cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7ht92p7
title: Data from: Conspecific olfactory preferences and interspecific divergence in odor cues in a chickadee hybrid zone

description: Understanding how mating cues promote reproductive isolation upon
 secondary contact is important in describing the speciation process in
 animals. Divergent chemical cues have been shown to act in reproductive
 isolation across many animal taxa. However, such cues have been overlooked
 in avian speciation, particularly in passerines, in favor of more
 traditional signals such as song and plumage. Here we aim to test the
 potential for odor to act as a mate choice cue, and therefore contribute
 to premating reproductive isolation between the black-capped (Poecile
 atricapillus) and Carolina chickadee (P. carolinensis) in eastern
 Pennsylvania hybrid zone populations. Using gas chromatography-mass
 spectrometry, we document significant species differences in uropygial
 gland oil chemistry, especially in the ratio of ester to non-ester
 compounds. We also show significant preferences for conspecific over
 heterospecific odor cues in wild chickadees using a Y-maze design. Our
 results suggest that odor may be an overlooked but important mating cue in
 these chickadees, potentially promoting premating reproductive isolation.
 We further discuss several promising avenues for future research in
 songbird olfactory communication and speciation.
description: GC Peak Relative
 AbundancesThis file contains
 information for 81 chickadees. The first four columns contain the species,
 sex, sampling date, and simplified sampling season for each individual.
 The remaining columns contain the gas chromatogram relative abundances of
 compounds eluted at the specified retention time
 (minutes).GC_peaks.csvPreen Oil AnalysisThis file contains the R code to be used with the "GC_peaks.csv" file.Odor PreferencesThis data contains information for two no-choice trials conducted on 55 chickadees. In order, the columns specify: sex, percent black-capped ancestry, species, test date for black-capped odor, time spent with black-capped odor (seconds), test date for Carolina odor, time spent with Carolina odor (seconds), time spent with conspecific odor (seconds), time spent with heterospecific odor (seconds), the difference between time spent with conspecific odor and time spent with heterospecific odor (seconds), and Julian day.odor_preferences.csvOdor Preferences CodeThis file contains the R code to be used with the "odor_preferences.csv" file.
DOI: 10.5061/dryad.5qv7v47
title: Data from: Parasite infections in a social carnivore: evidence of their fitness consequences and factors modulating infection load

description: There are substantial individual differences in parasite composition and
 infection load in wildlife populations. Few studies have investigated the
 factors shaping this heterogeneity in large wild mammals or the impact of
 parasite infections on Darwinian fitness, particularly in juveniles. A
 host’s parasite composition and infection load can be shaped by factors
 that determine contact with infective parasite stages and those that
 determine the host’s resistance to infection, such as abiotic and social
 environmental factors, and age. Host-parasite interactions and synergies
 between co-infecting parasites may also be important. We test predictions
 derived from these different processes to investigate factors shaping
 infection loads (faecal egg/oocyte load) of two energetically costly
 gastrointestinal parasites: the hookworm Ancylostoma and the intracellular
 Cystoisospora, in juvenile spotted hyenas (Crocuta crocuta) in the
 Serengeti National Park, in Tanzania. We also assess whether parasite
 infections curtail survival to adulthood and longevity. Ancylostoma and
 Cystoisospora infection loads declined as the number of adult clan members
 increased, a result consistent with an encounter-reduction effect whereby
 adults reduced encounters between juveniles and infective larvae, but were
 not affected by the number of juveniles in a clan. Infection loads
 decreased with age, possibly because active immune responses to infection
 improved with age. Differences in parasite load between clans possibly
 indicate variation in abiotic environmental factors between clan den
 sites. The survival of juveniles (&lt; 365 days old) to adulthood
 decreased with Ancylostoma load, increased with age and was modulated by
 maternal social status. High-ranking individuals with low Ancylostoma
 loads had a higher survivorship during the first four years of life than
 high-ranking individuals with high Ancylostoma loads. These findings
 suggest that high infection loads with energetically costly parasites such
 as hookworms during early life can have negative fitness consequences.
description: Ferreira_hyena_parasites_Ecol_EvolDataset of juvenile spotted hyenas from 3 clans in the Serengeti National Park, Tanzania. EPG = eggs per gram; Age = Age at time of sampling; Num_of_adults/cubs = Number of adults/cubs in the clan at the time of sampling; Total_Ancylostoma/Cystoisospora_co.infecting_taxa = Number of parasite taxa present other than Ancylostoma/Cystoisospora.Ferreira_et_al_Ecol_Evol.csv
DOI: 10.5061/dryad.g0t911k
title: Data from: Long‐term follow‐up, quality of life and survival of Lambert‐Eaton myasthenic syndrome patients

