cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.msbcc2fz5
title: Morphological bluethroat dataset

description: In temperate mountain ranges, sharp spatial variations in habitat
 heterogeneity and climate provide a perfect study setup to assess genetic
 and phenotypic differentiation in bird populations. In this paper, we
 analyzed morphological divergence patterns across geographic and
 environmental gradients, in correlation with genetic differentiation and
 geographic isolation, in the breeding grounds of a long-distance migrant
 passerine. Location NorthWestern Iberian mountains. Major taxa studied
 Iberian bluethroat, Luscina svecica azuricollis. Methods We collected a
 sample of 625 Iberian bluethroats across their whole breeding distribution
 area to measure body weight and tarsus length, as well as wing length and
 pointedness. Morphological differentiation across geographic (latitude and
 altitude) and environmental (climate and vegetation) gradients was
 assessed using GLMMs. Additionally, the role of genetic distance and
 geographic isolation as drivers of morphological differentiation was
 evaluated with Mantel tests. Results Bird morphology varied significantly
 with latitude and altitude, but not with climate or vegetation. In the
 case of latitude, morphological differences in body size were contrary to
 what was expected according to Bergmann’s rule. All biometric and
 morphometric variables diverged significantly among localities. A similar
 trend was found for genetic clusters, except for the case of wing shape.
 Body weight and wing length were both correlated to geographical distance,
 while only the former varied with genetic differentiation. The greatest
 genetic and phenotypic differentiation was detected in the southernmost
 mountain range that holds the most geographically isolated genetic group.
 Main conclusion As expected, Iberian breeding bluethroats show strong
 latitudinal phenotypic differentiation that correlates with geographic
 isolation and genetic distance. Nevertheless, some deviances from this
 pattern occur for biometric variables with greater selective pressure,
 which points to local adaptations related to migratory strategies. On the
 opposite of what was hypothesized, body size was inversely correlated to
 latitude.
DOI: 10.5061/dryad.n8pk0p2vr
title: Inbreeding reduces fitness of seed beetles under thermal stress

description: Human-induced environmental change can influence populations both at the
 global level through climatic warming and at the local level through
 habitat fragmentation. As populations become more isolated, they can
 suffer from high levels of inbreeding which contributes to a reduction in
 fitness, termed inbreeding depression. However, it is still unclear if
 this increase in homozygosity also results in a corresponding increase in
 sensitivity to stressful conditions, which could intensify the already
 detrimental effects of environmental warming. Here, in a fully factorial
 design, we assessed the life-long impact of increased inbreeding load and
 elevated temperature on key life history traits in the seed beetle,
 Callosobruchus maculatus. We found that beetles raised at higher
 temperatures had far reduced fitness and survival than beetles from
 control temperatures. Importantly, these negative effects were exacerbated
 in inbred beetles as a result of increased inbreeding load, with further
 detrimental effects manifesting on individual eclosion probability and
 lifetime reproductive success. These results reveal the harmful impact
 that increasing temperature and likelihood of habitat fragmentation due to
 anthropogenetic changes in environmental conditions could have on
 populations of organisms worldwide.
DOI: 10.5061/dryad.d2547d833
title: The species richness-productivity relationship varies among regions and productivity estimates, but not with spatial resolution

description: The relationship between species richness and productivity (SRPR) has been
 a long-studied and hotly debated topic in ecology. Different studies have
 reported different results with variable shapes (i.e. unimodal, linear)
 and directions (i.e. positive, negative) of SRPRs depending on spatial
 grain (i.e. size of sampling unit for species richness), productivity
 estimates, and study extent. In this study, we quantified the effect of
 multiple estimates of productivity (aboveground, belowground and total
 biomass, and various measures of soil fertility) on species richness
 across three spatial grains (0.04 m2, 1 m2, and 25 m2) across temperate
 grasslands from two regions in Central Europe. We analyzed SRPR in each of
 the two regional datasets separately, as well as the two datasets pooled
 together. Our results have revealed that differences caused by spatial
 grain were unexpectedly small, and the direction of the SRPR was
 consistent within each productivity estimate, but differed between
 regions. Productivity estimates (across all spatial scales) had different,
 sometimes contrasting effects on SRPR (together with predictive power)
 within a region, and this pattern was more pronounced when compared
 between regions. The combination of different datasets led to very
 different results than when these were analyzed separately. We did not
 find any evidence for a unimodal response. This study points to the
 necessity of careful assessing when combining datasets from different
 regions, even if the plant communities belong to the same vegetation type.
 The dataset combination may blur the role of different drivers, which
 likely determine the shape and strength of SRPR. We suggest that data and
 study comparability may be enhanced by consistently using the same
 productivity estimates, which would allow for more robust interpretation
 of possible ecological drivers underlying the SRPR.
DOI: 10.57841/casdc.0007105
title: 环丙烯氢烷基化反应过程数据和测试表征数据
DOI: 10.5061/dryad.w0vt4b8rj
title: Hot-headed peckers: thermographic changes during aggression among juvenile pheasants (Phasianus colchicus)

