cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dt3s7
title: Data from: Artificial selection reveals heritable variation for developmental instability

description: Fluctuating (nondirectional) asymmetry (FA) of bilaterally paired
 structures on a symmetrical organism is commonly used to assay the
 developmental instability (DI) caused by environmental or genetic factors.
 Although evidence for natural selection to reduce FA has been reported,
 evidence that FA (and by extension DI) is heritable is weak. We report the
 use of artificial selection to demonstrate heritable variation in the
 fluctuating asymmetry of wing veins in an outbred population of Drosophila
 melanogaster. Our estimates for the heritability of FA range from 0% to 1%
 and result in estimates for the heritability of DI as large as 20%,
 comparable to values typical for life-history traits. These values
 indicate the existence of evolutionarily relevant genetic variation for DI
 and the effectiveness of selection for reduced FA suggests that natural
 selection has not fixed all the genetic variants that would improve
 developmental stability in these populations.
description: carter-houle-evol2011-descriptionThis file contains descriptions of data column headings in other files. It is attached to each other file as a readme.carter-houle-evol2011-U1Data for the U1 line as described in the paper.carter-houle-evol2011-U2Data for the U2 line as described in the paper.carter-houle-evol2011-D1Data for the D1 line as described in the paper.carter-houle-evol2011-D2Data for the D2 line as described in the paper.
DOI: 10.5061/dryad.cr1c1
title: Data from: Variation in setal micromechanics and performance of two gecko

description: Biomechanical models of the gecko adhesive system typically focus on setal
 mechanics from a single gecko species, Gekko gecko. In this study, we
 compared the predictions from three mathematical models with experimental
 observations considering an additional gecko species Phelsuma grandis, to
 quantify interspecific variation in setal micromechanics. We also
 considered the accuracy of our three focal models: the frictional adhesion
 model, work of detachment model, and the effective modulus model. Lastly,
 we report a novel approach to quantify the angle of toe detachment using
 the Weibull distribution. Our results suggested the coupling of frictional
 and adhesive forces in isolated setal arrays, first observed in G. gecko
 is also present in P. grandis although P. grandis displayed a higher toe
 detachment angle, suggesting they produce more adhesion relative to
 friction than G. gecko. We also found the angle of toe detachment
 accurately predicts a species’ maximum performance limit when fit to a
 Weibull distribution. When considering the energy stored during setal
 attachment, we observed less work to remove P. grandis arrays when
 compared with G. gecko, suggesting P. grandis arrays may store less energy
 during attachment, a conclusion supported by our model estimates of stored
 elastic energy. Our predictions of the effective elastic modulus model
 suggested P. grandis arrays to have a lower modulus, E eff, but our
 experimental assays did not show differences in moduli between the
 species. The considered mathematical models successfully estimated most of
 our experimentally measured performance values, validating our three focal
 models as template models of gecko adhesion (see Full and Koditschek in J
 Exp Biol 202(23):3325–3332, 1999), and suggesting common setal mechanics
 for our focal species and possibly for all fibular adhesives. Future
 anchored models, built upon the above templates, may more accurately
 predict performance by incorporating additional parameters, such as
 variation in setal length and diameter. Variation in adhesive performance
 may affect gecko locomotion and as a result, future ecological
 observations will help to determine how species with different performance
 capabilities use their habitat.
description: Gecko biomechancis
 analyses_JanThe R code that analyses
 the raw dataArray_HeightArray_Areatokay_analysis_jonphelsuma_analysis_jon2010-05-042010-04-272010-04-282010-04-292010-04-302010-05-032010-05-052010-05-062010-05-072010-06-092010-06-102010-06-112010-06-142010-06-152010-06-19
DOI: 10.5061/dryad.vm72v
title: Data from: Large-scale biomonitoring of remote and threatened ecosystems via high-throughput sequencing

