The document discusses three schools of systematics: phenetics, cladistics, and evolutionary classification, outlining their approaches to classifying organisms based on similarities and evolutionary relationships. It explains concepts such as homologous and analogous features, monophyletic and paraphyletic groups, and the importance of derived characteristics in understanding phylogenetic relationships. Additionally, it touches on the methodologies used in cladistics, including outgroup comparison and maximum parsimony, while highlighting the challenges in traditional taxonomic classifications.

1. Systematics
Inferring Relationships

2. Three Schools of Systematics
• Phenetics
• Cladistics
• Evolutionary Classification

3. Phenetic analysis
• Phenetics also known as taximetrics, is an attempt to classify
organisms based on overall similarity, usually
in morphology or other observable traits, regardless of their
phylogeny or evolutionary relation.
• A numerical taxonomy which is concerned with the use of
numerical methods for taxonomic classification. Many people
contributed to the development of phenetics, but the most
influential were Peter Sneath and Robert R. Sokal.
• Phenetic techniques include various forms of clustering and
ordination. These are sophisticated ways of reducing the
variation displayed by organisms to a manageable level. In
practice this means measuring dozens of variables, and then
presenting them as two- or three-dimensional graphs.

4. Phenetic analysis

5. Cladistic Analysis
• The Phylogeny of an organism is traced back,
it connects through shared ancestors to
lineages of other organisms.
**phylogenetic tree
Cladistics or Phylogenetic Systematics

6. • Given that closely related species share a
common ancestor and often resemble each
other, it might seem that the best way to uncover
the evolutionary relationships would be with
overall 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?

7. • Overall similarity may be misleading
because there are actually two
reasons why organisms have similar
characteristics and only one of
them is due to evolutionary
relatedness.
• homologous feature (or
homology)- When two species have
a similar characteristic because it
was inherited by both from a
common ancestor
• Ex: Morphological Divergence
Among Vertebrate Forelimbs

8. • analogous feature (or homoplasy)- When two
species have a similar characteristic because of
convergent evolution
• Convergent evolution - when unrelated species
adopt a similar way of life, their body parts may
take on similar functions and end up resembling
one another

9. • 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 they
are closest relatives?
• YES or NO?
• a homology may be recently derived or an
ancient retained feature; only shared recent
homologies (called synapomorphies) are
evidence that two organisms are closely
related.

10. • 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 just a single digit
with a hoof.
• Clearly, humans are more closely related to horses, zebras and
donkeys, even though they have 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 was modified and reduced to
just one digit in the common ancestor of horses, donkeys and
zebras.

11. • In common cladistic usage, a
monophyletic group is a taxon
(group of organisms) which forms
a clade, meaning that it contains
all the descendants of the possibly
hypothetical closest common
ancestor of the members of the
group.
• The term is synonymous with the
uncommon term holophyly.
• Monophyletic groups are typically
characterized by shared derived
characteristics (synapomorphies).

12. • In current usage, a paraphyletic group
consists of all of the descendants of a
possibly hypothetical closest 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 a monophyletic group or a
paraphyletic group, which like a
paraphyletic group contains only some
of the descendants of their closest
common ancestor, but unlike a
paraphyletic group is not characterized
by the missing descendants forming
one (or more) monophyletic groups.

13. • A clade is a group of taxa consisting
only of an ancestor taxon and all of
its descendant taxa.
• 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.

14. The relationship between clades
can be described in several
ways:
1. A clade is basal to another clade if
it contains that 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.)

15. • 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.

16. • Terminology for characters
The following terms are used to identify shared
or distinct characters among groups:
• Plesiomorphy ("close form") or ancestral
state, also symplesiomorphy ("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, its presence 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.

17. • Apomorphy ("separate form") or
derived state is a characteristic
believed to have evolved within the
tree. It can thus be used to
separate one group in the tree
from the rest.
• Within the group which shares the
apomorphy it is a synapomorphy
("shared apomorphy", 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.

18. •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.

19. • In an important work (first published in
English in 1966) by the German entomologist
Willi Hennig, it was argued that only shared
derived characters could possibly give us
information about phylogeny.
• The method that groups organisms that share
derived characters is called cladistics or
phylogenetic systematics.
• Taxa that share many derived characters are
grouped more closely together than those
that do not. The relationships are shown in a
branching hierarchical tree called a
cladogram.

20. • If the character has only two states, then the task of
distinguishing primitive and derived character states is
fairly simple: The state which is in the outgroup is
primitive 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 are
going to calculate trees by hand, this will certainly
make your calculations easier.
• On the other hand, if you are using a computer
program to calculate a tree, it isn’t necessary to
designate the plesiomorphic state as 0 (zero):

21. • The first step in basic cladistic analysis is to determine which
character states are primitive and which are derived.
• The outgroup comparison method is the primary one in use today.
• In outgroup comparison, if a taxon that is not a member of the
group of organisms being classified has a character state that is the
same as some of the organisms in the group, then that character
state can be considered to be plesiomorphic.
• The outside taxon is called the outgroup and the organisms being
classified are the ingroup.