description: In group-living vertebrates, dominance status often covaries with
 physiological measurements (e.g. glucocorticoid levels), but it is unclear
 how dominance is linked to dynamic changes in physiological state over a
 shorter, behavioural timescale. In this observational study, we recorded
 spontaneous aggression among captive juvenile pheasants (Phasianus
 colchicus) alongside infrared thermographic measurements of their external
 temperature, a non-invasive technique previously used to examine stress
 responses in non-social contexts, where peripheral blood is redirected
 towards the body core. We found low but highly significant repeatability
 in maximum head temperature, suggesting individually consistent thermal
 profiles, and some indication of lower head temperatures in more active
 behavioural states (e.g. walking compared to resting). These individual
 differences were partly associated with sex, females being cooler on
 average than males, but unrelated to body size. During pairwise aggressive
 encounters, we observed a non-monotonic temperature change, with head
 temperature dropping rapidly immediately prior to an attack and increasing
 rapidly afterwards, before returning to baseline levels. This nonlinear
 pattern was similar for birds in aggressor and recipient roles, but
 aggressors were slightly hotter on average. Our findings show that
 aggressive interactions induce rapid temperature changes in dominants and
 subordinates alike, and highlight infrared thermography as a promising
 tool for investigating the physiological basis of pecking orders in
 galliforms.
description: Thermographic, behavioural and morphometric measurements
 collected from captive juvenile pheasants. All processing done within
 accompanying R script.
description: Variables are defined in the accompanying ReadMe files. Missing
 values are coded as NA.
DOI: 10.5061/dryad.r2280gbdb
title: Clinical Trial Transparency and Data-Sharing Among Bio-Pharmaceutical Companies and the Role of Company Size, Location, and Product Type: A Cross-Sectional Descriptive Analysis

description: Objective: To examine company characteristics associated with better
 transparency and to apply a tool used to measure and improve clinical
 trial transparency among large companies and drugs, to smaller companies
 and biologics. Design: Cross-sectional descriptive analysis. Setting and
 participants. Novel drugs and biologics FDA approved in 2016 and 2017, and
 their company sponsors. Using established Good Pharma Scorecard (GPS)
 measures, companies and products were evaluated on their clinical trial
 registration, results dissemination, and FDA Amendments Act (FDAAA)
 implementation; Companies were ranked using these measures and a
 multi-component data sharing measure. Associations between company
 transparency scores with company size (large vs non-large), location (US
 vs non-US), and sponsored product type (drug vs biologic) were also
 examined. 26% of products (16/62) had publicly available results for all
 clinical trials supporting their FDA approval and 67% (39/58) had public
 results for trials in patients by 6 months after their FDA approval; 58%
 (32/55) were FDAAA compliant. Large companies were significantly more
 transparent than non-large companies (overall median transparency score of
 95% [IQR 91-100] vs 59% [IQR 41-70], p&lt;0.001), attributable to
 higher FDAAA compliance (median of 100% [IQR 88-100] vs 57% [0-100],
 p=0.01) and better data sharing (median of 100% [IQR 80-100] vs 20% [IQR
 20-40], p&lt;0.01). No significant differences were observed by
 company location or product type. It was feasible to apply the GPS
 transparency measures and ranking tool to non-large companies and
 biologics. Large companies are significantly more transparent than
 non-large companies, driven by better data sharing procedures and
 implementation of FDAAA trial reporting requirements. Greater research
 transparency is needed, particularly among non-large companies, to
 maximize the benefits of research for patient care and scientific
 innovation.  
description: Using established Good Pharma Scorecard (GPS) measures, companies
 and products were evaluated on their clinical trial registration, results
 dissemination, and FDA Amendments Act (FDAAA) implementation; Companies
 were ranked using these measures and a multi-component data sharing
 measure. Associations between company transparency scores with company
 size (large vs non-large), location (US vs non-US), and sponsored product
 type (drug vs biologic) were also examined.
DOI: 10.5061/dryad.gtht76hmq
title: Phylogenomic assessment of biodiversity using a reference-based taxonomy: An example with Horned Lizards (Phrynosoma)

