cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9s4mw6mds
title: HyRAD-X Exome Capture Museomics Unravels Giant Ground Beetle Evolution

description: Abstract Advances in phylogenomics contribute toward resolving
 long-standing evolutionary questions. Notwithstanding, genetic diversity
 contained within more than a billion biological specimens deposited in
 natural history museums remains recalcitrant to analysis owing to
 challenges posed by its intrinsically degraded nature. Yet that
 tantalizing resource could be critical in overcoming taxon sampling
 constraints hindering our ability to address major evolutionary questions.
 We addressed this impediment by developing phyloHyRAD, a new bioinformatic
 pipeline enabling locus recovery at a broad evolutionary scale from
 HyRAD-X exome capture of museum specimens of low DNA integrity using a
 benchtop RAD-derived exome-complexity-reduction probe set developed from
 high DNA integrity specimens. Our new pipeline can also successfully align
 raw RNAseq transcriptomic and ultraconserved element reads with the
 RAD-derived probe catalog. Using this method, we generated a robust
 timetree for Carabinae beetles, the lack of which had precluded study of
 macroevolutionary trends pertaining to their biogeography and
 wing-morphology evolution. We successfully recovered up to 2,945 loci with
 a mean of 1,788 loci across the exome of specimens of varying age.
 Coverage was not significantly linked to specimen age, demonstrating the
 wide exploitability of museum specimens. We also recovered fragmentary
 mitogenomes compatible with Sanger-sequenced mtDNA. Our phylogenomic
 timetree revealed a Lower Cretaceous origin for crown group Carabinae,
 with the extinct Aplothorax (Waterhouse, 1841) nested within the genus
 Calosoma (Weber, 1801) demonstrating the junior synonymy of
 Aplothorax syn. nov., resulting in the new combination Calosoma burchellii
 (Waterhouse, 1841) comb. nov. This study compellingly illustrates that
 HyRAD-X and phyloHyRAD efficiently provide genomic-level data sets
 informative at deep evolutionary scales.
DOI: 10.1594/pangaea.774183
title: Analysis of symptoms of rural workers exposed to pesticides

description: This cross-sectional study was conducted in southern Minas Gerais, in two counties: São Gonçalo do Sapucaí and Silvianópolis. Presented as objective to verify the important variables associated with the occurrence of symptoms of subacute intoxication related to pesticides exposure. A questionnaire was dedicated to a sample of 412 workers. An analysis of non-conditional logistic regression was applied gradually. The likelihood ratio method was used to define the significant variables in the final model. Of the analysed population, 59.2% reported symptoms typical of subacute intoxication. Of the respondents, 91.5% reported knowing the deleterious effects associated with exposure to pesticides. The adjusted model was found with the significant variables: being male that presented Prevalence Odds Ratio (POR) adjusted . PORof 0.54 (95% CI 0.36 to 0.81), already hospitalized for poisoning with pesticides, POR of 3.26 (95% CI 1.08 to 9.82), living in the rural area of residence., POR of 2.17 (95% CI 1.20 to 3.93) and type of employment relationship or temporary employment, POR of 2.32 (95% CI 1.08 to 4.95).
description: Ordinal number gives the ID.
DOI: 10.5061/dryad.5mkkwh746
title: Supplementary figures for SpeciesTopoTestR: likelihood-based tests of species trees

