Biol375 2017: Difference between revisions
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<center>'''Room:''' 926 HN (Seminar Room, North Building)</center> | <center>'''Room:''' 926 HN (Seminar Room, North Building)</center> | ||
<center>'''Hours:''' Mon. & Thur 4:10-5:25 pm</center> | <center>'''Hours:''' Mon. & Thur 4:10-5:25 pm</center> | ||
<center>'''Office Hours:''' Belfer Research Building ([https://www.google.com/maps/place/413+E+69th+St,+New+York,+NY+10021/@40.7655886,-73.9561743,17z/data=!3m1!4b1!4m2!3m1!1s0x89c258c3d235f76f:0x4f3d0d5d8a78fe6?hl=en Google Map]) BB-402; | <center>'''Office Hours:''' Belfer Research Building ([https://www.google.com/maps/place/413+E+69th+St,+New+York,+NY+10021/@40.7655886,-73.9561743,17z/data=!3m1!4b1!4m2!3m1!1s0x89c258c3d235f76f:0x4f3d0d5d8a78fe6?hl=en Google Map]) BB-402; Thursdays 1-3 pm or by appointment</center> | ||
<center>'''Course Website:''' http://diverge.hunter.cuny.edu/labwiki/ | <center>'''Course Website:''' http://diverge.hunter.cuny.edu/labwiki/Biol375_2018</center> | ||
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[[File:Borreliabase-screenshot-1.png|350px|thumbnail]] | [[File:Borreliabase-screenshot-1.png|350px|thumbnail]] | ||
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! Assignment 1 (10 pts; Due: 8/31, TH) | ! Assignment 1 (10 pts; Due: 8/31, TH) | ||
|- | |- | ||
|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. [[File:Pretest.pdf|thumbnail]] | | | ||
* (5 pts) Install R, and then R-studio; Run command <code>getwd()</code>; Print screenshot to show output. | |||
* (5 pts) 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. [[File:Pretest.pdf|thumbnail]] | |||
|} | |} | ||
* 8/31 (M). Introduction (Continued). Tutorial: R & R-Studio <font color="red">(Bring your own computer)</font>. Lecture slides [ | * 8/31 (M). Introduction (Continued). | ||
** Tutorial: R & R-Studio <font color="red">(Bring your own computer)</font>. Follow [[Biol20N02_2017#Feb_2._Introduction_.26_R_Demo|this link]]. | |||
** Lecture slides [[File:Intro-2017.pdf|thumbnail]] | |||
{| class="wikitable sortable mw-collapsible" | {| class="wikitable sortable mw-collapsible" | ||
! Assignment 2 (10 pts; Due: 9/7, Thursday) | ! Assignment 2 (10 pts; Due: 9/7, Thursday) | ||
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* 9/7 (TH). Intro to trees. In-class exercise 1. | * 9/7 (TH). Intro to trees. In-class exercise 1. | ||
* 9/11 (M). Intro to trees. In-class exercise 2. Textbook Chapter 5: "Molecular Phylogenetics" (pages 170-175; 201-202) | * 9/11 (M). Intro to trees. In-class exercise 2. Textbook Chapter 5: "Molecular Phylogenetics" (pages 170-175; 201-202) | ||
* 9/14 (TH). Species Tree & Lineage Sorting. Textbook Chapter 5: "Molecular Phylogenetics" (pages 177-180) | * 9/14 (TH). Species Tree & Lineage Sorting. Textbook Chapter 5: "Molecular Phylogenetics" (pages 177-180). <font color="blue">Bring laptop & we will work on the following R exercise together in class.</font> | ||
{| class="wikitable sortable mw-collapsible" | {| class="wikitable sortable mw-collapsible" | ||
! Assignment 3 (10 pts; Due: 9/ | ! Assignment 3 (10 pts; Due: 9/18, Monday) | ||
|- | |- | ||
| R exercises | | R exercises | ||
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## setwd("/Users/john/Documents") (to set the working directory to where you saved your mt_primate.txt file) | ## setwd("/Users/john/Documents") (to set the working directory to where you saved your mt_primate.txt file) | ||
## library(ape) (this is to load the ape library) | ## library(ape) (this is to load the ape library) | ||
## mt | ## mt <- read.FASTA("mt_primate.txt") (to read the alignment and save it in an object called "mt") | ||
## mt (to show result, copy & paste into your report) | ## mt (to show result, copy & paste into your report) | ||
## dist.mt | ## dist.mt <- dist.dna(mt) (to obtain a pair-wise distance matrix) | ||
## dist.raw | ## dist.raw <- dist.dna(mt, model = "raw") (to obtain raw, un-corrected pair-wise sequence differences, in fractions) | ||
## dist.raw * 888 (888 is the length of aligned DNA bases, to show raw counts of base differences; copy & paste into your report) | ## dist.raw * 888 (888 is the length of aligned