cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0bq52
title: Data from: Modeling seasonal surface temperature variations in secondary tropical dry forests

description: Secondary tropical dry forests (TDFs) provide important ecosystem services
 such as carbon sequestration, biodiversity conservation, and nutrient
 cycle regulation. However, their biogeophysical processes at the
 canopy-atmosphere interface remain unknown, limiting our understanding of
 how this endangered ecosystem influences, and responds to the ongoing
 global warming. To facilitate future development of conservation policies,
 this study characterized the seasonal land surface temperature (LST)
 behavior of three successional stages (early, intermediate, and late) of a
 TDF, at the Santa Rosa National Park (SRNP), Costa Rica. A total of 38
 Landsat-8 Thermal Infrared Sensor (TIRS) data and the Surface Reflectance
 (SR) product were utilized to model LST time series from July 2013 to July
 2016 using a radiative transfer equation (RTE) algorithm. We further
 related the LST time series to seven vegetation indices which reflect
 different properties of TDFs, and soil moisture data obtained from a
 Wireless Sensor Network (WSN). Results showed that the LST in the dry
 season was 15–20 K higher than in the wet season at SRNP. We found that
 the early successional stages were about 6–8 K warmer than the
 intermediate successional stages and were 9–10 K warmer than the late
 successional stages in the middle of the dry season; meanwhile, a minimum
 LST difference (0–1 K) was observed at the end of the wet season. Leaf
 phenology and canopy architecture explained most LST variations in both
 dry and wet seasons. However, our analysis revealed that it is
 precipitation that ultimately determines the LST variations through both
 biogeochemical (leaf phenology) and biogeophysical processes
 (evapotranspiration) of the plants. Results of this study could help
 physiological modeling studies in secondary TDFs.
description: Data files, figures, and
 tables for the paperData_files.zip
DOI: 10.5061/dryad.rs806
title: Data from: Signatures of soft sweeps across the Dt1 locus underlying determinate growth habit in soybean [Glycine max (L.) Merr.]

description: Determinate growth habit is an agronomically important trait associated
 with domestication in soybean. Previous studies have demonstrated that the
 emergence of determinacy is correlated with artificial selection on four
 non-synonymous mutations in the Dt1 gene. To better understand the
 signatures of the soft sweeps across the Dt1 locus and track the origins
 of the determinate alleles, we examined patterns of nucleotide variation
 in Dt1 and the surrounding genomic region of approximately 800 kb. Four
 local, asymmetrical hard sweeps on four determinate alleles, sized
 approximately 660, 120, 220 and 150 kb were identified, which constitute
 the soft sweeps for the adaptation. These variable-sized sweeps
 substantially reflected the strength and timing of selection, and
 indicated that the selection on the alleles had been completed rapidly
 within half a century. Statistics of EHH, iHS, H12 and H2/H1 based on
 haplotype data had the power to detect the soft sweeps, revealing distinct
 signatures of extensive long-range LD and haplotype homozygosity, and
 multiple frequent adaptive haplotypes. A haplotype network constructed for
 Dt1 and a phylogenetic tree based on its extended haplotype block implied
 independent sources of the adaptive alleles through de novo mutations or
 rare standing variation in quick succession during the selective phase,
 strongly supporting multiple origins of the determinacy. We propose that
 the adaptation of soybean determinacy is guided by a model of soft sweeps
 and that this model might be indispensable during crop domestication or
 evolution.
description: SNPdataSequence dataoriginal sequence data
DOI: 10.5061/dryad.gj3vj
title: Data from: Light availability impacts structure and function of phototrophic stream biofilms across domains and trophic levels

