deep time

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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.org. On 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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What Is a Plant, and Why Should I Care? part three

“If it wasn’t for the plants, and if it wasn’t for the invertebrates, our ancestors’ invasion of land could never have happened. There would have been no food on land. There would have been no ecosystems for them to populate. So really the whole ecosystem that Tiktaalik and its cousins were moving into back in the Devonian was a new ecosystem. … This didn’t exist a hundred million years before – shallow fresh water streams with soils that are stabilized by roots. Why? Because it took plants to do that – to make the [habitats] in the first place. So really plants, and the invertebrates that followed them, made the habitats that allowed our distant relatives to make the transition from life on water to life on land.” – Neil Shubin, author of Your Inner Fish, in an interview with Cara Santa Maria on episode 107 of her podcast, Talk Nerdy To Me

Plants were not the first living beings to colonize land – microorganisms have been terrestrial for what could be as long as 3.5 billion years, and lichens first formed on rocks somewhere between 550 and 635 million years ago – however, following in the footsteps of these other organisms, land plants paved the way for all other forms of terrestrial life as they migrated out of the waters and onto dry land.

The botanical invasion of land was a few billion years in the making and is worth a post of its own. What’s important to note at this point, is that the world was a much different place back then. For one, there was very little free oxygen. Today’s atmosphere is 21% oxygen; the first land plants emerged around 470 million years ago to an atmosphere that was composed of a mere 4% oxygen. Comparatively, the atmosphere back then was very carbon rich. Early plants radiated into numerous forms and spread across the land and, through processes like photosynthesis and carbon sequestration, helped to dramatically increase oxygen levels. A recent study found that early bryophytes played a major role in this process. The authors of this study state, “the progressive oxygenation of the Earth’s atmosphere was pivotal to the evolution of life.”

A recreation of a Cooksonia species - one of many early land plants. (photo credit: wikimedia commons)

A recreation of a Cooksonia species – one of many early land plants (photo credit: wikimedia commons)

The first land plants looked very different compared to the plants we are used to seeing today. Over the next few hundred million years plants developed new features as they adapted to life on land and to ever-changing conditions. Roots provided stability and access to water and nutrients. Vascular tissues helped transport water and nutrients to various plant parts. Woody stems helped plants reach new heights. Seeds offered an alternative means of preserving and disseminating progeny. Flowers – by partnering with animal life – provided a means of producing seeds without having to rely on wind, water, or gravity. And that’s just scratching the surface. Rooted in place and barely moving, if at all, plants appear inanimate and inactive, but it turns out they have a lot going on.

But what is a plant again? In part one and two, we listed three major features all plants have in common – multicellularity, cell walls composed of cellulose, and the ability to photosynthesize – and we discussed how being an autotroph (self-feeder/producer) sets plants apart from heterotrophs (consumers). Joseph Armstrong writes in his book, How the Earth Turned Green, “photosynthetic producers occupy the bottom rung of communities.” In other words, “all modern ecosystems rely upon autotrophic producers to capture energy and form the first step of a food chain because heterotrophs require pre-made organic molecules for energy and raw materials.”

So, why should we care about plants? Because if it wasn’t for them, there wouldn’t be much life on this planet to speak of, including ourselves.

Plants don’t just provide food though. They provide habitat as well. Plus they play major roles in the cycling of many different “nutrients,” including nitrogen, phosphorous, carbon, sulfur, etc. They are also a major feature in the water cycle. It is nearly impossible to list the countless, specific ways in which plants help support life on this planet, and so I offer two examples: moss and dead trees.

The diminutive stature of mosses may give one the impression that they are inconsequential and of little use. Not so. In her book, Gathering Moss, Robin Wall Kimmerer describes how mosses support diverse life forms:

There is a positive feedback loop created between mosses and humidity. The more mosses there are, the greater the humidity. More humidity leads inexorably to more mosses. The continual exhalation of mosses gives the temperate rain forest much of its essential character, from bird song to banana slugs. … Without mosses, there would be fewer insects and stepwise up the food chain, a deficit of thrushes.

Mosses are home to numerous invertebrate species. For many insects, mosses are a place to deposit their eggs and, consequentially, a place for their larvae to mature into adults. Banana slugs traverse the moss feeding on “the many inhabitants of a moss turf, and on the moss itself.” In the process they help to disperse the moss.

Moss is used as a nesting material by various species of birds, as well as squirrels, chipmunks, voles, bears, and other animals. Patches of moss can also function as “nurseries for infant trees.” In some instances, mosses inhibit seed germination, but they can also help protect seeds from drying out or being eaten. Kimmerer writes, “a seed falling on a bed of moss finds itself safely nestled among leafy shoots which can hold water longer than the bare soil and give it a head start on life.”

moss as nurse plant

Virtually all plants, from the tiniest tufts of grass to the tallest, towering trees have similar stories to tell about their interactions with other living things. Some have many more interactions than others, but all are “used” in some way. And even after they die, plants continue to interact with other organisms, as is the case with standing dead trees (a.k.a. snags).

