Find research datasets worth reusing

opennotspecifiedOct 2024View details →

FIGURE 3. Species Richness per Ecoregion. The richness data per ecoregion were categorized into classes with equal intervals, using 14 in Revealing the Baja California Peninsula's Hidden Treasures: An Annotated checklist of the native bees (Hymenoptera: Apoidea: Anthophila)

FIGURE 3. Species Richness per Ecoregion. The richness data per ecoregion were categorized into classes with equal intervals, using 14 breaks. However, the map displays only the eight categories where ecoregional richness is concentrated. Ecoregion: Coastal Sage Matorral (CSM); Chaparral (Ch); Baja California Mountains (BCM); Succulent Coastal Matorral (SCM); Lower Colorado Desert (LCD); Central Desert (CD); Vizcaíno Desert (VD); Gulf Coast (GC); La Giganta Ranges (GR); Magdalena Plains (MP); Tropical Dry Forest (TDF); Cape Mountains (CM); Sarcocaulescent Shrubland (SS).

opencc-by-4.0Oct 2024View details →

Samples and 4-class predictions of agroforest-forest frontiers mapping in Peru

This is a database for the study of agroforest-forest frontiers mapping conducted by Wanting Yang, etc. The data contained in the repository includes two parts. 1. the training samples(polygons and rectagle_roi) annotated with Google Earth as reference. We used Google Earth Pro to make the date of Google Earth imagery match with PlanetScope imagery. 2. the prediction from the 4-class model. Users can visualize the data with QGIS or other GIS software.

opencc-by-4.0Sep 2023View details →

Data and code for: Re-drawing Köppen-Geiger classes with microclimate: implications for nature and society

Data and R code for reproducing analyses and visualizations for the paper: Klinges, D.H., Maclean, I.M.D., Scheffers, B.R. Re-drawing Köppen-Geiger classes with microclimate: implications for nature and society. Frontiers in Ecology and the Environment 2024 (in press)

opencc-by-4.0Nov 2024View details →

Observations and Modeling Investigations of Ionospheric Response to April 23-24, 2023, G4-Class Geomagnetic Storm over Indian Sector

This study explores the ionospheric response over the Indian sector to the G4-class geomagnetic storm of April 23-24, 2023. Utilizing multi-instrument observations and SAMI2 modeling, ionospheric behavior was examined during the storm's main phase (17:41 UT, April 23 - 04:03 UT, April 24) and the recovery phase (04:03 UT - 22:44 UT, April 24). During the main phase, ionosonde data from Tirunelveli showed rapid F-layer height (h’F) variations driven by westward and eastward prompt penetration electric fields (PPEFs). The westward PPEF, induced by undershielding, led to an initial decrease in h’F followed by an increase, suppressing pre-existing Equatorial Plasma Bubbles (EPBs) within two hours of the storm’s onset. Despite a late-night rise in h’F due to overshielding, no new EPB formed. The recovery phase exhibited a positive storm effect at low latitudes and a negative effect at higher latitudes, linked to disturbance dynamo electric fields (DDEFs) and thermospheric composition changes (O/N₂). Isofrequency analysis of CADI ionosonde and GNSS TEC data revealed large-scale traveling ionospheric disturbances (LSTIDs) with a ~2-hour period, ~2,450 km wavelengths, and ~340 m/s equatorward propagation speed. These LSTIDs were likely driven by atmospheric gravity waves or auroral heating. The westward DDEF suppressed the equatorial ionization anomaly (EIA) and inhibited post-sunset EPBs, while eastward DDEF increased h’F post-midnight without EPB formation. We speculate this absence might be due to a lack of seeding mechanisms. SAMI2 simulations incorporating E×B drift data reproduced several storm-time features in the main and recovery phases.

opencc-zeroDec 2017View details →

Data from: What determines prey selection in owls? Roles of prey traits, prey class, environmental variables, and taxonomic specialization

Ecological theory suggests that prey size should increase with predator size, but this trend may be masked by other factors affecting prey selection, such as environmental constraints or specific prey preferences of predator species. Owls are an ideal case study for exploring how predator body size affects prey selection in the presence of other factors due to the ease of analyzing their diets from owl pellets and their widespread distributions, allowing interspecific comparisons between variable habitats. Here, we analyze various dimensions of prey resource selection among owls, including prey size, taxonomy (i.e., whether or not particular taxa are favored regardless of their size), and prey traits (movement type, social structure, activity pattern, and diet). We collected pellets of five sympatric owl species (Athene noctua, Tyto alba, Asio otus, Strix aluco, and Bubo bubo) from 78 sites across the Mediterranean Levant. Prey intake was compared between sites, with various environmental variables and owl species as predictors of abundance. Despite significant environmental impacts on prey intake, some key patterns emerge among owl species studied. Owls select prey by predator body size: Larger owls tend to feed on wider ranges of prey sizes, leading to higher means. In addition, guild members show both specialization and generalism in terms of prey taxa, sometimes in contrast with the expectations of the predator–prey body size hypothesis. Our results suggest that while predator body size is an important factor in prey selection, taxon specialization by predator species also has considerable impact.

