cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dv41ns1wc
title: Data files from nonreciprocal acoustics in viscous environment

description: It is demonstrated that acoustic transmission through a phononic crystal
 with anisotropic solid scatterers becomes nonreciprocal if the background
 fluid is viscous. In an ideal (inviscid) fluid, the transmission along the
 direction of broken P symmetry is asymmetric. This asymmetry is compatible
 with reciprocity since time-reversal symmetry (T symmetry) holds. Viscous
 losses break T symmetry, adding a nonreciprocal contribution to the
 transmission coefficient. The nonreciprocal transmission spectra for a
 phononic crystal of metallic circular cylinders in water are
 experimentally obtained and analyzed. The surfaces of the cylinders were
 specially processed in order to weakly break P symmetry and increase
 viscous losses through manipulation of surface features. Subsequently, the
 nonreciprocal part of transmission is separated from its asymmetric
 reciprocal part in numerically simulated transmission spectra. The level
 of nonreciprocity is in agreement with the measure of broken P symmetry.
 The reported study contradicts commonly accepted opinion that linear
 dissipation cannot be a reason leading to nonreciprocity. It also opens a
 way for engineering passive acoustic diodes exploring natural viscosity of
 any fluid as a factor leading to nonreciprocity.
description: The transmission spectra for the experiments were measured using
 a thru-transmission setup. The detail information is written in the
 manuscript. The data was collected using the oscilloscope and processed in
 Matlab. The dissipated energy was calculated through the numerical
 simulation using COMSOL multiphysics and processed in Matlab.
DOI: 10.25338/b8hs6b
title: The core seed mycobiome of P. menziesii var. menziesii across provenances of the Pacific Northwest, USA

description: Fungal symbionts occur in all plant tissues, and many aid their host
 plants with critical functions, including nutrient acquisition, defense
 against pathogens, and tolerance of abiotic stress. “Core” taxa in the
 plant mycobiome, defined as fungi present across individuals, populations,
 or time, may be particularly crucial to plant survival during the
 challenging seedling stage. However, studies on core seed fungi are
 limited to individual sampling sites, raising the question of whether core
 taxa exist across large geographic scales. We addressed this question
 using both culture-based and culture-free techniques to identify the fungi
 found in individual seeds collected from nine provenances across the range
 of Coastal Douglas-fir (Pseudotsuga menziesii var. menziesii), a
 foundation tree species in the Pacific Northwest and a globally important
 timber crop that is propagated commercially by seed. Two key findings
 emerged: 1) Seed mycobiome composition differed among seed provenances. 2)
 Despite spatial variation in the seed mycobiome, we detected four core
 members, none of which is a known pathogen of Douglas-fir: Trichoderma
 spp., Hormonema macrosporum, Mucor plumbeus and Talaromyces rugulosus. Our
 results support the concept of a core seed microbiome, yet additional work
 is needed to determine the functional consequences of core taxa for
 seedling germination, growth, survival and competition.
DOI: 10.5061/dryad.bk3j9kd98
title: Selection on phenotypic plasticity favors thermal canalization

description: Climate change affects organisms worldwide with profound ecological and
 evolutionary consequences, often increasing population extinction risk.
 Climatic factors can increase the strength, variability or direction of
 natural selection on phenotypic traits, potentially driving adaptive
 evolution. Phenotypic plasticity in relation to temperature can allow
 organisms to maintain fitness in response to increasing temperatures,
 thereby “buying time” for subsequent genetic adaptation and promoting
 evolutionary rescue. Although many studies have shown that organisms
 respond plastically to increasing temperatures, it is unclear if such
 thermal plasticity is adaptive. Moreover, we know little about how natural
 and sexual selection operate on thermal reaction norms reflecting such
 plasticity. Here, we investigate how natural and sexual selection shape
 phenotypic plasticity in two congeneric and phenotypically similar
 sympatric insect species. We show that the thermal optima for longevity
 and mating success differ, suggesting temperature-dependent trade-offs
 between survival and reproduction in both sexes. Males in these
 species have similar thermal reaction norm slopes but have diverged in
 baseline body temperature (intercepts), being higher for the more northern
 species. Natural selection favoured reduced thermal reaction norm slopes
 at high ambient temperatures, suggesting that the current level of thermal
 plasticity is maladaptive in the context of anthropogenic climate change
 and that selection now promotes thermal canalization and robustness.
  Our results show that ectothermic animals also at high latitudes
 can suffer from overheating and challenge the common view of phenotypic
 plasticity as being beneficial in harsh and novel environments.
description: Data was collected in natural field populations at a sympatric
 site containing both Calopteryx splendens and C. virgo in southern Sweden:
 Klingavälsån at Sövdemölla Gård in Region Skåne (Latitude 55.601492,
 Longitude 13.657340 ) during the summers 2013-2016 (mainly June and July).
 Daily field work consisted of capturing and marking males and females
 individually, as well as re-capturing marked individuals and recording
 longevity and mating succcess. We also measured
 microenvironmental variaton using thermal loggers (iButtons) and
 quantified individual variation in thermal plasticity (heating rates)
 using thermal imaging (infrared camera). Demographic data on survivorship
 and mating success were subsequently used to estimate natural and sexual
 selection on thermal plasticity traits (slopes and intercepts).
description: We provide all raw data as well as R-code needed to replicate all
 the statistical analyses, main figures, supporting figures and
 supplemental statistical tables in this paper. The
 R-scripts are annotated, so that it will be possible to re-generate all
 the statistical analyses and all figures using the code we
 provide.
DOI: 10.5061/dryad.pnvx0k6kd
title: Data from - A new tale of lost tails: correlates of tail breakage in the worm lizard Amphisbaena vermicularis

