Process of Evolution

Process of Evolution

• Modern organisms evolved from ancient ancestors
• Evolution accounts for both life's similarities and differences
• Genetic variation is acted upon by selective pressures to drive evolution

Microevolution vs. Macroevolution

• A population evolves because it contains a collection of genes called the gene pool
• Population evolution follows changes within the gene pool
• Microevolution is continuous evolutionary change within a lineage
• Microevolution can dramatically alter a lineage over time, depending on factors like the organism and circumstances
• Lineages can remain unchanged over time in a state called stasis
• Macroevolution involves the origin and extinction of lineages
• Macroevolution happens gradually or slowly
• Both micro and macroevolution are essential
• Microevolution is better understood and documented due to observable timescales

Population as the Unit of Microevolution

• An individual's genotype is set at birth
• Population is the smallest unit that can undergo evolutionary change
• Populations, unlike individuals, allow new alleles to arise through mutation causing a change in allele frequency through selection or genetic drift
• Individuals do not evolve, but populations and species do evolve

Population Genetics

• Population genetics observes and models allele frequencies and genetic change in population evolution
• Three key parameters:
  • Allele frequency: the specific allele proportion at a given locus
  • Genotype frequency: the specific genotype proportion at a given locus
  • Phenotype frequency: the proportion of individuals in a population that exhibit a given phenotype

Phenotype Frequencies

• To calculate phenotype frequency, count individuals with the phenotype and divide by the total number

Genotype Frequencies

• To calculate genotype frequency, find the number of individuals with the genotype and divide by the population size (N)
• f(AA) = #(AA)/N, f(Aa) = #(Aa)/N, f(aa) = #(aa)/N

Allele Frequencies

• The frequency of the dominant allele is represented by p, and the recessive allele by q, where q = 1 - p
• To calculate frequency of an allele, add the total number of homozygotes for that allele to half the heterozygotes, and divide by N
• For p: ((#AA) + (1/2)(#Aa))/N
• For q: ((#aa) + (1/2)(#Aa))/N
• Derived from genotype frequencies:
  • p = f(AA) + (1/2)f(Aa)
  • q = f(aa) + (1/2)f(Aa)

Evolutionary Change and Allele Frequencies

• Evolution occurs due to changes in allele frequencies
• Change between single-celled ancestors to modern humans requires the sequenced origination of new alleles, replacing older ones via gene duplication

Evolution and Allele/Genotype Frequency

• Microevolutionary change occurs with changing allele frequencies
• Determining if evolution occurs requires a comparison to the expectation if evolution does not occur
• Departure from the expectation demonstrates that evolution has occurred

The Hardy-Weinberg Equilibrium

• Hardy-Weinberg Equilibrium occurs when no evolution is happening maintaining genetic equilibrium
• Debunks the misconception that allele dominance or recessiveness alone causes evolutionary change
• It refers to a particular locus: one locus can undergo rapid allele frequency change while others remain in equilibrium

Assumptions of the Hardy-Weinberg Equilibrium

• A locus needs to meet five assumptions to be in Hardy-Weinberg Equilibrium:
  • Infinite population size: there are infinitely many individuals in the population
  • No allele flow: no movement of individuals from population to population
  • No mutation: no new alleles are created from biochemical changes in DNA
  • Random mating: individuals mate at random
  • No Selection: all genotypes have equal fitness for the genetic trait

Hardy-Weinberg Population - Diploid and Sexually Reproducing

• Population comprised of AA, Aa, and aa genotypes meet the five assumptions of Hardy-Weinberg Equilibrium

• Because mating is random, alleles combine randomly

• Because the population is infinitely large, the probability of getting a gamete with a particular allele is the frequency of that allele

• Determining probabilities of getting particular genotypes tells the genotype frequencies

• For AA, an egg with allele A with probability p and a sperm with allele A with probability p are required, so the probability is p²

• For aa, a sperm with "a" allele with a chance of q and the egg with an 'a' allele is also q, so: q²

