1. Genes and Their Evolution: Population Genetics
Chapter 4
So far we’ve looked at DNA, the cell, and the individual person with punnett square inheritance. Now we’ll look at the genetics of populations or species.

2. Population
A population is a group of individuals of the same species who share a geographic area and usually mate within the group
The total genetic variation of that population is the gene pool
The number of times different genes or alleles occur is the frequency
And evolution is change in allele frequency over generations
When we think of living things we think of the entire organism. An organism has 2 alleles for each trait (ex HH for right-handed). We must also learn to see things not as individual beings but as pools of just their alleles (this is a gene pool).
This will be important for the Hardy-Weinberg equation we’ll learn this chapter

3. Species h
We only look at reproductive populations of organisms. This is important because to be called a species, organisms must be able to mate and have fertile offspring
Are these different species?
Lion and tiger
Horse and donkey
Dog and wolf
The biological definition of a species is a group of animals that can mate and produce fertile offspring.
Practice this definition of these animals listed.
Lions live in Africa, tigers in Asia. They never meet in the wild and can only sometimes reproduce if humans do artificial insemination. Their offspring are sterile.  different species
Horses and donkeys can mate and produce a mule, but mules are sterile  different species
Dogs and wolves are identical in their DNA and can produce fertile offspring  same species

4. Species
When reproductive isolation occurs, this means that two populations are kept from mating h
If enough time passes, these two groups will become two different species
This is allopatric speciation
Example: two groups of beetles get separated by a river. Over time, enough differences arise that they become different species and would not be able to mate again
So how do we get new species? There has to be reproductive isolation, or something that keeps two groups from mating. After a long enough time separated, they will become different in their genes and will eventually become different species.

5. The river separated one population
The river separated one population. It just so happened that the beetles on one side were a little browner and on the other side they were a little greener. After many generations of being separated, even if the river dried up, there are now 2 separate beetle species: the green beetle and the brown beetle. The reproductive isolating mechanism in this example is the river.

6. Population Genetics This is the study of changes in genetic material
More specifically, the change in allele frequency
allele= different versions of genes
Frequency= how often they occur
Microevolution: small-scale; happens in a short period of time
Macroevolution: large-scale; occurs over many generations; speciation
Population genetics lets us look at how often (frequency) characteristics (alleles) are found in a population. We can see changes in allele frequency over generations, which is our definition of evolution.
There are different types of evolution. Darwin described microevolution, which is also called Gradualism. However, the fossil record shows that some animals (shark) have lived for millions of years virtually unchanged. Gould and Eldrege then created the idea of Punctuated Equilibrium, which means that if an animals is successful in its environment it won’t change until the environment changes. This causes long periods of equilibrium (no change) and then sudden (punctuated) change (evolution). These can be extinction events or speciation.

7. Different Views of Evolution
Darwin thought evolution was small changes accumulating over long periods of time
This is phyletic gradualism
Gould and Eldredge said evolution could have long periods of no or minor change, interrupted by sudden change, such as speciation or extinction
This is punctuated equilibrium h

8. The Two Views

9. More Types of Evolution
We know evolution shows common ancestry
When two related species share phenotypic traits because of common ancestry, this is parallel evolution
All primates have eyes close together and nails
When distantly related species develop similar adaptations to similar environments, this is convergent evolution
Crocodyles and cats have tails because they walk on 4 legs
Chickens, bees, and bats all have wings to fly
When we look at animals’ features, sometimes features are similar due to a common evolutionary ancestry, and sometimes it is just coincidence.
In parallel evolution animals have the same features because they are closely related and have a common ancestor. Example: primates have nails because all primates share a common ancestor.
With convergent evolution, animals have features not because of a shared ancestor but because they just both happened to adapt to their environment in the same way. Example: lots of animals have wings, but you wouldn’t say a cockroach and a pigeon are closely related just because they can both fly.

10. Parallel Evolution
When determining the type of evolution, look not only at one feature but at many aspects of the animals, including their DNA, intelligence, reproduction, etc.
All apes (seen in the picture) are closely related because they all lack tails. But, they also have similar skeletons, large brains, Y-5 molars, and only one offspring at a time that they spend many years raising.

11. Convergent Evolution
These animals all have wings but they are all very different. A bat is a mammal and has fur, feeds its young with milk, and has the same bones in its arm as any other mammal (a cat, a whale, a human, etc.).
Birds have hollow bones, lay eggs and have feathers.
Insects have no bones and have larvae…etc.
These animals are not closely related but just have a similar adaptation for flying.

