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  • Statistical Tests of the Coalescent Model Based on the Haplotype Frequency Distribution and the Number of Segregating Sites
    Hideki Innan, Kangyu Zhang, Paul Marjoram, Simon Tavaré, Noah A. Rosenberg
    Genetics March 2005 169: 1763-1777; https://doi.org/10.1534/genetics.104.032219
    ...CB2 2XZ, United Kingdom Manuscript received June 18, 2004 Accepted for publication December 8, 2004 ABSTRACT Several tests of neutral evolution employ the observed number of segregating sites and properties of the haplotype frequency distribution as summary statistics and use simulations to obtain ~~~
  • Investigation of the Properties of Non-gypsy Suppressor of Hairy-wing-Binding Sites
    Emily J. Kuhn-Parnell, Cecilia Helou, David J. Marion, Brian L. Gilmore, Timothy J. Parnell, Marc S. Wold, Pamela K. Geyer
    Genetics July 2008 179: 1263-1273; https://doi.org/10.1534/genetics.108.087254
    ...that interactions occur between two SI 62D elements, but not between SI 62D and the gypsy insulator, limiting the scope of genomic gypsy insulator interactions. Enhancer blocking by SI 62D requires fewer Su(Hw)-binding sites than needed for gypsy insulator function, with these target regions having distinct zinc ~~~
  • Quantitative Trait Locus Mapping of Genes Under Selection Across Multiple Years and Sites in Avena barbata: Epistasis, Pleiotropy, and Genotype-by-Environment Interactions
    Robert G. Latta, Kyle M. Gardner, David A. Staples
    Genetics May 2010 185: 375-385; https://doi.org/10.1534/genetics.110.114389
    ...transgressive segregation, but also show significant epistasis giving hybrid breakdown. This epistasis is the result of sharply lower fitness in only one of the recombinant genotypes, suggesting that the loci may contain synergistically acting mutations. Within each trial (year/site combination), we can explain ~~~
  • The Role of MITF Phosphorylation Sites During Coat Color and Eye Development in Mice Analyzed by Bacterial Artificial Chromosome Transgene Rescue
    Georg L. Bauer, Christian Praetorius, Kristín Bergsteinsdóttir, Jón H. Hallsson, Bryndís K. Gísladóttir, Alexander Schepsky, Deborah A. Swing, T. Norene O'Sullivan, Heinz Arnheiter, Keren Bismuth, Julien Debbache, Colin Fletcher, Søren Warming, Neal G. Copeland, Nancy A. Jenkins, Eiríkur Steingrímsson
    Genetics October 2009 183: 581-594; https://doi.org/10.1534/genetics.109.103945
    ...results in phosphorylation of MITF on serine residues 73 and 409. However, the precise role of signaling to MITF in vivo remains largely unknown. Here, we use a BAC transgene rescue approach to introduce specific mutations in MITF to study the importance of specific phospho-acceptor sites and protein ~~~
  • Distal Recognition Sites in Substrates Are Required for Efficient Phosphorylation by the cAMP-Dependent Protein Kinase
    Stephen J. Deminoff, Vidhya Ramachandran, Paul K. Herman
    Genetics June 2009 182: 529-539; https://doi.org/10.1534/genetics.109.102178
    ...to the sites of phosphorylation and were found to interact with a C-terminal region of PKA that was itself removed from the active site. Only a small set of PKA alterations resulted in a stable association with substrates, and the identified residues were clustered together within the hydrophobic core ~~~
  • Genome-Wide Characterization of Tetrahymena thermophila Chromosome Breakage Sites. I. Cloning and Identification of Functional Sites
    Eileen Hamilton, Peter Bruns, Cindy Lin, Virginia Merriam, Eduardo Orias, Linh Vong, Donna Cassidy-Hanley
    Genetics August 2005 170: 1611-1621; https://doi.org/10.1534/genetics.104.031401
    ...for publication May 10, 2005 ABSTRACT The chromosomes of the macronuclear (expressed) genome of Tetrahymena thermophila are generated by developmental fragmentation of the five micronuclear (germline) chromosomes. This fragmentation is site specific and directed by a conserved 15-bp chromosome breakage sequence ~~~
  • Positive Selection at the Binding Sites of the Male-Specific Lethal Complex Involved in Dosage Compensation in Drosophila
    Doris Bachtrog
    Genetics October 2008 180: 1123-1129; https://doi.org/10.1534/genetics.107.084244
    ...differ with respect to their sex chromosomes, and dosage compensation mechanisms have evolved to equalize X-linked gene transcription. In Drosophila, the male-specific lethal (MSL) complex binds to hundreds of sites along the male X chromosome and mediates twofold hypertranscription of the single male X ~~~
  • Effect of Misoriented Sites on Neutrality Tests With Outgroup
    Emmanuelle Baudry, Frantz Depaulis
    Genetics November 2003 165: 1619-1622;
    ...population of constant size. which is based on the total number of polymorphicDepartures from this model are typically attributed to sites, and Tajimas (1983) diversity (respectively) toselective or demographic effects. A rarely considered e, the number of derived unique mutations (mutationsalternative ~~~
  • Coincidence of P-Insertion Sites and Breakpoints of Deletions Induced by Activating P Elements in Drosophila
    Jyotsna Sudi, Sen Zhang, Gino Intrieri, Ximing Hao, Ping Zhang
    Genetics May 2008 179: 227-235; https://doi.org/10.1534/genetics.107.085498
    ...for publication February 26, 2008 ABSTRACT We isolated a set of seven deletions in the 67B region by activating a nearby P-element insertion. The structures of the deletions were characterized by cloning and sequencing. The results showed that the P-induced deletions occurred nonrandomly in the genomic sites. One ~~~
  • Estimation of the Amount of DNA Polymorphism When the Neutral Mutation Rate Varies Among Sites
    Kazuharu Misawa, Fumio Tajima
    Genetics December 1997 147: 1959-1964;
    ...of DNA polymorphism is essential to understand the mechanism of maintaining DNA polymorphism in a natural population. The amount of DNA polymorphism can be measured by the average number of nucleotide differences per site (T), the proportion of segregating (polymorphic) site (s) and the minimum number ~~~

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