Ambiguity in phylogenies

Jul 31 2012 Published by under Uncategorized

As I noted in an earlier post, thinking about branching phylogenies (which represent variational evolution) is very much an acquired skill that needs training. Without it, people are prone to mis-reading phylogenies. Understanding and perception are highly inter-twined, so that the way one "reads" a phylogeny influences understanding, but prior understanding also influences the way one "reads" a phylogeny in the first place.

This problem has been studied by many researchers; and I have listed some of them in the Further Reading below. In this post I will cover just a few of their more important findings about the most common mis-interpretations made by non-experts.

The basic theme will be familiar to you from my previous blog posts — people look for transformational evolution not variational evolution when they view a phylogeny. It is easier to grasp a simple linear sequence than it is to comprehend an inter-linked set of lineages. However, there are a number of ways in which a single lineage can be "extracted" from a phylogeny, either intentionally or unintentionally, and I will briefly introduce these to you in this post.

There have been a number of studies of students taking introductory biology courses at tertiary institutions (mostly in the U.S.A.), aimed at identifying the "major misconceptions" entertained by these students. Certain basic problems are discussed by almost all of the authors listed below, and I assume that these are therefore the ones that we need to be most aware of and guard against.

As I noted in the previous post, I think that the ultimate source of these problems is evolutionists themselves, as they sometimes present ambiguous evolutionary diagrams, ones that are left open to an unintended transformational interpretation in addition to the intended variational one. This problem can be corrected only by the evolutionists themselves.

The first issue is the one I identified above, that people incorrectly emphasize a single lineage in the phylogeny, which they see as the "main branch" of the tree, with the other lineages as side branches. People have a preference for simplified stories with unambiguous beginnings and ends, and a single lineage provides this.

As an example, consider the first phylogeny. It shows six (unlabeled) taxa at the top, which represents the present, and a single ancestor at the bottom, which is the past. The lineages branch progressively from the ancestor to the current taxa. The order of the branching indicates the relationships among the taxa, without any intended emphasis on any one lineage.

A phylogeny of six (unlabeled) taxa.

However, many people do apparently interpret this type of diagram as having a main lineage, with the other lineages as side branches, as shown by the bold line in the next figure. That is, the taxon on the right is seen (incorrectly) as the "goal" of an evolutionary series, rather than merely being one of six equal taxa linked by branches. Technically, this is an example of "good continuation", where a straight line can be seen as continuing though the diagram and is therefore treated as a single entity.

The same phylogeny, with one lineage emphasized.

The research shows that this potential mis-interpretation can often be avoided by using an angled or circular diagram, rather than one with sloping lines. A comparison of a sloped and angled phylogeny is shown in the next picture. The sloped diagram potentially has a main lineage leading to E, but this is not as obvious in the angled diagram, because there is no continuous straight line running through the diagram.

A phylogeny of five taxa, drawn in two different way.

Interestingly, circular trees are apparently the representation most disliked by students, but this type also gets interpreted correctly most often. It seems that the ambiguity is reduced, thus leading to correct interpretation, but the observer has to work harder because their (incorrect) preconceptions can't come into play.

The same phylogeny drawn in a circular manner.

Another concern is that phylogenies are sometimes drawn in what is called a "ladderized" manner that unnecessarily emphasizes a "main branch with side-branches", as shown on the left of the next picture. The non-ladderized version on the right shows exactly the same branching sequence but re-arranges the order of the taxa to reduce the ladder effect.

A ladderized version of a phylogeny, on the left, compared to a non-ladderized one.

Another potential problem is having the observer locate a well-known organism in the phylogeny and then treating the lineage to that organism as the "main branch" of the tree. This is shown in the next picture, where the non-humans have been visually relegated to side-branches. There may be little we can do to stop this, at least in cases where Homo sapiens is in the phylogeny.

A phylogeny of some vertebrates, with a well-known lineage highlighted.

