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Comparative analyses of the Hymenoscyphus fraxineus and Hymenoscyphus albidus genomes reveals potentially adaptive differences in secondary metabolite and transposable element repertoires
<p><strong>Background </strong>The dieback epidemic decimating common ash (<em>Fraxinus excelsior</em>) in Europe is caused by the invasive fungus <em>Hymenoscyphus fraxineus</em>. In this study we analyzed the genomes of <em>H. fraxineus</em> and <em>H. albidus</em>, its native but, now essentially displaced, non-pathogenic sister species, and compared them with several other members of <em>Helotiales</em>. The focus of the analyses was to identify signals in the genome that may explain the rapid establishment of <em>H. fraxineus</em> and displacement of <em>H. albidus</em>.</p> <p><strong>Results</strong> The genomes of <em>H. fraxineus</em> and <em>H. albidus </em>showed a high level of synteny and identity. The assembly of <em>H. fraxineus </em>is 13 Mb longer than that of <em>H. albidus’, </em>most of this difference can be attributed to higher dispersed repeat content ((i.e transposable elements [TEs]) in <em>H. fraxineus</em>. In general, TE families in <em>H. fraxineus</em>showed more signals of repeat-induced point mutations (RIP) than in <em>H. albidus</em>, especially in Long-terminal repeat (LTR)/Copia and LTR/Gypsy elements. Comparing gene family expansions and 1:1 orthologs, relatively few genes show signs of positive selection between species. However, several of those that did appeared to be associated with secondary metabolite genes families, including gene families containing two of the genes in the <em>H. fraxineus-</em>specific, <em>hymenosetin </em>biosynthetic gene cluster (BGC).</p> <p><strong>C</strong><strong>onclusion </strong>The genomes of <em>H. fraxineus</em> and <em>H. albidus</em> show a high degree of synteny, and are rich in both TEs and BGCs, but the genomic signatures also indicated that <em>H. albidus</em> may be less well equipped to adapt and maintain its ecological niche in a rapidly changing environment. </p> <p><strong>Data included</strong></p> <p>This post contains the alternate structural and functional annotations of the genomes of Helotealean fungi used in the study.</p>
Data in the analysis of Comparative Study of the Impact of Dummy Variables on Regression Coefficients and Canonical Correlation Indices: an Empirical perspective
<p>This data is used in the analysis related to the article Comparative Study of the Impact of Dummy Variables on Regression Coefficients and Canonical Correlation Indices: an Empirical perspective. The data contain Crude Oil Prices, Exchange Rates, and Dummy variables coded 1 for the era before the Covid-19 outbreak and 0 for the era of Covid-19.</p> <p> </p>
Convolutional Neural Network Formulation to Compare 4D Seismic and Reservoir Simulation Models
<p>This dataset contains the .npy (numpy) files of the simulation models and reference discussed in the paper "Convolutional Neural Network Formulation to Compare 4D Seismic and Reservoir Simulation Models".</p> <p>The folders contain all simulation models and reference maps already divided in subregions. Each .npy file is a numpy 2D array with delta IP or delta Sw values. The csv files contain the 3-tuples and the selected model in each.</p> <p>There are two csv files: the first is the dataset used for training the CNN, with 1280 labeled tuples evaluated by a single specialist. The second is the ground-truth, with 164 tuples evaluated by three specialists (in which 2 or more agreed on the selected model), used for validating the models and comparing different approaches.</p> <p>We also provide a Python code to read and visualize the .npy files.</p>
The complete genome sequence and comparative genomic analyses of four phages (NJ-P3, NB-P21, NC-P34 and NN-P42)
<p>We downloaded and reanalyzed the raw data of four phages genomes (NJ-P3, NB-P21, NC-P34, NN-P42). This is the reassembled whole genomes and comparative genomic analyses of four phages.</p>
A preliminary field trial to compare control techniques for invasive Berberis aquifolium in Belgian coastal dunes
Non-native Berberis aquifolium is notoriously invasive in Belgian coastal dunes. With its strong clonal growth through suckers, this evergreen shrub outcompetes native species and affects dune succession. To prevent further secondary spread and mitigate its impact, there was an urgent need for knowledge on the effectiveness of control measures, both at the plant and habitat level. Here, we report on a first control experiment. Individual B. aquifolium clones were subjected to one of four treatments (manual uprooting, foliar herbicide application, stem cutting followed by herbicide or salt application), with regrowth being measured up to one year after treatment. Plants proved most susceptible to foliar herbicide application (5% glyphosate solution), resulting in 77% of the clones apparently killed. We discuss the limitations of our experiment and the potential for actual field application of the different treatments. We present some guidelines for future control that may become further refined as experience builds up.
