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1.
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26 p, 17.4 MB |
High-depth African genomes inform human migration and health
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Choudhury, Ananyo (University of the Witwatersrand) ;
Aron, S. (University of the Witwatersrand) ;
Botigué, Laura (Centre de Recerca en Agrigenòmica) ;
Sengupta, D. (University of the Witwatersrand) ;
Botha, G. (University of Cape Town) ;
Bensellak, T. (Abdelmalek Essaadi University) ;
Wells, G. (University of the Western Cape) ;
Kumuthini, J. (University of the Western Cape) ;
Shriner, Daniel (National Institutes of Health (USA)) ;
Fakim, Y. J. (University of Mauritius) ;
Ghoorah, A. W. (University of Mauritius) ;
Dareng, E. (Institute of Human Virology Nigeria) ;
Odia, T. (Covenant University) ;
Falola, O. (Covenant University) ;
Adebiyi, E. (Covenant University) ;
Hazelhurst, S. (University of the Witwatersrand) ;
Mazandu, G. (University of Cape Town) ;
Nyangiri, O. A. (Makerere University) ;
Mbiyavanga, M. (University of Cape Town) ;
Benkahla, A. (Institute Pasteur of Tunis) ;
Kassim, S. K. (Ain Shams University (El Caire, Egipte)) ;
Mulder, N. (University of Cape Town) ;
Adebamowo, S. N. (University of Maryland Baltimore) ;
Chimusa, E. R. (University of Cape Town) ;
Muzny, D. (Baylor College of Medicine) ;
Metcalf, G. (Baylor College of Medicine) ;
Gibbs, R. A. (Baylor College of Medicine) ;
Rotimi, C. (National Institutes of Health (USA)) ;
Ramsay, M. (University of the Witwatersrand) ;
Adeyemo, Adebowale A (National Institutes of Health (USA)) ;
Lombard, Z. (University of the Witwatersrand) ;
Hanchard, N. A. (Baylor College of Medicine) ;
TrypanoGEN Research Group ;
H3Africa Consortium
The African continent is regarded as the cradle of modern humans and African genomes contain more genetic variation than those from any other continent, yet only a fraction of the genetic diversity among African individuals has been surveyed. [...]
2020 -  10.1038/s41586-020-2859-7
Nature, Vol. 586 (October 2020) , p. 741-748
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2.
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15 p, 4.1 MB |
Donkey genomes provide new insights into domestication and selection for coat color
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Wang, Changfa (Liaocheng University. Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding) ;
Li, Haijing (National Engineering Research Center for Gelatin-based Traditional Chinese Medicine) ;
Guo, Yu (BGI-Shenzhen) ;
Huang, Jinming (Shandong Academy of Agricultural Sciences. Dairy Cattle Research Center) ;
Sun, Yan (Shandong Academy of Agricultural Sciences. Dairy Cattle Research Center) ;
Min, Jiumeng (BGI-Shenzhen) ;
Wang, Jinpeng (Shandong Academy of Agricultural Sciences. Dairy Cattle Research Center) ;
Fang, Xiaodong (BGI-Shenzhen) ;
Zhao, Zicheng (City University of Hong Kong. Department of Computer Science) ;
Wang, Shuai (City University of Hong Kong. Department of Computer Science) ;
Zhang, Yanlin (City University of Hong Kong. Department of Computer Science) ;
Liu, Qingfeng (BGI-Shenzhen) ;
Jiang, Qiang (Shandong Academy of Agricultural Sciences. Dairy Cattle Research Center) ;
Wang, Xiuge (Shandong Academy of Agricultural Sciences. Dairy Cattle Research Center) ;
Guo, Yijun (BGI-Shenzhen) ;
Yang, Chunhong (Shandong Academy of Agricultural Sciences. Dairy Cattle Research Center) ;
Wang, Yinchao (National Engineering Research Center for Gelatin-based Traditional Chinese Medicine) ;
Tian, Fang (National Engineering Research Center for Gelatin-based Traditional Chinese Medicine) ;
Zhuang, Guilong (Shandong Academy of Agricultural Sciences. Dairy Cattle Research Center) ;
Fan, Yanna (Shandong Academy of Agricultural Sciences. Dairy Cattle Research Center) ;
Gao, Qican (Shandong Academy of Agricultural Sciences. Dairy Cattle Research Center) ;
Li, Yuhua (Liaocheng University. Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding) ;
Ju, Zhihua (Shandong Academy of Agricultural Sciences. Dairy Cattle Research Center) ;
Li, Jianbin (Shandong Academy of Agricultural Sciences. Dairy Cattle Research Center) ;
Li, Rongling (Shandong Academy of Agricultural Sciences. Dairy Cattle Research Center) ;
