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6,234 results for “phenotypes”
Data from: Phylogenomics, biogeography and morphometrics reveal rapid phenotypic evolution in pythons after crossing Wallace's line
<p>Ecological opportunities can be provided to organisms that cross stringent biogeographic barriers towards environments with new ecological niches. Wallace's and Lyddeker's lines are arguably the most famous biogeographic barriers, separating the Asian and Australo-Papuan biotas. One of the most ecomorphologically diverse groups of reptiles, the pythons, is distributed across these lines, and are remarkably more diverse in phenotype and ecology east of Wallace's line in Australo-Papua. We used an anchored hybrid enrichment approach, with near complete taxon sampling, to extract mitochondrial genomes and 376 nuclear loci to resolve and date their phylogenetic history. Biogeographic reconstruction demonstrates that they originated in Asia around 38-45 Ma and then invaded Australo-Papua around 23 Ma. Australo-Papuan pythons display a sizeable expansion in morphological space, with shifts towards numerous new adaptive optima in head and body shape, coupled with the evolution of new micro-habitat preferences. We provide an updated taxonomy of pythons and our study also demonstrates how ecological opportunity following colonization of novel environments can promotemorphological diversification in a formerly ecomorphologically conservative group.</p>
Data from: "A cleaner break": genetic divergence between geographic groups and sympatric phenotypes revealed in ballan wrasse (Labrus bergylta)
<p>Capture and long-distance translocation of cleaner fish to control lice infestations on marine salmonid farms has the potential to influence wild populations via overexploitation in source regions, and introgression in recipient regions. Knowledge of population genetic structure is therefore required. We studied the genetics of ballan wrasse, a phenotypically diverse and extensively used cleaner fish, from 18 locations in Norway and Sweden, and from Galicia, Spain. We detected two very distinct genetic groups in Scandinavia, northwest and southeast. These groups were split by a stretch of sandy beaches in southwest Norway, representing a habitat discontinuity for this rocky shore associated benthic egg laying species. The Galician sample was highly differentiated from all Scandinavian samples, but overall closer to northwestern samples. . Distinct genetic differences were observed between sympatric spotty and plain phenotypes in Galicia, but not in Scandinavia. The mechanisms underlying the geographical patterns between phenotypes are discussed, but not identified. We conclude that extensive aquaculture-mediated translocation of ballan wrasse from Sweden and southern Norway, to western and middle Norway, has the potential to mix genetically distinct populations. These results question the sustainability of the current cleaner fish practice.</p>
Identification of a genetic network for an ecologically relevant behavioral phenotype in Drosophila melanogaster
<p>Pupation site choice of <i>Drosophila </i>third-instar larvae is critical for the survival of individuals, as pupae are exposed to various biotic and abiotic dangers while immobilized during the 3-4 days of metamorphosis. This singular behavioural choice is sensitive to both environmental and genetic factors. Here we developed a high-throughput phenotyping approach to assay the variation in pupation height in <i>Drosophila melanogaster, </i>while controlling for possibly confounding factors. We find substantial variation of mean pupation height among sampled natural stocks and we show that the <i>Drosophila</i> Genetic Reference Panel (DGRP) captures this variation. Using the DGRP stocks for genome wide association (GWA) mapping, 16 loci involved in determining pupation height could be resolved. The candidate genes in these loci are enriched for high expression in the larval central nervous system. A genetic network could be constructed from the candidate loci, which places <i>scrib</i> at the centre, plus other genes known to be involved in nervous system development, such as <i>Egfr</i> and <i>p53</i>. Using gene disruption lines, we could functionally validate several of the initially identified loci, as well as additional loci predicted from network analysis. Our study shows that the combination of high throughput phenotyping with a genetic analysis of variation captured from the wild can be used to approach the genetic dissection of an environmentally relevant behavioural phenotype.</p>
Latent atrophy factors related to phenotypical variants of posterior cortical atrophy
<p><b>Objective:</b> To determine whether atrophy relates to phenotypical variants of posterior cortical atrophy (PCA) recently proposed in clinical criteria; dorsal, ventral, dominant-parietal and caudal, we assessed associations between latent atrophy factors and cognition.</p> <p><b>Methods:</b> We employed a data-driven Bayesian modelling framework based on latent Dirichlet allocation to identify latent atrophy factors in a multi-center cohort of 119 individuals with PCA (age:64<span>±7</span>, 38% male, MMSE:21<span>±5, 71% amyloid-β-positive, 29% amyloid-β status unknown</span>). The model uses standardized gray matter density images as input (adjusted for age, sex, intracranial volume, field-strength and whole-brain gray matter volume) and provides voxelwise probabilistic maps for a predetermined number of atrophy factors, allowing every individual to express each factor to a degree without <i>a-priori</i> classification. Individual factor expressions were correlated to four PCA-specific cognitive domains (object-perception, space-perception, non-visual/parietal functions and primary visual processing) using general linear models.<b> </b></p> <p><b>Results: </b>The model revealed four distinct yet partially overlapping atrophy factors; right-dorsal, right-ventral, left-ventral, and limbic. We found that object-perception and primary visual processing were associated with atrophy that predominantly reflects the right-ventral factor. Furthermore, space-perception was associated with atrophy that predominantly represents the right-dorsal and right-ventral factors. However, individual participant profiles revealed that the vast majority expressed multiple atrophy factors and had mixed clinical profiles with impairments across multiple domains, rather than displaying a discrete clinical-radiological phenotype.</p> <p><b>Conclusion:</b> Our results indicate that particular brain-behavior networks are vulnerable in PCA, but most individuals display a constellation of affected brain-regions and symptoms, indicating that classification into four mutually exclusive variants is unlikely to be clinically useful.</p>
