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  • Phylogeny  (50)
  • American Association for the Advancement of Science (AAAS)  (50)
  • American Association for the Advancement of Science
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  • 2009  (50)
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  • American Association for the Advancement of Science (AAAS)  (50)
  • American Association for the Advancement of Science
  • American Institute of Physics (AIP)
  • Annual Reviews
  • Oxford University Press
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  • 2010-2014
  • 2005-2009  (50)
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  • 1
    Publication Date: 2009-02-07
    Description: Biodiversity hotspots, representing regions with high species endemism and conservation threat, have been mapped globally. Yet, biodiversity distribution data from within hotspots are too sparse for effective conservation in the face of rapid environmental change. Using frogs as indicators, ecological niche models under paleoclimates, and simultaneous Bayesian analyses of multispecies molecular data, we compare alternative hypotheses of assemblage-scale response to late Quaternary climate change. This reveals a hotspot within the Brazilian Atlantic forest hotspot. We show that the southern Atlantic forest was climatically unstable relative to the central region, which served as a large climatic refugium for neotropical species in the late Pleistocene. This sets new priorities for conservation in Brazil and establishes a validated approach to biodiversity prediction in other understudied, species-rich regions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carnaval, Ana Carolina -- Hickerson, Michael J -- Haddad, Celio F B -- Rodrigues, Miguel T -- Moritz, Craig -- New York, N.Y. -- Science. 2009 Feb 6;323(5915):785-9. doi: 10.1126/science.1166955.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720-3160, USA. carnaval@berkeley.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19197066" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Anura/classification/*genetics ; Bayes Theorem ; *Biodiversity ; Brazil ; Conservation of Natural Resources ; DNA, Mitochondrial/genetics ; Demography ; *Ecosystem ; Geography ; Molecular Sequence Data ; Mutation ; Phylogeny ; Population Dynamics ; Time ; *Trees ; *Tropical Climate
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  • 2
    Publication Date: 2009-03-03
    Description: Plants have distinct RNA polymerase complexes (Pol IV and Pol V) with largely unknown roles in maintaining small RNA-associated gene silencing. Curiously, the eudicot Arabidopsis thaliana is not affected when either function is lost. By use of mutation selection and positional cloning, we showed that the largest subunit of the presumed maize Pol IV is involved in paramutation, an inherited epigenetic change facilitated by an interaction between two alleles, as well as normal maize development. Bioinformatics analyses and nuclear run-on transcription assays indicate that Pol IV does not engage in the efficient RNA synthesis typical of the three major eukaryotic DNA-dependent RNA polymerases. These results indicate that Pol IV employs abnormal RNA polymerase activities to achieve genome-wide silencing and that its absence affects both maize development and heritable epigenetic changes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Erhard, Karl F Jr -- Stonaker, Jennifer L -- Parkinson, Susan E -- Lim, Jana P -- Hale, Christopher J -- Hollick, Jay B -- New York, N.Y. -- Science. 2009 Feb 27;323(5918):1201-5. doi: 10.1126/science.1164508.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, CA 94720-3102, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19251626" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Sequence ; Base Sequence ; Computational Biology ; DNA-Directed RNA Polymerases/chemistry/genetics/*metabolism ; *Epigenesis, Genetic ; Gene Silencing ; Genes, Plant ; Molecular Sequence Data ; *Mutation ; Phylogeny ; Protein Subunits/chemistry/genetics/metabolism ; RNA, Plant/genetics/metabolism ; RNA, Small Interfering/genetics/metabolism ; Transcription, Genetic ; Zea mays/*enzymology/*genetics/growth & development
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  • 3
    Publication Date: 2009-02-07
    Description: Great-appendage arthropods, characterized by a highly modified anterior limb, were previously unknown after the Middle Cambrian. One fossil from the Lower Devonian Hunsruck Slate, Germany, extends the stratigraphic range of these arthropods by approximately 100 million years. Schinderhannes bartelsi shows an unusual combination of anomalocaridid and euarthropod characters, including a highly specialized swimming appendage. A cladistic analysis indicates that the new taxon is basal to crown-group euarthropods and that the great-appendage arthropods are paraphyletic. This new fossil shows that features of the anomalocaridids, including the multisegmented raptorial appendage and circular plated mouth, persisted long after the initial radiation of the euarthropods.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kuhl, Gabriele -- Briggs, Derek E G -- Rust, Jes -- New York, N.Y. -- Science. 2009 Feb 6;323(5915):771-3. doi: 10.1126/science.1166586.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Palaeontology, Steinmann Institute, University of Bonn, Nussallee 8, 53115 Bonn, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19197061" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arthropods/*anatomy & histology/*classification ; Extremities/anatomy & histology ; *Fossils ; Germany ; Mouth/anatomy & histology ; Phylogeny
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  • 4
    Publication Date: 2009-10-08
    Description: Hominid fossils predating the emergence of Australopithecus have been sparse and fragmentary. The evolution of our lineage after the last common ancestor we shared with chimpanzees has therefore remained unclear. Ardipithecus ramidus, recovered in ecologically and temporally resolved contexts in Ethiopia's Afar Rift, now illuminates earlier hominid paleobiology and aspects of extant African ape evolution. More than 110 specimens recovered from 4.4-million-year-old sediments include a partial skeleton with much of the skull, hands, feet, limbs, and pelvis. This hominid combined arboreal palmigrade clambering and careful climbing with a form of terrestrial bipedality more primitive than that of Australopithecus. Ar. ramidus had a reduced canine/premolar complex and a little-derived cranial morphology and consumed a predominantly C3 plant-based diet (plants using the C3 photosynthetic pathway). Its ecological habitat appears to have been largely woodland-focused. Ar. ramidus lacks any characters typical of suspension, vertical climbing, or knuckle-walking. Ar. ramidus indicates that despite the genetic similarities of living humans and chimpanzees, the ancestor we last shared probably differed substantially from any extant African ape. Hominids and extant African apes have each become highly specialized through very different evolutionary pathways. This evidence also illuminates the origins of orthogrady, bipedality, ecology, diet, and social behavior in earliest Hominidae and helps to define the basal hominid adaptation, thereby accentuating the derived nature of Australopithecus.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉White, Tim D -- Asfaw, Berhane -- Beyene, Yonas -- Haile-Selassie, Yohannes -- Lovejoy, C Owen -- Suwa, Gen -- WoldeGabriel, Giday -- New York, N.Y. -- Science. 2009 Oct 2;326(5949):75-86.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Human Evolution Research Center and Department of Integrative Biology, 3101 Valley Life Sciences Building, University of California, Berkeley, CA 94720, USA. timwhite@berkeley.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19810190" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Bone and Bones/anatomy & histology ; Dentition ; Diet ; Ecosystem ; Environment ; Ethiopia ; *Fossils ; Geologic Sediments ; Geological Phenomena ; *Hominidae/anatomy & histology/classification/genetics/physiology ; Humans ; Locomotion ; Paleodontology ; Pan troglodytes/genetics ; Phylogeny ; Skeleton ; Skull/anatomy & histology ; Social Behavior ; Tooth/anatomy & histology
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  • 5
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2009-07-11
    Description: Anaerobic methanotrophs help regulate Earth's climate and may have been an important part of the microbial ecosystem on the early Earth. The anaerobic oxidation of methane (AOM) is often thought of as a sulfate-dependent process, despite the fact that other electron acceptors are more energetically favorable. Here, we show that microorganisms from marine methane-seep sediment in the Eel River Basin in California are capable of using manganese (birnessite) and iron (ferrihydrite) to oxidize methane, revealing that marine AOM is coupled, either directly or indirectly, to a larger variety of oxidants than previously thought. Large amounts of manganese and iron are provided to oceans from rivers, indicating that manganese- and iron-dependent AOM have the potential to be globally important.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Beal, Emily J -- House, Christopher H -- Orphan, Victoria J -- New York, N.Y. -- Science. 2009 Jul 10;325(5937):184-7. doi: 10.1126/science.1169984.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Geosciences and Penn State Astrobiology Research Center, Pennsylvania State University, University Park, PA 16802, USA. ejbeal@gmail.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19589998" target="_blank"〉PubMed〈/a〉
    Keywords: Anaerobiosis ; Archaea/classification/genetics/isolation & purification/*metabolism ; Bacteria/classification/genetics/isolation & purification/*metabolism ; Bacteroides/classification/genetics/isolation & purification/metabolism ; California ; Carbon Dioxide/metabolism ; Crenarchaeota/classification/genetics/isolation & purification/metabolism ; Euryarchaeota/classification/genetics/isolation & purification/metabolism ; Ferric Compounds/*metabolism ; Geologic Sediments/*microbiology ; Manganese/*metabolism ; Methane/*metabolism ; Methanosarcinaceae/classification/genetics/isolation & purification/metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Oxides/*metabolism ; Phylogeny ; Proteobacteria/classification/genetics/isolation & purification/metabolism ; Thermodynamics
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  • 6
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2009-07-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Miller, Greg -- New York, N.Y. -- Science. 2009 Jul 3;325(5936):24-6. doi: 10.1126/science.325_24.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19574364" target="_blank"〉PubMed〈/a〉
    Keywords: Action Potentials ; Animals ; *Biological Evolution ; Central Nervous System/anatomy & histology/physiology ; Cnidaria/cytology/genetics/physiology ; Ctenophora/cytology/physiology ; Ion Channels/physiology ; Nerve Net/anatomy & histology/physiology ; Nervous System/*anatomy & histology ; *Nervous System Physiological Phenomena ; Neurons/*cytology/*physiology ; Phylogeny ; Porifera/cytology/genetics/physiology ; Synapses/physiology
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  • 7
    Publication Date: 2009-09-26
