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  • 1
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    Evolution of the African pygmy phenotype [Anthropology] (2014)
    National Academy of Sciences
    Details
    Publication Date: 2014-09-03
    Description: The evolutionary history of the human pygmy phenotype (small body size), a characteristic of African and Southeast Asian rainforest hunter-gatherers, is largely unknown. Here we use a genome-wide admixture mapping analysis to identify 16 genomic regions that are significantly associated with the pygmy phenotype in the Batwa, a rainforest hunter-gatherer...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 2
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    Ignoring Heterozygous Sites Biases Phylogenomic Estimates of Divergence Times: Implications for the Evolutionary History of Microtus Voles (2014)
    Oxford University Press
    Details
    Publication Date: 2014-03-22
    Description: Phylogenetic reconstruction of the evolutionary history of closely related organisms may be difficult because of the presence of unsorted lineages and of a relatively high proportion of heterozygous sites that are usually not handled well by phylogenetic programs. Genomic data may provide enough fixed polymorphisms to resolve phylogenetic trees, but the diploid nature of sequence data remains analytically challenging. Here, we performed a phylogenomic reconstruction of the evolutionary history of the common vole ( Microtus arvalis ) with a focus on the influence of heterozygosity on the estimation of intraspecific divergence times. We used genome-wide sequence information from 15 voles distributed across the European range. We provide a novel approach to integrate heterozygous information in existing phylogenetic programs by repeated random haplotype sampling from sequences with multiple unphased heterozygous sites. We evaluated the impact of the use of full, partial, or no heterozygous information for tree reconstructions on divergence time estimates. All results consistently showed four deep and strongly supported evolutionary lineages in the vole data. These lineages undergoing divergence processes split only at the end or after the last glacial maximum based on calibration with radiocarbon-dated paleontological material. However, the incorporation of information from heterozygous sites had a significant impact on absolute and relative branch length estimations. Ignoring heterozygous information led to an overestimation of divergence times between the evolutionary lineages of M. arvalis . We conclude that the exclusion of heterozygous sites from evolutionary analyses may cause biased and misleading divergence time estimates in closely related taxa.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    A human genome diversity cell line panel (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-04-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cann, Howard M -- de Toma, Claudia -- Cazes, Lucien -- Legrand, Marie-Fernande -- Morel, Valerie -- Piouffre, Laurence -- Bodmer, Julia -- Bodmer, Walter F -- Bonne-Tamir, Batsheva -- Cambon-Thomsen, Anne -- Chen, Zhu -- Chu, J -- Carcassi, Carlo -- Contu, Licinio -- Du, Ruofu -- Excoffier, Laurent -- Ferrara, G B -- Friedlaender, Jonathan S -- Groot, Helena -- Gurwitz, David -- Jenkins, Trefor -- Herrera, Rene J -- Huang, Xiaoyi -- Kidd, Judith -- Kidd, Kenneth K -- Langaney, Andre -- Lin, Alice A -- Mehdi, S Qasim -- Parham, Peter -- Piazza, Alberto -- Pistillo, Maria Pia -- Qian, Yaping -- Shu, Qunfang -- Xu, Jiujin -- Zhu, S -- Weber, James L -- Greely, Henry T -- Feldman, Marcus W -- Thomas, Gilles -- Dausset, Jean -- Cavalli-Sforza, L Luca -- New York, N.Y. -- Science. 2002 Apr 12;296(5566):261-2.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11954565" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Specimen Banks ; *Cell Line ; Continental Population Groups/genetics ; DNA/genetics ; Databases, Factual ; Female ; *Genetic Variation ; *Genome, Human ; Haplotypes ; Humans ; Informed Consent ; *Lymphocytes ; Male ; Polymorphism, Single Nucleotide
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    Comment on "Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens" and "Microcephalin, a gene regulating brain size, continues to evolve adaptively in humans" (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-07-15
    Description: Mekel-Bobrov et al. and Evans et al. (Reports, 9 Sept. 2005, p. 1720 and p. 1717, respectively) examined sequence data from modern humans within two gene regions associated with brain development, ASPM and microcephalin, and concluded that selection of these genes must be ongoing. We show that models of human history that include both population growth and spatial structure can generate the observed patterns without selection.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Currat, Mathias -- Excoffier, Laurent -- Maddison, Wayne -- Otto, Sarah P -- Ray, Nicolas -- Whitlock, Michael C -- Yeaman, Sam -- New York, N.Y. -- Science. 2006 Jul 14;313(5784):172; author reply 172.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16840683" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Biological ; Biological Evolution ; Brain ; Demography ; Founder Effect ; Gene Frequency ; *Haplotypes ; Humans ; Models, Theoretical ; Nerve Tissue Proteins/*genetics ; Organ Size ; Population Density ; *Population Growth ; Selection, Genetic ; *Sequence Analysis, DNA
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Deep human genealogies reveal a selective advantage to be on an expanding wave front (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-11-05
    Description: Since their origin, human populations have colonized the whole planet, but the demographic processes governing range expansions are mostly unknown. We analyzed the genealogy of more than one million individuals resulting from a range expansion in Quebec between 1686 and 1960 and reconstructed the spatial dynamics of the expansion. We find that a majority of the present Saguenay Lac-Saint-Jean population can be traced back to ancestors having lived directly on or close to the wave front. Ancestors located on the front contributed significantly more to the current gene pool than those from the range core, likely due to a 20% larger effective fertility of women on the wave front. This fitness component is heritable on the wave front and not in the core, implying that this life-history trait evolves during range expansions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Moreau, Claudia -- Bherer, Claude -- Vezina, Helene -- Jomphe, Michele -- Labuda, Damian -- Excoffier, Laurent -- New York, N.Y. -- Science. 2011 Nov 25;334(6059):1148-50. doi: 10.1126/science.1212880. Epub 2011 Nov 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre de Recherche, Hopital Sainte-Justine, Universite de Montreal, 3175 Cote Sainte-Catherine, Montreal, Quebec, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22052972" target="_blank"〉PubMed〈/a〉
