Big+Idea+1+Evolution


 * Big Idea 1: The process of evolution drives the diversity and unity of life.

Evolution is a change in the genetic makeup of a population over time, with natural selection its major driving mechanism. Darwin’s theory, which is supported by evidence from many scientific disciplines, states that inheritable variations occur in individuals in a population. Due to competition for limited resources, individuals with more favorable variations or phenotypes are more likely to survive and produce more offspring, thus passing traits to future generations.

In addition to the process of natural selection, naturally occurring catastrophic and human induced events as well as random __#|environmental__ changes can result in alteration in the gene pools of populations. Small populations are especially sensitive to these forces. A diverse gene pool is vital for the survival of species because environmental conditions change. Mutations in DNA and recombinations during meiosis are sources of variation. Human-directed processes also result in new genes and combinations of alleles that confer new phenotypes. Mathematical approaches are used to calculate changes in allele frequency, providing evidence for the occurrence of evolution in a population.

Scientific evidence supports the idea that both speciation and extinction have occurred throughout Earth’s history and that life continues to evolve within a changing environment, thus explaining the diversity of life. New species arise when two populations diverge from a common ancestor and become reproductively isolated. Shared conserved core processes and genomic analysis support the idea that all organisms — Archaea, Bacteria, and Eukarya, both extant and extinct — are linked by lines of descent from common ancestry. Elements that are conserved across all three domains are DNA and RNA as carriers of genetic information, a universal genetic code and many metabolic pathways. Phylogenetic trees graphically model evolutionary history and “descent with modification.” However, some organisms and viruses are able to transfer genetic information horizontally.

The process of evolution explains the diversity and unity of life, but an explanation about the //origin// of life is less clear. Experimental models support the idea that chemical and physical processes on primitive Earth could have produced complex molecules and very simple cells. Under laboratory conditions, complex polymers and self-replicating molecules can assemble spontaneously; thus, the first genetic material may not have been DNA, but short sequences of self-replicating RNA that may have served as templates for polypeptide synthesis. Protobiontic formation was most likely followed by the evolution of several primitive groups of bacteria that used various means of obtaining energy. Mutually beneficial associations among ancient bacteria are thought to have given rise to eukaryotic cells.


 * __ **Evidence for Evolution** __ **:** added by Maddy Harmon (concept 22.3 pages 460-465)

Essential Knowledge 1.A.4: Biological evolution is supported by scientific evidence from many disciplines including mathematics.

I've notice a lot of the questions and essays in the Ap practice tests/tests we already take ask for examples and explananations, so I decided to include a list of scientific evidence for evolution, each with a link to a specific example. 1: Direct observation of Evolutionary Change- This is actually tracking change in a population over time and looking for the environmental pressure that selected for it.

[] (Peppered Moth Example explained in a brittish accent)

2: Fossil Record- By being able to trace a line of ancestry back thousands of years scientists can __#|apply__ direct observation to a species that otherwise evolved too slowly to be observed.

[] (Nova clip on Fossil exapmples of the transition from fish to semi-aquatic animals to land animals)

3: Homology- This is when creatures share underlying similarities in their characteristics or structures(even if those structures serve different purposes __#|now__) because they evolved from a common ancestor.

[] (breif explanation with whales __#|fins__ and human arms as the examples, and a way to remember the difference between homologous and analogous)

4: Convergent Evolution- Similar evolutionary solutions to similar environmental pressures that don't indicated a close relatedness.

[] (Very nonscientific but it serves as a good visual for convergent evolution, similar evironmental pressures, and their similar solutions between species)

5: Biogeography- Species tend to be more closely related to the other species in their region than to species in far away places.

[] (explains how living on an island does not make a species more similar to species on other far away islands than it does to species on their own mainland.)

and finally Mr. Anderson sums it up: []


 * __**Genetic variation can be produced in sexual life cycles, contributing to evolution (Test book: Page 103)**:__ done by Bunyad Bhatti

Essential Knowledge 1.A.1: Natural selection is a major mechanism of evolution. Essential Knowledge 3C2: Biological systems have multiple processes that increase genetic variation.

An explanation of the processes used when answering a question, is what almost all of the AP questions consisted of. The three processes of meiosis that cause variation are:

1.Crossing over: Occurs in pro phase 1 of meiosis. When the homologous chromosomes exchange genetic material with non-sister chromatids, all four chromatids that make up the tetrad are different. Once the sister chromatids separate in meta phase 2, each chromatid is unique.

2. Independent Assortment of Chromosomes: Occurs in meta phase 1 of meiosis. When the homologous chromosomes are lined up at the meta phase plate, they are able to pair up in any combination, with any of the homologous pairs facing either pole. It gives the daughter cells a 50-50 chance of obtaining a maternal or a paternal chromosome, from the homologous pair.

3.Random Fertilization: as each egg and sperm is different, each combination becomes unique.

Concept 23.4: Natural Selection is the only mechanism that consistently causes adaptive evolution.


 * __**Natural selection acts more directly on the phenotype and indirectly on the genotype:( Test book: page 157_**__ Bunyad Bhatti

Natural selection can alter the frequency distribution of heritable traits in three ways:

1.Directional selection: the with one extreme phenotypic range are favored, and the curve shifts to that extreme. (Example: Large black bears survived extreme cold better than the smaller bears, and became more common in the glacier periods.)

2. Disruptive Selection: when a condition favors individuals on both extremes of a phenotypic range, rather than the intermediate phenotypes. (Example: A population of birds with either large or small beaks, not any of the intermediate size, as they cannot crack the common seeds.)

3. Stabilizing Selection: acts against both extreme phenotypes, favoring the intermediate variants. (Example: the birth rates of most babies lie in a narrow range.)




 * **__Genetic Drift__:** Gabriela Christian (Found on pages 475 to 478 in the text book!)

Essential knowledge a.A.3: Evolutionary change is also driven by random processes.

Genetic drift is when allele frequencies fluctuate unpredictably from one generation to the next, especially in small populations. A first allele could be lost from the gene pool by chance after a generation. It could be the result of environmental factors, reproductive rates, or any event associated with survival. This increases the chance that a second different allele would be passed on to the next generation. Genetic drift can also occur as a result of chance events that take place during fertilization. By chance alone, every egg and sperm that generated offspring could happen to carry the second allele and not the first.

