Evolution

• Basic tenet of science: everything in the natural world has a natural cause and explanation.

• How did life originate?

• There are many forms of life, displaying many similarities and differences. How did they get that way?

• Aristotle and his medieval European followers believed that all living things could be arranged on a scale, from lowest to highest: the Great Chain of Being. In this view, the work of biologists was to find the place of each organism in the Chain.

Geology

• The theory of evolution grew out of geology. Specifically, the realization that the Earth is very old.

• Current estimate of the age of the Earth is 4.6 billion years.

Geology• James Hutton (late 1700’s) and Charles Lyell in the 1820’s and 1830’s developed the theory of Uniformitarianism: that the

geological processes we see today are the same ones that operated in that past. For example, we can see rivers slowly eroding rocks. Carried on for a long enough time, a river can erode its way through a mile of rock to form the Grand Canyon.

• Another example: high mountains are raised gradually through a series of earthquakes and volcanic eruptions. Oceans lay down sediments that are washed off the land, and eventually they build up to miles deep deposits.

• If the geology we see is due to the same slow forces in operation today, the Earth must have been here for a very long time

• The contrasting theory in Lyell’s time was Catastrophism: specifically, the great Flood of Noah caused the visible geology of the Earth in a very short period of time.

Fossils

• Fossils are the remains of ancient life, turned to stone by chemical processes.

• They have been known since ancient times, but their significance wasn’t clear until the 1800’s. Fossils can be created by burying the remains of living things in sediments that slowly compress into layers of rock.

↑ The first good geological maps of the layers of rocks in England showed that each layer had its own distinct set of fossils. And, the older the rocks—the deeper the layer was—the simpler the fossils were.

Fossils

• Long before rocks could be dated, the geological ages were defined based on their characteristic fossils.

• Most fossils come from the hard parts: bones, teeth, shells. These structures first appeared about 600 million years ago. Fossils before this time are much more difficult to detect: mostly microscopic. And, very old rocks are hard to find and often very distorted. But, the earliest fossils come from about 3.8 billion years ago, in almost the oldest rocks known, close to the beginning of the Earth,

3.5 billion year old Apex Chert microfossils

Radioactive Dating

• Ancient rocks are dated by looking at radioactive isotopes. There are numerous methods, and ages are often estimated by several different methods.

• We will discuss the potassium-argon dating method. This method is used to find the age of volcanic deposits, and it has been heavily used to date the remains of ancient human ancestors in east Africa.

Radioactive Dating

• Potassium is a element that is common in volcanic rock. The isotope potassium-40 (atomic weight of 40 protons + neutrons) is radioactive: it decays into argon-40. The rate of decay is steady and not affected by external conditions at all. It takes 1.25 billion years for ½ of the potassium-40 to convert into argon-40.

• Argon is a “noble” gas: it has 8 electrons in its outer shell and doesn’t combine with other atoms to form compounds. Under all earthly conditions, argon is a gas.

• When a volcano erupts, the lava is molten, and all of the argon gas is released into the atmosphere. When the rock freezes, it contains potassium-40 but no argon-40. Over time, argon-40 builds up from the decay of the potssium-40. By measuring the ratio of potassium-40 to argon-40, the amount of time since the rock was molten can be determined.

Radioactive Dating

• Other dating methods use uranium and lead, or carbon-14, or a variety of other radioactive isotopes.

Radioactive Dating

• The time scale used in evolutionary studies is calibrated by counts of tree rings. In some places this scale goes back 9000 years.

Lamarck• By the end of the 1700’s, it was clear

from the diversity of life and the fossil record that organisms had changed over time. The force driving the change remained mysterious.

• One common idea was the “inheritance of acquired characteristics”, a theory associated with Jean Lamarck. This theory states that during the course of an individual’s life, various needs and desires bring about changes in the body’s internal state, and that these changes are then passed along to the offspring. For example, if you exercise heavily, your children will be born with heavier muscles than you were. Or, giraffes stretch their necks to reach leaves on tall tress, so their offspring have longer necks.

