Topic 7 Flashcards
(27 cards)
1
Q
mutation
A
- Mutation is the ultimate source of all variation within populations; without mutation there can be no variation, and no evolution.
- The fate of new mutations will depend on other factors, such as selection and genetic drift.
- Mutation is defined as any heritable change in DNA sequence, or DNA compliment (eg number of chromosomes)
2
Q
somatic mutations
A
- mutations in somatic cells, (e.g., your arm) that are not heritable, and hence are of no evolutionary consequence
3
Q
germline mutations
A
- occur as gametes are being produced, or in the cells that produce them and can be passed on to offspring.
4
Q
chromosomal mutations
A
- Changes in the number or structure of chromosomes
5
Q
inversions
A
- backwards sequence of DNA
- often caused by ionizing radiation
6
Q
polyploidization
A
- Some organisms have more than two sets of chromosomes and are referred to as being Polyploid. This can include tetraploids, Octoploids and so on.
- Polyploidy has been very important in the evolution of the flowering plants. It is less common in animals.
7
Q
why is polyploidy important
A
- It can result in new species being formed
- Doubled chromosomes can gain new functions, increasing potential for adaptation
- Important source of genetic variation in natural populations- especially plants
8
Q
point mutations
A
- Point mutations are single base pair changes e.g., G to C
- Two types: transitions and transversions
- Transitions are more common than transversions
- Point mutations can be synonymous (e.g., do not change amino acid) or non-synonymous (amino acid replacement)
- Many mutations are silent (synonymous) because of genetic code redundancy
- The substitution of a purine with a purine, or a pyrimidine with a pyrimidine is a transition
- The substitution of a purine with a pyrimidine or vise versa is a transversion
9
Q
Indels
A
- insertions and deletions
- These can be caused by a few different means, replication slippage, transposition etc. In coding regions, they can disrupt the reading frame and be highly deleterious
10
Q
gene duplication
A
- Often, genes, groups of genes or pieces of a chromosome can duplicate. This has been an important mode of evolution.
- For example, the major histo-compatibility complex is an example of a multi-gene family that has arisen by duplications. Duplications have been an important source of evolutionary novelty
- can result in: Loci that retain their function, gain a new function or become a pseudogene, and importantly, has also resulted in the evolution gene families
11
Q
paralogous
A
- Genes that are duplicated within a genome and diverge in function such as the hemoglobin genes
12
Q
orthologous
A
- Genes that share a common ancestral sequence, and are separated by a speciation event
13
Q
mutation rates
A
- Mutation rates can be expressed in different ways:
- For a locus: Mutations per locus/ per zygote (e.g., per generation)
- For a DNA sequence: mutations per nucleotide site/ generation (e.g., per zygote)
- Example: The mutation rate for albinism in humans is 3 X 10-5 mutations per generation (zygote). How many zygotes out of a population of 200,000 zygotes would be expected to possess this mutation?
3 X 10-5 (200,000) = 6 zygotes
14
Q
infinite alleles model
A
- The model of recurrent mutation is very useful for describing the persistence of disease-causing deleterious alleles, but it is unrealistic in certain cases. Genes consist of long strings of nucleotides, any one of which can mutate to any of the other three, and insertions and deletions can occur as well.
- This led to the development of the infinite alleles model, which assumes that each new mutation will create a new unique allele. Under the infinite alleles model, all copies of any given allele will be identical by descent by definition because each allele arises only once.
15
Q
another way to look at F (inbreeding coefficient)
A
- F gives the probability that an individual in the population is autozygous or has two alleles that are identical by descent.
- The autozygosity as traditionally defined by F is a relative concept because it gives the autozygosity relative to a non-inbred ancestral population where all alleles are arbitrarily defined as not being identical by decent (the autozygosity = zero).
- In reality, at least a portion of the alleles in the non-inbred ancestral population will be identical by descent, and the autozygosity will not be equal to zero.
- In such cases, we interpret F as the additional autozygosity that arises in the population because of inbreeding relative to the non-inbred ancestral population.
- In this course, we will always assume that we have an infinite alleles model unless otherwise stated, and all copies of the same allele (identical by state) are identical by descent.
- Under the infinite alleles model, the population homozygosity and autozygosity will always be equal, and we interpret F as the additional autozygosity that arises because of inbreeding relative to the non inbred ancestral population
16
Q
the infinite sites model
A
- With the infinite sites model, only one mutation can occur at each site in a nucleotide sequence alignment. As a result, each site can possess a maximum of two different nucleotides. This is similar to the infinite alleles model because each mutation will produce a new unique allele, but it is more conservative because there are less ways that new alleles can evolve.
- All copies of an allele will be identical by descent with the infinite sites model. As we discussed earlier, most single nucleotide polymorphisms (SNPs) are bi-allelic, and hence follow the infinite sites model
17
Q
the stepwise mutation model
A
- Microsatellite alleles mutate by the gain or loss of repeats.
- This process is described by the stepwise mutation model, where the length of alleles incrementally increases or decreases one repeat at a time via mutation.
- With this model, different copies of the same allele might not be identical by descent.
18
Q
autozygosity and homozygosity
A
- Under the infinite alleles model and infinite sites model, the homozygosity will always be equal to the autozygosity. All homozygotes will possess alleles that are identical by descent.
- Under the recurrent model and stepwise model, the homozygosity can differ from the autozygosity, and a homozygous individual can possess two copies of the same allele (identical by state) that are not identical by descent (allozygous)
19
Q
deleterious mutations
A
- these are mutations that result in lowered fitness. Selection that acts to remove or lower the frequency of a deleterious mutation is referred to as purifying selection.
- What can prevent selection from removing a deleterious mutation?:
- Continued Mutation
- Dominance Effects = Hiding in Heterozygotes
Genetic Drift
20
Q
neutral mutations
A
- Have no effect on fitness, for example silent mutations that do not change an amino acid are often (but definitely not always) neutral
21
Q
nearly neutral mutations
A
- Have very little effect on fitness, so little that they are effectively neutral
22
Q
codon bias
A
- is the non-random use of synonymous codons for a given amino acid. Most organisms only use one or two of the codons for a given amino acid.
23
Q
advantageous mutations
A
- Have the effect of increasing fitness and are rare in comparison to deleterious and neutral mutations.
- Selection that acts to increase the frequency of advantageous mutations is termed positive selection. Positive selection results in adaptive evolution.
24
Q
heterozygous (dominant) effect on fitness
A
- Here, we consider allele a to be the deleterious mutant allele. Any new mutation will initially exist in a heterozygote. So, it is useful to understand fitness effects in heterozygotes.
As it turns out, there is generally an inverse relationship between h and s. The larger s, the smaller h.
25
mutation selection balance
- Selection has trouble removing mutations (deleterious) as mentioned earlier.
- Given this is the case, at what point will the removal of a deleterious allele by selection be exactly balanced by its re-introduction by recurrent mutation?
26
mutational load
- Mutation selection balance (we are ignoring genetic drift) will result in a mutational load in populations, chiefly resulting in deleterious effects.
- This load is equivalent to the reduction in the relative population fitness, and under certain circumstances, it can be quite high.
- In 1950, H.J. Muller published an important paper entitled “Our load of Mutations” and won a Nobel prize for his work.
- Muller induced mutations with X rays and was very concerned about human exposure to them, above ground nuclear testing, and other phenomenon.
27
mutation summarized
- On its own, mutation changes allele frequencies quite slowly. However, it provides the genetic variation that the other evolutionary forces act on.
