A Y-chromosome signature of hegemony in Gaelic Ireland

Reproductive inequality in humans and other mammals

To address claims of human exceptionalism, we determine where humans fit within the greater mammalian distribution of reproductive inequality. We show that humans exhibit lower reproductive skew (i.e., inequality in the number of surviving offspring) among males and smaller sex differences in reproductive skew than most other mammals, while nevertheless falling within the mammalian range. Additionally, female reproductive skew is higher in polygynous human populations than in polygynous nonhumans mammals on average. This patterning of skew can be attributed in part to the prevalence of monogamy in humans compared to the predominance of polygyny in nonhuman mammals, to the limited degree of polygyny in the human societies that practice it, and to the importance of unequally held rival resources to women's fitness. The muted reproductive inequality observed in humans appears to be linked to several unusual characteristics of our species-including high levels of cooperation among males, high dependence on unequally held rival resources, complementarities between maternal and paternal investment, as well as social and legal institutions that enforce monogamous norms.

Millennium-old pathogenic Mendelian mutation discovery for multiple osteochondromas from a Gaelic Medieval graveyard

Only a limited number of genetic diseases are diagnosable in archaeological individuals and none have had causal mutations identified in genome-wide screens. Two individuals from the Gaelic Irish Medieval burial ground of Ballyhanna, Co. Donegal, showed evidence of bone tumours consistent with the autosomal dominant condition multiple osteochondromas. Genome sequencing of the earlier individual uncovered a missense mutation in the second exon of EXT1, a specific lesion that has been identified in several modern patients. The later individual lacked this but displayed a novel frameshift mutation leading to a premature stop codon and loss of function in the same gene. These molecular confirmations of a paleopathological diagnosis within a single rural ancient context are surprisingly disjunct, given the observation of clusters of this disease in modern isolated populations and a de novo mutation rate of only 10%.

On the Forensic Use of Y-Chromosome Polymorphisms

Nowadays, the use of Y-chromosome polymorphisms forms an essential part of many forensic DNA investigations. However, this was not always the case. Only since 1992 have we seen that some forensic scientists started to have an interest in this chromosome. In this review, I will sketch a brief history focusing on the forensic use of Y-chromosome polymorphisms. Before describing the various applications of short-tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) on the Y-chromosome, I will discuss a few often ignored aspects influencing proper use and interpretation of Y-chromosome information: (i) genotyping Y-SNPs and Y-STRs, (ii) Y-STR haplotypes shared identical by state (IBS) or identical by descent (IBD), and (iii) Y-haplotype database frequencies.

Is History the Same as Evolution? No. Is it Independent of Evolution? Certainly Not

History is full of violence and oppression within and between groups, and although group conflicts enhance within-group cooperation (mediated by oxytocin, which promotes parochial altruism) the hierarchy within groups ensures that spoils accrue very unevenly. Darwin suggested, and we now know, that sexual selection is as powerful as selection by mortality, and the main purpose of survival is reproduction. Male reproductive skew is greater than that among females in all societies, but the difference became much greater after the hunting-gathering era, and the rise of so-called "civilization" was everywhere a process of predatory expansion, producing kingdoms and empires where top males achieved astounding heights of reproductive success. This was shown by historical and ethnographic data now strongly confirmed by genomic science. Psychological research confirms that group identity, out-group stigmatization, leadership characterized by charisma, the will to power, narcissism, sociopathy, and cruelty, and followership characterized by hypnotic obedience, loss of individuality, and cruelty are integral parts of human nature. We can thank at least ten or twelve millennia of microevolutionary processes such as those described above, all more prominent in males than females. Followers in wars have faced a difficult risk-benefit analysis, but if they survived and won they too could increase their reproductive success through the rape and other sexual exploitation that have accompanied almost all wars. For modern leaders, social monogamy and contraception have separated autocracy from reproductive success, but only partly, and current worldwide autocratic trends still depend on the evolved will to power, obedience, and cruelty.

Fitness and Power: The Contribution of Genetics to the History of Differential Reproduction

Textual evidence from pre-modern societies supports the prediction that status differences among men translate to variance in reproductive success. In recent years, analysis of genetic data has opened up new ways of studying this relationship. By investigating cases that range over several millennia, these analyses repeatedly document the replacement of local men by newcomers and reveal instances of exceptional reproductive success of specific male lineages. These findings suggest that violent population transfers and conquests could generate considerable reproductive advantages for male dominants. At the same time, this does not always seem to have been the case. Moreover, it is difficult to link such outcomes to particular historical characters or events, or to identify status-biased reproductive inequalities within dominant groups. The proximate factors that mediated implied imbalances in reproductive success often remain unclear. A better understanding of the complex interplay between social power and genetic fitness will only arise from sustained transdisciplinary engagement.

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.