description: Phylogenomic investigations of biodiversity facilitate the detection of
 fine-scale population genetic structure and the demographic histories of
 species and populations. However, determining whether or not the genetic
 divergence measured among populations reflects species-level
 differentiation remains a central challenge in species delimitation. One
 potential solution is to compare genetic divergence between putative new
 species with other closely related species, sometimes referred to as a
 reference-based taxonomy. To be described as a new species, a population
 should be at least as divergent as other species. Here, we develop a
 reference-based taxonomy for Horned Lizards (Phrynosoma; 17 species) using
 phylogenomic data (ddRADseq data) to provide a framework for delimiting
 species in the Greater Short-horned Lizard species complex (P.
 hernandesi). Previous species delimitation studies of this species complex
 have produced conflicting results, with morphological data suggesting
 that P. hernandesi consists of five species, whereas
 mitochondrial DNA support anywhere from 1 to 10+ species. To help address
 this conflict, we first estimated a time-calibrated species tree
 for P. hernandesi and close relatives using SNP data.
 These results support the paraphyly of P. hernandesi; we
 recommend the recognition of two species to promote a taxonomy that is
 consistent with species monophyly. There is strong evidence for three
 populations within P. hernandesi, and demographic modeling and
 admixture analyses suggest that these populations are not reproductively
 isolated, which is consistent with previous morphological analyses that
 suggest hybridization could be common. Finally, we characterize the
 population-species boundary by quantifying levels of genetic divergence
 for all 18 Phrynosoma species. Genetic divergence
 measures for western and southern populations of P.
 hernandesi failed to exceed those of
 other Phrynosoma species, but the
 relatively small population size estimated for the northern population
 causes it to appear as a relatively divergent species. These comparisons
 underscore the difficulties associated with putting a reference-based
 approach to species delimitation into practice. Nevertheless, the
 reference-based approach offers a promising framework for the consistent
 assessment of biodiversity within clades of organisms with similar life
 histories and ecological traits.
description: MtDNA data was collected using Sanger sequencing. New sequences
 are on Genbank (MW662366 - MW662452; MZ313846 - MZ313861).
 SNP data was collected using ddRADseq. New data are on the NCBI
 SRA (BioProject PRJNA704386).
DOI: 10.5061/dryad.fttdz08t2
title: Systematic revision of the arboreal Neotropical ‘Thorellii’ clade of Centruroides Marx, 1890 bark scorpions (Buthidae c.l. Koch, 1837) with descriptions of six new species

