Biology subjects

Praebel, K.

Publications and source records attributed to Praebel, K..

17 recordsLinked to original sources

bioRxiv2024

Ancient DNA reveals historical demographic decline and genetic erosion in the Atlantic bluefin tuna

Overexploitation has depleted fish stocks during the past century, nonetheless its genomic consequences remain poorly understood. Characterising the spatiotemporal patterns of these consequences may provide baseline estimates of past diversity and productivity to aid management targets, help predict future dynamics, and facilitate the identification of evolutionary factors limiting fish population recovery. Here, we evaluate human impacts on the evolution of the iconic Atlantic bluefin tuna (Thunnus thynnus), one of the longest and most intensely exploited marine fishes, with a tremendous cultural and economic importance. We sequenced whole genomes from modern (n=49) and ancient (n=41) specimens dating up to 5000 years ago, uncovering several novel findings. First, we identify temporally stable patterns of population admixture, as bluefin tuna caught off Norway and in the eastern Mediterranean share a greater degree of ancestry with Gulf of Mexico bluefin tuna than western and central Mediterranean bluefin tuna. This suggests that Atlantic spawning areas are important mixing grounds for the genetic diversity of Mediterranean bluefin tuna. We model effective population size to show that Mediterranean bluefin tuna began to undergo a demographic decline by the year 1900 to an extent not observed across the previous millennia. Coinciding with this, we found that heterozygosity and nucleotide diversity was significantly lower in modern (2013-2020), than ancient (pre-1941) Mediterranean bluefin tuna, suggesting bluefin tuna underwent a genetic bottleneck. With this work we show how ancient DNA provides novel perspectives on ecological complexity with the potential to inform the management and conservation of fishes. SignificanceAchieving the aim of the current UN Ocean Decade to "protect and restore ecosystems and biodiversity" is stymied by a lack of historical knowledge on how human exploitation has impacted and therefore what should be restored. Here, we sequence DNA in ancient fish bones to evaluate the historical diversity of the Atlantic bluefin tuna; which has been of great commercial importance for centuries. We find that bluefin tuna began to undergo demographic decline by 1900, 70 years earlier than currently recognised. Correspondingly, we find modern bluefin tuna had lower levels of genetic diversity than historical ones. This suggests that human impacts on the diversity of marine fishes are likely to have begun earlier and be more complex than previously thought.

ecology↗

bioRxiv2024

Population divergence manifested by genomic rearrangements in a keystone Arctic species with high gene flow

Genomic rearrangements have in recent years gained attention due to their evolutionary role in processes related to adaptation to local environmental conditions as well as diversification and speciation. In this study, we report on genomic rearrangements in the cold-water adapted polar cod (Boreogadus saida), a keystone Arctic fish species. By taking advantage of a new chromosome-level genome assembly in combination with whole-genome population sequencing data from specimens across the northern Barents Sea and adjacent regions, we identified a substantial number of larger chromosomal inversions (n=20) and characterized the previously identified chromosomal fusions (n=5). These genomic features -- encompassing over 20% of the genome -- exhibited genetic divergence, strong internal linkage disequilibrium, and signals of selection. Two of the identified inversions were associated with the two previously described hemoglobin clusters, while a third chromosomal region was found to differentiate between males and females. Moreover, clustering analyses on genotype frequencies of inversions revealed sub- structuring according to five geographic sub-groups suggesting sub-populations and/or the existence of cryptic ecotypes. These results provide novel insights into the impact of genomic rearrangements in population divergence and thus, potentially local adaptation, especially in species with high gene flow.

genomics↗

bioRxiv2024

Chromosomal fusions and large-scale inversions are key features for adaptation in Arctic codfish species

