cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jr583
title: Data from: Major histocompatibility complex class I evolution in songbirds: universal primers, rapid evolution and base compositional shifts in exon 3

description: Genes of the Major Histocompatibility Complex (MHC) have become an
 important marker for the investigation of adaptive genetic variation in
 vertebrates because of their critical role in pathogen resistance.
 However, despite significant advances in the last few years the
 characterization of MHC variation in non-model species still remains a
 challenging task due to the redundancy and high variation of this gene
 complex. Here we report the utility of a single pair of primers for the
 cross-amplification of the third exon of MHC class I genes, which encodes
 the more polymorphic half of the peptide-binding region (PBR), in oscine
 passerines (songbirds; Aves: Passeriformes), a group especially
 challenging for MHC characterization due to the presence of large and
 complex MHC multigene families. In our survey, although the primers failed
 to amplify exon 3 from two suboscine passerine birds, they amplified exon
 3 of multiple MHC class I genes in all 16 species of oscine songbirds
 tested, yielding a total of 120 sequences. The 16 songbird species belong
 to 14 different families, primarily within the Passerida, but also in the
 Corvida. Using a conservative approach based on the analysis of cloned
 amplicons (n = 16) from each species, we found between 3 and 10 MHC
 sequences per individual. Each allele repertoire was highly divergent,
 with the overall number of polymorphic sites per species ranging from 33
 to 108 (out of 264 sites) and the average number of nucleotide differences
 between alleles ranging from 14.67 to 43.67. Our survey in songbirds
 allowed us to compare macroevolutionary dynamics of exon 3 between
 songbirds and non-passerine birds. We found compelling evidence of
 positive selection acting specifically upon peptide-binding codons across
 birds, and we estimate the strength of diversifying selection in songbirds
 to be about twice that in non-passerines. Analysis using comparative
 methods suggest weaker evidence for a higher GC content in the 3rd codon
 position of exon 3 in non-passerine birds, a pattern that contrasts with
 among-clade GC patterns found in other avian studies and may suggests
 different mutational mechanisms. Our primers represent a useful toolfor
 the characterization of functional and evolutionarily relevant MHC
 variation across the hyperdiverse songbirds.
description: Alcaide_etal_PeerJ_MHC_classI_alignmentThis alignment was used in the analysis of the paper in PeerJ by M. Alcaide, M. Liu and S. Edwards entitled "Major Histocompatibility Complex class I evolution in songbirds: universal primers, rapid evolution and base compositional shifts in exon 3". The alignment begins on the first position of the codon and was made according to methods described in the paper. Taxa without Genbank numbers are original data; Genbank nubmers for these sequences can be found on Genbank. Taxa with Genbank numbers were taken from Genbank.
DOI: 10.5061/dryad.5q67v
title: Data from: Ecologically dependent and intrinsic genetic signatures of postzygotic isolation between sympatric host races of the leaf beetle Lochmaea capreae

description: The fitness of hybrids might be compromised as a result of intrinsic
 isolation and/or because they fall between ecological niches due to their
 intermediate phenotypes (“extrinsic isolation”). Here, we present data
 from several crosses (parental crosses, F1, F2 and backcrosses) between
 the two host races of Lochmaea capreae on willow and birch to test for
 extrinsic isolation, intrinsic isolation, and environmentally dependent
 genetic incompatibilities. We employed a reciprocal transplant design in
 which offspring were raised on either host plant and their survival was
 recorded until adulthood. We also applied joint-scaling analysis to
 determine the genetic architecture of hybrid inviability. The relative
 fitness of the backcrosses switched between environments; furthermore, the
 additive genetic-environment interaction was detected as the strongest
 effect in our analysis. These results provide strong evidence that
 divergent natural selection has played a central role in the evolution of
 hybrid dysfunction between host races. Joint-scaling analysis detected
 significant negative epistatic effects which are most evident in the poor
 performance of F2-hybrids on willow, indicating signs of intrinsic
 isolation. We did not find any evidence that genetic incompatibilities are
 manifested independently of environmental conditions. Our findings suggest
 the outcome of natural hybridization between these host races is mainly
 affected by extrinsic isolation and a weak contribution of intrinsic
 isolation.
description: Soudi_et_al_data_survivalSurvival of individuals from both willow and birch host races of L. capreae leaf beetles and hybrids between them on willow and birch
DOI: 10.5061/dryad.n536ts2
title: Data from: Predicting nitrate retention at the groundwater- surface water interface in sandplain streams

