cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2bvq83bq4
title: Optimising bat bioacoustic surveys in human-modified neotropical landscapes

description: During the last decades, the use of bioacoustics as a non-invasive and
 cost-effective sampling method has greatly increased worldwide. For bats,
 acoustic surveys have long been known to complement traditional
 mist-netting, however, appropriate protocol guidelines are still lacking
 for tropical regions. Establishing the minimum sampling effort needed to
 detect ecological changes in bat assemblages (e.g., activity, composition
 and richness) is crucial in view of workload and project cost constraints,
 and because detecting such changes must be reliable enough to support
 effective conservation management. Using one of the most comprehensive
 tropical bat acoustic datasets, collected in the Amazon, we assessed the
 minimum survey effort required to accurately assess (1) the completeness
 of assemblage inventories and (2) habitat selection in fragmented forest
 landscapes for aerial insectivorous bats. We evaluated a combination of 20
 different temporal sampling schemes, which differed regarding: (i) number
 of hours per night, (ii) number of nights per site and (iii) sampling only
 during the wet or dry season, or both. This was assessed under two
 different landscape scenarios: (a) in primary forest fragments embedded in
 a matrix of secondary forest, and (b) in the same forest fragments, but
 after they had been re-isolated through clearing of the secondary forest.
 We found that the sampling effort required to achieve 90% inventory
 completeness varied considerably depending on the research aim and the
 landscape scenario evaluated, averaging ~80 and 10 nights before and after
 fragment re-isolation, respectively. Recording for more than four hours
 per night did not result in a substantial reduction in the required number
 of sampling nights. Regarding the effects of habitat selection, except for
 assemblage composition, bat responses in terms of richness, diversity, and
 activity were similar across all sampling schemes after fragment
 re-isolation. However, before re-isolation, a minimum of four to six
 sampling hours per night after dusk and three to five nights of sampling
 per site were needed to detect significant effects that could otherwise go
 unnoticed. Based on our results, we propose guidelines that will aid to
 optimize sampling protocols for bat acoustic surveys in the Neotropics.
DOI: 10.5061/dryad.ns1rn8psm
title: Mapping the páramo land cover in the Northern Andes: Figure S4 Expert land-cover classification of the Andean páramo and distribution according to three groups: natural vegetation, natural abiotic and anthropogenic, and 12 classes

description: The Andean páramo is a biodiverse and vulnerable tropical high-mountain
 region, whose spatio-ecological patterns remain understudied. The lack of
 general characterization of its overall extent, land-cover classes, and
 treeline spatial features hinders our capacity to understand its responses
 to human impacts and predict future land-system changes. To address this
 knowledge gap, we classified the land-cover of the páramo in the northern
 Andes. Moreover, we estimated 1) the páramo’s total extent and
 distribution among countries, 2) the relative extent of 12 of its main
 land-cover classes, categorized into natural vegetation, natural abiotic
 and anthropogenic groups, and 3) the preliminary position and
 anthropogenic influence of its bordering treeline. Relying on Landsat 8
 imagery, we performed hybrid manual-automated classifications using the
 Maximum Likelihood and Random Forest algorithms. The two resulting final
 classifications were manually checked for errors compared to Google Earth
 and VegPáramo data, and used to produce the expert classification.
 Finally, we delimited the treeline based on regional forest connectivity,
 and applied it to the expert classification to evaluate páramo elevations,
 surface areas and land-cover classes above the treeline. The páramo extent
 was estimated at 24,301 km2, distributed between Ecuador (47%), Colombia
 (43%), Venezuela (8%) and Peru (2%). Natural vegetation, especially
 shrublands, rosette plant communities and grasslands were dominant
 (altogether, 65%), whereas classes reflecting intense land-use covered 12%
 overall. The average treeline reached 3546 m and was bordered uphill at
 16% with anthropogenic land-cover classes. The páramo’s extent is smaller
 than previously suggested. It remains a (semi-) natural region, yet crop
 and pasture expansion towards high elevations is a critical concern for
 long-term sustainability. Future research can build on our findings to
 predict land-system changes and assess priority areas for conservation. We
 recommend for future research to focus on remnant forest patches and
 treeline connectivity in priority.
description: This dataset corresponds to the expert classification results for
 the 2019 Land-cover classification of the Andean páramo.
 This dataset is presented in a raster format, with a pixel
 resolution of 1 arc second (30 m). It was obtained by
 conducting Maximum Likelihood and Random Forest classifications of Landsat
 8 Imagery (2018-2019) for the páramo region. The obtained results were
 contrasted and validated to generate the expert classification, which was
 then cropped at the Andean forest - páramo treeline.
 Classes are coded as such: 1 - water, 2 - shrubland, 3 - forest,
 4 - crop, 5 - desert, 6 - rosette, 7 - glacier, 8 - grassland, 9 - meadow,
 10 - rock, 11 - periglacial desert, 12 - urban
DOI: 10.5061/dryad.73n5tb2wz
title: Data from: Nectar robbing rather than pollinator availability constrains reproduction of a bee-flowered plant at high elevations

