Happy Birthday, Darwin! And Please Enjoy a Slice of Phylogenetic Fruit Cake.

Today is Charles Darwin’s 209th birthday.

In an earlier post, I explained how to prepare a special list of music to honor the occasion. In this playlist—a “phylogenetic playlist”—songs are named for organisms and are arranged in order to reflect the evolutionary relationships among these organisms. The Beatles’ “Blackbird,” for example, might be paired with Prince’s “When Doves Cry,” consistent with the fact that Old World blackbirds and doves diverged approximately 80 million years ago.

Music is a great way to start a celebration. But no birthday party is really complete without cake and ice cream, and I’d like to address that need today.

Let’s start with the cake.

Over the years, people have prepared many clever and beautiful cakes, framed as tributes to Darwin. One cake charts the 1831-1836 journey of the HMS Beagle, on which Darwin served as a naturalist, gathering specimens from around the world. Other cakes capture stages of human evolution, or recreate famous portraits of Darwin, or laud Darwin as a personal friend.

Any one of these cakes would make a fitting birthday centerpiece. However, in this post, I’d like to argue in favor of another possibility—something I call a “phylogenetic fruit cake.”

Cake

In a classic fruit cake—or fruitcake—fruits are mixed together randomly. In a phylogenetic fruit cake, in contrast, the arrangement of the fruits is decidedly non-random.

Much like the songs in a phylogenetic playlist, the fruits in a phylogenetic fruit cake are arranged to illustrate evolutionary relationships. Both are constructed using the same rules as a phylogenetic tree—a diagrammatic tool long favored by evolutionary biologists.

In any phylogenetic creation, species are arranged at the tips of branches. Points at which branches intersect represent common ancestors. Relative degrees of relationship—whether species A is more closely related to species B or to species C, or is equally closely related to both—can be inferred by comparing the number of shared ancestors.

Fruits are produced by flowering plants. Many species can be assigned to one of two divisions: monocots or eudicots. Within the eudicots, many fruits belong to one of two large categories: either the asterids or the rosids. Within the rosids, in turn, many fruits belong to the family Rosaceae; these include blackberries, strawberries, apples, and cherries.

These divisions reflect the species’ evolutionary histories, and can therefore be directly applied to the design of a phylogenetic fruit cake.

To build my fruit cake, I started with ten different species of fruit. (In some cases, I used slices, in other cases whole specimens.) I positioned these pieces on the upper surface of a frosted cake, with an eye to diagramming the fruits’ evolutionary histories. Write-on frosting served as my “branches.”

For example, bananas and pineapples are monocots. So, I paired the banana slice and the pineapple slice, using write-on frosting to delineate the connection. Kiwis and blueberries are asterids. So, I paired the kiwi slice and the blueberry in just the same way.

The remaining six fruits are rosids. They include grapes and oranges, in addition to the four Rosaceae species that I outlined above. In order to sort out these relationships more finely, I took advantage of divergence time estimates available at Time Tree.org.

Fruit Phylogeny

To tease out these relationships, I was especially reliant on Time Tree’s “Load a List of Species” option, which can be found at the bottom of the page. Here, you can upload a list of species in .txt format, and Time Tree will propose a tree.

As I positioned the fruits, I used Time Tree’s proposed tree as a model. According to Time Tree’s estimates, for example, oranges are more closely related to Rosaceae species than the grapes are, and so I positioned both accordingly. Time Tree’s estimates also led me to pair the blackberry with the strawberry slice, and the apple slice with the cherry.

My cake constitutes just one example of the form. If and when you make your own phylogenetic fruit cake, I’d encourage you to incorporate your own favorite fruits.

Whatever design you settle on, however, try to space out your fruits as evenly as possible on the cake surface. Remember: at the end of your Darwin celebration, you’ll want to cut up this cake, and distribute a slice to each of your party guests. To make this division as slick as possible, you’d ideally like to have one—and only one—piece of fruit per slice.

Here’s another pro tip: without special preservation techniques, exposed pieces of fruit will rot quickly. So you should either makes plans to finish this cake in short order (and if your party is big enough, this shouldn’t be a problem) or else be careful to refrigerate the leftovers.

