DrosoPhyla: Resources for Drosophilid Phylogeny and Systematics

Abstract

The vinegar fly Drosophila melanogaster is a pivotal model for invertebrate development, genetics, physiology, neuroscience, and disease. The whole family Drosophilidae, which contains over 4,400 species, offers a plethora of cases for comparative and evolutionary studies. Despite a long history of phylogenetic inference, many relationships remain unresolved among the genera, subgenera, and species groups in the Drosophilidae. To clarify these relationships, we first developed a set of new genomic markers and assembled a multilocus data set of 17 genes from 704 species of Drosophilidae. We then inferred a species tree with highly supported groups for this family. Additionally, we were able to determine the phylogenetic position of some previously unplaced species. These results establish a new framework for investigating the evolution of traits in fruit flies, as well as valuable resources for systematics.

Keywords: Drosophilidae; phylogenomics; systematics.

Fig. 1.

Phylogram of the 704-taxon analyses. IQ-TREE maximum-likelihood analysis was conducted under the GTR+R+FO model. Support values obtained after 100 bootstrap replicates are shown for selected supragroup branches, and infragroup branches within the melanogaster group (all the support values are shown online). Black dots indicate support values of PP>0.9 and BP>90; gray dots 0.9 ≥ PP>0.75 and 90 ≥ BP>75; black squares only BP>90; gray squares only 90 ≥ BP>75. Scale bar indicates the number of changes per site. Groups and subgroups are numbered or abbreviated as follows: (1) montium, (2) takahashii sgr, (3) suzukii sgr, (4) eugracilis sgr, (5) melanogaster sgr, (6) ficusphila sgr, (7) elegans sgr, (8) rhopaloa sgr, (9) ananassae, (10) Collessia, (11) mesophragmatica, (12) dreyfusi, (13), coffeata, (14) canalinea, (15) nannoptera, (16) annulimana, (17) flavopilosa, (18) flexa, (19) angor, (20) Dorsilopha, (21) ornatifrons, (22) histrio, (23) macroptera, (24) testacea, (25) bizonata, (26) funebris, (27) Samoaia, (28) quadrilineata sgr, (29) Liodrosophila, (30) Hypselothyrea, (31) Sphaerogastrella, (32) Zygothrica I, (33) Paramycodrosophila, (34) Hirtodrosophila III, (35) Hirtodrosophila II, (36) Hirtodrosophila I, (37) Dettopsomyia, (38) Mulgravea, (39) Hirtodrosophila IV, (40) Zygothrica II, Chy, Chymomyza; Colo, Colocasiomyia; Dichae, Dichaetophora; immigr, immigrans; Lord, Lordiphosa; Mic, Microdrosophila; Myco, Mycodrosophila; pol, polychaeta; salt, saltans; Scap, Scaptodrosophila; trip, tripunctata; will, willistoni.

Fig. 2.

(A) Phylogram of the 83-taxon analyses. The overall matrix represents 14,961 nucleotides and 83 taxa, including 63 composite ones. Support values obtained after 100 bootstrap replicates and Bayesian posterior probabilities are shown for selected branches and mapped onto the ML topology (all the support values are shown in supplementary fig. S1, Supplementary Material online). The dotted line indicates that the placement of Dettopsomyia varies between ML and Bayesian trees. Scale bar indicates the number of changes per site. (B–H) Photos of species of particular interest in this article. (B) Drosophila oshimai female (top) and male (bottom) (Japan, courtesy of Japan Drosophila Database), (C and D) Collessia kirishimana (Japan, courtesy of Masafumi Inoue), (E and F) Drosophila annulipes (Japan, courtesy of Yasuo Hoshino), (G) Drosophila pruinosa (São Tomé, courtesy of Stéphane Prigent), (H) Drosophila adamsi (Cameroun, courtesy of Stéphane Prigent).

Fig. 3.

Concordance versus mutational saturation of the phylogenetic markers. The y axis indicates the percentage of concordant nodes, and the x axis indicates the saturation level. In comparison with published markers (black dots), the markers developed in this study (orange dots) generally show moderate saturation levels and satisfying concordance.