IB Biology
Option D
D5 Phylogeny and Systematics
All syllabus statements ©IBO 2007
All images CC or public domain or link to original material.
Jason de Nys
http://en.wikipedia.org/wiki/File:Tree_of_life_SVG.svg
"The affinities of all the beings of the same class have
sometimes been represented by a great tree... As
buds give rise by growth to fresh buds, and these if
vigorous, branch out and overtop on all sides many a
feebler branch, so by generation I believe it has been
with the great Tree of Life, which fills with its dead
and broken branches the crust of the earth, and
covers the surface with its ever branching and
beautiful ramifications."
Charles Darwin, 1859
Charlie sure could spit out a quotable piece of writing
D.5.1 Outline the value of classifying organisms
Identification of Organisms
Unknown organisms are easily identified if data about organisms
is organised. Classification allows for the creation of keys.
Remember 5.5
Classification?
Evolutionary Links
Classification allows us to see evolutionary
relationships. Organisms that are grouped together share a lot of
similar features (homologous structures). These shared
characteristics help us see how organisms have evolved from a
common ancestor.
e.g. Llamas were
originally compared to
sheep but a study of
their morphology later
placed them in the
camel family
http://www.flickr.com/photos/mrapplegate/2423991076/
http://www.flickr.com/photos/doug88888/3458057235/
Prediction of Characteristics
Characteristics that are shared by organisms within a
group would be expected to be found in other
species that are closely related.
e.g. no doubt more fossils
that can be categorised in
the Homo genus will be
found.
We can expect them to
have relatively big brains
(crazy “Hobbit” finds
excepted!)
http://commons.wikimedia.org/wiki/File:Hominins_2002.png
D.5.2 Explain the Biochemical evidence provided by the universality of DNA and protein
structures for the common ancestry of living organisms
1) All known
organisms use DNA as
genetic material
The genetic code is
universal. Gene
sequences inserted in
different organisms
express the same
proteins
http://commons.wikimedia.org/wiki/File:Bdna.gif
2) The same 20 amino
acids are used to make
all proteins
http://commons.wikimedia.org/wiki/File:Protein_primary_structure.svg
3) Most amino acids can exist in left or righthanded forms, i.e. as mirror images
Yet all living things use
left-handed amino acids
It is believed that this
was a chance
occurrence in the
oldest common
ancestor
The panspermia hypothesis may help explain this as
more amino acids found in meteorites are left-handed
than right-handed
http://commons.wikimedia.org/wiki/File:Chirality_with_hands.jpg
4) Cytochrome c is a protein involved in the
electron transport chain.
It consists of 100-104 amino acids and is
found in plants, animals, and many
unicellular organisms
It is too complex to have evolved
independently and so must come from a
common ancestor
Further
evidence of
common
descent
http://en.wikipedia.org/wiki/File:Cytochromec.png
D.5.3 Explain how variations in specific molecules can indicate phylogeny
Taking the example of the protein cytochrome c.
It is not identical in all species because single
point mutations in the DNA that codes for it can
lead to different amino acids making up the
protein.
Both humans and chimpanzees have the identical
cytochrome c molecules, while rhesus monkeys
share all but one of the amino acids: the 66th
amino acid is isoleucine in the former and
threonine in the latter.
This suggests that humans and chimpanzees are
more closely related to each other than to rhesus
monkeys
I didn’t want to be
closely related to
stinking humans
anyway!
http://www.flickr.com/photos/stuffinhergoose/571672799
TOK
Read this article:
Closer to man than ape
What reasons are given for
including chimps in genus
Homo? Do you think humans
will ever be reclassified Pan?
This is part of a molecular
phylogeny of all of the living
primates.
It clearly shows chimpanzees (Pan)
as being more closely related to
humans than to gorillas.
It was made by
comparing 34,927
base pairs
sequenced from
54 genes taken
from each of a
single species in
each genus.
D.5.4 Discuss how biochemical variations can be used as an evolutionary clock
An evolutionary clock involves
calculating the time since species
diverged by comparing the
number of differences in their
DNA and/or protein sequences.
Scientists who originated the idea
calibrated the amino acid
differences in haemoglobin with
times derived from the fossil
record.
http://commons.wikimedia.org/wiki/File:Nature_Clock.gif
The assumption is that these changes occur at a regular rate.
