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Table of Contents
Table of Contents
Purpose of a Phylogeny
Purpose of a Phylogeny
Hierarchical Classification
Hierarchical Classification
The system by which we categorize organisms is hierarchical. That is, the system narrows down from large, more inclusive groups to smaller, less inclusive groups. On the image shown, the least inclusive, or most specific, classification is found at the top, the species level. Somtimes classifications can get more specific to include subspecies, but that is beyond the scope of the course.
This system is not perfect but it does allow us to group together organisms based on shared characteristics. In other words, there are some traits that define a given genus, so all organisms found therein should have those traits.
Each of these levels on the hierarchy is known as a taxon (plural, taxa). From largest to smallest, the classifications are kingdom, phylum (plural, phyla), class, order, family, genus (plural, genera), and species. You may remember it more easily with the mnemonic, Kings Play Chess On Fine Glass Stools, although memorizing it is beyond the scope of the course.
https://sites.google.com/site/physics8atlaurel/linnaean-classification
Urry, L., Cain, M., Wasserman, S., Orr, R., & Minorsky, P. (2020). Campbell Biology in Focus, AP Edition (3rd ed.). Pearson Education.
This is a simplified evolutionary tree that also has the taxon to which each group belongs labeled along the top (i.e. order, family, etc.). This is not found on every phylogenetic tree, but is useful for showing the importance of that hierarchical structure.
The purpose of a tree like this is to show evolutionary relationships of the organisms. This means that a phylogenetic tree will show what organisms are most closely related (i.e. share the most recent common ancestor).
In the example shown, we can see that both the gray wolf and the coyote are in the genus Canis and family Canidae. This means that they will share a lot of traits and will likely be significantly different from organisms in another family, such as the leopard.
We can see that all of the organisms here do share ancestry, though. They all have a common ancestor farther back on the tree.
If you want to see how closely related two organisms are, trace them back to their common ancestor. Here we can see that the gray wolf connects with the American badger at the unlabeled node that split into Mustelidae and Canidae.
The gray wolf and leopard, however, have a common ancestor even further back where the Felidae family branched off. Thus, the gray wolf is more closely related to the American badger than to the leopard.
Significance of the Axis
Significance of the Axis
Some phylogenetic trees will include an axis labeled with time. This can show when the data indicate two particular groups had a common ancestor that branched off into two taxa.
Thus, the branch length is important, as it denotes time. So you have to be more careful when constructing a phylogeny such as this.
In this example, we can see that humans and mice diverged from their common ancestor about 75 million years ago.
It is important to keep in mind that this doesn't necessarily mean humans and mice are the most closely related species on Earth. There are plenty of taxa that are alive or were once alive that are not represented on this particular phylogeny.
Furthermore, humans and mice had many stepping stones along their branches that led to what is we see today. Along that path of stepping stones are innumerable branching paths, much like the node shown here.
Urry, L., Cain, M., Wasserman, S., Orr, R., & Minorsky, P. (2020). Campbell Biology in Focus, AP Edition (3rd ed.). Pearson Education.
Cladograms vs Phylogenies
Cladograms vs Phylogenies
Those evolutionary trees that show time on the axis are known as phylogenetic trees (phylogenies). However, this is uncommon for this course. Typically, we will be using cladograms, which show the same evolutionary relationships but lack the information about evolutionary time. Thus, they are less useful to scientists, but generally are easier to construct.
https://www.vecteezy.com/free-vector/caution
Limitations of Phylogenetic Trees & Cladograms
Limitations of Phylogenetic Trees & Cladograms
A scientific conclusion is only as sound as the data on which it was founded. Evolution can be a particularly difficult process to track within one's lifespan because it can be so slow. Also, often there are missing links, or taxa that once lived and are now extinct that would make it clearer where a given organism's evolutionary history originated. Perhaps fossils for that taxon never formed or have since been destroyed.
Furthermore, some traits or even DNA sequences that are used to construct these cladograms are actually common across taxa, but not via common ancestry. Instead, they evolved independently. This is an example of convergent evolution, when a similiarity exists between two organisms not due to shared ancestry, but through independent evolution as a result of similar selection pressures. This similarity is referred to as an analogy (contrast this with homologies, or homologous structures from before).
Cladograms as Hypotheses
Cladograms as Hypotheses
Keep in mind that these trees are essentially hypotheses. This means that they are a scientist's educated guess about evolutionary relationship based on data collected. Sometimes the available data is lacking, so phylogenies are always possibly incorrect (like all hypotheses). When more data becomes available, a true scientist will be willing (and excited) to change their mind in accordance with these data.
