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115 results for “brown trout”
Data from: Sex-specific life history affected by stocking in juvenile brown trout
<p>Salmonids are a socioeconomically and ecologically important group of fish that are often managed by stocking. Little is known about potential sex-specific effects of stocking, but recent studies found that the sexes differ in their stress tolerances already at late embryonic stage, i.e., before hatchery-born larvae are released into the wild and long before morphological gonad formation. It has also been speculated that sex-specific life histories can affect juvenile growth and mortality, and that a resulting sex-biassed demography can reduce population growth. Here we test whether juvenile brown trout (Salmo trutta) show sex-specific life histories and whether such sex effects differ in hatchery- and wild-born fish. We modified a genetic sexing protocol to reduce false assignment rates and used it to study the timing of sex differentiation in a laboratory setting, and in a large-scale field experiment to study growth and mortality of hatchery and wild-born fish in different environments. We found no sex-specific mortality in any of the environments we studied. However, females started sex differentiation earlier than males, and while growth rates were similar in the laboratory, they differed significantly in the field depending on location and origin of fish. Overall, hatchery-born males grew larger than hatchery-born females while wild-born fish showed the reverse pattern. Whether males or females grew larger was location-specific. We conclude that juvenile brown trout show sex-specific growth that is affected by stocking and by other environmental factors that remain to be identified.</p>
FIGURE 8 in A new perspective on the molecular dating of the brown trout complex with an extended phylogeographic information on the species in Serbia
FIGURE 8 Simplified palinspastic map for the Pliocene (compiled and modified after Popov et al., 2004, 2006; Neubauer et al., 2015) with the indication of hypothetic BT colonization routes (arrows). Interrupted lines mark migration routes that are, in our opinion, less likely. Green areas represent brackish environments, light blue freshwater lakes or marshes and rivers, dark blue seas, dark gray mountain ranges, and light gray land mass; all geographic features are tentatively positioned. 1 – Ancestral trout originated in the Ponto-Caspian system and crossed from the paleo-Danube into the Western Mediterranean basin via stream capture of Alpine rivers in Pliocene; 2 – Ancestral trout originated in the Balkans basin and colonized other parts of the Mediterranean Basin from here; 3 – Colonization of the Central Alps took place in the Pliocene after the paleo-Rhône separated from the paleo-Danube and reached the Mediterranean; 4 – Atlantic basin was colonized when the Rhine captured Central Alpine rivers; 5 – Atlantic basin was colonized along the Mediterranean coastline and via Gibraltar; 6 – Ponto-Caspian basin was colonized from the Mediterranean basin following a presumed sea corridor in the upper Euphrates valley or using the paleo-Euphrates, which might have been connected with the Mediterranean until the Middle Pliocene; 7 – Ponto-Caspian basin was colonized via a possible Pliocene gateway that connected the Dacic basin and the Aegean Sea; 8 – Ponto-Caspian basin was colonized through the Bosphorus gateway.
FIGURE 6 in A new perspective on the molecular dating of the brown trout complex with an extended phylogeographic information on the species in Serbia
FIGURE 6 Split graph of the Neighbor-Net phylogenetic network analysis of brown trout lineages. The colors of the haplotypes represent different lineages, and the scale bar represents the nucleotide substitutions per site.
FIGURE 4 in A new perspective on the molecular dating of the brown trout complex with an extended phylogeographic information on the species in Serbia
FIGURE 4 Median-joining network of CR mtDNA sequences belonging to Danubian haplogroups. Haplotypes are represented by colored circles whose size is proportional to haplotype frequencies detected and taken from the literature (supplementary tables S2 and S3). Haplotypes from this study are bolded and framed. Mutations are represented by hatch marks on the lines connecting the haplotypes. Missing or theoretical haplotypes are shown as black dots. The maps show the distribution of haplotypes from the network (A – DA-ES haplotypes, B – DA-INT haplotypes, C – DA-BS haplotypes), and their numbering corresponds to that in supplementary table S2.
FIGURE 3 in A new perspective on the molecular dating of the brown trout complex with an extended phylogeographic information on the species in Serbia
FIGURE 3 Reconstruction of the sequence evolution in the Danubian lineage. Defining variable nucleotide sites in the control region are all placed nearby in the central part of the control region, between the nucleotide positions 540-550 of our alignment. The 542 G → C transversion defines the split of the DAES + DA-INT and the DA-BS; 541 G → A split of the DA-ES + DA-INT (excluding DaBS9) from the DaBS9 haplotype; and 548 C → T defines the DA-ES.
