The peopling of Europe and the cautionary tale of Y chromosome lineage R-M269

de Pancorbo M, Calafell F. Y-chromosome target enrichment reveals rapid expansion of haplogroup R1b-DF27 in Iberia during the Bronze Age transition

The Y chromosome can yield a unique perspective into the study of human demographic history. However, due to the repetitive nature of part of its sequence, only a small set of regions are suitable for variant calling and discovery from short-read sequencing data. These regions combined represent 8.9 Mbp or 0.14% of a diploid human genome. Consequently, investing in whole-genome sequencing to resolve Y-chromosome questions is poorly efficient. Here we use, as an alternative, target enrichment technology to greatly increase sequencing effectiveness, validating and applying the technique to 181 males, for 162 of whom we obtained a positive result. Additionally, 75 samples sequenced for the whole genome were also included, for a total sample size of 237. These samples were chosen for their Y chromosome haplogroup: R1b-DF27. In the context of European populations, and particularly in Iberia, this haplogroup stands out for its high frequency and its demographic history. Current evidence indicates that the diffusion of this haplogroup is related to the population movements that mark the cultural Bronze Age transition, making it remarkably interesting for population geneticists. The results of this study show the effects of the rapid radiation of the haplogroup in Spain, as even with the higher discriminating power of whole sequences, most haplotypes still fall within the R1b-DF27* paragroup rather than in the main derived branches. However, we were able to refine the ISOGG 2019-2020 phylogeny, and its two main subbranches, namely L176.2 and Z272, which present geographical differentiation between the Atlantic and Mediterranean coasts of Iberia.

The Anglo-Saxon migration and the formation of the early English gene pool

The history of the British Isles and Ireland is characterized by multiple periods of major cultural change, including the influential transformation after the end of Roman rule, which precipitated shifts in language, settlement patterns and material culture1. The extent to which migration from continental Europe mediated these transitions is a matter of long-standing debate2-4. Here we study genome-wide ancient DNA from 460 medieval northwestern Europeans-including 278 individuals from England-alongside archaeological data, to infer contemporary population dynamics. We identify a substantial increase of continental northern European ancestry in early medieval England, which is closely related to the early medieval and present-day inhabitants of Germany and Denmark, implying large-scale substantial migration across the North Sea into Britain during the Early Middle Ages. As a result, the individuals who we analysed from eastern England derived up to 76% of their ancestry from the continental North Sea zone, albeit with substantial regional variation and heterogeneity within sites. We show that women with immigrant ancestry were more often furnished with grave goods than women with local ancestry, whereas men with weapons were as likely not to be of immigrant ancestry. A comparison with present-day Britain indicates that subsequent demographic events reduced the fraction of continental northern European ancestry while introducing further ancestry components into the English gene pool, including substantial southwestern European ancestry most closely related to that seen in Iron Age France5,6.

Phylogeographic review of Y chromosome haplogroups in Europe

The Y chromosome has been widely explored for the study of human migrations. Due to its paternal inheritance, the Y chromosome polymorphisms are helpful tools for understanding the geographical distribution of populations all over the world and for inferring their origin, which is really useful in forensics. The remarkable historical context of Europe, with numerous migrations and invasions, has turned this continent into a melting pot. For this reason, it is interesting to study the Y chromosome variability and how it has contributed to improving our knowledge of the distribution and development of European male genetic pool as it is today. The analysis of Y lineages in Europe shows the predominance of four haplogroups, R1b-M269, I1-M253, I2-M438 and R1a-M420. However, other haplogroups have been identified which, although less frequent, provide significant evidence about the paternal origin of the populations. In addition, the study of the Y chromosome in Europe is a valuable tool for revealing the genetic trace of the different European colonizations, mainly in several American countries, where the European ancestry is mostly detected by the presence of the R1b-M269 haplogroup. Therefore, the objective of this review is to compile the studies of the Y chromosome haplogroups in current European populations, in order to provide an outline of these haplogroups which facilitate their use in forensic studies.

Y-chromosome variability and genetic history of Commons from Northern Italy

Objectives

Genetic drift and admixture are driving forces in human evolution, but their concerted impact to population evolution in historical times and at a micro‐geographic scale is poorly assessed. In this study we test a demographic model encompassing both admixture and drift to the case of social‐cultural isolates such as the so‐called “Commons.”

Materials and methods

Commons are peculiar institutions of medieval origins whose key feature is the tight relationship between population and territory, mediated by the collective property of shared resources. Here, we analyze the Y‐chromosomal genetic structure of four Commons (for a total of 366 samples) from the Central and Eastern Padana plain in Northern Italy.

Results

Our results reveal that all these groups exhibit patterns of significant diversity reduction, peripheral/outlier position within the Italian/European genetic space and high frequency of Common‐specific haplogroups. By explicitly testing different drift‐admixture models, we show that a drift‐only model is more probable for Central Padana Commons, while additional admixture (~20%) from external population around the same time of their foundation cannot be excluded for the Eastern ones.

Discussion

Building on these results, we suggest central Middle Ages as the most probable age of foundation for three of the considered Commons, the remaining one pointing to late antiquity. We conclude that an admixture‐drift model is particularly useful for interpreting the genetic structure and recent demographic history of small‐scale populations in which social‐cultural features play a significant role.

The Y chromosome of autochthonous Basque populations and the Bronze Age replacement

Here we report on the Y haplogroup and Y-STR diversity of the three autochthonous Basque populations of Alava (n = 54), Guipuzcoa (n = 30) and Vizcaya (n = 61). The same samples genotyped for Y-chromosome SNPs were typed for 17 Y-STR loci (DYS19, DYS385a/b, DYS398I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, Y-GATA H4) using the AmpFlSTR Yfiler system. Six major haplogroups (R, I, E, J, G, and DE) were detected, being R-S116 (P312) haplogroup the most abundant at 75.0% in Alava, 86.7% in Guipuzcoa and 87.3% in Vizcaya. Age estimates for the R-S116 mutation in the Basque Country are 3975 ± 303, 3680 ± 345 and 4553 ± 285 years for Alava, Guipuzcoa and Vizcaya, respectively. Pairwise Rst genetic distances demonstrated close Y-chromosome affinities among the three autochthonous Basque populations and between them and the male population of Ireland and Gascony. In a MDS plot, the population of Ireland segregates within the Basque cluster and closest to the population of Guipuzcoa, which plots closer to Ireland than to any of the other Basque populations. Overall, the results support the notion that during the Bronze Age a dispersal of individuals carrying the R-S116 mutation reached the Basque Country replacing the Paleolithic/Neolithic Y chromosome of the region.

