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High level of male-biased Scandinavian admixture in Greenlandic Inuit shown by Y-chromosome analysis
Abstract
We have used binary markers and microsatellites on the Y chromosome to analyse diversity in a sample of Greenlandic Inuit males. This sample contains Y chromosomes typical of those found in European populations. Because the Y chromosome has a unique and robust phylogeny of a time depth that precedes the split between European and Native American populations, it is possible to assign chromosomes in an admixed population to either continental source. On this basis, 58+/-6% of these Y chromosomes have been assigned to a European origin. The high proportion of European Y chromosomes contrasts with a complete absence of European mitochondrial DNA and indicates strongly male-biased European admixture into Inuit. Comparison of the European component of Inuit Y chromosomes with European population data suggests that they have their origins in Scandinavia. There are two potential source populations: Norse settlers from Iceland, who may have been assimilated 500 years ago, and the Danish-Norwegian colonists of the eighteenth century. Insufficient differentiation between modern Icelandic and Danish Y chromosomes means that a choice between these cannot be made on the basis of diversity analysis. However, the extreme sex bias in the admixture makes the later event more likely as the source.
... The first European settlement in Greenland, by the Norse from Norway and Iceland, is dated to 985 AD [9]. The Norse primarily settled along the west and south coasts of Greenland [9,10]. ...
... The first European settlement in Greenland, by the Norse from Norway and Iceland, is dated to 985 AD [9]. The Norse primarily settled along the west and south coasts of Greenland [9,10]. However, it is thought that the Norse population did not survive, and after 1450 AD, there is no evidence of any Norse settlements in Greenland [9,10]. ...
... The Norse primarily settled along the west and south coasts of Greenland [9,10]. However, it is thought that the Norse population did not survive, and after 1450 AD, there is no evidence of any Norse settlements in Greenland [9,10]. In 1721 AD, Danish and Norwegian settlers arrived in Greenland [9,11]. ...
The human population in Greenland is characterized by migration events of Paleo- and Neo-Eskimos, as well as admixture with Europeans. In this study, the Y-chromosomal variation in male Greenlanders was investigated in detail by typing 73 Y-chromosomal single nucleotide polymorphisms (Y-SNPs) and 17 Y-chromosomal short tandem repeats (Y-STRs). Approximately 40% of the analyzed Greenlandic Y chromosomes were of European origin (I-M170, R1a-M513 and R1b-M343). Y chromosomes of European origin were mainly found in individuals from the west and south coasts of Greenland, which is in agreement with the historic records of the geographic placements of European settlements in Greenland. Two Inuit Y-chromosomal lineages, Q-M3 (xM19, M194, L663, SA01 and L766) and Q-NWT01 (xM265) were found in 23% and 31% of the male Greenlanders, respectively. The time to the most recent common ancestor (TMRCA) of the Q-M3 lineage of the Greenlanders was estimated to be between 4,400 and 10,900 years ago (y. a.) using two different methods. This is in agreement with the theory that the North Circumpolar Region was populated via a second expansion of humans in the North American continent. The TMRCA of the Q-NWT01 (xM265) lineage in Greenland was estimated to be between 7,000 and 14,300 y. a. using two different methods, which is older than the previously reported TMRCA of this lineage in other Inuit populations. Our results indicate that Inuit individuals carrying the Q-NWT01 (xM265) lineage may have their origin in the northeastern parts of North America and could be descendants of the Dorset culture. This in turn points to the possibility that the current Inuit population in Greenland is comprised of individuals of both Thule and Dorset descent.
... Genetic studies have shown that many modern Greenlanders have a substantial amount of European ancestry [6][7][8][9] inherited mainly from male Europeans. 6 Furthermore, a large genetic study based on DNA from historic samples from different arctic cultures including Saqqaq, Dorset, and Thule, as well as two whole genomes from presentday Greenlanders, was recently published. ...
... Genetic studies have shown that many modern Greenlanders have a substantial amount of European ancestry [6][7][8][9] inherited mainly from male Europeans. 6 Furthermore, a large genetic study based on DNA from historic samples from different arctic cultures including Saqqaq, Dorset, and Thule, as well as two whole genomes from presentday Greenlanders, was recently published. 10 This study provided genetic evidence showing that modern-day Inuit in Greenland are direct descendants of the first Inuit pioneers of the Thule culture. ...
... 2 A few attempts were made to answer this question with genetics, but all were unsuccessful; part of the reason is that the Norse Vikings came from the same or similar geographical regions as the later European colonizers, making it difficult to answer this question by inferring the source country of the European ancestors of the Greenlanders. 6 Moreover, any potential genetic contribution from the Norse Vikings is most likely small and would have left a very limited genetic footprint, making the amount of genetic data used in previous studies insufficient. ...
Because of past limitations in samples and genotyping technologies, important questions about the history of the present-day Greenlandic population remain unanswered. In an effort to answer these questions and in general investigate the genetic history of the Greenlandic population, we analyzed ∼200,000 SNPs from more than 10% of the adult Greenlandic population (n = 4,674). We found that recent gene flow from Europe has had a substantial impact on the population: more than 80% of the Greenlanders have some European ancestry (on average ∼25% of their genome). However, we also found that the amount of recent European gene flow varies across Greenland and is far smaller in the more historically isolated areas in the north and east and in the small villages in the south. Furthermore, we found that there is substantial population structure in the Inuit genetic component of the Greenlanders and that individuals from the east, west, and north can be distinguished from each other. Moreover, the genetic differences in the Inuit ancestry are consistent with a single colonization wave of the island from north to west to south to east. Although it has been speculated that there has been historical admixture between the Norse Vikings who lived in Greenland for a limited period ∼600-1,000 years ago and the Inuit, we found no evidence supporting this hypothesis. Similarly, we found no evidence supporting a previously hypothesized admixture event between the Inuit in East Greenland and the Dorset people, who lived in Greenland before the Inuit.
Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.
... Studies based on uniparentally inherited markers have shown that the Y-chromosomal gene pool of Greenlandic people comprises approximately equal numbers of European and Inuit lineages, [6][7][8][9] but the set of mtDNA haplogroups revealed an overwhelmingly Inuit component, with no European lineages detected. 10 More recently, Helgason et al 4 reported evidence of an intricate pattern of mtDNA variation in Greenlanders. ...
... Taking into account that data for X-chromosomal markers includes individuals from all around Greenland, the proportion of European ancestry observed in X-chromosome markers (13%) is lower than that observed for autosomal data (27%) (Supplementary Table S9); the t-test P-value was statistically significant (Po0.0001). This result is not completely unexpected, because previous studies of uniparentally inherited markers [4][5][6][7]10 reported that the matrilineal ancestry of the Greenlanders is mostly non-European. ...
... This work attested to the complexity of the genetic pool of Greenlanders, corroborating a number of previous reports. 1,[4][5][6][7][8][9][10]24 Taken as a whole, the results supported the historical and archaeological accounts of Greenland's demographic features. A hard-to-access geography, together with an adverse climate, rendered difficult not only the most ancient peopling of Greenland, initiated a few millennia ago, but also the settlement of the island. ...
The peopling of Greenland has a complex history shaped by population migrations, isolation and genetic drift. The Greenlanders present a genetic heritage with components of European and Inuit groups; previous studies using uniparentally inherited markers in Greenlanders have reported evidence of a sex-biased, admixed genetic background. This work further explores the genetics of the Greenlanders by analysing autosomal and X-chromosomal data to obtain deeper insights into the factors that shaped the genetic diversity in Greenlanders. Fourteen Greenlandic subsamples from multiple geographical settlements were compared to assess the level of genetic substructure in the Greenlandic population. The results showed low levels of genetic diversity in all sets of the genetic markers studied, together with an increased number of X-chromosomal loci in linkage disequilibrium in relation to the Danish population. In the broader context of worldwide populations, Greenlanders are remarkably different from most populations, but they are genetically closer to some Inuit groups from Alaska. Admixture analyses identified an Inuit component in the Greenlandic population of approximately 80%. The sub-populations of Ammassalik and Nanortalik are the least diverse, presenting the lowest levels of European admixture. Isolation-by-distance analyses showed that only 16% of the genetic substructure of Greenlanders is most likely to be explained by geographic barriers. We suggest that genetic drift and a differentiated settlement history around the island explain most of the genetic substructure of the population in Greenland.European Journal of Human Genetics advance online publication, 7 May 2014; doi:10.1038/ejhg.2014.90.
... However, STR alleles do carry information on the haplogroup background they are found on (and actually, STR variability is partitioned by haplogroups to a greater extent than by populations (Bosch et al. 1999)), to the point that main haplogroups can be reasonable predicted from the STR haplotypes they carry (Athey 2005;Schlecht et al. 2008), but see Larmuseau et al. (2014) for a counterexample. The fast mutation rate in STRs implies that they can be used to time relatively recent events in human evolution, at a prehistoric (Arredi et al. 2004;Alonso et al. 2005;Berniell-Lee et al. 2009;Balaresque et al. 2010;Batini et al. 2011) or historic time scale (Bosch et al. 2003;Adams et al. 2008), or to date specific patrilineal lineages, linked to historic figures or to surnames (Skorecki et al. 1997;Zerjal et al. 2003;Hammer et al. 2009;King and Jobling 2009a;Martinez-Cruz et al. 2012;Martínez-González et al. 2012). ...
... For instance, many urban mestizo populations throughout Latin America are the result of triple admixture from European, African, and Native American ancestries, although the proportions differ by sex. The contributions of Native American women and European men are larger than those of Native American men and European women (Torroni et al. 1994;Bosch et al. 2003;Mendizabal et al. 2008;Corach et al. 2010;Núñez et al. 2010;Guerra et al. 2011); among the first European colonizers of the Americas, men were much more frequent than women. Obviously, that sexual asymmetry stemmed also from the power inequality, manifest also in the fact that European admixture into African Americans is much larger for the NRY than for mtDNA (Stefflova et al. 2009;Lao et al. 2010;Battaggia et al. 2012;Torres et al. 2012). ...
Most of the length of the Y chromosome escapes recombination with the X chromosome and is strictly paternally inherited. This has profound evolutionary implications and provides (together with the matrilineal mitochondrial DNA) unique tools in human population genetics. Absence of recombination implies that a most parsimonious tree can be easily constructed from SNPs and other slowly mutating polymorphisms. The main branches of this tree, called haplogroups, have distinct geographic distributions and can be used to trace human migrations. Faster evolving polymorphisms, such as microsatellites provide readily time estimates for these migrations and other demographic events. Beyond sets of predefined polymorphism, sequencing of most of the non-recombining portion of the Y chromosome has yielded an accurate picture of the global evolution of this chromosome. Combining the Y chromosome with mitochondrial DNA has revealed sex-specific migrations, particularly in the Colonial period. Since surnames are also patrilineally inherited in many populations, the analysis of Y chromosome variation within surnames has shed light on the dynamics of surnames in populations, but has also contributed to the investigation of notorious lineages, such as the Columbus, Bourbons, and Draculs. However, it also raises the possibility of predicting a surname from an anonymous sample, which may be an important tool in forensic genetics but raises also privacy concerns for participants in genetic studies.
... Le génome mitochondrial contient une région non-codante dite de contrôle ou D-loop, au sein de laquelle Vigilant et al. 1991 ;Voskarides et al. 2016). En particulier, plusieurs études rapportent des asymétries entre sexes lors de tels événements (Wilkins 2006) : au Groenland, des chromosomes Y européens ont été retrouvés parmi un fond génétique très largement inuit (Pereira et al. 2015), alors qu'aucun ADN mitochondrial européen n'a été retrouvé (Bosch et al. 2003), ce qui suggère un métissage génétique entre des hommes européens et des femmes inuits locales. Un autre exemple célèbre est celui de la conquête des Amériques par des hommes européens, dont on retrouve les chromosomes Y associés à des ADN mitochondriaux amérindiens, mais à aucun ADN mitochondrial européen (Nuñez et al. 2010 ;Adhikari et al. 2016). ...
... Sex-specific patterns of genetic diversity have already been largely documented in humans, using the male-inherited Y chromosome and the female-inherited mitochondrial DNA (mtDNA) (Jorde et al., 2000), and sex-specific migrations of men and women are thought to be mostly responsible for these patterns. While human migrations are often pictured as being male-biased at a large geographical scale (Stoneking, 1998), notably during events of settlement (Bosch et al., 2003;Moreno-Estrada et al., 2013;Nuñez et al., 2010), such cases remain marginal and only a few have been demonstrated. On the contrary, most observations support a higher migration of women at a fine geographical scale (Lippold et al., 2014;Seielstad, Minch, & Cavalli-Sforza, 1998;Wilkins, 2006). ...
