AP Biology Unit 9: Natural Selection Notes Pt. 1

1- How does the concept of descent with modification explain both the unity and diversity of life?

The concept of descent with modification explains both the unity and diversity of life because it states that current species are descendants of ancestral species. This process is also called evolution and is considered a process as well as a pattern. The descent comes from the parents while the modifications are caused by slight diversity within a population. 

2- If you discovered a fossil of an extinct mammal that lived high in the Andes, would you predict that it would more closely resemble present-day mammals that live high in African mountains? Explain your answer

Yes, if I discovered a fossil of an extinct mammal that lived high in the Andes, I would predict that it would resemble present-day mammals that live high in African mountains. The principle of uniformitarianism states that the mechanisms of change are constant over time. Geologists also perceived that change on Earth's surface can result from slow continuous actions still operating today, called gradualism. These two concepts combined support the theory that the extinct mammal resembles present day mammals since both live in high mountainous regions. Although the Andes are in South America while the other mountains are in Africa, the mammals will be similar since they are both adapted to suit the high elevations. Natural selection also states that individuals with certain heritable characteristics survive and reproduce at a higher rate than other individuals. 

3- Look at the figure 22.12 in the Powerpoint. Explain how those mantids demonstrate the three key observations about life (in the ppt) that match between organisms and their environment, unity and diversity.

These mantids demonstrate the three key observations about life that match between organisms and their environment, unity and diversity is descent with modification by natural selection, which explains the adaptations of organisms and the unity and diversity of life. The theory of evolution supports this idea since current species are descendants of ancestral species, and the process is descent with modification where the descent comes from the parents and the modifications are caused by slight diversity within a population. Gradualism is a theory to support this statement since the Earth’s surface can change over time due to slow continuous changes. Uniformitarianism also states that the mechanisms of change are constant over time. Adaptation is also seen since the species that were once the same shifted to favor characteristics that were more fit to the environment that this new species is related to. 

1. The unity of life

2. The diversity of life

3. The match between organisms and their environment

   • Natural selection can cause microevolution (change in allele frequencies), with fitness-increasing alleles becoming more common in the population.

   • Fitness is a measure of reproductive success (how many offspring an organism leaves in the next generation, relative to others in the group).

   • Natural selection can act on traits determined by alternative alleles of a single gene, or on polygenic traits (traits determined by many genes).

   • Natural selection on traits determined by multiple genes may take the form of stabilizing selection, directional selection, or disruptive selection.

     • Stabilizing selection: Intermediate phenotypes have the highest fitness, and the bell curve tends to narrow.

     • Directional selection: One of the extreme phenotypes has the highest fitness. The bell curve shifts towards the more fit phenotype.

     • Disruptive selection: Both extreme phenotypes have a higher fitness than intermediate phenotypes. The bell curve develops two peaks.

     • Write a summary of this article (No less than 6 lines and in your own words)
       Natural selection is the process by which organisms that are adapted or better suited to the environment are chosen over those who are not based on their phenotypes, which are the visible traits of an organism. This can cause microevolution over time, which is the gradual shift in allele frequencies. Those with the high fitness alleles are able to survive and reproduce successfully, which may cause the successful allele to become common in a population. High fitness individuals are more likely to reproduce and pass down this successful trait to their offspring, which gradually leads to more offspring exhibiting this trait, phenotypically. Polygenic traits are controlled by multiple genes in the organism. They often create a bell curve distribution when examined on a histogram. There are three types of selections introduced which are stabilizing selection, directional selection, and disruptive selection. Stabilizing prefers the intermediate phenotypes over the extreme phenotypes, which leads to the bell curve to become more narrow, focused in the center of the population. Directional prefers one of the extremes in a population, which causes the entire bell curve to shift towards either extreme that is preferred. Disruptive rejects the intermediate phenotypes, which causes multiple peaks in the bell graph that are both extremes for the population. 

1- How does evolution account for (a) the similar mammalian forelimbs with different functions shown in the slide of PPT and (b) the similar lifestyle of the two distantly related mammals (sugar glider and flying squirrel)

1. The similar mammalian forelimbs with different functions are accounted for by evolution is because they come from an analogous trait. The common ancestor of all these mammals had a forelimb structure. Depending on the environment that the organisms survived in, they naturally adapted to fit the needs of the species, which caused all of the organisms shown to have common bone functions, but each is adapted to fit the specific needs of the one organism. 

