Chapter 8 Flashcards
Founder effect
Chance variation in the initial allele frequencies in a founding population may lead to dramatically different allele frequencies on an isolated island compared to on a mainland
OR
Change in allele frequencies that results from the sampling effects that occur when a small number of individuals from a large population initially colonize a new area and found a new population. Example: Manx cats
The manx cat is an example of what effect?
the founder effect; where the M allele become more common.
Law of large numbers
As the size of a random sample increasese, the realized frequencies—those frequencies that we actually observe— usually will be very close to the expected frequencies.
What happens with experiments with small sample sizes?
Realized frequencies are not always very close to the expected frequencies
With small populations?
- Realized genotype frequencies often DEVIATE SUBSTANTIALLY from expected frequencies*
- certain mating pairs may form more or less often than expected
- certain genotypes may reproduce more or fewer offspring than expected
- certain genotypes may survive more or less often than expected
Wright Fisher model
Model shrinks the population variable from Hardy W. model; there is no migration into the population from other populations (versus infinite population size)
What influence does the Wright Fisher model have on allele frequencies when the population size is small?
Accounts for chance events that influence allele frequencies. Even if Natural Selection isn’t happening, allelic frequencies is going to change.
Genetic drift
variation in the relative frequency of different genotypes in a small population, owing to the chance disappearance of particular genes as individuals die or do not reproduce
The rate of fluctuation (in genetic drift) is dependent on ____?
population size; more powerful in small populations, causing larger allele frequency fluctuations.
Selectively neutral alleles
No fitness difference between them
What is the probability that alleles at a neutral locus will become fixed?
Probability of fixation is equal to the frequency of that allele in the population at that time.
Although not sure which alleles will or won’t become fixed, it’s true that…
Every allele in a finite population will eventually be fixed or lost as a result of drift
Genetic drift will cause allele frequencies to drift causing evolutionary change in the absence of what?
Natural selection
Genetic drift effects amount of variation…
within and between populations
Example of heterozygosity and genetic drift at work
Overfishing results in loss of heterozygosity
When drift is the only evolutionary process acting on the small archipelago of small islands, what two conclusions can be drawn?
Genetic drift leading to divergence
Differences in allele frequencies and ultimately fixation of different alleles
Slippage-induced mutation
INCREASES REPEAT COPY NUMBER
When a repetitive base slides over, is not a big deal; but can help track changes as in the Galapagos lava lizard
Micro satellite marker study
Short stretches of DNA sequence in which a brief sequence is repeated several times; allows to check for subtle changes;
What occurs in the absence of gene flow during genetic drift? (divergence in Galapagos)
Should strongly influence diversity patterns. The smaller the island, the fewer microsatellite alleles
What is a good example of population division?
Limited or no gene flow between subpopulations of a larger population; Population subdivision can occur without physical barriers like behavioral differences.
Coalescent Theory
How gene copies spread through a finite (limited) population
Gene trees (2)
Genealogical relationships for a single locus
Tells the HISTORY OF THE GENE and NOT THE SPECIES/ POPULATION
Genealogical diagram
Depiction of which gene copy derived from which ancestral copy; you can trace gene copies back through time
What happens when gene copies coalesce
Two or more gene copies at some point are all descended from the same ancestral gene copy
What is the coalescent point?
The gene copy that is the most recent common ancestor of the two or more gene copies
What is a coalescent tree?
A tree that shows the branching pattern of relatedness among the gene copies in the populations
*a dead end means an extinct allele
What does coalescence strongly depend on?
Strongly depends on population demography= small populations coalescence take place quicker (because less variation to start off with since it’s small)
Any allelic differences among a set of gene copies at the same locus must have arisen from what?
Must have arisen by mutation next to the coalescent point for this set of gene copies; you can know everything about the variation in the present population
The deeper the coalescent event…
The more variation one expects to see; more populations
Variation at a locus arises by which two separate processes?
- Genealogical process by which a coalescent tree is formed (gene has to be formed)
- Mutation process by which variation arises along the coalescent tree (then randomly mutate)
Why can mutation processes be separated at a NEUTRAL locus?
Because at a neutral locus, all gene copies are equally likely to leave descendants, irrespective of their allele state (mutation process and allelic states of gene copies have no effect on the genealogical process and the shape of the coalescent tree) it’s completely random
What is the effect of RECENT selective events?
Results in a more recent coalescent point and less neutral variation
What happens to newly arising neutral alleles?
They will be LOST rather than fixed; because Natural Selection acts on variation, so if there’s none in neutral alleles, they’ll be lost
What happens in balancing selection?
Able to maintain 2 alleles; both alleles persist indefinitely as a balanced polymorphism maintained by selection
Positive Selection
Quickly replaces the ancestral alleles as a result of Natural Selection
Neutral mutation
SLOWLY replaces the ancestral allele by drift
Demography
Study of distributions of populations
Biogeography
Study of distributions of species
Drift
random fixation of different alleles
Population bottleneck
Brief period of small population size can affect allele frequencies significantly. Usually the surviving population will have much less variation than the original population
Genes found in a founder population usually only represent what fraction of the alleles present in the main population? What then happens to these genes?
Small fraction; These genes in the founder pop. then become much more common.
