S1: W1-W2 (Prof. Kelsey) Flashcards
Components of the biodiversity framework that we focus on? (4)
• Genes.
• Genetic structure & processes.
• Populations.
• Population structure.
Things to note when defining evolution & the variation that enables it? (3)
• Heritable change (gemline).
• Change due to imperfect DNA replication.
• Variation in success/fitness of variant/different DNA.
Macro-scale to micro-scale on the hierarchical nature on phylogenetic assessment? (2)
• Macro-scale deals with general taxa/animal groups.
• Micro-scale deals with detail within a group/taxon (pedigrees and stuff).
Difference between purines & pyramidines?
Purines have a double membrane while pyramidines have a single membrane.
Purines? (2)
• Adenine.
• Guanine.
Pyramidines? (2)
•Thymine.
• Cytosine.
Codon?
= a sequence of three nucleotide bases/letters in a DNA or RNA strand.
Central Dogma in Molecular Biology?
= unifying theme of evolutionary biology.
CDMB stands for?
Central Dogma in Molecular Biology.
CDMB components? (3)
• Replication.
• Transcription.
• Translation.
Replication?
= DNA is copied in cells.
Transcription?
= DNA is made into RNA expressed regions.
Translation?
= RNA is made into proteins, using DNA codons to select amino acids (mRNA, rRNA, tRNA).
Why is CDMB a unifying theme of evolutionary biology? (3)
• Enables nature’s flow of information (unidirectional flow).
• Used to identify individuals, populations & species.
• Study how changes to DNA alter biodiversity.
How does CDMB help to identify individuals, populations & species?
By different nucleotides being introduced at the same point during replication.
Locus/Loci?
= can be a gene or a neutral marker.
Genes attributes? (2)
• Have 2 alleles.
• Can be neutral markers.
Neutral marker attributes? (2)
• Multiple alleles.
• Not genes.
Microsatellite?
= short sequence of nucleotides repeated.
Monomorphic microsatellite?
= when the number of repeats is the same among individuals.
Polymorphic microsatellite?
= when the number of repeat varies between individuals.
Monomorphic microsatellite attribute?
• Not informative.
Polymorphic microsatellite attribute?
• Informative.
Where do genes come from? (3)
• Homology.
• Orthology.
• Paralogy.
Homology types? (2)
• Orthology.
• Paralogy.
Orthology?
= duplicates that share a common ancestor.
Paralogy?
= duplicates that don’t share a common ancestor.
Orthology attributes? (4)
• Related via speciation events.
• Within different species.
• Have similar functions.
• Retain original function.
Paralogy attributes? (4)
• Related via duplication event.
• Within the same species.
• Functions diverge.
• Evolves new function.
Why should we organize information with/using orthologs?
It’s because they enable one to find & compare data speedily.
Eg of paralogs?
Hox genes.
Why are duplicate genes important?
They provide a source of genetic material for mutation, drift and selection to act upon.
Why are paralogs helpful?
They provide useful information into the way genomes evolve.
Epistasis?
= gene-gene interaction.
Types of genes? (2)
• Structural/productive genes.
• Untranscribed genes.
Structural genes attributes? (2)
• Protein-coding genes.
• RNA-specifying genes.
Untranscribed genes attribute?
Non-functional.
Transcription factor?
= proteins involved in the process of transcribing/converting DNA into RNA.
Transcription factor functions? (2)
• Turn genes on/off.
• Regulate transcription of subsequent genes.
Intron?
= a nucleotide sequence that does not code for amino acids in a protein.
Eg of intron?
Neutral markers.
Why do introns make good neutral markers?
It’s because they are free to accumulate mutations at a higher rate than extrons with lower consequences.
Why do extrons make bad neutral markers?
It’s because they accumulate mutations at a slower rate than introns with higher consequences.
Genome types? (3)
• Nuclear DNA.
• Mitochondrial DNA.
• Chloroplast DNA.
Things to note when dealing with types of genomes? (3)
• Inheritance.
• ATP.
• Rubisco.
Chloroplast DNA vs Nuclear DNA vs Mitochondrial DNA regarding appearance?
• cpDNA = coiled.
• nDNA = round.