Genetic drift can result in either the **founder effect** or the **bottleneck effect**. The founder effect is when a few individuals become isolated from a larger population and establish their own new population whose gene pool differs from the original. For example, this could occur if a small amount of seeds got blown on to an island, away from their originating plant population. The bottleneck effect is when there is a severe drop in the population size, usually due to a sudden change in the environment. For example, a flood could leave only a few survivors from a population.

An example of genetic drift is when greater prairie chickens experienced this change. Millions of these chickens once lived in Illinois, but as the prairies were converted to farmland in the 1800s, their numbers plummeted. This would be the bottleneck effect. By 1993, less than 50 of these birds remained in Illinois, and they had very low levels of genetic variation and less than 50% of their eggs hatched. This suggests that genetic drift may have led to a loss of genetic variation and an increase of harmful alleles.


 * __**Species Concepts:**__ Gabriela Christian (pages 487-488 and 492)

Essential Knowledge 1C2: Speciation may occur when two populations become reproductively isolated from each other.

There are a few of these so I just thought I'd explain them all in order to keep them straight! There are many different definitions of what a "species" really is, and these are just a few that are used.

1. Biological Species Concept: this is the primary definition of species that we use. According to this concept, a species is a group of populations whose members have the potential to interbreed in natures and produce viable, fertile offspring--but do not produce viable, fertile offspring with members of other groups. Therefore the members of biological species are united by being reproductively compatible. *** most important one** *

2. Morphological Species Concept: A species is characterized by body shape and other structural features. This concept is advantageous in that it can be useful without information on the extent of gene flow. However, a downfall is that many researchers disagree on which structural features distinguish a species.

3. Ecological Species Concept: A species is characterized by its ecological niche. This concept can accommodate both sexual and asexual organisms, unlike the biological species concept.

4. Phylogenetic Species Concept: A species is the smallest group of individuals that share a common ancestor, forming one branch on the tree of life. Scientists compare characteristics of a species with those of other organisms, which can distinguish groups that are very different to be considered separate species. The disadvantage is determining the degree of difference required to indicate separate species.


 * __**Gene Flow**__ by Lea Adams (page 478-479)

Essential knowledge a.A.3: Evolutionary change is also driven by random processes.

The three major factors that alter allelic frequencies and bring about the most evolutionary change are natural selection, genetic drift, and gene flow. Gene flow is the transfer of alleles into or out of a population due to the movement of fertile individuals and their gametes. In other words, it occurs when a population gains or loses alleles from the addition or subtraction of genes. An example of this occurring would be in flowers where insects may bring pollen from a white flower to a yellow flower, so modifications in the gene pool would be made in the next generation. Gene flow tends to reduce the genetic differences between populations, which makes them more similar. It can also cause nearby populations to combine into a single population with a common gene pool. This occurs in humans today because people move more freely around, so members of different populations mate although they were once isolated. In addition, gene flow may prevent a population from fully adapting to its environment when neighboring populations live in different environments, as well as transferring beneficial alleles. For example, gene flow has resulted in the spread of many insectiside-resistant alleles in the mosquito. Gene flow is similar to mutation, but it occurs at a higher rate and is more likely to affect genes directly.


 * **Scientific Evidence That Support Evolution as an Ongoing Process**: By Christina Dykas ( page 391 and 572 in book)

Essential Knowledge 1.A.4: Biological evolution is supported by scientific evidence from many disciplines including mathematics.

Three examples of this include antibiotic resistance, pesticide resistance, and antiviral resistance. I was confused on the difference between each of these so hopefully this clears it up.

1. Antibiotic resistance is when bacteria is exposed to an antibiotic, but they survive. After a mutation, the bacteria are naturally selected and the bacteria that survive then continue to reproduce and the new bacteria are resistant to the antibiotic. This is significant in medicine because new drugs need to be produced to effectively prevent the bacteria. An example of this would be the streptococcus bacteria. There are many possible treatments for this bacteria because some are resistant to certain antibiotics as a result of natural selection and evolution.

2. Pesticide Resistance is similar to antibiotic resistance but is focused on the "pests" of the environment. A pesticide normally controls the pest population, but when there is a resistant pest, the population no longer is affected and continues to grow. This is an important concept in farms and farmers need to come up with new pesticides to help save the crops. This shows ongoing evolution because the pest that is more fit to survive in the environment and is resistant to the pesticide continues to reproduce and the population evolves into a resistant population.

3. Antiviral Resistance is similar to antibiotic resistance but involves a virus and an antiviral treatment instead of a bacteria and an antibiotic. After a mutation and natural selection, the viruses that are resistant reproduce and the population evolves to become resistant. An example of this would be influenza. The vaccine for influenza is changed to control the virus that have become immune to the previous vaccine.

https://www.youtube.com/watch?v=S7EhExhXOPQ This is a video about natural selection that has a good explanation of antibiotic resistance at the end.


 * **Phylogenetic Trees:** By Christina Dykas (page 539-539 in book)

Essential knowledge 1.B.2: Phylogenetic trees and cladograms are graphical representations (models) of evolutionary history that can be tested.

Phylogenetic trees demonstrate the evolutionary relationships/history between a group of organisms in a tree shaped diagram. They represent a hypothesis about evolutionary relationships which are displayed in dichotomies (two way branch points) that show the divergence from the common ancestor. When there is more than two way branch points, this is called a polytomy. Sister taxa are groups of organisms displayed in a phylogenetic tree that share an immediate common ancestor. Phylogenetic trees and be described as rooted or unrooted. A rooted tree is when the branch usually the farthest to the left represents the last common ancestor of all the taxa in the tree and an unrooted tree does not. Problems with phylogenetic trees include you cannot determine the age of organisms or the time through which they lived. The amount of genetic change that occurred between organisms cannot be determined as well. Benefits would be that we can see the last common ancestor of multiple organisms and it puts the evolution of an organism in a more visual way that is easier to comprehend.

http://www.youtube.com/watch?v=xwuhmMIIspo This is helpful to explain the relationships between organisms on a phylogenetic tree. http://apcentral.collegeboard.com/apc/public/repository/ap11_biology_form_b_q4.pdf This is link to the guidelines of the essay we did in class regarding phylogenetic trees.


