Tree building: Advanced concepts and practice of phylogenetic analysis | CCMAR
 

Tree building: Advanced concepts and practice of phylogenetic analysis

Segunda, 24 Setembro, 2018 a Sábado, 29 Setembro, 2018
 
Course Description 

The use of phylogenetic methods to reconstruct the evolutionary history of molecular sequences is a vital part of biological research. These methods underpin studies on the evolution and epidemiology of plant and animal parasites and disease-causing organisms, and more generally they allow an objective analysis of the patterns and processes generating biological diversity. To carry out phylogenetic analysis properly, it is necessary to have a good understanding of the strengths and weaknesses of the key methods and approaches. This EMBO Practical Course has been designed to provide the theoretical and practical skills needed to carry out state-of-the-art phylogenetic analyses.

The past few years have seen have an explosion in new methods of analysis including the application of Bayesian analysis methods, the development of improved non-stationary models that better represent the dynamics of sequence evolution, the application of population genetic theory to phylogenies through the use of multispecies coalescent, and the development of methods for high-throughput genome-wide analyses. This EMBO Practical Course has been designed to cater for these newest methods and for understanding how they relate to the more traditional methods. Our goal is to teach technical sophistication without losing sight of the need for a critical attitude to data and analyses.

Format 

Registration

  • Registration Deadline
  • 30 April 2018
  • Chosen Participants Will Be Notified By
  • 18 May 2018
  • Payment Deadline
  • 31 July 2018

Registration includes:

  • Accommodation 23 – 29 Sept 2018 inclusive (7 nights)
  • Lunch and coffee
  • Dinner, including Welcoming Dinner and Gala
  • Transport to and from hotel to UALG campus (Gambelas)
  • Registration administration
  • Course materials

Payment

Successful applicants will be sent payment details by e-mail. Payment will be by bank transfer and is expected to have been completed by 31 July 2018.

 

Selection criteria

Participants will be early-career postdoctoral researchers and advanced PhD students who will be chosen on merit, as judged from a motivational letter, CV, and abstract for a 10 minute oral presentation. The selection procedure will also consider the need to balance numbers of participants representing different nationalities, to avoid over-representation from the host country (Portugal), to include a majority of participants resident in EMBC countries, and to maintain a reasonable gender balance.

 

Abstract guidelines

Abstract for a 10 minute PowerPoint presentation that each student will present (200 words).

 

Travel grants

A limited number of travel grants are available for participants. Applicants do not need to apply separately for travel grants for this event but should indicate on the registration form if they wish to be considered for a travel grant. Selection of awardees is handled directly by the organizer who will notify all eligible participants. More information is available at EMBO Travel Grants' page.

Agenda 

Programme

Day 1 – 24 September 2018

 

09:00–10:00

Welcome and Introduction: An Introduction to the basic concepts and ideas behind using molecular sequences to infer relationships.

  • Martin Embley

 

10:00–10:30

Coffee break and discussion

 

10:30–12:00

An Introduction to tree building. Case studies illustrating different issues and classic problems that need to be considered when making trees.

  • Martin Embley

 

12:00–13:00

Student introduction and PowerPoint presentations (I)

  • All participants

 

13:00–14:00

Lunch

 

14:00–18:00

Practical session – Becoming familiar with the computers and software: alignments and trees.

  • Tom Williams and Naiara Rodriguez-Ezpeleta

 

18:00–19:00

Student PowerPoint presentations (continued) (II)

  • All participants

 

20:00–22:00

Welcoming Dinner

 

Day 2 – 25 September 2018

 

09:00–09:10

Morning Briefing

  • Martin Embley

 

09:10–10:00

Character evolution, maximum parsimony, and consensus trees

  • Naiara Rodriguez-Ezpeleta

 

10:00–10:30

Coffee break and discussion

 

10:30–12:00

Maximum likelihood and modelling. An introduction to the use of maximum likelihood phylogenetic models and substitution.

  • Peter Foster

 

12:00–13:00

Student PowerPoint presentations (continued) (III)

  • All participants

 

13:00–14:00

Lunch

 

14:00–18:00

Practical session – Maximum likelihood and Bayesian inference. Using common ML and Bayesian phylogenetic software to build trees.

  • Peter Foster and Tom Williams

 

18:00–19:00

Student PowerPoint presentations (continued) (IV)

  • All participants

 

20:00–22:00

Dinner

 

Day 3 – 26 September 2018

 

09:00–09:10

Morning Briefing

  • Martin Embley

 

09:10–10:00

Robustness of data and hypotheses. Interpretation of non-parameteric bootstrap analyses and additional measures of support.

  • Mark Wilkinson

 

10:00–10:30

Coffee break and discussion

 

10:30–12:00

Estimating evolutionary rates and times using phylogenetic and coalescent models. Bayesian priors on rates and the multispecies coalescent.