description: Objective To study survival and characterize long-term functional
 impairments as well as health-related quality of life (HRQOL) of
 Lambert-Eaton myasthenic syndrome (LEMS) patients. Methods In this
 observational study, survival of LEMS patients, separately for non-tumor
 (NT) and small-cell lung cancer (SCLC), was compared to the Dutch general
 population and to patients with SCLC. Disease course in LEMS patients was
 recorded retrospectively. Several scales for functional impairments and
 health-related quality of life were assessed. Results We included 150 LEMS
 patients. Survival was similar to the general population in 65 NT-LEMS
 patients. Tumor survival was significantly longer in 81 SCLC-LEMS patients
 compared to non-LEMS SCLC patients (overall median survival 17 vs. 7.0
 months, p&lt;0.0001). At diagnosis, 39 patients (62%) of 63 patients
 with complete follow-up data were independent for ADL activities,
 improving to 85% at 1-year follow-up. Physical HRQOL composite score
 (55.9) was significantly lower than in the general population (76.3,
 p&lt;0.0001) and comparable to myasthenia gravis (60.5) Mental HRQOL
 composite score was 71.8 in LEMS patients, comparable to the general
 population (77.9, p=0.19) and myasthenia gravis (70.3). Conclusions This
 study shows NT-LEMS patients have normal survival. SCLC-LEMS patients have
 an improved tumor survival, even after correcting for tumor stage. A
 majority of LEMS patients report a stable disease course and remain or
 become independent for self-care after treatment.
description: Supplemental Tables e-1,
 e-2, e-3Supplemental Tables,
 including survival percentages for LEMS patients without (e-1) and with
 associated tumor (e-2), SF36 subdomains for HRQOL in LEMS patients, MG
 patients and the Dutch population as a control group
 (e-3).Supplemental Tables
 06Apr19.docxFigure e-1 flow chart
 inclusionFlow chart for inclusion
 of LEMS patientsSTROBE_checklist_v4
 Lipka AF et al 28Apr19STROBE checklist for
 reports of observational studies
DOI: 10.5061/dryad.k6ck467
title: Data from: Freshwater hydrozoan blooms alter activity and behaviour of territorial cichlids in Lake Tanganyika

description: Jellyfish blooms pose multiple threats to wild fish. Yet, we still know
 little about how blooms impact fitness-related behaviours of fish caught
 within their areas of effect, e.g. for littoral fish that are not able to
 relocate to avoid incoming blooms of stinging jellyfish. Here, we
 documented the behavioural impacts of freshwater jellyfish (Limnocnida
 tanganjicae) blooms on a territorial cichlid (Variabilichromis moorii) as
 well as on the wider community of cichlids in a shallow-water rocky
 habitat of Lake Tanganyika. Compared to non-bloom conditions, V. moorii
 individuals reduced their swimming and territory defence activities during
 jellyfish blooms (each by ~ 50%), but not their foraging or affiliative
 behaviours. Despite this reduction in activity, V. moorii could not
 entirely avoid being stung and preferred to remain closer to the rocky
 substrata as opposed to the more open demersal zone. Many other fishes
 similarly hid among the benthic substrata, changing the composition of the
 fish community in the demersal zone during bloom conditions. Reductions in
 activity could have multiple fitness-related implications for individual
 fish. Understanding these behavioural consequences is an important topic
 of research as blooms are predicted to increase in severity in the future
 especially along coastal habitats.
description: Fish behavior scores and
 transect surveys in jellyfish bloom and non-bloom
 conditionsExcel sheet "fish
 behaviour": The dataset contains data on the observed nests of V.
 moorii (date of Observation, nest ID, number of adult fish in nest, Body
 length of fish), indicates bloom (1) and non-bloom (0) conditions and
 presence (1) and absence (2) of young, and the following data on fish
 behaviour: distance moved (in pixels and body length), as well as counts
 of jellyfish stings, scrapes, feeds, defences and affiliative behaviours.
 Excel sheet "transect surveys": The dataset contains the number
 of individuals per species counted along the transects during jellyfish
 bloom and non-bloom conditions.dryad
 file.csv
DOI: 10.5061/dryad.rd465d6
title: Unique genetic signatures of local adaptation over space and time for diapause, an ecologically relevant complex trait, in Drosophila melanogaster

