cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bc276
title: Data from: Investigating trehalose synthesis genes after cold acclimation in the Antarctic nematode Panagrolaimus sp. DAW1

description: Panagrolaimus sp. DAW1 is a freeze-tolerant Antarctic nematode which
 survives extensive intracellular ice formation. The molecular mechanisms
 of this extreme adaptation are still poorly understood. We recently showed
 that desiccation-enhanced RNA interference (RNAi) soaking can be used in
 conjunction with quantitative polymerase chain reaction (qPCR) to screen
 for phenotypes associated with reduced expression of candidate genes in
 Panagrolaimus sp. DAW1. Here, we present the use of this approach to
 investigate the role of trehalose synthesis genes in this remarkable
 organism. Previous studies have shown that acclimating Panagrolaimus sp.
 DAW1 at 5°C before freezing or desiccation substantially enhances
 survival. In this study, the expression of tps-2 and other genes
 associated with trehalose metabolism, as well as lea-1, hsp-70 and gpx-1,
 in cold-acclimated and non-acclimated nematodes was analyzed using qPCR.
 Pd-tps-2 and Pd-lea-1 were significantly upregulated after cold
 acclimation, indicating an inducible expression in the cold adaptation of
 Panagrolaimus sp. DAW1. The role of trehalose synthesis genes in
 Panagrolaimus sp. DAW1 was further investigated by RNAi. Compared to the
 controls, Pd-tps-2a(RNAi)-treated and cold-acclimated nematodes showed a
 significant decrease in mRNA, but no change in trehalose content or
 freezing survival. The involvement of two other trehalose synthesis genes
 (tps-2b and gob-1) was also investigated. These findings provide the first
 functional genomic investigation of trehalose synthesis genes in the
 non-model organism Panagrolaimus sp. DAW1. The presence of several
 trehalose synthesis genes with different RNAi sensitivities suggests the
 existence of multiple backup systems in Panagrolaimus sp. DAW1,
 underlining the importance of this sugar in preparation for freezing.
description: Spreadsheet containing
 expression dataThis file contains
 relative expression data for qPCR experiments both before and after RNAi,
 as well as freezing tolerance and trehalose content.AnnaTrehalose.xlsx
DOI: 10.5061/dryad.8g3j2
title: Data from: Interactive effects of pests increase seed yield

description: Loss in seed yield and therefore decrease in plant fitness due to
 simultaneous attacks by multiple herbivores is not necessarily additive,
 as demonstrated in evolutionary studies on wild plants. However, it is not
 clear how this transfers to crop plants that grow in very different
 conditions compared to wild plants. Nevertheless, loss in crop seed yield
 caused by any single pest is most often studied in isolation although crop
 plants are attacked by many pests that can cause substantial yield losses.
 This is especially important for crops able to compensate and even
 overcompensate for the damage. We investigated the interactive impacts on
 crop yield of four insect pests attacking different plant parts at
 different times during the cropping season. In 15 oilseed rape fields in
 Sweden, we estimated the damage caused by seed and stem weevils, pollen
 beetles, and pod midges. Pest pressure varied drastically among fields
 with very low correlation among pests, allowing us to explore interactive
 impacts on yield from attacks by multiple species. The plant damage caused
 by each pest species individually had, as expected, either no, or a
 negative impact on seed yield and the strongest negative effect was caused
 by pollen beetles. However, seed yield increased when plant damage caused
 by both seed and stem weevils was high, presumably due to the joint plant
 compensatory reaction to insect attack leading to overcompensation. Hence,
 attacks by several pests can change the impact on yield of individual pest
 species. Economic thresholds based on single species, on which pest
 management decisions currently rely, may therefore result in economically
 suboptimal choices being made and unnecessary excessive use of
 insecticides.
description: Gagic2016_EcoEvo_dataSeed yield, individual yield components and plant damage data
DOI: 10.5061/dryad.4t393
title: Data from: Species turnover through time: colonization and extinction dynamics across metacommunities

