cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.98sf7m0kt
title: Phylogenomic analyses reveal an allopolyploid origin of core Didymocarpinae (Gesneriaceae) followed by rapid radiation

description: Allopolyploid plants have long been regarded as possessing genetic
 advantages under certain circumstances due to the combined effects of
 their hybrid origins and duplicated genomes. However, the evolutionary
 consequences of allopolyploidy in lineage diversification remain to be
 fully understood. Here, we investigate the evolutionary consequences of
 allopolyploidy using 138 transcriptomic sequences of Gesneriaceae,
 including 124 newly sequenced, focusing particularly on the largest
 subtribe Didymocarpinae. We estimated the phylogeny of Gesneriaceae using
 concatenated and coalescent-based methods based on five different nuclear
 matrices and 27 plastid genes, focusing on relationships among major
 clades. To better understand the evolutionary affinities in this family,
 we applied a range of approaches to characterize the extent and cause of
 phylogenetic incongruence. We found that extensive conflicts between
 nuclear and chloroplast genomes and among nuclear genes were caused by
 both incomplete lineage sorting (ILS) and reticulation, and we found
 evidence of widespread ancient hybridization and introgression. Using the
 most highly supported phylogenomic framework, we revealed multiple bursts
 of gene duplication throughout the evolutionary history of Gesneriaceae.
 By incorporating molecular dating and analyses of diversification
 dynamics, our study shows that an ancient allopolyploidization event
 occurred around the Oligocene-Miocene boundary, which may have driven the
 rapid radiation of core Didymocarpinae.
DOI: 10.5061/dryad.9ghx3ffk6
title: Life-cycle greenhouse gas emissions in power generation using palm kernel shell

description: Although the Japanese feed-in tariff was introduced to expand renewable
 energy, leading to the expansion of palm kernel shell (PKS) use, the
 greenhouse gas (GHG) emission reduction effect is evaluated using the
 limited life-cycle of PKS, focusing on processes after PKS generation
 point. Therefore, this study aimed to elucidate the life-cycle GHG
 emissions of power generation using PKS. We targeted two PKS-firing power
 plants as these are the first two instances of the use of PKS in power
 plants in Japan. A system boundary was established to cover palm
 plantation management in Indonesia and Malaysia, as both power plants
 import PKS from these countries. The GHG emissions were derived from
 land-use change, palm plantation, oil extraction, PKS transportation, and
 power plants. Six scenarios were examined for the emissions based on the
 type of land-use change and the existence of biogas capture in oil
 extraction. CO2 emissions from PKS combustion were also calculated by
 assuming that carbon neutrality was lost because of cultivation
 abandonment. The GHG emissions in one scenario, where the plantations were
 replanted and continuously managed and no biogas capture implemented in
 oil extraction, exhibited an average of 0.134 kg-CO2eq/kWh reduction in a
 plant in Kyushu District, and 0.043 kg-CO2eq/kWh reduction in a plant in
 Shikoku District for liquid natural gas-fired steam power generation,
 respectively. More than 65% of life-cycle GHG emissions originate from
 biogas generated during oil extraction; thus, biogas capture is an
 effective strategy to reduce current emissions. In contrast, in the case
 of accompanying land-use change or collapse of carbon neutrality, the
 emissions considerably exceeded those of fossil fuels. These findings
 indicated that the FIT fails to consider the risk of increased emissions
 or further substantial emission reductions. Therefore, the feasibility of
 FIT application to PKS needs to be re-established by evaluating the entire
 PKS life-cycle. 
description: All the parameters used in this research were acquired from
 literature and survey to the company. The calculation
 was conducted in Excel files.
DOI: 10.5061/dryad.0rxwdbs2r
title: Data from: Correcting a bias in the computation of behavioral time budgets that are based on supervised learning

