and Phylogenetics Systematics
How to read phylogenetic trees Classification (Systematics) Types of phylogenetic trees How to make phylogenetic trees How to use phylogenetic trees
The fossil record provides information about the history and relationships among organisms
100 million year old dragonfly fossil
The fossil record
Is based on the sequence in which fossils have accumulated in such strata
Fossils reveal
Ancestral characteristics that may have been lost over time
Fossils dates
Provide minimum estimates of the age of a taxon
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But the history of organisms is also written in their features, and in their genes.
Biologists use morphological, biochemical, and molecular comparisons to infer evolutionary relationships. Molecular (sequence) data are now the dominant data source.
This is a cladogram. One type of phylogenetic tree.
Are you more closely related to a fungus or a plant? Is a tulip more closely related to a mushroom or a human?
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How to read a phylogenetic tree
Morphological and Molecular Homologies
In general, organisms that share very similar morphologies or similar DNA sequences are likely to be more closely related.
Homology vs. Analogy
A potential source of error in reconstructing relationships is similarity due to convergent evolution, called analogy, rather than shared ancestry. Homologous features held in common by a group due to shared ancestry Analogous features are due to convergent evolution
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Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages Marsupial mole Mole (placental) (The two animals above are exactly as closely related to one another as the two animals below) Human Kangaroo
These wings are analagous
Bat
Bird
Each bone is homologous
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To determine whether a character state is homologous or analagous
One needs to look at many characters
Lizard
Bird
Mammal
Four-chambered heart
(a) Mammal-bird clade
Lizard
Bird
Mammal
Four-chambered heart Four-chambered heart
(b) Lizard-bird c lade
Analogous (convergent) structures or molecular sequences that evolved independently
Are also called homoplasies
Molecular Homologies
Systematists use computer programs and mathematical tools to align comparable
DNA segments from different organisms
Deletion
Insertion
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Here are two unrelated DNA sequences They happen to share 25% of their sites Computer programs are used to separate these chance homoplasies, from similarities that imply relationships
ACGGATAGTCCACTAG GCACTA
TCACCGACAGGTCTTT GACTAG
Figure 26.9
Phylogenetic systematics connects classification with evolutionary history Taxonomy
Is the ordered division of organisms into categories based on a set of characteristics used to assess similarities and differences
Binomial Nomenclature
Binomial nomenclature
Is the two-part format of the scientific name of an organism developed by Carolus Linnaeus Genus species
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Hierarchical Classification
Linnaeus also introduced a system
For grouping species in increasingly broad categories
Panthera Species pardus Genus Family Order Class Phylum Kingdom Panthera Felidae Carnivora Mammalia Chordata Animalia Eukarya
Figure 26.3
Domain
Systematists often depict evolutionary relationships
In branching phylogenetic trees
Species Genus
Panthera Mephitis Lutra lutra Canis Canis pardus mephitis (European familiaris lupus (leopard) (striped skunk) otter) (domestic dog) (wolf)
Panthera
Mephitis
Lutra
Canis
Family
Felidae
Mustelidae
Canidae
Order
Carnivora
Figure 26.4
Each branch point
Represents the divergence of two lineages
Leopard
Domestic cat
Common ancestor
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Deeper branch points
Represent progressively greater amounts of divergence
Wolf
Leopard
Domestic cat
Common ancestor
Phylogenetic systematics informs the construction of phylogenetic trees based on shared homologous characteristics A cladogram
Is a depiction of shared ancestries among taxa
A clade within a cladogram
Is defined as a group of species that includes an ancestral species and all its descendants Clades can be nested within larger clades, but not all groupings or organisms qualify as clades
A valid clade is monophyletic
A monophyletic clade consists of the ancestor species and all its descendants
Grouping 1 D C E G F H J I K
B A (a) Monophyletic. In this tree, grouping 1, consisting of the seven species B H, is a monophyletic group, or clade. A monophyletic g roup is made up of an ancestral species (species B in this case) and all of its descendant species. Only monophyletic groups qualify as legitimate t axa d erived from cladistics.
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Fig. 26-10
A B C D E F G (a) Monophyletic group (clade) Group I
A B C D E F G (b) P araphyletic group Group II
A B C D E F G (c) Polyphyletic group Group III
Fig. 26-10a
A B C D E F G (a) Monophyletic group (clade)
A monophyletic group contains the common ancestor and all of its descendents. Examples: Mammalia, Aves (birds), angiosperms, insects, etc.
Group I
Fig. 26-10b
A B C D E F G (b) Paraphyletic group
A paraphyletic g roup contains a common ancestor and some but not all descendents. E xamples : Traditionally defined D inosauria, fish, gymnosperms.
Group II
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Fig. 26-10c
A B C D E F G (c) Polyphyletic group
A polyphyletic group contains t axa w ith different ancestors. Examples: marine mammals, flying vertebrates, trees.