• This theory is known to be wrong. Inherited changes do occur, but they are random in nature, not influenced by the needs of the individual. The cells that generate the sperm and eggs are separate from the rest of the body’s cells.

Lamarck• Many demonstrations disproving

inheritance of acquired characteristics: in the late 1800’s one researcher cut the tails off a groups of mice at birth for 200 generations. Even after that time their tails were as long as in the original generation.

• Another: take blood from black rabbits and transfuse it into white rabbits. The offspring of the white rabbits are still white, even though the blood was supposed to carry the germs of the acquired characteristics.

• The real problem for Lamarck is that no one was able to do an experiment that demonstrated inheritance of acquired characteristics under controlled conditions. If a theory is repeatedly tested and never successful, people start to doubt its truth.

Darwin and Wallace

• Charles Darwin and Alfred Russel Wallace independently came up with the key ideas of evolution through natural selection in the 1830’s -1850’s. Both spent years traveling to exotic locations and examining the plants and animals there. Darwin went first, but he spent years slowly thinking and writing. He was only prodded to publish when Wallace showed him his manuscript.

Charles Darwin Alfred Wallace

Evolution through Natural Selection

• Three basic conditions for natural selection to occur:– 1. There must be variation within the species.– 2. The variations must be inherited.– 3. Some variants must have a better ability to survive and

reproduce than others.

• Fitness = ability to survive and reproduce. More fit individuals have a better chance of producing offspring than less fit individuals.

• This means that the alleles present in the more fit individuals will increase their share of the population with each generation.

• In time, the alleles that increase fitness take over the population, and the less fit alleles disappear.

Artificial Selection

• In artificial selection, humans define fitness (ability to survive and reproduce) by only allowing the desired individuals to mate, then selecting the best offspring.

• Darwin noted many examples of this: he was devoted to pigeon breeding.

Natural Selection• It is easy to find examples in

nature where one original type has been converted to a number of similar types that differ in small ways. Darwin found a group of finches on the isolated Galapagos Islands that fit this description.

↑ Another example: moths in England had 2 main varieties, dark and light. In the 1800’s, the dark form was most common. At that time, trees were covered with soot from burning coal, and the dark moths were hard for predators to see. In more recent times, coal soot has decreased, so tree trunks are lighter. Now the lighter moths are more common, because the dark ones stand out.

Summary of Natural Selection

• 1. Any population can reproduce beyond the capacity of the environment to sustain it. Some resource will be in short supply if the population gets too large. In this case, individual organisms will compete with each other for that resource.

• 2. Within a species there are a number of different genetic variations (alleles) for many genes. Some of these alleles help the organisms outcompete other members of the population: increase their ability to obtain critical resources to survive and reproduce.

• 3. The individuals possessing the better alleles will have a better chance of reproducing, so their offspring will make up a larger portion of the next generation.

• 4. This process (called microevolution) increases the frequency of the more fit alleles in the population. Over time the population becomes better and better suited for its environment.

Gene Pool and Allele Frequencies• Selection (artificial or natural) involves changes in the “gene pool”: the

genetic resources of the entire population that can breed with each other.

• The gene pool is counted in terms of “allele frequencies”: how many copies of each allele are present in the population.

• For example, consider a gene with 2 alleles: A and a. In one population of 100 organisms, there are 30 AA individuals, 60 Aa individuals, and 10 aa individuals.

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Gene Pool and Allele Frequencies• Counting copies of A: 2 in each AA individual (30 x 2 = 60 A alleles) plus 1

in each Aa individual (= 60 more A alleles), for a total of 120 A alleles in this population

• Counting copies of a: 2 in each aa individual ( 10 x 2 = 20 a alleles) plus 1 in each Aa individual (= 60 more), for a total of 80 a alleles.

• There are 200 total alleles ( 2 in each of the 100 individual organisms), so the frequency of A is 120 / 200 = 0.6, and the frequency of a is 80 / 200 = 0.4

• Note that the total of the frequencies equals 1: 0.6 + 0.4 = 1. A frequency of 1 means that every allele is either A or a.

