Y-chromosome diversity in Catalan surname samples: insights into surname origin and frequency

Development and validation of YARN: A novel SE-400 MPS kit for East Asian paternal lineage analysis

Y-chromosomal short tandem repeat polymorphisms (Y-STRs) and Y-chromosomal single nucleotide polymorphisms (Y-SNPs) are valuable genetic markers used in paternal lineage identification and population genetics. Currently, there is a lack of an effective panel that integrates Y-STRs and Y-SNPs for studying paternal lineages, particularly in East Asian populations. Hence, we developed a novel Y-chromosomal targeted panel called YARN (Y-chromosome Ancestry and Region Network) based on multiplex PCR and a single-end 400 massive parallel sequencing (MPS) strategy, consisting of 44 patrilineage Y-STRs and 260 evolutionary Y-SNPs. A total of 386 reactions were validated for the effectiveness and applicability of YARN according to SWGDAM validation guidelines, including sensitivity (with a minimum input gDNA of 0.125 ng), mixture identification (ranging from 1:1-1:10), PCR inhibitor testing (using substances such as 50 μM hematin, 100 μM hemoglobin, 100 μM humic acid, and 2.5 mM indigo dye), species specificity (successfully distinguishing humans from other animals), repeatability study (achieved 100% accuracy), and concordance study (with 99.91% accuracy for 1121 Y-STR alleles). Furthermore, we conducted a pilot study using YARN in a cohort of 484 Han Chinese males from Huaiji County, Zhaoqing City, Guangdong, China (GDZQHJ cohort). In this cohort, we identified 52 different Y-haplogroups and 73 different surnames. We found weak to moderate correlations between the Y-haplogroups, Chinese surnames, and geographical locations of the GDZQHJ cohort (with λ values ranging from 0.050 to 0.340). However, when we combined two different categories into a new independent variable, we observed stronger correlations (with λ values ranging from 0.617 to 0.754). Overall, the YARN panel, which combines Y-STR and Y-SNP genetic markers, meets forensic DNA quality assurance guidelines and holds potential for East Asian geographical origin inference and paternal lineage analysis.

Opt-in or out? Public perspectives on forensic DNA kinship investigations within the Dutch-speaking community

Forensic DNA kinship investigation involves analyzing genetic relationships between individuals to offer new leads for solving (cold) cases. Familial DNA matching has become a valuable asset in criminal case investigations, especially when traditional DNA methods hit dead ends. However, concerns surrounding ethical and privacy implications raised questions about its implementation and acceptance among the general public. The present study investigated the public perspectives regarding forensic DNA kinship investigations among 1710 Dutch-speaking Belgians using an online cross-sectional survey. The questionnaire consisted of three categories, including personal information, DNA knowledge, and their opinion on several familial DNA searching and investigative genetic genealogy related questions. The participants' average DNA knowledge score was 71 %, indicating a relatively high level of understanding of DNA-related concepts. Remarkably, the study revealed that 92 % of the participants expressed willingness to cooperate as a volunteer in a forensic DNA kinship investigation, irrespective of their scientific background or educational level. Key factors influencing participation included assurance of painless sampling and robust privacy safeguards. Participants lacking familiarity with DNA hesitated more towards participating in forensic DNA analysis, referring to "the fear of the unknown". Despite ethical and privacy concerns, the highly positive attitude towards forensic DNA analysis reflects a level of empathy and willingness to contribute to the pursuit of justice. Nearly all participants (95 %) agreed to use online DNA databases for resolving violent crimes with forensic genetic genealogy, but half emphasized the need for prior informed consent, referring to the current "opt-in" system. The results underscore the need for stringent regulations and ethical oversight to ensure the responsible use of genetic data while striking a balance between public safety and the protection of individuals' privacy rights. These findings add to the growing body of evidence regarding the potential benefits of forensic DNA kinship matching as a tool in criminal investigations, suggesting its potential future utilization and legalization.

