Molecular systematics Spring 2018

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2 Credits- half-semester module, 19 March-29 April 2016

Lectures: M & W 11:00-12:15 Bio-Pharm 3rd floor conference room.

M 2:30-4:30; Th 2:00-4:00 (Each lab session starts in 3rd floor conference room then moves to BioPharm 325).

Chris Simon, Biopharm 305D, 6-4640, <> Graduate Assistant: Katie Taylor, TLS 479,, 6-5479

Readings: will be posted as PDF’s.

Optional reference books: 1) Paul Lewis's unpublished text; 2) The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); 4) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 5) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference.

Lecture Goals: The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts.

Laboratory Goals: Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones.

Short Assignments:

1) For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week).

2) The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.

3) There will be a short "secondary structure alignment assignment" during the semester.

4) Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus.

5) For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Ursula will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.

Final Exam: The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.

Final Due Dates: Sunday 1st May: Lab project and notebook due. Take Home FINAL EXAM handed out. Sunday 8th May: Take home final due.

Syllabus: Pdficon small.gif


Day Topics Reading/Assignment Lab
Mar 21
Lecture 1. Pdficon small.gifAn introduction to looking at your data: How molecules evolve.
Reading too big to post, sent out by Chris. How Molecules Evolve BibliographyPdficon small.gif Data checks at every step. Mechanics of Lab; Start Nucleospin kit extractions Pdficon small.gif.
Wednesday Mar 23 Lecture 2. ASRV, models of evoltion, and the history of molecular systematics Pdficon small.gif
Kjer & Honeycutt Pdficon small.gif, Soubrier et al. Pdficon small.gif, Sullivan & Swofford Pdficon small.gif, ASRV BibliographyPdficon small.gif Mini-presentation: Explanation of class Tettigades project Pdficon small.gif, DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Ursula Pdficon small.gif.

LAB: Plant extraction Pdficon small.gif. Finish Nucleospin extractions Pdficon small.gif

Mar 28
Lecture 3. History of ASRV (cont.) 1980-present. Weighting stems and loops and correlated changes, calculating the probability of substitution for sites, invariant sites models & negative binominal models, the two components of evolutionary trees, problems associated combining data, multiple gene histories for single taxa, history of combining data Pdficon small.gif
Bull et al 1993 Pdficon small.gif, Pagel and Mead 2004 Pdficon small.gif, Combining Data & Partitioning Bibliography Pdficon small.gif Read these few pages before lab: the introduction to the primer compilation at the end of Simon et al. 1994, in addition, study the primer comparisons among animals for the COI and COII genes in that same primer compilation. In addition, read the introduction to the primer compilation that is at the beginning of the supplemental information in Simon et al. 2006, Attached here: Pdficon small.gif
Mini-presentation: Primer Design- Primer exercise introduction; the beginning of Geneious. Ursula Pdficon small.gif

LAB: Run extractions on gels. Pdficon small.gif Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. Pdficon small.gif Pdficon small.gif
Homework: Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences. Homework due April 13th.

Wednesday Mar 30 Lecture 4. History of combining data (cont.), Lack of agreement among character subsets, Random error vs systematic error, Assumptions of combined analysis, Bull et al. vs. Chippindale & Wiens; “Homothermia”, comparing trees Pdficon small.gif Combining Data & Partitioning Bibliography Pdficon small.gif Mini-presentation: The Polymerase Chain Reaction- how it works & optimizing reactions. Kate Pdficon small.gif

LAB: Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel. Pdficon small.gif

Apr 4
Lecture 5. Tests for combining data; testing whether the same tree underlies each data partition (tests of topology), partitioning, choosing among models for pre-assigned partitions, automated partition assignment and partition simplification, model averaging and mixture models
Pdficon small.gif
Combining Data & Partitioning Bibliography Pdficon small.gif Sullivan and Joyce 2005. Pdficon small.gif Frandsen et al 2015 Pdficon small.gif Kainer and Landfear 2015. Pdficon small.gif (Due Mon April 11) Mini-presentation: Different methods for cleaning PCR products for sequencing reactions.Ursula. Pdficon small.gif

