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90 Cards in this Set

  • Front
  • Back
The genetic variation that natural selection and other evolutionary forces act on originates in?
What is the only evolutionary force that creates new alleles and genes?
The instructions for making and maintaining an organism are enclosed where?
In the DNA
Which strand of the DNA is transcribed, the coding or non-coding strand?
What is the result of a mutation in the hemoglobin?
The mutation is a result of a mutation in position 6 of the nucleotide sequence, altering in nucleotide 2(A) to 2(T).

Wild Type-GAG,GAA-Glutamate
Mutant- GTG, GTA-Valine
How are point mutations created?
Either by random errors in DNA synthesis or random errors in the repair of sites damaged by chemical mutagens or high energy radiation.
Why are transitions said to occur more often than transversions?
Because transitions cause much less disruption in the DNA helix so they are less likely to be recognized as errors and therefore less likely to be immediately corrected by DNA polymerase or later by mismatch repair enzymes.
What type of point mutation leads to sickle cell disease?
A transversion leading for A going to T.
Point mutations that results in an amino acid chage are called __________ ________.
Replcaement sibstituions (nonsynonymous)
Point mutations that result in no change are called ___ ___ ______
Silent site substitutions (synonymous)
Do the synonymous or nonsynonymous substituions create new alleles?
They both do.
Why was the traditional method of estimating mutation rates revamped?
Because the old method simply took large populations and counted the number of offspring that had observable mutant phenotypes in each generation. But all this simply did was count the observablemutant phenotypes due to loss of function mutations (change in DNA that inactivate a gene or lead to a complete loss of gene product).

The silent type mutations would go un detected and the new alleles created by these types of mutations go completely uncounted in traditional surveys.
What was a result of the traditional method in which mutation rates were obtained?
Mutation rate were scaled for generation time and reported on a per-genome, per cell-division basis, and all organisms seemed to have a roughly equal mutation rate. It seemed Natural Selection had led to a single, common mutation rate.
When Denver et al was obtaining a direct estimate of mutation rates using C. elegans, what was done to minimize the amount of natural selection and mutations that may occur in each line?
They made possible:
optimal temperature and humidity, minimal crowding, abundant food and no predators or parasites
How did Denver et Al get an estimate for mutation rates when the C. elegans had reproduced?
They sequenced tens of thousands of base pairs of DNA from the founding individual and from each of the 50 lines derived from that individual at generations 280,353, and 396.
Does nuclear DNA or Ribosomal DNA have a higher mutation rate?
Mitochondrial, because there are less DNA repair enzymes found in the nucleus.
When Denver et Al were studying the mutation rates in C, elegans, what mutations made up more than half of the 30 mutations detected?
More than half consisted of indels, small numbers of bases inserted into or removed from the genome
Understanding that DNA replication and repairing rarely make mistakes, one can assume what concerning selection?
The enzymes involved with DNA repair and replication are under intense selection
What example given in lecture presents an opportunity where a type of mutation, decreases the mutation rate of a DNA poly?
This is seen in T4. The single base substitution will decrease the rate at which the polymerase makes errors during DNA replication, thus reducing the overal mutation rate.
Mutants that increased _______ are slower than more error prone _______. This is discussion on how DNA polymerases have been seen to vary in accuracy.
Accuracy; mutants
When might having a higher mutation rate be a positive effect on an organism?
When organisms are colonized in new environments to which they are poorly adapted or when rapid copying of genes is advantageous.
If mutations accumlate what usually is affected?
The organisms fitness will decline, as well as, longevity and production of offspring.
The difference in fitness between each experimental population and the control.
Most mutations are only midly deleterious- each mutation reduces fitness by only about 2% when _____.
Most of the new alleles created by mutation are quickly eliminated from the population by natural selection. This is because?
Mutation accumulation.
When can silent mutations be subject to natural selection?
Codon bias
What is gene duplication?
Gene duplication (or chromosomal duplication or gene amplification) is any duplication of a region of DNA that contains a gene; it may occur as an error in homologous recombination, a retrotransposition event, or duplication of an entire chromosome
How are DNA double helixes stabilized?
Hydrophobic interations and hydrogen bonds
What is the result of a mutation in the hemoglobin?
The mutation is a result of a mutation in position 6 of the nucleotide sequence, altering nucleotide 2(A) to nucleotide 2(T)
With hemoglobin the alpha like clusters are on chromosome __ and the beta like clusters are on chromosome __.
Why is hemoglobin thought to be a product of gene duplications?
Due to the length and position of the exons and introns among the globin genes. Also due to the high sequence similarity among globin genes and their similar function.
It is believed that an ancestral gene was duplicated several times during evolution. IN several of the new genes, mutation changed the function of the _______ ______ in a way that was favored by natural selection, leading to the formation of a gene family
Protein Product
Do all gene duplications result in sequences that evolve different functions or no function?
No, for example in rRNA genes, multiple copies of the same gene have an identical or nearly identical base sequence and produce a product with the same function as the ancestral sequence.
Duplicated genes are homologous to the same common ancestral sequence. True or false?
What are paralogous genes?
They are duplcated and then diverge in sequence within a species, like alpha and beta hemo in humans
What are orthologus genes?
They diverge after speciation, like the a and b genes in horses and humans.
_______ are homologous genes found in different species and can be used to estimate the degree and timing of divergence among species.
________ form gene familes and are an important aspect of genome structure and function.
Where did the neutral theory see its original problem?
There was a high rate of molecular evolution and it was constant through time. This did not match natural selection since natural selection isn't based time but is rather episodic and correlated with changes in the environment. Allso under natural selection mutation rates shouldn't be high. This showed natural selection could not be responsible for most evolutionary change.
Explain the neutral theory of molecular evolution?
At the heart of the theory is molecular evolution is equal to the mutation rate.

