Evolutionary Biology Exam 1
Darwin viewed evolution as a branching process
"As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications." - Darwin, 1859, The Origin of Species
4. Which of the following is testable using the scientific method? (a) Evolutionary processes (b) Creationism (c) Intelligent design (d) The "works of God" (e) All of the above
(a) Evolutionary processes - The evolutionary process can be tested using scientific methods. This scientific method utilizes a step-wise process that relies on observable facts and evidence to form theories; it involves asking a question, forming a hypothesis, testing the hypothesis, and forming a theory.
13. Homologous traits: (a) are always inherited from a common ancestor (b) always perform the same function in different species (c) always perform a different function in different species (d) a and c are correct (e) b and c are correct
(a) are always inherited from a common ancestor - Homologous traits are traits that have shared ancestry. As species evolve over time because of adaptations to environments, these traits may change in function and in appearance. However, ultimately, they still share common genetics or embryonic structure.
6. The similarly streamlined bodies of these three classes of animals below (fish ==> shark, land reptile ==> ichthyosaur, land mammal ==> porpoise) is an example of: (a) convergent evolution (b) atavistic emergence of a suppressed trait (c) common ancestry (d) heritability = 1 (e) similarity due to homology
(a) convergent evolution
8. The geological fact that the lowest layer of a rock formation is the oldest, while the youngest layer is at the top, is called: (a) uniformitarianism (b) interposition (c) evolutionary theory (d) antidisestablishmentarianism (e) the principle of superposition
(a) uniformitarianism
2. Which of the following is NOT a place that scientists look to for evidence of evolution? (a) the fossil remains of extinct animals (b) changes within an individual organism (c) examination of similar traits in closely related species (d) changes in allele frequencies in wild populations (e) None of the above - scientists look to all of these sources
(b) changes within an individual organism - Evolution is the process that causes species to change to survive better in their environments, and there are various types of evidence for the course of evolution such as fossorial data of extinct species and the presence and absence of similar traits in organisms that are related or not, such as homologous and analogous structures.
11. Pseudogenes are an example of: (a) atavisms (b) vestiges (c) developmental anomalies (d) genes that have been deleted (e) none of the above
(b) vestiges
1. Darwin published his influential book, On the Origin of Species, in what year? (a) 1659 (b) 1756 (c) In 1859 (d) In 1856 (e) 65 mya
(c) In 1859
7. Which book did Charles Darwin famously carry with him on the Voyage of H.M.S. Beagle? (a) Treatises on Plant Hybrids, by Gregor Mendel (b) A Universe from Nothing, by Laurence Krauss (c) Principles of Geology, by Charles Lyell (d) An Essay on the Principle of Population, by Thomas Malthus (e) A Universe from Nothing, by Lawrence Krauss
(c) Principles of Geology, by Charles Lyell - H.M.S. Beagle was the ship on which Charles Darwin went for a voyage. The voyage lasted for about five years. The book that Charles Darwin famously carried with him on the Voyage of H.M.S. Beagle was Principle of Geology, by Charles Lyell.
12. Which of the following is not an atavism? (a) pelvic bones of a whale (b) a tail on a newborn human baby (c) hind limbs (legs) protruding from a dolphin's body (d) outside toes on a modern horse (e) teeth in the mouth of a chicken
(c) hind limbs (legs) protruding from a dolphin's body - An atavism is an evolutionary throwback to more primitive times. It is a genetic trait that reoccurs after skipping several generations. If a person has blue eyes like her great-great-grandmother, but her mother, grandmother, and great grandmother have brown eyes, then having blue eyes is an example of atavism. All of the given examples are of atavism except hind limbs in dolphins.
5. Evolution functions on the level of _______________. (a) individuals (b) species (c) populations (d) tissues (e) none of the above
(c) populations - Evolution is the change in the heritable characteristics of populations over several generations. It relies on the process of natural selection. It was first postulated by Charles Darwin in his book "On the Origin of Species" in 1859. According to this theory, all the life forms shares a single ancestor.
3. The following type(s) of evidence helped Darwin develop his theory of natural selection: (a) evidence from artificial selection experiments (b) evidence from the geological record (c) evidence from genetic analyses using Galápagos finches (d) all of the above (e) both a and b are correct
(d) all of the above - Darwin's visit to the Galapagos Islands in 1835 helped him to formulate ideas on natural selection through observations on finches. Darwin took Lyell's book on Principles of Geology which stated that the gradual geological processes have gradually shaped Earth's surface. He knew artificial selection could change domestic species over time, from which he inferred about the changes of species over time through natural selection.
9. In evolutionary studies, the "gene pool" refers to which of the following: (a) a common ancestor and all its descendants (b) individuals who move into or out of a stable population (c) a gene's favorite place to bask in the sun and jump off the high dive (d) all the gametes in a population (e) none of the above
(d) all the gametes in a population - Gene pool refers to the total number of every individual present in the population. If the population have a large gene pool it indicates that they have higher Genetic diversity and greater the Genetic diversity greater the chances of biological fitness and supply.
