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Evolution of genes and genomes on the Drosophila phylogeny

Clark, Andrew G. and Pachter, Lior (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature, 450 (7167). pp. 203-218. ISSN 0028-0836. doi:10.1038/nature06341.

[img] PDF (all methods for the project as well as further detail on certain sections. Also contains Supplementary Tables 1-10 and 13-20, and Supplementary Figures 1-10 with Legends) - Supplemental Material
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[img] MS Excel (Supplementary Table 11 which is a list of 44 lineage-specific genes arising in the melanogaster group or some subset of the melanogaster group phylogeny) - Supplemental Material
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[img] MS Excel (Supplementary Table 12 which shows median value of omega, the negative log of the P-value from the test of positive selection and dN for each of the 115 GO)
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Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

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Pachter, Lior0000-0002-9164-6231
Additional Information:© 2007 Macmillan Publishers Limited. Received 19 July 2007; Accepted 5 October 2007. Agencourt Bioscience Corporation, The Broad Institute of MIT and Harvard and the Washington University Genome Sequencing Center were supported by grants and contracts from the National Human Genome Research Insititute (NHGRI). T.C. Kaufman acknowledges support from the Indian Genomics Initiative. Author Contributions The laboratory groups of A. G. Clark (including A. M. Larracuente, T. B. Sackton, and N. D. Singh) and Michael B. Eisen (including V. N. Iyer and D. A. Pollard) played the part of coordinating the primary writing and editing of the manuscript with the considerable help of D. R. Smith, C. M. Bergman, W. M. Gelbart, B. Oliver, T. A. Markow, T. C. Kaufman and M. Kellis. D. R. Smith served as primary coordinator for the assemblies. The remaining authors contributed either through their efforts in sequence production, assembly and annotation, or in the analysis of specific topics that served as the focus of more than 40 companion papers. The author declares no competing financial interests.
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National Human Genome Research InstituteUNSPECIFIED
Indian Genomics InitiativeUNSPECIFIED
Issue or Number:7167
Record Number:CaltechAUTHORS:20170307-113900780
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:74850
Deposited By: George Porter
Deposited On:07 Mar 2017 20:41
Last Modified:11 Nov 2021 05:30

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