Lab members are bolded.
• 2023 & In Press
• Phylogenetic analysis under heterogeneity and discordance. Pease JB, Weinheimer EI. 2023. In Species tree Inference. LS Kubatko and LL Knowles, editors. Princeton University Press. .
  • https://press.princeton.edu/books/paperback/9780691207605/species-tree-inference
• 2022
Layered evolution of gene expression in “superfast” muscles for courtship Pease JB^*, Driver RJ^*, de la Cerda DA, Day LB, Lindsay WR, Schlinger BA, Schuppe ER, Balakrishnan CN, Fuxjager MJ. 2022. Proceedings of the National Academy of the USA 119(14) e2119671119.
• doi: 10.1073/pnas.2119671119
• PMID: 35363565
• Data: 10.5281/zenodo.6299082
• Software: PhyDGET
• 2020
• The catalytic-dependent and -independent roles of Lsd1 and Lsd2 lysine demethylases in heterochromatin formation in Schizosaccharomyces pombe Marayati BF, Tucker JF, de la Cerda DA, Huo T, Chen R, Sugiyama T, Pease JB, Zhang K. 2020. Cells 9(4) 955.
  • doi: 10.3390/cells9040955
  • PMID: 32295063
• 2019
• Group A Rotavirus VP1 polymerase and VP2 core shell proteins: Intergenotypic sequence variation and in vitro functional compatibility Steger CL, Boudreaux CE, LaConte LE, Pease JB, McDonald SM. 2019. Journal of Virology 93 (2) e01642-18.
  • doi: 10.1128/JVI.01642-18
  • PMID: 30355692
• A deep-sequencing-assisted, spontaneous suppressor screen in the fission yeast Schizosaccharomyces pombe Marayati BF, Pease JB, Zhang K. 2019. Journal of Visualized Experiments. (145), e59133.
  • doi: 10.3791/59133
  • PMID: 30907886
• 2018
• Why phylogenomic uncertainty enhances introgression analyses Pease JB. 2018. Molecular Ecology. 27(22): 4347–4349.
  • doi: 10.1111/mec.14851
  • PMID: 30474302
• Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life Pease JB, Brown JW, Walker JF, Hinchliff CE, Smith SA. 2018.American Journal of Botany. 105(3): 385–403.
  • doi: 10.1002/ajb2.1016
  • PMID: 29746719
  • Data: 10.5061/dryad.6m20j
  • Software: quartetsampling
• Encoding data using biological principles: the Multisample Variant Format for phylogenomics and population genomics Pease JB, Rosenzweig BK. 2018 IEEE/ACM Transactions on Computational Biology and Bioinformatics. 15(4) 1231–1238.
  • PDF
  • doi: 10.1109/tcbb.2015.2509997
  • PMID: 26701894
  • Software: MVFtools
• Loss of Elongation-Like Factor 1 spontaneously induces diverse, RNase H-related suppressor mutations in Schizosaccharomyces pombe Marayati BF, Drayton AL, Tucker JF, Huckabee RH, Anderson AM, Pease JB, Zeyl CW, Zhang K. 2018 Genetics. 209(4): 967–981.
  • doi: 10.1534/genetics.118.301055
  • PMID: 29844133
• 2017
• Heterogeneous molecular processes among the causes of how sequence similarity scores can fail to recapitulate phylogeny Smith SA, Pease JB. 2017. Briefings in Bioinformatics. 18: 451–457.
  • doi: 10.1093/bib/bbw034
  • PMID: 27103098
• 2016
• Molecular mechanisms of postmating prezygotic reproductive isolation uncovered by transcriptome analysis Pease JB, Guerrero RF, Sherman NA, Hahn MW, Moyle LC. 2016. Molecular Ecology. 25: 2592–2608.
  • doi: 10.1111/mec.13679
  • PMID: 27136303
  • Data: 10.5061/dryad.j3s5r and see Data Addenda
  • Software: MVFtools
• Powerful methods for detecting introgressed regions from population genomic data Rosenzweig BK, Pease JB, Besansky NJ, Hahn MW. 2016. Molecular Ecology. 25: 2387–2397.
  • PDF
  • doi: 10.1111/mec.13610
  • PMID: 26945783
  • Data: 10.5061/dryad.f7h13
  • Software: MVFtools
• Phylogenomics reveals three sources of adaptive variation during a rapid radiation Pease JB, Haak DC, Hahn MW, Moyle LC. 2016. PLoS Biology 14(2): e1002379.
  • doi: 10.1371/journal.pbio.1002379
  • PMID: 26871574
  • Data: 10.5061/dryad.182dv and see Data Addenda
  • Software: MVFtools, dfoil
• 2015
• Detection and polarization of introgression in a five-taxon phylogeny Pease JB, Hahn MW. 2015. Systematic Biology 64 (4): 651–662.
  • doi: 10.1093/sysbio/syv023
  • PMID: 25888025
  • Data: 10.5061/dryad.4h462
  • Software: dfoil
• Extensive introgression in a malaria vector species complex revealed by phylogenomics Fontaine, MC*, Pease JB*, Steele A, Waterhouse RM, Neafsey DE, Sharakhov IV, Jiang X, Hall AB, Catteruccia F, Kakani E, Mitchell SN, Wu Y, Smith HA, Love RR, Lawniczak MK, Slotman MA, Emrich SJ, Hahn MW, Besansky NJ. 2015. Science 347 (6217), 1258524.
  • doi: 10.1126/science.1258524
  • PMID: 25431491
  • Data: 10.5061/dryad.f4114
  • Software: dfoil
• 2014
• Quantitative genetic analysis indicates natural selection on leaf phenotypes across wild tomato species ( Solanum sect. Lycopersicon; Solanaceae) Muir CD, Pease JB, Moyle LC. 2014. Genetics 198:1629–43.
  • doi: 10.1534/genetics.114.169276
  • PMID: 25298519
  • Data: 10.5061/dryad.116td
• 2013
• More accurate phylogenies inferred from low-recombination regions in the presence of incomplete lineage sorting Pease JB, Hahn MW. 2013. Evolution 67:2376–84.
  • doi: 10.1111/evo.12118
  • PMID: 23888858
• 2012
• Sex chromosomes evolved from independent ancestral linkage groups in winged insects Pease JB, Hahn MW. 2012. Molecular Biology & Evolution 29: 1645–53.
  • doi: 10.1093/molbev/mss010
  • PMID: 22319158
• 2011
• No excess gene movement is detected off the Avian or Lepidopteran Z chromosome Toups MA, Pease JB, Hahn MW. 2011. Genome Biology & Evolution 3:1381–90.
  • doi: 10.1093/gbe/evr109
  • PMID: 22024813
• 2010
• On the possible role of robustness in the evolution of infectious diseases Ogbunugafor CB, Pease JB, Turner PE. 2010. Chaos 20(2):026108.
  • doi: 10.1063/1.3455189
  • PMID: 20590337

Data and Addenda

Below is a list of corrected or missing data files for published studies and datasets. Dryad repositories associated with publications are listed next to individual articles.

• From: “Molecular mechanisms of postmating prezygotic reproductive isolation uncovered by transcriptome analysis”
• testE.500.strict.tab
• ui_known_genes.xlsx
• From: “Phylogenomics reveals three sources of adaptive variation during a rapid radiation”
• solanum2016-chronotree.nwk (Ultrametric tree from Fig 2).