Cultural hitchhiking and competition between patrilineal kin groups explain the post-Neolithic Y-chromosome bottleneck

In human populations, changes in genetic variation are driven not only by genetic processes, but can also arise from cultural or social changes. An abrupt population bottleneck specific to human males has been inferred across several Old World (Africa, Europe, Asia) populations 5000–7000 BP. Here, bringing together anthropological theory, recent population genomic studies and mathematical models, we propose a sociocultural hypothesis, involving the formation of patrilineal kin groups and intergroup competition among these groups. Our analysis shows that this sociocultural hypothesis can explain the inference of a population bottleneck. We also show that our hypothesis is consistent with current findings from the archaeogenetics of Old World Eurasia, and is important for conceptions of cultural and social evolution in prehistory.

A population bottleneck 5000-7000 years ago in human males, but not females, has been inferred across several African, European and Asian populations. Here, Zeng and colleagues synthesize theory and data to suggest that competition among patrilineal kin groups produced the bottleneck pattern.

Insular Celtic population structure and genomic footprints of migration

Previous studies of the genetic landscape of Ireland have suggested homogeneity, with population substructure undetectable using single-marker methods. Here we have harnessed the haplotype-based method fineSTRUCTURE in an Irish genome-wide SNP dataset, identifying 23 discrete genetic clusters which segregate with geographical provenance. Cluster diversity is pronounced in the west of Ireland but reduced in the east where older structure has been eroded by historical migrations. Accordingly, when populations from the neighbouring island of Britain are included, a west-east cline of Celtic-British ancestry is revealed along with a particularly striking correlation between haplotypes and geography across both islands. A strong relationship is revealed between subsets of Northern Irish and Scottish populations, where discordant genetic and geographic affinities reflect major migrations in recent centuries. Additionally, Irish genetic proximity of all Scottish samples likely reflects older strata of communication across the narrowest inter-island crossing. Using GLOBETROTTER we detected Irish admixture signals from Britain and Europe and estimated dates for events consistent with the historical migrations of the Norse-Vikings, the Anglo-Normans and the British Plantations. The influence of the former is greater than previously estimated from Y chromosome haplotypes. In all, we paint a new picture of the genetic landscape of Ireland, revealing structure which should be considered in the design of studies examining rare genetic variation and its association with traits.

A recent genetic study of the UK (People of the British Isles; PoBI) expanded our understanding of population history of the islands, using newly-developed, powerful techniques that harness the rich information embedded in chunks of genetic code called haplotypes. These methods revealed subtle regional diversity across the UK, and, using genetic data alone, timed key migration events into southeast England and Orkney. We have extended these methods to Ireland, identifying regional differences in genetics across the island that adhere to geography at a resolution not previously reported. Our study reveals relative western diversity and eastern homogeneity in Ireland owing to a history of settlement concentrated on the east coast and longstanding Celtic diversity in the west. We show that Irish Celtic diversity enriches the findings of PoBI; haplotypes mirror geography across Britain and Ireland, with relic Celtic populations contributing greatly to haplotypic diversity. Finally, we used genetic information to date migrations into Ireland from Europe and Britain consistent with historical records of Viking and Norman invasions, demonstrating the signatures of these migrations the on modern Irish genome. Our findings demonstrate that genetic structure exists in even small isolated populations, which has important implications for population-based genetic association studies.

The Irish DNA Atlas: Revealing Fine-Scale Population Structure and History within Ireland

The extent of population structure within Ireland is largely unknown, as is the impact of historical migrations. Here we illustrate fine-scale genetic structure across Ireland that follows geographic boundaries and present evidence of admixture events into Ireland. Utilising the 'Irish DNA Atlas', a cohort (n = 194) of Irish individuals with four generations of ancestry linked to specific regions in Ireland, in combination with 2,039 individuals from the Peoples of the British Isles dataset, we show that the Irish population can be divided in 10 distinct geographically stratified genetic clusters; seven of 'Gaelic' Irish ancestry, and three of shared Irish-British ancestry. In addition we observe a major genetic barrier to the north of Ireland in Ulster. Using a reference of 6,760 European individuals and two ancient Irish genomes, we demonstrate high levels of North-West French-like and West Norwegian-like ancestry within Ireland. We show that that our 'Gaelic' Irish clusters present homogenous levels of ancient Irish ancestries. We additionally detect admixture events that provide evidence of Norse-Viking gene flow into Ireland, and reflect the Ulster Plantations. Our work informs both on Irish history, as well as the study of Mendelian and complex disease genetics involving populations of Irish ancestry.

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.

Detecting past male-mediated expansions using the Y chromosome

Males and females display biological differences that lead to a higher variance of offspring number in males, and this is frequently exacerbated in human societies by mating practices, and possibly by past socio-cultural circumstances. This implies that the genetic record might contain the imprint of past male-mediated expansions, which can be investigated by analysing the male-specific region of the Y chromosome (MSY). Here, we review studies that have used MSY data to infer such expansions. Sets of short-tandem repeats define haplotypes of very low average frequencies, but in a few cases, high-frequency haplotypes are observed, forming the core of descent clusters. Estimates of the ages of such clusters, together with geographical information, have been used to propose powerful historical founders, including Genghis Khan, although without direct supporting evidence. Resequencing of multi-megabase segments of MSY has allowed the construction of detailed phylogenies in which branch lengths are proportional to time, leading to the identification of lineage expansions in the last few millennia as well as the more distant past. Comparisons with maternally-inherited mitochondrial DNA sequence data allow the male specificity of some of these expansions to be demonstrated. These include expansions in Europe in the last ~5000 years that may be associated with a cultural shift during the Bronze Age, as well as expansions elsewhere in the world for which explanations from archaeological evidence are not yet clear.

