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The unsettled science of taxonomy: Can we categorise life in time to save it?

The unsettled science of taxonomy: Can we categorise life in time to save it? SHUTTERSTOCK/Protosov An
27 Aug
2021
Classifying a group of organisms as a separate species has implications for conservation. But the science behind it is far from settled

It could happen out in the field, perhaps in a steamy jungle or a parched desert or deep beneath the ocean surface where few people have been before. Or it might happen in a dusty, dimly lit archive. What matters is spotting something a little bit different, something you haven’t seen before.

The discovery of a new species is always an exciting event for the person whose job it is to make such finds: the taxonomist. It goes to the heart of the scientific endeavour – uncovering some previously hidden aspect of our world. But when it comes to species, we might reasonably ask: what’s really being discovered? What makes two different moths, which may look identical to an untrained eye, separate species, when a poodle (Canis lupus) and a great dane (also Canis lupus) are most definitely just the one?

The answer has repercussions beyond the closeted world of taxonomy. Most notably, it has implications for conservation. We define some organisms today as ‘endangered species’ and put them onto lists. But if our concept of what a species is shifts, or if a population originally deemed to be one species with lots of individuals turns out to be two species, one of which has far fewer individuals, these lists can, and indeed do, shift.

‘If you want to formulate species-specific conservation programmes, then clearly you need to know what your species are,’ says Wolfgang Wuster, a herpetologist (reptile and amphibian specialist) and taxonomist at Bangor University. ‘If you think you’ve got a very widespread species that’s found all over the place in many different habitats, then you might not worry about its conservation status. If you find out that it’s actually several species, then you might suddenly realise that there’s a completely different lineage about to go extinct.’

Given this, the answer to the question ‘what is a species’ is surprisingly difficult to pin down. Different people favour different definitions, a huge range of criteria come into play and it’s not uncommon to hear people argue that it’s actually a man-made concept – that species don’t really exist in nature, but are defined as such by humans as a useful form of categorisation.

Of course, all of this is taking place during a period of mass extinction, in which many species and subspecies are disappearing before they can even be identified. ‘We estimate that there are somewhere between ten million species on Earth and, at the very highest end, 100 million species. The 20 million range is the number I often use,’ says Richard Pyle, a Hawaii-based naturalist who spends his days scuba diving, sometimes uncovering new species of fish. ‘We’ve only named about two million of them. In other words, 250 years after this process began, we’re only a tiny bit of the way there. And we have lots of reasons to believe that the sixth great extinction is upon us. We’re losing biodiversity faster than we can even know that it ever existed. That’s the context around how we play this game.’

Resized1In order to identify the species near his home in Australia, amateur naturalist Donald Hobern traps and photographs hundreds of insects, including this wasp from the family Pteromalidae. Image: Donald Hobern

There was no concept of biological species in natural history before the 17th century. Modern taxonomy stems from the work of Carolus Linnaeus, the Swedish botanical taxonomist who, in the mid-1700s, formulated the binomial system of nomenclature, in which each specimen is identified by a generic name (genus) and a specific name (species) – Homo sapiens, for instance.

Linnaeus defined different species according to the natural characters of individual organisms, or morphological descriptions – something that still remains important in modern taxonomy. Today, morphology (essentially, the features that can be examined by the human eye) is used in combination with examination of DNA and of cells and behaviour to identify new species, which are then named according to a strict set of rules. For Linnaeus, operating a century before Charles Darwin formulated his theory of evolution, two organisms were the same species because they came from the same parents, as created by God. Modern taxonomists are interested in identifying organisms that are the same species because they have followed the same distinct evolutionary path, usually as a result of geographical isolation from others.

But none of this really defines a species. When does an organism become different enough from another one that it counts? The traditional definition, often encountered in school textbooks, is known as the ‘biological species concept’ and holds that two organisms are the same species if they can breed and produce fertile offspring. A donkey and a horse can breed but their offspring (a mule) will be infertile and they are therefore different species. All dogs, on the other hand, can produce fertile offspring (although human breeding has made this practically difficult in some cases) and are therefore the same species. They are, in fact, the same species as wolves, too (Canis lupus), although they’re considered to be a subspecies (Canis lupus familiaris).

