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4.2: Limitations of Phylogenetic Trees

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    Learning Objectives

    • Identify the limitations of phylogenetic trees as representations of the organization of life
    • Construct a simple phylogenetic tree

    Limitations of Phylogenetic Trees

    Phylogenetic trees represent hypotheses about the evolution of life. They are only as good as the data on which they are based. The data come from our studies of modern organisms and fossils. We do no know everything about modern organisms, and the fossil record includes very few of the organisms that actually lived. Thus, the data that scientists use to make phylogenetic trees will always be incomplete. We will never know enough about the ancestors to all modern organisms to reconstruct the tree of life perfectly. Thus, it is important to understand the strengths and limitations of the data used to make phylogenetic trees.

    Morphological Data

    Many phylogenetic trees are built using the morphology of organisms or fossils. Closely-related organisms often look alike; they share morphological traits. For example, humans, bonobos, and chimpanzees share more features with each other than they do with mice. While closely related organisms often look similar, it is not always true that lineages that share features are the most closely related. If two closely-related lineages evolved under significantly varied surroundings or after the evolution of a major new adaptation, it is possible for the two groups to appear more different than other groups that are not as closely related. For example, the phylogenetic tree shows that lizards and rabbits both have amniotic eggs, whereas frogs do not; yet lizards and frogs appear more similar than lizards and rabbits.


    Limitations of phylogenetic trees: This ladder-like phylogenetic tree of vertebrates is rooted by an organism that lacked a vertebral column. At each branch point, organisms with different characters are placed in different groups based on the characteristics they share.

    Distantly related organisms can also share morphological features. For example, many Bacteria are spherical in shape, as are many Archaea. All bacteria are more distantly related to all Archaea than lizards are to rabbits even though lizards and rabbits look much more different from each other. Thus, morphology is not particularly useful for determining evolutionary relationships among some groups of organisms. In fact, genetic data have shown that very closely related Cyanobacteria (a specific lineage of bacteria that perform oxygenic photosynthesis) can have very different cell shapes, and Cyanobacteria with similar shapes may be only distantly related to each other. Thus, understanding how morphology does or does not relate to evolutionary history is critically important when using morphological data as the basis for phylogenetic trees.

    Genetic Data

    Many phylogenetic trees are built using genetic data. Genes are the units of organisms that encode the results of evolution, making them particularly useful for building phylogenetic trees. However, different genes evolve in different ways, genes can be swapped among organisms, and genes can be lost by organisms. Thus, the choice of genes to use for a phylogenetic tree needs to reflect the scientific questions being asked. As an example, genes that encode for antibiotic resistance in bacteria can be shared among bacteria, even between relatively distantly related species. When a scientist makes a phylogenetic tree based on a gene that provides antibiotic resistance, the tree will reflect how that gene evolved, not necessarily how the organisms hosting the gene evolved. As another example, some genes are almost never shared among organisms, such as the genes encoding the machinery to convert DNA into RNA. These genes are critical for the organism to live, and they evolve very slowly. One of these genes, 16S rRNA, is commonly used to build phylogenetic trees showing the evolutionary relationships within Bacteria. These trees are often very reliable in terms of the branching order, but it turns out that there are large numbers of organisms that do not show up in the 16S rRNA data obtained using standard lab techniques. Other techniques have led to the identification of a huge diversity of bacteria (see Hug et al., 2016). As new techniques become available and more data are collected, the complexity of genes as a reflection of evolution is becoming more apparent. And all of the complexities provide information scientists can use to understand the processes and history of evolution. 

    Branch Length and Time

    Another aspect of phylogenetic trees is that, unless otherwise indicated, the branches do not account for length of time over which evolution occurred. Rather, they reflect the evolutionary difference and the order of divergence among lineages. In other words, a long branch does not typically mean more time passed; nor does a short branch mean less time passed, unless the data are specifically correlated to time with an evolutionary model. A phylogenetic tree may not indicate how much time passed between the evolution of amniotic eggs and hair. What the tree does show is the order in which things took place. For example, the tree in the diagram above shows that the oldest trait is the vertebral column, followed by hinged jaws, and so forth. Remember, any phylogenetic tree is an evolutionary hypothesis that represents part of the greater whole. The individual branches do not necessarily evolve at the same rate or in the same way. So, simply because a vertebral column evolved does not mean that invertebrate evolution ceased. It only means that two lineages diverged. Also, groups that are not closely related, but evolve under similar conditions, may appear more similar to each other than to a close relative.

    Key Points

    • Closely-related species may not always look more alike, while groups that are not closely related yet evolved under similar conditions, may appear more similar to each other.
    • In phylogenetic trees, branches do not usually account for length of time. They depict evolutionary order and evolutionary difference.
    • Phylogenetic trees  do not simply grow in only one direction after two lineages diverge; the evolution of one organism does not necessarily signify the evolutionary end of another.

    Questions to ponder

    • Choose some organisms that you are familiar with and try to construct a phylogenetic tree showing the relationships among them.
      • What features did you use to construct the tree?
      • What are some of the challenges you had to face?
      • What are some of the uncertainties in how accurately your tree reflects the evolutionary relationships among the organisms?


    Hug, L.A., Baker, B.J., Anantharaman, K., Brown, C.T., Probst, A.J., Castelle, C.J., Butterfield, C.N., Hernsdorf, A.W., Amano, Y., Ise, K., et al. A new view of the tree of life, Nature Microbiology, 2016, 1:16048. (link)

    This page titled 4.2: Limitations of Phylogenetic Trees is shared under a CC BY-NC-SA license and was authored, remixed, and/or curated by Dawn Sumner.

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