Today is Wednesday, September 10 th , 2014

1. In This Lesson: Population Evolution (Lesson 2 of 3) Today is Wednesday,September 10th, 2014 Pre-Class: What are three types of selection?

2. Today’s Agenda • Population Evolution • Hardy-Weinberg Equilibrium • Other important dynamics in evolution across a population. • Where is this in my book? • Chapter 23.

3. By the end of the lesson… • You should be able to describe Hardy-Weinberg equilibrium and use its formula to solve problems. • You should be able to identify other dynamics that can occur to populations and how they will affect genetic diversity. • You should be able to explain why places like Hawaii, Australia, and Madagascar have such weird life forms.

4. Quick Genetics Review • Gene: • A segment of DNA that codes for a particular protein. • Allele: • A version of a gene. • We all have the eye color gene, but we have different eye color alleles. • Genotype: • The underlying alleles (homozygous/heterozygous) behind an individuals’ traits. • Phenotype: • The outward manifestation of an individual’s genotype. • In other words, how an individual looks.

5. Quick Genetics Review • Complete Dominance (Simple Inheritance) • Purple flower + white flower = purple flower • Incomplete Dominance • Purple flower + white flower = pink flower • Codominance • Purple flower + white flower = purple/white flower • Multiple Allele Inheritance • More than two traits (eyes: hazel, brown, blue, etc.) • Polygenic Inheritance • More than one gene controls a trait.

6. Quick Genetics Review? • Locus • Where a gene is located within a chromosome. • (it’s a location in the DNA) • Plural: loci

7. Why populations? • We study the evolution of populations because the population is the smallest “unit” that can evolve. • Mutations must be passed on, so evolution doesn’t actually appear in individuals. • Rather, the evolution is between generations. • Evolution is therefore only viewed in aggregate. • So how do you know if a population is evolving?

8. Hardy-Weinberg Theorem • The Hardy-Weinberg Theorem was developed by two separate individuals (independently). • It is a way to determine whether evolution is occurring in a population OR how many individuals exhibit certain genotypes/phenotypes. • If no evolution is occurring, allele frequencies should be unchanging. • Here’s the deal: • Suppose we have a population of… • …Blue-Footed Boobies. http://www.duskyswondersite.com/wp-content/uploads/2010/07/blue-footed-booby-two.jpg

9. Hardy-Weinberg Equilibrium • It’s not true, but for an example let’s also say that blue-footed boobies can either have the dominant allele for blue feet (B) or the recessive allele for green feet (b). • In other words, for feet, there are two possible alleles in the gene pool– all the available alleles in the population. • Now, let’s also say that a particular booby population is not evolving. It is therefore in Hardy-Weinberg equilibrium. • This allows us to make some broad statements about the boo- er, “birds.” https://lh3.googleusercontent.com/-d8McO_hqskg/ULI0QJLMvsI/AAAAAAAAyJM/5DulqEI35Gk/w506-h714/Blue-footed_Booby_Guard.jpg

10. Hardy-Weinberg Equilibrium • Put bio on pause for a second. • If I flip a fair coin, what’s the likelihood of heads? • 50%. • If I flip a fair coin twice, what’s the likelihood of heads both times? • 50% * 50%, or 25%. • Okay, back to bio.

11. Hardy-Weinberg Equilibrium • Suppose, in the entire gene pool for foot color, B (blue) alleles represent 70% of the population. • That means b (green) alleles represent 30% of the population. • Therefore, those numbers should not change generation-to-generation if this population is not evolving. • We can also determine the frequency of genotypes (not just alleles) in the population, but we need a concept or two first.

12. Hardy-Weinberg Equation • To be BB, then, you are 70% likely to get B for the first allele and 70% likely to get B again. • 70% * 70% = 0.72 = 49% • To be bb, it’s 30% the first time and 30% again. • 30% * 30% = 0.32 = 9% • To be Bb, however, you could be 30% or 70% likely for the first allele, and then 70% or 30% for the second allele. • This is trickier.

13. Hardy-Weinberg Equation • Let’s suppose the sperm provides B and the egg provides b: • 70% * 30% = 21%. • Suppose the opposite: • 30% * 70% = 21%. • That’s a total of 42%, so the chance of being Bb is really B * b * 2.

14. Hardy-Weinberg Equation • Therefore, 49% of individuals are BB, 42% are Bb, and 9% are bb. • That adds to 100% - not a coincidence. • That’s just an example. As a formula, the Hardy-Weinberg Equation looks like this: • p2 + 2pq + q2 = 1

15. p2 + 2pq + q2 = 1 • WRITE THIS: • p = frequency of dominant allele • q = frequency of recessive allele • p2 = frequency of homozygous dominant individuals • 2pq = frequency of heterozygous individuals • q2 = frequency of homozygous recessive individuals • Again, what’s the point? • Either to determine if evolution is occurring, or to determine how many individuals exhibit certain traits or have certain genotypes.

