32 Organizing Life on Earth

By the end of this section, you will be able to do the following:

  • Discuss the need for a comprehensive classification system
  • List the different levels of the taxonomic classification system
  • Describe how systematics and taxonomy relate to phylogeny
  • Discuss a phylogenetic tree’s components and purpose

In scientific terms, phylogeny is the evolutionary history and relationship of an organism or group of organisms. A phylogeny describes the organisim’s relationships, such as from which organisms it may have evolved, or to which species it is most closely related. Phylogenetic relationships provide information on shared ancestry but not necessarily on how organisms are similar or different.

Phylogenetic Trees

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

Unlike a taxonomic classification diagram, we can read a phylogenetic tree like a map of evolutionary history. 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 do not 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 show 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)

In a rooted tree, the branching indicates evolutionary relationships (Figure 2). The point where a split occurs, a branch point, represents where a single lineage evolved into a distinct new one. We call a lineage that evolved early from the root that remains unbranched a basal taxon. We call two lineages stemming from the same branch point sister taxa. A branch with more than two lineages is a polytomy and serves to illustrate where scientists have not definitively determined all of the relationships. Note that although sister taxa and polytomy do share an ancestor, it does not mean that the groups of organisms split or evolved from each other. Organisms in two taxa may have split at a specific branch point, but neither taxon gave rise to the other.

Illustration shows a phylogenetic tree that starts at a root, indicating that all organisms on the tree share a common ancestor. Shortly after the root, the tree branches out. One branch gives rise to a single, basal lineage, and the other gives rise to all other organisms on the tree. The next branch forks at one point into four different lineages, an example of polytomy. The final branch gives rise to two lineages, an example of sister taxa.
Figure 2: A phylogenetic tree’s root indicates that an ancestral lineage gave rise to all organisms on the tree. A branch point indicates where two lineages diverged. A lineage that evolved early and remains unbranched is a basal taxon. When two lineages stem from the same branch point, they are sister taxa. A branch with more than two lineages is a polytomy.

The diagrams above can serve as a pathway to understanding evolutionary history. We can trace the pathway from the origin of life to any individual species by navigating through the evolutionary branches between the two points. Also, by starting with a single species and tracing back towards the “trunk” of the tree, one can discover species’ ancestors, as well as where lineages share a common ancestry. In addition, we can use the tree to study entire groups of organisms.

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 rotated and the taxon order changed, this would not alter the information because each taxon’s evolution 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; these disciplines together contribute to building, updating, and maintaining the “tree of life.” Systematics is the field that scientists use to organize and classify organisms based on evolutionary relationships. Researchers may use data from fossils, from studying the body part structures, or molecules that an organism uses, and DNA analysis. By combining data from many sources, scientists can construct an organism’s phylogeny Since phylogenetic trees are hypotheses, they will continue to change as researchers discover new types of life and learn new information.

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, 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 in Figure 3 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 3: An organism that lacked a vertebral column roots this ladder-like phylogenetic tree of vertebrates. At each branch point, scientists place organisms with different characters in different groups based on shared characteristics.

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, a branch’s length 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 3, 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 3, 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. Thus, for the organisms in Figure 3, 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.

Taxonomy (which literally means “arrangement law”) is the science of classifying organisms to construct internationally shared classification systems with each organism placed into increasingly more inclusive groupings. Think about a grocery store’s organization. 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. We call this organization from larger to smaller, more specific categories 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 domains: 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 4).

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 4: 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)

The kingdom Animalia stems from the Eukarya domain. Figure 4 above shows the classification for the common dog. Therefore, the full name of an organism technically has eight terms. For the dog it is: Eukarya, Animalia, Chordata, Mammalia, Carnivora, Canidae, Canis, and lupus. Notice that each name is capitalized except for species, and the genus and species names are italicized. Scientists generally refer to an organism only by its genus and species, which is its two-word scientific name, or binomial nomenclature. Therefore, the scientific name of the dog is Canis lupus. The name at each level is also a taxon. In other words, dogs are in order Carnivora. Carnivora is the name of the taxon at the order level; Canidae is the taxon at the family level, and so forth. Organisms also have a common name that people typically use, in this case, dog. Note that the dog is additionally a subspecies: the “familiaris” in Canis lupus familiaris. Subspecies are members of the same species that are capable of mating and reproducing viable offspring, but they are separate subspecies due to geographic or behavioral isolation or other factors.

Figure 5 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, they have determined more precise phylogenies.

VISUAL 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 5: 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)

At what levels are cats and dogs part of the same group?


Answer:
Cats and dogs are part of the same group at five levels: both are in the domain Eukarya, the kingdom Animalia, the phylum Chordata, the class Mammalia, and the order Carnivora.

LINK TO LEARNING


Visit this website to classify three organisms – bear, orchid, and sea cucumber – from kingdom to species. To launch the game, under Classifying Life, click the picture of the bear or the Launch Interactive button.

Recent genetic analysis and other advancements have found that some earlier phylogenetic classifications do not align with the evolutionary past; therefore, researchers must make changes and updates 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 whale’s closest living relative.

Glossary

basal taxon
branch on a phylogenetic tree that has not diverged significantly from the root ancestor
binomial nomenclature
system of two-part scientific names for an organism, which includes genus and species names
branch point
node on a phylogenetic tree where a single lineage splits into distinct new ones
class
division of phylum in the taxonomic classification system
family
division of order in the taxonomic classification system
genus
division of family in the taxonomic classification system; the first part of the binomial scientific name
kingdom
domain division in the taxonomic classification system
order
class division in the taxonomic classification system
phylogenetic tree
diagram that reflects the evolutionary relationships among organisms or groups of organisms
phylogeny
evolutionary history and relationship of an organism or group of organisms
phylum
(plural: phyla) kingdom division in the taxonomic classification system
polytomy
branch on a phylogenetic tree with more than two groups or taxa
rooted
single ancestral lineage on a phylogenetic tree to which all organisms represented in the diagram relate
sister taxa
two lineages that diverged from the same branch point
systematics
field of organizing and classifying organisms based on evolutionary relationships
taxon
(plural: taxa) single level in the taxonomic classification system
taxonomy
science of classifying organisms

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