    Description: To explore the mechanisms and evolution of cell-cycle control, we analyzed the position and conservation of large numbers of phosphorylation sites for the cyclin-dependent kinase Cdk1 in the budding yeast Saccharomyces cerevisiae. We combined specific chemical inhibition of Cdk1 with quantitative mass spectrometry to identify the positions of 547 phosphorylation sites on 308 Cdk1 substrates in vivo. Comparisons of these substrates with orthologs throughout the ascomycete lineage revealed that the position of most phosphorylation sites is not conserved in evolution; instead, clusters of sites shift position in rapidly evolving disordered regions. We propose that the regulation of protein function by phosphorylation often depends on simple nonspecific mechanisms that disrupt or enhance protein-protein interactions. The gain or loss of phosphorylation sites in rapidly evolving regions could facilitate the evolution of kinase-signaling circuits.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2813701/" 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/PMC2813701/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Holt, Liam J -- Tuch, Brian B -- Villen, Judit -- Johnson, Alexander D -- Gygi, Steven P -- Morgan, David O -- GM037049/GM/NIGMS NIH HHS/ -- GM50684/GM/NIGMS NIH HHS/ -- HG3456/HG/NHGRI NIH HHS/ -- R01 GM069901/GM/NIGMS NIH HHS/ -- R01 GM069901-06/GM/NIGMS NIH HHS/ -- R01 HG003456/HG/NHGRI NIH HHS/ -- R01 HG003456-06/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2009 Sep 25;325(5948):1682-6. doi: 10.1126/science.1172867.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departments of Physiology and Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19779198" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Ascomycota/chemistry/genetics/metabolism ; *Biological Evolution ; CDC2 Protein Kinase/antagonists & inhibitors/*metabolism ; *Cell Cycle ; Cell Physiological Processes ; Computational Biology ; *Evolution, Molecular ; Molecular Sequence Data ; Phosphopeptides/chemistry/*metabolism ; Phosphorylation ; Phylogeny ; Protein Conformation ; Protein Structure, Tertiary ; Saccharomyces cerevisiae/chemistry/genetics/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/*metabolism ; *Signal Transduction ; Substrate Specificity
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  • 8
    Publication Date: 2009-08-29
    Description: To understand the process by which antibiotic resistance genes are acquired by human pathogens, we functionally characterized the resistance reservoir in the microbial flora of healthy individuals. Most of the resistance genes we identified using culture-independent sampling have not been previously identified and are evolutionarily distant from known resistance genes. By contrast, nearly half of the resistance genes we identified in cultured aerobic gut isolates (a small subset of the gut microbiome) are identical to resistance genes harbored by major pathogens. The immense diversity of resistance genes in the human microbiome could contribute to future emergence of antibiotic resistance in human pathogens.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4720503/" 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/PMC4720503/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sommer, Morten O A -- Dantas, Gautam -- Church, George M -- P50 HG003170/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2009 Aug 28;325(5944):1128-31. doi: 10.1126/science.1176950.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. sommer@genetics.med.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19713526" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Bacterial Agents/pharmacology ; Antiporters/genetics/metabolism ; Bacteria/drug effects/*genetics/isolation & purification ; Bacteria, Aerobic/classification/drug effects/*genetics/isolation & purification ; Bacterial Proteins/genetics/metabolism ; Digestive System/*microbiology ; Drug Resistance, Bacterial/*genetics ; Feces/microbiology ; *Genes, Bacterial ; Humans ; *Metagenome ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Phylogeny ; Proteobacteria/classification/drug effects/genetics/isolation & purification ; Saliva/microbiology ; Transposases/genetics/metabolism ; beta-Lactamases/genetics/metabolism
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  • 9
    Publication Date: 2009-12-08
    Description: Although the nematode Caenorhabditis elegans produces self-fertile hermaphrodites, it descended from a male/female species, so hermaphroditism provides a model for the origin of novel traits. In the related species C. remanei, which has only male and female sexes, lowering the activity of tra-2 by RNA interference created XX animals that made spermatids as well as oocytes, but their spermatids could not activate without the addition of male seminal fluid. However, by lowering the expression of both tra-2 and swm-1, a gene that regulates sperm activation in C. elegans, we produced XX animals with active sperm that were self-fertile. Thus, the evolution of hermaphroditism in Caenorhabditis probably required two steps: a mutation in the sex-determination pathway that caused XX spermatogenesis and a mutation that allowed these spermatids to self-activate.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baldi, Chris -- Cho, Soochin -- Ellis, Ronald E -- New York, N.Y. -- Science. 2009 Nov 13;326(5955):1002-5. doi: 10.1126/science.1176013.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate School of Biomedical Sciences, University of Medicine and Dentistry of New Jersey, Stratford, NJ 08084, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19965511" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; *Biological Evolution ; Caenorhabditis/anatomy & histology/classification/*genetics/*physiology ; Caenorhabditis elegans/anatomy & histology/classification/*genetics/*physiology ; Caenorhabditis elegans Proteins/genetics/physiology ; Crosses, Genetic ; Disorders of Sex Development/genetics ; Female ; Genes, Helminth ; Germ Cells/physiology ; Male ; Membrane Proteins/genetics/physiology ; Molecular Sequence Data ; *Mutation ; Oogenesis ; Ovulation ; Phylogeny ; Reproduction ; Selection, Genetic ; Sex Determination Processes ; Spermatids/physiology ; Spermatogenesis
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  • 10
    Publication Date: 2009-12-08
    Description: Bacteria-mediated acquisition of atmospheric N2 serves as a critical source of nitrogen in terrestrial ecosystems. Here we reveal that symbiotic nitrogen fixation facilitates the cultivation of specialized fungal crops by leaf-cutter ants. By using acetylene reduction and stable isotope experiments, we demonstrated that N2 fixation occurred in the fungus gardens of eight leaf-cutter ant species and, further, that this fixed nitrogen was incorporated into ant biomass. Symbiotic N2-fixing bacteria were consistently isolated from the fungus gardens of 80 leaf-cutter ant colonies collected in Argentina, Costa Rica, and Panama. The discovery of N2 fixation within the leaf-cutter ant-microbe symbiosis reveals a previously unrecognized nitrogen source in neotropical ecosystems.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pinto-Tomas, Adrian A -- Anderson, Mark A -- Suen, Garret -- Stevenson, David M -- Chu, Fiona S T -- Cleland, W Wallace -- Weimer, Paul J -- Currie, Cameron R -- GM 18938/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2009 Nov 20;326(5956):1120-3. doi: 10.1126/science.1173036.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19965433" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylene/metabolism ; Animals ; Ants/metabolism/microbiology/*physiology ; Argentina ; Costa Rica ; *Ecosystem ; Fungi/growth & development/*physiology ; Klebsiella/isolation & purification/*metabolism ; Molecular Sequence Data ; Nitrogen/analysis/metabolism ; *Nitrogen Fixation ; Oxidation-Reduction ; Panama ; Pantoea/isolation & purification/*metabolism ; Phylogeny ; Plant Leaves/chemistry ; *Symbiosis
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  • 11
    Publication Date: 2009-02-07
    Description: Evolution may be dominated by biotic factors, as in the Red Queen model, or abiotic factors, as in the Court Jester model, or a mixture of both. The two models appear to operate predominantly over different geographic and temporal scales: Competition, predation, and other biotic factors shape ecosystems locally and over short time spans, but extrinsic factors such as climate and oceanographic and tectonic events shape larger-scale patterns regionally and globally, and through thousands and millions of years. Paleobiological studies suggest that species diversity is driven largely by abiotic factors such as climate, landscape, or food supply, and comparative phylogenetic approaches offer new insights into clade dynamics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Benton, Michael J -- New York, N.Y. -- Science. 2009 Feb 6;323(5915):728-32. doi: 10.1126/science.1157719.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth Sciences, University of Bristol, Bristol BS8 1RJ, UK. mike.benton@bristol.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19197051" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; *Biological Evolution ; Climate ; Fossils ; *Genetic Speciation ; Geography ; Geological Phenomena ; Logistic Models ; Models, Biological ; Phylogeny ; Time
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  • 12
    Publication Date: 2009-04-11
    Description: Picoeukaryotes are a taxonomically diverse group of organisms less than 2 micrometers in diameter. Photosynthetic marine picoeukaryotes in the genus Micromonas thrive in ecosystems ranging from tropical to polar and could serve as sentinel organisms for biogeochemical fluxes of modern oceans during climate change. These broadly distributed primary producers belong to an anciently diverged sister clade to land plants. Although Micromonas isolates have high 18S ribosomal RNA gene identity, we found that genomes from two isolates shared only 90% of their predicted genes. Their independent evolutionary paths were emphasized by distinct riboswitch arrangements as well as the discovery of intronic repeat elements in one isolate, and in metagenomic data, but not in other genomes. Divergence appears to have been facilitated by selection and acquisition processes that actively shape the repertoire of genes that are mutually exclusive between the two isolates differently than the core genes. Analyses of the Micromonas genomes offer valuable insights into ecological differentiation and the dynamic nature of early plant evolution.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Worden, Alexandra Z -- Lee, Jae-Hyeok -- Mock, Thomas -- Rouze, Pierre -- Simmons, Melinda P -- Aerts, Andrea L -- Allen, Andrew E -- Cuvelier, Marie L -- Derelle, Evelyne -- Everett, Meredith V -- Foulon, Elodie -- Grimwood, Jane -- Gundlach, Heidrun -- Henrissat, Bernard -- Napoli, Carolyn -- McDonald, Sarah M -- Parker, Micaela S -- Rombauts, Stephane -- Salamov, Aasf -- Von Dassow, Peter -- Badger, Jonathan H -- Coutinho, Pedro M -- Demir, Elif -- Dubchak, Inna -- Gentemann, Chelle -- Eikrem, Wenche -- Gready, Jill E -- John, Uwe -- Lanier, William -- Lindquist, Erika A -- Lucas, Susan -- Mayer, Klaus F X -- Moreau, Herve -- Not, Fabrice -- Otillar, Robert -- Panaud, Olivier -- Pangilinan, Jasmyn -- Paulsen, Ian -- Piegu, Benoit -- Poliakov, Aaron -- Robbens, Steven -- Schmutz, Jeremy -- Toulza, Eve -- Wyss, Tania -- Zelensky, Alexander -- Zhou, Kemin -- Armbrust, E Virginia -- Bhattacharya, Debashish -- Goodenough, Ursula W -- Van de Peer, Yves -- Grigoriev, Igor V -- New York, N.Y. -- Science. 2009 Apr 10;324(5924):268-72. doi: 10.1126/science.1167222.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039 USA. azworden@mbari.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19359590" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; *Biological Evolution ; Chlorophyta/classification/cytology/*genetics/physiology ; DNA Transposable Elements ; Ecosystem ; Gene Expression Regulation ; Genes ; Genetic Variation ; *Genome ; Introns ; Meiosis/genetics ; Molecular Sequence Data ; Oceans and Seas ; Photosynthesis/genetics ; Phylogeny ; Phytoplankton/classification/genetics ; Plants/*genetics ; RNA, Untranslated ; Repetitive Sequences, Nucleic Acid ; Sequence Analysis, DNA ; Transcription Factors/genetics
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  • 13
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2009-02-07
