Basic Cladistics

7/29/2019 Basic Cladistics

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• The Phylogeny of an organism is traced back,

it connects through shared ancestors to lineages

of other organisms.

**phylogenetic tree

Cladistics or Phylogenetic Systematics



• Given that closely related species share acommon ancestor and often resemble eachother, it might seem that the best way to uncover

the evolutionary relationships would be withoverall similarity.

• Q: In other words, out of a group of species, if two are most similar, can we reasonably

hypothesize that they are closest relatives?

YES or NO?



• Overall similarity may be misleading becausethere are actually two reasons why organisms

have similar characteristics and only one of them is due to evolutionary relatedness.

• homologous feature (or homology)- Whentwo species have a similar characteristicbecause it was inherited by both from acommon ancestor

• Ex. eventoed foot of the deer, camels, cattle,

pigs, and hippopotamus is a homologoussimilarity because all inherited the featurefrom their common paleodont ancestor.



• analogous feature (or homoplasy)- When twospecies have a similar characteristic because of convergent evolution

• Convergent evolution - when unrelated speciesadopt a similar way of life, their body parts maytake on similar functions and end up resemblingone another

• Ex. The paddle-like front limb and streamlinedbodies of the aquatic animals shown in the figurefor convergent evolution are examples of analogous features.



• Only homologous similarity is evidence that

two species are evolutionarily related.• Q: If two animals share the highest number of

homologies, can we reasonably assume theyare closest relatives?

• YES or NO?

• a homology may be recently derived or anancient retained feature; only shared recent

homologies (called synapomorphies) areevidence that two organisms are closelyrelated.



• Ex. The hand of the first vertebrates to live on

land had five digits (fingers).

• Many living terrestrial vertebrates (such as

humans, turtles, crocodiles and frogs) also

have five digits because they inherited them

from this common ancestor. This feature is

then homologous in all of these species.



• In contrast, horses, zebras and donkeys have justa single digit with a hoof.

• Clearly, humans are more closely related to

horses, zebras and donkeys, even though theyhave a homology in common with turtles,crocodiles and frogs.

• The key point is that the five digit condition is the

primitive state for the number of digits. It wasmodified and reduced to just one digit in thecommon ancestor of horses, donkeys and zebras.



• In an important work (first published inEnglish in 1966) by the German entomologistWilli Hennig, it was argued that only sharedderived characters could possibly give usinformation about phylogeny.

• The method that groups organisms that share

derived characters is called cladistics orphylogenetic systematics.

• Taxa that share many derived characters are

grouped more closely together than thosethat do not. The relationships are shown in abranching hierarchical tree called acladogram.



• The cladogram is constructed such that the

number of changes from one character state

to the next is minimized. The principle behind

this is the rule of parsimony - any hypothesis

that requires fewer assumptions is a more

defensible hypothesis.



0 1 2 30 to 1 = 1 step 1 to 0 = 1 step 1 to 2 = 2 steps



0 1 2 30 to 1 = 1 step 1 to 0 = 1 step 1 to 2 = 1 step



0 1 2 30 to 1 = 1 step 1 to 0 = NA 1 to 2 = 1 step



Titanotheres



0 1 2 30 to 1 = 1 step 1 to 0 = NA 1 to 2 = 1 step



Multiple origins

1

2

3



• If the character has only two states, then the task of distinguishing primitive and derived character states isfairly simple: The state which is in the outgroup isprimitive and the one found only in the ingroup is

derived.• It is common practice to designate the primitive states

as 0 (zero) and the derived states as 1 (one). If you aregoing to calculate trees by hand, this will certainlymake your calculations easier.

• On the other hand, if you are using a computerprogram to calculate a tree, it isn’t necessary todesignate the plesiomorphic state as 0 (zero):



• The first step in basic cladistic analysis is todetermine which character states are primitiveand which are derived.

• The outgroup comparison method is the primaryone in use today.

• In outgroup comparison, if a taxon that is not a

member of the group of organisms beingclassified has a character state that is the same assome of the organisms in the group, then thatcharacter state can be considered to be

plesiomorphic.

• The outside taxon is called the outgroup and theorganisms being classified are the ingroup.

Asteroidea



Asteroidea

Sea stars and starfishes

• Outgroup comparison



• In common cladistic usage, a monophyletic groupis a taxon (group of organisms) which forms aclade, meaning that it contains all thedescendants of the possibly hypothetical closestcommon ancestor of the members of the group.

