cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7fq07
title: Data from: Early- and late-flowering guilds respond differently to landscape spatial structure

description: 1. Species with unique phenologies have distinct trait syndromes and
 environmental affinities, yet there has been little exploration of whether
 community assembly processes differ for plants with different phenologies.
 In this study, we ask whether early- and late-blooming species differ in
 the ways that dispersal, persistence, and resource-acquisition traits
 shape plant occurrence patterns in patchy habitats. 2. We sampled plant
 communities in 51 Ozark dolomite glade grasslands, which range in size
 from &lt;1 ha to &gt;100 ha. We modelled the occurrence of 71
 spring- and 43 summer-blooming grassland species these patches, using as
 predictors both environmental variables (landscape structure, soil
 resources) and plant traits related to dispersal, longevity, and resource
 acquisition. We were especially interested in how the environmental
 variables and plant traits interacted to determine the occurrence of
 phenological strategies in habitats that vary in size and isolation. 3.
 Summer-blooming species with better persistence and dispersal abilities
 had higher relative frequencies in smaller, more isolated habitat patches,
 and summer-blooming species with higher specific leaf area—suggesting fast
 growth and low stress tolerance—were more likely to occur in patches with
 greater soil organic matter and clay content. However, spring-blooming
 species showed much weaker interactions between functional traits and
 environmental gradients, perhaps because environmental conditions are less
 harsh in spring than in summer. 4. Synthesis: Several axes of plant life
 history variation may simultaneously influence community responses to
 habitat connectivity. In this case, explicitly considering plant phenology
 helped identify generalizable relationships between functional traits and
 landscape spatial structure.
description: Species occurence and
 trait dataLong form community data
 showing each potential species X site combination, with species-level
 trait data and site-level environmental variables for
 each.oztrait data
 JoE.csv
DOI: 10.5061/dryad.107h6
title: Data from: Reconstructing geographic range size dynamics from fossil data

description: Ecologists and paleontologists alike are increasingly using the fossil
 record as a spatial data set, in particular to study the dynamics and
 distribution of geographic range sizes among fossil taxa. However, no
 attempts have been made to establish how accurately range sizes and
 range-size dynamics can be preserved. Two fundamental questions are: Can
 common paleo range-size reconstruction methods accurately reproduce known
 species’ ranges from locality (i.e., point) data? And, are some
 reconstruction methods more reliable than others? Here, we develop a
 methodological framework for testing the accuracy of commonly used paleo
 range-size reconstruction methods (maximum latitudinal range, maximum
 great-circle distance, convex hull, and alpha convex hull) in different
 extinction-related biogeographic scenarios. We use the current
 distribution of surface water bodies as a proxy for “preservable area,” in
 which to test the performance of the four methods. We find that maximum
 great-circle distance and convex-hull methods most reliably capture
 changes in range size at low numbers of fossil sites, whereas convex hull
 performs best at predicting the distribution of “victims” and “survivors”
 in hypothetical extinction scenarios. Our results suggest that
 macroevolutionary and macroecological patterns in the relatively recent
 past can be studied reliably using only a few fossil occurrence sites. The
 accuracy of range-size reconstruction undoubtedly changes through time
 with the distribution and area of fossiliferous sediments; however, our
 approach provides the opportunity to systematically calibrate the quality
 of the spatial fossil record in specific environments and time intervals,
 and to delineate the conditions under which paleobiologists can
 reconstruct paleobiogeographical, macroecological, and macroevolutionary
 patterns over critical intervals in Earth history.
description: Supplementary Figures,
 Tables, and textSupporting figures, data
 and analyses for Darroch and Saupe (2017).suppmat_final.docx
DOI: 10.5061/dryad.h4p2b
title: Data from: The chemical signatures underlying host plant discrimination by aphids

