospieszny L.
      • Price T.D.
      • Saag L.
      • Sablin M.
      • Shishlina N.
      • Smrcka V.
      • Soenov V.I.
      • Szeverenyi V.
      • Toth G.
      • Trifanova S.V.
      • Varul L.
      • Vicze M.
      • Yepiskoposyan L.
      • Zhitenev V.
      • Orlando L.
      • Sicheritz-Ponten T.
      • Brunak S.
      • Nielsen R.
      • Kristiansen K.
      • Willerslev E.
      Population genomics of bronze age Eurasia.
      ] following a massive and rapid expansion, especially into Northwestern Europe, associated with the appearance of Bell beaker pottery [
      • Olalde I.
      • Brace S.
      • Allentoft M.E.
      • Armit I.
      • Kristiansen K.
      • Booth T.
      • Rohland N.
      • Mallick S.
      • Szecsenyi-Nagy A.
      • Mittnik A.
      • Altena E.
      • Lipson M.
      • Lazaridis I.
      • Harper T.K.
      • Patterson N.
      • Broomandkhoshbacht N.
      • Diekmann Y.
      • Faltyskova Z.
      • Fernandes D.
      • Ferry M.
      • Harney E.
      • de Knijff P.
      • Michel M.
      • Oppenheimer J.
      • Stewardson K.
      • Barclay A.
      • Alt K.W.
      • Liesau C.
      • Rios P.
      • Blasco C.
      • Miguel J.V.
      • Garcia R.M.
      • Fernandez A.A.
      • Banffy E.
      • Bernabo-Brea M.
      • Billoin D.
      • Bonsall C.
      • Bonsall L.
      • Allen T.
      • Buster L.
      • Carver S.
      • Navarro L.C.
      • Craig O.E.
      • Cook G.T.
      • Cunliffe B.
      • Denaire A.
      • Dinwiddy K.E.
      • Dodwell N.
      • Ernee M.
      • Evans C.
      • Kucharik M.
      • Farre J.F.
      • Fowler C.
      • Gazenbeek M.
      • Pena R.G.
      • Haber-Uriarte M.
      • Haduch E.
      • Hey G.
      • Jowett N.
      • Knowles T.
      • Massy K.
      • Pfrengle S.
      • Lefranc P.
      • Lemercier O.
      • Lefebvre A.
      • Martinez C.H.
      • Olmo V.G.
      • Ramirez A.B.
      • Maurandi J.L.
      • Majo T.
      • McKinley J.I.
      • McSweeney K.
      • Mende B.G.
      • Modi A.
      • Kulcsar G.
      • Kiss V.
      • Czene A.
      • Patay R.
      • Endrodi A.
      • Kohler K.
      • Hajdu T.
      • Szeniczey T.
      • Dani J.
      • Bernert Z.
      • Hoole M.
      • Cheronet O.
      • Keating D.
      • Veleminsky P.
      • Dobes M.
      • Candilio F.
      • Brown F.
      • Fernandez R.F.
      • Herrero-Corral A.M.
      • Tusa S.
      • Carnieri E.
      • Lentini L.
      • Valenti A.
      • Zanini A.
      • Waddington C.
      • Delibes G.
      • Guerra-Doce E.
      • Neil B.
      • Brittain M.
      • Luke M.
      • Mortimer R.
      • Desideri J.
      • Besse M.
      • Brucken G.
      • Furmanek M.
      • Haluszko A.
      • Mackiewicz M.
      • Rapinski A.
      • Leach S.
      • Soriano I.
      • Lillios K.T.
      • Cardoso J.L.
      • Pearson M.P.
      • Wlodarczak P.
      • Price T.D.
      • Prieto P.
      • Rey P.J.
      • Risch R.
      • Rojo Guerra M.A.
      • Schmitt A.
      • Serralongue J.
      • Silva A.M.
      • Smrcka V.
      • Vergnaud L.
      • Zilhao J.
      • Caramelli D.
      • Higham T.
      • Thomas M.G.
      • Kennett D.J.
      • Fokkens H.
      • Heyd V.
      • Sheridan A.
      • Sjogren K.G.
      • Stockhammer P.W.
      • Krause J.
      • Pinhasi R.
      • Haak W.
      • Barnes I.
      • Lalueza-Fox C.
      • Reich D.
      The Beaker phenomenon and the genomic transformation of northwest Europe.
      ,
      • Lee E.J.
      • Makarewicz C.
      • Renneberg R.
      • Harder M.
      • Krause-Kyora B.
      • Müller S.
      • Ostritz S.
      • Fehren-Schmitz L.
      • Schreiber S.
      • Müller J.
      • von Wurmb-Schwark N.
      • Nebel A.
      Emerging genetic patterns of the European neolithic: perspectives from a late neolithic bell beaker burial site in Germany.
      ]. We detected significant differences in the distribution of two sublineages of R1b-M269 north and south of the Alps: notably lineages R1b-U106 and R1b-U152 (Fig. 4c and d). R1b-U106 is mainly spread along the river Rhine, reaching the largest proportions at the southern coast of the North Sea [
      • Cruciani F.
      • Trombetta B.
      • Antonelli C.
      • Pascone R.
      • Valesini G.
      • Scalzi V.
      • Vona G.
      • Melegh B.
      • Zagradisnik B.
      • Assum G.
      • Efremov G.D.
      • Sellitto D.
      • Scozzari R.
      Strong intra- and inter-continental differentiation revealed by Y chromosome SNPs M269, U106 and U152.
      ,
      • Valverde L.
      • Illescas M.J.
      • Villaescusa P.
      • Gotor A.M.
      • García A.
      • Cardoso S.
      • Algorta J.
      • Catarino S.
