cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17044/scilifelab.26894242
title: Another dark taxon comes to light: Semicentenialomycetes, a new class within the Pucciniomycotina (Basidiomycota), and its described living representative, <i>Semicentenialea rex</i>

description: Only a small fraction of the world’s fungi is described, and a large number of fungal sequences from environmental DNA (eDNA) currently lack relevant reference sequences for taxonomic identification in metabarcoding studies. Partially because there are several deeply divergent fungal lineages, including hypothesized class- and order-level lineages, currently known only by eDNA sequences. Here, we describe the first living representative of one such lineage (previously referred to as Clade GS25). We use a phylogenomic approach to test the placement and taxonomic rank hypothesized for this lineage, and present the formally described <i>Semicentenialea rex</i>, as the first known species in the novel class Semicentenialomycetes (Pucciniomycotina, Basidiomycota). Additionally, we provide the first phylogenomic resolution of Pucciniomycotina, using reference genomes from all described classes with the exception of Cryptomycocolacomycetes. We propose a set of practices that could be adopted by the research community to help facilitate more connections between living fungi and eDNA sequences. The use of such practices would in turn help to alleviate some of the complications associated with fungal DNA sequences in reference databases and contribute towards a more complete understanding of fungal diversity.
DOI: 10.17044/scilifelab.26894242.v1
title: Another dark taxon comes to light: Semicentenialomycetes, a new class within the Pucciniomycotina (Basidiomycota), and its described living representative, <i>Semicentenialea rex</i>

description: Only a small fraction of the world’s fungi is described, and a large number of fungal sequences from environmental DNA (eDNA) currently lack relevant reference sequences for taxonomic identification in metabarcoding studies. Partially because there are several deeply divergent fungal lineages, including hypothesized class- and order-level lineages, currently known only by eDNA sequences. Here, we describe the first living representative of one such lineage (previously referred to as Clade GS25). We use a phylogenomic approach to test the placement and taxonomic rank hypothesized for this lineage, and present the formally described <i>Semicentenialea rex</i>, as the first known species in the novel class Semicentenialomycetes (Pucciniomycotina, Basidiomycota). Additionally, we provide the first phylogenomic resolution of Pucciniomycotina, using reference genomes from all described classes with the exception of Cryptomycocolacomycetes. We propose a set of practices that could be adopted by the research community to help facilitate more connections between living fungi and eDNA sequences. The use of such practices would in turn help to alleviate some of the complications associated with fungal DNA sequences in reference databases and contribute towards a more complete understanding of fungal diversity.
DOI: 10.5061/dryad.5tb2rbp6z
title: Drought-driven shifts in relationships between plant biodiversity and productivity in temperate steppes

description: 1. Drought events induced by global climate change strongly modify
 ecosystem structure and function in grasslands. Higher plant biodiversity
 can enhance ecosystem resistance to drought, however the potential effects
 of drought on the relationships between aboveground productivity (ANPP)
 and biodiversity along a natural aridity gradient remain poorly
 understood. 2. Here, we studied the effects of experimental drought on
 plant community structure and ANPP during the two different dry years
 (2015 and 2017) spanning three temperate steppe sites with low, medium and
 high aridity levels. We also examined the effects of drought and aridity
 on the associations of plant species (richness and abundance), functional
 (community-weighted trait means and functional dispersion) and
 phylogenetic diversity (evolutionary lineages) with ANPP. A structural
 equation modeling (SEM) was used to elucidate how the drought affected
 ANPP by altering biodiversity attributes. 3. We found that experimental
 drought shaped the biodiversity-ANPP relationships, and the
 biodiversity-ANPP relationships differed among three sites. At the low
 aridity site, ANPP was correlated with plant functional traits, whereas
 ANPP was correlated with functional dispersion, species and phylogenetic
 diversity at the medium aridity site. At the high aridity site, ANPP was
 correlated with species richness, functional traits and phylogenetic
 diversity. As compared with 2015, natural drought in 2017 strengthened the
 associations of species diversity, functional dispersion, leaf dry matter
 content and leaf nitrogen content with ANPP across three sites. SEM
 further showed that both experimental and natural drought directly
 decreased ANPP, and indirectly decreased ANPP by reducing
 community-weighted mean of plant height. 4. Synthesis. These results
 suggest that the aridity increase or drought occurrence is likely to
 induce the shifts in the associations of ANPP with species and functional
 diversity, highlighting the important role of water availability or
 precipitation conditions in regulating the biodiversity-ANPP relationships
 in temperate steppes. Overall, functional trait related to plant size
 plays a crucial role in modulating the response of productivity to drought
 across three steppe sites. Thus, to buffer the negative effects of drought
 on steppe ANPP should pay attention to protect the species with large
 plant size.
DOI: 10.5061/dryad.1vhhmgqwk
title: BdSL47: A complete dataset of sign alphabet and digits of Bangla Sign Language (BdSL) using depth information via MediaPipe

