Evolution of the obscura group drosophila species. II. Phylogeny of ten species based on electrophoretic data

EVOLUTIONARY IMPLICATIONS OF DNA DIVERGENCE IN THE DROSOPHILA OBSCURA GROUP

Using DNA-DNA hybridization, we have determined the degree of single-copy DNA (scDNA) divergence among eight species of the Drosophila obscura group. These include Old World and New World species as well as members of two subgroups. Contrary to classical systematics, members of the affinis subgroup are more closely related to American members of the obscura subgroup than are Old World species. The Old World species are not a monophyletic group. The degree of scDNA divergence among species is not necessarily correlated with morphology, chromosomal divergence, or ability to form hybrids. A unique pattern of hybrid formation was found: species separated by a ΔT_m of 6.5°C can form hybrids whereas species separated by a ΔT_m of 2.5°C cannot. As with other groups of Drosophila, the obscura group has discrete parts of the genome evolving at very different rates. The slow evolving fraction of the nuclear genome is evolving at about the same rate as mitochondrial DNA. The additional scDNA divergence accompanying the step from partial reproductive isolation (between North American pseudoobscura and the isolated Bogotà population) to full isolation is very small. The resolution of the technique was challenged by five closely related taxa with a maximum ΔT_m of 2.5°C separating them; the taxa were unambiguously resolved and the "correct" phylogeny recovered. Finally, there is some indication that scDNA in the obscura group may be evolving considerably slower than in the melanogaster subgroup.

The phylogeny of nine species of the Drosophila obscura group inferred by the banding homologies of chromosomal regions. II. Element E

The phylogenetic relationships among nine species of Drosophila belonging to the obscura group were investigated by establishing (according to their banding similarities) the homologous chromosome segments of element E (equivalent to chromosome O of D. subobscura). The phylogenetic relationships were based on the existence of segments in different triads of species, which could only be produced by overlapping inversions. This permitted the ordering of the species belonging to each triad. Drosophila obscura, D. ambigua and D. tristis were found to be very closely related and thus forming a cluster in which D. ambigua occupies an intermediate position between the other two species. Drosophila obscura seems to be the species more directly linked to three other separate lineages, that of D. subsilvestris, the two African species (D. microlabis and D. kitumensis), and the subobscura cluster. The species from this last cluster may be ordered as follows: D. subobscura-D. madeirensis-D. guanche. It is not clear which species of this triad is the direct link to D. obscura. These results completely agree with those produced in an independent study, where element B was considered for the same nine species. Furthermore, the present study clarifies some ambiguities concerning the phylogenetic relationships which remained obscure due to the conservative nature of chromosome B.

Phylogenetic relationships between Drosophila subobscura, D. guanche and D. madeirensis based on Southern analysis of heat shock genes

A Southern analysis of genomic DNA using Drosophila melanogaster probes for the major heat shock protein genes (Hsp82, Hsp70, Hsps encoding small proteins) was made to study the phylogenetic relationships between three Drosophila species belonging to the obscura group (D. subobscura, D. guanche, and D. madeirensis). The phylogenetic trees showed that D. madeirensis and D. subobscura are the most closely related species in the triad, while D. guanche is the most distantly related one. As in other Drosophila species, Hsp82 is a single copy gene in D. subobscura, D. guanche, and D. madeirensis, while Hsp70 and Hsps, which encode small proteins, are genic families. At least four sequences homologous to D. melanogaster Hsp70 were found in the obscura group species. These species have sequences which showed similarity with the four small Hsps of D. melanogaster.

Evolution of gypsy endogenous retrovirus in the Drosophila obscura species group

The Ty3/gypsy family of retroelements is closely related to retroviruses, and some of their members have an open reading frame resembling the retroviral gene env. Sequences homologous to the gypsy element from Drosophila melanogaster are widely distributed among Drosophila species. In this work, we report a phylogenetic study based mainly on the analysis of the 5' region of the env gene from several species of the obscura group, and also from sequences already reported of D. melanogaster, Drosophila virilis, and Drosophila hydei. Our results indicate that the gypsy elements from species of the obscura group constitute a monophyletic group which has strongly diverged from the prototypic D. melanogaster gypsy element. Phylogenetic relationships between gypsy sequences from the obscura group are consistent with those of their hosts, indicating vertical transmission. However, D. hydei and D. virilis gypsy sequences are closely related to those of the affinis subgroup, which could be indicative of horizontal transmission.

