Unit 7: Evolution (Biology)

Origin Of Life

• Hadean Eon
  • 1st major eon. Hell on Earth. No forms of life.
• Archean Eon
  • 2nd major eon. First form of life.
• Proterozoic Eon
  • 3rd major eon. Transition to eukaryotes from prokaryotes. Post Oxygen Revolution
• Phanerozoic Eon
  • 4th major eon (right now). Massive explosion in diversity.

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• Biogenesis - all living things come from other living things
• Spontaneous Generation - a process by which living things come from nonliving things
• Francesco Redi’s Experiment
  • Proved that the flies did not come from rotting meat, disproving Dr. Jan Baptista van Helmon’s experiment showing mice appearing in the proper environment
• Lazzaro Spallanzani’s Experiment
  • Thought that air was what led to life because heated broth left open led to growth, while when the flask was sealed, there was no growth
• Louis Pasteur’s Experiment
  • Proved it wasn’t AIR itself, but things IN the air that led to life by using a type of flask that doesn’t allow for bigger particles in the air to pass through, so dust collected at the bottom
  • some of these samples remain unspoiled, even today
  • The idea of milk pasteurization was inspired by him

Abiogenesis

• How did first life originate?
  • The Oparin-Haldane Hypothesis proposed a gradual, step-by-step process of “chemical evolution”
  • Miller and Urey experimentally showed, under the Oparin-Haldane Hypothesis conditions, that inorganic molecules could fuse to make organic molecules
  • Later research proved that their conditions for early life were incorrect, but despite that, it still proved the theory of chemical evolution true.
  • Abiogenesis – life arising from simple organic compounds

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• Steps needed for life:

1. Simple organic molecules (RNA, amino acids) form from inorganic molecules.
2. Self-replicating RNA evolved.
3. Replicating RNA molecules are contained in a cell membrane
4. metabolism - some cells evolved metabolism that generated energy.

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• RNA WORLD
• The RNA World Hypothesis states that the first molecule of genetic storage was not DNA, but RNA!
  • RNA is simpler than DNA, can store information, can act like a protein and be an enzyme, and can code for proteins

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• Although the Hadean era was very rough (asteroids bombarding the earth, frequent volcanic eruptions, noxious atmosphere, high temperatures), around ~4 bya, there were signs of life
• Possible theories:
  • Shallow clay pools - a hypothesis on how life originated. this allows for the concentration of nutrients in one specific area, and the water evaporates out but the organic molecules remain.
  • Hydrothermal vents - a hypothesis on how life originated. mantle of the earth is in contact with the ocean there, and there is a LOT of life there, completely cut off from the sun. There’s no photosynthesis, but there is chemosynthesis. They use the chemicals in the water and convert it to sugars. Photosynthesis did not evolve until the oxygen revolution
  • Panspermia - life elsewhere in the universe, came to Earth, and kick-started the evolution of life on Earth
• Chemical evolution needs 8 reaction conditions as of now:

1. reductive gas phase
2. alkaline pH
3. freezing temperature
4. freshwater
5. dry/dry-wet cycle
6. coupling with high-energy reactions
7. heating-cooling cycle in water
8. extraterrestrial input of life's building blocks and reactive nutrients

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• First life forms were prokaryotic, anaerobic, heterotrophic, and unicellular
• Prokaryote: no nucleus/organelles
• Anaerobic: did not use oxygen
• Heterotrophic: must consume resources
• Unicellular: the whole organism is just one cell
• Endosymbiosis - modern eukaryotes developed from one prokaryote taking in another, but instead of digesting it, it lives inside the cell and provides energy/resources

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Evidence of Evolution

• European thinkers believed in a “great chain of being”, where every chain link was a species; unchanged from creation, and connecting life to spiritual beings
• From the 1700s to the 1800s, European colonizers began to travel across the world
  • 19th-century colonization led to the collection of samples worldwide. Colonizers found very similar, unique organisms in VERY different places.
  • When they compared these various plants and animals, they noticed lots of similarities and differences between them.
  • They noticed some traits/instructions had no function (vestigial structures)
  • They found fossils that did not look like any currently living organisms.
    • Georges Cuvier attempted to explain this by proposing that some species must’ve gone extinct (but people rejected this idea, because it messed with the “great chain of being” belief)
    • Extinct - not currently existing
    • Extant - still existing
    • Fossils are the only direct evidence we have of old organisms that led to modern species.