DNA bases, to show raw counts of base differences; copy & paste into your report) | ||
## tr.mt | ## tr.mt <- bionj(dist.mt) ( to create a tree based on the pairwise distance matrix) | ||
## plot(tr.mt) (to show tree; Export and save tree image) | ## plot(tr.mt) (to show tree; Export and save tree image) | ||
## library(phangorn) | ## library(phangorn) | ||
## tr.mid | ## tr.mid <- midpoint(tr.mt) (this creates a midpoint-rooted tree) | ||
## plot(tr.mid) (Export and save tree image) | ## plot(tr.mid) (Export and save tree image) | ||
## q() (to quit and save your R session, to your working directory) | ## q() (to quit and save your R session, to your working directory) | ||
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## Illustrating with your tree (by labeling ancestral nodes and groups of species), explain why "ape" excluding "human" does not constitute a monophyletic group. | ## Illustrating with your tree (by labeling ancestral nodes and groups of species), explain why "ape" excluding "human" does not constitute a monophyletic group. | ||
|} | |} | ||
* 9/18 (M). Consensus Tree & Review. Chapter 5. pages 199-200 (Figure 5.31) Lecture Slides: [[File:Part-1-tree-thinking- | * 9/18 (M). Consensus Tree & Review. Chapter 5. pages 199-200 (Figure 5.31) Lecture Slides: [[File:Part-1-tree-thinking-2017.pdf|thumbnail]] | ||
* 9/19 (Tuesday; Thursday schedule). 4:10 - 5:10pm '''Midterm Exam I''' <font color="red">Bring pencils, erasers, and a calculator</font> | * 9/19 (Tuesday; Thursday schedule). 4:10 - 5:10pm '''Midterm Exam I''' <font color="red">Bring pencils, erasers, and a calculator</font> | ||
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{| class="wikitable sortable mw-collapsible" | {| class="wikitable sortable mw-collapsible" | ||
|- style="background-color:lightsteelblue;" | |- style="background-color:lightsteelblue;" | ||
! Assignment #4 (10 pts; Due | ! Assignment #4 (10 pts; Due Monday, 10/2) | ||
|- style="background-color:white;" | |- style="background-color:white;" | ||
| | | | ||
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{| class="wikitable sortable mw-collapsible" | {| class="wikitable sortable mw-collapsible" | ||
|- style="background-color:lightsteelblue;" | |- style="background-color:lightsteelblue;" | ||
! Assignment #5 (10 pts; Due 10/ | ! Assignment #5 (10 pts; Due 10/12) | ||
|- style="background-color:white;" | |- style="background-color:white;" | ||
| | | | ||
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## Set working directory to where you have downloaded the DNA alignment file: e.g., setwd("/Users/ann/Document") | ## Set working directory to where you have downloaded the DNA alignment file: e.g., setwd("/Users/ann/Document") | ||
## Load library: library(ape) | ## Load library: library(ape) | ||
## Read alignment: aln.an | ## Read alignment: aln.an <- read.FASTA("lizard-aligned.txt") | ||
## Calculate pairwise distance matrix: dist.an | ## Calculate pairwise distance matrix: dist.an <- dist.dna(aln.an) | ||
## Estimate tree: tr.an | ## Estimate tree: tr.an <- bionj(dist.an) | ||
## Reroot tree: tr.root | ## Reroot tree: tr.root <- root(tr.an, outgroup = "Leiocephalus_barahonensis", resolve.root = T) | ||
## Save tree: write.tree(tr.root, "rerooted.dnd") | ## Save tree: write.tree(tr.root, "rerooted.dnd") | ||
## Read re-rooted tree: tr.2 | ## 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" | ## Download [http://diverge.hunter.cuny.edu/w/images/2/21/Pheno.txt the phenotype file] and save it as "pheno.txt" (or use your own file) | ||
## Read phenotype with the command: ph | ## Read phenotype with the command: ph <- read.table("pheno.txt", row.names = 1, header=F) | ||
## Assign column names: colnames(ph) | ## 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) | ## 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$tip.label, pos=4, font = 3) | ## Add species names: text(rep(0.2,17), 1:17, tr.2$tip.label, pos=4, font = 3) | ||
## | ## Reorder according to tree: ph <- ph[tr.2$tip.label,] | ||
## Add a column: text(rep(0.5,17), 1:17, ph[ | ## Add a column: text(rep(0.5,17), 1:17, ph[,1], pos=4, col = ph[,3]) | ||
## Add another column: text(rep(0.7,17), 1:17, ph[ | ## Add another column: text(rep(0.7,17), 1:17, ph[,2], pos=4, col = ph[,4]) | ||
## Add a heading: text(0.5, 18, "Ecomorph", font = 2, pos=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) | ## Add another heading: text(0.7, 18, "Geography", font = 2, pos=4) | ||
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|} | |} | ||
