There’s no such thing as a tree (phylogenetically)

by eukaryote7 min read3rd May 202130 comments


BiologyEvolutionPhilosophy of LanguageWorld Modeling

[Crossposted from Eukaryote Writes Blog.]

So you’ve heard about how fish aren’t a monophyletic group? You’ve heard about carcinization, the process by which ocean arthropods convergently evolve into crabs? You say you get it now? Sit down. Sit down. Shut up. Listen. You don’t know nothing yet.

“Trees” are not a coherent phylogenetic category. On the evolutionary tree of plants, trees are regularly interspersed with things that are absolutely, 100% not trees. This means that, for instance, either:

  • The common ancestor of a maple and a mulberry tree was not a tree.
  • The common ancestor of a stinging nettle and a strawberry plant was a tree.
  • And this is true for most trees or non-trees that you can think of.

I thought I had a pretty good guess at this, but the situation is far worse than I could have imagined.

CLICK TO EXPAND. Partial phylogenetic tree of various plants. TL;DR: Tan is definitely, 100% trees. Yellow is tree-like. Green is 100% not a tree. Sourced mostly from Wikipedia. 

I learned after making this chart that tree ferns exist (h/t seebs), which I think just emphasizes my point further. Also, h/t kithpendragon for suggestions on improving accessibility of the graph.

Why do trees keep happening?

First, what is a tree? It’s a big long-lived self-supporting plant with leaves and wood.

Also of interest to us are the non-tree “woody plants”, like lianas (thick woody vines) and shrubs. They’re not trees, but at least to me, it’s relatively apparent how a tree could evolve into a shrub, or vice-versa. The confusing part is a tree evolving into a dandelion. (Or vice-versa.)

Wood, as you may have guessed by now, is also not a clear phyletic category. But it’s a reasonable category – a lignin-dense structure, usually that grows from the exterior and that forms a pretty readily identifiable material when separated from the tree. (…Okay, not the most explainable, but you know wood? You know when you hold something in your hand, and it’s made of wood, and you can tell that? Yeah, that thing.)

All plants have lignin and cellulose as structural elements – wood is plant matter that is dense with both of these.

Botanists don’t seem to think it only could have gone one way – for instance, the common ancestor of flowering plants is theorized to have been woody. But we also have pretty clear evidence of recent evolution of woodiness – say, a new plant arrives on a relatively barren island, and some of the offspring of that plant becomes treelike. Of plants native to the Canary Islands, wood independently evolved at least 38 times!

One relevant factor is that all woody plants do, in a sense, begin life as herbaceous plants – by and large, a tree sprout shares a lot of properties with any herbaceous plant. Indeed, botanists call this kind of fleshy, soft growth from the center that elongates a plant “primary growth”, and the later growth from towards the outside which causes a plant to thicken is “secondary growth.” In a woody plant, secondary growth also means growing wood and bark – but other plants sometimes do secondary growth as well, like potatoes (in roots)

This paper addresses the question. I don’t understand a lot of the closely genetic details, but my impression of its thesis is that: Analysis of convergently-evolved woody plants show that the genes for secondary woody growth are similar to primary growth in plants that don’t do any secondary growth – even in unrelated plants. And woody growth is an adaption of secondary growth. To abstract a little more, there is a common and useful structure in herbaceous plants that, when slightly tweaked, “dendronizes” them into woody plants.

Dendronization – Evolving into a tree-like morphology. (In the style of “carcinization“.) From ‘dendro‘, the ancient Greek root for tree.

Can this be tested? Yep – knock out a couple of genes that control flower development and change the light levels to mimic summer, and researchers found that Arabidopsis rock cress, a distinctly herbaceous plant used as a model organism – grows a woody stem never otherwise seen in the species.

The tree-like woody stem (e) and morphology (f, left) of the gene-altered Arabidopsis, compared to its distinctly non-tree-like normal form (f, right.) Images from Melzer, Siegbert, et al. “Flowering-time genes modulate meristem determinacy and growth form in Arabidopsis thaliana.”Nature genetics 40.12 (2008): 1489-1492.

So not only can wood develop relatively easily in an herbaceous plant, it can come from messing with some of the genes that regulate annual behavior – an herby plant’s usual lifecycle of reproducing in warm weather, dying off in cool weather. So that gets us two properties of trees at once: woodiness, and being long-lived. It’s still a far cry from turning a plant into a tree, but also, it’s really not that far.

