tag:blogger.com,1999:blog-85733078119006762352024-03-03T16:25:54.210-08:00For the love of treesStacey Smithhttp://www.blogger.com/profile/00476159407653766652noreply@blogger.comBlogger8125tag:blogger.com,1999:blog-8573307811900676235.post-25626876327030504722022-04-21T10:57:00.007-07:002022-04-21T11:53:45.608-07:00Anything but the line-up<p></p><p class="MsoNoSpacing"></p><p class="MsoNoSpacing"><span style="font-family: arial;">You all know I’m always pondering
how progressive thinking sneaks into how we talk about evolution. And how if we could break some of these
habits, we might begin to dismantle the ladder-of-life, which is so deeply
engrained. Here is a common thing I see in lots of science communication
that I think is one of these (relatively) easy to break habits – lining up some
organisms when you talk about how some *trait* evolves. Let’s say you were
talking about the evolution of multicellularity and went with a diagram like
this: <o:p></o:p></span></p>
<p class="MsoNoSpacing"></p><div style="text-align: center;"><span style="font-family: arial; font-size: medium;"> <u>Evolution of Multicellularity</u></span></div><o:p><span style="font-family: arial;"><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEh7MvzT8GhopEVNryboVIZ8pTYjv02r6C3GkynWkhBVQNBisUxizkBNiO6urUXfeYIjML4fRWlgwVk1gE1zXytM0qYDLhn0Yw-P77vZ0ptsHphc9A2XLmTIGKR5JoPLVQk6V-UNkSwN8Q75K9Jvo3oZp9nvhFozPNWbslwo-swT9ju1qC7V-inNmJeV" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="241" data-original-width="736" height="105" src="https://blogger.googleusercontent.com/img/a/AVvXsEh7MvzT8GhopEVNryboVIZ8pTYjv02r6C3GkynWkhBVQNBisUxizkBNiO6urUXfeYIjML4fRWlgwVk1gE1zXytM0qYDLhn0Yw-P77vZ0ptsHphc9A2XLmTIGKR5JoPLVQk6V-UNkSwN8Q75K9Jvo3oZp9nvhFozPNWbslwo-swT9ju1qC7V-inNmJeV" width="320" /></a></div></span></o:p><p></p><p class="MsoNoSpacing"><span style="font-family: arial; font-size: small;">Show this and the audience
is likely to walk away with any number of ladder-y misconceptions. Or feel that
any ladder-y notions they came with are totally fine. Like humans evolved from 'simple' things like bacteria. Like being unicellular is less ‘advanced’. Like
humans are the most complex, really impressive, best species so evolution has
stopped. We could go on, but what would be some ways to dismantle any of these
and still talk about what we wanted talk about? Here’s an easy one – refocus on
the character states!</span></p><p class="MsoNoSpacing"><span style="font-family: arial; font-size: small;"></span></p><div class="separator" style="clear: both; text-align: center;"><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEiho2ym_S8vN83ACkvMupAbHs5tyl9PmsOny-Rs9flweWktoshRa77aCd92hqmvzzpm7NjZPUyNKpZSlTXBOtzwgRg3CqGX8quSlqW5sJOMDMihMZKSJhi9jwJHK3cqvV3iIT99TbCOUkXhwd5kd_C-VjgbiX4k5DnAIyA9V3vRaRNIAhQc4gkiFzF_" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="217" data-original-width="800" height="96" src="https://blogger.googleusercontent.com/img/a/AVvXsEiho2ym_S8vN83ACkvMupAbHs5tyl9PmsOny-Rs9flweWktoshRa77aCd92hqmvzzpm7NjZPUyNKpZSlTXBOtzwgRg3CqGX8quSlqW5sJOMDMihMZKSJhi9jwJHK3cqvV3iIT99TbCOUkXhwd5kd_C-VjgbiX4k5DnAIyA9V3vRaRNIAhQc4gkiFzF_=w353-h96" width="353" /></a></div><br /></div><span style="font-family: arial; font-size: small;">Now this is still feeling
pretty progressive, but perhaps the notions that some living taxa are ancestors
of other living taxa are disrupted a little? I also suspect that labeling these states
might trigger us to wonder about the evolutionary complexities here.</span><span style="font-family: arial; font-size: small;"> </span><span style="font-family: arial; font-size: small;">How many times have these kinds of transitions happened? Is evolution really so directional or can lineages revert to
being unicellular?</span><span style="font-family: arial; font-size: small;"> </span><span style="font-family: arial; font-size: small;">Are these states
fairly thought about as bins or is it more of a continuum? Now this, this is
really thinking about evolution. Understanding such character transformations was
a primary motivation for developing phylogenetic methods in the first place!</span><p class="MsoNoSpacing"><span style="font-family: arial;">And in fact we have plenty
of information to suggest that the stepwise directional path above is not right. We know that there have been evolutionary transitions
to <i style="mso-bidi-font-style: normal;">and</i> from multicellularity. There are plenty of lineages where we have a heck of a time trying to classify
them because the cells sometimes stick together and sometimes go their own
ways. So if we are going to be fair, it’s probably more like a spectrum or even
something non-linear altogether. What’s for sure is that we will never
understand the diversity of life forms, nor how and why this diversity came to
be, if we enter with the ladder-of-life mindset at the top.<o:p></o:p></span></p><p class="MsoNoSpacing"><span style="font-family: arial;"></span></p><div class="separator" style="clear: both; text-align: center;"><span style="font-family: arial;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEgsGdU9l28rVKMqHas88xidNpKOlBS2bBn8UIc6LUFkOLj7wuGOjZHSbFD4mMUKhsDToyUbcKxUDQ0CWZ8sJwpuQCbsJXNKSUhO7-aIEeY5YliaSB_dq8CtOZFBzAYbyg2bZrbsBiw9bas1CBnhZ_r_L1ALxFM4CxWXK8OpCJzBKwJIhXkNIf6o3UJt" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="106" data-original-width="599" height="57" src="https://blogger.googleusercontent.com/img/a/AVvXsEgsGdU9l28rVKMqHas88xidNpKOlBS2bBn8UIc6LUFkOLj7wuGOjZHSbFD4mMUKhsDToyUbcKxUDQ0CWZ8sJwpuQCbsJXNKSUhO7-aIEeY5YliaSB_dq8CtOZFBzAYbyg2bZrbsBiw9bas1CBnhZ_r_L1ALxFM4CxWXK8OpCJzBKwJIhXkNIf6o3UJt" width="320" /></a></span></div><span style="font-family: arial;"><br /></span><span style="font-family: arial; font-size: small;">My broader point here is to
say we do our field no favors by playing on misconceptions. I get it, we want
to make things simple, draw on ideas that will ‘click’ with audiences. But we
are selling evolution so short when we do it.</span><span style="font-family: arial; font-size: small;">
</span><span style="font-family: arial; font-size: small;">I am convinced that any talk or paper can be just as compelling, if not
more, by stepping away from the linear narrative. I know we can handle breaking
the norms and our audiences can too.</span><p></p><br /><p></p><p></p>Stacey Smithhttp://www.blogger.com/profile/00476159407653766652noreply@blogger.com0tag:blogger.com,1999:blog-8573307811900676235.post-4491503489094731062018-04-08T15:00:00.001-07:002020-09-15T20:35:30.348-07:00Tree responsibly: Part 2In part 2 of this series, I want to talk about how we can draw trees that promote tree thinking instead of undermining it. But first let’s consider whether we can or should worm our way out of this possibly time-consuming task. You might say, well, I just draw the trees – it’s the viewer’s job to interpret them correctly.* However, it is well established that the many members of any audience (whether students or practicing scientists) are not trained in tree-thinking and will come to incorrect conclusions about what a tree is meant to convey. <br />
<br />
