Misunderstandings of evolutionary trees are pervasive among students, in the media, and among other nonspecialists. Even more alarming, they also surface frequently in the peer-reviewed scientific literature, often with significant implications for the conclusions drawn from comparative analyses (see Crisp and Cook 2005 for several examples). The following sections describe and seek to correct ten of the most commonly encountered misconceptions about evolutionary trees. Several of these are interrelated and therefore overlap to an extent, but each can be illustrated using distinct examples. Learning (and teaching students) to avoid these misunderstandings represents a key step toward the development of adequate tree thinking skills.
Misconception #1: Higher and Lower
Notions of a “Great Chain of Being” or scala naturae (scales of nature), in which living species (and, in some cases, nonliving matter and/or the divine) are ranked from lowest to highest and extend back at least as far as Aristotle. Although Darwin (1837) himself noted early on that “It is absurd to talk of one animal being higher than another,” in many respects, his contribution merely shifted the explanation for the perceived rankings, replacing the scales of nature with an “evolutionary scale” or “evolutionary ladder” (Ruse 1996). Talk of “higher” and “lower” organisms, made in reference to contemporaneous species, persists in both public and professional scientific discourse. Not surprisingly, humans typically are (self-)designated as the “highest” organisms, with other living species ranked as higher or lower on the “evolutionary scale” according to how similar they are to this particular terminal node on the phylogeny of animals.
As many prominent authors have noted, there is no scientifically defensible basis on which to rank living species in this way, regardless of how interesting or unique some aspect of their biology may be to human observers (e.g., Dawkins 1992; Gould 1994, 1996). This error does not so much reflect a specific misunderstanding of phylogenetic diagrams per se but a failure to grasp the very concept of common descent. Therefore, the adjustment to be made in this case is from imagining evolution as a linear, progressive process that generates ladder-like ranks to one of branching and diversification of which trees are the result (e.g., O’Hara 1992, 1997; Nee 2005).
Misconception #2: Main Line and Side Tracks
Although it is clearly a critical first step, recognizing evolution as tree-like does not in itself eliminate progressionist interpretations of life’s history. Even those who acknowledge the branching nature of evolutionary change may continue to interpret it as a progressive process in which a “main line” has led to a distinct endpoint (namely Homo sapiens). In this narrative, all other modern species are derivatives of “side tracks,” anomalous offshoots of the main line to humans that all went astray for one reason or another. Even Huxley (1880) fell prey to this line of thinking when he suggested that the teleost fishes “appear to me to be off the main line of evolution—to represent, as it were, side tracks starting from certain points of that line.”
Figure 10a provides an illustration of how Huxley could reach such a false conclusion while still accepting the basic concept of tree-like branching. This represents an unbalanced, right-ladderized tree with representatives of several vertebrate lineages, including the cartilaginous fishes, teleost fishes, amphibians, birds, and the mammalian lineage as represented by humans. For many, an intuitive interpretation of this tree is that humans represent an endpoint of a “main line,” with all other lineages branching off from this line at some time in the past.
Two points can help to correct this misconception. First, recall from Fig. 3 that all siblings are equally related to their shared cousins. In this tree, all members of the clade that includes frogs, birds, and humans (tetrapods) are equally related to all members of the clade that includes goldfish and trout (teleost fishes). Second, a simple rotation of a few internal nodes or adding a better representation of some of the most diverse groups, as reflected in Fig. 10b, completely changes this perception without any effect on the accuracy of the tree. Few readers would interpret Fig. 10b as implying that a main line exists with perch as the endpoint and humans and other mammals as a minor, early branching offshoot, even given the fact that teleost fishes make up roughly 50% of all vertebrate diversity, whereas mammals represent about 10%. Still, the logic behind such an obviously silly reading of this tree is no more fallacious than of the intuitive “main line” interpretation of Fig. 10a. To quote O’Hara (1992),
When we come to realize that even among the vertebrates there are 50,000 different ‘vertebrate stories’, each one with a different ending and each one with a different narrative landscape; when we truly think in terms of the diverging tree, instead of the line; when we understand that it is absurd to talk of one animal being higher than another; only then will we see the full grandeur of the historical view of life.
