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824 results for “Discrimination”
Data for "A systematic evaluation of interneuron morphology representations for cell type discrimination"
<p>data_v1.1 contains all the data to reproduce the figures of the publication <em>A systematic evaluation of interneuron morphology representations for cell type discrimination (</em>https://doi.org/10.1101/591370<em>).</em></p> <p>statistic_descriptions.csv : links each feature's statistic_id with a short description</p> <p>classification: This folder holds the multi-class and the pairwise classification performances of all feature representations (relevant for figure 4 and figure 5). It also holds the pickled multi-class models trained on morphometric statistics which coefficients are visualized in figure S5.</p> <p>embedding_data: This folder holds all the data used for the t-SNE visualizations of figure 8 and S4.</p> <p>features: This folder holds all computed feature representations of each data set and each modality (full, axon, dendrite). Features are indexed by a statistic id. Some example features are shown in figure 2. Careful, this folder is large (~6GB)!</p> <p>reconstructions: This folder contains all the neural reconstructions used for figure 1.</p> <p>final morphologies: contains all pre-processed reconstructions used in this study.</p>
FIGURE 2 in Discrimination of Uranotaenia species (Diptera: Culicidae) from Madagascar based on morphology and wing morphometric traits
FIGURE 2. Twelve landmarks on the wing of the Uranotaenia specimens used in the morphometric analyses.
FIGURE 5 in Discrimination of Uranotaenia species (Diptera: Culicidae) from Madagascar based on morphology and wing morphometric traits
FIGURE 5. Variation of the centroid size of the wing for Uranotaenia sp1 from the Anorana forest (1) and the Maromizaha forest (2). Each box shows the group of median values separating the 10th and 90th quartiles.
Data from: Evaluating presence-only species distribution models with discrimination accuracy is uninformative for many applications
Aim: Species distribution models are used across evolution, ecology, conservation, and epidemiology to make critical decisions and study biological phenomena, often in cases where experimental approaches are intractable. Choices regarding optimal models, methods, and data are typically made based on discrimination accuracy: a model's ability to predict subsets of species occurrence data that were withheld during model construction. However, empirical applications of these models often involve making biological inferences based on continuous estimates of relative habitat suitability as a function of environmental predictor variables. We term the reliability of these biological inferences "functional accuracy." We explore the link between discrimination accuracy and functional accuracy. Methods: Using a simulation approach we investigate whether models that make good predictions of species distributions correctly infer the underlying relationship between environmental predictors and the suitability of habitat. Results: We demonstrate that discrimination accuracy is only informative when models are simple and similar in structure to the true niche, or when data partitioning is geographically structured. However, the utility of discrimination accuracy for selecting models with high functional accuracy was low in all cases. Main conclusions: These results suggest that many empirical studies and decisions are based on criteria that are unrelated to models' usefulness for their intended purpose. We argue that empirical modeling studies need to place significantly more emphasis on biological insight into the plausibility of models, and that the current approach of maximizing discrimination accuracy at the expense of other considerations is detrimental to both the empirical and methodological literature in this active field. Finally, we argue that future development of the field must include an increased emphasis on simulation; methodological studies based on ability to predict withheld occurrence data may be largely uninformative about best practices for applications where interpretation of models relies on estimating ecological processes, and will unduly penalize more biologically informative modeling approaches.
