Today’s Plan: 2/25/11

1. Today’s Plan: 2/25/11 • Bellwork: Go over test/fly counts (30 mins) • Amino Acid Sequence and Evolution Lab (30 mins) • Begin Natural Selection Notes (the rest of class) • Pack/Wrap-up (last few mins of class)

2. Today’s Plan: 2/26/10 • Bellwork: Finish Flies/Compile Class Data (30 mins) • Sexual Selection Video • Pack/Wrap-up (last few mins of class)

3. Today’s Plan: 3/1/10 • Bellwork: Go over lab/Do PTC (15 mins) • AP Lab 8: Population Genetics and Evolution-Part B Genetic Drift (20 mins) • Finish video • Continue Notes-if time • Pack/Wrap-up (last few mins of class)

4. Today’s Plan: 3/2/10 • Bellwork: Settle in/Grab cards (5 mins) • Finish Lab (30 mins) • Continue notes (25 mins) • Pack/Wrap-up (last few mins of class)

5. Today’s Plan: 3/3/10 • Finish Notes (30 mins) • Restriction Mapping Exercise (the rest of class) • Pack/Wrap-up (last few mins of class)

6. Today’s Plan: 3/4/10 • Bellwork: Finish Restriction Mapping (20 mins) • Finish Nat. Sel Notes (20 mins) • HB fun week (the rest of class)

7. Today’s Plan: 3/5/10 • HB Stations-the entire period!

8. Before Natural Selection • Recall that Darwin wasn’t the 1st to think about how species have changed over time • Aristotle’s Scala Naturae grouped species with similar “affinities” together • Linnaeus came up with Binomial Nomenclature and did much classifying based on physical similarity • Cuvier noted that fossils of species differed significantly from more modern forms (proposed the idea of Catastrophism-that changes happened b/c of catastrophic events, and not gradually) • Lamarck suggested that use/disuse and will could change an organism’s body to fit the environment (he thought that acquired traits were heritable) • Malthus also discussed population limits • Darwin bred pigeons for various traits (artificial selection) • Recall that besides thinking about species change, others before Darwin worked with how the planet changed • Hutton proposed that geologic features were the result of gradual changes that are still occurring today • Lyell took this a step further and proposed his principle of Uniformitarianism-mechanisms of change are constant over time

9. Aristotle proposed that species were organized into a sequence based on increased size and complexity, with humans at the top Humans Figure 24-1 Vertebrates Invertebrates Land plants Green algae Fungi Simple cells

10. Natural Selection • Aka “Descent with Modification” was Darwin’s proposal for how species change over time and was the result of careful ponderance over his Galapagos Island collections • Darwin’s main focus was on adaptations that allowed species to survive better in their environments-finches had beaks adapted to their food source • Recall that while Darwin came up with the idea first, Alfred Russel Wallace also had the same ideal later, with no knowledge of Darwin’s work • The term Natural Selection was coined by Darwin’s friend, T.H. Huxley, who was called “Darwin’s bulldog” because he staunchly defended Darwin’s hypothesis

11. Darwin’s Observations and Inferences • Observations: • Members of a population vary greatly in their traits • Traits are inherited from parents to offspring • All species are capable of producing more offspring than their environment can support • Because of lack of resources, many offspring don’t survive • Inferences (Summary of Natural Selection’s Mechanism): • Individuals whose inherited traits give them a higher probability of surviving and reproducing in an environment tend to leave more offspring (have greater reproductive success) • This inequality means that favorable traits accumulate in populations over multiple generations • Remember: • Populations evolve, individuals don’t • Traits influenced by natural selection must be heritable • Environments are moving targets, so there’s no “perfect” and what’s good in one population isn’t necessarily good in another

12. Current Directly Observable Evidence for Natural Selection • Predation and Coloration in Guppies • Pools of guppies w/high predation produce more drab colored males • There are numerous examples of these “natural experiments” done by scientists • Drug-resistant HIV and other “superbugs” • It’s natural for some viruses or bacteria to be resistant, but when you treat, what’s all that’s left to reproduce? • The Fossil Record • We can see trends in the evolution of species • Anatomical Features • Similar patterns of fetal development • Homology (forelimb picture) • Vestigial structures • Biogeography • Looking at what we think happened to the geographic features of the planet to explain distribution of species (ex: how Pangea’s split allowed us to predict where we’d find certain types of fossils) • Molecular Similarity • Studies of DNA sequence and amino acid sequence can be used to construct “molecular clocks” that give us clues to which organisms diverged from one another, and tells us relatively how long ago the divergance occurred

13. Figure 24-11 EVOLUTION OF DRUG RESISTANCE Lung tissue Bacteria with point mutation in rpoB gene M. tuberculosis 1. Large population of M. tuberculosis bacteria in patient’s lungs makes him sick. 2. Drug therapy begins killing most M. tuberculosis. Patient seems cured and drug therapy is ended. However, a few of the original bacteria had a point mutation that made them resistant to the drug treatment. 4. A second round of drug therapy begins but is ineffective on the drug-resistant bacteria. The patient dies. 3. The mutant cells proliferate, resulting in another major infection of the lungs. The patient becomes sick again.

