Divergent clades or cryptic species? Mito-nuclear discordance in a Daphnia species complex

Abstract

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.

Keywords: Adaptive introgression; Ancestral polymorphism; Cladocera; Daphnia longispina complex; Incomplete lineage sorting; Interspecific hybridization.

Fig. 1

Comparison of nuclear and mitochondrial DNA patterns in the Daphnia longispina species complex. Factorial correspondence analysis (a) demonstrating the position of the 49 individuals belonging to mtDNA clades I, II, or III in relation to the reference dataset (grey circles) consisting of 312 individuals belonging to D. galeata, D. longispina, and D. cucullata. Genetic relationships are depicted using the first two factors of an FCA based on multilocus genotypes from ten microsatellite loci (see Additional file 1 Fig. S1 for illustrations of factor 1 and 3 as well as 2 and 3). All individuals that were characterized as pure taxa according to their assignment probabilities calculated in Structure 2.3.4 [34] are encased by an oval. Patterns of variation of the 12S rDNA [derived and modified from 8] is shown in the inset Maximum Likelihood tree (b). The six divergent mitochondrial lineages firstly described by [8] are labelled I-VI and the remaining five divergent lineages are labelled according to their origin (N: Norway; J1, J2: Japan; R1, R2: Russia)

Fig. 2

Detection of the uppermost hierarchical level of genetic structure in the complete microsatellite dataset. Ln P(D) and convergence between replicates (open circles with error bars) as well as Delta K (filled circles) were used for the detection of the most likely number of K. The graph is modified from the output derived from Structure Harvester [36]. According to these results, K = 3 is adequate to describe the structure in the dataset

Fig. 3

Results of the admixture analysis of all 49 individuals belonging to mtDNA clades I, II, and III. Analysis was performed using Structure 2.3.4 [34] with K = 3 where each cluster associates to one of the well-recognized species D. galeata (green), D. longispina (blue), and D. cucullata (purple); reference data are not shown. The population identification code as well as the corresponding mtDNA clade are given on the x axis and the posterior probabilities on the y axis. For information on population codes see Table 1