The evolutionary impact of structural variants, such as chromosomal inversions, is well documented, especially for their role in local adaptation in high gene flow systems. However, the role of other genomic rearrangements like chromosomal fusions, fissions, and translocations is still relatively unexplored. Here we present six chromosome-level Gadid reference genomes for the non-migratory Atlantic cod (Gadus morhua) i.e., Norwegian coastal cod (NCC), Atlantic haddock (Melanogrammus aeglefinus), burbot (Lota lota), European hake (Merluccius merluccius) as well as two keystone Arctic codfishes: the polar cod (Boreogadus saida) and Arctic cod (Arctogadus glacialis). Within a comparative genomics framework, we uncovered several lineage-specific chromosomal fusions, resulting in a reduced number of chromosomes compared to the ancestral state in the two cold-water adapted codfishes. The identified fusions were not homologous, i.e., indicating that they originate from independent evolutionary events. Additionally, a high number of partly overlapping chromosomal inversions between the two species were detected. Using a smaller population dataset, we uncovered a high degree of conservation for some of the overlapping inversions (including some breakpoint regions), suggesting that these regions are under selection, and potentially of evolutionary importance. With the use of chromosome-level genome assemblies, we demonstrate how large genomic reorganizations are likely to play important roles in speciation processes and thus, in particular to adaptation to freezing environmental conditions. Moreover, we observe that such massive rearrangement events can take place across relatively short evolutionary time scales.

genomics↗

bioRxiv2024

Reference genome bias in light of species-specific chromosomal reorganization and translocations

Whole-genome sequencing efforts has during the past decade unveiled the central role of genomic rearrangements--such as chromosomal inversions--in evolutionary processes, including local adaptation in a wide range of taxa. However, employment of reference genomes from distantly or even closely related species for mapping and the subsequent variant calling, can lead to errors and/or biases in the datasets generated for downstream analyses. Here, we capitalize on the recently generated chromosome-anchored genome assemblies for Arctic cod (Arctogadus glacialis), polar cod (Boreogadus saida), and Atlantic cod (Gadus morhua) to evaluate the extent and consequences of reference bias on population sequencing datasets (approx. 15-20x coverage) for both Arctic cod and polar cod. Our findings demonstrate that the choice of reference genome impacts population genetic statistics, including individual mapping depth, heterozygosity levels, and cross-species comparisons of nucleotide diversity ({pi}) and genetic divergence (DXY). Further, it became evident that using a more distantly related reference genome can lead to inaccurate detection and characterization of chromosomal inversions, i.e., in terms of size (length) and location (position), due to inter-chromosomal reorganizations between species. Additionally, we observe that several of the detected species-specific inversions were split into multiple genomic regions when mapped towards a heterospecific reference. Inaccurate identification of chromosomal rearrangements as well as biased population genetic measures could potentially lead to erroneous interpretation of species-specific genomic diversity, impede the resolution of local adaptation, and thus, impact predictions of their genomic potential to respond to climatic and other environmental perturbations.

genomics↗

bioRxiv2023

High resolution longitudinal molecular and morphological tracking of planktonic threats to salmon aquaculture.

Marine-phase salmonid aquaculture is a major component of the coastal economies of Northern Europe, North America and Chile and is under threat from numerous challenges to gill health, many of which originate from the phyto- and zooplankton. Associated losses are growing as a proportion of production year on year. A first step towards mitigating losses is to characterize the biological drivers of poor gill health. Numerous planktonic species have been implicated, including toxic and siliceous microalgae, hydrozoans and scyphozoans; however, rigorous longitudinal surveys of planktonic diversity and gill health have been lacking. In the current study, we present and assess an exhaustive identification approach combining both morphological and molecular methods (environmental DNA metabarcoding) approaches in combination with robust statistical models to identify the planktonic drivers of complex gill disease (CGD) and fish mortality. We undertook longitudinal molecular and microscopic evaluation at two marine aquaculture facilities on the west coast of Scotland using daily data collected during the 2021 growing season (March-October). Examining these two different sites, one sheltered and one exposed to the open sea, we identified new, important, and unexpected planktonic drivers (e.g. doliolids and appendicularians) of CGD and mortality and confirmed the significance of some established threats (e.g. hydrozoans and diatoms). We also explored delayed or lagged effects of planktonic abundances on gill health and undertook a comparison of environmental DNA metabarcoding and microscopy in their ability to identify and quantify planktonic species. Our data highlight the diversity of planktonic threats to salmonid aquaculture as well as the importance of using both molecular and morphological approaches to detect those. Despite our study relying on two farm sites only, our results evidence the role of the different planktonic players on salmon gill disease; there is now an urgent need to expand systematic longitudinal molecular and morphological approach across multiple sites and over multiple years. The resultant catalogue of main biological drivers will enable early warning systems, new treatments and, ultimately, a sustainable platform for future salmonid aquaculture in the marine environment.

