# Difference between revisions of "Molecular systematics Spring 2019"

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|Thursday <br> 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: :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/%20EEB%205350%20Day%204%20Effects%20of%20ASRV%2C%20combining%20data%202019.ppt.pdf}} 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 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Pagel_and_Meade._2004._Mixture_Model.pdf}} ||Combining Data, Partitioning, Species Trees readings: | |Thursday <br> 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: :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/%20EEB%205350%20Day%204%20Effects%20of%20ASRV%2C%20combining%20data%202019.ppt.pdf}} 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 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Pagel_and_Meade._2004._Mixture_Model.pdf}} ||Combining Data, Partitioning, Species Trees readings: | ||

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|Tuesday <br/> 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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/%20EEB%205350%20Day%205%20Combining%20Data%20%28cont%29%202019.ppt.pdf}} EEB 5350 Day 5 Combining Data (cont) 2019.ppt.pdf || Read and Summarize for Class on Tuesday April 9th Kanier and Landfear 2015. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Kainer_and_Landfear._2015._Effects_of_Partitioning_on_Phylogen.pdf}} || | |Tuesday <br/> 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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/%20EEB%205350%20Day%205%20Combining%20Data%20%28cont%29%202019.ppt.pdf}} EEB 5350 Day 5 Combining Data (cont) 2019.ppt.pdf || Read and Summarize for Class on Tuesday April 9th Kanier and Landfear 2015. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Kainer_and_Landfear._2015._Effects_of_Partitioning_on_Phylogen.pdf}} || | ||

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− | |Thursday <br> 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: :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Day%206.%20Partitions%2C%20Mixtures%2C%20Long%20Branches%204Apr2019.pptx.pdf}}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. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Gruenheit_et_al._(Lockhart)_2008._Covarion_under_changing_proportions_var_sites.pdf}}|| Covarion, Heterotachy, Nucleotide Bias Readings | + | |Thursday <br> 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: :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Day%206.%20Partitions%2C%20Mixtures%2C%20Long%20Branches%204Apr2019.pptx.pdf}}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. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Gruenheit_et_al._(Lockhart)_2008._Covarion_under_changing_proportions_var_sites.pdf}}|| Covarion, Heterotachy, Nucleotide Bias Readings |

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|Tueday <br/> Apr 09 ||Lecture 7. ALRV: heterotachy, covarion models;Among Lineage rate variation: Covarion evolution: codon models. Lecture notes: :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Day%207%29%20Covarion%20evolution%2C%20heterotachy%202019.pptx.pdf}}Day 7) Covarion evolution, heterotachy 2019.pptx.pdf || || | |Tueday <br/> Apr 09 ||Lecture 7. ALRV: heterotachy, covarion models;Among Lineage rate variation: Covarion evolution: codon models. Lecture notes: :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Day%207%29%20Covarion%20evolution%2C%20heterotachy%202019.pptx.pdf}}Day 7) Covarion evolution, heterotachy 2019.pptx.pdf || || |

## Revision as of 14:04, 20 April 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**