Transition stages of molecular drive in multiple-copy DNA families in Drosophila

Abstract

Multigene and non‐genic DNA families are in a state of turnover and hence are continually being replaced throughout a population by new variant repeats. To quantify such molecular processes, in the absence of selection, it is necessary to find and compare stages of transistion during the homogenization of at least two non‐genic families evolving in parallel in a closely related group of species. Detailed sequence analysis of patterns of variation, at each nucleotide position considered independently, amongst repeats of two tandem DNA families from seven related Drosophila species, reveals all stages of transition during the spread of randomly produced variant repeats. Variant repeats are found at different stages of homogenization and fixation in a population, irrespective of the loci, chromosomes or individuals from which they were cloned. Differences between the families in the relatively small number of variants at each transition stage and the greater number of fully homogenized and fixed variants between species of greater divergence indicate that the process of spread (molecular drive) is rapid relative to the mutation rate and occurs at seemingly different constant rates for each family. Occasional gene conversions, in addition to unequal exchanges, have contributed to family turnover. The significance of these results to the evolution of functional multigene families and divergence and conservation of sequences is discussed.

Microgeographic variation in rDNA intergenic spacers of Anopheles gambiae in western Kenya

“…Restriction site variants could be homogenized but simple length variants will be continually regenerated. Other studies of natural populations have revealed varying degrees of homogenization of sequence variants of multigene families Strachan et a!., 1985;Learn and Schaal, 1987). In the present study, spacer restriction fragments of 400 bp and Collins, 1989) hybridizes only to the 300 bp, 1700 bp, and 2000 bp restriction fragments and not to the 400, 500, 900 or 1400 bp fragments.…”

Long-term conservation vs high sequence divergence: the case of an extraordinarily old satellite DNA in bivalve mollusks

“…The overall variability profile of satDNA monomers in a genome is a complex feature that depends on genomic Figure 4 The distribution of transition stages (in percentages) according to the classification described by Strachan et al (1985) and modified in Meštrović et al, 2006a (see explanation in Materials and methods). It should be noted that bars of unclassifiable mutations embody values of changes shared among species and assumed to represent ancestral mutational events.…”

“…In this study, original classes have been regrouped as in Meštrović et al (2006a): homogenized stage (class 1), intermediate transition stage (classes 2-4) and advanced stage showing the complete homogeneity of different nucleotides at the same position in each set, and subsequent introduction of a new mutation (classes 5-6). Non-homogenized nucleotide positions occurring concurrently in both sets of monomers could not be grouped according to the method of Strachan et al (1985). However, mutations shared by both groups of variants at a given position are assumed to be inherited from an ancestral set of monomer variants, and are, therefore, considered as a distinct subgroup (see also Mravinac et al, 2005).…”

“…On the contrary, in the comparison between V. verrucosa and V. rhomboides just one mutation is in the advanced stage of sequence homogenization. However, the highest number of mutations observed in all comparisons are actually unclassifiable according to the method used (Strachan et al, 1985). Unclassifiable changes include those shared between the two monomer sets assumed to result from homogenization events that occurred before taxa cladogenesis rather than being a consequence of independent mutational events at the same position (Mravinac et al, 2005).…”

“…Sequence divergence between satDNAs was evaluated through the analysis of transition stages (Strachan et al, 1985). Variations at each nucleotide position in two compared monomer sets are divided in classes from 1 to 6, which follow gradual accumulation of changes in one of the sets at a given position.…”