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As a SciShow viewer, you can keep building your STEM skills with a 30 day free trial and 20% off an annual premium subscription at Brilliant.org/SciShow. If I asked you “what is an animal,” you might start by saying it’s something like a cat or a dog or a lizard or a bug.

If I asked you to be more specific, you might come around to saying it’s one of the major groups of organisms whose cells have a nucleus and organelles with a membrane, along with plants and fungi. And that’s where it gets interesting, because those old groups – the kingdoms of eukaryotes, or nucleus-havers – are basically obsolete. Still in familiar use, but scientifically?

The idea of the “animal kingdom” doesn’t mean much. How surprised you are to hear that might depend on how recently you’ve taken a biology class. But even if you graduated this year – congrats, by the way – what you learned about these groups is probably not what’s up to date now.

See, the groups we sort eukaryotes into have changed hugely in the past 15 years or so. And this is a feature, not a bug. Science in action, updating what we know about organisms and their evolutionary relationships – and making our own place a little smaller all the time. [♪ INTRO] Scientists have been on a quest to create a map of life on this planet for more than a century.

We can use these so-called trees of life to map relationships both big and small, but today we’re looking at those nucleus-having eukaryotes, and our relationship to everyone else in that group. Pretty much ever since the eukaryote tree of life was created, it’s been sprouting new branches, or losing them, or having those branches moved. In 1859 Charles Darwin was one of the first to draw something resembling a tree to represent how life was interconnected by evolution.

But he used it more as a metaphor for understanding common descent than actually showing any real relationships between organisms. German naturalist Ernst Haeckel was probably the first to map out how living creatures like plants, animals and algae were related. He used a mix of information from paleontology, embryology and the physical features of the organisms themselves to create his tree, which he later revised several times.

Fast forward to the late 1960’s and you’ve got a tree that looks something like this, with eukaryotes clumped together into four groups: Plants, fungi, animals, and algae or protists. Now, this tree kind of skimmed over the whole evolution thing, instead grouping organisms based on how they got their energy. But it did introduce the idea of kingdoms, or big groups that all organisms fell into.

We don’t really talk about kingdoms today, partly because the word represents a time when we thought animals, and us humans, reigned over all other creatures. It’s too much of a loaded term. But the general concept of big groups, or supergroups, still dominates how the tree is organized.

Which might be why this tree is starting to look pretty familiar. Chances are you had a poster of something like this in your biology classroom. But even organizing eukaryotes into these massive groupings hasn’t been easy!

Around the early 2000s, supergroups were mostly based on a key characteristic that the group shared. Like chloroplasts for plants. In those days there were four supergroups, that then became six as researchers added genetic information into the mix, and now we’re looking at something like seven.

Basically, as scientists have discovered new organisms and figured out ever-cleverer ways of understanding how they’re related, the tree gets switched up. Which might make you wonder just how useful it actually is. Scientists and teachers care about categories because they help us understand the world.

Dividing things into groups is a big part of how we help our own brains grasp relationships, heredity, and common descent. Kind of like items in a supermarket. Having the bakery, fresh produce or frozen foods sections helps when you’re trying to check off your shopping list.

But sometimes putting things in those categories can be tricky. Like, why are eggs always lumped in with dairy? Just like those signs at the top of the supermarket aisle, the eukaryote tree of life is a tool, not an immutable truth.

Having those groupings, and arranging organisms in a way that shows how they evolved, helps both scientists and us understand the evolutionary processes that made those organisms what they are today. Plus, scientists can use these trees as a tool for studying cell biology, genomes, or how we went from single to multi-celled organisms. So although the eukaryote tree has always been a bit of a work in progress, it still has a ton of use.

In the last decade, there have been two major shake ups that have totally flipped the tree on its canopy. The first is phylogenomics. Scientists have been using genes to build eukaryote trees since the 1980s.

They were mostly doing phylogenetics, phylo- being a prefix that refers to sorting things by type and genetics being genetics. So the word refers to grouping organisms by segments of genetic material they have in common. Phylogenetics would typically use one gene coding for one particular protein, or even a smaller chunk of a gene, thanks to how limited sequencing was back in the day.

Now, phylogenetics already shook things up from what they were, since early trees were based on physical characteristics that organisms shared. Which doesn’t always help show evolutionary relationships, because those traits may have evolved separately a couple of times, just from being in similar environments. Whereas genes don’t lie, the reasoning goes, because as two organisms drift further apart from their common ancestor, the sequences of their shared genes accumulate mutations.

So more difference equals less closely related. But one gene is one gene, and if you tunnel vision on it, you might miss something completely wild going on over there on chromosome 9. Phylogenomics builds on phylogenetics, by creating trees using dozens to hundreds of genes.

Scientists still compare gene sequences between groups, but now they can see which whole sections of the genome have been added, taken away, or shifted around. And it’s kind of impossible to do those comparisons if you don’t have the entire genome. Otherwise, how would you know whether a section went missing or if it just hasn’t been sequenced?

So the whole reason phylogenomics is even a thing is because more labs around the world are sequencing genomes from a bunch of organisms. That’s not something we’ve had the ability to do for all that long – remember that sequencing the human genome was a huge deal around the year 2000. The second major shakeup is that scientists discovered a whole host of new organisms from what we used to think of as the protist group, or eukaryotes that aren’t plants, animals or fungi.

