Comprehensive Notes on Evolution: Darwin, Mechanisms, and Population Genetics
Evolution: Comprehensive Study Notes
Evolution is the process by which different kinds of living organisms are thought to have developed and diversified from earlier forms over the history of the Earth.
Genetic changes in a population over generations lead to the emergence of new species.
Over time, organisms change based on their traits and interactions with the environment, explaining both the diversity of life and the similarities among species.
What is Evolution?
Evolution is driven by natural selection, random chance events, and interactions of organisms with their environment.
The process of natural selection can only act on existing variation; it cannot conjure up new beneficial traits on demand. It must work with what it starts with.
-illustrative example: Birds arose from dinosaurs as their front forelimbs evolved into wings and feathers (from a structure that gave balance on the ground to pursue prey).
Darwin’s Core Concepts
Descent with modification (Darwin’s short popular definition) implies:
Species change over time
Give rise to new species
Share a common ancestor
Darwinism vs evolution: Darwinism is a theory of evolution based on natural selection.
Three principles of natural selection: Inheritance, Variation, Differential Reproductive Success.
Descent with modification: over time, descendant species arise and diverge from an ancestral taxon; evolution is a change in the genetic composition of a population over generations.
What evolution is and is not
Evolution (biological evolution): heritable changes in the genotypic and phenotypic characteristics of groups of related organisms over generations; changes in the gene pool of a population.
Not evolution: changes in an organism during development from zygote to adult (ontogeny) do not constitute evolution.
Darwin’s Precepts and the Darwinian Framework
Variations, Heredity, and the Struggle for Existence drive evolution by changing which variants leave more offspring.
Differential reproductive success determines which traits become more or less common over generations.
The main idea: all species share a common ancestor and have diverged over time.
Pre-Darwin Era: Thinkers who pondered evolution
Anaximander (~520 BC): variability in species; proposed that species changed over time and had a single origin; life simpler in the past and became more complex.
Xenophanes (~500 BC): fossils as clues to ancient life; land where fossils are found was underwater; world formed from condensation of water and primordial mud; fossils used as evidence for Earth’s history.
Plato (~350 BC): Essentialism – objects have fixed essences or forms; inherent and unchanging characteristics.
Aristotle (~350 BC): Species as types; differentiation by differentiae; cataloged many species across birds, mammals, fishes, insects, invertebrates.
Age of Enlightenment and Foundational Ideas
John Ray (1686): proposed early species concept; individuals of a species descend from a common ancestor; coined the term “species.”
Carolus Linnaeus (1753): hierarchical classification; fixed number of species; did not subscribe to evolution; naming of ~12,000 species (plants and animals).
Buffon (1749): proposed a modern species definition based on ability to produce fertile offspring; suggested evolution and possible single-origin for all animals.
Charles Bonnet (~1770): proposed organisms evolved in response to natural catastrophes along predetermined paths (not natural selection); first to use the term evolution biologically.
Georges Cuvier (~1800): founder of paleontology; catastrophism; argued extinctions occurred and that new species did not arise; rejected gradual evolution.
Fossil Record and Evidence in the Pre-Darwin Era
Fossils were used to argue for historical change and extinction; early scientists proposed non-evolutionary explanations (e.g., Cuvier’s catastrophism).
Fossil series show sequences and transitions that would later be interpreted in the light of evolution (e.g., links between land mammals and whales over time).
Key Geology and Social Science Contributions to Darwin’s Ideas
Geology:
James Hutton (Theory of the Earth, 1788): deep time; small, cumulative geological changes (gradualism).
Charles Lyell (Principles of Geology, 1830–1833): Uniformitarianism; present-day processes are the same as those in the past; Earth is old enough for slow change to accumulate.
Impact on Darwin: slow, continuous processes over long time scales support gradual biological evolution.
Social science:
Thomas Malthus: population growth tends to outpace food production; inevitable competition; differential survival leads to struggle and selection analogies in nature.
Darwin saw parallels between Malthus’s ideas on populations and natural selection in nature.
Darwin’s Voyage and Observations
Voyage of the Beagle (1831–1836): Darwin’s observations of species emphasized island-specific adaptations and variations.
Galápagos finches: similar species with different feeding strategies; differences among finches helped Darwin infer the role of environment and selection in driving divergence.
Major outputs: These observations shaped his theory that species are descendants of a common ancestor and that adaptation arises through natural selection.
Origin of Species and Mechanism of Evolution
1859: On the Origin of Species by Means of Natural Selection presented:
1) Evidence for evolution: descent with modification; living species are descendants of ancestral species.
2) Mechanism for evolution: natural selection.Natural selection = differential survival and reproduction of individuals with advantageous traits, leading to adaptation.
