cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5qfttdz76
title: Evolution of static allometry and constraint on evolutionary allometry in a fossil stickleback

description: Allometric scaling describes the relationship of trait size to body size
 within and among taxa. The slope of the population-level regression of
 trait size against body size (i.e., static allometry) is typically
 invariant among closely related populations and species. Such invariance
 is commonly interpreted to reflect a combination of developmental and
 selective constraints that delimit a phenotypic space into which evolution
 could proceed most easily. Thus, understanding how allometric
 relationships do eventually evolve is important to understanding
 phenotypic diversification. In a lineage of fossil Threespine Stickleback
 (Gasterosteus doryssus), we investigated the evolvability of static
 allometric slopes for nine traits (five armor, and four non-armor) that
 evolved significant trait differences across 10 samples over 8,500 years.
 The armor traits showed weak static allometric relationships and a
 mismatch between those slopes and observed evolution. This suggests that
 observed evolution in these traits was not constrained by relationships
 with body size, perhaps because prior, repeated adaptation to freshwater
 habitats by Threespine Stickleback had generated strong selection to break
 constraint. In contrast, for non-armor traits, we found stronger
 allometric relationships. Those allometric slopes did evolve on short time
 scales. However, those changes were small and fluctuating and the slopes
 remained strong predictors of the evolutionary trajectory of trait means
 over time (i.e., evolutionary allometry), supporting the hypothesis of
 allometry as a constraint.
description: Please see the published paper associated with these data.
description: Please see the R code associated with these data for more
 description of their structure and use.
DOI: 10.5061/dryad.kkwh70s66
title: Data from: Getting to the root of organic inputs in groundwaters: stygofaunal plant consumption in a calcrete aquifer

description: Groundwater environments interact with and support subterranean biota as
 well as superficial aquatic and terrestrial ecosystems. However, knowledge
 of subterranean energy flows remains incomplete. Cross-boundary
 investigations are needed to better understand the trophic structures of
 groundwater ecosystems and their reliance on carbon inputs from
 aboveground. In this study we used carbon and nitrogen stable isotope
 analyses combined with radiocarbon fingerprints to characterise organic
 flows in groundwater ecosystems. We coupled these data with DNA
 metabarcoding of the gut contents of consumers to further elucidate
 organic matter sources and shifts in diet preferences. Samples were
 collected from the arid zone Sturt Meadows calcrete aquifer under low
 rainfall (LR) and high rainfall (HR) conditions. Bayesian modelling of
 Δ14C, δ13C and δ15N data indicated that primary consumers (copepods)
 incorporated mainly particulate organic carbon (POC) under LR but during
 HR shifted to root derived material (either exudates or direct root
 grazing). By contrast, diets of secondary consumers (amphipods) were
 dominated by root material under both LR and HR. Our DNA
 metabarcoding-based results indicate that amphipods relied primarily on
 root inputs from perennial trees
 (likely Eucalyptus and Callitris) during the
 dry season (LR). Under HR, diets of both amphipods and copepods also
 included organic material derived from a broad range of more shallow
 rooted shrubs, and ephemeral herbs and grasses. Our findings illustrate
 the complexity of functional linkages between groundwater biota and
 terrestrial surficial ecosystems in environments where aboveground
 productivity, diversity and organic matter flux to groundwater are
 intimately linked to often episodic rainfall.
description: Specimens of AM1, AM2, C and H were used for gut DNA
 metabarcoding analysis targeting plant material (primer trnL g-h). Prior
 to DNA extraction, stygofaunal animals (three to five individuals per
 pool; <i>n</i> = 84) were placed in petri dishes containing
 ultrapure water and UV sterilized in a UV oven for 10 min to eliminate any
 environmental DNA species that may be contained on the exoskeleton.
 Details on the DNA extraction, controls, sequencing and blasting for
 stygofaunal gut analysis are described in detail in Saccò et al. (2021a).
 A minimum threshold of five OTU counts was established for the
 presence-absence analysis. Only taxa known to occur in the Goldfields
 Region of Western Australia (Florabase; Western Australian Herbarium,
 1988) were considered in this study.
DOI: 10.5061/dryad.v6wwpzgxm
title: Endocrine disruption from plastic pollution and warming interact to increase the energetic cost of growth in a fish

