mtDNA and the origin of the Icelanders: deciphering signals of recent population history

Previous attempts to investigate the origin of the Icelanders have provided estimates of ancestry ranging from a 98% British Isles contribution to an 86% Scandinavian contribution. We generated mitochondrial sequence data for 401 Icelandic individuals and compared these data with >2,500 other European sequences from published sources, to determine the probable origins of women who contributed to Iceland’s settlement. Although the mean number of base-pair differences is high in the Icelandic sequences and they are widely distributed in the overall European mtDNA phylogeny, we find a smaller number of distinct mitochondrial lineages, compared with most other European populations. The frequencies of a number of mtDNA lineages in the Icelanders deviate noticeably from those in neighboring populations, suggesting that founder effects and genetic drift may have had a considerable influence on the Icelandic gene pool. This is in accordance with available demographic evidence about Icelandic population history. A comparison with published mtDNA lineages from European populations indicates that, whereas most founding females probably originated from Scandinavia and the British Isles, lesser contributions from other populations may also have taken place. We present a highly resolved phylogenetic network for the Icelandic data, identifying a number of previously unreported mtDNA lineage clusters and providing a detailed depiction of the evolutionary relationships between European mtDNA clusters. Our findings indicate that European populations contain a large number of closely related mitochondrial lineages, many of which have not yet been sampled in the current comparative data set. Consequently, substantial increases in sample sizes that use mtDNA data will be needed to obtain valid estimates of the diverse ancestral mixtures that ultimately gave rise to contemporary populations.     

DNA diversity and population admixture in Anatolia

The Turkic language was introduced in Anatolia at the start of this millennium, by nomadic Turkmen groups from Central Asia. Whether that cultural transition also had significant population-genetics consequences is not fully understood. Three nuclear microsatellite loci, the hypervariable region I of the mitochondrial genome, six microsatellite loci of the Y chromosome, and one Alu insertion (YAP) were amplified and typed in 118 individuals from four populations of Anatolia. For each locus, the number of chromosomes considered varied between 51-200. Genetic variation was large within samples, and much less so between them. The contribution of Central Asian genes to the current Anatolian gene pool was quantified using three different methods, considering for comparison populations of Mediterranean Europe, and Turkic-speaking populations of Central Asia. The most reliable estimates suggest roughly 30% Central Asian admixture for both mitochondrial and Y-chromosome loci. That (admittedly approximate) figure is compatible both with a substantial immigration accompanying the arrival of the Turkmen armies (which is not historically documented), and with continuous gene flow from Asia into Anatolia, at a rate of 1% for 40 generations. Because a military invasion is expected to more deeply affect the male gene pool, similar estimates of admixture for female- and male-transmitted traits are easier to reconcile with continuous migratory contacts between Anatolia and its Asian neighbors, perhaps facilitated by the disappearance of a linguistic barrier between them.     

Origins and evolution of the Europeans' genome: evidence from multiple microsatellite loci

There is general agreement that the current European gene pool is mainly derived from Palaeolithic hunting-gathering and Neolithic farming ancestors, but different studies disagree on the relative weight of these contributions. We estimated admixture rates in European populations from data on 377 autosomal microsatellite loci in 235 individuals, using five different numerical methods. On average, the Near Eastern (and presumably Neolithic) contribution was between 46 and 66%, and admixture estimates showed, with all methods, a strong and significant negative correlation with distance from the Near East. If the assumptions of the model are approximately correct, i.e. if the Basques' and Near Easterners' genomes represent a good approximation to the Palaeolithic and Neolithic settlers of Europe, respectively, these results imply that half or more of the Europeans' genes are descended from Near Eastern ancestors who immigrated in Europe 10000 years ago. If these assumptions are incorrect, our results show anyway that clinal variation is the rule in the Europeans' genomes and that lower estimates of Near Eastern admixture obtained from the analysis of single markers do not reflect the patterns observed at the genomic level.     

