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My question concern the abbreviation of the genus of a species.

I talk about two species: Amphiprion clarkii and Amphiprion perideraion.

Question 1

Let's assume I haven't said a word about these species in my article yet. Should I say:

  • Amphiprion perideraion is a small fish and Amphiprion clarkii is a big fish

or

  • Amphiprion perideraion is a small fish and A. clarkii is a big fish

Question 2

If I talk about these two species in the abstract, should I use the abreviation the first time I cite them in the introduction or not?

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  • $\begingroup$ I would use the long form for the first citation in the main text end after that the short form. You also wouldn't put references into an abstract, so this is repeated later (even if its part of an abstract) and then correctly referenced. $\endgroup$ – Chris Jan 9 '14 at 10:28
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To avoid confusion all species names should be written in full at first, and can then be abbreviated. In this particular example it would probably not be a problem to use the second, shorter version. But what if you had four species divided into three genera with all names starting with 'A'? As for question 2, the full name usually only needs to be used in the title (if relevant) and once in the body text (which includes the abstract), so you can abbreviate after the abstract. However, this is really only a space issue, and you can use the full name at all instances (you may abbreviate, but don't have to), unless of course journal style prohibits this. I find it useful to write the name in full both in the abstract and once in the main text.

See The International Code of Zoological Nomenclature (Appendix B: General Recommendations) for a reference. To be picky, technically, authorship and year of species names should also be included at least once in each paper (e.g. Amphiprion clarkii Bennett, 1830), to clarify exactly what definition of a name you are using. However, this is often not done in practice (in fields outside taxonomy/systematics). What you often see is that people refer to a authoritative source, e.g. "... all species names used in the study follow Doe et al. (2008)."

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