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Selection Changes Allele Frequencies

• Individuals can’t change which alleles they have, but the frequency of different alleles in a population can change. “Individuals don’t evolve—populations do.”

• As an example of fitness, assume that the aa homozygotes have a genetic disease that makes them less fit than AA or Aa individuals. In an extreme case, assume that the aa individuals die before they can reproduce. Their fitness is 0, since they can’t pass their genes on to future generations.

• So, only the AA and Aa individuals mate. They still generate some aa offspring ( ¼ of the offspring when Aa x Aa), but the number of aa’s is low. The frequency of A increases while the frequency of a decreases.

• This change in allele frequencies within a species based on differences in fitness is called “microevolution”. It is the source of slow changes in the characteristics of a species.

Populations in Equilibrium

• Many populations are more or less in equilibrium: allele frequencies stay constant between generations, no selection occurs because all the genotypes are equally fit.

• These equilibrium populations are governed by the Hardy-Weinberg rule, which determines how many homozygotes and heterozygotes there will be, based on the allele frequencies.

Populations in Equilibrium

• Hardy-Weinberg rule: – if the frequency of A is called p and – the frequency of a is called q, then – the frequency of AA individuals is p2, – the frequency of Aa individuals is 2pq, and – the frequency of aa individuals is q2.

Hardy-Weinberg Equation: p2 (AA) + 2pq (Aa) + q2 (aa) = 1

Populations in Equilibrium

• For example, – if the frequency of A is 0.6 and– the frequency of a is 0.4, then– a population in equilibrium will

have (0.6)2 = 0.6 x 0.6 = 0.36 as the frequency of AA’s.

– The Aa’s will be at a frequency of 2pq = 2 x 0.6 x 0.4 = 0.48.

– The aa’s will be at q2 = 0.4 x 0.4 = 0.16 frequency.

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p = frequency of A = 0.6 q = frequency of a = 0.4

phenotypes

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# of alleles in gene pool

(total = 1000)

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Conditions Necessary for Equilibrium

• Once a population is in equilibrium, the frequencies of the different genotypes doesn’t change between generations.

• To be in equilibrium, a population must fulfill several conditions:– 1. population must be very large– 2. all mating must be random– 3. no fitness differences between individuals– 4. no migration in or out of the population– 5. No new mutations

Effects of Hardy-Weinberg Conditions

• Mutation. Mutations are the raw material of evolution. They occur at a slow but steady rate, and they provide alleles of greater or lesser fitness. However, mutations by themselves don’t influence allele frequencies significantly.

• Migration. The movement of organisms in and out of populations keeps a species from fragmenting into several different species. When two populations mix, the combined population has allele frequencies that are a mix of the two original sets of frequencies.

• Random mating. Most organisms don’t mate at random, especially among the animals. Mate selection is a constant factor. The main form of non-random mating is called “assortative mating”, which means mating with someone similar to you. Tall people with tall people, smart people with smart people, etc. Disassortative mating, where the types differ (“opposites attract”) is also found.

Non-random Mating

•Inbreeding, mating with close blood relatives, is another form of non-random mating. In humans, almost all cultures forbid brother-sister marriages, but different cultures have different views on first cousin marriage. Some cultures encourage it and others forbid it.

•Overall, humans are inbred are approximately equivalent to everyone marrying a third cousin (i.e. common great-great grandparents). In the US population, the inbreeding equivalent is approximately that of fifth cousins (common great-great-great-great grandparents: mine were born about 1780).

•Why does inbreeding occur? • Desire to keep wealth or power in the family• Most people live near where they were born: ½ of all living descendants of the people who came to the US on the Mayflower in 1620 live within 50 miles of their landing spot at Plymouth Rock, Massachusetts.• Opposites don’t attract: even distant, unknown relatives share cultural characteristics and appearance details that are attractive to each other.