• The term is synonymous with the uncommonterm holophyly.

• Monophyletic groups are typically characterizedby shared derived characteristics(synapomorphies).

http://en.wikipedia.org/wiki/Cladistic

http://en.wikipedia.org/wiki/Taxon

http://en.wikipedia.org/wiki/Clade

http://en.wikipedia.org/wiki/Holophyly

http://en.wikipedia.org/wiki/Synapomorphy


http://en.wikipedia.org/wiki/Holophyly

http://en.wikipedia.org/wiki/Clade


http://en.wikipedia.org/wiki/Cladistic



• In current usage, a paraphyletic group consists of all of the descendants of a possibly hypotheticalclosest common ancestor minus one or more

monophyletic groups (most usually one).• A paraphyletic group is thus 'nearly'

monophyletic (consistent with the meaning of the prefix 'para', namely 'near' or 'alongside'.)

• A polyphyletic group is any group other than amonophyletic group or a paraphyletic group,which like a paraphyletic group contains onlysome of the descendants of their closest

common ancestor, but unlike a paraphyleticgroup is not characterized by the missingdescendants forming one (or more) monophyleticgroups.



• A clade is a group of taxa consisting only of an





• A clade is a group of taxa consisting only of an

ancestor taxon and all of its descendant taxa.

• In the diagram provided (a cladogram), it is

hypothesized that all vertebrates, including ray-finned fishes (Actinopterygii), had a common

ancestor all of whose descendants were vertebrates,

and so form a clade.

• Within the vertebrates, all tetrapods, including

amphibians, mammals, reptiles (as traditionally

defined) and birds are hypothesized to have had a

common ancestor all of whose descendants were

tetrapods, and so also form a clade.

• The tetrapod ancestor was a descendant of the

original vertebrate ancestor, but is not an ancestor of

any ray-finned fish living today.


http://en.wikipedia.org/wiki/Actinopterygii

http://en.wikipedia.org/wiki/Actinopterygii




The relationship between clades can be

described in several ways:

1. A clade is basal to another clade if it containsthat other clade as a subset within it.

• In the example, the vertebrate clade is basal

to the tetrapod and ray-finned fish clades.Note:(Some authors have used "basal"

differently to mean a clade that is less species-

rich than a sister clade, with such a deficit

being taken as an indication of 'primitiveness'.

Others consider this usage to be incorrect.

http://en.wikipedia.org/wiki/Basal_%28phylogenetics%29

http://en.wikipedia.org/wiki/Basal_%28phylogenetics%29



• A clade located within a clade is said to be

nested within that clade. In the diagram, the

tetrapod clade is nested within the vertebrate

clade.

• Two clades are sisters if they have an

immediate common ancestor. In the diagram,

crocodiles and birds are sister clades, as aremodern amphibians and amniotes.

http://en.wikipedia.org/wiki/Lissamphibia






• Terminology for characters

The following terms are used to identify shared or distinct

characters among groups:

• Plesiomorphy ("close form") or ancestral state, alsosymplesiomorphy ("shared plesiomorphy", i.e. "shared close

form"), is a characteristic that is present at the base of a tree

(cladogram). Since a plesiomorphy that is inherited from the

common ancestor may appear anywhere in a tree, itspresence provides no evidence of relationships within the

tree. The traditional definition of reptiles (the blue group in

the diagram) includes being cold-blooded (i.e. not maintaining

a constant high body temperature), whereas birds are warm-

blooded. Since cold-bloodedness is a plesiomorphy, inherited

from the common ancestor of traditional reptiles and birds, it

should not be used to define a group in a system based on

cladistics.

http://en.wikipedia.org/wiki/Plesiomorphy

http://en.wikipedia.org/wiki/Plesiomorphy



http://en.wikipedia.org/wiki/Apomorphy



• Apomorphy ("separate form") or derived state

is a characteristic believed to have evolved

within the tree. It can thus be used toseparate one group in the tree from the rest.

• Within the group which shares the

apomorphy it is a synapomorphy ("sharedapomorphy", i.e. "shared separate form"). For

example, within the vertebrates, all tetrapods

(and only tetrapods) have four limbs; thus,

having four limbs is a synapomorphy for

tetrapods. All the tetrapods can legitimately

be grouped together because they have four

limbs.







