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Figure 4 in Age, growth and reproduction of the endangered jewelfish Hemichromis bimaculatus (Cichlidae) in the valley of Oued Righ (South-eastern Algeria)
Figure 4. - Monthly variation of the gonadosomatic index (GSI) of Hemichromis bimaculatus females and males in the valley of Oued Righ. The different letters indicate significant differences between sampling points. Error bars correspond to standard deviations.
Figure 2 in Age, growth and reproduction of the endangered jewelfish Hemichromis bimaculatus (Cichlidae) in the valley of Oued Righ (South-eastern Algeria)
Figure 2. - Scale of Hemichromis bimaculatus (3 years old, TL = 9.30 cm), caught in Oued Righ valley (r1 = first annulus, r2 = second annulus, r3 = third annulus; MI = marginal increment; R = total radius)
Figure 1 in Age, growth and reproduction of the endangered jewelfish Hemichromis bimaculatus (Cichlidae) in the valley of Oued Righ (South-eastern Algeria)
Figure 1. - Map of the Valley of Oued Righ with the location of the sampling localities. 1: Temacine Lake, 2: Oued Righ Channel.
Machine Learning based identification of putative coral pathogens in endangered Caribbean staghorn coral
<h1>Supplementary Files</h1> <p>SupplementaryFile1.csv.gz – Metadata for field collected samples with columns:</p> <ul> <li>“sample_id” – individual sample names.</li> <li>“health” – “H” healthy and “D” diseased fragments.</li> <li>“year” – year fragment collected.</li> <li> “season” – season fragment collected (“S” July and “W” January)</li> <li>“site” – location fragment collected from</li> <li>“lib.size” – total number of sequenced reads</li> <li>“norm.factors” – factor used to normalize read counts of ASVs</li> </ul> <p>SupplementaryFile2.csv.gz – Metadata for tank collected samples with columns:</p> <ul> <li> “sample_id”<a name="_Hlk163818341"></a> – individual sample names.</li> <li>“geno” – fragment genotype</li> <li> “fragment_id” – fragment identification tracked through repeated sampling</li> <li> “tank_id” – tank identification</li> <li>“time_treat” – concatenated metric for sampling time, exposure, and disease outcome separated by “_” <ul> <li> Time – 0, 2, 8</li> <li>Exposure – “D” Diseased, “N” Healthy</li> <li>Disease Outcome - “D” Diseased, “H” Healthy</li> </ul> </li> <li> “lib.size” – total number of sequenced reads</li> <li>“norm.factors” – factor used to normalize read counts of ASVs</li> </ul> <p>SupplementaryFile3.fasta – FASTA file including complete 16s sequences named with ASV identifier and taxonomy.</p> <p>SupplementaryFile4.csv.gz – Matrix of the number of reads of each ASV sequenced in each sample. Combined both field and tank samples.</p> <p>SupplementaryFile5.csv.gz – Matrix of the log2 CPM of each ASV sequenced in each sample. Combined both field and tank samples.</p> <p>SupplementaryFile6.csv.gz – Complete results for each ASV association.</p> <ul> <li> “top_classification” – lowest taxonomic classification with more than 80% confidence.</li> <li>“taxonomy” – Full taxonomy including confidence in each taxonomic level.</li> <li>“passedFilter” – indicates taxa filtered from analysis due to rarity and/or lack of observations across sample times.</li> <li> “rank_*” – machine learning model rankings, median ranking, and model estimated ranking along with standard error, confidence interval, and FDR adjusted p-value used to identify important ASVs.</li> <li>“ml_retained” – Indicates if the ASV was of above average importance to ML models. NA values indicate ASVs which were filtered prior to ML modelling.</li> <li>“fieldModel_*” – ANOVA table results for each ASV testing the effects of health, year, season and all possible interactions indicating: <ul> <li>Sums of squares, mean squares, numerator and denominator degrees of freedom, F statistic, p-value, and FDR corrected p-value.</li> <li>NA values are filled for ASVs filtered prior to differential abundance analysis.