cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7783j
title: Data from: Character evolution and missing (morphological) data across Asteridae

description: Premise of the study: Our current understanding of flowering plant
 phylogeny provides an excellent framework for exploring various aspects of
 character evolution through comparative analyses. However, attempts to
 synthesize this phylogenetic framework with extensive morphological
 datasets have been surprisingly rare. Here, we explore character evolution
 in Asteridae (asterids), a major angiosperm clade, using an extensive
 morphological data set and a well-resolved phylogeny. Methods: We scored
 15 phenotypic characters (spanning chemistry, vegetative anatomy, and
 floral, fruit, and seed features) across 248 species for ancestral state
 reconstruction using a phylogenetic framework based on 73 plastid genes
 and the same 248 species. Key results: Iridoid production, unitegmic
 ovules, and cellular endosperm were all reconstructed as synapomorphic for
 Asteridae. Sympetaly, long associated with asterids, shows complex
 patterns of evolution, suggesting it arose several times independently
 within the clade. Stamens equal in number to the petals is likely a
 synapomorphy for Gentianidae, a major asterid subclade. Members of
 Lamianae, a major gentianid subclade, are potentially diagnosed by adnate
 stamens, unilacunar nodes, and simple perforation plates. Conclusions: The
 analyses presented here provide a greatly improved understanding of
 character evolution across Asteridae, highlighting multiple characters
 potentially synapomorphic for major clades. However, several important
 parts of the asterid tree are poorly known for several key phenotypic
 features (e.g., degree of petal fusion, integument number, nucellus type,
 endosperm type, iridoid production). Further morphological, anatomical,
 developmental, and chemical investigations of these poorly known asterids
 are critical for a more detailed understanding of early asterid evolution.
description: Chloroplast Gene
 MatrixMatrix of 73
 concatenated chloroplast genes use to build the phylogenies for this
 study. See the partition file for the demarcation of individual gene
 regions.73genes.phyPartition File for Chloroplast GenesPartition file showing starting and ending positions of each chloroplast gene in the concatenated matrix.73genepartMaximum Likelihood Tree with Bootstrap Support UnrootedML tree obtained from RAxML, with bootstrap support, unrooted.RAxML.treMrBayes Maximum Clade Credibility TreeMCCT obtained from MrBayes.asterid_bayes_MCCT.treSample of MrBayes Trees for Ancestral State ReconstructionSample of trees used from MrBayes analysis for ancestral state reconstructionBayesTrees_FOR_ASR.treMorphological Character MatrixMatrix of morphological characters used for ancestral state reconstructionStull_etal_AJB2018_character_matrix
DOI: 10.17632/k56z7nft57
title: Effects of temperature on the developmental biology of Thaumatotibia batrachopa

description: The macadamia nut borer, Thaumatotibia batrachopa, is one of the major pests of macadamia in South Africa. However, there is a lack of information on the effects of temperature on the developmental biology of this pest. We compared the effects of different constant temperatures on the pre-oviposition period, fecundity, mated adults' longevity, and development duration of the life stages. In addition, we determined the models that best illustrate temperature-dependent development rate and estimated thermal requirements. There was a significant variation between temperatures in all tested parameters. The pre-oviposition period, longevity, and development duration significantly increased with decreased temperature. The fecundity was highest at lower temperatures and lowest at higher temperatures. The T. batrachopa required 564.72 degree days to develop from egg to adult, with a Tmin of 10 degrees Celsius, Topt of 30 degrees Celsius, and Tmax of 36 degrees Celsius. Our findings align with the general trend of development duration, which increases with decreased temperatures. The degree days from our study will provide an accurate prediction of T. batrachopa phenology based on field temperatures and have various implications for managing this pest.
DOI: 10.17632/k56z7nft57.1
title: Effects of temperature on the developmental biology of Thaumatotibia batrachopa

