Biol375 2015 - Revision history

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

2015-12-16T03:34:44Z

Part 4. Population Genetics

← Older revision		Revision as of 03:34, 16 December 2015
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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)?
	\|}		\|}
	* 12/14 (M). Review & Course evaluations. Review slides: [[File:Final-review-slides.pdf\|thumbnail]]. '''Submit your Teacher's Evaluation''', using either:		* 12/14 (M). Review & Course evaluations.
			[[File:Key-q2.png\|thumbnail\|Answer key to In-Class Exercise 8 Question 2]]
			Review slides: [[File:Final-review-slides.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]
	~~[[File:Key-q2.png\|thumbnail\|Answer key to In-Class Exercise 8 Question 2]]~~
	* 12/17 (TH) '''Comprehensive Final Exam''' (Regular class hours & Room)		* 12/17 (TH) '''Comprehensive Final Exam''' (Regular class hours & Room)
	* 12/31 (Wed). Grades Submitted to Registrar Offices (Hunter and Graduate Center)		* 12/31 (Wed). Grades Submitted to Registrar Offices (Hunter and Graduate Center)

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

2015-12-16T03:32:55Z

Part 4. Population Genetics

← Older revision		Revision as of 03:32, 16 December 2015
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	** 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]
			[[File:Key-q2.png\|thumbnail\|Answer key to In-Class Exercise 8 Question 2]]
	* 12/17 (TH) '''Comprehensive Final Exam''' (Regular class hours & Room)		* 12/17 (TH) '''Comprehensive Final Exam''' (Regular class hours & Room)
	* 12/31 (Wed). Grades Submitted to Registrar Offices (Hunter and Graduate Center)		* 12/31 (Wed). Grades Submitted to Registrar Offices (Hunter and Graduate Center)

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

2015-12-11T04:03:34Z

Part 4. Population Genetics

← Older revision		Revision as of 04:03, 11 December 2015
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	# 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>		# 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.		# 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); ~~cts~~ = ~~table(~~sample(pop1, 100))</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)		# 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 the above with a smaller sample of 10 individuals
	# Repeat with population 2 and a sample of 100 individuals		# Repeat with population 2 and a sample of 100 individuals

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

2015-12-11T03:43:43Z

Part 4. Population Genetics

← Older revision		Revision as of 03:43, 11 December 2015
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	\|- 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:
	# With R-studio, make two populations of N=1000 haploid individuals consisting of alleles "A" and "G": <code>pop1 = c(rep("A",500), rep("G",500)); pop2 = c(rep("A",100), rep("G",900))</code>		# 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?		# 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>		# 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>

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

2015-12-11T03:37:26Z

Part 4. Population Genetics

← Older revision		Revision as of 03:37, 11 December 2015
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	# 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>		# 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.		# 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); cts = table(sample(pop1, 100))</code>. Is the sample more or less diverse than the original population? Repeat 10 times and report all counts and diversity		# Permute population 1 and take a random sample of 100 individuals: <code>pop1=sample(pop1); cts = table(sample(pop1, 100))</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 the above with a smaller sample of 10 individuals
	# Repeat with population 2 and a ~~smaller~~ 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". <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?		# 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)?
	\|}		\|}
	* 12/14 (M). Review & Course evaluations. Review slides: [[File:Final-review-slides.pdf\|thumbnail]]. '''Submit your Teacher's Evaluation''', using either:		* 12/14 (M). Review & Course evaluations. Review slides: [[File:Final-review-slides.pdf\|thumbnail]]. '''Submit your Teacher's Evaluation''', using either:

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

2015-12-11T03:33:34Z

Part 4. Population Genetics

← Older revision		Revision as of 03:33, 11 December 2015
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	\|- 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:
	# With R-studio, make two ~~population~~ of N=1000 haploid individuals consisting of alleles "A" and "G": <code>pop1 = c(rep("A",500), rep("G",500)); pop2 = c(rep("A",100), rep("G",900))</code>		# With R-studio, make two populations of N=1000 haploid individuals consisting of alleles "A" and "G": <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?		# 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>		# 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>
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	# Repeat with population 2 and a smaller of 100 individuals		# Repeat with population 2 and a smaller 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 ~~drift~~"		# Define "genetic diversity" verbally (+2 pts for giving and using formula for calculating heterozygosity).
	# ~~Based on~~ results from the above four statistical experiments, discuss the effect of genetic drift to ~~gene~~ diversity within population.		# 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?
	\|}		\|}
	* 12/14 (M). Review & Course evaluations. Review slides: [[File:Final-review-slides.pdf\|thumbnail]]. '''Submit your Teacher's Evaluation''', using either:		* 12/14 (M). Review & Course evaluations. Review slides: [[File:Final-review-slides.pdf\|thumbnail]]. '''Submit your Teacher's Evaluation''', using either:

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

2015-12-11T03:21:49Z

Part 4. Population Genetics

← Older revision		Revision as of 03:21, 11 December 2015
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	\|- 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:
	# With R-studio, make two population of N=~~100~~ haploid individuals consisting of alleles "A" and "G": <code>pop1 = c(rep("A",500), rep("G",500)); pop2 = c(rep("A",10), rep("G",90))</code>		# With R-studio, make two population of N=1000 haploid individuals consisting of alleles "A" and "G": <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?		# 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); freq1=cts[1]/total; freq2=cts[2]/total; ~~cat~~(1-(freq1^2+freq2^2)) }</code>		# 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.		# Calculate heterozygosity of each population: <code>hg(pop1); hg(pop2)</code>. The results should match your answer to the 2nd question.
	# Permute a population and take a random sample: <code>pop1=sample(pop1); ~~sample.30~~ = sample(pop1, 100)~~; hg(sample~~.~~100);~~ sample.10 = sample~~(pop1,~~ 10~~); hg(~~sample.~~10)</code>~~		# Permute population 1 and take a random sample of 100 individuals: <code>pop1=sample(pop1); cts = table(sample(pop1, 100))</code>. Is the sample more or less diverse than the original population? Repeat 10 times and report all counts and diversity
			# Repeat the above with a smaller sample of 10 individuals
			# Repeat with population 2 and a smaller of 100 individuals
			# Repeat the above with a smaller sample of 10 individuals
			# Define "genetic drift"
			# Based on results from the above four statistical experiments, discuss the effect of genetic drift to gene diversity within population.
	\|}		\|}
	* 12/14 (M). Review & Course evaluations. Review slides: [[File:Final-review-slides.pdf\|thumbnail]]. '''Submit your Teacher's Evaluation''', using either:		* 12/14 (M). Review & Course evaluations. Review slides: [[File:Final-review-slides.pdf\|thumbnail]]. '''Submit your Teacher's Evaluation''', using either:

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

2015-12-11T00:53:07Z

Part 4. Population Genetics

← Older revision		Revision as of 00:53, 11 December 2015
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	\|- 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:
	# With R-studio, make two population of N=100 haploid individuals consisting of alleles "A" and "G": <code>pop1 = c(rep("A",50), rep("G",50)); pop2 = c(rep("A",10), rep("G",90))</code>		# With R-studio, make two population of N=100 haploid individuals consisting of alleles "A" and "G": <code>pop1 = c(rep("A",500), rep("G",500)); pop2 = c(rep("A",10), rep("G",90))</code>
	# Count alleles in each population: <code>table(pop1); table(pop2)</code>. Which population is more diverse? Why?		# 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); freq1=cts[1]/total; freq2=cts[2]/total; cat(1-(freq1^2+freq2^2)) }</code>		# Define a function to calculate heterozygosity: <code>hg = function(x) {cts = table(x); total=sum(cts); freq1=cts[1]/total; freq2=cts[2]/total; cat(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.		# Calculate heterozygosity of each population: <code>hg(pop1); hg(pop2)</code>. The results should match your answer to the 2nd question.
	# Permute a population and take a random sample: <code>pop1=sample(pop1); sample.30 = sample(pop1, 50); hg(sample.50); sample.10 = sample(pop1, 10); hg(sample.10)</code>		# Permute a population and take a random sample: <code>pop1=sample(pop1); sample.30 = sample(pop1, 100); hg(sample.100); sample.10 = sample(pop1, 10); hg(sample.10)</code>
	\|}		\|}
	* 12/14 (M). Review & Course evaluations. Review slides: [[File:Final-review-slides.pdf\|thumbnail]]. '''Submit your Teacher's Evaluation''', using either:		* 12/14 (M). Review & Course evaluations. Review slides: [[File:Final-review-slides.pdf\|thumbnail]]. '''Submit your Teacher's Evaluation''', using either:

