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  • 1
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    A phylogenomic study of birds reveals their evolutionary history (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-06-28
    Description: Deep avian evolutionary relationships have been difficult to resolve as a result of a putative explosive radiation. Our study examined approximately 32 kilobases of aligned nuclear DNA sequences from 19 independent loci for 169 species, representing all major extant groups, and recovered a robust phylogeny from a genome-wide signal supported by multiple analytical methods. We documented well-supported, previously unrecognized interordinal relationships (such as a sister relationship between passerines and parrots) and corroborated previously contentious groupings (such as flamingos and grebes). Our conclusions challenge current classifications and alter our understanding of trait evolution; for example, some diurnal birds evolved from nocturnal ancestors. Our results provide a valuable resource for phylogenetic and comparative studies in birds.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hackett, Shannon J -- Kimball, Rebecca T -- Reddy, Sushma -- Bowie, Rauri C K -- Braun, Edward L -- Braun, Michael J -- Chojnowski, Jena L -- Cox, W Andrew -- Han, Kin-Lan -- Harshman, John -- Huddleston, Christopher J -- Marks, Ben D -- Miglia, Kathleen J -- Moore, William S -- Sheldon, Frederick H -- Steadman, David W -- Witt, Christopher C -- Yuri, Tamaki -- New York, N.Y. -- Science. 2008 Jun 27;320(5884):1763-8. doi: 10.1126/science.1157704.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Zoology Department, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18583609" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Animals ; Biological Evolution ; Birds/*classification/*genetics ; Ecosystem ; Flight, Animal ; *Genome ; *Genomics ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Combinatorial binding predicts spatio-temporal cis-regulatory activity (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-11-06
    Description: Development requires the establishment of precise patterns of gene expression, which are primarily controlled by transcription factors binding to cis-regulatory modules. Although transcription factor occupancy can now be identified at genome-wide scales, decoding this regulatory landscape remains a daunting challenge. Here we used a novel approach to predict spatio-temporal cis-regulatory activity based only on in vivo transcription factor binding and enhancer activity data. We generated a high-resolution atlas of cis-regulatory modules describing their temporal and combinatorial occupancy during Drosophila mesoderm development. The binding profiles of cis-regulatory modules with characterized expression were used to train support vector machines to predict five spatio-temporal expression patterns. In vivo transgenic reporter assays demonstrate the high accuracy of these predictions and reveal an unanticipated plasticity in transcription factor binding leading to similar expression. This data-driven approach does not require previous knowledge of transcription factor sequence affinity, function or expression, making it widely applicable.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zinzen, Robert P -- Girardot, Charles -- Gagneur, Julien -- Braun, Martina -- Furlong, Eileen E M -- England -- Nature. 2009 Nov 5;462(7269):65-70. doi: 10.1038/nature08531.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉European Molecular Biology Laboratory, D-69117 Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19890324" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Genetically Modified ; Artificial Intelligence ; Chromatin Immunoprecipitation ; Conserved Sequence/genetics ; Databases, Genetic ; Drosophila melanogaster/*embryology/*genetics ; Enhancer Elements, Genetic/genetics ; *Gene Expression Regulation, Developmental/genetics ; Genes, Reporter/genetics ; Mesoderm/embryology/metabolism ; *Models, Genetic ; Protein Binding ; Time Factors ; Transcription Factors/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    Developmental biology. Home for the precious few (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-09-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉DiNardo, Steve -- Braun, Robert E -- New York, N.Y. -- Science. 2007 Sep 21;317(5845):1696-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104-6058, USA. sdinardo@mail.med.upenn.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17885122" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Male ; Mice ; Pluripotent Stem Cells/cytology ; Spermatogonia/*cytology ; Testis/*cytology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    Early hominin foot morphology based on 1.5-million-year-old footprints from Ileret, Kenya (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-03-03
    Description: Hominin footprints offer evidence about gait and foot shape, but their scarcity, combined with an inadequate hominin fossil record, hampers research on the evolution of the human gait. Here, we report hominin footprints in two sedimentary layers dated at 1.51 to 1.53 million years ago (Ma) at Ileret, Kenya, providing the oldest evidence of an essentially modern human-like foot anatomy, with a relatively adducted hallux, medial longitudinal arch, and medial weight transfer before push-off. The size of the Ileret footprints is consistent with stature and body mass estimates for Homo ergaster/erectus, and these prints are also morphologically distinct from the 3.75-million-year-old footprints at Laetoli, Tanzania. The Ileret prints show that by 1.5 Ma, hominins had evolved an essentially modern human foot function and style of bipedal locomotion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bennett, Matthew R -- Harris, John W K -- Richmond, Brian G -- Braun, David R -- Mbua, Emma -- Kiura, Purity -- Olago, Daniel -- Kibunjia, Mzalendo -- Omuombo, Christine -- Behrensmeyer, Anna K -- Huddart, David -- Gonzalez, Silvia -- New York, N.Y. -- Science. 2009 Feb 27;323(5918):1197-201. doi: 10.1126/science.1168132.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Conservation Sciences, Bournemouth University, Poole, BH12 5BB, UK. mbennett@bmth.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19251625" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biomechanical Phenomena ; Body Size ; Foot/*anatomy & histology/physiology ; *Fossils ; Gait ; Geologic Sediments ; Hallux/anatomy & histology ; Hominidae/*anatomy & histology/physiology ; Humans ; Kenya ; Locomotion ; Pressure ; Software ; Toes/anatomy & histology/physiology
    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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