phylogenetics

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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?

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On the Genus Euphorbia

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

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Suspicion

I collect cacti and succulents. The more I collect plants, the more and more I become interested in taxonomic and phylogenetic relationships between them. Not just my own plants – all of them. Most recently, the genus Euphorbia has been on my mind. My favorite species are E. meloformis var. valida and E. horrida.

I’m mostly familiar with the succulent and cacti-looking euphorbia (they are not true cacti) and a few ornamental annuals. Sometimes I would come across a species that I could determine was a euphorbia; but in trying to identify exactly which species, I found countless possibilities within the genus. It seemed odd to me that a single genus could contain so many different forms.

Turns out, Euphorbia consists of over 1800 separate species. What?! That is an insanely high number! Only about 20 genera of plants contain over 1000 separate species. Euphorbia is the fourth most populated genus among all genera of plants.

That staggering number got me thinking: how can a single genus have so many different species? How has the classification worked that out? Has the genus been phylogenetically examined? There’s no way a genus can be so huge. You know what breeders and collectors can do with that much genetic material in a single genus? The man-made hybrids seem endless.

Euphorbia globosa in bloom

Taxonomy

In older taxonomic practices, morphological similarities were the primary method of grouping individuals together. While that is still a common practice today, phylogenetic testing is now an accessible tool for organizing species into related groups.

Organizations such as the Angiosperm Phylogeny Group (APG) have been doing this advanced scientific research – analyzing DNA, doing detailed dissection, etc. Ultimately, they organize plant taxonomy and systematics with greater detail, and examine plant relationships genetically – phylogenetics.

Analyzing genomes is much more expensive and time consuming than observing morphologies. Now, a mix of methods is used, but DNA sequencing has definitely changed the systematics game in a big way. As a result of the APG’s incorporation of widespread phylogenetic DNA analyses, their taxonomical classifications are quickly becoming the generally accepted classifications among plant taxonomists.

Since the inclusion of genetic testing, many plant orders, families, and genera have been reorganized, renamed, expanded, or shrunk.

Euphorbia

One of the identifying features of euphorbias are their very unique flowers. All species in the genus have a cyathium, an inflorescence exclusively produced by euphorbias. Lacking in true petals, sepals, or nectaries, monoecious euphorbia flowers possess only the most essential parts of reproduction. However, bracts, extra-floral nectaries, and other structures surrounding the reproductive parts of the flowers make them appear superficially different.

It would be very time consuming to sequence the DNA of every member of this genus to see where they all fit. Approximately 10% of the euphorbias have been phylogenetically examined, and they confirm the traditional morphological placement. How about that?

Interestingly, of the species genetically analyzed, some were subsequently placed into the genus Euphorbia after historically being considered members of other genera.

Euphorbia horrida and Euphorbia obesa

So? What’s that mean?

Species within the same genus when crossed can (but not always) produce viable offspring. Sometimes they don’t because of differences in pollinators, flowering times, or geographic location, which prevents hybridization. Clades within plant genera also can affect intra-genus reproduction. For example, hard maples won’t naturally hybridize with soft maples, despite both being in the genus Acer. Perhaps the case is similar between the groups within Euphorbia.

As a plant collector and cacti and succulent enthusiast, imagining the endless amounts of hybrids within a massive genus is a fancy idea to me. The APG’s confirming of the initial classifications of Euphorbia into a massive genus makes the idea of endless hybrids all the more real.

Additional guest posts by Jeremiah Sandler:

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Jeremiah Sandler lives in southeast Michigan, has a degree in horticultural sciences, and is an ISA certified arborist. Follow him on Instagram: @j.deepsea

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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.  

Resources:

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Speaking of Food: A Recap

The theme for the past 15 posts has been the October 2014 Special Issue of American Journal of Botany, Speaking of Food: Connecting Basic and Applied Plant Science. After a brief introduction to the issue, I spent the next 14 posts (spanning a period of 5 weeks) reading and writing summaries of each of the 17 articles. If you actually read every post, you are a champion in my eyes, and I probably owe you a prize of some sort. And even if you just read one or two, thank you, and I hope you found value in what you read.

I have to admit that it was kind of a grueling process. Many of the articles, along with being lengthy, included high level discussions that were beyond my current understanding, especially concerning topics like genetics, genomics, and phylogenetics. I learned a lot while reading them, but I am still far from truly grasping many of the concepts. For that reason, I did not feel completely comfortable writing summaries of some of these discussions. I made an effort not to misrepresent or oversimplify the research, but I can’t say for sure that my attempts were always successful. I welcome any criticisms, corrections, complaints, or comments in this regard, and I am open to making edits or updates to any of the posts as necessary. I consider this blog my learning platform, as well as a place to share my phyto-curiosity. Perhaps you find it a place for learning, too?

The main purpose of this post is to provide a Table of Contents for the last 14 posts, something that will make it easier to navigate through this series without having to scroll through each post. If you are interested in reading the entire series (again, you’re a champion), you can access them all in order here by clicking on the titles. Otherwise, you can pick and choose whatever topics interest you the most.