Exploring genetic counselors' experiences with non-paternity in clinical settings

Non-paternity (NP) is a challenging dilemma faced by genetics providers and there is little consensus on whether this finding should be disclosed. Discussions in the literature are highly theoretical, with limited research regarding how disclosure decisions are enacted in practice. We explored genetic counselors' (GCs) clinical experiences with NP to understand if, how, and why this finding is communicated. Our semi-structured interviews with genetic counselors in the United States and Canada were analyzed using reflexive thematic analysis to analyze data inductively, describe themes, and present a meaningful interpretation of the data. Eighteen participants who responded to list-serv messages were interviewed. Our framework describes five salient themes: (1) GC-lab relationship: the GCs awareness of laboratory processes such as quality control metrics that can uncover NP findings and the way in which a finding of NP was disclosed by the laboratory had an impact on disclosure decisions. This triggered a decision-making trajectory that involved (2) consultation, (3) ethical reasoning, and (4) practical constraints. GCs frequently consulted other professionals during decision-making. These conversations impacted disclosure decisions with some consultations carrying greater weight than others. GCs weighed moral concepts of patient autonomy, medical relevance, and preventing harm to rationalize decisions. Access to patients and documentation requirements often dictated how disclosure occurred. Finally, once a decision had been made and enacted, GCs used the experience to reconsider their approach to (5) consenting in future cases, with some GCs altering their pre-test counseling to always include a discussion of NP. Although NP scenarios are frequently unique in context, our findings demonstrate several common decision-making factors GCs harness to navigate the identification of NP through clinical genetic testing.

A forensic population database in El Salvador: 58 STRs and 94 SNPs

We have genotyped the 58 STRs (27 autosomal, 24 Y-STRs and 7 X-STRs) and 94 autosomal SNPs in Illumina ForenSeq™ Primer Mix A in a sample of 248 men and 143 women from El Salvador, Central America. Regional division (Centro, Oriente, Occidente) showed in almost all cases F_ST values not significantly different from 0, and further analyses were applied only to the undivided, country-wide population. The overall random match probability (RMP) decreased from 6.79 × 10^-31 in length-based genotypes in the 27 autosomal STRs to 1.47 × 10^-34 in repeat-sequence based genotypes. Combining the autosomal loci in this set, RMP reaches 2.97 × 10^-70. In a population genetic analysis, El Salvador showed the lowest F_ST values with US Hispanics both for autosomal and X-STRs; however, it was much closer to Native Americans for the latter than for the former, in accordance with the well-known gender-biased admixture that created most Latin American populations.

The Unique Identification of an Unknown Soldier from the Estonian War of Independence

The identification of human remains is challenging mostly due to the bad condition of the remains and the available background information that is sometimes limited. The current case report is related to the identification of an unknown soldier from the Estonian War of Independence (1918-1920). The case includes an anthropological study of the remains, examinations of documents found with the exhumed remains, and kinship estimations based on archival documents, and DNA analyses. As the preliminary data pointed to remains of male origin, Y-chromosomal STR (short tandem repeat) analyses of 22 Y-STR loci were used to analyze the exhumed teeth. Reference samples from individuals from two paternal lineages were collected based on archival documents. Y-chromosomal STR results for the tooth samples were consistent with a patrilineal relationship to only one reference sample out of two proposed paternal lineages. Based on the provided pedigrees in the consistent case, the Y-STR results are approximately four million times more likely if the tooth sample originated from an individual related along the paternal line to the matching reference sample, than if the tooth sample originated from another person in the general population. Special considerations have to be met when limited evidence is available.

CSYseq: The first Y-chromosome sequencing tool typing a large number of Y-SNPs and Y-STRs to unravel worldwide human population genetics

