Week 3 in-class assignment
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Part 1: Creating a phylogeny
Develop a hypothesis of the relationships between the list of candy bars below.
Although this exercise may seem to be frivolous, the strategies that you will need to employ are the
same as if you were studying real organisms. Assume that these candy bars evolved by descent with
modification. What is the simplest scenario of descent (i.e., most parsimonious) that would explain the
distribution of features among the candy bars? Your goal is to create a phylogeny (hypothesis of
relationships) for these "organisms."
Note: There are many possible phylogenies so there is not
one single correct tree. Try to make the most parsimonious tree you can, but no need to stress
about whether your tree is "right".
Instructions:
Candy Bar "Organisms"
Kit Kat (milk chocolate)
Kit Kat (raspberry creme chocolate)
Three Musketeers
Peppermint twist hard candy
Snickers
Snickers Almond
Milky Way
Mr. Goodbar
Krakel
Hershey's Milk Chocolate Bar
Hershey's Special Dark
If on zoom, search the internet to find out what features each candy bar has if you are not familiar
with that candy bar. e.g.
https://en.wikipedia.org/wiki/3_Musketeers_(chocolate_bar)
. If you are in
person, you can observe your candy bars. If you need to cut one open, there is a “dissection station”
at the front of the room.
Try to determine which candy bar you want to use as the
outgroup
, or most dissimilar taxon. This is
the taxon that you will use to polarize all the characters (determine which state is ancestral and which
is derived). Keep in mind that evolution can simplify (absence as a character state) organisms as well
as make them more complex.
Organize your ideas in a table on the table provided. Create a column for each trait and then list the
character state for each taxon. For example, you could define "milk chocolate" as a character that is
either
present
(+) or
absent
(-)
for each candy bar. Chocolate is given as an example. You will want
to identify at least 5 more characters, though you may need more to define your clades so no need to
limit yourself to this number. You will upload your completed table in Question 4.
Use these characters to make your phylogeny (your hypothesis of relationships). Once you have your
phylogeny, map each of your characters onto your tree. You will upload your completed tree in
Question 5. You can either make a tree using lines and text boxes in a program like powerpoint &
save it as an image file, or just draw your tree and take an image with your phone or other device and
upload the image.
Questions
1) What characters were most useful in defining
monophyletic
groups? What characters were not
useful? Give one example of each along with a reason it was or was not helpful.
Nuts were not useful because there was not a common ancestor. For example, both snickers and Mr.
Goodbar had nuts, but they were very far apart on the tree, meaning they weren’t very related.
Crunch was very useful because we had a lot of groups that were crunchy, like Krakel, Kit Kat, and
Kit Kat Raspberry and we could use crunch as a common ancestor.
2) Do you have evidence of convergent evolution (
homoplasy
) in your phylogeny? Did similar
features arise more than once? In your answer, state which characters showed evidence of
homoplasy.
Note
: the answer may vary depending on your phylogeny.
We do have evidence of homplasy. Nuts arose twice, once with Mr. Goodbar and then with Snickers
and Snickers Almonds.
3) Choose one node and circle it on your phylogeny. What characters would you predict the common
ancestor that node represents would have?
The node I circled, I would predict that ancestor would have sugar, chocolate, milk chocolate, and
nougat.
4) Upload your completed table of characters
Character
Chocolate
Nut
s
Wafer
Carame
l
Nougat
Milk
Chocolate
Dark
Chocolate
Sugar
Crunchy
(not nuts)
Almonds
Kit Kat (milk
Chocolate)
Y
N
Y
N
N
Y
N
Y
Y
N
Kit Kat
(raspberry)
Y
N
Y
N
N
Y
N
Y
Y
N
Three
Musketeers
Y
N
N
N
Y
Y
N
Y
N
N
Peppermint
twist
N
N
N
N
N
N
N
Y
N
N
Snickers
Y
Y
N
Y
Y
Y
N
Y
N
N
Milky Way
Y
N
N
Y
Y
Y
N
Y
N
N
Mr. Goodbar
Y
Y
N
N
N
Y
N
Y
N
N
Krakel
Y
N
N
N
N
Y
N
Y
Y
N
Hershey's
Milk
chocolate bar
Y
N
N
N
N
Y
N
Y
N
N
Hershey's
Special Dark
Y
N
N
N
N
N
Y
Y
N
N
Snickers
Almond
Y
Y
N
Y
Y
Y
N
Y
N
Y
5) Upload your completed phylogeny. Make sure it has your mapped characters and the circled node
from #3.
