cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mgqnk98wh
title: Direct and indirect effects of native plants and herbivores on biotic resistance to alien aquatic plant invasions

description: 1- Biotic resistance to alien plant invasions is mainly determined by
 ecological interactions in two layers of the food web: competition with
 native plant species, and herbivory by native herbivores. While the direct
 effect of native plants on alien plant performance via competition has
 been well documented across ecosystems, less is known about the direct and
 indirect effects of herbivores in providing biotic resistance. Our main
 aims were to determine whether temperate native aquatic plants and
 herbivores can provide biotic resistance to plant invasions, understand
 the underlying mechanisms and search for potential interactive effects of
 competition and herbivory on invader performance (i.e. growth). 2- We
 mimicked natural temperate mesotrophic and eutrophic freshwater lakes in
 mesoscosms, by growing three native submerged plant species in
 monocultures (Ceratophyllum demersum, Myriophyllum spicatum and
 Potamogeton perfoliatus) at three competition levels (no, low and high)
 without and with the native aquatic generalist snail Lymnaea stagnalis. We
 subsequently simulated an early stage of establishment of the South
 American highly invasive alien plant species Egeria densa. 3- We found
 that competition by native plant biomass significantly reduced invader
 performance but depended on native species identity. Herbivory had no
 direct negative effect on invader performance as the snails fed mainly on
 the available filamentous algae, which are commonly found in meso- and
 eutrophic systems, instead of on the plants. However, the consumption of
 filamentous algae by herbivores indirectly had positive effects on the
 invader total biomass, thus facilitating the invasion by E. densa.
 Nonetheless, these indirect effects worked through different pathways
 depending on the native plant identity. 4. Synthesis. We found evidence
 for biotic resistance through competition by native plant species.
 However, we show that herbivores can indirectly facilitate South American
 plant E. densa invasion promoting its growth through selective feeding on
 filamentous algae, but this effect depends on the native plant species
 involved. Our experiment illustrates the important role of indirect
 interactions to understand the potential of biotic resistance in natural
 ecosystems.
description: This file contains all data used as input for the analyses, the
 piecewise structural equation modelling (Experiment explanatory notes +
 Experiment) and feeding trial (Feeding trial explanatory notes + Feeding
 trial).
DOI: 10.5061/dryad.2fqz612kr
title: Parallel CRISPR-Cas9 screens clarify impacts of p53 on screen performance

description: CRISPR-Cas9 genome engineering has revolutionised high-throughput
 functional genomic screens. However, recent work has raised concerns
 regarding the performance of CRISPR-Cas9 screens using TP53 wild-type
 human cells due to a p53-mediated DNA damage response (DDR) limiting the
 efficiency of generating viable edited cells. To directly assess the
 impact of cellular p53 status on CRISPR-Cas9 screen performance, we
 carried out parallel CRISPR-Cas9 screens in wild-type and TP53 knockout
 human retinal pigment epithelial cells using a focused dual guide RNA
 library targeting 852 DDR-associated genes. Our work demonstrates that
 although functional p53 status negatively affects identification of
 significantly depleted genes, optimal screen design can nevertheless
 enable robust screen performance. Through analysis of our own and
 published screen data, we highlight key factors for successful screens in
 both wild-type and p53-deficient cells.
description: Primarily the dataset contains the results of CRISPR screens.
 RPE-1 cells that are TP53-null or wild-type were infected with pooled
 plasmid libraries targeting selected genes and grown for up to 19 days.
 Samples were taken at 3, 15 & 19 days. Samples were havested
 and DNA extracted. PCR was used to isolate and amplify barcodes on
 plasmids in the CRISPR library. The barcode abundances were mapped to
 plasmids targeting specific genomic loci, and these abundances are
 included here. Abundances from other screens were downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE128210. MAGeCK (https://sourceforge.net/p/mageck) was used to obtain significance values for gene enrichment/depletion from the abundances, and the output files are included. Further analysis was performed using Python, and a Python notebook (.ipynb) is included.
description: Python version &gt;= 3.6 is required to run the notebook (it
 uses f-strings); and the packages: scipy, matplotlib, pandas, statsmodels,
 seaborn & jupyter (plus dependencies).
 Files: analysis_and_charts.ipynb –
 Python notebook that produces all the figures in the paper.
 all_magecks.csv – Table of significance and log2 fold change
 values of genes, calculated by mageck. *.counts.tsv –
 Guide/barcode abundances from different screens.
 sample_replicate_details.xlsx – Details about samples in our
 screen. transomics_ddr_v2-1.csv – Details of the
 library used in our screen. OR_gene_list.txt – Names
 of olfactory receptor genes. mageck_results/* – files
 output by MAGeCK
DOI: 10.5061/dryad.gb5mkkwkw
title: Canadian polar bear population structure using genome-wide markers

