Microsatellite markers for European Daphnia

We present 32 polymorphic microsatellite markers for species of the European Daphnia longispina group: D. galeata, D. hyalina, D. rosea, D. cucullata and D. curvirostris. Microsatellite markers were either isolated from genomic libraries or optimized based on previously published sequence information of sister taxa. Cross‐species tests revealed that all but one of the polymorphic markers are applicable to more than one species, which allows intra‐ and interspecific genetic studies on, i.e. population structure, hybridization events and introgression.     

Clonal diversity,clonal persistence and rapid taxon replacement in natural populations of species and hybrids of the Daphnia longispina complex

Hybridization is common among cyclical parthenogens, especially in zooplankton species assemblages of the genus Daphnia. To explore hybridization dynamics and the extent of clonal diversity in the Daphnia longispina complex, we analysed population structure in eight permanent lakes. Based on 15 microsatellite loci, three major taxonomic units emerged: two species, D. galeata and D. longispina and their F1 hybrids, supported by factorial correspondence analysis and two Bayesian methods. At the same time, the detection of backcross classes differed between methods. Mean clonal diversity was lowest in the F1 hybrids, as expected from the high rate of asexual reproduction. Within taxa, replicated genotypes were of clonal origin, but clonal lineages persisted in subsequent years in only one of three resampled lakes. In another lake, the taxon composition changed from being dominated by hybrids to complete dominance by one parental taxon. Such a year‐to‐year taxon replacement has not been reported for the D. longispina complex before. Our data on this hybrid complex illustrate that high‐resolution genotyping is essential for the understanding of ecological and evolutionary outcomes of hybridization in partially clonal taxa.     

Intra-specific rDNA-ITS restriction site variation and an improved protocol to distinguish species and hybrids in the Daphnia longispina complex

A collaborative research effort was undertaken to evaluate the robustness of a recently developed genetic tool for species identification of members in the morphologically variable Daphnia longispina species complex. This genetic method, based on restriction fragment length polymorphism (RFLP) of the internal transcribed spacer region (ITS) of nuclear ribosomal DNA (rDNA) with restriction enzymes Mwo I and Sau96 I [Billiones et al., 2004. Hydrobiologia 526: 43–53], was applied to many different European populations. Results were compared with two or more independently obtained characters (morphology, allozymes, mitochondrial DNA (mtDNA), or cloned rDNA-ITS sequences). Individuals of most taxa were readily identified, but unexpected ITS-RFLP patterns were found in many individuals indicated by other markers to be D. galeata or one of its hybrids. Among 43 investigated D. galeata populations (902 specimen analysed by ITS-RFLP), deviant RFLP fragment patterns occurred in 26 (i.e., more than half) of the populations. The deviant patterns could be attributed to the loss of one single restriction site in the ITS2 region. This loss made the distinction of D. galeata from other species unreliable, and F1 hybrids could not be identified. Future users should be aware of this shortcoming of the Billions et al. [2004. Hydrobiologia 526: 43–53] protocol. As a solution to this problem, we present an improved genetic identification protocol based on a simple double digestion of the rDNA-ITS region with the restriction enzymes BsrB I and EagI. Sequence analyses of rDNA-ITS clones and preliminary testing indicate that the new protocol is unaffected by the rDNA variation which troubled the Mwo I/Sau96 I protocol. Further, the new protocol identifies all European species of the D. longispina complex, as well as their F1 hybrids. However, a wider screening is required to verify its general utility for all species, since yet unknown variation may occur. Guest editor: Piet Spaak Cladocera: Proceedings of the 7th International Symposium on Cladocera     

Identifying hybridizing taxa within the <Emphasis Type="Italic">Daphnia longispina</Emphasis> species complex: a comparison of genetic methods and phenotypic approaches

Daphnia galeata Sars, D. longispina O. F. Müller and D. cucullata Sars (Crustacea: Cladocera) are closely related species which often produce interspecific hybrids in natural populations. Several marker systems are available for taxon determination in this hybridizing complex, but their performance and reliability has not been systematically assessed. We compared results from identifications by three molecular methods. More than 1,200 individuals from 10 localities in the Czech Republic were identified as parental species or hybrids by allozyme electrophoresis and the analysis of the restriction fragment length polymorphism of the internal transcribed spacer (ITS-RFLP); over 440 of them were additionally analyzed and identified by 12 microsatellite loci. Identification by microsatellite markers corresponded well with allozyme analyses. However, consistent discrepancies between ITS-RFLP and other markers were observed in two out of 10 studied localities. Although some marker discrepancies may have been caused by occasional recent introgression, consistent deviations between ITS-RFLP and other markers suggest a long-term maintenance of introgressed alleles. These results warn against its use as a sole identification method in field studies. Additionally, we quantitatively evaluated the discriminatory power of geometric morphometric (elliptic Fourier) analysis of body shapes based on photos of over 1,300 individuals pre-classified by allozyme markers. Furthermore, a randomly selected subset of 240 individuals was independently determined from photos by several experts. Despite a tendency for morphological divergence among parental Daphnia species, some taxa (especially D. galeata, D. longispina, and their hybrids) substantially overlapped in their body shapes. This was reflected in different determination success for particular species and hybrids in discriminant analysis based on shape data as well as from photographs.     

