Curriculum vitae of Dr. Nicholas J. Matzke

CV link at: http://phylo.wikidot.com/nicholas-j-matzke

Quick links: Google Scholar, Graphical overview website

Current postion:
Discovery Early Career Researcher Award (DECRA) Fellow
DECRA granted by ARC (Australian Research Council)
Division of Ecology, Evolution, and Genetics
Research School of Biology
The Australian National University
      
Mailing address:
Room 208
Building 116, Gould Wing
The Australian National University
ACT 2601 AUSTRALIA


Cell phone (preferred): +61 0410 726 191
Office phone (not preferred): +61 612 52 450
Email: nick.matzke@anu.edu.au

Cell phone (when in US): (510) 301-0179

Outline:
Education
Employment
Publications
Publication statistics
Research publications
Science education publications
Presentations
Research presentations
Science education-related presentations
Teaching and student advising
Teaching
Student advising
Public outreach and additional professional activities
Media Appearances
Press
Research assistance
Blogging and news pieces (selected)
Software and Programming
Professional memberships
Peer-reviewing
Other activities
Awards, funding, grants
Major grant applications I have contributed to
Awards/funding received
References


Education

Ph.D. Integrative Biology, University at California, Berkeley, 2013
 
M.A. Geography, University at California, Santa Barbara, 2003
  • Thesis title: "Remote Sensing and Geostatistical Analysis of Anthropogenic Biomass Burning and Forest Degradation in Madagascar." (Local pdf: screen resolution, 3.2 MB | print resolution, 27 MB)
  • Used manual and automated satellite image analysis to map fires, and geostatistical simulation techniques to ascertain uncertainty in burned area estimates.
 
B.S. B.S., Biology and B.S., Chemistry, Valparaiso University, 1998
  • Graduated summa cum laude
  • GPA: 3.876
  • Christ College (V.U. liberal arts honors college) Scholar
  • Senior Honors
 

Employment

July 2015-present DECRA (Discovery Early Career Researcher Award) Fellow, Craig Moritz Lab, Division of Evolution, Ecology and Genetics, Research School of Biology, ANU College of Medicine, Biology & Environment, The Australian National University, Canberra, Australian Capital Territory (ACT). (DECRA announcement)
Fall 2013-July 2015 NIMBioS Postdoctoral Fellow in Mathematical Biology, National Institute for Mathematical and Biological Synthesis (NIMBioS, www.nimbios.org), University of Tennessee, Knoxville. NIMBioS is an NSF-funded synthesis center. See my research profile at NIMBioS.
Mentors: Brian O'Meara, Dan Simberloff
2010-2013 Graduate Student Researcher, BiTS: Bivalves in Time and Space: Testing the accuracy of methods to reconstruct ancestral morphology, dates, geography, and diversification patterns, NSF grant, co-PIs Scott Steppan (FSU, molecular systematics), Ruediger Bieler (Field Museum, morphological systematics), Paula Mikkelsen (Paleontological Research Institution, morphological systematics), Jan Johan ter Poorten (Netherlands, morphological systematics of cardiids), David Jablonski (Univ. Chicago, paleobiology), and John Huelsenbeck (UC Berkeley, computational systematics). See also BiTS Home.
Spring 2013 Graduate Student Instructor, Letters and Science 121 - Origins in Science and Religion, Department of Letters and Science, U.C. Berkeley. Instructors: Kevin Padian (Department of Integrative Biology) and Ron Hendel (Department of Near Eastern Studies).
Spring 2011 Graduate Student Instructor, IB200b: Principles of Phylogenetics: Ecology and Evolution, Department of Integrative Biology, U.C. Berkeley
Spring 2010 Graduate Student Instructor, IB200a: Principles of Phylogenetics: Systematics, Department of Integrative Biology, U.C. Berkeley
Fall 2009 Graduate Student Instructor, IB164: Human Genetics, Department of Integrative Biology, U.C. Berkeley
Summer 2009 Graduate Student Researcher, Google Summer of Code (project link | Final description, links, and tutorial on BioPython Wiki)
 
Spring/Summer 2009, Spring 2008 Graduate Student Instructor, Bio1B: Intro Bio: Evolution, Ecology, Plants, Department of Integrative Biology, U.C. Berkeley
 
Summer/Fall 2008 Graduate Student Researcher, Department of Integrative Biology, U.C. Berkeley
 
Fall 2007 Graduate Student Instructor, IB160: Evolutionary Biology, Department of Integrative Biology, U.C. Berkeley
 
2005-2007 Public Information Project Director, National Center for Science Education
  • NCSE's representative and science consultant for the plaintiffs' legal team in Kitzmiller v. Dover
  • Research & writing on evolution & challenges to evolution education
  • Radio, TV, & print media appearances
 
2004-2005 Public Information Project Specialist, National Center for Science Education
  • Evolution & science education, public information
 
2000-2003 Graduate Research Assistant, Geography Dept., UC Santa Barbara
  • Extensive research and software experience
  • Land cover and fire mapping in Madagascar
  • Alexandria Digital Earth Prototype (ADEPT) Project
  • Lab construction for Geographic Information Systems course (ARCINFO8)
 
2003 Teaching Assistant, Geography Dept., UC Santa Barbara
  • Geographic Data Analysis (introductory Geostatistics)
  • Teaching students MATLAB and statistical analysis
  • Also TAed other courses on climate change, physical geography
 
1999 Research technician, U.S. Forest Service, Portland, OR
  • Air photo interpretation and juniper survey crew
 
1998 Research technician, Forest Science Dept., Oregon State University, Corvallis, OR
  • Old growth and canopy study
 
1995-1997 Research technician, McDonald Research Forest, Oregon State University, Corvallis, OR
  • Timber survey crew
  • Wildlife crew
  • Stream survey crew
 

Publications -- Google Scholar citations

Publication statistics

Research publications

          (* = co-first-author)


bioRxiv/in review

Matos-Maraví, Pável; Matzke, Nicholas J.; Larabee, Fredrick J.; Clousef, Ronald M.; Wheeler, Ward C.; Sorger, D. Magdalena; Suarez, Andrew V.; Janda, Milan (2017). Trans-Pacific long-distance dispersal and the interplay between abiotic factors and 2 ecology shaped the diversity of Indo-Pacific trap-jaw ants. Molecular Ecology, submitted. MEC-17-0457

Lam, Adriane; Stigall, Alycia; Matzke, Nicholas (2017). Dispersal in the Ordovician: Speciation patterns and paleobiogeographic analyses of brachiopods and trilobites. Palaeogeography, Palaeoclimatology, Palaeoecology, submitted.

Massana, Kathryn A.; Beaulieu, Jeremy M.; Matzke, Nicholas J.; O'Meara, Brian C. (2017). Non-null Effects of the Null Range in Biogeographic Models: Exploring Parameter Estimation in the DEC Model. Submitted, and at bioRxiv: http://biorxiv.org/content/early/2015/09/16/026914 (bioRxiv | DOI)

Published/Accepted

Perez-Escobar, Oscar Alejandro; Chomicki, Guillaume; Condamine, Fabien L.; Karremans, Adam P. ; Bogarin, Diego; Matzke, Nicholas J.; Silvestro, Daniele; Antonelli, Alexandre (2017). Recent origin of Neotropical orchids in the world's richest plant biodiversity hotspot. New Phytologist, accepted. (bioRxiv | DOI)

Matzke, Nicholas J.; Irmis, Randall (2017). Including autapomorphies in paleontological datasets is important for tip-dating with clocklike data, but not with non-clock data. PeerJ, accepted.

Badgley, Catherine; Smiley, Tara M.; Terry, Rebecca; Davis, Edward B.; DeSantis, Larisa R.G.; Fox, David L.; Hopkins, Samantha S.B.; Jezkova, Tereza; Matocq, Marjorie D.; Matzke, Nicholas J.; McGuire, Jenny L.; Mulch, Andreas; Riddle, Brett R.; Roth, V. Louise; Samuels, Joshua X.; Strömberg, Caroline A.E.; Yanites, Brian J. (2017). Biodiversity and topographic complexity: Modern and geohistorical perspectives. Trends in Ecology and Evolution, 32(3), 211-226. (DOI | Journal)

Dupin, Julia; Matzke, Nicholas J.; Sarkinen, Tiina; Knapp, Sandra; Olmstead, Richard; Bohs, Lynn; Smith, Stacey (2016). Bayesian estimation of the global biogeographic history of the Solanaceae. Journal of Biogeography, 44(4), 887-899. (DOI | Journal)

Turner, Alan H.; Pritchard, Adam C.; Matzke, Nicholas J. (2016). Empirical and Bayesian approaches to fossil-only divergence times: a study across three reptile clades. PLoS ONE, 12(2): e0169885. (DOI | Journal | Dryad)

Zhang, Guanyang; Basharat, Usmaan; Matzke, Nicholas; Franz, Nico (2017). Model selection in statistical historical biogeography of Neotropical insects -- the Exophthalmus genus complex (Curculionidae: Entiminae). Molecular Phylogenetics and Evolution, 109, 226–239. (DOI | Journal | bioRxiv)

Matzke, Nicholas J.; Wright, April (2016). Inferring node dates from tip dates in fossil Canidae: the importance of tree priors. Biology Letters, 12(8), 20160328. (Part of the "Putting Fossils in Trees" special issue.) (Journal | DOI | BioRxiv | BioRxiv DOI | Dryad | Twitter)

Bapst, D. W.; Wright, A. M.; Matzke, N. J.; Lloyd, G. T. (2016). Topology, divergence dates, and macroevolutionary inferences vary between different tip-dating approaches applied to fossil theropods (Dinosauria). Biology Letters 12(7), 20160237. (Part of the "Putting Fossils in Trees" special issue.) (Journal | DOI | Dryad)

Yuan, Z.-y.; Zhou, W.-w.; Chen, X.; Poyarkov, N.A.; Chen, H.-m.; Jang-Liaw, N.-h.; Chou, W.-h.; Matzke, N.J.; Iizuka, K.; Min, M.-s.; Kuzmin, S.L.; Zhang, Y.-p.; Cannatella, D.C.; Hillis, D.M.; Che, J. (2016). Spatiotemporal Diversification of the True Frogs (Genus Rana): A Historical Framework for a Widely Studied Group of Model Organisms. Systematic Biology. 65(5):824-842. (Journal | DOI | Dryad)

Shih, Patrick; Hemp, James; Matzke, Nicholas J.; Fischer, Woodward (2017). Crown group Oxyphotobacteria postdate the rise of oxygen. Geobiology. 5(1): 19-29. Published July 8, 2016. (Journal | DOI | PubMed)

Van Dam, Matthew; Matzke, Nicholas J. (2016). Evaluating the influence of connectivity and distance on biogeographic patterns in the south-western deserts of North America. Journal of Biogeography. 43(8):1514–1532. Special paper, published online 3 March 2016. (Journal | DOI | Altimetric)

Matzke, N.J. (2016). Trait-dependent dispersal models for phylogenetic biogeography, in the R package BioGeoBEARS. Integrative and Comparative Biology 56(suppl 1), E330-E330. (Meeting | PhyloWiki | DOI | Journal)

Matzke, Nicholas (2015). The Evolution of Antievolution Policies After Kitzmiller v. Dover. Science, 351(6268), 10-12. Published online at ScienceExpress on December 17, 2015; print January 1, 2016. (Bonus material, media links, FAQ, etc. at: http://phylo.wikidot.com/matzke-2015-science-paper-on-the-evolution-of-antievolution ) (Journal | DOI | Altimetric)

     Attention included: a mention on the cover of Science, a cover story in Australasian Science (Matzke, Nick (2016). "Creationism Evolves." Australasian Science,
          37(3), 14-16, April 2016. http://www.australasianscience.com.au/article/issue-april-2016/creationism-evolves.html) approximated 40 writeups, a interview on
          ABC 666 AM (The Australian Broadcasting Corporation), a podcast (Steve Mirsky), and about 20 blogs.
     References and links are archived at: http://phylo.wikidot.com/matzke-2015-science-paper-on-the-evolution-of-antievolution#media

Dembo, Mana; Matzke, Nicholas; Mooers, Arne; Collard, Mark (2015). Bayesian analysis of a morphological supermatrix sheds light on controversial fossil hominin relationships. Journal of the Royal Society: Proceedings B, Biological Sciences, 282(1812), 20150943. (Journal | DOI)

     Press attention:
     Choi, C. Q. (2015). "Human Evolution's Biggest Questions May Find Answers in New Analysis." LiveScience. July 22, 2015. (Link)
     Viegas, J. (2015). "First Humans Out of Africa Were Small, Scrappy." Discovery.com. July 21, 2015. (Link)

Matzke, Nicholas J. (2015). Bayesian tip-dating with continuous characters using BEASTmasteR. Journal of Vertebrate Paleontology, Program and Abstracts, 2015, p. 177. (PhyloWiki)

Matzke, Nicholas J. (2015). Review of: Michael Heads (2014), Biogeography of Australasia: A Molecular Analysis. Quarterly Review of Biology, 90(3), 327-328. September 2015. (JSTOR)

Matzke, Nicholas J. (2015). Ancient Forests and Peripatetic Primates: Alan de Queiroz's The Monkey's Voyage. Reports of the National Center for Science Education, 25(2), 1-8. March-April 2015. (Journal)

Matzke, Nicholas J. (2015) "Bayesian stochastic mapping for estimating biogeographic history on phylogenies." International Biogeography Society 7th Biennial Meeting. 8–12 January 2015, Bayreuth, Germany. (ed. by D. Gavin, C. Beierkuhnlein, S. Holzheu, B. Thies, K. Faller, R. Gillespie & J. Hortal), Frontiers of Biogeography 6(suppl. 1), 37-38. (Scholar | Journal | PhyloWiki)

Meyer, Erin; Matzke, Nicholas J.; Williams, Simon (2015). "Remote sensing of intertidal habitats predicts West Indian topsnail population expansion but reveals scale-dependent bias." Journal of Coastal Conservation. 19(2), 107-118. (Scholar | Journal | DOI)

Matzke, Nicholas J. (2014). "Model Selection in Historical Biogeography Reveals that Founder-event Speciation is a Crucial Process in Island Clades." Systematic Biology, 63(6), 951–970. (Journal | Scholar | DOI | Dryad)

     Press attention:
     University of Tennessee Press Release (2014). "Research Confirms Controversial Darwin Theory of Jump Dispersal." (NIMBioS version) October 1, 2014.
     Alford, Justine (2014). "Researcher Finds Support For One Of Darwin's Controversial Theories." IFLScience. October 2, 2014.
     Hannah Osborne (2014). "Darwin's Theories on Invasive Species and Jump Dispersal Confirmed by Experts." International Business Times. October 2, 2014.