New insights on intercontinental origins of paternal lineages in Northeast Brazil

Background

The current Brazilian population is the product of centuries of admixture between intercontinental founding groups. Although previous results have revealed a heterogeneous distribution of mitochondrial lineages in the Northeast region, the most targeted by foreign settlers during the sixteenth century, little is known about the paternal ancestry of this particular population. Considering historical records have documented a series of territorial invasions in the Northeast by various European populations, we aimed to characterize the male lineages found in Brazilian individuals in order to discover to what extent these migrations have influenced the present-day gene pool. Our approach consisted of employing four hierarchical multiplex assays for the investigation of 45 unique event polymorphisms in the non-recombining portion of the Y-chromosome of 280 unrelated men from several Northeast Brazilian states.

Results

Primary multiplex results allowed the identification of six major haplogroups, four of which were screened for downstream SNPs and enabled the observation of 19 additional lineages. Results reveal a majority of Western European haplogroups, among which R1b-S116* was the most common (63.9%), corroborating historical records of colonizations by Iberian populations. Nonetheless, F_ST genetic distances show similarities between Northeast Brazil and several other European populations, indicating multiple origins of settlers. Regarding Native American ancestry, our findings confirm a strong sexual bias against such haplogroups, which represented only 2.5% of individuals, highly contrasting previous results for maternal lineages. Furthermore, we document the presence of several Middle Eastern and African haplogroups, supporting a complex historical formation of this population and highlighting its uniqueness among other Brazilian regions.

Conclusions

We performed a comprehensive analysis of the major Y-chromosome lineages that form the most dynamic migratory region from the Brazilian colonial period. This evidence suggests that the ongoing entry of European, Middle Eastern, and African males in the Brazilian Northeast, since at least 500 years, was significantly responsible for the present-day genetic architecture of this population.

The Dutch Y-chromosomal landscape

Previous studies indicated existing, albeit limited, genetic-geographic population substructure in the Dutch population based on genome-wide data and a lack of this for mitochondrial SNP based data. Despite the aforementioned studies, Y-chromosomal SNP data from the Netherlands remain scarce and do not cover the territory of the Netherlands well enough to allow a reliable investigation of genetic-geographic population substructure. Here we provide the first substantial dataset of detailed spatial Y-chromosomal haplogroup information in 2085 males collected across the Netherlands and supplemented with previously published data from northern Belgium. We found Y-chromosomal evidence for genetic–geographic population substructure, and several Y-haplogroups demonstrating significant clinal frequency distributions in different directions. By means of prediction surface maps we could visualize (complex) distribution patterns of individual Y-haplogroups in detail. These results highlight the value of a micro-geographic approach and are of great use for forensic and epidemiological investigations and our understanding of the Dutch population history. Moreover, the previously noted absence of genetic-geographic population substructure in the Netherlands based on mitochondrial DNA in contrast to our Y-chromosome results, hints at different population histories for women and men in the Netherlands.

Estimating Y-Str Mutation Rates and Tmrca Through Deep-Rooting Italian Pedigrees

In the population genomics era, the study of Y-chromosome variability is still of the greatest interest for several fields ranging from molecular anthropology to forensics and genetic genealogy. In particular, mutation rates of Y-chromosomal Short Tandem Repeats markers (Y-STRs) are key parameters for different interdisciplinary applications. Among them, testing the patrilineal relatedness between individuals and calculating their Time of Most Recent Common Ancestors (TMRCAs) are of the utmost importance. To provide new valuable estimates and to address these issues, we typed 47 Y-STRs (comprising Yfiler, PowerPlex23 and YfilerPlus loci, the recently defined Rapidly Mutating [RM] panel and 11 additional markers often used in genetic genealogical applications) in 135 individuals belonging to 66 deep-rooting paternal genealogies from Northern Italy. Our results confirmed that the genealogy approach is an effective way to obtain reliable Y-STR mutation rate estimates even with a limited number of samples. Moreover, they showed that the impact of multi-step mutations and backmutations is negligible within the temporal scale usually adopted by forensic and genetic genealogy analyses. We then detected a significant association between the number of mutations within genealogies and observed TMRCAs. Therefore, we compared observed and expected TMRCAs by implementing a Bayesian procedure originally designed by Walsh (2001) and showed that the method yields a good performance (up to 96.72%), especially when using the Infinite Alleles Model (IAM).

Paternal lineages in southern Iberia provide time frames for gene flow from mainland Europe and the Mediterranean world

BACKGROUND

The geography of southern Iberia and an abundant archaeological record of human occupation are ideal conditions for a full understanding of scenarios of genetic history in the area. Recent advances in the phylogeography of Y-chromosome lineages offer the opportunity to set upper bounds for the appearance of different genetic components.

AIM

To provide a global knowledge on the Y haplogroups observed in Andalusia with their Y microsatellite variation. Preferential attention is given to the vehement debate about the age, origin and expansion of R1b-M269 clade and sub-lineages.

SUBJECT AND METHODS

Four hundred and fourteen male DNA samples from western and eastern autochthonous Andalusians were genotyped for a set of Y-SNPs and Y-STRs. Gene diversity, potential population genetic structures and coalescent times were assessed.

RESULTS

Most of the analysed samples belong to the European haplogroup R1b1a1a2-M269, whereas haplogroups E, J, I, G and T show lower frequencies. A phylogenetic dissection of the R1b-M269 was performed and younger time frames than those previously reported in the literature were obtained for its sub-lineages.

CONCLUSION

The particular Andalusian R1b-M269 assemblage confirms the shallow topology of the clade. Moreover, the sharing of lineages with the rest of Europe indicates the impact in Iberia of an amount of pre-existing diversity, with the possible exception of R1b-DF27. Lineages such as J2-M172 and G-M201 highlight the importance of maritime travels of early farmers who reached the Iberian Peninsula.

The evolutionary history of Southern Africa

The genomic variability of Southern African groups is characterized by an exceptional degree of diversity, which is the result of long-term local evolutionary history, migrations and gene-flow. Over the last few years several investigations have identified and described signatures related to these processes, revealing how ancient and more recent events have shaped the structure and ancestry composition of local populations. Here we discuss recent insights into the genetic history of the Southernmost part of the African continent provided by the analysis of modern and ancient genomes. Future work is expected to clarify the population dynamics associated with the emergence of Homo sapiens across Africa and the details of the process of dispersion and admixture associated with the arrival of Bantu-speaking groups in the region.

