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Advanced Courses in Life Sciences

3rd Edition

Quantitative Cladistics and Use of TNT

October 2nd-6th, 2017, Barcelona (Spain)

Quantitative Cladistics and Use of TNT

This course will cover the basics of parsimony analysis and character optimisation, tree-searches, diagnosing and summarising results efficiently, and measuring group supports.

This course will be informal, with extensive hands-on exercises which will help students get familiar with the main aspects of phylogenetic analysis using TNT. For each of the units in the course, there will be a lecture (one to two hours, depending on the topics), then switching to exercises illustrating the points just seen in the lecture. Switches between “lecture” and “hands-on” mode will be dynamic, depending on how students progress with the exercises.

This course will make extensive use of TNT. There will also be a demonstration and some practice with GB->TNT, a program to create TNT matrices from GenBank data (in turn, GB->TNT requires installation of an alignment program, ideally Mafft or Muscle and possibly BioEdit to inspect alignments).

LOCATION

Centre de Restauració i Interpretació Paleontològica

C/ Mestre J. Lladós, 1
08781 Els Hostalets de Pierola, Barcelona.

How to get there

LANGUAGE

English

COURSE LENGTH & ECTS

40 hours on-site.

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

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

PLACES

Places are limited to 18 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

Pablo Goloboff instructor for Transmitting Science

Dr. Pablo A. Goloboff
Fundación Miguel Lillo – CONICET
Argentina

Claudia A. Szumik instructor for Transmitting Science

Dr. Claudia A. Szumik
Fundación Miguel Lillo – CONICET
Argentina

Coordinators

Ana Rosa Gómez-Cano coordinator at Transmitting Science

Dr. Ana Rosa Gómez-Cano
Transmitting Science
Spain

Soledad De Esteban-Trivigno instructor at Transmitting Science

Dr. Soledad De Esteban-Trivigno
Transmitting Science
Spain

Requirements

Graduate or postgraduate degree in any Biosciences discipline (including palaeontologists no matter the degree), basic knowledge of statistics, cladistics and personal computers. All participants must bring their own personal laptop, Windows strongly recommended (the software works with Macintosh, though without a graphic interface).

Program

Monday, October 2nd, 2017. Intro and Basics.

Parsimony and phylogenetic systematics. Character optimisation and mapping. Most parsimonious reconstructions and specific changes. Input/output in TNT. Dataset formats. Using GB->TNT to create matrices. Instruction files. Options for graphic output (SVG, metafiles). Creation of “batch” files. Editing trees. Handling tree files. Groups of trees, characters and taxa.


Tuesday, October 3rd, 2017. Tree calculation.

Tree searches. Exact solutions, Wagner trees, branch-swapping. Local and global optima. Use of multiple addition sequences. Improving search strategies. Factors which affect the efficiency of tree-searches. Constraints and “timeouts”.


Tuesday, October 3rd and Wednesday, October 4th, 2017. Ambiguity and consensus; summarizing results.

Zero-length branches and collapsing rules. Types of consensus and their use; improving consensus trees; supertrees. Pruned consensus. Comparison of tree-topologies; SPR distances.


Wednesday, October 4th, 2017. Character weighting.

Successive and implied weighting. Auto-weighted optimization. Refining character weighting with blocks; taking into account missing entries. User-defined weighting functions.

Thursday, October 5th, 2017. Group supports.

Concept of group support. Bremer supports; how to calculate them; search of suboptimal trees. Problems with Bremer supports; absolute and relative Bremer support. Partitioned Bremer support and individual Bremer supports. Measures based on resampling; effect of search strategies and collapsing rules. Problems with resampling methods.



Thursday, October 5th and Friday, October 6th, 2017. Tree search in large and difficult data sets.

Special search algorithms. Sectorial searches. Ratchet and drifting. Tree fusing. Combining different algorithms. Driven searches and stabilization of consensus.



Friday, October 6th, 2017. Scripting.

Automation of decisions to go beyond simple commands. Flow control. Decisions. Expressions, user variables, and internal variables. Design of simple scripts.

Previous editions of this course

2nd Edition, June 29th-July 3rd, 2015

Course Quantitative Cladistics and Use of TNT - 2nd Edition, June 29th-July 3rd, 2015Eleven people belonging to the following countries and institutions participated in this edition:

  • Spain: Autonomous University of Madrid, Institut Català de Paleontologia Miquel Crusafont, Universitat de València, Universitat de Barcelona.
  • Germany: Bavarian State Collection for Palaeontology and Geology.
  • Denmark: Natural History Museum of Denmark – University of Copenhagen.
  • Portugal: Universidade Nova de Lisboa.
  • United Kingdom: University of Bath, University of Leicester.
  • Poland: University of Wroclaw.
  • Canada: York University.