      • Rouault K.
      • Férec C.
      • Hardiman O.
      • Zarrabeitia M.
      • Jiménez S.
      • Pinheiro M.F.
      • Jarreta B.M.
      • Olofsson J.
      • Morling N.
      • de Pancorbo M.M.
      New clues to the evolutionary history of the main European paternal lineage M269: dissection of the Y-SNP S116 in Atlantic Europe and Iberia.
      ,
      • Myres N.M.
      • Rootsi S.
      • Lin A.A.
      • Järve M.
      • King R.J.
      • Kutuev I.
      • Cabrera V.M.
      • Khusnutdinova E.K.
      • Pshenichnov A.
      • Yunusbayev B.
      • Balanovsky O.
      • Balanovska E.
      • Rudan P.
      • Baldovic M.
      • Herrera R.J.
      • Chiaroni J.
      • Di Cristofaro J.
      • Villems R.
      • Kivisild T.
      • Underhill P.A.
      A major Y-chromosome haplogroup R1b holocene era founder effect in central and Western Europe.
      ]. R1b-U106 evolved approximately at the same time than haplogroup R1b-P312/S116 [
      • Myres N.M.
      • Rootsi S.
      • Lin A.A.
      • Järve M.
      • King R.J.
      • Kutuev I.
      • Cabrera V.M.
      • Khusnutdinova E.K.
      • Pshenichnov A.
      • Yunusbayev B.
      • Balanovsky O.
      • Balanovska E.
      • Rudan P.
      • Baldovic M.
      • Herrera R.J.
      • Chiaroni J.
      • Di Cristofaro J.
      • Villems R.
      • Kivisild T.
      • Underhill P.A.
      A major Y-chromosome haplogroup R1b holocene era founder effect in central and Western Europe.
      ]. R1b-U152 is a sublineage of R1b-P312/S116 of younger origin [
      • Myres N.M.
      • Rootsi S.
      • Lin A.A.
      • Järve M.
      • King R.J.
      • Kutuev I.
      • Cabrera V.M.
      • Khusnutdinova E.K.
      • Pshenichnov A.
      • Yunusbayev B.
      • Balanovsky O.
      • Balanovska E.
      • Rudan P.
      • Baldovic M.
      • Herrera R.J.
      • Chiaroni J.
      • Di Cristofaro J.
      • Villems R.
      • Kivisild T.
      • Underhill P.A.
      A major Y-chromosome haplogroup R1b holocene era founder effect in central and Western Europe.
      ]. It has been suggested that it originates from a Franco-Cantabrian region and has been brought to the Alps and northern Italy by migration along the Mediterranean coast [
      • Valverde L.
      • Illescas M.J.
      • Villaescusa P.
      • Gotor A.M.
      • García A.
      • Cardoso S.
      • Algorta J.
      • Catarino S.
      • Rouault K.
      • Férec C.
      • Hardiman O.
      • Zarrabeitia M.
      • Jiménez S.
      • Pinheiro M.F.
      • Jarreta B.M.
      • Olofsson J.
      • Morling N.
      • de Pancorbo M.M.
      New clues to the evolutionary history of the main European paternal lineage M269: dissection of the Y-SNP S116 in Atlantic Europe and Iberia.
      ]. Today it reaches its highest percentages in northern Italy [
      • Cruciani F.
      • Trombetta B.
      • Antonelli C.
      • Pascone R.
      • Valesini G.
      • Scalzi V.
      • Vona G.
      • Melegh B.
      • Zagradisnik B.
      • Assum G.
      • Efremov G.D.
      • Sellitto D.
      • Scozzari R.
      Strong intra- and inter-continental differentiation revealed by Y chromosome SNPs M269, U106 and U152.
      ,
      • Myres N.M.
      • Rootsi S.
      • Lin A.A.
      • Järve M.
      • King R.J.
      • Kutuev I.
      • Cabrera V.M.
      • Khusnutdinova E.K.
      • Pshenichnov A.
      • Yunusbayev B.
      • Balanovsky O.
      • Balanovska E.
      • Rudan P.
      • Baldovic M.
      • Herrera R.J.
      • Chiaroni J.
      • Di Cristofaro J.
      • Villems R.
      • Kivisild T.
      • Underhill P.A.
      A major Y-chromosome haplogroup R1b holocene era founder effect in central and Western Europe.
      ]. Northwestern Italy has a very high percentage of haplogroup R1b (around 70 %) with the highest proportions in the area of Bergamo [
      • Grugni V.
      • Raveane A.
      • Mattioli F.
      • Battaglia V.
      • Sala C.
      • Toniolo D.
      • Ferretti L.
      • Gardella R.
      • Achilli A.
      • Olivieri A.
      • Torroni A.
      • Passarino G.
      • Semino O.
      Reconstructing the genetic history of Italians: new insights from a male (Y-chromosome) perspective.
      ]. In this pre-alpine region, located about 50 km from Ticino, the percentage of individuals with haplogroup R1b-U152 is around 50 %, just as for our Ticino sample (Table 5). This local present day hotspot for haplogroup R1b-U152 fits quite well the ancient habitats of Celtic cultures such as the Lepontii, being most probably at the origin of the name “Valle Leventina” for the upper part of the Ticino Valley, or the Orobii [
      • Vietti G.
      Lepontier, Historisches Lexikon der Schweiz (HLS), Schweizerische Akademie der Geistes- und Sozialwissenschaften, Bern.
      ,
      • Müller F.
      • Kaenel G.
      • Lüscher G.
      Die Schweiz vom Paläolithikum bis zum frühen Mittelalter - SPM IV - Eisenzeit, Schweizerische Gesellschaft für Ur- und Frühgeschichte, Basel.