• Homoplasy is a characteristic shared by

members of a tree but not present in their

common ancestor.• It arises by convergence or reversion. Both

mammals and birds are able to maintain a

high constant body temperature (i.e. they are'warm-blooded'). However, the ancestors of

each group did not share this character, so it

must have evolved independently. Mammals

and birds should not be grouped together on

the basis that they are warm-blooded.

http://en.wikipedia.org/wiki/Homoplasy

http://en.wikipedia.org/wiki/Homoplasy



CLADOGRAM

WHAT A CLADOGRAM ACTUALLY SAYS



WHAT A CLADOGRAM ACTUALLY SAYS

ABOUT RELATIONSHIPS

• The trees that result from cladistic analysis are relativestatements of relationship and do not indicateancestors or descendants.

• For example in the tree above, Prorodon teres and

Prorodon marina are hypothesized to be sister taxaand to share a more recent common ancestor witheach other than with Coleps; but the prorodontids (P.teres+P. marina+Coleps) all share a more recent common ancestor with one another than with the

Placidae (Placus + Spathidiopsis).• The tree does not explicitly hypothesize ancestor-

descendant relationships. In other words, the treehypothesizes that Prorodon and Coleps are related, but not that Prorodon evolved from Coleps or that Coleps

evolved from Prorodon.



TAXON

A B C D

Character

1 1 1 0 0

2 1 1 0 0

3 1 1 1 0

4 1 1 1 0

5 1 1 1 0

6 1 1 1 0

7 0 1 0 0

8 0 1 0 0

9 0 1 0 0

Applying cladisticsTAXON

A B C D

A 6 4

B

C

D

We now count the

derived similarities

between A and C.



TAXON

A B C D

Character

1 1 1 0 0

2 1 1 0 0

3 1 1 1 0

4 1 1 1 0

5 1 1 1 0

6 1 1 1 0

7 0 1 0 0

8 0 1 0 0

9 0 1 0 0


A B C D

A 6 4 0

B

C

D

And the similarities in

derived traits between

A and D.



TAXONA B C D

Character

1 1 1 0 0

2 1 1 0 0

3 1 1 1 0

4 1 1 1 0

5 1 1 1 0

6 1 1 1 0

7 0 1 0 0

8 0 1 0 09 0 1 0 0


A B C D

A 6 4 0

B 4 0

C 0

D

The completed table

shows all pairwise

similarities.



TAXON

A B C D

A 6 4 0

B 4 0

C 0

D

Phenetics Vs. cladistics

TAXON

A B C D

A 6 7 3

B 4 0

C 5

D

Notice that the matrices produced

by phenetics (right) and cladistics

are quite different.

P C



• The similarity

matrix is now used

to create the

cladogram.

• A is most similar to

B.

Applying cladistics

TAXON

A B C D

A 6 4 0

B 4 0

C 0

D

A B



• The similarity

matrix is now used

to create the

cladogram.

• Next, (A and B) are

together most

similar to C.

Applying cladistics

TAXON

A B C D

A 6 4 0

B 4 0

C 0

D

A B C



Phenetics Vs. cladistics

The phylogenies produced by

phenetics (right) and cladistics are

also quite different.

P C

A C B D A B C D



A B C D

Now what?

• We can now plot the

changes that

occurred on the tree,getting a feeling for

the actual process.



Reconstructing phylogenies (1)

• The number of possible trees quickly increases

as the number of taxa goes up.

A B

2 taxa

A B C C B A A C B

3 taxa

A B C D A B C D A C B D A C B D A D B C

4 taxa

+



• Mathematically, the number of possibletrees is:

Reconstructing phylogenies (2)

(2n - 3)!

2n-2(n-2)!

• This quickly gets out of control.

• With many taxa and characters, computer

algorithms must be used.

Taxa trees

4 156 9458 135135

10 34459425



Exhaustive

Branch-and-bound

Heuristic



Monophyly of Endomychidae

Consensus Tree Length:

89 CI: 57RI: 81




Nelsen Consensus Tree

Length: 89CI: 57

RI: 81

Monophyly Supported by:

Fronto-clypeal ridge present





Length: 89CI: 57

RI: 81



Head without antennal grooves

Tarsi 4-segmented, simple

h l f d h d





Length: 89CI: 57

RI: 81



Head without antennal grooves

Tarsi 4-segmented, simple

Basic Cladistics

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