Feralis (2018 FULL) Chapter 13: Evolution

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Baron Georges Cuvier

1. Baron Georges Cuvier Cuvier proposed the theory of catastrophism . He is also the founder of paleontology (study of fossils). Through observing fossil patterns, he proposed that there must have been sudden catastrophes that happened spontaneously throughout history causing mass extinction of species in that area. (dinosaurs, for example) After the catastrophe, the landscape is drastically changed and new life forms will eventually populate the area, giving oﬀ new fossil specimens.

theory of catastrophism

After covering the two theories of macroevolution, there are also a few patterns of evolution that we should familiarize ourselves with:

1. Divergent evolution: ○ When species diverge from a common ancestor through speciation. 2. Convergent evolution: ○ When two completely unrelated species grow more and more alike (development of analogous structures ) due to adaptations in similar environments. 3. Parallel evolution: ○ When two related species diverge oﬀ from a common ancestor but they both went through similar changes . Feedback? Email Ari at [email protected] 522 4. Coevolution: occurs when two species impart selective pressures on each other, resulting in the evolution of both species. Camouﬂage, aposematic coloration, and mimicry are examples of coevolution. Camouﬂage (cryptic coloration) allows animals to avoid visual detection through matching of their appearance to the environment. An insect appearing stick-like is an example of this. Aposematic coloration (warning coloration) is a vibrant, bright coloration of poisonous animals, which warns predators that they are poisonous. An example of aposematic coloration is the bright coloring of poison dart frogs. Mimicry refers to when one species evolves to resemble another species. Batesian mimicry: A non-harmful animal mimics the coloring of a harmful animal. An example is a harmless ﬂy that mimics the coloring of a stinging bee. Mullerian mimicry occurs when diﬀerent poisonous species that share a common predator evolve to resemble each other. This way, it is easier for the predator to learn to avoid these species. An example is of a stinging bee and a stinging wasp, which have evolved to share similar coloring and body size.

Genetic Drift

1. Genetic Drift As we've mentioned above, genetic drift is a change in allele frequencies in a gene pool by chance . The fact that luck is involved diﬀerentiates genetic drift from natural selection, where allele frequencies are selected by the environment to increase or decrease. This is why genetic drift has a much bigger impact on small populations than big populations. There are two signature eﬀects that result in genetic drift: Bottleneck eﬀect When there is a disaster that kill oﬀ most of the population. For example, a forest ﬁre kills oﬀ all squirrels, and by chance two albino squirrels survive. The new population may be albino (if new squirrels don't migrate to this area). What's left is a handful of lucky individuals that survived and a much more smaller gene pool. Some alleles may be lost from this (by chance). https://commons.wikimedia.org/wiki/File:Bottleneck_eﬀect_Figure_19_02_03.jpg In this picture, we can assume that the colors of the marbles refer to the diﬀerent alleles in a population. Inside the bottle, there were many green and red marbles. However, after passing Feedback? Email Ari at [email protected] 515 through the bottleneck, we have lost all red marbles and only a few green ones remain. This shows the loss of alleles during a disaster. Founder eﬀect When there are a couple of individuals that migrated to and settled in a new location, these individuals would have a much smaller gene pool than their original population. The successive generations will descend from the founders, and their unique genetic makeup. https://commons.wikimedia.org/wiki/File:Founder_eﬀect_Illustration.jpg This shows a small group of marbles that "migrated" out from its original population. Since the group is small, it is prone to genetic drift. After a few more generations, all of the original red marbles (alleles) are lost. 'Large Random M&M' Random = random mating. So our second cause of change would be non-random mating

Mutation

1. Mutation This is the most straightforward way to have a new allele, through genetic mutation. Note here that these mutation cannot be fatal! https://commons.wikimedia.org/wiki/File:Antithrombin-gene-strand-switch.gif

1. Once upon a time, the Earth had a primordial atmosphere that was made of many diﬀerent inorganic compounds, except for oxygen . It mostly consisted of:

1. Once upon a time, the Earth had a primordial atmosphere that was made of many diﬀerent inorganic compounds, except for oxygen . It mostly consisted of: methane (CH 4 ), ammonia (NH 3 ), carbon monoxide (CO), carbon dioxide (CO 2 ), hydrogen gas (H 2 ), nitrogen gas (N 2 ), water (H 2 O), hydrogen sulﬁde (HS). The fact that oxygen was not part of the primordial atmosphere is very important, because the primordial atmosphere is a reducing environment without oxygen. We will talk about this concept later down the timeline.

10. More complex eukaryotes and multicellular organisms came about

10. More complex eukaryotes and multicellular organisms came about That's the most important events that happened on Earth since its birth summarized in 10 points. Now, we will take a look at the famous Miller-Urey experiment that we talked about earlier. Miller-Urey Experiment: In short, the Miller-Urey experiment tried to mimic the primordial environments on Earth to test out the organic "soup" theory proposed by Oparin and Haldane. To mimic the reducing environment as proposed in the theory, Miller and Urey set up a ﬂask with methane (CH 4 ), ammonia (NH 3 ), hydrogen (H 2 ), and water (H 2 O) in a closed system connecting to another ﬂask that contains electrodes . Quiz question, which gas is missing? The answer is oxygen. So on one hand, they heated up the ﬂask containing various gases to imitate the high temperature on Earth back in the days. On the other hand, the electrodes produced sparks that imitated lightning (energy source). After a week, they observed several organic compounds that formed: amino acids and other organic acids . However, they did not ﬁnd any complete nucleic acid . This result echoed with the proposed abiotic chemical evolution requirements, and further conﬁrmed Oparin and Haldane's theory. Feedback? Email Ari at [email protected] 529 https://commons.wikimedia.org/wiki/File:Miller-Urey_experiment-en.svg Critical Review: ● Universe: 14 b years ago. ● Earth: 4.5 b years ago (roughly one third of the age of the Universe) ● First prokaryote: 3.5 b years ago. ● First eukaryote: 2 b years ago. ● Most common gas in Earth's atmosphere : Nitrogen ● Most common component in Earth's crust : Oxygen ● Primordial Earth had no oxygen (strong reducing environment) ○ Formation of autotrophic prokaryotes introduced oxygen —> changed environment into oxidizing . ● Endosymbiotic theory: membrane-bound organelles (chloroplasts and mitochondria) used to be free-ﬂoating prokaryotes —> eaten by other prokaryotes later on.

Biogeography

2. Biogeography Biogeography evidence explains the spread of diﬀerent species throughout the world. As the supercontinent Pangea separated into 7 diﬀerent continents, living organisms were also separated. As the organism's environment changed, evolution took place so that the organisms could better adapt to their new habitats. Feedback? Email Ari at [email protected] 498 https://commons.wikimedia.org/wiki/File:Pangaea_continents.svg For example, both penguins and polar bears thrive in bitter cold environments. But why are polar bears only found in the North Pole whereas penguins are in the South Pole? This is because geographical barrier made it impossible to go to the other pole, so they each adapted to their respective surroundings.

Pangea

Jean-Baptiste Lamarck

2. Jean-Baptiste Lamarck Lamarck was actually the ﬁrst biologist who believed in evolution, instead of special creation of life forms. He proposed two interesting hypotheses of evolution: ● Use and disuse ○ The more used the body part is, the more it will develop i.e. a giraﬀe's neck grows longer when it tries to feed from higher trees. ○ The less used the body part is, the more weakened it will be i.e. certain species of monkeys didn't use their tails much, so through disuse that species evolved to not have tails ● Inheritance of acquired traits ○ He believed that whatever characteristics the organism acquires throughout its life (through use and disuse) will be passed onto its oﬀsprings. ■ For example, if a giraﬀe stretches its neck continually, it will develop a longer neck, and will pass on the long neck to its oﬀspring. ○ This theory is incorrect because environmentally acquired characteristics are actually not heritable . They are changes to the organism, but don't represent a heritable change because the use/disuse doesn't change the genetic code, ie. the DNA.

Non-random mating

2. Non-random mating This is when individuals choose who they want to mate with. This is a consequence of sexual selection , which we've covered beforehand. When certain traits are favored over others, they get passed onto oﬀsprings and become more represented within the allele frequencies of future generations. Feedback? Email Ari at [email protected] 516 Outbreeding : breeding with individuals with no distinct family ties. Inbreeding : breeding with relatives. 'Large Random M &M' M = No Mutation. Mutations are a cause of change as well.

Sexual Reproduction

2. Sexual Reproduction This will create diversity in 3 ways, as we have seen in the cell division chapter. ● Crossing over Feedback? Email Ari at [email protected] 512 ● Independent assortment ● Random joining of gametes

Balanced polymorphism

3. Balanced polymorphism Poly- many, morphism = forms. Polymorphism = many diﬀerent forms. A balanced polymorphism means that diﬀerent phenotypes within the members of a population can be maintained, through these advantages: ● Heterozygote advantage: ○ When a heterozygote form is more ﬁtted to the environment than either homozygote forms. ○ An example would be sickle cell anemia genes thriving in Africa. AA alleles give normal hemoglobin, SS alleles give sickle cell anemia (likely to die before puberty), whereas AS alleles are beneﬁcial because it oﬀers resistance against malaria — a common killer in Africa. ● Minority advantage: ○ This is when a rare phenotype oﬀers higher ﬁtness than common phenotypes, just as we saw in disruptive selection ! ○ However, as the rare allele increases in frequency, it then becomes common again, and will be selected against, leading to decrease in frequency. Hence, rare phenotypes cycle between low and high frequency ○ Example: hunters usually develop a " search image " for their preys according to the most common appearance, and they hunt accordingly. Preys that the rare phenotype escape the predator, therefore are more 'ﬁt'. ● Hybrid advantage: ○ A hybrid is a result of breeding between two diﬀerent strains of organisms. More breeding options = more variety! Feedback? Email Ari at [email protected] 513 ○ The oﬀspring is usually more superior due to the combination of diﬀerent genes — avoiding deleterious homozygous diseases and maximizing heterozygous advantage. ○ *Interesting side note: humans are very good at producing hybrid veggies and fruits through selecting the best traits of each parent. ● Neutral variations: ○ These are variations that are passed down which do not cause any beneﬁt or harm to the organism. One day they may come in handy if the environment changes.