14. The story of peppered moth (Biston betularia) in industrial England represents a tangible example of what process? (a) artificial selection (b) genetic drift (c) evolution of divergence in mating behavior (d) natural selection (e) none of the above
(d) natural selection The story of the peppered moth or bistonbetularia in England is an example of a process called natural selection, and in this case changes in the environment, causes the color change in the moth or increased frequency of dark-colored moths, which helps in the survival of the organisms, and this concept is also called as industrial melanism.
10. Shared ancestry accounts for: (a) vestigial traits (b) some of the similarities between even distantly related species (c) the hierarchical structure of the evolutionary tree of life (d) homologous traits (e) all of the above
(e) all of the above - Common descent or shared ancestry is the process where speciation occurs in a common species, and one species evolves into two or more species over a period of time. Over a period of time, these species become completely different, but still there are a few traits that still remain similar.
15. In the cladogram above, which two plant types are the most distantly related (see picture)? (a) Lepidodendron and Clubmoss (b) Oak and Yew (f) Oak and Fern (g) Clubmoss and Psilotum (h) Yew and Fern
(g) Clubmoss and Psilotum
Adaptive radiation of Darwin's finches
- (Darwin) - Beak size evolution - Medium ground finch
What sort of evidence would support (or not support) evolution by natural selection?
- (Darwin) - Hypothesis: Evolution by natural selection ==> Non-random evolution - Alternative (null) hypothesis: Evolution by genetic drift ==> Random evolution ==> Need to reject the model of random evolution - Evidence 1: Convergent evolution - Evidence 2: Adaptive radiation
Conditions for evolution by selection
- (Darwin) 1. Variation 2. Heritability 3. Change in time / Differential fitness of variants ==> When 3 depends on the natural environment, it is natural selection. When 3 depends on selective breeding by humans, it is artificial selection.
Conditions for evolution by selection
- (Darwin) 1. Variation 2. Heritability 3. Differential fitness of variants - Outcome: Change in variant frequency such that the population will accumulate traits better fit for the environment
1. Atavistic legs in cetaceans
- 1 in 500 whales is born with a rear leg protruding outside the body wall - Structure varies, but many have a femur, tibia, and fibula - Some have feet and toes
1. Evolution of Hawaiian Honeycreepers
- 56 species known to have existed, but only 18 species are left (due to extinction from a lot of human influences) - Asian rosefinches are closest ancestor and hypothesized a large group sought greener pastures ~ 5-7 million years ago and landed on Hawaii. Since then, a adaptive radiation to fill a variety of empty niches
Science
- A body of knowledge about the natural world - The process of generating it by observations and experimentation ==> Evidence based knowledge and its generative process
Node
- A common ancestor - Depicts speciation events in ancestral populations
Advanced and primitive
- A primitive trait is the original condition of that trait in the common ancestor - Advanced indicates a notable change from the original condition
Taxon
- A taxonomic unit ==> EX: Genes, organisms, population
Phylogeny
- A tree that represents an evolutionary relationship ==> EX: Of genes, organisms, populations, species
Beak size evolution
- All birds feed on small, soft seeds in times plenty - But during droughts: ==> no small soft seeds ==> Predominantly caltrop (hard, woody seeds) in major droughts
Branch length
- Amount of time; amount of change - Evolution of populations between speciation events
Clade
- An ancestor and all of its descendants - A monophyletic group - A natural taxonomic group
Paraphyletic group
- An ancestor and some but not all of its descendants; unnatural grouping ==> EX: Fish, reptiles
Vestiges
- An evolutionary remnant that was an adaptation in an ancestor, but has either ===> 1. Lost its usefulness completely ==> 2. Been coopted for a new use (i.e. exaptation). - Identifiable by the similarity to homologous traits in related species - A trait is vestigial when it no longer performs the function for which it evolved. - Can be maintained by selection if useful
Evidence 2: Adaptive radiation
- An increased relative rate of speciation in one lineage, generating a variety of species with diverse ecological niches - Rapid accumulation of non-random, adaptive changes in closely related species - Involves intra/inter-specific competition for resources - Occurs when new opportunities for diversification arise
Evolution
- Any heritable change in a population over time ==> EX: Genes, development, morphology, physiology, behavior, habitat - Descent with modification from a common ancestor (Darwin)
Using "basal" as a description
- Basal' is a term in biology for 'primitive' or 'ancestral' - In phylogenetics, basal is the direction of the base (or root) of a rooted phylogenetic tree or cladogram
3. Human development
- Carnegie stages of human development ==> Sizable fishlike tail until 7 weeks into development - Human vestigial tail (coccyx) versus monkey tail (true tail) - Human atavistic tails ==> We still carry a developmental program for making tails, homologous to the one in our tailed ancestors ==> We carry, in fact, exactly the same genes responsible for tail development in mice - normally deactivated in human fetuses
2. Vestigial eyes
- Cavefish: ==> Cannot see ==> Vestigial ==> Not functional: Possibly some amount light detection - Eye development and degeneration in Astyanax mexicanus: why develop and then degenerate? ==> Eye development and degeneration in Astyanax mexicanus. Surface fish (A) and cavefish (B) adults. Surface fish (C) and cavefish (D) embryos at the 24 h stage showing eye primordia with lens (L) and optic cup (OC). Arrowheads indicate the ventral sector of the OC. (E) Diagram showing the timing of eye growth and development in surface fish (top) and eye degeneration in cavefish (bottom). Sightlessness a derived character from sighted ancestor.
