BIO120 - EXAM NOTES - EVOLUTIONARY BIOLOGY LECTURES

Exam Review!

• Central unifying concept of biology

• “Nothing in biology makes sense except in the light of evolution” - Dobzhansky

Theory of evolution

• Living things change over time

• Adaptations have arisen through natural selection

Two core tenets of evolution

Organisms on earth have changed through time (Gradually)

Biodiversity is generated by speciation, splitting lineages

All species have a single common ancestor

Biodiversity and Adaptation are products of Evolution

Conclusions about evolution verified by scientific study

The diversity of life on earth & the number and types of organisms in an area

Biodiversity (definition)

Noun: Any trait allowing an organism to better survive or reproduce in an environment

Verb: The evolutionary process leading to the origin and maintenance of these (noun) traits

Adaptation (definitions)

Major areas of evolutionary study

Microevolution: Evolutionary patterns/processes within species

Macroevolution: Evolutionary patterns/processes among species

Microevolution vs. Macroevolution

History focuses on macroevolution, but requires microevolution as well

Mechanisms are primarily microevolution, but require some knowledge of macroevolution

Both are interlinked - knowledge from 1 assists the other

Correlation between Micro/macroevolution and evolutionary history/mechanisms

Goals

• Determine long-term evolutionary relationships in terms of common ancestry to understand patterns in evolution

Practice

• Uses comparative data from other disciplines (ex. paleontology, morphology)

Evolutionary History - Goals and Present Practice

Phylogenetic tree, Phylogeny

Other terms for “evolutionary tree”

True

T/F: Tree graphs can be flipped at a node and still present the same information

Goals:

• Determine processes responsible for evolutionary change, ex. natural selection

• Identify forces of evolution

Practice

• Uses experimental, comparative studies of genetics, ecology of populations

• Focuses primarily on population level (qty)

Evolutionary Mechanisms - Goals and Modern Practice

• Observational: Describe, quantify experiments

• Theoretical: Develop models - graphical, mathematical, etc.

• Comparative: Obtain data from a number of species

• Experimental: Manipulate a system to address specific hypotheses (experimental design, statistical analysis)

How is evolution studied (4 approaches)

William Paley

Humans have special, intricate functions, and therefore must have a maker (as does a watch)

Argument from design: Argument and Creator

• First person to use the term evolution

  • Provided a hypothetical mechanism: the inheritance of acquired characters

Jean-Baptiste de Lamarck - Contributions

Simplest form is repeatedly created spontaneously and evolves through usage of traits (ex. giraffe neck gets longer through use, is passed down to next generation)

Explain the inheritance of acquired characters

• Disproved Lamarck

• August Weismann (1938)

• Genetic information can flow from DNA to protein, but never in reverse - thus, acquired traits can never be passed down

Germplasm Theory - Creator, Contributions

Charles Darwin and Alfred Russel Wallace discovered natural selection, but it was Darwin who developed the first comprehensive theory

Who discovered, and who developed, the theory of evolution

• All living things have descended from a single common ancestor, and thus, have changed over time

  • The process leading to evolution is natural selection operating on variation among individuals

What was Darwin & Wallace’s theory of evolution

• Voyaged on HMS beagle

• Collected and observed plants, animals, and fossils

  • Spent most time at the Down House afterwards

How did Darwin develop the theory of natural selection

Charles Lyell (1830)

• Argued for uniformitarianism

  • Processes that have shaped the earth’s surface remain unchanged to this day

• Notion of a dynamic world, gradual changes

• Convinced darwin of Gradualism

Who wrote Principles of Geology, and what did it argue/do?

Changes build up gradually by the same mechanisms today as used in the past

Define gradualism

• Similar species descended from a common ancestor

• Caused darwin to doubt fixity of species

How did galapagos mockingbirds affect darwin

Thomas Malthus’ “An Essay on the Principle of Population” (1978)

• Made Darwin & wallace realize that favourable variations would be preserved and unfavourable would be removed in given circumstances in order to maintain stable population numbers

What essay did Darwin/Wallace read, and what did it say

On the Origin of Species (1859)

What book did Darwin write

• Variation: There must be variation at an individual level

• Heredity: Individuals must be able to inherit these varying characteristics

• Fitness: Some forms are more successful at surviving, reproducing than others in a given environment

What are the three conditions for natural selection, according to Darwin

Natural selection is heritable variation in fitness

What was the ultimate conclusion developed for Natural Selection?

