Taxonomy Part 1: reproductive isolation, biodiversity, and why it matters what Latin name you put on a species

[Note: I am aware that I came, I saw, I posted four times, and I disappeared into the dread abyss of non-posting. It occurs to me now that perhaps October was not the most sensible month to embark on my blogging adventures. November is National Novel Writing Month, and I signed up for it this year for the first time in four years. This means I am attempting to ensure I write 1667 words of my planned novel per day, to complete 50,000 words by the end of the month. Now, the reason I could do that this year is that I finally submitted my PhD thesis back in June. Irony of ironies, my examination results came back at the end of October, and now I have to make minor amendments to that thesis, while trying to write a novel. At the same time my current paper is – and I quote – “so close!” to being submission ready that I can’t really put that down either. Between the novel, the thesis, and the paper, I’ve had quite enough writing projects. But I am determined to share my love of taxonomy so here is my – somewhat lengthy – prodigal return post. -KN]

“I’m having trouble,” I told my friend at the bar. “I’ve tried six times to write a post about taxonomy. Normally I don’t have any trouble conveying my enthusiasm or making things interesting, but every time I start it ends up somewhere… else.”

She gave me a puzzled look. “You look at dead animals trying to work out which Latin name to put on them.”

“Well, there’s more to it than that…”

Perhaps that is the problem: the public perception of taxonomy is very much about putting the appropriate name (Latin, Greek, or otherwise derived) on critters, plants, fungi, microbes, what have you; one pictures crotchety old men with magnifying glasses and ancient sea shells, far disconnected from the environment in which they were found – less a cataloguing of biodiversity than a process of formalin-soaked stamp collection. I have seen my share of such scenes, although to be fair taxonomists vary in age and gender, and they are only very occasionally crotchety.

To be honest, it’s not just the public perception of taxonomy that suffers from that image; other biologists and environmental scientists also appear to have this notion.

Taxonomist is one my many Science Hats, and is the reason for my recent short jaunt to the Land of the Long White Cloud (New Zealand, although I have yet to see the cloud in question) – which, incidentally, is why there was zero blog action for a few days.

I had to visit Dunedin, New Zealand, because I’m revising a genus (what does that mean?) of feather stars (of what?) and I had to examine a type specimen at the Otago Museum (what the hell is a type specimen?) to make sure it was the same as the species of the same name we have in Australia (why does that matter?).

You can see how quickly the whole thing becomes quite muddled. I’m actually going to leave feather stars/crinoids for another day (although I will provide a link at the bottom for the curious), because they are gorgeous and marvellous and deserve a post all of their own.

Taxonomy is an exercise in categorisation, and since the natural world works the way it does, it is inherently an attempt to impose order upon chaos. At no point does the multitudinous swarming life among which we live feel any justification to make things easy for us. The best example of this is probably the species concept.

In fact, the very best example of that is the fact that I am going to set aside plants, fungi and microbes in my discussion of the species concept; they all interbreed and hybridise; plants have a tendency to randomly multiple their chromosome number (ploidy level) for (as near as I can tell) shits and giggles; microbes just swap in and out bits and pieces that they seem to find useful; and I don’t even want to know what the fungi are doing. It’s hard enough to work out what comprises an individual organism in a fungus, let alone an entire species.

Animals – for the most part – make things a little bit easier. The most common species concept is based on the notion of reproductive isolation, i.e., can the animals that look like this produce viable offspring with animals that look like that?

I have made up some critters to illustrate this. We shall call them “Bongs” and Bings”, because then the hybrid of these two can be called “Boings” and that appeals to my sense of the ridiculous (which is, let us be honest, all that matters).

Reproductive isolation takes two basic forms: prezygotic and postzygotic.

