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730 results for “Trout”
Oxygen consumption of juvenile brown trout, Salmo trutta, under varying thermal conditions during embryogenesis
<p>Climate change is predicted to increase the future thermal conditions in northern latitudes with the potential effect of altering the metabolic scope and potential fitness of aquatic ectotherms. We experimentally tested the effect of elevated egg incubation temperature on the metabolic scope in juvenile brown trout (<i>Salmo trutta</i>). Brown trout cohorts from anadromous and resident crosses were raised from egg through exogenous feeding of juveniles in either natural river temperatures (cold) or elevated (+ 3 °C, warm) temperatures. In respirometry studies, we measured oxygen consumption rates of juvenile trout from both incubation temperatures and all possible breeding crosses after they were feeding exogenously and at an ambient temperature of 13 °C. These measures were taken over a period where the trout were resting, allowing for the determination of standard metabolic rate (SMR), and followed by a chase to exhaustion allowing for the measure of the maximum metabolic rate (MMR). The aerobic scope (AS) of these juveniles from four anadromous-resident crosses and from both incubation temperatures could then be calculated as AS = MMR – SMR. This dataset represents a key to all respiration trials including: fish embryonic incubation temperature, parental cross, fish total length (mm), calculated mass (g) per fish, ventilation rate (opercular beats/min), and water temperature per respiration trial. For each fish tested, the dissolved oxygen levels in the respirometry chamber were recorded continuously through periods of static respiration and recharge flow in 15 sec intervals for the duration of the trial testing periods (~ 5-7 hrs). These data were evaluated for SMR and MMR using a respiration program (respR) in the R statistical program.</p>
Data from: Hybridization between genetically modified Atlantic salmon and wild brown trout reveals novel ecological interactions
Interspecific hybridization is a route for transgenes from genetically modified (GM) animals to invade wild populations, yet the ecological effects and potential risks that may emerge from such hybridization are unknown. Through experimental crosses, we demonstrate transmission of a growth hormone transgene via hybridization between a candidate for commercial aquaculture production, GM Atlantic salmon (Salmo salar), and closely related wild brown trout (S. trutta). Transgenic hybrids were viable and grew more rapidly than transgenic salmon and other non-transgenic crosses in hatchery-like conditions. In stream mesocosms designed to more closely emulate natural conditions, transgenic hybrids appeared to express competitive dominance and suppressed the growth of transgenic and non-transgenic (wild-type) salmon by 82% and 54%, respectively. To the best of our knowledge, this is the first demonstration of environmental impacts of hybridization between a GM animal and a closely related species. These results provide empirical evidence of the first steps towards introgression of foreign transgenes into the genomes of new species and contribute to the growing evidence that transgenic animals have complex and context-specific interactions with wild populations. We suggest that interspecific hybridization be explicitly considered when assessing the environmental consequences should transgenic animals escape to nature.
Data from: RAD sequencing yields a high success rate for westslope cutthroat and rainbow trout species-diagnostic SNP assays
Hybridization with introduced rainbow trout threatens most native westslope cutthroat trout populations. Understanding the genetic effects of hybridization and introgression requires a large set of high-throughput, diagnostic genetic markers to inform conservation and management. Recently, we identified several thousand candidate single nucleotide polymorphism (SNP) markers based on RAD sequencing of 11 westslope cutthroat trout and 13 rainbow trout individuals. Here we used flanking sequence for 56 of these candidate SNP markers to design high-throughput genotyping assays. We validated the assays on a total of 92 individuals from 22 populations and seven hatchery strains. Forty-six assays (82%) amplified consistently and allowed easy identification of westslope cutthroat and rainbow trout alleles as well as heterozygote controls. The 46 SNPs will provide high power for early detection of population admixture and improved identification of hybrid and non-hybridized individuals. This technique shows promise as a very low-cost, reliable, and relatively rapid method for developing and testing SNP markers for non-model organisms with limited genomic resources.
