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  • *Biological Evolution  (23)
  • *Biodiversity  (15)
  • American Association for the Advancement of Science (AAAS)  (36)
  • 2005-2009  (36)
  • 2006  (36)
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  • American Association for the Advancement of Science (AAAS)  (36)
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  • 2005-2009  (36)
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  • 1
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    Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-09-02
    Description: Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and the sudden oak death pathogen Phytophthora ramorum. Oomycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae such as diatoms, and the presence of many Phytophthora genes of probable phototroph origin supports a photosynthetic ancestry for the stramenopiles. Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors, and, in particular, a superfamily of 700 proteins with similarity to known oomycete avirulence genes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tyler, Brett M -- Tripathy, Sucheta -- Zhang, Xuemin -- Dehal, Paramvir -- Jiang, Rays H Y -- Aerts, Andrea -- Arredondo, Felipe D -- Baxter, Laura -- Bensasson, Douda -- Beynon, Jim L -- Chapman, Jarrod -- Damasceno, Cynthia M B -- Dorrance, Anne E -- Dou, Daolong -- Dickerman, Allan W -- Dubchak, Inna L -- Garbelotto, Matteo -- Gijzen, Mark -- Gordon, Stuart G -- Govers, Francine -- Grunwald, Niklaus J -- Huang, Wayne -- Ivors, Kelly L -- Jones, Richard W -- Kamoun, Sophien -- Krampis, Konstantinos -- Lamour, Kurt H -- Lee, Mi-Kyung -- McDonald, W Hayes -- Medina, Monica -- Meijer, Harold J G -- Nordberg, Eric K -- Maclean, Donald J -- Ospina-Giraldo, Manuel D -- Morris, Paul F -- Phuntumart, Vipaporn -- Putnam, Nicholas H -- Rash, Sam -- Rose, Jocelyn K C -- Sakihama, Yasuko -- Salamov, Asaf A -- Savidor, Alon -- Scheuring, Chantel F -- Smith, Brian M -- Sobral, Bruno W S -- Terry, Astrid -- Torto-Alalibo, Trudy A -- Win, Joe -- Xu, Zhanyou -- Zhang, Hongbin -- Grigoriev, Igor V -- Rokhsar, Daniel S -- Boore, Jeffrey L -- BB/C509123/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2006 Sep 1;313(5791):1261-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA. bmtyler@vt.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16946064" target="_blank"〉PubMed〈/a〉
    Keywords: Algal Proteins/genetics/physiology ; *Biological Evolution ; DNA, Algal/*genetics ; Genes ; *Genome ; Hydrolases/genetics/metabolism ; Photosynthesis/genetics ; Phylogeny ; Physical Chromosome Mapping ; Phytophthora/classification/*genetics/*pathogenicity/physiology ; Plant Diseases/microbiology ; Polymorphism, Single Nucleotide ; Repetitive Sequences, Nucleic Acid ; Sequence Analysis, DNA ; Symbiosis ; Toxins, Biological/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Biodiversity. Confronting amphibian declines and extinctions (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-07-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mendelson, Joseph R 3rd -- Lips, Karen R -- Gagliardo, Ronald W -- Rabb, George B -- Collins, James P -- Diffendorfer, James E -- Daszak, Peter -- Ibanez D, Roberto -- Zippel, Kevin C -- Lawson, Dwight P -- Wright, Kevin M -- Stuart, Simon N -- Gascon, Claude -- da Silva, Helio R -- Burrowes, Patricia A -- Joglar, Rafael L -- La Marca, Enrique -- Lotters, Stefan -- du Preez, Louis H -- Weldon, Che -- Hyatt, Alex -- Rodriguez-Mahecha, Jose Vicente -- Hunt, Susan -- Robertson, Helen -- Lock, Brad -- Raxworthy, Christopher J -- Frost, Darrel R -- Lacy, Robert C -- Alford, Ross A -- Campbell, Jonathan A -- Parra-Olea, Gabriela -- Bolanos, Federico -- Domingo, Jose Joaquin Calvo -- Halliday, Tim -- Murphy, James B -- Wake, Marvalee H -- Coloma, Luis A -- Kuzmin, Sergius L -- Price, Mark Stanley -- Howell, Kim M -- Lau, Michael -- Pethiyagoda, Rohan -- Boone, Michelle -- Lannoo, Michael J -- Blaustein, Andrew R -- Dobson, Andy -- Griffiths, Richard A -- Crump, Martha L -- Wake, David B -- Brodie, Edmund D Jr -- New York, N.Y. -- Science. 2006 Jul 7;313(5783):48.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Zoo Atlanta, 800 Cherokee Avenue SE, Atlanta, GA 30315, USA. jmendelson@zooatlanta.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16825553" target="_blank"〉PubMed〈/a〉
    Keywords: *Amphibians ; Animals ; *Biodiversity ; Chytridiomycota ; Conservation of Natural Resources ; Ecosystem ; *International Agencies ; International Cooperation ; Mycoses/veterinary ; Population Dynamics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Sequencing and analysis of Neanderthal genomic DNA (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-11-18
