DOI: 10.5061/dryad.v0t0d
title: Data from: Phylogenetic patterns of geographical and ecological diversification in the subgenus Drosophila

description: Colonisation of new geographic regions and/or of new ecological resources
 can result in rapid species diversification into the new ecological niches
 available. Members of the subgenus Drosophila are distributed across the
 globe and show a large diversity of ecological niches. Furthermore,
 taxonomic classification of Drosophila includes the rank radiation, which
 refers to closely related species groups. Nevertheless, it has never been
 tested if these taxonomic radiations correspond to evolutionary
 radiations. Here we present a study of the patterns of diversification of
 Drosophila to test for increased diversification rates in relation to the
 geographic and ecological diversification processes. For this, we have
 estimated and dated a phylogeny of 218 species belonging to the major
 species groups of the subgenus. The obtained phylogenies are largely
 consistent with previous studies and indicate that the major groups
 appeared during the Oligocene/Miocene transition or early Miocene,
 characterized by a trend of climate warming with brief periods of
 glaciation. Ancestral reconstruction of geographic ranges and ecological
 resource use suggest at least two dispersals to the Neotropics from the
 ancestral Asiatic tropical disribution, and several transitions to
 specialized ecological resource use (mycophagous and cactophilic).
 Colonisation of new geographic regions and/or of new ecological resources
 can result in rapid species diversification into the new ecological niches
 available. However, diversification analyses show no significant support
 for adaptive radiations as a result of geographic dispersal or ecological
 resource shift. Also, cactophily has not resulted in an increase in the
 diversification rate of the repleta and related groups. It is thus
 concluded that the taxonomic radiations do not correspond to adaptive
 radiations.
description: Figure 1 xml
 filexml file used in the
 BEAST analyses of Drosophila using 218 ingroup species and 9 calibration
 points.alignment_analysis.xmlFigure 1 treeFigure 1. Summarized chronogram for the subgenus Drosophila obtained with BEAST using 218 species and 9 calibration points. It corresponds to the analysis run with the Figure 1 xml file.summary.treeFigure 2 xml filexml file used to run the BEAST analysis of Figure 2, using 153 species for which there was sequence data for 2 or 3 genes and 9 calibration points.partitioned_2-3genes_all_calibrations.xmlFigure 2 treeSummarized chronogram for the subgenus Drosophila obtained with BEAST using 153 species and 9 calibration points, corresponding to the Figure 2 xml file analysis.MCC_summary.treeFigure 3 xml fileFile used to run the BEAST analyses of the subgenus Drosophila obtained with BEAST using all 218 species and 5 calibration points. Corresponding to the Figure 3.partitioned_all_spp.xmlFigure 3 treeFigure 3. Summarized chronogram for the subgenus Drosophila obtained with BEAST using 218 species and 5 calibration points. It corresponds to the Figure 3 xml file.partitioned_summary.treFig4AAncestral reconstruction of geographic distribution. Tree showing the main dispersal events inferred to have occurred during the evolution of the Drosophila subgenus.Fig4BAncestral reconstruction of ecological niche. Trees showing the main ecological shifts inferred to have occurred during the evolution of the Drosophila subgenus.Fig5AFigure 5. Backbone topology used in the MEDUSA analyses. A) phylogeny backbone from analysis with 218 species and 9 calibration points. Tip names refer to the species groups (those polyphyletic were clustered into a single clade) and numbers in brackets refer to the species richness of the tip. Numbers on nodes indicate divergence times.Fig5BFigure 5. Backbone topology used in the MEDUSA analyses. Phylogeny backbone from analysis with 218 species and 5 calibration points. Tip names refer to the species groups (those polyphyletic were clustered into a single clade) and numbers in brackets refer to the species richness of the tip. Numbers on nodes indicate divergence times.