description: The macadamia nut borer, Thaumatotibia batrachopa, is one of the major pests of macadamia in South Africa. However, there is a lack of information on the effects of temperature on the developmental biology of this pest. We compared the effects of different constant temperatures on the pre-oviposition period, fecundity, mated adults' longevity, and development duration of the life stages. In addition, we determined the models that best illustrate temperature-dependent development rate and estimated thermal requirements. There was a significant variation between temperatures in all tested parameters. The pre-oviposition period, longevity, and development duration significantly increased with decreased temperature. The fecundity was highest at lower temperatures and lowest at higher temperatures. The T. batrachopa required 564.72 degree days to develop from egg to adult, with a Tmin of 10 degrees Celsius, Topt of 30 degrees Celsius, and Tmax of 36 degrees Celsius. Our findings align with the general trend of development duration, which increases with decreased temperatures. The degree days from our study will provide an accurate prediction of T. batrachopa phenology based on field temperatures and have various implications for managing this pest.
DOI: 10.5061/dryad.5bv7p
title: Data from: Anthropogenic N deposition increases soil C storage by reducing the relative abundance of lignolytic fungi

description: Atmospheric nitrogen (N) deposition has increased dramatically since
 preindustrial times and continues to increase across many regions of the
 Earth. In temperate forests, this agent of global change has increased
 soil carbon (C) storage, but the mechanisms underlying this response are
 not understood. One long-standing hypothesis proposed to explain the
 accumulation of soil C proposes that higher inorganic N availability may
 suppress both the activity and abundance of fungi which decay lignin and
 other polyphenols in soil. In field studies, elevated rates of N
 deposition have reduced the activity of enzymes mediating lignin decay,
 but a decline in the abundance of lignolytic fungi has not been
 definitively documented to date. Here, we tested the hypothesis that
 elevated rates of anthropogenic N deposition reduce the abundance of
 lignolytic fungi. We conducted a field experiment in which we compared
 fungal communities colonizing low-lignin, high-lignin, and wood substrates
 in a northern hardwood forest that is part of a long-term N deposition
 experiment. We reasoned that, if lignolytic fungi decline under
 experimental N deposition, this effect should be most evident among fungi
 colonizing high-lignin and wood substrates. Using molecular approaches, we
 provide evidence that anthropogenic N deposition reduces the relative
 abundance of lignolytic fungi on both wood and a high-lignin substrate.
 Furthermore, experimental N deposition increased total fungal abundance on
 a low-lignin substrate, reduced fungal abundance on wood, and had no
 significant effect on fungal abundance on a high-lignin substrate. We
 simultaneously examined these responses in the surrounding soil and forest
 floor, in which we did not observe significant reductions in the relative
 abundance of lignolytic fungi or in the size of the fungal community;
 however, we did detect a change in community composition in the forest
 floor that appears to be driven by a shift away from lignolytic fungi and
 towards cellulolytic fungi. Our results provide direct evidence that
 reductions in the abundance of lignolytic fungi are part of the mechanism
 by which anthropogenic N deposition increases soil C storage.
description: 28S_pipelineThis compressed folder includes documentation and files for the fungal 28S rRNA gene sequence processing pipeline described in this manuscript.taxonomic_summaryThis compressed folder contains a file with the taxonomic assignment output produced by our fungal 28S sequence processing pipeline for each sample. We indicate the taxa which we selected for subsequent relative abundance analyses with symbols; these are described in the README file also contained in this folder.qPCR_dataThis compressed file contains data files and documentation related to quantitative PCR of the fungal ITS1 gene for this study.
DOI: 10.17632/svvhrs7p8h
title: Exposure to Ambient Particulate Matter Pollution and risk of COPD exacerbation

description: We hypothesized that exposure to ambient particulate matter exacerbate chronic obstructive pulmonary disease in participants. We documented a markedly elevated COPD prevalence of 63.5%, substantially exceeding general population estimates reported from other low- and middle-income countries. These findings underscore a considerable and under-recognized burden of chronic respiratory disease among urban informal workers in Ghana and comparable sub-Saharan African (SSA) settings. A qualified technician and two medical personnel performed the lung function test to determine any obstructive or restrictive syndrome. If an obstruction was detected, the spirometry test was repeated after administering a bronchodilator (2 puffs of salbutamol) to reassess lung function. This process was done between 9 – 12 hours and was guided by the 2019 American Thoracic Society guidelines for spirometry. Forced vital capacity (FVC), forced expiratory volume in the first second of exhalation (FEV1), and the FEV1/FVC ratio were measured in sitting and standing positions for both participants. The data was collected from two high risk working groups -drivers and traders- at two of the busiest transport stations in Accra (Circle and Kaneshie). A consecutive sampling technique was adopted to ensure that participants who refused consent were replaced with the next participant. The lung function text should be interpreted based on universally agreed cut-off points. Any researcher interested in lung function test studies can use this data.
DOI: 10.5061/dryad.ff265
title: Data from: A genome-wide data assessment of the African lion (Panthera leo) population genetic structure and diversity in Tanzania