    Description: Our knowledge of Neanderthals is based on a limited number of remains and artifacts from which we must make inferences about their biology, behavior, and relationship to ourselves. Here, we describe the characterization of these extinct hominids from a new perspective, based on the development of a Neanderthal metagenomic library and its high-throughput sequencing and analysis. Several lines of evidence indicate that the 65,250 base pairs of hominid sequence so far identified in the library are of Neanderthal origin, the strongest being the ascertainment of sequence identities between Neanderthal and chimpanzee at sites where the human genomic sequence is different. These results enabled us to calculate the human-Neanderthal divergence time based on multiple randomly distributed autosomal loci. Our analyses suggest that on average the Neanderthal genomic sequence we obtained and the reference human genome sequence share a most recent common ancestor approximately 706,000 years ago, and that the human and Neanderthal ancestral populations split approximately 370,000 years ago, before the emergence of anatomically modern humans. Our finding that the Neanderthal and human genomes are at least 99.5% identical led us to develop and successfully implement a targeted method for recovering specific ancient DNA sequences from metagenomic libraries. This initial analysis of the Neanderthal genome advances our understanding of the evolutionary relationship of Homo sapiens and Homo neanderthalensis and signifies the dawn of Neanderthal genomics.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2583069/" 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/PMC2583069/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Noonan, James P -- Coop, Graham -- Kudaravalli, Sridhar -- Smith, Doug -- Krause, Johannes -- Alessi, Joe -- Chen, Feng -- Platt, Darren -- Paabo, Svante -- Pritchard, Jonathan K -- Rubin, Edward M -- 1-F32-GM074367/GM/NIGMS NIH HHS/ -- HL066681/HL/NHLBI NIH HHS/ -- R01 HG002772/HG/NHGRI NIH HHS/ -- R01 HG002772-01/HG/NHGRI NIH HHS/ -- R01 HG002772-1/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2006 Nov 17;314(5802):1113-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17110569" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Bone and Bones ; Cell Nucleus ; DNA/*genetics/isolation & purification ; DNA, Mitochondrial ; *Fossils ; Gene Pool ; Genome ; Genome, Human ; Genomic Library ; History, Ancient ; Hominidae/*genetics ; Humans ; Male ; Molecular Sequence Data ; Pan troglodytes/genetics ; Polymerase Chain Reaction ; Sequence Alignment ; *Sequence Analysis, DNA/methods ; Time
    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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  • 4
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    Comment on "Statistical independence of escalatory ecological trends in Phanerozoic marine invertebrates" (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-11-11
    Description: The analysis of Madin et al. (Reports, 12 May 2006, p. 897) of Phanerozoic diversity failed to support expected correlations between carnivores and noncarnivores, leading the authors to reject escalation as an important macroevolutionary process. The test, however, is based on a flawed model of causality, and the ecological groups are improperly delineated with regard to the hypothesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Roopnarine, Peter D -- Angielczyk, Kenneth D -- Hertog, Rachel -- New York, N.Y. -- Science. 2006 Nov 10;314(5801):925; author reply 925.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Invertebrate Zoology and Geology, California Academy of Sciences, 875 Howard Street, San Francisco, CA 94103, USA. proopnarine@calacademy.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17095679" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Biological ; Animals ; Biodiversity ; *Biological Evolution ; *Ecosystem ; *Fossils ; *Invertebrates ; Predatory Behavior ; *Seawater ; Statistics as Topic
    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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  • 5
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    Late Precambrian oxygenation; inception of the clay mineral factory (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-02-04