Synonymous rates at the RpII215 gene of Drosophila: variation among species and across the coding region

The region encompassing the RpII215 gene that encodes the largest component of the RNA polymerase II complex (1889 amino acids) has been sequenced in Drosophila subobscura, D. madeirensis, D. guanche, and D. pseudoobscura. Nonsynonymous divergence estimates (Ka) indicate that this gene has a very low rate of amino acid replacements. Given its low Ka and constitutive expression, synonymous substitution rates are, however, unexpectedly high. Sequence comparisons have allowed the molecular clock hypothesis to be tested. D. guanche is an insular species and it is therefore expected to have a reduced effective size relative to D. subobscura. The significantly higher rate of synonymous substitutions detected in the D. guanche lineage could be explained if synonymous mutations behave as nearly neutral. Significant departure from the molecular clock hypothesis for synonymous and nonsynonymous substitutions was detected when comparing the D. subobscura, D. pseudoobscura, and D. melanogaster lineages. Codon bias and synonymous divergence between D. subobscura and D. melanogaster were negatively correlated across the RpII215 coding region, which indicates that selection coefficients for synonymous mutations vary across the gene. The C-terminal domain (CTD) of the RpII215 protein is structurally and functionally differentiated from the rest of the protein. Synonymous substitution rates were significantly different in both regions, which strongly indicates that synonymous mutations in the CTD and in the non-CTD regions are under detectably different selection coefficients.

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.

Molecular and chromosomal phylogeny in the obscura group of Drosophila inferred from sequences of the rp49 gene region

A region of approximately 1.6 kb encompassing the ribosomal protein 49 gene (rp49) has been sequenced and compared in nine species of the obscura group of Drosophila: four species belonging to the obscura subgroup, three to the pseudoobscura subgroup, and two to the affinis subgroup. Our data provide strong support that the nearctic species (pseudoobscura and affinis subgroups) are monophyletic and place D. bifasciata with the other species of the obscura subgroup. Nucleotide sequence information at the rp49 gene region (located very close to one of the breakpoints of inversion O3) has also been used to infer the phylogeny of the O chromosome in the subobscura species cluster. Analysis based both on parsimony-informative sites and on genetic distances confirms that the O3 gene arrangement, present in D. guanche (together with inversion g) and in D. madeirensis, is ancestral to gene arrangements O3 + 4 and Ost present in extant populations of D. subobscura.

The muscle of lawrence in Drosophila: a case of repeated evolutionary loss

The muscle of Lawrence (MOL) is a bilaterally symmetrical muscle spanning the tergite of the fifth abdominal segment of adult male Drosophila melanogaster. It is not, however, a general feature of male-specific development within the subfamily Drosophilinae. Of 95 species surveyed within this subfamily, 67 exist with no MOL at all. By drawing comparisons with published cladograms of species relatedness, three conclusions regarding the evolutionary history of the MOL are made: (i) The MOL predates the major radiations of the genus Drosophila, given its presence in earlier-branching Chymomyza and Scaptodrosophila; the MOL has been subsequently excluded in at least one present species of each of these two primitive genera. (ii) Within the genus Drosophila the MOL is present sporadically in the radiation of the subgenus Sophophora, showing repetitive loss even in very close evolutionary lineages. (iii) The MOL may have been entirely excluded from the prolific radiation of the subgenus Drosophila. Thus the MOL shows a uniquely incongruous pattern of presence or absence relative to accepted drosophilid phylogeny.

Two distinct P element subfamilies in the genome of Drosophila bifasciata

The genome of Drosophila bifasciata harbours two distinct subfamilies of P-homologous sequences, designated M-type and O-type elements based on similarities to P element sequences from other species. Both subfamilies have some general features in common: they are of similar length (M-type: 2935 bp, O-type: 2986 bp), are flanked by direct repeats of 8 bp (the presumptive target sequence), contain terminal inverted repeats, and have a coding region consisting of four exons. The splice sites are at homologous positions and the exons have the coding capacity for proteins of 753 amino acids (M-type) and 757 amino acids (O-type). It seems likely that both types of element represent functional transposons. The nucleotide divergence of the two P element subfamilies is high (31%). The main structural difference is observed in the terminal inverted repeats. Whereas the termini of M-type elements consists of 31 bp inverted repeats, the inverted repeats of the O-type elements are interrupted by non-complementary stretches of DNA, 12 bp at the 5' end and 14 bp at the 3' end. This peculiarity is shared by all members of the O-type subfamily. Comparison with other P element sequences indicates incongruities between the phylogenies of the species and the P transposons. M-type and O-type elements apparently have no common origin in the D. bifasciata lineage. The M-type sequence seems to be most closely related to the P element from Scaptomyza pallida and thus could be considered as a more recent invader of the D. bifasciata gene pool. The origin of the O-type elements cannot be unequivocally deduced from the present data.(ABSTRACT TRUNCATED AT 250 WORDS)

