cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.w9ghx3fps
title: Phylogenomics and biogeography of Castanea (chestnut) and Hamamelis (witch-hazel): Choosing between RAD-seq and Hyb-Seq approaches

description: Target enrichment and RAD-seq are well-established high throughput
 sequencing technologies that have been increasingly used for phylogenomic
 studies. Each method has its own pros and cons. The choice between them is
 a practical issue for plant systematists studying the evolutionary
 histories of biodiversity of rela­tively recent origins. However, few
 studies have compared the congruence and conflict between results from the
 two methods within the same group of organisms in plants. In this study,
 we employed RAD-seq and Hyb-Seq of Angiosperm 353 genes in phylogenomic
 and biogeographic studies of Hamamelis (the witch-hazels) and Castanea
 (chestnuts), two classic examples exhibiting the well-known eastern Asian
 (EA)-eastern North American (ENA) disjunct distribution, and compared them
 side by side. Our results showed congruences in phylogenetic inference and
 divergence time dating between the two data sets obtained through our
 customized procedures of library preparation and sequence trimming,
 although they differed in the number of loci and informative sites, the
 amount of missing data, and sampling within species. We suggest the
 selection of the two methods based on fund availability and sampling
 scale. Our phylogenetic analyses of RAD-seq and Hyb-Seq data resulted in
 well-resolved species relationships, and ancient introgressions were
 revealed in both genera by D-statistic test and PhyloNet. Biogeographic
 analyses including fossil data using total evidence-based dated tree and
 DEC model, applying specific inter-area dispersal probabilities, revealed
 a complicated history for each genus, indicating multiple intercontinental
 dispersals and local extinctions in areas outside of the taxa's
 modern ranges in both the Paleogene and Neogene. The study demonstrates
 the importance of including fossil taxa for a more accurate reconstruction
 of biogeographic histories of taxa to understand the EA and ENA floristic
 disjunction. Our results support an “out of western North America”
 migration of Castanea but an “out of Asia” migration of Hamamelis during
 their initial diversification, and the origins of the EA-ENA disjunction
 in both genera were results of vicariance.
DOI: 10.6084/m9.figshare.31166463
title: Additional file 1 of Chromosome structural variation analysis reveals lung cancer-associated gene regulatory networks in rheumatoid arthritis patients

description: Supplementary Material 1.
DOI: 10.6084/m9.figshare.31166463.v1
title: Additional file 1 of Chromosome structural variation analysis reveals lung cancer-associated gene regulatory networks in rheumatoid arthritis patients

description: Supplementary Material 1.
DOI: 10.5061/dryad.kprr4xh4r
title: Leaf data of four families of broad-leaved plants

description: The data include two comma-delimited (csv) files and one word document.
 The data1.csv file saves the leaf raw data (including leaf lamina length,
 width, area, perimeter, fresh mass, and dry mass) from five groups of
 Phyllostachys edulis (Poaceae) differing in culm age. The bamboo plants
 grew in the Purple Mountain, Nanjing, China. The data2.csv file saves the
 leaf raw data (including leaf lamina length, width, area, perimeter, fresh
 mass, and dry mass) of 21 species from three families (nine Lauraceae
 species, six Fagaceae species and six Ulmaceae species) growing in
 Nanjing, China. Among the 21 species, we measured the data of leaf petiole
 fresh mass for the nine Lauraceae species. The word document (i.e.,
 the metadata.docx file) is the metadata used to show the
 meanings of the column variables in each table.
description: About how the data was collected, please refer to the following
 paper: Guo, X., Shi, P., Niinemets, Ü, Hölscher, D.,
 Wang, R., Liu, M., Li, Y., Dong, L., Niklas, K.J. "Diminishing
 returns" for leaves of five age-groups of <em>Phyllostachys
 edulis</em> culms. American Journal of
 Botany 2021, 108: 1662−1672.
 doi: 10.1002/ajb2.1738 Li, Y., Shi,
 P., Niinemets, Ü, Song, Y., Yu, K., Schrader, J., Niklas,
 K.J. Diminishing returns among lamina fresh and dry mass, surface area,
 and petiole fresh mass among nine Lauraceae species. American Journal of
 Botany 2021, 109: 377−392.
 doi: 10.1002/ajb2.1812
DOI: 10.6084/m9.figshare.31166482
title: Additional file 2 of Long-read genome sequencing enhances diagnostics of pediatric neurological disorders

