cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t53k5
title: Data from: Induction of sexual reproduction and genetic diversity in the cheese fungus Penicillium roqueforti

description: The emblematic fungus Penicillium roqueforti is used throughout the world
 as a starter culture in the production of blue-veined cheeses. Like other
 industrial filamentous fungi, P. roqueforti was thought to lack a sexual
 cycle. However, an ability to induce recombination is of great economic
 and fundamental importance, as it would make it possible to transform and
 improve industrial strains, promoting the creation of novel phenotypes and
 eliminating the deleterious mutations that accumulate during clonal
 propagation. We report here, for the first time, the induction of the
 sexual structures of P. roqueforti — ascogonia, cleistothecia and
 ascospores. The progeny of the sexual cycle displayed clear evidence of
 recombination. We also used the recently published genome sequence for
 this species to develop microsatellite markers for investigating the
 footprints of recombination and population structure in a large collection
 of isolates from around the world and from different environments. Indeed,
 P. roqueforti also occurs in silage, wood and human-related environments
 other than cheese. We found tremendous genetic diversity within P.
 roqueforti, even within cheese strains, and identified six highly
 differentiated clusters that probably predate the use of this species for
 cheese production. Screening for phenotypic and metabolic differences
 between these populations could guide future development strategies.
description: Genotypes
 ProqMicrosatellite alleles
 for Penicillium roqueforti strains
DOI: 10.5061/dryad.c6011
title: Data from: Anthropogenic noise affects behavior across sensory modalities

description: Many species are currently experiencing anthropogenically driven
 environmental changes. Among these changes, increasing noise levels are
 specifically a problem for species using acoustic signals (i.e., species
 relying on signals that use the same sensory modality as anthropogenic
 noise). Yet many species use other sensory modalities, such as visual and
 olfactory signals, to communicate. However, we have only little
 understanding of whether changes in the acoustic environment affect
 species that use sensory modalities other than acoustic signals. We
 studied the impact of anthropogenic noise on the common cuttlefish Sepia
 officinalis, which uses highly complex visual signals. We showed that
 cuttlefish adjusted their visual displays by changing their color more
 frequently during a playback of anthropogenic noise, compared with before
 and after the playback. Our results provide experimental evidence that
 anthropogenic noise has a marked effect on the behavior of species that
 are not reliant on acoustic communication. Thus, interference in one
 sensory channel, in this case the acoustic one, affects signaling in other
 sensory channels. By considering sensory channels in isolation, we risk
 overlooking the broader implications of environmental changes for the
 behavior of animals.
description: 54793
DOI: 10.5061/dryad.8hq3s
title: Data from: Enhancing gardens as habitats for flower-visiting aerial insects (pollinators): should we plant native or exotic species?

description: 1. Domestic gardens typically consist of a mixture of native and
 non-native plants which support biodiversity and provide valuable
 ecosystem services, particularly in urban environments. Many gardeners
 wish to encourage biodiversity by choosing appropriate plant taxa. The
 value of native and non-native plants in supporting animal biodiversity
 is, however, largely unknown. 2. The relative value of native and
 non-native garden plants to invertebrates was investigated in a replicated
 field experiment. Plots (deliberately akin to garden borders) were planted
 with one of three treatments, representing assemblages of plants based on
 origin (native, near-native and exotic). Invertebrates and resource
 measurements were recorded over four years. This paper reports the
 abundance of flower-visiting aerial insects (‘pollinators’) associated
 with the three plant assemblages. 3. For all pollinator groups on all
 treatments, greater floral resource resulted in an increase in visits.
 There was, however, a greater abundance of total pollinators recorded on
 native and near-native treatments compared with the exotic plots.
 Short-tongued bumblebees followed the same pattern whilst more hoverflies
 were recorded on the native treatment than the other treatments, and more
 honeybees on the near-native treatment. There was no difference between
 treatments in abundance of long-tongued bumblebees or solitary bees. The
 lack of difference in solitary bee abundance between treatments was
 probably due to a third of individuals from this group being recorded on
 one exotic plant species. 5. The number of flower visitors corresponded to
 the peak flowering period of the treatments, that is there were fewer
 flower visitors to the exotic treatment compared with the other treatments
 in early summer but relatively more later in the season. 5. Synthesis and
 applications. This experiment has demonstrated that utilizing plants from
 only a single region of origin (i.e. nativeness) may not be an optimal
 strategy for resource provision for pollinating insects in gardens.
 Gardens can be enhanced as a habitat by planting a variety of flowering
 plants, biased towards native and near-native species but with a selection
 of exotics to extend the flowering season and potentially provide
 resources for specialist groups.
description: Raw abundance data -
 PollinatorsThe raw abundance data
 for insects visiting flowers used in the publication.Data.xlsx
DOI: 10.5061/dryad.18df7
title: Data from: The cutaneous lipid composition of bat wing and tail membranes: a case of convergent evolution with birds

