Midterm 2 Content

Evolution

Genetic change across generations

Microevolution

changes in allele frequencies across generations

• Small scale changes over short time frame

Macroevolution

Accumulation of microevolutionary changes such that a new group arises

• Speciation  

• Large scale changes over long-time frames

Natural Selection

Increased survival and reproduction of some individuals compared to others based on differences in phenotype 

• specific type of change that leads to evolution

  • mechanism of change

  • acts on INDIVIDUALS

  • results in changes in allele frequencies over generations

Necessary and Sufficient Conditions for Natural Selection

• Variation → individuals with varied phenotype exist in population 

• Heritability → trait is somehow genetic and based down to offspring

  • the proportion of trait variation explained by inheritance

  • the degree to which parental phenotypes predict offspring phenotypes

• Differential Success → individuals with different traits have different survival/reproductive success (fitness)

  • Individuals with certain traits survive or reproduce more successfully than others

Fitness

An organism’s ability to survive and reproduce in a particular environment

Phenotype

An organism’s observable traits/characteristics

• Physical

  • Ex: eye color

• Behavioral

  • Ex: bird songs

• Physiological

  • Ex: blood type

Genotype

A genotype is an organism’s genetic makeup

• specific set of genes or alleles it carries

Absolute Fitness vs Relative Fitness

Absolute fitness → actually number of offspring that survive and reproduce  

Relative fitness → absolute fitness of / population mean fitness 

• Both terms can be used to describe one organism or a group of individuals with the same phenotype/genotype

When comparing the success of a phenotypes in different populations, compare the ratios between mean absolute fitness of each phenotype

• Ex: 1:5 → 2:10

  • same level of fitness

Breeder’s Equation

Predicts phenotypic change

R = h²S

• R → response to selection; magnitude of phenotype shift between generations

  • new mean - old mean

  • difference AFTER reproduction

• h² → heritability

  • h² is a term by itself (no square function)

• S → strength of selection 

  • magnitude of phenotypic difference between breeders and full population

  • Breeder phenotype - Average phenotype

  • difference BEFORE reproduction

Altruism

Behavior that reduces individual fitness and increases the fitness of others

• Ex: Alarm Calls

Altruism is supported by natural selection when:

• Fitness lost by altruist is less than fitness gained by recipient

Kin selection

selection that favors behaviors that increase the reproductive success of relatives

• Ex: raising offspring in groups

Inclusive Fitness

the sum of an individual’s own fitness and its contribution to the fitness of relatives

Directional selection

Phenotype at one extreme has highest fitness: mean trends toward that extreme

• graph shifts left/right, toward the extreme with greater fitness

Stabilizing selection

Mean phenotype has the highest fitness

• mean stays the same, variation is reduced

• graph shifts towards center

Disruptive (Diversifying) selection

phenotypes at both extremes have higher fitness than the mean

• Bimodal pattern emerges

Frequency Dependent Selection

Phenotype is beneficial based on its frequency in a population, not what is actual is

• In other selection types what is beneficial is the phenotype itself

Positive Frequency Dependence

The most common phenotype is most benefited

Negative Frequency Dependence

The rarest phenotype is most benefited

• phenotype fitness graph is a “zigzag” → oscillation

Balancing Selection

Selection that maintains phenotypic variation in a population

• Patterns of selection that maintain variation include (both extremes still exist):

  • Diversifying/Disruptive selection

  • Negative frequency dependent selection 

Spatial Variation

Type of balancing selection

phenotypic variation is maintained by phenotypes having different fitness in different locations

• which phenotype is beneficial changes in different parts of a species’ range

Temporal Variation

Type of balancing selection

phenotypic variation is maintained by phenotypes having different fitness in different time periods

• which phenotype is beneficial changes in different time periods

Lingering deleterious phenotypes

Recessive disease alleles are not eliminated from populations by selection because:

• Carriers are not harmed by the disease; they can pass down the recessive allele to their offspring

  • Carrier fitness unaffected

• Disease has delayed onset

  • phenotype is expressed AFTER reproductive years → does not affect fitness

    • Ex: Huntington’s Disease

• Heterozygous advantage

  • Carriers of disease might have higher fitness over both homozygous types → maintains deleterious allele in population

    • Ex: Sickle cell disease in regions with high malaria prevalence

Constraints of Natural Selection

Environmental change

• Which phenotypes are beneficial are not always the same. Natural selection can only favor which traits are currently beneficial

  • Environmental changes occur faster than natural selection can operate

Laws of Physics

• Limits which phenotypes are physically possible

  • Ex: insect size is dependent of rate of oxygen diffusion

Evolutionary history

• An organism's evolutionary history influences which phenotype options are available

• Organisms inherit traits from their ancestors, cannot be “redesigned” from scratch

Trade offs

• Phenotypes beneficial in one context can be harmful in another

• Resources are limited, certain traits that may increase an organism’s fitness may be too energetically costly to maintain

Lack of genetic diversity

• Natural selection does not create new phenotypes, it can only act on preexisting variation

  • a population can lack phenotypes that would grant them higher fitness in their environment; natural selection cannot change that

“Levels” of Genetics

• Genome → all the genetic material an organism carries

• Chromosome → long strand of DNA containing 100s-1000s of genes

• Gene → sections of DNA that codes for a particular protein

• Alleles → different versions of a gene

DNA Structure

• Comprised of 4 nitrogenous bases that form hydrogen bonds with each other

  • A:T (U in mRNA) → 2 hydrogen bonds

  • C:G → 3 hydrogen bonds

• Double helix structure for stability

• Coils up around histones, forming chromosomes

Central Dogma

Flow of genetic information

DNA → RNA → Protein

Transcription

DNA → RNA

• Occurs in cell nucleus

• DNA unwinds, RNA polymerase builds mRNA against Antisense strand (template)

• new mRNA is identical to sense strand (U in place of T)

“Change in script”

Translation

RNA → protein

• Occurs in cytoplasm with help of tRNA

  • ribosome reads mRNA in codons, set of 3 base pairs

• tRNA carries over amino acid that corresponds to codon

“Change in language”

Gene Structure

• Coding region → contains instructions for making proteins

• Regulatory region → determines how often a protein is built

  • how many times transcription/translation occurs

Start with AUG, end with end codon

Wobble

Multiple codons produce the same amino acids

redundancy in codons

Substitution Mutations

Substitution: one or more nucleotides are exchanged

• Missense mutation → amino acid replaced by a different one

• Nonsense mutation → amino acid replaced by a stop

• Synonymous mutation → amino acid unaffected by nucleotide exchange

Frameshift Mutations

Frameshift mutation → alters all subsequent codons

• Insertion: one or more nucleotides are added

• Deletion: one or more nucleotides are deleted

Human Genetic Variation

Average nucleotide diversity

• The average proportion of nucleotide differences between a randomly chosen pair of individuals

  • Among humans 1/1000 → 99.9% similarity

  • Between humans and chimps 1/100 → 99% similarity

Models of Inheritance in the 1800s

• Blending model

  • parental characteristics are irreversible blended in succeeding generations

• Particulate model

  • parental traits are passed down through genes (discrete particles)

    • dominant vs recessive traits

Mendel’s Pea Experiments

Experimental method

• cross pollinated two true breeding plants with contrasting traits

• observed traits of F1 and F2 generations

• breed plants to have hundreds-thousands of offspring

Conclusions

• rejected blended model hypothesis

• discovered simple/complete dominance

  • recessive vs dominant alleles

Mendel’s Pea Traits

Discovered many traits that followed the “pea model”

• Parental generation: homozygous dominant and homozygous recessive

• F1: all have dominant trait (all heterozygous)