description: Predator-prey interactions are important evolutionary drivers of defensive
 behaviours, but they are usually difficult to record. This lack of data on
 natural history and ecological interactions of species can be overcome
 through museum specimens, at least for some reptiles. When facing
 aggressive interactions, reptile species may exhibit the defensive
 behaviour of autotomy by losing the tail, which is also known as
 ‘urotomy’. The inspection of preserved specimens for scars of tail
 breakage can reveal possible ecological and biological correlates of
 urotomy. Herein we investigated how the probability of urotomy in the worm
 lizard Amphisbaena vermicularis is affected by sex, body size,
 temperature, and precipitation. We found higher chances of urotomy for
 specimens with larger body size and from localities with warmer
 temperatures or lower precipitation. There was no difference in urotomy
 frequency between sexes. Older specimens likely faced – and survived –
 more predation attempts through their lifetime than smaller ones.
 Specimens from warmer regions might be more active both below- and
 aboveground, increasing the odds to encounter predators, and hence
 urotomy. Probability of urotomy decreased with increased precipitation.
 Possibly, in places with heavier rainfall worm lizards come more
 frequently to the surface when galleries are filled with rainwater,
 remaining more exposed to efficient predators, which could result in less
 survival rates and fewer tailless specimens. This interesting defensive
 behaviour is widespread in squamates, but yet little understood among
 amphisbaenians. The novel data presented here improve our understanding on
 the correlates of tail breakage and help us to interpret more tales of
 lost tails.
description: All analyses in this study were performed in the software R v.
 3.5.3. The dataset is thus composed of two files: 1.
 R_script.R 2. raw_data.csv The
 R-script is commented by the authors and cointains all code used to
 manipulate and analyse data tables, and create the figures in the
 manuscript.
DOI: 10.15468/dl.56m4aj
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Lasionycteris noctivagans"
 ]
}

 The dataset includes 8 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002638-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.s4mw6m959
title: Queen pheromone modulates the expression of epigenetic modifier genes in the brain of honeybee workers

description: Pheromones are used by many insects to mediate social interactions. In the
 highly eusocial honeybee (Apis mellifera) queen mandibular pheromone (QMP)
 is involved in the regulation of the reproductive and other behaviour of
 workers. The molecular mechanisms by which QMP acts are largely unknown.
 Here we investigate how genes responsible for epigenetic modifications to
 DNA, RNA and histones respond to the presence of QMP in the environment.
 We show that several of these genes are upregulated in the honeybee brain
 when workers are exposed to artificial QMP. We propose that pheromonal
 communication systems, such as those used by social insects, evolved to
 respond to environmental signals by making use of existing epigenomic
 machineries.
description: Relative gene expression data were generated by RT-qPCR
 assays.
DOI: 10.5061/dryad.prr4xgxk3
title: Sampling data, colony runfiles, VCFs, and Rscripts for: genomic determination of reproductive mode in facultatively parthenogenetic Opiliones

description: Sexual reproduction may pose myriad short-term costs to females. Despite
 these costs, sexual reproduction is near ubiquitous. Facultative
 parthenogenesis is theorized to mitigate some of the costs of sex, as
 individuals can participate in occasional sex to limit costs while
 obtaining many benefits. However, most theoretical models assume sexual
 reproduction is fixed following mating, with no possibility of clutches of
 mixed reproductive ontogeny. Therefore, we asked: if coercive males are
 present at high frequency in a population of facultative parthenogens,
 will their clutches be solely sexually produced, or will there be evidence
 of sexually and asexually-produced offspring? How will their offspring
 production compare to conspecifics in low frequency male populations? We
 addressed our questions by collecting females and egg clutches of the
 facultatively parthenogenetic Opiliones species Leiobunum manubriatum and
 L. globosum. In L. manubriatum, females from populations with few males
 were not significantly more fecund than females from populations with
 higher male relative frequency, despite the potential release of the
 former from sexual conflict. We used three genotyping methods along with a
 custom set of DNA capture probes to reveal that offspring of L.
 manubriatum from these high male populations were primarily produced via
 asexual reproduction. This is surprising because sex ratios in these
 southern populations approach equality, increasing the probability for
 females to encounter mates and produce offspring sexually. We additionally
 found evidence for reproductive polymorphisms within populations. Rapid
 and accurate SNP genotyping data will continue to allow us to address
 broader evolutionary questions regarding the role of facultative
 reproductive modes in the maintenance of sex.
DOI: 10.5061/dryad.h18931zjj
title: Explaining the worldwide distributions of two highly mobile species: Cakile edentula and C. maritima