• mtDNA = round.
Chloroplast DNA vs Nuclear DNA vs Mitochondrial DNA regarding Inheritance?
• cpDNA = paternal.
• nDNA = maternal & paternal.
• mtDNA = maternal.
Barcode?
= unique gene region that work for a species.
Barcode uses? (3)
• Used for species identification.
• Provide evidence to refute/dispute morphological data.
• Help us understand biodiversity (Sting flowers).
Egs of barcodes? (3)
• tmK.
• tmS.
• trnL.
Cataloging life on earth using barcodes general process? (6)
• Collect specimen.
• Collect metadata.
• Tissue sample.
• DNA extraction.
• PCR amplification of DNA barcode.
• Sequencing of DNA barcode.
Polymerase Chain Reaction (PCR)?
= a method used to make many copies of a specific DNA region.
Kary Mullis?
= developed the method to amplify regions of DNA, automatically.
When was the PCR discovered?
1983.
List of PCR Reagents? (6)
• DNA.
• Primers.
• dNTPs (nucleotides As, Ts, Cs, Gs).
• Buffer.
• MgCl2.
• TAQ Polymerase.
DNA regarding PCR reagents?
= genomic/template.
Primers in terms of PCR reagents?
= identification region.
dNTPs in terms of PCR reagents?
= make new DNA.
Buffer in terms of PCR reagents?
= stabilizes reaction.
MgCl2 in terms of PCR reagents?
= enhance binding.
TAQ Polymerase in terms of PCR reagents?
= adds dNTPs to the template.
TAQ Polymerase attributes? (2)
• Found in the hot spring of a national park.
• Can handle really high temperatures (98°C) & performs optimally in this environment.
PCR main steps? (3)
• Denaturation of DNA & primers.
• Annealing a primer to template DNA.
• Elongation.
Temperature of Denaturing process of PCR?
95°C.
Temperature range of Annealing process of PCR?
45°C – 60°C.
Temperature of Elongation process in PCR?
72°C.
Why the Anealing temperature range?
It’s because the proportion of nucleotides (As, Cs, Ts, Gs) in your primer & DNA changes the temperature at which the primer will attach/anneal to your DNA successfully.
Low temperature in annealing = …?
Non-specific annealing.
High temperatures in annealing = …?
Specific.
Annealing step in PCR?
= process where primers bind to template DNA strands.
What does your PCR look like?
Gel electrophoresis image.
Types of molecular markers? (3)
• Single locus marker.
• Co-dominant & dominant markers.
• -Omics.
Process associated with single locus marker?
• Gene sequencing.
Process associated with co-dominant & dominant markers?
Fragment analyses.
Process associated with -omics marker?
Next genetic sequencing.
Molecular marker?
= a segment of DNA that is found at a specific location in a genome.
Gene sequencing?
= the ability to determine nucleotide sequences of DNA molecules.
Eg of Single locus marker?
Barcodes.
Gene sequencing uses? (2)
• Help you identify breeds (i.e., whether species are related).
• Used for DNA fingerprints.
Thing to note about gene sequencing & relatability?
If species relatability is >2%, it means that they are different species.
If a species >2% = …?
Different species.
Fragment analysis?
= the process of breaking down a DNA sample into various fragments using restriction enzymes, & visualizing and analyzing those fragments through the process of gel electrophoresis.
Dominant markers attributes? (3)
• Cannot distinguish between heterozygotes.
• Give inaccurate impression/lower estimate of genetic diversity.
• Represented as present or absent bands.
Why do dominant markers give a lower estimate of genetic diversity?
It’s because they mask the recessive gene.
Co-dominant markers attribute?
Can distinguish between heterozygotes.
Eg of Co-dominant markers?
Microsatellites.
Things to note regarding Microsatellites? (2)
• Way that fragment size changes is based on the number of repeats.
• Single locus has many alleles of different lengths.
Eg of Dominant markers?
DNA fingerprints.
-Omics markers attributes? (3)
• Blends concepts of single gene sequencing & fragment analysis.
• Parallel (simultaneous) sequencing of DNA fragments.
• Researchers sequence multiple regions of an organism’s genome.