Group III
Shared Derived an Shared Ancestral Characters
In phylogenetic analysis
Clades are defined by their evolutionary novelties
A shared ancestral character is a character that originated in an ancestor of the t axon or group. A shared derived character
Is an evolutionary novelty unique to a particular clade.
Fig. 26-11
TAXA
Salamander
Lancelet (outgroup)
Lancelet (outgroup) Leopard Turtle Lamprey
Lamprey
Tuna
Vertebral column (backbone)
CHARACTERS
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
Tuna Vertebral column Hinged jaws
Hinged jaws Four walking legs Amniotic (shelled) egg Hair
Salamander
Four walking legs 1 Amniotic egg 1 (b) P hylogenetic t ree Hair
Turtle
Leopard
(a) Character table
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Outgroups and Ingroups
An outgroup is a species or group of species from an evolutionary lineage that diverged prior to the most recent common ancestor of the species we are studying (the ingroup) Systematists use a method called outgroup comparison to determine which character state(s) is ancestral, and which is derived.
As a basis of comparison we need to designate an outgroup
which is a species or group of species that is closely related to the ingroup, the various species we are studying
Outgroup comparison
Is based on the assumption that homologies present in both the outgroup and ingroup m ust be primitive characters that predate the divergence of both groups from a common ancestor
Here is a character with two states: a and a
Caracter state a Species 1 a a 23 a 4
Did evolution go from a to a or from a to a? Need an outgroup to polarize the direction of character-state change.
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Here is a character with two states: a and a
Caracter state a Species 1 a a 23 a a 4 outgroup
Outgroup shared the same character state as species 1 and 2. What is the most parsimonious reconstruction of character state evolution?
Two possible reconstructions
Character state a Species 1 a a 23 a a a 4 outgroup 1
2 1
a a 23
a a 4 outgroup
Ancestral state
a One change from a to a
a Two changes. First from a to a. Second from a to a.
First reconstruction is most parsimonious (fewest changes). Outgroup analysis polarizes the direction of character state change (from a to a ).
The outgroup comparison
determine Helps the direction and order of character state change.
TAXA Lamprey Tuna Salamander Turtle
Lancelet (outgroup)
CHARACTERS
Hair Amniotic (shelled) egg
0 0
0 0 0 0 1
0 0 0 1 1
0 0 1 1 1
0 1 1 1 1
Four walking legs 0 Hinged jaws 0 Vertebral column (backbone) 0
Leopard
1 1 1 1 1
(a) Character table. A 0 indicates that a character is absent; a 1 indicates that a character is present.
Turtle Salamander Tuna Lamprey Lancelet (outgroup)
Leopard Hair
Amniotic egg Four walking legs Hinged jaws (b) Cladogram. Analyzing the distribution of these derived characters can provide insight into vertebrate phylogeny.
Vertebral column
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Three types of phylogenetic trees
Cladograms Phylograms Ultrametric trees
Cladograms
Imply the relative order of divergences of taxa, but provide no information about the amount of change, or the time-depth of various events
Phylograms
In a phylogram
The length of a branch in a phylogram reflects the number of genetic changes that have taken place in a particular DNA or RNA sequence in that lineage
ila ph so Dro t ele nc La
Am ph ib ia n
d Bir
Hu m a Ra n t M ou se
Fis h
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Ultrametric Trees
In an ultrametric tree
The branching pattern is the same as in a phylogram , but all the branches all end at the presence and the lengths of the branches are proportional to time. Branch lengths on an ultrameric tree represent an estimate of time
Am ph ibia Bir n d Hu m Ra an t M ou se
Dr os op hil a La nc ele t Fis h
Cenozoic Mesozoic Paleozoic Proterozoic
Maximum Parsimony and Maximum Likelihood
Systematists
Use several methods to discover the best trees from large data sets. Two methods we will briefly discuss are:
Maximum Parsimony Maximum Likelihood
Maximum parsimony
Among phylogenetic hypotheses
The most parsimonious tree is the one that requires the fewest evolutionary events to have occurred
Millions of years ago
542
251
65.5
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Fig. 26-15-1
Species I
Species II
Species III
Three phylogenetic hypotheses: I I II III III II
III II I
Fig. 26-15-2
Site 1 Species I Species II Species III Ancestral sequence C C A A 2 T T G G 3 A T A T 4 T C C T
Three possible relationships
1/C
I II III
1/C
I III
1/C
III II I
1/C
II
1/C
For each relationship, map change in site 1
Fig. 26-15-3
Site 1 Species I Species II Species III Ancestral sequence C C A A 2 T T G G 3 A T A T 4 T C C T
3/A 2/T 4/C 1/C 1/C
I II III
I III
1/C
III II I
1/C 3/A 4/C 2/T
II
1/C 2/T 3/A 4/C
I II III
I III II
III II I
3/A 4/C
2/T 4/C
2/T 3/A
Now map changes in the other characters
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Fig. 26-15-4
Site 1 Species I Species II Species III Ancestral sequence C C A A 2 T T G G 3 A T A T 4 T C C T
3/A 2/T 4/C 1/C 1/C
I II III
I III
1/C
III II I
1/C 3/A 4/C 2/T
II
1/C 2/T 3/A 4/C
I II III
I III II
III II I
3/A 4/C
2/T 4/C
2/T 3/A
I II III 6 events 7 events
I III II 7 events
III II I
Fewest total changes on tree in which s pecies I and II are sister
In this example, characters (numbers) are coded 0 i f they share the same state as an ancestor (outgroup, not shown) and 1 if the state has changed. A utapomorphies (character states posessed b y single t axa) are in blue. Informative characters (those with alternative states each posessed b y more than one species, in red.