Paternal portrait of populations of the middle Magdalena River region (Tolima and Huila, Colombia): New insights on the peopling of Central America and northernmost South America

The valley of the Magdalena River is one of the main population pathways in Colombia. The gene pool and spatial configuration of human groups in this territory have been outlined throughout three historical stages: the Native pre-Hispanic world, Spanish colonization, and XIX century migrations. This research was designed with the goal of characterizing the diversity and distribution pattern of Y-chromosome lineages that are currently present in the Tolima and Huila departments (middle Magdalena River region). Historic cartography was used to identify the main geographic sites where the paternal lineages belonging to this area have gathered. Twelve municipalities were chosen, and a survey that included genealogical information was administered. Samples collected from 83 male volunteers were analyzed for 48 Y-SNPs and 17 Y-STRs. The results showed a highly diverse region characterized by the presence of 16 sublineages within the major clades R, Q, J, G, T and E and revealed that 93% (n = 77) of haplotypes were different. Among these haplogroups, European-specific R1b-M269 lineages were the most representative (57.83%), with six different subhaplogroups and 43 unique haplotypes. Native American paternal ancestry was also detected based on the presence of the Q1a2-M3*(xM19, M194, M199) and Q1a2-M346*(xM3) lineages. Interestingly, all Q1a2-M346*(xM3) samples (n = 7, with five different haplotypes) carried allele six at the DYS391 locus. This allele has a worldwide frequency of 0.169% and was recently associated with a new Native subhaplogroup. An in-depth phylogenetic analysis of these samples suggests the Tolima and Huila region to be the principal area in all Central and South America where this particular Native lineage is found. This lineage has been present in the region for at least 1,809 (+/- 0,5345) years.

Effective resolution of the Y chromosome sublineages of the Iberian haplogroup R1b-DF27 with forensic purposes

Single-nucleotide polymorphisms (SNPs) found within the non-recombining region of the Y chromosome (NRY) represent a powerful tool in forensic genetics for inferring the paternal ancestry of a vestige and complement the determination of biogeographical origin in combination with other markers like AIMs. In the present study, we introduce a panel of 15 Y-SNPs for a fine-resolution subtyping of the haplogroup R1b-DF27, in a single minisequencing reaction. This is the first minisequencing panel that allows a fine subtyping of R1b-DF27, which displays high frequencies in Iberian and Iberian-influenced populations. This panel includes subhaplogroups of DF27 that display moderate geographical differentiation, of interest to link a sample with a specific location of the Iberian Peninsula or with Iberian ancestry. Conversely, part of the intricacy of a new minisequencing panel is to have all the included variants available to test the effectiveness of the analysis method. We have overcome the absence of the least common variants through site-directed mutagenesis. Overall, the results show that our panel is a robust and effective method for subtyping R1b-DF27 lineages from a minimal amount of DNA, and its high resolution enables to improve male lineage discrimination in Iberian and Southwest European descent individuals. The small length of the amplicons and its reproducibility makes this assay suitable for forensic and population genetics purposes.

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.

Defining Y-SNP variation among the Flemish population (Western Europe) by full genome sequencing

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.

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.

Mutation Rates and Discriminating Power for 13 Rapidly-Mutating Y-STRs between Related and Unrelated Individuals

Rapidly Mutating Y-STRs (RM Y-STRs) were recently introduced in forensics in order to increase the differentiation of Y-chromosomal profiles even in case of close relatives. We estimate RM Y-STRs mutation rates and their power to discriminate between related individuals by using samples extracted from a wide set of paternal pedigrees and by comparing RM Y-STRs results with those obtained from the Y-filer set. In addition, we tested the ability of RM Y-STRs to discriminate between unrelated individuals carrying the same Y-filer haplotype, using the haplogroup R-M269 (reportedly characterised by a strong resemblance in Y-STR profiles) as a case study. Our results, despite confirming the high mutability of RM Y-STRs, show significantly lower mutation rates than reference germline ones. Consequently, their power to discriminate between related individuals, despite being higher than the one of Y-filer, does not seem to improve significantly the performance of the latter. On the contrary, when considering R-M269 unrelated individuals, RM Y-STRs reveal significant discriminatory power and retain some phylogenetic signal, allowing the correct classification of individuals for some R-M269-derived sub-lineages. These results have important implications not only for forensics, but also for molecular anthropology, suggesting that RM Y-STRs are useful tools for exploring subtle genetic variability within Y-chromosomal haplogroups.

The evolutionary adaptation of the C282Y mutation to culture and climate during the European Neolithic

OBJECTIVES

The C282Y allele is the major cause of hemochromatosis as a result of excessive iron absorption. The mutation arose in continental Europe no earlier than 6,000 years ago, coinciding with the arrival of the Neolithic agricultural revolution. Here we hypothesize that this new Neolithic diet, which originated in the sunny warm and dry climates of the Middle East, was carried by migrating farmers into the chilly and damp environments of Europe where iron is a critical micronutrient for effective thermoregulation. We argue that the C282Y allele was an adaptation to this novel environment.

MATERIALS AND METHODS

To address our hypothesis, we compiled C282Y allele frequencies, known Neolithic sites in Europe and climatic data on temperature and rainfall for statistical analysis.

RESULTS

Our findings indicate that the geographic cline for C282Y frequency in Europe increases as average temperatures decrease below 16°C, a critical threshold for thermoregulation, with rainy days intensifying the trend.

DISCUSSION

The results indicate that the deleterious C282Y allele, responsible for most cases of hemochromatosis, may have evolved as a selective advantage to culture and climate during the European Neolithic.

Male Lineages in Brazil: Intercontinental Admixture and Stratification of the European Background

The non-recombining nature of the Y chromosome and the well-established phylogeny of Y-specific Single Nucleotide Polymorphisms (Y-SNPs) make them useful for defining haplogroups with high geographical specificity; therefore, they are more apt than the Y-STRs to detect population stratification in admixed populations from diverse continental origins. Different Y-SNP typing strategies have been described to address issues of population history and movements within geographic territories of interest. In this study, we investigated a set of 41 Y-SNPs in 1217 unrelated males from the five Brazilian geopolitical regions, aiming to disclose the genetic structure of male lineages in the country. A population comparison based on pairwise FST genetic distances did not reveal statistically significant differences in haplogroup frequency distributions among populations from the different regions. The genetic differences observed among regions were, however, consistent with the colonization history of the country. The sample from the Northern region presented the highest Native American ancestry (8.4%), whereas the more pronounced African contribution could be observed in the Northeastern population (15.1%). The Central-Western and Southern samples showed the higher European contributions (95.7% and 93.6%, respectively). The Southeastern region presented significant European (86.1%) and African (12.0%) contributions. The subtyping of the most frequent European lineage in Brazil (R1b1a-M269) allowed differences in the genetic European background of the five Brazilian regions to be investigated for the first time.