Data from: Phenotypic, ecological and genomic variation in common bully (Gobiomorphus cotidianus) populations along depth gradients in New Zealand's Southern Great Lakes
<p>Depth gradients in lakes are often key drivers of population divergence and speciation in fishes. New Zealand has many deep lakes but no known profundal specialist fishes or cases of intralacustrine speciation. We sampled a native benthic fish, the common bully, from 5–90 m depth in four South Island lakes, to test for morphological, ecological, or genetic differentiation associated with depth. Deeper fish consistently had narrower bodies, while other morphological traits showed variable relationships with depth. Carbon and nitrogen stable isotope values of fish increased with depth, largely tracking isotopic trends with depth of benthic invertebrate prey. Genotyping-by-sequencing showed some genome-wide differentiation between two of the lakes, but no evidence for within-lake genetic structuring along depth gradients. These results indicate that individual bullies associate with shallower or deeper habitats within their lifetimes, but we found no evidence of progress toward genetic divergence within lakes. The apparent lack of intralacustrine genetic divergence in New Zealand's fishes may be explained by a combination of environmental factors and constraints intrinsic to its marine-derived freshwater fish fauna.</p>
Predicting Phenotype from Multi-Scale Genomic and Environment Data using Neural Networks and Knowledge Graphs
<p><strong>Background: To mitigate the effects of climate change on public health and conservation, we need to better understand the dynamic interplay between biological processes and environmental effects. Machine learning (ML) methods in general, and Deep Learning (DL) methods in particular, are a potential way forward because they are able to cope with the nonlinearity of natural systems. However, there are several barriers that exist, including the absence of ML-ready data. We propose to develop a machine learning framework capable of predicting phenotypes based on multi-scale data about genes and environments. A critical part of this framework are data transformation methods that map the heterogeneous input data into formats that are consumable by the ML techniques. The central hypothesis of this research is that deep learning algorithms and biological knowledge graphs will predict phenotypes more accurately across more taxa and more ecosystems than do current numerical and traditional statistical modeling methods. Our long term goal is to develop predictive analytics for organismal response to environmental perturbations using innovative data science approaches. This pilot project on predicting emergent properties of complex systems and multidimensional interactions is funded by the NSF (Award # 1939945, 1940059, 1940062, 1940330). </strong></p> <p> </p> <p><strong>Results: We have established shared project governance, communication channels, project timeline, and data and computing environment across four universities. We have successfully reached out to three other projects for broader collaboration.</strong></p>
Museomics of tree squirrels: a dense taxon sampling of mitogenomes reveals hidden diversity, phenotypic convergence, and the need of a taxonomic overhaul
Background: Tree squirrels (Sciuridae, Sciurini), in particular the highly diverse Neotropical lineages, are amongst the most rapidly diversifying branches of the mammal tree of life but also some of the least known. Negligence of this group by phylogeneticists is likely a product of the scarcity or unavailability of fresh tissue samples for DNA sequencing. Lack of comprehensive phylogenies result in highly discrepant taxonomic arrangements that are based exclusively on morphological data—impressively, these are the only classification schemes available for the group. Here we used high-throughput sequencing and an unprecedented sampling effort of museum specimens to provide the first comprehensive phylogenetic analysis of tree squirrels, with a special emphasis on Neotropical taxa. Results: We gathered mitochondrial genome data from 232 modern and historical samples, representing 40 out of the 43 currently recognized species of Sciurini. We found no correlation between specimen age and completeness of mitogenomes recovered for historical samples. Our phylogenetic analyses—performed with datasets differing on levels of missing data and taxa under distinctanalytical methods— strongly support the monophyly of Sciurini and consistently recovered 12 major clades within the tribe. We found evidence that the diversity of Neotropical tree squirrels is underestimated, with at least seven lineages that might represent taxa to be named or revalidated. Ancestral state reconstructions of number of upper premolars and number of pairs of mammae indicated that alternative conditions of both characters must have evolved multiple times along the evolutionary history of tree squirrels. Conclusions: We were able to obtain complete mitogenomes for samples as old as 120 years, reinforcing the potential of historical samples for phylogenetic and evolutionary inferences of elusive lineages of the tree of life. None of the taxonomic arrangements ever proposed for tree squirrels fully corresponded to our phylogenetic reconstruction, with only a few of the currently recognized genera recovered as monophyletic. By investigating the evolution of two morphological traits widely employed in the taxonomy of the group, we revealed that their homoplastic nature can help to explain the incongruence between phylogenetic results and classification schemes presented so far, and we recommend a substantial taxonomic overhaul.