Application of -Omics markers?
SNP.
SNP stands for?
Single Nucleotide Polymorphism.
SNP?
= variation in a DNA sequence occurring when a single nucleotide in a genome is altered.
Molecular markers uses? (5)
• Genetic variation.
• Species identification.
• Invasion biology.
• Disease ecology.
• Identifying genetic conditions, viruses & other medical conditions.
How are molecular markers used in genetic variation? (2)
Via:
• Population structure.
• Evolution.
How are molecular markers used in Species identification? (2)
Via:
• Taxonomy.
• Systematics.
How are molecular markers used in Invasion biology?
Biocontrol.
How are molecular markers used in Disease Ecology? (2)
Via:
• Genetic predisposition/susceptibility.
• Infection routes.
How are molecular markers used in identifying genetic conditions, viruses, etc? (2)
Via:
• Medical practice.
• Genetic counseling.
Important thing to note of molecular markers?
Must not be under selection (i.e., must be in HWE).
Why must molecular markers not be under selection?
It’s because they are “neutral” regions of genomes.
How do you tell if something is under selection?
It is not in HWE.
Why are neutral markers important?/Why do you think you need neutral markers?
Shifts your view of genetic variation:
- If a marker is neutral, you get a good estimate of variation.
- If a marker is under selection, it is bad for variation.
Main causes of genetic variation? (2)
• Recombination.
• Mutations.
Recombination?
= the shuffling of genes (alleles) between chromosomes.
Mutation?
= heritable changes in genetic information.
External causes of mutations? (2)
• “Naturally” occurring causes.
• External influences.
Egs of external influences? (3)
• Sun.
• Chemicals.
• Radiation.
What happens when DNA mutates? (4)
• Nothing (it’s a neutral/synonymous mutation).
• Advantageous.
• Deleterious.
• Conservative.
Advantageous effect if a DNA mutates attributes? (2)
• Increases fitness.
• Rare.
Deleterious effect if a DNA mutates attributes? (2)
• Common.
• Changes gene function/shuts off your genes.
Eg of a Deleterious effect of a DNA mutating?
BRCA1.
Conservative effect when a DNA mutates?
= a change in amino acids but the new amino acid has similar chemical properties (doesn’t change much).
Types of mutations? (4)
• Point mutations.
• Indels.
• Frameshifts.
• Macromutations.
Point mutation?
= nucleotide substitutions (where one base is changed to a different base).
Types of point mutations? (3)
• Silent.
• Non-sense.
• Mis-sense.
Silent point mutation?
= muation where a single nucleotide base is changed, but that change does not affect the amino acid sequence.
Non-sense point mutation?
= mutation that changes an amino acid to a stop codon.
Mis-sense point mutation?
= point mutation where a single nucleotide is changed, resulting in a codon that codes for a different amino acid.
Types of Mis-sense point mutations? (2)
• Conservative.
• Non-conservative.
Silent point mutation illustration? (3)
● DNA level = TTC [to TTT]
● mRNA level = AAG [to AAA]
● Protein level = Lys [to Lys]
Non-sense point mutation illustration? (3)
● DNA level = TTC [to ATC]
● mRNA level = AAG [to UAG]
● Protein level = Lys [to STOP]
Conservative Mis-sense point mutation illustration? (3)
● DNA level = TTC [to TCC]
● mRNA level = AAG [to AGG]
● Protein level = Lys [to Arg]
Non-conservative Mis-sense point mutation illustration? (3)
● DNA level = TTC [to TGG]
● mRNA level = AAG [to ACG]
● Protein level = Lys [to Thr]
Egs of Mis-sense point mutations? (3)
• ALS (Amyotrophic Lateral Sclerosis).
• Cystic fibrosis.
• Sickle cell anaemia.
Indel mutation?
= mutation where larger gaps are deleted or inserted into a DNA sequence.
Important thing to note about Indel mutation?
They are much harder to predict in evolutionary models.
Why are Indel mutations harder to predict in evolutionary models?
It’s because we have to think about the homology of the nucleotides that are left in the gaps (parsimony).
Frameshift mutation?
= mutation that causes a shift in the reading frame of the genetic message.
