Biol375 2014 - Revision history

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

2014-12-16T01:43:44Z

Part 4. Population Genetics

← Older revision		Revision as of 01:43, 16 December 2014
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	* 12/8 (M). Neutral Theory & Molecular Clock		* 12/8 (M). Neutral Theory & Molecular Clock
	* 12/11 (TH). Tests of Natural Selection. Lecture Slides: [[File:Part-4-evol-mechanisms.pdf\|thumbnail]]		* 12/11 (TH). Tests of Natural Selection. Lecture Slides: [[File:Part-4-evol-mechanisms.pdf\|thumbnail]]
	* 12/15 (M). Review & Course evaluations. '''Submit your Teacher's Evaluation''', using either:		* 12/15 (M). Review & Course evaluations. 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]
	* 12/18 (TH) '''Comprehensive Final Exam''' (Regular class hours & Room)		* 12/18 (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 */

2014-12-15T20:22:02Z

Part 4. Population Genetics

← Older revision		Revision as of 20:22, 15 December 2014
Line 172:		Line 172:
	* 12/11 (TH). Tests of Natural Selection. Lecture Slides: [[File:Part-4-evol-mechanisms.pdf\|thumbnail]]		* 12/11 (TH). Tests of Natural Selection. Lecture Slides: [[File:Part-4-evol-mechanisms.pdf\|thumbnail]]
	* 12/15 (M). Review & Course evaluations. '''Submit your Teacher's Evaluation''', using either:		* 12/15 (M). 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,
	## 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 (TH) '''Comprehensive Final Exam''' (Regular class hours & Room)		* 12/18 (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 */

2014-12-15T20:21:27Z

Part 4. Population Genetics

← Older revision		Revision as of 20:21, 15 December 2014
Line 171:		Line 171:
	* 12/8 (M). Neutral Theory & Molecular Clock		* 12/8 (M). Neutral Theory & Molecular Clock
	* 12/11 (TH). Tests of Natural Selection. Lecture Slides: [[File:Part-4-evol-mechanisms.pdf\|thumbnail]]		* 12/11 (TH). Tests of Natural Selection. Lecture Slides: [[File:Part-4-evol-mechanisms.pdf\|thumbnail]]
	* 12/15 (M). Review & Course evaluations. '''Submit your ~~online~~ [~~https~~://~~owl~~.hunter.cuny.edu/ ~~Teacher's Evaluation~~]~~'''~~		* 12/15 (M). 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]
	* 12/18 (TH) '''Comprehensive Final Exam''' (Regular class hours & Room)		* 12/18 (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 */

2014-12-15T20:17:17Z

Part 4. Population Genetics

← Older revision		Revision as of 20:17, 15 December 2014
Line 171:		Line 171:
	* 12/8 (M). Neutral Theory & Molecular Clock		* 12/8 (M). Neutral Theory & Molecular Clock
	* 12/11 (TH). Tests of Natural Selection. Lecture Slides: [[File:Part-4-evol-mechanisms.pdf\|thumbnail]]		* 12/11 (TH). Tests of Natural Selection. Lecture Slides: [[File:Part-4-evol-mechanisms.pdf\|thumbnail]]
	* 12/15 (M). Review		* 12/15 (M). Review & Course evaluations. '''Submit your online [https://owl.hunter.cuny.edu/ Teacher's Evaluation]'''
	* 12/18 (TH) '''Comprehensive Final Exam''' (Regular class hours & Room)		* 12/18 (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 */

2014-12-12T01:22:02Z

Part 4. Population Genetics

← Older revision		Revision as of 01:22, 12 December 2014
Line 170:		Line 170:
	* 12/4 (TH). Genetic Drift		* 12/4 (TH). Genetic Drift
	* 12/8 (M). Neutral Theory & Molecular Clock		* 12/8 (M). Neutral Theory & Molecular Clock
	* 12/11 (TH). Tests of Natural Selection		* 12/11 (TH). Tests of Natural Selection. Lecture Slides: [[File:Part-4-evol-mechanisms.pdf\|thumbnail]]
	* 12/15 (M). Review		* 12/15 (M). Review
	* 12/18 (TH) '''Comprehensive Final Exam''' (Regular class hours & Room)		* 12/18 (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 */

2014-11-29T14:29:51Z

Part 4. Population Genetics

← Older revision		Revision as of 14:29, 29 November 2014
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	# List all haplotypes using the 2 SNP sites		# List all haplotypes using the 2 SNP sites
	# Calculate frequencies of all haplotypes		# Calculate frequencies of all haplotypes
	# Using the outgroup sequence, determine the ancestral and derived SNP, codon, and amino-acid states at each codon site. Without the outgroup sequence, could derived and ancestral states be determined (e.g., by majority)? Explain ~~by sketching~~ a tree ~~and performing parsimony reconstruction~~.		# Using the outgroup sequence, determine the ancestral and derived SNP, codon, and amino-acid states at each codon site. Without the outgroup sequence, could derived and ancestral states be determined (e.g., by majority)? Explain with a tree including the outgroup sequence.
	# (Bonus: +2) For sites that are fixed differences between the outgroup sequences and others (e.g., the 5th nucleotide site), could one determine which is the ancestral and which is the derived state? Explain ~~by using~~ a tree.		# (Bonus: +2) For sites that are fixed differences between the outgroup sequences and others (e.g., the 5th nucleotide site), could one determine which is the ancestral and which is the derived state? Explain with a tree.
	\|}		\|}
	* <font color="gray">12/1 (M). Instructor traveling. No class</font>		* <font color="gray">12/1 (M). Instructor traveling. No class</font>