Evidence of Evolutionary Change

• HOMOLOGOUS STRUCTURES - Other scientists focused on homologous structures, similar features that originated in a shared ancestor that evolved over time
  • Analogous structures have very similar functions and may look alike, but are developmentally and structurally different. This is NOT evidence of evolution.
• VESTIGIAL STRUCTURES - Vestigial structures were, at one point in time, useful structures to an evolutionary ancestor, but through evolution, are no longer necessary to the organisms that have them.
  • I.e. tailbones in humans.
• EMBRYOLOGY - Similarities in embryology show a shared common ancestor between all vertebrates because of a similar developmental pattern.
• MACROMOLECULES - Macromolecule (DNA/RNA protein) similarities show that all living things have a similar blueprint and share similar genes.
• BIOGEOGRAPHY - Shows how plants and animals spread across the planet, and how certain species are related to others. Similar organisms may occur in very far places because of them having a similar ancestor back when the continents were together as Pangea.
• FOSSIL RECORD

Selection

• Evolution - genetic changes in a population of organisms over time
• Selection - is the survival and reproduction of individuals with certain traits.
  • Populations evolve because of selection.
  • Selection decides which traits become more common.
• Fitness - is the ability of organisms to survive and reproduce for the next generation
• Survival - (did they live or did they die?)
• Mating success - (did they mate?)
• Fecundity - (# of babies made)

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• Artificial Selection: Humans select the traits of plants and animals that are passed onto the offspring.
• Natural Selection: Nature selects the traits that get passed to the next generation.
  • Only the traits that allow organisms to survive and reproduce in nature get passed on to their offspring.
  • Proposed by Charles Darwin in his book On The Origin of Species in 1859
  • Natural Selection is the only explanation for why organisms are so specifically suited for the environments they live in
• Sexual Selection: A type of natural selection where the best traits increase the chances of successfully having offspring.
  • Sexual selection usually leads to males being very different from females.
  • This is called sexual dimorphism.
  • Males either must compete for the attention of females with colors/songs/dances, OR compete directly with other males for access to females. (female choice vs male competition)
• Random Selection (genetic drift):  is when a trait survives because it was chosen at random.
  • Sometimes called a bottleneck effect, where only a few members survive to the next generation, only those traits are passed on (whether they are useful or not).
• sexual dimorphism - A trait that differs between males and females of a species.
• bottleneck - Reduction in population size so severe that it reduces genetic diversity.
• gene flow - The movement of alleles between populations.
• genetic drift - Change in allele frequency due to chance alone.
• inbreeding - Mating among close relatives.
• Selections can shift traits in three ways: Directional, Stabilizing, and Disruptive

1. Directional selection - For one extreme trait, against the other extreme
2. Stabilizing selection - For the middle trait, against the extremes
3. Disruptive selection - For both extremes, against the middle

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• Jean Baptiste de Lamarck was an incredibly influential biologist, who first proposed species descended from a common ancestor.
  • First proposed nested hierarchy, where clades (groups of organisms) were grouped as nested sets within larger groups.
  • Acquired Characteristics Hypothesis - Lamarck first proposed a theory of species modification over time, where traits gained over a lifetime are passed on to an organism’s offspring (aka acquired characteristics go from parents to offspring)
  • This is impossible because DNA does not change like this, and the truth is natural selection.

Charles Darwin

• Charles Darwin
  • English Naturalist
  • 1859 published On The Origin of Species
  • Served as a naturalist on the HMS Beagle and traveled around the world for over 5 years observing.
  • Darwin, a son of a wealthy British physician, attended the University of Edinburgh, then Cambridge University, before discovering botany, beetles, and natural history!
  • In 1831, Darwin began his voyage on the H.M.S. Beagle; a five-year mapping and collecting expedition to South America and the South Pacific
  • Observed fossils of extinct armadillos in South America.
  • Visited the Galapagos Islands, and was intrigued by the fact that many plants & animals resembled those found on the coast of Ecuador.
  • Read Thomas Malthus, who described how populations can not simply keep growing, and that there is a balance due to death.
    • The finches varied in size and beak size and shape.
    • Concluded that all these finches evolved from one species of finch
  • Darwin collaborated with a young naturalist, Alfred Russell Wallace
  • Published 2 major theories

1. Descent with Modification - Newer forms of organisms appearing in the fossil record (and in modern times) are the modified descendants of older species
2. Modification by Natural Selection -

