Download C tudi - DNA to Darwin

TEACHER’S GUIDE
Introduction
Introductory
activities
Dean Madden
NCBE, University of Reading
Version 1.0
Case Stu
Case Stud
introduction
Introductory activities
The activities in this section explain the basic principles behind the
construction of phylogenetic trees, DNA structure and sequence
alignment. Students are also intoduced to the Geneious software.
Before carrying out the activities in the DNA to Darwin Case studies,
students will need to understand:
•• the basic principles behind the construction of an evolutionary tree or
phylogeny;
•• the basic structure of DNA and proteins;
•• the reasons for and the principle of alignment;
•• use of some features of the Geneious computer software (basic version).
The activities in this introduction are designed to achieve this. Some of
them will reinforce what students may already know; others involve new
concepts. The material includes extension activities for more able students.
Evolutionary trees
In 1837, 12 years before the publication of On the Origin of Species, Charles
Darwin famously drew an evolutionary tree in one of his notebooks.
The Origin also included a diagram of an evolutionary tree — the only
illustration in the book. Two years before, Darwin had written to his friend
Thomas Henry Huxley, saying:
‘The time will come, I believe, though I shall not live to see it, when we shall
have fairly true genealogical trees of each great kingdom of Nature.’
Today, scientists are trying to produce the ‘Tree of Life’ Darwin foresaw,
using protein, DNA and RNA sequence data.
Evolutionary trees are covered on pages 2–7 of the Student’s guide and
in the PowerPoint and Keynote slide presentations. Page 3 of the Student’s
guide is the instructions for making the tree from biscuits.
DNA and protein structure
Although this is well-covered in all relevant textbooks, a DNA model and
animated (QuickTime) slideshow of DNA structure are provided.
Sequence alignment
This is shown using an animated (QuickTime) slideshow.
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1. Evolutionary trees
This activity introduces students to the use of tree diagrams
(phylogenies) to show evolutionary relationships.
General reading
The making of the fittest. DNA and the ultimate forensic record of evolution by
Sean B. Carroll (2009) Quercus Books (Paperback) ISBN: 978 1847247247.
A popular lay account of some of the molecular evidence for evolution.
Reading the story in DNA: A beginner’s guide to molecular evolution
by Lindell Bromham (2008) Oxford University Press (Paperback)
ISBN: 978 0199290918. An engaging textbook on molecular evolution, which
assumes no specialist mathematical knowledge and takes the reader from first
principles.
A science primer. Just the facts: A basic introduction to the science underlying
NCBI resources (2004) National Center for Biotechnology Information. This
document from the National Center for Biotechnology Information in the USA,
provides a clear introduction to the principles of systematics and molecular
phylogenetics. It can be read on-line at: http://www.ncbi.nlm.nih.gov/
About/primer/phylo.html
Scientific publications
These papers can be accessed free-of-charge, online.
Evolution of the domestic cat
Johnson, W. E. et al (2006) The late Miocene radiation of modern Felidae: A
genetic assessment. Science 311, 73–77. doi: 10.1126/science.1122277
Driscoll, C. A. et al (2007) The Near Eastern origin of cat domestication.
Science 317, 519–523. doi: 10.1126/science.1139518
Re-evolution of teeth in the marsupial frog, Gastrotheca guentheri
Wiens, J. J. (2011) Re-evolution of lost mandibular teeth in frogs after more
than 200 million years, and re-evaluating Dollo’s Law. Evolution (online
advance publication). doi: 10.1111/j.1558-5646.2011.01221.x
Requirements
Each student or working group will need:
•• cut-outs of the biscuits on page 6 of this document (these could be
laminated for re-use)
•• a sheet of A3 paper
•• a ruler and pencil or pen
•• copies of worksheets.
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Presentations
Teachers may find the PowerPoint or Keynote presentation helpful for
introducing this exercise.
Educational aims
The activity introduces the concept of showing evolutionary relationships
in a tree diagram (phylogeny). The ‘biscuit’ activity can be used as a
diagnositic tool to evaluate students’ understanding of evolution, before
or after teaching the subject. It emphasises how phylogenies based
on phenotype alone can be misleading and introduces the concept of
generating evolutionary trees based on nucleic acid and protein sequence
data.
