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We experiment on Drosophila melanogaster, because it provides a useful model of mutations and genetic inheritance.
These regions did not conform to the assumption of equal mutation rates throughout the sequence according to a certain model of mutations.
Nei's [52] distance model, is based on infinite isoallele model of mutations [55], where all loci have the same rate of neutral mutations, and that the genetic variability originally in the population is at equilibrium between mutations and genetic drift.
A hierarchical model of mutations, which contributed to the T leukemogenesis, was recently proposed [ 23].
These estimates are based on a Markov model of mutations, similar to the Dayhoff model of protein evolution [ 15].
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T. Ohta and M. Kimura, "A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a finite population," Genetical Research 22 (1973): 201-204.
We did not find evidence of inbreeding within fragments, but from the fitting tests into the infinite allele model of mutation no population was shown to be in equilibrium, indicating recent bottlenecks.
All alleles at each neutral locus were assumed to be equally related to one another (i.e., an infinite alleles model of mutation was assumed).
An infinite site model of mutation was applied to all loci.
Finally, we used a simple model of mutation rate, particularly for VNTR, where all loci had the same mutation rate.
Both the stepwise mutation model (SMM) and two-phase model of mutation (TPM) were used, with the latter model being considered the most appropriate for microsatellites.
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