cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.98sf7m0j4
title: Phenotypic plasticity is not a cline: thermal physiology of an intertidal barnacle over 20 degrees of latitude

description: 1. Our understanding of the plastic and evolutionary potential of
 ectothermic organisms and their populational impacts in the face of rapid
 global change remains limited. Studies attempting on the relationship
 between the magnitude of thermal variability across latitude and the
 degree of phenotypic plasticity exhibited by marine ectotherms are
 inconclusive. We state that the latter arises from the narrow range of
 thermal variability captured by the limited span of the latitudinal
 gradients studied to date. 2. Using a mechanistic ecophysiological
 approach and a satellite-based assessment of the relevant environmental
 variables (i.e. temperature and food availability), we studied individuals
 of the intertidal barnacle Jehlius cirratus from seven local populations
 widely spread along the Humboldt current System that spanning two
 biogeographic regions. At the same time, we synthesized published
 information on the local abundance of our study species across a total of
 76 sites representing 20 degrees of latitude, and spanning from 18 to
 42°S. 3. We examined the effects of latitude and environmental variability
 on metabolic rate plasticity, thermal tolerance (thermal breadth and
 thermal safety margins) and their impacts on the abundance of this
 widespread marine invertebrate. 4. We demonstrate that the phenotypic
 plasticity of metabolic rate in J. cirratus populations is not related to
 latitude. In turn, thermal breadth is explained by the temperature
 variability each population experiences. Furthermore, we found clinal
 variation with a poleward decrease of the critical thermal minimum,
 suggesting that episodic extreme low temperatures represent a ubiquitous
 selective force on the lower thermal limit for ectotherms. 5. Across our
 study gradient, plasticity patterns indicate that populations at the
 equatorial extreme are more vulnerable to a warming climate, while
 populations located in the biogeographic transitional zone (i.e. high
 environmental heterogeneity), on the center of the gradient, display
 higher levels of phenotypic plasticity, and may represent a genetic buffer
 for the effects of ocean warming. Together, our results suggest the
 existence of a fitness trade-off involving the metabolic cost of
 plasticity and population density that is evident only across the vast
 latitudinal gradient examined.
DOI: 10.5061/dryad.1jwstqjv7
title: Code from: Realistic genetic architecture enables organismal adaptation as predicted under the folk definition of inclusive fitness

description: A fundamental task of evolutionary biology is to explain the pervasive
 impression of organismal design in nature, including traits benefiting
 kin. Inclusive fitness is considered by many to be a crucial piece in this
 puzzle, despite ongoing discussion about its scope and limitations. Here
 we use individual-based simulations to study what quantity (if any)
 individual organisms become adapted to maximise when genetic architectures
 are more or less suitable for the presumed main driver of biological
 adaptation: namely, cumulative multi-locus evolution. As an expository
 device we focus on a hypothetical situation called Charlesworth’s paradox,
 in which altruism is seemingly predicted to evolve, yet altruists
 immediately perish along with their altruistic genes. Our results support
 a recently proposed re-definition of inclusive fitness, which is concerned
 with the adaptive design of whole organisms as shaped by multi-locus
 evolution, rather than with selection for any focal gene. They also
 illustrate how our conceptual understanding of adaptation at the
 phenotypic level should inform our choice of genetic assumptions in
 abstract simplified models.
DOI: 10.5281/zenodo.18277175
title: GNSS-Acoustic observation data off Hokkaido during 2019–2024

description: --- GNSS-A_Hokkaido_2019-2024.tar.gz ---GNSS-Acoustic datasets collected at G21, G22, and G23, off Hokkaido, during 2019-2024.

The site coordinates are listed in "./array_center.txt". Each GNSS-A site is compoased of four seafloor transponders, and thier positions are listed in "./site_name/pxp-ini.inp"Each line of "pxp-ini.inp" show the EW, NS, and UD positions in meter.EW and NS positions are projected from the site coordinate.

