ECOL335 S2025 Final Exam Review Notes

Building and Using Phylogenies

• How do we build phylogenies? How do we use them?

Homology

• Homology: Similarity in structure due to inheritance from a common ancestor.
  • Example: Human arm (humerus, radius, ulna, carpals, metacarpals, and phalanges), seal flipper, bat wing.

Constructing Evolutionary Trees

• Using homologies to construct evolutionary trees.
• Parsimony principle: Choosing the simplest explanation (tree with fewest evolutionary changes).
• Maximum likelihood: Choosing the tree that maximizes the probability of observing the data, given a model of evolution.
• Assessing confidence in a reconstructed tree: Bootstrapping (resampling data to see how consistently clades are recovered).

Relatedness

• Species A is more closely related to species B than to species C if the common ancestor of A and B is more recent than the common ancestor of A and C.

Evolutionary Trees

• Using evolutionary trees to predict character evolution.
  • Example: Placing the evolution of 'Two pairs of limbs' and 'Wings' on a phylogenetic tree including birds, crocodiles, mice, bats, amphibians, snakes, and turtles.
• Is the similarity of flight structures in birds and bats a homology? (No, it's an analogy - convergent evolution).
• Predicting homologies based on evolutionary trees.

Transitional Forms

• Using evolutionary trees to predict transitional forms.
  • Example: Evolution of tetrapods from fish.
    • Timeline: 415 to 365 Million years ago.
    • Key innovations: Bony skeleton, lungs, lobe fin (single large bone in fin attached to shoulder girdle), single large limb bone articulated with two smaller bones.
    • Groups: Ray-finned fish, Coelacanth, Lungfish, Living tetrapods.

Natural Selection and Adaptation

• How natural selection and adaptation work.

Natural Selection

• Natural selection occurs when:
  1. Heritable Variation: Traits vary among individuals, and trait variation can be transmitted to the next generation.
  2. Selection (Fitness) Differential: Individuals with different traits have different reproductive success or fitness.
     • Fitness = total number of offspring they produce over their lifetime.

Breeder's Equation

• Breeder’s equation: $R = S \\times h^2$
  • R = Response to selection.
  • S = Selection differential.
  • $h^2$ = Heritability.
• When can we expect natural selection to have large effects on a population?

Limits to Natural Selection and Adaptation

• Limits to natural selection and adaptation: History & tradeoffs.
  • Example: Tradeoff between average size of offspring and number of offspring in high-predation vs. low-predation sites.

Extravagant Traits

• Given such constraints on adaptation, how can we explain the evolution of traits that seem "extravagant"?

Sexual Selection

• Sexual selection
  • Intersexual selection: One sex displays, the other chooses.
  • Intrasexual selection: Interference competition within one sex.
  • Sexual conflict: Mates are gained in one sex at some cost to the other sex.

Genetic Variation

• Where does genetic variation come from?
• How does genetic variation translate into phenotypic variation?

Mendelian Inheritance

• Laws of Mendelian inheritance
  • Law of segregation
  • Law of independent assortment

Phenotypic Traits

• A phenotypic trait may be controlled by one major gene.
• A phenotypic trait may be controlled by many genes with small effects.
• Gene effects can interact: dominance, epistasis.

Mutations and Fitness

• The effect of mutations on fitness: Neutral, deleterious, or advantageous.
• Genetic code.
• Mutations at a codon’s 3rd base are often neutral.
• New alleles arise by random mutation.
• The rate of mutation varies greatly among organisms.

Hardy-Weinberg Principle

• Hardy Weinberg principle.
• Heterozygosity (H): measure of genetic diversity.
• Genetic drift: causes a population to lose heterozygosity.
• Effective population size ($N_e$): determines rate at which H is lost.
• Population bottleneck: why $N_e$ may be very small.
• The fate of neutral alleles.

Beneficial Alleles

• How can we identify alleles that are beneficial and contribute to adaptation?
• Linkage Disequilibrium!
• Beneficial alleles are expected:
  • To occur at relatively high frequency.
  • To be relatively young (i.e., mutation occurred relatively recently).
• High linkage disequilibrium:
  • Non-random association with other alleles nearby on the chromosome.
  • Supports recent mutation (« young allele »).