description: Predicting the consequences of environmental changes, including
 human-mediated climate change on species, requires that we quantify
 range-wide patterns of genetic diversity and identify the ecological,
 environmental, and historical factors that have contributed to it. Here,
 we generate baseline data on polar bear population structure across most
 Canadian subpopulations (n=358) using 13,488 genome-wide single nucleotide
 polymorphisms (SNPs) identified with double digest restriction
 site-associated DNA sequencing (ddRAD). Our ddRAD dataset showed three
 genetic clusters in the sampled Canadian range, congruent with previous
 studies based on microsatellites across the same regions; however due to a
 lack of sampling in Norwegian Bay, we were unable to confirm the existence
 of a unique cluster in that subpopulation. These data on the genetic
 structure of polar bears using SNPs provide a detailed baseline against
 which future shifts in population structure can be assessed, and
 opportunities to develop new non-invasive tools for monitoring polar bears
 across their range.
description: ddRAD libraries were constructed following the Peterson et al.
 (2012) protocol, using MluCI and PstI restriction enzymes and size
 selecting the DNA insert to 275-365 bp using a BluePippin Prep. Libraries
 were sequenced using paired-end 125 bp Illumina HiSeq 2500. PCR duplicates
 were removed and reads were assebled to the polar bear reference genome
 UrsMar_1.0 using BWA mem. Variant detection and genotype calling were done
 using samtools mpileup and bcftools call. Loci were filtered using
 VCFtools.
DOI: 10.25349/d9rk54
title: Data from: Hypoxia tolerance is unrelated to swimming metabolism of wild, juvenile striped bass (Morone saxatilis)

description: Juvenile striped bass reside in the Chesapeake Bay where they are likely
 to encounter hypoxia that could affect their metabolism and performance.
 The ecological success of this economically valuable species may depend on
 their ability to tolerate hypoxia and perform fitness-dependent activities
 in hypoxic waters. We tested whether there is a link between hypoxia
 tolerance (HT) and oxygen consumption rate (MO2) of juvenile striped bass
 measured while swimming in normoxic and hypoxic water, and to identify the
 interindividual variation and repeatability of these measurements. Fish (N
 = 18) had their HT (loss of equilibrium) measured twice collectively, 11
 weeks apart, between which each fish had their MO2 measured
 individually while swimming in low flow (10.2 cm s-1) and high flow (~ 67%
 Ucrit) under normoxia and hypoxia. Both HT and MO2 varied
 substantially among individuals. HT increased across 11 weeks while the
 rank order of individual HT was significantly repeatable. Similarly,
 MO2 increased in fish swimming at high flow in a repeatable
 fashion, but only within a given level of oxygenation. MO2 was
 significantly lower when fish were swimming against high flow under
 hypoxia. There were no clear relationships between HT and a
 fish&[prime]s MO2 while swimming under any conditions.
 Only the magnitude of increase in HT over 11 weeks and an
 individual&[prime]s MO2 under low flow were correlated.
 The results suggest that responses to the interacting stressors of hypoxia
 and exercise vary among individuals, and that HT and change in HT are not
 simple functions of aerobic metabolic rate. 
description: 1. Hypoxia tolerance was determined following hypoxia challange
 test protocol (see methods in published article). Hypoxia tolerance is
 expressed as cumulative oxygen deficit. Fish ID, size, and date of repeat
 tests are provided.  2. Oxygen consumption rates were
 measured in swim tunnel respirometer. Metabolic performance was measured
 in fish under normoxic and hypoxic conditions at low and high flow. Oxygen
 consumption data represent visually inspected data, after it was corrected
 for background respiration. Fish ID, size and date of tests are
 provided. 
description: Repeat hypoxia tolerance, oxygen consumption rates under hypoxia
 and normoxia and two flow rates, body size, and cost of transport data of
 individual juvenile striped bass. These data are supplementary to
 "Hypoxia tolerance is unrelated to swimming metabolism of wild,
 juvenile striped bass <em>(Morone saxatilis</em>)"
 manuscript accepted in the Journal of Experimantal Biology.
DOI: 10.5061/dryad.c59zw3r42
title: Ontogenetic consistency in oak defence syndromes