Ma thèse s’intéresse à l’influence des comportements culturels sur la diversité génétique neutre des populations humaines, en particulier les populations d’Asie intérieure. Notamment, ces travaux explorent comment certains comportements affectent l’histoire démographique des populations, en agissant sur l’intensité des migrations et de la dérive génétique. Pour ce faire, j’ai étudié des données génétiques, au regard de données ethnologiques, collectées dans des populations habitant actuellement en Asie intérieure, qui diffèrent, entre autres, par leur organisation sociale. La première partie de cette thèse cherche à retracer l’histoire du peuplement de l’Asie intérieure, de l’âge du Bronze jusqu’à nos jours à partir données génomiques d’ADN moderne et ancien. Les résultats montrent que les populations actuelles forment deux groupes génétiques distincts correspondant à deux groupes linguistiques (Turco-Mongol et Indo-Iranien) et reflétant des composantes ancestrales contrastées. En étudiant la diversité génétique de marqueurs uniparentaux, j’ai montré des différences génétiques sexe-spécifiques telles qu’une différenciation des populations réduite pour l’ADN mitochondrial par rapport à celle du chromosome Y. Cette homogénéité génétique des populations pourrait être causée par de la patrilocalité, une règle de résidence commune à toutes les populations étudiées et entrainant principalement des migrations féminines entre populations. D’autre part, j’ai observé des différences de diversité génétique entre les groupes d’Asie intérieure pour le chromosome Y, que j’ai interprété à la lumière des différences de règles de filiation suivies par ces deux groupes : l’un des groupes est patrilinéaire, c’est-à-dire que la filiation sociale est héritée du père ; l’autre groupe est cognatique, et la transmission est indifférenciée entre les parents. La patrilinéarité conduirait à la formation de noyaux d’hommes apparentés par la lignée masculine dans la population et donc partageant le même chromosome Y, ce qui réduirait la diversité génétique du chromosome Y des populations patrilinéaires, comparées aux cognatiques. La diversité mitochondriale est, par contre, similaire entre patrilinéaires et cognatiques, illustrant le fait que seule la diversité génétique masculine est affectée par la patrilinéarité. Enfin, pour étudier le processus d’ethnogénèse, j’ai calculé l’âge génétique des groupes ethniques patrilinéaires et j’ai montré que cet âge biologique est plus ancien que les âges historiques, suggérant que l’ethnie, du moins chez les Turco-Mongols d’Asie intérieure, est une construction en partie sociale, plutôt qu’une entité entièrement biologique. Dans la troisième partie, je me suis intéressée aux mécanismes d’évitement de la consanguinité, que j’ai estimée au moyen de données génomiques. J’ai notamment testé l’hypothèse selon laquelle des unions exogames, entre conjoints nés dans des villages différents, permettraient de réduire la consanguinité. Malgré une importante variabilité du taux d’exogamie entre populations et entre groupes linguistiques dans notre jeu de données, je n’ai trouvé aucune différence significative de consanguinité. A l’échelle des individus, j’ai pu mettre en évidence le fait que certains descendants de couples exogames sont néanmoins consanguins. Cette situation est particulièrement répandue pour des conjoints nés à moins de 40 km l’un de l’autre, à tel point que leurs descendants sont statistiquement plus consanguins que les descendants de couples endogames. Ces résultats illustrent que, chez l’Homme, des comportements culturels d’alliance peuvent s’opposer aux attendus de la biologie évolutive. Ainsi, mes travaux illustrent plusieurs cas de figure, à des échelles géographiques et temporelles différentes, où des comportements culturels ont modifié et laissé une signature génétique particulière sur la diversité des populations humaines d’Asie intérieure.
... All samples were investigated with Yfiler 1 Plus according to the manufacturer's protocol with modifications in the reaction volume (12.5 ml), the volume of input DNA (0.5 ml) and the number of PCRcycles (25)(26)(27)(28)(29). Prior to electrophoresis, 1 ml of the amplified products and 0.5 ml of GeneScan TM 600 LIZ 1 Size Standard v. 2.0 were added to 9.5 ml of deionized Hi-Di TM formamide and denatured for 3 min at 95 C. The samples were electrophoresed on an Applied Biosystems 1 3500 Â L Genetic Analyzer (Thermo Fisher Scientific, Waltham, MA, USA) according to the recommendations of the manufacturer except for a slight modification of the injection time (12 s). ...
... The male Greenlandic population is a mixture of Inuit and Europeans, mainly Scandinavians [28][29][30]. Approximately 40% of the Greenlandic Y chromosomes are of European origin [14,28]. These Greenlandic Y chromosomes grouped with the Danish Y chromosomes in the Yfiler 1 network. ...
Recently, the Yfiler(®) Plus PCR Amplification Kit (Yfiler(®) Plus, Thermo Fisher Scientific, Waltham, MA, USA) was introduced. Yfiler(®) Plus amplifies 27 Y-chromosomal short tandem repeat loci (Y-STRs) and adds ten new Y-STRs to those analysed with the commonly used AmpFlSTR(®) Yfiler(®) PCR Amplification Kit (Yfiler(®), Thermo Fisher Scientific, Waltham, MA, USA). Seven of the new Y-STRs are rapidly mutating Y-STRs (RM Y-STRs). In this study, 551 male individuals from Denmark, Greenland and Somalia were typed with Yfiler(®) Plus. The results were compared to those obtained with Yfiler(®) in the same individuals. Forensic and population genetic parameters were estimated for Yfiler(®) Plus. Yfiler(®) Plus had a higher power of discrimination than Yfiler(®) in all three populations. Compared to Yfiler(®), Yfiler(®) Plus offers increased power of discrimination, which is obviously an advantage in crime case investigations. However, the inclusion of seven RM Y-STRs in Yfiler(®) Plus makes it less attractive for relationship testing because of the relatively high combined mutation rate, approximately 15%.
Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.
... The post-colonial population might reflect the present Eskimo population better as it is known that there has been significant commingling between Europeans and Inuit [127,128]. We therefore specifically chose the more recent 17th and 18th century for this study. ...
... The modern Greenlandic sample had statistically significant lower absence frequencies than the ancient sample, yet still one in five Greenland adults in our study had an absent frontal sinus extending above the supra-orbital line. Such a reduction in absence frequencies could be a result of modern, post-colonial admixture with Caucasians [127,128]. ...
This is the full summary paper of a thesis to be defended at the University of Copenhagen, May 31st, 2013
... However, the Danish participants were few in number, being only eight of the 72 patients and 19 of the 72 controls [75]. The Greenland Inuit are also highly admixed, with 58% of their paternal ancestry being European [76]. ...
Vitamin D metabolism differs among human populations because our species has adapted to different natural and cultural environments. Two environments are particularly difficult for the production of vitamin D by the skin: the Arctic, where the skin receives little solar UVB over the year; and the Tropics, where the skin is highly melanized and blocks UVB. In both cases, natural selection has favored the survival of those individuals who use vitamin D more efficiently or have some kind of workaround that ensures sufficient uptake of calcium and other essential minerals from food passing through the intestines. Vitamin D scarcity has either cultural or genetic solutions. Cultural solutions include consumption of meat in a raw or boiled state and extended breastfeeding of children. Genetic solutions include higher uptake of calcium from the intestines, higher rate of conversion of vitamin D to its most active form, stronger binding of vitamin D to carrier proteins in the bloodstream, and greater use of alternative metabolic pathways for calcium uptake. Because their bodies use vitamin D more sparingly, indigenous Arctic and Tropical peoples can be misdiagnosed with vitamin D deficiency and wrongly prescribed dietary supplements that may push their vitamin D level over the threshold of toxicity.
... Previous genetic research has not provided support for gene flow between the Norse and Inuit. 2 However, since the 16 th century, thousands of Europeans from various countries either visited or moved to Greenland, and there has been substantial gene flow from Europe into the Greenlandic population. 2,[5][6][7] This European contact with Greenland can be divided into three time periods: pre-colonial; colonial; and post-colonial ( Figure 1). Pre-colonial contact was initially limited to exploration and trade, such as when a search for the Northwest Passage led English explorers to Greenland in the 1500s. ...
The Inuit ancestors of the Greenlandic people arrived in Greenland close to 1,000 years ago.¹
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Since then, Europeans from many different countries have been present in Greenland. Consequently, the present-day Greenlandic population has ∼25% of its genetic ancestry from Europe.²
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Uncovering the genetic history of the present-day Greenlandic population.Am. J. Hum. Genet. 2015; 96: 54-69
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In this study, we investigated to what extent different European countries have contributed to this genetic ancestry. We combined dense SNP chip data from 3,972 Greenlanders and 8,275 Europeans from 14 countries and inferred the ancestry contribution from each of these 14 countries using haplotype-based methods. Due to the rapid increase in population size in Greenland over the past ∼100 years, we hypothesized that earlier European interactions, such as pre-colonial Dutch whalers and early German and Danish-Norwegian missionaries, as well as the later Danish colonists and post-colonial immigrants, all contributed European genetic ancestry. However, we found that the European ancestry is almost entirely Danish and that a substantial fraction is from admixture that took place within the last few generations.
... Within north-western Europe, peninsular Scandinavia (Norway and Sweden) shows the highest frequencies of one MSY lineage, haplogroup (hg) R1a1 (26% in Norway [13], and 12% in Sweden [14]). The finding of the same haplogroup in the North Atlantic islands of Orkney (20% [15]), the Faroes (52% [16]) and Iceland (24% [17]), as well as in Greenland (9% [18]), with their well-evidenced histories of Viking settlement, led to the idea of hg R1a1 as a signature of recent male Scandinavian migration. This gains some support from the finding that the English regions of West Lancashire and the Wirral Peninsula (the north-western part of Cheshire [ Fig. 1a]), settled by Vikings in 902 CE, show significantly elevated proportions of hg R1a1 when samples are ascertained using local medieval surnames to minimise the effect of recent immigration [19]. ...
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.
... Sex-specific processes can create different patterns of genetic diversity at sex-linked loci [12][13][14][15][16] with an extensive literature reporting such patterns in humans (e.g. [17][18][19][20][21][22][23]). Recent work is providing increasingly precise descriptions of the genetic impact of kinship practices [24], as well as the genetic relationships between communities at fine geographical scales [25], while advances in modelling are revealing both the drivers of changes in kinship practices at global scales [26,27] and surprising diversity in the rate and manner of change more locally [28]. ...
Population genetics has been successful at identifying the relationships between human groups and their interconnected histories. However, the link between genetic demography inferred at large scales and the individual human behaviours that ultimately generate that demography is not always clear. While anthropological and historical context are routinely presented as adjuncts in population genetic studies to help describe the past, determining how underlying patterns of human sociocultural behaviour impact genetics still remains challenging. Here, we analyse patterns of genetic variation in village-scale samples from two islands in eastern Indonesia, patrilocal Sumba and a matrilocal region of Timor. Adopting a 'process modelling' approach, we iteratively explore combinations of structurally different models as a thinking tool. We find interconnected socio-genetic interactions involving sex-biased migration, lineage-focused founder effects, and on Sumba, heritable social dominance. Strikingly, founder ideology, a cultural model derived from anthropological and archaeological studies at larger regional scales, has both its origins and impact at the scale of villages. Process modelling lets us explore these complex interactions, first by circumventing the complexity of formal inference when studying large datasets with many interacting parts, and then by explicitly testing complex anthropological hypotheses about sociocultural behaviour from a more familiar population genetic standpoint.
... Looking at the diversity in samples of Greenlandic Inuit shows 58% of the y chromosomes have been assigned to European origin in contrasts with a complete absence of European mitochondrial DNA, it indicates a male-biased European admixture. (Bosch et al. 2003). ...
This book addresses the significant environmental changes experienced by high latitude and high altitude ecosystems at the beginning of the 21st c- tury. Increased temperatures and precipitation, reduction in sea ice and glacier ice, the increased levels of UV-radiation and the long-range tra- ported contaminants in arctic and alpine regions are stress factors that challenge terrestrial and aquatic ecosystems. The large natural variation in the physical parameters of these extreme environments is a key factor in structuring the biodiversity and biotic productivity, and the effect of the new stress factors can be critical for the population structures and the - teraction between species. These changes may also have socio-economic effects if the changes affect the bio-production, which form the basis for the marine and terrestrial food chains. The book is uniquely multidisciplinary and provides examples of va- ous aspects of contemporary environmental change in arctic and alpine - gions. The 21 chapters of the book are organised under the fields of •Climate change and ecosystem response, •Long range transport of poll- ants and ecological impacts, and •UV radiation and biological effects, each also including aspects of the •Socio-economic effects of environmental change. The introductory chapter presents and explains the internal c- nection and integration of all chapters. The added value of these reviews and review-like manuscripts from different disciplines hopefully yields new information about the integrated aspects of environmental change.
... This is often attributed to differential migration of males into a region and subsequent mating with local females excluding local males (assortative mating), leading to an overrepresentation of the Y chromosomes belonging to the incoming males and an overrepresentation of the mitochondrial genome belonging to the local females. Examples of unequal partitioning of genomic components in admixed populations are numerous and include the Icelandic population (Helgason et al., 2000), Greenland Inuit (Bosch et al., 2003), African Americans (Lind et al., 2006), the Mongol expansion (Zerjal et al., 2003), the "colored" population of South Africa (Quintana-Murci et al., 2010), and the European/Polynesian population of Norfolk Island (McEvoy et al., 2010). Using a highly admixed Caribbean population from the island of Puerto Rico, and data from the 1000 Genomes Project (The 1000 Genomes Project 2010), it is shown that in some cases the explanation of assortative mating might be overly simplistic and that other factors could account for some of the perceived indigenous female founder bias when mitochondrial sequences are utilized. ...