• F2: 3 dominant, 1 recessive 

  • 1 homozygous dominant, 2 heterozygous, 1 homozygous recessive

• Mendelian inheritance applies to: Single gene, 2 alleles with simple/complete dominance

Law of Segregation

when any individual produces gametes, the two copies of a gene separate so that each gamete receives only one copy

• keeps the number of chromosomes per individuals the same across generations

Law of Independent Assortment

Alleles of different genes assort independently of one another during gamete formation

• Ex: inheriting the dominant allele for color does not impact what allele you’d inherent for shape

Meiosis

• During metaphase 1, chromosomes line up randomly (independent assortment)

  • allows for many different combinations of alleles in gametes

Calculating Probabilities

General rules

• “and” → multiple probabilities (multiply)

• “or” → add probabilities (add)

For heterozygous genotypes, recall:

• Parents can give offspring different combinations of alleles (add probabilities)

• Ex: If offspring is Yyrr and parents are YyRr…

  • parent 1: Yr / parent 2: yr

  • OR

  • parent 1: yr / parent 2: Yr

Types of Dominance

• Simple/Complete Dominance

  • a single dominant allele produces the dominant phenotype

  • homozygous dominant and heterozygous genotypes → same phenotype

• Incomplete Dominance

  • heterozygous phenotype is intermediate between the two homozygous phenotypes

• Codominance

  • heterozygote’s phenotype is both homozygous phenotypes expressed fully

Pedigree Analysis

Determining if phenotype is dominant or recessive:

• Recessive → two unaffected individuals produce an affected child

• Dominant → prove that it’s not recessive

  • possibility: unaffected individuals produce unaffected children

Linked Genes

If genes are located on the same chromosome, we will not observe expected ¼ ratio of all gametes/phenotypes

• Parental phenotypes and nonrecombinant gametes will be more common

Crossing Over

Linked genes do not assort independently. However, recombinant alleles can still be produced through crossing over.

• Crossing-over allows genes located on the same chromosome to separate (recombination)

  • Chromosomes physically exchange DNA

The frequency of crossing over producing recombinant gametes depends on the distance between the target genes

• genes farther away from each other → more frequent separation

• genes closer together → less frequent separation 

Sex-Linked Inheritance

Females are less likely to express sex-linked disorders because they have two X-chromosomes 

• a dominant X can mask the impact of a harmful recessive X

• When considering X-linked traits, male genotypes → hemizygous

Pleiotropy

Mode of inheritance where one gene controls multiple traits

Polygenic Inheritance

One trait is additively controlled by many genes

• Ex: color genes

Environmental Influences on Phenotypes

Environmental conditions influence phenotype

• Ex: Soil pH and flower color

Quantitative Traits

Phenotypes are continuous, not discrete categories

• Influence of both genes and environment

  • Ex: Human height

    • multiple genes, nutrition 

Epistasis

multiple genes interact to determine phenotype

• Ex: Labrador coat color

  • Black/Brown Gene: Black shows complete dominance over brown

  • Extension Gene: recessive trait lacks pigment in the fur (yellow)

genes are not additive but affect the expression of one another

Population

An interbreeding group of organisms of the same species occurring in the same place and time

Evolution acts on populations

• Changes in allele frequencies across generations

• Changes in mean and variance of traits across generations

Allele frequencies

proportion of a particular allele across all individuals of a population

Number of X alleles / Number of total alleles

Genotype frequencies

proportion of individuals of a particular genotype in a population

Number of XX individuals / Number of total individuals

Hardy-Weinberg Equilibrium

In non-evolving conditions, population reach and stay at equilibrium

Used as a  baseline expectation for comparisons → null hypothesis

• Deviations from HWE can give us insight into what is happening within a population

