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Fig. 6. Majority Rules Consensus Tree from the 27 in A revision of the genus Rudolfina Roháček (Sphaeroceridae: Limosininae)
Fig. 6. Majority Rules Consensus Tree from the 27 recovered trees retained from Traditional Search (TNT).
Illustration for "Ten simple rules for making training materials FAIR"
<p>Illustration for paper "Ten simple rules for making training materials FAIR"</p>
Fig. 2. Bayesian majority rule consensus tree reconstructed for 90 in Phylogenetic analysis and systematic position of two new species of the ant genus Crematogaster (Hymenoptera, Formicidae) from Southeast Asia
Fig. 2. Bayesian majority rule consensus tree reconstructed for 90 taxa using five genes (ArgK, CAD, LWRh, Top1, Wg) in a MrBayes analysis. Most of the outgroups are not shown. Above node numbers indicate posterior probability, bootstrap value for MP, and bootstrap value for ML. Data were partitioned by PartitionFinder v.1.1.1 and analyzed using a best fit model for each gene and codon position, with 10 million generations and a burn-in of 25 %.
Supplementary material 2 from: Hofmann MM, Fleischmann A, Renner SS (2020) Foraging distances in six species of solitary bees with body lengths of 6 to 15 mm, inferred from individual tagging, suggest 150 m-rule-of-thumb for flower strip distances. Journal of Hymenoptera Research 77: 105-117. https://doi.org/10.3897/jhr.77.51182
Table S1
Figure 4 from: Hofmann MM, Fleischmann A, Renner SS (2020) Foraging distances in six species of solitary bees with body lengths of 6 to 15 mm, inferred from individual tagging, suggest 150 m-rule-of-thumb for flower strip distances. Journal of Hymenoptera Research 77: 105-117. https://doi.org/10.3897/jhr.77.51182
Figure 4 Mean flight distances (with standard deviations) calculated from the 450 bee re-sightings shown in Suppl. material 2: Table S1, with year of observation given for Osmia cornuta, studied in both 2017 and 2018. All remaining data are from 2017. Species body sizes are from Amiet et al. (2004) and Scheuchl (2006). For the smaller species Chelostoma florisomne, C. rapunculi, and Heriades truncorum, which were colour-tagged rather than number-tagged, we cannot exclude repeated observations of the same individual.
Figure 3 from: Hofmann MM, Fleischmann A, Renner SS (2020) Foraging distances in six species of solitary bees with body lengths of 6 to 15 mm, inferred from individual tagging, suggest 150 m-rule-of-thumb for flower strip distances. Journal of Hymenoptera Research 77: 105-117. https://doi.org/10.3897/jhr.77.51182
Figure 3 Marking of an Osmia cornuta male (photos: J. Kirndorfer) a application of the glue and b, c attaching of the apiarists' tag d a labeled male ready to take off.
Figure 2 from: Hofmann MM, Fleischmann A, Renner SS (2020) Foraging distances in six species of solitary bees with body lengths of 6 to 15 mm, inferred from individual tagging, suggest 150 m-rule-of-thumb for flower strip distances. Journal of Hymenoptera Research 77: 105-117. https://doi.org/10.3897/jhr.77.51182
Figure 2 Marking of an Osmia cornuta female (photos: J. Kirndorfer). a, b A female caught with an insect net is transferred to the queen-marking tube and c, d pushed with the plunger to immobilize it (e, f a stylus is used to put glue on the mesonotum g, h the numbered colour plate is attached and i the bee released.
Figure 1 from: Hofmann MM, Fleischmann A, Renner SS (2020) Foraging distances in six species of solitary bees with body lengths of 6 to 15 mm, inferred from individual tagging, suggest 150 m-rule-of-thumb for flower strip distances. Journal of Hymenoptera Research 77: 105-117. https://doi.org/10.3897/jhr.77.51182
Figure 1 Marked individuals of AChelostoma florisomneBC. rapunculiCHeriades truncorumDHoplitis aduncaEOsmia bicornis, and FOsmia cornuta.