(which may not always be the case)
Therefore if species A had 5 differences from species B and 10
differences from species C, then the lineages for A and C must
have split twice as long ago as for A and B
C
B
A
Time
D.5.5 Define clade and cladistics
Cladistics (From the
ancient Greek for
"branch") is a method of
classifying species of
organisms into groups
called clades, which
consist of an ancestor
organism and all its
descendants (and
nothing else).
Wikipedia
http://www.flickr.com/photos/aussiegall/4149475009/
For example, birds,
dinosaurs,
crocodiles, and all
descendants (living
or extinct) of their
most recent
common ancestor
form a clade Wikipedia
http://www.flickr.com/photos/kev
http://www.flickr.com/photos/mo
http://www.flickr.com/photos/tam
om/photos/emraya/2929959881/
Characteristics change over time,
thus the amount of change can
help determine relationships
Groups of organisms are
descended from a common
ancestor
There is a branching pattern in the
evolution of species and when a
split occurs, two distinct species
eventuate.
Shelled
eggs
Hair
Each clade
is determined by
common characteristics
of its members that are
different from that of the
other species from which
it has diverged
Amniotic Egg
Four Limbs
Bony Skeleton
Vertebrate
http://bridgeurl.com/xrmmmk/all
These traits which tie the clades together
are called shared derived characters
http://www.flickr.com/photos/29448992@N08/2970804257/
D.5.6 Distinguish, with examples, between analogous and homologous characteristics
Homologous
structures are
inherited from a
common ancestor
http://www.flickr.com/photos/opoterser/4189239614/
e.g. The fly on the previous page and
the mosquito on this page have
mouthparts adapted to their food
sources but the basic components
were inherited from a common
ancestor
Other examples include
pentadactyl limbs and finches’
beaks
http://www.flickr.com/photos/kclama/102002644/
Analogous structures have similar form
and function due to convergent
evolution, they do not stem
from a common ancestor
Bats…
http://www.flickr.com/photos/tjt195/105694980/
…birds…
http://www.flickr.com/photos/patrickwilken/112947862/
…and bugs all have wings for flight that evolved
independently
Other examples include:
-Streamlined shape for dolphins , sharks and
ichthyosaurs
-Long snout and tongue for capturing ants on the
anteater and echidna http://www.flickr.com/photos/hhoyer/3758550410/sizes/o/in/photostream/
D.5.7 Outline the methods used to construct cladograms and the conclusions that can be drawn
from them
AND
D.5.8 Construct a simple cladogram
• These two cladograms are identical (although they don’t look it)
• The shape and the order of the terminal nodes does not matter.
• The only information to be gathered from the cladograms below is the order of
nesting of sister clades and the relative relatedness of species
http://commons.wikimedia.org/wiki/File:Identical_cladograms.svg
Sister clades: have a
common ancestor
Terminal nodes
Human
Chimp
Gorilla
Nodes:
Common ancestors
Root
Chimp
Human
Out group: Defines
the ancestral
characters
Gorilla
Branches on a
cladogram can be
scaled or unscaled.
If the branches are
scaled, the length
of the branch often
indicates how much
evolutionary
change has
occurred in a
species since it split
from it’s sister clade
at the last node
http://www.ncbi.nlm.nih.gov/About/primer/phylo.html
Rooted cladograms
show evolutionary
relationships.
Unrooted trees just
show the
relationships
between clades
http://www.ncbi.nlm.nih.gov/About/primer/phylo.html
Cladograms are made by compiling data on
homologous characteristics shared by species.
These characteristics can be structural, physiological
and/or biochemical.
With increasing taxa comes increasing complexity.
Number of taxa
Possible number
of rooted
cladograms
23 4
5
6
7
8
9
10
N
1 3 15 105 945 10,395 135,135 2,027,025 34,459,425 1*3*5*7*...*(2N-3)
So software is often used to find the best possible tree
that has the fewest evolutionary steps.