A large discrepancy between the Amerindian contribution to the mitochondrial and nuclear genetic components of 55 Puerto Rican (PR) genomes from the 1000 Genomes Project is identified, with Amerindian mitochondrial haplotypes being highly represented (67.3%), in strong contrast to the Amerindian autosomal contribution (12.9%). I examine the potential causes behind this strong mitonuclear discordance. The Amerindian contribution to the X chromosome is 19.8%, implying assortative mating with Amerindian females during the establishment of the PR population. However, this scenario does not account for the extraordinarily high Amerindian mitochondrial contribution. Demographic simulation of simple assortative mating scenarios during establishment of the PR population indicates that the observed Amerindian mitochondrial contribution is higher than expected. The simulations show that expansion from a small founding population does not produce the observed frequencies, instead producing the frequencies expected under neutrality, with the Amerindian mitochondrial frequencies approximately twice the Amerindian autosomal proportion. In addition, multiple replicated simulations show that drift is an unlikely explanation for the elevated Amerindian mi-tochondrial frequency, as these are unable to produce the elevated Amerindian mitochondrial frequency observed in the PR genomic dataset, under a range of different starting conditions. I conclude that the mitonuclear discordance appears most consistent with adaptive mitochondrial benefit; however, the molecular mechanism(s) remain to be characterized before this can be confirmed and warrant further investigation. Lastly, I show potential evidence of selection on autosomes and allosomes, using admixture proportions. Interestingly, the major histocompatibility complex locus on chromosome 6 shows greatly elevated single nucleotide polymorphism density but is unaccompanied by strong admixture variance. The observations on mitonuclear discordance may affect the interpretation of apparent assortative mating in recent human admixture events, which should be treated with caution when relying only on mitochondrial haplotype frequencies.
... mostly responsible for these patterns. While human migrations are often pictured as being male-biased at a large geographical scale (Stoneking, 1998), notably during events of settlement (Bosch et al., 2003;Moreno-Estrada et al., 2013;Nuñez et al., 2010), such cases remain marginal and only a few have been demonstrated. On the contrary, most observations support a higher migration of women at a fine geographical scale (Lippold et al., 2014;Seielstad, Minch, & Cavalli-Sforza, 1998;Wilkins, 2006). ...
Objectives:
Sex-specific genetic structures have been previously documented worldwide in humans, even though causal factors have not always clearly been identified. In this study, we investigated the impact of ethnicity, geography and social organization on the sex-specific genetic structure in Inner Asia. Furthermore, we explored the process of ethnogenesis in multiple ethnic groups.
Methods:
We sampled DNA in Central and Northern Asia from 39 populations of Indo-Iranian and Turkic-Mongolic native speakers. We focused on genetic data of the Y chromosome and mitochondrial DNA. First, we compared the frequencies of haplogroups to South European and East Asian populations. Then, we investigated the genetic differentiation for eight Y-STRs and the HVS1 region, and tested for the effect of geography and ethnicity on such patterns. Finally, we reconstructed the male demographic history, inferred split times and effective population sizes of different ethnic groups.
Results:
Based on the haplogroup data, we observed that the Indo-Iranian- and Turkic-Mongolic-speaking populations have distinct genetic backgrounds. However, each population showed consistent mtDNA and Y chromosome haplogroups patterns. As expected in patrilocal populations, we found that the Y-STRs were more structured than the HVS1. While ethnicity strongly influenced the genetic diversity on the Y chromosome, geography better explained that of the mtDNA. Furthermore, when looking at various ethnic groups, we systematically found a genetic split time older than historical records, suggesting a cultural rather than biological process of ethnogenesis.
Conclusions:
This study highlights that, in Inner Asia, specific cultural behaviors, especially patrilineality and patrilocality, leave a detectable signature on the sex-specific genetic structure.
... Some researchers support genetic admixture between Inuit from Thule and Dorset (Helgason et al., 2006;Olofsson et al., 2015), while others advocate for a single Thule origin (Moltke et al., 2015;Raghavan et al., 2014). The analysis of Y chromosomes in different districts in Greenland revealed heterogeneity suggesting that, in addition to the Thule, other Paleo-Eskimo extinct groups most likely have contributed to the current-day genetic variation of Greenlanders (Bosch et al., 2003;Hallenberg et al., 2009;Helgason et al., 2006;Olofsson et al., 2015). The same hypothesis was advanced by Helgason et al. (2006) based on the study of mtDNA. ...
Objectives:
The Greenlandic population history is characterized by a number of migrations of people of various ethnicities. In this work, the analysis of the complete mtDNA genome aimed to contribute to the ongoing debate on the origin of current Greenlanders and, at the same time, to address the migration patterns in the Greenlandic population from a female inheritance demographic perspective.
Methods:
We investigated the maternal genetic variation in the Greenlandic population by sequencing the whole mtDNA genome in 127 Greenlandic individuals using the Illumina MiSeq(®) platform.
Results:
All Greenlandic individuals belonged to the Inuit mtDNA lineages A2a, A2b1, and D4b1a2a1. No European haplogroup was found.
Discussion:
The mtDNA lineages seem to support the hypothesis that the Inuit in Greenland are descendants from the Thule migration. The results also reinforce the importance of isolation and genetic drift in shaping the genetic diversity in Greenlanders. Based on the mtDNA sequences, the Greenlandic Inuit are phylogenetically close to Siberian groups and Canadian Inuit.
... Some of the individuals used in the training dataset have most likely some European ancestry, but the population profile reflects the current Greenlandic population. Recent estimates suggest that more than 80% of present day Greenlanders have some European admixture [9], and that at least half of the male population has European Y-chromosome lineages [1,10]. The HID SNP genotyper plugin does not currently allow for the inclusion of customized reference populations other than the ones provided by the software. ...
The HID-Ion AmpliSeq Ancestry Panel from Life Techologies includes 123 SNPs from the Seldin panel and 55 SNPs from Kidd panel in a single multiplex assay that helps to determine the continental biogeographic ancestry of individuals. We tested the panel on 104 Greenlanders, divided into a training set of 89 individuals and a test set of 15 individuals. All loci showed genotype distributions consistent with Hardy-Weinberg expectations. Linkage disequilibrium tests indicated that 14 pairs of loci were in association in Greenlanders. Population assignment of the training set to populations included in the HID SNP genotyper plugin placed most individuals in American, Asian, and in a few cases European populations. By including the genotype frequencies of this training set as a possible population of origin, all 15 individuals from the test set were correctly predicted to be Greenlanders using the Seldin SNPs, and nine were classified as Greenlanders using the Kidd SNPs. Population structure analysis indicated that Greenlanders have a genetic profile that is distinguishable from those of populations from America or Asia.
... Saloum de Neves Manta et al. (2013) also identified, in the nuclear DNA analysis, a European component that is absent in the mtDNAs of Santa Isabel Yanomami. The European genetic component could be absent in the mtDNA data because of the highly asymmetrical admixture pattern observed in Native South American populations as a consequence of male European colonization of the continent in the post-Columbian era (Bosch et al., 2003;Schurr, 2004;Toscanini et al., 2011). ...
Objectives:
The aim of this study was to explore the mitochondrial variability in the Yanomami population to reconstruct its demographic history and explore its genetic composition in relation to its cultural and linguistic features.
Methods:
A total of 174 human head hair shafts -collected in 1958- belonging to individuals from a Yanomami group living in Santa Isabel, Brazil, were analyzed. Automated extraction of the hairs was performed, and several methods were applied to optimize the analysis of the degraded DNA. The mtDNA hypervariable segments I-II, along with the 9-bp COII-tRNA(Lys) deletion, were investigated. Using published data from the Yanomami and other Amazonian populations, several statistical analyses were carried out to explore the genetic variability within the study population.
Results:
Ninety eight percent of the mitochondrial DNA (mtDNA) sequences analyzed belonged to Native American haplogroups, while 2% belonged to African haplogroups. Compared with the Yanomami groups previously studied, the Santa Isabel sample seemed more genetically similar to other Amazonian populations.
Conclusions:
Among the Yanomami samples studied to date, the Santa Isabel Yanomami show a higher genetic heterogeneity. This could be due to gene flow with non-Yanomami populations, as well as to the introduction of new mitochondrial haplotypes by gold miners. In both cases, the geographic location of Santa Isabel might have made this Yanomami village less isolated than the others, suggesting that the Rio Negro played a central role in increasing its genetic variability. On the whole, the Yanomami were quite genetically diversified, probably mirroring their great linguistic heterogeneity. Am. J. Hum. Biol., 2016. © 2016 Wiley Periodicals, Inc.
... Although they were unable to permanently settle this region, they left a genetic impact in the Greenland Inuit populations. These populations now exhibit almost entirely indigenous mtDNA lineages (E, F*, R1), but only 40% indigenous Y-chromosome lineages (C, Q), due to Viking/Norse admixture (Bosch et al. 2003;Helgason et al. 2006) (Figure 17). ...
... With regard to Eskimo-Aleut-speaking populations, we are investigating the peopling of the Arctic through our work with the Inuvialuit, who live in the Mackenzie Delta region and adjacent islands in the Arctic Sea. Data from this area is filling a crucial gap in the sampling of Inuit groups across the Arctic Coast, and will help to clarify the timing and process of expansion of one or more Eskimoan groups across the region (Bosch et al. 2003;Dulik et al. 2012a;Gilbert et al. 2008;Helgason et al. 2006;Rasmussen et al. 2010;Saillard et al. 2000;Starikovskaya et al. 1998;Vilar et al. 2014). ...
Based on archeological and genetic data, the Altai-Sayan region appears to be the area from which human populations began expanding eastward toward Beringia some 25,000 years ago, and then much later to the west with the expansion of Turkic- and Mongolic-speaking groups. The initial human expansion into the New World appears to have occurred around 15,000–20,000 BP, with most genetic data supporting a single early expansion into the Americas giving rise to Amerindian populations. The ancestors of Eskimo-Aleut- and Na-Dene-speaking groups entered northern North America around 8,000–10,000 years ago, having become genetically distinctive from Amerindian populations to the south. From a Eurasian perspective, mtDNA and Y-chromosome data indicate that southern Altaians and Native Americans shared a common genetic ancestor some 20,000–25,000 BP. Such data from indigenous Altaians also link them to Japanese and Koreans (possibly Tibetans), tentatively supporting connections among Altaic (Transeurasian) speakers. Within the Altai-Sayan region, northern Altaians show genetic affinities with Yeniseian, Ugric, and Samoyedic speakers to the north, whereas southern Altaians have greater affinities to other Turkic-speaking populations of southern Siberia and Central Asia, revealing complex population dynamics there. Turkic and Mongolic groups show genetic influences from both West and East Eurasia, reflecting the entry of steppe peoples into Central Asia several thousand years ago, while Mongols have strongly genetically influenced southern Altaians and Altaian Kazakhs (Y-chromosome haplogroups C3c and O3e). Overall, this research has yielded important insights into the phylogeography and ancestry of populations from across Eurasia and the Americas.
... This phenomenon has been used in interpreting the clinal pattern of Y-chromosomal variation in Europe (Rosser et al., 2000) and in islands of Southeast Asia (Kayser et al., 2001a). There are also some examples where mass migration of male lineages changed the complete scenario of paternal genepool, for instance, the expansion of Europeans into Americas and Oceania in the last 400 or more years adding European Y-chromosomes with retention of indigenous mtDNA lineages that is seen in Polynesia (Hurles et al., 1998), Greenland (Bosch et al., 2003) and South America (Carvajal-Carmona LG et al., 2000;Carvalho-Silva et al., 2001). Oota et al. (2001) suggested that variation in mtDNA and Y-chromosome are different in matrilocal and patrilocal communities in Thailand. ...
... These analyses also revealed that the patrilineal boundary between southern and northern populations was not pronounced. 种 遗 传 标 记 对 不 同 地 区 人 群 进 行 分 析91011121314151617 。 普 遍 应 用 的 遗 传 标 记 有 ： 线 粒 体 遗 传 标 记 的 分 析 ， 我 们 [7,8] 和 其 他 学 者 ...
... Nearly all of these 117 are shown on this map, except for one individual from the Talas valley in northern Kyrgyzstan and one Indian from Andhra Pradesh. For further explanations, consult Figure 8.3.The Icelandic finding contributes to a growing body of genetic evidence (if any genetic evidence were needed) that tribal confrontation between human males has at its core the reproductive control of women, as seen in Brazil(Alves-Silva et al. 2000), Central America(Torroni et al. 1994), Polynesia(Hurles et al. 1998), Greenland(Bosch et al. 2003) and the Caribbean(BBC 2003). ...
