Visiting a new invasion of Xenopus laevis near Lille

Over the years I have managed to visit quite a few of the invasive populations of African clawed frogs covering all 4 continents on which they are currently known (Measey et al 2012). When reviewing these invasions, we found that the pathways were mostly due to the release of animals from scientific laboratories, but in 2017 when I reviewed the sources of current trade in these same frogs (Measey 2017), I predicted that we would start to see an increase in populations introduced from the burgeoning pet trade. 

In September 2018, it was reported that a population of African clawed frogs was present in a pond of the small French town La Chapelle-d'Armentières, near Lille and close to the border with Belgium (van Doorn et al., 2022). Although we do not know much about the pathway of this introduction, it appears that the pond in question was renovated by the council around the same time as the discovery, making the pond both deeper and thereby permanent (using images from Google Earth). A swift survey of numerous water bodies on the Belgian side of the border suggested that this pond is currently the only location for this established population (van Doorn et al., 2022). 

As I was in northern France in late April 2022, I requested permission to trap at the pond and process samples for our ongoing work into native and invasive genetic diversity of this model species (see blog posts here and here). The pond had been partially drained and a sturdy drift fence was planted all around the perimeter in aid of the eradication of this species from the area (seeTechnical Reportfor more information).

I set 4 traps in the two remaining areas and the next morning found 21Xenopus laevis. 

Further Reading:

van Doorn, L., Speybroeck, J., Adriaens, T. & Brys, R. (2022). Environmental DNA sampling for African clawed frog in Flanders, Wallonia and France in 2020. Reports of the Research Institute for Nature and Forest 2022 (6). Research Institute for Nature and Forest , Brussels. DOI:doi.org/10.21436/inbor.71707757

Technical Report on removal of Xenopus laevis: 

Interview with Daniel Shea from Scholarly Communication

Daniel contacted me some time back about doing an interview for his podcast on Scholarly Communication. I had a listen to excerpts of some of his previous interviews and wrote back with enthusiasm. I had a copy of How to Write a PhD in Biological Sciences  delivered to Daniel and we set a date for the interview. I had spent some time working on the next book (How to Publish in Biological Sciences) and so did a quick recap of the contents of How to Write a PhD in Biological Sciences  in the morning before the interview. Nevertheless, I was not feeling particularly well prepared when we started talking. Daniel explained that he would give a prepared introduction, and after this would launch into the interview.

It was quite a shock when Daniel gave a very lengthy introduction including reading a quote from the book. What struck me most was that he had actually read the book - apparently from cover to cover (not something that I'd advise for anyone wanting to use it!). His insights were eye opening. He had picked up on exactly why I wrote the book and that it is likely to be of use to people beyond only those writing PhDs in Biological Sciences. Moreover, Daniel had me thinking very hard on my feet about exactly why it is that we have built up a system with so much assumed knowledge. 

I should qualify the statement on assumed knowledge by adding that this may not be the case for all students (PhD, MSc or others). There are certainly some students who are well informed, and have all the knowledge on the system that they are working within prior to starting their PhDs. It's hard to know exactly where this came from and whether it was in the form of curricula based activities or that they had benefited from exceptionally good contacts. Evidently, the book is not needed by all students, but my experience, both as an uninitiated student and as an advisor, suggests that a great many would gain some benefit from the contents.

I was also very happy that Daniel was enthusiastic for the Bookdown approach. I may not have given a particularly useful explanation of what Bookdown is or why it's so great, but I would encourage you to go look at a product: http://howtowriteaphd.org/

To listen to Daniel Shea's interview with me, visit: https://newbooksnetwork.com/how-to-write-a-phd-in-biological-sciences

A trip to Angola 13 years ago...

It seems like a long time ago when in January 2009 we set off up the N7 through Namibia to Angola to join a SANBI expedition to the southern highlands of Angola and Iona National Park. Our team on reptiles and amphibians consisted of Krystal Tolley and myself (then from SANBI) and Bill Branch and Werner Conradie (from BayWorld). We were just one component of many teams from different disciplines that joined forces to inventory the biodiversity of southern Angola.

As time has gone by, there have been many more trips to Angola with many more people involved. Together, all of this data represents an important resource, and has now been written up as an updated herpetofaunal inventory for Iona National Park by Javier Lobón-Rovira and colleagues, and published in the journal Check List.

With 5 amphibians (the park is essentially a desert) and 70 reptile species, the new check list records 40 of these for the first time in Iona National Park. This is a remarkable achievement.

Read the full paper Open Access here.

