Citations are a means of recognising that your work is built on the work of others. They are part of the fundamental tenets of science that we don’t start from scratch each time we conduct a study.
Isaac Newton (in a letter to Robert Hooke in 1675) wrote:
“If I have seen further it is by standing on the shoulders of Giants.”
Although the phrase is often attributed to Isaac Newton, it turns out that it was a well accepted phrase in Newton’s time and has been traced back to the 12th century.
Essentially, standing on the shoulders of giants (Figure 15.1 is a recognition that all research is built upon research that has gone before it, and this is the basis for citations in the text of scientific papers. Patrick Dunleavy (2017) argues that citations are required to meet 7 criteria with respect to academic writing. Others have suggested that there are more criteria (see Harwood, 2009), and that these are a fundamental premise of academic work. But it was not always thus. If we dwell a moment longer, we can look back at the World’s longest-running scientific journal: Philosophical Transactions of the Royal Society.
You can download the first of those papers of 1665 and note that there are no citations (other than to books or letters) because there were no previously published articles from which to draw (Figure 15.2). However, even then, authors noted that ideas came from previous authors and we can regularly find acknowledgements that refer back to Aristotle (~350 BC).
It would therefore be very unlikely that your idea/ideas has no basis in existing literature. If you can’t find it, the chances are that you haven’t looked in the right way. Try Google Scholar, Scopus, Web of Science and vary the search terms or try searching for articles citing something similar.
Citations demonstrate to readers where your ideas have come from. Citations can also be used to reduce what you need to write – especially with respect to methodology. If you (or others) have already provided the methodology in full then you can give a much simpler description and the citation.
Citations need to be used to back up any statements of fact that you make in your PhD chapter. Any examples need citations for where the examples came from, and when you make arguments, you add credibility to your arguments from each side by citing that these are from published works.
When you choose to cite one paper over another, you are making a statement about what you find credible in the literature and what you don’t. For example, if you choose to cite a poorly conducted study as the cornerstone for one of your arguments, then others may interpret that your arguments are built on shaky foundations. Experienced (often senior) readers who know the literature well will be able to judge the quality of your work not only by what you’ve written, but on what you’ve based your ideas through your citations. As we will see later on, there’s a lot to think about when deciding what to cite, and what not to cite.
Automatically, I’d suggest that you cite whenever you write. Using citations becomes habit forming, and you’ll end up wanting to use citations everywhere. Popular scientific writings tend not to have citations, but they can still be there but subtly different.
Within a manuscript for a scientific journal or in your thesis, you can expect that your introduction and discussion sections are going to be full of citations. The methodology will likely also be citation rich. By using a lot of citations in your methods, you can often save your needing to write a lot of sections which would otherwise be very detailed.
Later in the book (Writing with a Formula), I explain how to start writing with an outline, then flesh out the outline with citations from your reading, and plan which citations you are going to use carefully before you start. This won’t stop you from adding more later, but this ensures that your work is built on your scholarly endeavour.
I’ve seen many students try to write their text first and then only later fill in citations. I’ve had students hand in thesis chapters and manuscripts that have ‘[ref]’ written strategically at the end of many sentences. I’ve even had the experience of doing this myself when I was an early career researcher (I probably still have those manuscripts somewhere because it’s a sure way of never getting anything finished). I suggest that you do not do this. The reason is that if you write first and try to insert citations later, you are going to spend lots of time looking for the citation that fits your text. This is clearly not the right way around. Your text should be based on what’s present in the literature.
I was planning to write that no-one would ever write an entire manuscript without references, and then put them all in at the end. Then I came across a video by Pat Schloss, and realised that I’m wrong (Schloss, 2018). Pat states early on (in the video) that he prefers to write first and cite later. He’s clearly a very experienced researcher and knows his literature very well. Indeed, he knows it all so well that he already knows what citations fit what statements without needing to look them up. However, later on in the video, Pat admits that even he sometimes gets it wrong, and that means that he ends up having to rewrite text when he finds the publication that he was thinking of and notes that what they actually found did not fit what he wrote. Although I can identify with what Pat is saying, I would find this re-writing far too time consuming to take this approach myself. I am familiar with most of the pertinent literature in my specialist area, but I’d rather check things before I start writing than leave it until later. I find that my memory is not only wrong about what other people have found but also about what’s in my own work. Therefore, I’d suggest that while you may aspire to write like Pat later on in your career, right now it’d be better for you to plan your writing with citations in mind, and cite while you write (not afterwards).
