cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.r6h4h
title: Data from: The presence of bacterial microcolonies on the maxillary sinus ciliary epithelium in healthy young individuals

description: Objective: The aim of this cross-sectional in vitro study was to evaluate
 the mucosal surfaces of healthy maxillary sinuses, explore different forms
 of bacterial microorganism colonies present on the mucous membrane, and
 determine a mucosal surface area they occupy. Methods: Samples of the
 maxillary sinus mucosa were collected from 30 healthy patients (M=11;
 F=19). The material was obtained during the Le Fort I osteotomy performed
 during corrective jaw surgery. The morphological and morphometric analysis
 of sinus mucosa and bacterial film that was grown on it was performed
 using scanning electron microscopy (SEM) as well as imaging software.
 Results: Scanning electron microscopy analysis showed the presence of
 different bacterium and bacteria-like structures in all the analyzed
 samples. In most cases, the bacterial film was mostly composed of
 diplococci-like and streptococci-like structures on the mucosa of the
 paranasal sinus. In any case, the mucous layer did not cover the whole
 lining of the evaluated sample. Each colony consists of more than 20
 single bacterial cells, which has grown in aggregates. Conclusions: Under
 the conditions of normal homeostasis of the body, the maxillary sinuses
 present diverse bacterial colonization. The bacteria are dispersed or
 concentrated in single microcolonies of the biofilm on the border of the
 mucous covering the ciliary epithelium. There is no uniform layer of the
 biofilm covering the mucosa of the maxillary sinuses. Because the biofilm
 is detected on healthy individuals sinus mucosa, the clinical question if
 it may become pathogenic is unclear and require an explanation.
description: Sinus microbiologic
 cultureThe results of sinus
 bacterial culture in healthy individualsSinus
 microbiology.xlsx
DOI: 10.5061/dryad.2gj70
title: Data from: Density dependence, precipitation, and biological control agent herbivory influence landscape-scale dynamics of the invasive Eurasian plant Linaria dalmatica

description: 1. Resource availability and natural enemies are among the most commonly
 cited mechanisms affecting competitive ability of invasive plants, but
 their simultaneous effects on plant dynamics are seldom evaluated in the
 field. Understanding how endogenous and exogenous factors affect invasive
 plant abundance is essential when evaluating the impact of classical weed
 biological control agents because misinterpretations of the mechanisms
 regulating plant demography may bias inference of herbivore impact. 2. In
 this study we report results from a citizen-science monitoring program
 initiated to evaluate the effects of the stem–mining weevil Mecinus
 janthiniformis on the Eurasian invasive weed Dalmatian toadflax Linaria
 dalmatica. We used a discrete model of population dynamics to evaluate the
 relative importance of endogenous and exogenous processes affecting
 changes in ramet density of L. dalmatica at 38 spatially replicated sites
 in Idaho, USA. 3. Analysis of per capita population growth rates based on
 ramet density indicated the presence of direct density dependence, which
 was most likely due to intraspecific competition. Changes in ramet density
 were not influenced by the abundance of the resident plant community. 4.
 Precipitation had a strong, positive effect on ramet density of L.
 dalmatica while the abundance of M. janthiniformis had a weaker, but
 significant, negative effect after accounting for the density dependence.
 There was no support for an interactive effect between precipitation and
 herbivory. 5. Synthesis and applications. Our results indicate that
 biological control is an important factor affecting weed population growth
 at the landscape scale, but they also suggest that biological control
 impact may vary considerably on local infestations due to site-specific
 variation in rainfall and density-dependent processes. We recommend that
 invasive plant management strategies integrate precipitation and
 biological control agent monitoring into their programs to estimate
 expected biological control efficacy. Alternative control methods should
 be prioritized in areas where herbivore impact is expected to be low.
description: field sampling
 dataThis file includes the
 field sampling data of Linaria dalmatica, its biological control agent
 Mecinus janthiniformis, and resident plant community cover and
 environmental data at 38 sites in Idaho USA from 2007 to
 2011.DT_SIMP_DRYAD.csv
DOI: 10.5061/dryad.t783j
title: Data from: Home-field advantages of litter decomposition increase with increasing N deposition rates: a litter and soil perspective