Data from: A phylogenomic framework, evolutionary timeline and genomic resources for comparative studies of decapod crustaceans
Comprising over 15 000 living species, decapods (crabs, shrimp and lobsters) are the most instantly recognizable crustaceans, representing a considerable global food source. Although decapod systematics have received much study, limitations of morphological and Sanger sequence data have yet to produce a consensus for higher-level relationships. Here, we introduce a new anchored hybrid enrichment kit for decapod phylogenetics designed from genomic and transcriptomic sequences that we used to capture new high-throughput sequence data from 94 species, including 58 of 179 extant decapod families, and 11 of 12 major lineages. The enrichment kit yields 410 loci (greater than 86 000 bp) conserved across all lineages of Decapoda, more clade-specific molecular data than any prior study. Phylogenomic analyses recover a robust decapod tree of life strongly supporting the monophyly of all infraorders, and monophyly of each of the reptant, 'lobster' and 'crab' groups, with some results supporting pleocyemate monophyly. We show that crown decapods diverged in the Late Ordovician and most crown lineages diverged in the Triassic–Jurassic, highlighting a cryptic Palaeozoic history, and post-extinction diversification. New insights into decapod relationships provide a phylogenomic window into morphology and behaviour, and a basis to rapidly and cheaply expand sampling in this economically and ecologically significant invertebrate clade.
Methodology matters for comparing coarse wood and bark decay rates across tree species
<p>1. The importance of wood decay for the global carbon and nutrient cycles is widely recognized. However, relatively little is known about bark decay dynamics, even though bark represents up to 25% of stem dry mass. Moreover, bark presence versus absence can significantly alter wood decay rates. Therefore, it really matters for the fate of carbon whether variation in bark and wood decay rates is coordinated across tree species.</p> <p>2. Answering this question requires advances in methodology to measure both bark and wood mass loss accurately. Decay rates of large logs in the field are often quantified as loss in tissue density, in which case volume depletions of bark and wood can give large underestimations.</p> <p>3. To quantify the real decay rates, we assessed bark mass loss per stem surface area and wood mass loss based on volume-corrected density loss. We further defined the range of actual bark mass loss by considering bark cover loss. Then, we tested the correlation between bark and wood mass loss across 20 temperate tree species during 4 years of decomposition.</p> <p>4. The area-based method generally showed more than 3-fold higher bark mass loss than the density-based method (even higher if considering bark cover loss), and volume-corrected wood mass losses were 1.08-1.12 times higher than density-based mass loss. The deviation of bark mass loss between the two methods was higher for tree species with thicker inner bark. Bark generally decomposed twice as fast as wood across species, and faster decaying bark came with faster decaying wood (R2=0.26, P=0.006).</p> <p>5. We strongly suggest using corrected volume when assessing wood mass loss especially for the species with faster decomposable sapwood and all the wood at advanced decay stages. Further studies of coarse stem decomposition should consider trait "afterlife" effects of inner bark and estimate fraction of stem bark cover to obtain more accurate decay rates. 6. Our new method should benefit our understanding of the in situ dynamics of woody debris decay and monitoring research in different forest ecosystems worldwide, and should aid meta-analyses across diverse studies.</p>
Data from: Comparative phylogeography, genetic differentiation, and contrasting reproductive modes in three fungal symbionts of a multipartite bark beetle symbiosis
Multipartite symbioses are complex symbiotic relationships involving multiple interacting partners. These types of partnerships provide excellent opportunities in which to apply a comparative approach to identify common historical patterns of population differentiation and species-specific life history traits. Using three symbiotic blue stain fungal species (Ophiostomatacea) associated with outbreaking populations of the mountain pine beetle (Dendroctonus ponderosae Hopkins) in western Canada, we applied phylogenetic, population genetic, and demographic approaches to clarify phylogeographic patterns among the three fungal species. Broadly, the three species showed significant population differentiation, forming northern and southern populations, despite dramatic differences in haplotype diversity. Finer scale structuring and population demographic patterns were less consistent, showing some interspecific incongruence. By contrasting these species simultaneously, we were able to identify differences in recombination rate and ecological traits that can explain the observed patterns of incongruence among the fungal species. By applying a comparative approach to partners of a multipartite symbiosis we were able to distinguish congruent population structuring and species-specific differences that help us to understand the complexity and evolution of this symbiotic system.
