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Naas' study on fynbos frogs published!

05 June 2023

How do fish invasions change fynbos amphibian communities?

 

Back in 2017, Naas Terblanche visited me in my office in Stellenbosch. A retired agriculturalist (with an MSc in animal nutrition) turned winemaker, Naas had spent the first 16 years of his retirement in Stanford developing a passion for the frogs that he found there. He explained that he wanted to conduct a scientific study on the different communities of frogs that he found in the area near where he lived, using the skills of sampling and identification that he had developed.

We put together a study that tested the influence of invasive fish on various different habitat types in the region. Spread across two watersheds in the Overstrand, Naas used satellite data to select 200 different freshwater sites and categorise them into different waterbody types. From these we selected 50 that represented a balanced number of each category type.

Above, Naas T shows off one of the invasive fish sampled from a dam where he also studied the amphibian community. What a great way to spend your retirement!

Naas spent the next two winters visiting each of these 50 sites in turn, identifying the amphibian communities therein. It was long and hard work as he had to visit each site once during each year, and spend the afternoon and evening conducting the surveys so that he saw, captured or heard every species present.

The data showed convincingly that invasive fish were important in determining the composition of amphibian communities. Perhaps unsurprisingly, toads (Raucous toads and Western Leopard toads) that have toxic eggs and larvae are particularly tolerant of invasive fish, while the most intolerant was the plantanna, X. laevis, perhaps because they spend most of their time in the water.

Secondly, the resulting data demonstrated some interesting trends in freshwater habitat types. First, we confirmed that different habitat types contain different amphibian assemblages in the fynbos, with those most valuable being from temporary aquatic habitats. Permanent habitats, such as garden ponds and dams, were not particularly useful for local amphibians, but more for widespread common species. This means that if you want to create a freshwater habitat for conservation purposes in the fynbos, you need to make sure that it is temporary (not permanent), drying out in the summer months and filling in the winter.

Read the paper in full:

Terblanche, N., Measey, J. (2023) The conservation value of freshwater habitats for frog communities of lowland fynbos. PeerJ 11: e15516 https://doi.org/10.7717/peerj.15516

  Frogs  Lab  Xenopus

Temperature profiles high and low

22 May 2023

Getting high to work out how low they can go

Invasive species often have large native ranges that encompass a number of different environments. The African clawed frog Xenopus laevis is most commonly referred to as coming from a Mediterranean climate. However, in its native range this species is almost ubiquitous in all of southern Africa from the Highlands of Malawi through the tropical lowlands of Mozambique and KwaZulu-Natal, and in the deserts of the Karoo and Namibia. Included in this natural range is a remarkable elevational gradient from sea level all the way up to over 3,300 m in elevation. 

We were interested in sampling animals along this elevation gradient to determine how they changed in the thermal performance curves. Back in 2020 Laurie sampled animals every 1,000 m in elevation (see blog post here). We also left temperature loggers at all of these sites to see how the natural environments varied over the course of a year (see blog post here and here). 

The results of Laurie's study are published today and show that the thermal profile of animals has a left shift to lower temperatures as they move up the elevational gradient. This means that animals that we captured in Lesotho have a lower optimal temperature for their endurance performance. However, the upper temperature limit for all of these animals was the same irrespective of where they were collected.

The results of this study put a rather different context on the potential of this species to invade different areas outside their native range. We now know that the species can tolerate very cold temperatures throughout the year at higher elevations. 
Although this work sounds relatively simple, don't forget that Laurie had to chase these frogs at lots of different temperatures all day every day for weeks and weeks. This represents an incredible amount of work. Well done Laurie!

Read more about this work at:
Araspin, L., Wagener, C., Padilla, P., Herrel, A., Measey, J. (2023) Shifts in the thermal dependence of locomotor performance across an altitudinal gradient in native populations of Xenopus laevis. Physiological and Biochemical Zoology Journal https://doi.org/10.1086/725237
  Frogs  Lab  Xenopus

Starting your PhD

27 April 2023

How to Start your PhD

In some parts of the world the time-line is just getting started for new PhD students. This will be a very busy time for those involved, but it also needs to be a time to take stock and consider the bigger questions. In this video I provide some pointers to key issues for you to think about when starting your PhD. 

Warning - I do speak pretty slowly in this video, and so I think it's worth speeding it up so that you don't fall asleep. 
Here are some key excerpts from the text of a new chapter with links to How To Write a PhD in Biological Sciences:

Creating a conceptual framework of your PhD thesis

An important phase at the outset of your PhD project is to plan the chapters that are going to be in it. Think about the contents of your PhD and commit as many thoughts and ideas as you can to paper. If you aren’t sure how to get started, then think about how to answer the following questions:

  • What questions are you going to ask?