3. Vestigial legs
- Cetaceans: ==> Cannot walk or swim ==> Vestigial ==> Not functional: Vestigial hindlimb, includes pelvis and femur, no longer connected to rest of skeleton, embedded in tissue, no apparent function (as hindlimb)
Derived character state
- Changed from the ancestral condition - Apomorphy
Artificial selection
- Changes in population characteristics by artificial selection are evident all around us - The speed of evolution by selection depends on the amount of heritable variation and strength of selection
Three basic types of trees
- Cladogram - Phylogram - Chronogram
3. Theory of descent with modification from a common ancestor
- Common ancestry (Darwin) - Extinction
Why is convergence considered strong evidence for natural selection?
- Consider potential mechanisms for the evolution of similarity in different lineages: ==> a. Natural selection ==> b. Chance/Genetic drift ==> c. Common ancestry 1. Evolution of similarity in independent lineages suggests non-random evolution, and is inconsistent with b. 2. c is ruled out based on phylogeny. 3. Natural selection is the only mechanism that can plausibly explain convergence.
Answer 1: God
- Diversity as God's creation (15-17th C) ==> The Great Chain of Being - The role of natural sciences (Linnaeus) - New data and ideas started to emerge ==> 1. Extinction ==> 2. Uniformitarianism
What happened to the lichens?
- During the Industrial Revolution, coal burning caused air pollution that killed the lichens - After WWII, peppered morphs increased in frequency, coinciding with a decrease in coal use
Tree of life
- Eukaryotes - Bacteria - Archaea
What sort of evidence would support (or not support) common ancestry of different organisms? What is the evidence for common ancestry of humans and other species? What is the evidence for common ancestry across organisms?
- Evidence 1: Comparative Anatomy - Evidence 2: The Universal Genetic Code - Evidence 3: The Universal Membrane - Evidence 4: Eukaryotic Organelles - Evidence 5: Anterior-Posterior Patterning in Animal Embryos - Evidence 6: Molecular Sequence Data
Evolution is a fact and a theory
- Evolution as a fact refers to the heritable change over time - Evolution as a theory explains the mechanisms of heritable change over time
Evolution by natural selection
- Evolution by natural selection involves a combination of randomness and lawfulness: ==> Random: The random "indifference" of the mutation process ==> Lawful: Orders and filters the variation, keeping individuals better adapted to the environment and culling those less well adapted - "The non-random survival of random variants" (Dawkins)
Misconception 6: Evolution always proceeds from simple to complex
- Evolution can proceed from simple to complex ==> EX: Evolution of multicellularity and division of labor - But evolution can sometimes proceed from complex to simple ==> EX: Gene losses in the human genome (20 gene losses in humans)
Misconception 5: Evolution is a march of progress
- Evolution has no foresight or a predetermined goal, implied by progress - In addition, humans did not evolve from chimpanzees; we share a common ancestor
Misconception 1: Evolution is just a theory
- Evolution is not speculation, but is well supported by evidence - Evolution is not just a theory, but is also a fact, and they are different
Artificial selection in dogs
- Extant: 40 species of extant wild dogs - Extinct: triple or so that number - Domestic dog diversity created in last 10,000 years: ==>Wild dogs: 2-60 pounds ==> Domestic dogs: 2-180 pounds 1. Ample genetic variation for color, size, shape, and behavior in the ancestral dog lineage to create the 150 different domestic dog breeds 2. A small fraction of the variation was produced by new mutations 3. All of this happened in the past 10,000 years
Georges Cuvier (1769-1831)
- Extinction ==> EX: Mammoth and Mastodon - Father of Paleontology
Catastrophism
- Extinctions occurred due to catastrophes in the past 6000 years ==> EX: Flood
4. Evolution of streamlined shapes in swimmers
- Fish ==> shark - Land reptile ==> ichthyosaur - Land mammal ==> porpoise
What is the evidence for common ancestry across organisms?
