Hadjirin NF, Miller EL, Murray GGR, Yen PLK, Phuc HD, Wileman TM, Hernandez-Garcia J, Williamson SM, Parkhill J, Maskell DJ, Zhou R, Fittipaldi N, Gottschalk N, Tucker AW, Hoa NT, Welch JJ, Weinert LA (2021). Large scale genomic analysis of antimicrobial resistance in the zoonotic pathogen Streptococcus suis. BMC Biology (in press).

Hammel M, Simon A, Arbiol C, Villalba A, Burioli EAV, Pépin J-F, Lamy J-B, Benabdelmouna A, Bernard I, Houssin M, Charrière GM, Destoumieux-Garzon D, Welch JJ, Metzger MJ,  Bierne N (2021). Prevalence and polymorphism of a mussel transmissible cancer in Europe. Mol Ecol (in press).

Murray GGR*, Charlesworth* J, Miller EL, Casey MJ, Lloyd CT, Gottschalk M, Tucker AW, Welch JJ, Weinert LA (2021).  Genome reduction is associated with bacterial pathogenicity across different scales of temporal and ecological divergence. Mol Biol Evol 38: 1570-1579. doi: 10.1093/molbev/msaa323

Martinez J, Klasson L, Welch JJ, Jiggins FM. (2021). Life and death of selfish genes: comparative genomics reveals the dynamic evolution of cytoplasmic incompatibility. Mol Biol Evol 38: 2-15. doi: 10.1093/molbev/msaa209

Simon A, Fraïsse C, El Ayari T, Liautard-Haag C, Strelkov P, Welch JJ, Bierne N (2021). How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels. Journal of Evolutionary Biology 34: 208-223. doi: 10.1111/jeb.13709

Schneemann H*, De Sanctis B*, Roze D, Bierne N, Welch JJ (2020).  The geometry and genetics of hybridization. Evolution 74: 2575-2590. doi:10.1111/evo.14116

Butt BG, Owen DJ, Jeffries C, Ivanova L, Houghton JW, Ahmed MF, Antrobus F, Svergun DI, Welch JJ, Crump CM, Graham SC (2020).  Structure of herpes simplex virus pUL7:pUL51, a conserved complex required for efficient herpesvirus assembly. eLife 9: e53789 doi: 10.7554/eLife.53789

Simon A, Arbiol C, Nielsen EE, Couteau J, Sussarellu R, Burgeot T, Bernard I, Coolen JWP, Lamy J-B, Robert S, Skazina M, Strelkov P, Queiroga H, Cancio I, Welch JJ, Viard F, Bierne N (2020).  Replicated anthropogenic hybridisations reveal parallel patterns of admixture in marine mussels. Evolutionary Applications 13: 575-599. doi:10.1111/eva.12879

Charlesworth J, Weinert LA, Araujo-Jnr EV, Welch JJ (2019). Wolbachia, Cardinium and climate: an analysis of global data. Biology Letters 5: 20190273. doi:10.1098/rsbl.2019.0273

Gossmann TI, Shanmugasundram A, Börno S, Duvaux L, Lemaire C, Kuhl H, Klages S, Roberts LD, Schade S, Gostner JM, Hildebrand F, Vowinckel J, Bichet C, Mülleder M, Calvani E, Zelezniak A, Griffin JL, Bork P, Allaine D, Cohas A, Welch JJ*, Timmermann B,* Ralser M* (2019). Ice-age climate adaptations trap the Alpine marmot in a state of low genetic diversity. Current Biology 29: 1712-1720.  doi:10.1016/j.cub.2019.04.020

Fraïsse C, Welch JJ (2019). The distribution of epistasis on simple fitness landscapes. Biology Letters 15: 20180881. doi:10.1098/rsbl.2018.0881

Simon A, Bierne N, Welch JJ (2018). Coadapted genomes and selection on hybrids: Fisher's geometric model explains a variety of empirical patterns. Evolution Letters 2: 472-498. doi:10.1002/evl3.66

Fraïsse C, Roux C, Gagnaire P-A, Romiguier J, Faivre N, Welch JJ, Bierne N (2018). The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: the effects of sequencing techniques and sampling strategies. PeerJ 6: e51986.

Peck JR, Waxman D (2018) What is adaptation, and how should it be measured? J Theor Biol 447: 190-198.

Weinert LA, Welch JJ (2017). Why might bacterial pathogens have small genomes? Trends Ecol Evol 32: 936-947. doi:10.1016/j.tree.2017.09.006

Welch JJ (2017). What’s wrong with evolutionary biology? Biology and Philosophy 32: 263-279. doi:10.1007/s10539-016-9557-8

Fraïsse C, Gunnarsson PA, Roze D, Bierne N, Welch JJ (2016). The genetics of speciation: insights from Fisher’s geometric model. Evolution 70: 1450-1464. doi:10.1111/evo.12968.

Murray GGR, Weinert LA, Rhule EL, Welch JJ (2016). The Phylogeny of Rickettsia Using Different Evolutionary Signatures: How Tree-Like is Bacterial Evolution? Syst Biol 65: 265-279. doi: 10.1093/sysbio/syv084.