  • On the Origins of Agriculture – A deep dive into plant domestication and the beginnings of agriculture, including the revision of theoretical approaches to thinking about the history of plant domestication and a discussion of emerging methods and tools for exploring early domestication and emerging agriculture.
  • The Legacy of a Leaky Dioecy – Does pre-Colombian management of North American persimmon trees explain why non-dioecious individuals are found in an otherwise dioecious species?
  • Dethroning Industrial Agriculture: The Rise of Agroecology – The environmentally devastating effects of industrial agriculture can and must be replaced by a more sustainable, ecologically-focused from of agriculture. This will require reforming our economic system and rethinking our “one size fits all” approach to scientific research.
  • An Underutilized Crop and the Cousins of a Popular One – Safflower, an underutilized oilseed crop, could be improved by introducing genes from wild relatives. Soybean, a very popular and valuable crop, could also be improved by introducing genes from its perennial cousins.
  • Carrots and Strawberries, Genetics and Phylogenetics – An exploration of the genetics and phylogenetics of carrots and strawberries. Better understanding of their genetics will aid in crop improvements; better understanding of their phylogenetics gives us further insight into the evolution of plants.
  • Exploring Pollination Biology in Southwestern China – A fascinating look at the pollination biology of edible and medicinal plants in southwestern China, revealing significant gaps in scientific understanding and the need for conservation and continued research.
  • Your Food Is a Polyploid – Polyploidy is more prevalent in plants than we once thought. This article examines the role of polyploidy in crop domestication and future crop improvements.
  • Tales of Weedy Waterhemp and Weedy Rice – How agriculture influenced the transition to invasiveness in two important weed species.
  • Cultivated Sunflowers and Their Wild Relatives – An investigation into the flowering times of wild sunflowers reveals potential for improvements in cultivated sunflowers.
  • The Nonshattering Trait in Cereal Crops – Is there a common genetic pathway that controls the shattering/nonshattering trait in cereal crops?
  • Apples and Genetic Bottlenecks – Domestication generally leads to a loss of genetic variation compared to wild relatives, but apples have experienced only a mild loss. That loss may increase as commercial apple production relies on fewer and fewer cultivars.
  • Improving Perennial Crops with Genomics – The nature of perennial crops can be an impediment to breeding efforts, which makes the introduction of new perennial crop varieties both time consuming and costly. Advances in genomics may help change that.
  • Using Wild Relatives to Improve Crop Plants – Crop plants can be improved through the introduction of genes from wild relatives. They could potentially experience even greater improvement through systematic hybridization with wild relatives.
  • Developing Perennial Grain Crops from the Ground Up – Some of the environmental issues resulting from agriculture could be addressed by switching from annual to perennial grain crops, but first they must be developed from wild species.
A small harvest of sweet potatoes (Ipomoea batatas ' Hong Hong') from this year's backyard mini-farm. Ipomoea batatas ' Hong Hong.'

A small harvest of sweet potatoes (Ipomoea batatas ‘ Hong Hong’) from this year’s backyard mini-farm.

If I had to pick a favorite article in this issue it would be Think Globally, Research Locally: Paradigms and Place in Agroecological Research (Reynolds et al.). I know I said it in the post, but this article really sums up the reasons why this special issue of AJB is so important. Humans are incredibly resourceful, creative, and resilient, and as we have spread ourselves across the globe and grown our population into the billions, we have found ways to produce enormous amounts of food relatively cheaply. Frankly, the fact that anyone is going hungry or dying of starvation is shameful and appalling as there is plenty of food to go around…for now. But we are doing a lot of things wrong, and the earth is suffering because of it. If the biosphere is in trouble, we are all in trouble. Thus, we are overdue for some major shifts in the way we do things, particularly agriculture as that’s what this series of posts is all about. I advocate for science-based sustainable agriculture, and I am hopeful, thanks to this issue of AJB and other signs I’ve seen recently, that we are moving more in that direction. I’ll step off my soapbox now and leave you with an excerpt from the article by Reynolds, et al.

“There is increasing recognition that the current industrial model of agricultural intensification is unsustainable on numerous grounds. Powered by finite and nonrenewable stores of fossil fuels over the last 200 years, humans have come to see themselves, their technology, and their built environments as controllers of nature rather than interdependent with it, even as our activities threaten to exceed planetary boundaries of resilience in multiple environmental dimensions, such as climate, biodiversity, ozone, and chemical pollution. … In the ‘full world’ we now live in, continuing to use high input, highly polluting methods of food production to support continued economic growth is counterproductive to achieving food security. Continued growth of population and per capita consumption on a finite planet fails to meet the basic requirement of sustainability, that of meeting needs within the regenerative and assimilative capacity of the biosphere. And prolonging the shift to a sustainable economic paradigm risks a harder landing.”