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Advanced Courses in Life Sciences

1st Edition

Morphological phylogenetics: principles, applications and techniques

November 4th-8th, 2019, Crete (Greece)

Evolution

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Morphological phylogenetics principles applications and techniques

Course overview

An accurate reconstruction of evolutionary relationships among species is the cornerstone of evolutionary biology. Building phylogenetic trees thus provides the fundamental framework upon which systematic, biogeographic and evolutionary research operates. Morphological phylogenetics provides a unique toolkit for inferring relationships, considering that the vast majority of the species that have ever lived are now extinct and can only be assessed based on morphological data. Additionally, combining fossils and morphological data with molecular data from extant species is becoming the most comprehensive method of assessing phylogenetic relationships on deep time and the time of origin of major evolutionary lineages.

In this course, we will focus on the analysis of morphological data (and combining morphological data with molecular data) using multiple optimality criteria for phylogenetic inference. We will discuss the best available approaches to construct morphological data sets and their impact on phylogenies. We will follow with theory and hands-on practice of phylogenetic programs using maximum parsimony, maximum likelihood and Bayesian inference. Participants will learn how to combine morphological and molecular data for total evidence analyses, how to conduct time-calibrations using tip and node dating, different birth-death models, morphological clocks and combined evidence relaxed clock analyses.

Softwares: Mesquite, TNT, RAxML, IQTree, Mr. Bayes and BEAST.

LOCATION

Alexander Hotel

Gerakári, Municipality of Amari, 74 061
Rethymno
Crete, Greece

DATE

November 4th-8th, 2019

LANGUAGE

English

COURSE LENGTH & ECTS

35 hours on-site.

This course is equivalent to 2 ECTS (European Credit Transfer System) at the Life Science Zurich Graduate School.

The recognition of ECTS by other institutions depends on each university or school.

PLACES

Places are limited to 20 participants and will be occupied by strict registration order.

Participants who have completed the course will receive a certificate at the end of it.

Instructors

Tiago Simoes instructor for Transmitting Science

Dr. Tiago Simões
Harvard University
United States of America

Oksana Vernygora instructor for Transmitting Science

Oksana Vernygora
University of Alberta
Canada

Coordinator

Haris Saslis coordinator for Transmitting Science

Dr. Haris Saslis
Transmitting Science
Greece

Requirements

Prior knowledge of basic systematic concepts is recommended but not imposed. All participants must bring their own personal laptop.

Program

Monday, November 4th, 2019.

  • Morning:
    • Theory of morphological character construction:
      • Homology: assessment and tests.
      • Avoiding logical and biological biases in morphological characters.
      • Challenges behind morphological data sets in the era of big data.
    • Working with data files:
      • File structure of main types of data matrices (NEXUS, PHYLIP, TNT).
      • Creating and editing data files.
  • Afternoon:
    •  Practice:
      • Exercise 1.1: Morphological character construction.

Tuesday, November 5th, 2019.

  • Morning:
    • Maximum Parsimony:
      • Principles and assumptions.
      • Fitch, Farris, and Goloboff algorithms.
      • Tree search using New Technology (T.N.T) – introduction to the T.N.T. software.
  • Afternoon:
    • Practice: maximum parsimony analysis using T.N.T.:
      • Morphological data analysis using Traditional and New Technology search algorithms.
      • Implied weights parsimony analysis.
      • Working with trees – constructing consensus, calculating support values, mapping synapomorphies, etc.

Wednesday, November 6th, 2019.

  • Morning:
    • Probabilistic methods in phylogenetics:
      • Concepts and assumptions.
      • Differences between probabilistic methods and parsimony (includes discussion on the performance comparison MP vs ML and BI for morphological data).
    • Maximum likelihood:
      • Theory of maximum likelihood.
      • Application in phylogenetics.
  • Afternoon:
    • Exercise 1: Maximum likelihood analysis in IQ-tree using web-server.
    • Exercise 2: Maximum likelihood analysis using command line version of IQ-tree.

Thursday, November 7th, 2019.

  • Morning:
    • Bayesian inference:
      • Bayes theorem and its application in phylogenetics.
      • Introduction to Markov chain Monte Carlo (MCMC) method.
      • Metropolis coupling of MCMC chains.
      • Priors.
    • Introduction to Mr Bayes software.
    • Clock-based (time calibrated) Bayesian inference analysis:
      • Principle behind molecular clock.
      • Introduction to morphological clock.
      • Types of clocks (strict, autocorrelated, uncorrelated, local).
    • Tree priors:
      • Birth-Death model.
      • Fossilized Birth-Death model.
  • Afternoon:
    • Exercise 1: Bayesian inference analysis using Mr Bayes:
      • Writing and adding Mr Bayes block to a data set.
      • Performing non-clock analysis and overview of each component.
      • Analysing output.
    • Exercise 2: Model-fit analysis using Bayes factor.
    • Exercise 3: Time-calibrated analysis in Mr Bayes.


