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The Y-chromosome is a widely studied and useful small part of the genome providing different applications for interdisciplinary research. In many (Western) societies, the Y-chromosome and surnames are paternally co-inherited, suggesting a corresponding Y-haplotype for every namesake. While it has already been observed that this correlation may be disrupted by a false-paternity event, adoption, anonymous sperm donor or the co-founding of surnames, extensive information on the strength of the surname match frequency (SMF) with the Y-chromosome remains rather unknown. For the first time in Belgium and the Netherlands, we were able to study this correlation using 2,401 males genotyped for 46 Y-STRs and 183 Y-SNPs. The SMF was observed to be dependent on the number of Y-STRs analyzed, their mutation rates and the number of Y-STR differences allowed for a kinship. For a perfect match, the Yfiler® Plus and our in-house YForGen kit gave a similar high SMF of 98%, but for non-perfect matches, the latter could overall be identified as the best kit. The SMF generally increased due to less mismatches when encountering [1] deep Y-subhaplogroups, [2] less frequently occurring surnames, and [3] small geographical distances between relatives. This novel information enabled the design of a surname prediction model based on genetic and geographical distances of a kinship. The prediction model has an area under the curve (AUC) of 0.9 and is therefore useable for DNA kinship priority listing in estimation applications like forensic familial searching., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Paternity testing using genetic markers has shown that extra-pair paternity (EPP) is common in many pair-bonded species [1, 2]. Evolutionary theory and empirical data show that extra-pair copulations can increase the fitness of males as well as females [3, 4]. This can carry a significant fitness cost for the social father, who then invests in rearing offspring that biologically are not his own [5]. In human populations, the incidence and correlates of extra-pair paternity remain highly contentious [2, 6, 7]. Here, we use a population-level genetic genealogy approach [6, 8] to reconstruct spatiotemporal patterns in human EPP rates. Using patrilineal genealogies from the Low Countries spanning a period of over 500 years and Y chromosome genotyping of living descendants, our analysis reveals that historical EPP rates, while low overall, were strongly impacted by socioeconomic and demographic factors. Specifically, we observe that estimated EPP rates among married couples varied by more than an order of magnitude, from 0.4% to 5.9%, and peaked among families with a low socioeconomic background living in densely populated cities of the late 19 th century. Our results support theoretical predictions that social context can strongly affect the outcomes of sexual conflict in human populations by modulating the incentives and opportunities for engaging in extra-pair relationships [9-11]. These findings show how contemporary genetic data combined with in-depth genealogies open up a new window on the sexual behavior of our ancestors., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

The reliquary of Jacques de Vitry, a prominent clergyman and theologian in the early 13th century, has experienced several transfers over the last centuries, which seriously question the attribution of the remains to the late Cardinal. Uncertainty about the year of his birth poses an additional question regarding his age at death in 1240. The reliquary, located in the Saint Marie d'Oigines church, Belgium, was reopened in 2015 for an interdisciplinary study around his relics as well as the Treasure of Oignies, a remarkable cultural heritage notably built from Jacques de Vitry's donation. Anthropological, isotopic and genetic analyses were performed independently on the remains found in the reliquary. Results of the analyses provided evidence that the likelihood that these remains are those of Jacques de Vitry is very high: the remains belong to the same human male individual and the historical tradition about his age is confirmed. In addition, a separate relic (left tibia) was analysed and found to match with the remains of the reliquary (right tibia). The unique Jacques de Vitry's mitre, made of parchment, was sampled non-destructively and the extracted parchment collagen was analysed by a proteomic method in order to determine the animal species. The results showed that, surprisingly, not all parts of the mitre were made from the same species. All together, these findings are expected to fertilize knowledge carried by historical tradition around the relics of Jacques de Vitry and his related cultural heritage., Competing Interests: The authors have declared that no competing interests exist.