As a matter of fact, it is most likely that evolutionary history will be misconstrued as representing a progressive “main line” when there is only one obvious endpoint available. In what he called “life’s little joke,” Gould (1991) noted that only unsuccessful lineages with very few living representatives are taken as endpoints of a supposed main line.
Misconception #3: Reading across the Tips
Referring to a cladogram similar to the one shown in Fig. 11a, Baum et al. (2005) asked readers to consider the following question on the basis of their reading of the tree: “Is the frog more closely related to the fish or the human?” The expectation, which has been reinforced by additional studies (Meir et al. 2007), is that many people intuitively interpret the tree as indicating a closer relatedness between frog and fish than between frog and human. They do so because they incorrectly read meaning into the order of the terminal nodes, rather than assessing the pattern of branching that links these contemporary tips to one another historically.
As a means of correcting this misinterpretation, one may take the time to identify the clades depicted in the tree (Baum et al. 2005). Humans, cats, and their common mammalian ancestor represent one clade, as do birds, lizards, and their common ancestor. These lineages together with their shared ancestor represent a clade (amniotes) in which the first two clades are nested. Adding frogs and the ancestor linking them to the aforementioned species creates a yet larger clade (tetrapods). Adding fishes and the common ancestor of all species on this tree creates the final and largest clade (vertebrates). Because frogs can be included in a clade with humans before fishes can—in other words, because frogs and humans share a common ancestor that is not shared with fishes—frogs are more closely related to humans than to fishes. Indeed, frogs and humans are exactly equally related to fishes through this common ancestor (recall that two cousins are equally related to a third, more distant relative).
A more rapid approach is to mentally rotate a few internal nodes with no effect on the topology of the tree, as shown in Fig. 11b. In this modified tree, humans are still sister to cats and birds are sister to lizards, frogs are then sister to amniotes, and fishes are the outgroup to the tetrapods. This second tree is identical in topology and is therefore equally accurate as the first tree. However, it should be obvious that humans are not suddenly more closely related to frogs than to reptiles and birds.
Reading across the tips is not just problematic when interpreting relatedness. It can also lead readers and even authors of scientific publications to incorrectly intuit the existence of evolutionary trends where none exist or to overlook them where they do. For example, the phylogeny depicted in Fig. 12a may seem to show a trend toward increased body size in this snail clade. However, a simple rotation of a few internal nodes to produce an equivalent but nonladderized tree destroys this illusion (Fig. 12b). Conversely, although a reading across the tips in Fig. 12c would provide no indication of the fact, this tree indicates strong evidence for an evolutionary trend toward larger body size. In this case, information is available about the common ancestors, and it is clear that both descendants have been larger than their shared ancestor following every branching event. Only historical data or statistically rigorous inferences about history, and not a simple comparison of living species, can provide convincing support for claims of an evolutionary trend.
Misconception #4: Similarity versus Relatedness
The modern science of taxonomy is built upon the foundation laid by Carolus Linnaeus in the mid-eighteenth century. His system, which long predated the widespread scientific acceptance of common descent inspired by Darwin, categorized organisms on the basis of physical similarity. Notably, in the first edition of his Systema Naturae of 1735, whales were grouped with fishes—an oversight that he corrected in the tenth edition in 1758 by placing them with the other mammals. Today, the primary criterion for scientific classification is evolutionary relatedness, whereas differences in the degree of physical similarity across lineages are often a confounding variable. This can be so for two major reasons: First, as with whales and fishes, adaptation to similar environments can lead to a superficial convergence of physical appearance. Second, the rates of morphological change can vary considerably among lineages, with some remaining similar to a common ancestor and/or to more distantly related contemporary lineages and others becoming markedly different over the same time span (Baum et al. 2005).
