cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m63xsj3zc
title: Efficient targeted integration directed by short homology in zebrafish and mammalian cells

description: Efficient precision genome engineering requires high frequency and
 specificity of integration at the genomic target site. Here, we describe a
 set of resources to streamline precision gene targeting in zebrafish and
 demonstrate the broader utility of the method in mammalian cells. Our
 approach uses short homology of 24-48 bp to drive targeted integration of
 DNA reporter cassettes by homology-mediated end joining (HMEJ) at high
 frequency. Our vector series, pGTag (plasmids for Gene Tagging), contains
 reporters flanked by a universal CRISPR sgRNA sequence to target double
 strand breaks in vivo and expose homology arms. We observed high rates of
 germline transmission (22-100%) for targeted knock-ins at eight zebrafish
 loci and efficient integration at safe harbor loci in porcine and human
 cells. 1 kb long homology arms did not increase targeting efficiency. Our
 system provides a straightforward and cost-effective approach for high
 efficiency gene targeting applications in CRISPR and TALEN compatible
 systems.
description: sgRNA targeted mutagenesis efficiency was determined by measuring
 the frequency of indel mutations at the target site. Individual embryos
 were injected with 150 pg Cas9 mRNA and 25 pg sgRNA. PCR amplicons over
 the cut site were first examined for mutagenesis (or a smear) on a 2-3%
 agarose gels in 1X TAE.  For the <i>noto</i> exon
 1, <i>cx43.4</i> exon 2, <i>esama</i> exon
 2, <i>msna</i> exon 6, <i>rb1 </i>exon 2, exon 4
 and exon 25, <i>aqp1a1</i> exon 1
 and <i>aqp8a1</i> exon 1 sgRNAs, at 3 dpf 5 embryos were
 pooled in 50 ul of 50 mM NaOH, and 2 ul used as template for PCR. Barcoded
 libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for
 Illumina (NEB #E7645L) for MiSeq 250 bp single read sequencing at the
 University of Kansas Genome Sequencing Core. Indel analysis of MiSeq reads
 was performed using Cas-Analyzer at CRISPR RGEN Tools (http://www.rgenome.net/cas-analyzer/#!).
DOI: 10.5061/dryad.h9w0vt4fh
title: FT TFL1 bimolecular luciferase complementation assays

description: CORRECTION Ho, W.W.H., and Weigel, D. (2014). Structural Features
 Determining Flower-Promoting Activity of Arabidopsis FLOWERING LOCUS T.
 Plant Cell 26: 552-564. Published February 2014. DOI:
 https://doi.org/10.1105/tpc.113.115220. During the assembly of
 Supplemental Figure 7 and Figure 8, six luciferase images of individual
 leaves were inadvertently duplicated. These images served to illustrate
 the strength of interactions between FT and TFL1 proteins and their mutant
 variants with GRF and TCP proteins, as measured qualitatively in split
 luciferase assays and in support of independent, quantitative
 yeast-two-hybrid experiments. This Dryad data set includes the original
 photographs of bimolecular luciferase complementation assays after
 Agrobacterium tumefaciens mediated transient transformation
 of N. benthamiana leaves. The associated key links the constructs
 tested for bimolecular luciferase complementation with the
 photographs.
description: <strong>Bimolecular Luciferase Complementation Assays</strong> <i>Nicotiana benthamiana</i> was transiently transformed as described (Voinnet et al., 2003), and samples were analyzed 4 days after inoculation (Gou et al., 2011). Before measurement, leaves only infiltrated with luciferin (negative control) and leaves infiltrated with a 35S:<i>LUC</i> construct and luciferin (positive control) were used for calibrating the Orca 2-BT cooled CCD camera (Hamamatsu Photonics, Hamamatsu, Japan). Gou, J.Y., Felippes, F.F., Liu, C.J., Weigel, D., and Wang, J.W. (2011). Negative regulation of anthocyanin biosynthesis in Arabidopsis by a miR156-targeted SPL transcription factor. Plant Cell 23, 1512-1522.<br> <br> Voinnet, O., Rivas, S., Mestre, P., and Baulcombe, D. (2003). An enhanced transient expression system in plants based on suppression of gene silencing by the p19 protein of tomato bushy stunt virus. Plant J. 33, 949-956.
DOI: 10.5061/dryad.tdz08kpwq
title: Origin of the natural variation in the storage of dietary carotenoids in freshwater amphipod crustaceans