description: The water vapour permeability barrier of mammals and birds resides in the
 stratum corneum (SC), the outermost layer of the epidermis. The molar
 ratio and molecular arrangement of lipid classes in the SC determine the
 integrity of this barrier. Increased chain length and polarity of
 ceramides, the most abundant lipid class in mammalian SC, contribute to
 tighter packing and thus to reduced cutaneous evaporative water loss
 (CEWL). However, tighter lipid packing also causes low SC hydration,
 making it brittle, whereas high hydration softens the skin at the cost of
 increasing CEWL. Cerebrosides are not present in the mammalian SC; their
 pathological accumulation occurs in Gaucher's disease, which leads to
 a dramatic increase in CEWL. However, cerebrosides occur normally in the
 SC of birds. We tested the hypothesis that cerebrosides are also present
 in the SC of bats, because they are probably necessary to confer
 pliability to the skin, a quality needed for flight. We examined the SC
 lipid composition of four sympatric bat species and found that, as in
 birds, their SC has substantial cerebroside contents, not associated with
 a pathological state, indicating convergent evolution between bats and
 birds.
description: Sphingolipid composition
 in 4 species of batsTRi is torpor index
 calculated for each bat; ssCEWL is surface area specific cutaneous water
 lossDryad
 raw data PRSL Mar 18 2016.xlsx
DOI: 10.5061/dryad.65v10
title: Data from: Ongoing changes in the avifauna of La Selva Biological Station, Costa Rica: twenty-three years of Christmas Bird Counts

description: Tropical forest fragmentation influences community composition via
 differential species-level effects. Avian responses to fragmentation at La
 Selva Biological Station are, in part, responsible for the particular
 concern over the fate of understory insectivorous species. However, since
 the 1990s, much previously deforested land within and surrounding La Selva
 has reverted to forest, providing an opportunity to test hypotheses
 explaining ongoing avifaunal change. Analyses of 23 years (1989–2011) of
 Christmas Bird Counts reveal that 63 of 202 species have increased whereas
 44 are declining, with declines occurring more rapidly than increases.
 Habitat association was an important predictor of population trends, as
 understory birds continue to decline whereas forest generalists increased.
 Our results differ from previous work in the tropics by revealing that, at
 La Selva, insectivores are not currently suffering greater declines than
 birds of other dietary guilds. Instead, body size was more strongly
 associated with population change than was diet, with smaller birds having
 more negative population trends than larger birds. These results suggest
 that we must consider additional hypotheses that may explain ongoing
 population declines of tropical birds. In particular, the associations
 between population trends and body size implicate physiological mechanisms
 influencing population change, which may result from direct or indirect
 consequences of changing climates.
description: La Selva Bird Trends
 DatatableLaSelvaBirdTrendsDatatable.csv
DOI: 10.5061/dryad.hk1h26n
title: Data from: Increased temperature disrupts the biodiversity-ecosystem functioning relationship

description: Gaining knowledge of how ecosystems provide essential services to humans
 is of primary importance, especially with the current threat of climate
 change. Yet, little is known about how increased temperature will impact
 the biodiversity-ecosystem functioning (BEF) relationship. We tackled this
 subject theoretically and experimentally. We developed a BEF theory based
 on mechanistic population dynamic models, which allows the inclusion of
 the effect of temperature. Using experimentally established relationships
 between attack rate and temperature, the model predicts that temperature
 increase will intensify competition and consequently the BEF relationship
 will flatten or even become negative. We conducted a laboratory experiment
 with natural microbial microcosms and the results were in agreement with
 the model predictions. The experimental results also revealed that an
 increase of both temperature average and variation had a more intense
 effect than an increase of temperature average alone. Our results indicate
 that, under climate change, high diversity may not guarantee high
 ecosystem functioning.
description: Data and R codes for the
 analysesThe file
 "data.xlsx" contains a description of the variables (sheet
 "metadata") and data used for the analyses (sheet
 "data"). The analyses can be performed using the R code provided
 in the zip file, starting with the R file
 "data_extraction.R".Data_RCode.zip
DOI: 10.5061/dryad.08c2k
title: Data from: Order of arrival structures arbuscular mycorrhizal colonization of plants