description: Phototrophic biofilms are ubiquitous in freshwater and marine environments
 where they are critical for biogeochemical cycling, food webs and in
 industrial applications. In streams, phototrophic biofilms dominate
 benthic microbial life and harbor an immense prokaryotic and eukaryotic
 microbial biodiversity with biotic interactions across domains and trophic
 levels. Here, we examine how community structure and function of these
 biofilms respond to varying light availability, as the crucial energy
 source for phototrophic biofilms. Using metatranscriptomics, we found that
 under light limitation dominant phototrophs, including diatoms and
 cyanobacteria, displayed a remarkable plasticity in their photosynthetic
 machinery manifested as higher abundance of messenger RNAs (mRNAs)
 involved in photosynthesis and chloroplast ribosomal RNA. Under higher
 light availability, bacterial mRNAs involved in phosphorus metabolism,
 mainly from Betaproteobacteria and Cyanobacteria, increased, likely
 compensating for nutrient depletion in thick biofilms with high biomass.
 Consumers, including diverse ciliates, displayed community shifts
 indicating preferential grazing on algae instead of bacteria under higher
 light. For the first time, we show that the functional integrity of stream
 biofilms under variable light availability is maintained by
 structure-function adaptations on several trophic levels. Our findings
 shed new light on complex biofilms, or “microbial jungles”, where in
 analogy to forests, diverse and multi-trophic level communities lend
 stability to ecosystem functioning. This multi-trophic level perspective,
 coupling metatranscriptomics to process measurements, could advance
 understanding of microbial-driven ecosystems beyond biofilms, including
 planktonic and soil environments.
description: meta_dataMeta data file describing sample identification, treatments, measured biofilm and microcosm parameters and summary statistics for the sequencing data.mRNAsRaw sequence data (fastq files) of putative mRNA reads of biofilms from each microcosm after sortmeRNA filtering.SSU_rRNAsRaw sequence data (fastq files) of small subunit (SSU) rRNA reads of biofilms from each microcosm.Genera_SSUSequence counts (sheet 1) and taxonomic and functional classification (sheet 2) of genus-level taxa based on SSU rRNA reads. Classified using Silvamod taxonomy (CREST) and exported from MEGAN.mRNA_MGRASTSEED Subsystems classifications (sheet 1) and functional assignments (sheet 2) of mRNA reads, exported from MGRAST.
DOI: 10.5061/dryad.c65b4j5
title: Data from: Tooth microwear and occlusal modes of euharamiyidans from the Jurassic Yanliao Biota reveal mosaic tooth evolution in Mesozoic allotherian mammals

description: ‘Haramiyidans’ are extinct mammaliaforms often clustered with
 Multituberculata as Allotheria, and with a fossil record extending from
 the Upper Triassic to possibly the Upper Cretaceous. For many decades,
 ‘haramiyidans’ were known only from isolated teeth, and their
 relationships to other mammaliaforms remain unclear. With the discovery of
 several euharamiyidans represented by skeletal specimens from the Jurassic
 Yanliao Biota, north‐western China, our knowledge of this group has
 significantly advanced. Nonetheless, much morphology, including dentition
 and occlusal patterns, has only been briefly described for most taxa, and
 phylogenetic reconstruction and interpretation of the biology of the group
 still remain unclear or controversial. Here we provide systematic
 descriptions of the dental wear of shenshouids (Qishou and Shenshou) from
 the Yanliao Biota. We reconstruct the occlusal mode of shenshouids and
 compare it with those of other taxa based on our observation of specimens
 of most known ‘haramiyidan’ taxa. Several occlusal patterns are
 recognized. In particular, that of Thomasia, Haramiyavia and Maiopatagium
 is similar to the multituberculate M1/m1 occlusal relationship and
 probably represents the primitive occlusal condition in ‘haramiyidans’.
 The occlusal mode of shenshouids resembles the multituberculate M2/m2
 occlusion. The double‐engaged mode in Arboroharamiya and Vilevolodon, as
 well as that of Eleutherodon, represents a more advanced occlusal pattern.
 The diverse dental occlusions suggest diverse diet adaptations and
 resource partitioning from co‐existing taxa in the Jurassic forests; they
 also reflect mosaic evolutionary transformations and complicated
 phylogenetic relationships within the group. Some aspects of the dental
 evolution remain challenging and require further vigorous testing.
description: Supporting
 InformationThe file is the
 Supporting Information for a paper to be published in Palaeontology. The
 title of the paper is "Tooth microwear and occlusal modes of
 euharamiyidans from the Jurassic Yanliao Biota reveal mosaic tooth
 evolution in Mesozoic allotherian mammals". The file is in pdf format
 and contains figures and text.SUPPORTING
 INFORMATION-mao&meng-v1.pdfRaw data and
 reconstructed modelsQishou-Mao&Meng.zip
 contains the raw data in TIF format of the CT-scanned teeth used in the
 paper. In each folder containing the TIF files, there is a file with the
 ending “raw”; the number in the folder name represents X-Y-Z-resolution.
 The data should be openable using VG-Studio. There is also a folder
 containing the .stl files, in which the reconstructed model can be played
 using Preview or other programs. Some of the model images have been
 flipped from the original specimens. Please see the README.docx for
 further information.Qishou-Mao&Meng.zip
DOI: 10.5061/dryad.gp5j0
title: Data from: De novo transcriptome assembly and polymorphism detection in two highly divergent evolutionary units of Bosca's newt (Lissotriton boscai) endemic to the Iberian Peninsula

