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L06-donoghue - Chapter 7 Comparisons Phylogeny and Teaching...

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Unformatted text preview: Chapter 7 Comparisons, Phylogeny, and Teaching Evolution Michael]: Donog/me Introduction Comparisons are central to research and teaching in biology and are ubiquitous in both. Furthermore, biological comparisons generally take for granted some baseline knowledge of phylogenetic relationships. The main point of my paper is that the teaching of biology—wand of evolutionary biology in particular— would benefit greatly from making more explicit use of phylogenetic trees in formulating comparisons. In addition to providing far richer comparisons, this would have the ancillary benefit of making “tree thinking” (O’Hara, 1997) second nature to biology students. Success in this endeavor requires that we pay more attention to teaching the basics of phyloge— netic biology and overcoming the preconceptions that students have about phylogeny. Educators also need more ready access to phylogeneticlknowledge and will need to pay more attention to the variety of evolutionary messages that phylogenetic comparisons can support. Many people bring to bear some level of subliminal knowledge of phylogenetic relationships in making biological comparisons. Consider, for example, how we make generalizations relevant to humans from observations of other organisms. Which of the fol— lowing organisms would you want to know the most about in predicting how humans might respond to a particular disease treatment: a mushroom, a chimp, a corn plant, or a fruit fly? Most people will quickly pick the chimp out of this lineup. Bur why? Of course, the chimp looks the most like us. But Why is this? It’s because we share a much more recent com- mon ancestor with the chimp than we do with the others—we have had much less time to diverge from one another and we therefore share many attributes retained from our common ancestor. Of course, we also share common ancestors with the mushroom, the fruit fly, and the corn plant, but these existed in the much more distant past, and we have obviously all diverged very considerably since then. \When it comes down to it, it is only this phylogenetic reasoning that leads us to trust predictions about all sorts of attributes that we can’t immediately observe, such as responses to particular medicines. Yet phylogenetic knowledge is rarely directly acknowledged as the basis for so many of the comparisons that we make on a daily basis. Why might it help to make phylogenetic reasoning more explicit? Consider a family visiting an aquarium and observing a tunafish and a dolphin. Most parents seem to appreciate that tunas and dolphins are super- ficially similar but not very closely related to one another, and they commonly "explain" to their children that the tuna is a true fish while the dolphin is really a mammal. They are intending to express something about relationships but are doing so in a way that provides little real understanding. Noting that these organisms have been classified in different named groups amounts to just rephrasing that they differ from one another. It helps a bit, as parents often will, to list some differences between these organisms: fish have scales whereas mammals have hair, and so on.‘ But this still is nowhere near as revealing as bringing phylogenetic relationships explicitly into the discus— sion (figure 1). For example, it might then be noted that dolphins are more closely related to mice, ele- phants, and bats, not to mention to lizards, turtles, birds, and frogs, than they are to tunafish. Among other things, this perspective provides the basis for concluding that dolphins descended from ancestors that lived on the land and had regular limbs, which means that the dolphin lineage must have moved into the water where limbs were lost (or greatly modified). Tunafish, on the other hand, never had terrestrial organisms in their anceStry—they are ancestrally aquatic and have fins, not limbs. ‘ Notice that explicitly adding phylogeny into the discussion serves to highlight evolutionary change through time, as opposed to static differences (O’Hara, 1988). In this case, it implies that there was once a shift from living in the water to living on land, which, among other things, entailed the evolution W 69 mayhem exit; 'a‘ iii into water, lose limbs onto land, gain limbs Figure l. A greatly simplified phylogeny of the vertebrate animals showing -: that tanafish and dolphins are very distantly related, despite their similarity in body form. Evolutionary shifts in habitat (from water to land and back again) and in f characters (the gain and loss of limbs) are highlighted by making the phylogeny explicit. of limbs, and later a shift from the land back into the water and the loss of limbs (figure 1). The phylogeny provides us with a historical narrative about the direction of evolutionary change, and in this case it highlights convergence in the dolphin lineage