    Description: An enigmatic stepwise increase in oxygen in the late Precambrian is widely considered a prerequisite for the expansion of animal life. Accumulation of oxygen requires organic matter burial in sediments, which is largely controlled by the sheltering or preservational effects of detrital clay minerals in modern marine continental margin depocenters. Here, we show mineralogical and geochemical evidence for an increase in clay mineral deposition in the Neoproterozoic that immediately predated the first metazoans. Today most clay minerals originate in biologically active soils, so initial expansion of a primitive land biota would greatly enhance production of pedogenic clay minerals (the "clay mineral factory"), leading to increased marine burial of organic carbon via mineral surface preservation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kennedy, Martin -- Droser, Mary -- Mayer, Lawrence M -- Pevear, David -- Mrofka, David -- New York, N.Y. -- Science. 2006 Mar 10;311(5766):1446-9. Epub 2006 Feb 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth Science, University of California Riverside, Riverside, CA 92521, USA. martink@mail.ucr.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16456036" target="_blank"〉PubMed〈/a〉
    Keywords: *Aluminum Silicates/analysis ; Animals ; *Atmosphere/chemistry ; *Biological Evolution ; Carbon ; Evolution, Planetary ; Geologic Sediments/chemistry ; *Minerals/analysis/chemistry ; Oxygen/analysis ; Quartz/analysis ; *Soil ; Time
    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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  • 6
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    Ecology. Photosymbiosis and the evolution of modern coral reefs (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-05-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stanley, George D Jr -- New York, N.Y. -- Science. 2006 May 12;312(5775):857-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Montana Paleontology Center, Missoula, MT 59812, USA. george.stanley@umontana.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16690848" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Animals ; Anthozoa/growth & development/*physiology ; *Biological Evolution ; Calcification, Physiologic ; Calcium Carbonate/metabolism ; Carbon Dioxide/metabolism ; Climate ; *Ecosystem ; Eukaryota/growth & development/*physiology ; Fossils ; Photosynthesis ; Sunlight ; *Symbiosis
    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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  • 7
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    Plant genotypic diversity predicts community structure and governs an ecosystem process (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-08-19
    Description: Theory predicts, and recent empirical studies have shown, that the diversity of plant species determines the diversity of associated herbivores and mediates ecosystem processes, such as aboveground net primary productivity (ANPP). However, an often-overlooked component of plant diversity, namely population genotypic diversity, may also have wide-ranging effects on community structure and ecosystem processes. We showed experimentally that increasing population genotypic diversity in a dominant old-field plant species, Solidago altissima, determined arthropod diversity and community structure and increased ANPP. The effects of genotypic diversity on arthropod diversity and ANPP were comparable to the effects of plant species diversity measured in other studies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Crutsinger, Gregory M -- Collins, Michael D -- Fordyce, James A -- Gompert, Zachariah -- Nice, Chris C -- Sanders, Nathan J -- New York, N.Y. -- Science. 2006 Aug 18;313(5789):966-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA. gcrutsin@utk.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16917062" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Arthropods ; *Biodiversity ; *Ecosystem ; *Genetic Variation ; Genotype ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Population Density ; Solidago/*genetics/growth & development
    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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  • 8
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    Evolution of metazoa and fungi (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-04-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Redecker, Dirk -- New York, N.Y. -- Science. 2006 Apr 7;312(5770):53-4; author reply 53-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16601175" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; *Fungi/classification/genetics ; *Phylogeny
