Evolutionary and ecological consequences of interspecific hybridization in cladocerans

Ceriodaphnia (Cladocera: Daphniidae) in China: Lineage diversity, phylogeography and possible interspecific hybridization

The distribution and species/lineage diversity of freshwater invertebrate zooplankton remains understudied in China. Here, we explored the species/lineage diversity and phylogeography of Ceriodaphnia species across China. The taxonomy of this genus is under-explored. Seven morphospecies of Ceriodaphnia (C. cornuta, C. laticaudata, C. megops, C. pulchella, C. quadrangula, C. rotunda and C. spinata) were identified across 45 of 422 water bodies examined. Rather little morphological variation was observed within any single morphospecies regardless of country of origin. Nevertheless, we recognized that some or all of these morphospecies might represent species complexes. To investigate this, phylogenetic relationships within and among these morphospecies were investigated based on mitochondrial (partial cytochrome c oxidase subunit I gene) and nuclear (partial 28S rRNA gene) markers. The mitochondrial marker placed these populations in nine lineages corresponding to the morphospecies: C. laticaudata and C. pulchella were each represented by two lineages, suggesting that both are species complexes. The remaining five morphospecies were each represented by a single mtDNA lineage. Three of the nine mitochondrial lineages (belonging to C. pulchella, C. rotunda and C. megops) are newly reported and exhibited a restricted distribution within China. The nuclear-DNA phylogeny also recognized seven Ceriodaphnia taxa within China. We detected occasional mito-nuclear discordances in Ceriodaphnia taxa across China, suggesting interspecific introgression and hybridization. Our study contributes to an understanding of the species/lineage diversity of Ceriodaphnia, a genus with understudied taxonomy.

New lineages and old species: Lineage diversity and regional distribution of Moina (Crustacea: Cladocera) in China

The distribution and genetic diversity of freshwater zooplankton is understudied in the Eastern Palearctic. Here, we explored the lineage diversity and regional distribution of the genus Moina in China. Members of this genus are often keystone components of freshwater ecosystems and have been frequently subjected to toxicological and physiological studies. Four species of Moina were identified, based on morphology, in 50 of 113 Chinese water bodies examined, and their phylogenetic position was analyzed using both a mitochondrial (mitochondrial cytochrome c oxidase subunit I; COI) and a nuclear marker (the nuclear internal transcribed spacer; ITS-1). Both molecular markers identified four clades corresponding broadly to the morphological species. Mitochondrial DNA analysis showed the presence of four species complexes with eleven lineages across China, five of which were new. However, some lineages (and even individual haplotypes) were widespread in Eurasia, suggesting an ability to disperse over long distances. In contrast, a few lineages exhibited restricted distributions. The nuclear phylogeny also recognized four species of Moina within China and seven very distinct clades. Interestingly, one specimen possessing Moina cf. micrura mtDNA had ITS-1 alleles of the M. cf. brachiata clade. This discordance between mtDNA and nuclear ITS-1 phylogenies is indicative of interspecific introgression and hybridization. Additionally, our COI phylogeny showed apparent paraphyly in two Moina species groups, suggesting introgression of their mitochondrial genomes. Our data shows the regional distribution/diversity of the Moina species complex in a Eurasian context.

Daphnia diversity on the Tibetan Plateau measured by DNA taxonomy

Daphnia on the Tibetan Plateau has been little studied, and information on species diversity and biogeography is lacking. Here, we conducted a 4-year survey using the barcoding fragment of the mitochondrial COI gene to determine the distribution and diversity of Daphnia species found across the Plateau. Our results show that species richness is higher than previously thought, with total described and provisional species number doubling from 5 to 10. Six of the taxonomic units recovered by DNA taxonomy agreed well with morphology, but DNA barcoding distinguished three clades each for the D. longispina (D. galeata, D. dentifera, and D. longispina) and D. pulex (D. pulex, D. cf. tenebrosa, and D. pulicaria) complexes. The sequence divergence between congeneric species varied within a large range, from 9.25% to 30.71%. The endemic D. tibetana was the most common and widespread species, occurring in 12 hyposaline to mesosaline lakes. The lineage of D. longispina is the first confirmed occurrence in west Tibet.

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

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.