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Natural Selection

• Evolution by Natural Selection

1. VARIATION IN A POPULATION (Variation) - There are slight differences between organisms of a species.
2. CHALLENGE IN ENVIRONMENT (Struggle) - Some individuals are better suited to survive. Some traits are beneficial, and some are not.
3. SURVIVORS REPRODUCE & COMPETE (Differential fitness) - Over time, the organisms with the beneficial trait survive and reproduce passing on the favorable trait to the offspring.
4. FAVORABLE TRAITS PASS ON (Heredity) - The number of individuals with the beneficial trait increases in a population, and over long periods these changes accumulate. Populations evolve

• Beneficial traits increase fitness by helping organisms survive their harsh environment and successfully mate and produce offspring.

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Examples:

1. Giraffes and neck lengths
2. Darwin’s finches
3. Peppered moth

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Hardy-Weinberg Equilibrium

• Population Genetics - the study of evolution from a genetic perspective, focusing on the change of allele frequency over time

• Gene Pool - The total genetic information available in a population.

  • We can predict the proportion of possible phenotypes of a population based on the proportion of dominant and recessive alleles in a population!
  • Genotypic Frequency - how often a specific genotype occurs in a population

• Allele Frequency - the proportion of a specific allele in a population

  • P = frequency of one allele (usually the dominant)
  • Q = frequency of the other allele (usually the recessive)
  • In cases of codominance or incomplete dominance, p/q assignment for an allele makes no difference. Either allele can be p or q
  • Allele frequencies follow simple arithmetic rules.
  • P+Q = 1
    • P = 1-Q
    • Q = 1-P
    • If you know the numbers of homozygotes and heterozygotes:
    • TO FIND P: [2* (# of homozygous dom) + (# of heterozygous)]/2*total
    • TO FIND Q: [2* (# of homozygous recessive) + (# of heterozygous)]/2*total
      • Or you do 1-P
    • To check if you did it correctly, add the values of P and Q and check if the answer is

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• microevolution - Change in allele frequency of a gene in a single population

• macroevolution - significant evolutionary change in multiple populations

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• These concepts are used in the Hardy-Weinberg Equilibrium
  • A null hypothesis - hypothesizes that NOTHING is happening. If proven incorrect, then something (evolution) is happening
  • Assumes allele frequencies do not change in a population
  • I.e. NO EVOLUTION
  • Allows us to predict allele (and, thus, genotype) frequencies in subsequent generations
  • Biologically unlikely due to assumptions
• Five assumptions of HWE -

1. The population is very large
2. Individuals mate at random (NO sexual selection)
3. There are two equally viable alleles (NO natural selection)
4. No migration
5. No mutation

• I.E. no evolution.
• Violating HWE assumptions = Evolution

1. Mutation
2. Migration
3. Genetic drift
4. Sexual selection
5. Natural selection

• p^2=f(AA)
• q^2=f(aa)
• 2pq=f(Aa)
• p^2+2pq+q^2=1

Reproductive Isolation

• Reproductive isolation - the separation of a species or population so that they can no longer interbreed
  • The end of gene flow between populations
• Isolation Mechanisms - reproductive isolation results from barriers to successful breeding between populations in the same area.
  • Geographic Isolation - physical separation of populations
  • Habitat/Ecological Isolation - separation of populations due to differences in habitat (i.e. terrestrial vs. aquatic, underground vs. trees)
  • Temporal Isolation - timing separation of populations
  • Behavioral Isolation - an attraction barrier between organisms
  • Mechanical Isolation - it is physically impossible to reproduce

Postzygotic Barriers

• Reduced Hybrid Inviability
• Hybrid Sterility/ Reduced Hybrid Fertility
  • Hybrids such as ligers, zorses, mules, etc, are sterile and cannot reproduce.

