Reference no: EM133116271 , Length: 10 pages

Question 1) Decide on a dataset: use the plant (Myrtales; Lythraceae)

Question 2) Perform a parsimony tree search on the morphological AND molecular data

Question 3) Run either a traditional search OR implicit enumeration on your datasets to ensure you find the best trees. Use the best tree(s) for each dataset (ie: the shortest tree) to make your consensus trees. The outgroup taxon will be presented as the first entry in each matrix.

Question 4) Perform a maximum likelihood tree search on the molecular data ONLY

Question 5) Perform a Bayesian Inference tree search on the molecular dataset ONLY

Question 6) Create your tree figures: Include figures for all four trees. Your classification will be based on your preferred tree (explained below) but will use the other three for comparative and informational purposes. Use Mesquite or FigTree to format the trees.

i) Tree 1 will be a majority rule consensus tree (either heuristic or branch and bound) for morphological data. If only 1 shortest tree is made, use that tree, report the finding.
ii) Tree 2 will be a majority rule consensus tree (either heuristic or branch and bound) for molecular data. If only 1 shortest tree is made, use that tree, report the finding.
iii) Tree 3 will be a maximum likelihood tree for molecular data.
iv) Tree 4 will be a Bayesian inference tree (majority rule consensus) for molecular data.
v) Tree 5 will be your preferred tree. You will have to choose your preferred tree
from Trees 1-3. Consensus values can hint at which tree is likely better, but a good way to test this is to perform a bootstrapping analysis to determine branch support, and/or calculate CI and RI to look at overall tree reliability.

Calculate bootstrapping support and calculate CI and RI for Trees 1-3. Higher Bootstrap values indicate better branch support and higher CI and RI generally indicates a better tree topology. Compare the trees, taking this evidence into account, then decide which tree is most reliable; this will be your preferred tree.

On Tree 3, the maximum likelihood tree, you will include the model chosen that best fits your data, bootstrap values, Details on model choice can be found in the PS2 manual.

On Tree 4, the Bayesian tree, you will include posterior probabilities as support values and branch lengths. You will also be expected to include relevant information such as number of generations, model chosen, and burn-in proportion. Note that posterior probabilities of <90 may be considered low support.

On Tree 5, the preferred tree, you will include bootstrap and (if your preferred tree is based on maximum parsimony) Bremer support values on the branches. There is no need to include consensus values again on this tree. Only report bootstrap values of 50 or higher on your tree.

Your preferred tree will indicate which dataset (molecular or morphological) and method (maximum likelihood or parsimony) you will base your classification on, but you still need to present the data from all your trees. You will compare them in the discussion of your report.

NOTE: Remember that when tracing character history in Mesquite, you will first need to open the matrix (the ".tnt" file), and then open your tree files. For this pratice assignment, you will need to use the morphology matrix regardless of whether you are using trees made from molecular or morphology data, because only the morphological dataset includes detailed character information.

6) Include the morphological data matrix and a list of the characters (and states) as appendices: these characters and states will be used in the description and diagnosis sections in your report . You can save your matrix in Mesquite: first, you need to be in the character-taxon matrix window. In the Data Editor window, select File > Save Matrix as PDF... Alternatively, you can copy and paste the entire matrix into Excel and edit it as a spreadsheet (in mesquite, select Edit > copy to do this). Do not include the molecular dataset if this is your preferred tree.

NOTE: This matrix can still be quite large. Feel free to make the text and columns quite small. It can help to use numbers to indicate the characters in the matrix, as long as those numbers match the character list you provide in your report.

7) Create a classification for the ingroup of your tree: this classification should be based on the preferred tree (Tree 5) that you chose in step 3 above. This classification
may be nested or sequenced. This includes giving your new species a name and naming the other clades in the ingroup if necessary:
i) Your classification must be either nested or sequenced, and you must state which it is.
ii) You should note from which tree the classification was based.
iii) The classification must reflect the relationships shown in that tree and the tree must be able to be reconstructed from the classification.
iv) Taxonomic names should have appropriate endings (e.g. "-aceae" for plant families).
THE WRITTEN REPORT:
1) Formatting:

Your paper will be written as if you were going to submit it as a manuscript to the Canadian Journal of Zoology (CJZ).