description: The diversity of phytophagous insects is largely attributable to
 speciation involving shifts between host plants. These shifts are mediated
 by the close interaction between insects and plant metabolites. However,
 there has been limited progress in understanding the chemical signatures
 that underlie host preferences. We use the pea aphid (Acyrthosiphon pisum)
 to address this problem. Host-associated races of pea aphid discriminate
 between plant species in race-specific ways. We combined metabolomic
 profiling of multiple plant species with behavioural tests on two A. pisum
 races, to identify metabolites that explain variation in either acceptance
 or discrimination. Candidate compounds were identified using tandem mass
 spectrometry. Our results reveal a small number of compounds that explain
 a large proportion of variation in the differential acceptability of
 plants to A. pisum races. Two of these were identified as L-phenylalanine
 and L-tyrosine but it may be that metabolically-related compounds directly
 influence insect behaviour. The compounds implicated in differential
 acceptability were not related to the set correlated with general
 acceptability of plants to aphids, regardless of host race. Small changes
 in response to common metabolites may underlie host shifts. This study
 opens new opportunities for understanding the mechanistic basis of host
 discrimination and host shifts in insects.
description: EPG
 DataData of electrical
 penetration graph results used in the behavioural response of aphids to
 plants.Fecundity
 dataAphid fecundity data
 used in the validation of EPG results.Metabolomic
 data_Nonpolar phaseMetabolic results
 non-polar phase compounds of plant esxtracts, as measured with
 MALI-TOF.Metabolomic data_Polar
 phaseMetabolic results
 non-polar phase compounds of plant esxtracts, as measured with
 MALI-TOF.
DOI: 10.5061/dryad.2br8k
title: Data from: Open-top chambers for temperature manipulation in taller-stature plant communities

description: Open-top chambers simulate global warming by passively increasing air
 temperatures in field experiments. They are commonly used in low-stature
 alpine and arctic ecosystems, but rarely in taller-stature plant
 communities because of their limited height. We present a modified
 International Tundra Experiment (ITEX) chamber design for year-round
 outdoor use in warming taller-stature plant communities up to 1.5m tall.
 We report a full year of results for the chambers’ effects on air and soil
 temperature, relative humidity, and soil moisture in a northern hardwood
 forest clearing and a southern early successional grassland site located
 in Michigan, USA. Detailed construction plans are also provided. The
 chambers elevated daytime air temperatures at 1m height by 1.8ºC above
 ambient levels, on average over an entire year, at both the northern and
 southern site. The chambers did not affect relative humidity at either
 site. The chambers did not alter average soil temperature or moisture at
 the northern site and reduced soil temperatures and soil moisture at the
 southern site. The chambers increased variability in soil freeze/thaw
 cycles at both sites. The chambers achieved predicted levels of warming
 for mid-century (2046-2065) scenarios consistent with the majority of
 Representative Concentration Pathways (RCPs) in the International Panel on
 Climate Change 5th Assessment Report, with minimal experimental artifact.
 This design is a valuable tool for examining the effects of in situ
 warming on understudied taller-stature plant communities and creates the
 opportunity to expand future comparisons across a diversity of systems.
description: Northern Forest Clearing
 Microclimate DataDetailed microclimate
 data at the Northern Forest Clearing site at the University of Michigan
 Biological Station in Pellston, Michigan, USA.nfc_detailed_microclimate.csvSouthern Old Agriculture Field Microclimate DataDetailed microclimate data at the Southern Old Agriculture Field site at the Kellogg Biological Station in Hickory Corners, Michigan, USA.soaf_detailed_microclimate.csvNorthern Forest Clearing Pendant DataHourly temperature data at 1 meter height taken in warmed plots at the Northern Forest Clearing site at the University of Michigan Biological Station in Pellston, Michigan, USA.nfc_pendants.csvSouthern Old Agriculture Field Pendant DataHourly temperature data at 1 meter height taken in warmed plots at the southern old agriculture field site at the Kellogg Biological Station in Hickory Corners, Michigan, USA.soaf_pendants.csvREADMEIncludes a list of all data files, a description of the variables, and contact information.
DOI: 10.5061/dryad.2sd19
title: Data from: Multimodal in situ datalogging quantifies inter-individual variation in thermal experience and persistent origin effects on gaping behavior among intertidal mussels (Mytilus californianus)