Partly, there wasn’t a lot of information about that group because we just couldn’t be bothered looking – we were kind of wrapped up in ourselves and other animals. But partly it was because we couldn’t find the darn things if we wanted to. Lots of these newly-discovered protists were found from scooping up tiny plankton in the ocean and sequencing the single-celled organisms floating in the slush.

And that became possible thanks to lab techniques that could screen for new organisms, and ones that could sequence genomes from tiny amounts of genetic material. Some of these new organisms were truly wild. Some were gliding single cells with two tails, some were swimming amoebas, and some even had cells covered in hard scales.

But all these new protists had to go somewhere in the tree. The question was where. When they were first discovered, scientists thought these protists didn’t fit anywhere in the supergroups.

Eventually, after some more analysis, some of these new-found eukaryotes made their way into existing supergroups. But some were still left on their own. Researchers think some of these protists are really similar to the last common ancestor of eukaryotes, which means it’s hard to compare them to more modern members who have undergone a ton of change.

But if we do figure out where they fit, it would mean a better understanding of how early eukaryotes evolved. So after much rearranging, we’ve gone from a tree that looked like three vines, to a tree that looks something like a fan. At least, that’s what it looks like for now.

Depending on whom you ask, we’re rocking around seven supergroups. And here’s what I mean by animals sort of not being a thing. I mean, they are, once you zoom in enough, but definitely not on top any more.

Have a look there at the group Amorphea. This group has the opisthokonts, which are animals, fungi and some of their single-celled relatives; plus the amoebae and slime molds. We’re lumped in with mushrooms.

Slightly insulting, but also humbling to see how much more life there is outside of the familiar groups we’re used to. If you’re looking for plants, let me direct your attention to Archaeplastida: green algae, red algae, land plants and a group of freshwater algae – who all have photosynthetic chloroplasts. And there’s so much more.

You’ve got TSAR, which stands for telonemids, stramenopiles, alveolates, and rhizaria. It makes up more than half of all eukaryotes and includes microbial algae, large seaweeds, single-celled protozoa and a group of microscopic, single-celled swimming organisms. Or there’s Hemimastigotes – a group of predatory protists that are extremely genetically different from anything else in the eukaryote tree.

That’s made them the hardest to place and so, for now at least, they’re their own supergroup. Now, this newest tree is far from perfect. As you can see, there are still a bunch of orphan groups that don’t seem to fit anywhere.

Some researchers think some of these groups might make up their own supergroup called Excavates, but others don’t agree. We want to understand how these organisms are related genetically and, ultimately, understand how we went from something resembling them to something resembling us. And that means figuring out their place, not just lumping them in, or hanging them onto the tree somewhere.

So if there’s going to be big pruning or growing of the tree in the future, chances are it’ll come down to the supergroups. This tree is also missing one really important feature: a root. Like all good trees, the root grounds the whole thing and tells us where eukaryotes came from, or, put differently, who their last common ancestor was.

A root would also show which groups in the tree are the most ancient, which traits eukaryotes picked up first, and how the supergroups are related to each other. Since the rest of the tree has been jumbled around, it’s probably not surprising that there have been a couple of different roots proposed as this went on. In 2012, based on data from mitochondrial DNA, the root sat between Opisthokonts and Amoebozoa, and Excavata and SAR – an earlier version of what’s now called TSAR.

That theory was later supported based on DNA from proteins that were given to early eukaryotes by bacteria. In 2014, other researchers used a similar, but different, set of genes, to put the root between the excavates and everything else. They also sorted all the supergroups into megagroups, because more boxes!

And in April 2023, a team placed the root smack bang in the middle of Excavata, splitting this supergroup into four and siding with the hypothesis that Excavata isn’t a supergroup at all. But finding the root is harder than just digging for it. Scientists think that eukaryotes split from their last common ancestor some 2 billion years ago, so whatever genetic sign is left over in eukaryotes today is going to be pretty small.

The key will be finding organisms that split off from the root long ago, since they’re the ones who will be most genetically similar, and getting enough, good quality genome analysis out of them. And with every bit of additional data, we’ll probably end up shaking up the tree all over again. Trees of life are really just a snapshot of a solution at a given time.

Here’s how we think the messy, wonderful, uncategorizable wonder that is life fits into categories. So, you could go memorizing a list of supergroups, but it’s pretty likely that the actual names and order will change next year, if not next week. Still, it’s amazing that there’s just so much eukaryote life out there and that scientists have ways of revising the eukaryote tree to accommodate them.

Even if it isn’t perfect. And every time they do, we learn something more about life and our place in it. Categories are how we make sense of the world.

We have categories of life, like all of the cool ones covered in this video; categories of math, like algebra, geometry, and calculus; categories of science, like physics, chemistry, and biology; and categories for pretty much anything. And you can learn more about each of those categories with Brilliant: an online learning platform with thousands of lessons in science, computer science, and math. They have interactive courses, created in partnership with smarties at the University of Chicago, Duke, and other accredited universities that cover each of those categories.

You can start learning today at Brilliant.org/SciShow or in the link in the description down below. That link also gives you a free 30 day trial and 20% off an annual premium Brilliant subscription. Thanks to Brilliant for supporting this SciShow video! [♪ OUTRO]