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Taxonomy is a powerful tool, and one that modern biology wouldn't be able to function without. But trying to shoehorn the messy, complicated web of interrelationships that is biology into neat boxes has resulted in a pretty messy tree of life.

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Sources:

https://ucmp.berkeley.edu/glossary/gloss1/phyly.html
Irie et al 2018 https://zoologicalletters.biomedcentral.com/articles/10.1186/s40851-018-0114-y
Komarek and Beutel 2007 https://www.researchgate.net/publication/229077116_Problems_in_taxonomy_and_suggestions_for_a_standardized_description_of_new_insect_taxa
Satoh et al 2014 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4211455/
Padial et al 2010 https://frontiersinzoology.biomedcentral.com/articles/10.1186/1742-9994-7-16
de Queiroz 2012 http://hydrodictyon.eeb.uconn.edu/eebedia/images/5/55/2012DeQueiroz.pdf
https://www.royalsociety.org.nz/assets/Uploads/Report-National-Taxonomic-Collections-in-New-Zealand-2015.pdf
https://www.cbd.int/gti/importance.shtml
https://academic.oup.com/bioscience/article/61/12/942/390232
https://phys.org/news/2017-08-biodiversity-earth.html
https://www.cell.com/current-biology/fulltext/S0960-9822(16)30303-7?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0960982216303037%3Fshowall%3Dtrue
https://www.britannica.com/animal/turtle-reptile/Origin-and-evolution
https://www.britannica.com/animal/dinosaur
https://www.biotaxa.org/Zootaxa/article/view/zootaxa.3025.1.5
https://science.sciencemag.org/content/346/6215/1254449

Images:

https://en.wikipedia.org/wiki/File:Linnaeus_-_Regnum_Animale_(1735).png
https://en.wikipedia.org/wiki/File:Lamarck_1815_diagram_of_animal_evolution.png
https://en.wikipedia.org/wiki/File:Spindle_diagram.jpg
https://nautiluslive.org/video/2019/09/04/translucent-deepstaria-jelly-whorls-resident-isopod
https://commons.wikimedia.org/w/index.php?title=File%3ARhyssa_persuasoria_-_2014-08-28.webm
https://en.wikipedia.org/wiki/File:Linn%C3%A9-Praeludia_Sponsaliorum_Plantarum.jpg
[♪ INTRO].

In school, you likely learned about the ranks in the tree of life with some kind of clever mnemonic, like Dear King Philip Came Over For Great Soup. This probably gave you the impression that those ranks were pretty important.

Fixed, unchanging steps on the path from general to specific. And of course, one phylum or order must be treated the same as any other. Unfortunately, that's not true.

At all. That method for naming living things and sorting them into groups is called taxonomy. And it's a foundational part of studying life on Earth.

We use these names and ranks to understand evolutionary relationships and preserve biodiversity. But it's also more complicated than it seems on the surface. Trying to shoehorn the messy, complicated web of interrelationships that is biology into neat boxes has resulted in a pretty messy tree of life.

And straightening it out is going to take time and effort. Time and effort we're going to need to put in, because we might be running out of time to name organisms before they disappear forever. If you remember that King Phillip thing, you might also remember that taxonomy got its start in the 1700s due to the work of a Swedish botanist named Linnaeus.

He came up with a scheme to name and categorize life on Earth, with ranked categories and binomial, two-part names, like Homo sapiens or Felis catus. That system, now updated to reflect our understanding of evolution, forms the basis of what's called rank-based taxonomy. It runs from the very high-level domain down through kingdom, phylum, class, order, family, genus, and species, with each describing more narrowly defined groups of related organisms.

The names and naming process are regulated by international codes, like the ICZN, or International Code of Zoological Nomenclature. And these groups are generally organized by describing characteristics shared within the group, which can be anything from having a cell wall to laying eggs with shells. In general, this works fairly well, but there are some weird quirks to doing things this way.

Part of the problem arises from using a system and groups invented before Darwin, and trying to paste in evolutionary relationships over top of them. One of the ways scientists have updated the tree of life to reflect evolution is to try to keep groups like orders or families monophyletic. That means everything in the group is descended from a single common ancestor, and the group contains all the descendants of that ancestor.

The advantage is that this system can easily and quickly tell you about evolutionary relationships. Like, giant pandas are in the same family as bears, but not red pandas. So giant pandas are more closely related to a black bear than a red panda.

Easy. But not all groups are monophyletic. Consider the class of vertebrates called Reptilia.

It includes animals like alligators, turtles, and snakes; pretty much all of what we'd traditionally consider reptiles. In day-to-day life, it's usually not a problem to lump all of these critters together. They're all scaly, generally cold-blooded, and generally do similar things.

But when we start to think in terms of evolution, things get a little trickier. Because reptiles as a group are what's known as paraphyletic. In a paraphyletic group, all members of that group descend from a common ancestor, but the group doesn't contain all descendants from that common ancestor.

Someone really important is missing when we talk about reptiles: Birds. Birds, which are descended from dinosaurs, are actually an off-shoot of the reptile family tree. And a relatively recent one.

In fact, crocodiles, which we think of as reptiles, are more closely related to birds than they are to turtles, which we also think of as reptiles. And yet birds have their own class: Aves. You can't have a class within a class, so birds can't be included under Reptilia.

This makes Reptilia a paraphyletic group. So if you were simply comparing one class to another, you might not realize how close birds and crocodiles are, nor how ancient and unique turtles are. Taxonomy should ideally help us understand how life evolved, but in cases like this, it can be misleading.

Incidentally, we've mostly phased out “fish” as a group, since in order for it to be monophyletic, we'd have to include humans. Because we're also descended from the same ancestor. Over time, we've focused more and more on these systematic relationships, and we've retired some old groups when they stop making sense.

