Intro Genome Bio 2013 - Revision history

imported>Weigang: /* December 3. Genome Evolution (4) */

2013-12-10T21:05:17Z

December 3. Genome Evolution (4)

← Older revision		Revision as of 21:05, 10 December 2013
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	# BLAST the [http://www.ncbi.nlm.nih.gov/nuccore/NC_005100.3?report=genbank&from=41824255&to=41824668 Rat cytC] gene sequence against the mouse genome. Based on the top hit, Identify the first five nucleotide sequence differences '''within the coding region'''. Are they synonymous or non-synonymous differences? Show your work. [Hint: identify the first 3-5 codons using the GenBank file. Then find the matching sequences in the BLAST output file.]		# BLAST the [http://www.ncbi.nlm.nih.gov/nuccore/NC_005100.3?report=genbank&from=41824255&to=41824668 Rat cytC] gene sequence against the mouse genome. Based on the top hit, Identify the first five nucleotide sequence differences '''within the coding region'''. Are they synonymous or non-synonymous differences? Show your work. [Hint: identify the first 3-5 codons using the GenBank file. Then find the matching sequences in the BLAST output file.]
	# Build a molecular phylogeny of homologs of [http://www.ncbi.nlm.nih.gov/gene/672 human BRCA1 gene] using [http://www.phylogeny.fr www.phylogeny.fr website]. Show your work. [Hint: Follow the HomoloGene link to download protein sequences. Then use the phylogeny website to infer a tree. Use only species names for tip labels in your final tree.]		# Build a molecular phylogeny of homologs of [http://www.ncbi.nlm.nih.gov/gene/672 human BRCA1 gene] using [http://www.phylogeny.fr www.phylogeny.fr website]. Show your work. [Hint: Follow the HomoloGene link to download protein sequences. Then use the phylogeny website to infer a tree. Use only species names for tip labels in your final tree.]
			<gallery align="center">
			File:wkshop-assign3-1.png\|Answer key for Q1
			File:wkshop-assign3-2.png\|Answer key for Q2
			File:wkshop-assign3-3.png\|Answer key for Q3
			</gallery>

	===December 10. Review===		===December 10. Review===

imported>Weigang: /* November 26. Genome Evolution (3) */

2013-12-10T21:02:05Z

November 26. Genome Evolution (3)

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 ## Gorrilla is more related to the Common Chimp than to Human
 ## A gene sequence from Gorrila is expected to be more similar to its human homolog (i.e., a homologous gene) than to its Orangutan homolog
 # Describe the Tree of Life, including (a) three domains of life, (b) does it imply a single or multiple origins of life on Earth?, (c) at least one line of genetic evidence supporting the common origin of life.
 # Based on the Tree of Life, explain why it is harder to design drugs to treat fungal diseases than to treat bacterial diseases.
 ===December 3. Genome Evolution (4)===

imported>Weigang: /* December 10. Review */

2013-12-10T16:18:24Z

December 10. Review

← Older revision		Revision as of 16:18, 10 December 2013
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	===December 10. Review===		===December 10. Review===
			* Review Slides: [[File:Final-review.pptx\|thumbnail]]

	===December 17. Final Cumulative Exam===		===December 17. Final Cumulative Exam===
	* 12:45-1:30: Paper-only exam		* 12:45-1:30: Paper-only exam

imported>Weigang: /* December 3. Genome Evolution (4) */

2013-12-07T18:02:02Z

December 3. Genome Evolution (4)

