Gene Duplication, Concerted Evolution and Whole Genome Duplication Flashcards
Partial gene duplication
One portion of gene is duplicated (maybe an exon)
Segmental duplication
Duplication of multiple adjacent genes
Two major mechanisms of duplication
- Unequal crossing over - leads to tandem repeats
- Transposition - leads to dispersed duplicates
Unequal crossing over
Incorrect pairing of sequences during recombination
Homologous unequal crossing over
Incorrect alignment caused by highly similar sequences matching together
Non-homologous crossing over
Incorrect paring of dissimilar sequences
Parology
Homology due to DNA duplication
Paralogs
Genes that started diverging due to duplication
Orthology
Homology due to shared vertical descent
Orthologs
Genes that started diverging due to speciation
What is the largest gene family in mammals
Olfactory gene family - humans have 400 functional olfactory receptors and 400 unfunctional
Nonfunctionalism (gene loss)
.Most likely fate of a duplicated gene
. As long as onne copy of the gene is functioning normally, the other can accumulate mutations with no fitness effect - no purifying mutation
. Final result is a non-processed pseudogene
Neofunctionalisation
.One copy of the gene gains a new function
.Freed from selection constrains, one copy can accumulate mutations that may in time confer a new mutation
.Much more rare
Subfunctionalisation
Genes that produce multifunctional products can have these functions partitioned after duplication
Invariant repeats
Identical or near identical in sequence - can be maintained by purifying selection
Variant repeats
Homology is clear, but they differ in their sequences to a lesser or greater extent
Concerted evolution - non-independent evolution of genes
Horizontal spread of mutations to all members of a multigene family - occurs by unequal crossing over and gene conversion
What does unequal crossing over result in?
A sequence duplication in one chromatid/chromosome and a corresponding deletion in the other
Gene conversion
Non-reciprocal recombination process, in which two sequences interact so that one is converted to the other - there is no deletion or duplication of material
What s concerted evolution by gene conversion typically initiated by?
Double-stranded break repair
Double Holliday junction model
gene conversion - physical exchange
What does repeated gene conversion cause duplicates to become more?
Homogenized
Unequal crossing over vs Gene conversion 3p each
- Changes gene copy number - may cause dosage imbalance
- Fluctuations in copy number less likely to be deleterious for large gene families
- More efficient than gene conversion for converted evolution of tandem duplicates
- Doesn’t change copy number
- Can act on dispersed repeats
- Can be biases- thus more likely to get to fixation
Polyploidy
Whole genome duplication
3 examples of somatic endopolyploidy in tissues
- Silk glands of silk work up to 1048576-ploid
- Mammalian liver cells can reach octoploid level
- Up to 200000-ploid in Aplaysia giant neurons
When do polyploids arise?
When a meiotic or mitotic irregularity (e.g. nondisjunction) causes the formation of unreduced gametes with more than one set of chromosomes
Characteristic of odd numbered ploidies
Almost always sterile
Two major types of polyploidy
- Autopolyploidy - doubling of the same set of chromosomes (single species)
- Allopolyploidy - combining genetically distinct, but similar chromosome sets (different species)
Autopolylploidy
Common mutational occurance in nature, but low evolutionary survival. Account for 11.5% of spontaneous abortions in humans.
Allopolyploidy
Most commonly known route to speciation - especially common in plants
Observed in asexual and sexually reproducing species of insects, fish, reptiles and amphibians
Has played a major role in plant domestication in the past 10k years
Benefits of going tetraploid 3
- Increased number of alleles for any given gene
. can mask deleterious recessive mutations
. can maintain more than two alleles per locus -
more allozymes which may allow higher fitness
values
. Higher effective population size - increase power
of selection and reduces severity of drift - Hybrid vigour - allopolyploids can show enhancement of parental trains - increase in fitness from parent
- Can disrupt self-incompatability mechanisms in plants
Some disadvantages of polyploidy
- prolongation of cell division
- Unbalanced changes in genome size
- increase in chromosome disjunctions at meiosis
- Interference with sexual differentiation, when sex is determined by ratio between sex chromosomes and autosomes
Diploidisation
Tetraploids that survive eventually revert to a diploid state through chromosomal rearrangements and gene loss
Chromosomal rearrangements
Mutations involving long DNA sequences that change the location and/or order of gene. These can occur within or between chromosomes
Synteny
Two or more genes being present on the same chromosome, though no necessary link
Palaeopolyploids
After diploidization a polyploid is called a palaeopolyploid. Can be harder to find the further back
Palaeopolyploids
After diploidization a polyploid is called a palaeopolyploid. Can be harder to find the further back
How to find a palaeopolyploid?
- Compare phylogenies for duplicated genes in the genome and estimate divergence times - do a lot of gene duplications occur at a similar time, this would point to a single major duplication event
- Look for double synteny. Two or more regions of the genome containing paralogs with shared synteny and collinearity
