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

Abstract

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.

Figure 1

Saturation plots for nucleotide substitutions. For each comparison, ratios of ti/tv for pairs of sequences (Y-coordinate) are graphed versus the corresponding numbers of total substitutions (X-coordinate). (A) and (B), concatenated sequence of the mitochondrial genes, 1st+2nd and 3rd codon positions, respectively; (C) and (D), Adh sequence, 1st+2nd and 3rd codon positions, respectively.

Figure 2

Phylogenetic trees based on NT data. (A) A single MP tree constructed with un-weighted scheme (tree length = 3233; CI = 0.4930; RI = 0.5581); (B) A single MP tree constructed with six-parameter weighting scheme (tree length = 2313.3101, CI = 0.5016, RI = 0.6059); (C) ML tree (-ln L = 20990.05); (C) Bayesian tree. Numbers besides nodes indicate bootstrap values in (A), (B) and (C), but posterior probabilities in (D). Symbols indicate the taxonomic assignment of species: affinis subgroup (●); pseudoobscura subgroup (○); obscura subgroup (■); sinobscura subgroup (□); subobscura subgroup (◆); microlabis subgroup (◇).

Figure 3

Phylogenetic trees based on AA data set. (A) Strict consensus of 17 equally parsimonious trees (tree length = 433, CI = 0.7367, RI = 0.7355); (B) Bayesian tree inferred with the Poisson model, with gamma-distributed rate variation across sites and a proportion of invariable sites; (C) Bayesian tree inferred with the GTR model, with gamma-distributed rate variation across sites and a proportion of invariable sites. Numbers besides nodes are bootstrap values of 1000 replicates in (A); those in (B) and (C) are posterior probabilities. Symbols are same as in Figure 2.

Figure 4

Linearized ML tree deduced from concatenated nucleotide sequences of the 4 mitochondrial loci. A time interval of 30–35 Mya for the obscura-melanogaster divergence [9] was used as calibration. Shaded areas (gray) indicate the time span of temperate forest developing in the Northern Hemisphere [50]. The numbers in the circle indicate the calibration points, and those in the panes indicate the estimated intervals of divergence times in light of the calibration points. For some very recent divergences, the estimates are not shown. Abbreviations: Eo. = Eocene; Oligo. = Oligocene; Mio = Miocene; Plio. = Pliocene; Q. = Quaternary. Symbols are same as in Figure 2.

Figure 5

CFD of normalized branching times for the KITSCH trees of 27 obscura group species. The largest difference between empirical and expected CFDs is indicated.