The Extension material on pages 5 and 6 can be used for more able students
or as homework.
Prequisite knowledge
Some knowledge of the basic concepts of evolution, including selection and
speciation, would be useful. It is also helpful if students know the basic
terms used to describe evolutionary trees e.g., root, branch, node.
Classroom organisation
There are several ways of using the exercise. One strategy would be to
divide the class into small groups of 2–3 students and to ask each group
to devise an evolutionary tree using the biscuit cut-outs. Each group then
reports back to the entire class, explaining the reasons for their decisions
and describing how they think the biscuits have ‘evolved’.
To ensure that the discussion is meaningful, it may help to give students
a list of words and phrases that they must use in their descriptions. For
example: selection, speciation, convergent evolution, adaptation, mutation,
common ancestor, branch, node, outgroup etc.
A strategy that has proved effective is for the teacher to eavesdrop on the
discussion in each group as they are devising their trees, then to choose a
relatively articulate group to give their presentation first. This will then
‘set the tone’ for the other groups’ feedback. With large classes, it may prove
impractical for all groups to report back, in which case just three or four
groups may be asked to describe their trees verbally, then all groups can be
asked to produce a written description.
The exercise can also be undertaken using a selection of real biscuits,
although this activity is more open-ended and hence less predictable.
Health and safety regulations will have to be considered if the biscuits are
to be eaten afterwards.
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Other useful resources
Simulating evolution
A practical exercise in which students produce a phylogenetic tree using
screws, nuts and bolts, paperclips, etc. Devised by John Barker, based on
an Open University activity. Downloadable from: www.eurovolvox.org/
protocols.html
Building a phylogenetic tree
An exercise devised by Wojciech Grajkowski of the Science Festival School,
Warsaw, in which students construct data matrices for three groups of
organisms, then use them to generate phylogenies. Downloadable from:
www.eurovolvox.org/protocols.html
Wellcome Trust Tree of Life
The Wellcome Trust Tree of Life is a six-minute animated evolutionary history
presented by Sir David Attenborough. The video can be downloaded for
classroom use, as can the supporting interactive tree, to be viewed using a
Web browser (requires Adobe Flash 10+). An audio-free version of the video
is also available for dubbing with your own soundtrack. Several additional
educational resources and an animated video presentation of evolution are
all free to download.
www.wellcometreeoflife.org
Tree of Life Web Project
The Tree of Life Web Project is a collaborative effort of biologists from around
the world. On more than 9,000 Web pages, the project provides information
about the diversity of organisms on Earth, their evolutionary history
(phylogeny), and characteristics.
http://tolweb.org/tree/
Interactive Tree of Life (European Molecular Biology Laboratory)
This is an advanced online tool for the display and manipulation of
phylogenetic trees. It provides most of the features available in other tree
viewers, and offers a novel circular tree layout, which makes it easy to
visualize trees. Trees can be exported to several graphical formats, both
bitmap- and vector-based. Even if you don’t want to generate your own
trees, you can explore the pre-computed interactive diagrams on this site.
http://itol.embl.de/
National Center for Biotechnology Information (NCBI)
The NCBI hosts a major collection of databases of genetic information that
is used by research scientists world-wide. The Web site includes some
excellent educational materials, including a primer on systematics and
molecular phylogenetics.
http://www.ncbi.nlm.nih.gov/
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Existing (extant) species
Fossil
common
ancestor
Existing (extant) species
Fossil
common
ancestor
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Tree 1
Tree 2
Tree 3
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Answers to the questions on the worksheets
Page 3
There are three possible ways of constructing the evolutionary tree from
biscuits. These are shown here and in the slide presentations.