</li> </ul> </li> <li>“diffAbundance_healthAssociation” – Marks the health association of ASVs from differential abundance analysis of field samples: “H” health, “D” diseased, “N” none, NA – filtered prior to differential abundance analysis.</li> <li>“fieldLogFC_*” – Post-hoc contrasts for ML retained ASVs testing the significance of the log2 fold-change between disease and healthy fragments within each sampling time (year: 2016, 2017 & season: “S” July, “W” January) showing: <ul> <li>Mean estimate, standard error, degrees of freedom, lower and upper 95% confidence interval, t-statistic, p-value, FDR adjusted p-value.</li> <li>NA values are filled for ASVs which were not marked as important by ML models.</li> </ul> </li> <li> “field_consistent” – Indicates if the ASV was consistently healthy or disease associated across sampling times. NA values are filled for ASVs which were not marked as important by ML models.</li> <li>“tankModel_*” – ANOVA table results for each ASV testing the effect of the combination of time, disease exposure, and disease outcome, indicating: <ul> <li>Sums of squares, mean squares, numerator and denominator degrees of freedom, F statistic, p-value, and FDR corrected p-value.</li> <li>NA values are filled for ASVs filtered prior to tank experimental analysis.</li> </ul> </li> <li> “tankLogFC_*” – Post-hoc contrasts for ASVs tested in tank exposure experiments. <ul> <li>Contrasts include: <ul> <li>Post-exposure diseased vs healthy outcome regardless of exposure (DvH)</li> <li>Post-exposure diseased vs healthy exposure regardless of outcome (DvN)</li> <li>Post-exposure disease exposed corals with disease symptoms compared to disease exposed but still healthy corals (DDvDH)</li> <li>Post-exposure disease exposed corals with disease symptoms compared to healthy exposed and still healthy corals (DDvNH)</li> <li>Post-exposure disease exposed corals which stay healthy compared to healthy exposed and still healthy corals (DHvNH)</li> <li>Pre-exposure compared to Post-exposure in corals with the disease regardless of exposure (PostvPreD)</li> <li>Pre-exposure compared to Post-exposure in corals without the disease regardless of exposure (PostvPreH)</li> </ul> </li> <li>Mean estimate, standard error, degrees of freedom, lower and upper 95% confidence interval, t-statistic, p-value, FDR adjusted p-value.</li> <li>NA values are filled for ASVs which were not consistently associated with healthy or diseased corals in the field experiment.</li> </ul> </li> <li>“pathogen_classification” – Indicates the predicted microbial classification based on the tank results. Pathogen, Opportunist, Commensal <ul> <li>NA values are filled for ASVs which were not consistently associated with healthy or diseased corals in the field experiment.</li> </ul> </li> </ul>
Fig. 14 in Pollinia removal and suspected pollination of the endangered ghost orchid, Dendrophylax lindenii (Orchidaceae) by various hawk moths (Lepidoptera: Sphingidae): another mystery dispelled
Fig. 14. Monk skipper (Asbolis capucinus) visiting Dendrophylax lindenii flower (22 Jun 2018, 10:13 AM Eastern Standard Time).
Fig. 15 in Pollinia removal and suspected pollination of the endangered ghost orchid, Dendrophylax lindenii (Orchidaceae) by various hawk moths (Lepidoptera: Sphingidae): another mystery dispelled
Fig. 15. Brazilian skipper (Calpodes ethlius) visiting Dendrophylax lindenii flow- er (2 Jul 2018, 5:50 PM Eastern Standard Time).
Fig. 13 in Pollinia removal and suspected pollination of the endangered ghost orchid, Dendrophylax lindenii (Orchidaceae) by various hawk moths (Lepidoptera: Sphingidae): another mystery dispelled
Fig. 13. Unidentified Geometrid moth visiting Dendrophylax lindenii flower (15 Aug 2018, 9:25 PM Eastern Standard Time).
Fig. 9 in Pollinia removal and suspected pollination of the endangered ghost orchid, Dendrophylax lindenii (Orchidaceae) by various hawk moths (Lepidoptera: Sphingidae): another mystery dispelled
Fig. 9. Seagrape spanworm moth (Ametris nitocris) on Dendrophylax lindenii flower (20 Jul 2017, 12:04 AM EST).