    Keywords: *Demography ; Emigration and Immigration ; Family Characteristics ; Female ; Fertility ; *Gene Pool ; Genes ; *Genetic Fitness ; Humans ; Male ; Marriage ; *Pedigree ; *Population Dynamics ; Quebec ; Registries ; Reproduction ; *Selection, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    Comment on "Genetic structure of human populations" (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-06-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Excoffier, Laurent -- Hamilton, Grant -- New York, N.Y. -- Science. 2003 Jun 20;300(5627):1877; author reply 1877.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Computational and Molecular Population, Genetics LabZoological Institute, University of Bern, Batzerstrasse 63012, Bern, Switzerland. laurent.excoffier@zoo.unibe.ch〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12817127" target="_blank"〉PubMed〈/a〉
    Keywords: Africa South of the Sahara ; Alleles ; Americas ; Asia ; Europe ; *Genetic Variation ; *Genetics, Population ; Humans ; *Microsatellite Repeats ; Mutation ; Pacific Islands
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 7
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    Reconstructing Native American population history (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-07-18
    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〉
    Keywords: Americas ; Asia ; Cluster Analysis ; Emigration and Immigration/*history/statistics & numerical data ; Gene Flow ; Genetics, Population ; History, Ancient ; Humans ; Indians, North American/*genetics/*history ; Models, Genetic ; *Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Siberia
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 8
    Electronic Resource
    Electronic Resource
    HLA-DPB1 DNA POLYMORPHISM IN THE SWISS POPULATION: LINKAGE DISEQUILIBRIUM WITH OTHER HLA LOCI AND POPULATION GENETIC AFFINITIES (1994)
    Oxford, UK : Blackwell Publishing Ltd
    International journal of immunogenetics 21 (1994), S. 0 
    Details
    ISSN: 1744-313X
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: Allelic diversity at the HLA-DPB1 locus was determined by PCR-oligotyping in a sample of 125 healthy Swiss individuals. A total of 17 alleles were detected among which four main alleles (DPB 1*0401, *0201, *0301, *0402) reached a cumulative frequency of 74.8%. HLA-A and -B (by serology) and HLA-DRB1 (by oligotyping) allelic polymorphisms were analysed also. HLA-B and HLA-DRB1 loci were highly polymorphic with 25 and 28 alleles respectively and similar heterozygosity levels of 0.93 and 0.92. These two loci were found to be more polymorphic than expected under neutrality, while lower heterozygosity levels were found for HLA-A (0.87) and DPB1 (0.81) loci. This paper presents also a global comparison of DPB1 allelic frequencies among 15 populations from four continents. As opposed to the DRB1 locus, overall DPB1 is shown to have a lower level of polymorphism and may be considered as neutral in all tested populations. DPB 1 genetic diversity is correlated significantly with geography also, as found previously for DRB1. Two- and four-locus haplotype frequencies were determined and the significance of their linkage disequilibrium tested by an original non-parametric method. A significant positive linkage disequilibrium was found for 11 A-B, 16 B-DRB1, 7 DRB1-DPB1 and 3 A-B-DRB1-DPB1 haplotypes. The overall linkage disequilibrium between DRB1 and DPB1 was much lower than expected from the physical distance and lower than for A-B and B-DRB1 pairs. The implications of these results for bone marrow transplantation and for the evolution of HLA loci are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1744-313X.1994.tb00186.x
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  • 9
    Electronic Resource
    Electronic Resource
    Low levels of mitochondrial DNA variation among central and southern European Esox lucius populations (2004)
    Oxford, UK; Malden, USA : Blackwell Science Ltd
    Journal of fish biology 64 (2004), S. 0 
    Details
    ISSN: 1095-8649
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Low levels of mitochondrial DNA variation were observed among pike Esox lucius populations from major drainage systems of Europe. Populations from the Italian peninsula including southern Switzerland were genetically distinct from other samples.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.0022-1112.2004.00397.x
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  • 10
    Electronic Resource
    Electronic Resource
    Minisatellite mutational processes reduce Fst estimates (1999)
    Springer
    Human genetics 〈Berlin〉 105 (1999), S. 567-576 
    Details
    ISSN: 1432-1203
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract. We have used a new method for binning minisatellite alleles (semi-automated allele aggregation) and report the extent of population diversity detectable by eleven minisatellite loci in 2689 individuals from 19 human populations distributed widely throughout the world. Whereas population relationships are consistent with those found in other studies, our estimate of genetic differentiation (Fst) between populations is less than 8%, which is lower than comparative estimates of between 10%–15% obtained by using other sources of polymorphism data. We infer that mutational processes are involved in reducing Fst estimates from minisatellite data because, first, the lowest Fst estimates are found at loci showing autocorrelated frequencies among alleles of similar size and, second, Fst declines with heterozygosity but by more than predicted assuming simple models of mutation. These conclusions are consistent with the view that minisatellites are subject to selective or mutational constraints in addition to those expected under simple stepwise mutation models.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004399900185
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