description: This article reports the de novo transcriptomes of two highly divergent
 evolutionary units of the Iberian endemic Bosca’s newt, Lissotriton
 boscai. These two units are distributed allopatrically but meet in areas
 of secondary contact in central-southwestern coastal region of Portugal.
 The resources we provide include the raw sequence reads, the assembled
 transcripts and SNPs called for both lineages.
description: boscai_spain_contigsContigs generated by Trinity assembler from all the reads belonging to boscai from Spainboscai_spain.fastaboscai_portugal_contigsContigs generated by Trinity assembler from all the reads belonging to boscai from Portugal.boscai_portugal.fastaboscai_spain_annotationAnnotations generated by Sma3s software for contigs belonging to boscai from Spainboscai_spain.annotboscai_portugal_annotationAnnotations generated by Sma3s software for contigs belonging to boscai from Portugalboscai_portugal.annotSNPs_fixedSNPs fixed in boscai from Portugal and SpainfilterDP10MQ20_fix.vcfSNPs_exclusive_in_boscai_portugalExclusive SNPs in boscai from PortugalfilterDP10MQ20_polpor.vcfSNPs_exclusive_in_boscai_spainExclusive SNPs in boscai from SpainfilterDP10MQ20_polsp.vcfSNPs_shared_between_boscai_portugal_and_boscai_spainSNPs shared between boscai from Portugal and boscai from SpainfilterDP10MQ20_shared.vcf
DOI: 10.5061/dryad.h46jr1k
title: Data from: Electron backscatter diffraction (EBSD) analysis of maniraptoran eggshells with important implications for microstructural and taphonomic interpretations

description: Electron backscatter diffraction (EBSD) is a useful tool for gathering
 crystallographic information from carbonate biominerals because it maps
 out the orientation of crystal grains very precisely. EBSD has become
 popular in invertebrate palaeontology but its application in vertebrate
 palaeontology remains limited. However, the study of fossil eggshells is a
 field where EBSD has wide potential applicability and provides a
 quantitative approach to fossil eggshell research as well as new
 qualitative data. Here we analyse fossil and extant maniraptoran dinosaur
 eggshells using EBSD analysis emphasizing four different aspects. The
 mapping imaging clarifies previously ambiguous characters such as
 squamatic ultrastructure and allows a more objective evaluation of avian
 and non‐avian maniraptoran eggshell. In particular, our results imply that
 the presence of an external zone in the manirpatoran eggshell is not
 diagnostic of avian eggshell. EBSD analysis can be also used for
 differentiating true pore canals from cracks in the eggshell radial
 section, thereby determining the biological genuineness or otherwise of a
 pore‐like structure. Finally, the misorientation angle distribution of the
 material shows a clear dichotomy that may reflect reproductive brooding
 strategy, although further studies on contact incubation of palaeognaths
 and neognaths are needed to confirm this.
description: Fossil eggshell SEM
 imagesElongatoolithus sp.,
 Prismatoolithus levis and Gobioolithus minor secondary electron images.
 Note rugged grain boundaries in continuous layers.Modern avian eggshell
 SEM imagesRhea, chicken, duck,
 Japanese tit, Korean magpie eggshells in secondary electron mode. Note
 rugged grain boundaries in continuous layers.EBSD raw data for
 materialsChannel 5 files. Note
 that in case of Gobioolithus minor, a version that diagenetic calcite is
 removed is used for misorientation histogram. In each species, a complete
 EBSD data and a subset for mammillary layer analysis are included. A zero
 solution corrected version is provided as raw data.Misorientation (For
 Figure 9)Misorientation angles
 for neighbour-pair (correlated) and random-pair (uncorrelated)
 distributions. These data were used for histograms in Figure
 9.Misorientation (For
 Figure S2 and Table S2)Misorientation angles
 for neighbour-pair (correlated) and random-pair (uncorrelated)
 distributions. These data were used for histograms in Figure S2 and for
 Table S2.Contrast
 mapsContrast map of
 materials.10 Grain boundary
 mapsThese maps were used for
 measuring ruggedness of the grain boundaries in squamatic ultrastructure
 and an external layer.Supplementary Figures
 S1-S4Supplementary Figures
 cited in the text.Supplementary Tables
 S1-S3Supplementary Tables
 cited in the text.Raw data converted to
 Text filesThese are CRC files
 converted into text files for users who can not access CRC
 files
DOI: 10.5061/dryad.4rn55kq
title: Data from: Detection of somatic epigenetic variation in Norway spruce via targeted bisulfite sequencing

