Evolution Exam 2 Mississippi State University

Where is heritable variation stored

○ DNA
○ Deoxyribonucleic acid

What does DNA consist of

○ Two strands of nucleotides wound together
○ Double helix

What is a nucleotide made up of

○ Sugar (deoxyribose / ribose)
○ Nitrogen base
○ Phosphate

Four bases in DNA

○ Adenine (A)
○ Thymine (T)
○ Guanine (G)
○ Cytosine ( C )

How is DNA length measured

○ Base pairs

RNA vs DNA

○ RNA only has a single strand of nucleotides
○ Ribose instead of deoxyribose sugar
○ Nitrogen base uracil replaces thymine

Gene

○ Segment of dna that performs a function

Protein coding gene

○ Gene whose sequence codes for a protein
○ Amount varies per species

Central Dogma

○ DNA -> rna -> protein
○ Transcription into rna
○ Translation into protein

Transcription

○ Produces a complementary strand of rna from dna segment

mRNA

○ Messenger RNA
○ Carries genetic material to the ribosome, so protein can be made

Translation

○ mRNA -> protein
○ mRNA read in sets of 3 known as codon
○ tRNA brings in the amino acid based on the codon

Genetic code

○ Relates the codon to the amino acid they code for
○ Lots of redundancy where different codons code for the same amino acid

Regulatory sequences

○ Determines when, how, and where a cell transcribes and translates a gene
○ Can be cis or trans acting elements

Cis-Regulatory Elements

○ Located very close to gene they regulate
○ Ex) transcription factor binging sites

Trans-Regulatory Elements

○ Located far away from gene they regulate (could even be on a different chromosome)
○ Ex) transcription factors

Genome

○ All hereditary information of an organism

What is DNA organised into

○ Chromosome
○ Can vary in size, shape, ploidy, and number of genes or chromosomes

How many chromosome pairs are in the human genome

○ 23
○ Over 3 billion bp

Ploidy

○ Number of copies of unique chromosomes in a cell

What does it mean for the human genome to be diploid

○ Contain 2 homologous copies of each autosome

Autosome

○ Chromsomes that do not differ between the sexes

Sex chromosomes

○ Differ in copies between males and females
○ Lots of exceptions to the traditional sex chromosomes

How are karyotypes arranged

○ Largest to smallest bp
○ autosome and sex chromosomes separate

Ex) genome size

○ Varies greatly between species
○ Smallest = virus
○ Largest = amoeba (chaos chaos)

Ex) chromosome number

○ Ant = 1
○ Goldfish = 100
○ Adder's tounge fern = 630+

Ex) ploidy

○ Haploid = 1 unique copy of each chromosome
○ Diploid - 2
○ Triploid - 3
○ Tetraploid -4

Does genome size = genome number

○ No

Do genome size and genome number equal organismal complexity

○ No

Do humans, dogs, or nematodes have more protein coding genes

○ None
○ All have about the same around 20k

What percentage of human genome is noncoding

○ 98%
○ Shows that lots of the genome is not coding for proteins but either remnant of previous function or regulatory role

Locus

○ Basic unit of inheritance
○ Specific location of a gene or piece of dna sequence on a chromosome

Alleles

○ Different varients of DNA seuqence at the same locus

Genotype

○ Describes the genetic makeup of the organisms
○ The individual's alleles

Phenotypes

○ Describes the measurable characteristics of an organism

Do individuals inherit phenotypes

○ No, they inherit alleles
○ Alleles come together to form a genotype
○ Genotype comes together to produce the phenotype ... which determines the ability to survive and reproduce

Mutation

○ Important source of variation
○ Any change in the genetic sequence of an organism
○ Occurs because DNA replication machinery is not perfect

What would happen if mutations didn't occur

○ No variation, no evolution, no life

Somatic mutations

○ Affects cells in body of an organism
○ NOT HERRITABLE

Germ-line mutations

○ Affects gametes
○ ARE HERRITABLE

Cancer often results from what type of mutation

○ Somatic
○ Ex) UV radiation leading to dna damage and thymine dimers

Point mutation

○ Mutation of one nucleotide
○ Doesn't always produce an effect because of the redundancy in the genetic code

