Phylogeny Data Collection- PorcupinesTable 1:
Species:
Species:
Entry ID: B6VAC7
North American
Porcupine
Basic Species Information
Geographic range:
North America, between the Atlantic
Ocean and North Mexico.
Basic Species Information
Geographic range:
North Africa
Latin name: Hystrix cristata
Prediction:
Latin name: Erethizon dorsatum
Prediction:
Entry
Species Matches
ID
Q9G2U Proechimys cuvieri
4
O2180 Octodon degus
7
%
O2054
6
88.4
Tympanoctomys
barrerae
North African
Crested Porcupine
Entry ID:
A0A0K1W3N6
88.9
88.9
Table 2:
Phylogenetic Tree: Write species name, not ID
Entry
ID
Q0491
0
Species Matches
%
Hystrix
africaeaustralis
98.9
Phylogenetic Tree Analysis:
1. Are the two species of porcupines more closely related to each other or another
species?
2. Given the answer from one, does this mean they are closely related and share a
recent common ancestor, or did their appearance evolve separately of each other?
Explain, how the tree supports this statement.
3. Do these results match your original prediction, or is this finding surprising? Explain
your original thinking versus what the data shows you.
4. Depending on which theory your evidence supports (recent ancestor, or separate
evolutionary events) create a new phylogenetic tree below with the same species that
support the opposite theory. (How would a tree show they are closely related vs.
evolved separately?)
Phylogeny- Choice Investigation
Which investigation are you researching:
Species to be included (all investigations need at least 4 species):
1.
2.
3.
4.
Others:
Species Research:
Species 1:
Latin name:
Geographic range:
Species 2:
Latin name:
Geographic range:
Species 3:
Latin name:
Geographic range:
Species 4:
Latin name:
Geographic range:
Other Species:
Latin name:
Geographic range:
Other Species:
Latin name:
Geographic range:
Predict if you think your species are all closely related and just live far apart, or if they
evolved separately.
Complete the protein analysis for your species, following the directions from the
porcupine inquiry. Use the spaces below to record the Entry ID for each species you
add to your basket to compare. Remember you need these to interpret your tree!
Species: ____________ ID: _________
Species: ____________ ID: _________
Species: ____________ ID: _________
Species: ____________ ID: _________
Species: ____________ ID: _________
Species: ____________ ID: _________
Species: ____________ ID: _________
Species: ____________ ID: _________
Species: ____________ ID: _________
Species: ____________ ID: _________
Phylogenetic Tree: Write species name, not ID
Make a claim as to your final conclusion. Are your species closely related and share a
recent ancestor, or are they examples of convergent evolution? 3-5 sentences
minimum.
Exploring Evolution Through Phylogeny
In this activity you will be given some choices to reconstruct evolutionary history and solve problems. As you
know, scientists can compare mutations in DNA, amino acid sequences, and/or genomes to establish common
ancestry and phylogenetic relationships. Some of the more common proteins to consider are:
Hemoglobin
(HBB)
Actin (ACT)
Catalase
Keratin
Pax1
Cytochrome
b (cytb)
ATP
Synthase
GAPDH
Myosin
Ubiquitin
Zinc Finger
In this lab you will be expected to do two explorations:
1. Phylogeny of Two Porcupines
2. Inquiry of your Choice
A Tale of Two Porcupines
One of the more interesting questions in evolution is whether given the chance to reset time, organisms would
evolve the same way. The late evolutionary scientist Stephen J. Gould took the side that if you replay life
history over again, evolution would give a very different outcome. The idea that evolutionary direction is unique
in time. Contrary to this is paleontologist Conway Morris’s perspective. His idea is that there are only so many
ways that organisms can respond to nature, make a living and adapt. There should be convergence on ways of
life based on the best evolutionary outcome1.
One thing we can look for is what scientists call “convergent evolution”. This is defined as “independent
evolution of similar features in species of different lineages.”2 If given a chance, will ecological pressure shape
organisms into similar niches or adaptations in geographically distant areas?
One way to explore this is through the genome. We can use genes and their mutations to see if genetic
compositions between organisms separated by geography show common ancestry.
For example, you might know of two types of organisms that look similar but live on different continents. You might
scratch your head and wonder how these organisms that look so similar in adaptations could have evolved so far
away. There are at least two ways of thinking about this we can test.
1. Did these two organisms share a recent common ancestor with similar homologies, and then geography
isolated them to where they occur today?
2. Did these two organisms evolve separately without a direct common ancestor, but evolution shaped them in
a convergence on the same adaptations and lifestyle?
Guided Investigation 1 – The North American Porcupine and the African Crested Porcupine3
1
2
3
Before we begin, we need to know a little about these porcupine species.
1. In Table 1, do some basic research on your organisms.
2. Below Table 1, make a prediction using the two evolutionary points of view above regarding the porcupines.
3. Open www.uniprot.org. This is a protein database that scientists contribute to from all over the world. It contains
genomes at your fingertips in the form of proteins. We can use this database to compare organisms based on
their amino acid sequence differences.
a. In this example, we will choose cytochrome b protein found as a molecular homology in aerobic
organisms. Molecular homologies are DNA sequences or proteins that species have in common.
b. Cytochrome b is a protein found in the electron transport chain of the mitochondria. The DNA that codes
for this protein mutates every so often, so the amino acid sequence derived from it will be a bit different.