 * **__Three Domain System__:** Brian Millham (pg 567 table 27.2)

Essential knowledge 1B1: Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today.

The three domain system consists of Bacteria, Archae, and Eukarya. Bacteria and Archea have Prokaryotic organisms while Eukarya contain Eukaryotic organisms.

This is a table to show comparisons of the three groups.


 * Characteristic || Bacteria || Archea || Eukarya ||
 * Nuclear Envelope || no || no || yes ||
 * Membrane-enclosed organelles || no || no || yes ||
 * Introns || no || yes || yes ||
 * Histone proteins assoc. with DNA || no || yes || yes ||
 * Circular chromosome || yes || yes || no ||

Prokaryotes, Archea, and Eukarya are linked together and share a common ancestor because DNA and RNA are seen in the three domains.

This __#|video__ shows the three domains []


 * Cladistics** by Brian Millham (pg. 543)

Essential knowledge 1.B.2: Phylogenetic trees and cladograms are graphical representations (models) of evolutionary history that can be tested.

Clades are similar to Phylogenetic trees but they are groups of species which includes an ancestral species and all of its descendants. Clades are grouped along with larger clades. There are three types of groups that include a monophyletic group, a paraphyletic group and a polyphyletic group. a monophyletic group consists of an ancestral species and all of it's descendants a paraphyletic group consists of an anscestral species and some of its descendants a polyphyletic group means that some of its members have different ancestors.

this video talks about phylogenetics []

(pages 468-471, 485) Essential Knowledge 1.A.1: Natural selection is a major mechanism of evolution. Essential Knowledge 3C2: Biological systems have multiple processes that increase genetic variation.
 * **__Factors That Produce The Genetic Variation That Makes Evolution Possible__** by Amanda Seale

Genetic variation is an important factor in the process of evolution. These genetic characters that vary within a population may be discrete or quantative. Discrete characters are classified on an either or basis and many are determined by a single gene locus with different alleles producing distinct phenotypes. Geographic variation also ties in, and is defined as differences in the genetic composition of separate populations. Mutations also provide for genetic variation within an evolving species. A mutation is a change in the nucleotide sequence of an organisms DNA. Mutations occur randomly-most occur in somatic cells and are lost when the individual dies. Sexual reproduction between organisms mostly results from the unique combinations of alleles an organism receives. It works by shuffling existing alleles from the parent cells and dealing them out at random to determine individual genotypes. The three mechanisms of crossing-over, independent assortment, and fertilization contribute to this gene shuffling.

In the side bar there are links that go further into discussion concerning these topics- very helpful! []


 * __**Major Modes of Evolution**__ by Grace Goodfellow

Essential Knowledge 1.A.2: Natural selection acts on phenotypic variations in populations. Essential Knowledge 3C2: Biological systems have multiple processes that increase genetic variation.

1. Genetic Drift 2. Gene Flow (also called migration) 3. Mutation 4. Natural Selection

1 & 2 (See Gabby's and Lea's posts on Genetic Drift and Gene Flow)

3. **Mutation:** Mutations are always random in choosing which genes they are going to affect. A mutation that creates a new allele will change the allele frequencies in the offspring generation. Remember that allele frequencies for a given gene always add up to one. One mutation on its own does not have the potential to dramatically alter the allele frequencies in a population. Mutation is extremely important, however, because it is the basis of the variation we see in the first place and it is a very strong force when it is paired with natural selection.

4. **Natural Selection:** Natural selection is based on these three main conditions...
 * Variation: for natural selection to occur, a population must exhibit phenotypic variance; differences must exist between individuals.
 * Heritability: parents must be able to pass on the traits that are under natural selection. If a trait cannot be inherited, it cannot be selected for or against.
 * Differential Reproductive Success: reproductive success measures how many offspring you produce that survive relative to how many the other individuals in your population produce. The condition simply states that there must be variation between parents in how many offspring they produce as a result of the different traits that the parents have.

Darwin's finches on the Galapagos islands would be an example of how natural selection caused an evolution of that specific species. There were different types of plants and resources on each island that the finches had to adapt to. The ones who had a certain beak size or shape survived if that particular characteristic gave them an advantage at being able to reach their food. Eventually, therefore, the ones that were the fittest survived and were able to produce offspring who would also have that same beak that would enable them to reach their resources.

Different alleles create different advantages in different environments. An environment- which includes everything from habitat, to climate, to competitors, to predators, to food resources- is constantly changing. Species are therefore also constantly changing as the traits that give them an advantage also change. In cases where a trait becomes unconditionally advantageous, there is a such thing as fixed alleles. For example... all spiders have eight legs because the alternatives just aren't as good under any circumstances. But where there are heritable characters that both vary and confer fitness advantages (or disadvantages) on their host organisms, natural selection can occur.

http://www.youtube.com/watch?v=sBM9ZKTQ1PQ
 * Mr. Anderson's video on Natural Selection **

[]
 * This website has an awesome AP Biology Test review and goes over almost every topic! **


 * __**Evolution by** **Polyploidy**__ (pages 495-496) By Jake Barry

Essential knowledge 1.A.3: Evolutionary change is also driven by random processes.

Essential Knowledge 3C2: Biological systems have multiple processes that increase genetic variation.

A species may originate quickly form an accident during cell division, that results in an extra set of chromosomes, this is called **Polyploidy**. **Autopolyploidy** is an individual that has more that two chromosomes sets that are all derived from a single species. This can be caused by failure during cell division, which would double the number of chromosomes. This causes reproductive isolation because an organism can only reproduce with another organism that has the same number of chromosomes. The organism with the extra chromosomes is called a tetraploid. This means that in just one generation, a new species can be generated.