description: Energetic cost of growth determines how much food-derived energy is needed
 to produce a given amount of new biomass, and thereby influences energy
 transduction between trophic levels. Growth and development are regulated
 by hormones and are therefore sensitive to changes in temperature and
 environmental endocrine disruption. Here we show that the endocrine
 disruptor bisphenol A at an environmentally relevant concentration (BPA;
 10 µg l⁻¹) decreased fish (Danio rerio) size at 30 oC water temperature.
 Under the same conditions, it significantly increased metabolic rates and
 the energetic cost of growth across development. In contrast, BPA
 decreased cost of growth at cooler temperatures (24 °C). BPA-mediated
 changes in cost of growth were not associated with mitochondrial
 efficiency (P/O ratios [i.e., ADP used/oxygen consumed] and respiratory
 control ratios) although BPA did increase mitochondrial proton leak. In
 females, BPA decreased age at maturity at 24 oC but increased it at 30 oC,
 and it decreased the gonadosomatic index suggesting reduced investment
 into reproduction. Our data reveal a potentially serious emerging problem:
 increasing water temperatures resulting from climate warming together with
 endocrine disruption from plastic pollution can impact animal growth
 efficiency, and hence the dynamics and resilience of animal populations
 and the services these provide.
DOI: 10.5281/zenodo.6631808
title: SuperDARN data in netCDF format (2006-Jul)

description: 2006-Jul SuperDARN radar data in netCDF format. These files were produced using version 3.0 of the public FitACF algorithm, using the AACGM v2 coordinate system. Cite this dataset if using our data in a publication.


The RST is available here: https://github.com/SuperDARN/rst



The research enabled by SuperDARN is due to the efforts of teams of scientists and engineers working in many countries to build and operate radars, process data and provide access, develop and improve data products, and assist users in interpretation.
Users of SuperDARN data and data products are asked to acknowledge this support in presentations and publications.
A brief statement on how to acknowledge use of SuperDARN data is provided below.




Users are also asked to consult with a SuperDARN PI prior to submission of work intended for publication.
A listing of radars and PIs with contact information can be found here:
(SuperDARN Radar Overview)



Recommended form of acknowledgement for the use of SuperDARN data:



'The authors acknowledge the use of SuperDARN data. SuperDARN is a collection of radars funded by national scientific funding agencies of Australia, Canada, China, France, Italy, Japan, Norway, South Africa, United Kingdom and the United States of America.'
DOI: 10.5281/zenodo.18396948
title: SuperDARN data in netCDF format (2006-Jul)

description: 2006-Jul SuperDARN radar data in netCDF format. These files were produced using version 3.0 of the public FitACF algorithm, using the AACGM v2 coordinate system. Cite this dataset if using our data in a publication.


The RST is available here: https://github.com/SuperDARN/rst



The research enabled by SuperDARN is due to the efforts of teams of scientists and engineers working in many countries to build and operate radars, process data and provide access, develop and improve data products, and assist users in interpretation.
Users of SuperDARN data and data products are asked to acknowledge this support in presentations and publications.
A brief statement on how to acknowledge use of SuperDARN data is provided below.