2. The similar lifestyle of the two distantly related mammals is accounted for by the analogous traits. The similar gliding lifestyle of the sugar glider and flying squirrel over time made them have the same cape-like flap that connects their limbs. 

2- The fossil record shows that the dinosaurs originated 200-250 million years ago. Would you expect the geographic distribution of early dinosaur fossils to be brod (on many continents) or narrow (on one or a few continents only)? Explain your answer

I would expect the geographic distribution of early dinosaur fossils to be broad because the continents over time moved to separate locations. Since the continents were once connected in one landmass called Pangea, there would most likely be distribution of early dinosaur fossils to be on many continents. 

If p is the frequency of allele A, use the Hardy-Weinberg equation to predict the frequency of individuals that have at least one A allele.

If p is the frequency of allele A, the frequency of individuals that have at least one A allele is p^2+2pq. 

Allele A frequency is P

Allele a frequency is q

Genotypic frequency is p^2+2pq+q^2

This means that the individual with at least one A allele is p^2+2pq. 

1- In what sense is natural selection more predictable than genetic drift?

Natural selection is more predictable than genetic drift because genetic drift is random and there is no way of determining the gene pool that will remain. However natural selection will choose the individuals who fit the best criteria over time, so there will be more of a certain gene found in the population since it is the unique adaptation to the environment. 

2- Distinguish genetic drift from gene flow in terms of 

1. How they occur and (b) their implications for future genetic variation in a population

2. Gene flow is the movement of individuals between populations. Genetic drift is the process where organisms are randomly selected from a population and have reduced genetic variation.

3. Genetic drift will eventually may lose an allele since they are unnecessary, and are not being used by the population. Gene flow will have increased diversity since they will mix alleles with another population. 

3- Suppose two plant populations exchange pollen and seeds. In  one population, individuals of genotype AA are most common (9000 AA, 900 Aa, 100 aa), while the opposite is true in the other population (100 AA, 900 Aa, 9000 aa). If neither allele has a selective advantage, what will happen over time to the allele and genotype frequencies of these populations?

Over time, the population will most likely have more heterozygous individuals. This is because the genes will mix and give rise to more offspring that are hybrid and carriers. Since carriers have the recessive allele along with the dominant allele. Genetic drift will happen, no favorable allele. The populations will be similar. 

4- What is the relative fitness of a sterile mule? Explain

The relative fitness is zero since a sterile mule is unable to reproduce. They are also unable to pass on their traits due to their inability to create offspring. Therefore their fitness is none. Fitness is the ability to pass on their genes to offspring. 

5- Explain why natural selection is the only evolutionary mechanism that consistently leads to adaptive evolution

Natural selection is the only evolutionary mechanism that consistently leads to adaptive evolution because the habitat selects for the individuals that have mutations to fit the environment best. This means that the offspring will always have the adapted traits, since the only organisms that can consistently reproduce and survive are those who have the certain trait necessary to survive. The selective pressure will choose traits that are the best fit to the env. 

6- Consider a population in which heterozygotes at a certain locus have an extreme phenotype (such as being larger than homozygotes) that confers a selective advantage. Does such a situation represent directional, disruptive, or stabilizing selection? Explain your answer

    Directional selection since the population leads to one extreme phenotype. The larger extreme is at an advantage since they are able to reproduce. Over time, the population will favor those who are larger, so the diagram will shift towards that extreme. 

7- Would individuals who are heterozygous for the sickle-cell allele be selected for or against in a region free from malaria? Explain

    Individuals who are heterozygous for the sickle cell allele will be selected against in a region free from malaria because they are at an advantage only when the region has malaria. They are able to have AA alleles which are susceptible to malaria and aa individuals who have malaria. Aa individuals are immune, but there is no benefit in a region with no malaria. 

1- Write no less than 5 sentences about evidence regarding the common ancestry in eukaryotes.