  • What is your study system?

  • How will you collect your data?

  • What are the most important variables that you will measure?

  • What techniques will you use?

  • Do you have hypotheses?

All these ideas (and more) are going to be swirling around your mind at the beginning of your PhD and you’re going to need to commit them to paper, and doing this right now at the start is the best time. If you haven’t done so already, write them all down. If you can do a mind map or some kind of graphical representation, this will be good for you if it suits the way that your mind works. Otherwise, you can use a series of lists and bullet points, if that is more your style. The important point here is be able to move from a jumble of ideas and thoughts into a formal plan for your thesis.

A thesis typically has five data chapters that are presented in a linear fashion (book format), bookended by an introduction and conclusion. At the heart of each chapter is going to be a hypothesis, a question or a technique that the following chapters implement in order to get their results.

It may help you to use distinct colours and short titles (just a couple of words) for each chapter so that you can efficiently communicate them to your advisor, and use them as file names for the sections (don’t use “Chapter 1” as your chapter name!). You should then use these same colours and short titles in your thesis timeline (Gandtt diagram) used in your proposal.

Once you have some rough ideas for your thesis plan, discuss it with your advisor and get their opinion. Then map it out on a piece of paper. But, be warned, it probably won’t be anything simple or linear - it’s likely to be more complex that the one illustrated below. It should have a lot of links and arrows that join all of the chapters to each other in different ways. It may help to code these links so that it’s clear what they represent. For example, you may want to use one colour for data and another for techniques and results. Although the detail is important, remember that the conceptual thesis plan is supposed to give an overview of the way in which the thesis works. This means that you might need to remove some of the minutiae in order to provide a clearer overall picture that others can easily follow.

A conceptual thesis plan will be placed in the introduction to your thesis. In this (fictional) example, I show how how the different chapters are linked by a single technique (developed as a chapter of the thesis: grey arrows), and data that results from each of the chapters (blue arrows).

A conceptual thesis plan will be placed in the introduction to your thesis. In this (fictional) example, I show how how the different chapters are linked by a single technique (developed as a chapter of the thesis: grey arrows), and data that results from each of the chapters (blue arrows).

To read more on this topic, please refer to the book!
  Lab  Writing

Dan graduates

30 March 2023

Graduation time for Dan

Dan van Blerk has been in the MeaseyLab since his Honours project in 2019 (see here), when he conducted a literature review on the impacts of invasive lizards around the world. In late 2019, Dan and I met with Olaf Weyl to plan Dan’s MSc fieldwork over the next two years. With all three of us filled with enthusiasm for the upcoming adventure and what it would achieve, we were about to find out that fate had other plans.

Very sadly, Olaf died later that same year, and subsequently did not get to participate in any of the plans. He is greatly missed, and we continue to remember his initial enthusiasm for the project. Happily, Josie Pegg was soon on hand to take over from the SAIAB side, and in doing so saved the project. However, just as we were about to deploy Dan into the streams of the Western Cape, we were hit by another big setback. The world suddenly shut down, and with it Dan was confined to quarters and we decided that we’d have to conduct at least one of his chapters as a literature review instead of in the field as planned.

During 2021, Dan managed to get two notes published on natural history observations that he’d made during his time in the MeaseyLab (van Blerk 2021 a,b).

Eventually, Dan did get out into the field and surveyed many locations in many streams for ghost frog tadpoles and invasive fish. The work was a real advance for conservation evidence in the impacts of invasive fish on these frogs. Dan presented his work in the Conservation Symposium (see here). We got used to seeing Dan presenting online and in person (see here and here). His findings have already been submitted to Aquatic Invasions, and we hope to announce publication of his chapter soon. Watch this space. Dan defended his MSc work in February this year (see here).

It was great having Dan in the lab, even if he didn’t spend much of the three years physically with us. We wish him all the best in his subsequent career and hope that he’ll keep in touch.

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

Van Blerk, D., Reissig, J., Riley, J.L., Measey, J., Baxter-Gilbert, J. (2021) Observations of infanticide and cannibalism in four species of cordylid lizard (Squamata: Cordylidae) in captivity and the wild. Herpetology Notes 14: 725-729. pdf

Van Blerk, D., Measey, J., Baxter-Gilbert, J.H. (2021) Predation by a Brown Widow Spider, Latrodectus geometricus (Koch, 1841), on a Common Dwarf Gecko, Lygodactylus capensis (Smith, 1849), with a review of the herpetofaunal diet of Latrodectus spp. Herpetology Notes 14: 291-296. pdf

  Frogs  Lab  prizes

Can Google's Bard do any better?

