Phylogenetic Arts and Crafts

This is a guest post by Rachel Rodman.

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The foods we eat – namely fruits, vegetables, and grains – are all products of their own evolutionary stories. Some of the most well-known chapters in these stories are the most recent ones – dramatic changes in size and shape mediated by human selection.

One especially striking example is that of Brassica oleracea –the source of broccoli, cauliflower, kale, Brussels sprouts, kohlrabi, and cabbage. Each of these diverse vegetables belongs to the same species, and each is the product of a different kind of selection, exerted on different descendants of a common ancestor.

Corn is another famous chapter. The derivation of corn – with its thick cobs and juicy kernels developed from the ancestral grain teosinte, which it barely resembles – has been described as “arguably man’s first, and perhaps his greatest, feat of genetic engineering.”

But these, again, are recent chapters. Relatively. They unfolded over the course of consecutive human lifetimes –hundreds of years or thousands at the outset (sometimes much less). They are the final flourishes (for the moment) on a much older story — a story that significantly precedes agriculture as well as humans.

It is this older story that lies at the heart of truly deep differences, like those at play in the idiom “apples and oranges.” The contrast between these two fruits can be mapped according to many measures: taste, smell, texture, visual appearance, and so on. When used colloquially, the phrase serves as a proxy for unmanageable difference — to describe categories that differ along so many axes that they can no longer be meaningfully compared.

However, in evolutionary terms, the difference between apples and oranges is not ineffable. It is not a folksy aphorism or a Zen puzzle at which to throw up one’s hands. To the contrary, it can be temporalized and quantified; or at least estimated. In fact, in evolutionary terms, that difference comes down to about 100 million years. That is, at least, the date (give or take) when the last common ancestor of apples and oranges lived — a flowering plant from the mid-Cretaceous.

The best way to represent these deep stories is with a diagram called a phylogenetic tree. In a phylogenetic tree, each species is assigned its own line, and each of these lines is called a branch. Points at which two branches intersect represent the common ancestor of the species assigned to these branches.

Phylogenetic trees can serve many purposes. Their classical function is to communicate a hypothesis – a pattern of familial relationships supported by a particular set of data based on DNA sequence, fossils, or the physical characteristics of living organisms.

But here are two alternate reasons to build trees:

  • To inspire wonder
  • Or (my favorite) just because

To reflect these additional motivations – this conviction that trees are for everyone and for all occasions and that an evolutionary tree belongs on every street corner – when I build trees, I often avail myself of a range of non-traditional materials. I’ve written previously about creating edible trees using cake frosting and fruit, as well as building trees out of state symbols and popular songs. Now here are two additional building materials, which are arguably even more fun.

First: Stickers. This one is titled: “Like Apples and Oranges…and Bananas.”

Bananas split ways with the common ancestor of apples and oranges about 150 million years ago, 50 million years before the split between apples and oranges. On this tree, these relationships are represented like so: the banana branch diverges from the apple branch at a deeper position on the trunk, and the orange branch diverges from the apple branch at a shallower position. 

All of the data required to build this tree  (and essentially any tree) is available at TimeTree.orgOn TimeTree, select “Get Divergence Time For a Pair of Taxa” at the top of the page. This is where one can obtain a divergence time estimate for most pairs of species. The divergence time is an approximate date, millions of years ago, at which the organisms’ last common ancestors may have lived. For more heavy duty assistance, there is the “Load a List of Species” option at the bottom of the page. Here, one can upload a list of species names (.txt), and TimeTree will generate a complete tree – a schematic that can serve as a guide in patterning one’s own phylogenetic artwork.

Here, by way of additional illustration, are three more sticker trees, equally charming and equally mouthwatering:

Carrot, watermelon, broccoli, strawberry, and pear.

Onion, asparagus, tomato, cucumber, and cherry.

Raspberry, apricot, pea, grape, and green pepper.

Sticker trees are festive takes on traditional trees. They are brighter, livelier, and more lovely. But, like traditional trees, they are also 2D, restricted to a flat sheet of paper. To extend one’s phylogenetic art projects into three dimensions, one must modify the choice of materials. There are many options. The following 3D tree, for example, employs 13 pieces of plastic toy food, the accouterments of a typical play kitchen. Segments of yarn serve as branches.

Trees like these, made of stickers or toys, constitute playful takes on deep questions. In pencil and yarn, they sketch a network of primeval relationships. They tell the history of our foods, a narrative whose origins profoundly precede us, as well as our intention to selectively breed them. To the Way-Before, to the Way-Way-Way-Before, these projects give shape and color. If and where they succeed, it is because they manage to do two things at once: To communicate a vast biological saga extending across many millions of years, and to be completely cute. Perhaps best of all – and let it not go unmentioned – anyone can make them.

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Bio: Rachel Rodman has a Ph.D. in Arabidopsis genetics and presently aspires to recast all of art, literature, and popular culture in the form of a phylogenetic tree.

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Charles Darwin and the Phylogeny of State Flowers and State Trees

This is a guest post by Rachel Rodman. Photos by Daniel Murphy.

