cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.92n53
title: Data from: Enhancement of apoptosis by titanium alloy internal fixations during microwave treatments for fractures: an animal study

description: Objective: Microwaves are used in one method of physical therapy and can
 increase muscle tissue temperature which is useful for improving muscle,
 tendon and bone injuries. In the study, we sought to determine whether
 titanium alloy internal fixations influence apoptosis in tissues subjected
 to microwave treatments at 2,450 MHz and 40 W during the healing of
 fractures because this issue is not yet fully understood. Methods: In this
 study, titanium alloy internal fixations were used to treat 3.0-mm
 transverse osteotomies in the middle of New Zealand rabbits’ femurs. After
 the operation, 30-day microwave treatments were applied to the 3.0 mm
 transverse osteotomies 3 days after the operation. The changes in the
 temperatures of the muscle tissues in front of the implants or the 3.0 mm
 transverse osteotomies were measured during the microwave treatments. To
 characterize the effects of titanium alloy internal fixations on apoptosis
 in the muscles after microwave treatment, we performed TUNEL assays,
 fluorescent real-time (quantitative) PCR, western blotting analyses,
 reactive oxygen species (ROS) detection and transmission electron
 microscopy examinations. Results: The temperatures were markedly increased
 in the animals with the titanium alloy implants. Apoptosis in the muscle
 cells of the implanted group was significantly more extensive than that in
 the non-implanted control group at different time points. Transmission
 electron microscopy examinations of the skeletal muscles of the implanted
 groups revealed muscular mitochondrial swelling, vacuolization. ROS, Bax
 and Hsp70 were up-regulated, and Bcl-2 was down-regulated in the implanted
 group. Conclusion: Our results suggest that titanium alloy internal
 fixations caused greater muscular tissue cell apoptosis following 2,450
 MHz, 40 W microwave treatments in this rabbit femur fracture models.
description: data
DOI: 10.5061/dryad.15f51
title: Data from: Exploring the impact of habitat size on phylogeographic patterning in the Overberg velvet worm Peripatopsis overbergiensis (Onychophora: Peripatopsidae)

description: Evolutionary relationships in the velvet worm species, Peripatopsis
 overbergiensis, were examined in 3 forest areas in the Overberg region of
 South Africa to explore the impact of historical habitat fragmentation on
 the population genetic structure of the species. We collected 84 P.
 overbergiensis specimens from Grootvadersbosch, Koppie Alleen, and Marloth
 Nature Reserves and sequenced all these specimens for the cytochrome c
 oxidase subunit I (COI) locus, whereas a subset of 13 specimens were also
 sequenced for the 18S rRNA locus. Phylogenetic analyses of the 20 unique
 COI haplotypes revealed 4 genetically distinct clades, a result that is
 corroborated by the haplotype network. A hierarchical analysis of genetic
 variation was performed on the COI haplotype data within the 2 large
 forested areas, Grootvadersbosch and Marloth Nature Reserves, and across
 all 3 of the sample localities. These results revealed low haplotypic and
 nucleotide diversity within the largest Grootvadersbosch Nature Reserve
 forest and high haplotypic and nucleotide diversity within the fragmented
 Marloth Nature Reserve forest, whereas Koppie Alleen had the lowest
 haplotypic and nucleotide diversity. Across all 3 main localities
 statistically significant F ST values were found, together with the
 absence of shared haplotypes indicating the absence of maternal gene flow.
 Divergence time estimations based on the 20 COI haplotypes calculated in
 BEAST suggest a Pleistocene/Holocene divergence between the 4 clades as a
 result of habitat fragmentation and the aridification of the region. Our
 results indicate that conservation efforts should also prioritize linked,
 smaller fragmented habitats together with continuous habitats to maximize
 the genetic diversity of saproxylic fauna.
description: COIhaplotypesCOI Haplotypes among the Peripatopsis overbergiensis18S partial sequence18S haplotypes18SHap
DOI: 10.5061/dryad.p59n8
title: Data from: When environmental factors become stressors: interactive effects of vermetid gastropods and sedimentation on corals