Insertion / deletion mutation

○ Inserts or deletes one or more nucleotides
○ Shifts the reading frame
○ Can result in frameshifts and drastic changes in amino acid sequence down the line
○ Premature stop codons

Gene duplication mutation

○ Accidentally creates more than one copy of the gene

Inversion mutation

○ Accidentally inverts the order of the genes

Chromosome fusion / fission mutation

○ Different chromosomes coming together / a chromosomes breaking apart

Genome duplication mutation

○ Creates several copies of the entire genome

Structural mutations

○ Everything except point mutaitons

Mutations occur at different frequencies

○ Point mutations most frequent (least impact)
○ Small insertions / deletions = 2nd (little impact in noncoding areas)
○ Large duplications
○ Gain or loss of chromosomes - least frequent, largest impact

Why are there so many mutations

○ In general, mutation rate is low for a given DNA base
○ However, genomes are rather large

Average number of new mutations per human gamete

○ About 40
○ About 80 new mutations for human baby because two gametes

Is mutation rate the same among all species

○ No
○ In C. Elegans, much lower than humans
○ .27 compared to 41.2 new mutations per gamete

Can mutations impact protein structure

○ In the protein-coding region of gene = yes
○ In non-protein coding region of gene = also yes because it could impact regulatory elements

Synonymous mutation

○ Due to redundancy in code, leads to same amino acid being produced
○ Wobble of the third nucleotide in codon

Nonsynonymous mutation

○ Leads to a different amino acid being produced
○ Changes the codon to code for a different aa to be brought

What can result in frameshifts

○ Small insertions or deletions

What do frameshifts often cause

○ Premature stop codons

Premature stop codon

○ A result of a mutation that causes a codon to now code for a stop codon rather than for an amino acid to be brought in
○ Results in a truncated protein

Pseudogenes

○ Genes that no longer produce a functional molecule
○ A result of mutations
○ Resemble functional genes but cant produce a functional product
○ Have lost protein coding ability

Pseudogenes example

○ Whales in the mysticites clade still have remnants of teeth coding genes despite not having teeth
○ Only baleen is currently expressed

Impacts of mutation

○ Harmful
○ Beneficial
○ No effect

Are mutations random as to their effect on survival and reproduction

○ Yes

Can mutation rates increase as a response to stressful environments

○ Yes
○ Doesn't increase likelyhood that a given mutation will increase survivorship

Sexual reproduction

○ Production of offspring by combining genetic information from two individuals of different types
○ Female = larger gametes
○ Male = smaller gametes

How are gametes produced in sexually reproducing organisms

○ A type of cell division called meiosis

Impact of meiosis on ploidy

○ It reduces it
○ Ex) diploid -> haploid

Genetic recombination

○ Occurs early in meiosis
○ Homologous chromosomes pair up and exchange DNA segments
○ Produces new combinations of alleles not present in either of the parents

Segregation

○ During the final stage of meiosis
○ Pairs of chromosomes separate so there is only a single copy in each daughter chromosome

Independent assortment

○ During the final stage of meiosis
○ It is random which copy will end up in which daughter chromosome
○ Random for each of the chromosome pairs
○ 2^n to calculate number of different combinations with n = number of chromosome pairs

Population

○ A group of interacting and potentially interbreeding individuals of a species
○ Made up of individuals that carry alleles

Population genetics

○ The study of the distribution of alleles within populations and the mechanisms that cause allele frequencies to change over time
§ Leading to evolution

What did population genetics arise from

○ Modern synthesis mixing darwin's theories with facts of genetics

Modern synthesis

○ Established that adaptive evolution is caused by natural selection action on particulate inherritance

What was the new definition of evolution proposed by the modern synthesis

○ Evolution is the change in allele frequencies in a population from one generation to the next
○ Focus on allele frequencies
○ Recognized mechanisms of evolution such as gene flow, genetic drift, and mutations