Male-specific Y-chromosome (chrY) polymorphisms are interesting components of the DNA for population genetics. While single nucleotide polymorphisms (Y-SNPs) indicate distant evolutionary ancestry, short tandem repeats (Y-STRs) are able to identify close familial kinships. Detailed chrY analysis provides thus both biogeographical background information as paternal lineage identification. The rapid advancement of high-throughput massive parallel sequencing (MPS) technology in the past decade has revolutionized genetic research. Using MPS, single-base information of both Y-SNPs as Y-STRs can be analyzed in a single assay typing multiple samples at once. In this study, we present the first extensive chrY-specific targeted resequencing panel, the 'CSYseq', which simultaneously identifies slow mutating Y-SNPs as evolution markers and rapid mutating Y-STRs as patrilineage markers. The panel was validated by paired-end sequencing of 130 males, distributed over 65 deep-rooted pedigrees covering 1,279 generations. The CSYseq successfully targets 15,611 Y-SNPs including 9,014 phylogenetic informative Y-SNPs to identify 1,443 human evolutionary Y-subhaplogroup lineages worldwide. In addition, the CSYseq properly targets 202 Y-STRs, including 81 slow, 68 moderate, 27 fast and 26 rapid mutating Y-STRs to individualize close paternal relatives. The targeted chrY markers cover a high average number of reads (Y-SNP = 717, Y-STR = 150), easy interpretation, powerful discrimination capacity and chrY specificity. The CSYseq is interesting for research on different time scales: to identify evolutionary ancestry, to find distant family and to discriminate closely related males. Therefore, this panel serves as a unique tool valuable for a wide range of genetic-genealogical applications in interdisciplinary research within evolutionary, population, molecular, medical and forensic genetics.

The surname structure of Trentino (Italy) and its relationship with dialects and genes

BACKGROUND

Thanks to the availability of rich surname, linguistic and genetic information, together with its geographic and cultural complexity, Trentino (North-Eastern Italy) is an ideal place to test the relationships between genetic and cultural traits.

AIM

We provide a comprehensive study of population structures based on surname and dialect variability and evaluate their relationships with genetic diversity in Trentino.

SUBJECTS AND METHODS

Surname data were collected for 363 parishes, linguistic data for 57 dialects and genetic data for different sets of molecular markers (Y-chromosome, mtDNA, autosomal) in 10 populations. Analyses relied on different multivariate methods and correlation tests.

RESULTS

Besides the expected isolation-by-distance-like patterns (with few local exceptions, likely related to sociocultural instances), we detected a significant and geography-independent association between dialects and surnames. As for molecular markers, only Y-chromosomal STRs seem to be associated with the dialects, although no significant result was obtained. No evidence for correlation between molecular markers and surnames was observed.

CONCLUSION

Surnames act as cultural markers as do other words, although in this context they cannot be used as reliable proxies for genetic variability at a local scale.

Development of the decision tree model for distinguishing individuals of Chinese four surnames from Zhanjiang Han population based on Y-STR haplotypes

Co-separation studies between surnames and Y chromosome genetic markers are beneficial to revealing population migrations, surname origins, population formation histories and forensic familial searching. Genetic distributions of 27 Y-STRs in Chinese four surnames (Li, Lin, Chen and Huang) from Zhanjiang Han population were investigated. Meanwhile, we tried to develop a decision tree model for surname predictions based on Y-STR haplotypes. Allelic frequencies of 27 Y-STRs showed that unique alleles were only observed in a certain surname; besides, some alleles displayed higher frequencies in a certain surname than those in other surnames, implying these alleles might be employed as the useful indicators for surname predictions. Haplotype match probability values of 27 Y-STRs in these surnames revealed that the system could be used as a valuable tool for forensic male identification. The developed decision tree model performed well for the training set with the accuracy of 0.9860 and obtained the relatively high accuracy (>0.70) for surname predictions of the testing set. To sum up, we explored the power of the machine learning to the surname predictions based on obtained Y-STR haplotypes, which showed promising application values in forensic familial searching.

