Introduction to phylogenetics

Disclaimer: This intro to phylogenetics is criminally over-simplistic. There are links to much more in depth articles at the bottom of the post. Also, this post is a work in progress, and I will refine it as time goes on.

Phylogenetics is the organization of organisms according to their evolutionary relationships. Evolutionary relatedness is determined by comparing large numbers of characteristics between multiple organisms. These characters can be morphological features, molecular sequences, behavior, or bio-geographical distributions. The more characters two species share, the closer together they are phylogenetically. Phylogenetic relatedness can be displayed using a phylogenetic tree. Let’s familiarize ourselves with a generic phylogenetic tree:

The crucial components of a phylogenetic tree are nodes, branches, leaves, and the root. Each leaf represents an organism. Each node, represents the common ancestor of all the organisms that branch out of it. The root represents the common ancestor of every organism on the tree. Evolutionary time is represented along the “x” axis of the tree. On this tree, the common ancestor (node) of organisms A and B is more recent than the common ancestor of A and C. Now lets work backwards and talk about how this tree could have been built.

Morphological characters could have been used to make this tree. Let’s say this is a species tree depicting three species of arthropods:

We have morphological data for two characters, color and leg number. The three arthropods are all different colors, however A and B have six legs while C has eight. You can use this information to attribute each species a character difference score in comparison to the other species.

Difference score = number of different characters / number of total characters

A vs B = 1/2 = 0.5
A vs C = 2/2 = 1.0
B vs C = 2/2 = 1.0

The lower the difference score, the closer two animals are related. This tells us that organisms A and B are more closely related than A and C or B and C. Also, organisms A and B are equally different from organism C.  The phylogenetic tree is merely a graphical means of displaying the relationship implied by these character difference scores.

The tree in this demonstration could also have been derived from genetic characters:

Say you sequenced the same gene from these three species of arthropods.  For the sake of this simplistic example, let’s say this particular gene is three nucleotides long. Each nucleotide position is a character. Organisms A and B differ at one nucleotide position, the second position. Organism C differs from organisms A and B at two positions, the first and second. Now calculate the difference scores for these animals.

A vs B = 1/3 = 0.33
A vs C = 2/3 = 0.66
B vs C = 2/3 = 0.66

Again, A and B have a lower difference score between one another than with C. Therefore, A and B diverged more recently than A and C or B and C. A and B are equally distant from C.

The more characters you use, the more accurate your tree will be. You can also combine morphological characters with genetic characters to derive trees. Let’s calculate the difference scores of the two morphological characters plus the three genetic characters.

A vs B = 2/5 = 0.40
A vs C = 4/5 = 0.80
B vs C = 4/5 = 0.80

Notice that the difference scores change as you add more characters, but the evolutionary history they imply remains unchanged.  You can generate more accurate trees by including more characters and more species.

Well, that’s phylogenetics in a minuscule nutshell.  Again, I plan to develop and amend this post in the future, but I wanted to get it out as a primer for upcoming posts about arthropod phylogenetics.

Important additional notes about phylogenetics and evolutionary thinking:

  • There is no “true” phylogenetic tree. Trees are completely dependent on the coverage of organisms and characters you input.  Use different characters and you can get a tree that implies a different evolutionary history.
  • The example I used in this post is just one type of phylogenetic tree, called a cladogram.  In a cladogram all branches are the exact same length and all extant species reside at the same point in evolutionary time.  The central focus of a cladogram is the relative locations of nodes (common ancestors) between the species in the tree.  There are other types of phylogenetic trees that can covey other attributes of evolutionary history.
  • It is crucial to think of all the species on a phylogenetic tree as cousins. Some creatures are closer cousins than others, but we know from common descent that every living thing is cousin to every other living thing.
  • You can make phylogenetic trees not only for organisms, but also for individual genes, within a single organism or across many.
  • You can make your own phylogenetic trees using only online resources like the NCBI database and clustalW.  More info on this later.

Links to more information about phylogenetics:


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Arthropoda can now be found here.

Michael Bok is a graduate student studying the visual system of mantis shrimp.

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