zoology↗

bioRxiv2021

Genome-wide DNA methylation predicts environmentally-driven life history variation in a marine fish

The molecular mechanisms underlying intraspecific variation in life history strategies are still poorly understood, despite the importance of this question for understanding of organisms responses to environmental variability. Theoretical work proposed that epigenetic mechanisms such as DNA methylation might regulate intraspecific variation in life history strategies, however this assumption has rarely been verified empirically in wild populations. We examined associations between genome-wide methylation changes and environmentally-driven life history variation in two lineages of a marine fish that diverged approximatively 2.5 Mya, the capelin (Mallotus villosus), from North America and Europe. In both lineages, capelin harbour two contrasted life history strategies: some are strictly semelparous, experience fast actuarial senescence, but benefit from high hatching success by spawning on demersal sites where water temperature is low and relatively stable. In contrast, others are facultative iteroparous, have slower actuarial senescence, and suffer from lower hatching success by breeding in the intertidal zone where temperature is warmer, thermohaline parameters are less stable, and egg desiccation risk is high. Performing whole genome and epigenome sequencing, we showed that these contrasted life history strategies are more likely governed by epigenetic changes than by differences in DNA sequence. While genetic differentiation between the capelin harbouring different life history strategies was negligible, we detected parallel genome-wide methylation changes across lineages. We identified 1,067 differentially methylated regions (DMRs) comprising 15,818 CpGs, with 22% of them located within 5-kb around genes comprising promotor regions. We found that all DMRs were hypermethylated in demersal-spawning individuals. This striking result suggests that lower water temperature at demersal sites leads to an overall hypermethylation of the genome determined during the epigenetic reprogramming occurring over embryonic development. Our study emphasizes that parallel epigenetics changes in lineages with divergent genetic background could have a functional role in the regulation of intraspecific life history variation.

evolutionary biology↗

bioRxiv2020

The spatio-temporal axis for phenotypic change: a comparison of source and translocated Arctic charr populations after 25 generations

Evolution of morphological traits is hypothesized to act on an extended time scale, yet studies have suggested that these changes are possible within a few generations. Trophic polymorphism enabled through niche adaptations and ecological opportunity is one phenomenon that facilitate occurrence of rapid adaptive variation, common in many northern freshwater fish species. One such species is Arctic charr, which is known for its extensive variation in morphology and the occurrence of morphs. However, the speed at which such morphological variation arises is poorly studied despite the importance for understanding the onset of evolution. The aim of this study was to elucidate this process in a gradient of eight lakes that was stocked with Arctic charr in the period from 1910 to 1917 from Lake Tinnsjoen, Norway. We used morphological measurements to test for differences in traits between populations and Haldane and Darwins evolutionary rates to estimate divergence rates in traits. We also tested for correlation between putative genetic and morphological divergence. In addition, we contrasted the morphological divergence with that expected under neutral genetic expectations, using 12 microsatellite markers, to analyze whether and which morphological differences that is following early genetic divergence. A significant genetic differentiation was found between the source population and five of the translocated populations with corresponding differences in morphological traits for four of the populations. Population genetic structuring indicated six different genetic clusters. The translocated populations also exhibited trait divergence estimated with both Haldane and Darwins rates. Differences in morphological traits showed a significant correlation with genetic divergence, and the morphological differences were most likely affected by differences in lake parameters such as maximum depth, lake size and fish community. We conclude that intraspecific morphological and genetic divergence can form on short evolutionary time scales with important implications for conservation and management practices.

evolutionary biology↗

bioRxiv2020

Space-time dynamics in monitoring neotropical fish communities using eDNA metabarcoding