3. Charles Darwin

3. Charles Darwin Finally, the third and perhaps most well-known scientist in evolutionary biology, Charles Darwin. He proposed the theory of natural selection , which we will talk more about in the upcoming section.

Embryology

3. Embryology Embryological similarities are observed during the development stage in related organisms. For example, if we look at phylum chordata, it comprises of all organisms with a notochord . It includes a variety of animals ranging from small ﬁshes to humans. From the outside, there is a huge physical diﬀerence between a human and a ﬁsh. But on the embryology level, we can see a lineage because all chordates (e.g. human and ﬁsh embryos) have a gill slit at some point of their development. In the image below, notice how similar all of these diﬀerent chordates are in their early embryo appearance.

3. Gradually, the simple compounds became complex compounds and then became organic compounds .

3. Gradually, the simple compounds became complex compounds and then became organic compounds . Feedback? Email Ari at [email protected] 526 The ﬁrst organic compounds are: acetic acid, amino acids, formaldehydes. Now, let's revisit the idea of a reducing environment. A famous duo, Oparin and Haldane , proposed an interesting theory — the Organic "Soup" Theory . They said that since oxygen is very reactive, no organic chemical would have been formed if there were oxygen in the primordial atmosphere. They also said that the reactions to form complex molecules are driven by strong energy emitting naturally on the Earth e.g. lightning , volcanic heat , and most importantly, UV radiation from the Sun. Another scientist duo, Stanley Miller and Harold Urey, later provided strong evidence to support Oparin and Haldane's theory through their famous experiment known as the Miller-Urey experiment . We will talk about this experiment after our timeline overview,

Miller Urey

Mutations

3. Mutations Mutations (a heritable change in DNA) happen with varying damage, to all organisms. Some mutations can happen and go into a 'dormant' phase until there is sudden environmental changes and the mutated traits suddenly become favorable and ﬂourish. 'Large Random M & M' &: read it like "n". N = No natural selection

4. Coevolution:

4. Coevolution: occurs when two species impart selective pressures on each other, resulting in the evolution of both species. Camouﬂage, aposematic coloration, and mimicry are examples of coevolution. Camouﬂage (cryptic coloration) allows animals to avoid visual detection through matching of their appearance to the environment. An insect appearing stick-like is an example of this. Aposematic coloration (warning coloration) is a vibrant, bright coloration of poisonous animals, which warns predators that they are poisonous. An example of aposematic coloration is the bright coloring of poison dart frogs. Mimicry refers to when one species evolves to resemble another species. Batesian mimicry: A non-harmful animal mimics the coloring of a harmful animal. An example is a harmless ﬂy that mimics the coloring of a stinging bee. Mullerian mimicry occurs when diﬀerent poisonous species that share a common predator evolve to resemble each other. This way, it is easier for the predator to learn to avoid these species. An example is of a stinging bee and a stinging wasp, which have evolved to share similar coloring and body size.

Comparative Anatomy

4. Comparative Anatomy As the name suggests, comparative anatomy compares diﬀerent body parts from diﬀerent animals to see possible connections between them. Here, we will talk about three types of structures that are commonly tested on the DAT: Homologous structures: These are structures that may or may not perform the same function , but are derived from a common ancestor Some signature examples that you may want to remember: ○ Forearm of an bird and the forearm of a human ■ Forearms within wings and human arms have diﬀerent functions, but both have the same ancestral origin. Feedback? Email Ari at [email protected] 500 https://en.m.wikipedia.org/wiki/File:Homology_vertebrates-en.svg Analogous structures: These are structures that have the same functions but are not derived from a common ancestor. Both birds and bats evolved to have wings, but they originated from diﬀerent lineages. Some examples: ○ Wings of birds and wings of bats ○ Fins of sharks and penguins Feedback? Email Ari at [email protected] 501 https://commons.wikimedia.org/wiki/File:Figure_20_02_01.jpg Vestigial structures: These are structures that exist, but do not serve a purpose in an organism. Note: they are often homologous to structures that are functional in other organisms. Some examples: ○ Wings of ostrich (homologous to wings of eagles) ○ Appendix of humans (homologous to cecum of cows)

Natural Selection

4. Natural Selection As we've discussed, natural selection is the increase or decrease of allele frequency due to adaptations to the environment. No luck is involved, traits are selected for based on how they confer ﬁtness within an ecosystem. 'Large Random M& M ' The last M = No Migration/No Gene Flow

Polyploidy

4. Polyploidy Many animals are diploids , meaning that we have two copies of each chromosome, also two alleles for each gene. Diploidy is beneﬁcial because the dominant allele can mask the eﬀect of the recessive allele, which is very helpful in cases where the recessive allele is harmful, such as sickle cell anemia. Imagine if we only had one gene for hemoglobin, people who happen to have one copy of sickle cell gene would suﬀer from that disease. But since we are diploids, we would need two copies of the sickle cell gene to have the disease — greatly reducing the number of sickle cell patients! https://commons.wikimedia.org/wiki/File:Haploid_vs_diploid.svg Some plants are polyploids , meaning that they actually have multiple alleles for a gene. This introduces more variety and preservation of diﬀerent alleles in the genome. You never know, one day an allele may come in handy when the environment changes! Finally, we will cover the last part of microevolution — the causes.

4. Simple organic monomers gradually became polymers, forming proteinoids .

4. Simple organic monomers gradually became polymers, forming proteinoids . *Humanoid = someone who looks and behaves like a human. *Proteinoid = something that looks and behaves like a protein. Proteinoids are the abiotically produced version of the proteins we have nowadays. Recall proteins are derived from polypeptides, which form through chains of amino acids joining together from dehydration reaction. So what we can do is to simply heat and dry amino acids through brute force in the lab and we can get proteinoids.

proteinoids

Biochemical

5. Biochemical This is the newest type of evidence that supports the theory of evolution, as scientiﬁc analysis methods has gotten more and more advanced. When we compare DNA sequences in genomes, we see conserved DNA regions across species which are related. The higher the similarity, the stronger the relatedness. Chimpanzees have roughly 98% similarity with humans, showing a strong lineage connection. We also observe common conserved pathways in species that are related. For example, respiration (Kreb's cycle, ETC) can be seen in many eukaryotes like plants and animals, which provides evidence that both plant and animal eukaryotes evolved at one point from a common eukaryotic ancestor. Critical Review: ● 5 types of evidence that supports evolution: ○ Fossils, biogeography, embryology, comparative anatomy, biochemical ● Homologous structures may perform the same function, and must have the same ancestry. ● Analogous structures must perform the same function and must not have the same ancestry. ● Vestigial structures don't serve a purpose in the organism in which they exist.

Gene Flow

5. Gene Flow Though the name sounds pretty similar, gene ﬂow is actually portraying a diﬀerent concept than genetic drift. Genetic drift is the result of a random change in allele frequency. Gene ﬂow is the process of moving alleles between populations through individuals' migration . You can think of gene ﬂow like how we are living in a global village nowadays — people emigrate and immigrate around the world and breed amongst diﬀerent ethnicities. This cause alleles to mix and eventually making variations between populations smaller.

5. Protobionts arose.

5. Protobionts arose. Proto- = prototype. Protobionts = biological prototype. These are actually precursors to cells which have microsomes (membrane-like substance) and have proteinoids incorporated in them.

6. Heterotrophic prokaryotes form.

6. Heterotrophic prokaryotes form. Fastforwarding a couple of steps (more like millions of years), we have the simplest lifeform, heterotrophic prokaryotes! They obtain energy by consuming surrounding organic materials.

7. Autotrophic prokaryotes form.

7. Autotrophic prokaryotes form. As heterotrophic prokaryotes advance and evolve, they became capable of making their own food, hence autotrophs. A good example would be cyanobacteria, which are capable of photosynthesis. This is a very important milestone because photosynthesis = oxygen. With oxygen accumulating in the atmosphere, we will see some dramatic changes.

8. Oxygen accumulates and terminates abiotic chemical evolution.

8. Oxygen accumulates and terminates abiotic chemical evolution. Feedback? Email Ari at [email protected] 527 This is a very important step. We have seen many DAT questions asking about "what ended the abiotic chemical evolution?" and "which important molecule was introduced by autotrophs?". Questions can take many forms, but they ultimately want to ask you if you know the importance of oxygen . With the introduction of oxygen, the Earth transformed from a reducing environment to an oxidizing environment . As oxygen accumulates in the Earth's atmosphere, it reacts with the incoming UV rays and forms a thick ozone layer. Ozone layer blocks a great amount of UV entering the Earth. As we have seen before, UV is perhaps the biggest source of energy propelling the abiotic formation of organic compounds. Now that the supply of UV is cut short, abiotic chemical evolution is forced to terminate.

9. Primitive eukaryotes form.

9. Primitive eukaryotes form. Again, fast-forwarding a few steps, we get the formation of primitive eukaryotes! A theory that explains how eukaryotic cells form is the endosymbiotic theory . Now, let's cut this word up so we can understand it better. Endo means within, and symbiotic is a harmonious relationship where both the "host" and the "invader" provide mutual beneﬁts for each other. The endosymbiotic theory suggests that some membrane-bound organelles, such as mitochondria and chloroplasts , were actually once free-living prokaryotes . Probably through means of phagocytosis, these free-living prokaryotes become engulfed in other prokaryotes. Afterwards, they actually lived in symbiosis and eventually became modern eukaryotes. There are several evidences that support this theory: A. Mitochondria and chloroplasts have their own DNA that is unbound (just like in prokaryotes). B. Thylakoid membranes of chloroplasts resemble the outer cell membrane of cyanobacteria (autotrophs).

Allopatric speciation

Allopatric speciation This is when speciation occurs due to the presence of a geographical barrier. The geographical barrier will stop populations from breeding. As they continue to live in their respective environments, they are subject to the eﬀects of natural selection and will gradually diﬀer from the original group that they used to belong to. Eventually, they will go oﬀ to become a new species. One type of allopatric speciation is adaptive radiation . In this case, many new species form from a single ancestor as they adapt to their respective environments diﬀerently. An example of this would be Darwin's ﬁnches on Galapagos Island, which originated from the same ancestor from the mainland. As the ﬁnches ﬂew to each small islands, they grew apart from their ancestors and became diﬀerent species that "radiated" away from the main branch.

