Option D: Evolution

1. Option D: Evolution IB Biology HL II March 2008

2. D.1 Origin of Life on Earth Physical conditions Miller and Urey’s experiments Role of RNA Origin of prokaryotes Origin of eukaryotes (endosymbiosis) D.2 Origin of Species Lamarck and acquired characters Darwin-Wallace theory and natural selection Other theories and evidence D.3 Evidence for Evolution Geographical distribution Fossils and dating Biochemical evidence Homologous structures D.4 Human Evolution Classification Physical features of primates Fossil evidence Ecological pressures Bipedalism and brain size Genetic vs. cultural evolution D.5 Neo-Darwinism Mutations and examples Recombination Adaptations Speciation and isolation Gradualism Punctuated equilibrium D.6 The Hardy-Weinberg Principle Calculation of allele, genotype, and phenotype frequencies Conditions of HW equilibrium Outline of Option D See “Syllabus Details” in schedule/resource packet for specific objectives.

3. D.1 Origin of Life on Earth

4. D.1.1 Outline the conditions of pre-biotic Earth, including high temperature, lightning, UV light penetration and a reducing atmosphere • The Earth formed about 4.6 bya • Collisions of material (comets and meteorites) led to the formation of the planet • As the mass increased, gravity and radioactive decay caused the formation of the dense metal core surrounded by the liquid mantle and topped with the solid crust • Cooling of the crust led to the formation of a very hot, dense, reducing atmosphere • “Pre-biotic” Earth • Reducing atmosphere • No oxygen (O2) • Reducing (hydrogen-containing) agents present • hydrogen, water vapor, methane, ammonia, nitrogen, and hydrogen sulfide • High temperatures • High UV light levels • Frequent lightning storms

6. D.1.2 Outline the experiments of Miller and Urey into the origin of organic compounds. • Miller and Urey (1953) • Simulated conditions of early Earth in order to determine whether chemical evolution could occur in “primeval soup” • Sealed water, methane, ammonia, and hydrogen in sterile glass flasks connected by tubing • One flask contained water and another contained a set of electrodes • The water was heated to produce vapor and sparks were produced with the electrodes to simulate lightning • The mixture was allowed to cool and condense and drip back into the first flask to simulate processes likely to have occurred on Earth • This continued for one week, then M & U analyzed the contents to find: • 13 amino acids present (of the 20 that occur naturally) • High concentration of adenine

7. D.1.4 Discuss the possible role of RNA as the first molecule capable of replicating D.1.3 Discuss the hypothesis that the first catalysts responsible for polymerization reactions were clay minerals and RNA • Miller and Urey’s experiments provide a hypothesis for the origin of amino acids and nucleotides • Subsequent experiments produced all 20 amino acids, nucleic acids, sugars, lipids, and nucleoside triphosphates from inorganic compounds How did the compounds combine to form larger polymers? • RNA can act as both a form of genetic material and an enzyme • Rybozymes are short sequences of RNA that can act as enzymes and are capable of • Polymerizing nucleotides using ATP (and are thus capable of replication) • Cleaving chemical bonds, including peptide bonds • Ribosomes (composed of rRNA) are rybozymes • Clay minerals • RNA and other organic compounds adhered to clay particles • Clay exists in very close layers, concentrating amino acids and other monomers in a small area • Metal ions in the clay may have acted as catalysts for dehydration reactions • Clays provide stable environments for polymerization

8. Origin of Membranes All cells are surrounded by membranes, and formation of these was critical in the development of the first cells Closed membrane vesicles can form spontaneously from lipids Due to structure and hydrophobic properties (think about a phospholipid) The first prokaryotes required a genetic mechanism and a membrane enclosure Origin of Prokaryotic Cells Coacervates are like little bundles of organic material surrounded by a hydrophobic layer Protobionts are groups of abiotically produced molecules Probably preceded by coacervates Surrounded by a protein membrane (can form bilayer in the presence of lipids) Maintain fairly constant internal environment Probably the predecessors for the first prokaryotes With RNA, these molecules could replicate and pass on their characteristics D.1.5 Discuss a possible origin of membranes and prokaryotic cells

9. D.1.6 Discuss the endosymbiotic theory for the origin of eukaryotes • Anaerobic prokaryotes eventually developed chlorophyll and a simple form of photosynthesis, leading to the accumulation of oxygen in the atmosphere and aerobic life • Review—differences between prokaryotes and eukaryotes? • Endosymbiotic theory: chloroplasts and mitochondria are derived from free-living prokaryotes that were engulfed by larger prokaryotes but survived inside the cytoplasm • Mitochondria probably evolved from proteobacteria • Chloroplasts probably evolved from cyanobacteria • Evidence for endosymbiotic theory • Both mitochondria and chloroplasts contain DNA that is different from nuclear DNA and similar to bacterial DNA • Both are surrounded by double-membranes similar to prokaryotic membranes • New organelles are formed by a process similar to binary fission • Internal structure of chloroplasts similar to structure of cyanobacteria • Analysis of nuclear DNA in plants suggests that some genes were incorporated from DNA of the chloroplast • Ribosomes are found within mitochondria and chloroplasts and resemble bacterial ribosomes