- Fundamental similarities are found across the tree of life. - Fundamental similarities ==> common ancestry = homology (Darwin)
Taxa
- Groups of organisms distinguished as belong to a cohesive unit (Linnaeus) ==> EX: A species or Genera, or Families, Orders
5. Evolution of complex eyes
- Human eyes versus animal eyes - The tree of humans and animals of having eyes or no eyes
2. Atavistic digits in horses
- In modern horses only the middle finger (the hoof) remains - Horse development: 3 toes à 1 toe as growth of middle toe outpaces the others - In some cases, the other toes continue developing - Extra-toed horses were considered supernatural wonders, ridden by Julius Caesar and Alexander the Great - A character is homologous among species but a given character state may not be. ==> EX: Number of toes: - Five toes are homologous in humans and crocodiles - Three toes in guinea pigs and rhinoceroses are NOT homologous because these evolved the condition independently. - The diagram above shows the porpoise with 5 digits and the horse with only ONE digit. Both have been modified into "single structures" ==> EX: Diagram of atavistic digits in horses: - Angiosperm forests of the Eocene, made it such that it was advantageous for horses to walk on spread out toes, because the ground was soft and lush with foliage. - After the Eocene grasslands appeared which opened up the landscape and made horse susceptible to faster predators that could navigate the open grassland. So horse lineages began experimenting lengthening of limbs and the lifting of some toes from the ground in such a way that the weight of the body was gradually placed on one of the longest toes, the third.
Artificial selection in chickens
- In nature: 10-15 eggs/year - Average number of eggs produced by one hen in 1960: 160 - Average number of eggs produced by one hen in 2009: 325
Kettlewell
- In the 1950's, Kettlewell tested camouflage effectiveness and confirmed the hypothesis - Test hypothesis: Industrial area vs agricultural area - Experiments to test the hypothesis Kettlewell studies of 1905's: ==> 1. Quantitative ranking of camouflage effectiveness ==> 2. Direct observations of predation by birds (filmed) ==> 3. Recapture rates of moths released onto trees in polluted and unpolluted woodlands
Rooted tree
- Includes the focal group of species being studied, along with a closely related outgroup species - Contain information about the ancestral states of characters, and they can be used to trace the evolutionary history of groups of organisms through time
Evidence 1: Convergent evolution
- Independent evolution of similar traits in distinct lineages due to common environmental pressures of natural selection, and not due to common ancestry - Convergence <==> homology
6. Evolution of placental and marsupial mammals
- Marsupial mammals colonized and diversified in Australia and New Guinea - Placental mammals dominated the rest of the world - Both mammal lineages radiated to fill the same, virtually identical set of niches
Maximum Parsimony method
- Minimum number of changes 1. Step 1: List all possible tree topologies 2. Step 2: For each homologous character (i.e. site), determine the minimum number of changes necessary for each tree 3. Step 3: Sum the number over all sites to compute the minimum number of changes per tree.
4. Pseudogene
- Molecular Vestige - A non-functional DNA segment that shows sequence similarity to a functional gene - Contain insertions, deletions, truncations, and/or internal stop codons - Humans carry around ~2000 pseudogenes. - Usually non-deleterious, but why do they exist? ==> Molecular vestige; the ancestor had the functional version of the genes. ==> EX: Diatom bas1 alignment - Which are the pseudogenes? Stop codons: TAG, TAA, and TGA
Percentages of shared genes
- Monkeys: 96% identical in DNA sequence and >99% identical in AA sequence - Mice: 92% of human genes are shared with mice - Flies: 44 % of human genes are shared - Bacteria: 26 % of human genes are shared - Plants: 18 % of human genes are shared.