By way of example, consider the phylogeny presented in Fig. 13. This tree shows one of the more prominent hypotheses regarding the relationships of major groups of nonmammalian tetrapods. Frogs are given as the outgroup in this tree, with turtles being the next most distantly related lineage to the others. Snakes are the sister group to lizards, and in fact, both modern lizards and snakes may be descended from a more ancestral lizard lineage. Most of these considerations are reasonably intuitive, but many people find it surprising that phylogenetically birds are located within the “reptiles” and represent the sister group to crocodilians. Although physical similarities would seem to suggest otherwise, crocodiles are more closely related to birds than they are to lizards. The reason for this is that the bird lineage has experienced significant modification, whereas crocodilians have remained largely unchanged for tens of millions of years. It is important to note that birds and crocodiles represent each other’s closest living relatives but that birds are not descended from crocodiles nor vice versa—as taxonomic groups, crocodilians and birds both arose long after their respective lineages diverged from a common ancestor well over 200 million years ago. Birds are, in fact, descended from a lineage of theropod dinosaurs, making Tyrannosaurus rex far more similar to the last nonavian ancestor of modern birds than anything resembling a crocodile (see Prothero 2007).
Misconception #5: Sibling versus Ancestor
Mistaken assumptions that the ancestor of two modern groups must have been very similar to, or perhaps even was, one of the modern groups extend well beyond the case of crocodiles and birds. Any claim that two species represent each other’s closest living relative should not be construed as implying that one of the modern groups itself is an ancestor of the other nor even that the common ancestor looked anything like either of the two groups. For example, the hypothesis that whales and hippopotamuses are sister groups (e.g., Boisserie et al. 2005) does not imply that the ancestor of whales was a hippo nor that it would even have been thought of as being similar to a hippo were it encountered when it was alive. Not surprisingly, the fossil record of whales, which is becoming increasingly extensive, shows that the early ancestors of whales (e.g., Pakicetus, Ambulocetus) bore no substantial resemblance to modern hippos at all (Thewissen and Bajpai 2001; Thewissen and Williams 2002).
Nowhere is this misconception more pronounced than in discussions of human evolution. One often hears it expressed in the rhetorical challenges offered by those who exhibit the poorest comprehension of evolutionary concepts: “If humans are descended from chimps,” so the question goes, “then why are there still chimps?” “If humans are descended from monkeys, then why has no one observed a monkey giving birth to a human baby?” The answer is simple because the premise is flawed: Humans are not descended from chimpanzees or monkeys, and no sane biologist suggests otherwise.
Figure 14a shows a ladderized phylogeny of the anthropoid primates. Humans and chimpanzees are sister taxa whose next (equally) close relatives are the gorillas, then the orangutans. Humans and chimpanzees share a common ancestor that lived around 5–7 million years ago. This ancestor was neither chimpanzee nor human, and as with whales, the increasingly detailed fossil record of the hominin lineage shows the extensive changes that have taken place since this divergence. Although the fossil record of chimpanzee ancestors is currently sparse, it can be presumed that a great deal of change characterized the evolutionary history of that branch as well.
The notion that other primates should have disappeared now that humans have evolved is based on a false understanding of species formation. Specifically, it assumes a process in which one species gradually transforms as a whole into another (called “anagenesis”). The reality of species diversification is that it most often proceeds by “cladogenesis,” the branching of new species from common ancestral populations. Chimps continue to exist because they are part of a separate branch that formed through cladogenesis when an ancestral population of a species, which was neither chimp nor human, split into independent lineages. Being confused about the coexistence of humans and chimpanzees is akin to being puzzled by the coexistence of Canada and Australia. Once again, rotating some internal nodes (Fig. 14b) can help to correct the misperception that other living primates are ancestors of humans or offshoots of a main line leading to humans or of incorrectly assuming that the left- or bottom-most tip represents an ancestor to those at the terminal nodes of the other branches.