A different type of polyploidy is when two different species mate and cause a hybrid. The offspring are sterile because the chromosomes from one organism cannot pair with the chromosomes of another. The offspring may however be able to reproduce asexually. an **Allopolyploid** is when the sterile hybrid evolves into a fertile species. This can be seen in the tree frog //Hyla versicolor.//

[|Polyploidy is mentioned in Mr.Anderson's video]

L.O. 1.3: The student is able to apply mathematical methods to data from a real or simulated population to predict what will happen to the population in the future.
 * **__The Hardy-Weinberg Theorm__ - Kayla Kaufmann**
 * Text Pages (472-475)**

The Hardy-Weinberg theorm is used to describe a population that is __NOT__ evolving. It explains that the freuencies of alleles and gene's in a population's gene pool will remain constant over the course of generations unless they are acted upon by forces other than Mendelian Segregation and the recombination of alleles. If a population fits this description, it is in Hardy-Weinberg equilibrium.

To test for equilibrium the Hardy-Weinberg equation can be used. The equation is **p^2 + 2pq + q^2 = 1** In this equation, **p = the frequency of the dominant allele q = the frequency of the recessive allele.** It is important to remember when solving Herdy-Weinberg problems that __p+q = 1__ because the sum of allele frequencies for all the alleles at the locus must be 1.
 * p^2 = the frequency of the homozygous dominant genotype**
 * q^2 = the frequency of the homozygous recessive genotype**
 * 2pq = the frequency of a heterozygous phenotype**

Imagine in a plant population that red __#|flowers__ (R) are dominant to white flowers (r). In a popluation of 500 individuals, 25% show the recessive phenotype. How many individuals would be expected to be homozygous dominant and heterozygous for this trait?
 * EXAMPLE:**


 * q^2 = the frequency of the homozygous recessive which = 25% which = 0.25 as a decimal. Since q^2 = 0.25 then, q = 0.5
 * p+q must = 1 so since q= 0.5 then p = 0.5 because 1 - 0.5 =0.5
 * Homozygous dominant individuals are RR or p^2 = 0.25 and will represent (0.25)(500) = **125 individuals**
 * The heterozygous individuals are calculated from 2pq which = (2)(0.5)(0.5) = 0.5 and in a population of 500 individuals will be (0.5)(500) = **250 individuals**
 * See link below for more help on Hardy Weinberg Equations**

[|Solving Hardy Weinberg Problems Help Video]


 * **__The Origin Of Life Models: Focusing on the Oparin - Haldane Model__ By: Kayla Kaufmann**

Text Pages (508-509) Essential knowledge 1.D.1: There are several hypotheses about the natural origin of life on Earth, each with supporting scientific evidence.

Oparin and Heldane hypothesized that the early atmosphere, thick with water vapor, nitrogen, carbon dioxide methane, ammonia, hydrogen, and hydrogen sulfide, provided with energy from lightning and UV radiation, may have formed organic compounds, a primitive "soup" from which life originated (This model is referred to as the "soup" model).

This hypothesis was tested by Miller and Urey in a lab and it produced a variety of aimno acids. Miller filled a carefully assembled glass apparatus with methane, ammonia, and hydrogen. Miller diligently did not include oxygen. A flask of boiling water connected to the glassware indtroduced water vapor into the headspace and simulated Earth's oceans. Miller then passed a a continuous electric discharge through the gas mix to mimick lightning. After a few days, organic compounds including amino acids formed (these are found in organisms today). Miller and Urey type experiments show that the abiotic synthesis of organic molecules is possible.

See the image below outlining visually the process of the Miller-Urey experiment, testing the Oparin-Haldane hypothesis.



by Kenna Garrison (p. 507-510)
 * Concept j: Scientific evidence supporting key events in the origin of life on Earth**

How the first cells developed with evidence supporting:

a. Abiotic (Non-biological) synthesis of small organic molecules (monomers) à C + H = organic molecule
 * Oparin and Haldane hypothesized that the conditions on primitive Earth favored chemical reactions that could synthesize organic compounds from inorganic material, due to a reducing environment (no O2) and lots of energy from lightning, UV radiation, and volcanic activity
 * Miller and Urey tested this hypothesis by creating a simulated primitive Earth environment with these conditions from which they obtained organic compounds such as amino acids

b. Monomers joined together to form polymers (proteins, nucleic acids)
 * Monomers could have gone through a sort of natural selection in which they were more likely to keep existing in polymers

c. Origin of self-replicating molecules (inheritance of traits) à proteins and polynucleic acids (RNA?)
 * RNA likely the firs hereditary material
 * RNA has been synthesized abiotically in the laboratory
 * Thomas Cech discovered that RNA catalysts, called ribozymes, are important in modern cells to remove introns from RNA and catalyze the synhesis of new RNA polymers
 * RNA molecules may have been capable o ribozyme-catalyzed replication in the pre-biotic world

d. Packaging of these organic molecules into protobionts. à Aggregates of abiotically produced molecules that maintain an internal chemical environment and exhibit some of the properties associated with life (i.e. metabolism, excitability).
 * Protobionts have formed spontaneously in lab experiments from mixtures of organic molecules
 * Natural selection would have favored protobionts that grow and replicate, and ones that could obtain energy by photosynthesis or predation would be favored

By Kenna Garrison (p. 475-478, 490-491) Bottleneck effect: when there is a sharp reduction in population size due to environmental events or human activities
 * Concept h: How types of selection can affect future populations**
 * Can cause genetic drift if the original population’s allele distribution is different from the new one
 * Increases inbreeding which can reduce diversity in the population, causing it to be less able to adapt to a changing environment
 * Could lead to extinction if there aren’t enough individuals left or the survivors aren’t able to reproduce sufficiently to recover the population

Hybrid sterility: when offspring of a cross between different species aren’t able to reproduce
 * Future populations will not include more hybrids

Reproductive isolating mechanisms: prezygotic and postzygotic barriers that prevent different species from producing viable offspring
 * Prevents hybrids from developing / reproducing
 * Keeps populations separated so that their future populations will be different from each other


 * The Effects of Human Interactions on Species Extinction Rates and Phyenotypic Success. By: Kohl Romeiser**

Essential knowledge 1.C: Life continues to evolve within a changing environment.