description: Biodiversity metrics are critical for assessment and monitoring of
 ecosystems threatened by anthropogenic stressors. Existing sorting and
 identification methods are too expensive and labour-intensive to be scaled
 up to meet management needs. Alternately, a high-throughput DNA sequencing
 approach could be used to determine biodiversity metrics from bulk
 environmental samples collected as part of a large-scale biomonitoring
 program. Here we show that both morphological and DNA sequence-based
 analyses are suitable for recovery of individual taxonomic richness,
 estimation of proportional abundance, and calculation of biodiversity
 metrics using a set of 24 benthic samples collected in the Peace-Athabasca
 Delta region of Canada. The high-throughput sequencing approach was able
 to recover all metrics with a higher degree of taxonomic resolution than
 morphological analysis. The reduced cost and increased capacity of DNA
 sequence-based approaches will finally allow environmental monitoring
 programs to operate at the geographical and temporal scale required by
 industrial and regulatory end-users.
description: Benthic_PAD-June2012_F230-BE_Dryad_submissionJoel_benthic_June2012_F230-BE_Dryad_submission.zip
DOI: 10.5061/dryad.5sf19
title: Data from: Functional anatomy of the cervical region in the late Miocene amphicyonid Magericyon anceps (Carnivora, Amphicyonidae): implications for its feeding behaviour

description: We describe the skull and neck morphology of the late Miocene amphicyonid
 Magericyon anceps, focusing on aspects related to functional anatomy. This
 species, recorded only from the Vallesian sites of Batallones-1 and
 Batallones-3 (Madrid, Spain), is the last known amphicyonid in the fossil
 record of Western Europe, with the Batallones populations being one of the
 best-known of the family. The morphology of its skull and cervical
 vertebrae allows us to infer aspects of its associated musculature, such
 as muscle strength and range of movement. Magericyon anceps had
 well-developed neck muscles, suited for providing the head with a high
 capacity for lateral and rotatory movements, as well as for playing an
 important role in the extension and stabilization of the head and neck,
 improving its efficiency in killing and consuming prey. Magericyon anceps
 shared its habitat with other large carnivorans, which would have strongly
 influenced its behaviour. Rapid killing and processing of prey would have
 been an advantage for avoiding kleptoparasitism by other large predators,
 as well as reducing consumption time, during which M. anceps would have
 been more vulnerable to attack from competitors.
description: Skull and cervical
 vertebrae of Magericyon ancepsFull rotation of 3D
 articulated model of skull and cervical vertebrae of Magericyon
 anceps
DOI: 10.5061/dryad.mp5s3
title: Data from: Dopamine promotes motor cortex plasticity and motor skill learning via PLC activation

description: Dopaminergic neurons in the ventral tegmental area, the major midbrain
 nucleus projecting to the motor cortex, play a key role in motor skill
 learning and motor cortex synaptic plasticity. Dopamine D1 and D2 receptor
 antagonists exert parallel effects in the motor system: they impair motor
 skill learning and reduce long-term potentiation. Traditionally, D1 and D2
 receptor modulate adenylyl cyclase activity and cyclic adenosine
 monophosphate accumulation in opposite directions via different G-proteins
 and bidirectionally modulate protein kinase A (PKA), leading to distinct
 physiological and behavioral effects. Here we show that D1 and D2 receptor
 activity influences motor skill acquisition and long term synaptic
 potentiation via phospholipase C (PLC) activation in rat primary motor
 cortex. Learning a new forelimb reaching task is severely impaired in the
 presence of PLC, but not PKA-inhibitor. Similarly, long term potentiation
 in motor cortex, a mechanism involved in motor skill learning, is reduced
 when PLC is inhibited but remains unaffected by the PKA inhibitor. Skill
 learning deficits and reduced synaptic plasticity caused by dopamine
 antagonists are prevented by co-administration of a PLC agonist. These
 results provide evidence for a role of intracellular PLC signaling in
 motor skill learning and associated cortical synaptic plasticity,
 challenging the traditional view of bidirectional modulation of PKA by D1
 and D2 receptors. These findings reveal a novel and important action of
 dopamine in motor cortex that might be a future target for selective
 therapeutic interventions to support learning and recovery of movement
 resulting from injury and disease.
description: Ctrl-PLCinh, synaptic
 strength(Fig3)Synaptic strength:
 PLCinh groupCtrl-PLCinh
 SynStrength(Fig3).xlsxPKAinhibitor(Fig2)LTP: PKAinhib groupPLCag&Raclo-SynStrength(Fig5)Synaptic Strength: PLCagonist and PLCag+raclopride groupsPLCag&Raclo(Fig5)LTP: PLC agonist and PLCag+raclopride groupsPLCagonist-SynStrength(Fig5)Synaptic strength: PLC agonist groupPLCinh Ctrl(Fig2)LTP: Ctrl groupPLCinh(Fig2)LTP: PLCinhibitor grouppka plc mapk_resultsBehavior: PKA and PLC inhibitors, minipumpsPKA_PLC_single injectionsBehavior: PKA and PLC inhibitors, local injectionsPLC overtrain_dataBehavior: PLCinh. after learningresults_PLCago_SCH23390Behavior: PLCagonist+D1antagresults_raclo PLC agonistBehavior: PLCagonist+D2antagonist
DOI: 10.5061/dryad.sm12b53
title: Data from: Acetaminophen responsive miR-19b modulates SIRT1/Nrf2 signaling pathway in drug-induced hepatotoxicity