Genetic data improves niche model discrimination and alters the direction and magnitude of climate change forecasts
<p>Ecological niche models (ENMs) have classically operated under the simplifying assumptions that there are no barriers to gene flow, species are genetically homogeneous (i.e., no population-specific local adaptation), and all individuals share the same niche. Yet, these assumptions are violated for most broadly distributed species. Here we incorporate genetic data from the widespread riparian tree species narrowleaf cottonwood (<i>Populus angustifolia</i>) to examine whether including intraspecific genetic variation can alter model performance and predictions of climate change impacts. We found that (1) <i>P. angustifolia</i> is differentiated into six genetic groups across its range from México to Canada, and (2) different populations occupy distinct climate niches representing unique ecotypes. Comparing model discriminatory power, (3) all genetically-informed ecological niche models (gENMs) outperformed the standard species-level ENM (3-14% increase in AUC; 1-23% increase in pROC). Furthermore, (4) gENMs predicted large differences among ecotypes in both the direction and magnitude of responses to climate change, and (5) revealed evidence of niche divergence, particularly for the Eastern Rocky Mountain ecotype. (6) Models also predicted progressively increasing fragmentation and decreasing overlap between ecotypes. Contact zones are often hotspots of diversity that are critical for supporting species' capacity to respond to present and future climate change, thus predicted reductions in connectivity among ecotypes is of conservation concern. We further examined the generality of our findings by comparing our model developed for a higher elevation Rocky Mountain species with a related desert riparian cottonwood, <i>P. fremontii</i>. Together our results suggest that incorporating intraspecific genetic information can improve model performance by addressing this important source of variance. gENMs bring an evolutionary perspective to niche modeling and provide a truly "adaptive management" approach to support conservation genetic management of species facing global change.</p>
Evaluating Bayesian stable isotope mixing models of wild animal diet and the effects of trophic discrimination factors and informative priors
<blockquote> <p>1. Ecologists quantify animal diets using direct and indirect methods, including analysis of faeces, pellets, prey items and gut contents. For stable isotope analyses of diet, Bayesian stable isotope mixing models (BSIMMs) are increasingly used to infer the relative importance of food sources to consumers. Although a powerful approach, it has been hard to test BSIMM performance for wild animals because precise, direct dietary data are difficult to collect.<br> 2. We evaluated the performance of BSIMMs in quantifying animal diets when using δ13C and δ15N stable isotope ratios from the feathers and red blood cells of common buzzard Buteo buteo chicks. We analysed mixing model outcomes with various trophic discrimination factors (TDFs), with and without informative priors, and compared these to direct observations of prey provisioned to chicks by adults at nests, using remote cameras. <br> 3. Although BSIMMs with different TDFs varied markedly in their performance, the statistical package SIDER generated TDFs for both feathers and blood that resulted in model outputs that accorded well with direct observations of prey provisioning. Using feather TDFs derived from captive peregrines Falco peregrinus resulted in estimates of diet composition that were also similar to provisioned prey, though blood TDFs from the same study performed poorly. The inclusion of informative priors, based on conventional analysis of pellet and prey remains, markedly reduced model performance.<br> 4. BSIMMs can provide accurate assessments of diet in wild animals. TDF estimates from the SIDER package performed well. The inclusion of informative priors from conventional methods in Bayesian mixing models can transfer biases into model outcomes, leading to erroneous results.</p> </blockquote>
Dataset for: Sensitivity of a satellite algorithm for harmful algal blooms discrimination to the use of laboratory bio-optical data for training
<p>Two files relating to the publication by Martinez-Vicente et al. (2020).</p> <p>meris_data_karenia_alt_chla.xlsx : file containing the chlorophyll concentrations for the different areas in the MODIS images selected for training and evaluation of the algorithm.</p> <p>coefficients_for_LDA_Karenia_mikimotoi.zip: file containing the coefficients for the Linear Discriminant Analysis (LDA) resulting from the training datasets 1,2 and 3. </p> <p> </p>
Natural history, phenotypic spectrum, and discriminative features of multisystemic RFC1-disease
<p>Objective: To delineate the full phenotypic spectrum, discriminative features, piloting longitudinal progression data, and sample size calculations of RFC1-repeat expansions, recently identified as causing cerebellar ataxia, neuropathy, vestibular areflexia syndrome (CANVAS).</p> <p>Methods: Multimodal RFC1 repeat screening (PCR, southern blot, whole-exome/genome (WES/WGS)-based approaches) combined with cross-sectional and longitudinal deep-phenotyping in (i) cross-European cohort A (70 families) with ≥2 features of CANVAS and/or ataxia-with-chronic-cough (ACC); and (ii) Turkish cohort B (105 families) with unselected late-onset ataxia.