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Figure 3 in Three new species of free-living marine nematodes from the Bohai Sea and Yellow Sea, China
Figure 3. Parodontophora deltensis sp. nov. (a) Lateral view of male head-end; (b) lateral view of male tail; (c) lateral view of male copulatory apparatus; (d) lateral view of female head-end; (e) tail of female. Scale bar: 20 mm (a, c, d); 50 mm (b, e).
Figure 2 in Three new species of free-living marine nematodes from the Bohai Sea and Yellow Sea, China
Figure 2. Paranticoma tricerviseta sp. nov. (a) Lateral view of male anterior end, showing cervical setae (1000×); (b) lateral view of spicules (400×); (c) lateral view of male tail (200×); (d) lateral view of conical part of male tail, showing subventral setae (400×).
Figure 1 in Three new species of free-living marine nematodes from the Bohai Sea and Yellow Sea, China
Figure 1. Paranticoma tricerviseta sp. nov. (a) Lateral view of male head-end; (b) lateral view of female head-end; (c) lateral view of male copulatory apparatus and ventral-middle setae behind anus in the tail; (d) last part of the tail. Scale bar: 20 mm.
Data and code from: Reciprocity and interaction effectiveness in generalised mutualisms among free-living species
<p><span>Mutualistic interactions among free-living species generally involve low-frequency interactions and highly asymmetric dependence among partners, yet our understanding of factors behind their emergence is still limited. Using individual-based interactions of a super-generalist fleshy-fruited plant with its frugivore assemblage, we estimated the Resource Provisioning Effectiveness (RPE) and Seed Dispersal Effectiveness (SDE) to assess the balance in the exchange of resources. Plants were highly dependent on a few frugivore species, while frugivores interacted with most individual plants, resulting in strong asymmetries of mutual dependence. Interaction effectiveness was mainly driven by interaction frequency. Despite highly asymmetric dependences, the strong reliance on quantity of fruit consumed determined high reciprocity in rewards between partners (i.e., higher energy provided by the plant, more seedlings recruited), which was not obscured by minor variations in the quality of animal or plant service. We anticipate reciprocity will emerge in low-intimacy mutualisms where the mutualistic outcome largely relies upon interaction frequency.</span></p>
Fig. 1. SEM photos showing c.f in Latitudinal Diversity Gradients in Free-living Microorganisms - Hoogenraadia a Key Genus in Testate Amoebae Biogeography
Fig. 1. SEM photos showing c.f. Hoogenraadia humicola found from soils in Shennongjia Mountains of central China (the left picture is from Qin et al. 2011). This was previously identified as Planhoogenraadia africana by Qin et al. (2011). Scale bars: 50 µm (a) and 20 µm (b).
Fig. 3 in Latitudinal Diversity Gradients in Free-living Microorganisms - Hoogenraadia a Key Genus in Testate Amoebae Biogeography
Fig. 3. Relationship between shell width and shell length of each species of the genus Hoogenraadia. The sample sizes on which these measurements are based is unclear as the older literature often doesn't specify the number of tests measured (see Table 1).
Fig. 2 in Latitudinal Diversity Gradients in Free-living Microorganisms - Hoogenraadia a Key Genus in Testate Amoebae Biogeography
Fig. 2. Shell outline and SEM photos of six species of genus Hoogenraadia Gauthier-Lièvre and Thomas 1958, with scale bar 50 μm. a – H. cryptostoma Gauthier-Lièvre and Thomas 1958; b – H. sylvatica Vucetich 1974; c – H. africana Gauthier-Lièvre and Thomas 1958; d – H. humicola Bonnet 1976; e – H. ovata Bonnet 1976; f – H. asiatica Wang and Min 1987.
Fig. 1 in First Molecular Detection of Giardia duodenalis Assemblage B in a Free-Living European Wildcat (Felis s. silvestris) from Luxembourg
Fig. 1. Neighbor-joining distance analysis of the β-giardin nucleotide sequences. FS1 – sequence of partial β-giardin gene of the isolate from wildcat (KX685669). Reference human isolates: WB and KC8, (X85958 and AY072723); LD18, Nij5, VAN/90/UBC/44, GH- 202 (AY072727, AY072725, KP687755, AB618785); A101 and – cat isolate, (AY647264 and EU769206); P15 – reference cow isolate, (AY072729); A29 and A27 – reference dog isolates (AY545646 and AY545648). G. muris (AY258618) represents an outgroup.
Fig. 1A–D in Review paper A Half-century of Research on Free-living Amoebae (1965-2017): Review of Biogeographic, Ecological and Physiological Studies
Fig. 1A–D. Column graphs showing the number of published papers reviewed (ordinate) grouped by decades (abscissa). 1A – Total; 1B – Biogeography; 1C – Ecology; 1D – Physiology.
