Written Assignment 1: Candy Phylogeny
Phylogenetics is the science of evolutionary relationships. It is fundamental in our understanding of how life evolved, how characteristics are shared across the tree of life, and allows us to make testable predictions about the biology of organisms. However it is also a fairly jargon laden science. For example the description of a new species often includes detailed morphological data, each of which can be used as a character to build a phylogeny.
The purpose of this lab is to focus on exploring phylogenetic relationships without getting lost in the morphology of fishes (there will be plenty of time for that later), for now I want you to focus on how to build a tree. Therefore we are going to focus on the phylogeny of something you understand very well already – Candy.
In class we built several phylogenies of candy. Remember each phylogeny is an evolutionary hypothesis, there is no one “true” phylogeny, just one that is better supported by the evidence.
You have the following candy items to choose from:
Skittles (original flavor)
Hershey’s Chocolate (with almonds)
Starbursts (original flavor)
Twix (original flavor)
1) From the above choose an outgroup. What did you choose and why?
2) Construct a rooted cladogram. Label the nodes and tell me what synapomorphies each of those nodes
3) What are the monophyletic groups in your tree?
4) Think of the group defined by the character “fruit flavored” Based on your phylogeny is this group, monophyletic, polyphyletic, or paraphyletic?
5) Write your phylogeny in Newick format
Phylogenies are often constructed with multiple types of data. Now consider new information – the date of first manufacture for each of these candies and the company that first produced them. Phylogenies strive to show a shared common ancestry so with this new information construct a new phylogeny.
Skittles (original flavor) [1974, Mars]
Hershey’s Chocolate (with almonds) [1908, Hershey’s]
Hershey’s Chocolate [1900 Hershey’s]
Starbursts (original flavor) [1967, Mars]
Almond Joy [1946 Hershey’s]
Twix (original flavor) [Mars 1979]
Swedish Fish [1950 Malaco]
Peanut M&Ms [1954 Mars]
Peach [5000BC, China*]
*Cao, Ke, et al. “Comparative population genomics reveals the domestication history of the peach, Prunus persica, and human influences on perennial fruit crops.” Genome biology 15.7 (2014): 415.
6) How did your phylogeny change?
When incorporating new data scientists often grapple with how to weight characters that can often lead to differences in the resulting trees. Read
Near TJ. 2009. Conflict and resolution between phylogenies inferred from molecular and phenotypic data sets for hagfish, lampreys, and gnathostomes. J. Exp. Zool. (Mol. Dev. Evol.) 312B:749-761.
(also available on courseworks) and discuss:
7) What are the data sets used?
8) How they are weighted?
9) How different data sets provide different evolutionary hypotheses?
10) Which data set seems the most reasonable to you? Why and how would you justify this to someone who preferred a different data set?