Almost as essential as a birthday cake is birthday ice cream. And you can build a Darwin-worthy sundae using the very same skill set we’ve already discussed.

The example that I am presenting here contains the three basic flavors: strawberry, chocolate, and vanilla.

Ice Cream

Strawberries come from the genus Fragaria. Chocolate is produced from seeds of the plant Theobroma cacao. Both plants are eudicots. Even more specifically, both are rosids. So these two flavors are linked, using a pair of branches made of chocolate syrup.

Vanilla, however, is a derived from an orchid—a monocot. In this sundae, therefore, vanilla serves as the outgroup, and is positioned on an earlier-diverging branch.

What I’ve just described is a minimalist sundae. When you make your own sundae, I’d challenge you to incorporate some additional ice cream flavors, like pistachio, peanut butter, or peppermint.

You might also experiment with new ways to represent the branches. In my sundae, I’ve used chocolate syrup. But in your own sundae, you might try building your branches out of whipped cream or trails of sprinkles—just as you prefer.

Once the desserts are ready, it’s time to light the candles. If you’re feeling sparkly, you might position all 209 candles along the branches of your cake. (Imagine it: many lines of descent, lit up in 209 points of flame! What a gorgeous, gleaming, flickering tribute to make to the story of plant evolution! And to Darwin!) But if 209 candles feels too ambitious, you might settle for a simple “2018” candle. Or take clever advantage, somehow, of the fact that 209 can be factored into 11 and 19.

Either way, though: with the candles set, it is traditional to sing “Happy Birthday.”

To be clear: I am using the word “traditional” very loosely. Because, of course, “Happy Birthday” is anachronistic. It didn’t actually become a song until well after Darwin’s death.

Still, I think that, by now, any “true to Darwin’s time” principle has been thrown out the window.  In the playlist that I suggested previously, the oldest song was the 1967 “White Rabbit” by Jefferson Airplane. Let’s remember, too: all of the molecular data, available at Time Tree.org, which was so essential in constructing these birthday creations, came well after Darwin’s time.

So, I am not personally inclined to sweat these things. I’d say: go ahead and sing, “Happy Birthday.”

On top of that: I think that the appropriation of modern birthday trappings is in many ways concordant with concepts at the heart of evolutionary biology.

The past has shaped us; the past defines us. But we live—we must—in our present environment, not in the long ago. Change happens. And the here-and-now is the only place in which we can make our way.

So, really? As long as our hearts are in the right place, I can’t imagine that Darwin would begrudge us a few modern conventions.

Ultimately, though: these are quibbles. Because at the end of everything: after all of the careful preparation, and all of the talk—and once the candles have been blown out—we come to what is arguably the very most important part.

That’s right: You get to eat it.

So, anyway: sing, or not—just as you care to. But, above all, dig in.

Because it’s going to be delicious.

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

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Darwin Turns 209 Next Week. And Here’s the Perfect Playlist to Help Us All Celebrate.

February 12th is Charles Darwin’s birthday; this year he turns 209.

There are many ways to celebrate. You could crack open your old copy of On the Origin of Species, his groundbreaking work describing the theory of evolution. You could book a trip to Down House, where he lived and raised his family. Or, if you’re looking for something impactful, make a contribution to defend evolution education (for a good birthday present you can even do it in his name).

An additional way to celebrate is with music. Darwin-themed songs have been highlighted before, and this is a wonderful option to explore. However, in this post I am proposing a playlist of another sort, in which it is the songs’ arrangement, rather than their content, that honors Darwin.

Today, evolutionary relationships are often represented using a diagram called a phylogenetic tree. (In fact, Darwin sketched one as early as 1837.) In a phylogenetic tree, organisms are placed at the tips of lines called branches. At certain positions in the diagram, adjacent branches intersect. These points of intersection are called nodes. A node represents a common ancestor—a point in the past when a single ancestral population split to give rise to two separate lineages. Clusters of intersecting branches, incorporating all of the species that are descended from a given ancestor, are called clades.

My playlist is organized in exactly the same way. It has 16 songs, each named for a different biological organism. Each song is positioned at the end of a branch; these branches, in turn, are arranged to reflect genealogical relationships.