Figure 10 in Comparative morphology of the larvae of the palm weevils Dynamis borassi (Fabricius) and Rhynchophorus palmarum (Linnaeus) (Curculionidae: Dryophthorinae): Two major pests of peach palms in the Neotropics
Figure 10. Adult, habitus. Dynamis borassi (Fabricius): (A) male, lateral, note sexually dimorphic ventrally setose profemora; (B) female, lateral; (E) male, dorsal; (F) female, dorsal; (I) male, ventral; (J) female, ventral. Rhynchophorus palmarum (Linnaeus): (C) male, lateral, note sexually dimorphic dorsally setose rostrum; (D) female, lateral; (G) male, dorsal; (H) female, dorsal; (K) male, ventral; (L) female, ventral. Scale bars: 5 mm.
Figure 9 in Comparative morphology of the larvae of the palm weevils Dynamis borassi (Fabricius) and Rhynchophorus palmarum (Linnaeus) (Curculionidae: Dryophthorinae): Two major pests of peach palms in the Neotropics
Figure 9. First instar larva of Dynamis borassi (Fabricius): (A) head capsule, dorsal; (B) detail of right antenna; (C) head capsule, ventral. Scale bars: A and C = 0.2 mm, B = 0.02 mm.
Figure 8 in Comparative morphology of the larvae of the palm weevils Dynamis borassi (Fabricius) and Rhynchophorus palmarum (Linnaeus) (Curculionidae: Dryophthorinae): Two major pests of peach palms in the Neotropics
Figure 8. First instar larva. (A) Dynamis borassi (Fabricius), habitus dorsolateral; (B) Rhynchophorus palmarum (Linnaeus), habitus lateral. D. borassi: (C) head and pronotum, dorsal; (D) abdominal segments IV to VII, dorsal, showing egg bursters; (E) detail of egg burster; (F) terminal dorsal disc (abdominal tergites VIII and IX). Scale bars: A and B = 0.5 mm, D = 0.2 mm, E = 0.03 mm.
Figure 7 in Comparative morphology of the larvae of the palm weevils Dynamis borassi (Fabricius) and Rhynchophorus palmarum (Linnaeus) (Curculionidae: Dryophthorinae): Two major pests of peach palms in the Neotropics
Figure 7. Larval abdominal apex showing posterior disc, dorsal: (A) Dynamis borassi (Fabricius); (B) Rhynchophorus palmarum (Linnaeus). Spiracles of D. borassi (external view, not at same scale): (C) thoracic; (D) abdominal I; (E) abdominal IV. (F) Thoracic spiracle and trachea of R. palmarum, seen from inside of body. (G, H) Spiracles and tracheal system of D. borassi, seen from inside of body: thoracic, abdominal IV. Abdominal spiracle VIII: (I) D. borassi; (J) R. palmarum. Scale bars: A and B = 2 mm, C and F-H = 0.2 mm, D and E = 0.1 mm, I and J = 0.5 mm.
Figure 6 in Comparative morphology of the larvae of the palm weevils Dynamis borassi (Fabricius) and Rhynchophorus palmarum (Linnaeus) (Curculionidae: Dryophthorinae): Two major pests of peach palms in the Neotropics
Figure 6. Chaetotaxy of thorax and abdomen, mature larva, Rhynchophorus palmarum (Linnaeus). (A) Prothorax, mesothorax, metathorax and abdominal segment I. (B) Abdominal apex, segments VIII to X, caudal. Scale bars: A = 3 mm, B = 2 mm.
Figure 4 in Comparative morphology of the larvae of the palm weevils Dynamis borassi (Fabricius) and Rhynchophorus palmarum (Linnaeus) (Curculionidae: Dryophthorinae): Two major pests of peach palms in the Neotropics
Figure 4. Larval mouthparts. Dynamis borassi (Fabricius): (A) epipharynx; (C-D, G-H) mandible in dorsal, outer, ventral and inner views. Rhynchophorus palmarum (Linnaeus): (B) epipharynx; (E-F, I-J) mandible in dorsal, outer, ventral and inner views. Scale bars: 0.5 mm.
Figure 3 in Comparative morphology of the larvae of the palm weevils Dynamis borassi (Fabricius) and Rhynchophorus palmarum (Linnaeus) (Curculionidae: Dryophthorinae): Two major pests of peach palms in the Neotropics
Figure 3. Larval mouthparts. (A) Rhynchophorus palmarum (Linnaeus), clypeus and labrum; (B) Dynamis borassi (Fabricius), epipharynx; (C) R. palmarum, epipharynx. Scale bars: 0.5 mm.