Data from: Discovery and characterization of novel genetic markers for use in the management of Lahontan cutthroat trout (Oncorhynchus clarkii henshawi)
The Lahontan cutthroat trout (Oncorhynchus clarkii henshawi) is threatened by habitat destruction, over-harvest and hybridization with nonnative trout. Currently, three Geographic Management Units (GMUs) are recognized within the taxon. Here, we describe a suite of 68 single-nucleotide polymorphism (SNP) genetic markers for use in the study and management of Lahontan cutthroat trout and a closely related subspecies, the Paiute cutthroat trout (O. c. seleneris). These include markers variable within the two subspecies (n = 35), diagnostic for the two subspecies (n = 23) and diagnostic for Yellowstone cutthroat trout (O. c. bouvieri) and other closely related subspecies (n = 10). Sixty-three markers were discovered by Sanger sequencing of 171 EST loci in an ascertainment panel including Lahontan cutthroat trout from four populations representing all GMUs. Five markers were identified in a secondary sequencing effort with a single population of Lahontan cutthroat trout. TaqMan assays were validated on six Lahontan cutthroat trout populations and a diverse panel of other trout. Over 90% of the markers variable in Lahontan cutthroat trout were polymorphic in at least two populations, and 66% were variable within all three GMUs. All Lahontan diagnostic markers were also fixed for the Lahontan allele in Paiute cutthroat trout. Most of the Yellowstone diagnostic markers can also be used for this purpose in other cutthroat trout subspecies. This is the first set of SNP markers to be developed for Lahontan cutthroat trout, and will be an important tool for conservation and management.
Data from: Identifying footprints of selection in stocked brown trout populations: a spatio-temporal approach
Studies of interactions between farmed and wild salmonid fishes have suggested reduced fitness of farmed strains in the wild, but evidence for selection at the genic level is lacking. We studied three brown trout populations in Denmark which have been significantly admixed with stocked hatchery trout (19 to 64%), along with two hatchery strains used for stocking. The wild populations were represented by contemporary samples (2000-2006) and two of them by historical samples (1943-1956). We analyzed 61 microsatellite loci, nine of which showed putative functional relationships (EST-linked or quantitative trait loci). FST based outlier tests provided support for diversifying selection at chromosome regions marked by three loci, two anonymous and one EST-linked. Patterns of differentiation suggested that the loci were candidates for being under diversifying hitch-hiking selection in hatchery versus wild environments. Analysis of hatchery strain admixture proportions showed that in one wild population, two of the loci showed significantly lower admixture proportions than the putatively neutral loci, implying contemporary selection against alleles introduced by hatchery strain trout. In the most strongly admixed population, however, there was no evidence for selection, possibly due to immigration by stocked trout overcoming selection against hatchery-derived alleles or supportive breeding practices allowing hatchery strain trout to escape natural selection. To our knowledge, this is the first study demonstrating footprints of selection in wild salmonid populations subject to spawning intrusion by farmed fish.
Data from: Genetic structure of Pacific trout at the extreme southern end of their native range
Salmonid fishes are cold water piscivores with a native distribution spanning nearly the entire temperate and subarctic northern hemisphere. Trout in the genus Oncorhynchus are the most widespread salmonid fishes and are among the most important fish species in the world, due to their extensive use in aquaculture and valuable fisheries. Trout that inhabit northwestern Mexico are the southernmost native salmonid populations in the world, and the least studied in North America. They are unfortunately also facing threats to their continued existence. Previous work has described one endemic species, the Mexican golden trout (O. chrysogaster), and one endemic subspecies, Nelson's trout (O. mykiss nelsoni), in Mexico, but previous work indicated that there is vastly more biodiversity in this group than formally described. Here we conducted a comprehensive genetic analysis of this important group of fishes using novel genetic markers and techniques to elucidate the biodiversity of trout inhabiting northwestern Mexico, examine genetic population structure of Mexican trout and their relationships to other species of Pacific trout, and measure introgression from non-native hatchery rainbow trout. We confirmed substantial genetic diversity and extremely strong genetic differentiation present in the Mexican trout complex, not only between basins but also between some locations within basins, with at least four species-level taxa present. We also revealed significant divergence between Mexican trout and other trout species and found that introgression from non-native rainbow trout is present but limited, and that the genetic integrity of native trout is still maintained in most locations. This information will help to guide effective conservation strategies for this important group of fishes.