description: In complex habitats, environmental variation over small spatial scales can
 equal or exceed larger-scale gradients. This small-scale variation may
 allow motile organisms to mitigate stressful conditions by choosing benign
 microhabitats, whereas sessile organisms may rely on other behaviors to
 cope with environmental stresses in these variable environments. We
 developed a monitoring system to track body temperature, valve gaping
 behavior, and posture of individual mussels (Mytilus californianus) in
 field conditions in the rocky intertidal zone. Neighboring mussels'
 body temperatures varied by up to 14°C during low tides. Valve gaping
 during low tide and postural adjustments, which could theoretically lower
 body temperature, were not commonly observed. Rather, gaping behavior
 followed a tidal rhythm at a warm, high intertidal site; this rhythm
 shifted to a circadian period at a low intertidal site and for mussels
 continuously submerged in a tidepool. However, individuals within a site
 varied considerably in time spent gaping when submerged. This behavioral
 variation could be attributed in part to persistent effects of
 mussels' developmental environment. Mussels originating from a
 wave-protected, warm site gaped more widely, and they remained open for
 longer periods during high tide than mussels from a wave-exposed, cool
 site. Variation in behavior was modulated further by recent wave heights
 and body temperatures during the preceding low tide. These large ranges in
 body temperatures and durations of valve closure events - which coincide
 with anaerobic metabolism - support the conclusion that individuals
 experience "homogeneous" aggregations such as mussel beds in
 dramatically different fashion, ultimately contributing to physiological
 variation among neighbors.
description: MusselTracker data
 repository and analysisUpdated R analysis file
 (MusselTracker_workup.Rnw) and accompanying data files for the
 MusselTracker project. See the README.md file for information on the files
 contained with. Example output from the .Rnw analysis file is provided (in
 .tex and .pdf formats).MusselTracker_Dryad_v3.ziphttps://github.com/millerlp/MusselTrackerThis archive contains circuit board design files and Arduino-style software to build and program a MusselTracker datalogger. See the README file within for further explanation.
DOI: 10.5061/dryad.tj1ss
title: Data from: Evidence of genomic adaptation to climate in Eucalyptus microcarpa: implications for adaptive potential to projected climate change

description: Understanding whether populations can adapt in situ or whether
 interventions are required is of key importance for biodiversity
 management under climate change. Landscape genomics is becoming an
 increasingly important and powerful tool for rapid assessments of climate
 adaptation, especially in long-lived species such as trees. We
 investigated climate adaptation in Eucalyptus microcarpa using the DArTseq
 genomic approach. A combination of FST outlier and environmental
 association analyses were performed using &gt; 4,200 genome-wide
 single nucleotide polymorphisms (SNPs) from 26 populations spanning
 climate gradients in south-eastern Australia. Eighty-one SNPs were
 identified as putatively adaptive, based on significance in FST outlier
 tests and significant associations with one or more climate variables
 related to temperature (70 / 81), aridity (37 / 81) or precipitation (35 /
 81). Adaptive SNPs were located on all 11 chromosomes, with no particular
 region associated with individual climate variables. Climate adaptation
 appeared to be characterized by subtle shifts in allele frequencies, with
 no consistent fixed differences identified. Based on these associations,
 we predict adaptation under projected changes in climate will include a
 suite of shifts in allele frequencies. Whether this can occur sufficiently
 rapidly through natural selection within populations, or would benefit
 from assisted gene migration, requires further evaluation. In some
 populations, the absence, or predicted increases to near fixation of
 particular adaptive alleles hint at potential limits to adaptive capacity.
 Together, these results reinforce the importance of standing genetic
 variation at the geographical level for maintaining species’ evolutionary
 potential.
description: Eucalyptus microcarpa
 SNP datasetVCF file containing 4218
 SNPs for 580 Eucalyptus microcarpa samples used in climate adaptation and
 associated analysesEmicrocarpa_GenomicApdt_SNPs.vcf.gzMetadata for Eucalyptus microcarpa samplesMetadata regarding sampling locations and samples belonging to each siteEmicrocarpa_GenomicApdt_SNPs_metadata.xlsxREADME fileREADME file for Eucalyptus microcarpa SNP data
DOI: 10.5518/1506
title: Supplementary material for ‘Location retrieval using qualitative place signatures of visible landmarks’

