A joint meeting of the Herpetological Association of Africa and the African Amphibian Working Group in Wilderness, South Africa: 26 – 29 November 2024

Each of these groups usually meets every two years separately, so it was for the first time in their existance that they met in back-to-back meetings in Wilderness South Africa. First up was the 20th meeting of the AAWG, with plenty of familiar faces from across the globe. 

Next was the 16th meeting of the HAA, which also had great representation and considerably more delegates. 

   

The meeting featured presenters from 9 different African countries: Madagascar, Nigeria, Tanzania, Uganda, Ethiopia, Kenya, Ghana, Namibia and South Africa. This was certainly the best representation of the continent since each of the meetings started. 

The following talks featured MeaseyLab members:

Home and away: the gut microbiome of Xenopus laevis in native and invasive populations

John Measey; Jiankun Yu; Dareen Almojil; Stephane Boissinot; Laurie Araspin; Carla Wagener; Greg Pauly; Reed Ojala-Barbour; Claudio Soto-Azat

The vertebrate gut microbiome is a community largely composed of bacterial, fungal and viral components, whose molecular component equal that of the host. The influence of the microbiome is known to be significant both on an individual basis, and also on population scales in a wide range of host organisms. The gut microbiome is known to be involved with key attributes of animal health, including assimilation of nutrients, immuno-defensive functions and host behaviour. In this study, we used bacterial 16S rRNA amplicon-based sequencing for metataxonomic classification of the gut microbiome of individuals from 12 native populations of Xenopus laevis. These populations were selected to represent the native range of the host species. From the 16S rRNA community profiles, we determine the components of the core microbiome of X. laevis and ask whether deviations from the core are associated with the environmental context in which they live. In addition, we sampled populations from Chile (4) and USA (7) to determine what aspects of the core microbiome are retained by non-native populations. This represents the first time that the microbiome of X. laevis has been assessed across such diverse conditions and provides data that will help understand the role played by the environment within this model organism.

Southern Africa Amphibian Red List Project – updated assessments for the region lead the GAA3

Jeanne Tarrant; Joshua Weeber; Oliver Angus; Adrian J. Armstrong; Ninda L. Baptista; Francois S. Becker; Rebecca M. Brunner; Werner Conradie; Louis H. du Preez; James Harvey; Adriaan Jordaan; Keir Lynch; John Measey; Mohlamatsane Mokhatla; Darren W. Pietersen; Fortunate M. Phaka; Jennifer Swanby; Krystal A. Tolley; Andrew A. Turner; Luke Verburgt

As the most threatened vertebrate class on earth, amphibians are leading the biodiversity extinction crisis. The 2nd Global Amphibian Assessment (GAA2) found that 41.5% of species globally are at risk of extinction, these extraordinary and diverse creatures are experiencing the worst population declines and highest extinction risk of any vertebrate group. South Africa has a good history of updating Red List assessments and has done so consistently since 2004 with the publication of the Atlas and Red Data Book. As some of the first assessments to contribute to GAA3, regional updates are in process for 246 southern African amphibian species. A very high proportion (approximately 74%) are endemic to the region, emphasizing the need to understand their conservation status, and prioritize conservation resources. Over 150,000 records were collated from 16 institutions (including citizen science platforms) and numerous private collections. A team of twenty experts contributed to assessment updates, with the support of the IUCN Amphibian Red List Authority, Amphibian Arc, SANBI and Re:Wild. Applying the IUCN Red List criteria according to IUCN guidelines, the current assessments have resulted in category changes for over 40% of priority species, including assigning a status to all but one Data Deficient species and all Not Evaluated species. Future climate scenarios (2050s) were modelled for South Africa’s threatened frog species and predict a wide range of distributional impacts, which will be exacerbated by ongoing land-use change. 35% of threatened species are likely to be highly impacted by future climate change scenarios. The updated assessments will be published by IUCN in the first half of 2025, and the outcomes of this work will be invaluable in informing an updated conservation and research strategy, the National Biodiversity Assessment, and has already contributed to identifying species in need of urgent recovery in the next decade.

The BioSoundSCape project: Automating frog detection for ecological monitoring in the Cape Floristic Region

Andrew A. Turner; John Measey; Oliver Angus; Colleen Seymour; Alan Lee; Rose Snyder; Festus Adebgola; Leo Salas; Matt Clarke

Monitoring frogs has the potential to provide useful insights into measuring ecosystem health and the management of these ecosystems. Yet currently this monitoring is highly restricted, in space and time consuming. Data acquired from automated sound recording devices can extend the reach of ecological monitoring. The BioSCape project is a large, multi-party collaboration with NASA that aims to relate biodiversity patterns on the ground with remotely sensed, cutting edge spectral imaging that provides very high spectral resolution across the electromagnetic spectrum. One of the novel ways to measure biodiversity is to measure bioacoustic diversity. The BioSoundSCape project deployed a large number of automated sound recorders (AudioMoths) across the Cape Floristic Region and recorded nearly 1 million sound recordings. These recordings are freely available on NASA’s Distributed Active Archive Center. The project set up pattern matching algorithms to detect frog calls of 13 frog species, ran statistical pattern matching, validated results and used the resultant validated sound sonographic signatures for training input to a machine learning (computational neural network) system as implemented by RFCx in Arbimon. From this we calculated diversity indices and present examples of these outputs. Once the entire data collection, processing and analysis can be automated, it can realise the ability for large-scale, frog and ecosystem monitoring.