The other option is to warn the audience that the way the tree is drawn is likely to evoke some misconceptions. Indeed, this is essentially the approach taken on the <a href="https://www.evogeneao.com/en/learn/tree-of-life" target="_blank">evogeneao</a> website, which has an interactive tree of life and other teaching resources. This page has a long section about distortions and limitations that explains that their tree is drawn to tell the human’s story and thus makes it look like evolution is goal-oriented (with the goal being humans). I'm glad they included this section and it may provide its own learning goal (leading the reader to say, how does this tree make me think that? How could it be drawn <i>not</i> to make me think that?). But I remain nervous that readers won’t scroll and dig into what may be viewed as <span style="font-size: x-small;">details</span>, <span style="font-size: xx-small;">details</span>. So my opinion is that if we want readers to interpret trees correctly, we should actually draw them in ways that dispel misconceptions and encourage correct interpretation. Here are some of my suggestions and related thoughts:<br />
<br />
First, those of us that spend a lot of time wandering the phylogenetics literature know that trees more often look like what’s on the left than what’s on the right.<br />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiXHRqh-5cwt_iOpvTejLwc3lZJ4flAswqAoaq8PQ9SOWKVdY25rh6mXr2SENt-gQMnk6AP12_On1xi1-ELdaKj4zIrUU3wAA3m6kMFP2LHxxXhRcYXgg9w0cl8VS2z403cTxowLJuIgP4/s1600/RealnotReal.jpg" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="235" data-original-width="279" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiXHRqh-5cwt_iOpvTejLwc3lZJ4flAswqAoaq8PQ9SOWKVdY25rh6mXr2SENt-gQMnk6AP12_On1xi1-ELdaKj4zIrUU3wAA3m6kMFP2LHxxXhRcYXgg9w0cl8VS2z403cTxowLJuIgP4/s1600/RealnotReal.jpg" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Tree on the left adapted from <a href="https://www.nature.com/articles/s41586-018-0012-7/figures/7" target="_blank">here</a>. </td></tr>
</tbody></table>
<span style="white-space: pre;"> </span><br />
And what’s on the right looks a lot more like what’s in textbooks, review articles, and popular science. So guess what’s in the middle? People making choices about which taxa to show, how to draw the tree, and what story they want to tell with the tree. Given that, let’s talk choices.<br />
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<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgq6XTmbQrm48ldLMGf4bEA3cWGbZjmSqKugGR9spz0mbb78Lk6czmx3bRFKLCBcjuS4zND9ppdQi3wU06DBOvrcTHzQP-g7EWTQ2CuEH_Ts8xI5aF15h-29P5C0OW7D8w5f18os4bMAQo/s1600/LaddervsUltra.jpg" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="98" data-original-width="434" height="72" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgq6XTmbQrm48ldLMGf4bEA3cWGbZjmSqKugGR9spz0mbb78Lk6czmx3bRFKLCBcjuS4zND9ppdQi3wU06DBOvrcTHzQP-g7EWTQ2CuEH_Ts8xI5aF15h-29P5C0OW7D8w5f18os4bMAQo/s320/LaddervsUltra.jpg" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><br />Ladder-y versus ultrametric</td></tr>
</tbody></table>
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Both of the trees above have the same topology (implying the same set of relationships), but the one on the left is much more likely to trigger ladder-thinking because some of the tips are higher and others are lower. The easy fix is to make the tree ultrametric, as on the right, helping to communicate that all taxa are extant (as they are in this pretend example) and that all have continued to evolve towards the present. <br />
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We also choose which taxa to include, and by simply choosing those which make our trees a little more <a href="http://ib.berkeley.edu/courses/ib200b/lect/ib200b_lect16_Nat_Hallinan_Lindberg_tree_shape2.pdf" target="_blank">balanced</a>, we can make it harder to view any tip as ‘basal’. Berkeley's Understanding Evolution site has a quite a few other <a href="https://evolution.berkeley.edu/evolibrary/article/0_0_0/evotrees_zoos_02" target="_blank">nice tips</a> for making trees that are less prone to misinterpretation.<br />
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEim1DeLqefBq0P5OjEUJRk2wPGUzMklkQUZ-xekBC3qNWsAwE1du7Bf18_Vym3ILfA-DfrJqOyiwHdqHSvRRtlRhHzPEMBeyEOIPCL-4ut-MhRb4NwZe6RYxfCJU6lqWzShYF-4pSV2axs/s1600/Balance.jpg" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="149" data-original-width="576" height="82" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEim1DeLqefBq0P5OjEUJRk2wPGUzMklkQUZ-xekBC3qNWsAwE1du7Bf18_Vym3ILfA-DfrJqOyiwHdqHSvRRtlRhHzPEMBeyEOIPCL-4ut-MhRb4NwZe6RYxfCJU6lqWzShYF-4pSV2axs/s320/Balance.jpg" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><br />Maximally unbalanced versus more balanced (oh and I rotated it at one node)</td></tr>
</tbody></table>
<br />
So now a suggestion that is possibly more painful, which is that those of us that estimate phylogenies take on more of the burden of creating education-friendly, misconception-fighting, biology-celebrating tree diagrams. Work on flatworms? Awesome! Make a lively worm-y phylogeny for your homepage that can be freely downloaded and shared. Put it on your lab t-shirt! Put it in the corner of your lab posters! Take it to outreach events! I know that most of us phylogeneticists are not graphic designers, but I think the dividends to come from one glorious, engaging figure are worth the time (and/or monetary investment). And we have such a long way to go to outnumber the <a href="https://en.wikipedia.org/wiki/March_of_Progress" target="_blank">'march of progress' </a>type images that dominate the representation of evolution.<br />
<br />
And my last thought is just that I wish that some kind programmer would make a truly easy piece of software to draw trees for educational purposes. Because if you are wondering what I do to make tree figures for teaching (and blogging), I create a pretend dataset in Mesquite and manipulate the tree to fit my purposes. Which sometimes require tinkering in Illustrator. Most teachers don’t have the time to learn Mesquite solely for this purpose, much less the funding for Illustrator licenses. Please feel free to reply to this blog if there are programs you think meet this need.**<br />
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In closing, thanks (I guess) to Matt Hahn for trolling me with tree figures to provoke me into writing about this.<br />
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*And a few years ago that was more or less my view. We can’t ‘protect’ everyone from seeing trees that foster misconceptions, so it’s better that we teach them how to read trees. We certainly do need to do the latter, but it’s not enough. People who are experts in this area <a href="https://onlinelibrary.wiley.com/doi/full/10.1111/j.1756-8765.2009.01077.x" target="_blank">also think so</a>.<br />
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**I am aware of FigTree and TreeEdit, but I still think these are probably too fiddly as they require a user to start with a tree file. I’m picturing more like the user says, "I need X tips" and then they move the branches, annotate branches with words, change formats, etc. Mesquite can do most of theses things, but having taught with it, I don’t think it’s reasonable to expect a teacher to wander through the menus just to make a vertebrate phylogeny that’s less ladder-y than what is in the textbook. I also don't think it would be fair to put all the burden on Mesquite, which already serves many needs in the systematics community and does so beautifully. Maybe someone who is good at Java could make a MesquiteLite to pull out and adapt the drawing tools. Even better if it could be an interactive website that students could use! But I'm getting ahead of myself...<br />