The biodiverse Neotropical ecoregion remains insufficiently assessed, poorly managed, and threatened by unregulated human activities. Novel, rapid and cost-effective DNA-based approaches are valuable to improve understanding of the biological communities and for biomonitoring in remote areas. Here, we evaluate the potential of environmental DNA (eDNA) metabarcoding for assessing the structure and distribution of fish communities by analysing sediments and water from 11 locations along the Jequitinhonha River catchment (Brazil). Each site was sampled twice, before and after a major rain event in a five-week period and fish diversity was estimated using high-through-put sequencing of 12S rRNA amplicons. In total, 252 Molecular Operational Taxonomic Units (MOTUs) and 34 fish species were recovered, including endemic, introduced, and previously unrecorded species for this basin. Spatio-temporal variation of fish assemblages was detected, richness during the first campaign was nearly twice as high as in the second sampling round; though peaks of diversity were primarily associated with only four locations. No correlation between {beta}-diversity and longitudinal distance or presence of dams was detected, but low species richness observed at sites located near dams indicates that these anthropogenic barriers might have an impact on local fish diversity. Unexpectedly high -diversity levels recorded at the river mouth suggest that these sections should be further evaluated as putative "eDNA reservoirs" for rapid monitoring. By uncovering spatio-temporal changes, unrecorded biodiversity components, and putative anthropogenic impacts on fish assemblages, we further strengthen the potential of eDNA metabarcoding as a biomonitoring tool, especially in regions often neglected or difficult to access.

ecology↗

bioRxiv2019

And if you gaze long into an abyss, the abyss gazes also into thee: four morphs of Arctic charr adapting to a depth-gradient in Lake Tinnsjoen

BackgroundThe origin of species is a central topic in biology aiming at understanding mechanisms, level and rate of diversification. Ecological speciation is an important driver in adaptive radiation during post-glacial intra-lacustrine niche diversification in fishes. The Arctic charr Salvelinus alpinus L. species complex in the Northern hemisphere freshwater systems display huge morphological and life history divergence in lakes with one or several morphs present, thus offering a unique opportunity to address ongoing speciation mechanisms.\n\nWe studied Arctic charr in Lake Tinnsjoen by fishing in four nominal lake habitats (pelagial, littoral, shallow-moderate profundal, and deep-profundal habitats) down to 350 meters depth. Research topics addressed were; (1) to illuminate Holarctic phylogeography and lineages colonizing Lake Tinnsjoen, (2) to estimate reproductive isolation of morphs or fish using unbiased methods, and (3) to document eco-morphological and life history trait divergence. Also, we compared Lake Tinnsjoen with four Norwegian outgroup populations of Arctic charr.\n\nResultsFour field-assigned morphs were identified in Lake Tinnsjoen; the planktivore morph in all habitats except deep-profundal, the dwarf morph in shallow-moderate profundal, the piscivore morph in shallow-moderate profundal (less in littoral and deep-profundal), and an undescribed new morph - the abyssal morph in the deep-profundal only. The morphs displayed extensive life history variation based on age and size patterns. A moderate to high concordance was observed between field-assigned morphs and four unbiased genetic clusters obtained from microsatellite variation. MtDNA suggested the occurrence of two minor endemic clades in Lake Tinnsjoen likely originating from one widespread colonizing clade in the Holarctic. All morphs were genetically differentiated at microsatellites (FST: 0.12-0.20; with some ongoing gene flow among morphs, and for most mtDNA comparisons (FST: 0.04-0.38). Analyses of Norwegian outgroup lakes implied colonization from a river system below Lake Tinnsjoen.\n\nConclusionOur findings suggest post-glacial adaptive radiation of one colonizing mtDNA lineage with divergent niche specialization along a depth-temperature-productivity-pressure gradient. Concordance between reproductive isolation and the realized habitat of the morphs imply that ecological speciation may be the mechanism of divergence. Particularly novel is the extensive morph diversification with depth into the often unexplored deep-water profundal habitat, suggesting we may have systematically underestimated biodiversity present in lakes.

evolutionary biology↗

bioRxiv2019

Standing genetic variation and chromosomal rearrangements facilitate local adaptation in a marine fish

