Biol375 2016: Difference between revisions
imported>Weigang |
imported>Weigang |
||
Line 110: | Line 110: | ||
===Part 2. Trait & Sequence Evolution=== | ===Part 2. Trait & Sequence Evolution=== | ||
* 9/22 (Th). Traits & trait matrix | |||
{| class="wikitable sortable mw-collapsible" | |||
|- style="background-color:lightsteelblue;" | |||
! Assignment #4 (5 pts; Due Monday, 9/26) | |||
|- style="background-color:white;" | |||
| | |||
# Download or Copy/Paste [http://media.hhmi.org/biointeractive/activities/lizard/Anolis-DNA-sequences.txt the lizard DNA sequences] to your own computer and save the file as "lizard.txt" | |||
# Align the DNA sequences [http://www.phylogeny.fr/one_task.cgi?task_type=muscle using this website] and save the aligned DNA file ("Output->Alignment in Fasta format") as "lizard-aligned.txt" (No need to print or submit the above two DNA sequence files; save them for next week's assignment) | |||
# Based on [http://media.hhmi.org/biointeractive/activities/lizard/Lizard-Cards-Color.pdf the lizard card], construct a character-state matrix for all lizard species. For each species, list its character state for each of the following two characters (as columns): (1) Geographic origin, and (2) Habitat. Re-watch [http://media.hhmi.org/biointeractive/films/OriginSpecies-Lizards.html the video] may help this assignment. '''Hint''': use Excel & hand in a printout of your Excel sheet. | |||
|} | |||
* 9/26 (M). Homoplasy & consistency | |||
* 9/29 (Th). Parsimony reconstruction (Chapter 5). In-Class Exercise 4 | |||
{| class="wikitable sortable mw-collapsible" | |||
|- style="background-color:lightsteelblue;" | |||
! Assignment #5 (10 pts; Due 10/) | |||
|- style="background-color:white;" | |||
| | |||
# Use the DNA alignment from the last assignment to build a tree of ''Anolis'' species. | |||
## Set working directory to where you have downloaded the DNA alignment file: e.g., setwd("/Users/ann/Document") | |||
## Load library: library(ape) | |||
## Read alignment: aln.an = read.FASTA("lizard-aligned.txt") | |||
## Calculate pairwise distance matrix: dist.an = dist.dna(aln.an) | |||
## Estimate tree: tr.an = bionj(dist.an) | |||
## Reroot tree: tr.root = root(tr.an, outgroup = "Leiocephalus_barahonensis", resolve.root = T) | |||
## Save tree: write.tree(tr.root, "rerooted.dnd") | |||
## Read re-rooted tree: tr.2 = read.tree("rerooted.dnd") | |||
## Download [http://diverge.hunter.cuny.edu/w/images/2/21/Pheno.txt the phenotype file] and save it as "pheno.txt" | |||
## Read phenotype with the command: ph = read.table("pheno.txt", row.names = 1) | |||
## Assign column names: colnames(ph) = c("hab", "geo", "hab_id", "geo_id") | |||
## Plot re-rooted tree: plot(tr.2, x.lim = 1, y.lim = 18, show.tip.label = F) | |||
## Add species names: text(rep(0.2,17), 1:17, tr.2$tip.label, pos=4, font = 3) | |||
## Match species names to tree order: ord = match(tr.2$tip.label, rownames(ph)) | |||
## Add a column: text(rep(0.5,17), 1:17, ph[ord,1], pos=4, col = ph[ord,3]) | |||
## Add another column: text(rep(0.7,17), 1:17, ph[ord,2], pos=4, col = ph[ord,4]) | |||
## Add a heading: text(0.5, 18, "Ecomorph", font = 2, pos=4) | |||
## Add another heading: text(0.7, 18, "Geography", font = 2, pos=4) | |||
## Export & print two copies (in color, preferably) | |||
# On one copy, infer locations (i.e., islands) of all internal nodes using parsimony | |||
# On another copy, infer habitats (i.e., ecomorphs) of all ancestors | |||
# Based on your reconstructed trait evolution, count the number of character-state changes and calculate consistency index for each trait. | |||
# Compare the two consistency indices & explain why the molecular phylogeny supports convergent adaptive evolution to habitats. | |||
|} | |||
* 10/3 (No class) | |||
* 10/6 (TH). Genome & gene structure (Chapter 3) | |||
* <font color="gray">10/12 (M). No Class</font> | |||
* 10/10 (M). Genome and gene evolution. | |||
* 10/13 (Th). Review & Practices. | |||
* 10/17 (M). '''Midterm Exam 2''' | |||
===Part 3. Tree Algorithms=== | ===Part 3. Tree Algorithms=== | ||
===Part 4. Population Genetics === | ===Part 4. Population Genetics === |
Revision as of 16:01, 17 September 2016
Course Description
Molecular evolution is the study of the change of DNA and protein sequences through time. Theories and techniques of molecular evolution are widely used in species classification, biodiversity studies, comparative genomics, and molecular epidemiology. Contents of the course include:
- Population genetics, which is a theoretical framework for understanding mechanisms of sequence evolution through mutation, recombination, gene duplication, genetic drift, and natural selection.
