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292 results for “Indicator species”
Figure 3. - Phylogenetic relationships among Dicronocephalus species reconstructed with Bayesian inference using 16S rRNA sequences. Numbers above branches indicate ML bootstrap values and Bayesian posterior probabilities. Numbers below branches are bootstrap, symmetric resampling, and jacknife support from parsimony searches, respectively. Scale bar represents 10% nucleotide mutation rate.
Figure 3. - Phylogenetic relationships among Dicronocephalus species reconstructed with Bayesian inference using 16S rRNA sequences. Numbers above branches indicate ML bootstrap values and Bayesian posterior probabilities. Numbers below branches are bootstrap, symmetric resampling, and jacknife support from parsimony searches, respectively. Scale bar represents 10% nucleotide mutation rate.
Figure 1. - Mitotic metaphases, karyograms and idiogram of Euterpe species with 2n=36 chromosomes. Euterpeedulis (A–B), Euterpeoleracea (C-D) and Euterpeprecatoria (E–F). Arrows indicate secondary constrictions. Semi-reticulate interphase nuclei of Euterpeedulis (G), Euterpeoleracea (H) and Euterpeprecatoria (I). Bar: 10 µm.
Figure 1. - Mitotic metaphases, karyograms and idiogram of Euterpe species with 2n=36 chromosomes. Euterpeedulis (A–B), Euterpeoleracea (C-D) and Euterpeprecatoria (E–F). Arrows indicate secondary constrictions. Semi-reticulate interphase nuclei of Euterpeedulis (G), Euterpeoleracea (H) and Euterpeprecatoria (I). Bar: 10 µm.
Figure 11. - Fruits and galls produced by Epicephala species on Glochidionobovatum. A Fruit produced after pollination by Epicephalaobovatella (Tomogashima, Wakayama) B Gall induced on female flower by Epicephalacorruptrix (Takae, Okinawa) C Cross section of the gall induced by Epicephalacorruptrix. Arrow indicates the galled locule with feeding trace of Epicephala larva. Note that the irregularly developed ovules of the galled locule have merged indistinguishablly to septa. Scale bar 2 mm.
Figure 11. - Fruits and galls produced by Epicephala species on Glochidionobovatum. A Fruit produced after pollination by Epicephalaobovatella (Tomogashima, Wakayama) B Gall induced on female flower by Epicephalacorruptrix (Takae, Okinawa) C Cross section of the gall induced by Epicephalacorruptrix. Arrow indicates the galled locule with feeding trace of Epicephala larva. Note that the irregularly developed ovules of the galled locule have merged indistinguishablly to septa. Scale bar 2 mm.
Figure 7. - Section of the female proboscis of the Japanese Epicephala species. All photographs were taken from non-type specimens. A Epicephalaanthophilia (slide No. AK303) B Epicephalabipollenella (slide No. AK298) C Epicephalalanceolatella (slide No. AK300) D Epicephalaperplexa (slide No. AK301) E Epicephalaobovatella (slide No. AK307) F Epicephalacorruptrix (slide No. AK304) G Epicephalavitisidaea (slide No. AK297) H Epicephalaparasitica (slide No. AK308), arrows indicate rudimentary sensilla I Epicephalanudilingua (slide No. AK309). lp, labial palp. Scale bar: 0.1 mm.
Figure 7. - Section of the female proboscis of the Japanese Epicephala species. All photographs were taken from non-type specimens. A Epicephalaanthophilia (slide No. AK303) B Epicephalabipollenella (slide No. AK298) C Epicephalalanceolatella (slide No. AK300) D Epicephalaperplexa (slide No. AK301) E Epicephalaobovatella (slide No. AK307) F Epicephalacorruptrix (slide No. AK304) G Epicephalavitisidaea (slide No. AK297) H Epicephalaparasitica (slide No. AK308), arrows indicate rudimentary sensilla I Epicephalanudilingua (slide No. AK309). lp, labial palp. Scale bar: 0.1 mm.
Fig. 5 in Hrabeiella Periglandulata (Annelida: "Polychaeta") Do Apparent Differences In Chaetal Ultrastructure Indicate The Existence Of Several Species In Europe?
Fig. 5. Hrabeiellaperiglandulata – structureofchaetaewithfinefibresvisible (secondfixation
Fig. 1. Phylogenetic relationships of species of Eusurbus and Zentamyia. Tree generated from morpho- logical phylogenetic analysis, unambiguous apomorphies mapped on branches, black circles indicate non- homoplasious changes.
Fig. 1. Phylogenetic relationships of species of Eusurbus and Zentamyia. Tree generated from morpho- logical phylogenetic analysis, unambiguous apomorphies mapped on branches, black circles indicate non- homoplasious changes.
