cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3bk3j9knq
title: Data for: Analytical transfer function for volcano deformation with T-dependent viscoelasticity

description: Rocks can modulate the triggering, duration, and style of volcanic
 eruptions. When heated, the host rocks surrounding a magmatic reservoir is
 typically considered as a viscoelastic material. The viscoelastic rheology
 (viscosity especially) is temperature dependent; however, the dynamics and
 consequence on surface deformation resulting from heterogeneous crustal
 temperature and viscosity around magmatic reservoirs have not been
 explored systematically.  This dataset incorporates the
 parameters and numerical codes used for generating results in the
 manuscript 'History-dependent volcanic ground deformation from
 broad-spectrum viscoelastic rheology around magma reservoirs'
 submitted to GRL and authord by Yang Liao, Leif Karlstrom, and Brittany
 Erickson.  The dataset consists of a README file detailing the
 data structure, a matlab .mat file that contains the parameters assumed in
 the magma chamber model, and several matlab program .m files that can be
 applied to the .mat file to generate results presented in the
 manuscript. 
description: Codes are based on analytical solutions in frequency domain
 detailed in the supplementary material accompanying  the submitted
 manuscript.
description: Files are accessible using Matlab.
DOI: 10.5061/dryad.t76hdr83z
title: Data and code – Effects of climate on salmonid productivity: A global meta-analysis across freshwater ecosystems

description: Salmonids are of immense socio-economic importance in much of the world
 but are threatened by climate change. This has generated a substantial
 literature documenting effects of climate variation on salmonid
 productivity in freshwater ecosystems, but there has been no global
 quantitative synthesis across studies. We conducted a systematic review
 and meta-analysis to gain quantitative insight into key factors shaping
 the effects of climate on salmonid productivity, ultimately collecting
 1,321 correlations from 156 studies, representing 23 species across 24
 countries. Fisher’s Z was used as the standardized effect size, and a
 series of weighted mixed-effects models were compared to identify
 covariates that best explained variation in effects. Patterns in climate
 effects were complex, and were driven by spatial (latitude, elevation),
 temporal (time-period, age-class), and biological (range, habitat type,
 anadromy) variation within and among study populations. These trends were
 often consistent with predictions based on salmonid thermal tolerances.
 Namely, warming and decreased precipitation tended to reduce productivity
 when high temperatures challenged upper thermal limits, while opposite
 patterns were common when cold temperatures limited productivity. Overall,
 variable climate impacts on salmonids suggest that future declines in some
 locations may be counterbalanced by gains in others. In particular, we
 suggest that future warming should (1) increase salmonid productivity at
 high latitudes and elevations (especially &gt;60° and &gt;1,500m),
 (2) reduce productivity in populations experiencing hotter and dryer
 growing season conditions, (3) favor non-native over native salmonids, and
 (4) impact lentic populations less negatively than lotic ones. These
 patterns should help conservation and management organizations identify
 populations most vulnerable to climate change, which can then be
 prioritized for protective measures. Our framework enables broad
 inferences about future productivity that can inform decision-making under
 climate change for salmonids and other taxa, but more widespread,
 standardized, and hypothesis-driven research is needed to expand current
 knowledge.
description: See README document.
description: See README document and R code.
DOI: 10.5061/dryad.qrfj6q5kd
title: Data from: Differential gene expression and mitonuclear incompatibilities in fast- and slow-developing inter-population Tigriopus californicus hybrids