5 Assumptions of HWE

1. No mutations

2. No natural selection

3. No gene flow (migration)

4. No genetic drift (requires infinitely large population size)

5. Random mating

Determining if a Population is in HWE

• Find observed genotype frequencies

• Use calculated genotype frequencies to find allele frequencies

• Use calculated allele frequencies to find the expected genotype frequencies under HWE

  • p² + 2pq + q²

Deviations between observed genotype frequencies and expected genotype frequencies = population not in HWE

HWE with More than 2 alleles

• Frequency of homozygous genotype always → f(allele)²

• Frequency of heterozygous genotype always → 2 x f(allele1) x f(allele2)

Mutations

• Mutations generate new alleles, provide variation for selection to act upon

  • beneficial

  • deleterious

  • neutral

• Possible “paths” of Mutations

  • gets removed by natural selection

  • increases in frequency via natural selection

  • can become fixed in small populations via genetic drift

  • can be transferred to other populations through gene flow

Gene flow

migration of genes into new populations

• genes can travel without organisms have to move

  • ex: pollination

Genetic Drift

Random chance events that cause allele frequencies to fluctuate unpredictably from one generation to the next

• More prevalent in small populations

  • fewer chances for rare alleles to get passed on

• Reduces genetic diversity

  • one allele can become fixed while another becomes lost

Founder Effect

occurs when a new population is created from a few individuals from the same initial population

• new population has less diversity because it was created by a small portion of the original population

  • carries only a subset of the genetic variation present in the original population

  • less diverse

• species as a whole still has the genetic diversity of the original population to lean back on

Genetic Bottlenecks

occur when a species’ total population size is severely reduced

• much smaller population → less genetic diversity

• no background genetic diversity to lean on, small population is all that is left of the species

Consequences of Genetic Drift

• loss of genetic diversity

  • alleles become fixed (freq = 1)

  • alleles lost (freq = 0)

• Increase in homozygosity

• Possible increase in deleterious recessive conditions

  • if deleterious allele is the one that gets fixed

• Increased susceptibility to future stressors

  • Ex: pathogens can more easily harm population since everyone has similar genotypes

Non-Random Mating

• organisms have a preference for who they mate with

  • Alleles do not have equal chance of uniting with each other

Inbreeding

preference for similar genotypes/phenotypes/relatives

• closely genetically related

Outbreeding

preference for different genotypes/phenotypes

Consequences of Inbreeding

• Reduction in heterozygous genotypes

• Increase in homozygous genotypes 

• Concerning increase in homozygous recessive genotypes

  • deleterious recessive alleles can become more common if genetically similar individuals reproduce

    • higher chance of them both having the same deleterious recessive allele

• Allele frequency can remain the same, but GENOTYPE frequency changes

Natural Selection - Dominant vs Recessive Alleles

Natural selection operates on phenotypes

• When a dominant allele is beneficial, it increases in frequency quickly 

  • Fitness increase for homozygous dominant and heterozygous individuals 

• When a recessive allele is beneficial, it increases in frequency slowly

  • Fitness increase for homozygous recessive individuals only

Impacts of Hardy-Weinberg Violations

Inbreeding

• less heterozygotes, more homozygotes

  • genotype frequencies

Outbreeding

• more heterozygotes, less homozygotes

  • genotype frequencies

Genetic drift

• One allele increases in frequency at the expense of another

  • One homozygous increases, other decreases

    • If genetic drift is a possibility, ignoring fluctuations in the heterozygote

Other possibilities

• Increased frequency of genotype

  • gene flow → immigration of individuals with genotype

  • selection in favor of genotype

• Decreased frequency of genotype

  • gene flow → emigration of individuals with genotype

  • selection against genotype

Interspecific Interactions

between individuals from two different species

• can increase or decrease a specie’s carrying capacity

• can increase or decrease a species’ fundamental niche

  • realized niche

Communities

Groups of interacting species occurring together in space and time

Keystone species

Have an effect on community composition that is disproportionately large compared to their abundance

