cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2p80260
title: Data from: How do seabirds modify their search behaviour when encountering fishing boats?

description: Seabirds are well known to be attracted by fishing boats to forage on
 offal and baits. We used recently developed loggers that record accurate
 GPS position and detect the presence of boats through their radar
 emissions to examine how albatrosses use Area Restricted Search (ARS) and
 if so, have specific ARS behaviours, when attending boats. As much as
 78.5% of locations with a radar detection (contact with boat) during a
 trip occurred within ARS: 36.8% of all large-scale ARS (n=212) and 14.7%
 of all small-scale ARS (n=1476) were associated with the presence of a
 boat. During small-scale ARS, birds spent more time and had greater
 sinuosity during boat-associated ARS compared with other ARS that we
 considered natural. For, small-scale ARS associated with boats, those
 performed over shelves were longer in duration, had greater sinuosity, and
 birds spent more time sitting on water compared with oceanic ARS
 associated with boats. We also found that the proportion of small-scale
 ARS tend to be more frequently nested in larger-scale ARS was higher for
 birds associated with boats and that ARS behaviour differed between
 oceanic (tuna fisheries) and shelf-edge (mainly Patagonian toothfish
 fisheries) habitats. We suggest that, in seabird species attracted by
 boats, a significant amount of ARS behaviours are associated with boats,
 and that it is important to be able to separate ARS behaviours associated
 to boats from natural searching behaviours. Our study suggest that
 studying ARS characteristics should help attribute specific behaviours
 associated to the presence of boats and understand associated risks
 between fisheries.
description: How do seabirds modify
 their search behaviour when encountering fishing boats?tracks and interactions
 with boats for Wandering albatrosses of Crozet IslandsData_Corbeau et
 al_2019_PLOSONE.7z
DOI: 10.5061/dryad.pp281n6
title: Data from: Distribution and human‐caused mortality of Persian leopards Panthera pardus saxicolor in Iran, based on unpublished data and Farsi gray literature

description: Gray literature and data from unpublished sources can provide important
 scientific information that has not been published scientifically. The
 Persian leopard (hereafter leopard) Panthera pardus saxicolor is classed
 as endangered on the Red List of the International Union for Conservation
 of Nature and also is one of the least-studied subspecies of leopard. It
 occurs in the Caucasus and Central and Southwest Asia. Iran contains more
 than 75% of the leopard’s extant range, and the leopard population in this
 country serves as a source for neighboring countries. In this study, we
 determined the distribution and human caused mortality of leopards in
 Iran, by reviewing unpublished data and Farsi gray literature (which
 includes government reports) between 1 January 2010 and 30 December 2018.
 We created the most recent distribution map of the leopard in Iran. Our
 data display that human caused mortality of leopard in Iran mostly
 includes poaching and intentional poisoning, and road-kill.
description: Table S1 Records of
 Persian leopard presence in Iran between 1 January 2010 and 30 December
 2018.Records of Persian
 leopard presence in Iran between 1 January 2010 and 30 December
 2018.Table
 S1.xlsxTable S2 Details of
 Persian leopard mortalities recorded in Iran between 1 January 2010 and 30
 December 2018.Details of Persian
 leopard mortalities recorded in Iran between 1 January 2010 and 30
 December 2018.Table
 S2.xlsx
DOI: 10.5061/dryad.6t8vb41
title: Data from: Spatial and temporal variation in nest temperatures forecasts sex ratio skews in a crocodilian with environmental sex determination