opencc-zeroDec 2013View details →

Data from: MHC class II diversity of koala (Phascolarctos cinereus) populations across their range

Major histocompatibility complex class II (MHCII) genes code for proteins that bind and present antigenic peptides and trigger the adaptive immune response. We present a broad geographical study of MHCII DA β1 (DAB) and DB β1 (DBB) variants of the koala (Phascolarctos cinereus; n=191) from 12 populations across eastern Australia, with a total of 13 DAB and 7 DBB variants found. We identified greater MHCII variation and, possibly, additional gene copies in koala populations in the north (Queensland and New South Wales) relative to the south (Victoria), confirmed by STRUCTURE analyses and genetic differentiation using analysis of molecular variance. The higher MHCII diversity in the north relative to south could potentially be attributed to (i) significant founder effect in Victorian populations linked to historical translocation of bottlenecked koala populations and (ii) increased pathogen-driven balancing selection and/or local genetic drift in the north. Low MHCII genetic diversity in koalas from the south could reduce their potential response to disease, although the three DAB variants found in the south had substantial sequence divergence between variants. This study assessing MHCII diversity in the koala with historical translocations in some populations contributes to understanding the effects of population translocations on functional genetic diversity.

opennotspecifiedJun 2021View details →

FIGURE 1 in Observation on the morphological and gonadal aspects of Cladonema radiatum (Class: Hydrozoa) from Tuticorin Bay, Southeast coast of India

FIGURE 1: Morphological and gonadal features of C. radiatum from the Gulf of Mannar, Southeast coast of India; A & B indicates the aboral view and C, D, E & F indicate the lateral view.

opencc-zeroDec 2014View details →

Data from: An exon-capture system for the entire class Ophiuroidea

Exon-capture studies have typically been restricted to relatively shallow phylogenetic scales due primarily to hybridisation constraints. Here, we present an exon-capture system for an entire class of marine invertebrates, the Ophiuroidea, built upon a phylogenetically diverse transcriptome foundation. The system captures ~90% of the 1552 exon target, across all major lineages of the quarter-billion year old extant crown group. Key features of our system are: 1) basing the target on an alignment of orthologous genes determined from 52 transcriptomes spanning the phylogenetic diversity and trimmed to remove anything difficult to capture, map or align, 2) use of multiple artificial representatives based on ancestral state reconstructions rather than exemplars to improve capture and mapping of the target, 3) mapping reads to a multi-reference alignment, and 4) using patterns of site polymorphism to distinguish among paralogy, polyploidy, allelic differences and sample contamination. The resulting data gives a well-resolved tree (currently standing at 417 samples, 275,352 sites, 91% data-complete) that will transform our understanding of ophiuroid evolution and biogeography.

openodc-byJul 2021View details →

UML class diagrams for layout quality checking

We offer a dataset of labelled UML class diagrams. In this dataset, we supply for every diagrams the following information: 1) a manually established ground truth of the quality of the layout, 2) a value for the layout-quality of the diagram as predicted by our classifier, and 3) the values of key features of the layout of the diagram. These features are extracted automatically via image processing. This dataset can be used for replication of our study and for others to build on and improve on our work.

opencc-zeroDec 2017View details →

Data from: Similar hybrid composition among different age and sex classes in the Myrtle–Audubon's warbler hybrid zone

Hybrid zones provide a key natural context within which to study the barriers between incipient species. In some avian hybrid zones, there is indirect evidence of selection against hybrid offspring, yet the source of that selection is often unclear. We examined the frequency distribution of hybrids between Myrtle Warblers (Setophaga coronata coronata) and Audubon's Warblers (S. c. auduboni), using data to quantify—for the first time at a genomic scale—the composition of hybrids in this hybrid zone. We sampled birds during the breeding season and during fall migration and compared the frequencies of hybrids of different sex and age classes. Specifically, we tested for evidence of early-generation hybrids being significantly under- or over-represented in any of these classes, as would be expected if hybrids have lower or higher fitness than non-hybrids. We found that the genomic composition of birds in the hybrid zone spans the full ancestry spectrum. Across all our sampling periods, we found an excess of birds that had more Audubon's ancestry, with a stronger bias toward Audubon's ancestry in fall migrants than in breeding birds, consistent with asymmetric introgression. Notably, we did not find any differences in hybrid frequencies between juvenile and adult age classes or between males and females. Therefore, our results do not support large differences in viability between male and female hybrids or between different age classes of hybrids.