FIGURE 7 in A new perspective on the molecular dating of the brown trout complex with an extended phylogeographic information on the species in Serbia
FIGURE 7 Fossil and geologically calibrated chronogram of the genus Salmo created with a relaxed clock in BEAST 2. 95% highest posterior density (HPD) intervals are shown as gray bars at the nodes. Calibration points are indicated by arrows. Median node ages are shown as node labels. Time estimates are given in millions of years. Clades, that were a priori treated as monophyletic are indicated with a black star, while a red star indicates the clade, where posterior probability was> 90% only in BEAST analysis.
Figure 1 in Feeding habit of Brown trout (Salmo trutta fario) in upper parts of river Swat, Pakistan
Figure 1. Percentage of N,W, FO and IRI of various diet components. Table 2. GSI and fullness index of various length groups of brown trout.
Figure 1 in Haplotype diversity of brown trout Salmo trutta (L.) in the broader Iron Gate area
Figure 1. Sampling sites on the streams Brnjica (1), Dobrinjska reka (2), Kožica (3), Mala Boljetinska reka (4), Zlatica (5), Porečka reka (6), Rečka reka (7), Vratna (8), and Zamna (9) in the broader Iron Gate area with the position in the Balkan region given in small figure in lower left.
Figure 2 in Haplotype diversity of brown trout Salmo trutta (L.) in the broader Iron Gate area
Figure 2. Relationships between CR haplotypes of brown trout populations in the broader Iron Gate area constructed using maximum likelihood (A) and maximum parsimony (B) methods (numbers at particular branches represent bootstrap probabilities; bootstrap values under 40% are not represented).
Trout of Hokkaido data (Rainbow, Brown, Brook, and Sockeye)
<p>This is a data set of 928 presents points (and 3 NA locations) for invasive trout species across Hokkaido for the masters thesis "<strong>Perception of fishermen towards invasive salmonids in Hokkaido and the contribution of citizen science to their long-term monitoring</strong>". It is comprised of Scientific studies, gray literature, YouTube videos, social media sites, blogs, word of mouth, email, and iNaturalist data. Please feel free to use this data for research on these species.</p> <p>Columns are broken up into 10 parts.</p> <p>-------------------------------Columns are--------------------------------</p> <p><strong>Hits</strong>: Hits on the map one per site.</p> <p><strong>Paper/source</strong>: where the study or citizen data came from. (Please feel free to check out the blogs as they update with new data often) The key as follows</p> <p> FLK = Fliker / IG = Instagram / TW = Twitter / WEB = website / YTV = youtube</p> <p><strong>Contributor</strong>: then Name of the citizen sciences contributor. Blogs, Twitter names, Instagram names, Youtube channel names, etc... </p> <p><strong>Xcoord</strong>: the X coordinate</p> <p><strong>Ycoord</strong>: the y coordinate</p> <p><strong>Specie</strong>: one of 4 species denoted as its scientific name</p> <p><strong>Start Date</strong>: When the study or post started collecting data</p> <p><strong>End Date</strong>: When the study or post ended collecting data</p> <p><strong>Science / Citizen</strong>: denotes where the data came from.</p> <p> Broken up into a few groups,</p> <p> <strong>Science</strong>: from scientific source and grey litterture</p> <p> *Science (old) : data was used as a base line for the study</p> <p> <strong>Active</strong>: Citizen data that has been reported during the study period of the study</p> <p> Please go the the iNaturalist link to get that data. </p> <p> <strong> Passive</strong>: Citizen data that came from lots of different places.</p> <p> *Passive(site) : places that are mapped as fishing spots per speceis by fishing shops and tours</p> <p><strong>Number per hit</strong>: reported or counted species per hit point on the map (accuracy is not 100% ensured) </p> <p>Notes-----------------------------------------------------------------------------------------------</p> <p>River points should be close to actual points caught but lake points should not be used for precise data as much of it was not precisely listed and so guess work on location took place.</p> <p> </p>
Data from: Sex-specific effects of inbreeding in juvenile brown trout
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Phenotypes and genotypes of brown trout used for breeding experiments in 2014
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Data from: Sex-specific life history affected by stocking in juvenile brown trout
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Testing for population differences in evolutionary responses to pesticide pollution in brown trout (Salmo trutta)