Differences in gene activity in a Drosophila species cluster belonging to the Obscura group

The polytene chromosome puffing pattern of Drosophila madeirensis was established and compared with those of the related species D. subobscura and D. guanche. A total of 145 loci, active in some of the 12 developmental stages analysed, were described, 38 of which were found to form the puffing pattern characteristic to this species. Taking into account the number of puffs as well as the mean puff expression, D. madeirensis shows a similar activity level to D. guanche, both species being less active than D. subobscura. The low gene activity of D. madeirensis and D. guanche was explained as a consequence of their ecological characteristics.

The phylogeny of nine species of the Drosophila obscura group inferred by the banding homologies of the chromosomal regions. IV. Element C

Homologies of the sections of the polytene chromosomes of element C, among several species of the obscura group of the genus Drosophila, were established according to the similarity of their banding patterns. The information gathered was used to construct an unrooted phylogenetic tree based on qualitative criteria. This tree is compared to three other similar trees derived from independent information provided by the study of chromosomal elements B, D and E. The general congruence of the patterns of these trees proves the well-foundedness of this approach. A single exception to this congruence is discussed. Finally a consensus tree, encapsulating information from all chromosomal elements, is presented and its topology is compared to those derived from electrophoretic data.

Nuclear and mitochondrial ribosomal RNA variability in the obscura group of Drosophila

Parts of 28S (nuclear) and 12S (mitochondrial) ribosomal RNA of Palearctic, Nearctic and African species of the obscura group have been sequenced by the direct method of sequencing. Rates of nucleotide substitutions in both molecules were compared. The nucleotide divergence is higher in the mitochondrial rRNA. Average distances of species taken in pairwise were compared to results obtained with the melanogaster subgroup: the divergence of nuclear rRNA appears lower, that of the mtDNA higher whereas genetic distances (allozymes) and sncDNA distances are similar. Noticeable variability of evolutionary rates can be observed even in low taxonomical levels. Phylogenetic trees for the obscura group are in general agreement with those obtained with other characters.

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

The study of individual genes is essential to a comprehensive understanding of genome evolution. The wealth of information on alcohol dehydrogenase (Adh) in Drosophila makes this gene particularly suitable for such analysis. We have characterized more than 4 kb of the genomic Adh region in Drosophila ambigua and compared this region to Drosophila mauritiana and Drosophila pseudoobscura. The presence of two genes, Adh and 3'ORF (open reading frame), has been confirmed and some of their essential features have been inferred from primary structural analysis. Inter- and intraspecific comparisons have led us to support that both genes may have diverged from an ancient precursor. They appear to be evolving independently, and show a species-specific pattern. The Adh in the obscura group species lacks amino acids three and four when compared to the species of the melanogaster group and has accumulated most of its amino acid replacements in the third exon. Neither characteristic is observed when any other group species are compared, which suggests that these may be particular features of the evolution of the obscura group. The 3'ORF is highly conserved among the three species analyzed, although variability in the length of the third exon and the nucleotide substitution rate, which is much higher than in Adh, are worth noting. According to our data, both mutation/fixation rates and the distribution of mutations vary over time, which makes it difficult to predict the evolutionary dynamics of specific genome regions.

The Adh in Drosophila: chromosomal location and restriction analysis in species with different phylogenetic relationships

Restriction analysis of the genomic region containing the Adh gene and in situ hybridization assays were performed in six Drosophila species belonging to three different subgenera: D. ambigua, D. subobscura, D. madeirensis and D. guanche (sg. Sophophora); D. immigrans (sg. Drosophila); and D. lebanonensis (sg. Pholadoris). In agreement with previous observations, comparison of restriction maps of the Adh region shows that D. subobscura and D. madeirensis are very closely related. Partial homology is also observed with the rest of the obscura group species. Nevertheless, no resemblance at the restriction map level is detected when more distantly related species are compared. In D. ambigua, D. immigrans and D. lebanonensis in situ hybridization assays reveal a single chromosomal location for Adh, which in D. lebanonensis appears to be sex linked. In contrast, in D. subobscura, D. madeirensis and D. guanche multiple sites of hybridization with homologous and heterologous probes are observed. For example, in D. subobscura and D. madeirensis the functional Adh gene is located on the U chromosome and additional homologous retrosequences are found on the E chromosome.

