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3. Evolution makes sense of homologies
3. Evolution makes sense of homologies
Richard Owen (1848) introduced the
term “Homology” to refer to structural
similarities among organisms.
And why would homologous
structures be inefficient or even
useless?
To Owen, these similarities indicated
that organisms were created following
a common plan or archetype. Although
each species is unique, the plans for
each might share many features.
For example, certain cave-dwelling fish
have degenerate eyes that cannot see.
Darwin made sense of homologous structures by supplying an
evolutionary explanation for them:
If every organism were created independently, why are there so
many homologies among certain organisms, while so few among
others?
A structure is similar among related organisms because
those organisms have all descended from a common
ancestor that had an equivalent trait.
3. Evolution makes sense of homologies
3. Evolution makes sense of homologies
Example: The "Universal" Genetic Code
Example: The "Universal" Genetic Code
5’
5’
T
C
A
G
T
C
A
G
3’
TTT Phe (F)
TCT Ser (S)
TAT Tyr (Y)
TGT Cys (C)
T
TTC Phe (F)
TCC Ser (S)
TAC Tyr (Y)
TGC Cys (C)
C
TTA Leu (L)
TCA Ser (S)
TAA Stop
TGA Stop [Trp]
A
TTG Leu (L)
TCG Ser (S)
TAG Stop
TGG Trp (W)
G
CTT Leu (L)
CTC Leu (L)
CCT Pro (P)
CCC Pro (P)
CAT His (H)
CAC His (H)
CGT Arg (R)
CGC Arg (R)
T
CTA Leu (L)
CCA Pro (P)
CAA His (H)
CGA Arg (R)
A
CTG Leu (L)
CCG Pro (P)
CAG His (H)
CGG Arg (R)
G
ATT Ile (I)
ACT Thr (T)
AAT Asn (N)
AGT Ser (S)
T
ATC Ile (I)
ACC Thr (T)
AAC Asn (N)
AGC Ser (S)
C
ATA Ile (I) [Met]
ACA Thr (T)
AAA Lys (K)
AGA Ser (S) [Stop]
A
ATG Met (M)
ACG Thr (T)
AAG Lys (K)
AGG Ser (S) [Stop]
G
GTT Val (V)
GCT Ala (A)
GAT Asp (D)
GGT Gly (G)
T
GTC Val (V)
GCC Ala (A)
GAC Asp (D)
GGC Gly (G)
C
GTA Val (V)
GCA Ala (A)
GAA Glu (E)
GGA Gly (G)
A
GCG Ala (A)
GAG Glu (E)
GGG Gly (G)
G
GTG Val (V)
[Mammalian mitochondrial code in italics.]
C
T
Basic code is universal among
eukaryotes and prokaryotes.
Minor variants are observed
in mitochondrial genomes
and some nuclear ones (e.g.
Mycoplasma and Tetrahymena).
C
A
G
T
C
A
G
3’
T
TTT Phe (F)
TCT Ser (S)
TAT Tyr (Y)
TGT Cys (C)
TTC Phe (F)
TCC Ser (S)
TAC Tyr (Y)
TGC Cys (C)
C
TTA Leu (L)
TCA Ser (S)
TAA Stop
TGA Stop [Trp]
A
TTG Leu (L)
TCG Ser (S)
TAG Stop
TGG Trp (W)
G
CTT Leu (L)
CCT Pro (P)
CAT His (H)
CGT Arg (R)
CTC Leu (L)
CCC Pro (P)
CAC His (H)
CGC Arg (R)
C
CTA Leu (L)
CCA Pro (P)
CAA His (H)
CGA Arg (R)
A
CTG Leu (L)
CCG Pro (P)
CAG His (H)
CGG Arg (R)
G
ATT Ile (I)
ACT Thr (T)
AAT Asn (N)
AGT Ser (S)
T
ATC Ile (I)
ACC Thr (T)
AAC Asn (N)
AGC Ser (S)
C
ATA Ile (I) [Met]
ACA Thr (T)
AAA Lys (K)
AGA Ser (S) [Stop]
A
ATG Met (M)
ACG Thr (T)
AAG Lys (K)
AGG Ser (S) [Stop]
G
GTT Val (V)
GCT Ala (A)
GAT Asp (D)
GGT Gly (G)
GTC Val (V)
GCC Ala (A)
GAC Asp (D)
GGC Gly (G)
C
GTA Val (V)
GTG Val (V)
GCA Ala (A)
GCG Ala (A)
GAA Glu (E)
GAG Glu (E)
GGA Gly (G)
GGG Gly (G)
A
Of the millions of alternatives, why do all
organisms have virtually the same genetic code?