description: The arboreal Neotropical ‘thorellii’ clade
 of Centruroides Marx, 1890 bark scorpions (Buthidae C.L.
 Koch, 1837) is revised, using a novel approach to species delimitation. A
 phylogenetic analysis, based on 112 morphological characters and 1078
 aligned DNA nucleotides from the mitochondrial
 Cytochrome c Oxidase Subunit I (COI) gene, provided the
 framework for placing singletons from geographically disparate localities
 (and often with suboptimal preservation) using COI minibarcodes, thereby
 enlarging the taxon sample for diagnosis and delimitation of morphological
 species. Six new species are described, tripling the known
 diversity in the clade to
 nine: Centruroides berstoni, sp.
 nov.; Centruroides catemacoensis, sp.
 nov.; Centruroides chanae, sp.
 nov.; Centruroides cuauhmapan, sp.
 nov.; Centruroides hamadryas, sp.
 nov.; Centruroides yucatanensis, sp. nov.
 Revised diagnoses are presented for Centruroides
 hoffmanni Armas, 1996, Centruroides
 rileyi Sissom, 1995, and Centruroides
 schmidti Sissom, 1995. Comparative images, a key and distribution
 maps for all species of the clade are provided, along with a summary of
 available data for their ecology.
description: Genomic DNA was
 extracted from muscle tissue from the fourth leg of well-preserved
 specimens using the spin column extraction protocol of the Qiagen DNeasy
 Blood & Tissue Kit (Valencia, CA). PCR amplification of complete
 mitochondrial and nuclear genes proved impossible for many older museum
 samples, due to degradation and fragmentation of the DNA. Therefore, a 125
 base-pair (bp) hypervariable region of the Cytochrome <em style="text-align:justify;text-indent:24px;">c</em> Oxidase Subunit I (COI) gene was partially amplified (Musnier et al., 2008). Newly generated sequences were edited, forward and reverse primers removed, and complementary strands assembled into consensus sequences using Geneious v. 11.0.4 (Kearse et al<em style="text-align:justify;text-indent:24px;">.</em>,<em style="text-align:justify;text-indent:24px;"> </em>2012), by reference to a 1078 bp fragment of COI for <em style="text-align:justify;text-indent:24px;">C. rileyi</em> from GenBank (Esposito and Prendini, 2019). 
description: Label of each specimen is organized by scientific name (ex:
 Centruroides thorelli), followed by Museum accession code. Material
 deposited in the following collections: Ambrose Monell Cryocollection
 (AMCC) at the American Museum of Natural History, New York; Colección
 Nacional de Arácnidos, Instituto de Biología (CNAN), Universidad Nacional
 Autónoma de México, Mexico City; California Academy of Sciences (CASENT),
 San Francisco. Oxford University Museum of Natural History (OUMNH),
 U.K. Locality information provided in Appendix III of
 manuscript, and provided.
DOI: 10.5061/dryad.ngf1vhhv6
title: Microscopic marine invertebrate microbiomes do not reveal signatures of phylosymbiosis

description: Animals and microorganisms often establish close ecological relationships.
 However, much of our knowledge on animal microbiomes comes from two deeply
 studied groups: vertebrates and arthropods. To understand interactions on
 a broader scale of diversity, we characterized the bacterial microbiomes
 of close to 1,000 microscopic marine invertebrates from 21 phyla, covering
 most of the remaining tree of metazoans. Samples were collected from five
 temperate and tropical locations covering three marine habitats (sediment,
 water column and intertidal macroalgae) and bacterial microbiomes were
 characterized using 16S rRNA gene sequencing. Our data show that, despite
 their size, these animals harbour bacterial communities that differ from
 those in the surrounding environment. Distantly related but coexisting
 invertebrates tend to share many of the same bacteria, suggesting that
 guilds of microorganisms preferentially associated with animals, but not
 tied to any specific host lineage, are the main drivers of the ecological
 relationship. Host identity is a minor factor shaping these microbiomes,
 which do not show the kind of correlation with host phylogeny, or
 “phylosymbiosis”, observed in many large animals. Hence, the current
 debate on the varying strength of phylosymbiosis within selected lineages
 should be reframed to account for the possibility that such a pattern
 might be the exception rather than the rule.
DOI: 10.5061/dryad.2z34tmpmw
title: Electrostatic interactions contribute to the control of intramolecular thiol–disulfide isomerization in a protein