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Stacey Smithhttp://www.blogger.com/profile/00476159407653766652noreply@blogger.com1tag:blogger.com,1999:blog-8573307811900676235.post-76376670662927025642018-04-08T13:27:00.000-07:002018-04-09T09:54:55.914-07:00Tree responsibly: Part 1A few years ago I was at a talk that opened with an evolutionary context for the study and had a tree that looked about like this:<br />
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<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEguweMrnRoRYHgEUPOYYQ4cAMUnAulBC21T9cX1XtL1FzJts5jJPUv928LWx1sEL4PTMGcdmhYcX853ZnlcYzsw2AElKdfaDzzDV-8BWE7o4xyDKN5psQQL44F5kFVTUfOVAMrJTyL_o_E/s1600/LadderTree.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="110" data-original-width="206" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEguweMrnRoRYHgEUPOYYQ4cAMUnAulBC21T9cX1XtL1FzJts5jJPUv928LWx1sEL4PTMGcdmhYcX853ZnlcYzsw2AElKdfaDzzDV-8BWE7o4xyDKN5psQQL44F5kFVTUfOVAMrJTyL_o_E/s1600/LadderTree.jpg" /></a></div>
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I thought <a href="https://tenor.com/view/scoobydoo-gif-4303248" target="_blank">ruh-roh</a>, I feel some basal-ancient-ladderness coming on. And sure enough it was primitive [living] taxa from there on out. This got me thinking about the relationship between tree drawing and tree thinking. This relationship is well established in the science education literature, which has demonstrated that certain tree formats are more likely to trigger misconceptions about evolution (e.g., <a href="https://onlinelibrary.wiley.com/doi/full/10.1111/j.1756-8765.2009.01077.x" target="_blank">Novick et al. 2011</a>). Viewers are likely to see the tips that are literally 'lower' on a tree like the one above as being evolutionarily lower*. Moreover, they are likely to interpret this diagram not as a branching history but as a replacement series with a progressive evolutionary story. Heck, it is almost begging readers to view evolution as a timeline. If you let it keep slipping, that’s right where you end up.<br />
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhMuX1l8P4YSPSJ8KdFcifx-28xPCmS7HK-YzGQGQzzOduh84sh2bk3zPdaEMGCYAGfOD6kcZvdjn2OId7erj8epzyNzb3UJLelEAUusvcR0_ZqSSQYYgaG44-iMVG5LOOFxgYmUNTcwBw/s1600/SlippingTrees.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="251" data-original-width="198" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhMuX1l8P4YSPSJ8KdFcifx-28xPCmS7HK-YzGQGQzzOduh84sh2bk3zPdaEMGCYAGfOD6kcZvdjn2OId7erj8epzyNzb3UJLelEAUusvcR0_ZqSSQYYgaG44-iMVG5LOOFxgYmUNTcwBw/s1600/SlippingTrees.jpg" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><br />
Going, going, gone.</td></tr>
</tbody></table>
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It is then a very short hop for viewers to interpret that ‘tree’ as something like this.<br />
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<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhBgf-P0Vs6I4zwaiCtr4Zdcql8dlkPQX8F70RprBcMx5f8l0yafG2YcXjrCZMCqWiXwIZmDP0Kf2HhAAqQ_pc2G64umF-SPvW7S0M90N-PIJUR5QDYAIF6vDJypO65nzh2ylLjokiib68/s1600/BadArrow.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="119" data-original-width="265" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhBgf-P0Vs6I4zwaiCtr4Zdcql8dlkPQX8F70RprBcMx5f8l0yafG2YcXjrCZMCqWiXwIZmDP0Kf2HhAAqQ_pc2G64umF-SPvW7S0M90N-PIJUR5QDYAIF6vDJypO65nzh2ylLjokiib68/s1600/BadArrow.jpg" /></a></div>
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As I have argued before, this terrible depiction of evolution and its many off-shoots (like <a href="https://c1.staticflickr.com/6/5057/5483369103_0b27619987_b.jpg" target="_blank">this</a>) are not only misleading but <a href="http://for-the-love-of-trees.blogspot.com/2016/12/the-phylogenetics-of-equality.html" target="_blank">downright dangerous</a>. Not to beat a dead horse, but none of the other extant apes (e.g., gorillas, chimps, bonobos) are our ancestors, as implied by this figure (see this <a href="https://blogs.iu.edu/sciu/2017/09/26/why-are-there-still-apes/" target="_blank">great blog </a>by Fabio Mendes for a more complete discussion). In fact, we can’t even be very sure which of the many extinct hominins actually sits on the <a href="https://www.nature.com/scitable/knowledge/library/hominin-taxonomy-and-phylogeny-what-s-in-142102877" target="_blank">lineage that gave rise to <i>Homo sapiens</i></a> (i.e., actually could be correctly referred to as an ancestor).<br />
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In exploring the relationship between tree diagrams and tree-thinking in science ed research, there has been a strong emphasis on diagonal trees versus rectangular trees, which often go by <a href="http://psycnet.apa.org/record/2007-19455-003?doi=1)" target="_blank">“tree” and “ladder” format</a>, respectively. I prefer to stick with diagonal (as in the top diagram) and rectangular (below), because let’s be honest, a rectangular tree can be made to look just as ladder-y as a diagonal tree.<br />
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjzEglivJDaES4Ojnslh-f2yIrr5XeYiZUU0oL0ibMkyVqHBbattqJyDGyPVOXzTCdCtQQQ34BBDmsm6YhwebxkmCMxAXHJavItZGWzAXmRsn2lX3vZP_FPUdyxepJgrzKSCUR4qaXKCKw/s1600/LadderyRectangle.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="74" data-original-width="249" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjzEglivJDaES4Ojnslh-f2yIrr5XeYiZUU0oL0ibMkyVqHBbattqJyDGyPVOXzTCdCtQQQ34BBDmsm6YhwebxkmCMxAXHJavItZGWzAXmRsn2lX3vZP_FPUdyxepJgrzKSCUR4qaXKCKw/s1600/LadderyRectangle.jpg" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"> My Ladder-y Rectangular Tree</td></tr>
</tbody></table>
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What is scary to me is the ladder-y trees seems to be exploding, faster than stick-in-the-muds like me can complain about how they trigger evolutionary misconceptions and make the jobs of evolutionary biologists even harder. Worse yet, these ladder-y trees are often presented the context of trying to expand access to information about phylogenies and evolution. I won’t enumerate them here, but let’s just say that I’ve got sort of a mental burn-book of phylogeny figures that fall in this more-harm-than-good zone**. In part II of this blog entry, I’ll talk about how I think we can improve the state of affairs.<br />
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*This is not a thing. Calling a group of organisms 'lower' is just as nails-on-a-chalkboard to me as <a href="http://for-the-love-of-trees.blogspot.com/2016/09/the-ancestors-are-not-among-us.html" target="_blank">basal</a>.<br />
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*(I realize that I'm making tons of weird hyphenated adjectives today. That's why it's just a blog.<br />
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<br />Stacey Smithhttp://www.blogger.com/profile/00476159407653766652noreply@blogger.com2tag:blogger.com,1999:blog-8573307811900676235.post-1369085377314371562017-07-03T09:53:00.000-07:002017-07-03T09:56:47.851-07:00Moving the needle[Note, this post is not about phylogenies]<br />
