Download Anole_Phylogeny_Analysis

AP Lab #3 Anole Phylogeny Analysis
Name:______________________________
Video Link: http://www.youtube.com/watch?v=rdZOwyDbyL0
(watch up until 9:55)
DESCRIPTION
The more than 700 islands of the Caribbean are home to about 150 species of anoles, a closely related
group of lizards (genus Anolis) that occupy diverse habitats and niches. Research on these lizards is
enriching our understanding of evolutionary processes, such as adaptation by natural selection,
convergent evolution, and the formation of new species— and it is helping to illuminate how and why
there are so many different kinds of living organisms on Earth.
KEY CONCEPTS
 An adaptation is a structure or function that confers greater ability to survive and reproduce in a
particular environment.
 Islands are good natural laboratories for scientists to conduct experiments on the role of natural
selection in driving adaptations in populations because they are isolated and have relatively
simple ecosystems.
 Microevolution refers to evolutionary changes or adaptations that occur within populations, and
macroevolution refers to changes leading to the formation of new species.
 The biological definition of a species is a group of interbreeding individuals that are
reproductively, and thus genetically, isolated from other groups.
 When two groups within one species become geographically isolated—separated by a physical
barrier, such as a river, canyon, or mountain range—genetic changes in one group will not be
shared with members of the other, and vice versa. Over many generations, the two groups diverge
as their traits change in different ways.
 For two groups to become distinct species, traits must change in ways that will keep members of
each group reproductively isolated—meaning that they will not mate or produce fertile offspring
with members of the other group—even if they come to be in the same geographic location.
 DNA sequence comparisons among different populations and species allow scientists to
determine how distantly related different species are and how long ago they shared a common
ancestor.
 Organisms in different evolutionary lineages can independently evolve similar traits as a result of
adapting to similar environments or ecological niches, a process known as convergent evolution.
 One reason why there have been and continue to be so many different species on Earth is that
there are so many different types of habitats and niches.
Go to: http://www.phylogeny.fr
Under “Phylogeny analysis” select “One Click”.
On the next page, select a name for your analysis.
You will also notice a large box into which you will input your DNA sequences in the proper format.
The sequences you will use are a stretch of mitochondrial DNA that includes the NADH
dehydrogenase subunit 2 (ND2) gene and five tRNA genes. Use the following instructions to copy
and paste the DNA sequences of the anole lizards you just learned about:
Go to Dr. Marble’s webpage and find the Resources page. Find the file named “Anolis-DNA-sequences.txt” and open
it. You should find 17 homologous DNA sequences including species names on the top of each in the FASTA format.
Copy the entire selection (including the names), and paste it into the big sequence box back at phylogeny.fr.
Now click submit. It may take some time to analyze, up to a couple of minutes. Remember, this is
hard stuff. The software is making a bajillion comparisons per second.
When complete, let’s go back and figure out what the software just did for us. Click on the tabs listed
below and answer the questions:
Overview:
Describe what the Overview panel is showing:
Data & Settings:
Describe what the Data & Settings panel is showing:
Alignment:
What is in the left-most column?
What do you think it means if a letter is highlighted blue?
What do you think it means if a letter is highlighted gray?
What do you think a dash in the sequence means?
Curation:
What does it mean if a letter is highlighted black?
What does it mean if a letter NOT highlighted?
What do you think that blue line on the bottom of the sequences indicates?
When there is a lot of variation between anoles for a certain stretch of nucleotides, what does that tell
you about the importance of that part of the protein gene product?
Phylogeny:
Why were there 17 DNA sequences used for analysis, and not just the 16 anoles?
What do the nodes (branching points) on the tree represent?
Tree Rendering:
The numbers on the tree represent a measure of the parsimony of the tree-build. The parsimony
principle is basic to all science and tells us to choose the simplest scientific explanation that fits the
evidence. In terms of tree-building, that means that, all other things being equal, the best hypothesis is
the one that requires the fewest evolutionary changes. The higher the value, the greater confidence.
What does the length of the branches directly indicate? What does that imply indirectly?
At this point you could print out your tree as a PDF, but instead ask your instructor for your two
copies. They will likely be on one sheet.
Label one copy “Island of Origin”. On that copy, color each branch (up until it reaches a differently
colored node) according to the island of origin (Cuba=red, Jamaica=green, Puerto Rico=blue,
Hispaniola=yellow). If both branches at a node are the same color, color the root branch and continue
left to the next node. (Include a key on your graph too.)
Species name
Anolis alutaceus
Anolis angusticeps
Anolis chlorocyanus
Anolis cristatellus
Anolis cybotes
Anolis evermanni
Anolis grahami
Anolis lineatopus
Anolis occultus
Anolis olssoni
Anolis ophiolepis
Anolis porcatus
Anolis pulchellus
Anolis sagrei
Anolis shelpani
Anolis valencienni
Leiocephalus barahonensis
Island
Cuba
Cuba
Hispaniola
Puerto Rico
Hispaniola
Puerto Rico
Jamaica
Jamaica
Puerto Rico
Hispaniola
Cuba
Cuba
Puerto Rico
Cuba
Hispaniola
Jamaica
Ecomorph Habitat
Grass-bush
Twig
Trunk-crown
Trunk-ground
Trunk-ground
Trunk-crown
Trunk-crown
Trunk-ground
Twig
Grass-bush
Grass-bush
Trunk-crown
Grass-bush
Trunk-ground
Twig
Twig
Outgroup
Label the other copy “Ecomorph Distribution”. On that copy, color each branch (up until it reaches a
node) according to the ectomorph of that lizard shown above (Trunk-ground=red, Trunkcrown=green, Grass-bush=blue, Twig=yellow). (Include a key.)
Examine the phylogenic trees and discuss the following points:
What general patterns do you see in the tree?
Do species from the same ecomorph group together on a phylogenetic branch?
Do species from the same island group together on a branch?
What historical events explain your previous two answers?
Back to the video (9:55 to end):
What is the difference between microevolution and macroevolution?
Explain how one species could evolve into two species in this scenario:
What does sexual selection have to do with it?
Explain in detail how anoles evolve on the Caribbean islands (there is a bigger space here for a
reason, use it):
What are these types of evolution called in respect to the islands.
Do some investigations of your own on at least two of the following genes.
ATP synthase
28S rRNA
Myosin
Pax1
Ubiquitin
Referring to these genes, explain:
What is the specific function of the gene products (usually a protein) in humans? (Explain what they
actually do in cells.)
Would you expect the gene products in other organisms? If so, which ones? Why?
Is it possible to find the same gene in two different organisms, but not find the product that is
produced from that gene? Discuss your answer.
If you found the same gene in many other different organisms, what does it suggest about the
evolution of this gene in the history of life?
Staple your colored phylogenetic trees to this assignment and turn it in.