description: Aim: If we are able to determine the geographic origin of an invasion, as
 well as its known area of introduction, we can better appreciate the
 innate environmental tolerance of a species and the strength of selection
 for adaptation that colonising populations have undergone. It also enables
 us to maximise the success of searches for effective biological control
 agents. We determined the number of successful colonisation events that
 have occurred throughout the world for two Cakile species and compared the
 climates from which they originated, in which they established and then
 spread. Location: Worldwide Taxon: Sea-Rockets (Cakile spp.), Brassicaceae
 Methods: We used a high throughput sequencing and a genome skimming
 approach combined with Bayesian Inference phylogenetics to examine
 variation in entire chloroplast genomes and regions of nuclear ribosomal
 DNA within native and introduced areas. Databases were used to compare
 climates between native ranges and introduced regions for multiple clades
 within each species. Results: At least seven clades have invaded different
 regions of the world. In most cases we were able to identify their source
 regions and climates. The environmental bottlenecks differed in intensity:
 while some clades colonized into climates that were similar to climates in
 their native range, other clades had a very broad innate environmental
 tolerance such that new invasions succeeded beyond the climate range of
 native populations. We found clear evidence of hybridisation –
 specifically chloroplast capture - between two species in Australia.
 Conclusions: Results here show that these species are sometimes capable of
 colonizing in climates that are beyond the climate range of native
 populations. Whether successful colonization beyond native climate niches
 requires de novo adaptation, or whether it represents an innate broad
 fundamental niche requires further investigation. Cakile species provide
 an excellent opportunity to study replicated climate adaptation
 trajectories.
description: The data set comprises collected occurrence data from
 different sources included in the SI Table 1 and GBIF data for the native
 range of the two species. The first records of introduction into a region
 were taken from the earliest sample in GBIF or from published
 reports.  27,343 and 2,081
 native range records were extracted from GBIF
 for <em>C.
 maritima</em> and <em>C.
 edentula</em>, respectively. 
description: Subsetting the data allows you to obtain occurrences of species
 and clades in their respective ranges. Empty fields present missing
 values.
DOI: 10.15468/dl.5dy9u9
title: Occurrence Download

description: A dataset containing 1828 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Clitoria ternatea",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 1828 records from 185 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002639-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.dfn2z3502
title: Drainage basins serve as multiple glacial refugia for alpine habitats in the Sierra Nevada Mountains, California

description: The evolutionary histories of alpine species are often directly associated
 with responses to glaciation. Deep divergence among populations and
 complex patterns of genetic variation have been inferred as consequences
 of persistence within glacier boundaries (i.e. on nunataks), while shallow
 divergence and limited genetic variation is assumed to result from
 expansion from large refugia at the edge of ice shields (i.e. massifs de
 refuge). However, for some species, dependence on specific microhabitats
 could profoundly influence their spatial and demographic response to
 glaciation, and such a simple dichotomy may obscure the localization of
 actual refugia. In this study, we use the Nebria ingens complex
 (Coleoptera: Carabidae), a water-affiliated ground beetle lineage, to test
 how drainage basins are linked to their observed population structure. By
 analyzing mitochondrial COI gene sequences and genome-wide single
 nucleotide polymorphisms, we find that the major drainage systems of the
 Sierra Nevada Mountains in California best explain the population
 structure of the N. ingens complex. In addition, we find that an
 intermediate morphotype within the N. ingens complex is the product of
 historical hybridization of N. riversi and N. ingens in the San Joaquin
 basin during glaciation. This study highlights the importance of
 considering ecological preferences in how species respond to climate
 fluctuations and provides an explanation for discordances that are often
 observed in comparative phylogeographic studies.
description: The genetic data, including DNA sequences, single nucleotide
 polymorphisms (SNPs), and site allele frequency spectrum (sfs), is
 collected from <em>Nebria ingens</em> complex samples. The DNA
 sequences were used to reconstruct the phylogeny of this species complex,
 and the the SNP and sfs data were used to conduct analyses regarding
 population structure and demographic history. The phylogeny reconstruction
 includes Bayesian tree with BEAST2 and haplotype network with popart. We
 use SNP data to analyze the population structure using vcftools, sNMF,
 and conStruct. We also use sfs data to reconstruct the demographic history
 of this species complex using stairway plot and ∂a∂i.
description: This dataset includes data and major scripts to repeat the
 analyses. The raw data such as DNA reads are stored in NCBI.
DOI: 10.5061/dryad.qz612jmd4
title: Host genetics, phenotype and geography structure the microbiome of a foundational seaweed