description: Mitochondrial functions are intimately reliant on proteins and RNAs
 encoded in both the nuclear and mitochondrial genomes, leading to
 inter-genomic coevolution within taxa. Hybridization can break apart
 coevolved mitonuclear genotypes, resulting in decreased mitochondrial
 performance and reduced fitness. This hybrid breakdown is an important
 component of outbreeding depression and early-stage reproductive
 isolation. However, the mechanisms contributing to mitonuclear
 interactions remain poorly resolved. Here we scored variation in
 developmental rate (a proxy for fitness) among reciprocal
 F2 inter-population hybrids of the intertidal
 copepod Tigriopus californicus, and used RNA sequencing to assess
 differences in gene expression between fast- and slow-developing hybrids.
 In total, differences in expression associated with developmental rate
 were detected for 2,925 genes, whereas only 135 genes were differentially
 expressed as a result of differences in mitochondrial genotype.
 Up-regulated expression in fast developers was enriched for genes involved
 in chitin-based cuticle development, oxidation-reduction processes,
 hydrogen peroxide catabolic processes, and mitochondrial respiratory chain
 complex I. In contrast, up-regulation in slow developers was enriched for
 DNA replication, cell division, DNA damage, and DNA repair. Eighty-four
 nuclear-encoded mitochondrial genes were differentially expressed between
 fast- and slow-developing copepods, including twelve subunits of the
 electron transport system (ETS) which all had higher expression in fast
 developers than in slow developers. Nine of these genes were subunits of
 ETS complex I. Our results emphasize the major roles that mitonuclear
 interactions within the ETS, particularly in complex I, play in hybrid
 breakdown, and resolve strong candidate genes for involvement in
 mitonuclear interactions.
description: Developmental rate data - collected by daily monitoring naupliar
 (larval) development of individual <em>Tigriopus
 californicus</em> until stage 1 copepodid metamorphosis was
 observed RNA-seq count data - collected by isolated RNA
 from pools of fast- or slow-developing <em>Tigriopus
 californicus </em>copepodids from reciprocal hybrids lines; RNA was
 sequenced on a NovaSeq 6000; reads were mapped to a hybrid reference
 genome and counted using <em>STAR</em> and
 <em>featureCounts</em>; differences in gene expression were
 tested with <em>edgeR</em>; gene ontology enrichments among
 differentially expressed genes were assessed with
 <em>goseq</em>.
description: All files can be opened in text editors, spreadsheet programs or
 the statistical software R.
DOI: 10.5061/dryad.n5tb2rbzt
title: Flagellum tapering and midpiece volume in songbird spermatozoa

description: In contrast to numerous studies on spermatozoa length, relatively little
 work focuses on the width of spermatozoa, particularly the width of the
 midpiece and flagellum. In flagellated spermatozoa, the flagellum provides
 forward thrust while energy may be provided via mitochondria in the
 midpiece and/or through glycolysis along the flagellum itself. Longer
 flagella may be able to provide greater thrust but may also require
 stronger structural features and more or larger mitochondria to supply
 sufficient energy. Here we use SEM imaging to investigate the
 ultrastructure of spermatozoa from 55 passerine species in 26 taxonomic
 families in the Passerides infraorder. Our data confirm the qualitative
 observation that the flagellum tapers along its length, and we show that
 longer flagella are wider at the neck. This pattern is similar to mammals,
 and likely reflects the need for longer cells to be stronger against
 shearing forces. We further estimate the volume of the mitochondrial helix
 and show that it correlates well with midpiece length, supporting the use
 of midpiece length as a proxy for mitochondrial volume, at least in
 between-species studies where midpiece length is highly variable. These
 results provide important context for understanding the evolutionary
 correlations among different sperm cell components and dimensions.
description: In essence, we measured the width of the flagellum and the
 flagellum + mitochondrial helix at many points along the cells, as well as
 measured the major axis of the mitochondrial helix. Our main dataset used
 multiple 4000 x SEM images stitched together. Please see the paper for
 full methodological details. 
description: R
DOI: 10.5061/dryad.msbcc2g24
title: Data for: Determinants of resource use in lizard assemblages from the Neotropical semiarid Caatinga