* Lawing, Michelle; Matzke, Nicholas (2014). "Conservation paleobiology needs phylogenetic methods." Ecography. 37(11), 1109–1122, November 2014. (Journal | Scholar | DOI)

Gavin, Dan G.; Fitzpatrick, M. C.; Gugger, P. F.; Heath, K. D.; Rodríguez-Sánchez, F.; Dobrowski, S. Z.; Hampe, A.; Hu, F. S.; Ashcroft, M. B.; Bartlein, P. J.; Blois, Jessica L.; Carstens, B. C.; Davis, Edward B.; de Lafontaine, G.; Edwards, M. E.; Fernandez, M.; Henne, P. D.; Herring, E. M.; Holden, Z. A.; Kong, W-s; Liu, J.; Magri, D.; Matzke, Nicholas J.; McGlone, M. S.; Saltré, F.; Stigall, A. L.; Tsai, Y-H. E.; Williams, J. W. (2014). Climate refugia: joint inference from fossil records, species distribution models and phylogeography. New Phytologist, 204(1), 37–54. October 2014. (Journal | Scholar | DOI)

Matzke, Nicholas J.; Shih, Patrick M.; Kerfeld, Cheryl A. (2014). "Bayesian Analysis of Congruence of Core Genes in Prochlorococcus and Synechococcus and Implications on Horizontal Gene Transfer." PLoS One, 9(1), e85103. (Journal | Scholar | DOI)

Matzke, Nicholas J. (2013). "Probabilistic historical biogeography: new models for founder-event speciation, imperfect detection, and fossils allow improved accuracy and model-testing." Frontiers of Biogeography, 5(4), 242-248. (Scholar | Journal)

* Shih, Patrick M.; Matzke, Nicholas J. (2013). "Primary endosymbiosis events date to the later Proterozoic with cross-calibrated phylogenetic dating of duplicated ATPase proteins." Proceedings of the National Academy of Sciences, 110(30), 12355-12360. (Scholar | DOI | Journal)

Note: This article was featured on the cover and profiled in: Zhaxybayeva, Olga (2013). "Anciently duplicated genes reduce uncertainty in molecular clock estimates." Proceedings of the National Academy of Sciences, 110(30), 12168–12169. (Scholar | DOI | Journal)

Alexandrou, Markos A.; Swartz, Brian A.; Matzke, Nicholas J.; Oakley, Todd H. (2013). "Genome duplication and multiple evolutionary origins of complex migratory behavior in Salmonidae." Molecular Phylogenetics and Evolution, 69(3), 514-523. (Scholar | DOI | Journal)

Landis, Michael J., Matzke, Nicholas J.; Moore, Brian R.; Huelsenbeck, John P. (2013). "Bayesian Analysis of Biogeography when the Number of Areas is Large." Systematic Biology, 62(6), 789-804. (Scholar | DOI | Journal)

Wood, Hannah Marie; Matzke, Nicholas J.; Gillespie, Rosemary G.; Griswold, Charles E. (2013). "Treating Fossils as Terminal Taxa in Divergence Time Estimation Reveals Ancient Vicariance Patterns in the Palpimanoidea Spiders." Systematic Biology, 62(2), 264-284. (Scholar | DOI)

Goldsmith, Gregory; Matzke, Nicholas J.; Dawson, Todd (2013). "The incidence and implications of clouds for cloud forest plant water relations." Ecology Letters, 16(3), 307-314. (Scholar | DOI)
     Note: This paper received honorable mention (top four) in the 5th annual Outstanding Student Paper Award competition of the Organization for Tropical Studies.

Matzke, Nicholas J. (2012). Founder-event speciation in BioGeoBEARS package dramatically improves likelihoods and alters parameter inference in Dispersal-Extinction-Cladogenesis (DEC) analyses. Frontiers of Biogeography, 4(suppl. 1): 210, December 2012. (Link)

Barnosky, Anthony D.; Hadly, Elizabeth A.; Bascompte, Jordi; Berlow, Eric L.; Brown, James H.; Fortelius, Mikae; Getz, Wayne M.; Harte, John; Hastings, Alan; Marquet, Pablo A.; Martinez, Neo D.; Mooers, Arne; Roopnarine, Peter; Vermeij, Geerat; Williams, John W.; Gillespie, Rosemary; Kitzes, Justin; Marshall, Charles; Matzke, Nicholas; Mindell, David P.; Revilla, Eloy; Smith, Adam B. (2012). "Approaching a state-shift in Earth's biosphere." Nature 486(7401), 52-58. (Scholar | DOI | Link)

* Gong, Zhenqiang; Matzke, Nicholas J.; Ermentrout, Bard; Song, Dawn; Vendetti, Jann E.; Slatkin, Montgomery; Oster, George (2012). "Evolution of patterns on Conus shells." Proceedings of the National Academy of Sciences 109(5), E234-E241. (Scholar | DOI | Link)

Lippold, S.; Matzke, N.J.; Reissmann, M.; Hofreiter, M. (2011). "Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication." BMC Evolutionary Biology 11(1), 328. (Scholar | DOI | Link)

Barnosky, Anthony D.; Matzke, Nicholas; Tomiya, Susumu; Wogan, Guinevere O. U.; Swartz, Brian; Quental, Tiago B.; Marshall, Charles; McGuire, Jenny L.; Lindsey, Emily L.; Maguire, Kaitlin C.; Mersey, Ben; Ferrer, Elizabeth A. (2011). "Has the Earth's sixth mass extinction already arrived?" Nature 471(7336), 51-57. (Scholar | DOI | Link)

* Pallen, M., and Matzke, N. (2006). "From The Origin of Species to the Origin of Bacterial Flagella." Nature Reviews Microbiology. 4(10), 784-790. October 2006. http://www.doi.org/10.1038/nrmicro1493. (Local pdf | NCSE writeup)

Powell R. L., Matzke N., de Souza C., Clark M., Numata I., Hess L. L., Roberts D.A. (2004). "Sources of error in accuracy assessment of thematic land-cover maps in the Brazilian Amazon." Remote Sensing of Environment, 90, 221-234. http://dx.doi.org/10.1016/j.rse.2003.12.007. (Local pdf)

 

Science education-related publications

          (* = co-first-author; ** = peer-reviewed journal article, rather than book chapter or book review)

Matzke, Nick (2016). "Creationism Evolves." Australasian Science, 37(3), 14-16, April 2016. http://www.australasianscience.com.au/article/issue-april-2016/creationism-evolves.html

** Matzke, Nicholas (2010). "The Evolution of Creationist Movements." Evolution: Education and Outreach 3(2), 145-162. (Scholar | DOI | Link)

** Matzke, N. J. and Padian, K. (2009). "Evolution -- the great debate: the authors reply." The Biochemist. 31(2), 56. April 2009. (Journal)

** Matzke, N. J. (2009). "Alleged scientific opposition to evolution." The Biochemist. 31(1), 23. February 2009. (Journal | PDF)

*,** Padian, K. and Matzke, N. J. (2009). "Darwin, Dover, 'Intelligent Design' and textbooks." Biochemical Journal. 417(1), 29-42. January 2009. (Local pdf | DOI | Journal)

Also published as: Padian, K. and Matzke, N. J. (2009). "The struggle continues - Darwin, Dover, 'Intelligent Design' and textbooks." The Biochemist. 31(1), 8-22. February 2009. (journal)

Matzke, N. (2009). "But Isn't It Creationism? The beginnings of 'intelligent design' and Of Pandas and People in the midst of the Arkansas and Louisiana litigation." But Is It Science?: The Philosophical Question in the Creation/Evolution Controversy, Updated Edition, edited by Robert Pennock and Michael Ruse. Prometheus Books, Amherst, New York, pp. 377-413. (published PDF)

Matzke, N. (2007). "The Edge of Creationism." [Book review of: Michael J. Behe (2007), The Edge of Evolution: The Search for the Limits of Darwinism, New York: Free Press.] Trends in Ecology and Evolution, 22(11), 566-567. (DOI | (text online)

Matzke, N. J. and Elsberry, W. R., 2007. "The Collapse of 'Intelligent Design'," in: Stewart, R. B. (Ed.), Intelligent design : William A Dembski & Michael Ruse in dialogue, Fortress Press, Minneapolis, MN, pp. 70-87. Essay for a Greer-Heard Forum anthology, based on the 2006 "Debating Design" forum. pp. 70-87. (Local pdf | PDF of proofs | PDF of uncut ms | PSCF review)

*,** Scott, E. C., and Matzke, N. (2007). "Biological design in science classrooms." Proceedings of the National Academy of Sciences. 104(suppl. 1), 8669-8676. May 15, 2007. Part of the v. 104 supplement, "In the Light of Evolution I: Adaptation and Complex Design." Published online before print May 9, 2007. Also submitted for a Special Volume on the Arthur M. Sackler NAS Colloquium "In the Light of Evolution: Adaptation and Complex Design." Arnold and Mabel Beckman Center, Irvine, CA, November 30 - December 2, 2006. Organized by John C. Avise and Francisco J. Ayala. (DOI | PNAS | AOP | PT discussion #1 - #2 | Local PDF | NAS pages: description | program | Uncorrected proof of NAS book version) (Additional note: we were informed by PNAS that this was once of the top 20 most downloaded articles for May 2007)

Matzke, N. (2007). "New Creationist Book On the Way (Again)." Reports of the National Center for Science Education, 26(6), 15-16. (Local pdf)

Matzke, N., ed. (2007). "The testimony of Kevin Padian in Kitzmiller v. Dover." NCSE Online Kitzmiller Archive, http://www2.ncseweb.org/kvd/exhibits/. Transcript of Padian's Kitzmiller testimony with corrections, captions for slides, background, and organization and formatting. Padian's slides are also reproduced on a separate webpage without the transcript. (NCSE news story)

Matzke, N. (2007). "Needs more brimstone." [book review of E.O. Wilson's The Creation: An Appeal to Save Life on Earth.] Trends in Ecology and Evolution. 22(7), 335. July 2007. Published online 6 April 2007. (DOI | Local pdf | PT)

Matzke, N. (2007). "The Proper Place of Intelligent Design in the Curriculum [letter]." Chronicle of Higher Education, 53(27), p. B13. March 9, 2007. (online | Local pdf)

*,** Pallen, M., and Matzke, N. (2006). "From The Origin of Species to the Origin of Bacterial Flagella." Nature Reviews Microbiology. 4(10), 784-790. October 2006. http://www.doi.org/10.1038/nrmicro1493. (Local pdf | NCSE writeup)

This paper is discussed further here: http://www.pandasthumb.org/archives/2006/09/flagellum_evolu.html
And in an update to the 2003 essay: http://www.talkdesign.org/faqs/flagellum.html#update

Matzke, N., Akyol, M., Yahia, M. (2006). "The Evolution Debate (Part 2)." Live Dialogue at IslamOnline.net. September 3, 2006. http://www.islamonline.net/livedialogue/english/Browse.asp?hGuestID=a0iQ4n

Matzke, N., Akyol, M., Yahia, M. (2006). "Evolution vs. Intelligent Design." Live Dialogue at IslamOnline.net. August 21, 2006. http://www.islamonline.net/livedialogue/english/Browse.asp?hGuestID=QYL0zb

Matzke, N., and Gross, P. (2006). "Analyzing Critical Analysis: The Fallback Antievolutionist Strategy." Chapter 2 of Not in Our Classrooms: Why Intelligent Design is Wrong for Our Schools. Scott, E., and Branch, G., eds., Beacon Press, pp. 28-56. http://www.beacon.org/productdetails.cfm?SKU=3278. (Local pdf)

Matzke, N. (ed.) (2006). "Hendren v. Campbell: Decision Against a Creationist Textbook." Talk.Origins Archive. August 20, 2006. http://www.talkorigins.org/faqs/hendren/hendren_v_campbell.html

Matzke, N. (2006). "Survival of the Fittest [book review of The Evolution-Creation Struggle, by Michael Ruse]." Free Inquiry, 26(4), pp. 59-60. June/July 2006. Local pdf

** Bottaro, A., Inlay, M., and Matzke, N. (2006). "Immunology in the spotlight at the Dover "Intelligent Design' trial." Nature Immunology. 7(5), 433-435. May 2006. http://dx.doi.org/10.1038/ni0506-433. (Local pdf | Online Supplementary Material | Annotated Bibliography | Long Unannoted Bibliography | Press accounts | Cited in ENSIweb)

Matzke, N. (2006). "Design on Trial: How NCSE Helped Win the Kitzmiller Case." Reports of the National Center for Science Education. 26(1-2), 37-44. Jan-Apr. 2006. (Local pdf)

Matzke, N. (ed.) (2006). Online archive of all public legal documents in Kitzmiller v. Dover. http://www2.ncseweb.org/kvd/

Padian, K., and Matzke, N. (2006). "Discovery Institute tries to "swift-boat' Judge Jones." NCSE website: http://www.ncseweb.org/resources/articles/6161_discovery_institute_tries_to__1_4_2006.asp

Isaak, M. & Matzke, N. (2005). "Rebuttal to Creationist Claim CB200.1: The Bacterial Flagellum is Irreducibly Complex." In The Counter-Creationism Handbook by Mark Isaak, London: Greenwood Press, pp. 61-62. Online version: http://www.talkorigins.org/indexcc/CB/CB200_1.html. (Local pdf)

Matzke, N. (2005). "Design on Trial in Dover, Pennsylvania." Reports of the National Center for Science Education. 24(5):4-9. http://www.ncseweb.org/resources/rncse_content/vol24/4838_design_on_trial_in_dover_penn_12_30_1899.asp. (Local pdf)

Matzke, N. (2005). "Evolution of the Utricularia Bladder Trap: A Short Summary." Bay Area Carnivorous Plant Society Newsletter, Spring 2005. http://www.bacps.org/2005Spring.html#utrictrap

Scott, E., Branch G., and Matzke N. (2005). "Outside View: Creation sticker shock." Washington Times, January 18, 2005. http://washingtontimes.com/upi-breaking/20050116-015611-6340r.htm

Matzke, N., (ed.) (2004). "NCSE Resources page on Of Pandas and People, the foundational work of the "Intelligent Design' movement." NCSE website, December 2004. http://www.ncseweb.org/article.asp?category=21

Matzke, N. (2004). "Evolution as Religion: Stranger Hopes and Stranger Fears, Revised Edition [by Mary Midgley]" (book review). Reports of the National Center for Science Education. 24(3-4), pp. 46-48. (Local pdf)

Gishlick, A., Matzke, N., Elsberry, W. (2004). "Meyer's Hopeless Monster." Posted at the Panda's Thumb blog. http://www.pandasthumb.org/pt-archives/000430.html

This critical review of Stephen Meyer's "intelligent design' paper in the Proceedings of the Biological Society of Washington was the first public notice of the paper, and the blog critique was mentioned in news stories in Nature and The Scientist. It was later cited favorably in: Jenner, R. (2004). "The Tainting of Proc. Biol. Soc. Wash." The Paleontology Newsletter. 57, pp. 10-17. http://www.palass.org/pages/archive/News57a.pdf

Matzke, N. (2004). "Behe's Blunder: Irreducible Complexity and Change of Function." BASIS: Bay Area Skeptics Information Sheet, 21(2), pp. 7-9, April-June 2004. (Local pdf)

Scott, E. C., Matzke, N. J., Branch, G., Steves (2004). "The Morphology of Steve." Annals of Improbable Research. 10(4), pp. 24-29. http://www.improbable.com/airchives/paperair/volume10/v10i4/v10i4.html

Matzke, N. (2003). "Evolution in (Brownian) space: a model for the origin of the bacterial flagellum." Talk.Origins/TalkDesign Archive: http://www.talkdesign.org/faqs/flagellum.html

This essay was cited in the literature in: Pallen et al. (2006), "Evolutionary links between FliH/YscL-like proteins from bacterial type III secretion systems and second-stalk components of the FoF1 and vacuolar ATPases." Protein Science, 15(4), 935-941. http://dx.doi.org/10.1038/nrmicro1493. It is also linked from the Pallen and Matzke (2006) article (above).