14. Figure 24-3 50 myo bird tracks 110 myo ammonite shell 20,000 y-old sloth dung

15. Figure 24-9 Humerus Radius and ulna Carpals Metacarpals Phalanges Seal Horse Bird Bat Human Turtle

16. Figure 24-8 Gill pouch Gill pouch Gill pouch Tail Tail Tail Chick House cat Human

17. The human tailbone is a vestigial trait. Figure 24-5 Capuchin monkey tail Human coccyx (used for balance, locomotion) Goose bumps are a vestigial trait. Human goose bumps Erect hair on chimp (insulation, emotional display)

18. Figure 24-7 Gene: Amino acid sequence (single-letter abbreviations): Aniridia (Human) eyeless (Fruit fly) Only six of the 60 amino acids in these sequences are different. The two sequences are 90% identical.

19. Figure 27-7

20. Tree thinking vs. Convergent evolution • In many cases, evolutionary trees are created in order to show how species evolved from common ancestors • Sometimes, this happens b/c of adaptive radiation-when organisms evolve in a variety of directions in order to exploit different aspects of the environment • Occasionally, organisms resemble each other, not because they’re related, but because some characteristics are advantageous regardless of their ancestry • Ex: sugar gliders in Australia look like flying squirrels

21. Adaptive radiations produce star phylogenies. Star phylogeny (a large polytomy) Figure 27-11 Rapid speciation Hawaiian honeycreepers underwent adaptive radiation. Hawaiian silverswords underwent adaptive radiation.

22. Figure 24-15b Darwinian evolution produces a tree of life. Land plants Green algae Bacteria Archaea Vertebrates Fungi Invertebrates The branches on the tree represent populations through time. All of the species have evolved from a common ancestor. None is higher than any other Common ancestor of all species living today

23. Sexual Selection • This is a variation of natural selection where some traits persist, not because they’re advantageous, but because they’re attractive • In some cases, the traits that evolve are disadvantageous, but continue to persist • Intersexual Selection is based on the “female choice” model-the opposite sex chooses a mate • Intrasexual Selection is based on competition within the sex for access to mates or resources that will attract mates • Causes sexual dimorphism (variation between sexes)

24. Beetle Lion Scarlet tanager Figure 25-15 Females Males During the breeding season, males of the beetle Dynastes granti use their elongated horns to fight over females. Male scarlet tanagers use their bright coloration in territorial and courtship displays. Male lions are larger than females lions and have an elaborate ruff of fur called a mane.

25. Males compete to mate with females. Figure 25-14 Variation in reproductive success is high in males. Variation in reproductive success is relatively low in females.

26. The survival of the fittest. . . • Remember, fitness is relative, and “struggle” isn’t always direct conflict. • Depending on which traits are favored, there are 3 ways in which natural selection can influence phenotypic variation • Directional selection-one extreme phenotype is favored • Disruptive selection-both extreme phenotypes are favored • Stabilizing selection-average is favored

27. Figure 25-3 For example, directional selection caused average body size to increase in a cliff swallow population. Directional selection changes the average value of a trait. Normal distribution Original population (N = 2880) Before selection Survivors (N = 1027) Change in average value Low fitness High fitness During selection Change in average value After selection

28. Figure 25-4 Stabilizing selection reduces the amount of variation in a trait. For example, very small and very large babies are the most likely to die, leaving a narrower distribution of birth weights. Normal distribution Mortality Before selection Heavy mortality on extremes High fitness Low fitness Low fitness During selection Reduction in variation After selection

29. Figure 25-5 For example, only juvenile black-bellied seedcrackers that had very long or very short beaks survived long enough to breed. Disruptive selection increases the amount of variation in a trait. Normal distribution Before selection Only the extremes survived Only the extremes survived Low fitness High fitness High fitness During selection Increase in variation After selection

30. Evolution of Populations • This is fueled by genetic variation • For individuals, can be quantified using average heterozygosity (average % of genes for which an individual is heterozygous) • For populations, you can directly compare individual karyotypes or gene sequences from each population • Sometimes, the difference is dramatic, and sometimes the difference is a cline (gradual difference) • This often exists b/c of geographic variation (isolation) • Genetic Variation occurs for 2 reasons • Sexual Reproduction • Mutation is the ultimate source for most new genetic variations. Often these mutations are neutral, but occasionaly, you get an adaptive mutation. The rates at which mutation occurs varies between species.