T
T
G
3. Evolution makes sense of homologies
3. Evolution makes sense of homologies
Example: The "Universal" Genetic Code
5’
T
Because the anti-codon is at the
opposite end from the amino acid
binding site of a tRNA and does
not interact with the binding site,
there is no chemical necessity for
a codon to be assigned to a
particular amino acid.
C
A
G
T
C
A
Example: The "Universal" Genetic Code
G
3’
TCT Ser (S)
TAT Tyr (Y)
TGT Cys (C)
TTC Phe (F)
TCC Ser (S)
TAC Tyr (Y)
TGC Cys (C)
C
TTA Leu (L)
TCA Ser (S)
TAA Stop
TGA Stop [Trp]
A
TTG Leu (L)
TCG Ser (S)
TAG Stop
TGG Trp (W)
G
CTT Leu (L)
CCT Pro (P)
CAT His (H)
CGT Arg (R)
CTC Leu (L)
CCC Pro (P)
CAC His (H)
CGC Arg (R)
C
CTA Leu (L)
CCA Pro (P)
CAA His (H)
CGA Arg (R)
A
CTG Leu (L)
CCG Pro (P)
CAG His (H)
CGG Arg (R)
G
ATT Ile (I)
ACT Thr (T)
AAT Asn (N)
AGT Ser (S)
T
ATC Ile (I)
ACC Thr (T)
AAC Asn (N)
AGC Ser (S)
C
ATA Ile (I) [Met]
ACA Thr (T)
AAA Lys (K)
AGA Ser (S) [Stop]
A
ATG Met (M)
ACG Thr (T)
AAG Lys (K)
AGG Ser (S) [Stop]
G
GTT Val (V)
GCT Ala (A)
GAT Asp (D)
GGT Gly (G)
GTC Val (V)
GCC Ala (A)
GAC Asp (D)
GGC Gly (G)
C
GTA Val (V)
GTG Val (V)
GCA Ala (A)
GCG Ala (A)
GAA Glu (E)
GAG Glu (E)
GGA Gly (G)
GGG Gly (G)
A
The genetic code is homologous among living organisms: it is similar
despite the fact that there exist many equally good genetic codes.
3. Evolution makes sense of homologies
Example: The plasma membrane
The plasma membranes of all
organisms, eukaryotic and
prokaryotic, are structurally similar,
consisting of a phospholipid bilayer.
The similarity of the plasma membrane suggests that all living
cells have descended from an ancestor with a similar
membrane structure.
5’
T
TTT Phe (F)
T
T
T
Evolutionary descent from a
common ancestor makes sense of
the similarity among genetic codes.
C
A
G
G
T
C
A
G
TAT Tyr (Y)
TGT Cys (C)
TCC Ser (S)
TAC Tyr (Y)
TGC Cys (C)
C
TTA Leu (L)
TCA Ser (S)
TAA Stop
TGA Stop [Trp]
A
TTG Leu (L)
TCG Ser (S)
TAG Stop
TGG Trp (W)
G
CTT Leu (L)
CCT Pro (P)
CAT His (H)
CGT Arg (R)
CTC Leu (L)
CCC Pro (P)
CAC His (H)
CGC Arg (R)
C
CTA Leu (L)
CCA Pro (P)
CAA His (H)
CGA Arg (R)
A
CTG Leu (L)
CCG Pro (P)
CAG His (H)
CGG Arg (R)
G
ATT Ile (I)
ACT Thr (T)
AAT Asn (N)
AGT Ser (S)
T
ATC Ile (I)
ACC Thr (T)
AAC Asn (N)
AGC Ser (S)
C
ATA Ile (I) [Met]
ACA Thr (T)
AAA Lys (K)
AGA Ser (S) [Stop]
A
ATG Met (M)
ACG Thr (T)
AAG Lys (K)
AGG Ser (S) [Stop]
G
GTT Val (V)
GCT Ala (A)
GAT Asp (D)
GGT Gly (G)
GTC Val (V)
GCC Ala (A)
GAC Asp (D)
GGC Gly (G)
C
GTA Val (V)
GTG Val (V)
GCA Ala (A)
GCG Ala (A)
GAA Glu (E)
GAG Glu (E)
GGA Gly (G)
GGG Gly (G)
A
Over the ages, the genetic code has passed unchanged (or
nearly so) from parents to offspring, because mutations to the
genetic code would have reduced fitness (changing the amino
acid sequence of all proteins produced).