description: Supplementary Material 2.
DOI: 10.6084/m9.figshare.31166482.v1
title: Additional file 2 of Long-read genome sequencing enhances diagnostics of pediatric neurological disorders

description: Supplementary Material 2.
DOI: 10.5061/dryad.t76hdr814
title: Animal-borne video systems provide insight into the reproductive behavior of the Asian black bear

description: Previous studies on the mating system of the Asian black bear (Ursus
 thibetanus) have been limited to observations of captive populations and
 estimations of multiple paternities. Hence, the mating system of wild
 bears remains poorly understood. Animal-borne camera systems (i.e.,
 cameras mounted on animals) provide novel tools to study the behavior of
 elusive animals. Here, we used an animal-borne video system to record the
 activities of wild bears during the mating season. Video camera collars
 were attached to four adult Asian black bears (Male ‘A’ and ‘B’, and
 female ‘A’ and ‘B’) captured in Tokyo, central Japan, in May and June
 2018. The collars were retrieved in July 2018, after which the video data
 were downloaded and analyzed in terms of bear activity and mating
 behavior. All the bears were found to interact with other uniquely
 identifiable bears for some of the time (range 9–22 days) during the
 deployment period (range 36–45 days), and multiple mating in males were
 documented. Both males and females exhibited different behaviors on social
 days (i.e., days when the bear interacted with conspecifics) compared to
 solitary days (i.e., days with no observed interactions with
 conspecifics). Compared to solitary days, the bears spent a lower
 proportion of time on foraging activities, and higher proportion of time
 on resting activities on social days. Our results suggest that Asian black
 bears have a polygamous mating system, as both sexes consort and
 potentially mate with multiple partners during a given mating season.
 Furthermore, bears appeared to reduce their foraging activities on social
 days, and engaged more in social interactions.
DOI: 10.5061/dryad.x69p8czj6
title: Midgut transcriptome assessment of the cockroach-hunting wasp Ampulex compressa (Apoidea: Ampulicidae)

description: The emerald jewel wasp Ampulex compressa (Hymenoptera:
 Ampulicidae) is a solitary wasp that is widely known for its specialized
 hunting of cockroaches as larvae provision. Adult wasps mainly feed on
 pollen and nectar, while their larvae feed on the cockroachs’ body, first
 as ecto- and later as endoparsitoids. Little is known about the expression
 of digestive, detoxification and stress-response-related genes in the
 midgut of A. compressa, or about its transcriptional versatility between
 life stages. To identify gut-biased genes related to digestion,
 detoxification, and stress response, we explored the midgut transcriptome
 of lab-reared A. compressa, for both adults and larvae, by
 focusing on the top 100 significantly up- and down-regulated genes. From
 the top 100 significantly differentially expressed genes (DEGs), we
 identified 39 and 36 DEGs putatively related to digestion and
 detoxification in the adult wasps and larvae, respectively.
 The two carbohydrases alpha-glucosidase (containing an
 alpha-amylase domain) and glycosyl hydrolase family
 31, as well as the two proteinases chymotrypsin and trypsin,
 revealed the highest gene diversity. We identified six
 significant DEGs related to detoxification, which comprise glutathione
 S-transferase, cytochrome P450s and UDP-glucuronosyltransferase. The gene
 expression levels that were significantly expressed in both life
 stages vary strongly between life stages, as found in
 genes encoding for chymotrypsin and trypsin or glycosyl hydrolases family
 31. The number of genes related to alpha-glucosidase, glycosyl hydrolase
 family 31, and cytochrome P450s was found to be similar
 across nine reference hymenopteran species, except for
 the identified glycosyl hydrolase family 31 gene, which was absent in all
 reference bee species. Phylogenetic analyses of the latter candidate genes
 revealed that they cluster together with their homologous genes found in
 the reference hymenopteran species. These identified candidate genes
 provide a basis for future comparative genomic and proteomic studies on
 (ontogenetic) dietary transitions in Hymenoptera.
DOI: 10.6084/m9.figshare.31166493
title: Additional file 1 of A bench-to-data analysis workflow for respiratory syncytial virus whole-genome sequencing with short and long-read approaches