Supporting observations for natural selection: inheritance, variation, and differential reproductive success.
Descent with Modification and Examples
Descent with modification can be illustrated by elephant evolution through tusk morphology changes; populations change over generations, potentially leading to speciation.
Today’s diverse species in related groups share a direct common ancestry; many lineages are extinct (dagger symbol ∎ marks extinction).
Evidence: Natural Selection and Its Mechanisms
Natural selection was inferred from: inheritance, variation, and differential reproductive success.
An editing view: natural selection culls less fit individuals, increases frequency of favorable traits, leading to adaptation and possibly new species.
It is not goal-directed; environments change, so what is favorable changes over time.
The Finches as a Classic Example
Galápagos finches: a single ancestral species diversified into multiple species with different beak shapes/sizes for different seed sizes.
Example narrative: a small mainland population arrives on an island; beak sizes vary; droughts favor larger beaks that crack large seeds; over many generations, larger-beaked finches become more common, illustrating adaptation via natural selection.
Artificial Selection and Human Impact
Controlled breeding demonstrates how selection shapes traits rapidly (e.g., dog domestication from wolves; dramatic breed diversity in a few thousand years).
This serves as a model for understanding natural selection’s potential effects over longer time scales.
Important Points About Evolution
Individuals do not evolve; populations do.
Natural selection amplifies or diminishes heritable traits only; acquired traits (non-heritable) are not passed on.
Evolution is not perfection; trait favorability varies with changing environments.
Darwin’s Finches: Major Observations and Ongoing Studies
Rosemary and Peter Grant studied Darwin’s finches for over 20 years, demonstrating real-time evolution in response to environmental conditions (e.g., wet vs dry years affecting seed sizes and beak selection).
Example hypothesis: in dry years, larger seeds predominate; selection favors larger beaks in subsequent generations.
Daphne Major as a key site for long-term observation.
Hypothetical Beak-Depth Data (illustrative)
A drought can shift beak size distributions in a population by favoring alleles associated with larger beaks, observable as a shift in the mean beak depth across generations. See the focused study by Grant and colleagues on Daphne Major for a real-world illustration.
Pesticide Resistance and Other Adaptive Scenarios
Evolution of pesticide resistance in insects is a clear case of natural selection: initial pesticide use favors pre-existing resistant alleles; continued use increases late-appearing resistant individuals; frequency of resistance alleles rises over time.
This exemplifies natural selection acting on standing variation and/or new mutations.
Camouflage and Adaptive Coloration
Camouflage as an evolutionary adaptation shows how appearance can influence survival; examples include flower mantis and leaf mantid illustrating mimicry forms.
Fossil Record: Evidence for Evolution
Oldest fossils: prokaryotic cells; oldest eukaryotic fossils ~2.1 billion years old; multicellular fossils appeared later.
Fossils link ancient extinct species with species living today; e.g., transitions in whales from land-dwelling mammals to fully aquatic forms.
Comparative Anatomy and Descent with Modification
Homologous structures indicate common ancestry; same bone arrangements across diverse species despite different functions (e.g., humerus, radius, ulna, carpals, metacarpals, phalanges across human, cat, whale, bat).
Vestigial structures: remnants of ancestral features with little or no current function (e.g., pelvic bones in some whales; hindlimb bones in snakes); evidence of past inheritance from a common ancestor.
Embryology and Evidence of Relatedness
Embryological similarity among vertebrates suggests common ancestry; early vertebrate embryos show similar features such as tails and gill arches.
Biochemical and Genetic Evidence
All cells share fundamental biochemical features: DNA, RNA, ribosomes; the same 20 amino acids; ATP as energy carrier.
DNA sequence similarities reveal relatedness; e.g., the gene cytochrome c has 315 nucleotides in both humans and mice with only ~30 differences between the two species, illustrating close relatedness.
Evolutionary Tree and Homologies
Homologies (structural or genetic) help reconstruct evolutionary trees and branching patterns.
Tiktaalik (Devonian) represents an intermediate link between fishes and tetrapods, illustrating transitions in rib structure and limb evolution.
Tetrapod characteristics: ribs common to tetrapods.
Fish characteristics: scales typical of fish.
The Evolution of Populations (Population Genetics)
Populations, not individuals, are the units of evolution.
A population is a group of individuals of the same species living in the same place and time.
Evolution = change in heritable traits in a population across generations (i.e., changes in allele frequencies).
Gene pool = total collection of genes in a population at a given time.
Microevolution = change in allele frequencies within a population over time.
Population genetics studies how populations change genetically over time.
Hardy–Weinberg Equilibrium (HWE)
Used to test whether a population is evolving.
In a sexually reproducing, diploid population, allele and genotype frequencies remain in equilibrium unless outside forces act to change them.