The data files for each campaign are stored at an individual directory: "./site_name/campaign_name".Each campaign has three data files: "obsdata.inp", "ss_prof.inp", and "tr-ant.inp".The data format of these files is following the GNSS-A positioning software, SeaGap.https://f-tommy.github.io/SeaGapDocs/dataformat/

"obsdata.inp": GNSS-A observational file- 1: Seafloor transponder number (corresponding to the line number of "pxp-ini.inp")- 2: Two-way travel time [sec]- 3: Transmitted time [sec] (cumulative seconds from 2000-01-01 00:00:00)- 4-6: Sea-surface platform positions (EW, NS, UD) when transmitting [m]- 7-9: Sea-surface platform attitude (heading, pitch, roll) when transmitting [deg]- 10: Recieved time [sec] (cumulative seconds from 2000-01-01 00:00:00)- 11-13: Sea-surface platform positions (EW, NS, UD) when recieving [m]- 14-16: Sea-surface platform attitude (heading, pitch, roll) when recieving [deg]- 17: Flag for the kinematic positioning- 18: Identifying number of the sea surface platforms (corresponding to the line number of "tr-ant.inp")

"ss_prof.inp": XCTD measurement results with deeper (>~2000 m) extrapolation using WOA2018- 1: water depth [m]- 2: sound speed [m/sec]

"tr-ant.inp": relative position between a GNSS antenna and a sea surface transponder- 1: X-position [m]- 2: Y-position [m]- 3: Z-position [m] --- Supplementary_Table1-3.xlsx ---This file contains three sheets corresponding to Supplementary Table 1–3 in the original papar.Table S1: GNSS-A observation periodThe GNSS-A observation campaigns off Nemuro are listed. During campaigns 3, 4, 6, and 7, the research vessel and wave glider were employed simultaneously.Table S2: Array displacements at GNSS-A sitesThe estimated array displacements for each campaign at G21, G22, and G23 are listed. Zero displacement indicates the average position among the campaigns, and the temporal evolution of the displacements is provided in IGS14, realizing ITRF2014. The error in this table is defined as the 1σ standard deviation of the Markov chain Monte Carlo samples.Table S3: Horizontal array displacement rates of GNSS-A sitesThe displacement rates at G21, G22, and G23 relative to the onshore reference site (950101), with rates of 0.861 (EW) and −0.718 (NS) cm/yr in IGb14 realizing ITRF2014, are listed.
DOI: 10.5281/zenodo.18277176
title: GNSS-Acoustic observation data off Hokkaido during 2019–2024

description: --- GNSS-A_Hokkaido_2019-2024.tar.gz ---GNSS-Acoustic datasets collected at G21, G22, and G23, off Hokkaido, during 2019-2024.

The site coordinates are listed in "./array_center.txt". Each GNSS-A site is compoased of four seafloor transponders, and thier positions are listed in "./site_name/pxp-ini.inp"Each line of "pxp-ini.inp" show the EW, NS, and UD positions in meter.EW and NS positions are projected from the site coordinate.

The data files for each campaign are stored at an individual directory: "./site_name/campaign_name".Each campaign has three data files: "obsdata.inp", "ss_prof.inp", and "tr-ant.inp".The data format of these files is following the GNSS-A positioning software, SeaGap.https://f-tommy.github.io/SeaGapDocs/dataformat/

"obsdata.inp": GNSS-A observational file- 1: Seafloor transponder number (corresponding to the line number of "pxp-ini.inp")- 2: Two-way travel time [sec]- 3: Transmitted time [sec] (cumulative seconds from 2000-01-01 00:00:00)- 4-6: Sea-surface platform positions (EW, NS, UD) when transmitting [m]- 7-9: Sea-surface platform attitude (heading, pitch, roll) when transmitting [deg]- 10: Recieved time [sec] (cumulative seconds from 2000-01-01 00:00:00)- 11-13: Sea-surface platform positions (EW, NS, UD) when recieving [m]- 14-16: Sea-surface platform attitude (heading, pitch, roll) when recieving [deg]- 17: Flag for the kinematic positioning- 18: Identifying number of the sea surface platforms (corresponding to the line number of "tr-ant.inp")

"ss_prof.inp": XCTD measurement results with deeper (>~2000 m) extrapolation using WOA2018- 1: water depth [m]- 2: sound speed [m/sec]