description: Supervised learning of behavioral modes from body-acceleration data has
 become a widely used research tool in Behavioral Ecology over the past
 decade. One of the primary usages of this tool is to estimate behavioral
 time budgets from the distribution of behaviors as predicted by the model.
 These serve as the key parameters to test predictions about the variation
 in animal behavior. In this paper we show that the widespread computation
 of behavioral time budgets is biased, due to ignoring the classification
 model confusion probabilities. Next, we introduce the confusion
 matrix correction for time budgets -- a simple correction method for
 adjusting the computed time budgets based on the model’s confusion
 matrix. Finally, we show that the proposed correction is able to
 eliminate the bias, both theoretically and empirically in a series of data
 simulations on body acceleration data of a fossorial rodent species
 (Damaraland mole-rat, Fukomys damarensis). Our paper provides a simple
 implementation of the confusion matrix correction for time budgets, and we
 encourage researchers to use it to improve accuracy of behavioral time
 budget calculations.
description: We obtained this dataset from 16 Damaraland mole-rats (DMRs) that
 were collared with acceleration loggers (Technosmart LTD, Italy) for 1-3
 weeks, and videotaped during this period to match the acceleration records
 with known behaviours.
description: See README.txt
DOI: 10.5061/dryad.wpzgmsbph
title: Fast likelihood calculations for automatic identification of macroevolutionary rate heterogeneity in continuous and discrete traits

description: Understanding phenotypic disparity across the tree of life requires
 identifying where and when evolutionary rates change on phylogeny. A
 primary methodological challenge in macroevolution is therefore to develop
 methods for accurate inference of among-lineage variation in rates of
 phenotypic evolution. Here, we describe a method for inferring
 among-lineage evolutionary rate heterogeneity in both continuous and
 discrete traits. The method assumes that the present-day distribution of a
 trait is shaped by a variable-rate process arising from a mixture of
 constant-rate processes and uses a single-pass tree traversal algorithm to
 estimate branch-specific evolutionary rates. By employing dynamic
 programming optimization techniques and approximate maximum likelihood
 estimators where appropriate, our method permits rapid exploration of the
 tempo and mode of phenotypic evolution. Simulations indicate that the
 method reconstructs rates of trait evolution with high accuracy.
 Application of the method to datasets on squamate reptile reproduction and
 turtle body size recovers patterns of rate heterogeneity identified by
 previous studies but with computational costs reduced by many orders of
 magnitude. Our results expand the set of tools available for detecting
 macroevolutionary rate heterogeneity and point to the utility of fast,
 approximate methods for studying large scale biodiversity dynamics.
DOI: 10.25338/b87p8k
title: Contrasting genetic trajectories of endangered and expanding red fox populations in the western U.S.

description: As anthropogenic disturbances continue to drive habitat loss and range
 contractions, the maintenance of evolutionary processes will increasingly
 require targeting measures to the population level, even for common and
 widespread species. Doing so requires detailed knowledge of population
 genetic structure, both to identify populations of conservation need and
 value, as well as to evaluate suitability of potential donor populations.
 We conducted a range-wide analysis of the genetic structure of red foxes
 in the contiguous western U.S. with the objectives of contextualizing
 field observations of relative scarcity in the Pacific mountains and
 increasing abundance in the cold desert basins of the Intermountain West.
 Using 31 autosomal microsatellites, along with mitochondrial and
 Y-chromosome markers, we found that populations of the Pacific mountains
 were isolated from one another and genetically depauperate (e.g.,
 estimated Ne range = 3–9). In contrast, red foxe s in the Intermountain
 regions showed relatively high connectivity and genetic diversity.
 Although most Intermountain red foxes carried indigenous western
 matrilines (78%) and patrilines (85%), the presence of nonindigenous
 haplotypes at lower elevations indicated admixture with fur-farm foxes and
 possibly expanding midcontinent populations as well. Our findings suggest
 that some Pacific mountain populations could likely benefit from increased
 connectivity (i.e., genetic rescue) but that nonnative admixture makes
 expanding populations in the Intermountain basins a non-ideal source.
 However, our results also suggest contact between Pacific mountain and
 Intermountain basin populations is likely to increase regardless,
 warranting consideration of risks and benefits of proactive measures to
 mitigate against unwanted effects of Intermountain gene flow.
DOI: 10.5061/dryad.hdr7sqvkh
title: The yellow gene regulates behavioral plasticity by repressing male courtship in Bicyclus anynana butterflies