</p> <p>Results: Prevalence of RFC1-disease was 67% in cohort A, 14% in unselected cohort B, 68% in clinical CANVAS, and 100% in ACC. RFC1-disease was also identified in Western and Eastern Asians, and even by WES. Visual compensation, sensory symptoms, and cough were strong positive discriminative predictors (>90%) against RFC1-negative patients. The phenotype across 70 RFC1-positive patients was mostly multisystemic (69%), including dysautonomia (62%) and bradykinesia (28%) (=overlap with cerebellar-type multiple system atrophy [MSA-C]), postural instability (49%), slow vertical saccades (17%), and chorea and/or dystonia (11%). Ataxia progression was ~1.3 SARA points/year (32 cross-sectional, 17 longitudinal assessments, follow-up ≤9 years [mean 3.1]), but also included early falls, variable non-linear phases of MSA-C-like progression (SARA 2.5-5.5/year), and premature death. Treatment trials require 330 (1-year-trial) and 132 (2-year-trial) patients in total to detect 50% reduced progression.</p> <p>Conclusions: RFC1-disease is frequent and occurs across continents, with CANVAS and ACC as highly diagnostic phenotypes, yet as variable, overlapping clusters along a continuous multisystemic disease spectrum, including MSA-C-overlap. Our natural history data help to inform future RFC1-treatment trials.</p>
Data from: Mechanisms of kin discrimination inferred from pedigrees and the spatial distribution of mates
Where animals avoid inbreeding, different mechanisms of kin discrimination can leave different "signatures" in the patterns of observed mate relationship. For example, consider a species with no paternal care. If females avoid mating with familiar individuals, one would expect a deficit of offspring whose parents are maternal half-siblings, but paternal half-siblings would be unfamiliar with each other and thus mate at the frequency expected by chance. If spatial cues are used to avoid inbreeding, females would be expected to produce few offspring with males (even unrelated males) living near the female's birth site. We searched for these and other signatures with data from a long-term study of bannertailed kangaroo rats Dipodomys spectabilis in Arizona, USA, using a combination of intensive censusing, mapping of available dens, microsatellite-based parentage determination, and a randomization routine that determines the numbers of offspring expected if females in the population mate indiscriminately among the males available to them. The data are consistent with the hypothesis that kangaroo rats discriminate kin by association, rather than by using spatial cues or self-referential phenotype matching. Our randomization routine also demonstrates that in this species, dispersal alone is not particularly effective at eliminating opportunities for inbreeding. Our approach can be applied wherever the spatial distribution of individual mates and their pedigree relationships are known, and should be widely applicable as a means of assessing the degree to which both kin recognition and dispersal influence inbreeding.
Data from: Particle backtracking improves breeding subpopulation discrimination and natal-source identification in mixed populations
We provide a novel method to improve the use of natural tagging approaches for subpopulation discrimination and source-origin identification in aquatic and terrestrial animals with a passive dispersive phase. Our method integrates observed site-referenced biological information on individuals in mixed populations with a particle-tracking model to retrace likely dispersal histories prior to capture (i.e., particle backtracking). To illustrate and test our approach, we focus on western Lake Erie's yellow perch (Perca flavescens) population during 2006–2007, using microsatellite DNA and otolith microchemistry from larvae and juveniles as natural tags. Particle backtracking showed that not all larvae collected near a presumed hatching location may have originated there, owing to passive drift during the larval stage that was influenced by strong river- and wind-driven water circulation. Re-assigning larvae to their most probable hatching site (based on probabilistic dispersal trajectories from the particle backtracking model) improved the use of genetics and otolith microchemistry to discriminate among local breeding subpopulations. This enhancement, in turn, altered (and likely improved) the estimated contributions of each breeding subpopulation to the mixed population of juvenile recruits. Our findings indicate that particle backtracking can complement existing tools used to identify the origin of individuals in mixed populations, especially in flow-dominated systems.
Data from: Non-nest mate discrimination and clonal colony structure in the parthenogenetic ant Cerapachys biroi
Understanding the interplay between cooperation and conflict in social groups is a major goal of biology. One important factor is genetic relatedness, and animal societies are usually composed of related but genetically different individuals, setting the stage for conflicts over reproductive allocation. Recently, however, it has been found that several ant species reproduce predominantly asexually. Although this can potentially give rise to clonal societies, in the few well-studied cases, colonies are often chimeric assemblies of different genotypes, due to worker drifting or colony fusion. In the ant Cerapachys biroi, queens are absent and all individuals reproduce via thelytokous parthenogenesis, making this species an ideal study system of asexual reproduction and its consequences for social dynamics. Here, we show that colonies in our study population on Okinawa, Japan, recognize and effectively discriminate against foreign workers, especially those from unrelated asexual lineages. In accord with this finding, colonies never contained more than a single asexual lineage and average pairwise genetic relatedness within colonies was extremely high (r = 0.99). This implies that the scope for social conflict in C. biroi is limited, with unusually high potential for cooperation and altruism.
