cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vq83bk3ss
title: Larger cells have relatively smaller nuclei across the Tree of Life

description: Larger cells have larger nuclei, but the precise relationship between cell
 size and nucleus size remains unclear, and the evolutionary forces that
 shape this relationship are debated. We compiled data for almost 900
 species – from yeast to mammals – at three scales of biological
 organisation: among‐species, within‐species, and among‐lineages of a
 species that was artificially selected for cell size. At all scales, we
 showed that the ratio of nucleus size to cell size (the ‘N: C’ ratio)
 decreased systematically in larger cells. Size evolution appears more
 constrained in nuclei than cells: cell size spans across six orders of
 magnitude, whereas nucleus size varies by only three. The next important
 challenge is to determine the drivers of this apparently ubiquitous
 relationship in N:C ratios across such a diverse array of organisms.
description: We compiled from the scientific litterature an among‐species
 dataset on cell size and nucleus size covering 879 species, ranging from
 prokaryotes to mammals and also including the nucleoid (c.f. nucleus) of
 prokaryotes. For the within‐species dataset, we compiled from scientific
 articles 7929 observations across 20 species, ranging from yeast to plants
 to metazoans. Finally, we evolved in the laboratory 72 lineages of the
 green alga <em>Dunaliella tertiolecta</em> for 500 generations
 (ca. 3 years), artificially selecting for different cell sizes while
 tracking the fate of their N:C ratios.
description: Instructions: There are three main
 folders: (1) “Among-species (DNA and Nucleus)”
 generates Fig. 1 (2) "Within-species"
 generates Fig. 2  (3) “Dunaliella tertiolecta”
 generates Fig. 3 In each subfolder, open the .R script
 using the statistical software R. Within the script file: (1) check that
 all packages are installed in the computer (otherwise install before
 running the script), and (2) set the directory where the script is located
 in the computer. After having done that, everything else should work by
 simply running the file in R. The script will read all data, calculate
 statistics, plot images, and save the images in the same folder. The file
 is designed to run in Mac computers.
DOI: 10.5061/dryad.f4qrfj6w8
title: Transcriptome for: MYB42 inhibits hypocotyl cell elongation by coordinating brassinosteroid homeostasis and signaling in Arabidopsis

description: The precise control of brassinosteroids (BRs) homeostasis and
 signaling is a prerequisite for hypocotyl cell elongation in plants.
 Little is known, however, of such regulators of BR homeostasis and
 signaling. Here, we have demonstrated that MYB42 negatively regulates
 hypocotyl elongation through partial inhibition of
 BRASSINAZOLE-RESISTANT 1 (BZR1) signaling and promotion of BR
 inactivation. Transgenic Arabidopsis plants repressing the
 expression of MYB42 and its paralog MYB85 (MYB85
 RNAi;myb42) exhibited longer hypocotyls than wild-type (WT) plants in
 darkness, while MYB42 or MYB85 overexpression inhibits hypocotyl
 elongation. Hypocotyl length of MYB85 RNAi;myb42 plants can be
 resorted into WT level by MYB42 overexpression. MYB42 inhibits
 hypocotyl elongation by mediating BR signaling, because MYB42 expression
 is repressed with BR treatment and in the dominant BR mutant
 bzr1-1D, and mutation
 of both MYB42 and MYB85 enhances the
 dwarf phenotype of the BR receptor mutant bri1-5. BZR1 directly
 represses MYB42 expression in response to BR, and the hypocotyl
 length of bzr1-1D is reduced in MYB42 overexpression
 plants but increased in MYB85 RNAi;myb42 plants. These results
 show MYB42 is a negative target of BZR1. Transcriptome data revealed
 that a number of BZR1-induced genes associated with cell
 elongation are down-regulated by MYB42, suggesting that MYB42 may
 partially inhibit BZR1 signaling. In addition, MYB42 enlarges its action
 in BR signaling through feedback activation of the BR-inactivating
 enzyme DOGT1. The present study shows a MYB42-mediated
 multilevel system that contributes to fine regulation of
 BR-induced hypocotyl elongation.
description: Hypocotyls of
 5-day-old dark-grown <em>MYB85RNAi;myb42 </em>and wild-type
 seedlings with or without
 0.02 uM
 PCZ were sampled for
 total RNA extraction with the TRIzol reagent (Invitrogen). For each genotype, 3 independent lines including at least 100 plants were selected. After mRNA library construction, sequencing was performed on an Illumina HiSequation 2500 platform (Annoroad Gene). Sequence data with base-pair qualities in the Q&gt;20 were extracted by custom Perl scripts. The filtered reads were mapped to the <i>Arabidopsis</i> genome (TAIR10) using the splice-aware read aligner TopHat2 software with default parameters (Kim et al. 2013). To calculate gene expression intensity, read counts were normalized to the number of fragments per kilobase of transcript per million mapped reads (FPKM) according to the gene length and total mapped reads. The R package DEGseq was used to identify DEGs from RNA-Seq data. Genes with FPKM less than 1 were removed from analyses. DEGs were characterized according to the criterion of fold change (FC) &gt;2.0 and false discovery rate (FDR) &lt; 0.05.
DOI: 10.5061/dryad.0p2ngf21s
title: Zalophus hindflipper turning metrics and angle of attack