Aposematic coloration **//**

Aposematic coloration (warning coloration) is a vibrant, bright coloration of poisonous animals, which warns predators that they are poisonous. An example of aposematic coloration is the bright coloring of poison dart frogs.

Artiﬁcial Selection:

Artiﬁcial Selection: As the name suggests, this is not a type of natural selection. Artiﬁcial selection is usually carried out by humans when they selectively breed for favorable traits, such as breeding for certain traits in dogs. The artiﬁcial selection of dogs with certain characteristics to create a new, adorable dog breed for example.

Balanced polymorphism:

Balanced polymorphism: Let's imagine we have black and white butterﬂies of the same species due to polymorphism. They are living in an area with dark tree barks, and light tree lives. The white butterﬂies will stick to the leaves we're they're camouﬂaged, and the black moths to the dark bark. And where does this lead to? Reproductive isolation. If this continues for a long time (hundreds of thousands of years), the black and white butterﬂies can become an entirely diﬀerent species.

Batesian mimicry:

Batesian mimicry: A non-harmful animal mimics the coloring of a harmful animal. An example is a harmless ﬂy that mimics the coloring of a stinging bee.

cryptic coloration

Camouﬂage (cryptic coloration) allows animals to avoid visual detection through matching of their appearance to the environment. An insect appearing stick-like is an example of this.

Convergent evolution

Convergent evolution: ○ When two completely unrelated species grow more and more alike (development of analogous structures ) due to adaptations in similar environments.

Critical Review:

Critical Review: ● Cuvier —> catastrophism ● Lamarck: ○ Use and disuse ○ Inheritance of acquired traits (giraﬀe's neck) —> incorrect ● Darwin —> natural selection

Critical Review:

Critical Review: ● Evolution is a gradual and non-random process. ○ Evolution occurs at the population level , not individual level ● Two factors for ﬁtness: survivability and oﬀspring production ● Four requirements for natural selection: ○ There is competition ○ There is variation in traits ○ Traits are heritable ○ Traits must make a diﬀerence in survivability and/or oﬀspring production ● Three types of natural selection: ○ Stabilizing Selection (bell-curve) ○ Directional Selection (bell-curve that shifts towards one side) ○ Disruptive Selection (M-shaped curve)

Critical Review:

Critical Review: ● Hardy Weinberg equilibrium formulae: p+q=1 pqp 2+2 +q2 =1 Feedback? Email Ari at [email protected] 517 ● Conditions for genetic equilibrium ○ Large, random M&M ■ Large population ■ Random mating ■ No mutations ■ No natural selection ■ No migration/gene ﬂow ● When there is no genetic equilibrium —> evolution

Critical Review:

Critical Review: ● Species are a group of individuals that can interbreed. ● The ﬁrst step to speciation is reproductive isolation (prezygotic and postzygotic measures) ● Allopatric speciation: speciation due to the presence of geographical barrier. ○ Adaptive radiation: rapid branching of diﬀerent species from a common ancestor (Darwin's ﬁnches) ● Sympatric speciation: speciation without geographic separation. ● Phylogenetic tree: the simpler, the better

Critical Review:

Critical Review: ● Universe: 14 b years ago. ● Earth: 4.5 b years ago (roughly one third of the age of the Universe) ● First prokaryote: 3.5 b years ago. ● First eukaryote: 2 b years ago. ● Most common gas in Earth's atmosphere : Nitrogen ● Most common component in Earth's crust : Oxygen ● Primordial Earth had no oxygen (strong reducing environment) ○ Formation of autotrophic prokaryotes introduced oxygen —> changed environment into oxidizing . ● Endosymbiotic theory: membrane-bound organelles (chloroplasts and mitochondria) used to be free-ﬂoating prokaryotes —> eaten by other prokaryotes later on.

Directional Selection:

Directional Selection: This is the type of selection where one extreme is favored (as evolution occurs, the population evolves to traits in one direction). For example, black color is more favorable than white color during the Industrial Revolution (where there is lots of black soot around) for moths, so moths eventually develop darker colors that blend in. Another example would be bacteria resistant to a certain type of antibiotics. As we take penicillin for an infection, there might be a bacterium that is genetically Feedback? Email Ari at [email protected] 506 resistant to penicillin. After taking the drug, mainly drug resistant bacteria survive and is directionally selected to reproduce and pass on its resistance genes. https://commons.wikimedia.org/wiki/File:Selection_Types_Chart.png This is a diagram that shows directional selection that giraﬀes evolve to be taller (which enables them to reach leaves of taller trees and which contributes to ﬁtness). Note one extreme is favored by directional selection (red = before, blue = after).

Disruptive Selection:

Disruptive Selection: This is the type of selection that is the exact opposite of stabilizing selection. In this case, oddballs (rare traits) are favored, while mainstreams (common traits) are not. For example, there is a breed of snails that live both in low-vegetation areas (grassﬁelds, meadow) and high-vegetation areas (forests). In low-vegetation areas, predators can detect snails with black shells, so snails with white shells will thrive. In high-vegetation areas, predators feed on snails with white shells, so the ones with black shells will ﬂourish. Feedback? Email Ari at [email protected] 507 https://commons.wikimedia.org/wiki/File:Selection_Types_Chart.png Here, we can see that the middle shellﬁsh is selected against in disruptive selection (red = before, blue = after). There are other types of selections that we may have heard of, including sexual selection and artiﬁcial selection.

Divergent evolution

Divergent evolution: ○ When species diverge from a common ancestor through speciation

Clade

Every cluster you see on a phylogenetic tree is called a clade . It includes an ancestor and all descendants from that ancestor. Therefore, a clade could be as big as the entire tree, or just a small branch at the tip of the tree.

Evidences of Evolution

Evidences of Evolution There are many diﬀerent types of evidences that support the theory of evolution. Some were perceived and noted by Charles Darwin in the 1800s, and some were added later when modern biochemical technologies became available. For the DAT, we will need to know the following 5 lines of evidence. 1. Fossils The study of fossils is also called paleontology . Fossils reveal a lot of information about prehistoric living organisms, including anatomy, lineage, behavior, habitat etc. There are two types of fossils — one is fossils of the actual remains of the animal, another one is fossils of their traces ( ichnofossils ), which records down details like footprints and nests. You may also wonder, how do ﬂeshy living organisms turn into solid rocks? This can be achieved through the process of petriﬁcation . As the body of the living organism becomes buried under layers of sediments, minerals slowly seep into its body and replaces organic materials, hardening the corpse. As we compare diﬀerent fossils found in diﬀerent layers of sedimentations, we can see the transition in time from the deepest (oldest) to the shallowest (youngest). The anatomical change and timeline recorded through fossils is a solid piece of evidence to support the theory of evolution. Feedback? Email Ari at [email protected] 497 https://commons.wikimedia.org/wiki/File:Keichousaurus_hui_fossil.JPG 2. Biogeography Biogeography evidence explains the spread of diﬀerent species throughout the world. As the supercontinent Pangea separated into 7 diﬀerent continents, living organisms were also separated. As the organism's environment changed, evolution took place so that the organisms could better adapt to their new habitats. Feedback? Email Ari at [email protected] 498 https://commons.wikimedia.org/wiki/File:Pangaea_continents.svg For example, both penguins and polar bears thrive in bitter cold environments. But why are polar bears only found in the North Pole whereas penguins are in the South Pole? This is because geographical barrier made it impossible to go to the other pole, so they each adapted to their respective surroundings. 3. Embryology Embryological similarities are observed during the development stage in related organisms. For example, if we look at phylum chordata, it comprises of all organisms with a notochord . It includes a variety of animals ranging from small ﬁshes to humans. From the outside, there is a huge physical diﬀerence between a human and a ﬁsh. But on the embryology level, we can see a lineage because all chordates (e.g. human and ﬁsh embryos) have a gill slit at some point of their development. In the image below, notice how similar all of these diﬀerent chordates are in their early embryo appearance. Feedback? Email Ari at [email protected] 499 https://commons.wikimedia.org/wiki/File:Haeckel_drawings.jpg 4. Comparative Anatomy As the name suggests, comparative anatomy compares diﬀerent body parts from diﬀerent animals to see possible connections between them. Here, we will talk about three types of structures that are commonly tested on the DAT: Homologous structures: These are structures that may or may not perform the same function , but are derived from a common ancestor Some signature examples that you may want to remember: ○ Forearm of an bird and the forearm of a human ■ Forearms within wings and human arms have diﬀerent functions, but both have the same ancestral origin. Feedback? Email Ari at [email protected] 500 https://en.m.wikipedia.org/wiki/File:Homology_vertebrates-en.svg Analogous structures: These are structures that have the same functions but are not derived from a common ancestor. Both birds and bats evolved to have wings, but they originated from diﬀerent lineages. Some examples: ○ Wings of birds and wings of bats ○ Fins of sharks and penguins Feedback? Email Ari at [email protected] 501 https://commons.wikimedia.org/wiki/File:Figure_20_02_01.jpg Vestigial structures: These are structures that exist, but do not serve a purpose in an organism. Note: they are often homologous to structures that are functional in other organisms. Some examples: ○ Wings of ostrich (homologous to wings of eagles) ○ Appendix of humans (homologous to cecum of cows) 5. Biochemical This is the newest type of evidence that supports the theory of evolution, as scientiﬁc analysis methods has gotten more and more advanced. When we compare DNA sequences in genomes, we see conserved DNA regions across species which are related. The higher the similarity, the stronger the relatedness. Chimpanzees have roughly 98% similarity with humans, showing a strong lineage connection. We also observe common conserved pathways in species that are related. For example, respiration (Kreb's cycle, ETC) can be seen in many eukaryotes like plants and animals, which provides evidence that both plant and animal eukaryotes evolved at one point from a common eukaryotic ancestor. Critical Review: ● 5 types of evidence that supports evolution: ○ Fossils, biogeography, embryology, comparative anatomy, biochemical ● Homologous structures may perform the same function, and must have the same ancestry. ● Analogous structures must perform the same function and must not have the same ancestry. ● Vestigial structures don't serve a purpose in the organism in which they exist.