EVERYTHING must be double-spaced and each page must be numbered, including the title page. Keep standard margins (2.5 cm on all sides). You should aim for 8-12 pages of writing (not counting figures, appendices, or their captions). The maximum is 12 pages; The title
page and references should each appear on a separate page, and both count as part of your 8-12 page limit.

NOTE: You must follow the layout outlined above for your paper

NOTE: Along with the papers you will need to cite in your report, here are two other papers you may wish to consult to get a feel for systematics papers:

Burns, M.E., Currie, P.J., Sissons, R.L., and Arbour, V.M. 2011. Juvenile specimens of Pinacosaurus grangeri Gilmore, 1933 (Ornithischia: Ankylosauria) from the Late Cretaceous of China, with comments on the specific taxonomy of Pinacosaurus.
Cretaceous Res 32 (2):174-186.

NOTE: This paper is just an example of how a systematics paper may appear. If there are any discrepancies between this paper and the guidelines in these instructions, default to what is written in these instructions.

2) Citation style:
You must properly cite sources in your paper. This includes in-text citations and a Literature Cited section in your paper

3) Written Report Sections:
You will need to include the following sections in your report:

TITLE:
A good title will summarize the contents of the paper in the fewest words possible - it should be brief but descriptive. Take a look at titles of papers in scientific journals to get an idea of what a good title looks like. It must include the name of the group studied (Lythraceae), and should mention that a new species was described and that a phylogeny was constructed. Common names and correct taxonomic names should both be included in the title. Make sure the title goes on a separate page with the abstract (see below).

ABSTRACT:
This should be a descriptive paragraph that summarizes the main questions, the methods, the results, and the conclusions of your report. It is not a list of topics or an introduction, but rather a synopsis or concise summary of your paper. Its purpose is to tell people what they should expect from reading the whole paper. Main points that must be included: that a new species was discovered, its name, and where it fits in the group's phylogeny. The abstract should be no longer than 200 words. Although this section comes first, you should write it last after you have determined the main conclusions of your paper.

References should not be cited in the abstract. This also appears on the separate title page.

INTRODUCTION:
It should introduce the reader to what your report contains and why your study is important. Basically, you want to provide the background necessary for a person with a basic understanding of biology to understand what you did and why. For background information you will need to read the papers from which we took the data and cite them in your paper.

Briefly introduce your study group (what are they, where do they occur, in what types of environments, etc.) and describe the current state of knowledge and history regarding its phylogeny. What other similar studies on the group have been done? This should include information from the source papers provided. You are not required to consult additional scientific references. A good introduction will start with presenting very general information and it will then move on to more specific topics. Also, be specific about the objectives of the study: to describe and name a new species, to construct a nested or sequenced classification of the group, and to construct a phylogeny of it using morphological and molecular data.
The following questions should be answered in your introduction:
a) What knowledge already exists about this subject?
b) Why was this study performed?
c) What is the specific purpose of the study? MATERIALS AND METHODS:

The location where specimens of your new species are stored should be outlined/described in this section as well. Also note where you found them (the type locality) and the specimen number(s). Where did the data for the other taxa come from?

This section should include the methods used for your analysis. It must be sufficiently detailed to permit scientific reproduction but still concise and avoid lengthy descriptions of known procedures. It also needs to include the sources of the information/data you are using in the analysis. Where did the data for your new species come from?

Specify the types of searches (be specific, e.g., parsimony using a heuristic search, with a random addition sequence with 100 replicates), the number of characters (and their type; ordered, unordered, molecular, morphological, etc.), and the trees generated (molecular, morphological, heuristic, branch and bound, strict consensus, 50% majority rule consensus, etc.). Information about the bootstrap search should also contain this information, as well as the number of bootstrap replications done. When you include the information for how you found the decay values, remember that you used a heuristic search. Also remember to mention which tree, specifically, was used for morphological character mapping in Mesquite.

Mention the detailed version of the programs you used in the analysis (i.e., TNT 1.1). Cite the programs properly and include them in the literature cited. They are linked to actual scientific papers.

SYSTEMATICS:
This section will include the following subsections and should follow this format (I have used an ankylosaur in the genus Ankylosaurus as an example). The Characters and

References documents on loostrifes or wasps avaliable, will have the information needed to complete this section. Remember to take a look at some systematics sections in the published literature because the following is only an example - yours will likely not look exactly like it. Start off by listing the higher taxonomy pertinent to your new taxon based upon your classification. Family Ankylosauridae
Subfamily Ankylosaurinae
Genus Ankylosaurus Brown, 1908 (for when using a previously existing genus) or
Genus Ankylosaurus, gen. nov. (for naming a new genus)
Genotype: ONLY IF YOU NAME A NEW GENUS to contain your new species. Name the type species of the new genus.
Etymology: ONLY IF YOU NAME A NEW GENUS to contain your new species. What does the name of the new genus mean?