The principle of maximum likelihood
States that, given a certain hypothesis about how DNA changes over time, a tree can be found that maximizes the likelihood of the observed data. This tree reflects the most likely sequence of evolutionary events
Human Human Mushroom 0 Mushroom 30% 0 Tulip 40% 40% 0
Tulip
(a) Percentage differences between sequences
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The divergences are the same for both trees. However, in the tree on the right, plant sequences have changed 7 times more than fungi since their most recent common ancestor. If there is a single model of DNA change, such big differences are unlikely.
25%
15%
15%
20%
15%
10% 5% 5%
Tree 1: More likely (b) Comparison of possible trees
Tree 2: Less likely
7100 base pair gene sequenced from 4 great apes
chimp human chimp gorilla 0.016 gorilla 0.017 0.021 orangutan 0.034 0.038 0.037
Pairwise p ercent divergence
Inferred relationships among great apes
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Reconstruction methods
Maximum parsimony
Minimizes the number of character-state changes on the tree
Maximum likelihood
Finds the tree that maximizes the likelihood of observing the data, given a model of sequence evolution
Molecular Clocks
Linus Pauling s uggested that rates of molecular change (DNA or amino acid substitution) might be relatively constant among different organisms. If so, there will be a correlation between the amount of divergence and time since divergence. If the clock could be calibrated (say using the fossil record for some divergence times, one could then use molecular divergence as a yardstick for measuring the absolute time since divergence.
Neutral Theory
Neutral theory states that
Much evolutionary change in genes and proteins has no effect on fitness and therefore is not influenced by Darwinian selection And that the rate of molecular change in these genes and proteins should be regular like a clock
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Amino acid alignment of cytochrome c
Divergence times estimated from the fossil record plotted against amino acid divergence
Different molecules evolve at different rates, most keep fairly good time.
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Applying a Molecular Clock: The Origin of HIV
Phylogenetic analysis shows that HIV
Is descended from viruses that infect chimpanzees and other primates
How did the virus get from chimps to humans?
Bush meat trade is the usual hypothesis Hooper suggested instead, that early polio vacines may have been created using chimpanzee cells, a possible source of HIV. T his would have occurred in the late 50s
A comparison of HIV samples from throughout the epidemic
Has shown that the virus has evolved in a remarkably clocklike fashion How old is the transfer of HIV from chimps to humans?
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Phylogeny of H IV
Hypothesis testing using phylogenetic trees
Relationships among organisms Order of character state change Character states associated with increased diversification Biogeography
Vicariance Biogeography
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Similar fish in Africa and South America. Three possibilities:
1. Independent evolution of similar assemblages of fish on each continent 2. Long-distance (across ocean) dispersal brought similar forms to each continent 3. Vicariance (splitting by geographic barrier): Similar fish found on each continent because the separation of the continents split populations
1. Independent evolution of similar assemblages of fish on each continent
S. A. Africa
2. Long-distance dispersal brought similar forms to each continent
South America Africa South America Africa South America Africa
Pairs of similar fish on different continents diverged much more recently than the continents split apart
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Vicariance (splitting by geographic barrier
S.A. S.A.
Af. Af.
S.A.
Af.
(Africa a nd South America split apart about 90mya)
200MY
Vicariance Biogeography
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Moas. Extinct ratites from New Zealand
Phylogeny based on 10,000 base pair sequences of mitochondrial DNA (moas) NZ Aus. Aus. NZ Afr SA
moas
NZ Aus NZ Af SA
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Summary
Phylogenetic trees describe the nested relationships among organisms Systematic classification should also but some designations (e.g. fish) do not describe monophyletic clades. There are several types of phylogenetic trees and methods of construction.
Cladograms describe the order of divergences Phylograms add information on the amount of change along each branch Ultrameric trees are clock-like
There are many ways that phylogenetic trees can be used to test hypotheses.
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