      ,
      • Eska J.F.
      ]. Haplogroup R1b-U152 is significantly less frequent north of the Alps, but remains the most frequent haplogroup throughout the entire country (Table 5). Jörg Jenatsch, a Swiss national hero from the 17th century, also belonged to haplogroup R1b-U152 [
      • Haas C.
      • Shved N.
      • Ruhli F.J.
      • Papageorgopoulou C.
      • Purps J.
      • Geppert M.
      • Willuweit S.
      • Roewer L.
      • Krawczak M.
      Y-chromosomal analysis identifies the skeletal remains of Swiss national hero Jorg Jenatsch (1596–1639).
      ].
      We could also observe an uneven distribution of haplogroup E1b1b-M35 (Fig. 4e). However, this one does not follow a gradient from north to south but manifests as an enrichment of haplogroup E1b1b-M35 in the eastern part of the country, close to Austria. This pattern fits quite well with data from Tyrol, a region in Western Austria [
      • Niederstatter H.
      • Berger B.
      • Kayser M.
      • Parson W.
      Differences in urbanization degree and consequences on the diversity of conventional vs. rapidly mutating Y-STRs in five municipalities from a small region of the Tyrolean Alps in Austria.
      ], showing an important fraction of 16.9 % haplogroup E in this area, mostly attributed to E-M78, a subclade of E1b1b-M35.

      5. Concluding remarks

      In sum, we are presenting the first detailed study of the Y-chromosomal landscape in Switzerland. The outcome fits very well the expectations and the Y chromosomal data from neighboring regions. The modern Swiss population still mirrors the alpine divide as an important barrier for human migration on an intra-national level.

      Ethics statement

      All samples were collected with informed written consent. They were reversibly anonymized, to permit the donors to exert their right to withdraw their sample at any time. The Institute of Forensic Medicine, University of Bern, obtained the samples under an arbitrary number. The written consent documents with the names of the donors remained with the Red Cross. All documents distributed to the donors upon sampling were submitted to the responsible cantonal ethical committee and approval obtained.

      CRediT authorship contribution statement

      Martin Zieger: Writing - original draft, Writing - review & editing. Silvia Utz: Resources.

      Acknowledgements

      We thank all the donors for participating in the project and Ina Krebber (Interregionale Blutspende SRK), for her help in organizing the sample collection. Special thanks go also to Ludmilla Lieder for technical assistance, as well as to Maria Geppert and Jessica Rothe (both Institute of Legal Medicine and Forensic Sciences, Charité - Universitätsmedizin Berlin) for help with the SNaPshot multiplex assays. We would also like to thank Sandra Lösch (Anthropology Dept., Institute of Forensic Medicine, University of Bern) for helping out with literature about Swiss Iron Age populations. Finally M.Z. would especially like to thank Lutz Roewer (Institute of Legal Medicine and Forensic Sciences, Charité - Universitätsmedizin Berlin) for hosting him in his lab and for discussing the present manuscript.

      References

        • Kayser M.
        Forensic use of Y-chromosome DNA: a general overview.
        Hum. Genet. 2017; 136: 621-635
        • Willuweit S.
        • Roewer L.
        The new Y chromosome haplotype reference database.
        Forensic Sci. Int. Genet. 2015; 15: 43-48
        • Semino O.
        • Passarino G.
        • Oefner P.J.
        • Lin A.A.
        • Arbuzova S.
        • Beckman L.E.
        • De Benedictis G.
        • Francalacci P.
        • Kouvatsi A.
        • Limborska S.
        • Marcikiae M.
        • Mika A.
        • Mika B.
        • Primorac D.
        • Santachiara-Benerecetti A.S.
        • Cavalli-Sforza L.L.
        • Underhill P.A.
        The genetic legacy of Paleolithic Homo sapiens sapiens in extant Europeans: a Y chromosome perspective.
        Science. 2000; 290: 1155-1159
        • Underhill P.A.
        • Kivisild T.
        Use of y chromosome and mitochondrial DNA population structure in tracing human migrations.
        Annu. Rev. Genet. 2007; 41: 539-564
        • Brandt G.
        • Szécsényi-Nagy A.
        • Roth C.
        • Alt K.W.
        • Haak W.
        Human paleogenetics of Europe – the known knowns and the known unknowns.
        J. Hum. Evol. 2015; 79: 73-92
        • Zieger M.
        • Utz S.
        A "forensic biobank" to establish comprehensive genetic frequency data for Switzerland.
        Forensic Sci. Int. Genet. 2019; 40: 46-51
        • Athey W.T.
        Haplogroup prediction from Y-STR values using an allele-frequency approach.
        J. Genet. Geneal. 2005; : 1-7
        • Athey W.T.
        Haplogroup prediction from Y-STR values using a Bayesian-allele-frequency approach.
        J. Genet. Geneal. 2006; : 34-39
        • Niederstatter H.
        • Berger B.
        • Erhart D.
        • Willuweit S.
        • Geppert M.
        • Gassner C.
        • Schennach H.
        • Parson W.
        • Roewer L.
        Multiple recurrent mutations at four human Y-chromosomal single nucleotide polymorphism sites in a 37 bp sequence tract on the ARSDP1 pseudogene.
        Forensic Sci. Int. Genet. 2013; 7: 593-600
        • Geppert M.
        • Roewer L.
        SNaPshot® minisequencing analysis of multiple ancestry-informative Y-SNPs using capillary electrophoresis.
        in: Alonso A. DNA Electrophoresis Protocols for Forensic Genetics. Humana Press, Totowa, NJ2012: 127-140
        • Haas C.
        • Shved N.
        • Ruhli F.J.
        • Papageorgopoulou C.
