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Dr. James talks to the Cape Herp Club

28 November 2018

Mother of Dragons gives us a talk

It was great to hear Dr. Mother give a talk about his urban dragons. Happily, James has found a country where he can give a great talk to a fabulous audience while drinking a beer.

Next stop, James will be supplying his now infamous home brew to all Cape Herpers who come on the Cape Herp retreat in early 2019... watch this space.

Speaker: Dr. James Baxter-Gilbert

Title of talk: Australian Water Dragons: Urban Evolution and Ecology

Time: 16h00 (4pm)

Venue:  Natural Sciences building, Stellenbosch University, Room 2025 (lab at far end on first floor)

James is well known in Sydney as the crazy Canadian who chases dragons everywhere. He raised hundreds of individuals from eggs and raised them in urban vs rural settings, finding that the juveniles were really distinct. You can read more about James' PhD work here.

James was part of Martin Whiting's Lizard Lab at Macquarie University, Sydney (but he's alright now). 

In 2019, we're really privaledged to have James join the MeaseyLab at the CIB, continuing his globetrotting academic herping career in South Africa. 

  Lab  meetings

Getting started with the introduction

22 November 2018

Why do we need an introduction?

The introduction and discussion appear to be two common stumbling points for students writing chapters or manuscripts. First, what to put in and what to leave out. And second how to construct it. Right now, I’m going to tackle the introduction, and leave the discussion for another time.

The introduction is going to be the first part of your manuscript that anyone reads. Yes, they’ve already taken in the title and the abstract. These are almost like fishing bait to draw the readers in. The meat starts with the introduction. And it’s not only important to get all the correct content in there, it’s also important not to give misleading information that might distract the reader.

Earlier this month, we had the editor of The Conversation Africa, Caroline Southey, who told the CIB ARM that one of the most important things for a Conversation article was for the narrative to avoid getting side-tracked. She cunningly used the example of driving down a highway to your destination to explain how we are rarely tempted to turn off and explore side roads. Instead, we concentrate on driving straight to the place we set out for.

I’m not even going to apologise to those who love to explore the highways and byways of life, because Caroline was right. When we write the introduction to a paper we must not be tempted to stray away from what we are aiming to introduce. The aim of our introduction is to explain to the reader the hypothesis we are testing, and the approach we have taken to test it.

So what do we put into the introduction?

As I’ve said elsewhere (see blog entry), the hypothesis itself is made up of different parts, and each of these must be explained in the introduction. We also need to understand the approach that you’ve decided to take in your study (e.g. experimental, lab or field approach, observations or natural history). All of these decisions that you made were informed by the literature, as is your general understanding of the subject that you are studying. So making sure that you cite (read about citing here) the relevant literature is a key ingredient of the introduction.

However, this is where I think many people get side tracked. Researchers love reading, and it’s super easy to get sucked into all the amazing things that people have done in an ever expanding and increasingly interesting literature. We are often tempted to show exactly how well read we are. Or put in that fascinating tit-bit that we stumbled on by accident. However, Caroline had it right. You must keep focussed on the goal, to introduce the hypothesis to the reader, and try not to allow yourself (and consequently your reader) to get distracted.

And the construction…?

Previously, I’ve described the introduction like a funnel, where we channel the reader into our hypothesis by starting broad and ending up narrow (see that formula here). This drew some criticism on Twitter from @109Deb that journal articles are expected to fit a certain style. My objective there, as here, is to try to demystify writing and enable my students (and any other readers of this blog) to get started. The easiest way to get started is, I believe, through a formula. But it is important to say that the funnel isn’t the only way, and I’ve read some great papers where the first sentence of the introduction is the hypothesis. However you do it, the hypothesis is at the heart of your introduction because it is the reason for your work.

My suggestion is to keep to the funnel if you want to make life easier for yourself. Start by writing an outline of where you want your text to go. Then add in the references that are pertinent to each paragraph of the outline. Make sure that there aren’t any paragraphs with a single citation repeated over and again; it’s more likely that there is a lot more relevant information out there (see blog article here on citations).

Paragraph 1: Overview of the major theme.

Paragraph 2: Identify knowledge gaps in the field. 

Paragraph 3. Identify the problem and the gaps you intend to fill. Introduce the important variables that your hypothesis includes. It’s not impossible to mention others, just don’t get distracted.

Paragraph 4. Introduce the approach that you are using, and the organism of choice.

Paragraph 5. Clearly state the hypotheses that are to be tested.

Note that you can shuffle the above to the point where it still makes sense to the reader. Don’t be overly strict or dogmatic with this (or any) advice. For example, there may be more than 5 paragraphs, but use the framework to get started. Do what works for you in your situation.

