cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3r2280gcr
title: Negative effects of urbanisation on terrestrial arthropod communities: a meta-analysis

description: Aim: Urbanisation is one of the most significant anthropogenic alterations
 of the earth's surface, and constitutes a major threat to
 biodiversity at the global level. Arthropods are a very diverse group of
 organisms, with many species that provide essential ecosystem services.
 However, their response to urbanisation is still unclear. Here we
 conducted the first meta-analysis that evaluates the overall effects of
 urbanisation on terrestrial arthropod communities and drives factors
 related to cities, arthropods and methods. Location: Global. Time period:
 1979-2019. Major taxa studied: Arthropods. Methods: We compiled a dataset
 of 162 publications that evaluated urbanisation effects along rural-urban
 gradients that yielded 196 observations for diversity and 148 for
 abundance of arthropods. Moderator variables related to cities (climate
 region, size, age, air pollution level and vegetation cover), arthropods
 (taxonomic and functional group, mobility level) and methods (study
 duration and type of gradient) were considered. We analysed the data
 through a hierarchical meta-analysis that allowed us to take into account
 the dependency of multiple effect sizes obtained from one study. Results:
 Overall, urbanisation had a negative effect on diversity and abundance of
 terrestrial arthropods. The magnitude of the changes in diversity and
 abundance along the urban gradient depended on arthropod taxonomic group.
 Coleoptera and Lepidoptera were the most affected groups, suggesting that
 not all species respond in the same way to urbanisation. In addition, the
 age of the cities had a slightly negative influence but just on abundance.
 Main conclusions: Our results indicate that terrestrial arthropod
 communities are less diverse and abundant in more urbanised landscapes.
 Considering the current biodiversity crisis and the fact that urbanisation
 is one of the most extreme forms of global environmental change, the
 evidence here presented could be useful to support and direct new
 conservation efforts in urban habitats.
DOI: 10.5061/dryad.w3r2280mm
title: Nothing as it seems: Behavioral and morphological plasticity appear correlated but are not in a Neotropical tadpole

description: In response to environmental stressors, organisms often demonstrate
 flexible responses in morphology, life-history, or behaviour. However, it
 is currently unclear if such plastic responses are coordinated or operate
 independent of one another. In vertebrates, this may partly result from
 studies examining population- or species- level mean responses, as opposed
 to finer-grained analyses of individuals or families. We measured
 predator-specific morphological and colouration plasticity in 42 families
 of tadpoles of the treefrog Dendropsophus ebraccatus, and behavioural
 plasticity from 18 of these families, allowing us to examine the
 correlation between three predator-induced plastic responses. For all
 three plastic responses, tadpoles showed strong opposing responses to each
 of two predators, providing the appearance of co-variation in plasticity.
 However, examination of individual families revealed strong correlation
 between morphological and colouration plasticity, but no correlations
 between either morphology or colour and behavioural plasticity. Thus, our
 analysis shows that some aspects of the plastic phenotype develop together
 while others function independently. This highlights the importance of
 examining individual- and family-level variation for understanding the
 adaptive significance of developmental plasticity, which is crucial for a
 holistic appreciation of phenotypic plasticity and its importance in
 ecology and evolution.
DOI: 10.5061/dryad.51c59zw4z
title: Long-term logging residue loadings affect tree growth but not soil nutrients in lodgepole pine forests

