Biol375 2016 - Revision history

imported>Weigang: /* Part 4. Population Genetics (Chapter 2) */

2016-12-13T16:25:58Z

Part 4. Population Genetics (Chapter 2)

← Older revision		Revision as of 16:25, 13 December 2016
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	* 12/5 (M) Rates of nucleotide substitutions (pages 111-125). Part 4 slides: [[File:Part-4-evol-mechanisms-v2.pdf\|thumbnail]].		* 12/5 (M) Rates of nucleotide substitutions (pages 111-125). Part 4 slides: [[File:Part-4-evol-mechanisms-v2.pdf\|thumbnail]].
	* 12/8 (Thursday). (Last Lecture) Review & Course evaluations. Review slides: [[File:Final-review.pdf\|thumbnail]]		* 12/8 (Thursday). (Last Lecture) Review & Course evaluations. Review slides: [[File:Final-review.pdf\|thumbnail]]. '''Submit your Teacher's Evaluation''', using either:
	'''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]
	* 12/19 (Monday, 4-6pm) '''Comprehensive Final Exam'''		* 12/19 (Monday, 4-6pm) '''Comprehensive Final Exam'''
	* 12/31 (Sat). Grades Submitted to Registrar Offices (Hunter and Graduate Center)		* 12/31 (Sat). Grades Submitted to Registrar Offices (Hunter and Graduate Center)

imported>Weigang: /* Part 4. Population Genetics (Chapter 2) */

2016-12-13T16:25:02Z

Part 4. Population Genetics (Chapter 2)

← Older revision		Revision as of 16:25, 13 December 2016
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	# 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). <font color="blue">Answer: Heterozygosity is the probability that two randomly picked alleles are different</font>		# Define "genetic diversity" verbally (+2 pts for giving and using formula for calculating heterozygosity). <font color="blue">Answer: Heterozygosity is the probability that two randomly picked alleles are different</font>
	# Define "genetic drift". ~~<font color="blue">~~Using results~~</font>~~ 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)? <font color="blue">Genetic drift is random, non-selective fluctuation of allele frequencies due to random gamete sampling in a finite population. Genetic drift reduces genetic diversity within a population and increases genetic divergence between populations. The effect of drift is more pronounced in small populations, as shown by larger frequency variation in a sample of 10 individuals than in a sample of 100 individuals.</font>		# 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)? <font color="blue">Genetic drift is random, non-selective fluctuation of allele frequencies due to random gamete sampling in a finite population. Genetic drift reduces genetic diversity within a population and increases genetic divergence between populations. The effect of drift is more pronounced in small populations, as shown by larger frequency variation in a sample of 10 individuals than in a sample of 100 individuals.</font>
	\|}		\|}
	* 12/5 (M) Rates of nucleotide substitutions (pages 111-125). Part 4 slides: [[File:Part-4-evol-mechanisms-v2.pdf\|thumbnail]].		* 12/5 (M) Rates of nucleotide substitutions (pages 111-125). Part 4 slides: [[File:Part-4-evol-mechanisms-v2.pdf\|thumbnail]].

imported>Weigang: /* Part 4. Population Genetics (Chapter 2) */

2016-12-13T16:23:55Z

Part 4. Population Genetics (Chapter 2)