<p>Pesticides are often toxic to non-target organisms, especially to those living in rivers that drain agricultural land. The brown trout (<i>Salmo trutta</i>) is a keystone species in many such rivers, and natural populations have hence been chronically exposed to pesticides over multiple generations. The introduction of pesticides decades ago could have induced evolutionary responses within these populations. Such a response would be predicted to reduce the toxicity over time but also deplete any additive genetic variance for the tolerance to the pesticides. If so, populations are now expected to differ in their susceptibility and in the variance for the tolerance depending on the pesticides they have been exposed to. We sampled breeders from seven natural populations that differ in their habitats and that show significant genetic differentiation. We stripped them for their gametes and produced 118 families by <i>in vitro</i> fertilization. We then raised 20 embryos per family singly in experimentally controlled conditions and exposed them to one of two ecologically relevant concentrations of either the herbicide S-metolachlor or the insecticide diazinon. Both pesticides affected embryo and larval development at all concentrations. We found no statistically significant additive genetic variance for tolerance to these stressors within or between populations. Tolerance to the pesticides could also not be linked to variation in carotenoid content of the eggs. However, pesticide tolerance was linked to egg size, with smaller eggs being more tolerant to the pesticides than larger eggs. We conclude that an evolutionary response to these pesticides is currently unlikely, and that (i) continuous selection in the past has either depleted genetic variance in all the populations we studied, or (ii) that exposure to the pesticides never induced an evolutionary response. The observed toxicity selects against large eggs that are typically spawned by larger and older females.</p>
Data from: Genetic consequences of improved river connectivity in brown trout (Salmo trutta)
<p>Fragmentation of watercourses poses a significant threat to biodiversity, particularly for migratory fish species. Mitigation measures such as fishways, have been increasingly implemented to restore river connectivity and support fish migration. The effects of such restoration efforts are typically tested using telemetry and fisheries methods, which do not fully capture the broader population movements that may have important consequences for population viability. We performed a before-and-after control-impact (BACI) study using genetic tools (SNPs) to investigate the effect of a newly implemented fishway, aiming to enhance upstream spawning migration of brown trout (<em>Salmo trutta</em> Linnaeus) in a reservoir with two headwater tributaries fragmented by man-made weirs. Another reservoir with two barrier-free tributaries was also analysed as a control. Our results showed that the isolated brown trout population was spawning in the reservoir before the installation of the fishway, and we found genetic structuring and differentiation between fragmented headwater tributaries before the fishway construction, but not in the control reservoir. Unexpectedly, after the fishway construction we observed signals consistent with increased genetic differentiation between populations of newly recruited juvenile fish in the reservoir tributary and fish in the reservoir. We propose this was caused by newly enabled philopatric behaviour of brown trout to their natal spawning tributary. In contrast, we did not find any genetic changes in the tributary without a fishway or in the barrier-free reservoir system. Given the scarcity of similar studies, we advocate for an increased use of genetic analyses in BACI studies to monitor and evaluate the effect of efforts to restore habitat connectivity and inform future management strategies.</p>
Whole-genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes
<p>The sympatric existence of genetically distinct populations of the same species remains a puzzle in ecology. Coexisting salmonid fish populations are known from over 100 freshwater lakes. Most studies of sympatric populations have used limited numbers of genetic markers making it unclear if genetic divergence involves only certain parts of the genome. We return to the first reported case of salmonid sympatry, initially detected through contrasting homozygosity at a single allozyme locus (coding for lactate dehydrogenase A) in brown trout in the small Lakes Bunnersjöarna, Sweden. First, we verify the existence of the two coexisting demes using a 96-SNP fluidigm array. We then apply whole-genome resequencing of pooled DNA to explore genome-wide diversity within and between these demes; nucleotide diversity is higher in Deme I than in Deme II. Furthermore, strong genetic divergence is observed with genome-wide <i>F</i><sub>ST</sub>≈0.2. Comparing with similar data from other lakes, this divergence is of similar magnitude as that between reproductively isolated populations. Individual whole-genome resequencing of two individuals per deme suggests higher inbreeding in Deme II vs. Deme I, indicating different degree of isolation. Finally, we located two gene-copies for LDH-A<i> </i>and find divergence between demes in a regulatory section of one of these genes. However, we did not find a perfect fit between the sequence data and previous allozyme results, and this will require further research. Our data demonstrates genome-wide divergence governed mostly by genetic drift but also by diversifying selection in coexisting populations. This type of hidden biodiversity needs consideration in conservation management.</p>
Archived data for: Balancing selection, genetic drift, and human mediated-introgression interplay to shape MHC (functional) diversity in Mediterranean brown trout