Hardy-Weinberg equilibrium

○ Math theorem that shows that absent of outside forces, allele frequencies will remain constant
○ P + Q = 1
○ P^2 + 2PQ + Q^2 = 1
○ P = frequency of allele #1
○ Q = frequency of allele #2

P^2

○ Represents frequency of homozygous individuals for allele #1

2PQ

○ Represents frequency of heterozygous individuals that have both allele #1 and #2

Q^2

○ Represents frequency of homozygous individuals for allele #2

Using genotype frequencies to predict allele frequencies

○ P = F(AA) + 1/2 F(AB)
○ Q = F(BB) + 1/2 F(AB)

5 assumptions for H-W Equilibrium

○ No mutation
○ Infinitely large population
○ Genotypes don't differ in fitness
○ Random mating
○ No migration

Why is the H-W Equilibrium important

○ Math proof that shows in the absence of selection, drift, or mutation: allele frequencies don't change and evolution doesn't occur
○ Can be used as a null hypothesis to try and disprove in the case that evolution is occuring
○ Can be used to study the way allele frequencies do change

Null hypothesis

○ Hypothesis that says that there is no relationship between two measured phenomena
○ If rejected, shows that a relationship between the phenomena may exist

H-W hemoglobin example

1. Convert allele frequencies to genotype frequencies using P^2 + 2PQ + Q^2
2. Look at observed frequencies
3. Perform chi-square analysis

Chi-square

○ Sum up (observed - expected)^2 / expected for all genotypes

Degrees of freedom

○ Number of alleles - 1

What p value do you reject H-W

○ If below .05
○ 5% threshold

1950s Peter Buri experiment

○ Flies and their eye color
○ All started heterozygous orange, and ended up fixed as either red or white
○ Started with 107 populations, each with 8 males and 8 females
○ Each generation = randomly select 8 males and 8 females to reproduce

Which assumption of H-W equilibrium did Peter Buri experiment violate

○ It wasn't an infinite population
○ Result of random sampling error / genetic drift

Genetic drift

○ Occurs when a random, non-representative portion of the population produces the next generation
○ Occurs because populations aren't infinitely large
○ Mechanism for evolution because changes allele frequency from one generation to the next
○ Results from random sampling error

4 features of genetic drift

○ Causes populations that are initially identical to become different
○ It is unbiased, and allele frequencies are equally likely to go up or down
○ Causes variation to be lost
○ Evolution occurs without natural selection

Is genetic drift stronger in small or large populations

○ Small
○ Smaller populations are more likely to result in allelic fixation

What population is immune to genetic drift

○ Only ones that are infinitely large

Can genetic drift impact populations that are only temporarily reduced in numbers

○ Yes
○ Bottleneck effect
○ Despite population size regaining, the loss of the alleles that are no longer present are permanent

Genetic bottleneck

○ Type of genetic drift
○ Event where the number of individuals in a population are drastically reduced

Example of genetic bottleneck

○ Northern elephant seals
○ 23 (south) vs 2 (north) variable sites in a 300 bp mitochondrial sequence

Founder effect

○ Type of bottleneck effect
○ Loss of allelic variation resulting from new populations founded from a very small number of individuals
○ Can lead to rare alleles being more likely to be lost
○ OR can cause a random set of rare alleles to rise in frequency

Founder effect ex)

○ HMS bounty mutanied and settled on pitcairn island
○ 27 adults and 1 baby
○ Later, about 200 moved to Norfolk island
○ On Norfolk island, high percentage are afflicated with migrains (25%) that is rather rare in mainland populations

Founder effect ex2)

○ Polydactyly (more than 5 digits) in amish community
○ 7% frequency
○ 100x greater than normal

Natural selection

○ A mechanism that can lead to evolution whereby differences in survival and reproduction can cause some genetic types to replace others
○ Occurs when individuals vary in fitness

Fitness

○ The success of an individual at surviving and reproducing
○ Must contribute to the next generation