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Refereed Publications:

Leigh JW, Bryant D (2015). Monte Carlo strategies for selecting parameter values in simulation experiments. Syst Biol 64:741–751.[link]

Leigh JW, Bryant D (2015). PopART: Full-feature software for haplotype network construction. Methods Ecol Evol 6:1110–1116.[link]

Becker M, Gruenheit N, Deusch O, Steel M, Voelckel C, McLenachan PA, Heenan PB, Kardailsky O, Leigh JW, Lockhart P (2013). The potential of hybridization to alter outcomes of climate change. Nat Clim Chang 12:1039–1043.[link]

Leigh JW, Schliep K, Lopez P, Bapteste E (2011). Let them fall where they may: Congruence analysis in massive, phylogenetically messy data sets. Mol Biol Evol 28:2773–2785.[link]

Leigh JW, Lapointe F, Lopez P, Bapteste E (2011). Evaluating phylogenetic congruence in the post-genomic era. Genome Biol Evol 3:571–587.[link]

Silberfeld T, Leigh JW, Verbruggen H, Cruaud C, de Reviers B, Rousseau F (2010). A multi-locus time-calibrated phylogeny of the brown algae (Heterokonta, Ochrophyta, Phaeophyceae): Investigating the evolutionary nature of the “brown algal crown radiation”. Mol Phylogenet Evol 56:659–674.[link]

Halary S, Leigh JW, Cheaib B, Lopez P, Bapteste E (2010). Network analyses structure genetic diversity in independent genetic worlds. Proc Natl Acad Sci U S A 107:127–132.[link]

Liu Y, Leigh JW, Brinkmann H, Cushion MT, Rodriguez-Ezpeleta N, Philippe H, Lang BF (2009). Phylogenomic analyses support the monophyly of Taphrinomycotina, including Schizosaccharomyces fission yeasts. Mol Biol Evol 26:27–34.[link]

Hampl V, Hug L, Leigh JW, Dacks JB, Lang BF, Simpson AGB, Roger AJ (2009). Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic “supergroups”. Proc Natl Acad Sci U S A 106:3859–3864.[link]

Bapteste E, Susko E, Leigh J, Ruiz-Trillo I, Bucknam J, Doolittle WF (2008). Alternative methods for concatenation of core genes indicate a lack of resolution in deep nodes of the prokaryotic phylogeny. Mol Biol Evol 25:83–91.[link]

Kolisko M, Cepicka I, Hampl V, Leigh J, Roger AJ, Kulda J, Simpson AGB, Flegr J (2008). Molecular phylogeny of diplomonads and enteromonads based on SSU rRNA, alpha-tubulin and HSP90 genes: implications for the evolutionary history of the double karyomastigont of diplomonads. BMC Evol Biol 8:205.[link]

Leigh JW, Susko E, Baumgartner M, Roger AJ (2008). Testing congruence in phylogenomic analysis. Syst Biol 57:104–115.[link]

Susko E, Leigh J, Doolittle WF, Bapteste E (2006). Visualizing and assessing phylogenetic congruence of core gene sets: a case study of the gamma-proteobacteria. Mol Biol Evol 23:1019–1030.[link]

Goddard MR, Leigh J, Roger AJ, Pemberton AJ (2006). Invasion and persistence of a selfish gene in the Cnidaria. PloS One 1:e3.[link]

Bapteste E, Susko E, Leigh J, MacLeod D, Charlebois RL, Doolittle WF (2005). Do orthologous gene phylogenies really support tree-thinking? BMC Evol Biol 5:33.[link]

Seif E, Leigh J, Liu Y, Roewer I, Forget L, Lang BF (2005). Comparative mitochondrial genomics in zygomycetes: bacteria-like RNase P RNAs, mobile elements and a close source of the group I intron invasion in angiosperms. Nucleic Acids Res 33:734–744.[link]

Bapteste E, Boucher Y, Leigh J, Doolittle WF (2004). Phylogenetic reconstruction and lateral gene transfer. Trends Microbiol 12:406–411.[link]

Leigh J, Lang BF (2004). Mitochondrial 3’ tRNA editing in the jakobid Seculamonas ecuadoriensis: a novel mechanism and implications for tRNA processing. RNA 10:615–621.[link]

Bullerwell CE, Leigh J, Forget L, Lang BF (2003). A comparison of three fission yeast mitochondrial genomes. Nucleic Acids Res 31:759–768.[link]

Book Chapters:

French N, Yu S, Biggs P, Holland B, Fearnhead P, Binney B, Fox A, Grove-White D, Leigh JW, Miller W, Muellner P, Carter P (2013). Evolution of Campylobacter species in New Zealand. In: SK Sheppard, G Méric, editors. Campylobacter Ecology and Evolution. Chapter 17. Norfolk: Horizon Scientific Press, 221–240.

Barberà MJ, Ruiz-Trillo I, Leigh J, Hug LA, Roger AJ (2007). The diversity of mitochondrion-related organelles amongst eukaryotic microbes. In: W Martin, M Müller, editors. Origins of Mitochondria and Hydrogenosomes. Chapter 10. Heidelberg: Springer-Verlag, 239–276.

Leigh J, Seif E, Rodriguez N, Jacob Y, Lang B (2003). Fungal evolution meets fungal genomics. In: DK Arora, editor. Handbook of fungal biotechnology. Chapter 12. New York: CRC Press, 249–281.

Bullerwell C, Leigh J, Seif E, Longcore J, Lang B (2003). Evolution of the fungi and their mitochondrial genomes. In: GG Khachatourians, DK Arora, editors. Applied Mycology and Biotechnology: Fungal genomics. Amsterdam: Elsevier Science, 133–159.