Short Writing Assignment #7
MORPHOLOGICAL EVOLUTION AND PHYLOGENETIC ANALYSIS
For class discussion Wednesday, 7 April 2010
This writing assignment will give you an introduction to constructing phylogenetic trees based on
morphological characters, and how those trees compare to trees based on molecular data or fossil data. As in
all short writing assignments in Bio 340, your responses must be computer printed (with one exception
noted below) and will be turned in at the beginning of class on 7 April. In class, you will compare and discuss
your answers with those of your classmates.
While the large-scale phylogeny of sharks is thought to be well-understood, the relationship of shark species
within some orders and families is still controversial. For example, the hammerhead sharks show a diversity of
head shapes. Morphological data suggest that the hammerhead with the smallest head, the bonnethead shark
Sphyrna tiburo, is the most ancestral, while molecular data indicate that the hammerhead with the biggest head,
the winghead shark Eusphyrna blockii, is the most ancestral. The fossil record is not much help in this case. Over
99% of the shark fossil record is composed of teeth, thanks to cartilaginous skeletons (which do not fossilize
well) and the frequent replacement of teeth throughout a shark’s lifetime. In this case, hammerhead teeth are
fairly rare in the fossil record and non-existent for some hammerhead species.
We will examine sharks from the order Lamniformes, which includes white sharks, makos, and basking sharks.
The taxonomy for this order is as follows, in no particular evolutionary order:
• Isurus oxyrinchus, the shortfin mako
• Isurus paucus, the longfin mako
• Lamna ditropis, the salmon shark
• Lamna nasus, the porbeagle shark
• Carcharodon carcharias, the white shark
• Cetorhinus maximus, the basking shark
• Mitsukurina owstoni, the goblin shark
• Alopias vulpinus, the thresher shark
• Alopias pelagicus, the pelagic thresher
• Alopias superciliosus, the bigeye thresher
• Carcharias taurus, the sandtiger shark
• Odontaspis ferox, the smalltooth sandtiger
• Megachasma pelagios, the megamouth shark
• Pseudocarcharias kamoharai, the crocodile shark
Most of these species can be distinguished by their teeth alone, though there are plenty of non-dental
morphological characters as well. We will be using two shark species as outgroups: Carcharhinus plumbeus (the
sandbar shark) and Heterodontus francisci (the horn shark). The sandbar shark is in the order Carcharhiniformes,
Biology 340 – Evolution Morphological Evolution and Phylogenetic Analysis – 2
which is a sister taxon to Lamniformes, while the Heterdontiformes is a sister taxon to Lamniformes +
1. Based on the figures provided and the taxonomy above, compose a phylogenetic tree
illustrating your hypothesis for how these sharks are related to each other. This tree can
be hand drawn, but please print neatly! In general, how did you decide on these
relationships? In other words, what kinds of morphological features did you use? There is
no need to establish character coding or a formal list of characters. Rather, the goal of this part of the
assignment is to make a tree based on general similarity so that you can see how this differs from a formal
phylogenetic analysis. More information about Lamniform sharks can be found in the FAO Species Guide
(ftp://ftp.fao.org/docrep/fao/009/x9293e/X9293E00.pdf). There are better pictures of the teeth and
sharks in the FAO Guide. Heterodontus is also in this guide. For more information on Carcharhinus, go to this
FAO guide: ftp://ftp.fao.org/docrep/fao/009/ad123e/AD123e28.pdf
2. We will begin by making a morphological tree based on dental characters, which is what we would have in
the fossil record. These characters include the presence/absence of serrations (column 23 in the data file
described below) and whether the upper and lower jaws have teeth of different shapes (column 2). All trees
using morphological data will be made in a free program called PAST, which is available at:
http://folk.uio.no/ohammer/past/ . If you are using a Windows operating system, you can download this
to your computer.
3. We have also provided a data file for you with the characters and their codes, called “fossil.nex”.
Remember, these are characters taken from teeth only. Download this to your computer and open it using
“notepad”. It should look like this:
DIMENSIONS NTAX=17 NCHAR=26;
FORMAT MISSING=? GAP=- SYMBOLS= " 0 1 2 3";
NTAX is the number of taxa, NCHAR is the number of characters. ?=missing character state, -=n/a, and
numbers are the character states. Each column of numbers is one character.
4. Close notepad and open PAST. Open fossil.nex. Select all of the data on your screen and choose
'Parsimony analysis' in the Cladistics menu. Select the following options: Heuristic (NNI), Wagner, #
Biology 340 – Evolution Morphological Evolution and Phylogenetic Analysis – 3
reordering = 5, all other fields = 0. Then hit “Go!”. This might take a while, depending on the number
most parsimonious trees (MPTs) generated.
5. Once it’s done, a box should pop up with a tree on it. If there is more than one MPT, you should be able
to scroll through them in the upper left corner. If you click on a tree, another box will pop up that will
allow you to change. Then go to the bottom right and hit the Consensus button. This will give you a two
options for consensus trees: strict and majority rules. Click on majority, and print this tree (printer
button). Be sure to label it “Fossil Tree” and write down how many MPTs there were.
How does this compare to your hypothesized tree?
6. Now we will make a tree based on non-dental characters, which we will call the “morphological tree”. We
have provided a data file for you with the characters and their codes, called “morph.nex”. Follow the same
directions as you did for the fossil tree (steps 4 & 5). Print the majority rules consensus tree. Label
it “Morphological Tree” and write down how many MPTs there were. How does your
morph tree compare to the hypothesized tree? To the fossil tree?
7. Next make a majority rules consensus tree using the file “combo.nex”, which combines the fossil and
morphological data sets into one. In other words, we’ve made a data set that we’d be able to bring fossil
data into later on if we wanted to include extinct
sharks, and we’ve created a set of data that utilizes
all of the information that the shark has to offer.
Print this new tree, label it “Morphological
+ Fossil Tree”, and write down how many
MPTs there were. How does this tree
compare to the fossil and morphological
trees you’ve made?
8. Molecular trees have been published for the
Lamniformes based on cytochrome-b and NADH 2
mDNA (Naylor et al. 1997). The tree on the right is a
consensus tree based on these data. How does the
molecular tree compare to the other trees
you’ve made, including your hypothesized
9. You now have several trees. Which one do you
think is the “right tree” and why? How
would you argue your point to a classmate
The following do not need to be turned in, but will be discussed in class. Be prepared!
a. Notice the position of C. maximus and M. pelagios on each tree, and look at the FAO Guide’s
information on these sharks. Why do we see different relationships on the morphological trees
than we do on the molecular tree?
b. On the fossil tree, look at the position of C. plumbeus. Even though it’s an outgroup and not part of
Lamniformes, it seems to be included in Lamniformes on this tree and not the others. Why might
, • v
Figure 1 Modern lamniform species and tooth series (drawings based on Compagno, 1984) Bar
scale = 50 cm.
__ .h '
- - - /tamohara; Carcharodon
, , 17
A A A j],d,
..... oxyrlnchus - nasus
Figure 1 con't. Modem lamnifonn species and tooth series (drawings based on Compagno, 1984)
Bar scale = 50 cm.
Figure 2 Outgroup taxa and representitive teeth (drawings based on Compagno, 1984 and Reif,