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1.
  • DeGiorgio, Michael, et al. (creator_code:aut_t)
  • Explaining worldwide patterns of human genetic variation using a coalescent-based serial founder model of migration outward from Africa
  • 2009
  • record:In_t: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 106:38, s. 16057-16062
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • Studies of worldwide human variation have discovered three trends in summary statistics as a function of increasing geographic distance from East Africa: a decrease in heterozygosity, an increase in linkage disequilibrium (LD), and a decrease in the slope of the ancestral allele frequency spectrum. Forward simulations of unlinked loci have shown that the decline in heterozygosity can be described by a serial founder model, in which populations migrate outward from Africa through a process where each of a series of populations is formed from a subset of the previous population in the outward expansion. Here, we extend this approach by developing a retrospective coalescent-based serial founder model that incorporates linked loci. Our model both recovers the observed decline in heterozygosity with increasing distance from Africa and produces the patterns observed in LD and the ancestral allele frequency spectrum. Surprisingly, although migration between neighboring populations and limited admixture between modern and archaic humans can be accommodated in the model while continuing to explain the three trends, a competing model in which a wave of outward modern human migration expands into a series of preexisting archaic populations produces nearly opposite patterns to those observed in the data. We conclude by developing a simpler model to illustrate that the feature that permits the serial founder model but not the archaic persistence model to explain the three trends observed with increasing distance from Africa is its incorporation of a cumulative effect of genetic drift as humans colonized the world.
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2.
  • Francois, Olivier, et al. (creator_code:aut_t)
  • Demographic history of European populations of Arabidopsis thaliana
  • 2008
  • record:In_t: PLoS Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 4:5, s. e1000075-
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • The model plant species Arabidopsis thaliana is successful at colonizing land that has recently undergone human-mediated disturbance. To investigate the prehistoric spread of A. thaliana, we applied approximate Bayesian computation and explicit spatial modeling to 76 European accessions sequenced at 876 nuclear loci. We find evidence that a major migration wave occurred from east to west, affecting most of the sampled individuals. The longitudinal gradient appears to result from the plant having spread in Europe from the east ~10,000 years ago, with a rate of westward spread of ~0.9 km/year. This wave-of-advance model is consistent with a natural colonization from an eastern glacial refugium that overwhelmed ancient western lineages. However, the speed and time frame of the model also suggest that the migration of A. thaliana into Europe may have accompanied the spread of agriculture during the Neolithic transition.
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3.
  • Goldberg, Amy, et al. (creator_code:aut_t)
  • Ancient X chromosomes reveal contrasting sex bias in Neolithic and Bronze Age Eurasian migrations
  • 2017
  • record:In_t: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 114:10, s. 2657-2662
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • Dramatic events in human prehistory, such as the spread of agriculture to Europe from Anatolia and the late Neolithic/Bronze Age migration from the Pontic-Caspian Steppe, can be investigated using patterns of genetic variation among the people who lived in those times. In particular, studies of differing female and male demographic histories on the basis of ancient genomes can provide information about complexities of social structures and cultural interactions in prehistoric populations. We use a mechanistic admixture model to compare the sex-specifically-inherited X chromosome with the autosomes in 20 early Neolithic and 16 late Neolithic/Bronze Age human remains. Contrary to previous hypotheses suggested by the patrilocality of many agricultural populations, we find no evidence of sex-biased admixture during the migration that spread farming across Europe during the early Neolithic. For later migrations from the Pontic Steppe during the late Neolithic/Bronze Age, however, we estimate a dramatic male bias, with approximately five to 14 migrating males for every migrating female. We find evidence of ongoing, primarily male, migration from the steppe to central Europe over a period of multiple generations, with a level of sex bias that excludes a pulse migration during a single generation. The contrasting patterns of sex-specific migration during these two migrations suggest a view of differing cultural histories in which the Neolithic transition was driven by mass migration of both males and females in roughly equal numbers, perhaps whole families, whereas the later Bronze Age migration and cultural shift were instead driven by male migration, potentially connected to new technology and conquest.