description: 1. Differences in litter quality and in soil microbial community
 composition can influence the litter decomposition and “home-field
 advantage” (HFA). However, our knowledge about the relative role of litter
 and soil characteristics on litter decomposition and HFA effects is still
 limited, especially under long-term N deposition. 2. We collected soil and
 two types of litter (monospecific and mixed species litter) from five
 replicate plots from a long-term N-deposition field experiment with seven
 N-addition treatments (0, 2, 5, 10, 15, 20, 50 g N m-2 yr-1). We examined
 the effects of N-addition on litter quality and soil characteristics. We
 then carried out a three-pronged microcosm decomposition experiment with
 (i) litter from different N-addition treatments decomposed on a standard
 field soil; (ii) standard litter decomposed on soils from the different
 N-addition treatments; and (iii) litter decomposed on soil from the same
 N-addition treatment plot. 3. Decomposition of litter on standard soil was
 influenced strongly by the N-addition treatment, but did not consistently
 decrease or increase with increasing N-addition rates. Instead,
 decomposition of standard litter on soils collected from different
 N-addition treatments decreased with increasing rates of N-addition.
 Decomposition of litter on soil collected from the same plot increased
 with increasing N-addition rates. Soil characteristics explained more of
 the variation in litter decomposition than litter characteristics. 4.
 There was a clear HFA effect for litter decomposition; both from a litter
 and from a soil perspective. HFA effects increased when the dissimilarity
 in litter quality (N content and C: N ratio) increase among the different
 N-addition treatments and the soil effect was strongest at high N-addition
 rates. 5. N-addition influenced litter decomposition by changing both
 litter and soil characteristics. Importantly, N-addition decreased the
 capability of soils to decompose litter and it increased the home-field
 advantage effect indicating that soils decomposed local litter better than
 other litter, due to specialization in soil communities. Nitrogen
 deposition is an important threat to ecosystems worldwide and our study
 emphasizes that ecosystem functions such as decomposition can be greatly
 influenced by these global changes.
description: LiYingbin-FE-2016-00794_data
DOI: 10.5061/dryad.sg1pn
title: Data from: Ant mosaics in Bornean primary rain forest high canopy depend on spatial scale, time of day, and sampling method

description: Background: Competitive interactions in biological communities can be
 thought of as giving rise to “assembly rules” that dictate the species
 that are able to co-exist. Ant communities in tropical canopies often
 display a particular pattern, an “ant mosaic”, in which competition
 between dominant ant species results in a patchwork of mutually exclusive
 territories. Although ant mosaics have been well-documented in plantation
 landscapes, their presence in pristine tropical forests remained
 contentious until recently. Here we assess presence of ant mosaics in a
 hitherto under-investigated forest stratum, the emergent trees of the high
 canopy in primary tropical rain forest, and explore how the strength of
 any ant mosaics is affected by spatial scale, time of day, and sampling
 method. Methods: To test whether these factors might impact the detection
 of ant mosaics in pristine habitats, we sampled ant communities from
 emergent trees, which rise above the highest canopy layers in lowland
 dipterocarp rain forests in North Borneo (38.8–60.2 m), using both baiting
 and insecticide fogging. Critically, we restricted sampling to only the
 canopy of each focal tree. For baiting, we carried out sampling during
 both the day and the night. We used null models of species co-occurrence
 to assess patterns of segregation at within-tree and between-tree scales.
 Results: The numerically dominant ant species on the emergent trees
 sampled formed a diverse community, with differences in the identity of
 dominant species between times of day and sampling methods. Between trees,
 we found patterns of ant species segregation consistent with the existence
 of ant mosaics using both methods. Within trees, fogged ants were
 segregated, while baited ants were segregated only at night. Discussion:
 We conclude that ant mosaics are present within the emergent trees of the
 high canopy of tropical rain forest in Malaysian Borneo, and that sampling
 technique, spatial scale, and time of day interact to determine observed
 patterns of segregation. Restricting sampling to only emergent trees
 reveals segregatory patterns not observed in ground-based studies,
 confirming previous observations of stronger segregation with increasing
 height in the canopy.
description: Appendices for Yusah et
 al (2018)R code for analysis of
 within and between tree co-occurrence of ant species and data to be used
 with this analysis.
DOI: 10.5061/dryad.n0d03
title: Data from: Cooperation-mediated plasticity in dispersal and colonization