In this context, the term 'marker' needs to be explained. Occasionally, in the course of the millen-nia, mutations may occur in the DNA of an organ-ism, such as a human or a seed of grain, and these mutations are passed down to the descendants. If these descendants remain united by a common char-acteristic such as a language, a certain geographic area, or a resistance against cereal rust, the DNA mutation can be considered a marker for that char-acteristic, even though it does not cause the charac-teristic. The two best-characterized genetic systems for identifying evolutionary markers in humans are the Y chromosome (passed down exclusively from the father to his male children) and mitochondrial DNA (transmitted exclusively from the mother to her chil-dren). Individuals living today differ genetically from each other as a consequence of different mutation events which occurred in their past ancestry, irre-spective of whether these mutation events are inter-esting markers for any characteristic. To date there have been two approaches to analyzing data for the exploration of genetic patterning: the summary method and the lineage approach. The summary method treats the entire data set in terms of a population concept which con-siders all the different genetic types as a single herit-able unit, which is passed down through time. The lineage method looks at the geographic spread and mutational age of specific lineages which in turn reflect movement of prehistoric individuals (for a discussion of the two approaches see Richards et al. 1997; Forster et al. 2001). This contrast in approach is also reflected in the choice of methods for detecting geographic patterns in genetic data. We will com-pare available coarse-grained approaches to detect-ing genetic patterns in Europe with the finer-scaled methods we propose in the main part of this paper. Languages and DNA in Europe The precise geographical origins of English and In-sular Celtic languages on the European continent are obscure, especially so for Celtic languages. In North America, prehistoric language spread can now be traced using state-of-the art genetic markers, for example Na Dene speakers and Eskimo speakers each harbour high frequencies (up to 50 per cent) of distinctive mtDNA types not found elsewhere (Torroni et al. 1993; Saillard et al. 2000). However, the European situation contrasts with that of America: modern languages and human DNA do not appear to correspond particularly closely. Geographic dis-tance tends to be better at predicting how similar the DNA of any two European populations is (Rosser et al. 2000; Zerjal et al. 2001). Nevertheless, it would be overly pessimistic to conclude that in Europe, genetic markers have no hope of shedding light on the prehistory of languages. Genetic markers tracing language migrations may well exist and these markers could then tell us about the routes and, via the molecular clock, the times of such migrations. However, unlike in North America, these markers may represent only a small minority of the gene pool, especially if the spread occurred by élite dominance rather than by pioneer colonization, and the geneticist needs to identify and analyze the markers singly, otherwise their signal may be swamped. In this paper our interest is to investigate the genetic prehistory of Celtic and Germanic speakers in the British Isles. We aim to show that genetic markers tracing the prehistoric origins of Celtic and English speakers living today indeed exist and will be useful to linguists, archaeologists and historians to provide indirect evidence for the origins of the languages themselves.
... Evidence of European paternal gene flow has also been seen in studies of blood group markers and NRY variation in these populations (Bolnick 2004, Huoponen et al. 1997, Kaspirin et al. 1987, Pollitzer et al. 1962). In fact, nearly 60% of Greenlandic Inuit Y chromosomes may have European origins, with these most likely coming from Norse settlers who were assimilated into Inuit groups some 500 years ago (Bosch et al. 2003). Not surprisingly, many rural and urban mestizo groups show differing degrees of female and male genetic contributions from non-native populations, with most European genotypes being introduced by males. ...
▪ Abstract A number of important insights into the peopling of the New World have been gained through molecular genetic studies of Siberian and Native American populations. These data indicate that the initial migration of ancestral Amerindian originated in south-central Siberia and entered the New World between 20,000–14,000 calendar years before present (cal yr BP). These early immigrants probably followed a coastal route into the New World, where they expanded into all continental regions. A second migration that may have come from the same Siberian region entered the Americas somewhat later, possibly using an interior route, and genetically contributed to indigenous populations from North and Central America. In addition, Beringian populations moved into northern North America after the last glacial maximum (LGM) and gave rise to Aleuts, Eskimos, and Na-Dené Indians.
... we observed a marked east-west gradient in stature, with Greenland children taller, Nunavik children intermediate, and Nunavut children shorter relative to the total sample. Greater stature among Greenland children, particularly those living in Nuuk, undoubtedly reflects Danish influence, both through the socioeconomic influence of Danish governance (formally a part of the kingdom of Denmark since 1953, Greenland has had home rule for 30 years) and through genetic admixture [13]. The continuation of the east-west gradient within Canada is interesting, especially given the geographical contiguity of many communities. ...
Aim:
The present study reports findings from a study of preschool-age Inuit children living in the Arctic regions of Canada and Greenland.
Methods:
We compare stature and obesity measures using cutoffs from the Centers for Disease Control and the International Obesity Task Force references. The sample is comprised of 1121 Inuit children (554 boys and 567 girls) aged 3-5 years living in Nunavut (n=376) and Nunavik (n=87), Canada, in the capital city of Nuuk, Greenland (n=86), and in Greenland's remaining towns and villages (n=572).
Results:
Greenland Inuit children were significantly taller than their Canadian counterparts, with greatest height and weight observed among children from Nuuk. Overall prevalence of stunting was low with the three cutoffs yielding similar values for height-for-age z-scores. Obesity prevalence was higher among Canadian Inuit children than their Greenland counterparts.
Conclusions:
Inuit children have stature values consistent with those of the Centers for Disease Control reference and low prevalence of stunting, though geographic variability in mean stature values between Canadian and Greenlandic samples likely reflects differences in both socioeconomic status and genetic admixture. Obesity prevalence is high among both Canadian and Greenland Inuit preschoolers, with children living in the city of Nuuk exhibiting lower obesity prevalence than children living in either Nunavut or Nunavik, Canada or Greenland's towns and villages. Varying obesity prevalence may reflect varying degrees of food security in remote locations as well as the influence of stature and sitting height which have not been well studied in young Inuit children.
... Eighty-eight Y-chromosome binary genetic markers were hierarchically genotyped as AFLP (YAP, [30]), RFLP (M2 [31], SRY 10831.2 [32], M12 [33]; P15 [34]; M74 [35]; M34, M60, M61, M67, M70, M76, M78, M81, M175, M198, M207, M213 [36]; LLY22g, P36.2, P43 [37]; M123, M172 [38]; M242, M253, M285 [23]; V12, V13, V22 [39]; M377 [24]; P128, P287 [40]; M406 [41]; M269 [42]; Page08 [43]; V88 [44]; M458 [45]; PAGE55 [46]; L23, M412 [47]; L91 [48]; M527, M547, Page19, P303, U1 [49]), by DHPLC (M217 [50]; M25, M35, M47, M68, M69, M82, M92, M124, M170, M173, M174, M201, M205, M214, M216 [36]; M429 [51]; P209 [40]; M241, M267, M343 [23]; M357, M378, M410 [24]; M346 [40]; M434, M458 [45]; M530 [46]; L497, P16 [49]), and direct sequencing (M18 [33]; M42, M73, M75, M96 [52]; M33, PN2 [36]; MEH2 [53]; M317 [24]; M356 [54]; M438 [51]; P297 [40]). The nomenclature used for haplogroup labeling is in agreement with the YCC conventions [37] and recent updates [24], [40], [43], [45]–[][47], [49], [51]. ...
Knowledge of high resolution Y-chromosome haplogroup diversification within Iran provides important geographic context regarding the spread and compartmentalization of male lineages in the Middle East and southwestern Asia. At present, the Iranian population is characterized by an extraordinary mix of different ethnic groups speaking a variety of Indo-Iranian, Semitic and Turkic languages. Despite these features, only few studies have investigated the multiethnic components of the Iranian gene pool. In this survey 938 Iranian male DNAs belonging to 15 ethnic groups from 14 Iranian provinces were analyzed for 84 Y-chromosome biallelic markers and 10 STRs. The results show an autochthonous but non-homogeneous ancient background mainly composed by J2a sub-clades with different external contributions. The phylogeography of the main haplogroups allowed identifying post-glacial and Neolithic expansions toward western Eurasia but also recent movements towards the Iranian region from western Eurasia (R1b-L23), Central Asia (Q-M25), Asia Minor (J2a-M92) and southern Mesopotamia (J1-Page08). In spite of the presence of important geographic barriers (Zagros and Alborz mountain ranges, and the Dasht-e Kavir and Dash-e Lut deserts) which may have limited gene flow, AMOVA analysis revealed that language, in addition to geography, has played an important role in shaping the nowadays Iranian gene pool. Overall, this study provides a portrait of the Y-chromosomal variation in Iran, useful for depicting a more comprehensive history of the peoples of this area as well as for reconstructing ancient migration routes. In addition, our results evidence the important role of the Iranian plateau as source and recipient of gene flow between culturally and genetically distinct populations.
... In contrast, the other three major haplogroups found in Greenland (haplogroup I, R1a1 and R1b) are found in high frequencies in the Danish population. This substantiates the notion that almost 50% of the male Greenlanders are of European (Nordic) descent [5] and that the other half may originate from Siberian and North American Inuits. ...
We have developed a PCR-based assay with co-amplification of 25 DNA fragments and detection of 35 Y chromosome SNPs with the SNaPshot technique. The Y SNP package can define 34 Y chromosome haplogroups and it can identify the majority of the Y chromosome haplogroups of interest in the populations relevant to forensic genetics in Denmark. We typed 194 Danes, 215 Greenlanders, and 201 Somalis, all males. A total of 21 different haplogroups were identified. In Danes, 11 haplogroups with frequencies from 0.5% to 38% were identified and three of the haplogroups, I, R1b*(xR1b1, R1b6, R1b8) and R1a1*(xR1a1b), were found in ∼91% of the population. In Greenlanders, 10 haplogroups with frequencies from 0.5% to 50% were identified and the haplogroups P*(xQ3a, R1), R1b*(xR1b1, R1b6, R1b8) and I, were found in ∼86% of the population. In Somalis, 14 haplogroups with frequencies from 0.5% to 79% were identified and the haplogroups E3b1*(xE3b1b) and K*(xN3, O, P) were found in ∼88% of the population. The distribution of haplogroups was compared to the distribution found in 65 males from West Africa.
... Even though the chromosomes bearing M3 are the most frequent clade in Native populations, many research groups have tried to find out whether other haplogroups entered the American continent from Asia. In 1999, Bergen and collaborators described one SNP in the RPS4Y gene that defines what is now known as haplogroup C, present in populations of Asia, AustraloMelanesia and also the Americas, where they are can be found in populations belonging to the three major linguistic stocks, namely Eskimo-Aleuts, Na-Dene and Amerindians (Bergen et al. 1999, Karafet et al. 1999, Capelli et al. 2001, Hammer et al. 2001, Bosch et al. 2003, Malhi et al. 2008). C lineages with one further mutation at M217 belong to the C3b clade, which spread through central and eastern Asia and America. ...
... Unfortunately, high historical rates of male-mediated admixture into Native American communities have complicated the identification of Native American-specific Y chromosomes. One estimate places the degree of paternal admixture at 0.166 6 0.02 [21], indicating that over 16% of the more than 450 Y-chromosomes examined in Greenlandic Inuit samples derive from non-native populations. Analyses of NRY single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs) have identified two major Native American Y-chromosomal haplogroups, Q and C [22][23][24]. ...
... Male-biased dispersal has been documented in connection to matri- locality (Bolnick et al. 2006), which is rare in human societies compared to patrilocality, and immigration seems to be much less regulated in matrilocal compared to patrilocal populations (Hamilton et al. 2005a). MBD tends to be more associated with historical events than with cultural practices, for example the introgression of European Y chromosomes, but not mtDNA, in the Americas post 1492 (Mesa et al. 2000;Seielstad 2000;Bolnick et al. 2006; see Bosch et al. 2003;Al-Zahery et al. 2003 for examples from other regions). ...
Sex-biased dispersal is an almost ubiquitous feature of mammalian life history, but the evolutionary causes behind these patterns still require much clarification. A quarter of a century since the publication of seminal papers describing general patterns of sex-biased dispersal in both mammals and birds, we review the advances in our theoretical understanding of the evolutionary causes of sex-biased dispersal, and those in statistical genetics that enable us to test hypotheses and measure dispersal in natural populations. We use mammalian examples to illustrate patterns and proximate causes of sex-biased dispersal, because by far the most data are available and because they exhibit an enormous diversity in terms of dispersal strategy, mating and social systems. Recent studies using molecular markers have helped to confirm that sex-biased dispersal is widespread among mammals and varies widely in direction and intensity, but there is a great need to bridge the gap between genetic information, observational data and theory. A review of mammalian data indicates that the relationship between direction of sex-bias and mating system is not a simple one. The role of social systems emerges as a key factor in determining intensity and direction of dispersal bias, but there is still need for a theoretical framework that can account for the complex interactions between inbreeding avoidance, kin competition and cooperation to explain the impressive diversity of patterns.
... Therefore, Y-STR typing can be useful in paternal lineage studies and in typing male/female mixtures where the female component is substantially greater [4]. Although some data exist for Arctic region populations, such as the Siberian Eskimos and Canadian and Greenland Inuit populations [5][6][7], there are no data on the forensically relevant Y-STR loci in Native Alaskans. Because of the unique characteristics of the Y chromosome, the objective of this study was to determine genetic variation at 16 Y-STR loci for three of the major Native American Alaska populations. ...
