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Data from: One-shot learning and behavioral eligibility traces in sequential decision making
In many daily tasks we make multiple decisions before reaching a goal. In order to learn such sequences of decisions, a mechanism to link earlier actions to later reward is necessary. Reinforcement learning theory suggests two classes of algorithms solving this credit assignment problem: In classic temporal-difference learning, earlier actions receive reward information only after multiple repetitions of the task, whereas models with eligibility traces reinforce entire sequences of actions from a single experience (one-shot). Here we show one-shot learning of sequences. We developed a novel paradigm to directly observe which actions and states along a multi-step sequence are reinforced after a single reward. By focusing our analysis on those states for which RL with and without eligibility trace make qualitatively distinct predictions, we find direct behavioral (choice probability) and physiological (pupil dilation) signatures of reinforcement learning with eligibility trace across multiple sensory modalities.
Data from: Love the one you're with: proximity determines paternity success in the barnacle Tetraclita rubescens
A species' mating system sets limits on the strength of sexual selection. Sexual selection is widespread in dioecious species, but is less well documented in hermaphrodites, and may be less important. We used four highly polymorphic microsatellite markers to assign paternity to broods of the hermaphroditic eastern Pacific volcano barnacle Tetraclita rubescens. These data were used to describe the species' mating system and to examine factors affecting male reproductive success. Tetraclita can sire broods over distances of 11.2 cm, but proximity to the sperm recipient had a highly significant effect on the probability of siring success. There was no effect of body size or the mass of male reproductive tissues on siring success. Broods showed relatively low frequencies of multiple paternity; even at high densities, 75% of broods had only one father. High frequencies of single-paternity broods imply either that this species does not compete via sperm displacement, or that sperm displacement is extremely effective, potentially explaining the lack of a positive relationship between male investment and paternity. In addition, there was low variance in siring success among individuals, suggesting a lack of strong sexual selection on male traits. Low variance among sires and the strong effect of proximity are likely driven by the unusual biology of a sessile copulating species.
Data from: Next-generation museomics disentangles one of the largest primate radiations
Guenons (tribe Cercopithecini) are one of the most diverse groups of primates. They occupy all of sub-Saharan Africa and show great variation in ecology, behavior, and morphology. This variation led to the description of over 60 species and subspecies. Here, using next-generation DNA sequencing (NGS) in combination with targeted DNA capture, we sequenced 92 mitochondrial genomes from museum-preserved specimens as old as 117 years. We infer evolutionary relationships and estimate divergence times of almost all guenon taxa based on mitochondrial genome sequences. Using this phylogenetic framework, we infer divergence dates and reconstruct ancestral geographic ranges. We conclude that the extraordinary radiation of guenons has been a complex process driven by, among other factors, localized fluctuations of African forest cover. We find incongruences between phylogenetic trees reconstructed from mitochondrial and nuclear DNA sequences, which can be explained by either incomplete lineage sorting or hybridization. Furthermore, having produced the largest mitochondrial DNA dataset from museum specimens, we document how NGS technologies can 'unlock' museum collections, thereby helping to unravel the tree-of-life.
Data from: Genetic inference of epiphytic orchid colonization; it may only take one
Colonization of vacant habitat is a fundamental ecological process that affects the ability of species to persist and undergo range modifications in continually shifting landscapes. Thus, understanding factors that affect and limit colonization has important ecological and conservation implications. Epiphytic orchids are increasingly threatened by various factors, including anthropogenic habitat disturbance. As cleared areas (e.g. pastures) are recolonized by suitable host trees, the establishment and genetic composition of epiphytic orchid populations are likely a function of their colonization patterns. We used genetic analyses to infer the prevailing colonization pattern of the epiphytic orchid, Brassavola nodosa. Samples from three populations (i.e. individuals within a tree) from each of five pastures in the dry forest of Costa Rica were genotyped with neutral nuclear and chloroplast markers. Spatial autocorrelation and hierarchical genetic structure analyses were used to assess the relatedness of individuals within populations, among populations within pastures and among populations in different pastures. The results showed significant relatedness within populations (mean r = 0.166) and significant but lower relatedness among populations within a pasture (mean r = 0.058). Our data suggest that colonization of available habitats is by few individuals with subsequent population expansion resulting from in situ reproduction, and that individuals within a tree are not a random sample of the regional seed pool. Furthermore, populations within a pasture were likely colonized by seeds produced by founders of a neighbouring population within that pasture. These results have important ramifications for understanding conservation measures needed for this species and other epiphytic orchids.
