IB Biology

Option D
D5 Phylogeny and Systematics

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.
 KEY CONCEPTS
• Systematic biology: Quantitative science that
uses characteristics of living and fossil
organisms, or traits, to infer relationships
among organisms over time.

• Taxonomy: is the branch of systematic biology

that identifies, names, and organise
biodiversity into related categories.
 KEY CONCEPTS
• Taxon: General name of a group containing an
organisms or group of organisms that exhibit a
set of shared traits.

• Classification: Process of naming and

assigning organisms or group of organisms to
a taxon.
THREE DOMAIN SYSTEM
 THREE
5 KINGDOMS
DOMAIN
SYSTEM
Linnaean Classification Hierarchy
Linnaean Classification Hierarchy
 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.

http://commons.wikimedia.org/wiki/File:Hominins_2002.png
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 right-
handed 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 I didn’t want to be

more closely related to each other than to rhesus
monkeys
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 http://www.flickr.com/photos/kev
http://www.flickr.com/photos/mo
http://www.flickr.com/photos/tam
or extinct) of their om/photos/emraya/2929959881/

most recent
common ancestor
form a clade Wikipedia
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.
 Hair Shelled
eggs

Each clade Amniotic Egg

is determined by Four Limbs

common characteristics
Bony Skeleton
of its members that are
different from that of the Vertebrate
other species from which
it has diverged

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
 Out group: Defines
the ancestral
Terminal nodes Sister clades: have a
characters
common ancestor

Human Chimp Gorilla Chimp Human Gorilla

Nodes:
Common ancestors

Root
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 23 4 5 6 7 8 9 10 N
Possible number
of rooted 1 3 15 105 945 10,395 135,135 2,027,025 34,459,425 1*3*5*7*...*(2N-3)
cladograms

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

Two pairs of limbs X X X

Mammary glands X X

Placenta X

Modified from:
http://www.bu.edu/gk12/eric/cladogram.pdf
2) Use the data to construct
a Venn diagram,
Vertebrae:
Start with the Shark
characteristic
Two Pairs of
shared by all Limbs: Frog
taxa in the
Mammary
biggest circle Glands:
and work Kangaroo

inwards
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 Earth- Snail Fruit fly Starfish Human
worm

Cells with flagella X X X X X X X X

Symmetry X X X X X X X

Bilateral symmetry X X X X X X

Mesoderm X X X X X

Head develops first X X X

Anus develops first X X

Segmented body X X

Calcified shell X

Chitinous Exoskeleton X

Water Vascular system X

Vertebrae X
It should look Cells with flagella: Sponge

something
Symmetry: Jellyfish
like this:
Bilateral symmetry: Flatworm

Mesoderm

Head develops first Anus develops first

Segmented Body:
Earthworm Water
Calcified
Vascular Vertebrae:
Shell:
system: Human
Chitinous Snail
Starfish
exoskeleton:
Fruit fly

now make
the cladogram
 It should look something like this:
Flat-
Sponge Jellyfish worm Snail Earthworm Fruit fly Starfish Human

Calcified Water
shell Chitinous vascular
shell system Vertebrae
Segmented body

Head develops
first
Anus develops first

Some of the
characteristics in the
data table were unnecessary Mesoderm
for the construction of this Bilateral symmetry
cladogram. Symmetry

Flagella
Can you identify them?
 Unnecessary to use two characteristics to
differentiate between Starfish and Human.
Either would do the trick
Flat-
Sponge Jellyfish worm Snail Earthworm Fruit fly Starfish Human

Calcified Water
shell Chitinous vascular
shell system Vertebrae
Segmented body

Head develops
first
Anus develops first

Unnecessary to differentiate Snail.

Snail is the only species with head Unnecessary to use
Mesoderm
develops first and without two characteristics
Bilateral symmetry to split lineages
segmented body
Symmetry

Flagella
D.5.9 Analyse cladograms in terms of phylogenetic relationships

A B C 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
1 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 Tuatara

closely related to birds.

Crocodile 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
What this doesn’t
include the most recent common ancestor
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

↑Sir David Attenborough

↓Amazing site, not to be missed! + BBC = Brilliant