3. Evolution makes sense of homologies. 3. Evolution makes sense of homologies. 3. Evolution makes sense of homologies

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Gervase Malone
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1 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. 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 5 T C A G 3 TTT Phe (F) TCT Ser (S) TAT Tyr (Y) TGT Cys (C) T 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) CCT Pro (P) CAT His (H) CGT Arg (R) T C 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 A 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 G 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 [Mammalian mitochondrial code in italics.] Example: The "Universal" Genetic Code Basic code is universal among eukaryotes and prokaryotes. Minor variants are observed in mitochondrial genomes and some nuclear ones (e.g. Mycoplasma and Tetrahymena). 5 T C A G 3 T C A G 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) 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 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 GTG Val (V) GCG Ala (A) GAG Glu (E) GGG Gly (G) G Of the millions of alternatives, why do all organisms have virtually the same genetic code?

Example: The "Universal" Genetic Code Example: The "Universal" Genetic Code Because the anti-codon is at the opposite end from the amino acid binding site of a trna and does not interact with the

2 Example: The "Universal" Genetic Code Example: The "Universal" Genetic Code 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. 5 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 T 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) T CTC Leu (L) CCC Pro (P) CAC His (H) CGC Arg (R) C 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 A 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 G 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 Evolutionary descent from a common ancestor makes sense of the similarity among genetic codes. 5 T C A G 3 T C A G 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) 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 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 GTG Val (V) GCG Ala (A) GAG Glu (E) GGG Gly (G) G The common ancestor to all known organisms had a genetic code similar to what we see today. The genetic code is homologous among living organisms: it is similar despite the fact that there exist many equally good genetic codes. 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 bilayer. 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 Five Digit 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 Cow Whale Bat

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

Frog Lizard Bird Human Cow Whale Bat New structures evolve from pre-existing structures Even when two species function in completely different ways, they often use

Similarly, the stinger of wasps and bees is a modified ovipositor, not an entirely new structure. (Explaining why only females sting!

3 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 Cow Whale Bat 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. Vestiges e.g., eye bulbs of blind, cave-dwelling creatures, such as the grotto salamander (Typhlotriton spelaeus) Vestigial structures Vestigial structures e.g. pelvic girdle of a whale

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 Vestiges e.g., anthers and pollen of asexual dandelions 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. 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 B- D by three mutations. The nesting of homologies allows us to determine the "relatedness" among organisms by how many (and which) features they share

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

5 Example: Primate Phylogeny Morphologically, humans and chimps are much more similar than are humans and gibbons. Example: Primate Phylogeny 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. 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 Phylogeny 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. 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.

6 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

7 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 Example: 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

poor and incomplete, there are certain deposits where sedimentary layers remain in a nearly continuous series.

Example: Trilobite evolution Fossils from these series provide direct evidence of evolutionary change.

cfm Example: Trilobite evolution Samples were obtained from every three million years.

8 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 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. Example: Trilobite evolution Fossils from these series provide direct evidence of evolutionary change. Hagerman fossil bed 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 (rick@geo.ucalgary.ca).

9 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. 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; MYA), Pliocene (P; MYA) and Pleistocene (Q; 1.8 MYA - 10,000 YA)]. 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. 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.

10 Evidence for evolution 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). 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 Flexicalymene Rick Larush

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