A Post-doc and two PhD candidate positions in computational evolution are available in the Centre for Computational Evolution at the University of Auckland to work on developing next generation models for inferring evolutionary history aiming to be able to process next generation sequencing data. The research will include the design and development of new mathematical and computational models for Bayesian phylogenetic inference. The successful candidates will work with an international team of computational biologists, evolutionary biologists and linguists to both develop new methods and test them on a number of exciting data sets.
Project
The study of evolution and, in particular, phylogenetic analysis has been transformed in the last decade by new methods for inferring species trees from gene trees. Any species tree will be compatible with a multitude of discordant underlying gene trees. Conventional approaches assume a single underlying tree, which can bias parameter estimates.
The multispecies coalescent (MSC) provides a principled framework for modelling the evolution of gene trees within species trees. However, the approach cannot currently be applied to the kind of large scale data sets made available by the current wave of next generation sequencing studies. This project requires the development of radical new approaches to a Bayesian implementation of the multispecies coalescent that can explicitly model gene trees within species trees even for very large data sets.
We will answer questions about macro-scale patterns of evolution across two very different domains in which we have particular expertise - large species radiations and human language. This work will not only provide insight specific to the composition and expansion of major clades in the tree of life (squamate lizards and Australian marsupials) and language (Indo-European, Austronesian and Pama-Nyungan) but also elucidate general processes of biological and cultural evolution.
Positions
Postdoc-doc: (1.5-2 year) The post-doc will have strong programming skills, and will implement new methods in BEAST under guidance of Bouckaert and Drummond. The post-doc will do simulation studies ensuring the implementation is correct and will provide a user friendly interface to set up analyses by members of the team as well as other users of the software.
PhD 1: (3 year) This student will focus on developing new computational methods in order to scale up the multi species coalescent model for NGS data and apply these methods to NGS data provided by ANU through Prof Moritz or sourced from other phylogenomic studies.
PhD 2: (3 year) This student will focus on linguistic analyses, develop new computational models for language evolution in the context of the multi species coalescent model and apply these models to the latest available Indo-European language data from the CoBL database provided by the Max Planck Institute through Prof Gray.
Each PhD position comes with a stipend of $NZ27,500 per annum and payment of enrolment fees. There is no teaching requirement associated with the stipend.
The successful candidates will work with an international team including Dr Remco Bouckaert, Prof Alexei Drummond, Prof Quentin Atkinson (University of Auckland), Prof Russell Gray (Max Planck Institute, Jena) and Prof Craig Moritz (ANU), as well as expert collaborators with knowledge of specific linguistic datasets at the Max Planck Institute for the Science of Human History, and molecular data sets at the Australian National University.
The successful applicants will have a strong background in a quantitative subject (such as Computational Biology, Mathematics, Statistics, Computer Science, Physics or similar), an understanding of Bayesian statistics, some experience of coding and ideally have had some exposure to, or at least a strong interest in, phylogenetic methods. The exact nature of the work will depend on the strengths and background of the successful candidates.
For more information and to express interest for the PhD candidate positions, please send a cover letter, your CV and list of grades to Dr Remco Bouckaert (r.bouckaert@auckland.ac.nz). To apply for the post-doc position see the HR webpage.