Question

Question 1:Construct a phylogenetic tree for the following species of shark listed in the table below, using the cytochrome b gene. Use the round stingray (Urolophus concentricus) as an outgroup to root your tree.

Common name	Latin name	Order
Great White shark	Carcharodon carcharias	order Lamniformes
Shortfin mako shark	Isurus oxyrhyncus	order Lamniformes
Longfin mako shark	Isurus paucus	order Lamniformes
Salmon shark	Lamna ditropis	order Lamniformes
Porbeagle shark	Lamna nasus	order Lamniformes
Pelagic thresher shark	Alopias pelagicus	order Lamniformes
Common thresher shark	Alopias vulpinus	order Lamniformes
Basking shark	Cetorhinus maximus	order Lamniformes
Blue shark	Prionace glauca	order Carcharhiniformes
Tiger shark	Galeocerdo cuvier	order Carcharhiniformes
Lemon shark	Negaprion brevirostris	order Carcharhiniformes
Megamouth shark	Megachasma pelagios	order Lamniformes
Round stingray	Urolophus concentricus	order Myliobatiformes

Your essays should reflect the reasoning strategies that you followed to resolve these problems. Your figures should include short captions that complement your text answers.

Read the entire question carefully. Your tree should contain 13 species total. Once your tree is produced, answer the questions below:

1. Do your trees support the monophyly of the orders Lamniformes and Carcharhiniformes?

2. Is the genus Isurusmonophyletic, i.e. do all members of this genus appear to have a common ancestor? How about for Lamna? How about for Alopias?

3. There has been some controversy over the relationships between the white shark, mako sharks and porbeagle sharks (genus Lamna). Based upon some aspects of external and dental morphology, some authors believe white sharks are more closely related to the porbeagle sharks, although fossil evidence suggests the white shark is more closely related to the makos. Which relationship do your trees best support?

4. In 1979, off the Hawaiian Islands, a very unusual new species of shark was captured by the Navy. A large (to 15-16 feet total length) deep dwelling filter feeder, this unique shark represented not only a new species, but an entirely new genus and family! Named the megamouth shark, Megachasma pelagios, the shark has since been grouped as a member of the order Lamniformes. In addition, it has been hypothesized that its closest relative would be Cetorhinus maximus(the Basking shark), the only other member of this group that is a filter feeder. Find the cytochrome b sequence for the megamouth shark, and rerun your tree, including this species. Do your analyses support the placement of the megamouth in the Lamniform clade? Do your analyses support that the basking shark is the closest relative of the megamouth?

Answer 1

1. Answer: Yes. The tree supports the monophyly of both the orders

2. Answer: Yes. all the three genera are Monophyletic.

3. Answer: As per the results obtained from the phylogentic tree, "White sharks are closely related to Mako rather than with Lamna" (i.e fossil evidence is supported).

4. Answer:  basking shark is NOT the closest relative of the megamouth shark as per the present phylogram. As per the present phylogram (Cyt b gene), the inclusion of Megamouth shark in Lamniformes is supported