In his book, Welcome to Subirdia, John Marzluff explains that when “hole creators” use dead and dying trees, they benefit a host of “hole users:”

Woodpeckers are natural engineers whose abandoned nest and roost cavities facilitate a great diversity of life, including birds, mammals, invertebrates, and many fungi, moss, and lichens. Without woodpeckers, birds such as chickadees and tits, swallows and martins, bluebirds, some flycatchers, nuthatches, wood ducks, hooded mergansers, and small owls would be homeless.

As plants die, they continue to provide food and habitat to a variety of other organisms. Eventually they are broken down to their most rudimentary components, and their nutrients are taken up and used by “new life.” Marzluff elaborates on this process:

Much of the ecological web exists out of sight – underground and in rotting wood. There, molds, bacteria, fungi, and a world of invertebrates convert the last molecules of sun-derived plant sugar to new life. These organisms are technically ‘decomposers,’ but functionally they are among the greatest of creators. Their bodies and chemical waste products provide us with an essential ecological service: soil, the foundation of terrestrial life.

Around 470 million years ago, plants found their way to land. Since then life of all kinds have made land their home. Plants helped lead the way. Today, plants continue their long tradition of supporting the living, both in life and in death.

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Thoughts on Equisetum Phylogenesis

This a guest post. Words and photos by Jeremiah Sandler.

These notes do not discuss either anatomy or medicinal uses of Equisetum. Both topics are worthy of their own discourse.

Plants in the genus Equisetum can be found on each continent of our planet, except for Antarctica. The plants are collectively referred to as scouring rush or horsetail.  Equisetum is in the division of plants called Pteridophytes, which contains all of the ferns and fern-allies (lycopods, whisk ferns, etc.) Pteridophytes are characterized by having a vascular system and by reproducing with spores, rather than seeds. Equisetum is the only living genus within the entire class Equisetopsida.  Within this single genus, there are a mere 20 species.

Picture 1

Equisetums can live pretty much anywhere. They can tolerate lots of shade, lots of sun, and virtually any soil condition (including submerged soil). Rhizomatous stems make it difficult for either disease or insects to kill an entire population. They do not require pollinators because they reproduce with spores.  Sounds like a recipe for reproductive and evolutionary success. Yet with all of these traits working in their favor, there is only a single genus left.  

Where’d they all go?

Picture 2

Let’s briefly consider the origin of these plants first. In the late Paleozoic Era, during the end of the Cambrian Period, these plants began their takeover. Shortly thereafter (about 70 million years later), in the Devonian Period, land plants began to develop a tree-like habit, also called “arborescence.” Tree-sized ferns and fern-allies ruled the planet. They formed the ancient forests.

The elements required for photosynthesis were plentiful. The planet was warm. Competition from the Cambrian Explosion of flora and fauna drove plants upwards towards the sky. Larger plants can both shade their competition and remain out of reach of herbivores. None of the Equisetum species alive today are near their ancestors’ height.  

picture 3

It is rather obvious why we don’t see as many Equisetum species, and why they are not as large: The planet now is not the same planet it once was. Oxygen levels back in those times were about 15% higher than today’s levels. Seed plants can diversify much faster than non-seed-bearing plants; Equisetum cannot compete with the rate of diversification of seed-bearing plants.

The most interesting predicament comes when Equisetum is compared with other Pteridophytes. Some ancient Pteridophytes still do have diversity of genera. True Ferns, as they’re called, are broad-leaved ferns. In the class Filicopsida, there are 4 orders of True Ferns containing about 100 genera combined. Equisetum has 1 order and 1 genera.

What’s the primary difference between these two classes of Pteridophytes?  Broad leaves.

Most pteridophytes tolerate some shade; most other plants can’t tolerate as deep of shade as ferns. More specifically, the amount of shade the plants create could be a deciding factor in this question. True ferns have all of the traits equisetums have, with one additional physical trait that has pulled them ahead: Broad leaves allow true ferns to actively shade out local competition while creating more habitat for themselves. Equisetums don’t have this aggressive capacity.

Of course there are other biological and evolutionary pressures affecting equisetums beside their lack of broad leaves. The structure they do possess has benefited them at a time when it was advantageous to have it.  Otherwise why would it exist? Equisetums remind me of the dynamic nature of a planet. I don’t anticipate equisetums coming back. 

Although, I find it entertaining to humor the idea that they might return to their former glory. The planet’s climate could change toward any direction (I’m not a climatologist, though). Maybe equisetums are adequately prepared to adapt to whatever changes come – or maybe we are observing the gradual decline of an old branch on the tree of life.  

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