Molecular Biology & Genetics 6 - Population Genetics & Natural Selection+ Sequencing the Human Genome Flashcards
What is a population?
Localised group of individuals of the same species
What is the gene pool?
Total aggregate of genes (and their alleles) in the population at one time
Why do we need to estimate genotype frequencies?
To predict how many individuals will inherit a genetic disease and to estimate the proportion of individuals. who are carriers of a genetic disease as this can’t be observed
How do we estimate the genotype frequencies?
Using the hardy-weinberg equation
What is the hardy Weinberg equation?
p^2+2pq+q^2=1
What is p^2?
The proportion of homozygous dominant
What is 2pq?
The proportion of heterozygous
What is q^2?
The proportion of homozygous recessive
What is the allele frequency equation?
p+q=1
What is p?
The frequency of the dominant allele
What is q?
The frequency of the recessive allele
How can allele frequencies change?
By non random mating, random genetic drift, the bottleneck effect, the founder effect, natural selection, mutations and migration
What are types of non-random mating?
Assortative mating and inbreeding
What is assortative mating?
When a particular genotype is more likely to mate with the genotype the same as themselves
What is inbreeding?
Breeding with a related individual which isn’t always avoidable in smaller populations
What is random genetic drift?
A random change in the allele frequencies due to sampling error over generations
What does random genetic drift depend on?
The mating combinations and how many individuals mate
What is random genetic drift noticeable in?
Particularly in small populations
What is the result of a population bottleneck/reduction event?
Loss or decrease in frequency of some alleles and decreased genetic diversity
What is the founder effect?
A population bottleneck as a result of a new population being established
What is genetic diversity of new populations dependent on?
The founders and is often less diverse than the original population
What are the types of natural selection?
Stabilising selection, directional selection, disruptive selection and sexual selection and frequency dependent selection
What happens in stabilising selection?
The medium individual phenotype is favoured by natural selection. The peak gets higher and narrower
What is the result of stabilising selection?
Reduces variation but doesn’t change the mean
What happens in directional selection?
Larger or smaller individual phenotype is favoured by natural selection. The peak shifts in one direction.
What is the result of directional selection?
Changes the mean value towards one extreme
What happens in disruptive selection?
Large and small phenotypes are favoured by natural selection forming two peaks
What is the result of disruptive selection?
Favours two extremes producing two peaks
What is sexual selection?
When males have features (e.g. long tails/feathers) which attract females and the “better” this is the more likely they are to attract a female
What is frequency dependent selection?
The rare (low frequency) individual obtains more food and becomes more common but then the other individual does better and balances this effect out
What is a mutation?
Very slow to act and usually disadvantageous, its role is usually of macroevolutionary proportions
What is migration ?
When an individual from another population successfully mates and contributes gametes to the gene pool
What are the results of migration?
Bringing new alleles, changing proportions of existing alleles, changing population size, making two populations more similar
What is cline?
The gradual geographic change in genetic/phenotypic composition
When did the human genome project begin?
1990
What did the human genome project aim to identify?
All human genes and their roles
What did the human genome project aim to analyse?
Genetic variation between humans
What did the human genome project aim to sequence?
The genomes of several model organisms used in genetics
What did the human genome project aim to develop?
New sequences and computational analyses
What did the human genome project aim to share?
Genome information with scientists and the general public as fast as possible
What is a genome?
A complete set of DNA of an organism, including all its genes
What is genomics?
The study of genomes
What does nuclear DNA consist of?
22 autosomes, X and Y
What does mitochondrial DNA consist of?
Single, circular DNA
How many base pairs in nuclear DNA?
6 billion
How many base pairs in mitochondrial DNA?
16,569
Where does nuclear DNA come from?
Half from each parent
Where does mitochondrial DNA come from?
All from the mother
How many genes in nuclear DNA?
<21,000
How many genes in mitochondrial DNA?
37 genes
What is the human reference genome made up of?
Lots of different people
What were some of the key findings of the human genome?
There are fewer genes than expected, the genome is dynamic, most human genes are related to those of other animals
What do we still not know about the human genome?
What many of our protein coding genes do
How similar are humans?
All humans are 99.9% similar at sequence level
How much of the genome codes for proteins?
Less than 2%
How much of the genome codes for introns?
20%
How many genes have unknown function still?
About 25%
While any two human genomes are 99.9% similar…
across the population, there is a lot of variation and it is important (for natural selection)
What are single nucleotide polymorphisms (SNP’s)?
Sites in the DNA that commonly vary within populations- common single base pair changes or variants
How many SNP’s are there?
1.9 million
How common are SNP’s?
common- around 1 in every 300 nucleotides
Where do SNP’s come from?
Mostly from parents (half from mother and half from father)
What does each genome sequenced do?
Adds to the variation on record
What does diversity in genome sequencing do?
Adds to the knowledge of variation
What do many SNP’s do?
The don’t do anything, they are just inherited variations but that doesn’t mean they’re not useful
What can genotyping tell you?
Who you are related to, where (some of) your ancestors are from, disease risk/association, if you will lose your hair, your muscle type, how you might respond to drugs
What can genotyping also be used for?
In crime solving
What do some of our SNP’s reveal?
Our species ancestral interbreeding with other hominins
Where are linked SNP’s found and what do they do?
Found outside of a gene and have no effect on protein production or function
Where are causative SNP’s found?
In the gene
What are the two types of causative SNP’s?
Coding SNP’s and non-coding SNP’s
What do coding SNP’s do?
change the amino acid sequence and therefore the protein produced
What do non-coding SNP’s do?
change the amount of a protein produced
What happens if the second or third base is the SNP?
they are less likely to affect the amino acid, protein and therefore phenotype
What are short tandem repeats (STR’s)?
Repeats of 2-5 nucleotides found in specific regions of the genome
What does each person inherit with respect to STR’s?
2 alleles, one from each biological parent, which can be different lengths
What can STR’s be used for?
To create genetic profiles or “DNA fingerprints”
What are indels?
small insertions or deletions
Are insertions or deletions more common?
Deletions
What is the second most common variant type in the human genome?
Indels
How many indels are there?
0.2 million
What can indels cause?
A frameshift which is a change in the way DNA is read if in protein coding regions
What are copy number variations?
Chunks of DNA >500 base pairs that are present at different amounts or “copy numbers” relative to a reference genome
What can copy number variants be?
deleted or duplicated
What can copy number variations do?
Span multiple genes
How many CNV’s do humans have?
10,000 found within and between genes
What are many genes in CNV’s associated with?
Sensory perception and immunity
How many large CNV’s are there and how many genes do they affect?
23 and they effect 34 genes