description: Previous studies suggest that activation of SIRT1 protects liver from
 acetaminophen (APAP)-induced injury, however, the detailed mechanism of
 SIRT1 modulation in this process is still incompletely. Therefore, this
 study was to investigate the pathophysiological role of SIRT1 in
 APAP-mediated hepatotoxicity. We found that SIRT1 mRNA and protein were
 markedly upregulated in human LO2 cells and mouse liver upon APAP
 exposure. In vitro, the specific knockdown of SIRT1 expression ultimately
 aggravated APAP-evoked cellular antioxidant defense in LO2 cells.
 Moreover, lentivirus mediated knockdown of hepatic SIRT1 expression
 exacerbated APAP-induced oxidative stress and liver injury, especially
 reduction of Nrf2 and subsequent downregulation of several antioxidant
 genes. Intriguingly, 30 mg/kg SRT1720, the specific SIRT1 activator, which
 greatly enhanced Nrf2 expression and antioxidant defense, and then
 eventually reversed APAP-induced hepatic liver injury in mice.
 Furthermore, APAP responsive miR-19b played an important role in
 regulating SIRT1 expression, whereas overexpression miR-19b largely
 abolished the induction of SIRT1 by APAP in vitro and in vivo. Specific
 SIRT1 3’-UTR mutation, which disrupted the interaction of miRNA-3’UTR, and
 successfully abrogated the modulation by miR-19b. Notably, hepatic miR-19b
 overexpression worsened the APAP-induced hepatotoxicity. In general, our
 results support the notion that the strong elevation of SIRT1 by APAP
 responsive miR-19b may represent a compensatory mechanism to protect liver
 against the drug-induced damage, at least in part by enhancing
 Nrf2-mediated antioxidant capacity in the liver.
description: Western
 Blotmice data includes AST,
 MDA, GSH, qReal-time PCR.AST, MDA, GSH and
 Q-PCR.xlsx
DOI: 10.5061/dryad.1s3d4
title: Data from: Dietary responses of Sahul (Pleistocene Australia–New Guinea) megafauna to climate and environmental change

description: Throughout the late Quaternary, the Sahul (Pleistocene Australia–New
 Guinea) vertebrate fauna was dominated by a diversity of large mammals,
 birds, and reptiles, commonly referred to as megafauna. Since ca.
 450–400Ka, approximately 88 species disappeared in Sahul, including
 kangaroos exceeding 200kg in size, wombat-like animals the size of
 hippopotamuses, flightless birds, and giant monitor lizards that were
 likely venomous. Ongoing debates over the primary cause of these
 extinctions have typically favored climate change or human activities.
 Improving our understanding of the population biology of extinct megafauna
 as more refined paleoenvironmental data sets become available will assist
 in identifying their potential vulnerabilities. Here, we apply a
 multiproxy approach to analyze fossil teeth from deposits dated to the
 middle and late Pleistocene at Cuddie Springs in southeastern Australia,
 assessing relative aridity via oxygen isotopes as well as vegetation and
 megafaunal diets using both carbon isotopes and dental microwear texture
 analyses. We report that the Cuddie Springs middle Pleistocene fauna was
 largely dominated by browsers, including consumers of C4 shrubs, but that
 by late Pleistocene times the C4 dietary component was markedly reduced.
 Our results suggest dietary restriction in more arid conditions. These
 dietary shifts are consistent with other independently derived isotopic
 data from eggshells and wombat teeth that also suggest a reduction in C4
 vegetation after ~45 Ka in southeastern Australia, coincident with
 increasing aridification through the middle to late Pleistocene.
 Understanding the ecology of extinct species is important in clarifying
 the primary drivers of faunal extinction in Sahul. The results presented
 here highlight the potential impacts of aridification on marsupial
 megafauna. The trend to increasingly arid conditions through the middle to
 late Pleistocene (as identified in other paleoenvironmental records and
 now also observed, in part, in the Cuddie Springs sequence) may have
 stressed the most vulnerable animals, perhaps accelerating the decline of
 late Pleistocene megafauna in Australia.
description: Supplementary Files:
 Dietary responses of Sahul (Pleistocene Australia-New Guinea) megafauna to
 climate and environmental changeSupplementary Figures
 1-6, Supplementary Tables 1-14.DeSantisetal_PBLRCSupplementaryFiles.pdf
DOI: 10.5061/dryad.6hk4h
title: Data from: Variation in responses of fishes across multiple reserves within a network of marine protected areas in temperate waters