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

2015-12-11T00:50:59Z

Part 4. Population Genetics

← Older revision		Revision as of 00:50, 11 December 2015
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	# Define a function to calculate heterozygosity: <code>hg = function(x) {cts = table(x); total=sum(cts); freq1=cts[1]/total; freq2=cts[2]/total; cat(1-(freq1^2+freq2^2)) }</code>		# Define a function to calculate heterozygosity: <code>hg = function(x) {cts = table(x); total=sum(cts); freq1=cts[1]/total; freq2=cts[2]/total; cat(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.		# Calculate heterozygosity of each population: <code>hg(pop1); hg(pop2)</code>. The results should match your answer to the 2nd question.
	# Permute ~~the populations~~ and take a random sample: <code>pop1=sample(pop1); ~~pop2~~=sample(~~pop2~~)</code>		# Permute a population and take a random sample: <code>pop1=sample(pop1); sample.30 = sample(pop1, 50); hg(sample.50); sample.10 = sample(pop1, 10); hg(sample.10)</code>
	\|}		\|}
	* 12/14 (M). Review & Course evaluations. Review slides: [[File:Final-review-slides.pdf\|thumbnail]]. '''Submit your Teacher's Evaluation''', using either:		* 12/14 (M). Review & Course evaluations. Review slides: [[File:Final-review-slides.pdf\|thumbnail]]. '''Submit your Teacher's Evaluation''', using either:

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

2015-12-11T00:17:42Z

Part 4. Population Genetics

← Older revision		Revision as of 00:17, 11 December 2015
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	! Assignment # (10 pts; Due 12/14, Monday)		! Assignment # (10 pts; Due 12/14, 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:
	# With R-studio, make two population of N=100 haploid individuals consisting of alleles "A" and "G": <code>pop1 = c(rep("A",50), rep("G",50)); pop2 = c(rep("A",10), rep("G",90))</code>		# With R-studio, make two population of N=100 haploid individuals consisting of alleles "A" and "G": <code>pop1 = c(rep("A",50), rep("G",50)); pop2 = c(rep("A",10), rep("G",90))</code>
	# Count alleles in each population: <code>table(pop1); table(pop2)</code>. Which population is more diverse? Why?		# Count alleles in each population: <code>table(pop1); table(pop2)</code>. Which population is more diverse? Why?
	# ~~Make~~ a function to calculate heterozygosity: <code>hg = function(x) {cts = table(x); total=sum(cts); freq1=cts[1]/total; freq2=cts[2]/total; cat(1-(freq1^2+freq2^2)) }</code>		# Define a function to calculate heterozygosity: <code>hg = function(x) {cts = table(x); total=sum(cts); freq1=cts[1]/total; freq2=cts[2]/total; cat(1-(freq1^2+freq2^2)) }</code>
	# Calculate heterozygosity of each population: <code>hg(pop1); hg(pop2)</code>		# Calculate heterozygosity of each population: <code>hg(pop1); hg(pop2)</code>. The results should match your answer to the 2nd question.
			# Permute the populations and take a random sample: <code>pop1=sample(pop1); pop2=sample(pop2)</code>
	\|}		\|}
	* 12/14 (M). Review & Course evaluations. Review slides: [[File:Final-review-slides.pdf\|thumbnail]]. '''Submit your Teacher's Evaluation''', using either:		* 12/14 (M). Review & Course evaluations. Review slides: [[File:Final-review-slides.pdf\|thumbnail]]. '''Submit your Teacher's Evaluation''', using either: