RESUMO
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.
Assuntos
Cromossomos Humanos Y/genética , Polimorfismo de Nucleotídeo Único/genética , Evolução Molecular , Projeto HapMap , Humanos , Masculino , Filogenia , Análise de Sequência de DNARESUMO
BACKGROUND: Richard III was the last king of England to die in battle, but how he died is unknown. On Sept 4, 2012, a skeleton was excavated in Leicester that was identified as Richard. We investigated the trauma to the skeleton with modern forensic techniques, such as conventional CT and micro-CT scanning, to characterise the injuries and establish the probable cause of death. METHODS: We assessed age and sex through direct analysis of the skeleton and from CT images. All bones were examined under direct light and multi-spectral illumination. We then scanned the skeleton with whole-body post-mortem CT. We subsequently examined bones with identified injuries with micro-CT. We deemed that trauma was perimortem when we recorded no evidence of healing and when breakage characteristics were typical of fresh bone. We used previous data to identify the weapons responsible for the recorded injuries. FINDINGS: The skeleton was that of an adult man with a gracile build and severe scoliosis of the thoracic spine. Standard anthropological age estimation techniques based on dry bone analysis gave an age range between 20s and 30s. Standard post-mortem CT methods were used to assess rib end morphology, auricular surfaces, pubic symphyseal face, and cranial sutures, to produce a multifactorial narrower age range estimation of 30-34 years. We identified nine perimortem injuries to the skull and two to the postcranial skeleton. We identified no healed injuries. The injuries were consistent with those created by weapons from the later medieval period. We could not identify the specific order of the injuries, because they were all distinct, with no overlapping wounds. Three of the injuries-two to the inferior cranium and one to the pelvis-could have been fatal. INTERPRETATION: The wounds to the skull suggest that Richard was not wearing a helmet, although the absence of defensive wounds on his arms and hands suggests he was still otherwise armoured. Therefore, the potentially fatal pelvis injury was probably received post mortem, meaning that the most likely injuries to have caused his death are the two to the inferior cranium. FUNDING: The University of Leicester.
Assuntos
Traumatismos Faciais/patologia , Traumatismos Cranianos Penetrantes/patologia , Ossos Pélvicos/lesões , Costelas/lesões , Fraturas Cranianas/patologia , Armas , Adulto , Autopsia , Inglaterra , Traumatismos Cranianos Penetrantes/diagnóstico por imagem , História Medieval , Humanos , Masculino , Roupa de Proteção/história , Fraturas Cranianas/diagnóstico por imagem , Tomografia Computadorizada por Raios X , Ferimentos Penetrantes/diagnóstico por imagem , Ferimentos Penetrantes/patologiaRESUMO
The great majority of phenotypic characteristics are complex traits, complicating the identification of the genes underlying their expression. However, both methodological and theoretical progress in genome-wide association studies have resulted in a much better understanding of the underlying genetics of many phenotypic traits, including externally visible characteristics (EVCs) such as eye and hair color. Consequently, it has become possible to predict EVCs from human samples lacking phenotypic information. Predicting EVCs from genetic evidence is clearly appealing for forensic applications involving the personal identification of human remains. Now, a recent paper has reported the genetic determination of eye and hair color in samples up to 800 years old. The ability to predict EVCs from ancient human remains opens up promising perspectives for ancient DNA research, as this could allow studies to directly address archaeological and evolutionary questions related to the temporal and geographical origins of the genetic variants underlying phenotypes.
Assuntos
DNA Mitocondrial/genética , DNA/genética , Fenótipo , Pigmentação/genética , Arqueologia/métodos , Impressões Digitais de DNA , Cor de Olho , Fósseis , Genoma Humano , Cabelo , Humanos , Paleontologia/métodos , Polimorfismo de Nucleotídeo ÚnicoRESUMO
The male-specific region of the human Y chromosome (MSY) contains eight large inverted repeats (palindromes), in which high-sequence similarity between repeat arms is maintained by gene conversion. These palindromes also harbor microsatellites, considered to evolve via a stepwise mutation model (SMM). Here, we ask whether gene conversion between palindrome microsatellites contributes to their mutational dynamics. First, we study the duplicated tetranucleotide microsatellite DYS385a,b lying in palindrome P4. We show, by comparing observed data with simulated data under a SMM within haplogroups, that observed heteroallelic combinations in which the modal repeat number difference between copies was large, can give rise to homoallelic combinations with zero-repeats difference, equivalent to many single-step mutations. These are unlikely to be generated under a strict SMM, suggesting the action of gene conversion. Second, we show that the intercopy repeat number difference for a large set of duplicated microsatellites in all palindromes in the MSY reference sequence is significantly reduced compared with that for nonpalindrome-duplicated microsatellites, suggesting that the former are characterized by unusual evolutionary dynamics. These observations indicate that gene conversion violates the SMM for microsatellites in palindromes, homogenizing copies within individual Y chromosomes, but increasing overall haplotype diversity among chromosomes within related groups.