description: California sea lions (Zalophus californianus) are a highly maneuverable
 species of marine mammal. During uninterrupted, rectilinear swimming, sea
 lions oscillate their foreflippers to propel themselves forward without
 aid from the collapsed hindflippers, which are passively trailed. During
 maneuvers such as turning and leaping (porpoising), the hindflippers are
 spread into a delta-wing configuration. There is little information
 defining the role of otarrid hindflippers as aquatic control surfaces. To
 examine Z. californianus hindflippers during maneuvering, trained sea
 lions were video recorded underwater through viewing windows performing
 porpoising behaviors and banking turns. Porpoising by a trained sea lion
 was compared with sea lions executing the maneuver in the wild. Anatomical
 points of reference (ankle and hindflipper tip) were digitized from videos
 to analyze various performance metrics and define the use of the
 hindflippers. During a porpoising bout, the hindflippers were considered
 to generate lift when surfacing with a mean angle of attack of 14.6±6.3
 deg. However, while performing banked 180 deg turns, the mean angle of
 attack of the hindflippers was 28.3±7.3 deg, and greater by another 8-12
 deg for the maximum 20% of cases. The delta-wing morphology of the
 hindflippers may be advantageous at high angles of attack to prevent
 stalling during high-performance maneuvers. Lift generated by the
 delta-shaped hindflippers, in concert with their position far from the
 center of gravity, would make these appendages effective aquatic control
 surfaces for executing rapid turning maneuvers.
DOI: 10.5061/dryad.x95x69pjg
title: Soil N enrichment mediates carbon allocation in a dominant grass during drought

description: Carbon (C) allocation strategy plays a critical role in plant
 adaptability, with knock-on effects for community stability under
 environmental change. Based on optimal partitioning theory we asked two
 questions: (1) How is plant C allocation within tissues affected by
 long-term nutrient enrichment (N addition)? And (2) does N addition alter
 how plants allocate C under drought? To address these questions, we
 conducted a greenhouse experiment using the widespread perennial C3 grass,
 Leymus chinensis, under four treatments: “Watered”, “Dry”, “Watered+N” and
 “Dry+N”. 13CO2 pulse labelling was used to trace C transport through the
 plant-soil system. We found that, in combination, drought and N addition
 resulted in offsetting effects on C allocation. Greater aboveground
 biomass under N addition resulted in higher C loss via aboveground plant
 respiration even under drought, which plays a more important role in the
 adjustment of R/S ratio than does the trade-off between above and
 belowground compartments. Compared to the concept of active phenotype
 adjustment for maximized growth rate in traditional optimal partitioning
 theory, our results imply that pre-drought allometry, which changes under
 long-term resource addition, also determine how plants respond to drought
 and their adaptability to changing environmental conditions.
description: The
 <sup>13</sup>CO<sub>2</sub> pulse labeling
 experiments were immediately carried out after 35 days of drought
 treatment. Four pots from each of the treatments were randomly selected to
 measure natural background δ<sup>13</sup>C of each C pool from
 each block. The rest of the 36 pots in each block were equipped with a
 polymethyl methacrylate chamber (0.9 m × 0.6 m × 0.7 m, 95% light
 permeability) before labelling. To stabilize the transparent chamber and
 reduce leakage of <sup>13</sup>CO<sub>2</sub>, an
 iron groove with a seal ring was fixed to the soil in advance of pulse
 labeling. In addition to ice packs and four symmetrical electric fans,
 temperature stabilization and air circulation in the chambers was achieved
 by an external air circulation system composed of a pump and
 pressure-tight cool box. CO<sub>2</sub> concentration and
 interior air temperature were monitored by an infrared gas analyzer
 (LI-6400, LiCor Inc., Lincoln, NE, USA) and thermocouple thermometer.
 During pulse labelling,
 <sup>13</sup>CO<sub>2</sub> (&gt; 99.9%
 CO<sub>2</sub> with 99 atom% <sup>13</sup>C,
 Cambridge Isotope Laboratories, Andover, MA, USA) was repeatedly added
 over a period of 90 min to maintain CO<sub>2</sub>
 concentrations between 330 - 480 ppm. All pulse labeling was conducted on
 two consecutive sunny days between 8:30 - 10:30 am.
description: Please contact Bo Meng before using.
DOI: 10.5061/dryad.612jm643q
title: Photosynthesis from stolen chloroplasts can support sea slug reproductive fitness

