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96 results for “whitefish”
Photograph measurements of broad whitefish (Coregonus nasus) body size
<p>The dataset contains photograph measurements of broad whitefish (<em>Coregonus nasus</em>). Measurements (mm; with the scale set to the image) were taken using ImageJ. There are 15 measurements total; see the “Measurement Guide” file for details. Broad whitefish were harvested and photographed in the Gwich’in Settlement Area by community collaborators in 2017 & 2018, along the Peel Channel in the Mackenzie Delta and the Peel River.</p> <p>Measurements were used to predict fish weight using random forest analysis as a methodology for community-based data collection. The “Data Type” column refers to the dataset fish were randomly assigned to as part of this process. “True Fish Weight (g)” and “True Fish Length (mm)” were collected in the field by community monitors.</p> <p>Data collection was done as part of a research program that began in 2017 between Gwich’in community members, renewable resources organizations within the Gwich'in Settlement Area, and university scientists.</p>
Data from: A de novo chromosome-level genome assembly of Coregonus sp. "Balchen": one representative of the Swiss Alpine whitefish radiation
<p>Salmonids are of particular interest to evolutionary biologists due to their incredible diversity of life-history strategies and the speed at which many salmonid species have diversified. In Switzerland alone, over 30 species of Alpine whitefish from the subfamily Coregoninae have evolved since the last glacial maximum, with species exhibiting a diverse range of morphological and behavioural phenotypes. This, combined with the whole genome duplication which occurred in the ancestor of all salmonids, makes the Alpine whitefish radiation a particularly interesting system in which to study the genetic basis of adaptation and speciation and the impacts of ploidy changes and subsequent rediploidization on genome evolution. Although well curated genome assemblies exist for many species within Salmonidae, genomic resources for the subfamily Coregoninae are lacking. To assemble a whitefish reference genome, we carried out PacBio sequencing from one wild-caught <i>Coregonus sp. "Balchen" </i>from Lake Thun to ~90x coverage. PacBio reads were assembled independently using three different assemblers, Falcon, Canu and wtdbg2 and subsequently scaffolded with additional Hi-C data. All three assemblies were highly contiguous, had strong synteny to a previously published <i>Coregonus</i>linkage map, and when mapping additional short-read data to each of the assemblies, coverage was fairly even across most chromosome-scale scaffolds. Here, we present the first <i>de novo</i>genome assembly for the Salmonid subfamily Coregoninae. The final 2.2 Gb wtdbg2 assembly included 40 scaffolds, an N50 of 51.9 Mb, and was 93.3% complete for BUSCOs. The assembly consisted of ~52% TEs and contained 44,525 genes.</p>
Male sexual signaling and expected effects of hatchery-induced sperm competition vary with water depth at which whitefish are caught
<div> <div> <div> <div> <p>Salmonids like whitefish (<em>Coregonus</em> spp.) are often propagated in supportive breeding. Spawners are caught from their spawning locations, their gametes mixed, and the resulting offspring reared in a protected environment before being released into the wild. This procedure can affect sexual selection, for example, by enhancing the importance of sperm competition or by reducing the relevance of sexual signals. While it is often unclear how sperm competitiveness is affected by a male's overall genetic quality, there is accumulating evidence that sexual signals reveal good genes and that mate choice based on such signals can increase offspring viability (Auld et al. 2019). Therefore, supportive breeding may affect the genetic variance and the mean genetic quality of next generations. We sampled whitefish from various locations along a depth gradient to test how male characteristics that are likely to affect sexual selection under natural conditions correlate with characteristics that affect hatchery-induced sperm competition. Whitefish are external fertilizers, and multi-male spawning and hence sperm competition is common under natural conditions. Mate choice is not sufficiently understood but could be based on breeding tubercles. These are small conical structures that grow on scales before the breeding sea- son and fall off shortly afterwards. The size of breeding tubercles varies much among males and has repeatedly been found to correlate positively with offspring viability (Wedekind et al. 2001; Keka ̈la ̈inen et al. 2010). Male dominance is typically depend- ent on body size (Auld et al. 2019) and could also be relevant in whitefish. Body size itself can reflect individual inbreeding coefficients (Su et al. 1996) and be an indicator of heritable genetic quality in small or structured populations (Neff and Pitcher 2008). In another fish with