31. Hardy-Weinberg • Useful for testing whether or not a population is evolving • This is a mathematical model: • p2+2pq+q2=1 • p=frequency of the dominant allele • q=frequency of the recessive allele • When a population is in Hardy-Weinberg equilibrium, the equation works, but when populations are evolving, it is an inequation.

32. If heritable variation… A1A1 A1A1 A1A2 A1A2 Figure 24-10 A1A2 A1A2 A2A2 A2A2 A1A1 A2A2 Color varies among individuals primarily because of differences in their genotype … leads to differential success… A1A1 A1A2 A1A1 A2A2 Birds find and eat many more dark-winged moths than light-winged moths … then evolution results. Allele frequencies have changed in the surviving moths

33. Figure 25-1-1 A NUMERICAL EXAMPLE OF THE HARDY-WEINBERG PRINCIPLE 1. Suppose allele frequencies in the parental generation were 0.7 and 0.3. Allele frequencies in parental generation: Allele A1 = p = 0.7 Allele A2 = q = 0.3 Gene pool (gametes from parent generation) 2. 70% of gametes in the gene pool carry allele A1, and 30% carry allele A2. 3. Pick two gametes at random from the gene pool to form offspring. You have a 70% chance of picking allele A1 and a 30% chance of picking allele A2. A1 A1 A1 A2 A2 A1 A2 A2 0.3 0.3 = 0.09 0.7 0.7 = 0.49 0.7 0.3 = 0.21 0.3 0.7 = 0.21 Offspring q p = pq q p = pq pp = p2 qq = q2 0.21 + 0.21 = 0.42

34. Figure 25-1-2 A NUMERICAL EXAMPLE OF THE HARDY-WEINBERG PRINCIPLE 4. Three genotypes are possible. Calculate the frequencies of these three combinations of alleles. Frequency of A1A1 genotype is p2 = 0.49 Frequency of A1A2 genotype is 2pq = 0.42 Frequency of A2A2 genotype is q2 = 0.49 Offspring 5. When the offspring breed, imagine their gametes entering a gene pool. Calculate the frequencies of the two alleles in this gene pool. 49% of offspring have the A1A1 genotype. All will contribute A1 alleles to the new gene pool. 42% of offspring have the A1 A2 Genotype. Half of their gametes will carry the A1 allele and the other half will carry the A2 allele. 9% of offspring have the A2A2 genotype. All will contribute A2 alleles to the new gene pool. 6. The frequencies of A1 andA2 have not changed from parental to offspring generation. Evolution has not occurred. 1 1 (0.42) + 0.09 = 0.3 (0.42) = 0.7 q = p = 0.49 + Allele frequencies in offspring gene pool 2 2 q = frequency of allele A2 p = frequency of allele A1 Genotype frequencies will be given by p2 : 2 p q : q2 as long as all Hardy-Weinberg assumptions are met.

35. Conditions for Hardy-Weinberg • No mutation • Random Mating • No natural selection • Large population size • No gene flow • Rarely do all of these conditions exist at any given moment, but over time, populations tend to be in equilibrium

36. Altering Gene Frequencies • Genetic Drift-caused by small population size or random changes that make predicting gene frequency difficult. 2 examples: • The founder effect-a small number of individuals are isolated from the larger group and have to reestablish a gene pool • The bottleneck effect-catastrophic incidents drop population size quickly and dramatically • In either case, genetic variation is lost, and harmful alleles can persist • Gene Flow-occurs when genes transfer in and out of populations. Usually, this is negligible unless something causes any of the following factors to change dramatically: • Immigration • Emigration

37. Figure 25-6

38. Lupines colonize sites and form populations. Figure 25-8 Gene flow reduces genetic differences among populations. Year 1: Seed establishes new population Year 2: Gene flow between source population and new population New population New population Source population Source population Seed Gene flow A1A1 A1A1 A1A1 A1A2 A1A2 A1A1 A1A1 A1A2 A1A2 A1A1 A1A2 A1A2 A1A1 A1A1 A1A1 Frequency of A1 = 0.83 Frequency of A1 = 0.90 Frequency of A1 = 0.50 Frequency of A1 = 0.67 Frequency of A2 = 0.50 Frequency of A2 = 0.17 Frequency of A2 = 0.33 Frequency of A2 = 0.10 Initially, allele frequencies are very different Gene flow causes allele frequencies to become more similar