description: Some sea slugs are able to steal functional chloroplasts (kleptoplasts)
 from their algal food sources, but the role and relevance of
 photosynthesis to the animal host remain controversial. While some
 researchers claim that kleptoplasts are slowly digestible ‘snacks’, others
 advocate that they enhance the overall fitness of sea slugs much more
 profoundly. Our analysis show light-dependent incorporation of 13C and 15N
 in the albumen gland and gonadal follicles of the sea slug Elysia timida,
 representing translocation of photosynthates to kleptoplast-free
 reproductive organs. Long-chain polyunsaturated fatty acids with reported
 roles in reproduction were produced in the sea slug cells using labelled
 precursors translocated from the kleptoplasts. Finally, we report reduced
 fecundity of E. timida by limiting kleptoplast photosynthesis. The present
 study indicates that photosynthesis enhances the reproductive fitness of
 kleptoplast-bearing sea slugs, confirming the biological relevance of this
 remarkable association between a metazoan and an algal-derived organelle.
DOI: 10.5061/dryad.qnk98sfh0
title: Double burden of malnutrition in two Nigerian states

description: Background: Double burden of malnutrition (DBM) is the co-existence of
 overweight/obesity and undernutrition. Rising prevalence rates of
 childhood overweight/obesity in Nigeria have been reported, whilst
 undernutrition continues to be prevalent. This study aimed to estimate the
 prevalence and distribution of underweight, stunting, thinness,
 overweight/obesity, and the DBM among school-aged children and adolescents
 in Gombe and Osun States in Nigeria. Methods: This was a community-based
 cross-sectional study carried out in Osun and Gombe States in 2019 – 2020.
 A total of 1,200 children aged 6 – 19 years were recruited using
 multi-stage sampling technique. Weight, height and data on demographic,
 socio-economic, household/family characteristics of the children were
 collected using structured interviewer administered questionnaires.
 Nutritional status was calculated using the WHO 2007 reference values
 using BMI-for-age (thinness, overweight/obesity), height-for-age
 (stunting) and weight-for-age (underweight). DBM was described at the
 population and individual levels. Results: The mean age of the respondents
 was 11.6 ± 3.8 years. The overall prevalence rate of stunting was 34.9%,
 underweight was 13.5%, thinness was 10.3% and overweight/obese was 11.4%
 and 4.0% had individual level DBM, which typifies the DBM at individual
 and population levels. These rates differed significantly across
 demographic, socio-economic and household/family characteristics (p
 &lt; 0.05). Gombe State, which is in the Northern part of Nigeria, had
 significantly higher burden of stunted, underweight and thin children than
 Osun State, while Osun State, in the Southern part of Nigeria, had a
 significantly higher burden of overweight/obesity. Conclusions: The study
 found evidence of DBM both at population and individual levels. The
 overall prevalence rates of stunting, underweight, thinness and
 overweight/obesity in this study were high, and they differed
 significantly across the demographic, socio-economic and household/family
 characteristics. There is the need for government and all other
 stakeholders to design nutritional educational programmes that will target
 both under- and over-nutrition among older children in the different
 contexts
DOI: 10.5061/dryad.0rxwdbs0t
title: Chemical analyses and insect interactions of an easO mutant of Metarhizium brunneum