description: Priority effects – the impact of a species' arrival on subsequent
 community development – have been shown to influence species composition
 in many organisms. Whether priority effects among arbuscular mycorrhizal
 fungi (AMF) structure fungal root communities is not well understood.
 Here, we investigated whether priority effects influence the success of
 two closely related AMF species (Rhizophagus irregularis and Glomus
 aggregatum), hypothesizing that a resident AMF suppresses invader success,
 this effect is time-dependent and a resident will experience reduced
 growth when invaded. We performed two glasshouse experiments using
 modified pots, which permitted direct inoculation of resident and invading
 AMF on the roots. We quantified intraradical AMF abundances using
 quantitative PCR and visual colonization percentages. We found that both
 fungi suppressed the invading species and that this effect was strongly
 dependent on the time lag between inoculations. In contrast to our
 expectations, neither resident AMF was negatively affected by invasion. We
 show that order of arrival can influence the abundance of AMF species
 colonizing a host. These priority effects can have important implications
 for AMF ecology and the use of fungal inocula in sustainable agriculture.
description: Werner_full_fungal_dataWerner_full_plant_dataWerner_Kiers_2014This R-script performs all the analyses reported in Werner et al. 2014 and generates the figures (with the exception of Figure 1). Very minor adaptations to the figures were made manually in Adobe Illustrator (move position of the legends, change colours etc.).
DOI: 10.5061/dryad.0q524
title: Data from: Influence of hepatitis C virus and IL28B genotypes on liver stiffness

description: Objective: Liver fibrosis has been associated with hepatitis C virus (HCV)
 genotype and genetic variation near the interleukin 28B (IL28B) gene, but
 the relative contribution is unknown. We aimed to investigate the relation
 between HCV genotypes, IL28B and development of liver stiffness. Patients
 and Methods: This cross-sectional study consists of 369 patients with
 chronic hepatitis C (CHC). Liver stiffness was evaluated using transient
 elastograhy (TE). Factors associated with development of liver fibrosis
 were identified by logistic regression analysis. Results: We identified
 369 patients with CHC. 235 were male, 297 Caucasians, and 223 had been
 exposed to HCV through intravenous drug use. The overall median TE value
 was 7.4 kPa (interquartile range (IQR) 5.7–12.1). HCV replication was
 enhanced in patients carrying the IL28B CC genotype compared to TT and TC
 (5.8 vs. 5.4 log10 IU/mL, p = 0.03). Patients infected with HCV genotype 3
 had significantly higher TE values (8.2 kPa; IQR, 5.9–14.5) compared to
 genotype 1 (6.9 kPa; IQR, 5.4–10.9) and 2 (6.7 kPa; IQR, 4.9–8.8) (p =
 0.02). Within patients with genotype 3, IL28B CC genotype had the highest
 TE values (p = 0.04). However, in multivariate logistic regression, using
 various cut-off values for fibrosis and cirrhosis, only increasing age
 (odds ratio (OR) 1.09 (95% confidence interval (CI), 1.05–1.14 per year
 increment)), ALT (OR 1.01 (95% CI, 1.002–1.011), per unit increment) and
 HCV genotype 3 compared to genotype 1 (OR 2.40 (95% CI, 1.19–4.81), were
 consistently associated with cirrhosis (TE&gt;17.1 kPa). Conclusions:
 Age, ALT and infection with HCV genotype 3 were associated with cirrhosis
 assessed by TE. However, IL28B genotype was not an independent predictor
 of fibrosis in our study.
description: Hcv_data
DOI: 10.5061/dryad.961m4t8
title: Data from: An expanded molecular phylogeny of Plumbaginaceae, with emphasis on Limonium (sea lavenders): taxonomic implications and biogeographic considerations

