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Sökning: WFRF:(Jakobsson Mattias)

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41.
  • Fraser, Magdalena (författare)
  • People of the Dolmens and Stone Cists : An archaeogenetic Investigation of Megalithic Graves from the Neolithic Period on Gotland
  • 2018
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • The study of ancient genomics of pre-historic human remains has in recent years offered unprecedented knowledge regarding pre-historic migration and population structure on the European continent which has fundamentally altered the current views in the archaeological community. However, the merging of the two fields, archaeology and genetics, is still in its infancy and much work is still needed in order for these fields to integrate. In this thesis I explore how genetic analyses, in combination with contextual radiocarbon dating and isotopic analyses for diet and mobility can be used to investigate demographic events on a local and regional level. This is done through the investigation of people buried in five previously excavated megalithic tombs on the Island of Gotland dated to the Neolithic period. I present the genomic population structure and archaeological background for the pre-historic European reference data and show how this is used to investigate population continuity, demographic shifts, cultural duality, and admixture for local and regional contexts. I present new data and explore the Strontium-baseline for the Gotland biosphere which is used for the mobility analyses. I show that mitochondrial haplogroup data is especially useful in combination with isotopic data, and radiocarbon dating for investigation of demographic shifts on a larger scale. I also show that genomic data gives unique insights into the individuals’ life history which, together with the established demographic background allows for fine scale investigation of population demographic events within and between different archaeological contexts. Finally I show that the different Neolithic contexts on Gotland to a large extent involves immigration of new groups to the island, and that the contextual breaks seen in the archaeological record during the Neolithic period are connected with cultural and population demographic shifts. This dissertation demonstrates that genomic analyses, in combination with archaeology and isotopic analyses, as well as contextual osteological analyses and radiocarbon dating, present unique insights into the life history of the actual people who lived the lives we try to understand.
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43.
  • Fraser, Magdalena, et al. (författare)
  • The stone cist conundrum : A multidisciplinary approach to investigate Late Neolithic/Early Bronze Age population demography on the island of Gotland
  • 2018
  • Ingår i: Journal of Archaeological Science. - : Elsevier BV. - 2352-409X .- 2352-4103. ; 20, s. 324-337
  • Tidskriftsartikel (refereegranskat)abstract
    • The Late Neolithic period in Scandinavia [LN, c. 2350-1700 cal BCE] marks a time of considerable changes in settlement patterns, economy, and material culture. This shift also lays the foundation for the demographic developments in the Early Bronze Age [EBA, c. 1700-1100 cal BCE]. However, little is presently known regarding the developments from these time-periods on the island of Gotland in the Baltic Sea. During the Middle Neolithic period [MN, c. 3300-2350 cal BCE], Gotland was inhabited by groups associated with the Funnel Beaker culture [TRB, c. 4000-2700 cal BCE], and the sub-Neolithic Pitted Ware culture [PWC, c. 3300-2300 cal BCE]. Some indications of connections with the Bathe Axe/Corded Ware cultures [BAC/CWC, c. 2800-2300 cal BCE] have also been found, but no typical BAC/CWC burials have been located on the island to date. Here, we investigate the chronological and internal relationship of twenty-three individuals buried in four LN/EBA stone cist burials; Haffinds, Hagur, Suderkvie, and Utalskog on Gotland. We present eleven mitochondrial genomes [from 23 X to 1271 X coverage], and twenty-three new radiocarbon dates, as well as stable isotope data for diet. We examine the local Sr-baseline range for Gotland, and present new Sr-data to discuss mobility patterns of the individuals. The genetic results are compared and discussed in light of earlier cultural periods from Gotland [TRB and PWC], and CWC from the European continent, as well as contemporaneous LN secondary burials in the MN Ansarve dolmen. We find that all burials were used into the EBA, but only two of the cists showed activity already during the LN. We also see some mobility to Gotland during the LN/EBA period based on Strontium and mitochondrial data. We see a shift in the dietary pattern compared to the preceding period on the island [TRB and PWC], and the two LN individuals from the Ansarve dolmen exhibited different dietary and mobility patterns compared to the individuals from the LN/EBA stone cist burials. We find that most of the cist burials were used by individuals local to the area of the burials, with the exception of the large LN/EBA Haffinds cist burial which showed higher levels of mobility. Our modeling of ancestral mitochondrial contribution from chronologically older individuals recovered in the cultural contexts of TRB, PWC and CWC show that the best model is a 55/45 mix of CWC and TRB individuals. A 3-way model with a slight influx from PWC [5%] also had a good fit. This is difficult to reconcile with the current archaeological evidence on the island. We suggest that the maternal CWC/TRB contribution we see in the local LN/EBA individuals derives from migrants after the Scandinavian MN period, which possible also admixed with smaller local groups connected with the PWC. Further genomic analyses of these groups on Gotland will help to clarify the demographic history during the MN to EBA time periods.
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44.
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45.