The next potential problem is that people often pay more attention to the order of the taxa at the tips of the phylogeny than they do to the branching order of the lineages. Most commonly, they interpret a transformation series from left-to-right across the diagram or from top-to-bottom. That is, the organism in the top-left corner is treated as being the ancestor, with an evolutionary series starting there. Each taxon is then interpreted as being most closely related to the taxon next to it, rather than using the branching order to interpret the genealogical relationships. That is, there appears to be a natural progression in the order of the taxa, and this pattern dominates over the branching pattern.

Two ways of drawing the same phylogeny of six taxa are shown in the next picture. In the first diagram the taxa are arranged in an order that represents the most common preconception about evolutionary change of vertebrates, so that mis-interpretation is quite likely. In the second diagram there is likely to be much less incentive to see an evolutionary series from left-to-right, so that the branching order can take precedence in displaying the relationships.

Two phylogenies of the same set of six organisms. The top one is often mis-interpreted as showing an evolutionary series from left-to-right.

The top-left corner is a key location in any visual interpretation, particularly for anyone whose native language is read left-to-right and top-to-bottom. However, the ancestor is not one of the tips, and the order of the tips has no special meaning.

This potential problem particularly occurs when there is no direct reminder about the direction of time in the phylogeny, since it is then left to the observer to deduce it. If this is combined with an anthropocentric ordering of the taxa (eg. humans at the top-right corner), then clearly there is enormous potential for mis-understanding. This will also be true if the observer has the idea that "simpler" (or "primitive") organisms have evolved into more "complex" (or "advanced") ones, and the supposedly simpler ones are presented at the left.

One of the most blatant examples of this problem occurred in 2008, when the highly ranked journal Nature put out a press release concerning a paper they had published, which concerned the completion of the sequencing of the platypus genome. The press release contained a picture of a phylogeny, supposedly illustrating the evolutionary relationships of various animal species in various stages of having their complete genomes sequenced, as shown here.

Phylogeny from the Nature press release.

Given what I have said above, you can see that almost everything about the way this phylogeny is drawn is blatantly inappropriate. First, this is the sloped version of a phylogeny; second it has a sequence of organisms from top-to-bottom leading to humans; and third, just in case you missed the sequence, it is emphasized by a set of arrows down the left side. The branching sequence appears to be the least important thing for whoever drew this diagram. Worst of all, the branching sequence is wrong, as well!

And just to add salt to the wound, when the equally highly ranked journal Science covered the same topic they published a picture with the same wrong phylogeny! At least this one is drawn in the square manner, and does not have the inappropriate arrows. (I am grateful to the evolgen blog for drawing my attention to these two pictures.)

Phylogeny from Science magazine.

My basic theme in these posts has been that evolutionists are, in some ways, their own worst enemy, because they often use potentially ambiguous language and ambiguous pictures when communicating. However, most of the research studies listed below offer practical advice for overcoming ambiguity and mis-interpretation, and I have indicated some of the suggestions above. The point is that merely instructing someone in how to interpret a diagram is insufficient for understanding — the design of the diagram also needs to take into account the perceptual viewpoint of the viewer, and be adjusted to ensure that it is unambiguous.

Unfortunately, the problems listed above commonly manifest themselves both in textbooks and in museums, as well as in books specifically written for the general public. I have listed below some of the formal studies that have demonstrated that this is a widespread problem. Not unexpectedly, it is diagrams of hominoid relationships that suffer the worst treatment at the hands of the educators.

The example shown below is taken from Novick, Shade & Catley (2011). Part (A) of the figure is taken from a textbook (published in 2002), and it incorrectly emphasizes a transformational evolutionary series through time, leading from extinct horses (at the bottom) to the modern ones (at the top). Part (B) is a sloped version of the phylogeny, which inadvertently emphasizes the lineage to the modern horse Equus, both by having a straight line leading to Equus and by having a temporal sequence lead from left to right. It is reported that sloped diagrams are the most common form found in textbooks! Part (C) is the same phylogeny drawn in the angled style, which is an improvement over the other versions, but it still has the inappropriate left-right temporal sequence (especially with the horses running left-to-right!). So, even this last version leaves itself open to ambiguous interpretation.

