1.6 Introduction to Phylogenies

Evolution is defined as the gradual change in characteristics of a population of organisms over generations. As changes accumulate, new species can form. A phylogeny describes the relationships among groups of organisms (such as which groups are most closely related, which diverged most recently from a common ancestor, etc.  The groups of organisms being compared in a phylogeny might be populations, species or groups of species such as genera, kingdoms, etc.  When comparing groups, we often use the generic term taxa (singular, taxon) which could refer to any of these levels of groups.   Phylogenetic relationships provide information on shared ancestry among taxa.

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Phylogenetic Trees

Scientists use a diagram called a phylogenetic tree to show the evolutionary pathways and connections among taxa.  A phylogenetic tree is a hypothesis of the evolutionary past since one cannot go back to confirm the proposed relationships. In other words, a “tree of life” can be constructed to illustrate when different organisms evolved and to show the relationships among different organisms (Figure 1).

Many phylogenetic trees have a single lineage at the base representing a common ancestor. Scientists call such trees rooted, which means there is a single ancestral lineage (typically drawn from the bottom or left) to which all organisms represented in the diagram relate. Notice in the rooted phylogenetic tree that the three domains— Bacteria, Archaea, and Eukarya—diverge from a single point and branch off. The small branch that plants and animals (including humans) occupy in this diagram shows how recent and miniscule these groups are compared with other organisms. Unrooted trees don’t show a common ancestor but do show relationships among species.

 

The phylogenetic tree in part a is rooted and resembles a living tree, with a common ancestor indicated as the base of the trunk. Two branches form from the trunk. The left branch leads to the domain Bacteria. The right branch branches again, giving rise to Archaea and Eukarya. Smaller branches within each domain indicate the groups present in that domain. The phylogenetic tree in part B is unrooted. It does not resemble a living tree; rather, groups of organisms within the Archaea, Eukarya, and Bacteria domains are arranged in a circle. Lines connect the groups within each domain. The groups within Archaea and Eukarya are then connected together. A line from the Archaea/ Eukarya domains, and another from the Bacteria meet in the center of the circle. There is no root, and therefore no indication of which domain arose first.
Figure 1. Both of these phylogenetic trees shows the relationship of the three domains of life—Bacteria, Archaea, and Eukarya—but the (a) rooted tree attempts to identify when various species diverged from a common ancestor while the (b) unrooted tree does not. (credit a: modification of work by Eric Gaba)

 

The diagrams can help us understand evolutionary history. The pathway can be traced from the origin of life to any individual taxon by navigating through the evolutionary branches between the two points. Also, by starting with a single taxon and tracing back towards the “trunk” of the tree, one can discover that taxon’s ancestors, as well as where lineages share a common ancestry.

Another point to mention on phylogenetic tree structure is that rotation at branch points does not change the information. For example, if a branch point was rotated and the taxon order changed, this would not alter the information because the evolution of each taxon from the branch point was independent of the other.

Many disciplines within the study of biology contribute to understanding how past and present life evolved over time.  Data may be collected from fossils, from studying the structure of body parts or molecules used by an organism, and by DNA analysis. By combining data from many sources, scientists can put together the phylogeny of an organism; since phylogenetic trees are hypotheses, they will continue to change as new types of life are discovered and new information is learned.  Many phylogenietic trees are being re-evaluated in light of our increased ability to examine DNA evidence.

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Limitations of Phylogenetic Trees

It may be easy to assume that more closely related organisms look more alike, and while this is often the case, it is not always true. 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 (Figure 2) shows that lizards and rabbits both have amniotic eggs, whereas frogs do not; yet lizards and frogs appear more similar than lizards and rabbits.

 

The ladder-like phylogenetic tree starts with a trunk at the left. A question next to the trunk asks whether a vertebral column is present. If the answer is no, a branch leads downward to lancelet. If the answer is yes, a branch leads upward to another question: is a hinged jaw present? If the answer is no, a branch leads downward to lamprey. If the answer is yes, a branch leads upward to another question: are legs present? If the answer is no, a branch leads downward to fish. If the answer is yes, a branch leads upward to another question: does the egg have amnion? If the answer is no, the branch leads downward to frog. If the answer is yes, the branch leads upward to another question: is hair present? If the answer is no, the branch leads downward to lizard. If the answer is yes, the branch leads upward to rabbit.
Figure 2. 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.

 

Another aspect of phylogenetic trees is that, unless otherwise indicated, the branches do not account for length of time, only the evolutionary order. In other words, the length of a branch does not typically mean more time passed, nor does a short branch mean less time passed— unless specified on the diagram. For example, in Figure 2, the tree does 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. Again using Figure 2, the tree shows that the oldest trait is the vertebral column, followed by hinged jaws, and so forth. Remember that any phylogenetic tree is a part of the greater whole, and like a real tree, it does not grow in only one direction after a new branch develops. So, for the organisms in Figure 2, just because a vertebral column evolved does not mean that invertebrate evolution ceased, it only means that a new branch formed. Also, groups that are not closely related, but evolve under similar conditions, may appear more phenotypically similar to each other than to a close relative.