        • Purps J.
        • Geppert M.
        • Willuweit S.
        • Roewer L.
        • Krawczak M.
        Y-chromosomal analysis identifies the skeletal remains of Swiss national hero Jorg Jenatsch (1596–1639).
        Forensic Sci. Int. Genet. 2013; 7: 610-617
        • Nunez C.
        • Geppert M.
        • Baeta M.
        • Roewer L.
        • Martinez-Jarreta B.
        Y chromosome haplogroup diversity in a Mestizo population of Nicaragua.
        Forensic Sci. Int. Genet. 2012; 6: e192-5
        • van Oven M.
        • Van Geystelen A.
        • Kayser M.
        • Decorte R.
        • Larmuseau M.H.
        Seeing the wood for the trees: a minimal reference phylogeny for the human Y chromosome.
        Hum. Mutat. 2014; 35: 187-191
        • Nei M.
        • Tajima F.
        DNA polymorphism detectable by restriction endonucleases.
        Genetics. 1981; 97: 145-163
        • Andersen M.M.
        • Eriksen P.S.
        • Morling N.
        The discrete Laplace exponential family and estimation of Y-STR haplotype frequencies.
        J. Theor. Biol. 2013; 329: 39-51
        • Willuweit S.
        • Anslinger K.
        • Bäßler G.
        • Eckert M.
        • Fimmers R.
        • Hohoff C.
        • Kraft M.
        • Leuker C.
        • Molsberger G.
        • Pich U.
        • Razbin S.
        • Rothämel T.
        • Schneider H.
        • Schneider P.M.
        • Templin M.
        • Vennemann M.
        • Wächter A.
        • Weirich V.
        • Zierdt H.
        • Roewer L.
        Gemeinsame Empfehlungen der Projektgruppe „Biostatistische DNA-Berechnungen “und der Spurenkommission zur biostatistischen Bewertung von Y‑chromosomalen DNA-Befunden.
        Rechtsmedizin. 2018; 28: 138-142
        • Gouy A.
        • Zieger M.
        STRAF-A convenient online tool for STR data evaluation in forensic genetics.
        Forensic Sci. Int. Genet. 2017; 30: 148-151
        • R Core Team
        R: A Language and Environment for Statistical Computing.
        (URL:) R Foundation for Statistical Computing, Vienna, Austria2015
        • Babicki S.
        • Arndt D.
        • Marcu A.
        • Liang Y.
        • Grant J.R.
        • Maciejewski A.
        • Wishart D.S.
        Heatmapper: web-enabled heat mapping for all.
        Nucleic Acids Res. 2016; 44: W147-53
        • Gusmao L.
        • Butler J.M.
        • Linacre A.
        • Parson W.
        • Roewer L.
        • Schneider P.M.
        • Carracedo A.
        Revised guidelines for the publication of genetic population data.
        Forensic Sci. Int. Genet. 2017; 30: 160-163
        • Roewer L.
        Y-chromosome short tandem repeats in forensics—sexing, profiling, and matching male DNA.
        WIREs Forensic Sci. 2019; 1: e1336
        • Roewer L.
        • Willuweit S.
        Y‑Chromosomale STR-analyse in der forensischen praxis.
        Rechtsmedizin. 2018; 28: 149-164
        • Cruciani F.
        • Trombetta B.
        • Antonelli C.
        • Pascone R.
        • Valesini G.
        • Scalzi V.
        • Vona G.
        • Melegh B.
        • Zagradisnik B.
        • Assum G.
        • Efremov G.D.
        • Sellitto D.
        • Scozzari R.
        Strong intra- and inter-continental differentiation revealed by Y chromosome SNPs M269, U106 and U152.
        Forensic Sci. Int. Genet. 2011; 5: e49-52
        • Iacovacci G.
        • D’Atanasio E.
        • Marini O.
        • Coppa A.
        • Sellitto D.
        • Trombetta B.
        • Berti A.
        • Cruciani F.
        Forensic data and microvariant sequence characterization of 27 Y-STR loci analyzed in four Eastern African countries.
        Forensic Sci. Int. Genet. 2017; 27: 123-131
        • Serin A.
        • Canan H.
        • Alper B.
        • Kotan D.
        Molecular structure and genealogical characterization of the DYS458.2 allelic variants founded in Turkey population samples.
        Forensic Sci. Int. Genet. Suppl. Ser. 2011; 3: e281-e282
        • Lee E.Y.
        • Shin K.-J.
        • Rakha A.
        • Sim J.E.
        • Park M.J.
        • Kim N.Y.
        • Yang W.I.
        • Lee H.Y.
        Analysis of 22 Y chromosomal STR haplotypes and Y haplogroup distribution in Pathans of Pakistan.
        Forensic Sci. Int. Genet. 2014; 11: 111-116
        • Lee E.Y.
        • Lee H.Y.
        • Shin K.-J.
        Off-ladder alleles due to a single nucleotide polymorphism in the flanking region at DYS481 detected by the PowerPlex® Y23 System.
        Forensic Sci. Int. Genet. 2016; 24: e7-e8
        • Myres N.M.
        • Ritchie K.H.
        • Lin A.A.
        • Hughes R.H.
        • Woodward S.R.
        • Underhill P.A.
        Y-chromosome short tandem repeat intermediate variant alleles DYS392.2, DYS449.2, and DYS385.2 delineate new phylogenetic substructure in human Y-chromosome haplogroup tree.
        Croat. Med. J. 2009; 50: 239-249
        • Budowle B.
        • Aranda X.G.
        • Lagace R.E.
        • Hennessy L.K.
        • Planz J.V.
        • Rodriguez M.
        • Eisenberg A.J.
