DOI: 10.5061/dryad.q0j90
title: Data from: Molecular phylogeny and timing of diversification in Alpine Rhithrogena (Ephemeroptera: Heptageniidae)

description: Background Larvae of the Holarctic mayfly genus Rhithrogena Eaton, 1881
 (Ephemeroptera, Heptageniidae) are a diverse and abundant member of stream
 and river communities and are routinely used as bio-indicators of water
 quality. Rhithrogena is well diversified in the European Alps, with a
 number of locally endemic species, and several cryptic species have been
 recently detected. While several informal species groups are
 morphologically well defined, a lack of reliable characters for species
 identification considerably hampers their study. Their relationships,
 origin, timing of speciation and mechanisms promoting their
 diversification in the Alps are unknown. Results Here we present a
 species-level phylogeny of Rhithrogena in Europe using two mitochondrial
 and three nuclear gene regions. To improve sampling in a genus with many
 cryptic species, individuals were selected for analysis according to a
 recent DNA-based taxonomy rather than traditional nomenclature. A
 coalescent-based species tree and a reconstruction based on a supermatrix
 approach supported five of the species groups as monophyletic. A molecular
 clock, mapped on the most resolved phylogeny and calibrated using
 published mitochondrial evolution rates for insects, suggested an origin
 of Alpine Rhithrogena in the Oligocene/Miocene boundary. A diversification
 analysis that included simulation of missing species indicated a constant
 speciation rate over time, rather than any pronounced periods of rapid
 speciation. Ancestral state reconstructions provided evidence for
 downstream diversification in at least two species groups. Conclusions Our
 species-level analyses of five gene regions provide clearer definitions of
 species groups within European Rhithrogena. A constant speciation rate
 over time suggests that the paleoclimatic fluctuations, including the
 Pleistocene glaciations, did not significantly influence the tempo of
 diversification of Alpine species. A downstream diversification trend in
 the hybrida and alpestris species groups supports a previously proposed
 headwater origin hypothesis for aquatic insects.
description: 16S
 matrixThe mitochondrial 16S
 alignment in fasta format16S.fastacox1 matrixThe mitochondrial cox1 alignment in fasta formatcox1.fastaEF-1α matrixThe nuclear EF-1α alignment in fasta formatEF-1alpha.fastaPEPCK matrixThe nuclear PEPCK alignment in fasta formatPEPCK.fastawg matrixThe nuclear wg alignment in fasta formatwg.fastaSpecies tree *BEAST input fileThe species tree *BEAST input file in xml formatsp_tree_STARBEAST_input.xml16S *BEAST tree fileThe mitochondrial 16S *BEAST output tree16S_STARBEAST.treecox1 pos1-2_*BEAST tree fileThe mitochondrial cox1 *BEAST output tree for codon positions 1 and 2cox1_pos1-2_STARBEAST.treecox1 pos3 *BEAST tree fileThe mitochondrial cox1 *BEAST output tree for codon position 3cox1_pos3_STARBEAST.treeEF-1α *BEAST tree fileThe nuclear EF-1α *BEAST output treeEF-1alpha_STARBEAST.treePEPCK pos1-2 *BEAST tree fileThe nuclear PEPCK *BEAST output tree for codon positions 1 and 2PEPCK_pos1-2_STARBEAST.treePEPCK pos3-intron *BEAST tree fileThe nuclear PEPCK *BEAST output tree for codon position 3 and intronPEPCK_pos3-intron_STARBEAST.treewg *BEAST tree fileThe nuclear wg *BEAST output treewg_STARBEAST.treespecies tree *BEAST output fileThe *BEAST output species tree including the five genes (cox1 + 16S + PEPCK + EF-1α + wg)species_tree_STARBEAST.treemitochondrial MrBayes input fileThe concatenated mitochondrial (cox1 + 16S) MrBayes input file in nexus formatmt_MrBayes_input.nexnuclear MrBayes input fileThe concatenated nuclear (PEPCK + EF-1α + wg) MrBayes input file in nexus formatnuc_MrBayes_input.nexconcatenated MrBayes input fileThe concatenated (cox1 + 16S + PEPCK + EF-1α + wg) Mrbayes input file in nexus formatcombined_MrBayes_input.nexcox1 MrBayes tree fileThe mitochondrial cox1 MrBayes output treecox1_MrBayes_tree.nex16S MrBayes tree flleThe mitochondrial 16S MrBayes output tree16S_MrBayes_tree.nexPEPCK MrBayes treee fileThe nuclear PEPCK MrBayes output treePEPCK_MrBayes_treee.nexEF-1α MrBayes tree fileThe nuclear EF-1α MrBayes output treeEF-1alpha_MrBayes_tree.nexwg MrBayes tree fileThe nuclear wg MrBayes output treewg_MrBayes_tree.nexmitochondrial MrBayes tree fileThe concatenated mitochondrial (cox1 + 16S) MrBayes output treemt_MrBayes_tree.nexnuclear MrBayes tree fileThe concatenated nuclear (PEPCK + EF-1α + wg) MrBayes output treenuc_MrBayes_tree.nexconcatenated MrBayes tree fileThe concatenated (cox1 + 16S + PEPCK + EF-1α + wg) MrBayes output treecombined_MrBayes_tree.nexmitochondrial Garli tree fileThe concatenated mitochondrial (cox1 + 16S) Garli output treemt_Garli_tree.trenuclear Garli tree fileThe concatenated nuclear (PEPCK + EF-1α + wg) Garli output treenuc_Garli_tree.treconcatenated Garli tree fileThe concatenated (cox1 + 16S + PEPCK + EF-1α + wg) Garli output treecombined_Garli_tree.tremitochondrial BEAST input fileThe mitochondrial (cox1 + 16S) Beast input file (dating analysis) in xml formatmt_BEAST_input.xmlmitochondrial BEAST tree fileThe mitochondrial (cox1 + 16S) Beast (dating analysis) output treemt_BEAST.treeCorSiM R scriptthe R script of the CorSiM analyses for simulation of missing speciesCorSiM_script.R