SPECIATION
1.3 Genome: d (i) Phylogenetics and molecular clocks
From the Arrangements
(i) Phylogenetics and molecular clocks
The use of sequence data to study the evolutionary relatedness among groups
of organisms. Sequence divergence is used to estimate time sinc e lineages
diverged. For example, comparison of sequences provides evidence for three
main domains (bacteria, archaea and eukaryotes).
The use of sequence data and fossil evidence to determine the main sequence
of events in the evolution of life: cells, last universal ancestor,
photosynthesis, eukaryotes, multicellularity, animals, land plants, vertebrates.
Teacher’s notes
There are three activities in this section. Each activity has its own set of
learning objectives. When going over these activities remember to refer back
to the learning objectives in order to clarify what may be required for
assessment.
If possible start this section with solving the mystery of the Neanderthals;
this will put the second exercise into context for students , making the
summary questions more relevant.
1.
Solving the mystery of the Neanderthals
This web-based activity can be delivered via an overhead projector and
the interactive web pages (slides) talked through or given to students to
work through on their own. In either case, familiarise yourself with the
background information (page 2). Open the web address and work
through the activity. There is a commentary with the handout on p age 2
but the activity is self-explanatory.
When students are looking for mutations it is important to emphasise
the need for computers in analysing sequence information.
In pairs, get students to discuss the ‘What to do’ section on page 3
before making their notes. You may also get them to read through the
information card (page 5).
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2.
Summary questions
A straightforward exercise: students read over the information card
(page 5) and answer the ten questions.
If this is carried out straight after ‘Solving the mystery of the
Neanderthals’ you may notice there is a mistake in the fir st activity. In
the early slides the human/chimpanzee common ancestor has been given
an age equivalent of 56 mutations (1.2 million years), but this is
corrected on the second last slide. The students may not even notice
this.
3.
Web-based research activity
A series of questions: the first seven can be easily answered from
simple Google searches or even Wikipedia. The last set of questions, 8–
16, is based on the Wellcome Trust’s interactive ‘Tree of Life’ website
(an excellent resource).
Start off by watching the video. At any point you can pause the video
and enter the interactive tree of life. Explore the tree and pick up the
video where you paused it.
There is also a set of student worksheets and a Teacher’s Guide on the
website.
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Student activities
Solving the mystery of the Neanderthals
Learning objectives
You will be able to compare DNA sequences from two different species and
look for single nucleotide point mutations.
You will appreciate why computers are used to analyse and compare
genomes.
You will learn how a molecular clock can be calibrated using DNA sequence
differences.
You will learn how this information can be used to make a phylogenetic tree .
Background information
Neanderthals first appeared in Europe about 175 000 years ago and became
extinct about 27 000 years ago. In other words they coexisted with modern
humans both in time and place. This activity explores the theories that
Neanderthals either may be the direct ancestor of humans or may be
descendents of a common ancestor who lived before the last common ancestor
of all modern humans.
By looking at the single nucleotide mutations in mitochondrial DNA and
tying these into fossil records a molecular clock has been calibrated to
estimate the time of divergence of all modern humans from their common
ancestor. The same type of analysis is used to estimate the time of divergence
of Neanderthals from their common ancestor and a human – Neanderthal
comparison made.
Google: solving the mystery of the Neanderthals
Open the link: http://www.geneticorigins.org/mito/media2.html
Slide 1
The first slide very simply and elegantly outlines how a molecular clock
works by comparing human and chimpanzee descendants from a common
ancestor.
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Slide 2
This shows a 379 base pair nucleotide sequence from a human lined up
alongside the same region from a chimpanzee. The task is to count how many
differences there are between the two sequences. There are four options to
choose from if counting the sequences is too tedious.
This emphasises the need for computers to analyse and compare sequence
data.
Slide 3
Similar to the first slide but summarises the number of mutations between
humans and chimpanzees.
Slides 4, 5 and 6
Does the same exercise but compares the sequences from two humans ,
estimating that humans are descended from a common ancestor about 150 000
years ago.
Slide 7
Introduces the Neanderthals and their extinction at about 30 000 years ago.
Slide 8
Shows a map of where Neanderthals coexisted with Cro Magnon – the direct
ancestor of humans.
Slide 9
Poses the question, ‘Were Neanderthals the direct ancestor of modern humans
or a “dead end” in hominid evolution?’ There are two phylogenetic trees and
options to say which model is correct.
Slide 10
Introduces the German scientist and mitochondrial DNA analysis .
Slide 11
Compares the 379 base pair regions from a human and Neandert hal and asks
how many differences there are.
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Slides 12 and 13
By using the molecular clock it is possible to estimate the time divergence
between humans and Neanderthals.
Slides 14 and 15
Shows the same two phylogenetic trees as in slide 9 and asks which model is
correct:
What to do
Go through this exercise and make notes on how the molecular clock was
calibrated.
Using the data in the presentation, how long ago did humans diverge from
their common ancestor (look at the second last slide)?
What evidence do you think would prove the existence of an early common
ancestor to chimpanzees and humans?
Draw a phylogenetic diagram showing the relationship between the common
primate ancestor, common human ancestor, modern humans and
Neanderthals. Make sure you use a suitable scale to represent time , ie the
longer the time, the longer the line (look at the last slide and the stick
diagram on this page for some help).
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Summary questions
Learning objectives
By completing these questions you will understand how a molecular clock
can be used to estimate when two species diverged from a common ancestor.
You will learn that molecular clocks rely on mutations occurring over time
and the time can be quantified against a known dated event from the fossil
record.