Middle eastern genetic legacy in the paternal and maternal gene pools of Chuetas

Chuetas are a group of descendants of Majorcan Crypto-Jews (Balearic Islands, Spain) who were socially stigmatized and segregated by their Majorcan neighbours until recently; generating a community that, although after the seventeenth century no longer contained Judaic religious elements, maintained strong group cohesion, Jewishness consciousness, and endogamy. Collective memory fixed 15 surnames as a most important defining element of Chueta families. Previous studies demonstrated Chuetas were a differentiated population, with a considerable proportion of their original genetic make-up. Genetic data of Y-chromosome polymorphism and mtDNA control region showed, in Chuetas’ paternal lineages, high prevalence of haplogroups J2-M172 (33%) and J1-M267 (18%). In maternal lineages, the Chuetas hallmark is the presence of a new sub-branching of the rare haplogroup R0a2m as their modal haplogroup (21%). Genetic diversity in both Y-chromosome and mtDNA indicates the Chueta community has managed to avoid the expected heterogeneity decrease in their gene pool after centuries of isolation and inbreeding. Moreover, the composition of their uniparentally transmitted lineages demonstrates a remarkable signature of Middle Eastern ancestry—despite some degree of host admixture—confirming Chuetas have retained over the centuries a considerable degree of ancestral genetic signature along with the cultural memory of their Jewish origin.

Adaptive selection drives TRPP3 loss-of-function in an Ethiopian population

TRPP3 (also called PKD2L1) is a nonselective, cation-permeable channel activated by multiple stimuli, including extracellular pH changes. TRPP3 had been considered a candidate for sour sensor in humans, due to its high expression in a subset of tongue receptor cells detecting sour, along with its membership to the TRP channel family known to function as sensory receptors. Here, we describe the functional consequences of two non-synonymous genetic variants (R278Q and R378W) found to be under strong positive selection in an Ethiopian population, the Gumuz. Electrophysiological studies and 3D modelling reveal TRPP3 loss-of-functions produced by both substitutions. R278Q impairs TRPP3 activation after alkalinisation by mislocation of H⁺ binding residues at the extracellular polycystin mucolipin domain. R378W dramatically reduces channel activity by altering conformation of the voltage sensor domain and hampering channel transition from closed to open state. Sour sensitivity tests in R278Q/R378W carriers argue against both any involvement of TRPP3 in sour detection and the role of such physiological process in the reported evolutionary positive selection past event.

High rate of extrapair paternity in a human population demonstrates diversity in human reproductive strategies

Among nonhuman species, social monogamy is rarely accompanied by complete fidelity. Evolutionary theory predicts that the rate of extrapair paternity (EPP) should vary according to socioecological conditions. In humans, however, geneticists contend that EPP is negligible and relatively invariable. This conclusion is based on a limited set of studies, almost all of which describe European-descent groups. Using a novel, double-blind method designed in collaboration with a community of Himba pastoralists, we find that the rate of EPP in this population is 48%, with 70% of couples having at least one EPP child. Both men and women were very accurate at detecting cases of EPP. These data suggest that the range of variation in EPP across human populations is substantially greater than previously thought. We further show that a high rate of EPP can be accompanied by high paternity confidence, which highlights the importance of disaggregating EPP from the notion of "cuckoldry."

Ysurnames? The patrilineal Y-chromosome and surname correlation for DNA kinship research

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.

Relating Clans Ao and Aisin Gioro from northeast China by whole Y-chromosome sequencing

The Y-chromosome haplogroup C2b1a3a2-F8951 is the paternal lineage of the Aisin Gioro clan, the most important brother branch of the famous Mongolic-speaking population characteristic haplogroup C2*-Star Cluster (C2b1a3a1-F3796). However, investigations on its internal phylogeny are still limited. In this study, we used whole Y-chromosome sequencing to update its phylogenetic tree. In the revised tree, C2b1a3a2-F8951 and C2*-Star Cluster differentiated 3852 years ago (95% CI = 3295-4497). Approximately 3558 years ago (95% CI = 3013-4144), C2b1a3a2-F8951 was divided into two main subclades, C2b1a3a2a-F14753 and C2b1a3a2b-F5483. Currently, samples of C2b1a3a2-F8951 were mainly from the House of Aisin Gioro clan, the Ao family from Daur and some individuals mainly from northeast China. Although other haplogroups are also found in the Ao family, including C2b1a2-M48, C2b1a3a1-F3796, C2a1b-F845, and N1c-M178, the haplogroup C2b1a3a2-F8951 is still the most distinct genetic component. For haplogroup C2b1a3a2-F8951, the time of the most recent common ancestor of the House of Aisin Gioro clan and the Ao family were both very late, just a few hundred years ago. Some family-specific Y-SNPs of the House of Aisin Gioro and the Ao family were also discovered. This revision evidently improved the resolving power of Y-chromosome phylogeny in northeast Asia, deepening our understanding of the origin of these two families, even the Mongolic-speaking population.