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Every U.S. state has its own set of symbols: an official flower, an official tree, and an official bird. Collectively, these organisms form the stuff of trivia and are traditionally presented in the form of a list.

But, lists…well. As charming as lists can sometimes be, lists are rarely very satisfying.

So I decided to try something different.

I am not, of course, the first person to be unhappy with the eclectic, disordered nature of many biological assemblages. In the 18th century, Linnaeus developed a classification system in order to make sense of that untidiness. Kingdom, Phylum, Class, and so on.

In the 19th century, Darwin set biodiversity into an even more satisfying intellectual framework, outlining a model that linked organisms via descent from a series of common ancestors. And, as early as 1837, he experimented with a tree-like structure, in order to diagram these relationships.

Following Darwin’s lead, I’ve worked to reframe the state flowers and state trees in terms of their evolutionary history (*see the methods section below). And today, in honor of Darwin’s 209th birthday, I am delighted to present the results to you.

Let’s start with the state flowers.

In this tree, Maine’s “white pine cone and tassel” forms the outgroup. Among all the state “flowers,” it is the only gymnosperm—and therefore, in fact, not actually a flower.

Notice, also, that the number of branches in this tree is 39—not 50. Most of this stems from the untidy fact that there is no requirement for each state to select a unique flower. Nebraska and Kentucky, for example, share the goldenrod; North Carolina and Virginia share the dogwood.

With the branch labeled “Rose,” I’ve compressed the tree further. The state flowers of Georgia, Iowa, North Dakota, New York, and Oklahoma are all roses of various sorts; with my data set (*see methods below), however, I was unable to disentangle them. So I kept all five grouped.

This is a rich tree with many intriguing juxtapositions. Several clades, in particular, link geographical regions that are not normally regarded as having a connection. Texas’ bluebonnet, for example, forms a clade with Vermont’s red clover. So, similarly, do New Hampshire’s purple lilac and Wyoming’s Indian paintbrush.

Texas bluebonnet (Lupinus texensis) – the state flower of Texas

The second tree—the tree of state trees—is similarly rewarding. This tree is evenly divided between angiosperms (19 species) and gymnosperms (17 species).

Iowa’s state tree is simply the “oak”—no particular species was singled out. To indicate Iowa’s selection, I set “IA” next to the node representing the common ancestor of the three particular oak species: white oak, red oak, and live oak, which were selected as symbols by other states.

Arkansas’ and North Carolina’s state tree, similarly, is the “pine,”—no particular species specified. I’ve indicated their choice in just the same way, setting “AR” and “NC” next to the node representing the common ancestor of the eight particular pine species chosen to represent other states.

In this tree of trees, as with the tree of flowers, several clades link geographical regions that are not usually linked—at least not politically. Consider, for example, the pairing of New Hampshire’s white birch with Texas’ tree, the pecan.

Another phylogenetic pairing also intrigued me: Pennsylvania’s eastern hemlock and Washington’s western hemlock. It evokes, I think, a pleasing coast-to-coast symmetry: two states, linked via an east-west cross-country bridge, over a distance of 2,500 miles

The corky bark of bur oak (Quercus macrocarpa). Oak is the state tree of Iowa.

In this post, I’ve presented the U.S. state flowers and U.S. state trees in evolutionary framework. The point in doing that was not to denigrate any of the small, human stories that lie behind these symbols—all of the various economic, historical, and legislative vagaries, which led each state to select these particular plants to represent them. (Even more importantly, I have no wish to downplay the interesting nature of any of the environmental factors that led particular plants to flourish and predominate in some states and not others.)

The point, instead, was to suggest that these stories can coexist and be simultaneously appreciated alongside a much larger one: the many million year story of plant evolution.

With Darwin’s big idea—descent with modification—the eclectic gains depth and meaning. And trivia become a story—a grand story, which can be traced back, divergence point by divergence point: rosids from asterids (~120 mya); eudicots from monocots (~160 mya); angiosperms from gymnosperms (~300 mya), and so on and so on.

So today, on Darwin’s 209th, here, I hope, is one of the takeaways:

An evolutionary framework really does make everything—absolutely everything: U.S. state symbols included—more fun, more colorful, more momentous, and more intellectually satisfying.

Thanks, Darwin.

*Methods:

To build these two trees, I relied on a data set from TimeTree.org, a website maintained by a team at Temple University. At the “Load a List of Species” option at the bottom of the page, I uploaded two lists of species in .txt format; each time, TimeTree generated a phylogenetic tree, which served as a preliminary outline.

Later, once I’d refined my outlines, I used the “Get Divergence Time For a Pair of Taxa” feature at the top of the page in order to search for divergence time estimates. As I reconstructed my trees in LibreOffice, I used these estimates to make my branch lengths proportional.

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Rachel Rodman has a Ph.D. in Arabidopsis genetics and presently aspires to recontextualize all of history, literature, and popular culture in the form of a phylogenetic tree. Won’t you help her?