Evolution refers to

Evolution refers to the heritable changes in populations of species over generations. More speciﬁcally, evolution refers to the changes in allele frequencies in populations over time. For example, the allele that codes for white fur coat will become more common as a population of foxes begins to live in the arctic.

allele frequencies

Factors that causes microevolution

Factors that causes microevolution Feedback? Email Ari at [email protected] 514 Let's revisit our mnemonics 'Large Random M&M' for the conditions for Hardy-Weinberg equilibrium. Here, we will think in the opposite directions so that they become factors that cause changes. ' Large Random M&M' Large = large population, minimizing eﬀect of genetic drift . So we know that the ﬁrst factor to cause change is genetic drift. 1. Genetic Drift As we've mentioned above, genetic drift is a change in allele frequencies in a gene pool by chance . The fact that luck is involved diﬀerentiates genetic drift from natural selection, where allele frequencies are selected by the environment to increase or decrease. This is why genetic drift has a much bigger impact on small populations than big populations. There are two signature eﬀects that result in genetic drift: Bottleneck eﬀect When there is a disaster that kill oﬀ most of the population. For example, a forest ﬁre kills oﬀ all squirrels, and by chance two albino squirrels survive. The new population may be albino (if new squirrels don't migrate to this area). What's left is a handful of lucky individuals that survived and a much more smaller gene pool. Some alleles may be lost from this (by chance). https://commons.wikimedia.org/wiki/File:Bottleneck_eﬀect_Figure_19_02_03.jpg In this picture, we can assume that the colors of the marbles refer to the diﬀerent alleles in a population. Inside the bottle, there were many green and red marbles. However, after passing Feedback? Email Ari at [email protected] 515 through the bottleneck, we have lost all red marbles and only a few green ones remain. This shows the loss of alleles during a disaster. Founder eﬀect When there are a couple of individuals that migrated to and settled in a new location, these individuals would have a much smaller gene pool than their original population. The successive generations will descend from the founders, and their unique genetic makeup. https://commons.wikimedia.org/wiki/File:Founder_eﬀect_Illustration.jpg This shows a small group of marbles that "migrated" out from its original population. Since the group is small, it is prone to genetic drift. After a few more generations, all of the original red marbles (alleles) are lost. 'Large Random M&M' Random = random mating. So our second cause of change would be non-random mating. 2. Non-random mating This is when individuals choose who they want to mate with. This is a consequence of sexual selection , which we've covered beforehand. When certain traits are favored over others, they get passed onto oﬀsprings and become more represented within the allele frequencies of future generations. Feedback? Email Ari at [email protected] 516 Outbreeding : breeding with individuals with no distinct family ties. Inbreeding : breeding with relatives. 'Large Random M &M' M = No Mutation. Mutations are a cause of change as well. 3. Mutations Mutations (a heritable change in DNA) happen with varying damage, to all organisms. Some mutations can happen and go into a 'dormant' phase until there is sudden environmental changes and the mutated traits suddenly become favorable and ﬂourish. 'Large Random M & M' &: read it like "n". N = No natural selection. 4. Natural Selection As we've discussed, natural selection is the increase or decrease of allele frequency due to adaptations to the environment. No luck is involved, traits are selected for based on how they confer ﬁtness within an ecosystem. 'Large Random M& M ' The last M = No Migration/No Gene Flow 5. Gene Flow Though the name sounds pretty similar, gene ﬂow is actually portraying a diﬀerent concept than genetic drift. Genetic drift is the result of a random change in allele frequency. Gene ﬂow is the process of moving alleles between populations through individuals' migration . You can think of gene ﬂow like how we are living in a global village nowadays — people emigrate and immigrate around the world and breed amongst diﬀerent ethnicities. This cause alleles to mix and eventually making variations between populations smaller. Critical Review: ● Hardy Weinberg equilibrium formulae: p+q=1 pqp 2+2 +q2 =1 Feedback? Email Ari at [email protected] 517 ● Conditions for genetic equilibrium ○ Large, random M&M ■ Large population ■ Random mating ■ No mutations ■ No natural selection ■ No migration/gene ﬂow ● When there is no genetic equilibrium —> evolution

Fitness

Fitness measures the ability to survive and produce viable and fertile oﬀsprings . DAT Pro-Tip: These are the two key conditions for the being to be favored by natural selection. This also is frequently tested on the DAT, a typical question would be asking you to choose the "ﬁttest" organism, be sure to choose the one with the most viable and fertile oﬀspring!

Founder eﬀect

Founder eﬀect When there are a couple of individuals that migrated to and settled in a new location, these individuals would have a much smaller gene pool than their original population. The successive generations will descend from the founders, and their unique genetic makeup. https://commons.wikimedia.org/wiki/File:Founder_eﬀect_Illustration.jpg This shows a small group of marbles that "migrated" out from its original population. Since the group is small, it is prone to genetic drift. After a few more generations, all of the original red marbles (alleles) are lost. 'Large Random M&M' Random = random mating. So our second cause of change would be non-random mating.

Hardy-Weinberg Equilibrium:

Hardy-Weinberg Equilibrium: Example: Let's look at the peas again. We suppose that the green color is dominant and the yellow color is recessive. Therefore, GG = green , Gg = green , gg = yellow Let: = frequency of the dominant allele ( G )p = frequency of the recessive allele ( g )q = frequency of homozygous dominant ( GG )p 2 = frequency of heterozygous ( Gg )p q2 = frequency of homozygous recessive ( gg )q 2 Now the two important formulae are: p+q=1 pqp 2+2 +q2 =1 Let's try to understand the two equations a little bit. The ﬁrst equation says that which implies that all alleles of the same gene should add up to ,p +q=1 100% (if you take all the dominant alleles and add them to all the recessive alleles, we've considered 100% of the alleles in the population). The second equation says that which means that all individuals should add up to pq ,p 2+2 +q2 =1 100%. This variant of the fomula looks at the diﬀerent allele variations that any given individual could be, and in total all the variations add up to 100%. Feedback? Email Ari at [email protected] 510 = homozygous dominantp 2 = heterozygous (note the '2' in 2pq is because an individual could be pq OR could be qp - wep q2 need to account for both of these as both representing an individual with one p and one q allele, so we have 2pq to cover both of these cases). = homozygous recessiveq 2 Now, If both of the equations hold true , then the population would be under Hardy Weinberg equilibrium . However, if any of the two is not met, then the population is not under Hardy Weinberg equilibrium. Okay, now onto some calculations. If we go back to our peas example, say we're told that there is a population of peas that is 84% green and 16% yellow. And the question asks us what is the heterozygous frequency i.e. ? pq2 Approach: 1. We know that both homozygous dominant ( GG ) or heterozygous ( Gg ) peas will appear green. However, yellow is the recessive color, so they have to be homozygous recessive ( gg ). 2. We know that = frequency of gg q2 3. Therefore, knowing that 16% of the population is yellow, = 16% = 0.16q 2 = q .4 √0.16=0 = which is our frequency of q (recessive allele) in the populationq .40 4. Let's go back to plug this into equation #1: p+q=1 5. Since = 0.4 q p+q=1 0.4p + =1 = 0.6p 6. Now let's calculate our heterozygous frequency, 2pq Plug this into our heterozygous frequency component of the formula pq2 Substitute in the values we've determined, p=0.6 and q = 0.4 = 2*0.4*0.6 = 0.48p q2 = 48%p q2 These two formulas are only valid if the population is in Hardy Weinberg equilibrium. What allows us to determine whether this is the case? We need to see if the Hardy Weinberg conditions are met. To remember the requirements for Hardy-Weinberg equilibrium (ie. that a population is in Hardy Weinberg equilibrium), use the mnemonic " Large Random M&M ". ■ Large populations to minimize the eﬀects of genetic drift . Genetic drift is the random increase or decrease of allele frequencies. A special type of genetic drift is the "founder Feedback? Email Ari at [email protected] 511 eﬀect", which occurs when a group of emigrating individuals do not reﬂect the allele frequencies of the original population. ■ Random mating . Individuals do not seek a particular type of individual to mate with, for example they do not mate only with nearby individuals or express sexual selection. Random mating decreases the chances of a speciﬁc allele changing in frequency. ■ No Mutation : There cannot be any mutations to introduce new alleles in the population. ■ No Natural selection : The environment is not impacting the allele frequencies, and all traits are neutral. ■ No Migration : This can also be written as no gene ﬂow . To ensure that there is no gene ﬂow, the population must be isolated . No amount of gene ﬂow into or out of the population can occur. After reading through all this, you might be a little overwhelmed by the new terminologies like genetic drift, Founder eﬀect etc... But worry not, we will go through this list bullet-by-bullet soon later. The main idea to take away here is that these conditions are actually rarely , if ever, met in the real world . This means that allele frequencies do change from generation to generation, and that evolution will naturally occur. If we think reversely, the conditions that are listed above are actually the factors that propels evolution, because they introduce change into a population. Now, we will ﬁrst talk about the sources of genetic variation, then we will go on to explain the factors that introduce changes (Large Random M&M).

Hybridization

Hybridization: This is a similar idea as polyploidy in plants, but hybridization also occurs in animals. Some hybrids are infertile (mules), and are not deﬁned as a new species. However, some hybrids could be more ﬁt than the purebred species, and eventually form its own line of species.

Indeed, natural selection chooses the ﬁttest being. But in order for natural selection to occur, there are 4 requirements :

Indeed, natural selection chooses the ﬁttest being. But in order for natural selection to occur, there are 4 requirements : 1. There is more demand than supply If the world has an inﬁnite supply of resources, then organisms would reproduce and grow in exponential numbers, without needing to struggle to survive. In this case, there would be no natural selection. Natural selection occurs on the basis that there is always an insuﬃcient supply to the growing demand. Therefore, organisms are constantly competing for survival . Only members of the population who are most "ﬁt" can survive and pass on their genes. Without the competition for survival, there is no mechanism for variations to be selected for or against. 2. There is a diﬀerence in the level of ﬁtness If every individual is equally ﬁt, then there would be no way to select the "ﬁttest" one. Therefore, organisms must have variation in traits . Variation among members of the population diﬀerentiates their ability to compete to survive. For example, during the Industrial Revolution, white tree barks were covered by soot and turned black. At that time, the frequency of black peppered moths increased because of its camouﬂage color. After the Industrial Revolution was over, pollution was cleared and the white peppered moths became favored by natural selection. This shows how diﬀerent variations are favored under diﬀerent environments. 3. Traits must be heritable If traits are not heritable, even if they prompts an individual's survival, they cannot be passed down to the oﬀspring. Therefore, the diﬀerences in traits must be at genetically-inﬂuenced . 4. The variation of traits must be signiﬁcant to reproduction and/or survival Remember the two key conditions for evaluating ﬁtness? If the diﬀerences in traits do not impact reproductive success nor mortality , they would not participate in the process of natural selection. Feedback? Email Ari at [email protected] 505 Genes that improve survival and/or reproductive success will be favored and increase in frequency as generations go by. Genes that decrease survival and/or reproductive success will be ﬁltered out and decrease in frequency as generations go by.