    Description: Biologists have long been fascinated by the exceptionally high diversity displayed by some evolutionary groups. Adaptive radiation in such clades is not only spectacular, but is also an extremely complex process influenced by a variety of ecological, genetic, and developmental factors and strongly dependent on historical contingencies. Using modeling approaches, we identify 10 general patterns concerning the temporal, spatial, and genetic/morphological properties of adaptive radiation. Some of these are strongly supported by empirical work, whereas for others, empirical support is more tentative. In almost all cases, more data are needed. Future progress in our understanding of adaptive radiation will be most successful if theoretical and empirical approaches are integrated, as has happened in other areas of evolutionary biology.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gavrilets, Sergey -- Losos, Jonathan B -- GM56693/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2009 Feb 6;323(5915):732-7. doi: 10.1126/science.1157966.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology, National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, TN 37996, USA. sergey@tiem.utk.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19197052" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Biological ; Animals ; *Biodiversity ; *Biological Evolution ; Ecosystem ; Fossils ; *Genetic Speciation ; Genetic Variation ; Models, Biological ; Phylogeny ; Selection, Genetic
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  • 14
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2009-01-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Renfrew, Colin -- New York, N.Y. -- Science. 2009 Jan 23;323(5913):467-8. doi: 10.1126/science.1168953.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK. renfrew@mcdonald.cam.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19164735" target="_blank"〉PubMed〈/a〉
    Keywords: Anthropology ; Archaeology ; *Emigration and Immigration/history ; Genetic Drift ; Helicobacter pylori/classification/*genetics ; History, Ancient ; Humans ; *Language ; Linguistics ; *Oceanic Ancestry Group/history ; Pacific Islands ; Phylogeny ; Polynesia ; Stomach/*microbiology ; Taiwan
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  • 15
    Publication Date: 2009-04-18
    Description: An active microbial assemblage cycles sulfur in a sulfate-rich, ancient marine brine beneath Taylor Glacier, an outlet glacier of the East Antarctic Ice Sheet, with Fe(III) serving as the terminal electron acceptor. Isotopic measurements of sulfate, water, carbonate, and ferrous iron and functional gene analyses of adenosine 5'-phosphosulfate reductase imply that a microbial consortium facilitates a catalytic sulfur cycle. These metabolic pathways result from a limited organic carbon supply because of the absence of contemporary photosynthesis, yielding a subglacial ferrous brine that is anoxic but not sulfidic. Coupled biogeochemical processes below the glacier enable subglacial microbes to grow in extended isolation, demonstrating how analogous organic-starved systems, such as Neoproterozoic oceans, accumulated Fe(II) despite the presence of an active sulfur cycle.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mikucki, Jill A -- Pearson, Ann -- Johnston, David T -- Turchyn, Alexandra V -- Farquhar, James -- Schrag, Daniel P -- Anbar, Ariel D -- Priscu, John C -- Lee, Peter A -- New York, N.Y. -- Science. 2009 Apr 17;324(5925):397-400. doi: 10.1126/science.1167350.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA 02138 USA. jill.a.mikucki@dartmouth.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19372431" target="_blank"〉PubMed〈/a〉
    Keywords: Anaerobiosis ; Antarctic Regions ; Autotrophic Processes ; Bacteria/growth & development/*metabolism ; *Ecosystem ; Ferric Compounds/*metabolism ; Ferrous Compounds/*metabolism ; Heterotrophic Processes ; *Ice Cover ; Metabolic Networks and Pathways ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases Acting on Sulfur Group Donors/genetics/metabolism ; Oxygen/metabolism ; Oxygen Isotopes/analysis ; Phylogeny ; Seawater/chemistry/*microbiology ; Sulfates/metabolism ; Sulfites/metabolism ; Sulfur/*metabolism
    Print ISSN: 0036-8075
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  • 16
    Publication Date: 2009-08-29
    Description: A single-base pair resolution silkworm genetic variation map was constructed from 40 domesticated and wild silkworms, each sequenced to approximately threefold coverage, representing 99.88% of the genome. We identified ~16 million single-nucleotide polymorphisms, many indels, and structural variations. We find that the domesticated silkworms are clearly genetically differentiated from the wild ones, but they have maintained large levels of genetic variability, suggesting a short domestication event involving a large number of individuals. We also identified signals of selection at 354 candidate genes that may have been important during domestication, some of which have enriched expression in the silk gland, midgut, and testis. These data add to our understanding of the domestication processes and may have applications in devising pest control strategies and advancing the use of silkworms as efficient bioreactors.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3951477/" 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/PMC3951477/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xia, Qingyou -- Guo, Yiran -- Zhang, Ze -- Li, Dong -- Xuan, Zhaoling -- Li, Zhuo -- Dai, Fangyin -- Li, Yingrui -- Cheng, Daojun -- Li, Ruiqiang -- Cheng, Tingcai -- Jiang, Tao -- Becquet, Celine -- Xu, Xun -- Liu, Chun -- Zha, Xingfu -- Fan, Wei -- Lin, Ying -- Shen, Yihong -- Jiang, Lan -- Jensen, Jeffrey -- Hellmann, Ines -- Tang, Si -- Zhao, Ping -- Xu, Hanfu -- Yu, Chang -- Zhang, Guojie -- Li, Jun -- Cao, Jianjun -- Liu, Shiping -- He, Ningjia -- Zhou, Yan -- Liu, Hui -- Zhao, Jing -- Ye, Chen -- Du, Zhouhe -- Pan, Guoqing -- Zhao, Aichun -- Shao, Haojing -- Zeng, Wei -- Wu, Ping -- Li, Chunfeng -- Pan, Minhui -- Li, Jingjing -- Yin, Xuyang -- Li, Dawei -- Wang, Juan -- Zheng, Huisong -- Wang, Wen -- Zhang, Xiuqing -- Li, Songgang -- Yang, Huanming -- Lu, Cheng -- Nielsen, Rasmus -- Zhou, Zeyang -- Wang, Jian -- Xiang, Zhonghuai -- Wang, Jun -- R01 HG003229/HG/NHGRI NIH HHS/ -- R01 HG003229-05/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2009 Oct 16;326(5951):433-6. doi: 10.1126/science.1176620. Epub 2009 Aug 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Key Sericultural Laboratory of Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19713493" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bombyx/classification/*genetics ; Digestive System/metabolism ; Exocrine Glands/metabolism ; Female ; Gene Expression ; *Genes, Insect ; *Genetic Variation ; *Genome, Insect ; INDEL Mutation ; Linkage Disequilibrium ; Male ; Phylogeny ; Polymorphism, Single Nucleotide ; Principal Component Analysis ; Selection, Genetic ; *Sequence Analysis, DNA ; Testis/metabolism
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  • 17
    Publication Date: 2009-01-24
    Description: Two prehistoric migrations peopled the Pacific. One reached New Guinea and Australia, and a second, more recent, migration extended through Melanesia and from there to the Polynesian islands. These migrations were accompanied by two distinct populations of the specific human pathogen Helicobacter pylori, called hpSahul and hspMaori, respectively. hpSahul split from Asian populations of H. pylori 31,000 to 37,000 years ago, in concordance with archaeological history. The hpSahul populations in New Guinea and Australia have diverged sufficiently to indicate that they have remained isolated for the past 23,000 to 32,000 years. The second human expansion from Taiwan 5000 years ago dispersed one of several subgroups of the Austronesian language family along with one of several hspMaori clades into Melanesia and Polynesia, where both language and parasite have continued to diverge.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2827536/" 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/PMC2827536/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Moodley, Yoshan -- Linz, Bodo -- Yamaoka, Yoshio -- Windsor, Helen M -- Breurec, Sebastien -- Wu, Jeng-Yih -- Maady, Ayas -- Bernhoft, Steffie -- Thiberge, Jean-Michel -- Phuanukoonnon, Suparat -- Jobb, Gangolf -- Siba, Peter -- Graham, David Y -- Marshall, Barry J -- Achtman, Mark -- R01 DK062813/DK/NIDDK NIH HHS/ -- R01 DK062813-05/DK/NIDDK NIH HHS/ -- R01 DK62813/DK/NIDDK NIH HHS/ -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2009 Jan 23;323(5913):527-30. doi: 10.1126/science.1166083.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck-Institut fur Infektionsbiologie, Department of Molecular Biology, Chariteplatz 1, 10117 Berlin, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19164753" target="_blank"〉PubMed〈/a〉
    Keywords: Australia ; Bayes Theorem ; *Emigration and Immigration/history ; Haplotypes ; Helicobacter pylori/classification/*genetics/isolation & purification ; History, Ancient ; Humans ; Language ; Melanesia ; *Oceanic Ancestry Group/history ; Pacific Islands ; Phylogeny ; Polynesia ; Population Dynamics ; Stomach/*microbiology ; Taiwan
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  • 18
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2009-07-25
    Description: Biodiversity research typically focuses on species richness and has often neglected interactions, either by assuming that such interactions are homogeneously distributed or by addressing only the interactions between a pair of species or a few species at a time. In contrast, a network approach provides a powerful representation of the ecological interactions among species and highlights their global interdependence. Understanding how the responses of pairwise interactions scale to entire assemblages remains one of the great challenges that must be met as society faces global ecosystem change.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bascompte, Jordi -- New York, N.Y. -- Science. 2009 Jul 24;325(5939):416-9. doi: 10.1126/science.1170749.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Integrative Ecology Group, Estacion Biologica de Donana, Consejo Superior de Investigaciones Cientificas, Calle Americo Vespucio s/n, E-41092 Sevilla, Spain. bascompte@ebd.csic.es〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19628856" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biodiversity ; Biological Evolution ; *Ecology/methods ; Food Chain ; Phylogeny ; Plants
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  • 19
    Publication Date: 2009-01-20
    Description: Among cellular organisms, symbiotic bacteria provide the extreme examples of genome degradation and reduction. However, only isolated snapshots of eroding symbiont genomes have previously been available. We documented the dynamics of symbiont genome evolution by sequencing seven strains of Buchnera aphidicola from pea aphid hosts. We estimated a spontaneous mutation rate of at least 4 x 10(-9) substitutions per site per replication, which is more than 10 times as high as the rates previously estimated for any bacteria. We observed a high rate of small insertions and deletions associated with abundant DNA homopolymers, and occasional larger deletions. Although purifying selection eliminates many mutations, some persist, resulting in ongoing loss of genes and DNA from this already tiny genome. Our results provide a general model for the stepwise process leading to genome reduction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Moran, Nancy A -- McLaughlin, Heather J -- Sorek, Rotem -- New York, N.Y. -- Science. 2009 Jan 16;323(5912):379-82. doi: 10.1126/science.1167140.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA. nmoran@email.arizona.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19150844" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Aphids/*microbiology/physiology ; Base Composition ; Buchnera/*genetics/*physiology ; Evolution, Molecular ; *Gene Silencing ; *Genome, Bacterial ; INDEL Mutation ; Models, Genetic ; Molecular Sequence Data ; *Mutation ; Phylogeny ; Polymorphism, Single Nucleotide ; Selection, Genetic ; Sequence Analysis, DNA ; Sequence Deletion ; *Symbiosis