description: Plumbaginaceae is characterized by a history of multiple taxonomic
 rearrangements and lacks a broad molecular phylogenetic framework.
 Limonium is the most species‐rich genus of the family with ca. 600 species
 and cosmopolitan distribution. Its center of diversity is the
 Mediterranean region, where ca. 70% of all Limonium species are endemic.
 In this study, we sample 201 Limonium species covering all described
 infrageneric entities and spanning its wide geographic range, along with
 64 species of other Plumbaginaceae genera, representing 23 out of 29
 genera of the family. Additionally, 20 species of the sister family
 Polygonaceae were used as outgroup. Sequences of three chloroplast
 (trnL‐F, matK, and rbcL) and one nuclear (ITS) loci were used to infer the
 molecular phylogeny employing maximum likelihood and Bayesian analyses.
 According to our results, within Plumbaginoideae, Plumbago forms a
 non‐monophyletic assemblage, with Plumbago europaea sister to Plumbagella,
 while the other Plumbago species form a clade sister to Dyerophytum.
 Within Limonioideae, Ikonnikovia is nested in Goniolimon, rejecting its
 former segregation as genus distinct from Goniolimon. Limonium is divided
 into two major clades: Limonium subg. Pteroclados s.l., including L. sect.
 Pteroclados and L. anthericoides, and L. subg. Limonium. The latter is
 divided into three well‐supported subclades: the monospecific L. sect.
 Limoniodendron sister to a clade comprising a mostly non‐Mediterranean
 subclade and a Mediterranean subclade. Our results set the foundation for
 taxonomic proposals on sections and subsections of Limonium, namely: (a)
 the newly described L. sect. Tenuiramosum, created to assign L.
 anthericoides at the sectional rank; (b) the more restricted
 circumscriptions of L. sect. Limonium (= L. sect. Limonium subsect.
 Genuinae) and L. sect. Sarcophyllum (for the
 Sudano‐Zambezian/Saharo‐Arabian clade); (c) the more expanded
 circumscription of L. sect. Nephrophyllum (including species of the L.
 bellidifolium complex); and (d) the new combinations for L. sect.
 Pruinosum and L. sect. Pteroclados subsect. Odontolepideae and subsect.
 Nobiles.
description: trnLF and rbcL sequences
 from Lledo et al. 2005trnLF and rbcL sequences
 used in this study, provided to us directly by the authors of Lledó et al.
 (2005).
DOI: 10.5061/dryad.4t5q437
title: Data from: Plant functional diversity and nutrient availability can improve restoration of floating fens via facilitation, complementarity and selection effects

description: 1. Peat-forming wetlands, and particularly floating fens forming the
 initial stages of these ecosystems, are globally declining due to
 excavation, dehydration and eutrophication. Restoration of these valuable
 ecosystems typically involves re-establishment of early-successional
 open-water stages with oligotrophic conditions that are characteristic for
 these systems. However, restoration success is notoriously limited and a
 potential solution may be to initiate succession by re-introduction of
 target plant species. Knowledge is needed on (a) which plant functional
 groups should be re-introduced to stimulate fen formation; and (b) how to
 manage nutrient levels during restoration, considering that plant growth
 may be slow in oligotrophic conditions. 2. We hypothesized that (1)
 increasing functional diversity of introduced species would stimulate the
 formation of peat-forming target communities, their biomass accumulation
 and expansion onto open water; and that (2) nutrient availability would
 mediate the relative contribution of specific functional groups to these
 effects. We experimentally investigated this in 36 artificial outdoor
 ponds by manipulating plant functional diversity (clonal dominants, clonal
 stress-tolerators and interstitials) on constructed rafts with fen-forming
 communities and subjected these to a range of nutrient loadings over two
 years. 3. Increasing functional diversity as well as increasing nutrient
 loadings had stimulating effects on plant biomass accumulation, cover
 formation and rhizome growth onto open water. Both complementarity (due to
 niche partitioning or facilitation) and selection effects were mechanisms
 underlying the diversity effect, with a constant relative importance over
 the entire range of nutrient availabilities. Different functional groups
 were important for biomass production at different nutrient
 availabilities. Rhizome formation by clonal stress-tolerators contributed
 disproportionately to open water colonisation, identifying this functional
 group as key across all nutrient levels. 4. Synthesis and applications
 Restoration of floating fen communities (1) can be stimulated during the
 first two years by introducing a high functional diversity of plant
 species, including fast-growing clonal species, clonal stress-tolerators
 and interstitials, which facilitate each other, (2) is dependent on the
 presence of clonal stress-tolerators such as Calla palustris, Comarum
 palustre and Menyanthes trifoliata for expansion onto the open water, (3)
 can start under a wide range of water nutrient levels, including eutrophic
 conditions.11-Jul-2018
description: All experimental data
 from the matsBiomass, cover and
 rhizome growth on the mats with different treatments.Supporting data for Van Zuidam
 et al 2018 JAE.xlsx
DOI: 10.5061/dryad.fj5m5
title: Data from: Effects of the number of genome segments on primary and systemic infection for a multipartite plant RNA virus