New native South American Y chromosome lineages

Many single-nucleotide polymorphisms (SNPs) in the non-recombining region of the human Y chromosome have been described in the last decade. High-coverage sequencing has helped to characterize new SNPs, which has in turn increased the level of detail in paternal phylogenies. However, these paternal lineages still provide insufficient information on population history and demography, especially for Native Americans. The present study aimed to identify informative paternal sublineages derived from the main founder lineage of the Americas-haplogroup Q-L54-in a sample of 1841 native South Americans. For this purpose, we used a Y-chromosomal genotyping multiplex platform and conventional genotyping methods to validate 34 new SNPs that were identified in the present study by sequencing, together with many Y-SNPs previously described in the literature. We updated the haplogroup Q phylogeny and identified two new Q-M3 and three new Q-L54*(xM3) sublineages defined by five informative SNPs, designated SA04, SA05, SA02, SA03 and SA29. Within the Q-M3, sublineage Q-SA04 was mostly found in individuals from ethnic groups belonging to the Tukanoan linguistic family in the northwest Amazon, whereas sublineage Q-SA05 was found in Peruvian and Bolivian Amazon ethnic groups. Within Q-L54*, the derived sublineages Q-SA03 and Q-SA02 were exclusively found among Coyaima individuals (Cariban linguistic family) from Colombia, while Q-SA29 was found only in Maxacali individuals (Jean linguistic family) from southeast Brazil. Furthermore, we validated the usefulness of several published SNPs among indigenous South Americans. This new Y chromosome haplogroup Q phylogeny offers an informative paternal genealogy to investigate the pre-Columbian history of South America.Journal of Human Genetics advance online publication, 31 March 2016; doi:10.1038/jhg.2016.26.

Y chromosome diversity in a linguistic isolate (Mirandese, NE Portugal)

OBJECTIVES

The purpose of this study was to genetically characterize the male lineages of people who speak Mirandese, an interesting case of a linguistic relict that can still be found in the municipality of Miranda do Douro, NE Portugal. This region lies within the area of the Leonese dialects, which are remnants of the Romance dialects spoken in the Kingdom of Leon currently grouped in the Astur-Leonese linguistic continuum. We intended to disclose affinities with surrounding populations, namely from Spain where the Astur-Leonese is also spoken.

METHODS

Eighty-eight unrelated males (58 from Miranda and 30 from Bragança, the broad Portuguese region where Miranda is located) were genotyped with the combined use of 17 Y chromosome short tandem repeats (Y-STRs) and a high resolution Y chromosome single nucleotide polymorphism (Y-SNPs) strategy. Moreover, 236 males from Miranda and neighboring regions, previously classified as R-M269, were also genotyped.

RESULTS

R-P312 was the most frequent haplogroup in the Mirandese, followed by J-12f2.1 and T-M70. The male lineages J-12f2.1 and T-M70 were also well represented, and both were shared with descendants of Sephardic Jews. No signs of diversity reduction were detected.

CONCLUSIONS

Mirandese speakers display a Y chromosome gene pool that shows a subtle differentiation from neighboring populations, mainly attributable to the assimilation of lineages ascribed to be of Jewish ancestry. Although not revealing signs of geographic/linguistic isolation, no clear affinities with other Astur-Leonese populations were detected. The results suggest that in Miranda language sharing is not accompanied by significant gene flow between populations from both sides of the political border. Am. J. Hum. Biol. 28:671-680, 2016. © 2016 Wiley Periodicals, Inc.

Human paternal lineages, languages, and environment in the Caucasus

Publications that describe the composition of the human Y-DNA haplogroup in diffferent ethnic or linguistic groups and geographic regions provide no explicit explanation of the distribution of human paternal lineages in relation to specific ecological conditions. Our research attempts to address this topic for the Caucasus, a geographic region that encompasses a relatively small area but harbors high linguistic, ethnic, and Y-DNA haplogroup diversity. We genotyped 224 men that identified themselves as ethnic Georgian for 23 Y-chromosome short tandem-repeat markers and assigned them to their geographic places of origin. The genotyped data were supplemented with published data on haplogroup composition and location of other ethnic groups of the Caucasus. We used multivariate statistical methods to see if linguistics, climate, and landscape accounted for geographical diffferences in frequencies of the Y-DNA haplogroups G2, R1a, R1b, J1, and J2. The analysis showed significant associations of (1) G2 with wellforested mountains, (2) J2 with warm areas or poorly forested mountains, and (3) J1 with poorly forested mountains. R1b showed no association with environment. Haplogroups J1 and R1a were significantly associated with Daghestanian and Kipchak speakers, respectively, but the other haplogroups showed no such simple associations with languages. Climate and landscape in the context of competition over productive areas among diffferent paternal lineages, arriving in the Caucasus in diffferent times, have played an important role in shaping the present-day spatial distribution of patrilineages in the Caucasus. This spatial pattern had formed before linguistic subdivisions were finally shaped, probably in the Neolithic to Bronze Age. Later historical turmoil had little influence on the patrilineage composition and spatial distribution. Based on our results, the scenario of postglacial expansions of humans and their languages to the Caucasus from the Middle East, western Eurasia, and the East European Plain is plausible.

Genetic structure of the Kuwaiti population revealed by paternal lineages

OBJECTIVE

We analyzed the Y-chromosome haplogroup diversity in the Kuwaiti population to gain a more complete overview of its genetic landscape.

METHOD

A sample of 117 males from the Kuwaiti population was studied through the analysis of 22 Y-SNPs. The results were then interpreted in conjunction with those of other populations from the Middle East, South Asia, North and East Africa, and East Europe.

RESULTS

The analyzed markers allowed the discrimination of 19 different haplogroups with a diversity of 0.7713. J-M304 was the most frequent haplogroup in the Kuwaiti population (55.5%) followed by E-M96 (18%). They revealed a genetic homogeneity between the Kuwaiti population and those of the Middle East (FST  = 6.1%, P-value < 0.0001), although a significant correlation between genetic and geographic distances was found (r = 0.41, P-value = 0.009). Moreover, the nonsignificant pairwise FST genetic distances between the Kuwait population on the one hand and the Arabs of Iran and those of Sudan on the other, corroborate the hypothesis of bidirectional gene flow between Arabia and both Iran and Sudan.