Transformational (change within generations) for Lamarck,

Variational (change between generations) for Darwin

What were the differences between the Lamarckian and Darwinian models of evolution

• Evolution occurs at the population level (individuals don’t evolve)

• Variation is stochastic and does not have a goal (no induced adaptation)

• Most fit variant is based on the environment

• Evolution works with available variation, and does not necessarily achieve perfection

What are some additional important elements of Darwin’s theory

• Replaced the idea of a static world with a changing universe

• Introduced natural selection as a phenomenon with no purpose

What were the implications of Darwin’s model

• Geology

• Homology

• Biogeography

• Domestication

What are the four sources of evidence for evolution?

Found in Brazil

• Fossils of extinct mammals that resemble intermediate forms of modern creatures (transitional fossils)

Explain Darwin’s Evidence from Geology

• Age of the earth allows for immense biological evolution

• Intermediate forms/transitional fossils allow us to link seemingly dissimilar relatives

• Fossils in younger strata (closer to surface) more closely resemble modern species in same region

What lessons did Darwin take from Geology

Similarity of traits in two species due to derivation from a single common ancestor

Define homology

• Found on Galapagos

• Vestigial structures - structures inherited from common ancestor, but reduced in size/function

  • Functional variations present in related species

• Some structures are modifications of pre-existing structures (ex. whale adaptations for swimming vs. bats for flying)

• 500 genes shared across all life

Explain Darwin’s Evidence from Homology

• Vestigial traits can provide evidence of evolutionary ancestors

  • Can only be explained by presence of functional traits in ancestors, followed by degradation (all traits have an associated cost)

• Homologous structures are present in many organisms

  • Reflect common ancestry, but have evolved to serve many different functions

Explain Darwin’s Lessons from Homology

• Found on Galapagos, Australia

  Galapagos:

• Flora and fauna found were all descendants of animals good at long-distance dispersal

• Different, isolated islands had different prominent phenotypes for certain animals

  • Ex. tortoise shells, finch beaks

  Australia:

  • Distinct flora, fauna, high endemism, unique adaptations unlike what has been seen in other locales due to isolation

  • Endemic radiations convergent with those on other continents

  • Found that geographically close organisms can resemble each other despite being in different environments

Explain Darwin’s Evidence from Biogeography

• Remote islands

  • Dominated by good colonists

  • Different islands, even close by, can have different fit traits

  • Have unique species

• Biogeographically isolated regions

  • Have species adapted to niches that may not be standard elsewhere

  • Harbor endemic radiations convergent with radiations elsewehre

Explain the Lessons from Biogeography

• Found in Darwin’s Gardens at the Down House

• Teosinte Vs. Maize - same ancestor, domesticated for specific traits

• Wolves Vs. Dogs

• Pigeons

• Vast amounts of heritable variation that can be artificially selected to create dramatic changes over generations

Explain Evidence from Domestication

• Antibiotic resistance, herbicide resistance, etc.

• Strength of natural selection being potentially much higher than Darwin realized

• Genomic DNA evidence for vestigial traits, homology

• More fossil discoveries creating a better record, including transitional forms

What is more modern evidence for evolution?

Genetic constitution of an organism in relation to a particular gene, gene combinations - ex. Aa, AA, AaBB

Define genotype

Feature of an organism as observed - ex. size, fur color

Used when describing a trait that varies within an organism

Define Phenotype

The entirety of an organism’s DNA, including both genes and non-coding regions

Define genome

Mutation

Independent Assortment

Recombination

What are the three sources of genetic variation

• A stable, rare change in a DNA sequence

  • Mutation rates are partially predictable

• Can be beneficial, neutral, or deleterious (weakly detrimental to outright lethal)

Define and explain Mutations

• Inevitable

  • Checking isn’t perfect, will always inevitably end up with errors during replication

• Not directed by organism or environment

  • Random with respect to fitness

• Rate is dependent on type of mutation

• Environment can affect mutation rate

  • Ex. high temperature, mutagens

What are some characteristics of mutation

1. Point mutations (replaced letter inside sequence)

2. Indels (added/removed letter inside sequence)

3. Changes in repeat number (more frequent in long repeating chains)

4. Chromosomal rearrangements (ex. inversions)

What are the kinds of mutations?

False, can happen anywhere in the genome - is only visible in genes

T/F: Mutation can only happen inside of genes

Even small amounts of genomes can create major variation in offspring (ex. 2 diploid genes from each organism can create up to 16 different combinations)

2^n gamete combinations for organisms, where n is the number of chromosomal pairs

Explain Independent Assortment

Chromasome bivalents cross over → switch pieces → create recombinant chromosomes

Explain Recombination

Only one parent contributed to inheritance (sperm/ovule only)

Explain Preformationism (1700s)

Traits mix together irreversibly like paint

Incorrect as genes do not immediately blend after a mutation

Explain Theory of Blending Inheritance (1800s)

H: Pure bred lines would be crossed and make a hybrid gene for multiple generations

A: Recessive genes re emerged after a generation, dominant genes took precidence in the first generation

What were the hypothetical vs. actual results of Mendel’s experiment?

