BISC 495, Evolution, Spring 2018

Big paper

Choose a topic

You are required to write a "big paper" on some aspect of evolutionary biology (you'll also write a "little paper" later in the semester). You will start by finding a "focal paper" in the older literature, identifying one of the main topics of that paper, then summarizing both the older and more recent literature on that topic.

On Tuesday, Feb. 20, you must turn in:

On this an all other assignments, you must use a font with serifs, such as Palatino or Times, not a sans serif font such as Arial, Geneva or Helvetica. Serifs are the little hooks at the ends of letters. I'm sorry if I've offended your favorite font, but I just think sans serif fonts are ugly and harder to read. The font size must be 12 point (if you're using Times font) or 11 point (if you're using anything else).

You should think of the "main topic" of your focal paper (and thus the paper that you write) as the biological question that the paper is trying to answer. For example, if you used the Kong et al. (2012) paper that you read for the second day of class as your focal paper, you could think of the main topic as "What is the effect of father's age on mutation rate?" As you get into the literature research for your paper, you may find that you need to narrow the focus down, so that you don't have an overwhelming number of references to read. You might have to narrow down the topic to "What is the effect of father's age on mutation rate in humans?" Or, your initial topic might be so narrow that it would be difficult to write a 12-page paper about it, and you might need to make it broader: "What causes mutation rate differences among individuals in a species?" Try to think of a topic that you can research in depth, without getting overwhelmed by too much information or frustrated by too little information; I'll offer suggestions to help you.

Your topic choice assignment will be worth two percent of your overall grade for the class. One-half point will be deducted for each day it is late. It must be typed.

I want your focal paper to be from the older literature, so that you get practice in starting with an older paper and finding more recent information on a topic; and I want it to have evolution as the primary focus. For this reason, you must pick a focal paper from the journal Evolution, in the year that equals 2000 plus your birth month (2001 if your were born in January, 2002 for February, etc., up to 2012 for December). Your focal paper must have been cited at least 10 times.



To see the papers in Evolution from your year, use the Web of Science (see the Guide to searching for biological literature). Do a Basic search with "evolution" as the Publication Name and your year as Year Published, as shown above. This should give you a couple hundred papers to choose from. You can skim through all the titles, looking for something interesting, or if you have a particular topic in mind, you can add a Topic search box to your search.

Look through the titles, pick out some that sound interesting, and look at their abstracts. Get the full text of the most interesting papers, skim through them, then decide on the one you want for your focal paper. Identify the main topic of the paper; if there are more than one, choose the one you're going to concentrate your paper about. Make sure the paper has been cited at least 10 times; you might want to skim through the titles of the papers that have cited your focal paper, to make sure they'll give you something substantial to write about.

If at some point you decide you picked a horrible paper and you want a different one, send me an e-mail asking for approval of the new focal paper. It must still be in Evolution, published in your year, and it must have been cited at least 10 times. If at some point you want to keep the same focal paper, but concentrate on a different aspect of it than you originally planned, you don't need my approval.

If you really, really want to do a topic that isn't in the journal Evolution for your year, find a focal paper on your proposed topic. It must be from 2001 through 2012, and it must have been cited at least 10 times. If you want to do a non-Evolution focal paper, you must e-mail me all the information listed above for your proposed focal paper by 11:59 p.m. Friday, Feb. 16. I'll decide whether the paper has enough evolution and is narrow enough in focus. If it isn't, you'll have to pick a paper from Evolution.

Literature research

On Tuesday, Feb. 27, you must turn in a typed list of references on your topic. This will be worth 4 percent of your grade; one-half point will be deducted for each day it is late. The references must be in the format shown below. You must use a serif font.

You must staple your graded first assignment to the back of this assignment. Do not use a paper clip or binder clip; you must use a staple. You're an adult now, and part of being an adult is owning a stapler.

Your list of references should be thorough, including everything on your specific topic. Look at your focal paper, and find every reference that they cite that is relevant to the subject of your paper. Also look at the more recent papers that have cited your focal paper, and list every relevant paper. Keep doing this--for every paper you get, see who they cite and who has cited them--until you're not seeing anything new.

Your reference list will be graded based on its format (see the examples below) and its thoroughness. If I can quickly find references that are very relevant to your topic that you haven't listed, you'll get points off. In some fields of biology, such as cell and molecular biology, laboratory techniques are so important and improve so rapidly that papers from 20 years ago are only of quaint, historical interest. But for many topics in evolution, even very old references are important. Advances in evolutionary biology often depend less on technical advances and more on synthesizing scattered bits of information, and sometimes that information is found in papers that are many decades old. So don't limit yourself to recent publications, even though the older ones may be harder to obtain.