Data from: Isotopic turnover rates and diet-tissue discrimination depend on feeding habits of freshwater snails
Estimates of animal diets and trophic structure using stable isotope analysis are strongly affected by diet-tissue discrimination and tissue turnover rates, yet these factors are often unknown for consumers because they must be measured using controlled-feeding studies. Furthermore, these parameters may be influenced by diet quality, growth, and other factors. We measured the effect of dietary protein content on diet-tissue discrimination and tissue turnover in three freshwater snail species. We fed lettuce to individually housed snails (n = 450 per species) for ten weeks, then half were switched to a high-protein diet. Isotopic values of muscle and gonad tissue were assessed at 48 and 80 days post-diet change. Snail discrimination factors varied by diet (low-protein > high-protein) and usually differed among species for both N and C, although species had similar carbon discrimination when fed the low-protein diet. Carbon turnover rates were similar among species for a given tissue type, but nitrogen turnover varied more among species. In addition, diet affected growth of species differently; some species grew larger on high-protein (H. trivolvis) while others grew larger on low-protein diet (Lymnaea spp.). These differences among species in growth influenced turnover rates, which were faster in the species with the highest growth rate following the diet switch from low to high-protein. Thus, growth is one of the main processes that affects tissue turnover, but growth and feeding preference did not affect diet-tissue discrimination, which was greater on low-protein than high-protein diets for all species regardless of growth performance. These results suggest that diet might influence two key parameters of stable isotope analysis differently.
Data from: Stimulus discriminability may bias value-based probabilistic learning
Reinforcement learning tasks are often used to assess participants' tendency to learn more from the positive or more from the negative consequences of one's action. However, this assessment often requires comparison in learning performance across different task conditions, which may differ in the relative salience or discriminability of the stimuli associated with more and less rewarding outcomes, respectively. To address this issue, in a first set of studies, participants were subjected to two versions of a common probabilistic learning task. The two versions differed with respect to the stimulus (Hiragana) characters associated with reward probability. The assignment of character to reward probability was fixed within version but reversed between versions. We found that performance was highly influenced by task version, which could be explained by the relative perceptual discriminability of characters assigned to high or low reward probabilities, as assessed by a separate discrimination experiment. Participants were more reliable in selecting rewarding characters that were more discriminable, leading to differences in learning curves and their sensitivity to reward probability. This difference in experienced reinforcement history was accompanied by performance biases in a test phase assessing ability to learn from positive vs. negative outcomes. In a subsequent large-scale web-based experiment, this impact of task version on learning and test measures was replicated and extended. Collectively, these findings imply a key role for perceptual factors in guiding reward learning and underscore the need to control stimulus discriminability when making inferences about individual differences in reinforcement learning.
Data from: Behavioral evidence for fruit odor discrimination and sympatric host races of Rhagoletis pomonella flies in the western United States
The recent shift of Rhagoletis pomonella (Diptera: Tephritidae) from its native host downy hawthorn, Crataegus mollis, to introduced domesticated apple, Malus domestica, in the eastern U.S. is a model for sympatric host race formation. However, the fly is also present in the western U.S., where it may have been introduced via infested apples within the last 60 years. In addition to apple, R. pomonella also infests two hawthorns in the West, one the native black hawthorn, C. douglasii, and the other the introduced English ornamental hawthorn, C. monogyna. Here, we test for behavioral evidence of host races in the western U.S. through flight tunnel assays of western R. pomonella flies to host fruit volatile blends. We report that western apple, black hawthorn, and ornamental hawthorn flies showed significantly increased levels of upwind directed flight to their respective natal compared to non-natal fruit volatile blends, consistent with host race status. We discuss the implications of the behavioral results for the origin(s) of western R. pomonella, including the possibility that western apple flies were not introduced, but may represent a recent shift from local hawthorn fly populations.