• Two ways to get the heterozygous genotype, Aa:

  • "A" bearing sperm and an "a" bearing egg
  • "A" bearing egg and an "a" bearing sperm

• "A" bearing sperm with probability p and "a" bearing egg with probability q yields a probability of getting an Aa of p*q=pq

• Probability of getting aA (a sperm, A egg) is also (p)(q) = pq

• Probability of getting the Aa genotype sums the probabilities of getting the two ways, giving: (pq + pq = 2pq)

• As long as the conditions of the Hardy-Weinberg equilibrium are met, allele frequencies remain constant

• After one round of random mating, a stable mathematical set of genotype frequencies for any given allele frequencies exists

• If allele frequencies are known, expected genotype frequencies can be found

• Recessive allele frequency can infer the frequency of the recessive genotype as well

Hardy-Weinberg Equations

• The equations apply under Hardy-Weinberg equilibrium

• Freq(AA) = p²

• Freq(Aa) = 2pq

• Freq(aa) = q²

• p² + 2pq + q² = 1

Working with Allele Frequencies

• To obtain allele frequencies from the number of individuals

  • p = ((#AA) + (1/2)(#Aa))/N
  • q = ((#aa) + (1/2)(#Aa))/N

• Using genotype frequencies to obtain allele frequencies

  • p=f(AA)+(1/2)f(Aa)
  • q=f(aa)+(1/2)f(Aa)

• To go from allele frequency to genotype frequency, assume the population is in HWE

• An exception to HW may present multiple genotype frequencies from a single allele frequency

• The true values are unknown but using the HWE equation the estimates are generated

Example Question

• Albinism in rabbits is caused by a recessive allele, aa
• AA and Aa individuals are normally pigmented, while aa individuals are albino
• In a population w/ 9999 normally pigmented rabbits and 1 albino rabbit:
  • The frequency of the recessive phenotype, = Freq (aa) genotype = 1/10000 or 0.0001
  • Under Hardy-Weinberg equilibrium the expected allele frequency are calculated based on the expected Aa genotype
  • q² = 0.0001 gives q = 0.01
  • p = 1 – q gives p = 0.99
  • 2pq = (0.01)(0.99)(2) = 0.0198
• Though only 1 out of 10,000 rabbits is albino, roughly 1/50 rabbits carry the allele meaning that it is fairly common and selected against

Chi-Square Test

• To generates values from the HWE expectations and compare to the observed values

• The null hypothesis suggests the population is in HWE so evolution is not occurring

• For an enzyme locus (superoxide dismutase) in a river grape population the observed are:

  • 460 SODF SODF
  • 23 SODF SODS
  • 517 SODS SODS

• It gives the implication of whether of the population is in HWE

• Because there is no dominant locus and frequency of SODF p = (460+11.5)/1000 = 0.47 resulting in *q = *0. 53

• Observed vs Expected values

  • 460 SODF SODF vs 221 SODF SODF
  • 23 SODF SODS vs 498 SODF SODS
  • 517 SODS SODS vs 281 SOD SODS

• Chi-square equals approximately 910

• There is only one degree of freedom since we generated three variables from known values and q, so *df = *1

• The Chi-square is much larger than the critical value, meaning the locus is not in HWE

• A statistical test cannot answer that but there are not enough heterozygous values due to inbreeding and grape plants self-fertilization

• Alternatively, the differential success of two genotypes as both homozygotes in asexual reproduction grapes

Genetic Basis of Variation

• The study of Mendelian genetics and inheritance patterns
• Genetic variation and polymorphisms, including:
  • Types of genetic variation (SNPs, INDEL, CNV etc.)
  • Variation sources (mutation, recombination, gene conversion)
  • The impact of genetic variation on phenotype
• Human genome structure and organization
• Molecular Basis of Evolution:
  • Molecular evolution mechanisms gene duplication and gene regulation changes
  • Comparative genomics and phylogenetics
  • Molecular evidence for evolutionary relationships and patterns