12. Population Genetics
We focus on the idea of change over time, especially in the frequency of alleles
Example: we are looking at a trait, which we will call R
The two alleles are R and r (dominant and recessive)
Generation 1 has 50% R and 50% r
When we come back and look at Generation 2, the frequency has changed to 40% R and 60% r
This shows evolution
Population genetics looks at the evolution of an entire population. Remember that evolution is change in allele frequency over generations. Allele = different versions of a gene. Frequency = number of times you see that allele in a population.
Example: Eye color.
Alleles: brown, blue, green, hazel
Allele frequency of a population is how many people have each eye color

13. Population Genetics
We need evidence that evolution is occurring, and we do this by looking at the frequencies of alleles in populations
If they do not change, there is no evolution
If they do change, there is evolution
If something does not change at all, it is in equilibrium. So, equilibrium is the opposite of evolution.

14. Intro to Hardy-Weinberg h
If the frequency never changed, the population would be in equilibrium
So, there is an equation to test for equilibrium
If the numbers don’t change = equilibrium = no evolution
If they do change = no equilibrium = evolution
We can never prove something in science. There is always the chance that we find new information to change our theories.
However you can disprove something and show that it does not happen.
Hardy and Weinberg wanted to show evidence of evolution so they created an equation that tested equilibrium. If they disproved equilibrium, then they were basically showing evidence of evolution.

15. Hardy-Weinberg h
Godfrey Hardy and Wilhelm Weinberg developed a way to test for equilibrium in allele frequency
In order for equilibrium to exist, you must have:
No mutations
No natural selection
Completely random mating
An infinitely large population
Each organism having the exact same number of offspring
Would this ever occur in nature?
Look at the criteria for having equilibrium in a population. Would these circumstances every occur in nature? No!
Mutations are random and we can’t control them.
Nature of course influences every living thing.
Random mating is literally walking around and mating with any member of your species you bump into, without any preference.
We can count how many animals are in a population.
Not every organism has the exact same number of offspring or the same number of offspring survive.

16. Hardy-Weinberg Don’t let the equation intimidate you!
Focus on what each part stands for and follow the steps
There will only be a couple of questions of this on the midterm
Remember that the point of the equation is to show evolution by showing change.
You will learn how to use the equation to find the frequencies of alleles in a population.
They idea is that you would then go back to that population later and do the equation again. If any of the numbers differed at all, you’ve shown change in allele frequency over generations, which is evolution.
You have a handout on Canvas that shows you in detail how to do each step of the equation. There are also websites and videos on your module.

17. Hardy-Weinberg Here is the equation:
p2 + 2pq + q2 = 1.00 (100% of population)
p2 = all individuals who are homozygous dominant
q2 = all individuals who are homozygous recessive
2pq = all individuals who are heterozygous
Second part of equation: p + q = 1.00
p = the dominant allele
q = the recessive allele
I always write both equations at the top of my paper so I can keep tabs on which frequencies I’ve found. Like this:
p2 + 2pq + q2 = p + q = 1.00
The first equation deals with individuals but remember we also want to look at the pool of alleles in a population, or the gene pool. That is the second equation.

18. Hardy-Weinberg
Please use the document titled “HW Explanation” on Canvas to see details and how to solve a problem

19. Example
A population of snails has a trait for either spotted or striped shells. Striped shells are dominant. Out of 100 snails, 16 have spotted shells.
Find the frequencies of SS, Ss, and ss
The next year we return and find that 25 out of 100 have spotted shells. Why?
My populations are always magically 100 animals. 
The numbers I use should be easy! If you get a bunch of decimals you’re doing the math wrong!
Follow the steps; they will always be in the same order:
Steps:
I ALWAYS GIVE YOU STEP ONE.
You can tell who is homozygous recessive (ss) in a population just by looking at the population. In this snail population, I count 16 snails with the spotted shells. Can we tell of the reamining striped snails who is homozygous dominant (SS) and who is heterozygous (Ss)? No, because they look exactly the same.
So, step one, write down q2 = whatever number is given in the problem, written as a decimal.
q2 = 0.16
2. This is the “mathiest” part of the equation. We want to go from looking at actual organisms (snails in this case) to just the recessive allele. So, we jump to the second part of the equation to find q.
To do this, take q2 and square root it. q2 = 0.16… √0.16 = 0.40 (use a calculator to do this so the math is right!)
So q = 0.40
This means that there are 16 spotted snails (q2) but the recessive allele itself (q) is found in 40% (0.40) of the population. This is because the hetrozygous snails (2pq) are carrying a hidden recessive in their genotype (Ss)
3. Now we know that the recessive allele (q) is 40% of the population. We can use logic to see that the dominant allele (p) must be 60% (0.60) because these must add up to 100%.
p+q = 1.00
p = 1.00
p must = 0.60
4. Now that we know p, we can use it to find p2 in the first equation. p2 is just p x p. (Or put in p value (0.60) and hit the square button (x2) on the calculator). p2 = .36.
Let’s plug all these into our equation to see where we’re at:
p pq + q2 = p + q = 1.00
5. All we need now is 2pq. Add p2 + q2. This equals Think of it this way: you have .52 cents in your pocket but you need a dollar to buy a snack. How many more cents do you need?
1.00 – 0.52 = 0.48
So, 2pq = 0.48
This means there are 36 striped snails in the population that are completely dominant (SS); there are 48 snails that are striped but carry a hidden spotted recessive allele (Ss). There are 16 snails that are spotted and completely recessive (ss).
If you went back the next year (generation 2) and you saw that 25 snails were now spotted, if you did the equation again you would get different numbers, SO YOU WOULD HAVE MATHEMATICAL EVIDENCE THAT EVOLUTOIN OCCURRED 