LAB: Purify PCR products and set-up sequencing reactions. Pdficon small.gif

Wednesday Apr 6 Lecture 6. Mixtures of Trees and Species Trees. Pdficon small.gif Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy Pdficon small.gif Readings: Long Branches, Taxon Sampling, Big Trees Pdficon small.gif Readings for: Species Trees. Lecture 6 (part 1.)Pdficon small.gif
Mini-presentation: How Big Dye works, chromatograms, and troubleshooting. Kevin Pdficon small.gif

LAB: Sephadex and put samples on the ABI. Pdficon small.gif Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank

Apr 11
Lecture 7. Big Trees, Long Branches, & Simulations Pdficon small.gif Swofford et al. 2001 Pdficon small.gif Brandley et al. 2011 Pdficon small.gif Mini-presentation: - Cloning DNA. Alison Pdficon small.gif

LAB: Cloning- Long Lab.Pdficon small.gif Pdficon small.gif

Wednesday Apr 13 Lecture 8. Problems associated with nodal support Pdficon small.gif Nodal Support Bibliography Pdficon small.gif Salichos and Rokas 2013 Pdficon small.gif Betancur et al. 2014 Pdficon small.gif (Comments on Salichos and Rokas 2013) Pdficon small.gif Mini-presentation: Depositing sequences in GenBank Shareef

LAB: RNA isolation- TRIzol. Pdficon small.gif Pdficon small.gif

Apr 18
Lecture 9. ALRV: heterotachy, covarion models;Among Lineage rate variation: Covarion evolution: codon models Pdficon small.gif Lockhart et al. 2006. Heterotachy and trees Pdficon small.gif, Lockhart and Steel 2005. A tale of two processes Pdficon small.gif, Gruenheit et al. (Lockhart) 2008. Covarion under changing proportions var sites Pdficon small.gif Mini-presentation: Ancient DNA & Museum DNA protocols Kate Pdficon small.gif

LAB: PCR clones.Pdficon small.gif Pdficon small.gif

Wednesday Apr 20 Lecture 10: Heterotachous evolution continued, Covarion Models, The Case for Stationary Genes, Mixture of Branch Lengths for building trees and studying selection. Covarion Mixture Models.Pdficon small.gif Mini-presentation: Numts Pdficon small.gif

LAB: Sephadex and put clone samples on ABI.

Apr 25
Lecture 11: Secondary structure & alignment. Pdficon small.gif Secondary structure & alignment readings Pdficon small.gif
Cladistics editorial Pdficon small.gif
rRNA secondary structure assignment Pdficon small.gif
rRNA template Pdficon small.gif
Hickson et al 1996 (for reference only - no need to summarize) Pdficon small.gif
Cow rRNA secondary structure example Pdficon small.gif
Mini-presentation: RNA: extraction and what it can be used for

LAB: Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences.

Wednesday Apr 27 Lecture 12: Combining nuclear and organelle data for evolutionary insights on specition and hybridization (Dropbox link emailed).
Additional lecture material on Molecular Clocks Pdficon small.gif
Additional lecture material on comparing trees Pdficon small.gif
Ho, 2014. Changing molecular evolutionary clock Pdficon small.gif
Molecular Clock readings Pdficon small.gif
Guest Lecture: Ursula, Next Gen sequencing applications, Transcriptomics, Rad Tags.(Dropbox link emailed)
May 1
Lab notebook due. Take home final handed out. Nothing new No Lab
May 8
Final Exam due, emailed to Ursula Nothing new You are so done with this class

Final Exam Files
Final Exam Instuctions Pdficon small.gif, Shull et al Manuscript Pdficon small.gif, Shull et al figures Pdficon small.gif, Published Shul et al 2001 Pdficon small.gif.