description: Epigenetic mechanisms represent a possible mechanism for achieving a rapid
 response of long‐lived trees to changing environmental conditions.
 However, our knowledge on plant epigenetics is largely limited to a few
 model species. With increasing availability of genomic resources for many
 tree species, it is now possible to adopt approaches from model species
 that permit to obtain single‐base pair resolution data on methylation at a
 reasonable cost. Here, we used targeted bisulfite sequencing (TBS) to
 study methylation patterns in the conifer species Norway spruce (Picea
 abies). To circumvent the challenge of disentangling epigenetic and
 genetic differences, we focused on four clone pairs, where clone members
 were growing in different climatic conditions for 24 years. We targeted
 &gt;26.000 genes using TBS and determined the performance and
 reproducibility of this approach. We characterized gene body methylation
 and compared methylation patterns between environments. We found highly
 comparable capture efficiency and coverage across libraries. Methylation
 levels were relatively constant across gene bodies, with 21.3 ± 0.3%, 11.0
 ± 0.4% and 1.3 ± 0.2% in the CG, CHG, and CHH context, respectively. The
 variance in methylation profiles did not reveal consistent changes between
 environments, yet we could identify 334 differentially methylated
 positions (DMPs) between environments. This supports that changes in
 methylation patterns are a possible pathway for a plant to respond to
 environmental change. After this successful application of TBS in Norway
 spruce, we are confident that this approach can contribute to broaden our
 knowledge of methylation patterns in natural tree populations.
description: Pabies1.0-HC.1000mRNA1000Reference fasta file used for mapping the reads containing all high confidence genes from the Picea genome (Nystedt et al. 2013) with 1000 bp before and after the mRNA if availablePabies1.0-HC.1000mRNA1000.gene.sortedgff file with annotations for CDS regions of the high confidence genes in the Picea abies genome (Nystedt et al. 2013)Pabies1.0-HC.1000mRNA1000.probes.sortedgff file with information on all probe regions in the SeqCap Epi probe set used in this publicationmethylation_bed_filesbed files with information on methylation status for CG, CHG and CHH methylation in the eight sequenced libraries.
DOI: 10.5061/dryad.50v83
title: Data from: Early treatment response in non-small cell lung cancer patients using diffusion-weighted imaging and functional diffusion maps - a feasibility study

description: Objective: The aim of this study was to prospectively evaluate the
 feasibility of monitoring treatment response to chemotherapy in patients
 with non-small cell lung carcinoma using functional diffusion maps (fDMs).
 Materials and Methods: This study was approved by the Cantonal Research
 Ethics Committee and informed written consent was obtained from all
 patients. Nine patients (mean age = 66 years; range = 53–76 years, 5
 females, 4 males) with overall 13 lesions were included. Imaging was
 performed within two weeks before initiation of chemotherapy and at one,
 two, and six weeks after initiation of chemotherapy. Imaging included a
 respiratory-triggered diffusion-weighted sequence including three
 b-factors (100, 600, and 800 s/mm2). Treatment response was defined by
 change in tumor diameter on computed tomography (CT) after two cycles of
 chemotherapy. Changes in the apparent diffusion coefficient (ADC) on a
 per-lesion basis and the percentages of voxel with significantly increased
 or decreased ADCs on fDMs were analyzed using repeated measures analysis
 of variance (ANOVA). Changes in tumor size were used as covariate to
 examine the ability of ADCs and fDM parameters to predict treatment
 response. Results: Repeated measures ANOVA revealed that the percentage of
 voxels with increased ADCs on fDMs (p = 0.002) as well as the mean ADC
 increase (p = 0.011) were significantly higher in good responders with a
 large reduction in tumor size on CT. Conclusion: Our results indicate that
 the percentage of voxels with significantly increased ADCs on fDMs seems
 to be a promising biomarker for early prediction of treatment response in
 patients with non-small cell lung carcinoma. Contrary to averaged values,
 this approach allows the spatial heterogeneity of treatment response to be
 resolved.
description: Longitudinal Lung Cancer
 DataThe zip-File includes
 all longitudinal MR data files for each patient separately which were used
 to determine treatment monitoring in non-small cell lung cancer patients
 using diffusion-weighted imaging and functional diffusion maps. The
 detailed scan parameters and acquisition time points can be found in the
 manuscript.LungCancerData.zip
DOI: 10.5061/dryad.bn7j3
title: Data from: Elevated CO2 and temperature increase soil C losses from a soybean-maize ecosystem