As you assemble your list of references, you should start obtaining them so you can read them. Some will be available online, some will be in print in the Morris library, and you'll have to obtain some by Interlibrary Loan. Don't wait until the last minute to obtain your references; the ones you get by Interlibrary Loan, in particular, may take a while to arrive.

Your reference list must contain at least 25 references. You may include web pages on your list, but they do not count towards the 25 references. You may not include Wikipedia; it can be a valuable place to start looking for some kinds of information, but you should trace the information back to its original source and cite that instead. If you are having trouble finding 25, keep in mind that you'll want some more general references in addition to everything on your narrow topic. For example, if you were researching the adaptive radiation of Hawaiian spiders, you'd want a few references on the general topics of adaptive radiations, a few references on spiders, and a few references on the geologic history of the Hawaiian islands, in addition to all of the references you can find that are specifically about the adaptive radiation of Hawaiian spiders.

You will not need to use all of this initial list of references in your final paper--as you read them, you may find that some are not as relevant as the titles suggested. You may add additional references between now and writing the paper.


An outline of the paper is due Thursday, March 8 Tuesday, March 13. It is worth 4 percent of your grade; one-half point will be deducted for each day it is late. You must attach the previous two assignments (the topic choice and the reference list) to the back of the outline.

One of the things I'll be looking for in the term paper is clear organization. You may want to organize your paper chronologically, starting with the earliest research on your topic and moving forward. You may want to organize by different techniques used to address your topic, or by different aspects of the general topic, or by different individuals or groups of people who have investigated your topic. The important thing is that there be some kind of clear organization, not just a random jumble of unconnected facts.

When writing your outline, you can use Roman numerals for the top level, then capital letters, then numerals, then lower-case letters. You don't have to have four levels. This format is not required; you can use any outline format you want, as long as the heirarchy of topics and subtopics is clear.

You should probably have one line at the lowest level of the outline for each paragraph in the final paper. At this level, you must include some of the citations you'll use, in the format shown below. You don't need to reprint the reference list; I'll look at the previous, graded one if I want to look up one of your citations.

Here's part of an outline of a paper on adaptive radiations in Hawaiian spiders. I've made up some of the citations, because I'm lazy and I'm not getting graded on this:

I. What is an adaptive radiation? 
   A. History of the concept (Schluter 2000)
   B. Classic examples of adaptive radiations
      1. Galapagos finches (Darwin 1859; Lack 1940; Grant and Grant 2003)
      2. Lake Victoria cichlid fish (Kornfield and Smith 2000; Salzburger et al. 2005)
II. Evolution of spiders in general
   A. Systematics (Parker and Jameson 2003)
   B. Fossil record (Spinne and Makari 2007)
   C. Anatomy
      1. Feeding structures (Araña and Geomi 1983; Kumo 2009)
      2. Web-spinning structures (Anlalawa 2000)
III. Spiders in Hawaii
   A. Geological history of the Hawaiian islands (Pele and Haleakala 1982)
   B. etc., etc.

The finished paper

The final version of your term paper is due in class on Tuesday, April 10. You should not attach any of the previous assignments to the term paper. Three points (out of a possible 23) will be deducted for each full day that the paper is late; you will get two points off if you turn it in after class but before 7 p.m. on April 11. As with all assignments, if you have printer problems, car problems, etc. and can't turn in the print version on time, your lateness penalty will depend on when you e-mail me the paper; you must then give me the print version at the next class or at my office (322 Wolf).

Everyone must e-mail the paper to me by the end of the day on April 10 (not just those with printer problems). The file can be in any format (Word, OpenOffice, Pages, pdf, plain text, etc.), and the name of the file must be your name (such as "JaneStudent.doc"). Unfortunately, I have had several cases of plagiarism in the past in this assignment. If I suspect your paper is plagiarized, the file will make it easier to search the web for matching sentences.

The paper must be typed and have at least 12 full pages (i.e., to the bottom of page 12) of double-spaced text, not including figures or the reference list. The reference list may be either single- or double-spaced. Do not use unusually wide margins, large font, increased line spacing, etc. to make the 12-page limit; just grit your teeth and write some more. You must have some figures, but they don't count towards the 12 pages; thus if you have four half-page figures, your paper must be at least 14 pages long.