    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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  • 9
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    Nonrandom processes maintain diversity in tropical forests (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-01-28
    Description: An ecological community's species diversity tends to erode through time as a result of stochastic extinction, competitive exclusion, and unstable host-enemy dynamics. This erosion of diversity can be prevented over the short term if recruits are highly diverse as a result of preferential recruitment of rare species or, alternatively, if rare species survive preferentially, which increases diversity as the ages of the individuals increase. Here, we present census data from seven New and Old World tropical forest dynamics plots that all show the latter pattern. Within local areas, the trees that survived were as a group more diverse than those that were recruited or those that died. The larger (and therefore on average older) survivors were more diverse within local areas than the smaller survivors. When species were rare in a local area, they had a higher survival rate than when they were common, resulting in enrichment for rare species and increasing diversity with age and size class in these complex ecosystems.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wills, Christopher -- Harms, Kyle E -- Condit, Richard -- King, David -- Thompson, Jill -- He, Fangliang -- Muller-Landau, Helene C -- Ashton, Peter -- Losos, Elizabeth -- Comita, Liza -- Hubbell, Stephen -- Lafrankie, James -- Bunyavejchewin, Sarayudh -- Dattaraja, H S -- Davies, Stuart -- Esufali, Shameema -- Foster, Robin -- Gunatilleke, Nimal -- Gunatilleke, Savitri -- Hall, Pamela -- Itoh, Akira -- John, Robert -- Kiratiprayoon, Somboon -- de Lao, Suzanne Loo -- Massa, Marie -- Nath, Cheryl -- Noor, Md Nur Supardi -- Kassim, Abdul Rahman -- Sukumar, Raman -- Suresh, Hebbalalu Satyanarayana -- Sun, I-Fang -- Tan, Sylvester -- Yamakura, Takuo -- Zimmerman, Jess -- New York, N.Y. -- Science. 2006 Jan 27;311(5760):527-31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0116, USA. cwills@ucsd.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16439661" target="_blank"〉PubMed〈/a〉
    Keywords: *Biodiversity ; *Ecosystem ; Population Density ; Population Dynamics ; *Trees/growth & development ; Tropical Climate
    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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  • 10
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    Gene regulatory networks and the evolution of animal body plans (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-02-14
    Description: Development of the animal body plan is controlled by large gene regulatory networks (GRNs), and hence evolution of body plans must depend upon change in the architecture of developmental GRNs. However, these networks are composed of diverse components that evolve at different rates and in different ways. Because of the hierarchical organization of developmental GRNs, some kinds of change affect terminal properties of the body plan such as occur in speciation, whereas others affect major aspects of body plan morphology. A notable feature of the paleontological record of animal evolution is the establishment by the Early "Cambrian of virtually all phylum-level body plans. We identify a class of GRN component, the kernels" of the network, which, because of their developmental role and their particular internal structure, are most impervious to change. Conservation of phyletic body plans may have been due to the retention since pre-Cambrian time of GRN kernels, which underlie development of major body parts.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Davidson, Eric H -- Erwin, Douglas H -- HD37105/HD/NICHD NIH HHS/ -- New York, N.Y. -- Science. 2006 Feb 10;311(5762):796-800.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology 156-29, California Institute of Technology, Pasadena, CA 91125, USA. davidson@caltech.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16469913" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Biological/genetics ; Animals ; *Biological Evolution ; Body Patterning/*genetics ; Embryonic Development ; Fossils ; *Gene Expression Regulation, Developmental ; Genes, Regulator ; Genetic Speciation ; Morphogenesis/*genetics ; Signal Transduction/genetics ; Transcription Factors/genetics/metabolism
    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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