cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0722b
title: Data from: Definition and estimation of vital rates from repeated censuses: choices, comparisons and bias corrections focusing on trees

description: 1.Mortality and recruitment rates are fundamental measures of population
 dynamics. Ecologists and others have defined and estimated these vital
 rates in various ways. We review these alternatives focusing on tree
 population census data in fixed area plots, though many aspects have wider
 application when similar data characteristics and assumptions apply: our
 goal is to guide choices and facilitate comparisons. 2.We divide our
 estimates into ‘instantaneous’ and ‘annual’ rates, corresponding to
 continuous- or discrete-time dynamics respectively. In each case, vital
 rate estimates can be further divided into those based on population
 density (‘per-capita’ rates) and those based on census area (‘per-area’
 rates). We also examine how all such rate estimates relate to each other
 and can thus be interconverted and compared. 3.In a heterogeneous
 population (e.g., trees in forest stand) comprising subpopulations (e.g.,
 species, locations, exposure classes), estimates of vital rates that
 assume homogeneity (equal likelihood of mortality and equal likelihood of
 recruitment for all individuals) are biased towards lower vital rates in
 stable mixed populations (due to survivorship bias) and towards lower
 absolute values of population change rate (due to changing-frequency
 bias). 4.We describe and illustrate an individual-based Bayesian procedure
 for estimating vital rates that reduces biases by accounting for
 demographic heterogeneity and sampling errors among and within
 subpopulations.
description: Supporting Information
 S1R
 tutorial for the Bayesian estimation of vital ratesS1.pdfYakushima30Sample data file for S1: stem census data in Yakushima Island (four sites) in 1983 and 2013.
DOI: 10.5061/dryad.cd65p
title: Data from: Phenotypic integration in response to incubation environment adaptively influences habitat choice in a tropical lizard

description: Phenotypic integration, in which a suite of traits change in a correlated
 or covarying response to shifts in environmental conditions, may enhance
 an organism’s fitness. In skinks, rocky environments select for longer
 limbs and rapid running and climbing. We examined whether differences in
 nest temperature coincident with specific habitats caused phenotypically
 integrated effects on morphology, locomotor performance, and behavior in
 the skink Carlia longipes. Specifically, we determined whether
 microhabitat choices were integrated with adaptive morphology for each
 habitat. Using a split-clutch design, we incubated eggs at thermal regimes
 that mimicked the thermal environments of nests from two habitat types
 (forest = warm; rocky = cool). Hatchlings from cool incubation
 environments had longer limbs and greater running and climbing speeds,
 which are likely to be beneficial for rocky habitats. In addition,
 individuals from cool incubation environments selected rocky microhabitats
 more frequently than did hatchlings from warm incubation environments. We
 demonstrate phenotypic integration in response to nest temperature that
 affected morphology, performance, and ultimately habitat selection in a
 way that should increase hatchling fitness.
description: Hatchling morphology and
 performanceThese data are the
 direct morphological measures and locomotor performance (sprinting and
 climbing) of hatchling Carlia longipes from two egg clutches randomly
 allocated to either the forest-high or rocky outcrop-low temperature
 incubation treatment.Nest Temperature Logger
 DataThese are the nest
 temperatures of eleven nest of Carlia longipes from a site near Cooktown,
 QLD, Australia. The nests were located in rock outcrop (n = 5) and forest
 habitat (n = 6) sites.Microhabitat enclosure
 trials-Hatchling Carlia longipesThese data are based on
 video footage of the duration that hatchling Carlia longipes lizards used
 various microhabitat types available within an enclosure. The hatchlings
 where from the two nest temperature environments.
DOI: 10.5061/dryad.56s5d84
title: Data from: A widespread thermodynamic effect, but maintenance of biological rates through space across life’s major domains

