Stadler (nee Gernhard), Tanja, Dr.

Research Interest

I am a mathematician applying analytical tools to problems arising in evolutionary biology. Some of the topics I am currently working on:

• Modelling transmission of infectious diseases
• Modelling speciation and extinction via birth-death processes
• Developing tree shape statistics for testing evolutionary hypothesis
• Investigating gene trees evolving on species trees

Publications

• Sampling trees from evolutionary models
  K. Hartmann, D. Wong, T. Stadler⁺
  Syst. Biol. in press.
• Analyzing and reconstructing reticulation networks under timing constraints
  S. Linz^*, C. Semple^*, T. Stadler^*+
  J. Math. Biol. in press.
• On incomplete sampling under birth-death models and connections to the sampling-based coalescent
  T. Stadler
  J. Theo. Biol. (2009) 261: 58-66
• A method for investigating relative timing information on phylogenetic trees
  D. Ford^*, E. Matsen^*+, T. Stadler^*
  Syst. Biol. (2009) 58(2): 167-183.
• Lineages-through-time plots of neutral models for speciation
  T. Stadler
  Math. Biosciences (2008) 216: 163-171.
• Stochastic properties of generalised Yule models, with biodiversity applications
  T. Gernhard^*, K. Hartmann^*+, M. Steel
  J. Math. Biol. (2008) 57: 713–735.
• The conditioned reconstructed process
  T. Gernhard
  J. Theo. Biol. (2008) 253(4): 769-778.
• New analytic results for speciation times in neutral models
  T. Gernhard
  Bull. Math. Biol. (2008) 70(4): 1082-1097.
• Estimating the relative order of speciation or coalescence events on a given phylogeny
  T. Gernhard⁺, D. Ford, R. Vos, M. Steel
  Evolutionary Bioinformatics Online (2006) 2: 309-317.

• Amazonia through time: Evolution of a tropical ecosystem influenced by mountain uplift and climate change.
  Carina Hoorn⁺, F. Wesselingh, H.ter Steege, T. Stadler, I. Sanmartín, A. Sanchez-Meseguer, C. Lisa Anderson, C. Jaramillo, M. Bermudez, J. Figueiredo, D. Riff, F.R. Negri, H. Hooghiemstra, J. Lundberg, H. P. Linder, T. Sarkinen, A. Mora, A. Antonelli.
  submitted, 2009.
• Virus genotype largely determines HIV viral load.
  Samuel Alizon⁺, Viktor von Wyl^*, Tanja Stadler^*, Roger Kouyos^*, Sabine Yerly, Jürg Böni, Cyril Shah, Thomas Klimkait, Philipp Bürgisser, Huldrych F. Günthard, Sebastian Bonhoeffer and the Swiss HIV Cohort Study.
  submitted, 2009.
• Quantifying species-level selection for sexual reproduction in aphids.
  J. Engelstädter⁺, T. Stadler.
  submitted, 2009.
• Approximate Bayesian computation of density-dependent speciation and extinction rates
  T. Stadler, F. Bokma⁺
  submitted, 2009.
• A unified multi-resolution coalescent: Markov lumpings of the Kingman-Tajima n-coalescent
  R. Sainudiin^*+, T. Stadler^*
  submitted, 2009.
• Testing the temporal framework of speciation in an ancient lake species flock: the genus Dina (Hirudinea: Erpobdellidae) in Lake Ohrid
  S. Trajanovski⁺, C. Albrecht, R. Schultheiß, T. Gernhard, M. Benke, T. Wilke
  submitted, 2008.

^* equal contribution
⁺ corresponding author

Software

You might ask why I develop tree simulation tools even though there are several commonly used tools around: well, the commonly used tools work inappropiate for most models and simulate incorrect trees which might yield to wrong conclusions, see our paper "Sampling trees from evolutionary models".

• TreeSim
  Last update - Nov 10th, 2009.
  An R library for simulating trees on a fixed number of species under models which may include mass extinction events and rate shifts through time.
  This library extends simulation methods implemented in TreeSample and Cass.
  Install from within R with the command: install.packages("TreeSim_1.0.tar.gz", repos=NULL, type="source")
  The package requires the libraries Ape and Geiger.
  Implemented by Tanja Stadler.
• Cass
  Last update - May 18th, 2009.
  A Python tool for analyzing and manipulating phylogenetic trees (simulating trees under birth-death processes with incomplete sampling, estimating dates in supertrees, testing for neutrality with our runs statistic, the Colless statistic, drawing LTT plots etc). Details are found in the ReadMe.
  Installing Python on your computer is easy and straightforward, so it should not prevent you from using the Cass package! An installation guide is included in the ReadMe of the Cass package.
  Implemented by Tanja Stadler.
• TreeSample
  Program for simulating phylogenetic trees with a fixed number of species. In our paper "Sampling trees from evolutionary models" we explain why other existing simulation programs return inappropriate trees.
  Implemented by Klaas Hartmann.
• Beast
  Bayesian Evolutionary Analysis Sampling Trees by Alexei Drummond and Andrew Rambaut. The birth-death prior is implemented using the results in the paper The conditioned reconstructed process.

Thesis

• PhD: Evolving Trees - Models for Speciation and Extinction in Phylogenetics
  awarded best PhD thesis 2008 of the Technical University of Munich
• Diplom: Stochastic Models for Speciation Events in Phylogenetic Trees
  awarded at the DMV (German Math Society) conference 2006 with a main prize

Short CV

• 10/2008-now: PostDoc with Prof. Sebastian Bonhoeffer at the ETH Zürich, Switzerland
• 06/2008: Le Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier, France
• 04/2008: Invited talks in Berkeley, Michigan University, New York City College
• 01/2007-04/2007 & 01/2008-03/2008: Biomathematics Research Institute Christchurch, New Zealand
• 09/2006-09/2008: PhD student at the TU München, Germany, advisor Prof. Anusch Taraz
• 09/2005-03/2006: Diplom thesis at Biomathematics Research Institute Christchurch, New Zealand, advisor Prof. Mike Steel
• 01/2005-06/2005: study abroad in Cardiff, Wales
• 10/2001-07/2006: studies of Mathematics with minors in Biology and Computer Science (Diplom), TU München, Germany
• 07/2001: Abitur, Germany
• 06/1999: High School Diploma, USA

Scholarships

• PhD scholarship within the Graduiertenkolleg Angewandte Algorithmische Mathematik (09/2006-09/2008)
• Allan Wilson Summerstudentship (2005 & 2006 & 2007)
• Friedrich-Ebert-Stiftung scholarship (2003-2006)
• e-fellows scholarship (since 2001)

My previous homepage at the Technical University of Munich:

http://www-m9.ma.tum.de/twiki/bin/view/Allgemeines/TanjaGernhard