Mitochondrial Genomes, Phylogenetic Associations, and SNP Recovery for the Key Invasive Ponto-Caspian Amphipods in Europe.
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ABSTRACT:
SUBMITTER: Mamos T
PROVIDER: S-EPMC8509019 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The Ponto-Caspian region is an endemicity hotspot that harbours several crustacean radiations, among which amphipods are the most diverse. These poorly known species are severely threatened in their native range, while at the same time they are invading European inland waters with significant ecological consequences. A proper taxonomic knowledge of this fauna is paramount for its conservation within the native region and monitoring outside of it. Here, we assemble a DNA barcode reference library for nearly 60% of all known Ponto-Caspian amphipod species. We use several methods to define molecular operational taxonomic units (MOTUs), based on two mitochondrial markers (COI and 16S), and assess their congruence with current species-level taxonomy based on morphology. Depending on the method, we find that 54-69% of species had congruent morpho-molecular boundaries. The cases of incongruence resulted from lumping distinct morphospecies into a single MOTU (7-27%), splitting a morphospecies into several MOTUs (4-28%), or both (4-11%). MOTUs defined by distance-based methods without a priori divergence thresholds showed the highest congruence with morphological taxonomy. These results indicate that DNA barcoding is valuable for clarifying the diversity of Ponto-Caspian amphipods, but reveals that extensive work is needed to resolve taxonomic uncertainties. Our study advances the DNA barcode reference library for the European aquatic biota, paving the way towards improved taxonomic knowledge needed to enhance monitoring and conservation efforts.
| S-EPMC9256591 | biostudies-literature
Project description:Legally certified sturgeon fisheries require population protection and conservation methods, including DNA tests to identify the source of valuable sturgeon roe. However, the available genetic data are insufficient to distinguish between different sturgeon populations, and are even unable to distinguish between some species. We performed high-throughput single-nucleotide polymorphism (SNP)-genotyping analysis on different populations of Russian (Acipenser gueldenstaedtii), Persian (A. persicus), and Siberian (A. baerii) sturgeon species from the Caspian Sea region (Volga and Ural Rivers), the Azov Sea, and two Siberian rivers. We found that Russian sturgeons from the Volga and Ural Rivers were essentially indistinguishable, but they differed from Russian sturgeons in the Azov Sea, and from Persian and Siberian sturgeons. We identified eight SNPs that were sufficient to distinguish these sturgeon populations with 80% confidence, and allowed the development of markers to distinguish sturgeon species. Finally, on the basis of our SNP data, we propose that the A. baerii-like mitochondrial DNA found in some Russian sturgeons from the Caspian Sea arose via an introgression event during the Pleistocene glaciation. In the present study, the high-throughput genotyping analysis of several sturgeon populations was performed. SNP markers for species identification were defined. The possible explanation of the baerii-like mitotype presence in some Russian sturgeons in the Caspian Sea was suggested.
| S-EPMC3930046 | biostudies-literature
Project description:Temperature is a crucial factor determining biology and ecology of poikilothermic animals. It often constitutes an important barrier for invasive species originating from different climate zones but, on the other hand, may facilitate the invasion process of animals with wide thermal preferences and high resistance to extreme temperatures. In our experimental study, we investigated the thermal behaviour of two Ponto-Caspian amphipod crustaceans-Dikerogammarus villosus and Dikerogammarus haemobaphes. Both species are known to live under a wide range of thermal conditions which may promote their invasion. Moreover, both these amphipods are hosts for microsporidian parasites which co-evolved with them within the Ponto-Caspian region and spread in European waters. As the presence of a parasite may influence the thermal preferences of its host, we expected to observe behavioural changes in infected individuals of the studied amphipods leading to (1) behavioural fever (selecting a warmer habitat) or (2) anapyrexia (selecting a colder habitat). The experiment (N = 20) was carried out for 30 min in a 100 cm. 20 cm from boths sides were not avaliable for amphipods long thermal gradient (0-40 °C), using 30 randomly selected adult amphipod individuals of one species. At the end of each trial, we checked the position of amphipods along the gradient and determined their sex and infection status (uninfected or infected by one of microsporidium species). D. villosus was infected with Cucumispora dikerogammari whereas D. haemobaphes was a host for C. dikerogammari, Dictyocoela muelleri or D. berillonum. Thermal preferences of amphipods depended on their species and sex. Females of D. villosus preferred warmer microhabitats (often much above 30 °C) than conspecific males and females of D. haemobaphes, whereas no significant differences were found among males of both species and both sexes of D. haemobaphes. Moreover, infected males of D. villosus stayed in warmer water more often than uninfected males of this species, selecting temperatures higher than 30 °C, which may be explained either as a behavioural fever constituting a defence mechanism of a host against the infection, or as a parasite manipulation of the host behaviour increasing the parasite fitness. On the other hand, none of the parasite species affected the thermal preferences of D. haemobaphes, including also C. dikerogammari, changing the behaviour of D. villosus. Our research presents the complexity of the thermal behaviour of studied amphipods and the evidence that microsporidia may trigger a change in temperature preferendum of their host species and those observations may be the result of different host-parasite coevolution time which may vary for the two host species (Poulin, 2010).