Mutation

• Biochemical change in DNA creates new alleles

• Rare event resulting in slow evolution

• Ultimately the source of genetic variation

• Other forms of evolution depends upon it being present

• Mutation is random in terms of allele fitness and produces high or low fitness outcomes independently of the evolutionary "need"

• Mutation changes include the organism's DNA

• Mutations may affect somatic (nonreproductive tissue) and germ line (reproductive tissue), the latter of which it is heritable

• Heritable mutations change one allele into another, sometimes creating novel alleles

• Mutations create dominant, recessive, or codominant alleles

• Mutations include harmful or lethal, neutral, and favorable traits that depends upon environmental factors

Some Types of Mutations

• Point mutations occur versus chromosomal mutations

• Substitution occurs when one nucleotide is substituted for another

• Insertion occurs when DNA is inserted into a gene

• Deletion removes DNA bases and is a small insertion and deletions can inactivate stretches of a gene by frameshift

• Duplication duplicates an entire gene

• Transposition relocates DNA to occurs because due to viruses, errors, or transposable elements

• Random events with independent selective incidence, and don't occur when they are needed

• Mutations at any single locus are rare events with a standard of 1 in 10⁶ gametes

• Cumulatively mutations lead to many effects, e.g. about 7% of us have become mutants

Genetic Variation

• Mutations are the only source of new alleles excluding when it's transferred by viruses
• Creates the raw material for natural selection to act upon

Example-of interesting mutation

• In humans, the variation known as the CCR-delta32 allele has a locus named CCR and gives a 32 base pair deletion that makes the protein nonfunctional
• lacking this protein on blood cells, homozygous individuals are essentially resistant to HIV infections
• predates the evolution of HIV evolution by hundreds of years and was neutral to the HIV species

Population Genetics

• Population genetics includes HWE and its implications
• Genetic drift, gene flow, and population structure
• Natural selection to describe its role in shaping genetic variation
• Adaptation and Evolutionary Processes, e.g. descriptions of physiological, behavioral, or morphological variations
• Evolutionary mechanisms
• Evolutionary theories: Darwinian evolution, modern synthesis, punctuated equilibrium

Genetic Drift

• Genetic Drift results in a change in allele frequency because the population is not of an infinite
• Passing of alleles from generation results in a change through randomness
• There is always some genetic drift occurring, the effect is greater in small populations

Genetic Drift Effects

• Does not lead to adaptation
• In larger populations it has minimal effects versus if an enormous span of time were to pass
• Over vast spans of time, the cumulative drift can lead to use as a molecular clock used in systematics
• In small populations, rare alleles may be lost, and the rest fixed by frequency
• Variation is lost and the population can become homozygous at many loci

Genetic Drift Consequences

• Reduction of genetic diversity and puts the population at risk of extinction

• With greater randomness it effects the genetic differentiation between two populations resulting in speciation through isolation

• Genetic differentiation alters new mutations that effect epistasis that may become favorable in one population but not another

• This is a demonstration of Wright's balance theory

• This leads to the evolution of human blood types (ex. In Blackfoots and Navajos groups) are due to neutral effects and drift

• In the past isolation of human populations lead to genetic drift and blood group differences

• Great effect exists when genes bottleneck out of a large population via mutations and selection

Founder Effect

• When some invade a new area and establish a population, this is genetic drift that represents only a fraction of alleles
• California Cypruses Amishes

Bottlenecks

• Periods of low population size or extinction that is a special case of genetic drift that has drastically reduced
• Cheetahs and their limited number
• In the 19th century Northern Elephant Seals bottlenecked numbers to their populations
• Ashkenazi Jews had rebounds

Allele Flow/Gene Flow/Migration

• Change in allele frequencies because of individuals move
• Shift the allele frequencies in a new population
• Evolutionary migrations because of seeds and spores provided that is a subspecies where there is at least two types of species