Murray GGR, Wang F, Harrison EM, Paterson GK, Mather AE, Harris SR, Holmes MA, Rambaut A, Welch JJ (2016). The effect of genetic structure on molecular dating and tests for temporal signal. Methods Ecol Evol 7: 80-89.

Welch JJ (2016). Selfish Gene. Entry for the SAGE Encyclopedia of Political Behavior. Ed. F. M. Moghaddam.

Fraïsse C, Belkhir K, Welch JJ, Bierne N (2016). Local inter-species introgression is the main cause of extreme levels of intra-specific differentiation in mussels. Mol Ecol 25: 269-286. doi:10.1111/mec.13299.

Longdon B, Murray GGR, Palmer WJ, Day JP, Parker DJ, Welch JJ, Obbard DJ, Jiggins FM (2015). The evolution, diversity and host associations of rhabdoviruses. Virus evolution 1: vev014.

Ahmed MZ, Araujo-Jnr EV, Welch JJ, Kawahara AY (2015). Wolbachia in butterflies and moths: geographical structure in infection frequency. Front Zool 12: 16.

Weinert LA*, Araujo-Jnr EV, Ahmed MZ, Welch JJ (2015). The incidence of bacterial endosymbionts in terrestrial arthropods. Proc R Soc B 282: 20150249. doi: 10.1098/rspb.2015.0249.

Weinert LA, Depledge DP, Kundu S, Gershon AA, Nichols RA, Balloux F, Welch JJ, Breuer J (2015). Rates of vaccine evolution show strong effects of latency: implications for Varicella Zoster virus epidemiology. Mol Biol Evol 32: 1020-1028. doi: 10.1093/molbev/msu406.

Paterson GK*, Harrison EM*, Murray GGR, Welch JJ, Warland JH, Holden MTG, Morgan FJE, Ba X, Koop G, Harris SR, Maskell DJ, Peacock SJ, Herrtage ME, Parkhill J, Holmes MA (2015) Capturing the cloud of diversity reveals complexity and heterogeneity of MRSA carriage, infection and transmission. Nature Comms 6: 6560. doi:10.1038/ncomms7560.

Armitage AE, Deforche K, Welch JJ, Van Laethem K, Camacho R, Rambaut A, Iversen AKN (2014) Possible footprints of APOBEC3F and/or other APOBEC3 deaminases – but not APOBEC3G – on HIV-1 from patients during acute/early and chronic infectionJ Virol 88: 12882-12894. doi:10.1128/JVI/01460-14.

Longdon B, Brockhurst MA, Russell CA, Welch JJ, Jiggins FM (2014) The evolution and genetics of virus host shifts. PLoS Pathogens 10: e1004395. doi:10.1371/journal.ppat.1004395.

Welch JJ, Jiggins CD (2014) Standing and flowing: The complex origins of adaptive variation. Mol Ecol 23: 3935-3937. doi:10.1111/mec.12859.

Fraïsse C, Roux C, Welch JJ, Bierne N (2014) Gene-flow in a mosaic hybrid zone: is local introgression adaptive? Genetics 197: 939-951. doi:10.1534/genetics.114.161380.

Waxman D*, Weinert LA*, Welch JJ (2014) Inferring host range dynamics from comparative data: the protozoan parasites of New World monkeys. Am Nat 184: 65-74.

Harrison EM, Weinert LA, Holden MTG, Welch JJ, Wilson K, Morgan FJE, Harris SA, Loeffler A, Boag AK, Peacock SJ, Paterson GK, Waller AS, Parkhill J, Holmes MA (2014) A shared population of epidemic MRSA-15 circulates in humans and companion animals. MBio 5: e00985-13. doi:10.1128/mBio.00985-13

        Press coverage:

            Vaccine news, VetMedResource

Fraïsse C*, Elderfield JAD*, & Welch JJ (2014) The Genetics of Speciation: Are complex incompatibilities easier to evolve? J Evol Biol 27: 688-699. doi:10.1111/jeb.12339.

Ahmed MZ, Greyvenstein OFC, Erasmus C, Welch JJ & Greef JM (2013) Consistently high incidence of Wolbachia in global fig wasp communities. Ecol Entomol 38: 147-154. doi:10.1111/een/12002.

Bierne N, Roze D & Welch JJ (2013) Pervasive selection or is it…? why are Fst outliers sometimes so frequent? Mol Ecol 22: 2061-64. doi:10.1111/mec.12241

Thomas JA, Trueman JWH, Rambaut A & Welch JJ (2013) Relaxed phylogenetics and the palaeoptera problem: Resolving deep ancestral splits in the insect phylogeny. Syst Biol 62: 285-297. doi:10.1093/sysbio/sys093.

Richardson MF, Weinert LA, Welch JJ, Linheiro RS, Magwire MM, Jiggins FM & Bergman CM (2012) Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster. PLoS Genetics. 8: e1003129. doi:10.1371/journal.pgen.1003129.

Peck JR, Waxman D & Welch JJ (2012) Hidden epistatic interactions can favour the evolution of sex and recombination. PLoS One 7: e48382.

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 8: 829-832.

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, 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 R 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.

* Equal contributions.


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