Hou, Minghai (Shandong Academy of Agricultural Sciences. Dairy Cattle Research Center) ;
Yang, Guiwen (Shandong Normal University. College of Life Science) ;
Liu, Guiqin (Liaocheng University. Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding) ;
Liu, Wenqiang (Liaocheng University Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding.) ;
Guo, Jiao (BGI-Shenzhen) ;
Pan, Shanshan (BGI-Shenzhen) ;
Fan, Guangyi (BGI-Shenzhen) ;
Zhang, Wei (Shandong Academy of Agricultural Sciences. Dairy Cattle Research Center) ;
Zhang, Ruitao (Liaocheng University. Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding) ;
Yu, Jie (National Engineering Research Center for Gelatin-based Traditional Chinese Medicine) ;
Zhang, Xinhao (National Engineering Research Center for Gelatin-based Traditional Chinese Medicine) ;
Yin, Qi (BGI-Shenzhen) ;
Ji, Chuanliang (National Engineering Research Center for Gelatin-based Traditional Chinese Medicine) ;
Jin, Yuanchun (BGI-Shenzhen) ;
Yue, Guidong (BGI-Shenzhen) ;
Liu, Mei (Nanjing Normal University. Jiangsu Key Laboratory for Molecular and Medical Biotechnology) ;
Xu, Jiake (The University of Western Australia . School of Biomedical Sciences) ;
Liu, Shimin (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments) ;
Jordana i Vidal, Jordi (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments) ;
Noce, Antonia (Centre de Recerca en Agrigenòmica) ;
Amills i Eras, Marcel (Centre de Recerca en Agrigenòmica) ;
Wu, Dong-Dong (Chinese Academy of Sciences. Center for Excellence in Animal Evolution and Genetics) ;
Li, Shuaicheng (City University of Hong Kong. Department of Computer Science) ;
Zhou, Xiangshan (East China University of Science and Technology. State Key Laboratory of Bioreactor Engineering) ;
Zhong, Jifeng (Jiangsu Academy of Agricultural Sciences. Institute of Animal Science)
Current knowledge about the evolutionary history of donkeys is still incomplete due to the lack of archeological and whole-genome diversity data. To fill this gap, we have de novo assembled a chromosome-level reference genome of one male Dezhou donkey and analyzed the genomes of 126 domestic donkeys and seven wild asses. [...]
2020 - 10.1038/s41467-020-19813-7
Nature communications, Vol. 11 (December 2020) , art. 6014
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3.
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6 p, 700.6 KB |
IMKT : the integrative McDonald and Kreitman test
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Murga-Moreno, Jesus (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Coronado-Zamora, Marta (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Hervás Fernández, Sergi (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Casillas Viladerrams, Sònia (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Barbadilla Prados, Antonio (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia)
The McDonald and Kreitman test (MKT) is one of the most powerful and widely used methods to detect and quantify recurrent natural selection using DNA sequence data. Here we present iMKT (acronym for integrative McDonald and Kreitman test), a novel web-based service performing four distinct MKT types. [...]
2019 - 10.1093/nar/gkz372
Nucleic acids research, Vol. 47, issue W1 (Jan. 2019) , p. W283-W288
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4.
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10 p, 3.7 MB |
PopHumanScan : the online catalog of human genome adaptation
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Murga-Moreno, Jesus (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Coronado-Zamora, Marta (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Bodelon de Frutos, Alejandra (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Barbadilla Prados, Antonio (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia) ;
Casillas Viladerrams, Sònia (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Since the migrations that led humans to colonize Earth, our species has faced frequent adaptive challenges that have left signatures in the landscape of genetic variation and that we can identify in our today-s genomes. [...]
2019 - 10.1093/nar/gky959
Nucleic acids research, Vol. 47, issue D1 (Jan 2019) , p. D1080-D1089
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5.
