3. Evolution mak es sense of homologiesbio336/Bio336/Lectures06/Lecture5.pdf · Evolution works pr...

Richard Owen (1848) introduced the term “Homology” to refer to structural similarities among organisms.

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.

3. Evolution makes sense of homologies

If every organism were created independently, why are there so many homologies among certain organisms, while so few among others?

And why would homologous structures be inefficient or even useless?

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:

A structure is similar among related organisms because those organisms have all descended from a common

ancestor that had an equivalent trait.

Example: The "Universal" Genetic Code


[Mammalian mitochondrial code in italics.]

5’ T C A G 3’

T

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

C

CTT Leu (L) CCT Pro (P) CAT His (H) CGT Arg (R) T

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

A

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

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

GTG Val (V) GCG Ala (A) GAG Glu (E) GGG Gly (G) G



5’ T C A G 3’

T





C





A





G





Basic code is universal among eukaryotes and prokaryotes.

Minor variants are observed in mitochondrial genomes and some nuclear ones (e.g. Mycoplasma and Tetrahymena).

Of the millions of alternatives, why do all organisms have virtually the same genetic code?



5’ T C A G 3’

T





C





A





G





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.

The genetic code is homologous among living organisms: it is similar despite the fact that there exist many equally good genetic codes.



5’ T C A G 3’

T





C





A





G





Evolutionary descent from a common ancestor makes sense of the similarity among genetic codes.

The common ancestor to all known organisms had a genetic code similar to what we see today.

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).

Example: The plasma membrane


The plasma membranes of all organisms, eukaryotic and prokaryotic, are structurally similar, consisting of a phospholipid bi-layer.

The similarity of the plasma membrane suggests that all living cells have descended from an ancestor with a similar

membrane structure.

Example: The Pentadactyl limb


All tetrapods (= four legged) have limbs with five digits, at least at some stage in development.

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?

Frog Lizard Bird

Human BatCow Whale

“Five” “Digit”

Example: The Pentadactyl limb


The five digits are not functionally necessary, but they represent a genetic artefact inherited from the ancestors of birds.

Homology explained by descent from a common ancestor.

Frog Lizard Bird

Human BatCow Whale

New structures evolve from pre-existing structures


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!!)

Evolution works primarily by modifying pre-existing structures.

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.

e.g. pelvic girdle of a whale

“Vestigial structures”

Vestiges


e.g., eye bulbs of blind, cave-dwelling creatures, such as the grotto salamander (Typhlotriton spelaeus)

“Vestigial structures”

Vestiges


e.g., anthers and pollen of asexual dandelions

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

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).


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 B-D by three mutations.

Consider a sequence of DNA in four species:

The nesting of homologies allows us to determine the "relatedness" among organisms by how many (and which) features they share


Morphologically, humans and chimps are much more similar than are humans and gibbons.

Example: Primate Phylogeny

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.


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

Example: Primate Phylogeny

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.

Example: Bird Phylogeny4. Homologies are nested

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.

4. Homologies are nestedExample: 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.


Archosauria• hard-shelled eggs

• single openings in each side 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


Dinosauria• reduced fourth and fifth

digits on the hand

• foot reduced to three main toes

• three or more vertebrae composing the sacrum

• an open hip socket


Saurischia• a grasping hand

• asymmetrical fingers

• long, mobile neck

• pelvis with a pubis that points downward and forward


Therapoda• hollow, thin-walled bones


Coelurosauria• elongated arms

• well-developed hinge-like ankles

• (some coelurosaurs have open nests like birds in which eggs were brooded)


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


Aves• feathers

• wings

• wishbone

• opposable big toe

4. Homologies are nestedExample: Bird Phylogeny

This nested series is thought to represent the evolutionary trajectory of dinosaurs along the lineage leading to birds.


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

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

Although the fossil record is often poor and incomplete, there are certain deposits where sedimentary layers remain in a nearly continuous series.

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 recordExample: Trilobite 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]).


Samples were obtained from every three million years. The number of ribs of each species of trilobite changed over time

(=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 recordExample: 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)].


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.


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


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


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