But this is really just one method of identification, not a definition. For starters, there are exceptions. Ligers, the offspring of tigers and lions, can sometimes produce fertile offspring, but tigers and lions are considered to be different species. Then there’s a whole host of animals, plants and bacteria that reproduce asexually and, in any case, the margins between species are often blurred – most individuals don’t interbreed, but some do and their offspring are sometimes fertile.

Richard Pyle diving with rebreather in Fiji Photo Cat Holloway NAIA Fiji 2Scuba diver and ichthyologist Richard Pyle collects specimens in Hawaiian waters. Image: Richard Pyle

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‘Science has no clear definition for what a species is. It always has been, and probably always will be, a matter of subjective decision,’ says Pyle. ‘The one that I use is the one that’s been around for the entire time and which we will always use, which is that a species is what a community of taxonomists says it is. That’s a little bit snarky, but it also underpins another debate in our world: are species actual entities in nature that exist independently of humans?’

Pyle’s feeling is that they don’t, but that doesn’t mean the exercise of categorisation is worthless. ‘My school of thought comes from the idea that evolution doesn’t produce species,’ he says, ‘evolution produces populations of organisms that have different levels of interbreeding with each other over time. Those populations change over time because of climate change and other circumstances. It’s just a kind of amorphous mix of things that definitely cluster but don’t necessarily have hard boundaries between species.’

Mostly, none of this a problem. Taxonomists are okay with uncertainty. Science is the gradual accumulation of knowledge, followed by correction – in other words, tinkering. And taxonomists like to tinker. But having no fixed definition does leave things open for debate and the debate can heat up. One of the hot topics today is the increasing use of genetic analysis to identify species. This concept defines a species as the smallest group that can be genetically distinguished from another species but still share a clear ancestor.

Differences in the genetic make-up of organisms are certainly a useful way of distinguishing between populations, but more traditional taxonomists balk at the idea that a species can be defined solely based on DNA – something that’s becoming much more common in the scientific literature and that’s contributing to what has been described as a ‘new age of discoveries’. This new age has seen more than 400 species of mammal discovered since 1993, an acceleration that has led some taxonomists to point to ‘taxonomic inflation’.

Sometimes, these new discoveries result from exploration of previously neglected regions (the deep sea, for example), but often they are made in the lab and result in what was once considered one species being divided in two, or what was considered a subspecies being elevated to species level. In early 2020, for example, a research paper announced the discovery of a new species of primate called the Popa langur. Found exclusively in Myanmar, near the extinct volcano Mount Popa, these animals weren’t unknown to humans before the paper came out, but were considered members of a wider species called Phayre’s langur (or leaf monkey), found right across Southeast Asia. The new categorisation meant that the Popa langur was critically endangered from the moment it was ‘discovered’ – there are just 200–250 individuals – although the categorisation is so new it doesn’t yet appear on the International Union for Conservation of Nature’s (IUCN) Red List (Phayre’s langur is listed as ‘endangered’). Like most other recently described primates, the Popa langur was first identified in a lab using genetic information, in this case taken from a 100-year-old skin and skull housed at the Natural History Museum in London. The genetic information was then supplemented by very subtle physical differences.

Similarly, scientists used to recognise two different subspecies of the red panda (Ailurus fulgens): the Chinese red panda and the Himalayan red panda. However, another 2020 study by researchers from the Chinese Academy of Sciences pointed out that the pandas fall into two clear genetic clusters, which they argue are distinct enough to classify them as separate species. (Again, just the one species appears on the Red List.) But the question remains: what is distinct enough?

‘It has been a hot topic now for about ten years and it has been heating up a little bit more recently,’ says Pyle. ‘Now that we have relatively inexpensive ability to access the DNA of specimens, it’s almost like the perfect characteristic to determine whether or not two species are the same or different. I say almost because we don’t quite understand how to translate the genetic information into the context of how species have historically been named. There’s a little bit of tension in the sense that people who only look at the genetics sometimes find different patterns than people who look at it in a more traditional way. And, if the names are changing every year, it gets really hard to put things into evolutionary context or biodiversity context.’