Directional Selection

• The simplest form of selection is directional selection: one extreme phenotype is less fit than the rest of the phenotypes.

• Plot the distribution of the trait being selected on a graph. Usually get a bell-shaped curve (normal distribution, Gaussian distribution)—most individuals are more or less average, with a few extremes at each end.

• Don’t let individuals at one extreme breed.

• In later generations, the population average shifts away from the less fit extreme.

Examples of Directional Selection

• Pesticide resistance. In the absence of pesticides, a few insects are naturally resistant. They have a combination of genes that does them no particular good in the absence of pesticides. However, when pesticides are used, suddenly these insects are the only ones who survive. Many of their descendants get the same resistance genes. After several generations of spraying pesticides to kill the insects, all the insects are resistant.

• Antibiotic resistance. Same phenomenon applied to disease-causing bacteria. If the antibiotic leaves some of them alive, their descendents are all resistant and the antibiotic no longer works. A growing problem—antibiotic resistance is spreading faster than new antibiotics are being developed.

• Cancer cell progression. If chemotherapy doesn’t kill all the tumor cells, the ones left living are the most resistant ones. They multiply, creating a new tumor that isn’t sensitive to chemotherapy.

• One solution: use multiple drugs—much more difficult to be resistant to several different antibiotics.

Stabilizing Selection• Selection can act to favor the most

common type, the middle of the distribution. This can happen when both extreme types are attacked. The status quo is maintained.

• Human birth weight: a small baby will survive the birth process better than a big one (and so will the mother). However, small baby will have a harder time surviving after birth than a big one. Leads to opposing forces that result in an average size of baby.

• Example: The fly Eurosta solidaginis lays its eggs on goldenrod plants. The larvae hatch, then bore into the stem, creating a gall, a swollen area of the stem. The larvae have 2 predators that eat them. One is a wasp that can only penetrate small galls. The other is a woodpecker that can penetrate any gall, but prefers the larger ones. So, both small galls and large galls are attacked. The intermediate ones have the highest rate of survival. Selection favors intermediate sizes.

Disruptive Selection

• Disruptive selection is the opposite of stabilizing selection. In disruptive selection, the average type is the least fit. Only the extremes survive, creating a population with two different alternatives. This is one of the forces that drives the splitting of one species into 2.

• This would seem to be an odd form of selection. Often it occurs with sudden changes in the environment.

• Example: grasses that find themselves near mines. Mine tailings containing heavy metals are toxic to most plants. Some grasses are resistant to heavy metal poisoning, so they can grow on the mine tailings. Less resistant members of the species grow on uncontaminated ground. Since heavy metal resistance is expensive, the resistant plants are less successful on uncontaminated ground. So, the species is being cut into 2 groups: the resistant variety growing on the mine tailings and the sensitive variety growing on clean soil.

Sexual Selection• No trait is more important to

producing offspring than finding a mate. And, selecting a high quality mate increase the chance that your offspring will survive to adulthood. For these reasons, much selection is aimed at increasing attractiveness to the opposite sex and signaling (or faking) good genes and good health. This is sexual selection.

• In the situations common in birds and mammals, the males must drive away their rivals, and the females must pick the “best” male as a mate.

• This leads to ritual fighting among males in many species: male elk fighting during mating season is an example. The winner drives off the loser, leaving the winner in possession of a territory that he can keep females in.

More Sexual Selection

• To show that they are in good health, one sex often puts on a showy display. The bright coloration of male birds is a good example. It serves no end other than to attract females, and it makes them easier prey for predators. But, it can lead to strong selection for very extreme appearances.

Heterozygote Advantage

• Sometimes selection works on the single gene level, by conferring an advantage on the heterozygotes. This allows 2 alleles to be maintained in a population even though both homozygotes are less fit than the heterozygote.

• Good example: sickle cell hemoglobin. The heterozygote is resistant to malaria and is otherwise normal under most conditions. Homozygotes for sickle cell hemoglobin die early with severe anemia. Homozygous normal people die of malaria. The relative death rates between these 3 genotypes causes an allele frequency of about 0.2 for sickle cell hemoglobin in areas affected by malaria. (That is, 20% of the alleles in the population are the sickle cell type.)