"tr-ant.inp": relative position between a GNSS antenna and a sea surface transponder- 1: X-position [m]- 2: Y-position [m]- 3: Z-position [m] --- Supplementary_Table1-3.xlsx ---This file contains three sheets corresponding to Supplementary Table 1–3 in the original papar.Table S1: GNSS-A observation periodThe GNSS-A observation campaigns off Nemuro are listed. During campaigns 3, 4, 6, and 7, the research vessel and wave glider were employed simultaneously.Table S2: Array displacements at GNSS-A sitesThe estimated array displacements for each campaign at G21, G22, and G23 are listed. Zero displacement indicates the average position among the campaigns, and the temporal evolution of the displacements is provided in IGS14, realizing ITRF2014. The error in this table is defined as the 1σ standard deviation of the Markov chain Monte Carlo samples.Table S3: Horizontal array displacement rates of GNSS-A sitesThe displacement rates at G21, G22, and G23 relative to the onshore reference site (950101), with rates of 0.861 (EW) and −0.718 (NS) cm/yr in IGb14 realizing ITRF2014, are listed.
DOI: 10.5061/dryad.vt4b8gtrz
title: Proteomic traits vary across taxa in a coastal Antarctic phytoplankton bloom

description: Production and use of proteins is under strong selection in microbes, but
 it is unclear how proteome-level traits relate to ecological strategies.
 We identified and quantified proteomic traits of eukaryotic microbes and
 bacteria through an Antarctic phytoplankton bloom using in situ
 metaproteomics. Different taxa, rather than different environmental
 conditions, formed distinct clusters based on their ribosomal and
 photosynthetic proteomic proportions, and we propose that these
 characteristics relate to ecological differences. We defined and used a
 proteomic proxy for regulatory cost, which showed that SAR11 had the
 lowest regulatory cost of any taxa we observed at our summertime Southern
 Ocean study site. Haptophytes had lower regulatory cost than diatoms,
 which may underpin haptophyte-to-diatom bloom progression in the Ross Sea.
 We were able to make these proteomic trait inferences by assessing various
 sources of bias in metaproteomics, providing practical recommendations for
 researchers in the field. We have quantified several proteomic traits
 (ribosomal and photosynthetic proteomic proportions, regulatory cost) in
 eukaryotic and bacterial taxa, which can then be incorporated into
 trait-based models of microbial communities that reflect resource
 allocation strategies.
description: Samples were collected at the Antarctic sea ice edge in the Ross
 Sea, and metagenomic, metatranscriptomic, and metaproteomic analyses were
 conducted on each sample. Contained in this data submission are the
 metaproteomic bioinformatic pipeline output, database configurations,
 metaproteomic simulation output, cofragmentation bias analysis output,
 targeted proteomics data summaries, and culture proteomic data
 summaries.
DOI: 10.5061/dryad.mcvdnck12
title: Characteristics of patients admitted to hospital with COVID-19 during the first wave of the pandemic in Malta

description: Introduction: The COVID-19 pandemic has posed major challenges to
 all aspects of healthcare. Malta's population density, large
 proportion of elderly and high prevalence of diabetes and obesity put the
 country at risk of uncontrolled viral transmission and high mortality.
 Despite this, Malta achieved low mortality rates compared to figures
 overseas. The aim of this paper is to identify key factors that
 contributed to these favorable outcomes. Methods: This is a
 retrospective, observational, nationwide study which evaluates outcomes of
 patients during the first wave of the pandemic in Malta, from the 7th of
 March to the 24th of April 2020. Data was collected on demographics and
 mode of transmission. Hospitalization rates to Malta's main general
 hospital, Mater Dei Hospital, length of in-hospital stay, intensive care
 unit admissions and 30-day mortality were also analyzed.
 Results: There were 447 confirmed cases in total; 19.5% imported,
 74.2% related to community transmission and 6.3% nosocomially transmitted.
 Ninety-three patients (20.8%) were hospitalized, of which 4 were children.
 Patients with moderate-severe disease received hydroxychloroquine and
 azithromycin, in line with evidence available at the time. A total of 4
 deaths were recorded, resulting in an all-cause mortality of 0.89%.
 Importantly, all admitted patients with moderate-severe disease survived
 to 30-day follow up. Conclusion: Effective public health
 interventions, widespread testing, remote surveillance of patients in the
 community and a low threshold for admission are likely to have contributed
 to these favorable outcomes. Hospital infection control measures were key
 in preventing significant nosocomial spread. These concepts can
 potentially be applied to stem future outbreaks of viral diseases.
 Patients with moderate-severe disease had excellent outcomes with no
 deaths reported at 30-day follow up.
DOI: 10.5061/dryad.05qfttf2s
title: Resolving the consequences of gradual phenotypic plasticity for populations in variable environments

