Evolutionary Biology Final Study Guide

Evolution - Fact, Theory, Pattern, Process (FTPP)

• Descent (splitting of lineages) with modification (i.e. change over time).

• Dinosaur fossils and other transition fossils are evidence of evolution.

• aDaptions caused by evolution lead to a good 'fit of form' (think coevolution, or dolphins losing their quadrapeds to swim).

Time Scale of Evolution:

Evolution occurs on broad and short time scales:

• Humans evolved around 200,000 years ago.
• Covid-19 evolved Spike Protein - Delta, Alpha, and Omicron variants in the span of two years.
• HIV uses reverse transcriptase to undergo translation of new HIV proteins, leaves the cell, and repeats this process.

Darwin vs. Lamarck vs. Wallace:

Darwin:

• Variation Under Domestication: title of first two chapters of On the Origin of Species (1859), suggests human have used artificial selection in domestication.

• Darwin Mechanism: natural selection passed through gametes.

Lamarck (1744 - 1829):

• First to propose a mechanism for evolutionary change: environments create a need that organisms fill by evolving within one generation. 

• Lamarck Mechanism: Pangenesis - all somatic cells carry traits.

Wallace:

• Co-discovered natural selection with Darwin.

Discussion Material

Discussion 1 Notes:

• Struggle for Existence: environment contributes to the struggle to reproduce alongside competition. 

• Organisms propensity for increase: more individuals are born than can reproduce. Parallel to Malthus' belief that populations grow exponentially before food supplies catch up. 

• Intra vs. Interspecific Struggle: Intraspecific struggle is the most severe, as they compete for the exact same niche.

Discussion 2 Notes:

• Modern human hybdridized with other species of Homo

• To find the genes that affect quantitative, continuous traits, we scan the genome for nucleotide sites that co-vary with the phenotype.

• In cases of mutation, adjacent SNPs are linked to the mutation. We must use phasing and genome sequencing to determine where these SNPs came from in the unphased form.

Discussion 3 Notes:

• Candidate Gene: gene that researchers suspect is linked to a trait of interest.

• Haplotype: a set of genes/alleles that are inherited together on a chromosome.

• Mitochondrial DNA: has NO effect on coat color, but does affect population history. mtDNA cannot result in speciation based on coat color.

Eidos, or Essentialism

Plato (427-347 B.C.):

• Eidos: concept of idealized form, with essential properties defining group, or species membership. Similar 
• Demiurge: the creative power that organized the universe.

Aristotle (384 - 322): Founder of Natural History

• Great Chain of Beings: there is a hierarchy of life arranged according to the degree to which they have the potential to change. Similar to Plenitude.

Scientific Reawakening and its Soldiers

Carl Linnaeus (1707 - 1778):

• System Naturae (1735); variation among/within species became evident as he emassed a collection of species.

George Buffon: Histoire Naturelle

• Developed Biogeography; demonstrated that fossils proved a problem for the model of Plenitude

George Cuvier (1769 - 1832):

• Founder of paleontology and comparative anatomy.

• Paris Basin: lower strate of soil had fossils of fauna and flora that were increasingly different from current organisms.

James Hutton (1726 - 1797):

• Uniformitarianism: the present is the key to the past.

• Forces on the past act today (erosion, sedimentation)

Sir Charles Lyell (1797 - 1875):

• Principles of Geology; supported uniformitarianism which supported Darwin's development.

Lamarck (1744 - 1829):

• First to propose a mechanism for evolutonary change in which environments create a need, and organisms respond in turn.

• Believed that evolution takes place within a generation, and is passed on through pangenesis, in which all somatic cells carry traits.

Tree Thinking Terms

• Clade = monophyletic group

• Taxa = groups of organisms/species | Taxon = individual organism/species | Taxa/Taxon are OTUs.

• Nodes: Terminal = most recent species | Internal = MRCA, or root 

• Monophylyl: group with a single common ancestor.

• Polyphylyl: group with multiple common ancestors

• Paraphylyl: group not containing all descendants of a single common ancestor

Homology vs. Analogy: Non/Convergent Evolution

• Homology: similarity in form due to descent from a common ancestor.

• Analogy: similarity in form DESPITE descenet from different ancestors, or convergent evolution.

Nucleotide Differences and Time

The relationship between nucleotide differences, i.e. speciation, and time is linear. Meaning that as time progresses, speciation and changes co-ocurr.

Natural Selection:

Natural selection: statistical differences in reproductive success among organisms that favors fitness, leading to evolution.

Adaptation: increases the fitness of its carrier;

• Physiological: you get hot = you sweat

• Biological: you get hot = you move to shade

• Genetic: you get hot = you develop reflective skin

• Design and Engineering: do adaptations make sense for form and structure?

