cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pp700
title: Data from: Long-term stoichiometry and fates highlight animal egestion as nutrient repackaging, not recycling, in aquatic ecosystems

description: 1. Animal defecation, or egestion, is a pronounced transformation of
 organic matter in many ecosystems. However, because egesta have been
 presumed recalcitrant and low-nutrient, their significance and variability
 as an animal nutrient flux in aquatic settings - especially relative to
 mineralization via excretion - are poorly known. 2. We compared carbon
 (C), nitrogen (N), and phosphorus (P) dynamics over short- to long-term
 (up to 107 days) microbial decomposition of egesta from the aquatic
 shredders Allocapnia spp., Lirceus spp., and Tipula spp. fed low- or
 high-P content Platanus occidentalis litter to investigate roles of egesta
 in aquatic nutrient dynamics. 3. Tipula produced N- and P-deplete egesta
 of higher N:P compared to Lirceus and Allocapnia, and high-P diets
 increased egesta P content compared to low-P diets. Despite measurable C
 losses to decomposition, these differences in nutrient content persisted
 through decomposition, showing diet and species control both immediate and
 long-term properties of egested particles. 4. Egesta switched between
 uptake and release of dissolved phosphorus and ammonium during
 decomposition, and exhibited consistent net N uptake as nitrate-nitrite.
 Across species and diets, lower N:P egesta tended to exhibit greater
 uptake of dissolved inorganic N, suggesting P enrichment of egesta drove
 stronger dissolved N demand by decomposer microbes. 5. Shredder egesta
 exhibit stable nutrient contents long-term and, counter to assumptions
 that they are negligible or minor net sources, can be strong, extended
 sinks of dissolved inorganic nutrients. Future studies should consider
 contrasts between animal nutrient fluxes as excretion, which facilitates
 nutrient recycling via mineralization, versus egestion, which slows
 nutrient recycling via organic nutrient repackaging and can create sinks
 of dissolved nutrients.
description: Egesta dissolved
 nutrient release, elemental contents, and respiration over
 time.Data are divided among 3
 sheets. The first sheet gives nutrient release recorded on each
 measurement day over 107 days. The second sheet gives egesta carbon,
 nitrogen, and phosphorus contents over the 107 d period. C contents were
 used to calculate long-term decomposition rates. The third sheet gives
 total respiration of egesta over the first 7 days of decomposition, used
 to calculate short-term decomposition rates.DryadData_Halvorson_FunctEcol.xlsx
DOI: 10.5061/dryad.fb48n
title: Data from: Signal diversification in Oecanthus tree crickets is shaped by energetic, morphometric, and acoustic trade-offs

description: Physiology, physics, and ecological interactions can generate trade-offs
 within species, but may also shape divergence among species. We tested
 whether signal divergence in Oecanthus tree crickets is shaped by
 acoustic, energetic, and behavioral trade-offs. We found that species with
 faster pulse rates, produced by opening and closing wings up to twice as
 many times per second, did not have higher metabolic costs of calling. The
 relatively constant energetic cost across species is explained by
 trade-offs between the duration and repetition rate of acoustic signals –
 species with fewer stridulatory teeth closed their wings more frequently
 such that the number of teeth struck per second of calling and the
 resulting duty cycle were relatively constant across species. Further
 trade-offs were evident in relationships between signals and body size.
 Calling was relatively inexpensive for small males, permitting them to
 call for much of the night, but at low amplitude. Large males produced
 much louder calls, reaching up to four times more area, but the energetic
 costs increased substantially with increasing size and the time spent
 calling dropped to only 20% of the night. These trade-offs indicate that
 the trait combinations that arise in these species represent a limited
 subset of conceivable trait combinations.
description: Mass and
 CO2Each line provides
 information for one individual cricket (mass, percent time spent calling,
 and CO2 production). Data correspond to Figure 2.Pulse rate and tooth
 numberEach line provides the
 pulse rate for an individual cricket and the number of teeth in the file
 of that cricket. Raw data for figure 4Mass, amplitude, and
 time spent callingSheet 1 contains the
 mass and percent of time spent calling. Sheet 2 contains mass and call
 amplitude. In both cases, each line represents a measurement on one
 cricket. Raw data for Figure 5.Supplemental amplitude
 dataProvides mass and
 relative amplitude (used to create supplemental
 figure).
DOI: 10.5061/dryad.941r8h0
title: Data from: A pollen fatty acid enhances learning and survival in bumblebees

