File Name: techniques in molecular systematics and evolution .zip
- Next-generation Molecular Systematics and Evolution: insights into Medicago
- Molecular Systematics
- Molecular systematics: A synthesis of the common methods and the state of knowledge
Molecular evolution is the process of change in the sequence composition of cellular molecules such as DNA , RNA , and proteins across generations. The field of molecular evolution uses principles of evolutionary biology and population genetics to explain patterns in these changes.
Next-generation Molecular Systematics and Evolution: insights into Medicago. Sousa, Filipe. Patterns of phylogenetic incongruence in Medicago L.
Next-generation Molecular Systematics and Evolution: insights into Medicago
Labs: Tu Each lab session starts in 3rd floor conference room then moves to BioPharm Haji uconn. 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. 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. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.
Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. 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. Sunday 12th May: Take home final due. Jump to: navigation , search. Tree thinking. Optimality criteria, properties of trees. An introduction to looking at your data: How molecules evolve. Too large to post, will be emailed to you. How molecules evolve cont. Sullivan and Swofford Sullivan and Swofford Classic paper from the Hillis Lab on partitioning and combing data, Bull et al. Thursday Mar 28 Lecture 4.
That is the question. Lack of agreement among character subsets, Random error vs systematic error, Assumptions of combined analysis. Bull et al. Partitioning; Choosing among models for pre-assigned partitions. 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?
Accuracy of different phylogenetic methods; Swofford et al. Bias in Phylogeny estimation due to long branches: Parsimony vs. Partitions, Mixtures, Long Branches 4Apr Gruenheit, Nicole, Peter J. Lockhart, Mike Steel, and William Martin.
Covarion Mixture Models. Novel information theory-based measures for quantifying incongruence among phylogenetic trees. Molecular Biology and Evolution No need to summarize the derivation, just the introduction and the applications.
Tuesday Apr 16 Lecture 9. Site stripping. Problems associated with branch support. Part 1. Spectral analysis, Internode certainty, SplitsTrees. Tuesday Apr 23 Lecture 11 Part 1. Tests of Topology. Comparing Trees; Tests of Topoogy Molecular Clocks, Types of dating studies, Fossil calibration of nodes Tip dating; Fossilized birth-death model, Examples. Lecture: Read and summarize for class Tuesday April 30th Maddison Gene trees in species trees.
Take home final handed out. Category : EEB Courses. Navigation menu Personal tools Log in. Namespaces Page Discussion. Views Read View source View history. This page was last modified on 4 May , at Lecture 1. Read and summarize for class Thursday March 14th, Simon et al. Lecture 2. Read and summarize for class for Thursday March 28th. Lecture 3. Read and summarize for class for Tuesday April 2nd, Bull et al. Lecture 4. Lecture 5. Lecture 6. Read and Summarize for Class on Thursday, April 11th.
Lecture 7. Lecture 8. Read and Summarize for class, Tuesday April 16th. Lecture 9. Lecture Nodal support continued. Read and Summarize for class Tuesday April 23rd: Hickson et al.
Lecture 11 Part 1. Secondary structure assignment:: EEB secondary structure assignment Sp Lecture Guest lecture by Eric Gordon. Read and summarize for class Tuesday April 30th Maddison Molecular clock readings: Brown and Smith Brown on Bayesian methods. Species tree and hybridization readings: Liu et al. 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.
Labs: Tu Each lab session starts in 3rd floor conference room then moves to BioPharm Haji uconn. 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.
PDF | The amount of information that can be obtained by using molecular techniques in evolution, systematics and ecology has increased.
Molecular systematics: A synthesis of the common methods and the state of knowledge
Instructor: Derek S. The course outline is available here. However, the PDF of the course outline does not have the assigned readings or other notes that are listed below - so consider this webpage to be the definitive outline. Note: I will try to post PDFs of lecture notes before lecture so you can print them out and bring them to lecture.
Metrics details. The comparative and evolutionary analysis of molecular data has allowed researchers to tackle biological questions that have long remained unresolved. The evolution of DNA and amino acid sequences can now be modeled accurately enough that the information conveyed can be used to reconstruct the past. In general, molecular systematics provides a powerful statistical framework for hypothesis testing and the estimation of evolutionary processes, including the estimation of divergence times among taxa. The field of molecular systematics has experienced a revolution in recent years, and, although there are still methodological problems and pitfalls, it has become an essential tool for the study of evolutionary patterns and processes at different levels of biological organization. This review aims to present a brief synthesis of the approaches and methodologies that are most widely used in the field of molecular systematics today, as well as indications of future trends and state-of-the-art approaches. Page, R.
Sneddon, S. Hunter, M. Settles, Z. Kronenberg, J. Demboski, J.
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