1. The Evolution Of Populations

2. Evolution and Variation
Microevolution- small scale evolution; change in allele frequencies in a population over generations.
Discrete Characters- classified on an either-or basis
Quantitative Characters- vary along a continuum
Average Heterozygosity- (gene variability) the average percent of loci that are heterozygous.
Nucleotide Variability- comparing DNA sequences of two individuals
Geographic Variation- differences in genetic composition of separate populations.
Populations evolve, not its individual members. (ie: galapagos finches- beak shape for hard seeds during drought)
Microevolution- caused by natural selection, genetic drift, and gene flow. Only natural selection consistently improves the match between organisms and their environment, thus bringing about the type of change we refer to as adaptive evolution.
Some phenotypic variation is not heritable and is a result of environmental influences and lifestyle (ie: bodybuilders- they don’t pass on their muscles to offspring). Only the genetic part of variation can have evolutionary consequences.
Some geographic variation occur as a cline, a graded change in a character along a geographic axis. (ie: genes in fish that codes for an enzyme that allows them to swim faster in cold water because it is a cold water catalyst. On the Atlantic coast in Maine, the allele frequency for this enzyme is high, but as you move down to Georgia where it is warmer, you begin to see other forms of this enzyme). Clines such as this probably result from natural selection.
Characters that vary within a population may be discrete or quantitative. Discrete characters such as the purple or white flower colors of Mendel’s pea plants can be classified on an either-or basis (either purple or white)./ Many discrete characters are determined by a single gene locus with different alleles that produce distinct phenotypes. However most heritable variation influences quantitative characters, which vary along a continuum within a population. Heritable quantitative variation usually results form the influence of two or more genes on a single phenotypic character.
Whether considering discrete or quantitative characters, biologists can measure genetic variation in a population at both the whole-gene level (gene variability) and the molecular level of DNA (nucleotide variability). Gene variability can be quantified as the average heterozygosity. Consider the fruit fly which has about 13,700 genes in its genome. On average, a fruit fly is heterozygous for about 1,920 of its loci (14%) and homozygous for all the rest. This means that it has an average heterozygosity of 14%.
Nucleotide variability is measured by comparing the DNA sequences of two individuals in the population and then averaging the data from many such comparisons. The genome of D. melanogaster has about 180 million nucleotides and the sequences of any two fruit flies differ on average by approximately 1.8 million (1% ) of their nucleotides. Thus the nucleotide variability of D. melanogaster populations is about 1%.
Gene variability (or average heterozygosity) tends to be greater than nucleotide variability because a gene can consist of thousands of nucleotides. A difference at only one of these nucleotides can be sufficient to make two alleles of that gene different and thereby increasing gene variability.

