cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.b5mkkwhdt
title: Halophila johnsonii phylogenetic analysis alignments

description: Halophila johnsonii is an endangered seagrass species that is restricted
 to the Florida Bay region of Florida, USA. Its taxonomic status has been
 called into question, in particular, given the close morphological and
 genetic similarity of H. johnsonii and the widely distributed and
 morphologically variable H. ovalis, which is largely restricted to the
 Indo-Pacific region. While a close relationship to H. ovalis is
 uncontroversial, it remains uncertain whether H. johnsonii represents a
 distinct lineage or is a recent introduction to the Florida region. Given
 the conservation status of H. johnsonii, distinguishing these alternatives
 has important implications for the management of the species and its
 habitat. Here, we develop molecular data sets for samples of H. johnsonii
 and H. ovalis including DNA sequences, genome-wide SNPs and
 microsatellites with the view to resolving the affinities of H. johnsonii
 with respect to the wider H. ovalis complex. Phylogenetic hypotheses based
 upon plastid (~18000 bp) and low copy nuclear DNA (~6500 bp) sequences
 derived from hybrid capture, along with 990 genome-wide ddRAD SNPs
 consistently resolved H. johnsonii within H. ovalis. Specifically, we
 found a close affinity between H. johnsonii and H. ovalis sampled from the
 east coast of Africa. In addition, Halophila specimens collected in
 Antigua, which are within the range of morphological variation typical for
 H. ovalis, are virtually identical to H. johnsonii and the East African H.
 ovalis samples based upon DNA sequence analyses and these group together
 using Bayesian clustering analyses of microsatellites and ddRAD SNPs. We
 conducted population genetic analyses using large number of H. johnsonii
 samples collected over a 17-year period. Genotypic data generated through
 microsatellites and ddRAD SNPs revealed genetic uniformity for all 132 H.
 johnsonii samples across the Indian River Lagoon, Florida, while samples
 of H. ovalis from Antigua shared the same genotype as H. johnsonii. We
 conclude that the lack of genetic diversity and the absence of sexual
 reproduction strongly indicates that the total range of H. johnsonii is
 actually one clone that is closely related to populations in Africa and
 Antigua and may be derived from a recent introduction from one of those
 regions.
description: Three types of data were collected to create independent
 alignments to assess the origin and nature of the seagrass Halophila
 johnsonii. First a ddRAD reaction was perfomed on a range of samples
 within the Halophila ovalis species complex, 990 nuclear snps were
 extracted, concatenated and aligned. Hybdrid capture was performed on a
 similar but larger dataset. The Ozbaits_CP (plastid) and OzBaits_NR
 (nuclear) (<i>bioRxiv</i><b>,</b>
 2021.2009.2006.456727) were used to capture targeted genes and two
 alginments were generated, the plastid being ~18000 bp long and the low
 copy nuclear alignment was ~6500 bp.
DOI: 10.5061/dryad.jdfn2z3bx
title: Water temperatures inside and outside an oak tree hibernaculum used by spotted turtles in central Pennsylvania

description: Water temperatures inside a swamp white oak tree hibernaculum used by
 spotted turtles, and at the bottom of the pool outside the tree, recorded
 every 30 minutes from December 2020 through mid–March 2021 with a Hobo
 U12-008 data logger and TMC temperature sensors (Onset Computer, Pocasset,
 MA). Sensors were placed at the bottom of the pool inside the tree
 (verified with the endoscopic camera) and at the bottom of the center of
 the pool outside the tree.
DOI: 10.5061/dryad.z08kprrdd
title: CircNRIP1 drives the malignant phenotypes in gastric cancer through mediating the miR-148b-5p/CYR61 axis