Species and hybrids in the genus Diaphanosoma Fischer, 1850 (Crustacea: Branchiopoda: Cladocera)

Cladocerans are well-studied planktonic crustaceans, especially those of the genus Daphnia in which interesting evolutionary questions have been addressed on speciation processes. The aim of the present study is to demonstrate that other genera of cladocerans show similar levels of cryptic diversity, intraspecific gene flow, and thus become useful model systems for comparison. In order to do so, we chose the genus Diaphanosoma, widespread in tropical and temperate areas. We started with a survey of species diversity in the genus Diaphanosoma in Asia using a morphological approach, then obtained sequences from a mitochondrial and a nuclear marker from multiple individuals of different species, performed tests on DNA taxonomy and molecular phylogenies, and assessed the role of hybridization in explaining the cases of mitonuclear discordance. The results are that cryptic diversity occurs in Diaphanosoma, and mitonuclear discordance was found in about 6% of the sequenced animals. Past hybridization is supported as the most likely explanation for the discordance: no evidence was found of first generation hybrids with heterozygous sequences. Our analysis on patterns of genetic diversity in Diaphanosoma supports similarities and differences with what is known in Daphnia.

Diversification of mitochondrial genome of Daphnia galeata (Cladocera, Crustacea): Comparison with phylogenetic consideration of the complete sequences of clones isolated from five lakes in Japan

To characterize genetic diversity and gene flow among Daphnia galeata populations, the complete nucleotide (nt) sequences of the mitochondrial (mt) DNAs of D. galeata clones isolated from five lakes in Japan (Lakes Shirakaba, Suwa, Kizaki, Kasumigaura, and Biwa) were determined. Comparison of non-synonymous (amino acid altering) substitution rates with synonymous substitution rates of D. galeata mt protein-coding genes demonstrated that ATPase8 and COI genes were the most and least susceptible, respectively, to the evolutional forces selecting the aa substitutions. Several non-synonymous substitutions were found in ATPase8 and ATPase6 even in the comparison that no synonymous substitution was found. Comparison of the total number of nt variations among the mt DNAs suggested the phylogenetic relationship ((((Shirakaba/Suwa, Kizaki), Kasumigaura), Biwa), D. pulex). Maximum-likelihood analysis using the total nt sequences of mt protein-coding genes confirmed this relationship with bootstrap values higher than 98%. All the mtDNAs of the analyzed Japanese D. galeata clones contained a control region of essentially the same structure that is distinct from those of the previously reported European Daphnia species of the D. longispina complex. The two control regions of different structures spread among mtDNAs of the Japanese and European Daphnia species, respectively, probably after the divergence of the Japanese D. galeata under different selection pressures associated with their habitats.

Genetic structure of Daphnia galeata populations in Eastern China

This study presents the first examination of the genetic structure of Daphnia longispina complex populations in Eastern China. Only one species, D. galeata, was present across the eight investigated lakes; as identified by taxon assignment using allelic variation at 15 microsatellite loci. Three genetically differentiated D. galeata subgroups emerged independent of the type of statistical analysis applied. Thus, Bayesian clustering, discriminant analysis based on results from factorial correspondence analysis, and UPGMA clustering consistently showed that populations from two neighbouring lakes were genetically separated from a mixture of genotypes found in other lakes, which formed another two subgroups. Clonal diversity was high in all D. galeata populations, and most samples showed no deviation from Hardy-Weinberg equilibrium, indicating that clonal selection had little effect on the genetic diversity. Overall, populations did not cluster by geographical origin. Further studies will show if the observed pattern can be explained by natural colonization processes or by recent anthropogenic impact on predominantly artificial lakes.

Population structure of a microparasite infecting Daphnia: spatio-temporal dynamics

Background

Detailed knowledge of spatial and temporal variation in the genetic population structure of hosts and parasites is required for understanding of host − parasite coevolution. As hot-spots of contemporary coevolution in natural systems are difficult to detect and long-term studies are restricted to few systems, additional population genetic data from various host − parasite systems may provide important insights into the topic. This is particularly true for parasites, as these players have been under-investigated so far due to the lower availability of suitable molecular markers. Here, we traced genetic variation (based on sequence variants in the internal transcribed spacer region, ITS) among seven geographically isolated populations of the ichthyosporean Caullerya mesnili, a common microparasite of the cladoceran Daphnia (here, the D. longispina hybrid complex). At three sites, we also studied parasite genetic variation over time (three to four sampling points) and tested for associations between parasite genotypes and host species.

