The Adh genomic region of Drosophila ambigua: evolutionary trends in different species

Molecular phylogeny of the Drosophila obscura species group, with emphasis on the Old World species

Background

Species of the Drosophila obscura species group (e.g., D. pseudoobscura, D. subobscura) have served as favorable models in evolutionary studies since the 1930's. Despite numbers of studies conducted with varied types of data, the basal phylogeny in this group is still controversial, presumably owing to not only the hypothetical 'rapid radiation' history of this group, but also limited taxon sampling from the Old World (esp. the Oriental and Afrotropical regions). Here we reconstruct the phylogeny of this group by using sequence data from 6 loci of 21 species (including 16 Old World ones) covering all the 6 subgroups of this group, estimate the divergence times among lineages, and statistically test the 'rapid radiation' hypothesis.

Results

Phylogenetic analyses indicate that each of the subobscura, sinobscura, affinis, and pseudoobscura subgroups is monophyletic. The subobscura and microlabis subgroups form the basal clade in the obscura group. Partial species of the obscura subgroup (the D. ambigua/D. obscura/D. tristis triad plus the D. subsilvestris/D. dianensis pair) forms a monophyletic group which appears to be most closely related to the sinobscura subgroup. The remaining basal relationships in the obscura group are not resolved by the present study. Divergence times on a ML tree based on mtDNA data are estimated with a calibration of 30–35 Mya for the divergence between the obscura and melanogaster groups. The result suggests that at least half of the current major lineages of the obscura group originated by the mid-Miocene time (~15 Mya), a time of the last developing and fragmentation of the temperate forest in North Hemisphere.

Conclusion

The obscura group began to diversify rapidly before invading into the New World. The subobscura and microlabis subgroups form the basal clade in this group. The obscura subgroup is paraphyletic. Partial members of this subgroup (D. ambigua, D. obscura, D. tristis, D. subsilvestris, and D. dianensis) form a monophyletic group which appears to be most closely related to the sinobscura subgroup.

Phylogeny of Drosophilinae (Diptera: Drosophilidae), with comments on combined analysis and character support

Drosophilidae (Diptera) is a diverse, cosmopolitan family of flies. Here, we present a combined analysis phylogeny of Drosophilinae, one of the two subfamilies of Drosophilidae, based on data from six different data partitions, including both molecular and morphological characters. Although our data show support for the monophyly of the Hawaiian Drosophilidae, and the subgenus Sophophora, neither the genus Drosophila nor the subgenus Drosophila is monophyletic. Partitioned Bremer support (PBS) indicates that morphological data taken from Grimaldi's monograph (Grimaldi, 1990a), as well as sequences from the mitochondrial (mt) 16S rDNA and the nuclear Adh gene, lend much support to our tree's topology. This is particularly interesting in the case of Grimaldi's data, since his published hypothesis conflicts with ours in significant ways. Our combined analysis cladogram phylogeny reflects the catch-all designation that the name Drosophila has become, in that the cladogram does not support the monophyly of either the genus or subgenus Drosophila.

Isolation and characterization of the genomic region from Drosophila kuntzei containing the Adh and Adhr genes

The nucleotide sequences of the Adh and Adhr genes of Drosophila kuntzei were derived from combined overlapping sequences of clones isolated from a genomic library and from cloned PCR and inverse-PCR fragments. Only a proximal promoter was detected upstream of the Adh gene, indicating that D. kuntzei Adh is regulated by a one-promoter system. Further upstream of the Adh structural gene, an adult enhancer region (AAE) was found that contains most of the regulatory sequences described for AAEs of other Drosophila species. Analysis of the ADH protein showed an amino acid change from valine to threonine in the active site at position 189 which is also found in D. funebris but is otherwise unique among Drosophila. This difference alone may be responsible for the very low ADH activity found in this species and may cause a difference in substrate usage pattern. Codon bias in Adh and Adhr was comparable and found to be very low compared with other species. Phylogenetic analysis showed that D. kuntzei is closest related to D. funebris and D. immigrans. The time of divergence between D. kuntzei and D. funebris was estimated to be 14.2-20.2 Myr and that between D. kuntzei-D. funebris and D. immigrans to be 30.8-44.0 Myr. An analysis of the genetic variation in the Adh gene and upstream sequences of four European strains showed that this gene was highly variable. Overall nucleotide diversity (pi) was 0.0139, which is two times higher than that in D. melanogaster.

