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5,864 results for “species diversity”
Lepidoptera species abundance: Trophic Structure: Insect Species Diversity, Abundance and Body Size
The goal of this study was to examine the populations of insects in prairies and savannas. Most of the prairies had developed after being abandoned from agriculture, but none of the savannas had been cultivated. The history of burning varied between sites. The main sampling for this study was conducted in 1992 by the lead investigators: John Haarstad, Evan Siemann, and David Tilman. Insects were sampled via sweep-net sampling, pitfalls and ant scent plates throughout the growing season in each of 49 grassland fields and savannas. In total, 89,596 individuals of 1,167 species were captured and enumerated. Body size was measured for a subset of grasshoppers collected. In 2004, John Haarstad conducted two similar studies by identifying and enumerating all insects collected in sweepnet samples taken in old fields (prairies) as part of E014 grasshopper studies and from sweepnet samples taken in savannas.
Miscellaneous inscet species abundance: Trophic Structure: Insect Species Diversity, Abundance and Body Size
The goal of this study was to examine the populations of insects in prairies and savannas. Most of the prairies had developed after being abandoned from agriculture, but none of the savannas had been cultivated. The history of burning varied between sites. The main sampling for this study was conducted in 1992 by the lead investigators: John Haarstad, Evan Siemann, and David Tilman. Insects were sampled via sweep-net sampling, pitfalls and ant scent plates throughout the growing season in each of 49 grassland fields and savannas. In total, 89,596 individuals of 1,167 species were captured and enumerated. Body size was measured for a subset of grasshoppers collected. In 2004, John Haarstad conducted two similar studies by identifying and enumerating all insects collected in sweepnet samples taken in old fields (prairies) as part of E014 grasshopper studies and from sweepnet samples taken in savannas.
Orthoptera species abundance: Trophic Structure: Insect Species Diversity, Abundance and Body Size
The goal of this study was to examine the populations of insects in prairies and savannas. Most of the prairies had developed after being abandoned from agriculture, but none of the savannas had been cultivated. The history of burning varied between sites. The main sampling for this study was conducted in 1992 by the lead investigators: John Haarstad, Evan Siemann, and David Tilman. Insects were sampled via sweep-net sampling, pitfalls and ant scent plates throughout the growing season in each of 49 grassland fields and savannas. In total, 89,596 individuals of 1,167 species were captured and enumerated. Body size was measured for a subset of grasshoppers collected. In 2004, John Haarstad conducted two similar studies by identifying and enumerating all insects collected in sweepnet samples taken in old fields (prairies) as part of E014 grasshopper studies and from sweepnet samples taken in savannas.
Formicidae species (ants) abundance: Trophic Structure: Insect Species Diversity, Abundance and Body Size
The goal of this study was to examine the populations of insects in prairies and savannas. Most of the prairies had developed after being abandoned from agriculture, but none of the savannas had been cultivated. The history of burning varied between sites. The main sampling for this study was conducted in 1992 by the lead investigators: John Haarstad, Evan Siemann, and David Tilman. Insects were sampled via sweep-net sampling, pitfalls and ant scent plates throughout the growing season in each of 49 grassland fields and savannas. In total, 89,596 individuals of 1,167 species were captured and enumerated. Body size was measured for a subset of grasshoppers collected. In 2004, John Haarstad conducted two similar studies by identifying and enumerating all insects collected in sweepnet samples taken in old fields (prairies) as part of E014 grasshopper studies and from sweepnet samples taken in savannas.
All Insect Savanna Sweepnet Sampling 2004:Trophic Structure: Insect Species Diversity, Abundance and Body Size
The goal of this study was to examine the populations of insects in prairies and savannas. Most of the prairies had developed after being abandoned from agriculture, but none of the savannas had been cultivated. The history of burning varied between sites. The main sampling for this study was conducted in 1992 by the lead investigators: John Haarstad, Evan Siemann, and David Tilman. Insects were sampled via sweep-net sampling, pitfalls and ant scent plates throughout the growing season in each of 49 grassland fields and savannas. In total, 89,596 individuals of 1,167 species were captured and enumerated. Body size was measured for a subset of grasshoppers collected. In 2004, John Haarstad conducted two similar studies by identifying and enumerating all insects collected in sweepnet samples taken in old fields (prairies) as part of E014 grasshopper studies and from sweepnet samples taken in savannas.