description: Island biogeography and metacommunity theory often use equilibrium
 assumptions to predict local diversity, yet non-equilibrium dynamics are
 common in nature. In non-equilibrium communities, local diversity
 fluctuates through time as the relative importance of colonization and
 extirpation change. Here, we test the prevalence and causes of
 non-equilibrium dynamics in metacommunities of mites associated with
 rubber trees distributed over large spatial (&gt;1000 km) and temporal
 (&gt; 30-60 generations) scales in Brazil. We measured colonization
 and extirpation rates to test species turnover and non-equilibrium
 dynamics over a growing season. Mite metacommunities exhibited
 non-equilibrium dynamics for most months of the year, and these dynamics
 tracked climatic conditions. Monthly shifts in temperature of more than
 one degree Celsius resulted in non-equilibrium dynamics, as did mean
 temperatures outside of two critical ranges. Non-equilibrium dynamics were
 caused by a change in colonization with temperature change, and changes in
 both colonization and extirpation with absolute temperature. Species
 turnover showed different trends; high relative humidity increased both
 colonization and extirpation rates, increasing turnover but not
 non-equilibrium dynamics. Our study illustrates that testing
 non-equilibrium dynamics can provide new insights into the drivers of
 colonization, extinction and diversity fluctuations in metacommunities.
description: mite distributions by
 tree, month and site and climatic conditions by site and
 monthMite distributions on
 rubber trees in Brazil. Mites organized by tree, month and site and
 climatic conditions by site and month.Dryad
 data.zip
DOI: 10.5061/dryad.ch06v
title: Data from: Ambient temperature, body condition and sibling rivalry explain feather corticosterone levels in developing black kites

description: In birds, the steroid hormone corticosterone (CORT) is considered a major
 mediator in a number of physiological mechanisms and behaviours critical
 for the regulation of an organism's energy balance. However, the
 question of whether the way in which circulating plasma CORT is
 incorporated into feathers actually reflects this regulation, and
 consequently whether feather CORT (CORT-F) measures allow to make
 inferences on past levels of energetic demands (also known as the
 allostatic load), remains unclear. While previous studies have yielded
 promising results, the technique still wants further study and validation
 in a wider range of bird species, across life-history stages and under
 different ecological situations. Here, we tested whether CORT-F levels in
 a sample of 427 nestling black kites (Milvus migrans) reflected
 interindividual variation in a number of environmental, social and
 physiological variables known to elevate allostatic load during
 development. We found that nestlings exposed to low ambient temperatures
 exhibited high CORT-F, suggesting that feathers registered the expected
 rise in circulating CORT levels inducing thermogenesis in response to cold
 stress. CORT-F was also negatively related to body condition, supporting
 the notion that allostasis becomes less affordable as energy stores become
 depleted. Finally, CORT-F also reflected brood hierarchy rank, with
 subordinate chicks exhibiting the highest levels, followed by
 first-hatched (dominant) chicks and lastly singleton nestlings. Moreover,
 CORT-F levels in nestlings from multiple-chick broods (but not in
 singletons) declined with age, mirroring the dynamics of establishment and
 stabilization of sibling hierarchies in black kites. Altogether, our
 results underscore the potential of using CORT-F to infer allostatic load
 in wild avian populations and their potential power as indicator tools in
 conservation biology.
description: Data for the response
 and predictor variables used in the statistical analysis of this
 studyDryad.xlsx
DOI: 10.5061/dryad.5g0mr64
title: Data from: Short-term precipitation exclusion alters microbial responses to soil moisture in a wet tropical forest

description: Many wet tropical forests, which contain a quarter of global terrestrial
 biomass carbon stocks, will experience changes in precipitation regime
 over the next century. Soil microbial responses to altered rainfall are
 likely to be an important feedback on ecosystem carbon cycling, but the
 ecological mechanisms underpinning these responses are poorly understood.
 We examined how reduced rainfall affect- ed soil microbial abundance,
 activity, and community compo- sition using a 6-month precipitation
 exclusion experiment at La Selva Biological Station, Costa Rica.
 Thereafter, we ad- dressed the persistent effects of field moisture
 treatments by exposing soils to a controlled soil moisture gradient in the
 lab for 4 weeks. In the field, compositional and functional re- sponses to
 reduced rainfall were dependent on initial condi- tions, consistent with a
 large degree of spatial heterogeneity in tropical forests. However, the
 precipitation manipulation sig- nificantly altered microbial functional
 responses to soil mois- ture. Communities with prior drought exposure
 exhibited higher respiration rates per unit microbial biomass under all
 conditions and respired significantly more CO2 than control soils at low
 soil moisture. These functional patterns suggest that changes in microbial
 physiology may drive positive feed- backs to rising atmospheric CO2
 concentrations if wet tropical forests experience longer or more intense
 dry seasons in the future.
description: WaringandHawkes_precip_exclusion_field_data
DOI: 10.5061/dryad.2s590
title: Data from: Elevated temperature and acclimation time affect metabolic performance in the heavily exploited Nile perch of Lake Victoria