description: Supplementary Material 1.
DOI: 10.6084/m9.figshare.31166493.v1
title: Additional file 1 of A bench-to-data analysis workflow for respiratory syncytial virus whole-genome sequencing with short and long-read approaches

description: Supplementary Material 1.
DOI: 10.5061/dryad.905qfttks
title: Illustrating potential effects of alternate control populations on real-world evidence-based statistical analyses

description: Objective: Case-control study designs are commonly used in retrospective
 analyses of Real-World Evidence (RWE). Due to the increasingly wide
 availability of RWE, it can be difficult to determine whether findings are
 robust or the result of testing multiple hypotheses. Materials and
 Methods: We investigate the potential effects of modifying cohort
 definitions in a case-control association study between depression and
 Type 2 Diabetes Mellitus (T2D). We used a large (&gt;75 million
 individuals) de-identified administrative claims database to observe the
 effects of minor changes to the requirements of glucose and hemoglobin A1c
 tests in the control group. Results: We found that small permutations to
 the criteria used to define the control population result in significant
 shifts in both the demographic structure of the identified cohort as well
 as the odds ratio of association. These differences remain present when
 testing against age and sex-matched controls. Discussion: Analyses of RWE
 need to be carefully designed to avoid issues of multiple testing. Minor
 changes to control cohorts can lead to significantly different results and
 have the potential to alter even prospective studies through selection
 bias. Conclusion: We believe this work offers strong support for the need
 for robust guidelines, best practices, and regulations around the use of
 observational RWE for clinical or regulatory decision making.
description: Included are the code and bootstrap results from our analysis on
 a large nationwide commercial insurance claims dataset covering &gt;75
 million individuals from Jan 1, 2008 to Aug 31, 2019. Results can be used
 to recreate our figures. Due to licensing reasons we are unable to share
 the source data. 
description: T2D Data prep.ipynb creates helper tables from source data which
 are used for T2D case/control, as well as depression
 phenotyping. Exploration.ipynb generates the phenotyped
 cohorts and performs bootstrap association testing. This file also
 includes queries for population characteristics. Paper
 figs.ipynb generates the figures shown in our manuscript from results
 stored in figdata/. ndclookup.py is a helper script to
 map NDC drug codes to RxCUI ingredient codes.
DOI: 10.6084/m9.figshare.31166497
title: Additional file 1 of Mitochondria dysfunctional diseases among African population since the discovery of mitochondrial pathologies: a systematic review

description: Additional file 1: Excluded Data.
DOI: 10.6084/m9.figshare.31166497.v1
title: Additional file 1 of Mitochondria dysfunctional diseases among African population since the discovery of mitochondrial pathologies: a systematic review

description: Additional file 1: Excluded Data.
DOI: 10.5061/dryad.p2ngf1vqq
title: Data from: Predicting southern zigzag salamander (Plethodon ventralis) occupancy in a fragmented landscape

description: We used repeated sampling of random quadrats and occupancy models to
 evaluate how the local distribution of the Southern Zigzag Salamander
 (Plethodon ventralis) in an urban and suburban landscape is
 influenced by: 1) forest patch size; 2) dominant lithology; and 3)
 invasive groundcover.
DOI: 10.5061/dryad.hx3ffbgdq
title: Relational values help explain green infrastructure preferences: The case of managing crane habitat in Hokkaido, Japan

description: The initial purpose of our study was to understand preferences of
 stakeholders on green infrastructure for flood control using a discrete
 choice experiment. However, the results of our study included unexpected
 findings. According to the utility theory of economics, an inexpensive
 green infrastructure scenario should have been chosen under ceteris
 paribus conditions, but our results differed from this expectation.
 Inconsistent results like ours are often interpreted as indicating bias
 and/or questionnaire design issues. However, our results can be
 interpreted using relational values. We studied green infrastructure in a
 large-scale flood control basin in Naganuma, a town in the Hokkaido
 prefecture in Northern Japan. We conducted a discrete choice experiment
 with town residents as stakeholders of the green infrastructure. Through
 the examination of choice and membership parameters of our results, we
 interpreted that individual identity and place attachment, which are types
 of relational values, are taken into consideration in the choice situation
 of the discrete choice experiment. We also found that a notion of social
 responsibility, which is also a relational value, can help us to
 understand unexpected findings that cannot be interpreted in terms of
 economic theory alone. Relational values contribute to our interpretation
 of preferences related to managing ecosystem services with implications
 for green infrastructure, culturally significant wildlife,
 wildlife-related recreation, and flood control.
DOI: 10.5061/dryad.ghx3ffbp0
title: Sampling plot × species matrix from: Climate-driven elevational variation in range sizes of vascular plants in the central Himalayas: a supporting case for Rapoport’s rule