Three ways of drawing the phylogeny of horses. The figure is adapted from Novick, Shade & Catley (2011).

Clearly, people bring certain pre-conceptions into any educational setting, which may not be appropriate for that setting. These natural pre-conceptions come from their prior training and from their own personal experiences. What is being learned will be fitted into the pre-existing thought processes, and what is said and shown will be interpreted in the light of the pre-conceptions. Ambiguity of words and icons is fatal under these circumstances, as it allows multiple interpretations, most of which are not intended by the presenter. Sadly, the studies done to date make it clear that ambiguity on the part of evolutionists simply re-inforces pre-conceptions rather than providing new knowledge about evolutionary biology.

Interestingly, this problem of ambiguity is not confined to evolutionary biology. In his first book of anecdotes about his life (Surely You're Joking, Mr Feynman! 1985), the Nobel-prize-winning physicist Richard P. Feynman criticized almost all of the physics schoolbooks available in the state of California at the time he was on the State Curriculum Commission. His comment was:

"Everything was written by by somebody who didn't know what the hell he was talking about, so it was a little bit wrong, always! ... [The books] were false. They were hurried. They would try to be rigorous, but they would use examples which were almost OK, but in which there were always some subtleties. The definitions weren't accurate. Everything was a little bit ambiguous — they weren't smart enough to understand what was meant by 'rigor'. They were faking it. They were teaching something they didn't understand ... And how we are going to teach well by using books written by people who don't quite understand what they're talking about, I cannot understand. I don't know why, but the books were lousy; UNIVERSALLY LOUSY!"

This is a comment that all textbook authors should heed. Understanding phylogenies as representations of evolutionary relatedness is a cognitively complex task that requires instruction, and ambiguity can play no part in that process. Moreover, diagrams of all sorts are important in science, not just as tools for communicating ideas but as tools for learning and reasoning. If one is to be a biologist, reasoning and communicating about evolution is essential, and this can only be done if one can interpret a phylogeny correctly.

To me, the most surprising result of the research listed below is that students who had previously completed a course in evolution were not necessarily any better at interpreting phylogenies than were other students. Apparently, evolution students are not taught phylogenetics, at least in a way that allows the students to connect their knowledge of evolutionary biology (usually micro-evolutionary processes) to the study of phylogeny (a macro-evolutionary process). So, phylogenetics ends up being taught as a subject independent of evolutionary biology, which is a ridiculous situation.

Further Reading

Distorted pictures occur in several ways in modern evolutionary biology. This topic has received considerable attention in the literature, and there are a number of very readable expositions of various parts of it.

Gregory T.R. (2008) Understanding evolutionary trees. Evolution: Education and Outreach 1: 121-137.

O'Hara R.J. (1992) Telling the tree: narrative representation and the study of evolutionary history. Biology and Philosophy 7: 135-160.

Crisp M.D., Cook L.G. (2005) Do early branching lineages signify ancestral traits? Trends in Ecology and Evolution 20: 122-128.

Krell F.-T., Cranston P.S. (2004) Which side of a tree is more basal? Systematic Entomology 29: 279-281.

Omland K.E., Cook L.G., Crisp M.D. (2008) Tree thinking for all biology: the problem with reading phylogenies as ladders of progress. BioEssays 30: 854-867.

Sandvik H. (2009) Anthropocentrisms in cladograms. Biology and Philosophy 24: 425-440.

Communication with non-experts has been a fundamental theme in these blog posts. A number of people have investigated how well evolutionists communicate in various educational settings, such as in the classroom, in textbooks, and in museums.

Catley K.M., Novick L.R. (2008) Seeing the wood for the trees: an analysis of evolutionary diagrams in biology textbooks. BioScience 58: 976-987.

Clark C.A. (2001) Evolution for John Doe: pictures, the public, and the Scopes Trial debate. Journal of American History 87: 1275-1303.

