cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sc38b
title: Data from: Life in the fat lane: seasonal regulation of insulin sensitivity, food intake, and adipose biology in brown bears

description: Grizzly bears (Ursus arctos horribilis) have evolved remarkable metabolic
 adaptations including enormous fat accumulation during the active season
 followed by fasting during hibernation. However, these fluctuations in
 body mass do not cause the same harmful effects associated with obesity in
 humans. To better understand these seasonal transitions, we performed
 insulin and glucose tolerance tests in captive grizzly bears,
 characterized the annual profiles of circulating adipokines, and tested
 the anorectic effects of centrally administered leptin at different times
 of the year. We also used bear gluteal adipocyte cultures to test insulin
 and beta-adrenergic sensitivity in vitro. Bears were insulin resistant
 during hibernation but were sensitive during the spring and fall active
 periods. Hibernating bears remained euglycemic, possibly due to
 hyperinsulinemia and hyperglucagonemia. Adipokine concentrations were
 relatively low throughout the active season but peaked in mid-October
 prior to hibernation when fat content was greatest. Serum glycerol was
 highest during hibernation, indicating ongoing lipolysis. Centrally
 administered leptin reduced food intake in October, but not in August,
 revealing seasonal variation in the brain’s sensitivity to its anorectic
 effects. This was supported by strong phosphorylated signal transducer and
 activator of transcription 3 labeling within the hypothalamus of
 hibernating bears; labeling virtually disappeared in active bears.
 Adipocytes collected during hibernation were insulin resistant when
 cultured with hibernation serum but became sensitive when cultured with
 active season serum. Heat treatment of active serum blocked much of this
 action. Clarifying the cellular mechanisms responsible for the physiology
 of hibernating bears may inform new treatments for metabolic disorders.
description: Data to accompany Rigano
 et. al. (2016) J.Comp.Physiol, Bdata to accompany
 manuscriptRigano_etal_JCPB_2016.zip
DOI: 10.5061/dryad.n4c7j
title: Data from: Social call divergence in bats: a comparative analysis

description: Acoustic signals mediate important life history events in a variety of
 species, providing new vistas for understanding speciation. It has been
 proposed that animal acoustic signals undergo complex interactions among
 morphology, ecology, social pressure, and phylogenetic history. Yet, the
 relative importance of these factors in shaping acoustic divergence is
 rarely assessed within a comparative framework. Herein, we aim to
 investigate the key determinants of social call divergence across 31 bat
 species from 5 families. We compiled a wide data set on bat aggressive
 calls, body size, foraging habitats, foraging modes, climatic conditions,
 colony size, and phylogenetic components. We identified remarkable
 interspecific divergence versus within-species variation in aggressive
 vocalizations. Despite weak effects of ecological factors, colony size,
 body size, and phylogenetic components accounted for the majority of
 variation in call parameters among species. The colony size and body size
 played a major role in influencing spectral parameters, whereas
 phylogenetic relationships determined call duration and minimum frequency.
 Together, our findings constitute convincing evidence that sociality,
 morphological constraint, and phylogenetic constraint mold social call
 divergence in bats. This study expands our limited knowledge of the
 evolution of bat social calls, and highlights the importance of sociality
 in driving acoustic phenotype diversity.
description: Supplementary
 materialThe raw data and
 alternative linear mixed models are listed in the tables. The video is
 recorded via an infrared camera (SonyHDR- CX760PJ760, Japan) in the in
 temporary field station near the bat roost.
DOI: 10.5061/dryad.93mn0
title: Data from: The contemporary distribution of Trypanosoma cruzi infection in humans, alternative hosts and vectors