Your paper should summarize the literature on your topic. It should be clearly organized, either chronologically or by sub-topic. For example, the Hawaiian spider paper could start with the oldest studies on adaptive radiation in Hawaiian spiders, then work up to the most recent research; or it could have different sections for different groups of spiders, or different islands, or different adaptations. Even if I said your outline (due March 8) was good enough, when I see the finished paper, I might decide that it is badly organized and take points off.

In addition to the results of the different studies, describe how those results were obtained. If you are struggling to fill 12 pages, this is probably what you need more of. What kinds of experiments and observations did people make? How did they interpret them? What were the competing hypotheses? Have later researchers interpreted earlier results in different ways, or come up with new hypotheses?

Do not use jargon that your classmates would not understand without explaining it. In particular, do not use phrases that you have read if you don't understand them. If you can't figure something out, ask me and I'll try to help.

The reference list must include at least 25 references, strictly following the format shown below. You may include web pages, but they don't count towards the minimum of 25. You may not cite Wikipedia; it can be a useful first step in researching a topic, but for this paper, you should look at the original references cited by the Wikipedian rather than trusting their interpretation.

One of the key things I'll be looking at is the thoroughness of your literature research. I will pick one or two key references on your topic, then take a quick look at their reference lists, and the papers that have cited them. If I find some papers that you didn't cite that are very relevant to your topic, you'll get points off. Even if I said your initial reference list (due Feb. 27) was good enough, I might do a more thorough job of checking, realize that you missed some obvious references, and take points off.

Text format

You must follow these formatting rules. They may seem picky, but following them demonstrates your ability to follow instructions exactly, an important skill for both research biologists and medical professionals.


You must include figures that illustrate the main points of your paper. Because this is a student paper, and not something that you're going to publish, you may copy figures from books, articles, and the Internet without asking for permission from the authors. You must, however, cite the original source of the figure in the figure legend. You must write your own, original figure legend; don't just copy the figure legend from the source of the figure.

To copy a figure from a web page, control-click on the figure (Mac) or right-click on the figure (Windows) and choose "Copy Image" from the menu. Then go to your document and Paste. To resize, click on the image, then drag a corner to make it smaller or larger.

Copying from a pdf is a little more complicated; you'll have to do a screen capture, copying the image as it is shown on your computer screen:

Macintosh: While viewing the pdf, zoom in until the figure you want fills as much of the screen as possible (this will make it look less pixellated when you copy and paste it). Then hit the Control, Command, Shift, and 4 keys simultaneously. The cursor will change from an arrow to a crosshairs. Drag the crosshairs from one corner of the region you want to copy to the other corner. When you release the mouse, the area of screen that you dragged across will be copied to the clipboard. Paste it into your document and resize it.

Windows: While viewing the pdf, zoom in until the figure you want fills as much of the screen as possible. Get the cursor out of the way. Then hit the Print Screen key (it may say PrtScn). The entire screen is now copied to the clipboard. Open up a graphics program, such as Microsoft Paint (this should come with Windows). Paste the image of the screen into Paint. Choose the rectangular select tool (the dashed rectangle) and select the area you want. Copy it, then Paste it into your document, then resize it.

If you want to use a figure from a printed book or journal, you can use a scanner; there is one you can use in the basement of the Morris library. Or you can take a picture of the printed figure. If you have to scan or photograph a figure, make sure you do a good job; don't paste a blurry, dim, slanted figure into your paper.


Copying someone else's writing and pretending that it is yours is a serious violation of the University's Code of Conduct. If you copy text from a book, article, web page, or other source, you will receive a 0 for the paper. If the copying is particularly extensive or egregious, you will receive an F for the course. This is not an empty threat; there have been several students in the past who didn't graduate in the spring because they needed this class to graduate and earned an F due to plagiarism.

To illustrate what is and isn't plagiarism, here's a passage from Hudson et al. (1987):

The presence of a balanced polymorphism in the coding region of Adh could explain the relatively high level of polymorphism observed in that region. The existence of a balanced polymorphism at a single site can lead to higher levels of neutral polymorphism at linked sites (Strobeck 1983). The reason this can occur is that during the time that the balanced polymorphism is maintained by selection, new mutations will tend to accumulate in the region tightly linked to the selected site.