        Null allele sequence structure at the DYS448 locus and implications for profile interpretation.
        Int. J. Leg. Med. 2008; 122: 421-427
        • Sánchez C.
        • Barrot C.
        • Xifró A.
        • Ortega M.
        • de Aranda I.G.
        • Huguet E.
        • Corbella J.
        • Gené M.
        Haplotype frequencies of 16 Y-chromosome STR loci in the Barcelona metropolitan area population using Y-Filer™ kit.
        Forensic Sci. Int. 2007; 172: 211-217
        • Park M.J.
        • Shin K.-J.
        • Kim N.Y.
        • Yang W.I.
        • Cho S.-H.
        • Lee H.Y.
        Characterization of deletions in the DYS385 flanking region and null alleles associated with AZFc microdeletions in Koreans.
        J. Forensic Sci. 2008; 53: 331-334
        • Kuroda-Kawaguchi T.
        • Skaletsky H.
        • Brown L.G.
        • Minx P.J.
        • Cordum H.S.
        • Waterston R.H.
        • Wilson R.K.
        • Silber S.
        • Oates R.
        • Rozen S.
        • Page D.C.
        The AZFc region of the Y chromosome features massive palindromes and uniform recurrent deletions in infertile men.
        Nat. Genet. 2001; 29: 279-286
        • Mizuno N.
        • Nakahara H.
        • Sekiguchi K.
        • Yoshida K.
        • Nakano M.
        • Kasai K.
        16 Y chromosomal STR haplotypes in Japanese.
        Forensic Sci. Int. 2008; 174: 71-76
        • Parkin E.J.
        • Kraayenbrink T.
        • Opgenort J.R.M.L.
        • van Driem G.L.
        • Tuladhar N.M.
        • de Knijff P.
        • Jobling M.A.
        Diversity of 26-locus Y-STR haplotypes in a Nepalese population sample: isolation and drift in the Himalayas.
        Forensic Sci. Int. 2007; 166: 176-181
        • Chang Y.M.
        • Perumal R.
        • Keat P.Y.
        • Kuehn D.L.C.
        Haplotype diversity of 16 Y-chromosomal STRs in three main ethnic populations (Malays, Chinese and Indians) in Malaysia.
        Forensic Sci. Int. 2007; 167: 70-76
        • Ye Y.
        • Gao J.
        • Fan G.
        • Liao L.
        • Hou Y.
        Population genetics for 23 Y-STR loci in Tibetan in China and confirmation of DYS448 null allele.
        Forensic Sci. Int. Genet. 2015; 16: e7-e10
        • Yang Y.
        • Wang W.
        • Cheng F.
        • Chen M.
        • Chen T.
        • Zhao J.
        • Chen C.
        • Shi Y.
        • Li C.
        • Chen C.
        • Liu Y.
        • Yan J.
        Haplotypic polymorphisms and mutation rate estimates of 22 Y-chromosome STRs in the Northern Chinese Han father–son pairs.
        Sci. Rep. 2018; 8: 7135
        • Roewer L.
        • Krüger C.
        • Willuweit S.
        • Nagy M.
        • Rodig H.
        • Kokshunova L.
        • Rothämel T.
        • Kravchenko S.
        • Jobling M.A.
        • Stoneking M.
        • Nasidze I.
        Y-chromosomal STR haplotypes in Kalmyk population samples.
        Forensic Sci. Int. 2007; 173: 204-209
        • Balaresque P.
        • Bowden G.R.
        • Parkin E.J.
        • Omran G.A.
        • Heyer E.
        • Quintana-Murci L.
        • Roewer L.
        • Stoneking M.
        • Nasidze I.
        • Carvalho-Silva D.R.
        • Tyler-Smith C.
        • de Knijff P.
        • Jobling M.A.
        Dynamic nature of the proximal AZFc region of the human Y chromosome: multiple independent deletion and duplication events revealed by microsatellite analysis.
        Hum. Mutat. 2008; 29: 1171-1180
        • Purps J.
        • Siegert S.
        • Willuweit S.
        • Nagy M.
        • Alves C.
        • Salazar R.
        • Angustia S.M.
        • Santos L.H.
        • Anslinger K.
        • Bayer B.
        • Ayub Q.
        • Wei W.
        • Xue Y.
        • Tyler-Smith C.
        • Bafalluy M.B.
        • Martinez-Jarreta B.
        • Egyed B.
        • Balitzki B.
        • Tschumi S.
        • Ballard D.
        • Court D.S.
        • Barrantes X.
        • Bassler G.
        • Wiest T.
        • Berger B.
        • Niederstatter H.
        • Parson W.
        • Davis C.
        • Budowle B.
        • Burri H.
        • Borer U.
        • Koller C.
        • Carvalho E.F.
        • Domingues P.M.
        • Chamoun W.T.
        • Coble M.D.
        • Hill C.R.
        • Corach D.
        • Caputo M.
        • D'Amato M.E.
        • Davison S.
        • Decorte R.
        • Larmuseau M.H.
        • Ottoni C.
        • Rickards O.
        • Lu D.
        • Jiang C.
        • Dobosz T.
        • Jonkisz A.
        • Frank W.E.
        • Furac I.
        • Gehrig C.
        • Castella V.
        • Grskovic B.
        • Haas C.
        • Wobst J.
        • Hadzic G.
        • Drobnic K.
        • Honda K.
        • Hou Y.
        • Zhou D.
        • Li Y.
        • Hu S.
        • Chen S.
        • Immel U.D.
        • Lessig R.
        • Jakovski Z.
        • Ilievska T.
        • Klann A.E.
        • Garcia C.C.
        • de Knijff P.
        • Kraaijenbrink T.
        • Kondili A.
        • Miniati P.