description: 1. Plant species allocate resources to multiple defensive traits
 simultaneously, which often leads to so-called defence syndromes, i.e.
 suites of traits that are co-expressed. While reports of ontogenetic
 variation in plant defences are commonplace, no research to date has
 tested for ontogenetic shifts in defence syndromes. In addition, we still
 know little about how ecological and evolutionary factors concurrently
 shape plant defence syndromes via ontogeny. 2. We tested for ontogenetic
 variation in plant defence syndromes by measuring a suite of defensive and
 nutritional traits on saplings and adult trees of 29 oak (Quercus,
 Fagaceae) species distributed across Europe, North America, and Asia. In
 addition, we investigated if these syndromes exhibited a phylogenetic
 signal to elucidate their macro-evolutionary nature, whether they were
 associated with levels of herbivore pressure and climatic conditions, and
 if such evolutionary and ecological patterns were contingent on ontogeny.
 3. Our analyses revealed three distinct defence syndromes: the first one
 including species with high defences, the second one including species
 with high defences and low nutrient levels, and the third one including
 species with high nutrients and thinner leaves. Interestingly, these
 defence syndromes remained virtually unchanged across the two ontogenetic
 stages sampled. In addition, our analyses indicated no evidence for a
 phylogenetic signal in oak syndromes, a result consistent for both
 ontogenetic stages. Finally, with respect to ecological factors, we found
 no effect of climatic conditions on defences for either ontogenetic stage,
 whereas herbivory levels differed among defence syndromes in adults but
 not saplings suggesting an association between herbivore pressure and
 syndrome type that is contingent on ontogeny. 4. Synthesis. Together,
 these findings indicate that defence syndromes remain remarkably
 consistent across oak ontogenetic stages, are evolutionarily labile, and
 while they appear unrelated to climate they are associated with herbivory
 levels in an ontogenetic-dependent manner. Overall, this study builds
 towards a better understanding of ecological and evolutionary factors
 shaping multivariate plant defensive phenotypes.
description: Readme tab of spreadsheet defines variables.
DOI: 10.5061/dryad.70rxwdbtf
title: Data from: Allopatric divergence and hybridization within Cupressus chengiana (Cupressaceae), a threatened conifer in the northern Hengduan Mountains of western China

description: Having a comprehensive understanding of population structure, genetic
 differentiation and demographic history is important for the conservation
 and management of threatened species. High‐throughput sequencing (HTS)
 provides exciting opportunities to address a wide range of factors for
 conservation genetics. Here, we generated HTS data and identified 266,884
 high‐quality single nucleotide polymorphisms from 82 individuals
 of Cupressus chengiana , to assess population genomics
 across the species' full range, comprising the Daduhe River (DDH),
 Minjiang River (MJR) and Bailongjiang River (BLJ) catchments in western
 China. admixture , principal components analysis and
 phylogenetic analyses indicated that each region contains a distinct
 lineage, with high levels of differentiation between them (DDH, MJR and
 BLJ lineages). MJR was newly distinguished compared to previous surveys,
 and evidence including coalescent simulations supported a hybrid origin of
 MJR during the Quaternary. Each of these three lineages should be
 recognized as an evolutionarily significant unit (ESU), due to isolation,
 differing genetic adaptations and different demographic history.
 Currently, each ESU faces distinct threats, and will require different
 conservation strategies. Our work shows that population genomic approaches
 using HTS can reconstruct the complex evolutionary history of threatened
 species in mountainous regions, and hence inform conservation efforts, and
 contribute to the understanding of high biodiversity in mountains.
description: We identified 266,884
 high-quality SNPs from 82 individuals to assess population genomics of
 <i>Cupressus chengiana</i> across its full
 range.  To get a high-quality reference,
 single-molecule real-time (SMRT) sequencing was used to obtain the
 full-length transcriptome of <i>C. chengiana</i>. A total of
 82 samples were collected for RNA-seq. We used bwa-mem  to align the
 quality-filtered reads of each individual to the refences sequences. We
 used the “mpileup” command in SAMTOOLS to identify SNPs. Data were
 filtered with the following processes: SNPs with a mapping quality
 &lt;30, a mapping depth &lt;10, genotyping rate &lt;50% per
 group, minor allele frequency (MAF) &lt;5%, or in 5bps windows around
 any indel.
DOI: 10.5281/zenodo.17979729
title: Reconstructed Efficiency Parameters from Superconducting Qubit Relaxation Data