Page 5
a. Variations in the rate of evolution may lead to organisms being placed
in the wrong place on an evolutionary tree (they may look very
different when they are in fact closely-related).
b. Any examples of convergent evolution could be suggested here, for
example, wings in bats and birds, camera-like eyes in primates and
cephalopods, streamlined body shapes in dolphins and sharks.
c. For example, the genes controlling skin colour in humans have
diverged very rapidly, meaning that humans look different when in
fact they are all the same species.
d. For evolution to go ‘in reverse’, similar selection pressures would
have to apply, but once genetic diversity has been lost, the chances of
successive mutations occurring to exactly recreate the original trait
are remote.
e. If a tree is prepared based on similarity, a re-evolved trait may cause a
species to be incorrectly grouped with distantly-related organisms.
f. All organisms have DNA or RNA, so there is a direct means for
comparing them, which is not necessarily the case with other
characteristics. Sequence data lends itself to computer-based analysis
and statisitical techniques can also be applied to the data.
High rates of mutation in stretches of non-coding DNA, which are
not eliminated by natural selection, can be misleading however. In
addition, since there are only four character states for DNA bases (C,
A, G and T) the probability of any one base being shared at a particular
position by chance is high.
Page 6
g. i. Cat (all are mammals, the other three organisms are rodents).
ii. Oak tree (the other two trees are coniferous).
iii. Snail (all are molluscs, but the octopus and squid are more closely
related to each other than they are to snails).
iv. Wombat (all except the wombat (a marsupial) are placental
mammals).
v. Lemur (all are primates, but the lemur is a prosimian, while the
others are simians).
vi. Platypus (the kangaroo (a marsupial) and the bear (a mammal)
are more closely-related to one another than they are to the egg
laying platypus (a monotreme)).
vii. Snail (the other two are chordates).
viii. Traditionally, classification of the rosaceae (all of the species
listed here) relied upon fruit type, which would imply that the
strawberry is the outgroup, but genetic studies have shown that
fruit type is a poor guide to evolutionary relationships here).
ix. Onion (it is the only monocotyledon).
x.
Escherichia coli (the other two are fungi).
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2. A model of DNA
In this activity, students make a 3-D paper model of B-DNA. There
is also a QuickTime animation showing the structure of DNA.
Modeling the helix
This model is cheap and easy to make and shows the key features of
DNA structure, including the major and minor grooves of the helix. The
templates must be cut and folded with care however, and this may take a
considerable time. The exercise is therefore best set as a group activity in
which students prepare a few base pair templates each then combine them
to build one or more models.
If the nucleotide pairs are photocopied or printed onto overhead
transparency sheets instead of card, these can be assembled to make a
particularly attractive model.
General reading
The double helix. A personal account of the discovery of the structure of DNA by
James D. Watson [Gunther Stent, Ed.] (1980) New York: W. W. Norton
and Company. ISBN: 0 393 95075 1.
What mad pursuit. A personal view of scientific discovery by Francis Crick
(1988) New York: Basic Books. ISBN: 0 465 09138 5.
Rosalind Franklin: The Dark Lady of DNA by Brenda Maddox (2003) London:
HarperCollins. ISBN: 978 0006552116.
Maurice Wilkins — The third man of the double helix by Maurice Wilkins
(2005) Oxford: Oxford University Press. ISBN: 978 0192806673.
Francis Crick: Discoverer of the genetic code by Matt Ridley (2008) London:
HarperPerennial. ISBN: 978 0007213313.
Requirements
Each student or working group will need:
Equipment
• Scissors
• Bodkin or strong needle, for punching holes through card
• OPTIONAL: Sharp craft knife and cutting board
Materials
• Nucleotide templates, copied onto thin card
(At least 16 templates will be needed to show the structure clearly)
• Glue suitable for paper
• Drinking straws
• Fine string or strong sewing thread
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Educational aims
Knowledge of the base-pairing mechanism is essential for use of the the
bioinformatics software in the DNA to Darwin Case studies. This activity
can be used to introduce or revise DNA structure. Models can be made for
homework or as a group activity.
Prequisite knowledge
Prior knowledge of the basic structure of DNA would be useful e.g., names
of bases and base-pairing mechanism; sugar-phosphate backbone.