| S-EPMC5985147 | biostudies-literature
Project description:Sturgeons (Order Acipenseriformes) represent an extremely valuable natural resource that is now facing depletion. In the current study we evaluate if the traditional classification in subspecies of Acipenser gueldenstaedtii, Acipenser stellatus and Huso huso, endemic to Ponto-Caspian region is sustained by molecular analysis and if these represent Evolutionary Significant Units (ESUs) that should be managed separately in conservation programs. To examine the classification of taxonomic entities we sequenced a fragment of the mitochondrial control region in case of three sturgeon species that inhabit the North-western of Black Sea and migrate for reproduction in the Lower Danube. Beside these sequences, we used previously published sequences from sturgeon individuals sampled in the Black Sea, Azov Sea and Caspian Sea. We determined the genetic diversity and genetic differentiation, conducted a Population Aggregation Analysis (PAA) and inferred an intraspecific molecular phylogeny and haplotype network. The results indicated a low level of genetic differentiation between the geographically designated subspecies and did not support a significant divergence or reciprocal monophyly between them. Our results confirm previous genetic studies with smaller samples sizes, but additional analyses including nuclear markers should be conducted for proper recommendations aiming at the development of conservation programs.
| S-EPMC4171761 | biostudies-literature
Project description:Dikerogammarus villosus is a freshwater amphipod of the Ponto-Caspian origin recognized as one of the 100 worst alien species in Europe, having negative impact on biodiversity and functioning of the invaded aquatic ecosystems. The species has a wide ecophysiological tolerance and during the last 20 years it has rapidly spread throughout European inland waters. In consequence, it presents a major conservation management problem. We describe eight polymorphic microsatellite loci developed for D. villosus by combining a biotin-enrichment protocol and new generation 454GS-FLX Titanium pyrosequencing technology. When genotyped in 64 individuals from two locations, the loci exhibited a mean diversity of 4.87 alleles per locus (2-13). The mean observed and expected heterozygosities were, respectively, 0.439 (0.091-0.844) and 0.468 (0.089-0.843). Gametic disequilibrium was not detected for any pair of loci. The microsatellite markers will be a valuable tool in assessing the demographic processes associated with invasion of the killer shrimp from a genetic point of view.
| S-EPMC4306734 | biostudies-literature
Project description:Suspension feeders play pivotal roles in the nutrient cycling of almost all aquatic ecosystems. Since sufficiently large differences in the filter mesh size (FMS) can lead to different food web positions, the inter- and intraspecific variability of this trait might be of community-level importance. The aim of this study was to quantify the range of FMS variation within the three invasive Ponto-Caspian Chelicorophium species based on a large material representing various conditions (1,224 specimens from 40 samples across Central Europe), characterize the components of variation within populations, identify the main factors determining intraspecific differences, and reveal how intraspecific variation affects the FMS overlaps among species. The FMS of the most widespread invader, C. curvispinum, varied within the broadest range (between 2.34-8.28 μm, compared to 2.51-5.97 μm in C. robustum and 1.08-3.23 μm in C. sowinskyi); nevertheless, the contribution of intraspecific plasticity to the invasion success of the species is not evident based on the present study. The within-individual variability of FMS increased with the individual mean of the trait and decreased with body size; however, it showed little differences among samples. The among-individual variation within samples could be partitioned into components related to body size (ontogenetic niche shift/differences among cohorts) and sex (ecological sexual dimorphism) as well as a seemingly random component (individual specialization), varying widely in extent and relative contributions. The FMS of C. curvispinum was significantly larger in the presence of C. sowinskyi than in allopatry, likely reflecting character displacement; however, it did not show further increase when C. robustum was also present. Similar differences could not be observed in C. sowinskyi. The FMS ranges of C. curvispinum and C. robustum never overlapped with that of C. sowinskyi in co-occurrence despite the considerable intraspecific differences among sites, suggesting that their interaction can be seen as a clear case of niche differentiation by food particle size. On the contrary, the strong overlaps observed between C. curvispinum and C. robustum indicate that other factors might play the primary role in their coexistence. The studied species appear to be suitable model organisms for identifying the drivers and mechanisms of FMS variability.