description: The African lion (Panthera leo), listed as a vulnerable species on the
 IUCN Red List of Threatened Species (Appendix II of CITES), is mainly
 impacted by indiscriminate killing and prey base depletion. Additionally,
 habitat loss by land degradation and conversion has led to the isolation
 of some subpopulations, potentially decreasing gene flow and increasing
 inbreeding depression risks. Genetic drift resulting from weakened
 connectivity between strongholds can affect the genetic health of the
 species. In the present study, we investigated the evolutionary history of
 the species at different spatiotemporal scales. Therefore, the
 mitochondrial cytochrome b gene (N = 128), 11 microsatellites (N = 103)
 and 9,103 SNPs (N = 66) were investigated in the present study, including
 a large sampling from Tanzania, which hosts the largest lion population
 among all African lion range countries. Our results add support that the
 species is structured into two lineages at the continental scale
 (West-Central vs East-Southern), underlining the importance of reviewing
 the taxonomic status of the African lion. Moreover, SNPs led to the
 identification of three lion clusters in Tanzania, whose geographical
 distributions are in the northern, southern and western regions.
 Furthermore, Tanzanian lion populations were shown to display good levels
 of genetic diversity with limited signs of inbreeding. However, their
 population sizes seem to have gradually decreased in recent decades. The
 highlighted Tanzanian African lion population genetic differentiation
 appears to have resulted from the combined effects of anthropogenic
 pressure and environmental/climatic factors, as further discussed.
description: Sampling information;
 microsatellite and SNP genotypesFirst sheet includes the
 following information on the sampling: sample name, collection year,
 country and region of origin, as well as sample type. Second, third and
 fourth sheets include the microsatellite and SNP databases, respectively,
 used in the present study.DRYAD-P.leo_SNP_msat.xlsx
DOI: 10.17632/svvhrs7p8h.1
title: Exposure to Ambient Particulate Matter Pollution and risk of COPD exacerbation

description: We hypothesized that exposure to ambient particulate matter exacerbate chronic obstructive pulmonary disease in participants. We documented a markedly elevated COPD prevalence of 63.5%, substantially exceeding general population estimates reported from other low- and middle-income countries. These findings underscore a considerable and under-recognized burden of chronic respiratory disease among urban informal workers in Ghana and comparable sub-Saharan African (SSA) settings. A qualified technician and two medical personnel performed the lung function test to determine any obstructive or restrictive syndrome. If an obstruction was detected, the spirometry test was repeated after administering a bronchodilator (2 puffs of salbutamol) to reassess lung function. This process was done between 9 – 12 hours and was guided by the 2019 American Thoracic Society guidelines for spirometry. Forced vital capacity (FVC), forced expiratory volume in the first second of exhalation (FEV1), and the FEV1/FVC ratio were measured in sitting and standing positions for both participants. The data was collected from two high risk working groups -drivers and traders- at two of the busiest transport stations in Accra (Circle and Kaneshie). A consecutive sampling technique was adopted to ensure that participants who refused consent were replaced with the next participant. The lung function text should be interpreted based on universally agreed cut-off points. Any researcher interested in lung function test studies can use this data.
DOI: 10.5061/dryad.h2c0c
title: Data from: Genetic basis of photosynthetic responses to cold in two locally adapted populations of Arabidopsis thaliana