on a fishlike solution to living in the water. From this perspective, many observations fall into place. For example, it makes sense that dolphins have hair, mammary glands, and lungs, all of which were retained from their terrestrial mammalian ancestors. Many new questions also open up. For example, the observation of convergent evolution properly frames the question, What’s so great about being shaped like a torpedo when you move through the water? In short, phylogenies make biological comparisons more productive. In the process, making explicit use of phylogenetic trees raises consciousness about evolu- tionary change, making it easier for students to absorb evolutionary thinking and incorporate it naturally into their learning. Reading Trees A critical first step in making use of phylogenetic information is becoming comfortable with what phy— logenetic trees are; that is, what they are meant to represent, how they should (and should not) be read, and how we converse about them. Perhaps the best way to get started is simply by drawing (growing) a phylogenetic tree from the bottom up. Start with a single ancestral species moving through time, have it branch in tvvo at some point, have one or both of the descendant species branch again later on, perhaps have some species go extinct along the way, and so forth, on up to a set of species that exist in the present. Now think about the meaning of “phylogenetic relationship.” We say that two (or more) species are more closely related to one another than either one is to a third species, if and only if they share a more recent common ancestor (figure 2). And, to refer to a complete branch of a phylogenetic tree—-one that includes an ancestor and all its descendants—we use the words “monophyletic group” or “clade.” It is critical to appreciate that the definitions of phylogenetic relationship and of monophyly that I have just given never refer to organismal similarity. Closely related species (members of a clade) may often, in fact, be more similar to one another than they are to more distant relatives (in the example above, for instance, humans and chimps are more similar to one another than either one is to a corn plant), but phylogenetic relationship is ultimately measured only in terms of the recency of common ancestry and not by the simi- larity of organisms to one another. The importance of this distinction will become clear in the following, when we explore in a little more detail divergence and convergence along the branches of a phylogenetic tree. Figure 2. ”Phylogenetic relationship" refers to sharing common ancestors, not to similarityaB and C are more closely related to one another than either one is tort because 3 and C share a more recent common ancestor (at l2 as opposed to Tl ). The shaded area marks a manophyletic group (or clade), which contains an ancestor and all of its descendants. Note that this is not the only clode that could be shown on this tree; for example, everything descended from the ancestor (at time ll) of A, B, and [forms a clade. The change in branch color from white to black (which is also marked by a bar across the branch) signifies on evolutionary change in a character from one state to another. Two other points are worth noting about reading phylogenetic trees, since they often seem to confuse beginners. First, a phylogenetic tree is like an Alexander Calder mobile in the sense that the branches can be swiveled around any particular node in every which way, but the relationships remain the same. Second, there is no favored side or tip of the tree toward which everything is heading. There is a tendency for ' novices to read trees from left to right, and therefore to consider the branches on the left to be “primitive” and the one farthest to the right to be the most ‘advanced.” Another common mistake is to interpret _ a less diverse “basal” clade as possessing the ancestral state of a character as compared with its more diverse but, of course, equally basal sister clade (Crisp 86 Cook, 2005). Often, it seems that the authors of published trees even cater to these preconceptions, for example, by placing the branches that they hap- pen to be most interested in as far to the right as pos- sible. This is especially true whenever Homo sapiens is included in a tree, and in general it seems difficult for ' people to resist reading phylogenetic trees as though everything leads up to humans. This is a holdover from the much earlier, pro-Darwinian image of life as a ladder leading from pond scum on a bottom rung to humans at the very top. But, as Robert O’Hara (1992) has stressed, phylogenetic trees are ramifying structures and can be read from the base toward any tip one wishes to focus on. The story of evolution, in . other words, can be "told" from the standpoint of a mushroom (with everything viewed as leading up to it) just as much as from the vantage point of a human. There is no one natural perspective—it depends only on what one is interested in and wishes to highlight at the moment. It