CONCLUSION

Overall, we have revealed that the Kuwaiti population has experienced significant gene flow from neighboring populations like Saudi Arabia, Iran, and East Africa. Therefore, we have confirmed that the population of Kuwait is genetically coextensive with those of the Middle East.

mtDNA analysis of 174 Eurasian populations using a new iterative rank correlation method

In this study, we analyse 27-dimensional mtDNA haplogroup distributions of 174 Eurasian, North-African and American populations, including numerous ancient data as well. The main contribution of this work was the description of the haplogroup distribution of recent and ancient populations as compounds of certain hypothetic ancient core populations immediately or indirectly determining the migration processes in Eurasia for a long time. To identify these core populations, we developed a new iterative algorithm determining clusters of the 27 mtDNA haplogroups studied having strong rank correlation among each other within a definite subset of the populations. Based on this study, the current Eurasian populations can be considered as compounds of three early core populations regarding to maternal lineages. We wanted to show that a simultaneous analysis of ancient and recent data using a new iterative rank correlation algorithm and the weighted SOC learning technique may reveal the most important and deterministic migration processes in the past. This technique allowed us to determine geographically, historically and linguistically well-interpretable clusters of our dataset having a very specific, hardly classifiable structure. The method was validated using a 2-dimensional stepping stone model.

New clues to the evolutionary history of the main European paternal lineage M269: dissection of the Y-SNP S116 in Atlantic Europe and Iberia

The dissection of S116 in more than 1500 individuals from Atlantic Europe and the Iberian Peninsula has provided important clues about the controversial evolutionary history of M269. First, the results do not point to an origin of M269 in the Franco-Cantabrian refuge, owing to the lack of sublineage diversity within M269, which supports the new theories proposing its origin in Eastern Europe. Second, S116 shows frequency peaks and spatial distribution that differ from those previously proposed, indicating an origin farther west, and it also shows a high frequency in the Atlantic coastline. Third, an outstanding frequency of the DF27 sublineage has been found in Iberia, with a restricted distribution pattern inside this peninsula and a frequency maximum in the area of the Franco-Cantabrian refuge. This entire panorama indicates an old arrival of M269 into Western Europe, because it has generated at least two episodes of expansion in the Franco-Cantabrian area. This study demonstrates the importance of continuing the dissection of the M269 lineage in different European populations because the discovery and study of new sublineages can adjust or even completely revise the theories about European peopling, as has been the case for the place of origin of M269.

Large-scale recent expansion of European patrilineages shown by population resequencing

The proportion of Europeans descending from Neolithic farmers ∼ 10 thousand years ago (KYA) or Palaeolithic hunter-gatherers has been much debated. The male-specific region of the Y chromosome (MSY) has been widely applied to this question, but unbiased estimates of diversity and time depth have been lacking. Here we show that European patrilineages underwent a recent continent-wide expansion. Resequencing of 3.7 Mb of MSY DNA in 334 males, comprising 17 European and Middle Eastern populations, defines a phylogeny containing 5,996 single-nucleotide polymorphisms. Dating indicates that three major lineages (I1, R1a and R1b), accounting for 64% of our sample, have very recent coalescent times, ranging between 3.5 and 7.3 KYA. A continuous swathe of 13/17 populations share similar histories featuring a demographic expansion starting ∼ 2.1-4.2 KYA. Our results are compatible with ancient MSY DNA data, and contrast with data on mitochondrial DNA, indicating a widespread male-specific phenomenon that focuses interest on the social structure of Bronze Age Europe.

High Y-chromosomal diversity and low relatedness between paternal lineages on a communal scale in the Western European Low Countries during the surname establishment

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.

Genetic stratigraphy of key demographic events in Arabia

At the crossroads between Africa and Eurasia, Arabia is necessarily a melting pot, its peoples enriched by successive gene flow over the generations. Estimating the timing and impact of these multiple migrations are important steps in reconstructing the key demographic events in the human history. However, current methods based on genome-wide information identify admixture events inefficiently, tending to estimate only the more recent ages, as here in the case of admixture events across the Red Sea (∼8–37 generations for African input into Arabia, and 30–90 generations for “back-to-Africa” migrations). An mtDNA-based founder analysis, corroborated by detailed analysis of the whole-mtDNA genome, affords an alternative means by which to identify, date and quantify multiple migration events at greater time depths, across the full range of modern human history, albeit for the maternal line of descent only. In Arabia, this approach enables us to infer several major pulses of dispersal between the Near East and Arabia, most likely via the Gulf corridor. Although some relict lineages survive in Arabia from the time of the out-of-Africa dispersal, 60 ka, the major episodes in the peopling of the Peninsula took place from north to south in the Late Glacial and, to a lesser extent, the immediate post-glacial/Neolithic. Exchanges across the Red Sea were mainly due to the Arab slave trade and maritime dominance (from ∼2.5 ka to very recent times), but had already begun by the early Holocene, fuelled by the establishment of maritime networks since ∼8 ka. The main “back-to-Africa” migrations, again undetected by genome-wide dating analyses, occurred in the Late Glacial period for introductions into eastern Africa, whilst the Neolithic was more significant for migrations towards North Africa.

Portuguese crypto-Jews: the genetic heritage of a complex history

The first documents mentioning Jewish people in Iberia are from the Visigothic period. It was also in this period that the first documented anti-Judaic persecution took place. Other episodes of persecution would happen again and again during the long troubled history of the Jewish people in Iberia and culminated with the Decrees of Expulsion and the establishment of the Inquisition: some Jews converted to Catholicism while others resisted and were forcedly baptized, becoming the first Iberian Crypto-Jews. In the 18th century the official discrimination and persecution carried out by the Inquisition ended and several Jewish communities emerged in Portugal. From a populational genetics point of view, the worldwide Diaspora of contemporary Jewish communities has been intensely studied. Nevertheless, very little information is available concerning Sephardic and Iberian Crypto-Jewish descendants. Data from the Iberian Peninsula, the original geographic source of Sephardic Jews, is limited to two populations in Portugal, Belmonte, and Bragança district, and the Chueta community from Mallorca. Belmonte was the first Jewish community studied for uniparental markers. The construction of a reference model for the history of the Portuguese Jewish communities, in which the genetic and classical historical data interplay dynamically, is still ongoing. Recently an enlarged sample covering a wide region in the Northeast Portugal was undertaken, allowing the genetic profiling of male and female lineages. A Jewish specific shared female lineage (HV0b) was detected between the community of Belmonte and Bragança. In contrast to what was previously described as a hallmark of the Portuguese Jews, an unexpectedly high polymorphism of lineages was found in Bragança, showing a surprising resistance to the erosion of genetic diversity typical of small-sized isolate populations, as well as signs of admixture with the Portuguese host population.

