Download Making Phylogenetic Trees

Making Phylogenetic Trees
Scientists use a variety of evidence to create phylogenetic trees to demonstrate evolutionary relationships among species or
other taxa. For this assignment you will use two sets of data to construct two different trees.
Part 1: Vertebrates
The subphylum Vertebrata contains all the animals that have spines (vertebrae). Table 1 describes several characteristics of
vertebrates for six different species. The lobe-finned fish is the “outgroup”, meaning its ancestors split from the other species
the longest ago.
Table1. Characteristics for Six Vertebrates
Trait
Outgroup
(Lobe-finned
fish)
Human
Turtle
Frog
Mouse
Kangaroo
Dorsal Nerve Yes
Cord
Yes
Yes
Yes
Yes
Yes
Legs
No
Yes
Yes
Yes
Yes
Yes
Nature of
egg
ExternalRequires
water
Develops
inside the
mother
External-Has
hard shell, on
land
ExternalRequires
water
Develops
inside the
mother
Develops
inside the
mother
Development In egg
Placental
In egg
In egg
Placental
Marsupial
Lives mostly
in water
Yes
No
No
Yes
No
No
Hair
No
Yes
No
No
Yes
Yes
Pouch
No
No
No
No
No
Yes
Warmblooded
No
Yes
No
No
Yes
Yes
Limited to
Australia
No
No
No
No
No
Yes
To evaluate the evolutionary relationships among the species you must consider the similarities. To do this, you must quantify
the number of similarities the species share. Perform this by drawing the matrix below into your journal. If the trait you
are considering is partially shared, you may use decimals, e.g. a trait may be counted as 0.5 instead of 0 or 1. Note: Two
“no’s” constitute a similarity.
Lobefinned fish
Lobed-fin fish
Turtle
Frog
Mouse
Human
Kangaroo
Turtle
Frog
Mouse
Human
Kangaroo
NA
NA
NA
NA
NA
NA
Now, draw the tree that has already been constructed below into your journal. Fill in the boxes at the end of each
branch with the correct species based on your measurement of similarities. Those that share the most similarities with the
lobe-finned fish will be written in the box directly to the right, and so on.
Lobe-finned
fish
Part 2: Across Kingdoms
In the past, biologists relied upon physical traits to construct phylogenetic trees like the ones you used in Part 1. Nowadays,
most phylogenies are constructed with molecular evidence.
Cytochrome c is a common large protein found in nearly all organisms. This protein varies, however, in its composition.
Table 2 shows how amino acids vary within the protein depending on the species. The amino acids are written in one of the
top rows. If the species contains that same amino acid, a “+” is indicated. If it does not contain that amino acid, then the
amino acid that is present is listed instead. The assumption is the more similarities that are shared between two molecules, the
more recently they have evolved from a common ancestral molecule, and thus a common ancestor species.
Table 2. Molecular Data For the Protein Cytochrome c
1
2
3
4
5
6
7
8
9
10 11 12
13
14 15 16
17 18 19
20 21 22
Gly Asp Val Glu Lys Gly Lys Lys Ile Phe Ile Met Lys Cys Ser Gln Cys His Thr Val Glu Lys
Human
Chicken
Dogfish
+
+
+
+
+
+
+ +
Ile +
+ +
+
+
+
+
+
+
+
+
+
+ + + + + +
+ + + Val Gln +
+ Val + Val Gln +
+
+ Lys Thr +
+ + +
+ + +
+ Ala +
+
+
+
+
+
+
+
+
+
+
+
+
+ +
+ +
+ Asn
+ Ala +
+
+
+
+ Asp Ala
Wheat
+ Asn Pro Asp Ala + Ala +
Yeast
+ Ser Ala Lys +
+ Ala Thr Leu + Lys Thr Arg + Glu Leu
+
+
+
+
+
+
Chimpanzee
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Pig
+
+
+
+
+
+
+
+
+
+ Val Gln +
+ Ala +
+
+
+
+
+
+
Fruit flies
+
+
+
+
+
+
+
+ Leu + Val Gln Arg + Ala +
+
+
+
+
+ Ala
+
+
+
+
+
In your journal, draw a matrix containing the 8 species listed in Table 2. Use the data from Table 2 to complete the
matrix. Do this by counting the number of shared amino acids between each pair of species and write the number in your
matrix.
Humans
Chicken
Dogfish
Wheat
Yeast
Chimps
Pig
Fruit flies
Humans
NA
Chicken
Dogfish
Wheat
Yeast
Chimps
Pig
Fruit flies
NA
NA
NA
NA
NA
NA
NA
Now, construct a phylogenetic tree in your journal for the eight species you’ve studied. The species that shares the
fewest similarities with the given example is the outgroup species (just like the lobe-finned fish in Part 1). Your tree
should look very similar to the tree in Part 1 but will have eight branches instead of six.