cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.76hdr7st3
title: Data from: The role of browsers in maintaining the openness of savanna grazing lawns

description: 1. In savannas, ruminant herbivores can have divergent impacts on
 tree recruitment and resulting woody cover. Heavy grazing by cattle
 results in woody thickening, whereas intensive grazing by wildlife instead
 tends to be associated with lower woody cover. 2. To disentangle why woody
 cover is low in areas heavily grazed by wildlife, we tested (I) whether
 short-grass environments attract indigenous mammalian browsers; (II)
 whether preference for short grass decreases with browser body mass
 because of differences in predator susceptibility; and (III) whether these
 translate into suppression of seedlings and saplings on grazing lawns,
 thus maintaining their openness.  3. This work was conducted in
 Kruger National Park (KNP) and Hluhluwe iMfolozi Park (HiP), South Africa.
 In KNP, the effect of grass height on browser abundance (estimated using
 dung counts), and on the utilisation of woody plants by browsers (using a
 bite-score approach) was tested. An exclosure experiment tested the effect
 of grass height and browser removal on seedling survival and sapling
 growth of a dominant woody plant species in a short- and tall-grass
 mosaic. Finally, in HiP, the effect of grass height and browser removal
 were tested on the growth rates of a range of woody species, monitored
 over ten years, across ten sites. 4. Steenbok and impala selected short-
 over tall-grass as preferred browsing sites, while elephant preferred tall
 grass. Browser abundance on short grass decreased with browser body mass,
 indicating that predator avoidance might be a key factor driving
 small-bodied browsers to utilize grazing lawns. Grass height did not
 explain variation in the utilisation of woody plants by browsers. 5.
 Seedling survival was lowest in short grass and when browsers were
 present, with mortality occurring in two out of every three seedlings.
 Also, sapling growth was lowest in short grass, although browser removal
 had no effect. Evidence for increased browser impact on grazing lawns was
 clearest from our long-term exclosure experiment in HiP, which
 demonstrated that the effect of browsers on sapling growth rates was
 strongly modified by the presence of short grass. 6. Synthesis. These
 results provide support for the hypothesis that browsers, particularly
 small-bodied browsers and mixed feeders, are attracted to short-grass
 habitats, and that, they help maintain grazing lawn openness by
 suppressing woody seedling survival and sapling growth where grass is kept
 short by grazers.
DOI: 10.5061/dryad.00000001h
title: Temperature and predator cues interactively affect ontogenetic metabolic scaling of aquatic amphipods

description: A common belief is that body-mass scaling of metabolic rate results
 chiefly from intrinsic body-design constraints. However, several studies
 have shown that multiple ecological factors affect metabolic
 scaling.  The mechanistic basis of these effects is largely
 unknown. Here, we explore whether abiotic and biotic environmental factors
 have interactive effects on metabolic scaling. To address this question,
 we studied the simultaneous effects of temperature and predator cues on
 the ontogenetic metabolic scaling of amphipod crustaceans inhabiting two
 different aquatic ecosystems, a freshwater spring and a saltwater lagoon.
 We assessed effects of phenotypic plasticity on metabolic scaling by
 exposing amphipods in the laboratory to water with and without fish-cues
 at multiple temperatures. Temperature interacts significantly with
 predator cues to affect metabolic scaling. Our results suggest that
 metabolic scaling is highly malleable in response to short-term
 acclimation. The interactive effects of temperature and predators show the
 importance of studying effects of global warming in realistic ecological
 contexts.
DOI: 10.5061/dryad.b2rbnzsbf
title: Data from: Contrasting the seasonal and elevational prevalence of generalist avian haemosporidia in co-occurring host species

description: Understanding the ecology and evolution of parasites is contingent on
 identifying the selection pressures they face across their infection
 landscape. Such a task is made challenging by the fact that these
 pressures will likely vary across time and space, as a result of seasonal
 and geographical differences in host susceptibility or transmission
 opportunities. Avian haemosporidian blood parasites are capable of
 infecting multiple co-occurring hosts within their ranges, yet whether
 their distribution across time and space varies similarly in their
 different host species remains unclear. Here we applied a new PCR method
 to detect avian haemosporidia (genera Haemoproteus, Leucocytozoon, and
 Plasmodium) and to determine parasite prevalence in two closely related
 and co-occurring host species, blue tits (Cyanistes caeruleus, N = 529)
 and great tits (Parus major, N = 443). Our samples were collected between
 autumn and spring, along an elevational gradient in the French Pyrenees
 and over a three-year period. Most parasites were found to infect both
 host species, and while these generalist parasites displayed similar
 elevational patterns of prevalence in the two host species, this was not
 always the case for seasonal prevalence patterns. For example,
 Leucocytozoon group A parasites showed inverse seasonal prevalence when
 comparing between the two host species, being highest in winter and spring
 in blue tits but higher in autumn in great tits. While Plasmodium relictum
 prevalence was overall lower in spring relative to winter or autumn in
 both species, spring prevalence was also lower in blue tits than in great
 tits. Together these results reveal how generalist parasites can exhibit
 host-specific epidemiology, which is likely to complicate predictions of
 host-parasite co-evolution.
DOI: 10.5061/dryad.sxksn030m
title: Data from: Adaptive niche‐based sampling to improve ability to find rare and elusive species: Simulations and field tests

