Biology 203 Lab

Phylogeny

Useful Reading

Campbell, Biology 6th Ed - Chapter 25, pgs 484-507

Campbell, Biology 7th Ed - Chapter 25, pgs 491-509

Vocabulary

Phylogenetics- a discipline of evolutionary biology which seeks to accurately depict the evolutionary relationships among living and non-living taxa.

Homology/homologs- when traits are similar due to shared ancestry (the trait was inherited from a shared ancestor).

Synapomorphy – a derived trait shared by taxa due to common ancestry. A derived homology.

Analogy/analogs – when traits are similar due to convergent evolution; the traits were not inherited from a common ancestor.

Taxa- general term for a taxonomic group (e.g. species, genera, families). Sister taxa are those presented as most-closely related in a phylogeny.

Clade- a group in a phylogenetic tree which begins with a node (ancestor) and includes everything more distal to the node (all descendents of the ancestor).

Monophyletic group- a proper clade; that is, a group which contains a common ancestor and all descendents of that ancestor (and no non-descendents).

Paraphyletic group- a group which contains a common ancestor and some, but not all, descendents of that ancestor.

Phylogenetics and Phylogenies

Phylogenetics is a discipline that aims to determine the true evolutionary relationships among organisms (The Tree of Life). Evolutionary biologists use a type of diagram, called a cladogram, to represent these evolutionary relationships or phylogenies. Cladograms (or phylogenetic trees) are sequentially branching trees. In these diagrams, you can gain information of the temporal pattern of diversification and shared ancestry.

Nodes on the trees (where branches meet) represent the common (shared) ancestor of all taxa beyond the node. If two taxa share a closer node than either share with a third taxon, then they share a more recent ancestor (they are more-closely related). Cladograms usually do not contain information about absolute time (e.g. in millions of years), but phylogenetic trees can be drawn which do depict the timing of events.

Reference the cladograms below, and make sure you understand how the following terms relate to the cladograms: sister taxa, node, branch, ancestor, descendent, most recent common ancestor.

Classification of organisms into the hierarchical system you are familiar with (e.g. Kingdom, Phylum, Class, etc.) is what the field of Taxonomy focuses on. Evolutionary biologists today believe that classification should represent true evolutionary relationships among organisms. Therefore, phylogenies are widely used for classification, and understanding the accurate phylogenetic relationships of organisms is important.

Taxa are best classified according to monophyletic groups, or clades. In these monophyletic groups, an ancestor (node) and all descendents are included. For example, “mammals” are a monophyletic group when we include the most recent common ancestor (MRCA) of all known mammals. “Reptiles” are not a monophyletic group if we exclude birds, since the MRCA of all reptiles is also a common ancestor of birds. Without birds included, “reptiles” is a paraphyletic group. Groups are polyphyletic when they include multiple taxa, but not the common ancestors.

Determining Phylogenetic Relationships

Phylogenetic relationships are established by analyzing homologous traits. Homologous traits are traits which are similar in two taxa because of shared ancestry. In contrast, analogous traits are similar because of convergent evolution of the two traits rather than inheritance from a shared ancestor. If we want to determine the accurate phylogeny of taxa, we need to concentrate on traits which are similar due to shared ancestry while ignoring analogies.

Because traits are constantly modified throughout evolutionary history, some components of a trait may be homologous, while others are analogous. For example, wings in birds and bats are analogous and due to convergent evolution. However, certain components of wings are homologous – e.g. finger and humerus bones.

Homologies are considered derived or ancestral depending on what clade you are looking at. Derived homologies (synapomorphies=shared, derived characters) are new to a clade of interest (first seen in ancestor of clade). Ancestral homologies (symplesiomorphies=shared, ancestral characters) arose before the common ancestor of the clade.

When determining phylogenetic relationships, we look only at the derived homologies (synapomorphies).

Synapomorphies which define clades are often included in cladograms, as seen in the examples below.

