cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0k6djhb15
title: Soil chemistry determines whether defensive plant secondary metabolites promote or suppress herbivore growth

description: Plant secondary (or specialized) metabolites mediate important
 interactions in both the rhizosphere and the phyllosphere. If and how such
 compartmentalized functions interact to determine plant-environment
 interactions is not well understood. Here, we investigated how the dual
 role of maize benzoxazinoids as leaf defenses and root siderophores shapes
 the interaction between maize and a major global insect pest, the fall
 armyworm. We find that benzoxazinoids suppress fall armyworm growth when
 plants are grown in soils with very low available iron but enhance growth
 in soils with higher available iron. Manipulation experiments confirm that
 benzoxazinoids suppress herbivore growth under iron-deficient conditions
 and in the presence of chelated iron, but enhance herbivore growth in the
 presence of free iron in the growth medium. This reversal of the
 protective effect of benzoxazinoids is not associated with major changes
 in plant primary metabolism. Plant defense activation is modulated by the
 interplay between soil iron and benzoxazinoids but does not explain fall
 armyworm performance. Instead, increased iron supply to the fall armyworm
 by benzoxazinoids in the presence of free iron enhances larval
 performance. This work identifies soil chemistry as a decisive factor for
 the impact of plant secondary metabolites on herbivore growth. It also
 demonstrates how the multifunctionality of plant secondary metabolites
 drives interactions between abiotic and biotic factors, with potential
 consequences for plant resistance in variable environments.
DOI: 10.5061/dryad.c2fqz618m
title: Gudgeon fish with and without genetically determined countershading coexist in heterogeneous littoral environments of an ancient lake

description: Countershading, characterized by a darker dorsal surface and lighter
 ventral surface, is common among many animals. This dorsoventral pigment
 polarity is often thought to be adaptive coloration for camouflage. By
 contrast, non-countershaded (melanistic) morphs often occur within a
 species due to genetic color polymorphism in terrestrial animals. However,
 the polymorphism with either countershaded or melanistic morphs is poorly
 known in wild aquatic animals. This study explored the genetic nature of
 diverged color morphs of a lineage of gudgeon fish (genus
 Sarcocheilichthys) in the ancient Lake Biwa, and propose this system as a
 novel model for testing hypotheses of functional aspects of countershading
 and its loss in aquatic environments. This system harbors two color morphs
 that have been treated taxonomically as separate species; S. variegatus
 microoculus which occurs throughout the littoral zone, and S. biwaensis
 which occurs in and around rocky areas. First, we confirmed that the
 divergence of dorsoventral color patterns between the two morphs is under
 strict genetic control at the levels of chromatophore distribution and
 melanin-related gene expression under common garden rearing. The former
 morph displayed sharp countershading coloration, whereas the latter morph
 exhibited a strong tendency towards its loss. The crossing results
 indicated that this divergence was likely controlled by a single locus in
 a two-allele Mendelian-inheritance pattern. Furthermore, our population
 genomic and genome-wide association study analyses detected no genome-wide
 divergence between the two morphs, except for one region near a locus that
 may be associated with the color divergence. Thus, these morphs are either
 in a state of intraspecific color polymorphism or two incipient species.
 Evolutionary forces underlying this polymorphism appears to be associated
 with heterogeneous littoral environments in this lake. Future ecological
 genomic research will provide insight into adaptive functions
 of this widespread coloration, including the eco-evolutionary
 drivers of its loss, in the aquatic world.
description: Please see corresponding manuscript for all the methods for the
 collection and processing of data.
description: The file contains data about chromatophore distribution patterns
 of the <i>Sarcocheilichthys variegatus microoculus</i>
 (S<sub>V</sub>) and<i> Sarcocheilichthys
 biwaensis</i> (S<sub>B</sub>) morphs. The cell numbers
 (per mm<sup>2</sup> on scale skin) of melanophores and
 xanthophores for each of five selected regions (area A–E ) in each family
 (<i>n</i> = 6 individuals per family) were shown.
DOI: 10.5061/dryad.2rbnzs7p1
title: Morphological and phylogenetic characterization of fungi within Hymenochaetales: Introducing two new species from southern China