The more differences between organisms the longer i t has been since they
diverged from a common ancestor.
You will understand how this information can be represented in a
phylogenetic tree.
You will understand why mitochondrial DNA is often the preferred source for
this type of sequence analysis.
Use the information card to help you answer these questions :
1.
When a new species is formed what will it continue to accumulate and
pass on to its offspring?
2.
What two pieces of information are needed to calibrate a molecular
clock?
3.
What three assumptions are made when calibrating a molecular clock?
4.
If the rate of mutations was five per 100 000 years and two species had
an average difference of 15 mutations, how long ago did they diverge
from a common ancestor?
5.
Using evidence from the phylogenetic tree explain where modern
humans first appeared.
6.
When did our relative Homo habilis become extinct?
7.
Roughly, how genetically different were Homo habilis and Homo
erectus from modern humans?
8.
Place in age order the three species mentioned in question 7.
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9.
Why is mitochondrial DNA often used for sequence comparisons in
phylogenetic studies?
10.
How does the mitochondrial genome differ from that of a typical
eukaryote?
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Information card
Molecular clocks
Evolutionary biologists have revolutionised their field using a combination of
DNA sequencing and bioinformatics. By comparing inherited DNA
substitution mutations, or single nucleotide polymorphisms (SNPs), it is
possible to establish relationships between different population groups within
the same species or between different closely related species. When two new
species develop from a common ancestor each will inherit and continue to
accumulate a unique set of random mutations. Assuming the mutations
accumulate at a constant rate, the number of mutations will be prop ortional to
the length of time that two groups have been separated. In other words the
number of mutations will be equivalent to a set period of time – a molecular
clock. Knowing the rate at which the changes occur and the number of
differences between two organisms allows you to estimate when the
separation from the common ancestor occurred.
Before using the clock, it has to be calibrated. For example, by extrapolating
from fossil evidence and DNA sequences from other primates it is thought
that chimpanzees and humans diverged from a last common ancestor about 5
to 6 million years ago. By measuring the number of sequence differences
between chimpanzees and humans it is possible to set the clock. However,
this is a controversial process, for example it reli es on having fossil evidence
which can be accurately dated and the assumption that the average rate of
mutation will be the same in all regions of the genome and for different
organisms.
Once the clock has been calibrated it is then possible to determine when other
events in human evolution occurred, for example fossils of our own species,
Homo sapiens, have been found throughout the old world dating to 100 000
years ago but molecular clock analysis suggest s that humans have been
around for 150 000 years. Could there still be fossils waiting to be
discovered?
Phylogenetic tree showing the evolution of humans (from Wikipedia) .
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Molecular clock analysis can be used to build up a phylogenetic tree , as in the
above example. A timescale in millions of years is provided along with a
genetic distance: this shows that humans and chimp anzees have DNA
sequence differences of about 2%.
Which part of the genome to use?
Two regions of DNA which are routinely used in this sort of phylogenetic
analysis can be found on the male Y chromosome or on the mitochondrial
DNA. This allows the molecular clock to be traced through the male or
female ancestral lines. (When a sperm fertilises an egg, only the egg’s
mitochondria are present in the zygote, so the mitochondria are derived from
the mother.)
One advantage of using mitochondrial DNA is the simplicity of a single small
chromosome, a haploid genome, which does not have a matching homologous
partner with different alleles or crossing over events to complicate the
sequence. Mitochondrial chromosomes also have very little non-coding DNA,
with genes tightly packed together and with few introns. This is in contrast to
normal eukaryote genes, which are usually widely dispersed on a linear
chromosome and have numerous introns.
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Web-based research activity
Learning objectives
You should find out about the main sequence of events in the evolution of
life.
You should know there are three main domains of life, each originating from
the last universal common ancestor.
You should be able to figure out why green plants are fundamental to life on
Earth.
Know that the only record of many creatures is to be found in fossils.
1.
What is meant by a ‘niche’?
2.
What are the three phylogenetic domains in the classification of life?
3.
What sequence data was used to divide life into three domains and why
do you think this was chosen?
4.
What is meant by the last universal ancestor?
5.
Sketch a simplified phylogenetic tree showing the three domains
originating from a common ancestor and some of the kingdoms
branching from each domain.
6.
In which environments would you expect to find members of the
archaea?
7.
Describe the differences between generalised prokaryotic and
eukaryotic cells.
Google ‘tree of life’ and click on the following link:
http://www.wellcometreeoflife.org/?gclid=CKrxmsmInqYCFY9O4Qod
Wj79Xw
Watch the short video then go to the interactive link. It is possible to
skip between the video and the interactive tree of life without losing
your place in the video.
8.
Look at the tree in two dimensions with no scaling (the red cube is to
the left of the box at the bottom of the screen). What do you notice
about the numbers of organisms as time has elapsed since the first signs
of life?
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9.
When did life first appear?
It is easier to navigate through the tree if you collapse it. This shows
the branches but does not give any information about time. Hover your
cursor over a node or line end to find out relevant information.
10.
Find the three main domains originating from life on Earth. When do
green plants appear on the tree relative to reptiles?
11.
Which type of green plants was first on the scene? ( Click on the nodes
land plants and green plants then the blue sub tree symbol to zoom in on
a section of the tree.)
12.
Why do you think green plants were important for life on Earth?
13.
When did the first armoured creatures appear on the land?
14.
When did the amphibians first appear?
15.
What happened to many creatures about 65 million years ago and how
do we know they existed?
16.
Which two types of land vertebrates capitalised on the vacant niches?
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