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      Dosage analysis of the 7q11.23 Williams region identifies BAZ1B as a major human gene patterning the modern human face and underlying self-domestication

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          Abstract

          Dissecting the BAZ1B genetic circuitry in the neural crest brings out its critical role in shaping the modern human face.

          Abstract

          We undertook a functional dissection of chromatin remodeler BAZ1B in neural crest (NC) stem cells (NCSCs) from a uniquely informative cohort of typical and atypical patients harboring 7q11.23 copy number variants. Our results reveal a key contribution of BAZ1B to NCSC in vitro induction and migration, coupled with a crucial involvement in NC-specific transcriptional circuits and distal regulation. By intersecting our experimental data with new paleogenetic analyses comparing modern and archaic humans, we found a modern-specific enrichment for regulatory changes both in BAZ1B and its experimentally defined downstream targets, thereby providing the first empirical validation of the human self-domestication hypothesis and positioning BAZ1B as a master regulator of the modern human face. In so doing, we provide experimental evidence that the craniofacial and cognitive/behavioral phenotypes caused by alterations of the Williams-Beuren syndrome critical region can serve as a powerful entry point into the evolution of the modern human face and prosociality.

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          The complete genome sequence of a Neandertal from the Altai Mountains

          We present a high-quality genome sequence of a Neandertal woman from Siberia. We show that her parents were related at the level of half siblings and that mating among close relatives was common among her recent ancestors. We also sequenced the genome of a Neandertal from the Caucasus to low coverage. An analysis of the relationships and population history of available archaic genomes and 25 present-day human genomes shows that several gene flow events occurred among Neandertals, Denisovans and early modern humans, possibly including gene flow into Denisovans from an unknown archaic group. Thus, interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene. In addition, the high quality Neandertal genome allows us to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neandertals and Denisovans.
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            A high-coverage genome sequence from an archaic Denisovan individual.

            We present a DNA library preparation method that has allowed us to reconstruct a high-coverage (30×) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation of Denisovan heterozygosity indicating that genetic diversity in these archaic hominins was extremely low. It also allows tentative dating of the specimen on the basis of "missing evolution" in its genome, detailed measurements of Denisovan and Neandertal admixture into present-day human populations, and the generation of a near-complete catalog of genetic changes that swept to high frequency in modern humans since their divergence from Denisovans.
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              A high-coverage Neandertal genome from Vindija Cave in Croatia

              To date the only Neandertal genome that has been sequenced to high quality is from an individual found in Southern Siberia. We sequenced the genome of a female Neandertal from ~50 thousand years ago from Vindija Cave, Croatia to ~30-fold genomic coverage. She carried 1.6 differences per ten thousand base pairs between the two copies of her genome, fewer than present-day humans, suggesting that Neandertal populations were of small size. Our analyses indicate that she was more closely related to the Neandertals that mixed with the ancestors of present-day humans living outside of sub-Saharan Africa than the previously sequenced Neandertal from Siberia, allowing 10-20% more Neandertal DNA to be identified in present-day humans, including variants involved in LDL cholesterol levels, schizophrenia and other diseases.
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                Author and article information

                Journal
                Sci Adv
                Sci Adv
                SciAdv
                advances
                Science Advances
                American Association for the Advancement of Science
                2375-2548
                December 2019
                04 December 2019
                : 5
                : 12
                : eaaw7908
                Affiliations
                [1 ]Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy.
                [2 ]Laboratory of Stem Cell Epigenetics, IEO, European Institute of Oncology, IRCCS, Milan, Italy.
                [3 ]University of Barcelona, Barcelona, Spain.
                [4 ]University of Barcelona Institute of Complex Systems (UBICS), Barcelona, Spain.
                [5 ]Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
                [6 ]Institute of Human Genetics, University Hospital Cologne, Cologne, Germany.
                [7 ]Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany.
                [8 ]Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy.
                [9 ]D-HEST Institute for Neuroscience, ETH Zürich, Switzerland.
                [10 ]Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Germany.
                [11 ]Institute of Biomedicine and Biotechnology of Cantabria, University of Cantabria, Cantabria, Spain.
                [12 ]Catalan Institute for Advanced Studies and Research (ICREA), Barcelona, Spain.
                [13 ]Human Technopole, Center for Neurogenomics, Via Cristina Belgioioso 171, Milan, Italy.
                Author notes
                [*]

                These authors contributed equally to this work.

                [†]

                Present address: Evotec SE, Hamburg, Germany.

                Author information
                http://orcid.org/0000-0002-1614-4370
                http://orcid.org/0000-0002-1462-8064
                http://orcid.org/0000-0003-2590-5650
                http://orcid.org/0000-0003-0987-7856
                http://orcid.org/0000-0002-4105-7164
                http://orcid.org/0000-0003-2231-8450
                http://orcid.org/0000-0001-7261-3162
                http://orcid.org/0000-0002-3142-6747
                http://orcid.org/0000-0003-3418-4218
                http://orcid.org/0000-0001-7478-2509
                http://orcid.org/0000-0001-5078-928X
                http://orcid.org/0000-0001-8882-9718
                http://orcid.org/0000-0002-9104-0918
                Article
                aaw7908
                10.1126/sciadv.aaw7908
                6892627
                31840056
                4e764557-c356-404c-b5b3-f6b87bcd55a8
                Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).

                This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.

                History
                : 24 January 2019
                : 26 September 2019
                Funding
                Funded by: doi http://dx.doi.org/10.13039/100009647, Ministry of Health;
                Funded by: doi http://dx.doi.org/10.13039/501100000781, European Research Council;
                Award ID: 616441-DISEASEAVATARS
                Funded by: doi http://dx.doi.org/10.13039/501100002426, Fondazione Telethon;
                Award ID: GGP14265
                Funded by: doi http://dx.doi.org/10.13039/501100002809, Generalitat de Catalunya;
                Award ID: 2017-SGR-341
                Funded by: doi http://dx.doi.org/10.13039/501100004710, Fondazione Umberto Veronesi;
                Funded by: doi http://dx.doi.org/10.13039/501100004895, European Social Fund;
                Award ID: BES-2017-080366
                Funded by: Spanish Ministry of Economy and Competitiveness;
                Award ID: FFI2016-78034-C2-1-P
                Funded by: MEXT/JSPS Grant-in-Aid for Scientific Research on Innovative Areas 4903;
                Award ID: JP17H06379
                Funded by: Marie Curie International Reintegration Grant from the European Union;
                Award ID: PIRG-GA-2009-256413
                Funded by: EPIGEN Flagship Project of the Italian National Research Council;
                Funded by: doi http://dx.doi.org/10.13039/501100007601, Horizon 2020;
                Funded by: Ricerca Corrente granted by the Italian Ministry of Health;
                Funded by: IEO Foundation;
                Funded by: Portuguese Foundation for Science and Technology;
                Award ID: SFRH/BD/131640/2017
                Categories
                Research Article
                Research Articles
                SciAdv r-articles
                Evolutionary Biology
                Evolutionary Biology
                Custom metadata
                Monica Bilog

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