I selected my songs based on two considerations. First, I wanted a diverse range of organisms, belonging to several different phyla. At the same time, I also wanted to restrict my playlist to famous songs—titles that most people would recognize immediately.

At the top of my list, “Who Let the Dogs Out” is paired with “Hungry Like the Wolf,” reflecting a close evolutionary relationship between dogs and wolves.

Positions 3 and 4 of the playlist are occupied by two more distantly-related carnivores: “The Fox” (better known as “What does the Fox Say?”) and “Eye of the Tiger.”

At positions 5-7 is a second clade of mammals, which diverged from the carnivores approximately 100 million years ago. This clade consists of a lagomorph-themed song: “White Rabbit,” together with a pair of songs named for primates: “Piano Man” and “Shock the Monkey.”

Bird-themed songs form a clade at positions 8-10: “Blackbird,” “When Doves Cry,” and “Peacock.”

Invertebrates occupy positions 11-13. Two arthropods, “Rock Lobster” and “Fireflies,” are paired; a mollusk-themed song, “Octopus’ Garden,” is present on an adjacent branch.

The remaining branches, rounding out the playlist, are devoted to plants and plant products: The Presidents of the United States of America’s “Peaches,” Eric Clapton’s “Cocaine” (cocaine is derived from any of several plants in the genus Erythroxylum), and Maroon 5’s “Sugar.”

The only thing more fun than this playlist is the process of creating one of your own. And you can do that, just like I did, in five easy steps.

Playlist

The full playlist!

1) Select your songs

Your selection criteria—and musical tastes—will likely differ from mine. You might also wish to challenge yourself by honing in on one specific section of the tree of life. Consider, for example, a playlist that is devoted just to flowering plants, or just to protostomes, or just to vertebrates.

Whatever your criteria, though, a variety of search engines can assist you. At Songfacts.com, for example, you can search for “songs with flowers in the title”.  Or for “songs with animals.”

2) Convert your song titles to species names. (Sites like Wikipedia can help.) In this conversion, for example, “Peaches” becomes Prunus persica.

3) Save a list of the species in .txt format

4) Visit TimeTree.org

Scroll to the bottom of the page. At “Load a List of Species,” upload your .txt list. Then, Bam!, Time Tree will generate a phylogenetic tree.

5) Recreate the tree replacing the species names with the song titles

And then, Voilà!: You have a playlist.

As you play around with your playlist, you should also remember: equivalent trees can be written in many different ways. So feel free to headline your playlist with whatever song you’d like: “The Yellow Rose of Texas,” “Hound Dog,” “I Am the Walrus,” whatever. Then tweak the arrangements of the other songs accordingly. And you’ll still have a perfectly accurate tree.

Whatever your plans for February 12th, I hope that you’ll consider making a phylogenetic playlist a part of the celebration. Use mine—you are very welcome to it. Or else build one of your own.

As you listen to your playlist, reflect upon the deep familial connections that link all forms of life. Think, too, about Darwin: the author of the revolutionary conceptual framework that underlies your playlist—the same framework that today enables us to make sense of biology.

And wish him, with all your heart, a happy 209th.

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

The dinosaur you’re eating for Thanksgiving dinner

I giggle a little every time people ask about the dinosaur extinction (on the inside because giggling in peoples’ faces is rude (so I’ve been told… repeatedly)). Dinosaurs, in the strictest sense, are not extinct. They are walking and flying around us everyday.

And this week, they are sitting in the middle of the table.

But, in all fairness, I should mention that this is an ongoing debate. Not whether or not Thanksgiving is going to be delicious (that should be settled soon), but whether dinosaurs still walk amongst us (and will soon be in your belly).

HAPPY THANKSGIVING! ENJOY YOUR DINOSAUR!

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When talking about phylogenies, don’t use words like “basal”

Over at the blog “For the love of treesStacey Smith has recently posted an interesting (and somewhat twitter controversial) post about how to correctly talk about evolution and phylogenies.

For starters, don’t use the word basal. She states that by her estimation the term “basal” is misused ~90% of the time, and it perpetuates a number of misconceptions about how evolution works.

