Tag Archives: systematics

December 21, 2016 · 9:30 am

Phylogenetics is Moon Man Talk

Phylogenetics is the study of the evolutionary history and relationships among extant and extinct organisms. More than any other organizational scheme, this is the way biologists think about the living world. In vertebrate paleontology in particular, an understanding of the evolutionary relationships of animals as identified via minute anatomical details is absolutely fundamental to our science. One might even argue that most new discoveries and inferences in this field are meaningless without some knowledge of the basic shape of the tree of life.

I’ve spent about eight years so far teaching science in museums, parks, and classrooms. And based on my anecdotal experience, most discussion of phylogeny comes across as incomprehensible babble to a plurality of people. For instance, one of the most commonly used definitions of “dinosaur” among paleontologists is “the most recent common ancestor of Triceratops and modern birds, and all it’s descendants” (there’s also the similar “most recent common ancestor of Megalosaurus and Iguanodon, and all it’s descendants”). This definition is not meaningful to most people. As evidence, I submit the following set of questions, all of which I have been asked by intelligent and well-meaning adults:

Did whales and dolphins evolve from marine reptiles?
Did giraffes evolve from sauropods?
Are [dromaeosaurs] related to cats?
Are dinosaurs related to sharks?
How can birds be dinosaurs if dinosaurs are reptiles?
Did the plant-eating dinosaurs evolve into mammals?
Are bats a kind of bird?
Are pterodactyls a kind of bird?

I don’t mean to ridicule or disparage people for asking these questions. Again, these all come from educated adults – museum and park visitors, undergraduate students, T.A.s, and at least one veterinarian! While these questions clearly show unfamiliarity with evolutionary relationships and how evolution works in general, they also show an effort to build a logical framework when none is available. For example, when a person asks if whales are descended from marine reptiles, he or she is hypothesizing that all large marine animals are related. This is incorrect, but it’s a sensible connection to make (and one that past naturalists have certainly explored).

For science communicators, this deficit of phylogenetic understanding is a serious problem which continuously undermines attempts to interpret zoology and paleontology. For example, think about how little meaning a statement like “Dimetrodon isn’t a dinosaur” has to somebody who can’t articulate what a mammal is or what a dinosaur is, much less the evolutionary distance between both groups. This is what we should expect from most of our audience, which means there is always a lot of catch-up work to do when explaining something as simple as the basic identity of a given organism. By the time you’ve satisfactorily defined “dinosaur” (good luck with that), explained the synapsid-diapsid split, discussed the tree of extinct stem-mammals, and positioned each of these things in deep time, you’re five minutes deep into a lecture when all you were asked was “what is it?”

USNM 8635, a handsome non-dinosaur. Photo by the author.

How can we solve this conundrum? The first step is to divide the issue into a number of smaller problems:

People don’t understand the fundamentals of how evolution works
People are unfamiliar with basic vertebrate classification
People lack knowledge of key evolutionary events through deep time
People don’t understand what traits are significant when assessing evolutionary relationships

The first problem is well known and has been discussed in-depth elsewhere (e.g. MacFadden et al. 2007, Spiegel et al. 2006, Spiegel et al. 2012), so I’m going to breeze over it and focus on the other three.

Basic Vertebrate Classification

It’s easy to toss out words like “mammal”, “reptile”, and “amphibian”, and take for granted that your audience will know what they mean. But even the most basic elements of vertebrate classification are specialized knowledge, and science communicators would do well to remember it. When I was teaching an undergraduate human anatomy course, I found that most of the class was familiar with the word “mammal”, and could name some examples. However, the students couldn’t articulate what sets mammals apart from other animals, and the relationship of mammals to other vertebrates within the tree of life was all new to them.

I think this is fairly typical, even among individuals with a background in biology. People are introduced to these categories in grade school, and you’d be hard-pressed to find somebody who couldn’t tell you whether (say) a cat is a mammal or a reptile. What is missing is what that actually means. We can’t assume that just because somebody knows a cat is a mammal, they know that fur and milk glands (much less auditory ossicles, a solid mandible, and heteromorphic teeth) are things to look for when categorizing mammals. They also may not know that “mammal” is an evolutionary group – that all the animals that fall under this banner are more closely related to each other than they are to anything else. No mammal is going to spontaneously become a bird or a fish. This is obvious to specialists, but not to most of our audience.