Friday, November 8th, 2019.

  • Morning:
    • Combined data sets:
      • Combining different types of data (molecular and morphological.
      • Divergence time estimation using combined evidence clocks.
      • Analysing output.
    • Clock analysis using BEAST:
      • Major differences to Mr Bayes
      • Overview of the modular configuration of BEAST 2.
  • Afternoon:
    • Exercise 1: Data partitioning and running combined evidence analysis.
    • Exercise 2: Time-calibrated analysis using BEAST 2 (Morphology and combined evidence datasets).

Fees

  • Course Fee
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  • Early bird (until July 31st, 2019):
  • 580 *
  • Regular (after July 31st, 2019):
  • 720 *
  • This includes course material, coffee breaks and lunches (VAT included).
    * Participants from companies/industry will have an extra charge of 100 €.
  • Course Fee + Accommodation Package
  • {{content-1}}
  • Early bird (until July 31st, 2019):
  • 580 * + 350 = 930
  • Regular (after July 31st, 2019):
  • 720 * + 350 = 1,070
  • This includes course material, coffee breaks, transportation between the Venue and Heraklion or Chania city, accommodation from Sunday to Friday, breakfasts, lunches and dinners (VAT included).
    * Participants from companies/industry will have an extra charge of 100 €.

20 % discount will be applied to your fee If you belong to any of the Institutions listed HERE. Discounts (see Funding below) are not cumulative and apply only on the fee.

We offer the possibility of paying in two instalments (contact the course coordinator).

Accommodation

If you choose the Accommodation Package you will be hosted at Alexander Hotel in Gerakári village (take a look at the venue), in shared en-suite twin rooms, although you will only share rooms with other course participants. There is a possibility that the rooms will be mixed. If this is an inconvenience for you, and you would prefer to stay in an all-female or all-male room, please indicate so in the “Comments” field of the Registration form (below).

If you prefer to stay in a single en-suite room, you can do so with a supplementary charge.

The Accommodation Package includes transportation from the centre of both Heraklion and Chania (the two main cities of Crete with airports) to the venue and back, at the start and end of the course, respectively. The trip takes around 1 hour 50 minutes each way. Once you have booked your flights, please let the course coordinator know which airport you are flying in and out of, in order to arrange your transportation.

If you do not wish to take the Accommodation Package, you can find a few other options in the surrounding area. However, please be aware that access to and travelling around the area requires a private vehicle as public transport is scarce. Therefore, course participants will find choosing the Accommodation Package more convenient.

Alexander Hotel, Gerakári

Alexander Hotel 1

Alexander Hotel twin room

Alexander Hotel, Gerakári

Alexander Hotel 2

Alexander Hotel, Gerakári

Alexander Hotel 3

Schedule

Course Schedule
  • Monday to Friday:
    • 9:30 to 13:30 Lessons.
    • 13:30 to 15:00 Lunch (included).
    • 15:00 to 18:00 Lessons.
Accommodation Package Schedule
  • Sunday:
    • 18:30 Meeting in Heraklion (Archaeological Museum) or Chania (Coach Station) to take the bus to Gerakári.
    • 20:15 Check-in at Alexander Hotel.
    • 20:45 Dinner.
  • Tuesday to Thursday:
    • 8:30 to 9:00 Breakfast.
    • 20:30 Dinner.
  • Friday:
    • 8:30 to 9:00 Breakfast.
    • 18:30 Meeting at Alexander Hotel to take the bus to Heraklion or Chania.
    • 20:15 Arrival in Heraklion (Archaeological Museum) or Chania (Coach Station).

The schedule is approximate; it is possible that the content of one day may run into the next and a working day may be longer than advertised.

Funding

Discounts

Former participants will have a 5 % discount on the Course Fee.

Furthermore, a 20 % discount on the Course Fee is offered for members of some organizations (Organizations with discount). If you want to apply to this discount please indicate it in the Registration form (proof will be asked later).

Unemployed scientists living in Greece, as well as PhD students based in Greece without any grant or scholarship to develop their PhD, could benefit from a 40 % discount on the Course Fee. If you want to ask for this discount, please contact the course coordinator. That would apply for a maximum of 2 places and they will be covered by strict inscription order.

Discounts are not cumulative and apply only on the fee, not to Accommodation Package or other options.

Organizers

Transmitting Science Logo

Collaborators

Colegio Oficial de Biólogos de Castilla y León Logo
Col·legi Oficial de Biòlegs de la Comunitat Valenciana Logo
Colexio Oficial de Biólogos de Galicia Logo
Colegio Oficial de Biólogos de Euskadi Logo

Registration