N-population size
2N-alleles of the locus of interest
v-rate of selectively neutral mutations per allele, per generation.
Also you must assume that each mutation creates an allele that has not existed previously in the population.

There will be 2Nv new alleles created by mutation each generation.

Each new allele has same chance of drifitng to fixation, frequency of new allele=1/2N

Therefore, each generation the number of new alleles that are created by mutation and are destined to drift to fixation is:
2Nv * 1/2N=v
v is then the rate of evolution at the locus of interest
Why is it ok to say genetic drift is the process at work in the neutral theory of evolution?
Because we assume that all new alleles are selectively neutral
Why was Kimura's theory alarming?
Because size of population had no role

Positive natural selection is excluded
What proved the neutral selection theory?
The evolution of pseudogenes, since these are neutral, they should have a high level and go to fixation.
2Nv equals what
2Nv equals the new alleles created by mutation each generation.
In the neutral theory, since we assume that new alleles are selectively neutral, what is at work here?
Genetic drift
Each new allele has the same chance of drifting to fixation and the chance is equal to the frequency of a new allele, equation=?
What is v?
The rate of selectively neutral alleles per allele per generation.
Besides the pseudogenes what else proves the neutral theory of evolution?
Silent sites change faster than replacement sites; showing neutral mutations have a higher rate of molecular evolution.
What was the nearly neutral theory of evolution trying to address?
The fact that v should be very reflective of generation size, but it was not. It is expected with shorter generation size, there should be more neutral mutations. This wasn't seen as some protein sequences were seen to undergo some clocklike evolution, independent of generation size.
Given the problems with the neutral theory of evolution, not corresponding with generation size, what was postulated?
That nearly neutral mutations must effect phenotypes and with this these mutations can depend on either selection or drift, depending on population size.
Species with long generation times, usually have a _____ population size.
What does the nearly neutral model of evolution state?
That drift fixes a larger percentage of mutations in organisms with small pop sizes. Hence an increase in evolutionary rate due to the fixation of nearly nuetral mutations in small-population, long generation species offsets the higher mutation rate in short generation species and results in the molecular clock.
Where are the more mutations, short generation time or long generation time?
Short, few are effectively neutral because population size is large.

Long generation time, there are few mutations on a per year basis. Many are effectively neutral, because pop size is small.
Using the rate of nonsynonymous substitutions (dn) and rate of synonymous substitutions (ds). Give the ratios when replacements are neutral, adv, and deleterious?
dn/ds =1
When sequences evolve by drift and negative selection, _______ ______ will outnumber _______ _____
synonymous substituions
replacement substituions
What test is more sensitive method for detecting positive selection?
The McDonald-Kreitman test
What is at the heart of the MK test?
The ratio of replacement to silent mutations between species should be the same as the ratio of nonsynonymous to synonymous polymorphisms in within-species comparisions.
What explains why synonymous mutations may not accumulate as quickly as pseudogenes?
Codon bias and other synonymous mutations may experience selection as a result of their effects on mRNA stability or exon splicing.

Also hitchhiking
What is hitchhiking?
Strong positive selection acts on a particular amino acid change.Neutral or even slightly deleterious mutations closely linked to favarable site will increase in frequency along with the beneficial locus.

This only occurs when recombination fails to break up the linkage between hitchhiking sites and the site that is under selection.

Hitchhiking usually results in reductions in polymorphism.
What is the difference of microevolution and macroevolution?
Microevolution is bio evolution that occurs within individual species, such as change in beak shape, form of an enzyme, selection for a flower color.