Old Field All Arthropod Sweepnet Sampling 2004 :Trophic Structure: Insect Species Diversity, Abundance and Body Size
The goal of this study was to examine the populations of insects in prairies and savannas. Most of the prairies had developed after being abandoned from agriculture, but none of the savannas had been cultivated. The history of burning varied between sites. The main sampling for this study was conducted in 1992 by the lead investigators: John Haarstad, Evan Siemann, and David Tilman. Insects were sampled via sweep-net sampling, pitfalls and ant scent plates throughout the growing season in each of 49 grassland fields and savannas. In total, 89,596 individuals of 1,167 species were captured and enumerated. Body size was measured for a subset of grasshoppers collected. In 2004, John Haarstad conducted two similar studies by identifying and enumerating all insects collected in sweepnet samples taken in old fields (prairies) as part of E014 grasshopper studies and from sweepnet samples taken in savannas.
Supplementary material 3 from: Gbedomon RC, Salako VK, Schlaepfer MA (2020) Diverse views among scientists on non-native species. NeoBiota 54: 49-69. https://doi.org/10.3897/neobiota.54.38741
Distribution of respondents across the clusters regarding their opinions on values associated to non-native species
Figure 1 in Diversity and species composition of Araneidaeı Tetragnathidae and Nephilidae in different levels of disturbed habitats in Trinidadı West Indies
Figure 1. Map of Trinidad showing the location of sampling localities of natural (∙) and disturbed (O) habitats.
FIGURE 1 in Uncovering a hidden diversity: a new species of freshwater shrimp Macrobrachium (Decapoda: Caridea: Palaemonidae) from Neotropical region (Brazil) revealed by morphological review and mitochondrial genes analyses
FIGURE 1. Characterization and location of the São Francisco river basin in Brazil. The red border indicates the location of Grande Sertão Veredas National Park and the distribution range of Macrobrachium veredensis sp. nov. Modified from MMA 2006 and ANA 2016.
Supplementary material 1 from: Oumarou Ngoute C, Kekeunou S, Lecoq M, Nzoko Fiemapong AR, Um Nyobe PCA, Bilong Bilong CF (2020) Effect of anthropogenic pressure on grasshopper (Orthoptera: Acridomorpha) species diversity in three forests in southern Cameroon. Journal of Orthoptera Research 29(1): 25-34. https://doi.org/10.3897/jor.29.33373
: Explanation note: Effect of anthropogenic pressures on floristic composition from the forests of three localities of southern Cameroon.
FIGURE 6. X in Unexpected species diversity within Sri Lanka's snakehead fishes of the Channa marulius group (Teleostei: Channidae)
FIGURE 6. X-radiographs of members of the Marulius group in Sri Lanka. A, Channa ara, 2020.02.01.NH, neotype, 300 mm SL, Angammedilla, Mahaweli River; B, C. marulius, DZ 4900, 350 mm SL, Rajanganaya, Kala Oya; C, C. cf. ara, DZ 4330, 230 mm SL, Lewwanduwa, Bentara River.
FIGURE 8 in Unexpected species diversity within Sri Lanka's snakehead fishes of the Channa marulius group (Teleostei: Channidae)
FIGURE 8. Colouration of Channa pseudomarulius. A, before preservation, ZRC 22869, 363 mm SL, South India, Chalakudy River, photo courtesy of Rohan Pethiyagoda; B, in preservation, WHT 30815, 217 mm SL, South India, Kerala, Alleppey.