* <font color="gray">10/10 (M). No Class (Columbus Day)</font> | * <font color="gray">10/10 (M). No Class (Columbus Day)</font> | ||
* 10/12 (TH). | * 10/12 (TH). In-class exercises | ||
* 10/16 (M). Review & Practices. Lecture Slides: [[File:Part-2-trait-evolution-2017.pdf|thumbnail]] | |||
* 10/19 (TH). '''Midterm Exam 2''' | * 10/19 (TH). '''Midterm Exam 2''' | ||
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{| class="wikitable sortable mw-collapsible" | {| class="wikitable sortable mw-collapsible" | ||
|- style="background-color:lightsteelblue;" | |- style="background-color:lightsteelblue;" | ||
! Assignment #6 ( | ! Assignment #6 (10 pts; Due 10/30, Monday) | ||
|- style="background-color:white;" | |- style="background-color:white;" | ||
| Based on the [http://www.ncbi.nlm.nih.gov/gene/54205 NCBI Gene Page for cytochrome C (CYCS)], answer the following questions: | | Based on the [http://www.ncbi.nlm.nih.gov/gene/54205 NCBI Gene Page for cytochrome C (CYCS)], answer the following questions: | ||
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|} | |} | ||
* 10/26 (TH). Genetic distances & Sequence-evolutionary models (Chapter 3, pages 79-88) | * 10/26 (TH). Genetic distances & Sequence-evolutionary models (Chapter 3, pages 79-88) | ||
* 10/30 (M). Maximum parsimony (Chapter 5, pages 191-194). In class exercise #6 | * 10/30 (M). Maximum parsimony (Chapter 5, pages 191-194). | ||
* 11/2 (TH). Distance methods (Chapter 5, pages 184-187). In class exercise #6; In-class computer exercise: | |||
{| class="wikitable sortable mw-collapsible" | {| class="wikitable sortable mw-collapsible" | ||
|- style="background-color:lightsteelblue;" | |- style="background-color:lightsteelblue;" | ||
! Assignment #7 (10 pts | ! Assignment #7 (10 pts). Due 11/6 (Monday) | ||
|- style="background-color:white;" | |- style="background-color:white;" | ||
| | | | ||
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## Use the graph to explain (1) Why it is necessary to correct for raw distances when comparing sequences from distantly related species; (2) What is the key difference between the K80 and JC models | ## Use the graph to explain (1) Why it is necessary to correct for raw distances when comparing sequences from distantly related species; (2) What is the key difference between the K80 and JC models | ||
|} | |} | ||
* 11/ | * 11/6 (M). Likelihood & Bayesian methods (Chapter 5, pages 194-198). Lecture slides posted: [[File:Part-3-tree-construction-posted.pdf|thumbnail]] | ||
In-class exercise: | |||
{| class="wikitable sortable mw-collapsible" | {| class="wikitable sortable mw-collapsible" | ||
|- style="background-color:lightsteelblue;" | |- style="background-color:lightsteelblue;" | ||
! Assignment #8 (10 pts | ! Assignment #8 (10 pts). Due 11/13 (Monday) | ||
|- style="background-color:white;" | |- style="background-color:white;" | ||
| | | | ||
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## Explain (1) Does bootstrap test for tree precision or tree accuracy? (2) What does a bootstrap value of 80% mean? | ## Explain (1) Does bootstrap test for tree precision or tree accuracy? (2) What does a bootstrap value of 80% mean? | ||
|} | |} | ||
* 11/9 (TH). Tree-testing & Review (Chapter 5, pages 207-209). Lecture slides | * 11/9 (TH). Tree-testing & Review (Chapter 5, pages 207-209). Lecture slides posted in the last session | ||
* 11/13 (M). '''Midterm Exam 3''' | * 11/13 (M). '''Midterm Exam 3''' | ||
===Part 4. Population Genetics (Chapter 2) === | ===Part 4. Population Genetics (Chapter 2) === | ||
* 11/16 (TH). Mechanism of molecular evolution: Overview (pages 35-38) | * 11/16 (TH). Mechanism of molecular evolution: Overview (pages 35-38); SNP statistics | ||
* 11/20 (M). | * 11/20 (M). No class (instructor traveling) | ||
{| class="wikitable sortable mw-collapsible" | {| class="wikitable sortable mw-collapsible" | ||