description: Both above- and below-ground characteristics are affected by logging
 residue loadings. Long-term monitoring of tree growth and soil nutrients
 was conducted. We found that tree growth but not soil nutrients were
 affected. There were dynamic relationships between tree growth and logging
 residue loadings.
description: The experiment was conducted near Satah Mountain
 (52<sup>o</sup>28’N, 124<sup>o</sup>43’W), located
 about 110 km northwest of Alexis Creek, west-central British Columbia,
 Canada. The region has a mean annual precipitation which varies between
 300 and 800 mm, and much of it comes as snow during the winter. The mean
 annual temperature is 1.3°C and the snowing cover is usually from November
 to April. Four experimental treatments were randomly arranged into five
 blocks which are over 100 ha each in lodgepole pine plantations. Four 20 m
 × 20 m plots were established in each block.The treatments were (1)
 removal of all logging residues (N, 0 Mg ha<sup>-1</sup>),
 removed manually; (2) logging residue loading similar to
 whole-tree-harvesting residuals left on site (W, 35-45 Mg
 ha<sup>-1</sup>); (3) logging residue loading similar to
 stem-only-harvesting residuals left on site (S, 60-70 Mg
 ha<sup>-1</sup>); and (4) logging residue loading similar to
 double that of stem-only-harvesting and more similar to disease and
 insects killed stands (D, 100-120 Mg ha<sup>-1</sup>). The N,
 W, S, and D treatments were randomly assigned to the plots within each
 block and no further measurements of the debris weight change over time
 were made. For tree height and base diameter data, we
 sampled in each plot were measured 10 times (years 1, 2, 3, 5, 6, 9, 10,
 11, 14 and 19) over the study period (1996 to 2015). The units for data is
 cm. For soil  nutrients data, we sampled in each
 plot in 2001, 2006 and 2015. All soil samples were collected from 0-20 cm
 mineral layer.  All soil samples were analyzed for total carbon (C), total
 nitrogen (N), available phosphorus (P) and exchangeable cations (Ca, K,
 Mg). For foliar nutrients, we sampled in each plot in
 2015. Foliage samples were analyzed for N, P, Ca, K, Mg, Zn, Cu, B and
 sulphur (S). Soil and foliage samples were analyzed at the chemistry
 laboratory of the British Columbia Ministry of Forests, Lands and Natural
 Resource Operations following their standard analytical protocols (Carter
 and Gregorich 2006). C and N were analyzed by elemental analyzer (Thermo
 Electron Corporation, MA, USA), metal elements mentioned above were
 analyzed by inductively coupled plasma mass spectrometer (ICP-MS, Agilent,
 Santa Clara, CA, USA) and available P was measured with a UV-visible
 spectrophotometer after extraction with acid-ammonium fluoride
 solution.
DOI: 10.5061/dryad.79cnp5hs0
title: Environmental cues for dispersal in a filamentous fungus in simulated islands

description: Airborne dispersal is a key part of the life history of many saprotrophic
 fungi. Theory suggests a transition from growth and resource capture to
 airborne dispersal at some point as the resource availability in a patch
 declines, but in the absence of an experimental model system this theory
 has not been empirically tested. For saprobes, resources are arrayed in an
 ever-shifting archipelago of islands with the quality of each island being
 defined by patch size and resource density. We tracked how Phacidium
 lacerum, a saprotrophic fungus, allocated resources to dispersal in small
 and large islands of varying resource density through production of
 fruiting bodies. We found that Phacidium altered the timing and rate of
 dispersal allocation in response to both patch size and resource density.
 On small resource islands, Phacidium drastically increased dispersal
 allocation after reaching the edge of the patch; if resource density was
 sufficient, on larger resource islands, Phacidium began allocation to
 dispersal prior to reaching the edge of the island, suggesting an
 additional absolute total resource level cue. These results are consistent
 with a two-cue model for the switch to allocation to airborne dispersal:
 1) absolute resource level controlled by the fungus, 2) the fungus’
 perception of patch size. This can be thought of as a mix between a full
 resource allocation switch (bang-bang) if the fungus perceives the patch
 is fully occupied with a smaller magnitude early shift (bet-hedging) if
 absolute resource level crosses a threshold.
description: This data was collected via a lab experiment exploring resource
 allocation towards dispersal in a filamentous fungus <em>Phacidium
 lacerum </em>on malt extract agar. The species were grown on varying
 levels of nutrient concentration and Petri-dish size to track the
 difference in production of fruiting bodies in vitro.  
description: There are equations in some of the columns to calculate relative
 growth rate.
DOI: 10.5061/dryad.1g1jwstrv
title: Presents-absents of woody species on termite mounds and the savanna matrix in Africa

