cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pg4f4qrmq
title: Data from: Cropland connectivity affects genetic divergence of Colorado potato beetle along an invasion front

description: The population genetic structure of invasive species can be strongly
 affected by environmental and landscape barriers to dispersal.
 Disentangling the relative contributions of these factors to genetic
 divergence among invading populations is a fundamental goal of landscape
 genetics with important implications for invasion management. Here, we
 relate patterns of genetic divergence in a global invasive agricultural
 pest, Colorado potato beetle (CPB; Leptinotarsa decemlineata), to
 environmental and landscape factors along an invasion front in
 Northwestern China. We first used microsatellite markers and
 spatial-temporal samples to assess broad patterns of genetic diversity as
 well as fine-scale changes in patterns of genetic divergence. We then
 distinguished the relative contributions of five factors to genetic
 divergence among front populations: geographic distance (isolation by
 distance), climate dissimilarity (isolation by environment), and
 least-cost distances (isolation by resistance) modelled with three
 factors: climate suitability, cropland cover, and road networks. Genetic
 diversity broadly decreased from West to East, with the exception being
 Eastern China. Low levels of genetic diversity and varying degrees of
 divergence were observed in Northwestern China, reflecting the potential
 effect of landscape heterogeneity. Least-cost distance across cropland
 cover was most positively correlated with genetic divergence, suggesting a
 role of croplands in facilitating gene flow. The contribution of climate
 to genetic divergence was secondary, whether modelled in terms of local
 adaptability or connectivity of the climatic landscape, suggesting that
 constraints to CPB gene flow imposed by a harsh climate may be ameliorated
 in agricultural landscapes. No evidence was found for an obvious effect of
 road networks on genetic divergence and population structuring. Our study
 provides an example of how agricultural landscape connectivity can
 facilitate the spread of invasive pests, even across a broad climatic
 gradient. More broadly, our findings can guide decisions about future land
 management for mitigating further spread.
description: CPB_all_9SSR_GenAlEx.xlsx Microsatellite
 loci for all populations of Colorado potato beetle. Read with GenAlEx in
 Excel. resistance surfaces.zip
 Resistance surfaces for Isolation by resistance models, as tif
 format. R_scripts.R R Scripts for
 landscape genetics analysis
DOI: 10.5061/dryad.s7h44j152
title: Energy consumption and greenhouse gas emissions data of activated carbon production using different biomass

description: This dataset includes the energy consumption and Greenhouse Gas emissions
 data of activated carbon production using 73 different types of
 woody biomass. Understanding the environmental implications of activated
 carbon (AC) produced from diverse biomass feedstocks is critical for
 biomass screening and process optimization for sustainability. Many
 studies have developed Life Cycle Assessment (LCA) for biomass-derived AC.
 However, most of them either focused on individual biomass species with
 differing process conditions or compared multiple biomass feedstocks
 without investigating the impacts of feedstocks and process variations.
 Developing LCA for AC from diverse biomass is time-consuming and
 challenging due to the lack of process data (e.g., energy and mass
 balance). This study addresses these knowledge gaps by developing a
 modeling framework that integrates artificial neural network (ANN), a
 machine learning approach, and kinetic-based process simulation. The
 integrated framework is able to generate Life Cycle Inventory data of AC
 produced from 73 different types of woody biomass with 250
 characterization data samples. The results show large variations in energy
 consumption and GHG emissions across different biomass species (43.4–277
 MJ/kg AC and 3.96–22.0 kg CO2-eq/kg AC). The sensitivity analysis
 indicates that biomass composition (e.g., hydrogen and oxygen content) and
 process operational conditions (e.g., activation temperature) have large
 impacts on energy consumption and GHG emissions associated with AC
 production.
description: The energy consumption and
 greenhouse gas emissions data of activated production were generated by
 the integrated modeling framework that was developed in this study.
 The modeling framework coupled artificial neural network (ANN), a machine
 learning approach, and kinetic-based process simulation.
DOI: 10.5061/dryad.zw3r2286m
title: Data from: The intrinsically disordered N-terminus of the voltage-dependent anion channel