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I’ve sensed some ‘what’s-the-big-deal’-ness in response to recent discussion about inappropriate behavior at the recent Evolution meetings, so I want to explain why I take this so seriously. I think you should care too, assuming you are interested in making science more diverse and inclusive. I’ll speak from my own experience here, making this a perhaps uncommonly personal post. First, I should say that I have been lucky throughout my career to have exceptional mentors (both men and women) who strongly encouraged my interest in science and always made me feel supported. But early on, it became apparent to me (and my female peers) that being a woman in science was going to present extra challenges. None of my experiences are unique and I have colleagues who had a much harder time*. One thing it seems like we all discovered was the amount of caution that was needed in interacting with male scientists, especially senior ones. Being friendly was sometimes taken as openness to flirtation, which could escalate to unwanted touching or worse. So as young woman in science, I learned how to tread carefully and how to be friendly but divert conversations when there were red flags. I learned what the flags are (“looks like you’ve been working out!” or “why is someone like you single?”**). I learned to avoid places and situations where inappropriate behavior is likely to happen, even if it meant sometimes missing out on networking***, and I found friends with whom I could safely discuss these issues. Friends who understood that it’s not as simple as ‘not putting up’ with bad behavior, especially from senior scientists in a community that is so tightly woven through letters of recommendation, reviews, grant panels, and committees.<br />
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For me, these social acrobatics became part of the fabric of interacting with other scientists. Another skill like presenting posters, or making aesthetically appealing slides. It wasn’t until a few years ago that I realized how much mental and emotional energy I wasted on these acrobatics as a younger scientist. Energy that I could have devoted to science or something else! Energy that some of my peers never had to spend****. Now that I am a faculty member, inappropriate behavior towards me has become less common, but I worry for my students and other young scientists. I wish I could prevent unprofessional behavior from clouding their experiences. I wish I could save them from the wasted energy of handling those who behave inappropriately. I wish I could keep them from ever having to become social acrobats themselves. They shouldn’t have to. But it doesn’t seem like things have changed that much in the 16 years I’ve been in this field. For my mentees, I try to prepare them, let them know that I know it happens, welcome them to come talk with me about their concerns, and ask them to brainstorm with me on how to make things better. With regard to the Evolution meetings, the Society for Systematic Biology has called for <a href="https://docs.google.com/forms/d/e/1FAIpQLSeS2lwOyZ0ftsvZiGlun_HZVS8WssBwXvrqvIL8vlvVflaH9w/viewform">suggestions</a>. I’m hoping that together we’ll come up with ideas that could actually move the needle. <br />
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*To get a sense, peruse the nearly 900 responses to <a href="https://twitter.com/gbaucom/status/872446177580593152">Gina Baucom’s post</a> about crappy things said to or about women in academia.<br />
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**I know that these may seem incredibly obvious but when it’s someone senior, someone you respect, and someone that you would never imagine would hit on you, it takes a while (at least for me) to realize what it is. I have learned now to look past rank and listen to my gut. <br />
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***If we want access to science for everyone, no one should have to make these choices.<br />
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****These are my experiences but I imagine the same goes for other underrepresented groups in STEM.<br />
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Stacey Smithhttp://www.blogger.com/profile/00476159407653766652noreply@blogger.com6tag:blogger.com,1999:blog-8573307811900676235.post-58773798080559488112017-05-15T14:46:00.000-07:002017-05-15T14:46:00.197-07:00Back to the futureOne of the most pervasive carryovers from ladder-of-life thinking is that some living species are older than others. These are often thought of as sitting on the lower rungs of the ladder. Of course, tree-thinking rejects this notion as all living species have evolved the same amount of time from their shared common ancestor at the base. Nonetheless I hear so many phrases that reflect the continuing influence of ladder-thinking, even among evolutionary biologists. So here's a good one - '<i>That trait goes all the way back to echinoderms</i>' [or insert any taxon perceived to be old]. The speaker almost certainly wanted to communicate that the trait was present in the common ancestor of echinoderms and vertebrates. So what's the problem with using the shorthand 'back to echinoderms'? Well, it suggests that an echinoderm was the common ancestor of echinoderms and vertebrates (not true even if that ancestor *looked* more like an echinoderm) and/or that echinoderms haven't been evolving since their split with other deuterostomes. This is particularly dangerous as it often leads to poor experimental design -- using living species perceived to be old or primitive as stand-ins for ancestors. Certainly studying echinoderms can help us make inferences about that common ancestor, but so would studying any other descendant.<br />
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So in summary:<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjocjekz2jsJmA2Azjw-CpT70ZhpCUYrCXSPmpKcbWUqGqFBvomWZCaEXWMcO_pE_-8v5JdZQ9PHuW9hJgkHcurSOoPj1GTJWj1S0mH3a-sTqNsdrp5kAu3Wx4mpKasO6cw_Lv5ofGWfIs/s1600/echinoderm.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="253" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjocjekz2jsJmA2Azjw-CpT70ZhpCUYrCXSPmpKcbWUqGqFBvomWZCaEXWMcO_pE_-8v5JdZQ9PHuW9hJgkHcurSOoPj1GTJWj1S0mH3a-sTqNsdrp5kAu3Wx4mpKasO6cw_Lv5ofGWfIs/s320/echinoderm.jpg" width="320" /></a></div>
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p.s. I think it would be a little better to say 'out to echinoderms' -- if your listener assumes humans are starting point, then going 'out' to echinoderms spans the clade that captures both humans and echinoderms, which maps to a particular ancestral node. But why not just use a couple more words and say the trait was present in the common ancestor of deuterostomes.Stacey Smithhttp://www.blogger.com/profile/00476159407653766652noreply@blogger.com1tag:blogger.com,1999:blog-8573307811900676235.post-21226704710122957302017-05-07T10:32:00.002-07:002017-05-15T14:46:58.650-07:00Naming nodes<span style="font-family: inherit;"><span style="font-family: verdana, sans-serif;">A friend texted me today to share a ‘crazy’ biology fact –
that ‘a slug is not a critter but a fungus’.</span><span style="font-family: verdana, sans-serif;">
</span><span style="font-family: verdana, sans-serif;">Of course, I had to protest immediately.</span><span style="font-family: verdana, sans-serif;">
</span><span style="font-family: verdana, sans-serif;">A slug is not a fungus, it is a mollusk! (Which I guess would colloquially be a critter?) This interchange made me think about how that kind of
statement translates for an evolutionary biologist.</span><span style="font-family: verdana, sans-serif;"> </span><span style="font-family: verdana, sans-serif;">When we say, a [species] is a [taxonomic