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14 p, 2.2 MB |
Adaptive responses of animals to climate change are most likely insufficient
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Radchuk, V. (Leibniz Institute for Zoo and Wildlife Research) ;
Reed, T. (University College Cork. School of Biological. Earth and Environmental Sciences) ;
Teplitsky, C. (Université de Montpellier) ;
van de Pol, M. (Netherlands Institute of Ecology. Department of Animal Ecology) ;
Charmantier, A. (Université de Montpellier) ;
Hassall, C. (University of Leeds. School of Biology. Faculty of Biological Sciences) ;
Adamík, P. (Palacký University. Department of Zoology) ;
Adriaensen, F. (University of Antwerp. Evolutionary Ecology Group) ;
Ahola, M. P. (Swedish Museum of Natural History) ;
Arcese, P. (Department of Forest and Conservation Sciences) ;
Miguel Avilés, J. (Experimental Station of Arid Zones (EEZA-CSIC). Department of Functional and Evolutionary Ecology.) ;
Balbontin, J. (Universidad de Sevilla) ;
Berg, K. S. (University of Texas Rio Grande Valley. Department of Biological Sciences.) ;
Borras, Antoni (Museu de Ciències Naturals de Barcelona) ;
Burthe, S. (Centre for Ecology and Hydrology. Bush Estate) ;
Clobert, J. (University Paul Sabatier) ;
Dehnhard, N. (University of Antwerp. Behavioural Ecology and Ecophysiology Group) ;
de Lope, F. (Universidad de Extremadura) ;
Dhondt, A. A. (Cornell University) ;
Dingemanse, N. J. (Ludwig-Maximilians University of Munich. Department of Biology) ;
Doi, H. (University of Hyogo. Graduate School of Simulation Studies) ;
Eeva, T. (University of Turku. Department of Biology) ;
Fickel, J. (Potsdam University. Institute for Biochemistry and Biology) ;
Filella, Iolanda (Centre de Recerca Ecològica i d'Aplicacions Forestals) ;
Fossøy, F. (Norwegian University of Science and Technology) ;
Goodenough, A. E. (University of Gloucestershire. School of Natural and Social Sciences) ;
Hall, Stephen (Estonian University of Life Sciences) ;
Hansson, B. (Lund University. Department of Biology) ;
Harris, M. (Centre for Ecology and Hydrology. Bush Estate) ;
Hasselquist, D. (Lund University. Department of Biology) ;
Hickler, Thomas (Senckenberg Biodiversity and Climate Research Center (BiK-F)) ;
Joshi, J. (Institute for Landscape and Open Space.) ;
Kharouba, H. (University of Ottawa. Department of Biology) ;
Martínez, J. G. (Universidad de Granada. Departamento de Zoología) ;
Mihoub, J. B. (Sorbonne Université. Muséum National d'Histoire Naturelle) ;
Mills, J. A. (3 Miromiro Drive) ;
Molina-Morales, M. (Universidad de Extremadura) ;
Moksnes, A. (Centre de Recerca Ecològica i d'Aplicacions Forestals) ;
Ozgul, A. (University of Zurich. Department of Evolutionary Biology and Environmental Studies) ;
Parejo, D. (Universidad of Extremadura) ;
Pilard, P. (LPO Mission Rapaces) ;
Poisbleau, M. (University of Antwerp. Behavioural Ecology and Ecophysiology Group) ;
Rousset, F. (Université de Montpellier) ;
Rödel, M. O. (Leibniz Institute for Evolution and Biodiversity Science) ;
Scott, D. (University of Georgia. Savannah River Ecology Laboratory) ;
Senar, Joan Carles (Museu de Ciències Naturals de Barcelona) ;
Stefanescu, C. (Natural History Museum of Granollers) ;
Stokke, B. G. (Norwegian Institute for Nature Research) ;
Kusano, T. (Tokyo Metropolitan University. Department of Biological Sciences.) ;
Tarka, M. (Lund University. Department of Biology) ;
Tarwater, C. E. (University of Wyoming. Department of Zoology and Physiology) ;
Thonicke, Kirsten (Potsdam Institute for Climate Impact Research (PIK)) ;
Thorley, J. (University of Cambridge. Department of Zoology) ;
Wilting, Andreas (Leibniz Institute for Zoo and Wildlife Research (IZW)) ;
Tryjanowski, P. (Poznan University of Life Sciences. Institute of Zoology) ;
Merilä, J. (University of Helsinki. Ecological Genetics Research Unit) ;
Sheldon, B. C. (University of Oxford. Edward Grey Institute) ;
Pape Møller, A. (Université Paris-Sud. Ecologie Systématique Evolution) ;
Matthysen, Erik (University of Antwerp. Evolutionary Ecology Group) ;
Janzen, F. (Iowa State University) ;
Dobson, F. S. (Auburn University. Department of Biological Sciences) ;
Visser, M. E. (Netherlands Institute of Ecology. Department of Animal Ecology) ;
Beissinger, S. R. (University of California. Department of Environmental Science. Policy and Management and Museum of Vertebrate Zoology) ;
Courtiol, A. (Leibniz Institute for Zoo and Wildlife Research) ;
Kramer-Schadt, S. (Technische Universität Berlin. Department of Ecology)
Biological responses to climate change have been widely documented across taxa and regions, but it remains unclear whether species are maintaining a good match between phenotype and environment, i. e. [...]