3. Evolution makes sense of homologies
Example: The Pentadactyl limb
Certain tetrapods lose some of
these digits during development,
as in the bird wing shown here.
But if the bird wing does not need
five digits, why do five initially
develop in the growing embryo?
T
TCT Ser (S)
TTC Phe (F)
The common ancestor to all known organisms had a genetic
code similar to what we see today.
“Five” “Digit”
All tetrapods (= four legged) have
limbs with five digits, at least at
some stage in development.
3’
TTT Phe (F)
Frog
Lizard
Bird
Human
Bat
Cow Whale
T
T
G
3. Evolution makes sense of homologies
Example: The Pentadactyl limb
Frog
3. Evolution makes sense of homologies
New structures evolve from pre-existing structures
Lizard
Bird
The five digits are not functionally
necessary, but they represent a
genetic artefact inherited from the
ancestors of birds.
Human
Bat
Cow Whale
Homology explained by descent from
a common ancestor.
Even when two species function in
completely different ways, they
often use homologous structures
to carry out those functions
(e.g., wings of birds and bats).
Similarly, the stinger of wasps and
bees is a modified ovipositor, not
an entirely new structure.
(Explaining why only females sting!!)
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Evolution works primarily by modifying pre-existing structures.
3. Evolution makes sense of homologies
3. Evolution makes sense of homologies
Vestiges
Vestiges
Structures that are functionless in a species but homologous to
a functioning structure in other species are particularly difficult
to explain except under the theory of common descent.
“Vestigial structures”
e.g. pelvic girdle of a whale
e.g., eye bulbs of blind, cave-dwelling creatures, such as the
grotto salamander (Typhlotriton spelaeus)
“Vestigial structures”
3. Evolution makes sense of homologies
Vestiges
e.g., anthers and pollen of asexual dandelions
4. Homologies are nested
One of the striking features about similar structures are that
they cluster.
Certain species share many
similarities at every level of
organization (e.g. humans and
chimpanzees), whereas other
species only share certain nearly
universal homologies (e.g.
humans and Escherichia coli).
Vestigial structures are puzzling if each creature were
independently created, but they make sense if organisms inherit
traits from their ancestors with gradual modification over time.
4. Homologies are nested
4. Homologies are nested
Consider a sequence of DNA in four species:
Evolutionary descent from
a common ancestor makes
sense of this nesting.
We expect the number of
shared homologies to be
high for closely related
species and to decrease
over time as the species
diverge from each other.
Species C and D would
have identical sequences,
species A and B would
differ by one mutation,
whereas A-C and A-D
would differ by four
mutations and B-C and BD by three mutations.
The nesting of homologies allows us to determine the "relatedness"
among organisms by how many (and which) features they share
4. Homologies are nested
4. Homologies are nested
Example: Primate Phylogeny
Example: Primate Phylogeny
Morphologically, humans and chimps are much more similar
than are humans and gibbons.
Three phylogenetic trees were reconstructed based on the
DNA sequences of:
(a) 4700 bp of mitochondrial DNA
(b) Testis specific protein on the Y chromosome
(c) Noncoding regions of the ß-globin gene
If this were because humans and chimps are more closely
related (=have had a common ancestor more recently), then
we would expect DNA sequences of humans and chimps to
be more similar as well.
4. Homologies are nested
Example: Bird Phylogeny
Nested series of homologous
characters can also be
identified in fossil organisms.
Some dinosaur fossils share
few traits in common with
birds while others share
several.
All three trees show that human and
chimp DNA sequences are more
similar on average than are human
and gibbon or human and orangutan
sequences.
4. Homologies are nested
Example: Bird Phylogeny
Maniraptors share more traits
with modern birds than do any
other type of dinosaurs.
Coelurosauria besides
maniraptors share some, but
not as many features of birds.