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6.
  • Huang, Lucy, et al. (creator_code:aut_t)
  • Haplotype variation and genotype imputation in African populations
  • 2011
  • record:In_t: Genetic Epidemiology. - : Wiley. - 0741-0395 .- 1098-2272. ; 35:8, s. 766-780
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • Sub-Saharan Africa has been identified as the part of the world with the greatest human genetic diversity. This high level of diversity causes difficulties for genome-wide association (GWA) studies in African populationsfor example, by reducing the accuracy of genotype imputation in African populations compared to non-African populations. Here, we investigate haplotype variation and imputation in Africa, using 253 unrelated individuals from 15 Sub-Saharan African populations. We identify the populations that provide the greatest potential for serving as reference panels for imputing genotypes in the remaining groups. Considering reference panels comprising samples of recent African descent in Phase 3 of the HapMap Project, we identify mixtures of reference groups that produce the maximal imputation accuracy in each of the sampled populations. We find that optimal HapMap mixtures and maximal imputation accuracies identified in detailed tests of imputation procedures can instead be predicted by using simple summary statistics that measure relationships between the pattern of genetic variation in a target population and the patterns in potential reference panels. Our results provide an empirical basis for facilitating the selection of reference panels in GWA studies of diverse human populations, especially those of African ancestry.
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7.
  • Jakobsson, Mattias, et al. (creator_code:aut_t)
  • The Relationship Between F-ST and the Frequency of the Most Frequent Allele
  • 2013
  • record:In_t: Genetics. - : Oxford University Press (OUP). - 0016-6731 .- 1943-2631. ; 193:2, s. 515-528
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • F-ST is frequently used as a summary of genetic differentiation among groups. It has been suggested that F-ST depends on the allele frequencies at a locus, as it exhibits a variety of peculiar properties related to genetic diversity: higher values for biallelic single-nucleotide polymorphisms (SNPs) than for multiallelic microsatellites, low values among high-diversity populations viewed as substantially distinct, and low values for populations that differ primarily in their profiles of rare alleles. A full mathematical understanding of the dependence of F-ST on allele frequencies, however, has been elusive. Here, we examine the relationship between F-ST and the frequency of the most frequent allele, demonstrating that the range of values that F-ST can take is restricted considerably by the allele-frequency distribution. For a two-population model, we derive strict bounds on F-ST as a function of the frequency M of the allele with highest mean frequency between the pair of populations. Using these bounds, we show that for a value of M chosen uniformly between 0 and 1 at a multiallelic locus whose number of alleles is left unspecified, the mean maximum F-ST is similar to 0.3585. Further, F-ST is restricted to values much less than 1 when M is low or high, and the contribution to the maximum F-ST made by the most frequent allele is on average similar to 0.4485. Using bounds on homozygosity that we have previously derived as functions of M, we describe strict bounds on F-ST in terms of the homozygosity of the total population, finding that the mean maximum F-ST given this homozygosity is 1 - In 2 approximate to 0.3069. Our results provide a conceptual basis for understanding the dependence of F-ST on allele frequencies and genetic diversity and for interpreting the roles of these quantities in computations of F-ST from population-genetic data. Further, our analysis suggests that many unusual observations of F-ST, including the relatively low F-ST values in high-diversity human populations from Africa and the relatively low estimates of F-ST for microsatellites compared to SNPs, can be understood not as biological phenomena associated with different groups of populations or classes of markers but rather as consequences of the intrinsic mathematical dependence of F-ST on the properties of allele-frequency distributions.
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8.