  • Gattepaille, Lucie, et al. (författare)
  • Inferring Past Effective Population Size from Distributions of Coalescent Times
  • 2016
  • Ingår i: Genetics. - : Oxford University Press (OUP). - 0016-6731 .- 1943-2631. ; 204:3, s. 1191-1206
  • Tidskriftsartikel (refereegranskat)abstract
    • Inferring and understanding changes in effective population size over time is a major challenge for population genetics. Here we investigate some theoretical properties of random-mating populations with varying size over time. In particular, we present an exact solution to compute the population size as a function of time, N-e(t), based on distributions of coalescent times of samples of any size. This result reduces the problem of population size inference to a problem of estimating coalescent time distributions. To illustrate the analytic results, we design a heuristic method using a tree-inference algorithm and investigate simulated and empirical population-genetic data. We investigate the effects of a range of conditions associated with empirical data, for instance number of loci, sample size, mutation rate, and cryptic recombination. We show that our approach performs well with genomic data ( 10,000 loci) and that increasing the sample size from 2 to 10 greatly improves the inference of Ne(t) whereas further increase in sample size results in modest improvements, even under a scenario of exponential growth. We also investigate the impact of recombination and characterize the potential biases in inference of Ne(t). The approach can handle large sample sizes and the computations are fast. We apply our method to human genomes from four populations and reconstruct population size profiles that are coherent with previous finds, including the Out-of-Africa bottleneck. Additionally, we uncover a potential difference in population size between African and non-African populations as early as 400 KYA. In summary, we provide an analytic relationship between distributions of coalescent times and Ne(t), which can be incorporated into powerful approaches for inferring past population sizes from population-genomic data.
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46.
  • Gattepaille, Lucie M., et al. (författare)
  • Combining Markers into Haplotypes Can Improve Population Structure Inference
  • 2012
  • Ingår i: Genetics. - : Oxford University Press (OUP). - 0016-6731 .- 1943-2631. ; 190:1, s. 159-174
  • Tidskriftsartikel (refereegranskat)abstract
    • High-throughput genotyping and sequencing technologies can generate dense sets of genetic markers for large numbers of individuals. For most species, these data will contain many markers in linkage disequilibrium (LD). To utilize such data for population structure inference, we investigate the use of haplotypes constructed by combining the alleles at single-nucleotide polymorphisms (SNPs). We introduce a statistic derived from information theory, the gain of informativeness for assignment (GIA), which quantifies the additional information for assigning individuals to populations using haplotype data compared to using individual loci separately. Using a two-loci-two-allele model, we demonstrate that combining markers in linkage equilibrium into haplotypes always leads to non-positive GIA, suggesting that combining the two markers is not advantageous for ancestry inference. However, for loci in LD, GIA is often positive, suggesting that assignment can be improved by combining markers into haplotypes. Using GIA as a criterion for combining markers into haplotypes, we demonstrate for simulated data a significant improvement of assigning individuals to candidate populations. For the many cases that we investigate, incorrect assignment was reduced between 26% and 97% using haplotype data. For empirical data from French and German individuals, the incorrectly assigned individuals can, for example, be decreased by 73% using haplotypes. Our results can be useful for challenging population structure and assignment problems, in particular for studies where large-scale population-genomic data are available.
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47.
  • Gattepaille, Lucie M., et al. (författare)
  • Inferring population size changes with sequence and SNP data : lessons from human bottlenecks
  • 2013
  • Ingår i: Heredity. - : Springer Science and Business Media LLC. - 0018-067X .- 1365-2540. ; 110:5, s. 409-419
  • Forskningsöversikt (refereegranskat)abstract
    • Reconstructing historical variation of population size from sequence and single-nucleotide polymorphism (SNP) data is valuable for understanding the evolutionary history of species. Changes in the population size of humans have been thoroughly investigated, and we review different methodologies of demographic reconstruction, specifically focusing on human bottlenecks. In addition to the classical approaches based on the site-frequency spectrum (SFS) or based on linkage disequilibrium, we also review more recent approaches that utilize atypical shared genomic fragments, such as identical by descent or homozygous segments between or within individuals. Compared with methods based on the SFS, these methods are well suited for detecting recent bottlenecks. In general, all these various methods suffer from bias and dependencies on confounding factors such as population structure or poor specification of the mutational and recombination processes, which can affect the demographic reconstruction. With the exception of SFS-based methods, the effects of confounding factors on the inference methods remain poorly investigated. We conclude that an important step when investigating population size changes rests on validating the demographic model by investigating to what extent the fitted demographic model can reproduce the main features of the polymorphism data. 
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48.
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49.
  • Gattepaille, Lucie, 1984- (författare)
  • Population Genetic Methods and Applications to Human Genomes
  • 2015
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • Population Genetics has led to countless numbers of fruitful studies of evolution, due to its abilities for prediction and description of the most important evolutionary processes such as mutation, genetic drift and selection. The field is still growing today, with new methods and models being developed to answer questions of evolutionary relevance and to lift the veil on the past of all life forms. In this thesis, I present a modest contribution to the growth of population genetics. I investigate different questions related to the dynamics of populations, with particular focus on studying human evolution. I derive an upper bound and a lower bound for FST, a classical measure of population differentiation, as functions of the homozygosity in each of the two studied populations, and apply the result to discuss observed differentiation levels between human populations. I introduce a new criterion, the Gain of Informativeness for Assignment, to help us decide whether two genetic markers should be combined into a haplotype marker and improve the assignment of individuals to a panel of reference populations. Applying the method on SNP data for French, German and Swiss individuals, I show how haplotypes can lead to better assignment results when they are supervised by GIA. I also derive the population size over time as a function of the densities of cumulative coalescent times, show the robustness of this result to the number of loci as well as the sample size, and together with a simple algorithm of gene-genealogy inference, apply the method on low recombining regions of the human genome for four worldwide populations. I recover previously observed population size shapes, as well as uncover an early divergence of the Yoruba population from the non-African populations, suggesting ancient population structure on the African continent prior to the Out-of-Africa event. Finally, I present a case study of human adaptation to an arsenic-rich environment.
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50.
  • Goldberg, Amy, et al. (författare)
  • Ancient X chromosomes reveal contrasting sex bias in Neolithic and Bronze Age Eurasian migrations
  • 2017
  • Ingår i: 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
  • Tidskriftsartikel (refereegranskat)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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