description: The role of structural factors and of electrostatic interactions with the
 environment on the outcome of thiol–disulfide exchange reactions were
 investigated in a mutated immunoglobulin domain (I27*) under mechanical
 stress. An extensive ensemble of molecular dynamics trajectories was
 generated by means of QM/MM simulations for a total sampling of 5.7 μs. A
 significant number of thiol–disulfide exchanges were observed, and the
 Cys32 thiolate preferred to attack Cys55 over Cys24, in agreement with
 previous experimental and computational studies. The structural features
 as well as electronic structures of the thiol–disulfide system along the
 reaction were analyzed, as were the electrostatic interactions with the
 environment. The previous findings of better accessibility of Cys55 were
 confirmed. Additionally, the reaction is found to be directed by the
 electrostatic interactions of the involved sulfur atoms with the molecular
 environment. The relationships of atomic charges, which stem from the
 electrostatic interactions, lead to the kinetic preference of the attack
 on Cys55. Further, QM/MM metadynamics simulations of thiol–disulfide
 exchange in a small model system with varied artificial external electric
 potentials revealed changes in reaction kinetics of the same magnitude as
 in I27*. Therefore, the electrostatic interactions are confirmed to play a
 role in the regioselectivity of the thiol–disulfide exchange reactions in
 the protein.
description: The dataset consists of trajectories from 334 individual unbiased
 QM/MM MD simulations of thiol–disulfide exchange in the mutated
 immunoglobulin domain I27*. These were generated with a local version of
 Gromacs 5, containing the implementation of the semi-empirical DFT method
 DFTB3. The trajectories in .xtc format only contain the protein (738) but
 not the solvent. Additionally provided are time series of (i) electric
 potentials on the QM atoms created by the MM system, and (ii) DFTB
 Mulliken atomic charges of the QM atoms, recorded along the
 simulations.
DOI: 10.5061/dryad.6wwpzgmzw
title: Intraspecific variation in plant economic traits predicts trembling aspen resistance to a generalist insect herbivore

description: Patterns of trait expression within some plant species have recently been
 shown to follow patterns described by the leaf economics spectrum
 paradigm. Resistance to herbivores is also expected to covary with leaf
 economics traits. We selected multiple mature Populus tremuloides
 genotypes from a common garden to assess whether aspen leaf economics
 patterns follow those observed among species globally. We also evaluated
 leaf economics strategies in the context of insect resistance by
 conducting bioassays to determine the effects of plant traits on
 preference and performance of Lymantria dispar. We found that: 1)
 intraspecific trait patterns of P. tremuloides parallel those exhibited by
 the interspecific leaf economics spectrum, 2) herbivores preferred leaves
 from genotypes with resource-acquisitive strategies, and 3) herbivores
 also performed best on genotypes with resource-acquisitive strategies. We
 conclude that a leaf economics spectrum that incorporates defense traits
 is a useful tool for explaining intraspecific patterns of variation in
 plant strategies, including resistance to herbivores.
DOI: 10.5061/dryad.05qfttf35
title: Periphyton carbon and nitrogen stable isotopes detect agricultural stressors in low-order streams

description: Shifts in the stable isotope signatures of carbon (C) and nitrogen (N) in
 ecological materials have the potential to indicate environmental
 disturbances. This study examined the δ13C‰ and δ15N‰ ratios of stream
 water and periphyton from low-order streams in a landscape influenced by
 agricultural activities. Our key purpose was to assess the influence of
 best management practice (BMP) presence and age on C and N isotope values
 as a potential water-quality assessment. We collected stream water and
 periphyton from 19 streams within the Upper Delaware River watershed in
 New York, USA, in each of 4 management categories: 1) recently applied BMP
 treatments, 2) long-standing BMPs, 3) streams lacking BMPs, and 4)
 minimally disturbed reference streams. We sampled and analyzed water and
 periphyton for δ13C‰ and δ15N‰ in a repeated-measures design (BMP category
 ´ time) from April to November 2013. There were large seasonal differences
 in stream water δ13C-dissolved organic C (DIC)‰ and δ15NO3-N‰, with strong
 differences between reference and agricultural streams. Periphyton δ13C‰
 and δ15N‰ values also differed strongly across streams draining land with
 agricultural activities, with 85% higher periphyton δ15N‰ signals in all
 agricultural categories vs reference streams. Periphyton diatom and
 chlorophyte taxonomic proportions showed the strongest relationship with
 periphyton δ13C‰ values, where diatoms were negatively associated with
 increasing δ13C‰. These results suggest that aqueous and periphytic stable
 isotopes were sensitive in detecting persistent effects of agriculture on
 these streams despite BMP mitigation, where nutrient (orthosphosphate,
 nitrite, and ammonia) levels were non-indicative. These results also
 suggest that BMPs may not have fully eliminated the negative impacts of
 agricultural stressors on water quality in impacted streams.
description: Please see associated manuscript methods for sample collection
 and data generation processes. 
description: Use Excel to read data. ReadMe.txt file contains definitions for
 all variables. Please see published manuscript for methodologies for all
 variables.