3. Evolution of Marsupial Mammals
- Mostly confined to the Southern Hemisphere - The predominant mammal group in Australia and New Guinea (>200 species) - One species in North America, the Virginia Opossum - The earliest marsupial fossils (80 Mya) are North American: - Southward migration à South America (~40 Mya) - Reached Australia 30 Mya à major diversification - The breakup of Pangaea - The breakup of Gondwana - Did they swim across the South Atlantic? Perhaps not, could have migrated through Antarctica - North America ==> South America ==> Antartica ==> Australia -Prediction: Antarctica should have marsupial fossils 30-40 Mya in age: ==> 1982 - discovery of an extinct, rat-sized marsupial on Seymour Island ==> Eocene-aged (35-40 Mya) ==> Antarctica was much warmer; pole à equator temperature gradient less severe ==> Antarctica was probably tropical in the early Eocene ==> Glaciers began advancing ~34 Mya ==> Marsupial fossils in Antartica - Phylogeny of marsupial mammals - Convergent evolution in placental and marsupial mammals: ==> Marsupial mammals colonized and diversified in Australia and New Guinea (adaptive radiation) ==> Placental mammals dominated the rest of the world ==> Both mammal lineages radiated to fill the same, virtually identical set of niches
Scientific ideas
- Must be falsifiable - There is no absolute certainty in science, but a differing degree of confidence - So, any statement in science should be considered a hypothesis
Generation of heritable variation (ultimately) by mutation
- Mutation - Migration
2. Transformational theory of evolution by inheritance of acquired characteristics
- New heritable characteristics can be acquired through the effect of use or the environment (Lamarck) ==> EX: August Weismann's Germplasm Theory and giraffes - The unit of evolution are individuals
3. Evolution of "vultures"
- New world vultures - Storks and their relatives - Birds of Prey - Old world vultures ==> New and Old World "vultures" look a lot alike, but they have evolved independently from different ancestors
4. Variational theory of evolution by natural selection
- No transformation of individuals during their lifetime, but the frequency of genetically distinct variants in a population changes over time due to differences in survival and reproductive rates (Darwin and Wallace) - The unit of evolution is population
Selection
- Nonrandom sorting based on differences in the ability of variants to survive and reproduce ==> EX: Differential fitness
Industrial Melanism in Peppered Moths
- Observation: Frequencies of melanic (dark) morphs increased in museum collections from 1849-1880s - Hypothesis: Since moths frequently rest on tree trunks, melanic morphs are better camouflaged on darker tree trunks - Prediction: Peppered morphs have higher fitness on lichen-covered trees; melanic morphs have higher fitness on dark soot-covered trees - "Carbonaria" vs "typica"
Adaptive radiations in Oceanic Islands
- Oceanic islands were never connected to a continent ==> Arose from the seafloor as volcanoes or coral reefs ==> Initially lacking terrestrial life ==> EX: Hawaiian Islands and Galápagos archipelago - Oceanic islands are a blank canvas, full of empty habitats and niches, with few predators and competitors - Initial colonization followed by adaptive radiation
Selective Breeding
- Only individuals with a particular trait or a combination of traits are allowed to breed, - Or for quantitative traits, only individuals that exceed some threshold are allowed to breed
Misconception 2: Evolution is natural selection
- Oversimplification - Natural selection is one of the mechanisms of evolution; there are additional mechanisms that are involved in evolution ==> EX: Mutation and genetic drift
Taxonomic system
- Represents a nested hierarchy (Linnaeus) ==> EX: Humans are in the genus Homo, which belongs to another group of taxa called "Hominidae", which belongs to even bigger group of taxa called Primata, etc.
Anestral versus Derived
- Rooted trees in this book will be depicted so that earlier (ancestral) character states are to the left, and later (derived) character states are to the right - Ancestral and derived characters are relative to specific locations on the phylogeny
38. Explain the relationship between heritability (h2) and the selection differential (S) when a trait is under directional selection
- S is the selection differential, which is the difference of the base population mean and the mean of the selected parents - h2 is the heritability, which is a measure of the genetic component that is contributed by the additive genetic variance. - The response to selection can thus be derived by multiplying the heritability by the selection differential. (R=h2*S)
Sorting of heritable variation
- Selection - Random genetic drift
When shared by multiple taxa
- Shared derived character state, or - Synapomorphy: ==> EX: Backbone in vertebrates - Basis for monophyly
UPGMA (Unweighted Pair Group Method with Arithmetic mean)
- Shortest pairwise distance - Sequential clustering algorithm - Assumes linearity between evolutionary distance and divergence time (i.e. constant rates of evolution 1. Step 1: Generate a distance matrix (e.g. % difference in sequence identity 2. Step 2: Identify the pair that has the shortest distance and cluster them 3. Step 3: Make a new matrix with combined taxa 4. Step 4: Repeat until the last pair is clustered.
Phylogram
- Shows extent of divergence <== Amount of change ==>
Cladogram
- Shows relationships only <== No meaning ==>
Chronogram
- Shows time to last common ancestor(s) <== Amount of time ==>
Homology
- Similarity due to common ancestry (Darwin) ==> EX: Vestiges and atavisms
5 fly species differ in body color and eye color. What is history of trait evolution?
