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  • 1
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    Novel Information Theory-Based Measures for Quantifying Incongruence among Phylogenetic Trees (2014)
    Oxford University Press
    Details
    Publication Date: 2014-04-23
    Description: Phylogenies inferred from different data matrices often conflict with each other necessitating the development of measures that quantify this incongruence. Here, we introduce novel measures that use information theory to quantify the degree of conflict or incongruence among all nontrivial bipartitions present in a set of trees. The first measure, internode certainty (IC), calculates the degree of certainty for a given internode by considering the frequency of the bipartition defined by the internode (internal branch) in a given set of trees jointly with that of the most prevalent conflicting bipartition in the same tree set. The second measure, IC All (ICA), calculates the degree of certainty for a given internode by considering the frequency of the bipartition defined by the internode in a given set of trees in conjunction with that of all conflicting bipartitions in the same underlying tree set. Finally, the tree certainty (TC) and TC All (TCA) measures are the sum of IC and ICA values across all internodes of a phylogeny, respectively. IC, ICA, TC, and TCA can be calculated from different types of data that contain nontrivial bipartitions, including from bootstrap replicate trees to gene trees or individual characters. Given a set of phylogenetic trees, the IC and ICA values of a given internode reflect its specific degree of incongruence, and the TC and TCA values describe the global degree of incongruence between trees in the set. All four measures are implemented and freely available in version 8.0.0 and subsequent versions of the widely used program RAxML.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Evidence for a high frequency of simultaneous double-nucleotide substitutions (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-02-26
    Description: Point mutations are generally assumed to involve changes of single nucleotides. Nevertheless, the nature and known mechanisms of mutation do not exclude the possibility that several adjacent nucleotides may change simultaneously in a single mutational event. Two independent approaches are used here to estimate the frequency of simultaneous double-nucleotide substitutions. The first examines switches between TCN and AGY (where N is any nucleotide and Y is a pyrimidine) codons encoding absolutely conserved serine residues in a number of proteins from diverse organisms. The second reveals double-nucleotide substitutions in primate noncoding sequences. These two complementary approaches provide similar high estimates for the rate of doublet substitutions, on the order of 0.1 per site per billion years.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Averof, M -- Rokas, A -- Wolfe, K H -- Sharp, P M -- New York, N.Y. -- Science. 2000 Feb 18;287(5456):1283-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Biotechnology (IMBB)-FORTH, Vassilika Vouton, 711 10 Iraklio, Crete, Greece.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10678838" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Substitution ; Animals ; *Codon ; Evolution, Molecular ; Globins/*genetics ; Haplorhini/genetics ; Humans ; Models, Genetic ; *Mutation ; Nucleotides/*genetics ; Phylogeny ; Serine/*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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  • 3
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    The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-02-15
    Description: Choanoflagellates are the closest known relatives of metazoans. To discover potential molecular mechanisms underlying the evolution of metazoan multicellularity, we sequenced and analysed the genome of the unicellular choanoflagellate Monosiga brevicollis. The genome contains approximately 9,200 intron-rich genes, including a number that encode cell adhesion and signalling protein domains that are otherwise restricted to metazoans. Here we show that the physical linkages among protein domains often differ between M. brevicollis and metazoans, suggesting that abundant domain shuffling followed the separation of the choanoflagellate and metazoan lineages. The completion of the M. brevicollis genome allows us to reconstruct with increasing resolution the genomic changes that accompanied the origin of metazoans.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2562698/" 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/PMC2562698/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉King, Nicole -- Westbrook, M Jody -- Young, Susan L -- Kuo, Alan -- Abedin, Monika -- Chapman, Jarrod -- Fairclough, Stephen -- Hellsten, Uffe -- Isogai, Yoh -- Letunic, Ivica -- Marr, Michael -- Pincus, David -- Putnam, Nicholas -- Rokas, Antonis -- Wright, Kevin J -- Zuzow, Richard -- Dirks, William -- Good, Matthew -- Goodstein, David -- Lemons, Derek -- Li, Wanqing -- Lyons, Jessica B -- Morris, Andrea -- Nichols, Scott -- Richter, Daniel J -- Salamov, Asaf -- Sequencing, J G I -- Bork, Peer -- Lim, Wendell A -- Manning, Gerard -- Miller, W Todd -- McGinnis, William -- Shapiro, Harris -- Tjian, Robert -- Grigoriev, Igor V -- Rokhsar, Daniel -- R01 CA058530/CA/NCI NIH HHS/ -- R01 CA058530-14/CA/NCI NIH HHS/ -- R01 GM077197/GM/NIGMS NIH HHS/ -- R01 HG004164/HG/NHGRI NIH HHS/ -- R01 HG004164-01/HG/NHGRI NIH HHS/ -- R37 HD028315/HD/NICHD NIH HHS/ -- England -- Nature. 