description: The voltage-dependent anion channel (VDAC) is a beta-barrel membrane
 protein of the mitochondrial outer membrane (MOM), which controls the
 transport of ions and ATP between mitochondria and the
 cytoplasm. The present dataset includes all data and
 scripts generated in the study "The
 intrinsically-disordered N-terminus of the voltage-dependent anion
 channel" by J. Preto and I. Krimm, where we performed
 all-atom simulations to investigate the disordered properties of VDAC’s
 N-terminus (i) as a free peptide in solution (ii) as part of the channel
 (mVDAC1-WT) or (iii) as part of a mVDAC1 mutant (mVDAC1-Cys) characterized
 by a disulfide bond affixing the N-terminus against the beta-barrel wall.
 The last two studies involve the channel embedded in a DOPC/DOPE lipid
 bilayer representing the MOM. Our data comprise molecular dynamics (MD)
 and accelerated MD (aMD) trajectories of the three systems performed for
 exploratory purposes. In the case of mVDAC1-Cys, MD/aMD simulations were
 performed upon different transmembrane (TM) potential values (0mV, +40mV
 and -40mV). At all voltages, GCMC/BD calculations were run to probe for
 possible low-conducting conformers of the channel. At +40mV, our aMD
 trajectory shows detachment of the N-terminus from the
 beta-barrel and the emergence of long-lived
 subconducting conformations. The stability of these conformations is
 further confirmed from standard MD simulations at +40mV, starting from
 each of the subconducting conformers identified in GCMC/BD. For each
 trajectory, the numbers of cations and anions crossing the channel were
 recorded to keep track of the intensity and of the conductance of each
 state.
DOI: 10.5061/dryad.cz8w9gj23
title: Predicting patch occupancy reveals the complexity of host range expansion

description: Specialized plant-insect interactions are a defining feature of life on
 earth, yet we are only beginning to understand the factors that set limits
 on host ranges in herbivorous insects. To better understand the recent
 adoption of alfalfa as a host plant by the Melissa blue butterfly, we
 quantified arthropod assemblages and plant metabolites across a wide
 geographic region, while controlling for climate and dispersal inferred
 from population genomic variation. The presence of the butterfly is
 successfully predicted by direct and indirect effects of plant traits and
 interactions with other species. Results are consistent with the
 predictions of a theoretical model of parasite host range in which
 specialization is an epiphenomenon of the many barriers to be overcome
 rather than a consequence of trade-offs in developmental physiology.
DOI: 10.5061/dryad.cc2fqz64d
title: How mitonuclear discordance and geographic variation have confounded species boundaries in a widely studied snake

description: As DNA sequencing technologies and methods for delimiting species with
 genomic data become more accessible and numerous, researchers have more
 tools than ever to investigate questions in systematics and
 phylogeography. However, easy access to sophisticated computational tools
 is not without its drawbacks. Choosing the right approach for one’s
 question can be challenging when presented with multitudinous options,
 some of which fail to distinguish between species and intraspecific
 population structure. Here, we employ a methodology that emphasizes
 intensive geographic sampling, particularly at contact zones between
 populations, with a focus on differentiating intraspecific genetic
 clusters from species in the Pantherophis guttatus complex, a group of
 North American ratsnakes. Using a mitochondrial marker as well as ddRADseq
 data, we find evidence of mitonuclear discordance which has contributed to
 historical confusion about the relationships within this group.
 Additionally, we identify geographically and genetically structured
 populations within the species Pantherophis emoryi that are congruent with
 previously described morphological variation. Importantly, we find that
 these structured populations within P. emoryi are highly admixed
 throughout the range of the species and show no evidence of any
 reproductive isolation. Our data support a revision of the taxonomy of
 this group, and we recognize two species within the complex and three
 subspecies within P. emoryi. This study illustrates the importance of
 thorough sampling of contact zones and consideration of gene flow when
 delimiting species in widespread complexes containing parapatric lineages.
DOI: 10.5061/dryad.zpc866t73
title: Individual differences in risk‐taking affect foraging across different landscapes of fear