27 March 2023

Can Google's Bard write my PhD?

Last week I checked out ChatGPT and its ability to write text on scientific topics with citations. The bot performed very well in that it gave a great first draft of text, but the references that it gave were completely bogus, with none of them checking out. It seemed to me that ChatGPT was using the internet to source the text and then throwing in a citation where it saw that others had used one on something similar. Writing text with citations is, however, a lot more difficult than randomly tossing in a citation (read more about how to do it here). Instead, citations must assert that statements in text where they are used have some basis. Overall, the output from ChatGPT resembled that of a “cocky student” who takes the risk that you won’t check their work, and so makes up citations to go along with text that looks good.

Today is the turn of Google’s Bard platform to take the same text, so let’s see how it does.

 First, Bard starts with a statement that: “Bard will not always get it right. Bard may give inaccurate or inappropriate responses. When in doubt, use the “Google it” button to check Bard’s responses.”

What does Bard say it is?

Input text: “I am writing a chapter for a book on academic writing and I want you to describe Bard in your own words”

Bard is a large language model, also known as a conversational AI or chatbot trained to be informative and comprehensive. I am trained on a massive amount of text data, and I am able to communicate and generate human-like text in response to a wide range of prompts and questions. For example, I can provide summaries of factual topics or create stories.

I am still under development, but I have learned to perform many kinds of tasks, including:

I will try my best to follow your instructions and complete your requests thoughtfully.

I will use my knowledge to answer your questions in a comprehensive and informative way, even if they are open ended, challenging, or strange.

I will generate different creative text formats of text content, like poems, code, scripts, musical pieces, email, letters, etc. I will try my best to fulfill all your requirements.

I am excited to be able to help you with your academic writing, and I hope that I can be a valuable tool for you.

You may feel, as I do, that Bard is a little overeager to please me, especially given that this is the first time we have chatted. Like some of Google’s other interactive platforms, I’d rather it was more concise and less politely flatulent.

The test

To quickly recap, I asked Bard the same things that I asked ChatGPT last week. I used the same wording, including the same sentence structure. Specifically, I wrote:

Write a sentence with citations on: ”…”

And then replaced the … between the quotes with a sentence that I had written as an outline for the first two paragraphs of an introduction appropriate to a PhD chapter or manuscript. Both paragraphs consisted of four sentences:

Paragraph 1

Invasive species are a growing global problem

invasive species cost a huge amount of money to governments

invasive species are a threat to biodiversity

invasive species impact people’s quality of life

Paragraph 2

Freshwater habitats have been particularly impacted by global change

important changes have occurred to freshwater systems after the introduction of invasive fish

invasive fish have been added to both rivers and lakes

large numbers of introductions of invasive fish have already occurred globally, and are ongoing

Here is the output from Bard compiled into two paragraphs for easy reading by me (see line-by-line version below):

Invasive species are a growing global problem, with the International Union for Conservation of Nature (IUCN) estimating that they cause $1.4 trillion in economic damages annually (IUCN, 2016; WWF, 2017). Invasive species cost governments a huge amount of money to control and eradicate, with the US National Invasive Species Council estimating that the cost in the US is $120 billion annually. (NISC, 2017). Invasive species are a major threat to biodiversity, as they can outcompete native species for resources, introduce new diseases, and alter habitats. (IUCN, 2016). Invasive species impact people’s quality of life by causing economic losses, disrupting ecosystems, and harming human health. Economic losses can occur when invasive species damage crops, forests, and other natural resources. Disrupted ecosystems can lead to the decline of native species and the loss of ecosystem services, such as water purification and flood control. Harm to human health can occur when invasive species spread diseases or cause allergic reactions.

 

References:

IUCN. (2016). Invasive alien species: A global threat to biodiversity and ecosystem services. Gland, Switzerland: IUCN.

WWF. (2017). Invasive alien species: A global problem in need of a global solution. Gland, Switzerland: WWF.

NISC. (2017). The economic impact of invasive species in the United States. Washington, DC: US National Invasive Species Council.