39. Preserving Genetic Variation • Diploidy-Since organisms get 2 copies of each gene, recessive alleles can be preserved • Balancing Selection-occurs when natural selection maintains 2 forms of a trait in a population • The heterozygote advantage-sickle cell disease and malaria symptom resistance • Frequency-Dependent selection-as a phenotype becomes more common, it loses its advantage • Neutral Variation-occurs when mutation has little to no effect on phenotype or on reproductive success

40. Why isn’t there a “perfect” organism • Selection can only act on existing variations (and each intermediate step between phenotypes must be adaptive) • You can’t scrap ancestral anatomy to build something new (see above statement) • Adaptations are often compromises (multifunctionality means you have to choose a primary function. Ex: seals don’t have legs b/c they also swim) • Chance, natural selection, and the environment have to interact

41. Types of evolution • Microevolution-evolution of allele frequencies within gene pools • Macroevolution-patterns of evolution over long time spans (like the emergence of new species)

42. The Biological Species Concept • This is the classic definition of the term “species” put forth by Ernst Mayr • A species is a group of populations whose members interbreed in nature to produce fertile offspring • Species are held together by proximity and interbreeding

43. Making new species • Requires Reproductive isolation-barriers that prevent the production of viable offspring (remember that hybrids can exist, but are sterile: ligers, mules, etc) • Prezygotic barriers-block fertilization • Blocking mating • Blocking the successful completion of mating • Preventing successful fertilization • Postzygotic barriers-prevent a hybrid from mating successfully

44. Types of Prezygotic Mechanisms • Habitat Isolation-2 species occupy different habitats • Temporal Isolation-species breed at different times • Behavioral Isolation-courtship rituals differ • Mechanical Isolation-differences in shape/form prevent mating • Gametic Isolation-the gametes may not be able to fuse

45. Types of postzygotic Mechanisms • Reduced Hybrid viability-parental genes prevent the hybrid’s survival • Reduced Hybrid Fertility-sterility due to inability to produce normal gametes • Hybrid Breakdown-Some hybrids can mate with one another, but their offspring are not viable

46. Limitations of Biological Species • It’s hard to evaluate the reproductive isolation of fossils, nor does it address species that reproduce asexually • Other species definitions • Morphological species concept-characterizes species by body shape and structure (can be applied to sexual and asexual reproducers, however this relies on subjective criteria) • Ecological species concept-characterizes a species based on its ecological niche (also can be applied to sexual and asexual reproducers, and emphasizes the role of disruptive selection in species definition) • Phylogenetic species concept-a species is defined by the smallest group of individuals that share a common ancestor (difficult to deterime the degree of difference required to separate one species from another)

47. Allopatric Speciation • “other country” speciation-occurs when species are geographically isolated • Populations become divided and evolve differently because of different environments, genetic drift, and different mutations • Remember that they’re not different species until they’re reproductively isolated. If the populations are put back together and can still mate, they’re not different species

48. DISPERSAL AND COLONIZATION CAN ISOLATE POPULATIONS. Figure 26-5 Island Continent 1. Start with one continuous population. Then, colonists float to an island on a raft. 2. Island population begins to diverge due to drift and selection. 3. Finish with two populations isolated from one another. VICARIANCE CAN ISOLATE POPULATIONS. River River changes course 1. Start with one continuous population. Then a chance eventoccurs that changes the landscape (river changes course.) 2. Isolated populations begin to diverge due to drift and selection. 3. Finish with two populations isolated from one another.

49. Sympatric Speciation • “same country” speciation-occurs when organisms are in the same area but speciate • Can occur via several mechanisms: • Polyploidy-having an extra set of chromosomes • Autopolyploid-more than 2 sets of chromosomes from a single species (failure of cell division) • Allopolyploid-caused by an extra set of chromosomes via hybridization of 2 species (fertile when mating with one another only) • Habitat Differentiation-when a subpopulation exploits a resource that the rest of the population doesn’t • Sexual Selection-when different groups of females prefer different groups of males

50. Soapberry bugs use their beaks to reach seeds inside fruits. Feeding on the fruit of a nonnative species Feeding on the fruit of a native species Figure 26-7 Nonnative fruits are much smaller than native fruits. Nonnative plant (small fruit) Native plant (large fruit) Evidence for disruptive selection on beak length Long-beaked population growing on native plants Short-beaked population growing on nonnative plants