II. Darwin’s Contributions A. Overview B. Argument: Evidence for Evolution by Common Descent C. Mechanism: Natural Selection D. Dilemmas: “Long before having arrived at this part of my work, a crowd of difficulties will have occurred to the reader. Some of them are so grave that to this day I can never reflect on them without being staggered; but, to the best of my judgment, the greater number are only apparent, and those that are real are not, I think, fatal to my theory.” – Charles Darwin, The Origin of Species (1859).

II. Darwin’s Contributions A. Overview B. Argument: Evidence for Evolution by Common Descent C. Mechanism: Natural Selection D. Dilemmas: 1. The evolution of complex structures – addressing Paley “Can we believe that natural selection could produce, on the one hand, organs of trifling importance, such as the tail of a giraffe, which serves as a fly-flapper, and, on the other hand, organs of such wonderful structure, as the eye, of which we hardly as yet fully understand the inimitable perfection?”– Charles Darwin, The Origin of Species (1859).

II. Darwin’s Contributions A. Overview B. Argument: Evidence for Evolution by Common Descent C. Mechanism: Natural Selection D. Dilemmas: 1. The evolution of complex structures “To suppose that the eye, with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest possible degree. Yet reason tells me, that if numerous gradations from a perfect and complex eye to one very imperfect and simple, each grade being useful to its possessor, can be shown to exist; if further, the eye does vary ever so slightly, and the variations be inherited, which is certainly the case; and if any variation or modification in the organ be ever useful to an animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, can hardly be considered real. Charles Darwin, The Origin of Species (1859).

Dawkins: Evolution of the Camera Eye

D. Dilemmas: 1. The evolution of complex structures

D. Dilemmas: 1. The evolution of complex structures 2. Where are modern and fossil intermediates? “…why, if species have descended from other species by insensibly fine gradations, do we not everywhere see innumerable transitional forms? Why is not all nature in confusion instead of the species being, as we see them, well defined? … as by this theory innumerable transitional forms must have existed, why do we not find them embedded in countless numbers in the crust of the earth?” – Charles Darwin, The Origin of Species (1859)

X X X X X X ? D. Dilemmas: 1. The evolution of complex structures 2. Where are modern and fossil intermediates? ?

D. Dilemmas: 1. The evolution of complex structures 2. Where are modern and fossil intermediates? “As natural selection acts solely by the preservation of profitable modifications, each new form will tend in a fully-stocked country to take the place of, and finally to exterminate, its own less improved parent or other less-favoured forms with which it comes into competition. Thus extinction and natural selection will, as we have seen, go hand in hand. Hence, if we look at each species as descended from some other unknown form, both the parent and all the transitional varieties will generally have been exterminated by the very process of formation and perfection of the new form.” –,The Origin of Species (Darwin 1859)

X X D. Dilemmas: 1. The evolution of complex structures 2. Where are modern and fossil intermediates? Better adapted descendant outcompetes ancestral type

X X X X D. Dilemmas: 1. The evolution of complex structures 2. Where are modern and fossil intermediates? Better adapted descendant outcompetes ancestral type

X X X X X X D. Dilemmas: 1. The evolution of complex structures 2. Where are modern and fossil intermediates? Better adapted descendant outcompetes ancestral type

X X X X X X ? D. Dilemmas: 1. The evolution of complex structures 2. Where are modern and fossil intermediates? “…I believe the answer mainly lies in the record being incomparably less perfect than is generally supposed…” - Charles Darwin, The Origin of Species (1859)

D. Dilemmas: 1. The evolution of complex structures 2. Where are modern and fossil intermediates? 1861 – Archaeopteryx lithographica “…and still more recently, that strange bird, the Archeopteryx, with a long lizardlike tail, bearing a pair of feathers on each joint, and with its wings furnished with two free claws, has been discovered in the oolitic slates of Solenhofen. Hardly any recent discovery shows more forcibly than this, how little we as yet know of the former inhabitants of the world.” – Charles Darwin, The Origin of Species, 6 th ed. (1876)

D. Dilemmas: 1. The evolution of complex structures 2. Where are modern and fossil intermediates? 3. What is the source of heritable variation?

