Unit Notes - Ch. 19 Descent with Modification

Fundamental Concepts of Evolution and Natural Selection

• Common Descent: The principle that all species alive today share common ancestors.
• Fitness: Defined as the likelihood that an individual contributes offspring to the next generation. It is a measure of reproductive success rather than just physical strength or size.
• Trait Distribution: Traits that assist individuals in surviving and reproducing become more common in the population over time.
• Evolution: The gradual change of a population through time. It is a process that occurs over generations.
• Natural Selection: The specific mechanism of how and why populations evolve. It is the process by which individuals with favorable traits are more likely to survive and reproduce.
• Relationship between Concepts:     * Natural selection is the cause/explanation for how evolution (the effect/observation) occurs.     * Natural selection leads to adaptation.
• Adaptation: A specific trait that makes an organism well-suited to its environment.
• Defining Statements:     * Natural Selection (NS) Evidence: A camouflaged caterpillar is more likely to reproduce because it is less likely to be eaten by a bird.     * Evolution (E) Evidence: Fossil data indicating that early ancestors of modern horses were less than $\frac{1}{2}\,\text{meter}$ tall and that horse ancestors got larger over time.     * Common Descent (E) Evidence: The fact that the closest living relatives of birds are alligators and crocodiles leads to the expectation that birds share many traits with reptiles.

Biological Paradigms: Typological vs. Population Thinking

• Typological Thinking:     * Based on ideas from Plato.     * Species are described based on an "ideal" form.     * Variation is viewed as an error or deviation from the ideal.     * Species descriptions are static (unchanging over time) and do not include diversity or variation.     * An individual is compared to one "type" or ideal.
• Population Thinking:     * The species description depends on the population.     * The description will change over time.     * The description explicitly includes the population's variation.     * Variation from all individuals is considered important data rather than error.     * Modern biology relies on population thinking to understand evolution and natural selection.
• Examples of Thinking Types:     * Typological (T): "Normal height for a human female is $5\,\text{ft}\,5\,\text{in}$."     * Population (P): "The mean length of a birch tree leaf is $7 \pm 2.5\,\text{cm}$."     * Typological (T): "A jaguar or leopard with abnormally dark coloration is called a 'black panther'."     * Typological (T): "The eastern gray squirrel is a rodent with uniform gray fur weighing between $400$ and $600\,\text{g}$."

Hierarchies: Ladder vs. Tree Thinking

• Ladder Thinking (Scala Naturae):     * Historical view created by Aristotle, also known as the "Great Chain of Being."     * Ordered species from low complexity (minerals/plants) to high complexity (humans).     * Species were considered unchanging and fixed on their specific "rung" of the ladder.     * Focus is on species hierarchy and fixed levels of complexity.
• Tree Thinking:     * Modern view where species change through common descent.     * The focus is on evolutionary relationships rather than a hierarchy of perfection.     * All extant (currently living) populations have been evolving for the same amount of time.     * Variation is explained by distinct evolutionary histories.     * Common ancestry explains the similarities observed between diverse organisms.

Reading and Interpreting Phylogenetic Trees

• Phylogenetic Trees: Graphical representations used to understand species' relationships based on common descent.
• Branches: Represent a lineage over time.
• Nodes: Represent a common ancestor where branches originate.
• Relatedness: Relatedness is determined by how recent in the tree a common node (ancestor) exists. The more recent the node, the more closely related the organisms.
• Identifying Ancestry (Example: Birds):     * Emu: Closely related to the Cassowary if they share the most recent node.     * Common Ancestor: A point on the tree (node) from which two or more lineages stem.
• Identifying Ancestry (Example: Plants):     * In a tree containing Cucumber, Apple, Pear, Cotton, Orange, and California Poppy:     * The most recent common ancestor between Pears and Cucumbers is identified by the node where their lineages first meet (e.g., Node D).     * If Cucumber is shown to branch from the same node as a group containing Apples and Pears, it is equally related to both.

Geological Foundations of Evolutionary Thought

• General Take-away: The Earth is old and changes slowly over time.
• James Hutton ($1726$-$1797$):     * Proposed that the Earth was much older than a few thousand years.     * In the late $1700\text{s}$, geology began challenging ideas of an unchanging Earth.
• Charles Lyell ($1797$-$1875$):     * Popularized modern geological thinking in his book Principles of Geology.     * Uniformitarianism: The theory that geological processes occurring today are the same as those that occurred in the past; therefore, change is gradual.     * Lyell's book directly influenced Charles Darwin's thinking during his voyage.
• Georges Cuvier ($1769$-$1832$):     * Specialized in fossils and is known as the "Father of Paleontology."     * Fossil records showed that life is different today than in the past, demonstrating both extinctions and progression.

Early Theories: Lamarck and the Inheritance of Acquired Traits

• Jean-Baptiste de Lamarck ($1744$-$1829$): Proposed a mechanism for evolution based on two principles that are now known to be incorrect:     1. Use and Disuse: Traits can become more or less developed in an organism's lifetime depending on how much they are used.     2. Inheritance of Acquired Traits: These developed traits can be passed down to offspring.
• Corrective Take-away: Changes that occur during an individual organism's lifetime (acquired traits) are not inherited via DNA. Genetics and inheritance were not understood scientifically until the early $1900\text{s}$.
• Lamarckian Example (Kangaroo):     * Hypothesis: An ancestor had average-sized limbs. Because it used its hind limbs for jumping, they became larger and stronger (Use). Its forelimbs were not used, so they became weaker (Disuse).     * Error: These physical changes in the parent would not be coded into the gametes and therefore would not be inherited by the offspring.

