ALBERT

Description: The peopling of the Americas has been the subject of extensive genetic, archaeological and linguistic research; however, central questions remain unresolved. One contentious issue is whether the settlement occurred by means of a single migration or multiple streams of migration from Siberia. The pattern of dispersals within the Americas is also poorly understood. To address these questions at a higher resolution than was previously possible, we assembled data from 52 Native American and 17 Siberian groups genotyped at 364,470 single nucleotide polymorphisms. Here we show that Native Americans descend from at least three streams of Asian gene flow. Most descend entirely from a single ancestral population that we call 'First American'. However, speakers of Eskimo-Aleut languages from the Arctic inherit almost half their ancestry from a second stream of Asian gene flow, and the Na-Dene-speaking Chipewyan from Canada inherit roughly one-tenth of their ancestry from a third stream. We show that the initial peopling followed a southward expansion facilitated by the coast, with sequential population splits and little gene flow after divergence, especially in South America. A major exception is in Chibchan speakers on both sides of the Panama isthmus, who have ancestry from both North and South America.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3615710/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3615710/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reich, David -- Patterson, Nick -- Campbell, Desmond -- Tandon, Arti -- Mazieres, Stephane -- Ray, Nicolas -- Parra, Maria V -- Rojas, Winston -- Duque, Constanza -- Mesa, Natalia -- Garcia, Luis F -- Triana, Omar -- Blair, Silvia -- Maestre, Amanda -- Dib, Juan C -- Bravi, Claudio M -- Bailliet, Graciela -- Corach, Daniel -- Hunemeier, Tabita -- Bortolini, Maria Catira -- Salzano, Francisco M -- Petzl-Erler, Maria Luiza -- Acuna-Alonzo, Victor -- Aguilar-Salinas, Carlos -- Canizales-Quinteros, Samuel -- Tusie-Luna, Teresa -- Riba, Laura -- Rodriguez-Cruz, Maricela -- Lopez-Alarcon, Mardia -- Coral-Vazquez, Ramon -- Canto-Cetina, Thelma -- Silva-Zolezzi, Irma -- Fernandez-Lopez, Juan Carlos -- Contreras, Alejandra V -- Jimenez-Sanchez, Gerardo -- Gomez-Vazquez, Maria Jose -- Molina, Julio -- Carracedo, Angel -- Salas, Antonio -- Gallo, Carla -- Poletti, Giovanni -- Witonsky, David B -- Alkorta-Aranburu, Gorka -- Sukernik, Rem I -- Osipova, Ludmila -- Fedorova, Sardana A -- Vasquez, Rene -- Villena, Mercedes -- Moreau, Claudia -- Barrantes, Ramiro -- Pauls, David -- Excoffier, Laurent -- Bedoya, Gabriel -- Rothhammer, Francisco -- Dugoujon, Jean-Michel -- Larrouy, Georges -- Klitz, William -- Labuda, Damian -- Kidd, Judith -- Kidd, Kenneth -- Di Rienzo, Anna -- Freimer, Nelson B -- Price, Alkes L -- Ruiz-Linares, Andres -- BB/1021213/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- GM057672/GM/NIGMS NIH HHS/ -- GM079558/GM/NIGMS NIH HHS/ -- GM079558-S1/GM/NIGMS NIH HHS/ -- HG006399/HG/NHGRI NIH HHS/ -- MH075007/MH/NIMH NIH HHS/ -- NS037484/NS/NINDS NIH HHS/ -- NS043538/NS/NINDS NIH HHS/ -- R01 GM079558/GM/NIGMS NIH HHS/ -- R01 GM100233/GM/NIGMS NIH HHS/ -- R01 HG006399/HG/NHGRI NIH HHS/ -- R21 DK073818/DK/NIDDK NIH HHS/ -- Canadian Institutes of Health Research/Canada -- England -- Nature. 2012 Aug 16;488(7411):370-4. doi: 10.1038/nature11258.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. reich@genetics.med.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22801491" target="_blank"〉PubMed〈/a〉