description: Chagas is a potentially fatal chronic disease affecting large numbers of
 people across the Americas and exported throughout the world through human
 population movement. It is caused by the Trypanosoma cruzi parasite, which
 is transmitted by triatomine vectors to humans and a wide range of
 alternative host species. The database described here was compiled to
 allow the risk of vectorial transmission to humans to be mapped using
 geospatial models. The database collates all available records, published
 since 2003, for prevalence and occurrence of infection in humans, vectors
 and alternative hosts, and links each record to a defined time and
 location. A total of 16,802 records of infection have been extracted from
 the published literature and unpublished sources. The resulting database
 can be used to improve our understanding of the geographic variation in
 vector infection prevalence and to estimate the risk of vectorial
 transmission of T. cruzi to humans.
description: Data file 1: Prevalence
 of T. cruzi infections in humansSurvey data for T. cruzi
 infection prevalence (seroprevalence) in humans, linked to individual
 locations and, if available, times.1_prevalence_humans.csvMetadata_file.xlsData file 2: Acute T. cruzi infections in humansReports of presence or absence of acute T. cruzi infections humans, linked to individual locations and, if available, times.2_acute_humans.csvMetadata_file.xlsData file 3: Reports of T. cruzi infections in humansReports of T. cruzi infections in humans, linked to individual locations and, if available, times. Prevalence data (for a community cross-section) are excluded because they can be found in Data file 1. Reports of confirmed acute infections are also excluded because they can be found in Data file 2.3_occurrence_humans.csvMetadata_file.xlsData file 4: Prevalence of T. cruzi infections in vector speciesSurvey data for prevalence of T. cruzi infections in vector species, linked to individual locations and, if available, times.4_prevalence_vectors.csvMetadata_file.xlsData file 5: Occurrence of T. cruzi infections in vector speciesReports of T. cruzi infections in vector species. Prevalence data are excluded because they can be found in Data file 4.5_occurrence_vectors.csvMetadata_file.xlsData file 6: Prevalence of T. cruzi infections in reservoir speciesSurvey data for T. cruzi infection prevalence in reservoir species, linked to individual locations and, if available, times.6_prevalence_alt-hosts.csvMetadata_file.xlsData file 7: Occurrence of T. cruzi infections in reservoir speciesReports of T. cruzi infections in reservoir species. Prevalence data are excluded because they can be found in Data file 6.7_occurrence_alt-hosts.csvMetadata_file.xls
DOI: 10.5061/dryad.3p121
title: Data from: Accuracy of climate-based forecasts of pathogen spread

description: Species distribution models (SDMs) are a tool for predicting the eventual
 geographical range of an emerging pathogen. Most SDMs, however, rely on an
 assumption of equilibrium with the environment, which an emerging
 pathogen, by definition, has not reached. To determine if some SDM
 approaches work better than others for modelling the spread of emerging,
 non-equilibrium pathogens, we studied time-sensitive predictive
 performance of SDMs for Batrachochytrium dendrobatidis, a devastating
 infectious fungus of amphibians, using multiple methods trained on
 time-incremented subsets of the available data. We split our data into
 timeline-based training and testing sets, and evaluated models on each set
 using standard performance criteria, including AUC, kappa, false negative
 rate and the Boyce index. Of eight models examined, we found that boosted
 regression trees and random forests performed best, closely followed by
 MaxEnt. As expected, predictive performance generally improved with the
 length of time series used for model training. These results provide
 information on how quickly the potential extent of an emerging disease may
 be determined, and identify which modelling frameworks are likely to
 provide useful information during the early phases of pathogen expansion.
description: Modeling and analytic
 codeThe zip file contains
 four folders: Data, Preliminary Code, Modeling, and Other Files. These
 folders correspond to sections in the READ-ME, and each contains a set of
 related code files.Schatz-Kramer-Drake-archive.zip
DOI: 10.5061/dryad.gb786
title: Data from: Bioenergetics modeling of the annual consumption of zooplankton by pelagic fish feeding in the Northeast Atlantic