Effect of a frameshift mutation?
Alters the protein tremendously.
Frameshift mutation illustration?
● Original = The fat cat sat
● Mutated = hef atc ats at
Macromutations?
= large changes in gene regions (sometimes due to recombination).
Macromutations attributes? (2)
• Happen on chromosome level.
• Polyploidy-genome duplication.
What causes polyploidy-genome duplication?
Non-disjunction.
Eg of Macromutations?
Tragopogon (goat’s beard).
Explain eg of Macromutations?
Pieces of chromosomes translocate (mixed colour chromosome).
Type of Macromutations?
Aneuploidy.
Aneuploidy?
= the gaining/losing of a chromosome.
Polyploidy?
= the gaining/losing of a whole set of chromosomes.
Do mutations have patterns?
Yes.
How is it that mutations have patterns? (2)
• Mutations are accumulated non-randomly (predictable).
• G & C mutate more readily than A & T.
Eg of where patterns of mutations are observed?
Tarsir’s genome (where transitions are more common than transversions).
Types of Nucleotide substitutions? (2)
• Transition.
• Transversion.
Transition?
= when a purine converts to a purine, or a pyrimidine converts to a pyrimidine.
Transversion?
= when a purine converts to a pyrimidine, or pyrimidine to a purine.
Why are transition & transversion important when thinking about protein coding genes?
To enable us to predict the downstream effects, especially of transversion.
Why do we conduct evolutionary analyses? (6)
• Better understand evolutionary effects of mutations.
• Identify closely related sequences or genes.
• Understand gene families & function.
• Consider evolutionary history of a species.
• Identify genes under selection.
• Estimate the timing of variation & evolution.
Explain what you mean that we conduct evolutionary analyses to understand genes families & function?
That we get better ideas of gene relatability.
What do you mean that we conduct evolutionary analyses to estimate the timing of variation & evolution?
We mean that we can date phylogenies.
How do mutations help us understand the evolutionary implications of variation?
By generating the genetic variation that evolutionary processes depend on to act on organisms.
What is the 3rd position of a codon called?
Wobble.
Why is the 3rd position of a codon called a wobble?
It’s because it can change but the codon can still.produce the same protein.
Which position(s) of a codon undergo strong selection?
1st & 2nd positions of a codon.
Thing to note about the 3rd position of a codon?
Undergoes a high rate of mutation.
Rate?
= change over time.
Why is there rate variation among regions? (3)
• Nucleotide substitutions
• Pseudogenes.
• Each codon changes differently over time.
Pseudogenes?
= non-functional fragments of DNA that resemble a functional gene.
Pseudogenes attributes? (2)
• Free to change.
• Have a high rate of variation.
Why do Pseudogenes have a high rate of variation?
It’s because they are not under strong selection.
Factors affecting genetic diversity? (4)
• Mutation.
• Genetic drift.
• Inbreeding.
• Gene flow.
Types of genetic variation? (2)
• Neutral.
• Adaptative.
Neutral genetic variation?
= where there’s no selective advantage/disadvantage.
Eg of Neutral genetic variation?
Eye colour.
Adaptive genetic variation?
= where there’s a selective advantage/disadvantage.
Egs of Adaptive genetic variation? (2)
• Venom.
• Darwin’s finches.
Hierarchical organization of genetic diversity? (bottom to top) [4]
Within individual
|
Individual
|
Within populations
|
Among populations
Implications of genetic variation/diversity within populations? (3)
• Critical factor in population/species survival.
• High chances for survival as environment changes.
• Small, isolated populations are less likely to survive drastic/any change.
Why are small, isolated populations less likely to survive drastic/any change?
It’s because of low genetic variation & decreased drift.
Genetic diversity/variance among populations use?
Help us think about how populations are changing through time.
Why is genetic variation/diversity high among populations?
It’s because of various evolutionary processes such as NS, mutations & genetic drift.
Implication of genetic diversity/variation among populations?
Population divergence/structuring.
Use of population divergence/structuring?
Helps you to figure out where diverge took place.
Contributors to population divergence/structuring? (2)
• Co-adapted gene complexes.
• Speciation.
Co-adapted gene complexes?