Copying these words exactly is plagiarism, even if you put "(Hudson et al. 1987)" at the end. It's also plagiarism if you just change a few words, like this:

A balanced polymorphism in the coding region of Adh could explain the high level of polymorphism in that region. The existence of a balanced polymorphism at a single site can cause higher levels of neutral polymorphism at linked sites (Strobeck 1983). This is because during the time that the balanced polymorphism is maintained by selection, new mutations will accumulate in the region tightly linked to the selected site (Hudson et al. 1987).

Instead of copying or trying to rewrite a passage, you should paraphrase it, summarizing the information in your own words:

There is an area around an amino acid polymorphism in Adh that has a relatively high level of silent polymorphism. This may be caused by balancing selection (Hudson et al. 1987).

If you find yourself staring at a sentence in a paper, struggling to think of a way to rearrange the words in that sentence just enough to keep it from being plagiarism, you're going down the wrong path. Read several paragraphs, set them aside, then write down a summary of the main points. Don't try to write about things you don't understand.

For more examples of plagiarism, see this report on a paper in a major scientific journal that was retracted due to plagiarism that I helped to detect.

Direct quotes

In papers in other fields, such as English or history, it is common to use many direct quotes, putting phrases or sentences from sources in quotation marks. This is because the exact words are important; if you're writing a paper on "The meanings of dust in Kafka's Metamorphosis," it's important to quote exactly what Kafka wrote about dust; his words are your "data," and you want to represent the data accurately. As long as you cite the source correctly, using quotes in quotation marks is not plagiarism.

In scientific writing, however, we rarely use direct quotes. Partly, this is just a cultural tradition; partly, it's because when scientists cite another paper, it's because they're writing about the information in the paper, and the exact words used to convey that information are not important. You may use a quotation or two, if you come across a particularly pithy statement of an important concept, but you will get points off for excessive use of direct quotes (because it can be a lazy way to fill up space).

Active vs. passive voice

Most scientific papers are written in the passive voice: "Two cm was cut from the end of each mouse tail, DNA was extracted from the tail segment, and the FOX2P gene was sequenced." Some people hate the passive voice and prefer the active voice: "I cut two cm from the end of each mouse tail, then I extracted DNA from the tail segment and I sequenced the FOX2P gene." The active voice is livelier and more interesting to read; it creates a more vivid word picture, it's easier to imagine the razor blade slicing through the poor mouse's tail in the second sentence. However, the active voice can be difficult to use accurately. Most scientific papers have multiple authors, so the active voice would use "we." However, if Johnson, Hussein, Ramachandran and Xie write "We cut two cm from the end of each mouse tail, then we extracted DNA from the tail segment and we sequenced the FOX2P gene," it could be a little inaccurate. Hussein may have cut the mouse tails, Johnson and Ramachandran may have extracted the DNA, and someone at a core DNA sequencing facility (whose name isn't even on the paper) may have done the DNA sequencing. Xie may have gotten the grant money and helped write the paper, but never actually touched a mouse or its DNA. It may seem trivial, but any hint of inaccuracy in a scientific paper is a big, big deal.

You may use either the passive or active voice for your paper. If you use the active voice, you must be accurate: don't say "we" if you mean "I", don't say "I" if you mean "we", and don't say "we" without explaining who the "we" are.

Names and pronouns

When a paper has two or more authors, refer to them as "they"; don't ignore the "et al." and refer to the author as "he" or "she": "Hudson et al. (1987) developed a new statistical test for selection, which they first applied to DNA sequence data on Adh."

If a paper has a single author, use "he" or "she" if you're confident in the correct pronoun: "McDonald (2013) studied allozyme variation in the amphipod Megalorchestia californiana, but he didn't find anything very interesting." If you don't know an author's gender (or if you know that the author prefers "they"), you should use "they" as the pronoun: "Weiner (1937) reviewed the evidence on earlobes, and they concluded that earlobes did not fall into two discrete categories, 'free' and 'attached." Using "they" as the "singular indefinite pronoun" will make some strict grammarians cringe, but it has a long history in English, going back at least to Shakespeare, and is a useful, sensible, and understandable solution when you don't know someone's gender. Do not assume that just because a paper is very old, its author was male. Despite the tremendous obstacles put in their way, women have been doing research and publishing scientific papers throughout the history of scientific publishing, so don't use "he" unless you know the author is male.