Matzke, N. (2003). "Comparative analysis of DMSP, MODIS, and GLOBSCAR burn area estimation capabilities for Madagascar." Presented at the Remote Sensing Specialty Group Competition, American Association of Geographers Annual Meeting, March 2003. (Local pdf)

Matzke, N., (2003). "Remote Sensing and Geostatistical Analysis of Anthropogenic Biomass Burning and Forest Degradation in Madagascar." Master's Thesis, University of California, Santa Barbara, Geography Department, pp. 1-158. (Local pdf: screen resolution, 3.2 MB | print resolution, 27 MB)

Matzke, N. (2002). "Icon of Obfuscation: Jonathan Wells' book Icons of Evolution and why most of what it teaches about evolution is wrong." Talk.Origins Archive. http://www.talkorigins.org/faqs/wells/iconob.html

This critical review of Icons of Evolution, a pernicious book written by intelligent design advocate Jonathan Wells of the Discovery Institute, was the first detailed critique to come out. The review (originally written under the marginally clever pen name "Nic Tamzek") was cited in Annual Review of Genomics and Human Genetics (Pennock, R., 2003, "Creationism and Intelligent Design." Ann. Rev. Genomics Hum. Genet., 4: 143-163, online: http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.genom.4.070802.110400).

The web essay was used in a study by Steven D. Verhey, "The Effect of Engaging Prior Learning on Student Attitudes Toward Creationism and Evolution" (2005, BioScience, 55(11): 996-1003, online: http://www.bioone.org/bioone/?request =get- abstract&issn=0006-3568&volume=055&issue=11&page =0996). Verhey split his college class split into 2 groups. In the group which read Icons and my rebuttal, 61% reported a change in views, while in the control group only 21% reported a change. Students classified themselves on a 6-step spectrum of evolution/creationism. After the course, in the non-Icons group, only 3 steps towards the evolutionary end of the spectrum were reported, and 0 the opposite direction. In the Icons + rebuttal group, 23 steps towards the evolutionary end were reported, and 5 steps towards the creationism end.

Matzke, N., and Battersby, S. (2001). ArcInfo8 labs. Originally at: http://www.geog.ucsb.edu/~ta176/, now widely reproduced in other online instructions for Geographic Information Systems courses.


Presentations (selected)

Research-related

Matzke, Nicholas J. (2017). Measuring how the probability of long-distance dispersal depends on geographic distance, environmental distance, and co-evolving seed dispersal traits: BioGeoBEARS on a mega-phylogeny of angiosperms. Accepted abstract for the special symposium "Key questions on angiosperm macroevolution: where do we stand, and where are we heading now? (two sessions)." The XIX International Botanical Congress (IBC 2017), Shenzhen Convention and Exhibition Center in Shenzhen, China, July 23-29, 2017.

Matzke, Nicholas J; Säilä, Laura (2017). Phylogenetic biogeography of fossil Canidae: combining models of imperfect detection, fossil databases as taphonomic controls, and Biogeographical Stochastic Mapping. Evolution 2017, Portland, Oregon. June 23-27, 2017. http://www.evolutionmeetings.org/evolution-2017---portland-oregon.html

Matzke, Nicholas J. (2017). Model-based inference of environmental niches and niche evolution: fundamental and practical issues for discussion. TEA Talk for the Centre for Biodiversity Analysis (CBA), Division of Evolution and Ecology, Research School of Biology, The Australian National University, Canberra, Australia. 12-2 pm, May 5, 2017. E&E Seminar Room, Gould Building 116, Daley Rd, ANU. http://cba.anu.edu.au/news-events/model-based-inference-environmental-niches-and-niche-evolution-fundamental-and-practical

Matzke, Nicholas J. (2017). Models matter: Better models for better inference in phylogenomic dating and biogeography. Weekly seminar series, Institute for Applied Ecology, University of Canberra, 3B12 (Building 3, Level B, room 12). April 19, 2017, 12:30 p.m. Hosted by Jonas.Bylemans & Emory Ingles.

Matzke, Nicholas J. (2017). "Biogeography with jumps, distance, and trait-based dispersal: Adding realism fits the data better than traditional models in historical biogeography." University of Auckland, School of Biological Sciences (SBS). 2017 Seminar Series. Federation of Graduate Women's Room, Old Government House (102), 1-2pm. April 11, 2017. (Poster link | seminar series link)

Matzke, Nicholas J. (2017). Models matter: Better models for better inference in phylogenomic dating and biogeography. Biology Department, Western Washington University. Room BI234, 4 p.m., February 8, 2017.

Matzke, Nicholas J. (2017). Measuring the influence of an evolving trait on evolutionary dispersal probability with Pacific rails, global legumes, and Indo-Pacific Cryptoblepharus lizards. Programa de Doctorado en Sistemática y Biodiversidad, Universidad de Concepción. Concepción, Chile. Thursday, January 19, 2017. Sponsored by Cristián E. Hernández, Laboratorio de Ecología Evolutiva y Filoinformática, Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas. Universidad de Concepción, Casilla 160-C, Concepción, Chile.

Matzke, Nicholas J.; Warren, Dan L. (2017). Joint Bayesian estimation of niche models and niche evolution: Comparing algorithms. International Biogeography Society, 2017 Biennial Meeting. Tucson, Arizona. January 10, 2017, talk MT2-5. Conference Programs and Abstracts, 8th Biennial Conference of The International Biogeography Society, Tucson, AZ, USA, January 9th-13th, 2017, p. 82.

Matzke, Nicholas J. (2016). Trait-dependent dispersal models for phylogenetic biogeography in the R package BioGeoBEARS. Ringvorlesung Biodiversität (RUB), University of Bochum. Bochum, Germany. Speaker for Wintersemester 2016/2017 seminar series, December 6, 2016. 4:15 pm, room ND03/99. Hosted by Kristina Klaus.

Bapst, David W.; Hopkins, Melanie; Wright, April; Matzke, Nicholas J.; Lloyd, Graeme T. (2016). Inferring ancestor-descendant relationships in the fossil record (with statistics). Geological Society of America Abstracts with Programs, 48(7). Geological Science of America Annual Meeting in Denver, Colorado. Session No. 289: T151. New Approaches to Phylogenetic Paleobiology. Wednesday, 28 September 2016: 8:00 AM-12:00 PM, Mile High Ballroom 4AB (Colorado Convention Center). Paper No. 289-6, Presentation Time: 9:15 a.m. (Abstract | doi: 10.1130/abs/2016AM-277591 | PDF

Matzke, Nicholas J. (2016). The Evolution of Anti-evolutionism. Keynote at Centre for Biodiversity Analysis (CBA) Workshop on "The interface of evolutionary biology and policy impact." Canberra, Australia. September 6, 2016. http://cba.anu.edu.au/news-events/interface-evolutionary-biology-and-policy-impact

Lam, Adriane R.; Matzke, Nicholas J.; Stigall, Alycia L. (2016). "Testing Dispersal of Benthic Invertebrates during the Richmondian Invasion using Bayesian and Maximum-Likelihood Analyses." International Geoscience Programme Project 591 (IGCP 591). Ghent, Belgium. 2 pm, July 6-9, 2016. Session 9 (Refter Room): Large scale biodiversity patterns and palaeo-ecology. http://www.igcp591.ugent.be/

Matzke, Nicholas J. (2016). "Trait-dependent dispersal models for phylogenetic biogeography, in the R package BioGeoBEARS." Poster #577, Society for Molecular Biology and Evolution Conference 2016. Poster session B, Hall 1, 6:00pm-8:00pm, July 5, 2016. (Meeting | Abstract | Poster PDF | Twitter)

Matzke, Nicholas J. (2016). "iEvoBio Lightning Talk: Trait-dependent dispersal models for phylogenetic biogeography, in the R package BioGeoBEARS." 2:12 pm, in room MR9C. at: Evolution 2016, Austin, TX, Austin Convention Center, June 17-21, 2016. (talk PDF)

Matzke, Nicholas J. (2016). "Introduction to Symposium; and phyloSDM: Bayesian hierarchical model for joint estimation of ecological niche models and niche evolution." 8:15 am, Ballroom C. Part of: "SSB Special Symposium at Evolution 2016: Putting evolution into ecological niche modeling: Building the connection between phylogenies, paleobiology, and species distribution models" at: Evolution 2016, Austin, TX, Austin Convention Center, June 17-21, 2016. (talk PDF)

Matzke, Nicholas J.; Warren, Dan (2016). Co-organizers of "SSB Special Symposium at Evolution 2016: Putting evolution into ecological niche modeling: Building the connection between phylogenies, paleobiology, and species distribution models." Sunday, June 19, 8:15 am-11:45 am. At: Evolution 2016, Austin, TX, Austin Convention Center, June 17-21, 2016.

Dupin, Julia; Matzke, Nicholas J.; Saarkinen, Tiina; Knapp, Sandra; Olmstead, Richard G.; Bohs, Lynn; Smith, Stacey D. (2016). "Bayesian estimation of the global biogeographic history of the Solanaceae." Botany Society of America 2016. July 31-August 3, Savannah, Georgia. (Meeting | PhyloWiki)

Matzke, Nicholas J. (2016). The Evolution of Anti-evolutionism. Dinner Presentation for Australian Skeptics. West Reid, Sydney, Australia. April 9, 2016. http://www.skeptics.com.au/2016/03/06/sydney-dinner-april-9-the-evolution-of-antievolutionism/

Matzke, Nicholas J. Ground-truthing tip-dating methods and models using fossil Canidae reveals major differences in performance. Molecular Paleobiology of Australia's Terrestrial Vertebrates Conference. Melbourne, Victoria, Australia. Melbourne Museum, 11-11:15 a.m., Tuesday, April 5, 2016. (Conference website | PhyloWiki)

Matzke, N.J. (2016). Trait-dependent dispersal models for phylogenetic biogeography, in the R package BioGeoBEARS. ANU Research School of Biology. Poster at Early-and Mid-Career Conference (#RSBEMCR16). R. N. Robertson Lecture Theatre, Bldg. 46. Feb. 11th, 2016, 4:45 pm. (PhyloWiki)

Matzke, Nicholas J. (2017). Modeling the influence of traits and distance on dispersal probability in historical biogeography with BioGeoBEARS. Invited speaker for the 2017 meeting of the International Botanical Congress (IBC 2017) to take place in Shenzhen, China, 23-29 July 2017 (http://www.ibc2017.cn/)

Matzke, Nicholas J.; Warren, Dan (2016). Symposium (accepted): “Putting Evolution Into Ecological Niche Modeling: Building the Connection Between Phylogenies, Paleobiology, and Species Distribution Models.” Accepted Symposium for 2016 SSB Symposium at Evolution 2016, Austin, Texas (June 17-21).

Matzke, Nicholas J. (2016). The Evolution of Antievolutionism before and after Kitzmiller v. Dover (2005). Sponsor: Lindell Bromham, Tempo and Mode Seminar. [postponed]

Matzke, Nicholas J. (2016). When Darwin Visited Valparaiso (Chile). Darwin Day Lecture at Valparaiso University, Friday, Jan. 15, 3:30-4:30 pm, Christopher Center Library. Sponsor: Robert Swanson.

Matzke, Nicholas J. (2016). Trait-dependent dispersal models for phylogenetic biogeography, in the R package BioGeoBEARS. Speciation and Biogeography session, Society of Integrative and Comparative Biology Annual Meeting, Jan. 3-8, 2016. Wednesday, January 6, 3:30-4:30 pm. 3:30 pm, Wed. Jan. 6, Poster P3-12. http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=1674 http://phylo.wikidot.com/abstracts-for-presentations-by-nicholas-j-matzke#trait

Matzke, N. (2015). Trait-dependent dispersal models for phylogenetic biogeography, in the R package BioGeoBEARS. Annual Meeting of the Society of Australian Systematic Biologists, 2015. Tuesday, December 8, 2015. Sirius Room: From R to ecology, 3:50-4:10 pm.

Matzke, Nicholas J. (2015). Putting Evolution Into Ecological Niche Modelling (And: Statistical model choice in phylogenetic biogeography more generally). At: Stochastic Modelling meets Phylogenetics (SMMP), collaborative workshop November 16-18, University of Tasmania, Hobart. November 16, 2015, 12:30 pm. Mathematics & Physics Building, University of Tasmania. (#SMMP2015) (SMMP website PDF)

Matzke, Nicholas (2015). Bayesian tip-dating with continuous characters using BEASTmasteR. Presentation at Society of Vertebrate Paleontology, Technical Session V, Histology and Methods, Wednesday, October 14, 2015, 1:45-4:15 p.m. Journal of Vertebrate Paleontology, Program and Abstracts, 177. http://phylo.wikidot.com/local--files/beastmaster/2015-10-14_Matzke_SVP_continuous_traits_v3.pdf

Matzke, Nicholas J. (2015). "Biogeographical Stochastic Mapping: Bayesian estimation of the history and timing of biogeographical events on phylogenies." Craig Moritz Lab Group, Gould Meeting Room, 2 pm, August 5, 2015.

06/30/15 - Matzke, Nicholas J. (2015). "Historical biogeography models with dispersal probability as a function of distance(s)." SSE symposium: Frontiers in Parametric Biogeography, Presentation for the SSB Biogeography Symposium in Guarujá, Brasil, Evolution 2015. 10:45-11:15 a.m.

06/30/15 - Massana, Kathryn; Beaulieu, Jeremy; Matzke, Nicholas J.; O'Meara, Brian (2015). "Non-null effects of a null range: Exploring parameter estimation in the dispersal-extinction-cladogenesis model." SSE symposium: Frontiers in Parametric Biogeography, Presentation for the SSB Biogeography Symposium in Guarujá, Brasil, Evolution 2015. 8:45-9:15 a.m.

