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How to Write a PhD - Published!

30 November 2021

Published today

What started right here as a series of blog posts is published today as a book from CRC Press.

As you should know by now, this book is available to read free online at

Of course, you can still access the blog posts which are curated together on a page here. But don't be surprised if the book is quite a bit different. This time last year, I had completed a first draft of this book - and actually the next one on publishing. After signing the deal with CRC Press and getting a manuscript due date on 30 April 2021, I found that I needed to rewrite the book from start to finish. This was, in part, because the original book I had written needed to be split into two, and because it turns out that a first draft is just that. 

I received the copy edits and then proofs in July and August 2021. I was quite surprised at how much work was still needed on the copy edits. I had submitted the book in LaTex, and had quite a few formatting points that hadn't worked out well. By that time I had also signed another contract to submit the second book in August: How to publish in Biological Sciences. As you can imagine, August was a busy month. At this point though, I could make sure that the second book did not have the same problems as the first (and indeed I have already returned the copy edits on that and it was all good).

So, it turned out to be quite a bit more work to get the blog posts into the form of a book. The Bookdown (online) version is already growing and having chapters added. That's the really nice aspect of this guide book, that it can continue to evolve online. Please do take a look and see what you think. All contributions are welcome. If you can't find a section that you are looking for, let me know.

The book itself contains a long list of acknowledgements, but I feel that it is necessary to name some of those people here too. Firstly to my brother, Richard, who maintains this website and has rescued it from hackers and systems crashes over the years. My wife, Thalassa, has had to read (and correct) a lot of this book as blog posts, and also when I was rewriting it. All of the MeaseyLab folk who have been the source of great inspiration for many of the chapters, but for also discussing a lot of the topics in lab meetings and contributing so much to my understanding of the writing process. Lastly, to all the support I had from the CIB over the last 8 years, especially Christy who has been absolutely fantastic.

Curious to see what the book looks like?

You can see a preview of the book on Google Books. Just click this link

Measey J (2021) How to publish in Biological Sciences: a guide for the uninitiated. CRC Press, Boca Raton.  ISBN: 9781032116419      

Great to see this in hard copy!

  Lab  Writing

Another online CIB-ARM

19 November 2021

Centre for Invasion Biology - Annual Research Meeting - online again

By May 2021 it seemed that we could have started planning for an in-person Annual Research Meeting (ARM) for the Centre for Invasion Biology (CIB), but decided to err on the side of caution and keep it online only. That turned out to be the best plan as the third wave of COVID hit us in July and still hadn't entirely left by September. 

We managed to fit all CIB students into 4 pods led by all remaining post-docs, and had some great presentations from all members of the MeaseyLab. Below you will find images of everyone giving their talks. 

Sam Peta, M.Sc. An army marches on its stomach: diet composition and prey preference of guttural toad (Sclerophrys gutturalis) populations along a native-invasive and natural-urban gradient. 

John Measey How to write a PhD in Biological Sciences - book launch

SESSION 03: Distribution, spreading and impacts of invasive species Introduced and chaired by
Dr Andrea Melotto

Dan Van Blerk, M.Sc. Impacts of invasive fish on amphibians in lentic and lotic systems: a meta-analysis 

Laurie Araspin, Ph.D. Temperature dependence of locomotor performance across an altitudinal gradient in an invasive frog, Xenopus laevis

Of course, you can watch the full meeting (only 7.5 hours) on YouTube (below) if you want!

Getting the address right

12 November 2021

Why is your institutional address important?

When you are ready to submit your manuscript to a journal, one of the first pieces of metadata that you are required to enter in the editorial management software is your address. It is usually also on the first page of your manuscript after the title and your name. Moreover, you will also be asked to enter the addresses of all of your co-authors. It is very important to get this correct, but why?