description: Phenotypic adjustments following environmental change are ubiquitous and
 trait changes arising through phenotypic plasticity often lag behind their
 environmental stimuli. Evolutionary biologists seeking to understand how
 adaptive plasticity can evolve have extensively studied this phenomenon.
 However, the ecological consequences of common features of plastic
 responses to environmental variability, including gradual phenotypic
 change (i.e., slower than the pace of environmental change), are
 underappreciated. We present a framework based on the unifying concept of
 phenotype x environment performance landscapes that encompasses gradual
 plasticity. Then, we experimentally investigate the environmental contexts
 where gradual plasticity is important, using freshwater phytoplankton
 populations exposed to thermal variation. Finally, based on our conceptual
 framework, we develop a mathematical model of gradual plasticity that
 explains population dynamics in variable environments better than common
 alternative models. Understanding and accounting for the ecological
 effects of plasticity in variable environments is critical to making vital
 predictions and advancing ecology.
DOI: 10.5061/dryad.sf7m0cg67
title: Data from: Facebook groups as citizen science tools for plant species monitoring

description: Species list of the vascular flora of Sicily and related plant
 traits analysed in the paper "Facebook groups as citizen science
 tools for plant species monitoring". These include: floral traits,
 vegetative traits, life form, plant size, traditional use (edible/healing
 plants only). All traits were extracted from the digital
 archives of the Flora of Italy (Pignatti et al. 2017-2019) except
 for the conservation status of species, which was taken from Raimondo et
 al. (2011) and from the related updates proposed by
 Orsenigo et al. (2018). The number of records of a given
 species in the Facebook group "Flora Spontanea Siciliana" and in
 the subset of vegetation plots from Sicily extracted from the
 "European Vegetation Archive" are reported in the first two
 columns after the species name.
description: Please, note: the file consists of two spreadsheets. The first
 one is the dataset, the second includes the description of the variables
 included in the dataset.
 <strong>References</strong> Orsenigo, S., Montagnani, C., Fenu, G., Gargano, D., Peruzzi, L., Abeli, T., … Rossi, G. (2018). Red Listing plants under full national responsibility: Extinction risk and threats in the vascular flora endemic to Italy. <i>Biological Conservation</i>, <i>224</i>, 213–222. https://doi.org/10.1016/j.biocon.2018.05.030 Pignatti, S., Guarino, R., & La Rosa, M. (2017-2019). <i>Flora d’Italia</i>, 2nd edition, Vols. 1-4. Edagricole, Edizioni agricole di New Business Media, Bologna Raimondo, F. M., Bazan, G., & Troia, A. (2011). Taxa a rischio nella flora vascolare della Sicilia. <i>Biogeographia – The Journal of Integrative Biogeography</i>, <i>30</i>(1), 229-239. https://doi.org/10.21426/B630110586
DOI: 10.5061/dryad.w9ghx3fpp
title: Supplementary files from: Improving inference and avoiding over-interpretation of hidden-state diversification models: Specialized plant breeding has no effect on diversification in frogs