description: Questions: Although the biogeography of plant communities has been well
 studied, mechanisms controlling plant community diversity are still poorly
 understood. Stochastic and deterministic processes are hotly debated as
 being key in structuring communities across taxa. Here we ask, to what
 extent are plant communities on termite mounds shaped by either stochastic
 or deterministic processes within and between regions on the African
 continent? Methods: We performed a meta-analysis on 23 studies that
 satisfied our selection criteria out of 369 that we initially identified.
 All these studies sampled woody plants that occurred on termite mounds and
 the surrounding matrix. In order to disentangle the relative importance of
 deterministic and stochastic processes in generating β-diversity between
 mound-mound and matrix-matrix plots, within and between regions, we
 applied null models. We also assessed the relationship between species
 richness and environmental variables for each site. Results: Of the
 environmental variables assessed at each site, only altitude had a
 significant (negative) relationship with species richness. Within each
 region comparison of mound-mound, matrix-matrix and matrix-mound species
 composition did not significantly deviate from the null models of random
 expectation. Between regions, the observed pattern was significantly
 higher than expected for both mound-mound and matrix-matrix plots between
 East and West Africa. Surprisingly, the comparison between southern Africa
 and both East and West Africa did not significantly deviate from the null
 expectation, regardless of increased spatial separation. We attributed the
 within region pattern to homogenizing dispersal and reliance on the same
 species pool (γ) for matrix and mound plots. Between regions pattern, was
 influenced by both deterministic and stochastic processes. 
 Conclusion: Our results suggest that the processes responsible for
 vegetation composition between mound-mound, matrix-matrix and mound-matrix
 are stochastic in nature due to lack of difference from the null
 expectation. However, regional patterns are governed by both deterministic
 and stochastic processes. 
description: Meta-analysis
DOI: 10.5061/dryad.9zw3r22b8
title: Agricultural intensification and land use change: assessing country-level induced intensification, land sparing and rebound effect

description: In the context of growing societal demands for land based products, crop
 production can be increased through expanding cropland or intensifying
 production on cultivated land. Intensification can allow sparing land for
 nature, but it can also drive further expansion of cropland, i.e. a
 rebound effect. Conversely, constraints on cropland expansion may induce
 intensification. We tested those hypotheses by investigating the
 bidirectional relations between changes in cropland area and intensity,
 using a global cross-country panel dataset over 1961-2016. We used a
 cointegration approach with additional tests to disentangle long and
 short-run causal relations between variables, and total factor
 productivity and yields as two measures of intensification. Over the long
 run we found support for the induced intensification thesis for low income
 countries. In the short run, intensification resulted in a
 rebound effect in middle-income countries, which include many key
 agricultural producers strongly competitive in global agricultural
 commodity markets. This rebound effect manifested for commodities with
 high price-elasticity of demand, including rubber, flex crops (sugarcane,
 palm oil and soybean), and tropical fruits. Over the long run,
 strong rebound effects remained for key commodities such as flex crops and
 rubber. Staple cereals such as wheat and rice manifested significant land
 sparing. In low-income countries, intensification driven by
 increases in total factor productivity was associated with a stronger
 rebound effect than yields increases. Agglomeration economies may drive
 yields increases for key tropical commodity crops. Our study design could
 allow addressing other complex long and short run causal dynamics in land
 and social-ecological systems.
description: This database has been created by gathering variables
 retreived from: i) Well known data sources such as the World Bank, the
 Food and Agriculture Organization and the United States Department of
 Agriculture; ii) Less well known data sources iii) Other researchers'
 work. These data was downloaded and stored on a commond folder.
 Afterwards, the data was gathered and homogenized (same format and country
 names) on a unique database using STATA sofware. 
description: The database and the codes should be used after reading the
 "Supplementary information" of the paper this data was used for.
 Specially the section of the "Long and short run causal dynamics".
DOI: 10.25934/pr00012556.0
title: Available datapackage for study 'A Confectionary-Based Screening Tool for Assessing Chemosensory Loss in COVID-19 Patients'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.5061/dryad.xd2547ddf
title: Data from: A de novo chromosome-level genome assembly of Coregonus sp. “Balchen”: one representative of the Swiss Alpine whitefish radiation