description: For over a century, the hypothesis of temperature compensation, the
 maintenance of similar biological rates in species from different thermal
 environments, has remained controversial. An alternative idea, that
 fitness is greater at higher temperatures (the thermodynamic effect), has
 gained increasing traction. This alternative hypothesis is also being used
 to understand large-scale biodiversity responses to environmental change.
 Yet evidence in favour of each of these contrasting hypotheses continues
 to emerge. In consequence, the fundamental nature of organismal thermal
 responses and its implications remain unresolved. Here we investigate
 these ideas explicitly using a global dataset of 619 observations of four
 categories of organismal performance, spanning 14 phyla and 403 species.
 In agreement with both hypotheses, we show a positive relationship between
 the temperature of maximal performance rate (Topt) and environmental
 temperature (Tenv) for all traits. Next we demonstrate that relationships
 between Tenv and the maximal performance rate (Umax) are rarely
 significant and positive, as expected if a thermodynamic effect
 predominates. By contrast, a positive relationship between Topt and Umax
 is always present, but markedly weaker than theoretically predicted. These
 outcomes demonstrate that while some form of thermodynamic effect exists,
 ample scope is present for biochemical and physiological adaptation to
 thermal environments in the form of temperature compensation.
description: Database for
 publicationDatabase used for
 analysesLegend and references
 for databaseLegend and references
 for database
DOI: 10.5061/dryad.97p31jr
title: Data from: Deconstruction of an African folk medicine uncovers a novel molecular strategy for therapeutic potassium channel activation

description: A third of the global population relies heavily upon traditional or folk
 medicines, such as the African shrub Mallotus oppositifolius. Here, we
 used pharmacological screening and electrophysiological analysis in
 combination with in silico docking and site-directed mutagenesis to
 elucidate the effects of M. oppositifolius constituents on KCNQ1, a
 ubiquitous and influential cardiac and epithelial voltage-gated potassium
 (Kv) channel. Two components of the M. oppositifolius leaf extract,
 mallotoxin (MTX) and 3-ethyl-2-hydroxy-2-cyclopenten-1-one (CPT1),
 augmented KCNQ1 current by negative shifting its voltage dependence of
 activation. MTX was also highly effective at augmenting currents generated
 by KCNQ1 in complexes with native partners KCNE1 or SMIT1; conversely, MTX
 inhibited KCNQ1-KCNE3 channels. MTX and CPT1 activated KCNQ1 by hydrogen
 bonding to the foot of the voltage sensor, a previously unidentified drug
 site which we also find to be essential for MTX activation of the related
 KCNQ2/3 channel. The findings elucidate the molecular mechanistic basis
 for modulation by a widely used folk medicine of an important human Kv
 channel and uncover novel molecular approaches for therapeutic modulation
 of potassium channel activity.
description: De Silva-Manville et al
 2018 Supplementary TablesSupplementary tables
 describing functional effects of M. oppositifolius leaf extract components
 on KCNQ1 channels, alone and with regulatory proteins. Effects of the leaf
 extract components on mutant KCNQ1 and KCNQ2/3 channels are also
 described.De Silva-Manville et al
 Repository Data 9_11_18.pdf
DOI: 10.5061/dryad.4h31p
title: Data from: Body size and allometric shape variation in the molly Poecilia vivipara along a gradient of salinity and predation