__The Peppered Moth Scenario:__

Prior to the Industrial Revolution, most of the peppered moth (Biston bitularia) population displayed the dominant white/gray allele which enabled the moth to camouflage within white lichen on the trees within its habitat. This white phenotype gave the majority of peppered moths a reproductive advantage over the darker recessive trait that is also found within the population. Darker moths were more likely to be spotted and eaten by predators, so they would reproduce less often and spread their recessive dark trait to offspring.

During the Industrial Revolution of the 1800s, human soot pollution turned tree species black, killing the lichen used for camouflage by the peppered moths. Suddenly, the white moths became a very easy target for predators because they could be seen and fed on. Without the lichen camouflage to protect them, the dominant white phenotype of the peppered moth rapidly died off, while the recessive darker moths survived to reproduce because they could not be so easily detected by predators on the darker soot covered trees.

This is an excellent example of how human interaction with the environment can change the phenotypic success of a species. Although the allele frequency of the peppered moths changed, the species did not die out. This illustrates the concept that species are able to evolve with a changing environment to avoid extinction.



__The Thylacine:__



Thylacines were present on the island of Tasmania over 200 years ago, when Europeans first arrived and inhabited the island. The main reason for their rapid decline was human driven. Thylacines had become virtually extinct from the mainland of Australia due to competition with other dominant predators of the region. As humans began settling in Tasmania, the Thylacine population posed a great threat to livestock on the island. Tasmania offered great agriculture land, and soon the Thylacine population dwindled due to over-hunting and habitat loss. Unfortunately, the Thylacine is just one of many species that have been wiped from the face of the earth due to human interaction. Today, many species such as the right whale face extreme endangerment and the possibility of extinction. Unlike the peppered moth, the Thylacine was unable to adapt to the rapid change of environment.


 * The Endosymbiotic Theory By: Kohl Romeiser**

Essential knowledge 1.B: Organisms are linked by lines of descent from common ancestry

[]

Most scientists agree with the endosymbiotic theory stating that eukaryotes formed from prokaryotes during the first few billion years of life. It is thought that the mirochondrion and chloroplast organelles were once individual cells that were swallowed by larger cells, escaping digestion. This relationship turned out to be excellent for both cells. The chloroplast and mitochondrion were provided with a stable home, while providing energy for their host cell.
 * 1) Mitochondrion: consumes oxygen and obtains energy through carbon sources like glucose and produces water and carbon dioxide.
 * 2) Choloroplast: consumes water and carbon dioxide while capturing energy from the sun and forms glucose as a result releasing oxygen.
 * 3) Mitochondrion and Chloroplasts are very similar to some prokaryotes and even have their own circular DNA.

Here's a Mr. Anderson video link if you need some clarification: []

Concept 25.1, page 508 Appendix A- Big Idea 1 (elaboration on part k because I didnt understand how exactly it happened)
 * How the Synthesis of Simple Cells May Have Occurred on Early Earth- Submitted by Maddy Harmon**

The first, simple cells on early Earth may have been produced through 4 main theorized steps 1: The Abiotic (having nothing to do with anything alive- they just reacted chemically) synthesis of small organic molecules. (this could include amino acids or neucleotides, but nothing large and complicated like fully folded protiens or strings of DNA) 2: the joining of these small molecules into larger macromolecules (this could include some protiens and nucleic acids-- larger and slightly more complicated) 3: Packaging the newly formed macromolecules into protobionts (droplets or bubbles that maintained a somewhat different internal environment than their surroundings--like early membranes) 4: The origin of self replicating molecules that eventually made inheritance possible (a big leap-- helped along by the emergence of the power of natural selection- that labratory experiments such as the oparin model have still not been able to replicate-- they're still waiting on protobionts)

heres a video showing the 4 main stages-- [] jump to 2:31, the beginning is just about spontaneous generation

Appendix A: Essential knowledge 1.B.1: Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today (Letter B)
 * __**Structural Evidence Supports the Relatedness of all Eukaryotes**__ by Grace Goodfellow
 * Structural Similarities
 * Cytoskeleton
 * A network of structural proteins that facilitate cell movement, morphological integrity, and organelle transport
 * Microfilaments are the smallest at 4 to 6 µm in diameter and are made of actin. These lie beneath the surface of the cell membrane and are anchored to it, forming a web inside the cell. They dictate the cell's shape and can also be involved in motility by contraction or expansion of the filament. Filaments may also tether organelles to the membrane and help move them around the cell. This movement can be important for modulation of organelle function.
 * Involved in cell division, allowing the separation of chromosomes into each of the daughter cells
 * Membrane-bound organelles
 * Because eukaryotes are larger than prokaryotes, they require a variety of specialized internal membrane-bound organelles to carry out metabolism, provide energy, and transport chemicals throughout the cell
 * Linear Chromosomes
 * Eukaryotes possess multiple large linear contained in the cell's nucleus
 * Each chromosome has one centromere, with one or two "arms" projecting from the centromere
 * Eukaryotes have a small circular mitochondrial genome
 * In nuclear chromosomes, un-condensed DNA exists in a semi-ordered structure, where it is wrapped around histones (structural proteins), forming a composite material called chromatin
 * Endomembrane systems, including the nuclear envelope
 * Compartmentalizes the cell for various different but interrelated cellular functions
 * A vesicle buds off of one organelle and transports materials when it fuses with another membrane
 * Eukaryotic cells possess a distinct nucleus surrounded by two membranes that constitute the nuclear membrane

Video on how eukaryotes (and prokaryotes) arose (theory) http://www.youtube.com/watch?v=DwbbkH4oV6o

(pages 492-498)
 * __Allopatric and Sympatric Speciation__ by Amanda Seale**

Appendix A: Essential knowledge 1.C.1: Speciation and extinction have occurred throughout the Earth’s history.