| S-EPMC8061577 | biostudies-literature
Project description:Predators shape prey populations by elimination of individuals (consumptive effects) and by inducing modifications in prey behaviour, physiology or morphology (NCE-non-consumptive effects). Due to the resource allocation to defence, decreased feeding and higher stress, the costs of predator NCEs can be considerable. Therefore, the resistance to NCEs may be crucial for population growth and interspecific competition. We tested the resistance of Ponto-Caspian gammarids Dikerogammarus villosus and Pontogammarus robustoides to NCEs imposed by their predator, the racer goby Babka gymnotrachelus. As D. villosus is often avoided by predators in the presence of alternative food, we hypothesised that it would bear lower behavioural and physiological costs of anti-predator responses. We tested gammarid feeding in short-time experiments (2-4 h) with food (chironomid larvae) located at various distances from the stony shelter (to enforce food searching, Experiment I) or in the direct gammarid proximity (no searching needed, Experiment II). Moreover, we checked the predator effect on gammarid growth in a 2-week Experiment III. Both gammarids exposed to predators reduced feeding efficiency outside the shelter (Experiment I). Contrary to our expectations, the response of D. villosus was stronger. When food was provided in their direct proximity (Experiment II), the feeding of both species was unaffected by predators, indicating that a shelter supplied with food can reduce predator NCEs. The growth of P. robustoides was reduced in the presence of predators (Experiment III), whereas that of D. villosus was unaffected. Although D. villosus has a more effective defence strategy than P. robustoides, it bears similar or even higher behavioural costs of NCEs. However, it exhibits the higher resistance to the long-term predator presence, sustaining its growth rate under such conditions. This may be one of the factors contributing to the great invasion success of D. villosus, currently taking place in European fresh waters.
| S-EPMC5542608 | biostudies-literature
Project description:Microsporidia are common parasites infecting animals and protists. They are specifically common pathogens of amphipods (Crustacea, Malacostraca), with Dictyocoela spp. being particularly frequent and highly prevalent, exhibiting a range of phenotypic and ecological effects. Until now, seven species of Dictyocoela were defined, predominantly based on the genetic distance. However, neither the taxonomic status of this provisionally erected genus (based on eight novel sequences and one micrograph of the spore), nor its internal phylogenetic relationships have been clearly revealed. The formal description of the genus and of most of the putative species are still lacking. Here we aimed to fill this gap and performed both ultrastructural and molecular studies (based on SSU, ITS and partial LSU) using different species delimitation methods. As a consensus of these results and following conservative data interpretation, we propose to distinguish five species infecting gammarid hosts, and to keep the names introduced by the authors of the type sequences: Dictyocoela duebenum, D. muelleri, D. berillonum and D. roeselum. We provide full descriptions of these species. Moreover, thanks to our extensive sampling, we extend the known host and geographic range of these Microsporidia.
| S-EPMC5997659 | biostudies-literature
Project description:Adaptive radiations are bursts of evolutionary species diversification that have contributed to much of the species diversity on Earth. An exception is modern Europe, where descendants of ancient adaptive radiations went extinct, and extant adaptive radiations are small, recent and narrowly confined. However, not all legacy of old radiations has been lost. Subterranean environments, which are dark and food-deprived, yet buffered from climate change, have preserved ancient lineages. Here we provide evidence of an entirely subterranean adaptive radiation of the amphipod genus Niphargus, counting hundreds of species. Our modelling of lineage diversification and evolution of morphological and ecological traits using a time-calibrated multilocus phylogeny suggests a major adaptive radiation, comprised of multiple subordinate adaptive radiations. Their spatio-temporal origin coincides with the uplift of carbonate massifs in South-Eastern Europe 15 million years ago. Emerging subterranean environments likely provided unoccupied, predator-free space, constituting ecological opportunity, a key trigger of adaptive radiation. This discovery sheds new light on the biodiversity of Europe.
| S-EPMC8211712 | biostudies-literature
Project description:BackgroundAmphipods (Crustacea) of Lake Baikal are a very numerous and diverse group of invertebrates generally believed to have originated by adaptive radiation. The evolutionary history and phylogenetic relationships in Baikalian amphipods still remain poorly understood. Sequencing of mitochondrial genomes is a relatively feasible way for obtaining a set of gene sequences suitable for robust phylogenetic inferences. The architecture of mitochondrial genomes also may provide additional information on the mechanisms of evolution of amphipods in Lake Baikal.ResultsThree complete and four nearly complete mitochondrial genomes of Baikalian amphipods were obtained by high-throughput sequencing using the Illumina platform. A phylogenetic inference based on the nucleotide sequences of all mitochondrial protein coding genes revealed the Baikalian species to be a monophyletic group relative to the nearest non-Baikalian species with a completely sequenced mitochondrial genome - Gammarus duebeni. The phylogeny of Baikalian amphipods also suggests that the shallow-water species Eulimnogammarus has likely evolved from a deep-water ancestor, however many other species have to be added to the analysis to test this hypothesis. The gene order in all mitochondrial genomes of studied Baikalian amphipods differs from the pancrustacean ground pattern. Mitochondrial genomes of four species possess 23 tRNA genes, and in three genomes the extra tRNA gene copies have likely undergone remolding. Widely varying lengths of putative control regions and other intergenic spacers are typical for the mitochondrial genomes of Baikalian amphipods.ConclusionsThe mitochondrial genomes of Baikalian amphipods display varying organization suggesting an intense rearrangement process during their evolution. Comparison of complete mitochondrial genomes is a potent approach for studying the amphipod evolution in Lake Baikal.
| S-EPMC5249044 | biostudies-literature