description: Seasonal plasticity in male courtship in Bicyclus anynana butterflies is
 due to variation in levels of the steroid hormone 20E (20-hydroxyecdysone)
 during pupation. Wet season (WS) males have high levels of 20E and become
 active courters. Dry season (DS) males, have lower levels of 20E and
 reduced courtship rates, although WS courtship rates can be achieved if DS
 male pupae are injected with 20E at 30% of pupation. Here we investigated
 the genes involved in male courtship plasticity and examine whether 20E
 plays an organizational role in the pupal brain that later influences the
 sexual behaviour of adults. We show that DS pupal brains have a 7-fold
 upregulation of the yellow gene relative to the WS and that knocking out
 yellow leads to increased male courtship. We find that injecting 20E into
 DS pupa reduced yellow expression although not significantly. Our results
 show that yellow is a repressor of the neural circuity for male courtship
 behaviour in B. anynana. 20E levels experienced during pupation could play
 an organizational role during pupal brain development by regulating yellow
 expression, however, other factors might also be involved. Our findings
 are in striking contrast to Drosophila where yellow is required for male
 courtship.
description: Behavioural assays (two males and two females) was conducted by
 recording the duration and frequency of different courtship elements
 (localisation, flickering, thrusting, attempting) in male
 <em>Bicyclus anynana</em> (Day 4 - 8). Courtship latency (time
 taken for first mating between male and female) and mating duration was
 recorded as well. All behavioural assays lasted one hour, or once the
 first mating occurred (i.e. even if one male has mated, the other
 male's behavior is still quantified until its own mating or one hour
 has lapsed). Assays are done in a temperature-controlled behavioural room
 set at 23 degrees Celcius. There are two types of
 assays done: using live females and decapitated females. Data inputted
 into Microsoft Excel, analysed using R packages 'pscl' and
 'tweedie' for count and continuous data respectively. Figures
 are also made in R using the 'ggplot2' package.
description: Data from live assays are all collapsed into the same excel sheet
 ("Compare ws and ds live.4grps"), while data from decapitation
 assays are collapsed into another excel sheet ("Compare ws and ds
 decap.4grps"). Included a "README.txt" file to better
 understand the variable names in dataset. Data was analysed using R
 software.  For count/frequency and continuous/duration
 data, read R script "zipandtweediemodels".
 For how figures were made, read R script
 "yellow_graphs_rscript".
DOI: 10.5061/dryad.b5mkkwhfn
title: Genetic differentiation of a critically endangered population of the limpet Patella candei candei d’Orbigny, 1840, in the Canary Islands

description: The adoption of measures to protect the viability of threatened
 populations should be supported by empirical data identifying appropriate
 conservation units and management strategies. The global population of the
 majorera limpet, P. candei candei d’Orbigny, 1840, is restricted to the
 Macaronesian islands in the NE Atlantic, including near-to-extinct and
 healthy populations in Fuerteventura and Selvagens, respectively. The
 taxonomic position, genetic diversity and intra- and interspecific
 relationships of these populations are unclear, which is hindering the
 implementation of a recovery plan for the overexploited majorera limpet on
 Fuerteventura. In this study, ddRAD-based genome scanning was used to
 overcome the limitations of mitochondrial DNA-based analysis. As a result,
 P. candei candei was genetically differentiated from the closely related
 P. candei crenata for the first time. Moreover, genetic differentiation
 was detected between P. candei candei samples from Selvagens and
 Fuerteventura, indicating that translocations from the healthy Selvagens
 source population are inadvisable. In conclusion, the majorera limpet
 requires population-specific management focused on the preservation of
 exceptional genetic diversity with which to face future environmental
 challenges.
DOI: 10.5281/zenodo.18399752
title: Dataset for paper "First principles study of photocatalytic activity in ZnO-Janus van der Waals heterostructures" (https://doi.org/10.1039/D4CP03691C)
DOI: 10.5281/zenodo.18399753
title: Dataset for paper "First principles study of photocatalytic activity in ZnO-Janus van der Waals heterostructures" (https://doi.org/10.1039/D4CP03691C)
DOI: 10.5061/dryad.jdfn2z3cv
title: The closest relative of Archaeplastida is revealed by phylogenomic analyses that include Microheliella maris