description: Learning associations between food-related stimuli and nutrients allows
 foragers to collect resources efficiently. In turn, the nutrients foragers
 consume can themselves affect learning performance, through innate
 preferences for pre-ingestive stimuli, as well as post-ingestive
 reinforcement. Bees are insect models of learning and memory, yet the vast
 majority of this research concerns nectar (carbohydrate) rather than
 pollen (protein/lipid) rewards, despite the fact that many bees collect
 both simultaneously. We asked how one component of pollen surface
 chemistry, a free fatty acid (oleic acid), affected bees’ performance in a
 nectar-learning task. We found that ingestion of oleic acid enhanced
 visual learning, likely through positive post-ingestive reinforcement.
 This was supported by our finding that although bees did not prefer to
 consume the oleic acid solution, its ingestion both decreased motor
 activity and increased survival. These results are a step towards
 understanding how nutritionally complex floral rewards may affect
 cognitive processes that underlie pollination mutualisms.
description: Muth data for
 DryadData for Muth et al A
 pollen fatty acid enhances learning and survival in bumblebees. Each tab
 relates to each experiment in the manuscript (as
 labelled).
DOI: 10.5061/dryad.v676m
title: Data from: Local and landscape metrics identify opportunities for conserving cavity-nesting birds in a rapidly urbanizing ecoregion

description: Urban centers are rapidly expanding globally, resulting in regional
 forest-cover transformations that shift from temperate forest biomes to a
 heterogeneous mix of urban development, forest patches, and agriculture.
 Data on habitat use within remaining forest patches embedded across land
 use types, particularly in urban land use, are needed to optimize
 conservation strategies as urban growth continues. In the rapidly
 urbanizing southern Piedmont, USA, small pine patches have become more
 frequent across the landscape and are found embedded within second-growth
 forest, agricultural, and urban land use matrices. We used point-count
 surveys and N-mixture models to determine the effect of patch- and
 landscape-scale drivers on cavity-nesting bird abundance, including the
 threatened Brown-headed Nuthatch (Sitta pusilla), in pine forest patches.
 Model-averaged estimates suggest Brown-headed Nuthatches are more abundant
 in large patches in a heterogeneous matrix that includes urban residential
 development. Three other cavity-nesting species declined in abundance as a
 function of reduced canopy cover. White-breasted Nuthatches increased and
 Tufted Titmice decreased in abundance in response to patch area. By
 identifying factors that predict abundance at local and landscape scales
 for ecologically sensitive and generalist species, we can more effectively
 contribute to regional conservation efforts in urban ecosystems, extending
 conservation in practice beyond protected areas.
description: Species Counts and
 CovariatesThis data set contains
 .csv files used to estimate abundance of nine cavity nesting species in
 the southern Piedmont ecoregion of the southeast United States. Data are
 formatted to be analyzed with the unmarked package in
 R.DataforDryad.zip
DOI: 10.5061/dryad.550p3
title: Data from: Blood-stage parasitaemia and age determine Plasmodium falciparum and P. vivax gametocytaemia in Papua New Guinea