description: Salmonids are of particular interest to evolutionary biologists due to
 their incredible diversity of life-history strategies and the speed at
 which many salmonid species have diversified. In Switzerland alone, over
 30 species of Alpine whitefish from the subfamily Coregoninae have evolved
 since the last glacial maximum, with species exhibiting a diverse range of
 morphological and behavioural phenotypes. This, combined with the whole
 genome duplication which occurred in the ancestor of all salmonids, makes
 the Alpine whitefish radiation a particularly interesting system in which
 to study the genetic basis of adaptation and speciation and the impacts of
 ploidy changes and subsequent rediploidization on genome evolution.
 Although well curated genome assemblies exist for many species within
 Salmonidae, genomic resources for the subfamily Coregoninae are lacking.
 To assemble a whitefish reference genome, we carried out PacBio sequencing
 from one wild-caught Coregonus sp. “Balchen” from Lake Thun to ~90x
 coverage. PacBio reads were assembled independently using three different
 assemblers, Falcon, Canu and wtdbg2 and subsequently scaffolded with
 additional Hi-C data. All three assemblies were highly contiguous, had
 strong synteny to a previously published Coregonuslinkage map, and when
 mapping additional short-read data to each of the assemblies, coverage was
 fairly even across most chromosome-scale scaffolds. Here, we present the
 first de novogenome assembly for the Salmonid subfamily Coregoninae. The
 final 2.2 Gb wtdbg2 assembly included 40 scaffolds, an N50 of 51.9 Mb, and
 was 93.3% complete for BUSCOs. The assembly consisted of ~52% TEs and
 contained 44,525 genes.
description: For detailed methods please see the associated publication.
description: This repository contains supplementary files for De-Kayne, Zoller
 and Feulner 2020 Coregonus sp
 "Balchen" genome assembly GCA_902810595.1
 The main assembly was produced with wtdbg2 and is on ENA:
 https://www.ebi.ac.uk/ena/browser/view/GCA_902810595.1
 The files included are:
 AWG_v2.AED0.6_pseudo_contigs.embl.gz - the embl format
 annotation for unscaffolded contigs
 AWG_v2_GO_annotation.out - the functional 'GO'
 annotation for the full GCA_902810595.1 assembly (made using
 Pannzer2) AWG_v2_MakerOutput.gff - the unfiltered/raw
 Maker annotation for the full GCA_902810595.1 assembly
 Canu.AWG.fasta.gz - the scaffolded Canu assembly containing 40
 scaffolds and 3513 contigs Falcon.AWG.fasta.gz - the
 scaffolded Falcon assembly containing 40 scaffolds and 3705
 contigs WF_RepeatLibrary.lib - the repeat library
 used to identify repeats in the whitefish genome (methods can be found in
 the paper)
DOI: 10.5281/zenodo.17954991
title: 16S rRNA Sequencing Analysis of Intestinal Microbiota Structure in Mice After Fecal Microbiota Transplantation
DOI: 10.5061/dryad.1g1jwstrw
title: Data from: Genetic analysis of Boletus edulis suggests that intra-specific competition may reduce local genetic diversity as a woodland ages