Misconception #6: Long Branch Implies no Change (or “Less Diverse Equals Basal Equals Ancestral”)
When viewing unbalanced trees such as those presented as Figs. 10a, 11a, 13, and 14a, there is a tendency among many people to misinterpret the long branch leading to the lone outgroup taxon in two ways. First, it is sometimes assumed that this species, although actually a contemporary of all others on the tree, is ancestral to the other lineages or at least is more similar to the root ancestor than any of the other species included in the tree (Crisp and Cook 2005). Second, this long branch is often taken to imply that no further branching has occurred along this lineage.
Figure 15 exposes the fallacy of both interpretations. In this case, humans are accurately included as the outgroup—the so-called basal lineage—to the echinoderms. It should go without saying that the branch leading from the common ancestor of echinoderms and vertebrates to modern mammals such as humans has not been devoid of additional divergence. In actuality, there have been hundreds of thousands, if not millions, of branching events along that lineage. The corollary of this observation, that humans do not resemble the ancestral echinoderm, should be even more obvious. Nonetheless, equally false interpretations of “basal” lineages are not uncommon, even in the scientific literature (Crisp and Cook 2005).
As with several of the other misconceptions discussed here, the problem of “basal equals primitive” is most likely to emerge when the tree under consideration is unbalanced and ladderized. It must be borne in mind that even if the unbalanced nature of a phylogeny reflects real differences in species diversity (which it often does not, as most trees include an incomplete sample of species), the relative diversity of major lineages can change over time, with one being the most diverse now and the other having been so in the past (Crisp and Cook 2005).
Finally, it must be pointed out that the relevant comparison is not between “primitive” (as in the sense of “poorly developed”) versus “advanced.” The only legitimate comparison is between “primitive” in the technical sense, meaning more like the last common ancestor (also called “ancestral”), versus “derived” (i.e., different from the ancestor). Any other interpretation runs the risk of invoking the fallacy of a progressive evolutionary scale. Moreover, as Crisp and Cook (2005) put it,
Once two lineages have separated, each evolves new characters independently of the other and, with time, each will show a mixture of plesiomorphic [inherited largely unchanged from the ancestor] and apomorphic [newly evolved and thus not possessed by the ancestor] character states. Therefore, extant species in both lineages resemble, to varying degrees, their common ancestor. Consequently, whereas character states can be relatively ancestral (plesiomorphic) or derived (apomorphic), these concepts are nonsensical when applied to whole organisms.
Misconception #7: Different Lineage Ages for Modern Species
Groups of species recognized as taxonomically distinct on the basis of particular characteristics (say, “flowering plants” or “beetles”) may have appeared at different times in the history of life and thus may be of different ages. However, the overall lineage leading to any modern species is of exactly the same age as that leading to any other modern species with whom an ancestor is shared (Fig. 16). This is a fundamental consequence of the principle of common descent, but there nevertheless can be a tendency to conflate taxon age with lineage age. For example, the group identified as teleost fishes is thought to be older—that is, to have appeared as a recognizable taxonomic group earlier—than mammals. Similarly, the first organisms that would be recognized as rainbow trout (Oncorhynchus mykiss) probably lived and died before the first individuals that would have been classified as Homo sapiens were born. However, rainbow trout and humans are contemporary species, meaning that the lineages of which they are currently terminal nodes have been evolving for exactly the same amount of time since their divergence from a distant common ancestor. As a result, any notion that one of these lineages is “more evolved” or that one has had more time to accumulate differences is flawed.
