Prepare a short presentation (~5 minutes). The presentation is due on October 26, 2011




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2011
Phylogenetic reconstructions by using mitochondrial protein coding genes from completely sequenced mitochondria (Final Assignments for Undergraduate Students)
The objective of the final assignment is to use the tools of bioinformatics to study the evolutionary relationships among taxa. Each student is assigned an individual assignment. The first part of the work will consist of a very short summary of the current taxonomic knowledge pertaining to the ingroup taxa in the assignment. This summary will be presented in class. In the second part, each student will perform a comprehensive study and submit a written report in the form of a scientific paper.

1. A list of taxa for each student is found at the end of this document. Use the NCBI Taxonomy Browser to find the relevant ingroup species.


2. Search the literature for previous studies on the phylogeny of the taxon or taxa under study based on molecular and/or morphological data.
3. Prepare a short presentation (~5 minutes). The presentation is due on October 26, 2011. Please base your presentation on at least three scientific sources. In your talk:

  • Describe the taxa that you are going to study.

  • Outline the current phylogenetic view or views pertaining to the taxa under study.

  • What methods have been used in these studies?

  • What questions are still open (in your opinion)?

4. 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

(If you cannot find all genes in all taxa, please consult with the TA.)
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. Run the multiple-sequence alignment through HoT and use only the reliable parts.

  3. Build NJ and MP trees for each reliable protein alignment.

  4. Bootstrap each tree 100 times.

  5. Estimate the lengths of the branches of each tree.

  6. 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 completed assignment is due on December 12, 2009 at 4:30 PM. Please submit a hard copy in my mailbox (Room 349, 3rd Floor, Science and Research Building II).
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.


Bonus points:

  • For one taxon in your assignment: are there statistically significant differences in codon usage for amino acid Alanine between the protein coding genes located on the two DNA strands?

  • Compare the arrangement of all genes (protein coding genes, tRNAs, rRNAs) between two species in your study. Enumerate the differences.

ID number is followed by Assignment choices. Choose 1
0629609 1 or 21

0480119 2 or 12

0623197 13 or 23

0623272 4 or 24

0859347 5 or 15

0551459 16 or 26

0815672 17 or 27

0506162 8 or 18

0195295 19 or 29

0926327 10 or 20


Assignment List:

1. Identify the phylogenetic relationships within Nematoda. Your study should include: 1 species belonging to Mermithidae, 1 species belonging to Onchocercidae, 1 species belonging to Rhabditida, 1 species belonging to Toxocara, 2 species belonging to Strongylida, 1 Ascaris species + the closest outgroup to all these taxa that you can find.


