The MEEP Lab runs workshops on methods for evolutionary analysis. Our annual Sydney Phylogenetics Workshop is held in July each year and is free to attend. We have also run workshops at other venues, including the National Herbarium of NSW, Australian National University, University of Melbourne, University of New South Wales, and University of Gothenburg (Sweden). Some of our workshops have been offered in conjunction with COMBINE or with the annual conference of the Genetics Society of Australasia.
Sydney Phylogenetics Workshop
28–29 January 2021
The 11th annual Sydney Phylogenetics Workshop will be held as an online event in January. This workshop is normally held in July but was postponed because of COVID-19 and to avoid clashing with online conferences in later 2020.
The 2-day workshop will provide an introduction to phylogenetic analysis using maximum-likelihood and Bayesian methods. The workshop will comprise a series of lectures (delivered in Zoom webinar format) and practical exercises (provided in the form of self-guided tutorials).
Day 1 of the workshop will cover interpreting phylogenetic trees, molecular data, sequence alignment, evolutionary models, and phylogenetic methods, and maximum-likelihood analysis using IQ-TREE. Day 2 will provide an introduction to Bayesian phylogenetic analysis and will include models and priors, molecular clocks, estimating timescales, and pathogen phylodynamics. Prior knowledge of basic phylogenetics is helpful but not essential.
Registration is free but limited to 100 participants, with 80 places reserved for early career researchers (students and postdocs). Please note that the workshop is fully booked; registration is now closed.
Speakers include Simon Ho and Fred Jaya (University of Sydney), Minh Bui (author of IQ-TREE, Australian National University), David Duchêne (University of Copenhagen), and Barbara Brito-Rodriguez (University of Technology Sydney).
Recent workshops and conferences
Phylomania: Sydney hub
25–27 November 2020, University of Sydney
Phylomania 2020, the Twelfth Theoretical Phylogenetics Meeting at University of Tasmania, was run as an online event in November 2020. The University of Sydney hosted a local hub at the Charles Perkins Centre for attendees from the Sydney region.
Morning tea was provided by Taste Baguette CPC.
Phylomania 2020 was organised by Venta Terauds and Nick Fountain-Jones from the UTAS Mathematical Biology Research Group. The Sydney hub was organised by Simon Ho and Fred Jaya.
Genomes and Biodiversity
This three-day event comprised seminars by research leaders in genomics and biodiversity, hands-on training sessions in analyses of ‘big data’, and a career development workshop. It concluded with a public lecture by Dr Rebecca Johnson, Director of the Australian Museum Research Institute. Attendance was limited to 50 early- to mid-career researchers from Australia and New Zealand.
The workshop was supported by the Australian Academy of Science, University of Sydney, and University of Copenhagen. The organising committee comprised early- and mid-career researchers from the Australian Museum (Jackie Nguyen), Australian National University (Dan Rosauer, David Duchene, Xia Hua), and University of Sydney (Cara Van Der Wal, Jackie Mahar, Mang Shi, Simon Ho).
Sydney Phylogenetics Workshop
15–16 July 2019, University of Sydney
The most recent Sydney Phylogenetics Workshop was held on 15–16 July 2019. The teaching team was led by Simon Ho (University of Sydney) and David Duchene (Australian National University), and included Nate Lo, Cara Van Der Wal, Perry Beasley-Hall, and Yi-Kai Tea.
This free two-day workshop provided an introduction to phylogenetic analysis, including practical exercises based on the software MEGA and BEAST2. Day 1 dealt with interpreting phylogenetic trees, molecular data, sequence alignment, evolutionary models, and phylogenetic methods. Day 2 provided an introduction to Bayesian phylogenetic analysis and includes Bayesian statistics, priors, and molecular dating. All of the teaching materials are available on GitHub.
Languages, Genes, and Prehistory
14 June 2019, University of Sydney
Linguistics and genetics have traditionally pursued different approaches to the reconstruction of human prehistories, applying different methods and often working at different time-scales). In recent years, however, research has emerged which attempts a direct correlation of linguistic and genetic indicators of population migrations, and a rapidly growing field of inquiry applies methods developed in the context of computational phylogenetics and cladistics to various types of language data to derive probabilistic models of language evolution and, therefore, language relationships.
This day-long interdisciplinary workshop brought together world-leading scholars to focus on intersections between theory and method in evolutionary biology and linguistics, with a special focus on the Asia-Pacific region. The workshop included talks by researchers from the University of Sydney (Mark Post, Paul Sidwell), Australian National University (Lindell Bromham, Xia Hua), and Universität Bern (George van Driem), as well as a software clinic run by Simon Ho.
Taming the BEAST Down Under
17–22 February 2019, University of Sydney
In February 2019 we hosted the week-long workshop Taming the BEAST Down Under, which focussed on Bayesian phylogenetic analysis using BEAST2. The workshop consisted of invited talks, lectures, and hands-on tutorial sessions given by core BEAST2 developers and experts in phylogenetics. The aim of the workshop was to provide participants with a firm grasp of the theory behind the methods central to phylogenetics, as implemented in BEAST2. The workshop covered Bayesian phylogenetics, phylogenetic model selection, molecular clocks, total-evidence dating, species trees and gene trees, and pathogen phylodynamics.
The teaching team included leading international and Australian reseachers from the University of Auckland, ETH Zurich, University of Sydney, Flinders University, University of Melbourne, and Australian National University. The workshop was organised by Simon Ho and several members of the MEEP Lab.