a somewhat comparable mating system, the size of breeding tubercles and male size was not correlated but could both be used to predict male reproductive success under close to natural conditions (Jacob et al. 2009). We study whitefish from Lake Hallwil (Switzerland). This lake has suffered so much from anthropogenic eutrophication that it is being artificially aerated since 1985. Three hatcheries around the lake are likely to have played a key role in maintaining the whitefish population, as concluded also from a recent mark–recapture experiment (Vonlanthen 2015). However, eutrophication combined with possible hybridization in hatcheries can have led to a speciation reversal (Vonlanthen et al. 2012) and may thereby have destroyed any genetic structure linked to water depth. Hatchery protocols now focus on maintaining over-all genetic variance by pooling milt of many males before adding the mix to eggs of multiple females. Milt volume varies among sires, for example, because males often lose milt when being pulled up from deep locations (Figure 1), an effect that likely depends on how much the swim bladder is inflated by the change in pressure. This variance in milt volume is likely to affect the genetic variance that, in combination with the average genetic quality, may then affect the long-term survival of a population. The extent to which hatchery protocols affect genetic quality can be estimated by the correlations between male quality indicators and traits that affect hatchery-induced sperm competition, that is, sperm number, velocity, and longevity (summarized here as "milt potency," see also Supplementary Material). Many breeding protocols are likely to promote genetic quality if male attractiveness or dominance are positively correlated to milt potency. If there are no such correlations or negative ones because of life-history trade-offs, hatchery-induced sperm competition is likely to reduce the average genetic quality in future generations. We sampled fish from various depths and determined their age, size, breeding ornamentation, and milt potency (see methods in the Supplementary Material) to test whether and how different male characteristics affect reproductive success in supportive breeding in a heavily managed population.</p> </div> </div> </div> </div>
Male sexual signaling and expected effects of hatchery-induced sperm competition vary with water depth at which whitefish are caught
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Data from: A de novo chromosome-level genome assembly of Coregonus sp. “Balchen”: one representative of the Swiss Alpine whitefish radiation
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Data from: Ecological speciation in European whitefish is driven by a large‐gaped predator
<p>Lake‐dwelling fish that form species pairs/flocks characterized by body size divergence are important model systems for speciation research. Although 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 studied the initial stages of speciation in European whitefish (<i>Coregonus lavaretus</i>) using data from 358 populations of varying age (26–10,000 years). We find that whitefish speciation is driven by a large‐growing predator, the northern pike (<i>Esox lucius</i>). 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 pike's 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.</p>
Data from: A taxonomic revision of the whitefish radiation of lakes Brienz and Thun, Switzerland, with descriptions of four new species (Teleostei: Coregonidae)
<p>The alpha taxonomy of the endemic whitefish of lakes Brienz and Thun, Switzerland, is revised. We evaluate the status of seven known species: <em>Coregonus steinmanni </em>sp. nov., <em>Coregonus profundus</em> sp. nov. and <em>Coregonus acrinasus</em> sp. nov. are endemic to Lake Thun; <em>Coregonus brienzii </em>sp. nov. is endemic to Lake Brienz; and <em>C. alpinus, C. albellus,</em> and <em>C. fatioi</em> from lakes Brienz and Thun are redescribed. One of these species, <em>C. alpinus</em>, is revised, since the lectotype for this species is incongruent with the species description given by Kottelat (1997) and Kottelat and Freyhof (2007). The name <em>C. alpinus</em> is thus retained for the lectotype designated by Kottelat (1997) and a new description of this taxon provided. For the species otherwise described by Kottelat (1997) and Kottelat and Freyhof (2007) as C. alpinus the new name C. profundus is designated. <em>Coregonus acrinasus </em>is genetically partially of allochthonous origin, closely related to the radiation of Lake Constance, and we therefore compare it to all recognized species of Lake Constance, <em>C. wartmanni, C. macrophthalmus, C. arenicolus,</em> and <em>C. gutturosus.</em></p>
Data from: Genomic insights into the vulnerability of sympatric whitefish species flocks