Users are also asked to consult with a SuperDARN PI prior to submission of work intended for publication.
A listing of radars and PIs with contact information can be found here:
(SuperDARN Radar Overview)



Recommended form of acknowledgement for the use of SuperDARN data:



'The authors acknowledge the use of SuperDARN data. SuperDARN is a collection of radars funded by national scientific funding agencies of Australia, Canada, China, France, Italy, Japan, Norway, South Africa, United Kingdom and the United States of America.'
DOI: 10.5061/dryad.n5tb2rbxc
title: Habitat-complexity regulates the intensity of facilitation along an environmental stress gradient

description: Positive interactions between foundation species and their associated
 species are expected to be influenced by the degree of environmental
 stress as well as trait variations of the species involved. However, there
 is scarce empirical evidence regarding how these two factors interact and
 shape the intensity of facilitation. To test how facilitation varies with
 stress, a colonization experiment using artificial algal units that varied
 in a functional trait (morphological complexity) was conducted at
 different intertidal height levels. The isolated effects of shore-height
 and host-complexity are as expected: the number of species and overall
 abundance of epifauna decreased with lower complexity host units and
 greater exposure to environmental stress. However, in contrast to the
 initially proposed model, based on the Stress Gradient Hypothesis, the
 magnitude of positive interactions increased at lower tidal heights (those
 levels with, presumably, milder environmental conditions). An additional
 predation exclusion experiment ruled out the effects of predation pressure
 as a major factor driving the structure of mobile epifaunal assemblages in
 these intertidal habitats. Thus, further studies are needed to identify
 the factors that explain the patterns of facilitation intensity found in
 the present study.
description: The upload files contains the abundance of each taxa obtained
 throught the study (both the main experiment and the additional predation
 experiment).
DOI: 10.5061/dryad.pvmcvdnnm
title: Alteration of DNA supercoiling serves as a trigger of short-term cold shock repressed genes of E. coli

description: Cold shock adaptability is a key survival skill of gut bacteria of
 warm-blooded animals. Escherichia coli cold shock responses are controlled
 by a complex multi-gene, timely-ordered transcriptional program. We
 investigated its underlying mechanisms. Having identified short-term, cold
 shock repressed genes, we show that their responsiveness is unrelated to
 their transcription factors or global regulators, while their single-cell
 protein numbers’ variability increases after cold shock. We hypothesized
 that some cold shock repressed genes could be triggered by high propensity
 for transcription locking due to changes in DNA supercoiling (likely due
 to DNA relaxation caused by an overall reduction in negative
 supercoiling). Concomitantly, we found that nearly half of cold shock
 repressed genes are also highly responsive to gyrase inhibition (albeit
 most genes responsive to gyrase inhibition are not cold shock responsive).
 Further, their response strengths to cold shock and gyrase inhibition
 correlate. Meanwhile, under cold shock, nucleoid density increases, and
 gyrases and nucleoid become more colocalized. Moreover, the cellular
 energy decreases, which may hinder positive supercoils resolution.
 Overall, we conclude that sensitivity to diminished negative supercoiling
 is a core feature of E. coli’s short-term, cold shock transcriptional
 program, and could be used to regulate the temperature sensitivity of
 synthetic circuits.
description: Collection and data generation are described in the section
 'Materials and Methods' of the main manuscript and Sections
 I-III of Supplementary Information. Data processing
 methods and the software packages used are described in Supplementary
 Information.
DOI: 10.5061/dryad.1vhhmgqvd
title: Breeding site fidelity is lower in polygamous shorebirds and male-biased in monogamous species

description: Sex-bias in breeding dispersal is considered the norm in many taxa, and
 the magnitude and direction of such sex-bias is expected to correlate with
 the social mating system. We used local return rates in shorebirds as an
 index of breeding site fidelity, and hence as an estimate of the
 propensity for breeding dispersal, and tested whether variation in site
 fidelity and in sex-bias in site fidelity relates to the mating system.
 Among 111 populations of 49 species, annual return rates to a breeding
 site varied between 0–100%. After controlling for body size (linked to
 survival) and other confounding factors, monogamous species showed higher
 breeding site fidelity compared to polyandrous and polygynous species.
 Overall, there was a strong male bias in return rates, but the sex-bias in
 return rate was independent of the mating system and did not covary with
 the extent of sexual size dimorphism. Our results bolster earlier findings
 that the sex-biased dispersal is weakly linked to the mating system in
 birds. Instead, our results show that return rates are strongly correlated
 with the mating system in shorebirds regardless of sex. This suggests that
 breeding site fidelity may be linked to mate fidelity, which is only
 important in the monogamous, biparentally incubating species, or that the
 same drivers influence both the mating system and site fidelity. The
 strong connection between site fidelity and the mating system suggests
 that variation in site fidelity may have played a role in the coevolution
 of the mating system, parental care, and migration strategies.
DOI: 10.5061/dryad.n02v6wx03
title: The cost of noise: Stochastic punishment falls short of sustaining cooperation in social dilemma experiments

