The importance of genetic cluster recognition for the conservation of migratory fish species: the example of the endangered European huchen Hucho hucho (L.)

Genome-Wide Reconstruction of Rediploidization Following Autopolyploidization across One Hundred Million Years of Salmonid Evolution

The long-term evolutionary impacts of whole-genome duplication (WGD) are strongly influenced by the ensuing rediploidization process. Following autopolyploidization, rediploidization involves a transition from tetraploid to diploid meiotic pairing, allowing duplicated genes (ohnologs) to diverge genetically and functionally. Our understanding of autopolyploid rediploidization has been informed by a WGD event ancestral to salmonid fishes, where large genomic regions are characterized by temporally delayed rediploidization, allowing lineage-specific ohnolog sequence divergence in the major salmonid clades. Here, we investigate the long-term outcomes of autopolyploid rediploidization at genome-wide resolution, exploiting a recent "explosion" of salmonid genome assemblies, including a new genome sequence for the huchen (Hucho hucho). We developed a genome alignment approach to capture duplicated regions across multiple species, allowing us to create 121,864 phylogenetic trees describing genome-wide ohnolog divergence across salmonid evolution. Using molecular clock analysis, we show that 61% of the ancestral salmonid genome experienced an initial "wave" of rediploidization in the late Cretaceous (85-106 Ma). This was followed by a period of relative genomic stasis lasting 17-39 My, where much of the genome remained tetraploid. A second rediploidization wave began in the early Eocene and proceeded alongside species diversification, generating predictable patterns of lineage-specific ohnolog divergence, scaling in complexity with the number of speciation events. Using gene set enrichment, gene expression, and codon-based selection analyses, we provide insights into potential functional outcomes of delayed rediploidization. This study enhances our understanding of delayed autopolyploid rediploidization and has broad implications for future studies of WGD events.

Effects of multiple stressors on the distribution of fish communities in 203 headwater streams of Rhine, Elbe and Danube

Fishes in European rivers are threatened by manifold stressors such as structural degradation, water pollution, overexploitation, land-use changes in the catchment, invasive species and global processes including climate change. Identifying main stressors in a stream/river system is of utterly importance for efficiently utilizing the scarce funds for conservation measures in order to achieve the best possible outcome. Within 203 headwater streams of Rhine, Elbe and Danube, we quantified the relative influence of different environmental stressors (water chemistry, food availability (macroinvertebrates), terrestrial predators) and anthropogenic stressors (land use, structural modification of streams) on fish assemblages at different spatial scales based on multivariate biota-environment models. In our analyses, the predictor variables percentage of impoundments, crop farming (especially erosion-prone crops such as maize) and ground sealing in the catchments, the number of wastewater treatment plants and biogas plants in the catchments as well as structural modifications of river banks were most often identified as stressors influencing fish community composition. However, the effects of the stressors varied between the investigated survey-area scales (two different catchments sizes and riparian strips) and regionally (entire study area, major drainage systems, river catchments, stream sizes, geographical subregions). In most cases, fish community composition was simultaneously affected by multiple stressors, underpinning the need for a more holistic and ecosystem-based approach in freshwater conservation and restoration.

Fish conservation in the land of steppe and sky: Evolutionarily significant units of threatened salmonid species in Mongolia mirror major river basins

Mongolia's salmonids are suffering extensive population declines; thus, more comprehensive fisheries management and conservation strategies are required. To assist with their development, a better understanding of the genetic structure and diversity of these threatened species would allow a more targeted approach for preserving genetic variation and ultimately improve long-term species recoveries. It is hypothesized that the unfragmented river basins that have persisted across Mongolia provide unobstructed connectivity for resident salmonid species. Thus, genetic structure is expected to be primarily segregated between major river basins. We tested this hypothesis by investigating the population structure for three salmonid genera (Hucho, Brachymystax and Thymallus) using different genetic markers to identify evolutionarily significant units (ESUs) and priority rivers to focus conservation efforts. Fish were assigned to separate ESUs when the combined evidence of mitochondrial and nuclear data indicated genetic isolation. Hucho taimen exhibited a dichotomous population structure forming two ESUs, with five priority rivers. Within the Brachymystax genus, there were three B. lenokESUs and one B. tumensisESU, along with six priority rivers. While B. tumensiswas confirmed to display divergent mtDNA haplotypes, haplotype sharing between these two congeneric species was also identified. For T. baicalensis,only a single ESU was assigned, with five priority rivers identified plus Lake Hovsgol. Additionally, we confirmed that T. nigrescens from Lake Hovsgol is a synonym of T. baicalensis. Across all species, the most prominent pattern was strong differentiation among major river basins with low differentiation and weak patterns of isolation by distance within river basins, which corroborated our hypothesis of high within-basin connectivity across Mongolia. This new genetic information provides authorities the opportunity to distribute resources for management between ESUs while assigning additional protection for the more genetically valuable salmonid rivers so that the greatest adaptive potential within each species can be preserved.