description: Species displaying temperature-dependent sex determination (TSD) are
 especially vulnerable to the effects of a rapidly changing global climate
 due to their profound sensitivity to thermal cues during development.
 Predicting the consequences of climate change for these species, including
 skewed offspring sex ratios, depends on understanding how climatic factors
 interface with features of maternal nesting behavior to shape the
 developmental environment. Here, we measure thermal profiles in 86 nests
 at two geographically distinct sites in the northern and southern regions
 of the American alligator’s (Alligator mississippiensis) geographic range
 and examine the influence of both climatic factors and maternally-driven
 nest characteristics on nest temperature variation. Changes in daily
 maximum air temperatures drive annual trends in nest temperatures, while
 variation in individual nest temperatures is also related to local habitat
 factors and microclimate characteristics. Without any compensatory nesting
 behaviors, nest temperatures are projected to increase by 1.6° - 3.7°C by
 the year 2100, and these changes are predicted to have dramatic
 consequences for offspring sex ratios. Exact sex ratio outcomes vary
 widely depending on site and emission scenario as a function of the unique
 temperature-by-sex reaction norm exhibited by all crocodilians. By
 revealing the ecological drivers of nest temperature variation in the
 American alligator, this study provides important insights into the
 potential consequences of climate change for crocodilian species, many of
 which are already threatened by extinction.
description: Alligator nest
 temperature and nest characteristic dataNest temperature data
 and descriptive data on nest characteristics at Kennedy Space
 Center/Merritt Island National Wildife Refuge (KSC) from American
 alligator nests monitored between 2010-2017.NESTMODEL_SharedData.xlsx
DOI: 10.5061/dryad.j4d7r61
title: Data from: Impacts of nutrient subsidies on salt marsh arthropod food webs: a latitudinal survey

description: Anthropogenic nutrient inputs into native ecosystems cause fluctuations in
 resources that normally limit plant growth, which has important
 consequences for associated foodwebs. Such inputs from agricultural and
 urban habitats into nearby natural systems are increasing globally and can
 be highly variable. Despite the global increase in
 anthropogenically-derived nutrient inputs into native ecosystems, the
 consequences of variation in subsidy amount on native plants and their
 associated foodwebs are poorly known. Salt marshes represent an ideal
 system to address the differential impacts of nutrient inputs on ecosystem
 and community dynamics because human development and other anthropogenic
 activities lead to recurrent introductions of nutrients into these natural
 systems. Previously, we have found in manipulative experiments that
 arthropod abundance increases in response to nutrient enrichment, with
 predators being the trophic group most strongly affected. We conducted a
 survey of Atlantic coastal Spartina marshes to test whether such local
 responses are indicative of responses at a landscape level. We examined
 the most abundant arthropod species associated with Spartina coastal
 marshes that receive variable amounts of anthropogenic nitrogen, and
 tested how this response varied across different arthropod functional
 groups (herbivores, epigeic feeders, and predators). Similar to what we
 found at a local scale, nutrient subsidies alter the trophic structure of
 the arthropod assemblage by changing the relative abundances of various
 feeding groups. Variable responses among predators to nitrogen density
 could be partly explained by diet breadth (e.g. generalists vs.
 specialists). Herbivores had a negative response to increasing plant
 nitrogen density; specialist predators tracked their herbivore prey and
 thus also responded negatively to nitrogen density. However, generalists
 were not negatively affected by nitrogen density and indeed some
 generalist predators responded positively to nitrogen density. Thus, the
 overall predator-to-herbivore ratio was also positively associated with
 nitrogen density. Our research helps us to understand how long-term
 nutrient enrichment of native ecosystems by human activities affects
 arthropod assemblages and foodweb dynamics.
description: MarshSurveyData for
 FrontiersPlant data and arthropod
 data.
DOI: 10.5061/dryad.64t161m
title: Fluorescent biomarkers demonstrate prospects for spreadable vaccines to control disease transmission in wild bats

description: Vaccines that autonomously transfer among individuals have been proposed
 as a strategy to control infectious diseases within wildlife populations.
 However, understanding rates of spread and epidemiological efficacy in
 real world systems remain elusive. Here, we investigated whether topical
 vaccines that transfer among bats through social contacts can control
 vampire bat rabies, a medically and economically important zoonosis in
 Latin America. Field experiments in 3 Peruvian bat colonies which used
 fluorescent biomarkers as a proxy for the bat-to-bat transfer and
 ingestion of an oral vaccine revealed that vaccine transfer would increase
 population-level immunity up to 2.6 times beyond the same effort using
 conventional, non-spreadable vaccines. Mathematical models demonstrated
 that observed levels of vaccine transfer would reduce the probability,
 size, and duration of rabies outbreaks, even at low, but realistically
 achievable levels of vaccine application. Models further predicted that
 existing vaccines provide substantial advantages over culling bats, the
 policy currently implemented in North, Central, and South America. Linking
 field studies with biomarkers to mathematical models can inform how
 spreadable vaccines may combat pathogens of health and conservation
 concern prior to costly investments in vaccine design and testing.
description: Data.S1.CaptureDataThis file contains capture histories, fluorescent biomarker application histories and fluorescent biomarker detection histories for 709 individually marked vampire bats from 3 colonies in Peru.
DOI: 10.5281/zenodo.18393036
title: Long-History PCA in a Dynamic Factor Model with Weak Loadings

description: To reproduce the results reported in “Long-History PCA in a Dynamic Factor Model with Weak Loadings,” users must download the accompanying data files and place them in the designated directory. Detailed instructions are provided in the ReadMe.txt file available on the journal’s website.
description: IMPORTANT NOTICE

The raw data files included in previous versions of this repository have been removed due to licensing restrictions imposed by the data vendor (WRDS).