description: Non-sessile animals could partition the use of resources in different
 axes, reducing the effects of competition and allowing coexistence. Here,
 we investigated the spatial and trophic niche dimensions in four lizard
 assemblages in the Neotropical semiarid Caatinga to investigate the
 determinants of resource use and the extent which lizards partition their
 niches. We sampled each lizard assemblage once, for ten days, in the dry
 season of 2017 and 2018. In two lizard assemblages, we detected non-random
 niche overlap patterns that were higher or lower than expected by chance.
 The high niche overlap patterns suggests that either there is intense
 current competition for available microhabitats or an abundance of
 microhabitats. The lower niche overlap may be influenced by the presence
 of species adapted to sandy habitats (psamophilous), suggesting that
 spatial partitioning detected has historical basis, which is supported by
 the pPCA results and by the lack of patterns in the realized niche
 distribution of species across niche space. We detected trophic niche
 partitioning in three lizard assemblages. In one assemblage, we discovered
 random spatial and trophic niche overlap patterns, revealing that
 competition is not a determining factor in the structure of that
 assemblage. In fact, phylogenetic effects were predominantly the main
 determinants of resource use in the four studied lizard assemblages. Arid
 and semiarid habitats cover about one third of land surface of the world.
 Comparisons between our findings and those from other regions of the world
 may aid identify general trends in the lizard ecology of dry environments.
DOI: 10.5061/dryad.1rn8pk0xn
title: Data for: The significance of Apis cerana cerana (Hymenoptera: Apidae) gnawing off the old brood cells

description: Apis cerana cerana has the biological characteristic of gnawing off the
 old brood cells for rearing multiple generations of workers. This study
 investigated the internal structure of newly built, old, and semi-rebuilt
 brood cells and their effects on the morphological development of workers
 to understand the significance of Apis cerana cerana gnawing off the old
 brood cells. The structural dimensions of the brood cells and the
 morphological characteristics of the newly emerged workers were measured.
 The results showed that Apis cerana cerana gnaw off the old brood cells
 mainly in two ways either by removing the whole cell or only the cell
 walls keeping the bases. The workers construct semi-rebuilt brood cells on
 the foundation of these old cell bases. The main shapes of the newly
 built, old, and semi-rebuilt brood cells are hexagonal prism, hexagonal
 prismatic table, and hexagonal prism having three rhombuses, hemisphere,
 and hemisphere-shaped bases, respectively. The average thickness of the
 newly built or semi-rebuilt brood comb was significantly smaller than that
 of the old brood comb (P&lt;0.05), while it was almost the same for
 the newly built and semi-rebuilt brood combs (P&gt;0.05). The depth of
 brood cells showed no significant difference between the three types of
 brood cells (P&gt;0.05), but the brood cell volumes were significantly
 different (P&lt;0.05). There was no significant difference among the
 three diameters (at the top, middle, and bottom positions) of newly built
 or semi-rebuilt brood cells (P&gt;0.05), but these changed within the
 old brood cells (P&lt;0.05). The top, middle, and bottom diameters of
 the newly built or semi-rebuilt brood cells were significantly larger than
 those of the old brood cells (P&lt;0.05), but were almost the same
 between the newly built and the semi-rebuilt brood cells (P&gt;0.05).
 The weight and base thickness of the cocoon were significantly greater in
 the old brood cells than those in the semi-rebuilt brood cells
 (P&lt;0.05). Importantly, the birth weight, body length, and the
 tested 6 external morphological indices did not show a significant
 difference between the newly built and the semi-rebuilt brood cells
 (P&gt;0.05), but were significantly larger than those of old brood
 cells (P&lt;0.05). The size of brood cell and the external morphology
 of the workers showed a positive correlation. This study highlights the
 significance of Apis cerana cerana gnawing off the old brood cells
 providing a reference for its scientific breeding.
DOI: 10.5061/dryad.866t1g1td
title: Reducing the number of accepted species in Aspergillus series Nigri