Y chromosome short tandem repeat (Y-STR) loci are important genetic markers for forensic biological evidence analyses. However, paternal inheritance, reduced effective population size, and lack of independence between loci can reduce Y-STR diversity and may yield greater population substructure effects on a locus-by-locus basis compared with the autosomal STR loci. Population studies are necessary to assess the genetic variation of forensically relevant markers so that proper inferences can be made about the rarity of DNA profiles. This study examined 16 Y-STRs in three sampled populations of Native Americans from Alaska: Inupiat, Yupik, and Athabaskan. Population genetic and statistical issues addressed were: (1) the degree of diversity at locus and haplotype levels, (2) determination of the loci that contribute more so to haplotype diversity, and (3) the effects of population substructure on forensic statistical calculations of the rarity of a Y-STR profile. All three population samples were highly polymorphic at the haplotype level for the 16 Y-STR markers; however, the Native Americans demonstrated reduced genetic diversity compared with major US populations. The degree of substructure indicated that the three populations were related and admixed in terms of paternal lineage. The examination of more polymorphic loci may be needed to increase the power of discrimination of Y-STR systems in these populations.
... In both of these treatments male migrants, and the paternal lineages they introduce, are overrepresented in subsequent generations, whereas native Aleut maternal lineages, as measured by mtDNA haplogroups, continue to predominate. This asymmetry in admixture at contact or during historic colonization events is not uncommon (e.g., Batista dos Santos et al. 1999; Bosch et al. 2003; Quintana-Murci, et al. 2010). These migration events are " observed " and can be precisely documented with historical sources. ...
Academic research focusing on the population and culture history of the Aleut (Unangan) people began in the late 19th century and continues to the present. The papers in this special issue of Human Biology summarize the latest results from archaeological, linguistic, genetic, and morphometric research approaches that bear on our current understanding of Unangan history and prehistory. Although these new analyses have provided a level of description and resolution previously unattainable, explanatory models and mechanisms for the patterned variation observed over time in the biological and cultural record of the Aleutian region remains elusive. Bringing the diverse data sets into concordance to represent an integrated synthesis of Aleut population and culture history and of Unangan origins and their relationships with other groups in the region remains a goal for future investigators.
Introduction. The use of ancient nucleic acids to infer population history and phylogeny is now entering its third decade, with the initial demonstration of the possibility and utility of the approach pioneered by Higuchi et al. (1984) on museum specimens of the extinct quagga, and by Pääbo (1985) on preserved soft tissue from Egyptian mummies. Now uniformly termed ancient DNA (aDNA) studies, the approach has exploded in the past decade to encompass studies of modern human origins, regional history and dynamics of prehistoric human populations, as well as phylogenetic studies of nonhuman organisms. A full review of this vast and rapidly growing literature is beyond the scope of this chapter, and interested readers are directed to several excellent and recent reviews of the field from a variety of disciplinary perspectives (e.g. Wayne et al., 1999; O'Rourke et al., 2000a; Hofreiter et al., 2001a; Kaestle and Horsburgh, 2002, Pääbo et al., 2004, Cipollaro et al., 2005). The study of contemporary patterns of human genetic variation has proven a powerful approach to inferring human population history and evolution, although such approaches are bound by assumptions of evolutionary rates in the markers under study, effective population sizes over time, rates of population movement, levels of admixture, etc. The use of aDNA analyses in conjunction with such modern genetic studies affords a temporal perspective on human genetic variation that is, to some degree, independent of model assumptions.
For decades, the peopling of the Americas has been explored through the analysis of uniparentally inherited genetic systems in Native American populations and the comparison of these genetic data with current linguistic groupings. In northern North America, two language families predominate: Eskimo-Aleut and Na-Dene. Although the genetic evidence from nuclear and mtDNA loci suggest that speakers of these language families share a distinct biological origin, this model has not been examined using data from paternally inherited Y chromosomes. To test this hypothesis and elucidate the migration histories of Eskimoan- and Athapaskan-speaking populations, we analyzed Y-chromosomal data from Inuvialuit, Gwich’in, and Tłįchǫ populations living in the Northwest Territories of Canada. Over 100 biallelic markers and 19 chromosome short tandem repeats (STRs) were genotyped to produce a high-resolution dataset of Y chromosomes from these groups. Among these markers is an SNP discovered in the Inuvialuit that differentiates them from other Aboriginal and Native American populations. The data suggest that Canadian Eskimoan- and Athapaskan-speaking populations are genetically distinct from one another and that the formation of these groups was the result of two population expansions that occurred after the initial movement of people into the Americas. In addition, the population history of Athapaskan speakers is complex, with the Tłįchǫ being distinct from other Athapaskan groups. The high-resolution biallelic data also make clear that Y-chromosomal diversity among the first Native Americans was greater than previously recognized.
Escape from recombination makes the Y chromosome a useful tool for studying human genetic history. A unique phylogeny of Y haplogroups has been constructed using binary markers such as SNPs (single nucleotide polymorphisms), and diversity within haplogroups can be analyzed using multiple microsatellites. The time-depth of the phylogeny and geographical distribution of the deepest-rooting haplogroups are compatible with a recent African origin for modern humans. Haplogroup distributions are highly geographically differentiated, which allows past population movements to be studied, and sex-biased admixture to be recognized.Keywords:Y chromosome;haplotype;genetic drift;population;selection;SNP;microsatellite;admixture;patrilocality
Background
Variation in genes involved in alcohol metabolism is associated with drinking patterns worldwide. We compared variation in these genes among the Inuit with published results from the general population of Denmark and, due to the Asian ancestry of the Inuit, with Han Chinese. We analysed the association between gene variations and drinking patterns among the Inuit.
Methods
We genotyped 4,162 Inuit participants from two population health surveys. Information on drinking patterns was available for 3,560. Seven single nucleotide polymorphisms (SNPs) were examined: ADH1B arg48his, ADH1C ile350val, ADH1C arg272gln, ALDH2 glu504lys, ALDH2 5’-UTR A-357G, ALDH1B1 ala86val and ALDH1B1 arg107leu.
Results
The allele distribution differed significantly between Inuit and the general population of Denmark. A protective effect on heavy drinking was found for the TT genotype of the ALDH1B1 arg107leu SNP (OR = 0.59; 95% CI 0.37-0.92), present in 3% of pure Inuit and 37% of Danes. The ADH1C GG genotype was associated with heavy drinking and a positive CAGE test (OR 1.34; 95% CI 1.05-1.72). It was present in 27% of Inuit and 18% of Danes. The Asian genotype pattern with a high frequency of the ADH1B A allele and an ALDH2 gene coding for an inactive enzyme was not present in Greenland.
Conclusions
ADH1C and ALDH1B1 arg107leu SNPs play a role in the shaping of drinking patterns among the Inuit in Greenland. A low frequency of the ALDH1B1 arg107leu TT genotype compared with the general population in Denmark deserves further study. This genotype was protective of heavy drinking among the Inuit.
Different data types have previously been shown to have the same microevolutionary patterns in worldwide data sets. However, peopling of the New World studies have shown a difference in migration paths and timings using multiple types of data, spurring research to understand why this is the case. This study was designed to test the degree of similarity in evolutionary patterns by using cranial and dental metric and nonmetric data, along with Y-chromosome DNA and mtDNA. The populations used included Inuits from Alaska, Canada, Siberia, Greenland, and the Aleutian Islands. For comparability, the populations used for the cranial and molecular data were from similar geographic regions or had a shared population history. Distance, R and kinship matrices were generated for use in running Mantel tests, PROTEST analyses, and Procrustes analyses. A clear patterning was seen, with the craniometric data being most highly correlated to the mtDNA data and the cranial nonmetric data being most highly correlated with the Y-chromosome data, while the phenotypic data were also linked. This patterning is suggestive of a possible male or female inheritance, or the correlated data types are affected by the same or similar evolutionary forces. The results of this study indicate cranial traits have some degree of heritability. Moreover, combining data types leads to a richer knowledge of biological affinity. This understanding is important for bioarchaeological contexts, in particular, peopling of the New World studies where focusing on reconciling the results from comparing multiple data types is necessary to move forward. Am J Phys Anthropol, 2014. © 2014 Wiley Periodicals, Inc.
We used the JC virus genotyping method to investigate the origins of Greenland Inuits. Using polymerase chain reaction, we detected six JC virus isolates in urine samples collected from Inuits in northwestern and southeastern Greenland. Phylogenetic analysis of the complete and partial DNA sequences of these isolates demonstrated that all isolates belonged to the EU-al/Arc cluster previously identified in native northeastern Siberians (e.g. Chukchis and Koryaks) and Canadian Inuits. This finding suggests a close contact or affinity between Greenland Inuits and other circumarctic populations.
Recent research indicates that anthropometrics can be used to study microevolutionary forces acting on humans. We examine the use of morphological traits in reconstructing the population history of Aleuts and Eskimos of the Bering Sea. From 1979 to 1981, W. S. Laughlin measured a sample of St. Lawrence Island Eskimos and Pribilof Island Aleuts. These samples included adult participants from St. George and St. Paul in the Pribilof Islands and from Gambell and Savoonga on St. Lawrence Island. The Relethford-Blangero method was used to examine the phylogenetic relationship between Aleuts and Eskimos. Anthropometric measurements for Native North Americans (measured by Boas and a team of trained anthropometrists in 1890–1904) and Native Mesoamericans (compiled from the literature for 1898–1952) were used for comparison. A principal components analysis of means for measurements and a neighbor-joining tree were constructed using Euclidean distances. All these tests revealed the same strong relationship among the focus populations. The R matrix from the Relethford-Blangero method clusters Aleuts and Eskimos separately and accounts for 97.3% of the variation in the data. Phenotypic variation within the population is minimal and therefore minimum FST values are low. Genetic distances were compared to a Euclidean distance matrix of anthropometric measurements using a Mantel test and gave a high but not significant correlation. Our results provide evidence of a close phylogenetic relationship between Aleut and Eskimo populations in the Bering Sea. However, it is apparent that history has affected the relationship among the populations. Despite previous findings of higher European admixture in Gambell (based on blood group markers) than in Savoonga, Savoonga has greater within-group variation in anthropometric measurements. Anthropometrics reveal a close relationship between Gambell and St. Paul as a result of European admixture. The St. George population was the most divergent of the populations, indicating that it diverged from the Eskimos and St. Paul because of the compounding effects of genetic drift and limited European gene flow. These findings are in agreement with previous anthropometric and genetic studies of the Aleut and Eskimo populations and support the utility of anthropometrics in inferring population history and structure.
Academic research focusing on the population and culture history of the Aleut (Unangan) people began in the late 19th century and continues to the present. The papers in this special issue of Human Biology summarize the latest results from archaeological, linguistic, genetic, and morphometric research approaches that bear on our current understanding of Unangan history and prehistory. Although these new analyses have provided a level of description and resolution previously unattainable, explanatory models and mechanisms for the patterned variation observed over time in the biological and cultural record of the Aleutian region remains elusive. Bringing the diverse data sets into concordance to represent an integrated synthesis of Aleut population and culture history and of Unangan origins and their relationships with other groups in the region remains a goal for future investigators.
The remains of the Greenland Norse provide unique biological anthropological material for the investigation of human and environmental interaction. As a population, they were generally secluded from most of the contemporary European medieval society, and land suitable for their way of life was limited in Greenland. The archaeological and historical record is excellent, clearly establishing the 500-year period of colonisation. In other words, the Greenland Norse represent a relatively isolated population, constrained in both space and time.
Living in an environment with very little buffering capacity, ecological changes immediately had repercussions. Ten years of research have shown a direct climatic impact on the humans as well as changing subsistence patterns. It seems that the Norse in Greenland responded to these changes, although inside ‘cultural’ limits. Demographic modelling indicates that emigration may have accounted for the final abandonment of the settlements. A changing ecology thus seems to have pushed the Greenland Norse out of Greenland, because their sedentary way of life, relying on animal husbandry, and probably with a strong cultural sense of identity focused on farmsteads and domestication, became unsustainable. A further step will be clarifying the genetic history of the Norse as well as of the Thule Culture Inuit. These analyses have commenced by examining mtDNA variation and Y-chromosomal diversity among present-day Greenlandic Inuit, and preliminary results appear to provide some information as to the fate of the Norse people.
Molecular genetic studies of Siberian and Native American populations indicate that ancestral Native Americans originated in south-central Siberia and entered the New World between 20 000 and 15 000 years before present (ybp), after thousands of years of isolation in Beringia. These early immigrants probably followed a coastal route into the New World, where they expanded into all continental regions. A second expansion, possibly coming from the same area of Siberia, may have entered the Americas, and genetically influenced North American populations. Beringian populations moved into northern North America after the Last Glacial Maximum (LGM) and gave rise to Aleuts, Eskimos and Na-Dene Indians.