This cladogram for
bacteria is
computer
generated
1) Compile a table of the characters being compared
Characters
Shark
Frog
Kangaroo
Human
Vertebrae
X
X
X
X
X
X
X
X
X
Two pairs of limbs
Mammary glands
Placenta
X
Modified from:
http://www.bu.edu/gk12/eric/cladogram.pdf
2) Use the data to construct
a Venn diagram,
Start with the
characteristic
shared by all
taxa in the
biggest circle
and work
inwards
Vertebrae:
Shark
Two Pairs of
Limbs: Frog
Mammary
Glands:
Kangaroo
Placenta:
Human
3) Convert the Venn diagram into a cladogram
Shark
Frog
Kangaroo
Human
Placenta
Mammary Glands
Lungs
Vertebrae
Now you try! Make a Venn diagram for this data.
Characters
Sponge
Jellyfish
Flatworm
Earthworm
Snail
Fruit fly
Starfish
Human
Cells with flagella
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
Mesoderm
X
X
X
X
X
Head develops first
X
X
X
X
X
Symmetry
Bilateral symmetry
Anus develops first
Segmented body
Calcified shell
Chitinous Exoskeleton
Water Vascular system
Vertebrae
X
X
X
X
X
X
It should look
something
like this:
Cells with flagella: Sponge
Symmetry: Jellyfish
Bilateral symmetry: Flatworm
Mesoderm
Head develops first
Segmented Body:
Earthworm
Chitinous
exoskeleton:
Fruit fly
Calcified
Shell:
Snail
Anus develops first
Water
Vascular
system:
Starfish
Vertebrae:
Human
now make
the cladogram
It should look something like this:
Sponge
FlatJellyfish worm Snail
Earthworm
Fruit fly Starfish
Calcified
shell
Chitinous
shell
Water
vascular
system
Human
Vertebrae
Segmented body
Head develops
first
Some of the
characteristics in the
data table were unnecessary
for the construction of this
cladogram.
Can you identify them?
Anus develops first
Mesoderm
Bilateral symmetry
Symmetry
Flagella
Unnecessary to use two characteristics to
differentiate between Starfish and Human.
Either would do the trick
Sponge
FlatJellyfish worm Snail
Earthworm
Fruit fly Starfish
Calcified
shell
Chitinous
shell
Water
vascular
system
Human
Vertebrae
Segmented body
Head develops
first
Unnecessary to differentiate Snail.
Snail is the only species with head
develops first and without
segmented body
Anus develops first
Unnecessary to use
two characteristics
Bilateral symmetry
to split lineages
Mesoderm
Symmetry
Flagella
D.5.9 Analyse cladograms in terms of phylogenetic relationships
A
B
C
1
D
Of the three nodes,
3 is most recent and 1
3
occurred earliest.
Node 3 is the most recent
2
common ancestor for C and D
Node 2 is the most recent common
ancestor for B and C
Node 3 is the common ancestor of all taxa
And so on…
D.5.10 Discuss the relationship between cladograms and the classification of living organisms
Mammals have the
unique homologous
characteristic of
producing milk
They form a clade
http://www.flickr.com/photos/chavals/3720930469/
Likewise, birds share the
common characteristic of
feathers
They too form a clade
http://www.flickr.com/photos/bestrated1/47581481/
Lizard
Tortoise
Reptiles, as a group, consist of
the crocodilians, lizards and
snakes, tortoises and turtles
and tuatara.
However, they are not a clade.
One of them is actually more
closely related to birds.
Crocodile
Tuatara
Care to guess which one?
http://www.flickr.com/photos/audreyjm529/155024495/
http://www.flickr.com/photos/mg-muscapix/3288435589/
http://www.flickr.com/photos/8363028@N08/2665814123/
http://www.flickr.com/photos/sidm/5253662054/
Crocodiles are more closely related
to birds than to lizards!
Monophyletic: A recent common ancestor and all it’s
descendants
Paraphyletic: Does not include all descendants from a
common ancestor
Polypheletic: A group of organisms that does not
include the most recent common ancestor
What this doesn’t
show is that birds are
the last descendants of
the dinosaurs!
http://en.wikipedia.org/wiki/File:Phylogenetic-Groups.svg
*ornithologists study birds, herpetologists study amphibians and reptiles
‘herp’ is a polyphylatelic grouping whereas birds are monophylatelic
Fish are paraphylatelic
Dinosaurs are paraphylatelic
http://xkcd.com/867/
Further information:
↑An excellent series that covers
most of the content
↑The tree of life
↓Amazing site, not to be missed!
↑Sir David Attenborough
+ BBC = Brilliant