description: The present study uses bioenergetics modeling to estimate the annual
 consumption of the main zooplankton groups by some of the most
 commercially important planktivorous fish stocks in the Northeast
 Atlantic, namely Norwegian spring-spawning (NSS) herring (Clupea
 harengus), blue whiting (Micromesistius poutassou) and NEA mackerel
 (Scomber scombrus). The data was obtained from scientific surveys in the
 main feeding area (Norwegian Sea) in the period 2005-2010. By
 incorporating novel information about ambient temperature, seasonal growth
 and changes in the diet from stomach content analyses, annual consumption
 of the different zooplankton groups by pelagic fish is estimated. The
 present study estimates higher consumption estimates than previous studies
 for the three species and suggests that fish might have a greater impact
 on the zooplankton community as foragers. This way, NEA mackerel, showing
 the highest daily consumption rates, and NSS herring, annually consume
 around 10 times their total biomass, whereas blue whiting consume about 6
 times their biomass in zooplankton. The three species were estimated to
 consume an average of 135 million (M) tonnes of zooplankton each year,
 consisting of 53-85 M tonnes of copepods, 20-32 M tonnes of krill, 8-42 M
 tonnes of appendicularians and 0.2-1.2 M tonnes of fish, depending on the
 year. For NSS herring and NEA mackerel the main prey groups are calanoids
 and appendicularians, showing a peak in consumption during June and
 June-July, respectively, and suggesting high potential for inter-specific
 feeding competition between these species. In contrast, blue whiting
 maintain a low consumption rate from April to September, consuming mainly
 larger euphausiids. Our results suggest that the three species can coexist
 regardless of their high abundance, zooplankton consumption rates and
 overlapping diet. Accordingly, the species might have niche segregation,
 as they are species specific, showing annual and inter-annual variability
 in total consumption of the different prey species. These estimates and
 their inter-annual and inter-specific variation are fundamental for
 understanding fundamental pelagic predator-prey interactions as well as to
 inform advanced multispecies ecosystem models.
description: ConsNS_dataData used to estimate annual consumption of zooplankton by small pelagic fish in the Northeast Atlantic. Bioenergetics modeling has been used to make such estimations. Therefore diet composition data, fish length & growth data (length distribution), ambient temperatura data, energy density data, stock biomass information, etc. are included.Mackerel Energy Data
DOI: 10.5061/dryad.s056d
title: Data from: Asexual queen succession mediates an accelerated colony life cycle in the termite Silvestritermes minutus

description: Mixed modes of reproduction, combining sexual processes with thelytokous
 parthenogenesis, occur in all major clades of social insects. In several
 species of termites, queens maximize their genetic input into
 nondispersing replacement queens through parthenogenesis, while
 maintaining genetically diverse sterile offspring and dispersing
 reproductives via sexual reproduction. This so-called asexual queen
 succession (AQS) has multiple independent origins and its presumed
 advantages are diverse as well, ranging from multiplication of colony
 reproductive potential to extension of its lifespan beyond that of the
 foundress. However, how AQS shapes colony life cycles under natural
 conditions remains poorly known. The neotropical termite Silvestritermes
 minutus inhabits small but conspicuous nests, offering a unique
 opportunity to investigate the impact of AQS on life history. We report on
 its breeding system, life cycle and sex allocation using social structure
 census in 137 nests and genotyping of 12 colonies at 12 microsatellite
 loci. We show that colonies are established by an outbred pair of primary
 reproductives. In less than 2 years, the foundress is replaced by multiple
 neotenic queens, arising mostly through automixis with central fusion.
 Sterile castes, male and most (93%) female dispersers are produced
 sexually. Colony reproduction is usually restricted to a single dispersal
 of alates with unbiased sex ratio, taking place after 3 years. We conclude
 that S. minutus benefits from AQS to maximize colony growth rate and alate
 production within a very short life cycle rather than to extend colony
 lifespan. This highlights the versatile role of AQS in different cases of
 its polyphyletic origin.
description: Silvestritermes minutus
 microsatellite lociSequences for 8
 microsatellite loci developed from Silvestritermes minutus (Sm) and 3
 microsatellite loci developed from Embiratermes neotenicus
 (En).Dryad_Roy.xlsxFougeyrollas et al GENOTYPESGenotypes recorded in 12 colonies of Silvestritermes minutus at 12 microsatellite loci (inf., inferred; gen. genotyped)
DOI: 10.5061/dryad.bq015
title: Data from: Evidence toads may modulate landing preparation without predicting impact time