10. Endosymbiosis

11. D.2 Origin of Species

12. D.2.1 Outline Lamarck’s theory of evolution by the inheritance of acquired characteristicsD.2.2 Discuss the mechanism of, and lack of evidence for, the inheritance of acquired characteristics • Lamarck (1809) proposed a theory based on the inheritance of acquired characteristics • Acquired characters are those that are acquired during an organism’s lifetime • For example, if muscles are used, they grow stronger • Giraffe example: The ancestors of modern giraffes had short necks. According to Lamark’s theory, the giraffes had to stretch up to the trees to reach their food, so their necks lengthened slightly. The next generation inherited the lengthened necks and stretched more. After many generations, long-necked giraffes came into existence. • No significant cases of acquired characters have been found, and Lamarck’s theory does not fit in with the principles of inheritance—no mechanism exists for the acquired character to cause a mutation in the gene controlling the trait

13. D.2.3 Explain the Darwin-Wallace theory of evolution by natural selection • Darwin and Wallace proposed the theory of evolution by natural selection in 1858 • Evolution is the accumulation of changes in the heritable characteristics of a population • A series of observations and deductions led to the development of this theory

14. Other theories for the origin of species exist… Spontaneous Generation Life arises from non-life Pasteur’s experiments disproved theory Special creation God created life Panspermia Organic material arrived on Earth from space This theory has not been scientifically excluded In a 2001 study, experiments simulated interstellar dust clouds containing ammonia, CO2, and methanol mixed with ice crystals at low temperatures and high levels of UV Organic compounds were formed The scientific method cannot be used to test these Modern experiments will never determine with certainty what happened billions of years ago Experiments (such as Miller & Urey’s) determine what is possible in conditions known to have existed D.2.4 Discuss other theories for the origin of species including special creation and panspermia D.2.5 Discuss the evidence for all these theories and the applicability of the scientific method for further investigation

15. D.3 Evidence for Evolution

16. Types of Evidence There are three basic types of evidence for a common ancestor: • Geographic • Similar organisms exist in areas of the world known to have been connected by land at some point in the Earth’s history • Biochemical • Comparisons of DNA and amino acid sequences reveal similarities among all organisms • Paleontological • The fossil record provides information about organisms that lived in the past—some of which are similar to modern organisms When all available evidence is compiled, phylogenies can be constructed.

17. D.3.1 Describe the evidence for evolution as shown by the geographical distribution of living organisms, including the distribution of placental, marsupial and monotreme mammals.

18. Evolution of monotremes, marsupials, and placental mammals • The groups of mammals • Monotremes • Egg-laying mammals • Examples: platypus and some anteaters • Marsupials • Young carried in “pouch” until fully developed • Examples: kangaroo, koala • Placental mammals • Young carried in uterus until fully developed and nourished by placenta • Examples: humans, dogs, horses • Looking at the way in which continents have drifted over time and examining the fossils in them we can map out the development of different sorts of mammals • Monotremes and marsupials developed in Gondwanaland (about 165mya) • Native mammals in Australia are monotremes and marsupials (due to geographical isolation) • Placental mammals developed later (about 135mya) and replaced almost all of the monotremes and marsupials in the other continents • Mammal groups were geographically isolated and evolved independently • Similar organisms evolved to fit similar niches on different continents

19. Role of the Bering Land Bridge • Asia and North America are only separated by a small, shallow sea—the Bering Straight • The sea level has risen and fallen several times through the Earth’s history, allowing several periods of exposure of a “land bridge” between the continents • About 1,000 miles long at longest point • Allowed land mammals to pass • Believed to have enabled human migration to the Americas from Asia about 25,000 years ago (some disagreement on time frame) • Both continents have similar mammal life • Ancestors of cows, sheep, horses, rhinos and other mammals may have evolved in Asia and migrated to North America • Migration from North America to Asia likely occurred as well—horses and camels originated in N.A. and spread to S.A. and Asia

20. D.3.2 Outline how remains of past living organisms have been preserved Ancient bird skull preserved in peat • Fossils are the preserved remains of an organism • The remains of organisms can be preserved in many ways… • They may be trapped in resins (sap) which become amber • They may be frozen • They may be trapped in acid peat (partially decomposed organic material), which prevents decay • The may be trapped in sediments that become rock Insect preserved in amber Scallop fossils preserved in sediment

21. D.3.4 Define half-life and D.3.5 Deduce the approximate age of materials based on a simple decay curve for a radioisotope • Half-life: the time for half of the radioactive atoms in a sample to undergo decay • Radioactive decay takes place at a constant rate independent of physical conditions • Decay depends only on time! Questions: • After three half-lives, what fraction of the original radioactive isotope remains in a sample? • A piece of fossilized wood has a carbon14 radioactivity that is 1/4 that of new wood. The half-life of carbon14 is 5730 years. How old is the fossilized wood?