Filamentous cyanobacteria alter the relative fitness in a Daphnia hybrid species complex

相似文献   

Does global warming threaten the dynamics of Arctic charr in Lake Geneva?

In France, the Arctic charr (Salvelinus alpinus) is native in only two lakes (Lakes Bourget and Geneva), in the most southerly part of its distribution area. It is a profundal morph living at depths of between 30 and 100 m in Lake Geneva. Following considerable stocking of Lake Geneva with juvenile Arctic charr and some good results during the 1980s, catches are currently declining. Several hypotheses have been proposed to explain this decrease, but the potential influence of warming of the lake in the 1990s has not been considered. This article studies the relationship between the strength of the cohorts and the temperature in Lake Geneva from 1992 to 2002, and discusses the various potential causes of the population collapse observed. The findings reveal close correlation between water temperature and the strength of the cohorts. It is concluded that the recent warming of Lake Geneva may have a significant direct or indirect impact on the Arctic charr population.     

Bidirectional mitochondrial introgression between Korean cobitid fish mediated by hybridogenetic hybrids

Genomic introgression through interspecific hybridization has been observed in some species of the freshwater fish family Cobitidae. Within this family, a Cobitis hankugensis–Iksookimia longicorpa diploid–triploid hybrid species complex on the Korean peninsula is unique in displaying hybridogenesis, a unisexual reproduction mode that allows hybrids to mediate the transfer of mitochondrial DNA (but not nuclear DNA) between the two parent species. However, populations of the parental species in the wild have never been examined for the potential effect of introgression on their genomes. To address the genetic consequences of unisexual hybridization on the parental species, we examined genetic structure of the two parental species, C. hankugensis and I. longicorpa, in three independent natural habitats where they coexist with their hybrid complex using DNA sequence data of one mitochondrial gene and three nuclear genes. We found that mitochondrial introgression between the two species was extensive in all the examined localities, while there was no evidence of nuclear introgression across the species boundary. This result indicates that the hybridogenetic individuals mediate mitochondrial introgression from one species to the other, producing mito‐nuclear mosaic genomes such as C. hankugensis nuclear genomes associated with I. longicorpa mitochondrial DNA and the reverse. The direction and degree of introgression varied among the three localities, but the underlying mechanisms for this observation proved elusive. Introgression might depend on which species serves as the predominant sperm or ovum donor or the environmental conditions of the localities. The present study suggests that introgressive hybridization between pure C. hankugensis and I. longicorpa species is highly likely where the two species co‐occur with hybridogenetic individuals, but the consequence of introgression could be variable due to the history and environmental characteristics of particular populations across the parental species’ ranges.     

Genetic diversity and differentiation of Daphnia galeata in the middle and lower reaches of the Yangtze River,China

Mitochondrial 16S rDNA and CO I gene were used as molecular markers for the analysis of the genetic diversity and differentiation of Daphnia galeata populations in nine water bodies in the middle and lower reaches of the Yangtze River. In the combined 16S rDNA and CO I gene sequences, 54 variable sites and 44 haplotypes were observed among 219 individuals belonging to nine D. galeata populations. Average haplotype diversity and nucleotide diversity were, respectively, 0.72% and 0.56%. The F‐statistics (F_ST) value of the D. galeata populations was 0.149. According to the results of the neutral test, D. galeata in the middle and lower reaches of the Yangtze River had experienced a bottleneck effect in the history. Molecular variance analysis indicated that the genetic differentiation of the D. galeata populations mainly occurred within populations (85.09%). Greater genetic differentiations of D. galeata among individuals within populations appeared in the populations from the Huaihe River basin, whereas smaller genetic differentiations occurred in the populations from the middle reaches of the Yangtze River. Strong gene flows were all observed between Group I (four populations from the middle reaches of the Yangtze River) and Group ΙΙ (three populations from the middle and lower reaches of the Yangtze River), and Group ΙΙΙ (two populations from the Huaihe River basin). The effective migration rates (M) were 851.49 from Group I to Group ΙΙ and 685.96 from Group I to Group ΙΙΙ, respectively. However, no significant relationship was observed between the genetic differentiation and geographical distance of the nine populations (r = .137, p > .05). Results suggested that the genetic differentiation of D. galeata in the water bodies in the middle and lower reaches of the Yangtze River resulted mainly from geographical isolation.     