3. Mutation Mutation- the ultimate source of new alleles
Point mutations- a change in one base in a gene
Neutral and Beneficial Mutations
Mutations Rates
Plants/Animals- 1/100,000 genes per generation
Prokaryotes- fewer mutations, shorter generation span, more genetic variation
Viruses- more mutations, shorter generation span, RNA genome with fewer repair mechanisms
Mutations result from a change in the nucleotide sequence of an organism’s DNA. Organisms reflect thousands of generations of past selection, and hence their phenotypes generally provide a close match to their environment.
*Are mutations passed on to offspring? (yes, if they are in cells that produce gametes)
Point mutation- a change in one base in a gene- can have a significant effect on the phenotype, as in sickle-cell disease (GUA is now GAA). How might a point mutation not have an affect on the protein? (A change in one base pair may still code for the same amino acid). *Come up with an example. Even if there is a change in the amino acid, this may not affect the protein’s shape and function. In some cases, a mutant allele may actually make its bearer better suited to the environment, enhancing reproductive success.
Chromosomal changes that delete, disrupt, or rearrange many loci at once are almost certain to be harmful. However, when these mutations leave genes intact, their effect on organisms may be neutral. (If they rearranged introns, which do not code for genetic information). In rare cases, chromosomal rearrangements may even be beneficial if they link DNA in a way that results in a positive effect. Duplications of large chromosome segments may often be harmful, but the duplication of smaller pieces of DNA may not be. Gene duplications that do not have severe effects can persist over generations, allowing mutations to accumulate. The result is an expanded genome with new loci that may take on new functions. (if you are duplicating the coding part of DNA. You may also be able to mutate previously un-useful parts of DNA and make it something that codes for something, this could code for something good or bad). This can be seen in olfactory genes. Early mammals carried a single gene for detecting odors, which has been duplicated many times and now mice have 1300 olfactory receptor genes. Humans have lost about 60% of olfactory receptor genes. *Why would this be? (Mice are hunters and rely on their sense of smell more than humans do!)
Plants and animals have relatively low mutation rats. Prokaryotes are lower, but they have shorter lifespans so mutations can quickly generate genetic variation. Same is true for viruses regarding short lifespan. They however have a higher mutation rate because they have a RNA genome rather than a typical DNA genome. RNA has a higher mutation rate because of lack of repair mechanisms in host cells. For this reason, it is unlikely that a single-drug treatment would ever be effective against HIV because mutant forms of the virus are resistant to the drugs. The most effective HIV treatments have been drug cocktails that combine several medications. It is less likely that multiple mutations would resist all the drugs in a short time period.

4. Gene Pools and Allele Frequency
Population- a group of individuals of the same species that live in the same area and interbreed, producing fertile offspring.
Gene pool- all of the alleles for all the loci in all individuals of the population.
Fixed- only one allele exists for a particular locus and all individuals are homozygous for that allele
Gene pool- used to characterize a population’s genetic makeup. If only one allele exists for a particular locus in a population, that allele is said to be fixed in the gene pool, and all individuals are homozygous for that allele. *What problem does this pose for reproduction? How could you increase genetic variation?

5. Hardy-Weinberg Principle
H-W Equilibrium describes a constant frequency of alleles within a gene pool.
p2 + 2pq + q2 = 1
where p2 and q2 represent the frequencies of the homozygous genotypes and 2pq represents the frequency of the heterozygous genotype
If you observe no change at a loci across a population, you can conclude that the gene pool of that population is not evolving and is therefore at Hardy Weinberg equilibrium. The Hardy Weinberg Principle states that the frequencies of alleles and genotypes in a population will remain constant from generation to generation, provided that only Mendelian segregation and recombination of alleles are at work. Such a gene pool is said to be in Hardy Weinberg Equilibrium.
Imagine that alleles for a given locus for all of the individuals in a population could be mixed together in a large bin. We can think of this bin as holding the population’s gene pool for that locus. “Reproduction” occurs by selecting alleles at random from the bin. By viewing reproduction as a random selection of alleles from the bin (the gene pool), we are in effect assuming that mating occurs at random- that is, that all male-female matings are equally likely.
CR= red flower, CW=red flower, CRCW=pink flower *Which inheritance pattern is this? (incomplete dominance)
P = 0.8, q = 0.2 (p is dominant allele, q is recessive) Thus a bin holding 1000 alleles for 500 wildflowers will have 800 CR alleles and 200 CW alleles. The frequency of CWCW=0.2x0.2=0.04 or 4%. The frequency of a CRCR=0.8x0.8=0.64 or 64%. The frequency of a heterozygote is 0.8x x0.8= =0.32 or 32%. As you can see, these frequencies add up to 1, or 100% regardless of whether or not the population is in hardy weinberg equilibrium. Hardy Weinberg is only achieved if the ACTUAL frequencies are what they are predicted to be by this equation. As long as random mating continues to occur, the population should remain constant, or in HW equilibrium because the allele frequencies should not change (much like the frequencies of aces or jacks do not change after repeated shuffling of a deck of cards).
Alleles in the population
Frequencies of alleles
Gametes produced
p = frequency of
Each egg:
Each sperm:
CR allele = 0.8
q = frequency of
80%
chance
20%
chance
80%
chance
20%
chance
CW allele = 0.2