22. D.3.3 Outline the method for dating rocks and fossils using radioisotopes, with reference to 14C and 40K • Radioisotopes are radioactive isotopes of chemical elements • Isotopes of an element have the same number of protons but differing numbers of neutrons, giving them different masses • The amount of a radioisotope in a preserved sample can be measured and, the decay curve of the isotope can be used to determine the age of the sample • 14C and 40K are commonly used in dating • Radiocarbon dating using 14C • The percentage of surviving 14C atoms in a sample is measured • The half-life of 14C is 5730 years, so it is most useful in dating fossils between 1000 and 100,000 years of age • Can be used to date organic material produced by living organisms; as long as the organism is living, it contains the same proportion of 14C as the atmosphere. When it dies, the 14C begins to decay into 14N • Potassium-argon dating using 40K • 40K decays into 40Ar over time • The proportions of both are measured • The half-life of 40K is 1250 million years, so it is useful in dating samples older than 100,000 years • Can be used to date rocks and mineral-containing samples

23. D.3.6 Outline the paleontological evidence for evolution using one example • Paleontological evidence for evolution is provided in the fossil record • The fossil record is the sum total of fossils discovered to date • Fossils are organized based on age and the similarities of structures • It is incomplete—why? Example of paleontological evidence: • Acanthostega may be a “missing link” between terrestrial and aquatic organisms • Characteristics: • Eight digits on each “hand” and “foot” linked by webbing • Lungs as well as gills • Limbs not particularly well-adapted to bearing weight • Primarily aquatic

24. D.3.7 Explain the biochemical evidence provided by the universality of DNA and protein structures for the common ancestry of living organisms • Remember the idea of the “Universal Genetic Code”… all organisms utilize the standard genetic code • All have DNA • DNA is transcribed into RNA • RNA is translated into chains of amino acids based on the genetic code… • Exceptions: • Small deviations from the code in the protein synthesis of yeast and some protozoans • It is thought that since all organisms have a VERY similar (if not identical) code, then the genetic code was present in the first common ancestor • Analysis of biomolecules including proteins provides further evidence for common descent • The protein cytochrome c is an electron carrier that is required for aerobic respiration • It is a complex molecule found in plants, animals, unicellular aerobes • Provides strong evidence that all aerobic organisms descended from a common ancestor—it is very unlikely that unrelated organisms would have independently evolved the ability to produce this complex enzyme

25. D.3.8 Explain how variations in specific molecules can indicate phylogeny • Researchers have the capability of determining the sequence of amino acids in a protein or nucleotides in a molecule of DNA • Comparisons of these sequences can be made between organisms to determine how closely they are related • Remember the amino acid comparison of primates we did last year? • Humans and chimpanzees have identical amino acid sequences in both alpha and beta hemoglobin • Orangutans differ from humans in two amino acids • Humans are more closely related to _______ than _______

26. βhemoglobin comparison The number of “changes” is the number of differences in the amino acid sequence of the protein between the divergent groups.

27. Evolutionary Clock D.3.9 Discuss how biochemical variations can be used as an evolutionary clock • The more closely related the species, the fewer variations in amino acid or DNA sequence, and the shorter period of time since divergence • More distant relatives have more variations and diverged earlier • The idea of an evolutionary clock allows us to organize the species based on when divergence occurred • Assumptions: • The rate of change of any protein or DNA sequence is approximately constant over time • The rate of DNA replication is constant over time and across all species • So, there is some uncertainty, but the approximate time since divergence can be determined based on the number of differences in a DNA sequence

28. D.3.10 Explain the evidence for evolution provided by homologous anatomical structures, including vertebrate embryos and the pentadactyl limb • Homologous character: a structural or biochemical trait which is shared between two or more organisms because of a common ancestor • Examples: • vertebral columns in vertebrates • pentadactyl limbs • vertebrate embryos

29. Pentadactyl (5-digit) Limbs X • Nearly all vertebrates have a pentadactyl limb • Structure is similar in all, despite different uses for the limb