Other useful resources
The Wellcome Trust has several (Adobe Flash) animations of DNA structure,
function and sequencing methods which can be downloaded free-ofcharge from its web site: www.wellcome.ac.uk/Education-resources/
Teaching-and-education/Animations/DNA/index.htm
Fernand Schroeder of the Lycée de Garçons, Esch/Alzette (Luxemborg)
has devised a cut-out ‘computer’ showing the codons that correspond to
each amino acid. The reverse of the ‘computer’ shows the structure of each
amino acid: www.eurovolvox.org/Animations and models/geneticcode.
html
The same web site also includes several interactive DNA animations devised
by Tago Sarapuu and his colleagues from the Science Didactics Department,
University of Tartu (Estonia).
Molecule of the Month
The Protein Data Bank has a tutorial on DNA structure and function,
including a 3-D cut-out paper model: http://www.rcsb.org/pdb/101/motm.
do?momID=23
NCBE DNA50
The NCBE has several materials on this mini web site created to celebrate
50 years of the double helix in 2003: www.ncbe.reading.ac.uk/DNA50/
menu.html
Acknowledgements
The model upon which this one is based was devised by Van Rensselaer Potter
in 1958 and appeared the following year in his book Nucleic Acid Outlines.
This article is adapted from one by the same author which first appeared in
the on-line journal Bioscience Explained: www.bioscience-explained.org
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Screenshots from the QuickTime animation
1.Use the space bar, forward or back arrow keys or
mouse to move through the animation.
2.The first slide shows the components that DNA is
made from and give an overview of the structure.
3.Base pairs are highlighted. Note the antiparallel
arrangment of the two strands.
4.Hydrogen bonds between the bases are shown.
5.The phosphate groups are highlighted. Note the
negative charge on the oxygen atoms.
6.The sugars are highlighted. Another slide shows the
numbering of the carbon atoms.
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H
O
CH2
O
P
-O
N
O
N
H
H
O
H3C
O
N H
N
N H
O
N
CH2
O
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H
N
GC
H N
O
H
O P O-
N
O
N
TA
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CH2
O
N
O
CH2
O
H
N
N H
O
O
H
O
O
O P O-
H N
O
O P O-
N
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CH2
O
N
O
O
H N
N
O
O
P
O
N
N
CH2
O
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H
O
O
N
H N
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H
CH2
O
N
H N
CG
O P O-
N
O
N H
CH2
O
H
H
O
N
AT
H
O P O-
CH3
H
O
N
O
N H
O
O P OO
-O
H
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RNA code
DNA code
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3. Alignment
This animation is useful to highlight why alignment is necessary
to detect underlying relationships between nucleic acid or protein
sequences.
Note that inversions are not shown in the animation, as these cannot be
identified by most alignment software. Generally, inverted sequences
are treated by the software like any other sequence and consequently
underlying relationships may not be detected. The identification of
inversions in sequence data is a non-trivial and computationally-expensive
task.
Alignments can be produced using DNA or protein sequence data. Amino
acid sequences are of course a third of the length of their nucleic acid
equivalents, so they carry less information. Because of the redundancy in
the Genetic Code (with one amino acid being represented by more than one
codon), for a particular sequence, protein alignments show less variation
than their nucleic acid equivalents. Consequently, a phylogenetic tree
generated from a protein alignment may be different from that generated
by the equivalent nucleic acid sequence.
Requirements
• Computer with QuickTime installed. QuickTime may be downloaded freeof-charge from the Apple web site: www.apple.com/quicktime
• QuickTime animation showing alignment.
Screenshots from the QuickTime animation
1.The animation shows three types of mutation and
the alignment of four DNA sequences.
Copyright © Dean Madden, 2011
2.You can use the space bar, forward or back arrow
keys or mouse to move through the animation.
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3.Pauses (requiring a click to advance) allow you to
explain the process and to question students.
4.At the end of each section, there is a static one-screen
summary of the process.
5.The three derived sequences and the original DNA
sequence are aligned.
6.Note how insertions affect the alignment of all other
sequences; substitutions can be seen here too.
7.An example of aligned DNA sequences in Geneious.
The inserted dashes can clearly be seen.
Copyright © Dean Madden, 2011
8.Aligned protein sequences. The asterisks on a black
background show unknown amino acids.
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