The Y chromosome pool of Jews as part of the genetic landscape of the Middle East

A sample of 526 Y chromosomes representing six Middle Eastern populations (Ashkenazi, Sephardic, and Kurdish Jews from Israel; Muslim Kurds; Muslim Arabs from Israel and the Palestinian Authority Area; and Bedouin from the Negev) was analyzed for 13 binary polymorphisms and six microsatellite loci. The investigation of the genetic relationship among three Jewish communities revealed that Kurdish and Sephardic Jews were indistinguishable from one another, whereas both differed slightly, yet significantly, from Ashkenazi Jews. The differences among Ashkenazim may be a result of low-level gene flow from European populations and/or genetic drift during isolation. Admixture between Kurdish Jews and their former Muslim host population in Kurdistan appeared to be negligible. In comparison with data available from other relevant populations in the region, Jews were found to be more closely related to groups in the north of the Fertile Crescent (Kurds, Turks, and Armenians) than to their Arab neighbors. The two haplogroups Eu 9 and Eu 10 constitute a major part of the Y chromosome pool in the analyzed sample. Our data suggest that Eu 9 originated in the northern part, and Eu 10 in the southern part of the Fertile Crescent. Genetic dating yielded estimates of the expansion of both haplogroups that cover the Neolithic period in the region. Palestinian Arabs and Bedouin differed from the other Middle Eastern populations studied here, mainly in specific high-frequency Eu 10 haplotypes not found in the non-Arab groups. These chromosomes might have been introduced through migrations from the Arabian Peninsula during the last two millennia. The present study contributes to the elucidation of the complex demographic history that shaped the present-day genetic landscape in the region.     

Evaluation of Group Genetic Ancestry of Populations from Philadelphia and Dakar in the Context of Sex-Biased Admixture in the Americas

Background

Population history can be reflected in group genetic ancestry, where genomic variation captured by the mitochondrial DNA (mtDNA) and non-recombining portion of the Y chromosome (NRY) can separate female- and male-specific admixture processes. Genetic ancestry may influence genetic association studies due to differences in individual admixture within recently admixed populations like African Americans.

Principal Findings

We evaluated the genetic ancestry of Senegalese as well as European Americans and African Americans from Philadelphia. Senegalese mtDNA consisted of ∼12% U haplotypes (U6 and U5b1b haplotypes, common in North Africa) while the NRY haplotypes belonged solely to haplogroup E. In Philadelphia, we observed varying degrees of admixture. While African Americans have 9–10% mtDNAs and ∼31% NRYs of European origin, these results are not mirrored in the mtDNA/NRY pools of European Americans: they have less than 7% mtDNAs and less than 2% NRYs from non-European sources. Additionally, there is <2% Native American contribution to Philadelphian African American ancestry and the admixture from combined mtDNA/NRY estimates is consistent with the admixture derived from autosomal genetic data. To further dissect these estimates, we have analyzed our samples in the context of different demographic groups in the Americas.

Conclusions

We found that sex-biased admixture in African-derived populations is present throughout the Americas, with continual influence of European males, while Native American females contribute mainly to populations of the Caribbean and South America. The high non-European female contribution to the pool of European-derived populations is consistently characteristic of Iberian colonization. These data suggest that genomic data correlate well with historical records of colonization in the Americas.     

Estimating the impact of prehistoric admixture on the genome of Europeans

We inferred past admixture processes in the European population from genetic diversity at eight loci, including autosomal, mitochondrial and Y-linked polymorphisms. Admixture coefficients were estimated from multilocus data, assuming that most current populations can be regarded as the result of a hybridization process among four or less potential parental populations. Two main components are apparent in the Europeans' genome, presumably corresponding to the contributions of the first, Paleolithic Europeans, and of the early, Neolithic farmers dispersing from the Near East. In addition, only a small fraction of the European alleles seems to come from North Africa, and a fourth component reflecting gene flow from Northern Asia is largely restricted to the northeast of the continent. The estimated Near Eastern contribution decreases as one moves from east to west, in agreement with the predictions of a model in which (Neolithic) immigrants from the Near East contributed a large share of the alleles in the genome of current Europeans. Several tests suggest that probable departures from the admixture models, due to factors such as choice of the putative parental populations and more complex demographic scenarios, may have affected our main estimates only to a limited extent.     