description: This document provides the supplementary material to the manuscript ‘Location retrieval using qualitative place signatures of visible landmarks’ published in the to the ’International Journal of Geographical Information Science’. It should be read in conjunction with the main manuscript.
DOI: 10.5061/dryad.fm03p
title: Data from: Taxonomic revision of the flavopalliata species group of Signiphora (Hymenoptera: Signiphoridae)

description: The flavopalliata species group of Signiphora Ashmead (Hymenoptera:
 Signiphoridae) is revised. Twelve species are redescribed: Signiphora
 aleyrodis Ashmead, S. aspidioti Ashmead, S. borinquensis Quezada et al.,
 S. coquilletti Ashmead, S. fax Girault, S. flavella Girault, S.
 flavopalliata Ashmead, S. lutea Rust, S. maculata Girault, S. merceti
 Malenotti, S. perpauca Girault and S. xanthographa Blanchard. Signiphora
 townsendi Ashmead is synonymized under S. aleyrodis n. syn.; Thysanus
 insularis Dozier and S. flavopalliata desantisi De Santis are synonymized
 under S. fax n. syns.; S. basilica Girault, S. euclidi Girault, S. flava
 Girault, S. caridei Brèthes, S. thoreauini Girault and Thysanus louisianae
 Dozier are synonymized under S. flavella n. syns.; and S. woolleyi Hayat
 is synonymized under S. perpauca n. syn. Thirteen new species are
 described: S. bennetti n. sp., S. biloba n. sp., S. brachyptera n. sp., S.
 curepensis n. sp., S. dozieri n. sp., S. ehleri n. sp., S. ensifera n.
 sp., S. falcata n. sp., S. jojobae n. sp., S. longitibia n. sp., S.
 plaumanni n. sp., S. renuncula n. sp. and S. tridentata n. sp. Lectotypes
 are designated for S. aleyrodis, S. townsendi, S. fax, S. flavella, S.
 occidentalis, S. lutea, S. maculata and S. xanthographa.
description: S1 morphological and
 anatomical terms and HAO entriescomma-delimited list of
 all anatomical and morphological terms used in the paper, along with links
 to Hymenoptera Anatomy OntologyS2 material
 examinedcomma-delimited file
 with records for specimens examined for each species description, along
 with specimen accession numbers, repositories, latitude and longitude, and
 verbatim label datadistribution map
 fileskml files with records
 for all material examined and type material for each species, to be used
 for visualizing species distributions. See Readme file for more
 details.
DOI: 10.5061/dryad.p4sg5
title: Data from: Huygens' clocks revisited

description: In 1665, Huygens observed that two identical pendulum clocks, weakly
 coupled through a heavy beam, soon synchronized with the same period and
 amplitude but with the two pendula swinging in opposite directions. This
 behaviour is now called anti-phase synchronization. This paper presents an
 analysis of the behaviour of a large class of coupled identical
 oscillators, including Huygens' clocks, using methods of equivariant
 bifurcation theory. The equivariant normal form for such systems is
 developed and the possible solutions are characterized. The transformation
 of the physical system parameters to the normal form parameters is given
 explicitly and applied to the physical values appropriate for
 Huygens' clocks, and to those of more recent studies. It is shown
 that Huygens' physical system could only exhibit anti-phase motion,
 explaining why Huygens observed exclusively this. By contrast, some more
 recent researchers have observed in-phase or other more complicated motion
 in their own experimental systems. Here, it is explained which physical
 characteristics of these systems allow for the existence of these other
 types of stable solutions. The present analysis not only accounts for
 these previously observed solutions in a unified framework, but also
 introduces behaviour not classified by other authors, such as a
 synchronized toroidal breather and a chaotic toroidal breather.
description: Video of a synchronized
 breather solutionThis video shows a
 three-dimensional projection of a quasiperiodic solution on an invariant
 2-torus for the four-dimensional normal form for a system with Huygens
 (exchange) symmetry near a double Hopf bifurcation. The visual result of
 this projection is a trajectory riding the surface of a breathing
 torus.breather.mp4Video of a chaotic breather solutionThis video shows a three-dimensional projection of a chaotic solution for the four-dimensional normal form for a system with Huygens (exchange) symmetry near a double Hopf bifurcation. The visual result of this projection is a trajectory riding the surface of a breathing torus but filling a three-dimensional space.breather_chaotic.mp4
DOI: 10.5061/dryad.82600
title: Data from: A novel adenine-based-MOF derived nitrogen-doped nanoporous carbon for flexible solid-state supercapacitor