description: Organisms living in seasonally variable environments utilize cues such as
 light and temperature to induce plastic responses, enabling them to
 exploit favorable seasons and avoid unfavorable ones. Local adapation can
 result in variation in seasonal responses, but the genetic basis and
 evolutionary history of this variation remains elusive. Many insects,
 including Drosophila melanogaster, are able to undergo an arrest of
 reproductive development (diapause) in response to unfavorable conditions.
 In D. melanogaster, the ability to diapause is more common in high
 latitude populations, where flies endure harsher winters, and in the
 spring, reflecting differential survivorship of overwintering populations.
 Using a novel hybrid swarm-based genome wide association study, we
 examined the genetic basis and evolutionary history of ovarian diapause.
 We exposed outbred females to different temperatures and day lengths,
 characterized ovarian development for over 2800 flies, and reconstructed
 their full phased genomes. We found that diapause scored at two different
 developmental cutoffs has modest heritability, and we identified hundreds
 of SNPs associated with each of the two phenotypes. Alleles associated
 with one of the diapause phenotypes tend to be more common at higher
 latitudes, but these alleles do not show predictable seasonal variation.
 The collective signal of many small-effect, clinally varying SNPs can
 plausibly explain latitudinal phenotypic variation seen in North America.
 SNPs associated with diapause do not exhibit signs of recent selective
 sweeps, but most are segregating at relatively high frequencies in Africa,
 suggesting that variation in diapause relies on ancestral polymorphisms.
 Finally, we utilized outdoor mesocosms to track diapause under natural
 conditions. We found that hybrid swarms reared outdoors evolved increased
 propensity for diapause in late fall, whereas indoor control populations
 experienced no such change. Our results indicate that diapause is a
 complex, quantitative trait with different evolutionary patterns across
 time and space.
description: All file names should match the file names found in the code for
 this analysis, located at:
 https://github.com/ericksonp/diapause-scripts-clean
DOI: 10.5061/dryad.g6kh12j
title: Data from: Cooperation with closely bonded individuals reduces cortisol levels in long-tailed macaques

description: Many animal species cooperate with conspecifics in various social
 contexts. While ultimate causes of cooperation are being studied
 extensively, its proximate causes, particularly endocrine mechanisms, have
 received comparatively little attention. Here, we present a study
 investigating the link between the hormone cortisol, cooperation and
 social bonds in long-tailed macaques (Macaca fascicularis). We tested 14
 macaques in a dyadic cooperation task (loose-string paradigm), each with
 two partners of different social bond strength and measured their salivary
 cortisol before and after the task. We found no strong link between the
 macaques’ cortisol level before the task and subsequent cooperative
 success. In contrast, we did find that the act of cooperating in itself
 led to a subsequent decrease in cortisol levels, but only when cooperating
 with closely bonded individuals. Two control conditions showed that this
 effect was not due to the mere presence of such an individual or the
 pulling task itself. Consequently, our study shows an intricate way in
 which the hypothalamic-pituitary-adrenal axis is involved in cooperation.
 Future studies should reveal whether and how our findings are driven by
 the anxiolytic effect of oxytocin, which has been associated with social
 bonding.
DOI: 10.5061/dryad.n710qb3
title: Extinction debt in local habitats: quantifying the roles of random drift, immigration, and emigration

