Molecular Phylogenetics Workshop

Praveen Karanth lab, IISc Bangalore

Molecular phylogenetics workshop

August 1-5, 2016

Seminar hall, Centre for Ecological Sciences, New Biology building, IISc

Day 1 (August 1, Monday)

9:30 AM -12:30 PM

ORigin of tree building

Introduction, Taxonomy vs. Systematics
Schools of Systematics: Cladistics, Phenetic, Evolutionary systematics
Phylogenetic terminologies -monophyly, polyphyly, rooting trees Molecular vs. morphological data

2:00-2:30 PM

Testing the limits of phylogenomics with the bird tree of life: Exploring the impacts of taxon sampling and data type

Invited talk by Sushma Reddy, Loyola University, Chicago

2:30-4:00 PM

Methods of tree building using DNA sequence data-I

Distance approach: NJ, UPGMA, Least square, Minimum evolution Estimating pairwise genetic distance and nucleotide substitution models

4:00-6:00 PM

Computer lab:

Installation of programs, working with the program MEGA (TAChinta, Maitreya)

Day 2 (August 2, Tuesday)

9:30 AM -11:30 AM

Methods of tree building using DNA sequence data-II

Character state approach (discrete methods): Parsimony, Maximum likelihood

11:30-12:30 PM

Plant phylogenetics- from morphology to molecules

Invited talk by Vinita Gowda, IISER, Bhopal

2:00-3:00 PM

Methods of tree building using DNA sequence data-II

Character state approach (discrete methods): Bayesian approach

3:30-5:30/6:00 PM

Computer lab:

Working with the programs MEGA (Chinta, Maitreya), PAUP Demo (Roy, Kunal), Partitionfinder (Roy, Maitreya)

Day 3 (August 3, Wednesday)

9:30 AM -11:30 AM

Comparing different methods of tree building

Clustering (algorithmic) vs. search (optimality criteria) methods Character state approach (discrete methods) vs. distance approach Heuristic searches Statistical tests Bootstrap (BT), Likelihood ratio test and applications Test for monophyly (parametic BT, S-H test)

11:30 AM -12:30 PM

Morphological Evolution, Diversification and Speciation: A Phylogenetic Perspective

Invited talk by KrushnameghKunte, NCBS, Bangalore

2:00 -3:00 PM

Phylogenetic Diversity: methods and applications

Divya B. CES, IISc

3:30/4:00-6:00 PM

Computer lab:

Working with the programs RAxML and MrBayes (TA: Roy and Aparna)

Day 4 (August 4, Thursday)

9:30 AM -11:30 AM

Molecular markers: powers and pitfalls

Homologous sequences (orthologous vs. paralogous) Nuclear copies of mtDNA genes Gene tree vs. species tree Different types of molecular markers (Plants and Animals) What gene/region to select for the question to be addressed Nuclear vs. mtDNA vs. Y-chromosome markers Applications of molecular phylogenetics Molecular phylogenetics: frequently asked questions

11:30 AM -12:00 PM

Plant molecular markers and Insights into the Phylogeny and Biogeography of the mint genus Leucas (Lamiaceae)

Invited talk by Sunojkumar P. University of Calicut

12:00-12.30 PM

Tools to study microbial phylogenetic diversity

Invited talk by DevanitaGhosh, CEaS, IISc

2:00-3:00 PM

Introduction to biogeography

Praveen Karanth CES, IISc

3:00-4:00 PM

Species delimitation in Sitana complex

V. Deepak CES, IISc

4:00-6:00 PM

Computer lab:

Working with the programs S-DIVA, Lagrange (Roy)

Day 5 (August 5, Friday)

9:30 AM -10:30 AM

Molecular Dating

Molecular clock hypothesis, strict molecular clock, relaxed molecular clocks Species trees Multispecies coalescent models

10:30-11:30 AM

Evolution of Avian malaria

Farah Ishtiaq

11:30 AM -12:30 PM

Computer lab:

Working with the programs BEAST and *BEAST SVDquartet(TA: Deepak, Kunal)

2:00-3:00 PM

Phylogenetic approach to character evolution and ancestral state reconstruction

Jahnavi Joshi National Centre for Biological Sciences, Bangalore

3:30-6:00 PM

Computer lab:

Working with the program Mesquite (TA: Aparna and Jahnavi)

Extra time for discussing topics covered thus far (if needed); discussion on individual projects