Evolutionary History Through Deep Time

The situation is further complicated by the element of time. Somebody may know that a modern cat and lizard differ in several fundamental ways, but do they know that both groups still evolved from a common ancestor? Or that said ancestor lived more than 300 million years ago? Unfortunately, much of the public would appear to lack any knowledge of how the past is related to the present. I’ve had visitors insist on calling fossil turtles “dinosaur turtles” and Teleoceras a “rhino-saur.” For them, extinct animals (all labeled “dinosaurs”) are a category all their own, wholly independent from the categories that describe modern animals.

For specialists, it’s obvious that modern animals exist within a continuum that extends into the deep past. It’s also obvious that groups like “mammals” and “reptiles” had starting points, and are embedded within larger, more ancient groups. None of this can be considered common knowledge, but it’s critical to any discussion about the identity or categorization of a given taxon.

Box diagrams are a simple and intuitive way to ground students’ understanding of the diversity of life.

How can educators hope to cover so much ground without confusing, distracting, or alienating their audiences? One option is to use a cladogram, or evolutionary tree. Trees are absolutely the most precise and accurate way to portray relationships over time, but as Torrens and Barahona demonstrate, they are regularly misinterpreted by the public. When I’m dealing with a general audience, I prefer box diagrams like the one above. Boxes within boxes show tiers of relatedness in a way that is more intuitive and easily understood than a tree. Box diagrams allow educators to cover a lot of unfamiliar ground quickly, and it’s easy to test visitors’ comprehension by asking them to point to where an example taxon should be placed. While this visualization of vertebrate relationships lacks a time axis, people can at least grasp the relative order in which each group evolved (fish before amphibians, amphibians before reptiles and mammals, etc).

How Scientists Discover Evolutionary Relationships

Going back to the list of misguided questions at the top of this post, we can generally surmise the thought process that led to each inquiry. The person who asked if whales and marine reptiles are related was classifying based on shared habitat. The person who asked if giraffes evolved from sauropods was classifying based on similar body shape. We can also see classifications based on diet, and based on shared activities, like flight or attacking prey with clawed feet. All these questions reflect a misunderstanding of what kinds of traits researchers look for when working out evolutionary relationships. So how do we quickly and clearly explain which traits are relevant, and which ones are not?

This is a tricky problem, and one I have not found a perfect solution to. The most important distinction is between plesiomorphic and apomorphic traits: plesiomorphic traits are inherited from an ancestral form, while apomorphic traits are novel developments. Put simply, working out a phylogenetic tree is all about grouping organisms based on shared apomorphies. The more apomorphic traits between two species, the more closely related they are. Once introduced, this is a fairly intuitive distinction. You don’t even need to use the jargon – “old traits” and “new traits” will often suffice. Going back to our problem of defining Dimetrodon, we can clarify that the lizardy shape and general toothiness are “old traits” – so they don’t tell us much about what the animal actually is. Instead, scientists look at “new traits”, like the number of postorbital fenestrae, to work out Dimetrodon‘s evolutionary affinities.

All of this is a long-winded way of saying that relating phylogeny to the public is challenging, but very important. Too often, science educators assume visitors have more background than they do, and the discussion comes across as so much moon man talk. Alternatively, educators push past complicated parts too quickly, which leads to confusion or misunderstanding. Ultimately, being a good educator comes down to two things: knowing your content and knowing your audience. Both are equally important, and both need to be practiced and refined in equal measure to ensure successful communication.

References

Macfadden, B.J., Dunckel, B.A., Ellis, S., Dierking, L.D., Abraham-Silver, L., Kisiel, J., and Koke, J. 2007. BioScience 57:10:875-882.

Spiegal, A.N., Evans, E.M., Gram, W., and Diamond, J. 2006. Museums and Social Issues 1:1:69-86.

