cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1g3r5
title: Data from: Response of bats to light with different spectra: light-shy and agile bat presence is affected by white and green, but not red light

description: Artificial light at night has shown a remarkable increase over the past
 decades. Effects are reported for many species groups, and include changes
 in presence, behaviour, physiology and life-history traits. Among these,
 bats are strongly affected, and how bat species react to light is likely
 to vary with light colour. Different spectra may therefore be applied to
 reduce negative impacts. We used a unique set-up of eight field sites to
 study the response of bats to three different experimental light spectra
 in an otherwise dark and undisturbed natural habitat. We measured activity
 of three bat species groups around transects with light posts emitting
 white, green and red light with an intensity commonly used to illuminate
 countryside roads. The results reveal a strong and spectrum-dependent
 response for the slow-flying Myotis and Plecotus and more agile
 Pipistrellus species, but not for Nyctalus and Eptesicus species. Plecotus
 and Myotis species avoided white and green light, but were equally
 abundant in red light and darkness. The agile, opportunistically feeding
 Pipistrellus species were significantly more abundant around white and
 green light, most likely because of accumulation of insects, but equally
 abundant in red illuminated transects compared to dark control.
 Forest-dwelling Myotis and Plecotus species and more synanthropic
 Pipistrellus species are thus least disturbed by red light. Hence, in
 order to limit the negative impact of light at night on bats, white and
 green light should be avoided in or close to natural habitat, but red
 lights may be used if illumination is needed.
description: bat passes per transect
 per nightFile contains (only
 valid nights included) number of bat passes per night per transect. For
 detailed information on the setup of the experiment, please see Spoelstra
 et al. 2015, Experimental illumination of natural habitat—an experimental
 set-up to assess the direct and indirect ecological consequences of
 artificial light of different spectral composition. nightNR=night number,
 with first night January 1, 2012; yearperiod=June/July(1),
 August/September(2); lightonoff=experimental light on (1) or off
 (0).BatsPerTransectPerNight_sonochiro_min5_3gr.txt
DOI: 10.5061/dryad.q755t
title: Data from: Towards smarter harvesting from natural palm populations by sparing the individuals that contribute most to population growth or productivity

description: 1. Natural populations deliver a wide range of products that provide
 income for millions of people and need to be exploited sustainably. Large
 heterogeneity in individual performance within these exploited populations
 has the potential to improve population recovery after exploitation and
 thus help sustaining yields over time. 2. We explored the potential of
 using individual heterogeneity to design smarter harvest schemes, by
 sparing individuals that contribute most to future productivity and
 population growth, using the understorey palm Chamaedorea elegans as a
 model system. Leaves of this palm are an important non-timber forest
 product and long-term inter-individual growth variability can be evaluated
 from internode lengths. 3. We studied a population of 830 individuals,
 half of which was subjected to a 67 % defoliation treatment for three
 years. We measured effects of defoliation on vital rates and leaf size – a
 trait that determines marketability. We constructed integral projection
 models in which vital rates depended on stem length, past growth rate, and
 defoliation, and evaluated transient population dynamics to quantify
 population development and leaf yield. We then simulated scenarios in
 which we spared individuals that were either most important for population
 growth or had leaves smaller than marketable size. 4. Individuals varying
 in size or past growth rate responded similarly to leaf harvesting in
 terms of growth and reproduction. By contrast, defoliation-induced
 reduction in survival chance was smaller in large individuals than in
 small ones. Simulations showed that harvest-induced population decline was
 much reduced when individuals from size and past growth classes that
 contributed most to population growth were spared. Under this scenario
 cumulative leaf harvest over 20 years was somewhat reduced, but long-term
 leaf production was sustained. A three-fold increase in leaf yield was
 generated when individuals with small leaves are spared. 5. Synthesis and
 applications This study demonstrates the potential to create smarter
 systems of palm leaf harvest by accounting for individual heterogeneity
 within exploited populations. Sparing individuals that contribute most to
 population growth ensured sustained leaf production over time. The
 concepts and methods presented here are generally applicable to exploited
 plant and animal species which exhibit considerable individual
 heterogeneity.
description: Vital rate and internode
 dataThis data file contains
 annual vital rate data (stem length growth, fruit production, survival and
 leaf production) of 830 individuals of the understorey palm Chamaedorea
 elegans, collected in a 0.7 ha plot in Chiapas, Mexico, during the period
 November 2012 - November 2015. A 2/3 defoliation treatment was repeatedly
 applied to half of the individuals. The data file also contains
 measurements of the lengths of all internodes of all
 individuals.
DOI: 10.5061/dryad.8nr13
title: Data from: Existing infection facilitates establishment and density of malaria parasites in their mosquito vector