description: Two new wood-inhabiting fungal species, Lyomyces niveus and L.
 ochraceoalbus spp. nov. are proposed based on a combination of
 morphological and molecular evidence.
 Lyomyces ochraceoalbus is characterised by
 resupinate basidiomata with tuberculate, cracking hymenial
 surface, clavate basidia with a median
 constriction, gathering numerous irregular crystals and
 thin-walled basidiospores with one or two globules.
 Lyomyces niveus is characterised by
 resupinate basidiomata, smooth to grandinioid
 hymenial surface, presence of three kinds of cystidia, and broadly
 ellipsoid basidiospores. Sequences of ITS and nLSU gene regions
 were generated, and phylogenetic analyses were performed with maximum
 likelihood, maximum parsimony and Bayesian inference methods. The
 phylogenetic reconstruction of Schizoporaceae based on a concatenated
 ITS+nLSU dataset showed that two new species nested in Lyomyces.
 A second phylogenetic analysis, of the genus Lyomyces, demonstrated that
 multiple isolates of L. niveus forms a monophyletic
 lineage and is sister to a clade
 comprising of L. crustosus, L.
 juniperi, L. ochraceoalbus, and L.
 vietnamensis. Moreover, L. ochraceoalbus is closely
 related to L. crustosus.
DOI: 10.5061/dryad.hqbzkh1gt
title: Effects of land use and climate change on functional and phylogenetic diversity of terrestrial vertebrates in a Himalayan biodiversity hotspot

description: Aim: Land use and climate change interact to impact functional and
 phylogenetic diversity globally, but this pattern is largely unknown in
 the eastern Himalayas. We aim to discern the response of community
 diversity and structure of terrestrial mammals and birds to anthropogenic
 land use and climate change in this hitherto understudied landscape.
 Location: Himalayan biodiversity hotspot, Bhutan Methods: We used camera
 trap and point-count transect data to estimate taxonomic, functional, and
 phylogenetic diversity while accounting for detectability. We calculated
 the abundance-weighted standardised effect sizes (ses) of mean pairwise
 distance and mean nearest taxon distance. The ses metrics were regressed
 against land use (agriculture and forest) and climate (temperature and
 precipitation) variables using linear mixed effect models. Results:
 Community diversity declined with agriculture in both groups. Mammal
 diversity was higher farther from the settlement but birds remained
 indifferent. Temperature and precipitation were positively associated with
 mammal diversity, but birds displayed a mixed response: negative with
 temperature and positive with precipitation. Agriculture had a strong
 negative effect on the functional structure of birds but not mammals. The
 functional and phylogenetic structure declined farther from the settlement
 for mammals but increased for birds. Except for the functional structure,
 all other metrics increased with temperature and precipitation for
 mammals. Except for the positive relationship between functional structure
 and temperature, other metrics showed a mixed response to climate in
 birds.  Main conclusions: Our findings provide evidence that land
 use rather than climate has an imminent effect in shaping local and
 regional patterns of terrestrial vertebrate diversity in a Himalayan
 biodiversity hotspot. Climate effects, although weak, may reduce
 functional traits and consequently diminish functional roles. Species that
 can persist in human-modified environments are clustered within a
 phylogeny, suggesting possible loss of phylogenetic diversity.
description: Mammal: camera trap survey (refer to Penjor et al., 2018
 (EcoEvol), 2019 (BioCon), 2020 (EcolInd) for details.
 Bird: transect, point count survey, repeated observation (Penjor
 et al., 2021, J Applied Ecology). Detection,
 non-detection data (binary), occupancy models (MacKenzie et al., 2002
 Ecol)
description: Follow the script to run MSOM, obtain detection-corrected site x
 species matrix (z-matrix) and use this matrix to calculate FD and PD (eg.,
 Chapman et al., 2018, J Applied Ecol).
DOI: 10.5061/dryad.j0zpc86fj
title: 3D microelectrode cluster and stimulation paradigm yield powerful analgesia without noticeable adverse effects

