Organizing Life on Earth

Phylogenetic Trees

Phylogenetic trees illustrate the hypothetical evolution of organisms and their relationship to other species.

Learning Objectives

Describe the various types of phylogenetic trees and how they organize life

Key Takeaways

Key Points

  • Rooted trees have a single lineage at the base representing a common ancestor that connects all organisms presented in a phylogenetic diagram.
  • Branch points in a phylogenetic tree represent a split where a single lineage evolved into a distinct new one, while basal taxon depict unbranched lineages that evolved early from the root.
  • Unrooted trees portray relationships among species, but do not depict their common ancestor.
  • Phylogenetic trees are hypotheses and are, therefore, modified as data becomes available.
  • Systematics uses data from fossils, the study of bodily structures, molecules used by a species, and DNA analysis to contribute to the building, updating, and maintaining of phylogenetic trees.

Key Terms

  • polytomy: a section of a phylogeny in which the evolutionary relationships cannot be fully resolved to dichotomies
  • basal taxon: a lineage, displayed using a phylogenetic tree, that evolved early from the root and from which no other branches have diverged
  • systematics: research into the relationships of organisms; the science of systematic classification
  • phylogeny: the visual representation of the evolutionary history of organisms; based on rigorous analyses

Phylogenetic Trees

Scientists use a tool called a phylogenetic tree, a type of diagram, to show the evolutionary pathways and connections among 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, a “tree of life”, as it is sometimes called, can be constructed to illustrate when different organisms evolved and to show the relationships among different organisms.

Unlike a taxonomic classification diagram, a phylogenetic tree can be read 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 don’t show a common ancestor but do show relationships among species.

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Phylogenetic trees: 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.

In a rooted tree, the branching indicates evolutionary relationships. The point where a split occurs, called a branch point, represents where a single lineage evolved into a distinct new one. A lineage that evolved early from the root and remains unbranched is called basal taxon. When two lineages stem from the same branch point, they are called sister taxa. A branch with more than two lineages is called a polytomy and serves to illustrate where scientists have not definitively determined all of the relationships. It is important to 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 apart at a specific branch point, but neither taxa gave rise to the other.

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Rooted phylogenetic trees: The root of a phylogenetic tree 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.

Rooted phylogenetic trees can serve as a pathway to understanding evolutionary history. The pathway can be traced 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 that species’ ancestors, as well as where lineages share a common ancestry. In addition, the tree can be used 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 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; together, these disciplines contribute to building, updating, and maintaining the “tree of life.” Information is used to organize and classify organisms based on evolutionary relationships in a scientific field called systematics. 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.

Limitations of Phylogenetic Trees

Limitations of phylogenetic trees include the inability to distinguish evolutionary time and relatedness between distinct species.

Learning Objectives

Identify the limitations of phylogenetic trees as representations of the organization of life

Key Takeaways

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 and only depict evolutionary order.
  • Phylogenetic trees are like real trees in that they do not simply grow in only one direction after a new branch forms; the evolution of one organism does not necessarily signify the evolutionary end of another.

Key Terms

  • phenotypical: of or pertaining to a phenotype: the appearance of an organism based on a multifactorial combination of genetic traits and environmental factors

Limitations of Phylogenetic Trees

It may be easy to assume that more closely-related organisms look more alike; 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 shows that lizards and rabbits both have amniotic eggs, whereas frogs do not; yet lizards and frogs appear more similar than lizards and rabbits.

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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.

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. A 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 shows that the oldest trait is the vertebral column, followed by hinged jaws, and so forth. Remember, any phylogenetic tree is a part of the greater whole and, as with a real tree, it does not grow in only one direction after a new branch develops. So, simply 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.

The Levels of Classification

Taxanomic classification divides species in a hierarchical system beginning with a domain and ending with a single species.

Learning Objectives

Describe how taxonomic classification of organisms is accomplished and detail the levels of taxonomic classification from domain to species

Key Takeaways

Key Points

  • Categories within taxonomic classification are arranged in increasing specificity.
  • The most general category in taxonomic classification is domain, which is the point of origin for all species; all species belong to one of these domains: Bacteria, Archaea, and Eukarya.
  • Within each of the three domains, we find kingdoms, the second category within taxonomic classification, followed by subsequent categories that include phylum, class, order, family, genus, and species.
  • At each classification category, organisms become more similar because they are more closely related.
  • As scientific technology advances, changes to the taxonomic classification of many species must be altered as inaccuracies in classifications are discovered and corrected.

Key Terms

  • binomial nomenclature: the scientific system of naming each species of organism with a Latinized name in two parts
  • taxon: any of the taxonomic categories such as phylum or subspecies
  • Linnaeus: Swedish botanist, physician and zoologist who laid the foundations for the modern scheme of nomenclature; known as the “father of modern taxonomy”

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.

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Hierarchical models: 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.

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.

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Levels in taxonomic classification: 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.

The kingdom Animalia stems from the Eukarya domain. The full name of an organism technically has eight terms. For dogs, it is: Eukarya, Animalia, Chordata, Mammalia, Carnivora, Canidae, Canis, and lupus. Notice that each name is capitalized except for species and that 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, in what is called binomial nomenclature. Therefore, the scientific name of the dog is Canis lupus. The name at each level is also called 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 considered separate subspecies due to geographic or behavioral isolation or other factors.

Dogs actually share a domain (Eukarya) 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 physical characteristics, but as DNA technology developed, more precise phylogenies have been determined.

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 to the whale.