6. Hardy-Weinberg Assumptions
No mutations
Random mating
No natural selection
Extremely large population size
No gene flow
*Departure from any of these conditions usually results in evolutionary change.
This can result in the deletion or duplication of an entire gene- mutations modify the gene pool
if individuals mate preferentially within a subset of the population, such as their close relatives (inbreeding) random mixing of gametes does not occur and genotype frequencies change.
differences in the survival and reproductive success of individuals carrying different genotypes can alter allele frequencies
the smaller the population, the more likely it is that allele frequencies will fluctuate by chance from one generation to the next (genetic drift)
by moving alleles into or out of populations, gene flow can alter allele frequencies.
Departure from any of these conditions usually results in evolutionary change which is common in natural populations. One would think that any
evolutionary change would not allow for HWE, but this is not true. Rather, the population can be evolving at some loci yet simultaneously in HWE
at another loci. Also, some populations evolve so slowly that their evolution is hard to distinguish form a nonevolving population.
*Aside from accounting for evolution, the equation also has medical applications such as estimating the percentage of a population carrying the allele for an inherited disease. For example, PKU, a metabolic disorder that results from homozygosity for a recessive allele, occurs in about 1/10,000 babies born in the US. Left untreated, PKU results in mental retardation and other problems although symptoms can be lessened with a phenylalanine free diet. (warnings on diet cokes)
To apply the HWE, we must assume that PKU meets these assumptions. Few mutations in PKU, inbreeding not likely in US, selection only occurs against rare homozygotes (and only then if dietary restrictions are not followed), US population is very large, and the frequency of PKU around the world is similar to that of the US. If all of these assumptions hold true, then the number of people born with PKU will be equivalent to q2. (q= frequency of recessive alleles, q squared = frequency of homozygotes)
SOLVE PROBLEM:
PKU occurs in 1/10,000 births, so it has a probability of = q2. Solving for q, we get The frequency of the dominant allele is p=1-q=1-0.01= The number of carriers is then 2pq=2(0.99)(0.01)= (about 2% of the population). Remember this is an approximation, or expected value, although observed values may be different.

7. Practice Hardy-Weinberg Problem
For a locus with two alleles (A and a) in a population at risk from an infections neurodegenerative disease, 16 people had genotype AA, 92 had genotype Aa, and 12 had genotype aa. Use the Hardy-Weinberg equation to determine whether this population appears to be evolving.

8. mechanisms that alter allele frequency
Natural selection
Leads to adaptive radiation
Genetic drift
Founder Effect
Bottleneck Effect
Gene flow
These violate the conditions for hardy-weinberg equilibrium and therefore alter allele frequencies directly, causing the most evolutionary change.
Fruit flies select for an allele that confers resistance to several insecticides, including DDT. Early in the 1930s, none of the flies in laboratory strains had this allele, likely because DDT wasn’t used. 30 years later, in the 60’s, (after 20 years of DDT usage) the allele frequency is 37%. This allele either arose from mutation, or was very rare in the 30s. Either way, it has now been selected for. By consistently favoring some alleles over others, natural selection can cause adaptive evolution (evolution that results in a better match between organisms and their environment).
See next slide. Genetic drift- chance events that cause allele frequencies to fluctuate unpredictably from one generation to the next. It tends to reduce genetic variation through the loss of alleles. (the smaller the sample, the greater the chance of deviation from a predicted result).
Founder Effect- occurs when a few individuals become isolated from a larger population. This smaller group may establish a new population whose gene pool and allele frequencies differs from the source population. (ie: a storm blows members of a population to a new island. This is an example of genetic drift because the allele frequencies are altered). The founder effect probably accounts for the relatively high frequency of certain inherited disorders among isolated human populations. (Tay Sachs increased probabilities in certain populations).
Bottleneck Effect- (see image next slide)- a sudden change in the environment such as a fire or flood, may drastically reduce the size of a population