Fig. 6 in Pollinia removal and suspected pollination of the endangered ghost orchid, Dendrophylax lindenii (Orchidaceae) by various hawk moths (Lepidoptera: Sphingidae): another mystery dispelled
Fig. 6. Photo sequence of Protambulyx strigilis nectaring on Dendrophylax lindenii flower, with proboscis fully inserted into the nectar spur in the bottom image (17 Aug 2018, 10:07 PM Eastern Standard Time).
Fig. 11 in Pollinia removal and suspected pollination of the endangered ghost orchid, Dendrophylax lindenii (Orchidaceae) by various hawk moths (Lepidoptera: Sphingidae): another mystery dispelled
Fig. 11. Unidentified Geometrid moth resting on the labellum of Dendrophylax lindenii flower. The head of the insect is positioned over the concave labellum's upper surface where moisture droplets from dew and rain have been known to accumulate (6 Aug 2018, 2:02 PM Eastern Standard Time).
Fig. 10 in Pollinia removal and suspected pollination of the endangered ghost orchid, Dendrophylax lindenii (Orchidaceae) by various hawk moths (Lepidoptera: Sphingidae): another mystery dispelled
Fig. 10. Palamedes swallowtail butterfly (Papilio palamedes) visiting Dendrophylax lindenii flower during daylight hours (9 Aug 2017, 10:59 AM Eastern Standard Time).
Fig. 4 in Pollinia removal and suspected pollination of the endangered ghost orchid, Dendrophylax lindenii (Orchidaceae) by various hawk moths (Lepidoptera: Sphingidae): another mystery dispelled
Fig. 4. Dolba hyloeus photographed with Dendrophylax lindenii pollinia at base of proboscis (23 Aug 2018, 8:19 PM Eastern Standard Time).
Fig. 5 in Pollinia removal and suspected pollination of the endangered ghost orchid, Dendrophylax lindenii (Orchidaceae) by various hawk moths (Lepidoptera: Sphingidae): another mystery dispelled
Fig. 5. Top image: Eumorpha fasciatus in the act of inserting its proboscis into the nectar spur, opening just beneath the column of the flower (4 Jul 2018, 2:49 AM Eastern Standard Time). Bottom image: Eumorpha fasciatus flying towards Dendrophylax lindenii flower (2 Sep 2018, 9:33 PM Eastern Standard Time).
Fig. 3 in Pollinia removal and suspected pollination of the endangered ghost orchid, Dendrophylax lindenii (Orchidaceae) by various hawk moths (Lepidoptera: Sphingidae): another mystery dispelled
Fig. 3. Pachylia ficus shown inserting its proboscis into the nectar spur opening (top). In the bottom image, pollinia are shown affixed to the proboscis itself (26 Jul 2018, 8:29 PM Eastern Standard Time).
Fig. 2 in Pollinia removal and suspected pollination of the endangered ghost orchid, Dendrophylax lindenii (Orchidaceae) by various hawk moths (Lepidoptera: Sphingidae): another mystery dispelled
Fig. 2. Stages of proboscis insertion by a female Pachylia ficus (8 Jul 2018, 8:40 PM Eastern Standard Time). Note the close proximity of the insect's head to the column following complete insertion of the proboscis into the nectar spur (lower image).
Fig. 1 in Pollinia removal and suspected pollination of the endangered ghost orchid, Dendrophylax lindenii (Orchidaceae) by various hawk moths (Lepidoptera: Sphingidae): another mystery dispelled
Fig. 1. Pachylia ficus, shown nectaring on Dendrophylax lindenii in top 2 images (3 Jul 2018, 8:55 PM Eastern Standard Time), and carrying pollinia in lower image (5 Jul 2018, 5:43 AM Eastern Standard Time). Pollinia are yellow in color, and can be observed on the moth's forehead, at base of proboscis.
Fig. 2 in Syzygium setosum (Myrtaceae), a rare and endangered peat swamp tree in Southeast Asia: lectotypification, conservation status and a new record in Sumatra
Fig. 2. – Geographical distribution of Syzygium setosum (King) I.M. Turner. Extant populations of the taxon are represented by black solid circles, while likely extinct populations are represented by white circles.