Molecular organization of the Drosophila melanogaster Adh chromosomal region in D. repleta and D. buzzatii, two distantly related species of the Drosophila subgenus

The molecular organization of a 1.944-Mb chromosomal region of Drosophila melanogaster around the Adh locus has been analyzed in two repleta group species: D. repleta and D. buzzatii. The extensive genetic and molecular information about this region in D. melanogaster makes it a prime choice for comparative studies of genomic organization among distantly related species. A set of 26 P1 phages from D. melanogaster were successfully hybridized using fluorescence in-situ hybridization (FISH) to the salivary gland chromosomes of both repleta group species. The results show that the Adh region is distributed in D. repleta and D. buzatii over six distant sites of chromosome 3, homologous to chromosomal arm 2L of D. melanogaster (Muller's element B). This observation implies a density of 2.57 fixed breakpoints per Mb in the Adh region and suggests a considerable reorganization of this chromosomal element via the fixation of paracentric inversions. Nevertheless, breakpoint density in the Adh region is three times lower than that estimated for D. repleta chromosome 2, homologous to D. melanogaster 3R (Muller's element E). Differences in the rate of evolution among chromosomal elements are seemingly persistent in the Drosophila genus over long phylogenetic distances.

Reevaluation of phylogeny in the Drosophila obscura species group based on combined analysis of nucleotide sequences

The Drosophila obscura species group has served as an important model system in many evolutionary and population genetic studies. Despite the amount of study this group has received, some phylogenetic relationships remain unclear. While individual analysis of different nuclear, mitochondrial, allozyme, restriction fragment, and morphological data partitions are able to discern relationships among closely related species, they are unable to resolve relationships among the five obscura species subgroups. A combined analysis of several nucleotide data sets is able to provide resolution and support for some nodes not seen or well supported in analyses of individual loci. A phylogeny of the obscura species group based on combined analysis of nucleotide sequences from six mitochondrial and five nuclear loci is presented here. The results of several different combined analyses indicate that the Old World obscura and subobscura subgroups form a monophyletic clade, although they are unable to resolve the relationships among the major lineages within the obscura species group.

The phylogenetic position of Drosophila eskoi deduced from P element and Adh sequence data

PCR screening with primers specific for the T-, M-, and O-type P element subfamilies was performed to investigate the interspecific distribution in 18 species and to reconstruct the phylogenetic history of the various types within the obscura species group. T-type elements occur in D. ambigua, D. tristis, D. obscura, D. subsilvestris, and D. eskoi. In the genomes of D. subobscura, D. madeirensis, and D. guanche they are present in the form of terminally truncated T-type derivatives. The wide distribution suggests that the T-type subfamily had a long evolutionary history in the obscura lineage. In contrast, the patchy occurrence of M- and O-type elements can be ascribed to four independent events of horizontal invasion of different lineages. The cladogenesis of the obscura group was investigated using a partial sequence of the Adh gene as a marker. In contrast to earlier findings, the position of D. eskoi had to be revised. D. eskoi appears as the closest relative of the D. ambigua clade, whereas D. tsukubaensis is the sister taxon of the species pair D. bifasciata/D. imaii. This result is in good accordance with the P element data, where high sequence similarity (95%) was found among the T-type elements of D. eskoi and those of D. ambigua and D. tristis.

The Adh-related gene of Drosophila melanogaster is expressed as a functional dicistronic messenger RNA: multigenic transcription in higher organisms

Essentially all eukaryotic cellular mRNAs are monocistronic, and are usually transcribed individually. Two tandemly arranged Drosophila genes, alcohol dehydrogenase (Adh) and Adh-related (Adhr), are transcribed as a dicistronic transcript. From transcripts initiated from the Adh promoter, two classes of mRNA are accumulated, one is monocistronic and encodes Adh alone, the other is dicistronic and includes the open reading frames of both Adh and Adhr. The dicistronic transcript is found in polysomes and the Adhr protein product is detected by antibody staining. We present evidence that the accumulation of the dicistronic mRNA is controlled at the level of the 3' end processing.