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  • 20
    Publication Date: 2009-02-07
    Description: Male animals of many species deploy conditional reproductive strategies that contain distinct alternative phenotypes. Such facultatively expressed male tactics are assumed to be due to a single developmental threshold mechanism switching between the expression of two alternative phenotypes. However, we discovered a clade of dung beetles that commonly expresses two threshold mechanisms, resulting in three alternative phenotypes (male trimorphism). Once recognized, we found trimorphism in other beetle families that involves different types of male weapons. Evidence that insects assumed to be dimorphic can express three facultative male forms suggests that we need to adjust how we think about animal mating systems and the evolution of conditional strategies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rowland, J Mark -- Emlen, Douglas J -- New York, N.Y. -- Science. 2009 Feb 6;323(5915):773-6. doi: 10.1126/science.1167345.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA. rowland@unm.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19197062" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Beetles/*anatomy & histology/classification/genetics/physiology ; Behavior, Animal ; *Biological Evolution ; Body Size ; Female ; Genetic Speciation ; Male ; Phenotype ; Phylogeny ; Reproduction ; Sexual Behavior, Animal
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  • 21
    Publication Date: 2009-05-02
    Description: Africa is the source of all modern humans, but characterization of genetic variation and of relationships among populations across the continent has been enigmatic. We studied 121 African populations, four African American populations, and 60 non-African populations for patterns of variation at 1327 nuclear microsatellite and insertion/deletion markers. We identified 14 ancestral population clusters in Africa that correlate with self-described ethnicity and shared cultural and/or linguistic properties. We observed high levels of mixed ancestry in most populations, reflecting historical migration events across the continent. Our data also provide evidence for shared ancestry among geographically diverse hunter-gatherer populations (Khoesan speakers and Pygmies). The ancestry of African Americans is predominantly from Niger-Kordofanian (approximately 71%), European (approximately 13%), and other African (approximately 8%) populations, although admixture levels varied considerably among individuals. This study helps tease apart the complex evolutionary history of Africans and African Americans, aiding both anthropological and genetic epidemiologic studies.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2947357/" 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/PMC2947357/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tishkoff, Sarah A -- Reed, Floyd A -- Friedlaender, Francoise R -- Ehret, Christopher -- Ranciaro, Alessia -- Froment, Alain -- Hirbo, Jibril B -- Awomoyi, Agnes A -- Bodo, Jean-Marie -- Doumbo, Ogobara -- Ibrahim, Muntaser -- Juma, Abdalla T -- Kotze, Maritha J -- Lema, Godfrey -- Moore, Jason H -- Mortensen, Holly -- Nyambo, Thomas B -- Omar, Sabah A -- Powell, Kweli -- Pretorius, Gideon S -- Smith, Michael W -- Thera, Mahamadou A -- Wambebe, Charles -- Weber, James L -- Williams, Scott M -- 1R01GM083606-01/GM/NIGMS NIH HHS/ -- F32 HG003801/HG/NHGRI NIH HHS/ -- F32 HG003801-01A1/HG/NHGRI NIH HHS/ -- F32HG03801/HG/NHGRI NIH HHS/ -- R01 GM076637/GM/NIGMS NIH HHS/ -- R01 GM076637-01/GM/NIGMS NIH HHS/ -- R01 GM083606/GM/NIGMS NIH HHS/ -- R01 GM083606-01/GM/NIGMS NIH HHS/ -- R01 HL065234/HL/NHLBI NIH HHS/ -- R01 HL065234-01/HL/NHLBI NIH HHS/ -- R01 HL65234/HL/NHLBI NIH HHS/ -- R01GM076637/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2009 May 22;324(5930):1035-44. doi: 10.1126/science.1172257. Epub 2009 Apr 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of Maryland, College Park, MD 20742, USA. tishkoff@mail.med.upenn.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19407144" target="_blank"〉PubMed〈/a〉
    Keywords: Africa ; African Americans/ethnology/*genetics ; African Continental Ancestry Group/ethnology/*genetics ; Bayes Theorem ; Cluster Analysis ; Continental Population Groups/genetics ; Emigration and Immigration ; Ethnic Groups/genetics ; Gene Flow ; *Genetic Variation ; Genotype ; Geography ; Humans ; INDEL Mutation ; Language ; Microsatellite Repeats ; Phylogeny ; Polymorphism, Single Nucleotide ; Principal Component Analysis
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  • 22
    Publication Date: 2009-05-02
    Description: Molecular preservation in non-avian dinosaurs is controversial. We present multiple lines of evidence that endogenous proteinaceous material is preserved in bone fragments and soft tissues from an 80-million-year-old Campanian hadrosaur, Brachylophosaurus canadensis [Museum of the Rockies (MOR) 2598]. Microstructural and immunological data are consistent with preservation of multiple bone matrix and vessel proteins, and phylogenetic analyses of Brachylophosaurus collagen sequenced by mass spectrometry robustly support the bird-dinosaur clade, consistent with an endogenous source for these collagen peptides. These data complement earlier results from Tyrannosaurus rex (MOR 1125) and confirm that molecular preservation in Cretaceous dinosaurs is not a unique event.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schweitzer, Mary H -- Zheng, Wenxia -- Organ, Chris L -- Avci, Recep -- Suo, Zhiyong -- Freimark, Lisa M -- Lebleu, Valerie S -- Duncan, Michael B -- Vander Heiden, Matthew G -- Neveu, John M -- Lane, William S -- Cottrell, John S -- Horner, John R -- Cantley, Lewis C -- Kalluri, Raghu -- Asara, John M -- AA 13913/AA/NIAAA NIH HHS/ -- CA 125550/CA/NCI NIH HHS/ -- DK 55001/DK/NIDDK NIH HHS/ -- DK 61866/DK/NIDDK NIH HHS/ -- DK 62987/DK/NIDDK NIH HHS/ -- R01 AA013913/AA/NIAAA NIH HHS/ -- R01 CA125550/CA/NCI NIH HHS/ -- R01 DK055001/DK/NIDDK NIH HHS/ -- R01 DK062987/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 2009 May 1;324(5927):626-31. doi: 10.1126/science.1165069.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉North Carolina State University, Raleigh, NC 27695, USA. schweitzer@ncsu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19407199" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Birds/classification ; Bone Demineralization Technique ; Bone Matrix/chemistry ; Collagen/analysis/*chemistry/isolation & purification ; *Dinosaurs/classification ; Elastin/analysis ; Femur/blood supply/*chemistry/ultrastructure ; *Fossils ; Hemoglobins/analysis ; Immunologic Techniques ; Laminin/analysis ; Mass Spectrometry ; Microscopy, Electron, Scanning ; Molecular Sequence Data ; Osteocytes/ultrastructure ; Peptide Fragments/chemistry/isolation & purification ; Phylogeny ; Proteins/analysis/*chemistry/isolation & purification ; Sequence Alignment
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  • 23
    Publication Date: 2009-11-07
    Description: We report a high-quality draft sequence of the genome of the horse (Equus caballus). The genome is relatively repetitive but has little segmental duplication. Chromosomes appear to have undergone few historical rearrangements: 53% of equine chromosomes show conserved synteny to a single human chromosome. Equine chromosome 11 is shown to have an evolutionary new centromere devoid of centromeric satellite DNA, suggesting that centromeric function may arise before satellite repeat accumulation. Linkage disequilibrium, showing the influences of early domestication of large herds of female horses, is intermediate in length between dog and human, and there is long-range haplotype sharing among breeds.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3785132/" 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/PMC3785132/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wade, C M -- Giulotto, E -- Sigurdsson, S -- Zoli, M -- Gnerre, S -- Imsland, F -- Lear, T L -- Adelson, D L -- Bailey, E -- Bellone, R R -- Blocker, H -- Distl, O -- Edgar, R C -- Garber, M -- Leeb, T -- Mauceli, E -- MacLeod, J N -- Penedo, M C T -- Raison, J M -- Sharpe, T -- Vogel, J -- Andersson, L -- Antczak, D F -- Biagi, T -- Binns, M M -- Chowdhary, B P -- Coleman, S J -- Della Valle, G -- Fryc, S -- Guerin, G -- Hasegawa, T -- Hill, E W -- Jurka, J -- Kiialainen, A -- Lindgren, G -- Liu, J -- Magnani, E -- Mickelson, J R -- Murray, J -- Nergadze, S G -- Onofrio, R -- Pedroni, S -- Piras, M F -- Raudsepp, T -- Rocchi, M -- Roed, K H -- Ryder, O A -- Searle, S -- Skow, L -- Swinburne, J E -- Syvanen, A C -- Tozaki, T -- Valberg, S J -- Vaudin, M -- White, J R -- Zody, M C -- Broad Institute Genome Sequencing Platform -- Broad Institute Whole Genome Assembly Team -- Lander, E S -- Lindblad-Toh, K -- 098051/Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2009 Nov 6;326(5954):865-7. doi: 10.1126/science.1178158.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA. c.wade@usyd.edu.au〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19892987" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Domestic/genetics ; Centromere/genetics ; Chromosome Mapping ; Chromosomes, Mammalian/*genetics ; Computational Biology ; DNA Copy Number Variations ; Dogs ; Evolution, Molecular ; Female ; Genes ; *Genome ; Haplotypes ; Horses/*genetics ; Humans ; Molecular Sequence Data ; Phylogeny ; Repetitive Sequences, Nucleic Acid ; *Sequence Analysis, DNA ; Synteny
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  • 24
    Publication Date: 2009-02-14
    Description: Infection by human rhinovirus (HRV) is a major cause of upper and lower respiratory tract disease worldwide and displays considerable phenotypic variation. We examined diversity by completing the genome sequences for all known serotypes (n = 99). Superimposition of capsid crystal structure and optimal-energy RNA configurations established alignments and phylogeny. These revealed conserved motifs; clade-specific diversity, including a potential newly identified species (HRV-D); mutations in field isolates; and recombination. In analogy with poliovirus, a hypervariable 5' untranslated region tract may affect virulence. A configuration consistent with nonscanning internal ribosome entry was found in all HRVs and may account for rapid translation. The data density from complete sequences of the reference HRVs provided high resolution for this degree of modeling and serves as a platform for full genome-based epidemiologic studies and antiviral or vaccine development.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3923423/" 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/PMC3923423/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Palmenberg, Ann C -- Spiro, David -- Kuzmickas, Ryan -- Wang, Shiliang -- Djikeng, Appolinaire -- Rathe, Jennifer A -- Fraser-Liggett, Claire M -- Liggett, Stephen B -- R01 HL091490/HL/NHLBI NIH HHS/ -- U19 AI070503/AI/NIAID NIH HHS/ -- U19-AI070503/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2009 Apr 3;324(5923):55-9. doi: 10.1126/science.1165557. Epub 2009 Feb 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Molecular Virology, University of Wisconsin, Madison, WI 53706, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19213880" target="_blank"〉PubMed〈/a〉
