Nicholas J Matzke
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Welcome to the PhyloWiki page on Nicholas J. Matzke.

My research is focused on integrating ecological and historical biogeography with statistical phylogenetics. Biogeography is the study of where species live, and why. Traditionally, the "why" has been divided into "Ecological Biogeography" and "Historical Biogeography." Ecological biogeography has focused on environmental and ecological controls on distribution, such as temperature and precipitation. "Historical" biogeography (evolutionary history, not human history) has focused on geographical distributions over phylogenies on geological timescales, primarily dealing with rare dispersal and vicariance events. I believe that it is high time that these two traditions were re-integrated, not just in verbal models and interpretation, but with formal probabilistic models, using the computational tools of statistical phylogenetics. My work aims to build these tools, and using them to answer Big Questions in evolution and biogeography.

Major projects at the moment include:

  1. New models for historical biogeography that integrate geographical distances, environmental distances, and the co-evolution of geographic distributions with traits that influence dispersal. This work is done in the R package BioGeoBEARS, which is continually being upgraded at: http://phylo.wikidot.com/biogeobears
  2. New methods for historical biogeography: Biogeographical Stochastic Mapping, again in BioGeoBEARS
  3. Applications of these methods to: global angiosperm phylogeny (NIMBioS Dispersal Biology Working Group); Canidae (living and fossil dog relatives); and numerous other collaborations
  4. Hierarchical Bayesian models for joint inference of niche-evolution and present-day Ecological Niche Models.
  5. Phylogenetic dating of Northern Australian Gehyra lizards (with the lab of Craig Moritz at ANU)

This PhyloWiki page serves as a flexible introduction to information about me and my software, including:

  1. The historical biogeography R package BioGeoBEARS, and its accessory packages rexpokit and cladoRcpp.
  2. BEASTmasteR, an R package in development for setting up custom analyses in the Bayesian phylogenetics program BEAST. BEASTmasteR sets up "tip-dating" analyses where the tips of the tree can include fossils with dates. The position of fossils on the tree is jointly inferred using morphological characters and fossil dates, and the dating of nodes on the tree occurs simultaneously.
  3. BioGeoBEARS workshops and BEASTmasteR workshops
  4. Another R package I have done is modiscloud, for processing satellite data from the MODIS cloud-cover product. (Also, google me on various R and phylogenetics listservs for additional code.)

If you found me from the QR code on a meeting poster, welcome!

About Nicholas J. Matzke

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Nicholas Matzke is currently a Discovery Early Career Researcher Award fellow in the Division of Evolution, Ecology, and Genetics, Research School of Biology, at the Australian National University in Canberra, Australian Capital Territory (ACT) — (Nicholas Matzke ANU page)

CVs

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Short-form CV (2-pager)

Long-form CV, and links to publications (see also: Matzke CV files)

Webpages

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Overview website: http://nickmatzke.weebly.com (in development)

Google Scholar for Nicholas J. Matzke — Google Scholar, and my CV, are the ONLY things I try to keep up to date.

  • I might accidentally be on other profile services, but YMMV (your mileage may vary).
  • My ORCid is: http://orcid.org/0000-0002-8698-7656, and my ResearchID is L-4109-2015 — again, I do not plan to maintain these closely.

National Institute for Mathematical and Biological Synthesis (NIMBioS) webpage on Postdoctoral Fellow Nicholas J. Matzke

Link to my mobile online business card with Vizibility. This will supply my contact information to your smartphone (you get the same effect if you scan the QR code on my poster).

Abstracts for presentations by Nicholas J. Matzke — in meeting websites, the abstracts are usually (a) hard to find, (b) hard to google, and (c) disappear at some point. This is can be problematic when the author tries to find them later. So, I will archive mine here.

Defending public education in evolutionary science: see (and join!) the National Center for Science Education, where I worked from 2004-2007, and The Panda's Thumb, a now-venerable group science blog, where I still blog on occasion when the creationists get annoying enough (see Nick Matzke posts archive). I mostly find myself too busy with science to do much blogging, plus I have found it much faster to do a twitter post instead of a whole blog. See my Twitter feed and the #IDerrors hashtag. See also: Nick Matzke on science education.

Events coming up

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

Monday, November 28-Friday, December 2, 2016: Model-Based Statistical Inference in Ecological and Evolutionary Biogeography. Week-long workshop in Barcelona, Spain. http://www.transmittingscience.org/courses/biog/statistical-biogeography/

Tuesday, September 6, 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 http://phylo.wikidot.com/matzke-2015-science-paper-on-the-evolution-of-antievolution

Sunday, June 19, 2016: Putting evolution into ecological niche modeling, a symposium, co-organized with Dan Warren, on building the connection between phylogenies, paleobiology, and species distribution models. At Evolution 2016, in Austin, Texas.

R Packages, Code, and Demos

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"Matzke 2015 Science Paper On The Evolution Of Antievolution" — This paper in Science, published online on December 17, 2015, contains a tip-dated, sampled-ancestors phylogenetic analysis of U.S. creationist/antievolution bills from 2004-2015. (Tracing how creationism involves!) The PhyloWiki page archives bonus material, including a free preprint, figures under Creative Commons license, and supplemental data and code.

"BioGeoBEARS" — an R package, on CRAN (but actively developing), which allows inference of historical biogeography down an phylogeny. Allows running LAGRANGE-like models as well as many more models. See IBS poster

"rexpokit" — an R package on CRAN bundling the FORTRAN EXPOKIT library for exponentiation of large sparse matrices.

"cladoRcpp" — an R package on CRAN using C++ code to rapidly calculate the conditional probabilities of cladogenetic range-inheritance events.

"BEASTmasteR" — R code for converting NEXUS data file(s) (DNA, amino acids, and/or discrete morphological characters), plus an Excel settings file, into Beast2 XML format. Primarily aimed at enabling tip-dating analyses using fossils as dated terminal taxa. The Birth-Death-Skyline-Serial-Sampling tree model is used, enabling different birth, death, and sampling rates through time.

"TNTR" — R code (and some TNT scripts) for converting data and trees from R into TNT format, running TNT analyses, and parsing the results back into R (and then conversion to standard formats and graphics). See also tntwiki.

"modiscloud" — an R package for processing MODIS Level 2 Cloud Mask products. Constructed for analyzing clouds & weather for Goldsmith, Matzke, & Dawson (2012), Ecology Letters.

"TreeRogue" — R code for digitizing phylogenetic trees from published figures. I devised this because I could never get TreeThief (or TreeSnatcher) to work on my Mac.

"BioGeoNick" — R code for plotting where I've travelled over my lifetime. Pretty groovy.

BioGeography module for Biopython — Google Summer of Code 2009 grant.

Gists on GitHub — These are short code snippets that can be easily shared without the infrastructure of an R package.

Seeking help/information?

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I get enough questions about various phylogenetics / software/ evolution topics that I have started to accumulate online help pages. If you email me, I may just give you the link, if it is a common question. Major links to resources I have made, or participate in, include:

BioGeoBEARS Google Group

BEASTmasteR Google Group

BEAST users group

R-sig-phylo, for phylogenetics in R

Lab Exercises for Berkeley's IB200a/b Phylogenetics courses

Intro to statistics in R, written for the 2014/2015 Research Experience for Undergraduates (REU) program at NIMBioS

Hominin cranial capacity through time

National Center for Science Education

Talk.Origins

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