Hellström N.P. (2011) The tree as evolutionary icon: TREE in the Natural History Museum, London. Archives of Natural History 38: 1-17.

Ladouceur R. (2010) 20th century high school biology textbooks reviewed and ranked. http://www.textbookhistory.com/?p=52

MacDonald T., Wiley E.O. (2012) Communicating phylogeny: evolutionary tree diagrams in museums. Evolution: Education and Outreach 5: 14-28.

Torrens E., Barahona A. (2012) Why are some evolutionary trees in natural history museums prone to being misinterpreted? Evolution: Education and Outreach 5: 76–100.

Other researchers have carefully investigated how students respond when confronted with a phylogeny, and what things can be done to improve their understanding and interpretational skills.

Baum D.A., Smith S.D., Donovan S.S. (2005) The tree-thinking challenge. Science 310: 979-980.

Catley K.M., Novick L.R., Shade C.K. (2010) Interpreting evolutionary diagrams: when topology and process conflict. Journal of Research in Science Teaching 47: 861-882.

Gendron R.P. (2000) The classification & evolution of caminalcules. American Biology Teacher 62: 570-576.

Goldsmith D.W. (2003) Presenting cladistic thinking to biology majors & general science students. American Biology Teacher 65: 679-682.

Halverson K.L., Pires C.J., Abell S.K. (2011) Exploring the complexity of tree thinking expertise in an undergraduate systematics course. Science Education 95: 794-823.

Meir E., Perry J., Herron J.C., Kingsolver J. (2007) College students’ misconceptions about evolutionary trees. American Biology Teacher 69: e71-e76

Miesel R.P. (2010) Teaching tree-thinking to undergraduate biology students. Evolution: Education and Outreach 3: 621-628.

Morabito N.P., Catley K.M., Novick L.R. (2010) Reasoning about evolutionary history: post-secondary students' knowledge of most recent common ancestry and homoplasy. Journal of Biological Education 44: 166-174.

Novick L.R., Catley K.M. (2012) Reasoning about evolution’s grand patterns: college students’ understanding of the Tree of Life. American Educational Research Journal 49: in press.

Novick L.R., Catley K.M., Funk D.J. (2010) Characters are key: the effect of synapomorphies on cladogram comprehension. Evolution: Education and Outreach 3: 539-547.

Novick L.R., Shade C.K., Catley K.M. (2011) Linear versus branching depictions of evolutionary history: implications for diagram design. Topics in Cognitive Science 3: 536-559.

Sandvik H. (2008) Tree thinking cannot taken for granted: challenges for teaching phylogenetics. Theory in the Biosciences 127: 45–51.

3 responses so far

  • Isabel says:

    " This will also be true if the observer has the idea that "simpler" (or "primitive") organisms have evolved into more "complex" (or "advanced") ones, and the supposedly simpler ones are presented at the left."

    Thanks for the reference list. Do you know of any articles that specifically tackled the issue of supposedly "simple" vs "complex" taxa? I have not even been able to find a definition of "simple" or "complex" used in this context.

    Also, as I have mentioned, this is the only way I have ever encountered plant evolution taught. Do you know of any exceptions?

    Check out this Wired-Science blog post title for example. Yet in the article there is no evidence that the algae are "simple".

    http://www.wired.com/wiredscience/2011/02/seaweed-fossils-edicaran/

    • Isabel, In the Wired blog post "simple" appears only in the title, which suggests to me that the title and the main text are quite separate! Anyway, algal genomes are quite complex even if the organism looks simple to us. For your first question, the reference by Crisp & Cook talks about plants. However, the explanation at the Understanding Evolution website may be more accessible to you. As for your second question, I think that the best of the current crop of plant books that cover this topic is: Walter S. Judd, Christopher S. Campbell, Elizabeth A. Kellogg, Peter F. Stevens, Michael J. Donoghue (2007) Plant Systematics: A Phylogenetic Approach, Third Edition. Sinauer Associates. /David

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