        • Vouropoulou M.
        • Kovacevic L.
        • Marjanovic D.
        • Lindner I.
        • Mansour I.
        • Al-Azem M.
        • Andari A.E.
        • Marino M.
        • Furfuro S.
        • Locarno L.
        • Martin P.
        • Luque G.M.
        • Alonso A.
        • Miranda L.S.
        • Moreira H.
        • Mizuno N.
        • Iwashima Y.
        • Neto R.S.
        • Nogueira T.L.
        • Silva R.
        • Nastainczyk-Wulf M.
        • Edelmann J.
        • Kohl M.
        • Nie S.
        • Wang X.
        • Cheng B.
        • Nunez C.
        • Pancorbo M.M.
        • Olofsson J.K.
        • Morling N.
        • Onofri V.
        • Tagliabracci A.
        • Pamjav H.
        • Volgyi A.
        • Barany G.
        • Pawlowski R.
        • Maciejewska A.
        • Pelotti S.
        • Pepinski W.
        • Abreu-Glowacka M.
        • Phillips C.
        • Cardenas J.
        • Rey-Gonzalez D.
        • Salas A.
        • Brisighelli F.
        • Capelli C.
        • Toscanini U.
        • Piccinini A.
        • Piglionica M.
        • Baldassarra S.L.
        • Ploski R.
        • Konarzewska M.
        • Jastrzebska E.
        • Robino C.
        • Sajantila A.
        • Palo J.U.
        • Guevara E.
        • Salvador J.
        • Ungria M.C.
        • Rodriguez J.J.
        • Schmidt U.
        • Schlauderer N.
        • Saukko P.
        • Schneider P.M.
        • Sirker M.
        • Shin K.J.
        • Oh Y.N.
        • Skitsa I.
        • Ampati A.
        • Smith T.G.
        • Calvit L.S.
        • Stenzl V.
        • Capal T.
        • Tillmar A.
        • Nilsson H.
        • Turrina S.
        • De Leo D.
        • Verzeletti A.
        • Cortellini V.
        • Wetton J.H.
        • Gwynne G.M.
        • Jobling M.A.
        • Whittle M.R.
        • Sumita D.R.
        • Wolanska-Nowak P.
        • Yong R.Y.
        • Krawczak M.
        • Nothnagel M.
        • Roewer L.
        A global analysis of Y-chromosomal haplotype diversity for 23 STR loci.
        Forensic Sci. Int. Genet. 2014; 12: 12-23
        • Aliferi A.
        • Thomson J.
        • McDonald A.
        • Paynter V.M.
        • Ferguson S.
        • Vanhinsbergh D.
        • Syndercombe Court D.
        • Ballard D.
        UK and Irish Y-STR population data-A catalogue of variant alleles.
        Forensic Sci. Int. Genet. 2018; 34: e1-e6
        • Valverde L.
        • Illescas M.J.
        • Villaescusa P.
        • Gotor A.M.
        • García A.
        • Cardoso S.
        • Algorta J.
        • Catarino S.
        • Rouault K.
        • Férec C.
        • Hardiman O.
        • Zarrabeitia M.
        • Jiménez S.
        • Pinheiro M.F.
        • Jarreta B.M.
        • Olofsson J.
        • Morling N.
        • de Pancorbo M.M.
        New clues to the evolutionary history of the main European paternal lineage M269: dissection of the Y-SNP S116 in Atlantic Europe and Iberia.
        Eur. J. Hum. Genet. 2016; 24: 437-441
        • Olalde I.
        • Brace S.
        • Allentoft M.E.
        • Armit I.
        • Kristiansen K.
        • Booth T.
        • Rohland N.
        • Mallick S.
        • Szecsenyi-Nagy A.
        • Mittnik A.
        • Altena E.
        • Lipson M.
        • Lazaridis I.
        • Harper T.K.
        • Patterson N.
        • Broomandkhoshbacht N.
        • Diekmann Y.
        • Faltyskova Z.
        • Fernandes D.
        • Ferry M.
        • Harney E.
        • de Knijff P.
        • Michel M.
        • Oppenheimer J.
        • Stewardson K.
        • Barclay A.
        • Alt K.W.
        • Liesau C.
        • Rios P.
        • Blasco C.
        • Miguel J.V.
        • Garcia R.M.
        • Fernandez A.A.
        • Banffy E.
        • Bernabo-Brea M.
        • Billoin D.
        • Bonsall C.
        • Bonsall L.
        • Allen T.
        • Buster L.
        • Carver S.
        • Navarro L.C.
        • Craig O.E.
        • Cook G.T.
        • Cunliffe B.
        • Denaire A.
        • Dinwiddy K.E.
        • Dodwell N.
        • Ernee M.
        • Evans C.
        • Kucharik M.
        • Farre J.F.
        • Fowler C.
        • Gazenbeek M.
        • Pena R.G.
        • Haber-Uriarte M.
        • Haduch E.
        • Hey G.
        • Jowett N.
        • Knowles T.
        • Massy K.
        • Pfrengle S.
        • Lefranc P.
        • Lemercier O.
        • Lefebvre A.
        • Martinez C.H.
        • Olmo V.G.
        • Ramirez A.B.
        • Maurandi J.L.
        • Majo T.
        • McKinley J.I.
        • McSweeney K.
        • Mende B.G.
        • Modi A.
        • Kulcsar G.
        • Kiss V.
        • Czene A.
        • Patay R.
        • Endrodi A.
        • Kohler K.
        • Hajdu T.
        • Szeniczey T.
        • Dani J.
        • Bernert Z.
        • Hoole M.
        • Cheronet O.
        • Keating D.
        • Veleminsky P.
        • Dobes M.