description: Background: Phenotypic diversity among populations may result from
 divergent natural selection acting directly on traits or via correlated
 responses to changes in other traits. One of the most frequent patterns of
 correlated response is the proportional change in the dimensions of
 anatomical traits associated with changes in growth or absolute size,
 known as allometry. Livebearing fishes subject to predation gradients have
 been shown to repeatedly evolve larger caudal peduncles and smaller
 cranial regions under high predation regimes. Poecilia vivipara is a
 livebearing fish commonly found in coastal lagoons in the north of the
 state of Rio de Janeiro, Brazil. Similar to what is observed in other
 predation gradients, lagoons inhabited by P. vivipara vary in the presence
 of piscivorous fishes; contrary to other poeciliid systems, populations of
 P. vivipara vary greatly in body size, which opens the possibility of
 strong allometric effects on shape variation. Here we investigated body
 shape diversification among six populations of P. vivipara along a
 predation gradient and its relationship with allometric trajectories
 within and among populations.ResultsWe found substantial body size
 variation and correlated shape changes among populations. Multivariate
 regression analysis showed that size variation among populations accounted
 for 66% of shape variation in females and 38% in males, suggesting that
 size is the most important dimension underlying shape variation among
 populations of P. vivipara in this system. Changes in the relative sizes
 of the caudal peduncle and cranial regions were only partly in line with
 predictions from divergent natural selection associated with predation
 regime.ConclusionsOur results suggest the possibility that adaptive shape
 variation among populations has been partly constrained by allometry in P.
 vivipara. Processes governing body size changes are therefore important in
 the diversification of this species. We conclude that in species
 characterized by substantial among-population differences in body size,
 ignoring allometric effects when investigating divergent natural
 selection?s role in phenotypic diversification might not be warranted.
description: Morphometric data of
 Poecilia viviparaThe dataset has the
 Procrustes coordinates on ten anatomical landmarks
 (ProcCoord1-ProcCoord20), as well as centroid size (CS) and its logarithm
 (logCS). Specimens have a unique identification code (Id) and are
 classified according to sex and population of origin.Dataset.csv
DOI: 10.5061/dryad.71dq2
title: Data from: Trait integration and macroevolutionary patterns in the pollination biology of conifers

description: Integration influences patterns of trait evolution, but the relationship
 between these patterns and the degree of trait integration is not well
 understood. In order to explore this further, we study a specialized
 pollination mechanism in conifers whose traits are linked through function
 but not development. This mechanism depends on interactions among three
 characters: pollen that is buoyant, ovules that face downward at
 pollination, and the production of a liquid droplet that buoyant grains
 float through to enter the ovule. We use a well-sampled phylogeny of
 conifers to test correlated evolution among these characters and specific
 sequences of character change. Using likelihood models of character
 evolution, we find that pollen morphology and ovule characters evolve in a
 concerted manner, where the flotation mechanism breaks down irreversibly
 following changes in orientation or drop production. The breakdown of this
 functional constraint, which may be facilitated by the lack of
 developmental integration among the constituent traits, is associated with
 increased trait variation and more diverse pollination strategies.
 Although this functional “release” increases diversity in some ways, the
 irreversible way in which the flotation mechanism is lost may eventually
 result in its complete disappearance from seed plant reproductive biology.
description: Character Data for
 Leslie et al.This file contains
 character scorings in a more readily usable txt format. For information on
 data sources, please see the Data Table and Sources file also included
 here.Leslie
 et al_Character Data.txtData Table and
 SourcesInformation in this
 table can also be found in the online Supporting Materials associated with
 the paper. It lists the data and data sources for all analyzed species, as
 well as which conifer species were not included due to missing
 data.
DOI: 10.5061/dryad.3g14b02
title: Data from: Fire, fragmentation, and windstorms: a recipe for tropical forest degradation