The address that appears alongside your name assigns credit to the institution where the work was conducted. In these days when institutions are held to account for the research that they conduct, having their address correctly entered may be of direct significance to them. The smaller your institution, the more important this will be as your research (or that of your co-authors) will be one of fewer products. Many institutions will rely on pulling lists of publications from databases (such as Web of Science, Scopus or Dimensions). An automated search may not pull out all publications if the name of the institution has been misspelled, misses appropriate accents, or is inverted (e.g. University of Stellenbosch instead of Stellenbosch University). Some databases code names of institutions, so that you may be asked to select yours from a (very long) drop down menu.

Remember that adding the name of your institution, and that of your coauthors, also adds the reputation and endorsement of that establishment to the work. You should already have sufficient confidence in the work that you are doing in order to warrant adding your institution’s address. Some institutions will ask that manuscripts are submitted to a committee for official endorsement before they are submitted for publication. If you are a postgraduate student, you are likely to need your advisor's consent before submitting a manuscript for publication. Because the institutional endorsement is important, institutions are quite picky about who can publish with their name. Thus, any contract that you sign with your institution may well have a clause about not bringing their name into disrepute.

Clearly, there could be a fine line between your freedom to publish your academic opinion and the interests of your institution and their name. In the US, where academic freedom is protected by the First Amendment, legal assertion usually arises following claims against colleagues, administrators and trustees from the same institution, or against the state (Euben 2002). Happily, in the biological sciences, you are less likely to come up against this line than in some other areas. Most institutions are liberal, and you are unlikely to ever face difficulties. This is most likely to happen when you conduct research that can garner controversy in the traditional or social media. Different periods of time have different trends for what subjects are sensitive to the public. You should be aware of these from your own reading of traditional media, and this is a great reason for staying in touch with what is happening more generally in the world around you.

All this means that although it is arduous, correctly capturing the address of yourself and your coauthors in the initial submission is very important. In order to get ready for this, you should engage your co-authors prior to submission to ask them to provide the exact address that they want you to use.

Figurative, physical or postal address?

Some journals require a detailed postal address (with post code), which harks back to the days of when readers wrote letters to authors. Some may only require this for the corresponding author. Other journals appear happy to have a physical address, or even a more figurative address, that stipulates only the department, institutional name and country - this makes sense in terms of acknowledging the affiliation where the work was done. My preference is for a short figurative address that contains all the important information.

Multiple addresses

These days, it is possible that you and/or your coauthors will want to use multiple addresses. There could be many reasons for this. They may have roles at more than one institution (including joint appointments, or honorary affiliations). Again, you may not be aware of this, so it is worth engaging with all coauthors ahead of submission. 

Some funders ask you to add a line to your address to denote a virtual team. This can easily be done within your institutional address (usually as the first line) and doesn’t require any additional address.

There does not seem to be any limit on the number of addresses that you can use. If you have a legitimate need for adding additional addresses, then you can go to town.

What if your institutional affiliation changes?

If you are a postgraduate student or Early Career Researcher, then you are likely to change your address when you finish your degree, or start a new job. Should you use your new address, where people can find you now, or your old address where you conducted the work?

Essentially, you should use the address where you did the work. If you move after completion (before submission) then you can list your new address as a "corresponding address". If you have used work time and resources at your new address in order to finish the submission (which may well be the case) you should include them. However, the PI on the study should know before you submit if you are planning to add another institutional address as this may impact the way in which their institution considers the work.  

Article Processing Charges

Your address may give you access to funds for publishing your article in Open Access journals, or when there is an article publishing charge (APC). It may be the case that your new address has access to funds for APC, but your old address does not. Is this a legitimate reason for adding the new address? 

Some might consider that access to APC may constitute additional funding towards a study and therefore warrant addition of an address. My feeling is that this is a contentious issue and that you shouldn’t make any assumptions. Rather discuss this openly with your co-authors and try to determine whether they all agree on adding an address, or whether there is another way toward paying an APC. 