    Keywords: 3' Untranslated Regions ; 5' Untranslated Regions ; Base Composition ; Base Sequence ; Codon, Terminator ; *Evolution, Molecular ; *Genome, Viral ; Humans ; Molecular Sequence Data ; Mutation ; Nucleic Acid Conformation ; Open Reading Frames ; Phylogeny ; Picornaviridae Infections/virology ; Polyproteins/biosynthesis/chemistry/genetics ; RNA, Viral/chemistry/*genetics ; Recombination, Genetic ; Respiratory Tract Infections/virology ; Rhinovirus/classification/*genetics/ultrastructure ; Sequence Alignment ; Sequence Analysis, RNA ; Serotyping ; Viral Proteins/biosynthesis/chemistry/genetics
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  • 25
    Publication Date: 2009-11-11
    Description: Oxygen minimum zones, also known as oceanic "dead zones," are widespread oceanographic features currently expanding because of global warming. Although inhospitable to metazoan life, they support a cryptic microbiota whose metabolic activities affect nutrient and trace gas cycling within the global ocean. Here, we report metagenomic analyses of a ubiquitous and abundant but uncultivated oxygen minimum zone microbe (SUP05) related to chemoautotrophic gill symbionts of deep-sea clams and mussels. The SUP05 metagenome harbors a versatile repertoire of genes mediating autotrophic carbon assimilation, sulfur oxidation, and nitrate respiration responsive to a wide range of water-column redox states. Our analysis provides a genomic foundation for understanding the ecological and biogeochemical role of pelagic SUP05 in oxygen-deficient oceanic waters and its potential sensitivity to environmental changes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Walsh, David A -- Zaikova, Elena -- Howes, Charles G -- Song, Young C -- Wright, Jody J -- Tringe, Susannah G -- Tortell, Philippe D -- Hallam, Steven J -- New York, N.Y. -- Science. 2009 Oct 23;326(5952):578-82. doi: 10.1126/science.1175309.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology, 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/19900896" target="_blank"〉PubMed〈/a〉
    Keywords: Biomass ; British Columbia ; Carbon/metabolism ; *Chemoautotrophic Growth ; *Ecosystem ; Energy Metabolism ; Gammaproteobacteria/*genetics/metabolism/physiology ; Genes, rRNA ; *Genome, Bacterial ; *Metagenome ; Molecular Sequence Data ; Nitrates/metabolism ; Oxidation-Reduction ; Oxygen/*analysis ; Pacific Ocean ; Phylogeny ; Seasons ; Seawater/chemistry/*microbiology ; Sulfur/metabolism ; Symbiosis
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  • 26
    Publication Date: 2009-02-07
    Description: Morphological diversity within closely related species is an essential aspect of evolution and adaptation. Mutations in the Melanocortin 1 receptor (Mc1r) gene contribute to pigmentary diversity in natural populations of fish, birds, and many mammals. However, melanism in the gray wolf, Canis lupus, is caused by a different melanocortin pathway component, the K locus, that encodes a beta-defensin protein that acts as an alternative ligand for Mc1r. We show that the melanistic K locus mutation in North American wolves derives from past hybridization with domestic dogs, has risen to high frequency in forested habitats, and exhibits a molecular signature of positive selection. The same mutation also causes melanism in the coyote, Canis latrans, and in Italian gray wolves, and hence our results demonstrate how traits selected in domesticated species can influence the morphological diversity of their wild relatives.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2903542/" 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/PMC2903542/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Anderson, Tovi M -- vonHoldt, Bridgett M -- Candille, Sophie I -- Musiani, Marco -- Greco, Claudia -- Stahler, Daniel R -- Smith, Douglas W -- Padhukasahasram, Badri -- Randi, Ettore -- Leonard, Jennifer A -- Bustamante, Carlos D -- Ostrander, Elaine A -- Tang, Hua -- Wayne, Robert K -- Barsh, Gregory S -- P01 DK068384/DK/NIDDK NIH HHS/ -- P01 DK068384-050001/DK/NIDDK NIH HHS/ -- R01 GM068882/GM/NIGMS NIH HHS/ -- R01 GM068882-04/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2009 Mar 6;323(5919):1339-43. doi: 10.1126/science.1165448. Epub 2009 Feb 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departments of Genetics and Pediatrics, Stanford University, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19197024" target="_blank"〉PubMed〈/a〉
    Keywords: Agouti Signaling Protein/genetics ; Animals ; *Biological Evolution ; Coyotes/genetics ; Dogs/genetics ; *Ecosystem ; Gene Flow ; Hair Color/*genetics ; Haplotypes ; Linkage Disequilibrium ; Melanins/metabolism ; Molecular Sequence Data ; *Mutation ; Phenotype ; Phylogeny ; Pigmentation/*genetics ; Polymorphism, Single Nucleotide ; Receptor, Melanocortin, Type 1/genetics ; Selection, Genetic ; Sequence Deletion ; Wolves/*genetics ; beta-Defensins/*genetics
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  • 27
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2009-04-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2009 Apr 3;324(5923):28-31. doi: 10.1126/science.324.5923.28.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19342565" target="_blank"〉PubMed〈/a〉
    Keywords: *Angiosperms/anatomy & histology/classification/genetics ; Biodiversity ; *Biological Evolution ; *Flowers/anatomy & histology ; Fossils ; Gene Duplication ; Genes, Plant ; Genetic Variation ; Genome, Plant ; Gymnosperms/classification/genetics ; Phylogeny ; Pollen ; Seeds/anatomy & histology ; Time
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  • 28
    Publication Date: 2009-10-10
    Description: The definitive mammalian middle ear (DMME) is defined by the loss of embryonic Meckel's cartilage and disconnection of the middle ear from the mandible in adults. It is a major feature distinguishing living mammals from nonmammalian vertebrates. We report a Cretaceous trechnotherian mammal with an ossified Meckel's cartilage in the adult, showing that homoplastic evolution of the DMME occurred in derived therian mammals, besides the known cases of eutriconodonts. The mandible with ossified Meckel's cartilage appears to be paedomorphic. Reabsorption of embryonic Meckel's cartilage to disconnect the ear ossicles from the mandible is patterned by a network of genes and signaling pathways. This fossil suggests that developmental heterochrony and gene patterning are major mechanisms in homplastic evolution of the DMME.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ji, Qiang -- Luo, Zhe-Xi -- Zhang, Xingliao -- Yuan, Chong-Xi -- Xu, Li -- New York, N.Y. -- Science. 2009 Oct 9;326(5950):278-81. doi: 10.1126/science.1178501.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Geology, Chinese Academy of Geological Sciences, Beijing 100037, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19815774" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Cartilage/embryology/physiology ; Chondrogenesis ; Dentition ; Ear Ossicles/anatomy & histology/embryology ; *Ear, Middle/anatomy & histology/embryology ; Embryo, Mammalian/anatomy & histology ; *Fossils ; Gene Expression Regulation, Developmental ; Intercellular Signaling Peptides and Proteins/metabolism ; *Mammals/anatomy & histology/classification/embryology/genetics ; Mandible/anatomy & histology ; Mice ; Mice, Mutant Strains ; *Osteogenesis ; Phylogeny ; Signal Transduction
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  • 29
    Publication Date: 2009-08-22
    Description: Blast disease is a devastating fungal disease of rice, one of the world's staple foods. Race-specific resistance to blast disease has usually not been durable. Here, we report the cloning of a previously unknown type of gene that confers non-race-specific resistance and its successful use in breeding. Pi21 encodes a proline-rich protein that includes a putative heavy metal-binding domain and putative protein-protein interaction motifs. Wild-type Pi21 appears to slow the plant's defense responses, which may support optimization of defense mechanisms. Deletions in its proline-rich motif inhibit this slowing. Pi21 is separable from a closely linked gene conferring poor flavor. The resistant pi21 allele, which is found in some strains of japonica rice, could improve blast resistance of rice worldwide.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fukuoka, Shuichi -- Saka, Norikuni -- Koga, Hironori -- Ono, Kazuko -- Shimizu, Takehiko -- Ebana, Kaworu -- Hayashi, Nagao -- Takahashi, Akira -- Hirochika, Hirohiko -- Okuno, Kazutoshi -- Yano, Masahiro -- New York, N.Y. -- Science. 2009 Aug 21;325(5943):998-1001. doi: 10.1126/science.1175550.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉QTL Genomics Research Center, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan. fukusan@affrc.go.jp〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19696351" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Motifs ; Amino Acid Sequence ; Chromosome Mapping ; Cloning, Molecular ; Genes, Plant ; Genetic Variation ; Haplotypes ; Immunity, Innate/*genetics ; Magnaporthe/*pathogenicity ; Molecular Sequence Data ; Oryza/*genetics/metabolism/*microbiology ; Phylogeny ; Plant Diseases/*microbiology ; Plant Proteins/chemistry/*genetics/*physiology ; Proline/analysis ; Protein Interaction Domains and Motifs ; Protein Structure, Tertiary ; Quantitative Trait Loci ; Sequence Deletion ; Transformation, Genetic
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  • 30
    Publication Date: 2009-09-19
    Description: Microorganisms have been repeatedly discovered in environments that do not support their metabolic activity. Identifying and quantifying these misplaced organisms can reveal dispersal mechanisms that shape natural microbial diversity. Using endospore germination experiments, we estimated a stable supply of thermophilic bacteria into permanently cold Arctic marine sediment at a rate exceeding 10(8) spores per square meter per year. These metabolically and phylogenetically diverse Firmicutes show no detectable activity at cold in situ temperatures but rapidly mineralize organic matter by hydrolysis, fermentation, and sulfate reduction upon induction at 50 degrees C. The closest relatives to these bacteria come from warm subsurface petroleum reservoir and ocean crust ecosystems, suggesting that seabed fluid flow from these environments is delivering thermophiles to the cold ocean. These transport pathways may broadly influence microbial community composition in the marine environment.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hubert, Casey -- Loy, Alexander -- Nickel, Maren -- Arnosti, Carol -- Baranyi, Christian -- Bruchert, Volker -- Ferdelman, Timothy -- Finster, Kai -- Christensen, Flemming Monsted -- Rosa de Rezende, Julia -- Vandieken, Verona -- Jorgensen, Bo Barker -- P 20185/Austrian Science Fund FWF/Austria -- New York, N.Y. -- Science. 2009 Sep 18;325(5947):1541-4. doi: 10.1126/science.1174012.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biogeochemistry Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany. chubert@mpi-bremen.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19762643" target="_blank"〉PubMed〈/a〉
    Keywords: Anaerobiosis ; Arctic Regions ; *Bacteria/classification/isolation & purification ; Bacterial Physiological Phenomena ; *Biodiversity ; *Cold Climate ; Cold Temperature ; *Ecosystem ; Fatty Acids, Volatile/metabolism ; Fermentation ; Geologic Sediments/*microbiology ; Hot Temperature ; Oxidation-Reduction ; Phylogeny ; Spores, Bacterial/*physiology ; Sulfates/metabolism
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  • 31
    Publication Date: 2009-05-26