description: The Aspergillus series Nigri contains
 biotechnologically and medically important species. They can produce
 hazardous mycotoxins, which is relevant due to the frequent occurrence of
 these species on foodstuffs and in the indoor environment. The taxonomy of
 the series has undergone numerous rearrangements, and currently, there are
 14 species accepted in the series, most of which are considered cryptic.
 Species-level identifications are, however, problematic or impossible for
 many isolates even when using DNA sequencing or MALDI-TOF mass
 spectrometry, indicating a possible problem in the definition of species
 limits or the presence of undescribed species diversity. To re-examine the
 species boundaries, we collected DNA sequences from three phylogenetic
 markers (benA, CaM and RPB2) for 276 strains
 from series Nigri and generated 18 new whole-genome
 sequences. With the three-gene dataset, we employed phylogenetic methods
 based on the multispecies coalescence model, including four single-locus
 methods (GMYC, bGMYC, PTP and bPTP) and one multilocus method (STACEY).
 From a total of 15 methods and their various settings, 11 supported the
 recognition of only three species corresponding to the three main
 phylogenetic lineages: A. niger, A.
 tubingensis and A. brasiliensis. Similarly, recognition
 of these three species was supported by the GCPSR approach (Genealogical
 Concordance Phylogenetic Species Recognition) and analysis in DELINEATE
 software. We also showed that the phylogeny based
 on benA, CaM and RPB2 is
 suboptimal and displays significant differences from a phylogeny
 constructed using 5 752 single-copy orthologous proteins; therefore, the
 results of the delimitation methods may be subject to a higher than usual
 level of uncertainty. To overcome this, we randomly selected 200 genes
 from these genomes and performed ten independent STACEY analyses, each
 with 20 genes. All analyses supported the recognition of only one species
 in the A. niger and A.
 brasiliensis lineages, while one to four species were
 inconsistently delimited in the A. tubingensis lineage.
 After considering all of these results and their practical implications,
 we propose that the revised series Nigri includes six
 species: A. brasiliensis, A. eucalypticola, A.
 luchuensis (syn. A. piperis), A.
 niger (syn. A. vinaceus and A.
 welwitschiae), A. tubingensis (syn. A.
 chiangmaiensis, A. costaricensis, A.
 neoniger and A. pseudopiperis) and A. vadensis.
 We also showed that the intraspecific genetic variability in the
 redefined A. niger and A.
 tubingensis does not deviate from that commonly found in other
 aspergilli. We supplemented the study with a list of accepted species,
 synonyms and unresolved names, some of which may threaten the stability of
 the current taxonomy.
DOI: 10.7280/d1mh5z
title: Revealing the role of ionic liquids in promoting fuel cell catalysts reactivity and durability

description: Ionic liquids have shown to be promising additives to the
 catalyst layer to enhance oxygen reduction reaction in polymer electrolyte
 fuel cells. However, fundamental understanding of their role
 in complex catalyst layers in practically relevant membrane
 electrode assembly environment is needed for rational design of highly
 durable and active platinum-based catalysts. Here
 we explore three imidazolium-derived ionic liquids,
 selected for their high proton conductivity and oxygen
 solubility, and incorporate them into high surface area carbon
 black support. Further, we establish a correlation between the physical
 properties and electrochemical performance of the ionic
 liquid-modified catalysts by providing direct evidence of ionic
 liquids role in altering hydrophilic/hydrophobic interactions within the
 catalyst layer
 interface. The resulting catalyst with
 optimized interface design achieved a high mass activity of 347 A
 g-1Pt at 0.9 V H2/O2, power density of 0.909 W
 cm-2 under H2/air and 1.5 bar and had only 0.11
 V potential decay at 0.8 A cm-2 after 30 k
 accelerated stress test cycles. This performance stems from substantial
 enhancement in Pt utilization, which is buried inside the mesopores and is
 now accessible due to ILs addition.
DOI: 10.5061/dryad.5mkkwh78q
title: Data from: Nutrigonometry I: using right-angle triangles to quantify nutritional trade-offs in performance landscapes

