DOI: 10.5061/dryad.6jd34
title: Data from: Divergent clades or cryptic species? Mito-nuclear discordance in a Daphnia species complex

description: Background: Genetically divergent cryptic species are frequently detected
 by molecular methods. These discoveries are often a byproduct of molecular
 barcoding studies in which fragments of a selected marker are used for
 species identification. Highly divergent mitochondrial lineages and
 putative cryptic species are even detected in intensively studied animal
 taxa, such as the crustacean genus Daphnia. Recently, eleven such
 lineages, exhibiting genetic distances comparable to levels observed among
 well-defined species, were recorded in the D. longispina species complex,
 a group that contains several key taxa of freshwater ecosystems. We tested
 if three of those lineages represent indeed distinct species, by analyzing
 patterns of variation of ten nuclear microsatellite markers in six
 populations. Results: We observed a discordant pattern between
 mitochondrial and nuclear DNA, as all individuals carrying one of the
 divergent mitochondrial lineages grouped at the nuclear level with
 widespread, well-recognized species coexisting at the same localities
 (Daphnia galeata, D. longispina, and D. cucullata). Conclusions: A likely
 explanation for this pattern is the introgression of the mitochondrial
 genome of undescribed taxa into the common species, either in the distant
 past or after long-distance dispersal. The occurrence of highly divergent
 but rare mtDNA lineages in the gene pool of widespread species would
 suggest that hybridization and introgression in the D. longispina species
 complex is frequent even across large phylogenetic distances, and that
 discoveries of such distinct clades must be interpreted with caution.
 However, maintenance of ancient polymorphisms through selection is another
 plausible alternative that may cause the observed discordance and cannot
 be entirely excluded.
description: Multilocus genotype data
 of Daphnia longispina complexThis file contains the
 microsatellite data from the publication formatted as input file for the
 program Genetix, which was used to calculate a factorial correspondence
 analysis that is presented in the publication.Genetix data
 file.txtStructure data
 file_complete datasetThis is an input file
 for the clustering software Structure that contains multilocus genotype
 data of several taxa of the Daphnia longispina complex (Daphnia longispina
 = 103 individuals; D. galeata = 134 individuals; D. cucullata = 75
 individuals; Daphnia divergent mitochondrial clade I = 3 individuals;
 Daphnia divergent mitochondrial clade II = 11; Daphnia divergent
 mitochondrial clade III = 35 individuals). Information on the
 microsatellite loci as well as the populations are available in the
 publication or in the additional file associated to the
 publication.Structure results
 K=1-10_complete datasetThis file contains the
 results of the Structure analysis presented in the publication using the
 whole dataset. The zipfile includes the Evanno table as well as the
 indfiles for K1-10 that were obtained from Structure
 Harvester.Structure_results_complete_dataset.zipStructure parameter file_complete datasetThis file summarizes the Structure parameters that were used to obtain the results for the whole dataset presented in the publication.Structure date file_subset longispinaThis is an input file for the clustering software Structure that contains multilocus genotype data of Daphnia longispina (N = 103), Daphnia divergent mitochondrial clade II (N = 8), and Daphnia divergent mitochondrial clade III (N = 9). Information on the microsatellite loci as well as the populations are available in the publication or in the additional file associated to this publication.Structure parameter file_subset longispinaThis file summarizes the Structure parameters that were used to obtain the results of the taxon D. longispina (including individuals belonging to mitochondrial clade II and III) presented in the publication.Structure results K=1-15_subset longispinaThis file contains the results of the Structure analysis of D. longispina (including individuals belonging to divergent clades II and III) presented in the publication. The zipfile includes the Evanno table as well as the indfiles for K1-15 that were obtained from Structure Harvester.Structure_results_subset_longispina.zip