To look at it another way, as Andrew T. Groover put it:

“Obviously, in the search for which genes make a tree versus a herbaceous plant, it would be folly to look for genes present in poplar and absent in Arabidopsis. More likely, tree forms reflect differences in expression of a similar suite of genes to those found in herbaceous relatives.”

So: There are no unique “tree” genes. It’s just a different expression of genes that plants already use. Analogously, you can make a cake with flour, sugar, eggs, sugar, butter, and vanilla. You can also make frosting with sugar, butter, and vanilla – a subset of the ingredients you already have, but in different ratios and use

But again, the reverse also happens – a tree needs to do both primary and secondary growth, so it’s relatively easy for a tree lineage to drop the “secondary” growth stage and remain an herb for its whole lifespan, thus “poaizating.” As stated above, it’s hypothesized that the earliest angiosperms were woody, some of which would have lost that in become the most familiar herbaceous plants today. There are also some plants like cassytha and mistletoe, herbaceous plants from tree-heavy lineages, who are both parasitic plants that grow on a host tree. Knowing absolutely nothing about the evolution of these lineages, I think it’s reasonable to speculate that they each came from a tree-like ancestor but poaized to become parasites. (Evolution is very fond of parasites.)

Poaization: Evolving into an herbaceous morphology. From ‘poai‘, ancient Greek term from Theophrastus defining herbaceous plants (“Theophrastus on Herbals and Herbal Remedies”).

(I apologize to anyone I’ve ever complained to about jargon proliferation in rationalist-diaspora blog posts.)

The trend of staying in an earlier stage of development is also called neotenizing. Axolotls are an example in animals – they resemble the juvenile stages of the closely-related tiger salamander. Did you know very rarely, or when exposed to hormone-affecting substances, axolotls “grow up” into something that looks a lot like a tiger salamander? Not unlike the gene-altered Arabidopsis.

A normal axolotl (left) vs. a spontaneously-metamorphosed “adult” axolotl (right.) [Photo of normal axolotl from By th1098 – Own work, CC BY-SA 3.0, Photo of metamorphosed axolotl from deleted reddit user, via this thread: ]

Does this mean anything?

A friend asked why I was so interested in this finding about trees evolving convergently. To me, it’s that a tree is such a familiar, everyday thing. You know birds? Imagine if actually there were amphibian birds and mammal birds and insect birds flying all around, and they all looked pretty much the same – feathers, beaks, little claw feet, the lot. You had to be a real bird expert to be able to tell an insect bird from a mammal bird. Also, most people don’t know that there isn’t just one kind of “bird”. That’s what’s going on with trees.

I was also interested in culinary applications of this knowledge. You know people who get all excited about “don’t you know a tomato is a fruit?” or “a blueberry isn’t really a berry?” I was one once, it’s okay. Listen, forget all of that.

There is a kind of botanical definition of a fruit and a berry, talking about which parts of common plant anatomy and reproduction the structure in question is derived from, but they’re definitely not related to the culinary or common understandings. (An apple, arguably the most central fruit of all to many people, is not truly a botanical fruit either).

Let me be very clear here – mostly, this is not what biologists like to say. When we say a bird is a dinosaur, we mean that a bird and a T. rex share a common ancestor that had recognizably dinosaur-ish properties, and that we can generally point to some of those properties in the bird as well – feathers, bone structure, whatever. You can analogize this to similar statements you may have heard – “a whale is a mammal”, “a spider is not an insect”, “a hyena is a feline”…

But this is not what’s happening with fruit.  Most “fruits” or “berries” are not descended from a common “fruit” or “berry” ancestor. Citrus fruits are all derived from a common fruit, and so are apples and pears, and plums and apricots – but an apple and an orange, or a fig and a peach, do not share a fruit ancestor.