description: One of the strongest determinants of behavioural variation is the tradeoff
 between resource gain and safety. Although classical theory predicts
 optimal foraging under risk, empirical studies report large unexplained
 variation in behaviour. Intrinsic individual differences in risk-taking
 behaviour might contribute to this variation. By repeatedly exposing
 individuals of a small mesopredator to different experimental landscapes
 of risks and resources, we tested 1) whether individuals adjust their
 foraging behaviour according to predictions of the general tradeoff
 between energy gain and predation avoidance and 2) whether individuals
 differ consistently and predictably from each other in how they solve this
 tradeoff. Wild-caught individuals (n = 42) of the jumping spider Marpissa
 muscosa, were subjected to repeated release and open-field tests to
 quantify among-individual variation in boldness and activity.
 Subsequently, individuals were tested in four foraging tests that differed
 in risk level (white/dark background colour) and risk variation (constant
 risk/variable risk simulated by bird dummy overflights) and contained
 inaccessible but visually perceivable food patches. When exposed to a
 white background, individuals reduced some aspects of movement and
 foraging intensity, suggesting that the degree of camouflage serves as a
 proxy of perceived risk in these predators. Short pulses of acute
 predation risk, simulated by bird overflights, had only small effects on
 aspects of foraging behaviour. Notably, a significant part of variation in
 foraging was due to among-individual differences across risk landscapes
 that are linked to consistent individual variation in activity, forming a
 behavioural syndrome. Our results demonstrate the importance of
 among-individual differences in behaviour of animals that forage under
 different levels of perceived risk. Since these differences likely affect
 food-web dynamics and have fitness consequences, future studies should
 explore the mechanisms that maintain the observed variation in natural
 populations.
description: Most values were collected from recorded videos using the program
 EthoVision (Noldus).
DOI: 10.5061/dryad.f4qrfj6tr
title: A core competency model for clinical informationists

description: Objectives: Access to high-quality information improves the quality of
 patient care, but lack of time and sufficient skills in
 information-seeking can prevent access to information by clinicians. To
 solve this problem, clinical informationists can provide high-quality,
 filtered information for clinical team members. In this study, we
 identified the core competencies needed by clinical informationists to
 effectively fulfill their role in clinical teams. Methods: Participants
 were selected purposefully from clinicians and medical librarians. Data
 were collected through semi-structured interviews and analyzed using
 qualitative content analysis. Results: We identified six
 competencies—communication, research, education and training, domain
 knowledge, information services, and technology—which together were used
 to develop a CREDIT model of core competencies for clinical
 informationists. Conclusions: The CREDIT model can be used as criteria for
 evaluating the performance of clinical informationists as well as for
 developing and assessing clinical informationist educational programs and
 curriculum.
description: The data were collected through semi-structured
 interviews. Qualitative content analysis used to analyze data. 
description: This is a semi-processed data transcript from an interview with 10 librarianship professions who provided CI services for at least 2 years in clinical settings and 12 clinicians who received CI services for at least 2 years to identify the competencies needed by clinical informationist. Data were collected through semi-structured interviews. A qualitative content analysis led to the identification of 6 main categories and 25 subcategories. In this transcript, there are quotations from participants below each subcategory. Similar quotations have been removed.
DOI: 10.15468/dl.h73bmd
title: Occurrence Download

description: A dataset containing 79 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Calamus merrillii"
 ]
}

 The dataset includes 79 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002575-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.6djh9w0zz
title: Female fiddler crabs, Austruca lactea (Decapoda: Ocypodidae), adjust their rate of mate sampling based on remaining days until oviposition under a size-dependent temperature constraint