While macroevolution is refered to changes in organisms which are significant enough that, over time, the newer organisms would be considered an entirely new species. Macroevolution includes:
Classification and phylogenetic reconstruction
Uses phylogenies to understand coevolution
Fossil record
What is the difference between strong and weak inference?
Strong inference: testing hypothesis under carefully constructed control factors.
Causation can be inferred wwith a high degree of confidence.

Weak inference:
Testing a hypothesis when experiments are not fully controlled.
Can lead to false inferences due to correlation.
True or False?
Saturated fats are less energetically expensive and produce and yield less energy than unsaturated
False, yield more
Unsaturated fats have much ______ mp than saturated fats
Germination temp are ______ at ____ latitudes and altitudes
The morphospecies concept is the careful analysis of phenotypic differences. What are the benefits of this?
Define species that are extinct, living, or species that reproduce sexually or asexually
What is the difficulties of the morphospecies concept?
Small organisms
Fossils that differed in characters that aren't preserved
Populations that are similar in morphology but differ in other characteristics (habitat use, courtship display,drought tolerace)-cryptic species
Under the biological species concept the criterion for identifying evolutionary independence is reproductive isolation.
What is the strength of the biological species concept?
Reproductive isolation is a meaningful criterion for identifying species because it confirms a lack of gene flow
What are negative to bio species?
If populations don't overlap, there is no way to know they are reproductively isolated.

Inability to test fossil forms

No meaning in asexual population

Hard in many plant groups where hybridization between strongly divergent populations is routine.
How do phylogenetic species concept and monophyly intertwine?
The phylogenetic species concept uses monophyletic groups, groups defined as lineages that contain all of the known descendants of a single common ancestor.

The species are then defined by using the closely related populations and finding the smallest monophyletic groups.
What species concept can be allied to any type of organism, sexual, asexual, fossil?
Phylogenetic species concept
What is a negative of the phy species concept?
It takes a lot of time, money and careful anaylsis
What is good and wrong with the recognition species concept?
Good-provides a role for sexual selection in speciation (its like bio spec concept, the emphaseis is on what causes the species to chose each other as mates rather than what isolates them from other orgnaisms)

Organisms that release their gametes into the air or water
Use vectors to move their gametes
Where is the cohesion mechanism seen?
Recognition species concept
What are usually the three steps that lead to speciation?
1. An isolation in populations
2. Divergence in traits such as mating system or habitat use
3. A step that produces reproductive isolation
The first two steps of speciation was thought to occur over extended time while the populations were located in different geo area AND the third happens when they come back together, but what happens?
The first two steps can occur together in the same place and the third may never happen.
Gene flow tends to homogenize gene ________ and reduce differentiation of populations
Geographic isolation can be made by what?
Dispersal and Colonization
Besides physcial isolation, how else might there be a barrier to gene flow?
Sympatric speciation, polyploidization.
Also this polyploid may lead to other characteristics such as flower shape and the timing of flowering will be different.

There also, besides polyploidy, might be an increase in chromosome number.

Genetic drift and natural selection

Sexual selection
What are the two evolutionary forces that play a part in divergence?
Genetic drift and natural selection.
Genetic drift is powerful because?
Random fixation and random loss of alleles
What has been the problem with saying genetic drift is a major cause of divergence
It has been shown that in bottleneck only very rare alleles are lost.

GD must work in extremely small populations and the population must remain small for a sig time.

Lots of small pop have been introduced but few dramatic changes in genotype and no speciation events have resulted.
What is the result of secondary contact, or what can occur?
The diverged species that hybiridze can now have a lower fitness than the parental species

Develop new characteristics and create a new population

May thrive and interbreed with parental erasing the previous divergence
If a hybrid species occupies a new habitat than either of the parents, is there a chance that they will have a higher fitness than both of them?
Yes, and they may make new species
What is a hybrid zone?
The hybrid zone is a region where interbreeding between diverged pop occurs and hybrid offspring are frequent.
When are hybrid zones usually produced?
When secondary contact occurs between species that diverged while allopatric.
What determines the type of hybrid zones that are formed and eventual outcome of the populations that hybridize?
The fitness of hybrid individuals
When the fitness of hybrids equals to parental species, hybrid zones are:
Hybrid zone is _____
Allele frequency change are dominated by ____
Individuals with hybrid traits are found at high frequency at the ________ of the zone.

The width of the zone depends on how far indv.from each pop are disperesed each generation and how long the zone has existed.
When the fitness of hybrids lower to parental species, hybrid zones are:

Hybrid zone depends on the strength of selection against ______; if selection strong and reinforcement, hybrid zone is ______ and short lived.
When the fitness of hybrids higher to parental species, hybrid zones are:

The fate of the hybrid zone depends on the extent of ________ in which hybrids have an advantage.

If hybrids achieve higher fitness in eviro outside the ranges of parental species, then a new species may form in the new habitat.