description: Adaptive niche-based sampling (ANBS) is an iterative sampling strategy
 that relies on the predictions of species distribution models (SDMs). By
 predicting highly suitable areas to guide prospection, ANBS could improve
 the efficiency of sampling effort in terms of finding new locations for
 rare species. Its iterative quality could potentially mitigate the effect
 of small and initially biased samples on SDMs. In this study, we compared
 ANBS with random sampling by assessing the gain in terms of new locations
 found per unit of effort. The comparison was based on both simulations and
 two field surveys of mountain birds.We found an increasing probability of
 contacting the species through iterations if the focal species showed
 specialization in the environmental gradients used for modelling. Overall,
 ANBS is an effective and flexible strategy that can contribute to a better
 understanding of distribution drivers in rare species. The datasets stored
 in this repository were used to implement and assess ANBS using 2 mountain
 bird species as biological models, complementarily to simulations.
description: Opportunistic and standardized counts data on rock thrush
 Monticola saxatilis and snowfinch Montifringilla nivalis, Pyrenees, 2014 -
 2016. Dataset used for species distribution modelling,
 method comparison, and model checking.
description: Initial datasets ("Opportunistic data and point
 counts.zip") are opportunistic data and standardized point count
 data, extracted from local citizen science databases (GOPA and Pyrenees
 National Park). We recommend to open those files with R cran for data
 exploration and analysis. Both opportunistic and point counts data were
 used for initial species distribution modelling, and point counts data
 were also used for method comparison. Transects
 trajectories ("TRANSECTS_2015-2017.zip") and counts ("DATA_TRANSECTS.zip"), are compressed QGIS shapefile (1 shapefile is made of 5 files with same name but different extensions). They were used to implement ANBS,  species distribution modelling iterations 1 and 2, and finally, for method comparison, and finally for field-based assessment of models performed previously. We recommand to use Quantum GIS for data exploration (opening .shp file), or to use R cran -rgeos package for data analysis (use .shp file again to get all information at once).
DOI: 10.5061/dryad.dncjsxkwh
title: Data from: Suitable habitat of the wild Asian elephant in the western Terai of Nepal

description: Background: There are very few researches on habitat suitability, the
 influence of infrastructure on distribution, and the extent and
 connectivity of habitat in parts of Asian elephant (Elephas maximus).
 Information related to the habitat is crucial for conservation of this
 species. Methods: In this study, we identified suitable habitat for Asian
 Elephants in the western Terai region of Nepal using elephant presence
 points and environmental variables by the help of Maximum Entropy (MaxEnt)
 software. Results: Out of 9,207 km2, we identified 3,194.82 km2 as
 suitable habitat for elephants in the study area. Approximately 40% of
 identified habitat occurs in existing protected areas. Most of these
 habitat patches are smaller than previous estimations of the species home
 range, and this may reduce the probability of the species continued
 survival in the study area. Proximity to roads was identified as the most
 important factor defining habitat suitability, with elephants preferring
 habitats far from roads. Conclusions: We conclude that further habitat
 fragmentation in the study area can be reduced by avoiding the
 construction of new roads and that connectivity between areas of existing
 suitable habitat is increased through the identification and management of
 wildlife corridors between habitat patches.
description: Wild Asian elephant (Elephas maximus) is conflict causing animal
 of Nepal. Here we collected 76 occurrence points of wild Asian elephants
 from Banke, Bardia and Kanchanpur Districts of Nepal. Data were collected
 during filed visit and from secondary sources (offices of the protected
 areas: Banke National Park, Bardia National Park and Suklaphanta National
 Park). Data can be useful for the researchers and managers for academic
 and managerial purpose. Data were collected during
 filed visit and from secondary sources (offices of the protected areas:
 Banke National Park, Bardia National Park and Suklaphanta National
 Park).
DOI: 10.5061/dryad.x95x69pfb
title: Data from: Applied use of alternate stable state modeling in restoration ecology