Prezygotic isolation involves the case where ne’er shall egg and sperm meet. There are a host of plausible mechanisms here. Maybe Bings and Bongs live on different continents (but does that make them different species?). Perhaps Bings are fertile in summer and Bongs are only fertile in winter. Perhaps Bings produce eggs that float up onto the surface of the water and Bongs produce sperm that sink to the sea floor. Perhaps the mating call of the female Bing, an irresistable siren song to the randy male Bing, is simply quite uninteresting to the randy male Bong. The same could apply to mating dances, plumage, pheromones, or any other behavioural cue. At the absolute farthest edge of what we can safely call “prezygotic”, perhaps male Bong sperm (you may giggle any time. I shall not judge you) cannot penetrate the envelope of the female Bing egg, due to a lack of protein recognition.

But wait! Reproductive isolation can be asymmetrical, meaning that perhaps a female Bong and a male Bing can get busy and experience a successful breeding season together, but a male Bong and a female Bing are utterly uninterested in one another. Due to the behavioural and chemical complexities of sexual reproduction, this is more likely than not.

Postzygotic isolation involves the case where a delightful Boing zygote is produced. Perhaps it doesn’t develop past a certain point. There is a spectrum here on which a hybrid offspring might be considered inviable – even if it survives to maturity, it may not produce useful gametes and thus it won’t be able to breed a second generation.

Unfortunately, while that seems simple, the definition of “viable” is somewhat fungible (see what I did there?). Imagine our Boing reaches adulthood and sexual maturity, and is entirely capable of producing worthwhile eggs and/or sperm which will be enable it to produce offspring with other Bings, other Bongs, or both.

But maybe those offspring are not quite as good. Maybe they are a bit less fertile than they should be, or a bit smaller and less competitive for food or mates, or perhaps a bit prone to disease, and over several generations they are eclipsed and outcompeted by purebred Bings and Bongs.

That’s called outbreeding depression, and it makes the species concept a bit more of a grey area than we would generally prefer.

The problem taxonomists face is that reproductive isolation is often not something that is easy to test. When someone throws you a dead animal (note: do not throw), you don’t have the opportunity to drop it into a tank with a similar looking animal and wait for them to get busy – or rather, if you do, all that will happen is you’ll end up listening to Barry White for a while and staring at a dead animal in a tank.

What I do, as a molecular biologist, is to look at DNA samples from a large number of animals from various groups and to work out whether they are swapping genes around. If you look at enough different genes (one is not enough, but that’s another story), you can get a very good idea of whether the Bings and Bongs living under the same rock are able to successfully get busy (because, as a general rule, if they can, they will).

Even then, however, you have to assume that

1)   you have access to enough fresh tissue for DNA analysis (DNA can be extracted and used from very old specimens, but it’s extremely fiddly and expensive)

and

2)   you have the money to embark on DNA analysis (even though whole genome sequencing, or WGS, is becoming a great deal cheaper and more accessible, molecular biology as a whole is another entire world of expense on top of just collecting the animal)

Often, this is not the case, and this is illustrated my most recent adventure to New Zealand. In that case, all you have to go on is morphology (what the animal looks like, often specifically what it looks like when preserved in formalin or ethanol), and working out what key feature (a.k.a. “diagnostic character”) separates one species from another can be tricky.

I was trying to explain the species concept to some friends of friends at a party. They brought up dog breeds, and there was some confusion about the term “breed” versus “species”.

Dog breeds can, obviously, interbreed (although there are some mechanical difficulties if you try to breed a Great Dane to, say, a chihuahua). They are the same species, and yet they look stupendously different from one another. Dogs are not a great example, since we deliberately bred them to look different and it can hardly be called natural selection, but it is a useful illustration nonetheless.

When it comes to a lot of the animals that I look at, many of them look almost identical to one another; and yet their DNA is telling me that not only do they not interbreed, but they probably haven’t shared a common ancestor for a few million years.

Morphology is an essential piece of the puzzle – without it, field surveys would be almost impossible (or prohibitively expensive); we wouldn’t know what animals are living where; and we wouldn’t be able to look at interesting things like the evolution of various features. At the same time, it’s important to realise that there is often no apparent relationship between the degree of morphological difference and how distant something might be genetically. Species that diverged at least six million years ago might be nearly impossible to distinguish, while humans of various different ethnicities who are all quite clearly the same species (but who, to our eyes, can look quite different) probably first diverged only a paltry few thousand years ago.

