Understanding Evolution: Key Concepts and Theories

Evolution as a Core Unifying Principle

• Evolution connects many different interdisciplinary fields in biology.
• All life results from evolution.
• Understanding the past through evolution is essential for predicting future biological trends.

Relevance of Evolution in Everyday Life

• Medicine: Antibiotic resistance increases with drug use, highlighting evolutionary adaptation in microorganisms; CRISPR technology development.
• Agriculture: Selective breeding demonstrates artificial selection, seen in the diversification of mustard plants into vegetables like cabbage, cauliflower, and kale.

Patterns Defined as Evolution

• Antimicrobial resistance
• Artificial selection in crops

Biological Definition of Evolution

• Change over time in the characteristics of a population of organisms.

What Evolution Is and Is Not

• Evolution involves change in populations of organisms, is not limited to common misconceptions

Evolution as a Scientific Theory

• Evolution meets the criteria of a scientific theory, supported by a substantial body of evidence and explanatory power.

Darwin's Influences

• Before the 1850s, theories were rooted in Plato and Aristotle.
• Platonic Idealism: This philosophical view posits ideal forms imperfectly represented on Earth, explaining variation as imperfections.
• Aristotle: He believed species were immutable and classified them on a scala naturae, reflecting increasing complexity.
• Essentialism: Aristotle's view that species are defined by unchanging properties.
• Carolus Linnaeus: He established modern taxonomy in Systema Naturae (1735) to understand God's creation, not to infer evolution.
• Type specimens: Represent the ideal form of a species.
• George Cuvier: Known as the 'father of modern paleontology,' he advanced zoology and paleontology by comparing species, articulating the concept of extinction.
• Catastrophism: Cuvier's idea that species were created after catastrophic extinction events shaped changes in species composition.
• The Enlightenment emphasized logic and reason to explain natural phenomena, influencing astronomers and geologists to propose "deep time," that the earth is older than 4000 years.
• James Hutton: He proposed volcanic upwelling formed rocks subsequently eroded by water and uniformitarianism -- natural processes in the past are the same as today.
• Charles Lyell: Influenced Darwin; popularized Hutton's uniformitarianism in Principles of Geology.
• Jean-Baptiste Lamarck: Proposed that evolution occurs through the inheritance of acquired characteristics.
• Lamarckism suggested giraffes elongate their necks over time by reaching for trees, passing this trait to offspring through the accumulation of nervous fluid.
• Lamarckism, or transformism, was dismissed by Cuvier and included ideas of spontaneous origins and inheritance of acquired characteristics but didn't believe in extinction.
• Thomas Malthus: His "Essay on the Principle of Population" states human population growth outpaces food supply.
• Malthus argued unchecked populations grow exponentially until limited by resources.
• Darwin recognized competition for limited resources leads to the survival and reproduction of individuals with advantageous traits.
• Malthusian crisis is the idea that population will increase to a point where we cant feed everyone
• Alfred Russel Wallace: Conducted fieldwork in the Amazon and Malay Archipelago.
• An early transmutation of species believer, influenced by Lamarck and Malthus.
• Wallace sent Darwin his theory in 1858 just before Darwin published Origin of Species, Darwin later secured a British government pension for Wallace.
• Darwin and Wallace jointly presented their findings.

Key Event in 1859

• Darwin published "On the Origin of Species," detailing evolution via natural selection.

Significance of the Voyage of the Beagle

• Darwin served as a companion to Captain Fitzroy on the HMS Beagle in 1831.
• The voyage lasted five years and included a visit to the Galapagos Islands.
• Darwin experienced an earthquake in Chile, witnessing uniformitarianism firsthand.
• He observed biodiversity and variation across Galapagos Islands, including tortoises and finches.

Darwin's Sub-Theories

• Darwin's On the Origin of Species in November 1859 outlined evolution and natural selection.
• Evolution by natural selection comprises five interconnected theories:

  • Evolution as Such: Lineages change over time.

  • Common Descent: Divergence from a common ancestor results in different species.

  • Gradualism vs. Saltation: Gradualism is the slow, incremental change over time saltation is large leaps without intermediate forms.

  • Population Variation vs. Platonic Idealism: Emphasizes variation within populations rather than fixed ideal forms.

  • Natural Selection: Key mechanism involves selection.

Missing Elements in Darwin's Theory

• A mechanism of inheritance.
• Darwin proposed natural selection operates on phenotypic variation, with better-adapted individuals producing more offspring.

Darwin vs. Mendel on Inheritance

• Darwin: Phenotypes are intermediate between parents (blended inheritance).
• Mendel: Traits are inherited through particles.
• Mendelians Studied large differences, discrete traits, and rejected natural selection.
• Biometricians Studied small differences, quantitative traits, and supported natural selection.
• Relatively few loci approximate continuous variation in a trait.

Modern Synthesis/Neo-Darwinism

• R.A. Fisher used quantitative and population genetic theory; all biometrician results derive from Mendelian inheritance principles.
• J.B.S. Haldane and Sewall Wright showed natural selection and Mendelian inheritance could produce evolutionary change, explaining speciation through population genetics.

Key Figures of the Modern Synthesis

• R.A. Fisher
• J.B.S. Haldane
• Sewall Wright

Conditions for Evolution by Natural Selection

• Selection + heritable genetic variation = evolution.
• Strong heritability and strong selection = fast evolution; weak heritability and weak selection = slow evolution.
• Phenotype: morphological, physiological, biochemical, and behavioral traits
• Genotype: set of genes possessed by an individual organism
• Three conditions for evolution by natural selection:
  • Phenotypic Variation: Individuals differ in the focal trait.
  • Heritability: Phenotypic variation has a genetic basis.
  • Variation in Fitness: Traits influence lifetime reproductive success.