Inferring the history of surname Ye based on Y chromosome high-resolution genotyping and sequencing data

Paternal inheritance of both Y chromosome and surnames makes it possible to trace the origin and migration histories of surnames based on high-resolution Y chromosome phylogeny. In this study, 292 male samples with surname Ye () in China were collected to unravel the history of this surname. Among these samples, O-F492 showed the highest frequency (26.71%). Analysis based on Y chromosome genotyping data of 52,798 males from virtually the whole China revealed a close correlation between O-F492 and surname Ye. High-throughput sequencing of 131 unrelated male individuals covering all sub-haplogroups in O-F492 was conducted to update the phylogeny of O-F492. Most of the Ye individuals (43/64, 67.19%) are embedded in three major branches, i.e., O-MF1461, O-MF15219, and O-FGC66159, deriving from the same node (O-FGC66168). These three clades restrictively distributed in different regions, likely attributed to independent differentiations. Coalescent ages of the three subclades are estimated ranging from 1,925 to 1,775 years ago, probably driven by the massive migration from north to south China after Yongjia riot in Jin Dynasty, consistent with the migration history of surname Ye. Our study thus shed important light on the history of the surname Ye from genetic perspective.

People from Ibiza: an unexpected isolate in the Western Mediterranean

In this study, we seek to understand and to correlate the genetic patterns observed in the population of the island of Ibiza in the Western Mediterranean basin with past events. Genome-wide genotypes of 189 samples representing 13 of 17 regions in Spain have been analyzed, in addition to 105 samples from the Levant, 157 samples from North Africa, and one ancient sample from the Phoenician Cas Molí site in Ibiza. Before the Catalans conquered the island in 1235 CE, Ibiza (Eivissa) had already been influenced by several cultures, starting with the Phoenicians, then the Carthaginians, followed by the Umayyads. The impact of these various cultures on the genetic structure of the islanders is still unexplored. Our results show a clear distinction between Ibiza and the rest of Spain. To investigate whether this was due to the Phoenician colonization or to more recent events, we compared the genomes of current Ibizans to that of an ancient Phoenician sample from Ibiza and to both modern Levantine and North African genomes. We did not identify any trace of Phoenician ancestry in the current Ibizans. Interestingly, the analysis of runs of homozygosity and changes in the effective population size through time support the idea that drift has shaped the genetic structure of current Ibizans. In addition to the small carrying capacity of the island, Ibiza experienced a series of dramatic demographic changes due to several instances of famine, war, malaria and plague that could have significantly contributed to its current genetic differentiation.

Ancient DNA of Phoenician remains indicates discontinuity in the settlement history of Ibiza

Ibiza was permanently settled around the 7th century BCE by founders arriving from west Phoenicia. The founding population grew significantly and reached its height during the 4th century BCE. We obtained nine complete mitochondrial genomes from skeletal remains from two Punic necropoli in Ibiza and a Bronze Age site from Formentara. We also obtained low coverage (0.47X average depth) of the genome of one individual, directly dated to 361-178 cal BCE, from the Cas Molí site on Ibiza. We analysed and compared ancient DNA results with 18 new mitochondrial genomes from modern Ibizans to determine the ancestry of the founders of Ibiza. The mitochondrial results indicate a predominantly recent European maternal ancestry for the current Ibizan population while the whole genome data suggest a significant Eastern Mediterranean component. Our mitochondrial results suggest a genetic discontinuity between the early Phoenician settlers and the island's modern inhabitants. Our data, while limited, suggest that the Eastern or North African influence in the Punic population of Ibiza was primarily male dominated.

Ovulation, Sex Hormones, and Women's Mating Psychology

The dual mating strategy hypothesis proposes that women's preferences for uncommitted sexual relationships with men displaying putative fitness cues increase during the high-fertility phase of the menstrual cycle. Results consistent with this hypothesis are widely cited as evidence that sexual selection has shaped human mating psychology. However, the methods used in most of these studies have recently been extensively criticized. Here we discuss (i) new empirical studies that address these methodological problems and largely report null results and (ii) an alternative model of hormonal regulation of women's mating psychology that can better accommodate these new data.

