Female and Male Perspectives on the Neolithic Transition in Europe: Clues from Ancient and Modern Genetic Data
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{"title"=>"Female and Male Perspectives on the Neolithic Transition in Europe: Clues from Ancient and Modern Genetic Data", "type"=>"journal", "authors"=>[{"first_name"=>"Rita", "last_name"=>"Rasteiro", "scopus_author_id"=>"22135887600"}, {"first_name"=>"Lounès", "last_name"=>"Chikhi", "scopus_author_id"=>"6603662722"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"23613761", "isbn"=>"1932-6203", "doi"=>"10.1371/journal.pone.0060944", "issn"=>"19326203", "scopus"=>"2-s2.0-84876262517", "pui"=>"368743297", "sgr"=>"84876262517"}, "id"=>"92dd4b42-7ca0-3e33-bc9e-9a1826c34ccd", "abstract"=>"The arrival of agriculture into Europe during the Neolithic transition brought a significant shift in human lifestyle and subsistence. However, the conditions under which the spread of the new culture and technologies occurred are still debated. Similarly, the roles played by women and men during the Neolithic transition are not well understood, probably due to the fact that mitochondrial DNA (mtDNA) and Y chromosome (NRY) data are usually studied independently rather than within the same statistical framework. Here, we applied an integrative approach, using different model-based inferential techniques, to analyse published datasets from contemporary and ancient European populations. By integrating mtDNA and NRY data into the same admixture approach, we show that both males and females underwent the same admixture history and both support the demic diffusion model of Ammerman and Cavalli-Sforza. Similarly, the patterns of genetic diversity found in extant and ancient populations demonstrate that both modern and ancient mtDNA support the demic diffusion model. They also show that population structure and differential growth between farmers and hunter-gatherers are necessary to explain both types of data. However, we also found some differences between male and female markers, suggesting that the female effective population size was larger than that of the males, probably due to different demographic histories. We argue that these differences are most probably related to the various shifts in cultural practices and lifestyles that followed the Neolithic Transition, such as sedentism, the shift from polygyny to monogamy or the increase of patrilocality.", "link"=>"http://www.mendeley.com/research/female-male-perspectives-neolithic-transition-europe-clues-ancient-modern-genetic-data", "reader_count"=>66, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>4, "Researcher"=>14, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>19, "Student > Postgraduate"=>2, "Student > Master"=>10, "Other"=>5, "Student > Bachelor"=>6, "Lecturer"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>4, "Researcher"=>14, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>19, "Student > Postgraduate"=>2, "Student > Master"=>10, "Other"=>5, "Student > Bachelor"=>6, "Lecturer"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>7, "Agricultural and Biological Sciences"=>36, "Arts and Humanities"=>10, "Philosophy"=>1, "Social Sciences"=>8, "Immunology and Microbiology"=>1, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Social Sciences"=>{"Social Sciences"=>8}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>36}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>7}, "Unspecified"=>{"Unspecified"=>2}, "Arts and Humanities"=>{"Arts and Humanities"=>10}, "Philosophy"=>{"Philosophy"=>1}}, "reader_count_by_country"=>{"United States"=>1, "United Kingdom"=>3, "Portugal"=>2}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1026602"], "description"=>"<p>In (<b>A</b>) are represented the posterior distributions of the Palaeolithic contribution (<i>HG</i> contribution to modern European), for each of the populations analysed, using mtDNA data. Each curve corresponds to the analysis of a specific admixed population (Armenia − red, Caucasus – dashed red, Azeri – dotted red, Egypt – dotdash red, Iran – twodash red, Central Mediterranean − black, East Mediterranean – dashed black, West Mediterranean – dotted black, Southeast Europe – green, North and Central Europe – blue, Northeast Europe – dashed blue, Northwest Europe – dotted blue, Alps, dotdash blue and Scandinavia − aquamarine). (<b>B</b>) Linear regression of Neolithic contribution, against geographical distance from Near East. For each of the samples, one 1−<i>p<sub>1</sub></i> value was randomly sampled from the corresponding posterior distribution. A linear regression was then calculated between this set of values and geographic distance. This process was repeated 1,000 times to obtain the empirical distribution of regression curves. The fitted values using mtDNA data are plotted for each of the 1,000 replicates. As fitted values are plotted, they can occur outside the range (0–1). Mean values for each population are represented by solid circles (mtDNA data) and open triangles and circles (for two different NRY datasets, Rosser et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060944#pone.0060944-Rosser1\" target=\"_blank\">[23]</a> and Semino et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060944#pone.0060944-Semino1\" target=\"_blank\">[17]</a>, respectively). In (<b>C</b>) a similar approach was used to represent the linear regression of <i>t<sub>h</sub></i> (drift in the admixed populations) against geographic distance from the Near East. Mean values for each population for mtDNA and NRY datasets are plotted, with symbol codes as in (B). The close-up inset shows the mtDNA regression on a different scale for the Y-axis. Mean values for each population are represented for the sake of clarity. Calibrated radiocarbon dates of Neolithic archaeological sites <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060944#pone.0060944-Pinhasi1\" target=\"_blank\">[13]</a> (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060944#pone.0060944.s013\" target=\"_blank\">table S4</a>) are also plotted against the distance from the Near East (blue open circles), with the linear regression represented by the blue line.