Diagnosis: This is the diagnosis for the genus to which your new species belongs. This includes the derived states for the branch leading to this part of the tree. This should be taken from characters traced onto this clade of the tree in Mesquite. It should be in telegraphic style. See example below:

Telegraphic style diagnosis example:
Apomorphies of taxon: Highest point of skull roof anterior to orbits, external nares facing laterally, tooth crown lacking cingulum. Differs from all other ankylosaurines except Tianzhenosaurus and Nodocephalosaurus in: narial region lacking accessory openings, median dermal ossification overlying dorsum of nasal region.

Included species: A list of the included species of the genus to which your new species belongs. This only needs to include the species on your tree, not any others out there in the real world. Don't forget to include your new species as well.
Ankylosaurus magniventris, sp. nov.
Fig. 1
You will need the image in which the type specimen is figured in your paper, and it should be cited in the text (e.g., Figure 1). This may be found in the Characters and References document. Although the figure is cited here, it should appear at the end of the report with the rest of the figures.

Holotype: Give the specimen # of the holotype, and where it is stored (this is on the Characters and References document for your organism).

Type locality: Where the specimen is from.

Etymology: What the new name means. Its gender should be consistent with the generic name.

Diagnosis: This is the diagnosis for the new species, based on the derived states that make it unique from its sister species (or group). This should again be based on the tree with the characters traced on it. It should be in telegraphic style. If you named a new genus for your species, this will be the same as for the genus.

Description: This is a detailed description of your new species. This includes both derived diagnostic characters and the others that (in our case) were used in the phylogenetic analysis. I suggest starting with the characters that define the other clades to which your new species belongs. You should use full sentences (i.e., not telegraphic style) for this part and group characters into short paragraphs that are related (e.g., a head paragraph and leg paragraph, or a flower paragraph and a seed paragraph, etc.). The description, for this project, should most definitely not exceed 1 page.

Habitat: Briefly describe the habitat of the new species (the internet is a good resource for info, but make sure you cite the websites!). This is the only section of the report for which you are permitted to use a website for cited information.

Results: Here you will present the results of your computer analysis. Make sure you present all five trees as outlined on page 1 of this handout as figures. The figures themselves should be at the end of the paper. The figure captions should be highly detailed/descriptive. If the tree is your preferred tree, this should be noted in the caption. All figures must be referred to in the text and should be numbered in the order that they appear in the text. The trees should be the correct ones and presented in an organized and legible fashion.

In the text, describe each tree. The "preferred" tree (this is the one your classification is based on) should be described in detail (with references to support values, general topology, etc.), and any similarities/differences from the "non-preferred" trees should be noted. Where does the new species fit? The tree length, consistency index, and retention index should be stated for the applicable trees from each data set. Additionally, state the number of most-parsimonious trees obtained from each search.

DISCUSSION:
The Discussion section should not rehash results and should not contain new findings that have not already been mentioned in the Results section. Conclusions should be put under Discussion, not as a separate section.

Discuss the differences and similarities in the structure of the tree and why you chose one data set over the other. You should also justify your selection of the preferred tree among trees 1-3(this is a good place to use branch support, overall resolution, and the distribution of characters and/or taxa on your trees). Take a few sentences to describe Tree 4. Is the Bayesian inference tree congruent with the others? Does it provide any information that the other analysis methods do not? Are the differences between it and both the parsimony and maximum likelihood trees congruent? Would you have chosen Tree 4 as your preferred tree if the instructions allowed? Justify your decision.

How did the trees from this study compare to those found in other studies? Refer to the source papers. If there were differences between your results and those of other researchers, why might this have been so? Justify the identification and classification of your new taxon. Can you further refine this based upon an analysis of the character distributions on our tree? Does the data provided by your new taxon warrant a revision of any other accepted groups/clades?

Finally, can you expand your results to say anything about the broader evolution of characters or biogeographic distribution of the organisms in your family? Any other insights will result in a higher mark than otherwise given.

Attachment:- Practice Assigment systematics.rar