← Older revision		Revision as of 18:02, 7 December 2013
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	* Lecture Slides: [[File:Session-11.pptx\|thumbnail]]		* Lecture Slides: [[File:Session-11.pptx\|thumbnail]]
	* Workshop IV. Human evolution		* Workshop IV. Human evolution
	* Workshop Assignment 3 (~~Tentative~~. 15 pts).		* Workshop Assignment 3 (Finalized 12/7 1pm. 15 pts).
	[[File:Ch04f11.jpg\|thumbnail]]		[[File:Ch04f11.jpg\|thumbnail]]
	# Based on ~~amino-acid~~ sites #61-90 in the thioredoxin alignment (see figure at right), ~~draw~~ a phylogenetic tree of these four species. Show your work [Hint: Calculate pairwise differences. Then group two most similar species together. Proceed to adding the next-similar species. End by adding the least similar species.]		# Based on sites #61-90 in the thioredoxin alignment (see figure at right), draft a phylogenetic tree of these four species. Show your work [Hint: Calculate pairwise differences. Then group two most similar species together. Proceed to adding the next-similar species. End by adding the least similar species.]
	# BLAST the [http://www.ncbi.nlm.nih.gov/nuccore/NC_005100.3?report=genbank&from=41824255&to=41824668 Rat cytC] gene sequence against the mouse genome. Based on the top hit, Identify the first five nucleotide sequence differences '''within the coding region'''. Are they synonymous or non-synonymous differences? Show your work ~~(including~~ the BLAST output).		# BLAST the [http://www.ncbi.nlm.nih.gov/nuccore/NC_005100.3?report=genbank&from=41824255&to=41824668 Rat cytC] gene sequence against the mouse genome. Based on the top hit, Identify the first five nucleotide sequence differences '''within the coding region'''. Are they synonymous or non-synonymous differences? Show your work. [Hint: identify the first 3-5 codons using the GenBank file. Then find the matching sequences in the BLAST output file.]
	# Build a molecular phylogeny of homologs of [http://www.ncbi.nlm.nih.gov/gene/672 human BRCA1 gene] using [http://www.phylogeny.fr www.phylogeny.fr website]. Show your work. [Hint: Follow the HomoloGene link to download protein sequences. ~~Use~~ the phylogeny website to infer a tree. Use only species names for tip labels]		# Build a molecular phylogeny of homologs of [http://www.ncbi.nlm.nih.gov/gene/672 human BRCA1 gene] using [http://www.phylogeny.fr www.phylogeny.fr website]. Show your work. [Hint: Follow the HomoloGene link to download protein sequences. Then use the phylogeny website to infer a tree. Use only species names for tip labels in your final tree.]

	===December 10. Review===		===December 10. Review===

imported>Weigang: /* December 3. Genome Evolution (4) */

2013-12-05T20:59:42Z

December 3. Genome Evolution (4)

← Older revision		Revision as of 20:59, 5 December 2013
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	* Workshop IV. Human evolution		* Workshop IV. Human evolution
	* Workshop Assignment 3 (Tentative. 15 pts).		* Workshop Assignment 3 (Tentative. 15 pts).
	# Based on amino-acid sites #61-90 in the thioredoxin alignment, draw a phylogenetic tree of these four species. Show your work (Hint: ~~Start by grouping~~ two most similar species together. Proceed to adding the next-similar species. End by adding the least similar species.)		[[File:Ch04f11.jpg\|thumbnail]]
	# BLAST the Rat cytC gene sequence against the mouse genome. Identify the first five nucleotide sequence differences. Are they synonymous or non-synonymous differences? Show your work (including the BLAST output)		# Based on amino-acid sites #61-90 in the thioredoxin alignment (see figure at right), draw a phylogenetic tree of these four species. Show your work [Hint: Calculate pairwise differences. Then group two most similar species together. Proceed to adding the next-similar species. End by adding the least similar species.]
	# Build a molecular phylogeny of homologs of human BRCA1 gene using www.phylogeny.fr website. Show your work.		# BLAST the [http://www.ncbi.nlm.nih.gov/nuccore/NC_005100.3?report=genbank&from=41824255&to=41824668 Rat cytC] gene sequence against the mouse genome. Based on the top hit, Identify the first five nucleotide sequence differences '''within the coding region'''. Are they synonymous or non-synonymous differences? Show your work (including the BLAST output).
			# Build a molecular phylogeny of homologs of [http://www.ncbi.nlm.nih.gov/gene/672 human BRCA1 gene] using [http://www.phylogeny.fr www.phylogeny.fr website]. Show your work. [Hint: Follow the HomoloGene link to download protein sequences. Use the phylogeny website to infer a tree. Use only species names for tip labels]

	===December 10. Review===		===December 10. Review===

imported>Weigang: /* December 17. Final Exam */

2013-12-05T20:32:23Z

December 17. Final Exam

← Older revision		Revision as of 20:32, 5 December 2013
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	===December 10. Review===		===December 10. Review===
	===December 17. Final Exam===		===December 17. Final Cumulative Exam===
			* 12:45-1:30: Paper-only exam
			* 1:30-2:10: Computer practicum

	==Links==		==Links==

imported>Weigang: /* December 3. Genome Evolution (4) */

2013-12-05T14:24:53Z

December 3. Genome Evolution (4)

← Older revision		Revision as of 14:24, 5 December 2013
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	* Lecture Slides: [[File:Session-11.pptx\|thumbnail]]		* Lecture Slides: [[File:Session-11.pptx\|thumbnail]]
	* Workshop IV. Human evolution		* Workshop IV. Human evolution
	* Workshop Assignment 3 (15 pts).		* Workshop Assignment 3 (Tentative. 15 pts).
			# Based on amino-acid sites #61-90 in the thioredoxin alignment, draw a phylogenetic tree of these four species. Show your work (Hint: Start by grouping two most similar species together. Proceed to adding the next-similar species. End by adding the least similar species.)
			# BLAST the Rat cytC gene sequence against the mouse genome. Identify the first five nucleotide sequence differences. Are they synonymous or non-synonymous differences? Show your work (including the BLAST output)
			# Build a molecular phylogeny of homologs of human BRCA1 gene using www.phylogeny.fr website. Show your work.

