A phylogeny of Drosophilidae using the Amyrel gene: questioning the Drosophila melanogaster species group boundaries

Abstract

In this study, the phylogenetic relationships of 164 species of the family Drosophilidae are discussed, using the Amyrel gene, a member of the a-amylase multigene family. This study focuses on numerous species groups in the subgenera Sophophora and Drosophila of the genus Drosophila but also includes other closely related genera. Nucleotide data were analysed by several methods: maximum parsimony, neighbour joining, maximum likelihood and Bayesian inference. Heterogeneity of base composition (mainly low GC contents in the species groups willistoni and saltans) has been addressed. In all analyses, the genus Drosophila appeared paraphyletic. The subgenus Sophophora clearly appeared to be a monophyletic group, showing well-resolved clades, with the Neotropical groups arising in a basal position. Here, it is proposed to raise the species subgroups ananassae and montium to the rank of species group, and to restrict the melanogaster species group to the melanogaster subgroup plus the ÔOrientalÕ subgroups, among which the suzukii subgroup is polyphyletic. Some related genera such as Zaprionus, Liodrosophila, Scaptomyza and Hirtodrosophila are clustered with, or inside the subgenus Drosophila, which is therefore paraphyletic and should be reviewed.

Connecting systematic and ecological studies using DNA barcoding in a population survey of Drosophilidae (Diptera) from Mt Oku (Cameroon)

“…4) even though the dentissima group is considered to be distinct from the melanogaster group (Tsacas 1980). This result is, however, in agreement with the proposition of raising the ananassae and montium species subgroups to species groups (Da Lage et al 2007). A barcode in the genus Lissocephala was sequenced for the first time and branched within the subgenus Sophophora, an unexpected observation needing confirmation, since this genus is generally given a basal position in Drosophilinae based on morphology (Throckmorton 1975) or molecular data (Harry et al 1996(Harry et al , 1998Yassin 2013).…”

“…The molecular phylogeny of Drosophila has been thoroughly studied using a number of markers (e.g., Pelandakis & Solignac 1993;Remsen & O'Grady 2002;Da Lage et al 2007;van der Linde et al 2010), including whole genomes (Drosophila 12 genomes consortium 2007). These studies were searching deep nodes in order to identify the main groups in this very large genus.…”

Species-Wide Genetic Variation and Demographic History of Drosophila sechellia, a Species Lacking Population Structure

“…The recent survey of 136 olfactory and gustative receptor genes in D. sechellia has revealed an increase in gene loss due to a high rate of lack-offunction mutations (Mcbride 2007). D. sechellia is also the only species showing deletions that cause genes that are highly conserved among species of the melanogaster subgroup and Drosophila in general to be nonfunctional, like Amyrel (see results; Da Lage et al 2007) and Amy (Shibata and Yamazaki 1995). All these observations are consistent with a stronger effect of genetic drift in a historically small-sized population of D. sechellia.…”

Tropical Africa as a cradle for horizontal transfers of transposable elements between species of the genera Drosophila and Zaprionus

“…However, studies using different molecular markers have continued to corroborate the original positioning of Zaprionus within the genus Drosophila. [21][22][23][24][25] Despite these results, the scientific community still considers Zaprionus as a separate genus. Regardless of the phylogenetic position adopted for the genus Zaprionus, their species and those of the melanogaster subgroup (subgenus Sophophora, genus Drosophila), the focus of this review, have evolved separately for at least 40 Mya and may be as old as 60 Mya.…”