= set of alleles/genes that increase the fitness in a specific environment.
Genetic diversity within populations attributes? (5)
• High gene flow.
• High mutations.
• Decreased NS.
• Decreased genetic drift.
• Decreased inbreeding.
Genetic diversity among populations attributes? (4)
• High NS.
• High genetic drift.
• High mutations.
• Decreased gene flow.
Eg of Hierarchical organization of genetic diversity?
Tragopogon miscellus.
Genetic diversity within individual attributes?
Genetic diversity in individual attributes?
Explain Elongation process of PCR?
It’s where DNA polymerase (TAQ) is used to extend the DNA fragment between the primers.
Desirable properties for molecular markers? (5)
• Polymorphism.
• Co-dominant inheritance•••
Egs of Frameshift mutations? (2)
• Insertions.
• Deletions.
What do Macromutations include? (4)
• Deletions.
• Duplications.
• Translocations.
• Inversions.
Deletion (chromosomal)?
= loss of all or part of a chromosome.
Duplication (chromosomal)?
= produces an extra copy of all or part of a chromosome.
Inversion (chromosomal)?
= reverses the direction of parts of a chromosome.
Translocation?
= occurs when part of one chromosome breaks off and attaches to another.
What causes a Frameshift mutation?
Insertion or deletion.
Types of molecular markers? (2)
• Neutral markers.
• Adaptive markers.
Genetic diversity/variation hierarchy? (3)
• Individual.
• Among individuals within populations.
• Among populations.
What do evolution analyses depend on?
Rate of mutation (eg substitutions).
Evolutionary analyses uses? (4)
• Help us estimate the timing of divergence.
• Help us estimate selection on on genes & populations.
• History of biodiversity.
• Evolutionary history of species, populations & genes/gene regions.
Rate attributes?
• vary within & among organisms, genes, regions of genes & nuclear vs organellar genomes (mtDNA & cpDNA).
1st codon position name?
Non-degenerate sites.
2nd codon position name?
Twofold degenerate sites.
3rd codon position name?
Fourfold degenerate sites.
COVID-19 mutation rates?
An eg of where a gene has a different rate than the whole genome.
Eg of Point mutation in general?
SNP.
Why should we model evolution? (4)
• Describes the changes of fixed mutations.
• Amount of change, i.e., function of time since divergence.
• Incorporate what we know about rates of change.
• Estimate genetic differences or similarities.
Substitution model assumptions? (3)
• Sites (A,T,G,C) are independent of each other & site homogeneity.
• Current base & future substitutions are independent of the past (no relationship).
• Temporal homogeneity (mutations occur per unit time).
Note about Substitution model assumptions?
Only apply to gene regions that are not undergoing selection (i.e., neutral markers).
Foundation of models?
Each p = probability of a change between the 2 nucleotides & 12 independent probabilities have to be considered.
List models of evolution? (4)
• Jukes-Canter model (JC).
• Kimura 2-parameter model (K2P).
• Hasegawa-Kishino-Yano 85 model (HKY85).
• General Time Reversable model (GTR).
Jukes-Canter (JC) model attributes? (5)
• Simplest model.
• One parameter (mu).
• Equal base frequencies (0.25).
• Assumes a single rate of change among nucleotides.
• Equal probabilities (mu).
JC scenarios?
EG1 EG2
t=0 A A
t=1 A Not A
t=2 A A
Therefore, in EG2 we lost information because we don’t know what nucleotide was changed.
K2P model attributes? (5)
• 2 parameters (mu & beta).
• Equal base frequencies (0.25).
• 1 parameter for transitions (alpha).
• 1 parameter for transversions (beta).
• Different probabilities of
K2P scenarios?
EG1 EG2 EG3 EG4
t=0 A A A A
t=1 A G C T
t=2 A A A A
Therefore, in EG2 you have transition (alpha), EG3 you have transversion (beta), EG4 you have transversion (beta).
HKY85 model attributes? (3)
• Unequal base frequencies.
• Account for transition/transversion rate difference (K = alpha / beta).
• Put nucleotides in a matrix as each has a different base frequency.
Why put nucleotides in a matrix?
It’s because each nucleotide has a different base frequency.