description: BdSL47 is the first open-access complete dataset in Bangla Sign Language
 that contains hand signs from both 10 sign digits (from sign ০ to sign ৯)
 and 37 sign alphabet (from sign অ to sign ँ). Dataset summary : 100 RGB
 images per sign (total 47 signs) from each of 10 users Total input images
 : 100×47×10 = 47000 Input images are processed via MediaPipe, which
 provided an output image with hand key-points being detected 3D coordinate
 values of 21 predefined key-points Total 63 coordinate values for each
 sample The values are stored in csv files 1 CSV file contains values from
 100 samples of 1 sign from 1 user Total CSV files : 47×10 = 470 The
 dataset has been made public for further research purposes. It is also
 available upon request here.
DOI: 10.5061/dryad.p5hqbzksb
title: Plankton community respiration and POC in the Kuroshio east of Taiwan

description: This dataset contains data collected from six shipboard
 measurements taken from the R/V Ocean Researcher
 I between April 2014 and November 2015, which covered the entire
 season: April, July, September, and November 2014 and March, June,
 September, and November 2015 in the Kuroshio, east of Taiwan
 described in the paper: “Chung-Chi Chen, Pei-Ji Meng, Chih-hao Hsieh, Sen
 Jan (2022). Plankton community respiration and
 particulate organic carbon in the Kuroshio, east of
 Taiwan. Plants“. The main results of this study included seven
 figures, which show: 1). The sampling stations; 2). Typical depth profile
 contour plots of temperature, nitrate, chlorophyll a and particulate
 organic carbon within 250 m water depth along the KTV1 transect in
 September 2015; 3). Temporal and spatial variations of the mean values of
 nitrate and phosphate across the KTV1 transect of the Kuroshio; 4).
 Temporal and spatial variations of the mean values of chlorophyll a,
 particulate organic carbon, and plankton community respiration across the
 KTV1 transect of the Kuroshio; 5). Relationships between the concentration
 of plankton community respiration vs. particulate organic carbon,
 chlorophyll a, heterotrophic bacterioplankton, and all picophytoplankton;
 6). Relationships between the concentration of particulate organic carbon
 vs. chlorophyll a and picophytoplankton for all pooled data; and 7).
 Temporal and spatial variations of the mean values of picophytoplankton in
 terms of abundance and biomass across the KTV1 transect of the Kuroshio.
description: To understand the coastal
 uplift effect on the Kuroshio ecosystem, eight stations
 (K101–K108) along a transect (KTV1) between 121.72°
 and 123° E at 23.75° N were repeatedly surveyed across the Kuroshio, east
 of Taiwan.
 At each station, seawater
 was sampled at eight depths (2–5, 10, 30, 50, 100, 150, 200, and 250 m), using
 Teflon-coated Go-Flo
 bottles (20 l, General Oceanics Inc., USA) mounted on a General Oceanic
 rosette assembly. Sub-samples were taken for analyses of dissolved
 inorganic nutrients (e.g., nitrate and phosphate), particulate organic
 carbon (POC), chlorophyll <em>a</em> (Chl
 <em>a</em>), autotrophic picoplankton (e.g.,
 <em>Synechococcus</em>, <em>Prochlorococcus</em>,
 and picoeukaryotes) and heterotrophic bacteria abundances, and plankton
 community respiration. The
 analyzed methods for each variable can be found in the paper. The data has
 been processed by simple and multiple linear regression analyses using
 “SigmaStat” (ver. 3.5,
 Systat Software, Inc.) to
 produce a manuscript for publication in
 <em>Plants</em>.
description: The “Readme_Plankton CR and
 POC” file contains an explanation of each of the variables in
 the dataset and its
 measurement units. Information on how the measurements were done or data
 were retrieved can be found in the associated manuscript referenced
 above.
DOI: 10.6084/m9.figshare.31168579
title: Soil organic carbon loss decreases microbial diversity and accelerates carbon turnover