description: Kin selection theory predicts that costly cooperative behaviors evolve
 most readily when directed toward kin. Dispersal plays a controversial
 role in the evolution of cooperation: dispersal decreases local population
 relatedness and thus opposes the evolution of cooperation, but limited
 dispersal increases kin competition and can negate the benefits of
 cooperation. Theoretical work has suggested that plasticity of dispersal,
 where individuals can adjust their dispersal decisions according to the
 social context, might help resolve this paradox and promote the evolution
 of cooperation. Here, we experimentally tested the hypothesis that
 conditional dispersal decisions are mediated by a cooperative strategy: we
 quantified the density-dependent dispersal decisions and subsequent
 colonization efficiency from single cells or groups of cells among 6
 genetic strains of the unicellular Tetrahymena thermophila that differ in
 their aggregation level (high, medium and low), a behavior associated with
 cooperation strategy. We found that the plastic reaction norms of
 dispersal rate relative to density differed according to aggregation
 level: highly aggregative genotypes showed negative density-dependent
 dispersal, whereas low-aggregation genotypes showed maximum dispersal
 rates at intermediate density, and medium-aggregation genotypes showed
 density-independent dispersal with intermediate dispersal rate. Dispersers
 from highly aggregative genotypes had specialized long-distance dispersal
 phenotypes, contrary to low-aggregation genotypes; medium-aggregation
 genotypes showing intermediate dispersal phenotype. Moreover, highly
 aggregation genotypes showed evidence for beneficial kin-cooperation
 during dispersal. Our experimental results should help to resolve the
 evolutionary conflict between cooperation and dispersal: cooperative
 individuals are expected to avoid kin-competition by dispersing long
 distances, but maintain the benefits of cooperation by dispersing in small
 groups.
description: Dispersal rate
 dataData supporting Figure
 1a: dispersal rate function of population density and cooperation
 levelDispersal_rate.txtDispersal phenotype dataData supporting Figure 1b: dispersal phenotype function of population density and cooperation levelDispersal_phenotype.txtColonization from single cell dataData supporting Figure 2a: colonization from a single cell function of population density and cooperation levelColonization_from_single_cell.txtColonization from a group dataData supporting Figure 2b: colonization from a group function of population density and cooperation levelColonization_from_a_group.txt
DOI: 10.5061/dryad.0v346
title: Data from: Vertical root distribution of individual species in a mountain grassland community: does it respond to neighbours?