Intrigued? Go check out the post. Or enjoy this phylogeny of basil posted by Maggie Schedl (which is the most basal basil?!?)

The Basil-Lineage problem: which is the #mostprimitivebasil

The Basil-Lineage problem: which is the #mostprimitivebasil

 

How the squashes hitched a ride with humans

Squashes are funny, as fruits go. Even after years of selection for human consumption they have thick, hard rinds, they’re not particularly sweet — in fact, they contain bitter compounds called cucurbitacins — and their seeds don’t separate from their flesh very easily. That all suggests that the wild ancestors of butternuts and pumpkins were dispersed by large mammals, but squashes are native to the Americas, and there haven’t been many large mammals of the sort that would eat them since humans showed up there, back at the end of the last ice age. Of course, those humans since domesticated squashes, which would obviate the need for seed dispersal — and a new genetic study of wild and domesticated squash species provides support for exactly that hypothesis.

Ed Yong has a nice write-up over at Phenomena:

[Squashes’] old dispersers were gone and the most likely substitutes were small rodents with diverse diets, who could have chiselled through the fruits and carried the seeds to pastures new. But Kistler found that these same animals are the most likely to be put off by the squashes’ bitter tastes. Compared to larger animals like elephants or rhinos, he found that smaller ones like mice and shrews have far more TAS2R genes, which allow them to taste bitter compounds.

Humans can’t stomach cucurbitacins either. People who’ve been unfortunate enough to swallow high levels of these chemicals have come down with a severe diarrhoeal illness called Toxic Squash Syndrome. But perhaps some ancient hunter-gatherers became skilled at finding individual squashes that produced low or tolerable levels. After eating such plants, they would have pooped the seeds out, inadvertently sowing the land with more palatable strains.

I am not personally a great fan of pumpkin pie, particularly since I tried sweet potato last Thanksgiving — but maybe this finding will make for some nice chatter over coffee after dinner. Unless you happen to have an uncle who’s into Pleistocene rewilding, anyway.

Reference

Kistler L., L.A. Newsom, T.M. Ryan, A.C. Clarke, B.D. Smith, & G.H. Perry. 2015. Gourds and squashes (Cucurbita spp.) adapted to megafaunal extinction and ecological anachronism through domestication
Proc. Nat. Acad. Sci.; published ahead of print November 16, 2015, doi: 10.1073/pnas.1516109112.

Biologist Having Too Much Fun Testing Evolution Education Game To Actually Study Evolution

Phylogenetics has never been this much fun. Seriously. (Screenshot: Evolution Lab)

Phylogenetics has never been this much fun. Seriously. (Screenshot: Evolution Lab)

NOVA, the flagship science program on U.S. Public Television, has just launched a new Evolution Lab website, which is chocked full of great information about the history of life on Earth, and how we study it. But my favorite thing has got to be the accompanying online game, which asks you to assemble organisms into evolutionary trees based on their traits and even their DNA sequences — it’s slick and pretty and it guides you into the logic of evolutionary relationships without explaining them point-by-point, unless you want that. I’ll be keeping this in mind for the next time I teach a basic class in phylogenetics.

Understanding the evolution of nocturnal mammals by studying their extinct relatives

Humans are diurnal. We sleep at night and are active during the day. (That isn’t to say that I feel particularly diurnal most mornings, given that my alarm has to make it through a few snooze cycles to wake me up and coffee is the only thing keeping me from napping under my desk at work.) Most mammals, though, don’t share our ostensible predilection for daylight; only 20% of mammal species are diurnal like us. Of our mammalian relatives, nearly 70% are nocturnal. The rest are crepuscular (active at dawn and dusk) or cathemeral (active during both day and night).

A tarsier (Flickr: )

A tarsier from Borneo. (Flickr: Erwin Bolwidt)

Mammalogists like myself often think nocturnality is a particularly mammalian thing because—let’s be honest here—nearly all of the coolest nocturnal vertebrates are mammals. How can you compete with the likes of tarsiers, vampire bats, leopards, and—strangest of them all—the aye-aye? I’ll throw the ornithologists a bone and acknowledge the enduring awesomeness of owls, but they are the odd birds out in a group that’s mostly diurnal.

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