Those organisms with the least number of differences in their cytochrome b will be more genetically
related in time.
4. In the search box, type in the name of the species you are researching followed by cytb abbreviation. Click
Search.
a. Ex. “North African Crested Porcupine cytb”
5. In the results table, note the number of amino acids (Length) listed in the far right of the chart. If multiple results
come up with different lengths, choose one entry from the most common result. Under “Entry” click the box and
then click “Add to basket”.
6. In Table 1, there is a spot for the Entry ID- this is the series of numbers/ letters next to the check box. Record this
in the table- if you do not you’ll be confused later!
a. Example: Entry ID for the cytb sequence for the Gray Wolf (above) is Q6Y8J2
7. In the menu above the results table click BLAST. This will search the database for other organisms that have
similar amino acid sequences in their cytochrome b protein. Leave the BLAST search on Default.
8. When your results come in, you will see a number of organisms listed under “Overview”. This shows you the other
organisms that are similar to yours in terms of the amino acid sequence. In your Table 1 write the top 3 matches
that are within a 93.4% match. If there is only one match within 93.4%, only record one; if there are more than
3, record the 3 highest match percentages. Be sure not to repeat organisms.
9. Look at the alignment table under the results. Click the boxes next to the organisms you recorded in Table 1 and
add them to your basket.
10. Do steps 4-9 for the African Crested Porcupine. Complete Table 2.
11. Click on your Basket (top right of the screen) and select all of the checkboxes.
12. Click “Align”. The database will now align your amino acid sequences and show you similarities and differences.
Some look the same, while others look like they have amino acids missing. If you are curious, you can select the
“Similarity” checkbox on the left and it will show you all of the amino acids they all have in common. THIS MAY
TAKE A MINUTE. LET IT RUN!
13. Scroll down in the alignment window to find the phylogenetic tree of these species.
14. One this runs, it will create a tree for you using the Entry IDs instead of species names—this is why you needed
to write them down before!!! Copy the phylogenetic tree you create into the space below Table 1 and 2. Replace
the Entry IDs with the species names for easy analysis.
15. Answer the questions to make your conclusion as to whether these animals are examples of convergent or
divergent evolution.
For the second protein analysis, choose one of the topics on the next page to study. Use the instructions
above to do the protein analysis for the new species.
Examples
Placentals vs.
Marsupials
Question to Explore
●
Are placental and marsupial animals separated by
geography a result of descendance from a recent
common ancestor or are they a product of
convergent evolution.
Species
Use the Cytochrome c (COX1) protein
instead of cytb!
Species:
●
●
●
●
●
●
Old World vs.
New World
Monkeys
●
Armadillos and
Anteaters
●
Are old world and new world monkeys separated
by geography a result of descendance from a
recent common ancestor or are they a product of
convergent evolution.
New World Monkeys:
Are these species of armadillos and anteaters
separated by geography a result of descendance
from a recent common ancestor or did they evolve
separately on different continents?.
Species:
● Black howler monkey
● Common squirrel monkey
● Black-handed spider monkey
● Venezuelan red howler
Old World Monkeys
● Mandrill
● Vervet monkey
● Hamadryas baboon
●
●
●
●
●
Large, Flightless
Birds
●
Are these species of flightless birds separated by
geography a result of descendance from a recent
common ancestor or are they a product of
convergent evolution.
●
Are these egg laying mammals a result of a recent
common egg laying ancestor or has egg laying in
mammals arisen multiple times?
●
●
●
●
●
Are these species of awesome animals separated
by geography a result of descendance from a
recent common ancestor or are they a product of
convergent evolution.
Ostrich
Emu
Cassowary
Kiwi
Kakapo
Species:
●
●
●
●
Manatee and
Dugongs
Indian pangolin
Giant anteater
Giant armadillo
Southern anteater
Silky anteater
Species:
●
Monotremes
(egg laying
mammals)
Tasmanian devil
Common Wombat
Yellow-sided opossum
Norway rat
Groundhog
Southern brown Bandicoot
Platypus
Short-beaked echidna
Western long-beaked echidna
European hedgehog (not egg-laying, but
similar appearance)
Species:
●
●
●
●
Dugongs
West Indian Manatees
West African Manatees
Amazonian manatees
Marine
Mammals
●
Examine two species from three of the following
categories to evaluate the phylogenetic history of
aquatic mammals: whales, seals, sea lions,
walrus, and dolphin.
Need two species from each category.
Elephants
●
Explore protein sequences to evaluate the
phylogenetic history for all elephants, and all
extinct mammoths and mastodons.
Use the Cytochrome c (COX1) protein instead of
cytb!
Species:
● Asian elephants
●
●
African Elephants
Wooly mammoth
●
Mastodons
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