- Simple reconstruction: ==> Parsimony ==> Minimize changes. ==> (Look at body color alone for example) - A different reconstruction: ==> 1 change (purple to orange) More parsimonious
1. Theory of Organic Progression
- Species first originate by spontaneous generation and evolve up the scale of organization from simple to complex forms of life, leading to the pattern of the Great Chain of Being (Lamarck) - No common ancestry - No extinction
Atavism
- Sporadic expression/recapitulation of a "lost" ancestral trait by misfiring of an ancestral, but suppressed, developmental program - Rare - Absent in parents or the species of the individual displaying the trait - Completely useless
Misconception 4: Evolution violates the 2nd law of thermodynamics
- The 2nd law of thermodynamics states that disorder (entropy) increases in an isolated system, where no energy or matter can enter or leave, toward a random state with maximum entropy - Because Earth is an isolated system and life represents a non-random state, life could not have resulted from natural processes such as evolution - The Earth is not an isolated system, the Sun provides a constant supply of energy
The Great Chain of Being
- The divine plan of creation from inanimate objects and barely animate forms of life, up through ever "higher" forms - Complete and no gaps -Permanent and unchanging - No change in diversity over time; species are fixed entities
Root
- The last common ancestor of all taxa of interest - A taxon (or taxa) that is is ancestral to every thing else
Carl Linnaeus (1707-1778)
- The role of natural sciences - Father of modern taxonomy ==> Kingdom (Animalia), Phylum (Chordata), Class (Mammalia), Order (Primata), Family (Hominidae), Genus (Homo), Species (Homo sapiens) - He thought of taxonomy as a road map to some sort of Divine plan; all diversity that exists is the same diversity that was created in the beginning - He did however, allow for some change. Given that he intensely studied many different types of organisms, he excepted that hybrids could produce entirely new species -Established the framework of hierarchical classification -Relatedness meant similarity in God's design and not in genealogy
Topology
- The topology is the branching structure of the tree - It indicates patterns of relatedness among taxa, meaning that trees with the same topology and root have the same biological interpretation
Jean-Baptiste Lamarck (1744-1829)
- Theory of Organic Progression - Transformational theory of evolution by inheritance of acquired characteristics - No common ancestry - No extinction
Charles Darwin (1809-1882)
- Theory of descent with modification from a common ancestor - Variational theory of evolution by natural selection
Misconception 3: Evolution is entirely random
- There is randomness in evolution ==> EX: Mutation and drift - But natural selection is a non random/deterministic sorting process ==> EX: The tree of humans and animals of having eyes or no eyes
How to read phylogeny
- Time proceeds forward from the root to the tips of the tree: ==> Younger (top) ^ | | Older (bottom) ==> Derived ^ | | Ancestral - Trees illustrate patterns of shared ancestry - Rotating at an interior node does not change the tree; Taxa can be rotated around nodes and still depict the same relationships - Phylogenies can be drawn in any orientation - Phylogenies can be drawn in different styles - Trees can be rooted or unrooted - Trees consist of a nested series of clades, each comprising a node and all of its descendent lineages - Trees can be drawn with more or less information: ==> The trees show the same evolutionary relationships. ==> The branch lengths have different meanings ==> All show the same evolutionary relationships, or branching orders, between the taxa - Lateral lines or lengths have no meaning
Homologous characters
- Traits shared by common descent: ==> 1. Ancestral character state ==> 2. Derived character state ==> When shared by multiple taxa
40. Considering radiometric dating, both C14 and U235 are often used. Which one would be used to date a rock that is 2.9 billion years old? ______ Which would be used to date human remains that are 1600 years old? ______ Explain why the different elements would be used for the different analyses: ____
- U235 - C14 - C14: An organism acquires carbon from carbon dioxide during its lifetime. When an organism dies, it ceases to take in new carbon-14 and the existing isotope decays. - U235: Uranium-lead dating can be used to find the age of a uranium-containing mineral.
Ancestral character state
- Unchanged from the ancestral condition ==> EX: Bilateral symmetry in vertebrates
James Hutton (1726-1797) and Charles Lyell (1797-1875)
- Uniformitarianism - The Earth must be VERY old - James Hutton is the Father of Geology
Medium ground finch
- Variation in beak morphology exists - Beak morphology is heritable - Variation in beak size influences efficiency at eating different types of seeds
2. Evolution of Darwin's finches
- Woodpecker finch, Camarhynchus pallidus: Uses cactus spines or twigs to pry insects from trees (there are no woodpeckers on the Galapagos) - Vampire finch, Geospiza difficilis septentrionalis: Wounds the rear ends of seabirds to feed on their blood. - Galapagos finches: Common ancestor from South American mainland
Are we still evolving? Do we generate heritable variation by mutation? If so, does sorting of heritable variation occur by selection and/or drift?
- Yes, we are still evolving - Yes - Selection, maybe; Drift, yes (N = finite)
How did the diversity of life come about?
1. Answer 1: God 2. Answer 2: Evolution
Examples of evolution by artificial selection
1. Artificial selection in chickens 2. Artificial selection in crop production 3. Artificial selection in dogs 4. Artificial selection for herbicide resistance in plants 5. Artificial selection for pesticide resistance in houseflies
Atavism Examples
1. Atavistic legs in cetaceans 2. Atavistic digits in horses 3. Human development
Homology vs. Convergence/Analogy
1. Common ancestor of humming bird and butterflies: ==> Wings in this context are convergent ==>Why? Because wings were likely not present in common ancestor ==> Showing just the hummingbird, are the wings homologous or analogous? Can't tell - we need context. 2. Common ancestor of flies and butterflies: ==> Wings in this context are homologous ==> Why? Wings were likely present in common ancestor
For artificial selection, the selected/desired traits must:
1. Display variation that can be selected for 2. Be heritable
Phylogeny reconstruction methods differ in the definition of the "best" tree
1. Distance method 2. Maximum Parsimony method 3. Maximum likelihood method 4. Baysian method
What are the mechanisms for the diversity of life seen today on Earth?