School for Climate Studies (SCS) and Centre for Invasion Biology (CIB) Annual Research Meeting

Regular readers of this blog will be familiar with the CIB-ARM which is hosted annually in November. This year (after a 2 year interim), we see the new SCS-CIB ARM: a joint venture where Masters and PhD students present on their latest research. This event provides an important forum for networking for post-docs and students alike. For the CIB, the entire Core Team is invited to come together with their students from universities up and down South Africa.

Policy from Science

This year, there was a promient flavour of policy from science both at the national and international level. Prof. Melodie McGeogh (Monash University) provided a plenary from her perspectives after participating in the recent IPBES report Thematic Assessment Report on Invasive Alien Species and their Control. 

In addition, Peter Lukey (Chief Director: Environment Knowledge and Information at DFFE) provided an overview of his experience as a policy maker in the South African government.

In addition to these plenary talks, we had a host of marvellous talks from postgraduate students from the SCS and CIB. This included Jonathan Bell who presented an update on his MSc work on improving the efficacy of the Gutteral Toad eradication programme.

Another great ARM from another year of research for 10s of students working on invasions and climate change. We look forward to next year when the intersection of these two disciplines will be dissected in more detail.

A talk for the University of Portsmouth

Readers of the blog will be familiar with my repeated visits to the University of Portsmouth and in particular the European Xenopus Resource Centre (EXRC). In January 2024 (see here) I became a Visiting Researcher, School of Biological Sciences, University of Portsmouth, and so during a brief visit to Portsmouth this week, I was asked to give a talk to the School.

The EXRC is a special place for anyone working on Xenopus as they hold breeding stock for anyone in Europe working on Xenopus frogs. Recently, we were able to supply them with some gametes from the progeny of wild caught animals from South Africa. I hope to report more on that project here on the blog in future.

Matt Guille leads the EXRC and received a flashing Xenopus neon sign for the EXRC lab.

Measey, J. (2024) What can biological invasions teach us about rapid evolutionary change? 1 November 2024 School of Biological Sciences at University of Portsmouth

Insights from marking a peer review assignment

As part of my course on writing and publishing, my postgraduate students do a workshop on conducting peer review (here), attend a lecture (here), and they are set a peer review assignment for their course mark. They are told to follow the workshop on a specific unpublished manuscript selected by me from bioRxiv. This gives them the opportunity to write, putting in place some of the writing skills that they are taught during the course, and lets them put into practice what they are taught about the spirit of peer review.

During the lecture on peer review, I emphasise how peer review should always be about helping authors to improve their manuscript. How to avoid making judgements and instead place an emphasis on critiquing the manuscript – including positive comments where they are warranted.

It should be stressed that the manuscript did not fall into the specialist subject of any of the students. Some of them may have had more insight into the molecular methods used than others, but for most of them their review fell firmly within science, and the biological sciences, but outside of anything familiar.

Before I start marking the assignments, I re-read the manuscript (having already read it once when I selected it) and carry out my own peer review exercise. This gives me familiarity with the manuscript and some ideas of the merits and problems therein. It also means that when I read the student reviews, I am able to assess them compared to my viewpoints and comments. 

The points that are well addressed, common mistakes and insights that follow are illustrative of general problems when dealing with peer review:

Well addressed

Many students spotted some very minor typos and errors made by the authors. For example, a single missing % sign was spotted by about a third of students, and those same students also saw that one figure was incorrectly referred to in the text. Similarly, a poorly labelled figure and colours that were too close together to distinguish were also regularly picked up.

Some students noticed that the authors failed to discuss any caveats relating to their study in the discussion. This had been a part of the coursework on writing a discussion, which is gratifying. However, no students noticed the failure of the authors to suggest new fruitful directions for their research.

Common mistakes

When summing up the manuscript contents, many of the students repeated a claim of novelty made by the authors even though this was false. This was interesting as there was no real need to repeat the claim, but the prominent claim of novelty in the abstract and the introduction was clearly very attractive and picked out by many students in the class to be repeated. I couldn’t have expected the students to know whether or not the claim was correct (it wasn’t), but very interesting that they were prepared to repeat it even though the claim was not substantiated and they had no knowledge to contribute themselves. This may go partway to explaining why claims of novelty are regularly published in many journals even though they are false. This is more common in high-ranking journals where editors are looking for novelty.

Although the manuscript clearly stated that it aimed to study one species, most students suggested that the study should be widened to increase the number of species studied. This mistake in review, expecting authors to go beyond the scope of their stated aims, was common in the class last year. The importance of the aims of a study was repeated continually throughout the writing course, yet students failed to recognise how the stated aims in a manuscript set the bounds of the manuscript contents. No students suggested that the idea of widening the experiment to further taxa, and which taxa to prioritise, should be a discussion point.