20. Sources of Evolution h
So, evolution is change over time, but how do these changes arise?
4 sources:
Mutation
Natural Selection
Gene Flow
Genetic Drift
OK, moving on!
There are four ways evolution occurs. These four sources are very important for understanding how evolution takes place.

21. Mutation h Small errors in DNA, especially during replication
Most go unnoticed. Some can be harmful and some beneficial
They occur at random
They are the only source of new genetic variation in a population
Not all mutations are negative. Please note that mutations are the only source of new genetic variation in a population
The other three sources just shuffle around existing alleles, but mutation can create new alleles

22. Mutations Point mutation: a single base is changed h
ATCGGTC  ATCGGTA
Frameshift mutation: caused by a deletion or insertion of genetic information; causes codons to be read incorrectly
Parts of chromosomes can be mutated, or entire chromosomes can be mutated
Kleinfelter’s Syndrome: males have extra sex chromosome: XXY
Trisomy 21: person has extra 21st chromosome. AKA Down Syndrome h
A point mutation is when one single DNA base (and A,T,C, or G) is changed.
In a frameshift mutation, one base is deleted or added; all the bases after this error will be moved up or down, causing all of those bases to also be incorrect.
Example: Think of DNA as our language:
Correct DNA: THE FAT CAT ATE RAT
Point Mutation: THE HAT CAT ATE RAT (only one base is changed)
Frameshift Mutation (insertion): THE FHA TCA TAT ERA T (everything after the insertion of “H” is now wrong)

24. Mutation Example
A point mutation changes the hemoglobin blood cell in some people
This causes sickle-cell anemia. Their blood cells are deformed and cannot carry enough oxygen
It is often fatal
Why do so many sub-Saharan Africans have this mutation?
Sickle-cell anemia is caused by a point mutation. You would expect nature to select against this mutation because it causes a person’s blood cells to be sickle-shaped and not carry enough oxygen. However, we find this mutation in high frequencies in Africa, which means that nature is selecting for this mutation? Why?

25. Mutation Example
A point mutation changes the hemoglobin blood cell in some people
This causes sickle-cell anemia. Their blood cells are deformed and cannot carry enough oxygen
It is often fatal
Why do so many sub-Saharan Africans have this mutation?
Because it protects against malaria, the #1 killer in Africa
If a person is heterozygous for the sickle-cell trait, he/she will have enough normal blood to carry oxygen and enough affected blood to kill malaria parasites that enter body h
Watch:
If a person has full sickle-cell, then they may die from lack of oxygen.
If a person has normal blood, they may die from the #1 killer in Africa, the malaria parasite
BUT if they are heterozygous, they have just enough oxygen to be healthy and if malaria enters their blood, the mutation causes the cell to collapse and kill it, meaning these people are immune to malaria
Life lesson: nature is awesome and things we may think are bad end up being good for us

26. Malaria and Sickle-Cell h
The malaria/sickle-cell relationship is a balanced polymorphism h
Two seemingly negative things cancel each other out and are positive for a person’s health
The heterozygous trait balances one negative trait with another, giving the person a better chance of surviving
This is selected for, and is also an example of natural selection

27. Natural Selection h
Survival of those best adapted to current environmental pressures
Based on the idea of fitness: number of offspring produced in a lifetime
Has nothing to do with strength, speed, or intelligence
Is just how good are you at surviving and making babies
We don’t really say “survival of the fittest” because people don’t know what fitness really means.
It means how many babies you’ve had!
The goal of life is to 1) not die and 2) make babies. Fitness is how good you are at that.

