Assessing freshwater fish biodiversity of Kumbe River, Papua (Indonesia) through environmental DNA metabarcoding

Context. The ability to accurately assess biodiversity is a critical first step towards effective conservation and management. However, assessment of biodiversity using conventional monitoring programs is often constrained by high cost and a lack of taxonomic expertise. Environmental DNA (eDNA) metabarcoding may be a useful tool to efficiently catalogue biodiversity in areas that cannot be easily assessed using other methods. Aims. Here, we evaluated the potential of eDNA metabarcoding for assessing fish biodiversity and distribution in the Kumbe River, Papua Province, Indonesia. Methods. We selected four sampling locations and collected seven eDNA samples from each location. We used eDNA metabarcoding of the Cytochrome-b gene to characterise the fish community. Key results. A total of 23 species were detected, three of which comprised 92% of sequence reads detected: Melanotaenia goldiei (32%), Craterocephalus randi (31%), and the invasive tilapia Oreochromis niloticus (29%). Only five species that were previously detected using conventional methods were detected by metabarcoding: M. goldiei, Craterocephalus stercusmuscarum, O. niloticus, Neoarius graeffei, and Arius arius. We detected 18 species (70% native) that have never been recorded from the Kumbe River. Conclusions. This work has demonstrated that fish biodiversity is substantially underestimated in the Kumbe River. Environmental DNA metabarcoding is a promising rapid, non-invasive and cost-effective method for assessing fish biodiversity in Papua. Implications. The findings support future investment in eDNA metabarcoding to characterise the fish biodiversity in Papua. This will assist in allocating the limited resources for conservation and management to areas most at risk from anthropogenic impacts

Changes in the spatio-temporal genetic structure of Baltic sea trout (Salmo trutta L.) over two decades: direct and indirect effects of stocking

Several countries have implemented stocking programmes to enhance abundance and fish production by releases of hatchery-reared fish. However, due to fluctuations in population size, stocking history, and potential indirect effects of straying of hatchery-reared fish, it is often difficult to predict how these factors will affect genetic diversity and differentiation patterns among wild populations. This study characterized the population genetic structure and temporal variability of four Estonian sea trout populations by evaluating the degrees of direct and indirect genetic impacts of stocking over two decades using 14 microsatellite loci. Our results demonstrate considerable temporal change combined with weak genetic structuring among studied sea trout populations. We found a reduction of the overall level of genetic differentiation combined with the tendency for increased genetic diversity, and an effective number of breeders (N-b) over the study period. Furthermore, we found that immigration rates (m) from hatchery stocks were highest in the population subjected to direct stocking and in non-stocked populations that were located geographically closer to the stocked rivers. This work suggests that hatchery releases have influenced the genetic diversity and structuring of studied sea trout populations. However, the impact of hatchery releases on the adaptive variation and fitness-related traits in wild trout populations remains to be revealed by more informative genetic markers. This study illustrates the dynamic nature of the population genetic structure of sea trout and the value of long-term genetic monitoring for management and conservation

Subtle transcriptomic response of Eurasian perch (Perca fluviatilis) associated with Triaenophorus nodulosus plerocercoid infection

Determining the physiological effects of parasites and characterizing genes involved in host responses to infections are essential to improving our understanding of host-parasite interactions and their ecological and evolutionary consequences. This task, however, is complicated by high diversity and complex life histories of many parasite species. The use of transcriptomics in the context of wild-caught specimens can help ameliorate this by providing both qualitative and quantitative information on gene expression patterns in response to parasites in specific host organs and tissues. Here, we evaluated the physiological impact of the widespread parasite, the pike tapeworm (Triaenophorus nodulosus), on its second intermediate host, the Eurasian perch (Perca fluviatilis). We used an RNAseq approach to analyse gene expression in the liver, the target organ of T. nodulosus plerocercoids, and spleen which is one of the main immune organs in teleost fishes. We compared perch collected from multiple lakes consisting of individuals with (n = 8) and without (n = 6) T. nodulosus plerocercoids in the liver. Results revealed a small number of differentially expressed genes (DEGs, adjusted p-value <= 0.05) in both spleen (n = 22) and liver (n = 10). DEGs in spleen consisted of mostly upregulated immune related genes (e.g., JUN, SIK1, THSB1), while those in the liver were often linked to metabolic functions (e.g., FABP1, CADM4, CDAB). However, Gene Ontology (GO) analysis showed lack of functional enrichment among DEGs. This study demonstrates that Eurasian perch displays a subtle response at a gene expression level to T. nodulosus plerocercoid infection. Given that plerocercoids are low-metabolic activity transmission stages, our results suggest that moderate T. nodulosus plerocercoid infection most likely does not provoke an extensive host immune response and have relatively low physiological costs for the host. Our findings illustrate that not all conspicuous infections have severe effects on host gene regulation