Instead of trying to get uppity about this, may I recommend the following:

  • Acknowledge that all of our categories are weird and a little arbitrary
  • Look wistfully of pictures of Welwitschia
  • Send a fruit basket to your local botanist/plant evolutionary biologist for putting up with this, or become one yourself
While natural selection is commonly thought to simply be an ongoing process with no “goals” or “end points”, most scientists believe that life peaked at Welwitschia. [Photo from By Sara&Joachim on Flickr – Flickr, CC BY-SA 2.0,]

Some more interesting findings:

  • A mulberry (left) is not related to a blackberry (right). They just… both did that.
[ Mulberry photo by Cwambier – Own work, CC BY-SA 4.0, Blackberry photo by By Ragesoss – Own work, CC BY-SA 3.0, ]
  • Avocado and cinnamon are from fairly closely-related tree species.
  • It’s possible that the last common ancestor between an apple and a peach was not even a tree.
  • Of special interest to my Pacific Northwest readers, the Seattle neighborhood of Magnolia is misnamed after the local madrona tree, which Europeans confused with the (similar-looking) magnolia. In reality, these two species are only very distantly related. (You can find them both on the chart to see exactly how far apart they are.)
  • None of [cactuses, aloe vera, jade plants, snake plants, and the succulent I grew up knowing as “hens and chicks”] are related to each other.
  • Rubus is the genus that contains raspberries, blackberries, dewberries, salmonberries… that kind of thing. (Remember, a genus is the category just above a species – which is kind of a made-up distinction, but suffice to say, this is a closely-related groups of plants.) Some of its members have 14 chromosomes. Some of its members have 98 chromosomes.
  • Seriously, I’m going to hand $20 in cash to the next plant taxonomy expert I meet in person. God knows bacteriologists and zoologists don’t have to deal with this.

And I have one more unanswered question. There doesn’t seem to be a strong tend of plants evolving into grasses, despite the fact that grasses are quite successful and seem kind of like the most anatomically simple plant there could be – root, big leaf, little flower, you’re good to go. But most grass-like plants are in the same group. Why don’t more plants evolve towards the “grass” strategy?

Let’s get personal for a moment. One of my philosophical takeaways from this project is, of course, “convergent evolution is a hell of a drug.” A second is something like “taxonomy is not automatically a great category for regular usage.” Phylogenetics are absolutely fascinating, and I do wish people understood them better, and probably “there’s no such thing as a fish” is a good meme to have around because most people do not realize that they’re genetically closer to a tuna than a tuna is to a shark – and “no such thing as a fish” invites that inquiry.

(You can, at least, say that a tree is a strategy. Wood is a strategy. Fruit is a strategy. A fish is also a strategy.)

At the same time, I have this vision in my mind of a clever person who takes this meandering essay of mine and goes around saying “did you know there’s no such thing as wood?” And they’d be kind of right.

But at the same time, insisting that “wood” is not a useful or comprehensible category would be the most fascinatingly obnoxious rhetorical move. Just the pinnacle of choosing the interestingly abstract over the practical whole. A perfect instance of missing the forest for – uh, the forest for …

… Forget it.


Timeless Slate Star Codex / Astral Codex Ten piece: The categories were made for man, not man for the categories.

Towards the end of writing this piece, I found that actual botanist Dan Ridley-Ellis made a tweet thread about this topic in 2019. See that for more like this from someone who knows what they’re talking about.


29 comments, sorted by Highlighting new comments since Today at 11:40 AM
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Acknowledge that all of our categories are weird and a little arbitrary

That is not the moral! The moral is that the cluster-structure of similarities induced by phylogenetic relatedness exists in a different subspace from the cluster-structure of similarities induced by convergent evolution! (Where the math jargon "subspace" serves as a precise formalization of the idea that things can be similar in some aspects ("dimensions") while simultaneously being different in other aspects.) This shouldn't actually be surprising if you think about what the phrase "convergent evolution" means!

For more on the relevant AI/philosophy-of-language issues, see "Where to Draw the Boundaries?" and "Unnatural Categories Are Optimized for Deception".

That's a good expanded takeaway of part of it! (Obviously "weird and a little arbitrary" is kind of nebulous, but IME it's a handy heuristic you've neatly formalized in this case.) To be clear, it doesn't sound like we disagree?

On the specific example of trees, John Wentworth recently pointed out that neural networks tend to learn a "tree" concept: a small, local change to the network can add or remove trees from generated images. That kind of correspondence between human and unsupervised (!) machine-learning model concepts is the kind of thing I'd expect to happen if trees "actually exist", rather than trees being weird and a little arbitrary. (Where things are closer to "actually existing" rather than being arbitrary when different humans and other AI architectures end up converging on the same concept in order to compress their predictions.)