Secondary contact zones of closely-related Erebia butterflies overlap with narrow phenotypic and parasitic clines
Zones of secondary contact between closely related taxa are a common legacy of the Quaternary ice ages. Despite their abundance, the factors that keep species apart and prevent hybridisation are often unknown. Here we study a very narrow contact zone between three closely related butterfly species of the Erebia tyndarus species complex. Using genomic data, we first determined if gene flow occurs and then assessed whether it might be hampered by differences in chromosome number between some species. We found interspecific gene flow between sibling species that differ in karyotype by one chromosome. Conversely, only F1 hybrids occurred between two species that have the same karyotype, forming a steep genomic cline. In a second step, we fitted clines to phenotypic, ecological and parasitic data to identify the factors associated with the genetic cline. We found clines for phenotypic data and the prevalence of the endosymbiont parasite Wolbachia to overlap with the genetic cline, suggesting that they might be drivers for separating the two species. Overall our results highlight that some gene flow is possible between closely-related species despite different chromosome numbers, but that other barriers restrict such gene flow.
Data from: ApoE is a correlate of phenotypic heterogeneity in Alzheimer's disease in a national cohort
Objective: To compare the proportion of APOEε4 genotype carriers in aphasic versus amnestic variants of Alzheimer's disease (AD). Method: The proportion of APOEε4 carriers was compared among 3 groups. 1) Forty-two patients with primary progressive aphasia (PPA) and AD pathology (PPA/AD) enrolled in the Northwestern Alzheimer Disease Center Clinical Core. 2) 1,418 patients with autopsy confirmed AD and amnestic dementia of the Alzheimer-type (DAT/AD); 3) 2,608 cognitively normal controls (NC). The latter two groups were compiled from the National Alzheimer Coordinating Center (NACC) database. Logistic regression models analyzed the relationship between groups and APOEε4 carrier status, adjusting for age of onset and sex as needed. Results: Using NC as the reference and adjusting for sex and age, the DAT/AD group was 3.97 times more likely to be APOEε4 carriers. Adjusting for sex and age at symptom onset, the DAT/AD group was 2.46 times as likely to be carriers compared to PPA/AD. There was no significant difference in the proportion of APOEε4 carriers for PPA/AD compared to NC. PPA subtypes included 24 logopenic, 10 agrammatic nonfluent, and eight either mixed (n=5) or too severe (n=3) to subtype. The proportion of carriers and non carriers was similar for logopenic and agrammatic subtypes, both having fewer carriers. Conclusion: The proportion of APOEε4 carriers was elevated in amnestic but not aphasic manifestations of AD. These results suggest that APOEε4 is an anatomically selective risk factor that preferentially increases the vulnerability to AD pathology of memory-related medial temporal areas rather that language-related neocortices.
