1,036 research outputs found
Étude du surf génétique dans un contexte de sélection balancée
No full textAu cours de l'évolution, de nombreuses expansions de populations se sont produites et elles ont indéniablement modifié la diversité génétique des espèces, humains compris. Lors de ces expansions (spatiales et démographiques), plusieurs études ont montré qu'un nouvel allèle pouvait parfois surfer génétiquement sur le front de la vague d'expansion pour atteindre une haute fréquence et une dissémination sur un grand territoire. Ce travail de maîtrise universitaire décrit donc la diffusion d'un allèle apparaissant à un locus soumis à sélection balancée à la lumière de ce phénomène, par le biais de simulations informatiques, dans la continuité de celles effectuées par Klopfstein, Currat et Excoffier pour un locus neutre, dans un article publié en 2006. L'intérêt de ma recherche est de constituer des attendus théoriques afin d'aider l'interprétation des données réelles dans un contexte spécifique d'expansion de population et de sélection balancée
Setting files from: Spatially explicit paleogenomic simulations support cohabitation with limited admixture between Bronze Age Central European populations.
No full textSimulated Data and Custom Scripts
This dataset release permits to simulate the expansion of populations from the Pontic Steppes to Central Europe with the version of SPLATCHE3 which is included. There are 2 main zipped folders: i) the one called "SPLATCHE3executableAndSettings" contains a "ReadMe.txt" file that contains all required information to make the simulations: the resulting ".prop" file contains proportions of genomic ancestry of the P2 layer, ancestry from P1 layer is equal to 1-(proportion from P2) ; ii) the other one called "HowToMakeFigure2" contains the R script and the tables necessary to reproduce Figure 2. See Rio J, Quilodrán CS & Currat M., Communications Biology (2021), for background.
Acknowledgments
This project was financially supported by the Swiss National Research Foundation grants n° 31003A_182577 to MC and n° P400PB_183930 to CQ, as well as the IGE3 Student Salary Award to JR
Modern humans did not admix with Neanderthals during their range expansion into Europe.
No full textThe process by which the Neanderthals were replaced by modern humans between 42,000 and 30,000 before present is still intriguing. Although no Neanderthal mitochondrial DNA (mtDNA) lineage is found to date among several thousands of Europeans and in seven early modern Europeans, interbreeding rates as high as 25% could not be excluded between the two subspecies. In this study, we introduce a realistic model of the range expansion of early modern humans into Europe, and of their competition and potential admixture with local Neanderthals. Under this scenario, which explicitly models the dynamics of Neanderthals' replacement, we estimate that maximum interbreeding rates between the two populations should have been smaller than 0.1%. We indeed show that the absence of Neanderthal mtDNA sequences in Europe is compatible with at most 120 admixture events between the two populations despite a likely cohabitation time of more than 12,000 y. This extremely low number strongly suggests an almost complete sterility between Neanderthal females and modern human males, implying that the two populations were probably distinct biological species
Mauersegler weiter Wege. Mathias Enard: Kompass
No full textAnalysis of the peculiar scientific narrative in the novel of the Prix-Goncourt winning author Mathias Enard
Early farmers from across Europe directly descended from Neolithic Aegeans
No full textFarming and sedentism first appeared in southwestern Asia during the early Holocene and later spread to neighboring regions, including Europe, along multiple dispersal routes. Conspicuous uncertainties remain about the relative roles of migration, cultural diffusion, and admixture with local foragers in the early Neolithization of Europe. Here we present paleogenomic data for five Neolithic individuals from northern Greece and northwestern Turkey spanning the time and region of the earliest spread of farming into Europe. We use a novel approach to recalibrate raw reads and call genotypes from ancient DNA and observe striking genetic similarity both among Aegean early farmers and with those from across Europe. Our study demonstrates a direct genetic link between Mediterranean and Central European early farmers and those of Greece and Anatolia, extending the European Neolithic migratory chain all the way back to southwestern Asia
Inferring Population Dynamics During Past Expansion Events Using Spatiotemporal Molecular Patterns
No full textPopulation expansions have a major evolutionary impact on the genetic diversity of species. When a population expands into a new territory, it often encounters other populations of the same or closely related species. Interbreeding between the migrating population and the local one occurs can generate specific molecular patterns in both populations. These patterns can potentially be used to infer the migratory and demographic dynamics of the expansion. However, the effect of interbreeding during population expansions on the spatiotemporal patterns of molecular diversity in the involved populations has not been studied yet. In the present thesis, I used palaeogenomic data to investigate spatiotemporal patterns of molecular diversity that were created during past expansions of the species Homo sapiens, and I used these patterns to make inferences about these important evolutionary processes. The thesis mainly focused on patterns of genomic introgression. In Chapter 2, we used spatially explicit simulations to investigate the expected pattern of introgression after an expansion with interbreeding. We showed that the levels of introgression from the local population in the expanding one are expected to increase with distance from the source of the expansion, while the opposite cline is expected in the local population. We reported the existence of such empirical introgression patterns in various species that underwent an expansion with interbreeding, in accordance with our theoretical expectation. In Chapter 3, we used palaeogenomic data to investigate the spatiotemporal pattern of Neanderthal introgression in Eurasian anatomically modern human populations at different periods of time. In accordance with the theoretical expectations from Chapter 2, we found that during the expansion of modern humans in Eurasia, a spatial cline of Neanderthal introgression developed, increasing with distance from the Near