(Now I'm wondering if there's some sort of fruitful analogy to be made between convergence of tree concepts in different maps, and convergent evolution in the territory; in some sense, the fact that evolution keeps rediscovering the tree strategy makes them less "arbitrary" than if trees had only been "invented once" and all descended from the same ur-tree ...)

Oh, I think you're over-extrapolating what I meant by arbitrary - like I say toward the end of the essay, trees are definitely a meaningful category. Categories being "a little arbitrary" doesn't mean they're not valuable - is there a clear difference between a tree and a shrub? Maybe, but I don't know what it is if so, and it seems like plausibly not. The fruit example is even clearer - is a grape a berry? Is a pumpkin a fruit? Who cares? Probably lots of people, depending on the context? Most common human categories work like this around the edges if you try and pin them down - hence, a little arbitrary.  Seems fine.

I'm standing by "weird." That's definitely weird. I don't think of nature as going in for platonic forms! What's going on here?! Weird as hell.

If you're at all like me, part of that feeling is definitely having not internalized [genes as lego bricks] rather than [genes as fragile tightly coupled organism recipie].  The notion that the Blind Idiot God invented reusable loosly coupled code and is halfway to a functioning package manager is more than a bit of a shocker.  And crazier yet has had those capabilities long enough that they're fixed in substantially all life on Earth (albiet with serious regressions in animals).

Apparently there's some ideas that are convergent enough substaintially any optimizer finds them eventually.

The notion that the Blind Idiot God invented reusable loosly coupled code and is halfway to a functioning package manager is more than a bit of a shocker.

I appreciate this way of putting it.

Or I'm speaking a slightly different dialect of English from you?? As a point of terminology, I think "fuzzy" is a better word than "arbitrary" for this kind of situation, where I agree that, as a human having a casual conversation, my response to "Is a pumpkin a fruit?" is usually going to be something like "Whatever; if it matters in context, I'll ask for more specifics", but as a philosopher of science, I claim that there definite mathematical laws governing the relationship between what communication signals are sent, and what probabilistic inferences a receiver can infer, and the laws permit things like soft k-means clustering, where given some set of data points representing data about plants, the algorithm could say that this-and-such plant has a membership coefficient of 0.34 in the "shrub" cluster and 0.66 in the "tree" cluster, and there would be nothing arbitrary about those numbers as the definite, precise result of what happens when you run this particular clustering algorithm against that particular data. (But the number 0.34 in this blog comment is arbitrary, because I made it up for concreteness while trying to explain what fuzzy clustering is; there's no reason I couldn't have chosen a different coefficient.)

But then when I actually look up "arbitrary" and "fuzzy" on Wiktionary, it seems common usage is not unequivocally on my side: your usage of arbitrary fits with the first part of definition 1 ("Based on individual discretion or judgment"), whereas my usage is centered on the second part of definition 1 ("not based on any objective distinction, perhaps even made at random"), with influence from the mathematician's usage, definition 3 ("Any, out of all that are possible"). And the meaning of fuzzy I want barely even makes the list as a technical reference ("Employing or relating to fuzzy logic") ...

Agreed on weirdness.

This is more of a contrast but this line of thinking could be used to remedy that dolphins are fishes. That is the branch of tree fo life "fish" is a different concept than "thing that swims to survive".

In this sense "fishes" don't inherently breathe or have gills. A whole lot of properties would probably be A freedom degree" while the phylogenetics probbaly has a lot of "accidental" properties. 

Why don’t more plants evolve towards the “grass” strategy?

I suspect it's related to the the distinction between C3 and C4 photosynthesis - both are common in grasses and C4 species tend to do better in hot climates, but trees seem to have trouble evolving C4 pathways even though that happened on 60+ separate occasions.

(also IMO monocots top out at "kinda tree-ish" - they do have a recognisable trunk, but more fibrous than woody)

My hypothesis after 30 seconds of thinking was that trees evolve independently because height = good for competing for sunlight, while grasses must specialize a ton to 'afford' passing up on the height advantage. So once a grass is established somewhere it might be hard for an up-and-coming-almost-grass species to nudge out of its niche. Maybe this is related?