description: Carotenoids are diverse lipophilic natural pigments which are stored in
 variable amounts by animals. Given the multiple biological functions of
 carotenoids, such variation may have strong implications in evolutionary
 biology. Crustaceans such as Gammarus amphipods store large amounts of
 these pigments and inter-population variation occurs. While differences in
 parasite selective pressure have been proposed to explain this variation,
 the contribution of other factors such as genetic differences in the
 gammarid ability to assimilate and/or store pigments, and the
 environmental availability of carotenoids cannot be dismissed. This study
 investigates the relative contributions of the gammarid genotype and of
 the environmental availability of carotenoids in the natural variability
 in carotenoid storage. It further explores the link of this natural
 variability in carotenoid storage with major crustacean immune parameters.
 We addressed these aspects using the cryptic diversity in the amphipod
 crustacean Gammarus fossarum and a diet supplementation protocol in the
 laboratory. Our results suggest that natural variation in G. fossarum
 storage of dietary carotenoids results from both the availability of the
 pigments in the environment and the genetically-based ability of the
 gammarids to assimilate and/or store them, which is associated to levels
 of stimulation of cellular immune defences. While our results may support
 the hypothesis that carotenoids storage in this crustacean may evolve in
 response to parasitic pressure, a better understanding of the specific
 roles of this large pigment storage in the crustacean physiology is
 needed.
DOI: 10.5281/zenodo.18388806
title: Gravity = Magnetism + Heat

description: Absolutely everything in our universe is dual. Gravity is not an exception. There are only two different types of energy: magnetism, which is the energy inside matter (i.e., inside atoms or molecules), and heat, the energy outside matter. Gravity is, therefore, the equilibrium between magnetic and heat energies. Spherical tridimensional magnetism rules the cosmological systems—it's 100% attractive—any repulsion is converted into attraction by torque. Modern Physics claims to know it, however, where is the mathematical formalization of it? Einstein's Special and General Relativity theories are built upon Maxwell's Equations on magnetism, that are theoretical, because it only works at frozen time in constrained objects. Planets, stars and galaxies are, obviously, not suited for Einstein's Relativity. Furthermore, neither Newton nor Einstein ever took into consideration thermal attraction. This paper rescues Modern Physics, initiating the post-Einsteinian era.
DOI: 10.6071/m3m08p
title: Iterative evolution of large-bodied hypercarnivory in canids benefits species but not clades

description: Ecological specialization has costs and benefits at various scales: traits
 benefitting an individual may disadvantage its population, species or
 clade. In particular, large body size and hypercarnivory (diet over 70%
 meat) have evolved repeatedly in mammals; yet large hypercarnivores are
 thought to be trapped in a macroevolutionary “ratchet”, marching
 unilaterally toward decline. Here, we weigh the impact of this
 specialization on extinction risk using the rich fossil record of North
 American canids (dogs). In two of three canid subfamilies over the past 40
 million years, large-bodied hypercarnivory appears to constrain
 diversification at the clade level, biasing specialized lineages to
 extinction. However, despite shorter species durations, extinction rates
 of large hypercarnivores have been mostly similar to those of all other
 canids. Extinction was size- and carnivory-selective only at the end of
 the Pleistocene epoch 11,000 years ago, suggesting that large
 hypercarnivores were not disadvantaged at the species level before
 anthropogenic influence.
DOI: 10.5061/dryad.b8gtht78t
title: Data from: Digit ratio and length asymmetry in calves’ limbs