GTR model attributes? (3)
• Unequal base frequencies (meaning 4 equilibrium base frequencies).
• Allows all 6 substitutions to have different rates.
• Each nucleotide has its own probability.
What do we mean when we say it allows for all 6 substitutions to have different rates?
We mean that you now have different rates for different transitions & different rates for different transversions, which ALL have different probabilities.
What do we mean by 4 equilibrium base frequencies?
We mean that each nucleotide has an equilibrium frequency.
What to think about when dealing with models of evolution? (2)
• Base frequencies (whether they’re equal or not).
• Substitutions & their rates (are substitution rates equal).
Why do we use models of evolution?
• Help us calculate genetic distance.
Genetic distance?
= estimate of the amount of genetic divergence between sequences/microsatellite regions.
Genetic distance AKA?
Net nucleotide distance.
How do we calculate genetic distance? (4)
● Use sequence data.
● Count no. of subs / total #sites.
● Use a model of evolution to estimate substitutions.
● Interpret data.
How to interpret the data after calculating genetic distance? (3)
• Range is 0 to 1.
• Lower values = sequences are more similar to each other.
• Higher values (closer to 1) = sequences are different from each other.
Sequence data vs Microsatellites?
● Sequence data
= deals with substitutions.
● Microsatellite
= deal with allele frequencies (presence/absence in sample).
Genetic distance uses?
Estimate population diversity.
Genetic distance uses?
Estimate population diversity.
Stepwise mutation model use?
Infinite allele model?
= model that allows for more microsatellites in any direction.
Types of genetic distance?
• Heterozygosity.
Heterozygosity attributes? (3)
• Based on alleles (haplotype for sequences).
• Observed vs expected heterozygosity.
• Locus, individual & population variation.
Things to look for when interpreting heterozygosity estimates (“summary statistics” in genetics)? [2]
• Site = nucleotide = position in sequence.
• HsubscriptE = heterozygosity (consider the evolutionary processes contributing to this).
Evolutionary processes that affect genetic variation/diversity? (4)
• Mutation.
• Gene flow.
• Drift.
• Selection.
Which evolutionary processes that affect genetic diversity increases heterozygosity? (3)
• Mutations.
• Gene flow.
• Selection.
Which evolutionary processes that affect genetic diversity decreases heterozygosity? (2)
• Drift.
• Selection.
Which evolutionary processes that affect genetic diversity increases differentiation? (3)
• Mutation.
• Drift.
• Selection.
Which evolutionary processes that affect genetic diversity decreases differentiation? (2)
•Gene flow.
• Selection.
Which evolutionary processes that affect genetic diversity affect all loci equally? (2)
• Gene flow.
• Drift.
Which evolutionary processes that affect genetic diversity DON’T affect all loci equally? (3)
• Mutation.
• Selection.
Why do mutation & selection not affect all loci equally?
It’s because they are loci-specific & therefore a change in locus can happen in 1 individual but not the other.
Why do gene flow & drift affect all loci equally?
It’s because they happen in individuals & therefore in all of the loci.
Difference between neutral markers & adaptive markers regarding location?
● Neutral markers
= on gene regions.
● Adaptive markers
= on genes.
G
Where do we apply the
Types of balances? (2)
• Mutation-selection balance.
• Migration-selection balance.
Mutation-selection balance?
= where because most mutations are deleterious, selection tries to eliminate them but cannot due to mutations having higher frequencies than selection can act on.
How/In what ways do mutations remain in populations? (2)
• Heterozygotes (via masking of deleterious mutation).
• Drift.
How does genetic drift ensure that deleterious mutations stay in the population?
Egs of Mutation-selection balance? (2)
• Waser & Price (1981) with Delphinium melsonii.
• Cystic fibrosis.
Explain Waser & Price (1981)? (2)
● Found that pollinators didn’t visit white morphs of Delphinium melsonii but these morphs persisted even though they had low fitness.
● Selection couldn’t act on it as some pollinators were still visiting some of the white morphs.
Explain Cystic fibrosis?
• Caused by mutations in the CFTR gene and was selected against because males with it are infertile.
Cystic fibrosis?