description: The files contain data on the floral ecology of Clinopodium alpinum
 collected along an elevational gradient in the Berchtesgaden National Park
 in Germany in 2017. The data are presented in the work entitled
 "Nectar robbing rather than pollinator availability constrains
 reproduction of a bee-flowered plant at high elevations" by Patrick
 L. Kohl and Ingolf Steffan-Dewenter. Files include data on flower visitor
 observations (including raw data on the number of visits by individual
 specifmens), data on seed/ovule ratios (both open pollinated and bagged
 flowers), data on the incidence of nectar robbing by bumble bees (the
 frequency of corolla perforations) and of flower herbivory by Eulophidae,
 and data on basic flowering traits of C. alpinum (number of flowers per
 inflorescence, corolla tube length, display size).
description: The methods of how the data were collected are described in the
 work entitled "Nectar robbing rather than pollinator availability
 constraints reproduction of a bee-flowered plant at high elevations"
 by Patrick L. Kohl and Ingolf Steffan-Dewenter
description: The precise data file content is described in the
 "README.txt" document.
DOI: 10.5061/dryad.n2z34tmwm
title: Dataset for analysing spatiotemporal dynamics of large carnivores in Kasungu National Park, Malawi

description: Effective conservation management requires an understanding of the
 spatiotemporal dynamics driving large carnivore density and resource
 partitioning. In African ecosystems, reduced prey populations and the loss
 of competing guild members, most notably lion (Panthera leo), are expected
 to increase levels of competition between remaining carnivores.
 Consequently, intraguild relationships can be altered, potentially
 increasing the risk of further population decline. Kasungu National Park
 (KNP), Malawi, is an example of a conservation area that has experienced
 large-scale reductions in both carnivore and prey populations, leaving a
 resident large carnivore guild consisting of only leopard (Panthera
 pardus) and spotted hyaena (Crocuta crocuta). Here we quantify the
 spatiotemporal dynamics of these two species and their degree of
 association, using a combination of co-detection modelling, time-to-event
 analyses, and temporal activity patterns from camera trap data. Detection
 of leopard and spotted hyaena was significantly associated with the
 detection of preferred prey and competing carnivores, increasing the
 likelihood of species interaction. Temporal analyses revealed sex-specific
 differences in temporal activity, with female leopard activity patterns
 significantly different to those of spotted hyaena and male conspecifics.
 Heightened risk of interaction with interspecific competitors and male
 conspecifics may have resulted in female leopards adopting temporal
 avoidance strategies to facilitate co-existence. Female leopard
 behavioural adaptations increased overall activity levels and diurnal
 activity rates, with potential consequences for overall fitness and
 exposure to sources of mortality. As both species are currently found at
 low densities in KNP, increased risk of competitive interactions, that
 infer a reduction in fitness, could have significant implications for
 large carnivore demographics. Protection of remaining prey populations is
 necessary to mitigate interspecific competition and avoid further
 alterations to the large carnivore guild.
DOI: 10.5061/dryad.5x69p8d2r
title: Data from: Mesozoic cupules and the origin of the angiosperm second integument