Now that you’ve fleshed out your outline with relevant citations, it’ll be time to pass it by your advisor to check that you are moving in the right direction before you start writing. My suggestion is always to use your advisor to get the advice that you need – that’s what they’re there for!

  Lab  Writing

Frogs eating tadpoles

18 November 2018

Corey's second MSc chapter is published

African clawed frogs (Xenopus laevis) appear to select against their own tadpoles and for those of a threatened congener, Xenopus gilli. That's the punchline for Corey's second MSc chapter, recently published in African Journal of Ecology. He also found that the behaviour and developmental rate of the two species was different, with X. gilli developing much faster than X. laevis

Corey conducted several experiments that are written up in this paper. The results are very interesting in the light of the threat of high numbers of X. laevis throughout the distribution of X. gilli

Read more about Corey's other published thesis chapter on functional response here.

Read this article here:

Thorp, C.J., Vonesh, J.R. & Measey, J. (in press) Cannibalism or congeneric predation? The African clawed frog (Xenopus laevis Daudin) preferentially predate on larvae of Cape platannas (X. gilli Rose & Hewitt). African Journal of Ecology DOI:10.1111/aje.12577 pdf

  Frogs  Lab  Xenopus

The 2018 CIB Annual Research Meeting

09 November 2018

Nitya takes the big prize at the CIB Annual Research Meeting

Following in the lab tradition, Nitya has added to our collective pride by taking the prize for the best PhD at the CIB ARM. This year, contestants for the prizes had to write an articles for The Conversation, an online magazine written entirely by academics. 

Top Left - Natasha, John & Nitya represented the lab. Top Right - Natasha talked about her tadpole behavioural experiments.

Bottom Left - Nitya talked about his tadpole survival experiments. Bottom Right - Nitya receives his prize from Sarah Davies.

The talks (see above) were all done in the style of the FameLab, and although neither won this heat, Nitya was invited to present his talk among the finalists. His catch phrase "babies can be mean" went down well with the crowd as well as his interjection with "spoiler alert" when Olaf Weyl guessed his tadpoles' survival had gone to zero.

It was a great meeting with lots of antics that were topped off by a great meal at Middelvlei Wine Estate

Top - John meets Oz and Candice from The Conversation

Middle left - John W & Inderjit post for a shot. Middle middle - Bo Li, Inderjit and Dave Richardson Pose for the camera. Middle right - Nitya removes his glasses for the group photo

Bottom left - Dave, Christy & Corlia are the 3 monkeys. Bottom middle - Oonsie Biggs takes questions from the audience. Bottom Right - Tricksy Ming poses with Inderjit

  Frogs  Lab  meetings  prizes  Xenopus

What literature is actually out there on herp invasions?

08 November 2018

A great new systematic review on invasive herp literature tells us that we have a biased information base

Today we're publishing a great new study that collects all of the literature on invasive reptiles and amphibians and asks what's out there, and how will it help us with risk analysis? 

Building a comprehensive view of risk analysis for invasive and potentially invasive species requires scientific studies that provide a basis for the assessments. National assessments have suggested that studies are inadequate, but no systematic assessment of literature for any group has been undertaken. In a new paper led by Nicola van Wilgen (of the Cape Research Centre, SANParks, and a CIB associate), the authors trawled literature associated with alien reptiles and amphibians. They found 836 papers that cover a vast 1116 species of herpetofauna that were alien to the countries where they were studied, but 95% of these species had <12 studies. Most of this had a focus on frogs, and especially cane toads in Australia, although we know very little of what cane toads do in other countries. This is significant as although we can do a good job of assessing the risk of cane toads in Australia, we have a poor basis for knowing what happens elsewhere. 

Most of the herpetofaunal literature (~50%) as assessed the impacts that alien species have on the environment, with very little information on trade (~2%), which is considered to be of prime importance for new invasions. The world is also uneven when it comes to research on invasive reptiles and amphibians. One hotspot is Florida, but there are plenty more areas with very little information, including China. This study provides an insight into the way in which scientists still need to gather much more information on alien species so that we can make meaningful assessments on their future risk.


Other groups, like crocodiles and turtles, are much better documented relative to the total number of species in the group. This is mostly because there are very few species in the group and so the ones that have been studied make up a high proportion. 

There's lots more interesting stats and discussion, so please read the paper and see what you think!

Van Wilgen, N.J., Gillespie, M.S., Richardson, D.M. & Measey, J. (2018) A taxonomically and geographically constrained information base limits non-native reptile and amphibian risk assessment: a systematic review. PeerJ   10.7717/peerj.5850

  Frogs  Lab  Xenopus
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