From Arabia to Iberia: A Y chromosome perspective

At different times during recent human evolution, northern Africa has served as a conduit for migrations from the Arabian Peninsula. Although previous researchers have investigated the possibility of the Strait of Gibraltar as a pathway of migration from North Africa to Iberia, we now revisit this issue and theorize that although the Strait of Gibraltar, at the west end of this corridor, has acted as a barrier for human dispersal into Southwest Europe, it has not provided an absolute seal to gene flow. To test this hypothesis, here we use the spatial frequency distributions, STR diversity and expansion time estimates of Y chromosome haplogroups J1-P58 and E-M81 to investigate the genetic imprints left by the Arabian and Berber expansions into the Iberian Peninsula, respectively. The data generated indicate that Arabian and Berber genetic markers are detected in Iberia. We present evidence that suggest that Iberia has received gene flow from Northwest Africa during and prior to the Islamic colonization of 711A.D. It is interesting that the highest frequencies of Arabia and Berber markers are not found in southern Spain, where Islam remained the longest and was culturally most influential, but in Northwest Iberia, specifically Galicia. We propose that Moriscos' relocations to the north during the Reconquista, the migration of cryptic Muslims seeking refuge in a more lenient society and/or more geographic extensive pre-Islamic incursions may explain the higher frequencies and older time estimates of mutations in the north of the Peninsula. These scenarios are congruent with the higher diversities of some diagnostic makers observed in Northwest Iberia.

The Y-chromosome tree bursts into leaf: 13,000 high-confidence SNPs covering the majority of known clades

Many studies of human populations have used the male-specific region of the Y chromosome (MSY) as a marker, but MSY sequence variants have traditionally been subject to ascertainment bias. Also, dating of haplogroups has relied on Y-specific short tandem repeats (STRs), involving problems of mutation rate choice, and possible long-term mutation saturation. Next-generation sequencing can ascertain single nucleotide polymorphisms (SNPs) in an unbiased way, leading to phylogenies in which branch-lengths are proportional to time, and allowing the times-to-most-recent-common-ancestor (TMRCAs) of nodes to be estimated directly. Here we describe the sequencing of 3.7 Mb of MSY in each of 448 human males at a mean coverage of 51×, yielding 13,261 high-confidence SNPs, 65.9% of which are previously unreported. The resulting phylogeny covers the majority of the known clades, provides date estimates of nodes, and constitutes a robust evolutionary framework for analyzing the history of other classes of mutation. Different clades within the tree show subtle but significant differences in branch lengths to the root. We also apply a set of 23 Y-STRs to the same samples, allowing SNP- and STR-based diversity and TMRCA estimates to be systematically compared. Ongoing purifying selection is suggested by our analysis of the phylogenetic distribution of nonsynonymous variants in 15 MSY single-copy genes.

Different waves and directions of Neolithic migrations in the Armenian Highland

Background

The peopling of Europe and the nature of the Neolithic agricultural migration as a primary issue in the modern human colonization of the globe is still widely debated. At present, much uncertainty is associated with the reconstruction of the routes of migration for the first farmers from the Near East. In this context, hospitable climatic conditions and the key geographic position of the Armenian Highland suggest that it may have served as a conduit for several waves of expansion of the first agriculturalists from the Near East to Europe and the North Caucasus.

Results

Here, we assess Y-chromosomal distribution in six geographically distinct populations of Armenians that roughly represent the extent of historical Armenia. Using the general haplogroup structure and the specific lineages representing putative genetic markers of the Neolithic Revolution, haplogroups R1b1a2, J2, and G, we identify distinct patterns of genetic affinity between the populations of the Armenian Highland and the neighboring ones north and west from this area.

Conclusions

Based on the results obtained, we suggest a new insight on the different routes and waves of Neolithic expansion of the first farmers through the Armenian Highland. We detected at least two principle migratory directions: (1) westward alongside the coastline of the Mediterranean Sea and (2) northward to the North Caucasus.

Electronic supplementary material

The online version of this article (doi:10.1186/s13323-014-0015-6) contains supplementary material, which is available to authorized users.

The place of Slovakian paternal diversity in the clinal European landscape

BACKGROUND

Several demographic events have been postulated to explain the contemporaneous structure of European genetic diversity. First, an initial settlement of the continent by anatomically modern humans; second, the re-settlement of northern latitudes after the Last Glacial Maximum; third, the demic diffusion of Neolithic farmers from the Near East; and, fourth, several historical events such as the Slavic migration.

AIM

The aim of this study was to provide a more integrated picture of male-specific genetic relationships of Slovakia within the broader pan-European genetic landscape.

SUBJECTS AND METHODS

This study analysed a new Y-chromosome data-set (156 individuals) for both SNP and STR polymorphisms in population samples from five different Slovakian localities.

RESULTS

It was found that the male diversity of Slovakia is embedded in the clinal pattern of the major R1a and R1b clades extending over the continent and a similar pattern of population structure is found with Y-specific SNP or STR variation.

CONCLUSION

The highly significant correlation between the results based on fast evolving STRs on one hand and slow evolving SNPs on the other hand suggests a recent timeframe for the settlement of the area.

Traces of medieval migrations in a socially stratified population from Northern Italy. Evidence from uniparental markers and deep-rooted pedigrees

Social and cultural factors had a critical role in determining the genetic structure of Europe. Therefore, socially stratified populations may help to focus on specific episodes of European demographic history. In this study, we use uniparental markers to analyse the genetic structure of Partecipanza in San Giovanni in Persiceto (Northern Italy), a peculiar institution whose origins date back to the Middle Ages and whose members form the patrilineal descent of a group of founder families. From a maternal point of view (mtDNA), Partecipanza is genetically homogeneous with the rest of the population. However, we observed a significant differentiation for Y-chromosomes. In addition, by comparing 17 Y-STR profiles with deep-rooted paternal pedigrees, we estimated a Y-STR mutation rate equal to 3.90 * 10(-3) mutations per STR per generation and an average generation duration time of 33.38 years. When we used these values for tentative dating, we estimated 1300-600 years ago for the origins of the Partecipanza. These results, together with a peculiar Y-chromosomal composition and historical evidence, suggest that Germanic populations (Lombards in particular) settled in the area during the Migration Period (400-800 AD, approximately) and may have had an important role in the foundation of this community.