← Older revision		Revision as of 16:23, 13 December 2016
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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). <font color="blue">Answer: Heterozygosity is the probability that two randomly picked alleles are different</font>
	# Define "genetic drift". <font color="blue">Using results</font> 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". <font color="blue">Using results</font> 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)? <font color="blue">Genetic drift is random, non-selective fluctuation of allele frequencies due to random gamete sampling in a finite population. Genetic drift reduces genetic diversity within a population and increases genetic divergence between populations. The effect of drift is more pronounced in small populations, as shown by larger frequency variation in a sample of 10 individuals than in a sample of 100 individuals.</font>
	\|}		\|}
	* 12/5 (M) Rates of nucleotide substitutions (pages 111-125). Part 4 slides: [[File:Part-4-evol-mechanisms-v2.pdf\|thumbnail]]		* 12/5 (M) Rates of nucleotide substitutions (pages 111-125). Part 4 slides: [[File:Part-4-evol-mechanisms-v2.pdf\|thumbnail]].
	* 12/8 (Thursday). (Last Lecture) Review & Course evaluations. '''Submit your Teacher's Evaluation''', using either:		* 12/8 (Thursday). (Last Lecture) Review & Course evaluations. Review slides: [[File:Final-review.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]
	* 12/19 (Monday, 4-6pm) '''Comprehensive Final Exam'''		* 12/19 (Monday, 4-6pm) '''Comprehensive Final Exam'''
	* 12/31 (Sat). Grades Submitted to Registrar Offices (Hunter and Graduate Center)		* 12/31 (Sat). Grades Submitted to Registrar Offices (Hunter and Graduate Center)

imported>Weigang: /* Part 4. Population Genetics (Chapter 2) */

2016-12-08T02:51:10Z

Part 4. Population Genetics (Chapter 2)

← Older revision		Revision as of 02:51, 8 December 2016
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	# Define "genetic drift". <font color="blue">Using results</font> 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". <font color="blue">Using results</font> 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)?
	\|}		\|}
	* 12/5 (M) Rates of nucleotide substitutions (pages 111-125)		* 12/5 (M) Rates of nucleotide substitutions (pages 111-125). Part 4 slides: [[File:Part-4-evol-mechanisms-v2.pdf\|thumbnail]]
	* 12/8 (Thursday). (Last Lecture) Review & Course evaluations. '''Submit your Teacher's Evaluation''', using either:		* 12/8 (Thursday). (Last Lecture) Review & Course evaluations. '''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,

imported>Weigang: /* Part 4. Population Genetics (Chapter 2) */

2016-12-05T18:20:42Z

Part 4. Population Genetics (Chapter 2)

← Older revision		Revision as of 18:20, 5 December 2016
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	* 12/5 (M) Rates of nucleotide substitutions (pages 111-125)		* 12/5 (M) Rates of nucleotide substitutions (pages 111-125)
	* 12/8 (Thursday). (Last Lecture) Review & Course evaluations.		* 12/8 (Thursday). (Last Lecture) Review & Course evaluations. '''Submit your Teacher's Evaluation''', using either:
	* '''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]
	* 12/19 (Monday, 4-6pm) '''Comprehensive Final Exam'''		* 12/19 (Monday, 4-6pm) '''Comprehensive Final Exam'''
	* 12/31 (Sat). Grades Submitted to Registrar Offices (Hunter and Graduate Center)		* 12/31 (Sat). Grades Submitted to Registrar Offices (Hunter and Graduate Center)

imported>Weigang: /* Part 4. Population Genetics (Chapter 2) */

2016-12-05T18:20:11Z

Part 4. Population Genetics (Chapter 2)

← Older revision		Revision as of 18:20, 5 December 2016
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	* 12/5 (M) Rates of nucleotide substitutions (pages 111-125)		* 12/5 (M) Rates of nucleotide substitutions (pages 111-125)
	* 12/8 (Thursday). (Last Lecture) Review & Course evaluations.		* 12/8 (Thursday). (Last Lecture) Review & Course evaluations.
	'''Submit your Teacher's Evaluation''', using either:		* '''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]
	* 12/19 (Monday, 4-6pm) '''Comprehensive Final Exam'''		* 12/19 (Monday, 4-6pm) '''Comprehensive Final Exam'''
	* 12/31 (Sat). Grades Submitted to Registrar Offices (Hunter and Graduate Center)		* 12/31 (Sat). Grades Submitted to Registrar Offices (Hunter and Graduate Center)