description: Background: Gastric cancer (GC) is a frequent disease with a poor
 prognosis worldwide. Circular RNAs (circRNAs) are considered to be
 important regulators that mediate the occurrence and development of
 cancers, including GC. However, the regulatory mechanism of circRNAs in GC
 progression is not fully understood. Methods: The expression of circular
 RNA nuclear receptor-interacting protein 1 (circNRIP1), microRNA
 (miR)-148b-5p and Cysteine-rich 61 (CYR61) was gauged using quantitative
 real-time polymerase chain reaction (qRT-PCR). The stability of circNRIP1
 was determined by Ribonuclease R (RNase R) assay. Results: CircNRIP1 was
 upregulated in GC tissues and cells, and it was a stable circular RNA.
 CircNRIP1 overexpression facilitated cell proliferation, cycle
 progression, colony formation, invasion, migration and angiogenesis, while
 circNRIP1 knockdown exhibited opposite effects in GC cells.
 Mechanistically, miR-148b-5p could mediate the regulation of circNRIP1 on
 GC cell progression by serving as a target of circNRIP1. Furthermore,
 miR-148b-5p inhibited GC cell malignant behaviors by sponging CYR61.
 Meanwhile, circNRIP1 could regulate CYR61 expression via downregulating
 miR-148b-5p. Besides, circNRIP1 knockdown suppressed tumor growth in
 xenograft models. Conclusion: CircNRIP1 contributed to GC progression
 through regulating the miR-148b-5p/CYR61 axis, hinting that circNRIP1
 might be a new target for GC treatment.
DOI: 10.5061/dryad.4b8gthtdf
title: Data from: Downregulation of circATXN7 represses non-small cell lung cancer growth by releasing miR-7-5p

description: Circular RNAs (circRNAs) participate in the occurrence and progression of
 many cancers. CircRNA ataxin 7 (circATXN7) (circBase ID: hsa_circ_0066436)
 plays a promoting influence on gastric cancer progression. However, the
 biological role of circATXN7 in non-small cell lung cancer (NSCLC) is
 indistinct. CircATXN7 and PFN2 were highly expressed in NSCLC, whereas
 miR-7-5p expression had the opposite trend. CircATXN7 overexpression
 constrained apoptosis and promoted proliferation, metastasis, invasion,
 and epithelial-mesenchymal transition (EMT) of NSCLC cells, but circATXN7
 silencing played the opposing influence and repressed xenograft tumor
 growth in vivo. CircATXN7 served as a miR-7-5p sponge, and circATXN7
 regulated malignant behaviors of NSCLC cells through sponging miR-7-5p.
 PFN2 acted as a miR-7-5p target. PFN2 silencing overturned the promoting
 effect of miR-7-5p inhibitor on NSCLC cell malignancy, while PFN2
 overexpression reversed the inhibitory impact of miR-7-5p mimic on NSCLC
 cell malignancy. CircATXN7 accelerated the malignancy of NSCLC cells
 through adsorbing miR-7-5p and upregulating PFN2, offering evidence to
 support circATXN7 as a might target for NSCLC treatment.
DOI: 10.15468/dl.vunsde
title: Occurrence Download

description: A dataset containing 1315 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-5000.0",
 "TaxonKey is Excoecaria agallocha"
 ]
}

 The dataset includes 1315 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002936-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.wh70rxwp2
title: Multiple mitochondrial haplotypes within individual specimens affect biodiversity estimation by DNA metabarcoding

description: In the global action for biodiversity conservation, the most urgent need
 is to delimit and identify species. DNA barcoding and metabarcoding based
 on molecular markers have been increasingly used in species delimitation
 and species diversity assessment, respectively, owing to their advantages
 of standardization and high throughput. The molecular markers used in
 these methods for animals are mainly derived from mitochondrial DNA. The
 principle involved is that inter-specific genetic distances are greater
 than intra-specific genetic distances. However, if multiple mitochondrial
 haplotypes exist within individual specimens and the divergence between
 these haplotypes is greater than the assumed maximum intra-specific
 divergence, the species delimitation and species diversity assessment may
 be affected. In our recent studies, a widespread phenomenon of multiple
 mitochondrial haplotypes within individual specimens was discovered in fig
 wasps (Hymenoptera, Insecta), having negative impact on DNA barcoding and
 metabarcoding. In this study, we expanded the taxa to include up to 480
 specimens from 82 species, 66 genera, 45 families, and 13 orders of
 Insecta and Arachnida. By high-throughput sequencing of mitochondrial cox1
 fragments within individual specimens, we studied the pattern of multiple
 mitochondrial haplotypes within individual specimens. Three DNA
 metabarcoding strategies, one of which was simulated, were applied. The
 results revealed that multiple mitochondrial haplotypes within individual
 specimens could lead to an overestimation of species diversity by
 metabarcoding. Simultaneously, we found that the infection with
 intracellular endosymbiotic bacteria Wolbachia was significantly
 negatively related with this effect. These results suggest that additional
 attention should be paid to the interference of multiple mitochondrial
 haplotypes within individual specimens on the results of DNA metabarcoding
 in species diversity assessment of animals.
DOI: 10.5061/dryad.np5hqbztr
title: Seed dispersal by wind decreases when plants are water-stressed, potentially counteracting species coexistence and niche evolution