description: A better understanding of human-to-mosquito transmission is crucial to
 control malaria. In order to assess factors associated with gametocyte
 carriage, 2083 samples were collected in a cross-sectional survey in Papua
 New Guinea. Plasmodium species were detected by light microscopy and qPCR
 and gametocytes by detection of pfs25 and pvs25 mRNA transcripts by
 reverse-transcriptase PCR (qRT-PCR). The parasite prevalence by PCR was
 18.5% for Plasmodium falciparum and 13.0% for P. vivax. 52.5% of all
 infections were submicroscopic. Gametocytes were detected in 60% of P.
 falciparum-positive and 51% of P. vivax-positive samples. Each 10-fold
 increase in parasite density led to a 1.8-fold and 3.3-fold increase in
 the odds of carrying P. falciparum and P. vivax gametocytes. Thus the
 proportion of gametocyte positive and gametocyte densities was highest in
 young children carrying high asexual parasite densities and in symptomatic
 individuals. Dilution series of gametocytes allowed absolute
 quantification of gametocyte densities by qRT-PCR and showed that pvs25
 expression is 10-20 fold lower than pfs25 expression. Between 2006 and
 2010 parasite prevalence in the study site has decreased by half. 90% of
 the remaining infections were asymptomatic and likely constitute an
 important reservoir of transmission. However, mean gametocyte densities
 were low (approx. 1-2 gametocyte/μL) and it remains to be determined to
 what extent low-density gametocyte positive individuals are infective to
 mosquitos.
description: PNG_2010cross-sectional_DryadMicroscopy and qPCR results on P. falciparum and P. vivax parasite and gametocyte carriage in Papua New Guinea, and clinical status of participants.
DOI: 10.5061/dryad.b81n1
title: Data from: Downregulation of autophagy is associated with severe ischemia-reperfusion-induced acute kidney injury in overexpressing C-reactive protein mice

description: C-reactive protein (CRP), was recently reported to be closely associated
 with poor renal function in patients with acute kidney injury (AKI), but
 whether CRP is pathogenic or a mere biomarker in AKI remains largely
 unclear. Impaired autophagy is known to exacerbate renal
 ischemia-reperfusion injury (IRI). We examined whether the pathogenic role
 of CRP in AKI is associated with reduction of autophagy. We mated
 transgenic rabbit CRP over-expressing mice (Tg-CRP) with two autophagy
 reporter mouse lines, Tg-GFP-LC3 mice (LC3) and Tg-RFP-GFP-LC3 mice
 (RG-LC3) respectively to generate Tg-CRP-GFP-LC3 mice (PLC3) and
 Tg-CRP-RFP-GFP-LC3 mice (PRG-LC3). AKI was induced by IRI. Compared with
 LC3 mice, PLC3 mice developed more severe kidney damage after IRI. Renal
 tubules were isolated from LC3 mice at baseline for primary culture. OKP
 cells were transiently transfected with GFP-LC3 plasmid. CRP addition
 exacerbated lactate dehydrogenase release from both cell types.
 Immunoblots showed lower LC-3 II/I ratios and higher levels of p62,
 markers of reduced autophagy flux, in the kidneys of PLC3 mice compared to
 LC3 mice after IRI, and in primary cultured renal tubules and OKP cells
 treated with CRP and H2O2 compared to H2O2 alone. Immunohistochemistry
 showed much fewer LC-3 punctae, and electron microscopy showed fewer
 autophagosomes in kidneys of PLC3 mice compared to LC3 mice after IRI.
 Similarly, CRP addition reduced GFP-LC3 punctae induced by H2O2 in primary
 cultured proximal tubules and in GFP-LC3 plasmid transfected OKP cells.
 Rapamycin, an autophagy inducer, rescued impaired autophagy and reduced
 renal injury in vivo. In summary, it was suggested that CRP be more than
 mere biomarker in AKI, and render the kidney more susceptible to
 ischemic/oxidative injury, which is associated with down-regulating
 autophagy flux.
description: Human
 dataThis is the human data
 of our study.Animal
 dataanimal
 data.xlsx
DOI: 10.5061/dryad.d15d4
title: Data from: Genetic isolation within the malaria mosquito Anopheles melas

