The exciting potential of Overlay Journals

Having already said on this blog that preprints won’t replace the role of peer review:

• What if we did have good, editorially coordinated peer review of preprints?
• What if, instead of these manuscripts effectively leaving the preprint system, they were updated together with the reviews that prompted the updates, each with their own linked DOI?
• What if the journals themselves were simply pointing to collections of papers that had been curated in this way?
• Simply, this could be a website that throws a veneer of a journal as waypoints to peer reviewed journals?

This world has already been imagined and is functioning in mathematics, where Overlay Journals have begun to prosper.

According to Brown (2010), the idea of overlaying has been with us for some time, and exist as websites that offer a series of links to other papers. It makes me think of the early days of the internet where there were websites that consisted of lists of other websites, before the days of search engines. Thinking about it in this way, a review article could be considered an ‘overlay paper,’ the contents of Web of Science as an ‘overlay database.’ But, for me at least, this is not where the real potential lies. Instead, imagine the overlay journal as a way in which academics entirely remove the need for publishers. The need for this is increasingly evident as we become more familiar with the ways in which we rely on traditional publishing models to pervade our scientific project with confirmation bias. Overlay journals no longer require a publisher to store the publication. This is done at the preprint server. The reviews are housed at the same arXiv site (or would be in an ideal and transparent version)(Rittman 2020), as is the manuscript in its final form after being accepted by the overlay journal editor. The authors themselves are responsible for the final layout. The Overlay Journal co-ordinates the reviews and conducts the editorial work, and then simply acts as a pointer to the finished product: no papers, no publishers, no editorial management software, no costs and all papers are Diamond OA!

The math journal Discrete Analysis (indexed in both Web of Science and Scopus) was the first of these new ‘arXiv overlay journals’ (since 2015, and indexed since 2017), and following on this link will allow you to quickly appreciate what an Overlay Journal is. Each ‘published’ paper still sits on its original preprint server. The overlay journal itself offers a brief editorial summary of what you’ll find if you click through to the paper. This is a fantastic idea in that it pitches editors back into being responsible content curators. As an editor I’d want to be motivated to publish a paper that I liked in order to write an editorial summary about it.

Because only the accepted version is provided with an ‘article number’ and the style file of the journal layout, the author then produces the final version of record (VoR) of the accepted manuscript by running the style file with LaTex. All of this is possible with free software, for example by using Rmarkdown (Xie, Allaire, and Grolemund 2018).

Using preprint servers also allows the entire process to be transparent, very quickly becoming associated with other great initiatives like the Centre for Open Science - OSF.

The highs and lows of being a tadpole

Some species are wide ranging, either across latitudes or from montane areas to the sea. The African clawed frog, Xenopus laevis, is one such species that occurs from the sub-tropical regions at sea-level to ~3000 m in the Lesotho highlands. In this study, (then) Honours student Carla Wagener collected adults from (close to) sea-level in iSimangaliso National Park, and up at ~2000 m at the foot of the Drakensburg mountains (see blog post here).

Adults were brought back to the lab in Stellenbosch and bred in a common garden experiment. Crucially, she also cross bred males from high altitude with females from low, and vice versa. With the progeny that resulted from these crosses, Carla measured their swimming performance at different temperatures. We knew that tadpoles swim faster as higher temperatures, but we wanted to determine the difference in temperature of peak performance between the two populations adapted to different altitudes - and what would happen when adults were crossed.

The results were amazing. The difference in peak performance between the two populations was ~15 C (see graph A below), but when parents from different populations were crossed, they followed the performance peak of the mother.

It could be that individuals from high altitude are carrying a gene for performing well at low temperatures in their mtDNA, which is maternally inherited. Although there are other explanations, the common garden nature of this experiment suggests that these populations have strong adaptations to their altitudes that are can be inherited when mixed, instead of becoming diluted.

This has some relevance for invasive populations, particularly in France which is a population made up of a lot of different genetic sources. It has been speculated that the reason that they have done so well in the much colder French midlands is because of this variation in genetics. This study by Carla suggests that progeny of different populations retain their peak performance at different temperatures, and that could explain some of the benefits seen by invasive populations in France.

Read the study here:

Wagener, C., Kruger, N., Measey, J. (2021) Progeny of Xenopus laevis from altitudinal extremes display adaptive physiological performance. J Exp Biol 1 April 2021; 224 (7): jeb233031. doi: https://doi.org/10.1242/jeb.233031

Fieldwork at last for Sam 

Lockdown has taken it's toll on many projects in the MeaseyLab, and no more so than with Sam Peta who has been prevented from doing much of the fieldwork that was envisioned for his MSc. Happily, domestic travel was still an option for Sam, and so he has been able to conduct a trip to Durban this April to collect some needed samples for his work.

Despite it being very late in the toad season, Sam has done a fantastic job of getting all of the samples he needs to complete his second MSc chapter. 

Sam captures another Guttural toad for his work, and completes his sampling.

Battle of the dwarfs: Guttural Toads turn out to be the largest known shrinkage of any anuran island dwarf

Large analyses reveal a good idea of how major systems have shifted on an evolutionary scale. Yesterday a new paper published inNature Ecology & Evolutionby Ana Benítez-López and colleaguesbrought together more than a thousand species of vertebrates to explore the ‘island rule’:  insular dwarfism in large-bodied species and island gigantism in small-bodied species.