description: Likelihood-based tests of phylogenetic trees are a foundation of modern
 systematics, and examples of such tests are among the most
 widely-referenced scientific literature of all time. Over the past decade,
 an enormous wealth and diversity of model-based approaches have been
 developed for phylogenetic inference of both gene trees and species trees.
 However, while many techniques exist for conducting formal
 likelihood-based tests of gene trees, such frameworks are comparatively
 underdeveloped and underutilized for testing species-level hypotheses. To
 date, widely-used tests of tree topology are designed to assess the fit of
 classical models of molecular sequence data and individual gene trees, and
 thus, are not readily applicable to the problem of species tree inference.
 We derive several analogous likelihood-based approaches for testing
 species-level topologies using modern species tree models and algorithms
 for maximum likelihood estimation under the multispecies coalescent. For
 the purpose of comparing support for species-level relationships, these
 tests leverage the statistical procedures of their original gene
 tree-based counterparts that have a long history for testing phylogenetic
 hypotheses at single loci. We discuss and demonstrate a number of
 applications, limitations, and important considerations of these tests
 using simulated and empirical phylogenomic datasets that include both
 bifurcating topologies and reticulate network models of species
 relationships. Finally, we introduce the open-source R
 package SpeciesTopoTestR (Species Topology Tests in R) that includes a suite of functions for conducting formal likelihood-based tests of species topologies.
DOI: 10.1594/pangaea.68013
title: Station list of SONNE cruise SO143
DOI: 10.1594/pangaea.846146
title: Benthic and substrate cover data derived from a time series of photo-transect surveys for the Eastern Banks, Moreton Bay Australia in 2012-06
DOI: 10.1594/pangaea.846185
title: Benthic and substrate cover data derived from a time series of photo-transect surveys for the Eastern Banks, Moreton Bay Australia in 2013-02
DOI: 10.1594/pangaea.846186
title: Benthic and substrate cover data derived from a time series of photo-transect surveys for the Eastern Banks, Moreton Bay Australia in 2013-05
DOI: 10.1594/pangaea.846266
title: Benthic and substrate cover data derived from a time series of photo-transect surveys for the Eastern Banks, Moreton Bay Australia in 2014-07
DOI: 10.1594/pangaea.846142
title: Benthic and substrate cover data derived from a time series of photo-transect surveys for the Eastern Banks, Moreton Bay Australia in 2007-08
DOI: 10.1594/pangaea.846143
title: Benthic and substrate cover data derived from a time series of photo-transect surveys for the Eastern Banks, Moreton Bay Australia in 2011-06
DOI: 10.5061/dryad.vmcvdncr3
title: Data from: Differential effects of fertilisers on pollination and parasitoid interaction networks

description: Grassland fertilisation drives non-random plant loss resulting in areas
 dominated by perennial grass species. How these changes cascade through
 linked trophic levels, however, is not well understood. We studied how
 grassland fertilisation propagates change through the plant assemblage
 into the plant-flower visitor, plant-leaf miner and leaf miner-parasitoid
 networks using a year’s data collection from a long-term grassland
 fertiliser application experiment. Our experiment had three fertiliser
 treatments each applied to replicate plots 15 m2 in size: mineral
 fertiliser, farmyard manure, and mineral fertiliser and farmyard manure
 combined, along with a control of no fertiliser. The combined treatment
 had the most significant impact, and both plant species richness and
 floral abundance decreased with the addition of fertiliser. While insect
 species richness was unaffected by fertiliser treatment, fertilised plots
 had a significantly higher abundance of leaf miners and parasitoids and a
 significantly lower abundance of bumblebees. The plant-flower visitor and
 plant-herbivore networks showed higher values of vulnerability and lower
 modularity with fertiliser addition, while leaf miner-parasitoid networks
 showed a rise in generality. The different groups of insects were impacted
 by fertilisers to varying degrees: while the effect on abundance was the
 highest for leaf miners, the vulnerability and modularity of flower
 visitor networks was the most affected. The impact on the abundance of
 leaf miners was positive and three times higher than the impact on
 parasitoids, and the impact on bumblebee abundance was negative and double
 the magnitude of impact on flower abundance. Overall our results show that
 while insect species richness was unaffected by fertilisers, network
 structure changed significantly as the replacement of forbs by grasses
 resulted in changes in relative abundance across trophic levels, with the
 direction of change depending on the type of network. By studying multiple
 networks simultaneously, we were able to rank the relative impact of
 habitat change on the different groups of species within the community.
 This provided a more holistic picture of the impact of agricultural
 intensification and provides useful information when deciding on
 priorities for mitigation. 01-Oct-2020
description: Insect data were hand collected or reared from host.
 Insect identification was done or confirmed by taxonomists (see
 methods in the paper).
description: In flower count,  we used information on the number of flowers
 per flower unit (capitulum or umbel) by: Baldock KCR et
 al. 2015 Where is the UK’s pollinator biodiversity? The importance of
 urban areas for flower-visiting insects. Proc. R. Soc. B 282: 20142849.
 http://dx.doi.org/10.1098/rspb.2014.2849
DOI: 10.1594/pangaea.846144
title: Benthic and substrate cover data derived from a time series of photo-transect surveys for the Eastern Banks, Moreton Bay Australia in 2012-02
DOI: 10.1594/pangaea.867188
title: Benthic and substrate cover data derived from a time series of photo-transect surveys for the Eastern Banks, Moreton Bay Australia in 2015-06
DOI: 10.5061/dryad.0gb5mkkzw
title: Making sense of virus size and the tradeoffs shaping viral fitness