• Have a big effect despite low abundance

Trophic Casacade

Indirect effects of predators on biomass at least two trophic levels away

• Predators can increase the biomass of plants by eating herbivores

• Predators can decrease the biomass of plants by eating other predators that eat herbivores

Foundation Species

Affect other species because of their high biomass and habitat forming characteristics 

• have big effect because of their abundance/size

• Can be benefited or unaffected by the species they facilitate

  • Ex: Trees, corals

Competitive exclusion principle

two species that use the same resources in the same way cannot coexist; one will drive the other to extinction

• In order for two species to coexist, they must differ in the way they use resources / use different resources

  • Intraspecific competition is strong relative to interspecific competition

Resource Partitioning

major way competitors can coexist in the same ecosystem.

• Occurs when competing species use different resources or use the same resources in different ways

  • small resource overlap

  • competition exists, but it's minimized

    • each species' carrying capacity is still lower than it would be alone

Species can coexist when they partition resources

• Intraspecific competition is strong relative to interspecific competition 

Niche Utilization Curves

Graph of niches in terms of performance across a range

• The overlap of different species’ niche utilization curves represents their degree of competition

  • Less overlap → more likely to coexist

Obligate Mutualism

Type of mutualism where both species need depend on each other for survival

Facultative mutualism

Type of mutualism where the interaction between two species is not required for either of them to survive

• Can be thought of as two separate commensalisms

• Outcomes of relationship vary with environment

  • No stress → changes to exploitation

Positive interaction

Interaction in which at least one species benefits and none are harmed

• Involves one species that is resistant to a stress (a facilitator) locally reducing that stress

  • benefits species that are susceptible to that stress

Strength of positive interactions vary with intensity of stress

• Strong in high stress environments

• Weak in low stress environments

  • Can switch to negative

Predator-prey oscillations

Some natural populations of predators and prey display coupled oscillations (stable coexistence)

• both intraspecific competition and predation contribute to stabilization of predator-prey cycles

  • predators AND competition among prey act together to stabilize population dynamics and prevent extinction

5 Givens on Pathogen-Host interactions

• Disease is caused by organisms (pathogens)

• Pathogens can be transmitted between individuals (hosts) either:

  • directly 

  • through the environment

• Hosts resist pathogens either: 

  • by chemical defense 

  • through an immune system

• Immunity can be:

  • innate (genetic) 

  • acquired (immune memory)

• Many pathogens are host specific 

  • infecting only 1 species or one genotype with a species

Disease Outbreak

Outbreaks occur if the fraction of the population that is infected is increasing

• S > d/B

  • susceptible individuals > recovery rate / transmission rate

Threshold Density

S > / (recovery rate / transmission rate)

• outbreaks end once S drops below threshold

  • restart once S rises → immigration and births

Strategies for Disease Management

• Decrease transmission rate

  • masking

• Increase recovery rate

  • prescribe medication to infected individuals

• Decrease number of susceptible individuals

  • vaccination

Herd Immunity

Reducing frequency of S so that the rate of new infections is much lower than the recovery rate will effectively allow even those that aren’t vaccinated to benefit

• Immunizations reduce S

  • S becomes R without becoming infected

• The vaccination rates needed to achieve herd immunity depends on a disease's rate of transmission

• If S increases because of vaccine opt outs, herd immunity can be lost

Character Displacement

Evolution toward niche divergence as a result of interspecific competition

• If two species have somewhat overlapping resource pools, individuals that consume resources from the regions without overlap will have higher fitness

  • More intraspecific competition than interspecific 

Phenotypes in allopatry differ from those in sympatry

Host-Pathogen Evolution

• Hosts can evolve in response to pathogens

  • Susceptible individuals die, leaving resistant individuals with higher fitness

    • resistant allele frequency increases across generation

• Pathogens evolve in response to hosts as well 

  • Evolving to be less lethal is favored when population density is low

    • Killing hosts too quickly decreases rate of transmission