Bioinformatic pipeline: Vast differences in strain-level diversity in the gut microbiota of two closely related honey bee species
<p>This data-set contains the full bioinformatic pipeline used to analyze metagenomic samples in the study "Vast differences in strain-level diversity in the gut microbiota of two closely related honey bee species" (Ellegaard et al. 2020, Current Biology). </p> <p>New metagenomic samples were generated for the study, for which the raw data is available on the NCBI Sequence Read Achive, under accession: PRJNA59809.</p> <p>The data of this submission consist of 9 tar-balls, as further described here below. Download and unpack to view the contents (tar -zxvf filename.tar.gz). For each tarball, all directories contain README.txt files, describing the contents of the directory. Due to size constraints, some intermediate files have been omitted, and some workflows are demonstrated for a subset of the data. However, the full analysis can be reproduced from the raw data, using the provided scripts.</p> <p>All scripts are included within the directories where they were applied. Perl-scripts contain documentation, which can be viewed by typing: "perl script_name.pl -h". For R scripts, the usage is indicated as a comment in the top lines of each script. Note that many of the scripts require specific input-files to be present in the run-directory. Their usage is demonstrated within the workflow directories in bash-scripts (*.sh). Commands used for generating plots and some statistics are given within workflow directories in text-files "R.commands" when applicable.</p> <p>Aside from custom code, the pipeline also utilizes various open-source Software packages, which are detailed in the file "software_dependencies.txt". Note, while many of the scripts will run fast on any computer, some steps of the pipeline are computationally demanding, and will require significant computing time, as well as storage space. When scripts are known to be time-consuming, this is indicated in the script help message.</p> <p>Description of tarballs.</p> <p>raw_data_processing.tar.gz: Describes the quality-control and trimming of raw data, and includes info on the sequencing run.</p> <p>databases.tar.gz: Contains all databases used for analysis, in addition to relevant meta-data.</p> <p>mapping_stats.tar.gz: Contains a file with the number of reads mapped to the honey bee gut microbiota database and the host genomes, for each sample. Bash-scripts are provided, detailing how the mapping was done and quantified.</p> <p>orthologs_phylogenies.tar.gz: Contains the pipeline for inferring orthologous gene-families and core genome phylogenies, as well as scripts for filtering of single-copy core gene families.</p> <p>assemblies.tar.gz: Contains the final de novo metagenome assembly files (contig fasta-files), gener<br> ated for both complete and rarefied read subsets. Bash-scripts detailing the assembly commands are also provided.</p> <p>SDP_validation.tar.gz: Contains the pipeline for metagenomic validation of candidate SDPs. Final output-files, containing the percentage identity of recruited metagenomic ORFs to database core genes, are provided for each candidate SDP. Additionally, a small example dataset is provided, where the intermediate result-files can be viewed.</p> <p>community_profiling.tar.gz: Contains the pipeline for community profiling, i.e. the quantification of individual community members (SDPs) across samples. Final output files are provided, including mapped read coverage on core gene families and corresponding plots. A small bam-file (containing data from a single subset sample), is also provided, in order to demonstrate the pipeline, together with all scripts used.</p> <p>snv_profiling.tar.gz: Contains the pipeline used for SNV profiling, including filtering and analysis. Final filtered vcf-files are provided for each SDP. Analytical output files are also provided, including data on shared SNV fractions, distance matrices, and cumulative curves.</p> <p>metagenomic_ORF_analyses.tar.gz: Contains the pipeline for analysis of metagenomic ORFs. This includes prediction of ORFs, clustering, annotation and functional characterization. ORF sequences, annotation files, and cluster-files are provided.</p>
FIGURE 8 in Accessing cryptic diversity in Neotropical rattlesnakes (Serpentes: Viperidae: Crotalus) with the description of two new species
FIGURE 8. Crotalus ehecatl in life, (A) ECO-CH-H 3778, holotype from San José Tintonishac, Las Margaritas, Chiapas; (B) adult specimen from Tuxtla Gutiérrez, Chiapas; (C) UTA-R 51456, adult male from Santa Inés, Santa María Chimalapa, Oaxaca; (D) neonate specimen from Santa María Mixtequilla, Oaxaca; (E) neonate specimen from San Pedro Tapanatepec, Oaxaca; (F) adult specimen from San Pedro Totolápam, Oaxaca. Photos by J.A. Hidalgo García (A), E.B. Jiménez Díaz (B), E.N. Smith courtesy of J.A. Campbell (C), I.T. Ahumada Carrillo (D), HERP.MX (E), and F. Martínez Belmar (F).
