UNIT 23 - EVOLUTIONARY PROCESSES

Genetics
● Our basic traits are determined by genes
○ Location where gene can occur: Locus (pl. loci)
○ Particular version of a gene is called an allele
■ Complex organisms usually have two alleles at each locus (Can be same or
different)

Loci
● Complex organisms usually have two alleles at each locus (same or diff)
○ Organisms with different alleles at a particular locus: heterozygous (heterozygote)
○ Organisms with two copies of the same allele at a particular locus are homozygous
(homozygote)

Two definitions of Evolution:

1. Lecture: Heritable changes in species traits over time
2. Book: Changes in allele frequencies

Genotype & Phenotype

● Genotype - collection of individual's genes
● Phenotype - collection of an individual's physiological and physical traits
○ Observational traits
○ Largely, but not 100% determined by genotype

Example: Peppered Moths

● Two different alleles possible at the wing color gene: A1 & A2
○ A1A1 genotype = Light-winged phenotype
○ A2A2 genotype = Dark-winged phenotype
○ A1A2 genotype = ?
● If individuals that have genotype XY have the same phenotype (on average) as those with XX,
we say that X is a dominantand Y is a recessive allele
● If XY individuals have an intermediate phenotype (Between XX and YY, we say that X and Y
are incompletely dominant)
 ○ Incomplete dominance is a blend of the two qualities:

Co-dominance
● When both phenotypes are expressed
○ Ex: If a red and white flower mate, both colours are expressed in the hybrid

Analyzing Genotype Frequencies

● We analyze genotype frequencies as follows;
○ Calculate expected frequencies under our assumptions
○ Measure observed frequencies in the population
 ■ Expected frequencies are usually calculated by assuming that alleles assort
randomly and independently, like flipping two coins, or rolling two dice

Hardy-Weinberg Distribution
● Expected if alleles work random and independent
○ Frequency of genotype A1A1 is p^2
○ Frequency of genotype A2A2 is q^2
○ Frequency of genotype A1A2 is 2pq

● Key Terms:
○ Observed # of People = Total People
○ Observed Genotype Frequency = Number of frequency / Total # of people

Allele frequency formula

Genotype Frequency Formula

FORMULA FOR ALLELE FREQUENCIES:

WORKED EXAMPLE

Hardy-Weinberg Assumption
1. No Natural Selection at the gene in question
1. There is no difference in fitness between genes, all are treated equally
2. No genetic drift, or random allele frequency changes, affecting the gene in question
1. Assumes that alleles are picked in their exact frequencies and that the frequencies weren't
lost or gained by chance. Model behaves as though population is infinitely large
3. No gene flow
1. No new alleles are being added or lost by immigration / emigration
4. No mutation
1. No new alleles (A3 / A4 ) are introduced into the gene pool
5. Random mating with respect to the gene in question
1. Module assumes that gametes from the gene pool combine at random. Individuals are not
allowed to choose a mate (No inbreeding)

Differences from equilibrium

● If we observe large differences from the HWE, usually a sign that mating is not random, or that
natural selection is operating
○ HWE is a null model, telling us what to expect if complicating effects are absent

Example: HLA Genes

● Why might more people be heterozygous for HLA genes than predicted by HWE?
○ Heterozygous might be more likely to survive
○ Heterozygous people may have more offspring

Types of Natural Selection

1. Directional Selection
1. Tends to move a population in a particular direction (Reduces genetic diversity)
1. It favours one allele over the other, and over time if the trend continues, the
favoured alleles with approach a frequency of 1.0 while the disadvantageous
alleles will approach a frequency of 0.0
1. Example: Cliff Swallows
1. A population of cliff swallows native to the Great Plains endured
a six-day period of exceptionally cold, rainy weather. They feed
on insects, however they disappeared as a result of the cold snap.
This led to a great number of Cliff Swallows dying of starvation.
When conditions improved, they re-captured cliff swallows and
found that they were bigger than average than the birds who
died. Assumed that the larger ones survived because they had
more fat reserves to depend on.
2. Multi-Directional Selection
1. Directional selection can change through time with the environment
1. Swallows may get larger during extreme cold spells, smaller again
during normal weather

● When directional selection stays in a specific state for a long time, it implies that the population
arrived at the target and that direction selection turned into stabilizing selection

1. Stabilizing Selection
1. Tends to keep population where it is (Genetic variation is reduced, and no change in
average value of a trait over time)
1. Disruptive Selection
1. Favors phenotypes different from the average value. (Increases overall amount of genetic
variation)
1. (Unlike stabilizing selection, instead of favouring phenotypes near the average
value and eliminating extreme phenotypes, it eliminates phenotypes near the
average value and favours extreme phenotypes)
2. Could lead to speciation - formation of a new species
1. Example: Black-Bellied Seedcrackers vs Beak Size
1. When there is a great amount of small beaked birds, disruptive
selection favours large beaked birds because the smaller ones are
all competing for the same food. Conversely, if there are more
big, small is favoured because there is more food for them and
less competition