imported>Weigang: /* Part 4. Population Genetics */

2016-11-16T19:05:14Z

Part 4. Population Genetics

imported>Weigang: /* Part 4. Population Genetics */

2016-11-09T23:35:17Z

Part 4. Population Genetics

← Older revision		Revision as of 23:35, 9 November 2016
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	# Using the outgroup sequence, determine the ancestral and derived SNP, codon, and amino-acid states at each codon site. Explain with a tree including the outgroup sequence.		# Using the outgroup sequence, determine the ancestral and derived SNP, codon, and amino-acid states at each codon site. Explain with a tree including the outgroup sequence.
	\|}		\|}
	* <font color="gray">12/3 (TH). Instructor traveling. No class</font>
	* 11/28 (M). Neutral Theory & Molecular Clock		* 11/28 (M). Neutral Theory & Molecular Clock
	* 12/1 (TH). Tests of Natural Selection.		* 12/1 (TH). Tests of Natural Selection.

imported>Weigang: /* Part 4. Population Genetics */

2016-11-09T23:34:13Z

Part 4. Population Genetics

← Older revision		Revision as of 23:34, 9 November 2016
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	===Part 4. Population Genetics ===		===Part 4. Population Genetics ===
			* 11/17 (Th). Mechanism of molecular evolution: Overview; Analogy with language evolution
			* 11/21 (Mon). SNP statistics & Genetic Drift
			{\| class="wikitable sortable mw-collapsible"
			\|- style="background-color:lightsteelblue;"
			! Assignment #9 (10 pts; Due 12/7, Monday)
			\|- style="background-color:lightblue;"
			\|[[File:Snp-pa1.png\|thumbnail]]
			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 (<font color="red">with the outgroup sequence excluded.</font>) <font color="green">Do not print the figure directly. Hand-copy the sequences to a graph sheet, include only sequences at the two variable codon positions</font>:
			# There are two SNP sites. For each SNP, determine whether it is a synonymous or nonsynonymous change (could be both if more than 2 states). You may simply list the codons and their corresponding amino acids, at each aligned codon site.
			# Calculate allele frequencies at each SNP site (for 3 SNP states, calculate frequencies of all three separately)
			# List all haplotypes using the 2 SNP sites
			# Calculate frequencies of all haplotypes
			# Using the outgroup sequence, determine the ancestral and derived SNP, codon, and amino-acid states at each codon site. Explain with a tree including the outgroup sequence.
			\|}
			* <font color="gray">12/3 (TH). Instructor traveling. No class</font>
			* 11/28 (M). Neutral Theory & Molecular Clock
			* 12/1 (TH). Tests of Natural Selection.
			{\| class="wikitable sortable mw-collapsible"
			\|- style="background-color:lightsteelblue;"
			! Assignment # (10 pts; Due 12/14, Monday)
			\|- style="background-color:lightblue;"
			\|Statistical experiments to explore gene-frequency change due to genetic drift:
			# With R-studio, make two populations of N=1000 haploid individuals consisting of alleles "A" and "G" at a SNP site: <code>pop1 = c(rep("A",500), rep("G",500)); pop2 = c(rep("A",100), rep("G",900))</code>
			# Count alleles in each population: <code>table(pop1); table(pop2)</code>. Which population is more diverse? Why?
			# Define a function to calculate heterozygosity: <code>hg = function(x) {cts = table(x); total=sum(cts); if (length(cts)==1) {return(0) } else { freq1=cts[1]/total; freq2=cts[2]/total; return(1-(freq1^2+freq2^2)) } }</code>
			# Calculate heterozygosity of each population: <code>hg(pop1); hg(pop2)</code>. The results should match your answer to the 2nd question.
			# Permute population 1 and take a random sample of 100 individuals: <code>pop1=sample(pop1); s = sample(pop1, 100); counts=table(s); heterozygosity = hg(s)</code>. Is the sample more or less diverse than the original population? Repeat 10 times and report all counts and diversity (e.g., with a table)
			# Repeat the above with a smaller sample of 10 individuals
			# Repeat with population 2 and a sample of 100 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 drift". <font color="blue">Using results</font> 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)?
			\|}
			* 12/5 (M)
			* 12/8 (M). (Last Lecture) Review & Course evaluations.
			'''Submit your Teacher's Evaluation''', using either:
			** 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]
			* 12/19 (Monday, 4-6pm) '''Comprehensive Final Exam'''
			* 12/31 (Sat). Grades Submitted to Registrar Offices (Hunter and Graduate Center)