description: 1.Vertical differentiation in root placement is one of the potential
 mechanisms of plant niche differentiation. It can be due to the remarkable
 plasticity of roots in response to nutrients and neighbours, but most data
 on it come from pot or garden experiments. The roles of vertical
 differentiation and of plasticity in it in the field are thus not well
 known. 2.We examined species-specific root vertical distribution in a
 montane grassland using quantitative Real-Time PCR. We asked whether
 individual species differ in their rooting depths, whether such
 differences are associated with aboveground functional traits (such as
 height or specific leaf area), and whether they respond to the presence of
 a competitor. This response was assessed by comparison of species-specific
 vertical profiles between control plots and plots where the dominant
 species, Festuca rubra, had been removed. 3.Vertical profiles of
 individual species varied considerably, from species with most root
 biomass concentrated in the uppermost (&lt;2 cm) soil layer, through
 species with uniform vertical distribution, to a species with roots
 predominantly below 8 cm (Nardus stricta). Species at the fast end of the
 plant economy spectrum were more likely to place their roots in the
 uppermost layers. Grassland species thus exploit different parts of the
 belowground resources in spite of their short stature, minor differences
 in height aboveground and shallow soil. 4.While belowground and
 aboveground biomasses of most species were higher in the removal plots,
 species rooting patterns did not change in response to the removal. The
 interspecific differences in vertical profiles were thus due to species’
 innate differences, not to plastic responses to the presence of the
 dominant species. 5.Synthesis. The findings imply that vertical root
 differentiation in the field is strong and can contribute to niche
 differentiation. However, the role of root plasticity in natural systems
 may be considerably weaker than in artificial systems with few species and
 strong nutrient gradients. This absence of the plastic response in the
 field is likely to be due to a fairly homogeneous distribution of
 nutrients in the soil and to the predominantly symmetric nature of
 belowground competition.
description: aboveground and
 belowground dataPlotwise ramet counts
 and belowground root densities of 13 species in 18 plots. Readme file is a
 part of the archive.data.zip
DOI: 10.5061/dryad.c194d
title: Data from: Genetic architecture and functional characterization of genes underlying the rapid diversification of male external genitalia between Drosophila simulans and Drosophila mauritiana

description: Male sexual characters are often among the first traits to diverge between
 closely related species and identifying the genetic basis of such changes
 can contribute to our understanding of their evolutionary history.
 However, little is known about the genetic architecture or the specific
 genes underlying the evolution of male genitalia. The morphology of the
 claspers, posterior lobes and anal plates exhibit striking differences
 between Drosophila mauritiana and Drosophila simulans. Using QTL and
 introgression-based high-resolution mapping, we identified several small
 regions on chromosome arms 3L and 3R that contribute to differences in
 these traits. However, we found that the loci underlying the evolution of
 clasper differences between these two species are independent from those
 that contribute to posterior lobe and anal plate divergence. Furthermore,
 while most of the loci affect each trait in the same direction and act
 additively, we also found evidence for epistasis between loci for clasper
 bristle number. In addition, we conducted an RNAi screen in D.
 melanogaster to investigate if positional and expression candidate genes
 located on chromosome 3L, are also involved in genital development. We
 found that six of these genes, including components of Wnt signaling and
 male-specific lethal 3 (msl3), regulate the development of genital traits
 consistent with the effects of the introgressed regions where they are
 located and that thus represent promising candidate genes for the
 evolution these traits.
description: Recombination
 breakpoints in the 3rd chromosome introgression linesRecombination
 breakpoints calculated using the MSG pipeline (Andolfatto et al. 2011).
 Coordinates in the gff files correspond to the D. simulans w501 genome (Hu
 et al. 2013). File names refer to chromosome and introgression
 ID.gff.zip
DOI: 10.5061/dryad.2044d
title: Data from: The early record of halysitid tabulate corals, and morphometrics of Catenipora from the Ordovician of north-central China

description: Catenipora is one of the most common tabulate coral genera in the Upper
 Ordovician Jinghe and Beiguoshan formations on the southern margin of the
 Ordos Basin, north-central China. We distinguish and identify the species
 of Catenipora using multivariate morphometric procedures. Cluster analysis
 based on morphological characters of coralla yields a dendrogram showing
 five morphospecies. The validity and distinctiveness of the morphospecies
 are evaluated by discriminant analysis and non-metric multidimensional
 scaling. To identify the species represented by the morphospecies, type
 specimens of species that are morphologically similar from north-central
 China (Sino-Korean Block) and surrounding palaeocontinents are compared
 with the morphospecies by non-metric multidimensional scaling and
 descriptive statistics. The result indicates that one morphospecies
 represents C. daliangensis (Yu), another represents C. subovata Yu, and
 the others are considered to be new species named C. tongchuanensis, C.
 jingyangensis and C. tiewadianensis. Catenipora tongchuanensis from the
 middle of the Jinghe Formation (Sandbian; early Late Ordovician) is the
 earliest confirmed halysitid tabulate. Species of Catenipora in
 north-central China (Sino-Korean Block) show the highest morphological
 diversity (i.e. disparity) in terms of corallite size and shape, compared
 with other palaeocontinents in China. Species of Catenipora in North
 Qilian share more common components with those from north-central China
 than any other palaeocontinent in China. The different morphological
 characteristics in terms of corallite shape and ranks in some Katian
 species of Catenipora from East Junggar, Mongolia, South China and Estonia
 suggest that some species may have originated separately during the Great
 Ordovician Biodiversification Event, and Catenipora is possibly
 polyphyletic.
description: Supplemental
 Data
DOI: 10.5281/zenodo.17980471
title: SHM_415394_HST_3D