Macroevolution

Macroevolution So far we have covered the micro side of evolution (allele frequencies), here we will expand our vision and see the macro side of things. In short, macroevolution looks at changes that occur at the level that is at or higher than species . Recall the 7 levels of taxonomy (Kingdom, Phylum, Class, Order, Family, Genus, Species). Since we are at least at the level of species, evolution will take time. We need to look from a long-term perspective to see evolutionary patterns. This is unlike microevolution, where genes can change within one generation. Remember, species are individuals that can interbreed . Therefore, two diﬀerent species are reproductively separated , which means that their respective gene pool is also isolated, denying gene ﬂow between species. Nature secures reproductive isolation for each species through two ways: prezygotic and postzygotic isolating mechanisms.

Main components of modern Earth's atmosphere :

Main components of modern Earth's atmosphere : ● Nitrogen gas (78%) ○ Most commoNNNNNNNN (N is for Nitrogen!) ● Oxygen gas (21%) ○ Though this is what we rely on to survive, it is only the second most abundant. ● Argon gas (0.9%) ○ Noble gas here ● The rest is small traces of carbon dioxide, methane, and ozone.

Main components of modern Earth's crust (ranked by % by weight):

Main components of modern Earth's crust (ranked by % by weight): ● Oxygen atom (47%) ○ Careful here, in the Earth's crust oxygen is the most abundant atom. Whereas in the atmosphere, it is ranked second. ● Silicon atom (28%) ○ Think of all the sand we can ﬁnd on the beach, plenty of silicon! ● Aluminum (8%)

Microevolution

Microevolution In this section, we will take on evolution from a micro perspective, which will revolve around the concept of allele frequencies . Allele frequency = gene frequency (could be used interchangeably). Recall from the genetics chapter, we learned that alleles refer to diﬀerent forms of a gene (yellow vs. green pea genes). Hence, allele frequencies basically means how often you can ﬁnd a yellow allele vs. a green allele (gene variant) in a pea population. Microevolution refers to the process when gene frequencies change within a population from generation to generation. Genes that translate into traits that best suit the environment will proliferate — they increase in frequency; whereas genes which become traits that suit the environment less optimally will die out — these unfavorable alleles decrease in frequency. Feedback? Email Ari at [email protected] 509 Before we talk about all the factors that cause changes, let's talk about a state of no change — gene equilibrium . In this state of equilibrium, there is no change in gene frequencies, hence there would be no evolution. Now, when there is genetic equilibrium, how do we calculate gene frequency? A smart duo, G. H. Hardy and W. Weinberg came up with a formula for this: the famous Hardy-Weinberg formula . This frequency formula is the basis for a common tested question on the DAT, so let's go through an example together to make sure we know how the calculation works.

Miller-Urey Experiment:

Miller-Urey Experiment: In short, the Miller-Urey experiment tried to mimic the primordial environments on Earth to test out the organic "soup" theory proposed by Oparin and Haldane. To mimic the reducing environment as proposed in the theory, Miller and Urey set up a ﬂask with methane (CH 4 ), ammonia (NH 3 ), hydrogen (H 2 ), and water (H 2 O) in a closed system connecting to another ﬂask that contains electrodes . Quiz question, which gas is missing? The answer is oxygen. So on one hand, they heated up the ﬂask containing various gases to imitate the high temperature on Earth back in the days. On the other hand, the electrodes produced sparks that imitated lightning (energy source). After a week, they observed several organic compounds that formed: amino acids and other organic acids . However, they did not ﬁnd any complete nucleic acid . This result echoed with the proposed abiotic chemical evolution requirements, and further conﬁrmed Oparin and Haldane's theory.

Mimicry

Mimicry refers to when one species evolves to resemble another species. Batesian mimicry: A non-harmful animal mimics the coloring of a harmful animal. An example is a harmless ﬂy that mimics the coloring of a stinging bee. Mullerian mimicry occurs when diﬀerent poisonous species that share a common predator evolve to resemble each other. This way, it is easier for the predator to learn to avoid these species. An example is of a stinging bee and a stinging wasp, which have evolved to share similar coloring and body size.

Mullerian mimicry

Mullerian mimicry occurs when diﬀerent poisonous species that share a common predator evolve to resemble each other. This way, it is easier for the predator to learn to avoid these species. An example is of a stinging bee and a stinging wasp, which have evolved to share similar coloring and body size.

Natural Selection

Natural Selection Evolution refers to the heritable changes in populations of species over generations. More speciﬁcally, evolution refers to the changes in allele frequencies in populations over time. For example, the allele that codes for white fur coat will become more common as a population of foxes begins to live in the arctic. Natural selection is the gradual , non-random process where alleles become more or less common as a result of the individual's interactions with the environment (as we'll discuss coming up - the genetic variations that lead to diﬀerent traits in organisms are random, but natural selection itself is a non-random process). Those organisms better adapted to survive and reproduce are more successful in passing on their genes, resulting in the evolution of populations over time . Individuals do not evolve, populations evolve over generations . https://commons.wikimedia.org/wiki/File:Mutation_and_selection_diagram.svg Note in the image above: mutation happens randomly. Mutations that lead to successful organisms for that environment allow that speciﬁc genetic variant to thrive. This increases the number of organisms in that population that have the favorable genetics over successive generations. This brings us to the concept of " survival of the ﬁttest ". Feedback? Email Ari at [email protected] 504 Here, note that the term "ﬁtness" doesn't measure the strength or athleticism of an organism. Fitness measures the ability to survive and produce viable and fertile oﬀsprings . DAT Pro-Tip: These are the two key conditions for the being to be favored by natural selection. This also is frequently tested on the DAT, a typical question would be asking you to choose the "ﬁttest" organism, be sure to choose the one with the most viable and fertile oﬀspring! Indeed, natural selection chooses the ﬁttest being. But in order for natural selection to occur, there are 4 requirements : 1. There is more demand than supply If the world has an inﬁnite supply of resources, then organisms would reproduce and grow in exponential numbers, without needing to struggle to survive. In this case, there would be no natural selection. Natural selection occurs on the basis that there is always an insuﬃcient supply to the growing demand. Therefore, organisms are constantly competing for survival . Only members of the population who are most "ﬁt" can survive and pass on their genes. Without the competition for survival, there is no mechanism for variations to be selected for or against. 2. There is a diﬀerence in the level of ﬁtness If every individual is equally ﬁt, then there would be no way to select the "ﬁttest" one. Therefore, organisms must have variation in traits . Variation among members of the population diﬀerentiates their ability to compete to survive. For example, during the Industrial Revolution, white tree barks were covered by soot and turned black. At that time, the frequency of black peppered moths increased because of its camouﬂage color. After the Industrial Revolution was over, pollution was cleared and the white peppered moths became favored by natural selection. This shows how diﬀerent variations are favored under diﬀerent environments. 3. Traits must be heritable If traits are not heritable, even if they prompts an individual's survival, they cannot be passed down to the oﬀspring. Therefore, the diﬀerences in traits must be at genetically-inﬂuenced . 4. The variation of traits must be signiﬁcant to reproduction and/or survival Remember the two key conditions for evaluating ﬁtness? If the diﬀerences in traits do not impact reproductive success nor mortality , they would not participate in the process of natural selection. Feedback? Email Ari at [email protected] 505 Genes that improve survival and/or reproductive success will be favored and increase in frequency as generations go by. Genes that decrease survival and/or reproductive success will be ﬁltered out and decrease in frequency as generations go by. Now that we have covered the requirements for natural selection to take place, we will move onto the 3 diﬀerent types of natural selection. 1. Stabilizing Selection 2. Directional Selection 3. Disruptive Selection Stabilizing Selection: This is the type of selection where mainstream is favored, oddballs are selected against. For example, an average newborn weighs around 3.5kg, babies who are born too small are fragile and risk losing too much body heat, whereas babies who are born too big may face complications during the birth process. https://commons.wikimedia.org/wiki/File:Selection_Types_Chart.png This diagram shows the signature bell curve of stabilizing selection in regards to tail length of geckos. Here, red = before selection and blue = after selection. Note that through the evolutionary process, more geckos have medium length tails and less have short/long tails. Directional Selection: This is the type of selection where one extreme is favored (as evolution occurs, the population evolves to traits in one direction). For example, black color is more favorable than white color during the Industrial Revolution (where there is lots of black soot around) for moths, so moths eventually develop darker colors that blend in. Another example would be bacteria resistant to a certain type of antibiotics. As we take penicillin for an infection, there might be a bacterium that is genetically Feedback? Email Ari at [email protected] 506 resistant to penicillin. After taking the drug, mainly drug resistant bacteria survive and is directionally selected to reproduce and pass on its resistance genes. https://commons.wikimedia.org/wiki/File:Selection_Types_Chart.png This is a diagram that shows directional selection that giraﬀes evolve to be taller (which enables them to reach leaves of taller trees and which contributes to ﬁtness). Note one extreme is favored by directional selection (red = before, blue = after). Disruptive Selection: This is the type of selection that is the exact opposite of stabilizing selection. In this case, oddballs (rare traits) are favored, while mainstreams (common traits) are not. For example, there is a breed of snails that live both in low-vegetation areas (grassﬁelds, meadow) and high-vegetation areas (forests). In low-vegetation areas, predators can detect snails with black shells, so snails with white shells will thrive. In high-vegetation areas, predators feed on snails with white shells, so the ones with black shells will ﬂourish. Feedback? Email Ari at [email protected] 507 https://commons.wikimedia.org/wiki/File:Selection_Types_Chart.png Here, we can see that the middle shellﬁsh is selected against in disruptive selection (red = before, blue = after). There are other types of selections that we may have heard of, including sexual selection and artiﬁcial selection. Sexual Selection: Sexual selection occurs in nature when there is diﬀerential, non-random mating between a male and a female. In nature, and perhaps in our daily lives as well, females can be very picky and they are the ones who choose which male to mate with. This is because compared to males, females have a limited capacity to reproduce due to the relatively long labor period. Hence, females need to carefully pick the superior males to boost the quality of her oﬀsprings. In some species, males even ﬁght for the chance to mate. This preferentially selects males with bigger muscles, stronger horns, and larger stature to pass on their genes. Since the cost of fathering an oﬀspring is very low for most male animals, males increase their ﬁtness by boosting the quantity of his oﬀsprings (trying to impregnate as many females as possible). . Artiﬁcial Selection: As the name suggests, this is not a type of natural selection. Artiﬁcial selection is usually carried out by humans when they selectively breed for favorable traits, such as breeding for certain traits in dogs. The artiﬁcial selection of dogs with certain characteristics to create a new, adorable dog breed for example. Feedback? Email Ari at [email protected] 508 @thatdogdobby Critical Review: ● Evolution is a gradual and non-random process. ○ Evolution occurs at the population level , not individual level ● Two factors for ﬁtness: survivability and oﬀspring production ● Four requirements for natural selection: ○ There is competition ○ There is variation in traits ○ Traits are heritable ○ Traits must make a diﬀerence in survivability and/or oﬀspring production ● Three types of natural selection: ○ Stabilizing Selection (bell-curve) ○ Directional Selection (bell-curve that shifts towards one side) ○ Disruptive Selection (M-shaped curve)