As genetic technology has boomed in recent years, phylogenies have changed faster than publications can keep up. There are still cases where scientists disagree about evolutionary relationships, but ultimately it comes down to what is best supported by the data.
Anatomy of a Cladogram
Anatomy of a Cladogram
Components
Components
The branches will split at a node, which represents the common ancestor that is shared by the taxa downstream. In this example, there is a node that represents the common ancestor of A & B.
Phylogenies can be very dense with information, so it is important that we can discuss certain components of a tree with specificity. The tips of the tree (shown at the top on this tree) are where the taxa (A, B, C, D, & E) are listed.
The lines that end in tips are referred to as branches, and they represent an evolutionary lineage that led to the taxa being represented. These branches can be labeled with specific traits or characteristics that have evolved and that all taxa downstream have.
The branches will split at a node, which represents the common ancestor that is shared by the taxa downstream. In this example, there is a node that represents the common ancestor of A & B. A branch should never split into three lines, always two. This would be referred to as a polytomy, and is the result of missing data.
The tree begins at the root, which represents the oldest node on the tree.
Urry, L., Cain, M., Wasserman, S., Orr, R., & Minorsky, P. (2020). Campbell Biology in Focus, AP Edition (3rd ed.). Pearson Education.
This phylogeny shows the evolutionary relationships between 5 taxa.
Please note that we could expand on some of these groups (like fishes or lizards) and have many, many branches therein.
But that would make the phylogeny too busy and it might be difficult to use it to answer scientific questions. It is normal to only include relevant information.
There is a common ancestor for all taxa represented on the phylogeny. It can be found all the way at the leftmost node. That ancestor led to all organisms found downstream on the tree.
Clades
Clades
When constructing or analyzing phylogenetic trees, it is useful to speak in terms of clades (aka monophyletic groups). These are groups of organisms that includes an ancestral species and all of its descendants. These clades, which all share some trait(s) that evolved with that ancestral species, are given names.
In the example shown, the name given to the highlighted group is Reptilia, commonly referred to as reptiles. Included within that group are birds (Aves), so technically birds are reptiles (and are more specifically dinosaurs, but that's for another time).
https://fossil.fandom.com/wiki/Clade
In fact, most taxa you've heard of would be considered clades: mammals, insects, birds, etc. Sometimes our names get a little messier when we learn more about the taxon's evolutionary history, however.
Sometimes the scientific community tends to scrap the name and sometimes the name becomes more inclusive. That's why every time you eat turkey or chicken, you know what dinosaur tastes like.
Interestingly, the term fish is not scientifically accurate because the clade fish would include humans, as we share a common ancestor!
https://www.businessinsider.com/fish-do-not-exist-2016-8
Outgroups
Outgroups
Within every phylogenetic tree, you will find a number of taxa represented at the tips. However, you can find one taxon that stands out from the rest because the common ancestor it shares with the rest is way in the backmost node. This is referred to as the outgroup (see yellow highlight in image).
This is referred to as the outgroup because it is missing some attribute or trait that is common to every other taxon on the tree. In other words, the ingroup represents a clade that the outgroup is not a part of. We will see this more clearly later when traits are explicitly labeled, but for now remember that it is the group that branched off the furthest back in evolutionary time.
https://en.wikipedia.org/wiki/Outgroup_%28cladistics%29
Ancestral vs Derived Characteristics
Ancestral vs Derived Characteristics
One of the most useful aspects of the phylogenetic trees is the ability to trace traits, or characters, and when they evolved. A shared ancestral character is a trait that originated in an ancestor of the taxon in question. A shared derived character is a new, or novel, trait that is unique to a clade. A given trait can be either a derived or an ancestral character depending on what taxon you are examining.
To clarify this, look at the phylogeny shown here. Examine the purple clade (species D & E). Whiskers evolved and define this group, so that would be a derived character. However, those taxa also have fuzzy tails and big ears, but those evolved way back in an ancestor, so those are shared ancestral characters.
https://www.khanacademy.org/science/ap-biology/natural-selection/phylogeny/a/building-an-evolutionary-tree
Sister Taxa
Sister Taxa
As shown in this diagram, mammals and cynodonts are sister taxa, groups of organisms that share a common ancestor unique to those groups. Sister taxa can refer to species, genera, families, etc. - essentially any taxon that is represented on the tree.
Different Formats - Same Representation
Different Formats - Same Representation
Different Orientations
Different Orientations
Phylogenies can be represented vertically, horizontally, diagonally, and even in circles! The same information can be displayed in any of these ways, so it is important that you are able to recognize the basics in any of these trees.
Start with the tips of the trees and work your way backward. You should be able to trace the ancestry and identify when groups split and formed new taxa.