9. Generation 1 Generation 2 Generation 3 p (frequency of CR) = 0.7
Fig
CR CR
CR CR
CW CW
CR CR
CR CR
CR CW
CR CW
CR CR
CR CR
CW CW
CR CR
CR CR
CR CR
CW CW
CR CR
CR CW
CR CW
CR CR
CR CR
CR CR
CR CW
CW CW
CR CR
CR CR
CR CR
CR CW
CR CW
CR CW
CR CR
CR CR
Generation 1
Generation 2
Generation 3
p (frequency of CR) = 0.7
p = 0.5
p = 1.0
q (frequency of CW ) = 0.3
q = 0.5
q = 0.0

10. Original population Bottlenecking event Surviving population
Fig. 23-9
Bottleneck Effect
By chance alone, certain alleles, represented here by blue marbles, may become overrepresented among the survivors. Ongoing genetic drift is likely to have substantial effects on the gene pool until the population becomes large enough that chance events have less of an effect. Even after a bottleneck population recovers in size, it may still have low levels of genetic variation for a long period of time- a legacy of the genetic drift hat occurred when the population was small.
Sometimes human actions can also create a bottleneck for certain species. Ex: the greater prairie chicken: loss of prairie habitat (habitat was converted to farmland) caused a severe reduction in the population of greater prairie chickens in Illinois. The surviving birds had low levels of genetic variation, and only 50% of their eggs hatched. When comparing allele counts of birds before and after the bottleneck, you can see a loss of alleles at several different loci. Researchers introduced greater prairie chickens from population in other states and were successful in introducing new alleles and increasing the egg hatch rate to 90%
Original
population
Bottlenecking
event
Surviving
population

11. Effects of Genetic Drift
Genetic drift is significant in small populations
Genetic drift causes allele frequencies to change at random
Genetic drift can lead to a loss of genetic variation within populations
Genetic drift can cause harmful alleles to become fixed
It alters alleles frequencies more and has a greater effect in small populations
Allele frequencies could increase one year and decrease another year, thus it is not predictable. Unlike natural selection, genetic drift works at random
Some alleles can be eliminated from the population (as seen in flowers) this may effect how well a population can adapt to change and could ultimately lead to the extinction of a population
Because genetic drift works at random, it can increase or decrease beneficial or detrimental alleles, this may result in a fixed population, such as that of the chickens, also evident in the flowers diagram

12. mechanisms that alter allele frequency
Natural selection
Leads to adaptive radiation
Genetic drift
Founder Effect
Bottleneck Effect
Gene flow
the transfer of alleles into or out of a population due to the movement of fertile individuals or their gametes.
These violate the conditions for hardy-weinberg equilibrium and therefore alter allele frequencies directly, causing the most evolutionary change.
Gene Flow- the transfer of alleles into or out of a population due to the movement of fertile individuals or their gametes
Refers to how alleles are exchanged among populations (ie: insects pollinating flowers in one population with pollen from plants in another population). Gene flow thereby tends to reduce the genetic differences between populations. If it is extensive enough, gene flow can result in neighboring populations combining into a single population with a common gene pool.
Gene flow can also result in populations not fully adapting to their environments (because of the constant influx of new alleles)
Sometimes beneficial alleles are transferred very widely. Insecticide resistant alleles in a specific mosquito (arose by mutation). In original population, these alleles increased because of natural selection. As a result of mating with other populations, the alleles were also transmitted to new populations, and again selected for by natural selection. On the other hand, it can also cause the frequency of a beneficial allele to decrease.
*mutations can introduce new alleles into a population, but because it can occur at a higher rate than mutation, it is more likely to alter alleles frequencies directly. Natural selection can then select for or against it.