description: Very little is known about how vector-borne pathogens interact within
 their vector and how this impacts transmission. Here we show that
 mosquitoes can accumulate mixed strain malaria infections after feeding on
 multiple hosts. We found that parasites have a greater chance of
 establishing and reach higher densities if another strain is already
 present in a mosquito. Mixed infections contained more parasites but these
 larger populations did not have a detectable impact on vector survival.
 Together these results suggest that mosquitoes taking multiple infective
 bites may disproportionally contribute to malaria transmission. This will
 increase rates of mixed infections in vertebrate hosts, with implications
 for the evolution of parasite virulence and the spread of drug-resistant
 strains. Moreover, control measures that reduce parasite prevalence in
 vertebrate hosts will reduce the likelihood of mosquitoes taking multiple
 infective feeds, and thus disproportionally reduce transmission. More
 generally, our study shows that the types of strain interactions detected
 in vertebrate hosts cannot necessarily be extrapolated to vectors.
description: survival of
 mosquitoesSurvival and infection
 status data for mosquitoes.vector.mortality.csvParasite densities in primary infectionsFirst.infection.as.focal.csvEstablishment of infection from second feedData showing that mosquitoes can accumulate infections from multiple feeds.establishment.of.2nd.infection.csvParasite density in infections established from a secondary feeddensity.of.2nd.infections.csv
DOI: 10.5061/dryad.pn30v
title: Data from: Unexpected collective larval dispersal but little support for sweepstakes reproductive success in the highly dispersive brooding mollusk Crepidula fornicata

description: In many marine invertebrates, long-distance dispersal is achieved during
 an extended pelagic larval phase. Although such dispersal should result in
 high gene flow over broad spatial scales, fine-scale genetic structure has
 often been reported, a pattern attributed to interfamilial variance in
 reproductive success and limited homogenization during dispersal. To
 examine this hypothesis, the genetic diversity of dispersing larvae must
 be compared with the post-dispersal stages, i.e. benthic recruits and
 adults. Such data remain however scarce due to the difficulty to sample
 and analyze larvae of minute size. Here we carried out such an
 investigation using the marine gastropod Crepidula fornicata. Field
 sampling of three to four larval pools was conducted over the reproductive
 season and repeated over three years. The genetic composition of larval
 pools, obtained with 16 microsatellite loci, was compared with that of
 recruits and adults sampled from the same site and years. Conversely to
 samples of juveniles and adults, large genetic temporal variations between
 larval pools produced at different times of the same reproductive season
 were observed. In addition, full- and half-sibs were detected in early
 larvae and post-dispersal juveniles, pointing to correlated dispersal
 paths between several pairs of individuals. Inbred larvae were also
 identified. Such collective larval dispersal was unexpected given the long
 larval duration of the study species. Our results suggest that each larval
 pool is produced by a small effective number of reproducers but that, over
 a reproductive season, the whole larval pool is produced by large numbers
 of reproducers across space and time.
description: MEC-17-0564
DOI: 10.5061/dryad.3hf5gb3
title: Data from: Ultrasonic cavitation induces necrosis and impairs growth in three-dimensional models of pancreatic ductal adenocarcinoma