I could imagine lots of plants getting stuck in a local maximum of fitness where they are still pretty tree-like but would need to simultaneously lose some tree features and gain C4 photosynthesis in order to succeed as grasses, so the gap to jump in adaptation-space is too large.

Height is also useful for reducing impact of fires, herbivores, some parasites, etc.; and gives you substantially better volume-of-airflow-over-leaves which can be helpful - a flat sheet of leaf-material would underperform substantially for respiration, even before considering the variable angle of sunlight for photosynthesis.

With some handwaving, we seem to agree that "the absence of trees becoming grass-like indicates that there's no nice/large path in evolution-trajectory-space which is continuously competitive" and I'm gesturing towards the known-to-be-difficult C3/C4 distinction as a potentially-relevant feature of that space.

Note that while our non-expert speculation might turn up interesting relevant considerations, the space is very complicated and high-dimensional, and I at least have very little data or subject matter expertise. I therefore expect my analysis to be wrong, though I do enjoy and learn from doing it.

First off, thanks for the reminder that thingspace can map very differently depending on which dimensions you choose to filter on! It's difficult to really grok that idea in a sufficiently general way, I've noticed, and I feel like this was much more surprising that it should have been. I think reframing "tree" and "fish" as strategies may end up being an important takeaway.

Question: Apples not (botanically) a fruit how? Are they not the seed-bearing mature ovum of a plant? I feel like I missed something there.

Accessibility note: I totally might have started with the same colors you chose for your tree diagram! To my eye, they scream "woody thing" and "leafy thing" and "something like both". But also, the yellow and the brown are nearly indistinguishable on my monitor with the blue-reducer turned on, and all three hues sit in the part of color-space that gets kinda muddy to folks with certain kinds of reduced-color vision. Possible adjustments: you could add a shape component to each node (e.g. rounded corners, lozenge, square corners, hexagons), use different border styles (e.g. thin, thick, dotted, double-lined), and/or choose colors with very different values if you want to keep those (admittedly information-rich) hues (e.g. pastel green (maybe with dark text), walnut brown (maybe with white text), mossy green (maybe the text has a border to make it stand out)). The goal is to be able to distinguish the differences easily in a grayscale rendering of the image.

Thank you so much!
Re: question: Well, they're not "normal" fruits, at least - they're accessory fruits. I don't know much else about the botanical definitions other than that.

Also, the accessibility point is very much appreciated. I've updated the graphic to take that into account - would love your thoughts on the improved one? Either way, I very much appreciate both the raising-the-issue and the suggestions on improvements!

Not a "real" fruit because the flesh is a product of some tissue adjacent to the ovum instead of within it. That sounds oddly nit-picky to me, even for scientists. Do you think this might be an important distinction for some non-taxes reason, or are botanists just really pedantic sometimes?

Well done on the new graphic! It's much easier to read now: I like the choice to use the darkest color and heaviest border for the "Definitely a tree" category, since that makes them pop out. When I look at it in greyscale (camera filter on my phone), the "Kind of a tree" green and "Definitely not a tree" orange are pretty close in value, but the borders make them easy to differentiate. Given that the goal was ostensibly to highlight the distribution of true trees, I think that's entirely appropriate. And when I turn on my laptop's blue blocker, I still have no problem seeing the difference between the categories.

When I showed the new graphic to my family, Partner suddenly started examining it and making connections. ("🧐 Look how closely related tea is to pitcher plants!") And the 5yo was even trying to make sense of it! Neither of them seemed interested yesterday, so I'm declaring success!

…Okay, not the most explainable, but you know wood? You know when you hold something in your hand, and it’s made of wood, and you can tell that? Yeah, that thing.

Missed chance to refer to this classic, imo.

I identify strongly with the excitement of discovery and enquiry in this post!

OP or readers may enjoy some additional examples of extinct or living-fossil tree-strategizing clades: (extant, includes larger extinct tree species) (extinct 'seed fern' tree group) (a few extant, includes larger extinct tree species) (extinct tree 'club mosses' - not really mosses) (not even a plant probably!)

