Mario dos Reis
On Friday 28th of July in the morning I will be providing an overview of Bayesian species delimitation, with theory and practical examples. I will also discuss how to calibrate multispecies coalescent trees to geological time.
Mario was born in Venezuela, where he studied Biology at Universidad Simón Bolívar. In 2000 he moved to London where he did an MSc and a PhD at Birkbeck College in computational biology under the supervision of Lorenz Wernisch. He then did postdocs at the NIRM (now the Francis Crick institute), with Richard Goldstein, and at University College London, with Ziheng Yang. Since 2015 Mario has been faculty at Queen Mary University of London. His main research interests include development and application of Bayesian methods to estimate species divergence times, and development of mutation-selection models of codon evolution.
- Bayesian methods to estimate species divergence times
- Codon models to detect positive selection
- Bayesian species delimitation
Arrival and Departure
Thursday July 20 - Sunday July 30
Friday's morning lecture on Bayesian inference under the multispecies coalescent:
Demo and Tutorials
On Friday 28th of July in the afternoon we will be running a tutorial on Bayesian species delimitation using BPP. The PDF slides for the practical can be accessed from the link below.
Please also download BPP's paper here.
Phylogenetics MCMC in R
If you want something to do during the open lab sessions (Tue 24th and Sun 30th), you may want to try the phylogenetics MCMC tutorial I co-wrote with @thednainus and @zihengyang. The tutorial accompanies a forthcoming review paper (more soon!). The tutorial guides the user on how to write a full phylogenetic MCMC program in R! Tutorial here! GitHub files here!
Mouse lemur analysis with BPP
I've uploaded the mouse lemur example from my lecture to GitHub, so that you can see how to calibrate multispecies coalescent trees to geological divergence times. Code in  and full tutorial explained in .
- Angelis K, dos Reis M. 2015. The impact of ancestral population size and incomplete lineage sorting on Bayesian estimation of species divergence times. Current Zoology, 61: 874–885. 
- Rannala B. 2015. The art and science of species delimitation. Current Zoology, 61: 846–853. 
- Rannala B., Zhu T., Yang Z. 2012. Tail paradox, partial identifiability and influential priors in Bayesian branch length inference. Molecular Biology and Evolution 29: 325-335.  (This explains the Gamma-Dirichlet prior used to estimate branch lengths, for example in BPP)
- Xu B, Yang Z. 2016. Challenges in species tree estimation under the multispecies coalescent model. Genetics, 204: 1353–1368. 
- Yang Z. 2015. The BPP program for species tree estimation and species delimitation. Current Zoology, 61: 854–865. 
- Yoder A., et al. 2015. Geogenetic patterns in mouse lemurs (genus Microcebus) reveal the ghosts of Madagascar’s forests past. PNAS, 113: 8049–8056.