description: This dataset contains reconstructed efficiency parameters derived from publicly available relaxation measurements of superconducting qubit systems operated on IBM quantum processors (Fez and Marrakesh backends).

The dataset is based on entropy-like and energy-proxy quantities reported by the hardware during irreversible relaxation following state preparation. Informational entropy changes are reconstructed using standard information-theoretic normalization, and an effective efficiency parameter is inferred by comparing dissipated energy to entropy production scaled by thermal bandwidth.

The analysis is presented independently of any interpretive or foundational framework. It is intended to support quantitative characterization of thermodynamic efficiency in quantum measurement and relaxation processes and to enable reproducibility and cross-platform comparison by other researchers.

All reconstruction steps, assumptions, and aggregation procedures are documented within the dataset.Used as validation example in A Minimal Admissibility Constraint for Irreversible Physical UpdatesThis dataset is used as a proof-of-concept validation in a study of admissibility constraints for irreversible physical updates. It demonstrates operational extraction of energetic cost, informational entropy change, and an effective bandwidth proxy in a controlled quantum platform. The dataset does not assert universality or invariance across domains and is not tied to any particular interpretation of quantum measurement.
DOI: 10.5061/dryad.3r2280gcn
title: Experimental evolution of competing bean beetle species reveals long-term reversals of short-term evolution, but no consistent character displacement

description: Interspecific competition for shared resources should select for
 evolutionary divergence in resource use between competing species, termed
 character displacement. Many purported examples of character displacement
 exist, but few completely rule out alternative explanations. We reared
 genetically-diverse populations of two species of bean beetles,
 Callosobruchus maculatus and C. chinensis, in allopatry and sympatry on a
 mixture of adzuki beans and lentils, and assayed oviposition preference
 and other phenotypic traits after four, eight, and twelve generations of
 (co)evolution. C. maculatus specializes on adzuki beans; the generalist C.
 chinensis uses both beans. C. chinensis growing in allopatry emerged
 equally from both bean species. In sympatry, the two species competing
 strongly and coexisted via strong realized resource partitioning, with C.
 chinensis emerging almost exclusively from lentils and C. maculatus
 emerging almost exclusively from adzuki beans. However, oviposition
 preferences, larval survival traits, and larval development rates in both
 beetle species did not vary consistently between allopatric vs. sympatric
 treatments. Rather, traits evolved in treatment-independent fashion, with
 several traits exhibiting reversals in their evolutionary trajectories.
 For example, C. chinensis initially evolved a slower egg-to-adult
 development rate on adzuki beans in both allopatry and sympatry, then
 subsequently evolved back towards the faster ancestral development rate.
 Lack of character displacement is consistent with a previous similar
 experiment in bean beetles, and may reflect lack of evolutionary
 trade-offs in resource use. However, evolutionary reversals were
 unexpected and remain unexplained. Together with other empirical and
 theoretical work, our results illustrate the stringency of the conditions
 for character displacement.
DOI: 10.6078/d1x98s
title: Data from: Low temperatures impact species distributions of jumping spiders across a desert elevational cline