4. Homologies are nested
4. Homologies are nested
Archosauria
• hard-shelled eggs
• single openings in each side
Dinosauria
• reduced fourth and fifth
•
•
•
•
of the skull in front of the
eyes (antorbital fenestrae)
openings in the lower jaw
(the mandibular fenestra)
a high narrow skull with a
pointed snout
teeth set in sockets
4. Homologies are nested
Saurischia
• a grasping hand
• asymmetrical fingers
• long, mobile neck
• pelvis with a pubis that
points downward and
forward
•
•
digits on the hand
foot reduced to three main
toes
three or more vertebrae
composing the sacrum
an open hip socket
4. Homologies are nested
Therapoda
• hollow, thin-walled bones
4. Homologies are nested
Coelurosauria
• elongated arms
• well-developed hinge-like
•
ankles
(some coelurosaurs have
open nests like birds in
which eggs were brooded)
4. Homologies are nested
Aves
• feathers
• wings
• wishbone
• opposable big toe
4. Homologies are nested
Maniraptora
• the semilunate carpal
•
•
•
present in wrist
modified forelimb (elevated
forelimb capable of folding)
a fused collar bone and
sternum
pelvis with a pubis that
points downwards
4. Homologies are nested
Example: Bird Phylogeny
This nested series is thought
to represent the evolutionary
trajectory of dinosaurs along
the lineage leading to birds.
4. Homologies are nested
The earliest known fossil bird
(Archaeopteryx) shares these
features of birds but also has
many ancestral features of
therapods including:
• teeth
• extensive tail vertebrae
• claws
• lack of a keeled breastbone
5. Evidence for evolution from the fossil record
Although the fossil record is
often poor and incomplete,
there are certain deposits where
sedimentary layers remain in a
nearly continuous series.
Archaeopteryx probably did not fly. It lacked the prominent
keel of modern birds upon which flight muscles attach.
5. Evidence for evolution from the fossil record
Example: Trilobite evolution
Fossils from these series provide
direct evidence of evolutionary
change.
Hagerman fossil bed
http://www2.nature.nps.gov/Geology/parks/hafo/index.cfm
5. Evidence for evolution from the fossil record
Example: Trilobite evolution
Samples were obtained from every three million years. The
number of ribs of each species of trilobite changed over time
(=evolution).
Sheldon (1987) examined a
series of sedimentary layers
from the Ordovician period
(500 MYA) containing trilobite
fossils (extinct marine
arthropods).
Flexicalymene
Rick Larush ([email protected]).
5. Evidence for evolution from the fossil record
Example: Trilobite evolution
Some of these changes over time were so large that the animals
at the end of the series are assigned to a new genus.
5. Evidence for evolution from the fossil record
Example: Foraminiferan evolution
An even finer scale analysis was performed by Malmgren et
al. (1983) on a species of foraminiferan (shell-bearing
protozoans) from 10MYA to recent times.
[Three epochs are represented:
Miocene (M; 23.8-5.2 MYA), Pliocene (P; 5.2-1.8 MYA) and Pleistocene (Q; 1.8 MYA - 10,000 YA)].
5. Evidence for evolution from the fossil record
Example: Foraminiferan evolution
Over this period, the fossil
shells evolved a larger,
thicker shell, with a more
pronounced ridge.
Although the fossil record
indicates continuous
change over time, the rate
was not always the same.
Shaped changed most
around the Miocene/
Pliocene boundary.
5. Evidence for evolution from the fossil record
Example: Foraminiferan evolution
These changes were large
enough that the lineage is
assigned to the species
Globorotalia plesiotumida
in the Miocene, but to
the species Globorotalia
tumida afterwards.
5. Evidence for evolution from the fossil record
The fossil record demonstrates evolutionary changes do occur.
The disadvantage of the fossil record is that it is generally
difficult to determine the selective forces that may have
contributed to these changes.
The advantage of the fossil record over present-day
observations of evolution is that higher order evolutionary
changes may be tracked (e.g. the origin of new species, new
genera, etc).
Flexicalymene
Rick Larush ([email protected]).
Evidence for evolution
SOURCES:
•
•
•
•
•
Pentadactyl limbs: Ridley (1997) Evolution.
Whale, salamander, primate trees: Freeman and Herron (1998) Evolutionary Analysis.
Membrane photo: Wessells and Hopson (1988) Biology.
Dinosaur information: UC Museum of Paleontology.
Trilobite and foraminiferan fossil record: Futuyma (1998) Evolutionary Biology.
Flexicalymene
Rick Larush ([email protected]).