description: Environmental stressors often interact, but most studies of multiple
 stressors have focused on combinations of abiotic stressors. Here we
 examined the potential interaction between a biotic stressor, the vermetid
 snail Ceraesignum maximum, and an abiotic stressor, high sedimentation, on
 the growth of reef-building corals. In a field experiment, we subjected
 juvenile massive Porites corals to four treatments: (i) neither stressor,
 (ii) sedimentation, (iii) vermetids or (iv) both stressors. Unexpectedly,
 we found no effect of either stressor in isolation, but a significant
 decrease in coral growth in the presence of both stressors. Additionally,
 seven times more sediment remained on corals in the presence (versus
 absence) of vermetids, likely owing to adhesion of sediments to corals via
 vermetid mucus. Thus, vermetid snails and high sedimentation can interact
 to drive deleterious effects on reef-building corals. More generally, our
 study illustrates that environmental factors can combine to have negative
 interactive effects even when individual effects are not detectable. Such
 ‘ecological surprises' may be easily overlooked, leading to
 environmental degradation that cannot be anticipated through the study of
 isolated factors.
description: VermetidSedimentData_ZillGilOsenbergThis data corresponds to a manipulative field experiment conducted in 2012 by Julie Zill, Michael Gil, and Craig Osenberg in Moorea, French Polynesia. Experimental corals were used for two separate data sets: (1) the combined and separate effects of vermetid gastropod presence and sedimentation on coral growth, and (2) the sediment removal rate data obtained via timelapse video over 6 hour periods, using ImageJ to determine the fractions of sediment removed.
DOI: 10.5061/dryad.4d15b08
title: Data from: Temperature effects on prey and basal resources exceed that of predators in an experimental community

description: Climate warming alters the structure of ecological communities by
 modifying species interactions at different trophic levels. Yet, the
 consequences of warming-led modifications in biotic interactions at higher
 trophic levels on lower trophic groups are lesser known. Here, we test the
 effects of multiple predator species on prey population size and traits,
 and subsequent effects on basal resources along an experimental
 temperature gradient (12-15C, 17-20C, and 22-25C). We experimentally
 assembled food web modules with two congeneric predatory mites (Hypoaspis
 miles and Hypoaspis aculeifer), and two Collembola prey species (Folsomia
 candida and Proisotoma minuta) on a litter and yeast mixture as the basal
 resources. We hypothesized that warming would modify interactions within
 and between predator species, and that these alterations would cascade to
 basal resources via changes in the density and traits (body size and
 lipid: protein ratio) of the prey species. The presence of congeners
 constrained the growth of the predatory species independent of warming
 despite warming increased predator density in their respective
 monocultures. We found that warming effects on both prey and basal
 resources were greater than the effects of predator communities. Our
 results further showed opposite effects of warming on predator (increase)
 and prey densities (decrease), indicating a warming-induced trophic
 mismatch, which are likely to alter food web structures. We highlight that
 warmer environments can restructure food webs by its direct effects on
 lower trophic groups rather than via modifying top-down effects.
description: Thakur et al.
 Ecol&Evol_Data
DOI: 10.5061/dryad.q3c3t
title: Data from: Repeatability of circadian behavioural variation revealed in free-ranging marine fish

description: Repeatable between-individual differences in the behavioural manifestation
 of underlying circadian rhythms determine chronotypes in humans and
 terrestrial animals. Here, we have repeatedly measured three circadian
 behaviours, awakening time, rest onset and rest duration, in the
 free-ranging pearly razorfish, Xyrithchys novacula, facilitated by
 acoustic tracking technology and hidden Markov models. In addition, daily
 travelled distance, a standard measure of daily activity as fish
 personality trait, was repeatedly assessed using a State-Space Model. We
 have decomposed the variance of these four behavioural traits using linear
 mixed models and estimated repeatability scores (R) while controlling for
 environmental co-variates: year of experimentation, spatial location of
 the activity, fish size and gender and their interactions. Between- and
 within-individual variance decomposition revealed significant Rs in all
 traits suggesting high predictability of individual circadian behavioural
 variation and the existence of chronotypes. The decomposition of the
 correlations among chronotypes and the personality trait studied here into
 between- and within-individual correlations did not reveal any significant
 correlation at between-individual level. We therefore propose circadian
 behavioural variation as an independent axis of the fish personality, and
 the study of chronotypes and their consequences as a novel dimension in
 understanding within-species fish behavioural diversity.
description: Full data-set used in
 the analysisId is the identification
 code of the fish, day is date (dd/mm/yyyy) of tracking, the year of
 tagging experiment , sex is the gender of the individuals, the fish size
 is in total length nearest the mm of the individual, grain size and depth
 are the characteristics of the habitat, latitude and longitude are the
 locations of the centre of the home range (centre of activity) of each
 individual in m and refereed to the central point of the study area, rest
 duration (hours) is the time difference between the rest onset of the
 previous day and the awakening time of the current day (n= 148), wakening
 time is the time relative to sunrise (min) when fish started their daily
 active behaviour (n= 159), rest onset is the time related to sunset (min)
 when fish fished their daily active behaviour, and iii) (n= 159) and
 activity is the daily distance travelled in m (n= 159).DataBase_Alos etal 2017
 RSOS.csv
DOI: 10.5061/dryad.85709
title: Data from: Conservation implications of ameliorating survival of little brown bats with White-Nose Syndrome