Supplementary material 1 from: Hofmann MM, Fleischmann A, Renner SS (2020) Foraging distances in six species of solitary bees with body lengths of 6 to 15 mm, inferred from individual tagging, suggest 150 m-rule-of-thumb for flower strip distances. Journal of Hymenoptera Research 77: 105-117. https://doi.org/10.3897/jhr.77.51182
Figure S1. Map showing the garden lay-out and location of the nest boxes at with bees were tagged
Data from: Multifaceted functional diversity for multifaceted crop yield: towards ecological assembly rules for varietal mixtures
<p>Data and code for the study "Multifaceted functional diversity for multifaceted crop yield: towards ecological assembly rules for varietal mixtures"</p> <p>Two data files are available:</p> <ul> <li>"CWM_D.csv" contains one row per experimental plot with community-weighted mean (CWM) and Rao quadratic diversity (D) indices computed on the 19 functional traits.</li> </ul> <p>The first two columns ("genotype_1" & "genotype_2") are the identity of the two genotypes in the plot, which are identical in single-variety plots. The third column ("assoc") refers to the plot type: single-variety ("M") or mixed-variety ("P") plot. Then, all trait CWMs and Ds are reported as "CWM_trait_name" and "D_trait_name" , respectively. For single-variety plots, only CWMs are reported but in this case they correspond to unweighted-averaged trait values across replicated measurements within plots. Root trait names are followed by "sem" or "adv" depending if they were measured on seminal or adventitious roots. Reported traits are: "Angle_aer" (Aerial angle, °), "Angle_root" (Root angle, °), "Diam_sem/adv" (mean root diameter, mm), "SRL_sem/adv" (specific root length, m/g), "RTD_sem/adv" (root tissue density, g/cm3), "RBI_sem/adv" (root branching intensity, nb of root tips/cm), "RLD_sem/adv" (root length density, cm root/cm3 soil), "Till_nb" (tiller number per capita), "Ear_bio" (early biomass per capita, g), "SLA" (specific leaf area, m²/kg), "LNC" (leaf nitrogen content, %), "Height" (plant height, cm), "Heading" (heading date, Growing Degree Days), and "Maturity" (maturity date, Growing Degree Days).</p> <ul> <li>"RAW_RYT.csv" contains one row per experimental plot with absolute and relative measures of performance on several agronomic variables.</li> </ul> <p>The first two columns ("genotype_1" & "genotype_2") are the identity of the two genotypes in the plot, which are identical in single-variety plots. The third column ("assoc") refers to the plot type: single-variety ("M") or mixed-variety ("P") plot. Then, all absolute and relative measures of agronomic performance are reported as "RAW_performance_variable_name" and "RYT_performance_variable_name", respectively. For single-variety plots, only absolute performances are reported. Reported performance variable are "GY" (Grain yield, g/m²), "GNb" (Grain number per m²), "SY" (Spike yield, g/m²), "SNb" (Spike number per m²), "BY" (Biomass yield, g/m²), "PY" (Protein yield, g/m²), "TKW" (Thousand kernel weight, g), "SeY" (Semolina yield, %), "GPC" (Grain protein content, %), "TW" (Test weight, kg/hL), "RLVA" (Rate of loss of vitreous aspect, %), "YI" (Yellowness index), "GPD" (Grain protein deviation, %).</p> <p>One R code file is available:</p> <ul> <li>"Mu_FD_Mu_CY_Analysis.R" contains all statistical analysis performed to produce the results presented in the main text and in the Supplementary Information of the study. It uses "CWM_D.csv" and "RAW_RYT.csv" files as inputs.</li> </ul>
Harrison's rule scales up to entire parasite assemblages but is determined by environmental factors
<p>Harrison's rule states that parasite body size and the body size of their hosts tend to be positively correlated. After it was proposed a century ago, a number of studies have investigated this trend, but the support level has varied greatly between parasite/host associations. Moreover, while the rule has been tested at the individual species level, we still lack knowledge on whether Harrison's rule holds at the scale of parasite and host communities.</p> <p>Here, we mapped flea (parasites) and rodent (hosts) body sizes across Mongolia and asked whether Harrison's rule holds for parasite/host assemblages (i.e., whether a parasite's average body size in a locality is positively correlated with its host's average body size). In addition, we attempted to disentangle complex relationships between flea size, host size, and environmental factors by testing alternative hypotheses for the determinants of fleas' body size variation.</p> <p>We gathered occurrence data for fleas and rodents from 2370 sites across Mongolia, constructed incidence matrices for both taxa, and calculated the average body sizes of fleas and their hosts over half-degree cells. Then, we applied a path analysis, accounting for spatial autocorrelation, trying to disentangle the drivers of the correlation between parasite and host body sizes.</p> <p>We found a strong positive correlation between average flea and host size across assemblages. Surprisingly though, we found that environmental factors simultaneously affected the body sizes of both fleas and hosts in the same direction, leading to a most likely deceptive correlation between parasite and host size across assemblages.</p> <p>We suggest that environmental factors may, to a great extent, reflect the environmental conditions inside the hosts' burrows where fleas develop and attain their adult body size, thus influencing their larval growth. Similarly, rodent body size is strongly influenced by air temperature, in the direction predicted by Bergmann's rule. If our findings are valid in other host-parasite associations, this may explain the dissenting results of both support and lack thereof for Harrison's rule.</p>