description: Meta-analyses of field studies have shown that biomass, density, species
 richness, and size of organisms protected by no-take marine reserves
 generally increase over time. The magnitude and timing of changes in these
 response variables, however, vary greatly and depend upon the taxonomic
 groups protected, size and type of reserve, oceanographic regime, and time
 since the reserve was implemented. We conducted collaborative,
 fishery-independent surveys of fishes for seven years in and near newly
 created marine protected areas (MPAs) in central California, USA. Results
 showed that initially most MPAs contained more and larger fishes than
 associated reference sites, likely due to differences in habitat quality.
 The differences between MPAs and reference sites did not greatly change
 over the seven years of our study, indicating that reserve benefits will
 be slow to accumulate in California’s temperate eastern boundary current.
 Fishes in an older reserve that has been closed to fishing since 1973,
 however, were significantly more abundant and larger than those in
 associated reference sites. This indicates that reserve benefits are
 likely to accrue in the California Current ecosystem, but that 20 years or
 more may be needed to detect significant changes in response variables
 that are due to MPA implementation. Because of the high spatial and
 temporal variability of fish recruitment patterns, long-term monitoring is
 needed to identify positive responses of fishes to protection in the
 diverse set of habitats in a dynamic eastern boundary current. Qualitative
 estimates of response variables, such as would be obtained from an expert
 opinion process, are unlikely to provide an accurate description of MPA
 performance. Similarly, using one species or one MPA as an indicator is
 unlikely to provide sufficient resolution to accurately describe the
 performance of multiple MPAs.
description: CPUE data and complete
 model resultsThis Excel document
 contains 4 tabs: 1) "Models-7 year analyses" - mixed-model
 repeated measures analysis of BPUE and mean length estimates for each MPA.
 2) "Models-Network analyses" - mixed-model repeated measures
 analysis of BPUE and mean length estimates across all MPAs. 3)
 "CCFRP_CPUE_by_gridcell_07-13" - raw data of CPUE for each grid
 cell each year. 4) "Species codes" - A key for 3 letter codes
 used for fishes in CPUE table.CCFRP_publication_supplemental_data.xlsx
DOI: 10.5061/dryad.7fh4q
title: Data from: Rodent reservoirs of future zoonotic diseases

description: Forecasting reservoirs of zoonotic disease is a pressing public health
 priority. We apply machine learning to datasets describing the biological,
 ecological, and life history traits of rodents, which collectively carry a
 disproportionate number of zoonotic pathogens. We identify particular
 rodent species predicted to be novel zoonotic reservoirs and geographic
 regions from which new emerging pathogens are most likely to arise. We
 also describe trait profiles—complexes of biological features—that
 distinguish reservoirs from nonreservoirs. Generally, the most permissive
 rodent reservoirs display a fast-paced life history strategy, maximizing
 near-term fitness by having many altricial young that begin reproduction
 early and reproduce frequently. These findings may constitute an important
 lead in guiding the search for novel disease reservoirs in the wild.
description: Global rodents, traits,
 and zoonotic reservoir statusThese data combine
 rodent species and life history traits from the PanTHERIA database
 (defined in associated metadata), in addition to a number of derived
 variables (defined in the published PNAS paper).pan for PNAS
 Dryad.csv
DOI: 10.5061/dryad.md7ph
title: Data from: The legacy of large regime shifts in shallow lakes

