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Optional reference books: 1) Paul Lewis's unpublished text; 2) The Phylogenetic Handbook (eds.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 and we will pursue a class project.

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.



Day Topics Reading/Assignment/Bibliography Lab
Mar 19
Lecture 1. An introduction to looking at your data: How molecules evolve.

Pdficon small.gif

Read Simon et al. 1994. 651-670 (up to the section that starts on the bottom of the second column). Too large to post, will be emailed to you. LAB: Data checks at every step. Mechanics of Lab; Nucleospin extractions. Pdficon small.gif
Wednesday Mar 21 Lecture 2. ASRV, models of evolution, and the history of molecular systematics
Mini-presentation: DNA extraction (Katie)
LAB: Nucleospin extractions continued and Phenol-chloroform plant extractions
Mar 26
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 Mini-presentation: Primer Design ( )
LAB: Making gels, running extractions on gels, DNA extraction quantification, Troubleshooting and improving “universal” primers for COI and COII

Wednesday Mar 28 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 Mini-presentation:The polymerase chain reaction ( )
LAB: Setting-up PCR reactions
Apr 2
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 Mini-presentation: Different methods for cleaning PCR products for sequencing reactions ( )
LAB: Running PCR products on gels, purifying PCR products with ExoSAP-IT, and setting-up sequencing reactions
Wednesday Apr 4 Lecture 6. Mixtures of Trees and Species Trees. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy
Mini-presentation: Numts ( )
LAB: Cleaning and putting samples on the ABI; Looking at sequences using Geneious
Apr 09
Lecture 7. Big Trees, Long Branches, & Simulations Mini-presentation: How Big Dye works, chromatograms, and troubleshooting ( )
LAB: Viewing and interpreting sequencing results, setting up long range PCR
Wednesday Apr 11 Lecture 8. Problems associated with nodal support
Mini-presentation: : Depositing sequences in GenBank ( )
LAB: Running long rage PCR gel, cleaning long range PRC product, setting up 2nd short PCR
Apr 16
Lecture 9. ALRV: heterotachy, covarion models;Among Lineage rate variation: Covarion evolution: codon models Mini-presentation: Ancient DNA & Museum DNA protocols ( )
LAB: Running short rage PCR gel, cleaning PRC product, setting up sequencing reaction
Wednesday Apr 18 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. Mini-presentation: RNA: extraction and what it can be used for ( )
LAB: Cleaning and putting samples on the ABI, and starting RNA isolation with Trizol
Apr 23
Lecture 11: Secondary structure & alignment. Mini-presentation: Gel electrophoresis ( )
LAB: Finish RNA isolation, Compare sequencing results from long range and typical PCR
Wednesday Apr 25 Lecture 12: Combining nuclear and organelle data for evolutionary insights on speciation and hybridization Mini-presentation:
Sunday April 29th
Lab notebook due. Take home final handed out.
May 6th
Final Exam due, emailed to Katie who will transmit the anonymous papers to Chris along with a list of pseudonyms

Final Exam Files