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Methods: Detection of nonneutral substitution rates on mammalian phylogenies
- Katherine S. Pollard,
- Melissa J. Hubisz,
- Kate R. Rosenbloom,
- and Adam Siepel
Genome Res. January 2010 20: 110-121; Published in Advance October 26, 2009, doi:10.1101/gr.097857.109
...of individual nucleotides. In this study, we examine the problem of detecting nonneutral substitution rates from aligned genomic sequences, focusing on what is possible with currently available data for the eutherian mammals. Our contributions consist of four main components: (1) a detailed comparison of four...
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ARTICLE: Patterns of Insertions and Their Covariation With Substitutions in the Rat, Mouse, and Human Genomes
- Shan Yang,
- Arian F. Smit,
- Scott Schwartz,
- Francesca Chiaromonte,
- Krishna M. Roskin,
- David Haussler,
- Webb Miller,
- and Ross C. Hardison
Genome Res. April 2004 14: 517-527; doi:10.1101/gr.1984404
...Sequencing Consortium 2002 ) provide an opportunity to better understand rates and mechanisms of eutherian evolution. Previous analysis of whole- alignments between human and mouse showed that the rates of several processes by which DNA diverges, including neutral nucleotide substitution, insertions...
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ARTICLE: Comparative Recombination Rates in the Rat, Mouse, and Human Genomes
- Michael I. Jensen-Seaman,
- Terrence S. Furey,
- Bret A. Payseur,
- Yontao Lu,
- Krishna M. Roskin,
- Chin-Fu Chen,
- Michael A. Thomas,
- David Haussler,
- and Howard J. Jacob
Genome Res. April 2004 14: 528-538; doi:10.1101/gr.1970304
...insights into the factors that covary with, and therefore may be affecting or affected by, recombination that are seen in only one species. Data from more mammals will likely reveal lineage-specific patterns in the evolution of recombination. Genetic maps are available for a number of additional species...
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Research: The (r)evolution of SINE versus LINE distributions in primate genomes: Sex chromosomes are important
- Erika M. Kvikstad and
- Kateryna D. Makova
Genome Res. May 2010 20: 600-613; Published in Advance March 10, 2010, doi:10.1101/gr.099044.109
...of recombination-driven deletion in driving TE distributions over evolutionary time. Thus, Alu and L1 densities have been influenced by the combination of distinct local landscapes and the unique evolutionary dynamics of sex chromosomes. [Supplemental material is available online at http://www..org.] Transposable...
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LETTER: Reduced purifying selection prevails over positive selection in human copy number variant evolution
- Duc-Quang Nguyen,
- Caleb Webber,
- Jayne Hehir-Kwa,
- Rolph Pfundt,
- Joris Veltman,
- and Chris P. Ponting
Genome Res. November 2008 18: 1711-1723; Published in Advance August 7, 2008, doi:10.1101/gr.077289.108
...for the accumulation of deleterious substitutions to be apparent in increased d N /d S values. We present evidence in a separate manuscript that, indeed, recombination rates are an ancestral trait of metatherian and eutherian mammals (C. Webber and C.P. Ponting, in prep.). A model of inefficient purifying selection...
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Chicken Special/Letters: Evolution and functional classification of vertebrate gene deserts
- Ivan Ovcharenko,
- Gabriela G. Loots,
- Marcelo A. Nobrega,
- Ross C. Hardison,
- Webb Miller,
- and Lisa Stubbs
Genome Res. January 2005 15: 137-145; Published in Advance December 8, 2004, doi:10.1101/gr.3015505
..., transposition, and recombination during eutherian evolution. Genome Res. 13 : 13 -26. ↵ Hasse, A. and Schulz, W.A. 1994 . Enhancement of reporter gene de novo methylation by DNA fragments from the α-fetoprotein control region. J. Biol. Chem. 269 : 1821 -1826. ↵ International Chicken Genome Sequencing Consortium...
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LETTER: An analysis of the gene complement of a marsupial, Monodelphis domestica: Evolution of lineage-specific genes and giant chromosomes
- Leo Goodstadt,
- Andreas Heger,
- Caleb Webber,
- and Chris P. Ponting
Genome Res. July 2007 17: 969-981; Published in Advance May 10, 2007, doi:10.1101/gr.6093907
...for the portions of the human X chromosome that are syntenic to the Monodelphis chromosomes 4 and 7 and that appear to have conjoined the rest of the X chromosome early in eutherian evolution ( Glas et al. 1999 ) ( Figs. 2B , 3C ; Supplemental Table 1). Moreover, nucleotide substitution rates and overall G...
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ARTICLE: Genomic Regionality in Rates of Evolution Is Not Explained by Clustering of Genes of Comparable Expression Profile
- Martin J. Lercher,
- Jean-Vincent Chamary,
- and Laurence D. Hurst
Genome Res. June 2004 14: 1002-1013; doi:10.1101/gr.1597404
...2003 ; Filatov and Gerrard 2003 ; Hellmann et al. 2003 ), possibly indicating a mutagenic effect of recombination. GC and recombination rates are known to covary ( Eyre-Walker 1993 ; Fullerton et al. 2001 ), and it has recently been argued that substitutional GC biases are directly associated...
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LETTER: Patterns of Evolutionary Constraints in Intronic and Intergenic DNA of Drosophila
- Daniel L. Halligan,
- Adam Eyre-Walker,
- Peter Andolfatto,
- and Peter D. Keightley
Genome Res. February 2004 14: 273-279; doi:10.1101/gr.1329204
...eutherian evolution. Genome Res. 13 : 13 -26. ↵ Hellmann, I., Zollner, S., Enard W., Ebersberger, I., Nickel, B., and Pääbo, S. 2003 . Selection on human genes as revealed by comparisons to chimpanzee cDNA. Genome Res. 13 : 831 -837. ↵ International Human Genome Sequencing Consortium. 2001 . Initial...
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Review: What fraction of the human genome is functional?
- Chris P. Ponting and
- Ross C. Hardison
Genome Res. November 2011 21: 1769-1776; Published in Advance August 29, 2011, doi:10.1101/gr.116814.110
..., Yang S, Diekhans M, KentWJ,Weber R, Elnitski L, Li J, O’Connor M, Kolbe D, et al. 2003. Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Res 13: 13–26. Jordan IK, Rogozin IB, Glazko GV, Koonin EV. 2003. Origin of a substantial...
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