CHAPTER 26
PHYLOGENY AND SYSTEMATICS
Evolutionary history of a species, Relationships between organisms and
Classification
Phylogeny (Evolutionary History of a species- a timeline) are based on:
• Continental Drift helps explain the current geographic distribution of species.
– Ex: volcanic islands such as the Galapagos highlight the role of geographic isolation in speciation
• Fossil record - unfortunately, only long lived hard bodied species tend to be found
• Morphological and Molecular Homologies
– Number and arrangement of bones in an appendage – DNA similarities
Systematics
• Attempts to understand the diversity and relationships between organisms
– Tree of life. Systematists have proposed a
classification system that would recognize only groups that include a common ancestor and all its descendants
• Utilize
– Morphologies
– Biochemical similarities – Molecular systematics
• Analysis of DNA, RNA, ribosomes, etc
• Similarities in sequence, # of changes, substitutions or deletions
http://learn.genetics.utah.edu/content/variation/hoxgenes/
Phylogenic (Evolutionary lineage)
Systematics Connects Classification with Evolutionary History
Taxonomy: hierarchical system
• Linnean system
• binomial system - Genus species , or Genus species
• Hierachical classification - organisms grouped into
progressively broader
categories: family, order, class, phylum, kingdom and domain.
• All of these are taxons - a taxonomic unit
Panthera pardus Panthera
Felidae Carnivora Mammalia Chordata Animalia Eukarya Domain
Kingdom Phylum
Class Order
Family Genus
Species
Modern phylogenetic systematics uses cladistic analysis
• Willi Hennig, cladogram - series of dichotomies (forks).
• sequence of branching symbolizes historical chronology.
• Each branch or clade can be nested within larger clades.
• Each branch (isolation of a group/species) is justified by a statement(Synapomorphie – shared derived character)
• A clade consists of an ancestral species and all its descendents, a monophyletic group. NOT poly or paraphyletic
• A valid clade is monophyletic, signifying that it consists of the ancestor species and all its
descendants
• A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants
• A polyphyletic grouping includes distantly related species but does not include their most recent
common ancestor
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(a) Monophyletic group
(clade) (b) Paraphyletic group (c) Polyphyletic group
Group III Group
Group II I
Important to distinguish homology - (due to shared ancestry)… from analogy – (due to
convergent evolution)
Analogous structures that evolved independently of one another can be called homoplasies (or, simply, “analogous structures”)
Marsupial, Australian
Eutherian, North
American
Basics of Cladistics
• As a general rule: 1) many homologous parts closely related species
• 2) increased complexity of many like parts not likely to have evolved independently
• A shared derived character (synapomorphic) is unique to a particular clade.
– A derived character might seem primitive (loss of legs in snakes)
• useful in establishing a phylogeny ex: hair within tetrapods
• A shared primitive character (plesiomorphic) – shared by several clades
• Ex: among vertebrates, the backbone http://highered.
mcgraw-hill.com/
sites/9834092339 /student_view0/c hapter23/animati on_-_phylogeneti c_trees.html
Basic Cladistic Diagram with Synapomorphies
Salamander
TAXA
Turtle Leopard
Tuna
Lamprey
Lancelet (outgroup)
0 0 0 0 0 1
0 0 0 0 1 1
0 0 0 1 1 1
0 0 1 1 1 1
0 1 1 1 1 1
Hair Amniotic (shelled) egg Four walking legs
Hinged jaws Vertebral column (backbone)
Leopard Hair Amniotic egg Four walking legs Hinged jaws
Vertebral column Turtle Salamander
Tuna Lamprey Lancelet (outgroup)
(a) Character table. A 0 indicates that a character is absent; a 1 indicates that a character is present.
(b) Cladogram. Analyzing the distribution of these derived characters can provide insight into vertebrate phylogeny.
CHARACTERS
Synapomorphie: a derived or changed character state
In Group, Out Group & insuring Derived Characters
• A key step in cladistic analysis is outgroup comparison which is used to differentiate shared ancestral characters from shared derived ones.