When you submit a draft of your chapter to your advisor, they may suggest additional citations that are known to them. Don’t simply add blindly, but look them up and check their relevance to the statement concerned. They may require recrafting of the statement, or a query back to your advisor.
There are a number of different styles, and this is likely to depend on the journal that you are writing for (see Pandey et al., 2020). The two most prevalent styles in biological sciences are often referred to as Harvard (name, year) and Vancouver1 (superscript numbers that are listed in the reference section). Most universities and journals require Harvard style. The intricacies of how exactly this will get carried out will change from institution to institution and journal to journal. You will have to find out what is relevant to you.
Vancouver style dates back to medical journals in the 1970s and refers to conventions to avoid fraud in medical sciences. You are probably familiar with it, even if you don’t know the name. It is the convention that uses small superscript numbers to denote the place of citations in the main text, and the full reference given at the end of the document is provided in order of the citations (and their numbers), instead of alphabetical order. In biological sciences, Vancouver style is not used as widely as Harvard style, but is chosen as the superscript numbers tend not to impede the flow of the text for the reader.
Each style has its pros and cons. Vancouver style is more equitable and anonymous, as all cited people are represented only in the references and do not have their names plastered throughout the text. The diminutive numbers take up less space, allowing the reader and writer to concentrate more on their prose. On the other hand, if you are familiar with the literature, or you are interested in learning more about the literature, you’ll find that the little numbers take much more time to cross-reference with the list at the end, than does Harvard style. Reference strings in Vancouver style can either be separate numbers, or numbers listed as a series. Because citations are numbered in the order in which they first mentioned, citation strings later in documents often end up as a list of non-sequential numbers separated by commas.
Here is an example of text (from Measey et al., 2016) with citations in Vancouver style:
Amphibian populations are currently declining across the globe1-3 and alien amphibians are at least partially driving these declines through competition4, hybridization5 and introduction of novel pathogens6-9.
The standard way is to use the name and year in parentheses at the end of the statement to which the citation is relevant. Names of three or more authors are frequently reduced to ‘et al.’ (often written in italics: et al.) which is short for the Latin et alia, meaning ‘and others’. References strings in Harvard style can go on for an entire line of text or more. Some journals have rules that mean on the first mention, the citation should have all authors (up to a certain number). This can become tedious when citations start taking up more space than text.
A repeat of the above example, except with Harvard style shows how much more space these same citations take up.
Amphibian populations are currently declining across the globe (Wake and Vredenburg, 2008; Collins et al., 2009; Pimm et al., 2014) and alien amphibians are at least partially driving these declines through competition (Kupferberg, 1997), hybridization (Dufresnes et al., 2015) and introduction of novel pathogens (Berger et al., 1999; Daszak et al., 2003; La Marca et al., 2005; Martel et al., 2013).
From here on (and throughout the book - because the book uses a form of Harvard style), I concentrate on Harvard style as this provides more freedom for how citations can differ.
Moving within styles is always a hassle, especially as formatting the references can take a long time, but moving between these styles is especially tricky as it may require you to re-evaluate the way in which you use the citations.
Moving from Harvard to Vancouver style means that every time you would have had the year and date, you will replace this with a superscript denoting the number for that particular citation. However, Vancouver style does not allow for much variation in how you cite. You can’t use (e.g. 1,2) or (see 3 for a review). This means that when you originally wrote for a Harvard style journal, but then change the manuscript to submit it to a journal that uses Vancouver style, you’ll need to remove any explanations of citations. That doesn’t mean removing the citations themselves, but it may mean re-writing some sentences. Simply changing your reference manager to use a different referencing style will only be the start of your work.