Fine-scale human genetic structure in Western France

The difficulties arising from association analysis with rare variants underline the importance of suitable reference population cohorts, which integrate detailed spatial information. We analyzed a sample of 1684 individuals from Western France, who were genotyped at genome-wide level, from two cohorts D.E.S.I.R and CavsGen. We found that fine-scale population structure occurs at the scale of Western France, with distinct admixture proportions for individuals originating from the Brittany Region and the Vendée Department. Genetic differentiation increases with distance at a high rate in these two parts of Northwestern France and linkage disequilibrium is higher in Brittany suggesting a lower effective population size. When looking for genomic regions informative about Breton origin, we found two prominent associated regions that include the lactase region and the HLA complex. For both the lactase and the HLA regions, there is a low differentiation between Bretons and Irish, and this is also found at the genome-wide level. At a more refined scale, and within the Pays de la Loire Region, we also found evidence of fine-scale population structure, although principal component analysis showed that individuals from different departments cannot be confidently discriminated. Because of the evidence for fine-scale genetic structure in Western France, we anticipate that rare and geographically localized variants will be identified in future full-sequence analyses.

Demographic events and evolutionary forces shaping European genetic diversity

Europeans have been the focus of some of the largest studies of genetic diversity in any species to date. Recent genome-wide data have reinforced the hypothesis that present-day European genetic diversity is strongly correlated with geography. The remaining challenge now is to understand more precisely how patterns of diversity in Europe reflect ancient demographic events such as postglacial expansions or the spread of farming. It is likely that recent advances in paleogenetics will give us some of these answers. There has also been progress in identifying specific segments of European genomes that reflect adaptations to selective pressures from the physical environment, disease, and dietary shifts. A growing understanding of how modern European genetic diversity has been shaped by demographic and evolutionary forces is not only of basic historical and anthropological interest but also aids genetic studies of disease.

Phylogenetic applications of whole Y-chromosome sequences and the Near Eastern origin of Ashkenazi Levites

Previous Y-chromosome studies have demonstrated that Ashkenazi Levites, members of a paternally inherited Jewish priestly caste, display a distinctive founder event within R1a, the most prevalent Y-chromosome haplogroup in Eastern Europe. Here we report the analysis of 16 whole R1 sequences and show that a set of 19 unique nucleotide substitutions defines the Ashkenazi R1a lineage. While our survey of one of these, M582, in 2,834 R1a samples reveals its absence in 922 Eastern Europeans, we show it is present in all sampled R1a Ashkenazi Levites, as well as in 33.8% of other R1a Ashkenazi Jewish males and 5.9% of 303 R1a Near Eastern males, where it shows considerably higher diversity. Moreover, the M582 lineage also occurs at low frequencies in non-Ashkenazi Jewish populations. In contrast to the previously suggested Eastern European origin for Ashkenazi Levites, the current data are indicative of a geographic source of the Levite founder lineage in the Near East and its likely presence among pre-Diaspora Hebrews.

Population genetics studies continue to debate whether Ashkenazi Levites originated in Europe or the Near East. Here, Rootsi et al. use whole Y-chromosome DNA sequences to unravel the phylogenetic origin of the Ashkenazi Levite and suggest an origin for the Levite founder lineage in the Near East.

An ancient Mediterranean melting pot: investigating the uniparental genetic structure and population history of sicily and southern Italy

Due to their strategic geographic location between three different continents, Sicily and Southern Italy have long represented a major Mediterranean crossroad where different peoples and cultures came together over time. However, its multi-layered history of migration pathways and cultural exchanges, has made the reconstruction of its genetic history and population structure extremely controversial and widely debated. To address this debate, we surveyed the genetic variability of 326 accurately selected individuals from 8 different provinces of Sicily and Southern Italy, through a comprehensive evaluation of both Y-chromosome and mtDNA genomes. The main goal was to investigate the structuring of maternal and paternal genetic pools within Sicily and Southern Italy, and to examine their degrees of interaction with other Mediterranean populations. Our findings show high levels of within-population variability, coupled with the lack of significant genetic sub-structures both within Sicily, as well as between Sicily and Southern Italy. When Sicilian and Southern Italian populations were contextualized within the Euro-Mediterranean genetic space, we observed different historical dynamics for maternal and paternal inheritances. Y-chromosome results highlight a significant genetic differentiation between the North-Western and South-Eastern part of the Mediterranean, the Italian Peninsula occupying an intermediate position therein. In particular, Sicily and Southern Italy reveal a shared paternal genetic background with the Balkan Peninsula and the time estimates of main Y-chromosome lineages signal paternal genetic traces of Neolithic and post-Neolithic migration events. On the contrary, despite showing some correspondence with its paternal counterpart, mtDNA reveals a substantially homogeneous genetic landscape, which may reflect older population events or different demographic dynamics between males and females. Overall, both uniparental genetic structures and TMRCA estimates confirm the role of Sicily and Southern Italy as an ancient Mediterranean melting pot for genes and cultures.

The phylogenetic and geographic structure of Y-chromosome haplogroup R1a

R1a-M420 is one of the most widely spread Y-chromosome haplogroups; however, its substructure within Europe and Asia has remained poorly characterized. Using a panel of 16 244 male subjects from 126 populations sampled across Eurasia, we identified 2923 R1a-M420 Y-chromosomes and analyzed them to a highly granular phylogeographic resolution. Whole Y-chromosome sequence analysis of eight R1a and five R1b individuals suggests a divergence time of ∼25,000 (95% CI: 21,300-29,000) years ago and a coalescence time within R1a-M417 of ∼5800 (95% CI: 4800-6800) years. The spatial frequency distributions of R1a sub-haplogroups conclusively indicate two major groups, one found primarily in Europe and the other confined to Central and South Asia. Beyond the major European versus Asian dichotomy, we describe several younger sub-haplogroups. Based on spatial distributions and diversity patterns within the R1a-M420 clade, particularly rare basal branches detected primarily within Iran and eastern Turkey, we conclude that the initial episodes of haplogroup R1a diversification likely occurred in the vicinity of present-day Iran.

