phylogeny_teachers_guidex - Computational Biology

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AP Biology


Teacher’s Guide

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1

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Le
arning Evolution Using


Phylogenetic Analysis

For more information contact Yulia Newton at ynewton@soe.ucsc.edu

Pre
-
requisite skills:

Introduction knowledge of evolution.

Required equipment:

1.

Students will need to
use a computer individually or in groups

2.

Students will need an internet access

The purpose of this hands
-
on practice is to
learn how to utilize Bioinformatics tools

to help
students

learn about
E
volution
.

Students learn through
an in
-
class discussion and
c
ompleting a hands
-
on
worksheet.

The lesson unit includes the following components:

1.

This document (teacher’s guide)

2.

Power point presentation for an in
-
class discussion

3.

Student worksheet to be completed by students in class (we suggest groups of 2 students
but
individual work is perfectly acceptable as well)

There are 5 parts in the student

worksheet:

1.

Big Picture of the worksheet lists an overview of the steps involved in constructing a
phylogenetic tree. It provides students with a big picture of the proces
s.

2.

Part A of the worksheet is
an exercise of inferring phylogenetic relationship from purely
morphological features
.

3.

Part B
is
a step
-
by
-
step walk through performing a phylogenetic analysis. Beta globin
sequences from various specie

are used for this part of the worksheet
.

4.

In part C students work on their own, using what they learned in part B, to analyze SIV and
HIV sequences to determine which SIV strand HIV evolved from
.

GAG protein sequences are
used in this part of the worksheet
.

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Teacher’s Guide

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5.

In
Part D

students
perform phylogenetic analysis on various placentals and marsupials to
determine relationship of platypus and kangaroo rats to other specie
.

Students should get the
following tree as a part of their analysis.


Big Picture

1.

Gather your
characteristics

based on which you want to compare the desired
species/entities.

2.

Perform multiple sequence alignment

on the selected sequences.

3.

Calculate the distance matrix

from the multiple sequence alignment.

4.

Build a phylogenetic tree
.

5.

Visualize the

tree

in graphical output from the text representation of the tree produced by the
previous step.

In class discussion and presentation

The included power point is optional but is strongly encouraged to be used. Below is a discussion
guideline for the foll
owing topics:



Rooted and un
-
rooted trees



Cladograms vs. Phylograms


AP Biology


Teacher’s Guide

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Start this workshop by talking about evolution.

1.

What is evolution?
Descent with modification.

2.

Talk about the time frames (geological time vs. family genealogy)

3.

How can we infer relatedness of species (morphology, fossil record, genetic makeup, protein
sequence, etc.)?

4.

What are the differences for inferring relatedness between species that still exist and species
that are now extinct (Neanderthals, Wooly Mammoth,

etc.)?

5.

Talk about examples of morphological features (bipedalism, shape of limbs, digits vs. hooves,
etc.)

6.

Give examples of situations when using morphological features makes it hard to determine
evolutionary relationship (Quagga) or produces phylogeny th
at is wrong (Bankisia, Horseshoe
crab).

7.

Can you think of any reasons when it is adventageous to use genomic over proteomic
sequences and visa versa?

a.

It makes sense to use genomic sequences when there has not been enough
evolutionary divergence between the
sequences. For example, when looking at fairly
young species or recent evolutionary changes. Oherwise, proteomic sequences are
best to use.

Rooted and un
-
rooted trees

Let’s talk about rooted and unrooted trees. This is a very important concept to understa
nd.

Computational phylogeny is a discipline that lives in the intersection of Computer Science and
Biology. However, there are some concepts that mean different things to a computer scientist and to
a biologist. Tree root is one of those concepts. To a compute
r scientist a root is a special node that
sits above other nodes in the tree. To a biologist examining a phylogenetic tree, a root means an
evolutionary common ancestor.

Below are different examples of drawing a tree:


One has to be careful about whether

the tree they are working with is rooted or unrooted. Unrooted
trees provide information about evolutionary relatedness. Those entities that are more closely
grouped are more closely related than those entities that are not as closely grouped. Rooted tree
s
provide information about the evolutionary ancestry in addition to the evolutionary relatedness. The
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Teacher’s Guide

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same tree could be drawn to look rooted or unrooted. In the example below, A appears to be a root of
the left tree and therefore we could infer that A is

an evolutionary ancestor of all other nodes.
However, if that tree is not truly rooted but only drawn as rooted then our analysis is incorrect. The
tree on the right is the same tree as the one on the left, only drawn differently. A is not a root in this
tree. When using Bioinformatics tools to produce and draw phylogenetic trees, you have to be extra
careful about whether the tree is rooted or unrooted. Usually these details are a part of the manual or
the readme file.