In summary

In my view, you should use the address where you did the work. To give a new address when work was done at the old one is denying the old institute the credit that they deserve in having supported you at that time. Of course, addresses change and the amount of support may not be important any more. For example, I published some work this year for which the data was collected >15 years ago. I didn't include the address where I was back then, but I did make sure that there was an acknowledgement to the funding. 

  Lab  Writing

Do toads shit in the woods?

05 November 2021

Expanding populations of toads shit in the woods

A recent study by CIB MSc student, Carla Wagener, and CIB researcher John Measey, found that the gut microbiome on invasive toads shifts in expanding populations. 

The study, published this month inMicrobial Ecology, examined the faecal microbiome of three invasive populations of the Guttural Toad,Sclerophrys gutturalis, Mauritius, Reunion and Cape Town, as well as their origin population in Durban. The Mauritius and Reunion populations, despite being introduced ~100 years ago, contained a microbiome that most closely resembled the native Durban population. 

Guttural toads from Cape Town had the most distinct microbiome recorded for these toads. Although this population is only ~20 years old, the animals are believed to have arrived accidentally in Cape Town as eggs or tadpoles. This would mean that the gut microbiome of the adults was acquired after metamorphosis in their new environment. Moreover, toads collected from the periphery of the invasion were found to have a microbiome that had shifted from those at the invasion core. 

This is the first time that a study has shown rapid alteration of the faecal microbiome during a population expansion, such as that during the movement of individuals during an invasion. It seems likely that this difference is due to the proximity of other Guttural Toads during the expansion process. 

Read the article here:

Wagener, C., du Plessis, M., Measey, J. (2021) Invasive amphibian gut microbiota and functions shift differentially in an expanding population but remain conserved across established populations.Microbial Ecology

Talks at the Conservation Symposium

04 November 2021

A session dedicated to the Guttural Toad (Sclerophrys gutturalis)

The Conservation Symposium (1-4 November 2021) had a special session on the morning of 4 November 2021 where five MeaseyLab members presented their work on Guttural Toads. Because these presentations were recorded ahead of time, we are able to share them for your interest in a playlist here.

The humble guttural toad (Sclerophrys gutturalis): Lessons of plasticity and adaptation following invasion: John Measey

Introduction of guttural toads (Sclerophrys gutturalis) produces marked shifts in the endemic western leopard toad (Sclerophrys pantherina) gut microbiome: Carla Wagener

Does urban adaptation enhance invasiveness? A case study of tadpoles of a successful invasive amphibian: Max Mühlenhaupt

Conqueror toads: Comparing behaviour, performance and competitive potential in a successful invader and its native congeners: Andrea Melotto

An army marches on its stomach: Diet composition and prey preference of guttural toad (Sclerophrys gutturalis) populations along a native-invasive and natural-urban gradient: Sam Peta

The session was well attended with 140 people online. You may recognise some of the people below who showed up to face the questions...
Measey, J. 2021. The humble guttural toad (Sclerophrys gutturalis): Lessons of plasticity and adaptation following invasion. The Conservation Symposium, 1-5 November 2021

Wagener, C., Measey, J. 2021. Introduction of guttural toads (Sclerophrys gutturalis) produces marked shifts in the endemic western leopard toad (Sclerophrys pantherina) gut microbiome. The Conservation Symposium, 1-5 November 2021

Mühlenhaupt, M., Baxter-Gilbert, J., Riley, J., Makhubo, B., Measey, J. 2021. Does urban adaptation enhance invasiveness? A case study of tadpoles of a successful invasive amphibian. The Conservation Symposium, 1-5 November 2021

Melotto, A. 2021. Conqueror toads: Comparing behaviour, performance and competitive potential in a successful invader and its native congeners. The Conservation Symposium, 1-5 November 2021

Peta, S., Baxter-Gilbert, J., Measey, J. 2021. An army marches on its stomach: Diet composition and prey preference of guttural toad (Sclerophrys gutturalis) populations along a native-invasive and natural-urban gradient. The Conservation Symposium, 1-5 November 2021
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