description: A fundamental yet controversial topic in biogeography is how and why
 species range sizes vary along spatial gradients. To advance our
 understanding of these questions and to provide insights into biological
 conservation, we assessed elevational variations in the range sizes of
 vascular plants with different life forms and biogeographical affinities
 and explored the main drivers underlying these variations in the longest
 valley in China’s Himalayas, the Gyirong Valley. Elevational range sizes
 of vascular plants were documented in 96 sampling plots along an
 elevational gradient ranging from 1,800 to 5,400 m above sea level. We
 assessed the elevational variations in range size by averaging the range
 sizes of all recorded species within each sampling plot. We then related
 the range size to climate, disturbance, and the mid-domain effect, and
 explored the relative importance of these factors in explaining the range
 size variations using the Random Forest model. A total of 545 vascular
 plants were recorded in the sampling plots along the elevational gradient.
 Of these, 158, 387, 337, and 112 were woody, herbaceous, temperate, and
 tropical species, respectively. The range size of each group of vascular
 plants exhibited uniform increasing trends along the elevational gradient,
 which was consistent with the prediction of Rapoport’s rule. Climate was
 the main driver of the increasing trends of vascular plant range sizes in
 the Gyirong Valley. The climate variability hypothesis and mean climate
 condition hypothesis could both explain the elevation-range size
 relationships. Our results reinforce the previous notion that Rapoport’s
 rule applies to regions where the influence of climate is the most
 pronounced, and call for close attention to the impact of climate change
 to prevent species range contraction and even extinction due to global
 warming. 
description: Sampling plot × species presence/absence matrix for vascular
 plants in the Gyirong valley.
DOI: 10.5061/dryad.1c59zw3vm
title: Optimizing parameters for using the parallel auditory brainstem response (pABR) to quickly estimate hearing thresholds

description: Objectives: Timely assessments are critical to providing early
 intervention and better hearing and spoken language outcomes for children
 with hearing loss. To facilitate faster diagnostic hearing assessments in
 infants, the authors developed the parallel auditory brainstem response
 (pABR), which presents randomly timed trains of tone pips at five
 frequencies to each ear simultaneously. The pABR yields high-quality
 waveforms that are similar to the standard, single-frequency serial ABR
 but in a fraction of the recording time. While well-documented for
 standard ABRs, it is yet unknown how presentation rate and level interact
 to affect responses collected in parallel. Furthermore, the stimuli are
 yet to be calibrated to perceptual thresholds. Therefore, this study aimed
 to determine the optimal range of parameters for the pABR and to establish
 the normative stimulus level correction values for the ABR stimuli.
 Design: Two experiments were completed, each with a group of 20 adults (18
 – 35 years old) with normal hearing thresholds (≤ 20 dB HL) from 250 to
 8000 Hz. First, pABR electroencephalographic (EEG) responses were recorded
 for six stimulation rates and two intensities. The changes in component
 wave V amplitude and latency were analyzed, as well as the time required
 for all responses to reach a criterion signal-to-noise ratio of 0 dB.
 Second, behavioral thresholds were measured for pure tones and for the
 pABR stimuli at each rate to determine the correction factors that relate
 the stimulus level in dB peSPL to perceptual thresholds in dB nHL.
 Results: The pABR showed some adaptation with increased stimulation rate.
 A wide range of rates yielded robust responses in under 15 minutes, but 40
 Hz was the optimal singular presentation rate. Extending the analysis
 window to include later components of the response offered further
 time-saving advantages for the temporally broader responses to low
 frequency tone pips. The perceptual thresholds to pABR stimuli changed
 subtly with rate, giving a relatively similar set of correction factors to
 convert the level of the pABR stimuli from dB peSPL to dB nHL.
 Conclusions: The optimal stimulation rate for the pABR is 40 Hz, but using
 multiple rates may prove useful. Perceptual thresholds that subtly change
 across rate allow for a testing paradigm that easily transitions between
 rates, which may be useful for quickly estimating thresholds for different
 configurations of hearing loss. These optimized parameters facilitate
 expediency and effectiveness of the pABR to estimate hearing thresholds in
 a clinical setting.
description: Methods information is provided in the manuscript as well as the
 README and accompanying files to the datasets.
description: All necessary information is provided in the manuscript, a README
 file for the entire dataset, as well as README and sidecar files in the
 datasets.
DOI: 10.5061/dryad.cc2fqz662
title: Sperm length divergence as a potential pre-zygotic barrier in a passerine hybrid zone

