- Research article
- Open Access
Divergent clades or cryptic species? Mito-nuclear discordance in a Daphnia species complex
© The Author(s). 2017
- Received: 8 June 2017
- Accepted: 8 November 2017
- Published: 22 November 2017
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.
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).
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.
- Interspecific hybridization
- Adaptive introgression
- Ancestral polymorphism
- Incomplete lineage sorting
- Daphnia longispina complex
Since the plea for DNA taxonomy  and the introduction of the DNA barcoding concept  the use of mitochondrial DNA (mtDNA) as genetic marker in animals has become an inherent part not only of taxonomic research but is also widely used in systematics, phylogeography, population genetics, ecology and evolutionary biology. One initial goal of integrating genetic markers into traditional taxonomy was to uncover hidden diversity [2–4]. Especially genetically divergent cryptic species, i.e., those pooled under a single name due to their morphological similarity [5, 6], could be easily detected by the use of molecular markers. Since the introduction of the polymerase chain reaction (PCR) in the 1980s, the number of reports of cryptic species increased exponentially .
Interestingly, divergent mitochondrial lineages are still detected even in well-studied groups. This is also true for the freshwater crustacean genus Daphnia (Cladocera: Anomopoda), in which previously undescribed lineages were recovered in most biogeographical regions . Within the Daphnia longispina species complex, a dominant taxonomic group of Daphnia in lake plankton of northern temperate zone, an extensive amount of mitochondrial lineages was reported recently [8–11], with eleven divergent clades without applicable names. The levels of genetic differentiation of seven lineages reported from Europe [8, 11] are as high or even higher than the genetic differentiation among well-recognized species of that complex. Specifically, the sequence divergence from their closest sister clade, expressed as Kimura 2-parameter distance calculated for the mitochondrial gene for the 12S ribosomal ribonucleic acid (12S rRNA), ranged from 10.8 to 17.6% . It was thus suggested that these lineages may represent distinct biological species .
However, not every divergent mitochondrial DNA lineage should be considered as species [e.g., [12–14]. Several studies show that the divergence detected at the mitochondrial level is not always supported by nuclear DNA data [e.g., 15, 16]. The reasons for such a discrepancy in mitochondrial and nuclear DNA patterns are diverse . On the one hand, nuclear mitochondrial pseudogenes (numts) or pseudogenes from the mitochondrial genome that originate from duplication events might be amplified rather than the functional target gene . On the other hand, cyto-nuclear discordance may be caused by various biological processes, like hybridization and subsequent introgression of the mitochondrial genome [15, 16, 19], incomplete lineage sorting of ancestral polymorphisms [19–21], or selection acting on mitochondrial genes, either direct due to, e.g., environmental factors [22, 23], or through indirect selection induced by maternally inherited symbionts [reviewed by 24]. Thus, firm conclusions about the delimitations of species based on genetic data should be drawn from a combination of different approaches, e.g., combining mtDNA and nuclear DNA, and assessing evidence on the level of gene flow between putative species.
The main aim of our study was to analyze at least some of the distinct mitochondrial lineages of the Daphnia longispina species complex reported recently from Europe , to gather additional evidence in favor or against the hypothesis that they represent cryptic species. Therefore, we studied individuals belonging to three distinct mitochondrial lineages from six geographically distant localities using nuclear microsatellite markers  in addition to the mitochondrial gene for the 12S rRNA.
Data on populations from which analyzed individuals belonging to mtDNA clades I, II and III were obtained.
Neuhofener Altrhein (oxbow lake)
As no distinguishing morphological characters were reported for the respective mitochondrial lineages, we screened for these lineages by sequencing mitochondrial 12S rDNA in randomly selected individuals from the respective populations (in total, 508 individuals were studied at the mitochondrial level; for more information on sample sizes per population see Table 1). Total DNA was extracted either by using HotSHOT  or H3 extraction method [according to 29].
We aimed for the amplification of an approximately 600 bp fragment of the mitochondrial gene for 12S rRNA [following 11]. If DNA samples had low quality and the amplification of the target marker failed, shorter fragments that still allowed discrimination within the Daphnia longispina complex were amplified, either according to a previously published protocol [30; fragment length approximately 150 bp] or using newly designed primer pairs (segment 1 with an approximate length of 190 bp: forward 5′ CAGGGTATCTAATCCTGG 3′, reverse 5′ GCGACGGCTGGCACGATTT 3′; segment 2 with an approximate length of 230 bp: forward 5′ CTGCACCTTGACCTGAAGT 3′, reverse 5′ CAGGGTATCTAATCCTGG 3′). All amplification products were sequenced using forward and reverse primer on a capillary sequencer (either 3130xl or 3730 Genetic Analyzer; Applied Biosystems). The sequences were manually checked using Geneious 4 (Biomatters Ltd) with a particular focus on possible presence of double peaks or other ambiguities, and aligned using MUSCLE algorithm  implemented in MEGA 6 .
Individuals which belonged to one of the previously undescribed mtDNA lineages (clade I = 3 individuals, clade II = 11 individuals, and clade III = 35 individuals) were subsequently analyzed at the nuclear level by characterizing the variation at ten microsatellite loci (DaB17/17, Dgm105, Dgm109, Dgm112, Dp196NB, Dp281NB, Dp519, SwiD6, SwiD14, SwiD18) that were originally developed for D. galeata, D. longispina, D. cucullata and other taxa of the D. longispina complex [27, 33]. Each individual was assigned to a multilocus genotype (MLG), based on the allelic variation at all ten loci. We compared the allelic variation with a reference dataset consisting of 312 individuals of D. galeata, D. longispina, and D. cucullata from 21 European locations [see Additional file 1: Table S1 for information on reference populations; partly published in 33].
To test if individuals with previously undescribed mtDNA lineages were also divergent at the nuclear level, we used a model-based assignment test implemented in Structure 2.3.4  to identify the number of genetic clusters in the total dataset (i.e., 312 reference individuals and 49 individuals belonging to the three divergent mitochondrial lineages). As we were only interested in the interspecific patterns, we limited the number of expected groups to a range of K = 1–10 (the upper bound already exceeding the number of expected taxa within the dataset).
For each value of K we conducted ten independent replicates using 100,000 burn-in iterations and 900,000 Markov Chain Monte Carlo (MCMC) steps and we used the admixture modus (ancestry model) as well as independent allele frequencies (allele frequency model). For the assessment of the most likely value of K, we employed the ΔK method  implemented in Structure Harvester  and evaluated Ln P(D), convergence between replicates as well as individual assignment probabilities. Individuals with a probability to belong to a certain cluster exceeding 90% were regarded as pure-taxon individuals while the others were regarded as hybrids or individuals showing some level of backcrossing or introgression [according to 37]. In addition to the model-based assignment test, the pattern of similarity among individuals from the whole dataset, based on their MLGs, was characterized using an factorial correspondence analysis (FCA) implemented in Genetix 4.05 .
Furthermore, we conducted a hierarchical Structure analysis using all individuals assigned to D. longispina, including 103 reference individuals, eight individuals belonging to clade II and nine individuals belonging to clade III. The number of K was set to 1–15 with ten replicates for each K using 50,000 burn-in iterations and 450,000 MCMC steps for each replicate. As in the preceding Structure analysis description, we used the admixture modus as well as independent allele frequencies among populations and employed ΔK, Ln P(D) and convergence between replicates to assess the most likely number of K in the D. longispina data set. With this additional analysis, we wanted to evaluate if within one taxon a substructure is apparent that would support the distinct status of the divergent lineages.
We sequenced 508 individuals from the six studied localities and detected 49 individuals belonging to one of the previously undescribed mtDNA clades (Table 1). Three were assigned to clade I (Druksiai, Lithuania), eleven to clade II (three from Norrviken, Sweden; and eight from Seragah, Iran), and 35 to clade III (seven from Želivka, Czechia; 27 from Neuhofener Altrhein, Germany; and one from Esch-sur-Sûre, Luxembourg). Clades I and III were only represented by a single already reported haplotype . Clade II, however, was represented by two haplotypes, one found in the Swedish population  and the other one in the Iranian population (GenBank accession number: KY652589). In all locations, other coexisting Daphnia taxa were detected when sequencing the mitochondrial 12S rDNA (Table 1); in three sites (Druksiai, Želivka, and Neuhofener Altrhein), three different hybridizing species coexisted (D. longispina, D. galeata, and D. cucullata).
Analysis of the structure within D. longispina (including 103 reference individuals and individuals of clade II and III) resulted in a most likely number of seven or eight clusters, respectively (Additional file 1: Figure S2). These clusters corresponded mainly to geographically distinct populations, and the resulting pattern did not support a separation of D. longispina, clade II and clade III (Additional file 1: Figure S3).
The distinctness of the 49 focal individuals, each belonging to one of the three studied mtDNA clades according to 12S rDNA, was not confirmed at the nuclear level. On the contrary, all these individuals were assorted to one of the coexisting species of the complex (Fig. 1): D. galeata (clade II), D. longispina (clade II and III), and D. cucullata (clade I). This finding explains the lack of earlier nuclear evidence (based on allozyme and ITS-RFLP studies) of an unknown taxon in the reservoir Želivka [see 8]. An additional study analyzing in detail Daphnia population structure from the same locality by ten microsatellite markers also failed to find any evidence of an additional distinct taxon . Our data also show that the divergent mtDNA lineages are not a short-term phenomenon but rather persist over longer time periods: Lineage III was detected at different times over one growing season in Neuhofener Altrhein (Table 1) and lineage II was still detected in lake Norrviken after almost two decades.
The reason for these discordant patterns of mitochondrial and nuclear DNA could be, in principle, a methodological artifact in case we failed to amplify the functional mtDNA gene under study and sequenced pseudogenes instead. Especially, the so-called numts (nuclear copies of mitochondrial DNA) are reported frequently . These numts are, in general, observed for protein-coding genes [but see 40 for an example of ribosomal DNA] and some of them still look functional (i.e., exhibit no signs of stop codons or frameshifts within the coding region). In addition, cases are known where those numts are diverged enough that they were inappropriately considered as evidence for the presence of different species [see 18 for more information]. Besides numts, mitochondrial pseudogenes due to gene duplication have also been observed  but they are assumed to be very rare.
However, we consider the pseudogene scenarios an unlikely explanation for the observed patterns. First, the original study reporting the divergent lineages  already evaluated whether the secondary structures of obtained sequences correspond to that expected from functional ribosomal RNAs. Second, for some individuals from the reservoir Želivka  and the lake Seragah (unpublished data), additional partial sequences of mitochondrial genes for the cytochrome c oxidase subunit 1 (COI) and for the reduced nicotine adenine dinucleotide dehydrogenase subunit 2 (ND2) were obtained, confirming the distinctness of the mitochondrial genomes of those lineages.
There are, however, further explanations for the discordant patterns of mitochondrial and nuclear DNA that should be considered when evaluating the hypothesis that divergent mitochondrial lineages represent cryptic species within the D. longispina complex.
For example, cases of mito-nuclear discordances are observed after hybridization and subsequent introgression of the mitochondrial genome [15, 16, reviewed by 17]. The authors of a recent meta-analysis on freshwater and marine fish emphasized that discordance is expected to be higher in freshwater fish due to greater historical hybridization and introgression within this group . Individuals of the genus Daphnia and especially of the D. longispina complex are known to hybridize regularly . In the D. longispina complex, D. galeata is reported as the most “aggressively” hybridizing taxon  and its interspecific hybrids with at least five other taxa (D. mendotae, D. lacustris, D. dentifera, D. longispina, and D. cucullata) have been detected [e.g., 9, 33, 45, 46]. Most hybrids of the D. longispina complex are categorized as F1 hybrids, but also later-generation hybrids and backcrosses have been frequently detected [e.g., 33, [47–50], which confirms that gene flow between the parental species, although reduced , is not entirely restricted. This is also supported by studies that detected mitochondrial introgression within the D. longispina complex [50, 52–54] as well as mitochondrial capture in other Daphnia species . Thus, the discordant patterns found in our study may indeed be explained by introgressive hybridization. However, the source taxa of the mitochondrial genomes are not known, either because individuals of the original taxon have not yet been discovered, or because they are extinct. This would not be an exception; the authors of other studies concluded in comparable cases that mitochondrial introgression did cause cyto-nuclear discrepancies, although they failed to identify the source species [13: leaf beetle Chrysomela, 56: Drosophila quinaria].
Incomplete lineage sorting (ILS) of ancestral polymorphisms is another possible scenario [17, 19] as assumed for example for the mito-nuclear discordance observed in the Drosophila serido haplogroup . Distinguishing between ILS and introgression is difficult and often the only indications might be drawn from genetic data. It was suggested that haplotypes which hold a phylogenetically basal position are hints for ancestral polymorphisms and that no predictable geographical pattern is expected from ILS . However, these criteria are inadequate to distinguish ancient mitochondrial introgression from ILS. Most of the previously reported divergent mtDNA lineages in the D. longispina complex  are phylogenetically basal compared to the mtDNA lineages of well-recognized species and so far no geographic pattern is visible (but the number of observations is very low at the moment). This would support the idea that the mtDNA variation we observed is due to ILS according to the above-mentioned criteria. However, the divergence among mtDNA lineages in this complex  is so high (10.8 to 17.6% sequence divergence from their closest sister clade expressed as Kimura 2-parameter distance) that stochastically driven ILS is highly unlikely as lineage sorting in mitochondrial loci progresses fast .
Direct balancing selection may preserve ancestral polymorphisms within a population indefinitely . Often, it is assumed that mitochondrial DNA is selectively neutral; however, various recent studies show deviations from these assumptions [e.g. 22, 23, 57] and propose that mitochondrial DNA variation might be determined also by natural selection. Even in the Daphnia longispina complex, experimental evidence was collected indicating a higher fitness of certain haplotypes under various temperature regimes . Additionally, simulations have shown that uniparentally inherited loci may display strong phylogeographic structures generated by weak selection . Therefore, it is possible that we detected rare ancestral mitochondrial lineages in the D. longispina species complex that are favored under specific environmental conditions, like temperature, predation, food quality or quantity. However, we have no experimental evidence yet to verify the potential adaptive value of the divergent mtDNA lineages.
Besides direct selection, indirect selection induced by maternally inherited symbionts (including parasites), might also explain mito-nuclear discordance [reviewed by 24]. In these cases, certain mitochondrial genomes might be linked to the transmission of those symbionts. The maintenance of different symbionts via natural selection could, therefore, result in mitochondrial differentiation between populations despite ongoing gene flow. However, also selective sweeps, occurring in one population but not in others, might induce this pattern . This is reported for the intracellular bacteria of the genus Wolbachia (which is not known to infect Daphnia ), but a few studies of other vertically transmitted symbionts indicate that this is not genus-specific . Most symbionts so far studied in Daphnia (mostly microparasites) are nevertheless transmitted horizontally and not vertically , even though many Daphnia species, including those of the D. longispina complex [e.g., 62], carry them. Intracellular parasites that are known to transmit vertically in Daphnia are species of the microsporidian genus Hamiltosporidium . Yet, to our knowledge, there is no published study presenting a case of mito-nuclear discordance caused by a microsporidian. Irrespective thereof, the mitochondrial divergence caused by such a process is expected to be lower than the deep divergence we observed in Daphnia.