description: The concept of alternate stable states is important in ecological theory
 and models, but the application and implementation of these models have
 the potential to make significant future advances in the field of
 patterned landscapes. The bi-stable, ridge and slough landscape is a
 central feature of Everglades restoration and provides an important
 opportunity to test stable state theory with multistate transition models.
 We used these models to estimate environmental parameters associated with
 state changes (water depths, edaphic factors, etc.) to develop a
 quantitative method to measure resilience and stability. The multistate
 model indicates that long-term, local hydrology (15-year mean maximums and
 15-year mean amplitude) and edaphic factors control the local scale shifts
 between ridge and slough states. We show that multistate models can
 provide hydrologic envelopes for managers, produce a tool to help assess
 future water management scenarios, and address issues of sustainability,
 resilience, and restoration for any bi-stable system.
DOI: 10.15468/dl.jzv879
title: Occurrence Download

description: A dataset containing 883 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((159.00094 -48.95058,200.03306 -48.95058,200.03306 -32.54476,159.00094 -32.54476,159.00094 -48.95058))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Weymouthia mollis"
 ]
}

 The dataset includes 883 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002340-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u9bj4x
title: Occurrence Download

description: A dataset containing 543 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aphanocalyx microphyllus",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 543 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002341-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2jm63xskt
title: Data from: Risk factors for possible REM sleep behavior disorders: a community-based study in Beijing

description: Objective: To explore the risk factors for idiopathic REM sleep behavior
 disorder (RBD) in a community population in Beijing. Methods: Participants
 aged 55 years and above were recruited from the Beijing Longitudinal Study
 on Aging II (BLSA II) cohort. We identified individuals with possible RBD
 (pRBD) using the validated RBD questionnaire-Hong Kong in 2010. A series
 of environmental, lifestyle and other potential risk factors were assessed
 via standardized questionnaires in 2009. Multivariable logistic regression
 analysis was performed to investigate the association between the studied
 factors and pRBD. Results: Of 7225 participants who were free of
 parkinsonism and dementia, 219 (3.0%) individuals were considered as
 having pRBD. Participants with pRBD reported more non-motor and motor
 symptoms of Parkinson’s disease (PD) with adjusted odds ratios (ORs)
 ranging from 1.10 to 4.40. Participants with pRBD were more likely to
 report a family history of parkinsonism or dementia (OR 3.03, 95%
 Confidence interval [CI] 1.23–7.46). There was a significant association
 between pRBD and self-reported hyperlipidemia (OR 1.51, 95% CI 1.09–2.10),
 ever smoking (OR 1.79, 95% CI 1.20–2.65), prior carbon monoxide (CO)
 poisoning (OR 2.30, 95% CI 1.39–3.83) and nonoccupational exposure to
 pesticides (OR 2.21, 95% CI 1.40–3.50). Conclusion: Our study replicated
 previously reported associations between pRBD and hyperlipidemia, smoking,
 pesticide exposure, and several prodromal PD symptoms. We also found
 previously unreported links with a positive family history of
 parkinsonism/dementia and CO poisoning. Risk factor profiles for pRBD
 partially resemble those defined for PD, but also differ in distinct ways.
DOI: 10.5061/dryad.n8pk0p2s5
title: Multiple drainage reversal episodes and glacial refugia in a Patagonian fish revealed by sequenced microsatellites

description: The rise of the southern Andes and the Quaternary glacial cycles
 influenced the landscape of Patagonia, affecting the phylogeographic and
 biogeographic patterns of its flora and fauna. Here we examine the
 phylogeography of the freshwater fish, Percichthys trucha, using 53
 sequenced microsatellite DNA markers. Fish (N=835) were collected from 16
 river systems (46 locations) spanning the species range on both sides of
 the Andes. Eleven watersheds drain to the Pacific, five of which are
 trans-Andean (headwaters east of Andes). The remaining five drainages
 empty into the Atlantic. Three analytical approaches (neighbour-joining
 tree, hierarchical AMOVAs, STRUCTURE) revealed evidence of historic
 drainage reversals: Fish from four of the five trans-Andean systems
 (Puelo, Futalaufquen/Yelcho, Baker, Pascua) exhibited greater genetic
 similarity with Atlantic draining systems than with Pacific systems with
 headwaters west of Andes. Present-day drainage (Pacific vs. Atlantic)
 explained only 5% of total genetic variance, while ancestral drainage
 explained nearly 27% of total variance. Thus, the phylogeographic
 structure of Percichthys trucha is consistent with episodes of drainage
 reversal in multiple systems and suggests a major role for deglaciation in
 the genetic and indeed the geographic distribution of P. trucha in
 Patagonia. The study emphasizes the significant role of historical
 processes in the current pattern of genetic diversity and differentiation
 in a fish from a southern temperate region.
description: Fish field collections by gillnetting and electrofishing,
 microsatellite DNA markers identified by sequencing.
DOI: 10.5061/dryad.47d7wm39j
title: Data from: Evaluating Sphagnum traits in the context of resource economics and optimal partitioning theories