Speciation

• Previously, species were defined by:
  • Morphological Species Concept
  • Based on external appearance
  • Problematic because some species look very alike.
  • Biological Species Concept
  • A certain species can only successfully interbreed with their own, and not other groups
  • Problematic because some species were extinct, asexual organisms
• Species - a unique type of organism that has a genus name and specific epithet. Also, a group of individuals that can potentially interbreed, produce fertile offspring, and do not interbreed with other groups.
• Speciation - the formation of a new species. Occurs when members of a species become isolated and can no longer reproduce.
  • Allopatric - barrier forms + in isolation = new species
  • a physical barrier, a geographical difference
  • Peripatric - new niche enters + niche in isolation = new species
  • Parapatric - new niche enters + in adjacent niche = new species
  • Sympatric - genetic polymorphism + within same population = new species
  • a mutation
  • genetic polymorphism

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• adaptive radiation - A lineage undergoes a burst of genetic divergences that gives rise to many species.
• coevolution - The joint evolution of two closely interacting species; each species is a selective agent for traits of the other.
• exaptation - A trait that has been repurposed during evolution.
• extinct - Refers to a species that no longer has living members.
• key innovation - An evolutionary adaptation that gives its bearer the opportunity to exploit a particular environment much more efficiently or in a new way.
• macroevolution - Large-scale evolutionary patterns and trends.
• stasis - Evolutionary pattern in which a lineage persists with little or no change over evolutionary time

Taxonomy

• Taxonomy: the branch of biology that names and groups organisms according to characteristics and evolutionary history.
• Modern classification is a nested hierarchy, with each group made up of several smaller groups
• Does King Phillip Come Over For Good Soup

1. domain (bacteria, archaea, Eukaryota)
2. kingdom
3. phylum
4. class
5. order
6. family
7. genus
8. species

Phylogenies/Cladograms

• Combining all of the evidence we know about evolutionary history helps scientists build a phylogeny
  • Phylogeny - the evolutionary history of a species.
• Phylogenetics is the study of evolutionary relationships among biological entities - often species, individuals, or even genes.
• Phylogenies are graphs with one axis, time.
  • In a phylogeny, branch length = time elapsed
• Cladograms are sometimes seen as a hypothesis, while phylogeny reflects true evolutionary history based on empirical data.
  • Cladograms will have traits on the diagram itself. Phylogenies don’t.
• This is NOT UNIVERSAL/CONSISTENT within the community. Phylogeny/cladogram are used interchangeably.
• Reading phylogenies
  • In a phylogenetic tree, the species of interest are at the tips of the branches, and branches are split into two parts at branch points (nodes)
  • The branching pattern of the tree represents how a species or other groups evolved from a series of common ancestors
  • Don’t read the tips, read the nodes!
• Reading cladograms
  • Traits are placed directly on the tree. EVERY organism after the trait has that trait!
  • These are graphs with one axis - time!
  • Character tables
• Key to cladogram/phylogenetic construction is the concept of parsimony, or that the simplest explanation of evolutionary relationships is the best one. (may not always be true!)
• clade - A group whose members share one or more defining derived traits.
• cladogram - Evolutionary tree diagram that shows evolutionary connections among a group of clades.
• derived trait - A novel trait present in a clade but not in any of the clade’s ancestors.
• phylogenetic tree - Diagram showing evolutionary connections.
• phylogeny - Evolutionary history of a species or group of species.
• sister groups - The two lineages that emerge from a node on a cladogram.

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Final Overview

• Important People
  • Dr. Jan Baptista van Helmon
  • theorized that life magically appears from the right conditions
  • Francesco Redi
  • proved that life doesn’t just appear from the right conditions
  • Lazzaro Spallanzani
  • believed air was what led to life
  • Louis Pasteur
  • proved that it wasn’t air, but the things in the air that led to life.
  • Oparin-Haldane Hypothesis
  • proposed the idea of chemical evolution
  • Miller and Urey
  • experimented under the Oparin Haldane Hypothesis using early life conditions. later, we learned that the life conditions were incorrect, but the idea of chemical evolution was proved.
  • Georges Cuvier
  • proposed the idea that some species have gone extinct after finding fossils that did not look anything like any currently living organisms.
  • Jean Baptiste de Lamarck
  • theorized that species modified over time and traits gained over a lifetime were passed on to an organism’s offspring. this is incorrect because DNA doesn’t work like that.
  • Charles Darwin
  • visited the Galapagos islands and studied finches. concluded that the finches evolved from one species of finch. published 2 theories in natural selection, descent by modification, and modification by natural selection.
  • Alfred Russell Wallace
  • was second in publicizing his findings on natural selection, so Darwin got to it first.
  • Thomas Robert Malthus
  • wrote about how populations cannot keep growing and things die eventually, leading to a balance.

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• how to solve hardy weinberg equilibrium problems

1. figure out what the question is asking
2. if whether or not it’s in the hardy weinberg equilibrium
3. if there’s an unknown amount of genotypes

• CONCEPT MAPPING.

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