Y-chromosomal single nucleotide polymorphisms (Y-SNPs) represent a powerful tool in forensic research and casework, especially for inferring paternal ancestry of unknown perpetrators and unidentified bodies. However, the wealth of recently discovered Y-SNPs, the 'jungle' of different evolutionary lineage trees and nomenclatures, and the lack of population-wide data of many phylogenetically mapped Y-SNPs, limits the use of Y-SNPs in routine forensic approaches. Recently, a concise reference phylogeny of the human Y chromosome, the 'Minimal Reference Y-tree', was introduced aiming to provide a stable phylogeny with optimal global discrimination capacity by including the most resolving Y-SNPs. Here, we obtained a representative sample of 270 whole-genome sequences (WGS) to grasp the Y-SNP variation within the autochthonous Flemish population (Belgium, Western Europe) according to this reference Y-tree. The high quality of the Y-SNP calling was guaranteed for the WGS sample as well as its representativeness for the Flemish population based on the comparison of the main haplogroup frequencies with those from earlier studies on Flanders and the Netherlands. The 270 Flemish Y chromosomes were assigned to 98 different sub-haplogroups of the Minimal Reference Y-tree, showing its high potential of discrimination and confirming the spectrum of evolutionary lineages within Western Europe in general and within Flanders in particular. The full database with all Y-SNP calls of the Flemish sample is public available for future updates including forensic and population genetic studies. New initiatives to categorise Y-SNP variation in other populations according to the reference phylogeny of the Y chromosome are highly encouraged for forensic applications. Recommendations to realise such future population sample sets are discussed based on this study., (Copyright © 2017 Elsevier B.V. All rights reserved.)

There is limited knowledge on the biological relatedness between citizens and on the demographical dynamics within villages, towns and cities in pre-17th century Western Europe. By combining Y-chromosomal genotypes, in-depth genealogies and surname data in a strict genetic genealogical approach, it is possible to provide insights into the genetic diversity and the relatedness between indigenous paternal lineages within a particular community at the time of the surname adoption. To obtain these insights, six Flemish communities were selected in this study based on the differences in geography and historical development. After rigorous selection of appropriate DNA donors, low relatedness between Y chromosomes of different surnames was found within each community, although there is co-occurrence of these surnames in each community since the start of the surname adoption between the 14th and 15th century. Next, the high communal diversity in Y-chromosomal lineages was comparable with the regional diversity across Flanders at that time. Moreover, clinal distributions of particular Y-chromosomal lineages between the communities were observed according to the clinal distributions earlier observed across the Flemish regions and Western Europe. No significant indication for genetic differences between communities with distinct historical development was found in the analysis. These genetic results provide relevant information for studies in historical sciences, archaeology, forensic genetics and genealogy.

Y-chromosomal short tandem repeats (Y-STRs) are often used in addition to Y-chromosomal single-nucleotide polymorphisms (Y-SNP) to detect subtle patterns in a population genetic structure. There are, however, indications for Y-STR haplotype resemblance across different subhaplogroups within haplogroup R1b1b2 (R-M269) which may lead to erosion in the observation of the population genetic pattern. Hence the question arises whether Y-STR haplotypes are still informative beyond high-resolution Y-SNP genotyping for population genetic studies. To address this question, we genotyped the Y chromosomes of more than 1000 males originating from the West-European regions of Flanders (Belgium), North-Brabant and Limburg (the Netherlands) at the highest resolution of the current Y-SNP tree together with 38 commonly used Y-STRs. We observed high resemblance of Y-STR haplotypes between males belonging to different subhaplogroups of haplogroup R-M269. Several subhaplogroups within R-M269 could not be distinguished from each other based on differences in Y-STR haplotype variation. The most likely hypothesis to explain this similarity of Y-STR haplotypes within the population of R-M269 members is a recent radiation where various subhaplogroups originated within a relatively short time period. We conclude that high-resolution Y-SNP typing rather than Y-STR typing might be more useful to study population genetic patterns in (Western) Europe., (© 2014 John Wiley & Sons Ltd/University College London.)