group], we are saying, that species belongs to a clade, a branch of the tree of
life, that we have given a name.</span><span style="font-family: verdana, sans-serif;"> </span><span style="font-family: verdana, sans-serif;">So it’s
really a statement about evolutionary history.</span><span style="font-family: verdana, sans-serif;"> </span><span style="font-family: verdana, sans-serif;"> A slug does not belong to the clade that we call fungi. A slug is in the mollusk clade, which is a branch of lophotrochozoans, which is a branch of animals, which is a branch of eukaryotes, etc. So a slug *is* all of those. The limit on the number of these statements is only the number of nodes (and
corresponding clades) which we have assigned names.</span><span style="font-family: verdana, sans-serif;"> </span><span style="font-family: verdana, sans-serif;">Since all species share common ancestors back
in time, at some point, the slug’s history will intersect with the fungus; that
is, we will eventually arrive at a node which sits along both of their evolutionary histories.</span><span style="font-family: verdana, sans-serif;"> </span><span style="font-family: verdana, sans-serif;">Currently, this node is the opisthokonts, whose
descendants are eukaryotes with a single posterior flagellum.</span><span style="font-family: verdana, sans-serif;"> </span><span style="font-family: verdana, sans-serif;">Naming these nodes give us a handy way to
remember traits that the species belonging to that clade possess (although some
may have subsequently lost those synapomorphies).</span><span style="font-family: verdana, sans-serif;"> </span><span style="font-family: "verdana" , sans-serif; font-size: small;">So then you might wonder, how do we decide
which nodes to name?<span style="mso-spacerun: yes;"> </span>Anyone who
publishes a phylogeny is free to name any node they wish, although typically
only nodes that are well-supported by various sources of evidence would be
named.<span style="mso-spacerun: yes;"> </span>Among those with good support, authors
often pick those that correspond to some previously named group (like a genus)
in order to carry that information (whatever characteristics originally resulted in the group's description as a separate genus). Many nodes however don’t contain members
that had a traditional name (pre-phylogenetics), but nonetheless correspond to
a group with some distinctive features, like the Opisthokonts. <span style="mso-spacerun: yes;"> </span>Thus, taxonomy and classification return to
the same principles that have long guided the field – that names function to
convey information about organisms – about their evolutionary history (their
relatedness to other organisms) and their traits.<span style="mso-spacerun: yes;"> In this sense, naming is a choice -- about which information we think is interesting or important to communicate. I always think if bacteria were doing the taxonomy instead of humans we would have many fewer named nodes within the animal clade and many more along branches in their part of the tree.</span></span></span><br />
<span style="font-family: inherit;"><span style="font-family: "verdana" , sans-serif; font-size: small;"><span style="mso-spacerun: yes;"><br /></span></span><span style="font-family: inherit; font-size: small;"><span style="font-family: "verdana" , sans-serif; mso-spacerun: yes;">P.S. The title 'naming nodes' will only be entertaining to those of you who are also fans of Best in Show. Taxonomy is a far more valuable endeavor than naming nuts, but certainly less funny.</span></span></span><br />
<span style="font-family: inherit;"><br /></span>
Stacey Smithhttp://www.blogger.com/profile/00476159407653766652noreply@blogger.com0tag:blogger.com,1999:blog-8573307811900676235.post-30883927339475091922016-12-02T15:34:00.000-08:002019-01-15T09:17:52.064-08:00The phylogenetics of equality<!--[if gte mso 9]><xml>
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In previous articles (<a href="http://digitalcommons.unl.edu/bioscifacpub/105/">here</a> and <a href="http://www.oxfordbibliographies.com/view/document/obo-9780199941728/obo-9780199941728-0052.xml">here</a>*), I have argued that
understanding phylogenetic trees is a core part of understanding evolution, and
thus biology as a whole.<span style="mso-spacerun: yes;"> </span>My <a href="http://for-the-love-of-trees.blogspot.com/2016/09/the-ancestors-are-not-among-us.html">last blogpost</a> emphasized that using terms like basal and early-diverging to refer to taxa
misrepresents what phylogenies communicate, and therefore leads to
misunderstanding about how evolution works. I would guess that at least some
readers thought, "Well is that so bad?<span style="mso-spacerun: yes;">
</span>So what if I casually talk about a group of species as basal, and some
in the audience incorrectly take this to mean less evolved? I just mean to say
that they have retained some ancestral character states that I am interested
in, and saying 'basal' as a shorthand is convenient."<o:p></o:p></div>
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Here I'd like to stress that contributing to ladder-of-life
thinking** with sloppy tree-speaking has real tangible consequences, that we
should take seriously, not just as biologists, but as citizens.<span style="mso-spacerun: yes;"> Today </span><a href="http://www.dan-lowe.com/">Dan Lowe</a>, friend in political philosophy sent me <a href="https://slate.com/news-and-politics/2016/11/the-majority-of-trump-supporters-surveyed-described-black-people-as-less-evolved.html">this article</a>,
written by a group of political scientists. They conducted a survey in which
they asked 2000 participants (who were all white) to rank how 'evolved' they believe
blacks and whites to be using a 0-100 scale placed below a popular depiction of
the "ascent of man", an image which undoubtedly stirs up ladder-of-life
thinking.***<o:p></o:p></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjChwW98BrUHbXP6QRr-bCbdeh3cG442pKBKnRuyNnxM_47OJVj18nam6MDqcZRtmc2vvYpfDg5wDyQwXErPC0tu5Vhh-ahtXd35TZoSjj24ZQ00xFXRF_mlfdX3iCXZfq-Fphnl4E8Nf8/s1600/161107_POL_Ascent.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="114" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjChwW98BrUHbXP6QRr-bCbdeh3cG442pKBKnRuyNnxM_47OJVj18nam6MDqcZRtmc2vvYpfDg5wDyQwXErPC0tu5Vhh-ahtXd35TZoSjj24ZQ00xFXRF_mlfdX3iCXZfq-Fphnl4E8Nf8/s320/161107_POL_Ascent.jpg" width="320" /></a></div>
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Thirty-eight percent of the respondents rated blacks less evolved, with rationales including being more 'closer to' or 'like animals'. The researchers report being surprised by these results, but I am not at all surprised. Not just because we know that racism is prevalent in our country, but also because the public understanding of evolution, and <a href="http://www-personal.umich.edu/~evansem/JCC_Pol_Evans.pdf">particularly common ancestry</a>, is depressingly low. </div>
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Anyone who has been taught evolution (including tree
thinking) should protest, no humans could ever be considered less 'evolved' than
any other! All humans are more closely related to each other than to any other
species, so none of us is 'closer to animals'! Anyway, all of us <i style="mso-bidi-font-style: normal;">are</i> animals. We belong to a branch of
the tree that we call animals, and we are all equally related to <i>other</i> animals.
