Dr Nicholas Joseph Matzke

PhD Integrative Biology (UC Berkeley); MA Geography (UC Santa Barbara); BS Biology/Chemistry (Valparaiso)

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Senior Lecturer

Biography

I work in phylogenetic biogeography: the dispersal history of species around the globe over millions of years. I specialise in taking model-based inference techniques (Maximum Likelihood and Bayesian methods) from statistical phylogenetics and applying them to biogeographical problems. This often involves linking unusual datasets for improved inference (e.g. linking biogeography, paleogeography, and organismal traits and structures to more traditional DNA and fossil datasets). Recent papers focus on using statistical model comparison to learn the role that organismal traits play in the probability of long-distance dispersal events. My R package for biogeographical analysis is BioGeoBEARS.

I am also a leader in evolution education. I worked at the U.S. nonprofit National Center for Science Education during the 2005 Kitzmiller v. Dover trial. I also tracked the "evolution of antievolutionism" after Kitzmiller using phylogenetic analysis of the evolutionary history of creationist policies. This was published in Science magazine. It is an example of "phylomemetics", studying how texts and other human cultural products ("memes") evolve in part through Darwin's process of "descent with modification."

I invite students to work with me on any topics related to these (the University of Auckland has rolling admissions, so postgraduate applications are accepted at any time during the year; see also UoA Summer Research Projects). I am also regularly involved in research collaborations, symposia at scientific meetings, and workshops on methods in phylogenetic biogeography.
 

Research Projects

Available July 2019: Funded PhD project: Improving model-based inference in phylogenetic biogeography. See also: FindAThesis: New models in phylogenetic biogeography. Regulations: University of Auckland Marsden Grant PhD Scholarship in Phylogenetic Biogeography

December 2019-Feb. 2020: Phylogenetics of the bacterial flagellum. See listing at: https://www.auckland.ac.nz/en/study/scholarships-and-awards/scholarship-types/undergraduate-scholarships/summer-research-scholarships/summer-research-projects/science/biological-sciences.html

December 2019-Feb. 2020: Speed benchmarking of state-dependent speciation/extinction models in the open-source computing language, Julia. See listing at: https://www.auckland.ac.nz/en/study/scholarships-and-awards/scholarship-types/undergraduate-scholarships/summer-research-scholarships/summer-research-projects/science/biological-sciences.html

See also at FindAThesisThe current research of Dr Nicholas Matzke

Research | Current

Revolutionising biogeography by adding extinction, fossils, organismal traits, and paleogeography in a computationally efficient way. Part of a funded Marsden grant and further proposals, this work aims to overcome the major limitations in current methods for inferring biogeographical history at phylogenetic timescales. Students who work in this area will get experience with phylogenetics, Maximum Likelihood/Bayesian inference, programming (in R, Julia, etc.), Geographic Information Systems, paleogeography modeling (GPlates, Paleobiology Database), etc. Currently available (as of July 2019; email me with enquiries): University of Auckland Marsden Grant PhD Scholarship in Phylogenetic Biogeography

Reconstructing the evolution of the bacterial flagellum. The bacterial flagellum is a famous example of a complex molecular adaptation, and its evolutionary history has attracted public attention for that reason. This work is a collaboration between Matt Baker at UNSW (experimental evolution, ancestral protein reconstruction) and Matzke (bioinformatics, phylogenetics); students may work in these areas, or their interface.

Phylogenetics and Phylogenetic Comparative Methods (PCMs). Biology is vast, and many areas have yet to be addressed by modern inference methods; similarly, many modern inference methods used quite crude models with simple assumptions. Motivated students therefore are welcome to propose projects in these areas; Matzke’s interests include phylomemetics, carnivorous plants, evolution education, and evolution of complex adaptations.