        • Candilio F.
        • Brown F.
        • Fernandez R.F.
        • Herrero-Corral A.M.
        • Tusa S.
        • Carnieri E.
        • Lentini L.
        • Valenti A.
        • Zanini A.
        • Waddington C.
        • Delibes G.
        • Guerra-Doce E.
        • Neil B.
        • Brittain M.
        • Luke M.
        • Mortimer R.
        • Desideri J.
        • Besse M.
        • Brucken G.
        • Furmanek M.
        • Haluszko A.
        • Mackiewicz M.
        • Rapinski A.
        • Leach S.
        • Soriano I.
        • Lillios K.T.
        • Cardoso J.L.
        • Pearson M.P.
        • Wlodarczak P.
        • Price T.D.
        • Prieto P.
        • Rey P.J.
        • Risch R.
        • Rojo Guerra M.A.
        • Schmitt A.
        • Serralongue J.
        • Silva A.M.
        • Smrcka V.
        • Vergnaud L.
        • Zilhao J.
        • Caramelli D.
        • Higham T.
        • Thomas M.G.
        • Kennett D.J.
        • Fokkens H.
        • Heyd V.
        • Sheridan A.
        • Sjogren K.G.
        • Stockhammer P.W.
        • Krause J.
        • Pinhasi R.
        • Haak W.
        • Barnes I.
        • Lalueza-Fox C.
        • Reich D.
        The Beaker phenomenon and the genomic transformation of northwest Europe.
        Nature. 2018; 555: 190-196
        • Huszar T.I.
        • Jobling M.A.
        • Wetton J.H.
        A phylogenetic framework facilitates Y-STR variant discovery and classification via massively parallel sequencing.
        Forensic Sci. Int. Genet. 2018; 35: 97-106
        • Muzzio M.
        • Ramallo V.
        • Motti J.M.B.
        • Santos M.R.
        • López Camelo J.S.
        • Bailliet G.
        Software for Y-haplogroup predictions: a word of caution.
        Int. J. Legal Med. 2011; 125: 143-147
        • Athey W.
        Comments on the article, "Software for Y haplogroup predictions, a word of caution.
        Int. J. Legal Med. 2011; 125 (author reply 905-906): 901-903
        • Emmerova B.
        • Ehler E.
        • Comas D.
        • Votrubova J.
        • Vanek D.
        Comparison of Y-chromosomal haplogroup predictors.
        Forensic Sci. Int. Genet. Suppl. Ser. 2017; 6: E145-E147
        • Petrejcikova E.
        • Carnogurska J.
        • Hronska D.
        • Bernasovska J.
        • Boronova I.
        • Gabrikova D.
        • Bozikova A.
        • Macekova S.
        Y-SNP analysis versus Y-haplogroup predictor in the Slovak population.
        Anthropol. Anz. 2014; 71: 275-285
        • Rootsi S.
        • Magri C.
        • Kivisild T.
        • Benuzzi G.
        • Help H.
        • Bermisheva M.
        • Kutuev I.
        • Barac L.
        • Pericic M.
        • Balanovsky O.
        • Pshenichnov A.
        • Dion D.
        • Grobei M.
        • Zhivotovsky L.A.
        • Battaglia V.
        • Achilli A.
        • Al-Zahery N.
        • Parik J.
        • King R.
        • Cinnioglu C.
        • Khusnutdinova E.
        • Rudan P.
        • Balanovska E.
        • Scheffrahn W.
        • Simonescu M.
        • Brehm A.
        • Goncalves R.
        • Rosa A.
        • Moisan J.P.
        • Chaventre A.
        • Ferak V.
        • Furedi S.
        • Oefner P.J.
        • Shen P.
        • Beckman L.
        • Mikerezi I.
        • Terzic R.
        • Primorac D.
        • Cambon-Thomsen A.
        • Krumina A.
        • Torroni A.
        • Underhill P.A.
        • Santachiara-Benerecetti A.S.
        • Villems R.
        • Semino O.
        Phylogeography of Y-chromosome haplogroup I reveals distinct domains of prehistoric gene flow in europe.
        Am. J. Hum. Genet. 2004; 75: 128-137
        • Cinnioğlu C.
        • King R.
        • Kivisild T.
        • Kalfoğlu E.
        • Atasoy S.
        • Cavalleri G.L.
        • Lillie A.S.
        • Roseman C.C.
        • Lin A.A.
        • Prince K.
        • Oefner P.J.
        • Shen P.
        • Semino O.
        • Cavalli-Sforza L.L.
        • Underhill P.A.
        Excavating Y-chromosome haplotype strata in Anatolia.
        Hum. Genet. 2004; 114: 127-148
        • Semino O.
        • Magri C.
        • Benuzzi G.
        • Lin A.A.
        • Al-Zahery N.
        • Battaglia V.
        • Maccioni L.
        • Triantaphyllidis C.
        • Shen P.
        • Oefner P.J.
        • Zhivotovsky L.A.
        • King R.
        • Torroni A.
        • Cavalli-Sforza L.L.
        • Underhill P.A.
        • Santachiara-Benerecetti A.S.
        Origin, diffusion, and differentiation of Y-chromosome haplogroups E and J: inferences on the neolithization of Europe and later migratory events in the Mediterranean area.
        Am. J. Hum. Genet. 2004; 74: 1023-1034
        • Balaresque P.
        • Bowden G.R.
        • Adams S.M.
        • Leung H.Y.
        • King T.E.
        • Rosser Z.H.
        • Goodwin J.
        • Moisan J.P.
        • Richard C.
        • Millward A.
        • Demaine A.G.
        • Barbujani G.
        • Previdere C.
        • Wilson I.J.
        • Tyler-Smith C.