1. Earth is Old 2. Gradual change over time (Lyle & Hutton) 3. Organisms of varying complexity, perhaps can change form over time (Larmarck) 4. Organisms 'created' or appear in fossil record and organisms can go extinct
Darwin's major contributions
1. Established the fact of evolution 2. Proposed a mechanism of evolution of natural selection.
Misconceptions about evolution
1. Evolution is just a theory 2. Evolution is natural selection 3. Evolution is entirely random 4. Evolution violates the 2nd law of thermodynamics 5. Evolution is a march of progress 6. Evolution always proceeds from simple to complex
41. Give three examples of adaptive radiations.
1. Evolution of Hawaiian Honeycreepers 2. Evolution of Darwin's finches 3. Evolution of Marsupial Mammals
Adaptive radiation examples
1. Evolution of Hawaiian Honeycreepers 2. Evolution of Darwin's finches 3. Evolution of Marsupial Mammals
Convergent examples
1. Evolution of wings 2. Evolution of beak shapes in birds 3. Evolution of "vultures" 4. Evolution of streamlined shapes in swimmers 5. Evolution of complex eyes 6. Evolution of placental and marsupial mammals 7. Evolution of Anoles lizards
New data and ideas started to emerge...
1. Extinction (Cuvier) 2. Uniformitarianism (Hutton and Lyell)
Examples of vestiges
1. Flightless birds 2. Vestigial eyes 3. Vestigial legs 4. Pseudogene
How does evolution occur?
1. Generation of heritable variation (ultimately) by mutation 2. Sorting of heritable variation
1. Flightless birds
1. Ostrich: ==> Cannot fly ==> Vestigial ==> Functional: Balance, mating, threatening enemies, but why wings? It is because the common ancestor of modern birds was winged and could fly. 2. Penguins: ==> Cannot fly ==> Vestigial ==> Functional: Flippers for swimming with incredible speed and grace. 3. Kiwi: ==> Cannot fly ==> Vestigial ==> Not functional: No apparent function. Why exists? No Mammalian predators in Australia, New Zealand when this bird was evolving and adapting to its environment.
How to read a phylogenetic tree
1. Taxon 2. Branch length 3. Node 4. Root 5. Clade 6. Paraphyletic group 7. Sister groups 8. Outgroup
Answer 2: Diversity as a product of change over time
1. Theory of Organic Progression (Lamarck) 2. Transformational theory of evolution by inheritance of acquired characteristics (Lamarck) 3. Theory of descent with modification (Darwin) 4. Variational theory of evolution by natural selection (Darwin and Wallace)
Distance method
1. UPGMA (Unweighted Pair Group Method with Arithmetic mean) 2. Neighbor-joining
35. List the three requirements needed for evolution by natural selection to occur:
1. Variation 2. Heritability 3. Change in time / Differential fitness of variants
Character state reconstruction rules
1. Work from the tips to the root, and then back to tips. 2. The set at an internal node is the intersection of the two sets at its immediate descendant nodes if the intersection is not empty. ==> {CT} Ç {AGT} = {T} 3. If the intersection is empty, the set at an internal node is the union of the two sets at its immediate descendant. ==> {GT} È {A} = {AGT} 4. Character states are assigned to each descendant node based on which character state it shares with its parent.
Evidence 2: The Universal Genetic Code
==> EX: Codons - Nearly universal across prokaryotes and eukaryotes - Potentially millions of genetic codes - Why are they all the same? - Encodes the traits we see - often times an unbiased and better record of homology and analogy.
Evidence 4: Eukaryotic Organelles
==> EX: Diagram of different eukaryotic cells
Evidence 5: Anterior-Posterior Patterning in Animal Embryos
==> EX: Drosophillia embryo and mouse embryo of posterior and anterior
Evidence 1: Comparative Anatomy
==> EX: Human arm versus seal flipper versus bat wing, shark versus human
2. Evolution of beak shapes in birds
==> EX: Hummingbird - Beak shape has evolved to match tubular flowers in many unrelated lineages
Evidence 6: Molecular Sequence Data
==> EX: Nucleotide alignment, codon position, amino acid alignment of different animals, and chromosome, nucleus, cell, DNA, and gene
Evidence 3: The Universal Membrane
==> EX: Phospholipid bilayer (hydrophilic head group and lipid hydrophobic fatty acids) architecture across prokaryotic and eukaryotic cells and organelles ==> EX: Archae have Isopreen (branched) lipid hydrophobid side-chains
39. Considering the idea of contingency in evolution, give two reasons why mammals could not have arisen 2.6 billion years ago.
?