1. Inheritance comes from discrete particles (genes)

2. Each diploid organism has 2 copies of a gene (dominant/recessive)

   • Gametes only hold one allele per gene

3. Gametes fuse to make offspring (sperm/egg, pollen/ovule)

4. Offspring inherit one gene from each parent at random

What were the conclusions from Mendel’s pea experiments?

Discrete: Have few genes contributing in large quantities to a trait (ex. plant color)

Continuous: Many genes with minor effect on trait (ex. height, IQ)

Explain discrete vs. continuous traits

• More traits → more continuous possible variations with smaller effects

Explain quantitative traits

• Genome (gene A,B,C,D)

• Environment (Factor 1,2,3,4)

What dictates a phenotype

Discrete:

• “Mendelian”

• Genes of major effect, dominant, recessive

• Spread of alleles, change in allele frequency

Continuous

• “Quantitative”

• Many genes with alleles of small effect, importance of environment

• Selection response as change in average trait value

When analyzing genetic variation, describe the difference between Discrete & Continuous variation

Invented by R.A. Fisher, J.B.S. Haldane, and S. Wright in 1920s-1950s

Merged darwin’s ideas with mendelian understanding of genetics

Proved that continuous variation and darwinian selection are consistent with Mendel’s laws

Demonstrated evolutionary significance of genetic variation

Who created the ideas of Population Genetics, and when? What did they do?

Mutation: Increases genetic diversity - biggest source of variation

Recombination: Increases genetic diversity (creates new combinations)

Genetic Drift: Decreases genetic diversity (random sampling) - more prevalent on smaller populations

Purifying selection: Reduces genetic diversity (removes deleterious)

Directional selection: Reduces genetic diversity (Fixes favourable alleles)

Selection for diversity: Increases diversity (selection acting to maintain diversity)

Gene flow: Increases genetic diversity (migration of new alleles)

What forces influence genetic diversity, and how?

Heterozygosity (H):

• Fraction of population’s individuals that are heterozygous

Polymorphism (P):

• Proportion of gene loci with 2+ possible alleles - can be polymorphic but not heterozygous

What are the two metrics of genetic variation?

• Mutation-selection balance

  • Less fit types are reintroduced by mutation

  • Followed by selection acting to remove them

• Selection maintaining variation

  • Heterozygote advantage

  • Frq-dependent selection

  • Fitness varies in space or time

  • “balancing selection”

What maintains genetic variation?

Classical School: T.H. Morgan, H.J. Muller

• Low heterozygosity, low polymorphism, selection is usually negative, wild type is normal genotype

Balance School: E.B. Ford, T. Dobzhansky

• Heterozygote advantage, high heterozygosity, high polymorphism, selection favours diversity

What are the two schools of thought, and who participated in them?

• Morphological

  • Snail colour polymorphism

• Cytological

  • Chromosomal inversions

How did they study genetic diversity pre-1966?

• Focus on continuous traits

• Classical view says its possible to exhaust variation

• Perform selection experiments on variety of organisms

• Found that heritable variation does exist, relaxing artificial selection undoes selection responses

Early tests for genetic variation:

• Richard Lewontin

• Allozyme gel electrophoresis provided a way to find the proportion of P and H

Who invented Gel electrophoresis?

• Many loci can be examined

• almost universally usable

• Can identify heterozygotes

• Data is found closer to DNA level

What are the advantages of studying polymorphism through electrophoresis?

Motoo Kimura

Neutral theory (negative eliminates deleterious, positive fixes beneficial, only variant genes are selectively neutral)

What was the ‘new’ theory of genetic variation and who created it?

By checking for which changes in a genome alter a protein compared to those that don’t

How do they measure for genetic variation at the DNA level?

Measure DNA sequencing diversity

What did Alivia Dey do?

• Corn has reduced genetic diversity due to population bottlenecks during domestication

How did Maize and Teosinte demonstrate DNA variation?

Lower DNA diversity after glaciation, genetic drift due to small population affected this diversity

How did Arabidopsis lyrata demonstrate Polymorphism

• Humans have lost variation as distance from East Africa increases - result of Founder Events from source population

How do humans demonstrate genetic variation?

Fill in the Blanks:

Parthenogenesis: Asexual production in which an embryo develops from an egg without fertilization

Clonal Propagation: Asexual reproduction that does not involve an egg (ex. budding plants)

Define Parthenogenesis and Clonal Propagation:

2 parents (sex) vs 1 parent (asex) contribute genetic material to form offspring

Meiotic reductive division (sex) vs not (asex) to form gametes

Fusion of gametes (sex) vs clones of parent (asex)

What is the difference between sexual and asexual reproduction?