Palenque de San Basilio in Colombia: genetic data support an oral history of a paternal ancestry in Congo

The Palenque, a black community in rural Colombia, have an oral history of fugitive African slaves founding a free village near Cartagena in the seventeenth century. Recently, linguists have identified some 200 words in regular use that originate in a Kikongo language, with Yombe, mainly spoken in the Congo region, being the most likely source. The non-recombining portion of the Y chromosome (NRY) and mitochondrial DNA were analysed to establish whether there was greater similarity between present-day members of the Palenque and Yombe than between the Palenque and 42 other African groups (for all individuals,n= 2799) from which forced slaves might have been taken. NRY data are consistent with the linguistic evidence that Yombe is the most likely group from which the original male settlers of Palenque came. Mitochondrial DNA data suggested substantial maternal sub-Saharan African ancestry and a strong founder effect but did not associate Palenque with any particular African group. In addition, based on cultural data including inhabitants' claims of linguistic differences, it has been hypothesized that the two districts of the village (Abajo and Arriba) have different origins, with Arriba founded by men originating in Congo and Abajo by those born in Colombia. Although significant genetic structuring distinguished the two from each other, no supporting evidence for this hypothesis was found.

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.

Genomic signals of migration and continuity in Britain before the Anglo-Saxons

The purported migrations that have formed the peoples of Britain have been the focus of generations of scholarly controversy. However, this has not benefited from direct analyses of ancient genomes. Here we report nine ancient genomes (∼ 1 ×) of individuals from northern Britain: seven from a Roman era York cemetery, bookended by earlier Iron-Age and later Anglo-Saxon burials. Six of the Roman genomes show affinity with modern British Celtic populations, particularly Welsh, but significantly diverge from populations from Yorkshire and other eastern English samples. They also show similarity with the earlier Iron-Age genome, suggesting population continuity, but differ from the later Anglo-Saxon genome. This pattern concords with profound impact of migrations in the Anglo-Saxon period. Strikingly, one Roman skeleton shows a clear signal of exogenous origin, with affinities pointing towards the Middle East, confirming the cosmopolitan character of the Empire, even at its northernmost fringes.

Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome

The Neolithic and Bronze Age transitions were profound cultural shifts catalyzed in parts of Europe by migrations, first of early farmers from the Near East and then Bronze Age herders from the Pontic Steppe. However, a decades-long, unresolved controversy is whether population change or cultural adoption occurred at the Atlantic edge, within the British Isles. We address this issue by using the first whole genome data from prehistoric Irish individuals. A Neolithic woman (3343-3020 cal BC) from a megalithic burial (10.3× coverage) possessed a genome of predominantly Near Eastern origin. She had some hunter-gatherer ancestry but belonged to a population of large effective size, suggesting a substantial influx of early farmers to the island. Three Bronze Age individuals from Rathlin Island (2026-1534 cal BC), including one high coverage (10.5×) genome, showed substantial Steppe genetic heritage indicating that the European population upheavals of the third millennium manifested all of the way from southern Siberia to the western ocean. This turnover invites the possibility of accompanying introduction of Indo-European, perhaps early Celtic, language. Irish Bronze Age haplotypic similarity is strongest within modern Irish, Scottish, and Welsh populations, and several important genetic variants that today show maximal or very high frequencies in Ireland appear at this horizon. These include those coding for lactase persistence, blue eye color, Y chromosome R1b haplotypes, and the hemochromatosis C282Y allele; to our knowledge, the first detection of a known Mendelian disease variant in prehistory. These findings together suggest the establishment of central attributes of the Irish genome 4,000 y ago.

Prevalence and correlates of diagnosed and undiagnosed type 2 diabetes mellitus and pre-diabetes in older adults: Findings from the Irish Longitudinal Study on Ageing (TILDA)

AIMS

The prevalence of type 2 diabetes and pre-diabetes has increased rapidly in recent decades and this trend will continue as the global population ages. This study investigates the prevalence of, and factors associated with, diagnosed and undiagnosed type 2 diabetes mellitus and pre-diabetes in older adults in Ireland.

METHODS

Cross-sectional data from 5377 men and women aged 50 and over from Wave 1 of the Irish Longitudinal Study on Ageing (TILDA) was analysed. Diagnosed diabetes was defined using self-reported doctors' diagnosis and medications data. Glycated haemoglobin (HbA1c) analysis was used to identify undiagnosed and pre-diabetes. Age and sex-specific prevalence estimates were generated. Logistic regression was used to investigate the association between diabetes classification and the demographic, health and lifestyle characteristics of the population.