description: The escalating pace of anthropogenic activities is exacerbating soil organic carbon (SOC) loss and altering microbial community structure and ecological functions. However, how soil microbiomes reorganize under SOC dynamics and feed back to carbon depletion, especially at micro-to-millimeter scale remain unresolved. Here, croplands spanning a SOC gradient under varying cultivation duration were used to examine microbial diversity trajectories across bacteria, fungi and protists, together with carbon decomposition in bulk soils and individual aggregate fractions. Metagenomics, <sup>13</sup>C‐tracing and literature synthesis were integrated to interlink microbial functions with alterations of carbon substrates and microenvironment. The results derived from these data imply that incorporating microscale physical structure and associated biological processes into SOC turnover models is paramount to develop practices improving biodiversity conservation and carbon persistence under intensifying anthropogenic activity and climate changes.
DOI: 10.6084/m9.figshare.31168579.v1
title: Soil organic carbon loss decreases microbial diversity and accelerates carbon turnover

description: The escalating pace of anthropogenic activities is exacerbating soil organic carbon (SOC) loss and altering microbial community structure and ecological functions. However, how soil microbiomes reorganize under SOC dynamics and feed back to carbon depletion, especially at micro-to-millimeter scale remain unresolved. Here, croplands spanning a SOC gradient under varying cultivation duration were used to examine microbial diversity trajectories across bacteria, fungi and protists, together with carbon decomposition in bulk soils and individual aggregate fractions. Metagenomics, <sup>13</sup>C‐tracing and literature synthesis were integrated to interlink microbial functions with alterations of carbon substrates and microenvironment. The results derived from these data imply that incorporating microscale physical structure and associated biological processes into SOC turnover models is paramount to develop practices improving biodiversity conservation and carbon persistence under intensifying anthropogenic activity and climate changes.
DOI: 10.5061/dryad.8w9ghx3qh
title: Banding and recovery data on several game bird species to study hunting selectivity

description: Selective hunting has various impacts that need to be considered for the
 conservation and management of harvested populations. The consequences of
 selective harvest have mostly been studied in trophy hunting and fishing,
 where selection of specific phenotypes is intentional.  Recent
 studies however show that selection can also occur unintentionally. With
 at least 52 million birds harvested each year in Europe, it is
 particularly relevant to evaluate the selectivity of hunting on this
 taxon. Here we considered 211 806 individuals belonging to 7
 hunted bird species to study unintentional selectivity in harvest. Using
 linear mixed models, we compared morphological traits (mass, wing and
 tarsus size) and body condition at the time of banding between birds that
 were subsequently recovered from hunting during the same year as their
 banding, and birds that were not recovered. We did not find any patterns
 showing systematic differences between recovery categories, among our
 model species, for the traits we studied. Moreover, when a difference
 existed between recovery categories, it was so small that its biological
 relevance can be challenged. Hunting of birds in Europe therefore does not
 show any form of strong selectivity on the morphological and physiological
 traits that we studied, and should hence not lead to any change of these
 traits either by plastic or evolutionary response. 
description: These data were collected in
 the framework of several ringing programmes of the CRBPO (Centre de
 Recherche sur la Biologie des Populations d'Oiseaux), OFB (Office
 Français de la biodiversité) and Tour du Valat. 
 These data are ringing and
 recovery data for 7 huntable species:  Mallard (<em>Anas
 platyrhynchos</em>), Eurasian Teal (<em>Anas
 crecca</em>), Tufted Duck (<em>Aythya</em>
 <em>fuligula</em>), Common Pochard (<em>Aythya
 ferina</em>), Common Snipe (<em>Gallinago
 gallinago</em>), Eurasian Coot (<em>Fulica atra</em>),
 and Blackbird (<em>Turdus merula</em>). All individuals were
 ringed in France between 1953 and 2020. They  include ring recoveries reported from
 Europe, covering several putative flyways and including individuals
 potentially pertaining to distinct populations. With the exception of blackbirds, some banding
 seasons are missing before 2000. In addition, for Anatidae and Rallidae,
 no banding data were available between 1978 and
 2000.  Apart from
 information on recovery date, country of recovery and the cause of
 recovery, all other information was collected at the time of banding.
 Information on sex, age or morphology of the individuals is therefore
 collected at the time of banding
 only. 
description: These data can be opened with the R software and have been
 analysed with this software. They can also be opened via Excel or
 LibreOffice Calc
DOI: 10.5061/dryad.kh189328w
title: Stay in shape: assessing the adaptive potential of shell morphology and its sensitivity to temperature in the invasive New Zealand Mud Snail Potamopyrgus antipodarum through phenotypic plasticity and natural selection in Europe