Data from: Potential of a no-take marine reserve to protect home ranges of anadromous brown trout (Salmo trutta)
1. The extent to which no‐take marine reserves can benefit anadromous species requires examination. 2. Here, we used acoustic telemetry to investigate the spatial behavior of anadromous brown trout (sea trout, Salmo trutta) in relation to a small marine reserve(~1.5 km2) located inside a fjord on the Norwegian Skagerrak coast. 3. On average, sea trout spent 42.3 % (±5.0% SE) of their time in the fjord within the reserve, a proportion similar to the area of the reserve relative to that of the fjord. 4. On average, sea trout tagged inside the reserve received the most protection, although the level of protection decreased marginally with increasing home range size. Furthermore, individuals tagged outside the reserve received more protection with increasing home range size, potentially opposing selection toward smaller home range sizes inflicted on fish residing within reserves, or through selective fishing methods like angling. 5. Monthly sea trout home ranges in the marine environment were on average smaller than the reserve, with a mean of 0.430 (±0.0265 SE) km2. Hence, the reserve is large enough to protect the full home range of some individuals residing in the reserve. 6. Synthesis and applications: In general, the reserve protects sea trout to a varying degree depending on their individual behavior. These findings highlight evolutionary implications of spatial protection and can guide managers in the design of marine reserves and networks that preserve variation in target species' home range size and movement behavior.
Data from: Increased natural reproduction and genetic diversity one generation after cessation of a steelhead trout (Oncorhynchus mykiss) conservation hatchery program
Spatial and temporal fluctuations in productivity and abundance confound assessments of captive propagation programs aimed at recovery of Threatened and Endangered populations. We conducted a 17 year before-after-control-impact experiment to determine the effects of a conservation hatchery program for anadromous steelhead trout (Oncorhynchus mykiss) on a key indicator of natural reproduction (naturally produced nests or 'redds'). The supplemented population exhibited a significant (2.6-fold) increase in redd abundance in the generation following supplementation. Four non-supplemented (control) populations monitored over the same 17 year period exhibited stable or decreasing trends in redd abundance. Expected heterozygosity in the supplemented population increased significantly. Allelic richness increased, but to a lesser (non-significant) degree. Estimates of the effective number of breeders increased from a harmonic mean of 24.4 in the generation before supplementation to 38.9 after supplementation. Several non-conventional aspects of the captive rearing program may have contributed to the positive response in the natural population.
Data from: Genetic changes caused by restocking and hydroelectric dams in demographically bottlenecked brown trout in a transnational subarctic riverine system
Habitat discontinuity, anthropogenic disturbance, and overharvesting have led to population fragmentation and declines worldwide. Preservation of remaining natural genetic diversity is crucial to avoid continued genetic erosion. Brown trout (Salmo trutta L.) is an ideal model species for studying anthropogenic influences on genetic integrity, as it has experienced significant genetic alterations throughout its natural distribution range due to habitat fragmentation, overexploitation, translocations, and stocking. The Pasvik River is a subarctic riverine system shared between Norway, Russia and Finland, subdivided by seven hydroelectric power dams that destroyed about 70% of natural spawning and nursing areas. Stocking is applied in certain river parts to support the natural brown trout population. Adjacent river segments with different management strategies (stocked versus not stocked) facilitated the simultaneous assessment of genetic impacts of dams and stocking based on analyses of 16 short tandem repeat loci. Dams were expected to increase genetic differentiation between and reduce genetic diversity within river sections. Contrastingly, stocking was predicted to promote genetic homogenization and diversity, but also potentially lead to loss of private alleles and to genetic erosion. Our results showed comparatively low heterozygosity and clear genetic differentiation between adjacent sections in non-stocked river parts, indicating that dams prevent migration and contribute to genetic isolation and loss of genetic diversity. Furthermore, genetic differentiation was low and heterozygosity relatively high across stocked sections. However, in stocked river sections, we found signatures of recent bottlenecks and reductions in private alleles, indicating that only a subset of individuals contribute to reproduction, potentially leading to divergence away from the natural genetic state. Taken together, these results indicate that stocking counteracts the negative fragmentation effects of dams, but also that stocking practices should be planned carefully in order to ensure long-term preservation of natural genetic diversity and integrity in brown trout and other species in regulated river systems.