description: Groundwater-surface water ecotones present opportunities for nitrate
 retention because changes in organic carbon availability, redox potential
 and nitrate demand often occur at these locations. Although there have
 been many measurements of nitrate retention and denitrification at the
 groundwater-surface water interface few investigators have quantitatively
 predicted where nitrogen transformation occurs in this zone. Our main
 objective was to describe and predict spatial variation in nitrate
 retention and removal in shallow groundwater among and within streams in
 the central sand plains of Wisconsin. We predicted that nitrate
 transformation rates would be positively related to nitrate and
 particulate organic carbon availability, a negative nonlinear function of
 dissolved oxygen availability and would peak at intermediate rates of
 groundwater discharge. Five sites on 4 streams were chosen that spanned an
 order of magnitude in groundwater nitrate concentration. Nitrate retention
 and N2 production were quantified by determining how nitrate and N2 fluxes
 changed along nominal 60 cm groundwater flow paths. Nitrogen
 transformation was widespread but highly variable within the study sites.
 Partial least squares regression models explained a much larger amount of
 variation in nitrate retention and N2 production at the local scale than
 at the regional scale. Dissolved oxygen (DO) availability and ground water
 discharge were the most consistent predictors of nitrate retention at both
 scales. We conclude that nitrate retention at the groundwater-surface
 water interface can be predicted but that more research is necessary to
 determine if nitrate transformation at this ecotone can be modeled at
 broader scales.
description: Nitrate retention and
 denitrification data at the groundwater-surface water interface in streams
 within the Wisconsin central sand plainsThe file includes data
 from 5 sites on 4 streams in Central Wisconsin, USA. The data are
 organized by piezometer location and include solute concentrations of
 groundwater at 3 sediment depths (5, 25, 60 cm) at upwelling locations.
 Nitrate retention and N2 production rates are also included for the
 piezometer locations.Stelzer and Scott Data 081618
 FOR DRYAD (1).xlsx
DOI: 10.5061/dryad.bs385
title: Data from: Experimental evolution reveals trade-offs between mating and immunity

description: Immune system maintenance and upregulation is costly. Sexual selection
 intensity, which increases male investment into reproductive traits, is
 expected to create trade-offs with immune function. We assayed
 phenoloxidase (PO) and lytic activity of individuals from populations of
 the Indian meal moth, Plodia interpunctella, which had been evolving under
 different intensities of sexual selection. We found significant divergence
 among populations, with males from female-biased populations having lower
 PO activity than males from balanced sex ratio or male-biased populations.
 There was no divergence in anti-bacterial lytic activity. Our data suggest
 that it is the increased male mating demands in female-biased populations
 that trades-off against immunity, and not the increased investment in
 sperm transfer per mating that characterizes male-biased populations.
description: PO and Lytic for Plodia
 selection linesExcel data file for both
 phenoloxidase and lytic analyses. FB = female biased lines, MB =
 male-biased lines and ESR = equal sex ratio lines.
DOI: 10.5061/dryad.50584
title: Data from: Seasonal variation in the biocontrol efficiency of bacterial wilt is driven by temperature-mediated changes in bacterial competitive interactions

description: 1. Microbe-based biocontrol applications hold the potential to become an
 efficient way to control plant pathogen disease outbreaks in the future.
 However, their efficiency is still very variable, which could be due to
 their sensitivity to the abiotic environmental conditions. 2. Here we
 assessed how environmental temperature variation correlates with the
 Ralstonia pickettii, an endophytic bacterial biocontrol agent, ability to
 suppress Ralstonia solanacearum pathogen during different tomato crop
 seasons in China. 3. We found that the pathogen suppression was highest
 when the seasonal mean temperatures were around 20 °C and rapidly
 decreased with increasing mean crop season temperatures. Interestingly,
 low levels of disease incidence did not correlate with low pathogen or
 high biocontrol agent absolute densities. Instead, the biocontrol to
 pathogen density ratio was more important predictor of disease incidence
 levels between different crop season. To understand this mechanistically,
 we measured the growth and strength of competition between the biocontrol
 agent and the pathogen over a naturally occurring temperature gradient in
 vitro. We found that the biocontrol strain grew relatively faster at low,
 and the pathogen at high temperature ranges, and that similar to field
 experiments, pathogen suppression peaked at 20° C. 4. Together our results
 suggest that temperature-mediated changes in the strength of bacterial
 competition could potentially explain the variable R. solanacearum
 biocontrol outcomes between different crop seasons in China. 5. Synthesis
 and applications. Bacterial strains that can retain their functionality
 regardless of the environmental conditions (i.e. have flat reaction
 norms), could be good candidate species for developing more consistent
 biocontrol applications.
description: All
 dataAll the data are put in
 this fileAll
 Data.xlsx
DOI: 10.6084/m9.figshare.31154038
title: Supplementary Material for: Concurrent Monkeypox, HHV8, and other opportunistic infections in a HIV patient with disseminated Kaposi sarcoma: a case report

description: Introduction. Human immunodeficiency virus (HIV) infection predisposes patients to opportunistic infections. Kaposi sarcoma (KS) is a soft tissue sarcoma caused by human herpesvirus-8 (HHV8). Patients with high HHV8 and HIV viremia can develop KS inflammatory cytokine storm (KICS), a rare condition characterized by severe sepsis-like symptoms and high mortality.