 

Research history

Teaching | Current

Course

Title

Semester

BIOSCI 109

Ecology and Evolution: The Continuum of Life

One

BIOINF 702

Comparative Bioinformatics

One

BIOSCI 210

Evolution and The Origins of Life

Two

BIOSCI 322

Evolution of Genes, Populations and Species

Two

BIOSCI 733

Molecular Ecology and Evolution

Two

Postgraduate supervision

Degree, Institution

Student

Role

Ph.D., U. Auckland

Luke Liddell

Supervisor

Ph.D., U. Auckland

Ben Potter

Supervisor

Ph.D., U. Auckland

Christiaan Swanepoel

Co-advisor

Ph.D., ANU

Kirrily Apthorp

Co-advisor

Ph.D., ANU

Alex Skeels

Co-advisor

Selected publications and creative works (Research Outputs)

  • Nicolaï MPJ, & Matzke, N. J. (2019). Trait-based range expansion aided in the global radiation of Crocodylidae. Global Ecology and Biogeography, 28 (9), 1244-1258. 10.1111/geb.12929
  • Lu, L., Fritsch, P. W., Matzke, N. J., Wang, H., Kron, K. A., Li, D.-Z., & Wiens, J. J. (2019). Why is fruit colour so variable? Phylogenetic analyses reveal relationships between fruit-colour evolution, biogeography and diversification. GLOBAL ECOLOGY AND BIOGEOGRAPHY, 28 (7), 891-903. 10.1111/geb.12900
    URL: http://hdl.handle.net/2292/48391
  • Blom, M. P. K., Matzke, N. J., Bragg, J. G., Arida, E., Austin, C. C., Backlin, A. R., ... Hathaway, S. A. (2019). Habitat preference modulates trans-oceanic dispersal in a terrestrial vertebrate. Proceedings of the Royal Society B: Biological Sciences, 286 (1904), 20182575-20182575. 10.1098/rspb.2018.2575
  • Klaus, K. V., & Matzke, N. J. (2019). Statistical Comparison of Trait-dependent Biogeographical Models indicates that Podocarpaceae Dispersal is influenced by both Seed Cone Traits and Geographical Distance. Systematic Biology, online first10.1093/sysbio/syz034
    URL: http://hdl.handle.net/2292/48315
  • Ishida, T., Ito, R., Clark, J., Matzke, N., Sowa, Y., & Baker, M. A. B. (2018). Sodium-powered stators of the bacterial flagellar motor can generate torque in the presence of phenamil with mutations near the peptidoglycan-binding region. 10.1101/507533
    URL: http://hdl.handle.net/2292/47990
  • Matos-Maraví P, Matzke, N. J., Larabee, F. J., Clouse, R. M., Wheeler, W. C., Sorger, D. M., ... Janda, M. (2018). Taxon cycle predictions supported by model-based inference in Indo-Pacific trap-jaw ants (Hymenoptera: Formicidae: Odontomachus). Molecular ecology, 27 (20), 4090-4107. 10.1111/mec.14835
    URL: http://hdl.handle.net/2292/43698
  • Flammensbeck, C. K., Pollerspock, J., Schedel, F. D. B., Matzke, N. J., & Straube, N. (2018). Of teeth and trees: A fossil tip-dating approach to infer divergence times of extinct and extant squaliform sharks. ZOOLOGICA SCRIPTA, 47 (5), 539-557. 10.1111/zsc.12299
    URL: http://hdl.handle.net/2292/43885
    Other University of Auckland co-authors: Christina Flammensbeck
  • Matzke, N. J., & Irmis, R. B. (2018). Including autapomorphies is important for paleontological tip-dating with clocklike data, but not with non-clock data. PeerJ, 610.7717/peerj.4553
    URL: http://hdl.handle.net/2292/43488

Contact details

Alternative contact

The auckland.ac.nz email sometimes fails due to spam filters or large attachments. As backup, try: nickmatzke.ncse@gmail.com

Primary office location

COMMERCE A - Bldg 114
3A SYMONDS ST
AUCKLAND CENTRAL
AUCKLAND 1010
New Zealand