Advanced Molecular Systematics

General Introduction to Molecular Systematics: Evolutionary theory and Tree of Life, Tree thinking, Convergent Vs. Divergent evolution, Homologous and Analogous traits, Character states: Synapomorphy, Symplesiomorphy and Homoplasy, Types of Clades: Monophyly, Paraphyly and Polyphyly, Orthologous Vs. Paralogous Sequences, Phenetics Vs. Cladistics, DNA Barcoding, and Major Loci Used in Molecular Systematics.

1. BAST, F. 2015. Tutorial on Phylogenetic Inference Part-1. Resonance 20 (4) 360-367 PDF
2. BAST, F. 2015. Tutorial on Phylogenetic Inference Part-2. Resonance 20 (5) 445-457 PDF
3. Introduction to Molecular Systematics PPT

Videos

1. Phenetics vs Cladistics
2. Orthologues vs. Paralogues
3. Types of evolution: Divergent vs Convergent vs. Parallel
4. Homoplasy vs. Apomorphy vs. Plesiomorphy
5. DNA Taxonomy

Molecular Evolution: Neutral theory of molecular evolution, Models of nucleotide substitution, p-distance, Poisson correction, Jukes-Cantor 69, Kimura-2-Parameter, Felsenstein 81, Hasegawa, Kishino and Yano 85, General Time Reversible (GTR), Rate heterogeneity (G), Rate Invariability (I), Model selection, Hierarchical Likelihood Ratio Test (hLRT), and locus selection.

1. Molecular evolution and Substitution models PPT
2. DAMBE
3. Drosophila ADH alignment
4. K Tamura, D Peterson, N Peterson, G Stecher… - Molecular biology and …, 2011
5. Assessing substitution saturation with DAMBE
6. X Xia, P Lemey - The Phylogenetic Handbook, 2009 - dambe.bio.uottawa.ca

Sequence Analysis: Basics of DNA Sequencing, Base calling, Sequence Assembly and Contig construction, Consensus Sequences, Multiple Sequence Alignment, Concatenation of datasets and construction of supermatrix, Sequence annotation and deposition in Genbank, DNA Flatfiles, rDNA Secondary structure construction, and in-silico translation. NCBI BLAST and its variants, Vienna RNA Package and RNAalifold, Primer design using primer BLAST, CodonCodeAligner, Geneious, and MEGA.

1. Base calling PPT
2. Alignment PPT
3. Alignment Chapter of the Phylo Handbook
4. Zufall-Current protocols
5. Vienna RNA Webserver

Videos

1. DNA Barcoding: Primer Design, Sequencing and Contig Assembly
2. Base Call Auditing and BLAST
3. Multiple Sequence Alignment and BLAST
4. Annotation and Genbank submission

Computational Phylogenetics: Theoretical framework of phylogenetics, Distance Vs. Discrete methods, Minimum Evolution, UPGMA, Neighbor Joining, Maximum Likelihood, Maximum Parsimony, Bayesian Inference, reconstruction of phylogeny from morphological data, Gene Tree Vs. Species tree, and lineage sorting.

1. Understanding trees
2. Tree thinking
3. Methods of PI 1
4. Methods of PI 2
5. Roderic Page: Introduction to Computational Phylogenetics
6. Whelan Goldman Review of Molecular Phylogenetics
7. Phylogeny for the Faint Heart

Taxonomy: Morphometry using ImageJ, Specimens and Curation, Herbarium Voucher preparation, Typification, Geographical sampling design, Taxonomic literature survey, Species description, Taxonomic publication and codes, Rules of nomenclature

Suggested readings:

1. Describing Species, Judith Winston, Columbia University Press,978-0231068253
2. Phylogenetic Analysis of Morphological Data (Smithsonian Series in Comparative Evolutionary Biology), John J. Wiens. Smithsonian Books, 978-1560988168
3. Phylogenetics: Theory and Practice of Phylogenetic Systematics, E. O. Wiley & Bruce S. Lieberman, Wiley-Blackwell, 978-0470905968
4. Phylogenetic Trees Made Easy: A How-To Manual, Fourth Edition, Barry G. Hall, Sinauer Associates, Inc. 978-0878936069
5. Inferring Phylogenies, Joseph Felsenstein, Sinauer Associates, 978-0878931774
6. Phylogenetics (Oxford Lecture Series in Mathematics and Its Applications), Charles Semple & Mike Steel, Oxford University Press, 978-0198509424
7. Plant Systematics: A Phylogenetic Approach, Walter S. Judd, Christopher S. Campbell, Elizabeth A. Kellog, Peter F. Stevens & Michael J. Donoghue, Sinauer Associates, 978-0878934072
8. Bast, F (2013) Sequence Similarity Search, Multiple Sequence Alignment, Model Selection, Distance Matrix and Phylogeny Reconstruction. Nature Protocol Exchange. Nature Publishing Group. doi: 10.1038/protex.2013.065 Accessible at: http://www.nature.com/protocolexchange/protocols/2740
9. Bast, F (2015) Tutorial on Phylogenetic Inference Part-1. Resonance 20 (4) 360-367
10. Bast, F (2015) Tutorial on Phylogenetic Inference Part-2. Resonance 20 (5) 445-457
11. Tree Thinking 2015) An Introduction to Phylogenetic Biology. David Baum and Stacey Smith. Roberts and Company Publishers
12. The Phylogenetic Handbook