Data from: Evolutionary and plastic phenotypic change can be just as fast as changes in population densities
<p>Evolution and plasticity can drive population-level phenotypic change (e.g., changes in the mean phenotype) on time scales comparable to changes in population densities. However, it is unclear if phenotypic change has the potential to be just as fast as changes in densities, or if comparable rates of change only occur when densities are changing slow enough for phenotypes to keep pace. Moreover, it is unclear if this depends on the mode of adaptation. Using scaling theory and fast-slow dynamical systems theory, we develop a method for comparing maximum rates of density and phenotypic change estimated from population-level time series data. We apply our method to 30 published empirical studies where changes in morphological traits are caused by evolution, plasticity, or an unknown combination. For every study, the maximum rate of phenotypic change was 0.5 to 2.5 times faster than the maximum rate of change in density. Moreover, there were no systematic differences between systems with different modes of adaptation. Our results show that plasticity and evolution can drive phenotypic change just as fast as changes in densities. We discuss the implications of our results in terms of the strengths of feedbacks between population densities and traits.</p>
Data from: Gene expression in the phenotypically plastic Arctic charr (Salvelinus alpinus): a focus on growth and ossification at early stages of development
Gene expression during development shapes the phenotypes of individuals. Although embryonic gene expression can have lasting effects on developmental trajectories, few studies consider the role of maternal effects, such as egg size, on gene expression. Using qPCR, we characterize relative expression of 14 growth and/or skeletal promoting genes across embryonic development in Arctic charr (Salvelinus alpinus). We test to what extent their relative expression is correlated with egg size and size at early life‐stages within the study population. We predict smaller individuals to have higher expression of growth and skeletal promoting genes, due to less maternal resources (i.e., yolk) and prioritization of energy toward ossification. We found expression levels to vary across developmental stages and only three genes (Mmp9, Star, and Sgk1) correlated with individual size at a given developmental stage. Contrary to our hypothesis, expression of Mmp9 and Star showed a non‐linear relationship with size (at post fertilization and hatching, respectively), whilst Sgk1 was higher in larger embryos at hatching. Interestingly, these genes are also associated with craniofacial divergence of Arctic charr morphs. Our results indicate that early life‐stage variation in gene expression, concomitant to maternal effects, can influence developmental plasticity and potentially the evolution of resource polymorphism in fishes.
Seasonal patterns of melatonin alter aggressive phenotypes of female Siberian hamsters
<p>Many animal species exhibit year-round aggression, a behaviour that allows individuals to compete for limited resources in their environment (e.g., food and mates).<br> Interestingly, this high degree of territoriality persists during the non-breeding season, despite low levels of circulating gonadal steroids (i.e., testosterone [T] and oestradiol<br> [E<sub>2</sub>]). Our previous work suggests that the pineal hormone melatonin mediates a 'seasonal switch' from gonadal to adrenal regulation of aggression in Siberian hamsters<br> (<em>Phodopus sungorus</em>); solitary, seasonally breeding mammals that display increased aggression during the short, 'winter-like' days (SDs) of the non-breeding season. To test<br> the hypothesis that melatonin elevates non-breeding aggression by increasing circulating and neural steroid metabolism, we housed female hamsters in long days (LDs)<br> or SDs, administered them timed or mis-timed melatonin injections (mimic or do not mimic a SD-like signal, respectively), and measured aggression, circulating hormone<br> profiles, and aromatase (ARO) immunoreactivity in brain regions associated with aggressive or reproductive behaviours (paraventricular hypothalamic nucleus [PVN],<br> periaqueductal gray [PAG], and ventral tegmental area [VTA]). Females that were responsive to SD photoperiods (SD-R) and LD females given timed melatonin injections<br> (Mel-T) exhibited gonadal regression and reduced circulating E<sub>2</sub>, but increased aggression and circulating dehydroepiandrosterone (DHEA). Furthermore, aggressive challenges differentially altered circulating hormone profiles across seasonal phenotypes; reproductively inactive females (ie, SD-R and Mel-T females) reduced circulating<br> DHEA and T, but increased E<sub>2</sub> after an aggressive interaction, whereas reproductively active females (i.e., LD females, SD non-responder females, and LD females given mis-timed melatonin injections) solely increased circulating E<sub>2</sub>. Although no differences in neural ARO abundance were observed, LD and SD-R females showed distinct associations between ARO cell density and aggressive behaviour in the PVN, PAG, and VTA. Taken together, these results suggest that melatonin increases non-breeding<br> aggression by elevating circulating steroid metabolism after an aggressive encounter and by regulating behaviourally relevant neural circuits in a region-specific manner.</p>
A multidimensional approach to the expression of phenotypic plasticity
<p>Phenotypic plasticity is increasingly recognized as a key element of eco-evolutionary dynamics, but it remains challenging to assess because of its multidimensional nature. Indeed, organisms live in complex environments where numerous factors can impact the phenotypic expression of traits (inter-environment axis), possess multiple traits that can influence each other's expression (inter-trait axis), and differ in their genetic background (inter-genotype axis), which can not only impact the traits' values but also their plasticity.</p> <p>We addressed six questions related to phenotypic plasticity: (1) do different environmental gradients show similar effects on a given trait? (2) Are the effects of two environmental gradients on a trait additive? (3) Do different traits show similar plastic response to a given environmental gradient? (4) Do the (co)variances between traits vary across environmental gradients? (5) Do genotypes differ in their plastic response to a given environmental gradient? (6) Are some genotypes more plastic than others across all traits?</p> <p>We designed a microcosm experiment using the protist Tetrahymena thermophila aimed at encompassing all these aspects of phenotypic plasticity. We exposed 15 distinct genotypes to 25 combinations of temperature and nutrient availability and assessed the plasticity of five phenotypic traits.</p> <p>Our results show strong differences in the plastic response depending on the environmental gradient, not only regarding the shape of the reaction norm of the different traits tested, but also in the overall plasticity of the organisms. We did not find any covariance between traits that was consistent across all environments.</p> <p>Overall, our results suggest independent impacts of the environmental dimension considered on the observed plastic response. These results underline potential difficulties in generalising findings about plasticity to all environments and all traits.</p>