= condition where you have autosomal recessive inheritance.
Migration-selection balance?
= where local adaptation in subpopulations is caused by selection & migrated by migration.
Migration-selection balance attributes? (3)
• Movement of alleles balances out selective pressures.
• Differentiation occurs if s>m (i.e., if selection is overpowering migration).
• Differentiation ONLY at the loci affecting traits that selection is acting on (the single trait).
Symbols in s>m?
• s = selection coefficient across subpopulations.
• m = fraction of migrants each generation.
Egs of Migration-selection balance? (2)
• Industrial melanism is moths.
• Snake venom.
Explain Industrial melanism in moths? (2)
• Local adaptation occurred.
• Selection acted stronger than migration.
Explain Snake venom?
Dietary needs is what caused the change in the venom.
Migration & drift in terms of Migration-selection balance?
Because most alleles are lost in small populations through drift, new alleles are replaced through migrants to balance it out.
Equation for Migration & Drift in terms of Migration-selection balance?
Fsub(ST) = 1/ (1+4Ne m)
Symbols of Migration & Drift relating to Migration-selection balance? (3)
• Ne = effective population size.
• m = migrant.
• Fsub(ST) = population differentiation.
Fsub(ST) attributes? (2)
• How different your populations are.
• Takes into account how Ne (population size) is different from migrants.
Ne?
Tells you about drift.
Drift effect on subpopulation differentiation?
Increases differentiation among subpopulations.
Migration effect on subpopulation differentiation?
Decreases differentiation among subpopulations.
Selection & Drift in terms of Migration-selection balance?
In order for for selection to counteract drift in small populations, it needs to be much stronger (high s).
Thing to consider for Migration-selection balance?
Migration & selection try to counteract drift effects in small populations. Migration counteracts it by bringing in new alleles, while selection counteracts it by acting strongly on them.
When does selection determine allele frequency?
When:
s > 1/2Ne.
1/2Ne?
= rate of genetic drift.
Eg of Selection in drift?
Purple loosestrife flowers.
Explain Purple loosestrife flowers?
3 morphs (long style, mid style, short style) are maintained by negative frequency dependent selection, but morphs can be lost in small populations due to drift.
How do populations survive changing environments (adapt)? (3)
• Dispersal.
• Phenotypic plasticity.
• Adaptation.
Focus is on…?
Adaptation.
Why do we need to consider genetics in understanding selection on phenotypes?
It’s because genetics are underlying mechanisms of phenotypes.
Adaptation in terms of genetic basis attributes? (3)
• Can drive increase or decrease in genetic distribution.
• One genotype can produce multiple phenotypes.
• Multiple genotypes can produce one phenotype.
Eg of where one genotype produces multiple phenotypes?
Daphnia species having helmets in the presence of predators & no helmets in their absence.
- Helmet = phenotype.
Eg of multiple genotypes producing one phenotype?
Tetrahymena (is an eg of Phenotypic parallelism, which overrides genetic divergence).
Genetic basis of adaptation questions asked? (2)
• Does adaptation involve 1 gene or multiple genes?
• Are the same genes involved in adaptations across diverse groups?
Eg of genetic basis of adaptation?
Antarctic ice fishes (Nototheinoid fishes) & Arctic Gadids.
Explain Nototheinoid fishes & Arctic Gadids? (3)
• Partial de novo gene evolution.
• Both fish have anti-freeze protein (AFGP).
• Essentially, scientists “turned” on an unrelated ancestral gene to a functional gene in Arctic gadids (hence the de novo evolution).
Things to consider in terms of genetic variation & adaptive potential? (3)
• How genetic variation is related to fitness.
• Populations genetic composition (allele/haplotype frequencies).
• Measuring the fitness of variable phenotypes.
What is key for adaptive potential? (2)
• Fitness.
• Diversity.
Egs under Genetic variation & adaptive potential? (2)
• Geospiza finches.
• Opposum shrimp.
Opposum shrimp attributes? (2)
• Model organism for conservation genetics in changing environments.
• Tells us that genetic diversity is important in changing environments.
What enables diversity for adaptation?
Adaptive markers!
Adaptive marker?
= gene/DNA region that’s under selection.