Key equation: p^2 + 2pq + q^2 = 1 where p and q are the frequencies of two alleles, and p + q = 1.
Conditions for HWE (no evolution):
No mutation
No gene flow between populations (no migration)
Very large population size (no genetic drift)
Random mating
No natural selection
If these conditions hold, allele/genotype frequencies remain constant across generations.
Mutation and Genetic Variation
Mutation is the ultimate source of new alleles and genetic variation; mutations are rare but important, occurring at roughly
ext{mutation rate} \,\approx\, 10^{-5} \text{ to } 10^{-6} per gene per generation in humans.Mutations are not goal-directed; some may improve adaptation, others may be neutral or deleterious.
Chromosomal duplications provide raw material for evolution; a duplicated gene can accumulate new mutations while the original copy maintains function.
Sexual reproduction shuffles alleles via independent assortment, crossing over during meiosis, and random fertilization, producing novel combinations.
Gene Flow, Genetic Drift, and Population Size Effects
Gene flow: movement of alleles among populations due to migration and interbreeding; alters allele frequencies.
Genetic drift: random changes in allele frequencies, strongest in small populations; causes loss of genetic variation over time.
Population bottlenecks: drastic reduction in population size leading to loss of genetic diversity and potentially altered allele frequencies; can be caused by natural disasters or human activities (e.g., hunting).
Founder effects (implied by bottleneck discussions): new populations established by a small number of individuals can have non-representative allele frequencies compared to the source population.
Nonrandom Mating and Natural Selection
Nonrandom mating: mating biases (e.g., snow geese with color morphs preferring same-color mates) can influence genotype frequencies independent of selection.
Natural selection as a driver of adaptive evolution: individuals with higher fitness leave more offspring; can alter trait distributions across generations.
Penetrance of trade-offs: a trait that increases fitness in one context (e.g., long neck for combat) may incur costs in another (e.g., vulnerability while drinking).
Sexual and Social Selection
Sexual selection can cause dimorphism: males and females evolve different appearances due to competition for mates.
Intrasexual competition (often male–male) drives evolution of traits used in combat or intimidation.
Altruism: behaviors that reduce an individual's own reproductive success but benefit others (e.g., yearling Florida scrub jay feeding younger siblings).
Kin Selection and Kin Recognition in Behavior
Some species exhibit kin recognition and preferentially avoid harming close relatives (e.g., cannibalistic spadefoot toad tadpoles distinguish kin and avoid consuming them).
Practical Takeaways and Implications
Darwin’s theory integrates multiple lines of evidence (fossil record, comparative anatomy, embryology, biochemistry, and observed selection).
Evolution operates on populations across generations; time scales and environmental contexts shape adaptive outcomes.
Understanding evolution has practical implications in medicine (e.g., pesticide and antibiotic resistance), conservation (genetic drift and bottlenecks), and agriculture (artificial selection).
Key Formulas and Notation
Hardy–Weinberg equilibrium: p^2 + 2pq + q^2 = 1, ag{1} with p + q = 1. ag{2}
Mutation rate (approximate): \mu \approx 10^{-5} \text{ to } 10^{-6} \text{ per gene per generation}.
Descent with modification and the concept of common ancestry are qualitative, but the math of population genetics revolves around allele frequencies p and q and their changes over time.
Notable Historical Timelines and Figures
2.1 billion years ago: oldest eukaryotic fossils appear; prokaryotic fossils are older.
~230 MYA: Trilobites extinct; ~150 MYA: seed ferns extinct in deeper strata; ~65 MYA: dinosaurs extinct.
1788–1830s: Hutton and Lyell promoted gradualism/uniformitarianism, shaping Darwin’s thinking about long timescales.
1831–1836: Darwin’s Beagle voyage influences; Galápagos finches underscore variation and adaptation.
1859: Origin of Species published; presents descent with modification and natural selection as core ideas.
Common Misconceptions Clarified
Individuals do not evolve; populations do over generations.
Natural selection acts on existing heritable variation, not on acquired characteristics.
Evolution is not goal-directed or perfect; it is contingent on current environmental conditions.
The fossil record, comparative anatomy, embryology, and molecular data all support a single, branching tree of life.
Quick Summary of Evolutionary Mechanisms (three main sources of change)
Mutation: introduces new alleles; source of variation.
Gene flow: moves alleles among populations; changes allele frequencies.
Genetic drift: random changes in small populations; can fix or lose alleles independent of fitness.
Natural selection: differential reproduction based on heritable variation; leads to adaptation.
Sexual selection: selection for traits that improve mating success; can produce sexual dimorphism.
Nonrandom mating: assortative mating shapes genotype frequencies.
Artificial selection: humans deliberately select for desired traits, illustrating natural selection principles in a controlled context.