Part 2: Computing the consequences of a phylogeny
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Related Questions
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4.Take a picture of your phylogenetic tree and submit it with this document.
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Gibbons
Orangutans
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the offspring, while in others only the female feeds the offspring. You imagine that having bright males
near the nest may tend to attract predators to the young.
You want to distinguish between two hypotheses to explain the patterns you see:
1) Males not feeding the young is an adaptation to dimorphism
2) If males don’t feed the young in a species, it will allow them to become brightly colored
To begin to address this question, map the characters changes in dimorphism and males feeding
the young onto each of the trees on the previous page.
CHARACTER
SEXUAL DIMORPHISM
MALES FEED YOUNG
Cassin's Vireo
Red Fox Sparrow
Cape May Warbler
Cedar Waxwing
Golden-Crowned Kinglet…
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Below is a list of seven hypothetical, currently-living species (A-G), and eleven of their character
states (i.e., traits). You will use these traits to construct your tree.
Species
Character states
green
еyes
green
no
no
egg
wings claws
hair
A
scales
tail
carnivore
teeth
spots
horns
layer
green
eyes
green
no
egg
В
scales
wings
horns
tail
carnivore
hair
teeth
spots
claws
layer
egg
layer
green
green
no
no
scales
wings claws
tail
carnivore
hair
spots
eyes
horns
teeth
no
no
no
egg
no
no
scales
red eyes
wings
claws
layer
no tail
carnivore
spots
horns
hair
teeth
no
no
egg
layer
no
no
E
spots
red eyes
horns
scales
claws
tail
carnivore
wings
hair
teeth
no
no
no
live
no
F
spots
red eyes
wings claws
carnivore
tail
hair
scales
horns
birth
teeth
no
no
no
live
no
G
spots
red eyes
wings claws
tail
herbivore
hair
scales
horns
birth
teeth
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It provides a drawing the reflects the proven relationships between living and extinct species.
b
It provides a hypothetical model of the relationships between extinct species.
c
It provides a hypothetical model of the relationships between living and extinct species.
d
It a diagram used by scientists that provides a model of evolutionary relationships without the need for scientific data.
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organisms descended from
common ancestors
Structures that do not
serve a function and are
similar to those found in
earlier organisms
1. Transitional Species
Compares the age of fossils
to each other based on the
layers of rock they are
found in
2. Vestigial structure
3. Fossil Record
4. Relative Dating
Evidence of gradual change
between a new species and
its ancestor
5. Radiometric Dating
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species have inherited from
a common ancestor
6. Homologous Structures
uses radioactive elements
to narrow down the age of
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1. Which two organisms are most closely related?
2. The green dot indicates a trait that is shared
by every animal on the diagram. Suggest a trait
that would apply.
3. Animals A & B share a trait that animal C does
not have, indicated by the orange circle.
Suggest a trait that would apply.
Source: https//commons wikimedia org/wiki/File Identical cladograms svg
B.
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lizards, 4 from each island.
b. Following the module, group the lizards by morphology.
i. How many groups did you find?_
ii. What sorts of traits or characters did you use to group the lizards?
c. Then take some more careful measurements as shown and regroup them if
needed.
i. Did your measurements match the reference set?
ii. Compare Lamellae Count, Relative Hindlimb Length, and Relative Tail
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characters.
iii. Did your groupings change? If so, how?
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