There are a number of different styles, and this is likely to depend on the journal that you are writing for. The standard way is to use the name and year in parentheses at the end of the statement to which the citation is relevant.
The impact of all invasive amphibians is similar to that of invasive birds and mammals (Measey et al., 2016).
But there may be a lot of papers that have found the same result, and you might want to only cite one as an example.
Invasive amphibians have some serious impacts on their recipient environments (e.g. Measey et al., 2016).
You’ll see that sometimes the names are brought into the sentence and become the central agents of the text.
Sometimes, instead of ‘et al.’ you can write ‘and colleagues’ or ‘and others’. This is something to do occasionally when you are looking to diversify some text. Don’t over do it though.
Measey and others (2016) found that the impact of invasive amphibians is comparable to that of birds and mammals.
This technique is very useful when you then want to add another sentence or two about this same study.
Measey and colleagues (2016) found that the impact of invasive amphibians is comparable to that of birds and mammals. They did this by constructing GISS scores for all individuals in all groups.
Because the authors are the subjects of the first sentence, the citation becomes implicit in the second sentence. Then you don’t need to use the same citation again within the paragraph.
Sometimes you’ll see a citation with a colon and page number after. This really only needs to be used if you are quoting specific text on a particular page:
Measey et al. (2016: 976) proposed that using GISS scores could show that “some amphibians can have devastating impacts to the environment”.
Citations use brackets, and brackets are also used for other parts in writing. The problems with brackets often come when trying to combine citations that have brackets with the other parts of writing that also need the brackets. This is compounded when trying to do all this in citation software when you don’t have complete control over it.
Most citation software allows for flexibility of how you will use your citation. In the above examples we have seen the full citation, a version where just the year is included in the brackets, some text occurs before (prefix) or after (suffix) the citation within the brackets, or even a combination of these:
- The classic: (Measey et al., 2016)
- Omitting the authors: Measey et al. (2016)
- Using a prefix: (e.g. Measey et al., 2016)
- Using a suffix: (Measey et al., 2016: 976)
- A combination of the above: Measey et al. (2016: 976)
Citation software handles producing these different ways by omitting the author, adding a prefix, or adding a suffix, respectively. However, the default will be to use the classic version, and you will need to alter this to one of the others in the software as you are citing it (i.e. as you add it to the document).
It is very common that people simply don’t know how to do these different ways of citing within their citation software. The easiest is to look up “how to add suffix” or whatever it is that you want to do in the respective manual or in your search engine. The result of not being sufficiently skilled in your citation software, is that you end up with confused text - and usually a surfeit of brackets. The examples below are all mistakes that I regularly see in theses and manuscripts:
Measey et al. (Measey et al., 2016) found that the impact of invasive amphibians is comparable to that of birds and mammals.
Invasive amphibians have some serious impacts on their recipient environments (e.g. Measey et al. (2016)).
Invasive amphibians have some serious impacts on their recipient environments (e.g. (Measey et al., 2016)).
The above examples are obviously wrong (i.e. obvious to an examiner or reviewer), and immediately suggest that the writer hasn’t invested enough time in mastering the citation software, or isn’t aware that what they have produced is incorrect. I’d encourage you to take the time to correct these kinds of errors in a timely manor, or at least before submitting your thesis or manuscript.
It is better to combine information into one set of continuous brackets instead of having back to back sets of brackets. You can do this by using a prefix or a suffix as below:
Some invasive amphibians have been investigated insufficiently compared to their impact (e.g. Asian common toads: Measey et al., 2016).
Instead of back to back bracketing as follows:
Some invasive amphibians have been investigated insufficiently compared to their impact (e.g. Asian common toads)(Measey et al., 2016).
If you must have brackets nested within each other (and I would argue that this is very unusual), then rather use different types of brackets, such as square brackets inside round brackets. But make sure that you do this consistently throughout your thesis or manuscript.
A citation string is a list of two or more citations that all assert the statement given. When you provide a string of citations, you will need to decide which one comes first. Normally, this is given in the order of precedence: the oldest citation comes first, the youngest last. However, journals have their own styles and these may dictate how citation strings are ordered. For example, they could be alphabetical. If your referencing software has a style then you can relax. Otherwise, you’ll need to look it up!