description: Animals regulate their food intake to maximise the expression of fitness
 traits but are forced to trade-off optimal expression of some fitness
 traits due to differences in nutrient requirements of each trait
 (‘nutritional trade-offs’). Nutritional trade-offs have been
 experimentally uncovered using the Geometric Framework for Nutrition (GF).
 However, current analytical methods to measure such responses rely on
 either visual inspection or complex models of vector calculations applied
 to multidimensional performance landscapes, making these approaches
 subjective, or conceptually difficult, computationally expensive, and in
 some cases inaccurate. Here, we present a simple trigonometric model to
 measure nutritional trade-offs in multidimensional landscapes
 (Nutrigonometry), which relies on the trigonometric relationships of
 right-angle triangles and thus, is both conceptually and computationally
 easier to understand and use than previous quantitative approaches. We
 apply Nutrigonometry to a landmark GF dataset for the comparison of
 several standard statistical models to assess model performance in finding
 regions in the performance landscapes. This revealed that polynomial
 (Bayesian) regressions can be used for precise and accurate predictions of
 peaks and valleys in performance landscapes, irrespective of the
 underlying structure of the data (i.e., individual food intakes vs fixed
 diet ratios). We then identified the known nutritional trade-off between
 lifespan and reproductive rate both in terms of nutrient balance and
 concentration for validation of the model. This shows Nutrigonometry
 enables a fast, reliable, and reproducible quantification of nutritional
 trade-offs in multidimensional performance landscapes, thereby broadening
 the potential for future developments in comparative research on the
 evolution of animal nutrition.
description: The data was collected by Lee et al., 2008 and is available here
 and in the Dryad entry for the previous manuscript of this series
 (Morimoto and Lihoreau, 2019 Am Nat). The data consists of measures of
 life-histories in <em>Drosophila</em> based on diets, using
 the Geometric Framework for Nutrition. 
description: R software is required, along with the suitable packages needed
 for the analysis. The specifications of the versions of each package are
 given in the PDF Demo file deposited alongside the data and the raw R
 scripts. q
DOI: 10.5061/dryad.zpc866tc1
title: Data and code from: Functional rarity of plants in German hay meadows - patterns on the species level and mismatches with community species richness

description: Functional rarity (FR) - a feature combining a species’ rarity with the
 distinctiveness of its traits - represents a promising tool to better
 understand the ecological importance of rare species and consequently to
 protect functional diversity more efficiently. Yet, we lack a systematic
 understanding of FR on both the species level (which species are
 functionally rare and why) and the community level (how is FR associated
 with biodiversity and environmental conditions). Here, we quantify FR for
 218 plant species from German hay meadows on a local, regional, and
 national scale by combining data from 6500 vegetation relevés and 15
 ecologically relevant traits. We investigate the association between
 rarity and trait distinctiveness on different spatial scales via
 correlation measures and show which traits lead to low or high trait
 distinctiveness via distance-based redundancy analysis. We test how
 species richness and FR are correlated and use boosted regression trees to
 determine environmental conditions driving species richness and FR. On the
 local scale, only rare species showed high trait distinctiveness while on
 larger spatial scales rare and common species showed high trait
 distinctiveness. As infrequent trait attributes (e.g., legumes, low
 clonality) led to higher trait distinctiveness, we argue that functionally
 rare species are either specialists or transients. While specialists
 occupy a particular niche in hay meadows leading to lower rarity on larger
 spatial scales, transients display distinct but maladaptive traits
 resulting in high rarity across all spatial scales. More functionally rare
 species than expected by chance occurred in species-poor communities
 indicating that they prefer environmental conditions differing from
 characteristic conditions of species-rich hay meadows. Finally, we argue
 that functionally rare species are not necessarily relevant for nature
 conservation, since many were transients from surrounding habitats. Yet,
 FR can facilitate our understanding of why species are rare in a habitat
 and under which conditions these species occur.
description: Data in this dataset were requested from external resources and
 are either:<br>a) publicly available, or<br>b) not publicly
 available due to privacy or ethical restrictions.
 <br>Data sources and instructions to request/download the
 data are given in the README file.
description: Required software:<br>R (4.1.2) to load ".RData"
 files<br>RStudio to open ".R" files containing the code
 used to carry out the analysis