The erosion of habitat heterogeneity can reduce species diversity directly but can also lead to the loss of distinctiveness of sympatric species through speciation reversal. We know little about changes in genomic differentiation during the early stages of these processes, which can be mediated by anthropogenic perturbation. Here, we analyse three sympatric whitefish species (Coregonus spp) sampled across two neighbouring and connected Swiss pre-alpine lakes, which have been differentially affected by anthropogenic eutrophication. Our data set comprises 16,173 loci genotyped across 138 whitefish using restriction-site associated DNA sequencing (RADseq). Our analysis suggests that in each of the two lakes the population of a different, but ecologically similar, whitefish species declined following a recent period of eutrophication. Genomic signatures consistent with hybridisation are more pronounced in the more severely impacted lake. Comparisons between sympatric pairs of whitefish species with contrasting ecology, where one is shallow benthic and the other one more profundal pelagic, reveal genomic differentiation that is largely correlated along the genome, while differentiation is uncorrelated between pairs of allopatric provenance with similar ecology. We identify four genomic loci that provide evidence of parallel divergent adaptation between the shallow benthic species and the two different more profundal species. Functional annotations available for two of those loci are consistent with divergent ecological adaptation. Our genomic analysis indicates the action of divergent natural selection between sympatric whitefish species in pre-alpine lakes and reveals the vulnerability of these species to anthropogenic alterations of the environment and associated adaptive landscape.
Monitoring growth of whitefish (Coregonus cf. suidteri) in Lake Hallwil
<p><span>Many lakes of the pre-Alpine region suffered from severe eutrophication that affected the natural reproduction of whitefish (<em>Coregonus </em>spp.) and necessitated large-scale supportive breeding programs. With the advanced reoligotrophication, it is now important to evaluate the relevance of continued artificial breeding for population dynamics. We focused on a whitefish population of a lake that has reached phase III of the reoligotrophication, i.e., lake biomass production is declining since 2012 in response to low phosphorus concentrations. We show that most eggs are naturally spawned, the observed oxygen concentrations would again support embryo development at all depths, and ready-to-hatch embryos can indeed be found on spawning grounds. We marked all hatchery-produced eggs of the 2014 cohort with Alizarin red, stocked them as usual (at larval or early juvenile stages), and recaptured them over a period of five years. Fish were aged from yearly growth rings on scales, and otoliths were checked for marks. We found 90.3% of the 2014 cohort to be hatchery-born. This ratio did not decline with fish age. We also determined juvenile growth of the cohorts 2012-2020 (based on the first annual ring on scales) and found that stocking intensity predicted juvenile growth (r<sup>2</sup> = 0.67). This strong density dependence suggest that stocking has largely determined population size over the first nine years of reoligotrophication phase III. We conclude that large areas of spawning grounds allow again for successful embryogenesis, that large quantities of eggs are naturally spawned, but that natural recruitment is significantly reduced by ecological or evolutionary factors, e.g., competition with hatchery-born fish, desynchronization of trophic interactions, or long-term effects of fishing- or hatchery-induced evolution</span></p>
High-density genomic data reveal fine-scale population structure and pronounced islands of adaptive divergence in lake whitefish (Coregonus clupeaformis) from Lake Michigan
<p>Understanding patterns of genetic structure and adaptive variation in natural populations is crucial for informing conservation and management. Past genetic research using 11 microsatellite loci identified six genetic stocks of lake whitefish (<em>Coregonus clupeaformis</em>) within Lake Michigan, USA. However, ambiguity in genetic stock assignments suggested those neutral microsatellite markers did not provide adequate power for delineating lake whitefish stocks in this system, prompting calls for a genomics approach to investigate stock structure. Here, we generated a dense genomic dataset to characterize population structure and investigate patterns of neutral and adaptive genetic diversity among lake whitefish populations in Lake Michigan. Using Rapture sequencing, we genotyped 829 individuals collected from 17 baseline populations at 197,588 SNP markers after quality filtering. Although the overall pattern of genetic structure was similar to the previous microsatellite study, our genomic data provided several novel insights. Our results indicated a large genetic break between the northwestern and eastern sides of Lake Michigan, and we found a much greater level of population structure on the eastern side compared to the northwestern side. Collectively, we observed five genomic islands of adaptive divergence on five different chromosomes. Each island displayed a different pattern of population structure, suggesting that combinations of genotypes at these adaptive regions are facilitating local adaptation to spatially heterogenous selection pressures. Additionally, we identified a large linkage disequilibrium block of ~8.5 Mb on chromosome 20 that is suggestive of a putative inversion but with a low frequency of the minor haplotype. Our study provides a comprehensive assessment of population structure and adaptive variation that can help inform management of Lake Michigan's lake whitefish fishery and highlights the utility of incorporating adaptive loci into fisheries management. </p>
