ITS1 chromatogramsThe folder contains all the chromatograms of the rotifer clones newly sequenced for this study. The folder also contains the Sequencher file of assembled sequence reads (“Sequencer_aligned_chromatograms.spf”) with *_H1 in the name of the sample indicating a single nucleotide heterozygote and “_LVH” indicating a length variant heterozygote.0_ITS1_chromatograms.tar.bz2AlignmentThe folder contains the LocARNA alignment result file for all the studied ITS1 sequences. The file “Haplotype_mapping.xlsx” contains the association between the haplotypes used in this study and those of Papakostas et al. (2016) Systematic Biology, 65: 508-524.1_Alignment.tar.bz2jModeltest2_BIC_resultThe file contains the BIC result of the model likelihoods calculated with jModeltest2 for the studied ITS1 alignment.BEAST runThis folder contains the files associated with the BEAST analysis used in the manuscript.3_BEAST.tar.bz2Result of GMYCThis file contains the result of the GMYC species delimitation analysis on the tree selected using TreeAnnotator as described in the manuscript. Haplotype numbers are as inferred for this study (check file "Haploype mapping.xlsx" at the "Alignment" datafile of this Dryad submission for drawing a connection with the haplotypes used in Papakostas et al. (2016) Systematic Biology, 65: 508-524).Rotifer_microphotographsThis file contains Rotifer microphotographs analysed for the morphometric analysis of the four species described in the manuscript in addition to the '9_Rotifer microphotographs' of Papakostas et al 2016: Systematic Biology 65: 508-524S1 TableThis file contains the results of the Redundancy analysis (RDA) showing the amount of morphometric variation explained by species identity for each pair of the investigated speciesS2 TableThis file contains the summary statistics for the selection of morphometric traits measured on individuals of the four speciesS3 TableThis files contains the results of the Classification functions of the stepwise discriminant analysis performed on species A, B, C, and DS4 TableThis file contains the results of the Classification functions of the stepwise discriminant analysis performed on species B, C, and DS1 textThis file contains Records of Brachionus calyciflorus with notes on the name used.

The discovery and exploration of cryptic species have been profoundly expedited thanks to developments in molecular biology and phylogenetics. In this study, we apply a reverse taxonomy approach to the Brachionus calyciflorus species complex, a commonly studied freshwater monogonont rotifer. By combining phylogenetic, morphometric and morphological analyses, we confirm the existence of four cryptic species that have been recently suggested by a molecular study. Based on these results and according to an exhaustive review of the taxonomic literature, we name each of these four species and provide their taxonomic description alongside a diagnostic key.