Les Christidis, an ornithologist at Southern Cross University in New South Wales, is more outspoken. ‘The problem with just relying on genetic information or DNA data is, what is the threshold of differentiation that qualifies for species recognition? Is it two per cent, five per cent, 20 per cent? There’s no consistency in the application of genetic distances as a species boundary. There’s a tendency to over-inflate the significance of the genetic differences in order to define a new species. Your paper is more cited if you’re describing a new species as opposed to a subspecies and there are conservation-funding implications. The primates are a classic example of where every slightly differentiated population is now classified as a separate species.’

DNA DETECTION

Donald Hobern is executive secretary of the International Barcode of Life Consortium (iBOL), an organisation working to use DNA to reveal species across the globe, including their dynamics and interactions. As the iBOL website states: ‘While study has delivered a basic understanding of biodiversity, it cannot discover and identify species on a planetary scale. Our vision is to illuminate biodiversity for the benefi t of all life.’

iBOL is centred on DNA barcoding, which involves isolating DNA from a specimen (which might be a small organism or just a small part of an organism) and turning it into a barcode sequence that is then stored in a searchable reference database. You don’t need to map the whole genome of a specimen (although other projects are underway that do so, such as the Earth Biogenome Project); for animals, the barcode is taken from a small section of 650 base pairs in the loop of DNA found in the mitochondria of cells.

‘Within this loop, a difference in DNA between two organisms of a few per cent [the amount varies within different taxonomic groups] seems fairly reliably to match, for many groups, the sort of difference that would traditionally identify different species,’ says Hobern. ‘The level of difference is not a black-and-white test, but it’s a very useful tool, because we can standardise it across most animals and these days it’s relatively cheap.’

The first iBOL research programme barcoded 500,000 species, reflecting an investment of US$150 million by research organisations in 25 nations. Its second programme, BIOSCAN, aims to extend barcode coverage to 2.5 million species by 2026.

Hobern points out that there’s a wide range of uses for such a database. Not only could it aid taxonomists in their work, but sequencing DNA from a sample and comparing it to the reference database can verify that fish being sold are indeed one of the species listed on the packet, rather than a threatened species, or enable rapid detection of rare forest timbers or bushmeat in a market.

‘One of the other advantages is that, not only can you do this with a bit of flesh, you can do it with all kinds of other samples in the environment,’ he says. ‘If you take soil, you’ll find trace DNA from animals that have passed there and that have either dropped skin cells or left faeces behind. If you take water from streams, you can detect what fish are elsewhere in the stream.’ This is known as a ‘metagenomic’ study and it can very quickly provide a genetic snapshot of an entire ecosystem.

With the cost of sequencing coming down all the time, Hobern is looking forward to seeing environmental sensors that are based on cheap portable DNA sequencers, which could simply be placed in the field or at sea and then sequence the DNA of all of the species present in that area. ‘At that point, the world’s a different place, and we’re probably not that far from it,’ he says.

51264346159 f6946affdb oA specimen caught in the trap, identified as belonging to the order Hemiptera. Image: Donald Hobern

By and large, taxonomists have a high tolerance for this type of healthy academic debate, but it can prove frustrating for conservation professionals. For them, a clear list of species is important in order to carry out conservation work. It was partly this divide that led to an intellectual sparring match, only recently resolved, in which the question ‘what is a species’ came to the fore. It all kicked off with an article written by Christidis and Stephen Garnett, a professor of conservation and sustainable livelihoods at Charles Darwin University in Darwin, Australia. They argued that the lack of concrete definitions and the lack of oversight when it comes to identifying new species contribute to a chaotic system. ‘The assumption that species are fixed entities underpins every international agreement on biodiversity conservation, all national environmental legislation and the efforts of many individuals and organisations to safeguard plants and animals. Yet for a discipline aiming to impose order on the natural world, taxonomy... is remarkably anarchic,’ they wrote. ‘“Species” are often created or dismissed arbitrarily, according to the individual taxonomist’s adherence to one of at least 30 definitions.'