Daphnia Galeata × D. Longispina Hybrids in Western Norway

We describe the occurrence of D. galeata×longispina hybrids in two lakes of western Norway. Parental species and interspecific hybrids were characterised by both nuclear and mitochondrial molecular markers. In one of the populations, hybrids were shown to dominate the population over several years. A few individuals in both populations were probably not F1 hybrids, but possibly backcrosses or F2 hybrids. Most (possibly all) F1 hybrids were of D. galeata maternal origin. In addition, interspecific hybrids could be identified based on morphological characters, which were intermediate between the parental species. Interspecific hybridisation between these two species is remarkable, since they are distantly related.     

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.     

Identification of the Daphnia species (Crustacea: Cladocera) in the lakes of the Ob and Yenisei River basins: morphological and molecular phylogenetic approaches

The morphological and genetic variability of Daphnia species from 16 lakes in the upper watersheds of the Ob and Yenisei Rivers were investigated. Four species, namely D. galeata Sars 1863, D. cristata Sars 1862, D. curvirostris Eylmann, 1887 and D. longispina O.F. Müller, 1776 inhabit these lakes. In addition, longispina-like individuals in Lake Borzu-Khol (the Bolshoi Yenisei River basin) were found which were, however, clearly distinguishable from the other species by morphometric and mitochondrial DNA analyses and could belong to D. umbra based on the 12S sequences.     

Molecular genetic analysis of Daphnia in the English Lake District: species identity, hybridisation and resting egg banks

• 1 Taxonomic issues in many Daphnia species complexes are often confused by a high degree of phenotypic plasticity and by interspecific hybridisation. Here, we employ molecular genetic tools to confirm the species composition and incidence of hybridisation in extant and resting egg populations of Daphnia from Windermere and Esthwaite Water in the English Lake District.
• 2 A combination of species‐diagnostic allozymes and mtDNA, confirms that contemporary populations are dominated by a single species, D. galeata.
• 3 We present the first account of genetic characterisation of dated ‘resting’ eggs using microsatellites and mtDNA, employing PCR‐based DNA recovery, thus providing a temporal dimension to taxonomic patterns. Thirty years ago, two species were present in Esthwaite, D. galeata and D. hyalina, but Windermere populations were dominated by D. galeata only.
• 4 The use of PCR‐based mtDNA RFLP analysis as a species‐diagnostic tool, and microsatellites to monitor clonal diversity, provide a valuable approach for long‐term studies, especially in populations free from the complicating effect of frequent hybridisation. The detailed limnological records available for many large lakes, and associated changes in land‐use, pollutants and climate, combined with long‐term ephippial molecular genetic data, provide opportunities for exploring natural and anthropogenic impacts on genetic and community structure.

     

Differences in genetic structure and ecological diversity between parental forms and hybrids in a Daphnia species complex

Hybridization is a common phenomenon in Daphnia species complexes. Hybrids often dominate in Daphnia populations; therefore it is worthwhile to look for principal differences between parental and hybrid populations with respect to their genetic structure and clonal differentiation. We studied natural populations of members of the Daphnia galeata/hyalina/cucullata complex in three lakes. In one of these lakes, one parental species (D. galeata) and one hybrid (D. galeata × cucullata) were investigated more intensively. The frequency of sexual reproduction was higher in parental populations, whereas clonal diversity was higher in hybrid populations. Ecological differentiation among clonal groups was more pronounced in the D. galeata × cucullata hybrid compared to D. galeata, whereas selection intensity was weaker. These results are discussed with respect to stability of clonal groups, multiple hybridizations and selective constraints.     

Amplified Fragment Length Polymorphism (AFLP) Reveals Species-Specific Markers in the Daphnia Galeata–HyalinaSpecies Complex

Daphnia often occur in species complexes that consist of two or more co-occurring species and their hybrids. Hybrid individuals are often capable of sexual reproduction and so backcrossing with introgression occurs. To better understand hybridization and backcrossing frequency, we sought to develop PCR-based, species-specific markers in the Daphnia galeata–hyalina species complex using amplified fragment length polymorphism (AFLP). This technique produces large numbers of reproducible markers for assessing diversity across the nuclear genome and provides several advantages over mtDNA and microsatellite approaches. We examined 28 clones of D. galeata, D. hyalina, and their hybrids isolated from Lake Constance on the Swiss-German border. Using a single AFLP primer combination we found five potential species-specific markers, defined as bands that occurred in >80% of one parental species and <20% of the other. Two bands appeared to be co-dominant and were present (homozygous) in D. galeata, absent in D. hyalina, and heterozygous in the hybrid. We conclude AFLP could provide enough PCR-based, species-specific markers to identify species, hybrids, and backcrosses from even small amounts of tissue (i.e. resting eggs).     