Natural selection is

Natural selection is the gradual , non-random process where alleles become more or less common as a result of the individual's interactions with the environment (as we'll discuss coming up - the genetic variations that lead to diﬀerent traits in organisms are random, but natural selection itself is a non-random process).

Now that we have covered how species form in general, we will cover the two main theories of macroevolution :

Now that we have covered how species form in general, we will cover the two main theories of macroevolution : 1. Phyletic gradualism 2. Punctuated equilibrium

Now that we have covered the requirements for natural selection to take place, we will move onto the 3 diﬀerent types of natural selection.

Now that we have covered the requirements for natural selection to take place, we will move onto the 3 diﬀerent types of natural selection. 1. Stabilizing Selection 2. Directional Selection 3. Disruptive Selection Stabilizing Selection: This is the type of selection where mainstream is favored, oddballs are selected against. For example, an average newborn weighs around 3.5kg, babies who are born too small are fragile and risk losing too much body heat, whereas babies who are born too big may face complications during the birth process. https://commons.wikimedia.org/wiki/File:Selection_Types_Chart.png This diagram shows the signature bell curve of stabilizing selection in regards to tail length of geckos. Here, red = before selection and blue = after selection. Note that through the evolutionary process, more geckos have medium length tails and less have short/long tails. Directional Selection: This is the type of selection where one extreme is favored (as evolution occurs, the population evolves to traits in one direction). For example, black color is more favorable than white color during the Industrial Revolution (where there is lots of black soot around) for moths, so moths eventually develop darker colors that blend in. Another example would be bacteria resistant to a certain type of antibiotics. As we take penicillin for an infection, there might be a bacterium that is genetically Feedback? Email Ari at [email protected] 506 resistant to penicillin. After taking the drug, mainly drug resistant bacteria survive and is directionally selected to reproduce and pass on its resistance genes. https://commons.wikimedia.org/wiki/File:Selection_Types_Chart.png This is a diagram that shows directional selection that giraﬀes evolve to be taller (which enables them to reach leaves of taller trees and which contributes to ﬁtness). Note one extreme is favored by directional selection (red = before, blue = after). Disruptive Selection: This is the type of selection that is the exact opposite of stabilizing selection. In this case, oddballs (rare traits) are favored, while mainstreams (common traits) are not. For example, there is a breed of snails that live both in low-vegetation areas (grassﬁelds, meadow) and high-vegetation areas (forests). In low-vegetation areas, predators can detect snails with black shells, so snails with white shells will thrive. In high-vegetation areas, predators feed on snails with white shells, so the ones with black shells will ﬂourish. Feedback? Email Ari at [email protected] 507 https://commons.wikimedia.org/wiki/File:Selection_Types_Chart.png Here, we can see that the middle shellﬁsh is selected against in disruptive selection (red = before, blue = after). There are other types of selections that we may have heard of, including sexual selection and artiﬁcial selection. Sexual Selection: Sexual selection occurs in nature when there is diﬀerential, non-random mating between a male and a female. In nature, and perhaps in our daily lives as well, females can be very picky and they are the ones who choose which male to mate with. This is because compared to males, females have a limited capacity to reproduce due to the relatively long labor period. Hence, females need to carefully pick the superior males to boost the quality of her oﬀsprings. In some species, males even ﬁght for the chance to mate. This preferentially selects males with bigger muscles, stronger horns, and larger stature to pass on their genes. Since the cost of fathering an oﬀspring is very low for most male animals, males increase their ﬁtness by boosting the quantity of his oﬀsprings (trying to impregnate as many females as possible). . Artiﬁcial Selection: As the name suggests, this is not a type of natural selection. Artiﬁcial selection is usually carried out by humans when they selectively breed for favorable traits, such as breeding for certain traits in dogs. The artiﬁcial selection of dogs with certain characteristics to create a new, adorable dog breed for example.

Origins of Life

Origins of Life In this chapter, we will condense the long journey from the birth of the Universe to the birth of life in a couple of paragraphs. There are several facts that we need to remember for the DAT: Timeline Facts: ● The Big Bang gave rise to the Universe ~14 billion years ago. ● The Earth came ~4.5 billion years ago. ○ *Tip: The DAT won't likely be testing you the speciﬁcs e.g. if the Earth was born 4.3 or 4.5 billion years ago. Even scientists today can't be sure of the exact date! We just need to know the ballpark number and we are good to go. ○ We can think of the Earth as ⅓ as old as the Universe! ● The ﬁrst prokaryotes came ~3.5 billion years ago. ○ One billion years after Earth was born, we got the simplest life forms. ● The ﬁrst eukaryotes came ~2 billion years ago. ○ 1.5 billion years after prokaryotes! Another very common question tests you for the most common compound/atom in the Earth's atmosphere and crust. Since these questions are purely factual, let's ace them and get some free points! Main components of modern Earth's atmosphere : ● Nitrogen gas (78%) ○ Most commoNNNNNNNN (N is for Nitrogen!) ● Oxygen gas (21%) ○ Though this is what we rely on to survive, it is only the second most abundant. ● Argon gas (0.9%) ○ Noble gas here ● The rest is small traces of carbon dioxide, methane, and ozone. Feedback? Email Ari at [email protected] 525 https://commons.wikimedia.org/wiki/File:Atmosphere3.svg Main components of modern Earth's crust (ranked by % by weight): ● Oxygen atom (47%) ○ Careful here, in the Earth's crust oxygen is the most abundant atom. Whereas in the atmosphere, it is ranked second. ● Silicon atom (28%) ○ Think of all the sand we can ﬁnd on the beach, plenty of silicon! ● Aluminum (8%) Now, let's brace ourselves and go through the sequence of events that led to the formation of modern life.

Parallel evolution:

Parallel evolution: ○ When two related species diverge oﬀ from a common ancestor but they both went through similar changes .

Phyletic gradualism:

Phyletic gradualism: This theory says that evolution happened gradually with the accumulation of many small intermediate changes . But when we look at fossils, we cannot see those intermediary stages, hence this theory is not likely to be true.

Polyploidy:

Polyploidy: Polyploidy is a common phenomenon that occurs in plants, often resulting from nondisjunction when chromosomes separate during cell division, speciﬁcally meiosis. Let's imagine plant A, which normally contains 10 chromosomes (2n = 10). During meiosis, if nondisjunction occurs and two of the four gametes have 0 chromosomes, the other two will have 10 chromosomes (2n). Whereas under normal conditions all four gametes should each have 5 chromosomes (n). So what happens next? If one of the 2n gametes fuse with another normal n gamete, there will be a 15 chromosome (3n) zygote. This 3n zygote will be sterile , unless it encounters another polyploidy 3n gamete. This will result in reproductive isolation and could eventually result in polyploidy speciation, if two 3n organisms meet and are reproductively compatible.

Postzygotic Isolation

Postzygotic Isolation There's always needs be a plan B for things if plan A fails. Postzygotic isolation is the backup in case a hybrid zygote actually forms. ● Hybrid mortality ○ This is when a hybrid zygote is not viable and dies before reaching reproductive age. ○ Usually, diﬀerent species have diﬀerent # of chromosomes. When gametes with diﬀerent # of chromosome fuse, the maternal and paternal genetic information cannot match properly. ● Hybrid sterility ○ This is when a hybrid zygote is sterile and cannot reproduce. ○ The most well-known example would be the mule (hybrid of a horse and a donkey). It's viable (doesn't die) but is infertile (can't produce new oﬀspring) ● Hybrid F2 breakdown ○ F2 refers to the next generation of hybrids. In this case, even if hybrids can reproduce, their oﬀspring would suﬀer from decreased ﬁtness.

Preview

Preview: Evolution is the gradual development and change of heritable traits in populations over successive generations. It is a long process that brings about biodiversity. (From a single bacterium to a spectrum of plants and animals, all thanks to evolution!)