Population genetic theory states that adaptation most frequently occurs from standing genetic variation, which results from the interplay between different evolutionary processes including mutation, chromosomal rearrangements, drift, gene flow and selection. To date, empirical work focusing on the contribution of standing genetic variation to local adaptation in the presence of high gene flow has been limited to a restricted number of study systems. Marine organisms are excellent biological models to address this issue since many species have to cope with variable environmental conditions acting as selective agents despite high dispersal abilities. In this study, we examined how, demographic history, standing genetic variation linked to chromosomal rearrangements and shared polymorphism among glacial lineages contribute to local adaptation to environmental conditions in the marine fish, the capelin (Mallotus villosus). We used a comprehensive dataset of genome-wide single nucleotide polymorphisms (25,904 filtered SNPs) genotyped in 1,359 individuals collected from 31 spawning sites in the northwest Atlantic (North America and Greenland waters). First, we reconstructed the history of divergence among three glacial lineages and showed that they diverged from 3.8 to 1.8 MyA. Depending on the pair of lineages considered, historical demographic modelling provided evidence for divergence with gene flow and secondary contacts, shaped by barriers to gene flow and linked selection. We next identified candidate loci associated with reproductive isolation of these lineages. Given the absence of physical or geographic barriers, we thus propose that these lineages may represent three cryptic species of capelin. Within each of these, our analyses provided evidence for large Ne and high gene flow at both historical and contemporary time scales among spawning sites. Furthermore, we detected a polymorphic chromosomal rearrangement leading to the coexistence of three haplogroups within the Northwest Atlantic lineage, but absent in the other two clades. Genotype-environment associations revealed molecular signatures of local adaptation to environmental conditions prevailing at spawning sites. Altogether, our study shows that standing genetic variation associated with both chromosomal rearrangements and ancestral polymorphism contribute to local adaptation in the presence of high gene flow.

genomics↗

bioRxiv2019

Case studies and mathematical models of ecological speciation. V. Adaptive divergence of whitefish in Fennoscandia.

Modern speciation theory has greatly benefited from a variety of simple mathematical models focusing on the conditions and patterns of speciation and diversification in the presence of gene flow. Unfortunately the application of general theoretical concepts and tools to specific ecological systems remains a challenge. Here we apply modeling tools to better understand adaptive divergence of whitefish during the postglacial period in lakes of northern Fennoscandia. These lakes harbor up to three different morphs associated with the three major lake habitats: littoral, pelagic, and profundal. Using large-scale individual-based simulations, we aim to identify factors required for in situ emergence of the pelagic and profundal morphs in lakes initially colonized by the littoral morph. The importance of some of the factors we identify and study - sufficiently large levels of initial genetic variation, size- and habitat-specific mating, sufficiently large carrying capacity of the new niche - is already well recognized. In addition, our model also points to two other factors that have been largely disregarded in theoretical studies: fitness-dependent dispersal and strong predator pressure in the ancestral niche coupled with the lack of it in the new niche(s). We use our theoretical results to speculate about the process of diversification of whitefish in Fennoscandia and to identify potentially profitable directions for future empirical research.

evolutionary biology↗

bioRxiv2019

From metabarcoding to metaphylogeography: separating the wheat from the chaff

Metabarcoding is by now a well-established method for biodiversity assessment in terrestrial, freshwater and marine environments. Metabarcoding datasets are usually used for - and {beta}-diversity estimates, that is, interspecies (or inter-MOTU) patterns. However, the use of hypervariable metabarcoding markers may provide an enormous amount of intraspecies (intra-MOTU) information - mostly untapped so far. The use of cytochrome oxidase (COI) amplicons is gaining momentum in metabarcoding studies targeting eukaryote richness. COI has been for a long time the marker of choice in population genetics and phylogeographic studies. Therefore, COI metabarcoding datasets may be used to study intraspecies patterns and phylogeographic features for hundreds of species simultaneously, opening a new field which we suggest to name metaphylogeography. The main challenge for the implementation of this approach is the separation of erroneous sequences from true intra-MOTU variation. Here, we develop a cleaning protocol based on changes in entropy of the different codon positions of the COI sequence, together with co-occurrence patterns of sequences. Using a dataset of community DNA from several benthic littoral communities in the Mediterranean and Atlantic seas, we first tested by simulation on a subset of sequences a two-step cleaning approach consisting of a denoising step followed by a minimal abundance filtering. The procedure was then applied to the whole dataset. We obtained a total of 563 MOTUs that were usable for phylogeographic inference. We used semiquantitative rank data instead of read abundances to perform AMOVAs and haplotype networks. Genetic variability was mainly concentrated within samples, but with an important between-seas component as well. There were inter-group differences in the amount of variability between and within communities in each sea. For two species the results could be compared with traditional Sanger sequence data available for the same zones, giving similar patterns. Our study shows that metabarcoding data can be used to infer intra- and interpopulation genetic variability of many species at a time, providing a new method with great potential for basic biogeography, connectivity and dispersal studies, and for the more applied fields of conservation genetics, invasion genetics, and design of protected areas.