	===December 10. Review===		===December 10. Review===

imported>Weigang: /* November 19. Genome Evolution (2) */

2013-12-04T02:37:35Z

November 19. Genome Evolution (2)

← Older revision		Revision as of 02:37, 4 December 2013
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	## If the female philopatry is disapproved by Y-chromosome haplotypes, describe a possible explanation [Hint: Re-phrase one of the first two bullet points on pg.77]		## If the female philopatry is disapproved by Y-chromosome haplotypes, describe a possible explanation [Hint: Re-phrase one of the first two bullet points on pg.77]
	## Conclude with how geographic distribution of Y-chromosome haplotypes would support or dis-approve the female philopatry hypothesis		## Conclude with how geographic distribution of Y-chromosome haplotypes would support or dis-approve the female philopatry hypothesis
	<pre style="white-space: pre-wrap;">[The following answer is contributed by student in the class]		<pre style="white-space: pre-wrap;">[The following answer is contributed by a student in the class]
	1. One possible explanation for the current geographic separation of haplotypes in brown bear population in northwest North America is the female philopatry hypothesis. This means female bears tend to live and breed within home ranges that are smaller than male bears and daughter bears often set up home ranges within their mother’s home range.		1. One possible explanation for the current geographic separation of haplotypes in brown bear population in northwest North America is the female philopatry hypothesis. This means female bears tend to live and breed within home ranges that are smaller than male bears and daughter bears often set up home ranges within their mother’s home range.

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	## Explain why the Mal'ta Boy genome support the "after-interbreeding" hypothesis, using evidence of its mitochondrial and Y-chromosome haplotypes.		## Explain why the Mal'ta Boy genome support the "after-interbreeding" hypothesis, using evidence of its mitochondrial and Y-chromosome haplotypes.
	## Conclude by describing how the Mal'ta Boy genome revised the theory on the geographic and genetic origins of Native Americans.		## Conclude by describing how the Mal'ta Boy genome revised the theory on the geographic and genetic origins of Native Americans.
	<pre style="white-space: pre-wrap;">[The following answer is contributed by student in the class]		<pre style="white-space: pre-wrap;">[The following answer is contributed by a student in the class]
	1. The source of European DNA in Native American genomes has long been assumed to occur after Christopher Columbus introduced the new world to Europe and is a result of the interbreeding between the native population and Europeans after the colonization of the Americas (circa 1492). However, the recent revelation of the genetic identity of the Mal’ta boy (which is closely related to Native Americans) seems to suggest the source of European DNA present in Native Americans are pre-historic and not post-Columbus, as we had assumed. In analyzing the genetic identity of the Mal’ta Boy and Native Americans, we may draw two hypotheses on the origin of Native Americans. The first hypothesis suggests that the ancestral population of Native Americans migrated to North American after the interbreeding between West Eurasian and East Asian populations. The second hypothesis suggests this ancestral population migrated before the interbreeding took place.		1. The source of European DNA in Native American genomes has long been assumed to occur after Christopher Columbus introduced the new world to Europe and is a result of the interbreeding between the native population and Europeans after the colonization of the Americas (circa 1492). However, the recent revelation of the genetic identity of the Mal’ta boy (which is closely related to Native Americans) seems to suggest the source of European DNA present in Native Americans are pre-historic and not post-Columbus, as we had assumed. In analyzing the genetic identity of the Mal’ta Boy and Native Americans, we may draw two hypotheses on the origin of Native Americans. The first hypothesis suggests that the ancestral population of Native Americans migrated to North American after the interbreeding between West Eurasian and East Asian populations. The second hypothesis suggests this ancestral population migrated before the interbreeding took place.

imported>Weigang: /* November 19. Genome Evolution (2) */

2013-12-04T02:35:04Z

November 19. Genome Evolution (2)

← Older revision		Revision as of 02:35, 4 December 2013
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	## If the female philopatry is disapproved by Y-chromosome haplotypes, describe a possible explanation [Hint: Re-phrase one of the first two bullet points on pg.77]		## If the female philopatry is disapproved by Y-chromosome haplotypes, describe a possible explanation [Hint: Re-phrase one of the first two bullet points on pg.77]
	## Conclude with how geographic distribution of Y-chromosome haplotypes would support or dis-approve the female philopatry hypothesis		## Conclude with how geographic distribution of Y-chromosome haplotypes would support or dis-approve the female philopatry hypothesis
	<pre style="white-space: pre-wrap;">[~~Edited from a~~ student~~'s work~~]		<pre style="white-space: pre-wrap;">[The following answer is contributed by student in the class]
	1. One possible explanation for the current geographic separation of haplotypes in brown bear population in northwest North America is the female philopatry hypothesis. This means female bears tend to live and breed within home ranges that are smaller than male bears and daughter bears often set up home ranges within their mother’s home range.		1. One possible explanation for the current geographic separation of haplotypes in brown bear population in northwest North America is the female philopatry hypothesis. This means female bears tend to live and breed within home ranges that are smaller than male bears and daughter bears often set up home ranges within their mother’s home range.