Recent evidence suggests that seeking out extra-pair paternity (EPP) can be a viable alternative reproductive strategy for both males and females in many pair-bonded species, including humans. Accurate data on EPP rates in humans, however, are scant and mostly restricted to extant populations. Here, we provide the first large-scale, unbiased genetic study of historical EPP rates in a Western European human population based on combining Y-chromosomal data to infer genetic patrilineages with genealogical and surname data, which reflect known historical presumed paternity. Using two independent methods, we estimate that over the last few centuries, EPP rates in Flanders (Belgium) were only around 1–2% per generation. This figure is substantially lower than the 8–30% per generation reported in some behavioural studies on historical EPP rates, but comparable with the rates reported by other genetic studies of contemporary Western European populations. These results suggest that human EPP rates have not changed substantially during the last 400 years in Flanders and imply that legal genealogies rarely differ from the biological ones. This result has significant implications for a diverse set of fields, including human population genetics, historical demography, forensic science and human sociobiology.

Allele frequencies and haplotypes for 12 Y-chromosomal STR loci included in the Powerplex System (Promega, Madison, USA) were determined in a sample of 113 unrelated males of Belgian origin. Ninety-nine different haplotypes were observed with an overall haplotype diversity of 0.997.

The allele and genotype distributions for 15 STR loci included in the AmpFlSTR SGM Plus and AmpFlSTR Profiler kits (Applied Biosystems, Foster City, USA) were determined in a sample of 222 unrelated individuals of Belgian origin.

A protocol for simultaneous amplification of the tetrameric STR loci HUMVWA, HUMTH01, D21S11 and HPRT has been developed in this study. Fluorescent amplified alleles were detected by laser scanning on the ALF DNA sequencer, and identified with locus specific allelic ladders. A sequencing survey of these STR loci was performed in 40 selected individuals from three major ethnic groups and confirmed the data reported previously. At the D21S11 locus, a new allele of 207 bp, was found in a Belgian Caucasian individual and designated as allele 25.2. Sequence analysis of this allele revealed that it contained a 14 bp deletion of (TCTA)3 TA at the beginning of the constant region. A nonconsensus allele of 245 bp, described and designated as allele 33.2.3(2x) by Brinkmann et al. (1996), was identified in an individual of central African origin. In addition, three new sequence variants of the allele 29, 30 and 32 were observed at D21S11.

The PCR technique was used to analyze the DXYS17 locus in the pseudoautosomal region of the X and the Y chromosomes. Analysis on an automated DNA sequencer allowed for sensitive and highly accurate typing of 16 different alleles with a size between 480 and 1,100 bp. Two DXYS17 alleles migrated with the same size on agarose or denaturing polyacrylamide gels but with different mobilities on nondenaturing polyacrylamide gels. Sequence analysis showed that, while an identical number of repeats were present in both alleles, differences in the composition of the units were observed. The origin of these differences was found in the 28- and 33-bp units, which only had a specific repeat pattern at the 5' and 3' ends of the region. The genotype distribution for DXYS17 in a Caucasian population did not deviate from the values expected under Hardy-Weinberg equilibrium. However, the frequency of one allele and one genotype was significantly different between males and females. Segregation analysis showed that this difference was the result of a nonrandom distribution of certain alleles on the sex chromosomes in males.

Using Southern blotting and the polymerase chain reaction, the prevalence of the haplotypes for XV2c, CS7, KM19 and D9 on CF and on normal chromosomes could be determined in 35 Belgian families. A set of primers complementary to the DNA sequence of the CF gene around the delta F508 deletion was used to amplify this particular segment of the gene. In a total of 57 families, deletion screening showed that 69 out of 116 CF chromosomes (59.5%) carried the delta F508 deletion. Both the delta F508 deletion and another mutation(s) showed strong association with the haplotype 1-2-2-2.