Identification of sawflies and horntails (Hymenoptera, ‘Symphyta’) through DNA barcodes: successes and caveats

The ‘Symphyta’ is a paraphyletic assemblage at the base of the order Hymenoptera, comprising 14 families and about 8750 species. All have phytophagous larvae, except for the Orussidae, which are parasitoids. This study presents and evaluates the results of DNA barcoding of approximately 5360 specimens of ‘Symphyta’, mainly adults, and 4362 sequences covering 1037 species were deemed of suitable quality for inclusion in the analysis. All extant families are represented, except for the Anaxyelidae. The majority of species and specimens are from Europe, but approximately 38% of the species and 13% of the specimens are of non‐European origin. The utility of barcoding for species identification and taxonomy of ‘Symphyta’ is discussed on the basis of examples from each of the included families. A significant level of cryptic species diversity was apparent in many groups. Other attractive applications include the identification of immature stages without the need to rear them, community analyses based on metabarcoding of bulk samples and association of the sexes of adults.     

Vertical distribution and chemical character of sediment phosphorus in two shallow estuaries in the Baltic Sea

The vertical distribution of various phosphorus (P) forms and their relation to physico-chemical properties of estuary sediment material were studied to better understand the potential release and burial of P. Core samples were taken from two dissimilar estuaries in the Baltic Sea: one in the Archipelago Sea (AS) and one in the Gulf of Finland (GoF). The P reserves were characterized by a sequential extraction procedure including the analysis of simultaneously dissolved elements in two extraction steps. The sediment material was also analysed for particle size distribution and total elements. In addition, several environmental variables were determined. The occurrence of the various forms of P varied with sediment depth among different sites. Reductant soluble, iron (Fe) bound P was the most dynamically changing P form in the sediment, while P bound to other metal oxides and apatite-P were the most stable fractions. High sedimentation rate was a dominating factor for sediment P burial. In addition, the content of organic matter, the amount of erosion-transported sorption components, and the oxygen (O₂) conditions in the near-bottom water were important determinants of the behaviour of sediment P. The results indicate that, over the long term, both estuaries have acted as sinks for deposited P and restricted the transport of P to the AS and the open GoF, thereby partly alleviating the eutrophication process.     

Efficacy and accuracy of portable PIT-antennae when locating fish in ice-covered streams

Active tracking of passive integrated transponder (PIT)-tags using portable antennae is becoming an increasingly common technique in fish habitat studies in shallow rivers. We carried out “blind testing” to test the efficacy (% tags found) and accuracy (distance between predicted and true tag location) of a portable antenna system (Texas Instruments) in winter conditions using 23-mm PIT-tags. Up to 90 cm reading range was achieved and signals penetrated ice, rock, wood and water. In the “blind test” trials, a majority of the hidden tags (N = 12–30) were found indicating high tracking efficacy. PIT-tags that were oriented with their cylindrical axis parallel to the plane of the antenna coil inductor loop resulted in a bimodal detection field that had low detection range in the centre of the loop. The utilization of this bimodal detection field proved to be a very accurate method for identifying tag position (mean ± SE distance from predicted to true tag location 10.9 ± 1.4 cm) and thus well suited for microhabitat and activity studies in winter conditions. Aggregations of tags (multiple tags within 1 m²) and obstacles for the antenna maneuvering (e.g., boulders, logjams) reduced the pinpointing accuracy (mean ± SE 13.3 ± 1.8 cm), but the reduction in accuracy was statistically non-significant between the single and aggregated tags.     