causal knowledge rules
<p>The rules we learned from our rule learning framework.</p> <p>It can also be seen as a causal knowledge graph.</p>
Data: Generalized evidence for Bergmann's rule body size variation in a cosmopolitan owl genus
<p><strong>Aim:</strong> The eco-geographic Bergmann's rule predicts that animals have smaller body size in warmer regions than in cold environments because of thermoregulatory reasons. Although this rule has been widely investigated, intraspecific analyses on cosmopolitan taxa are rare. We examined whether geographic variation in wing length, a proxy of body size, shows a Bergmannian pattern and can be explained by three mechanisms known to affect animal body size (heat conservation, resource availability and starvation resistance) in seven species of nocturnal raptors of the genus <i>Tyto</i>.</p> <p><strong>Location:</strong> World.</p> <p><strong>Taxon:</strong> Genus <i>Tyto</i>.</p> <p><strong>Methods:</strong> We measured wing length of 9033 museum specimens covering the entire distributional range of each species and linked it with geographic (absolute latitude, elevation) and climatic predictors associated with heat conservation, resource availability and starvation resistance hypotheses of spatial variation in body size.</p> <p><strong>Results:</strong> All the species show a trend of increasing wing length with increasing latitude and/or elevation, and in five of them either or both geographic predictors are statistically significant. In all the species showing a Bergmannian pattern, wing length significantly decreases with temperature, thus supporting the heat conservation hypothesis. Conversely, we found less generalized support for the other hypotheses, although in some species significant trends between wing length and proxies of climatic seasonality and/or primary productivity emerged.</p> <p><strong>Main conclusions:</strong> Consistent clines in body shrinking in warm environments are observed in species living in different continents at different latitudinal and temperature ranges, as well as exploiting different habitats. These findings thus support the hypothesis that body size is, at least partly, selected for heat maintenance depending on the thermal environment, even in nocturnal species which are not directly exposed to solar radiation. However, different selective pressures may also have concomitantly acted to promote body size evolution in this bird group.</p>
Rule-based Synthetic Data for Japanese GEC
<pre>Title: Rule-based Synthetic Data for Japanese GEC <strong>Dataset Contents:</strong> This dataset contains two parallel corpora intended for the training and evaluating of models for the NLP (natural language processing) subtask of Japanese GEC (grammatical error correction). These are as follows: <strong>Synthetic Corpus - *synthesized_data.tsv*</strong> This corpus file contains 2,179,130 parallel sentence pairs synthesized using the process described in [1]. Each line of the file consists of two sentences delimited by a tab. The first sentence is the erroneous sentence while the second is the corresponding correction. These paired sentences are derived from data scraped from the keyword-lookup site <yourei.jp>. The data within this file is primarily intended to serve as or augment a training set for a Japanese GEC model. Overall the sentences cover a broad array of primarily simple Japanese grammatical errors. <strong>Teacher Corpus - *teacher_data.tsv*</strong> This corpus file contains 6,345 parallel sentence pairs created via what we call the "teacher-sourcing" project [2]. The corpus sentences were created by Japanese language teachers, and this "teacher-sourcing" was funded by the Japan Foundation, Los Angeles. The overall format of the file is similar to that of *synthesized_data.tsv*, with each line containing an erroneous sentence and a corresponding correction separated by a comma. In addition, each erroneous sentence and correction sentence also contain pairs of characters that delimit the specific location within the sentence where the error/correction occur. For the erroneous sentence, these characters are `<` and `>`, while for the correction sentence, these are `(` and `)`. For example, consider the following sentence pair: - Error: <汚れる服>をあらいました。 - Correction: (汚れた服)をあらいました。 The delimiter characters indicate that the error phrase is `汚れる服` while the corresponding correction is `汚れた服` These paired sentences were written to mimic commonly grammatical errors produced by Japanese langauge learners; thus this file's data is primarily intended to serve as a evaluation set for Japanese GEC models. ______ In addition, the dataset contains the rule file used to generate the synthetic data within *synthesized_data.tsv*: ### Rule File - *rule_set.tsv* This file contains the 400 "syntactic rules" used to generate the data within *synthesized_data.tsv*. Each line contains a single rule, with different attributes delimited by tabs. Consult pages 41-66 of [1] for a more detailed analysis of these "syntactic rules" and the manner in which they are used to produce the synthetic data. </pre>