Antonelli, Alexandre; Bacon, Christine D.; Carvalho, Fernanda A.; Hettling, Hannes; Matzke, Nicholas J.; Obst, Matthias; Scharn, Ruud; Silvestro, Daniele; Vilhena, Daril; Vos, Rutger; Zizka, Alexander (2015). "Comparative biogeography: A framework for cross-taxonomic inference of bioregions, range shifts and diversification." SSE symposium: Frontiers in Parametric Biogeography, Presentation for the SSB Biogeography Symposium in Guarujá, Brasil, Evolution 2015. 4:00-4:30 p.m.

06/27/15 - Dupin, Julia; Matzke, Nicholas; Knapp, Sandra; Bohs, Lynn; Olmstead, Richard; Särkinen, Tiina; Smith, Stacey D. (2015). "Solanaceae biogeography: dispersal patterns over space and time." Poster session, 7 p.m., Sala de exposições room, at Evolution 2015 in Guarujá, Brasil.

05/22/15 - Matzke, Nicholas J. (2015). "BEASTmasteR: Tip-dating with fossils in Beast2, using R to convert NEXUS data files to XML input." Lightning Talk, Society of Systematic Biology Standalone Meeting 2015 (SSB2015), Ann Arbor, Michigan. 1:30 pm, session C, Michigan Union, Pendleton room. http://ssb2015standalone.weebly.com/program.html http://phylo.wdfiles.com/local--files/beastmaster/2015-05-21_Matzke_SSB2015_BEASTmasteR_v1.pdf

05/21/15 - Zhang, Guanyang; Barashat, Usmaan; Matzke, Nicholas J.; Franz, Nico (2015). Biogeography of Caribbean weevils highlights the importance of founder-event speciation. Society for Systematic Biologists Standalone Meeting 2015 (SSB2015), Ann Arbor, Michigan, May 21, 2015. http://ssb2015standalone.weebly.com/program.html http://www.slideshare.net/GYZhang1/b-100-zhang

03/05/2015 - Matzke, Nicholas J. Statistical model choice in historical biogeography. Lecture for Zoogeography, taught by Sandy Echternacht and Dan Simberloff. Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville. March 5, 2015.

02/28/15 - Matzke, N. (2015). Dating dinos by putting fossils in trees: simultaneous estimation of evolutionary relationships and phylogenetic divergence times of dinosaurs (and other groups) with Bayesian MCMC techniques. Howard University Math Department. Room 213 Academic Support Building B. Department of Math, Howard University. Host Alex Burstein. Part of the NIMBioS Minority-Serving Institutions Outreach Program.

02/12/15 - Matzke, Nicholas J. et al. (2015). Panel Discussion on Evolution Education, Darwin Day at University of Tennessee, Knoxville. February 12, 2015.

01/28/15 - Matzke, N. (2015). Model selection in historical biogeography: when is founder-event speciation important? Botanische Staatssammlung München (Bavarian State Collection for Botany, Munich, Bavaria, Germany). Host Suzanne Renner. Wednesday, January 28, 2015, 2 pm-2:45 pm

01/16/15 - Matzke, N. (2015). Model selection in historical biogeography: when is founder-event speciation important? Geosciences Department, University of Helsinki, Finland. Host Laura K. Saila. Friday, January 16, 2015, 2 pm-2:45 pm

01/08/15 - Matzke, N. (2015). Biogeographical Stochastic Mapping: Bayesian estimation of the history and timing of biogeographical events on phylogenies. International Biogeography Society (IBS) Biannual Meeting, Bayreuth, Germany. Saturday, January 10, 2015, 1:30-1:45 pm, H 22, RW II.

11/19/14 - Matzke, N. (2014). Introduction to Likelihood and Bayesian methods in phylogenetics. Guest lecture for Stephanie Drumheller-Horton's Geology 320: Paleobiology. 9 a.m., Earth & Planetary Sciences room 400.

11/07/14 - Matzke, N., Wright, A., Bapst, D. (2014). Incorporation of absolute and relative fossil dating information in bayesian tip-dating analyses using the R package BEASTmasteR: examples from assassin spiders, salmonids, and hominids. Moderators: Nicholas J. Matzke and April Wright. In: Symposium 3: Putting fossils in trees: new methods for combining morphology, time, and molecules to estimate phylogenetic and divergence times of living and fossil taxa. 8:00 a.m., Estrel Berlin, Hall A.

11/07/14 - Turner, A., Pritchard, A., Matzke, N. J. (2014). 'Tip-dating' when all you have are fossils: comparing traditional and bayesian approaches to fossil divergence times. Moderators: Nicholas J. Matzke and April Wright. In: Symposium 3: Putting fossils in trees: new methods for combining morphology, time, and molecules to estimate phylogenetic and divergence times of living and fossil taxa. 11:00 a.m., Estrel Berlin, Hall A.

11/07/14 - Wright, A., Lloyd, G., Matzke, N. (2014). Fossils-only tip-dating of deinonychosaurian theropods: a comparison of methods and models. Moderators: Nicholas J. Matzke and April Wright. In: Symposium 3: Putting fossils in trees: new methods for combining morphology, time, and molecules to estimate phylogenetic and divergence times of living and fossil taxa. 11:15 a.m., Estrel Berlin, Hall A.

11/05/2014 - Matzke, Nicholas J.; Wright, April; Lloyd, Graeme; Bapst, David W., co-convenors (2014, approved). Moderators for symposium: New methods for combining morphology, time, and molecules to estimate phylogenetic position and divergence times of living and fossil taxa. Approved symposium at the 74th Annual Meeting of the Society of Vertebrate Paleontology (Estrel Convention Center, Berlin, Germany, November 2014).

10/09/14 - Matzke, N. (2014). Model selection in historical biogeography: when is founder-event speciation important? Evolutionary Morphology Seminar, Department of of Geophysical Sciences, University of Chicago. Thursday, October 9, 2014 7:30–8:30 p.m.

09/30/2014 - Matzke, Nicholas J. "Science and Intelligent Design Creationism on Trial." Lecture for ANTH/EEB305 Evolution and Society, co-taught by Michael Gilchrist, University of Tennessee, Knoxville. 2:10 pm, 405 EPS, September 30, 2014.

09/19/2014 - Matzke, Nicholas J. "The Kitzmiller v. Dover Trial: the evolution of creationism and the importance of history." Departmental seminar, Department of Earth & Planetary Sciences, University of Tennessee, Knoxville. 3:40 pm, September 18, 2014.

06/20/14 - Matzke, Nicholas J. (2014). Accuracy assessment of historical biogeography methods under a variety of simulated conditions. Evolution 2014 Annual Meeting, Raleigh, North Carolina. June 19-24, 2014.

06/08/14 - Matzke, Nicholas J.; Shih, Patrick M. (2014). Primary endosymbiosis events date to the later Proterozoic with cross-calibrated phylogenetic dating of duplicated ATPase proteins. Society for Molecular Biology and Evolution, 2014 Annual Meeting, Puerto Rico. June 8-12, 2014.

04/12/14 - Dembo, Mana; Matzke, Nicholas J.; Mooers, Arne; Collard, Mark (2014). A reanalysis of fossil hominin phylogeny using a craniodental supermatrix. The 83rd Annual Meeting of the American Association of Physical Anthropologists. Telus CC Exhibit Hall E2. April 12, 2014. (Link)

03/03/14 - Matzke, Nicholas J. (2014). Discussion of reviews of DEC+J model. HOFF Lab Meeting, University of Tennessee, Knoxville. March 3, 2014.

02/28/14 - Matzke, Nicholas J. (2014). Statistical model choice in phylogenetic biogeography: Inference of speciation processes and ancestral range, and prospects for integration with species distribution modeling (SDM). Invited speaker for the Bioinformatics Program at the University of Texas, El Paso. Feb. 28 2014.

02/12/14 - Matzke, Nicholas J. (2014). History matters: the 2005 Kitzmiller v. Dover case, the defeat of “Intelligent Design”, and the aftermath. Invited talk for Darwin Day at University of Tennessee, Knoxville. Buehler, room 511. February 12, 2014.

02/08/14 - Matzke, Nicholas J. (2014). Invited talk and panel member for a continuing education event for teachers, sponsored by NIMBioS and Darwin Day at University of Tennessee, Knoxville. NIMBioS. February 8, 2014.

01/25/14 - Matzke, Nicholas J. (2014). Co-led tour of Dayton, Tennessee, site of the 1925 "Scopes Monkey Trial" and now a National Historic Site. Part of activities for 2014 Darwin Day at University of Tennessee, Knoxville. January 25, 2014

01/09/14 - Matzke, Nicholas J. (2014). Model selection reveals differences in cladogenesis processes opera)ng in island versus continental clades. International Biogeography Society Early Career Meeting. Australian National University, Canberra, Australia. 2-2:15 pm, ANU Commons. January 9, 2014.

11/12/2013 - Matzke, Nicholas J. (2013). Model choice in phylogenetic biogeography. Jetz Lab, Department of Ecology and Evolution, Yale University. 12-1 pm, Osborn Memorial Laboratories (OML) room 40, November 12, 2013.

11/01/13 - Matzke, Nicholas J. (2013). BioGeoBEARS: An R package for inference and model tesinng in historical biogeography. KRUG (Knoxville R User's Group) fall meeting, University of Tennessee, Knoxville. November 1, 2013.

10/29/13 - Matzke, Nicholas J. (2013). Statistical model choice in phylogenetic biogeography: Inference of speciation processes and ancestral range, and prospects for integration with species distribution modeling (SDM). NIMBioS Seminar Series. Room 105, Claxton Building, 1122 Volunteer Blvd., University of Tennessee, Knoxville. October 29, 2013. Video online at: http://youtu.be/HaSObNiox18. (Link to abstract, flyer, and video)

09/23/13 - Matzke, Nicholas J. (2013). Statistical model choice for old and new biogeographical cladogenesis models: comparing DEC, DIVA, BayArea, and measuring the importance of founder-event speciation, with and without model for imperfect detection of fossils. Invited talk for France-Berkeley-Fund Workshop: Integrating Molecular Phylogenies and the Fossil Record, organized by Helene Morlon, Tiago Quental, Charles Marshall, September 23-25, 2013.

09/16/13 - Matzke, Nicholas J. (2013). Statistical model choice for old and new biogeographical cladogenesis models. HOFF Lab Meeting, University of Tennessee, Knoxville. September 16, 2013.

08/12/13 - Matzke, Nicholas J. (2013). BioGeoBEARS R Package. Accepted talk for NESCENT Catalyis Meeting: Integrating Historical Biogeography and Phylogeography with the Fossil Record and Landscape History. August 12, 2013. Travel expenses covered.

07/08/13 - Matzke, Nicholas J.; Schraiber, Joshua G.; Collard, Mark; Dembo, Mana; Yang, Melinda A. (2013). "Tighter estimation of hominoid divergence times by Bayesian joint analysis of dated fossil morphology and incompletely sorted genes." Poster at Society of Molecular Biology 2013 Annual Meeting, Chicago, IL. July 8, 2013.

06/25/13 - Matzke, Nicholas J. (2013). BioGeoBEARS: R package for model comparison in historical biogeography. iEvoBio Lightning Talk. June 23, 2013. Received Travel Award, $500.

06/23/13 - Matzke, Nicholas J. (2013). Founder-event speciation dramatically improves likelihoods and alters parameter inference in Dispersal-Extinction-Cladogenesis (DEC) analyses. Selected talk for the Ernst Mayr Symposium. Evolution 2013, Snowbird, Utah. June 23, 2013.

05/07/13 - Matzke, Nicholas J. (2013). Founder-event speciation dramatically improves likelihoods and alters parameter inference in Dispersal-Extinction-Cladogenesis (DEC) analyses. Ph.D. Finishing Talk, Department of Integrative Biology, University of California, Berkeley. May 7, 2013.

04/13/13 - Matzke, Nicholas J. (2013). Founder-event speciation dramatically improves likelihoods and alters parameter inference in Dispersal-Extinction-Cladogenesis (DEC) analyses. California Botanical Society, Centennial Meeing, Berkeley, CA April 13-14, 2013.

03/11/13 -- Matzke, Nicholas J. (2013). Genome size variability and its correlates. Talked and then led discussion for lab meeting of the Center for Theoretical Evolutionary Genomics. Department of Integrative Biology, University of California, Berkeley. March 11, 2013.

03/08/13 -- Matzke, Nicholas J. (2013). What Galileo Saw. Guest lecture for Letters & Science 121: Origins in Science and Religion, University of California, Berkeley. March 8, 2013.

02/14/13 -- Matzke, Nicholas J. (2013). Origins(s) of Life. Guest lecture giving and overview and recent developments in origin-of-life research, for Letters & Science 121: Origins in Science and Religion, University of California, Berkeley. February 14, 2013.

02/13/13 -- Matzke, Nicholas J. (2013). Social Media and Online Presence in Science. Invited Panel Member for meeting of Integrative Biology Women in Science, University of California, Berkeley. February 13, 2013.

01/09/13 - Matzke, Nicholas J. (2013). Founder-event speciation in BioGeoBEARS package dramatically improves likelihoods and alters parameter inference in Dispersal-Extinction-Cladogenesis (DEC) analyses. International Biogeography Society Biannual Meeting, Miami, Florida. January 9-13, 2013. Submitted. (IBS Miami 2013 meeting)

11/17/12 - Matzke, Nicholas J. (2012). Founder-event speciation in BioGeoBEARS package dramatically improves likelihoods and alters parameter inference in Dispersal-Extinction-Cladogenesis (DEC) analyses. Computational and Genomic Biology Retreat. Submitted. (2012 Annual Retreat)

10/17/12 - Matzke, Nicholas J. (2012). Kitzmiller v. Dover, and the future of the evolution-creationism battle. Presentation for the DeCal course "Politics for Scientists." 2-4 pm, 174 Barrows.

9/20/12 - Matzke, Nicholas J. (2012). Inclusion of detection models in historical biogeography - Directed Acyclic Graphs (DAGs). Seminar for the Berkeley Initiative for Global Change Biology.

09/11/12 - Matzke, Nicholas J. (2012). Micro and Macro for the Millenial Generation. Bay Area Biosystematists Meeting. Berkeley, CA. Invited speaker and moderator. Speaker with Brian Swartz and Josh Schraiber. (BABS website | PDF)

7/9/12 - Landis, Michael; Matzke, Nick; Moore, Brian; Huelsenbeck, John. Statistical analysis of biogeography when the number of areas is large. Evolution 2012, Biogeography, bioinformatics & computational biology session. Ottawa, Canada.

7/8/12 - Wood, Hannah; Matzke, Nicholas; Gillespie, Rosemary; Griswold, Charles (2012). Treating fossils as terminal taxa in divergence time estimation reveals ancient vicariance patterns in the Palpimanoidea spiders. Evolution 2012, Biogeography 2 session. Ottawa, Canada.

5/15/12 - Matzke, Nicholas J. (2012). Estimating ancestral cone snail shell patterns: Creative application of models for the evolution of continuous characters. Genomes, Development, and Evolution Annual Meeting, Berkeley, CA.

