Understanding Phylogenies: Terminology

I was inspired several months ago by this tweet from Drew Lab in which they made a phylogeny of candy bars. Besides thinking, “what a delicious lab project,” I also thought it was an intuitive way to understand the basic evolutionary concept of how species (or candy bars as it may be) are related to each other. Candy bars are accessible in a way species are not; kids and adults, scientists and non-scientists alike understand candy and can debate how the candy bars are related to each other based on their tasty traits. Bringing us to an important point about phylogenies: they are debatable! Phylogenies represent hypotheses about how species are related to each other. Some phylogenies are well supported and even have multiple lines of evidence to support the tree topology such as molecular sequence data, morphological data, and fossil records. However, some phylogenies are not well supported and scientists gather new data to resolve these phylogenies.

To understand phylogenies let’s start with some basic terminology (Figure 1).
Taxon (plural: taxa): the species/candy bars we will infer relationships between in a phylogeny
Tips: the terminal unit in the phylogeny. There will be one tip for every taxon included in the phylogeny.
Node: point that joins two groups together. Nodes represent the most recent common ancestor of the two groups that were joined.
Branch: the portion of the tree that joins tips and nodes, or nodes with other nodes. In a cladogram, branches are equidistant between nodes; while in a phylogeny representing time, the length of the branch estimates the amount of time that has passed between evolutionary events.
Clade: A group of similar taxa. Figure 1 represents the peanut clade.
Traits: information about the taxa that may be unique to a single taxon or shared by multiple taxa.

Figure 1- Phylogeny terminology using the peanut clade.  This clade has three tips represented by the three candy bar taxa.  The clade has five branches and two nodes.

Figure 1- Phylogeny terminology using the peanut clade. This clade has three tips represented by the three candy bar taxa. The clade has five branches and two nodes.

Biologists describe how clades are related to each other using the following terms:
Sister taxa: Two taxa (could be one or multiple species/candy bars) that arise from a common node. (Example- Mounds and Almond Joy in Figure 2)
Monophyletic: A clade formed by all of the species/candy bars sharing a common ancestral node. (Example- M&Ms are monophyletic)
Paraphyletic: A group of taxon descended from a common ancestral node that does not include all of the taxa descended from that node.
Polyphyletic: A group formed by shared traits even when a single common ancestral node is not shared. (Example- In Figure 2 peanuts independently arise three times on the candy bar phylogeny)

Figure 2- Fully bifurcating candy bar phylogeny with traits mapped onto tree topology.  Red slash over a trait means "loss of" that trait on the tree.

Figure 2- Fully bifurcating candy bar phylogeny with traits mapped onto tree topology. Red slash over a trait means “loss of” that trait on the tree.

With this background we can begin understanding how phylogenies allow for evolutionary insight. More to come on Understanding Phylogenies including Polytomies and Use in Conservation Planning.

Updates
The candy bar phylogeny uses American candy bars. If you recreate with your country’s candy, please tweet a picture to WildlifeSNPits! We would love to see candy phylogenies from around the world.

You can download the data here: CandyBarPhylogenyData.

About these ads

10 thoughts on “Understanding Phylogenies: Terminology

  1. Pingback: Nibbles: Genebanks trifecta, Marley Coffee, Sorghum noodles, Biofortification Q&A, African oils, Cow diversity, Coffee course, Fructose deconstructed, Vanuatu chocolate, Candy bar phylogenies, Japanese copycats, Charger beer

  2. Pingback: Nibbles: Genebanks trifecta, Marley Coffee, Sorghum noodles, Biofortification Q&A, African oils, Cow diversity, Coffee course, Fructose deconstructed, Vanuatu chocolate, Candy bar phylogenies, Japanese copycats, Charger beer | Gaia Gazette

  3. This is of course a great exercise, but have the hypotheses so generated been tested by the “fossil record”, the actual order in which these confections appeared? Hey, that’s what makes it science! Hershey’s milk chocolate bar likes to make that claim, but note above, it’s not a basal lineage. :-( Tootsie roll is even older, but maybe that isn’t in the Bar family.

  4. Pingback: Links 3/24/14 | Mike the Mad Biologist

  5. Interesting visual aid. I’m still trying to figure out where a Baby Ruth bar could be best placed to avoid creating a paraphyletic clade! It would also be interesting to see a divergence tree – Hershey’s bars go way back!

  6. Pingback: I’ve Got Your Missing Links Right Here (29 March 2014) – Phenomena: Not Exactly Rocket Science

  7. Pingback: I’ve Got Your Missing Links Right Here (29 March 2014) | Gaia Gazette

  8. Reblogged this on The Flibberatic Skreebles and commented:
    Genius! Delicious genius!

    I’m fairly used – now – to cladograms and phylogenic classification because of my long obsession with dinosaurs and animals as a whole, but I have to say that this takes it to a whole new level of awesome. And I am now tempted to do a UK version!

  9. I’d be very grateful if you could share your data (candy bars, features, and phylogenetic tree) – I’d really like to use it as an example in Software Carpentry.

    • Thanks for your interest. I updated the post with a link to the data at the bottom. Here’s the Nexus string for the tree I created but as others have pointed out there are other possibilities given how the data is weighted:
      ((((‘Peanut M&Ms’, ‘Peanut Butter M&Ms’), ‘M&Ms’), ((((‘Hershey’s w/ Almonds’, ‘Cookies & Cream’), Hershey’s), ‘Crunch’))),((((((‘Snickers’, ‘Snickers w/ Almonds’),(‘Milky Way’, ‘Milky Way Dark’)), ’3 Musketeers’),(((‘Rolo’, ’100 Grand’),(‘Twix’, ‘Kit Kat’)), ‘Heath’)),((‘Reece’s Peanut Butter Cups’, ‘Pay Day’), ‘Butterfinger’)),((‘Almond Joy’, ‘Mounds’), (‘York’, ‘Cherry Mash’)))

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s