description: Climate change may force organisms to adapt genetically or plastically to
 new environmental conditions. Invasive species show a remarkable potential
 for rapid adaptation. The ovoviviparous New Zealand mud snail (NZMS),
 Potamopyrgus antipodarum, has successfully established across Europe with
 two clonally reproducing mitochondrial lineages since its arrival in the
 first half of the 19th century. Its remarkable variation in shell
 morphology was shown to be fitness relevant. We investigated the effects
 of temperature on shell morphology across eleven populations from Germany
 and the Iberian Peninsula in a common garden across three temperatures. We
 analysed size and shape using geometric morphometrics. For both, we
 compared reaction norms and estimated heritabilities. For size, the
 interaction of temperature and haplotype explained about 50% of the total
 variance. We also observed more genotype by environment interactions
 indicating a higher degree of population differentiation than in shape.
 Across the three temperatures, size followed the expectations of the
 temperature-size rule, with individuals growing larger in cold
 environments. Changes in shape may have compensated changes in size
 affecting space for brooding embryos. Heritability estimates were
 relatively high. As indicated by the very low coefficients of variation
 for clonal repeatability (CVA), they can probably not be compared in
 absolute terms. However, they showed some sensitivity to temperature, in
 haplotype t more so than in z, which was only found in Portugal. The low
 CVA-values indicate that genetic variation among European populations is
 still restricted with low potential to react to selection. A considerable
 fraction of the genetic variation was due to differences between the
 clonal lineages. The NZMS has apparently not been long enough in Europe to
 accumulate significant genetic variation relevant for morphological
 adaptation. As temperature is obviously not the sole factor influencing
 shell morphology, their interaction will probably not be a factor limiting
 population persistence under a warming climate in Europe.
DOI: 10.15468/dl.r75fgv
title: Occurrence Download

description: A dataset containing 37423 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Alternanthera philoxeroides",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Human Observation, Observation, Machine Observation, Occurrence evidence)"
 ]
}

 The dataset includes 37423 records from 78 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003253-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.x3ffbg7nn
title: Progress in understanding middle Eocene nassellarian (Radiolaria, Polycystinea) diversity; new insights from the western equatorial Atlantic Ocean

description: Middle Eocene deep-sea sediment sequences cored at Ocean Drilling Program
 Site 1260 (Leg 207; equatorial Atlantic Ocean), yielded diverse and
 abundant radiolarian faunas which are conducive to biostratigraphic and
 palaeoceanographic researchs, as well as to the study of radiolarian
 diversity dynamics during this epoch of dramatic climate changes. However,
 many species present in these sediments still have not been formally
 described and are therefore neglected in most biodiversity surveys. In an
 effort to improve the taxonomic resolution of middle Eocene radiolaria, 15
 new species of nassellarian are described and illustrated. The species
 are: Cymaetron ? dilatatus n. sp., Eucyrtidium levisaltatrix n. sp.
 (Eucyrtidiidae), Siphocampe pollen n. sp., Spirocyrtis ? renaudiei n. sp.
 (Artostrobiidae), Pterocyrtidium eep n. sp. (Rhopalosyringiidae),
 Petalospyris cometa n. sp., Petalospyris castanea n. sp.
 (Cephalospyrididae), Velicucullus armatus n. sp. (Theophormididae),
 Lychnocanium nimrodi n. sp. (Lithochytrididae), Aphetocyrtis zamenhofi n.
 sp., Aphetocyrtis ? columboi n. sp., Aphetocyrtis ? spheniscus n. sp.
 (Lophocyrtiidae), Albatrossidium regis n. sp., Albatrossidium
 annikasanfilippoae n. sp. and Phormocyrtis lazari n. sp.
 (Pterocorythidae). Stratigraphic range data are provided for each new
 species, as well as the orbitally tuned ages for their first and last
 occurrences. In addition to these new species, we also illustrated and
 documented the stratigraphic distribution of three species described in
 early radiolarian studies and rarely reported since.
DOI: 10.5061/dryad.95x69p8p0
title: Immunohistochemistry of wild type and hjv-/- iron manipulated mouse livers and spleens treated with LPS or Hepcidin

