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 dataset 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.

Phylogenomic analyses of the genusDrosophilareveals genomic signals of climate adaptation

“…Our phylogenies (Figure 1) agree with the generally accepted view that the genus Drosophila is paraphyletic to other genera and can be divided into two large clades (Finet et al, 2021; et al, 1995) or closest to either the immigrans-tripunctata (Zhou & Bachtrog, 2015) or Hawaiian-repleta radiations (Finet et al, 2021) within the Drosophila. We placed Z. bogoriensis, the only Zaprionus species in our data set, together with the immigrans-tripunctata radiation, which concurs with three earlier studies (Finet et al, 2021;O'Grady & DeSalle, 2018;Yassin, 2013) that grouped at least some Zaprionus species with that radiation. Within the immigranstripunctata radiation, we placed D. rubida as an outgroup to both D. immigrans and D. albomicans/D.…”

“…Comparative genomic studies on such a broad scale require a well resolved phylogeny. However, despite numerous phylogenetic studies of Drosophila species, many relationships among them remain controversial and the genus also now appears to be paraphyletic to several other genera (Finet et al, 2021;van der Linde & Houle, 2008;van der Linde et al, 2010;O'Grady & DeSalle, 2018).…”

Repression precedes independent evolutionary gains of a highly specific gene expression pattern

“…The genes included the 15 nuclear markers Amyrel ( Amyrel ), Distal-less ( Dll ), Dopa decarboxylase ( Ddc ), ebony ( e ), engrailed ( en ), even-skipped ( eve ), hedgehog ( hh ), Notum ( Notum ), patched ( ptc ), wingless ( wg ), 28S ribosomal RNA ( 28S ), Alcohol dehydrogenase ( Adh ), Glycerol-3-phosphate dehydrogenase ( Gpdh ), Superoxide dismutase ( Sod ), Xanthine dehydrogenase ( Xdh ), and the two mitochondrial markers cytochrome oxidase subunit 1 ( COI ) and cytochrome oxidase subunit 2 ( COII ). Nucleotide sequences of the 20 drosophilid species were retrieved from the DrosoPhyla project ( Finet et al, 2021 ), and nucleotide sequences of M. domestica were collected from the NCBI database. Alignments for each individual gene were generated using MUSCLE ( Edgar, 2004 ) with default parameters.…”

“…Unreliably aligned positions were excluded using trimAl with parameters −gt 0.5 and −st 0.001 ( Capella-Gutiérrez et al, 2009 ). In-house Python scripts were used to concatenate the aligned sequences ( Finet et al, 2021 ). Maximum-likelihood searches were performed using PhyML 3.0 ( Guindon et al, 2010 ) under the GTR+Γ 4 +I model, and 100 bootstrap replicates were conducted for support estimation.…”

“…Percentages on key nodes indicate probability of bond EB expression in the ancestor. Phylogeny was constructed using data from Finet et al (2021) . Scale bar indicates the number of nucleotide changes per site.…”