30. Comparison of vertebrate embryos

31. Galapagos Finches The 1977 drought in the Galapagos led to a 4% increase in beak size of finch species Geospiza fortis—afterwards the average beak was short and wide; the diet consisted of large, hard seeds El Niño event in 1982-3 caused an increase in precipitation and changed the vegetation—fruits became smaller and softer Finch population grew exponentially due to rains and increase in food, then fell By 1987 average beak was longer and narrower than pre-1982 Ladybugs The majority of ladybugs in industrial (high smog) areas of Europe in 1960 had a black phenotype black absorbs more light, and so the black bugs have an advantage staying warm when sunlight levels are low After 1960 as smog levels decreased the proportion of black ladybugs decreased proportionally By 1980, both smog and black butterflies reached constant low level Post-1980, the majority of ladybugs were red red coloring warns predators that they are poisonous and is more effective at improving survival when light levels are normal D.3.11 Outline two modern examples of observed evolution. One example must be the changes to the size and shape of the beaks of Galapagos finches.

32. D.4 Human Evolution

33. D.4.1 State the full classification of human beings from kingdom to sub-species

34. D.4.2 Describe the major physical features, such as adaptations for tree life, that define humans as primates Characteristics of all members of the Primate order: • Hands and feet • Able to grasp, with long fingers and an opposable thumb • Sensitive fingers • Limbs • Highly mobile arms and hands (able to rotate) • Vision • Stereoscopic = able to see objects in 3 dimensions • Forward-facing eyes on flattened face, giving overlapping fields of view • Enhanced depth-perception and hand-eye coordination • Olfaction • Reduced sense of smell, allowing flatter face • Skull • Enlarged and expanded for cerebrum (site of perception, imagination, thought, judgment, decision) • Modified for upright posture • Brain • Increased sensory/motor areas • Few offspring • Social dependency Arboreal Adaptations

35. D.4.3 Discuss the anatomical and biochemical evidence which suggests that humans are a bipedal and neotenous species of African ape that spread to colonize new areas • Humans and apes… • care for their young for a long time • have delayed puberty • have dexterous hands and similar hips and muscles • We may be neotenous – evolved to retain juvenile ape characteristics • Humans show more physical similarities with young apes than mature ones • 98% of human and chimpanzee DNA is exactly the same • Fossils have been found of intermediate species in the evolution of humans from apes.

36. D.4.4 Outline the trends illustrated by the fossils of Australopithecus and Homo • See chart • Over time, trends show… • Increasing skull size with respect to body mass • Increasing brain capacity • Posture becoming more erect • Increasing degree of bipedalism • Decreased size of neck muscle • Forward movement of foramen magnum (site in the skull through which the spinal cord passes) • Jaw becoming more V-shaped and less U-shaped • Canines and molars reduced in size due to changes in diet • Increasing ability to grasp with hands

37. D.4.5 Discuss the possible ecology of these species and the ecological changes that may have prompted their origin • Climate changes: • Eastern Africa became drier with thin woodlands instead of forests (about 5 mya) • Led to evolution of bipedal ground-adapted species that could move on land for long distances and gather scattered food • Later (about 2.5 mya) Africa became much cooler and drier • Mostly savanna and grasslands • May have prompted the evolution of the Homo genus which used tools and group work to hunt large animals for food

38. D.4.6 Discuss the incompleteness of the fossil record and the resulting uncertainties with respect to human evolution • As previously discussed, the fossil record provides one type of evidence for change over time • Criticisms of using fossils in support of evolution include the lack of continuous record, many gaps or “missing links” • Possible explanations for incompleteness of fossil record: • Punctuated equilibrium • Intermediate organisms would exist in few numbers, making fossilization less likely • Decomposition or consumption of dead organisms by scavengers • Relatively rare fossilization of soft-bodied organisms • Relatively rare conditions favorable for fossilization • Fossilized organisms infrequently unearthed

39. D.4.7 Discuss the origin and consequences of bipedalism and increase in brain size • Increased brain size • Greater ability to adapt to different environmental circumstances • Tool-making • Construction of shelters • Use of fire • Transmission of cultural behaviors between generations • Longer gestation and care of young after birth during period of brain development • Critical period from birth to two years • Bipedalism • Led to shorter arms, longer and stronger legs • Knee allows leg to fully straighten • Rigid foot with shorter, non-opposable toes

40. D.4.8 Outline the difference between genetic and cultural evolution D.4.9 Discuss the relative importance of genetic and cultural evolution in the evolution of humans • Genetic evolution • Genetic changes that have occurred during hominid evolution; differences observed between individuals of different racial or cultural groups • Cultural evolution • Changes in the actions and ideas of society, including transmission of these from one generation to the next • Typically involves writings, spoken word, and images • Unique to human societies! • Hominization: “becoming human” • Involved concurrent physical and social changes • Example: changes in sexual behavior (due to physical changes) led to formation of monogamous pairs which lived together with their children; led to formation of communities which shared food and resources

41. “Becoming Human” www.becominghuman.org Evidence Anatomy Lineages Culture