Neutral Mutations

• In Darwin’s time, natural selection was thought to be the only force driving evolution. This led to “social Darwinism”, theories that glorified competition above all else. The catchphrase “nature red in tooth and claw” comes from this era.

• However, it became clear that many traits seem to be selectively neutral, or at least there was no obvious selection pressure on them. For example, much of the DNA is not part of any gene. How could a base change mutation in DNA outside of a gene affect fitness? Genetic variants that don’t affect fitness are called “neutral mutations” and they are said to be “selectively neutral”.

• An example: detached vs. attached earlobes. Hard to see how this would affect fitness.

• Another example: blood type.

My Boyfriend is Type B

Japanese Blood Type Personality Chart

Type A

Best Traits

Conservative, reserved, patient, punctual, perfectionist and good with plants.

Worst Traits

Introverted, obsessive, stubborn, self conscious, and uptight

Type B

Best Traits

Creative and passionate. Animal loving. Optimistic and flexible

Worst Traits

Forgetful, irresponsible, individualist

Type AB

Best Traits

Cool, controlled, rational. Sociable and popular. Empathic

Worst Traits

Aloof, critical, indecisive and unforgiving

Type O

Best Traits

Ambitious, athletic, robust and self-confident. Natural leaders

Worst Traits

Arrogant, vain and insensitive. Ruthless in Korean, written and directed by Choi Seok-Won

Genetic Drift• Genetic drift is the random change in allele frequencies due to chance alone. It happens in all

populations, but it is most significant in small populations.• Genetic drift is largely the result of sampling error: the variation in results that occurs when too

small a sample is taken. For example, if a population contains only 3 individuals, 2 males and 1 female, the allele frequencies of the next generation will be heavily influenced by the female’s choice of a mate. Any alleles found only in the unmated male will be lost.

• If a population stays small, genetic drift leads to the fixation of one allele and the loss of other alleles. Fixation = the allele has a frequency of 1, all alleles in the population are of this one type.

• The time until fixation is random, but it is proportional to the size of the population. In large populations fixation by genetic drift is rare.

Bottlenecks

• A bottleneck is a severe reduction in the size of a population. Whatever the allele frequencies were before, the allele frequencies after the bottleneck are based solely on the alleles found in the survivors.

Bottlenecks• Small islands are especially subject to

bottlenecks—it is very easy to lose a significant portion of the population. A typhoon hit Pingalap Atoll, a small Pacific Ocean island, in 1780. All but 30 people died. One of the 9 male survivors was a high ranking man who had the recessive genetic condition achromatopsia. This causes complete colorblindness, cataracts, and often complete blindness due to retinal degeneration. Today between 4 and 10% of the people on this island are homozygous for the disease. The allele frequency before the typhoon was low, but due to the vagaries of survival, it became very high.

• The entire human population is thought to have gone through a bottleneck about 100,000 years ago. One consequence is that there is less genetic variation among the 6 billion humans than there is among, for example, one 55-member social group of chimpanzees living in West Africa.

• Cheetahs in Africa went through a very bad bottleneck within the last 10,000 years. Their population was reduced to fewer than 100 individuals. The population has since grown much larger, but the amount of genetic diversity among them is very low because there were so few founders.

Founder Effect

• The founder effect is very similar: when a small group leaves a large population, the allele frequencies in the newly established population are based on which alleles were in the small group of founders.

• Example of founder effect: the Amish are a group descended from 30 Swiss founders who renounced technological progress. Most Amish mate within the group. One of the founders had Ellis-van Crevald syndrome, which causes short stature, extra fingers and toes, and heart defects. Today about 1 in 200 Amish are homozygous for this syndrome, which is very rare in the larger US population.

• Note the effect inbreeding has here: the problem comes from this recessive condition becoming homozygous due to the mating of closely related people.