Reconstructing the genetic structure of the Kazakh from clan distribution data

Applying quasigenetic markers - non-biological traits which are nevertheless inherited in generations - is one of the research fields within human population genetics. For the West European, East European, and Caucasus populations, surnames are typical quasigenetic markers. For Central Asian populations, particularly Kazakh, the clan affiliation serves as a good marker: a set of papers demonstrated that many clans include mainly persons which biologically descent from a recent common ancestor. In this study, we analyzed a large (~4.2 million persons) dataset on quasigenetic markers - the geographic distribution of 50 Kazakh clans at the beginning of the 20th century, and compared the dataset with the direct data of the Y-chro-mosomal diversity in modern Kazakh populations. The analysis included three steps: the isonymy method, which is standard for quasigenetic markers, comparing frequencies of quasigenetic markers, and comparing the quasigenetic and genetic datasets. We constructed 50 maps of frequency of the distribution of each clan and revealed that these maps correlate with the maps of genetic distances. The Mantel test also demonstrated a significant correlation between geographic and quasigenetic distances (г = 0.60; p < 0.05). The analysis of inter-population variability revealed the largest diversity between geographic territories corresponding to the social-territorial groups of the Kazakh Khanate (zhuzes) rather than to other historical groups that existed on the territory of Kazakhstan in preceding and modern epochs. The same is evidenced by the principal components and multidimensional scaling plots, which grouped geographic populations into three clusters corresponding to three zhuzes. This indicates that the final structuring of the Kazakh gene pool might have occurred during the Kazakh Khanate period.

Mediterranean Y-chromosome 2.0-why the Y in the Mediterranean is still relevant in the postgenomic era

CONTEXT

Due to its unique paternal inheritance, the Y-chromosome has been a highly popular marker among population geneticists for over two decades. Recently, the advent of cost-effective genome-wide methods has unlocked information-rich autosomal genomic data, paving the way to the postgenomic era. This seems to have announced the decreasing popularity of investigating Y-chromosome variation, which provides only the paternal perspective of human ancestries and is strongly influenced by genetic drift and social behaviour.

OBJECTIVE

For this special issue on population genetics of the Mediterranean, the aim was to demonstrate that the Y-chromosome still provides important insights in the postgenomic era and in a time when ancient genomes are becoming exponentially available.

METHODS

A systematic literature search on Y-chromosomal studies in the Mediterranean was performed.

RESULTS

Several applications of Y-chromosomal analysis with future opportunities are formulated and illustrated with studies on Mediterranean populations.

CONCLUSIONS

There will be no reduced interest in Y-chromosomal studies going from reconstruction of male-specific demographic events to ancient DNA applications, surname history and population-wide estimations of extra-pair paternity rates. Moreover, more initiatives are required to collect population genetic data of Y-chromosomal markers for forensic research, and to include Y-chromosomal data in GWAS investigations and studies on male infertility.

Ripples on the surface. Surnames and genes in Sicily and Southern Italy

BACKGROUND

Southern Italy and Sicily played a key role in the peopling history of the Mediterranean. While genetic research showed the remarkable homogeneity of these regions, surname-based studies instead suggested low population mobility, hence potential structuring.

AIM

In order to better understand these different patterns, this study (1) thoroughly analysed the surname structure of Sicily and Southern Italy and (2) tested its relationships with a wide set of molecular markers.

SUBJECTS AND METHODS

Surname data were collected from 1213 municipalities and compared to uniparental and autosomal genetic markers typed in ∼300 individuals from 8-10 populations. Surname analyses were performed using different multivariate methods, while comparisons with genetic data relied on correlation tests.

RESULTS

Surnames were clearly structured according to regional geographic patterns, which likely emerged because of recent isolation-by-distance-like population dynamics. In general, genetic markers, hinting at a pervasive homogeneity, did not correlate with surname distribution. However, long autosomal haplotypes (>5 cM) that compared to genotypic (SNPs) data identify more "recent" relatedness, showing a clear association with surname patterns.