Impact of catchment land use on fish community composition in the headwater areas of Elbe, Danube and Main

Intensification of catchment land-use and the corresponding habitat degradation pose a threat to freshwater biodiversity and ecosystem health, yet few studies comprehensively quantified the effects of specific land-use variables on fish communities for different catchments within the same climatic region. Herein, we investigated the influence of catchment land use on fish community composition in the headwater areas of the European main river systems Elbe, Danube and Main/Rhine. The analyses comprising 289 streams and rivers in Bavaria, southern Germany, revealed that the influence of urbanization (e.g. ground sealing), potamalisation (impoundment of water courses), and erosion-prone, agricultural land-use types (e.g. root crop, maize) were significantly related to the fish community composition. In addition, multiple stressors were effective indicators and their importance differed between survey-area scales, geographical regions, and stream sizes. The findings suggest that terrestrial effects of land-use and urbanization need to be more strongly considered in the conservation of endangered stream fishes, ideally including combined measures of erosion control, restoration of environmental flows and mitigation of structural degradation.

Miniature circulatory systems: A new exposure system for ecotoxicological effect assessments in riverine organisms

Long-term effect assessments in ecotoxicological investigations are important, yet there is a lack of suitable exposure systems for these experiments that can be used for riverine species. A cost-efficient miniature circulatory system was developed that was evaluated for its applicability in long-term exposures in 2 stream-dwelling species: brown trout (Salmo trutta) and an amphipod (Gammarus roeseli). In an egg-to-fry exposure of S. trutta, the toxicity of 2 reverse osmosis concentrates was investigated as examples. Control hatching rate of yolk sac fry was 75 ± 7% and thus complies with the Organisation for Economic Co-operation and Development validity criterion (≥66%). The reverse osmosis concentrates did not impair the hatching rate in any tested concentration. In G. roeseli, mortality rates remained below 20% during a 21-d cultivation, fulfilling the common validity criterion in ecotoxicological testing. Mortality was significantly lower when the species was fed with conditioned alder leaves instead of an artificial shrimp food. Finally, a toxicity test on G. roeseli using copper as the test substance revealed median lethal concentration (LC50) values of 156 μg/L after 96 h and 99 μg/L after 264 h, which is in line with literature findings using other accepted exposure units. In conclusion, the miniature circulatory system provides a novel and cost-efficient exposure system for long-term investigations on riverine species that may also be applicable for other species of fishes and macroinvertebrates. Environ Toxicol Chem 2016;35:2827-2833. © 2016 SETAC.

Genetic analysis of four European huchen (Hucho hucho Linnaeus, 1758) broodstocks from Poland, Germany, Slovakia, and Ukraine: implication for conservation

Four broodstocks of European huchen (Hucho hucho) from: Poland, Germany, Slovakia, and Ukraine were investigated using ten microsatellite DNA loci. Microsatellite DNA analysis was successfully applied for the first time in the Polish broodstock of this fish species. The genetic variation and genetic distance between these broodstocks were evaluated. In addition, we examined the potential effects of a genetic bottleneck on the genetic variation of the broodstocks. The European huchen broodstocks exhibited moderate genetic diversity (PIC = 0.405–0.496 and I = 0.831–1.047) with the exception of German broodstock which presented higher genetic diversity (PIC = 0.590 and I = 1.254). Observed (Ho) and expected (He) heterozygosity across the investigated loci in all broodstocks ranged from 0.434 to 0.686 and from 0.452 to 0.650, respectively. Overall, the studied broodstocks were in Hardy-Weinberg equilibrium (HWE); however, from 8 to 42 % of the loci deviated from HWE in each stock. The Garza-Williamson index (M = 0.146–0.279) and values of the heterozygosity excess revealed a reduction of genetic variation in all studied broodstocks because of the founder or bottleneck effect. The analysis of genetic differentiation (Fst) and Nei’s genetic distance between pairs of broodstocks revealed that Polish and Ukrainian broodstocks of European huchen were characterized by the closest genetic distance. In contrast, the highest genetic divergence parameters (Fst and Nei’s distance) were observed among German, Slovak, and Ukrainian broodstocks.