D. Dilemmas: 1. The evolution of complex structures 2. Where are modern and fossil intermediates? 3. What is the source of heritable variation? "These laws, taken in the largest sense, being Growth with Reproduction; Inheritance which is almost implied by reproduction; Variability from the indirect and direct action of the external conditions of life, and from use and disuse; a Ratio of Increase so high as to lead to a Struggle for Life, and as a consequence to Natural Selection…". - The Origin of Species (Darwin 1859). - Inheritance of acquired characters – (wrong) - Use and disuse – (sort of, but not as he envisioned it) - Blending heredity and the action of selection should reduce variation in a population over time. - gemmules and grafting experiments….

D. Dilemmas: 1. The evolution of complex structures 2. Where are modern and fossil intermediates? 3. What is the source of heritable variation? 4. How do instincts evolve? - if there is heritable variation in behavior, then selection can act on that, also…

D. Dilemmas: 1. The evolution of complex structures 2. Where are modern and fossil intermediates? 3. What is the source of heritable variation? 4. How do instincts evolve? 5. How can sterility, and the evolution of entire sterile castes (like in social insects) evolve? - Sterile organisms don’t reproduce; how can they be favored by selection? Some form of group selection… groups with steriles do bet and their reproductives outperform the combined reproductive success of sexual competitors.

II. Darwin’s Contributions A. Overview B. Argument: Evidence for Evolution by Common Descent C. Mechanism: Natural Selection D. Dilemmas: E. Darwin’s Model of Evolution

II. Darwin’s Contributions A. Overview B. Argument: Evidence for Evolution by Common Descent C. Mechanism: Natural Selection D. Dilemmas: E. Darwin’s Model of Evolution Sources of VariationAgents Causing Evolution ? VARIATIONVARIATION Natural Selection

III. Post-Darwinian Developments A. Physics 1. The Age of the Earth a William Thompson - "Lord Kelvin“ - Earth was 15-20mya. b Henri Becquerel - discovers emission of Uranium c Pierre and Marie Curie - discover emission from new element - Radium d Ernst Rutherford - "The discovery of the radio-active elements, which in their disintegration liberate enormous amounts of energy, thus increases the possible limit of the duration of life on this planet, and allows the time claimed by the geologist and biologist for the process of evolution."

III. Post-Darwinian Developments A. Physics 1. The Age of the Earth 2. Radioactive Decay and Geological Clocks - measure amt of parent and daughter isotopes = total initial parental - with the measureable1/2 life, determine time needed to decay this fraction - K40-Ar40 suppose 1/2 of total is Ar40 = 1.3by (Now, you might say "be real"! How can we measure something that is this slow?) Well, 40 grams of Potassium (K) contains: 6.0 x atoms (Avogadro's number, remember that little chemistry tid-bit?). So, For 1/2 of them to change, that would be: 3.0 x atoms in 1.3 billion years (1.3 x 10 9 ) So, divide 3.0 x by 1.3 x 10 9 = 2.3 X atoms/year. Then, divide 2.3 x by 365 (3.65 x 10 2 ) days per year = 0.62 x atoms per day ( shift decimal = 6.2 x ) Then, divide 6.2 x by 24*60*60 = 86,400 seconds/day: (= 8.64 x 10 4 ) = 0.7 x 10 7 atoms per second 0.7 x 10 7 = 7 x 10 6 = 7 million atoms changing from Potassium to Argon every second!!!

Ichthyostega FISH AMPHIBIANS XXX - Struts in the tailfin (FISH) - Feet (AMPHIBIANS) - After fish, before amphibians (just where evolution predicts it should be) III. Post-Darwinian Developments A. Physics B. Paleontology and Transitional Fossils 1. Ichthyostega and the fish-amphibian transition

D. Devonian ( mya) - Placoderms - Sharks - Lobe-finned Fishes 385 mya 365 mya

III. Post-Darwinian Developments A. Physics B. Paleontology and Transitional Fossils 1. Ichthyostega and the fish-amphibian transition

Eusthenopteron

Tiktaalik roseae

Acanthostega gunnari

Ichthyostega sp.