description: Photogrammetric 3D model of a Middle Neolithic double-edged battle axe collected from Kalmar and currently held in the collections of the National Historical Museums in Stockholm.

Link to the Dynamic Collection platform  

https://dyncolldev.ht.lu.se/plus/artifact_view.php?item=695

Link to Sök I Samlingarna  

https://samlingar.shm.se/object/6327BC25-56E6-4D45-800F-14C2515B2077
DOI: 10.5061/dryad.7k4k6
title: Data from: Microsatellite length variation in candidate genes correlates with habitat in the gilthead sea bream Sparus aurata

description: The genetic basis and evolutionary implications of local adaptation in
 high gene flow marine organisms are still poorly understood. In several
 Mediterranean fish species, alternative migration patterns exist between
 individuals entering coastal lagoons that offer favorable conditions for
 growth and those staying in the sea where environmental conditions are
 less subject to rapid and stressful change. Whether these coexisting
 strategies are phenotypically plastic or include a role for local
 adaptation through differential survival needs to be determined. Here, we
 explore the genetic basis of alternate habitat use in western
 Mediterranean populations of the gilthead sea bream (Sparus aurata).
 Samples from lagoonal and open sea habitats were typed for 3 candidate
 gene microsatellite loci, 7 anonymous microsatellites and 44 AFLP markers
 to test for genotype-environment associations. While anonymous markers
 globally indicated high levels of gene flow across geographic locations
 and habitats, non-neutral differentiation patterns correlated with habitat
 type were found at two candidate microsatellite loci located in the
 promoter region of the Growth hormone and Prolactin genes. Further
 analysis of these two genes revealed that a mechanism based on habitat
 choice alone could not explain the distribution of genotype frequencies at
 a regional scale, thus implying a role for differential survival between
 habitats. We also found an association between allele size and habitat
 type, which, in the light of previous studies, suggests that polymorphisms
 in the proximal promoter region could influence gene expression by
 modulating transcription factor binding, thus providing a potential
 explanatory link between genotype and growth phenotype in nature.
description: Sparus_aurata_genotypes_data_filesThis ZIP archive contains 3 data files (as described in Table 1), "3_CANDIDATE_SSR_10_pops.gtx" is the GENETIX input file matrix for the 3 candidate genes SSRs genotyped in 10 locations, "7_ANONYMOUS_3_CANDIDATE_SSR_5_pops.gtx" is the GENETIX input file matrix for the 7 anonymous SSRs and 3 candidate genes SSRs genotyped in 5 locations, and "Sparus_44loci_AFLPSURV.txt" is the AFLPSURV input file table for the 44 AFLP markers in 10 locations.
DOI: 10.5281/zenodo.17980470
title: SHM_415394_HST_3D

description: Photogrammetric 3D model of a Middle Neolithic double-edged battle axe collected from Kalmar and currently held in the collections of the National Historical Museums in Stockholm.

Link to the Dynamic Collection platform  

https://dyncolldev.ht.lu.se/plus/artifact_view.php?item=695

Link to Sök I Samlingarna  

https://samlingar.shm.se/object/6327BC25-56E6-4D45-800F-14C2515B2077