1. Balancing Selection
1. Tends to maintain allele diversity (No single best allele)
1. In this case, there is no specific phenotype or allele frequency with advantage,
there is diversity and they are all maintained.
2. Occurs when:
1. Heterozygous individuals have higher fitness than homozygous
individuals (Heterozygote Advantage)
2. Environment varies over time or in different geographic areas occupied
by a population (Certain alleles are favoured by natural selection at
different times or in different places, overall the genetic variation in the
population is maintained)
3. Certain alleles are favoured when they are rare, but not when they are
common (Frequency Dependent Selection)
1. Ex: Rare alleles responsible for colouration in guppies are
favoured because predators learn to recognize common colour
patterns. As a result, alleles for common colours get eliminated
while the alleles for rare colours increase in frequency.

Other evolution Mechanisms

Genetic Drift
● Change in allele frequencies due to random sampling (Defined as any change in allele frequencies
in a population that is due to chance)
○ Named because allele frequencies drift up and down randomly over time. This change
occurs due to blind luck (sampling error)
■ Occurs in every population, but smaller populations are more susceptible
■ Ex: If you have 5 kids, there will be different variations / combinations of mother
vs father genes. In the end, you may find that one of the genes appears more or
 less often than the other, this is what Genetic Drift is- a random change in allele
frequencies due to chance.
● Much stronger in small populations as opposed to larger ones (Law of averages) [Had the couple
produced 50 children as opposed to 5, it is likely that the frequencies would be closer to 0.5]
● Founder Effects - When a new population is started by a small number of individuals
● Bottlenecks - When a population becomes small, then large again

Fixation and Loss

● Advantageous Alleles are often (not always) fixed (1)
● Disadvantageous Alleles are often (not always) lost (0)
● Alleles with neutral differences (no selective difference) will be fixed or lot at random
● Drift tends to reduce genetic variation

Gene Flow
● Movement of alleles from one population to another (Through immigration and emigration)
○ Occurs when individuals move from one population to another and breed
○ Usually has one outcome- equalized allele frequencies between the source population and
the recipient population.
○ Increases genetic diversity in a recipient population if new alleles arrive with immigrants,
HOWEVER, it may also decrease genetic variation in the source population if alleles
leave with emigrating individuals.

Mutation
● Heritable errors in copying DNA (Leads to an increase in genetic diversity over time)
● Very rare, by themselves don't cause much evolution
● Extremely important to evolution as it provides variation on natural selection and is the only
source of new alleles

Types of Mutations:
1. A single DNA base might change (ACGT)
2. Chunks of DNA can be added or subtracted
3. Whole genes (or whole chromosomes) can be duplicated
1. These come from copying errors or other organisms (Lateral Gene Transfer - transfer of
genes from one species to another)
2. Most mutations are deleterious - bad for fitness
3. Very rarely mutations are beneficial - good for fitness
1. These are the only ones favoured by natural selection
 Sex
● Does not directly change allele frequencies
● Brings alleles together and splits them apart
● Not a source of new alleles, rather a source of new combinations

Mating Patterns

Inbreeding
● Mating between close relatives
● Increases homozygosity
● Does not cause evolution because allele frequencies do not change in the population as a whole
○ Inbreeding only changes genotype frequencies, not allele frequencies so it is not an
evolutionary mechanism
● Observed that inbred individuals have lower fitness
○ More likely to be homozygous for rare genetic defects
○ Less likely to be heterozygous for immune-system genes

Sexual Selection
● Form of natural selection
● Occurs when there is a heritable variation in traits related to success in obtaining mates
○ Occurs when individuals within a population differ in their ability to attract mates
■ Favours individuals with heritable traits that enhance their ability to obtain mates
■ Intersexual Selection - When you are trying to attract someone from another
gender
■ Intrasexual Selection - When you are trying to compete against the same gender
for a mate

● Males often have traits that females lack, that they use in courtship or to compete against other
males
● Sexual Dimorphism - Trait differences between males and females
○ If females invest a lot in each offspring, they can maximize fitness by being choosy about
mates
○ If males invest little in each offspring, they can maximize fitness by mating as much as
possible
 UNIT 24 - SPECIATION

How are species defined?

