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  • 1
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    Genes mirror geography within Europe (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-09-02
    Description: Understanding the genetic structure of human populations is of fundamental interest to medical, forensic and anthropological sciences. Advances in high-throughput genotyping technology have markedly improved our understanding of global patterns of human genetic variation and suggest the potential to use large samples to uncover variation among closely spaced populations. Here we characterize genetic variation in a sample of 3,000 European individuals genotyped at over half a million variable DNA sites in the human genome. Despite low average levels of genetic differentiation among Europeans, we find a close correspondence between genetic and geographic distances; indeed, a geographical map of Europe arises naturally as an efficient two-dimensional summary of genetic variation in Europeans. The results emphasize that when mapping the genetic basis of a disease phenotype, spurious associations can arise if genetic structure is not properly accounted for. In addition, the results are relevant to the prospects of genetic ancestry testing; an individual's DNA can be used to infer their geographic origin with surprising accuracy-often to within a few hundred kilometres.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2735096/" 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/PMC2735096/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Novembre, John -- Johnson, Toby -- Bryc, Katarzyna -- Kutalik, Zoltan -- Boyko, Adam R -- Auton, Adam -- Indap, Amit -- King, Karen S -- Bergmann, Sven -- Nelson, Matthew R -- Stephens, Matthew -- Bustamante, Carlos D -- R01 GM083606/GM/NIGMS NIH HHS/ -- R01 GM083606-01/GM/NIGMS NIH HHS/ -- R01 GM083606-02/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Nov 6;456(7218):98-101. doi: 10.1038/nature07331. Epub 2008 Aug 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, Interdepartmental Program in Bioinformatics, University of California-Los Angeles, Los Angeles, California 90095, USA. jnovembre@ucla.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18758442" target="_blank"〉PubMed〈/a〉
    Keywords: Emigration and Immigration ; Europe/ethnology ; Genetic Variation/*genetics ; *Genetics, Population ; Genome, Human/genetics ; Genome-Wide Association Study ; Genotype ; *Geography ; Humans ; Phylogeny ; Polymorphism, Single Nucleotide ; Principal Component Analysis ; Quantitative Trait, Heritable ; Sample Size
    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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  • 2
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    Proportionally more deleterious genetic variation in European than in African populations (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-02-22
    Description: Quantifying the number of deleterious mutations per diploid human genome is of crucial concern to both evolutionary and medical geneticists. Here we combine genome-wide polymorphism data from PCR-based exon resequencing, comparative genomic data across mammalian species, and protein structure predictions to estimate the number of functionally consequential single-nucleotide polymorphisms (SNPs) carried by each of 15 African American (AA) and 20 European American (EA) individuals. We find that AAs show significantly higher levels of nucleotide heterozygosity than do EAs for all categories of functional SNPs considered, including synonymous, non-synonymous, predicted 'benign', predicted 'possibly damaging' and predicted 'probably damaging' SNPs. This result is wholly consistent with previous work showing higher overall levels of nucleotide variation in African populations than in Europeans. EA individuals, in contrast, have significantly more genotypes homozygous for the derived allele at synonymous and non-synonymous SNPs and for the damaging allele at 'probably damaging' SNPs than AAs do. For SNPs segregating only in one population or the other, the proportion of non-synonymous SNPs is significantly higher in the EA sample (55.4%) than in the AA sample (47.0%; P 〈 2.3 x 10(-37)). We observe a similar proportional excess of SNPs that are inferred to be 'probably damaging' (15.9% in EA; 12.1% in AA; P 〈 3.3 x 10(-11)). Using extensive simulations, we show that this excess proportion of segregating damaging alleles in Europeans is probably a consequence of a bottleneck that Europeans experienced at about the time of the migration out of Africa.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2923434/" 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/PMC2923434/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lohmueller, Kirk E -- Indap, Amit R -- Schmidt, Steffen -- Boyko, Adam R -- Hernandez, Ryan D -- Hubisz, Melissa J -- Sninsky, John J -- White, Thomas J -- Sunyaev, Shamil R -- Nielsen, Rasmus -- Clark, Andrew G -- Bustamante, Carlos D -- P50 GM065509/GM/NIGMS NIH HHS/ -- P50 GM065509-070006/GM/NIGMS NIH HHS/ -- R01 HG003229/HG/NHGRI NIH HHS/ -- R01 HG003229-03/HG/NHGRI NIH HHS/ -- R01 HL072904/HL/NHLBI NIH HHS/ -- England -- Nature. 2008 Feb 21;451(7181):994-7. doi: 10.1038/nature06611.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18288194" target="_blank"〉PubMed〈/a〉