  • Rachel Warnock

 

12:00–13:00

Student PowerPoint presentations (continued) (V)

  • All participants

 

13:00–14:00

Lunch

 

14:00–18:00

Practical session – Multispecies coalescent analyses. Guide to using coalescent models for phylogenetic reconstruction.

  • Rachel Warnock and Mark Wilkinson

 

18:00–19:00

Round-table discussion (I)

  • All participants

 

20:00–22:00

Dinner

 

Day 4 – 27 September 2018

 

09:00–09:10

Morning Briefing

  • Martin Embley

 

09:10–10:00

Advanced phylogenetic models. Fitting complex phylogenetic models in a Bayesian setting using p4 and Phylobayes, and testing model assumptions.

  • Peter Foster

 

10:00–10:30

Coffee break and discussion

 

10:30–12:00

Constructing supertrees and detecting rogue taxa. Methods for building supertrees and identifying poorly-fitting taxa.

  • Mark Wilkinson

 

12:00–13:00

Round-table discussion (II)

  • All participants

 

13:00–14:00

Lunch

 

14:00–18:00

Practical session - Advanced model application in a Bayesian setting. Using p4 and Phylobayes, and testing model assumptions.

  • Peter Foster and Tom Williams

 

18:00–19:00

Round-table discussion (III)

  • All participants

 

20:00–22:00

Dinner

 

Day 5 – 28 September 2018

 

09:00–09:10

Morning Briefing

  • Martin Embley

 

09:10–10:00

Causes and resolution of phylogenetic conflict. Biological and systematic sources of tree conflict are described in detail.

  • Naiara Rodriguez-Ezpeleta

 

10:00–10:30

Coffee break and discussion

 

10:30–12:00

Phylogenomics and phylogenomic networks. The use of network models that enable reconstruction of both vertical and lateral gene transfer events.

  • Tal Dagan

 

12:00–13:00

Round-table discussion (IV)

  • All participants

 

13:00–14:00

Lunch

 

14:00–17:00

Practical session – Constructing and interpreting networks. Using network models to interpret reticulation.

  • Tal Dagan and Naiara Rodriguez-Ezpeleta

 

17:00–18:00

Round-table discussion (V)

  • All participants

 

18:00–19:00

Research seminar and case study - Applying phylogenetics to resolving ancient eukaryotic relationships

  • Martin Embley

 

20:00–22:00

Course Gala Dinner

 

Day 6 – 29 September 2018

 

09:00–09:10

Morning Briefing

  • Martin Embley

 

09:10–10:00

Phylogenetic reconstruction of horizontal gene transfer. Exploring gene acquisition by LGT: an important mechanism for natural evolution.

  • Tal Dagan

 

10:00–10:30

Coffee break and discussion

 

10:30–13:00

Roots, gene trees, and species trees. Synthesising recent progress on the methods that enable trees to be rooted as part of the analysis.

  • Tom Williams

 

13:00–14:00

Lunch

 

14:00–16:00

Round table discussion (VI)

  • All participants

 

16:00–17:00

Final comments; course ends

  • All participants

 

19:00–21:00

Dinner

Intended Audience 
Academics, Postdoctoral Researchers, PhD students, and MSc Students
Scientific Organisation 
Instructors 

Martin Embley

University of Newcastle, UK

Tal Dagan

University of Kiel, DE

Peter Foster

Natural History Museum (London), UK

Rachel Warnock

ETH Zurich, CH

Mark Wilkinson

Natural History Museum (London), UK

Tom Williams

University of Bristol, UK
Accomodation 

Accommodation 23 – 29 Sept 2018 inclusive (7 nights) is included in the Registration, and will be a room, or shared room, in a hotel in central Faro.

Venue 

Centro de Ciencia do Mar (CCMAR),

Universidade do Algarve,

Campus de Gambelas,

Faro, Portugal

Accommodation

Hotel accommodation (7 nights, with breakfast) will be provided in central Faro close to the marina and shopping area. We will try to accommodate all participants in single rooms but most likely participants will be asked to share 2 to a room.

Transport

The host institute, CCMAR at the University of the Algarve (UAlg), Faro, is 5 km from the international airport (FAO). The venue can also be reached from Lisbon by taking a train to the Faro railway station, or via major roads in Portugal and Spain.

About the Area

See these websites for further information about the Algarve and Faro areas.

Location 
Activity type 
Other
Presentation Language 
English
Fee (starting from...) 
€ 300.00
Fee Covers 

Academics/Industry: 400€

Postdocs/Students: 300€

Registration includes:

  • Accommodation 23 – 29 Sept 2018 inclusive (7 nights)
  • Lunch and coffee
  • Dinner, including Welcoming Dinner and Gala
  • Transport to and from hotel to UALG campus (Gambelas)
  • Registration administration
  • Course materials

Payment

Successful applicants will be sent payment details by e-mail. Payment will be by bank transfer and is expected to have been completed by 31 July 2018.

 

Keywords 
Molecular Evolution, Phylogeny, Modeling, Population genetics, networks