16. Wait…what? • What’s the difference between “alleles” and “individuals?” • AKA what’s the difference between “q” and “q2?” • Let’s explain it with an example – eye color. • Suppose you can either have brown eyes (B) or blue eyes (b), and brown eyes are dominant. • I can look at a room of people and determine the frequency of people with blue eyes (that’s q2). • However, I can’t look at the room and determine how many blue alleles are out there (that’d be q). • Some people with brown eyes could be heterozygous, and therefore carry a blue allele without showing it. • This is why we need the equation, and it only works if the population is at equilibrium.

17. Hardy-Weinberg Equation • We’re going to practice, but first, some assumptions of Hardy-Weinberg equilibrium. • To be at H-W equilibrium, a population must: • Not have mutation (no DNA changes). • Have random mating (no sexual selection). • Not have natural selection (no “fitter” genotypes). • Be large (smaller ones fluctuate through genetic drift). • Not have gene flow (no individuals come in or out). • Any violation of these conditions indicates evolution.

18. H-W Practice Problem • The frequency of the “not caring” allele (N) in honey badgers is 95%. • If the population is at Hardy-Weinberg equilibrium, how many honey badgers don’t care in a population of 5000? • If 95% of alleles in the gene pool are N, 5% are n. • p2 + 2pq + q2 = 1. • (0.95)2 + 2(0.95)(0.05) + (0.05)2 = 1 • 90.25% are NN, 9.5% are Nn, 0.25% are nn, or in other words, 90.25% + 9.5% = 99.75% don’t care. • 99.75% of 5000 is 4987 badgers.

19. H-W Practice Problem 2 • This one’s adapted from your textbook (p. 486). • Phenylketonuria (PKU) is a rare disease caused by a recessive allele. It can cause mental disability and other symptoms as a result of being unable to metabolize the amino acid phenylalanine, but is relatively easily treated. • If 1 in 10,000 births in the USA is phenylketonuric, what percent of the population are carriers of the allele?

20. H-W Practice Problem 2 • Okay, this is a bit of a weird one. • First, let’s make sure we can even use Hardy-Weinberg: • Are new PKU mutations being introduced? Nope. • Do people mate with others based on PKU? Nope. • Are people with PKU dying off? Nope. • Is there a large population size? Yep. • Is there gene flow? Yes, but other populations have similar PKU rates. • Proceed.

21. What percent of people are heterozygous (carriers) for PKU? • Since PKU is recessive, q2 represents the frequency of PKU-positive individuals. • q2 = 1/10,000 = 0.0001 • q = √0.0001 = 0.01(1% of all alleles are PKU) • Therefore, the non-PKU dominant allele has a 99% frequency. • p2 + 2pq + q2 = 1 • (0.99)2 + 2(0.99)(0.01) + (0.01)2 = 1 • We care about the highlighted part because those are the carriers. • 2(0.99)(0.01) = 0.0198, or 1.98% of the population carries PKU.

22. H-W Practice Problem 3 • In a population of 1000 Polish Frizzle chickens, 342 have a recessive phenotype for tan feathers. Determine how many chickens are homozygous dominant and heterozygous. • 342 out of 1000 is 34.2%, or 0.342 (q2). • q = 0.585 (√q2). • p = 0.415 (p + q = 1) • p2 = 0.172; 2pq = 0.486; q2 = 0.342. • But! That’s not good enough. They gave us a starting population size (1000 individuals). • So 0.172, or 17.2%, is 172 chickens homozygous dominant. 2pq = 0.486 (or 48.6%) means 486 chickens are heterozygous. http://memberfiles.freewebs.com/00/26/41242600/photos/Diane-Spisak/cwhfriz.JPG

23. Hardy-Weinberg Takeaways • A gene pool is the sum of all the individual alleles (“gene letters”) in a population. • In order to have no evolution, you need the five assumptions of Hardy-Weinberg equilibrium. • If there is no evolution, allele frequencies in the gene pool are unchanging. • When allele changes are in equilibrium, we can estimate genotypes in a population. • If actual numbers show considerable difference from Hardy-Weinberg probabilities, evolution is occurring. • Letters are allele frequencies; terms in the equation are genotype frequencies.