This version provides all codes required to download the data directly from the authorized data source and to reproduce all results in the paper for users with legitimate access to the data.
DOI: 10.5061/dryad.gt160v2
title: Data from: Presynaptic GABAB receptors functionally uncouple somatostatin interneurons from the active hippocampal network

description: Information processing in cortical neuronal networks relies on properly
 balanced excitatory and inhibitory neurotransmission. A ubiquitous motif
 for maintaining this balance is the somatostatin interneuron (SOM-IN)
 feedback microcircuit. Here, we investigate the modulation of this
 microcircuit by presynaptic GABAB receptors (GABABRs) in the rat
 hippocampus. Whole-cell recordings from SOM-INs reveal that both
 excitatory and inhibitory synaptic inputs are strongly inhibited by
 GABABRs, while optogenetic activation of the interneurons shows that their
 inhibitory output is also strongly suppressed. Electron microscopic
 analysis of immunogold-labelled freeze-fracture replicas confirms that
 GABABRs are highly expressed presynaptically at both input and output
 synapses of SOM-INs. Activation of GABABRs selectively suppresses the
 recruitment of SOM-INs during gamma oscillations induced in vitro. Thus,
 axonal GABABRs are positioned to efficiently control the input and output
 synapses of SOM-INs and can functionally uncouple them from local network
 with implications for rhythmogenesis and the balance of entorhinal versus
 intrahippocampal afferents.
description: Booker-et-al-eLife-SOM-IN-GABAB-SourceData-20190905 Electrophysiological, optogenetic and quantitative electron microscopic data sets presented on the manuscript by Booker et al. 2019 eLife submitted. Excel spreadsheet contains tabs associated with figures from the manuscript.
DOI: 10.5061/dryad.g003051
title: Data from: Increased dystrophin production with golodirsen in patients with Duchenne muscular dystrophy

description: Objective To report safety, pharmacokinetics, exon 53 skipping, and
 dystrophin expression in golodirsen-treated patients with Duchenne
 muscular dystrophy (DMD) amenable to exon 53 skipping. Methods Part 1 was
 a randomized, double-blind, placebo-controlled, 12-week dose titration of
 once-weekly golodirsen; Part 2 is an ongoing, open-label evaluation.
 Safety and pharmacokinetics were primary and secondary objectives of Part
 1. Primary biological outcome measures of part 2 were blinded exon
 skipping and dystrophin protein production on muscle biopsies (baseline,
 Week 48) evaluated, respectively using reverse transcription PCR and
 western blot and immunohistochemistry. Results Twelve patients were
 randomized to receive golodirsen (n=8) or placebo (n=4) in Part 1. All
 from Part 1 plus 13 additional patients received 30 mg/kg golodirsen in
 Part 2. Safety findings were consistent with those previously observed in
 pediatric DMD patients. Most of the study drug was excreted within 4 hours
 following administration. A significant increase in exon 53 skipping was
 associated with ~16-fold increase over baseline in dystrophin protein
 expression at Week 48, with a mean percent normal dystrophin protein
 standard of 1.019% (range, 0.09%-4.30%). Sarcolemmal localization of
 dystrophin was demonstrated by significantly increased dystrophin positive
 fibers (Week 48, p&lt;0.001); and a positive correlation
 (Spearman-r=0.663; p&lt;0.001) between dystrophin protein change from
 baseline, measured by western blot and immunohistochemistry.
description: Supplementary Materials include additional methodology details,
 e-tables and e-figures. Please refer to the updated file, dated June 18,
 2020
DOI: 10.5061/dryad.t38b3k2
title: Data from: Female loggerhead sea turtles (Caretta caretta L.) rarely remate during nesting season

