Evidence for time dependency of molecular rate estimates

Ho, Simon Y.W., Shapiro, Beth, Phillips, Matthew J., Cooper, Alan, & Drummond, Alexei J. (2007) Evidence for time dependency of molecular rate estimates. Systematic Biology, 56(3), pp. 515-522.

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Long-term changes in the genetic composition of a population occur by the fixation of new mutations, a process known as substitution. The rate at which mutations arise in a population and the rate at which they are fixed are expected to be equal under neutral conditions (Kimura, 1968). Between the appearance of a new mutation and its eventual fate of fixation or loss, there will be a period in which it exists as a transient polymorphism in the population (Kimura and Ohta, 1971). If the majority of mutations are deleterious (and nonlethal), the fixation probabilities of these transient polymorphisms are reduced and the mutation rate will exceed the substitution rate (Kimura, 1983). Consequently, different apparent rates may be observed on different time scales of the molecular evolutionary process (Penny, 2005; Penny and Holmes, 2001). The substitution rate of the mitochondrial protein-coding genes of birds and mammals has been traditionally recognized to be about 0.01 substitutions/site/million years (Myr) (Brown et al., 1979; Ho, 2007; Irwin et al., 1991; Shields and Wilson, 1987), with the noncoding D-loop evolving several times more quickly (e.g., Pesole et al., 1992; Quinn, 1992). Over the past decade, there has been mounting evidence that instantaneous mutation rates substantially exceed substitution rates, in a range of organisms (e.g., Denver et al., 2000; Howell et al., 2003; Lambert et al., 2002; Mao et al., 2006; Mumm et al., 1997; Parsons et al., 1997; Santos et al., 2005). The immediate reaction to the first of these findings was that the polymorphisms generated by the elevated mutation rate are short-lived, perhaps extending back only a few hundred years (Gibbons, 1998; Macaulay et al., 1997). That is, purifying selection was thought to remove these polymorphisms very rapidly.

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ID Code: 50532
Item Type: Journal Article
Refereed: Yes
Keywords: genetic composition , mutations, substitution
DOI: 10.1080/10635150701435401
ISSN: 1063-5157
Subjects: Australian and New Zealand Standard Research Classification > BIOLOGICAL SCIENCES (060000) > EVOLUTIONARY BIOLOGY (060300)
Australian and New Zealand Standard Research Classification > BIOLOGICAL SCIENCES (060000) > GENETICS (060400)
Divisions: Current > QUT Faculties and Divisions > Science & Engineering Faculty
Deposited On: 24 May 2012 01:56
Last Modified: 30 Jun 2014 01:43

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