Restriction map variation in the Adh region of Drosophila.

Abstract

Restriction maps of a 12,000-nucleotide region containing the alcohol dehydrogenase (Adh) locus of the second chromosome of Drosophila were determined for (i) 18 independent second chromosome stocks of D. melanogaster established from several natural populations and (ii) five closely related Drosophila species. All of the detected map differences appear to lie outside the Adh coding block. Four polymorphic restriction sites and four insertion/deletion variants were identified among D. melanogaster chromosomes. The estimated heterozygosity per nucleotide site was 0.006. The relative distributions of restriction sites and insertion/deletion variations among subpopulations and species suggest that the insertion/deletion variation may be mildly deleterious.In recent years it has become possible to survey organisms for DNA sequence variation detected as differences in distributions of restriction endonuclease sites along specific regions of DNA (1). Both nuclear and cytoplasmic DNAs show variation in laboratory strains. These differences are important in localizing mutational lesions and functional regions. Restriction map variation also has been systematically surveyed in natural populations of several species, including Drosophila melanogaster, simulans, and virilis (2); the deer mouse (3); and man (4). These studies have allowed the estimation of .sequence diversity among individuals, populations, and species in DNA sequences that have been inaccessible (e.g., noncoding regions and mitochondrial genomes).Goldberg reported the cloning ofthe DNA in and around the alcohol dehydrogenase locus (Adh) of D. melanogaster (5). A single transcript was found from this region-that of Adh (5). The availability of this cloned sequence afforded us the opportunity to survey restriction map variation in this region. We report here the restriction maps from 18 independent second chromosome stocks of D. melanogaster established from several natural populations. We also present restriction maps for five other species closely related to D. melanogaster. From these maps, estimates of sequence diversity over a 12,000-nucleotide region can be made. Insertion/deletion variation was found both within and between species. The distribution over individuals, subpopulations, and species suggests some selective effect of insertions/deletions outside the transcriptional unit.MATERIALS AND METHODS Drosophila Stocks. Eighteen stocks of D. melanogaster homozygous for independent second chromosomes isolated from several natural populations were received from C. C. Laurie-Ahlberg (6). Ten

The size differences among mammalian introns are due to the accumulation of small deletions

“…The imbalance between these two mutagenic events can be a driving force that decreases the genome size and also the intron size. We observed gaps (insertions and deletions) of fairly small sizes in non-coding sequences, the longest one being a 16 nt deletion, which is consistent with the previous observations of short deletions [20][21][22]. The dis- tribution of gap lengths found in the alignment of human/ rodent introns also indicates a higher frequency of smaller gaps (data not shown).…”

Long-Term and Short-Term Evolutionary Impacts of Transposable Elements onDrosophila

“…This theoretical prediction suggests that the selective benefit of a host allele increases with the number of TE copies whose transposition it can suppress. Given the TE transposition rate [10 25 10 24 (Nuzhdin and Mackay 1995;Nuzhdin et al 1997;Maside et al 2000Maside et al , 2001 For example, a host allele that can reduce half of the transposition rate of a subset of TE families with a total of 1000 copies can have a selection coefficient as large as 10 25 , which would be strong enough to overcome the effect of genetic drift in D. melanogaster [N e 10 6 (Langley et al 1982;Kreitman 1983)]. Accordingly, unlike the arms race between host and horizontally transferred pathogens, where strong selective benefit comes from the precise targeting of the host allele to a specific pathogen variant, the antagonistic interaction between TEs and host variants that can target the aggregated influence of multiple vertically inherited TE families could be the main force driving the fast evolution of host TE-interacting genes…”

Variation at the 87A heat shock locus in Drosophila melanogaster

“…Heterozygosity per nucleotide has been estimated to be 0.001, with 0.5% of the nucleotide sites polymorphic (8) (8,9) but in Drosophila the two appeared to be similar (7,12 (25) reported a strain difference in the size of the spacer region at the 87A7 hsp70 locus. This difference corresponds to insertion B in Fig.…”

“…1 (unpublished data). In a detailed study of the hsp70 genes from 87A7 and 87C1 using DNA sequence analysis, Mason (53,54), although Tn5 appears to insert at random (55 (12), this suggests that selection can detect the effects of DNA insertion at some distance from coding elements and prevent such variants from becoming fixed in the species. In the f3-globin gene cluster of higher primates it has recently been suggested that even the rate of nucleotide substitution may be lower outside the coding regions than that for silent substitutions within them (57).…”

“…This work has generally involved mapping restriction site polymorphisms and various approaches to the analysis of such data have now been published (6)(7)(8)(9)(10). The study of DNA-level variation in nuclear genes is technically more complex and to date three systematic population surveys have been completed-one on the ,B-globin region in man (11) and two on the alcohol dehydrogenase (Adh) locus in Drosophila melanogaster (12,13). Much information has been collected at other loci in man (14)(15)(16)(17)(18) but, in general, those studies were conditioned by the prior discovery of variation and do not provide an unbiased estimate of its overall level.…”