Data and code from: Reciprocity and interaction effectiveness in generalised mutualisms among free-living species
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Vocal communication is seasonal in social groups of wild, free-living house mice
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Human presence shifts the landscape of fear for a free-living mammal
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Data from: Early-life exposure to artificial light at night elevates physiological stress in free-living songbirds
<p>Artificial light at night (ALAN) can disrupt adaptive patterns of physiology and behavior that promote high fitness, resulting in physiological stress and elevation of steroid glucocorticoids (corticosterone, CORT in birds). Elevated CORT may have particularly profound effects early in life, with the potential for enduring effects that persist into adulthood. Research on the consequences of early-life exposure to ALAN remains limited, especially outside of the laboratory, and whether light exposure affects CORT concentrations in wild nestling birds particularly remains to be elucidated. We used an experimental setup to test the hypothesis that ALAN elevates CORT concentrations in developing free-living birds, by exposing nestling great tits (Parus major) to ALAN inside nest boxes. We measured CORT in feathers grown over the timeframe of the experiment (7 nights), such that CORT concentrations represent an integrative metric of hormone release over the period of nocturnal light exposure, and of development. We also assessed the relationships between feather CORT concentrations, body condition, nestling size rank and fledging success. In addition, we evaluated the relationship between feather CORT concentrations and telomere length. Nestlings exposed to ALAN had higher feather CORT concentrations than control nestlings, and nestlings in poorer body condition and smaller brood members also had higher CORT. On the other hand, telomere length, fledging success, and recruitment rate were not significantly associated with light exposure or feather CORT concentrations. Results indicate that exposure to ALAN elevates CORT concentrations in nestlings, which may reflect physiological stress. In addition, the organizational effects of CORT are known to be substantial. Thus, despite the lack of an effect on telomere length and survivorship, elevated CORT concentrations in nestlings exposed to ALAN may have subsequent impacts on later-life fitness and stress sensitivity.</p>
Data from: Thinking outside the box: problem-solving in free-living lizards
<p>Despite evidence that organisms are more likely to exhibit their full range of cognitive abilities under conditions found in nature, studies evaluating cognition under such conditions remain rare, particularly in vertebrate species. Here we conducted an experiment to evaluate problem solving and motor-self regulation in free-living arboreal lizards, Anolis sagrei, under natural conditions. We presented lizards with a novel detour problem which challenged individuals to circumvent a transparent barrier in order to obtain a food reward. Individuals varied in their ability to solve the detour problem. Furthermore, those that solved the problem were able to improve their performance across trials by modifying the natural response of attempting to strike the reward trough the transparent barrier, providing evidence of motor self-regulation. Solving the problem required individuals to modify their typical foraging behavior, as approaching the prey in a single burst of movement that culminated with an attack was an unsuccessful strategy. Contrary to expectations our findings provide evidence of motor self-regulation in a visually-oriented, sit-and-wait predator under natural conditions, suggesting motor-self-regulation is not limited by foraging strategy. Our results also underscore the need to evaluate the cognitive abilities of free-living organisms in the wild, particularly for taxa that perform poorly under laboratory conditions.</p>
Anthropogenic noise is associated with telomere length and carotenoid-based coloration in free-living nestling songbirds
<p>Growing evidence suggests that anthropogenic noise has deleterious effects on the behavior and physiology of free-living animals. These effects may be particularly pronounced early in life, when developmental trajectories are sensitive to stressors, yet studies investigating developmental effects of noise exposure in free-living populations remain scarce. To elucidate the effects of noise exposure during development, we examined whether noise exposure is associated with shorter telomeres, duller carotenoid-based coloration and reduced body mass in nestlings of a common urban bird, the great tit (Parus major). We also assessed how the noise environment is related to reproductive success. We obtained long-term measurements of the noise environment, over a ~24-h period, and characterized both the amplitude (measured by LAeq, LA90, LA10, LAmax) and variance in noise levels, since more stochastic, as well as louder, noise regimes might be more likely to induce stress. In our urban population, noise levels varied substantially, with louder, but less variable, noise characteristic of areas adjacent to a highway. Noise levels were also highly repeatable, suggesting that individuals experience consistent differences in noise exposure. The amplitude of noise near nest boxes was associated with shorter telomeres among smaller, but not larger, brood members. In addition, carotenoid chroma and hue were positively associated with variance in average and maximum noise levels, and average reflectance was negatively associated with variance in background noise. Independent of noise, hue was positively related to telomere length. Nestling mass and reproductive success were unaffected by noise exposure. Results indicate that multiple dimensions of the noise environment, or factors associated with the noise environment, could affect the phenotype of developing organisms, that noise exposure, or correlated variables, might have the strongest effects on sensitive groups of individuals, and that carotenoid hue could serve as a signal of early-life telomere length.</p>
