Contact details +64 (06) 356 9099

Dr David Winter PhD


School of Fundamental Sciences



  • Doctor of Philosophy - University of Otago (2012)

Research Projects

Summary of Research Projects

Position Current Completed
Project Leader 1 1

Current Projects

Project Title: Treasure from the junk pile. Do transposable elements drive the evolution of gene expression?

Date Range: 2019 - 2022

Funding Body: Royal Society of New Zealand

Project Team:

Research Outputs


Winter, D., Charlton, N., Krom, N., Shiller, J., Bock, C., Cox, M., . . . Young, C. (2019). Chromosome-level genome reference of Venturia effusa, causative agent of pecan scab.
[Journal article]Authored by: Cox, M., Winter, D.
Hassing, B., Winter, D., Becker, Y., Mesarich, CH., Eaton, CJ., & Scott, B. (2019). Analysis of Epichloëfestucae small secreted proteins in the interaction with Lolium perenne. PLoS ONE. 14(2)
[Journal article]Authored by: Mesarich, C., Scott, D., Winter, D.
Chujo, T., Lukito, Y., Eaton, CJ., Dupont, PY., Johnson, LJ., Winter, D., . . . Scott, B. (2019). Complex epigenetic regulation of alkaloid biosynthesis and host interaction by heterochromatin protein I in a fungal endophyte-plant symbiosis. Fungal Genetics and Biology. 125, 71-83
[Journal article]Authored by: Cox, M., Lukito, Y., Scott, D., Winter, D.
Winter, DJ., Ganley, ARD., Young, CA., Liachko, I., Schardl, CL., Dupont, PY., . . . Cox, MP. (2018). Repeat elements organise 3D genome structure and mediate transcription in the filamentous fungus Epichloë festucae. PLoS Genetics. 14(10)
[Journal article]Authored by: Berry, D., Cox, M., Scott, D., Winter, D.
Winter, DJ., Wu, SH., Howell, AA., Azevedo, RBR., Zufall, RA., & Cartwright, RA. (2018). accuMUlate: a mutation caller designed for mutation accumulation experiments. Bioinformatics (Oxford, England). 34(15), 2659-2660
[Journal article]Authored by: Winter, D.
Winter, DJ. (2017). rentrez: An R package for the NCBI eUtils API. R Journal. 9(2), 520-526
[Journal article]Authored by: Winter, D.
Wu, SH., Schwartz, RS., Winter, DJ., Conrad, DF., & Cartwright, RA. (2017). Estimating error models for whole genome sequencing using mixtures of Dirichlet-multinomial distributions. Bioinformatics. 33(15), 2322-2329
[Journal article]Authored by: Winter, D.
Wallis, GP., Cameron-Christie, SR., Kennedy, HL., Palmer, G., Sanders, TR., & Winter, DJ. (2017). Interspecific hybridization causes long-term phylogenetic discordance between nuclear and mitochondrial genomes in freshwater fishes. Molecular Ecology. 26(12), 3116-3127
[Journal article]Authored by: Winter, D.
Michonneau, F., Brown, JW., & Winter, DJ. (2016). rotl: an R package to interact with the Open Tree of Life data. Methods in Ecology and Evolution. 7(12), 1476-1481
[Journal article]Authored by: Winter, D.
Smith, AM., Key, MM., Henderson, ZE., Davis, VC., & Winter, DJ. (2016). Pretreatment for removal of organic material is not necessary for x-ray-diffraction determination of mineralogy in temperate skeletal carbonate. Journal of Sedimentary Research. 86(12), 1425-1433
[Journal article]Authored by: Winter, D.
Long, H., Winter, DJ., Chang, AYC., Sung, W., Wu, SH., Balboa, M., . . . Zufall, RA. (2016). Low base-substitution mutation rate in the germline genome of the ciliate tetrahymena thermophila. Genome Biology and Evolution. 8(12), 3629-3639
[Journal article]Authored by: Winter, D.
Smith, AM., Clark, DE., Lamare, MD., Winter, DJ., & Byrne, M. (2016). Risk and resilience: Variations in magnesium in echinoid skeletal calcite. Marine Ecology Progress Series. 561, 1-16
[Journal article]Authored by: Winter, D.