Lessons learned from microsatellite development for nonmodel organisms using 454 pyrosequencing

Microsatellites, also known as simple sequence repeats (SSRs), are among the most commonly used marker types in evolutionary and ecological studies. Next Generation Sequencing techniques such as 454 pyrosequencing allow the rapid development of microsatellite markers in nonmodel organisms. 454 pyrosequencing is a straightforward approach to develop a high number of microsatellite markers. Therefore, developing microsatellites using 454 pyrosequencing has become the method of choice for marker development. Here, we describe a user friendly way of microsatellite development from 454 pyrosequencing data and analyse data sets of 17 nonmodel species (plants, fungi, invertebrates, birds and a mammal) for microsatellite repeats and flanking regions suitable for primer development. We then compare the numbers of successfully lab‐tested microsatellite markers for the various species and furthermore describe diverse challenges that might arise in different study species, for example, large genome size or nonpure extraction of genomic DNA. Successful primer identification was feasible for all species. We found that in species for which large repeat numbers are uncommon, such as fungi, polymorphic markers can nevertheless be developed from 454 pyrosequencing reads containing small repeat numbers (five to six repeats). Furthermore, the development of microsatellite markers for species with large genomes was also with Next Generation Sequencing techniques more cost and time‐consuming than for species with smaller genomes. In this study, we showed that depending on the species, a different amount of 454 pyrosequencing data might be required for successful identification of a sufficient number of microsatellite markers for ecological genetic studies.     

Chromosomal fusion and life history‐associated genomic variation contribute to within‐river local adaptation of Atlantic salmon

Chromosomal inversions have been implicated in facilitating adaptation in the face of high levels of gene flow, but whether chromosomal fusions also have similar potential remains poorly understood. Atlantic salmon are usually characterized by population structure at multiple spatial scales; however, this is not the case for tributaries of the Miramichi River in North America. To resolve genetic relationships between populations in this system and the potential for known chromosomal fusions to contribute to adaptation, we genotyped 728 juvenile salmon using a 50 K SNP array. Consistent with previous work, we report extremely weak overall population structuring (Global F_ST = 0.004) and failed to support hierarchical structure between the river's two main branches. We provide the first genomic characterization of a previously described polymorphic fusion between chromosomes 8 and 29. Fusion genomic characteristics included high LD, reduced heterozygosity in the fused homokaryotes, and strong divergence between the fused and the unfused rearrangement. Population structure based on fusion karyotype was five times stronger than neutral variation (F_ST = 0.019), and the frequency of the fusion was associated with summer precipitation supporting a hypothesis that this rearrangement may contribute local adaptation despite weak neutral differentiation. Additionally, both outlier variation among populations and a polygenic framework for characterizing adaptive variation in relation to climate identified a 250‐Kb region of chromosome 9, including the gene six6 that has previously been linked to age‐at‐maturity and run‐timing for this species. Overall, our results indicate that adaptive processes, independent of major river branching, are more important than neutral processes for structuring these populations.     

Top-down or Bottom-up Effects by Fish: Issues of Concern in Biomanipulation of Lakes

A large-scale biomanipulation trial was carried out on Lake Vesijärvi in Finland during 1989–1993. Following the mass removal of coarse fish the biomass of cyanobacteria collapsed from 1.4 g/m^?3 to below 0.4 g/m^?3, while total phosphorus concentration declined from 45 μ g/L to 30 μ g/L. No relevant changes in zooplankton communities were observed. The results suggest that the success of food web manipulation as a tool for lake restoration is not necessarily dependent on the grazing rate of zooplankton. The effects of reduced fish-mediated internal loading and recycling of nutrients are in many cases stronger than those of reduced planktivory. Alternative stable states of water quality may also exist in lakes not covered by macrophytes, owing to the changes in the behavior of fish stocks. Year-to-year variation in the littoral zone may cause large oscillations in lake ecosystems—for example, through the recruitment of fish. In addition, the nutrients translocated by fish from the littoral zone may affect the nutrient dynamics of the pelagial plankton community. In terms of phytoplankton species composition and the ratio of phosphorus to chlorophyll a, the water quality in Lake Vesijärvi has improved in a stepwise fashion within the last 10 years. This is probably due to the fact that the five-year mass removal of fish in Enonselkä fulfilled the requirement of sustained management of fish stocks in order to maintain nonequilibrial conditions between alternate stable states. The prediction of the water quality development is obscured, however, by spatial and temporal within-lake variation, which sets high requirements for sampling programs.