ecology↗

bioRxiv2019

Ecological speciation in European whitefish is driven by a large-gaped predator

Lake-dwelling fish that form species pairs/flocks characterized by body size divergence are important model systems for speciation research. While several sources of divergent selection have been identified in these systems, their importance for driving the speciation process remains elusive. A major problem is that in retrospect, we cannot distinguish selection pressures that initiated divergence from those acting later in the process. To address this issue, we reconstructed the initial stages of speciation in European whitefish (Coregonus lavaretus) using data from 357 populations of varying age (26-10 000 years). We find that whitefish speciation is driven by a large-growing predator, the northern pike (Esox lucius). Pike initiates divergence by causing a largely plastic differentiation into benthic giants and pelagic dwarfs; ecotypes that will subsequently develop partial reproductive isolation and heritable differences in gill raker number. Using an eco-evolutionary model, we demonstrate how pikes habitat specificity and large gape size are critical for imposing a between-habitat trade-off, causing prey to mature in a safer place or at a safer size. Thereby, we propose a novel mechanism for how predators may cause dwarf/giant speciation in lake-dwelling fish species.

evolutionary biology↗

bioRxiv2018

Dispersal routes of climate-induced marine range expansions into the Arctic

As a result of ocean warming, the species composition of the Arctic seas has begun to shift in a boreal direction. One ecosystem prone to fauna shifts is the Northeast Greenland shelf. The dispersal route taken by boreal fauna to this area is, however, not known. This knowledge is essential to predict to what extent boreal biota will colonise Arctic habitats. Using population genetics, we show that Atlantic cod (Gadus morhua), beaked redfish (Sebastes mentella), and deep-sea shrimp (Pandalus borealis) specimens recently found on the Northeast Greenland shelf originate from the Barents Sea, and suggest that pelagic offspring were dispersed via advection across the Fram Strait. Our results indicate that boreal invasions of Arctic habitats can be driven by advection, and that the fauna of the Barents Sea can project into adjacent habitats with the potential to colonise putatively isolated Arctic ecosystems such as Northeast Greenland.

ecology↗

bioRxiv2018

Convergent transcriptomic landscapes under polygenic selection accompany inter-continental parallel evolution within a Nearctic Coregonus (Salmonidae) sister-species complex.

In contrast to the plethora of studies focusing on the genomic basis of adaptive phenotypic divergence, the role of gene expression during speciation has been much less investigated and consequently, less understood. Yet, the convergence of differential gene expression patterns between closely related species-pairs might reflect the role of natural selection during the process of ecological speciation. Here, we test for intercontinental convergence in differential transcriptional signatures between limnetic and benthic sympatric species-pairs of Lake Whitefish (Coregonus clupeaformis) and its sister-lineage, the European Whitefish (C. lavaretus), using six replicated sympatric species-pairs (two in North America, two in Norway and two in Switzerland). We characterized both sequence variation in transcribed regions and differential gene expression between sympatric limnetic and benthic species across regions and continents. Our first finding was that differentially expressed genes (DEG) between limnetic and benthic whitefish tend to be enriched in shared polymorphism among sister-lineages. We then used both genotypes and co-variation in expression in order to infer polygenic selection at the gene level. We identified parallel outliers and DEG involving genes primarily over-expressed in limnetic species relative to the benthic species. Our analysis finally revealed the existence of shared genomic bases underlying parallel differential expression across replicated species pairs from both continents, such as a cis-eQTL affecting the pyruvate kinase expression level involved in glycolysis. Our results are consistent with a longstanding role of natural selection in maintaining transcontinental diversity at phenotypic traits involved in ecological speciation between limnetic and benthic whitefishes.

evolutionary biology↗

bioRxiv2017

Environmental DNA: a new low-cost monitoring tool for pathogens in salmonid aquaculture.