Keywords:
mtDNA;
Y-chromosome;
Asia;
Siberia;
migrations
For decades, the peopling of the Americas has been explored through the analysis of uniparentally inherited genetic systems in Native American populations and the comparison of these genetic data with current linguistic groupings. In northern North America, two language families predominate: Eskimo-Aleut and Na-Dene. Although the genetic evidence from nuclear and mtDNA loci suggest that speakers of these language families share a distinct biological origin, this model has not been examined using data from paternally inherited Y chromosomes. To test this hypothesis and elucidate the migration histories of Eskimoan- and Athapaskan-speaking populations, we analyzed Y-chromosomal data from Inuvialuit, Gwich'in, and Tłįch populations living in the Northwest Territories of Canada. Over 100 biallelic markers and 19 chromosome short tandem repeats (STRs) were genotyped to produce a high-resolution dataset of Y chromosomes from these groups. Among these markers is an SNP discovered in the Inuvialuit that differentiates them from other Aboriginal and Native American populations. The data suggest that Canadian Eskimoan- and Athapaskan-speaking populations are genetically distinct from one another and that the formation of these groups was the result of two population expansions that occurred after the initial movement of people into the Americas. In addition, the population history of Athapaskan speakers is complex, with the Tłįch being distinct from other Athapaskan groups. The high-resolution biallelic data also make clear that Y-chromosomal diversity among the first Native Americans was greater than previously recognized.
The linguistically distinctive Haida and Tlingit tribes of Southeast Alaska are known for their rich material culture, complex social organization, and elaborate ritual practices. However, much less is known about these tribes from a population genetic perspective. For this reason, we analyzed mtDNA and Y-chromosome variation in Haida and Tlingit populations to elucidate several key issues pertaining to the history of this region. These included the genetic relationships of Haida and Tlingit to other indigenous groups in Alaska and Canada; the relationship between linguistic and genetic data for populations assigned to the Na-Dene linguistic family, specifically, the inclusion of Haida with Athapaskan, Eyak, and Tlingit in the language family; the possible influence of matrilineal clan structure on patterns of genetic variation in Haida and Tlingit populations; and the impact of European entry into the region on the genetic diversity of these indigenous communities. Our analysis indicates that, while sharing a "northern" genetic profile, the Haida and the Tlingit are genetically distinctive from each other. In addition, Tlingit groups themselves differ across their geographic range, in part due to interactions of Tlingit tribes with Athapaskan and Eyak groups to the north. The data also reveal a strong influence of maternal clan identity on mtDNA variation in these groups, as well as the significant influence of non-native males on Y-chromosome diversity. These results yield new details about the histories of the Haida and Tlingit tribes in this region.
A global picture is emerging of sex-specific transmission of language change in quite different regions and continents.
X-chromosome markers have become a useful set of markers of choice when certain complex kinship cases need to be unravelled. The Argus X-12 kit allows the co-amplification in a single PCR reaction of 12 X-chromosome short tandem repeats located in four linkage groups. A number of 507 unrelated individuals from Greenland, Denmark and Somalia together with two generation families were typed using the Argus X-12 kit. Silent alleles for the DXS10148 and DXS10146 systems were observed in males, mostly from Somalia. High levels of intrapopulation variability and therefore high forensic parameter values were calculated for the three studied populations. The population in Greenland showed a significantly lower intrapopulation variability and a high genetic differentiation compared with 13 other populations. Significant levels of linkage disequilibrium were observed between markers belonging to the same linkage group, mainly in the populations in Greenland and Somalia. Family studies allowed the calculation of mutation and recombination frequencies. A higher male versus female mutation rate was obtained, with an average value of 3.3 × 10(-3). Recombination fraction calculations performed on two generation families showed, as previously described, a not complete independence between X-chromosome linkage groups 3 and 4.
Recent research indicates that anthropometrics can be used to study microevolutionary forces acting on humans. We examine the use of morphological traits in reconstructing the population history of Aleuts and Eskimos of the Bering Sea. From 1979 to 1981, W. S. Laughlin measured a sample of St. Lawrence Island Eskimos and Pribilof Island Aleuts. These samples included adult participants from St. George and St. Paul in the Pribilof Islands and from Gambell and Savoonga on St. Lawrence Island. The Relethford-Blangero method was used to examine the phylogenetic relationship between Aleuts and Eskimos. Anthropometric measurements for Native North Americans (measured by Boas and a team of trained anthropometrists in 1890-1904) and Native Mesoamericans (compiled from the literature for 1898-1952) were used for comparison. A principal components analysis of means for measurements and a neighbor-joining tree were constructed using Euclidean distances. All these tests revealed the same strong relationship among the focus populations. The R matrix from the Relethford-Blangero method clusters Aleuts and Eskimos separately and accounts for 97.3% of the variation in the data. Phenotypic variation within the population is minimal and therefore minimum F(ST) values are low. Genetic distances were compared to a Euclidean distance matrix of anthropometric measurements using a Mantel test and gave a high but not significant correlation. Our results provide evidence of a close phylogenetic relationship between Aleut and Eskimo populations in the Bering Sea. However, it is apparent that history has affected the relationship among the populations. Despite previous findings of higher European admixture in Gambell (based on blood group markers) than in Savoonga, Savoonga has greater within-group variation in anthropometric measurements. Anthropometrics reveal a close relationship between Gambell and St. Paul as a result of European admixture. The St. George population was the most divergent of the populations, indicating that it diverged from the Eskimos and St. Paul because of the compounding effects of genetic drift and limited European gene flow. These findings are in agreement with previous anthropometric and genetic studies of the Aleut and Eskimo populations and support the utility of anthropometrics in inferring population history and structure.
Reading the human Y chromosome: the emerging DNA markers and human genetic history.
A polymorphic C-->T transition located on the human Y chromosome was found by the systematic comparative sequencing of Y-specific sequence-tagged sites by denaturing high-performance liquid chromatography. The results of genotyping representative global indigenous populations indicate that the locus is polymorphic exclusively within the Western Hemisphere. The pre-Columbian T allele occurs at > 90% frequency within the native South and Central American populations examined, while its occurrence in North America is approximately 50%. Concomitant genotyping at the polymorphic tetranucleotide microsatellite DYS19 locus revealed that the C-->T mutation displayed significant linkage disequilibrium with the 186-bp allele. The data suggest a single origin of linguistically diverse native Americans with subsequent haplotype differentiation within radiating indigenous populations as well as post-Columbian European and African gene flow. The mutation may have originated either in North America at a very early time during the expansion or before it, in the ancestral population(s) from which all Americans may have originated. The analysis of linkage of the DYS199 and the DYS19 tetranucleotide loci suggests that the C-->T mutation may have occurred around 30,000 years ago. We estimate the nucleotide diversity over 4.2 kb of the nonrecombining portion of the Y chromosome to be 0.00014. compared to autosomes, the majority of variation is due to the smaller effective population size of the Y chromosome rather than selective sweeps. There begins to emerge a pattern of pronounced geographical localization of Y-specific nucleotide substitution polymorphisms.
Recently, a set of highly polymorphic chromosome Y specific microsatellites became available for forensic, population genetic
and evolutionary studies. However, the lack of a mutation frequency estimate for these loci prevents a reliable application.
We therefore used seven chromosome Y tetranucleotide repeat loci to screen 42 males who are descendants from 12 ‘founding
fathers’ by a total number of 213 generations. As a result, we were able to estimate an average chromosome Y tetranucleotide
mutation frequency of 0.20% (95% CIL 0.05–0.55). This closely matches the often cited Weber and Wong estimate of 0.21% for
a set of autosomal tetranucleotide repeats. Expanding the set of microsatellites with two more loci (a tri- and a penta-nucleotide
repeat locus) an average chromosome Y microsatellite mutation frequency of 0.21% (95% CIL 0.06–0.49) was found. These estimates
suggest that microsatellites on the Y chromosome have mutation frequencies comparable to those on the autosomes. This supports
the hypothesis that slippage-generated growth is the driving force behind the microsatellite variability.
According to Jewish tradition, following the Exodus from Egypt, males of the tribe of Levi, of which Moses was a member, were assigned special religious responsibilities, and male descendants of Aaron, his brother, were selected to serve as Priests (Cohanim). To the extent that patrilineal inheritance has been followed since sometime around the Temple period (roughly 3,000-2,000 years before present), Y chromosomes of present-day Cohanim and Levites should not only be distinguishable from those of other Jews, but - given the dispersion of the priesthood following the Temple's destruction - they should derive from a common ancestral type no more recently than the Temple period. Here we show that although Levite Y chromosomes are diverse, Cohen chromosomes are homogeneous. We trace the origin of Cohen chromosomes to about 3,000 years before present, early during the Temple period.
Mitochondrial DNA and the Y chromosome have been used extensively in the study of modern human origins and other phylogenetic questions, but not in the context of their sex-specific modes of transmission. mtDNA is transmitted exclusively by females, whereas the Y chromosome is passed only among males. As a result, differences in the reproductive output or migration rate of males and females will influence the geographic patterns and relative level of genetic diversity on the Y chromosome, autosomes and mtDNA (ref. 1). We have found that Y chromosome variants tend to be more localized geographically than those of mtDNA and the autosomes. The fraction of variation within human populations for Y chromosome single nucleotide polymorphisms (SNPs) is 35.5%, versus 80-85% for the autosomes and mtDNA (refs 6-8). A higher female than male migration rate (via patrilocality, the tendency for a wife to move into her husband's natal household) explains most of this discrepancy, because diverse Y chromosomes would enter a population at a lower rate than mtDNA or the autosomes. Polygyny may also contribute, but the reduction of variation within populations that we measure for the Y chromosome, relative to the autosomes and mitochondrial DNA, is of such magnitude that differences in the effective population sizes of the sexes alone are insufficient to produce the observation.
Polymorphic Y-chromosome-specific microsatellites are becoming increasingly used in evolutionary and forensic studies and, in particular, in dating the origins of Y-chromosomal lineages. Previously, haplotyping of Y chromosomes from males belonging to a set of deep-rooting pedigrees was used to estimate a conservative average Y-chromosomal microsatellite mutation rate of 2.1 x 10(-3)per locus per generation. A number of males showed multiple differences in haplotypes compared with other males within their pedigrees, and these were excluded from the calculation of this estimate, on the grounds that non-paternity was a more probable explanation than multiple mutation within a lineage. Here we reanalyse the pedigrees using an independent highly polymorphic system, the Y-specific minisatellite, MSY1. This supports the hypothesis of non-paternity where more than one microsatellite difference was observed, provides further support for the previously deduced microsatellite mutation rate and throws light on the mutation dynamics of MSY1 itself, suggesting that single-step changes are not the only mode of mutation.
Binary polymorphisms associated with the non-recombining region of the human Y chromosome (NRY) preserve the paternal genetic legacy of our species that has persisted to the present, permitting inference of human evolution, population affinity and demographic history. We used denaturing high-performance liquid chromatography (DHPLC; ref. 2) to identify 160 of the 166 bi-allelic and 1 tri-allelic site that formed a parsimonious genealogy of 116 haplotypes, several of which display distinct population affinities based on the analysis of 1062 globally representative individuals. A minority of contemporary East Africans and Khoisan represent the descendants of the most ancestral patrilineages of anatomically modern humans that left Africa between 35,000 and 89,000 years ago.
Clinal patterns of autosomal genetic diversity within Europe have been interpreted in previous studies in terms of a Neolithic demic diffusion model for the spread of agriculture; in contrast, studies using mtDNA have traced many founding lineages to the Paleolithic and have not shown strongly clinal variation. We have used 11 human Y-chromosomal biallelic polymorphisms, defining 10 haplogroups, to analyze a sample of 3,616 Y chromosomes belonging to 47 European and circum-European populations. Patterns of geographic differentiation are highly nonrandom, and, when they are assessed using spatial autocorrelation analysis, they show significant clines for five of six haplogroups analyzed. Clines for two haplogroups, representing 45% of the chromosomes, are continentwide and consistent with the demic diffusion hypothesis. Clines for three other haplogroups each have different foci and are more regionally restricted and are likely to reflect distinct population movements, including one from north of the Black Sea. Principal-components analysis suggests that populations are related primarily on the basis of geography, rather than on the basis of linguistic affinity. This is confirmed in Mantel tests, which show a strong and highly significant partial correlation between genetics and geography but a low, nonsignificant partial correlation between genetics and language. Genetic-barrier analysis also indicates the primacy of geography in the shaping of patterns of variation. These patterns retain a strong signal of expansion from the Near East but also suggest that the demographic history of Europe has been complex and influenced by other major population movements, as well as by linguistic and geographic heterogeneities and the effects of drift.
We examined 43 biallelic polymorphisms on the nonrecombining portion of the Y chromosome (NRY) in 50 human populations encompassing a total of 2,858 males to study the geographic structure of Y-chromosome variation. Patterns of NRY diversity varied according to geographic region and method/level of comparison. For example, populations from Central Asia had the highest levels of heterozygosity, while African populations exhibited a higher level of mean pairwise differences among haplotypes. At the global level, 36% of the total variance of NRY haplotypes was attributable to differences among populations (i.e., Phi(ST) = 0.36). When a series of AMOVA analyses was performed on different groupings of the 50 populations, high levels of among-groups variance (Phi(CT)) were found between Africans, Native Americans, and a single group containing all 36 remaining populations. The same three population groupings formed distinct clusters in multidimensional scaling plots. A nested cladistic analysis (NCA) demonstrated that both population structure processes (recurrent gene flow restricted by isolation by distance and long-distance dispersals) and population history events (contiguous range expansions and long-distance colonizations) were instrumental in explaining this tripartite division of global NRY diversity. As in our previous analyses of smaller NRY data sets, the NCA detected a global contiguous range expansion out of Africa at the level of the total cladogram. Our new results support a general scenario in which, after an early out-of-Africa range expansion, global-scale patterns of NRY variation were mainly influenced by migrations out of Asia. Two other notable findings of the NCA were (1) Europe as a "receiver" of intercontinental signals primarily from Asia, and (2) the large number of intracontinental signals within Africa. Our AMOVA analyses also supported the hypothesis that patrilocality effects are evident at local and regional scales, rather than at intercontinental and global levels. Finally, our results underscore the importance of subdivision of the human paternal gene pool and imply that caution should be exercised when using models and experimental strategies based on the assumption of panmixia.