2008 Feb 14;451(7180):783-8. doi: 10.1038/nature06617.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology and the Center for Integrative Genomics, University of California, Berkeley, California 94720, USA. nking@berkeley.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18273011" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Adhesion ; Conserved Sequence ; Eukaryotic Cells/classification/cytology/*metabolism ; Evolution, Molecular ; Extracellular Matrix/metabolism ; Gene Expression Regulation ; Genetic Speciation ; Genome/*genetics ; Hedgehog Proteins/chemistry/genetics ; Humans ; Introns/genetics ; Phosphotyrosine/metabolism ; *Phylogeny ; Protein Structure, Tertiary/genetics ; Receptors, Notch/chemistry/genetics ; Signal Transduction/genetics ; Transcription Factors/genetics/metabolism ; Transcription, Genetic
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 4
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    Remarkably ancient balanced polymorphisms in a multi-locus gene network (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-02-19
    Description: Local adaptations within species are often governed by several interacting genes scattered throughout the genome. Single-locus models of selection cannot explain the maintenance of such complex variation because recombination separates co-adapted alleles. Here we report a previously unrecognized type of intraspecific multi-locus genetic variation that has been maintained over a vast period. The galactose (GAL) utilization gene network of Saccharomyces kudriavzevii, a relative of brewer's yeast, exists in two distinct states: a functional gene network in Portuguese strains and, in Japanese strains, a non-functional gene network of allelic pseudogenes. Genome sequencing of all available S. kudriavzevii strains revealed that none of the functional GAL genes were acquired from other species. Rather, these polymorphisms have been maintained for nearly the entire history of the species, despite more recent gene flow genome-wide. Experimental evidence suggests that inactivation of the GAL3 and GAL80 regulatory genes facilitated the origin and long-term maintenance of the two gene network states. This striking example of a balanced unlinked gene network polymorphism introduces a remarkable type of intraspecific variation that may be widespread.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2834422/" 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/PMC2834422/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hittinger, Chris Todd -- Goncalves, Paula -- Sampaio, Jose Paulo -- Dover, Jim -- Johnston, Mark -- Rokas, Antonis -- 2T32HG00045/HG/NHGRI NIH HHS/ -- 5R01GM032540/GM/NIGMS NIH HHS/ -- R01 GM032540/GM/NIGMS NIH HHS/ -- R01 GM032540-27/GM/NIGMS NIH HHS/ -- T32 HG000045/HG/NHGRI NIH HHS/ -- T32 HG000045-10/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2010 Mar 4;464(7285):54-8. doi: 10.1038/nature08791. Epub 2010 Feb 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20164837" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; *Evolution, Molecular ; Galactose/metabolism ; Gene Regulatory Networks/*genetics ; Genes, Fungal/*genetics ; Genome, Fungal ; Japan ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Genetic/*genetics ; Portugal ; Pseudogenes/genetics ; Repressor Proteins/genetics/metabolism ; Saccharomyces/classification/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 5
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    Genomics. Genomics and the tree of life (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-09-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rokas, Antonis -- New York, N.Y. -- Science. 2006 Sep 29;313(5795):1897-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Broad Institute of Massachusetts Institute of Technology and Harvard University, Microbial Genome Analysis and Annotation, 7 Cambridge Center, Cambridge, MA 02142, USA. arokas@mit.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17008515" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Animals ; *Biological Evolution ; Computational Biology ; Genome ; *Genomics ; *Phylogeny ; Polymorphism, Genetic ; Sequence Analysis, DNA
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
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    The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-06-30