Assuntos
Conversão Gênica , Sequências Repetidas Invertidas/genética , Repetições de Microssatélites/genética , Mutação , Cromossomos Humanos Y/genética , Humanos , Modelos GenéticosRESUMO
Relevant for various areas of human genetics, Y-chromosomal short tandem repeats (Y-STRs) are commonly used for testing close paternal relationships among individuals and populations, and for male lineage identification. However, even the widely used 17-loci Yfiler set cannot resolve individuals and populations completely. Here, 52 centers generated quality-controlled data of 13 rapidly mutating (RM) Y-STRs in 14,644 related and unrelated males from 111 worldwide populations. Strikingly, >99% of the 12,272 unrelated males were completely individualized. Haplotype diversity was extremely high (global: 0.9999985, regional: 0.99836-0.9999988). Haplotype sharing between populations was almost absent except for six (0.05%) of the 12,156 haplotypes. Haplotype sharing within populations was generally rare (0.8% nonunique haplotypes), significantly lower in urban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). Analysis of molecular variance revealed 99.98% of variation within populations, 0.018% among populations within groups, and 0.002% among groups. Of the 2,372 newly and 156 previously typed male relative pairs, 29% were differentiated including 27% of the 2,378 father-son pairs. Relative to Yfiler, haplotype diversity was increased in 86% of the populations tested and overall male relative differentiation was raised by 23.5%. Our study demonstrates the value of RM Y-STRs in identifying and separating unrelated and related males and provides a reference database.
Assuntos
Cromossomos Humanos Y/química , Impressões Digitais de DNA/métodos , Genética Populacional , Haplótipos , Repetições de Microssatélites , África , Alelos , América , Ásia , Impressões Digitais de DNA/estatística & dados numéricos , Europa (Continente) , Frequência do Gene , Variação Genética , Humanos , Masculino , Paternidade , Linhagem , População Rural , População UrbanaRESUMO
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.
Assuntos
Cromossomos Humanos Y , População Branca/genética , Emigração e Imigração , Europa (Continente) , Variação Genética , Geografia , Haplótipos , Humanos , Masculino , Repetições de Microssatélites , Dinâmica PopulacionalRESUMO
Heritable surnames are highly diverse cultural markers of coancestry in human populations. A patrilineal surname is inherited in the same way as the non-recombining region of the Y chromosome and there should, therefore, be a correlation between the two. Studies of Y haplotypes within surnames, mostly of the British Isles, reveal high levels of coancestry among surname cohorts and the influence of confounding factors, including multiple founders for names, non-paternities and genetic drift. Combining molecular genetics and surname analysis illuminates population structure and history, has potential applications in forensic studies and, in the form of 'genetic genealogy', is an area of rapidly growing interest for the public.
Assuntos
Cromossomos Humanos Y/genética , Genealogia e Heráldica , Nomes , Linhagem , Diversidade Cultural , Variação Genética , Humanos , Reino UnidoRESUMO
The influence of Viking-Age migrants to the British Isles is obvious in archaeological and place-names evidence, but their demographic impact has been unclear. Autosomal genetic analyses support Norse Viking contributions to parts of Britain, but show no signal corresponding to the Danelaw, the region under Scandinavian administrative control from the ninth to eleventh centuries. Y-chromosome haplogroup R1a1 has been considered as a possible marker for Viking migrations because of its high frequency in peninsular Scandinavia (Norway and Sweden). Here we select ten Y-SNPs to discriminate informatively among hg R1a1 sub-haplogroups in Europe, analyse these in 619 hg R1a1 Y chromosomes including 163 from the British Isles, and also type 23 short-tandem repeats (Y-STRs) to assess internal diversity. We find three specifically Western-European sub-haplogroups, two of which predominate in Norway and Sweden, and are also found in Britain; star-like features in the STR networks of these lineages indicate histories of expansion. We ask whether geographical distributions of hg R1a1 overall, and of the two sub-lineages in particular, correlate with regions of Scandinavian influence within Britain. Neither shows any frequency difference between regions that have higher (≥10%) or lower autosomal contributions from Norway and Sweden, but both are significantly overrepresented in the region corresponding to the Danelaw. These differences between autosomal and Y-chromosomal histories suggest either male-specific contribution, or the influence of patrilocality. Comparison of modern DNA with recently available ancient DNA data supports the interpretation that two sub-lineages of hg R1a1 spread with the Vikings from peninsular Scandinavia.