Case Presentation. We present a patient with poorly controlled HIV and 2-weeks of fevers, dyspnea, abdominal pain, weight loss, and tender umbilicated plaques on the face, trunk, and extremities. Along with HIV, concomitant infections included HHV8, herpes simplex virus, cytomegalovirus, methicillin-resistant Staphylococcus aureus, adenovirus, and rhinovirus/enterovirus. Skin biopsy was positive for monkeypox. Lymph node biopsy was positive for monkeypox and HHV8, and morphologically consistent with KS. The patient also had pan-cytopenia with multiple increased inflammatory markers. 

Conclusion. This case highlights a diagnostic challenge. While numerous infections can cause inflammatory presentations with skin lesions and lymphadenopathy, only HHV8 is characterized by hypergammaglobulinemia. Further, in the setting of KS, HHV8-viremia is concerning for KICS. Recognizing this distinction is essential, as it shifts management from targeting infection to controlling the underlying inflammatory response.
DOI: 10.6084/m9.figshare.31154038.v1
title: Supplementary Material for: Concurrent Monkeypox, HHV8, and other opportunistic infections in a HIV patient with disseminated Kaposi sarcoma: a case report

description: Introduction. Human immunodeficiency virus (HIV) infection predisposes patients to opportunistic infections. Kaposi sarcoma (KS) is a soft tissue sarcoma caused by human herpesvirus-8 (HHV8). Patients with high HHV8 and HIV viremia can develop KS inflammatory cytokine storm (KICS), a rare condition characterized by severe sepsis-like symptoms and high mortality.

Case Presentation. We present a patient with poorly controlled HIV and 2-weeks of fevers, dyspnea, abdominal pain, weight loss, and tender umbilicated plaques on the face, trunk, and extremities. Along with HIV, concomitant infections included HHV8, herpes simplex virus, cytomegalovirus, methicillin-resistant Staphylococcus aureus, adenovirus, and rhinovirus/enterovirus. Skin biopsy was positive for monkeypox. Lymph node biopsy was positive for monkeypox and HHV8, and morphologically consistent with KS. The patient also had pan-cytopenia with multiple increased inflammatory markers. 

Conclusion. This case highlights a diagnostic challenge. While numerous infections can cause inflammatory presentations with skin lesions and lymphadenopathy, only HHV8 is characterized by hypergammaglobulinemia. Further, in the setting of KS, HHV8-viremia is concerning for KICS. Recognizing this distinction is essential, as it shifts management from targeting infection to controlling the underlying inflammatory response.
DOI: 10.5061/dryad.d8mq37r7
title: Data from: Hybridization alters early life-history traits and increases plant colonization success in a novel region

description: Hybridization is hypothesized to promote invasiveness, but empirical tests
 comparing the performance of hybrid versus parental taxa in novel regions
 are lacking. We experimentally compared colonization ability of
 populations of wild radish (Raphanus raphanistrum) versus populations of
 advanced-generation hybrids between wild and cultivated radish (R.
 sativus) in a southeast Texas pasture, well beyond the known invasive
 range of hybrid radish. We also manipulated the strength of interspecific
 competition to better generalize across variable environments. In both
 competitive environments, hybrid populations produced at least three times
 more seeds than wild radish populations, a distinction that was driven by
 greater hybrid seedling emergence, earlier hybrid emergence and more
 hybrid seedlings surviving to flower, rather than by greater individual
 fecundity. Flowering duration in hybrids was less negatively affected by
 competition than it was in wild radishes, while early emergence was
 associated with subsequent high seed output in both biotypes. Our data
 show that hybridization can enhance colonization success in a novel
 region, and, by comparison with previous studies, that the life-history
 traits enhancing hybrid success can differ across regions, even for
 lineages originating from the same hybridization event. These results
 imply a much larger arena for hybrid success than previously appreciated.
description: Radish
 DATA_PLOTRadish
 DATA_IND
DOI: 10.15468/dl.82mj53
title: Occurrence Download

description: A dataset containing 1004 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Tuta absoluta"
 ]
}