Allele Flow Effects

• Small effects will negate drift
• Genetic flow is a force that may oppose adaptations that lead to genetic convergences
• Genetic drift is countered if the population of migrants exceed more than one every two times the number of individuals in the population

Allele Flow and Selection

• Can also oppose
• Specialized conditions may be in selected populations
• With influxes, selection can cause an imbalance between the unsuited vs less fit alleles

Random Mating

• Non-random influences can result in evolution by how individuals select based upon characteristics
• Natural selection occurs with fitness difference
• These are both ways that mating can influence evolution

Mating

• Non-random mating comes in many evolution influencing parts
• Inbreeding as a consequence
• Selfing that is a form of high inbreeding and is high risk
• High levels of loss of heterozygosity but no change to number of alleles
• Exposes alleles to recessions that can reduce recessions because of the homozygous populations

Assortative Mating

• From resemblance to a certain phenotype
• Positive for like genes
• Negative for dissimilar
• Dwarfism and height
• As the list goes there are ways that assortative patterns present themselves to the number of offspring that is expressed

Natural Selection

• Natural selection includes variation, heritability, differential reproductive success as the main traits
• Acts on phenotypes to cause change
• Alleles that affect the ability of an organism leads to surviving producing will be able to subject to selection
• Operates whenever individuals present in the ability to reproduce
• Change with genetic variation to have to ability

Principles

• Must have variation with individuals in the population and variation must affect survival that has a genetic basis that is able to change through the ability of fitness- alleles

Fitness

• Ability of the alleles that are represented in the next generation that depends on success as the same as its lifetime reproductive performance

• Not physical and will be attributed to those that survive long and leave success

Absolute Fitness vs Relative Fitness

• the number of surviving offspring that an individual produces during its lifetime
• Things that cause this: Survivorship, number offspring, and components of fitness are
• Used through mathematic practices to represent relative fitness
• Genotypes and phenotypes are presented to where the ones with the highest absolute fitness shows the relative fitness of the fittest
• Given every other that is the fitness against the best phenotype

Example for Absolute Fitness vs Relative Fitness

• With birds and its polymorphism depending on the chance of success those traits is used to determine its likeliness of the value of its dominance
• In respect, for more clear reference and use against frequencies and its comparison can calculate relative ratios
• Selection will take note on where there is what difference that can be between its value and ideal

Directional Selection

• The most phenotype is often the most fit versus the loss from losing the old genetics
• Can cause genetic varience

Example Directional Selection

• Peppered moth evolution
• two traits light and dark genetic control controlled by alleles
• darker are typically dominence
• moths rest on the tree in the morning to use for protection
• In 1848 it became visible
• By museum collections the melanic trait had almost full increase
• soot darkened the dark that created a higher presence of visibility

Stabilizing Selection

• Most phenotypes stay close and the heterozygote traits are favored
• Value shows decreasing genetic variations
• Special genetic variants will maintain and both are maintained

Examples

• Probable in nature
• Weight influences mortality
• eggs that hatch out of the ordinary will have less of a reproductive advantage
• Lack’s optimum that the more may not be favored over the fewer eggs

Examples 2 balancing

• Example balance for Sickle cell defomers under conditions
• Hemoglobin that give illness
• The HbSHbS allele cause a genetic disease

Malaria

• malaria comes with resistance which leads to plasmodium
• heteroxyzotes have high resistantce that balance maintains because the is favored
• This is most common where the illness is favored
• There is no favor that doesn’t influence
• Can be affected by the population so has to work with that type

Freuqncy Selection

• Can be affected by frequency for more or less
• The more frequent tend to have a more desirable trait

Selection documented

• has many documentation in nature because they are rapid
• environments also affect what direction one needs to take
• there are many different traits when species are affected such as what they eat

Population Structure

• Affect how species work
• This variation as the genetic influence
• With different ethnic and races it will become influenced in different ways

Reverse Election Effects

• This takes place naturally because it is hard to determine what exactly it can measure
• When low some of those genetics can be lost
• Most structure needs to be known for its genetic diversity