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Cape Herp Club talks

28 February 2019

First Cape Herp Club of 2019

We kicked off late in 2019 on the last day of February, and very appropriately for Leap Frog Day we had two froggy talks from the MeaseyLab:

Natasha started off the talks with her (much practiced) talk on:

"The effects of range expansion on the survival and development of invasive Xenopus laevis tadpoles." Natasha Kruger (Stellenbosch University)

Then Carla told us about some of the work that she did for her thesis on toads in Brazil in the Caatinga, as well as some work she's currently doing on tegu lizards. 

"Relationship between seasonality, stress and immunity in anurans and lizards" Dr Carla Madelaire (Physiology Department, Univ. of São Paulo)

Both talks were well received.

It was a splendid venue at the Manor House next to the CapeNature Scientific Services centre in Jonkershoek. We got a rather special misty rain the came down as we all settled down to talks under the yellow-wood beams and the thatched roof.

  Frogs  Lab  meetings  Xenopus

Publication of our meta-analysis

27 February 2019

What do invasive species do to amphibians?

Today our amazing global meta-analysis on the impacts of alien species on amphibians was published. This MeaseyLab project was the brainchild of Ana Nunes. Way back in July 2015, Ana spotted that while there had been some great reviews of impacts of invasive species on amphibians, so far there hadn't been a meta-analysis. She introduced the idea to the lab, and then kept us busy for many months reading and scoring papers on impacts. It has now paid off with our paper being published today in Proceedings of the Royal Scociety B. It's been a long haul, but it was certainly worth it.

So what did we find?

What we found was quite surprising. While most people focus on the negative impacts of fish being most deleterious to amphibians, we found that the biggest effect was in fact from invertebrates. Moreover, most of the studies of invertebrates on amphibians featured the impacts of crayfish on tadpoles. Ana did her PhD in exactly this area, and so we got some great insight into exactly what the mechanisms involved were.

Other important findings involved the holes in our knowledge of impacts of alien species on amphibians. Very few studies have been conducted on adults, especially the impacts of invasive plants. These insights really help when planning future work.

Ana left us in June 2017, and now works for the IUCN in Cambridge. But if you want a really good look at the lab group that took part in this work, look no further than the infamous MeaseyLab Mannequin Challenge

Nunes, A.L., Fill, J.M., Davies, S.J., Louw, M., Rebelo, A.D., Thorp, C.J., Vimercati, G. & Measey, J. (2019) A global meta-analysis of the ecological impacts of alien species on native amphibians. Proceedings of the Royal Society B  20182528. http://dx.doi.org/10.1098/rspb.2018.2528

  Frogs  Lab

"Invasive Alien Species" is not a thing

26 February 2019

Why “Invasive Alien Species” is not a thing

Many invasion biologists are fond of the term “Invasive Alien Species” (often abbreviated to IAS), but for me it’s logically inconsistent and encompasses redundancy. Perhaps, the original reason for placing the three words together was in recognition that not all alien species are invasive, therefore we’d need to add the term invasive to underline the point that we are only referring to the subset of alien species, those that are invasive. However, the implication in this phrase is that it’s possible to be invasive and not alien; i.e. that “invasive native species” is another category. But it’s not. Most would agree that to be invasive you would first need to be alien. To this end, perhaps I should have titled this blog: Why "invasive native species" is not a thing... but there is a school of thought that suggests that invaders can be native (see Valéry et al 2008).

The Blackburn et al (2011) scheme (pictured below) formalised this in a way that makes this easy to understand.

To make it even easier, I’ve adapted the scheme into sets so that you can appreciate that each group of species is a subset of the other (this scheme is not to scale, as we’d expect to see much smaller sets inside each set – maybe even following the tens rule?). Note that if “invasive native species” were a thing, we could draw another set inside “All species” but separate from all the other sets. Does this seem logical?

If I said that this was an “invasive species”, would you then have to ask: “is it alien or native”?

Invasive species are a subset of alien species (i.e. the ones that spread), but we shouldn’t be adding words to each growing subset; otherwise we’d have the term “invasive established alien species” to distinguish between those that are merely “established alien species” or just “alien species”.

My appeal is to think about these terms instead of blindly following those who have gone before.

Yes, this is another rant on the blog, and I’d like to point the finger at John Wilson for infecting me with this particular pernicious titbit. Now I can only hope that it’ll spread and you’ll be able to point to this to help in your own war on IAS. We don't want to join those silly mechanistic definition folk with their non-biogeographic ideas of invasions. Otherwise we might end up going down an alley labelled 'invasion syndromes'.

  Lab  Writing

Pseudoreplication

24 February 2019

What is pseudoreplication?

It is very rare that we can measure every animal in a population, or every measure available in the environment. Instead of such exhaustive sampling, we try to take a representative sample. This sample is something that we can achieve over the period of our study, and which we can use to represent the population or environment of interest. Each data point within the sample should be a replicate, the same measure taken on an equivalent animal. For example, 20 replicate measures of the right hind leg of a frog should involve 20 individuals.