description: In this article, we have synthesized a series of nitrogen-doped nanoporous
 carbon (NPC) from metal organic framework (MOF) of UiO-66 with different
 ratio of adenine and coated on carbon nanotube film (CNTF) to obtain a
 flexible porous electrode (NPC/CNTF). It is worth noting that the
 introduction of adenine at different ratio did not change the structure of
 UiO-66. We also investigated the effect of carbonization temperature from
 800 to 1000 °C on the electrochemical properties of the NPC. The ratio (1,
 4-benzendicarboxylate: adenine) 9:1 and the NPC carbonized at 900 °C
 (noted as NPC-1-900) exhibits better electrochemical properties. The
 results show that NPC-1-900/CNTF electrode exhibits an exceptionally areal
 capacitance of 121.5 mF cm-2 than that of PC-900/CNTF electrode (22.8 mF
 cm-2) at 5 mV s-1 in a three-electrode system, indicating that the
 incorporation of nitrogen is beneficial to the electrochemical properties
 of nanoporous carbon. A symmetric flexible solid-state supercapacitor of
 NPC-1-900/CNTF has also been assembled and tested. Electrochemical date
 shows that the device exhibited superior areal capacitance (43.2 mF cm-2)
 at the scan rate of 5 mV s-1, the volumetric energy density is 57.3 µWh
 cm-3 and the volumetric power density is 2.4 mW cm-3 at the current
 density of 0.5 mA cm-2 based on PVA/H3PO4 gel electrolyte. For practical
 application, we have also studied the bending tests of the device, which
 show that the device exhibits the outstanding mechanical stability under
 different bending angles. Furthermore, the flexible device shows excellent
 cyclic stability, which can retain 91.5% of the initial capacitance after
 2000 cycles.
description: Original data for
 figures in the manuscriptThe zip file includes
 the original data of Figures from Fig.1 to Fig 8, SFig.1 to SFig.7. The
 files can be accessed by common softwares such as origin edit software,
 Jade 5.0 for XRD, NOVAWIN for N2 adsorption/desorption isotherms, PEAK 4.1
 for XPS, EC-LAB and Landt programs for electrochemical
 data.Revised
 Data.zip
DOI: 10.5061/dryad.6697t
title: Data from: Evidence of opposing fitness effects of parental heterozygosity and relatedness in a critically endangered marine turtle?

description: How individual genetic variability relates to fitness is important in
 understanding evolution and the processes affecting populations of
 conservation concern. Heterozygosity-fitness correlations (HFCs) have been
 widely used to study this link in wild populations, where key parameters
 that affect both variability and fitness, such as inbreeding, can be
 difficult to measure. We used estimates of parental heterozygosity and
 genetic similarity (‘relatedness’) derived from 32 microsatellite markers
 to explore the relationship between genetic variability and fitness in a
 population of the critically endangered hawksbill turtle, Eretmochelys
 imbricata. We found no effect of maternal MLH (multilocus heterozygosity)
 on clutch size or egg success rate, and no single-locus effects. However,
 we found effects of paternal MLH and parental relatedness on egg success
 rate that interacted in a way that may result in both positive and
 negative effects of genetic variability. Multicollinearity in these tests
 was within safe limits, and null simulations suggested the effect was not
 an artefact of using paternal genotypes reconstructed from large samples
 of offspring. Our results could imply a tension between inbreeding and
 outbreeding depression in this system, which is biologically feasible in
 turtles: female-biased natal philopatry may elevate inbreeding risk and
 local adaptation, and both processes may be disrupted by male-biased
 dispersal. Although this conclusion should be treated with caution due to
 a lack of significant identity disequilibrium, our study shows the
 importance of considering both positive and negative effects when
 assessing how variation in genetic variability affects fitness in wild
 systems.
description: all_data_and_analysis_scriptsAll data and analysis scripts. An explainer text file is included in the zipped folderphillips2017_hawksbill_HFC_dataForDryad.zip