description: This study considered possible sexual dimorphism in the relative lengths
 of the second, third and fourth digits (digit ratio), in calves.
 Furthermore, a different length of the bone structures of the third (3D)
 and of the fourth (4D) digits has been examined as an evolutionary
 adaptation to locomotion on soft ground. The length of the digital bones
 of the right fore-limb of 33 females and 15 male calves was measured in
 vivo using a portable X-ray machine. The vestigial structure of the second
 digit (2D), and 3D and 4D, from metacarpus to the third phalanx were
 considered in a mixed model, as well as some ratios between 2D and
 different parts of 3D or 4D (2D:3D and 2D:4D). A covariate for the mean
 finger length was considered for digit ratios to control for possible
 biases due to shape allometry. Shorter first phalanx and trotter were
 found in 3D than in 4D, and the reverse for the third phalanx. The 2D was
 significantly shorter in females, as well as the second phalanges of 3D
 and 4D. Significant sex differences in 2D:3D and 2D:4D were found for some
 digit parts of 3D and 4D and for the first phalanges of 3D:4D. These
 ratios were always shorter in females, in contrast to that found in most
 mammals. The asymmetry between 3D and 4D could mean a functional
 adaptation for locomotion. Sex differences in 2D:4D and 3D:4D were found,
 but with a reverse pattern than in most mammal species
 (males &gt; females rather than
 males &lt; females). In this regard digit ratio in
 calves was similar to that of Old World monkeys. This study is the first
 investigation of digit ratio in Ungulates, whose limbs differ from the
 limbs of most Mammals, maintaining five digits. The reverse pattern of sex
 differences (digit ratios: males &gt; females) could
 be due to the peculiar nature of the vestigial dewclaw of 2D and to the
 hormone patterns acting on this digit during development, but further
 research is required around this topic.
description: The dataset consists in radiographic measurements of the right
 foreleg of newborn calves taken using a portable X-ray unit. Images were
 acquired using a portable scanner and then  imported into a
 image-processing software. The measures of the digital bones of interest
 were therefore obtained by a trained operator. Two radiographic images
 were obtained using the X-ray machine and then acquired and measured for
 a sample of individuals to assess the repeatability. Additional digit
 measures and digit ratios were obtained by summing some digital measures
 or by performing ratios. Further details are provided directly into the
 dataset (Excel sheet).
description: The dataset includes all the data that have been used in the
 manuscript. Variable definition is reported directly within the
 spreadsheet.
DOI: 10.5061/dryad.v6wwpzgs2
title: Differences in oxidative status explain variation in thermal acclimation capacity between individual mosquitofish (Gambusia holbrooki)

description: 1. Evolutionary theory predicts that the capacity to acclimate should be
 favoured in variable environments. However, perfect compensation for
 thermal variation is rare and the capacity for thermal acclimation can
 vary considerably between individuals within natural populations. This
 variation may be explained by costs associated with acclimation, but it is
 not clear what these costs are. 2. We tested the hypothesis that oxidative
 stress is a cost of acclimation that could explain the variation between
 individuals in acclimation capacity. We acclimated individual mosquitofish
 (Gambusia holbrooki, n = 416) to 18oC and 28oC sequentially, and
 determined swimming performance at each temperature to evaluate their
 acclimation capacity. Fish were then acclimated to either cold (18oC) or
 warm (28oC) conditions, and we increased antioxidant capacities of a
 subset of fish experimentally by administering N-acetyl cysteine (NAC). We
 measured H2O2 production, catalase antioxidant activities, and oxidative
 damage to proteins and membranes. 3. We show that there is significant
 variation in acclimation capacity between individuals, and that there is a
 trade-off between acclimation capacity and swimming performance in warm
 conditions. Mean swimming performance across both acclimation temperatures
 increased with increasing acclimation capacity, but the increase was small
 biologically. Hence, greater thermal plasticity (high acclimation
 capacity) resulted in only minor performance benefits across acclimation
 conditions. We verified this rather surprising result in replicate
 populations grown in outdoor mesocosms. 4. ROS production, antioxidant
 activities, and oxidative damage were higher in cold-acclimated fish, and
 particularly in those fish with low capacity for acclimation. However,
 experimentally increasing antioxidant capacities with NAC alleviated these
 changes to oxidative status, suggesting a causal relationship. Hence,
 oxidative stress may be a cost that constrains the capacity for
 acclimation. Together, the performance trade-off and oxidative cost
 indicate that phenotypic plasticity is not always advantageous in variable
 environments, and instead bet-hedging may be a more beneficial strategy,
 particularly in short-lived species.
description: Data were collected in a laboratory experiment, and from a
 mesocosm experiment. Details are given in the main manuscript and in the
 Explanatory Notes tab of the Excel sheet providing the data.
description: Raw data and details of treatments are provided in the data Excel
 sheet, as well as Explanatory notes regarding data collection.
DOI: 10.5061/dryad.k0p2ngf5b
title: Data from: Identifying error and accurately interpreting eDNA metabarcoding results: a case study to detect vertebrates at arid zone waterholes