Changes to classifications mean that conservation legislation often fails to keep pace. For example, the authors made the point that changes to taxonomy since Chinese wildlife legislative lists were last updated in 1989 have left 25 species exposed to illegal trade. Given this, they went on to argue that the scientific community’s failure to govern taxonomy threatens the effectiveness of global efforts to halt biodiversity loss and proposed that any changes to the taxonomy of complex organisms be overseen by the highest body in the global governance of biology, the International Union of Biological Sciences.

This suggestion didn’t go down well. Taxonomists argued that such an oversight would limit scientific freedom. In one paper, a group of taxonomists accused Garnett and Christidis of trying to suppress freedom of scientific thought, likening them to Stalin’s science advisor Trofim Lysenko.

As Wuster says: ‘Taxonomy isn’t a service industry that serves up classifications on demand. It’s a science with its own body of theory, its own concepts. We’re constantly generating new evidence that causes us to review our previous conclusions, which is the way science works. So the idea that we should be able to produce, on demand, a fixed species list is just completely out of tune with how taxonomy actually works.’

Thankfully, things came to a more fruitful conclusion. After some back and forth (or ‘strongly worded ripostes’ as one summary of the debate put it), each side came together to discuss the problem at Charles Darwin University. ‘The workshop was collegiate once we had explained that we weren’t about stopping taxonomists naming things or academic freedom, but rather having a system of independent quality control on which species are accepted,’ explains Christidis.

‘In fact, it has been a very constructive engagement,’ agrees Wuster. ‘There are several follow-up papers, which make the point that there are efforts to be made on both sides to try to generate more consensus and evidence-based lists of species, which is what decision-makers really want. They don’t want to know about why it’s complicated; they want a list of species and to know what we need to protect. But the fundamental issue, that taxonomy isn’t just a service industry, I think is a really important one.’

The individuals involved, who included taxonomists, scientific-governance experts, philosophers of science, administrators of the nomenclatural (naming) codes and the creators of national species lists, agreed that a global list of species – representing a consensus view of the world’s taxonomists at a particular time – was an important goal. Such a list would need to be underpinned by a set of principles that would at least partially control what could and couldn’t be added. Some early principles were agreed, others are now being thrashed out.

Luckily, they aren’t starting from scratch with this list. The Catalogue of Life is the most comprehensive attempt to date, bringing together a wide range of existing species databases in one place. The catalogue currently includes 1.4 million animal species, 374,236 plant species, 146,155 fungus species and 81,445 other species (including bacteria), all freely searchable online. The hope is that the new set of principles could be applied to the catalogue to give it greater weight.

One important principle of any such list is to make sure that it’s guided by science. Some taxonomists are very keen to keep out what have become known as ‘taxonomic vandals’ – people who indiscriminately name new species without any scientific rigour. This can prove difficult because, unlike the (lack of) rules for what is and isn’t a species, the rules for how you name a species are strict, leading to a bizarre situation in which a person can name a new species based on flimsy/no criteria and, in the process, ensure that the new name is set in stone.

Naming rules are set out in the International Code of Zoological Nomenclature (for animals) and the International Code of Nomenclature (for fungi and plants). The full rules fill many chapters but, simply put, each new species must have a two-part name, as originally set out by Linnaeus, with the first part denoting the genus and the second the species. The second word must be unique within the genus, can’t be rude and you can’t use your own name. You can, however, use someone else’s – hence the spider Aphonopelma johnnycashi (all names must be translated into Latin).

shutterstock 759344008The same species and subspecies, whatever it may look like. Image: SHUTTERSTOCK/Best Animal Photos

SUBSPECIES
Since determining a species is complicated, it’s unsurprising that the next category down - the subspecies - is equally so. Yet identifying subspecies is just as important for conservation. Take tigers (Panthera tigris). The WWF website states that there are two recognised subspecies of tiger – the continental (Panthera tigris tigris) and the Sunda (Panthera tigris sondaica) – but other organisations recognise a number of other subspecies.