• Darwinian: do adaptations make sense for increased fitness/reproduction?

DNA - the Central Dogma

DNA: Deoxyribonucleic Acid, Sugar-Phosphate backbone, 5'-3' Carbon Bonds

• Purines = A, G
• Pyrimidines = C, T

Central Dogma:

• DNA transcription by RNA Polymerase
• RNA translation via tRNA decoding mRNA
• Amino acids are produced, with synonymous codons expressing the same proteins.

Prokaryotic vs. Eukaryotic Gene Structure:

• Prokaryotes = continous coding sequence.
• Eukaryotic = interrupted coding sequence due to introns, with the removal of specific introns leading to one gene expressing multiple proteins.

Genetics Terminology:

• Chromatid: DNA double helix + protein.

• Chromosome: pair of chromatids, segregate in mitosis and meiosis.

• Homologous Chromosomes: one chromatid from each parent.

• Autosomes: non-sex chromosomes.

• Locus: a place in the genome.

• Gene: string of DNA that codes for some trait.

• Allele: a variant of a gene that can code/express for different things.

Mendel's Laws:

Mendel's 1st Law:

• Factors segregate, i.e., become discrete alleles that code for discrete things.

Mendel's 2nd Law:

• Independent assortment of factors, i.e., genes for different traits are inherited independently from each other.

Mendelian Genotype Ratios:

• Complete Dominance: a heterozygote is characterized by the dominant allele - 3:1
• Incomplete Dominance: heterozygote is a blend of the two alleles, leading to partial dominance - 1:2:1
• Dihybrid Cross - 9:3:3:1

Variation in Geno/Phenotype:

Sources of Variation: measured by nucleotide diversity, π, or pairwise differences between all DNA sequences.

• Genetic mutations
• Phenotypic Plasticity is induced by environment effect on gene expression and development.

Weismann's Doctrine: mutations pass only through germ line cells.

Single Nucleotide Polymorphisms (SNPs):

• Within haplotypes (groups of variable alleles), there is one variable nucleotide for every 1000 base pairs, with the difference between one human haploid genome and another being 3,000,000 base pairs.

Types of Mutation:

Point Mutations:

• Synonymous vs Nonsynonymous
• Transitions from purines to purines and from pyrimidines to pyrimidines
• Transversions from purines to pyrimidines and vice versa.

Deletions

Duplications

Inversions

Fission/Fusion

Translocation

Schools of Variation:

"Classical School: H.J. Muller

• Low levels of genetic variation in natural populations, i.e. the Wild Type is favored to ""purify"" populations from deleterious alleles.

Balance School: T. Dozhansky

• Genetic variation is common in natural populations and is maintained by balancing selection.
• Heterozygotes are favored to maintain both alleles.

"

Population Genetics - Predicting Genotype Frequencies from Allele Frequencies:

Hardy-Weinberg Law: p^2 + 2qp + q^2

• Genotype frequencies stay constant under random mating, and can be restored after one generation of random mating.
• Expected genotype frequencies are given by HWEquilibrum, regardless of starting (observed) frequencies.
• The HWE is a Null Model of an idealized population given the following assumptions: 
• Alleles are diploid
• Random mating
• Infinite population size
• There is no selection, mutation, or migration.

Variable Number of Tandem Repeat Locus (VNTRs):

• Different patterns and repetitions of VNTRs contribute to the diversity of haplotypes.
• Microsatellite loci: tandem repeats of short motifs.

Effective Population Size:

Effective Population Size (Ne): number of breeding individuals contributing to the gene pool.

• Genetic Drift vs. Effective Population Size: GD wins when Ne is smaller than the inverse of selection coefficient

Sex Ratio Effects on Ne:

• Nf and Nm = number of breeding females/males

• The real Ne (harmonic mean) is always lower than the average Ne when accounting for bottlenecks and sex ratios.

Fitness:

Peppered Moth Example: dark form is favored under pollution (natural selection) but eliminated when pollution is regulated (reverse direction).

A model of natural selection and fitness:

• Fitness: wii = lii (survivorship) x mii (fecundity)

A model of selection based on changes in genotype frequencies:

• Absolute Fitness = freq.(after selection)/freq.(before selection)
• Relative Fitness = (abs fitness of a genotype)/(best abs fitness of all of the genotypes)
• Selection Coefficients: measures the relative fitness disadvantage of a genotype compared to the most fit genotype. How strong natural selection acts against the genotype.
  
• Selection is inversely proportional to the strength of selection, where higher values of s correspond to faster changes in allele frequency, and thus fewer generations for fixation or loss.
  