Repeated horizontal transfer of P transposons between Scaptomyza pallida and Drosophila bifasciata

Two distinct P element subfamilies, designated M-type and O-type, reside in the genome of D. bifasciata. PCR-screening of 65 Drosophila species revealed that only D. bifasciata and its closest relative D. imaii possess O-type elements. Outside the genus, O-type elements were detected in Scaptomyza pallida. Restriction analyses show that the general structure of the O-type elements from S. pallida and D. bifasciata is the same. Sequence divergence turned out to be extremely low (0.43%). These results suggest that the O-type subfamily of D. bifasciata has been received by horizontal transfer from an external source, most probably from the genus Scaptomyza, as has been previously suspected for the M-type family. Since the sequence divergence between M-type elements from S. pallida and D. bifasciata is eighteen-fold higher than that between O-type elements, two independent intergeneric transfer events have to be postulated. In order to re-examine the taxonomic status of S. pallida, a partial sequence (489 bp) of the Adh gene was analysed. The data clearly prove that S. pallida has to be placed far outside the D. obscura group.

Maintenance of pre-mRNA secondary structure by epistatic selection

Linkage disequilibrium between polymorphisms in a natural population may result from various evolutionary forces, including random genetic drift due to sampling of gametes during reproduction, restricted migration between subpopulations in a subdivided population, or epistatic selection. In this report, we present evidence that the majority of significant linkage disequilibria observed in introns of the alcohol dehydrogenase locus (Adh) of Drosophila pseudoobscura are due to epistatic selection maintaining secondary structure of precursor mRNA (pre-mRNA). Based on phylogenetic-comparative analysis and a likelihood approach, we propose secondary structure models of Adh pre-mRNA for the regions of the adult intron and intron 2 where clustering of linkage disequilibria has been observed. Furthermore, we applied the likelihood ratio test to the phylogenetically predicted secondary structure in intron 1. In contrast to the other two structures, polymorphisms associated with the more conserved stem-loop structure of intron 1 are in low frequency, and linkage disequilibria have not been observed. These findings are qualitatively consistent with a model of compensatory fitness interactions. This model assumes that mutations disrupting pairing in a secondary structural element are individually deleterious if they destabilize a functionally important structure; a second "compensatory" mutation, however, may restabilize the structure and restore fitness.

ADH evolution and the phylogenetic footprint

The evolution of any given protein reflects the interplay between proximal selective forces involving the conservation of protein structure and function and more general populational factors that shape the action and efficiency of natural selection. In an attempt to address that interplay, we have analyzed patterns of amino acid replacement within a well-conserved molecule, alcohol dehydrogenase (ADH), in the Drosophilidae. A sliding window, moved along the protein sequence in order to quantify the extent of change at each amino acid position, reveals heterogeneous amounts of replacement across the molecule when all ADH sequences are analyzed simultaneously. Surprisingly, the replacement profile for ADH differs significantly in the melanogaster, mulleri, and Hawaiian subgroups, reflecting the imprint of the differing evolutionary histories of each of these assemblages on the evolution of this conservative molecule.

Structure of the Drosophila melanogaster glutathione-dependent formaldehyde dehydrogenase/octanol dehydrogenase gene (class III alcohol dehydrogenase). Evolutionary pathway of the alcohol dehydrogenase genes

The glutathione-dependent formaldehyde dehydrogenase gene (gfd) of Drosophila melanogaster encodes an enzyme that is active toward S-hydroxymethylglutathione, an adduct of formaldehyde with glutathione, and also with long-chain primary alcohols, both properties typical of class III alcohol dehydrogenases, gfd hybridizes at the 86D division of the third chromosome, in agreement with the known location of the Drosophila octanol dehydrogenase gene (odh), gfd/odh was isolated from a lambda EMBL-4 genomic library and consists of three exons (with coding segments of 21, 90 and 1029 bp) and two introns (69 bp and 70 bp, respectively). The introns are small in size like the Drosophila interrupting sequences and are located at the 5' end of the coding region. Comparisons with the homologous genes of Saccharomyces, Candida and humans provide information on the evolution of the class III alcohol dehydrogenases. Moreover, results from analysis of exon/intron distributions in eleven dehydrogenases are compatible with the hypothesis of intron loss accounting for aspects of the present structure of these genes.