Genetic structure of the paternal lineage of the Roma people

According to written sources, Roma (Romanies, Gypsies) arrived in the Balkans around 1,000 years ago from India and have subsequently spread through several parts of Europe. Genetic data, particularly from the Y chromosome, have supported this model, and can potentially refine it. We now provide an analysis of Y-chromosomal markers from five Roma and two non-Roma populations (N = 787) in order to investigate the genetic relatedness of the Roma population groups to one another, and to gain further understanding of their likely Indian origins, the genetic contribution of non-Roma males to the Roma populations, and the early history of their splits and migrations in Europe. The two main sources of the Roma paternal gene pool were identified as South Asian and European. The reduced diversity and expansion of H1a-M82 lineages in all Roma groups imply shared descent from a single paternal ancestor in the Indian subcontinent. The Roma paternal gene pool also contains a specific subset of E1b1b1a-M78 and J2a2-M67 lineages, implying admixture during early settlement in the Balkans and the subsequent influx into the Carpathian Basin. Additional admixture, evident in the low and moderate frequencies of typical European haplogroups I1-M253, I2a-P37.2, I2b-M223, R1b1-P25, and R1a1-M198, has occurred in a more population-specific manner.     

Skin colorimetry and admixture measurement: Some further considerations

Several techniques for using skin colorimetric data to measure admixture contributions to a hybrid population have been reviewed by Lees and Relethford ('78), who find this general approach to be useful. This paper extends their evaluation, providing a method for obtaining an error term and considering at greater length certain potential sources of estimate bias. Questions are raised about their discussion of the appropriate employment of distance statistics in this context, and an alternative procedure for obtaining a single estimate of admixture proportions jointly over all reflectance measurements is offered. While it is shown that the hybrid reflectance curves do not support entirely an assumption of unlinked loci contributing equally and additively to skin color, preliminary findings indicate that admixture estimates made from these data are apparently unbiased and reasonably efficient.     

Analysis of the region V mitochondrial marker in two Black communities of Ecuador,and in their parental populations

Data on the frequency of the mtDNA region V deletion were used to estimate the relative maternal contribution from the parental populations to the gene pools of the two Black communities of Rio Cayapas and Viche in northern Ecuador. Ethnohistorical records and nuclear DNA data indicate that these populations are hybrids of West African and Amerindian populations. The unique distribution of the DNA marker in these parental groups provided good admixture estimates. The fraction of mtDNA of Amerindian origin in the population of Rio Cayapas is quite small (8%±5%), whereas in the community of Viche the native Americans contributed the major portion of the gene pool (51%±15). The mtDNA estimate for Rio Cayapas is similar to that of some protein polymorphisms, which confirms the cultural and genetic isolation of this community from the neighboring native population. On the other hand, the admixture value obtained from nuclear genes in Viche is statistically different from the estimate obtained from mtDNA data. This supports the traditional belief, gathered from historical records and cultural data, that the contribution from Indian females was higher than that of Indian males, at least in the primary settlements of the African-American population of Esmeraldas.     

The Gm and Inv allotypes of some Ashkenazic Jews living in Northern U.S.A

Determination of the Gm haplotypes among the serum samples of 249 Ashkenazic Jews living in northern U.S.A. has confirmed the presence of Black African admixture and has established the presence of San (Bushman) admixture. A rough estimate indicates that the haplotypes from these sources contribute about 2% of the genome of the people sampled. The Inv allele frequency is very low (0.037 ± 0.009). This has been found in other Jewish populations and may be characteristic of Jews.     

Estimating European admixture in African Americans by using microsatellites and a microsatellite haplotype (CD4/Alu)

We have analyzed 10 unlinked microsatellites and a linked Alu deletion polymorphism at the CD4 locus in an African American population sample from Chicago (USA). Heterozygosity estimates at the microsatellite loci range from 0.727±0.025 (D3S1358) to 0.873±0.017 (D18S51), with an average of 0.794±0.016. These values are comparable to or higher than those reported for Europeans, with only one exception (D3S1358). The CD4/Alu haplotypic diversity (0.887±0.012) is comparable to diversity levels observed in sub-Saharan African populations and is higher than the diversity levels reported in European populations. No consistent pattern of within, between, or multi-locus deviations from Hardy-Weinberg expectations is observed, suggesting a low sub-heterogeneity within the sampled population. We have applied a maximum likelihood method and estimated the proportion of European admixture to the African American gene pool to be 0.26±0.02. The narrow confidence interval indicates that allele frequency data from multiple microsatellite loci, whether analyzed independently or as haplotypes, are particularly useful for estimating genetic admixture. Received: 9 September 1998 / Accepted: 3 November 1998     