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

2014-11-29T14:26:28Z

Part 4. Population Genetics

← Older revision		Revision as of 14:26, 29 November 2014
Line 159:		Line 159:
	\|- style="background-color:lightblue;"		\|- style="background-color:lightblue;"
	\|[[File:Snp-pa1.png\|thumbnail]]		\|[[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>):		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.		# 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)		# 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		# List all haplotypes using the 2 SNP sites
	# Calculate frequencies of all haplotypes		# Calculate frequencies of all haplotypes
	# Using the outgroup sequence, determine the ancestral and derived SNP, codon, and amino-acid states at each codon site. Without the outgroup sequence, could derived and ancestral states be determined? Explain by sketching a tree and performing parsimony reconstruction.		# Using the outgroup sequence, determine the ancestral and derived SNP, codon, and amino-acid states at each codon site. Without the outgroup sequence, could derived and ancestral states be determined (e.g., by majority)? Explain by sketching a tree and performing parsimony reconstruction.
			# (Bonus: +2) For sites that are fixed differences between the outgroup sequences and others (e.g., the 5th nucleotide site), could one determine which is the ancestral and which is the derived state? Explain by using a tree.
	\|}		\|}
	* <font color="gray">12/1 (M). Instructor traveling. No class</font>		* <font color="gray">12/1 (M). Instructor traveling. No class</font>

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

2014-11-28T21:26:50Z

Part 4. Population Genetics

← Older revision		Revision as of 21:26, 28 November 2014
Line 159:		Line 159:
	\|- style="background-color:lightblue;"		\|- style="background-color:lightblue;"
	\|[[File:Snp-pa1.png\|thumbnail]]		\|[[File:Snp-pa1.png\|thumbnail]]
	The left is 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>):		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>):
	# 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)		# 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)		# Calculate allele frequencies at each SNP site (for 3 SNP states, calculate frequencies of all three separately)
	~~# Calculate the amino-acid frequencies at each polymorphic codon site~~
	# List all haplotypes using the 2 SNP sites		# List all haplotypes using the 2 SNP sites
	# Calculate frequencies of all haplotypes		# Calculate frequencies of all haplotypes
	# Using the outgroup sequence, determine the ancestral and derived SNP states at each		# Using the outgroup sequence, determine the ancestral and derived SNP, codon, and amino-acid states at each codon site. Without the outgroup sequence, could derived and ancestral states be determined? Explain by sketching a tree and performing parsimony reconstruction.
	\|}		\|}
	* <font color="gray">12/1 (M). Instructor traveling. No class</font>		* <font color="gray">12/1 (M). Instructor traveling. No class</font>

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

2014-11-28T18:41:13Z

Part 4. Population Genetics

← Older revision		Revision as of 18:41, 28 November 2014
Line 159:		Line 159:
	\|- style="background-color:lightblue;"		\|- style="background-color:lightblue;"
	\|[[File:Snp-pa1.png\|thumbnail]]		\|[[File:Snp-pa1.png\|thumbnail]]
	The left is a codon alignment of 38 strains of a ~~bacteria and~~ an outgroup sequence (which ~~contains~~ a string of SNPs: "....g...c..ca..", etc), answer the following questions (<font color="red">~~exclude~~ the outgroup sequence</font>):		The left is 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>):
	# 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)		# 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)
	# Calculate allele frequencies at each SNP site (for 3 SNP states, calculate frequencies of all three separately)		# Calculate allele frequencies at each SNP site (for 3 SNP states, calculate frequencies of all three separately)
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	# List all haplotypes using the 2 SNP sites		# List all haplotypes using the 2 SNP sites
	# Calculate frequencies of all haplotypes		# Calculate frequencies of all haplotypes
	# Using the outgroup sequence, determine the ancestral and derived SNP states at each		# Using the outgroup sequence, determine the ancestral and derived SNP states at each
	\|}		\|}
	* <font color="gray">12/1 (M). Instructor traveling. No class</font>		* <font color="gray">12/1 (M). Instructor traveling. No class</font>

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

2014-11-28T18:33:47Z

Part 4. Population Genetics

← Older revision		Revision as of 18:33, 28 November 2014
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	! Assignment #10 (10 pts; Due 12/4, Thursday)		! Assignment #10 (10 pts; Due 12/4, Thursday)
	\|- style="background-color:lightblue;"		\|- style="background-color:lightblue;"
	\| The left is a codon alignment of 38 strains of a bacteria and an outgroup sequence (which contains a string of SNPs: "....g...c..ca..", etc), answer the following questions (<font color="red">exclude the outgroup sequence</font>):		\|[[File:Snp-pa1.png\|thumbnail]]
			The left is a codon alignment of 38 strains of a bacteria and an outgroup sequence (which contains a string of SNPs: "....g...c..ca..", etc), answer the following questions (<font color="red">exclude the outgroup sequence</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)		# 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)
	# Calculate allele frequencies at each SNP site (for 3 SNP states, calculate frequencies of all three separately)		# Calculate allele frequencies at each SNP site (for 3 SNP states, calculate frequencies of all three separately)