Results

Parasite (and host) populations were significantly structured across space, indicating limited dispersal. Moreover, the frequency of parasite genotypes varied significantly over time, suggesting rapid evolutionary change in Caullerya. However, the distribution of parasite genotypes was similar across different host species, which might in turn have important consequences for parasite epidemiology.

Conclusions

The approach proposed here can be applied to track spatial and temporal changes in the population structure of other microparasite species for which sequence variation in the ITS or other highly variable genome regions has been documented but other types of polymorphic markers are lacking. Screening of parasite sequence variants allows for reliable detection of cross-species infections and, using advanced sequencing techniques in the near future, for detailed studies of parasite evolution in natural host − parasite systems.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-014-0247-3) contains supplementary material, which is available to authorized users.

Fine-scale temporal and spatial variation of taxon and clonal structure in the Daphnia longispina hybrid complex in heterogeneous environments

Background

Cyclical parthenogenetic water fleas of the genus Daphnia have become a prominent model organism in ecology and evolution. In the past, analyses of their population structure have been limited by the prevailing use of allozyme markers, which in general do not allow for the distinction of individual clones. In this study, we used 10 microsatellite markers to track changes in the taxonomic and clonal composition of Daphnia populations, and traced the abundance of the most common clones in two European reservoirs. One of the localities was inhabited by a single species of the Daphnia longispina complex (D. galeata), the other by two parental species (D. galeata and D. longispina) and their interspecific hybrids. The study took place during the transition from summer stratification to autumn mixing, representing a period of major environmental change within lake habitats.

Results

In both reservoirs, we observed temporal (generation-to-generation) and spatial (along the heterogeneous reservoir environment) changes in Daphnia community structure. In the single-species reservoir, the clonal diversity of D. galeata increased with time, as a few dominant clones were replaced by a higher number of less common clones. A loss in selective advantage for the dominant clones may have been due to gradual changes in the environment, or due to selection acting in a negative frequency-dependent manner. In the multispecies reservoir, there were no apparent temporal trends in clonal diversity but we observed significantly lower clonal diversity in the interspecific hybrids than in the coexisting parental species, supporting the existence of reproductive barriers between the parental genomes.

Conclusions

Our study, tracing clonal lineages of Daphnia in time and space by the fine-resolution markers, contributes to the understanding of how clonal reproduction impacts community structure in cyclically parthenogenetic organisms.

Speciation with gene flow and the genetics of habitat transitions

Whether speciation can advance to completion in the face of initially high levels of gene flow is a very controversial topic in evolutionary biology. Extensive gene exchange is generally considered to homogenize populations and counteract divergence. Moreover, the role of introgressive hybridization in evolution remains largely unexplored in animals, particularly in freshwater zooplankton in which allopatric speciation is considered to be the norm. Our work investigates the genetic structure of two young ecological species: the pond species, Daphnia pulex and the lake species, Daphnia pulicaria. Phylogenetic and population genetics analyses were conducted on mitochondrial NADH dehydrogenase 5 (ND5) gene, the nuclear Lactate dehydrogenase (Ldh) gene and 21 nuclear microsatellite markers in 416 individuals from habitats with various degrees of permanence. The strong and consistent phylogenetic discordance between nuclear and mitochondrial markers suggests a complex evolutionary history of multiple independent habitat transition events that involved hybridization and introgression between lake and pond Daphnia. On the other hand, the low level of contemporary gene flow between adjacent populations indicates the presence of effective habitat isolating barriers. The Daphnia system provides strong evidence for a divergence-with-gene flow speciation model that involves multiple habitat transition events.

Porous genomes and species integrity in the branchiopod Artemia

Over the years, studies on interspecific hybridization have highlighted cases where gene exchange between taxa continues for a significant amount of time after speciation. The reasons for this lag of reproductive isolation relative to genetic isolation are largely unclear, and the question still remains whether the resulting hybrids represent novel biological (and taxonomic) diversity or merely an evolutionary liability. We provide strong indications in the branchiopod Artemia that hybrids between distantly related species may not be evolutionary inconsequential. Based on a global sampling of published and newly derived nuclear (ITS1) and mitochondrial (16S rRNA) sequence data from all representatives of the genus, we have identified natural hybrids between Artemia species (A. persimilisxA. franciscana, A. salinaxA. franciscana) separated by evolutionary interludes of tens of millions of years. Our combined analytical framework of cladistic and network methods provides evidence that hybridizations are the result of recent secondary contact following pronounced allopatric differentiation. The detection of mitochondrial introgression from A. persimilis to A. franciscana attests F(1) hybrid fertility. The reasons for this apparent unidirectionality of introgression are currently unknown but a likely explanation is provided based on morphometric divergence. We discuss the evolutionary implications of our results within the broader context of continental zooplankters.