description: The second integument of the angiosperm ovule is unique among seed plants,
 with developmental genetics that are distinct from those of the inner
 integument. Understanding how the second integument should be compared to
 structures in other seed plants is therefore crucial to resolving the
 long-standing question of the origins of angiosperms. Attention has
 focused on several extinct plants with recurved cupules that are
 reminiscent of the anatropous organization of the basic bitegmic ovules of
 angiosperms, but interpretations have been hampered by inadequate
 information on the relevant fossils. Here we describe abundant
 exceptionally well-preserved recurved cupules from a newly discovered
 silicified peat dating to the Early Cretaceous epoch (around 125.6 million
 years ago) in Inner Mongolia, China. The new material, combined with
 re-examination of potentially related fossils, indicates that the recurved
 cupules of several groups of Mesozoic plants are all fundamentally
 comparable, and that their structure is consistent with the recurved form
 and development of the second integument in the bitegmic anatropous ovules
 of angiosperms. Recognition of these angiosperm relatives (angiophytes)
 provides a partial answer to the question of angiosperm origins, will help
 to focus future work on seed plant phylogenetics and has important
 implications for ideas on the origin of the angiosperm carpel.
description: See Shi et al. 2021 Methods and Material section for
 details.
DOI: 10.5061/dryad.866t1g1qm
title: The effect of temperature on appetite in fish

description: Temperature has a dramatic effect on the physiology of ectothermic
 animals, impacting most of their biology. When temperatures increase above
 optimal for an animal, their growth gradually decreases. The main
 mechanism behind this growth rate reduction is unknown.  Here, we
 suggest the ‘aerobic scope protection’ hypothesis as a mechanistic
 explanation for the reduction in growth.  After a meal, metabolic
 rate, and hence oxygen consumption rate, transiently increases in a
 process called specific dynamic action (SDA). At warmer temperatures, the
 SDA response usually becomes temporally compressed, leading to a higher
 peak oxygen consumption rate. This peak in oxygen consumption rate risks
 taking up much of the animal’s aerobic scope (the difference between
 resting and maximum rates of oxygen consumption), which would leave little
 residual aerobic scope for other aerobic functions.  We propose
 that water-breathing ectothermic animals will protect their postprandial
 residual aerobic scope by reducing meal sizes in order to regulate the
 peak SDA response during times of warming, leading to reductions in
 growth. This hypothesis is consistent with the published literature on
 fishes, and we suggest predictions to test it.
description: The file contains data extracted from the literature on the
 effect of temperature on fish appetite.
DOI: 10.5061/dryad.9kd51c5h2
title: The association between obesity and chronic rhinosinusitis with nasal polyps: A national population-based study

description: Objectives: We performed a cross-sectional analysis of data from the
 nationwide Korea National Health and Nutrition Examination Survey
 (KNHANES) to evaluate the association between obesity and chronic
 rhinosinusitis with nasal polyps (CRSwNP) or without nasal polyp (CRSsNP).
 Design: Retrospective cross-sectional analysis of health survey data
 Setting: Voluntary survey of representative South Korean populations
 Participants: In total, 32,384 individuals aged 19 years or older with
 available data on CRS and obesity were included. Primary and Secondary
 Outcome Measures: Diagnosis of CRSwNP or CRSsNP was performed by trained
 otolaryngologists through sinus endoscopy and surveys of medical history.
 General and central obesity was diagnosed using body mass index (BMI) and
 waist circumference (WC), respectively. Methods: A multivariate logistic
 regression analysis was used to clarify the association between CRSwNP or
 CRSsNP and obesity according to BMI and WC. Non-obese individuals were
 recruited as controls. Results: The prevalence of CRSwNP was higher in the
 general (odds ratio [OR] 1.438; 95% confidence interval [CI] 1.170-1.768;
 P &lt; 0.001) and central (OR 1.251; 95% CI 1.031-1.520; P=0.033)
 obesity groups than in the control group. Prevalence of CRSsNP was not
 correlated with obesity. In a logistic regression analysis, olfactory
 dysfunction (OR 1.329; 95% CI 1.137-1.553; P ˂ 0.001) and purulent
 discharge (OR 1.383; 95% CI 1.193-1.603; P ˂ 0.001) showed a higher
 incidence in the central obesity group than in the control group.
 Conclusions: We demonstrated an association between CRSwNP and general and
 central obesity. Further investigations on the mechanism underlying this
 correlation are necessary for an improved understanding of the
 pathogenesis of CRSwNP.
DOI: 10.5061/dryad.f7m0cfxw2
title: Data from: Topographic and vegetation drivers of thermal heterogeneity along the boreal–grassland transition zone in western Canada: implications for climate change refugia

