Are the Elasmobranchii monophyletic?
Required skills: Biology, Biotechnology
Are the Elasmobranchii monophyletic? Your study should include: 7 species belonging to Elasmobranchii + the closest outgroup to all these taxa that you can find.
The objective is to use the tools of bioinformatics to study the evolutionary relationships among taxa. Need a comprehensive study and a written report in the form of a scientific paper.
1. Search the literature for previous studies on the phylogeny of the taxon or taxa under study based on molecular and/or morphological data.
2. Retrieve the following protein sequences for each ingroup taxon:
NADH dehydrogenase subunit 1
NADH dehydrogenase subunit 2
cytochrome c oxidase subunit I
cytochrome c oxidase subunit II
ATP synthase F0 subunit 8
ATP synthase F0 subunit 6
cytochrome c oxidase subunit III
NADH dehydrogenase subunit 3
NADH dehydrogenase subunit 4L
NADH dehydrogenase subunit 4
NADH dehydrogenase subunit 5
NADH dehydrogenase subunit 6
cytochrome b
5. By using the amino acid sequences of the cytochrome c oxidase subunit I from all the species in the ingroup taxa, identify through BLAST a closely related outgroup species. This species is identified as follows: Use tBLASTn to BLAST the query sequence against refseq_genomics (the database of complete genomes only), using the Entrez query to limit the search to animalia[orgn] NOT XXX[orgn], where XXX = the ingroup taxon name. Repeat this process for each of the proteins. Compile the first 5 results in each of your searches. Arrange the species in descending order of appearance. Chose the most abundant result for which you can find a completely sequenced mitochondrial genome in the database. This species will be the outgroup species. (Sometimes you may need more than one outgroup.)
1. Construct multiple sequence alignments at the protein level by using ClustalW with default parameters.
2. Build NJ and MP trees for each protein alignment.
3. Bootstrap each tree 100 times.
4. Estimate the lengths of the branches of each tree.
5. For the NJ trees, determine by eye groups of congruent trees.
Based on your work, answer the following questions:
1. Does your analysis solve the phylogenetic assignment?
2. Are there contradicting trees? If so, what do you think may be the reason for the incongruence?
3. Does your study agree with previous studies? If not, explain what in your opinion is the cause for the difference.
4. Are there large differences in the rate of evolution among lineages?
The study, written as a scientific paper, should include the following sections:
Abstract
Summarize briefly all aspects of the study including objectives, hypotheses, data, methods, results, and conclusions.
Introduction (most of it you already prepared for your class presentation)
State purpose of the study.
Review previous literature (make proper citations in the bibliography).
List phylogenetic hypothesis that were tested.
Materials and Methods
Provide details of sequences and methods (with proper references)
Present succinct and orderly description of data collection procedure
Provide sufficient detail to allow precise replication of the study
Results
Summarize data in tabular or graphic form with appropriate titles and legends.
Use text to describe important aspects of data (refer to tables and figures)
Present data without interpretation
Discussion
Provide interpretation of results with regard to the hypotheses
Compare results of your study to those of previous studies
Address limitations and sources of errors in your study
Summarize major conclusion(s)
Bibliography
Cite at least three references.
I have attached these details and two sample papers. The paper does not have to be as detailed as the sample papers but they are just to give an idea.
Additional files submitted:
turtle%2520phylogeny.pdf
Lamprologiniphylogenysample.pdf
Are+the+Elasmobranchii+monophyletic.doc
The objective is to use the tools of bioinformatics to study the evolutionary relationships among taxa. Need a comprehensive study and a written report in the form of a scientific paper.
1. Search the literature for previous studies on the phylogeny of the taxon or taxa under study based on molecular and/or morphological data.
2. Retrieve the following protein sequences for each ingroup taxon:
NADH dehydrogenase subunit 1
NADH dehydrogenase subunit 2
cytochrome c oxidase subunit I
cytochrome c oxidase subunit II
ATP synthase F0 subunit 8
ATP synthase F0 subunit 6
cytochrome c oxidase subunit III
NADH dehydrogenase subunit 3
NADH dehydrogenase subunit 4L
NADH dehydrogenase subunit 4
NADH dehydrogenase subunit 5
NADH dehydrogenase subunit 6
cytochrome b
5. By using the amino acid sequences of the cytochrome c oxidase subunit I from all the species in the ingroup taxa, identify through BLAST a closely related outgroup species. This species is identified as follows: Use tBLASTn to BLAST the query sequence against refseq_genomics (the database of complete genomes only), using the Entrez query to limit the search to animalia[orgn] NOT XXX[orgn], where XXX = the ingroup taxon name. Repeat this process for each of the proteins. Compile the first 5 results in each of your searches. Arrange the species in descending order of appearance. Chose the most abundant result for which you can find a completely sequenced mitochondrial genome in the database. This species will be the outgroup species. (Sometimes you may need more than one outgroup.)
1. Construct multiple sequence alignments at the protein level by using ClustalW with default parameters.
2. Build NJ and MP trees for each protein alignment.
3. Bootstrap each tree 100 times.
4. Estimate the lengths of the branches of each tree.
5. For the NJ trees, determine by eye groups of congruent trees.
Based on your work, answer the following questions:
1. Does your analysis solve the phylogenetic assignment?
2. Are there contradicting trees? If so, what do you think may be the reason for the incongruence?
3. Does your study agree with previous studies? If not, explain what in your opinion is the cause for the difference.
4. Are there large differences in the rate of evolution among lineages?
The study, written as a scientific paper, should include the following sections:
Abstract
Summarize briefly all aspects of the study including objectives, hypotheses, data, methods, results, and conclusions.
Introduction (most of it you already prepared for your class presentation)
State purpose of the study.
Review previous literature (make proper citations in the bibliography).
List phylogenetic hypothesis that were tested.
Materials and Methods
Provide details of sequences and methods (with proper references)
Present succinct and orderly description of data collection procedure
Provide sufficient detail to allow precise replication of the study
Results
Summarize data in tabular or graphic form with appropriate titles and legends.
Use text to describe important aspects of data (refer to tables and figures)
Present data without interpretation
Discussion
Provide interpretation of results with regard to the hypotheses
Compare results of your study to those of previous studies
Address limitations and sources of errors in your study
Summarize major conclusion(s)
Bibliography
Cite at least three references.
I have attached these details and two sample papers. The paper does not have to be as detailed as the sample papers but they are just to give an idea.
Additional files submitted:
turtle%2520phylogeny.pdf
Lamprologiniphylogenysample.pdf
Are+the+Elasmobranchii+monophyletic.doc
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