CONCLUSION

The apparent contradiction between surname structure and genetic homogeneity was resolved by figuring surnames as recent "ripples" deposited on a vast and ancient homogeneous genetic "surface".

The black legend on the Spanish presence in the low countries: Verifying shared beliefs on genetic ancestry

OBJECTIVES

War atrocities committed by the Spanish army in the Low Countries during the 16th century are so ingrained in the collective memory of Belgian and Dutch societies that they generally assume a signature of this history to be present in their genetic ancestry. Historians claim this assumption is a consequence of the so-called "Black Legend" and negative propaganda portraying and remembering Spanish soldiers as extreme sexual aggressors. The impact of the presence of Spaniards during the Dutch Revolt on the genetic variation in the Low Countries has been verified in this study.

MATERIALS AND METHODS

A recent population genetic analysis of Iberian-associated Y-chromosomal variation among Europe is enlarged with representative samples of Dutch (N = 250) and Flemish (N = 1,087) males. Frequencies of these variants are also compared between donors whose oldest reported paternal ancestors lived in-nowadays Flemish-cities affected by so-called Spanish Furies (N = 116) versus other patrilineages in current Flemish territory (N = 971).

RESULTS

The frequencies of Y-chromosomal markers Z195 and SRY2627 decline steeply going north from Spain and the data for the Flemish and Dutch populations fits within this pattern. No trend of higher frequencies of these variants has been found within the well-ascertained samples associated with Spanish Fury cities.

DISCUSSION

Although sexual aggression did occur in the 16th century, these activities did not leave a traceable "Spanish" genetic signature in the autochthonous genome of the Low Countries. Our results support the view that the 'Black Legend' and historical propaganda on sexual aggression have nurtured today's incorrect assumptions regarding genetic ancestry.

Whole Y-chromosome sequences reveal an extremely recent origin of the most common North African paternal lineage E-M183 (M81)

E-M183 (E-M81) is the most frequent paternal lineage in North Africa and thus it must be considered to explore past historical and demographical processes. Here, by using whole Y chromosome sequences from 32 North African individuals, we have identified five new branches within E-M183. The validation of these variants in more than 200 North African samples, from which we also have information of 13 Y-STRs, has revealed a strong resemblance among E-M183 Y-STR haplotypes that pointed to a rapid expansion of this haplogroup. Moreover, for the first time, by using both SNP and STR data, we have provided updated estimates of the times-to-the-most-recent-common-ancestor (TMRCA) for E-M183, which evidenced an extremely recent origin of this haplogroup (2,000-3,000 ya). Our results also showed a lack of population structure within the E-M183 branch, which could be explained by the recent and rapid expansion of this haplogroup. In spite of a reduction in STR heterozygosity towards the West, which would point to an origin in the Near East, ancient DNA evidence together with our TMRCA estimates point to a local origin of E-M183 in NW Africa.

Analysis of the R1b-DF27 haplogroup shows that a large fraction of Iberian Y-chromosome lineages originated recently in situ

Haplogroup R1b-M269 comprises most Western European Y chromosomes; of its main branches, R1b-DF27 is by far the least known, and it appears to be highly prevalent only in Iberia. We have genotyped 1072 R1b-DF27 chromosomes for six additional SNPs and 17 Y-STRs in population samples from Spain, Portugal and France in order to further characterize this lineage and, in particular, to ascertain the time and place where it originated, as well as its subsequent dynamics. We found that R1b-DF27 is present in frequencies ~40% in Iberian populations and up to 70% in Basques, but it drops quickly to 6–20% in France. Overall, the age of R1b-DF27 is estimated at ~4,200 years ago, at the transition between the Neolithic and the Bronze Age, when the Y chromosome landscape of W Europe was thoroughly remodeled. In spite of its high frequency in Basques, Y-STR internal diversity of R1b-DF27 is lower there, and results in more recent age estimates; NE Iberia is the most likely place of origin of DF27. Subhaplogroup frequencies within R1b-DF27 are geographically structured, and show domains that are reminiscent of the pre-Roman Celtic/Iberian division, or of the medieval Christian kingdoms.