description: The saltmarsh sparrow Ammospiza caudacuta and the Nelson’s sparrow A.
 nelsoni differ in ecological niche, mating behavior, and plumage, but they
 hybridize where their breeding distributions overlap. In this advanced
 hybrid zone, past inter-breeding and current back-crossing result in
 substantial genomic introgression in both directions, although few hybrids
 are currently produced in most locations. However, because both species
 are non-territorial and have only brief male-female interactions, it is
 difficult to determine to what extent assortative mating explains the low
 frequency of hybrid offspring. Since females often copulate with multiple
 males, a role of sperm as a post-copulatory pre-zygotic barrier appears
 plausible. Here we show that sperm length differs between the two species
 in the hybrid zone, with low among-male variation consistent with strong
 post-copulatory sexual selection on sperm cells. We hypothesize that
 divergence in sperm length may constitute a reproductive barrier between
 species, as sperm length co-evolves with the size of specialized female
 sperm storage tubules. Sperm does not appear to act as a post-zygotic
 barrier, as sperm from hybrids was unexceptional.
description: Males were captured and measured for 13 plumage characters
 reflecting species identity; these were summed to give plumage index (see,
 e.g., Shriver, W.G., Gibbs, J.P., Vickery, P.D., Gibbs, H.L.,
 Hodgman, T.P., Jones, P.T., Jacques, C.N., 2005. Concordance between
 morphological and molecular markers in assessing hybridization between
 sharp-tailed sparrows in New England. Auk 122, 94–107.
 https://doi.org/10.1642/0004-8038(2005)122[0094:CBMAMM]2.0.CO;2). Hybrid
 index was determined from 135 SNPs showing fixed differences between the
 species. The index reflects the proportion of these SNPs with the
 saltmarsh sparrow genotype. Genotyping was performed with ddRAD
 sequencing. Sperm morphology was measured for three sperm segments which
 sum to total sperm length, using light microscopy. Up to 10
 morphologically normal cells were measured per male, depending on cell
 availability.
DOI: 10.5061/dryad.12jm63xxz
title: Revisiting of Carex sect. Confertiflorae s.l. (Cyperaceae): new data from molecular and morphological evidence and first insights on Carex biogeography in East Asia

description: Carex sect. Confertiflorae s.l., contains ca. 40 species and diverse in E
 Asia. It has one of the most unstable delimitations in the literature, and
 the section was proposed to split into two sections up to five different
 ones. Recent phylogenetic reconstructions showed Confertiflorae s.l. not
 to be monophyletic. In this study we investigate the phylogenetic
 structure, morphological affinities, and biogeographic history of sect.
 Confertiflorae s.l. We performed a taxon-based approach to explore the
 morphological affinities of the species considered in sect.
 Confertiflorae. We studied macromorphological observations and
 micromorphology of the nutlets using SEM, and used five molecular markers
 to reconstruct the phylogeny. The placement of all the species on a
 previously published megaphylogeny was tested in a preliminary exploration
 using a scaffolding approach. Then a core of species was selected to run
 the main analyses. The phylogenetic analyses confirmed the polyphyly of
 sect. Confertiflorae s.l., whose representatives were found within five
 distinct clades, with sect. Confertiflorae s.s. and sect. Molliculae
 clades were found to be closely related and contained the majority of the
 species. The composition of the two clades agreed with the morphological
 structure of the group, and we confirmed an exclusive combination of
 features. The origin of the two clades was found to be in the early
 Pliocene while the majority of the diversification events within each
 clade took place during the Pleistocene. Eventually, we proposed the
 rearrangement of sect. Confertiflorae as previously conceived as three
 independent sections: sects. Alliiformes, Molliculae, and Paludosae.