A pseudoreplicate is a problem with the experimental design. Using our example above, if we measured the same leg on the same animal 20 times, we could not claim to have taken a sample of all frog in a population. Similarly, if 20 measures of 20 individuals all came from the same pond, these animals would probably represent the pond well, but not necessarily the entire population (which is presumably made from more than one pond). Thus, pseudoreplication occurs when the measurements taken have a degree of dependence on each other, and therefore aren’t independent.

In this image, I’ve used the mean of the length of the frogs’ rear legs to be represented by the intensity of the shading. Taking 20 samples from the blue population would need to involve sampling several of the ponds, similarly for the green population. But in the yellow and red populations, the animals move so frequently between the ponds that all the means are the same. Thus, if you only needed to compare red to yellow populations (for your question), then you only need to sample 20 animals from one of their ponds.

However, this is where the subtlety of pseudoreplication sets in. We may have good reason to believe that the frogs in the pond we’re sampling actually do represent the entire population. We may know that animals in all the ponds in that population regularly move around, and hence measuring 20 animals from any of the ponds is the equivalent to measuring animals from all of the ponds. If the opposite were true, that we believe that the frogs in each pond represent a discrete unit, then we’d have a bigger problem. We’d have to sample evenly across all the ponds in the population to make up our sample, or the alternative would be to take lots of samples from each pond and use the pond as a factor in our analysis. By now you can see that the task is getting more onerous, mostly because the question is becoming more complex. This is a really important point, your experimental design is going to depend entirely on your hypothesis, and (as I’ve stated before – see here) it is really important to know what this is from the start.

If our hypothesis was that the legs of animals in one population were longer from those of another (perhaps because of selective sorting), then we might presume that animals within one pond are closely related (especially at the range edge), and so the ponds would become our smallest repeatable unit. We should then measure only a few animals from each pond, and repeat this for lots of ponds for each population. You can build the ponds into your model when you test you hypothesis, given that you have sufficient statistical power (see here for more on this).

Pseudoreplication in experiments

When it comes to conducting experiments, there tend to be a greater number of points at which you might be pseudoreplicating. A good example is the use of incubators to raise 10 sets of tadpoles from 10 pairs of parents at different temperatures. When each incubator is set at a different temperature (i.e. a different treatment) then this is fine, but if two incubators are used to house 5 of the tadpoles sets each, the largest unit becomes the incubator instead of the parental set of tadpoles. This is because the incubators are unlikely to be able to keep exactly the same conditions (incubators are fickle things). Likewise, this could be a room or some other unit in which you are treating the samples. Imagine that you wanted to extract the gut microbiome of these tadpoles and that you used one kit to extract nearly all of them, but suddenly this became unobtainable and you had to buy another brand to finish off the remaining samples. The kits would become your largest unit, and you’d be falling into the realms of pseudoreplication.

As I’ve emphasised above, pseudoreplication is a problem of experimental design. This is because if you’d designed your experiment properly, you’d know that you’d have ordered the right number of extraction kits, or see that not all your animals are going to fit into a single incubator. When you know about these problems in advance, you’ll be able to make allowances for them by including them as a term in your analysis (essentially testing to make sure that the different kit or extra incubator isn’t an issue - you wouldn’t expect it to be, otherwise it wouldn’t be worth going ahead with the experiment). However, you can’t simply go adding extra terms into your analysis. At some point you’ll run out of statistical power, and you must know that you’re going to have enough before you start. That is, you’ll stand an unacceptably high chance of failing to reject the null hypothesis when it is false (Type II error).

Summary

In summary, pseudoreplication is something that you need to beware of before you start your sampling. A good way of checking if you have a problem with pseudoreplication is to present it to a group (like in a lab meeting), with enough detail in your study design so that they’ll be able to spot it. If you are aware of potential problems in your study, conduct a power analysis to decide how many samples you can take in order to take account of the problem.

Sometimes it might be impossible to avoid pseudoreplication in your study design. If you think it's going to be important, then you'll have to redesign your experiment. If you think it's not important, you'll need to be able to reason intelligently, and be honest about the possibility of pseudoreplication in your write-up (see an example of this here). 

  Lab  Writing

Going Crazy for Toads in Durban

19 February 2019

Adriana, Carla and Carla go Crazy for Durban Guttural Toads

Sometimes, research takes you to places that you wouldn't have dreamt of going. Often these are experiences that you'll remember for the rest of your life, but some are memorable for touching your soul with beauty, while others are memorable for other reasons.

Adriana, Carla & Carla left for Durban last weekend to collect Guttural toads to compare with the invasive population in Cape Town (see blog entry here). While their Cape work took them into the gardens of elite homes, the Durban work has seen them in less salubrious surroundings. 

Trawling city streets after dark for the chance of picking up a warty friend is not for everyone, that's why Carla and Adriana came from USP!

Carla is much more familiar with hanging around fetid water after dark. Can you see the toad that she sees?

I'm sure that the trip will be very memorable, even if not for the joy to their souls. But hopefully the toads they find will unlock the secrets to what it takes to be an unstressed city anuran.

  Frogs  Lab
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