        • Jobling M.A.
        A predominantly neolithic origin for European paternal lineages.
        PLoS Biol. 2010; 8e1000285
        • Myres N.M.
        • Rootsi S.
        • Lin A.A.
        • Järve M.
        • King R.J.
        • Kutuev I.
        • Cabrera V.M.
        • Khusnutdinova E.K.
        • Pshenichnov A.
        • Yunusbayev B.
        • Balanovsky O.
        • Balanovska E.
        • Rudan P.
        • Baldovic M.
        • Herrera R.J.
        • Chiaroni J.
        • Di Cristofaro J.
        • Villems R.
        • Kivisild T.
        • Underhill P.A.
        A major Y-chromosome haplogroup R1b holocene era founder effect in central and Western Europe.
        Eur. J. Hum. Genet.: EJHG. 2011; 19: 95-101
        • Haak W.
        • Lazaridis I.
        • Patterson N.
        • Rohland N.
        • Mallick S.
        • Llamas B.
        • Brandt G.
        • Nordenfelt S.
        • Harney E.
        • Stewardson K.
        • Fu Q.
        • Mittnik A.
        • Banffy E.
        • Economou C.
        • Francken M.
        • Friederich S.
        • Pena R.G.
        • Hallgren F.
        • Khartanovich V.
        • Khokhlov A.
        • Kunst M.
        • Kuznetsov P.
        • Meller H.
        • Mochalov O.
        • Moiseyev V.
        • Nicklisch N.
        • Pichler S.L.
        • Risch R.
        • Rojo Guerra M.A.
        • Roth C.
        • Szecsenyi-Nagy A.
        • Wahl J.
        • Meyer M.
        • Krause J.
        • Brown D.
        • Anthony D.
        • Cooper A.
        • Alt K.W.
        • Reich D.
        Massive migration from the steppe was a source for Indo-European languages in Europe.
        Nature. 2015; 522: 207-211
        • Allentoft M.E.
        • Sikora M.
        • Sjogren K.G.
        • Rasmussen S.
        • Rasmussen M.
        • Stenderup J.
        • Damgaard P.B.
        • Schroeder H.
        • Ahlstrom T.
        • Vinner L.
        • Malaspinas A.S.
        • Margaryan A.
        • Higham T.
        • Chivall D.
        • Lynnerup N.
        • Harvig L.
        • Baron J.
        • Della Casa P.
        • Dabrowski P.
        • Duffy P.R.
        • Ebel A.V.
        • Epimakhov A.
        • Frei K.
        • Furmanek M.
        • Gralak T.
        • Gromov A.
        • Gronkiewicz S.
        • Grupe G.
        • Hajdu T.
        • Jarysz R.
        • Khartanovich V.
        • Khokhlov A.
        • Kiss V.
        • Kolar J.
        • Kriiska A.
        • Lasak I.
        • Longhi C.
        • McGlynn G.
        • Merkevicius A.
        • Merkyte I.
        • Metspalu M.
        • Mkrtchyan R.
        • Moiseyev V.
        • Paja L.
        • Palfi G.
        • Pokutta D.
        • Pospieszny L.
        • Price T.D.
        • Saag L.
        • Sablin M.
        • Shishlina N.
        • Smrcka V.
        • Soenov V.I.
        • Szeverenyi V.
        • Toth G.
        • Trifanova S.V.
        • Varul L.
        • Vicze M.
        • Yepiskoposyan L.
        • Zhitenev V.
        • Orlando L.
        • Sicheritz-Ponten T.
        • Brunak S.
        • Nielsen R.
        • Kristiansen K.
        • Willerslev E.
        Population genomics of bronze age Eurasia.
        Nature. 2015; 522: 167-172
        • Lee E.J.
        • Makarewicz C.
        • Renneberg R.
        • Harder M.
        • Krause-Kyora B.
        • Müller S.
        • Ostritz S.
        • Fehren-Schmitz L.
        • Schreiber S.
        • Müller J.
        • von Wurmb-Schwark N.
        • Nebel A.
        Emerging genetic patterns of the European neolithic: perspectives from a late neolithic bell beaker burial site in Germany.
        Am. J. Phys. Anthropol. 2012; 148: 571-579
        • Grugni V.
        • Raveane A.
        • Mattioli F.
        • Battaglia V.
        • Sala C.
        • Toniolo D.
        • Ferretti L.
        • Gardella R.
        • Achilli A.
        • Olivieri A.
        • Torroni A.
        • Passarino G.
        • Semino O.
        Reconstructing the genetic history of Italians: new insights from a male (Y-chromosome) perspective.
        Ann. Hum. Biol. 2018; 45: 44-56
        • Vietti G.
        Lepontier, Historisches Lexikon der Schweiz (HLS), Schweizerische Akademie der Geistes- und Sozialwissenschaften, Bern.
        2008
        • Müller F.
        • Kaenel G.
        • Lüscher G.
        Die Schweiz vom Paläolithikum bis zum frühen Mittelalter - SPM IV - Eisenzeit, Schweizerische Gesellschaft für Ur- und Frühgeschichte, Basel.
        1999
        • Eska J.F.
        The Linguistic Position of Lepontic, Proceedings of the Twenty-Fourth Annual Meeting of the Berkeley Linguistics Society: Special Session on Indo-European Subgrouping and Internal Relation, Linguistic Society of America1998: 2-11
        • Niederstatter H.
        • Berger B.
        • Kayser M.
        • Parson W.
        Differences in urbanization degree and consequences on the diversity of conventional vs. rapidly mutating Y-STRs in five municipalities from a small region of the Tyrolean Alps in Austria.
        Forensic Sci. Int. Genet. 2016; 24: 180-193