- Molecular systematics, which introduces statistical models of sequence evolution and methods for reconstructing species phylogeny.
- Bioinformatics, which provides hands-on training on data acquisition and the use of software tools for phylogenetic analyses.
This 3-credit course is designed for upper-level biology-major undergraduates. Hunter pre-requisites are BIOL203, and MATH150 or STAT113.
Please note that starting from fall 2015, completing this course no longer counts towards research credits for biology majors.
Textbooks
- (Required) Graur, 2016, Molecular and Genome Evolution, First Edition, Sinauer Associates, Inc. ISBN: 978-1-60535-469-9. Publisher's Website (Student discount: a 15% discount and receive free UPS standard shipping)
http://www.sinauer.com/molecular-and-genome-evolution.html)
- (Recommended) Baum & Smith, 2013. Tree Thinking: an Introduction to Phylogenetic Biology, Roberts & Company Publishers, Inc.
Learning Goals
- Be able to describe evolutionary relationships using phylogenetic trees
- Be able to use web-based as well as stand-alone software to infer phylogenetic trees
- Understand mechanisms of DNA sequence evolution
- Understand algorithms for building phylogenetic trees
Links for phylogenetic tools
- NCBI sequence databases
- R Tools
- R source: download & install from a mirror site
- R Studio: download & install
- APE package
- A Molecular Phylogeny Web Server
- EvolView: an online tree viewer
Exams & Grading
- Attendance (or a note in case of absence) is required. Bonus for active participation in classroom discussions.
- Assignments. All assignments should be handed in as hard copies only. Email submission will not be accepted. Late submissions will receive 10% deduction (of the total grade) per day.
- Three Mid-term Exams (30 pts each)
- Comprehensive Final Exam (50 pts)
Academic Honesty
While students may work in groups and help each other for assignments, duplicated answers in assignments will be flagged and investigated as possible acts of academic dishonesty. To avoid being investigated as such, do NOT copy anyone else's work, or let others copy your work. At the least, rephrase using your own words. Note that the same rule applies regarding the use of textbook and online resources: copied sentences are not acceptable and will be considered plagiarism.
Hunter College regards acts of academic dishonesty (e.g., plagiarism, cheating on examinations, obtaining unfair advantage, and falsification of records and official documents) as serious offenses against the values of intellectual honesty. The College is committed to enforcing the CUNY Policy on Academic Integrity and will pursue cases of academic dishonesty according to the Hunter College Academic Integrity Procedures.
Course Schedule
Part 1. Tree Thinking
- 8/25 (TH). Overview & Introduction. Textbook Chapter: "Introduction" (pages 1-3)
Assignment 1 (10 pts; Due: 8/29, Monday) |
---|
Pre-test: Full credits will be given as long as each question is answered with some reasoning. In other words, it will NOT be graded on being right or wrong. It's an assessment tool, to be compared with later test outcomes to show teaching/learning results. |
- 8/29 (M). Introduction (Continued). Tutorial: R & R-Studio (Bring your own computer). Lecture slides:
- 9/1 (TH). Intro to trees. In-class exercise 1.
Assignment 2 (10 pts; Due: 9/8, Thursday) |
---|
Watch Origin of Species: Lizards in an Evolutionary Tree. Provide short answer (1-3 sentences) to each of the following three questions.
|
R exercises
|
- 9/5 (M). Labor Day. No class
- 9/8 (TH). Intro to trees. In-class exercise 2. Textbook Chapter 5: "Molecular Phylogenetics" (pages 170-175; 201-202)
- 9/12 (M). Species Tree & Lineage Sorting. Textbook Chapter 5: "Molecular Phylogenetics" (pages 177-180)
Assignment 3 (10 pts; Due: 9/19, Monday) |
---|
R exercises
|
- 9/15 (TH). Consensus Tree & Review. Chapter 5. pages 199-200 (Figure 5.31) Lecture Slides:
- 9/19 (M). 4:10 - 5:10pm Midterm Exam I Bring pencils, erasers, and a calculator
Part 2. Trait & Sequence Evolution
- 9/22 (Th). Traits & trait matrix
Assignment #4 (5 pts; Due Monday, 9/26) |
---|
|
- 9/26 (M). Homoplasy & consistency
- 9/29 (Th). Parsimony reconstruction (Chapter 5). In-Class Exercise 4
Assignment #5 (10 pts; Due 10/) |
---|
|
- 10/3 (No class)
- 10/6 (TH). Genome & gene structure (Chapter 3)
- 10/12 (M). No Class
- 10/10 (M). Genome and gene evolution.
- 10/13 (Th). Review & Practices.
- 10/17 (M). Midterm Exam 2