2. Identify the phylogenetic relationships within Rodentia. Your study should include: 1 hystricognath species, 1 sciurognath species, 1 Mus species, 1 Rattus species, 1 Microtus species, 1 Cricetulus species, 1 Nannospalax species + the closest outgroup to Rodentia that you can find.
3. Identify the phylogenetic relationships within the genus Taenia: Your study should include: 6 Taenia species + the closest 2 outgroup species to all these taxa that you can find.
4. Identify the phylogenetic relationships within the Arachnida. Your study should include: 1 species belonging to Acari, 1 species belonging to Scorpiones, 1 species belonging to Araneae, 1 species belonging to Solifugae, 1 species belonging to Amblyphygi, 1 species belonging to Thelyphonida + the closest outgroup to all these taxa that you can find.
5. Are lampshells related to mollusks? Your study should include: 2 species belonging to the Brachiopoda, 1 species belonging to the Gastropoda, 1 species belonging to the Bivalvia, 1 species belonging to the Polyplacophora, 1 species belonging to the Scaphopoda, 1 species belonging to Cephalopoda + the closest outgroup to all these taxa that you can find.
6. Identify the phylogenetic relationships within Decapoda. Your study should include: 1 species belonging to the genus Penaeus, 1 species belonging to the genus Litopenaeus, 1 species belonging to Portunidae, 1 species belonging to Anomura, 1 species belonging to Grapsoidea, 1 species belonging to the Caridea, 1 species belonging to Heterotremata + the closest outgroup to all these taxa that you can find.
7. (a) Are Brachycera monophyletic? (b) Are Nematocera monophyletic? Your study should include: 1 species belonging to Muscomorpha, 1 species belonging to Stratiomyomorpha, 1 species belonging to Tabanomorpha, 1 species belonging to Blephericeromorpha, 1 species belonging to Culicimorpha, 1 species belonging to Psychodemorpha, 1 species belonging to Ptychopteromorpha + the closest outgroup to all these taxa that you can find.
8. Identify the phylogenetic relationships within the hydei subgroup of Drosophila. Your study should include: 7 species belonging to the hydei subgroup of Drosophila + the closest outgroup to all these taxa that you can find.
9. Determine the phylogenetic relationships among unclassified Musca species (in particular their relationships to the housefly, Musca domestica. Your study should include: Musca domestica, M. asiatica, M. autumnalis, M. confiscata, M. formosana, M. inferior, M. vitripennis + the closest outgroup species that you can find.
10. Identify the phylogenetic relationships within true oysters? Your study should include: 1 species belonging to each of the genera Crassostrea, Dendostra, Lopha, Ostrea, Ostreola. Saccostrea, Striostrea + the closest outgroup to all these taxa that you can find.
11. (a) Are the Orthogastropoda monophyletic? (b) are the Pulmonata monophyletic? Your study should include: 3 different genera belonging to Orthogastropoda, 3 different genera belonging to Pulmonata, Lottia digitalis + the closest outgroup to all these taxa that you can find.
12. Are the Pteriomorphia monophyletic? Your study should include: 4 species belonging to Pteriomorphia, 2 species belonging to Heteroconchia, 1 species belonging to Unionidae + the closest outgroup species that you can find.
13. Are the Hexacorallia monophyletic? Your study should include: 1 species belonging to Antipatharia, 1 species belonging to Zoanthidea, 1 species belonging to Corallimorpharia, 1 species belonging to Actinaria, 1 species belonging to Scleractinia, 1 species belonging to Alcyonacea, and 1 species belonging to Gorgonacea.
14. Are the Sternorrhyncha monophyletic? Your study should include: 2 species belonging to Clypeorrhyncha, 2 species belonging to Neohemiptera, 1 species belonging to Aleyrodiformes, 1 species belonging to Aphidiformes, 1 species belonging to Psylliformes, + the closest outgroup to all these taxa that you can find.
15. Is the genus Bemisia monophyletic? Your study should include: 4 species belonging to Bemisia, 3 species belonging to Aleyrodinae (other than Bemisia), + Doogie Howzer’s whitefly.
16. Identify the phylogenetic relationships within Paraneoptera. Your study should include: 4 species belonging to Hemiptera, 1 species belonging to Phthiraptera, 1 species belonging to Thysanoptera, 1 species belonging to Psocoptera + the closest outgroup species you can find.
17. Identify the phylogenetic relationships within Echinodermata. Your study should include: 3 species belonging to Asterozoa, 3 species belonging to Echinozoa, 1 species belonging to Pelmatozoa + the closest outgroup to all these taxa that you can find.
18. Are wingless insects monophyletic? Your study should include: 3 species belonging to Collembola, 1 species belonging to Diplura, 1 species belonging to Archaeognatha, 2 species belonging to Thysanura + the closest outgroup species from within the Pterygota.
19. Identify the phylogenetic relationships within insects. Your study should include: 1 species belonging to Diptera, 1 species belonging to Hemiptera, 1 species belonging to Lepidoptera, 1 species belonging to Hymenoptera, 1 species belonging to Coleoptera, 1 species belonging to Orthoptera, 1 species belonging to Thysanoptera + the closest outgroup to all these taxa that you can find.
20. Identify the phylogenetic relationships within Amphibia. Your study should include: 1 species belonging to Anura, 1 species belonging to Caudata, 1 species belonging to Caeciliidae, 1 species belonging to Ichthyophiidae, 1 species belonging to Rhinatrematidae, 1 species belonging to Scolecomorphidae, 1 species belonging to Uraeotyphlidae + the closest outgroup species that you can find.
21. Identify the phylogenetic relationships within Anura. Your study should include: 3 species belonging to Archeobatrachia, 3 species belonging to Neobatrachia, 1 species belonging to Mesobatrachia + the closest outgroup to all these taxa that you can find.
22. Are the Chiropterans monophyletic? Your study should include: one species from each of the following genera: Chalinolobus, Pipistrellus, Mystacina, Rhinolophus, Artibeus, Pteropus, Rousettus + a primate outgroup.
23. Identify the phylogenetic relationships within Neobatrachia. Your study should include: 4 species belonging to Ranoidea, 2 species belonging to Microhyloidea, 1 species belonging to Hyloidea, + the closest outgroup to all these taxa that you can find.
24. Identify the phylogenetic relationships within Caudata. Your study should include: 2 species belonging to Cryptobranchioidea, 5 species belonging to Salamandroidea + the closest outgroup to all these taxa that you can find.
25. (a) Are the Neognathae monophyletic? (b) Are the Paleognathae monophyletic? Your study should include: 3 species belonging to Neognathae, 3 species belonging to Paleognathae, 1 species belonging to Tinamiformes + the closest outgroup to all these taxa that you can find.
26. Does the phylogeny of ratites follow their geographic distribution? Your study should include: 1 Anomalopteryx species, 1 Apterix species, 1 Casuarius species, 1 Dromaius species, 1 Eudromia species, 1 Rhea species, 1 Struthio species + the closest outgroup to all these taxa that you can find.
27. Identify the phylogenetic relationships within Neognathae. Your study should include: 1 species belonging to Galliformes, 1 species belonging to Anseriformes, 1 species belonging to Charadriiformes, 1 species belonging to Falconiformes, 1 species belonging to Casuariiformes, 1 species belonging to Ciconiiformes, 1 species belonging to Passeriformes + the closest outgroup to all these taxa that you can find.
28. (a) Identify the phylogenetic relationships within the genus Gallus. (b) Are subspecies belonging to the species Gallus gallus monophyletic? Your study should include: Gallus lafayettei, Gallus sonneratii, 1 Gallus varius, 3 Gallus gallus subspecies (for which the subspecies is known) + the closest 2 outgroups to all these taxa that you can find.
29. Which of the three avian families (Anseriformes, Galliformes, Passeriformes) are more closely related to each other to the exclusion of the third? Your study should include: 2 species belonging to Anseriformes, 2 species belonging to Galliformes, 2 species belonging to Passeriformes + the closest 2 outgroup species that you can find.
30. Are the Elasmobranchii monophyletic? Your study should include: 7 species belonging to Elasmobranchii + the closest outgroup to all these taxa that you can find.
31. (a) Are the Fissipedia monophyletic? (b) Are the Pinnipedia monophyletic? Your study should include: 1 species belonging to Canidae, 1 species belonging to Felidae, 1 species belonging to Herpestidae, 1 species belonging to Ursidae, 1 species belonging to Otariidae, 1 species belonging to Phocidae, 1 species belonging to Odobenidae + the closest outgroup to all these taxa that you can find.

Changes in assignment or independent suggestions must be approved in advance by Dr. Graur.


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