APS11006 Principles of Evolution- Slate Lectures Flashcards
First theory of inheritance
- Jean Baptiste de Lamarck (1744-1829)
- Inheritance of acquired characteristics
- WRONG
Causes of mutations
- Tend to be spontaneous but can be induced
- Radiation, UV, X-Rays
- Mutagens, any agent that increases mutation rate
- Disasters such as Chernobyl provide a ‘natural laboratory’ for testing the effects of radiation on mutation rates across Western Europe
Karyotype
-Number or organisation of chromosomes in an individual
Polyploidy
- More than diploid
- Dispermy occurs when two sperm simultaneously fertilise egg, resulting in 3 complete sets of chromosomes, happens in 1-3% conceptions, always lethal
- Bacteria usually monoploid
- Plants can be diploid, tetraploid, hexaploid…
Aneuploidy
- One set of chromosomes is incomplete (missing or extra)
- On autosomes can be nullisomy (both missing, lethal), monosomy (one missing, lethal in humans) or trisomy (one extra, usually lethal)
- On sex chromosomes, missing chromosome (45X, turners syndrome, causes infertility, 45Y inviable), extra chromosomes (minor effects, reasonably common)
Translocations
Exchange of parts between non-homologous chromosomes, evolutionary dead end
Deletions
- Part of chromosome missing
- Consequence depends on size
- Deletion on chromosome 5, Cri-du-Chat syndrome
Inversions
- Chromosome breaks during replication but is repaired in different order
- Paracentric doesnt include centromere, no problems in meiosis
- Pericentric inversions include centromere, possible meiosis problems
Human genome length
3 billion base-pairs long
Codon
- Three nucleotides
- Specifies one amino acid
- An amino acid can be encoded by more than one codon
- Start (met) and stop codons
Organisation of human genome
- 20-30,000 genes
- 1.5% encodes proteins, most conserved
- 3% regulate protein expression, highly conserved
- 45% caused by transposons
- 6.6% not transcribed
- 44% non conserved, repetitive DNA, regulating DNA and structure and folding
DNA substitutions
- Most common mutation form
- E.g., CAT<>CAC, switching of one base to another
- Can be silent or synonymous, CAT and CAC both code for histidine, however CAA and CAG code for glutamine
DNA insertions and deletions
- Indels
- Causes change in amino acid from indel onwards
- Serious consequences, different protein is encoded
Albinism
- Caused by a single substitution in codon for tyrosinase
- Stops melanin production in gorillas
Sickle cell anaemia
- Caused by mutation from GAA to GTA in the haemoglobin beta gene
- GAA codes for glutamic acid, and GTA valine
- Valine causes individuals to have sickled red blood cells
Single nucleotide polymorphisms
- 100,000,000 SNPs discovered in humans
- Non-coding region mutations
- Around 3% of genome contains polymorphisms, leading to variation amongst individuals
Satellite DNA, or simple tandem repeats
- Nearly always harmless
- Sequences with repeated parts
- Widely used in finding disease genes, conservation genetics, evolutionary genetics, agricultural improvement
Pisum sativum
- Garden pea
- Wide variety of phenotypes
- Single gene, readily available
- Short generation time
- Self-pollinates (true breeding)
Cross-pollination
- Anthers removed before they shed pollen, stops self-pollination
- Transfer pollen by brushing
Chi-square goodness-of-fit test
- X^2 = sum of (((O-E)^2)/E)
- Degrees of freedom = categories - parameters - 1
- Null hypothesis always that O and E are good fit
- To reject null when df = 1, chi-square must be greater than 3.841
Exceptions to independent assortment law
-Two genes physically proximate on same chromosome do not assort independently
Mendel-Fisher controversy
- Ratios were always very close to expected
- Probability of this is 7x10^-5
- Fisher attributed the alleged forgery to an unknown assistant
Mendelian or monogenetic disease
One gene involved
Multifactorial or polygenic disease
- Many genes involved
- Most diseases
Pedigrees
- Show several generations
- Used to infer mode of inheritance or genetic counselling
Consanguineous
-Inbreeding
Autosomal dominant diseases
- Achondroplasia, form of dwarfism
- Polydactyly, extra digits
- Hairy mid-digit
- Widow’s peak
Autosomal recessive diseases
- Carriers and non-carriers indistinguishable without genetic testing
- 2 carriers mate, 1 in 4 chance of affected offspring, 1 in 2 carrier
- Albinism, sickle cell disease, cystic fibrosis, attached ear lobes
Cystic fibrosis
- Two inactive copies of the CFTR gene (CF transmembrane conductance regulator)
- Large gene, lots of mutations, some more severe
- Most common is at codon 508
Examples of x-linked recessive disorders
- Duchenne’s muscular dystrophy
- Red-green colour blindness
- Haemophilia
Lyonization
- X-inactivation
- In each cell of females, one X chromosome is randomly inactivated
- Occurs early in development
- Some cells express one X, others will express the other
How many genes do humans have?
Around 20,500
Recombination/crossing over
- Non-independent assortment of linked genes
- Closer the genes together, less likely to cross over
Recombination fraction
- Recombinant individuals/total individuals
- Measure of distance between two genes in centiMorgans
Loci
Physical position of a gene or genetic marker along chromosome
Estimating allele frequencies example in scarlet tiger moth (Panoxia dominula)
- Three forms controlled by 2 alleles A1 (p) and A2 (q)
- Sample of 18,385 moths, 17,062 were A1A1, 1,295 A1A2, 28 A2A2
- p + q = 1
- Number of A1 alleles is (2 x 17,062) + (1,295) =35,419
- A1 frequency = 35,419/36,770 = 96.3%
- A2 = 1 - 0.963 = 3.7%
Hardy-Weinberg equilibrium
- p^2 + 2pq + q^2 = 1
- Assumes random mating, no natural selection at that gene, a large pop size, no migration, no mutation
- Useful as it provides description of how genetic variation is maintained in population