Data from: Effects of host genetics and environment on egg-associated microbiotas in brown trout (Salmo trutta)
Recent studies found fish egg-specific bacterial communities that changed over the course of embryogenesis, suggesting an interaction between the developing host and its microbiota. Indeed, single-strain infections demonstrated that the virulence of opportunistic bacteria is influenced by environmental factors and host immune genes. However, the interplay between a fish embryo host and its microbiota has not been studied yet at the community level. To test whether host genetics affects the assemblage of egg-associated bacteria, adult brown trout (Salmo trutta) were sampled from a natural population. Their gametes were used for full-factorial in vitro fertilizations to separate sire from dam effects. In total, 2520 embryos were singly raised under experimental conditions that differently support microbial growth. High-throughput 16S rRNA amplicon sequencing was applied to characterize bacterial communities on milt and fertilized eggs across treatments. Dam and sire identity influenced embryo mortality, time until hatching and composition of egg-associated microbiotas, but no link between bacterial communities on milt and on fertilized eggs could be found. Elevated resources increased embryo mortality and modified bacterial communities with a shift in their putative functional potential. Resource availability did not significantly affect any parental effects on embryo performance. Sire identity affected bacterial diversity that turned out to be a significant predictor of hatching time: embryos associated with high bacterial diversity hatched later. We conclude that both host genetics and the availability of resources define diversity and composition of egg-associated bacterial communities that then affect the life history of their hosts.
Data from: Historical citizen science to understand and predict climate-driven trout decline
Historical species records offer an excellent opportunity to test the predictive ability of range forecasts under climate change, but researchers often consider that historical records are scarce and unreliable, besides the datasets collected by renowned naturalists. Here, we demonstrate the relevance of biodiversity records developed through citizen-science initiatives generated outside the natural sciences academia. We used a Spanish geographical dictionary from the mid-nineteenth century to compile over 10 000 freshwater fish records, including almost 4 000 brown trout (Salmo trutta) citations, and constructed a historical presence–absence dataset covering over 2 000 10 × 10 km cells, which is comparable to present-day data. There has been a clear reduction in trout range in the past 150 years, coinciding with a generalized warming. We show that current trout distribution can be accurately predicted based on historical records and past and present values of three air temperature variables. The models indicate a consistent decline of average suitability of around 25% between 1850s and 2000s, which is expected to surpass 40% by the 2050s. We stress the largely unexplored potential of historical species records from non-academic sources to open new pathways for long-term global change science.
Data from: Metabolic traits of westslope cutthroat, introduced rainbow trout and their hybrids in an ecotonal hybrid zone along an elevation gradient
In the Upper Oldman River, Alberta, introduced non-native hatchery rainbow trout hybridize with native westslope cutthroat trout, resulting in a hybrid swarm. Rainbow trout dominate at low elevations (<1250 m) in the river mainstem, cutthroat in high elevation tributaries (>1400 m), and hybrids are numerically dominant in the mid-elevation range. We hypothesized that metabolism of rainbow trout would exceed that of cutthroat trout, and that the elevation gradient in genetic makeup would be mirrored by a gradient in metabolic traits, with intermediate traits in the hybrid dominated ecotone. Metabolic traits were measured and regressed against the genetic makeup of individuals and elevation. Rainbow trout had higher oxygen consumption rates (OCR), higher white muscle lactate dehydrogenase (LDH) and citrate synthase (CS) activity, and higher plasma acetylcholinesterase (AchE) than cutthroat trout. Hybrids had intermediate OCR and AchE, but LDH activity as high as rainbow trout. While hybrid zones are usually modeled as a balance between cross species mating and selection against hybrids, ecotonal hybrid zones, where hybrids proliferate in intermediate habitats and have traits that appear well suited to ecotonal conditions, have been proposed for some plants and animals, and may have important implications for resource management and conservation.