Spiegel, A.N., Evans, E.M., Frazier, B., Hazel, A., Tare, M., Gram, W., and Diamond, J. 2012. Changing Museum Visitors’ Conceptions of Evolution. Evolution: Education and Outreach 5:1:43-61.

Torrens, E. and Barahona, A. 2012. Why are Some Evolutionary Trees in Natural History Museums Prone to Being Misinterpreted?” Evolution: Education and Outreach 1-25.

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Filed under education, opinion, science communication, systematics

Tagged as education, paleontology, science communication, scientific literacy, systematics

June 20, 2012 · 9:41 am

Communicating Systematics, Part 2

In the previous post, I discussed how phylogenetic trees, while powerful and informative to trained eyes, can be misinterpreted by lay audiences. These misunderstandings are easy to diagnose, but actually finding solutions to the problem is challenging.

In a perfect world, every child would be introduced to evolutionary theory early and often in their obligatory science education, and everybody would be able to interpret phylogenetic trees the way scientists do. This is unlikely to happen anytime soon, especially in the United States, so educators are going to have to get creative. One option is to provide additional information to aid in the interpretation of the diagram. On the surface, adding more information is always an attractive prospect, but unfortunately it does not always work as intended. Attention spans are perilously short, and the goal of a visual representation should be to make the content immediately intuitive and easier to understand.

If conventional shapes and symbols in evolutionary trees are not getting the intended message across to target audiences, then perhaps we need to rethink how we are structuring these trees. I don’t have a catch-all solution, but the following might be enough to at least start a conversation.

Change the shape of the tree

Torrens and Barahona argue that many misinterpretations of trees stem from ideas of essentialism and teleology that are deeply ingrained in and continually reinforced by western culture. Likewise, equating up with good and down with bad is a recurring, internalized motif. Therefore, trees that illustrate evolution and diversification proceeding upward or to the right only encourage presuppositions of linear, goal-oriented evolution.

One solution that has been experimented with (at AMNH, for example) is to draw trees as circles (see below). This eliminates the problem of associating up with good and bad with down, or upward movement with progress. A circular “tree” has no orientation, and thus does not imply any taxa to be better than the rest. Personally, I find circle diagrams confusing to read, but I appreciate what they are intended to accomplish. A diagram of evolutionary relationships could theoretically take any shape, since the crucial information is in the branching order, not the nature of the lines.

A circular tree. From eplanetscience.com.

Be careful with representation of ancestors

Many phylogenetic diagrams place specific fossil taxa at nodes along the tree in order to illustrate the course of evolution. This is informative of general evolutionary trends, but it can also be confusing. As a case in point, I just did an image search for a horse evolution diagram to use as an example, and found that many of the top results came from creationist websites. These sites aren’t worth linking to (although they are easy enough to find), but they erroneously assume that fossil taxa are thought to be directly ancestral to modern Equus caballus. Evolutionary scientists think no such thing, but looking at the image below I can see how that conclusion could be reached.

This diagram of the evolutionary history of horses can lead to the mistaken assumption that earlier species are thought to be directly ancestral to later ones. That polytomy that leads to three unlabeled nodes doesn’t help either.

In a proper cladogram, taxa are only placed at the ends of branches. Direct ancestry is (almost) never inferred, because the scarcity of the fossil record prevents us from ever knowing exactly what evolved into what when. The cladogram below shows the relationships between the seven modern-day species of Equus. Systematists have determined a series of branching relationships based on anatomical and molecular data, and even provide a suggestion of when these divergences occurred, via the time scale. Each node represents a common ancestor that definitely existed, but we will probably never find or identify their fossils.

A cladogram of modern horse species. From Hooper Virtual Natural History Museum.

In this case, I would prefer if books or exhibits for popular audiences nixed images like the first one and instead went with cladograms that do not suggest specific ancestor-descendant relationships. Obviously the cladogram could be spiced up with colors and illustrations, but it is important to use a format that represents precisely what scientists do and do not know.