Foraging behavior and extended phenotype independently affect foraging success in spiders
<p>Multiple phenotypic traits often interact with each other to determine an individual's fitness. Behavioral and extended phenotypic traits, such as architectural constructions, can contribute to fitness in an integrated way. The goal of this study was to understand how the interaction between behavioral and extended phenotypic traits can affect foraging success. We tested this question using black widow spiders, where spiders that are aggressive in a foraging context tend to build more gumfooted silk lines that aid in prey capture, while non-aggressive spiders build webs with fewer gumfooted lines. We repeatedly assessed behavior and web structure to quantify relationships between these traits, and then allowed spiders to forage for live prey on their own web or the web of a conspecific that differed in structure. Thus, we assessed how varying combinations of behavior and web structure affect foraging success, and if correlational selection might act on them. We confirmed that aggressiveness and number of gumfooted lines are positively correlated and found that capture success increased with both aggressiveness and the number of gumfooted lines. Yet, we did not find any evidence for correlational selection: aggressiveness and number of gumfooted lines appeared to affect foraging success independently of each other. These findings highlight that a correlation between traits that contribute towards the same ecological function does not necessarily imply correlational selection. Taking advantage of the experimental convenience afforded by extended phenotypic traits can provide insight into the functional consequences of phenotypic variation within and between individuals.</p>
DNA methylation and phenotypic data from: Environmentally induced phenotypic plasticity and DNA methylation changes in a wild potato growing in two contrasting Andean experimental gardens
<p>DNA methylation can be environmentally modulated and play a role in phenotypic plasticity. To understand the role of environmentally induced epigenetic variation and its dynamics in natural populations and ecosystems, it is relevant to place studies in a real-world context. Our experimental model is the wild potato <i>Solanum kurtzianum</i>, a close relative of the cultivated potato <i>S. tuberosum</i>. It was evaluated in its natural habitat, an arid Andean region in Argentina characterised by spatial and temporal environmental fluctuations. The dynamics of phenotypic and epigenetic variability (with Methyl Sensitive Amplified Polymorphism markers, MSAP) was assayed in three genotypes across three growing seasons. These genotypes were cultivated permanently and also reciprocally transplanted between experimental gardens (EG) differing in ca. 1000 m of altitude. In two seasons, the genotypes presented differential methylation patterns associated to the EG. In the reciprocal transplants, a rapid epigenomic remodelling occurred according to the growing season. Phenotypic plasticity, both spatial (between EGs within season) and temporal (between seasons), was detected. The epigenetic and phenotypic variability were positively correlated. The lack of an evident mitotic epigenetic memory would be a common response to short-term environmental fluctuations. Thus, the environmentally induced phenotypic and epigenetic variation could contribute to populations persistence through time. These results have implications for understanding the great ecological diversity of wild potatoes.</p>
Results of Neuron Phenotype Ontology competency queries
<p>Full list of neurons with human readable labels returned from competency queries against the Neuron Phenotype Ontology as described in Gillespie et al. (2020). Three .CSV files are included with the number of competency query (Q1, Q2 and Q3) appended. The DL query used for the query is given in the column header of column A. The numbers provided for Q1 and Q2 in columns B-E represent the count of neurons returned for each of the 3 evidence based models (EBMs) described in the paper and the Common Usage Types (CUTs) The total number of neurons returned across all categories is shown in column F.</p>
Data from: Positive relationships between association strength and phenotypic similarity characterize the assembly of mixed-species bird flocks worldwide
Competition theory predicts that communities at small spatial scales should consist of species more dissimilar than expected by chance. We find a strikingly different pattern in a multi-continent dataset (55 presence-absence matrices from 24 locations) on the composition of mixed-species bird flocks, important subunits of local bird communities the world over. Using null models and randomization tests followed by meta-analysis, we find the association strength of species in flocks to be strongly related to similarity in body size and foraging behavior, and higher for congeneric compared with non-congeneric species pairs. Given the small spatial scale of our individual analyses, differences in habitat preferences of species are unlikely to have caused these association patterns; therefore, the patterns are most likely the outcome of species interactions. Extending group-living and social information use theory to a heterospecific context, we discuss potential behavioral mechanisms leading to positive interactions among similar species in flocks as well as ways in which competition costs are reduced. Our findings highlight the need to consider positive interactions along with competition when seeking to explain community assembly.