In 2004, Malayan tigers were recognised as a new subspecies by one team of scientists. The distinction was made based on genetic analysis and the new subspecies was dubbed Panthera tigris jacksoni after naturalist Peter Jackson. Later research found no clear morphological differences between tigers from Peninsular Malaysia and those elsewhere in Indochina. Nevertheless, the IUCN and other conservation groups have provisionally accepted the Malayan tiger as a subspecies, triggering significant conservation efforts. With just 80–120 mature individuals found only on the Malay Peninsula and along the southern tip of Thailand, the Malayan tiger is critically endangered. Its plight has caught the attention of the Malaysian government and local conservation agencies, as well as conservation partners around the world. One example is the Woodland Park Zoo in Seattle, Washington, which has partnered with the global conservation organisation Panthera on a ten-year, million-dollar preservation plan.

The issue with taxonomic vandalism lies in the fact that the code operates according to the ‘principle of priority’. This means that the first person to name a species according to the code gets that name and everyone else is expected to use it. The key criterion for securing the name is to have it published in a place that exists ‘for the purpose of providing a public and permanent scientific record’ – which isn’t that difficult as many journals and scientific websites exist and not all are reputable.

‘What taxonomic vandals do is they go around and find things for which there isn’t a name available yet,’ explains Wuster, ‘and quickly throw one at it. So they may go across distribution maps of species and wherever you have a species that’s distributed in multiple places, they quickly throw a name at each of the populations that haven’t been named yet on the off chance that somebody later comes along and says, “Oh, yeah, that’s actually a different species”.’

This secondary investigator might do all the hard work to prove that such a population really is a new species, but when they go to record it, find that a name has already been given. Wuster is well aware of the problem because the snake world has been particularly affected, with a few vandals naming thousands of species. ‘There’s a guy called Raymond Hoser who loves to name things after his dogs, after his wife, after his kids. And it becomes a big problem. In the year 2020, he coined 404 scientific names. Clearly it’s not quality controlled. It’s somebody who throws a lot of names out there and hopes that some of them will stick and then they will be the author of that name and they will go down in history for that.’

The rules of nomenclature are some of the oldest in science and are usually strictly followed. As the code’s website states: ‘The system of naming organisms is the first truly global scientific standard, predating even standard calendars and units of measurement.’ Nevertheless, some taxonomists, Wuster included, feel they have no choice but to override this prestigious institution when vandalism takes place.

The vandalism issue perfectly highlights just how complex and fraught the identification and naming of species can be. A perfect list of all the species on Earth will never truly exist. Even if the human resources could be worked out, the biology can’t be – species are constantly shifting. Nevertheless, there is merit in working towards such a list – one that can be relied upon. ‘It’s sort of bridging the gap between the taxonomy world and the rest of biology and coming to some sort of agreement,’ says Pyle. ‘We’re going to acknowledge that taxonomy still happens – we call it the bubbling cauldron of debate about what are the valid species – but then there’s this filter between that world and the world of people who need to use names in a more stable way. The Catalogue of Life theoretically serves that function, but in practice hasn’t done so. So this new initiative is mostly about empowering the Catalogue of Life to actually serve in that capacity.’

Such an attempt involves thousands of people working in every corner of the world, very gradually improving our knowledge of the life that surrounds us. In the meantime, that life will keep on carrying on, oblivious to our attempts to organise it.

SUBSCRIBE TO OUR MONTHLY PRINT MAGAZINE!
Subscribe to Geographical today for just £38 a year. Our monthly print magazine is packed full of cutting-edge stories and stunning photography, perfect for anyone fascinated by the world, its landscapes, people and cultures. From climate change and the environment, to scientific developments and global health, we cover a huge range of topics that span the globe. Plus, every issue includes book recommendations, infographics, maps and more!

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