III. Matching (#29 - #33). The following timeline includes 12 important dates relevant to the evolution of life on Earth. CHOOSE A TOTAL OF 5 DATES ONLY, and match an event from the list below to the corresponding date on the timeline by writing the letter in the blank provided, as shown for the 15 Bya date for the origin of the universe. If you fill in more than 5 blanks, only the first 5 (left à right) will be graded. (10 pts total). Bya = billion years ago, Mya = million years ago A Origin of the universe B Origin of flowering plants C Oldest fossil cyanobacteria D Origin of land plants E Burgess Shale F Oldest fossil tetrapods G Cambrian explosion H Breakup of Pangaea I Out-gassing of O2 from oceans J Origin of Earth K Origin of eukaryotes M Extinction of dinosaurs N Oldest human fossil O Oldest fossil eukaryote resembling a living species (red algae) 15 Bya 4.5 Bya 3.5 Bya ~ 2.0 Bya 1.2 Bya 1.80-0.85 Bya 542-488 Mya 505 Mya 450 Mya 370 Mya 250 Mya 65 Mya
?
Fact
A hypothesis so firmly supported by evidence that scientists believe it is true
Theory
A mature, coherent body of interconnected statements (hypotheses), based on reasoning and evidence, that explain a variety of observations
Sister groups
A pair of clades descending from their last common ancestor
Hypothesis
A statement of what might be true
Outgroup
A taxon or taxa outside of the group of interest (ingroup); useful to determine the root of the ingroup.
Plesiomorphy
Ancestral
34. Define evolution:
Any heritable change in a population over time
37. Based on the graph above (#36), is tail length a heritable trait? (1 pt) How do you know? (Explain your answer.) (See picture)
Because the tail lengths of song birds increased over time of generations.
Apomorphy
Derived
Artificial selection for herbicide resistance in plants
Evolution of resistance to Herbicides
18. T or F. Charles Darwin used Gregor Mendel's work on inheritance as a starting point for his theory.
F
21. T or F. Evolution and natural selection are the same thing.
F
22. T or F. Oceanic islands have more mammals than continental ones.
F
26. T or F. Natural selection only "sees" the genotype, not the phenotype.
F
Character state reconstruction
Fitch parsimony (1971): The evolutionary scenario that requires the least number of changes is assumed to represent the true history (i.e. most parsimonious).
Uniformitarianism
Geological processes observable at present were operational throughout earth's history (Hutton and Lyell)
Artificial selection in crop production
Gradual increase in cob size documented by archaeologists
Maximum likelihood method
Highest P (data|tree, evolutionary model)
Baysian method
Highest P (tree|data, evolutionary model)
Are extinctions imperfection in God's plan?
Not necessarily
Random genetic drift
Random sorting due to sampling errors that occur during reproduction in a finite population
Disruptive selection
See scratch work for problem set 1 and powerpoint lecture 7 and 8
Problem Set 1
See scratch work for problem set 1 and powerpoint lecture 7 and 8
Truncation selection
See scratch work for problem set 1 and powerpoint lecture 7 and 8
Synapomorphy
Shared derived
Neighbor-joining
Shortest total distance
Linnaean classifications
Some Linnaean classifications are not monophyletic
16. T or F. Evolution by natural selection favors traits that benefit the overall good of the species.
T
17. T or F. Natural selection is best described as a process, not a force.
T
19. T or F. Plant species with dense, large-sized seeds typify the native flora of most oceanic islands.
T
20. T or F. Marsupial mammals originated in the Americas and migrated south and eastward through Antarctica, eventually reaching Australia and diversifying.
T
23. T or F. Carolus Linnaeus is considered "The Father of Modern Taxonomy".
T
24. T or F. Ecology is important for understanding evolution and biogeographic distributions of species.
T
25. T or F. The more closely related two species are, the more homologous traits they share
T
27. T or F. Tiktaalik roseae, found in Antarctica, represents an animal transition from water to land.
T
28. T or F. Cetaceans are more closely related to the rhinoceros than they are to the hippopotamus.
T
Hybrids
The process by which two different species producing a viable offspring
Use UPGMA to determine their phylogeny with branch lengths.
The table below shows pairwise distances (per 1000 nucleotides) between tarsier, galago, cow and opossum
The role of natural sciences
To catalogue the plan of creation by God (Linnaeus)
What is the evidence for Darwin's view of evolution?
Ubiquity of homologies, including vestiges and atavisms, across the tree of life (Darwin)
Alfred Rusel Wallace (1823-1913)
Variational theory of evolution by natural selection
1. Evolution of wings
Wings of a fly versus wings of an eagle
36. This graph is a linear regression showing the heritability of tail length in a population of song birds. Label the X and Y axes on this graph (units of measure are not important). The labels should be brief, but should clearly demonstrate that you know what the graph is showing. (see picture)
X: Time over generations of song birds Y: Tail length of song birds