RESULTS

The prevalence of diagnosed and undiagnosed type 2 diabetes was 8.6% (95% confidence interval (CI): 7.6-9.5%) and 0.9% (95% CI: 0.6-1.1%) respectively. Diabetes was more prevalent in men than women and increased with age. The prevalence of pre-diabetes was 5.5% (95% CI: 4.8-6.3%) and increased with age. Diabetes and pre-diabetes were independently associated with male sex, central obesity and a history of hypertension, while undiagnosed diabetes was associated with geographic location and medical costs cover.

CONCLUSION

Despite high rates of obesity and other undiagnosed health conditions, the prevalence of undiagnosed and pre-diabetes is relatively low in community-dwelling older adults in Ireland. Addressing lifestyle factors in this population may help to further reduce the prevalence of pre-diabetes and improve outcomes for those with a previous diagnosis.

The relationship between surname frequency and Y chromosome variation in Spain

In most societies, surnames are passed down from fathers to sons, just like the Y chromosome. It follows that, theoretically, men sharing the same surnames would also be expected to share related Y chromosomes. Previous investigations have explored such relationships, but so far, the only detailed studies that have been conducted are on samples from the British Isles. In order to provide additional insights into the correlation between surnames and Y chromosomes, we focused on the Spanish population by analysing Y chromosomes from 2121 male volunteers representing 37 surnames. The results suggest that the degree of coancestry within Spanish surnames is highly dependent on surname frequency, in overall agreement with British but not Irish surname studies. Furthermore, a reanalysis of comparative data for all three populations showed that Irish surnames have much greater and older surname descent clusters than Spanish and British ones, suggesting that Irish surnames may have considerably earlier origins than Spanish or British ones. Overall, despite closer geographical ties between Ireland and Britain, our analysis points to substantial similarities in surname origin and development between Britain and Spain, while possibly hinting at unique demographic or social events shaping Irish surname foundation and development.

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.

Surnames and Y-chromosomal markers reveal low relationships in Southern Spain

A sample of 416 males from western and eastern Andalusia has been jointly analyzed for surnames and Y-chromosome haplogroups and haplotypes. The observed number of different surnames was 222 (353 when the second surname of the Spanish system of naming is considered). The great majority of recorded surnames have a Castilian-Leonese origin, while Catalan or Basque surnames have not been found. A few Arab-related surnames appear but none discernible of Sephardic-Jewish descent. Low correlation among surnames with different population frequencies and Y-chromosome markers, at different levels of genetic resolution, has been observed in Andalusia. This finding could be explained mainly by the very low rate of monophyletic surnames because of the historical process of surname ascription and the resulting high frequencies of the most common Spanish surnames. The introduction of surnames in Spain during the Middle Ages coincided with Reconquest of the territories under Islamic rule, and Muslims and Jews progressively adopted the present male line surname system. Sampled surnames and Y-chromosome lineages fit well a power-law distribution and observed isonymy is very close to that of the general population. Besides, our data and results show that the reliability of the isonymy method should be questioned because of the high rate of polyphyletic surnames, even in small geographic regions and autochthonous populations. Random isonymy would be consistently dependent of the most common surname frequencies in the population.

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.

Y-chromosome descent clusters and male differential reproductive success: young lineage expansions dominate Asian pastoral nomadic populations

High-frequency microsatellite haplotypes of the male-specific Y-chromosome can signal past episodes of high reproductive success of particular men and their patrilineal descendants. Previously, two examples of such successful Y-lineages have been described in Asia, both associated with Altaic-speaking pastoral nomadic societies, and putatively linked to dynasties descending, respectively, from Genghis Khan and Giocangga. Here we surveyed a total of 5321 Y-chromosomes from 127 Asian populations, including novel Y-SNP and microsatellite data on 461 Central Asian males, to ask whether additional lineage expansions could be identified. Based on the most frequent eight-microsatellite haplotypes, we objectively defined 11 descent clusters (DCs), each within a specific haplogroup, that represent likely past instances of high male reproductive success, including the two previously identified cases. Analysis of the geographical patterns and ages of these DCs and their associated cultural characteristics showed that the most successful lineages are found both among sedentary agriculturalists and pastoral nomads, and expanded between 2100 BCE and 1100 CE. However, those with recent origins in the historical period are almost exclusively found in Altaic-speaking pastoral nomadic populations, which may reflect a shift in political organisation in pastoralist economies and a greater ease of transmission of Y-chromosomes through time and space facilitated by the use of horses.