description: Climate-change refugia are areas that are relatively buffered from
 contemporary climate change and may be important safe havens for wildlife
 and plants under anthropogenic climate change. Topographic variation is an
 important driver of thermal heterogeneity, but it is limited in relatively
 flat landscapes, such as the boreal plain and prairie regions of western
 Canada. Topographic variation within this region is mostly restricted to
 river valleys and hill systems, and their effects on local climates are
 not well documented. We sought to quantify thermal heterogeneity as a
 function of topography and vegetation cover within major valleys and hill
 systems across the boreal–grassland transition zone. Using iButton data
 loggers, we monitored local temperature at four hill and 12 river valley
 systems that comprised a wide range of habitats and ecosystems in Alberta,
 Canada (N = 240) between 2014 and 2020. We then modelled monthly
 temperature by season as a function of topography and different vegetation
 cover types using general linear mixed effect models. Summer maximum
 temperatures (Tmax) varied nearly 6 oC across the elevation gradient
 sampled. Local summer mean (Tmean) and maximum (Tmax) temperatures on
 steep, north-facing slopes (i.e., low levels of potential solar radiation)
 were up to 0.70 oC and 2.90 oC cooler than highly exposed areas,
 respectively. Tmax in incised valleys was between 0.26 and 0.28 oC cooler
 than other landforms, while areas with greater terrain roughness
 experienced maximum temperatures that were up to 1.62 oC cooler. We also
 found that forest cover buffered temperatures locally, with coniferous and
 mixedwood forests decreasing summer Tmean from 0.23 to 0.72 oC, and
 increasing winter Tmin by up to 2 oC, relative to non-forested areas.
       Spatial predictions of
 temperatures from iButton data loggers were similar to a gridded climate
 product (ClimateNA), but the difference between them increased with
 potential solar radiation, vegetation cover and terrain roughness. Species
 that can track their climate niche may be able to compensate for regional
 climate warming through local migrations to cooler microsites. Topographic
 and vegetation characteristics that are related to cooler local climates
 should be considered in the evaluation of future climate-change impacts
 and to identify potential refugia from climate change.
DOI: 10.5061/dryad.hmgqnk9gn
title: De novo genome assembly of Leptodactylus fuscus

description: This presents a de novo genome assembly
 of Leptodactylus fuscus. High molecular weight DNA was
 extracted from a L. fuscus embryo which had been preserved in
 ethanol upon collection in Garzón, Huila, Colombia. The library was
 prepared and sequenced with 10X Genomics Chromium. Linked
 reads were processed by Long Ranger basic v2.2.2 and assembled
 with Supernova v2.1.1. The assembled genome is 2.42 Gb with
 16,530 scaffolds &gt;=10 kb, and scaffold N50 = 363 kb. The assembly
 size of contigs larger than 10 kb (1.26 Gb) is about half of the
 estimated genome size (2.4 Gb). 72.6% of the BUSCO Tetrapoda gene
 annotations (version odb10) were identified.
description: High-molecular-weight genomic DNA was isolated from a single
 <i>Leptodactylus</i> <i>fuscus</i> individual and
 used to prepare a 10x Genomics Chromium library that was sequenced on
 Illumina HiSeq X sequencer (HudsonAlpha Institute of Biotechnology,
 Alabama, USA.). Barcodes were removed using the Long Ranger basic v2.2.2
 (https://support.10xgenomics.com/genome-exome/software/downloads/latest). Trimmed reads were used for k-mer estimation in Jellyfish (v2.2.7). The k-mer (k=21) frequency distribution was processed in GenomeScope to estimate the genome size, heterozygosity, and percentage of repeat content. The linked-reads were assembled using the Supernova v2.1.1 assembler using default settings and the “–accept-extreme-coverage” flag. A summary of the assembly is provided in the Table S3 of the associated publication. The assembled genome is 2.42 Gb (16,530 scaffolds &gt;=10 kb, scaffold N50 = 363 kb) and was outputted in the pseudohap2 format. The assembly size of contigs larger than 10 kb (1.26 Gb) is only ~1/2 of the estimated genome size (2.4 Gb). Effective depth coverage (48X) was in the middle of the recommended range (38-56X) which may have limited the success of the assembly. The completeness of the genome assembly was assessed using Benchmarking Universal Single-Copy Orthologs (BUSCOs, v4.0.5), and 72.6% of the BUSCO Tetrapoda gene annotations (version odb10) were identified.
description: 1. The assembly is outputted in the pseudohap2 format. Other
 formats like megabubbles and pseudohap are also available upon
 request.  2. The coverage of this genome to be ~50X
 which is within the recommended sequencing depth of 38-56X coverage.
 However, a flag "--accept-extreme-coverage" was used for
 assembling because dropping it caused the assembler to crash. While we
 tested other methods, like increasing the memory, only adding
 –accept-extreme-coverage seemed to resolve the issue.
DOI: 10.5061/dryad.69p8cz91z
title: Secondary Contact LTREB: Lake metadata