description: Anopheles melas is a brackish water-breeding member of the An. gambiae
 complex that is distributed along the coast of West Africa and is a major
 malaria vector within its range. Because little is known about the
 population structure of this species, we analyzed 15 microsatellite
 markers and 1,161 bp of mtDNA in 11 An. melas populations collected
 throughout its range. Compared to its sibling species An. gambiae, An.
 melas populations have a high level of genetic differentiation between
 them, representing its patchy distribution due to its fragmented larval
 habitat which is associated with mangroves and salt marsh grass.
 Populations clustered into three distinct groups representing Western
 Africa, Southern Africa, and Bioko Island populations that appear to be
 mostly isolated. Fixed differences in the mtDNA are present between all
 three clusters, and a Bayesian clustering analysis of the microsatellite
 data found no evidence for migration from mainland to Bioko Island
 populations, and little migration was evident between the Southern to the
 Western cluster. Surprisingly, mtDNA divergence between the three An.
 melas clusters is on par with levels of divergence between other species
 of the An. gambiae complex, and no support for monophyly was observed in a
 maximum likelihood phylogenetic analysis. Finally, an Approximate Bayesian
 Analysis of microsatellite data indicates that Bioko Island An. melas
 populations were connected to the mainland populations in the past, but
 became isolated, presumably when sea levels rose after the last glaciation
 period (≥10,000-11,000 years ago). This study has exposed species level
 genetic divergence within An. melas, and also has implications for control
 of this malaria vector.
description: Anopheles melas genotype
 data for 15 microsatellite lociThe datafile is in
 GENEPOP format, and comprises genotype scores for 15 Anopheles
 melas-specific microsatellite loci. A total of 617 wild-caught specimens
 from 11 populations are included in the datafile. Locus names are listed
 at the beginning of the file under the title line, and correspond with the
 lines of data, left to right. Missing genotypes are coded as
 "000". Allele scores for each locus are concatenated into six
 digits, with the first three letters representing allele "A",
 and the second three letters representing allele
 "B".Deitz_et_al_Anopheles_melas.Genepop.txt
DOI: 10.5061/dryad.8k015
title: Data from: Rapidly fluctuating environments constrain coevolutionary arms races by impeding selective sweeps

description: Although pervasive, the impact of temporal environmental heterogeneity on
 coevolutionary processes is poorly understood. Productivity is a key
 temporally heterogeneous variable, and increasing productivity has been
 shown to increase rates of antagonistic arms race coevolution, and lead to
 the evolution of more broadly resistant hosts and more broadly infectious
 parasites. We investigated the effects of the grain of environmental
 heterogeneity, in terms of fluctuations in productivity, on bacteria–phage
 coevolution. Our findings demonstrate that environmental heterogeneity
 could constrain antagonistic coevolution, but that its effect was
 dependent upon the grain of heterogeneity, such that both the rate and
 extent of coevolution were most strongly limited in fine-grained, rapidly
 fluctuating heterogeneous environments. We further demonstrate that rapid
 environmental fluctuations were likely to have impeded selective sweeps of
 resistance alleles, which occurred over longer durations than the fastest,
 but not the slowest, frequency of fluctuations used. Taken together our
 results suggest that fine-grained environmental heterogeneity constrained
 the coevolutionary arms race by impeding selective sweeps.
description: resistance data from
 cross-infection assaysLaboratory selection
 experiment, cross-infection assay dataRAW
 DATA.xlsx
DOI: 10.5061/dryad.91741
title: Data from: A test of hybrid growth disadvantage in wild, free-ranging species pairs of threespine sticklebacks (Gasterosteus aculeatus) and its implications for ecological speciation