Genetic-genealogy approach reveals low rate of extrapair paternity in historical Dutch populations

OBJECTIVE

Evolutionary theory has shown that seeking out extrapair paternity (EPP) can be a viable reproductive strategy for both sexes in pair-bonded species, also in humans. As yet, estimates of the contemporary or historical EPP rate in human population are still rare. In the present study, we estimated the historical EPP rate in the Dutch population over the last 400 years and compared the rate with those obtained for other human populations to determine the evolutionary, cultural, and socio-demographic factors that influence human cuckoldry behavior.

METHODS

We estimated the historical EPP rate for the Dutch population via the "genealogical pair method", in which the EPP rate is derived from Y-chromosome mismatches between pairs of individuals that, based on genealogical evidence, share a common paternal ancestor.

RESULTS

Based on the analysis of 68 representative genealogical pairs, separated by a total of 1013 fertilization events, we estimated that the historical EPP rate for the Dutch population over the last 400 years was 0.96% per generation (95% confidence interval 0.46%-1.76%).

CONCLUSION

The Dutch EPP rate fits perfectly within the range reported for other contemporary and historical populations in Western Europe and was highly congruent with that estimated for neighboring Flanders, despite the socio-economic and religious differences between both populations. The estimated low EPP rate challenges the "dual mating strategy hypothesis" that states that women could obtain fitness benefits by securing investment from one man while cuckolding him to obtain good genes from an affair partner.

Human Y-chromosome variation in the genome-sequencing era

The properties of the human Y chromosome - namely, male specificity, haploidy and escape from crossing over - make it an unusual component of the genome, and have led to its genetic variation becoming a key part of studies of human evolution, population history, genealogy, forensics and male medical genetics. Next-generation sequencing (NGS) technologies have driven recent progress in these areas. In particular, NGS has yielded direct estimates of mutation rates, and an unbiased and calibrated molecular phylogeny that has unprecedented detail. Moreover, the availability of direct-to-consumer NGS services is fuelling a rise of 'citizen scientists', whose interest in resequencing their own Y chromosomes is generating a wealth of new data.

Cuckolded Fathers Rare in Human Populations

Contemporary data of extra-pair paternity (EPP) in human populations may be biased by the use of modern contraceptives. Studies have now estimated historical EPP rates in several human populations. The observed low EPP rates challenge the idea that women routinely 'shop around' for good genes by engaging in extra-pair copulations.

Group membership, geography and shared ancestry: Genetic variation in the Basotho of Lesotho

OBJECTIVES

The investigation of the evolution of cultural and genetic traits and how they interact represents a vibrant area of research in evolutionary genetics, whose dynamics are particularly relevant for our species. One of the key assumptions of the "gene-culture coevolution" framework is the coinheritance of cultural and genetic traits. A corollary of the model is that culturally defined groups with a unique (or a limited number of) common origin(s) whose membership is inherited only through the male or female line are expected to show a relatively low intragroup variation for genetic markers similarly transmitted. Across human societies this is expected to be the case for cultural toponymies and family names within patrilineal and matrilineal groups considered in association with the nonrecombining region of the Y chromosome (NRY) and the mitochondrial DNA (mtDNA) portion of the genome, respectively. This study aims at exploring the degree of correlation between culture and genetics by investigating the genetic variation of culturally and geographically defined groups.

METHODS

We analyzed the genetic variation at NRY and mtDNA in 181 individuals from the Basotho, a Southern African patrilineal population from Lesotho, in combination with information about group membership and geographic origin.

RESULTS

Our results show that (a) the genetic distance between individuals belonging to the same culturally defined group is lower than the population as a whole when NRY markers are considered; (b) cultural traits have a bigger impact than geography for the within-group variation of Y chromosome, but not mtDNA; and (c) within-group genetic variation is compatible with a more homogeneous origin for less common groups.

CONCLUSIONS

Our results provided additional evidence for the relevance of the dual inheritance model (culture and genetics) in understanding the patterns of human genetic variation, as implied by gene-culture coevolution theory.