When I came across these facts, upon a little wider reading I had a similar additional mind-blowing moment around the whole set of circumstances of the 'alternation of generations' ( exhibited by plants, fungi and a few other groups. For me, this exploded my conception of what reproduction strategies can look like (and my conception was probably already not even that narrow by most standards). Wait til you read about seed development and ploidy!

I really enjoyed this post!  Look wistfully at pictures of Welwitschia, indeed!  I got to see some in person a few years ago when we went to the Kirstenbosch Botanical Gardens in Cape Town, and my wife was very forbearing with my gaping at the unassuming piles of green straps.

If you're interested in learning more about what the plant developmental toolbox looks like and how it's been deployed throughout plant evolution, I'd recommend David Beerling's Making Eden.  It's a pop-science book but pitched at the upper end of that range.  Merlin Sheldrake's Entangled Life is also fun if you want an intro to the crazy stuff that happens in the fungal kingdom.

Cladistics is useful not only for biology but also for analyzing things like cultures. If your whole experience comes from a particular clade then you a probably missing most of the picture. Systematically exploring an evolutionary tree is a simple way to gain broader perspective.

Cladistics is useful not only for biology but also for analyzing things like cultures.

Would love to see some examples if you have any to share. 

A really enjoyable and informative read. I noticed on your graphic that the starting point for the entire graphic is the very first land plant, and its a moss. The very first evolutionary step from that point has to do with vascularity. This makes me wonder what was before the first land plant? Some sort of water plant obviously but I'm curious what the major evolutionary step from the ocean to land was - what it means to be 'moss'. 

My second question is more open ended I guess, but thinking about all the various strategies life on Earth has developed to create such diversity in the plant world, and seeing as how many of them are quite similar across species, if you consider the vascularity of the post-moss plants as similar to the vascular system of animals, and the tightly packed wooden structure of trees as similar to bones of the skeleton, and the reproductive systems as similar as well, what do you see as constituting the "brain" or nervous system of a plant, if anything? I know it's a weird question. 

And this is not exactly a deep observation, but It seems like the discussion of classification of plants - but also the post you linked to - involve the idea in relation to rationality and maybe to AI, that these are all examples of things which are hard to define in a true/false way, and this is at the heart of rationality from what I'm gathering. I think I want to do a bit more research about apples as well after reading this.

I got a feel of this growing sunflowers last year. They got quite big, significantly taller than me. They died in autumn as herbaceous plants do, but as I cut them down I noticed the part where the stem meets the root was seriously woody. Like, I could have cut out a small piece and convinced someone it was a piece of wood.

And, conversely, Palm "trees" do not actually have wood - they are just very large stems with lots of layers. Kind of like Ogres.

Enjoyed the Attenborough Galapagos series recently, discovering most of the trees on the Galapagos are actually dandelions.

That common-ancestors-being-totally-different thing is wonderful. But really, wood is just wood, it's not even "the" "interesting" feature compared to, say, the placement of the next-season(s) buds (which is an instrumental thing in itself, but at least a higher-order instrumental thing.)

I'd love to see an ELI5 explanation of high the MADS-box genes coordinate about making wood in an Arabidopsis plant, that has to be some serious challenge for them.

So: There are no unique “tree” genes. It’s just a different expression of genes that plants already use. Analogously, you can make a cake with flour, sugar, eggs, sugar, butter, and vanilla. You can also make frosting with sugar, butter, and vanilla – a subset of the ingredients you already have, but in different ratios and use

Actually, you can even make a frosting with flour, sugar, eggs, sugar (uh… you listed ‘sugar’ twice), butter, and vanilla—i.e., the exact same ingredients!

(The flour and the butter make a roux, the eggs and the sugar make a zabaglione base, then you mix both things together, add vanilla, and bam! Meanwhile, a cake made from the given ingredients would be a chiffon cake.)

EDIT: But I would not recommend using this type of frosting with this type of cake.

This was a great read! 

a subset of the ingredients you already have, but in different ratios and use

This sentence seems to cut off in the middle, probably unintentionally.

I thought that, them decided he meant "use" as a noun, (yoos) not a verb (yooze).

decided he meant "use" as a noun, (yoos) not a verb (yooze).

Not a big deal (I think), but this is accidentally misgendering the author (generally on the internet I would use the gender-neutral "they").

How is mistletoe herbaceous? (Edit - we were taught it's a shrub.)