A five-day introductory course on parsimony based and probabilistic phylogenetic analysis in paleontology and morphological studies, for students and professionals, to be held online, by members of the Department of Earh Sciences, NOVA School of Sciences and Technology.
Phylogenetic analyses are a key tool for palaeontologists. The aim of this course is to provide the participants the basic skills need to perform a morphological phylogenetic analysis and publish their results. The basics of parsimony and probabilistic methods will be covered. Training sessions using TNT, Mesquite, MrBayes and Beast will be held via Zoom.
Open to anyone but targeted to students and professionals in evolutionary biology and palaeontology.Diploma will be provided upon fulfilment of the academic requirements by FCT-UNL.
Miguel Moreno Azanza and Filippo Maria Rotatori (FCT- University NOVA of Lisbon)
The course is fully online and will be held by Zoom. Participants should have a computer to run the programs. Windows OS strongly recommended (MacOS versions of the software available but without user interface).
April 26th to April 30th of 2021. The course will have 10 sessions, each with theoretical and practical lessons.
Total hours of training: 30.
Day 1- Phylogenetics 101
Introduction to phylogenetic analysis
What makes a good character?
How to write a good character
How to read a tree
Introduction to parsimony
Hands on: Building a matrix in Mesquite
Day 2 -Basic TNT
TNT workspace and workflow
Search strategies: how to choose the most suitable. Implicit enumeration and traditional searchers
Summarizing the tree space: consensus trees
Character optimization in TNT
Day 3 – More on TNT
Edit your data in TNT. Step matrices, character weighting. A solution to inapplicable characters.
Branch support
Implied weighting
Scripting in TNT
Hans on: writing the phylogenetic section of a paper
Day 4 – Introduction to probabilistic methods in phylogeny
Introduction to probability theory
Principles of Bayesian inference
The tripartite model
How to perform a Bayesian analysis
Hands-on: non-clock analysis on MrBayes
Day 5 – Introduction to Clock analysis
Integrating and modelling stratigraphic data within the analysis
introduction to tip-dating
importance of modelling uncertainty
Birth-date processes
Basic Model
Fossilized Birth-Death Model
Exploring anagenetic processes: the sampled ancestor (SA)
Time partitioning: The Skyline Fossilized Birth-Death with sampled Ancestor model (SFBDSA)
Rates of character evolution (with parsimony and with probabilistic methods)
Characters transformation with Paul and Rauhut algorithm (MP)
Characters transformation within a probabilistic framework.
Hands-on: clock analysis with Beast
Language: English
Registration: Send an email to Miguel Moreno-Azanza (mmazanza@fct.unl.pt) including your name, email, professional situation, institution and where you learn about this course.
REGISTRATION HAS ENDED.
PLEASE CONTACT mmazanza@fct.unl.pt IF YOU ARE INTERESTED IN FUTURE EDITIONS OF THE COURSE.