How genomics can help biodiversity conservation

The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics

Decades of warming alters maturation and reproductive investment in fish

How does warming affect maturation and reproductive investment in ectotherms? Younger age and smaller size at maturation, as well as altered reproduction processes, have been found in a few species subjected to elevated temperatures. These observations, however, come from studies that do not distinguish effects of warming on maturation from those on growth, are also restricted to single generation responses to warming, or have additional stressors besides warming in the study system. Here, we study warming effects on maturation and reproductive investment in wild, unexploited fish populations using a whole-ecosystem heating experiment. The experiment is conducted on Eurasian perch (Perca fluviatilis) in a heated and control area (with > 5 degrees C temperature difference) in the Baltic Sea. We compare female perch size at maturation using estimated probabilistic maturation reaction norms (PMRNs) and the gonado-somatic index over 17 years of heating, spanning approximately five to eight perch generations. Using the PMRN approach, we show that warming has substantial effects on maturation size independent of warming-induced changes in body growth. We found that young fish mature at a smaller size and invest more in developing their gonads in the heated population than in the unheated population. Our findings suggest that warming effects on reproductive investment may initially compensate for the cost of warming-induced decrease in maturation size caused by the trade-off between early maturation and size-dependent fecundity. After multiple additional generations of warming, maturation and reproduction traits in perch differed from those in the first generations following the onset of warming, which suggests that warming-induced evolution may have occurred. Our study is particularly relevant in the context of climate change because of the unusually large temperature difference between the areas and the fact that the heating occurred on an ecosystem level. We call for experimental studies resolving mechanisms of trait responses to warming across generations, complemented with genomic analyses, to aid understanding of organisms' long-term responses to climate change

Status and monitoring of the buff-tailed bumblebee Bombus terrestris Linnaeus (Hymenoptera: Apidae) in Southern Finland

Bombus terrestris can cause pollination disturbance in native plants and compete with native bumblebees and other pollinators. The accompanying non-native parasites may also threaten native bees. We report new observations of the commercially used Bombus terrestris (Linnaeus, 1758) using trapping data and sporadic samples identified with a PCR–RFLP-method for degraded DNA. A total of 863 individuals (355 queens, 442 workers, 66 drones) of Bombus sensu stricto were collected during the years 2008–9, of which, 642 were B. lucorum, ten B. cryptarum, four B. terrestris and none were B. magnus. Three trap types were compared in two modified transects near areas that use the commercial B. terrestris for pollination in Southern Finland: the tree trap that was hung at approximately 3 metres height was the most effective. Regular monitoring is important in the risk assessment of B. terrestris, and for correct species identification, molecular methods are recommended

Draft genome assembly of the freshwater apex predator wels catfish (Silurus glanis) using linked-read sequencing

The wels catfish (Silurus glanis) is one of the largest freshwater fish species in the world. This top predator plays a key role in ecosystem stability, and represents an iconic trophy-fish for recreational fishermen. S. glanis is also a highly valued species for its high-quality boneless flesh, and has been cultivated for over 100 years in Eastern and Central Europe. The interest in rearing S. glanis continues to grow; the aquaculture production of this species has almost doubled during the last decade. However, despite its high ecological, cultural and economic importance, the available genomic resources for S. glanis are very limited. To fulfill this gap we report a de novo assembly and annotation of the whole genome sequence of a female S. glanis. The linked-read based technology with 10X Genomics Chromium chemistry and Supernova assembler produced a highly continuous draft genome of S. glanis: ∼0.8Gb assembly (scaffold N50 = 3.2 Mb; longest individual scaffold = 13.9 Mb; BUSCO completeness = 84.2%), which included 313.3 Mb of putative repeated sequences. In total, 21,316 protein-coding genes were predicted, of which 96% were annotated functionally from either sequence homology or protein signature searches. The highly continuous genome assembly will be an invaluable resource for aquaculture genomics, genetics, conservation, and breeding research of S. glanis

Effect of environmental factors and an emerging parasitic disease on gut microbiome of wild salmonid fish