Underwater video of lake whitefish Coregonus clupeaformis spawning in lake Michigan
<p>The lake whitefish <em>Coregonus clupeaformis,</em> <em>dikameg</em> in Anishinaabemowin, holds cultural importance, and is a mainstay of commercial, recreational, and subsistence fisheries throughout North America. In the Laurentian Great Lakes, declines in recruitment, since the early 2000s, have raised concerns among stewards and fishery managers. A more detailed understanding of the lake whitefish mating system could help resolve potential recruitment bottlenecks and thus inform appropriate stewardship actions. Herein, we describe, for the first time, a single lake whitefish spawning event captured using high-resolution underwater videography. From 94 h spent on the water, we captured and analyze a 4.5 min video clip that shows pre-mating, mating, and post-mating behaviour of a male and female lake whitefish from Lake Michigan. The clip shows a number of what we interpret as courtship, site-selection, and spawning behaviours culminating in release of about 20 eggs in a single spawning event. Behaviours that included travelling, physical contact, chasing, circling, orienting, and gamete release are described and time-referenced to a video supplement. This single observation is part of a larger project to assess lake whitefish spawning behaviour in the wild but is noteworthy in that it provides new insights into the spawning behaivour of lake whitefish and appears consistent with reproductive behaviours observed in European coregonines.</p>
Data from: How "simple" methodological decisions affect interpretation of population structure based on reduced representation library DNA sequencing: a case study using the lake whitefish
Reduced representation (RRL) sequencing approaches (e.g., RADSeq, genotyping by sequencing) require decisions about how much to invest in genome coverage and sequencing depth (library quality), as well as choices of values for adjustable bioinformatics parameters. To empirically explore the importance of these "simple" decisions, we generated two independent sequencing libraries for the same 142 individual lake whitefish (Coregonus clupeaformis) using a nextRAD RRL approach: (1) A small number of loci and low sequencing depth (library A); and (2) more loci and higher sequencing depth (library B). The fish were selected from populations with different levels of expected genetic subdivision. Each library was analyzed using the STACKS pipeline followed by three types of population structure assessment (FST, DAPC and ADMIXTURE) with iterative increases in the stringency of sequencing depth and missing data requirements, as well as more specific a priori population maps. Library B was always able to resolve strong population differentiation in all three types of assessment regardless of the selected parameters. In contrast, library A produced more variable results; increasing the minimum sequencing depth threshold (-m) resulted in a reduced number of retained loci, and therefore lost resolution at high -m values for FST and ADMIXTURE, but not DAPC. FST and DAPC were robust to varying the population map and increasing the stringency of missing data requirements. In contrast, ADMIXTURE was unable to resolve strong population differentiation when increasing these same parameters in library A. Similarly, when examining fine scale population subdivision, library B was robust to changing parameters but library A lost resolution depending on the parameter set. We used library B to examine actual subdivision in our study populations. All three types of analysis found complete subdivision among populations in Lake Huron, ON and Dore Lake, SK, Canada using 10,640 SNP loci. Weak population subdivision was detected in Lake Huron with fish from sites in the north-west, Search Bay, North Point and Hammond Bay, showing slight differentiation. Overall, we show that apparently simple decisions about library quality and bioinformatics parameters can have potentially important impacts on the interpretation of population subdivision. Although costly, the early investment in a high-quality library and more conservative stringency settings on STACKS parameters lead to a final dataset that was more consistent and robust when examining both weak and strong population differentiation.