</p>", "links"=>[], "tags"=>["Computational biology", "population genetics", "Population modeling", "ecology", "Ecological metrics", "Population growth", "Evolutionary biology", "Organismal evolution", "Human evolution", "Paleontology", "genetics", "Human genetics", "Population biology", "Population metrics", "anthropology", "Biological anthropology", "Cultural anthropology", "Paleoanthropology", "Sociology", "demography", "admixture"], "article_id"=>684145, "categories"=>["Biological Sciences", "Sociology"], "users"=>["Rita Rasteiro", "Lounès Chikhi"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0060944.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Spatial_variation_of_admixture_and_drift_across_Europe_/684145", "title"=>"Spatial variation of admixture and drift across Europe.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-17 01:09:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/1026603"], "description"=>"<p>Three different demographic models were tested using ancient and modern mtDNA data. The Total Panmixia (TP) model (<b>A</b>) follows the assumptions of Bramanti et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060944#pone.0060944-Bramanti1\" target=\"_blank\">[27]</a>, where <i>HG</i> and farmers were part of the same panmictic population over Central Europe and were never separated in different populations or communities. This model was used assuming a single modern female effective population size N<sub>M</sub> and two periods of exponential growth: i) the first starting with an Upper Palaeolithic (UP) population of effective size N<sub>UP</sub>, sampled from an ancestral African female population of constant size, corresponding to the initial colonization of Central Europe 45,000 years ago and ii) the second following the Neolithic Transition 7,500 years ago, from a population of effective size N<sub>N</sub>. Both N<sub>UP</sub> and N<sub>N</sub> population sizes were allowed to vary using the same priors as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060944#pone.0060944-Bramanti1\" target=\"_blank\">[27]</a>. In the Split Model (S) (<b>B</b>), the UP population was structured in two sub-populations of equal size, 45,000 years ago. These sub-populations were assumed to grow independently (no gene flow), until they joined together at the beginning of the Neolithic, in Central Europe. The Split with Differential Growth (SDG) model (<b>C</b>) is similar to the S model but has a more complex splitting, in which one of the two sub-populations was allowed to have a higher growth rate between 10,000 and 7,500 years ago. In (<b>D</b>) are represented the posterior probabilities under each model, calculated using the ABC framework, for two different types of post-rejection adjustments: MLR (white bars) and NCH (grey bars).</p>", "links"=>[], "tags"=>["Computational biology", "population genetics", "Population modeling", "ecology", "Ecological metrics", "Population growth", "Evolutionary biology", "Organismal evolution", "Human evolution", "Paleontology", "genetics", "Human genetics", "Population biology", "Population metrics", "anthropology", "Biological anthropology", "Cultural anthropology", "Paleoanthropology", "Sociology", "demography", "adna", "posterior"], "article_id"=>684146, "categories"=>["Biological Sciences", "Sociology"], "users"=>["Rita Rasteiro", "Lounès Chikhi"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0060944.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Demographic_models_used_in_the_aDNA_analysis_and_their_posterior_probabilities_/684146", "title"=>"Demographic models used in the aDNA analysis and their posterior probabilities.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-17 01:09:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/1026604"], "description"=>"<p>The panels in each row correspond to data simulated under the TP model (<b>A, B, C</b>), the S model (<b>D, E, F</b>) and the SDG model (<b>G, H, I</b>) (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060944#pone-0060944-g002\" target=\"_blank\">Figure 2</a>, for models definitions). Each column corresponds to a specific pairwise <i>F<sub>ST</sub></i> comparison, namely between <i>HG</i> and early farmers (<b>A, D, G</b>), <i>HG</i> and modern Europeans (<b>B, E, H</b>), and early farmers and modern Europeans (<b>C, F, I</b>). The x- and y-axis represent the values used for the female effective size N<sub>N</sub> (at the onset of the Central European Neolithic 7,500 years ago) and N<sub>UP</sub> (45,000 years ago), respectively. The colour key gives the probability of obtaining a <i>F<sub>ST</sub></i> value equal or greater than that observed. The white shaded area corresponds to parameter combinations for which this probability is greater than 0.05.