description: Identifying mechanisms able to sustain costly cooperation among
 self-interested agents is a central problem across social and biological
 sciences. One possible solution is peer punishment: when agents have an
 opportunity to sanction defectors, classical behavioral experiments
 suggest that cooperation can take root. Overlooked from standard
 experimental designs, however, is the fact that real-world human
 punishment---the administration of justice---is intrinsically noisy. Here
 we show that stochastic punishment falls short of sustaining cooperation
 in the repeated public good game. As punishment noise increases, we find
 that contributions decrease and punishment efforts intensify, resulting in
 a 45% drop in gains compared to a noiseless control. Moreover, we
 observe that uncertainty causes a rise in antisocial punishment, a
 mutually harmful behavior previously associated with societies with a weak
 rule of law. Our approach brings to light challenges to cooperation that
 cannot be explained by economic rationality and strengthens the case for
 further investigations of the effect of noise---and not just bias---on
 human behavior.
description: The experiments were conducted from March to July 2021 using
 oTree. We recruited participants using the online platform Prolific.co.
 The sole reason for exclusion was prior participation in a study.
  Participants were paid a fixed compensation of £3.75 with the opportunity
 to earn a bonus of up to £6 based on their income in the game. In total,
 384 participants in 96 groups finished the experiment. After removing
 groups with repeated non-responses in order to eliminate bias, 80 groups
 remained for the analysis, involving 320 participants from 41 countries
 (sex ratio 2:1). These are distributed on the experimental conditions in
 the following way: 21 groups in the control condition, and 20 (resp. 20,
 19) groups in the low (resp. medium, high) noise treatment
 condition.
DOI: 10.5061/dryad.mpg4f4r20
title: Chemical defense acquired via pharmacophagy can lead to protection from predation for conspecifics in a sawfly

description: Predation is an important selection pressure acting on organisms, with
 organisms evolving diverse anti-predator strategies to combat it. One such
 strategy is chemical defense in which organisms either synthesize or
 extrinsically acquire defensive chemicals. Little is known about the
 intraspecific transfer of such chemicals and if such chemicals acquired
 from conspecifics can also serve as defense against predation. Here, we
 used adults of the turnip sawfly, Athalia rosae, which can acquire the
 plant chemicals ‘clerodanoids’ via pharmacophagy after exposure to the
 plant, Ajuga reptans. We show that clerodanoid access mediates protection
 against predation by mantids for the sawflies. Moreover, even indirect
 access to clerodanoids, via nibbling on conspecifics that had access to
 the plant, resulted in protection against predation albeit to a lower
 degree than direct access. Furthermore, sawflies that had no direct access
 to clerodanoids were less consumed by mantids when they were grouped with
 conspecifics that had direct access. Most of such initially undefended
 sawflies could acquire clerodanoids from conspecifics that had direct
 access to the plant, although in low quantities. Together our results
 demonstrate that clerodanoids serve as chemical defense that can be
 intraspecifically transferred. Moreover, the presence of chemically
 defended individuals in a group can confer protection onto conspecifics
 that had no direct access to clerodanoids, suggesting a ‘herd-protection’
 effect.
DOI: 10.5061/dryad.hmgqnk9jm
title: SNPs genotypes of Italian wild boar (Sus scrofa) populations