description: The hidden-state speciation and extinction (HiSSE) model helps avoid
 spurious results when testing whether a character affects diversification
 rates. However, care must be taken to optimally analyze models and
 interpret results. Recently, Tonini et al. (2020; TEA hereafter) studied
 anuran (frog and toad) diversification with HiSSE methods. They concluded
 that their focal state, breeding in phytotelmata, increases net
 diversification rates. Yet this conclusion is counterintuitive, because
 the state that purportedly increases net diversification rates is 14 times
 rarer among species than the alternative. Herein I revisit TEA’s analyses
 and demonstrate problems with inferring model likelihoods, conducting
 post-hoc tests, and interpreting results. I also re-evaluate their top
 models and find that diverse strategies are necessary to reach the
 parameter values that maximize each model’s likelihood. In contrast to
 TEA, I find no support for an effect of phytotelm breeding on net
 diversification rates in Neotropical anurans. In particular, even though
 the most highly supported models include the focal character, averaging
 parameter estimates over hidden states shows that the focal character does
 not influence diversification rates. Finally, I suggest ways to better
 analyze and interpret complex diversification models – both
 state-dependent and beyond – for future studies in other organisms.
description: Phenotypic and phylogenetic data come from a previous publication
 (Tonini et al. 2020 <em>Evolution</em>). All new files result
 from novel analyses of the data files, including R code, results files,
 and starting parameter values for likelihood searches.
description: Please see README.txt for full information.
DOI: 10.25338/b8z91n
title: Quantitative interactions: the disease outcome of Botrytis cinerea across the plant kingdom

description: Botrytis cinerea is a fungal pathogen that causes necrotic disease on more
 than a thousand known hosts widely spread across the plant kingdom. How B.
 cinerea interacts with such extensive host diversity remains largely
 unknown. To address this question, we generated an infectivity matrix of
 98 strains of B. cinerea on 90 genotypes representing eight host plants.
 This experimental infectivity matrix revealed that the disease outcome is
 largely explained by variations in either the host resistance or pathogen
 virulence. However, the specific interactions between host and pathogen
 account for 16% of the disease outcome. Furthermore, the disease outcomes
 cluster among genotypes of a species but are independent of the
 relatedness between hosts. When analyzing the host specificity and
 virulence of B. cinerea, generalist strains are predominant. In this
 fungal necrotroph, specialization may happen by a loss in virulence on
 most hosts rather than an increase of virulence on a specific host. To
 uncover the genetic architecture of Botrytis host specificity and
 virulence, a genome-wide association study (GWAS) was performed and
 revealed up to 1492 genes of interest. The genetic architecture of these
 traits is widespread across B. cinerea genome. The complexity of the
 disease outcome might be explained by hundreds of functionally diverse
 genes putatively involved in adjusting the infection to diverse hosts.
  
description: This study is based on a collection of 98 strains of
 <i>Botrytis cinerea </i>that samples fourteen plant hosts and
 to a smaller degree geographical origins. We generated an infectivity
 matrix of 98 strains of <i>B. cinerea</i> on 90 genotypes
 representing eight host plants, resulting in a dataset of 51,920 visible
 lesions at 72hpi. Least-square means and linear modeling was applied. GWAS
 was performed to assess the genetic architecture in Botrytis.
description: Accession list = all plant genotypes. isolate
 host origin = list of isolates with info. SNP data =
 SNP matrix for B. cinerea strains used for GWAS. LSmean
 files = least-square means of lesion area in either the column or row
 format to do plotting and linear modeling. Full meta
 data = all lesion area data. Lmer = full results of the
 linear mixed models for each of the 7 crops. Rnotebook
 = explanation on the R pipelines and associated R codes.
DOI: 10.5061/dryad.ncjsxksv5
title: Deep-time convergent evolution in animal communication presented by shared adaptations for coping with noise in lizards and other animals

description: Convergence in communication appears rare compared to other forms of
 adaptation. This is puzzling, given communication is acutely dependent on
 the environment and expected to converge in form when animals communicate
 in similar habitats. We uncover deep-time convergence in territorial
 communication between two groups of tropical lizards separated by over 140
 million years of evolution: the Southeast Asian Draco and Caribbean
 Anolis. These groups have repeatedly converged in multiple aspects of
 display along common environmental gradients. Robot playbacks to
 free-ranging lizards confirmed the most prominent convergence in display
 is adaptive, as it improves signal detection. We then provide evidence
 from a sample of the literature to further show convergent adaptation
 among highly divergent animal groups is almost certainly widespread in
 nature. Signal evolution is therefore curbed towards the same set of
 adaptive solutions, especially when animals are challenged with the
 problem of communicating effectively in noisy environments.
description: See main paper and associated online supporting information for
 details on methods. 
description: Missing values are presented as empty spaces. Please cite the
 dryad repository using the accepted "Data from: Ord, TJ ..."
 format in your reference list.