description: Management of wildlife populations impacted by novel threats is often
 challenged by a lack of data on temporal changes in demographic response.
 Populations may suffer rapid declines from the introduction of new
 stressors, but how demography changes over time is critical to determining
 long-term outcomes for populations. White-nose syndrome (WNS), an
 infectious disease of hibernating bats, has caused massive and rapid
 population declines in several hibernating species of bats in North
 America since the disease was first observed on the continent in 2006.
 Estimating annual survival rates and demographic trends among remnant
 colonies of hibernating bats that experienced mass mortality from WNS is
 needed to determine long-term population viability of species impacted by
 this disease. Using mark–recapture data on infected little brown bats
 (Myotis lucifugus), we estimated the first apparent annual survival rates
 for four years following WNS detection at a site. We found strong support
 for an increasing trend in annual survival, which improved from 0.68 (95%
 CI = 0.44–0.85) to 0.75 (95% CI = 0.51–0.89) for males and 0.65 (95% CI =
 0.44–0.81) to 0.70 (95% CI = 0.50–0.84) for females. These results suggest
 that stabilization at remnant colonies after mass mortality from WNS may
 be due to improved survival and not from immigration from other areas.
 Despite ameliorating survival, our stochastic matrix projection model
 predicts continued declines for little brown bat populations (λ = 0.95),
 raising concern for the regional persistence of this species. We conducted
 a vital rate sensitivity analysis and determined that adult and juvenile
 survival, as opposed to fecundity, are the demographic parameters most
 important to target to maximize recovery potential of little brown bat
 populations in areas impacted by WNS.
description: MyLuSurvival-datadryadencounter histories for marked individuals in the survival study
DOI: 10.15468/dl.fwkxre
title: Occurrence Download

description: A dataset containing 505 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Macleania insignis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 505 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001353-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2010
title: Data from: Paternity covaries with laying and hatching order in the collared flycatcher Ficedula albicollis

description: Females in most bird species engage in extra-pair copulations. Although
 this behaviour is widespread, benefits for females of doing so are less
 understood. The most widely accepted hypothesis is that they improve their
 previous choice of social partner and gain genetic benefits for their
 offspring. Some evidence for this comes from studies that find that
 extra-pair young (EPY) have greater fitness than their half-sibs. However,
 this might be also caused by maternal, non-genetic effect, a possibility
 that remains largely untested. Here we test whether EPY are laid in larger
 eggs or eggs laid early in the laying sequence in the collared flycatcher
 (Ficedula albicollis). The size of eggs bearing EPY and within-pair young
 (WPY) did not differ, however, EPY were laid in early eggs and
 consequently hatched earlier than WPY. As hatching asynchrony is a strong
 determinant of offspring size and survival in many species, including
 collared flycatcher, our results suggest that a caution is needed when
 paternal genetic effects are to be inferred from comparison of naturally
 occurring half-sibs.
description: chicksmales
DOI: 10.5061/dryad.4t85s
title: Data from: Additive negative effects of anthropogenic sedimentation and warming on the survival of coral recruits