description: Multipartite plant viruses were discovered because of discrepancies
 between the observed dose response and predictions of the independent
 action hypothesis (IAH) model. Theory suggests that the number of genome
 segments predicts the shape of the dose response, but a rigorous test of
 this hypothesis has not been reported. Here Alfalfa mosaic virus (AMV), a
 tripartite Alfamovirus, and transgenic Nicotiana tabacum plants expressing
 none (wild-type), one (P2) or two (P12) viral genome segments were used to
 test whether the number of genome segments necessary for infection
 predicts dose response. Dose response for wild-type plants was steep and
 congruent with predicted kinetics for a multipartite virus, confirming
 previous results. Moreover, for P12 plants the data support the IAH model,
 showing that the expression of virus genome segments by the host plant can
 modulate the infection kinetics of a tripartite virus to those of a
 monopartite virus. However, the different types of virus particles
 occurred at different frequencies, with a ratio 116:45:1 (RNA1:RNA2:RNA3),
 which will affect infection kinetics and required analysis with a more
 comprehensive infection model. This analysis showed that each type of
 virus particle has a different probability of invading the host plant,
 both at the primary- and systemic-infection levels. Whilst the number of
 genome segments affects dose response, taking into consideration
 differences in the infection kinetics of the three types of AMV virus
 particles results in a better understanding of the infection process.
description: Dose response
 dataAn excel file containing
 data from dose response experiments performed in a greenhouse. Please
 refer to readme file for more detais.
DOI: 10.5061/dryad.53h16
title: Data from: Understanding patterns of land-cover change in the Brazilian Cerrado from 2000 to 2015

description: Clearing tropical vegetation impacts biodiversity, the provision of
 ecosystem services, and thus ultimately human welfare. We quantified
 changes in land cover from 2000 to 2015 across the Cerrado biome of
 northern Minas Gerais state, Brazil. We assessed the potential biophysical
 and social-economic drivers of the loss of Cerrado, natural regeneration
 and net cover change at the municipality level. Further, we evaluated
 correlations between these land change variables and indicators of human
 welfare. We detected extensive land cover changes in the study area, with
 the conversion of 23,446 km2 and the natural regeneration of 13,926 km2,
 resulting in a net loss of 9,520 km2. The annual net loss (-1.2% per year)
 of the cover of Cerrado is higher than that reported for the whole biome
 in similar periods. We argue that environmental and economic variables
 interact to underpin rates of conversion of Cerrado, most severely
 affecting more humid Cerrado lowlands. While rates of Cerrado regeneration
 are important for conservation strategies of the remaining biome, their
 integrity must be investigated given the likelihood of encroachment. Given
 the high frequency of land abandonment in tropical regions, secondary
 vegetation is fundamental to maintain biodiversity and ecosystem services.
 Finally, the impacts of Cerrado conversion on human welfare likely vary
 from local to regional scales, making it difficult to elaborate land use
 policies based solely on social-economic indicators.
description: Espírito-Santo et al
 (2016) - Philosophical TransactionsThis is an excel file
 containing several variables for each of the 89 municipalities of the
 north of Minas Gerais region in two years (2000 and 2015). It includes
 biophysical and social-economic drivers of land use change, welfare
 indicators, Cerrado gross area lost and gained, and Cerrado net area
 change between 2000 and 2015. These variables include social-economic
 indicators obtained from public databases (Brazilian Institute for
 Geography and Statistics-IBGE and United Nations Development
 Programme-UNDP) and biophysical variables obtained through Geographic
 Information Systems.Espírito-Santo et al (2016) -
 DRYAD.xlsx