description: Warming temperatures and increasing CO2 are likely to have large effects
 on the amount of carbon stored in soil, but predictions of these effects
 are poorly constrained. We elevated temperature (canopy: +2.8 °C; soil
 growing season: +1.8 °C; soil fallow: +2.3 °C) for 3 years within the
 9th–11th years of an elevated CO2 (+200 ppm) experiment on a maize–soybean
 agroecosystem, measured respiration by roots and soil microbes, and then
 used a process-based ecosystem model (DayCent) to simulate the decadal
 effects of warming and CO2 enrichment on soil C. Both heating and elevated
 CO2 increased respiration from soil microbes by ~20%, but heating reduced
 respiration from roots and rhizosphere by ~25%. The effects were additive,
 with no heat × CO2 interactions. Particulate organic matter and total soil
 C declined over time in all treatments and were lower in elevated CO2
 plots than in ambient plots, but did not differ between heat treatments.
 We speculate that these declines indicate a priming effect, with increased
 C inputs under elevated CO2 fueling a loss of old soil carbon. Model
 simulations of heated plots agreed with our observations and predicted
 loss of ~15% of soil organic C after 100 years of heating, but simulations
 of elevated CO2 failed to predict the observed C losses and instead
 predicted a ~4% gain in soil organic C under any heating conditions.
 Despite model uncertainty, our empirical results suggest that combined,
 elevated CO2 and temperature will lead to long-term declines in the amount
 of carbon stored in agricultural soils.
description: SoyFACE_SOM_Black_etal_2016Soil respiration, particulate organic matter, and DayCent simulations from a fully open-air heating + CO2 experiment in soybean & maize at SoyFACE, Urbana IL USA, 2009-2011.soyface_dryad.zip
DOI: 10.5061/dryad.5856q415
title: Data from: Ring distributions leading to species formation: a global topographic analysis of geographic barriers associated with ring species

description: BACKGROUND: In the mid 20th Century, Ernst Mayr and Theodosius Dobzhansky
 championed the significance of circular overlaps or ring species as the
 perfect demonstration of speciation, yet in over 50 years since only a
 handful of such taxa are known. We developed a topographic model to
 evaluate whether the geographic barriers that favor processes leading to
 ring species are common or rare, and to predict where other candidate ring
 barriers might be found. RESULTS: Of the 952,147 geographic barriers
 identified on the planet, only about 1% are topographically similar to
 barriers associated with known ring taxa, with most of the likely
 candidates occurring in under-studied parts of the world (e.g., marine
 environments, tropical latitudes). Predicted barriers separate into two
 distinct categories: (i) single cohesive barriers (&lt;50,000 km2),
 associated with taxa that differentiate at smaller spatial scales
 (salamander: Ensatina eschscholtzii; tree: Acacia karroo); and (ii)
 composite barriers – formed by groups of barriers (each 184,000 to 1.7
 million km2) in close geographic proximity (totaling 1.9 to 2.3 million
 km2) – associated with taxa that differentiate at larger spatial scales
 (birds: Phylloscopus trochiloides and Larus [sp. argentatus and fuscus]).
 When evaluated globally, we find a large number of cohesive barriers that
 are topographically similar to those associated with known ring taxa. Yet,
 compared to cohesive barriers, an order of magnitude fewer composite
 barriers are similar to those that favor ring divergence in species with
 higher dispersal. CONCLUSIONS: While these findings confirm that the
 topographic conditions that favor evolutionary processes leading to ring
 speciation are in fact rare, they also suggest that many understudied
 natural systems could provide valuable demonstrations of continuous
 divergence towards the formation of new species. Distinct advantages of
 the model are that it (i) requires no a priori information on the relative
 importance of features that define barriers, (ii) can be replicated using
 any kind of continuously distributed environmental variable, and (iii)
 generates spatially explicit hypotheses of geographic species formation.
 The methods developed here – combined with study of the geographical
 ecology and genetics of taxa in their environments – should enable
 recognition of ring species phenomena throughout the world.
description: TopographicBarrierModel_v1.0Complete results from the topographic model of ring barriers published in BMC Biology (2012) -- Ring distributions leading to species formation: a global topographic analysis of geographic barriers associated with ring species, Monahan, William B., Pereira, Ricardo J., Wake, David B.