Winter, D., Pacheco, M., Vallejo, AF., Schwartz, R., Arevalo-Herrera, M., Herrera, S., . . . Escalante, A. (2015). Whole genome sequencing of field isolates reveals extensive genetic diversity in Plasmodium vivax from Colombia.
[Journal article]Authored by: Winter, D.
Long, H., Winter, D., Chang, AY-C., Sung, W., Wu, S., Balboa, M., . . . Zufall, R. (2015). Low base-substitution mutation rate in the germline genome of the ciliate Tetrahymena thermophila.
[Journal article]Authored by: Winter, D.
Winter, DJ., Pacheco, MA., Vallejo, AF., Schwartz, RS., Arevalo-Herrera, M., Herrera, S., . . . Escalante, AA. (2015). Whole Genome Sequencing of Field Isolates Reveals Extensive Genetic Diversity in Plasmodium vivax from Colombia. PLoS Neglected Tropical Diseases. 9(12)
[Journal article]Authored by: Winter, D.
Donald, KM., Winter, DJ., Ashcroft, AL., & Spencer, HG. (2015). Phylogeography of the whelk genus Cominella (Gastropoda: Buccinidae) suggests long-distance counter-current dispersal of a direct developer. Biological Journal of the Linnean Society. 115(2), 315-332
[Journal article]Authored by: Winter, D.
Smith, AM., Berman, J., Key, MM., & Winter, DJ. (2013). Not all sponges will thrive in a high-CO<inf>2</inf> ocean: Review of the mineralogy of calcifying sponges. Palaeogeography, Palaeoclimatology, Palaeoecology. 392, 463-472
[Journal article]Authored by: Winter, D.
Smith, AM., Riedi, MA., & Winter, DJ. (2013). Temperate reefs in a changing ocean: Skeletal carbonate mineralogy of serpulids. Marine Biology. 160(9), 2281-2294
[Journal article]Authored by: Winter, D.
Byrne, M., Lamare, M., Winter, D., Dworjanyn, SA., & Uthicke, S. (2013). The stunting effect of a high CO<inf>2</inf> ocean on calcification and development in sea urchin larvae, a synthesis from the tropics to the poles. Philosophical Transactions of the Royal Society B: Biological Sciences. 368(1627)
[Journal article]Authored by: Winter, D.
Winter, DJ. (2012). MMOD: An R library for the calculation of population differentiation statistics. Molecular Ecology Resources. 12(6), 1158-1160
[Journal article]Authored by: Winter, D.
Smith, AM., Sutherland, JE., Kregting, L., Farr, TJ., & Winter, DJ. (2012). Phylomineralogy of the Coralline red algae: Correlation of skeletal mineralogy with molecular phylogeny. Phytochemistry. 81, 97-108
[Journal article]Authored by: Winter, D.
Donald, KM., Preston, J., Williams, ST., Reid, DG., Winter, D., Alvarez, R., . . . Spencer, HG. (2012). Phylogenetic relationships elucidate colonization patterns in the intertidal grazers Osilinus Philippi, 1847 and Phorcus Risso, 1826 (Gastropoda: Trochidae) in the northeastern Atlantic Ocean and Mediterranean Sea. Molecular Phylogenetics and Evolution. 62(1), 35-45
[Journal article]Authored by: Winter, D.
Fraser, CI., Winter, DJ., Spencer, HG., & Waters, JM. (2010). Multigene phylogeny of the southern bull-kelp genus Durvillaea (Phaeophyceae: Fucales). Molecular Phylogenetics and Evolution. 57(3), 1301-1311
[Journal article]Authored by: Winter, D.
Steens, MI., Winter, DJ., Morris, R., McCartney, J., & Greenslade, P. (2007). New Zealand's giant Collembola: New information on distribution and morphology for Holacanthella Börner, 1906 (Neanuridae: Uchidanurinae). New Zealand Journal of Zoology. 34(1), 63-78
[Journal article]Authored by: Winter, D.

Supervision and Teaching

Summary of Doctoral Supervision

Position Current Completed
Co-supervisor 1 0

Current Doctoral Supervision

Co-supervisor of:

  • Sidra Hussain - Doctor of Philosophy
    Evolution of Cytonuclear Coordination in Tragopogon (Asteraceae) Allopolyploids

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