  • Kopelman, Naama M., et al. (creator_code:aut_t)
  • Clumpak : a program for identifying clustering modes and packaging population structure inferences across K
  • 2015
  • record:In_t: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 15:5, s. 1179-1191
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • The identification of the genetic structure of populations from multilocus genotype data has become a central component of modern population-genetic data analysis. Application of model-based clustering programs often entails a number of steps, in which the user considers different modelling assumptions, compares results across different predetermined values of the number of assumed clusters (a parameter typically denoted K), examines multiple independent runs for each fixed value of K, and distinguishes among runs belonging to substantially distinct clustering solutions. Here, we present Clumpak (Cluster Markov Packager Across K), a method that automates the postprocessing of results of model-based population structure analyses. For analysing multiple independent runs at a single K value, Clumpak identifies sets of highly similar runs, separating distinct groups of runs that represent distinct modes in the space of possible solutions. This procedure, which generates a consensus solution for each distinct mode, is performed by the use of a Markov clustering algorithm that relies on a similarity matrix between replicate runs, as computed by the software Clumpp. Next, Clumpak identifies an optimal alignment of inferred clusters across different values of K, extending a similar approach implemented for a fixed K in Clumpp and simplifying the comparison of clustering results across different K values. Clumpak incorporates additional features, such as implementations of methods for choosing K and comparing solutions obtained by different programs, models, or data subsets. Clumpak, available at , simplifies the use of model-based analyses of population structure in population genetics and molecular ecology.
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9.
  • Pemberton, Trevor J., et al. (creator_code:aut_t)
  • Sequence determinants of human microsatellite variability
  • 2009
  • record:In_t: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 10, s. e612-
  • swepub:Mat_researchreview_t (swepub:level_refereed_t)abstract
    • BackgroundMicrosatellite loci are frequently used in genomic studies of DNA sequence repeats and in population studies of genetic variability. To investigate the effect of sequence properties of microsatellites on their level of variability we have analyzed genotypes at 627 microsatellite loci in 1,048 worldwide individuals from the HGDP-CEPH cell line panel together with the DNA sequences of these microsatellites in the human RefSeq database.ResultsCalibrating PCR fragment lengths in individual genotypes by using the RefSeq sequence enabled us to infer repeat number in the HGDP-CEPH dataset and to calculate the mean number of repeats (as opposed to the mean PCR fragment length), under the assumption that differences in PCR fragment length reflect differences in the numbers of repeats in the embedded repeat sequences. We find the mean and maximum numbers of repeats across individuals to be positively correlated with heterozygosity. The size and composition of the repeat unit of a microsatellite are also important factors in predicting heterozygosity, with tetra-nucleotide repeat units high in G/C content leading to higher heterozygosity. Finally, we find that microsatellites containing more separate sets of repeated motifs generally have higher heterozygosity.ConclusionsThese results suggest that sequence properties of microsatellites have a significant impact in determining the features of human microsatellite variability.
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10.
  • Rosenberg, Noah A., et al. (creator_code:aut_t)
  • The relationship between homozygosity and the frequency of the most frequent allele
  • 2008
  • record:In_t: Genetics. - : Oxford University Press (OUP). - 0016-6731 .- 1943-2631. ; 179:4, s. 2027-2036
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • Homozygosity is a commonly used summary of allele-frequencydistributions at polymorphic loci. Because high-frequency allelescontribute disproportionately to the homozygosity of a locus,it often occurs that most homozygotes are homozygous for themost frequent allele. To assess the relationship between homozygosityand the highest allele frequency at a locus, for a given homozygosityvalue, we determine the lower and upper bounds on the frequencyof the most frequent allele. These bounds suggest tight constraintson the frequency of the most frequent allele as a function ofhomozygosity, differing by at most and having an average difference of – 2/18 0.1184. The close connection between homozygosityand the frequency of the most frequent allele—which weillustrate using allele frequencies from human populations—hasthe consequence that when one of these two quantities is known,considerable information is available about the other quantity.This relationship also explains the similar performance of statisticaltests of population-genetic models that rely on homozygosityand those that rely on the frequency of the most frequent allele,and it provides a basis for understanding the utility of extendedhomozygosity statistics in identifying haplotypes that havebeen elevated to high frequency as a result of positive selection.
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