description: Within anurans (frogs and toads), cane toads (Bufo marinus) perform
 particularly controlled landings in which the forelimbs are exclusively
 used to decelerate and stabilize the body after impact. Here we explore
 how toads achieve dynamic stability across a wide range of landing
 conditions. Specifically, we suggest that torques during landing could be
 reduced by aligning forelimbs with the body's instantaneous velocity
 vector at impact (impact angle). To test whether toad forelimb orientation
 varies with landing conditions, we used high-speed video to collect
 forelimb and body kinematic data from six animals hopping off platforms of
 different heights (0, 5 and 9 cm). We found that toads do align forelimbs
 with the impact angle. Further, toads align forelimbs with the
 instantaneous velocity vector well before landing and then track its
 changes until touchdown. This suggests that toads may be prepared to land
 well before they hit the ground rather than preparing for impact at a
 specific moment, and that they may use a motor control strategy that
 allows them to perform controlled landings without the need to predict
 impact time.
description: RawPlatformDigitizedPointsThe raw digitized forelimb points in three dimensionsAnimalInfoArmAnglePaper2hop events timing (takeoff, touchdown, etc) by hop
DOI: 10.5061/dryad.q3670
title: Data from: Combining familiarity and landscape features helps break down the barriers between movements and home ranges in a non-territorial large herbivore

description: Recent advances in animal ecology have enabled identification of certain
 mechanisms that lead to the emergence of territories and home ranges from
 movements considered as unbounded. Among them, memory and familiarity have
 been identified as key parameters in cognitive maps driving animal
 navigation, but have been only recently used in empirical analyses of
 animal movements. At the same time, the influence of landscape features on
 movements of numerous species and on space division in territorial animals
 has been highlighted. Despite their potential as exocentric information in
 cognitive maps and as boundaries for home ranges, few studies have
 investigated their role in the design of home ranges of non-territorial
 species. Using step selection analyses, we assessed the relative
 contribution of habitat characteristics, familiarity preferences and
 linear landscape features in movement step selection of 60 GPS-collared
 Mediterranean mouflon Ovis gmelini musimon × Ovis sp. monitored in
 southern France. Then, we evaluated the influence of these
 movement-impeding landscape features on the design of home ranges by
 testing for a non-random distribution of these behavioural barriers within
 sections of space differentially used by mouflon. We reveal that
 familiarity and landscape features are key determinants of movements,
 relegating to a lower level certain habitat constraints (e.g. food/cover
 trade-off) that we had previously identified as important for this
 species. Mouflon generally avoid crossing both anthropogenic (i.e. roads,
 tracks and hiking trails) and natural landscape features (i.e. ridges,
 talwegs and forest edges) while moving in the opposite direction,
 preferentially toward familiar areas. These specific behaviours largely
 depend on the relative position of each movement step regarding distance
 to the landscape features or level of familiarity in the surroundings. We
 also revealed cascading consequences on the design of home ranges in which
 most landscape features were excluded from cores and relegated to the
 peripheral areas. These results provide crucial information on landscape
 connectivity in a context of marked habitat fragmentation. They also call
 for more research on the role of landscape features in the emergence of
 home ranges in non-territorial species using recent methodological
 developments bridging the gap between movements and space use patterns.
description: Marchand_et_al_raw_data_DRYAD
DOI: 10.5061/dryad.4f775
title: Data from: Drosophila clock is required in brain pacemaker neurons to prevent premature locomotor aging independently of its circadian function