<p>The extraordinary polymorphism of Major Histocompatibility Complex (MHC) genes is considered a paradigm of pathogen-mediated balancing selection, although empirical evidence is still scarce. Furthermore, the relative contribution of balancing selection to shape MHC population structure and diversity, compared to that of neutral forces, as well as its interaction with other evolutionary processes such as hybridization, remains largely unclear. To investigate these issues, we analysed adaptive (MHC-DAB gene) and neutral (11 microsatellite loci) variation in 156 brown trout (<i>Salmo trutta </i>complex) from six wild populations in central Italy exposed to introgression from domestic hatchery lineages (assessed with the LDH gene). MHC diversity and structuring correlated with those at microsatellites, indicating the substantial role of neutral forces. However, individuals carrying locally rare MHC alleles/supertypes (regardless of the zygosity status and degree of sequence dissimilarity of MHC) were in better body condition (a proxy of individual fitness/parasite load), hence supporting balancing selection under rare allele advantage, but not heterozygote advantage or divergent allele advantage. The association between specific MHC supertypes and body condition confirmed in part this finding. Across populations, MHC allelic richness increased with increasing admixture between native and domestic lineages, indicating introgression as a source of MHC variation. Furthermore, introgression across populations appeared more pronounced for MHC than microsatellites, possibly because initially-rare MHC variants are expected to introgress more readily under rare allele advantage. Providing evidence for the complex interplay among neutral evolutionary forces, balancing selection and human-mediated introgression in shaping the pattern of MHC (functional) variation, our findings contribute to a deeper understanding of the evolution of MHC genes in wild populations exposed to anthropogenic disturbance.</p>
Supplementary information for: Redundancy analysis, genome-wide association studies, and the pigmentation of brown trout (Salmo trutta L.)
<p><span>The association of molecular variants to phenotypic variation is a main issue in biology, often tackled with genome-wide association studies (GWAS). GWAS are challenging, with increasing, but still limited use in evolutionary biology. We used redundancy analysis (RDA) as a complimentary ordination approach to single- and multi-trait GWAS to explore the molecular basis of pigmentation variation in brown trout (<em>Salmo</em> <em>trutta</em>) belonging to wild populations impacted by hatchery fish. Based on 75,684 single nucleotide polymorphic (SNP) markers, RDA, single- and multi-trait GWAS allowed us to extract 337 independent "colour patterning loci" (CPLs) associated with trout pigmentation traits, such as the number of red and black spots on flanks. Collectively, these CPLs (<em>i</em>) mapped onto 35 out of 40 brown trout linkage groups indicating a polygenic genomic architecture of pigmentation, (<em>ii</em>) were found associated with</span><span> 218 </span><span>candidate genes, including 197 genes </span><span>formerly mentioned in the literature dealing with skin pigmentation, skin patterning, differentiation or structure notably in a close relative, the rainbow trout (<em>Onchorhynchus</em> <em>mykiss</em>)</span><span>, and (<em>iii</em>) related to functions relevant to pigmentation variation (e.g., calcium- and ion-binding, cell adhesion). Annotated CPLs include genes with well-known pigmentation effects (e.g., PMEL, SLC45A2, SOX10), but also markers associated with genes formerly found expressed in rainbow or brown trout skins. RDA was also shown useful to investigate management issues, especially the dynamics of trout pigmentation submitted to several generations of hatchery introgression.</span></p>
SNP genotype dataset from brown and anadromous trout
<p>Populations of anadromous brown trout, also known as sea trout, have suffered recent marked declines in abundance due to multiple factors, including climate change and human activities. While much is known about their freshwater phase, less is known about the species' marine feeding migrations. This situation is hindering the effective management and conservation of anadromous trout in the marine environment. Using a panel of 95 single nucleotide polymorphism markers we developed a genetic baseline, which demonstrated strong regional structuring of genetic diversity in trout populations around the English Channel and adjacent waters. Extensive baseline testing showed this structuring allowed the high-confidence assignment of known-origin individuals to the region of origin. This study presents new data on the movements of anadromous trout in the English Channel and southern North Sea. Assignment of anadromous trout sampled from 12 marine and estuarine localities highlighted contrasting results for these areas. The majority of these fisheries are composed predominately of stocks local to the sampling location. However, there were multiple cases of long-distance movements of anadromous trout, with several individuals originating from rivers in northeast England being caught in the English Channel and southern North Sea, in some cases more than 1000 km from their natal region. These results have implications for the management of sea trout in inshore waters around the English Channel and southern North Sea.</p>
Figure 2 in Feeding habit of Brown trout (Salmo trutta fario) in upper parts of river Swat, Pakistan
Figure 2. Month wise number of stomach and empty stomachs.
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