description: 1. Widespread degradation of tropical forests is caused by a variety of
 disturbances that interact in ways that are not well understood. 2. To
 explore potential synergies between edge effects, fire and windstorm
 damage as causes of Amazonian forest degradation, we quantified vegetation
 responses to a 30-minute high-intensity windstorm that in 2012, swept
 through a large-scale fire experiment that borders an agricultural field.
 Our pre- and post-windstorm measurements include tree mortality rates and
 modes of death, aboveground biomass, and airborne LiDAR-based estimates of
 tree heights and canopy disturbance (number and size of gaps). The
 experimental area in the southeastern Amazonia includes three 50-ha plots
 established in 2004 that were unburned (Control), burned annually (B1yr),
 or burned at three-year intervals (B3yr). 3. The windstorm caused greater
 damage to trees (&gt;10 cm DBH) in the burned plots (B1yr: 13±9% of
 785 trees; B3yr: 17±13% of 433) than in the Control plot (8±4% of 2300;
 ±CI). It substantially reduced vegetation height by 14% in B1yr, 20% in
 B3yr and 12% in the Control plots, while it reduced aboveground biomass by
 18% of 77.7 Mg ha-1 (B1yr), 31% of 56.6 (B3yr) and 15% of 120 (Control).
 Tree damage was greatest near the agricultural field edge in all three
 plots, especially among large trees and in B3yr. Trunk snapping (70%) and
 uprooting (20%) were the most common modes of tree damage and mortality,
 with the height of trunk failure on the burned plots often corresponding
 with the height of historical fire scars. Of the windstorm-damaged trees,
 80% (B1yr), 90% (B3yr), and 57% (Control) were dead four years later.
 Trees that had crown damage experienced the least mortality (22–60%),
 followed by those that were snapped (55–94%) and uprooted (88–94%). 4.
 Synthesis. We demonstrate the synergistic effects of three kinds of
 disturbance on a tropical forest. Our results show that the effects of
 windstorms are exacerbated by prior degradation by fire and fragmentation.
 We highlight that understory fires can produce long-lasting effects on
 tropical forests not only by directly killing trees but also by increasing
 tree vulnerability to wind damage due to fire-scars and a more-open
 canopy.
description: Silverio_et_al_2018_joecol_master_windstormPost-windstorm inventory of tree damage conducted on the Tanguro Farm, in Mato Grosso, Brazil. The columns names are as follows: "genera" = the scientific name of genus; "transect" = each of transects; "xx" = long utm; "yy" = lat utm; "x" = x distance from the plot corner; "y" = x distance from the plot corner (edge distance); "plot" = fire treatment plots; "DBH" = diameter at breast height (1.3 m); "wood_density" = wood density value; "fire_scar" = post-burn scars present (P) or absent (A); "neighbors" = number of neighbors (20 m); "snapped, uprooted, and crown-damage" = 1 indicate damage.
DOI: 10.15468/dl.hhh3zm
title: Occurrence Download

description: A dataset containing 3294 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-86.791 34.448,-75.904 34.448,-75.904 38.67,-86.791 38.67,-86.791 34.448))",
 "OccurrenceStatus is Present",
 "TaxonKey is Lucanidae"
 ]
}

 The dataset includes 3294 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000661-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.4p800
title: Data from: Experimental hybridization in allopatric species of the Drosophila repleta group (Diptera, Drosophilidae): implications in the mode of speciation

description: The Pleistocene refugia theory proposes that recurrent expansions and
 contractions of xerophytic vegetation over climate change periods affected
 the evolution of cactophilic Drosophila in South American continent. The
 resulting demographic fluctuations linked to the available patches of
 vegetation should have been prone to bottlenecks and founder events,
 affecting the fate of gene pool dynamics. However, these events also
 promoted the diversification of cacti, creating an ecological opportunity
 for host specialization. We tested the hypothesis of ecological speciation
 in the D. buzzatii group. We assessed adaptive footprints and examined the
 genetic architecture of fitness related traits in the sibling allopatric
 species D. koepferae and D. antonietae. Overall our results are in line
 with the idea that these species evolved under different ecological
 scenarios. Joint-scaling analysis comparing both species and their hybrids
 revealed that additive genetic variance was the major contributor to
 phenotypic divergence, but dominance, epistasis and maternal effects were
 also important factors. Correlation analysis among functionally-related
 traits suggested divergent selection on phenotypic integration associated
 with fitness. These findings support the hypothesis of adaptive evolution
 driving the phylogenetic radiation of the group through independent events
 of host shifts to chemically complex columnar cacti.
description: Data
 fileSample sites - life
 history traits - wing morphologyData.xls
DOI: 10.5061/dryad.4mb11
title: Data from: Drosophila increase exploration after visually detecting predators