But it's an ongoing process, and we still have wonky groups like Reptilia. There are also some weird problems with the idea of the ranks themselves. At the most basic level, there are tricky problems with how we define species.

But there are also questions about how some of those higher-order groups are organized as well, like orders or phyla. That's because there isn't an objective test for whether something should count as a class or phylum. It's not like 99% DNA match is a genus, 95% is a family, 90% is a class, et cetera.

This can create situations where groups of the same rank aren't comparable to one another; they're not equivalent. Take Cnidaria, a group that includes critters like jellyfish and coral. Cnidaria is a phylum, a high-level rank just below kingdom.

As vertebrates, our phylum is Chordata. And since they're both phyla, you might be tempted to think of them as roughly “equal”. Like, maybe the groups are roughly as old as each other, or contain about the same amount of genetic diversity, or the same number of species.

But depending on how you look at it, Cnidaria is actually a much bigger group. In fact, the genetic difference between true jellyfish and box jellyfish is about the same as between a human and a sea urchin; a group that belongs to another phylum altogether. So, again, for a system that's supposed to help us understand the world, it's got some serious flaws.

Now, don't get me wrong: Taxonomy is really useful. Life is a continuum, and classification is a tool that we use to understand it. Without it, we'd struggle to describe the organisms around us or understand evolutionary relationships.

But we've also seen some of the quirks of our current system. And those quirks can have consequences. For one, we need the insights taxonomy gives us to be able to protect the natural world.

For countries or governments to make policy decisions about animal and plant species, they need to know what species are out there. Like, if a national park is trying to understand the diversity of animals in their borders, it's important to know whether two populations of fish are related. Or if crops are being attacked by a new invasive species of insect, knowing exactly what species it is can help farmers, scientists, and policymakers protect the food supply.

So if our systems and ranks aren't clear, it can become harder to understand these kinds of problems. And of course, taxonomy can really affect researchers, too. For example, a paper published in 2016 in the journal Current Biology claimed that it's not uncommon for researchers to treat these ranks as actual biological patterns rather than human-made aids.

They're there as a tool to aid our understanding, not as an absolute rule. Yet as long as they exist, the paper suggests, people will be tempted to focus on them. To fix things, some researchers have proposed standardizing taxonomic ranks, like by using when different groups diverged in Earth's history as a yardstick for assigning ranks.

But it's worth noting that re-organizing things can sometimes be cumbersome, due to the way those rank names work. While many of the classic groups like Reptilia or Mammalia have names that wouldn't change, taxonomic convention dictates that certain categories, like family or subfamily, have precise suffixes. This means that, by convention, if you upgrade or downgrade a group, it might need to have its name changed.

And that can cause headaches for future researchers. So why not just ditch the idea of trying to classify life by characteristics, like those body plans or egg shells? Some researchers have proposed and backed a whole new system called PhyloCode.

First published in 2000, it's based on evolutionary relationships from the get-go. So a group like Reptilia could be described as “the group that contains crocodiles and turtles, but not frogs.” Traditional orders and phyla would still exist as part of these groupings, but wouldn't necessarily be assigned any special rank. There's been pushback around things like how stable and useful these new categories would be long term, like how often they'd need to be rearranged or reclassified, as well as whether or not people could still use Latin names.

Since the first draft in 2000, the idea has been updated to make things easier, but it's a big undertaking. In the end, this problem is complicated, because we've had the old system for literally centuries. So revamping it would, well, take a bit of work.

And to make things more complicated, it's work we may not be able to afford. Because the biggest problem facing taxonomy today is probably a lack of resources. There aren't enough taxonomists, and they're facing serious funding shortages.

A 2015 report published by the Royal Society of New Zealand, for instance, suggests that New Zealand was losing its taxonomists to a lack of investment and staff not being replaced. This is a problem, because although we've described about 1.5 million species so far, and though about 20,000 new animal species alone are described each year, it's still only a fraction of the tree of life. By one estimate, there might be at least 10 million species on the planet.

And that's only considering eukaryotic species, those whose cells have a nucleus. Another study estimated that nearly 90% of those eukaryotes have yet to be described. And there are some habitats, like the deep sea, that are so remote that scientists find new species every time they visit.

Many fields do rely on amateur collectors. Entomology, which is the study of insects, is a major example. And those folks are great to have.

But to describe a species, there are a lot of things people need to keep in mind, like providing enough descriptions, potentially including illustrations, as well as making everything fit within the existing ranks. That takes time, and we're kind of on the clock. Climate change and other human activity puts us on a timer as species disappear.

So it's a messy problem. To get around the lack of taxonomists, some researchers have proposed basing taxonomy not on painstaking analysis of body parts or ranges, but on DNA barcodes. For example, a 2019 paper proposed that for hyper-diverse groups of animals, like parasitoid wasps, that new species be described by comparing specific sequences of DNA, rather than by analyzing their bodies or homes.

However, not everyone wants to do things this way. For one thing, it'd mean that you might need to have a DNA lab to investigate whether something you found is a new species, which could put taxonomic work out of the reach of amateurs or people working in less developed areas. So yeah, it's really complicated.

And there's probably not one easy solution, either. In the end, taxonomy is a powerful tool, and one that modern biology would not be able to function without. But some scientists have argued that it needs to change with the times, the way biology as a whole has done.

Linnaeus didn't know what a gene was, and he also predated Darwin by more than a century. So while his binomial system has gotten us this far, it doesn't always reflect what we now know. Ultimately, it might be time to prune a few branches on the tree of life.

Thanks for watching this deep dive, and thanks to our patrons who make it possible for us to make episodes just like this one. You guys are awesome. If you want to help us keep making SciShow, head over to patreon.com/scishow to get started. [♪ OUTRO].