Data from: Testing mechanisms of Bergmann's rule: phenotypic but no genetic change in body size in three passerine bird populations
Bergmann's rule predicts a decrease in body size with increasing temperature and has much empirical support. Surprisingly, we know very little about whether 'Bergmann size clines' are due to a genetic response or is a consequence of phenotypic plasticity. Here we use data on body size (mass and tarsus length) from three long-term (1979-2008) study populations of great tits (Parus major), in which there has been a temperature increase, to examine mechanisms behind Bergmann's rule. We show that adult body mass decreased over the study period in all populations and that tarsus length increased in one population. Both body mass and tarsus length were heritable and under weak positive directional selection, predicting an increase, rather than decrease, in body mass. There was no support for micro-evolutionary change and thus the observed declines in body mass were a result of phenotypic plasticity. Interestingly, this plasticity was not in direct response to temperature changes but seemed to be due to changes in prey dynamics. Our results caution against interpreting recent phenotypic body size declines as an adaptive evolutionary response to temperature changes and highlight the importance of considering alternative environmental factors when testing size clines.
Data from: Ornament complexity is correlated with sexual selection: (a comment on Raia et al., "Cope's rule and the universal scaling law of ornament complexity")
Raia et al. propose that the evolution of the shape and complexity of animal ornaments (e.g., deer antlers) can be explained by interspecific variation in body size and is not influenced by sexual selection. They claim to show that ornament complexity is related to body size by an 0.25-power law and argue that this finding precludes a role for sexual selection in the evolution of ornament complexity. However, their study does not test alternative hypotheses and mismeasures antler shape allometry by omitting much of the published data. We show that an index of sexual selection (sexual size dimorphism) is positively correlated with size-corrected antler complexity and that the allometric slope of complexity is substantially greater than 0.25, contra Raia et al. We conclude that sexual selection and physical constraints both affect the evolution of antler shape.
Data from: Is high-sensitivity troponin, alone or in combination with copeptin, sensitive enough for ruling out NSTEMI in very early presenters at admission? A post-hoc analysis performed in emergency departments
Objectives: Copeptin and high-sensitivity cardiac troponin (HS-cTn) assays improve the early detection of NSTEMI. Their sensitivities may however be reduced in very early presenters. Setting: We performed a post-hoc analysis of three prospective studies that included patients who presented to the Emergency Department for chest pain onset (CPO) of less than 6 hours. Participants: 449 patients were included, in whom 12% had NSTEMI. CPO occurred <2h from ED presentation in 160, between 2-4h in 143, and >4h in 146 patients. The prevalence of NSTEMI was similar in all groups (9%, 13% and 12%, respectively, p=0.281). Measures: Diagnostic performances of HS-cTn and copeptin at presentation were examined according to CPO. The discharge diagnosis was adjudicated by 2 experts, including cTnI. HS-cTn and copeptin were blindly measured. Results: Diagnostic accuracies of cTnI, cTnI+copeptin and HS-cTnT (but not HS-cTnT+copeptin) lower through CPO categories. For patients with CPO<2h, the choice of a threshold value of 14 ng/L for HS-cTnT resulted in 3 false negative (Sensitivity 80% [95%CI: 51-95]; specificity 85% [78-90]; 79% of correctly ruled-out patients) and that of 5 ng/L in 2 false negative ( Sensitivity 87% [59-98]; specificity 58% [50-66]; 52% of correctly ruled-out patients). The addition of copeptin to HS-cTnT induced a decrease of misclassified patients to 1 in patients with CPO<2h (Sensitivity 93% [66-100]; specificity 41% [33-50]). Conclusion: A single measurement of HS-cTn, alone or in combination with copeptin at admission, seems not safe enough for ruling out NSTEMI in very early presenters (with CPO<2h). Trial registrations: French Health Ministry (no. DC-2009-1052), French Local Ethic comity « Comité de Protection des Personnes Ile-de-France » III (Hôpital Cochin) et VI (CHU Pitié-Salpétrière).
