Thursday, August 11, 2022

Chapter 2: The Evolution of Sloppy Genomes

Pufferfish, lungfish, frogs, and the C-Value Paradox. (pp. 33-34)
The complexity of genomes
Reassociation kinetics (C0t curves). Highly repetitive DNA, moderately repetitive DNA, unique sequence DNA. (pp. 34-35)
Variation in genome size
Junk DNA explains the variations in genome size. The C-Value Enigma. You don't need new genes to explain complexity. (pp. 35-37)
Instantaneous genome doubling
Polyploidy. Brassica species. Organisms can tolerate extra DNA. (pp. 38-39)
The Onion Test

The Onion test is a way of testing your junk DNA hypotheses. (pp. 39-40)
[The Onion Test]

Modern evolutionary theory

Evolution is a change in the frequency of alleles in a population. Adaptation, fixation, postive selection, negative selection, purifying selection. (pp. 40-41)
[Is the Modern Synthesis effectively dead?] [Kevin Laland's view of "modern" evolutionary theory (again)]

Random genetic drift
Beanbag genetics and population genetics. Fixation by random genetic drift. (pp. 41-43)
[On the importance of random genetic drift in modern evolutionary theory] [Evolution by chance] [The role of chance in evolution] [One philosopher's view of random genetic drift] [A philosopher's view of random genetic drift]
Neutral Theory

Kimura and the promotion of the neutral theory. Random genetic drift as a major cause of evolution. (pp. 43-44)
[Celebrating 50 years of Neutral Theory]

Nearly neutral Theory
Ohta and the nearly neutral Theory. The fixation of slightly deleterious alleles.(pp. 44-45)
Population genetics

Population size and selection coefficients. Probability of fixation. Population size and the fixation of slightly deleterious alleles. Drift-Barrier Hypothesis. (pp. 45-49)
[Learning about modern evolutionary theory: the drift-barrier hypothesis]

   Box: Are humans are still evolving? (pp. 49-50)

On the evolution of sloppy genomes

Insertions, deletions, and random genetic drift. (pp. 50-54)
[Evolution by Accident]

   Box: Chromosome dynamics (p. 54)
   [Segmental duplications in the human genome]

Bacteria have small genomes
Why do bacteria have small genomes? (pp. 54-56)

Notes for Chapter 2 (pp. 318-320)

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