Sensitivity and responses of diatoms to climate warming in lakes heavily influenced by humans

相似文献   

Molecular genetic data reveal hybridization between Typha angustifolia and Typha latifolia across a broad spatial scale in eastern North America

A recent increase in the abundance of cattails (Typha spp.) in North American wetlands has been anecdotally linked with hybridization between Typha latifolia and Typha angustifolia. In this study, we used molecular genetic markers (microsatellites) to investigate whether the hybrid lineage (Typha × glauca) is restricted to The Great Lakes region, or exists across a much broader spatial scale. We also investigated the possibility of backcrossing and genetic introgression in natural populations. Parental species could be distinguished from one another based on the distribution of alleles at six microsatellite loci. Species identification based on genetic data corresponded well with species identifications based on leaf width, a key morphological trait that can distinguish the two parental species. We found that hybrids occur in Ontario, Quebec, New Brunswick, and Nova Scotia, but we did not detect hybrids in Maine. F₁s are more abundant than backcrossed or intercrossed hybrids, although we also found evidence of backcrossing, particularly in Ontario. This indicates that hybrids are fertile, and are therefore potential conduits of gene flow between the parental species. Further work is needed to determine whether T. × glauca is particularly successful in the Great Lakes region relative to other areas in which the two parental species co-exist, and to assess whether introgression may lead to increased invasiveness in the species complex.     

New microsatellite primers for Daphnia galeata mendotae

In order to study genetic changes in populations of Daphnia galeata mendotae, I characterized seven polymorphic microsatellite loci. Primers to amplify these loci were tested on individual eggs from the resting egg bank of Onondaga Lake, NY. Levels of polymorphism and cross‐amplification in D. g. galeata indicate that they will be useful markers for ecological genetic studies on both adults and diapausing eggs of these species.     

Sequential adaptive introgression of the mitochondrial genome in Drosophila yakuba and Drosophila santomea

Interspecific hybridization provides the unique opportunity for species to tap into genetic variation present in a closely related species and potentially take advantage of beneficial alleles. It has become increasingly clear that when hybridization occurs, mitochondrial DNA (mtDNA) often crosses species boundaries, raising the possibility that it could serve as a recurrent target of natural selection and source of species' adaptations. Here we report the sequences of 46 complete mitochondrial genomes of Drosophila yakuba and Drosophila santomea, two sister species known to produce hybrids in nature (~3%). At least two independent events of mtDNA introgression are uncovered in this study, including an early invasion of the D. yakuba mitochondrial genome that fully replaced the D. santomea mtDNA native haplotypes and a more recent, ongoing event centred in the hybrid zone. Interestingly, this recent introgression event bears the signature of Darwinian natural selection, and the selective haplotype can be found at low frequency in Africa mainland populations of D. yakuba. We put forward the possibility that, because the effective population size of D. santomea is smaller than that of D. yakuba, the faster accumulation of mildly deleterious mutations associated with Muller's ratchet in the former species may have facilitated the replacement of the mutationally loaded mitochondrial genome of D. santomea by that of D. yakuba.     

Life history patterns of parental and hybrid Daphnia differ between lakes

1. We investigated whether Daphnia galeata × hyalina hybrids of Lake Constance and Lake Greifensee show the same pattern of life history parameters as previously reported for D. galeata × cucullata hybrids and whether such a pattern is consistent between Daphnia populations from those two lakes. 2. Hybrids in Lake Constance were intermediate in size compared with the parental species. Hybrids in Lake Greifensee were smaller than D. galeata. The intrinsic growth rate (r) of hybrids from Lake Constance was not significantly different from the faster growing parental taxon D. galeata. However, r of hybrids from Lake Greifensee was significantly lower than that of D. galeata. 3. The observed juvenile body length differences between the taxa varied with the clutch number. The first clutch juvenile lengths of the three taxa did not differ for Lake Constance. First clutch juveniles of Lake Greifensee D. galeata were smaller than hybrid first clutch juveniles. The third clutch juvenile length did not differ between taxa from Lake Greifensee, but D. galeata juveniles from Lake Constance were bigger than those of D. hyalina. 4. The life history pattern found in Lake Constance corresponds to previous findings from other studies. The hybrids in this lake combine the faster population growth of one parental species with a relatively small size. In the case of Lake Greifensee hybrids, the relatively large size of first clutch juveniles and the small size of the adults could be interpreted as dual adaptations to invertebrate and fish predation. We speculate that the lower population growth rate of the hybrids is a trade‐off for this twofold protection.