    Description: Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the presence of lignin. The only organisms capable of substantial lignin decay are white rot fungi in the Agaricomycetes, which also contains non-lignin-degrading brown rot and ectomycorrhizal species. Comparative analyses of 31 fungal genomes (12 generated for this study) suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and mycorrhizal species. Molecular clock analyses suggest that the origin of lignin degradation might have coincided with the sharp decrease in the rate of organic carbon burial around the end of the Carboniferous period.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Floudas, Dimitrios -- Binder, Manfred -- Riley, Robert -- Barry, Kerrie -- Blanchette, Robert A -- Henrissat, Bernard -- Martinez, Angel T -- Otillar, Robert -- Spatafora, Joseph W -- Yadav, Jagjit S -- Aerts, Andrea -- Benoit, Isabelle -- Boyd, Alex -- Carlson, Alexis -- Copeland, Alex -- Coutinho, Pedro M -- de Vries, Ronald P -- Ferreira, Patricia -- Findley, Keisha -- Foster, Brian -- Gaskell, Jill -- Glotzer, Dylan -- Gorecki, Pawel -- Heitman, Joseph -- Hesse, Cedar -- Hori, Chiaki -- Igarashi, Kiyohiko -- Jurgens, Joel A -- Kallen, Nathan -- Kersten, Phil -- Kohler, Annegret -- Kues, Ursula -- Kumar, T K Arun -- Kuo, Alan -- LaButti, Kurt -- Larrondo, Luis F -- Lindquist, Erika -- Ling, Albee -- Lombard, Vincent -- Lucas, Susan -- Lundell, Taina -- Martin, Rachael -- McLaughlin, David J -- Morgenstern, Ingo -- Morin, Emanuelle -- Murat, Claude -- Nagy, Laszlo G -- Nolan, Matt -- Ohm, Robin A -- Patyshakuliyeva, Aleksandrina -- Rokas, Antonis -- Ruiz-Duenas, Francisco J -- Sabat, Grzegorz -- Salamov, Asaf -- Samejima, Masahiro -- Schmutz, Jeremy -- Slot, Jason C -- St John, Franz -- Stenlid, Jan -- Sun, Hui -- Sun, Sheng -- Syed, Khajamohiddin -- Tsang, Adrian -- Wiebenga, Ad -- Young, Darcy -- Pisabarro, Antonio -- Eastwood, Daniel C -- Martin, Francis -- Cullen, Dan -- Grigoriev, Igor V -- Hibbett, David S -- New York, N.Y. -- Science. 2012 Jun 29;336(6089):1715-9. doi: 10.1126/science.1221748.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biology Department, Clark University, Worcester, MA 01610, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22745431" target="_blank"〉PubMed〈/a〉
    Keywords: Basidiomycota/classification/*enzymology/*genetics ; Bayes Theorem ; *Evolution, Molecular ; *Genome, Fungal ; Indoles ; Lignin/*metabolism ; Peroxidases/*genetics/metabolism ; Wood/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 7
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    Animal evolution and the molecular signature of radiations compressed in time (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-12-24
    Description: The phylogenetic relationships among most metazoan phyla remain uncertain. We obtained large numbers of gene sequences from metazoans, including key understudied taxa. Despite the amount of data and breadth of taxa analyzed, relationships among most metazoan phyla remained unresolved. In contrast, the same genes robustly resolved phylogenetic relationships within a major clade of Fungi of approximately the same age as the Metazoa. The differences in resolution within the two kingdoms suggest that the early history of metazoans was a radiation compressed in time, a finding that is in agreement with paleontological inferences. Furthermore, simulation analyses as well as studies of other radiations in deep time indicate that, given adequate sequence data, the lack of resolution in phylogenetic trees is a signature of closely spaced series of cladogenetic events.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rokas, Antonis -- Kruger, Dirk -- Carroll, Sean B -- New York, N.Y. -- Science. 2005 Dec 23;310(5756):1933-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Laboratory of Molecular Biology, R. M. Bock Labs, University of Wisconsin-Madison, 1525 Linden Drive, Madison, WI 53706, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16373569" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Computer Simulation ; DNA, Complementary ; Fungi/classification ; Genes ; Humans ; Invertebrates/classification/genetics ; Models, Biological ; Phylogeny ; Sequence Analysis, DNA ; 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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  • 8
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    Non-optimal codon usage is a mechanism to achieve circadian clock conditionality (2013)
    Nature Publishing Group (NPG)
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    Publication Date: 2013-02-19
    Description: Circadian rhythms are oscillations in biological processes that function as a key adaptation to the daily rhythms of most environments. In the model cyanobacterial circadian clock system, the core oscillator proteins are encoded by the gene cluster kaiABC. Genes with high expression and functional importance, such as the kai genes, are usually encoded by optimal codons, yet the codon-usage bias of the kaiBC genes is not optimized for translational efficiency. We discovered a relationship between codon usage and a general property of circadian rhythms called conditionality; namely, that endogenous rhythmicity is robustly expressed under some environmental conditions but not others. Despite the generality of circadian conditionality, however, its molecular basis is unknown for any