    Description: Since its identification in April 2009, an A(H1N1) virus containing a unique combination of gene segments from both North American and Eurasian swine lineages has continued to circulate in humans. The lack of similarity between the 2009 A(H1N1) virus and its nearest relatives indicates that its gene segments have been circulating undetected for an extended period. Its low genetic diversity suggests that the introduction into humans was a single event or multiple events of similar viruses. Molecular markers predictive of adaptation to humans are not currently present in 2009 A(H1N1) viruses, suggesting that previously unrecognized molecular determinants could be responsible for the transmission among humans. Antigenically the viruses are homogeneous and similar to North American swine A(H1N1) viruses but distinct from seasonal human A(H1N1).〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3250984/" 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/PMC3250984/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Garten, Rebecca J -- Davis, C Todd -- Russell, Colin A -- Shu, Bo -- Lindstrom, Stephen -- Balish, Amanda -- Sessions, Wendy M -- Xu, Xiyan -- Skepner, Eugene -- Deyde, Varough -- Okomo-Adhiambo, Margaret -- Gubareva, Larisa -- Barnes, John -- Smith, Catherine B -- Emery, Shannon L -- Hillman, Michael J -- Rivailler, Pierre -- Smagala, James -- de Graaf, Miranda -- Burke, David F -- Fouchier, Ron A M -- Pappas, Claudia -- Alpuche-Aranda, Celia M -- Lopez-Gatell, Hugo -- Olivera, Hiram -- Lopez, Irma -- Myers, Christopher A -- Faix, Dennis -- Blair, Patrick J -- Yu, Cindy -- Keene, Kimberly M -- Dotson, P David Jr -- Boxrud, David -- Sambol, Anthony R -- Abid, Syed H -- St George, Kirsten -- Bannerman, Tammy -- Moore, Amanda L -- Stringer, David J -- Blevins, Patricia -- Demmler-Harrison, Gail J -- Ginsberg, Michele -- Kriner, Paula -- Waterman, Steve -- Smole, Sandra -- Guevara, Hugo F -- Belongia, Edward A -- Clark, Patricia A -- Beatrice, Sara T -- Donis, Ruben -- Katz, Jacqueline -- Finelli, Lyn -- Bridges, Carolyn B -- Shaw, Michael -- Jernigan, Daniel B -- Uyeki, Timothy M -- Smith, Derek J -- Klimov, Alexander I -- Cox, Nancy J -- DP1 OD000490-01/OD/NIH HHS/ -- DP1-OD000490-01/OD/NIH HHS/ -- HHSN266200700010C/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2009 Jul 10;325(5937):197-201. doi: 10.1126/science.1176225. Epub 2009 May 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉WHO Collaborating Center for Influenza, Centers for Disease Control and Prevention (CDC), Atlanta, GA 30333, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19465683" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antibodies, Viral/immunology ; Antigens, Viral/genetics/*immunology ; Disease Outbreaks ; Evolution, Molecular ; Genes, Viral ; Genetic Variation ; Genome, Viral ; Hemagglutination Inhibition Tests ; Hemagglutinin Glycoproteins, Influenza Virus/chemistry/genetics/immunology ; Humans ; Influenza A Virus, H1N1 Subtype/classification/*genetics/*immunology/isolation & ; purification ; Influenza A Virus, H3N2 Subtype/genetics ; Influenza A virus/genetics ; Influenza, Human/epidemiology/immunology/*virology ; Mutation ; Neuraminidase/genetics ; Orthomyxoviridae Infections/veterinary/virology ; Phylogeny ; Reassortant Viruses/genetics ; Swine ; Swine Diseases/virology ; Viral Matrix Proteins/genetics ; Viral Nonstructural Proteins/genetics
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  • 32
    Publication Date: 2009-07-11
    Description: Since the discovery of the Marburg and Ebola species of filovirus, seemingly random, sporadic fatal outbreaks of disease in humans and nonhuman primates have given impetus to identification of host tropisms and potential reservoirs. Domestic swine in the Philippines, experiencing unusually severe outbreaks of porcine reproductive and respiratory disease syndrome, have now been discovered to host Reston ebolavirus (REBOV). Although REBOV is the only member of Filoviridae that has not been associated with disease in humans, its emergence in the human food chain is of concern. REBOV isolates were found to be more divergent from each other than from the original virus isolated in 1989, indicating polyphyletic origins and that REBOV has been circulating since, and possibly before, the initial discovery of REBOV in monkeys.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Barrette, Roger W -- Metwally, Samia A -- Rowland, Jessica M -- Xu, Lizhe -- Zaki, Sherif R -- Nichol, Stuart T -- Rollin, Pierre E -- Towner, Jonathan S -- Shieh, Wun-Ju -- Batten, Brigid -- Sealy, Tara K -- Carrillo, Consuelo -- Moran, Karen E -- Bracht, Alexa J -- Mayr, Gregory A -- Sirios-Cruz, Magdalena -- Catbagan, Davinio P -- Lautner, Elizabeth A -- Ksiazek, Thomas G -- White, William R -- McIntosh, Michael T -- New York, N.Y. -- Science. 2009 Jul 10;325(5937):204-6. doi: 10.1126/science.1172705.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Foreign Animal Disease Diagnostic Laboratory, National Veterinary Services Laboratories, Animal and Plant Health Inspection Services, United States Department of Agriculture, Plum Island Animal Disease Center, New York, NY 11944, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19590002" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antibodies, Viral/blood ; Disease Outbreaks/veterinary ; Disease Reservoirs ; Ebolavirus/classification/genetics/immunology/*isolation & purification ; Filoviridae Infections/complications/epidemiology/*veterinary/virology ; Hemorrhagic Fever, Ebola/epidemiology/veterinary/virology ; Humans ; Molecular Sequence Data ; Philippines/epidemiology ; Phylogeny ; Porcine Reproductive and Respiratory Syndrome/epidemiology/*virology ; Porcine respiratory and reproductive syndrome ; virus/classification/genetics/*isolation & purification ; Sus scrofa ; Swine Diseases/epidemiology/*virology
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  • 33
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2009-04-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Friedman, Matt -- New York, N.Y. -- Science. 2009 Apr 17;324(5925):341-2. doi: 10.1126/science.1172783.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Committee on Evolutionary Biology, University of Chicago, 1025 East 57th Street, Chicago, IL 60637, USA. mattf@uchicago.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19372416" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Fishes/anatomy & histology/growth & development/physiology ; Forelimb/*anatomy & histology/growth & development/physiology ; *Fossils ; Humerus/*anatomy & histology/growth & development/physiology ; Locomotion ; Muscle, Skeletal/physiology ; Phylogeny ; Vertebrates/*anatomy & histology/growth & development/physiology
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  • 34
    Publication Date: 2009-06-27
    Description: Diatoms and other chromalveolates are among the dominant phytoplankters in the world's oceans. Endosymbiosis was essential to the success of chromalveolates, and it appears that the ancestral plastid in this group had a red algal origin via an ancient secondary endosymbiosis. However, recent analyses have turned up a handful of nuclear genes in chromalveolates that are of green algal derivation. Using a genome-wide approach to estimate the "green" contribution to diatoms, we identified 〉1700 green gene transfers, constituting 16% of the diatom nuclear coding potential. These genes were probably introduced into diatoms and other chromalveolates from a cryptic endosymbiont related to prasinophyte-like green algae. Chromalveolates appear to have recruited genes from the two major existing algal groups to forge a highly successful, species-rich protist lineage.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Moustafa, Ahmed -- Beszteri, Bank -- Maier, Uwe G -- Bowler, Chris -- Valentin, Klaus -- Bhattacharya, Debashish -- R01ES013679/ES/NIEHS NIH HHS/ -- T32 GM98629/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2009 Jun 26;324(5935):1724-6. doi: 10.1126/science.1172983.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Interdisciplinary Program in Genetics, University of Iowa, Iowa City, IA 52242, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19556510" target="_blank"〉PubMed〈/a〉
    Keywords: Biological Evolution ; Cell Nucleus/genetics ; Chlorophyta/classification/*genetics/physiology ; Diatoms/classification/*genetics/physiology ; Gene Transfer, Horizontal ; Genes ; *Genome ; Phylogeny ; Plastids/*genetics ; Rhodophyta/classification/*genetics/physiology ; *Symbiosis
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  • 35
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2009-08-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cohen, Jon -- New York, N.Y. -- Science. 2009 Aug 7;325(5941):663. doi: 10.1126/science.325_663a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19661392" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Ape Diseases/parasitology ; *Biological Evolution ; Erythrocytes/*parasitology ; Genetic Speciation ; Genetic Variation ; Malaria/parasitology/veterinary ; Malaria Vaccines ; Malaria, Falciparum/*parasitology ; Mutation ; Pan troglodytes/*virology ; Phylogeny ; Plasmodium/classification/*genetics/immunology/pathogenicity ; Plasmodium falciparum/classification/*genetics/pathogenicity
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  • 36
    Publication Date: 2009-12-08
    Description: Rates and mechanisms of intron gain and loss have traditionally been inferred from alignments of highly conserved genes sampled from phylogenetically distant taxa. We report a population-genomic approach that detected 24 discordant intron/exon boundaries between the whole-genome sequences of two Daphnia pulex isolates. Sequencing of presence/absence loci across a collection of D. pulex isolates and outgroup Daphnia species shows that most polymorphisms are a consequence of recent gains, with parallel gains often occurring at the same locations in independent allelic lineages. More than half of the recent gains are associated with short sequence repeats, suggesting an origin via repair of staggered double-strand breaks. By comparing the allele-frequency spectrum of intron-gain alleles with that for derived single-base substitutions, we also provide evidence that newly arisen introns are intrinsically deleterious and tend to accumulate in population-genetic settings where random genetic drift is a relatively strong force.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3878872/" 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/PMC3878872/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, Wenli -- Tucker, Abraham E -- Sung, Way -- Thomas, W Kelley -- Lynch, Michael -- R01 GM036827/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2009 Nov 27;326(5957):1260-2. doi: 10.1126/science.1179302.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biology Department, Indiana University, Bloomington, IN 47405, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19965475" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; Base Sequence ; Computational Biology ; DNA Breaks, Double-Stranded ; DNA Repair ; Daphnia/*genetics ; Exons ; *Genome ; *Introns ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Genetic ; Polymorphism, Single Nucleotide ; Repetitive Sequences, Nucleic Acid ; Time Factors
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  • 37
    Publication Date: 2009-10-08
    Description: The Middle Awash Ardipithecus ramidus sample comprises over 145 teeth, including associated maxillary and mandibular sets. These help reveal the earliest stages of human evolution. Ar. ramidus lacks the postcanine megadontia of Australopithecus. Its molars have thinner enamel and are functionally less durable than those of Australopithecus but lack the derived Pan pattern of thin occlusal enamel associated with ripe-fruit frugivory. The Ar. ramidus dental morphology and wear pattern are consistent with a partially terrestrial, omnivorous/frugivorous niche. Analyses show that the ARA-VP-6/500 skeleton is female and that Ar. ramidus was nearly monomorphic in canine size and shape. The canine/lower third premolar complex indicates a reduction of canine size and honing capacity early in hominid evolution, possibly driven by selection targeted on the male upper canine.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Suwa, Gen -- Kono, Reiko T -- Simpson, Scott W -- Asfaw, Berhane -- Lovejoy, C Owen -- White, Tim D -- New York, N.Y. -- Science. 2009 Oct 2;326(5949):94-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University Museum, University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan. suwa@um.u-tokyo.ac.jp〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19810195" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Evolution ; Cuspid/anatomy & histology ; Dental Enamel/anatomy & histology ; *Dentition ; Diet ; Ethiopia ; Female ; *Fossils ; Hominidae/*anatomy & histology/classification ; Incisor/anatomy & histology ; Male ; Molar/anatomy & histology ; Odontometry ; Paleodontology ; Phylogeny ; Sex Characteristics ; Tooth/*anatomy & histology ; Tooth Crown/anatomy & histology