description: Introduction: Pancreatic ductal adenocarcinoma (PDAC) is a rapidly
 increasing cause of mortality whose dismal prognosis is mainly due to
 overwhelming chemoresistance. New therapeutic approaches include physical
 agents such as ultrasonic cavitation, but clinical applications require
 further insights in the mechanisms of cytotoxicity. Three dimensional in
 vitro culture models such as spheroids exploit realistic spatial,
 biochemical and cellular heterogeneity that may bridge some of the
 experimental gap between conventional in vitro and in vivo experiments.
 Purpose: to assess the feasibility and efficiency of inertial cavitation
 associated or not with chemotherapy, in a spheroid model of PDAC. Methods:
 we used DT66066 cells ,derived from a genetically-engineered murine PDAC,
 isolated from KPC-transgenic mice (LSL-KrasG12D/+; LSL-Trp53R172H/+;
 Pdx-1- Cre). Spheroids were obtained by either a standard
 centrifugation-based method, or by using a magnetic nano-shuttle method
 allowing the formation of spheroids within 24 hours and facilitating their
 handling. The spheroids were exposed to ultrasonic inertial cavitation in
 a specially designed setup. Four conditions were studied: control,
 gemcitabine alone , US cavitation alone , US cavitation + gemcitabine.
 Five US inertial cavitation indexes, corresponding to increased US
 intensities, were evaluated . The effectiveness of treatment was assessed
 after 24 hours with the following criteria: spheroid size (growth), ratio
 of phase S cells (proliferation), proportion of cells in apoptosis or
 necrosis (cellular mortality). These parameters were assessed by
 quantitative immunofluorescence techniques. Results: The 3D culture model
 presented excellent reproducibility. Eight or nine spheroids were analyzed
 for each condition. Cavitation induced a significant decrease in the size
 of spheroids , an effect significantly correlated to an increasing
 cavitation index (p &lt; 0.0001). The treatment induced cell death
 whose predominant mechanism was necrosis (p &lt; 0.0001). There was a
 tendency to a synergistic effect of US cavitation and gemcitabine at 5μM
 concentration, however significant in only one of the cavitation indexes
 used (p = 0. 013). Conclusion: Ultrasonic inertial cavitation induced a
 significant reduction of tumor growth in a spheroid model of PDAC., with
 necrosis rather than apoptosis as a Cell dominant mechanism of cell death.
 More investigations are needed to understand the potential role of
 inertial cavitation in overcoming chemoresistance.
description: DATA file for article
 10.1371/journal.pone.0209094All the data file of
 experiments described in the article: Ultrasonic cavitation induces
 necrosis and impairs growth in three-dimensional models of pancreatic
 ductal adenocarcinoma.ABOU ALI E. et alDATA FILE article plos
 one.zip
DOI: 10.5061/dryad.c2j05
title: Data from: Whole mitochondrial genomes provide increased resolution and indicate paraphyly in deer mice

description: Background: Recent phylogenies of deer mice, genus Peromyscus, have relied
 heavily on mitochondrial markers. These markers provided resolution at and
 below the level of species groups, but relationships among species groups
 and Peromyscus affiliated genera have received little support. Here, we
 present the mitochondrial genomes of 14 rodents and infer the phylogeny of
 Peromyscus and related taxa. Results: Our analyses support results from
 previous molecular phylogenies, but also yield support for several
 previously unsupported nodes throughout the Peromyscus tree. Our results
 also confirm several instances of paraphyly within the clade and suggest
 additional taxonomic work will be required to clarify some relationships.
 Conclusions: Our findings greatly enhance our understanding of the
 evolution of Peromyscus providing support for previously unsupported
 relationships. However, the results also highlight the need to address
 paraphyly that may exist in this clade.
description: Peromyscus
 proteincodingNexus file containing
 concatenated and aligned protein coding gene data for Bayesian and maximum
 likelihood analysis.Peromyscus_proteincoding.nex
DOI: 10.5061/dryad.9dd42
title: Data from: Brazilian marsupial frogs are diphyletic (Anura: Hemiphractidae: Gastrotheca)