When populations are separated for long periods and then brought into contact for a brief episode in part of their range, this can result in genetic admixture. To analyze this type of event we considered a simple model under which two parental populations (P1 and P2) mix and create a hybrid population (H). After that event, the three populations evolve under pure drift without exchange during T generations. We developed a new method, which allows the simultaneous estimation of the time since the admixture event (scaled by the population size t(i) = T/N(i), where N(i) is the effective population size of population i) and the contribution of one of two parental populations (which we call p1). This method takes into account drift since the admixture event, variation caused by sampling, and uncertainty in the estimation of the ancestral allele frequencies. The method is tested on simulated data sets and then applied to a human data set. We find that (i) for single-locus data, point estimates are poor indicators of the real admixture proportions even when there are many alleles; (ii) biallelic loci provide little information about the admixture proportion and the time since admixture, even for very small amounts of drift, but can be powerful when many loci are used; (iii) the precision of the parameters' estimates increases with sample size n = 50 vs. n = 200 but this effect is larger for the t(i)'s than for p1; and (iv) the increase in precision provided by multiple loci is quite large, even when there is substantial drift (we found, for instance, that it is preferable to use five loci than one locus, even when drift is 100 times larger for the five loci). Our analysis of a previously studied human data set illustrates that the joint estimation of drift and p1 can provide additional insights into the data.
Questions about the timing and geographic origins of the migrations that led to the peopling of the Americas have been examined through use of a wide array of approaches. Greenberg et al. (1986) used linguistic, dental, and genetic evidence to propose a tripartite migration model through which the Amerinds (of North, Central, and South America), Na-Dene (of northwestern North America) and Eskimo-Aleuts (of the subarctic) emerged. Studies of maternally inherited mtDNA variation (e.g., Schurr et al. 1990; Torroni et al. 1992, 1993a, 1993b, 1994; Horai et al. 1993; Shields et al. 1993; Forster et al. 1996; Merriwether et al. 1996) have generally supported the tripartite model of Native American origins, although the number of migrations that gave rise to the Amerinds, as well as the Amerinds' interrelationship with the Na-Dene and Eskimo-Aleuts, has been subject to differences in interpretation.
Human paternal population history was studied in 9 populations [three Native American, three Asian, two Caucasian and one African-derived sample(s)] using sequence and short tandem repeat haplotype diversity within the non-pseudoautosegmal region of the Y chromosome. Complete coding and additional flanking sequences (949 base pairs) of the RPS4Y locus were determined in 59 individuals from three of the populations, revealing a nucleotide diversity of 0.0147%, consistent with previous estimates from Y chromosome resequencing studies. One RPS4Y sequence variant, 711C>T, was polymorphic in Asian and Native American populations, but not in African and Caucasian population samples. The RPS4Y 711C>T variant, a second unique sequence variant at DYS287 and nine Y chromosome short tandem repeat (YSTR) loci were used to analyze the evolution of Y chromosome lineages. Three unambiguous lineages were defined in Asian, Native American and Jamaican populations using sequence variants at RPS4Y and DYS287. These lineages were independently supported by the haplotypes defined solely by YSTR alleles, demonstrating the haplotypes constructed from YSTRs can evaluate population diversity, admixture and phylogeny.
Polymorphic Y-chromosome-specific microsatellites are becoming increasingly used in evolutionary and forensic studies and, in particular, in dating the origins of Y-chromosomal lineages. Previously, haplotyping of Y chromosomes from males belonging to a set of deep-rooting pedigrees was used to estimate a conservative average Y-chromosomal microsatellite mutation rate of 2.1 × 10 -3 per locus per generation. A number of males showed multiple differences in haplotypes compared with other males within their pedigrees, and these were excluded from the calculation of this estimate, on the grounds that non-paternity was a more probable explanation than multiple mutation within a lineage. Here we reanalyse the pedigrees using an independent highly polymorphic system, the Y-specific minisatellite, MSY1. This supports the hypothesis of non-paternity where more than one microsatellite difference was observed, provides further support for the previously deduced microsatellite mutation rate and throws light on the mutation dynamics of MSY1 itself, suggesting that single-step changes are not the only mode of mutation.
Recent discoveries of many new genes have made it clear that there is more to the human Y chromosome than a heap of evolutionary debris, hooked up to a sequence that happens to endow its bearer with testes. Coupled with the recent development of new polymorphic markers on the Y, making it the best-characterized haplotypic system in the genome, this gives us new opportunities to assess its role in disease and selection, through association studies with phenotypes such as infertility and cancers. However, the peculiar genetics of this bizarre chromosome means that we should interpret such studies particularly cautiously.
What triggered the collapse of the medieval Norse colony on Greenland? Theories have ranged from a cold climate to warring
Thule hunters, ancestors of the modern Inuit. New studies combine data from ice cores, archaeological digs, and fossil flies to create a picture of desperation and disaster in the
final days of one settlement—and finger climate as well as culture as causes of the settlers' demise.
Oxygen isotope analysis of anew ice core from the crest of the Greenland ice sheet reveals a climatic record of the past 1,420 years. Climatic changes of medium frequencies are in phase with corresponding changes in Iceland and England, whilst long-term changes at mid Atlantic longitudes are out of phase with Europe and North America. Reconciliation with Norse history suggests a strong climatic impact, and a parallel is drawn to the present critical situation of the human society.
Brief accounts of methods for estimating proportions of admixture in populations and individuals of hybrid origin are presented with the objective of appraising their underlying assumptions. In view of the uncertainties introduced by assumptions under which admixture estimates are obtained, it is concluded that the reliability of estimates derived from different methods cannot be formally compared. With examples from several admixed populations, it is shown that all methods do not necessarily give discordant results when identical data are used to obtain admixture estimates.
Even though past experiences using admixed populations to detect selection or to understand disease etiology have not been very successful, it is believed that admixed human populations can be regarded as a natural experiment. Hence, they are suitable for microevolutionary and epidemiological studies.
The proper identification of ancestral populations and the degree of asymmetry in gene flow (sex-biased admixture) are important issues in admixture studies. These aspects can be examined in the statistical properties of allele frequency distributions, but corroboration of particular models should be made from in-depth investigations of historical demography and social structure of admixed populations.
Future studies of admixture with DNA polymorphism data may resolve some of the uncertainties associated with current techniques of detecting genetic polymorphisms. Because of the abundance of genetic data, it is argued that morphological traits are of limited use in resolving current problems of human admixture studies.
Clinal patterns of autosomal genetic diversity within Europe have been interpreted in previous studies in terms of a Neolithic demic diffusion model for the spread of agriculture; in contrast, studies using mtDNA have traced many founding lineages to the Paleolithic and have not shown strongly clinal variation. We have used 11 human Y-chromosomal biallelic polymorphisms, defining 10 haplogroups, to analyze a sample of 3,616 Y chromosomes belonging to 47 European and circum-European populations. Patterns of geographic differentiation are highly nonrandom, and, when they are assessed using spatial autocorrelation analysis, they show significant clines for five of six haplogroups analyzed. Clines for two haplogroups, representing 45% of the chromosomes, are continentwide and consistent with the demic diffusion hypothesis. Clines for three other haplogroups each have different foci and are more regionally restricted and are likely to reflect distinct population movements, including one from north of the Black Sea. Principal-components analysis suggests that populations are related primarily on the basis of geography, rather than on the basis of linguistic affinity. This is confirmed in Mantel tests, which show a strong and highly significant partial correlation between genetics and geography but a low, nonsignificant partial correlation between genetics and language. Genetic-barrier analysis also indicates the primacy of geography in the shaping of patterns of variation. These patterns retain a strong signal of expansion from the Near East but also suggest that the demographic history of Europe has been complex and influenced by other major population movements, as well as by linguistic and geographic heterogeneities and the effects of drift.
Eleven biallelic polymorphisms and seven short-tandem-repeat (STR) loci mapping on the nonrecombining portion of the human Y chromosome have been typed in men from northwestern Africa. Analysis of the biallelic markers, which represent probable unique events in human evolution, allowed us to characterize the stable backgrounds or haplogroups of Y chromosomes that prevail in this geographic region. Variation in the more rapidly mutating genetic markers (STRs) has been used both to estimate the time to the most recent common ancestor for STR variability within these stable backgrounds and to explore whether STR differentiation among haplogroups still retains information about their phylogeny. When analysis of molecular variance was used to study the apportionment of STR variation among both genetic backgrounds (i.e., those defined by haplogroups) and population backgrounds, we found STR variability to be clearly structured by haplogroups. More than 80% of the genetic variance was found among haplogroups, whereas only 3.72% of the genetic variation could be attributed to differences among populations—that is, genetic variability appears to be much more structured by lineage than by population. This was confirmed when two population samples from the Iberian Peninsula were added to the analysis. The deep structure of the genetic variation in old genealogical units (haplogroups) challenges a population-based perspective in the comprehension of human genome diversity. A population may be better understood as an association of lineages from a deep and population-independent gene genealogy, rather than as a complete evolutionary unit.
The Y chromosome contains the largest nonrecombining block in the human genome. By virtue of its many polymorphisms, it is now the most informative haplotyping system, with applications in evolutionary studies, forensics, medical genetics, and genealogical reconstruction. However, the emergence of several unrelated and nonsystematic nomenclatures for Y-chromosomal binary haplogroups is an increasing source of confusion. To resolve this issue, 245 markers were genotyped in a globally representative set of samples, 74 of which were males from the Y Chromosome Consortium cell line repository. A single most parsimonious phylogeny was constructed for the 153 binary haplogroups observed. A simple set of rules was developed to unambiguously label the different clades nested within this tree. This hierarchical nomenclature system supersedes and unifies past nomenclatures and allows the inclusion of additional mutations and haplogroups yet to be discovered.
[Supplementary Table 1, available as an online supplement at www.genome.org , lists all published markers included in this survey and primer information.]
We have used Y-chromosomal polymorphisms to trace paternal lineages in Polynesians by use of samples previously typed for mtDNA variants. A genealogical approach utilizing hierarchical analysis of eight rare-event biallelic polymorphisms, seven microsatellite loci, and internal structural analysis of the hypervariable minisatellite, MSY1, has been used to define three major paternal-lineage clusters in Polynesians. Two of these clusters, both defined by novel MSY1 modular structures and representing 55% of the Polynesians studied, are also found in coastal Papua New Guinea. Reduced Polynesian diversity, relative to that in Melanesians, is illustrated by the presence of several examples of identical MSY1 codes and microsatellite haplotypes within these lineage clusters in Polynesians. The complete lack of Y chromosomes having the M4 base substitution in Polynesians, despite their prevalence (64%) in Melanesians, may also be a result of the multiple bottleneck events during the colonization of this region of the world. The origin of the M4 mutation has been dated by use of two independent methods based on microsatellite-haplotype and minisatellite-code diversity. Because of the wide confidence limits on the mutation rates of these loci, the M4 mutation cannot be conclusively dated relative to the colonization of Polynesia, 3,000 years ago. The other major lineage cluster found in Polynesians, defined by a base substitution at the 92R7 locus, represents 27% of the Polynesians studied and, most probably, originates in Europe. This is the first Y-chromosomal evidence of major European admixture with indigenous Polynesian populations and contrasts sharply with the picture given by mtDNA evidence.
Haplotypes constructed from Y-chromosome markers were used to trace the origins of Native Americans. Our sample consisted of 2,198 males from 60 global populations, including 19 Native American and 15 indigenous North Asian groups. A set of 12 biallelic polymorphisms gave rise to 14 unique Y-chromosome haplotypes that were unevenly distributed among the populations. Combining multiallelic variation at two Y-linked microsatellites (DYS19 and DXYS156Y) with the unique haplotypes results in a total of 95 combination haplotypes. Contra previous findings based on Y- chromosome data, our new results suggest the possibility of more than one Native American paternal founder haplotype. We postulate that, of the nine unique haplotypes found in Native Americans, haplotypes 1C and 1F are the best candidates for major New World founder haplotypes, whereas haplotypes 1B, 1I, and 1U may either be founder haplotypes and/or have arrived in the New World via recent admixture. Two of the other four haplotypes (YAP+ haplotypes 4 and 5) are probably present because of post-Columbian admixture, whereas haplotype 1G may have originated in the New World, and the Old World source of the final New World haplotype (1D) remains unresolved. The contrasting distribution patterns of the two major candidate founder haplotypes in Asia and the New World, as well as the results of a nested cladistic analysis, suggest the possibility of more than one paternal migration from the general region of Lake Baikal to the Americas.