Data from: The effects of Medieval dams on genetic divergence and demographic history in brown trout populations
Background: Habitat fragmentation has accelerated within the last century, but may have been ongoing over longer time scales. We analyzed the timing and genetic consequences of fragmentation in two isolated lake-dwelling brown trout populations. They are from the same river system (the Gudenå River, Denmark) and have been isolated from downstream anadromous trout by dams established ca. 600-800 years ago. For reference, we included ten other anadromous populations and two hatchery strains. Based on analysis of 44 microsatellite loci we investigated if the lake populations have been naturally genetically differentiated from anadromous trout for thousands of years, or have diverged recently due to the establishment of dams. Results: Divergence time estimates were based on 1) Approximate Bayesian Computation and 2) a coalescent-based isolation-with-gene-flow model. Both methods suggested divergence times ca. 600-800 years bp, providing strong evidence for establishment of dams in the Medieval as the factor causing divergence. Bayesian cluster analysis showed influence of stocked trout in several reference populations, but not in the focal lake and anadromous populations. Estimates of effective population size using a linkage disequilibrium method ranged from 244 to > 1,000 in all but one anadromous population, but were lower (153 and 252) in the lake populations. Conclusions: We show that genetic divergence of lake-dwelling trout in two Danish lakes reflects establishment of water mills and impassable dams ca. 600-800 years ago rather than a natural genetic population structure. Although effective population sizes of the two lake populations are not critically low they may ultimately limit response to selection and thereby future adaptation. Our results demonstrate that populations may have been affected by anthropogenic disturbance over longer time scales than normally assumed.
Data from: Estimates of gene flow and dispersal in wild riverine Brook Trout (Salvelinus fontinalis) populations reveal ongoing migration and introgression from stocked fish
As anthropogenic impacts accelerate changes to landscapes across the globe, understanding how genetic population structure is influenced by habitat features and dispersal is key to preserving evolutionary potential at the species level. Furthermore, knowledge of these interactions is essential to identifying potential constraints on local adaptation and for the development of effective management strategies. We examined these issues in Brook Trout (Salvelinus fontinalis) populations residing in the Upper Hudson River watershed of New York State by investigating the spatial genetic structure of over 350 fish collected from 14 different sampling locations encompassing three river systems. Population genetic analyses of microsatellite data suggest that fish in the area exhibit varying degrees of introgression from nearby State-directed supplementation activities. Levels of introgression in these populations correlate with water-way distance to stocking sites, although genetic population structure at the level of individual tributaries as well as their larger, parent river systems is also detectable and is dictated by migration and influenced by habitat connectivity. These findings represent a significant contribution to the current literature surrounding Brook Trout migration and dispersal, especially as it relates to larger interconnected systems. This work also suggests that stocking activities may have far-reaching consequences that are not directly limited to the immediate area where stocking occurs. The framework and data presented here may aid in the development of other local aquatic species-focused conservation plans that incorporate molecular tools to answer complex questions regarding diversity mapping, and genetically important conservation units.