</p>", "links"=>[], "tags"=>["Computational biology", "population genetics", "Population modeling", "ecology", "Ecological metrics", "Population growth", "Evolutionary biology", "Organismal evolution", "Human evolution", "Paleontology", "genetics", "Human genetics", "Population biology", "Population metrics", "anthropology", "Biological anthropology", "Cultural anthropology", "Paleoanthropology", "Sociology", "demography", "obtaining", "differentiation", "larger", "observed"], "article_id"=>684147, "categories"=>["Biological Sciences", "Sociology"], "users"=>["Rita Rasteiro", "Lounès Chikhi"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0060944.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Probability_of_obtaining_genetic_differentiation_F_ST_values_larger_than_those_observed_in_the_real_data_/684147", "title"=>"Probability of obtaining genetic differentiation (<i>F<sub>ST</sub></i>) values larger than those observed in the real data.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-17 01:09:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1026605", "https://ndownloader.figshare.com/files/1026606", "https://ndownloader.figshare.com/files/1026607", "https://ndownloader.figshare.com/files/1026608", "https://ndownloader.figshare.com/files/1026609", "https://ndownloader.figshare.com/files/1026610", "https://ndownloader.figshare.com/files/1026611", "https://ndownloader.figshare.com/files/1026613", "https://ndownloader.figshare.com/files/1026615", "https://ndownloader.figshare.com/files/1026616", "https://ndownloader.figshare.com/files/1026617", "https://ndownloader.figshare.com/files/1026618", "https://ndownloader.figshare.com/files/1026620", "https://ndownloader.figshare.com/files/1026621"], "description"=>"<div><p>The arrival of agriculture into Europe during the Neolithic transition brought a significant shift in human lifestyle and subsistence. However, the conditions under which the spread of the new culture and technologies occurred are still debated. Similarly, the roles played by women and men during the Neolithic transition are not well understood, probably due to the fact that mitochondrial DNA (mtDNA) and Y chromosome (NRY) data are usually studied independently rather than within the same statistical framework. Here, we applied an integrative approach, using different model-based inferential techniques, to analyse published datasets from contemporary and ancient European populations. By integrating mtDNA and NRY data into the same admixture approach, we show that both males and females underwent the same admixture history and both support the demic diffusion model of Ammerman and Cavalli-Sforza. Similarly, the patterns of genetic diversity found in extant and ancient populations demonstrate that both modern and ancient mtDNA support the demic diffusion model. They also show that population structure and differential growth between farmers and hunter-gatherers are necessary to explain both types of data. However, we also found some differences between male and female markers, suggesting that the female effective population size was larger than that of the males, probably due to different demographic histories. We argue that these differences are most probably related to the various shifts in cultural practices and lifestyles that followed the Neolithic Transition, such as sedentism, the shift from polygyny to monogamy or the increase of patrilocality.</p></div>", "links"=>[], "tags"=>["Computational biology", "population genetics", "Population modeling", "ecology", "Ecological metrics", "Population growth", "Evolutionary biology", "Organismal evolution", "Human evolution", "Paleontology", "genetics", "Human genetics", "Population biology", "Population metrics", "anthropology", "Biological anthropology", "Cultural anthropology", "Paleoanthropology", "Sociology", "demography", "perspectives", "neolithic", "clues"], "article_id"=>684148, "categories"=>["Biological Sciences", "Sociology"], "users"=>["Rita Rasteiro", "Lounès Chikhi"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0060944.s001", "https://dx.doi.org/10.1371/journal.pone.0060944.s002", "https://dx.doi.org/10.1371/journal.pone.0060944.s003", "https://dx.doi.org/10.1371/journal.pone.0060944.s004", "https://dx.doi.org/10.1371/journal.pone.0060944.s005", "https://dx.doi.org/10.1371/journal.pone.0060944.s006", "https://dx.doi.org/10.1371/journal.pone.0060944.s007", "https://dx.doi.org/10.1371/journal.pone.0060944.s008", "https://dx.doi.org/10.1371/journal.pone.0060944.s009", "https://dx.doi.org/10.1371/journal.pone.0060944.s010", "https://dx.doi.org/10.1371/journal.pone.0060944.s011", "https://dx.doi.org/10.1371/journal.pone.0060944.s012", "https://dx.doi.org/10.1371/journal.pone.0060944.s013", "https://dx.doi.org/10.1371/journal.pone.0060944.s014"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Female_and_Male_Perspectives_on_the_Neolithic_Transition_in_Europe_Clues_from_Ancient_and_Modern_Genetic_Data_/684148", "title"=>"Female and Male Perspectives on the Neolithic Transition in Europe: Clues from Ancient and Modern Genetic Data", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-04-17 01:09:08"}

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Relative Metric

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