description: The dataset contains the underlying data for the figures in the paper
 "3D microelectrode cluster and stimulation paradigm yield powerful
 analgesia without noticeable adverse effects" by M. Forni et al.,
 Science Advances, 2021. In the reported study, we present a newly
 developed biocompatible gelatin-embedded cluster of microelectrodes that
 enable higly customizable stimulation in the periaqueductal gray/dorsal
 raphe nucleus in awake rats. We were able to select a subset of electrodes
 for each individual, that upon stimulation provided significant pain
 inhibition during both normal and hyperalgesia conditions, without
 noticable side effects. Pain responses were quantified in terms of evoked
 field potentials (FP) and neuronal activity (z score), as well as
 withdrawal rate (WR) resulting from stimulating the skin with either a
 CO2-laser or a tactile stimulator, and analyzed with respect to multiple
 variables, such as time from stimulation onset, effect in comparison to
 morphine administration etc. Also, the effects of stimulation were
 quantified in terms of gait parameters (speed and paw-usage symmetry). The
 location of implanted electrodes was verified using computed tomography
 (CT) imaging and superimposition to the Waxholm brain atlas. The dataset
 contains the CT images for each anaimal, as obtained after alignment to
 the atlas.
description: See methods section of the paper "3D microelectrode cluster
 and stimulation paradigm yield powerful analgesia without noticeable
 adverse effects" by M. Forni et al.
description: The filenames refer to the figure names in the paper "3D
 microelectrode cluster and stimulation paradigm yield powerful analgesia
 without noticeable adverse effects" by M. Forni et al.. The dataset
 is structured according to the figures presented in the paper, i.e. names
 of datafiles correspond to figure names in the paper (e.g. the file
 "Fig3A.xlsx" contains the data underlying the plots in Fig. 3A).
 Each xlsx-file contains several sheets, each corresponding to the
 subpanels of the figures. CT-images are in Nifti format and are aligned
 and resampled to match the Waxholm Brain atlas (https://www.nitrc.org/projects/whs-sd-atlas) which is used for localizing the stimulation electrodes within the brain. The images can be opened using any software for 3D-image analysis. The corresponding figures in the paper were obtained using Matlab, but they can be opened and viewed using e.g. itk-SNAP (http://www.itksnap.org). For more information, please refer to the readme file.
DOI: 10.5061/dryad.ffbg79cvs
title: Climate differently influences genomic patterns of two sympatric marine fish species

description: 1- Climate influences population genetic variation of marine
 species. Capturing those impacts remains challenging for marine
 fishes dispersing over a large geographic scale
 spanning steep environmental gradients. This requires an
 extensive spatial sampling of individuals or populations, representative
 of seascape heterogeneity, combined with a set
 of highly informative molecular markers able to
 reveal climatic-associated genomic variations. 2- We explored how
 space, dispersal and environment shape the genomic patterns of two marine
 fish species. We hypothesized that population structure
 and climate-associated genomic signatures of
 selection will be stronger in the less mobile species, as
 restricted gene flow tends to facilitate the fixation of locally adapted
 alleles. 3- To investigate our hypothesis, we genotyped two
 species that share a common environment but have contrasting dispersal
 abilities, the white seabream (Diplodus sargus) and striped red mullet
 (Mullus surmuletus). We collected 823 samples across the Mediterranean
 Sea, which ranks among the oceanic basins the most affected by climate
 change and human pressures. We used genotyping by sequencing
 (GBS) to detect 8 206 Single Nucleotides Polymorphisms (SNPs) for seabream
 and 2 794 for mullet. For each species, we identified
 highly differentiated genomic regions and disentangled the relative
 contribution of space, dispersal
 and environmental (climate, productivity) variables on
 genetic structure to test the prevalence of gene flow and local
 adaptation. 4- We observed contrasted patterns of gene flow
 and adaptive genetic variation between the two species.
 The seabream showed a separate Alboran sea population but further
 panmictia across the Mediterranean Sea, while the mullet
 revealed additional differentiation. The
 within-Mediterranean differentiation of mullet was significantly
 correlated to summer – and winter temperatures as well as
 productivity. Functional annotation
 of climate-associated
 outlier SNPs then identified candidate
 genes involved in heat tolerance that could be examined to
 further predict species’ responses to climate change. 5- Our results
 illustrate the key steps of a comparative seascape genomics study that
 aims to unravel the evolutionary processes at play in marine species, in
 order to better anticipate their response to climate change. Defining
 population adaptation capacities and climatic niches can then serve
 to include complementary evolutionary processes
 in species conservation planning. 
description: SNP data for each species considering all filtered SNP,
 putatively neutral SNP and outlier SNP as detected by PCAdapt.
DOI: 10.5281/zenodo.17943825
title: KaML-ESM v1.0.0 ensemble weights (ESM2)
DOI: 10.5281/zenodo.18397706
title: KaML-ESM v1.0.0 ensemble weights (ESM2)
DOI: 10.5061/dryad.m905qfv1r
title: MorphoGraphX2: Datasets that demonstrate how to create positional information with local coordinate systems