Urry, L., Cain, M., Wasserman, S., Orr, R., & Minorsky, P. (2020). Campbell Biology in Focus, AP Edition (3rd ed.). Pearson Education.
Rotating Around a Node
Rotating Around a Node
Every branch can also be rotated around its node. It does not matter which taxon you put on top or on bottom - what matters is that you did not change the evolutionary relationships.
Rotating around a node changes only the presentation. Analyze these two phylogenies with very different looks, but the same data and conclusions.
Urry, L., Cain, M., Wasserman, S., Orr, R., & Minorsky, P. (2020). Campbell Biology in Focus, AP Edition (3rd ed.). Pearson Education.
Creating a Cladogram with the Basics
Creating a Cladogram with the Basics
Parsimony
Parsimony
When constructing your first phylogeny for a given group of organisms, it is best to follow the principle of parsimony, sometimes referred to as Occam's razor. Essentially, this idea states that the simplest solution is usually correct, if all other elements are equal.
So how does this weird philosophical idea pertain to phylogenies? Essentially, we could create a potential phylogeny that makes sense, but is less parsimonious than another person's phylogeny.
Think about all the traits you have - hair, skin, toe nails, etc. Isn't it possible that your clade evolved all of those, and those are shared, derived characters? Other organisms have some of those traits too, though.
https://www.khanacademy.org/science/ap-biology/natural-selection/phylogeny/a/building-an-evolutionary-tree
So what is more likely... did we evolve the same traits as those organisms independently? Or were those traits passed down through common ancestry. In general, common ancestry is how those traits came to be in common.
This is exemplified beautifully in these example phylogenies. They show the same organisms and the same traits, but one is more parsimonious than the other because it requires the evolution of a trait (jaws, in this example) only once, whereas it must have evolved twice in the second phylogeny.
Both are valid hypotheses and could be supported by further data, but one is more parsimonious, and thus more likely given the limited data provided.
https://www.khanacademy.org/science/ap-biology/natural-selection/phylogeny/a/building-an-evolutionary-tree
Morphology
Morphology
Morphology is the most common data used to create phylogenetic trees to represent hypotheses about evolutionary relationships. Morphology is essentially anything about an organism's body structure. It is used so commonly because it is really cheap and easy - just look at it!
However, this can lead to misconceptions and incorrect evolutionary relationships. There are many examples of this in practice, but just imagine how difficult something like wings might be. Bats, birds, and insects all have wings, so one might first group them closely together on a cladogram.
However, using genetic data (and many other traits), we know that they all evolved wings independently. So use caution when relying solely on morphology.
https://www.quora.com/How-is-convergent-evolution-evidence-for-evolution
DNA Sequences
DNA Sequences
As genetic technologies have become more precise, accessible, and cheaper, DNA sequencing is often the most reliable way to create a phylogeny. Both large and small mutations can be used to determine when and where taxa diverged from one another.
Large-scale mutations such as insertions and deletions tend to accumulate over time, particularly in non-coding regions of the genome because natural selection will not act on those portions.
Even when using something a precise and impressive as genetic sequencing, you have to be careful of convergent evolution, however. Two DNA sequences from distantly related species have sometimes been found to share large portions of their genomes.
There are many factors that contribute to this phenomenon, and it is overall much more reliable that morphology, but you should be cautious regardless.
Urry, L., Cain, M., Wasserman, S., Orr, R., & Minorsky, P. (2020). Campbell Biology in Focus, AP Edition (3rd ed.). Pearson Education.
Using Matrices
Using Matrices
When it is time to make a phylogeny, it can be rather intimidating, particularly if you are given tons of data (or traits). The easiest way to go from data to phylogeny is to create a matrix. In this context, a matrix is simply a table that has organisms on one side and traits on the other.
In order to fill in the matrix, simply examine the organism. If it has the trait, give it a symbol that represents this. If that trait is missing, use a different symbol. Some of the most common symbols are 1/0 (present/absent), +/- or ✓/0.
Once your matrix is completed, organize it by most common trait to least common trait and fewest present traits to most present traits (see example below). From here, you can very easily create clades that clearly mark the evolution of those traits along the way. The taxon that lacks all (or the most) of the traits will easily be identifiable as the outgroup. The taxa with the most traits should be further down the evolutionary tree.
Urry, L., Cain, M., Wasserman, S., Orr, R., & Minorsky, P. (2020). Campbell Biology in Focus, AP Edition (3rd ed.). Pearson Education.
This method is slightly limited in that it will not always represent the most accurate phylogeny, but it can be a quick and easy start to making a parsimonious tree. I recommend you start with this method, and then check all the organisms to ensure that no one has a trait that they actually lack. If all of the traits and organisms seem to be accurately represented, that will suffice for the scope of this course.
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