description: By clarifying the phylogenetic positions of “orphan” protists (unicellular
 micro-eukaryotes with no affinity to extant species/lineages), we may
 uncover the novel affiliation between two (or more) major lineages in
 eukaryotes. Microheliella maris was an orphan protist, which failed to be
 placed within the previously described species/lineages by pioneering
 phylogenetic analyses. In this study, we analyzed a 319-gene alignment and
 demonstrated that M. maris represents a basal lineage of one of the major
 eukaryotic lineages, Cryptista. We here propose a new clade name
 “Pancryptista” for Cryptista plus M. maris. The 319-gene analyses also
 indicated that M. maris is a key taxon to recover the monophyly of
 Archaeplastida and the sister relationship between Archaeplastida and
 Pancryptista, which is collectively called as “CAM clade” here.
 Significantly, Cryptophyceae tend to be attracted to Rhodophyta depending
 on the taxon sampling (ex., in the absence of M. maris and Rhodelphidia)
 and the particular phylogenetic ‘signal’ most likely hindered the stable
 recovery of the monophyly of Archaeplastida in previous studies.
DOI: 10.5061/dryad.qfttdz0jx
title: Realisation of solid-state electrochromic devices based on gel electrolyte

description: Background: Since the last decade, there has been much interest in solid
 polymer electrolyte (SPE) to address the issues of electrolyte leakage and
 evaporation in electrochromic devices (ECD). ECD is a state-of-the-art
 technology having the ability to change from transparent state to opaque
 state under the influence of a small applied voltage for energy saving
 applications. Methods: In this work, tungsten oxide (WO3) films were
 fabricated via the sol-gel spin-coating method. Subsequently, ECDs were
 assembled based on SPE and liquid polymer electrolyte (LPE) respectively,
 using indium doped tin oxide (ITO) coated glass as conducting electrodes
 and WO3 films as working electrode. Results: Cyclic voltammetry (CV)
 results revealed reduced ionic conductivity of conducting ions in SPE
 based ECD (SECD) owing to increased viscosity by addition of PMMA.
 However, lesser time was required for the colouration process. LPE based
 ECD (LECD) showed higher colouration efficiency (CE) compared to its SECD
 counterpart. This is attributed to its larger optical modulation.
 Conclusions: This work presents a comparison between the performance of
 LECD and SECD in terms of electrochromic (EC) and optical properties. They
 were analyzed through CV, chronoamperometry (CA) and ultraviolet-visible
 (UV-Vis) spectrophotometer. Furthermore, this work provides an insight on
 the employment of solid-state electrolytes in ECDs in view of the
 persistent leakage and evaporation problems in ECD implementation.
description: Experimental data was collected based on transmittance using
 UV-Vis spectrophotometer, cyclic voltammetry and chronoamperometry using
 potentiostat/galvanostat measurement methods. Measured data are extracted
 and further analysed through the relevant equations.
DOI: 10.5061/dryad.8sf7m0cqh
title: Data for: Environmental responses of fruiting fungal communities are phylogenetically structured