The impact of human-made ecological changes on the genetic architecture of Daphnia species

The overenrichment (eutrophication) of aquatic ecosystems with nutrients leading to algal blooms and anoxic conditions has been a persistent and widespread environmental problem. Although there are many studies on the ecological impact of elevated phosphorus (P) levels (e.g., decrease in biodiversity and water quality), little is known about the evolutionary consequences for animal species. We reconstructed the genetic architecture of a Daphnia species complex in 2 European lakes using diapausing eggs that were isolated from sediment layers covering the past 100 years. Changes in total P were clearly associated with a shift in species composition and the population structure of evolutionary lineages. Although environmental conditions were largely re-established after peak eutrophication during the 1970s and 1980s, original species composition and the genetic architecture of species were not restored but evolved along new evolutionary trajectories. Our data demonstrate that anthropogenically induced temporal alterations of habitats are associated with long-lasting changes in communities and species via interspecific hybridization and introgression.

Daphnia hybridization along ecological gradients in pelagic environments: the potential for the presence of hybrid zones in plankton

The relative homogeneity of pelagic environments has been regarded as the reason for the absence of hybrid zones for hybridizing planktonic Daphnia (Crustacea: Cladocera); occasional dominance of interspecific hybrids over parental species was explained by their temporal superiority in fluctuating environments. However, water bodies with spatially varying environmental conditions might facilitate the formation of hybrid zones in plankton. We studied the distribution of species and hybrids of the Daphnia longispina complex in 11 canyon-shaped reservoirs, localities characterized by horizontal environmental gradients (particularly of food supply and size-selective predation); we also analysed patterns of carapace size and fecundity among coexisting taxa. Spatial distribution of taxa agreed with their ecological characteristics; those showing different affinities along longitudinal reservoir profiles differed in size according to the presumed fish predation gradient. Only hybrids of Daphnia galeata with Daphnia cucullata and D. longispina (=hyalina) were recorded. The latter two species preferred opposite ends of gradients, such spatial segregation probably explaining the absence of their hybrids. Distributional patterns were relatively stable in two consecutive summers, apart from a substantial decline of D. galeata X cucullata in the second year. The observed pattern of a hybrid-dominated zone in intermediate conditions suggests that local Daphnia hybrid zones may indeed form within reservoirs.

Effects of food availability on the acute and chronic toxicity of the insecticide methomyl to Daphnia spp

The widespread increase of pesticides application in crops threats vicinal freshwater lentic ecosystems, frequently leading to their contamination. Due to their position in the aquatic food web, the responses to these pesticide inputs of freshwater filter-feeding zooplankters, as daphnids, provide relevant information the general risk to the ecosystem of xenobiotics. Moreover, cladoceran grazers often face fluctuations in food availability due to the phytoplankton dynamics in lentic water bodies, and food acquisition naturally conditions their fitness. In this study, the responses of Daphnia magna, and of three genotypes within the Daphnia longispina complex, to acute and chronic exposures of methomyl, were assessed. In addition, we focused on whether the food level can model the Daphnia life-history responses to the insecticide. Results showed that methomyl was acutely and chronically toxic to both D. magna and the D. cf longispina populations at very low concentrations, and remarkable differences in sensitivity were noticed when comparing the responses to the toxic among taxa/genotypes. Furthermore, food availability conditioned the overall fitness of the species although not interacting specifically on the response to the toxicant stress.