description: The goal of this study was to assess the consequences of single versus
 multiple paternity by identifying paternity of clutches per female to
 identify if there were detectable costs or benefits. Multiple mating can
 occur when the benefits of mating outweigh the costs, but if costs and
 benefits are equal, no pattern is expected. Previous research on
 loggerhead sea turtle (Caretta caretta) populations found male-biased
 breeding sex ratios and multiple mating by many females nesting in
 southwestern Florida. A sample of nesting loggerhead females who laid more
 than one nest over the course of the season and a subset of their
 hatchlings were examined from 36 clutches in 2016 on Sanibel Island,
 Florida. Males that fathered hatchlings in the first clutch sampled were
 identified in subsequent clutches. Interestingly, 75% of the females
 analyzed had mated singly. No male was represented in more than one
 female’s clutches. The results suggest that females likely mate at the
 beginning of the season and use stored sperm for multiple clutches.
 Evidence for mating between laying events was limited. There was no
 consistent pattern across the subsequent multiple paternity clutches,
 suggesting benefits to loggerhead females likely equal their costs and
 subsequent mating is likely determined by female preference.
description: Repeating Nests FSA
 Files.fsa files for up to 20
 hatchlings per nest of all repeat nests from 2016.
 Zipped.Cc
 Repeat Nests FSA.zipRepeating Females
 FSA.fsa files of repeating
 females from 2016 on Sanibel Island Florida.Nesters and Hatchling
 Data 2016First tab is raw data of
 nesters from 2016 on Sanibel Island. Includes morphometrics of encountered
 females, nest date, hatch date, number of males identified in nests,
 emergence and hatch success. Second tab is hatchling raw data
 morphometrics, including nest ID, straight carapace length and
 width.
DOI: 10.5061/dryad.td3fb01
title: Data from: Microbiome responses during virulence adaptation by a phloem-feeding insect to resistant near-isogenic rice lines

description: The microbiomes of phloem feeding insects include functional bacteria and
 yeasts essential for herbivore survival and development. Changes in
 microbiome composition are implicated in virulence adaptation by
 herbivores to host plant species or host populations (including crop
 varieties). We examined patterns in adaptation by the green leafhopper,
 Nephotettix virescens, to near-isogenic rice lines (NILs) with one or two
 resistance genes and the recurrent parent T65, without resistance genes.
 Only the line with two resistance genes was effective in reducing
 leafhopper fitness. After 20 generations on the resistant line, selected
 leafhoppers attained similar survival, weight gain and egg laying to
 leafhoppers that were continually reared on the susceptible recurrent
 parent, indicating that they had adapted to the resistant host. By
 sequencing the 16s rRNA gene, we described the microbiome of leafhoppers
 from colonies associated with five collection sites, and continually
 reared or switched between NILs. The microbiomes included 69-119 OTUs of
 which 44 occurred in ≥ 90% of samples. Of these, 14 OTUs were assigned to
 the obligate symbiont Candidatus sulcia clade. After 20 generations of
 selection, collection site had a greater effect than host plant on
 microbiome composition. Six bacteria genera, including Candidatus sulcia,
 were associated with leafhopper virulence. However, there was significant
 within-treatment, site-related variability in the prevalence of these taxa
 such that the mechanisms underlying their association with virulence
 remain to be determined. Our results imply that these taxa are associated
 with leafhopper nutrition. Ours is the first study to describe microbiome
 diversity and composition in rice leafhoppers. We discuss our results in
 light of the multiple functions of herbivore microbiomes during virulence
 adaptation in insect herbivores.
description: Bacterial OTUs
 associated with leafhopper colonies from the PhilippinesExcel file containing
 lists of OTUs based on targeted sequencing of 16s rRNA gene from green
 leafhopper, Nephotettix virescens, populations artificially selected on
 near-isogenic rice lines with GRH2, GRH4 or GRH2+GRH4 resistance genes and
 on the recurrent parent T65 without resistance genes. Classification of
 bacterial OTUs based on megablast (NCBI Resource Coordinators 2016) used
 against the NCBI database are provided for each numbered OTU. The
 leafhopper colonies were collected at 5 locations in the Philippines:
 Batangas, Quezon, Laguna, Rizal, and San PabloOTU data
 microbiome.xls
DOI: 10.5061/dryad.qc23720
title: Data from: Conservation and novelty in the microRNA genomic landscape of hyperdiverse cichlid fishes

