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Classification and Phylogeny:
What’s In a Name?
Alice in Wonderland
“What’s the use of their having
names,” the Gnat said, “if they don’t
answer to them?”
“No use to them,” said Alice,
“but it’s useful to the people that
name them, I suppose.”
What’s in a name?
Carolus Linnaeus: the father of
modern taxonomy
In the 1700s a Swedish
physician and biologist,
Carolus Linnaeus, refined
classification into a hierarchy
where groups of similar
organisms can be subdivided
into smaller more distinctive
groups.
Linnaeus classified organisms into
a hierarchy of groups:
• Eventually, as one
works through such a
system, each unique
form of organism is
left to occupy its own
small, but distinct
category.
• Domain, Kingdom,
Phylum, Class, Order,
Family, Genus,
Species
Here are the classification hierarchies for
several different species of organisms:
A bee by any other name…
Scientific name: Genus species
Taxonomy= the science of naming and classifying living things
The science of taxonomy underwent a
fundamental revolution when Darwin
published On the Origin of Species
Darwin suggested organisms cluster together due to
common ancestry:
Species that are in the same genus have a more recent
common ancestor than those in different genera
Likewise, genera within the same family have a more
Recent common ancestor than those in different families
Systematics
Darwin showed that the classification of living
organisms has a natural basis:
their evolutionary history
Taxonomy expanded into systematics: the study
of the diversity of living organisms and their
evolutionary relationships
How do we determine evolutionary
relationships?
• Homology: the same component and structures
of organisms are repeated in many forms
• Darwin viewed homology as evidence that
development of one structure is a
modification or variant of the development of
another (implies a common origin as a feature
present in a common ancestor)
Evolutionary Homologies
features that share common origin in a common ancestor
humerus
Recognizing
homologies:
position relative
to other parts and
of its parts to
each other
ulna
radius
Evolutionary Homologies
features that share common origin in a common ancestor
Recognizing homologies:
Transitional forms
Ex: horses run on their toes (actually on
the tip of a single toe on each foot) Which
toe?
the fossil record for horses is exceptional,
and we can trace the transitional stages
through time to discover that it is the third
toe
IN FACT, we can trace to a common
ancestor with rhinos and tapirs
(Hyracotherium) and discover that
the habit of walking on the 3rd toe is
homologous in this group
Why do we care about homologies?
Homologies imply that the most recent common ancestor had the trait
Nesting
homologies
allows us to
heirarchically
classify
organisms in an
evolutionarily
meaningful way
Homoplasy
Homoplasy (also analogy or analogous traits)
same or similar character in two or more taxa was not
present in the most recent common ancestor
Can be difficult to distinguish from homology
Homoplasy results from convergent evolution
similar structure/trait has arisen in 2 or more species, but is not possessed
by a common ancestor (and all intervening ancestors)
• cooperative hunting in canids and felids
• growth form of aloe (related to lillies) and
agave (cactus)
Homoplasy results from evolutionary reversals
similar structure/trait has arisen in 2 or more species, but is not possessed
by a common ancestor (and all intervening ancestors)
• secondary wing loss in birds and insects
• eye loss in cave fish and cave salamanders
Texas blind salamander
Typhlomolge rathbuni
Eyed (surface dwelling) and eyeless
(cave dwelling) Astyanax mexicanus
Evolutionary modifications
Evolutionary change (modification) is a change in a
character state
• Do not confuse character with character state
• eg.,
Characters include:
number of digits, eye color,
Characters states are: 3, 4, 5
blue, green
height
2m, 2.5m, 3m
Character state changes can be any character, behavioral, physiological,
morphological, biochemical, molecular, etc.
1) presence/absence (0,1) for any character
2) qualitative, multistate - arbitrarily 1, 2, 3 for any character
3) quantitative, multistate - difficult to handle. How do you separate variation
from difference?
Systematics
systematists infer the historical pattern of evolutionary
descent for an organism to build a
PHYLOGENY - the genealogy of a group of taxa (the
practice of developing phylogenies is called phylogenetics)
outgroup
A
B
C
D
‘tips’- represent terminal
taxa (extant species)
1
2
3
Nodes’ - represent common
ancestors that no longer exist
Interpretation:
B&C evolved from a common ancestor 1;
1 is no longer present, only B&C.
Cladistics
• Cladistics is a modern approach
• Goal is to group organisms according to evolutionary
history (phylogeny)
• Note: in practice, collect data on character states and
then reconstruct topology
• Use data to construct cladograms
Cladistics
• cladograms can be derived by observing shared
character states
– 3 types:
1. shared derived character states -- synapomorphy
2. shared ancestral states -- sympleisiomorphy
3. shared but independently evolved state -- homoplasy
• Only #1 are useful in constructing cladograms
• SYNAPOMORPHIES DEFINE CLADES, and are evidence of
a most recent common ancestor
• individual taxa are recognized by unique, unshared character
states (autapomorphies)
Ancestral vs. Derived
• If a character state was
present before a clade
split off, it is ancestral
• If a character state is
new to a group, it is
derived
• Ancestral vs. derived
can be answered with
outgroups (which
define the ancestral
state for a clade)
autopomorphy
synapomorphy
sympleisiomorphy
Constructing a cladogram
How many
synapomorphies
do each pair of
organisms share?
How many trees?
With 3 taxa, there are the following possible trees:
A
B
C
B
A
C
C
B
A
The problem that arises is that even with complete knowledge of
shared derived characters, there are many possible phylogenies
that can be generated:
# of taxa
bifurcating trees
3
3
4
15
5
105
6
945
How do we chose between them?
Choosing the correct tree
There are many possible methods for selecting trees, most are
built on the principle of parsimony - the most likely alternative is
the simplest and least complex in the phylogenetic context, the
favored phylogeny includes the fewest number of changes in
character state
There are other ways to choose between trees (e.g., Maximum
likelihood) that weight some kinds of character state changes
differently than others
e.g., for molecular data, we know that transversions (A, G <--> C,
T) are less common than transitions (A<-->T, C<-->G) - we can
calculate the probabilities for any taxon and weight each change
differently
Defining Groups: Cladistics
Monophyletic:
includes all taxa
from a single
common ancestor
Paraphyletic:
does not include
all taxa from a
single common
ancestor
Polyphyletic:
includes all taxa
not from a
common ancestor
Impact of cladistics
• Cladistics argues that many traditional
groups are paraphyletic
• Example: Reptiles are not a valid group
Reptiles are a paraphyletic group
Cladistics would group birds with the reptiles
Traditional and cladistic classification of vertebrates