description: Ecological shifts in shallow lakes from clear-water macrophyte-dominated
 to turbid-water phytoplankton-dominated are generally thought of as rapid
 short-term transitions. Diatom remains in sediment records from shallow
 lakes in the Prairie Pothole Region of North America provide new evidence
 that the long-term ecological stability of these lakes is defined by the
 legacy of large regime shifts. Here we examine the modern and historical
 stability of eleven shallow lakes. Currently, four of the lakes are in a
 clear-water state, three are consistently turbid-water, and four have been
 observed to change state from year to year (transitional). Lake sediment
 records spanning the past 150-200 years suggest that: 1) the diatom
 assemblage is characteristic of either clear or turbid lakes; 2) prior to
 significant landscape alteration, all of the lakes existed in a regime of
 a stable clear-water state; 3) lakes that are currently classified as
 turbid or transitional have experienced one strong regime shift over the
 past 150-200 years, and have since remained in a regime where turbid-water
 predominates; and 4) top-down impacts to the lake food web from fish
 introductions appear to be the dominant driver of strong regime shifts,
 and not increased nutrient availability. Based on our findings we
 demonstrate a method that could be used by lake managers to identify lakes
 that have an ecological history close to the clear-turbid regime
 threshold; such lakes might more easily be returned to a clear-water state
 through biomanipulation. The unfortunate reality is that many of these
 lakes are now part of a managed landscape and will likely require
 continued intervention.
description: Ramstack
 Hobbs_Ecological Applications_2016This file contains
 diatom species data from eleven shallow lake sediment cores from the
 Prairie Pothole Region of Minnesota, USA. The file also contains diatom
 species and environmental data for a 145-lake calibration set from the
 state of Minnesota. The first sheet of this spreadsheet gives a full
 description of the data.
DOI: 10.5061/dryad.3062c
title: Data from: Fe-S cluster biosynthesis controls uptake of aminoglycosides in a ROS-less death pathway

description: All bactericidal antibiotics were recently proposed to kill by inducing
 reactive oxygen species (ROS) production, causing destabilization of
 iron-sulfur (Fe-S) clusters and generating Fenton chemistry. We find that
 the ROS response is dispensable upon treatment with bactericidal
 antibiotics. Furthermore, we demonstrate that Fe-S clusters are required
 for killing only by aminoglycosides. In contrast to cells, using the major
 Fe-S cluster biosynthesis machinery, ISC, cells using the alternative
 machinery, SUF, cannot efficiently mature respiratory complexes I and II,
 resulting in impendence of the proton motive force (PMF), which is
 required for bactericidal aminoglycoside uptake. Similarly, during iron
 limitation, cells become intrinsically resistant to aminoglycosides by
 switching from ISC to SUF and down-regulating both respiratory complexes.
 We conclude that Fe-S proteins promote aminoglycoside killing by enabling
 their uptake.
description: Fig1Fig2ABFig2CFig2DFig2EFig2FFig3AFig3BFig4BFig3C
 Fig4AFig4CFig4Dfig4E
 IscSFig4E
 NuoFfig4E
 sufC
DOI: 10.5061/dryad.8710
title: Data from: Relative risks of inbreeding and outbreeding depression in the wild in endangered salmon

description: Conservation biologists routinely face the dilemma of keeping small,
 fragmented populations isolated, wherein inbreeding depression may ensue,
 or mixing such populations, which may exacerbate population declines via
 outbreeding depression. The joint evaluation of inbreeding and outbreeding
 risks in the wild cannot be readily conducted in endangered species, so a
 suggested 'safe' strategy is to mix ecologically and genetically
 similar populations. To evaluate this strategy, we carried out a
 reciprocal transplant experiment involving three neighbouring populations
 of endangered Atlantic salmon (Salmo salar) now bred in captivity and
 maintained in captive and wild environments. Pure, inbred, and outbred
 (first and second generation) cross types were released and recaptured in
 the wild to simultaneously test for local adaptation, inbreeding
 depression and outbreeding depression. We found little evidence of
 inbreeding depression after one generation of inbreeding and little
 evidence of either heterosis or outbreeding depression via genetic
 incompatibilities after one or two generations of outbreeding. A trend for
 outbreeding depression via the loss of local adaptation was documented in
 one of three populations. The effects of inbreeding were not significantly
 different from the effects of outbreeding. Hence, at the geographic scale
 evaluated (34-50 km), inbreeding for one generation and outbreeding over
 two generations may have similar effects on the persistence of small
 populations. The results further suggested that outbreeding outcomes may
 be highly variable or unpredictable at small genetic distances. Our work
 highlights the necessity of evaluating the relative costs of inbreeding
 and outbreeding in the conservation and management of endangered species
 on a case-by-case basis.
description: data_Houde_EA_2011length, weight, family assignment