description: Ecological speciation is the evolution of reproductive isolation as a
 direct or indirect consequence of divergent natural selection. Reduced
 performance of hybrids in nature is thought to be an important process by
 which natural selection can favour the evolution of assortative mating and
 drive speciation. Benthic and limnetic sympatric species of threespine
 stickleback (Gasterosteus aculeatus) are adapted to alternative trophic
 niches (bottom browsing versus open water planktivory, respectively) and
 reduced feeding performance of hybrids is thought to have contributed to
 the evolution of reproductive isolation. We tested this
 “hybrid-disadvantage hypothesis” by inferring growth rates from otoliths
 sampled from wild, free-ranging benthic, limnetic, and hybrid sticklebacks
 from two lakes. There were significant differences in growth rate between
 lakes, life-history stages, and among years (maximum P = 0.02), as well as
 interactions between most factors, but not between hybrid and parental
 species sticklebacks in most comparisons. Our results provide little
 evidence of a growth disadvantage in hybrid sticklebacks when free-ranging
 in nature. While trophic ecology per se may contribute less to ecological
 speciation than envisioned, it may act in concert with other aspects of
 stickleback biology, such as interactions with parasites, predators,
 competitors and/or sexual selection, to present strong multifarious
 selection against hybrids.
description: Stickleback age and
 otolith growth dataThe file is an excel
 spreadsheet with different tabs holding data for stickleback fish, their
 estimated ages (from otolith growth ring counts) and the size of the
 otolith used to age the fish, from which otolith growth rates were
 calculated. Also shown are the id's of each fish and their estimated
 admixture/hybridity coefficients.dryadentry.xls
DOI: 10.5061/dryad.895jb
title: Data from: Limited oxygen availability in utero may constrain the evolution of live-birth in reptiles

description: Although viviparity (live birth) has evolved from oviparity (egg laying)
 at least 140 times in vertebrates, nearly 120 of these independent events
 occurred within a single reptile taxon. Surprisingly, only squamate
 reptiles (lizards and snakes) are capable of facilitating embryonic
 development to increasingly advanced stages inside the mother during
 extended periods of oviducal egg retention. Viviparity has never evolved
 in turtle lineages, presumably because embryos enter and remain in an
 arrested state until after eggs are laid, regardless of the duration of
 egg retention. Until now, the limiting factor that initiates and maintains
 developmental arrest has remained elusive. Here, we show that oviducal
 hypoxia arrests embryonic development. We demonstrate that hypoxia can
 maintain developmental arrest after oviposition and that subsequent
 exposure of arrested embryos to normoxia triggers resumption of their
 development. We discovered remarkably low oxygen partial pressure in the
 oviducts of gravid turtles and found that secretions produced by the
 oviduct retard oxygen diffusion. Our results suggest that an extremely
 hypoxic environment in the oviduct arrests embryonic development and may
 constrain the evolution of viviparity in turtles, with the reduced
 diffusive capacity of oviducal secretions possibly creating or
 contributing to this hypoxia. We anticipate that these findings will allow
 us to better understand the mechanisms underlying the evolutionary
 transition between reproductive modes.
description: DRYAD_Raffertyetal
DOI: 10.5061/dryad.j646b
title: Data from: Accuracy of popular media reporting on tobacco cessation therapy in substance abuse and mental health populations

description: Background: Tobacco cessation therapy is not consistently provided for
 alcohol, drug abuse and mental health (ADM) populations, despite the
 enormous health consequences of tobacco addiction in these groups and
 research supporting the effectiveness of treatment. Policymakers, however,
 tend to rely on popular media reports rather than the scientific
 literature in regulating treatment. Our goal was to determine whether
 popular reporting accurately reflects findings from the scientific
 literature on tobacco cessation treatment for ADM populations in
 treatment. Methods: We compared the results of systematic reviews on
 tobacco cessation therapy published before 2004 with articles published in
 traditional media and on the internet over the following 8 years. We
 searched LexisNexis and Google and assessed them using the Index of
 Scientific Quality (ISQ). Results: We found that popular reporting on this
 topic was consistent with findings reported in contemporaneous scientific
 literature. Our results suggest that the failure to consistently provide
 tobacco cessation therapy to ADM populations in treatment is not due to
 poor research translation. Conclusions: Our findings also suggest that in
 this topic area, scientific research findings have diffused relatively
 quickly. Further study of journalism in this area may suggest new
 strategies for effective translation of scientific findings into popular
 reporting on tobacco control.
description: DatabaseOur dataset contains the quality scores for each criterion assessed in both traditional and internet media. We also provide the standard deviation and mean values for each criterion.