genome size and complexity (as told by michael lynch)
TRANSCRIPT
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Genome size and Complexity
(as told by Michael Lynch)
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Genome size and complexity varies across the tree of life
Lynch 2007
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Some Big Questions
• What is the relationship between genomic and organismal size/complexity?
• Are genome size changes adaptive, or passively acquired?
• How do these changes occur mechanistically?
• How do study all this?
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Proximal mechanisms of genomic expansion/contraction
• Mobile element proliferation• Segmental duplications• Strand slippage• DS DNA breaks
– Insertion propagation (biased gene conversion)– Microdeletions (nonhomologous end repair)
• Unequal crossing over• Illegitimate recombination• Selection for or against such modifications
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Explaining variation in genome size
• Adaptive, neutral, deleterious
• Selfish DNA hypothesis• Bulk DNA hypothesis• Metabolic cost of DNA• Petrov neutral hypothesis• Mutation Hazard Hypothesis
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Lynch and Conery 2003: “Mutation Hazard” Hypothesis
1• Body size / complexity increase
2• Reduced Ne
3• Reduced efficacy of selection
4
• Non-coding DNA proliferates • duplicate genes retained
Increases in genome size and complexity are a drift-driven consequence of reducing efficacy of selection
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Lynch and Conery 2003
Neu scales inversely with genome size
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Lynch and Conery 2003
Half life of duplicate genes greater in larger genomes
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Intron number and size greater in larger genomes
Lynch and Conery 2003
Threshold effect
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TE size/number scales with genome size; threshold effect
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Whitney and Garland, 2010
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Whitney and Garland, 2010
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Whitney and Garland, 2010
Conclusion: no mechanistic connection between Ne and genome complexitySubtext: Adaptive processes account for variations in genome size?
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Lynch 2011 rebuttal
• Neu has no shared evolutionary history– Comparative methods inappropriate
• Topology and branch lengths of phylogeny is suspect
• Threshold effect is most important prediction of MH; not addressed in W&G
• OLS is unbiased
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Whitney et al. counterpoints
• Significant phylogenetic signal (K) for all traits examined (genome size, etc)
• Life history and other factors underlying Neu can and do have phylogenetic signal
• Consistent results with different phylogenies
• Too few data to conduct threshold tests• OLS clearly biased