● Species -Evolutionarily independent population or group of populations
○ "Evolutionary Units"
■ Individuals of different species evolve independently

1.1 Biological Species Concept

● Defined by reproductive isolation, in other words there is no gene flow
○ Logical because no gene flow occurs between populations that are reproductively isolated
from each other
● Species are distinct, or are consider different if:
○ Two species don't breed in nature
○ They breed but fail to produce offspring
○ Produce inviable offspring ( Do not develop into adulthood)
○ Produce sterile offspring (Offspring that cannot themselves reproduce)
■ These two are known as Post-zygotic isolation

Prezygotic vs Postzygotic Isolation

1. Prezygotic Isolation - Refers to any mechanism that prevents successful mating
2. Postzygotic Isolation - Refers to any mechanism that prevents offspring from producing offspring
of their own (Ex: Inviable offspring or Sterile Offspring)

Which should be adaptively favoured?

● Prezygotic = Less Wasted Effort (You didn't produce the offspring)

Disadvantages of Biological Species Concepts

● Doesn't apply for: Asexual Organisms
● Extinct Species (Fossils)
● May be hard to evaluate (Not all populations come into contact so how do you know?)

Morphospecies Concept (Morphological Species Concept)

● Distinguished by differences in size, shape, or other morphological features
○ Species is group if they have the same body shape and features
○ If they look different, they are different
■ Useful for working with fossils, or very diverse groups (e.g. insects)
 ■ A lot of expertise and experience guides morphospecies decisions

Disadvantages of Morphospecies Concept

● Can be misleading; convergent evolution can make us believe that species look familiar / possess
similar features but they were by chance
● Can be subjective (Some may argue for / against certain aspects)

Ecological Species Concept

● Set of related organisms occupying the same ecological niche (area)
○ Exploit similar resources
○ Tolerate similar environments
○ Face similar natural enemies
● Commonly used for small things: particularly small asexual things
○ Ex: Bacteria, Archaea, Asexual Eukaryotes

Phylogenetic Species Concept

● Species is defined as a group of organisms with a common ancestor
● A phylogenetic species is a monophyletic group of populations
○ Must not be divisible into smaller species
● A monophyletic group is a group defined by a single common ancestor

Advantages
● Well defined
● Broadly applicable
● Made via morphological & molecular data

Disadvantages
● Hard to estimate phylogenies
● Requires a lot of information about populations

Defining Species
● Formally defining species can be tricky

Generating Species
● We believe new species are generated from old species
● One species can gradually evolve into another
● Species can also diverge: one species splits into two species
○ Divergence is the origin of diversity

How do species split?

● Genetic Isolation
● Genetic divergence
○ Usually divergence comes first (Isolation > divergence > natural selection for more
isolation)

Species Divergence in allopatry

● Allopatry : Refers to organisms living apart from each other
○ We expect two populations that are isolated from each other to diverge because:
■ Genetic Drift
■ Natural Selection (as a result of different environments / adaptive measures)

Dispersal
● When parts of species move to new location, settle and reproduce
○ Isolated populations of the same species can develop if some individuals disperse to a
new area and colonize it.

Vicariance
● Vicariance : Physical splitting of habitat (Ex: Forests destroyed, ice patch

Species Divergence in sympatry

● Sympatry : Refers to organisms living in the same geographic area (close enough so that they can
breed)
○ In general, hard for populations of the same species living in sympatry to diverge

Polyploidy
● Reproductive mistakes can occur that produce individuals with extra copies of each chromosome
○ Sometimes these polyploid individuals survive, and can even mate
● Autopolyploid - Individuals are produced when a mutation results in a doubling of chromosome
number and the chromosomes all come from the same species
● Allopolyploid - Individuals are created when parents that belong to different species mate and
produce an offspring where chromosome number doubles. These individuals have chromosome
sets from different species
 Fusion
● When two isolated populations come into contact, they may fuse - go back together

Reinforcement
● In some cases, hybrid offspring may have low fitness
○ Incompatible Alleles
○ Disruptive Selection
○ If parents of the new species are each adapted to different climates, the hyrid will not be
adapted to either and therefore have lower fitness
● In these cases, we expect natural selection for traits that reinforce the distinction between two
species
○ They avoid mating, using coloration, timing, courtship rituals

Hybrid Zones
● When hybrid offspring are functional, and well-adapted to the overlap zone, there may be a zone
where hybrids occur

Exclusion
● One species might eliminate the other species, either by competition, or by better success in
mating

UNIT 25 - PHYLOGENY

Tools for Studying History: Phylogenetic Trees

● Evolutionary history of a group of organisms is called its Phylogeny
○ Phylogenetic Tree - graphical summary of this history, showing the evolutionary
relationships among genes, populations, species, or higher taxa.
■ Model of how a group of organisms descended from a common ancestor