24. Hardy-Weinberg Tips • Because heterozygous individuals “hide” recessive alleles, start your analysis with the homozygous recessive genotype/phenotype. • Frequently, but not always, problems require you to find q2, then q, then p, and then use the Hardy-Weinberg equation. • Keep your allele frequencies as decimals unless percentages are specifically required by the problem.

25. Final Hardy-Weinberg Note • Polymorphism…what’s that? • Think root words! • Poly- = many. • -morph = form. • So polymorphisms are different forms of an organism within a population. • For example, white-handed gibbons can be either black or blond (not related to gender). • That’s a color polymorphism. • There can even be single nucleotide polymorphisms (SNPs), which are when DNA bases change at certain points (loci). http://blogs.ucl.ac.uk/museums/files/2012/05/White-handed-gibbons-showing-colour-morphs.jpg

26. Practice • Let’s first try another way of measuring allele frequencies: • Lab 8 – Population Genetics and Evolution • Followed by: • Hardy-Weinberg Practice Problems (odd numbers)

27. Onward! • Now that that’s done, let’s look at some broad population-level evolutionary trends: • Genetic Drift • Bottleneck Effect • Founder Effect • Gene Flow • Mutations • Natural Selection • Directional Selection • Diversifying Selection • Stabilizing Selection • Sexual Selection

28. Genetic Drift • Genetic drift has occurred when allele frequencies have changed due to chance. • Prevalent in small populations. • Decreases variation and thus adaptability. • Non-biology example: • If you flip a coin 1000 times, what percent of flips will be heads? • About 50%, or maybe slightly more. It’s unlikely to be that far off. • If you flip a coin 5 times, what percent of flips will be heads? • Well, it should be 50%, but with fewer flips it’s not entirely unlikely you could even get 100% heads. Or 0%.

29. Small Populations • So how do populations shrink, leading to genetic drift? • Bottleneck Effect • Disaster, famine, loss of habitat shrinks population. • Importantly, genetic fitness has no correlation with the alleles lost from gene pool. It’s chance only.

30. Bottleneck Effect Case in Point • Cheetahs: • Very small number of alleles in the cheetah gene pool. • Caused by a bottleneck during the last ice age (~10,000 years ago) and more recently from poaching. • Zoo populations and other captive cheetahs must be managed carefully to outcross (avoid inbreeding).

31. Founder Effect • The founder effect occurs when a new population is started with a small group of individuals (founders). • The new gene pool may not resemble the old gene pool. • This frequently leads to microevolution. • This is much like a small sample size in an experiment. • A small group leads to sampling error.

32. About sampling error… • Suppose I wanted to poll the school on which sport we all like the best. • I ask only the football team. • I then conclude that football is our school’s favorite. Fair? • Nope, this is sampling error. • Similarly, if a group of birds settles on an island and starts a new population, but their gene pool does not have the same allele frequency as the “starting” gene pool, we may experience sampling error as the birds all appear “red” for example. • It’s sampling error because we end up with a different gene pool composition from the “previous” gene pool.

33. Founder Effect Example #1 • Amish people have higher-than-average rates of polydactyly (extra digits). • It has nothing to do with being Amish – it’s just that the Amish community was founded by a relatively small group with higher-than-average polydactyly rates. • Since the Amish usually do not reproduce outside the community, the skewed allele frequency is maintained. http://www.whodiscoveredit.com/wp-content/uploads/2010/06/Polydactyly.jpg

34. Founder Effect Example #2 • AIDS • AIDS (caused by HIV – human immunodeficiency virus)has nothing to do with being homosexual, however in the virus’s early days of public awareness, it was considered a “gay disease.” • Why, then, is it so prevalent in the homosexual community? • Because the initial human patient (Patient Zero – likely GaëtanDugas) was homosexual, and most homosexuals don’t suddenly turn heterosexual. GaëtanDugas Patient Zero?

35. Genetic Drift: Alternate Example • Here’s something weird: • We all know DNA can be mutated by UV radiation. • UV radiation doesn’t just harm our DNA. It can also mutate viral DNA. • Some research suggests that UV radiation might cause the mutations that lead to pandemics. • The crazy part? In the 20th century, 6 out of 9 massive flu outbreaks were accompanied by increased sunspot activity – when the sun releases a bunch more radiation than normal. • The acquisition of these novel genes by viruses is known as antigenic drift.

36. Okay, next… • Another population-level pattern in evolution: gene flow. • When a population’s alleles are spread to another population, gene flow has occurred. • For most of human history, for example, people tended to not move very far. • Once modern transportation came about, however, populations that would never have come in contact with one another now are. • When these formerly-isolated groups reproduce, alleles from each “flow” into the other population.