    Keywords: Africa/ethnology ; Alleles ; Computational Biology ; Emigration and Immigration ; Europe/ethnology ; Exons/genetics ; Genome, Human/*genetics ; Heterozygote ; Homozygote ; Humans ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide/*genetics ; United States
    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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  • 3
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    Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-03-20
    Description: Advances in genome technology have facilitated a new understanding of the historical and genetic processes crucial to rapid phenotypic evolution under domestication. To understand the process of dog diversification better, we conducted an extensive genome-wide survey of more than 48,000 single nucleotide polymorphisms in dogs and their wild progenitor, the grey wolf. Here we show that dog breeds share a higher proportion of multi-locus haplotypes unique to grey wolves from the Middle East, indicating that they are a dominant source of genetic diversity for dogs rather than wolves from east Asia, as suggested by mitochondrial DNA sequence data. Furthermore, we find a surprising correspondence between genetic and phenotypic/functional breed groupings but there are exceptions that suggest phenotypic diversification depended in part on the repeated crossing of individuals with novel phenotypes. Our results show that Middle Eastern wolves were a critical source of genome diversity, although interbreeding with local wolf populations clearly occurred elsewhere in the early history of specific lineages. More recently, the evolution of modern dog breeds seems to have been an iterative process that drew on a limited genetic toolkit to create remarkable phenotypic diversity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3494089/" 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/PMC3494089/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vonholdt, Bridgett M -- Pollinger, John P -- Lohmueller, Kirk E -- Han, Eunjung -- Parker, Heidi G -- Quignon, Pascale -- Degenhardt, Jeremiah D -- Boyko, Adam R -- Earl, Dent A -- Auton, Adam -- Reynolds, Andy -- Bryc, Kasia -- Brisbin, Abra -- Knowles, James C -- Mosher, Dana S -- Spady, Tyrone C -- Elkahloun, Abdel -- Geffen, Eli -- Pilot, Malgorzata -- Jedrzejewski, Wlodzimierz -- Greco, Claudia -- Randi, Ettore -- Bannasch, Danika -- Wilton, Alan -- Shearman, Jeremy -- Musiani, Marco -- Cargill, Michelle -- Jones, Paul G -- Qian, Zuwei -- Huang, Wei -- Ding, Zhao-Li -- Zhang, Ya-Ping -- Bustamante, Carlos D -- Ostrander, Elaine A -- Novembre, John -- Wayne, Robert K -- R01 GM083606/GM/NIGMS NIH HHS/ -- R01 GM083606-03/GM/NIGMS NIH HHS/ -- ZIC HG200365-01/Intramural NIH HHS/ -- ZIC HG200365-02/Intramural NIH HHS/ -- ZIC HG200365-03/Intramural NIH HHS/ -- England -- Nature. 2010 Apr 8;464(7290):898-902. doi: 10.1038/nature08837. Epub 2010 Mar 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, 621 Charles E. Young Drive South, University of California, Los Angeles, California 90095, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20237475" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Domestic/classification/*genetics ; Animals, Wild/classification/genetics ; Breeding ; Computational Biology ; Dogs/classification/*genetics ; Evolution, Molecular ; Far East/ethnology ; Genome/*genetics ; Haplotypes/*genetics ; Middle East/ethnology ; Phenotype ; Phylogeny ; Polymorphism, Single Nucleotide/*genetics ; Wolves/classification/genetics
    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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  • 4
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    Reply to Wang et al: Central Asian origin of dogs [Biological Sciences] (2016)
    National Academy of Sciences
    Details
    Publication Date: 2016-05-12
    Description: We welcome the additional data and analyses of Wang et al. (1), but believe there are some misunderstandings regarding the methods and findings of Shannon et al. (2). First, although we merged Nepal and Mongolia when plotting linkage disequilibrium (LD) decay in figure 5B of ref. 2 for legibility, we...