Deuterostomy is a synapomorphy (derived homology) of the clade containing chordates and echinoderms.
Multicellularity is a symplesiomorphy (ancestral homology) of the same clade.

Hair is a derived homology of all mammals.
Having a backbone is an ancestral homology of all mammals.
A backbone is a derived homology for the vertebrate clade.

The Principle of Parsimony is employed when using homologies to make a phylogeny. This principle favors the hypothesis that requires the fewest or simplest assumptions to explain an observation. In phylogenetics, the principle of parsimony invokes the minimal number of evolutionary changes to infer phylogenetic relationships. For example, it is more parsimonious to infer that a vertebral column evolved only once in a common ancestor of all living vertebrates than to infer that it evolved multiple times, once for fish, once for amphibians, etc. The first option requires fewer evolutionary changes.

The Principle of Parsimony states that trait origination is much less likely than trait inheritance in an ancestor-descendent relationship. The single origination and subsequent evolutionary inheritance of a trait is more likely than multiple originations of the same trait. When determining a phylogeny, we look at a number of traits in our taxa which are 1) not similar, 2) similar due to homology, or 3) similar due to convergence (analogy). Parsimony is invoked to construct a phylogeny that minimizes the number of changes in these traits (maximizes homology and minimizes analogy). In essence, we minimize the number of “tick marks” we have to make on the cladogram (see “tick marks” in the synapomorphy examples above.

For more advanced detail on how phylogenies are determined and cladograms made, click here.

For a quiz on phylogenetics, click here, then go to the "Readings" link in the left hand column, then click on “Phylogenetic Systematics exercise” on the main screen.

What can be learned from phylogenies and homologies?

	There is a single phylogeny for all of life. Based on homologies seen in all life forms (e.g. nucleic acids, metabolic pathways), it is most parsimonious to conclude that all of life as we know it (currently and historically) shares a common ancestor. You can find out more about efforts to determine the true tree of life here: TOL website This link shows you what important taxa originated during different periods of geologic time - click here
	Humans are a third chimp DNA homology suggests that humans are more closely related to living chimps than either are to other living primates.
	Birds are dinosaurs. Based on traits common with mammals (e.g. endothermy), it was long thought that birds were more closely related to mammals than to other vertebrates. When looking at various skull and hip characteristics, however, birds share more traits with certain lineages of dinosaurs. When evidence arose that some dinosaurs had beak-like traits and feathers, it became clear that these bird traits were all homologous with dinosaurs and that the clade of living birds was, in fact, within the clade of dinosaurs. A cladogram of the phylogenetic relationships of dinosaurs and birds. A cladogram of all reptiles, including birds.
	Origin of traits Phylogenetics is used to identify where in a phylogeny traits first evolved. Once we have established an accurate phylogeny, we can make “tick marks” on a cladogram to indicate where a trait first appeared. These marks are usually placed on the branch before the MRCA of all taxa which share the trait. For example, we know that whales and their relatives (cetaceans) all have long, torpedo-shaped bodies. The closest relatives of cetaceans, the artiodactyls (e.g. cows, deer) do not have this body shape. Therefore, we know that this body shape must have arisen on the branch between the common ancestor of cetaceans and artiodactyls and the MRCA of all known cetaceans. Review Questions

- Construct a tree of the following taxa:

Dolphin

Human

Gorilla

Bluebird

Rattlesnake

Bullfrog

Tiger Shark

Clam

Sponge

- How easily (evolutionarily speaking) do you think it is for diet to change compared to number of limbs in an organism? What would happen if we made a phylogeny of mammals based on diet? Do you think it would accurately reflect true evolutionary relationships?

- How do we know that there is one Tree of Life?

- Based on vertebrate evolutionary relationships, are the dorsal fins of dolphins and sharks homologous or analogous?

- Is the group currently recognized as Fish monophyletic or paraphyletic? You may want to refer to a text to look at a phylogeny of jawless, cartilaginous, and bony fish and tetrapods.

- What does a node in a cladogram represent?