Speciation is the process by which a unique species arises from an existing species. In allopatric speciation, gene flow is interrupted when a population is divided into geographically isolated subpopulations. This could happen by a river changing course and dividing a population of animals unable to cross, or a water level in a lake subsiding and resulting in two smaller lakes with two separate populations. It can also occur when individuals just begin to colonize in a remote area, having their descendants become geographically isolated from the parent population. Once geographic separation has occurred, gene pools can differentiate using mechanisms such as natural selection, mutations, and genetic drift. Highly isolated populations have very little gene flow and are more likely to undergo allopatric speciation. Sympatric speciation occurs in populations living in the same geographical area. Reproductive barriers originate in the form of polyploidy, habitat differentiation, and sexual selection (these can also promote allopatric speciation). Polyploidy is an accident during cell division resulting in extra chromosome sets. Two distinct forms of polyploidy include the autopolyploid, which refers to an individual who has more than two chromosome sets all derived from a single species, and the allopolyploid, which is a fertile polyploid that originally a sterile hybrid. Habitat differentiation occurs when genetic factors enable a subpopulation to utilize a habitat or resource not used by the parent generation. Sexual selection can drive sympatric speciation, which is evident in cases where several species originate in a single lake or area.

Thank god for Mr Anderson: []



Emily Bernardi

1.C.2: Speciation may occur when two populations become reproductively isolated from each other

Speciation is t he evolutionary formation of new biological species, usually by the division of a single species into two or more genetically distinct ones. An example of this occurring is something such as the finch observation that Charles Darwin made. The finches migrated to different islands, causing geographical isolations and adapting into a different species which were better for their environments. New species arise from reproductive isolation over time, and this can involve up to millions of years. Speciation can also occur very rapidly such as polyploidy in plants. It can occur in a diversity of life forms and usually happens when they are separated by a geographic barrier (such as an ocean or mountain range).



Mr. Anderson does an awesome job of explaining speciation and extinction in this video: @http://www.youtube.com/watch?v=yJLRl2G41nQ

Maggie Garrahan 1.D.2: Scientific evidence from many different disciplines supports models of the origin of life

By studying geological, physical, and chemical data, you can get a better understanding of the origin of life on Earth. 1. Geological evidence: a. The Earth formed about 4.6 billion years ago b. Earth began to support life 3.9 billion years ag c. Earliest fossils date back to 3.5 billion years ago d. This evidence provides dates of when the origin of life could have occurred 2. Chemical evidence: a. Chemical experiments have shown that it’s possible to form complex organic molecules from inorganic molecules in the absence of life b. Therefore organic molecules could have produced before the origin of life c. Scientific evidence includes molecular building blocks which are common to all life forms. 3. Physical evidence: a. Molecular and genetic evidence from extant and extinct organisms shows that all organisms on Earth share a common ancestral origin of life. b. Study of common genetic code An example of the origin of life based on biochemical evidence would be seeing the relationship between the chemicals that make up a mammal and the chemicals that make up a fungus. Many of those chemicals are exactly the same and work by using the same molecules. RNA experiments can serve as proof of the origin of life. If a particular chemical reaction happens in a modern lab under conditions similar to those on early Earth, the same reaction could have happened on early Earth and could have played a role in the origin of life.

http://evolution.berkeley.edu/evosite/evo101/IIE2bStudyorigins.shtml http://www.youtube.com/watch?v=SWY3FKbtEz8

1.C.3: Populations of organisms continue to evolve. by Maeve Dalpe

Scientific evidence supports the idea that evolution has occurred in all species and that evolution continues to occur. Fossil records show past organisms that differ from present day organisms while still resembling each other. They indicate that most mammals were once terrestrial. Chemical resistance is an example of continuing evolution of drug-resistant pathogens. The human immunodeficiency virus is one that causes AIDS. Drugs have been made to silence the virus and may be partially successful. Those that survive the drug, reproduce, and pass on the alleles that make them resistant to that drug. Scientists have tried the drug 3TC to alter reverse transcriptase. HIV uses the enzyme to make a structure similar to its RNA and inserts it into the DNA of a host cell. The error this causes, allows for the termination of DNA elongation and blocks AIDS reproduction. But hope falls short when the 3TC resistant type of HIV is able to identify the real nucleotide verses the false one. Instead of halting or even slowing the replication, the virus favors the survival of resistant HIV pathogens. Other examples of evolution continuation include emergent diseases, evolution in systems within a species and directional phenotypic change in populations (Darwin's finches in the Galapagos Islands) (pg 461).

F.) Explain how the different lines of data (morphological, biochemical, genetic) support the concept of a common ancestry within a phylogenetic domain and for all life. by Maeve Dalpe

Morphological homologies represent features shared by common ancestry. Biochemical and genetic similarities, in particular DNA nucleotide and protein sequences, provide evidence for evolution and ancestry. Organisms with similar morphologies or similar DNA sequences are likely to be more closely related than organisms with vastly different structures or sequences. Molecular comparisons of nucleic acids cause frustration to scientists because they must align comparable sequences from the species being studied. If sequences are different from one another but the organisms are in fact related, scientists conclude that their sequences have diverged greatly since their common ancestor. Vestigial structures are remnants of functional structures, which can be compared to fossils and provide evidence for evolution. Fossils can be dated by a variety of methods that provide evidence for evolution. These include the age of the rocks where a fossil is found, the rate of decay of isotopes including carbon-14, the relationships within phylogenetic trees, and the mathematical calculations that take into account information from chemical properties and geographical data. (pg 540 & 541)


 * __Preservation of genetic variation__** by Lea Adams (Page 483)

Genetic variation is preserved in a population through diploidy and heterozygote advantage. A diploid cell contains two sets of chromosomes, inheriting one from each parent. Because most eukaryotes are diploid, they are capable of hiding genetic variation or recessive alleles from selection and only showing the dominant allele. This allows organisms to display one trait but pass on another, thus preserving variation. The heterozygote advantage says that individuals who are heterozygous at a certain locus have an advantage for survival. For example, in sickle cell disease, being homozygous for normal hemoglobin are more likely to get malaria, and homozygous recessive organisms suffer from the complications of sickle cell disease. Luckily, heterozygotes benefit from protection from malaria and do not have the disease, so the mutant allele is common and heterozygous individuals have an advantage.