Evidence that supports common ancestry are membrane bound organelles, linear chromosomes, and genes that contain introns. Membrane bound organelles such as chloroplast and mitochondria are one piece of evidence that supports common ancestry since they have double membranes, ribosomes, circular genomes, and it supports the endosymbiotic theory. The nucleus also is similar since it has linear chromosomes, that also has a nucleolus. Other organelles that have similar structures and functions are the ER, Golgi apparatus, lysosomes and vacuoles. Linear chromosomes are evidence for eukaryotes having a common ancestor. Linear chromosomes are made up of tightly coiled DNA and histone proteins, that are capped with telomeres, found in the nucleus, and have large genomes. Prokaryotes have single circular chromosomes, occur in the cytoplasm and have small genomes. Introns are in all eukaryotes, it doesn't code for proteins and RNA processing removes before protein synthesis. 

2- There are specific segments of the DNA inside the eukaryotic genome which cannot be found in the prokaryotic genome. What is the name of those segments? Can they be considered as an evidence for common ancestry in eukaryotes?

The specific segments of the DNA inside the eukaryotic genome which cannot be found in the prokaryotic genome are called introns. They can be considered evidence for common ancestry in eukaryotes because it doesn't code for proteins and RNA processing removes before protein synthesis. 

3- Explain about the picture in the Lesson Skill practice. (Just about the procedure which is depicted in the picture of the question)

The process is called created recombinant DNA. It is done by taking a plasmid from a bacterial cell. There is also a segment of eukaryotic DNA that is cut out using restriction enzymes to isolate the specific genes. The restriction enzymes are used to cut the plasmid, and by chance, the plasmid becomes a recombinant plasmid, with the specific gene that is desired. 

Choice C is the correct choice in the question. 

4- What are some mechanisms of genetic change?

Evolution is the ongoing process in all living organisms in a changing environment. Genomic changes lead to evolution such as DNA changes, cell  and environmental disruptions. Changes in DNA include gene mutation and chromosomal mutations. Cell division includes sexual reproduction increasing gamete diversity, independent assortment, and crossing over. Environmental disruptions include sudden environmental changes, and changes in allele or gene frequencies in a population. 

5- How can fossil records prove the change in evolution? Your answer should be directly from the video including concepts like Transition fossil.

Fossils records prove the change in evolution since they are a preservation or impression of an organism over time. Strata layers are able to arrange the fossils in the order they were deposited. New fossils mark environmental changes and natural selective pressures can result in changes in the frequency of certain adaptations in a population. Transition fossils can show the evolutionary changes as one group evolves into another group. However, the fossil record is incomplete, and gaps also exist.

6- What could be the reason for increasing the frequency of resistance in a population?

    The reason for increasing the frequency of resistance in a population is natural selection. Mutations may result in resistance, which could be selected for in conditions where the trait is advantageous. This allele frequency may increase over time if the trait continues to provide better fitness to the organism and population.

7- Give some examples of Pathogens’ evolution.

Some examples of pathogens evolution are high mutation rates. Since the mutation rate is high, there is an increased diversity. They evolve and cause emergent diseases. They are also chemically compatible with the host, in a way that they can coevolve, and the presence of the pathogen can even change the phenotype that is selected for or against in the population.

8- Lesson skill practice for the video 7.8 is focused on which concept pertaining to the scientific method? Explain about it using the example in the practice MC question.

    Lesson skill practice for the video 7.8 is focused on testing to see if the experiment is successful or not in the scientific method. This answer is b, which is increasing the number of traits and the number of mice in each treatment group. It is essential to collect all necessary data and a large population is necessary. 

1- (a) Which species concept(s) could you apply to both asexual and sexual species? (b) which would be most useful for identifying species in the field? Explain

1. All of the species concepts could be applied to both asexual and sexual species, with the exception of biological. Considering that asexual organisms all have the same genes, it will not be optimal for the biological species concept. 

2. The most useful for identifying species in the field would be morphological since it relies on the appearance of the organisms, being distinguished by structural features. It is the most simple since it only relies on the organisms and its appearance. 

2- Suppose you are studying two bird species that live in a forest and are not known to interbreed. One species feeds and mates in the treetops and the other on the ground. But in captivity, the birds can interbreed and produce viable, fertile offspring. What type of reproductive barriers most likely keeps these species separate in nature? Explain your answer

The reason these species are kept separate in nature is prezygotic isolation. Considering that they are able to produce viable, fertile offspring in captivity, it is not postzygotic isolation. The type of prezygotic isolation is based on their habitat, since they do not live in the same area of the forest. Different habitat preferences. It is habitat isolation. 

1- The first appearance of free oxygen in the atmosphere likely triggered  a massive wave of extinction among the prokaryotes of the time. Why?

