Download 2/9/2015 Phylogeny and the Tree of Life Chapter 26:

2/9/2015
Chapter 26:
Phylogeny and the Tree of Life
1. Key Concepts Pertaining to Phylogeny
2. Determining Phylogenies
3. Evolutionary History Revealed in Genomes
1. Key Concepts Pertaining to Phylogeny
Cell
division
error
PHYLOGENY – the evolutionary history
of species or group
Species:
Panthera pardus
Genus:
Panthera
TAXONOMY – system by which
organisms are named and classified
Family:
Felidae
• based on morphological and molecular
(DNA, proteins) data
Order:
Carnivora
• not necessarily based on evolutionary
history, though it can be
Class:
Mammalia
TAXONOMIC HIERARCHY – series of nested
groupings used to categorize organisms
• developed by Carolus Linnaeus of Sweden
in the mid-18th century and still used today
Phylum:
Chordata
Domain:
Bacteria
Kingdom:
Animalia
Domain:
Archaea
Domain:
Eukarya
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TAXON – a specific category or level in the
taxonomic hierarchy (e.g., “class” or “family”)
BINOMIAL NOMENCLATURE – how organisms
are named
• genus & specific epithet (e.g., Homo sapiens,
Escherichia coli, Tyrannosaurus rex)
o both terms are “latinized” and written in italics
o the specific epithet is an adjective and is not
capitalized
o the genus is a noun and is capitalized
• also developed by Carolus Linnaeus
Order
Family Genus
Phylogenetic Trees
Species
Felidae
Panthera
Panthera
pardus
(leopard)
Taxidea
taxus
(American
badger)
Lutra lutra
(European
otter)
Lutra
Mustelidae
Taxidea
Carnivora
A PHYLOGENITIC TREE is a branching
diagram representing a hypothesis
of evolutionary relationships
1
Canis
Canidae
2
• each branch point indicates
divergence from a common ancestor
• shows patterns of descent, NOT
morphological similarity
Canis
latrans
(coyote)
SISTER TAXA – groups that share an
immediate common ancestor
(e.g., wolf and coyote)
Canis
lupus
(gray wolf)
BASAL TAXON – earliest
lineage to diverge
from the remainder of a
group
Branch point:
where lineages diverge
Taxon A
3
Taxon B
4
Taxon C
ROOTED – if all taxa in a
group have the same
common ancestor they
are said to be “rooted”
POLYTOMY – more than
two lineages diverge from
a single branch point (due
to uncertain divergence)
Sister
taxa
2
Taxon D
ANCESTRAL
LINEAGE
1
5
Taxon E
Taxon F
Taxon G
This branch point
represents the
common ancestor of
taxa A–G.
Basal
taxon
This branch point forms
a polytomy: an
unresolved pattern of
divergence.
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Homology vs Analogy
HOMOLOGY – similarities due to common ancestry
• Molecular Homology – similarity in DNA, protein sequences
• Morphological Homology – skeletal & fossil similarities
ANALOGY – morphological similarity
due to convergent evolution (e.g.,
bird vs bat wings)
• analogous structures that arise
independently are referred to as
homoplasies
Australian marsupial “mole”
North American eutherian mole
2. Determining Phylogenies
All available information, molecular, morphological and
physiological, are used in determining phylogenetic relationships.
Geckos
ANCESTRAL
LIZARD
(with limbs)
No limbs
Snakes
Iguanas
Monitor lizard
When molecular and
morphological data contradict,
molecular data takes precedence.
Eastern glass lizard
No limbs
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Using DNA Homology to
Construct Phylogenies
Cell
1 C C A T C AG AG T C C
division
2 C C A T C A
G AG T C C
error
Deletion
1 C C A T C AG AG T C C
2 C C A T C AG AG T C C
Sequences in non-conserved regions of DNA (i.e.,
sequences not subject to Natural Selection) are
aligned since they are presumably free to mutate
G T A Insertion
o computers are used to find the best alignment
accounting for deletions, insertions, etc
1 C C A T C AAG T C C
2 C C A T G TA C AG AG T C C
The degree of homology in similar regions can
be used to construct a phylogeny
o greater homology = more recent common ancestor
1 C C A T
C A
AG T C C
NOTE: Random chance would result in 25% homology
between sequences, so true homology must be >25%.
2 C C A T G TA C AG AG T C C
Using Cladistics to Construct Phylogenies
CLADE – an ancestral species and all descendants
• all descendants have a single common ancestor
(a) Monophyletic group (clade)
• all members of clade have unique shared
derived characters
A
1
• clades are a monophyletic groups
B
Group I
C
SHARED ANCESTRAL CHARACTERS (SAC)
D
• characters that originated before the clade
E
SHARED DERIVED CHARACTERS (SDC)
F
• characters found only within the clade
PARAPHYLETIC group – consists
of a single common ancestor and
some (not all) of its descendants
(b) Paraphyletic group
G
Paraphyletic group
Common
ancestor of
even-toed
ungulates
Other even-toed
ungulates
(c) Polyphyletic group
Hippopotamuses
A
A
B
B
C
D
2
Group III
Cetaceans
C
3
D
E Group II
E
F
F
G
G
Seals
Bears
POLYPHYLETIC group – consists of
organisms with more than 1
common ancestor
Polyphyletic group
Other
carnivores
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Constructing phylogenies based on shared derived characters (SDCs):
• start with an outgroup (group that diverged before the lineage of interest) and construct the
phylogeny based on multiple SDCs
• a character table can be used to identify successive branch points, each being due to a SDC
found in successively fewer members of the phylogeny
Bass
Frog
Turtle
Leopard
Lancelet
(outgroup)
Lamprey
CHARACTERS
Lancelet
(outgroup)
TAXA
Vertebral column
(backbone)
0
1
1
1
1
1
Hinged jaws
0
0
1
1
1
1
4 walking legs
0
0
0
1
1
1
Amnion
0
0
0
0
1
1
Hair
0
0
0
0
0
1
Lamprey
Bass
Vertebral
column
Hinged jaws
Frog
Turtle
Four walking legs
Amnion
Leopard
Hair
(b) Phylogenetic tree
(a) Character table
Using the Principle of “Maximum Parsimony”
to Construct Phylogenies
A phylogeny should be constructed based on maximum parsimony, i.e., the
simplest solution that is consistent with the facts.
