Entries from 2010-02-01 to 1 month

PPR

Hernandez Mora JR, Rivals E, Mireau H & Budar F 2010 Sequence analysis of two alleles reveals that intra-and intergenic recombination played a role in the evolution of the radish fertility restorer (Rfo). BMC Plant Biol 10:35. some PPR pro…

PPR

O'Toole N, Hattori M, Andres C, Iida K, Lurin C, Schmitz-Linneweber C, Sugita M & Small I 2008 On the expansion of the pentatricopeptide repeat gene family in plants. Mol Biol Evol 25:1120-1128. a large majority of the PPR genes in each of…

phylogeography

Brito PH & Edwards SV 2009 Multilocus phylogeography and phylogenetics using sequence-based markers. Genetica 135:439-455. the phylogenetic tradition the discordance found was often ascribed not to independent realizations of the lineage s…

adaptive evolution

Halligan DL, Oliver F, Eyre-Walker A, Harr B & Keightley PD 2010 Evidence for pervasive adaptive protein evolution in wild mice. PLoS Genet 6:e1000825. estimates of the proportion of adaptive amino acid changes (α) vary greatly between tax…

evolutionary rate

Charlesworth D 2010 Don't forget the ancestral polymorphism. Heredity 105:509-510.

evolutionary rate

Peterson GI & Masel J 2009 Quantitative prediction of molecular clock and Ka / Ks at short timescales. Mol Biol Evol 26:2595-2603. the apparent acceleration of the molecular clock at short timescales can be explained by segregating polymor…

evolutionary rate

Gillespie JH & Langley CH 1979 Are evolutionary rates really variable? J Mol Evol 13:27-34. Langley and Fitch (1973, 1974) concluded that the evolutionary rates of four proteins in vertebrates are temporally variable the statistical analys…

weak selection

Traulsen A 2010 Mathematics of kin and group selection: formally equivalent? Evolution 64:316-323. the underlying mathematics of game theory is fundamentally different from the approach of inclusive fitness does a single cooperator have a …

transcriptional regulation

Weirauch MT & Hughes TR 2010 Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same. Trends Genet 26:66-74. cis- and trans-regulatory changes can contribute to sequence divergence wi…

diffusion method

Ohta T & Kimura M 1971 Genetic load due to mutations with very small effects. Jpn J Genet 46:393-401. Φ(p, x) = νm∫0∞φ(p, x; t)dt Φ(p, x) gives the steady flux distribution Φ(p, x)dt represents the expected number of sites in which the fre…

diffusion method

Maruyama T & Kimura M 1971 Some methods for treating continuous stochastic process in population genetics. Jpn J Genet 46:407-410. let us calculate the sum of heterozygosity for the paths leading to fixation H1(1)(p) = F1(1)(p) / p = (4Ne …

fixation time

Maruyama T & Kimura M 1974 A note on the speed of gene frequency changes in reverse directions in a finite population. Evolution 28:161-163. assuming no selection, it can be shown that under irreversible mutation from A to A', the average …

fixation time

Ewens WJ 2004 Mathematical population genetics I. Theoretical introduction. 2nd ed. Springer. ISBN:9780387201912 t*(x; p) is symmetric about x = 0.5 the mean time spent in any interval (x, x + δx) is the same as the mean time spent in (1 −…

fixation time

Otto SP & Whitlock MC 2008 Fixation probabilities and times. Encyclopedia Life Sci a0005464. when selection is very strong the fixation time is much shorter and is inversely proportional to the strength of selection although deleterious al…

fixation time

Otto SP & Whitlock MC 1997 The probability of fixation in populations of changing size. Genetics 146:723-733. deleterious alleles have a much lower probability of fixation, but conditional on fixation the expected time until fixation is th…

cis versus trans effects

Main BJ, Bickel RD, McIntyre LM, Graze RM, Calabrese PP & Nuzhdin SV 2009 Allele-specific expression assays using Solexa. BMC Genomics 20:422. to test for cis-by-trans, we compared allelic imbalance in the heterozygote and the introgressio…

cis versus trans effects

Jovelin R 2009 Rapid sequence evolution of transcription factors controlling neuron differentiation in Caenorhabditis. Mol Evol Biol 26:2373-2386. the role of transcription factor (TF) divergence in developmental evolution may be underesti…

transcriptional regulation

Odom DT, Dowell RD, Jaconbsen ES, Gordon W, Danford TW, MacIsaac KDRolfe PA, Conboy CM, Gifford DK & Fraenkel E 2007 Tissue-specific transcriptional regulation has diverged between human and mouse. Nat Genet 39:730-732. the binding sites f…

cis-trans compensation

Landry CR, Wittkopp PJ, Taubes CH, Ranz JM, Clark AG & Hartl DL 2005 Compensatory cis-trans evolution and the dysregulation of gene expression in interspecific hybrids of Drosophila. Genetics 171:1813-1822. cis- and trans-regulatory elemen…

cis versus trans effects

Wittkopp PJ, Haerum BK & Clark AG 2008 Independent effects of cis- and trans-regulatory variation on gene expression in Drosophila melanogaster. Genetics 178:1831-1835. over half of the yeast genes for which two quantitative trait loci (QT…

cis versus trans effects

Wittkopp PJ, Haerum BK & Clark AG 2004 Evolutionary changes in cis and trans gene regulation. Nature 430:85-88. the distribution of cis- and trans-regulatory changes provides insight into the evolution of regulatory networks these networks…