description: Temperature is known to influence many aspects of organisms and is
 frequently linked to geographical species distributions. Despite the
 importance of a broad understanding of an animal’s thermal biology, few
 studies in- corporate more than one metric of thermal biology. Here we
 examined an elevational assemblage of Habronattus jumping spiders to
 measure different aspects of their thermal biology including thermal
 limits (CTmin , CTmax), thermal preference, V̇CO2 as proxy for metabolic
 rate, locomotor behavior and warming tolerance. We used these data to test
 whether thermal biology helped explain how species were distributed across
 elevation. Habronattus had high CTmax values, which did not differ among
 species across the elevational gradient. The highest-eleva- tion species
 had a lower CTmin than any other species. All species had a strong thermal
 preference around 37 °C. With respect to performance, one of the middle
 elevation species was significantly less temperature-sensitive in
 metabolic rate. Differences between species with respect to locomotion
 (jump distance) were likely driven by differences in mass, with no
 differences in thermal performance across elevation. We suggest that
 Habronattus distributions follow Brett’s Rule, a rule that predicts more
 geographical variation in cold tolerance than heat. Additionally, we
 suggest that physiological tolerances interact with biotic factors,
 particularly those related to courtship and mate choice to influence
 species distributions. Habronattus also had very high warming tolerance
 values (&gt;20 °C, on average). Taken together, these data suggest
 that Habronattus are resilient in the face of cli- mate-change related
 shifts in temperature.
description: Please see specific methods for data collection in online
 supplement for published article. Contact the author if
 unavailable.
description: Please see metadata files that describe columns for each
 dataset
DOI: 10.5061/dryad.63xsj3v00
title: Quantification of uncertainties introduced by data-processing procedures of sap flow measurements using the cut-tree method on a large mature tree

description: Motivation: Sap flow sensors are crucial instruments to understand
 whole-tree water use. The lack of direct calibration of the available
 methods on large trees and the application of several data-processing
 procedures may jeopardize our understanding of water uptake dynamics by
 increasing the uncertainties around sensor-based estimates. We directly
 compared the heat ratio method (HRM) sap flow measurements to water uptake
 measured gravimetrically using the cut-tree method on a large mature aspen
 tree to quantify those uncertainties for ten consecutive days. Dataset: In
 this dataset, we provide sap flux density (ten-minutes intervals;
 g.cm-2.hr-1; corrected for wounding and sapwood thermal diffusivity)
 obtained from four HRM sap flow sensors installed at 2.5 m high on the
 focus tree (20 m tall, 60 years old trembling aspen in the boreal
 mixedwood region of Alberta) between July 18th and August 22nd 2017. We
 present the code and data (weather data from neighboring weather station)
 used to calculate whole-tree sap flux (L.hr-1) from each of the individual
 sensors using different methods of radial integration of sap flux density
 across the sapwood area estimated via different calculations, as well as
 different zero-flow corrections used. The cut-tree procedure was applied
 to the focus tree, and gravimetric measurements of water uptake
 (ten-minutes intervals) were made using a recording scale. We directly
 compared the different estimates of hourly, daily and cumulative sap flows
 obtained with gravimetric measurement of water uptake. We present the code
 providing the statistical analysis and results reported in the associated
 publication (Merlin, M., Solarik, K.A., Landhäusser, S.M. Quantification
 of uncertainties introduced by data-processing procedures of sap flow
 measurements using the cut-tree method on a large mature tree. 2020.
 Agricultural and Forest Meteorology,
 http://dx.doi.org/10.1016/j.agrformet.2020.107926)
description: See methods of the associated publication (Merlin, M., Solarik,
 K.A., Landhäusser, S.M. Quantification of uncertainties introduced by
 data-processing procedures of sap flow measurements using the cut-tree
 method on a large mature tree. 2020. Agricultural and Forest Meteorology,
 http://dx.doi.org/10.1016/j.agrformet.2020.107926).
description: A metadata file is provided with description and units of each of
 the variables presented in all the datafiles.
 Individual data files are provided. A unique R
 script is provided with ample annotations within the script to run the
 entire data processing, analysis and visualization presented in the
 association publication (Merlin, M., Solarik, K.A., Landhäusser, S.M.
 Quantification of uncertainties introduced by data-processing procedures
 of sap flow measurements using the cut-tree method on a large mature tree.
 2020. Agricultural and Forest Meteorology,
 http://dx.doi.org/10.1016/j.agrformet.2020.107926).