Oxygen is very reactive, so it is toxic to many cells. This is why there was most likely a massive wave of extinction among prokaryotes at the time. They were also unable to adapt to the oxygen because the environment changed largely. Oxygen bonding causes toxic material, and the prokaryotes did not have a method of detoxifying the cell. 

2- What evidence supports the hypothesis that mitochondria preceded plastids in the evolution of eukaryotic cells?

    Plastids such as chloroplast are not found in all eukaryotic cells but mitochondria is found in all organisms. This means that there were first eukaryotes with mitochondria and then some took in chloroplasts through the endosymbiotic theory. It is called serial endosymbiosis, which states that some organelles like mitochondria came into the cell before the chloroplast. The more prevalent an organelle is, the older it was absorbed by the cell. 

3- What would a fossil record of life today look like?

    A fossil record would have many species from currency life that are not endangered. No particular structures other than bones and teeth will become fossils. Only animals with the skeleton would be preserved as a fossil since softer material would deteriorate. Fossils will not have been formed for endangered species because they will not encounter the situation with the necessary conditions for fossilization. 

1- The amino acid sequence of cytochrome c was determined for five different species of vertebrates. The table below shows the number of differences in the sequences between each pair of species

(a) Using the data in the table, create a phylogenetic tree on the template provided to reflect the evolutionary relationships of the organisms. Provide reasoning for the placement on the tree of the species that is least related to the others. Following is the template so draw the same in your notebook and paste the picture here.

The D.polylepis is the outgroup because it has the most amino acid sequence differences, when compared to all of the organisms. The E.africanus and E.ferus are the most closely related, so they branch from the same stem. The G.gallus and A.forsteri are also on the same stem, since they only have 3 amino acid differences. Since E.ferus and D.polylepis have the most amino acid sequence differences of 21 in the entire chart, they must be on completely different ends of the phylogenetic tree. 

(b) Identify whether morphological data or amino acid sequence data are more likely to accurately represent the true evolutionary relationships among the species, and provide reasoning for your answer.

Amino acid sequence data is more likely to accurately represent the true evolutionary relationships because they are concrete evidence to be able to determine the relationship of organisms. However, morphological data is not always accurate. There can be two completely unrelated organisms with no common ancestor, but have similar analogous structures, due to their habitat or niches being similar. Morphology may cause organisms to develop to be similar.

1- Directions: Answers must be in essay form. Outline form is not acceptable. Labeled diagrams may be used to supplement discussion, but in no case will a diagram alone suffice. It is important that you read each question completely before you begin.

Evolution is one of the unifying themes of biology. Evolution involves change in the frequencies of alleles in a population. For a particular genetic locus in a population, the frequency of the recessive allele (a) is 0.4 and the frequency of the dominant allele (A) is 0.6.

(a) What is the frequency of each genotype (AA, Aa, aa) in this population? What is the frequency of the dominant phenotype?

Allele frequency

P+q=1

P=A=0.6

q=a=0.4

Genotype frequency

P^2+2pq+q^1=1

P^2=AA=0.36

2pq=Aa=0.48

q^2=aa=0.16

AA+Aa=0.36+0.48=0.84

The genotype AA frequency is 0.36, and the genotype Aa frequency is 0.48, and the genotype aa frequency is 0.16. Since the allele frequency for A is 0.6 and the allele frequency for a is 0.4, the AA is the A value squared, which is 0.36. The Aa value is 0.48 and the aa value is 0.16. The dominant phenotype is the AA genotype and Aa genotype added together, so it is 0.84. 

(b) How can the Hardy-Weinberg principle of genetic equilibrium be used to determine whether this population is evolving?

The Hardy-Weinberg principle of genetic equilibrium can be used to determine whether the population is evolving since it measures the allele frequencies as well as the genotype frequencies in a given population. In the case that the allele frequency is changing in a population, that means that there is evolution taking place. For the Hardy-Weinberg equilibrium to be reached, there has to be a large population size, isolation, random mating, no mutations, and no natural selection.

(c) Identify a particular environmental change and describe how it might alter allelic frequencies in this population. Explain which condition of the Hardy-Weinberg principle would not be met.