• this is the principle of “Occam’s Razor” in which the hypothesis with the
fewest assumptions is favored
Applying the principle of maximum likelihood to phylogenies based on
DNA sequences:
• the hypothesis that requires the least number of mutational events is favored
Technique
3
1/C
I
1/C
I
II
III
III
II
III
II
1/C
I
1/C
Species I
1
Species II
Three phylogenetic hypotheses:
I
I
4
III
II
III
II
III
II
I
1
Site
2 3
Species I
C
T
A
T
Species II
C
T
T
C
Species III
Ancestral
sequence
A
G
A
C
G
T
T
2
A
1/C
Species III
4
3/A
2/T
I
2/T
3/A
II
4/C
III
II
II
I
2/T 3/A
I
I
II
III
III
III
2/T
2/T 4/C
6 events
3/A
4/C
III
4/C
3/A 4/C
Results
I
II
7 events
III
II
I
7 events
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Phylogenetic Bracketing
Phylogenetic bracketing is the process of inferring unknown characters in
extinct species based on the principle of maximum parsimony:
• in this example the shared
characters of crocodiles and
birds are also attributed to 2
groups of dinosaurs
• this example of phylogenetic
bracketing exhibits maximum
parsimony since the simplest
explanation for these shared
characters would be a single
common ancestor from which
all 4 groups evolved
Lizards
and snakes
Crocodilians
Ornithischian
dinosaurs
Common
ancestor of
crocodilians,
dinosaurs,
and birds
Saurischian
dinosaurs
Birds
Evidence Supporting a Case of
Phylogenetic Bracketing
Front
limb
Hind
limb
This fossil supports a prediction based
on phylogenetic bracketing – that
dinosaurs, like crocodiles and birds,
engaged in brooding, the bodily
warming of eggs.
Eggs
(a) Fossil remains of Oviraptor
and eggs
(b) Artist’s reconstruction of the
dinosaur’s posture based on the
fossil findings
Phylogenetic Branch Lengths can be used to
Indicate the Degree of Genetic Differences…
Drosophila
Lancelet
Zebrafish
Frog
Chicken
Human
Mouse
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Phylogenetic Branches can also Indicate Time
Drosophila
Lancelet
Zebrafish
Frog
Chicken
Human
Mouse
542
CENOZOIC
MESOZOIC
PALEOZOIC
251
Millions of years ago
65.5
Present
3. Evolutionary History
Revealed in Genomes
Orthologous vs Paralogous Genes
ORTHOLOGOUS GENES – homologous genes in different species
PARALOGOUS GENES – homology between different genes in the same species due
to duplication
Formation of orthologous genes:
a product of speciation
Ancestral gene
Ancestral gene
Ancestral species
Species C
Speciation with
divergence of gene
Gene duplication and divergence
Orthologous genes
Species A
Formation of paralogous genes:
within a species
Species B
Gene families result
from repeated
duplication of an
original gene followed
by subsequent
mutation.
Paralogous genes
Species C after many generations
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Molecular Clocks
Certain genes or other regions of genomes tend to change (i.e., evolve) at a
constant rate and thus serve as a molecular clock.
Number of mutations
For example, the number sequence differences (i.e., nucleotide
substitutions) in orthologous genes can reveal:
• the amount of time that has passed
since 2 species diverged from a
common ancestor
90
60
• the amount of time that has passed
since the gene was duplicated
30
0
0
60
90
30
Divergence time (millions of years)
120
This is best determined with
neutral mutations (mutations that
are neither selected for or against).
Problems with Molecular Clocks
A molecular clock will not give accurate predictions if the rate of
mutation is not constant which will be the case if:
• there is natural selection (i.e., a mutation is not neutral)
• changes in selective factors over time (i.e., under some conditions a
mutation may be neutral and under other conditions it may not be)
• for these or other reasons the mutation rate may change over time
One can increase the number of genes and taxa analyzed as molecular
clocks to dilute any inaccuracies associated with any particular gene,
however the problems indicated above can never be entirely eliminated.
Cell
division
error
Euglenozoans
Forams
Diatoms
Red algae
Green algae
Land plants
Domain Eukarya
Ciliates
Amoebas
Fungi
Animals
Methanogens
COMMON
ANCESTOR
OF ALL LIFE
Thermophiles
Domain
Archaea
Nanoarchaeotes
Proteobacteria
Chlamydias
Spirochetes
Gram-positive
bacteria
Cyanobacteria
(Chloroplasts)*
Domain Bacteria
(Mitochondria)*
Current Model of the
“Tree of Life”
• this model, as with previous models,
will no doubt change over time as
more information pertaining to
current and extinct species becomes
available
• as new information becomes
available, we get closer and closer to
the true evolutionary relationships
among all species, both past and
present
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