description: Local adaptation is common, but the traits and genes involved are often
 unknown. Physiological responses to cold probably contribute to local
 adaptation in wide-ranging species, but the genetic basis underlying
 natural variation in these traits has rarely been studied. Using a
 recombinant inbred (495 lines) mapping population from locally adapted
 populations of Arabidopsis thaliana from Sweden and Italy, we grew plants
 at low temperature and mapped quantitative trait loci (QTLs) for traits
 related to photosynthesis: maximal quantum efficiency (Fv/Fm), rapidly
 reversible photoprotection (NPQfast), and photoinhibition of PSII
 (NPQslow) using high-throughput, whole-plant measures of chlorophyll
 fluorescence. In response to cold, the Swedish line had greater values for
 all traits, and for every trait, large effect QTLs contributed to parental
 differences. We found one major QTL affecting all traits, as well as
 unique major QTLs for each trait. Six trait QTLs overlapped with
 previously published locally adaptive QTLs based on fitness measured in
 the native environments over 3 years. Our results demonstrate that
 photosynthetic responses to cold can vary dramatically within a species,
 and may predominantly be caused by a few QTLs of large effect. Some
 photosynthesis traits and QTLs probably contribute to local adaptation in
 this system.
description: photosynthesis_alldays_alltraits_fordryadFile containing data for all traits measured for all days of the experiment. Column names are as follows: batch_ID indicates a unique batch ID that contains the date; flat_ID indicates a unique flat ID; camera indicates which camera recorded the data; genotype indicates the RIL (numeric) or parental (It = Italy; Sw = Sweden) genotype ID; replicate identifies different replicates of an individual genotype within a batch; the 9 day columns represent daily means (individual values for Fv/Fm) for each of the days of the DEPI experiment (day0 was in the initial warm conditions, subsequent days were at 4C).RIL LSM phenotypes formatted for RqtlGenotype file formatted for Rqtl. Least square mean phenotypes for the three traits included in the QTL mapping (Fv/Fm, NPQfast, and NPQslow). A prefix of "QN_" indicates the quantile normalized value for a particular trait. The last column (id) gives the numeric RIL ID.pheno.csvRIL genotypes formatted for RqtlGenotype matrix for the RILs used in this study, formatted for input into Rqtlgeno.csv
DOI: 10.17632/mdxdntzfwm
title: Raw Data from: Targeted Screening Studies on Endemic Propolis Extracts for Selective Cytotoxicity Against Melanoma Cells

description: The aim of this study was to determine the cytotoxicity of propolis from endemic areas of Nepal, Greece, Kazakhstan, Ukraine, and Georgia against the malignant melanoma cell lines: A375 and SK-MEL-3, as well as against normal human skin fibroblasts (BJ). Within this study following propolis extracts were tested: Nepal – NE-TRI (no. 1), Greece – GR-PA (no. 8), Kazakhstan – region Bozovoe – KA-BO (no. 7), Ukraine – UK-TA (no. 9), Georgia – region Orgora – GE-OR (no. 4), Georgia region Ota – GE-OT (no. 3), Georgia – region Qvakhvreli sample 1 – GE-Q1 (no. 2), Georgia – region Qvakhvreli sample 2 – GE-Q2 (no. 6), Georgia – region Vazisubani sample 1 – GE-VA1 (no. 5), Georgia – region Vazisubani sample 2 – GE-VA2 (no. 10). Biological properties were evaluated by analyzing cell viability, apoptosis (fluorescent staining and confocal laser scanning microscope imaging), and caspase-6 activity (fluorometric assay). The results showed that 3 propolis samples from Georgian endemic regions (GE-OR, GE-VA1, and GE-Q2) exhibited the highest anticancer activity, with low toxicity towards normal cells (Si &gt;1).

Folder entitled ‘Cytotoxicity evaluation’ contains 3 folders for 3 cell lines used: BJ, A375, and SK-MEL-3. Each folder (named with the cell line code) contains several Microsoft Excel files (.xlsx) presenting raw MTT results for various propolis extracts (the name of the file indicates cell line used and propolis tested: NE-TRI (no. 1), GR-PA (no. 8), KA-BO (no. 7), UK-TA (no. 9), GE-OR (no. 4), GE-OT (no. 3), GE-Q1 (no. 2), GE-Q2 (no. 6), GE-VA1 (no. 5), GE-VA2 (no. 10)).

Folder entitled ‘Apoptosis Necrosis Assay’ contains raw confocal laser scanning microscope images (.TIF) of the propolis-treated cells. The name of the image indicates cell line used (BJ, A375, and SK-MEL-3) and propolis tested (no. 4 – GE-OR, no. 5 – GE-VA1, and no. 6 – GE-Q2). 