description: This dataset contains metadata for the core lakes of the Secondary Contact
 LTREB and other lakes that are occasionally sampled by the
 project. 
description: Much of the lake data were originally collected from public
 records and published in:  Post, David M., Eric P.
 Palkovacs, Erika G. Schielke, and Stanley I. Dodson. 2008.
 "Intraspecific variation in a predator affects community structure
 and cascading trophic interactions." Ecology 89 (7): 2019-2032.
 https://doi.org/10.1890/07-1216.1 Jones, A.W., E. P.
 Palkovacs, and D. M. Post. 2013. "Recent parallel divergence in body
 shape and diet source of alewife life history forms." Evolutionary
 Ecology 27: 1175-1187.
 https://doi.org/10.1007/s10682-013-9650-2.
description: Area is in hectares and maximum depth is in meters. Percent
 pelagic is the percent of the lake area with a depth &gt;3m,
 calculated from the bathymetry of the lakes studied by Jones et al.
 (2013).
DOI: 10.5061/dryad.sxksn032t
title: Warming of aquatic ecosystems disrupts aquatic-terrestrial linkages in the tropics

description: Aquatic ecosystems are tightly linked to terrestrial ecosystems by
 exchanges of resources, which influence species interactions, community
 dynamics and functioning in both ecosystem types. However, our
 understanding of how this coupling responds to climate warming is
 restricted to temperate, boreal, and arctic regions, with limited
 knowledge from tropical ecosystems. We investigated how warming aquatic
 ecosystems impacts cross-ecosystem exchanges in the tropics, through the
 export of aquatic resources into the terrestrial environment and the
 breakdown of terrestrial resources within the aquatic environment. We
 experimentally heated 50 naturally assembled aquatic communities,
 contained within different sized tank-bromeliads, to a 23.5 - 32°C
 gradient of mean water temperatures. The biomass, abundance, and richness
 of aquatic insects emerging into the terrestrial environment all declined
 with rising temperatures over a 45-day experiment. Structural equation and
 linear mixed-effects modelling suggested that these impacts were driven by
 deleterious effects of warming on insect development and survival, rather
 than being mediated by aquatic predation, nutrient availability, or
 reduced body size. Decomposition was primarily driven by microbial
 activity. However, total decomposition by both microbes and
 macroinvertebrates increased with temperature in all but the largest
 ecosystems, where it decreased. Thus, warming decoupled aquatic and
 terrestrial ecosystems, by reducing the flux of aquatic resources to
 terrestrial ecosystems but variably enhancing or reducing terrestrial
 resource breakdown in aquatic ecosystems. In contrast with increased
 emergence observed in warmed temperate ecosystems, future climate change
 is likely to reduce connectivity between tropical terrestrial and aquatic
 habitats, potentially impacting consumers in both ecosystem types. As
 tropical ectotherms live closer to their thermal tolerance limits compared
 to temperate species, warming can disrupt cross-ecosystem dynamics in an
 interconnected tropical landscape and should be considered when
 investigating ecosystem-level consequences of climate change. 
description: Further methodological
 details on data collection can be found within the published paper and its
 supplementary material.
description: This archive contains the dataset used for all modelling,
 analysis and plotting carried out in this paper. Please see the
 "ReadMe" sheet within the Excel file for further descriptive
 information on the contents of the dataset and the units of each column.
 Any missing data are indicated by “NA”. All additional methodological
 details are present in the main and supplementary components of the
 published paper.