4/3/12 - Matzke, Nicholas J. (2012). Putting detection models, spatial autocorrelation, and phylogenetic autocorrelation into biogeography. Computational and Genomic Biology Designated Emphasis Seminar, Tuesday, 4/3/2012, Campbell 001.

4/30/2012 - Matzke, Nicholas J. (2012). Phylogenetics for: 1. reconstructing extinct species 2. Linking species distribution modeling and historical biogeography. Tien Fellowship presentation.

3/20/2012 - Matzke, Nicholas J. (2012). Evolution: What the Public Needs to Know. Presentation for the students in Introductory Biology at San Quentin Prison, San Francisco, CA. This course is run by the Prison University Project (http://www.prisonuniversityproject.org/), which recently added a biology course as part of its addition of an Associate's Degree program (a 2-year college degree). I was invited to be a guest lecturer.

Matzke, N. J.; Maguire, K. C. (2011). "Effect of fossil range and extinction data in DEC analyses: a case study with Canidae." Society of Vertebrate Paleontology Annual Meeting, November 2011, Las Vegas. (Scholar)

Atterholt, Jessie; Matzke, N. J. (2011). "Evolution of life history traits using a dated phylogeny derived from combined-analysis dataset of dinosaurs and birds." Society of Vertebrate Paleontology Annual Meeting, November 2011, Las Vegas. (Scholar)

Matzke, Nicholas J. (2011). Testing old and new methods in historical biogeography using simulation: the role of extinction and fossils. 5th International conference of the International Biogeography Society. Irakleio, Crete, Greece, 147. (Scholar | Link)

11/2/11 - Ferrer, Elizabeth; Matzke, N. J. (2011). Are raw taxic counts really reflecting shifts in diversity dynamics? A case study using canids. Society of Vertebrate Paleontology Annual Meeting, November 2011, Las Vegas)

9/25/2011 - Matzke, Nicholas J. (2011). Moving from historical biogeographic inference in discrete space to historical biogeographic inference in continuous space, by moving from species distribution modeling to phylogenetic lineage distribution modeling. SESSION 8: Topics in Biogeography, at: Advances in Biogeography: Early Career Conference, 23-25 September, 2011. Oxford University Centre for the Environment.

5/26/11 - Matzke, Nicholas J. (2011). Talk and workshop on "R-and-Biogeography." Invited presentation, all expenses paid. At: "Methodological Workshop On Biodiversity Dynamics", on May 26th. Evolution of Life on Pacific Islands and Reefs: Past, present, and future. May 26-30, 2011, East-West Center, Honolulu, Hawaii. (Workshop notes announcement | Demos and code at PhyloWiki)

04/19/11 - Matzke, Nicholas J. (2011). Biogeography II -- New tools, databases, and research possibilities. Lecture for IB200B: Phylogenetics Applications in Ecology and Evolution. (PDF lecture notes | course link)

03/03/11 - Matzke, Nicholas J. (2011). Gene family evolution; comparative genomics. Lecture for IB200B: Phylogenetics Applications in Ecology and Evolution. (PDF lecture notes | course link)

02-08-11 - Matzke, Nicholas J. (2011). Dating in the 21st Century: Theoretical and Empirical Issues in Putting Dates on Phylogenies. Bay Area Biosystematists Meeting. Berkeley, CA. Invited speaker and moderator. Panelist with Sarah Werning, Pat Holroy, and Tracy Heath. (Scholar | Link | Local PDF)

01/25/11 - Matzke, Nicholas J. (2011). Introduction to Statistical Thinking. Lecture for IB200B: Phylogenetics Applications in Ecology and Evolution. With course professors. (PDF lecture notes | course link)

01/09/11 - Matzke, Nicholas J. (2011). Testing old and new methods in historical biogeography using simulation: the role of extinction and fossils. 5th International conference of the International Biogeography Society. Irakleio, Crete, Greece, 147. (Scholar | Link | Poster PDF | Poster PPT)

Matzke, Nicholas J. (2010). The Modern Synthesis Revisited. A rank-free discussion of microevolution and macroevolution: Avoiding the fallacy of retrospective significance. Bay Area Biosystematists Meeting. B. Mishler. Berkeley, CA. (Scholar | Link)

10/19/10 - Matzke, Nicholas J. "Biogeographical Methods." Presentation for Island Biodiversification Seminar, taught by Rosie Gillespie, Fall 2010. (PDF)

Barnosky, Anthony D.; Matzke, Nicholas; Tomiya, Susumu; Lindsey, Emily L.; Wogan, Guinevere O. U. (2010). How present extinction rates compare with mass extinction rates: insights from mammals. Journal of Vertebrate Paleontology 30, Society of Vertebrate Paleontology Program and Abstracts. Pittsburgh, Pennsylvania. 57A. (Scholar | Link)

09/10/10 - Matzke, Nicholas J. (2010). The Modern Synthesis Revisited. A rank-free discussion of microevolution and macroevolution: Avoiding the fallacy of retrospective significance. Bay Area Biosystematists Meeting. Berkeley, CA. Invited speaker along with Jessie Atterholt, Brian Swartz; organizer, Brent Mishler. (Scholar | Link | Local PDF)

Bieler, Ruediger; Mikkelsen, Paula M.; Jablonski, David; Steppan, Scott J.; Huelsenbeck, John P.; Sartori, Andre F.; Robles, Rafael; Tomaovch, Adam; ter Poorten, Jan Johan; Herrera, Nathanael; Matzke, Nicholas J. (2010). Bivalves in Time and Space (BiTS): Testing Macroevolutionary Methods against the Bivalve Fossil Record. Abstracts of the 2010 Joint Meeting of The American Malacological Society & The Western Society of Malacologists.. (Scholar)

Bieler, Ruediger; Mikkelsen, Paula M.; Jablonski, David; Steppan, Scott J.; Huelsenbeck, John P.; Sartori, Andre F.; Robles, Rafael; Tomaovch, Adam; ter Poorten, Jan Johan; Herrera, Nathanael; Matzke, Nicholas J. (2010). Bivalves in Time and Space (BiTS): Developing Bivalves as a Preeminent Model for Macroevolutionary Studies. Abstracts of the 2010 World Congress of Malacology. (Scholar)

06/30/10 - Matzke, Nicholas J. (2010). Biopython (bio) Geography Module. iEvoBio 2010 Conference, June 29-30, 2010. Portland State University, Portland, Oregon. (Scholar | Link)

06/29/10 - Matzke, Nicholas J. (2011). Testing old and new methods in historical biogeography using simulation: the role of extinction and fossils. Evolution 2010 Conference, June 25-29, 2010. Portland State University, Portland, Oregon, American Society of Naturalists, Society for the Study of Evolution, Society of Systematic Biologists, 147. (Scholar | Link)

04/30/10 - Matzke, Nicholas J.; Shih, Patrick. "Bayesian Phylogenetic Analysis of Horizontal Gene Transfer in Prochlorococcus and Synechococcus." Lab talk, 4/30/2010 (ppt).

04/22/10 - Matzke, Nicholas J. (2010). Historical Biogeography: event-based methods. Lecture for IB200A: Systematics. (PDF lecture notes | course link)

03/09/10 - Matzke, Nicholas J. (2010). Phylogenetic trees VI - Bayesian methods. Lecture for IB200A: Systematics. (PDF lecture notes | course link)

10/1/09 - Macguire, Kaitlin C., Matzke, N. J. (2009). "Maximum Likelihood Estimation of Biogeographic Histories Using the Horse Fossil Record." Society of Vertebrate Paleontology Annual Meeting, Fall 2009.(SVP abstract)

06/16/09 - Presentation on applying community phylogenetics methods to the historical biogeography of temperate tree species. 8 a.m., Evolution 2009, Moscow Idaho

11/21/08 - Computational Biology Annual retreat, biogeography methods talk

11/17/08 - Computational Biology DE student seminar, review of the history of biogeography talk

10/06/08 -- lab talk, flagellum evolution update

6/20/2008 -- talk on flagellum evolution at Evolution2008, Minneapolis, MN

December 2008 - beta-phylodiversity of trees of northern hemisphere temperate forest regions

May 2008 -- amino acid substitution models, Stat C141: Statistics for Bioinformatics

May 2008 -- IB200A, Phylogenetics, flagellum evolution

February 2008 -- Evolution and the Latitudinal Diversity Gradient, group presentation for IB250: Tropical Diversity seminar

Science education-related

04/11/11 - Science and religion and the history of the evolution/creationism issue. St. Ignatius High School. With Jeremy Brown.

09/03/09 - The origin of adaptive immunity in evolution and creationism: transposition in the Kitzmiller v. Dover case. Invited talk for the Evolution 2009 Symposium at the University of Nebraska, Kansas. $1700 honorarium.

03/04/09 - invited talk on the Kitzmiller case, University of Oklahoma Zoology Department

10/17/08 -- invited talk, National Association of Biology Teachers, Conflicts over evolution: past/present/future

February 2008 -- moderated AAAS session on Major Transitions in Evolution, AAAS Annual Meeting, Boston

01/30/2008 -- chalk talk for grad. students; with Kevin Padian on science and the media: "How to talk to the media -- and why you should". Graduate Louge (5047 VLSB) at 5:10pm, Wednesday, Jan. 30

11/29/07 -- invited talk, National Association of Biology Teachers, "The Road to Dover"

11/25/07: IB 303 -- Science education, evolution misconceptions discussion

"Communicating with the public about evolution." Part of an invited panel session, "Communicating Science without the Jargon." Monday, June 18, 2007, Session 53, 1:30-3:00. First Pan-American Congress in Developmental Biology. Cancun, Mexico, June 16-20, 2007. (Local Powerpoint - 25 MB)

"Evolution versus creationism: courts and classrooms." For a course taught by David Stronk on Methods of Teaching Single Subject Science. California State University " East Bay, Hayward, CA, April 30, 2007. (Local Powerpoint - 25 MB)

"Evolution versus "intelligent design' at the Kitzmiller v. Dover trial." University of California, Berkeley, Botany Lunch. February 16, 2007. (Local Powerpoint - 25 MB)

"From McLean to Kitzmiller: The Rise and Fall of "Intelligent Design'." Willamette University Darwin Day event, "Creationism on Trial." Salem, Oregon. February 9, 2007. (Local Powerpoint - 10 MB)

"Deep geological time, age-dating techniques, and the evolution of life in national parks." Oregon State University Geosciences Department, GEO 307 - National Park Geology and Preservation. Corvallis, Oregon. February 9, 2007. (Local Powerpoint - 7.7 MB)

"Science and the Law: The Kitzmiller v. Dover evolution case." EPA Lab, Corvallis, Oregon. February 8, 2007. (Local Powerpoint - 26 MB)

"What is Science? Evolution vs. "Intelligent Design' in Court." Oregon State University Philosophy Club. February 7, 2007. (Local Powerpoint - 27 MB)

"The Evolutionary Origin of Intelligent Design: Kitzmiller vs. Dover Case." Americans United for Separation of Church and State, San Fernando Valley Chapter. January 28, 2007. http://www.ausfv.org

"Challenges to Teaching Evolution: "Theory not Fact'." SETI session on evolution education. California Science Teachers Annual Meeting. October 21, 2006.

"The Evolutionary Origin of "Intelligent Design' and the Kitzmiller vs. Dover Case." Kern County Chapter of Americans United for Separation of Church and State. Bakersfield College, CA, September 21, 2006. (PDF of flyer)

"Complex adaptations in plants: Darwin and botanical gardens." Invited talk for the a session on "Evolution: What role should botanical gardens play in sustaining evolution?" Other speakers: Peter Raven, Steve Clemants. Annual meeting of the American Public Gardens Association. San Francisco, CA, June 29, 2006. http://publicgardens.org/ac2006/concurrent.htm. (Local Powerpoint - 18 MB)

"Design on Trial in Dover, PA." Annual meeting of Coalition for Excellence in Science Education/New Mexicans for Science and Reason, Albuquerque, NM, June 11, 2006. http://www.cesame-nm.org/news/Beacon/0609.pdf. (Online summary of talk | Local Powerpoint - 34 MB)

"Evolution Forum." Final topic in the Conscious Event series at Pacific Union College. Angwin, CA, June 6, 2006. (Local Powerpoint - 47 MB)

"The Evolutionary Origin of Intelligent Design: Science & History in the Pennsylvania Evolution versus Creationism Trial." Silicon Valley chapter of Americans United for Separation of Church and State. Campbell, CA, May 6, 2006. http://www.ausv.org

"The Evolutionary Origin of "Intelligent Design.'" Course for science teachers taught by David Stronk. California State University " East Bay, Hayward, CA, April 25, 2006.

"The Evolution of Creationism." Lecture for a course taught by Adrian Leveen, "Religious Studies 180 -- Confronting Genesis: Sex, Science and Faith in the 21st Century. Stanford University." Stanford, CA, April 24, 2006.

"Science on Trial in the Pennsylvania Evolution Case." Spring meeting of the Women Chemists Committee, American Chemical Society, California Section. Mills College, Oakland, CA, April 22, 2006. http://www.calacs.org/calendar/WCCSpringMeet.html

"The evolution wars: Organizing resistance." Panel session on "Dispatches from the Evolution Wars." Annual meeting of the National Association of Research in Science Teaching (NARST). San Francisco, CA, April 6, 2005.

"The Politics of Intelligent Design." Columbia Political Union Forum. Columbia University, February 27, 2006. Video online: http://www.cupolitics.org/videos/0506/id_panel/

"On the Origin of Intelligent Design." Darwin Day 2006. University of Birmingham, February 10, 2006.

"Irreducible Complexity: Irreducible Confusion." Stanford University Skeptics Group. May 10, 2005. (Local Powerpoint - 5 MB)

"Evolution and Education." Talk before an Education Extension Course taught by David Stronck, California State University - Hayward. May 6, 2005.

"Evolution of the Utricularia Bladder Trap." Invited talk before the Bay Area Carnivorous Plant Society. University of California, Berkeley Botanic Garden, May 1, 2005. Summary online at: http://www.bacps.org/2005Spring.html#utrictrap

"The Evolution of Creationism." Portola Valley Community Church. Portola Valley, CA, February 13, 2005.

"History of creation/evolution." East Bay Skeptics Meeting. January 23, 2005.