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	## Explain why the Mal'ta Boy genome support the "after-interbreeding" hypothesis, using evidence of its mitochondrial and Y-chromosome haplotypes.		## Explain why the Mal'ta Boy genome support the "after-interbreeding" hypothesis, using evidence of its mitochondrial and Y-chromosome haplotypes.
	## Conclude by describing how the Mal'ta Boy genome revised the theory on the geographic and genetic origins of Native Americans.		## Conclude by describing how the Mal'ta Boy genome revised the theory on the geographic and genetic origins of Native Americans.
			<pre style="white-space: pre-wrap;">[The following answer is contributed by student in the class]
			1. The source of European DNA in Native American genomes has long been assumed to occur after Christopher Columbus introduced the new world to Europe and is a result of the interbreeding between the native population and Europeans after the colonization of the Americas (circa 1492). However, the recent revelation of the genetic identity of the Mal’ta boy (which is closely related to Native Americans) seems to suggest the source of European DNA present in Native Americans are pre-historic and not post-Columbus, as we had assumed. In analyzing the genetic identity of the Mal’ta Boy and Native Americans, we may draw two hypotheses on the origin of Native Americans. The first hypothesis suggests that the ancestral population of Native Americans migrated to North American after the interbreeding between West Eurasian and East Asian populations. The second hypothesis suggests this ancestral population migrated before the interbreeding took place.

			2. In the scenario of the first hypothesis, we would expect the genetic composition of Native American genomes to be a mixture of West Eurasian and East Asian populations. Also, as descendents of this mixture, the Native American genome should be homogenous in the distribution of haplotypes that may be unique to this mixture.

			3. In the scenario of the second hypothesis, we would expect the genetic composition of Native American genomes to resemble either West Eurasian or East Asian. If the migration of both populations occurred prior to interbreeding, there should be pockets of Native American populations that reflect “founder effects,” having haplotypes unique only to West Euroasians or East Asians.

			4. By examining the Mal’ta Boy’s genome, it would seem the “after-interbreeding” hypothesis on the origin of Native Americans is much more plausible. First, both mitochondrial DNA and Y-chromosome indicate the Mal’ta Boy’s genes come from Europe and West Asia. We may conclude he is part of a regional population that has a steady gene flow of the mixed DNA of Europeans and West Asian. This is important as both his maternal and paternal inheritance reflects this mixture of West Eurasian. Second, his autosomal DNA shows he is closed related to Native Americans. Since the Mal’ta boy is dated at 24,000 years old and Native Americans are identified as approximately 15,000 year old, he is most likely an early ancestor of the Native American population. Lastly, the absence of East Asian DNA in the Mal’ta Boy strongly suggests that although he is an early ancestor, he is not part of the ancestral population that migrated to North America. The two-third proportion of East Asian DNA present in the Native America genome was most liked introduced to the Mal’ta Boy’s West Eurasian population and only after interbreeding were the ancestral population of Native America created.

			5. In conclusion, the revelation of Mal’ta Boy genome offers new insights to the genetic makeup and migration patterns of the first Americans that may revise our current theories on the origin of Native Americans. Mal’ta Boy provides genetic evidence that would suggest (1) the source of European DNA present in Native Americans was most like pre-historic and not post-Columbus and (2) there was an ancestral population of Native Americans that migrated to North America by crossing the Beringia carrying both European and East Asian DNA.
			</pre>

	===November 26. Genome Evolution (3)===		===November 26. Genome Evolution (3)===

imported>Weigang: /* November 19. Genome Evolution (2) */

2013-12-04T02:29:52Z

November 19. Genome Evolution (2)

@@ Line 197: / Line 197: @@
 ## If the female philopatry is disapproved by Y-chromosome haplotypes, describe a possible explanation [Hint: Re-phrase one of the first two bullet points on pg.77]
 ## Conclude with how geographic distribution of Y-chromosome haplotypes would support or dis-approve the female philopatry hypothesis
 # '''Mal'ta Boy and origin of Native Americans''' (see links above). The Mal'ta Boy genome suggests that European sequence types in Native Americans are pre-historic and not post-Columbus. Describe evidence supporting this conclusion. Structure your paragraph in the following way:
 ## Start with the main question ("source of European DNA in Native American genomes") and the previous theory [Hint: "post-Columbus gene flow"]