Microsoft Excel file (.xlsx) entitled ‘Caspase 6 48h’ contains the raw results of Caspase-6 activity assay for selected propolis extracts (no. 4 – GE-OR, no. 5 – GE-VA1, and no. 6 – GE-Q2).
DOI: 10.5061/dryad.mr875
title: Data from: Restriction site-associated DNA sequencing for SNP discovery and high-density genetic map construction in southern catfish (Silurus meridionalis)

description: Single nucleotide polymorphism (SNP) markers and high-density genetic maps
 are important resources for marker-assisted selection, mapping of
 quantitative trait loci (QTLs), and genome structure analysis. Although
 linkage maps in certain catfish species have been obtained, high-density
 maps remain unavailable in the economically important southern catfish
 (Silurus meridionalis). Recently developed restriction site-associated DNA
 (RAD) markers have proven to be a promising tool for SNP detection and
 genetic map construction. The objective of this study was to construct a
 high-density linkage map using SNPs generated by next-generation RAD
 sequencing in S. meridionalis for future genetic and genomic studies. An
 F1 population of 100 individuals was obtained by intraspecific crossing of
 two wild heterozygous individuals. In total, 77,634 putative high-quality
 biallelic SNPs between the parents were discovered by mapping the parents’
 paired-end RAD reads onto the reference contigs from both parents, of
 which 54.7% were transitions and 45.3% were transversions
 (transition/transversion ratio of 1.2). Finally, 26,714 high-quality RAD
 markers were grouped into 29 linkage groups by using de novo clustering
 methods (Stacks). Among these markers, 4,514 were linked to the female
 genetic map, 23,718 to the male map, and 6,715 effective loci were linked
 to the integrated map spanning 5,918.31 centimorgans (cM), with an average
 marker interval of 0.89 cM. High-resolution genetic maps are a useful tool
 for both marker-assisted breeding and various genome investigations in
 catfish, such as sequence assembly, gene localisation, QTL detection, and
 genome structure comparison. Hence, such a high-density linkage map will
 serve as a valuable resource for comparative genomics and fine-scale QTL
 mapping in catfish species.
description: Supplementary
 material
DOI: 10.17632/mdxdntzfwm.1
title: Raw Data from: Targeted Screening Studies on Endemic Propolis Extracts for Selective Cytotoxicity Against Melanoma Cells

description: The aim of this study was to determine the cytotoxicity of propolis from endemic areas of Nepal, Greece, Kazakhstan, Ukraine, and Georgia against the malignant melanoma cell lines: A375 and SK-MEL-3, as well as against normal human skin fibroblasts (BJ). Within this study following propolis extracts were tested: Nepal – NE-TRI (no. 1), Greece – GR-PA (no. 8), Kazakhstan – region Bozovoe – KA-BO (no. 7), Ukraine – UK-TA (no. 9), Georgia – region Orgora – GE-OR (no. 4), Georgia region Ota – GE-OT (no. 3), Georgia – region Qvakhvreli sample 1 – GE-Q1 (no. 2), Georgia – region Qvakhvreli sample 2 – GE-Q2 (no. 6), Georgia – region Vazisubani sample 1 – GE-VA1 (no. 5), Georgia – region Vazisubani sample 2 – GE-VA2 (no. 10). Biological properties were evaluated by analyzing cell viability, apoptosis (fluorescent staining and confocal laser scanning microscope imaging), and caspase-6 activity (fluorometric assay). The results showed that 3 propolis samples from Georgian endemic regions (GE-OR, GE-VA1, and GE-Q2) exhibited the highest anticancer activity, with low toxicity towards normal cells (Si &gt;1).

Folder entitled ‘Cytotoxicity evaluation’ contains 3 folders for 3 cell lines used: BJ, A375, and SK-MEL-3. Each folder (named with the cell line code) contains several Microsoft Excel files (.xlsx) presenting raw MTT results for various propolis extracts (the name of the file indicates cell line used and propolis tested: NE-TRI (no. 1), GR-PA (no. 8), KA-BO (no. 7), UK-TA (no. 9), GE-OR (no. 4), GE-OT (no. 3), GE-Q1 (no. 2), GE-Q2 (no. 6), GE-VA1 (no. 5), GE-VA2 (no. 10)).

Folder entitled ‘Apoptosis Necrosis Assay’ contains raw confocal laser scanning microscope images (.TIF) of the propolis-treated cells. The name of the image indicates cell line used (BJ, A375, and SK-MEL-3) and propolis tested (no. 4 – GE-OR, no. 5 – GE-VA1, and no. 6 – GE-Q2). 

Microsoft Excel file (.xlsx) entitled ‘Caspase 6 48h’ contains the raw results of Caspase-6 activity assay for selected propolis extracts (no. 4 – GE-OR, no. 5 – GE-VA1, and no. 6 – GE-Q2).