2019 - 10.1038/s41467-019-10924-4
Nature communications, Vol. 10 Núm. 1 (january 2019) , p. 3109
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6.
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13 p, 3.5 MB |
Unprecedented reorganization of holocentric chromosomes provides insights into the enigma of lepidopteran chromosome evolution
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Hill, Jason (Uppsala University. Department of Medical Biochemistry and Microbiology) ;
Rastas, Pasi (University of Helsinki. Institute of Biotechnology) ;
Hornett, Emily A. (Liverpool School of Tropical Medicine. Department of Vector Biology) ;
Neethiraj, Ramprasad (Stockholm University. Department of Zoology. Population Genetics) ;
Clark, Nathan (University of Pittsburgh. Department of Computational and Systems Biology) ;
Morehouse, Nathan (University of Cincinnati. Department of Biological Sciences) ;
de la Paz Celorio-Mancera, Maria (Stockholm University. Department of Zoology. Population Genetics) ;
Carnicer i Cols, Jofre (Centre de Recerca Ecològica i d'Aplicacions Forestals) ;
Dircksen, Heinrich (Stockholm University. Department of Zoology. Functional Morphology) ;
Meslin, Camille (INRA. Institute of Ecology and Environmental Sciences of Paris. Department of Sensory Ecology) ;
Keehnen, Naomi (Stockholm University. Department of Zoology. Population Genetics) ;
Pruisscher, Peter (Stockholm University. Department of Zoology. Population Genetics) ;
Sikkink, Kristin (University of Mississippi. Department of Biology) ;
Vives Ingla, Maria (Centre de Recerca Ecològica i d'Aplicacions Forestals) ;
Vogel, Heiko (Max Planck Institute for Chemical Ecology. Department of Entomology) ;
Wiklund, Christer (Stockholm University. Department of Zoology. Population Genetics) ;
Woronik, Alyssa (New York University. Department of Biology. Center for Developmental Genetics) ;
Boggs, Carol L. (University of South Carolina. Department of Biological Sciences) ;
Nylin, Sören (Stockholm University. Department of Zoology. Population Genetics) ;
Wheat, Christopher W. (Stockholm University. Department of Zoology. Population Genetics)
Chromosome evolution presents an enigma in the mega-diverse Lepidoptera. Most species exhibit constrained chromosome evolution with nearly identical haploid chromosome counts and chromosome-level gene collinearity among species more than 140 million years divergent. [...]
2019 - 10.1126/sciadv.aau3648
Science advances, Vol. 5, Núm. 6 (Jun 2019) , p. eaau3648
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7.
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10 p, 860.4 KB |
Population structure of eleven Spanish ovine breeds and detection of selective sweeps with BayeScan and hapFLK
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Manunza, Arianna (Centre de Recerca en Agrigenòmica) ;
Cardoso, Tainã Figueiredo (Centre de Recerca en Agrigenòmica) ;
Noce, Antonia (Centre de Recerca en Agrigenòmica) ;
Martinez, Amparo (Universidad de Córdoba. Departamento de Genética) ;
Pons Barro, Agueda (Servei de Millora Agrària i Pesquera (SEMILLA)) ;
Bermejo Asensio, Luis Alberto (Universidad de La Laguna) ;
Landi, Vincenzo (Universidad de Córdoba. Departamento de Genética) ;
Sánchez Bonastre, Armando (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments) ;
Jordana i Vidal, Jordi (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments) ;
Delgado Bermejo, Juan Vicente (Universidad de Córdoba. Departamento de Genética) ;
Adán Belmonte, Silvia (Federación de Razas Autóctonas de Galicia (BOAGA)) ;
Capote, Juan (Instituto Canario de Investigaciones Agrarias) ;
Vidal i Fàbrega, Oriol (Universitat de Girona. Departament de Biologia) ;
Ugarte Sagastizabal, Eva (Neiker-Tecnalia) ;
Arranz Santos, Juan José (Universidad de León. Departamento de Producción Animal) ;
Calvo Lacosta, Jorge Hugo (Centro de Investigación y Tecnología Agroalimentaria de Aragón) ;
Casellas Vidal, Joaquim (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments) ;
Amills i Eras, Marcel (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments)
The goals of the current work were to analyse the population structure of 11 Spanish ovine breeds and to detect genomic regions that may have been targeted by selection. A total of 141 individuals were genotyped with the Infinium 50 K Ovine SNP BeadChip (Illumina). [...]
2016 - 10.1038/srep27296
Scientific reports, Vol. 6 (June 2016) , art. 27296
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