Remember that evolution is a fluid process? Evolutionary changes are slow and settle, when looking
at any short periods of time. Usually when building phylogenetic trees, the common ancestor of two
currently existing specie is often extinct and no longer e
xists. Such common ancestor is indicated in a
tree as a junction of two branches.

Adding an outlier entity/group to our set of characteristics (in our case sequences) allows creating a
tree topology that shows the position of the common ancestor for our g
roup of interest. It causes
representing the phylogeny of our entities/specie as a subtree, which indicates a grouping together.
The outlier sequence is usually completely unrelated to the other sequences in your analysis and will
lie on the outside of all

the other groups. It will not group together with any other sequences. This
technique allows all the sequences of interest to group together in a subtree, by which separating all
of them from the outlier entity. Below is an example of using an outlier gro
up. Eubacteria is used as
an outlier in the analysis of eukaryotes based on some enzymes. Without the use of an outgroup it
would be impossible to infer an relationship to a common ancestor just from the tree topology.


Da
-
Fei Feng, Glen Cho, and Russell
F. Doolittle. Determining divergence times with a protein clock: Update and reevaluation, PNAS,
1997.

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A subtree with two or more nodes is called a clade. Nodes within the same clade are more closely related than
those in two different clades.


There are m
any ways to draw a tree

Everything is derived from the common ancestor. Many algorithms do not actually give us the root.

Part c: what does evolutionary time means (in cladograms, everything is now

Cladograms vs. Phylograms

Another important concept we need to tackle is the difference between the
cladograms

and
phylograms
. Both of these types of trees can be drawn as rooted and unrooted. However, there is
one big difference between cladograms and phylograms. The length of a t
ree arm (called an “edge” in
computer science and mathematics) in phylograms indicates evolutionary time since the last common
ancestor while the length of a tree arm in a cladogram is irrelavant and has no special meaning. In
phylogram, the longer the edg
e is the more time has passed since the last common ancestor and
very short edges indicate a very young (in evolutionary time) node.

Answers to the worksheet questions:

Part A

Exercise 1

Quagga and Zebra are more closely related.

Exercise 2

Banksia and Ha
kea are more closely related.

Exercise 3

Horseshoe crab and Aquatic spider are more closely related.

Exercise 4

Barnacle and Shrimp are more closely related.

Exercise 5

Species that are more closely related may have more similar DNA sequences and, therefore, we can use
those sequences. When the species we are comparing are more distantly related then the appropriate
genomic sequences might not align well while the protein

sequences still show conservation. In that case, it is
better to use protein sequences.

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Part B

Exercise 1

Q11


Exercise

3

Q9



Exercise 4

A

Students should see a tree that looks similar to this:


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Q8

Different.

Q9

Chimp (displayed as Pan in the tree).

Q10

Gorilla.

Exercise 4B

Students should see trees similar to this:



Q9

Rooted. It says so in the
Standard output (
Report
)

field.

Q13

Salmon (appears as Salmo in the tree).

Q14

Logically, this relationship does not make sense. As was discussed in the in
-
class presentation and class
discussion, we should use an outgroup to fix this.

Q22

The root should be drawn on the edge leading to Salmo node.

Exercise 4C

Students should see a

tree similar to this:



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Q10

Unrooted. It says so in
Standard output (
Report
)

field.

Q14

The root should be drawn on the edge leading to Salmo node.

Q29

The tree produced in step 8 is a phylogram. It tells you how much
evolution occurred from the time of

speciation between any two given species
.

In other words, it tells us how closely two species are related.

For
example, from this tree we can conclude that there has passed more evolutionary time between
Salmo
(salmon) and Mus (mouse) than between Rattus

(rat) and Mus (mouse).

The tree produced in step 26 is a cladogram. It tells us how much time has passed since the speciation
between the species in the exercise. For example, we can tell that more evolutionary time passed from the
time
of speciation betw
een
Mus (mouse) and Rattus (Rat)
than

Mus (mouse) and Otolemur (galago).

Exercise 5

Students should see trees similar to this:




Q8

Chicken (Gallus) is most related to the mouse and the rat (Mus and Rattus).

Part C

Exercise 1

Students
should see a tre
e similar to one of these trees
:

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Q3

HIV is most closely related to SIV Chimp.

Part D

Students should see a tree similar to one of these trees:




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Q7

Platypus is most closely related to other
marsupials
: Opassum, Quokka, Rock
wallaby
, Nail tail
wallaby,
Swamp wallaby).

Q8

Kangaroo rats don’t belong to the same immediate clade. They are more distantly related to platypus than the
species listed in Q7. Actually, kangaroo rats are not marsupials at all.

Q9

Kangaroo rats are more closely related to other species of rats and mice.