Moreover, it is meaningless and biologically incorrect to consider any group of
living organisms primitive or 'less evolved'. The real danger of any suggestion
otherwise is that there is some biological or evolutionary rationale for
racism.<span style="mso-spacerun: yes;"> </span>We must be emphatic that there
is not.<span style="mso-spacerun: yes;"> </span><o:p></o:p></div>
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<span style="mso-spacerun: yes;"><br /></span></div>
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Right now, many of us are thinking, what can we do to
celebrate diversity and support inclusiveness? Here's one thing.<span style="mso-spacerun: yes;"> </span>We can teach evolutionary biology and teach
it well.<span style="mso-spacerun: yes;"> </span>We can make a point to state
that humans are part of evolutionary history just like everything else on the
planet and the same principles that apply to other living organisms apply to
us, too.<span style="mso-spacerun: yes;"> </span>Just as we, as humans, are not
more 'evolved' than a fern, none of the populations of humans are any more
evolved than any other.<o:p></o:p></div>
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p.s. Thanks to <a href="http://www.colorado.edu/lab/taylor/">Scott Taylor </a>for comments.</div>
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p.p.s. Hateful comments in response to this post will be deleted.</div>
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*full text versions available from <a href="http://www.colorado.edu/smithlab/">my website</a><o:p></o:p></div>
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**ladder-of-life thinking = thinking that promotes the idea that some species are more primitive (less 'evolved') than others; is associated with the ladder-of-life or <a href="http://www.nature.com/nature/journal/v435/n7041/full/435429a.html">the great chain of being</a> (scala naturae), in which species are ranked from least to most evolved. The ladder-of-life is not consistent with the tree-like structure of evolution. Although it has been rejected since Darwin, the vestiges of progressive thinking remain and are the source of <a href="https://www.ncbi.nlm.nih.gov/pubmed/18693264">many misconceptions</a> regarding phylogenies. </div>
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***I think I am going to have to write a post just about this depiction, and probably I'll make a new version, with a tree and all rotated around, that would have the opposite effect, i.e. stimulate tree-thinking instead of ladder-thinking. </div>
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Stacey Smithhttp://www.blogger.com/profile/00476159407653766652noreply@blogger.com0tag:blogger.com,1999:blog-8573307811900676235.post-38843802525768123402016-09-19T21:42:00.000-07:002016-09-20T13:39:47.226-07:00The ancestors are not among us<div class="MsoNormal" style="text-align: center;">
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>>Terms like 'basal', 'early-diverging', and 'first-branching'
reflect persistent misconceptions about evolution and phylogenies</div>
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<o:p></o:p></div>
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<b style="mso-bidi-font-weight: normal;">Why take the time to
blog about the issues with the use of the word "basal" and similar
terms?<o:p></o:p></b></div>
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This a good question because, indeed, many tree-thinking
papers have directly discussed misconceptions related to interpreting
phylogenies (e.g., <a href="http://www.ncbi.nlm.nih.gov/pubmed/18693264">Omland
et al.</a> and <a href="https://www.nabt.org/websites/institution/File/pdfs/publications/abt/2007/069-07-0040.pdf">Meir
et al.</a>).<span style="mso-spacerun: yes;"> </span>In fact, several have tackled
issues surrounding the term "basal" specifically (see <a href="http://onlinelibrary.wiley.com/doi/10.1111/j.0307-6970.2004.00262.x/abstract">Krell
and Cranston</a> and <a href="http://www.ncbi.nlm.nih.gov/pubmed/16701355">Crisp
and Cook</a>). Given these efforts, I hoped that the use of this term (and the
associated misconceptions) would begin to erode.<span style="mso-spacerun: yes;"> </span>Unfortunately I feel as though, if anything,
the problem is becoming more widespread.<span style="mso-spacerun: yes;">
</span>I think this is largely for several good reasons -- building phylogenies
is continually becoming easier, even for large datasets, and many researchers
from a range of fields are seeking to incorporate an evolutionary perspective
into their research.<span style="mso-spacerun: yes;"> </span>However, it's
important to point out that the misinterpretation of phylogenies is just as
common in evolutionary biology as in any other field.<span style="mso-spacerun: yes;"> </span>So in short, the “basal” problem is not going
to disappear without active efforts to teach tree-thinking to all biologists at
all stages.<o:p></o:p></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<b style="mso-bidi-font-weight: normal;">So what is the
problem with 'basal', exactly?<o:p></o:p></b></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
The problem is that the term is used incorrectly and/or in
misleading ways in talks, papers, and proposals, roughly 90% of the time (by my
estimate). <span style="mso-spacerun: yes;"> </span>Moreover, the use of basal
and similar terms perpetuates a large suite of misconceptions about how
evolution works.<span style="mso-spacerun: yes;"> </span>So in order to
communicate effectively and accurately about evolution, we must also
communicate effectively and accurately about trees.<span style="mso-spacerun: yes;"> </span>As I have struggled to understand the desire
to describe some taxa as basal (or early-diverging or early-branching), I've
assembled a mental list of the various ideas that speakers and writers seem to
be aiming to communicate with the use of these terms.<span style="mso-spacerun: yes;"> </span>I've listed these below along with comments
about relevant misconceptions.<span style="mso-spacerun: yes;"> </span>This list
overlaps with what has been described in the publications listed above.<o:p></o:p></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<b style="mso-bidi-font-weight: normal;">1) A basal species is
one that has given rise to another species, i.e. some ancestral lineage.<span style="mso-spacerun: yes;"> </span><o:p></o:p></b></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
I think this use of the term is related to the misconception
that some living taxa are the ancestors of other living taxa.<span style="mso-spacerun: yes;"> </span>Unless something has changed with respect to
the space-time continuum, this is not possible.<span style="mso-spacerun: yes;">
</span>The ancestors are lineages that are no longer present -- they are
represented in the tree as internal nodes and internal branches.<o:p></o:p></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<b style="mso-bidi-font-weight: normal;">2) A basal taxon is one
that is older than other taxa in the tree.<o:p></o:p></b></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
If all of the taxa at the tips are extant (i.e., not
extinct), then all of them are the same age.<span style="mso-spacerun: yes;">
</span>They all have the same root-to-tip distance in terms of time. In other
words, they have all evolved the same amount of time from the base of the tree.