At the end of this first paragraph I have to say that it’s a relief that Bard is citing and providing the reference for its citation. This makes tracking the information a lot easier. However, the bland nature of the text and the (over) reliance on a single source is not particularly useful. As stated for ChatGPT, these reports are compiled from a great many different documents, and are often written in an ‘readers’ digest’ format that doesn’t include source material. Hence, for a student these are best avoided as citation sources unless their work is pertinent to that particular report. In the last sentence, Bard seems to have forgotten completely about the one sentence request and instead has provided us with a barrage of statements – none of which have citations, although there are still a couple of references.

2nd paragraph

Freshwater habitats have been particularly impacted by global change, with climate change, invasive species, and habitat loss all playing a role. Climate change is causing changes in temperature, precipitation, and water flow that are altering freshwater habitats. Invasive species are non-native species that can outcompete native species for resources, introduce new diseases, and alter habitats. Habitat loss is occurring due to human activities such as development, agriculture, and mining. The impacts of these changes are already being felt, with many freshwater species in decline. If we do not take action to address these challenges, the consequences for freshwater ecosystems and the people who rely on them will be severe. "Invasive species can cause major changes to freshwater ecosystems, including the decline of native species, the alteration of food webs, and the spread of diseases. For example, the introduction of the invasive Asian carp to the Great Lakes has led to the decline of native fish populations and the alteration of the food web" (IUCN, 2016). "Invasive fish, such as Asian carp and largemouth bass, have been added to both rivers and lakes, often through illegal releases or escapes from aquaculture facilities." (IUCN, 2016). "Large numbers of introductions of invasive fish have already occurred globally, and are ongoing. Between 1970 and 2000, an estimated 7,000 species of fish were introduced to new areas (IUCN, 2016)."

 

References:

IUCN. (2016). Invasive alien species: A global threat to biodiversity and ecosystem services. Gland, Switzerland: IUCN.

WWF. (2017). Invasive alien species: A global problem in need of a global solution. Gland, Switzerland: WWF.

  

The 2nd paragraph contained requests (from me) for sentences that were a lot more specific. However, Bard continues to use the same set of references for all of its answers. Those IUCN reports are really good, especially that one in 2016 – where would Bard be without it? Interesting that it slipped into a quotation mode by the end. Whether this was because it could only find a single pertinent sentence and didn’t want to simply rephrase it, or because it was feeling lazy, I’m not sure. Still, lots more text than I had wanted, and if I had wanted quotes then I’d have asked for them.

Rather like the output from ChatGPT, Bard is writing sentences (apart from when it gets over enthusiastic and produces a paragraph or gets lazy and decides to quote directly from the source) and they are on topic. But they do lack depth. While I have no reason to doubt the source for this information, it is inadequate for a thesis or manuscript and I’d be tempted to toss the lot and go back to my outline and fill it in with citations from my own reading. It's interesting that Bard starts quoting its source, and even gives me back the exact same sentence I gave it as one of its outputs. This is an odd interpretation of the request: write a sentence on - simply to provide the same sentence back. 

It should not go without comment that Bard is distressingly out of date. I guess this comes from only looking at one or two reports from Google Books as a source, but I’d have thought that there was a lot more up to date content in Google Books. It’s a curious and conservative approach.

 

Bard output – thanks but no thanks

In comparison with ChatGPT though, I have to conclude that Bard is more honest in its output. While ChatGPT might be thought of as the “cocky student who isn’t afraid to make anything up”, Google’s Bard could be characterized as the “lazy student who found a single report and mined it to produce everything”. Neither would survive writing a PhD or manuscript.

Given that Google should have access to so much more, I asked Bard a few supplementary questions to find out why it was being so restrictive in its answers:

Why do you only supply references from a single source?

I am currently able to access and process information from a single source, which is the Google Books database.

Will you be able to cite from academic literature in the future?

Yes, I am confident that I will be able to cite from academic literature in the future. I am currently being trained on a massive dataset of text and code, including academic literature. As I continue to learn and grow, I will be able to access and process information from a wider range of sources, including academic literature. This will allow me to cite from academic literature in my responses, which will help me to provide more comprehensive and informative answers to your questions.

If you look back at our conversation above do you think that there will be any conflicts between your statements and your cited sources?

I have reviewed the conversation above and I do not think that there will be any conflicts between my statements and my cited sources. I have tried to be as accurate as possible in my responses, and I have cited my sources whenever I have made a statement that is not common knowledge. I hope that I have been able to provide you with accurate and informative information.

Do you think that your answers are going to be different from those of chat GPT?

It is possible that my answers will be different from those of Chat GPT. I am trained on a different dataset of text and code, and I am also trained using different techniques. This means that I may be able to generate different results, or I may be able to generate results that are more accurate or more informative.