Data from: Willet be one species or two?: a genomic view of the evolutionary history of Tringa semipalmata
The Willet (Tringa semipalmata; Scolopacidae) is composed of 2 morphologically and vocally distinct subspecies with broadly disjunct breeding distributions in North America. Nominate T. s. semipalmata breeds in coastal salt and brackish marshes along the Atlantic and Gulf coasts of eastern North America and the West Indies, and T. s. inornata breeds in wet grasslands and prairies in the northwestern interior of North America. To assess divergence and test for hybridization between the 2 subspecies, we sampled breeding and wintering populations and collected morphological data, mitochondrial DNA sequences from the ND2 locus, and nuclear DNA sequences from genomic libraries enriched for ultraconserved elements (UCEs). Mitochondrial haplotypes were reciprocally monophyletic between the 2 subspecies and indicated divergence approximately 700,000 yr ago. The UCE dataset included 4,635 loci containing 19,322 single nucleotide polymorphisms (SNPs), and, based on these data, individuals clustered by subspecies with no evidence of admixture between them and no substructure within subspecies. We identified 42 nuclear loci that contained SNPs fixed for alternate alleles between the 2 subspecies. Of the 42 loci with fixed differences, a statistically disproportional 17 were Z-linked, indicating a role for sexual selection in the divergence of the 2 subspecies. Genetic, morphological, ecological, and behavioral differences suggest that the 2 Willet subspecies may merit treatment as separate species. Further studies are needed to determine the presence of pre- or post-mating reproductive isolation.
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: A few large roads or many small ones? How to accommodate growth in vehicle numbers to minimise impacts on wildlife
Roads and vehicular traffic are among the most pervasive of threats to biodiversity because they fragmenting habitat, increasing mortality and opening up new areas for the exploitation of natural resources. However, the number of vehicles on roads is increasing rapidly and this is likely to continue into the future, putting increased pressure on wildlife populations. Consequently, a major challenge is the planning of road networks to accommodate increased numbers of vehicles, while minimising impacts on wildlife. Nonetheless, we currently have few principles for guiding decisions on road network planning to reduce impacts on wildlife in real landscapes. We addressed this issue by developing an approach for quantifying the impact on wildlife mortality of two alternative mechanisms for accommodating growth in vehicle numbers: (1) increasing the number of roads, and (2) increasing traffic volumes on existing roads. We applied this approach to a koala (Phascolarctos cinereus) population in eastern Australia and quantified the relative impact of each strategy on mortality. We show that, in most cases, accommodating growth in traffic through increases in volumes on existing roads has a lower impact than building new roads. An exception is where the existing road network has very low road density, but very high traffic volumes on each road. These findings have important implications for how we design road networks to reduce their impacts on biodiversity.
Data from: Altitudinal clinal variation in wing form in African Drosophila melanogaster: one cline or many?
Geographical patterns of morphological variation have been useful in addressing hypotheses about environmental adaptation. In particular, latitudinal clines in phenotypes have been studied in a number of Drosophila species. Some environmental conditions along latitudinal clines—for example, temperature—also vary along altitudinal clines, but these have been studied infrequently and it remains unclear whether these environmental factors are similar enough for convergence or parallel evolution. Most clinal studies in Drosophila have dealt exclusively with univariate phenotypes, allowing for the detection of clinal relationships, but not for estimating the directions of covariation between them. We measured variation in wing shape and size in D. melanogaster derived from populations at varying altitudes and latitudes across sub-Saharan Africa. Geometric morphometrics allows us to compare shape changes associated with latitude and altitude, and manipulating rearing temperature allows us to quantify the extent to which thermal plasticity recapitulates clinal effects. Comparing effect vectors demonstrates that altitude, latitude, and temperature are only partly associated, and that the altitudinal shape effect may differ between Eastern and Western Africa. Our results suggest that selection responsible for these phenotypic clines may be more complex than just thermal adaptation.