description: Hydrology is a major environmental factor determining plant fitness, and
 hydrological niche segregation (HNS) has been widely used to explain
 species coexistence. Nevertheless, the distribution of plant species along
 hydrological gradients does not only depend on their hydrological niches
 but also on their seed dispersal, with dispersal either weakening or
 reinforcing the effects of HNS on coexistence. However, it is poorly
 understood how seed dispersal responds to hydrological conditions. To
 close this gap, we conducted a common-garden experiment exposing five
 wind-dispersed plant species (Bellis perennis, Chenopodium album, Crepis
 sancta, Hypochaeris glabra, and H. radicata) to different hydrological
 conditions. We quantified the effects of hydrological conditions on seed
 production and dispersal traits, and simulated seed dispersal distances
 with a mechanistic dispersal model. We found species-specific responses of
 seed production, seed dispersal traits, and predicted dispersal distances
 to hydrological conditions. Despite these species-specific responses,
 there was a general positive relationship between seed production and
 dispersal distance: plants growing in favourable hydrological conditions
 not only produce more seeds but also disperse them over longer distances.
 This arises mostly because plants growing in favourable environments grow
 taller and thus disperse their seeds over longer distances. We postulate
 that the positive relationship between seed production and dispersal may
 reduce the concentration of each species to the environments favourable
 for it, thus counteracting species coexistence. Moreover, the resulting
 asymmetrical gene flow from favourable to stressful habitats may slow down
 the microevolution of hydrological niches, causing evolutionary niche
 conservatism. Accounting for context-dependent seed dispersal should thus
 improve ecological and evolutionary models for the spatial dynamics of
 plant populations and communities.
description: Deed production and seed dispersal traits are from a
 common-garden experiment conducted at Heidfeldhof, University of
 Hohenheim, Germany. Physical dispersal environments
 (wind speeds) were from the LAFO project
 (https://lafo.uni-hohenheim.de/en/1670). Seed dispersal
 data was from simulation using the mechanistic dispersal model WALD (Katul
 et al. 2005, American Naturalist).
DOI: 10.5061/dryad.8931zcrrk
title: Data and scripts from: Phylogenomic analysis points to a South American origin of Manihot and illuminates the primary gene pool of cassava

description: The genus Manihot, with around 120 known
 species, is native to a wide range of habitats and regions in the
 tropical and subtropical Americas. Its high species richness and recent
 diversification only ~6Mya have significantly complicated previous
 phylogenetic analyses. Several basic elements
 of Manihot evolutionary history therefore remain
 unresolved. Here, we conduct a comprehensive phylogenomic analysis
 of Manihot, focusing on exhaustive sampling of South American
 taxa.  We find that two recently described species from northeast
 Brazil’s Atlantic forest were the earliest to diverge, strongly suggesting
 a South American common ancestor of Manihot. Ancestral state
 reconstruction indicates early Manihot diversification
 in dry forests, with numerous independent episodes of new habitat
 colonization including into savannas and rainforests within South America.
 We identify the closest wild relatives to M.
 esculenta including the crop cassava, and we quantify extensive
 wild introgression into the cassava gene pool from at least five wild
 species including M. glaziovii, a species used widely in
 breeding programs. Finally, we show that this wild-to-crop introgression
 substantially shapes the mutation load in cassava. Our findings provide a
 detailed case study for neotropical evolutionary history in a diverse and
 widespread group, and a robust phylogenomic framework for
 future Manihot and cassava research.
description: Methods for genomic data collection, processing, and analysis are
 described in detail in Simon et al, 2021<i> New
 Phytologist</i>.
DOI: 10.5061/dryad.547d7wm8v
title: SMRT sequencing data on four hypersuppressive Saccharomyces cereviciae mitochondrial DNAs