FIGURE 5 in Accessing cryptic diversity in Neotropical rattlesnakes (Serpentes: Viperidae: Crotalus) with the description of two new species
FIGURE 5. Dorsal and lateral view of the head of the holotype of Crotalus mictlantecuhtli (SDNHM 22416).
FIGURE 3 in Accessing cryptic diversity in Neotropical rattlesnakes (Serpentes: Viperidae: Crotalus) with the description of two new species
FIGURE 3. (A), Results of the principal component analyses between the members of the Crotalus durissus species complex with 95% confidence regions. PC1 and PC2 together explain 33.4% of the total variance. (B), Reanalysis including only members of norhten clade (Crotalus culminatus); (C), members of southern clade (Crotalus durissus) with morphological data available. (D), Bivariate plots with 95% confidence regions for the first two axes derived from scores of discriminant analyses for members of Crotalus durissus species complex.
FIGURE 1 in Accessing cryptic diversity in Neotropical rattlesnakes (Serpentes: Viperidae: Crotalus) with the description of two new species
FIGURE 1. (A) Maximum-likelihood phylogram of the four genes (cyt b, ND4, ND2, c-mos, 2596 bp) analysis (-ln L=- 17,270.83). Tip labels are as follows: 3-letter subspecies code for the Crotalus durissus species complex, following Campbell & Lamar (2004), locality and haplotypes in parentheses, see Appendix 1. Numbers along branches indicate bootstrap support-ML and Bayesian posterior probability. For clarity, support is only shown for important nodes. (B) Maximum-likelihood phylogram of the four genes (cyt b, ND4, ND2, c-mos, 2596 bp) analysis (-ln L=-17,270.83). Tip labels are as follows: 3-letter subspecies code for the Crotalus molossus species complex and outgroups, following Campbell & Lamar (2004) and Anderson & Greenbaum (2012), locality and haplotypes in parentheses, see Appendix 1. Numbers along branches indicate bootstrap support-ML and Bayesian posterior probability. For clarity, support is only shown for important nodes.
FIGURE 8. A in New species, diversity, systematics, and conservation assessment of the Puppet Toads of Sumatra (Anura: Bufonidae: Sigalegalephrynus)
FIGURE 8. A) Elevational distribution of Sigalgalephrynus species in Sumatra. B) Map showing probability of presence of Sigalegalephrynus species. C) Map showing suitable habitats of Sigalegalephrynus species (according to 10 percentile rule in MaxEnt).
FIGURE 7 in New species, diversity, systematics, and conservation assessment of the Puppet Toads of Sumatra (Anura: Bufonidae: Sigalegalephrynus)
FIGURE 7. Spectral graphs of known calls for species of Sigalegalephrynus, S. gayoluesensis sp. nov. (MZB.Amph.30411) and S. mandailinguensis (MZB.Amph.25736). Oscillograms (A and C, S. gayoluesensis sp. nov.; F and H, S. mandailinguensis); spectrograms (B and D, S. gayoluesensis sp. nov.; G and I, S. mandailinguensis); oscillograms of a single pulse within call (E, S. gayoluesensis sp. nov.; J, S. mandailinguensis).
FIGURE 6 in New species, diversity, systematics, and conservation assessment of the Puppet Toads of Sumatra (Anura: Bufonidae: Sigalegalephrynus)
FIGURE 6. Palmar and plantar surfaces of Sigalegalephrynus specimens in alcohol (Scale bar = 5 mm). Holotypes of Sigalegalephrynus burnitelongensis (A, MZB.Amph.30413), S. gayoluesensis sp. nov. (B, MZB.Amph.30411), S. mandailinguensis (C, MZB.Amph.25736), S. minangkabauensis (D, MZB.Amph.25738), and S. harveyi sp. nov. (E, MZB.Amph.30412).
ScienceDex guides
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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.