13. Natural Selection and Adaptive Evolution
Relative Fitness- the contribution an individual makes to the gene pool of the next generation, relative to the contributions of other individuals.
Natural selection is the only evolutionary mechanism that continually leads to adaptive evolution.
Evolution by natural selection is a blend of chance and “sorting”- chance in the creating of new genetic variations (originally by mutation) and sorting as natural selection favors some alleles over others. Because of this sorting effect, only natural selection consistently increases the frequencies of alleles that provide reproductive advantage and thus leads to adaptive evolution.
Relative fitness basically implies the same thing as “survival of the fittest” but is a more scientific term. It is an adaptive advantage.
Remember that natural selection acts on the organism as a whole. The whole organism however is a combination of its phenotypes, therefore selection acts more on the phenotype, rather than the genotype (Aa and AA are the same). The genotype is affected indirectly though, because the genotype determines the phenotype.
Adaptations arise gradually over time as natural selection increase the frequencies of alleles that enhance survival and reproduction. As the proportion of individuals that have favorable traits increases, the match between a species and its environment improves; that is, adaptive evolution occurs. The physical and biological components of an organism’s environment may change over time. As a result, what constitutes a “good match” between an organism and its evolutionary environment can be a moving target, making adaptive evolution a continuous dynamic process.
Natural selection is the only evolutionary mechanism that continually leads to adaptive evolution
**What is the relative fitness of a sterile mule? Explain?

14. Directional Selection
Original population
Frequency of individuals
Occurs when conditions favor individuals exhibiting one extreme of a phenotypic range, thereby shifting the frequency curve for the phenotypic character in one direction or another.
Phenotypes (fur color)
Is common when a population’s environment changes or when members of a population migrate to a new (and different) habitat. For instance, fossil evidence indicates that the average size of black bears in Europe increase during each frigid glacial period, only to decrease again during warmer interglacial periods. Larger bears, with a smaller surface-to-volume ration, are better at conserving body heat and surviving periods of extreme cold.
*include discussion of fig (captions)
Original population
Evolved population
(a) Directional selection

15. Fig b
Disruptive Selection
Original population
Frequency of individuals
Occurs when conditions favor individuals at both extremes of a phenotypic range over individuals with intermediate phenotypes.
Phenotypes (fur color)
One example is a population of black-bellied seedcracker finches in Cameroon whose members display two distinctly different beak sizes. Small-billed birds feed mainly on soft seeds, whereas large-billed birds specialize in cracking hard seeds. It appears that birds with intermediate-sized bills are relatively inefficient at cracking both types of seeds and thus have lower relative fitness.
Evolved population
(b) Disruptive selection

16. Stabilizing Selection
Fig c
Stabilizing Selection
Original population
Frequency of individuals
Acts against both extreme phenotypes and favors intermediate variants.
Phenotypes (fur color)
This mode of selection reduces variation and tends to maintain the status quo for a particular phenotypic character. (ie: the birth weights of most human babies lie in the range of pounds, but babies who are either much smaller or much larger suffer higher rates of mortality).
Regardless of the mode of selection, the basic mechanism remains the same. Selection favors individuals whose heritable phenotypic traits provide higher reproductive success than do the traits of other individuals.
Evolved population
(c) Stabilizing selection