Electrochemical and thermodynamic properties of 1-phenyl-3-(phenylamino)propan -1-one with Na2WO4 on N80 Steel
<p>The corrosion inhibition effect and adsorption behavior of 1-phenyl-3-(phenylamino)propan-1-one(PPAPO) on N80 steel in hydrochloric solution have been investigated by Fourier transform infrared (FTIR), electrochemical method and scanning electron microscopy (SEM). The corrosion inhibition mechanism of PPAPO with Na<sub>2</sub>WO<sub>4</sub> was interpreted from the point of view of the thermodynamic. The results indicated that PPAPO with Na<sub>2</sub>WO<sub>4</sub> acted as a mixed type inhibitor. The inhibition film formed on N80 steel surface can increase the charge transfer resistance and prevent the occurrence of corrosion reaction, thereby reducing the corrosion rate of metal surface. The inhibition efficiency was up to 99.65%; and the inhibitor PPAPO with Na<sub>2</sub>WO<sub>4</sub> showed good synergistic effect on N80 corrosion behavior in HCl solution. The adsorption behavior of inhibitors on N80 steel surface was in accordance with the Langmuir adsorption model, and mainly belonged to chemisorption. The adsorption process of PPAPO on N80 surface was spontaneous and irreversible endothermic reaction.</p>
Data from: One species for one island? Unexpected diversity and weak connectivity in a widely distributed tropical hydrozoan
Isolation by distance (IBD) is one of the main modes of differentiation in marine species, above all in species presenting low dispersal capacities. This study reports the genetic structuring in the tropical hydrozoan Lytocarpia brevirostris α (sensu Postaire et al, 2016b), a brooding species, from 13 populations in the Western Indian Ocean (WIO) and one from New Caledonia (Tropical Southwestern Pacific). At the local scale, populations rely on asexual propagation at short distance, which was not found at larger scales; identical genotypes were restricted to single populations. After the removal of repeated genotypes, all populations presented significant positive FIS values (between 0.094*** and 0.335***). Gene flow was extremely low at all spatial scales, between sites within islands (<10 km distance) and among islands (100 to>11 000 km distance), with significant pairwise FST values (between 0.012*** and 0.560***). A general pattern of IBD was found at the Indo-Pacific scale, but also within sampled ecoregions of the WIO province. Clustering analyses identified each sampled island as an independent population, whereas analysis of molecular variance indicated that population genetic differentiation was significant at small (within island) and intermediate (among islands within province) spatial scales. The high population differentiation might reflect the life cycle of this brooding hydrozoan, possibly preventing regular dispersal at distances more than a few kilometres and probably leading to high cryptic diversity, each island housing an independent evolutionary lineage.
Data from: Global biodiversity assessment and hyper-cryptic species complexes: more than one species of elephant in the room?
Several recent estimates of global biodiversity have concluded that the total number of species on Earth lies near the lower end of the wide range touted in previous decades. However, none of these recent estimates formally explore the real 'elephant in the room', namely, what proportion of species are taxonomically invisible to conventional assessments, and thus, as undiagnosed cryptic species, remain uncountable until revealed by multi-gene molecular assessments. Here we explore the significance and extent of so-called 'hyper-cryptic' species complexes, using the Australian freshwater fish Galaxias olidus as a proxy for any organism whose taxonomy ought to be largely finalized when compared to those in little-studied or morphologically undifferentiated groups. Our comprehensive allozyme (838 fish for 54 putative loci), mtDNA (557 fish for 605bp of cytb), and morphological (1963–3389 vouchers for 17–58 characters) assessment of this species across its broad geographic range revealed a 1500% increase in species-level biodiversity, and suggested that additional taxa may remain undiscovered. Importantly, while all 15 candidate species were morphologically diagnosable a posteriori from one another, single-gene DNA barcoding proved largely unsuccessful as an a priori method for species identification. These results lead us to draw two strong inferences of relevance to estimates of global biodiversity. First, hyper-cryptic complexes are likely to be common in many organismal groups. Second, no assessment of species numbers can be considered 'best practice' in the molecular age unless it explicitly includes estimates of the extent of cryptic and hyper-cryptic biodiversity.