The complete mitochondrial genome of the endangered Hucho hucho (Salmonidae: Huchen)

Hucho hucho, one of the most endangered members of the family Salmonidae, is endemic to the Danube basin. In this study, the complete mitochondrial genome of H. hucho was sequenced and characterized. The genome is 16,751 bp in length and contains 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs and a noncoding control region. The gene arrangement and nucleotide composition of the mitochondrial genome are similar to those of H. bleekeri. An 82 bp tandem repeat was identified in the control region, which is variable in length and copy number of repeat between and within species. The complete mitochondrial DNA of H. hucho should be useful to study population genetics, biogeography and adaptive evolution of this lineage.

Timing matters: species-specific interactions between spawning time, substrate quality, and recruitment success in three salmonid species

Substratum quality and oxygen supply to the interstitial zone are crucial for the reproductive success of salmonid fishes. At present, degradation of spawning grounds due to fine sediment deposition and colmation are recognized as main factors for reproductive failure. In addition, changes in water temperatures due to climate change, damming, and cooling water inlets are predicted to reduce hatching success. We tested the hypothesis that the biological effects of habitat degradation depend strongly on the species-specific spawning seasons and life-history strategies (e.g., fall- vs. spring-spawners, migratory vs. resident species) and assessed temperature as an important species-specific factor for hatching success within river substratum. We studied the species-specific differences in their responses to such disturbances using egg-to-fry survival of Danube Salmon (Hucho hucho), resident brown trout (Salmo trutta fario), and migratory brown trout (Salmo trutta lacustris) as biological endpoint. The egg incubation and hatching success of the salmonids and their dependence on temperature and stream substratum quality were compared. Hatching rates of Danube salmon were lower than of brown trout, probably due to higher oxygen demands and increased interstitial respiration in spring. Increases in maximum water temperature reduced hatching rates of resident and migratory brown trout (both fall-spawners) but were positively correlated with hatching rates of Danube salmon (a spring-spawner). Significantly longer incubation periods of resident and migratory brown trout coincided with relatively low stream substratum quality at the end of the egg incubation. Danube salmon seem to avoid low oxygen concentrations in the hyporheic zone by faster egg development favored by higher water temperatures. Consequently, the prediction of effects of temperature changes and altered stream substratum properties on gravel-spawning fishes and biological communities should consider the observed species-specific variances in life-history strategies to increase conservation success.

Mitochondrial DNA variation and introgression in Siberian taimen Hucho taimen

Siberian taimen Hucho taimen is the largest representative of the family Salmonidae inhabiting rivers of northern Eurasia. The species is under intensive aquaculture activity. To monitor natural taimen populations we have sequenced a portion (8,141 bp) of the mitochondrial (mt) genome in 28 specimens of H. taimen from six localities in the Amur River basin. Nucleotide variability is low (π = 0.0010), but structured in two divergent haplotype groups. A comparison of the data with the GenBank H. taimen mt genome (HQ897271) reveals significant differences between them in spite of the fact that the fish specimens come from neighboring geographical areas. The distribution of divergence is non-uniform with two highly pronounced divergent regions centered on two genes, ND3 and ND6. To clarify the pattern of divergence we sequenced the corresponding portion of the mt genome of lenok Brachymystax tumensis and analyzed the GenBank complete mt genomes of related species. We have found that the first and second divergent regions are identical between the GenBank H. taimen and two lenok subspecies, B. lenok and B. lenok tsinlingensis, respectively. Consequently, both divergent regions represent introgressed mtDNA resulting from intergeneric hybridization between the two lenok subspecies and H. taimen. Introgression is, however, not detected in our specimens. This plus the precise identity of the introgressed fragments between the donor and the recipient GenBank sequence suggests that the introgression is local and very recent, probably due to artificial manipulations involving taimen – lenok intergeneric hybridization. Human-mediated hybridization may become a major threat to aquatic biodiversity. Consequently we suggest that due attention needs to be given to this threat by means of responsible breeding program management, so as to prevent a potential spread of hybrid fishes that could jeopardize the resilience of locally adapted gene pools of the native H. taimen populations.

Salmonid-egg floating boxes as bioindication for riverine water quality and stocking success

The salmonid-egg floating box provides an easy bioindication tool for an assessment of water quality, as demonstrated here for the reintroduction of Europe's largest salmonid species, the huchen Hucho hucho.