description: We developed a time-dependent stochastic neutral model for predicting
 diverse temporal trajectories of biodiversity change in response to
 ecological disturbance (i.e., habitat destruction) and dispersal dynamic
 (i.e., emigration and immigration). The model is general and predicts how
 transition behaviors of extinction may accumulate according to different
 combination of random drift, immigration rate, emigration rate, and the
 degree of habitat destruction. We show that emigration, the areal size of
 the destroyed habitat, and initial species abundance distribution can
 impact the total biodiversity loss in an intact local area. Among these,
 the species abundance distribution plays the most deterministic role, as
 it directly determines the initial species richness in the local target
 area. In contrast, immigration was found to slow down total biodiversity
 loss and can drive the emergence of species credits (i.e., a gain of
 species) over time. However, emigration process would increase the
 extinction risk of species and accelerate biodiversity loss. Finally but
 notably, we found that a shift in the emigration rate after a habitat
 destruction event may be a new mechanism to generate species credits.
description: R code for generating
 Figs. 1-2 of main text This is the detailed R
 script for generating Figs. 1-2 of the main text. Annotations are provided
 for each command line of the code.
DOI: 10.7272/q62z13fs
title: Frontotemporal Lobar Degeneration (FTLD)

description: This data set was acquired with the aim of determining the structural and
 chemical changes that occur in the brain as a result of frontotemporal
 lobar degeneration (FTLD). The data includes proton density, T1, and
 T2-weighted neuroimages from subjects suffering from FTLD and
 Alzheimer's Disease, as well as a population of matched controls.
description: Data Acquisition Location: San Francisco VA Medical Center;
 Scanner Type: Siemens Vision 1.5T; Coronal T1 MPRAGE (orthogonal to long
 axis of hippocampus): TR=9ms, TE=4ms, TI=300ms, 1x1mm2, 1.5mm slice
 thickness; Coronal MPRAGE (orthogonal to PD, T2): TR=10ms, TE=7ms,
 TI=300ms, 1x1mm2, 1.4mm slice thickness; Axial double spin echo PD
 & T2: TR=2500ms, TE=20/80ms, 1x1.25mm2, 3mm slice
 thickness.
DOI: 10.5061/dryad.tq645ft
title: Data from: Scientific output scales with resources. A comparison of US and European Universities

description: By using a comprehensive dataset of US and European universities, we
 demonstrate super-linear scaling between university revenues and their
 volume of publications and (field-normalized) citations. We show that this
 relationship holds both in the US and in Europe. In terms of resources,
 our data show that three characteristics differentiate the US system: (1)
 a significantly higher level of resources for the entire system, (2) a
 clearer distinction between education-oriented institutions and doctoral
 universities and (3) a higher concentration of resources among doctoral
 universities. Accordingly, a group of US universities receive a much
 larger amount of resources and have a far higher number of publications
 and citations when compared to their European counterparts. These results
 demonstrate empirically that international rankings are by and large
 richness measures and, therefore, can be interpreted only by introducing a
 measure of resources. Implications for public policies and institutional
 evaluation are finally discussed.
description: ETER_IPEDS_ISCED6 -
 data_publicationStata file with all
 variables needed for the analysis
DOI: 10.5061/dryad.3nd978g
title: Data from: Aircraft sound exposure leads to song frequency decline and elevated aggression in wild chiffchaffs

description: 1. The ubiquitous anthropogenic low-frequency noise impedes communication
 by masking animal signals. To overcome this communication barrier, animals
 may increase the frequency, amplitude and delivery rate of their acoustic
 signals, making them more easily heard. However, a direct impact of
 intermittent, high-level aircraft noise on birds’ behaviour living close
 to a runway has not been studies in detail. 2. We recorded common
 chiffchaffs Phylloscopus collybita songs near two airports and nearby
 control areas, and we measured sound levels in their territories at
 Manchester airport. The song recordings were made in between aircraft
 movements, when ambient sound levels were similar between airport and
 control populations. We also conducted playback experiments at the airport
 and a control population to test the salience of airport, and control
 population specific songs. 3. In contrast to the general pattern of
 increased song frequency in noisy areas, we show that common chiffchaffs
 at airports show a negative relationship between noise exposure level and
 song frequency. 4. Experimental data show that chiffchaffs living near
 airports also respond more aggressively to song playback. 5. Since the
 decrease in song frequency results in increased overlap with aircraft
 noise, these findings cannot be explained as an adaptation to improve
 communication. The increased levels of aggression suggests that
 chiffchaffs, like humans, might be affected behaviourally by extreme noise
 pollution. These findings should influence environmental impact
 assessments for airport expansions globally.
description: JAE-Wolfenden-et-al-2019-SonganalysisThis file contains the data that was used for the songanalysis in this paperJAE-Wolfenden-et-al-2019-PlaybackBehavioural response data to playback of airport type and control type stimuli
DOI: 10.5061/dryad.vn5js14
title: Data from: “Gaming the System”: a qualitative study on the price of drugs for multiple sclerosis