Intraspecific Genetic Admixture and the Morphological Diversification of an Estuarine Fish Population Complex

The North-east American Rainbow smelt (Osmerus mordax) is composed of two glacial races first identified through the spatial distribution of two distinct mtDNA lineages. Contemporary breeding populations of smelt in the St. Lawrence estuary comprise contrasting mixtures of both lineages, suggesting that the two races came into secondary contact in this estuary. The overall objective of this study was to assess the role of intraspecific genetic admixture in the morphological diversification of the estuarine rainbow smelt population complex. The morphology of mixed-ancestry populations varied as a function of the relative contribution of the two races to estuarine populations, supporting the hypothesis of genetic admixture. Populations comprising both ancestral mtDNA races did not exhibit intermediate morphologies relative to pure populations but rather exhibited many traits that exceeded the parental trait values, consistent with the hypothesis of transgressive segregation. Evidence for genetic admixture at the level of the nuclear gene pool, however, provided only partial support for this hypothesis. Variation at nuclear AFLP markers revealed clear evidence of the two corresponding mtDNA glacial races. The admixture of the two races at the nuclear level is only pronounced in mixed-ancestry populations dominated by one of the mtDNA lineages, the same populations showing the greatest degree of morphological diversification and population structure. In contrast, mixed-ancestry populations dominated by the alternate mtDNA lineage showed little evidence of introgression of the nuclear genome, little morphological diversification and little contemporary population genetic structure. These results only partially support the hypothesis of transgressive segregation and may be the result of the differential effects of natural selection acting on admixed genomes from different sources.     

Demographic and genetic structures of two partially isolated communities of Santa Catarina Island,southern Brazil

The objectives of this study were to analyze the population structure and genetic variability of two communities, Costa da Lagoa (CLG) and S?o Jo?o do Rio Vermelho (SJRV), located on Santa Catarina Island in southern Brazil. The two populations descend from Azores Archipelago immigrants (Portuguese), with a minor contribution of sub-Saharan Africans and Amerindians. To estimate the relative contribution of the different ethnic groups to the current gene pool of the two communities, values of admixture were obtained using the weighted least-squares method based on allelic frequencies of the loci ABO, RHD-RHCE, GPA-GPB (MNSs), HBB, HP, TF, CP, AK, and ACP1. The origins of the studied populations can be quantified as follows: for CLG, sub-Saharan Africans (A) = 17.3%, Iberian Europeans (P) = 75.0%, and Southern Amerindians (I) = 7.7%; for SJRV, A = 48.8%, P = 44.5%, and I = 6.7%. Because haplotype frequencies of the GPA-GPB loci in SJRV were unusual, possibly as a consequence of random genetic drift, the values of admixture were recalculated after exclusion of GPA-GPB, as follows: A = 28.0%; P = 53.3%, and I = 18.7%. The total diversity (HT) was estimated as 42.29%, of which 99.6% can be attributed to the intrapopulational variability (HS). The interpopulational genetic variation (or standard distance, DST) corresponds to 0.19%, while the gene differentiation coefficient is 0.28%, indicative of low genetic difference. These results led to the conclusion that random genetic drift may have had an important effect on the Costa da Lagoa community, while presently gene flow might be the predominant evolutionary factor potentially capable of changing allele frequencies in SJRV.     

Gm and Inv [Km] allotypes among Libyan and Ashkenazi Jews,and Armenians living in Israel

Summary Serum samples from Armenians, and from Libyan and Ashkenazi Jews living in Israel were tested for Gm (1, 2, 3, 5, 6, 10, 11, 13, 14, 17, 21, 24, 26) and for Inv(1) [Km(1)].The Gm data indicate that all three populations have Negroid and Mongoloid admixture. The minimum amount of admixture varies from 3.1% (Armenians) to 5.5% (Libyan Jews). This admixture had not been detected by the study of other polymorphisms, thus once again underlining the sensitivity of the Gm system. The haplotype frequencies among the Libyan Jews are markedly different from those among the Ashkenazi Jews. Surprisingly (coincidentally?) the haplotype frequencies among the Ashkenazi Jews and the Armenians are similar.The Libyan Jews have a significantly higher frequency of Inv ¹ than do the Ashkenazi Jews and among the latter, Inv ¹ is at least twice as frequent among Polish Jews as it is among Russian Jews.     