description: Several fungi, including the plant root symbiont and insect pathogen
 Metarhizium brunneum, produce lysergic acid amides via a branch of the
 ergot alkaloid pathway. Lysergic acid amides include important
 pharmaceuticals and pharmaceutical lead compounds and have potential
 ecological significance, making knowledge of their biosynthesis relevant.
 Many steps in the biosynthesis of lysergic acid amides have been
 determined, but terminal steps in the synthesis of lysergic acid
 α-hydroxyethylamide (LAH)––by far the most abundant lysergic acid amide in
 M. brunneum––are unknown. Ergot alkaloid synthesis (eas) genes are
 clustered in the genomes of fungi that produce these compounds, and the
 eas clusters of LAH producers contain two uncharacterized genes (easO and
 easP) not found in fungi that do not produce LAH. Knockout of easO via a
 CRISPR-Cas9 approach eliminated LAH and resulted in accumulation of
 alternate lysergic acid amides lysergyl-alanine and ergonovine. Despite
 the elimination of LAH, the total concentration of lysergic acid
 derivatives was not affected significantly by the mutation.
 Complementation with a wild-type allele of easO restored the ability to
 synthesize LAH. Substrate feeding studies indicated that neither
 lysergyl-alanine nor ergonovine were substrates for the product of easO
 (EasO). EasO had structural similarity to Baeyer-Villiger monooxygenases
 (BVMOs), and labeling studies with deuterated alanine supported a role for
 a BVMO in LAH biosynthesis. The easO knockout had reduced virulence to
 larvae of the insect Galleria mellonella, indicating that LAH contributes
 to virulence of M. brunneum on insects and that LAH has biological
 activities different from ergonovine and lysergyl-alanine.
description: Data were collected as described in Steen et al. 2021. Applied
 and Environmental Microbiology 88:e00748-21. 
description: Data are contained in an excel file with separate tabs for each
 of the major data set.  The tab labeled “hplc data” contains data
 contributing to Table 1 of the Applied and Environmental Microbiology
 article.  The “deu ala” tab contains data supporting the statistical
 analyses in Fig. 3.  The tab labeled “insect survival” contains insect
 survival data used to prepare Figure 4.  The “spores” tab contains data
 used to prepare Figure 5.  The data in each tab are arrayed to be copied
 and pasted into a JMP worksheet.
DOI: 10.5061/dryad.2fqz612pf
title: Diversity and biogeography of Mediterranean freshwater blennies (Blenniidae, Salaria)

description: Aim: In the Mediterranean Biodiversity Hotspot freshwater fishes are key
 biogeographical indicators while their habitats are vulnerable to ongoing
 anthropogenic pressures. The freshwater blenny is a widespread endemic
 taxon in this area. However, our understanding of the overall diversity of
 specific populations and their phylogenetic relationships is sparse. Thus,
 we aim to investigate the genetic diversity, infer relationships among
 sampled populations related to major paleoenvironmental changes and
 suggest insights for future research and conservation targets. Location:
 Mediterranean Basin Methods: We studied
 171 Salaria specimens from 51 rivers and lakes, and from
 13 countries surrounding the Mediterranean Sea. For assessing the
 phylogenetic relationships among different locations, we used mtDNA d-loop
 and Intron S7 sequences. Furthermore, we inferred absolute divergence
 times as well as demographic changes using secondary calibrations and
 investigated the diversity within major lineages using haplotype networks
 as well as several geographical and genetic clustering methods. Results:
 We found eight well differentiated lineages, each of which being confined
 to a particular geographic region. The onset of the freshwater blenny
 radiation was dated around the Messinian salinity crisis. Further
 differentiation happened during the Plio- and Pleistocene with signatures
 of population expansion after the Last Glacial Maximum in some of the main
 lineages. Main Conclusions: Due to their unusual widespread distribution,
 the freshwater blennies represent an excellent model for studying
 phylogeographic structure across the Mediterranean basin biodiversity
 hotspot. The extant diversity and distribution of the
 freshwater Salaria species mirrors
DOI: 10.5061/dryad.5tb2rbp48
title: Subannual phenology and the effect of staggered fruit ripening on dispersal competition