Speciation

• Explaining the origin of new species…

Biological Species Definition

• Biological species definition
• Speciation requires:
  • Population split (geographical, ecological)
  • Reproductive isolation
• Evolution of reproductive isolation:
  • Post-zygotic: Dobzhansky-Muller genetic incompatibility.
  • Pre-zygotic: assortative mating… often involves sexual selection.

Positive Selection

• How can we detect the effect of positive selection and adaptation in the evolutionary divergence of two species?
  • → We compare DNA sequences from these two species and look for a genomic signature of positive selection.

Gene Selection

• A gene being under selection means that nonsynonymous mutations in the gene do have some fitness effect.
• Nonsynonymous mutations that are deleterious will be eliminated by purifying selection.
• Nonsynonymous mutations that are beneficial will be driven to fixation by positive selection.
• The $K<em>a/K</em>s$ (also called $d<em>N/d</em>S$) test of selection.

$K<em>a/K</em>s$ Test

• The $K<em>a/K</em>s$ (or $d<em>N/d</em>S$) test of selection
• When we find more nonsynonymous substitutions per nonsynonymous site ($K<em>a$) compared to the number of synonymous substitutions per synonymous site ($K</em>s$), this strongly supports that positive selection has acted on the gene and is responsible for this excess of nonsynonymous substitutions.

Nonsynonymous vs Synonymous

• Nonsynonymous (Val - Thr - Pro - Glu - Glu - - Lys Ser)
• Synonymous

Molecular Clock

• The molecular clock.
• Within a clade, substitutions tend to accumulate at a constant rate.
• We can use the molecular clock to date the divergence of species based on differences in their DNA sequences.
• How can we date speciation events?

Tree of Life

• Three domains: Bacteria, Archaea, Eukaryotes
• Striking abundance of lineages without isolated representatives.
• Make majority of life’s current diversity!
• A look at the whole Tree Of Life…

Human Evolution

• Looking into the evolutionary history of our own lineage…

Hominin Divergence

• Divergence of Hominins from other great apes
• From 6 to 4 Mya, from 4 to 2 Mya… The last 2 My…
• 3 waves out of Africa

Homo Species

• Examples of Homo species:
  • Homo ergaster
  • Homo habilis
  • Homo erectus (About 1.6 Mya)
  • Homo heidelbergensis (About 1 Mya)
  • Homo naledi
  • Neanderthals
  • Homo sapiens
  • Homo luzonensis
  • Homo floresiensis

Genetic Variation in Humans

• Genetic variation in modern human species shaped by interbreeding.
• Timeline:
  • Super-archaic (4 million-900 ka)
  • Super-archaic and archaic humans split (765-550 ka)
  • Archaic humans split into Denisovans and Neanderthals (473-381 ka)
  • Lineages of archaic humans and modern humans split.
  • Denisovans and Neanderthals gone by ~40,000 years ago
• Arrows indicate known incidents of interbreeding
• By sequencing ancient and modern DNA, comparing differences and calculating how much time was needed for the variations to accumulate, scientists can create timelines for when different populations split.

Human Adaptation

• Genomic evidence for human adaptation: coping with low oxygen in Tibet, as one example.

Genetic Diseases

• How can we explain the persistence of genetic diseases in contemporary human populations?
  1. Genetic drift can drive deleterious mutations to fixation.
  2. Deleterious alleles may persist in mutation-selection balance.
  3. Deleterious alleles may persist due to heterozygote advantage.

Infectious Diseases

• What evolutionary biology can tell us about infectious diseases.

HIV

• HIV as a case study
• Making sense of HIV virulence
  • Role of within-host selection
• Evolutionary biology to help design effective treatments
  • How to delay the evolution of drug resistance

Origin of HIV

• Where does HIV come from?
  • Phylogenetic reconstruction points to ‘jump’ from chimps or gorillas to humans
• When did HIV arise?
  • Using the molecular clock approach

Theodosius Dobzhansky

• "Nothing in biology makes sense except in the light of evolution." - Theodosius Dobzhansky (1900-1975)