description: Environmental DNA (eDNA) metabarcoding surveys enable rapid, non-invasive
 identification of taxa from trace samples with wide-ranging applications
 from characterising local biodiversity to identifying food-web
 interactions. However, the technique is prone to error from two major
 sources: i) contamination through foreign DNA entering the workflow, and
 ii) misidentification of DNA within the workflow. Both types of error have
 the potential to obscure true taxon presence or to increase taxonomic
 richness by incorrectly identifying taxa as present at sample sites but
 multiple error sources can remain unaccounted for in metabarcoding
 studies.  Here, we use data from an eDNA metabarcoding study
 designed to detect vertebrate species at waterholes in Australia’s arid
 zone to illustrate where and how in the workflow errors can arise, and how
 to mitigate those errors. We detected the DNA of 36 taxa spanning 34
 families, 19 orders and 5 vertebrate classes in water samples from
 waterholes, demonstrating the potential for eDNA metabarcoding surveys to
 provide rapid, non-invasive detection in remote locations, and to widely
 sample taxonomic diversity from aquatic through to terrestrial taxa.
 However, we initially identified 152 taxa in the samples, meaning there
 were many false positive detections. We identified the sources of these
 errors, allowing us to design a stepwise process to detect and remove
 error, and provide a template to minimise similar errors that are likely
 to arise in other metabarcoding studies. Our findings suggest eDNA
 metabarcoding surveys need to be carefully conducted and
 screened for errors to ensure their accuracy.
description: eDNA water samples collected from waterholes in central
 Australia. Metabarcoding analyses targeting vertebrates. Sequenced on
 Illumina MiSeq. See paper for full method details. 
description: Sequence data have been deconvoluted to link sequences to each
 individual sample.
DOI: 10.5061/dryad.w3r2280mp
title: Phylogenetic tree of S-protein genes of selected betacoronaviruses

description: The emergence of SARS-CoV-2 has resulted in more than 200,000 infections
 and nearly 9,000 deaths globally so far. This novel virus is thought to
 have originated from an animal reservoir, and acquired the ability to
 infect human cells using the SARS-CoV cell receptor hACE2. In the wake of
 a global pandemic it is essential to improve our understanding of the
 evolutionary dynamics surrounding the origin and spread of a novel
 infectious disease. One way theory predicts selection pressures should
 shape viral evolution is to enhance binding with host cells. We first
 assessed evolutionary dynamics in select betacoronavirus spike protein
 genes to predict where these genomic regions are under directional or
 purifying selection between divergent viral lineages at various scales of
 relatedness. With this analysis, we determine a region inside the
 receptor-binding domain with putative sites under positive selection
 interspersed among highly conserved sites, which are implicated in
 structural stability of the viral spike protein and its union with human
 receptor hACE2. Next, to gain further insights into factors associated
 with coronaviruses recognition of the human host receptor, we performed
 modeling studies of five different coronaviruses and their potential
 binding to hACE2. Modeling results indicate that interfering with the salt
 bridges at hot spot 353 could be an effective strategy for inhibiting
 binding, and hence for the prevention of coronavirus infections. We also
 propose that a glycine residue at the receptor binding domain of the spike
 glycoprotein can have a critical role in permitting bat variants of the
 coronaviruses to infect human cells.
description: The most similar genomes to SARS-CoV-2 MN908947 were retrieved
 using BLASTp vs the NR database of GenBank. Genomes were then aligned
 using MAUVE and the S-protein gene was trimmed. The extracted genomic
 sections were aligned using a translation align option of Geneious with a
 MAFFT plugin. The phylogenetic reconstruction of S-protein genes was
 performed with PhyML, using a GTR+I+G model, using 100 non-parametric
 bootstrap replicates.
DOI: 10.5061/dryad.08kprr500
title: Biodiversity components mediate the response to forest loss and the effect on ecological processes of plant-frugivore assemblages

