Advanced Courses in Life Sciences

We will host Prof. Dr. Donald L. Swiderski, and Prof. Dr. M. Zelditch for a period of one week at Koç University from 01 to 08 May 2023. After a one-day seminar on analyzing mammalian macro-evolution, Dr. Swiderski, and Dr. M. Zelditch will hold a course on geographic analysis of biodiversity (integrating geographic, shape, and phylogenetic data) on the following days of the week. In this course instructors will introduce different conceptual biological reasons why it might be interesting to examine biodiversity data in a geographic context, focusing on the relationships between species richness, trait similarity, and phylogeny, as well as patterns of turnover in those relationships. In this overview, they will discuss what these can reveal about patterns of community assembly, in situ diversification vs immigration, as well as the potential connections between these patterns and environmental/climatic/elevational gradients.

Prof. Dr. Donald L. Swiderski
Research Laboratory Specialist
Intermediate and Adjunct Assistant Research Scientist
Ecology and Evolutionary Biology
University of Michigan
Ann Arbor, USA

I am an evolutionary biologist interested primarily in the relationship between morphological changes and functional transitions in both evolution and ontogeny. I use quantitative analyses of skeletal shape data to gain a better understanding of (a) what morphological attributes actually differ between species or growth stages in different ecological roles, and (b) the relevance of morphological change to functional or ecological change. My recent research has focused on the relationship between diversity and disparity in squirrels, using quantitative analyses of jaw shape. I also am interested in locomotion and the relationship between locomotory and dietary transitions, and in form-function relationships throughout the animal kingdom.

Website

Prof. Dr. M. Zelditch
Associate Research Scientist
Museum of Paleontology
University of Michigan
Ann Arbor, USA

I am an evolutionary biologist interested in the relationship between diversification and morphological evolution.  The geographic landscape is central to theories of diversification, and the adaptive landscape is equally central to theories of adaptive evolution, so integrating these two landscapes promises a general theory for the generation and maintenance of diversity of both species and their morphologies. I use models of adaptive evolution, combined with geographic distributions of species and their morphologies, to analyze the relationship between species richness and morphological diversity over time and space.

Websit

Syllabus
Introduction
1.      Basics of geometric morphometrics
2.      Overview of the course
3.      Resources
4.      Software
Introduction to shape data
1.      Landmarks and semilandmarks
2.      Objectives of a shape analysis: How to think about landmark selection
3.      Criteria for selecting landmarks
4.      When to include semilandmarks
5.      How landmarks and semilandmarks differ
6.      Digitizing landmarks and semilandmarks
Getting shape data from landmark coordinates
1.      Operations that remove non-shape variation
2.      Procrustes superimposition
3.      Landmarks
4.      Semilandmark sliding
5.      Loading datafiles, sliders file, superimposition
Statistical Theory of Shape
1.      Theoretical foundations of shape analysis
2.      Shape spaces and distances
a.      Configuration space
b.      Space of centered shapes
c.      Pre-shape space
d.     The Space Of Aligned Pre-shapes at CS=1
e.      Kendall’s shape space
f.       Tangent space
g.      Revisiting semilandmarks
Coordinate Systems and Ordination Methods
1.      Getting a basis for the tangent space
2.      Visualizing variation and interpreting patterns
a.      Within groups (Principal Components Analysis (PCA))
b.      Between groups (Canonical Variates Analysis, Between-group PCA, Finite-Mixture Analysis
Statistics (1)
1.      Introduction to statistics
2.      Statistical models
3.      Testing for statistical significance
4.      Measuring the size of an effect
Statistics (2): More complex designs
1.      Multifactorial models
2.      Interaction terms and phenotypic trajectory analysis
a.      Testing for differences in trajectory direction
b.      Testing for differences in trajectory length
3.      Mixed models
4.      Unbalanced designs
5.      Types of sums of squares
Phylogenetic Comparative Methods
1.      Phylogenetic Generalized Least Squares
2.      Visualizing shape variation in phylogenetic context
a.      Phylomorphospace
b.      Phylogenetic Principal components Analysis
3.      Modeling the dynamics of phenotypic Evolution
Geographic analyses of shape and phylogenetic disparity
1.      Metrics of shape and phylogenetic disparity
2.      Analyzing disparity in geographic context
a.      Getting geographic data
b.      Integrating geographic, shape and phylogenetic data
3.      Analyzing relationships between geographic, shape and phylogenetic data
 
When to include semilandmarks
How landmarks and semilandmarks
Digitizing landmarks
 
Shape Data
            Landmarks
            Semilandmarks
Getting from Landmarks to shape
 
Landmarks and Semilandmarks
 
Statistical theory of shape
Ordination Methods
Principal Components Analysis
Canonical Variates Analysis
Between-groups Principal Components Analysis
Relative eigenanalysis
Statistical Methods
Statistical Methods: Ordinary Least Squares
Statistical Methods: Generalized Least Squares
Modeling dynamics of Phenotypic Evolution

May can be considered the unofficial start of the summer in Istanbul, and with an average temperature of 20°C and precipitation 34 mm. May is great for city sightseeing and museum hopping, staying outdoors, and a good month for some popular festivals and events.

Reserve 01 – 08 May 2023 in your calendar, Come to Istanbul and join this workshop. For any inquiry about this wonderful workshop please contact mnaderi@ku.edu.tr

Registration:

Registration until the end of Feb. 2023 will be as follows:
Students fee: Turkish participants: 700 TL, Other countries: 250 Euro,
Academicians fee: Turkish participants: 900 TL, Other countries: 350 Euro

For Earlybird registration please contact the mentioned email address. After Feb. 2023, all fees will be increased by 15 percent. Accommodation and daily subsistence will be upon the participants, but we are negotiating with some hotels to get discounted fees for the workshop participants. In the workshop venue, there are various economic restaurants and students’ dining halls that can be used by the participants

An attendance certificate will be given to the participants upon their request

Registration Link: https://docs.google.com/forms/d/e/1FAIpQLSdz7u9g4hfwlTAaJbs5e7A2NcWCfDASns50t42KZEUStZWYpQ/viewform?usp=sf_link

https://forms.gle/PWRtNLRVa6mwmcP87

Coordinator: Associ. prof. Dr. Morteza Naderi