Data from: Maternal allocation of carotenoids increases tolerance to bacterial infection in brown trout
Life-history theory predicts that iteroparous females allocate their resources differently among different breeding seasons depending on their residual reproductive value. In iteroparous salmonids there is typically much variation in egg size, egg number, and in the compounds that females allocate to their clutch. These compounds include various carotenoids whose functions are not sufficiently understood yet. We sampled 37 female and 35 male brown trout from natural streams, collected their gametes for in vitro fertilizations, experimentally produced 185 families in 7 full-factorial breeding blocks, raised the developing embryos singly (n = 2960), and either sham-treated or infected them with Pseudomonas fluorescens. We used female redness (as a measure of carotenoids stored in the skin) and their allocation of carotenoids to clutches to infer maternal strategies. Astaxanthin contents largely determined egg colour. Neither egg weight nor female size was correlated with the content of this carotenoid. However, astaxanthin content was positively correlated with larval growth and with tolerance against P. fluorescens. There was a negative correlation between female skin redness and the carotenoid content of their eggs. Although higher astaxanthin contents in the eggs were associated with an improvement of early fitness-related traits, some females appeared not to maximally support their current offspring as revealed by the negative correlation between female red skin colouration and egg carotenoid content. This correlation was not explained by female size and supports the prediction of a maternal trade-off between current and future reproduction.
Data from: Relative contributions of neutral and non-neutral genetic differentiation to inform conservation of steelhead trout across highly variable landscapes
Mounting evidence of climatic effects on riverine environments, and adaptive responses of fishes has elicited growing conservation concerns. Measures to rectify population declines include assessment of local extinction risk, population ecology, viability, and genetic differentiation. While conservation planning has been largely informed by neutral genetic structure, there has been a dearth of critical information regarding the role of non-neutral or functional genetic variation. We evaluated genetic variation among steelhead trout of the Columbia River Basin, which supports diverse populations distributed among dynamic landscapes. We categorized 188 SNP loci as either putatively neutral or candidates for divergent selection (non-neutral) using a multi-test association approach. Neutral variation distinguished lineages and defined broad-scale population structure consistent with previous studies, but fine-scale resolution was also detected at levels not previously observed. Within distinct coastal and inland lineages, we identified 9 and 22 candidate loci (respectively) commonly associated with precipitation or temperature variables, and putatively under divergent selection. Observed patterns of non-neutral variation suggest overall climate is likely to shape local adaptation (e.g., potential rapid evolution) of steelhead trout in the Columbia River region. Broad geographic patterns of neutral and non-neutral variation demonstrated here can be used to accommodate priorities for regional management and inform long-term conservation of this species.
Data from: Step-patterned survivorship curves: mortality and loss of equilibrium responses to high temperature and food restriction in juvenile rainbow trout (Oncorhynchus mykiss)
<p>While survivorship curves typically exhibit smooth declines over time, step-patterned curves can occur with multiple stressors within a life stage. To explore this process, we examined the effects of heat (24 ºC) and food restriction on juvenile rainbow trout (<i>Oncorhynchus mykiss</i> Walbaum) in challenge experiments. We observed step-patterned survivorship curves determined by mortality and loss of equilibrium (LOE) endpoints. To examine the cause of heterogeneity in the stress responses from early to late mortality and LOE, we measured indices of energetic reserves. The step transition in the survivorship curves, the peak mortality rates, and start of when individuals reached a critical energetic threshold (14% dry mass; 4.0 kJ·g<sup>-1</sup> energy) all occurred at around days 10-15 of the challenge. The coherence in these temporal patterns suggest heterogeneity in the cohort stress responses, in which an early subgroup died from heat stress and a late subgroup died from starvation. Thus, their endpoint sensitivities resulted in step-patterned survivorship curves. We discuss the implications of the study for understanding effects of multiple stressors on population heterogeneity and note the possible significance of stress response selection under climate change in which heat stress and food limitations occur in concert.</p>
Data from: Environmental stress linked to consumption of maternally derived carotenoids in brown trout embryos (Salmo trutta)
The yellow, orange, or red colors of salmonid eggs are due to maternally derived carotenoids whose functions are not sufficiently understood yet. Here, we studied the significance of naturally acquired carotenoids as maternal environmental effects during embryo development in brown trout (Salmo trutta). We collected eggs from wild females, quantified their egg carotenoid content, fertilized them in vitro in full-factorial breeding blocks to separate maternal from paternal effects, and raised 3,278 embryos singly at various stress conditions until hatching. We found significant sire effects that revealed additive genetic variance for embryo survival and hatching time. Dam effects were 5.4 times larger than these sire effects, indicating that maternal environmental effects play an important role in determining embryo stress tolerance. Of the eight pigment molecules that we targeted, only astaxanthin, zeaxanthin (that both affected egg redness), and lutein were detected above our confidence thresholds. No strong link could be observed between carotenoid content in unfertilized eggs and embryo mortality or hatching timing. However, the consumption of carotenoids during our stress treatment was negatively correlated to embryo survival among sib groups and explained about 14% of the maternal environmental variance. We conclude that maternally derived carotenoids play a role in the ability of embryos to cope with environmental stress, but that the initial susceptibility to the organic pollution was mainly determined by other factors.