Reconstructing phylogenies from intraspecific data (such as human mitochondrial DNA variation) is often a challenging task because of large sample sizes and small genetic distances between individuals. The resulting multitude of plausible trees is best expressed by a network which displays alternative potential evolutionary paths in the form of cycles. We present a method ("median joining" [MJ]) for constructing networks from recombination-free population data that combines features of Kruskal's algorithm for finding minimum spanning trees by favoring short connections, and Farris's maximum-parsimony (MP) heuristic algorithm, which sequentially adds new vertices called "median vectors", except that our MJ method does not resolve ties. The MJ method is hence closely related to the earlier approach of Foulds, Hendy, and Penny for estimating MP trees but can be adjusted to the level of homoplasy by setting a parameter epsilon. Unlike our earlier reduced median (RM) network method, MJ is applicable to multistate characters (e.g., amino acid sequences). An additional feature is the speed of the implemented algorithm: a sample of 800 worldwide mtDNA hypervariable segment I sequences requires less than 3 h on a Pentium 120 PC. The MJ method is demonstrated on a Tibetan mitochondrial DNA RFLP data set.
Human paternal population history was studied in 9 populations [three Native American, three Asian, two Caucasian and one African-derived sample(s)] using sequence and short tandem repeat haplotype diversity within the non-pseudoautosegmal region of the Y chromosome. Complete coding and additional flanking sequences (949 base pairs) of the RPS4Y locus were determined in 59 individuals from three of the populations, revealing a nucleotide diversity of 0.0147%, consistent with previous estimates from Y chromosome resequencing studies. One RPS4Y sequence variant, 711C > T, was polymorphic in Asian and Native American populations, but not in African and Caucasian population samples. The RPS4Y 711C > T variant, a second unique sequence variant at DYS287 and nine Y chromosome short tandem repeat (YSTR) loci were used to analyze the evolution of Y chromosome lineages. Three unambiguous lineages were defined in Asian, Native American and Jamaican populations using sequence variants at RPS4Y and DYS287. These lineages were independently supported by the haplotypes defined solely by YSTR alleles, demonstrating the haplotypes constructed from YSTRs can evaluate population diversity, admixture and phylogeny.
We have analyzed 247 Brazilian mtDNAs for hypervariable segment (HVS)-I and selected restriction fragment-length-polymorphism sites, to assess their ancestry in different continents. The total sample showed nearly equal amounts of Native American, African, and European matrilineal genetic contribution but with regional differences within Brazil. The mtDNA pool of present-day Brazilians clearly reflects the imprints of the early Portuguese colonization process (involving directional mating), as well as the recent immigrant waves (from Europe) of the last century. The subset of 99 mtDNAs from the southeastern region encompasses nearly all mtDNA haplogroups observed in the total Brazilian sample; for this regional subset, HVS-II was analyzed, providing, in particular, some novel details of the African mtDNA phylogeny.
Recent discoveries of many new genes have made it clear that there is more to the human Y chromosome than a heap of evolutionary debris, hooked up to a sequence that happens to endow its bearer with testes. Coupled with the recent development of new polymorphic markers on the Y, making it the best-characterized haplotypic system in the genome, this gives us new opportunities to assess its role in disease and selection, through association studies with phenotypes such as infertility and cancers. However, the peculiar genetics of this bizarre chromosome means that we should interpret such studies particularly cautiously.
The Eskimo-Aleut language phylum is distributed from coastal Siberia across Alaska and Canada to Greenland and is well distinguished from the neighboring Na Dene languages. Genetically, however, the distinction between Na Dene and Eskimo-Aleut speakers is less clear. In order to improve the genetic characterization of Eskimos in general and Greenlanders in particular, we have sequenced hypervariable segment I (HVS-I) of the mitochondrial DNA (mtDNA) control region and typed relevant RFLP sites in the mtDNA of 82 Eskimos from Greenland. A comparison of our data with published sequences demonstrates major mtDNA types shared between Na Dene and Eskimo, indicating a common Beringian history within the Holocene. We further confirm the presence of an Eskimo-specific mtDNA subgroup characterized by nucleotide position 16265G within mtDNA group A2. This subgroup is found in all Eskimo groups analyzed so far and is estimated to have originated <3,000 years ago. A founder analysis of all Eskimo and Chukchi A2 types indicates that the Siberian and Greenland ancestral mtDNA pools separated around the time when the Neo-Eskimo culture emerged. The Greenland mtDNA types are a subset of the Alaskan mtDNA variation: they lack the groups D2 and D3 found in Siberia and Alaska and are exclusively A2 but at the same time lack the A2 root type. The data are in agreement with the view that the present Greenland Eskimos essentially descend from Alaskan Neo-Eskimos. European mtDNA types are absent in our Eskimo sample.
We present findings based on a study of Y-chromosome diallelic and microsatellite variation in 181 Icelanders, 233 Scandinavians, and 283 Gaels from Ireland and Scotland. All but one of the Icelandic Y chromosomes belong to haplogroup 1 (41.4%), haplogroup 2 (34.2%), or haplogroup 3 (23.8%). We present phylogenetic networks of Icelandic Y-chromosome variation, using haplotypes constructed from seven diallelic markers and eight microsatellite markers, and we propose two new clades. We also report, for the first time, the phylogenetic context of the microsatellite marker DYS385 in Europe. A comparison of haplotypes based on six diallelic loci and five microsatellite loci indicates that some Icelandic haplogroup-1 chromosomes are likely to have a Gaelic origin, whereas for most Icelandic haplogroup-2 and -3 chromosomes, a Scandinavian origin is probable. The data suggest that 20%-25% of Icelandic founding males had Gaelic ancestry, with the remainder having Norse ancestry. The closer relationship with the Scandinavian Y-chromosome pool is supported by the results of analyses of genetic distances and lineage sharing. These findings contrast with results based on mtDNA data, which indicate closer matrilineal links with populations of the British Isles. This supports the model, put forward by some historians, that the majority of females in the Icelandic founding population had Gaelic ancestry, whereas the majority of males had Scandinavian ancestry.
Protocadherins are members of the cadherin superfamily involved in cell-cell interactions critical in the development of the central nervous system. This paper describes the isolation, sequence, and expression analysis of two novel protocadherin genes from the hominid specific Yp11.2/Xq21.3 block of homology between the sex chromosomes. The X-(PCDHX) and Y-linked (PCDHY) genes share 98.1% nucleotide and 98.3% amino acid identity and have an identical gene structure of six exons. The open reading frames of PCDHX and PCDHY encode proteins of 1025 and 1037 amino acids respectively and specify seven extracellular cadherin domains. Small differences in amino acid sequence affect regions that potentially have a large impact on function: thus, the X and Y genes may be differentiated in this respect. Sequence analysis of cDNA clones shows that both the X and Y loci are transcribed. RT-PCR expression analysis of mRNA from a variety of tissues and cell lines has demonstrated that both transcripts are expressed predominantly in the brain, with differential regional expression. From studies in the NTERA pluripotential cell line (which differentiates along neuronal and spermatogenic pathways in response to retinoic acid), it emerges that the X and Y-linked genes are regulated differently. This indicates that PCDHX and PCDHY possess different promoter regions. These findings suggest a role for PCDHX and PCDHY in the brain, consistent with the involvement of protocadherins in segmental brain morphogenesis and function. The implications of Y-linked genes expressed predominantly in tissues and organs other than the testis are considered within the context of the concept of sexual selection.
Historical and genetic evidences suggest that the recently founded population of Antioquia (Colombia) is potentially useful for the genetic mapping of complex traits. This population was established in the 16th-17th centuries through the admixture of Amerinds, Europeans, and Africans and grew in relative isolation until the late 19th century. To examine the origin of the founders of Antioquia, we typed 11 markers on the nonrecombining portion of the Y chromosome and four markers on mtDNA in a sample of individuals with confirmed Antioquian ancestry. The polymorphisms on the Y chromosome (five biallelic markers and six microsatellites) allow an approximation to the origin of founder men, and those on mtDNA identify the four major founder Native American lineages. These data indicate that approximately 94% of the Y chromosomes are European, 5% are African, and 1% are Amerind. Y-chromosome data are consistent with an origin of founders predominantly in southern Spain but also suggest that a fraction came from northern Iberia and that some possibly had a Sephardic origin. In stark contrast with the Y-chromosome, approximately 90% of the mtDNA gene pool of Antioquia is Amerind, with the frequency of the four Amerind founder lineages being closest to Native Americans currently living in the area. These results indicate a highly asymmetric pattern of mating in early Antioquia, involving mostly immigrant men and local native women. The discordance of our data with blood-group estimates of admixture suggests that the number of founder men was larger than that of women.
We examined DNA polymorphisms in the nonrecombining portion of the Y-chromosome to investigate the contribution of distinct patrilineages to the present-day white Brazilian population. Twelve unique-event polymorphisms were typed in 200 unrelated males from four geographical regions of Brazil and in 93 Portuguese males. In our Brazilian sample, the vast majority of Y-chromosomes proved to be of European origin. Indeed, there were no significant differences when the haplogroup frequencies in Brazil and Portugal were compared by means of an exact test of population differentiation. Y-chromosome typing was quite sensitive in the detection of regional immigration events. Distinct footprints of Italian immigration to southern Brazil, migration of Moroccan Jews to the Amazon region, and possible relics of the 17th-century Dutch invasion of northeast Brazil could be seen in the data. In sharp contrast with our mtDNA data in white Brazilians, which showed that > or =60% of the matrilineages were Amerindian or African, only 2.5% of the Y-chromosome lineages were from sub-Saharan Africa, and none were Amerindian. Together, these results configure a picture of strong directional mating between European males and Amerindian and African females, which agrees with the known history of the peopling of Brazil since 1500.
Y-chromosome DNA profiles are promising tools in population genetics and forensic science. Here we present DNA profiles of 300 unrelated Y-chromosomes of Norwegian origin. The profile is composed of eight short tandem repeats (STRs) and one single nucleotide polymorphism (SNP). In more than 2/3 of the haplotypes the modular structure in the 5' end of the minisatellite locus DYF155S1 was revealed by minisatellite variant repeat PCR (MVR-PCR) These haplotypes were also typed for deletions of fragment 50f2C (DYF155S2). Allele distribution and paternity exclusion parameters are given for each marker. The degree of haplotype diversity and its implication for statistics are evaluated. In the 300 samples 177 different haplotypes were encountered, of which 137 were observed once only. Analysis showed that the main source of variation is within the population. The Fst values were less than 0.015 in general. Haplotype grouping by the SNP demonstrated two haplogroups (Tat/T and Tat/C). Haplogroup Tat/C--found in 5.7% of the present material - is the same haplogroup as encountered in 60% of Finnish males [Am. J. Hum. Genet. 62 (1998) 1171]. Mutation analysis in 150 father/son pairs (a total of 1200 meiotic events) revealed an average mutation frequency of 0.0042 (95% CI 0.0014-0.0097).
The genetic variance at seven Y-chromosomal microsatellite loci (or short tandem repeats [STRs]) was studied among 986 male individuals from 20 globally dispersed human populations. A total of 598 different haplotypes were observed, of which 437 (73.1%) were each found in a single male only. Population-specific haplotype-diversity values were.86-.99. Analyses of haplotype diversity and population-specific haplotypes revealed marked population-structure differences between more-isolated indigenous populations (e.g., Central African Pygmies or Greenland Inuit) and more-admixed populations (e.g., Europeans or Surinamese). Furthermore, male individuals from isolated indigenous populations shared haplotypes mainly with male individuals from their own population. By analysis of molecular variance, we found that 76.8% of the total genetic variance present among these male individuals could be attributed to genetic differences between male individuals who were members of the same population. Haplotype sharing between populations, phi(ST) statistics, and phylogenetic analysis identified close genetic affinities among European populations and among New Guinean populations. Our data illustrate that Y-chromosomal STR haplotypes are an ideal tool for the study of the genetic affinities between groups of male subjects and for detection of population structure.
The reference database of highly informative Y-chromosomal short tandem repeat (STR) haplotypes (YHRD), available online at http://ystr.charite.de, represents the largest collection of male-specific genetic profiles currently available for European populations. By September 2000, YHRD contained 4688 9-locus (so-called "minimal") haplotypes, 40% of which have been extended further to include two additional loci. Establishment of YHRD has been facilitated by the joint efforts of 31 forensic and anthropological institutions. All contributing laboratories have agreed to standardize their Y-STR haplotyping protocols and to participate in a quality assurance exercise prior to the inclusion of any data. In view of its collaborative character, and in order to put YHRD to its intended use, viz. the support of forensic caseworkers in their routine decision-making process, the database has been made publicly available via the Internet in February 2000. Online searches for complete or partial Y-STR haplotypes from evidentiary or non-probative material can be performed on a non-commercial basis, and yield observed haplotype counts as well as extrapolated population frequency estimates. In addition, the YHRD website provides information about the quality control test, genotyping protocols, haplotype formats and informativity, population genetic analysis, literature references, and a list of contact addresses of the contributing laboratories.