Molecular systematics Spring 2019

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Molecular Systematics EEB 5350 Spring 2019

2 Credits- half-semester module

Lectures: Tu & Th 2:00-3:15 Bio-Pharm 3rd floor conference room.

Tu 3:30-5:30 (Each lab session starts in 3rd floor conference room then moves to BioPharm 325).

Chris Simon, Biopharm 305D, 6-4640, <> Graduate Assistant: Diler Haji, TLS 479,, 6-3947

Readings: will be posted as PDF’s.

Reference books: 1) Paul Lewis's unpublished text; 2) The Phylogenetic Handbook (eds.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.

SEE: Molecular Systematics Google Docs

EEB 5350 Lab Syllabus

EEB 5350 shared Lab folder

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 May 5th: Lab project and notebook due. Take Home FINAL EXAM handed out. Sunday 12th May: Take home final due.



Day Topics Reading/Assignment Bibliography
Mar 12
Lecture 1. An introduction to looking at your data: How molecules evolve. Read and summarize for class Thursday March 14th, 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. How Molecules Evolve & Model Choice Bibliography:Pdficon small.gifHow molecules evolve, model choice Readings 2019.pdf
Mar 14
Lecture 2.ASRV, models of evolution, and the history of molecular systematics. Calculating the probability of substitution for sites, Fitch and Margoliash invariant sites models & negative binominal models,Weighting stems and loops. Read and summarize for class for Tuesday March 26th. Sullivan and Swofford 2001 Among Site Rate Variation Readings: Pdficon small.gif EEB 5350 ASRV readings 2019.pdf
Mar 19 and Thursday March 21
Spring Break Spring Break Spring Break
Mar 26
Lecture 3. Correlated changes- should consider stems vs loops; How much to down weight and how to partition when weighting is problematic; Different methods for calculating & accommodating ASRV; For probability of substitution, using a tree is more effective than an alignment; The interaction of tree shape and ASRV; The two components of evolutionary trees; (equal weights aka evenly weighted; misnomer “unweighted” parsimony); Effects of Ignoring ASRV Read and summarize for class for Thursday March 28th, Bull et al. 1993. Classic paper from the Hillis Lab on partitioning and combing data, Bull et al. 1993. Pdficon small.gif
Mar 28
Lecture 4. History of “combining data”, As many kinds of data as possible, non-specificity hypothesis, To combine or not to combine? That is the question. Lack of agreement among character subsets, Random error vs systematic error, Assumptions of combined analysis, Bull et al. vs. Chippindale & Wiens; ASRV &ALRV, Homothermia Read and Summarize for Class by Tuesday April 2nd Pagel and Meade 2004 Pdficon small.gif Combining Data, Partitioning, Species Trees readings
Apr 2
Lecture 5.Tests for combining data; testing whether the same tree underlies each data partition. Partitioning; Choosing among models for pre-assigned partitions; Automated partition assignment and partition simplification; Model averaging and mixture models Read and Summarize for Class on Thursday, April 4th Kanier and Landfear 2015. Pdficon small.gif
Apr 4
Lecture 6. What is a long branch?; The meaning of “basal”; Node density artifacts; Felsenstein 1978- when will parsimony be positively misleading?; Penny & Hendy 1989- long branch attraction; Huelsenbeck & Hillis simulations to explore tree space. Accuracy of different phylogenetic methods; Swofford et al. 2001. Bias in Phylogeny estimation due to long branches: Parsimony vs. likelihood in tree space; Remaining uncommitted Read and Summarize for Class on Tuesday, April 9th. Sullivan et al. 2001 Covarion, Heterotachy, Nucleotide Bias Readings
Apr 09
Lecture 7. ALRV: heterotachy, covarion models;Among Lineage rate variation: Covarion evolution: codon models Read and summarize for Class (Due Monday, April 16) Gruenheit, Nicole, Peter J. Lockhart, Mike Steel, and William Martin. 2008. Pdficon small.gif
Apr 11
Lecture 8. Heterotachous evolution continued, Covarion Models, The Case for Stationary Genes, Mixture of Branch Lengths for building trees and studying selection. Covarion Mixture Models.
Apr 16
Lecture 9. Problems associated with nodal support Read and Summarize for Next week.... Monday 23 April 18. Salichos L, Stamatakis A, Rokas A. 2014. Novel information theory-based measures for quantifying incongruence among phylogenetic trees. Molecular Biology and Evolution 31:1261-1271.Pdficon small.gif (No need to summarize the derivation, just the introduction and the applications). Nodal Support Readings
Thursday Apr 18 Lecture 10: Nodal support continued. Spectral analysis, Internode certainty, SplitsTrees. Misc. topics: Big Trees; more taxa or more sequences.
Apr 23
Lecture 11: Secondary structure & alignment. Read and Summarize for class: Hickson et al. 1996 Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12s rRNA. Pdficon small.gif Secondary structure assignment Pdficon small.gif and templates for Magicicada Pdficon small.gif and conserved motif template Pdficon small.gif. Structure and alignment readings:
Thursday Apr 25 Lecture 12: Molecular Clocks Molecular clock readings:
April 30
Lecture 13: Complications to Phylogenetic Inference (Guest lecture by Eric Gordon). Incomplete lineage sorting; Rationale for failure of concatenation in certain situations; Coalescence-based methods (ASTRAL *BEAST, SVDQuartets); Problems (including a little bit about combinability of data--also address in lecture 5)"Concatalescence"; Reticulate evolution- Various causes, Summary of how some methods work, Examples, Problems
May 2
Lecture 14: Applications of molecular phylogenetic datasets beyond a traditional phylogeny (Guest lecture by Eric Gordon). Dating. Types of dating studies (Brief mention of) molecular clocks (if already covered). Fossil calibration of nodes Tip dating; Fossilized birth-death model, Examples. Possible systemic problems in dating studies, Macroevolution genomic studies, Investigation of Pseudogenes, Gene family diversification (CAFE, COUNT), Investigating selection (PAML); Examples, Species delimitation methods, Methodology, Tools and Examples, Problems, Brief mention of some other population level methods, Brief mentions of ASR, correlated trait evolution and diversification and biogeographic methods.
Sunday May 5th
Lab notebook due. Take home final handed out.
May 12th
Final Exam due, emailed to Associate Editor Diler who will transmit the anonymous papers to Editor-in-Chief Chris along with a list of pseudonyms; keep your pseudonym secret because answers will be posted with pseudonyms credited