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

Abstract

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.

Phylogeny of the Subgenus Sophophora (Diptera: Drosophilidae) Based on Combined Analysis of Nuclear and Mitochondrial Sequences

“…The hypothesis supported by morphology, biogeography, and molecular mt 16S (DeSalle, 1991) and nu Adh (Russo et al, 1995) data is shown on the left. The hypothesis supported by analysis of nu 28S rRNA (Pelendakis et al, 1991;Pelendakis and Solignac, 1993) is on the right. …”

“…Pelendakis et al (1991) and Pelendakis and Solignac (1993), based on neighbor joining analysis of the 28S rRNA locus, suggest that the melanogaster species group, as traditionally defined, is not a monophyletic lineage. The ananassae subgroup, which has traditionally been placed in the melanogaster species group, was shown to be the sister taxon of the obscura species group (Fig.…”

“…Alignment of the 28S locus was exactly as in Pelendakis et al (1991) and Pelendakis and Solignac (1993). The alignment of the COII and Adh coding regions was trivial.…”

“…We have examined these data, along with previously published data from the 28S rRNA locus (Pelendakis et al, 1991;Pelendakis and Solignac, 1993), in both individual and combined analyses, to test the monophyly of Sophophora and its component groups. Although we were unable to address the monophyly of Sophophora relative to Lordiphosa (see below), we (1) determined the relationships among the major groups defined within the subgenus Sophophora (the melanogaster, obscura, saltans, and willistoni species groups; the Neotropical clade; and the melanogaster-obscura clade) and (2) tested whether these groups are monophyletic.…”

Chromosomal Rearrangement Inferred From Comparisons of 12 Drosophila Genomes

“…They estimate the divergence between the D. montium subgroup and D. melanogaster to be $12.7 MY. Although there are some reports to the contrary (Yang et al 2004), a majority of the other studies estimate that D. ananassae branched off prior to the D. montium subgroup and after the D. obscura group (Pelandakis et al 1991;Pelandakis and Solignac 1993;Clark et al 1998;Harr et al 2000;Goto and Kimura 2001;Tamura et al 2004). We have chosen an approximate estimate of 20 MY for the divergence between D. melanogaster and D. ananassae on the basis of these observations (Table 1).…”