East, and it persists until the present. In Chapter 4, we inferred the population dynamics of two human migrations that created the observed spatiotemporal pattern of Neanderthal introgression in Europe, by using a novel spatially explicit simulation framework of three populations. We showed that the observed cline of Neanderthal introgression is indicative of the direction from which the first humans arrived in Europe and that the reduction of Neanderthal introgression levels during the Neolithic transition can be explained by drift, and demographic and migratory processes. Lastly, in Chapter 5, we investigated in more depth the Neolithic transition in Europe, by following two different approaches and using two palaeogenomic datasets. Our results are compatible with a model of “demic diffusion with delayed admixture”, meaning that early farmer populations migrated into Europe from Anatolia and that the assimilation of local hunter-gatherers increased with time. Altogether, my thesis shows that population expansions with interbreeding create clear spatiotemporal patterns of local introgression in the migrating population, which can provide information both on the direction of past expansions and on the demography and interactions of the involved populations. Although focused on specific events of human evolution, our approach and results offer a framework for using the introgression levels in genomic data to study other instances of spatial processes between populations, in humans or other species.</p
Estimation of Population Admixture from Paleogenomic Data using Spatially Explicit Simulations
No full textGenomes are full of informations related to our evolutionary history. In this thesis I'm interested in making inferences on past human population interactions by simulating paleogenomic data under different historical contexts. The originality of this approach lies on the simulation of paleogenomes in a spatially explicit simulation framework that integrates demograhy, migration and admixture of populations. Chapter 2 and 3 are related to the test of population continuity, in two different contexts. Chapter 4 and 5 are exploratory analyses in which (i) I explore the effect of spatio-temporally heterogeneous environments on the population continuity test and (ii) I explore different methods to identify a subset of paleogenomes from a database base filling the requirements of our spatially explicit approach. In Chapter 6, I extend the simulation approach to study populations of the Bronze Age in Central Europe under different demographic scenarios
Inférence de l'histoire démographique post-néolithique européenne par simulation informatique
No full textLes analyses d'ADN mitochondrial des populations contemporaines d'Europe centrale suggèrent un peuplement continu depuis la période néolithique alors que les analyses d'ADN ancien tiré de fossiles datant de cette période montrent au contraire une discontinuité. Ce travail a cherché à expliquer comment réconcilier ces résultats discordants à l'aide de simulations informatiques. Sur la base de ces simulations, nous avons pu écarter la possibilité que des fluctuations ou de fortes chutes démographiques après le Néolithique aient pu conduire à la diversité génétique observée aujourd'hui. En revanche, des scénarios impliquant une importante migration d'une population provenant de l'Est de l'Europe après le Néolithique n'ont pas pu être écartés. Enfin, le développement d'une méthode originale permettant la création d'haplogroupes à partir de séquences simulées, nous a permis de conclure que la baisse de fréquence de l'haplogroupe mitochondrial N1a observée en Europe depuis le Néolithique était possible par dérive génétique, sans aucune perturbation démographique
Investigation of the Neolithic transition in Europe through spatially explicit simulations applied to ancient DNA
No full textThe increasing availability of DNA from prehistoric skeletal remains changed drastically the focus of the human population genetics field during the last decade. It is now possible to use ancient DNA to formally test evolutionary hypotheses built by inter-disciplinary studies on the basis of archaeological or anthropological information. Spatially explicit simulations offer the advantage of taking into account the spatial and temporal dynamics of populations by representing explicitly the migration of individuals within the geographic area under study. This PhD thesis is a first attempt to analyse ancient genetic material with spatially explicit simulations. Using this original approach, we analysed a large dataset of ancient, and modern, mitochondrial DNA from European populations, under various evolutionary hypotheses. We focused on the relation between past populations during the period of the Neolithic transition that started in Europe around 8,000 years ago
Models of hybridization during range expansions and their application to recent human evolution
No full textSeveral lines of genetic, archeological and paleontological evidence suggest
that anatomically modern humans (Homo sapiens) colonized the world
in the last 60,000 years by a series of migrations originating from Africa (e.g.
Liu et al., 2006; Handley et al., 2007; Prugnolle, Manica, and Balloux, 2005;
Ramachandran et al. 2005; Li et al. 2008; Deshpande et al. 2009; Mellars,
2006a, b; Lahr and Foley, 1998; Gravel et al., 2011; Rasmussen et al., 2011).
With the progress of ancient DNA analysis, it has been shown that archaic
humans hybridized with modern humans outside Africa. Recent direct analyses
of fossil nuclear DNA have revealed that 1–4 percent of the genome of Eurasian
has been likely introgressed by Neanderthal genes (Green et al., 2010; Reich
et al., 2010; Vernot and Akey, 2014; Sankararaman et al., 2014; Prufer et al.,
2014; Wall et al., 2013), with Papua New Guineans and Australians showing
even larger levels of admixture with Denisovans (Reich et al., 2010; Skoglund
and Jakobsson, 2011; Reich et al., 2011; Rasmussen et al., 2011). It thus appears
that the past history of our species has been more complex than previously
anticipated (Alves et al., 2012), and that modern humans hybridized several
times with local hominins during their expansion out of Africa, but the exact
mode, time and location of these hybridizations remain to be clarifi ed (Ibid.;
Wall et al., 2013). In this context, we review here a general model of admixture
during range expansion, which lead to some predictions about expected patterns
of introgression that are relevant to modern human evolution
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