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New Methods in Molecular Phylogenetics


Project Description

Phylogenies form the backbone of our understanding of much of life on earth. We are looking for a candidate with experience in bioinformatics, mathematics, computer science, or machine learning to help us build and apply the next generation of phylogenetic methods.

A famous evolutionary biologist, Dobzhansky, once wrote that ’nothing in biology makes sense except in the light of evolution’. And the way that we start to understand evolution is, most often, by understanding how organisms are related using molecular phylogenetics. New sequencing methods mean that we now have vastly more data to estimate phylogenies than we have ever had before. But the huge increase in the size of our datasets means that we need new methods to analyse all of this data.

This PhD project will involve designing and testing the next generation of methods for estimating phylogenetic trees from genome-scale sequencing data. There are a large number of potential directions that the research could take, and the details will depend on your interests and experience. Potential directions include: developing rapid phylogenetic methods using machine learning; new approaches to phylogenetic model selection; co-estimating multiple trees; developing empirical benchmark datasets in phylogenomics.

The Lanfear Lab

The Lanfear lab is a vibrant and supportive research group, with an open-source and open-access ethos. Students in the lab have a lot of freedom to pursue projects of their own choosing, and there is a lot of potential and support for collaboration both within and outside Australia. We work on various widely-used software packages including IQ-TREE (http://iqtree.org), PartitionFinder (http://www.robertlanfear.com/partitionfinder/), and RWTY (https://cran.r-project.org/web/packages/rwty/index.html). We also work on empirical biological questions, which currently focus on genomics and phylogenomics in Eucalytpus. More details about the Lanfear lab can be found here: http://www.robertlanfear.com/research/. And a full list of our publications is available here: https://scholar.google.com.au/citations?hl=en&user=Se6txrMAAAAJ


The Division of Ecology and Evolution

The Division of Ecology and Evolution at the Australian National University (ANU) (https://biology.anu.edu.au/research/divisions/ecology-and-evolution) provides an outstanding research environment with a world-class reputation. We work hard to provide excellent supervision and we take pride in providing an atmosphere that values intellectual rigour, inclusion, mentorship and fun. Graduate research students are well supported through internal funding, including for conference travel, and our research facilities are second to none. We have a thriving community of PhD students and Postdoctoral Fellows from around the world. Our graduates go on to productive careers in many areas of science and beyond.


Canberra and the ANU

The ANU campus is situated in the heart of Australia’s capital city, Canberra, which is ranked as the third best city in the world according to Lonely Planet (2018) and is Australia’s most liveable city (Life in Australia Report 2019). The ANU has an international reputation for research excellence and is ranked among the best universities in the world (QS World University Ranking 2019).

Funding Notes

Candidates: These scholarships are only open to citizens and permanent residents of Australia and New Zealand. ANU scholarships are highly competitive, and cover all fees and a ~$27K stipend. In order to be put forward, you will need outstanding undergraduate marks and a first class honours or Masters by research (or be expecting to gain one by the end of 2019) or equivalent research experience.

Expressions of interest: To send in an expression of interest, please email with a detailed CV, full academic transcripts, and a brief description of your research interests and how they intersect with this project.

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