Data for: A taxonomic revision of ten whitefish species from lakes Lucerne, Sarnen, Sempach, and Zug, Switzerland, with descriptions of seven new species (Teleostei, Coregonidae)
<p><span>The taxonomy of the endemic whitefish of the lakes of the Reuss River system (Lucerne, Sarnen, Zug) and Lake Sempach, Switzerland, is reviewed and revised. Lake Lucerne harbours five species. <em>Coregonus</em> <em>intermundia</em> </span><span><strong>sp. nov.</strong> </span><span>and <em>C</em>. <em>suspensus</em> </span><strong><span>sp. nov.</span></strong><span>, are described. <em>Coregonus</em> <em>nobilis</em> Haack, 1882, <em>C</em>. <em>suidteri</em> Fatio, 1885, and <em>C</em>. <em>zugensis</em> Nüsslin, 1882, are redescribed. Genetic studies have shown that <em>C</em>. <em>suidteri</em> and <em>C</em>. <em>zugensis</em> are composed of several distinct species endemic to different lakes. The names <em>C</em>. <em>suidteri</em> and <em>C</em>. <em>zugensis</em> are restricted to the species of lakes Sempach and Zug, respectively. The whitefish populations previously referred to as <em>C</em>. <em>suidteri</em> and <em>C</em>. <em>zugensis</em> from Lake Lucerne are described as <em>C</em>. <em>litoralis</em> </span><span><strong>sp. nov.</strong> </span><span>and <em>C</em>. <em>muelleri</em> </span><strong><span>sp. nov.</span></strong><span>, respectively. Furthermore, the whitefish from Lake Zug that were previously referred to as <em>C</em>. <em>suidteri</em> are described as <em>C</em>. <em>supersum</em> </span><strong><span>sp. nov</span></strong><span><strong>.</strong> A holotype is designated for <em>C</em>. <em>supersum</em> that was previously one of two syntypes of <em>C</em>. <em>zugensis</em>. The other syntype is retained for <em>C</em>. <em>zugensis</em>. <em>Coregonus</em> <em>obliterus</em> </span><span><strong>sp. nov.</strong> </span><span>is described from Lake Zug, and <em>C</em>. <em>obliterus</em> and <em>C</em>. <em>zugensis</em> from Lake Zug are extinct. Finally, we describe <em>C</em>. <em>sarnensis</em> </span><span><strong>sp. nov.</strong> </span><span>from lakes Sarnen and Alpnach. <em>Coregonus</em> <em>suidteri</em> from Lake Sempach shows strong signals of introgression from deliberately translocated non-native whitefish species, which questions if the extant population still carries a genetic legacy from the original species and thus may need to be considered extinct. <em>Coregonus</em> <em>suspensus</em> is genetically partially of allochthonous origin, closely related to the radiation of Lake Constance. It is therefore compared to all known and described species of Lake Constance: <em>C</em>. <em>wartmanni</em> Bloch, 1784, <em>C</em>. <em>macrophthalmus</em> Nüsslin, 1882, <em>C</em>. <em>arenicolus</em> Kottelat,1997, and <em>C</em>. <em>gutturosus</em> Gmelin, 1818.</span></p>
Monitoring growth of whitefish (Coregonus cf. suidteri) in Lake Hallwil
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Data from: How “simple” methodological decisions affect interpretation of population structure based on reduced representation library DNA sequencing: a case study using the lake whitefish
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Data for: A taxonomic revision of ten whitefish species from lakes Lucerne, Sarnen, Sempach, and Zug, Switzerland, with descriptions of seven new species (Teleostei, Coregonidae)
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Data from: Genomic insights into the vulnerability of sympatric whitefish species flocks
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Data from: A taxonomic revision of the whitefish radiation of lakes Brienz and Thun, Switzerland, with descriptions of four new species (Teleostei: Coregonidae)
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Data from: Genomic insights on conservation priorities for North Sea houting and European lake whitefish (Coregonus spp.)
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High-density genomic data reveal fine-scale population structure and pronounced islands of adaptive divergence in lake whitefish (Coregonus clupeaformis) from Lake Michigan
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