In the case of a small population being isolated geographically such as on an island, this would become the founder's effect. The smaller population that is now isolated has a different genotypic frequency, and allele frequency. In the case that the isolated population has a higher dominant allele frequency, there is a chance that the recessive allele would eventually disappear from the population. This would cause less genetic diversity and would have less of a chance of survival. In this example, the condition that is not met from the Hardy-Weinberg principle is the large population size. In order to have an ecosystem with Hardy-Weinberg equilibrium, there must be a large gene pool, to have the allele frequency constantly remain the same. 

2- Directions: Answers must be in essay form. Outline form is not acceptable. Labeled diagrams may be used to supplement discussion, but in no case will a diagram alone suffice. It is important that you read each question completely before you begin.

Mammalian milk contains antibodies that are produced by the mother's immune system and passed to offspring during feeding. Mammalian milk also contains a sugar (lactose) and may contain proteins (protein A, protein B, and casein), as indicated in the table.

Using the data in the table, construct a cladogram on the template provided to indicate the most likely evolutionary relationships among the different mammals. Indicate on the cladogram where each of the characters most likely arose in the evolutionary process, and justify the placement of the characters on the cladogram.

As lactose and protein A characters are present in all mammals listed in the table, it must be a trait that was developed prior to the common ancestor of the two groups. Therefore, it is placed all the way to the left of the diagram. Two organisms only have these characters, and they are cats and humans, which are located on the bottom branch. The 3 organisms that do have lactose, protein a, protein b, and casein in their milk are cows, horses, and pigs. As these three species contain all characters listed, the newly developed traits in these organisms must be the protein b and casein. Therefore, this trait must have developed after the oldest common ancestor, but before they developed into different species.

1- What is the difference between homologous and analogous structures?

Homologous structures are the same structure in organisms that are shared because they are related with a common ancestor. Analogous structures are not of a shared ancestor, but they come from similar habitats. Since they are from similar environments, they over time develop similar characteristics. 

2- In the following choices, which one cannot be observation or inference on which natural selection is based?

A- There is a heritable variation among individuals

B- poorly adapted individuals never produce offspring.

C- Species produce more offspring that the environment can support

D- Individuals whose characteristics are best suited to the environment generally leave more offspring than those whose characteristics are less well suited.

Explain your answer:This can not be observed or inferred on what natural selection is based. Organisms must have variation for the population to survive. Species can produce more offspring, and individuals who are best suited can leave more offspring with the exhibited favored trait. However, it is impossible to definitely state that poorly adapted individuals will never produce offspring, since their fitness would have to be zero. The individual would have to have a fitness of 0, and most likely be infertile to definitely say that offspring would not be produced for poorly adapted individuals.

2- What did Darwin mean by the phrase; Unity of life?

Darwin meant that all living things have a common ancestor, which leads to the conclusion that living organisms share common heritable structures, such as DNA, RNA and proteins. Since all organisms have a shared ancestor, it is assumed that they also have underlying commonalities. 

3- We should know that individuals do not evolve; populations evolve over time.

4- ln some animals, the ability to hear specific frequencies is

inherited as a simple dominant characteristic. Suppose you found out that

360 out of 1000 of those individual animals could not hear the specific frequencies.

State the frequency of the gene for hearing specific frequencies.

p^2 plus 2pq Hh and HH  ability to hear specific frequencies is dominant : 640 out of 1000

q^2 hh inability to hear specific frequencies is recessive :360 out of 1000 =0.36

q^2=0.36

2pq=2 times 0.4 times 0.6=0.48

p^2=0.4 squared=0.16

q=square root of 0.36=0.6

p=1-0.6=0.4

p+q=1

The frequency of the gene for hearing specific frequencies is p which is the dominant allele. This means that p is 0.4 since using the equation of hardy weinberg, it can be solved.

5- What is gene pool? State in your own words

Gene pool is all of the alleles of a population. This includes dominant and recessive alleles. It is calculated by multiplying 2 times the number of homozygous individuals plus 1 times the number of heterozygous. THis is the same for both dominant and recessive. 

6- Those meadow-larks that have average-sized wings survive severe storms better than those with longer or shorter wings, illustrating

A- the bottleneck effect.

B- disruptive selection.

C- frequency-dependent selection.

D- neutral variation

E- stabilizing selection

Explain your answer: The intermediate phenotype is preferred over the extreme because of the habitat. This causes the graph to peak at the average, where most of the individuals will become centered over time.