• ingroup: those to be classified
• outgroup: a distant relative (ingroup more closely related to each other than to the outgroup)
• In an outgroup analysis: any homologies shared by the
ingroup and outgroup must be primitive characters already present in the ancestor common to both groups. Ex:
notochord
• Any homologies present in some or all of the ingroup taxa must have evolved after the divergence of the ingroup and outgroup taxa. These would be derived characters
Figure 26.5a
Parts of a Tree Common
ancestor Fishes
Frogs
Lizards
Chimps
Sister taxa Humans
An
evolutionary lineage
An ancestor in the
lineage
Figure 26.5a
Parts of a Tree Common
ancestor Fishes
Frogs
Lizards
Chimps
Sister taxa Humans
An
evolutionary lineage
An ancestor in the
lineage
Figure 26.5c
Rotating Around Branch Points Fishes Frogs
Lizards
Chimps Humans
Frogs Humans
Chimps Lizards Fishes
Figure 26.5b
Alternative Forms of Tree Diagrams
Fishes Frogs Lizards Chimps Humans
Vertical tree
Fishes Frogs Lizards Chimps Humans
Diagonal tree
Systematists can infer phylogeny from molecular data
• comparing genes and proteins
• Aligning DNA sequences
– Comparing homologous segments length and sequence – Can establish a parsimonious phylogeny
– Parsimony – simple. Organize by fewest evolutionary events (shared derived characters)
• Comparison of conserved organelles ex:
mitochondrial DNA, rRNA
Figure 26.15
I II
I III II
III II I
I II III
I III II
III II I
III
I II III
I III II
III II I
I II III
I III II
III II I
Technique
Species I Species II Species III Three phylogenetic hypotheses:
Species I Species II Species III Ancestral sequence
1
C C A A
Site 2
T T G G
A T A T
4
T C C T
3
1/C 1/C
1/C
1/C 1/C
2/T 3/A 3/A
3/A 2/T
4/C
4/C 3/A 4/C
4/C 2/T 4/C
2/T 2/T 3/A
Results
6 events 7 events 7 events
1
2
4 3
Figure 26.8_4
1 2
1 2
1 2
1 2
C
Deletion
G T A Insertion
C A T C A G A G T C C C C A T C A G A G T C C
C C A T C A G A G T C C C C A T C A G A G T C C
C C A T C A A G T C C
C C A T G T A C A G A G T C C
C C A T G T A C A G A G T C C A G T C C C A
C C A T
Phylogenetic trees are hypotheses
• How good is the evidnece?
• Homologies: morphological, DNA, mDNA, rRNA, etc
• Conflicting information?
– An analogous feature is mistaken as a homologous one?
• Strongest hypothesis: multiple lines of morphological, molecular and fossil evidence
An Organisms genome Documents its Evolutionary History
• Not all genes change at the same rate – DNA coding for rRNA: slow
• Investigate divergences mya
– Mitochondrial DNA: relatively fast
• Relatively recent speciation
• Orthologous genes - 1 copy in a genome
– Beta hemoglobin in humans & mice
• Paralogous genes - result of gene duplication,multiple copies in a genome
– Olfactory receptor genes vary widely allowing sensitivity to numerous odors
Molecular clocks may keep track of evolutionary time
• Use a shared conserved gene - orthologous gene
• Graph Time vs. Changes in AA or nucleotides
• Neutral Theory - some genes do not influence the fitness of an organism and therefore change at a consistent rate. These genes make a good clock.
• Problems?
– Punctuated Equilibrium – Choosing the right gene – Always been neutral?
The Universal Tree of Life
• If life only emerged once, how are we all related?
Bacteria Eukarya Archaea
4 Symbiosis of chloroplast ancestor with ancestor of green plants
3 Symbiosis of mitochondrial ancestor with ancestor of eukaryotes 2 Possible fusion
of bacterium and archaean, yielding ancestor of eukaryotic cells
1 Last common ancestor of all living things 4
3
2
1 1
2
3
4
Billion years ago
Origin of life
Horizontal gene transfer through transposable
elements,
transduction or transformation