A genetic variant at 12p11 significantly modifies breast cancer risk in a genetically homogenous island population

Genome-wide association studies have identified novel breast cancer susceptibility loci at 12q24 (rs1292011), 12p11 (rs10771399) and 21q21 (rs2823093). The aim of our study was to investigate the prevalence of variants at these three loci in an Irish sample, and to examine the association between these variants and breast cancer in this cohort. DNA was extracted from the blood or buccal swabs of Irish patients with breast cancer (cases), as well as from healthy Irish female controls. Genotyping was performed for each target using a Taqman-based platform. Data were analysed using IBM Statistical Package for the Social Sciences version 22. Genotyping was performed on samples from 1,267 patients with breast cancer and 841 cancer-free controls. The per-allele odds ratio associated with the minor allele at 12p11 was found to be 0.67 (0.54-0.81, p < 0.001). Genotype-specific odds ratios showed an allele dosage effect with odds ratio of 0.76 (0.6-0.95) for heterozygotes, and 0.23 (0.1-0.51) for rare homozygotes. Minor allele frequencies of the variants at 12q24 and 21q21 did not differ significantly between cases or controls. All three investigated variants were identified in the Irish population. The polymorphism rs10771399 was strongly associated with breast cancer risk in this cohort, and was shown to be associated with reduced odds ratio for all molecular subtypes.

General method to unravel ancient population structures through surnames, final validation on Italian data

We analyze the geographic location of 77,451 different Italian surnames (17,579,891 individuals) obtained from the lists of telephone subscribers of the year 1993. By using a specific neural network analysis (Self-Organizing Maps, SOMs), we automatically identify the geographic origin of 49,117 different surnames. To validate the methodology, we compare the results to a study, previously conducted, on the same database, with accurate supervised methods. By comparing the results, we find an overlap of 97%, meaning that the SOMs methodology is highly reliable and well traces back the geographic origin of surnames at the time of their introduction (Late Middle Ages/Renaissance in Italy). SOMs results enables one to distinguish monophyletic surnames from polyphyletic ones, that is surnames having had a single geographic and historic origin from those that started to be in use, with an identical spelling, in different locations (respectively, 76.06% and 21.05% of the total). As we are interested in geographic origins, polyphyletic surnames are excluded from further analyses. By comparing the present location of each monophyletic surname to its inferred geographic origin in late Middle Ages/Renaissance, we measure the extent of the migrations having occurred in Italy since that time. We find that the percentage of individuals presently living in the very area where their surname started to be in use centuries ago is extremely variable (ranging from 22.77% to 77.86% according to the province), thus meaning that self-assessed regional identities seldom correspond to the "autochthony" they imply. For example the upper part of the Thyrennian coast (Northern Latium, Tuscany) has a strong identity but few "autochthonous" inhabitants (∼28%) having been a passageway from the North to the South of Italy.

The impact of recent events on human genetic diversity

The historical record tells us stories of migrations, population expansions and colonization events in the last few thousand years, but what was their demographic impact? Genetics can throw light on this issue, and has mostly done so through the maternally inherited mitochondrial DNA (mtDNA) and the male-specific Y chromosome. However, there are a number of problems, including marker ascertainment bias, possible influences of natural selection, and the obscuring layers of the palimpsest of historical and prehistorical events. Y-chromosomal lineages are particularly affected by genetic drift, which can be accentuated by recent social selection. A diversity of approaches to expansions in Europe is yielding insights into the histories of Phoenicians, Roma, Anglo-Saxons and Vikings, and new methods for producing and analysing genome-wide data hold much promise. The field would benefit from more consensus on appropriate methods, and better communication between geneticists and experts in other disciplines, such as history, archaeology and linguistics.

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

Recently, the debate on the origins of the major European Y chromosome haplogroup R1b1b2-M269 has reignited, and opinion has moved away from Palaeolithic origins to the notion of a younger Neolithic spread of these chromosomes from the Near East. Here, we address this debate by investigating frequency patterns and diversity in the largest collection of R1b1b2-M269 chromosomes yet assembled. Our analysis reveals no geographical trends in diversity, in contradiction to expectation under the Neolithic hypothesis, and suggests an alternative explanation for the apparent cline in diversity recently described. We further investigate the young, STR-based time to the most recent common ancestor estimates proposed so far for R-M269-related lineages and find evidence for an appreciable effect of microsatellite choice on age estimates. As a consequence, the existing data and tools are insufficient to make credible estimates for the age of this haplogroup, and conclusions about the timing of its origin and dispersal should be viewed with a large degree of caution.

Genetic polymorphisms of 17 short tandem repeat loci on Y chromosome in central Croatian population

In forensic casework, Y-chromosome short tandem repeat (STR) haplotyping is used in human identification, paternity testing and sexual assault cases where Y-STRs provide a male-specific DNA profile. The aim of this study was to describe the genetic structure of Y chromosome in a central Croatian population. We carried out a statistical analysis of the data from previously performed genetic analyses collected during routine forensic work by the Forensic Science Centre "Ivan Vučetić". A total of 220 unrelated healthy men from central Croatia were selected for the purpose of this study. Genomic DNA was extracted using a Chelex procedure from FTA(®) cards. Y-chromosomal STRs were determined using the AmpFISTR Yfiler PCR amplification kit. The haplotype frequencies were determined by direct counting and analyzed using Arlequin 3.1 and analysis of molecular variance calculated with the Y chromosome haplotype reference database online analysis tool. A total of 212 haplotypes were identified, 204 of which were unique. Total haplotype diversity was 0.993. Locus diversity varied from 0.325 for DYS392 to 0.786 for DYS385. Discrimination capacity was 92.7%. Allele frequencies diversity was 0.615. Intermediate alleles 17.2, 18.2 and 19.2 were found at DYS458 locus. A comparison with published data for the European minimal haplotype set showed the closest relationship to the Croatian capital of Zagreb and Bosnia and Herzegovina with significant genetic distance from Slovenia and Austria. The central Croatian population is now well characterized in terms of Y-chromosome STRs, thus providing a solid basis for further forensic and genetic epidemiology studies.