description: Human activities can globally modify natural ecosystems determining
 ecological, demographic and range perturbations for several animal
 species. These changes can jeopardize native gene pools in different ways,
 leading either to genetic homogenization or, conversely, to the split into
 genetically divergent demes.   In the past decades, most European
 wild boar (Sus scrofa) populations were heavily managed by humans.
 Anthropic manipulations have strongly affected also Italian populations
 through heavy hunting, translocations and reintroductions that might have
 deeply modified their original gene pools.   In this study,
 exploiting the availability of the well-mapped porcine genome, we applied
 genomic tools to explore genome-wide variability in Italian wild boar
 populations, investigate their genetic structure and detect signatures of
 possible introgression from domestic pigs and non-native wild boar.
 Genomic data from 134 wild boar sampled in six areas of peninsular Italy
 and in Sardinia were gathered using the Illumina Porcine SNP60 Beadchip
 (60k Single Nucleotide Polymorphisms – SNPs) and compared with reference
 genotypes from European specimens and from domestic pigs (both commercial
 and Italian local breeds), using multivariate and maximum-likelihood
 approaches.   Pairwise FST values, multivariate analysis and
 assignment procedures indicated that Italian populations were highly
 differentiated from all the other analyzed European wild boar populations.
   Overall, a lower heterozygosity was found in the Italian
 population than in the other European regions. The most diverging
 populations in Castelporziano Presidential Estate and Maremma Regional
 Park can be the result of long-lasting isolation, reduced population size
 and genetic drift. Conversely, an unexpected similarity was found among
 Apennine populations, even at high distances. Signatures of introgression
 from both non-Italian wild boar and domestic breeds were very limited.
   To summarize, we successfully applied genome-wide procedures to
 explore, for the first time, the genomic diversity of Italian wild boar,
 demonstrating that they represent a strongly heterogeneous assemblage of
 demes with different demographic and manipulation histories. Nonetheless,
 our results suggest that a native component of genomic variation is
 predominant over exogenous ones in most populations.
DOI: 10.15468/dl.zdasf5
title: Occurrence Download

description: A dataset containing 3074 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Caulacanthus ustulatus"
 ]
}

 The dataset includes 3074 records from 109 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003034-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.tdz08kq1n
title: Assessment of biogeographic variation in traits of Lewis flax (Linum lewisii) for use in restoration and agriculture

description: Lewis flax (Linum lewisii) is widely distributed across western North
 America and is currently used in native ecosystem restoration. There is
 also growing interest in de novo domestication of Lewis flax as a
 perennial oilseed crop. To better understand this species and facilitate
 both restoration and domestication, we used common gardens to assess
 bio-geographical variation in a variety of seed and growth traits from 37
 flax accessions, consisting of 35 wild populations from the Intermountain
 West region, the pre-variety germplasm Maple Grove (L. lewisii) and the
 cultivar ‘Appar’ (L. perenne) and related this variation to collection
 site geography and climate. Results from linear mixed models suggest there
 is extensive phenotypic variation among populations of Lewis flax within
 the Intermountain West. Using a multivariate approach, we identify a key
 suite of traits that are related to latitude and climate and may
 facilitate adaptation, including flowering indeterminacy, seed mass, and
 stem number. These traits should be taken into account when considering
 the release of new germplasm for restoration efforts. We also find that
 Lewis flax seed contains desirably high amounts of alpha-linolenic acid
 and is otherwise mostly indistinguishable in fatty acid composition from
 oil-type varieties of domesticated flax (L. usitatissimum), making it a
 strong candidate for domestication. This study provides fundamental
 knowledge for future research into the ecology and evolution of Lewis
 flax, which will inform its use in both restoration and agriculture.
description: See manuscript in AoBP for details.
description: Code for analysis is available at:
 https://github.com/peterinnes/Lile_common_garden