description: Confocal image data sets and segmented meshes from various plant organs
 including the Arabidopsis root, flower, gynoecium, meristem, embryo and
 ovule. The data sets are used to demonstrate features available in
 MorphoGraphX software (www.MorphoGraphX.org), and how to use positional
 information to add spatial context to quantitative cellular data. Also
 included are longform video tutorials, and source code for the
 MorphoGraphX software.
description: The data was collected using confocal microscopy on fixed or live
 imaged samples. Please see the publication for detailed methods for each
 dataset.
description: Confocal files are provided in original microscope formats,
 and/or as tifs exported from Fiji. Meshes extracted
 from the data are in .mgxm (MorphoGraphX mesh) format.
 Source code for MorphoGraphX is included, and has been compiled
 and tested on Ubuntu 20.04 with Cuda 11.4. Tutorials
 are in standard mp4 format.
DOI: 10.5061/dryad.ngf1vhhvb
title: Data from: BIOVERA-Tree: tree diversity, community composition, forest structure and functional traits along gradients of forest-use intensity and elevation in Veracruz, Mexico

description: Here, we describe BIOVERA-Tree, a database on tree diversity, community
 composition, forest structure, and functional traits collected in 120
 forest plots distributed along an extensive elevational gradient in
 Veracruz State, Mexico. BIOVERA-Tree includes information on forest
 structure from three levels of forest-use intensity, namely old-growth,
 degraded, and secondary forest, replicated across eight elevations from
 sea-level to near the tree line at 3500 m and on size and location of 4549
 tree individuals with a diameter at breast height ≥ 5 cm belonging to 216
 species, 154 genera, and 80 families. We also report measurements of eight
 functional traits, namely wood density for 143 species, maximum
 height for 216 species and leaf traits including: specific leaf area,
 lamina density, leaf thickness, chlorophyll content, and leaf area for
 148 species and leaf dry matter content for 145 species.
DOI: 10.5061/dryad.12jm63xzd
title: Data from: Alternative food sources interfere with removal of a fungal amphibian pathogen by zooplankton

description: 1. While the amphibian disease chytridiomycosis is causing ongoing
 population declines and biodiversity losses around the globe, efficient
 mitigation strategies are lacking. The free-living zoospores of the
 causative agents of this disease, the chytrid
 pathogens Batrachochytrium dendrobatidis (Bd)
 and Batrachochytrium salamandrivorans (Bsal), are a
 potential food source for filter-feeding micropredators as part of the
 aquatic food web. While consumption of zoospores can lower environmental
 pathogen loads, alternative food sources may interfere with pathogen
 removal rates. 2. We compared the ability of three filter-feeding
 zooplankton species, i.e. the cladoceran Daphnia magna, the
 rotifer Brachionus calyciflorus and the
 ostracod Heterocypris incongruens, to remove Bd
 zoospores in water and investigated the effect of alternative food
 sources, i.e. the green algae Pseudokirchneriella
 subcapitata and Chlorella vulgaris, on zoospore
 ingestion by D. magna. 3. D. magna was the only
 micropredator candidate that effectively removed Bd zoospores from its
 environment, with an average removal rate of 1,012 ± 542 GE
 ind.-1 h-1 within our test system. High concentrations
 (1x105 cells/mL) of large and easily ingestible P.
 subcapitata reduced pathogen removal rates, whereas the small and
 less edible C. vulgaris did not interfere with pathogen
 removal. 4. Synthesis and applications: We showed
 that Daphnia spp., which are keystone species in all sorts of
 aquatic habitats worldwide, are promising target agents for biologically
 mitigating chytridiomycosis infections and how natural food sources may
 interfere with this strategy. We also suggest potential management actions
 for biological disease mitigation, aiming to optimize environmental
 conditions for these target filter-feeders, thereby reducing pathogen
 densities and eventually infection pressure in amphibian hosts. Examples
 of such management actions include, but are not limited to, removal of
 planktivorous fish, habitat restoration, nutrient control or agrochemical
 regulation in the vicinity of amphibian breeding ponds. Further studies,
 including field trials, are needed to confirm the effects of pathogen
 consumption on infection dynamics in natural situations and investigate
 the impact of intervention actions.
description: The README file contains an explanation of all variables in the
 csv data files. Statistical analyses and graphical representations were
 performed in R and are also included in the dataset. Information about the
 experimental and statistical methods can be found in the associated
 manuscript.
DOI: 10.5061/dryad.j3tx95xf5
title: Cohen and Schenk (2021) Data from: Investigating phylogenetic placement and species-level relationships in a recent radiation of Mentzelia section Bartonia (Loasaceae) from the Mojave Desert