17. Intrasexual Selection
a form of natural selection in which individuals with certain inherited characteristics are more likely than other individuals to obtain mates.
Sexual Dimorphism
marked differences between the two sexes in secondary sexual characteristics, which are not directly associated with reproduction or survival.
Intrasexual Selection
Selection within the same sex. Individuals of one sex compete directly for mates of the opposite sex.
Intersexual Selection
“mate choice”- individuals of one sex (usually females) are choosy in selecting their mates from the other sex.
Described by Darwin
These distinctions include differences in size, color, ornamentation, and behavior.
In many species, intrasexual selection occurs among males. For example, a single male may patrol a group of females and prevent other males from mating with them. The patrolling male may defend his status by defeating smaller, weaker, or less fierce males in combat. More often, this male is the psychological victor in ritualized displays that discourage would-be competitors but do not risk injury that would reduce his own fitness.
In many cases, the females choice depends on the showiness of the male’s appearance or behavior. One thing that Darwin noted is that the showiness may not seem adaptive in any other way, and may in fact pose some risk. For example, bright plummage may make male birds more visible to predators. But if such characteristics help a male gain a mate, and if this benefit outweigh the risk from predation, then both the bright plummage and the female preference for it will be reinforced because they enhance overall reproductive success.
How do female preferences for certain male characteristics evolve in the first place? One hypothesis is that females prefer male traits that are
correlated with “good genes.” If the trait preferred by females is indicative of a male’s overall genetic quality, both the male trait and female
preference for it should increase in frequency.

18. Preservation of Genetic Variation
Diploidy
Hides genetic variation from selection in the form of recessive alleles
Balancing Selection
Occurs when natural selection maintains two or more forms in a population.
Heterozygote Advantage
Individuals who are heterozygous at a particular locus have greater fitness than do both kinds of homozygotes
Frequency-Dependent Selection
The fitness of a phenotype declines if it becomes too common in the population
Neutral Variation
Has no selective advantage or disadvantage
Diploidy hides genetic variation from selection in the form of recessive alleles. Recessive alleles that are less favorable than their dominant counterparts, or even harmful in the current environment, can persist by propagation in heterozygous individuals. This latent variation is exposed to natural selection only when both parents carry the same recessive allele and two copies end up in the same zygote. This happens only rarely if the frequency of the recessive allele is very low. Heterozygote protection maintains a huge pool of alleles that might not be favored under present conditions, but which could bring new benefits if the environment changes.
Includes heterozygote advantage and frequency-dependent selection
Ex: sickle cell for malaria- discuss how it is different over populations (here vs. w. africa)
Left mouthed or right mouthed feature of a specific type of fish. Each year selection favors whichever phenotype is least common. As a result, the frequency of left and right mouthed fish oscillates over time and balancing selection keeps the frequency of each phenotype close to 50%. This is an example of simple Mendelian inheritance.
Nucleotide differences on noncoding region of DNA appears to have no advantage or disadvantage because they have little or no effect on protein function and reproductive fitness. Over time, the frequencies of alleles that are not affected by natural selection may increase or decrease as a result of genetic drift.

19. Why Natural Selection Cannot Fashion Perfect Organisms
Selection can only act on existing variations.
Evolution is limited by historical constraints.
Adaptations are often compromises
Chance, natural selection, and the environment interact.
Natural selection favors only the fittest phenotypes among those currently in the population, which may not be the ideal traits. New advantageous alleles do not arise on demand.
Each species has a legacy of descent with modification from ancestral forms. Evolution does not scrap the ancestral anatomy and build each new complex structure from scratch; rather evolution co-opts existing structures and adapts them to new situations. It operates on the traits and organism already has. Thus in birds, and bats, an existing pair of limbs took on new functions for flight as these organisms evolved from walking ancestors.
We have adaptations to do many things. Our flexible limbs allow us to do many things but also makes us prone to sprains, torn ligaments, and dislocations. Structural reinforcement has been compromised for agility. Seals live on rocks and in ocean. It could benefit from feet for the rocks, but then wouldn’t be able to swim well in the ocean.
Chance events can affect the subsequent evolutionary history of populations. (ie: when a storm blows insects and organisms to a new island, it doesn’t necessarily mean that it is a place best suited for their survival)
With these four constraints, evolution cannot craft perfect organisms. Natural selection operates on a “better than” basis. We can see this
evidence in the many imperfections of organisms

20. Exit Slip
Of all the mutations that occur in a population, why do only a small fraction become widespread among the population’s members?
If a population stopped reproducing sexually (but still reproduced asexually), how would its genetic variation be affected over time? Explain.