How old are chimpanzee communities? Time to the most recent common ancestor of the Y-chromosome in highly patrilocal societies

Many human societies are patrilineal, with males passing on their name or descent group affiliation to their offspring. Y-chromosomes are also passed on from father to son, leading to the simple expectation that males sharing the same surname or descent group membership should have similar Y-chromosome haplotypes. Although several studies in patrilineal human societies have examined the correspondence between Y-chromosome variation and surname or descent group membership, similar studies in non-human animals are lacking. Chimpanzees represent an excellent species for examining the relationship between descent group membership and Y-chromosome variation because they live in strongly male philopatric communities that arise by a group-fissioning process. Here we take advantage of recent analytical advances in the calculation of the time to the most recent common male ancestor and a large sample size of 273 Y-chromosome short tandem repeat haplotypes to inform our understanding of the potential ages of eight communities of chimpanzees. We find that the times to the most recent common male ancestor of chimpanzee communities are several hundred to as much as over two thousand years. These genetic estimates of the great time depths of chimpanzee communities accord well with behavioral observations suggesting that community fissions are a very rare event and are similar to genetic estimates of the time depth of patrilineal human groups.

A genetic atlas of human admixture history

Modern genetic data combined with appropriate statistical methods have the potential to contribute substantially to our understanding of human history. We have developed an approach that exploits the genomic structure of admixed populations to date and characterize historical mixture events at fine scales. We used this to produce an atlas of worldwide human admixture history, constructed by using genetic data alone and encompassing over 100 events occurring over the past 4000 years. We identified events whose dates and participants suggest they describe genetic impacts of the Mongol empire, Arab slave trade, Bantu expansion, first millennium CE migrations in Eastern Europe, and European colonialism, as well as unrecorded events, revealing admixture to be an almost universal force shaping human populations.

An unbiased resource of novel SNP markers provides a new chronology for the human Y chromosome and reveals a deep phylogenetic structure in Africa

Sequence diversity and the ages of the deepest nodes of the MSY phylogeny remain largely unexplored due to the severely biased collection of SNPs available for study. We characterized 68 worldwide Y chromosomes by high-coverage next-generation sequencing, including 18 deep-rooting ones, and identified 2386 SNPs, 80% of which were novel. Many aspects of this pool of variants resembled the pattern observed among genome-wide de novo events, suggesting that in the MSY, a large proportion of newly arisen alleles has survived in the phylogeny. Some degree of purifying selection emerged in the form of an excess of private missense variants. Our tree recapitulated the previously known topology, but the relative lengths of major branches were drastically modified and the associated node ages were remarkably older. We found significantly different branch lengths when comparing the rare deep-rooted A1b African lineage with the rest of the tree. Our dating results and phylogeography led to the following main conclusions: (1) Patrilineal lineages with ages approaching those of early AMH fossils survive today only in central-western Africa; (2) only a few evolutionarily successful MSY lineages survived between 160 and 115 kya; and (3) an early exit out of Africa (before 70 kya), which fits recent western Asian archaeological evidence, should be considered. Our experimental design produced an unbiased resource of new MSY markers informative for the initial formation of the anatomically modern human gene pool, i.e., a period of our evolution that had been previously considered to be poorly accessible with paternally inherited markers.

Y-chromosomal DNA analysis in French male lineages

French population, despite of its crucial geographic location for repopulation movements of Europe across time, it has been insufficiently characterized at the genetic level, especially for Y-chromosomal DNA variation. In order to make a genetic structure characterization, we have analyzed the Y-chromosome diversity of 558 male individuals, scattered along 7 different French regions: Alsace (Strasbourg), Auvergne (Clermont-Ferrand), Bretagne (Rennes), Île-de-France (Paris), Midi-Pyrénées (Toulouse), Nord-Pas-de-Calais (Lille) and Provence-Alpes-Côte d'Azur (Marseille). A total of 17 Y-chromosome STRs and 27 Y-chromosome SNPs were genotyped for each individual. Even though we find that most of the individual populations in France were not differentiated from each other, Bretagne population shows population substructure, an important fact to be considered when establishing general population databases.

Low historical rates of cuckoldry in a Western European human population traced by Y-chromosome and genealogical data

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.

Demographic histories, isolation and social factors as determinants of the genetic structure of Alpine linguistic groups

Great European mountain ranges have acted as barriers to gene flow for resident populations since prehistory and have offered a place for the settlement of small, and sometimes culturally diverse, communities. Therefore, the human groups that have settled in these areas are worth exploring as an important potential source of diversity in the genetic structure of European populations. In this study, we present new high resolution data concerning Y chromosomal variation in three distinct Alpine ethno-linguistic groups, Italian, Ladin and German. Combining unpublished and literature data on Y chromosome and mitochondrial variation, we were able to detect different genetic patterns. In fact, within and among population diversity values observed vary across linguistic groups, with German and Italian speakers at the two extremes, and seem to reflect their different demographic histories. Using simulations we inferred that the joint effect of continued genetic isolation and reduced founding group size may explain the apportionment of genetic diversity observed in all groups. Extending the analysis to other continental populations, we observed that the genetic differentiation of Ladins and German speakers from Europeans is comparable or even greater to that observed for well known outliers like Sardinian and Basques. Finally, we found that in south Tyroleans, the social practice of Geschlossener Hof, a hereditary norm which might have favored male dispersal, coincides with a significant intra-group diversity for mtDNA but not for Y chromosome, a genetic pattern which is opposite to those expected among patrilocal populations. Together with previous evidence regarding the possible effects of “local ethnicity” on the genetic structure of German speakers that have settled in the eastern Italian Alps, this finding suggests that taking socio-cultural factors into account together with geographical variables and linguistic diversity may help unveil some yet to be understood aspects of the genetic structure of European populations.

Afghan Hindu Kush: where Eurasian sub-continent gene flows converge

Despite being located at the crossroads of Asia, genetics of the Afghanistan populations have been largely overlooked. It is currently inhabited by five major ethnic populations: Pashtun, Tajik, Hazara, Uzbek and Turkmen. Here we present autosomal from a subset of our samples, mitochondrial and Y- chromosome data from over 500 Afghan samples among these 5 ethnic groups. This Afghan data was supplemented with the same Y-chromosome analyses of samples from Iran, Kyrgyzstan, Mongolia and updated Pakistani samples (HGDP-CEPH). The data presented here was integrated into existing knowledge of pan-Eurasian genetic diversity. The pattern of genetic variation, revealed by structure-like and Principal Component analyses and Analysis of Molecular Variance indicates that the people of Afghanistan are made up of a mosaic of components representing various geographic regions of Eurasian ancestry. The absence of a major Central Asian-specific component indicates that the Hindu Kush, like the gene pool of Central Asian populations in general, is a confluence of gene flows rather than a source of distinctly autochthonous populations that have arisen in situ: a conclusion that is reinforced by the phylogeography of both haploid loci.