|- style="background-color:lightsteelblue;" | |- style="background-color:lightsteelblue;" | ||
! Assignment #9 (10 pts; Due | ! Assignment #9 (10 pts; Due 11/30, Thursday) | ||
|- style="background-color:lightblue;" | |- style="background-color:lightblue;" | ||
|[[File:Snp-pa1.png|thumbnail]] | |[[File:Snp-pa1.png|thumbnail]] | ||
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* 11/27 (M). No class (Instructor traveling) | * 11/27 (M). No class (Instructor traveling) | ||
* 11/30 (TH). Neutral Theory & Molecular Clock (pages 58-59; 72-74) | * 11/30 (TH). Neutral Theory & Molecular Clock (pages 58-59; 72-74) | ||
* 12/4 (M). | * 12/4 (M). Genetic Drift (pages 47-49). Computer exercises of Assignment #10 (below) will be done in class. | ||
{| class="wikitable sortable mw-collapsible" | {| class="wikitable sortable mw-collapsible" | ||
|- style="background-color:lightsteelblue;" | |- style="background-color:lightsteelblue;" | ||
! Assignment # (10 pts; Due 12/ | ! Assignment # (10 pts; Due 12/11, Monday) | ||
|- style="background-color:lightblue;" | |- style="background-color:lightblue;" | ||
|Statistical experiments to explore gene-frequency change due to genetic drift: | |Statistical experiments to explore gene-frequency change due to genetic drift: | ||
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# Repeat with population 2 and a sample of 100 individuals | # Repeat with population 2 and a sample of 100 individuals | ||
# Repeat the above with a smaller sample of 10 individuals | # Repeat the above with a smaller sample of 10 individuals | ||
# Define "genetic diversity" verbally (+2 pts for giving and using formula for calculating heterozygosity). | # Define "genetic diversity" verbally (+2 pts for giving and using formula for calculating heterozygosity). | ||
# Define "genetic drift". Using results from the above four statistical experiments, discuss the effect of genetic drift to genetic diversity within population. What's the general trend (increase or decrease) of genetic diversity as a result of random sampling of gametes? Is the gain or loss of genetic diversity due to genetic drift more rapid in small or large population (contrasting results with different sample sizes)? | # Define "genetic drift". Using results from the above four statistical experiments, discuss the effect of genetic drift to genetic diversity within population. What's the general trend (increase or decrease) of genetic diversity as a result of random sampling of gametes? Is the gain or loss of genetic diversity due to genetic drift more rapid in small or large population (contrasting results with different sample sizes)? | ||
|} | |} | ||
* 12/7 (TH) Rates of nucleotide substitutions (pages 111-125). Part 4 slides: [[File:Part-4-evol-mechanisms- | * 12/7 (TH) Rates of nucleotide substitutions (pages 111-125). Part 4 slides: [[File:Part-4-evol-mechanisms-2017.pdf|thumbnail]] | ||
* 12/11 (M). (Last Lecture) Review & Course evaluations. Review slides: [[File:Final-review.pdf|thumbnail]]. '''Submit your Teacher's Evaluation''', using either: | * 12/11 (M). (Last Lecture) Review & Course evaluations. Review slides: [[File:Final-review-2017.pdf|thumbnail]]. '''Submit your Teacher's Evaluation''', using either: | ||
** Personal computer at [http://www.hunter.cuny.edu/te www.hunter.cuny.edu/te]; or, | ** Personal computer at [http://www.hunter.cuny.edu/te www.hunter.cuny.edu/te]; or, | ||
** Smartphone at [http://www.hunter.cuny.edu/mobilete www.hunter.cuny.edu/mobilete] | ** Smartphone at [http://www.hunter.cuny.edu/mobilete www.hunter.cuny.edu/mobilete] | ||
* 12/18 (Monday, 4-6pm) '''Comprehensive Final Exam''' | * 12/18 (Monday, 4-6pm) '''Comprehensive Final Exam''' | ||
* 12/30 (Sat). Grades Submitted to Registrar Offices (Hunter and Graduate Center) | * 12/30 (Sat). Grades Submitted to Registrar Offices (Hunter and Graduate Center) |
Latest revision as of 20:18, 27 August 2018
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
- Bonus for full attendance (or a note in case of absence) & 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
- 8/28 (M). Overview & Introduction. Textbook Chapter: "Introduction" (pages 1-3)
Assignment 1 (10 pts; Due: 8/31, TH) |
---|
|
- 8/31 (M). Introduction (Continued).
