Evolution__3rd_Edition

192 PART 2 / Evolutionary Genetics
Further reading
The texts by Graur & Li (2000), Page & Holmes (1998), and Li (1997) introduce the
topic. The classic works, in order of decreasing age, are: Lewontin (1974), Kimura
(1983), and Gillespie (1991). Kimura (1991) up-dated his views.
The Festschrift for Lewontin (Singh & Krimbas 2000) contains a number of chapters
on the topic. See Hardison (1999) on hemoglobin. Golding & Dean (1998) review
studies of adaptation at the molecular level. Eanes (1999) reviews studies of enzyme
polymorphism. The texts include material on levels of variation and rates of evolution.
Przeworski et al. (2000) describe variation in human DNA. Mitton (1998) reviews
classic, pregenomic studies of selection.
On molecular clocks, see Cutler (2000) on irregularity or overdispersion. The mutation
process matters for the generation time effects in the molecular clock. For number
of germ line divisions see Ridley (2001, p. 234). Mutations are mainly internal copying
accidents: see Ridley (2001), and Sommer (1995), for example. However, Kumar &
Subramanian (2002) provide evidence that some synonymous evolution rates, and
therefore perhaps mutation rates, in mammals do not depend on generation time.
For nearly neutral theory, see the general texts. Ohta (1992) is a review, Ohta &
Gillespie (1996) a historic perspective, and Ohta (2002) a recent update. The exchange
between Ohta and Kreitman included in Ridley (1997) shows how various facts can be
explained by the nearly neutral theory or selective evolution. Gillespie (2001) questions
whether population size affects the rate of evolution, because the effect via hitch-hiking
(Chapter 8) is the opposite of the effect on drift at one site.
On testing for selection in genomic data, Nielsen (2001) reviews the statistical tests.
Brookfield (2001) introduces one case study. Hughes (1999) looks at ratios of nonsynonymous
to synonymous evolutionary rates.
Another test, similar to the test of McDonald and Kreitman (1991), was devised by
Hudson, Kreitman, & Aguade (1987). The “HKA” test is also enjoying a revival with
genomic data. It can be seen in action recently in Rand (2000) on mitochondrial
genomics, and Wang et al. (1999) on genetic change during maize domestication.
Bustamente et al. (2002) is another paper using the MK test with genomic data, like the
two discussed in the text. They agree that fruitflies have substituted many advantageous
non-synonymous changes, and add an inference that Arabidopsis has substituted more
disadvantageous changes. The Ohta–Kreitman exchange cited above considers the MD
and HKA tests further.
On codon biases, see Kreitman & Antezana (2000), Mooers & Holmes (2000), and
Duret & Mouchiroud (1999).
Research on this topic can be followed in Trends in Ecology and Evolution, Trends in
Genetics, Bioessays, and the December special issue each year of Current Opinion in
Genetics and Development.
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