Always clarify orientation

Proboscidea phylogeny from academic.reed.edu.

Individuals well-versed in evolutionary science automatically read trees from the basal node out to the tips. Typically, and in the elephant phylogeny above, that would be from the bottom up. It can therefore come as a surprise (it certainly did for me) that non-specialists frequently attempt to read phylogenetic trees from left to right. Viewers may assume that the horizontal order of taxa across the top is significant, representing either the course of evolution or time. Neither would be correct, as Mammut on the far left and Mammuthus on the far right were roughly contemporaneous, and Loxodonta africana and Elephas maximus in the middle are the only extant elephants. Although it may not occur to specialists, it is a simple and necessary precaution to label the orientation of the tree and avoid such confusion.

Avoid calling anything “more evolved”

This is more of a nomenclature issue than a visual one, but poor graphics can exacerbate this misconception. All contemporary species, from sponges to frogs to humans, have been evolving for the same amount of time. An amphibian or reptile is not “primitive”; it is just as adapted to its environment as we are. Using this sort of terminology is attractive as a shortcut when referring to less-diverse sister groups to more-diverse clades, but it misrepresents the nature of evolution and should be discouraged.

References

MacDonald, Teresa E. “Communicating Phylogeny: Evolutionary Tree Diagrams in Museums.” 2010. Paper presented at the NARST (National Association for Research in Science Teaching).

Torrens, Erica and Barahona, Ana. “Why are Some Evolutionary Trees in Natural History Museums Prone to Being Misinterpreted?” 2012 Evolution: Education and Outreach 1-25.

Communicating Systematics

In case you forgot, only 15% of Americans polled by Gallup accept that human beings evolved from other animals through natural processes*. This statistic has not changed meaningfully since Gallup started asking this question in 1982. This fact should be in the back of the mind of every science educator, and for that matter, every scientist, each and every day we go to work. It is a scientifically well-established fact that all life has evolved over long periods of time, and that all forms of life are related to each other. This fact is fundamental to our understanding of life on Earth. The goal of both educators and scientists is to expand our knowledge and awareness of our world, and it is therefore disconcerting that so few people are willing (or have had to opportunity to) acknowledge the wealth of information that an understanding of evolution provides.

*A couple complaints about that link. First, the phrasing of the question, “human beings evolved over millions of years from less advanced forms of life” (emphasis mine) is poor, read on for reasons why. Second, belief that humans evolved “with God’s guidance” does not seem like a meaningful distinction to me, and does not suggest a proper understanding of evolution.

The overwhelming number of people who do not accept evolution is intimidating. The fact that our politicians and leaders are often among this number is even more troubling. It can be tempting to retreat into academia and whine about the problem to our peers, or perhaps ignore it entirely. However, 30 years of unchanging results on the Gallup poll indicate that the issue is not going to go away. Both educators and scientists need to take the offensive and directly address misconceptions and misunderstandings about evolution, as well as find effective means to mitigate them.

Phylogenetic Trees

In the world of science education, one of the trickiest issues is supplying appropriate context. Although all good science can be explained in clear, readily-understandable language, most research still requires some background on the Big Ideas in science. Two huge examples are evolution by natural selection and the scientific method, which I briefly discussed here and here. Without an understanding of how scientific ideas or generated or how evolution works, discussing the finer points of, say, feeding strategies of tyrannosaurs is quite pointless. Unfortunately, even among people who accept the fact that evolution is a real phenomenon, this background all too often does not exist.

Educators need to supply the public with the context they need to understand current science, and one good area to focus is the reading of phylogenetic trees. A phylogenetic tree is a branching diagram that depicts inferred evolutionary relationships among organisms. A tree implicitly shows that included organisms descended and diversified from a common ancestor. As such, phylogenetic trees are a visual embodiment of evolutionary theory, and provide an informative narrative of the history of life.