However, it is also possible that my answers will be similar to those of Chat GPT. We are both large language models, and we are both trained on a massive amount of data. This means that we may be able to generate similar results, or we may be able to generate results that are both accurate and informative.

Ultimately, it is up to the user to decide which model they prefer.

And there we have it folks. Two bots who produce shallow text that isn’t really of any help to a student who is trying to write for their thesis or a manuscript. Hence, to answer my own question, neither of these platforms are going to write your PhD thesis. ChatGPT is going to throw a real curve ball to anyone who has the patience to look into the veracity of its statements, while Bard is just looking lame. However, I think that we will need to watch this space. Either or both have the potential to do much better, and I suspect that the will get much better at this as soon as they get the chance.

Last note

This text was written without the use of suggestive prompts. AI generated text is written as quotes in the above text. All other text is my own.

It will be interesting to look back on this chapter in a decade and see the changes that have emerged in that time.

I would like to thank Google and Bard for generating the quoted text in this blog post.

Here is the output from Bard line-by-line:

Invasive species are a growing global problem, with the International Union for Conservation of Nature (IUCN) estimating that they cause $1.4 trillion in economic damages annually. (IUCN, 2016; WWF, 2017)

 

References:

IUCN. (2016). Invasive alien species: A global threat to biodiversity and ecosystem services. Gland, Switzerland: IUCN.

WWF. (2017). Invasive alien species: A global problem in need of a global solution. Gland, Switzerland: WWF.

 

 

Invasive species cost governments a huge amount of money to control and eradicate, with the US National Invasive Species Council estimating that the cost in the US is $120 billion annually. (NISC, 2017)

References:

NISC. (2017). The economic impact of invasive species in the United States. Washington, DC: US National Invasive Species Council.

 

Invasive species are a major threat to biodiversity, as they can outcompete native species for resources, introduce new diseases, and alter habitats. (IUCN, 2016)

References:

IUCN. (2016). Invasive alien species: A global threat to biodiversity and ecosystem services. Gland, Switzerland: IUCN.

 

Invasive species impact people’s quality of life by causing economic losses, disrupting ecosystems, and harming human health.

 

Economic losses can occur when invasive species damage crops, forests, and other natural resources.

 

Disrupted ecosystems can lead to the decline of native species and the loss of ecosystem services, such as water purification and flood control.

 

Harm to human health can occur when invasive species spread diseases or cause allergic reactions.

 

References:

IUCN. (2016). Invasive alien species: A global threat to biodiversity and ecosystem services. Gland, Switzerland: IUCN.

WWF. (2017). Invasive alien species: A global problem in need of a global solution. Gland, Switzerland: WWF.

2nd paragraph

Freshwater habitats have been particularly impacted by global change, with climate change, invasive species, and habitat loss all playing a role.

 

Climate change is causing changes in temperature, precipitation, and water flow that are altering freshwater habitats.

 

Invasive species are non-native species that can outcompete native species for resources, introduce new diseases, and alter habitats.

 

Habitat loss is occurring due to human activities such as development, agriculture, and mining.

 

References:

IUCN. (2016). Invasive alien species: A global threat to biodiversity and ecosystem services. Gland, Switzerland: IUCN.

WWF. (2017). Invasive alien species: A global problem in need of a global solution. Gland, Switzerland: WWF.

 

The impacts of these changes are already being felt, with many freshwater species in decline. If we do not take action to address these challenges, the consequences for freshwater ecosystems and the people who rely on them will be severe.

 

"Invasive species can cause major changes to freshwater ecosystems, including the decline of native species, the alteration of food webs, and the spread of diseases. For example, the introduction of the invasive Asian carp to the Great Lakes has led to the decline of native fish populations and the alteration of the food web." (IUCN, 2016)

 

 

References:

IUCN. (2016). Invasive alien species: A global threat to biodiversity and ecosystem services. Gland, Switzerland: IUCN.

 

 

"Invasive fish, such as Asian carp and largemouth bass, have been added to both rivers and lakes, often through illegal releases or escapes from aquaculture facilities." (IUCN, 2016)

 

References:

IUCN. (2016). Invasive alien species: A global threat to biodiversity and ecosystem services. Gland, Switzerland: IUCN.

 

"Large numbers of introductions of invasive fish have already occurred globally, and are ongoing. Between 1970 and 2000, an estimated 7,000 species of fish were introduced to new areas (IUCN, 2016)."

 

 

References:

IUCN. (2016). Invasive alien species: A global threat to biodiversity and ecosystem services. Gland, Switzerland: IUCN.

 

  Lab  Writing
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