description: Corals worldwide are facing population declines due to global climate
 change and local anthropogenic impacts. Global climate change effects are
 hard to tackle but recent studies show that some coral species can better
 handle climate change stress when provided with additional energy
 resources. The local stressor that most undermines energy acquisition is
 sedimentation because it impedes coral heterotrophic feeding and their
 ability to photosynthesize. To investigate if reducing local sedimentation
 will enable corals to better endure ocean warming, we quantitatively
 assessed the combined effects of increased temperature and sedimentation
 (concentration and turbidity) on the survival of coral recruits of the
 species, Porites astreoides. We used sediment from a reef and a boat basin
 to mimic natural sediment (coarse) and anthropogenic (fine) sediment
 (common in dredging), respectively. Natural sediment did not negatively
 impact coral survival, but anthropogenic sediment did. We found that the
 capacity of coral recruits to survive under warmer temperatures is less
 compromised when anthropogenic sedimentation is maintained at the lowest
 level (30 mg.cm−2). Our study suggests that a reduction of US-EPA
 allowable turbidity from 29 Nephelometric Turbidity Units (NTU) above
 background to less than 7 NTU near coral reefs would facilitate coral
 recruit survival under current and higher temperatures.
description: Survival of coral
 recruits at all combinations of temperature (26 and 30°C) and deposited
 sediment concentration (30, 60, 90 and 120 mg/cm2) using natural
 sedimentData set arranged for
 survival analysis: Temperature (Celsius), Sediment (deposited natural
 sediment mg/cm2), Time (Weeks), Status (1- dead, 0 -
 alive).Natural.csvSurvival of coral recruits at all combinations of temperature (26 and 30°C) and deposited sediment concentration (30, 60, 90 and 120 mg/cm2) using anthropogenic sedimentData set arranged for survival analysis: Temperature (Celsius), Sediment (deposited natural sediment mg/cm2), Time (Weeks), Status (1- dead, 0 - alive).Anthropogenic.csv
DOI: 10.5061/dryad.18qv7ks
title: Data from: Oxygen limitation is not the cause of death during lethal heat exposure in an insect

description: Oxygen- and capacity-limited thermal tolerance (OCLTT) is a controversial
 hypothesis claiming to explain variation in, and mechanistically
 determine, animal thermal limits. The lack of support from Insecta is
 typically argued to be a consequence of their high-performance respiratory
 systems. However, no studies have reported internal body oxygen levels
 during thermal ramping so it is unclear if changes in ambient gas are
 partially or fully offset by a compensatory respiratory system. Here we
 provide such an assessment by simultaneously recording haemolymph oxygen
 (pO2) levels – as an approximation of tissue oxygenation - while
 experimentally manipulating ambient oxygen and subjecting organisms to
 thermal extremes in a series of thermolimit respirometry experiments using
 pupae of the butterfly Pieris napi. The main results are that while P.
 napi undergo large changes in haemolymph pO2 that are positively
 correlated with experimental oxygen levels, haemolymph pO2 is similar pre-
 and post-death during thermal assays. OCLTT predicts that reduction in
 body oxygen level should lead to a reduction in CTmax. Despite finding the
 former, there was no change in CTmax across a wide range of body oxygen
 levels. Thus, we argue that oxygen availability is not a functional
 determinant of the upper thermal limits in pupae of P. napi.
description: Data used for all
 analysesThis single-sheet excel
 file contains the raw data extracted from the CO2, O2 and temperature
 datafiles.Data_181212.xlsx
DOI: 10.5061/dryad.4gk4f
title: Data from: New species in the Sitalcina sura species group (Opiliones, Laniatores, Phalangodidae), with evidence for a biogeographic link between California desert canyons and Arizona sky islands