description: The iron hormone hepcidin is transcriptionally activated by iron or
 inflammation via distinct, partially overlapping pathways. We addressed
 how iron affects inflammatory hepcidin levels and the ensuing hypoferremic
 response. Dietary iron overload did not mitigate hepcidin induction in
 LPS-treated wt mice but prevented effective inflammatory hypoferremia.
 Likewise, LPS modestly decreased serum iron in hepcidin-deficient Hjv-/-
 mice, model of hemochromatosis. Synthetic hepcidin triggered hypoferremia
 in control but not iron-loaded wt animals. Furthermore, it dramatically
 decreased hepatic and splenic ferroportin in Hjv-/- mice on standard or
 iron-deficient diet, but only triggered hypoferremia in the latter.
 Mechanistically, iron antagonized hepcidin responsiveness by inactivating
 IRPs in the liver and spleen, to stimulate ferroportin mRNA translation.
 Prolonged LPS treatment eliminating ferroportin mRNA permitted
 hepcidin-mediated hypoferremia in iron-loaded mice. Thus, de novo
 ferroportin synthesis is critical determinant of serum iron and finetunes
 hepcidin-dependent functional outcomes. Our data uncover a crosstalk
 between hepcidin and IRE/IRP systems that controls tissue ferroportin
 expression and determines serum iron levels. Moreover, they suggest that
 hepcidin supplementation therapy is more efficient combined with iron
 depletion.
description: Tissue specimens were fixed in 10% buffered formalin and embedded
 in paraffin. Samples from 3 different mice for each experimental condition
 were cut at 4-µm, placed on SuperFrost/Plus slides (Fisher) and dried
 overnight at 37°C. The slides were then loaded onto the Discovery XT
 Autostainer (Ventana Medical System) for automated immunohistochemistry.
 Slides underwent de-paraffinization and heat-induced epitope retrieval.
 Immunostaining was performed by using 1:500 diluted rabbit polyclonal
 antibodies against ferroportin and an appropriate detection kit (Omnimap
 rabbit polyclonal HRP, #760-4311 and ChromoMap-DAB #760-159; Roche).
 Negative controls were performed by the omission of the primary antibody.
 Slides were counterstained with hematoxylin for four minutes, blued with
 Bluing Reagent for four minutes, removed from the autostainer, washed in
 warm soapy water, dehydrated through graded alcohols, cleared in xylene,
 and mounted with Permount (Fisher). Sections were analyzed by conventional
 light microscopy and quantified by using the Aperio ImageScope software
 (Leica Biosystems).
description: Aperio ImageScope
DOI: 10.5061/dryad.tx95x6b1t
title: Data for: Sensory biases in response to novel complex acoustic signals in male and female gray treefrogs, Hyla chrysoscelis

description: The sensory bias hypothesis proposes that female preferences for male
 sexual signaling traits evolved in contexts other than mating. Individuals
 of both sexes may experience similar selection pressures in these
 contexts, thus males may have similar biases to females for variation in
 signal traits. We tested this prediction in the gray treefrog, Hyla
 chrysoscelis, in which males produce simple advertisement calls, but
 females are more attracted to certain novel complex stimuli. We recorded
 males’ responses to playbacks of both simple advertisement calls and
 complex calls consisting of the advertisement call with an acoustic
 appendage (filtered noise, or heterospecific call pulses) either leading
 or following the call. We tested females’ preferences for the same stimuli
 in phonotaxis tests. We found evidence for a sensory bias in both sexes:
 males gave more aggressive calls in response to complex stimuli and
 females sometimes preferred complex over simple calls. These biases were
 not universal and depended on both temporal order and appendage
 characteristics, but how these effects manifested differed between the
 sexes. Ultimately, our approach of studying biases of both sexes in
 response to novel mating signals will shed light on the origin of mating
 preferences, and the mechanisms by which sensory biases operate.