Topic of the Week_Lab 6_2023

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University of Victoria *

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BIOL-186

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Biology

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Feb 20, 2024

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Name: Anna Hale Total: /10 ‘Topic of the Week’ Literature Assignment – Lab 6 The learning objectives of this assignment are to: 1) Find a scholarly article related a topic from Lab 6 using a keyword search on Web of Science. 2) Describe in your own words the i ntroduction , one of the methods used , and one result from the chosen article. Submission and Grading: Fill in the required information on this worksheet and submit it to Topic of the Week Dropbox in the Assignments module on Brightspace as a .doc or .docx file (no PDFs). Late assignments will not be accepted and will receive a grade of zero. Assignment submissions will be time-stamped by the Brightspace website.  Please upload your assignment well-before the deadline to avoid a late assignment. Always back up your work.  Lost assignments due to computer crashes, file corruption or other computer related issues will not be excused. Exercise 1. Using Web of Science , accessed through the UVic library, find a PRIMARY SCHOLARLY article using a chosen keyword related to a topic from Lab 6. Enter the bibliographic information in the table below. This table will be marked for content, not formatting. (2 marks) Keyword used Nudibranchs Title of article Cryptic ecological and geographic diversification in coral- associated nudibranchs Author(s) Fritts-Penniman, AL (Fritts-Penniman, Allison L.); Gosliner, TM (Gosliner, Terrence M.); Mahardika, GN (Mahardika, G. Ngurah); Barber, PH (Barber, Paul H.) Title of journal (Source) Molecular Phylogenetics and Evolution Date of publication 2020 Volume 144 Page Numbers (if applicable)* N/A

DOI (digital object identifier) if found 10.1016/j.ympev.2019.106698 * some articles are only available electronically and may not have page numbers Exercise 2. Refer to the links about Research Papers (primary scholarly articles) on Brightspace. Other sources may also be used. Read the introduction, have a look at the methods, and read the results. Answer the following questions. (i) In your own words and using 2-3 sentences, briefly summarize the introduction of the chosen article (2 marks) . Aeolid nudibranchs, known for specializing on cnidarian prey, offer a unique opportunity to study ecological speciation. Their specialization on specific genera or species of scleractinian corals and limited mobility could lead to reproductive isolation and speciation. This study aims to reconstruct the evolutionary history of these nudibranchs to assess the roles of host shifting and geography in their diversification. (ii) Have a look at the methods section of the chosen article. In your own words, briefly describe one experiment from the chosen scientific research article (1 mark) . 2.2 Molecular Markers The study involved sequencing genetic markers for each nudibranch in the phylogeny, including two mitochondrial genes (COI and 16S) and one nuclear gene (H3), commonly used in gastropod phylogenetics. Additional sequences from Genbank were incorporated into the dataset. To identify cryptic species and clades, the researchers amplified COI using specific primers and PCR conditions and then chose a subset of samples from each COI clade for further sequencing of 16S and H3. The coral hosts were also studied by amplifying a section of the nuclear histone 2 (H2) coding region using specific primers and PCR conditions. Sequencing was carried out using the ABI 3730 sequencer at UC Berkeley's DNA Sequencing Facility and the California Academy of Sciences Center for Comparative Genomics. (iii) In your own words, briefly describe the purpose of the results section in a scientific research article (1 mark) . The purpose of the results section is to present the findings and outcomes of the research study/studies in the article in a clear and concise manner. (iv) How are results presented, i.e. the format(s) (1 mark) ?

They are presented in tables, figures, and cladograms; with paragraphs and figure titles explaining the findings and results. (v) Provide a screenshot of one of the results from the chosen scientific research article that interests you (1 mark) . (vi) In your own words, briefly summarize the results from (v) above (1 mark) . This is a table presenting the locations and the coral hosts of the coral feeding nudibranchs in this study. (vii) Briefly describe how one of the data analyses was performed in the chosen article (1 mark) . Hint: you may also need to look in the methods section. In the data analysis, the researchers used the Analyses of Phylogenetics and Evolution (APE) package in R version 3.5, to estimate the ancestral coral host genera at the nodes of a Bayesian three-gene tree. Since the ancestral character estimation function required a bifurcating tree with branch lengths greater than zero, the researchers converted all the zero branch lengths to 1/1000000 of the total tree length because the tree had a polytomy. They used pie charts to plot the likelihoods of each character state at each node.

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