• Higher s = faster change | Smaller s = slower change

Selective Sweep and Hitchhiking:

• Selective Sweep: a beneficial allele rapidly increases in frequency in a population, often due to fixation, reducing polymorphism. Selective sweep is the causal force behind hitchhiking.

• Hitchhiking: an allele inreases in frequency because it is physically linked to a nearby allele that is under positive selection.

• Mutation and recombination reintroduce polymorphisms into populations after hitchhiking.
  

Dominance and Kinds of Natural Selection Under Wright's Adaptive Landscape:

R.A. Fisher: The rate of natural selection is proportional to the genetic variation in the population.

Dominance:

• Co-dominance: the heterozygote has a fitness exactly in between the two homozygotes.

• Partial Dominance: the heterozygote has fitness closer to either of the homozygotes.

• Dominance: the heterozygote has the same fitness as one of the homozygotes.

Wright's Adaptive Landscape Under Three Kinds of Selection:

1. Positive Selection: Frequency has a linear trend towards a peak in fitness.

2. 'Marginal' Overdominance: Fitness peaks for heterozygotes over homozygotes, (regardless of environment).

3. Underdominace: Fitness peaks for homozygotes over heterozygote.

Mutation:

Mutation: source of new variation, increases recessive allele presence.

Modeling Mutation: A --u> <---v a

• u = probability of mutation

• 1-u = probability of NO mutation

• v = probability of reverse mutation

Mutation vs. Selection

Mutation:

• Mutation introduces 'bad' recessive allele while selection eliminates the bad recessive allele. This helps maintain polymorphism.

• Mutation acts on all loci simultaneously.

Selection:

• Multiple-Niche Polymorphism: selection maintains polymorphism because of variable niches which can provide fitness advantages depending on the environment.

• Selection acts on specific loci.

Continent-Island Model of Migration:

• m = the proportion of the Island that migrates in from a continent.

• (1-m) = the proportion of the Island that does NOT migrate from the continent.

Genetic Drift: acts on all loci simultaneously

Genetic Drift: changes in genotype frequency due to random sampling of breeding individuals in SMALL populations.

• Features of Genetic Drift: unbiased, results in the fixation or loss of alleles with NO selection.
  
• Example - Founder Effect: islands have LARGE GD.

Population Structure:

Population Structure: The distribution of genetic variation within and among populations. How is variation partitioned in and among populations? 

• FST: Fixation of alleles in the sub population relative to the total population (p can = 0.5 but if heterozygotes are present, FST = 0. If homozygotes are present, FST can = 1.0)
• Population Structure (Fst) and Effective Migration (Nem): Low gene flow causes strong population differentiation = high FST. High gene flow causes low population differentiaton = low FST.
• Mutation (u) and Drift Equilibrium (Ne): 4Neu (where Ne is large and unknown and u is small and unknown)

How do we integrate Selection, Mutation, Migration, and Genetic Drift as evolutionary forces?

• Wright's Adaptive Landscape: Positive, Overdominance, Underdominance Selection - tends to increase mean fitness of the population.

DNA Evolution - Heterozygosity vs. Inbreeding Coefficient

Substitution: when repeated over time, leads to DNA divergence. Caused by: Mutation, Polymorphism, Fixation/

• Divergence = number of base pair differences / length of sequence
• Rate = sequence Divergence / age of common ancestor

Consequences of DNA evolution, or lack thereof:

• Heterozygosity (H) = 2pq: H, or proportion of heterozygotes, decays due to genetic drift and inbreeding.
• Inbreeding Coeffcient (F) = the probability that two alleles are IDENTICAL by descent.
• H and F are opposites, think of it like that!

Molecular Evolutionary Clocks

• Molecular Evolutionary Clocks: different genes/regions have different functional constraints, and therefore are bound by the amount of synonymous vs. nonsynonymous mutations they are allowed to have by the biological importance of their processes.

• I.e., Histones have LOW rates of mutation and take forever to evolve while coding genes have high rates of mutation and evolve much faster.

Neutralist-Selectionist Debate:

Mooto Kimura: proponent of the Neutral theory of molecular evolution. Some substitutions are adaptive but most are neutral.

• Neutral mutations are defined by selection coefficients being smaller than 1/2Ne: Selection is non-neutral in large populations, while it is neutral in smaller populations.

Protein Coding DNA and Neutrality:

• dN = non-synonymous changes per non-synonymous site.
• dS = synonymous changes per synonymous site.
• dN/dS = 1 indicates neutrality
• dN/dS > 1 indicates positive selection for avantageous alleles
• dN/dS < 1 indicates purifying (negative) selection, or the removal of deleterious alleles.
• The ratio of dN/dS suggests the ability to be variant and the capacity for genetic mutability.