description: Increasing water temperatures due to anthropogenic climate change are
 predicted to negatively impact the aerobic metabolic performance of
 aquatic ectotherms. Specifically, it has been hypothesized that thermal
 increases result in reductions in aerobic scope (AS), which lead to
 decreases in energy available for essential fitness and performance
 functions. Consequences of warming are anticipated to be especially severe
 for warm-adapted tropical species as they are thought to have narrow
 thermal windows and limited plasticity for coping with elevated
 temperatures. In this study we test how predicted warming may affect the
 aerobic performance of Nile perch (Lates niloticus), a
 commercially-harvested fish species in the Lake Victoria basin of East
 Africa. We measured critical thermal maxima (CTmax) and key metabolic
 variables such as AS and excess post-exercise oxygen consumption (EPOC)
 across a range of temperatures, and compared responses between acute
 (3-day) exposures and 3-week acclimations. CTmax increased with
 acclimation temperature, however 3-week acclimated fish had higher overall
 CTmax than acutely-exposed individuals. Nile perch also showed the
 capacity to increase or maintain high AS even at temperatures well beyond
 their current range, however acclimated Nile perch had lower AS compared
 to acutely-exposed fish. These changes were accompanied by lower EPOC,
 suggesting that drops in AS may reflect improved energy utilization after
 acclimation, a finding that is supported by improvements in growth at high
 temperatures over the acclimation period. Overall, the results challenge
 predictions that tropical species have limited thermal plasticity, and
 that high temperatures will be detrimental due to limitations in AS.
description: Nile perch metabolic
 traits and CTmaxSheet 1 contains
 standard and maximum metabolic rates (SMR and MMR), aerobic scope (AS),
 excess post-exercise oxygen consumption (EPOC), and recovery time (RT)
 data for Nile perch acutely exposed to a range of treatment temperatures.
 Sheet 2 contains the same data for Nile perch acclimated for 21 days
 (3-weeks) plus standard growth rate (SGR) and condition data. Sheet 3
 contains CTmax data for both acclimated and acutely exposed Nile perch.
 Final fish mass (W), standard length (SL) and total length (TL) are
 included in each sheet.Data_Nile
 perch_metabolism_CTmax.xlsx
DOI: 10.5061/dryad.5tv5d
title: Data from: Two complete mitochondrial genomes from Praticolella mexicana Perez, 2011 (Polygyridae) and gene order evolution in Helicoidea (Mollusca, Gastropoda)

description: Helicoidea is a diverse group of globally distributed land snails. While
 much is known regardingthe relationships of helicoid taxa, comparatively
 little is known about the evolution of themitochondrial genome in the
 superfamily. We sequenced two complete mitochondrial genomesfrom
 Praticolella mexicana Perez, 2011 representing the first such data from
 the helicoid familyPolygyridae, and used them in an evolutionary analysis
 of mitogenomic gene order. We foundthe mitochondrial genome of P. mexicana
 to be 14,008 bp in size, possessing the typical 37metazoan genes. Multiple
 alternate stop codons are used, as are incomplete stop codons,
 andmitogenome size and nucleotide content is consistent with other
 helicoid species. Our analysis ofgene order suggested that Helicoidea has
 undergone five mitochondrial rearrangements in thepast. Four
 rearrangements were limited to tRNA genes, including one
 homoplasticrearrangement in Helicidae and (Bradybaenidae+Camaena+P.
 mexicana). The fifthrearrangement, unique to Aegista, involved a protein
 coding gene.
description: mt gene
 orderMitochondrial gene order
 data from 18 taxa (both P. mexicana samples included) coded for use in
 MLGO. Names are abbreviated since MLGO does not support long taxon names.
 See manuscript for how genes and strand orientation were
 coded.geneorder.txtIndividual gene filesThirteen fasta files, one for each protein-coding mt gene, containing the translated amino acid sequence for 18 taxa. Sequences in each file are not aligned.genesequences.zip
DOI: 10.5061/dryad.172hm
title: Data from: Natural and anthropogenic influences on the population structure of white-tailed eagles in the Carpathian Basin and Central Europe