Of course, this brings us to a problem (you may have spotted it already). If a species has natural variation within it (and they all do), how do you at any point confidently describe what a species actually looks like, such that it can’t be confused with another species?

Enter – the type specimen.

How much does a gram weigh? How long is a metre? They’re not rhetorical questions; to avoid variation over time, these things are measured against a universal standard. We do the same thing with species.

When you find a new species, you pick one of the specimens you have (hopefully you have more than one, but that is not always the case) and you declare, “This is the type specimen! This is what Doorbellius bingius looks like! It has all the requisite bits and pieces for us to know what it is.” Then you take photos and make drawings and describe it in excruciating, tedious detail and publish it so that everyone knows your species exists and where to find the type specimen. That way, when they are handed a box of specimens, they will be able to see that one might actually be D. bingius instead of actually being D. bongius (I am enjoying that far more than I should).

That standard is called the holotype. If you’re fortunate enough to have a reasonable number of specimens and you are sure they are the same species as the holotype, you can pick a number of them and declare them to be paratypes. This is so they can capture the natural variation. You might choose a Bing with curly fur, for example, because the holotype has straight fur and you want to make it clear that the fur of a Bing can be straight or curly. You might choose a big one and a little one, because maybe they look different when they are different sizes (a very common problem in taxonomy, particularly invertebrate taxonomy, is that juveniles have different features from adults).

Although I have at most recent count eleven species to describe as a result of my PhD work (eleven!), I have only at this stage described one species. We thought they were all the same species, but some of the animals we had were different. Then it turned out that they produced different larvae, and they were very differentin their DNA, and when it came right down to it and after complicated multi-dimensional scaling analyses yes, alright, alright, they were different colours.

I designated a holotype and a paratype and they live at the museum where I do my taxonomic work, and no doubt I shall repeat that process another eleven times.

But what does it matter, Kate? you may ask. Why does it matter that the species are different?

It matters for a lot of reasons. Some of it, I suppose, comes down to a philosophy of valuing biodiversity that I hold dear; and I don’t know how we can value something properly if we don’t know that we have it. A great deal of it is related to our understanding of the natural world, how species form, how they persist and change over time, and how that process will continue into the future – these are good and important things to know.

For me, personally, it comes down to conservation. If we are going to take care of our environment, we are going to have to keep an eye on it. In order to effectively monitor our environment, we need to be able to recognise what’s in it. That species I described was a cute little biscuit star (yes, I think starfish are cute. Sue me) that produced unusual larvae that could not swim. If the larvae can’t disperse, that means that all the different populations of that star are relatively isolated from one another, and in turn that means that if one population is wiped out due to a natural disaster or pollution event, it is less likely to recover.

Before I described it, no-one knew it existed. They all thought it was the same as the other biscuit star that mostly occurred in exactly the same environments. It could have suffered a silent extinction, and no-one would ever have noticed because the other species was still there. Perhaps it performed an interesting ecosystem function, like preying on an invasive sponge, and its disappearance would have a knock-on effect. These kinds of questions are bread and butter for ecologists, and once they have the taxonomic information they can ask some truly marvellous questions about the natural world.

But in summary, if people think that Bings and Bongs are the same species, and think they are all Bings, then they won’t notice the decline of the Bongs and the loss of biodiversity.

I am not saying that my description of one little biscuit star (no matter how awesome I think the animal is and no matter how cheered I am by seeing it on a dive) is particularly momentous. It’s not. There are numerous taxonomists who describe tens of species a year. It is incremental work. Our estimates of biodiversity, particularly in Australia, are turning out to be very short of the actual value.

As to how all this resulted in my recent trip to New Zealand, and what happened with the specimens there, that is a tale for another time. 

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