Biol375 2017 - Revision history

imported>Weigang at 20:18, 27 August 2018

2018-08-27T20:18:00Z

← Older revision		Revision as of 20:18, 27 August 2018
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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; ~~Tuesdays 5~~-7 pm or by appointment</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; Thursdays 1-3 pm or by appointment</center>
	<center>'''Course Website:''' http://diverge.hunter.cuny.edu/labwiki/~~Biol375_2017~~</center>		<center>'''Course Website:''' http://diverge.hunter.cuny.edu/labwiki/Biol375_2018</center>
	----		----
	[[File:Borreliabase-screenshot-1.png\|350px\|thumbnail]]		[[File:Borreliabase-screenshot-1.png\|350px\|thumbnail]]

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

2017-12-11T21:41:47Z

Part 4. Population Genetics (Chapter 2)

← Older revision		Revision as of 21:41, 11 December 2017
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	* 12/7 (TH) Rates of nucleotide substitutions (pages 111-125). Part 4 slides: [[File:Part-4-evol-mechanisms-2017.pdf\|thumbnail]]		* 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-2017.pdf\|thumbnail]]		* 12/11 (M). (Last Lecture) Review & Course evaluations. Review slides: [[File:Final-review-2017.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]
	* 12/18 (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)

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

2017-12-11T21:41:13Z

Part 4. Population Genetics (Chapter 2)

← Older revision		Revision as of 21:41, 11 December 2017
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	* 12/7 (TH) Rates of nucleotide substitutions (pages 111-125). Part 4 slides: [[File:Part-4-evol-mechanisms-2017.pdf\|thumbnail]]		* 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: ~~to be posted~~. '''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)

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

2017-12-09T17:24:02Z

Part 4. Population Genetics (Chapter 2)

← Older revision		Revision as of 17:24, 9 December 2017
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	# 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)?
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	* 12/7 (TH) Rates of nucleotide substitutions (pages 111-125). Part 4 slides: ~~to be posted~~.		* 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: to be posted. '''Submit your Teacher's Evaluation''', using either:		* 12/11 (M). (Last Lecture) Review & Course evaluations. Review slides: to be posted. '''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) */

2017-12-05T18:39:34Z

Part 4. Population Genetics (Chapter 2)

← Older revision		Revision as of 18:39, 5 December 2017
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	\|- style="background-color:lightsteelblue;"		\|- style="background-color:lightsteelblue;"
	! Assignment # (10 pts; Due 12/8, ~~Thursday~~)		! 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:

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

2017-11-13T21:35:48Z

Part 4. Population Genetics (Chapter 2)

← Older revision		Revision as of 21:35, 13 November 2017
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	===Part 4. Population Genetics (Chapter 2) ===		===Part 4. Population Genetics (Chapter 2) ===
	* 11/16 (TH). Mechanism of molecular evolution: Overview (pages 35-38); SNP statistics ~~& Genetic Drift (pages 47-49)~~		* 11/16 (TH). Mechanism of molecular evolution: Overview (pages 35-38); SNP statistics
	* 11/20 (M). No class (instructor traveling)		* 11/20 (M). No class (instructor traveling)
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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). ~~Tests~~ of ~~Natural Selection~~		* 12/4 (M). Genetic Drift (pages 47-49). Computer exercises of Assignment #10 (below) will be done in class.
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imported>Weigang: /* Part 4. Population Genetics (Chapter 2) */

2017-11-13T21:30:17Z

Part 4. Population Genetics (Chapter 2)

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

2017-11-13T21:28:30Z

Part 3. Tree Algorithms

← Older revision		Revision as of 21:28, 13 November 2017
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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~~: to be~~ posted		* 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'''

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

2017-11-13T05:41:18Z

Part 4. Population Genetics (Chapter 2)

← Older revision		Revision as of 05:41, 13 November 2017
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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). ~~<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).
	# 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>		# 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-v2.pdf\|thumbnail]].		* 12/7 (TH) Rates of nucleotide substitutions (pages 111-125). Part 4 slides: [[File:Part-4-evol-mechanisms-v2.pdf\|thumbnail]].

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

2017-11-05T01:10:42Z

Part 3. Tree Algorithms

← Older revision		Revision as of 01:10, 5 November 2017
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	\|- style="background-color:lightsteelblue;"		\|- style="background-color:lightsteelblue;"
	! Assignment #7 (10 pts). Due 11/7 (Monday)		! Assignment #7 (10 pts). Due 11/6 (Monday)
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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
	\|}		\|}
	* 11/6 (M). Likelihood & Bayesian methods (Chapter 5, pages 194-198). In-class exercise:		* 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:
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	\|- style="background-color:lightsteelblue;"		\|- style="background-color:lightsteelblue;"
	! Assignment #8 (10 pts)		! Assignment #8 (10 pts). Due 11/13 (Monday)
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← Older revision		Revision as of 21:30, 13 November 2017
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	\|- style="background-color:lightsteelblue;"		\|- style="background-color:lightsteelblue;"
	! Assignment #9 (10 pts; Due 12/1, Thursday)		! Assignment #9 (10 pts; Due 11/30, Thursday)
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	\|[[File:Snp-pa1.png\|thumbnail]]		\|[[File:Snp-pa1.png\|thumbnail]]
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	# 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-v2.pdf\|thumbnail]]~~.		* 12/7 (TH) Rates of nucleotide substitutions (pages 111-125). Part 4 slides: to be posted.
	* 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: to be posted. '''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)