Find research datasets worth reusing

opencc-by-4.0Mar 2017View details →

Raw data used for COI delineation of the Eupolybothrus species: Authors: Stoev et al. 2013 Data type: genomic The archive contains the following data: 1) fasta-Alignment as the basis for all analyses (.FASTA), 2) mega-file for the calculation of the genetic distances and the NJ tree (.MDSX), 3) NJ-tree in Newick format (.NWK), 4) graph of the TCS Software for the Statistical Parsimony method (.GRAPH) File: E_cavernicolus.rar from: Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data - Biodiversity Data Journal 1: e1013 (28 October 2013) https://doi.org/10.3897/BDJ.1.e1013

Authors: Stoev et al. 2013 Data type: genomic The archive contains the following data: 1) fasta-Alignment as the basis for all analyses (.FASTA), 2) mega-file for the calculation of the genetic distances and the NJ tree (.MDSX), 3) NJ-tree in Newick format (.NWK), 4) graph of the TCS Software for the Statistical Parsimony method (.GRAPH) File: E_cavernicolus.rar

opencc-zeroDec 2023View details →

Atlas of Heritage Trees

Atlas of Heritage Trees This dataset is a collection of laser scanned heritage trees of exceptional historical, cultural, and ecological significance. The trees have been archived in laz, e57, pcd, ply, xyz, and 3dm format point clouds. The project was directed by <a href="https://baharmon.github.io/">Brendan Harmon</a> and <a href="https://hynam.org/">Hye Yeon Nam</a>. Contributors include Cecil Chapman, Carlos Roman, Jocelynne Crandall, Javier Zamora, Huan Guo, William Reinhardt, Julie Whitbeck, Kaiti Fink, and Jeff Boucher. This project was funded by an LSU Big Idea Grant and the LSU Arts & Humanities Support Fund. It was supported by the LSU Center for Computation and Technology, the LSU Center for GeoInformatics, and the LSU Coastal Ecosystem Design Studio. The point clouds are released under the <a href="https://creativecommons.org/share-your-work/public-domain/cc0/">Creative Commons Zero</a> public domain dedication. See the collection online at <a href="https://xyz.cct.lsu.edu/">xyz.cct.lsu.edu</a>. License This dataset is released under the <a href="https://creativecommons.org/publicdomain/zero/1.0/">Creative Commons Zero 1.0</a> Universal Public Domain Dedication by Brendan Harmon.

opencc-by-4.0Oct 2023View details →

TLS Z+F Imager 5010 point clouds of hybrid poplar trees from short-rotation crops after 5, 6, and 7 growing seasons

The point clouds are obtained from hybrid poplar crops installed in NE Romania, managed in short rotation (SRWCs) between 5, 6, and 7 growing seasons. The crops were planted every spring, outside the growing season, at a depth of 0.6 m in the ground with two clones: AF8 and Pannonia. Rods (2-meter-long cuttings) were used as planting material at a density of 1667 trees per ha (3 x 2 m). The scanning of the sample areas (3 x 10 trees for each variant, about 6 x 10 m) was outside the growing seasons.The 3D model was obtained using the Z+F Imager 5010 (Zoller and Fröhlich, Wangen, Germany), phase-shift type, providing a distance estimation accuracy of ±1 mm at 25 m and a nominal range of 187 m, and the tree individualization was done in CloudCompare v.2.12 (public license). A total of six station points and eight fixed targets or remarks (200 mm spheres) for co-registration were adopted for scanning. Trees included in the survey (without leaves) were marked with a ring of adhesive tape (black with yellow, 50 mm wide) at 1.4 m height on the tree spindle to adjust the results for calibration. Individually segmented trees can be sent on request, the database has a limit of 100 files. They can be converted into different formats via the CloudCompare application.File code: clone type _ number of growing seasons _ plot number

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Efficient genomics based 'end-to-end' selective tree breeding framework

Since their initiation in the 1950s, worldwide selective tree breeding programs followed the recurrent selection scheme of repeated cycles of selection, breeding (mating), and testing phases and essentially remained unchanged to accelerate this process or address environmental contingences and concerns. Here, we introduce an "end-to-end" selective tree breeding framework that: 1) leverages strategically preselected GWAS-based sequence data capturing trait architecture information, 2) generates unprecedented resolution of genealogical relationships among tested individuals, and 3) leads to the elimination of the breeding phase through the utilization of readily available wind-pollinated (OP) families. Individuals' breeding values generated from multi-trait multi-site analysis were also used in an optimum contribution selection protocol to effectively manage genetic gain/co-ancestry trade-offs and traits' correlated response to selection. The proof-of-concept study involved a 40-year-old spruce OP testing population growing on three sites in British Columbia, Canada, clearly demonstrating our method's superiority in capturing most of the available genetic gains in a substantially reduced timeline relative to the traditional approach. The proposed framework is expected to increase the efficiency of existing selective breeding programs, accelerate the start of new programs for ecologically and environmentally important tree species, and address climate-change caused biotic and abiotic stress concerns more effectively.