(Note that this is a correct use of base -- the base is the earliest part of
the tree, the root, and time proceeds forward from that point.)<span style="mso-spacerun: yes;"> </span>It is worth noting that in molecular
phylogenies, some tips may be longer or shorter (i.e., the tree may not be ultrametric).<span style="mso-spacerun: yes;"> </span>This is due to a combination of stochasticity
in the substitution process as well as differences in substitution rates across
lineages. However, we would not say that the taxa on longer branches are
"more evolved" than the other taxa on the tree. <o:p></o:p></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<b style="mso-bidi-font-weight: normal;">3) A basal taxon is
primitive morphologically or in some other sense.<o:p></o:p></b></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
All species, extant or extinct, possess a mixture of characteristics
that are, in cladistic terminology, ancestral (plesiomorphic) or derived (apomorphic)
relative to other species.<span style="mso-spacerun: yes;"> </span>For example,
in reptiles having scales and four limbs is the ancestral state. Snakes have
retained the ancestral state of having scales but have the derived state of no
limbs. <span style="mso-spacerun: yes;"> </span>This highlights the fact that no
species can be accurately described in evolutionary terms as 'primitive',
'ancestral', 'lower', or 'basal' any more than they can be described as
'derived', 'advanced', or 'higher'. In this sense, the tree-thinking view of
species diversity is rather egalitarian.<span style="mso-spacerun: yes;">
</span>All of the species on earth have evolved the same amount of time from
the <a href="http://evolution.berkeley.edu/evolibrary/article/side_0_0/origsoflife_05">last
common ancestor of all life</a> some 3 to 4 billion years ago, and their
diverse forms reflect the accumulation of changes during their unique pathways
along the tree to the present. It's worth noting that this misconception (that
not all species are equally 'evolved', or equally 'advanced') has been linked
to the history of progressive ideas in evolution, and specifically, the notion
that <a href="http://www.nature.com/nature/journal/v435/n7041/full/435429a.html">humans
sit at the apex of a ladder of life</a>. This is exactly why terms like basal
are more than just poor wording; they perpetuate the incorrect interpretation
of phylogenies as ladders of progress. We can't expect to improve
understanding of the tree-like nature of evolution while continuing to use
misleading terminology.<o:p></o:p></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<b style="mso-bidi-font-weight: normal;">4) Basal lineages sit
at the base of the tree or at the bottom of the tree diagram.</b><o:p></o:p></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
The observation that certain lineages are near the bottom of
a tree does not reflect any aspect of evolutionary history; it is simply a
reflection of the choices made in drawing the tree. These choices are generally
guided by aesthetic and didactic motivations.<span style="mso-spacerun: yes;">
</span>That is, the tree is drawn to best communicate the results of the
phylogenetic analysis in a visually appealing way. The root could be towards
the top or towards the bottom, and the authors can rotate trees at nodes and
bend branches.<span style="mso-spacerun: yes;"> </span>None of these drawing
choices alters the relationships depicted in the tree.<span style="mso-spacerun: yes;"> </span>Thus, the two trees below communicate the
same phylogenetic information (e.g., lizards are more closely related to humans
that to frogs), despite the fact that the nodes have been rotated.<span style="mso-spacerun: yes;"> </span>This exercise makes it apparent why you
cannot learn interpret a phylogeny from the order of the tips, only from the
order of the nodes.<span style="mso-spacerun: yes;"> </span>For more practice in
reading trees without being distracted by tip order or tree format, look <a href="http://digitalcommons.unl.edu/cgi/viewcontent.cgi?article=1104&context=bioscifacpub">here</a>
and <a href="http://www.nature.com/scitable/topicpage/reading-a-phylogenetic-tree-the-meaning-of-41956">here</a>.<o:p></o:p></div>
<div class="MsoNormal">
<br /></div>
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<o:p><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgxqK3kJpZdDcPXE7AALkv9wgIQV-DFmtVMNYZ08ZyDm8Zv_BBCJ7-ARd5rBaDO1xSFIxf08wk-qxIrEThid2yH_mGa5DYvBpLczYUDuZL-E9Bb3YtJ7WViiCjlFHUpAg3zla0HgOpQrHY/s1600/tetrapods.jpg" imageanchor="1"><img border="0" height="173" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgxqK3kJpZdDcPXE7AALkv9wgIQV-DFmtVMNYZ08ZyDm8Zv_BBCJ7-ARd5rBaDO1xSFIxf08wk-qxIrEThid2yH_mGa5DYvBpLczYUDuZL-E9Bb3YtJ7WViiCjlFHUpAg3zla0HgOpQrHY/s400/tetrapods.jpg" width="400" /></a></o:p></div>
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<o:p><br /></o:p></div>
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<div class="MsoNormal">
You may be wondering, so if the order across the tips can be
rotated without changing the tree, how do authors choose among possible rotated
versions? Since we read from left to right, it is common to show the 'focal'
taxon toward the right and if humans are in the tree, we are almost always put
in that prime position! Just take a look at most biology textbook depictions of
primate phylogeny, like this <a href="https://www.mun.ca/biology/scarr/Phylogeny_of_Primata.html">one</a>. <o:p></o:p></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
Some of these drawing choices may also not be apparent to
novice users of phylogenetics software. Most inference software and tree
drawing programs will automatically <a href="http://evolution.berkeley.edu/evolibrary/article/0_0_0/evotrees_zoos_02">'ladderize'</a>
trees, which places the sparsely sampled outgroups on the left of an upright
tree as above or on the top or bottom of a horizontal tree. <span style="mso-spacerun: yes;"> </span>Thus, the order of the tips that a program
produces is drawing convention and never the outcome of an analysis (e.g., you
could never say that 'the maximum likelihood analysis placed lemurs at the base
of the primate phylogeny').<o:p></o:p></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<b style="mso-bidi-font-weight: normal;">So what should I say,
if not basal?<o:p></o:p></b></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
I realize that this whole post may be a big bummer.<span style="mso-spacerun: yes;"> </span>Especially if what you wanted from a
phylogeny was to learn which species were ancestral or which diverged first
(reminder, neither are possible or realistic, see above and below). Once you
have reconciled yourself with the fact that the ancestors are not among us,
here are some 100% not-confusing, evolutionarily-consistent, and still
interesting things you can say about a tree like the <i style="mso-bidi-font-style: normal;">Platanthera</i> orchid phylogeny below from this <a href="http://www.colorado.edu/smithlab/sites/default/files/attached-files/Smith2010NewPhy.pdf">review
paper</a>. <o:p></o:p></div>
<div class="MsoNormal">
<br /></div>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj8Vp8ooQvcr0bJjlfkTlRuVam2PnbNsKRGNfjYW5S1mmYg8UuUfMNObWzpSPvXu3A7ndBatcn4Owep4HyoJPUUMYzs-0mSrsBnRw079wZXPPQkZnL1Yf8U1irCa3sz3-mfr0WcWIXNKPY/s1600/Platanthera.jpg" imageanchor="1"><img border="0" height="304" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj8Vp8ooQvcr0bJjlfkTlRuVam2PnbNsKRGNfjYW5S1mmYg8UuUfMNObWzpSPvXu3A7ndBatcn4Owep4HyoJPUUMYzs-0mSrsBnRw079wZXPPQkZnL1Yf8U1irCa3sz3-mfr0WcWIXNKPY/s640/Platanthera.jpg" width="640" /></a><br />
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal" style="margin-left: .25in;">
</div>
<ul>
<li>The ancestors of extant <i>Platanthera</i> had nocturnally pollinated
flowers. [<i>Not, e.g., 'Nocturnally
pollinated </i>Platanthera<i> are ancestral.' Because this could connote that some living </i>Platanthera<i> are ancestors of others. See space-time-continuum above</i>]</li>
<li>Diurnal pollination has arisen
multiple times in <i>Platanthera</i>. [<i>Not, e.g., 'Diurnally pollinated </i>Platanhera<i> are evolutionarily derived.' Because