True! Ex. water hyacinth, water fleas

T/F: Some species can be both asexual and sexual

Costs:

• 50% gene contribution

• Negative transmission bias

• Creation of unfavourable allele combinations

• Energy costs, predation risks, for finding and attracting mates, actually performing mating

• Cost of producing males

What are the costs of sexual reproduction?

Benefits:

• Quicker fixation of positive alleles, elimination of deleterious alleles

  • From independent assortment, recombination

• Provides greater genetic variation in unpredictable environments (“lottery models”)

  • Spatially heterogenous: Tangled Bank Hypothesis

  • Temporally heterogenous: Red Queen Hypothesis

What are the benefits of sexual reproduction?

High rates of extinction due to variety of factors

• Premature stop codons

• Higher mutation rates for protein sequence evolution

• Accumulation of deleterious mutations

• Low genetic variation

Why are many asexual organisms recent lineages?

• Used rotifer with both asexual and sexual possible reproduction

• measured 3 environments: 2 homogenous, 1 heterogenous

• Found that sexual organisms persisted with heterogeneity, decreased with homogeneity

Who performed experiments for spatial heterogeneity? What did they do?

Parthenogenesis:

• Rarely found in animal kingdom

• More common in invertibrates, rare in vertibrates

Clonal Propagation:

• Fairly common in plants

• Few exclusively asexual species

Macroevolutionarily, describe where parthenogenesis and clonal propagation are found

Outbreeding: Less closely related than random

Inbreeding: Rates are more closely related than random

*Note: Is a continuum!

What is the difference between outbreeding and inbreeding?

Outcross:

• Mate with another organism

• Fusion of gametes from 2 parents

Selfing:

• Self-mating

• Most extreme form of inbreeding

• NOT asexual

• Fusion of gametes from single parent

Explain outcrossing vs. selfing

• Timing offset between male, female reproduction (plants)

• Self-incompatibility

• Dispersal of one sex

• Delayed maturation between generations

• Extra-pair copulation

• Kin recognition

What are some methods of inbreeding avoidance in populations?

• Change in genotype frequencies

  • Decreases heterozygosity

• Does NOT change polymorphism, allele frequencies

What are the population effects of inbreeding?

Inbreeding Depression: Reduction in fitness of inbred offspring compared to outcrossed offspring

Can cause:

• Homozygosity of recessive, deleterious alleles

• Reduction of heterozygosity by 50% each generation (selfing)

• Reduction of polymorphism due to selection and drift in small populations

• CHANGES IN ALLELE FREQUENCIES

What is inbreeding depression? Explain the effects.

Inherent transmission bias (2:3, outcross:self)

Beneficial in the short-term (but harmful in the long-term)

Why does selfing reproduction continually re-emerge?

• Selfing spreads under specific, favourable conditions

• Eventually, low diversity and inefficient selection can increase extinction rates and cause outcrosisng to prevail

Explain the short-term and long-term frequency changes of selfing.

False, it is a relative quantity

T/F: Fitness is an absolute value in a population

• Positive/directional selection (brings alleles to fixity)

• Negative/purifying selection (removes negative alleles)

• Selection to maintain variation (balancing selection)

What are the 3 types of natural selection?

Stabilizing selection - favouring average traits

Directional selection - favours a singular extreme in one direction

Disruptive Selection: Favours both extremes compared to the average

What are the graphical modes of selection on continuous traits?

True - speciation occurs if trait divergence reduces gene flow

T/F: Disruptive selection can lead to speciation and divergence of traits - if true, under what condition does speciation occur?

• Testing correlations of alleles with an environent across space/time

• Analyzing distinctive patterns of genes targeted by selection

• Experimental manipulations

In what ways can adaptation be studied?

• Fewer convincing cases to document in natural populations

  • Difficult to link evolution with ecology

What are the challenges of determining the agents of selection?

• Evolution due to pollution (ex. color changes in moths, metal tolerance in grasses)

• Malaria-Protective Genes/SC Anemia

• DNA variation

• Experimental evolution (ex. study of E. Coli)

In what ways can we correlate ecology to evolutionary biology?

New mutations increasing in frequency so quickly that nearby alleles hitchhike

Define “selective sweep”

• Similar adaptations emerge in similar situations

What was a relevant conclusion in Richard Lenski’s E. Coli experiment?

A group of individuals in a single species occupying a given area at the same time

Define “Population”

The movement of individuals from one population to another

Define “migration”