Yes. One of the most common ways in which students mis-cite a paper is to use statements made in the introduction (or discussion) which were not the subject of the study. For example, in the introduction of their paper, Measey et al. (2016) make comments on amphibian decline (see above).
However, it would be wrong to give a statement on amphibian decline and cite Measey et al. (2016). They did not study amphibian decline. Instead, you should read the papers that they cite (e.g. Wake & Vredenburg, 2008; Collins, Crump & Lovejoy III, 2009; Pimm et al., 2014), and read around those to find studies on amphibian decline that are appropriate for your context. This kind of mis-citation has been called an ‘empty citation’ (Todd et al., 2007), and underlines one important aspect of choosing citations where the statement that you make relates directly to the study carried out in the citation.
Todd et al. (2007) looked at mis-citation rates in ecology, concluding that only around three quarters of papers were correctly cited. They found that 11% of citations were ambiguous, and 7% had citations that did not support the statement. Around 5% of citations were classed as empty - citing works that cite works with relevance - also known as ‘lazy author syndrome’.
Another common mistake is to forget which paper has which information. You can try to make sure that you don’t do this by taking better notes or write a more accurate plan. And do the citations before or as you write, not afterwards!
No. When you are citing a study, you should be sufficiently familiar with the publication that you are endorsing the study in relation with the statement that you make (but see below). If you are not convinced by the nature of the study that you are tempted to cite, then rather don’t cite it and use another one. If you can’t get hold of the paper, this is another reason why you might not cite it. This is a regular reason given for why Open Access journals attract more citations.
This does depend on the journal you are writing for. Some journals don’t permit citations to unpublished data or web sites. My suggestion would be to avoid such sources anyway (with particular exceptions – see below), unless it is really important that you include it. Other examples of texts to avoid are: text books (use the original paper instead), newspapers or magazines, blog posts, Facebook pages (or other social media sites), predatory journals (or any non-peer-reviewed article). These are all examples of grey literature.
There are, of course, exceptions. When you are writing about social media sites, or newspaper coverage, you will want to cite those sources.
I don’t like citations to guide-books or general text books. This has become very common, but really smacks of laziness. Most of what’s written in a guidebook has already been documented in the scientific literature, but guide-books generally don’t provide sources for the information that they provide. Thus, it’s easy to look up and find something in a guide-book but suggests (to me) that you haven’t spent enough time or effort reading the literature. Some guide-books are excellent and the authors have gone to a lot of trouble to incorporate original data and observations. But this is unusual, and most data can be found in publications.
One exception to not citing websites is the IUCN Red List. Note that all entries on this site now have DOIs, and this might be a good guide for what is available to cite. The Digital Object Identifier (DOI) is very useful as it means that there is a consistent record of that version. Otherwise, you could cite any website and then the owner can go and change the site and it no longer says what you thought it did. The DOI removes this problem; there will always be an archived version with that particular DOI.
You should not cite papers that have been retracted.
The primary literature consists of studies or experiments that are done in order to test a hypothesis. Secondary literature includes reviews, syntheses or meta-analyses. Primacy (see below) is important, but this depends on the space you have and whether the review contains all the information you need to cite. Sometimes reviews (especially meta-analyses) provide more information. It’s preferable to use primary literature, but sometimes reviews (or meta-analyses) are actually more expedient to use, especially if they are not the focus of your study. You can even cite both when relevant. Todd et al. (2007) suggested that citing review articles might occur when postgraduate students do not have access to sufficient literature because of pay-walls.
The rule of priority (or primacy) in the literature is that those paper/s where the authors first provide the original idea or concept, or evidence for this are the ones that are cited (Strevens, 2003). Papers that are published afterwards, are simply seen as repeating the same story as those who published first, even if the time-lines of the research itself don’t reflect this. The rule of priority makes sense, in that we have an obligation to name the shoulders on which we stand (Figures 15.1. Thus, it is important in that you should give credit to original ideas over those who copy or simply repeat them, or even those who review them. Tracing back the origins of ideas makes for interesting reading and a deeper understanding of your subject.
