Genome size and Complexity

(as told by Michael Lynch)

Genome size and complexity varies across the tree of life

Lynch 2007

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?

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

Explaining variation in genome size

• Adaptive, neutral, deleterious

• Selfish DNA hypothesis• Bulk DNA hypothesis• Metabolic cost of DNA• Petrov neutral hypothesis• Mutation Hazard Hypothesis

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

Lynch and Conery 2003

Neu scales inversely with genome size

Lynch and Conery 2003

Half life of duplicate genes greater in larger genomes

Intron number and size greater in larger genomes

Lynch and Conery 2003

Threshold effect

TE size/number scales with genome size; threshold effect

Whitney and Garland, 2010

Whitney and Garland, 2010

Whitney and Garland, 2010

Conclusion: no mechanistic connection between Ne and genome complexitySubtext: Adaptive processes account for variations in genome size?

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

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