description: European populations of the white-tailed eagle (Haliaeetus albicilla)
 suffered a drastic decline during the 20th century. In many countries,
 only a few dozen breeding pairs survived or the species disappeared
 completely. By today, the populations have recovered, naturally or through
 restocking (e.g. in Scotland or the Czech Republic). In the Carpathian
 Basin, which is now a stronghold in southern Europe for the species in the
 southern part of the distribution range with more than 500 breeding pairs,
 only about 50 pairs survived the bottleneck. This region provides
 important wintering places for individuals arriving from different regions
 of Eurasia. In the present study, we investigated 249 DNA samples from
 several European countries, using 11 microsatellites and mitochondrial
 control region sequences (499 bp), to answer two main questions: 1) Did
 the Carpathian Basin population recover through local population expansion
 or is there a significant gene flow from more distant populations as well?
 2) Does the Czech population show signs in its genetic structure of the
 restocking with birds of unknown origin? Our microsatellite data yielded
 three genetically separate lineages within Europe: northern, central and
 southern, the latter being present exclusively in the Carpathian Basin.
 Sequencing of mitochondrial DNA revealed that there is one haplotype (B12)
 which is not only exclusive to the Carpathian Basin but it is frequent in
 this population. Our results suggest that in accordance with the
 presumably philopatric behaviour of the species, recovery of the
 Carpathian Basin population was mainly local, but some of the wintering
 birds coming from the northern and central populations contributed to its
 genetic composition as well. We detected considerably higher proportions
 of northern birds within the Czech Republic compared to the neighbouring
 areas, making it likely that parents of the reintroduced birds came from
 northern populations.
description: Individual genotypes of
 European white-tailed eaglesThis TAB-delimited text
 file contains genotypes from 11 nuclear microsatellite loci and
 approximate locations of white-tailed eagles from across Europe.
 Additionally, haplotypes from the mitochondrial control region based on
 499 bp fragments are shown for each sequenced individual. Further details
 are described in the file.individual_genotypes_for_DRYAD-TAB_delimited-20160329.txt
DOI: 10.5061/dryad.qh03c
title: Data from: Psychostimulant-induced testicular toxicity in mice: evidence of cocaine and caffeine effects on the local dopaminergic system

description: Several organ systems can be affected by psychostimulant toxicity.
 However, there is not sufficient evidence about the impact of
 psychostimulant intake on testicular physiology and catecholaminergic
 systems. The aim of the present study was to further explore potential
 toxic consequences of chronic exposure to cocaine, caffeine, and their
 combination on testicular physiology. Mice were injected with a 13-day
 chronic binge regimen of caffeine (3x5mg/kg), cocaine (3×10mg/kg), or
 combined administration. Mice treated with cocaine alone or combined with
 caffeine showed reduced volume of the seminiferous tubule associated to a
 reduction in the number of spermatogonia. Cocaine-only and combined
 treatments induced increased lipid peroxidation evaluated by TBARS assay
 and decreased glutathione peroxidase mRNA expression. Importantly,
 caffeine-cocaine combination potentiated the cocaine-induced germ cell
 loss, and induced pro-apoptotic BAX protein expression and diminished
 adenosine receptor A1 mRNA levels. We analyzed markers of dopaminergic
 function in the testis and detected the presence of tyrosine hydroxylase
 (TH) in the cytoplasm of androgen-producing Leydig cells, but also in
 meiotic germs cells within seminiferous tubules. Moreover, using
 transgenic BAC-Drd1a-tdTomato and D2R-eGFP mice, we report for the first
 time the presence of dopamine receptors (DRs) D1 and D2 in testicular
 mouse Leydig cells. Interestingly, the presence of DRD1 was also detected
 in the spermatogonia nearest the basal lamina of the seminiferous tubules,
 which did not show TH staining. We observed that psychostimulants induced
 downregulation of DRs mRNA expression and upregulation of TH protein
 expression in the testis. These findings suggest a potential role of the
 local dopaminergic system in psychostimulant-induced testicular pathology.
description: Gonzalez et al
 Dataraw data and statistical
 analysisGonzalez et al
 Dryad.xlsx
DOI: 10.5061/dryad.h6qm7
title: Data from: Monoamine abnormalities in the SAPAP3 knockout model of obsessive-compulsive disorder-related behaviour