description: Viruses span an impressive size range, with genome length varying a
 thousandfold and virion volume nearly a millionfold. For cellular
 organisms the scaling of traits with size is a pervasive influence on
 ecological processes, but whether size plays a central role in viral
 ecology is unknown. Here we focus on viruses of aquatic unicellular
 organisms, which exhibit the greatest known range of virus size. We
 outline hypotheses within a quantitative framework, and analyze data where
 available, to consider how size affects the primary components of viral
 fitness. We argue that larger viruses have fewer offspring per infection
 and slower contact rates with host cells, but a larger genome tends to
 increase infection efficiency, broaden host range, and potentially
 increase attachment success and decrease decay rate. These countervailing
 selective pressures may explain why a breadth of sizes exist and even
 coexist when infecting the same host populations. Oligotrophic ecosystems
 may be enriched in “giant” viruses, because environments with
 resource-limited phagotrophs at low concentrations may select for broader
 host range, better control of host metabolism, lower decay rate, and a
 physical size that mimics bacterial prey. Finally, we describe where
 further research is needed to understand the ecology and evolution of
 viral size diversity.
description: All tables are measurements of viral traits compiled from the
 literature. Details on the compiled data and their sources are provided in
 the Excel files.
DOI: 10.1594/pangaea.915002
title: Spectrum gamma ray borehole logging of MeBo sediment core GeoB23711-5

description: Logging was performed with the sea floor drill rig MARUM-MeBo70 in a borehole drilled with a 103 mm diameter bit. The 1460 Slimhole Memory SGR instrument developed by ANTARES Datasystems GmbH was used. A CsI(Na) crystal with outer diameter of 37 mm and 250 mm length is used as detector. The probe provides Natural Gamma Ray counts and analyses the spectrum for the concentrations of the natural gamma ray emitters potassium, thorium and uranium with an accuracy of about 10%. The probe was deployed in the memory mode with the logging string being inserted into the drill string. The measurement was conducted as upcast hooking up the logging string with a wire inside the drill string. Wire speed was about 2 cm/s and the logging frequency was 0.5 Hz. Data Processing including the correction for bore hole diameter and signal attenuation by the drill string was conducted using the Antares software GeoBase 6.22.1
DOI: 10.1594/pangaea.915003
title: Spectrum gamma ray borehole logging of MeBo sediment core Geob23725-2

description: Logging was performed with the sea floor drill rig MARUM-MeBo70 in a borehole drilled with a 103 mm diameter bit. The 1460 Slimhole Memory SGR instrument developed by ANTARES Datasystems GmbH was used. A CsI(Na) crystal with outer diameter of 37 mm and 250 mm length is used as detector. The probe provides Natural Gamma Ray counts and analyses the spectrum for the concentrations of the natural gamma ray emitters potassium, thorium and uranium with an accuracy of about 10%. The probe was deployed in the memory mode with the logging string being inserted into the drill string. The measurement was conducted as upcast hooking up the logging string with a wire inside the drill string. Wire speed was about 2 cm/s and the logging frequency was 0.5 Hz. Data Processing including the correction for bore hole diameter and signal attenuation by the drill string was conducted using the Antares software GeoBase 6.22.1
DOI: 10.5061/dryad.sf7m0cg4b
title: Data from: Harvester ant seed removal in an invaded sagebrush ecosystem: implications for restoration