Data from: Discrimination of fast click series produced by tagged Risso's dolphins (Grampus griseus) for echolocation or communication
Early studies that categorized odontocete pulsed sounds had few means of discriminating signals used for biosonar-based foraging from those used for communication. This capability to identify the function of sounds is important for understanding and interpreting behavior; it is also essential for monitoring and mitigating potential disturbance from human activities. Archival tags were placed on free-ranging Grampus griseus to quantify and discriminate between pulsed sounds used for echolocation-based foraging and those used for communication. Two types of rapid click-series pulsed sounds, buzzes and burst pulses, were identified as produced by the tagged dolphins and classified using a Gaussian mixture model based on their duration, association with jerk (i.e., rapid change of acceleration), and temporal association with click trains. Buzzes followed regular echolocation clicks and coincided with a strong jerk signal from accelerometers on the tag. They consisted of series averaging 359 ± 210 (mean ± SD) clicks with an increasing repetition rate and relatively low amplitude. Burst pulses consisted of relatively short click series averaging 45 ± 54 clicks with decreasing repetition rate and longer inter-click interval that were less likely to be associated with regular echolocation and the jerk signal. These results suggest that the longer, relatively lower amplitude, jerk-associated buzzes are used in this species to capture prey, mostly during the bottom phase of foraging dives, as seen in other odontocetes. In contrast, the shorter, isolated burst pulses that are generally emitted by the dolphins while at or near the surface are used outside of a direct, known foraging context.
Data from: DNA metabarcoding reveals that 200-μm-size-fractionated filtering is unable to discriminate between planktonic microbial and large eukaryotes
Microeukaryotic plankton (0.2–200 μm) are critical components of aquatic ecosystems and key players in global ecological processes. High-throughput sequencing is currently revolutionizing their study on an unprecedented scale. However, it is currently unclear whether we can accurately, effectively and quantitatively depict the microeukaryotic plankton communities using traditional size-fractionated filtering combined with molecular methods. To address this, we analysed the eukaryotic plankton communities both with, and without, prefiltering with a 200 μm pore-size sieve –by using SSU rDNA-based high-throughput sequencing on 16 samples with three replicates in each sample from two subtropical reservoirs sampled from January to October in 2013. We found that ~25% reads were classified as metazoan in both size groups. The species richness, alpha and beta diversity of plankton community and relative abundance of reads in 99.2% eukaryotic OTUs showed no significant changes after prefiltering with a 200 μm pore-size sieve. We further found that both >0.2 μm and 0.2–200 μm eukaryotic plankton communities, especially the abundant plankton subcommunities, exhibited very similar, and synchronous, spatiotemporal patterns and processes associated with almost identical environmental drivers. The lack of an effect on community structure from prefiltering suggests that environmental DNA from larger metazoa is introduced into the smaller size class. Therefore, size-fractionated filtering with 200 μm is insufficient to discriminate between the eukaryotic plankton size groups in metabarcoding approaches. Our results also highlight the importance of sequencing depth, and strict quality filtering of reads, when designing studies to characterize microeukaryotic plankton communities.
Data from: Adaptive genetic markers discriminate migratory runs of Chinook salmon (Oncorhynchus tshawytscha) amid continued gene flow
Neutral genetic markers are routinely used to define distinct units within species that warrant discrete management. Human-induced changes to gene flow however may reduce the power of such an approach. We tested the efficiency of adaptive vs. neutral genetic markers in differentiating temporally divergent migratory runs of Chinook salmon (Oncorhynchus tshawytscha) amid high gene flow owing to artificial propagation and habitat alteration. We compared seven putative migration timing genes to ten microsatellite loci in delineating three migratory groups of Chinook in the Feather River, CA: offspring of fall run hatchery broodstock that returned as adults to freshwater in fall (fall run), spring run offspring that returned in spring (spring run), and fall run offspring that returned in spring (FRS). We found evidence for significant differentiation between the fall and federally-listed threatened spring groups based on divergence at three circadian clock genes (OtsClock1b, OmyFbxw11 and Omy1009UW), but not neutral markers. We thus demonstrate the importance of genetic marker choice in resolving complex life history types. These findings directly impact conservation management strategies and add to previous evidence from Pacific and Atlantic salmon indicating that circadian clock genes influence migration timing.