22. • 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
• parsimony - any hypothesis that requires
fewer assumptions is a more defensible
hypothesis.
• the most parsimonious tree requires the
fewest base changes.

24. 0 1 2 3
0 to 1 = 1 step 1 to 0 = 1 step 1 to 2 = 1 step
0 to 2 = 2 steps

25. 0 1 2 3
0 to 1 = 1 step 1 to 0 = 1 step 1 to 2 = 1 step

26. 0 1 2 3
0 to 1 = 1 step 1 to 0 = NA 1 to 2 = 1 step

27. 0 1 2 3
0 to 1 = 1 step 1 to 0 = NA 1 to 2 = 1 step

28. • Maximum parsimony
– In the case of trees based on morphology, the most parsimonious tree
requires the fewest evolutionary events, as measured by the origin of
shared derived morphological characters.
– For phylogenies based on DNA, the most parsimonious tree requires the
fewest base changes.
Maximum Parsimony

29. Applying Parsimony

30. Applying Parsimony

31. Applying Parsimony

32. Applying Parsimony

33. Applying Parsimony

34. WHAT A CLADOGRAM ACTUALLY SAYS ABOUT RELATIONSHIPS
• The trees that result from cladistic
analysis are relative statements of
relationship and do not indicate
ancestors or descendants.
• For example in the tree above,
Prorodon teres and Prorodon marina
are hypothesized to be sister taxa
and to share a more recent common
ancestor with each 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 tree
hypothesizes that Prorodon and
Coleps are related, but not that
Prorodon evolved from Coleps or that
Coleps evolved from Prorodon.

35. Sample Exercise
You have discovered the skeletons of five new fossil animals, and you would like to
investigate their phylogenetic relationships. After being told that species "A" is
very primitive, you decide to use it as the outgroup for a phylogenetic analysis.

36. Sample Exercise
You have constructed the following character matrix:

37. Sample Exercise
1
2
3
4
5
67
7 character changes

38. Sample Exercise
1
2
3
4
5
6 7
3
3
4
5
11 character changes

39. Sample Exercise
Which is the most parsimonious tree?
A B

42. Monophyly of Endomychidae
Consensus Tree
Length: 89
CI: 57
RI: 81

43. Monophyly of Endomychidae
Nelsen Consensus Tree
Length: 89
CI: 57
RI: 81
Monophyly Supported by:
Fronto-clypeal ridge present

44. Monophyly of Endomychidae
Nelsen Consensus Tree
Length: 89
CI: 57
RI: 81
Monophyly Supported by:
Fronto-clypeal ridge present
Head without antennal grooves
Tarsi 4-segmented, simple

45. Monophyly of Endomychidae
Nelsen Consensus Tree
Length: 89
CI: 57
RI: 81
Monophyly Supported by:
Fronto-clypeal ridge present
Head without antennal grooves
Tarsi 4-segmented, simple

75. Phenogram
A C B D
A B C D
Cladogram

77. • Like the phenetic/cladistic system, this
classification groups organisms according to
basic similarity, but unlike the two, it demands
an evolutionary explanation for these
similarities.
• Evolutionary taxonomists regard phenotypic
specialization and degree of change after
divergence from a common ancestor as
important components of classification.

78. • Traditionally, classical evolutionary taxonomists
have considered a taxon worthy of separate
status if its members show a high degree of
specialization relative to those of a closely
related taxon.
• The problem arises in the subjectivity of this
judgment.

79. • Ex. Genetic and ontogenetic data indicate that
birds share a most recent common ancestor
with crocodilians.

80. • The Traditional Phylogeny diagram shows that some unknown common
ancestor evolved into mammals and another unknown common ancestor.
That second unknown ancestor evolved into turtles and a third unknown
ancestor. The third unknown ancestor evolved into the common ancestor
of birds and crocodiles and the common ancestor of tuataras and
squamates. Turtles evolved early, and have remained unchanged for a
long time.
• But DNA evidence (“molecular phylogeny”) shows a different picture. It
shows, for example, that turtles and crocodiles evolved recently from a
common ancestor that also had birds for descendants.

81. • However, because birds have
feathers, are "warm blooded",
and are superficially very different
from crocodilians, the classical
evolutionary biologist places them
in Class Aves, and the crocodilians
in Class Reptilia.
• This means that Class Reptilia
does not include all the species
that descended from the original
ancestral reptile that gave rise to
lizards, snakes, crocodilians, and
birds. Such an artificial taxon,
which does not include all
descendants of a single ancestor,
is said to be paraphyletic

82. • Similarly, Homo sapiens has traditionally been
assigned to its own family (Hominidae),
although there is no objective reason to
taxonomically separate it from the great apes
(Pongidae). Like Reptilia, Pongidae not
including Homo sapiens is paraphyletic.