description: Ectomycorrhizal fungi are key players in terrestrial ecosystems yet their
 mating systems and population dynamics remain poorly understood. We
 investigated the fine-scale relatedness structure and genetic diversity of
 Boletus edulis, one of the world’s most commercially important wild
 mushrooms. Microsatellite genotyping of fruiting bodies from 14 different
 sites around Bielefeld in Germany revealed little in the way of population
 structure over a geographic scale of several kilometers. However, on a
 more local scale we found evidence for elevated relatedness as well as
 inbreeding. We also observed a significant negative association between
 the genetic diversity of fruit and the age of the trees under which they
 were sampled. Taken together, our results suggest that as genets mature,
 they compete and potentially create conditions under which further spores
 struggle to become established. By implication, even though this species
 is widely picked, propagules remain common enough to create strong
 competition when new habitats become available.
description: A total of 134<i> B. edulis</i> sporocarps were
 sampled during 2015 from around Bielefeld in northwest Germany. In order
 to sample the sporocarps as comprehensively as possible, all of the sites
 were visited between two and four times a week from mid-August until
 mid-October 2015. We downloaded the <i>B. edulis </i>genome
 sequence version 1.0 from
 https://mycocosm.jgi.doe.gov/Boled1/Boled1.home.html and searched for
 perfect di- tri- and tetranucleotide motifs using MISA-web. Primers were
 designed for microsatellites with unusually large numbers of repeats
 (<i>B. edulis</i> tends to have short microsatellites, so in
 practice this meant more than eight pure repeats for dinucleotides, and
 more than four pure repeats for tri- and tetranucleotides). Primers were
 designed using Primer3Plus. Testing was then conducted in multiplexes on a
 panel of 96 <i>B. edulis</i> samples, and primers revealing
 three or more alleles were combined into multiplexes for genotyping. Total
 genomic DNA was extracted using a standard proteinase K digestion followed
 by glass milk extraction. For each PCR reaction, 1µl of DNA was added to
 3µl H<sub>2</sub>O and 4µl Qiagen 2X multiplex PCR mastermix
 to which PCR primers had already been added. Resulting PCR products were
 subsequently resolved by electrophoresis and allele sizes were called
 using GeneMarker version 2.6.2 (SoftGenetics®: State College,
 Pennsylvania, USA).
DOI: 10.5061/dryad.k0p2ngf56
title: Effects of trading networks on the risk of bovine tuberculosis incidents on cattle farms in Great Britain

description: Trading animals between farms and via markets can provide a conduit for
 spread of infections. By studying trading networks we might better
 understand the dynamics of livestock diseases. We constructed ingoing
 contact chains of cattle farms in Great Britain that were linked by
 trading, to elucidate potential pathways for the transmission of
 infection, and to evaluate their effect on the risk of a farm experiencing
 a bovine tuberculosis (bTB) incident. Our findings are consistent with
 variation in bTB risk associated with region, herd size, disease risk area
 and history of previous bTB incidents on the root farm and nearby farms.
 However, we also identified effects of both direct and indirect trading
 patterns, such that connections to more farms in the England High Risk
 Area up to three movements away from the root farm increased the odds of a
 bTB incident, while connections with more farms in the England Low Risk
 Area up to eight movements away decreased the odds. Relative to other risk
 factors for bTB, trading behaviours are arguably more amenable to change,
 and consideration of risks associated with indirect trading, as well
 direct trading, might therefore offer an additional approach to bTB
 control in Great Britain.
description: Extensive trading data and disease history data collated by
 Animal and Plant Health Agency.  We are making our code
 available in line with the Data accessibility manuscript:
 "Underlying data consist of every movement of cattle between all farms in Great Britain and their disease history. Aside from the size of the dataset, there are substantial issues of confidentiality (locations, trading practices) and commercial sensitivity in these data. They are collated and managed by Defra, via the Animal and Plant Health Agency, who grant access to the data with specific permissions for specific studies. In practice, this means that the data can be used for the stated purpose only, and making the data publicly accessible would not conform to the licence the authors have been granted to use these data. With the agreement of the journal's Editorial Office, the authors will not be able to make the dataset available on this occasion, but encourage readers, referees and editors to contact the Animal and Plant Health Agency data manager for data access requests. At the time of submission, the data manager is Andy Mitchell (andrew.mitchell@apha.gsi.gov.uk). Code used to run our analysis is available at Dryad data repository."
description: Trading data and disease data may be available by agreement with
 the Animal and Plant Health Agency. We are making our code available. In
 case of any queries, please contact the first or corresponding
 authors.