Misconception #8: Backwards Time Axes
Among the common misconceptions identified by Meir et al. (2007) was the tendency for many students to misread the time axis on evolutionary trees. Many students interpreted the location of the terminal nodes as indicating time, for example by reading from left to right or from the leftmost tip to the root. In Fig. 17a, for example, many students read time as proceeding from birds (oldest) to the root W (youngest) or from birds (oldest) to kangaroos (youngest). Neither is correct, as time extends from the root to the terminal nodes, all of which are contemporary. This misinterpretation may have been exacerbated by the fact that the tree used in the quiz placed mammals—which many students assume to be the most “advanced” and hence most recent group—alone on the less diverse branch at the far right of an unbalanced, ladderized tree (unfortunately, a tendency to place humans or some other preferred taxon at the top or right of every tree appears to be an unshakable habit among many phylogeneticists, although there is no objective reason for doing so). As indicated in Fig. 5, even on cladograms, in which the lengths of the branches are not scaled to time, the historical order in which ancestors lived extends from the most distant past at the root, through a series of increasingly recent branching events, to the tips representing contemporary species.
Misconception #9: More Intervening Nodes Equals More Distantly Related
In the study by Meir et al. (2007), many students demonstrated a tendency to assess relatedness in a phylogeny like the one depicted in Fig. 17a by “counting nodes.” For example, because birds on this tree are separated from mammals by four internal nodes (Z, Y, X, W), whereas the separation of turtles and mammals consists of only two internal nodes (X, W), many students incorrectly concluded that birds must be more distantly related to mammals than are turtles. The important point in calculating relatedness is not the number of intervening nodes along a given branch but the number of shared ancestors.
In Fig. 17a, both turtles and birds share one ancestor with mammals (node W), making them equally closely related to mammals. By contrast, birds share three common ancestors with crocodilians (nodes Z, Y, and X) but only two with turtles (nodes X and W), which makes birds and crocodilians more closely related to one another than either is to turtles. To illustrate the basic notion that all modern species in a tree are equally distant from their common ancestor, one can plot the same phylogeny as in Fig. 17a with different patterns for each branch (Fig. 17b) and then splice those branches together to show that the total distance from the root (node W) to any of the terminal nodes is exactly equal (Fig. 17c). The only difference is the number of branching events that occurred within the lineages, whereas the relatedness of the lineages themselves is not affected by this. Misconceptions about relatedness based on node counting also could be countered by balancing the tree, for example by deleting all but one species of birds/reptiles, resulting in a symmetrical V-shaped tree, regardless of which species remains along with mammals, or by adding an equal number of mammals to the sample to even out the diversity along the major branches.
Misconception #10: Change Only at Nodes
There is a legitimate debate among professional evolutionary biologists regarding the patterns of species formation, such as whether it occurs comparatively rapidly (in a geological sense) or is more gradual. Proponents of the punctuated equilibrium model of speciation argue that species remain largely unchanged morphologically for the duration of their existence, with most physical diversification occurring concomitant with species formation events (Eldredge and Gould 1972; Gould 2002; Eldredge 2008). If punctuated equilibrium were established conclusively to represent the exclusive mode of species formation in a clade and an accurate and complete phylogenetic tree were available for that clade that included all living and extinct species, then one could reasonably interpret the internal nodes as the points at which most morphological divergence took place among species. As Meir et al. (2007) noted, many students do draw such a conclusion, although of course this is not because they possess the requisite knowledge on which to base it.
The fact is that one should not assume that an internal node indicates the exact moment (again, geologically speaking) when particular physical changes came about, any more than one should interpret a long, node-free branch as indicating that no change has occurred. More accurately, an internal node represents the time at which a formerly cohesive population diverged into two genetically isolated descendant populations, with morphological change possible both at this time and long afterward (Baum et al. 2005).
Finally, one must bear in mind that terminal nodes can also be misinterpreted if the diversity that they sometimes represent is neglected. For example, the tree in Fig. 11 shows only a single fish, a frog, a lizard, a bird, a cat, and a human, but in actuality, these six terminal nodes together represent more than 50,000 species of living vertebrates and an untold number of ancestors. The important point is that any given node, whether internal or at the tips, represents a diverse assemblage of organisms with a complex evolutionary history.