Prezygotic Isolation

Prezygotic Isolation As its name suggests, this mechanism prevents fertilization even if mating is attempted, hence preventing the formation of a zygote. Some types of isolation include: ● Habitat Isolation ○ Even if two species reside in the same geographical area, if they occupy diﬀerent habitats , it will hinder mating. ○ For example, many diﬀerent species are restricted to only one layer of the canopy in tropical rainforests. ● Temporal Isolation ○ Species breed and reproduce at diﬀerent times/seasons . ○ " Well, if you are only active past midnight whereas I am an early bird, I don't think we are right for each other. " ● Behavioral Isolation ○ Many species perform courtship rituals to signal to his/her partner, such as singing songs in birds or pheromones in ants. ○ Diﬀerent species would not perform the right type of rituals, hence preventing mating. ● Mechanical Isolation Feedback? Email Ari at [email protected] 518 ○ Male and female genitalia are not compatible between diﬀerent species. ● Gamete Isolation ○ This is when gametes cannot recognize and fertilize each other. ○ If you recall from the reproduction chapter, mammalian oocytes have a structure called the zona pellucida that blocks the binding of sperm from alien species. This is an example of gametic isolation.

Punctuated equilibrium:

Punctuated equilibrium: This theory says that there are short spurs of evolutionary changes during long periods of stasis (no evolution). This theory is more supported by the fossil evidence.

Sexual Selection:

Sexual Selection: Sexual selection occurs in nature when there is diﬀerential, non-random mating between a male and a female. In nature, and perhaps in our daily lives as well, females can be very picky and they are the ones who choose which male to mate with. This is because compared to males, females have a limited capacity to reproduce due to the relatively long labor period. Hence, females need to carefully pick the superior males to boost the quality of her oﬀsprings. In some species, males even ﬁght for the chance to mate. This preferentially selects males with bigger muscles, stronger horns, and larger stature to pass on their genes. Since the cost of fathering an oﬀspring is very low for most male animals, males increase their ﬁtness by boosting the quantity of his oﬀsprings (trying to impregnate as many females as possible). .

Sources of genetic variation:

Sources of genetic variation: As humans, we have around 20,000 genes in our genome. And since we are a diploid organism, we will have about 40,000 alleles (two variations for each gene). Here, we will explain how each organism is unique, all thanks to the massive genetic diversity! 1. Mutation This is the most straightforward way to have a new allele, through genetic mutation. Note here that these mutation cannot be fatal! https://commons.wikimedia.org/wiki/File:Antithrombin-gene-strand-switch.gif 2. Sexual Reproduction This will create diversity in 3 ways, as we have seen in the cell division chapter. ● Crossing over Feedback? Email Ari at [email protected] 512 ● Independent assortment ● Random joining of gametes https://commons.wikimedia.org/wiki/File:Meiosis_Overview_new.svg 3. Balanced polymorphism Poly- many, morphism = forms. Polymorphism = many diﬀerent forms. A balanced polymorphism means that diﬀerent phenotypes within the members of a population can be maintained, through these advantages: ● Heterozygote advantage: ○ When a heterozygote form is more ﬁtted to the environment than either homozygote forms. ○ An example would be sickle cell anemia genes thriving in Africa. AA alleles give normal hemoglobin, SS alleles give sickle cell anemia (likely to die before puberty), whereas AS alleles are beneﬁcial because it oﬀers resistance against malaria — a common killer in Africa. ● Minority advantage: ○ This is when a rare phenotype oﬀers higher ﬁtness than common phenotypes, just as we saw in disruptive selection ! ○ However, as the rare allele increases in frequency, it then becomes common again, and will be selected against, leading to decrease in frequency. Hence, rare phenotypes cycle between low and high frequency ○ Example: hunters usually develop a " search image " for their preys according to the most common appearance, and they hunt accordingly. Preys that the rare phenotype escape the predator, therefore are more 'ﬁt'. ● Hybrid advantage: ○ A hybrid is a result of breeding between two diﬀerent strains of organisms. More breeding options = more variety! Feedback? Email Ari at [email protected] 513 ○ The oﬀspring is usually more superior due to the combination of diﬀerent genes — avoiding deleterious homozygous diseases and maximizing heterozygous advantage. ○ *Interesting side note: humans are very good at producing hybrid veggies and fruits through selecting the best traits of each parent. ● Neutral variations: ○ These are variations that are passed down which do not cause any beneﬁt or harm to the organism. One day they may come in handy if the environment changes. 4. Polyploidy Many animals are diploids , meaning that we have two copies of each chromosome, also two alleles for each gene. Diploidy is beneﬁcial because the dominant allele can mask the eﬀect of the recessive allele, which is very helpful in cases where the recessive allele is harmful, such as sickle cell anemia. Imagine if we only had one gene for hemoglobin, people who happen to have one copy of sickle cell gene would suﬀer from that disease. But since we are diploids, we would need two copies of the sickle cell gene to have the disease — greatly reducing the number of sickle cell patients! https://commons.wikimedia.org/wiki/File:Haploid_vs_diploid.svg Some plants are polyploids , meaning that they actually have multiple alleles for a gene. This introduces more variety and preservation of diﬀerent alleles in the genome. You never know, one day an allele may come in handy when the environment changes! Finally, we will cover the last part of microevolution — the causes.

Stabilizing Selection:

Stabilizing Selection: This is the type of selection where mainstream is favored, oddballs are selected against. For example, an average newborn weighs around 3.5kg, babies who are born too small are fragile and risk losing too much body heat, whereas babies who are born too big may face complications during the birth process. https://commons.wikimedia.org/wiki/File:Selection_Types_Chart.png This diagram shows the signature bell curve of stabilizing selection in regards to tail length of geckos. Here, red = before selection and blue = after selection. Note that through the evolutionary process, more geckos have medium length tails and less have short/long tails.

Sympatric speciation

Sympatric speciation Realistically, being physically separated is probably the most straightforward way to stop species from mating. However, there are still other ways that will prevent mating and induce speciation without necessarily being isolated. In the case of sympatric speciation, speciation occurs WITHOUT the presence of a geographical barrier. Feedback? Email Ari at [email protected] 520 There are three main ways to achieve this: 1. Balanced polymorphism 2. Polyploidy 3. Hybridization Balanced polymorphism: Let's imagine we have black and white butterﬂies of the same species due to polymorphism. They are living in an area with dark tree barks, and light tree lives. The white butterﬂies will stick to the leaves we're they're camouﬂaged, and the black moths to the dark bark. And where does this lead to? Reproductive isolation. If this continues for a long time (hundreds of thousands of years), the black and white butterﬂies can become an entirely diﬀerent species. Polyploidy: Polyploidy is a common phenomenon that occurs in plants, often resulting from nondisjunction when chromosomes separate during cell division, speciﬁcally meiosis. Let's imagine plant A, which normally contains 10 chromosomes (2n = 10). During meiosis, if nondisjunction occurs and two of the four gametes have 0 chromosomes, the other two will have 10 chromosomes (2n). Whereas under normal conditions all four gametes should each have 5 chromosomes (n). So what happens next? If one of the 2n gametes fuse with another normal n gamete, there will be a 15 chromosome (3n) zygote. This 3n zygote will be sterile , unless it encounters another polyploidy 3n gamete. This will result in reproductive isolation and could eventually result in polyploidy speciation, if two 3n organisms meet and are reproductively compatible. Hybridization: This is a similar idea as polyploidy in plants, but hybridization also occurs in animals. Some hybrids are infertile (mules), and are not deﬁned as a new species. However, some hybrids could be more ﬁt than the purebred species, and eventually form its own line of species.

The Big Bang

The Big Bang gave rise to the Universe ~14 billion years ago.

The Earth

The Earth came ~4.5 billion years ago. ○ *Tip: The DAT won't likely be testing you the speciﬁcs e.g. if the Earth was born 4.3 or 4.5 billion years ago. Even scientists today can't be sure of the exact date! We just need to know the ballpark number and we are good to go. ○ We can think of the Earth as ⅓ as old as the Universe!

Parsimony

The idea of parsimony is very important in evolutionary biology. Parsimony refers to the idea: 'the simpler, the better' . The tree with the least number of evolutionary reversals , convergent evolution , and parallel evolution is the most parsimonious- or the simplest. This is often how biologists formulate phylogenetic trees.

paleontology

The study of fossils is also called paleontology . Fossils reveal a lot of information about prehistoric living organisms, including anatomy, lineage, behavior, habitat etc.

The ﬁrst eukaryotes

The ﬁrst eukaryotes came ~2 billion years ago. ○ 1.5 billion years after prokaryotes!

The ﬁrst prokaryotes

The ﬁrst prokaryotes came ~3.5 billion years ago. ○ One billion years after Earth was born, we got the simplest life forms.

Theories of Evolution

Theories of Evolution In this chapter, we will talk about three scientists and their respective theories that contributed to the hypothesis of evolution. 1. Baron Georges Cuvier Cuvier proposed the theory of catastrophism . He is also the founder of paleontology (study of fossils). Through observing fossil patterns, he proposed that there must have been sudden catastrophes that happened spontaneously throughout history causing mass extinction of species in that area. (dinosaurs, for example) After the catastrophe, the landscape is drastically changed and new life forms will eventually populate the area, giving oﬀ new fossil specimens. 2. Jean-Baptiste Lamarck Lamarck was actually the ﬁrst biologist who believed in evolution, instead of special creation of life forms. He proposed two interesting hypotheses of evolution: ● Use and disuse ○ The more used the body part is, the more it will develop i.e. a giraﬀe's neck grows longer when it tries to feed from higher trees. ○ The less used the body part is, the more weakened it will be i.e. certain species of monkeys didn't use their tails much, so through disuse that species evolved to not have tails ● Inheritance of acquired traits ○ He believed that whatever characteristics the organism acquires throughout its life (through use and disuse) will be passed onto its oﬀsprings. ■ For example, if a giraﬀe stretches its neck continually, it will develop a longer neck, and will pass on the long neck to its oﬀspring. ○ This theory is incorrect because environmentally acquired characteristics are actually not heritable . They are changes to the organism, but don't represent a heritable change because the use/disuse doesn't change the genetic code, ie. the DNA. 3. Charles Darwin Finally, the third and perhaps most well-known scientist in evolutionary biology, Charles Darwin. He proposed the theory of natural selection , which we will talk more about in the upcoming section. Critical Review: ● Cuvier —> catastrophism ● Lamarck: ○ Use and disuse ○ Inheritance of acquired traits (giraﬀe's neck) —> incorrect ● Darwin —> natural selection

There are two modes of speciation:

There are two modes of speciation: allopatric and sympatric speciation.

ichnofossils

There are two types of fossils — one is fossils of the actual remains of the animal, another one is fossils of their traces ( ichnofossils ), which records down details like footprints and nests.