    Keywords: Letters
    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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  • 5
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    Reply to Ge and Sang: A single origin of domesticated rice (2011)
    National Academy of Sciences
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    Publication Date: 2011-09-07
    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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  • 6
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    Molecular evidence for a single evolutionary origin of domesticated rice (2011)
    National Academy of Sciences
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    Publication Date: 2011-05-02
    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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  • 7
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    Genetic structure and domestication history of the grape [Agricultural Sciences] (2011)
    National Academy of Sciences
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    Publication Date: 2011-03-02
    Description: The grape is one of the earliest domesticated fruit crops and, since antiquity, it has been widely cultivated and prized for its fruit and wine. Here, we characterize genome-wide patterns of genetic variation in over 1,000 samples of the domesticated grape, Vitis vinifera subsp. vinifera, and its wild relative, V. vinifera subsp. sylvestris from the US Department of Agriculture grape germplasm collection. We find support for a Near East origin of vinifera and present evidence of introgression from local sylvestris as the grape moved into Europe. High levels of genetic diversity and rapid linkage disequilibrium (LD) decay have been maintained in vinifera, which is consistent with a weak domestication bottleneck followed by thousands of years of widespread vegetative propagation. The considerable genetic diversity within vinifera, however, is contained within a complex network of close pedigree relationships that has been generated by crosses among elite cultivars. We show that first-degree relationships are rare between wine and table grapes and among grapes from geographically distant regions. Our results suggest that although substantial genetic diversity has been maintained in the grape subsequent to domestication, there has been a limited exploration of this diversity. We propose that the adoption of vegetative propagation was a double-edged sword: Although it provided a benefit by ensuring true breeding cultivars, it also discouraged the generation of unique cultivars through crosses. The grape currently faces severe pathogen pressures, and the long-term sustainability of the grape and wine industries will rely on the exploitation of the grape's tremendous natural genetic diversity.
    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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  • 8
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    Molecular evidence for a single evolutionary origin of domesticated rice [Evolution] (2011)
    National Academy of Sciences
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    Publication Date: 2011-05-18
    Description: Asian rice, Oryza sativa, is one of world's oldest and most important crop species. Rice is believed to have been domesticated ∼9,000 y ago, although debate on its origin remains contentious. A single-origin model suggests that two main subspecies of Asian rice, indica and japonica, were domesticated from the wild rice O. rufipogon. In contrast, the multiple independent domestication model proposes that these two major rice types were domesticated separately and in different parts of the species range of wild rice. This latter view has gained much support from the observation of strong genetic differentiation between indica and japonica as well as several phylogenetic studies of rice domestication. We reexamine the evolutionary history of domesticated rice by resequencing 630 gene fragments on chromosomes 8, 10, and 12 from a diverse set of wild and domesticated rice accessions. Using patterns of SNPs, we identify 20 putative selective sweeps on these chromosomes in cultivated rice. Demographic modeling based on these SNP data and a diffusion-based approach provide the strongest support for a single domestication origin of rice. Bayesian phylogenetic analyses implementing the multispecies coalescent and using previously published phylogenetic sequence datasets also point to a single origin of Asian domesticated rice. Finally, we date the origin of domestication at ∼8,200–13,500 y ago, depending on the molecular clock estimate that is used, which is consistent with known archaeological data that suggests rice was first cultivated at around this time in the Yangtze Valley of China.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 9
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    Reply to Ge and Sang: A single origin of domesticated rice [Letters (Online Only)] (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-09-28
    Description: In a recent study using two different methods of analysis and two different datasets, we concluded that domesticated Asian rice had a single origin (1). Ge and Sang (2) suggest that our analyses were flawed and that the origin of rice remains an open question.The first objection is that we did not take into account ancestral population structure in our models. Although we did not explicitly account for population structure, this should affect our estimates of divergence times in the model and not the relationships between populations. Our estimates of divergence/domestication times are not predetermined but inferred from the models...
    Keywords: Letters
    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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  • 10
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    Population Variation Revealed High-Altitude Adaptation of Tibetan Mastiffs (2014)
    Oxford University Press
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    Publication Date: 2014-04-23
    Description: With the assistance of their human companions, dogs have dispersed into new environments during the expansion of human civilization. Tibetan Mastiff (TM), a native of the Tibetan Plateau, was derived from the domesticated Chinese native dog and, like Tibetans, has adapted to the extreme environment of high altitude. Here, we genotyped genome-wide single-nucleotide polymorphisms (SNPs) from 32 TMs and compared them with SNPs from 20 Chinese native dogs and 14 gray wolves ( Canis lupus ). We identified 16 genes with signals of positive selection in the TM, with 12 of these candidate genes associated with functions that have roles in adaptation to high-altitude adaptation, such as EPAS1 , SIRT7 , PLXNA4 , and MAFG that have roles in responses to hypoxia. This study provides important information on the genetic diversity of the TM and potential mechanisms for adaptation to hypoxia.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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