opencc-zeroDec 2022View details →

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Exaggerated mandibles are correlated with enhanced foraging efficacy in male Auckland tree wētā

Sexual selection has driven the evolution of weaponry for males to fight rivals to gain access to females. Although weapons are predicted to increase males' reproductive success, they are also expected to incur costs and may impair functional activities, including foraging. Using feeding assays, we tested whether the enlarged mandibles of Auckland tree wētā (Hemideina thoracica) impact feeding activity (the total volume of biomass consumed, bite rate, and number of foraging visits) and foraging behaviour (time spent moving, feeding, or stationary). We predicted that increased mandible length in male wētā would hinder their feeding rates. However, we found that wētā with longer heads fed at a faster rate and spent less time foraging than wētā with smaller heads, regardless of sex. Contrary to expectations that weapons impede functional activities, our results demonstrate that exaggerated traits can improve feeding performance and may offer benefits other than increased mating success.

opencc-zeroOct 2023View details →

Figure 2 in Cicada minimum age tree: Cryptic speciation and exponentially increasing base substitution rates in recent geologic time

Figure 2. Cicada timetree built by BEAST v1.X, applying 1,534 bp COI sequence. OUTs with isolate number: our own analyzed specimens shown in Table 1, and others: from GenBank/DDJB. In outgroup Hemiptera; #: analyzed family by Johnson et al. (2018); % analyzed family by Misof et al. (2014). Inserted figure: Base substitution rate (= rate median shown at each node; substitutions per site per million year; s/s/myr) vs age (= posterior age shown at each node) diagram. Red approximate curve with its formula was drawn by Excel function, with the intersection for the curve = 0.0128 s/s/myr, the rate median shown on Tracer.

Figure 4 in Cicada minimum age tree: Cryptic speciation and exponentially increasing base substitution rates in recent geologic time

Figure 4. Number of base changes of transition and tansversion vs corrected pairwide distance diagram for whole mitochondrial gene.

Figure 1 in Cicada minimum age tree: Cryptic speciation and exponentially increasing base substitution rates in recent geologic time

Figure 1. Simplified cicada timetree built by BEAST v1.X, applying a 1,534 bp in maximum COI sequence. Inserted figure: Base substitution rate (= ratemedian shown at each node; substitutions per siteper millionyear; s/s/ myr) vsage (= posterior age shown at each node) diagram. Red approximate curve with its formula was drawn by an Excel function, with the intersection for the curve = 0.0128 s/s/myr, the rate median shown on Tracer.

Figure 3 in Cicada minimum age tree: Cryptic speciation and exponentially increasing base substitution rates in recent geologic time

Figure 3. Cicada timetree built by BEAST v1.X, applying 1,534 bp COI and 874 bp 18S rRNA sequences. OUTswith isolate number: our own analyzed specimens shown in Table 1, and others: from GenBank/DDJB. In outgroup Hemiptera; #: analyzed family by Johnson et al. (2018); % analyzed family by Misof et al. (2014). Inserted figure: Base substitution rate (= rate median shown at each node; substitutions per site per million year; s/s/myr) vs age (= posterior age shown at each node) diagram. Red approximatecurve with its formulawas drawn by Excel function, with the intersection for the curve = 0.0114 s/s/myr, the rate median shown on Tracer. Note that this rate is a little slower than thatsolely of COI in Figures 1 and 2, reflecting slowerrate of 18S rRNAthan COI (see Osozawa et al. 2017a).

opencc-by-4.0Jun 2022View details →

Time trees and Clock genes: a Systematic Review and Comparative Analysis of Contemporary Avian Migration Genetics (Dataset)

Complete dataset of Clock and Adcyap1 alleles, distance matrices, and migration data used in the review and meta-analysis "Time trees and Clock genes: a Systematic Review and Comparative Analysis of Contemporary Avian Migration Genetics".

opencc-by-4.0Oct 2023View details →

Fig. 11. Bayesian inference trees. A. 16S rRNA dataset. B. Cytochrome oxidase I in Designation of a neotype for Myxicola infundibulum (Montagu, 1808) (Annelida: Sabellidae) and a new species from the UK

Fig. 11. Bayesian inference trees. A. 16S rRNA dataset. B. Cytochrome oxidase I gene dataset. The first value at each node represents maximum likelihood bootstrap support, the second the Bayesian posterior probabilities and the third the maximum parsimony bootstrap support.