Data from: Current and projected global distribution of Phytophthora cinnamomi, one of the world's worst plant pathogens
Globally, Phytophthora cinnamomi is listed as one of the 100 worst invasive alien species and active management is required to reduce impact and prevent spread in both horticulture and natural ecosystems. Conversely, there are regions thought to be suitable for the pathogen where no disease is observed. We developed a CLIMEX model for the global distribution of P. cinnamomi based on the pathogen's response to temperature and moisture and by incorporating extensive empirical evidence on the presence and absence of the pathogen. The CLIMEX model captured areas of climatic suitability where P. cinnamomi occurs that is congruent with all available records. The model was validated by the collection of soil samples from asymptomatic vegetation in areas projected to be suitable by the model for which there were few records. DNA was extracted and the presence or absence of P. cinnamomi determined by high throughput sequencing (HTS). While not detected using traditional isolation methods, HTS detected P. cinnamomi at higher elevations in eastern Australia and central Tasmania as projected by the CLIMEX model. Further support for the CLIMEX model was obtained by using the large dataset from southwest Australia where the proportion of positive records in an area is related to the Ecoclimatic Index value for the same area. We provide for the first time a comprehensive global map of the current P. cinnamomi distribution, an improved CLIMEX model of the distribution, and a projection to 2080 of the distribution with predicted climate change. This information provides the basis for more detailed regional scale modelling and supports risk assessment for governments to plan management of this important soil-borne plant pathogen.
Data from: When one phenotype is not enough - divergent evolutionary trajectories govern venom variation in a widespread rattlesnake species
Understanding the origin and maintenance of phenotypic variation, particularly across a continuous spatial distribution, represents a key challenge in evolutionary biology. For this, animal venoms represent ideal study systems: they are complex, variable, yet easily quantifiable molecular phenotypes with a clear function. Rattlesnakes display tremendous variation in their venom composition, mostly through strongly dichotomous venom strategies, which may even coexist within single species. Here, through dense, widespread population-level sampling of the Mojave rattlesnake, Crotalus scutulatus, we show that genomic structural variation at multiple loci underlies extreme geographic variation in venom composition, which is maintained despite extensive gene flow. Unexpectedly, neither diet composition nor neutral population structure explain venom variation. Instead, venom divergence is strongly correlated with environmental conditions. Individual toxin genes correlate with distinct environmental factors, suggesting that different selective pressures can act on individual loci independently of their co-expression patterns or genomic proximity. Our results challenge common assumptions about diet composition as the key selective driver of snake venom evolution and emphasise how the interplay between genomic architecture and local-scale spatial heterogeneity in selective pressures may facilitate the retention of adaptive functional polymorphisms across a continuous space.
Data from: Don't put all eggs in one nest - spread them and cut time at risk
In many egg-laying animals, some females spread their clutch among several nests. The fitness effects of this reproductive tactic are debated. Using mathematical modelling and field observations we analyse an unexplored benefit of egg spreading in brood parasitic and other breeding systems: reduced time at risk for offspring. If a clutch takes many days to lay until incubation and embryo development starts after the last egg, a parasitic female by spreading her eggs can reduce offspring time in the vulnerable nest, at risk of predation or other destruction. The model suggests that she can achieve much of this benefit already by spreading her eggs among a few nests, even if her total clutch is large. Field data from goldeneye ducks Bucephala clangula show that egg spreading enables a fecund female to lay a much larger than average clutch, without increasing offspring time at risk in a nest. This advantage increases with female condition (fecundity) and can markedly raise female reproductive success. These results help explain the puzzle of nesting parasites in some precocial birds, which lay eggs in the nests of other females before laying in their own nest. Risk reduction by egg spreading may also play a role in the evolution of other breeding systems, for instance some forms of polyandry with male parental care.
Figure 5 in Natural history of the fireflies of the Serra dos Órgãos mountain range (Brazil: Rio de Janeiro) - one of the 'hottest' firefly spots on Earth, with a key to genera (Coleoptera: Lampyridae)
Figure 5. Diversity of Photurinae fireflies of the Serra dos Órgãos. A – Bicellonycha albilatera, B – Bicellonycha tenuicornis, C – Photuris velox, D – Photuris elliptica, E – Photuris femoralis (modified from Souto et al. 2019), F – Photuris lugubris, G – Pyrogaster moestus, H – Pyrogaster lunifer, I – Pyrogaster vestitus, J – Pyrogaster elongatior, K – Pyrogaster aureus, L – Pyrogaster angustatus, M – Pyrogaster nigrolineatus, N – Pyrogaster telephorinus, O – Pyrogaster margipallens, P – Pyrogaster atrocinctus, Q – Pyrogaster coxalis. Scale bar: 2 mm.