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The Levels of Classification

Taxonomy (which literally means “arrangement law”) is the science of classifying organisms to construct internationally shared classification systems with each organism placed into more and more inclusive groupings. Think about how a grocery store is organized. One large space is divided into departments, such as produce, dairy, and meats. Then each department further divides into aisles, then each aisle into categories and brands, and then finally a single product. This organization from larger to smaller, more specific categories is called a hierarchical system.

The taxonomic classification system (also called the Linnaean system after its inventor, Carl Linnaeus, a Swedish botanist, zoologist, and physician) uses a hierarchical model. Moving from the point of origin, the groups become more specific, until one branch ends as a single species. For example, after the common beginning of all life, scientists divide organisms into three large categories called a domain: Bacteria, Archaea, and Eukarya. Within each domain is a second category called a kingdom. After kingdoms, the subsequent categories of increasing specificity are: phylum, class, order, family, genus, and species (Figure 3).

 

The illustration shows the classification of a dog, which belongs in the domain Eukarya, kingdom Animalia, phylum Chordata, class Mammalia, order Carnivore, family Canidae, genus Canis, species Canis lupus, and the subspecies is Canis lupus familiaris.
Figure 3. The taxonomic classification system uses a hierarchical model to organize living organisms into increasingly specific categories. The common dog, Canis lupus familiaris, is a subspecies of Canis lupus, which also includes the wolf and dingo. (credit “dog”: modification of work by Janneke Vreugdenhil)

 

Figure 4 shows how the levels move toward specificity with other organisms. Notice how the dog shares a domain with the widest diversity of organisms, including plants and butterflies. At each sublevel, the organisms become more similar because they are more closely related. Historically, scientists classified organisms using characteristics, but as DNA technology developed, more precise phylogenies have been determined.

 

ART CONNECTION
 
Illustration shows the taxonomic groups shared by various species. All of the organisms shown are in the domain Eukarya: plants, insects, fish, rabbits, cats, foxes, jackals wolves, and dogs. Of theses, insects, fish, rabbits, cats, foxes, jackals, wolves and dogs are in the kingdom Animalia. Within the kingdom Animalia, fish, rabbits, cats, foxes, jackals, wolves, and dogs are in the phylum Chordata. Rabbits, cats, foxes, jackals, wolves, and dogs are in the class Mammalia. Cats, foxes, jackals, wolves, and dogs are in the order Carnivora. Foxes, jackals, wolves, and dogs are in the family Canidae. Jackals, wolves and dogs are in the genus Canis. Wolves and Dogs and have the species name Canis lupus. Dogs have the subspecies name Canis lupus familiaris.
Figure 4. At each sublevel in the taxonomic classification system, organisms become more similar. Dogs and wolves are the same species because they can breed and produce viable offspring, but they are different enough to be classified as different subspecies. (credit “plant”: modification of work by “berduchwal”/Flickr; credit “insect”: modification of work by Jon Sullivan; credit “fish”: modification of work by Christian Mehlführer; credit “rabbit”: modification of work by Aidan Wojtas; credit “cat”: modification of work by Jonathan Lidbeck; credit “fox”: modification of work by Kevin Bacher, NPS; credit “jackal”: modification of work by Thomas A. Hermann, NBII, USGS; credit “wolf”: modification of work by Robert Dewar; credit “dog”: modification of work by “digital_image_fan”/Flickr)

 

Recent genetic analysis and other advancements have found that some earlier phylogenetic classifications do not align with the evolutionary past; therefore, changes and updates must be made as new discoveries occur. Recall that phylogenetic trees are hypotheses and are modified as data becomes available. In addition, classification historically has focused on grouping organisms mainly by shared characteristics and does not necessarily illustrate how the various groups relate to each other from an evolutionary perspective. For example, despite the fact that a hippopotamus resembles a pig more than a whale, the hippopotamus may be the closest living relative of the whale.

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Section Summary

Scientists continually gain new information that helps understand the evolutionary history of life on Earth. Each group of organisms went through its own evolutionary journey, called its phylogeny. Each organism shares relatedness with others, and based on morphologic and genetic evidence, scientists attempt to map the evolutionary pathways of all life on Earth. Historically, organisms were organized into a taxonomic classification system. However, today many scientists build phylogenetic trees to illustrate evolutionary relationships.

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Glossary

branch point
node on a phylogenetic tree where a single lineage splits into distinct new ones
phylogenetic tree
diagram used to reflect the evolutionary relationships among organisms or groups of organisms
phylogeny
evolutionary history and relationship of an organism or group of organisms
taxon
(plural: taxa) group of organisms (could be a species, genus, order, etc.)
taxonomy
science of classifying organisms

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Human Biology 2nd edition Copyright © by Sarah Malmquist and Kristina Prescott is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License, except where otherwise noted.

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