The data table of eleven invasive species in Hungary and Romania: Invasive species' cover, invasive species' traits, basic characteristics, trait composition, functional diversity indices and soil parameters of recipient plant communities
<p>We studied 11 widespread herbaceous invasive alien species of East-Central Europe and their 16 impact metrics (resident plant communities' ecological characteristics, trait composition, functional diversity, and soil parameters) by sampling invaded and similar, uninvaded sites (space-for-time substitution method). Our aim was to (1) investigate the detailed ecological impacts of invasive plants on native plant communities; (2) explore the type of cover-impact relationships across impact metrics and their consistency across species; (3) study whether the cover-impact relationship depends on functional traits of invasive species. We present the data table with the 11 invasive species: the status of the sites (invaded, uninvaded), the cover of invasive species at plot level, the invasive species traits (lifespan, height, SLA, seed mass, clonal spread, flowering duration), community characteristics (species richness and diversity, native vegetation cover and bare ground cover at plot level), trait composition of native plant communities (native vegetation height, CWM height, CWM SLA, CWM seed mass, CWM clonal spread), functional diversity (functional richness, functional evenness, functional divergence, functional distance, RaoQ) and soil properties (N, P, organic C, pH).</p>
Data from: Acoustic indices estimate breeding bird species richness with daily and seasonally variable effectiveness in lowland temperate Białowieża forest
<p><span>Biodiversity monitoring is important to follow temporal changes of the environment. We examined whether acoustic indices can be used as a rapid and easy-to-apply tool for bird biodiversity estimation in one of the least changed European lowland forests – the Białowieża Forest.</span></p> <p><span>We collected soundscape recordings in early and late spring at 84 randomly chosen recording points. At each recording point, we analysed 72 1-min sound samples to evaluate how well acoustic indices predict bird species richness from the perspective of a single sound sample, single survey, and recording point, and how they follow the daily pattern of singing activity. For each 1-min sound sample, we prepared a list of vocalizing bird species and calculated three acoustic indices: Bioacoustic Index (BI), Acoustic Complexity Index (ACI), and Acoustic Diversity Index (ADI)</span>.</p> <p><span>We found that from the perspective of a single 1-min sound sample, BI best predicts the bird species richness, independently of time in the season but variably across the day, while ACI and ADI showed weaker and seasonally and daily variable dependency. The correlation between each index and the number of bird species was stronger in the early survey than in the late survey. All acoustic indices followed daily bird activity patterns, yet they provided greater values before the peak of the species richness estimated by manual spectrogram scanning and listening to recordings.</span></p> <p><span>We showed that acoustic indices correlate moderately to strongly with the bird species richness obtained by manual spectrogram scanning and listening to recordings by humans. Therefore, acoustic indices can be used as a tool for rapid estimation of bird biodiversity in temperate forests. However, daily and seasonal variation in effectiveness of acoustic indices should be taken into account in the analysis.</span></p>
The species coalescent indicates possible bat and pangolin origins of the COVID-19 pandemic
<p>A consensus species tree is reconstructed from 11 gene trees for human, bat, and pangolin beta coronaviruses from samples taken early in the pandemic (prior to April 1, 2020). Using coalescent theory, the shallow (short branches relative to the hosts) consensus species tree provides evidence of recent gene flow events between bat and pangolin beta coronaviruses predating the zoonotic transfer to humans. The consensus species tree was also used to reconstruct the ancestral sequence of human SARS-CoV-2, which was 2 nucleotides different from the Wuhan sequence. The time to most recent common ancestor was estimated to be Dec 8, 2019, with a bat origin. Some human, bat, and pangolin coronavirus lineages found in China are phylogenetically distinct, a rare example of a class II phylogeography pattern (Avise et al. in Ann Rev Eco Syst 18:489–422, 1987). The consensus species tree is a product of evolutionary factors, providing evidence of repeated zoonotic transfers between bat and pangolin as a reservoir for future zoonotic transfers to humans.</p>
AQUAVITAE_Fish key performance indicators for diets from low-trophic species
<p>This dataset presents the key performance indicators from gilthead seabream (Sparus aurata) juveniles fed diets containing mussel meal.</p>
The species coalescent indicates possible bat and pangolin origins of the COVID-19 pandemic
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The data table of eleven invasive species in Hungary and Romania: Invasive species' cover, invasive species' traits, basic characteristics, trait composition, functional diversity indices and soil parameters of recipient plant communities
Open the record for dataset details and reuse information.