description: Novel stimuli elicit behaviors that are collectively known as specific
 exploration. These behaviors allow the animal to become more familiar with
 the novel objects within its environment. Specific exploration is
 frequently suppressed by defensive reactions to predator cues. Herein, we
 examine if this suppression occurs in Drosophila melanogaster by measuring
 the response of these flies to wild harvested predators. The flies used in
 our experiments have been cultured and had not lived under predator threat
 for multiple decades. In a circular arena with centrally-caged predators,
 wild type Drosophila actively avoided the pantropical jumping spider,
 Plexippus paykulli, and the Texas unicorn mantis, Phyllovates
 chlorophaena, indicating an innate defensive reaction to these predators.
 Interestingly, wild type Drosophila males also avoided a centrally-caged
 mock spider, and the avoidance of the mock spider became exaggerated when
 it was made to move within the cage. Visually impaired Drosophila failed
 to detect and avoid the Plexippus paykulli and the moving mock spider,
 while the broadly anosmic orco2 mutants were fully capable of detecting
 and avoiding Plexippus paykulli, indicating that these flies principally
 relied upon vison to perceive the predator stimuli. During early
 exploration of the arena, exploratory activity increased in the presence
 of Plexippus paykulli and the moving mock spider. The elevated activity
 induced by Plexippus paykulli disappeared after the fly had finished
 exploring, suggesting the flies were capable of habituating the predator
 cues. Taken together, these results indicate that despite being isolated
 from predators for decades Drosophila will visually detect these
 predators, retain innate defensive behaviors, respond by increasing
 exploratory activity in the arena rather than suppressing activity, and
 may habituate to normal predator cues.
description: Spider
 DataThis file contains
 several worksheets, each representing a separate experiment. Each
 worksheet contains the minimal data set for each data panel in the
 paper.
DOI: 10.5061/dryad.rr0v479
title: Data from: How to quantify animal activity from radio-frequency identification (RFID) recordings

description: Automated animal monitoring via radio-frequency identification (RFID)
 technology allows efficient and extensive data sampling of individual
 activity levels, and is therefore commonly used for ecological research.
 However, processing RFID data is still a largely unresolved problem, which
 potentially leads to inaccurate estimates for behavioural activity. One of
 the major challenges during data processing is to isolate independent
 behavioural actions from a set of superfluous, non-independent detections.
 As a case study, individual blue tits (Cyanistes caeruleus) were
 simultaneously monitored during reproduction with both video recordings
 and RFID technology. We demonstrated how RFID data can be processed based
 on the time spent in- and outside a nest box. We then validated the number
 and timing of nest visits obtained from the processed RFID dataset by
 calibration against video recordings. The video observations revealed a
 limited overlap between the time spent in- and outside the nest box, with
 the least overlap at 23 seconds for both sexes. We then isolated exact
 arrival times from redundant RFID registrations by erasing all successive
 registrations within 23 seconds after the preceding registration. After
 aligning the processed RFID data with the corresponding video recordings,
 we observed a high accuracy in three behavioural estimates of parental
 care (individual nest visit rates, within-pair alternation and
 synchronization of nest visits). We provide a clear guideline for future
 studies that aim to implement RFID technology in their research. We argue
 that our suggested RFID data processing procedure improves the precision
 of behavioural estimates, despite some inevitable drawbacks inherent to
 the technology. Our method is useful, not only for other cavity breeding
 birds, but for a wide range of (in)vertebrate species that are large
 enough to be fitted with a tag and that regularly pass near or through a
 fixed antenna.
description: Iserbyt et al. 2018
 Ecol&EvolThis file includes two
 datasets. The first one (Inside_outside) supports the density plots in
 Figure 2. The second one (Validation) supports the validation in Figure 3
 and Table 1.
DOI: 10.15468/dl.xwgcu9
title: Occurrence Download

description: A dataset containing 358 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Germany",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Nyctalus noctula",
 "Year 2024-2026"
 ]
}

 The dataset includes 358 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000662-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.