Figure 2 in Natural history of the fireflies of the Serra dos Órgãos mountain range (Brazil: Rio de Janeiro) - one of the 'hottest' firefly spots on Earth, with a key to genera (Coleoptera: Lampyridae)
Figure 2. Regional climate at the study area is marked by a warm season between October‒April, and a cool season between May‒September. Lines represent the monthly mean, and the shaded area represents the range between the monthly maximum and minimum, from 2007–2017. Inter-annual variation in precipitation is higher in the warm than in the cool season. Data were obtained from an automated weather station at the PNSO at 991 m, Latitude: −22.448922º, Longitude: −42.987146º.
Figure 3 in Natural history of the fireflies of the Serra dos Órgãos mountain range (Brazil: Rio de Janeiro) - one of the 'hottest' firefly spots on Earth, with a key to genera (Coleoptera: Lampyridae)
Figure 3. Diversity of fireflies of the Serra dos Órgãos, including Amydetinae, Psilocladinae, Lampyrinae, and Incertae sedis taxa. A – Amydetes fastigiata, B – Magnoculus obscurus, C – Cladodes pauper, D – Cladodes illigeri, E – Cladodes stellata, F – Vesta thoracica, G – Araucariocladus hiems (modified from Silveira and Mermudes 2017), H – Psilocladus grandis, I – Psilocladus sigillatus, J – Psilocladus pulcher, K – Scissicauda disjuncta (modified from Silveira et al. 2016a), L – Ethra axillaris, M – Ethra marginata, N – Ethra addita, O – Ethra inculta. Scale bar: 2 mm.
Figure 4 in Natural history of the fireflies of the Serra dos Órgãos mountain range (Brazil: Rio de Janeiro) - one of the 'hottest' firefly spots on Earth, with a key to genera (Coleoptera: Lampyridae)
Figure 4. Diversity of Lampyrinae fireflies of the Serra dos Órgãos. A – Aspisoma sticticum, B – Aspisoma lineatum, C – Aspisoma pallens, D – Cratomorphus besckei, E – Cratomorphus cossyphinus (modified from Campos et al. 2018), F – Cratomorphus splendidus, G – Cratomorphus distinctus, H – Lucernuta savignii (modified from Silveira et al. 2019), I – Lychnacris flabellata subopaca, J – Phaenolis basalis, K – Luciuranus takiyae (modified from Silveira et al. 2018), L – Luciuranus desideratus (modified from Silveira et al. in 2018), M – Luciuranus josephi (modified from Silveira et al. 2016b), N – Luciuranus jameshooki (modified from Silveira et al. 2016b), O – Lucidota flabellicornis, P – Lucidota tricolor, Q – Photinus infuscatus, R – Photinus laticollis, S – Macrolampis varicollis, T – Photinus succensus, U – Photinus augustalisi, V – Macrolampis frater, W – Photinus nodieri, X – Ybytyramoan praeclarum (modified from Silveira and Mermudes 2014b), Y – Ybytyramoan diasi (modified from Silveira and Mermudes 2014b), Z – Ybytyramoan monteirorum (modified from Silveira and Mermudes 2014b). Scale bar: 2 mm.
Figure 1 in Natural history of the fireflies of the Serra dos Órgãos mountain range (Brazil: Rio de Janeiro) - one of the 'hottest' firefly spots on Earth, with a key to genera (Coleoptera: Lampyridae)
Figure 1. The Serra dos Órgãos National Park (blue) and the Guapiaçu Ecological Reserve (red), in the Rio de Janeiro State (Southeastern Brazil) are protected areas within the domains of the Serra do Mar Mountain Range (green), Southeastern Brazil.
One Cent, Lincoln Memorial
This is a 3D Scan of the Lincoln Memorial on the reverse side of the Lincoln Memorial Cent. It is one of the most difficult 3D scans I have ever attempted. The coin is small and the relief is shallow, making it hard to capture the image with significant detail. The model includes only one side of the coin. If you want to 3D print this coin put it on its side to capture all the detail. For printing on an fdm printer scale the model sufficiently for your printer's nozzle. More information about the scanner and the scanning process can be found here: https://www.muellerr.ch/raspberry-pi-3d-coin-scanner/ Source: Objaverse 1.0 / Sketchfab
ScienceDex guides
Understand access before you commit
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.