__How Reproductive isolation can occur__ by Owen Gaffney ch 24 p 489-491

I always got confused about what forms of isolation there were so here is a quick summary. Reproductive isolation can occur through a number of pathways. reproductive isolation is the existence of by psychological factors that impede members of two species from producing viable fertile offspring. Some of the most basic forms include geographical barriers were species cannot enter me due to physical obstacles. Other forms include temporal where to species do not interact at the same time or mechanical where things just don't fit together. These are forms of pre-zygotic barriers before the zygospore the block fertilization from occurring altogether. Sperm cell from one species overcomes pre-zygotic barriers realizes another species variety of posts I got there is they contribute to the reproductive isolation after the hybrid zygote is formed. For example problems afterbirth may cause hybrids to be infertile or may decrease the chance of them surviving long enough to reproduce. Reduced hybrid viability is when the genes of different parent species may interact in ways that impair the hybrids development of survival and its environment. Produced hybrid fertility the carriers even if the hybrids are vigorous and maybe staff if the chromosomes of the two parent species differ in number structure miosis and the hybrid may fail to produce normals gametes. Finally hybrid breakdown is when some first-generation hybrids are viable or fertile and then mate with one another or with either parent species and offspring of the next-generation are feeble or sterile.

__What can the fossil record prove about evolution?__ by Owen Gaffney ch. 24 p 502

One of the strongest forms of evidence that supports claims of evolution that can be undisputed by scientists is the fossil record. Since the dawn of time an index of all organisms and their development is buried beneath our feet. The fossil record includes many episodes in which new species appear suddenly in the geological strata, persist essentially unchanged through several strata, and then disappear. There are two basic terms used to describe periods of change in the fossil record. The one stated above refers to punctuated equilibrium which means periods of apparent status punctuated by sudden change. A second form of evolution seen in the fossil record is gradualism in which small changes occur in the history of the species over many millions of years and can be seen with small changes in the structures of individual organisms. Punctuated equilibrium can tell us a lot about species. Depending on the time it occurred punctuated equilibrium can specifically give time references in accordance to a big events changed on the earth including the presence of oxygen and meteor strikes. Before the presence of oxygen much life on earth was simple and did not you've all rapidly in any sense. However once oxygen enter the atmosphere and explosion of evolution is seen the fossil record in the development of multicellular organisms origins' are seen.

Essential knowledge 1.B.2: Phylogenetic trees and cladograms are graphical representations (models) of evolutionary history that can be tested. By Maggie Garrahan

Phylogenetic trees are used to trace evolutionary history. They show all the descendants from a common ancestor and show the relationships and evolutionary time. They show traits that had either been derived from a common ancestor over evolutionary time, or it shows how traits can be loss due to environmental change or other changes throughout time. This can be seen through many aquatic animals. Some, over time, have lost their legs and formed fins and gills in order to survive in the aquatic environment. Also, opposable thumbs can be traced, which actually shows a relationship between humans and chimpanzees. Another example would be the comparison between the wings of bats and the fins on fish. Phylogenetic trees can trace speciation, or when two species separated from a previous single specie. Phylogenetic trees, or caladograms, can be made from observing live organisms or fossils. This can be difficult if extinct species do not have any fossils that can be recorded. Computer programs can also be used in order to create the tree. They can be compared based on their appearance or their DNA.

Examples:

http://www.nature.com/scitable/topicpage/reading-a-phylogenetic-tree-the-meaning-of-41956

http://highered.mcgraw-hill.com/sites/9834092339/student_view0/chapter23/animation_-_phylogenetic_trees.html

http://evolution.berkeley.edu/evolibrary/article/phylogenetics_01

http://media.collegeboard.com/digitalServices/pdf/ap/10b_2727_AP_Biology_CF_WEB_110128.pdf

Mariah Pennington Appendix A, letter a: Applying mathematical methods to data from a real or simulated population and predict what will happen to the population in the future based on the Hardy-Weinberg equilibrium model. To prove if a population is NOT evolving, the Hardy-Weinberg principle is applied. Factors that must all be present to reach this equilibrium are The equation for the genotypes is p^2 + 2pq+q^2 = 1. The term p^2 represents the homozygous dominant genotype. The 2pq term is for the heterozygous individuals and the q^2 is the homozygous recessive genotypes. The phenotypic equation is p + q = 1. P is for the percentage for the dominant expression of the trait and q is for the recessive trait percentage being expressed. For example, if the recessive allele frequency in the original population is 30%, it will remain that way through the generations. This shows that the population is in equilibrium and therefore NOT evolving. (textbook 472-474).
 * 1) Random mating
 * 2) Large population size
 * 3) No natural selection
 * 4) No mutations
 * 5) No migration in or out

Mariah Pennington Appendix A, letter d: Conserved core processes and features that support common ancestry within and across domains of life. (pgs 852-858 in txt) Systems that are still in effect today had to have come from something before it. The respiratory system, for example, shows unity across life forms of past and present. What is essentially happening in all organisms that undergo cellular respiration is the intake of oxygen and releasing carbon dioxide and water vapor. A very basic life form, such as a marine worm, is surrounded by water (which is vital for proper exchange of gases). The o2 and co2 can be diffused through the moist membrane of the skin surface through up to three tissue layers. Fish gills are external. The water filters through the gill filaments and the gills absorb the o2 from the water and release co2 back into the water around them. An earthworm does not live in an aquatic environment, so its skin needs to be slimy enough to allow gas exchange to occur on the surface. Insects respire through the tiny holes on their sides that lead directly into and out of them (these chambers are called tracheae). As creatures moved from water to land and increased in complexity and size, the moist membranes needed to be protected. Internal lungs became the solution because it conserved the moist membrane and efficiently stored large surface area. The universal moist membrane that aids in gas exchange is a conserved feature and shows common ancestry.

Biotechnology and genetic engineering - Kylie Dolan
 * "Human-directed processes also result in new genes and combinations of alleles that confer new phenotypes." (Appendix A)
 * Restriction enzymes - enzymes that cut DNA at particular sequences called restriction sites
 * Recombinant DNA - combining DNA sequences that would not normally occur together to form one piece of DNA.
 * DNA ligase - an enzyme that is added to seal the recombinant DNA strands together


 * Example:
 * Golden rice is a type of rice made from genetic engineering. This type ofrice was created to provide vitamin A to Third-World countries where malnutrition is prevalent. Scientists used recombinant DNA to produce carotenoids or organic pigments in the endosperm (the edible part of the grain). These scientists added genes to the rice genome. They added Phytoene synthase which is derived from daffodils, and Lycopene cyclase which is derived from the soil bacteria //Erwinia uredovora//. These essentially code to produce enzymes and catalysts for the biosynthesis of carotenoids (beta carotene) in the endosperm.