description: Trade-offs between key aspects of plant performance such as resource
 acquisition and allocation underpin several trait-based theories that have
 been derived for vascular plants. However, due to difficulty in
 quantifying traits in nonvascular plants, our theoretical understanding of
 how traits govern the physiological and ecological preferences of
 nonvascular plant species is quite limited. Here, we used the resource
 economics theory (RET) and optimal partitioning theory (OPT) to evaluate
 functional traits in mosses. We evaluated aspects of these theories in two
 common but ecologically different Sphagnum moss species. We used a suite
 of morpho-physiological traits across a range of environmental treatments
 to test whether Sphagnum is capable of functional tissue partitioning and
 whether the two Sphagnum species studied conform to a fast or slow
 strategy often observed in vascular plants. Consistent with the
 predictions of RET, the fast-growing species maintained a faster growth
 rate and low biomass across treatments. However, some of the traits
 responded contrary to predictions for respiration and photosynthetic
 rates. Consistent with OPT, Sphagnum diverted biomass from branch to
 capitulum to connect with the primary source of moisture when under
 drought stress. Overall, this study showed that moss traits could be used
 to test ecological theories that were developed primarily for vascular
 plants.
description: The data was collected from an experimental study
DOI: 10.25338/b8vs52
title: Data from: Wildfire reveals transient changes to individual traits and population responses of a native bumble bee (Bombus vosnesenskii)

description: 1. Fire-induced changes in the abundance and distribution of organisms,
 especially plants, can alter resource landscapes for mobile consumers
 driving bottom-up effects on their population sizes, morphologies, and
 reproductive potential. We expect these impacts to be most striking for
 obligate visitors of plants, like bees and other pollinators, but these
 impacts can be difficult to interpret due to the limited information
 provided by forager counts in the absence of survival or fitness proxies.
 2. Increased bumble bee worker abundance is often coincident with the
 pulses of flowers that follow recent fire. However, it is unknown if
 observed postfire activity is due to underlying population growth or a
 stable pool of colonies recruiting more foragers to abundant resource
 patches. This distinction is necessary for determining the net impact of
 disturbance on bumble bees: are there population-wide responses or do just
 a few colonies reap the rewards? 3. We estimated colony abundance before
 and after fire in burned and unburned areas using a genetic mark-recapture
 framework. We paired colony abundance estimates with measures of body
 size, counts of queens, and estimates of foraging and dispersal to assess
 changes in worker size, reproductive output, and landscape-scale
 movements. 4. Higher floral abundance following fire not only increased
 forager abundance, but also the number of colonies from which those
 foragers came. Importantly, despite a larger population size we also
 observed increased mean worker size. Two years following fire, queen
 abundance was higher in both burned and unburned sites, potentially due to
 the dispersal of queens from burned into unburned areas. The effects of
 fire were transient; within two growing seasons, worker abundance was
 substantially reduced across the entire sampling area and body sizes were
 similar between burned and unburned sites. 5. Our results reveal how
 disturbance can temporarily release populations from resource limitation,
 boosting the genetic diversity, body size, and reproductive output of
 populations. Given that the effects of fire on bumble bees acted
 indirectly through pulsed resource availability, it is likely our results
 are generalizable to other situations, such as habitat restorations, where
 resource density is enhanced within the landscape.
description: Full data description provided in text. Data was collected at
 McLaughlin Reserve before and after wildfire. Genetic data is provided as
 called genotypes and inputs to program COLONY.
description: All further code for generation of the manuscript figures and
 results can be found on github at
 https://github.com/John-Mola/bb-response-to-fire A
 README file is provided
DOI: 10.5061/dryad.x0k6djhg6
title: Mass spectrometry data of Chalmydomonas reinhardtii central pair mutants

description: The following data includes the mass spectrometry results from 5 different
 strains of Chlamydomonas reinhardtii. The first strain
 is CC-124 or more commonly referred to as the wild type strain. The second
 strain is a mutant that lacks the central pair pf15. Other
 central pair mutants are pf16, pf6 and cpc1. All strains were cultured
 under identical conditions and the doublet microtubules were purified and
 treated twice with NaCl before mass spectrometry. Biological triplicates
 were performed on each strain for mass spectrometry.
description: Cilia were purified from Chlamydomonas, salt-treated to remove
 outside proteins. The samples were subjected to tandem mass spectrometry
 according to the protocol described in Dai et al. 2019, bioRxiv. (https://doi.org/10.1101/739383).
description: Mass Spectrometry Core Data File (.sf3 file) - can be opened
 using the Proteome Software Scaffold free viewer (http://www.proteomesoftware.com/products/scaffold/download/).