Data from: Phenotypically plastic responses to predation risk are temperature dependent
Predicting how organisms respond to climate change requires that we understand the temperature dependence of fitness in relevant ecological contexts (e.g., with or without predation risk). Predation risk often induces changes to life history traits that are themselves temperature dependent. We explore how perceived predation risk and temperature interact to determine fitness (indicated by the intrinsic rate of increase, r) through changes to its underlying components (net reproductive rate, generation time, and survival) in Daphnia magna. We exposed Daphnia to predation cues from dragonfly naiads early, late, or throughout their ontogeny. Predation risk increased r differentially across temperatures and depending on the timing of exposure to predation cues. The timing of predation risk likewise altered the temperature dependent response of T and R0. Daphnia at hotter temperatures responded to predation risk by increasing r through a combination of increased R0 and decreased T that together countered an increase in mortality rate. However, only D. magna that experienced predation cues early in ontogeny showed elevated r at colder temperatures. These results highlight the fact that phenotypically plastic responses of life history traits to predation risk can be strongly temperature dependent.
Multivariate phenotypic divergence along an urbanization gradient
A growing body of evidence suggests that natural populations can evolve to better tolerate the novel environmental conditions associated with urban areas. Invariably, studies of adaptive divergence in urban areas examine only one or a few traits at a time from populations residing only at the most extreme urban and nonurban habitats. Thus, whether urbanization is driving divergence in many traits simultaneously in a manner that varies with the degree of urbanization remains unclear. To address this gap, we generated seed families of white clover (Trifolium repens) collected from 27 populations along an urbanization gradient in Toronto, Canada, and grew them in a common garden to measure 14 phenotypic traits. Overall, families from urban sites had evolved later phenology and germination, larger flowers, thinner stolons, reduced cyanogenesis, greater biomass, and greater seed set. Pollinator observations revealed near complete turnover of pollinator morphological groups between urban and nonurban sites, which may explain some of the observed divergence in floral traits and phenology. Our results suggest that adaptation to urban environments involves multiple organismal traits.
Thermal tolerance and cardiac phenotypes
<p>Adaptation to local environments involves the evolution of ecologically important traits and underlying physiological processes. Here, we used low coverage whole-genome resequencing (lcWGR) on individuals to identify genome regions involved in thermal adaptation in wild redband trout <i>Oncorhynchus mykiss gairdneri</i>, a subspecies of rainbow trout that inhabits ecosystems ranging from cold montane forests to high elevation deserts. This study includes allele frequency-based analyses for selective sweeps among populations, followed by multiple association tests for specific sets of phenotypes measured under thermal stress (acute and chronic survival/mortality; high or low cardiac performance groups). Depending on the groups in each set of analyses, sequencing reads covered between 43-75% of the genome at ≥15X and each analysis included millions of SNPs across the genome. In tests for selective sweeps among populations, a total of six chromosomal regions were significant. However, association tests for specific phenotypes revealed that the region on chromosome 4 was consistently the most significant and contains the <i>cerk</i> gene (ceramide kinase). This study provides insight into a potential genetic mechanism of local thermal adaptation and suggests c<i>erk</i> may be an important candidate gene. However, further validation of this <i>cerk</i> gene is necessary to determine if the association with cardiac performance results in a functional role to influence thermal performance when exposed to high water temperatures and hypoxic conditions. </p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.