Teaching and student advising

Teaching experience

I have extensive experience teaching college-level material in the following (courses where I was a Graduate Student Instructor are listed in parentheses). I was awarded U.C. Berkeley's "Outstanding Graduate Student Instructor" Award in 2013. Often, the labs, course websites, and materials I assembled are used for years afterwards (see links below).
  • Accredited as an Associate Fellow of The Higher Education Academy (AFHEA) in recognition of attainment against the UK Professional Standards Framework for teaching and learning support in higher education. Recognition reference: PR125089. https://www.international.heacademy.ac.uk/
  • Prepared and taught 5 lectures for ANU's Biol. 1003: Biology 1: Evolution, Ecology and Genetics, February 28-March 8, 2017. Class size: ~400 students. Course coordinator: Andras Keszei. http://programsandcourses.anu.edu.au/course/BIOL1003
  • Evolutionary Biology (Integrative Biology 160)
  • Phylogenetics (Integrative Biology IB200A and IB200B)
  • General Biology (Integrative Biology 1B)
  • Human Genetics (Integrative Biology 164)
  • Biogeography (Lectures for many courses and workshops)
  • GIS and remote sensing (Geography MA) (search for ArcGIS courses still using these labs
  • Species Distribution Modeling (workshops, research, student advising)
  • Science and Society, The History of Science, and cultural/religious controversies about science (many guest lectures, and U.C. Berkeley's Interdisciplinary Studies course "Origins in Science and Religion")
  • Statistical inference in biology - both theoretical (maximum likelihood, Bayesian) and practical (computational) aspects. In particular, I specialize on "what biology students really need to know" about statistical inference with the kinds of problems that biologists face, which are often distant from the idealized situations often taught in introductory statistics course.
  • The programming languages R and Python (several of the above courses, also workshops)
Other topics I am familiar with by education and work experience include ecology, field techniques and vegetation/forestry surveying. I have led or assisted with many course field trips for field courses.

Student advising

  • Ph.D. student advising: As a DECRA fellow at ANU, I am currently co-advising a Ph.D. student in biological anthropology, Kirrily Apthorp, on niche modeling endangered primates in SE Asia.
  • Ph.D. student advising: I am on the supervisory committee of ANU Ph.D. student Alex Skeels (with Craig Moritz and Marcel Cardillo)
  • Assisting and advising on student-led research: I work extremely well with graduate and undergraduate student researchers, and am often sought out to assist with students who are learning statistical inference methods in historical biogeography and phylogenetics. This work has led to at least 7 articles published in good peer-reviewed journals. Many of my co-authored publications (often second author, reflecting extensive assistance in the paper) result from this. (See e.g. the seven articles marked with "s" in my short CV.)


Additional professional activities

Broadcast Media Appearances (selected)

Matzke, Nicholas J. (2016). The Evolution of Antievolutionism. Podcast, "Maynard's Spooky Action" segment of The Skeptic Zone, April 10, 2016. Starts at 0:05:15. http://skepticzone.libsyn.com/the-skeptic-zone-390-10april2016

Matzke, Nicholas (2015). Interview on 666 ABC Canberra, Breakfast with Philip Clark. Australian Broadcasting Corporation. December 21, 2015, 7:30 a.m. http://ab.co/666live http://www.abc.net.au/canberra/ https://twitter.com/NickJMatzke/status/678669055822135296

Mirsky, Steve (2015). Evolution Still on Trial, 10 Years After Dover. Science Talk, Scientific American podcasts. December 20, 2015 http://www.scientificamerican.com/podcast/episode/evolution-still-on-trial-10-years-after-dover/

NTN24 (2012). Interview of Nick Matzke about Barnosky et al. (2012) "tipping point" article. June 7, 2012. NTN24 "airs in all Latin America, the Caribbean and the United States, through different cable systems; in the USA is channel 418 of Directv. We also air in Europe through streaming in the following site: http://www.ntn24.com/senal.html."

Redell, Bob (2011). Interview of Nick Matzke, NBC Bay Area Morning Show. NBC Bay Area. Bay Area, 2 hours. Filmed in front of the T. rex at the UCMP. March 4, 2011. (Scholar)

Welch, Kris (2011). Interview of Nick Matzke. Saturday Morning Talkies, KPFA radio. Berkeley, CA, 1 hour. March 5, 2011. (Link | Local mp3)

PBS - Nova. "Judgment Day: Intelligent Design on Trial" November 13, 2007. (The 2-hour special is free online at the PBS website; an additional chunk of the interview with me is (or at least was) online here. It also received a lot of good press.)

The Sci Phi Show with Jason Rennie. "Can the Flagellum Evolve?" May 4, 2007. Part of "Darwin Or Design?" audiobook (show description | mp3 download | PT)

The Innoculated Mind with Karl J. Mogel. "Discussion of intelligent design and Kitzmiller." March 1, 2007. (show description | mp3 download | PT)

Talk of the Nation: Science Friday with Ira Flato. "Evolution Roundup: Edward Humes and 'Monkey Girl' / 'Flock of Dodos' Movie / Teaching Evolution." National Public Radio, February 23, 2007. (show description | mp3 download | PT)

Michael Medved Show. "Creation as Science." Salem Radio Network, November 24, 2006. Debate with Hugh Ross over Ross's book Creation as Science. http://www.pandasthumb.org/pt-archives/000690.html

The Sci Phi Show. "Outcast #18 - Interview with Nick Matzke." This is a web-podcast show about science-fiction and philosophy. October 27, 2006. http://thesciphishow.com/?p=75 (mp3 - 16MB | PT post)

NMSR's Science Watch with Dave Thompson and Kim Johnson. "Inside the Dover ID Trial." KABQ 1350 AM Progressive Talk. Albuquerque, NM, June 10, 2006. http://www.nmsr.org/goradio.htm

CNN, Lou Dobbs Tonight. "Intelligent design." January 12, 2006. http://transcripts.cnn.com/TRANSCRIPTS/0601/12/ldt.01.html

Philosophy Talk. "Intelligent design." KALW (San Francisco NPR affiliate), January 17, 2006. http://www.philosophytalk.org/IntelligentDesign.htm

Forum with Michael Krasny. "Intelligent Design Decision." KQED (San Francisco NPR affiliate), December 22, 2005. http://www.kqed.org/epArchive/R512220900

Channel 2 Oakland . Live studio interview with a legal commentator about Kitzmiller v. Dover decision. Mornings on Two. Channel 2 (KTVU) Oakland. December 21, 2005.

City Visions Radio with Yumi Wilson. "Intelligent Design -- the next science curriculum?" KALW 91.7 San Francisco. December 5, 2005. (Show description | Streaming audio)

Talk of the Nation: Science Friday with Ira Flato. "Teaching Evolution Update." National Public Radio, November 11, 2005. http://www.sciencefriday.com/pages/2005/Nov/hour2_111105.html

Interview with John Grayson. KMOX radio. November 10, 2005.

Numerous media interviews (print, radio, TV) during the Kitzmiller vs. Dover trial in Harrisburg, PA. September 26, 2005 - November 4, 2005.

BBC Scotland morning show. Rebuttal to Stephen C. Meyer of the Discovery Institute. BBC Scotland. September 26, 2005.

Talk of the Nation: Science Friday with Ira Flato. "Dover Evolution Court Case." National Public Radio, September 16, 2004. http://www.sciencefriday.com/pages/2005/Sep/hour2_091605.html

To The Point with Warren Olney. "Intelligent Design vs. Evolution." National Public Radio, August 23, 2005. http://www.kcrw.org/cgi-bin/db/kcrw.pl?show_code=tp&air_date=8/23/05&tmplt_type=show

Hot Talk with Scott Hennen. WDAY Minnesota. August 10, 2005. http://www.wday.com/hottalk/

AgriTalk. Interview with Nick Matzke and John Calvert. August 10, 2005. http://www.agritalk.com/mail.php3

Weekend Live with Tony Snow. (Opposing ID advocate Stephen C. Meyer.) Fox News, August 6, 2005. http://www.pandasthumb.org/archives/2006/04/my_encounter_wi.html

Diane Rehm Show. "Evolution and Intelligent Design." WAMU/National Public Radio, August 4, 2005. http://www.wamu.org/programs/dr/05/08/04.php

Dayside. (Opposing ID advocate Jay Wesley Richards). Fox News, July 6, 2005.

Interview with KTHO, South Lake Tahoe. February 16, 2005.

Interview on The Infidel Guy. "Nick Matzke: Creationist Challenges to Evolution." February 11, 2005. (Tape 259 in show archives | direct link (subscription required))

BBC Northern Ireland morning show. (Responding to comments by Richard Thompson of the Thomas More Law Center.) January 17, 2005.

Michael Medved Show. "Intelligent Design." Salem Radio Network, December 22, 2004. Description online: "Mopping Up on the Medved Show." http://www.pandasthumb.org/pt-archives/000690.html

Mike Romigh Show. Interview about evolution, intelligent design, and Dover. KDKA Pittsburgh. November 29, 2004. http://kdkaradio.com/mikeromigh.shtml

Talk of the Nation: Science Friday with Ira Flato. "Teaching Evolution." National Public Radio, November 19, 2004. http://www.sciencefriday.com/pages/2004/Nov/hour1_111904.html

Danny Fontana Show. Interview with Danny Fontana and local creationist David Chadwick. WBT News Talk, 1110 AM/99.3 FM, Charlotte, North Carolina. November 18, 2004.

Radio Inside Scoop with Mark Levine. "How Kansas Failed to Evolve." August 9, 2004. http://radioinsidescoop.com/mt-posts-archive/000162.html


Press (selected)

University of Tennessee Press Release (2014). "Research Confirms Controversial Darwin Theory of Jump Dispersal." (NIMBioS version) October 1, 2014.

Alford, Justine (2014). "Researcher Finds Support For One Of Darwin's Controversial Theories." IFLScience. October 2, 2014.

Hannah Osborne (2014). "Darwin's Theories on Invasive Species and Jump Dispersal Confirmed by Experts." International Business Times. October 2, 2014.

Keim, B. (2012). "Sperm Trajectories, Evolving Humans and a Tomato Tapestry: The Best Scientific Figures of 2012." Wired. Retrieved December 5, 2012, from: http://www.wired.com/wiredscience/2012/12/science-figures-2012/?utm_source=twitter&utm_medium=socialmedia&utm_campaign=wiredscienceclickthru&pid=5582&viewall=true.

A quote:

Evolution Reconstructed

Though the fossil record preserves physical shapes, ancient colors and patterns are usually lost to deep time. Here researchers have combined what's known about pigmentation and physiological development in existing Conus sea snails to infer what their ancestors probably looked like, computationally resurrecting lost appearances.

Citation: "Evolution of patterns on Conus shells." By Zhenqiang Gong, Nicholas J. Matzke, Bard Ermentrout, Dawn Song, Jann E. Vendetti, Montgomery Slatkin, and George Oster. Proceedings of the National Academy of Sciences, 4 January 2012.

Image: Gong et al./PNAS (Larger image)



Matzke, Nicholas J. (2012). "Predicting a state shift in the biosphere, and communicating it." The Panda's Thumb (blog). This is my discussion of the press surrounding: Barnosky et al. (2012), "Approaching a state shift in Earth's biosphere." Nature, 486, 52-58. June 7, 2012. This was part of the cover story (timed to coincide with the United Nations Rio+20 Earth Summit in Rio de Janeiro) and got worldwide press, far more than can be listed. The best summary was the Berkeley press release, listed below.

Sanders, Robert (2012). "Scientists uncover evidence of impending tipping point for Earth." UC Berkeley News Center, June 6, 2012. (Link)

ScienceDaily. (2012). "Breakthrough Model Reveals Evolution of Ancient Nervous Systems Through Seashell Colors." Retrieved January 12, 2012, from http://www.sciencedaily.com/releases/2012/01/120112142301.htm.

Huber, B. R. (2012). "Pitt Researchers' Breakthrough Model Reveals Evolution of Ancient Nervous Systems Through Analysis of Seashell Color Patterns: Mathematics, engineering used to collect space-time information by studying 19 different species of the predatory sea snail Conus." Retrieved January 12, 2012, from http://www.news.pitt.edu/CONUSSHELLS.

          The "mass extinctions" paper in Nature (Barnosky, Anthony D.; Matzke, Nicholas; Tomiya, Susumu; Wogan, Guinevere O. U.; Swartz, Brian; Quental, Tiago B.; Marshall, Charles; McGuire, Jenny L.; Lindsey, Emily L.; Maguire, Kaitlin C.; Mersey, Ben; Ferrer, Elizabeth A. (2011). "Has the Earth's sixth mass extinction already arrived?" Nature 471(7336), 51-57) got a huge amount of press. Here are some of the primary accounts: Matzke, Nicholas J. (2011). "Extinctions paper: Why grad school is cool, and what creationists don't get about evolutionary biology." The Panda's Thumb (blog). March 2, 2011.http://pandasthumb.org/archives/2011/03/extinctions-pap.html

Sanders, Robert. (2011). "Has the Earth's sixth mass extinction already arrived?" Retrieved March 2, 2011, from http://newscenter.berkeley.edu/2011/03/02/has-the-sixth-mass-extinction-already-arrived/.

NSF. (2011). "Earth's Sixth Mass Extinction: Is It Almost Here?" Retrieved March 2, 2011, 2011, from http://www.nsf.gov/news/news_summ.jsp?cntn_id=118804&WT.mc_id=USNSF_51&WT.mc_ev=click (NSF front page with banner linking to the story).

Pappas, Stephanie (2011). 6th mass extinction looms but preventable, study says. LiveScience, MSNBC. (Scholar | Link)

Drake, Nadia (2011). Scientists try to determine whether life on Earth is quickly heading toward extinction. San Jose Mercury News. San Jose, CA. March 3, 2011. (Scholar | Link)

Gibbons, Ann (2011). "Are We in the Middle of a Sixth Mass Extinction?" ScienceNOW. (Scholar | Link)

Redell, Bob (2011). Interview of Nick Matzke, NBC Bay Area Morning Show. NBC Bay Area. Bay Area, 2 hours. Filmed in front of the T. rex at the UCMP. March 4, 2011. (Scholar)

Welch, Kris (2011). Interview of Nick Matzke. Saturday Morning Talkies, KPFA radio. Berkeley, CA, 1 hour. March 5, 2011. (Link | Local mp3)

Karlamangla, Soumya (2011). Mass Extinction May Occur in 300 Years, Scientists Say. The Daily Californian. Berkeley, CA, 1-2. (Scholar | Link)

          My work on the Kitzmiller v. Dover trial and the flagellum has been described in various journalist accounts.

Travis, J. (2009). "Nicholas Matzke: From Chat Rooms to the Courthouse, Taking on Intelligent Design." Interview posted on the Science magazine blog "Origins: a history of beginnings." May 19, 2009. (Link | Newer Link | PT)

Travis, J. (2009). "On the Origin of the Immune System." Science. 324(5927), 580-582. (DOI | Journal | PT #1 | PT #2)

Lebo, Lauri (2008). The Devil in Dover: An Insider's Story of Dogma v. Darwin in Small-Town America. New York: The New Press, pp. 1-238. (Amazon)

Zimmer, Carl (2008). Microcosm: E. coli and the New Science of Life. New York: Pantheon Books, 1-256. (Book discusses the Kitzmiller case and the Matzke/Pallen article.) (Amazon)

Timmer, John (2008). "Misperceptions meet state of the art in evolution research." Arc Technica, February 26, 2008. (Link; this was a report on a special session I moderated at the 2008 AAAS meeting devoted to "The State of the Art in Major Transitions in Evolution.")