The impact of founder effects, gene flow, and European admixture on native American genetic diversity

Recent studies have concluded that the global pattern of neutral genetic diversity in humans reflects a series of founder effects and population movements associated with our recent expansion out of Africa. In contrast, regional studies tend to emphasize the significance of more complex patterns of colonization, gene flow, and secondary population movements in shaping patterns of diversity. Our objective in this study is to examine how founder effects, gene flow, and European admixture have molded patterns of neutral genetic diversity in the Americas. Our strategy is to test the fit of a serial founder effects process to the pattern of neutral autosomal genetic variation and to examine the contribution of gene flow and European admixture to departures from fit. The genetic data consist of 678 autosomal microsatellite loci assayed by Wang and colleagues in 530 individuals in 29 widely distributed Native American populations. We find that previous evidence for serial founder effects in the Americas may be driven in part by high levels of European admixture in northern North America, intermediate levels in Central America, and low levels in eastern South America. Geographically patterned admixture may also account for previously reported genetic differences between Andean and Amazonian groups. Though admixture has obscured the precise details of precontact evolutionary processes, we find that genetic diversity is still largely hierarchically structured and that gene flow between neighboring groups has had surprisingly little impact on macrogeographic patterns of genetic diversity in the Americas.     

Estimation of race admixture--a new method.

The contribution of a parental population in the gene pool of a hybrid population which arose by hybridization with one or more other populations is estimated here at the population level from the probability of gene identity. The dynamics of accumulation of such admixture is studied incorporating the fluctuations due to finite size of the hybrid population. The method is illustrated with data on admixture in Cherokee Indians.     

Estimation of admixture proportions: a likelihood-based approach using Markov chain Monte Carlo.

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.     

Gender and population history: sex bias revealed by studying genetic admixture of Ngazidja population (Comoro Archipelago)

The peopling of Comoro Archipelago is defined by successive waves of migration from three main areas: the East African Coast (Bantu-speaking populations), the Persia and Arabian Peninsula, and Southeast Asia (especially Indonesia). It follows an apparent classic trihybrid admixture model. To better understand the Comorian population admixture dynamics, we analyzed the contributions of these three historical parental components to its genetic pool. To enhance accuracy and reliability, we used both classical and molecular markers. Samples consist of published data: blood group frequencies, 14 KIR genes, 19 mitochondrial DNA SNPs (to highlight female migrations), 14 Y chromosome SNPs (male migrations). We revealed distinct admixture patterns for autosomal and uniparental markers. KIR gene frequencies had never been used to estimate admixture rates, this being a first assessment of their informative power in admixture studies. To avoid major methodological and statistical bias, we determined admixture coefficients through nine well-tried estimators and their associated software programs (ADMIX95, ADMIX, admix 2.0, LEA, LEADMIX, and Mistura). Results from mtDNA and Y chromosome markers point to an important sex-bias in the admixture event. The original Bantu gene pool received a predominant male-mediated contribution from the Arabian Peninsula and Persia, and a female-mediated contribution from Southeast Asia. Admixture rates estimated from autosomal KIR gene markers point also to an unexpected elevated Austronesian contribution.     

Changes in the genetic structure of Atlantic salmon populations over four decades reveal substantial impacts of stocking and potential resiliency

While the stocking of captive‐bred fish has been occurring for decades and has had substantial immediate genetic and evolutionary impacts on wild populations, its long‐term consequences have only been weakly investigated. Here, we conducted a spatiotemporal analysis of 1428 Atlantic salmon sampled from 1965 to 2006 in 25 populations throughout France to investigate the influence of stocking on the neutral genetic structure in wild Atlantic salmon (Salmo salar) populations. On the basis of the analysis of 11 microsatellite loci, we found that the overall genetic structure among populations dramatically decreased over the period studied. Admixture rates among populations were highly variable, ranging from a nearly undetectable contribution from donor stocks to total replacement of the native gene pool, suggesting extremely variable impacts of stocking. Depending on population, admixture rates either increased, remained stable, or decreased in samples collected between 1998 and 2006 compared to samples from 1965 to 1987, suggesting either rising, long‐lasting or short‐term impacts of stocking. We discuss the potential mechanisms contributing to this variability, including the reduced fitness of stocked fish and persistence of wild locally adapted individuals.