description: Understanding species level relationships is a central goal in systematic
 botany; however complexes of closely related and morphologically similar
 species often pose considerable challenges to that goal. The North
 American west is home to many notable genera that notoriously have
 difficult species complexes (e.g., Astragalus, Eriogonum, Penstemon).
 Mentzelia section Bartonia (Loasaceae) is a recently evolved and diverse
 clade that occurs across the North American west. Phylogenetic studies
 have resolved many relationships, but the relationships within a species
 complex of perennial, subshrub species that occurs in the Mojave Desert,
 Great Basin, and Colorado Plateau remains elusive. This arid-adapted
 clade, which is referred to as the Mojave clade, has significant
 conservation implications, due to three narrowly endemic
 species:  Mentzelia polita and Mentzelia tiehmii are state
 listed, and Mentzelia leucophylla is federally listed. Species
 relationships within the Mojave clade are not fully understood.
 Populations of Mentzelia oreophila from California and Nevada, for
 example, are not monophyletic. We generated restriction site associated
 DNA sequence data (RADSeq) to address evolutionary relationships in the
 Mojave clade. Our results corroborated previous studies in continued
 recognition of Mentzelia polita, Mentzelia leucophylla, and Mentzelia
 tiehmii; however, Mentzelia oreophila was recovered in three clades that
 includes a California clade, a Nevada clade, and one with Mentzelia
 puberula. Incomplete lineage sorting and hybridization might have
 generated conflicting phylogenetic signal between Mentzelia oreophila and
 Mentzelia puberula. Increasing population level sampling will aid in
 species delimitation and further help to understand how gene flow and/or
 hybridization is influencing population level dynamics in the Mojave
 Desert.
description: RADSeq was used to collect SNP data from randomly across the
 genome. Raw sequences were filtered, clustered, and combined in the python
 program ipyrad. A total of nine alignments were created using multiple
 clustering thresholds and different minimum sample requirements to be
 included in the final alignment.
DOI: 10.5061/dryad.bnzs7h4bs
title: Analytical kinetic model of native tandem promoters in E. coli

description: Closely spaced promoters in tandem formation are abundant in bacteria. We
 investigated the evolutionary conservation, biological functions, and the
 RNA and single-cell protein expression of genes regulated by tandem
 promoters in E. coli. We also studied the sequence (distance between
 transcription start sites ‘dTSS’, pause sequences, and distances from
 oriC) and potential influence of the input transcription factors of these
 promoters. From this, we propose an analytical model of gene expression
 based on measured expression dynamics, where RNAP-promoter occupancy times
 and dTSS are the key regulators of transcription interference due to TSS
 occlusion by RNAP at one of the promoters (when dTSS ≤ 35 bp) and RNAP
 occupancy of the downstream promoter (when dTSS &gt; 35 bp). Occlusion
 and downstream promoter occupancy are modeled as linear functions of
 occupancy time, while the influence of dTSS is implemented by a continuous
 step function, fit to in vivo data on mean single-cell protein numbers of
 30 natural genes controlled by tandem promoters. The best-fitting step is
 at 35 bp, matching the length of DNA occupied by RNAP in the open complex
 formation. This model accurately predicts the squared coefficient of
 variation and skewness of the natural single-cell protein numbers as a
 function of dTSS. Additional predictions suggest that promoters in tandem
 formation can cover a wide range of transcription dynamics within
 realistic intervals of parameter values. By accurately capturing the
 dynamics of these promoters, this model can be helpful to predict the
 dynamics of new promoters and contribute to the expansion of the
 repertoire of expression dynamics available to synthetic genetic
 constructs.
description: Data processing methods and the software packages used are
 described in S1 Appendix.