description: A better understanding of seed movement in plant community dynamics is
 needed, especially in light of disturbance-driven changes and investments
 into restoring degraded plant communities. A primary agent of change
 within the sagebrush-steppe is wildfire and invasion by non-native forbs
 and grasses, primarily cheatgrass (Bromus tectorum). Our objectives were
 to quantify seed removal and evaluate ecological factors influencing seed
 removal within degraded sagebrush-steppe by granivorous Owyhee harvester
 ants (Pogonomyrmex salinus Olsen). In 2014, we sampled 76 harvester ant
 nests across 11 plots spanning a gradient of cheatgrass invasion (40-91%
 cover) in southwestern Idaho, USA. We presented seeds from four plant
 species commonly used in post-fire restoration at 1.5 and 3.0 m from each
 nest to quantify seed removal. We evaluated seed selection for presented
 species, monthly removal, and whether biotic and abiotic factors (e.g.,
 distance to nearest nest, temperature) influenced seed removal. Our top
 model indicated seed removal was positively correlated with nest height,
 an indicator of colony size. Distance to seeds and cheatgrass canopy cover
 reduced seed removal, likely due to increased search and handling time.
 Harvester ants were selective, removing Indian ricegrass (Achnatherum
 hymenoides) more than any other species presented. We suspect this was due
 to ease of seed handling and low weight variability. Nest density
 influenced monthly seed removal, as we estimated monthly removal of 1,890
 seeds for 0.25 ha plots with 1 nest and 29,850 seeds for plots with 15
 nests. Applying monthly seed removal to historical restoration treatments
 across the western U.S. showed harvester ants can greatly reduce seed
 availability at degraded sagebrush sites; for instance, fourwing saltbush
 (Atriplex canescens) seeds could be removed in &lt;2 months.
 Collectively, these results shed light on seed removal by harvester ants
 and emphasize their potential influence on post-fire restoration within
 invaded sagebrush communities.
DOI: 10.1594/pangaea.915004
title: Spectrum gamma ray borehole logging of MeBo sediment core GeoB23731-2 (first run)

description: Logging was performed with the sea floor drill rig MARUM-MeBo70 in a borehole drilled with a 103 mm diameter bit. The 1460 Slimhole Memory SGR instrument developed by ANTARES Datasystems GmbH was used. A CsI(Na) crystal with outer diameter of 37 mm and 250 mm length is used as detector. The probe provides Natural Gamma Ray counts and analyses the spectrum for the concentrations of the natural gamma ray emitters potassium, thorium and uranium with an accuracy of about 10%. The probe was deployed in the memory mode with the logging string being inserted into the drill string. The measurement was conducted as upcast hooking up the logging string with a wire inside the drill string. This was the first of two subsequent runs. Wire speed was about 9 cm/s and the logging frequency was 0.5 Hz. Data Processing including the correction for bore hole diameter and signal attenuation by the drill string was conducted using the Antares software GeoBase 6.22.1
DOI: 10.1594/pangaea.915008
title: Spectrum gamma ray borehole logging of MeBo sediment core GeoB23731-2 (second run)

description: Logging was performed with the sea floor drill rig MARUM-MeBo70 in a borehole drilled with a 103 mm diameter bit. The 1460 Slimhole Memory SGR instrument developed by ANTARES Datasystems GmbH was used. A CsI(Na) crystal with outer diameter of 37 mm and 250 mm length is used as detector. The probe provides Natural Gamma Ray counts and analyses the spectrum for the concentrations of the natural gamma ray emitters potassium, thorium and uranium with an accuracy of about 10%. The probe was deployed in the memory mode with the logging string being inserted into the drill string. The measurement was conducted as upcast hooking up the logging string with a wire inside the drill string. This was the second of two subsequent runs. Wire speed was about 9 cm/s and the logging frequency was 0.5 Hz. Data Processing including the correction for bore hole diameter and signal attenuation by the drill string was conducted using the Antares software GeoBase 6.22.1
DOI: 10.1594/pangaea.915130
title: Magnetic susceptibility borehole logging of MeBo sediment core GeoB23711-5

description: Logging was performed with the sea floor drill rig MARUM-MeBo70 in a borehole drilled with a 103 mm diameter bit. The 1188 Slimhole Memory Magnetic Susceptibility instrument developed by ANTARES Datasystems GmbH was used. Three coils are used for measuring the apparent magnetic susceptibility with an alternating magnetic field tuned to resonate at 1 kHz. The accuracy is within 5 %. The vertical resolution is about 20 cm. The probe was deployed in the memory mode with the logging string being inserted into the drill string and the sensors located below the drill bit. The measurement was conducted as upcast while the drill string was pulled back to the seafloor out of the borehole. The trip out speed was about 1 cm/s and the logging frequency was 0.5 Hz. Data Processing was conducted using the Antares software GeoBase 6.22.1
DOI: 10.5061/dryad.d7wm37q02
title: Data from: Body size and shape responses to warming and resource competition