28. Who has better fitness? Male, Harvard degree, $500,000 salary, no kids
Male, high school drop out, unemployed, 7 kids
If the guy on the left fell off that cliff, he would have no fitness.
If the guy on the right had a heart attack lifting the remote, he has passed his genes down 7 times so he is really fit!

29. Types of Natural Selection h
Directional: selection shifts in one direction
Example: large beak sizes in finches when droughts leave only hard food to eat
There are 3 “shapes” of selection.
The first is directional: the middle of the graph is the average; in this type of selection the average is moved higher or lower due to a change in the environment.

30. Types of Natural Selection h
Stabilizing: selection favors the average and is against the extremes
Example: birth weight. Babies in the normal range survive more than premature ones or obese ones
Stabilizing selection means being average is very good, so the average is selected for and the extremes are selected against and die off.

31. Types of Natural Selection h
Disruptive: selection favors the extremes, and against the average. Leads to speciation
Example: beetles are reproductively isolated until 2 new species are created.
Disruptive selection is when the average is not good and is not selected for and the extremes are good and are selected for. After enough time this can cause a speciation event.

32. Example of Natural Selection
In Great Britain, most moths were light colored to blend in to the environment
With the Industrial Revolution in the 1800s, the smog and soot produced changed the environment to be darker
Did the light moths have the advantage still?
No, they were eaten and darker moths survived. This changed allele frequencies

34. Practical Example #2 (from lecture 2)
Can you see viruses or bacteria?
They are alive and, like everything else, they evolve
Can evolve in a matter of hours
This is why not taking antibiotics/medication correctly leads to drug resistance

35. When people do not take medication correctly
Yellow = weak bacteria
Purple = medium bacteria
Red = strong bacteria

36. When people do not take medication correctly
Yellow = weak bacteria
Purple = medium bacteria
Red = strong bacteria

37. Genetic Drift
This is an over-representation or an under-representation of traits because of a small sample size h
Example: In a class of 25 people, I find that 20 have Type B blood, 3 have Type O and 2 have Type AB
Does this accurately reflect the frequency of blood types in the entire human population?
What about Type A?
The third source of evolution happens when a small group breaks off of the larger population. Whatever traits the group members happen to have is all they will ever have, if they do not rejoin the population.
Example: we go on a field trip to the Galapagos islands and become stranded there. It just so happens that in our group there are only two people with brown eyes and 17 with green eyes. There are no people with blue eyes. Is this an accurate representation of the frequencies in the larger population? No!

38. Genetic Drift
This shows why large populations are healthier…there is more variation
Endogamous groups only breed within their population
Exogamous groups breed with members outside their population
Which is better for variation and health?
Remember, variation is the key to success and survival!

39. 2 Types of Genetic Drift h
1. Founder Effect: a small group breaks off from the original population and forms its own group
Will that small group accurately reflect all the variation of the original population?
Tay Sachs: genetic defects that are exaggerated due to founder effect and genetic drift
2. Population Bottleneck: when a population is reduced drastically, there is not enough variation to keep it going
Can cause extinction
This is what happens to endangered species
Be sure to know these examples of genetic drift.
Founder Effect: A group of Dutch people came to America and settled in Pennsylvania. Due to cultural and religious reasons they were endogamous. They also, by chance, had a high percentage of carriers for Tay Sachs, which is fatal at birth. So, sadly, many babies were born that didn’t survive.
Population Bottleneck: Foundation behind endangered species. When a population is drastically reduced, there is not enough variation to keep it going. The magic number for this is around 500. Under 500 members really means extinction.

40. Genetic Drift: Founder Effect
A small group of original population creates new population
Some traits will be over-represented
Some traits will be lost
Is this “rare” gene rare anymore in the new founder population?

41. Genetic Drift: Bottleneck
Severe reduction in population
Loss of variation
What is the pigs’ variation like now? What happens if there is a bad mutation on the recessive allele? Extinction. 

42. Gene Flow Movement of genes and mixture of them through breeding h
Not only migration: have to mate as well, in order to add variation
So it is migration and nonrandom mating
If there is no gene flow between 2 populations, they could evolve into 2 different species
With global travel and more open-mindedness in cultural ideals, our human gene pool has had a large increase in gene flow and variation
The last source happens when one population migrates and encounters another population of the same species and mates with them. This merges two gene pools and creates more variation.

43. Gene Flow Variation is the key to success! Why is inbreeding so bad?
It limits variation in the gene pool and can increase harmful mutations

44. Review Questions
What is the difference between microevolution and macroevolution?
How does the Hardy-Weinberg equation show that evolution occurs?
What are the sources of evolution? What are some examples?