As is often the case, David Hone has already provided a wonderful explanation of how scientists construct trees and how to read them correctly, so I’ll just drop that link and move on. The problem is that although evolutionary trees are often used to convey ideas in museum displays and general interest science articles, many lay-viewers are interpreting them inaccurately. Reading a tree requires practice and expertise that shouldn’t be taken for granted, because misinterpretations only provide fodder for the anti-evolution/anti-science lobby. Let’s go through the common misinterpretations one at a time (many of these are discussed in Torrens and Barahona 2012, a few are my own additions).

Evolution is goal-oriented. In fact, evolution is not progressive, but is the product of organisms adapting to their specific environment. When that environment changes, taxa that were once well-adapted often die out. Being “well-evolved” is therefore fluid and transitory state. The misconception of directed evolution is probably related to ingrained western religious views of human superiority over nature. Rather annoyingly, cultural anthropologists often buy into the erroneous idea of progressive evolution, and attempt to use it as evidence that science is but one of many equally correct world-views.

There is a “main line” of evolution. This is largely the product of late 19th century drawings of trees of life which used literal trees as the basis of the diagram. Most famously, German natualist Ernst Haeckel illustrated the Systematischer Stammbaum des Menschen in his book Anthropogenie in 1874. In this drawing, the diversity of life is overlaid on a tree, which has a thick trunk running straight up to humans and other primates at the top. Again, this plays into concepts of human superiority and inevitability that have nothing to do with biological evolution.

Some contemporary species are more or less evolved than others. All contemporary species, from sponges to frogs to humans, have been evolving for the same amount of time, and are just as adapted to their environments as we are. Unfortunately, placing humans or mammals at the top or the right of phylogenetic trees seems to be an unshakable habit, even for systematists, which only encourages the notion that these taxa are somehow better.

Similarity among taxa always implies relatedness. Determining evolutionary relationships is a complex process. Modern systematists use huge matrices of independent characters to calculate the most parsimonious trees. Furthermore, Hennigean cladistics requires that relationships only be determined using synapomorphies (shared derived traits) rather than plesiomorphies (shared primitive conditions). Although the salmon and the lungfish below superficially appear more like one another than the cow, similarities like a fishy shape and a lack of a neck are primitive conditions, not specializations. The synapomorphies shared by the lungfish and cow, such as jointed limbs and the ability to breathe air, inform us that they shared a more recent common ancestor than either did with ray-finned fish.

A counter-intuitive cladogram. Subjective similarity does not always mean relatedness.

Change only occurs at nodes. The nodes in a phylogenetic tree do not represent literal evolutionary events. Rather, evolution is a continuous process. This is a case where I like to ask people who make this misconception, “how could we know that?” This can get people thinking about what evidence is available to scientists, what conclusions can be reached from these data, and what isn’t known.

Example taxa illustrated lower in the tree represent direct ancestors of taxa higher in the tree. It can be helpful to use fossil species to illustrate the general state of an evolutionary lineage at varying points in time (this is done all the time with diagrams of horse evolution). However, with few exceptions, the incomplete nature of the fossil record makes it impossible to know exactly which species were directly ancestral to others.

Traditional Linnean categories are directly applicable to trees. In fact, most (sensible) modern systematists prefer the cladistic methodology, which requires that all groups be monophyletic (that is, made up of all descendents of a common ancestor, with no exclusions). For example, the traditonal Linnean definition of reptiles, which includes turtles, lizards, snakes, tuataras and crocodiles, is not monophyletic, because any cladistic unification of these taxa would also have to include birds.

The traditional definition of reptiles, which excludes birds, is paraphyletic.

This went on a bit longer than I expected, so I’m going to leave these issues hanging for the time being. But do not fret, I will finish this train of thought soon with a discussion of potential solutions to these misinterpretations that have been attempted, and some that may be attempted in the future.

References

MacDonald, Teresa E. “Communicating Phylogeny: Evolutionary Tree Diagrams in Museums.” 2010. Paper presented at the NARST (National Association for Research in Science Teaching).

Torrens, Erica and Barahona, Ana. “Why are Some Evolutionary Trees in Natural History Museums Prone to Being Misinterpreted?” 2012 Evolution: Education and Outreach 1-25.

Tag Archives: systematics