The gastrointestinal tract (GIT) of fish supports a dynamic microbial ecosystemthat is intimately linked to host nutrient acquisition, epithelial development,immune system priming, and disease prevention, and we are far from understandingthe complex interactions among parasites, symbiotic gut bacteria, and host fitness.Here, we analyzed the effects of environmental factors and parasitic burdens on themicrobial composition and diversity within the GIT of the brown trout (Salmo trutta).We focused on the emerging dangerous salmonid myxozoan parasite Tetracapsuloidesbryosalmonae, which causes proliferative kidney disease in salmonid fish, todemonstrate the potential role of GIT micobiomes in the modulation of host-parasiterelationships. The microbial diversity in the GIT displayed clear clustering accordingto the river of origin, while considerable variation was also found among fish fromthe same river. Environmental variables such as oxygen concentration, water temperature,and river morphometry strongly associated with both the river microbialcommunity and the GIT microbiome, supporting the role of the environment in microbialassemblage and the relative insignificance of the host genotype and gender.Contrary to expectations, the parasite load exhibited a significant positive relationshipwith the richness of the GIT microbiome. Many operational taxonomic units(OTUs; n 202) are more abundant in T. bryosalmonae-infected fish, suggesting thatbrown trout with large parasite burdens are prone to lose their GIT microbiome homeostasis.The OTUs with the strongest increase in infected trout are mostly nonpathogenicaquatic, anaerobic sediment/sludge, or ruminant bacteria. Our results underscorethe significance of the interactions among parasitic disease, abiotic factors,and the GIT microbiome in disease etiology.IMPORTANCE Cohabiting microorganisms play diverse and important roles in thebiology of multicellular hosts, but their diversity and interactions with abiotic and bioticfactors remain largely unsurveyed. Nevertheless, it is becoming increasinglyclear that many properties of host phenotypes reflect contributions from the associatedmicrobiome. We focus on a question of how parasites, the host genetic background,and abiotic factors influence the microbiome in salmonid hosts by using ahost-parasite model consisting of wild brown trout (Salmo trutta) and the myxozoanTetracapsuloides bryosalmonae, which causes widely distributed proliferative kidneydisease. We show that parasite infection increases the frequency of bacteria fromthe surrounding river water community, reflecting impaired homeostasis in the fishgut. Our results also demonstrate the importance of abiotic environmental factorsand host size in the assemblage of the gut microbiome of fish and the relative insignificanceof the host genotype and gender.</p

Discovery and application of insertion-deletion (INDEL) polymorphisms for QTL mapping of early life-history traits in Atlantic salmon

<p>Abstract</p> <p>Background</p> <p>For decades, linkage mapping has been one of the most powerful and widely used approaches for elucidating the genetic architecture of phenotypic traits of medical, agricultural and evolutionary importance. However, successful mapping of Mendelian and quantitative phenotypic traits depends critically on the availability of fast and preferably high-throughput genotyping platforms. Several array-based single nucleotide polymorphism (SNP) genotyping platforms have been developed for genetic model organisms during recent years but most of these methods become prohibitively expensive for screening large numbers of individuals. Therefore, inexpensive, simple and flexible genotyping solutions that enable rapid screening of intermediate numbers of loci (~75-300) in hundreds to thousands of individuals are still needed for QTL mapping applications in a broad range of organisms.</p> <p>Results</p> <p>Here we describe the discovery of and application of insertion-deletion (INDEL) polymorphisms for cost-efficient medium throughput genotyping that enables analysis of >75 loci in a single automated sequencer electrophoresis column with standard laboratory equipment. Genotyping of INDELs requires low start-up costs, includes few standard sample handling steps and is applicable to a broad range of species for which expressed sequence tag (EST) collections are available. As a proof of principle, we generated a partial INDEL linkage map in Atlantic salmon (<it>Salmo salar</it>) and rapidly identified a number of quantitative trait loci (QTLs) affecting early life-history traits that are expected to have important fitness consequences in the natural environment.</p> <p>Conclusions</p> <p>The INDEL genotyping enabled fast coarse-mapping of chromosomal regions containing QTL, thus providing an efficient means for characterization of genetic architecture in multiple crosses and large pedigrees. This enables not only the discovery of larger number of QTLs with relatively smaller phenotypic effect but also provides a cost-effective means for evaluation of the frequency of segregating QTLs in outbred populations which is important for further understanding how genetic variation underlying phenotypic traits is maintained in the wild.</p