character states can be derived but taxa cannot be</i>]</li>
<li>The
sonoharae-fuscescens-ussuriensis-japonica clade is sister to the rest of the
genus <i>Platanthera</i>. [<i>Not, e.g., 'The sonoharae-fuscescens-ussuriensis-japonica
clade is basal to the rest of </i>Platanthera<i>.' or 'The sonoharae-fuscescens-ussuriensis-japonica group is an early
diverging clade of </i>Platanthera<i>.' More on early-diverging below</i>]</li>
<li>The evolution of white flowers
evolved after the transition to diurnal pollination in the clades that
includes. <i>P. blephariglottis</i> and <i>P. nivea</i>.</li>
<li>The basal nodes of the tree are
reconstructed as nocturnally pollinated. [<i>It
is fine to describe the earliest nodes in the tree as basal because they did in
fact occur earlier than the nodes towards the tips. Although personally, I prefer 'deeper' nodes</i>.] </li>
</ul>
<br />
<div class="MsoNormal">
Notice that in this list, I use basal to refer to nodes,
sisters to refer to taxa, and ancestral/derived to refer to characters.<span style="mso-spacerun: yes;"> </span>My intuition is that many who use basal to
refer to taxa are actually most interested in characters (what did the ancestor
look like, not who was it exactly).<span style="mso-spacerun: yes;"> </span>So
if this is the case, talk about the characters! This is a good strategy for
avoiding tree mis-speak.<o:p></o:p></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<b style="mso-bidi-font-weight: normal;">How about calling
some taxa 'early-diverging' or 'first-branching' instead of 'basal' or
'lower'?<span style="mso-spacerun: yes;"> </span>Doesn't this do the trick?<o:p></o:p></b></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
In short, no. These terms are equally uninformative, and
since many listeners will equate them with basal, equally misleading.<span style="mso-spacerun: yes;"> </span>I'll walk through an example that may help to
reveal why early-diverging is not meaningful.<o:p></o:p></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
Let's first consider a very simple tree with just two tips.<o:p></o:p></div>
<div class="MsoNormal">
<br /></div>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjlq_MOmI_YV0apegKBtKHmjHO7bZPKMU7vpePOQMRravTsYGv8GgDS2Fq1Ot8Bdkc5kH2jM69lvZ3E4D6RmUGzrlLgHJcY7-ruq6MAqj9bpPIw1BXqT6l3S9FsLXX0EhV3XFPlek3Tidw/s1600/turtlehuman.jpg" imageanchor="1"><img border="0" height="57" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjlq_MOmI_YV0apegKBtKHmjHO7bZPKMU7vpePOQMRravTsYGv8GgDS2Fq1Ot8Bdkc5kH2jM69lvZ3E4D6RmUGzrlLgHJcY7-ruq6MAqj9bpPIw1BXqT6l3S9FsLXX0EhV3XFPlek3Tidw/s200/turtlehuman.jpg" width="200" /></a><br />
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
We would look at this tree and say there are two tips that
have diverged from a common ancestor and have evolved for the same period of
time since that split.<span style="mso-spacerun: yes;"> </span>We can add
another taxon to this tree.<o:p></o:p></div>
<div class="MsoNormal">
<br /></div>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhFgrOEym6PQbICjxq51WUDlU_7CSRKBPu8YRE2UImiSx2HehVPKmMArP3xjWc9DTae5VDVMZpqN9Dwp4fFcK7iCD451IpFcg-mZJhKmnmtHwaudh2N9C93IiXoDpGTy8ITx8oMQG9ajHI/s1600/threetaxa.jpg" imageanchor="1"><img border="0" height="96" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhFgrOEym6PQbICjxq51WUDlU_7CSRKBPu8YRE2UImiSx2HehVPKmMArP3xjWc9DTae5VDVMZpqN9Dwp4fFcK7iCD451IpFcg-mZJhKmnmtHwaudh2N9C93IiXoDpGTy8ITx8oMQG9ajHI/s320/threetaxa.jpg" width="320" /></a><br />
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
It is still true in this tree that the turtle and the human
have evolved the same amount of time since the earliest node in the tree.<span style="mso-spacerun: yes;"> </span>And so has the bird, remembering that its ancestry
includes the branch shared with the turtle.<span style="mso-spacerun: yes;">
</span>Looking at this sort of topology, there is a tendency to call the branch
labeled human as 'early diverging', but of course the bird-turtle branch
diverged at the same moment.<span style="mso-spacerun: yes;"> </span>Thus, this
term seems to instead to be applied to whichever branch has given rise to fewer
descendants given the taxon sampling. Taxon sampling, like tree drawing, is a
choice, and I could instead have chosen a different set of three taxa, e.g.,<o:p></o:p></div>
<div class="MsoNormal">
<br /></div>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgifDD2daNZBYVI_ONUYUwZ0zUN9JPL65hznp5QxzjnBy0XvyKms-sXpixjNKomjoxXQqxO_GY35LVXhYQe53eRWbCaI4ATdJu-dX2jwLKcOhWB4rW1E7Dn2B38Lp6nwnlw9qx2iWwYu5w/s1600/threeothertaxa.jpg" imageanchor="1"><img border="0" height="100" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgifDD2daNZBYVI_ONUYUwZ0zUN9JPL65hznp5QxzjnBy0XvyKms-sXpixjNKomjoxXQqxO_GY35LVXhYQe53eRWbCaI4ATdJu-dX2jwLKcOhWB4rW1E7Dn2B38Lp6nwnlw9qx2iWwYu5w/s320/threeothertaxa.jpg" width="320" /></a><br />
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
Calling the turtle an early-diverging amniote based on this
tree is just as odd as calling the human an early-diverging amniote based on
the previous tree.<span style="mso-spacerun: yes;"> </span>Even if we had all of
the amniotes sampled in this tree, one of the two branches arising from the
root node would be less speciose than the other. Tree drawing software will typically
ladderize the tree and thus would place the less speciose clade at the bottom
of the figure.<span style="mso-spacerun: yes;"> </span>This placement does not
making it earlier-diverging -- just as with any pair of sister taxa, the two
descendent branches emerged from the node at the same time and have evolved for
the same time to reach the present. This is not affected by how many times
those branches have split.<o:p></o:p></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
I have also seen a tendency for some to say, well, what I
mean by early-diverging or basal is indeed species-poor sister group, so as
long as that's clear to the audience, I will continue to use this term.<span style="mso-spacerun: yes;"> </span>My first response is that pointing out that
one group is species-poor is not an interesting observation by itself.<span style="mso-spacerun: yes;"> </span>All real trees are unbalanced and one of the
two branches descending from the root will almost always have more descendants.
Second, I think this choice of wording is simply too dangerous.<span style="mso-spacerun: yes;"> </span>Using terms like basal and early-diverging
carry strong connotations, and most audiences will assume taxa carrying this
label have retained more primitive characters or will fall into one of the many
misconceptions listed above.<span style="mso-spacerun: yes;"> </span><o:p></o:p></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<b style="mso-bidi-font-weight: normal;">Looking forward</b><br />
<br />
So what do I hope to result from this long exposition on
tree terminology?<span style="mso-spacerun: yes;"> </span>Most of all to have
convinced you that it's not about the terms, it's about the ideas. <span style="mso-spacerun: yes;"> </span>Evolutionary biologists, me included, spend
tremendous energy to learn about the history of life -- when groups diverged
from each other, what changes occurred along the different branches, what
factors may have caused these changes.<span style="mso-spacerun: yes;">
</span>But this effort is wasted if sloppy terminology allows the inferred
history to be misconstrued as a ladder of progress, or yet another living
fossil. I believe that we don't need such familiar and comfortable storytelling
to make evolution interesting or relevant, to our peers or to the general
public.<span style="mso-spacerun: yes;"> </span>The truth is that all living
taxa have traversed fascinating paths to reach the present and all of their
stories are worth telling.</div>
<div class="MsoNormal">
<o:p></o:p></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
**I'd like to acknowledge advice from Emily Sessa, Brian O'Meara, and Eric Schranz on this post, as well as helpful comments from Matt Hahn.</div>
Stacey Smithhttp://www.blogger.com/profile/00476159407653766652noreply@blogger.com31