Molecular phylogeny of the subgenus Sophophora of Drosophila derived from large subunit of ribosomal RNA sequences

RNA sequencing has been used to assess the relationships among species of the subgenus Sophophora of the genus Drosophila. Two divergent domains, D1 and D2, of the large ribosomal RNA (28S), totalling 550 nucleotides have been sequenced using the rRNA direct sequencing method. A tree has been reconstructed from the neighbor-joining algorithm and the confidence intervals were evaluated by the bootstrap procedure. Results have shown that the branching of the willistoni and saltans groups of the subgenus Sophophora is very ancient and probably predates that of the subgenus Drosophila. The other groups and subgroups of Sophophora are clustered in three main lineages: 1) the melanogaster and oriental subgroups; 2) the montium subgroup; 3) the ananassae subgroup of the melanogaster group clustered with the fima and obscura groups. Thus, in comparison with our results, several taxa of various ranks appear paraphyletic (the genus Drosophila, the subgenus Sophophora and the melanogaster group). Our biochemical phylogeny is only in partial agreement with the pattern of Throckmorton's radiations as well as with classical taxonomy, both based on morphological data.

Mitochondrial DNA evolution in the obscura species subgroup of Drosophila

Mitochondrial DNA (mtDNA) restriction site maps for nine species of the Drosophila obscura subgroup and for Drosophila melanogaster were established. Taking into account all restriction enzymes (12) and strains (45) analyzed, a total of 105 different sites were detected, which corresponds to a sample of 3.49% of the mtDNA genome. Based on nucleotide divergences, two phylogenetic trees were constructed assuming either constant or variable rates of evolution. Both methods led to the same relationships. Five differentiated clusters were found for the obscura subgroup species, one Nearctic, represented by Drosophila pseudoobscura, and four Palearctic, two grouping the related triads of species Drosophila subobscura, Drosophila madeirensis, Drosophila obscura, Drosophila subsilvestris, and two more represented by one species each, Drosophila bifasciata, and Drosophila tristis. The different Palearctic clusters are as distant between themselves as with the Nearctic one. For the related species D. subobscura, D. madeirensis, and D. guanche, the pair D. subobscura-D. madeirensis is the closest one. The relationships found by nucleotide divergence were confirmed by differences in mitochondrial genome size, with related species sharing similar genome lengths and differing from the distant ones. The total mtDNA size range for the obscura subgroup species was from 15.5 kb for D. pseudoobscura to 17.1 for D. tristis.

Functional and biochemical features of alcohol dehydrogenase in four species of the obscura group of Drosophila

The biochemical features of ADH of four Drosophila species of the obscura group have been studied. The relationship between ethanol tolerance and ADH activity has been investigated. Propan-2-ol and acetone concentrations have been determined in propan-2-ol treated flies and ADH activity has been followed during 96 h of propan-2-ol treatment. Data on the ADH system confirm constructed phylogenies based on electrophoretic variation and chromosome homologies.

Chromosomal locations of actin genes are conserved between the melanogaster and obscura groups of Drosophila

The actin genes of D. subobscura and D. madeirensis were mapped by in situ hybridization, using a D. melanogaster probe. Six loci were detected, and they were strikingly similar in chromosomal location to the six actin loci previously characterized in D. melanogaster.

The banding pattern of polytene chromosomes of Drosophila guanche compared with that of D. subobscura

A detailed map of the salivary gland chromosomes of Drosophila guanche is presented and compared to the standard gene arrangements of D. subobscura. Generally, the polytene chromosome banding patterns of the two species show a high degree of homology. Only Segment I of the sex chromosome (Chromosome A) shows marked differences. The banding pattern proposed for this segment in D. guanche could have originated from a cluster of overlapping inversions including A1 arrangement.

Genomic blot hybridization as a tool of phylogenetic analysis: evolutionary divergence in the genus Drosophila

Comparative, quantitative Southern analysis of genomic DNA, using single-copy sequence probes, potentially is valuable for phylogenetic analysis. We have examined 27 Drosophila species, belonging to two subgenera, seven species groups, and ten subgroups, using a variety of cloned and characterized probes: twelve cloned sequences from D. melanogaster, two from D. pseudoobscura, and two from D. grimshawi. The data are generally congruent with accepted phylogenetic relationships in Drosophila, and confirm or clarify some previously uncertain relationships. The potential and limitations of the method are discussed.