Students called for more citations to be made in the introduction and discussion. They did this without any making reference to specific statements that lacked citations.

  

Insights

Many of the students asked for experiments to be repeated, often adding that more replicates must be made. This request came regardless of the results or size effect, but they regularly drew attention to a lack of significance and high variance. Many implied a Type II error adding that no reporting should be made unless significant results could be achieved by repeating experiments. This was also interesting as a good part of the course stressed the importance of transparency and the realities of publication bias. Nonetheless, the idea of rejecting publication based on data that did not show significance was very strong, suggesting that this is a deeply held belief and not one that can be swayed by a course that stresses how this approach is bad science.

Students often requested experiments conducted in the field part of the study to be repeated with more controls on fluctuating environmental factors, although never stating which factors they wanted to be controlled. This lack of insight into the difficulty of field experimentation from a class of biology postgraduates was particularly disappointing. This may be because few of the students have sufficient experience in conducting field experiments. Nonetheless, the lack of empathy for authors who successfully carried out a field experiment and presented the results, limited though they may be, was surprising.

I had asked students to draw attention to the good in the manuscript for praise as well as negative aspects. However, those who wrote much of their review as praise did so without drawing attention to any specific points in the manuscript. Much in the same way that other students were highly critical without being able to say why. I think that this “arm-waving” approach to peer review is indicative of someone who really doesn’t understand what they are reading but feels the need to write something (in this case because they had to for an assignment). Again, this felt familiar to many reviews received where reviewers try to set a tone of their impression, but then fail to find any specifics that can back up that feeling.

Although these students were not experts on the contents of the manuscript, and are unlikely ever to be called upon to review something similar, many of the comments that they made felt familiar and could even be considered generic of a bad review. This despite being coached immediately prior to the assignment in how to conduct a good review.

In conclusion

I think post-graduate students conducting peer review is a great learning exercise, but that it is also very insightful for me when reading what they decide to pull out. Peer review is difficult. It appears to bring out prejudices even when we know that these should be suppressed. These insights should be useful for editors when assessing manuscripts on the basis of peer review.

A testimonial from Sam and the importance of saying thank you

Today was another long day. I got back from the office to find a whole bunch of messages on different platforms and I made myself a cup of tea before sitting down and going through them. One was a voice note from Sam Peta. Sam did a MSc with me and James Baxter-Gilbert, defending his thesis back in 2022 (see here). The voice note really surprised me. I've asked Sam, and he's given his consent to transcribe it here for the blog:

“Morning John, I hope you're good.

I think I forgot to tell you this but some time last year I had a job interview. I think it was a research field assistant for the Cape Parrot Project in Hogsback. It was like a brief interview to ask about who I am and what I do what was my MSc was about.

I told the lady, I don't remember her name, that I was supervised by Prof John Measey, and she said “Oh, I know John Measey!”

I was like whoa, okay, that's nice. And then she started telling me about her project with the leopard toad and that was quite amazing.

Even with one of the guys that I work with, he said that you taught him, I think when he was in Stellies.

So yeah, I think that the point that I'm trying to make is that I wouldn't be where I am now if it wasn't for you. The amazing skills that I've learned from you, the amazing mindset that I have when it comes to research, or looking at the world the way I look at things. So I'm grateful for the support that you've given me all these years, and now I have the confidence to say that I would like to believe that there's a great future in terms of research, and in terms of finding my way around. They're the small parts of life when it comes to working, is because of the skills that I've learned from people like you and James [Baxter-Gilbert] have helped me so much. I'll forever be grateful for that.

Even when I hear people talk about you, I get that kind of inspiration to say, okay, I've been under the supervision of one of the most incredible scientists in the world. So yeah, I'd like to believe that, hopefully in some way we can just keep in touch enough to work together at some point in the future. Yeah, I'm just wanting to say, before I start my new working day, thanks so much John for everything.”

Firstly, I’m incredibly grateful to Sam for reaching out and saying such nice things. It’s so great to hear that there’s been a lasting positive effect on students that have worked in my lab. Second, is that I have learned that it’s so very important to actually say these things to people. To actually thank them instead of just thinking that it would be nice. It’s not just important that they hear you say it, but also because you might be surprised what you hear in reply.

Here’s my response to Sam:

“Hey Sam – Thanks so much for your kind words. I think what you forget is that this does not only go in one direction. I learn an incredible amount from my students, including you. This is one of the things that makes being an advisor such an enjoyable experience, because I get to work with such enthusiastic people. It’s really my privilege to have worked with you.”

I used to think when I heard aged professors talking about their wonderful postgraduate students that they were just paying lip service to the team of people who really did all the work, but with no thanks. However, what I’ve learned, over the fullness of time, is that for many professors they truly do appreciate their team and the benefit goes both ways.

So, if you have read this far and you have someone in your life that you are thinking – yeah, they really helped me – I’m asking you to reach out to them now and say thank you. If you can, leave a voice note (like Sam did) so that they can hear your voice and know that you really do mean it. It will mean so much to them, and like Sam you may well get some words of wisdom to continue to propel you forwards.