Figure 2 in Comparative morphology of the larvae of the palm weevils Dynamis borassi (Fabricius) and Rhynchophorus palmarum (Linnaeus) (Curculionidae: Dryophthorinae): Two major pests of peach palms in the Neotropics
Figure 2. Head of larva, anterodorsal: (A) Dynamis borassi (Fabricius); (B) Rhynchophorus palmarum (Linnaeus). (C) D. borassi, postoccipital membrane showing cervical sclerites; (D) R. palmarum, antenna, apical. Scale bars: A and B = 2 mm, C = 0.4 mm, D = 0.1 mm.
Figure 1 in Comparative morphology of the larvae of the palm weevils Dynamis borassi (Fabricius) and Rhynchophorus palmarum (Linnaeus) (Curculionidae: Dryophthorinae): Two major pests of peach palms in the Neotropics
Figure 1. Habitus of mature larva (lateral, ventral, dorsal). (A-C) Dynamis borassi (Fabricius); (D-F) Rhynchophorus palmarum (Linnaeus). Scale bars: 5 mm.
Figure 5 in Comparative morphology of the larvae of the palm weevils Dynamis borassi (Fabricius) and Rhynchophorus palmarum (Linnaeus) (Curculionidae: Dryophthorinae): Two major pests of peach palms in the Neotropics
Figure 5. Maxillae and labium of larva. Dynamis borassi (Fabricius): (A) ventral; (C) dorsal; (E) detail of mala, dorsal. Rhynchophorus palmarum (Linnaeus): (B) ventral; (D) dorsal; (F) detail of mala, dorsal; (G) detail of dorsal malar setae; (H) detail of ventral malar setae; (I) detail of maxillary palp. Scale bars: A-D = 1 mm, E and F = 0.2 mm, G and I = 0.1 mm, H = 0.2 mm.
Data from: Feeding capability in the extinct giant Siamogale melilutra and comparative mandibular biomechanics of living Lutrinae
At 50 kg in estimated weight, the extinct Siamogale melilutra is larger than all living otters, and ranks among the largest fossil otters. The biomechanical capability of S. melilutra jaws as related to their large size is unknown but crucial to reconstructing the species' potentially unique ecological niche. Here we compare the mandibular biomechanics of S. melilutra using engineering-based performance measures against ten extant otter biomechanical models. Despite a wide range of feeding preferences from durophagy to piscivory, living otter species exhibit a linear relationship between mandible stiffness and volume, as expected in isometric model scaling. In contrast, S. melilutra models exhibit a six-fold increase in stiffness from expected stiffness-volume relationships calculated from extant species models. Unlike stiffness, mechanical efficiency of biting is conserved among living otters and in S. melilutra. These findings indicate that although similar to living bunodont otters in morphology and biting efficiency, jaw strength in S. melilutra far surpasses molluscivores such as sea otters and Cape clawless otters, even after accounting for size. Therefore, Siamogale represents a feeding ecomorphology with no living analog, and its giant size and high mandibular strength confer shell-crushing capability matched only by other extinct molluscivores such as the marine bear Kolponomos.
Data from: Comparative landscape genetics of two frugivorous bats in a biological corridor undergoing agricultural intensification
Agricultural intensification in tropical landscapes poses a new threat to the ability of biological corridors to maintain functional connectivity for native species. We use a landscape genetics approach to evaluate impacts of expanding pineapple plantations on two widespread and abundant frugivorous bats in a biological corridor in Costa Rica. We hypothesize that the larger, more mobile Artibeus jamaicensis will be less impacted by pineapple than the smaller Carollia castanea. In 2012 and 2013, we sampled 735 bats in 26 remnant forest patches surrounded by different proportions of forest, pasture, crops and pineapple. We used 10 microsatellite loci for A. jamaicensis and 16 microsatellite loci for C. castanea to estimate genetic diversity and gene flow. Canonical correspondence analyses indicate that land cover type surrounding patches has no impact on genetic diversity of A. jamaicensis. However, for C. castanea, both percentage forest and pineapple surrounding patches explained a significant proportion of the variation in genetic diversity. Least-cost transect analyses (LCTA) and pairwise G″st suggest that for A. jamaicensis, pineapple is more permeable to gene flow than expected, while as expected, forest is the most permeable land cover for gene flow of C. castanea. For both species, LCTA indicate that development may play a role in inhibiting gene flow. The current study answers the call for landscape genetic research focused on tropical and agricultural landscapes, highlights the value of comparative landscape genetics in biological corridor design and management and is one of the few studies of biological corridors in any ecosystem to implement a genetic approach to test corridor efficacy.
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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
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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.
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