Founder effect in Island populations are very important
How is the loss of heterozygosity due to DRIFT balanced by?
Balanced by the gain of heterozygosity due to MUTATION
How are selection and drift related in evolutionary change?
They are NOT mutually exclusive modes of evolutionary change (they can happen at the same time)
Are favored alleles guaranteed to become fixed in a population?
No, or we’d all look alike
What model of selection did Motoo Kimura show? (mathematically showed)
Interplay between selection and drift depends on the strength of selection and the population size:
- If population is large, then selection is weak.
- If population is small, then selection is strong
If selection is STRONG and population size is LARGE, what largely determines the change in allele frequencies?
SELECTION largely determines the change in allele frequencies
If selection is WEAK and population size is SMALL, what largely determines the change in allele frequencies?
DRIFT largely determines the change in allele frequencies
What does Neutral theory explain?
How DNA and RNA sequences change over time; ubiquity of molecular variation; why molecular variation in populations is very common.
Problems that Neutral Theory addressed?
If there is so much variation, natural selection can’t be the whole explanation. There isn’t enough natural selection occurring to account for the amount of observed variation.
What does neutral theory contradict?
Selection may not be acting on this variation
Neutral theory of evolution proposes what two things, at the molecular level of DNA sequence or amino acid sequence?
- Most of the variation present within a population is selectively neutral
- Most of the changes in DNA or AA sequence over time and thus many of the molecular differences between related species- are selectively neutral.
According to Neutral Theory, what process does it suggest is responsible for change in DNA sequences over time, other than Natural Selection?
Neutral Theory suggests genetic drift is the process.
What are Allelic Substitutions? When does it occur?
The rate at which new alleles become fixed in the population;
A substitution occurs when a new allele arises by mutation and is thereby fixed in the population. (substitutions over generations)
What is an important distinction Neutral Theory proposes?
Neutral Theory proposes that most substitutions are neutral, NOT that most mutations are neutral. (Most mutations are deleterious and will be removed from the population.
What is the Naturalist-Selectionist debate?
NOT a dispute about the effects of typical mutations, instead, it is a dispute about WHETHER DRIFT OR SELECTION is the primary driver of evolutionary change in that subset of mutations that reach a high frequency in populations.
What are the three biological reasons why allelic differences might have no fitness consequences? (reasons for selective neutrality)
- Synonymous substitution
- Many molecular changes don’t cause changes in phenotype
- Degeneracy of the genetic code
Non-coding regions (in eukaryotes)? What effect do mutations in these regions have on fitness?
In eukaryotes, only a small fraction of the genome encodes proteins. The rest if the genome is untranslated, left for enhancers/regulatory elements)
Many mutations in untranslated regions will have minor effects or none on fitness
What is a pseudogene? What’s special about mutations on these genes?
Nonfunctional and typically untranslated segment of DNA that arise from previous functional genes via gene-duplication; subject to neutral drift.
Mutations in pseudogenes tend to be neutral and accumulate rapidly.
What is retroposition? What does it lack? (from pseudogene slide)
mRNA from a funcitonal gene is reverse-transcribed by a retrotransposon and is inserted into the genome.
These often lack regulatory regions (such as a promoter) and WILL NOT BE EXPRESSED
What is deactivation? (from pseudogene slide)
Genes become pseudogenes without leaving behind a functional copy. Mutations accumulate and the gene becomes inactivated.
What is effective neutrality?
A mutation that does not have an effect on function and fitness because they’re sufficiently SMALL.
(You can only detect this if there’s a high transversion rate *from notes)
Molecular clock theory
Hypothesized that molecular evolution proceeds in a clocklike manner with AA sequences changing at a constant rate over time, and at the same rate in different lineages
Genetic equidistance principle, which is found in AA cytochrome c sequences, states…
If molecular evolution proceeds at the same constant rate over time in different lineages, all members of a clade should be genetically equidistant from an outgroup to the clade.
Do most molecular evolution exist in clocklike manner?
Turns out not to be the case; in primates mt DNA and nuclear DNA evolve at very different rates
Where do most of the differences accumulate after two species diverge?
At sites that were identical
For any particular gene, what happens to the number of substitutional differences between two lineages?
Will not increase indefinitely with time
As time PROCEEDS, differences are likely to accumulate where?
At the site that already differs; these changes don’t “increase” the amount of genetic divergence so rate of divergence will decrease.
Saturation results
Not going to accumulate changes; a sequence that has become saturated with substitutions and further substitutions will not be detected.
Why are silent third-codon positions good for looking at short evolutionary changes?
Changes often and quickly becomes saturated
What does neutral theory predict about species with similar mutation rates?
Neutral theory predicts a constant rate of synonymous substitution per generation.
What does empirical data suggest about the rate of synonymous substitution?
The rate is approximately constant per year despite differences in generation time across taxa; rat and elephant are examples
Why is it that the mutation rate/base pair is similar in long and short generation species?
Neutral theory; most substitutions are neutral/ mildly deleterious. So fate is determined by interplay between selections and drift (balance).
What does N.T. predict about substitution rate and population size?
It is independent of population size while the nearly neutral theory predicts that substitution rate is higher in smaller populations, where mildly deleterious alleles can drift to fixation.