Data from: Kin discrimination and outer membrane exchange in Myxococcus xanthus: a comparative analysis among natural isolates
Genetically similar cells of the soil bacterium Myxococcus xanthus cooperate at multiple social behaviours, including motility and multicellular development. Another social interaction in this species is outer-membrane exchange (OME), a behaviour of unknown primary benefit in which cells displaying closely related variants of the outer-membrane protein TraA transiently fuse and exchange membrane contents. Functionally incompatible TraA variants do not mediate OME, which led to the proposal that TraA incompatibilities determine patterns of intercellular cooperation in nature, but how this might occur remains unclear. Using natural isolates from a centimetre-scale patch of soil, we analyse patterns of TraA diversity and ask whether relatedness at TraA is causally related to patterns of kin discrimination in the form of both colony-merger incompatibilities (CMIs) and inter-strain antagonisms. A large proportion of predicted TraA functional diversity documented among global isolates is contained within the cm-scale population. We find evidence of balancing selection on the PA14-portion of TraA and extensive transfer of traA alleles across genomic backgrounds. CMIs are shown to be common among strains identical at TraA, suggesting that CMI kin discrimination is not generally caused by TraA dissimilarity. Finally, it has been proposed that inter-strain antagonisms might be caused by OME-mediated toxin transfer. However, we find that most strain pairs exhibiting strong antagonisms are predicted to be incapable of OME due to TraA dissimilarity. Overall, our results suggest that documented patterns of kin discrimination in a defined natural population of M. xanthus are not causally related to the degree of TraA relatedness among interactants.
Data from: Statolith morphometrics can discriminate among taxa of cubozoan jellyfishes
Identification of potentially harmful cubomedusae is difficult due to their gelatinous nature. The only hard structure of medusae, the statolith, has the potential to provide robust measurements for morphometric analysis. Traditional morphometric length to width ratios (L: W) and modern morphometric Elliptical Fourier Analysis (EFA) were applied to proximal, oral and lateral statolith faces of 12 cubozoan species. EFA outperformed L: W as L: W did not account for the curvature of the statolith. Best discrimination was achieved with Canonical Discriminant Analysis (CDA) when analysing proximal + oral + lateral statolith faces in combination. Normalised Elliptical Fourier (NEF) coefficients classified 98% of samples to their correct species and 94% to family group. Statolith shape agreed with currently accepted cubozoan taxonomy. This has potential to assist in identifying levels of risk and stock structure of populations in areas where box jellyfish envenomations are a concern as the severity of envenomation is family dependent. We have only studied 12 (27%) of the 45 currently accepted cubomedusae, but analyses demonstrated that statolith shape is an effective taxonomic discriminator within the Class.
Data from: Discrimination of grasshopper (Orthoptera: Acrididae) diet and niche overlap using next-generation sequencing of gut contents
Species of grasshopper have been divided into three diet classifications based on mandible morphology: forbivorous (specialist on forbs), graminivorous (specialist on grasses), and mixed feeding (broad-scale generalists). For example, Melanoplus bivittatus and Dissosteira carolina are presumed to be broad-scale generalists, Chortophaga viridifasciata is a specialist on grasses, and Melanoplus femurrubrum is a specialist on forbs. These classifications, however, have not been verified in the wild. Multiple specimens of these four species were collected, and diet analysis was performed using DNA metabarcoding of the gut contents. The rbcLa gene region was amplified and sequenced using Illumina MiSeq sequencing. Levins' measure and the Shannon–Wiener measure of niche breadth were calculated using family-level identifications and Morisita's measure of niche overlap was calculated using operational taxonomic units (OTUs). Gut contents confirm both D. carolina and M. bivittatus as generalists and C. viridifasciata as a specialist on grasses. For M. femurrubrum, a high niche breadth was observed and species of grasses were identified in the gut as well as forbs. Niche overlap values did not follow predicted patterns, however, the low values suggest low competition between these species.
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