Geographic and phylogenetic evidence for dispersed nuclear introgression in a daphniid with sexual propagules

The role of among-species gene flow in eukaryotic evolution remains controversial. Putative hybrid lineages are common in water fleas, but their ecological success is often associated with polyploidy and the production of asexual propagules. Advanced hybrid lineages with sexual propagules are expected to be geographically restricted because their successful dispersal is contingent on overcoming fertility complications, assimilation by parent taxa, and competition with parent taxa. Here we provide evidence that a diploid lineage of Daphnia has been formed by introgression between distantly related species and attained a broad distribution (Nearctic) despite its requirement for sexual propagules. The evidence is based on geographical discordance, phylogenetic discordance, recombinant genotypes and additive genotypes of the nuclear internal transcribed spacer regions (ITS) and mitochondrial DNA. Additive genotypes also provided evidence of hybridization between introduced European Daphnia and North American Daphnia. We argue that the unique biology of Holarctic lacustrine water fleas and the spatial separation of lineages during Pleistocene glaciation have promoted hybridization and its evolutionary consequences.

Gene flow across a climatic barrier between hybridizing avian species, California and Gambel's quail (Callipepla californica and C. gambelii)

Allopatric species commonly interbreed in a restricted margin between their ranges. The particular factors that permit interbreeding between species determine the extent of hybridization and its significance for evolution and conservation. Using California quail and Gambel's quail (Callipepla californica and C. gambelii) that naturally hybridize in a narrow region between relatively mesic and xeric environments, I assessed the exchange of genetic and phenotypic traits in relation to vegetative and climatic features (temperature and precipitation) that characterize the area of range overlap, and I examined genetic and phenotypic traits within the hybrid zone over a five-year period in relation to variation in precipitation. Using microsatellite markers, this study reveals that genetic, plumage, and morphometric traits are tightly associated with vegetation, rainfall, and temperature profiles through the abrupt transition from one parental species to the other across the hybrid zone. Results show that the hybrid zone has remained clinal, stationary, and bounded over the five-year study period. There was no evidence of introgression outside the narrow hybrid zone. Interannual climatic fluctuations are associated with internal hybrid zone dynamics but did not alter the shape and position of the zone. A transect through the hybrid zone revealed rapid and episodic genetic mixing within the zone. Possible long-term consequences of this restricted hybridization for the evolution of the two parental species are discussed in the light of changing environments.

Mitochondrial DNA variation in North American populations of Daphnia obtusa: continentalism or cryptic endemism?

The morphological stasis of many freshwater crustaceans has resulted in the prior delineation of cosmopolitan species and has been explained by their capacity for long-distance dispersal. This study examines the phylogeography of Daphnia obtusa, a cladoceran thought to be widespread in North America. However, sequence variation of the mitochondrial cytochrome c oxidase subunit I gene indicates that this taxon is composed of two morphologically cryptic species, designated D. obtusa NA1 and NA2. NA2 is restricted to the east, whereas NA1 is broadly distributed across the United States, and is subdivided into four phylogroups that show weak genetic differentiation over broad geographical areas, which likely reflects recent long-distance dispersal. The current distributions of the four phylogroups in NA1 can be explained by recent range expansion from different refugia following the last Pleistocene glacial advance. Interestingly, the mitochondrial phylogroups identified in this study do not correspond to lineages detected in a previous allozyme analysis. However, the latter groups are associated with a habitat shift suggesting that natural selection may have played a role in their divergence. The results of this and previous studies illustrate the complicated biogeographical history of freshwater cladocerans.

Molecular systematics of European Hyalodaphnia: the role of contemporary hybridization in ancient species

We examined phylogenetic relationships among Daphnia using mitochondrial DNA (mtDNA) sequences from the small subunit ribosomal RNA (12S), cytochrome c oxidase subunit I and nuclear DNA sequences from the first and second internal transcribed spacer representing 1612 base positions. Phylogenetic analyses using several species of the three main Daphnia subgenera, Ctenodaphnia, Hyalodaphnia and Daphnia, revealed that the Hyalodaphnia are a monophyletic sister group of the Daphnia. Most Hyalodaphnia species occur on one continent, whereas only three are found in North America and Europe. Endemicity of species is associated with variation in thermal tolerance and habitat differentiation. Although many species of the Hyalodaphnia are known to hybridize in nature, mtDNA divergence is relatively high ca. 9%) compared to other hybridizing arthropods (ca. 3%). Reproductive isolation in Daphnia seems to evolve significantly slower than genetic isolation. We related these findings to what is known about the ecology and genetics of Daphnia in order to better understand the evolutionary diversification of lineages. The relationship of these data to phylogenetic patterns is discussed in the context of speciation processes in Daphnia.