Data from: Neotropical wrens learn new duet rules as adults
Although song development in songbirds has been much studied as an analogue of language development in humans, the development of vocal interaction rules has been relatively neglected in both groups. Duetting avian species provide an ideal model to address the acquisition of interaction rules as duet structure involves time and pattern-specific relationships among the vocalizations from different individuals. In this study, we address the development of the most striking properties of duets: the specific answering rules that individuals use to link their own phrase types to those of their partners (duet codes) and precise temporal coordination. By performing two removal experiments in canebrake wrens (Cantorchilus zeledoni), we show that individuals use a fixed phrase repertoire to create new phrase pairings when they acquire a new partner. Furthermore, immediately after pairing, individuals perform duets with poor coordination and poor duet code adherence, but both aspects improve with time. These results indicate that individuals need a learning period to be able to perform well-coordinated duets that follow a consistent duet code. We conclude that both duet coordination and duet code adherence are honest indicators of pair-bond duration.
Data from: The relative importance of predation risk and water temperature in maintaining Bergmann's rule in a marine ectotherm
Bergmann's rule - an increase in body size with latitude - correlates with latitudinal declines in ambient temperature and predation risk, but relatively few studies simultaneously explore the relative importance of these factors. Along temperate Atlantic shorelines, the isopod Idotea balthica from high latitudes are 53% longer on average than are isopods from low latitudes. When reared at 6°- 24°C, juveniles increased growth and development rates with temperature. Because the increase in growth rate with temperature outstripped increases in development rate, female size at maturity increased with temperature. This thermal sensitivity of growth cannot account for the latitudinal pattern in body size. Within temperature treatments, females from low latitudes reached sexual maturity at younger ages and at a smaller size than did females from higher latitudes. This shift in life-history strategy is predicted by latitudinal declines in predation pressure, which we tested using field-tethering experiments. Overall, isopods at low latitudes had a 44% greater mortality risk from daytime predators relative to isopods at higher latitudes. We conclude that a latitudinal gradient in predation risk, and not temperature, is principally responsible for Bergmann's rule in I. balthica. Increases in body size during future warming of oceans may be constrained by local patterns of predation risk.
Data from: Mutation rules and the evolution of sparseness and modularity in biological systems
Biological systems exhibit two structural features on many levels of organization: sparseness, in which only a small fraction of possible interactions between components actually occur; and modularity – the near decomposability of the system into modules with distinct functionality. Recent work suggests that modularity can evolve in a variety of circumstances, including goals that vary in time such that they share the same subgoals (modularly varying goals), or when connections are costly. Here, we studied the origin of modularity and sparseness focusing on the nature of the mutation process, rather than on connection cost or variations in the goal. We use simulations of evolution with different mutation rules. We found that commonly used sum-rule mutations, in which interactions are mutated by adding random numbers, do not lead to modularity or sparseness except for in special situations. In contrast, product-rule mutations in which interactions are mutated by multiplying by random numbers – a better model for the effects of biological mutations – led to sparseness naturally. When the goals of evolution are modular, in the sense that specific groups of inputs affect specific groups of outputs, product-rule mutations also lead to modular structure; sum-rule mutations do not. Product-rule mutations generate sparseness and modularity because they tend to reduce interactions, and to keep small interaction terms small.
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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.