Weinert LA, Welch JJ, Suchard MA, Lemey P, Rambaut A, Fitzgerald JR (2012). Molecular dating of human to bovid host jumps in Staphylococcus aureus reveals an association with the spread of domestication. Biology Letters In Press.
Armitage AE, Deforche K, Chang C-h, Wee E, Kramer B, Welch JJ, Gerstoft J, Fugger L, McMichael A, Rambaut A, Iversen AKN (2012) APOBEC3G-induced hypermutation of Human Immunodeficiency Virus type-1 is typically a discrete "all or nothing" phenomenon. PLoS Genetics 8: e1002550.
Edwards CJ, Suchard MA, Lemey P, Welch JJ, Barnes I, Fulton TL, Barnett R, O'Connell TC, Coxon P, Monaghan N, Valdiosera CE, Lorenzen ED, WIllerslev E, Baryshnikov GF, Rambaut A, Thomas MG, Bradley DG & Shapiro B (2011) Ancient hybridization and an Irish origin for the modern polar bear matriline. Current Biology 21: 1251-1258.
Press coverage:
BBC News, The Guardian, Science, News of the World, Mirror, USA Today.
Gardner A, Welch JJ (2011) A formal theory of the selfish gene. J Evol Biol 24: 1801-1813.
Bierne N, Welch J, Loire E, Bonhomme F, David P (2011) The coupling hypothesis: why genome scans may fail to map local adaptation genes. Mol Ecol 20: 2044-2072.
Lanfear R, Welch JJ & Bromham L (2010) Watching the Clock: Studying variation in rates of molecular evolution between species. Trends Ecol Evol 25: 495-503.
Lemey P, Rambaut A, Welch JJ & Suchard MA (2010) Phylogeography takes a relaxed random walk in continuous space and time. Mol Biol Evol 27: 1877-1886.
Welch JJ (2010) The "island rule" and deep-sea gastropods: Re-examining the evidence. PLoS One 5: e8776.
Thomas JA, Welch JJ, Lanfear R & Bromham L (2010) A generation time effect on the rate of molecular evolution in invertebrates. Mol Biol Evol 27: 1173-1180.
Obbard DJ, Welch JJ, Kim K-W & Jiggins FM (2009) Quantifying adaptive evolution in the Drosophila immune system: a high throughput approach. PLoS Genetics 5: e1000698.
Weinert, LA, Welch JJ & Jiggins FM (2009) Conjugation genes are common throughout the genus Rickettsia and are transmitted horizontally. Proc Roy Soc B 276: 3619-3627.
Obbard DJ, Welch JJ & Little TJ (2009) Inferring selection in the Anopheles gambiae species complex: an example from immune-related serine protease inhibitors. Malaria Journal 8: 117.
Betancourt AJ, Welch JJ & Charlesworth B (2009) Reduced effectiveness of selection caused by a lack of recombination on the dot chromosome of Drosophila americana. Current Biology 19: 655-660.
Welch JJ (2009) Testing the Island Rule: Primates as a case study. Proc Roy Soc B 276: 675-682.
Welch JJ, Eyre-Walker A & Waxman D (2008) Divergence and polymorphism under the nearly neutral theory of molecular evolution. J Mol Evol 67: 418-26.
Armitage AE, Katzourakis A, de Oliveira T, Welch JJ, Belshaw R, Bishop KN, Kramer B, McMichael AJ, Rambaut A & Iversen AKN (2008) Conserved footprints of APOBEC3G on hypermutated HIV-1 and HERV-K(HML2) sequences. J Virol 82: 8743-8761.
Welch JJ, Bininda-Emonds ORP & Bromham L (2008) Correlates of substitution rate variation in mammalian protein-coding sequences. BMC Evol Biol 8: 53.
Welch JJ & Waxman D (2008) Calculating independent contrasts for the comparative study of substitution rates. J Theor Biol 251: 667-678.
Lanfear R, Thomas JA, Welch JJ, Brey T & Bromham L (2007) Metabolic rate does not calibrate the molecular clock. Proc Natl Acad Sci USA 104: 15388-15393.
Fontanillas E, Welch JJ, Thomas JA & Bromham L (2007) The influence of body size and net diversification rate on molecular evolution during the radiation of animal phyla. BMC Evol Biol 7: 95.
Welch JJ (2006) Estimating the genomewide rate of adaptive protein evolution in Drosophila. Genetics 173: 821-837.
Thomas JA, Welch JJ, Woolfit M & Bromham L (2006) There is no universal molecular clock for invertebrates, but rate variation does not scale with body size. Proc Natl Acad Sci USA 103: 7366-7371.
Waxman D & Welch JJ (2005) Fisher's Microscope and Haldane's Ellipse. Am Nat 166: 447-457.
Stoletzki N, Welch J, Hermisson J & Eyre-Walker A (2005) A dissection of volatility in yeast. Mol Biol Evol 22: 2022-2026.
Welch JJ, Fontanillas E & Bromham L (2005) Molecular dates for the "Cambrian explosion": the influence of prior assumptions. Syst Biol 54: 672-678.
Welch JJ & Bromham L (2005) Molecular dating when rates vary. Trends Ecol Evol 20: 320-327.
Welch JJ & Waxman D (2005) The nk model and population genetics. J Theor Biol 234: 329-340.
Welch JJ (2004) Accumulating Dobzhansky-Muller incompatibilities: reconciling theory with data. Evolution 58: 1145-1156.
Peck JR & Welch JJ (2004) Adaptation and species range. Evolution 58: 211-221.
Welch JJ & Waxman D (2003) Modularity and the cost of complexity. Evolution 57: 1723-1734.
Waxman D & Welch J (2003) Non-equivalent loci and mutation-selection balance. Theor Popul Biol 63: 339-345.
Welch JJ & Waxman D (2002) Non-equivalent loci and the distribution of mutant effects. Genetics 161: 897-904.
Publications
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