- Tutorial: R & R-Studio (Bring your own computer). Follow this link.
- Lecture slides
Assignment 2 (10 pts; Due: 9/7, Thursday) |
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Watch Origin of Species: Lizards in an Evolutionary Tree. Provide short answer (1-3 sentences) to each of the following three questions.
|
R exercises
|
- 9/4 (M). Labor Day. No class
- 9/7 (TH). Intro to trees. In-class exercise 1.
- 9/11 (M). Intro to trees. In-class exercise 2. Textbook Chapter 5: "Molecular Phylogenetics" (pages 170-175; 201-202)
- 9/14 (TH). Species Tree & Lineage Sorting. Textbook Chapter 5: "Molecular Phylogenetics" (pages 177-180). Bring laptop & we will work on the following R exercise together in class.
Assignment 3 (10 pts; Due: 9/18, Monday) |
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R exercises
|
- 9/18 (M). Consensus Tree & Review. Chapter 5. pages 199-200 (Figure 5.31) Lecture Slides:
- 9/19 (Tuesday; Thursday schedule). 4:10 - 5:10pm Midterm Exam I Bring pencils, erasers, and a calculator
Part 2. Trait & Sequence Evolution
- 9/25 (M). Traits & trait matrix
- Textbook Chapter 5, pages 180-183
Assignment #4 (10 pts; Due Monday, 10/2) |
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|
- 9/28 (TH). Homoplasy & consistency
- 10/2 (M). Parsimony reconstruction (Chapter 5).
- Textbook Chapter 5, pages 188-191
- In-Class Exercise 4
- 10/5 (TH). Genome & gene structure (Chapter 3)
- In-Class Exercise 5. Pretest Part 2 (molecular phylogenetics in forensics)
Assignment #5 (10 pts; Due 10/12) |
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|
- 10/10 (M). No Class (Columbus Day)
- 10/12 (TH). In-class exercises
- 10/16 (M). Review & Practices. Lecture Slides:
- 10/19 (TH). Midterm Exam 2
Part 3. Tree Algorithms
- 10/23 (M). BLAST & Alignments (Chapter 3. pages 93-100)
Assignment #6 (10 pts; Due 10/30, Monday) |
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Based on the NCBI Gene Page for cytochrome C (CYCS), answer the following questions:
|
- 10/26 (TH). Genetic distances & Sequence-evolutionary models (Chapter 3, pages 79-88)
- 10/30 (M). Maximum parsimony (Chapter 5, pages 191-194).
- 11/2 (TH). Distance methods (Chapter 5, pages 184-187). In class exercise #6; In-class computer exercise:
Assignment #7 (10 pts). Due 11/6 (Monday) |
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|
- 11/6 (M). Likelihood & Bayesian methods (Chapter 5, pages 194-198). Lecture slides posted:
In-class exercise:
Assignment #8 (10 pts). Due 11/13 (Monday) |
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|
- 11/9 (TH). Tree-testing & Review (Chapter 5, pages 207-209). Lecture slides posted in the last session
- 11/13 (M). Midterm Exam 3
Part 4. Population Genetics (Chapter 2)
- 11/16 (TH). Mechanism of molecular evolution: Overview (pages 35-38); SNP statistics
- 11/20 (M). No class (instructor traveling)
Assignment #9 (10 pts; Due 11/30, Thursday) |
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The left figure shows a codon alignment of 38 strains of a bacterium, with an outgroup sequence (which starts with a string of SNPs: "....g...c..ca..", etc), answer the following questions (with the outgroup sequence excluded.) Do not print the figure directly. Hand-copy the sequences to a graph sheet, include only sequences at the two variable codon positions:
|
- 11/27 (M). No class (Instructor traveling)
- 11/30 (TH). Neutral Theory & Molecular Clock (pages 58-59; 72-74)
- 12/4 (M). Genetic Drift (pages 47-49). Computer exercises of Assignment #10 (below) will be done in class.
Assignment # (10 pts; Due 12/11, Monday) |
---|
Statistical experiments to explore gene-frequency change due to genetic drift:
|
- 12/7 (TH) Rates of nucleotide substitutions (pages 111-125). Part 4 slides:
- 12/11 (M). (Last Lecture) Review & Course evaluations. Review slides: . Submit your Teacher's Evaluation, using either:
- Personal computer at www.hunter.cuny.edu/te; or,
- Smartphone at www.hunter.cuny.edu/mobilete
- 12/18 (Monday, 4-6pm) Comprehensive Final Exam
- 12/30 (Sat). Grades Submitted to Registrar Offices (Hunter and Graduate Center)