Description: Mexico harbors great cultural and ethnic diversity, yet fine-scale patterns of human genome-wide variation from this region remain largely uncharacterized. We studied genomic variation within Mexico from over 1000 individuals representing 20 indigenous and 11 mestizo populations. We found striking genetic stratification among indigenous populations within Mexico at varying degrees of geographic isolation. Some groups were as differentiated as Europeans are from East Asians. Pre-Columbian genetic substructure is recapitulated in the indigenous ancestry of admixed mestizo individuals across the country. Furthermore, two independently phenotyped cohorts of Mexicans and Mexican Americans showed a significant association between subcontinental ancestry and lung function. Thus, accounting for fine-scale ancestry patterns is critical for medical and population genetic studies within Mexico, in Mexican-descent populations, and likely in many other populations worldwide.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4156478/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4156478/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Moreno-Estrada, Andres -- Gignoux, Christopher R -- Fernandez-Lopez, Juan Carlos -- Zakharia, Fouad -- Sikora, Martin -- Contreras, Alejandra V -- Acuna-Alonzo, Victor -- Sandoval, Karla -- Eng, Celeste -- Romero-Hidalgo, Sandra -- Ortiz-Tello, Patricia -- Robles, Victoria -- Kenny, Eimear E -- Nuno-Arana, Ismael -- Barquera-Lozano, Rodrigo -- Macin-Perez, Gaston -- Granados-Arriola, Julio -- Huntsman, Scott -- Galanter, Joshua M -- Via, Marc -- Ford, Jean G -- Chapela, Rocio -- Rodriguez-Cintron, William -- Rodriguez-Santana, Jose R -- Romieu, Isabelle -- Sienra-Monge, Juan Jose -- del Rio Navarro, Blanca -- London, Stephanie J -- Ruiz-Linares, Andres -- Garcia-Herrera, Rodrigo -- Estrada, Karol -- Hidalgo-Miranda, Alfredo -- Jimenez-Sanchez, Gerardo -- Carnevale, Alessandra -- Soberon, Xavier -- Canizales-Quinteros, Samuel -- Rangel-Villalobos, Hector -- Silva-Zolezzi, Irma -- Burchard, Esteban Gonzalez -- Bustamante, Carlos D -- BB/I021213/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- ES015794/ES/NIEHS NIH HHS/ -- GM007546/GM/NIGMS NIH HHS/ -- GM061390/GM/NIGMS NIH HHS/ -- HL004464/HL/NHLBI NIH HHS/ -- HL078885/HL/NHLBI NIH HHS/ -- HL088133/HL/NHLBI NIH HHS/ -- HL111636/HL/NHLBI NIH HHS/ -- K23 HL004464/HL/NHLBI NIH HHS/ -- K23 HL111636/HL/NHLBI NIH HHS/ -- M01 RR000083/RR/NCRR NIH HHS/ -- P60 MD006902/MD/NIMHD NIH HHS/ -- P60MD006902/MD/NIMHD NIH HHS/ -- R01 ES015794/ES/NIEHS NIH HHS/ -- R01 GM083606/GM/NIGMS NIH HHS/ -- R01 GM090087/GM/NIGMS NIH HHS/ -- R01 HG003229/HG/NHGRI NIH HHS/ -- R01 HL078885/HL/NHLBI NIH HHS/ -- R01 HL088133/HL/NHLBI NIH HHS/ -- R01GM090087/GM/NIGMS NIH HHS/ -- R01HG003229/HG/NHGRI NIH HHS/ -- R13 MD008154/MD/NIMHD NIH HHS/ -- RR000083/RR/NCRR NIH HHS/ -- T32 GM007175/GM/NIGMS NIH HHS/ -- T32 GM007546/GM/NIGMS NIH HHS/ -- T32 HG000044/HG/NHGRI NIH HHS/ -- T32GM007175/GM/NIGMS NIH HHS/ -- T32HG000044/HG/NHGRI NIH HHS/ -- U01 GM061390/GM/NIGMS NIH HHS/ -- ZIA ES049019-14/Intramural NIH HHS/ -- ZIA ES049019-15/Intramural NIH HHS/ -- ZIA ES49019/ES/NIEHS NIH HHS/ -- New York, N.Y. -- Science. 2014 Jun 13;344(6189):1280-5. doi: 10.1126/science.1251688. Epub 2014 Jun 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. cdbustam@stanford.edu morenoe@stanford.edu esteban.burchard@ucsf.edu. ; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA. cdbustam@stanford.edu morenoe@stanford.edu esteban.burchard@ucsf.edu. ; Instituto Nacional de Medicina Genomica (INMEGEN), Mexico City, Mexico. ; Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. ; Escuela Nacional de Antropologia e Historia (ENAH), Mexico City, Mexico. Department of Genetics, Evolution and Environment, University College London, London, UK. ; Department of Medicine, University of California, San Francisco, CA, USA. ; Instituto de Investigacion en Genetica Molecular, Universidad de Guadalajara, Ocotlan, Mexico. ; Escuela Nacional de Antropologia e Historia (ENAH), Mexico City, Mexico. ; Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico City, Mexico. ; Department of Medicine, University of California, San Francisco, CA, USA. Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA. ; The Brooklyn Hospital Center, Brooklyn, NY, USA. ; Instituto Nacional de Enfermedades Respiratorias (INER), Mexico City, Mexico. ; Veterans Caribbean Health Care System, San Juan, Puerto Rico. ; Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. Instituto Nacional de Medicina Genomica (INMEGEN), Mexico City, Mexico. ; International Agency for Research on Cancer, Lyon, France. ; Hospital Infantil de Mexico Federico Gomez, Mexico City, Mexico. ; National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA. ; Department of Genetics, Evolution and Environment, University College London, London, UK. ; Instituto Nacional de Medicina Genomica (INMEGEN), Mexico City, Mexico. Facultad de Quimica, Universidad Nacional Autonoma de Mexico, Mexico City, Mexico. ; Department of Medicine, University of California, San Francisco, CA, USA. Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA. cdbustam@stanford.edu morenoe@stanford.edu esteban.burchard@ucsf.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24926019" target="_blank"〉PubMed〈/a〉

Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Acuna, V -- Datry, T -- Marshall, J -- Barcelo, D -- Dahm, C N -- Ginebreda, A -- McGregor, G -- Sabater, S -- Tockner, K -- Palmer, M A -- New York, N.Y. -- Science. 2014 Mar 7;343(6175):1080-1. doi: 10.1126/science.1246666.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Catalan Institute for Water Research, 17003 Girona, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24604183" target="_blank"〉PubMed〈/a〉

Description: The genetic diversity of 14 Japanese plum (Prunus salicina Lindl) landraces adapted to an ecosystem of alternating flooding and dry conditions was characterized using neutral simple sequence repeat (SSR) markers. Twelve SSRs located in six chromosomes of the Prunus persica reference genome resulted to be polymorphic, thus allowing identification of all the evaluated landraces. Differentiation between individuals was moderate to high (average shared allele distance (DAS) = 0.64), whereas the genetic diversity was high (average indices polymorphism information content (PIC) = 0.62, observed heterozygosity (Ho) = 0.51, unbiased expected heterozygosity (uHe) = 0.70). Clustering and genetic structure approaches grouped all individuals into two major groups that correlated with flesh color. This finding suggests that the intuitive breeding practices of growers tended to select plum trees according to specific phenotypic traits. These neutral markers were adequate for population genetic studies and cultivar identification. Furthermore, we assessed the SSR flanking genome regions (25 kb) in silico to search for candidate genes related to stress resistance or associated with other agronomic traits of interest. Interestingly, at least 26 of the 118 detected genes seem to be related to fruit quality, plant development, and stress resistance. This study suggests that the molecular characterization of specific landraces of Japanese plum that have been adapted to extreme agroecosystems is a useful approach to localize candidate genes which are potentially interesting for breeding.

Description: Motivation: In the context of studying whole metabolic networks and their interaction with the environment, the following question arises: given a set of target metabolites T and a set of possible external source metabolites , which are the minimal subsets of that are able to produce all the metabolites in T . Such subsets are called the minimal precursor sets of T . The problem is then whether we can enumerate all of them efficiently. Results: We propose a new characterization of precursor sets as the inputs of reaction sets called factories and an efficient algorithm to decide if a set of sources is precursor set of T . We show proofs of hardness for the problems of finding a precursor set of minimum size and of enumerating all minimal precursor sets T . We propose two new algorithms which, despite the hardness of the enumeration problem, allow to enumerate all minimal precursor sets in networks with up to 1000 reactions. Availability: Source code and datasets used in our benchmarks are freely available for download at http://sites.google.com/site/pitufosoftware/download . Contact: vicente77@gmail.com , pvmilreu@gmail.com or marie-france.sagot@inria.fr

Description: Motivation:  The increasing availability of metabolomics data enables to better understand the metabolic processes involved in the immediate response of an organism to environmental changes and stress. The data usually come in the form of a list of metabolites whose concentrations significantly changed under some conditions, and are thus not easy to interpret without being able to precisely visualize how such metabolites are interconnected. Results:  We present a method that enables to organize the data from any metabolomics experiment into metabolic stories. Each story corresponds to a possible scenario explaining the flow of matter between the metabolites of interest. These scenarios may then be ranked in different ways depending on which interpretation one wishes to emphasize for the causal link between two affected metabolites: enzyme activation, enzyme inhibition or domino effect on the concentration changes of substrates and products. Equally probable stories under any selected ranking scheme can be further grouped into a single anthology that summarizes, in a unique subnetwork, all equivalently plausible alternative stories. An anthology is simply a union of such stories. We detail an application of the method to the response of yeast to cadmium exposure. We use this system as a proof of concept for our method, and we show that we are able to find a story that reproduces very well the current knowledge about the yeast response to cadmium. We further show that this response is mostly based on enzyme activation. We also provide a framework for exploring the alternative pathways or side effects this local response is expected to have in the rest of the network. We discuss several interpretations for the changes we see, and we suggest hypotheses that could in principle be experimentally tested. Noticeably, our method requires simple input data and could be used in a wide variety of applications. Availability and implementation:  The code for the method presented in this article is available at http://gobbolino.gforge.inria.fr . Contact:   pvmilreu@gmail.com ; vincent.lacroix@univ-lyon1.fr ; marie-france.sagot@inria.fr Supplementary information: Supplementary data are available at Bioinformatics online.