New information about authorship for sale

From time to time new publications about publishing and writing appear and I make a note that I will need to update my book chapters accordingly. A preprint on rXiv by Abalkina (2022) prompted this particular revision to How to Publish in Biological Sciences. You can find the full book chapter here: When should you be an author?

When William Blake wrote about the dark satanic mills, he wasn't thinking of the paper mills (see here) that are now a growing feature of academic life. However, the description seems rather apt. Like other aspects of academic publishing, when money is involved there are forever increasing ways in which integrity in academic publishing is compromised. 

Paper Mills

The concept of a paper mill is rather different from ghost authors or even salami-slicing (Part IV). Paper mills involve third parties, often not included on the author line acting as intermediaries. A paper mill may either be producing material for publication from scratch: i.e. companies that specialise in producing content that will pass peer review for those who want to buy authorship. Or they may be third party organisations that sell a position in the author line of a legitimate paper. Given that the world of paper mills is particularly shady, there is likely no hard distinction between these types of paper mill but a large grey blur between completely fake at one end and legitimate novel research (including non-legitimate authors) at the other.

Ghost frogs are under threat from invasive fish - it's official

Dan van Blerk defended his MSc thesis today in what is likely one of the most anticipated events of 2023. Dan has been working for the last 2 years on getting enough data from as many streams as possible to establish whether or not invasive fish (most notably bass and trout) are impacting tadpoles of ghost frogs. The data were unambiguous. Invasive fish are having a major impact on the density of ghost frog tadpoles.

Having this unambiguous data is really good news. It is all very well to speculate that the invasive fish impact tadpoles, and there are a couple of annecdotal studies that show the same. But getting robust data from lots of sites on lots of rivers is no easy job. Dan worked tirelessly, trudging up and down some of the most beautiful scenery in South Africa's fynbos, to collect the necessary data. In truth, Dan greatly enjoyed his time in the field. It did give him a great excuse to play in water and catch fish - two of his most enjoyable pursuits.

Below one of Dan's pics shows the upper portion of a stream beyond which fish cannot reach, and the tadpoles are safe!

His work is critical to conservation managers who require evidence in order to base their conservation management decisions.

We look forward to seeing Dan's work in print shortly!

Read more:

van Blerk, D. (2023) The Impacts of Invasive Fish on Ghost Frog tadpoles. MSc thesis, Stellenbosch University. http://hdl.handle.net/10019/32356

A big step toward conservation of Rough Moss Frogs

Ten years is a relatively short period of monitoring data, yet it can reveal important ecological interactions that can inform conservation managers about on the ground decisions. In this study, published today, we show the clear synergistic relationship between fire and the invasion of pine trees on populations of moss frogs on the Klein Swartberg. 

In the figure below, you can see how the density of calling male Rough Moss Frogs increases in the absence of invasive pine trees, but declines in their presence. In addition, our analyses indicated that this decline was manifest when fire interacted with the invasion.  

We obtained the density estimates of calling frogs in this study from a microphone array using the aSCR methodology (described here). We employed this approach at 12 sites on the Klein Swartberg over 10 years with 35 recordings. This included the initial work undertaken by Debra Stark (see here). Debra's work is published in a book chapter (see here). Currently, the invasion of pines on the Klein Swartberg is incredible, but undergoing control through block burning. 

A picture of Oliver Angus among the pines on the Klein Swartberg in June 2021. 

Further reading:

Angus, O., Turner, A.A. & Measey, J. (in press) In a Rough Spot: Declines in Arthroleptella rugosa calling densities are explained by invasive pine trees. Austral Ecology https://doi.org/10.1111/aec.13273

Starting at Yunnan University

After a short spell in quarantine, I've finally made it to Kunming and to Yunnan University where I start as a faculty Professor today!

It will be a steep learning experience and I am grateful to all my new colleagues at YNU for making me feel so welcome. 

I'm hoping that the winter blues will soon be a thing of the past in Kunming, known as the Spring City. So far it's pretty cold and wet...

I will continue my role at Stellenbosch University for 3 months each year. For the other 9 months, I'll be based here in Kunming. 

The Cape Fold Mountains are the centre of African Clawed Frog genetic diversity

I'm really pleased to see this paper finally emerge. It's a fantastic study that took many years (more than 10!) to assemble all of the tissue samples used. A great many people helped assemble all of these, and the detailed resolution we now have of genetic diversity of this most widely distributed amphibian in southern Africa is excellent. 

What did we find?

In contrast to previous studies, we found that there are 5 mitochondrial clades of Xenopus laevis in southern Africa. You can see how these are distributed in the following map (Fig 2 below). 

Here you can see (on the right) that most of the area colonised by this species is from a single (yellow) clade. This shows signs of rapid expansion suggesting that even in it's native southern Africa, X. laevis  is a very successful species that has recently spread throughout a very large area. The next largest clade (blue) is from the winter rainfall area of the Cape. This includes animals that were sent all over the world for pregnancy testing (Van Sittert & Measey, 2016) and that are currently in the pet trade (Measey, 2017). The Cape Fold Mountains harbour the greatest genetic diversity of this species, and this includes a (green) clade that occurs in the lower Karoo. In the same area is the new (brown) clade, that appears to be co-distributed with the yellow clade up South Africa's east coast. But by far the most different animals in this species come from Nieuwoudtville (purple clade - see Fig 3 below) and adjacent areas of the northwest Karoo. This area is known for having many relict species, but how and why X. laevis  became isolated there so long ago is probably related to the large wetland areas that occur along the escarpment. Presumably these remained wet even when lowland areas dried up.

Overall, the picture of the distribution of this species in southern Africa is one of opportunism. These animals readily move into permanent water (e.g. irrigation dams) that is associated with modern farming practices. This has allowed expansion of this species into many arid areas where they might otherwise only appear after unusual rainfall events.

Our data is also the first to examine the entire genome of this model species. In the figure above you can see how the two different subgenomes differ (as X. laevis  is a tetraploid species). There is very little difference between the two genomes, suggesting that they are both under selection throughout its range. 

This is not the last study on the geographical differences of X. laevis,  but it is a great advance from our existing knowledge. 

Read More:

Premachandra, T., Cauret, C.M.S., Conradie, W., Measey, J., Evans, B.J. (2022) Population genomics of Xenopus laevis  in southern Africa. G3 Genes|Genomes|Genetics,  https://doi.org/10.1093/g3journal/jkac325 pdf

Measey, J. (2017). Where do African clawed frogs come from? An analysis of trade in live Xenopus laevis imported into the USA. Salamandra 53: 398-404. pdf

Van Sittert, L. & Measey, G.J. (2016) Historical perspectives on global exports and research of African clawed frogs (Xenopus laevis). Transactions of the Royal Society of South Africa  71: 157-166. https://doi.org/10.1080/0035919X.2016.1158747pdf