Intro to Evolution and Darwin (Notes)

1. Overview of Evolution

• Definition: Evolution is defined as change over time in organisms. It serves as a foundational core theme in biology to explain both similarities and differences across species.

• Internal Mechanisms: Morphological, physiological, and physical characteristics of organisms are driven internally by genetic material ($DNA$, $RNA$) and proteins.

• Scientific Status: Evolution is a well-supported scientific theory built on empirical data, holding the same scientific rigor and backing as the theory of gravity.

2. Lines of Evidence Supporting Evolution

• Fossil Record:

  • Provides long-term historical evidence showing changes in anatomical structures over time (e.g., limb structures in ancient vertebrates, hindlimb/pelvis structures in whale ancestors).

  • Limitations: The fossil record is incomplete because soft-bodied organisms and plants do not fossilize easily. Hard, calcified skeletal structures evolved long after early life established on Earth. It is primarily useful for analyzing animal evolution within the last $100 \times 10^6\text{ years}$.

• Morphology and Embryology:

  • Homologous Structures: Structures that share the same underlying skeletal layout due to common evolutionary ancestry, despite having different modern functions (e.g., the 1-bone, 2-bone, 5-bone forelimb layout found in humans, dogs, birds, whales, and bats).

  • Embryonic Development: Early developmental stages across vertebrates share remarkable structural similarities (e.g., presence of pharyngeal pouches and a post-anal tail in human, bird, tortoise, salamander, and fish embryos).

• Molecular Data:

  • Amino Acid Differences: Comparing monomers of essential proteins highlights evolutionary distance (e.g., human hemoglobin differs by only $32$ amino acids from dogs, compared to $125$ amino acids from lampreys).

  • Nucleotide Sequences: Gene sequence comparisons show precise relationships (e.g., Cytochrome c oxidase sequence of approximately $600\text{ base pairs}$ shows only $13$ base pair differences between humans and pigs, versus $66$ base pair differences between humans and yeast).

• Phylogenetics and Evolutionary Trees:

  • Branch lengths on phylogenetic trees quantify evolutionary relationships and shared ancestry (e.g., genetic and morphological data indicate crocodiles share a more recent common ancestor with birds than with lizards).

3. Key Historical Contributors and Concepts

1. Charles Darwin ($1809\text{--}1882$):

   • Served as a naturalist on the HMS Beagle ($1831\text{--}1836$), surveying South America and the Galápagos Islands.

   • Recognized that geographic proximity is a stronger indicator of evolutionary relatedness than environmental similarity alone.

   • Documented adaptive variation in Galápagos finches, where beak size and shape correlated directly with dietary sources (e.g., large seeds vs. insects).

   • Published On the Origin of Species in $1859$, introducing natural selection as the primary mechanism for evolution ("survival of the fittest").

2. Alfred Russel Wallace:

   • Independently co-discovered the theory of natural selection and co-authored a joint paper with Darwin in $1858$.

3. Other Major Influences:

   • James Hutton: Proposed gradualism, the concept that species and geological features change slowly over long periods.

   • Charles Lyell: Published Principles of Geology ($1830$), establishing uniformitarianism and the law of superposition (deeper strata are older).

   • Georges Cuvier: Paleontologist who analyzed dinosaur fossils and established the concept of extinction.

   • Jean-Baptiste Lamarck: Proposed the inheritance of acquired characteristics; while his mechanism was incorrect (e.g., ducks developing webbed feet during their lifetime through swimming), he correctly identified that organisms change over time.

   • Thomas Malthus: Mathematician who modeled exponential population growth and resource limitations.

   • Carl Linnaeus: Developed the binomial nomenclature system ($\text{genus}$ and $\text{species}$) for classifying organisms.

4. Evolutionary Scales and Mechanics

• Microevolution: Focuses on small-scale changes in allele frequencies within a population over generations.

• Macroevolution: Focuses on large-scale changes over extended timeframes, leading to speciation (formation of new species) and adaptive radiation.

• Genetic Basis: Physical traits (phenotypes) are determined by underlying genetic code, requiring two alleles (genes) to code for a given character.