system. Here we show that in the cyanobacterium Synechococcus elongate, non-optimal codon usage was selected as a post-transcriptional mechanism to switch between circadian and non-circadian regulation of gene expression as an adaptive response to environmental conditions. When the kaiBC sequence was experimentally optimized to enhance expression of the KaiB and KaiC proteins, intrinsic rhythmicity was enhanced at cool temperatures that are experienced by this organism in its natural habitat. However, fitness at those temperatures was highest in cells in which the endogenous rhythms were suppressed at cool temperatures as compared with cells exhibiting high-amplitude rhythmicity. These results indicate natural selection against circadian systems in cyanobacteria that are intrinsically robust at cool temperatures. Modulation of circadian amplitude is therefore crucial to its adaptive significance. Moreover, these results show the direct effects of codon usage on a complex phenotype and organismal fitness. Our work also challenges the long-standing view of directional selection towards optimal codons, and provides a key example of natural selection against optimal codons to achieve adaptive responses to environmental changes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3593822/" 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/PMC3593822/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xu, Yao -- Ma, Peijun -- Shah, Premal -- Rokas, Antonis -- Liu, Yi -- Johnson, Carl Hirschie -- GM062591/GM/NIGMS NIH HHS/ -- GM068496/GM/NIGMS NIH HHS/ -- R01 GM062591/GM/NIGMS NIH HHS/ -- R01 GM067152/GM/NIGMS NIH HHS/ -- R01 GM068496/GM/NIGMS NIH HHS/ -- R01 GM084283/GM/NIGMS NIH HHS/ -- R01 GM088595/GM/NIGMS NIH HHS/ -- England -- Nature. 2013 Mar 7;495(7439):116-20. doi: 10.1038/nature11942. Epub 2013 Feb 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23417065" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/genetics/metabolism ; Circadian Clocks/*genetics/*physiology ; Circadian Rhythm/genetics/physiology ; Circadian Rhythm Signaling Peptides and Proteins/genetics/metabolism ; Codon/*genetics ; Gene Expression Regulation, Bacterial/*genetics ; Genes, Bacterial/*genetics ; Multigene Family/genetics ; Phenotype ; Selection, Genetic ; Synechococcus/*genetics/*physiology ; Temperature
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 9
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    Inferring ancient divergences requires genes with strong phylogenetic signals (2013)
    Nature Publishing Group (NPG)
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    Publication Date: 2013-05-10
    Description: To tackle incongruence, the topological conflict between different gene trees, phylogenomic studies couple concatenation with practices such as rogue taxon removal or the use of slowly evolving genes. Phylogenomic analysis of 1,070 orthologues from 23 yeast genomes identified 1,070 distinct gene trees, which were all incongruent with the phylogeny inferred from concatenation. Incongruence severity increased for shorter internodes located deeper in the phylogeny. Notably, whereas most practices had little or negative impact on the yeast phylogeny, the use of genes or internodes with high average internode support significantly improved the robustness of inference. We obtained similar results in analyses of vertebrate and metazoan phylogenomic data sets. These results question the exclusive reliance on concatenation and associated practices, and argue that selecting genes with strong phylogenetic signals and demonstrating the absence of significant incongruence are essential for accurately reconstructing ancient divergences.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Salichos, Leonidas -- Rokas, Antonis -- England -- Nature. 2013 May 16;497(7449):327-31. doi: 10.1038/nature12130. Epub 2013 May 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23657258" target="_blank"〉PubMed〈/a〉
    Keywords: Candida/genetics ; Databases, Genetic ; *Evolution, Molecular ; *Genes, Fungal ; Genome, Fungal/genetics ; Models, Genetic ; *Phylogeny ; Saccharomyces/genetics ; Sequence Alignment ; Time Factors
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 10
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    Genomics. Lining up to avoid bias (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-01-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rokas, Antonis -- New York, N.Y. -- Science. 2008 Jan 25;319(5862):416-7. doi: 10.1126/science.1153156.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Vanderbilt University, VU Station B 35-1634, Nashville, TN 37235, USA. antonis.rokas@vanderbilt.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18218881" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Amino Acid Sequence ; Base Sequence ; Bias (Epidemiology) ; Computational Biology ; Evolution, Molecular ; *Genome, Fungal ; *Genomics ; Phylogeny ; Saccharomyces/*genetics ; Sequence Alignment/*methods/standards ; Software ; Uncertainty
    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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