 The dataset includes 1004 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000963-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.41356
title: Data from: Acceleration and novelty: community restoration speeds recovery and transforms species composition in Andean cloud forest

description: Community-based tropical forest restoration projects, often promoted as a
 win-win solution for local communities and the environment, have increased
 dramatically in number in the past decade. Many such projects are underway
 in Andean cloud forests, which, given their extremely high biodiversity
 and history of extensive clearing, are understudied. This study
 investigates the efficacy of community-based tree-planting projects to
 accelerate cloud forest recovery, as compared to unassisted natural
 regeneration. This study takes place in northwest Andean Ecuador, where
 the majority of the original, highly diverse cloud forests have been
 cleared, in five communities that initiated tree-planting projects to
 restore forests in 2003. In 2011, we identified tree species along
 transects in planted forests (n = 5), naturally regenerating forests (n =
 5), and primary forests (n = 5). We also surveyed 120 households about
 their restoration methods, tree preferences, and forest uses. We found
 that tree diversity was higher in planted than in unplanted secondary
 forest, but both were less diverse than primary forests. Ordination
 analysis showed that all three forests had distinct species compositions,
 although planted forests shared more species with primary forests than did
 unplanted forests. Planted forests also contained more animal-dispersed
 species in both the planted canopy and in the unplanted, regenerating
 understory than unplanted forests, and contained the highest proportion of
 species with use value for local people. While restoring forest increased
 biodiversity and accelerated forest recovery, restored forests may also
 represent novel ecosystems that are distinct from the region's
 previous ecosystems and, given their usefulness to people, are likely to
 be more common in the future.
description: Cloud forest tree
 dataThe data in this file is
 at the site level. Each site (AP, SL, and so on) is described in the paper
 with which this data is associated. Size class is denoted by SE -
 seedling, SA - sapling, and TR - tree.Size_class_site_data.xlsx
DOI: 10.5061/dryad.20860
title: Data from: Comparison of the abiotic preferences of macroinvertebrates in tropical river basins

description: We assessed and compared abiotic preferences of aquatic macroinvertebrates
 in three river basins located in Ecuador, Ethiopia and Vietnam. Upon using
 logistic regression models we analyzed the relationship between the
 probability of occurrence of five macroinvertebrate families, ranging from
 pollution tolerant to pollution sensitive, (Chironomidae, Baetidae,
 Hydroptilidae, Libellulidae and Leptophlebiidae) and physical-chemical
 water quality conditions. Within the investigated physical-chemical
 ranges, nine out of twenty-five interaction effects were significant. Our
 analyses suggested river basin dependent associations between the
 macroinvertebrate families and the corresponding physical-chemical
 conditions. It was found that pollution tolerant families showed no clear
 abiotic preference and occurred at most sampling locations, i.e.
 Chironomidae were present in 91%, 84% and 93% of the samples taken in
 Ecuador, Ethiopia and Vietnam. Pollution sensitive families were strongly
 associated with dissolved oxygen and stream velocity, e.g. Leptophlebiidae
 were only present in 48%, 2% and 18% of the samples in Ecuador, Ethiopia
 and Vietnam. Despite some limitations in the study design, we concluded
 that associations between macroinvertebrates and abiotic conditions can be
 river basin-specific and hence are not automatically transferable across
 river basins in the tropics.
description: Dataset including
 occurrences of macroinvertebrates in three river basinsDataset.xlsx
DOI: 10.5061/dryad.627fm05
title: Data from: Co-occurrence among three divergent plant-castrating fungi in the same silene host species

description: The competitive exclusion principle postulates that different species can
 only coexist in sympatry if they occupy distinct ecological niches. The
 goal of this study was to understand the geographical distribution of
 three species of Microbotryum anther-smut fungi that are distantly related
 but infect the same host plants, the sister species Silene vulgaris and S.
 uniflora, in western Europe. We used microsatellite markers to investigate
 pathogen distribution in relation to host specialization and ecological
 factors. Microbotryum violaceo-irregulare was only found on S. vulgaris at
 high elevations in the Alps. Microbotryum lagerheimii could be subdivided
 into two genetically differentiated clusters, one on S. uniflora in the UK
 and the second on S. vulgaris in the Alps and Pyrenees. The most abundant
 pathogen species, M. silenes-inflatae, could be subdivided into four
 genetic clusters, co-occurring in the Alps, the UK and the Pyrenees, and
 was found on both S. vulgaris and S. uniflora. All three fungal species
 had high levels of homozygosity, in agreement with the selfing mating
 system generally observed in anther-smut fungi. The three pathogen species
 and genetic clusters had large range overlaps, but occurred at sites with
 different elevations, temperatures and precipitation levels. The three
 Microbotryum species thus do not appear to be maintained by host
 specialization or geographic allopatry, but instead may occupy different
 ecological niches in terms of environmental conditions.
description: Multilocus
 microsatellite genotypes for 446 isolates of Microbotryum violaceum
 collected on Silene vulgaris and Silene unifloraThe dataset contains
 information about the biological (host) and geographical (country, GPS)
 origin of samples, and microsatellite data for 11
 markersMvSv_abbate_dryad.xlsx