Data from: Assessing thermal adaptation using family-based association and FST-outlier tests in a threatened trout
Discovering genetic markers associated with phenotypic or ecological characteristics can improve our understanding of adaptation and guide conservation of key evolutionary traits. The Lahontan cutthroat trout (Oncorhynchus clarkii henshawi) of the northern Great Basin Desert, USA, demonstrated exceptional tolerance to high temperatures in the desert lakes where it resided historically. This trait is central to a conservation hatchery effort to protect the genetic legacy of the nearly extinct lake ecotype. We genotyped full‐sibling families from this conservation broodstock and samples from the only two remaining, thermally distinct, native lake populations at 4,644 new single nucleotide polymorphisms (SNPs). Family‐based genome‐wide association testing of the broodstock identified nine and 26 SNPs associated with thermal tolerance (p < 0.05 and p < 0.1), measured in a previous thermal challenge experiment. Genes near the associated SNPs had complex functions related to immunity, growth, metabolism and ion homeostasis. Principal component analysis using the thermotolerance‐related SNPs showed unexpected divergence between the conservation broodstock and the native lake populations at these loci. FST outlier tests on the native lake populations identified 18 loci shared between two or more of the tests, with two SNPs identified by all three tests (p < 0.01); none overlapped with loci identified by association testing in the broodstock. A recent history of isolation and the complex genetic and demographic backgrounds of Lahontan cutthroat trout probably limited our ability to find shared thermal tolerance loci. Our study extends the still relatively rare application of genomic tools testing for markers associated with important phenotypic or environmental characteristics in species of conservation concern.
Data from: Return of a giant: DNA from archival museum samples helps to identify a unique cutthroat trout lineage formerly thought to be extinct
Currently one small, native population of the culturally and ecologically important Lahontan cutthroat trout (Oncorhynchus clarkii henshawi, LCT, Federally listed) remains in the Truckee River watershed of northwestern Nevada and northeastern California. The majority of populations in this watershed were extirpated in the 1940's due to invasive species, overharvest, anthropogenic water consumption and changing precipitation regimes. In 1977, a population of cutthroat trout discovered in the Pilot Peak Mountains in the Bonneville basin of Utah, was putatively identified as the extirpated LCT lacustrine lineage native to Pyramid Lake in the Truckee River basin based upon morphological and meristic characters. Our phylogenetic and Bayesian genotype clustering analyses of museum specimens collected from the large lakes (1872-1913) and contemporary samples collected from populations throughout the extant range provide evidence in support of a genetically distinct Truckee River basin origin for this population. Analysis of museum samples alone identified three distinct genotype clusters and historical connectivity among water bodies within the Truckee River basin. Baseline data from museum collections indicate that the extant Pilot Peak strain represents a remnant of the extirpated lacustrine lineage. Given the limitations on high quality data when working with a sparse number of preserved museum samples, we acknowledge that, in the end, this may be a more complicated story. However, the paucity of remnant populations in the Truckee River watershed in combination with data on the distribution of morphological, meristic and genetic data for Lahontan cutthroat trout, suggest that recovery strategies, particularly in the large lacustrine habitats should consider this lineage as an important part of the genetic legacy of this species.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.