The evolutionary significance of Red Sox nation: sport fandom as a by-product of coalitional psychology

Sport fandom has received considerable attention from social scientists, yet few have considered it from an evolutionary perspective. To redress this gap, we develop the hypothesis that team sports exhibit characteristics that activate mechanisms which evolved to facilitate the development of coalitions in the context of small-scale warfare. Based on this by-product hypothesis, we predicted a correlation between fandom and binding (i.e. group-relevant) concerns, especially loyalty. To test this prediction, we administered the Sport Spectator Identification Scale (SSI) and the Moral Foundations Questionnaire (MFQ) to 495 undergraduates. The MFQ measures three binding concerns, including loyalty, and two individualizing ones, harm and fairness. As predicted, fandom correlated significantly with loyalty (r = .27) and, within men, the two other binding concerns, authority (r =.22) and purity (r = .24). By contrast, fandom did not significantly correlate with harm or fairness. In addition, we predicted and found that men reported significantly higher levels of fandom (Cohen's d =.45) and loyalty (d = .27) than did women. In conclusion, this study presents data supporting the coalitional by-product hypothesis of fandom and should spur further research using fandom as a window into our evolved psychology.

The Evolutionary Significance of Red Sox Nation: Sport Fandom as a Byproduct of Coalitional Psychology

Sport fandom has received considerable attention from social scientists, yet few have considered it from an evolutionary perspective. To redress this gap, we develop the hypothesis that team sports exhibit characteristics that activate mechanisms which evolved to facilitate the development of coalitions in the context of small-scale warfare. Based on this by-product hypothesis, we predicted a correlation between fandom and binding (i.e. group-relevant) concerns, especially loyalty. To test this prediction, we administered the Sport Spectator Identification Scale (SSI) and the Moral Foundations Questionnaire (MFQ) to 495 undergraduates. The MFQ measures three binding concerns, including loyalty, and two individualizing ones, harm and fairness. As predicted, fandom correlated significantly with loyalty ( r = .27) and, within men, the two other binding concerns, authority ( r =.22) and purity ( r = .24). By contrast, fandom did not significantly correlate with harm or fairness. In addition, we predicted and found that men reported significantly higher levels of fandom (Cohen's d =.45) and loyalty ( d = .27) than did women. In conclusion, this study presents data supporting the coalitional by-product hypothesis of fandom and should spur further research using fandom as a window into our evolved psychology.

Population structure and genome-wide patterns of variation in Ireland and Britain

Located off the northwestern coast of the European mainland, Britain and Ireland were among the last regions of Europe to be colonized by modern humans after the last glacial maximum. Further, the geographical location of Britain, and in particular of Ireland, is such that the impact of historical migration has been minimal. Genetic diversity studies applying the Y chromosome and mitochondrial systems have indicated reduced diversity and an increased population structure across Britain and Ireland relative to the European mainland. Such characteristics would have implications for genetic mapping studies of complex disease. We set out to further our understanding of the genetic architecture of the region from the perspective of (i) population structure, (ii) linkage disequilibrium (LD), (iii) homozygosity and (iv) haplotype diversity (HD). Analysis was conducted on 3654 individuals from Ireland, Britain (with regional sampling in Scotland), Bulgaria, Portugal, Sweden and the Utah HapMap collection. Our results indicate a subtle but clear genetic structure across Britain and Ireland, although levels of structure were reduced in comparison with average cross-European structure. We observed slightly elevated levels of LD and homozygosity in the Irish population compared with neighbouring European populations. We also report on a cline of HD across Europe with greatest levels in southern populations and lowest levels in Ireland and Scotland. These results are consistent with our understanding of the population history of Europe and promote Ireland and Scotland as relatively homogenous resources for genetic mapping of rare variants.