Jones, Dan (2008). "Engines of evolution: The elegant complexity of the bacterial flagellum inspires awe, but its humble origins are becoming apparent." New Scientist, 197(2643), 40-43. February 16, 2008. (DOI | Journal | Local PDF | PT)

Whiting, Sam (2007). "Nick Matzke, in the evolutionist's corner, faces each new challenge the creationists bring." Interview for the San Francisco Chronicle Magazine, p. 4. Sunday, January 7, 2007. (HTML | photo | NCSE | PT | MHT archive | PDF color scan)

Slack, Gordy (2007). The Battle Over the Meaning of Everything: Evolution, Intelligent Design, and School Board in Dover, PA. New York: Jossey-Bass, 1-240. (Gordy Slack is a science journalist in Oakland who covered the trial for Salon.com.) (Amazon)

Chapman, Matthew (2007). 40 Days and 40 Nights: Darwin, Intelligent Design, God, OxyContin, and Other Oddities on Trial in Pennsylvania. New York: Collins, 1-288. (Matthew Chapman, Darwin's great-great grandson, was a reporter at the Dover trial.) (Amazon)

Humes, Edward (2007). Monkey Girl: Evolution, Education, Religion, and the Battle for America's Soul. New York: HarperCollins, 1-380 (Amazon)

Zimmer, Carl (2006). "A Fin Is A Limb Is A Wing." National Geographic, November 2006. The article discusses the Pallen & Matzke 2006 article. (HTML | Carl Zimmer's blogpost)

Wetterschneider, Molly (2006). "Nick Matzke: Legal Beagle." Seed: Science is Culture. 2(7), p. 62. November 2006. Part of "Revolutionary Minds" series in Seed magazine, 2(7), pp. 54-63. (PDF of proofs | PDF scan | NCSE | PT)

Dawkins, Richard (2006). The God Delusion. London: Houghton Mifflin. (Amazon | Local PDF of pages 131 and 133, which discuss the Kitzmiller case and the "irreducible complexity" argument. Page 133 recounts the immune system cross, relying on Bottaro et al. 2006 (note 64). I am not particularly fond of Dawkins' theological arguments, but it is good that he is paying close attention to the science issues.)

Branch, Glenn (2006). "Pallen and Matzke on the Bacterial Flagellum." Reports of the National Center for Science Education, 26(3), pp. 36-37. (Local pdf)

Chapman, Matthew (2006). "God or Gorilla: A Darwin descendant at the Dover monkey trial." Harper's Magazine, 312(1869), pp. 54-63. February 2006. http://www.wesjones.com/gorilla.htm. (Local pdf - 5MB)

Mason, Betsy (2006). "Origins Debate Escalates: Intelligent design has local roots." Contra Costa Times, 94(243), pp. A1, A8, A9. January 29, 2006. http://www.contracostatimes.com/mld/cctimes/living/science/13741453.htm. (Local pdf - 7 MB) | MHT | HTML | FindArticles)

Humburg, Burt & Brayton, Ed (2006). "Kitzmiller et al versus Dover Area School District: a report by Burt Humburg & Ed Brayton." Skeptic 12(2), 44-50. Spring 2006. Published online on December 20th, 2005. http://www.skeptic.com/eskeptic/05-12-20.html. (Local pdf)

Talbot, Margaret (2005). "Darwin in the Dock: Intelligent design has its day in court." The New Yorker, 81(38), pp. 66-77. December 5, 2005. http://www.wesjones.com/darwin.htm. (Local pdf -- I am not actually mentioned here, but this is an excellent summary of the trial.)

Lebo, Lauri (2005). "What's made Dover unique? Nation, world seek reasons this community became flashpoint for intelligent-design debate." York Daily Record/Sunday News. November 6, 2005. http://www.ydr.com/doverbiology/ci_3219242. (Local pdf | MHT | HTML)

Biever, Celeste (2005). "Book thrown at proponents of Intelligent Design." New Scientist. October 6, 2005. http://www.newscientist.com/article.ns?id=dn8061


Research assistance

          These are some publications in which I played a small part, e.g. as part of a field research crew or photo interpreter.

Azuma, Dave L., Hiserote, Bruce A., Dunham, Paul A. (2005). "The western juniper resource of eastern Oregon, 1999." Resource Bulletin PNW-RB-249. Portland, OR: U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station. 18 pages.
Online: http://www.fs.fed.us/pnw/publications/rbs.shtml
PDF: http://www.fs.fed.us/pnw/pubs/pnw_rb249.pdf

Campbell, S., Dunham, P., Azuma, D. (2004). "Timber resource statistics for Oregon." Resource Bulletin PNW-RB-242. Portland, OR: U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station. 67 pages.
Online: http://www.fs.fed.us/pnw/publications/rbs.shtml
PDF: http://www.fs.fed.us/pnw/pubs/pnw_rb242.pdf

North, M., Che, J., Oakley, B., Song, B., Rudnicki, M., Gray, A., Innes, J. (2004). "Forest Stand Structure and Pattern of Old-Growth Western Hemlock/Douglas-Fir and Mixed-Conifer Forests." Forest Science, 50(3), pp. 299-311(13), June 2004. Online: http://www.ingentaconnect.com/content/saf/fs/2004/00000050/00000003/art00004

Olszyk, D.M., Johnson, M.G., Tingey, D. T., Rygiewicz, P.T., Wise, C., VanEss, E., Benson, A., Storm, M.J., King, R. (2003). "Whole-seedling biomass allocation, leaf area, and tissue chemistry for Douglas-fir exposed to elevated CO2 and temperature for 4 years." Canadian Journal of Forest Research, 33, pp. 269"278. Online: http://dx.doi.org/10.1139/X02-186

Monleon, Vicente J., Gitelman, Alix L., Gray, Andrew N. (2002). "Multi-scale Relationships Between Coarse Woody Debris and Presence/Absence of Western Hemlock in the Oregon Coast Range." Chapter 17 in: Case Studies in Bayesian Statistics: Volume VI, edited by Gatsonis, C., Kass, R.E., Carriquiry, A., Gelman, A., Higdon, D.L., Pauler, D.K., Verdinelli, I. Series: Lecture Notes in Statistics, Vol. 167. New York: Springer-Verlag, pp. 311-318. Online: http://search.barnesandnoble.com/booksearch/isbnInquiry.asp?isbn=0387954724

Wimberly, Mike, and Spies, Thomas A. (2001). "Influences of Environment and Disturbance on Forest Patterns in Coastal Oregon Watersheds." Ecology, 82(5), pp. 1443-1459, May, 2001
Online at: http://www.esajournals.org/esaonline/?request=get-abstract&issn=0012-9658&volume=082&issue=05&page=1443
(Listed as "Nick Maetske" in the acknowledgements. Close!)

Azuma, D.L., Birch, K.R., DelZotto, P., Herstrom, A.A., Lettman, G.J. (1999). Land use change on non-federal land in western Oregon, 1973-1994. Salem, OR: Oregon Department of Forestry, pp. 1-55. December 1999. Updated version online: http://www.oregonsolutions.net/documents/ForestFarmsPeople.pdf
Press Release at: http://www.odf.state.or.us/DIVISIONS/resource_policy/public_affairs/News_Releases/NR02263.htm

Blogging and news pieces (selected)

Blogs have become an important part of the public discussion of science and science education. Often, important developments (such as the discovery of the drafts of Pandas) are announced or discussed here before other venues.

I do some of the NCSE news updates at: http://www.ncseweb.org/pressroom.asp?branch=current

NCSE website/law blog on Kitzmiller v. Dover case: http://www2.ncseweb.org/wp/. See especially:
      Missing Link discovered! -- http://www2.ncseweb.org/wp/?p=80

Numerous posts at The Panda's Thumb, the premier pro-evolution, anti-creationism blog on the internet: http://www.pandasthumb.org. Nature listed PT as one of the top five science blogs on the internet (http://www.nature.com/news/2006/060703/pf/442009a_pf.html). Some representative posts:




Software and Programming

Workshops:

Matzke, Nicholas J. (2017). September 26, 2017: Workshop on BioGeoBEARS and other biogeographical/phylogenetic methods. Bangalore, India. "Biogeography India", a meeting of the International Biogeography Society, September, 26-28, 2017. Sponsored by IBS. https://www.biogeography.in/

Matzke, Nicholas J. (2017). January 16-20, 2017: Workshop on BioGeoBEARS and other biogeographical/phylogenetic methods. Santiago, Chile. Sponsored by Cristian E. Hernandez.

Warren, Dan; Matzke, Nicholas J. (2016). "Model-Based Statistical Inference in Ecological and Evolutionary Biogeography" Hosted by Transmitting Science. Venue: Els Hostalets de Pierola, Barcelona, Spain. Monday, November 28-Friday, December 2, 2016, Times: 9:30 am-1:30 pm, 3-7 pm daily. http://www.transmittingscience.org/courses/biog/statistical-biogeography/

Matzke, Nicholas J. (2016). Guest speaker: "The evolution of antievolution policies." At: Centre for Biodiversity Analysis annual conference: The interface of evolutionary biology and policy impact. The Common Room, University House, 1 Balmain Crescent, Acton (ANU). 6:30-7:30, September 6, 2016. http://biology.anu.edu.au/news-events/cba-annual-conference-interface-evolutionary-biology-and-policy-impact

Matzke, Nicholas J. (2016). "Free your mind: Comparing and statistical testing of multiple models in historical biogeography, using the R package 'BioGeoBEARS'." Monday, June 27, 2016. 1-5 pm. Oregon State University. Room 164 Nash Hall. Sponsored by Brian Sidlauskus.

Matzke, Nicholas J. (2015). "Biogeographical analysis with the R package BioGeoBEARS." Wednesday, October 21, 2015, 10 am-3 pm. Texas A&M University. MSC 2507 (Memorial Student Center). Sponsored by Michelle Lawing & Open Source for Open Science (OSOS).

Matzke, Nicholas J. (2015). "Advanced probabilistic historical biogeography, with the R package BioGeoBEARS." Tuesday, August 25, 2015, The Australian National University, Canberra, Australia. 1-5 pm, Gould Meetings Room, Room 246, Building 116 (Gould Wing).

Matzke, Nicholas J. (2015). "Introduction to statistical model choice in historical biogeography, with the R package BioGeoBEARS." Tuesday, August 24, 2015, The Australian National University, Canberra, Australia. 1-5 pm, Gould Meetings Room, Room 246, Building 116 (Gould Wing).

Matzke, Nicholas J. (2015). "Introduction to R, starting from scratch." 2015 Summer Research Experiences (SRE) at NIMBioS for Undergraduates and Teachers. Given Monday, June 9, 1-3 pm, Claxton 206, National Institute of Mathematical and Biological Science (NIMBioS). http://www.nimbios.org/sre/sre2015

01/22/15 - Matzke, Nicholas J. (2015). BEASTmasteR workshop: "BEASTmasteR: An R package for designing phylogenetic dating analyses in Beast2, including dated fossils as tips." Invited, expenses & honorarium covered. Ludwig Maximilian University of Munich, Germany. Date: Thursday, January 22, 2015, 10am-4pm. http://phylo.wikidot.com/beastmaster-workshops#munich2015

01/19/15 - Matzke, Nicholas J. (2015). BioGeoBEARS workshop: "Free your mind: Comparing and statistical testing of multiple models in historical biogeography, using the R package 'BioGeoBEARS'." Invited, expenses & honorarium covered. Department of Geosciences, University of Helsinki, Finland. Date: Monday, January 19, 2015, 10am-4pm. http://phylo.wikidot.com/biogeobears-workshops#helsinki2015

01/14/15 - Matzke, Nicholas J. (2015). BEASTmasteR workshop: "BEASTmasteR: An R package for designing phylogenetic dating analyses in Beast2, including dated fossils as tips." Invited, expenses & honorarium covered. Department of Geosciences, University of Helsinki, Finland. Date: Wednesday, January 14, 2015, 10am-4pm. http://phylo.wikidot.com/beastmaster-workshops#helsinki2015

01/08/15 - Matzke, Nicholas J. (2015). BioGeoBEARS workshop: "Free your mind: Model comparison and model testing in historical biogeography with the R package 'BioGeoBEARS'." Invited, $1000 travel expenses paid. International Biogeography Society Biannual Meeting, Bayreuth, Germany. January 8, 2015, 1pm-4pm. http://www.bayceer.uni-bayreuth.de/ibs2015/en/top/gru/html.php?id_obj=11101 http://phylo.wikidot.com/biogeobears-workshops

11/04/2014 - Matzke, Nicholas J.; Wright, April (2014). "Tip-dating: Estimating dated phylogenies using fossils as terminal taxa." Workshop to be held at the 74th Annual Meeting of the Society of Vertebrate Paleontology at the 74th Annual Meeting of the Society of Vertebrate Paleontology (Estrel Convention Center, Berlin, Germany). Workshop held at the Leibnitz Institute, adjacent to the Berlin natural history museum (Museum für Naturkunde -- Leibniz-Institut für Evolutions- und Biodiversitätsforschung an der Humboldt-Universität zu Berlin). November 4, 2014, 10am-4pm.

Matzke, Nicholas J. (2014). "Introduction to R, starting from scratch." 2014 Summer Research Experiences (SRE) at NIMBioS for Undergraduates and Teachers. Given Monday, June 16, 9-11 am, Claxton 206, National Institute of Mathematical and Biological Science (NIMBioS). http://nimbios.org/sre/sre2014 | http://phylo.wikidot.com/2014-summer-research-experiences-sre-at-nimbios-for-undergra

02/28/14 - Matzke, Nicholas J. (2014). BioGeoBEARS workshop. Invited, travel expenses paid. Bioinformatics Program at the University of Texas, El Paso. February 28 2014.

01/07/14 - Matzke, Nicholas J. (2014). BioGeoBEARS workshop. Invited, travel expenses paid. International Biogeography Society Early Career Meeting. Australian National University, Canberra, Australia. January 7, 2014.

11/12/2013 - Matzke, Nicholas J. (2013). BioGeoBEARS workshop. Invited, travel expenses paid. Jetz Lab, Department of Ecology and Evolution, Yale University. 5-7 pm, Osborn Memorial Laboratories (OML) room 40, November 12, 2013.

10/10/13 - Matzke, Nicholas J. (2013). BioGeoBEARS workshop. Invited, travel expenses paid. 2013 CEBA Thematic School, Cayenne, French Guiana. CEBA is the French CEntre for the study of Biodiversity in Amazonia. October 10, 2013.

08/26/13 - Matzke, Nicholas J. (2013). BioGeoBEARS workshop. Department of Integrative Biology, University of California, Berkeley. August 26, 2013.