description: Through their ephemeral reproductive structures (fruiting bodies),
 ectomycorrhizal forest soil fungi provide a resource for a plethora of
 organisms. Thus, resolving what biotic and abiotic factors determine the
 occurrence and abundance of fruiting bodies is fundamental for
 understanding the dynamics of forest trophic networks. While the influence
 of abiotic factors such as moisture and temperature on fungal fruiting are
 relatively well established, little is known about how these processes
 interact with the evolutionary history of fungal species to determine
 when, where, and in which abundance fungal fruiting bodies will emerge. A
 specific knowledge gap relates to whether species’ responses to their
 environment are phylogenetically structured. Here, we ask whether related
 fungal taxa respond similarly to climatic factors and forest habitat
 characteristics, and whether such correlated responses will affect the
 assembly of fungal fruiting communities. To resolve these questions, we
 fitted joint species distribution models combining data on the species
 composition and abundance of fungal fruiting bodies, environmental
 variation, and phylogenetic relationships among fungal taxa. Our results
 show that both site-level forest characteristics (dominant tree species
 and forest age) and climatic factors related to phenology (effective heat
 sum) greatly influence the occurrence and abundance of fruiting bodies.
 More importantly, while different fungal species responded unequally to
 their shared environment, there was a strong phylogenetic signal in their
 responses, so that related fungal species tended to fruit under similar
 environmental conditions. Thus, not only are fruiting bodies short-lived
 and patchily distributed, but the availability of similar resources will
 be further aggregated in time and space. These strong constraints on
 resource availability for fungus-associated taxa highlight the potential
 of fungus-based networks as a model system for studies on the ecology and
 evolution of resource–consumer relations in ephemeral systems of high
 spatiotemporal patchiness.
description: This dataset contains field transect data of fungal fruiting
 bodies, collected in 2016 and 2017. Likewise, it contains environmental
 data from the transect sites as well as a phylotree of the detected fungal
 taxa. Transect counts were used using achievable taxonomic resolution.
 After that, transect data was used to perform NMDS and JSDM (HMSC)
 analysis to determine the effects of phylogeny and environment on fungal
 fruiting.
DOI: 10.5061/dryad.3xsj3txjb
title: Intermediate results for: Large differences in carbohydrate degradation and transport potential among lichen fungal symbionts

description: Lichen symbioses are thought to be stabilized by the transfer of fixed
 carbon from a photosynthesizing symbiont to a fungus. In other fungal
 symbioses, carbohydrate subsidies correlate with reductions in plant cell
 wall-degrading enzymes, but whether this is true of lichen fungal
 symbionts (LFSs) is unknown. We predicted genes encoding
 carbohydrate-active enzymes (CAZymes) and sugar transporters in 46 genomes
 from the Lecanoromycetes, the largest extant clade of LFSs. All LFSs
 possess a robust CAZyme arsenal including enzymes acting on cellulose and
 hemicellulose, confirmed by experimental assays. However, the number of
 genes and predicted functions of CAZymes vary widely, with some fungal
 symbionts possessing arsenals on par with well-known saprotrophic fungi.
 These results suggest that stable fungal association with a phototroph
 does not in itself result in fungal CAZyme loss, and lends support to
 long-standing hypotheses that some lichens may augment fixed CO2 with
 carbon from external sources.
description: The data provided are intermediate results from genome
 annotations performed with funannotate, phylogenomic trees calculated with
 phylociraptor and additional settings and configuration files used to run
 different analyses steps. The files are processed in a comparative genomic
 analysis pipeline (https://github.com/reslp/LFS-cazy-comparative) to create perform the final analyses and create figures for the publication.
description: They should be used together with the comparative genomic
 pipeline used in the paper, which is available here:
 https://github.com/reslp/LFS-cazy-comparative. If this
 pipeline is set up correctly, the data provided here should be downloaded
 automatically.
DOI: 10.6092/unibo/amsacta/8754
title: Ki67 density maps in canine tumors

description: This dataset contains aimed to evaluate the classification of the spatial distribution of the most proliferative areas in selected canine tumour types, using Ki67 immunohistochemistry. Tumour types analysed included melanomas, cutaneous mast cell tumours, canine mammary carcinomas and soft tissue sarcomas. Using im-age analysis, Ki67 density maps were generated from digital slides and classified according to their distribution pattern (focal/multifocal or diffuse) and location within the tumour (central, peripheral or scattered).