description: Objective: To describe pricing decisions, justifications, and attitudes
 among current and former biotech industry executives for companies that
 manufacture multiple sclerosis disease-modifying therapies. Methods: Four
 leaders in biotech who have been directly involved in multiple sclerosis
 disease-modifying therapy pricing and/or marketing volunteered to
 participate in 30-minute, semi-structured interviews conducted via
 telephone. An expert in qualitative methods moderated and analyzed the
 interviews alongside the Principal Investigator. Brief, pre-interview
 online surveys were also administered, to provide additional context and
 insight for discussion. Interviews were audio-recorded and professionally
 transcribed. Results: Participants consistently stated that initial price
 decisions were dictated by the price of existing competitors in the
 market. Revenue maximization and corporate growth were drivers of price
 escalations in the absence of continued market penetration. Lower revenue
 predictions outside the US also informed pricing strategies. The growing
 complexity and clout of drug distribution and supply channels was also
 cited as a contributing factor. Although decisions to raise prices were
 motivated by the need to attract investment for future innovation,
 recouping drug-specific research and development costs as a justification
 was not strongly endorsed as having a significant influence on pricing
 decisions. Conclusions: Contrary to prevailing narratives that underscore
 drug development costs, findings from our interviews suggest that the
 existing price ecosystem, overall corporate growth, international pricing
 disparities, and supply chain-related distortions may play a more central
 role to drug pricing decision.
description: AppendixSurveyResultsFile includes survey and survey results
DOI: 10.5061/dryad.7jj53hb
title: Data from: Prevalence of pelagic dependence among coral reef predators across an atoll seascape.

description: 1) Coral reef food webs are complex, vary spatially and remain poorly
 understood. Certain large predators, notably sharks, are subsidised by
 pelagic production on outer reef slopes, but how widespread this
 dependence is across all teleost fishery target species and within atolls
 is unclear. 2) North Malé Atoll (Maldives) includes oceanic barrier as
 well as lagoonal reefs. Nine fishery target predators constituting ca. 55%
 of the local fishery target species biomass at assumed trophic levels 3-5
 were selected for analysis. Data were derived from carbon (δ13C), nitrogen
 (δ15N) and sulfur (δ34S) stable isotopes from predator white dorsal muscle
 samples, and primary consumer species representing production source
 end-members. 3) Three-source Bayesian stable isotope mixing models showed
 that uptake of pelagic production extends throughout the atoll, with
 predatory fishes showing equal planktonic reliance between inner and outer
 edge reefs. Median plankton contribution was 65-80% for all groupers and
 68-88% for an emperor, a jack and snappers. 4) Lagoonal and atoll edge
 predators are equally at risk from anthropogenic and climate-induced
 changes which may impact the linkages they construct, highlighting the
 need for management plans that transcend the boundaries of this threatened
 ecosystem.
description: Skinner_JAnimEcol_PredatorPelagicDependence_2019.xlsxThis spreadsheet contains the raw data to accompany the publication in J Anim Ecology. The first sheet includes a README with details of all the data. The second sheet has information about each site where underwater visual census (UVC) was conducted, including GPS coordinates. The third sheet has the data collected during UVC where the abundance and size of all fishery target predators was recorded. The fourth sheet has all the carbon, nitrogen, and sulfur stable isotope data for all the predatory fish sampled. The fifth sheet has all the carbon, nitrogen, and sulfur stable isotope data for all the primary consumer species sampled to represent different food sources in the reef food web.