As keen readers of this blog will know we published a paper last year (Baxter-Gilbert et al 2020) about rapid shifts in the sizes of Guttural Toads introduced from Durban, South Africa to the islands of Mauritius and Réunion. That paper led by MeaseyLab postdoc, James Baxter Gilbert, revealed that female toads from Mauritius had significantly smaller snout vent length (SVL) than female toads from Durban by 33.9% (red data point below). Similarly female toads from Réunion had significantly smaller SVL than female toads from Durban by 25.9% (green data point below). For males the shift was somewhat smaller (and is not shown on the graph). 

We were quite surprised with the magnitude of these changes but we did not appreciate how large they really were until the publication of the study by Anna Bonita Lopez et al, yesterday.

Above I have graphed out their data on anuran SVL together with a one to one bar (blue) indicating size parity. Their data seems pretty globally comprehensive with 116 data points from 42 anuran species. You can see that most examples of frogs on islands show gigantism compared to their mainland counterparts. The two coloured data points represent mean size shifts between Durban and Mauritius (red) and Durban and Réunion (green). 

The biggest shift that they record for any taxon on from mainlands to islands is a 25% reduction from 43 mm to 32 mm from the Spanish mainland to Majorca for Alytes dickhilleni and A. muletensis, respectively (Arntzen & Garcia-Paris 1995). These sister taxa are believed to have been separated for more than 4 million years! 

As you can see, it is clear that the 33% shift we saw for female Guttural Toads (from Durban to Mauritius - red data point) in less than 100 years is not only remarkable but the largest reduction in body size of any anuran known on the planet! 

A nice fun fact for a Friday morning

 

References

Arntzen, J.W. and García-París, M., 1995. Morphological and allozyme studies of midwife toads (genus Alytes), including the description of two new taxa from Spain. Contributions to Zoology, 65(1), pp.5-34.

Baxter-Gilbert, J., Riley, J.L., Wagener, C., Mohanty, N.P. and Measey, J., 2020. Shrinking before our isles: the rapid expression of insular dwarfism in two invasive populations of guttural toad (Sclerophrys gutturalis). Biology letters, 16(11), p.20200651.

Benítez-López, A., Santini, L., Gallego-Zamorano, J. et al. The island rule explains consistent patterns of body size evolution in terrestrial vertebrates. Nat Ecol Evol (2021). https://doi.org/10.1038/s41559-021-01426-y

Graduation time

Every graduation is a celebration of achievements, and each year I am moved by how much our students achieve during their (relatively) short postgraduate studies. This April we had a double celebration of two MSc students, both of whom graduatedcum laude. Sadly, because of the ongoing pandemic situation, neither was able to attend the graduation ceremony in person. 

Nolwethu Jubase-Tshaliworked full-time during her MSc, including receiving a promotion to becoming Western Cape Regional Coordinator in SANBI’s Directorate on Biodiversity Evidence (DBE). Because Nolwethu worked full-time at her day job, we didn’t see her often in the lab. Nolwethu was co-supervised by Dr Ross Shackleton, previously a PhD student and post-doc at the CIB, but now Maitre assistant at the University of Lausanne, Switzerland. 

Nolwethu’s MSc thesis consists of 2 chapters. In the first, she asks what motivates volunteers to remove alien invasive plants in the Western Cape. In the second, she finds out what people from 8 towns in the Berg River catchment know about alien invasive species. Both chapters are placed into the framework of how to practically manage alien invasive species in the Western Cape province. Each progresses our understanding in the important topic of biological invasions. 

The first chapter: "Motivations and contributions of volunteer groups in the management of invasive alien plants in South Africa’s Western Cape province", is currently in press withBothalia, African Biodiversity & Conservation. 

The second chapter is being prepared for a special issue. For more news on this, stay tuned on the blog. 

Nolwethu’s graduation provides an important milestone for me, as she is my first student to graduate with a degree in Botany!

Carla Wagenerdid her undergraduate degree in Botany & Zoology, she did both her Honours project and MSc in the lab. Consequently, Carla had been in the department in Stellenbosch longer than anyone else, and knew the answers to practically anything we could think of. Carla’s MSc work was co-supervised by Dr Morne du Plessis (then) of SANBI at the Pretoria Zoo. Carla also received the covetedcum laudefor her thesis and presentation of her MSc in Zoology.

You can read blog posts about Carla’s work: 

Honours&fieldwork

With Brazilian guests:Carla&Adriana

Doing toady things inMauritius&Durban

Carla’s MSc has two chapters. One compares the gut microbiome of 1 native and 3 invasive populations of Guttural Toad,Sclerophrys gutturalis. The second chapter contains an experiment to determine the effect of transplanting gut microbial fauna from invasive to native populations, and vice versa. The first chapter is currently under review, while you can read a preprint of the second chapter here: 

The gut microbiome facilitates ecological adaptation in an invasive vertebrate

Last, but not least, Lisa Mertens, also graduated as a PhD. Due to some difficulties during the course of her studies, Lisa finally graduated with John as her supervisor. They both attended graduation on April 1st. 

Graduating theses:

Jubase-Tshali, N. (2021) Evaluating the effectiveness of citizen science to detect, report and control alien and invasive species in Western Cape, South AfricaMSc thesisStellenbosch University

Wagener, C. (2021) Spill your guts: the invasive amphibian gut microbiome.MSc thesisStellenbosch University

Mertens, L. (2021) Assessing the evolutionary and physiological resilience of southern African marine speciesPhD ThesisStellenbosch University