Nucleotide sequence of the genomic region encompassing Adh and Adh-dup genes of D. lebanonensis (Scaptodrosophila): gene expression and evolutionary relationships

The region of the genome of D. lebanonensis that contains the Adh gene and the downstream Adh-dup gene was sequenced. The structure of the two genes is the same as has been described for D. melanogaster. Adh has two promoters and Adh-dup has only one putative promoter. The levels of expression of the two genes in this species are dramatically different. Hybridizing the same Northern blots with a specific probe for Adh-dup, we did not find transcripts for this gene in D. lebanonensis. The level of Adh distal transcript in adults of D. lebanonensis is five times greater than that of D. melanogaster adults. The maximum levels of proximal transcript are attained at different larval stages in the two species, being three times higher in D. melanogaster late-second-instar larvae than in D. lebanonensis first-instar larvae. The level of Adh transcripts allowed us to determine distal and proximal initiation transcription sites, the position of the first intron, the use of two polyadenylation signals, and the heterogeneity of polyadenylation sites. Temporal and spatial expression profiles of the Adh gene of D. lebanonensis show qualitative differences compared with D. melanogaster. Adh and Adh-dup evolve differently as shown by the synonymous and nonsynonymous substitution rates for the coding region of both genes when compared across two species of the melanogaster group, two of the obscura group of the subgenus Sophophora and D. lebanonensis of the victoria group of the subgenus Scaptodrsophila. Synonymous rates for Adh are approximately half those for Adh-dup, while nonsynonymous rates for Adh are generally higher than those for Adh-dup. Adh shows 76.8% identities at the protein level and 70.2% identities at the nucleotide level while Adh-dup shows 83.7% identities at the protein level and 67.5% identities at the nucleotide level. Codon usage for Adh-dup is shown to be less biased than for Adh, which could explain the higher synonymous rates and the generally lower nonsynonymous substitution rates in Adh-dup compared with Adh. Phylogenetic trees reconstructed by distance matrix and parsimony methods show that Sophophora and Scaptodrosophila subgenera diverged shortly after the separation from the Drosophila subgenus.

Adh and Adh-dup sequences of Drosophila lebanonensis and D. immigrans: interspecies comparisons

We have cloned and sequenced the Adh genomic region of Drosophila lebanonensis (subgenus Scaptodrosophila) and D. immigrans (subgenus Drosophila). This region, which contains Adh, encoding the alcohol dehydrogenase enzyme, and Adh-dup (duplicate of Adh), has been compared with the same fragment from D. subobscura (subgenus Sophophora). Even though the flanking regions and introns of both genes have been affected by high substitution rates, the consensus sequences have been clearly identified. Although the overall homology of the coding regions was 76-78% among the species compared, there were differences in the exon distribution of the nucleotide substitutions when Adh or Adh-dup were compared, thus showing that these two genes differ in their evolutionary pattern.

Evolutionary genetics of the Drosophila alcohol dehydrogenase gene-enzyme system

Evolutionary genetics embodies a broad research area that ranges from the DNA level to studies of genetic aspects in populations. In all cases the purpose is to determine the impact of genetic variation on evolutionary change. The broad range of evolutionary genetics requires the involvement of a diverse group of researchers: molecular biologists, (population) geneticists, biochemists, physiologists, ecologists, ethologists and theorists, each of which has its own insights and interests. For example, biochemists are often not concerned with the physiological function of a protein (with respect to pH, substrates, temperature, etc.), while ecologists, in turn, are often not interested in the biochemical-physiological aspects underlying the traits they study. This review deals with several evolutionary aspects of the Drosophila alcohol dehydrogenase gene-enzyme system, and includes my own personal viewpoints. I have tried to condense and integrate the current knowledge in this field as it has developed since the comprehensive review by van Delden (1982). Details on specific issues may be gained from Sofer and Martin (1987), Sullivan, Atkinson and Starmer (1990); Chambers (1988, 1991); Geer, Miller and Heinstra (1991); and Winberg and McKinley-McKee (1992).

Evidence for retrotranscription of protein-coding genes in the Drosophila subobscura genome

Evidence is provided for the presence of retrosequences (also named retroposons) arising from Adh in the Drosophila subobscura genome. Restriction analysis and primary structure of two different retrosequence-containing clones, S812 and S135, are reported. The fact that these retrosequences lack introns and a recognizable promoter strongly supports their retrotranscriptional origin. Adjacent to the two retrosequences analyzed, a middle repetitive DNA element has been found which bears no clear similarity to any sequence reported to date in the GenBank/EMBL Data Library. A comparative analysis of these retrosequences with the functional Adh gene of D. subobscura is presented. In addition, a model concerning the origin, functionality, and propagation of these genome elements is discussed.