1st Edition, June 3rd-7th, 2013

Course Quantitative Cladistics and Use of TNT - 1st Edition, June 3rd-7th, 2013Thirteen people belonging to the following countries and institutions participated in this edition:

  • Germany: Bayerische Staatssmmlung für Paläontologie und Geologie.
  • People’s Republic of China: University of Hong Kong.
  • Spain: Universidad de Zaragoza.
  • Canada: York University.
  • Portugal: Faculdade de Ciências, Lisbon University.
  • South Korea: Hanyang University.
  • Lebanon: Lebanese American University.
  • Austria: Natural History Museum Vienna.
  • United States of America: American Museum of Natural History.
  • Turkey: Abant İzzet Baysal University.
  • Poland: University of Warsaw, Polish Academy of Sciences, University of Lodz.

Fees

  • Course Fee
  • Early bird (until May 31st, 2017):
  • 475
  • Regular (after May 31st, 2017):
  • 665
  • This includes course material, coffee breaks and lunches.
    (VAT included)
  • Accommodation Package
  • Early bird (until May 31st, 2017):
  • 360
  • Regular (after May 31st, 2017):
  • 360
  • This includes local transportation, lodging, breakfasts, dinners and social (tourist) activities.
    (VAT included)
  • Course Fee + Accommodation Package
  • Early bird (until May 31st, 2017):
  • 835
  • Regular (after May 31st, 2017):
  • 1,025
  • This includes course material, coffee breaks, local transportation, lodging, breakfasts, lunches, dinners and social (tourist) activities.
    (VAT included)

We offer the possibility of paying in two instalments (contact the course coordinators). Discounts (see Funding below) are not cumulative and apply only on the fee, not to Accommodation Package or other options.

Accommodation

If you take the Accommodation Package you will be hosted in the Youth Hostel Can Roviralta, in shared dormitories (common bathrooms), although you will only share rooms with other classmates. The possibility exists that the dormitories will be mixed. Therefore, if this is an inconvenience for you, and you require staying in a dormitory with only women, or only men, please indicate so in the “Comments” field of the Registration form (see below).

A supplemental charge will be added if you prefer to stay in a single room with private bathroom. The number of rooms is limited and if you prefer to have a single room, let us know it as soon as possible. If you want more information on this please contact the course coordinators.

Please be aware that from the centre of Barcelona city it takes about one hour by car and one hour and a half by public transport to arrive to Els Hostalets de Pierola. Course participants will find that staying in Els Hostalets de Pierola is more convenient.

If you do not want the Accommodation Package, accommodation is available in places other than Els Hostalets de Pierola. You may stay in Barcelona city, Martorell or Igualada. You will find information about Hotels in Martorell here, and information about Hotels in Igualada here.

How to get to Els Hostalets de Pierola from Barcelona city, Martorell and Igualada.

Youth Hostel Can Roviralta (Els Hostalets de Pierola, Barcelona, Spain)

Funding

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

Scholarship: Thanks to the donations of former participants, this year there is one scholarship for PhD students (the scholarship is in the form of tuition fee waivers only, it does not cover travelling and lodging). If you want to apply please fill up this form. You are expected to send us: 1- Full name and country, 2- Short project related with the course (maximum 2500 characters), 3- Letter of your advisor stating if you have any grant to develop your PhD. Deadline: March 31st. You should register for the course before applying.

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).

Spanish unemployed scientists, as well as Spanish PhD students 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 coordinators. 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.

Schedule

Course ScheduleCourse + Accommodation Package Schedule
Sunday, October 1st, 201719:00 Meeting point in Plaza Catalunya (Barcelona) to take the bus to Els Hostalets de Pierola. If you are planning to arrive later, you can find more information in How to get there.
20:00 Registration in the Youth Hostel.
20:30 Dinner.
Monday, October 2nd through Friday, October 6th, 20179:30 to 13:30 Lessons.
13:30 to 15:00 Lunch.
15:00 to 19:00 Lessons.

There will be two coffee breaks each day, halfway through each lesson session.

8:30 to 9:00 Breakfast.
9:30 to 13:30 Lessons.
13:30 to 15:00 Lunch.
15:00 to 19:00 Lessons.
20:30 Dinner.

There will be two coffee breaks each day, halfway through each lesson session.

Saturday, October 7th, 20178:30 to 9:00 Breakfast.
9:15 Meeting point in the Youth Hostel to take the bus to visit a wine cellar.
10:00 Arrival at the wine cellar.
11:30 Bus to Barcelona city.
13:00 Arrival at Plaza Catalunya (Barcelona).

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.

Organizers

Transmitting Science Logo
Research School in Biosystematics (ForBio) Logo
Centre de Restauració i Interpretació Paleontològica (CRIP) Logo
Institut Català de Paleontologia Miquel Crusafont (ICP) Logo

Collaborators

Colegio Oficial de Biólogos de Castilla y León Logo
Colegio Oficial de Biólogos de Euskadi Logo
Colexio Oficial de Biólogos de Galicia Logo
Col·legi Oficial de Biòlegs de la Comunitat Valenciana Logo
Distributed European School of Taxonomy (DEST) Logo
European Association of Vertebrate Palaeontologists (EAVP) Logo
Sociedade Brasileira de Paleontologia (SBP) Logo

Registration