description: Molecular phylogenetic analyses based on expanded taxonomic and geographic
 sampling support the monophyly of the marsupial frog genera (family
 Hemiphractidae), resolve six geographically circumscribed lineages within
 Gastrotheca, and, for the first time, reveal that two divergent lineages
 of Gastrotheca inhabit the Atlantic Coastal Forests of Brazil. Within
 Gastrotheca, the earliest diverging clade is confined to northeastern
 Brazil, whereas the three subsequent diverging lineages are restricted to
 northern Venezuela (G. walkeri), southeastern Brazil, and northwestern
 South America. All species in these clades inhabit humid forests at low to
 mid-elevations, and their life histories are characterized by lacking
 free-living tadpoles (i.e., direct development). Two derived clades
 inhabit the Andes, and both contain species with either direct development
 or tadpoles. One Andean clade of Gastrotheca ranges in the high Andes from
 Colombia to extreme northern Peru, whereas the other clade inhabits high
 elevations in the Andes of southern Ecuador, Peru, and Bolivia, and lower
 elevations in the Andes of northwestern Argentina. The presence of two
 non-sister lineages on each side of the Amazon Basin suggests that
 vicariance across this central region played an important role in
 diversification within Gastrotheca.
description: Gastrotheca_Blackburn&Duelman2013Nexus file containing aligned sequence data for four genes: 16S (mt), ND1 (mt), POMC (nuc), and RAG-1 (nuc). File also includes character sets and model settings for analysis.
DOI: 10.5061/dryad.s492m
title: Data from: Herbivore release drives parallel patterns of evolutionary divergence in invasive plant phenotypes

description: 1. Herbivory can drive rapid evolution of plant chemical traits mediating
 defensive and competitive ability. At a geographic scale, plant
 populations that escape selection from their ancestral herbivores may
 evolve decreased defense and increased competitiveness. While contrasts
 between native and invasive populations of plants lend support to this
 hypothesis, such experiments cannot establish causal links between
 herbivory and evolved invasive phenotypes. 2. Here, we conducted
 geographic contrasts, and coupled these with long-term selection
 experiments that directly test for evolutionary responses to
 herbivore-exclusion. In common gardens, we contrasted Solidago altissima
 genotypes that were historically exposed or protected from herbivory
 across two experimental timescales: 1) a natural experiment where plant
 populations evolved either with native herbivory (in Minnesota and New
 York), or evolved relatively free from herbivory for ~100 years in Japan,
 and 2) a 12-year manipulative experiment where plants were either exposed
 to ambient herbivory, or treated with insecticide. 3. In both experiments,
 plant populations responded to herbivore-release by evolving increased
 production of root allelochemicals and inter-specific competitive ability
 against Poa pratensis. While plant resistance to a beetle herbivore did
 not diverge between plant origins, we still observed parallel evolutionary
 shifts in leaf secondary metabolite and protease inhibitor production,
 which may confer resistance to diverse herbivore species. 4. Synthesis.
 Observed evolutionary convergence for multiple plant traits, between the
 natural and manipulative experiments, emphasises the role of insect
 herbivores as key drivers of plant adaptation and geographic
 differentiation.
description: congruent evolution
 dataData from Manipulative
 and Natural experiments, including plant growth, resistance, leaf and root
 secondary metabolite data.Uesugi&Kessler_data.xlsx
DOI: 10.5061/dryad.616gv
title: Data from: Regional difference in sex steroid action on formation of morphological sex differences in the anteroventral periventricular nucleus and principal nucleus of the bed nucleus of the stria terminalis