Those organisms better adapted to survive and reproduce are more successful in passing on their genes, resulting in the evolution of populations over time . Individuals do not evolve, populations evolve over generations . Note in the image above: mutation happens randomly. Mutations that lead to successful organisms for that environment allow that speciﬁc genetic variant to thrive. This increases the number of organisms in that population that have the favorable genetics over successive generations.

Timeline

Timeline 1. Once upon a time, the Earth had a primordial atmosphere that was made of many diﬀerent inorganic compounds, except for oxygen . It mostly consisted of: methane (CH 4 ), ammonia (NH 3 ), carbon monoxide (CO), carbon dioxide (CO 2 ), hydrogen gas (H 2 ), nitrogen gas (N 2 ), water (H 2 O), hydrogen sulﬁde (HS). The fact that oxygen was not part of the primordial atmosphere is very important, because the primordial atmosphere is a reducing environment without oxygen. We will talk about this concept later down the timeline. 2. Eventually, as the Earth cooled down signiﬁcantly, some of the gases in the primordial atmosphere condensed and formed the primordial sea . The primordial sea composed of mostly water and some minerals found in the Earth's crust. 3. Gradually, the simple compounds became complex compounds and then became organic compounds . Feedback? Email Ari at [email protected] 526 The ﬁrst organic compounds are: acetic acid, amino acids, formaldehydes. Now, let's revisit the idea of a reducing environment. A famous duo, Oparin and Haldane , proposed an interesting theory — the Organic "Soup" Theory . They said that since oxygen is very reactive, no organic chemical would have been formed if there were oxygen in the primordial atmosphere. They also said that the reactions to form complex molecules are driven by strong energy emitting naturally on the Earth e.g. lightning , volcanic heat , and most importantly, UV radiation from the Sun. Another scientist duo, Stanley Miller and Harold Urey, later provided strong evidence to support Oparin and Haldane's theory through their famous experiment known as the Miller-Urey experiment . We will talk about this experiment after our timeline overview, 4. Simple organic monomers gradually became polymers, forming proteinoids . *Humanoid = someone who looks and behaves like a human. *Proteinoid = something that looks and behaves like a protein. Proteinoids are the abiotically produced version of the proteins we have nowadays. Recall proteins are derived from polypeptides, which form through chains of amino acids joining together from dehydration reaction. So what we can do is to simply heat and dry amino acids through brute force in the lab and we can get proteinoids. 5. Protobionts arose. Proto- = prototype. Protobionts = biological prototype. These are actually precursors to cells which have microsomes (membrane-like substance) and have proteinoids incorporated in them. 6. Heterotrophic prokaryotes form. Fastforwarding a couple of steps (more like millions of years), we have the simplest lifeform, heterotrophic prokaryotes! They obtain energy by consuming surrounding organic materials. 7. Autotrophic prokaryotes form. As heterotrophic prokaryotes advance and evolve, they became capable of making their own food, hence autotrophs. A good example would be cyanobacteria, which are capable of photosynthesis. This is a very important milestone because photosynthesis = oxygen. With oxygen accumulating in the atmosphere, we will see some dramatic changes. 8. Oxygen accumulates and terminates abiotic chemical evolution. Feedback? Email Ari at [email protected] 527 This is a very important step. We have seen many DAT questions asking about "what ended the abiotic chemical evolution?" and "which important molecule was introduced by autotrophs?". Questions can take many forms, but they ultimately want to ask you if you know the importance of oxygen . With the introduction of oxygen, the Earth transformed from a reducing environment to an oxidizing environment . As oxygen accumulates in the Earth's atmosphere, it reacts with the incoming UV rays and forms a thick ozone layer. Ozone layer blocks a great amount of UV entering the Earth. As we have seen before, UV is perhaps the biggest source of energy propelling the abiotic formation of organic compounds. Now that the supply of UV is cut short, abiotic chemical evolution is forced to terminate. 9. Primitive eukaryotes form. Again, fast-forwarding a few steps, we get the formation of primitive eukaryotes! A theory that explains how eukaryotic cells form is the endosymbiotic theory . Now, let's cut this word up so we can understand it better. Endo means within, and symbiotic is a harmonious relationship where both the "host" and the "invader" provide mutual beneﬁts for each other. The endosymbiotic theory suggests that some membrane-bound organelles, such as mitochondria and chloroplasts , were actually once free-living prokaryotes . Probably through means of phagocytosis, these free-living prokaryotes become engulfed in other prokaryotes. Afterwards, they actually lived in symbiosis and eventually became modern eukaryotes. There are several evidences that support this theory: A. Mitochondria and chloroplasts have their own DNA that is unbound (just like in prokaryotes). B. Thylakoid membranes of chloroplasts resemble the outer cell membrane of cyanobacteria (autotrophs). Feedback? Email Ari at [email protected] 528 10. More complex eukaryotes and multicellular organisms came about That's the most important events that happened on Earth since its birth summarized in 10 points. Now, we will take a look at the famous Miller-Urey experiment that we talked about earlier.

Timeline Facts:

Timeline Facts: ● The Big Bang gave rise to the Universe ~14 billion years ago. ● The Earth came ~4.5 billion years ago. ○ *Tip: The DAT won't likely be testing you the speciﬁcs e.g. if the Earth was born 4.3 or 4.5 billion years ago. Even scientists today can't be sure of the exact date! We just need to know the ballpark number and we are good to go. ○ We can think of the Earth as ⅓ as old as the Universe! ● The ﬁrst prokaryotes came ~3.5 billion years ago. ○ One billion years after Earth was born, we got the simplest life forms. ● The ﬁrst eukaryotes came ~2 billion years ago. ○ 1.5 billion years after prokaryotes!

To recap, in this section of macroevolution, we began with Afterwards Finally

To recap, in this section of macroevolution, we began with the concept of a species and the mechanisms of reproductive isolation in nature. Afterwards, we went on to talk about how speciation occurs. Then, we presented two theories of evolution : phyletic gradualism and punctuated equilibrium, while showing that the latter is the more probable of the two. Finally, we wrapped up with the 4 patterns of evolution and how to design a good phylogenetic tree .

We have probably all seen a phylogenetic tree that looks like this:

We have probably all seen a phylogenetic tree that looks like this: Feedback? Email Ari at [email protected] 523 Note: this is an example of what a phylogenetic tree looks like, you do not need to know the details of the labels https://commons.wikimedia.org/wiki/File:Phylogenetic_tree.svg According to the deﬁnition, a phylogenetic tree is a branch diagram that shows the inferred evolutionary relationship between diﬀerent taxa. Here, the word inferred is very important, because we are tracing back in history, biologists can only infer the relationship between species using bits and pieces of the biological evidences of evolution we mentioned earlier (fossils, anatomical structures). Every cluster you see on a phylogenetic tree is called a clade . It includes an ancestor and all descendants from that ancestor. Therefore, a clade could be as big as the entire tree, or just a small branch at the tip of the tree. When designing a phylogenetic tree, the tree with the least amount of assumptions is preferred because it minimizes homoplasy. Homoplasy, also known as convergent evolution , is a phenomenon that describes when two distinct clades develop strikingly similar characteristics ( analogous structures ) despite the fact that there is no common ancestor with the trait. A well-known example of this is the convergent evolution of wings in both birds and bats . Rather than making it easy to develop phylogenetic trees, this tends to confound biologists who construct the tree. For instance, imagine a phylogenetic tree where ﬂight was viewed as the most important characteristic. This would lead you to determine that birds and bats are the most closely related of all vertebrates, which is simply not true. The idea of parsimony is very important in evolutionary biology. Parsimony refers to the idea: 'the simpler, the better' . The tree with the least number of evolutionary reversals , convergent evolution , and parallel evolution is the most parsimonious- or the simplest. This is often how biologists formulate phylogenetic trees. Feedback? Email Ari at [email protected] 524 To recap, in this section of macroevolution, we began with the concept of a species and the mechanisms of reproductive isolation in nature. Afterwards, we went on to talk about how speciation occurs. Then, we presented two theories of evolution : phyletic gradualism and punctuated equilibrium, while showing that the latter is the more probable of the two. Finally, we wrapped up with the 4 patterns of evolution and how to design a good phylogenetic tree . Critical Review: ● Species are a group of individuals that can interbreed. ● The ﬁrst step to speciation is reproductive isolation (prezygotic and postzygotic measures) ● Allopatric speciation: speciation due to the presence of geographical barrier. ○ Adaptive radiation: rapid branching of diﬀerent species from a common ancestor (Darwin's ﬁnches) ● Sympatric speciation: speciation without geographic separation. ● Phylogenetic tree: the simpler, the better

Homoplasy

When designing a phylogenetic tree, the tree with the least amount of assumptions is preferred because it minimizes homoplasy. Homoplasy, also known as convergent evolution , is a phenomenon that describes when two distinct clades develop strikingly similar characteristics ( analogous structures ) despite the fact that there is no common ancestor with the trait. A well-known example of this is the convergent evolution of wings in both birds and bats . Rather than making it easy to develop phylogenetic trees, this tends to confound biologists who construct the tree. For instance, imagine a phylogenetic tree where ﬂight was viewed as the most important characteristic. This would lead you to determine that birds and bats are the most closely related of all vertebrates, which is simply not true.

Bottleneck Effect

When there is a disaster that kill oﬀ most of the population. For example, a forest ﬁre kills oﬀ all squirrels, and by chance two albino squirrels survive. The new population may be albino (if new squirrels don't migrate to this area). What's left is a handful of lucky individuals that survived and a much more smaller gene pool. Some alleles may be lost from this (by chance). In this picture, we can assume that the colors of the marbles refer to the diﬀerent alleles in a population. Inside the bottle, there were many green and red marbles. However, after passing Feedback? Email Ari at [email protected] 515 through the bottleneck, we have lost all red marbles and only a few green ones remain. This shows the loss of alleles during a disaster.

petriﬁcation

You may also wonder, how do ﬂeshy living organisms turn into solid rocks? This can be achieved through the process of petriﬁcation . As the body of the living organism becomes buried under layers of sediments, minerals slowly seep into its body and replaces organic materials, hardening the corpse.

Feralis (2018 FULL) Chapter 13: Evolution

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