Continuous and Discrete Phenotypic Variation

• Discrete: Controlled by few loci and alleles, straightforward inheritance (e.g., Mendel's plant traits).
• Continuous: Controlled by many loci and alleles (polygenic), statistical inheritance (e.g., height).

Continuous Phenotypic Variation Example

• Average heights of human males in European countries, influenced by nutrition and genetics.
• Continuous variation combines gene action and environmental variation.

Phenotypes Without Genetic Change

• Phenotypic plasticity: The ability of a genotype to develop different phenotypes based on environmental conditions (e.g., Daphnia developing protective helmets due to predator cues)
• This can be either reversible or permanent.
• Reactions can be adaptive, maladaptive, or neutral.

Evidence for Genetic or Non-Genetic Inheritance

• Genetic variation reflects phenotypic variation due to DNA differences.
• Non-genetic forms of inheritance:
  • Cultural inheritance: Non-genetic traits based on imitation or learning (e.g., dialects in bird calls).
  • Maternal effects: Non-genetic maternal influence on offspring phenotype (e.g., stress affecting squirrel growth rate).
  • Epigenetic Inheritance: Inherited changes in gene expression or phenotype not based on DNA (DNA methylation). Holly more prickly leaves due to herbivory

Determining Genetic Influence

• To determine whether (or how much) a trait has a genetic basis:
  • Experimental crosses: Used for traits with simple genetic control.
  • Correlations among individuals: Relate offspring and parent phenotypes.
  • Common garden experiments: Raise offspring in a common environment to observe persistent phenotype variation.

Mutation Importance

• Mutations are the primary source of genetic variation.
• Mutations must be passed on

Effects of Mutations

• Phenotype: Subtle/quantitative or drastic/qualitative.
• Fitness: Most are neutral, but the average effect is deleterious.

Directed vs. Random Mutations

• Mutation is stochastic; environmental benefits do not influence likelihood (e.g., E. coli fitness).

Mutation Rate

• Mutation rate is the number of independent origins per base pair, locus, or genome per generation or time unit.

Estimating Mutation Rates

1. Screen offspring of genetically characterized parents.
2. Mutation accumulation experiments assess mutations over generations.
3. Compare fixed mutations across species indirectly.
4. Directly compare DNA sequences.

• Average mutation rate is 10⁻⁶ to 10⁻⁵ per gamete per generation.
• There are about 70 new mutations per human relative to parents.
• The larger the genome, the higher the mutation rate, but this doesn't hold for viruses.

Hardy-Weinberg Equilibrium

• Population genetics studies allele frequencies and causes of variation.
• Allele frequencies not influenced by genotype frequencies.
• Hardy-Weinberg Principle: Allele frequencies are conserved in a randomly mating population unless influenced by external forces.
• HWE is established after one generation of random mating. After establishment, frequencies remain unchanged.

Hardy-Weinberg Equilibrium Assumptions

1. Random mating
2. Infinitely large population
3. Closed population
4. No mutations
5. No selection

Studying HWE

• Much of evolutionary biology examines what happens when these assumptions fail.

Evolution Without Selection

• Genetic drift refers to random changes in allele frequencies.
• Average time to fixation of a new mutation = 4N generations.
• The probability a population becomes monomorphic for one allele equals the initial frequency.

Heterozygosity

• Heterozygosity declines as the frequency of one allele approaches 1.
• Can lead to maladaptive evolution.

Effective Population Size (Ne)

• Ne accounts for unequal reproductive contribution in a population, making populations susceptible to genetic drift.

Neutral Theory of Molecular Evolution

• Most molecular evolution is driven by neutral mutations fixed by genetic drift, not natural selection.
• "Neutralist-selectionist" debate: mutations occur at a constant rate (molecular clock).
• Neutral mutation rates expected to be highest in non-functional DNA.

Mutation Rate, Population Size, and Allele Fixation

• Rates of synonymous mutations are higher than non-synonymous mutations.
• Supports the idea that is synonymous mutations evolve neutrally and at a constant rate.
• Non-synonymous mutations evolve more slowly because there is a phenotypic effect

Inbreeding Coefficient

• It is the probability that a random pair of gene copies is identical by descent.
• Results in heterozygote deficiency, leading to inbreeding depression.

Inbreeding Depression Causes

• Exposure of deleterious recessive alleles
• Loss of heterozygote advantage as more diverse offspring are more likely to be able to respond to different environments, stressors….

Autozygous vs. Allozygous

• Autozygous: Alleles are identical by descent
• Allozygous: Alleles are not identical by descent

Heterozygosity Under Inbreeding

• Heterozygosity decreases under inbreeding.

Fitness Components

• Fitness is survival + reproductive success.

1. Probability of survival to reproductive age
2. Average offspring number via female route
3. Average offspring number via male route

Selection

• "Selection of" entities
• "Selection for" traits

Levels of Selection

• Natural selection is the differential fitness of classes of entities differing in one or more characteristics.
• Evolution requires: phenotypic variation, fitness differences, and heritability.

Different Levels of Selection

• Individual selection: Differing phenotypes contribute to generations differently.
• Genic selection: Single gene/allele drives selection.
• Group selection: Differential origination/extinction rates occur.
• Species selection: Species increase/decrease in number at different rates.

Natural Selection vs. Genetic Drift

• Differences in fitness are not just due to chance, natural selection = deterministic.

Adaptation

• Characteristic improving survival/reproductive success or genetic shift adapting the population.