Lobón-Rovira J, Vaz Pinto P, S. Becker F, Tolley KA, Measey J, Bennet B, Boon B, de Sá S, Conradie W (2022) An updated herpetofaunal species inventory of Iona National Park in southwestern Angola. Check List 18(2): 289-321. https://doi.org/10.15560/18.2.289

Downloading data from Hobo loggers

Sometimes you have to take a leap of faith and leave expensive equipment in the field in order to get much needed long-term data. This is what we did last February in a trip to KZN where we made an elevational transect while collecting African clawed frogs for Laurie (see Blog Post here). We placed four loggers at sea level, 1000 m, 2000 m and 3000 m asl. Sadly, the logger at 3000 m asl disappeared very soon after we placed it in a deluge of floods that hit Lesotho in March 2021. That meant that there were still three more loggers out in the field that needed to be retrieved. 

Fortunately, with the help of Bongani Ntloko from Letseng mine, we were able to redeploy another Hobo logger into a pond with Xenopus at ~3300 m asl. The results after one year (March to March 2022-23) are amazing.

Firstly, note that the scale on the y-axis only goes up to 20 C, and the water never gets that warm. For most of the year, the water is below 10 C. Only from around mid-October to late-March is the water above 10 C. This means that the frogs in Lesotho are more than half of their year in water less than 10 C. Even in summer, the water still regularly dips below 10 C on a daily basis.

Happily, the logger from 2000 m asl at the Fat Mulberry was retrieved by Marggie and she brought it to Stellenbosch where we could download the data.

This month I made a trip back to KZN to retrieve the outstanding loggers from near Dalton and at Bonamanzi:

The temperature of the water in a dam near Dalton never went below freezing, but it did get quite cold (as well as getting hot in the summer). 

Meanwhile at Bonamanzi, the temperature was nearly always above 10 C, and even went above 40 C! Contrast this with Lesotho when the water temperature rarely went above 10 C!

You may remember that Bonamanzi was where we had our traps vandalised by crocodiles. Happily though, you can see that the logger (right) didn't come to the same fate. The logger near Dalton (left) was still tied to the same stone sunk in the dam. 

Thanks to friends in Lesotho, we redeployed one of these Hobo devices there. Because you can replace their batteries, they are fantastic and just carry on working. We are hoping that the new logger won't go AWOL!

What is Sci-Hub?

Sci-Hub is a file sharing website that allows anyone to access to ~95% of all scientific articles that normally sit behind a paywall. While publishers see Sci-Hub as a pirate site that disseminates content that they own illegally, many of the world's scientists have come to rely on using it to quickly gain access to articles that they would otherwise be charged to read. Read more about Sci-Hub and its Kazakhstani founder Alexandra Elbakyan on Wikipedia. 

At first sight, this does seem to be a lawless exercise, but remember that none of the knowledge or content are paid for by the publishers. Indeed, many scientists are increasingly viewing the publishers' paywall as immoral, while sites like Sci-Hub are akin to a Robin Hood dissemination of knowledge already funded by civil society. To read more about the issues with publishing science, see How to Publish in Biological Sciences (Measey 2022). 

Who uses Sci-Hub?

Today, Alexandra Elbakyan gave us the stats on who uses Sci-Hub. What struck me most is that we might expect scientists from poorer economies to use Sci-Hub proportionately more because they lack the economic power to access the papers. 

What Alexandra revealed is that it is the more wealthy economies (who publish more) that use Sci-Hub the most. In other words - everyone uses Sci-Hub.

Here I have graphed on the x-axis GDP (Purchasing power parity; international dollars from IMF for 2021) of the top 50 countries downloading Sci-Hub (data taken 15-02-2022), while on the y-axis the number of papers each country has published so far in 2022 (from Scopus 15-02-2022). Size of bubbles are proportionate to the number of Sci-Hub downloads. Both axes are on log scales.

Although we might expect the bubbles to get proportionately bigger as the economies get poorer, what we see is that it is mostly the largest economies who are accessing Sci-Hub the most. 

Is this a mistake?

Surely, rich countries such as the USA and France (#2 and #3 on the Sci Hub download list) don't need to access Sci Hub as all of their institutions can subscribe to all content? This is how it might seem from afar, especially if you work in a low or middle income country. However, the idea that all academics work at wealthy institutions in rich countries is a fallacy. Countries, such as the USA, have very large numbers of tertiary institutions and most of these are not at all wealthy. Those who conduct research there need to obtain research from behind paywalls that their institutions don't subscribe to. Their only option is to use Sci Hub. I say that this is their 'only' option as paying $30-$50 for each article that they need to read is not really an option. 

Let's not forget that the better educated public in rich countries might also be more likely to try to access scientific articles, although I doubt that many will know of the Sci Hub option.

These same people (i.e. the vast majority of scientists in the world, even those from rich countries) suffer from the new price ticket on gold Open Access publications. Like those scientists from middle income countries, they cannot afford the prices that publishers charge and so have to look for alternatives. 

There are also some oddities in the list. As Alexandra Elbakyan points out, many places in the UK do not allow access to Sci Hub, and so there people might be using proxy servers to access it via the USA (also inflating their figures). But this is speculation.