A comparison of Y-chromosome variation in Sardinia and Anatolia is more consistent with cultural rather than demic diffusion of agriculture

Two alternative models have been proposed to explain the spread of agriculture in Europe during the Neolithic period. The demic diffusion model postulates the spreading of farmers from the Middle East along a Southeast to Northeast axis. Conversely, the cultural diffusion model assumes transmission of agricultural techniques without substantial movements of people. Support for the demic model derives largely from the observation of frequency gradients among some genetic variants, in particular haplogroups defined by single nucleotide polymorphisms (SNPs) in the Y-chromosome. A recent network analysis of the R-M269 Y chromosome lineage has purportedly corroborated Neolithic expansion from Anatolia, the site of diffusion of agriculture. However, the data are still controversial and the analyses so far performed are prone to a number of biases. In the present study we show that the addition of a single marker, DYSA7.2, dramatically changes the shape of the R-M269 network into a topology showing a clear Western-Eastern dichotomy not consistent with a radial diffusion of people from the Middle East. We have also assessed other Y-chromosome haplogroups proposed to be markers of the Neolithic diffusion of farmers and compared their intra-lineage variation—defined by short tandem repeats (STRs)—in Anatolia and in Sardinia, the only Western population where these lineages are present at appreciable frequencies and where there is substantial archaeological and genetic evidence of pre-Neolithic human occupation. The data indicate that Sardinia does not contain a subset of the variability present in Anatolia and that the shared variability between these populations is best explained by an earlier, pre-Neolithic dispersal of haplogroups from a common ancestral gene pool. Overall, these results are consistent with the cultural diffusion and do not support the demic model of agriculture diffusion.

Coercive paraphilic disorder

Sexual coercion is a manifestation of sexual conflict that is not in itself pathological according to Wakefield's (1992) criteria because sexual coercion can increase a man's Darwinian fitness. There are, however, differences among men in their propensity to commit rape and this propensity is linked to antisocial personality characteristics and relatively more sexual interest in brutal rape depictions. If highly rape-prone men were to be considered pathological, it would be possible to develop diagnostic criteria to identify them.

A predominantly neolithic origin for European paternal lineages

The relative contributions to modern European populations of Paleolithic hunter-gatherers and Neolithic farmers from the Near East have been intensely debated. Haplogroup R1b1b2 (R-M269) is the commonest European Y-chromosomal lineage, increasing in frequency from east to west, and carried by 110 million European men. Previous studies suggested a Paleolithic origin, but here we show that the geographical distribution of its microsatellite diversity is best explained by spread from a single source in the Near East via Anatolia during the Neolithic. Taken with evidence on the origins of other haplogroups, this indicates that most European Y chromosomes originate in the Neolithic expansion. This reinterpretation makes Europe a prime example of how technological and cultural change is linked with the expansion of a Y-chromosomal lineage, and the contrast of this pattern with that shown by maternally inherited mitochondrial DNA suggests a unique role for males in the transition.

Stratégies reproductives et transmission des gènes: grâce aux femmes et malgré les hommes ?

L’étude des comportements animaux montre que le souci majeur de tout être vivant est de transmettre ses gènes, quel que soit le type de société dans lequel il vit. Cela a conduit, au cours de l’évolution, à l’élaborationde stratégies reproductives variées, différentes selon les espèces, le mode de production des gamètes mais aussi selon le sexe. Chez les mammifères, un certain antagonismereproductif existe entre les mâles et les femelles, qui a trouvé un écho dans la mise en évidence de gènes soumis à empreinte parentale et dans la théorie de la guerre des sexes.

Y-chromosome short tandem repeat intermediate variant alleles DYS392.2, DYS449.2, and DYS385.2 delineate new phylogenetic substructure in human Y-chromosome haplogroup tree

AIM

To determine the human Y-chromosome haplogroup backgrounds of intermediate-sized variant alleles displayed by short tandem repeat (STR) loci DYS392, DYS449, and DYS385, and to evaluate the potential of each intermediate variant to elucidate new phylogenetic substructure within the human Y-chromosome haplogroup tree.

METHODS

Molecular characterization of lineages was achieved using a combination of Y-chromosome haplogroup defining binary polymorphisms and up to 37 short tandem repeat loci. DNA sequencing and median-joining network analyses were used to evaluate Y-chromosome lineages displaying intermediate variant alleles.

RESULTS

We show that DYS392.2 occurs on a single haplogroup background, specifically I1*-M253, and likely represents a new phylogenetic subdivision in this European haplogroup. Intermediate variants DYS449.2 and DYS385.2 both occur on multiple haplogroup backgrounds, and when evaluated within specific haplogroup contexts, delineate new phylogenetic substructure, with DYS449.2 being informative within haplogroup A-P97 and DYS385.2 in haplogroups D-M145, E1b1a-M2, and R1b*-M343. Sequence analysis of variant alleles observed within the various haplogroup backgrounds showed that the nature of the intermediate variant differed, confirming the mutations arose independently.

CONCLUSIONS

Y-chromosome short tandem repeat intermediate variant alleles, while relatively rare, typically occur on multiple haplogroup backgrounds. This distribution indicates that such mutations arise at a rate generally intermediate to those of binary markers and STR loci. As a result, intermediate-sized Y-STR variants can reveal phylogenetic substructure within the Y-chromosome phylogeny not currently detected by either binary or Y-STR markers alone, but only when such variants are evaluated within a haplogroup context.