DDT resistance in mosquitoes - Kylie Dolan Essential knowledge 1.A.2: Natural selection acts on phenotypic variations in populations. DDT has been an acronym thrown around that I was not entirely sure of. DDT is an insecticide that can be incredibly harmful in concentrated amounts. There are some insects that are naturally immune to its effects, and thus have a far greater chance of survival. Scientists with good intentions decided to use DDT on a large scale to kill mosquitoes and prevent malaria. However, in many countries, the insects are said to be largely immune to the effects, as there has been years of "selecting for" the mosquitoes who are immune (as the others did not live to reproduce). On a side note, the effects of DDT are scariest because it amplifies at each increasing trophic level. Because DDT does not break down easily (it is not water soluble), it is passed on to each group next in the food chain at an amplified amount (i.e. a small amount in ten fish that were all eaten by one bird essentially gets added together).

Evidence for Evolution in fossil records Emily Bernardi Remains of animals and plants found in sedimentary rock deposits give us an indisputable record of past changes through vast periods of time. This evidence attests to the fact that there has been a tremendous variety of living things. Some extinct species had traits that were transitional between major groups of organisms. Their existence confirms that species are not fixed but can evolve into other species over time. The evidence also shows that what have appeared to be gaps in the fossil record are due to incomplete data collection. The more that we learn about the evolution of specific species lines, the more that these so-called gaps or "missing links in the chain of evolution" are filled with transitional fossil specimens. One of the first of these gaps to be filled was between small bipedal dinosaurs and birds. Just two years after Darwin published On the Origin of Species, a 150-145 million year old fossil of Archaeopteryx was found in southern Germany. It had jaws with teeth and a long bony tail like dinosaurs, broad wings and feathers like birds, and skeletal features of both. This discovery verified the assumption that birds had reptilian ancestors.

Factors affecting Hardy-Weinberg Equilibrium Amanda Vespermann In order for a population to be in Hardy-Weinberg equilibrium, it must meet each of the five conditions required. The population must have no mutations, random mating, no natural selection, extremely large population size, and no gene flow. However, many different environmental factors can also take a population out of Hardy-Weinberg equilibrium. These factors include genetic drift and natural selection. Genetic drift occurs randomly within a population. The gene frequencies can not be expected to be exactly the same from one generation to the next, purely based on randomness. When a coin is flipped, it generally does not land on heads exactly half of the time. Similarly, the exact same genotypic and phenotypic ratios cannot be expected within a population from one generation to another. Natural selection can occur for a variety of reasons. If a temperature change occurs within the environment and a certain genotype is best suited, over several generations there will be a change in the allele frequencies of the population. Other environmental changes, such as the presence of a new chemical in the air could also affect allele frequencies. This demonstrates that a population in Hardy-Weinberg equilibrium is highly unlikely in the real world. (textbook pages 473-476) Examples:

[] (Kahn Academy video explaining Hardy Weinberg factors) [] (Bozeman Mr. Anderson video explaining Hardy Weinberg principle and factors).

Reproductive Isolation - Appendix A big idea 1.h Amanda Vespermann Reproductive isolation is when there are prezygotic or postzygotic barriers that prevent two organisms from different species from successfully reproducing, through preventing fertilization of prevention of viable fertile offspring. Prezygotic barriers include: Habitat isolation - two species live in different habitats, and therefore do not cross paths and are not given the opportunity to mate Temporal isolation - two species reproduce at different times of the day or different seasons, and are therefore never given the chance to mate Behavioral isolation - courtship rituals and mating behaviors between species prevent reproduction Mechanical isolation - morphological differences prevent successful reproduction Gametic isolation - the sperm of one species may not be able to fertilize the egg of the other species For postzygotic barriers, the offspring may not live a normal lifespan, due to hindrances in its development. If the offspring does live, it may be sterile and unable to reproduce. In hybrid breakdown, the hybrid species may survive and be non-sterile, but the following generation is not able to reproduce and is either feeble or sterile. (textbook pages 488-491) Examples: [] (quick video summing up the basics of speciation)

Essential Knowledge 1.C.2: Speciation may occur when two populations become reproductively isolated from each other Kayla Kaufmann (make-up work) Pages 487-492


 * Speciation- an evolutionary process in which one species splits into two or more species
 * Speciation results in diversity of life forms because more species and variety arise through this process. Species can be physically seperated by a geographic barrier like an ocean or moutain range for example, or different pre and post zygotic mechanisms can maintain reproductive isolation and prevent gene flow
 * New species come about from reproductive isolation over time which can be hundreds, thousands, or millions of years.
 * Speciation can happen rapidly through methods like polyploidy (a chromosomal alteration in which the organism posesses more than two complete chromosome sets. It is the result of an accident of cell division) in plants



Check out this cool interactive website on speciation []

Essential Knowledge 1.A.1: Natural Selection is a major mechanism of evolution Kayla Kaufmann (Make-up work) Pages 479-485 Other things play a role in natural selection Environments can be more or less stable or fluctuating and this affects evolutionary rate (how fast evolution is occuring) and direction, different genetic variations can be selected for in each generation based on what is happening in the environment *It is important to remember that in addition to natural selection, chance and random events can influence the evolutionary process, especially for small populations*
 * According to Darwin's theory of natural selection, competition for limited resources results in differential survival. Organisms with more helpful phenotypes have a better chance of surviving and producing more offspring. As a result, these organisms pass their traits to their next generations.
 * In other words traits that help a organism survive are the ones that are passed on because only the organisms with these traits stick around long enough to reproduce so the favorable traits are "selected" for
 * Evolutionary fitness is measured by succes with reproduction or producing offspring
 * These include mutation and genetic variation which cause a diverse gene pool - A diverse gene pool is important for the survival of a species in a changing envionment - leading to natural selection and evolution
 * Adaption- a genetic variation that is favored by selection and is apparent as a trait that provides an advantage to an organism in a certain environment