Sometimes primacy is less important, especially if the concept is well known and/or has changed substantially. Then you should cite the most recent work that shows the ideas that you are wanting to show. Other times, primacy is more important - especially when few have built on ideas or concepts since they were put forward, or in the taxonomic literature. If in doubt, place a citation to the original study and the most recent study, then flag this using a comment for your advisor to consider. The important point here is for you to give credit where it’s due and not to overlook those who put in the hard work to publish original content.
Some have argued that the rule of priority is of benefit to science as it drives competition and this spurs creativity. On the other hand, the winner-takes-all approach of being first with something drives secrecy and dishonesty, and does not genuinely reflect the team effort that is the science project (Casadevall & Fang, 2012).
Some journals have a word limit, or even a limit to the number of references that they allow. Others do not, and you should probably use what is recently published as a guide to what is acceptable. For the chapter of a thesis, you should err on the upper end; from 50 to 100 references. Note that citations may well be more as you may cite a paper more than once.
Obviously, everything you cite needs to be in the References (or Literature Cited) section, and you may well need to spend time deleting extra stuff. You can get around this common issue by using a citation manager like Mendeley, Zotero or EndNote. I’d always suggest that you use one of these tools as they can really help with your reading too. These days they are busy turning into a kind of scientific social network. They regularly make suggestions of what you could be reading based on what you read. This can be useful.
If you are looking for multiple examples of citations for a statement that you’ve made and there are many possibilities, I’d suggest that you aim to produce three. Make sure that you use a suffix (like ‘e.g.’) to show that you are aware that these are examples of a widely reported phenomenon. You can choose these as you like, but may want to consider using what you consider to be ‘the best’ examples, and/or references that you are planning to use elsewhere in your paper/chapter. This can drive the total number of citations down considerably, and helps to keep the citations more relevant to your work.
If you are publishing relevant and appropriate papers, then there is no reason not to cite yourself. In many cases (such as with your thesis work), your own publications are likely to be more relevant to methodology and subject matter than much of the other work that is out there. However, if you’ve previously published on termite fungus and now you’re publishing on rat toes, it’s unlikely to be relevant. Choosing citations should include your comfort with being transparent. If you know when citing yourself that citing another article would be more correct in showing where an idea came from, but citing your own is more relevant to the application, then you should feel comfortable in citing both.
I would avoid citing your thesis if possible, rather put it all into papers. There are times though when citing your thesis is unavoidable. Within your thesis, I would suggest that you do provide citations to different chapters as this will help the examiners see how the chapters relate to each other.
Take a look at this article on self-citation. They claim that self-citations in the Natural Sciences run at 33% (Raan, Moed & Leeuwen, 2007), which provides you with a nice idea of what is acceptable. Remember that this would include not only your citations to your articles, but all citations to your co-authors’ articles too.
It may be easier to cite your friends if you already know their work well. You may have heard them talk and know that the subject is relevant. They may be encouraging you to cite them, but should you?
In these days of scientometrics, we do need to acknowledge that citations act as a kind of currency. They count towards your H-index (Hirsch, 2005) and this can reflect on your prospects as a postdoc or employee. What’s also clear is that cited papers get cited more, so it could really help your friends if you cite them. Obviously, the inverse is also true, so beware of the politics of citing. However, the most important points have already been raised. The study must be relevant and appropriate before it gets included as a citation in your work.
Papers in journals with high impact factors are more likely to be cited because their contents are already thought to be of interest to a wide range of people. Indeed, there is evidence that for identical statements published in many journals, those with higher Impact Factors are cited more (Perneger, 2010). Sometimes (but not always) the impact factor of the journal can be an indication of the quality of the study. But you should judge this for yourself when you critically read the paper.
I find that the first paragraph of a paper is more likely to contain citations of higher impact journals. This is in part as these are likely to be more cross cutting (as is often the case for the first paragraph). In the end, if you need to make a choice, choose the paper that is most relevant, irrespective of impact factor.