imported>Weigang: /* Part 3. Tree Algorithms */

2016-11-05T15:58:27Z

Part 3. Tree Algorithms

← Older revision		Revision as of 15:58, 5 November 2016
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	{\| class="wikitable sortable mw-collapsible"		{\| class="wikitable sortable mw-collapsible"
	\|- style="background-color:lightsteelblue;"		\|- style="background-color:lightsteelblue;"
	! Assignment #7 (10 pts; <font color="red">Due 11/7, Monday</font>)		! Assignment #7 (10 pts; <font color="red">Due 11/7, Monday (Part-3 lecture slides posted below)</font>)
	\|- 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
	\|}		\|}
	* 11/3 (TH). Distance methods (Chapter 5, pages 184-187).		* 11/3 (TH). Distance methods (Chapter 5, pages 184-187). Lecture Slides: [[File:Part-3-tree-construction.pdf\|thumbnail]]
	* 11/7 (M). Likelihood & Bayesian methods (Chapter 5, pages 194-198)		* 11/7 (M). Likelihood & Bayesian methods (Chapter 5, pages 194-198)
	{\| class="wikitable sortable mw-collapsible"		{\| class="wikitable sortable mw-collapsible"

← Older revision		Revision as of 19:05, 16 November 2016
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	* 11/14 (M). '''Midterm Exam 3'''		* 11/14 (M). '''Midterm Exam 3'''

	===Part 4. Population Genetics ===		===Part 4. Population Genetics (Chapter 2) ===
	* 11/17 (Th). Mechanism of molecular evolution: Overview~~; Analogy with language evolution~~		* 11/17 (Th). Mechanism of molecular evolution: Overview (pages 35-38)
	* 11/21 (Mon). SNP statistics & Genetic Drift		* 11/21 (Mon). SNP statistics & Genetic Drift (pages 47-49)
	{\| class="wikitable sortable mw-collapsible"		{\| class="wikitable sortable mw-collapsible"
	\|- style="background-color:lightsteelblue;"		\|- style="background-color:lightsteelblue;"
	! Assignment #9 (10 pts; Due 12/7, ~~Monday~~)		! Assignment #9 (10 pts; Due 12/1, Thursday)
	\|- style="background-color:lightblue;"		\|- style="background-color:lightblue;"
	\|[[File:Snp-pa1.png\|thumbnail]]		\|[[File:Snp-pa1.png\|thumbnail]]
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	# Using the outgroup sequence, determine the ancestral and derived SNP, codon, and amino-acid states at each codon site. Explain with a tree including the outgroup sequence.		# Using the outgroup sequence, determine the ancestral and derived SNP, codon, and amino-acid states at each codon site. Explain with a tree including the outgroup sequence.
	\|}		\|}
	* 11/28 (M). Neutral Theory & Molecular Clock		* 11/28 (M). Neutral Theory & Molecular Clock (pages 58-59; 72-74)
	* 12/1 (TH). Tests of Natural Selection.		* 12/1 (TH). Tests of Natural Selection
	{\| class="wikitable sortable mw-collapsible"		{\| class="wikitable sortable mw-collapsible"
	\|- style="background-color:lightsteelblue;"		\|- style="background-color:lightsteelblue;"
	! Assignment # (10 pts; Due 12/14, ~~Monday~~)		! Assignment # (10 pts; Due 12/8, Thursday)
	\|- 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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	# Define "genetic drift". <font color="blue">Using results</font> 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". <font color="blue">Using results</font> 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)?
	\|}		\|}
	* 12/5 (M)		* 12/5 (M) Rates of nucleotide substitutions (pages 111-125)
	* 12/8 (M). (Last Lecture) Review & Course evaluations.		* 12/8 (Thursday). (Last Lecture) Review & Course evaluations.
	'''Submit your Teacher's Evaluation''', using either:		'''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,