description: The rate of mate sampling is one of the critical components associated
 with the sampling costs in female mate choice. In ectotherms,
 environmental temperature generally constrains locomotion performance. In
 addition, females will adjust the mate sampling rate depending on their
 breeding schedule because of the risk of remaining unfertilized eggs or a
 loss of benefits related to mating, if they lost the opportunity to
 copulate. This study investigated how these effects influence the rate of
 female mate sampling in the temperate fiddler crab (Austruca lactea) in
 the field. The number of sampled males per searching duration formed a
 convex curve against environmental temperature. The optimal environmental
 temperature increased with the female body size. These results suggest
 that the mate sampling rate would be under a size-dependent temperature
 constraint, and sampling costs would be lower for larger females than
 smaller individuals under high-temperature conditions. Furthermore, when
 there were fewer remaining days, the mate sampling rate increased. Females
 would hasten the sampling rate to ensure a suitable burrow for breeding.
 Mate sampling rate in female A. lactea is therefore associated with
 environmental temperature, female body size, and remaining days until
 oviposition.
description: Please see materials and methods.
DOI: 10.5061/dryad.mkkwh70xh
title: A place to land: spatiotemporal drivers of stopover habitat use by migrating birds

description: Migrating birds require en route habitats to rest and refuel. Yet habitat
 use has never been integrated with passage to understand factors that
 determine where and when birds stopover during spring and autumn
 migration. Here, we introduce the stopover-to-passage ratio (SPR), the
 percentage of passage migrants that stop in an area, and use eight years
 of data from 12 weather surveillance radars to estimate over 50% SPR
 during spring and autumn through the Gulf of Mexico and Atlantic coasts of
 the southeastern U.S., the most prominent corridor for North America’s
 migratory birds. During stopovers, birds concentrated close to the coast
 during spring and inland in forested landscapes during autumn, suggesting
 seasonal differences in habitat function and highlighting the vital role
 of stopover habitats in sustaining migratory communities. Beyond advancing
 understanding of migration ecology, SPR will facilitate conservation
 through identification of sites that are disproportionally selected for
 stopover by migrating birds.
DOI: 10.5061/dryad.pzgmsbcjc
title: A codon model for associating phenotypic traits with altered selective patterns of sequence evolution

description: Detecting the signature of selection in coding sequences and associating
 it with shifts in phenotypic states can unveil genes underlying complex
 traits. Of the various signatures of selection exhibited at the molecular
 level, changes in the pattern of selection at protein coding genes have
 been of main interest. To this end, phylogenetic branch-site codon models
 are routinely applied to detect changes in selective patterns along
 specific branches of the phylogeny. Many of these methods rely on a
 pre-specified partition of the phylogeny to branch categories, thus
 treating the course of trait evolution as fully resolved and assuming that
 phenotypic transitions have occurred only at speciation events. Here we
 present TraitRELAX, a new phylogenetic model that alleviates these strong
 assumptions by explicitly accounting for the uncertainty in the evolution
 of both trait and coding sequences. This joint statistical framework
 enables the detection of changes in selection intensity upon repeated
 trait transitions. We evaluated the performance of TraitRELAX using
 simulations and then applied it to two case studies. Using TraitRELAX, we
 found an intensification of selection in the primate SEMG2 gene in
 polygynandrous species compared to species of other mating forms, as well
 as changes in the intensity of purifying selection operating on sixteen
 bacterial genes upon transitioning from a free-living to an endosymbiotic
 lifestyle.
DOI: 10.5061/dryad.zkh189388
title: The complete mitochondrial genome of Eutrichosiphum pasaniae (Okajima, 1908) (Hemiptera: Aphididae: Greenideinae)

description: In this study, we sequenced the complete mitochondrial genome of
 Eutrichosiphum pasaniae through Illumina platform. The circular mitogenome
 is 16,500 bp in length and composed of 13 protein-coding genes (PCGs), 22
 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), a large control
 region and a special repeat region. The nucleotide composition of whole
 mitogenome is strongly AT-biased (85.5%). All PCGs start with ATN and end
 with TAA except for cox1 which terminates with an incomplete stop codon T.
 All tRNAs have a typical clover-leaf secondary structure except for trnS
 (AGN). The lengths of rrnL, rrnS and control region are 1276, 774 and 996
 bp, respectively. The repeat region with a length of 909 bp is located
 between trnE and trnF and consists of 4.1 repeat units. The phylogenetic
 tree supports the sister relationship of Eutrichosiphum pasaniae and
 Greenidea psidii.
description: The maximum-likelihood phylogenetic tree was constructed with
 RAxML v8.2.10 under the GTR+I+G model, based on the whole mitogenome
 sequences of <i>E.</i> <i>pasaniae</i> and 24
 other aphid species.  <strong>The compressed file Phylogenetic_analysis
 includes:</strong>
  <strong>The sequence of gene used</strong>
 37_genes.phy <strong>Gene
 partition</strong> partition.txt
 <strong>The maximum-likelihood
 tree</strong> RAxML_bestTree.T1
 RAxML_bipartitions.T1
 RAxML_bipartitionsBranchLabels.T1
 RAxML_bootstrap.T1
DOI: 10.5061/dryad.p2ngf1vp0
title: Data from: Spatial and environmental influences on selection in a clock gene coding trinucleotide repeat in Canada lynx (Lynx canadensis)