Data from: Acoustic indices estimate breeding bird species richness with daily and seasonally variable effectiveness in lowland temperate Białowieża forest
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Data package from: Mapping Atlantic rainforest degradation and regeneration history with indicator species using convolutional network
<p>This data package contains the very high resolution maps of natural forests as well as map of natural forests dominated by Cecropia hololeuca or Tibouchina pulchra presented in the Figure 8 of the paper "Mapping Atlantic rainforest degradation and regeneration history with indicator species using convolutional network". These maps have be produced with WorldView-2 and WorldView-3 very high resolution images and a deep learning method for image segmentation called U-net (methods and data are fully described in the article). When using this data, please cite the original article <a href="https://doi.org/10.1371/journal.pone.0229448">https://doi.org/10.1371/journal.pone.0229448</a>.</p> <p> </p>
Indicator Species Analysis Results
<p>Paper: Diversity and composition of fungal soil communities across prescribed burn areas in temperate hardwood forests</p> <p>Authors: S.D. Russell & M.C. Aime</p> <p>A spreadsheet containing the combined DESeq2 log2FoldChange and Random Forest MeanDecreaseAccuracy metrics for each OTU. Supplementary material for the paper above.</p>
Pairwise distance demarcation of species in the family Coronaviridae. a, Diagonal matrix of PPDs of 2,505 viruses clustered according to 49 coronavirus species, 39 established and 10 pending or tentative, and ordered from the most to least populous species, from left to right; green and white, PPDs smaller and larger than the inter-species threshold, respectively. Areas of the green squares along the diagonal are proportional to the virus sampling of the respective species, and virus prototypes of the five most sampled species are specified to the left; asterisks indicate species that include viruses whose intra-species PPDs crossed the inter-species threshold (threshold 'violators'). b, Maximal intra-species PPDs (x axis, linear scale) plotted against virus sampling (y axis, log scale) for 49 species (green dots) of the Coronaviridae. Indicated are the acronyms of virus prototypes of the seven most sampled species. Green and blue plot sections represent intra-species and intra-subgenera PPD ranges. The vertical black line indicates the inter-species threshold. c, Shown are the PDs of non-identical residues (y axis) for four viruses representing three major phylogenetic lineages (clades) of the species Severe acute respiratorysyndrome-related coronavirus (panel b) and all pairs of the 256 viruses of this species ('all pairs'). The PD values were derived from pairwise distances in the MSA that were calculated using an identity matrix. Panels a and b were adopted from the DEmARC v.1.4 output. in The species Severe acute respiratory syndromerelated coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2
Pairwise distance demarcation of species in the family Coronaviridae. a, Diagonal matrix of PPDs of 2,505 viruses clustered according to 49 coronavirus species, 39 established and 10 pending or tentative, and ordered from the most to least populous species, from left to right; green and white, PPDs smaller and larger than the inter-species threshold, respectively. Areas of the green squares along the diagonal are proportional to the virus sampling of the respective species, and virus prototypes of the five most sampled species are specified to the left; asterisks indicate species that include viruses whose intra-species PPDs crossed the inter-species threshold (threshold 'violators'). b, Maximal intra-species PPDs (x axis, linear scale) plotted against virus sampling (y axis, log scale) for 49 species (green dots) of the Coronaviridae. Indicated are the acronyms of virus prototypes of the seven most sampled species. Green and blue plot sections represent intra-species and intra-subgenera PPD ranges. The vertical black line indicates the inter-species threshold. c, Shown are the PDs of non-identical residues (y axis) for four viruses representing three major phylogenetic lineages (clades) of the species Severe acute respiratorysyndrome-related coronavirus (panel b) and all pairs of the 256 viruses of this species ('all pairs'). The PD values were derived from pairwise distances in the MSA that were calculated using an identity matrix. Panels a and b were adopted from the DEmARC v.1.4 output.