description: MicroRNAs (miRNAs) play crucial roles in the post-transcriptional control
 of messenger RNA (mRNA). These miRNA-mRNA regulatory networks are present
 in nearly all organisms and contribute to development, phenotypic
 divergence, and speciation. To examine the miRNA landscape of cichlid
 fishes, one of the most species-rich families of vertebrates, we profiled
 the expression of both miRNA and mRNA in a diverse set of cichlid
 lineages. Among these, we found that conserved miRNAs differ from recently
 arisen miRNAs (i.e. lineage specific) in average expression levels, number
 of target sites, sequence variability, and physical clustering patterns in
 the genome. Furthermore, conserved miRNA target sites tend to be enriched
 at the 5’ end of protein-coding gene 3'UTRs. Consistent with the
 presumed regulatory role of miRNAs, we detected more negative correlations
 between the expression of miRNA-mRNA functional pairs than in random
 pairings. Finally, we provide evidence that novel miRNA targets sites are
 enriched in genes involved in protein synthesis pathways. Our results show
 how conserved and evolutionarily novel miRNAs differ in their contribution
 of the genomic landscape and highlight their particular evolutionary roles
 in the adaptive diversification of cichlids.
description: mRNA_exp_tpm.tableNormalized expression values (TPM) of the 48 mRNA samples included in the study.miRNA_exp_norm.tableNormalized expression values of the 48 microRNA samples included in the study.Aall.strg.faReference-guided transcriptome assembly of the African cichlid species Astatoreochromis alluaudi.Acen.strg.faReference-guided transcriptome assembly of the Neotropical cichlid species Archocentrus centrarchus.Asiq.strg.faReference-guided transcriptome assembly of the Neotropical cichlid species Amatitlania siquia.Azal.strg.faReference-guided transcriptome assembly of the Neotropical cichlid species Amphilophus zaliosus.Hbur.strg.faReference-guided transcriptome assembly of the African cichlid species Astatotilapia burtoni.Mzeb.strg.faReference-guided transcriptome assembly of the African cichlid species Maylandia zebra.Nbri.strg.faReference-guided transcriptome assembly of the African cichlid species Neolamprologus brichardi.Pnye.strg.faReference-based transcriptome assembly of the African cichlid species Pundamilia nyererei.Aall_Trinity.faDe novo transcriptome assembly of the African cichlid species Astatoreochromis alluaudi.Asiq_Trinity.faDe novo transcriptome assembly of the Neotropical cichlid species Amatitlania siquia.
DOI: 10.5061/dryad.7k6502b
title: Data from: Soil functional responses to drought under range-expanding and native plant communities

description: 1. Current climate warming enables plant species and soil organisms to
 expand their range to higher latitudes and altitudes. At the same time,
 climate change increases the incidence of extreme weather events such as
 drought. While it is expected that plants and soil organisms originating
 from the south are better able to cope with drought, little is known about
 the consequences of their range shifts on soil functioning under drought
 events. 2. Here, we test how range-expanding plant species and soil
 communities may influence soil functioning under drought. We performed a
 full-factorial outdoor mesocosm experiment with plant communities of range
 expanders or related natives, with soil inocula from the novel or the
 original range, with or without summer drought. We measured litter
 decomposition, carbon mineralization and enzyme activities,
 substrate-induced respiration, and the relative abundance of soil
 saprophytic fungi immediately after drought and at 6 and 12 weeks after
 rewetting. 3. Drought decreased all soil functions regardless of plant and
 soil origin except one; soil respiration was less reduced in soils of
 range-expanding plant communities, suggesting stronger resistance to
 drought. After rewetting, soil functioning responses depended on plant and
 soil origin. Soils of native plant communities with a history of drought
 had more litter mass loss and higher relative abundance of saprophytic
 fungi than soils without drought and soils of range expanders. Functions
 of soil from range expanders recovered in a more conservative manner than
 soils of natives, as litter mass loss did not exceed the control rates. At
 the end of the experiment, after rewetting, most soil functions in
 mesocosms with drought history did not differ anymore from the control. 4.
 We conclude that functional consequences of range expanding plants and
 soil biota may interact with effects of drought, and that these effects
 are most prominent during the first weeks after rewetting of the soil.
description: Manrubia_etal_datasoil data, decomposition, enzyme activity and plant biomass