Assuntos
Cromossomos Humanos Y/genética , Haplótipos , Migração Humana , Evolução Molecular , Humanos , Masculino , Repetições Minissatélites , Linhagem , Polimorfismo de Nucleotídeo Único , Países Escandinavos e Nórdicos , Reino UnidoRESUMO
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.
Assuntos
Cromossomos Humanos Y/genética , Pai , Genealogia e Heráldica , Deriva Genética , Variação Genética , Nomes , Simulação por Computador , Haplótipos , Humanos , Repetições de Microssatélites/genética , Filogenia , Fatores de TempoRESUMO
Surnames are cultural markers of shared ancestry within human populations. The Y chromosome, like many surnames, is paternally inherited, so men sharing surnames might be expected to share similar Y chromosomes as a signature of coancestry. Such a relationship could be used to connect branches of family trees, to validate population genetic studies based on isonymy, and to predict surname from crime-scene samples in forensics. However, the link may be weak or absent due to multiple independent founders for many names, adoptions, name changes and nonpaternities, and mutation of Y haplotypes. Here, rather than focusing on a single name, we take a general approach by seeking evidence for a link in a sample of 150 randomly ascertained pairs of males who each share a British surname. We show that sharing a surname significantly elevates the probability of sharing a Y-chromosomal haplotype and that this probability increases as surname frequency decreases. Within our sample, we estimate that up to 24% of pairs share recent ancestry and that a large surname-based forensic database might contribute to the intelligence-led investigation of up to approximately 70 rapes and murders per year in the UK. This approach would be applicable to any society that uses patrilineal surnames of reasonable time-depth.
Assuntos
Cromossomos Humanos Y/genética , Nomes , Haplótipos/genética , Humanos , Masculino , Repetições de Microssatélites , População Branca/genéticaRESUMO
The genetic structures of past human populations are obscured by recent migrations and expansions and have been observed only indirectly by inference from modern samples. However, the unique link between a heritable cultural marker, the patrilineal surname, and a genetic marker, the Y chromosome, provides a means to target sets of modern individuals that might resemble populations at the time of surname establishment. As a test case, we studied samples from the Wirral Peninsula and West Lancashire, in northwest England. Place-names and archaeology show clear evidence of a past Viking presence, but heavy immigration and population growth since the industrial revolution are likely to have weakened the genetic signal of a 1,000-year-old Scandinavian contribution. Samples ascertained on the basis of 2 generations of residence were compared with independent samples based on known ancestry in the region plus the possession of a surname known from historical records to have been present there in medieval times. The Y-chromosomal haplotypes of these 2 sets of samples are significantly different, and in admixture analyses, the surname-ascertained samples show markedly greater Scandinavian ancestry proportions, supporting the idea that northwest England was once heavily populated by Scandinavian settlers. The method of historical surname-based ascertainment promises to allow investigation of the influence of migration and drift over the last few centuries in changing the population structure of Britain and will have general utility in other regions where surnames are patrilineal and suitable historical records survive.
Assuntos
Variação Genética , População Branca/genética , Cromossomos Humanos Y , Inglaterra , Genética Populacional , Haplótipos , Humanos , NomesRESUMO
The presence of Africans in Britain has been recorded since Roman times, but has left no apparent genetic trace among modern inhabitants. Y chromosomes belonging to the deepest-rooting clade of the Y phylogeny, haplogroup (hg) A, are regarded as African-specific, and no examples have been reported from Britain or elsewhere in Western Europe. We describe the presence of an hgA1 chromosome in an indigenous British male; comparison with African examples suggests a Western African origin. Seven out of 18 men carrying the same rare east-Yorkshire surname as the original male also carry hgA1 chromosomes, and documentary research resolves them into two genealogies with most-recent-common-ancestors living in Yorkshire in the late 18th century. Analysis using 77 Y-short tandem repeats (STRs) is consistent with coalescence a few generations earlier. Our findings represent the first genetic evidence of Africans among 'indigenous' British, and emphasize the complexity of human migration history as well as the pitfalls of assigning geographical origin from Y-chromosomal haplotypes.