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  • 38
    Publication Date: 2009-08-08
    Description: Protein synthesis involves the accurate attachment of amino acids to their matching transfer RNA (tRNA) molecules. Mistranslating the amino acids serine or glycine for alanine is prevented by the function of independent but collaborative aminoacylation and editing domains of alanyl-tRNA synthetases (AlaRSs). We show that the C-Ala domain plays a key role in AlaRS function. The C-Ala domain is universally tethered to the editing domain both in AlaRS and in many homologous free-standing editing proteins. Crystal structure and functional analyses showed that C-Ala forms an ancient single-stranded nucleic acid binding motif that promotes cooperative binding of both aminoacylation and editing domains to tRNA(Ala). In addition, C-Ala may have played an essential role in the evolution of AlaRSs by coupling aminoacylation to editing to prevent mistranslation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4559334/" 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/PMC4559334/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Guo, Min -- Chong, Yeeting E -- Beebe, Kirk -- Shapiro, Ryan -- Yang, Xiang-Lei -- Schimmel, Paul -- GM 15539/GM/NIGMS NIH HHS/ -- R01 GM015539/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2009 Aug 7;325(5941):744-7. doi: 10.1126/science.1174343.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Skaggs Institute for Chemical Biology and the Department of Molecular Biology, The Scripps Research Institute, BCC-379, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19661429" target="_blank"〉PubMed〈/a〉
    Keywords: Alanine-tRNA Ligase/*chemistry/*metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Bacteria/enzymology ; Base Sequence ; Crystallography, X-Ray ; Escherichia coli Proteins/chemistry/metabolism ; Evolution, Molecular ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA, Bacterial/chemistry/metabolism ; RNA, Transfer, Ala/*chemistry/*metabolism ; RNA, Transfer, Amino Acyl/chemistry/metabolism ; *Transfer RNA Aminoacylation
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  • 39
    Publication Date: 2009-09-19
    Description: Retroviruses can leave a "fossil record" in their hosts' genomes in the form of endogenous retroviruses. Foamy viruses, complex retroviruses that infect mammals, have been notably absent from this record. We have found an endogenous foamy virus within the genomes of sloths and show that foamy viruses were infecting mammals more than 100 million years ago and codiverged with their hosts across an entire geological era. Our analysis highlights the role of evolutionary constraint in maintaining viral genome structure and indicates that accessory genes and mammalian mechanisms of innate immunity are the products of macroevolutionary conflict played out over a geological time scale.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Katzourakis, Aris -- Gifford, Robert J -- Tristem, Michael -- Gilbert, M Thomas P -- Pybus, Oliver G -- New York, N.Y. -- Science. 2009 Sep 18;325(5947):1512. doi: 10.1126/science.1174149.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Zoology Department, University of Oxford, Oxford OX1 3PS, UK. aris.katzourakis@zoo.ox.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19762636" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; *Biological Evolution ; Endogenous Retroviruses/classification/*genetics ; *Evolution, Molecular ; Genome ; Genome, Viral ; Immunity, Innate ; Molecular Sequence Data ; Phylogeny ; Retroviridae Infections/veterinary/virology ; Sloths/classification/*genetics/immunology/*virology ; Spumavirus/classification/*genetics ; Time
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  • 40
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2009-01-10
    Description: Charles Darwin's theory of natural selection has been hailed as one of the most innovative contributions to modern science. When first proposed in 1859, however, it was widely rejected by his contemporaries, even by those who accepted the general idea of evolution. This article identifies those aspects of Darwin's work that led him to develop this revolutionary theory, including his studies of biogeography and animal breeding, and his recognition of the role played by the struggle for existence.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bowler, Peter J -- New York, N.Y. -- Science. 2009 Jan 9;323(5911):223-6. doi: 10.1126/science.1160332.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Philosophy and Anthropological Studies, Queen's University of Belfast, University Road Belfast, Belfast, Northern Ireland, BT7 1NN, UK. p.bowler@qub.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19131623" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Biological ; Animals ; *Biological Evolution ; Breeding/history ; Genetic Speciation ; Genetic Variation ; Geography ; History, 19th Century ; Humans ; Phylogeny ; *Selection, Genetic ; Sociology/history
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  • 41
    Publication Date: 2009-01-31
    Description: Kulp et al. (Reports, 15 August 2008, p. 967) described a bacterium able to photosynthetically oxidize arsenite [As(III)] via arsenate [As(V)] reductase functioning in reverse. Based on their phylogenetic analysis of As(V) reductase, they proposed that this enzyme was responsible for the anaerobic oxidation of As(III) in the Archean. We challenge this proposition based on paleogeochemical, bioenergetic, and phylogenetic arguments.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schoepp-Cothenet, B -- Duval, S -- Santini, J M -- Nitschke, W -- New York, N.Y. -- Science. 2009 Jan 30;323(5914):583; author reply 583. doi: 10.1126/science.1164967.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Bioenergetique et Ingenierie des Proteines, IFR88, CNRS, 13402 Marseille, France. schoepp@ifr88.cnrs-mrs.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19179513" target="_blank"〉PubMed〈/a〉
    Keywords: Arsenate Reductases/*metabolism ; Arsenites/*metabolism ; Bacteria/*metabolism ; *Biofilms ; California ; Hot Springs/*microbiology ; Oxidation-Reduction ; *Photosynthesis ; Phylogeny
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  • 42
    Publication Date: 2009-12-17
    Description: Characterizing the evolutionary history of early dinosaurs is central to understanding their rise and diversification in the Late Triassic. However, fossils from basal lineages are rare. A new theropod dinosaur from New Mexico is a representative of the early North American diversification. Known from several nearly complete skeletons, it reveals a mosaic of plesiomorphic and derived features that clarify early saurischian dinosaur evolution and provide evidence for the antiquity of novel avian character systems including skeletal pneumaticity. The taxon further reveals latitudinal differences among saurischian assemblages during the Late Triassic, demonstrates that the theropod fauna from the Late Triassic of North America was not endemic, and suggests that intercontinental dispersal was prevalent during this time.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nesbitt, Sterling J -- Smith, Nathan D -- Irmis, Randall B -- Turner, Alan H -- Downs, Alex -- Norell, Mark A -- New York, N.Y. -- Science. 2009 Dec 11;326(5959):1530-3. doi: 10.1126/science.1180350.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Paleontology, American Museum of Natural History, New York, NY 10024, USA. nesbitt@jsg.utexas.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20007898" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Bone and Bones/*anatomy & histology ; Bones of Lower Extremity/anatomy & histology ; Bones of Upper Extremity/anatomy & histology ; *Dinosaurs/anatomy & histology/classification ; *Fossils ; New Mexico ; Phylogeny ; Skeleton ; Skull/anatomy & histology ; Spine/anatomy & histology
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  • 43
    Publication Date: 2009-11-07
    Description: Elucidating the biogeography of bacterial communities on the human body is critical for establishing healthy baselines from which to detect differences associated with diseases. To obtain an integrated view of the spatial and temporal distribution of the human microbiota, we surveyed bacteria from up to 27 sites in seven to nine healthy adults on four occasions. We found that community composition was determined primarily by body habitat. Within habitats, interpersonal variability was high, whereas individuals exhibited minimal temporal variability. Several skin locations harbored more diverse communities than the gut and mouth, and skin locations differed in their community assembly patterns. These results indicate that our microbiota, although personalized, varies systematically across body habitats and time; such trends may ultimately reveal how microbiome changes cause or prevent disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3602444/" 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/PMC3602444/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Costello, Elizabeth K -- Lauber, Christian L -- Hamady, Micah -- Fierer, Noah -- Gordon, Jeffrey I -- Knight, Rob -- DK64540/DK/NIDDK NIH HHS/ -- DK78669/DK/NIDDK NIH HHS/ -- T32 GM065103/GM/NIGMS NIH HHS/ -- T32 GM065103-08/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2009 Dec 18;326(5960):1694-7. doi: 10.1126/science.1177486. Epub 2009 Nov 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19892944" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Bacteria/classification/genetics/*isolation & purification ; Biodiversity ; Cluster Analysis ; DNA, Bacterial/analysis/genetics/isolation & purification ; DNA, Ribosomal/analysis/genetics/isolation & purification ; Ear Canal/*microbiology ; Feces/*microbiology ; Female ; Genes, rRNA ; Hair/*microbiology ; Humans ; Male ; *Metagenome ; Middle Aged ; Mouth/*microbiology ; Nose/*microbiology ; Phylogeny ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Skin/*microbiology ; Time Factors
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  • 44
    Publication Date: 2009-09-05
    Description: Species that are habitat specialists make up much of biodiversity, but the evolutionary factors that limit their distributions have rarely been considered. We show that in Drosophila, narrow and wide ranges of desiccation and cold resistance are closely associated with the distributions of specialist and generalist species, respectively. Furthermore, our data show that narrowly distributed tropical species consistently have low means and low genetic variation for these traits as compared with those of widely distributed species after phylogenetic correction. These results are unrelated to levels of neutral variation. Thus, specialist species may simply lack genetic variation in key traits, limiting their ability to adapt to conditions beyond their current range. We predict that such species are likely to be constrained in their evolutionary responses to future climate changes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kellermann, Vanessa -- van Heerwaarden, Belinda -- Sgro, Carla M -- Hoffmann, Ary A -- New York, N.Y. -- Science. 2009 Sep 4;325(5945):1244-6. doi: 10.1126/science.1175443.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Environmental Stress and Adaptation Research, Department of Genetics, University of Melbourne, Parkville, Melbourne 3010, Australia. vanessa.kellermann@biology.au.dk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19729654" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptation, Physiological ; Animals ; *Biological Evolution ; *Climatic Processes ; Cold Temperature ; Dehydration ; Drosophila/anatomy & histology/*genetics/*physiology ; *Ecosystem ; *Genetic Variation ; Phylogeny ; Selection, Genetic ; Species Specificity ; Tropical Climate ; Wings, Animal/anatomy & histology