description: Clock genes exhibit substantial control over gene expression and
 ultimately life-histories using external cues such as photoperiod, and are
 thus likely to be critical for adaptation to shifting seasonal conditions
 and novel environments as species redistribute their ranges under climate
 change. Coding trinucleotide repeats (cTNRs) are found within several
 clock genes, and may be interesting targets of selection due to their
 containment within exonic regions and elevated mutation rates. Here, we
 conduct inter-specific characterization of the NR1D1 cTNR between Canada
 lynx and bobcat, and intra-specific spatial and environmental association
 analyses of neutral microsatellites and our functional cTNR marker, to
 investigate the role of selection on this locus in Canada lynx. We report
 signatures of divergent selection between lynx and bobcat, with the
 potential for hybrid-mediated gene flow in the area of range overlap. We
 also provide evidence that this locus is under selection across Canada
 lynx in eastern Canada, with both spatial and environmental variables
 significantly contributing to the explained variation, after controlling
 for neutral population structure. These results suggest that cTNRs may
 play an important role in the generation of functional diversity within
 some mammal species, and allow for contemporary rates of adaptation in
 wild populations in response to environmental change. We encourage
 continued investment into the study of cTNR markers to better understand
 their broader relevance to the evolution and adaptation of mammals.
description: See README file for notes on data contained within Excel
 spreadsheet.
DOI: 10.5061/dryad.rxwdbrv6b
title: VCF file of multiple single-cyst-derived Ro1 and Ro2 lines of New York fields on Globodera rostochiensis genome

description: The potato cyst nematode, Globodera rostochiensis, is a regulated pest
 posing a serious threat to potato production worldwide. Although the
 endemic pathotype (Ro1) of G. rostochiensis has been confined to New York
 State for several decades as a result of quarantine regulations and
 management with resistant potato cultivars, a virulent pathotype, Ro2, has
 emerged, for which control measures are scarce. The ability to detect Ro2
 early in fields is necessary to sustain the success of G. rostochiensis
 quarantine in the US. Here, we report the comparative analysis of
 whole-genome sequences of multiple single-cyst-derived Ro1 and Ro2 lines,
 propagated from original field populations. The identified discriminant
 variants are good targets for developing molecular diagnostic tools for
 differentiating G. rostochiensis pathotypes in NY.
description: DNA extractions of twenty cysts per population of New York
 <em>Globodera rostochiensis</em> Ro1/Ro2 lines. TruSeq DNA
 library construction and Illumina NextSeq500 sequencing were performed at
 Cornell Institute of Biotechnology. Sequencing reads were trimmed with
 Trimmomatic v0.36 (Bolger et al. 2014) to a minimum length of 50 bp and a
 minimum Phred quality score of 20. Unpaired reads were discarded and the
 remaining sequences were aligned to the <em>G.
 rostochiensis</em> reference genome nGr.v1.1 (Eves-van den Akker et
 al. 2016) using BWA-MEM v0.7.12 (Li et al. 2009). Variants were identified
 using FreeBayes v1.2.0 (Garrison and Marth 2012) with minimum mapping
 quality set at 30, minimum base quality at 20, minimum alternate count at
 2, minimum alternate fraction at 0.05. Additional filters were applied to
 keep only the variant calls with a minimum coverage of 5 in each of the 55
 lines and no missing data.