37. Gene Flow Example • GMO Plants • Some of the fear around genetically-modified organisms, plants in this example, is that their pollen, seeds, et cetera, will spread into the wild. • You might say the fear is of GMOGF, or genetically-modified organism gene flow. http://sustainablepulse.com/2013/11/12/spread-of-gm-crops-out-of-control-in-many-countries-breaking-news/#.U8mhoFbqsWY

38. Mutations • Any time DNA is copied or transcribed (to RNA), there are always mistakes. • Many are fixed but some slip through. • About one typo in every billion DNA bases goes uncorrected. • These mutations, over millions of years and coupled with genetic drift and/or natural selection, can ultimately lead to evolution. • They are not always positive. They are random*.

39. *Random Mutations • Recent research suggests that not all mutations are random. • Jumping genes have been documented across the biological world, but they were first found in corn by Barbara McClintock in the 1950s. • When corn plants were stressed by heat or drought, mutation rates soared. Entire genes were moving! • The movements were not random, however. • Genes went certain places significantly more frequently than others and their movement occurred as a result of environmental stimuli.

40. Natural Selection • We’ve covered this one, but obviously natural selection is usually applied at the population level, not just for the individual. • Note that there will never be a “perfect” individual produced through natural selection: • There are historical constraints (like the existence of vestigial structures – old adaptations now unneeded). • Mutations must occur for new and fitter phenotypes to occur than those already in existence. • Adaptations frequently represent compromises. One trait often can’t suit every possible use.

41. Types of Selection • Here’s the thing…selection manifests across a population in a few different ways: • Directional Selection • Diversifying/Disruptive Selection • Stabilizing Selection • Remember, these are responses to selective pressures.

42. Types of Selection Arrows represent selective pressures.

43. Directional Selection • When a population’s genetics shift in one direction toward an extreme phenotype. • Example: Male house sparrow’s black “bibs” are preferred by females. Over time, we would expect the bibs to become bigger and bigger. http://www.sparrowdove.com/wp-content/uploads/2012/07/house_sparrow.jpg

44. Diversifying/Disruptive Selection • When both extremes of a phenotype are preferred over the middle ground. • Example: Oysters. Being relatively light-colored helps blend in with rocks. Being dark-colored helps blend in with shadows. Being medium-colored helps you get eaten. http://bivalves.teacherfriendlyguide.org/index.php?option=com_content&view=article&id=42:types-of-natural-selection&catid=27&Itemid=124

45. Stabilizing Selection • When both extremes of a phenotype are not preferred over the middle ground (being in the middle is best). • Example: Birth weight. Being underweight or a big ol’ baby are not good. A middle-weight infant has the best chance of survival. http://circ.ahajournals.org/content/114/16/1687.figures-only

46. Sexual Selection • Where natural selection is all about being able to survive well enough to reproduce, this one’s about being able to win over the opposite sex. • Sexual selection is a process by which individuals more readily survive to reproduce because they have traits desired by mates. • …sometimes. • I know, we talked about this before. More details now; types and examples on the next slides…

47. Sexual Selection • Intrasexual selection occurs when individuals of the same sex (usually males) compete for the opportunity to mate. • Example: Young male lions that must oust an older male from his pride in order to win the harem. • Example: Buck Fight! • By the way, the male lion’s mane serves as a way to defend against another male’s “neck bite” attempt. http://blog.londolozi.com/wp-content/uploads/2012/02/Pic2.jpg

48. Sexual Selection • Intersexual selection occurs when individuals of the opposite sex select mates based on certain desirable traits. • Example: Female zebra finches that select the males with the reddest beaks and legs, and biggest cheek patches. http://www.mpg.de/663248/zoom.jpeg

49. Sexual Selection Key Points • Sexual selection is a form of non-random mating. • It can lead to sexual dimorphism – when males and females differ visibly. • For intersexual selection, females are using some kind of visual assessment as a proxy for good genes. • “If that stud can keep his beak so red, he must be good at securing food. He’ll be a great father.” http://media-cache-ec0.pinimg.com/236x/8a/55/1e/8a551eee45902d4c2de140f76b5903a5.jpg

50. Balancing Selection • Balancing selection is a form of selection that acts to preserve variation, or in other words, preserve allele variety: • Heterozygote advantage occurs when the heterozygote genotype is favored, thus preserving both alleles. • Example: Cystic Fibrosis has been shown to prevent Cholera. • Frequency-dependent selection is a condition when individuals with uncommon characteristics are favored: • Book example: Scale-eating fish in Lake Tanganyika Africa have mouths facing left or right (not both). • When most scale-eating fish have left-facing mouths, being able to attack from the opposite side is advantageous.