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  • 45
    Publication Date: 2009-01-24
    Description: Debates about human prehistory often center on the role that population expansions play in shaping biological and cultural diversity. Hypotheses on the origin of the Austronesian settlers of the Pacific are divided between a recent "pulse-pause" expansion from Taiwan and an older "slow-boat" diffusion from Wallacea. We used lexical data and Bayesian phylogenetic methods to construct a phylogeny of 400 languages. In agreement with the pulse-pause scenario, the language trees place the Austronesian origin in Taiwan approximately 5230 years ago and reveal a series of settlement pauses and expansion pulses linked to technological and social innovations. These results are robust to assumptions about the rooting and calibration of the trees and demonstrate the combined power of linguistic scholarship, database technologies, and computational phylogenetic methods for resolving questions about human prehistory.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gray, R D -- Drummond, A J -- Greenhill, S J -- New York, N.Y. -- Science. 2009 Jan 23;323(5913):479-83. doi: 10.1126/science.1166858.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Psychology, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19164742" target="_blank"〉PubMed〈/a〉
    Keywords: Bayes Theorem ; Databases, Factual ; *Emigration and Immigration/history ; History, Ancient ; Humans ; *Language ; Linguistics ; *Oceanic Ancestry Group/history ; Pacific Islands ; Philippines ; Phylogeny ; Polynesia ; Population Dynamics ; Taiwan ; Vocabulary
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  • 46
    Publication Date: 2009-05-30
    Description: Human skin is a large, heterogeneous organ that protects the body from pathogens while sustaining microorganisms that influence human health and disease. Our analysis of 16S ribosomal RNA gene sequences obtained from 20 distinct skin sites of healthy humans revealed that physiologically comparable sites harbor similar bacterial communities. The complexity and stability of the microbial community are dependent on the specific characteristics of the skin site. This topographical and temporal survey provides a baseline for studies that examine the role of bacterial communities in disease states and the microbial interdependencies required to maintain healthy skin.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2805064/" 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/PMC2805064/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Grice, Elizabeth A -- Kong, Heidi H -- Conlan, Sean -- Deming, Clayton B -- Davis, Joie -- Young, Alice C -- NISC Comparative Sequencing Program -- Bouffard, Gerard G -- Blakesley, Robert W -- Murray, Patrick R -- Green, Eric D -- Turner, Maria L -- Segre, Julia A -- Z01 HG000180-08/Intramural NIH HHS/ -- ZIA BC010938-02/Intramural NIH HHS/ -- ZIA HG000180-09/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2009 May 29;324(5931):1190-2. doi: 10.1126/science.1171700.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Genetics and Molecular Biology Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19478181" target="_blank"〉PubMed〈/a〉
    Keywords: Actinobacteria/classification/genetics/isolation & purification ; Adult ; Bacteria/classification/genetics/*isolation & purification ; Bacteroidetes/classification/genetics/isolation & purification ; Biodiversity ; Female ; Genes, rRNA ; Humans ; Male ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; Proteobacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S ; Skin/*microbiology ; Time Factors ; Young Adult
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  • 47
    Publication Date: 2009-07-18
    Description: Analysis of Neandertal DNA holds great potential for investigating the population history of this group of hominins, but progress has been limited due to the rarity of samples and damaged state of the DNA. We present a method of targeted ancient DNA sequence retrieval that greatly reduces sample destruction and sequencing demands and use this method to reconstruct the complete mitochondrial DNA (mtDNA) genomes of five Neandertals from across their geographic range. We find that mtDNA genetic diversity in Neandertals that lived 38,000 to 70,000 years ago was approximately one-third of that in contemporary modern humans. Together with analyses of mtDNA protein evolution, these data suggest that the long-term effective population size of Neandertals was smaller than that of modern humans and extant great apes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Briggs, Adrian W -- Good, Jeffrey M -- Green, Richard E -- Krause, Johannes -- Maricic, Tomislav -- Stenzel, Udo -- Lalueza-Fox, Carles -- Rudan, Pavao -- Brajkovic, Dejana -- Kucan, Zeljko -- Gusic, Ivan -- Schmitz, Ralf -- Doronichev, Vladimir B -- Golovanova, Liubov V -- de la Rasilla, Marco -- Fortea, Javier -- Rosas, Antonio -- Paabo, Svante -- New York, N.Y. -- Science. 2009 Jul 17;325(5938):318-21. doi: 10.1126/science.1174462.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany. briggs@eva.mpg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19608918" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bayes Theorem ; DNA Primers ; DNA, Mitochondrial/analysis/*genetics/isolation & purification ; Evolution, Molecular ; Female ; *Fossils ; Gene Library ; Genetic Variation ; Genome, Human ; *Genome, Mitochondrial ; Geography ; Hominidae/*genetics ; Humans ; Male ; Molecular Sequence Data ; Phylogeny ; Population Density ; *Sequence Analysis, DNA
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  • 48
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2009-06-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dagan, Tal -- Martin, William -- New York, N.Y. -- Science. 2009 Jun 26;324(5935):1651-2. doi: 10.1126/science.1175765.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Botanik III, Heinrich-Heine Universitaet Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19556490" target="_blank"〉PubMed〈/a〉
    Keywords: Biological Evolution ; Cell Nucleus/genetics ; Chlorophyta/*genetics/physiology ; Diatoms/*genetics/physiology ; Gene Transfer, Horizontal ; *Genome ; Phylogeny ; Plastids/genetics ; Rhodophyta/*genetics/physiology ; Symbiosis
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  • 49
    Publication Date: 2009-12-17
    Description: Asia harbors substantial cultural and linguistic diversity, but the geographic structure of genetic variation across the continent remains enigmatic. Here we report a large-scale survey of autosomal variation from a broad geographic sample of Asian human populations. Our results show that genetic ancestry is strongly correlated with linguistic affiliations as well as geography. Most populations show relatedness within ethnic/linguistic groups, despite prevalent gene flow among populations. More than 90% of East Asian (EA) haplotypes could be found in either Southeast Asian (SEA) or Central-South Asian (CSA) populations and show clinal structure with haplotype diversity decreasing from south to north. Furthermore, 50% of EA haplotypes were found in SEA only and 5% were found in CSA only, indicating that SEA was a major geographic source of EA populations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉HUGO Pan-Asian SNP Consortium -- Abdulla, Mahmood Ameen -- Ahmed, Ikhlak -- Assawamakin, Anunchai -- Bhak, Jong -- Brahmachari, Samir K -- Calacal, Gayvelline C -- Chaurasia, Amit -- Chen, Chien-Hsiun -- Chen, Jieming -- Chen, Yuan-Tsong -- Chu, Jiayou -- Cutiongco-de la Paz, Eva Maria C -- De Ungria, Maria Corazon A -- Delfin, Frederick C -- Edo, Juli -- Fuchareon, Suthat -- Ghang, Ho -- Gojobori, Takashi -- Han, Junsong -- Ho, Sheng-Feng -- Hoh, Boon Peng -- Huang, Wei -- Inoko, Hidetoshi -- Jha, Pankaj -- Jinam, Timothy A -- Jin, Li -- Jung, Jongsun -- Kangwanpong, Daoroong -- Kampuansai, Jatupol -- Kennedy, Giulia C -- Khurana, Preeti -- Kim, Hyung-Lae -- Kim, Kwangjoong -- Kim, Sangsoo -- Kim, Woo-Yeon -- Kimm, Kuchan -- Kimura, Ryosuke -- Koike, Tomohiro -- Kulawonganunchai, Supasak -- Kumar, Vikrant -- Lai, Poh San -- Lee, Jong-Young -- Lee, Sunghoon -- Liu, Edison T -- Majumder, Partha P -- Mandapati, Kiran Kumar -- Marzuki, Sangkot -- Mitchell, Wayne -- Mukerji, Mitali -- Naritomi, Kenji -- Ngamphiw, Chumpol -- Niikawa, Norio -- Nishida, Nao -- Oh, Bermseok -- Oh, Sangho -- Ohashi, Jun -- Oka, Akira -- Ong, Rick -- Padilla, Carmencita D -- Palittapongarnpim, Prasit -- Perdigon, Henry B -- Phipps, Maude Elvira -- Png, Eileen -- Sakaki, Yoshiyuki -- Salvador, Jazelyn M -- Sandraling, Yuliana -- Scaria, Vinod -- Seielstad, Mark -- Sidek, Mohd Ros -- Sinha, Amit -- Srikummool, Metawee -- Sudoyo, Herawati -- Sugano, Sumio -- Suryadi, Helena -- Suzuki, Yoshiyuki -- Tabbada, Kristina A -- Tan, Adrian -- Tokunaga, Katsushi -- Tongsima, Sissades -- Villamor, Lilian P -- Wang, Eric -- Wang, Ying -- Wang, Haifeng -- Wu, Jer-Yuarn -- Xiao, Huasheng -- Xu, Shuhua -- Yang, Jin Ok -- Shugart, Yin Yao -- Yoo, Hyang-Sook -- Yuan, Wentao -- Zhao, Guoping -- Zilfalil, Bin Alwi -- Indian Genome Variation Consortium -- New York, N.Y. -- Science. 2009 Dec 11;326(5959):1541-5. doi: 10.1126/science.1177074.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20007900" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Asia ; Asian Continental Ancestry Group/*genetics/history ; Bayes Theorem ; Cluster Analysis ; *Emigration and Immigration/history ; Ethnic Groups/*genetics/history ; Gene Flow ; Genotype ; Geography ; *Haplotypes ; History, Ancient ; Humans ; Language ; Linguistics ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; *Polymorphism, Single Nucleotide ; Principal Component Analysis
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 50
    Publication Date: 2009-09-19
    Description: Nearly all of the large-bodied predators (〉2.5 tons) on northern continents during the Late Cretaceous were tyrannosaurid dinosaurs. We show that their most conspicuous functional specializations--a proportionately large skull, incisiform premaxillary teeth, expanded jaw-closing musculature, diminutive forelimbs, and hindlimbs with cursorial proportions--were present in a new, small-bodied, basal tyrannosauroid from Lower Cretaceous rocks in northeastern China. These specializations, which were later scaled up in Late Cretaceous tyrannosaurids with body masses approaching 100 times greater, drove the most dominant radiation of macropredators of the Mesozoic.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sereno, Paul C -- Tan, Lin -- Brusatte, Stephen L -- Kriegstein, Henry J -- Zhao, Xijin -- Cloward, Karen -- New York, N.Y. -- Science. 2009 Oct 16;326(5951):418-22. doi: 10.1126/science.1177428. Epub 2009 Sep 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637, USA. dinosaur@uchicago.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19762599" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Body Size ; Bone and Bones/*anatomy & histology ; Cerebrum/anatomy & histology ; China ; *Dinosaurs/anatomy & histology/classification ; Forelimb/anatomy & histology ; *Fossils ; Hindlimb/anatomy & histology ; Phylogeny ; Skeleton ; Skull/anatomy & histology ; Tooth/anatomy & histology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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