description: Interactions between hosts and their microbiota are critical to the
 functioning and resilience of eukaryotic macro-organisms. Critically, for
 hosts that play foundational roles in communities, understanding what
 drives these interactions is essential for informing restoration and
 conservation of entire ecosystems. Here, we investigated the relative
 influence of host traits and the surrounding environment on microbial
 communities associated with the foundational seaweed Phyllospora comosa.
 We collected data on 16 morphological and functional phenotypic traits,
 host genetics (using 354 Single Nucleotide Polymorphisms) and
 surface-associated microbial communities (using 16S rRNA gene amplicon
 sequencing) from 160 individuals sampled from eight sites spanning
 Phyllospora’s entire latitudinal distribution (1300 km). Combined, these
 factors explained 54% of the overall variation in Phyllospora’s associated
 microbial community structure, much of which was related to the local
 environment (~32%). We found that putative “core” microbial taxa (i.e.
 present on all Phyllospora individuals sampled) exhibited slightly higher
 association with host traits when compared to “variable” taxa (not present
 on all individuals). We identified several key genetic loci and phenotypic
 traits in Phyllospora that were strongly related to multiple microbial
 amplicon sequence variants, including taxa with known associations to
 seaweed defense, disease and tissue degradation. This information on how
 host-associated microbial communities vary with host traits and the
 environment enhances our current understanding of holobionts and how they
 are structured. Such understanding can be used to inform management
 strategies of these important and vulnerable habitats.
description: raw amplicon sequence data (ASV table only), morphological data
 and SNP genotypes for 156 Phyllospora comosa individuals collected
 at eight sampling locations in Australia.
DOI: 10.5281/zenodo.18396229
title: CETΩ: Reproducible numerical pipeline for late-time background modifications of cosmology

description: This repository contains a minimal, fully reproducible numerical pipeline used to generate the results presented in the accompanying manuscript “A late–time informational modification of the cosmological background and the Hubble tension”.

The pipeline implements the CETΩ framework as a purely late–time, background-level modification of the cosmological expansion history, leaving recombination physics, the sound horizon, and linear perturbations unchanged by construction.

The modification is implemented directly in the background routines of CAMB, without introducing new propagating degrees of freedom or altering the Einstein–Boltzmann equations.

The pipeline produces:





background expansion curves H(z)H(z),




BAO distance observables and an effective BAO–inferred Hubble constant,




consistency checks with CMB low-ℓℓ temperature anisotropies (ISW regime),




growth observables fσ8(z)fσ8(z) and comparison with representative RSD measurements,




profile likelihood scans for the CETΩ deformation parameter.



All figures and numerical consistency checks reported in the manuscript can be reproduced by running the provided scripts.The pipeline is intended for transparency and reproducibility purposes and is not optimized for large-scale parameter inference or full MCMC analyses.

 





Cosmology




Dark energy




Hubble tension




Late-time cosmology




BAO




CMB




CAMB




Numerical pipeline




Reproducibility
DOI: 10.5281/zenodo.18396230
title: CETΩ: Reproducible numerical pipeline for late-time background modifications of cosmology

description: This repository contains a minimal, fully reproducible numerical pipeline used to generate the results presented in the accompanying manuscript “A late–time informational modification of the cosmological background and the Hubble tension”.

The pipeline implements the CETΩ framework as a purely late–time, background-level modification of the cosmological expansion history, leaving recombination physics, the sound horizon, and linear perturbations unchanged by construction.

The modification is implemented directly in the background routines of CAMB, without introducing new propagating degrees of freedom or altering the Einstein–Boltzmann equations.

The pipeline produces:





background expansion curves H(z)H(z),




BAO distance observables and an effective BAO–inferred Hubble constant,




consistency checks with CMB low-ℓℓ temperature anisotropies (ISW regime),




growth observables fσ8(z)fσ8(z) and comparison with representative RSD measurements,




profile likelihood scans for the CETΩ deformation parameter.



All figures and numerical consistency checks reported in the manuscript can be reproduced by running the provided scripts.The pipeline is intended for transparency and reproducibility purposes and is not optimized for large-scale parameter inference or full MCMC analyses.

 





Cosmology




Dark energy




Hubble tension




Late-time cosmology




BAO




CMB




CAMB




Numerical pipeline




Reproducibility