Archeopteryx lithographica REPTILES BIRDS XXX – 150 mya - Fingers, teeth, tail (Reptiles) - Feathers (birds) - After reptiles, before birds (just where evolution predicts it should be) B. Paleontology and Transitional Fossils 1. Ichthyostega and the fish-amphibian transition 2. The evolution of birds

B. Paleontology and Transitional Fossils 1. Ichthyostega and the fish-amphibian transition 2. The evolution of birds

B. Paleontology and Transitional Fossils 1. Ichthyostega and the fish-amphibian transition 2. The evolution of birds Epidipteryx – 165 mya

B. Paleontology and Transitional Fossils 1. Ichthyostega and the fish-amphibian transition 2. The evolution of birds Microraptor – 120 mya

B. Paleontology and Transitional Fossils 1. Ichthyostega and the fish-amphibian transition 2. The evolution of birds Anchiornis – 160mya

B. Paleontology and Transitional Fossils 1. Ichthyostega and the fish-amphibian transition 2. The evolution of birds Sinosauropteryx – 120mya

B. Paleontology and Transitional Fossils 1. Ichthyostega and the fish-amphibian transition 2. The evolution of birds Tianyulong – 200 mya

Therapsids REPTILES MAMMALS XXX - Mammalian skeleton - Intermediate ear - primitive dentition - After reptiles, before mammals (just where evolution predicts it should be) B. Paleontology and Transitional Fossils 1. Ichthyostega and the fish-amphibian transition 2. The evolution of birds 3. The evolution of mammals

Mammals from the Jurassic (185 mya) Pelycosaur Reptiles of the Carboniferous (300 mya) Therapsids from the Permian (280 mya) to the Triassic (200mya)

Australopithecines APES HUMANS XXX - After apes, before humans (just where evolution predicts it should be) - bipedal (human trait) - chimp-sized cranial volume B. Paleontology and Transitional Fossils 1. Ichthyostega and the fish-amphibian transition 2. The evolution of birds 3. The evolution of mammals 4. The evolution of humans

Australopithecines Australopithecus afarensis 4. The evolution of humans

Teeth 4. The evolution of humans

Legs 4. The evolution of humans

Skulls 4. The evolution of humans

III. Post-Darwinian Developments A. Physics B. Paleontology and Transitional Fossils C. Geology

III. Post-Darwinian Developments A. Physics B. Paleontology and Transitional Fossils C. Geology Continental Drift Alfred Wegener

- Not accepted until the 1960’s and 1970’s, when sea floor spreading was observed, sonar was used to map the ocean, and paleomagnetism demonstrated where continents had been in the past relative to magnetic north.

Explained disjunct distributions as a consequence of “vicariance”

III. Post-Darwinian Developments A. Physics B. Paleontology and Transitional Fossils C. Geology D. Genetics and Population Genetics 1. Heredity and Variation Hereditary units are ‘particulate’, and Chromosomes assort independently during gamete formation. Sexually reproducing species can produce an extraordinary amount of genetic variation in their offspring as a consequence of passing on different combinations of chromosomes and genes. A single pair of humans can produce any of 2 46 (~70 trillion) combinations of chromosomes in their offspring.

D. Genetics and Population Genetics 1. Heredity and Variation 2. Genetic Tests/Analyses of Phylogeny - gross chromosomal patterns

D. Genetics and Population Genetics 1. Heredity and Variation 2. Genetic Tests/Analyses of Phylogeny - gross chromosomal patterns - sequence analyses

D. Genetics and Population Genetics 1. Heredity and Variation 2. Genetic Tests/Analyses of Phylogeny 3. Population Genetics - demonstrated that selection and drift were the major agents of evolutionary change.

Sources of VariationAgents of Change MutationN.S. RecombinationDrift - crossing overMigration - independent assortmentMutation Non-random Mating VARIATION D. Genetics and Population Genetics 1. Heredity and Variation 2. Genetic Tests/Analyses of Phylogeny 3. Population Genetics 4. The Modern Synthesis

D. Genetics and Population Genetics 1. Heredity and Variation 2. Genetic Tests/Analyses of Phylogeny 3. Population Genetics 4. The Modern Synthesis 5. Beyond the Synthesis - Peripatric Speciation

D. Genetics and Population Genetics 1. Heredity and Variation 2. Genetic Tests/Analyses of Phylogeny 3. Population Genetics 4. The Modern Synthesis 5. Beyond the Synthesis - Peripatric Speciation - Punctuated Equilibrium

TIME VARIATION 1. Consider a large, well-adapted population

- Punctuated Equilibrium TIME VARIATION 1. Consider a large, well-adapted population Effects of Selection and Drift are small - little change over time

- Punctuated Equilibrium TIME VARIATION 2. There are always small sub-populations "budding off" along the periphery of a species range...