description: 1. Anthropogenic disturbances are jeopardizing ecosystem functioning
 globally. Yet we know very little about the effect of human impacts on
 ecological processes derived from trophic interactions. By focusing on
 biodiversity components of consumer and resource organisms, such as the
 diversity of phylogenetic lineages and the diversity of traits that
 influence species interactions, it is possible to simultaneously address
 the responses to disturbances and their effects on processes. 2. Here, we
 evaluate the consequences of forest loss on the ecological process of
 frugivory between fleshy-fruited plants and frugivorous birds. For two
 years, and at 14 sites representing a gradient of forest cover in the
 Cantabrian Range (N Iberian Peninsula), we monitored fruit and bird
 abundance, and fruit consumption. We compared the response to forest loss
 of both plants and birds by assessing changes in phylogenetic and
 trait-based functional diversity in relation to forest cover. We further
 evaluated how changes in these biodiversity components translate into
 functional changes by estimating the degree of functional complementarity
 of plant and bird species. 3. We found different responses of plants and
 birds to forest loss. The diversity of plant assemblages did not respond
 to changes in forest cover, whereas bird assemblages markedly lost
 phylogenetic and trait-based functional diversity at high levels of forest
 loss. Functional complementarity of birds was well predicted by
 phylogenetic and trait-based functional diversity, but functional
 complementarity of plants depended exclusively on the diversity of traits.
 4. Forest loss filtered avian phylogenetic lineages and traits, and
 influenced how birds contributed to the frugivory process. These results
 show how the diversity decay of one trophic level may compromise
 ecological processes derived from trophic interactions. Therefore, we
 suggest that a multitrophic response-effect framework, which includes
 measures of functional traits, lineages and species functional
 contributions across trophic levels, may be required to fully understand
 the ecological consequences of biodiversity decays.
description: Please see ReadMe file
DOI: 10.5061/dryad.dr7sqv9vp
title: Plant diversity enhances rehabilitation of degraded lands by spurring plant-soil feedbacks

description: Despite a rich history of theoretical and empirical work showing that
 increasing biodiversity results in higher ecosystem function, this
 research has not made a commensurate impact on the reclamation of degraded
 lands, where enhancing ecosystem function is of primary importance. 2. In
 this study, we manipulated plant diversity on heavily degraded mine lands
 and showed that increasing plant diversity greatly enhanced the
 reclamation of these lands. We found that high diversity assemblages were
 often associated with more biomass, higher stability and less toxic
 foliage than low diversity treatments, although the monocultures of
 Miscanthus sinensis (the most productive species) performed equally well
 as some of the polycultures. 3. Our results showed that species
 composition and richness explained most of the total variation in biomass
 yield of the experimental plots, indicating that both the selection and
 complementarity effects influenced the positive diversity effects observed
 in this study. 4. M. sinensis and legumes (as a functional group) were
 found to be the main contributors to the selection effect. The plots with
 M. sinensis tended to harbor fewer soil fungal pathogens than those
 without it and a similar pattern was observed for the legumes, indicating
 a poorly known plant-soil fungal pathogen feedback for these plants. This
 kind of feedback appeared to play an important role also in shaping the
 positive plant species richness-ecosystem function relationships recorded
 in the degraded mine land. More importantly, we provide the first evidence
 that the observed plant-soil fungal pathogen feedbacks were likely
 mediated by chitinolytic bacteria that release anti-fungal enzymes.
 Cellulose-degrading bacteria that aid in plant decomposition and nutrient
 cycling also attained higher abundances in plots with higher plant
 diversity, suggesting the contribution of another kind of plant-soil
 feedback to the positive diversity effects. 5. Synthesis and applications.
 Our findings reveal that high diverse plant assemblages are better able to
 spur plant-soil feedbacks and that increasing plant diversity is an
 important strategy to enhance land reclamation efficiency. Meanwhile, our
 results also indicate that some plants such as M. sinensis and legumes
 should be preferentially used to establish diverse plant communities for
 rapid reclamation of degraded lands.