is also critical to appreciate how phylogenetic trees are used to infer the conditions present in ancesrors (internal segments in the tree) and thereby the direction and sequence of evolutionary change (figure 2). Every characteristic present in any organism evolved at some point along the branches of the tree of life. Each one originated (via mutation) in some population and then (owing to natural selection or genetic drift) rose in frequency, eventually to fixation. Knowledge of phylogenetic relationships, combined with infor- mation on the features of known organisms, can be used to infer where in the tree (along which branches) particular features of interest most likely arose, and therefore what ancestors were like. There are a variety of methods for inferring both phylogenetic relationships and ancestral conditions (employing different optimality criteria, such as max— imum parsimony or maximum likelihood; reviewed in Felsenstein, 2003; Holderléc Lewis, 2003), but the details of these methods are perhaps not so critical from the standpoint of teaching biology at the K—12 level. A few simple examples tend to provide students with enough of an intuition to move forward in using trees. For instance, all other things being equal, if the members of two sister lineages all possess a cer- tain characteristic, say the presence of limbs, and this condition is absent in all more distant relatives, then the condition was most likely present in the common ancestor of the two lineages and retained by the descendants (figure 2). Of course, there are circum- stances where this conclusion might not be justified. For example, if the rate of evolution is high in the trait of interest and a long time has passed since the lineages diverged, then it may be more likely that the shared trait actually evolved independently. When possible, it also helps to have students play with interactive computer programs such as MacClade (Maddison 86 Maddison, 2000; see also Mesquite, www.mesquiteproject.org), which quickly drive home the connection between hypothesized phylogenetic relationships and inferred ancestral character states. Using Trees in Making Comparisons The use of phylogenetic trees in comparative biology has expanded dramatically over the past few decades, to the point that hardly an area of biology remains untouched. To provide a flavor of the possi— bilities, I will touch briefly here on several uses of phylogenies by referring to projects that I have recently been involved in. This, of course, is a highly biased sample, if for no other reason than the emphasis is on plants (and fungi). Also, my examples concern evolutionary biology and ecology, as opposed to the many uses of phylogeny in medicine, agriculture, conservation, and so on (for which see Yates, Salazar- Bravo, 8C Dragoo, 2004). In any case, I hope that the examples mentioned here will help interested readers locate the scores of other studies that have explored similar territory (see also Futuyma, 2004). The ability to infer where and when character changes occurred during the course of phylogeny opens up many exciting opportunities for under— standing the patterns and processes of evolution. For example, there are a variety of methods to assess whether the evolution of a particular trait of interest was correlated with the evolution of other traits, in which case there may be a causal connection between them (e.g., one trait may have promoted the evolution of the other). In one such study (Hibbett 66 Donoghue, 2000), we documented subtle evolutionary connec— tions between the type of wood decay mechanism and the genetic mating systems of basidiomycete fungi (mushrooms and relatives). It might also be that a particular trait change was historically correlated fl ll with certain environmental or biogeographic changes (e.g., movements from the tropics into the temperate zone, or movements from North America into South America). Phylogenies can also be used to infer whether particular directions of character change have been favored in evolution. For example, using a maximum likelihood approach, we argued that bilat— eral flower symmetry may have been lost more often than gained (Ree 66 Donoghue, 1999). By examining whole suites of character changes at once, it may even be possible to reconstruct what a particular ancestor looked like or how it probably functioned. In one such study (Chang, Jonsson, Kazmi, Donoghue, 8C Sakmar, 2002), we inferred the DNA sequence of the rhodopsin visual pigment gene for the Triassic ancestor of the archosaurs (the clade that includes alligators, dinosaurs, and birds). It was even possible to synthesize the hypothesized ancestral protein in the lab and measure the wavelengths of light that it absorbed, and therefore (by inference) the visual capacity of these organisms. It is also possible to make inferences about the geographic ranges of ancestors and hence the direction of movement of lineages in the past. For example, using a method that minimizes dispersal and extinction events (dispersal—vicariance analysis: Ronquist, 1997), we recently hypothesized that many plant groups in eastern North America had ancestors that once lived in Asia and that these lineages may have entered North America at several times during the Tertiary, perhaps mainly through the Bering land bridge (Donoghue & Smith, 2004). Likewise, by inferring the physiological and anatomical attributes of ancestors, it is possible to hypothesize the habitats that they once occupied. On this basis, we have suggested that the first flowering plants probably lived in shady, disturbed habitats—what we’re calling the “dark and disturbed” hypothesis (Field, Arens, Doyle, Dawson, 85 Donoghue, 2004). Finally, by combining inferred ancestral habitats with age estimates for key lineages, we have concluded that tropical rain forests probably originated in the mid—Cretaceous, quite a bit earlier than postulated by previous researchers (Davis, Webb, Wurdack, Jaramillo, & Donoghue, 2005). There are a variety of other uses of trees that don’t rely on inferring ancestral conditions (of charac— ters, ranges, habitats, and so on). It is now common, for instance, to compare phylogenetic trees obtained from different groups of organisms to test the degree to which these correspond, either in terms of their shapes and/ or in terms of the estimated ages of various events (Page, 2002). One obvious use of such com- parisons is in asking about the degree to which the diversification of a group of parasites has been driven by the diversification of their hosts. Trees are also often compared in studies of historical biogeography, where the idea is to discover the extent to which the relationships of organisms occupying particular geologic and biotic regions correspond to one another (e.g., are species from New Zealand and South America more closely related to one another than they are to species from Australia?) It is also worth noting that there are a variety of methods—using tree shape with or without information on the absolute ages of clades—for inferring where in a phylogenetic tree there may have been significant shifts in the rate ofdiversification (e.g., Nee, 2001; Moore, Chan, Sc Donoghue, 2004). Used in concert with methods for inferring ancestral character states, these approaches can be used to test whether particular character changes (“key innovations”) may have stimulated an increase in speciation rate, a decrease in extinction rate, or both. Finally, it should be mentioned that phylogenetic trees are beginning to be used in studies of community ecology (e.g., Webb, Ackerly, McPeek, SC Donoghue, 2002) and in measuring and elucidating global patterns of biodiversity (e.g., Wiens and Donoghue, 2004). Sometimes it is of great interest to compare trees obtained from different sorts of data. For example, in studies of plant evolution, it has become routine to compare a gene tree obtained from an analysis of one or more nuclear genes with one derived from the (typically) maternally inherited chloroplast genome. Discordance in this case might be attributable to hybridization in the past. Similarly, microbiologists compare trees from different genes to infer the occur- rence of lateral gene transfer events. Finally, it is important to draw attention to what is probably the most obvious and common use of trees, namely, to make generalizations that extend the knowledge obtained from organisms that have been studied in detail to those that have not. Much of our detailed knowledge of biology has been obtained from only a handful of model organisms, such as the fruit fly, Bitmap/silt: melanogaster; the nematode worm, Caenarkaévditis elegam; and the corn plant, Zea mayr. Generalizing this knowledge to other organisms that have not been studied in such detail, or perhaps not at all, relies directly upon phylogeny. In plants, for example, much of our knowledge of development comes from studies of com; the tiny mustard plant, Améz'dopris tkaiiam; and the snap— dragon, Antirr/az'num majm. Finding shared genes underlying particular developmental processes (and functions) in Amlaz'doprir and Antirr/ainum, but not in corn, allows us to predict that these were inherited from their shared ancestor and that all other plants derived from that ancestor also possess these genes/ functions. In this case, predictions can be made about well over 120,000 species that have not been examined in detail. Of course, such predictions may prove to be incorrect as we examine additional species in detail, but knowledge of phylogeny permits us to at least formulate working hypotheses about the distribution of genes and funcrions. The study of genome evolution falls in this same general category. At present, only a handfill of eukaryOtic genomes have been sequenced in their entirety, and when these are placed in a phylogenetic context we can begin to make generalizations about ' genome size, structure, and function. One important area of research concerns the diversification of gen...
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