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Many of the journal references in the bibliography of my thesis contain bird names. Journals use birds names in the titles of papers in at least four different ways:

  1. Titlecase, eg Teal
  2. Titlecase plus scientific name, eg Teal Anas crecca
  3. Lowercase, eg teal
  4. Lowercase plus scientific name, eg teal Anas crecca

These different ways of using bird names makes my bibliography look untidy and inconsistent.

Should I adjust the titles of the papers in my bibliography so all bird names are used in a consistent way? Or should I use paper titles exactly as how they are given?

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As a general academic principle you should not adjust the titles -- or other essential bibliographic data*, e.g. the form and ordering of the authors' names -- of papers that you reference in any way, with the possible exception of necessary typographical concessions for "exotic" characters.

(For instance, in my branch of mathematics is it common to use the cyrillic letter Sha for something named after a Russian mathematician whose name begins with this character. If you simply don't have cyrllic characters available, you have to do something else. But even in this case it would be better to try to take a little trouble to "get cyrillic characters".)

So my answer to your question is no: it is obviously not your fault that different papers you cite refer to teals in different ways. So if there is any untidiness and/or inconsistency, you are simply faithfully replicating it, as you are obliged to do.

This answer comes from someone with precisely zero avian-specific academic knowledge. So it couldn't hurt to get a second opinion from someone in your field.

*: I confess that I sometimes mess with "inessential" bibliographic data. For instance, most journals come with a volume number followed by a number of the issue within that volume, and I usually omit the second number: you simply don't need it to access the paper. I don't specifically endorse this practice and mention it only for "professional honesty", but in my defense I just checked around and I am far from the only one who does this.

Moreover in some fields there are different formats for referencing. In my field (mathematics), on the one hand we are not too picky about the format, and on the other hand we have standard repositories of all papers: MathReviews/MathSciNet and Zentralblatt, from which I assume that most contemporary authors simply copy the bibliographic data (and then the philistines among us delete the number of the journal within the volume). It is a good idea to choose a consistent format throughout all your bibliographic references: e.g. put last names first always or never, and so forth. But still: the title is not yours to monkey with, as far as I know.

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    Regarding omitting issue numbers, I always thought they were completely unnecessary, but then I learned that a few journals are paginated by issue rather than volume. If you're looking through hard copies or navigating the journal web site, then knowing the issue number becomes genuinely helpful. (But it's still irrelevant if you are doing a web search.) Commented Jul 12, 2014 at 4:01
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You should never add or remove words from the title of papers you cite. The reason you add citations is so that your readers can find these papers, and the title is one of the most important pieces of information. While it might be obvious to you that "Teal" and "Teal Anas crecca" mean the same thing, this might not be the case for others, e.g. scientists outside your field.

The issue of capitalization is a little less cut and dry. Different citation styles treat titles in different ways (title case, sentence case, or even all-caps), so you have more freedom here to be internally consistent. In addition, some automated reference systems mess up capitalization, so in my experience this is frequently something you have to fix by hand. If there is no semantic difference between "Teal" and "teal", I would pick one and apply it consistently.

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