very nice ppt of phylogeny

1. Sorting Homology from Analogy
• A potential misconception in constructing a
phylogeny is similarity due to convergent
evolution/with out common ancestor = called
analogy, rather than shared ancestry/homology
• Analogous structures or molecular sequences
that evolved independently are also called
homoplasies.
• Shared characters that result from common
ancestry are homologous.
• Independent evolution of similar characters that
are NOT homologous is called homoplasy

2. • 4. Phylogeny and the tree of life /evolutionary trees
• Investigating the Tree of Life
• A major goal of systematics is to infer the
evolutionary tree or phylogeny – the evolutionary
history of a species or group of related species.
• Phylogenies are inferred by identifying organismal
features, characters, that vary among species.
Morphological
Chromosomal
Molecular
Behavioral or ecological

3. Shared Primitive and Shared Derived Characteristics
• A shared primitive (ancestral) character:
=It is a homologous structure that predates the
branching of a particular clade from other members of
that clade.
Is shared beyond the taxon we are trying to define
– Example – mammals all have a backbone, but so do
other vertebrates
• A shared derived character
• = it is an evolutionary novelty unique to a
particular clade.
• E.g. All mammals have hair, and no other
animals have hair

4. • The form of the character that was present in the
common ancestor of the entire group is called
ancestral
• Variant forms of the character arose later and are
called derived character states.
• Determining polarity of a character involves
determining which state is ancestral or which is
derived
• Polarity is determined by using out-group
comparison.
– An out-group is closely related, but not part of the group
being examined (the in-group).
– If a character is found in both the study group and the
out-group, it is considered ancestral for the study group.
– Character groups found in the study groups but not the
out-groups are derived.

5. • Clades are organisms or species that share
derived character states and form a subset
within a larger group.
– A synapomorphy is a derived character shared
by the members of the clade
– A clade corresponds to a unit of evolutionary
common descent
• Ancestral character states for a taxon are
called plesiomorphic.
• Sharing these ancestral characters is
called symplesiomorphy.

6. • Maximum Parsimony and Maximum Likelihood
• Systematists can never be sure of finding
the single best tree in a large data set.
– Narrow the possibilities by applying the
principles of maximum parsimony and
maximum likelihood
• Among phylogenetic hypotheses the most
parsimonious tree is the one that
requires the fewest evolutionary events to
have occurred in the form of shared
derived characters.

7. • Phylogenetic Trees as Hypotheses:
• The best hypotheses for phylogenetic trees are
those that fit the most data: morphological,
molecular, and fossil.
In-group= taxa in which someone is interested
Out-group=closely related taxa to in-group
Allometry= d/t parts of body grow in different
proportion
Isometery=d/t parts of body grow proportionally
Homoplasy= resemblance not due to inheritance
from common ancestor/no genetic base
Convergence= similarity without common ancestor
Parallelism= similarity with common ancestor

8. • Polarity= determine primitive/advanced
• E.g. gills-primitive and lung -advanced
• presence of tail-primitive and absence of
tail- advanced
• Coding:
• Primitive=0 (ancestral)
• Advanced=1(derived)

9. • Methodology of a cladistic analysis
1. Choose the taxa=whose r/ships interest you
 2. Determine the character =all taxa must be unique
 3. Determine the polarity of character (original/derived)
 4. Group taxa by synapomorphies/shared derived character
 5. Workout conflicts (minimizeing the number of conflict)
 6. Build your cladogram, which is not evolutionary tree following
these rules
 All taxa go on the endpoints of the cladogram, never at nodes
 All cladogram nodes must have a list of synapomorphies, which
are common to all above the node (unless the character is later
modified)

10. character Primitive Derived
Extra embryonic membrane No(0) Yes(1)
Placenta No(0) Yes(1)
Temp. regulation Pokilothermy(0) Homeothermy(1)
Skeleton Cartilaginous(0) Bony(1)
Ruminant stomach Absence no(0) Presense yes(1)
Septation of auricles No(0) Yes(1)
1st Group taxa by synapomorphies
•In group-frog, snake, cow, human
•Out group-shark
2nd polarized out group comparism

11. 4th identification of synapomorphic/group taxa by snapomorphic
Character 4 is synapomorphic
Character 1&6 are synapomorphic in snake, cow , human
Character 2&3 are synapomorphic in cow and human
Character 5 is autapomorphic
Cow & human-together b/c share synapomorphic at Character 2&3
Snake, cow & human –together b/c synapomorphic at Character 1&6
Synapomorphic ch= Are homologous b/c there is no conflict, how by
Calculating
CI=Consistency index = M(minimum no. of steps/chx)
O(Observed no. of steps/chx)
CI=1= shows completely consistency/no conflict
CI=0= most characters are homoplesy, 1=homology
The length of the tree is 6 (steps) equal to the minimum
5th Workout conflict
6th constricting a tree