In the studied populations, we observed high mitochondrial divergence in the absence of nuclear divergence in the Daphnia longispina species complex. For the reasons discussed above, we would exclude methodological artifacts (like the amplification and sequencing of numts or pseudogenes instead of the functional gene) as explanation. In addition, the level of divergence among lineages is so high that we find stochastic ILS as well as indirect selection that arose from linkage disequilibrium with maternally transmitted symbionts highly unlikely. Likely explanations are that we observe polymorphisms resulting from past introgression from unknown source taxa, or maintained through selection. Both explanations are plausible, as hybridization and introgression are common phenomena in this species complex  and experimental evidence hints that selection of mitochondrial genomes may occur in Daphnia .
Altogether, we consider past hybridization and introgression as most probable explanation for the observed polymorphisms in the lineages I, II and III, assuming that the original parental lineages did not evolve efficient reproductive barriers. This is commonly observed also for other taxa in the D. longispina species complex and long-lasting introgressed lineages have been recorded before; a well-described example is D. mendotae, which arose from hybridization between D. galeata and D. dentifera but subsequently maintained its distinct character . The observed patterns in our study might be the legacy of long-range dispersal events that ended up in mitochondrial DNA introgression rather than establishment of separated lineages. If the presumed parental species of lineages I-III still exist somewhere as entities with distinct nuclear genomes, their distribution is either geographically restricted or scattered [as hypothesized in 8], possibly in understudied regions like Siberia or parts of eastern and north-eastern Europe.
The results of our study illustrate that the discovery of highly divergent mitochondrial DNA lineages does not necessarily translate into the discovery of previously undescribed species. Additional evidence, like the analyses of nuclear markers, morphology, biogeography, or behavior, is mandatory. Detailed studies of divergent mitochondrial lineages frequently reveal relevant, but small, phenotypic differences, supporting the conclusion that they are indeed distinct taxa [e.g., 64, 65]. Also in the genus Daphnia two such species have been recently described from Europe: Daphnia hrbaceki  and Daphnia inopinata . Considering the substantial yet undescribed and often unexplored variation within the genus , we assume that other new species descriptions will follow. However, our study indicates that high mtDNA divergence represents a precondition, but not a sufficient criterion for species delimitation.
We thank Kęstutis Arbačiauskas for the zooplankton sample from Lake Druksiai, Isabelle Thys for the sample from reservoir Esch-sur-Sûre, and Melanie Sinn, Irene Kregul, Linda Peters, and Jasna Vukić for laboratory support. In addition, we thank four anonymous reviewers for comments improving the manuscript.
The authors acknowledge the support by the Czech Science Foundations (project P506/10/P167) and by the Biodiversity and Climate Research Centre Frankfurt am Main (BiKF; “LOEWE–Landes-Offensive zur Entwicklung Wissenschaftlich-ökonomischer Exzellenz” of Hesse’s Ministry of Higher Education, Research and the Arts). In addition, AK received a support from the Charles University Mobility Fund.
Availability of data and materials
The microsatellite dataset of the 49 individuals belonging to the divergent mitochondrial lineages I, II and III as well as the reference data are published in Dryad Digital Repository (doi:https://doi.org/10.5061/dryad.6jd34) as input files for the programs Structure and Genetix. The Structure parameter files as well as the results of both analyses (complete dataset and D. longispina subset) are also stored in Dryad Digital Repository. The sequence data are stored in GenBank (accession number KY652589).
AP, AT and KS had the original idea for the study. AM, AP and AT obtained the samples. AK, AM and AT conducted the genetic analyses. AK and AT carried out the statistical analyses, interpreted the results with input from AP and KS. AT wrote the manuscript with input from all authors. All authors read and approved the final version.
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