Software:

Gupta, Rishabh; Matzke, Nicholas J. (2016). mod09nrt: Extraction of Bands from MODIS Surface Reflectance Product MOD09 NRT. R package, version 0.14, published July 24, 2016 at: https://cran.r-project.org/web/packages/mod09nrt/index.html

Matzke, Nicholas J. (2013). BioGeoBEARS: BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts. R package, version 0.2.1, published July 27, 2013 at: http://CRAN.R-project.org/package=BioGeoBEARS

Matzke, Nicholas J., and Sidje, Roger B. (2013). rexpokit: R wrappers for EXPOKIT. R package, version 0.24.2, published July 15, 2013 at: http://CRAN.R-project.org/package=rexpokit

Matzke, Nicholas J. (2013). cladoRcpp: C++ implementations of phylogenetic calculations. R package, version 0.14.2, published July 15, 2013 at: http://CRAN.R-project.org/package=cladoRcpp

Matzke, Nicholas J. (2013). modiscloud: R tools for processing Level 2 Cloud Mask products from MODIS. R package, version 0.14, published February 9, 2013 at: http://CRAN.R-project.org/package=modiscloud

Google Summer of Code, project title: "Biogeographical Phylogenetics for BioPython." Summary: Create a BioPython module, "Biogeography," that will enable users to (1) automatically access and parse species locality records from online biodiversity databases (e.g. GBIF); (2) link these to user-specified phylogenies (as in the Phylocomm/Phylomatic package); (3) calculate basic alpha- and beta- diversity summary statistics, and parallel phylodiversity statistics for the biogeographical regions of interest; (4) produce input files for input into the various inference algorithms available for inferring historical biogeography (primarily lagrange; older algorithms if there is time: parsimony, DIVA, etc.), and run these algorithms directly where feasible; (5) convert output from these programs into GIS files suitable for display in ArcGIS/GeoPhyloBuilder (e.g. shapefiles) and Google Earth (KML files).


Programming Skills/Training:

Ph.D. with an official Computational Biology Designated Emphasis at U.C. Berkeley

Python, including Enthought Python Distribution, IPython, BioPython, BioSQL, and various other packages. Took 10-day "Introductory Programming for Bioinformatics" course in Summer 2008. Have written a number of scripts to search, download, and process sequence data.

R, including packages APE, ACE, Geiger, laser, vegan, picante. Also have authored my own packages and simulations, and discovered bugs in released packages (lttplot in ape; phylosor in picante) and acknowledged (picante: http://picante.r-forge.r-project.org/ ).

Software/techniques used:
BEAST, MrBayes, PAUP*, Phyllip, other standard packages
Community phylogenetics software: Phylocom, Phylomatic
Online databases & tools (BLAST, PSI-BLAST, NCBI tools, etc.)
ClustalW, T-coffee, PROMALS3D
JALview, STRAP (alignment viewing/editing)
Mesquite, MacClade (sequence editing, display)
TreeView, Dendroscope
Phylogeny programs: PAUP, RAxML, MrBayes
Python, BioPython, bioSQL, some Perl

GIS: ArcInfo/ArcView (wrote labs, data analysis, cartography)

ENVI/IDL, ERDAS (remote sensing)

MATLAB, S-PLUS (statistical analysis)

Scripting: DOS, UNIX c-shell, ArcView, ENVI, MATLAB

Windows: Office (large, graphics-intensive word documents; Excel data analysis; Access database management; PowerPoint presentations)

Webpages, wikis, blogs, etc.



Professional memberships

Society of Systematic Biologists
Society for the Study of Evolution
International Biogeographical Society
American Society of Naturalists
American Association of Geographers
International Carnivorous Plant Society
National Center for Science Education



Peer-reviewing

Peer-reviewer for: University of Chicago Press (paid peer-review of unpublished book)
Diversity and Distributions (1)
Cladistics (2)
Proceedings of the Royal Society, Series B: Biological Sciences (2)
Systematic Biology (4)
Garamszegi, L. Z. (ed.) (2014). Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology.
Evolution (7)
Ecography (2)
PLoS One
Methods in Ecology and Evolution (3)
American Naturalist (2)
Journal of Biogeography (4)
Journal of Theoretical Biology
Naturwissenschaften
Evolution: Education and Outreach (3)
Trends in Microbiology
David A. Baum and Stacey D. Smith (2012). Tree thinking: An Introduction to Phylogenetic Biology.
Rosenhouse, Jason (2012). Among the Creationists.
New Scientist (flagellum evolution article, by Yeager)
Weezie Mead, NCSE/UCMP evolution curriculum
Eugenie Scott, revised edition of Evolution vs. Creationism
Mark Pallen, Rough Guide to Evolution, chapter on history of evolution/antievolution
Lawrence Hall of Science evolution/biodiversity unit 2 - SEPUP - June 2009
Lawrence Hall of Science evolution/biodiversity unit 2 - SEPUP - December 2008
Lawrence Hall of Science evolution/biodiversity unit - SEPUP - January 2008


Other Activities

April 22, 2017 - Assistant organizer of March for Science - Canberra, Australia; Participated as volunteer for "Ask a Scientist" event, and post-march cleanup.

November 19, 2016 - Speaker for Science in the Pub: Biology in the Pub. "Evolutionary biologist Nick Matzke (Biology@ANU) has analysed anti-evolution policies in the US. Guess what, they’ve evolved!" Saturday November 19, 2016. 7-9 pm, Smiths Alternative bookshop, Civic, Canberra, Australia. https://www.facebook.com/events/1749766278618789

5/26/2015 - Co-organized "21st-century college teaching strategies in biology and math." Speakers Elizabeth Schussler and Lou Gross. NIMBioS Career Development Session. Hesler 426, 3:30 pm, May 26, 2015.

Host, Darwin Day Speaker Alan de Queiroz, February 2015, University of Tennessee, Knoxville

Host, NIMBioS Distinguished Speaker Michael Lynch, February 2015, University of Tennessee, Knoxville

Guide, Darwin Day 2015 trip to Scopes Monkey Trial museum, Dayton, TN

Host, NIMBioS Distinguished Speaker Eugene Koonin, March 2014, University of Tennessee, Knoxville

Guide, Darwin Day 2014 trip to Scopes Monkey Trial museum, Dayton, TN

Organizer of "chalk talks" series for U.C. Berkeley Dept. Integrative Biology, 2009-2010

Organizer of "chalk talks" series for U.C. Berkeley Dept. Integrative Biology, 2008-2009

Organizer/leader of new student camping trip to U.C. Angelo Reserve, August 2008



Awards, funding, grants

Major grant applications I have contributed to

(pre-proposal submitted 2017) Understanding American Amphitropic Distributions (AAD): combining morphometric and genomic data for the first Bayesian tip-dating of an angiosperm group, Amsinckiinae (Boraginaceae), and application of biogeographical statistical model comparison. Pre-proposal for NSF-DEB. PI Matt Guilliams. Co-PIs Matzke, N.J.; Hasenstab-Lehman, K.

(funded 2017) Genomes, phenotypes and fossils: integrative models of species evolution (2016). Full proposal for Marsden Fund (New Zealand). 16-UOA-277. Principal Investigators: Drummond, Alexei J.; Welch, David. Associate Investigators: Stadler, Tanja; Matzke, Nicholas J.; Vaughn, T.G.

Does competition block range expansion or access to climate change refugia? (2016) Full proposal for Australian Research Council Discovery Projects (ARC DP). Chief Investigators: Moritz, Craig; Matzke, Nicholas J.; Kearney, Michael; Ranjard, Louis.

Diversification of the New Guinea weevils Eupholini: host plants and epizoics (2016). Preliminary proposal for National Science Foundation, DEB-Phylogenetic Systematics. Principal Investigator: Roderick, George K. Senior personnel: Van Dam, Matthew H.; Matzke, Nicholas J.; Balke, Michael; Bowie, Rauri C.K.; Gillespie, Rosemary G.; Riedel, Alexander.

Funding received

03/2016: $1800 funding to travel to NIMBioS Dispersal Biology Working Group Meeting, March 17-19, 2016, University of Tennessee, Knoxville.

06/2015: $1000 travel award, to Evolution 2015 Annual Meeting, Sao Paulo, Brazil. For invited participation in a symposium on Frontiers in Parametric Biogeography, sponsored by they Society for Systematic Biology, in Guarujá, Brazil.

06/2015: Brought Adriane Lam, student of Alycia Stigall, to collaborate on a project including fossils in BioGeoBEARS to look at dispersal patterns in Paleozoic invertebrates. ~$300

05/2015: Brought Fabiola Soto, Universidad Nacional Autónoma de México, as NIMBioS visiting scholar, to finish collaboration with Kathryn Massana and Ed Schilling, $800

05/2015: $500 travel award, to Evolution 2015 Satellite Meeting in Ann Arbor, Michigan

03/2015: ~$1000 travel award (all travel paid), to the Paleobiology Database Hackathon, Santa Cruz, California

02/2015: Brought Alan de Queiroz, author of The Monkey's Voyage, for collaborative brainstorming on biogeography models, and to speak at UT Knoxville's Darwin Day 2015, ~$1000

02/2015: Brought Laura K. Saila, University of Helsinki, Finland, to collaborate on biogeographic analysis of fossil carnivores, $3000

November 2014: Awarded Australia's Discovery Early Career Award (national competition). AUS$369,536 over 3 years. To start July 2015.

09/2014: Brought Dan Warren, Macquerie University, as NIMBioS visiting scholar, 10 days, $3000

09/2014: Brought Fabiola Soto, Universidad Nacional Autónoma de México, as NIMBioS visiting scholar, $800

2013-2015: NIMBioS Postdoctoral Fellowship, $55,000/year

2014: $4000 travel covered to attend International Biogeography Society meeting in Canberra, Australia, and teach BioGeoBEARS workshop, January 2014

2013: All expenses paid to attend CEBA Annual Meeting and teach BioGeoBEARS workshop in French Guiana, October 2013

2013: Outstanding Graduate Student Instructor (GSI) Award, for outstanding teaching at U.C. Berkeley

2012-2013: U.C. Berkeley Tien Fellowship, $20,000/year

2011-2012: U.C. Berkeley Tien Fellowship, $20,000/year

Summer 2011-present: Consultant for NSF-funded Voyage to the Galapagos

June 2011. Travel Grant for Evolution 2011, Norman, Oklahoma. $500

January 2011. Travel Grant for International Biogeography Society Biannual Meeting, Heraklion, Crete. $366

2009-2011: Graduate Student Research, NSF Bivalves in Time and Space project

Fall 2010: Wang Fellowship, $15,000

Department of Integrative Biology Hansen Travel Award: $200

Sacker Colloquium: In the Light of Evolution IV: The Human Condition, December 10-12, 2009. Travel award, $275

Google Summer of Code 2009: $5000 grant

Department of Integrative Biology GRAC Travel Award: $200

Sackler Colloquium: In the Light of Evolution III: Two Centuries of Darwin, January 15-17, 2009, UC Irvine; Travel award, $275

International Biogeography Society biannual meeting - Mexico, January 9-12, 2009; poster given, travel award received, $1300

Sackler NAS biogeography meeting - December 12-13, 2008; poster given, received travel award, $250

Presentation: "Comparative Analysis of DMSP, MODIS, and GLOBSCAR burn area estimation capabilities for Madagascar." Presented at the AAG Remote Sensing Specialty Group Student Honors Paper Competition, American Association of Geographers Annual Meeting, March 2003. Runner-up, prize: ERDAS-Imagine 8.6 software. (Local pdf of paper submitted | award announcement)

NASA Earth System Science Fellowship. "Remote Sensing of Anthropogenic Biomass Burning and Forest Degradation in Madagascar." $21,000/year, 3 years. (pdf final report)

NASA Space Calgrant, 2000. "Comparison of DMSP and Landsat ETM burn estimation capabilities." $5,000.

Service award, Valparaiso University, 1998.


Paid consulting, reviewing, and tutoring

2012, phylogenetics/R tutor, $50/hour

2011, Provided critical review of draft book by Bart Rask, $200/hour

2011, Reviewed draft of Tree Thinking: An Introduction to Phylogenetic Biology by David Baum and Stacey Smith, $200

2010, Tutor, IB164: Human Genetics, $50/hour

2009-2010, Reviewer, Lawrence Hall of Science SEPUP Evolution Unit

2008, Consultant on evolutionary dynamics for researcher developing project on the evolution of bacteria flora for dentistry, $50/hour



References

Main letter writers

John Huelsenbeck (Ph.D. advisor)
Department of Integrative Biology
University of California, Berkeley, CA 94720-3140
Phone (510) 502-5887 // Dept. fax (510) 643-6264
Email: johnh@berkeley.edu
https://ib.berkeley.edu/people/faculty/huelsenbeckj

Brian O'Meara (NIMBioS postdoc advisor)
Department of Ecology and Evolutionary Biology
University of Tennessee, Knoxville, TN 37996-3410
Phone (865) 974-2804 // Dept. fax (865) 974-3067
Email: bomeara@utk.edu
http://www.brianomeara.info/

Craig Moritz (DECRA supervisor)
Professor, Director, Centre for Biodiversity Analysis
Gould Building
Division of Ecology, Evolution, and Genetics
Research School of Biology
The Australian National University
Phone +61 2 6125 5651 (Office)
Email: gekkojessie@gmail.com
http://cba.anu.edu.au/about-us/people/craig-moritz

Kevin Padian (Past-president of NCSE Board of Directors, expert witness in Kitzmiller)
Professor and Curator
Department of Integrative Biology and Museum of Paleontology
University of California, Berkeley, CA 94720-3140
Phone (510) 642-7434 // Fax (510) 642-1822
Email: kpadian@berkeley.edu
http://www.ucmp.berkeley.edu/people/padian/webintro.html

Other references

Brent Mishler (Professor for Phylogenetics, which I took and then TAed)
Professor, Department of Integrative Biology
Director of the University & Jepson Herbaria
4156 Valley Life Sciences Building
University of California, Berkeley, CA 94720-3140
Phone (510) 642-6810 // Fax (510) 642-1822
Email: bmishler@berkeley.edu
http://ucjeps.berkeley.edu/people/mishler.html

Anthony Barnosky (Ph.D. Committee)
Professor, Department of Integrative Biology and Museum of Paleontology
5002/5008 Valley Life Sciences Building
University of California, Berkeley, CA 94720-3140
Phone (510) 643-6275 // Fax (510) 642-1822
Email: barnosky@berkeley.edu
http://ib.berkeley.edu/labs/barnosky/

Eugenie C. Scott (Former Executive Director, National Center for Science Education)
420 40th Street, Ste. 2
Oakland, CA 94609-2509
Phone: (510) 601-7203 x 301
Fax: (510) 601-7204
Email: eugeniescott1@gmail.com
http://ncse.com/

Eric Rothschild (Head attorney, Kitzmiller v. Dover)
Pepper Hamilton LLP
3000 Two Logan Square
Philadelphia, PA 19103
Phone: (215) 981-4813
Fax: (215) 981-4750
Email: rothschilde@pepperlaw.com