opencc-zeroJun 2022View details →

Annual mortality and growth index for 17 tree species across entire size classes in the Ogawa Forest Reserve, an old-growth deciduous forest, central Japan

We estimated demographic parameters across entire size classes for 17 tree species (Betula, Carpinus, Fagus, Quercus, Castanea, Acer, Cerasus, Swida, Kalopanax, and Styrax) using a dataset over 18 years obtained from the Ogawa Forest Reserve, an old-growth deciduous forest located in the southern part of the Abukuma Mountains, Ibaraki Prefecture, central Japan (36° 56', 140° 35', 610 m in elevation) 1). Size classes were represented by 12 categories defined based on age, height, and diameter at breast height (DBH): new seedling (age < 1), aged seedling (age ≥ 1 and height < 30 cm), sapling (height 30 cm to 2 m), juvenile (height ≥ 2 m and DBH < 5 cm), D10 (DBH 5–15 cm, D10 was denoted by the midpoint of this range; later classes were similarly defined), D20, D30, D40, D50, D60, D70, and D80 (including trees with DBH ≥ 85 cm). We derived the annual mortality and growth index (i.e., the probability of a living tree transitioning to the next size class) for each species and size class using estimates of transition probabilities between size classes (i.e., stasis, progression and retrogression)2). The stem densities of these 17 species in each size class are also presented3). File list 1) dataset - number of trees stagnating, progressing and retrogressing by size class.csv 2) estimates - mean and 95 percent credible intervals of demographic parameters by species and size class.csv 3) estimates - mean density of stems by species and size class.csv

opennotspecifiedJan 2009View details →

Figure 1 in Major histocompatibility complex Class II DRB exon-2 diversity of the Eurasian lynx (Lynx lynx) in China

Figure 1. Neighbour-joining tree of the 13 Eurasian lynx DRB nucleotide sequences. Distance was based on Kimura's two-parameter distance. The bootstrap values (percentage of 1000 replicates) supporting particular clusters are shown next to the node. Scale bar represents substitutions per site.

FIGURES 53–58. Representative valves from size class 2 in Climate-related morphological changes in Pantocsekiella (Mediophyceae) spanning 0-1.2 Ma in the Lake El'gygytgyn, northeastern Russia including Pantocsekiella elgygytgynensis sp. nov.

FIGURES 53–58. Representative valves from size class 2 (5–10 µm) and size class 3 (10–15 µm). Fig. 53) size class 2 external valve from 1.029 Ma (DC1600)showing flat valve face and large central area with many fovi, Fig. 54) size class 2 external valve 1126 ka (DC1750) with dissolution, Fig. 55) size class 3 external valve from 1.3 ka (LZ31) showing four depressions with small central area, Fig. 56) size class 3 external valve 70.2 ka (LZ688) showing five depressions, Fig. 57) size class 3 external valve 198.2 ka (LZ9-155) with flat valve face, granules, and scattered central fultoportulae, Fig. 58) size class 3 internal valve 214.2 ka (LZ10-65) showing scattered central fultoportulae.

FIGURES 47–52. Representative external valves from size class 2 in Climate-related morphological changes in Pantocsekiella (Mediophyceae) spanning 0-1.2 Ma in the Lake El'gygytgyn, northeastern Russia including Pantocsekiella elgygytgynensis sp. nov.

FIGURES 47–52. Representative external valves from size class 2 (5–10 µm). Fig. 47) Valve from 0.075 ka (LZ23) showing one central fultoportula (cf) and flat valve face with four depressions, Fig. 48) Valve from 29.12 ka (LZ491) showing flat valve face with three depressions, Fig. 49) Valve from 190.5 ka (LZ9-138) showing flat valve face with numerous fovi, Fig. 50) Valve from 198.2 ka (LZ9-155) showing flat valve face with five scattered central fultoportulae (cf), Fig 51) Valve of P. elgygytgynensis from 238.5 ka (LZ10-227), Fig. 52) Valve of P. elgygytgynensis from 417.4 ka (DC570) with white circles highlighting the clusters of central fultoportulae within the large depressions.

FIGURES 59–64. Representative valves from size class 3 in Climate-related morphological changes in Pantocsekiella (Mediophyceae) spanning 0-1.2 Ma in the Lake El'gygytgyn, northeastern Russia including Pantocsekiella elgygytgynensis sp. nov.

FIGURES 59–64. Representative valves from size class 3 (10–15 µm). Fig. 59) external valve of P. elgygytgynensis from 278.8 ka (LZ11- 125), Fig. 60) external valve of P. elgygytgynensis from 333.2 ka (LZ12-176), Fig. 61) external valve of P. elgygytgynensis from 484.1 ka (DC680), Fig. 62) external valve of P. elgygytgynensis from 406.7 ka (DC550), Fig. 63) internal valve of P. elgygytgynensis from 406.7 ka (DC550), Fig. 64) internal valve of P. elgygytgynensis from 302.5 ka (LZ12-54).

