EHJ352H1 Lecture Notes - Lecture 5: Mutation Rate, Single-Nucleotide Polymorphism, Genome Size

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Lecture 5: Evolution of Genome Complexity
What would a simple genome look like:
1. Just the protein coding genes ( and a minimal amount of additional regulatory DNA)
2. Protein coding genes not separated into pieces (exons) by other sequence (intron)
Gene number varies much less than gene density: Gene number is the amount of functional
genes, and that does not vary as much. Humans have 24000 and yeast has around 6000.
However humans gene density is a lot less than yeast since humans has a larger genome size
Variation in genome size and complexity is adaptive?
Maybe smaller organisms need to be able to replicate their genomes more quickly
1. Adaptive hypothesis: Larger organisms need larger genomes to adapt as a direct
response to selection
2. Non-adaptive hypothesis: The organisms get bigger physically due to adaptation,
and as a result their genomes also get larger (the latter is a non-adaptive
consequence).
Mutation Pressure:
Gains of sequence are more common than loss of sequences (transposable
elements)
Lynch argues that there is an insertional bias although data are somewhat mixed
Dangers of a larger genome:
1. Metabolic costs of DNA: energy is needed to replicate DNA
2. Increased mutational target size:
Non-functional neutral DNA can be target for deleterious “gain of function
“ mutations
Transcription factor (TF) binding motifs are under-represented in non-coding
regions, presumably as a result of selection
Insertion of TEs in non-coding regions often alters expression of neighboring
genes
Alpha-thalassemia
Human blood disease resulting from two few globins
Affected individuals have Single Nucleotide Polymorphism (SNP) in non-coding
region
SNP creates a new promoter-like element that interferes with normal activation of
all downstream alpha-like globin genes
Why are there still harmful mutations around? That could be because selection may often
be weak and effective neutrality happens if l4NeSl << 1
Lynch’s Hypothesis:
There is directional mutation pressure to increase genome size
Small increases in genome size are deleterious but very weakly so
Increases in genome size are more likely to be effectively neutral with smaller Ne since
selection is weak
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After genome sizes got larger, more complex patterns of gene regulation were able to
evolve
Mutation and drift both play a key role
Mutation pressure is the source of excess DNA
Drift reduces the efficiency of selection
Predicts that genome size and complexity should be positively correlated with mutation
rate
Predicts that genome size and complexity should be negatively correlated with Ne
It is more important for E coli to replicate their DNA than elephants
More bacteria than mice
Larger organisms tend to have lower Ne and less density
Ne estimated from silent-site diversity within species
Genome size and complexity should be positively correlated (since both results in lower Ne
and more mutation rate)
Evidence for Lynch’s Hypothesis:
Predicts genome size should be positively correlated with mutation rate
Predicts genome size should be negatively correlated with population size
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