Fig. 1 in Syzygium setosum (Myrtaceae), a rare and endangered peat swamp tree in Southeast Asia: lectotypification, conservation status and a new record in Sumatra
Fig. 1. – Syzygium setosum (King) I.M. Turner. A. Base of trunk showing the buttress; B. Close-up of the flush trunk showing pale cream inner bark and pale to dark cream sapwood; C. Close-up of a twig showing reddish-brown erect bristly hairs; D. Leafy branch showing opposite leaf arrangement; E. Adaxial (upper) leaf surface; F. Abaxial (lower) leaf surface; G. Immature terminal and axillary inflorescences; H. Mature inflorescences showing open flowers; I. Close-up of open flowers; J. Close-up of an infructescence; K. Apical view of a fruit; L. Seeds (left) and inner part of the carpel (right); M. Longitudinal section of a fruit. [Randi GB-052, BO] [Photos: A. Randi]
A New Record of Arisaema tylophorum C.E.C.Fisch (Araceae) an Endemic and Endangered Cobra Lily in the Nilgiri Mountains, India
<p>Arisaema tylophorum C.E.C. Fisch. (Araceae) is an endemic and endangered cobra lily discussed in the context of botanical exploration in the Nilgiri Mountains of India and its conservation implications. A rare plant from historical collections was last seen in 1932, and its rediscovery was first recorded in June 2019. It was documented as a new record for the region, specifically in the Kundah range of the Nilgiri Mountains. The species was identified using morphological information from live samples and herbarium specimens obtained from multiple herbaria. A key and images are included to accurately identify similar species in various locations. Based on recent collections, this study represents and provides clear information about the taxonomic range, characterization, risk, and conservation status of A. tylophorum.</p>
Inbreeding depression, functional traits and phenotypic plasticity in an endangered tree species from Congo basin with a mixed mating system
<h3><span>Inbreeding depression, functional traits and phenotypic plasticity in an endangered tree species from Congo basin with a mixed mating system</span></h3> <h1><a name="_Hlk166486742"></a><strong><span>Abstract</span></strong></h1> <p><span><span>1. Most tree species can suffer from inbreeding depression (ID), which they escape by reproducing predominantly through outcrossing. A remarkable exception is <em>Pericopsis elata</em>, an African timber species naturally producing 54% of self-fertilized seeds in the eastern Congo Basin. This species is highly logged and suffers from a deficit of natural regeneration, so that silviculture is needed for its sustainable management. While selecting good genetic material can increase the value of plantations, we lack fundamental biological knowledge on the effect of inbreeding and competition on growth potential, variability in leaf traits and phenotypic plasticity. We hypothesize that ID in <em>P. elata</em> could result from the expression of deleterious mutations affecting functional traits, or from a reduction of adaptive phenotypic plasticity in inbred genotypes.</span></span></p> <p><span><span>2. To test our hypotheses, 540 <em>P. elata</em> seedlings were monitored for 4 years in a Nelder-type device located in the DRC, in which trees were planted along concentric circles to generate a density gradient. Nine leaf morphological traits (including specific leaf area, stomata density and size), eight leaf chemical traits, diameter, and total height were measured regularly, while paternity analyses allowed distinguishing inbred and outbred plants. To explain the observed ID on growth, we tested whether inbreeding affected leaf traits and/or their plasticity expressed across years, across the density gradient or across sunlight exposure. </span></span></p> <p><span><span>3. Outbred plants grew faster than inbred ones, demonstrating ID for each level of competition. Despite the significant correlation found between specific leaf area and growth, and the impact of planting density, plant age, and leaf exposure to sunlight on multiple traits, mean leaf trait values did not differ according to inbreeding. However, </span></span><span><span>a few leaf traits (chlorophyl content, </span></span><span><span>maximum stomatal water vapor conductance</span></span><span><span>, and leaf fresh mass) showed significantly higher plasticity in outbred than inbred plants. </span></span></p> <p><span><span>4. Synthesis: the observed ID on growth was not explained by a direct effect of inbreeding on the mean values of functional traits but possibly by a reduction of phenotypic plasticity with inbreeding. Additional studies on the interplay between ID, functional traits and plasticity should be conducted at the intra-specific level to identify general patterns<em>.</em></span></span></p> <p><span><strong><span>Key-words : </span></strong></span><span><span>Inbreeding depression, phenotypic plasticity, silviculture, functionals traits, <em>Pericopsis elata</em>, mating system, Nelder device.</span></span></p>
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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)
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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.