opencc-by-4.0May 2011View details →

Fig. 2 in Characterization of leaf-rollers attacking forest and fruit trees in Azerbaijan (Lepidoptera: Tortricidae)

Fig. 2: Distribution of Tortrix viridana, Archips rosanus and Archips xylosteanus in different regions of Azerbaijan.

opencc-by-4.0Sep 2004View details →

Figure 2 in Occurrence of Quesada gigas on Schizolobium amazonicum trees in Maranhão and Pará States, Brazil

Figure 2. Exit holes of Quesada gigas (A), plants of Schizolobium amazonicum with symptoms of attack by this insect (B) and trap to capture nymphs (C).

opencc-by-4.0Nov 2023View details →

Low-frequency somatic mutations are heritable in tropical trees Dicorynia guianensis and Sextonia rubra

Somatic mutations potentially play a role in plant evolution, but common expectations pertaining to plant somatic mutation remain insufficiently tested. Unlike in most animals, the plant germline is assumed to be set aside late in development, leading to the expectation that plants accumulate somatic mutations along growth. Therefore, several predictions were made on the fate of somatic mutations: mutations have generally low frequency in plant tissues; mutations at high frequency have a higher chance of intergenerational transmission; branching topology of the tree dictates mutation distribution; and, exposure to UV radiation increases mutagenesis. To provide new insights into mutation accumulation and transmission in plants, we produced two high-quality reference genomes and a unique dataset of 60 high-coverage whole-genome sequences of two tropical tree species, Dicorynia guianensis (Fabaceae) and Sextonia rubra (Lauraceae). We identified 15,066 de novo somatic mutations in D. guianensis and  3,208 in S. rubra, surprisingly almost all found at low frequency. We demonstrate that: 1) low-frequency mutations can be transmitted to the next generation; 2) mutation phylogenies deviate from the branching topology of the tree; and 3) mutation rates and mutation spectra are not demonstrably affected by differences in UV exposure. Altogether, our results suggest far more complex links between plant growth, ageing, UV exposure, and mutation rates than commonly thought.

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Data for: Speciation in kleptoparasites of oak gall wasps often correlates with shifts into new tree habitats, tree organs, or gall morphospace

Host shifts to new plants can drive speciation for plant-feeding insects, but how commonly do host shifts also drive diversification for the parasites of those same insects? Oak gall wasps induce galls on oak trees, and shifts to novel tree hosts and new tree organs have been implicated as drivers of oak gall wasp speciation. Gall wasps are themselves attacked by many insect parasites, which must find their hosts on the correct tree species and organ, but which also must navigate the morphologically variable galls with which they interact. Thus, we ask whether host shifts to new trees, organs, or gall morphologies correlate with gall parasite diversification. We delimit species and infer phylogenies for two genera of gall kleptoparasites, Synergus and Ceroptres, reared from a variety of North American oak galls. We find that most species were reared from galls induced by just one gall wasp species, and no parasite species was reared from galls of more than four species. Most kleptoparasite divergence events correlate with shifts to non-ancestral galls. These shifts often involved changes in tree habitat, gall location, and gall morphology. Host shifts are thus implicated in driving diversification for both oak gall wasps and their kleptoparasitic associates.

opencc-zeroNov 2023View details →

Fig. 5 in Bird Diversity Differs Between Industrial Tree Plantations On Borneo: Implications For Conservation Planning

Fig. 5. Nonlinear multidimensional scaling of bird survey data pooled by point-transect. Vectors represent correlations between the ordination and habitat variables. Vectors and Pearson correlation coefficients are plotted for habitat variables with an r2> 0.200 for axis 1.

Fig. 4 in Bird Diversity Differs Between Industrial Tree Plantations On Borneo: Implications For Conservation Planning

Fig. 4. Plots of (A) species and (B) individual rates (from Fig. 1) versus number of species listed by www.birdlife.org (Table 1) per habitat type.

Fig. 1 in Bird Diversity Differs Between Industrial Tree Plantations On Borneo: Implications For Conservation Planning

Fig. 1. Map of forest occurrence in Borneo in 2005 (WWF-Malaysia, 2005) showing the localities of the Sarawak Planted Forest Project and Sabah Softwoods plantation.

Fig. 2. Bayesian consensus tree generated from partial 28S in Relationships Of The Heteronchocleidids (Heteronchocleidus, Eutrianchoratus And Trianchoratus) As Inferred From Ribosomal Dna Nucleotide Sequence Data

Fig. 2. Bayesian consensus tree generated from partial 28S rDNA sequences (D1 domain) with Diplectanum spp. and Gyrodactylus spp. as outgroups. Values shown at each node refer to Bayesian (BI) posterior probabilities/maximum likelihood (ML) percentages of the bootstrap values with 100 replicates. Bootstrap values lower than 50 are given as dashes (-).