Molecular systematics Spring 2019

Molecular Systematics EEB 5350 Spring 2019

2 Credits- half-semester module

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

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

Instructor:
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu> Graduate Assistant: Diler Haji, TLS 479, Diler.Haji@uconn.edu, 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Reference books: 1) Paul Lewis's unpublished text; 2) The Phylogenetic Handbook (eds.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

https://docs.google.com/document/d/1IbrXonoc63Ihj_vFEdT_le9Jl1IwzQzBwDmRgEPZ-RA/edit

EEB 5350 shared Lab folder

https://drive.google.com/drive/u/1/folders/16IODJWzL_8CZ605j83zl99nADRvoyy2g

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.

Syllabus:

Schedule

Day	Topics	Reading/Assignment	Bibliography
Tuesday Mar 12	Lecture 1. Tree thinking. Optimality criteria, properties of trees. An introduction to looking at your data: How molecules evolve. Lecture notes: EEB 5350 Day 1 Begin How Molecules evolve 2019.ppt.pdf	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:How molecules evolve, model choice Readings 2019.pdf
Thursday Mar 14	Lecture 2. How molecules evolve (cont.), Unrealistic assumptions of JC69, How RNA and proteins evolve, ASRV and structure-function, Fitch and Margoliash sites not free to vary, importance of partitioning, models of evolution summary diagram. Lecture notes: EEB 5350 Day 2 How Molecules evolve (cont.) 2019.ppt.pdf	Read and summarize for class for Thursday March 28th. Sullivan and Swofford 2001 Sullivan and Swofford 2001.pdf	Among Site Rate Variation Readings: EEB 5350 ASRV readings 2019.pdf
Tuesday Mar 19 and Thursday March 21	Spring Break	Spring Break	Spring Break
Tuesday Mar 26	Lecture 3. Molecular systematics decadal time line, 1950-2020, History of ASRV, Weighting stems and loops (don’t do it), Correlated changes- should consider stems vs loops. Lecture notes: : EEB 5350 Day 3 ASRV. History. 2019.ppt.pdf	Read and summarize for class for Tuesday April 2nd, Bull et al. 1993. Classic paper from the Hillis Lab on partitioning and combing data, Bull et al. 1993.
Thursday 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. Lecture notes: : EEB 5350 Day 4 Effects of ASRV, combining data 2019.ppt.pdf	Read and Summarize for Class by Thursday April 4th Pagel and Meade 2004	Combining Data, Partitioning readings: :Combining Data, Partitioning, Comparing Trees Readings 2019.doc.pdf
Tuesday Apr 2	Lecture 5. Bull et al. 1993, Tests for combining data; testing whether the same tree underlies each data partition. Partitioning; Choosing among models for pre-assigned partitions. Lecture notes: EEB 5350 Day 5 Combining Data (cont) 2019.ppt.pdf	Read and Summarize for Class on Tuesday April 9th Kanier and Landfear 2015.
Thursday Apr 4	Lecture 6. Finish partitioning: Automated partition assignment and partition simplification; Model averaging and mixture models; Long Branches. 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. Lecture notes: :Day 6. Partitions, Mixtures, Long Branches 4Apr2019.pptx.pdf	Read and Summarize for Class on Thursday, April 11th. Gruenheit, Nicole, Peter J. Lockhart, Mike Steel, and William Martin. 2008.	Covarion, Heterotachy, Nucleotide Bias Readings:Covarion, Heterotachy, bias, site stripping readings 2019.pdf
Tueday Apr 09	Lecture 7. ALRV: heterotachy, covarion models;Among Lineage rate variation: Covarion evolution: codon models. Lecture notes: :Day 7) Covarion evolution, heterotachy 2019.pptx.pdf
Thursday 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. Lecture notes: :Day 8) Covarion evolution, heterotachy 2019.pdf	Read and Summarize for class, Tuesday April 16th. 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. (No need to summarize the derivation, just the introduction and the applications).
Tuesday Apr 16	Lecture 9. Site stripping. Problems associated with branch support. Lecture notes: :Day 9) Site Stripping, Branch support. Part 1. 2019.pdf		Nodal support = Branch Support Readings: :Branch support readings Sp 2019.pdf
Thursday Apr 18	Lecture 10: Nodal support continued. Spectral analysis, Internode certainty, SplitsTrees. Lecture notes: :Day 10) Support & Conflict 2019.pdf	Read and Summarize for class Tuesday April 23rd: Hickson et al. 1996 Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12s rRNA.
Tuesday Apr 23	Lecture 11: Secondary structure & alignment.	Secondary structure assignment::EEB 5350 secondary structure assignment Sp19.pdf and templates for Magicicada and Cow template:COW rRNA secondary strucutre.pdf Third Domain conserved motifs Template:rRNA 12S 3rd Domain Template.pdf	Structure and alignment readings:
Thursday Apr 25	Lecture 12: Guest lecture by Eric Gordon. Molecular Clocks, Types of dating studies, Fossil calibration of nodes Tip dating; Fossilized birth-death model, Examples.		Molecular clock readings:
Tuesday April 30	Lecture 13: Guest lecture by Eric Gordon. Complications to Phylogenetic Inference, 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	Species tree readings:
Thursday May 2	Lecture 14: Guest lecture by Diler Haji- Hybridization and phylogenetic tree reconstruction
Sunday Sunday May 5th	Lab notebook due. Take home final handed out.
Sunday 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