description: Sex steroid action is critical to form sexually dimorphic nuclei, although
 it is not fully understood. We previously reported that masculinization of
 the principal nucleus of the bed nucleus of the stria terminalis (BNSTp),
 which is larger and has more neurons in males than in females, involves
 aromatized testosterone that acts via estrogen receptor-α (ERα), but not
 estrogen receptor-β (ERβ). Here, we examined sex steroid action on the
 formation of the anteroventral periventricular nucleus (AVPV) that is
 larger and has more neurons in females. Morphometrical analysis of
 transgenic mice lacking aromatase, ERα, or ERβ genes revealed that the
 volume and neuron number of the male AVPV were significantly increased by
 deletion of aromatase and ERα genes, but not the ERβ gene. We further
 examined the AVPV and BNSTp of androgen receptor knockout (ARKO) mice. The
 volume and neuron number of the male BNSTp were smaller in ARKO mice than
 those in wild-type mice, while no significant effect of ARKO was found on
 the AVPV and female BNSTp. We also examined aromatase, ERα, and AR mRNA
 levels in the AVPV and BNSTp of wild-type and ARKO mice on embryonic day
 (ED) 18 and postnatal day (PD) 4. AR mRNA in the BNSTp and AVPV of
 wild-type mice was not expressed on ED18 and emerged on PD4. In the AVPV,
 the aromatase mRNA level was higher on ED18, although the ERα mRNA level
 was higher on PD4 without any effect of AR gene deletion. Aromatase and
 ERα mRNA levels in the male BNSTp were significantly increased on PD4 by
 AR gene deletion. These results suggest that estradiol signaling via ERα
 during the perinatal period and testosterone signaling via AR during the
 postnatal period are required for masculinization of the BNSTp, whereas
 the former is sufficient to defeminize the AVPV.
description: Morphometrical analysis
 of the AVPVThis file contains the
 results of morphometrical analysis of the AVPV in adult AromKO, αERKO,
 βERKO, and ARKO mice of both sexesAVPV-AromKO, αERKO, βERKO,
 ARKO.xlsxMorphometrical analysis
 of the BNSTpThis file contains the
 results of morphometrical analysis of the BNSTp in adult ARKO mice of both
 sexes and male ARKO mice treated neonatally with testosterone
 propionateBNSTp-ARKO.xlsxAnalysis of gene expression in the AVPV of perinatal miceThis file contains the results of gene expression analysis using real-time PCR in the AVPV of perinatal WT and ARKO micereal-time PCR(AVPV).xlsxAnalysis of gene expression in the BNSTp of perinatal miceThis file contains the results of gene expression analysis using real-time PCR in the BNSTp of perinatal WT and ARKO micereal-time PCR(BNSTp).xlsx
DOI: 10.5061/dryad.h08r6
title: Data from: The puzzle of partial resource use by a parasitoid wasp

description: When there is conspicuous underexploitation of a limited resource, it is
 worth asking, what mechanisms allow presumably valuable resources to be
 left unused? Evolutionary biologists have generated a wide variety of
 hypotheses to explain this, ranging from interdemic group selection to
 selfishly prudent individual restraint. We consider a situation in which,
 despite high intraspecific competition, individuals leave most of a key
 resource unexploited. The parasitic wasp that does this finds virtually
 all host egg clusters in a landscape but parasitizes only about a third of
 the eggs in each and then leaves a deterrent mark around the cluster. We
 first test—and reject—a series of system-specific simple constraints that
 might limit full host exploitation, such as asynchronous maturation of
 host eggs. We then consider classical hypotheses for the evolution of
 restraint. Prudent predation and bet-hedging fail as explanations because
 the wasp lives as a large, well-mixed population. Additionally, we find no
 individual benefits to the parasitoid of developing in a sparsely
 parasitized host nest. However, an optimal foraging model, including
 empirically measured costs of superparasitism and hyperparasitism, can
 explain through individual selection both the consistently low rate of
 parasitism and deterrent marking.
description: All
 data.xlsxHyposoter ms data for
 Dryad.xlsx.zip
DOI: 10.5061/dryad.4s4t1
title: Data from: Catch reconstructions reveal that global marine fisheries catches are higher than reported and declining

description: Fisheries data assembled by the Food and Agriculture Organization (FAO)
 suggest that global marine fisheries catches increased to 86 million
 tonnes in 1996, then slightly declined. Here, using a decade-long
 multinational ‘catch reconstruction’ project covering the Exclusive
 Economic Zones of the world’s maritime countries and the High Seas from
 1950 to 2010, and accounting for all fisheries, we identify catch
 trajectories differing considerably from the national data submitted to
 the FAO. We suggest that catch actually peaked at 130 million tonnes, and
 has been declining much more strongly since. This decline in reconstructed
 catches reflects declines in industrial catches and to a smaller extent
 declining discards, despite industrial fishing having expanded from
 industrialized countries to the waters of developing countries. The
 differing trajectories documented here suggest a need for improved
 monitoring of all fisheries, including often neglected small-scale
 fisheries, and illegal and other problematic fisheries, as well as
 discarded bycatch.
description: Pauly&Zeller-data-F1-F2-F4-Nov-04-2015Data as used for and presented in Figures 1, 2 and 4 of the associated paperPauly&Zeller-data-F3-Nov-04-2015Data used for and presented in Figure 3 of the associated paper