List of tissue specimens of Hipposideros spp. used for cytochrome b sequencing and phylogenetic inference, with geographical data. Voucher refers to the location and/or accession number of the voucher, and tissue collection refers to the collection where the tissue is kept, and accession or collector numbers. Acronyms are as follows: Estación Biológica de DoZana, Sevilla, Spain (EBD), South Australia Museum, Adelaide, Australia (SAM), Senckenberg Museum, Frankfurt am Main, Germany (SMF), Instituto de Ecología, Xalapa, México (IEX), Louisiana State University, Baton Rouge, Louisiana, USA (LSU), Charles M. Francis, Canadian Wildlife Service, Ottawa, Ontario, Canada (CMF), Lao Department of Forestry, Vientiane, Lao PDR, no catalogued (LAO). Next column indicates GenBank accession numbers. More information about the specimens is available in the GenBank records in A new species of bat of the Hipposideros bicolor group (Chiroptera: Hipposideridae) from Central Laos, with evidence of convergent evolution with Sundaic taxa
List of tissue specimens of Hipposideros spp. used for cytochrome b sequencing and phylogenetic inference, with geographical data. Voucher refers to the location and/or accession number of the voucher, and tissue collection refers to the collection where the tissue is kept, and accession or collector numbers. Acronyms are as follows: Estación Biológica de DoZana, Sevilla, Spain (EBD), South Australia Museum, Adelaide, Australia (SAM), Senckenberg Museum, Frankfurt am Main, Germany (SMF), Instituto de Ecología, Xalapa, México (IEX), Louisiana State University, Baton Rouge, Louisiana, USA (LSU), Charles M. Francis, Canadian Wildlife Service, Ottawa, Ontario, Canada (CMF), Lao Department of Forestry, Vientiane, Lao PDR, no catalogued (LAO). Next column indicates GenBank accession numbers. More information about the specimens is available in the GenBank records
Automated flow control of a multi-lane swimming chamber for small fishes indicates species-specific sensitivity to experimental protocols
<p>In fishes, swimming performance is considered an important metric to measure fitness, dispersal, and migratory abilities. Swimming performance of individual larval fishes is often integrated into models to make inferences on how environmental parameters affect population-level dynamics (e.g., connectivity). However, little information exists regarding how experimental protocols affect the swimming performance of marine fish larvae. In addition, the technical setups used to measure larval fish swimming performance often lack automation and accurate control of water quality parameters and flow velocity. In this study, we automated the control of multi-lane swimming chambers for small fishes by developing an open-source algorithm. This automation allowed us to execute repeatable flow scenarios and reduce operator interference and inaccuracies in flow velocity typically associated with manual control. Furthermore, we made structural modifications to a prior design to reduce areas of lower flow velocity. We then validated the flow dynamics of the new chambers using computational fluid dynamics and particle tracking software. The algorithm provided accurate alignment between set and measured flow velocities and we used it to test whether faster critical swimming speed (<i>U</i><sub>crit</sub>) protocols (i.e., shorter time intervals and higher velocity increments) would increase <i>U</i><sub>crit</sub> of early life stages of two tropical fish species (4-10 mm standard length). The <i>U</i><sub>crit</sub> of barramundi (<i>Lates calcarifer</i>) and cinnamon anemonefish (<i>Amphiprion melanopus</i>) increased linearly with fish length, but in cinnamon anemonefish, <i>U</i><sub>crit</sub> started to decrease upon metamorphosis. Swimming protocols using longer time intervals (>2.5 times increase) negatively affected <i>U</i><sub>crit</sub> in cinnamon anemonefish but not in barramundi. These species-specific differences in swimming performance highlight the importance of testing suitable <i>U</i><sub>crit</sub> protocols prior to experimentation. Automated control of flow velocity will create more accurate and repeatable data on swimming performance of larval fishes. Integrating refined measurements into individual-based models will support future research on the effects of environmental change.</p>
Most cultural importance indices do not predict species cultural keystone status
<p>The use of quantitative indices to quantify the importance of a plant species to human societies is widespread. While quantifi- cation may yield support for standardized methodologies and facilitate generalizations, it is important to examine the potential limitations of these indices. Moreover, because these indices are calculated at the species level, failure to control for phylogenetic relatedness in predictive models may yield misleading conclusions. We test if commonly used cultural importance indices predict species cultural keystone status among the Shipibo-Konibo community of Paoyhan in the Peruvian Amazon. Eleven of the 12 indices were correlated with each other indicating most cultural importance indices are redundant. Most indices did not predict species cultural keystone status. Phylogenetic control improved our models indicating a significant part of the predictive power of even the best index was explained by species shared evolutionary history. Our findings highlight the need for the cautious use of cultural importance indices to infer species cultural keystone status. Newly developed indices should be tested for correlation with existing indices to avoid redundancy.</p>
Data from: Landscape genetics informs mesohabitat preference and conservation priorities for a surrogate indicator species in a highly fragmented river system
Poor dispersal species represent conservative benchmarks for biodiversity management because they provide insights into ecological processes influenced by habitat fragmentation that are less evident in more dispersive organisms. Here we used the poorly dispersive and threatened river blackfish (Gadopsis marmoratus) as a surrogate indicator system for assessing the effects of fragmentation in highly modified river basins and for prioritizing basin-wide management strategies. We combined individual, population and landscape-based approaches to analyze genetic variation in samples spanning the distribution of the species in Australia's Murray–Darling Basin, one of the world's most degraded freshwater systems. Our results indicate that G. marmoratus displays the hallmark of severe habitat fragmentation with notably scattered, small and demographically isolated populations with very low genetic diversity—a pattern found not only between regions and catchments but also between streams within catchments. By using hierarchically nested population sampling and assessing relationships between genetic uniqueness and genetic diversity across populations, we developed a spatial management framework that includes the selection of populations in need of genetic rescue. Landscape genetics provided an environmental criterion to identify associations between landscape features and ecological processes. Our results further our understanding of the impact that habitat quality and quantity has on habitat specialists with similarly low dispersal. They should also have practical applications for prioritizing both large- and small-scale conservation management actions for organisms inhabiting highly fragmented ecosystems.
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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.