What can you use to identify adaptive markers? (2)
• Genomics.
• Controlled crosses approach.
Controlled crosses approach attributes? (3)
• Help you figure out the proportion of phenotypes, which in turn helps you link it to gene region.
• Often needs whole genome coverage.
• SNPs.
Eg of adaptive markers?
Mimmulus flowers.
Egs of gene families used to quantify adaptive genetic diversity? (2)
• MHC genes.
• S loci.
What do we use to quantify adaptive genetic diversity?
Gene families.
How do we test for adaptations & gene differentiation? (3)
Use a combination of marker types & look for patterns of selection:
• Neutral markers.
• Adaptive markers.
• Sequence data.
Neutral marker in testing for adaptations & genetic differentiation?
Show similar levels of genetic divergence (low divergence).
Adaptive marker in testing for adaptations & genetic differentiation?
Show variable (anomalous) levels of divergence.
Sequence data in testing for adaptations & genetic differentiation?
Compare non-synonymous & synonymous substitutions.
Egs of testing for adaptations & genetic differentiation? (2)
• Stickleback fish.
• Mimmulus.
Explain Stickleback fish?
Genome scan of 45 000 SNPs indicates genomic differences between freshwater populations.
Explain Mimmulus? (2)
• Indicates genetic discordance.
• Where although other flowers are annual or perennial, this flower tends to be both annual & perennial.
Selection patterns that indicate adaptation? (2)
• Directional selection.
• Stabilizing selection.
Directional selection effects? (2)
• Increases population differentiation.
• Decreases
Stabilizing selection effects? (2)
• Decreases population differentiation.
• Increases
What is used to estimate selection?
Molecular data (protein coding genes & dN/ds ratio).
dN/ds ratio?
= proportion of non-synonymous to synonymous substitutions.
How do we calculate selection with molecular data?
Z-test.
Z-test Ho (null hypothesis)?
Ho: dN = ds.
Z-tedt HA (alternate hypothesis)? (3)
• dN = ds
• dN > ds
• dN < ds
dN = ds means…?
Test of neutrality.
dN > ds means…?
Positive selection.
dN < ds means…?
Purifying selection.
Positive selection means…?
Non-synonymous substitutions favoured.
Purifying selection means…?
Non-synonymous substitutions selected against.
Are changes in traits due to selection or drift?
Ho & Smith 2016 paper.
Summarize Ho & Smith 2016 paper?
If dN/ds ratio is close to 1?
Positive selection.
If dN/ds is close to 0?
Purifying selection.
Consequence of adaptation?
Isolation.
Eg of a consequence of adaptation?
White & purple flowers where bees pollinated the purple flowers & the white flowers were isolated.
How does adaptation drive genetic differentiation?
Populations ar the periphery tend to have low genetic diversity & high differentiation as a consequence of selection.
Eg of adaptation driving genetic differentiation?
Malaria mosquitoes.
Explain Malaria mosquitoes?
• Inversion is being selected for by the environment they live in.
• Dagilis & Kirkpatuck, 2016 & Ayala et al, 2013 papers.
Ayala et al, 2013 paper summary?
Dagilis & Kirkpatuck, 2016 paper summary?
Why do we use adaptive markers?
To examine inbreeding depression on populations.
Hypotheses for inbreeding depression? (2)
• Dominance.
• Overdominance.
Dominance hypothesis?
= where there’s unmasking of deleterious alleles through a reduction of heterozygotes.
Overdominance attributes? (2)
• Where you have heterozygote advantage.
• Increase in homozygotes = less fit heterozygotes.
What do we use to test which of the mechanisms in the competing hypotheses are prominent?
Adaptive markers.
Eg of inbreeding depression?
Drosophila.
Explain Drosophila in inbreeding depression? (2)
• Heat shock genes were upregulated in inbred Drosophila when they were exposed to high temperatures.
• Inbreeding acted as an environmental stressor.
Speed of inbreeding & adaptation?
Demontis et al, 2007 paper.
Explain Demontis et al, 2007 paper?
What represents the no. of subs when using sequence data to calculate genetic distance?
What represents the total # of sites when using sequence data to calculate genetic distance?
