Genetic Mechanisms Of Morphological Change Flashcards
Genetic mechanisms of morphological change
Finding the mutations that matter
Key qs under genetic mechanisms of morphological change
1) how important are “gene duplication” mutations
2) where in genes do key mutations occur? Exon vs cis-reg
3) reproducibility? Does convergent evolution use the same mutations?
4) can we track a pathway of mutations?
Do extra genes facilitate evolution?
- TG and WGD
TD
- v.Common
- 2v similar genes near each other in genome (pair wrongly @ meiosis)
- crossover in/near gene generated gametes w/ 3 copies/ 1 copy
TD: can start from one gene
- If there are TEs nearby
- 1 gene becomes 2/0
WGD
- evidence is in genome sequences
- e.g. human C13
- e.g. pufferfish C6&7
2R
- at the base of the vertebrates
- v. Important for structure of human genome
3R
At the base of the teleost fish
4R
In a few !
Seed plants
Ancestral polyploidy events
Possible consequences of gene duplication (can confound phylogenies)
- Nonfunctionalisation
- Subfunctionalisation
- Neofunctionalisation
Ortholog
Same gene, different sp.
Paralog
Different gene by duplication
Ortholog v paralog
Not always easy to work out due to
- gene loss
- gene conversion
Exon
Altered protein function
Cis-regulatory change
Altered time/place of expression
Methodology
1) breeding expts (aka trait mapping)
2) wild pops
3) domesticated sp.
Sliding Hox gene expression
- cis-regulatory elements near Hox clusters?
- changes to an upstream TF
Breeding experiments (aka trait mapping)
- need a breedable species w/ variation
- find a DNA variant inherited precisely w/ trait of interest
- co-segregation
Three-spiked sticklebacks (Gasterosteus aculeatus)
- ancestrally marine
- invaded freshwater when ice sheets retracted
- each pop evolved adaptations to the new habitat
- e.g. smaller spines
F1 gen
Boring! Virtually all the same
F2 gen
= 100s
- Some spiny, some not
- genotype by PCR/SNP arrays/sequencing
- co-inheritance of polymorphism and phenotype
Small spines map to
the tip to of chromosome 7, next to Pitx1
Pitx1 in 3-spine sticklebacks
- known limb/fin developmental gene
- coding sequence = identical
- expression pattern = different
- deletion removed enhancer region (independent across pops)
- KO mice: smaller; asymmetrical: left leg not reduced as much (bias)
- KO in fish: asymmetrical fins
Pitx2
- partially compensates Pitx1 KO
- left expressed (R gene)
Nine spined stickleback (Pungitius)
- different Genus
- also evolved some pops lacking pelvic spine
- also moved into freshwater occasionally
- is it the same gene?
Three x nine-spine stickleback interspecific cross
- mutations do not complement each other
- infertile hybrid has no spiky fin
- probably same locus
- not a perfect test
Manatees
- mammals
- Pelvic retention more L than R
Investigating manatee F1 hybrids
- comparing gene expt soon
- cis-regulatory behaviour is parental
- trans-regulatory (TFs), alleles change behaviour and cosegregate
Protein annotation of manatees
- compare many genomes for marine/freshwater
- sequence
- find correlating alleles
- 17%: aa change
- 41% regulatory (+42%?)
Snowshoe hares
- northern USA and Canada turn white @ winter moult photo period threshold; “winter white”
- West coast; “winter brown”
- phenotype spreading!
Scan snowshoe hare genome
- DNA variants close to Agouti gene co-segregate with unknown “winter brown” gene; likely to be Agouti allele
- cis-reg change
- jackrabbit origin
- rare interbreeding
Domesticated species
Look different due to artificial selection, but have v similar DNA
Twin-tailed goldfish
- 1000AD: domestication
- 1596: 1st twin-tail phenotype
Is there any zebrafish mutation causing
Tail twinning?
- yes, lethal!
- chordin: dorsal Bmp-antagonist in early embryo
- v. important
Candidate gene approach (no trait mapping):
- chordin: mutated in goldfish
- clone and sequence chordin from lots of goldfish strain
Candidate gene approach H
- 2 copies (ChordinA, ChordinB)
- 1 mutation: twin-tail
- 2 mutations: lethal
How to prove candidate gene approach H?
1) cross different genotypes in lab: perfect correlation!
2) rescue (inject -/- eggs w Chordin A); twin-tail
Goldfish pathway
1) duplication
2) subfunctionalisation (cis-reg)
3) mutation