The Contributors to Modern Evolutionary Theory

• Charles Darwin ($1809$-$1882$):     * From a wealthy family of intellectuals.     * Traveled the world on the HMS Beagle ($1831$-$1836$).     * Observed fossils (like the extinct giant ground sloth), geology (an earthquake in Chile), and organisms (unique island species like Galapagos finches).     * Spent $20$ years researching and developing his theory of natural selection.
• Alfred Russel Wallace ($1823$-$1913$):     * Limited formal education.     * Traveled to the Amazon ($1848$-$1852$) and the Malay Archipelago ($1854$-$1862$).     * Observed the distribution of species on different islands, identifying the "Wallace Line."     * In $1858$, he sent a letter to Darwin describing a nearly identical theory of natural selection.
• Publication: Darwin and Wallace's ideas were published jointly in $1858$. Darwin published On the Origin of Species in $1859$.

The Mechanism of Natural Selection

• Four Pillars of Natural Selection:     1. Variation: Individuals in a population have different traits (e.g., snowshoe hares turning white vs. staying brown).     2. Overproduction: Organisms produce more offspring than the environment can support (e.g., hares having many offspring per year).     3. Selection: Certain traits provide a survival advantage in specific environments (e.g., in a year with little snow, white hares are predated more easily).     4. Evolution: Over generations, the population changes (e.g., the future population will have fewer white hares if snow remains scarce).
• Key Insights:     * Requires heritable variation.     * Members of the same species are in competition.     * Fitness is relative and highly dependent on the environment.     * Populations evolve; individuals do not.     * Natural selection increases the frequency of adaptations to the current environment.

Evidence for Evolution

• Artificial Selection:     * The selective breeding of individuals with traits favored by humans (e.g., developing kale, broccoli, and cabbage from wild mustard Brassica oleracea).     * Darwin used artificial selection as a comparison to explain natural selection.
• Direct Observation of Evolution:     * Antibiotic Resistance: In a population of S. aureus (MRSA), some bacteria have a mutation for resistance. In the presence of antibiotics (selection), the resistant bacteria have higher fitness. The population evolves to become mostly resistant.     * Rock Pocket Mice: Variation in fur color (tan vs. black). On dark volcanic rock, black mice have higher fitness due to camouflage. Black fur becomes more common.     * Peppered Moths: In the early $1800\text{s}$, light-colored moths were camouflaged by lichen. During the Industrial Revolution, soot covered trees. Dark moths then had higher fitness. By the $1900\text{s}$, the population was mostly black. As pollution decreased later, the light-colored moths became common again.
• Homology: Traits with similar underlying structures that suggest a common ancestor (e.g., upper limb bones in whales, humans, and birds).
• Analogy: Functionally similar traits that have different evolutionary origins (e.g., wings in bees vs. wings in birds). This is the result of convergent evolution.

Specialized Homologies

• Vestigial Structures: Traits that have lost most or all of their original function (e.g., pelvic girdle in snakes, human goosebumps, eyes in blind cave salamanders).
• Embryologic Homology: Organisms share traits as embryos that are not present in adults (e.g., pharyngeal arches and post-anal tails in fish, birds, reptiles, and mammals).
• Molecular Homology: DNA and protein sequences are more similar in more closely related organisms. Genes like the MC1R gene (affecting hair/coat color) are homologous across many mammals.

Evidence from the Fossil Record

• Stratigraphy: Deeper layers of sedimentary rock (strata) are older. Fossils in deeper layers represent organisms from further back in time.
• Patterns: Fossil records demonstrate extinctions and gradual change.
• Transitional Forms: Fossils that fill gaps in evolutionary history.     * Example (Whales): The hypothesis that whales evolved from four-legged land ancestors is supported by fossils like Indohyus ($50\,\text{mya}$), Rodhocetus ($47\,\text{mya}$), and Dorudon ($40\,\text{mya}$) which show transitioning leg structures.     * Example (Birds): Archaeopteryx ($150\,\text{mya}$) shows a dinosaur-like skeleton (teeth, bony tail) but has bird-like feathers, indicating traits common in modern birds evolved before dinosaurs went extinct.

Common Misconceptions about Evolution

• "Evolution is just a theory": In science, a "theory" is a well-supported, widely accepted explanation of natural phenomena.
• "Individuals evolve": Individuals can acclimatize, but they do not evolve. Populations evolve over generations as allele frequencies change.
• "Acquired traits are inherited": Only traits coded in DNA (heritable variation) can be passed to offspring.
• "Fitness equals strength": Fitness refers specifically to reproductive success—how many offspring an individual contributes.
• "Organisms evolve toward a goal": Evolution is not proactive. Populations change in response to current environmental pressures. Adaptations from the past were not "working toward" modern forms.
• "Adaptations help the species": Natural selection acts on individuals within a population. It does not select for the "good of the species" but rather for the reproductive success of individuals.
• "Natural selection creates perfect organisms": Selection is limited by existing variation and involves trade-offs (e.g., a trait that helps in one area may be a disadvantage in another).