Some people change their name after they have started publishing scientific papers, which means one person will have publications under more than one name. Use their current name when referring to them as a person; use the name on each publication when referring to the work of that publication, since that's the name on the publication: "Cathy Laurie was one of the first researchers to study the fitness effects of non-coding DNA sequence variation. Laurie-Ahlberg and Stam (1987) used P-elements to transform lines of Drosophila melanogaster and study the effects of variation in an intron in the Adh gene, while Laurie et al. (1990) used a similar technique to compare Adh expression between D. melanogaster and D. simulans."

Citation format

Citations in the text must follow the author, year format: (Lewontin and Hubby 1966; Kreitman 1983; Hudson et al. 1987). There is no comma between the author and year, and multiple citations are separated by semicolons. Use "et al." for three or more authors. If the authors' names are part of the sentence, they are not in parentheses: "Lewontin and Hubby (1966) surveyed allozyme polymorphism in Drosophila pseudoobscura."; "The fly species Drosophila pseudoobscura has extensive allozyme polymorphism (Lewontin and Hubby 1966)." If there are multiple citations in a single set of parentheses, they are in chronological order from oldest to most recent.

Do not give the paper title or journal name in the body of the paper. Don't say, for example, "Richard Hudson, Martin Kreitman and Montserrat Aguadé, in a paper titled 'A test of neutral molecular evolution based on nucleotide data,' published in Genetics in 1987, developed a method to detect selection using variation in the ratio of polymorphism to divergence." Instead, say "Hudson et al. (1987) developed a method to detect selection using variation in the ratio of polymorphism to divergence."

Web pages should be cited using the author and year, if that information is available; this page would be cited as McDonald (2018), for example. If the web page does not say when it was written, say "undated." If there's an institutional author, list that; UD's home page could be cited as University of Delaware (2018), for example. If there's no apparent author of any kind, say Anonymous. Remember that while you may cite web pages, they do not count towards the minumum number of references.

The Literature Cited section must include all of the literature cited in the text, alphabetically by first author, in the following format. If there are more than one paper with the same first author, they go alphabetically by the second author's last name, etc. If there are multiple papers by the exact same author or set of authors, they go from oldest to most recent. If there are multiple papers by the same author from the same year, they are distinguished by an a, b, c, etc. after the year in both the Literature Cited and the in-text citations.

For journal articles, the format consists of the following, in order:

There are two kinds of books you're likely to use; I'll call them "regular books" and "edited collections." A "regular book" has a single author or set of authors for the whole book. It counts as a single reference for the term paper. A regular book is cited the same as a journal article, except instead of the journal, volume and page numbers, you give the publisher and the publisher's city. Do not abbreviate book titles. "Edited collections" have one or more editors for the whole book, but each chapter has a different author or authors. Each chapter that you cite counts as a separate reference for the term paper. You cite a book chapter the same as a journal article, except instead of the journal, volume and page numbers, you give the pages, the editors of the book, the title of the book, publisher and city.

Web pages can be tricky to cite, as it's often not clear what the author, title, and year are. Follow the format shown below as best you can, and don't worry if you're not exactly sure you're right; unlike journal articles and books, I won't be very picky about how you cite web pages. Remember that while you should cite web pages that you use as sources, they don't count towards the minimum number of references needed for the paper.

Here are some examples of citation format:

Journal articles

Hudson, R. R., Kreitman, M., and Aguadé, M. 1987. A test of neutral molecular evolution based on nucleotide data. Genetics 116:153-159.

Methe, B. A., Nelson, K. E., Deming, J. W., et al. (24 co-authors). 2005. The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses. Proc. Natl. Acad. Sci. USA 102: 10913-10918.

McDonald, J. H., and Kreitman, M. 1991a. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654.

McDonald, J. H., and Kreitman, M. 1991b. Scientific correspondence. Nature 354: 116.

Slater, G.J., Figueirido, B., Louis, L., Yang, P., and Van Valkenburgh, B. 2010. Biomechanical consequences of rapid evolution in the polar bear lineage. PLoS One 5: e13870.

Regular books

McDonald, J. H. 2014. Handbook of biological statistics, 3rd ed. Sparky House Publishing, Baltimore.

Book chapters in edited volumes

Hall, B. G. 1983. Evolution of new metabolic functions in laboratory organisms. Pp. 234-257 in Nei, M., and Koehn, R. K., eds. Evolution of genes and proteins. Sinauer Associates, Sunderland, Mass.

Web pages

Gregory, T. R. 2018. Animal genome size database.

University of California Museum of Paleontology. 2018. Understanding evolution.

Anonymous. Undated [viewed February 3, 2018]. Frequently asked questions about creationism and evolution.

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