Sequencing of environmental DNA (eDNA-seq) is an emergent new monitoring tool that promises to facilitate the accurate and cost effective detection of species in environmental samples. eDNA monitoring is likely to have a major impact on the ability of salmonid aquaculture industry producers and their regulators to detect the presence and abundance of pathogens and other biological threats in the surrounding environment. However, for eDNA-seq to develop into a useful bio-monitoring tool it is necessary to (a) validate that sequence datasets derived from amplification of meta-barcoding markers reflect the true species identity and abundances in biological samples, and (b) establish a low-cost sequencing method to enable the bulk processing of environmental samples. In this study, we employed an elaborate experimental design whereby different combinations of five biological agents were crossed at three abundance levels and exposed to pre-filtered and normal seawater, prior to coarse filtering and then eDNA ultrafiltration of the resultant material. We then benchmarked the low-cost, scalable, Ion Torrent sequencing method against the current gold-standard Illumina platform for eDNAseq detection in aquaculture. Based on amplicon-seq of the 18S SSU rDNA v9 region, we found that Illumina and Ion Torrent were equally good in identifying the two parasite species (Lepeophtheirus salmonis and Paramoeba perurans), whereas the microalgae species Prymnesium parvum, Pseudo-nitzschia seriata and P. delicatissima could be assigned correctly only to the genus level. Illumina and Ion Torrent were also equally able to reflect community composition in our samples, whereas Ion Torrent was more sensitive in detecting species richness when the medium was unfiltered seawater. Both methods were able to reflect the correct abundances of 4 out of 5 species in samples from unfiltered seawater, despite the significant amount of background noise from both bacteria and eukaryotes. Our findings indicate that eDNA-seq offers significant potential in the monitoring of species harmful to aquaculture and for this purpose, the low-cost Ion Torrent sequencing is equally as accurate as Illumina.

genetics↗

bioRxiv2017

Genetic fingerprinting of salmon louse (Lepeophtheirus salmonis) populations in the North-East Atlantic using a random forest classification approach

Caligid sea lice represent a significant threat to salmonid aquaculture worldwide. Lepeophtheirus salmonis is the predominant species that occurs in the Northern Hemisphere. Dispersal of sea lice between marine aquaculture sites and geographic regions is thought to occur rapidly via planktonic transport of larvae. Population genetic analyses have consistently shown minimal population genetic structure in North Atlantic L. salmonis, frustrating efforts to track louse populations, improve targeted control measures and understand local adaption to environmental conditions. The aim of this study was to test the power of reduced representation library sequencing (IIb-RAD sequencing) coupled with random forest machine learning algorithms to define markers for fine-scale discrimination of louse populations. We identified 1286 robustly supported SNPs among four L. salmonis populations from Ireland (N=2, 27 individuals), Scotland (N=1, 11 individuals) and North Norway (N=1, 12 individuals). Weak global structure (FSC = 0.018, p<0.0001) and only one significant pairwise FST comparison was observed (Scotland vs Kenmare Bay, (FST = 0.018, p<0.0001)) using all 1286 SNPs. The application of a random forest machine-learning algorithm identified 98 discriminatory SNPs that dramatically improved population assignment (DAPC assignment probability = 1), increased global Fsc = 0.098, (p<0.0001) and resulted in pairwise comparisons that all showed highly significant Fst-values (range = 0.081 - 0.096, p<0.0001). Out of 19 SNPs found to be under directional selection between populations, 12 corresponded to the discriminatory SNPs identified using random forest. Taken together our data suggest that L. salmonis SNP diversity exists with which it is possible to discriminate differences between nearby populations given suitable marker selection approaches, and that such differences might have an adaptive basis. We discuss these data in light of sea lice adaption to anthropogenic and environmental pressures as well as novel approaches to track and predict sea louse dispersal.

ecology↗