description: The western United States is home to numerous narrowly endemic harvestman
 taxa (Arachnida, Opiliones), including members of the genus Sitalcina
 Banks, 1911. Sitalcina is comprised of three species groups, including the
 monospecific S. californica and S. lobata groups, and the S. sura group
 with eight described species. All species in the S. sura group have very
 small geographic distributions, with group members distributed like
 disjunct “beads on a string” from Monterey south to southern California
 and southeast to the sky-island mountain ranges of southern Arizona. Here,
 molecular phylogenetic and species delimitation analyses were conducted
 for all described species in the S. sura group, plus several newly
 discovered populations. Species trees were reconstructed using
 multispecies coalescent methods implemented in *BEAST, and species
 delimitation was accomplished using Bayes Factor Delimitation (BFD). Based
 on quantitative species delimitation results supported by consideration of
 morphological characters, two new species (Sitalcina oasiensis sp. n.,
 Sitalcina ubicki sp. n.) are described. We also provide a description of
 the previously unknown male of S. borregoensis Briggs, 1968. Molecular
 phylogenetic evidence strongly supports distinctive desert versus coastal
 clades, with desert canyon taxa from southern California more closely
 related to Arizona taxa than to geographically proximate California
 coastal taxa. We hypothesize that southern ancestry and plate tectonics
 have played a role in the diversification history of this animal lineage,
 similar to sclerophyllous plant taxa of the Madro-Tertiary Geoflora.
 Molecular clock analyses for the S. sura group are generally consistent
 with these hypotheses. We also propose that additional Sitalcina species
 await discovery in the desert canyons of southern California and northern
 Baja, and the mountains of northwestern mainland Mexico.
description: Sitalcina_FinalPhased_forDryadPhylogenetic matrices, phased data, nexus format
DOI: 10.5061/dryad.ng785
title: Data from: Multi-trait mimicry and the relative salience of individual traits

description: Mimicry occurs when one species gains protection from predators by
 resembling an unprofitable model species. The degree of mimic-model
 similarity is variable in nature and is closely related to the number of
 traits that the mimic shares with its model. Here, we experimentally test
 the hypothesis that the relative salience of traits, as perceived by a
 predator, is an important determinant of the degree of mimic-model
 similarity required for successful mimicry. We manipulated the relative
 salience of the traits of a two-trait artificial model prey, and
 subsequently tested the survival of mimics of the different traits. The
 unrewarded model prey had two colour traits, black and blue, and the
 rewarded prey had two combinations of green, brown and grey shades. Blue
 tits were used as predators. We found that the birds perceived the black
 and blue traits similarly salient in one treatment, and mimic-model
 similarity in both traits was then required for high mimic success. In a
 second treatment, the blue trait was the most salient trait, and
 mimic-model similarity in this trait alone achieved high success. Our
 results thus support the idea that similar salience of model traits can
 explain the occurrence of multi-trait mimicry.
description: discrimination-data-exp1Data from the discrimination learning in Experiment 1.generalization-data-exp1Data from the generalization test in Experiment 1.salience-data-exp2Data from the salience test in Experiment 2.
DOI: 10.5061/dryad.0gg8n
title: Data from: Fat and happy in the city: eastern chipmunks in urban environments

description: Cities are rapidly expanding, and wildlife may experience different
 selection pressures in urban environments when compared to natural
 habitats. Phenotypic differences between urban and natural populations may
 occur because of the altered urban environment. Behavior, the activity of
 the hypothalamic-pituitary-adrenal (HPA) axis and body condition can be
 expected to differ between urban and natural habitats. We used the eastern
 chipmunk (Tamias striatus) to test for differences in behavior assayed
 from an open field test, hair and fecal cortisol concentrations, and body
 condition (size-corrected body mass), predicting that urban chipmunks
 would exhibit more exploratory behavior, higher cortisol concentrations,
 and higher body condition, than their counterparts from natural habitats.
 We sampled eastern chipmunks in 2 urban areas paired with natural habitats
 and subjected adult chipmunks to an open field test, collected hair and
 fecal samples for the determination of cortisol concentrations, and
 measured body size and body mass to estimate body condition. Eastern
 chipmunks in urban habitats had significantly different behavior, tending
 toward reduced locomotion and grooming, and greater latency, than their
 counterparts from natural habitats. Urban chipmunks also had lower fecal
 cortisol concentrations than those from natural habitats, and female
 chipmunks were in better body condition when captured in urban habitats.
 These results suggest that urban habitats may be relatively benign for
 urban chipmunks, perhaps because of reduced need for exploration and the
 availability of anthropogenic food subsidies associated with urban
 environments.
description: JerCor_MS1_dataData on body size, mass, behaviour, and fecal/hair cortisol for adult eastern chipmunks (Tamias striatus)