description: Body size is a fundamental trait that impacts many aspects of species
 biology and ecology. It is in turn influenced by a suite of environmental
 factors, and often decreases with warming. Although environmental
 conditions can also impact body shape, which is another functional trait
 that influences locomotion, resource acquisition, and potentially
 physiological processes, such responses are poorly understood and rarely
 quantified.  We experimentally tested the independent and
 combined effects of environmental temperature, resource level, and
 interspecific competition on the body shape and size responses of two
 model protist species. We also tested the degree to which these
 individual-level phenotypic responses are associated with population
 densities and species coexistence.  Body shape was strongly
 influenced by resource competition, whereas body size changes were mainly
 driven by environmental temperature. In both species, lower resource
 levels resulted in body shape elongation, suggesting that relatively more
 elongate individuals with potentially higher swimming speed were
 advantaged in the resource scarce environment. However, competition
 had contrasting influence on the body shape of the two species.
 Competition decreased the population densities of Blepharisma
 japonicum, which exhibited relative body shape elongation, similar to the
 response at low resource levels. In contrast, competition increased the
 population densities of Paramecium aurelia, which
 exhibited reduced elongation similar to body shape response at
 high resource levels. Hence, body shape responses could be indicative of
 changes in resource availability, aiding our understanding of competitive
 hierarchies and species interactions. Coexistence was observed in all
 treatment combinations, likely because body size of both species decreased
 similarly under warming, potentially maintaining constant per
 capita competitive intensity. These findings, along with recent
 research on phytoplankton, diverse pelagic invertebrates, and birds
 highlight the importance of body shape and morphology across different
 taxonomic groups. Hence, we call for body size and shape to be considered
 in concert when investigating ecological consequences of climate warming.
description: Temperature column reflects the two temperature levels: high
 temperature (HT - 25 °C) and low temperature (LT - 22 °C)
 Resource column reflects the two temperature levels: high
 resource (HR - 0.56 g L<sup>-1</sup> protozoa pellet) and low
 resource (LR - 0.28 g L<sup>-1 </sup>protozoa pellet) dissolved in spring water. Length, width, biovolume and aspect ratios are mean measurements obtained from 9-11 individuals per replicate.
DOI: 10.1594/pangaea.915131
title: Magnetic susceptibility borehole logging of MeBo sediment core GeoB23702-5

description: Logging was performed with the sea floor drill rig MARUM-MeBo70 in a borehole drilled with a 103 mm diameter bit. The 1188 Slimhole Memory Magnetic Susceptibility instrument developed by ANTARES Datasystems GmbH was used. Three coils are used for measuring the apparent magnetic susceptibility with an alternating magnetic field tuned to resonate at 1 kHz. The accuracy is within 5 %. The vertical resolution is about 20 cm. The probe was deployed in the memory mode with the logging string being inserted into the drill string and the sensors located below the drill bit. The measurement was conducted as upcast while the drill string was pulled back to the seafloor out of the borehole. The trip out speed was about 1 cm/s and the logging frequency was 0.5 Hz. Data Processing was conducted using the Antares software GeoBase 6.22.1
DOI: 10.1594/pangaea.915132
title: Magnetic Susceptibility borehole logging of MeBo sediment core Geob23725-2

description: Logging was performed with the sea floor drill rig MARUM-MeBo70 in a borehole drilled with a 103 mm diameter bit. The 1188 Slimhole Memory Magnetic Susceptibility instrument developed by ANTARES Datasystems GmbH was used. Three coils are used for measuring the apparent magnetic susceptibility with an alternating magnetic field tuned to resonate at 1 kHz. The accuracy is within 5 %. The vertical resolution is about 20 cm. The probe was deployed in the memory mode with the logging string being inserted into the drill string and the sensors located below the drill bit. The measurement was conducted as upcast while the drill string was pulled back to the seafloor out of the borehole. The trip out speed was about 1 cm/s and the logging frequency was 0.5 Hz. Data Processing was conducted using the Antares software GeoBase 6.22.1
DOI: 10.1594/pangaea.915155
title: Acoustic borehole logging of MeBo sediment core GeoB23711-3

description: Logging was performed with the sea floor drill rig MARUM-MeBo70 in a borehole drilled with a 103 mm diameter bit. The 1343 Slimhole Memory Acoustic instrument developed by ANTARES Datasystems GmbH was used. The probe consists of 1 transmitter and two receivers in 0.9 and 1.0 m distance, respectively. Sound velocity in the formation was calculated from the time difference of signal arrival at both receivers using the waveform processing module of the Antares software GeoBase 6.22. The vertical resolution is about 10 cm. The accuracy is better than 10 m/s.