- Punctuated Equilibrium TIME VARIATION 2. Most will go extinct, but some may survive... X X X

- Punctuated Equilibrium TIME VARIATION 2. These surviving populations will initially be small, and in a new environment...so the effects of Selection and Drift should be strong... X X X

- Punctuated Equilibrium TIME VARIATION 3. These populations will change rapidly in response... X X X

- Punctuated Equilibrium TIME VARIATION 3. These populations will change rapidly in response... and as they adapt (in response to selection), their populations should increase in size (because of increasing reproductive success, by definition). X X X

- Punctuated Equilibrium TIME VARIATION 3. As population increases in size, effects of drift decline... and as a population becomes better adapted, the effects of selection decline... so the rate of evolutionary change declines... X X X

- Punctuated Equilibrium TIME VARIATION 4. And we have large, well-adapted populations that will remain static as long as the environment is stable... X X X

- Punctuated Equilibrium TIME VARIATION 5. Since small, short-lived populations are less likely to leave a fossil, the fossil record can appear 'discontinuous' or 'imperfect' X X X

- Punctuated Equilibrium TIME VARIATION 5. Large pop's may leave a fossil.... X X X

- Punctuated Equilibrium TIME VARIATION 5. Small, short-lived populations probably won't... X X X

- Punctuated Equilibrium TIME VARIATION 6. So, the discontinuity in the fossil record is an expected result of our modern understanding of how evolution and speciation occur... X X X

- Punctuated Equilibrium TIME VARIATION 6. both in time (as we see), and in SPACE (as changing populations are probably NOT in same place as ancestral species). X X X

D. Genetics and Population Genetics 1. Heredity and Variation 2. Genetic Tests/Analyses of Phylogeny 3. Population Genetics 4. The Modern Synthesis 5. Beyond the Synthesis - Peripatric Speciation - Punctuated Equilibrium - Evo-Devo

1. Core Processes - Basic biological processes are CONSERVED, and the enzymes that perform them are CONSERVED: - Many enzymes are more than 50% similar in AA sequence in E. coli and H. sapiens, though separated by 2 billion years of divergence. - Of 548 metabolic enzymes in E. coli, 50% are present in ALL LIFE, and only 13% are unique to bacteria. - Evo-Devo – the influence of developmental programs

1. Core Processes - Basic biological processes are CONSERVED, and the enzymes that perform them are CONSERVED: - Many enzymes are more than 50% similar in AA sequence in E. coli and H. sapiens, though separated by 2 billion years of divergence. - Of 548 metabolic enzymes in E. coli, 50% are present in ALL LIFE, and only 13% are unique to bacteria. - So the variation and diversity of life is NOT due to changes in metabolic or structural genes... we are all built out of the same stuff, that works the same way at a cellular level. - Evo-Devo – the influence of developmental programs

- Variation is largely due to HOW these processes are REGULATED cell types in humans, all descended from the zygote; all genetically the same. - Best (and most fundamental) examples are HOX genes. These are 'homeotic genes' that produce a variety of transcription factors. The production and localization of these transcription factors are CRITICAL in determining the ‘developmental compartments' of bilaterally symmetrical animals. - Evo-Devo – the influence of developmental programs

- Effects can be profound - 'Master Switches' that initiate downstream cascades that can be very different... like compound or vertebrate eyes. - Evo-Devo – the influence of developmental programs

Sources of VariationAgents of Change Mutation Recombination Selection Drift Mutation Migration Non-Random Mating VARIATION PHYSIOLOGY DEVELOPMENT D. Genetics and Population Genetics 1. Heredity and Variation 2. Genetic Tests/Analyses of Phylogeny 3. Population Genetics 4. The Modern Synthesis 5. Beyond the Synthesis - Peripatric Speciation - Punctuated Equilibrium - Evo-Devo