FIGURES 41–46. Representative external valves from size class 1 in Climate-related morphological changes in Pantocsekiella (Mediophyceae) spanning 0-1.2 Ma in the Lake El'gygytgyn, northeastern Russia including Pantocsekiella elgygytgynensis sp. nov.

FIGURES 41–46. Representative external valves from size class 1 (3–5 µm). Fig. 41) Valve from 1.029 Ma (DC1600) showing numerous fovi and two central fultoportulae (cf), Fig. 42) Valve from 952.6 ka (DC1480) showing the rimoportula placement, Fig. 43) Valve of P. elgygytgynensis from 406.7 ka (DC550) showing the rimoportula placement,, Fig. 44) Valve of P. elgygytgynensis from 302.5 ka (LZ12- 54) showing three depressions and three central fultoportulae, Fig. 45) Valve from 119.3 ka (LZ6-60) showing less distinct depressions, and Fig. 46) Valve from 8.28 ka (LZ366) showing P. ocellata morphology.

opencc-zeroSep 2021View details →

Coarse woody debris density and carbon concentration by decay classes in mixed montane wet tropical forests (Dataset)

This dataset contains data from a study considering the relationship between decay class, wood density and C content of CWD in old-growth mixed monsoon montane tropical forests in Vietnam based on the inventory of 359 CWD pieces. The CWD inventories were conducted on forty one (3-4 per site) 50 m long and 4 m wide transects. The first dataset for contains site description, plot and transect numbers with geographical coordinates. All CWD pieces of more than 6 cm in diameter were inventoried. The dataset contains position of CWD: stumps, standing dead trees (snags), lying logs, leaning logs and branches, diameter, proportion consumed by termites, decay class, bulk density and moisture of wood and mass loss. The second dataset contains the data on the wood density of tree species present in the study area according to the global database compiled by Zanne et al. (2009).

opencc-zeroSep 2021View details →

Phytochemistry reflects different evolutionary history in traditional classes versus specialized structural motifs

Foundational hypotheses addressing plant-insect codiversification and plant defense theory typically assume a macroevolutionary pattern whereby closely related plants have similar chemical profiles. However, numerous studies have documented variation in the degree of phytochemical trait lability, raising the possibility that phytochemical evolution is more nuanced than initially assumed. We utilize proton nuclear magnetic resonance (1H NMR) data, chemical classification, and double digest restriction-site associated DNA sequencing (ddRADseq) to resolve evolutionary relationships and characterize the evolution of secondary chemistry in the Neotropical plant clade Radula (Piper; Piperaceae). Sequencing data substantially improved phylogenetic resolution relative to past studies, and spectroscopic characterization revealed the presence of 35 metabolite classes. Metabolite classes displayed phylogenetic signal, whereas the crude 1H NMR spectra featured little evidence of phylogenetic signal in multivariate tests of chemical resonances. Evolutionary correlations were detected in two pairs of compound classes (flavonoids with chalcones; p-alkenyl phenols with kavalactones), where the gain or loss of a class was dependent on the other's state. Overall, the evolution of secondary chemistry in Radula is characterized by strong phylogenetic signal of traditional compound classes and weak phylogenetic signal of specialized chemical motifs, consistent with both classic evolutionary hypotheses and recent examinations of phytochemical evolution in young lineages.

opencc-zeroOct 2021View details →

16S V4 raw read count data; 16S reads metadata; new MHC class II allele sequences

Pathogen-mediated selection at the major histocompatibility complex (MHC) is thought to promote MHC-based mate choice in vertebrates. Mounting evidence implicates odour in conveying MHC genotype, but the underlying mechanisms remain uncertain. MHC effects on odour may be mediated by odour-producing symbiotic microbes whose community structure is shaped by MHC genotype. In birds, preen oil is the primary source of body odour and similarity at MHC predicts similarity in preen oil composition. Hypothesizing that this relationship is mediated by symbiotic microbes, we characterized MHC genotype, preen gland microbial communities, and preen oil chemistry of song sparrows (Melospiza melodia). Consistent with the microbial mediation hypothesis, pairwise similarity at MHC predicted similarity in preen gland microbiota. Overall microbial similarity did not predict chemical similarity of preen oil, counter to this hypothesis. However, permutation testing identified a maximally predictive set of microbial taxa that best reflect MHC genotype, and another set of taxa that best predict preen oil chemical composition. The relative strengths of relationships between MHC and microbes, microbes and preen oil, and MHC and preen oil suggest that MHC may affect host odour both directly and indirectly. Thus, birds may assess MHC genotypes based on both host-associated and microbially-mediated odours.