Data from: Heritable variation in circulating glucocorticoids and endocrine flexibility in a free-living songbird
Phenotypic flexibility is a central way that organisms cope with challenging and changing environments. As endocrine signals mediate many phenotypic traits, heritable variation in hormone levels, or their context-dependent flexibility, could present an important target for selection. Several studies have estimated the heritability of circulating glucocorticoid levels under acute stress conditions, but little is known about the potential for either baseline hormone levels or rapid endocrine flexibility to evolve. Here we assessed the potential for selection to operate on the elevation (circulating hormone levels) and flexibility of glucocorticoid reaction norms to acute restraint stress. Multivariate animal models revealed low but significant heritability in baseline (h2=0.13-0.14) and stress-induced glucocorticoids (h2=0.18), and moderate heritability in glucocorticoid flexibility in response to acute stress (h2=0.38) in free-living juvenile tree swallows (Tachycineta bicolor; n=408). Baseline glucocorticoids were not genetically correlated with either stress-induced glucocorticoids or glucocorticoid flexibility. These findings indicate that baseline glucocorticoids and the acute stress response are distinct traits that can be independently shaped by selection. Microevolutionary changes that influence the expression or flexibility of these endocrine mediators of phenotype may be an important way that populations adapt to changing environments and novel threats.
Data from: Select and resequence reveals relative fitness of bacteria in symbiotic and free-living environments
Assays to accurately estimate relative fitness of bacteria growing in multistrain communities can advance our understanding of how selection shapes diversity within a lineage. Here, we present a variant of the "evolve and resequence" approach both to estimate relative fitness and to identify genetic variants responsible for fitness variation of symbiotic bacteria in free-living and host environments. We demonstrate the utility of this approach by characterizing selection by two plant hosts and in two free-living environments (sterilized soil and liquid media) acting on synthetic communities of the facultatively symbiotic bacterium Ensifer meliloti. We find (i) selection that hosts exert on rhizobial communities depends on competition among strains, (ii) selection is stronger inside hosts than in either free-living environment, and (iii) a positive host-dependent relationship between relative strain fitness in multistrain communities and host benefits provided by strains in single-strain experiments. The greatest changes in allele frequencies in response to plant hosts are in genes associated with motility, regulation of nitrogen fixation, and host/rhizobia signaling. The approach we present provides a powerful complement to experimental evolution and forward genetic screens for characterizing selection in bacterial populations, identifying gene function, and surveying the functional importance of naturally occurring genomic variation.
Primary data of thiotrophic free-living and ectosymbiotic genomes
<p><span>Thiotrophic symbioses between sulfur-oxidizing bacteria and various unicellular and metazoan eukaryotes are widespread in reducing marine environments. The giant colonial ciliate <em>Zoothamnium</em> <em>niveum</em> and its vertically transmitted ectosymbiont <em>Candidatus</em> <em>Thiobius</em> <em>zoothamnicola</em> (short Thiobius), however, is the only thiotrophic mutualism that has been cultivated so far. Because theoretical predictions posit a smaller genome in vertically transmitted endosymbionts compared to free-living relatives, we investigated whether this is true also for an ectosymbiont. We used metagenomics to recover the high-quality draft genome of this bacterial symbiont. For comparison, we have also sequenced a closely related free-living cultured but not formally described strain Milos ODIII6 (short ODIII6). We then performed comparative genomics to assess the functional capabilities at the gene, metabolic pathway, and trait levels. 16S rRNA gene trees and average amino acid identity confirmed the close phylogenetic relationship of both bacteria. Indeed, Thiobius had about a third smaller genome than its free-living relative ODIII6, with reduced metabolic capabilities and fewer functional traits. The functional capabilities of Thiobius were mostly a subset of those of the more versatile ODIII6, which possessed additional genes in the context of oxygen, sulfur, and hydrogen utilization and for the acquisition of phosphorus illustrating the adaptations to instable environmental conditions at hydrothermal vents. In contrast, Thiobius possessed genes for heterotrophy potentially enabling it to utilize lactate and acetate, which may be provided as byproducts by the host. The present study illustrates the effect of strict host-dependence of a bacterial ectosymbiont on genome evolution and host adaptation.</span></p>
Fig. 16 in XXII. Free-living Nematodes from Greenland, Land and Freshwater.
Fig. 16. Dorylaimus conicaudatus. Hind part.
Fig. 15 in XXII. Free-living Nematodes from Greenland, Land and Freshwater.
Fig. 15. Dorylaimus conicaudatus. Front end.
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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.