Inbreeding, pedigree size, and the most recent common ancestor of humanity

How many generations ago did the common ancestor of all present-day individuals live, and how does inbreeding affect this estimate? The number of ancestors within family trees determines the timing of the most recent common ancestor of humanity. However, mating is often non-random and inbreeding is ubiquitous in natural populations. Rates of pedigree growth are found for multiple types of inbreeding. This data is then combined with models of global population structure to estimate biparental coalescence times. When pedigrees for regular systems of mating are constructed, the growth rates of inbred populations contain Fibonacci n-step constants. The timing of the most recent common ancestor depends on global population structure, the mean rate of pedigree growth, mean fitness, and current population size. Inbreeding reduces the number of ancestors in a pedigree, pushing back global common ancestry times. These results are consistent with the remarkable findings of previous studies: all humanity shares common ancestry in the recent past.

Y chromosome variation in Europe: Continental and local processes in the formation of the extant gene pool

The polymorphism of the male-specific portion of the Y chromosome has been increasingly used to describe the composition of the European gene pool and to reconstruct its formation. Here the theoretical grounds and the limitations of this approach are presented, together with the different views on debated issues. The emerging picture for the composition of the male gene pool of the continent is illustrated, but local peculiarities that represent departures from the main trends are also highlighted, in order to illustrate the main unifying feature, i.e. the overlay of recent patterns onto more ancient ones. A synopsis of the main findings and conclusions obtained in regional studies has also been compiled.

Effects of Context and Relative Rank on Mate Choice and Affiliation Ratings

Female dominance has not often been studied as a factor in mate choice and other social interactions. When it has been examined, there have been a number of conflicting findings. The present study was designed to clarify interpretations of a study conducted by Brown and Lewis (2004) that found that men prefer subordinate women in a workplace context. We presented participants with information about the relative rank of physically attractive targets, in two very different contexts (work-related and recreational). We found that the context in which rank cues are presented has an impact on affiliation ratings, but that cues of rank do not affect mate choice ratings. Future studies of effects of dominance must take into account the context in which they are presented, and recognize that rank may not be a sufficient indicator of dominance for the purpose of mate choice by both men and women.

Founders, drift, and infidelity: the relationship between Y chromosome diversity and patrilineal surnames

Most heritable surnames, like Y chromosomes, are passed from father to son. These unique cultural markers of coancestry might therefore have a genetic correlate in shared Y chromosome types among men sharing surnames, although the link could be affected by mutation, multiple foundation for names, nonpaternity, and genetic drift. Here, we demonstrate through an analysis of 1,678 Y-chromosomal haplotypes within 40 British surnames a remarkably high degree of coancestry that generally increases as surnames become rarer. On average, the proportion of haplotypes lying within descent clusters is 62% but ranges from 0% to 87%. The shallow time depth of many descent clusters within names, the lack of a detectable effect of surname derivation on diversity, and simulations of surname descent suggest that genetic drift through variation in reproductive success is important in structuring haplotype diversity. Modern patterns therefore provide little reliable information about the original founders of surnames some 700 years ago. A comparative analysis of published data on Y diversity within Irish surnames demonstrates a relative lack of surname frequency dependence of coancestry, a difference probably mediated through distinct Irish and British demographic histories including even more marked genetic drift in Ireland.

Differential Greek and northern African migrations to Sicily are supported by genetic evidence from the Y chromosome

The presence or absence of genetic heterogeneity in Sicily has long been debated. Through the analysis of the variation of Y-chromosome lineages, using the combination of haplogroups and short tandem repeats from several areas of Sicily, we show that traces of genetic flows occurred in the island, due to ancient Greek colonization and to northern African contributions, are still visible on the basis of the distribution of some lineages. The genetic contribution of Greek chromosomes to the Sicilian gene pool is estimated to be about 37% whereas the contribution of North African populations is estimated to be around 6%.In particular, the presence of a modal haplotype coming from the southern Balkan Peninsula and of its one-step derivates associated to E3b1a2-V13, supports a common genetic heritage between Sicilians and Greeks. The estimate of Time to Most Recent Common Ancestor is about 2380 years before present, which broadly agrees with the archaeological traces of the Greek classic era. The Eastern and Western part of Sicily appear to be significantly different by the chi(2)-analysis, although the extent of such differentiation is not very high according to an analysis of molecular variance. The presence of a high number of different haplogroups in the island makes its gene diversity to reach about 0.9. The general heterogeneous composition of haplogroups in our Sicilian data is similar to the patterns observed in other major islands of the Mediterranean, reflecting the complex histories of settlements in Sicily.

An evolutionary perspective on Y-chromosomal variation and male infertility

Genetic variation on the Y chromosome is one of the best-documented causes of male infertility, but the genes responsible have still not been identified. This review discusses how an evolutionary perspective may help with interpretation of the data available and suggest novel approaches to identify key genes. Comparison with the chimpanzee Y chromosome indicates that USP9Y is dispensable in apes, but that multiple copies of TSPY1 may have an important role. Comparisons between infertile and control groups in search of genetic susceptibility factors are more complex for the Y chromosome than for the rest of the genome because of population stratification and require unusual levels of confirmation. But the extreme population stratification exhibited by the Y also allows populations particularly suitable for some studies to be identified, such as the partial AZFc deletions common in Northern European populations where further dissection of this complex structural region would be facilitated.