description: Circadian clocks control many self-sustained rhythms in physiology and
 behavior with approximately 24-hour periodicity. In many organisms,
 oxidative stress and aging negatively impact the circadian system and
 sleep. Conversely, loss of the clock decreases resistance to oxidative
 stress, and may reduce lifespan and speed up brain aging and
 neurodegeneration. Here we examined the effects of clock disruptions on
 locomotor aging and longevity in Drosophila. We found that lifespan was
 similarly reduced in three arrhythmic mutants (ClkAR, cyc0 and tim0) and
 in wild-type flies under constant light, which stops the clock. In
 contrast, ClkAR mutants showed significantly faster age-related locomotor
 deficits (as monitored by startle-induced climbing) than cyc0 and tim0, or
 than control flies under constant light. Reactive oxygen species
 accumulated more with age in ClkAR mutant brains, but this did not appear
 to contribute to the accelerated locomotor decline of the mutant. Clk, but
 not Cyc, inactivation by RNA interference in the pigment-dispersing factor
 (PDF)-expressing central pacemaker neurons led to similar loss of climbing
 performance as ClkAR. Conversely, restoring Clk function in these cells
 was sufficient to rescue the ClkAR locomotor phenotype, independently of
 behavioral rhythmicity. Accelerated locomotor decline of the ClkAR mutant
 required expression of the PDF receptor and correlated to an apparent loss
 of dopaminergic neurons in the posterior protocerebral lateral 1 (PPL1)
 clusters. This neuronal loss was rescued when the ClkAR mutation was
 placed in an apoptosis-deficient background. Impairing dopamine synthesis
 in a single pair of PPL1 neurons that innervate the mushroom bodies
 accelerated locomotor decline in otherwise wild-type flies. Our results
 therefore reveal a novel circadian-independent requirement for Clk in
 brain circadian neurons to maintain a subset of dopaminergic cells and
 avoid premature locomotor aging in Drosophila.
description: Vaccaro et al. 2016
 sleep raw dataData for S2
 FigLifespan
 dataData for S1A and S1B
 Figures (Prism .pzf format)Lifespan.zipStartle-induced negative geotaxis dataData for Fig 1-3, 6A and 7, and S1C, S2E and S4 (Prism .pzf format)SING.zipSpontaneous locomotor activity dataData for S1D Fig (Prism .pzf format)Spontaneous locomotor activity.zipDHE-ROS quantificationData for Fig 4B-D, and S5 (Prism .pzf format)Neuronal countsData for Fig5, 6A, S10 and S11A (Prism .pzf format)
DOI: 10.5061/dryad.n04g0
title: Data from: Organization of biogeochemical nitrogen pathways with switch-like adjustment in fluctuating soil redox conditions

description: Nitrogen is cycled throughout ecosystems by a suite of biogeochemical
 processes. The high complexity of the nitrogen cycle resides in an
 intricate interplay between reversible biochemical pathways alternatively
 and specifically activated in response to diverse environmental cues.
 Despite aggressive research, how the fundamental nitrogen biochemical
 processes are assembled and maintained in fluctuating soil redox
 conditions remains elusive. Here, we address this question using a kinetic
 modelling approach coupled with dynamical systems theory and microbial
 genomics. We show that alternative biochemical pathways play a key role in
 keeping nitrogen conversion and conservation properties invariant in
 fluctuating environments. Our results indicate that the biochemical
 network holds inherent adaptive capacity to stabilize ammonium and nitrate
 availability, and that the bistability in the formation of ammonium is
 linked to the transient upregulation of the amo-hao mediated nitrification
 pathway. The bistability is maintained by a pair of complementary
 subsystems acting as either source or sink type systems in response to
 soil redox fluctuations. It is further shown how elevated anthropogenic
 pressure has the potential to break down the stability of the system,
 altering substantially ammonium and nitrate availability in the soil, with
 dramatic effects on biodiversity.
description: Nitrogen_Biogeochemical_Network_Sanjay_Lamba_Chakraborty_ESMThis Auxiliary Material includes five supplementary tables (Table S1-S5), fifteen supplementary figures (Figs. S1-S15) and ten supplementary texts(Text S1-S10). Detailed methods and mathematical techniques are described in the supplementary texts; all the simulated model results in the form of tables and figures are presented in the auxiliary figures and tables. This material presents how the nitrogen biochemical system runs and is regulated over time and how it is responded to external ammonium supply.