Assuntos
População Negra/genética , Cromossomos Humanos Y/genética , Genética Populacional , Inglaterra , Haplótipos , Humanos , Masculino , Repetições de MicrossatélitesRESUMO
The Y-chromosomal binary marker P25 is a paralogous sequence variant, rather than a SNP: three copies of the P25 sequence lie within the giant palindromic repeats on Yq, and one copy has undergone a C to A transversion to define haplogroup R1b (designated C/C/A). Since gene conversion is known to be active in the palindromic repeats, we reasoned that P25 might be liable to back-mutation by gene conversion, yielding the ancestral state C/C/C. Through analysis of a set of binary markers in Y-chromosomes in two large samples from Great Britain and the Iberian Peninsula we show that such conversion events have occurred at least twice, and provide preliminary evidence that the reverse conversion event (yielding C/A/A) has also occurred. Because of its inherent instability, we suggest that P25 be used with caution in forensic studies, and perhaps replaced with the more reliable binary marker M269.
Assuntos
Cromossomos Humanos Y/química , Medicina Legal/métodos , Conversão Gênica , Marcadores Genéticos , Genética Populacional , Humanos , Masculino , Polimorfismo de Nucleotídeo Único , Valor Preditivo dos Testes , Espanha , Reino UnidoRESUMO
The proportion of Europeans descending from Neolithic farmers â¼ 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 â¼ 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.
Assuntos
Análise de Sequência de DNA , Teorema de Bayes , Evolução Biológica , Simulação por Computador , DNA Mitocondrial/genética , Demografia , Emigração e Imigração , Etnicidade/genética , Europa (Continente) , Variação Genética , Genética Populacional , Genômica , Geografia , Haplótipos , História Antiga , Humanos , Masculino , Oriente Médio , Mutação , Filogenia , Dinâmica Populacional , População Branca/genéticaRESUMO
In 2012, a skeleton was excavated at the presumed site of the Grey Friars friary in Leicester, the last-known resting place of King Richard III. Archaeological, osteological and radiocarbon dating data were consistent with these being his remains. Here we report DNA analyses of both the skeletal remains and living relatives of Richard III. We find a perfect mitochondrial DNA match between the sequence obtained from the remains and one living relative, and a single-base substitution when compared with a second relative. Y-chromosome haplotypes from male-line relatives and the remains do not match, which could be attributed to a false-paternity event occurring in any of the intervening generations. DNA-predicted hair and eye colour are consistent with Richard's appearance in an early portrait. We calculate likelihood ratios for the non-genetic and genetic data separately, and combined, and conclude that the evidence for the remains being those of Richard III is overwhelming.
Assuntos
Cromossomos Humanos Y/genética , Impressões Digitais de DNA , DNA Mitocondrial/análise , Genética Forense , Sequência de Bases , Antropologia Forense , Haplótipos , Humanos , Masculino , Dados de Sequência Molecular , PaternidadeRESUMO
We have characterized the Y chromosome carried by President Thomas Jefferson, the general rarity of which supported the idea that he, or a patrilineal relative, fathered the last son of his slave Sally Hemings. It belongs to haplogroup K2, a lineage representing only approximately 1% of chromosomes worldwide, and most common in East Africa and the Middle East. Phylogenetic network analysis of its Y-STR (short tandem repeat) haplotype shows that it is most closely related to an Egyptian K2 haplotype, but the presence of scattered and diverse European haplotypes within the network is nonetheless consistent with Jefferson's patrilineage belonging to an ancient and rare indigenous European type. This is supported by the observation that two of 85 unrelated British men sharing the surname Jefferson also share the President's Y-STR haplotype within haplogroup K2. Our findings represent a cautionary tale in showing the difficulty of assigning individual ancestry based on a Y-chromosome haplotype, particularly for rare lineages where population data are scarce.
Assuntos
Cromossomos Humanos Y/genética , Genética Populacional , Haplótipos/genética , Filogenia , Europa (Continente) , Pessoas Famosas , Variação Genética , Humanos , Masculino , Repetições de Microssatélites/genética , Oriente MédioRESUMO
We describe a new G to A transition polymorphism, designated Apt, on the human Y chromosome. The A allele chromosomes and the most closely related G allele chromosomes have been found only in India, where they make up about 1.3% of the population. They are found in several different social groups and show considerable microsatellite, minisatellite and major satellite diversity, suggesting that they do not have a recent origin.