description: Seed dispersal mutualisms evolve in complex communities of plants and
 frugivorous animals, within which indirect interactions such as
 competition and facilitation can occur. Many tropical plants reproduce
 subannually in multiple episodes per year. Yet, the consequences of
 episodic reproduction on interactions with seed dispersers remains largely
 unexplored. We studied Guarea guidonia (Meliaceae), a subannually
 reproducting tree, to examine temporal variation in seed dispersal within
 a tropical forested landscape in the central Dominican Republic. We
 hypothesized that foraging by seed dispersers would (a) increase with
 daily ripe fruit set on focal trees, (b) decrease with increasing ripe
 fruit biomass of neighboring plants, and (c) decrease in response to the
 fruiting periods of other taxa at the landscape scale. Over 18 months, we
 tracked the phenology of 24 focal trees and quantified foraging during
 fruiting phases through repeated observations, simultenously measuring
 seed dispersal in traps beneath isolated perches across the study
 landscape. Date was the only clear predictor of frugivore visitation, with
 early and late peaks in activity during the 5-month fruiting period. The
 midseason decline in foraging at focal trees matched a decline in Guarea
 dispersal to seed traps independently of fruit abundance. Declines in
 foraging associated with Guarea were inversely related to peak dispersal
 of higher quality lipid-rich fruiting species. Our results suggest that
 multiple flowering episodes and subsequent asynchronous fruit ripening of
 low-quality fruits can reduce competititive pressure from other high
 quality fruiting species, implying that this potentialy bet-hedging
 strategy may be an overlooked factor in the evolution of subannual
 reproduction.
description: Missing values in data files are denoted with "NA"
DOI: 10.5061/dryad.q573n5tjb
title: Moving beyond the diversity paradox: the limitations of competition-based frameworks in understanding species diversity

description: Over the last century, ecologists have attempted to understand patterns of
 species diversity by showing stable coexistence arising from a baseline
 expectation of competitive exclusion. This expectation stems from an
 explicit assumption of resource scarcity and implicit assumptions of
 Malthusian struggle and winner-take-all dynamics. Fidelity to the
 competitive exclusion principle (CEP) presents species diversity as a
 paradox: if species compete for limited resources, how can they coexist?
 In this essay, we investigate the contradiction between the theoretical
 expectation of competitive exclusion and the empirical prevalence of
 multispecies communities. We trace the persistence of the CEP in
 ecological research despite numerous challenges and explore publishing
 trends suggesting that this framework has resulted in a disproportionate
 focus on competition and exclusion in contemporary research. From a
 critical science studies perspective, we analyze the sociopolitical
 factors that have contributed to these patterns. We argue that we must
 excavate the ideological foundation upon which competition-based
 coexistence research has been built to move beyond the current perceived
 “diversity paradox.” To that end, we propose shifting the functional null
 hypothesis of coexistence research, introducing the notion of a
 “coexistence principle,” which positions the persistence of multispecies
 communities as the rule rather than the exception in nature.
description: This dataset contains several keyword searches that we used to
 assess the state of community ecology in its exploration of species
 coexistence. Several data files and R code are included along with a
 readme file that explains methods and the contents of each file.
DOI: 10.5061/dryad.t76hdr819
title: Data from: Vertebrate scavenging dynamics differ between carnivore and herbivore carcasses in the northern boreal forest

description: Vertebrate scavenging can impact food web dynamics, but our understanding
 of this process stems predominantly from monitoring herbivore carrion and
 extrapolating results across carcass types. Recent evidence suggests
 carnivores may avoid intraguild scavenging to reduce parasite
 transmission. If this behavior is widespread across diverse ecosystems,
 estimation of nutrient cycling and community scavenging rates are likely
 biased to a currently unknown degree. We examined whether the time to
 initiate scavenging, carcass persistence, or the richness of species
 scavenging in the boreal forest of Yukon, Canada, differed between
 carnivore and herbivore carcasses. Vertebrates took longer to initiate
 scavenging on carnivore carcasses (3.2 days) relative to herbivore
 carcasses (1.1 days), and carnivore carcasses persisted on the landscape
 for over a month longer (48.4 days and 5.5 days, respectively). The longer
 persistence times were due to the reduction in scavenging by carnivores
 such as Canada lynx (Lynx canadensis). Decreased scavenging was caused by
 changes in the propensity to consume carnivore carrion, as the number of
 species detecting a carcass within the first week did not differ between
 carnivore and herbivore carcasses. These results have ramifications for
 our understanding of nutrient cycling and food web dynamics in the boreal
 forest, and provide further support that carcass type should be included
 in future studies.