description: Obsessive-compulsive disorder (OCD) is a leading cause of illness-related
 disability, but the neuralmechanisms underlying OCDsymptoms are unclear.
 One potential mechanism of OCD pathology is monoamine dysregulation.
 Because of the difficulty of studying monoamine signalling in patients,
 animal models offer a viable alternative to understanding this aspect of
 OCD pathophysiology. We used HPLC to characterize post-mortem monoamine
 levels in lateral orbitofrontal cortex (OFC), medial OFC, medial
 prefrontal cortex and dorsal and ventral striatum of SAPAP-3 knockout (KO)
 mice, a well-validated model of compulsive-like behaviours in OCD. As
 predicted from previous studies, excessive grooming was significantly
 increased in SAPAP-3 KO mice. Overall levels of the serotonin metabolite
 5-hydroxyindoleacetic acid (HIAA) and the ratio of 5HIAA/serotonin
 (serotonin turnover) were increased in all cortical and striatal regions
 examined. In addition, dihydroxyphenylacetic acid/dopamine ratio was
 increased in lateral OFC, and HVA/dopamine ratio was increased in lateral
 and medial OFC. No baseline differences in serotonin or dopamine tissue
 content were observed.These data provide evidence of monoaminergic
 dysregulation in a translational model of OCD symptoms and are consistent
 with aberrant cortical and striatal serotonin and dopamine
 release/metabolism in SAPAP-3 KO mice. These results are guiding ongoing
 experiments using circuit and celltype specific manipulations of dopamine
 and serotonin to determine the contributions of these monoaminergic
 systems to compulsive behaviours, and serve here as a touchstone for an
 expanded discussion of these techniques for precise circuit dissection.
description: Raw
 DataThis file contains the
 raw data for each subject/brain regionJWood
 09.07.16.xlsx
DOI: 10.5061/dryad.d1nm3
title: Data from: Does landscape connectivity shape local and global social network structure in white-tailed deer?

description: Intraspecific social behavior can be influenced by both intrinsic and
 extrinsic factors. While much research has focused on how characteristics
 of individuals influence their roles in social networks, we were
 interested in the role that landscape structure plays in animal sociality
 at both individual (local) and population (global) levels. We used female
 white-tailed deer (Odocoileus virginianus) in Illinois, USA, to
 investigate the potential effect of landscape on social network structure
 by weighting the edges of seasonal social networks with association rate
 (based on proximity inferred from GPS collar data). At the local level, we
 found that sociality among female deer in neighboring social groups (n =
 36) was mainly explained by their home range overlap, with two exceptions:
 1) during fawning in an area of mixed forest and grassland, deer whose
 home ranges had low forest connectivity were more social than expected;
 and 2) during the rut in an area of intensive agriculture, deer inhabiting
 home ranges with high amount and connectedness of agriculture were more
 social than expected. At the global scale, we found that deer populations
 (n = 7) in areas with highly connected forest-agriculture edge, a high
 proportion of agriculture, and a low proportion of forest tended to have
 higher weighted network closeness, although low sample size precluded
 statistical significance. This result implies that infectious disease
 could spread faster in deer populations inhabiting such landscapes. Our
 work advances the general understanding of animal social networks,
 demonstrating how landscape features can underlie differences in social
 behavior both within and among wildlife social networks.
description: Koen_global_dataAverage network closeness for 7 groups of female white-tailed deer in southern and central Illinois, USA. Data include proportion of forest, agriculture, and forest-agriculture edge (and the average current density obtained from program Circuitscape for each of those classes) for each study area. Notes in the column headings in the .xls data file describe each column.Koen_local_dataSummarized data from GPS-collared female white-tailed deer in southern and central Illinois, USA. Data include, for each individual deer (by study area and season), social network characteristics (degree, average edge weight), home range overlap, and the proportion of forest, agriculture, and forest-agriculture edge (and the average current density obtained from program Circuitscape for each of those classes) within each home range (95% kernel density contour). Notes in the column headings in the .xls data file describe each column.