Parts of a Phylogenetic Tree

1. Node: Where groups split
2. Branches: Where evolution occurs
3. Tips: Representing observed taxa, also the endpoints of the process we are trying to model
4. Polytomy: Point where more than two branches diverge
5. Sister Taxa: Groups that occupy adjacent branches on a tree (can be defined at any level / node)
 Monophyletic Group
● Monophyletic Group - defined by a single common ancestor
○ Also called clades or taxa
● Test for monophyletic groups using the snip test (Snip every branch, that’s a monophyletic group)

Constructing Phylogenetic Trees

1. Measure characteristics of the taxa of interest (can be morphological or genetic)
2. Make inferences about the phylogenetic relationships
● Phenetic - Uses measures of distance between organisms
● Cladistic - Based on modeling how evolution occurs on the tree

Morphological vs Genetic Characteristics

● Usually have more information from genetic characteristics, and this information is easier to
measure precisely
● Use morphological characteristics when genetic information is not available (Ex: Fossil
Organisms)
○ Also, some viruses evolve fast that morphological traits are more stable

Phenetic vs Cladistic Analysis

● Cladistic analysis makes use of the phylogenetic model of organisms evolving from each other to
infer phylogenies
○ Based on ancestry and evolutionary relationships
○ Relationships among species can be reconstructed by identifying shared derived traits
(synapomorphies)
● Phenetic analysis ignores the phylogenetic model of organisms evolving from each other while
inferring phylogenies
○ Based on morphological and structural features

Which is better? When to use either?

● Cladistic Analysis is better
● Use Phenetic Analysis when data is only distances- no characters available. (Certain molecular
technique)
○ Not enough baseline evidence

Synapomorphies
● Classical Cladistic Analysis is based on synapomorphies - Shared, derived characters as
evidence that two taxa are related
○ Trait found in two or more taxa that is present in their most recent common ancestor but
is missing in more distance ancestors.

Derived Characteristics
● Characteristics of the common ancestor are called Basal / Ancestral characteristics
● Derived characteristic - Not shared by the common ancestor of the group that we are currently
thinking about
○ Phenetic Analysis treats derived and basal characters equally

● Ancestral Trait - character that existed in an ancestor

● Derived Trait - Modified form of the ancestral trait found in a descendant

● Outgroup - Sister group that shares a recent common ancestor with the taxa being studied, but is
not itself the focus of the study
○ Outgroup usually branches out from the group at the root, or beginning of the tree

Confusing the Phylogeny

● Two species may have the same trait because the trait evolved twice independently- convergent
evolution
● An organisms may also lack a character that its ancestors had - secondary loss

● Homoplasy - Occurs when traits are similar for reasons other than common ancestry
○ This is related to convergent evolution
● To address the problem of convergent evolution and homoplasy, consider multiple characteristics
when possible and it might help to use multiple taxa
 Parsimony
● Classical Cladistic analysis is based on searching for the tree that can be explained with the
fewest number of changes necessary (Parsimony)

Phylogenetic Trees are approximations

● The true history of life cannot be summarized by a tree
○ Sex, other forms of combination or gene transfer
● Trees constructed by humans are not necessarily even the best approximations to the true history
of life

Adaptive Radiations
● Adaptive Radiation - Occurs when a single lineage produces many descendant species, in a
short period of time, that make their living in a variety of different ways
○ Single Lineage > produces many descendant species with a wide range of adaptive forms
○ Triggered by opportunity, either in the environment or because of the evolution of the
organisms themselves
■ Extrinsic (External) to organisms- favourable new conditions in the environment
■ Intrinsic (Internal) - key morphological, physiological, or behavioural traits.

Triggers for Adaptive Radiation

1. Ecological Opportunity - Availability of new or novel types of resources
1. Organism arrives in an area with no similar organisms,
2. Group of competing species is driven extinct (or nearly extinct) by some other cause
2. Morphological Innovation: Organism comes up with a good, new idea
1. These traits often let species live in new areas, exploit new sources of food, select mates
in a new way, or move in new ways
1. Examples:
1. Flowers helped trigger the diversification of angiosperms
2. Feathers and wings gave some dinosaurs the ability to fly

Hox Gene
● Hox Genes - involved in determining the identity / function of different body parts
○ Taxa with simpler body structures tend to have fewer hox genes
● There is evidenfoce that new hox genes were largely created by gene duplication events
○ I.e. polyploidy: one or more genes may be accidentally duplicated so that the genome has
two copies of each gene
 ■ This may cause the organism to be less efficient, but it also might allow for
innovation
■ The first copy does the old functions while the new ones discover
different functions