description: Hypersuppressive mitochondrial DNAs are thought to be linear tandem
 repeats of the base unit of specific ORI regions on the mitochondrial
 genome. Here we confirm the linear tandem repeats using SMRT sequencing
 technology on four hypersuppressive clones. Mitochondrial DNA
 from four Saccharomyces cervisiae hypersuppressive mutants and a
 wild-type control was enriched and sequenced using SMRT sequencing
 technology.
description: The mtDNA isolation for SMRT sequencing was done using two phenol
 chloroform extractions on pellets enriched for mitochondria using
 differential ultracentrifugation. Isolated mtDNA was sequenced using SMRT
 sequencing technology on Pacific Biosciences Sequel II. 10kb insert size
 was selected for on 0.75% agarose Blue Pippin cassettes obtaining 12-13kb
 mean length inserts and mean read length of 6-7kb.
DOI: 10.5061/dryad.cvdncjt52
title: Turning old foes into new allies – harnessing drainage canals for biodiversity conservation in a desiccated European lowland region

description: 1. Drainage canals are widespread components of agricultural landscapes.
 Although canals have greatly contributed to biodiversity loss by
 desiccating wetlands, they have recently attracted conservation attention
 due to their potential to function as refugia for native species in
 intensively managed landscapes. However, their conservation role in
 complex landscapes composed of agricultural fields and desiccated but
 otherwise untransformed, semi-natural habitats, on which canals still pose
 a heavy burden, is unknown. Improved understanding of drainage canals and
 related biodiversity in these landscapes could help unlock their potential
 and support synergistic land management for nature conservation and water
 resource management. 2. We applied a multitaxon approach, including
 plants, butterflies, true bugs, spiders and birds, to (1) assess the
 conservation value of drainage canals with temporary water cover in a
 heavily drained European lowland region, (2) to test landscape-level and
 local canal parameters for aiding prioritization among canals, and (3) to
 propose a reconciliation-based management framework that suits the
 interest of all stakeholders. 3. We found that drainage canals and their
 banks concentrate more species across most taxa than semi-natural, mostly
 grassland habitats, possibly due to micro-environmental heterogeneity and
 the absence of low-intensity annual management compared to grasslands.
 Canals traversing semi-natural grasslands concentrate particularly high
 numbers of native species, but agricultural canals also support remarkable
 species richness. However, agricultural canals are important dispersal
 corridors for non-native invasive plants, which may negatively affect
 native biodiversity. Canal size has little effect on biodiversity but
 habitat stress is an important determinant. The higher the stress (due to
 sandiness and salinity), the higher is the added value of canals to
 landscape-wide biodiversity. Synthesis and applications. We show that
 drainage canals can harbour high biodiversity and should therefore be
 recognized as important novel ecosystems with high conservation value,
 even when cutting through semi-natural grassland habitats. Canals have
 previously been considered detrimental to nature conservation due to their
 association with loss of wetlands. However, by reducing water loss with
 reversible obstructions, controlling invasive species and applying
 specific conservation measures, they may be turned into conservation
 allies without compromising long-term interests of water management and
 agricultural land use.
description: See Material and methods in the associated paper
DOI: 10.5061/dryad.2547d7wr9
title: Demographic inferences and climatic niche modeling shed light on the evolutionary history of the emblematic cold-adapted Apollo butterfly at regional scale

description: Cold-adapted species escape climate warming by latitudinal and/or
 altitudinal range shifts, and currently occur in Southern Europe in
 isolated mountain ranges within ‘sky islands. Here we studied the genetic
 structure of the Apollo butterfly in five such alpine islands (above 1000
 m) in France, and infer its demographic history since the last
 interglacial, using single nucleotide polymorphisms (ddRADseq SNPs). The
 Auvergne and Alps populations show strong genetic differentiation but not
 alpine massifs, although separated by deep valleys. Combining three
 complementary demographic inference methods and species distribution
 models (SDMs) we show that the LIG period was highly defavorable for
 Apollo that probably survived in small population in the highest summits
 of Auvergne. The population shifted downslope and expanded eastward
 between LIG and LGM throughout the large climatically suitable Rhône
 valley between the glaciated summits of Auvergne and Alps. The Auvergne
 and Alps populations started diverging before the LGM but remained largely
 connected till the mid-Holocene. Population decline in Auvergne was more
 gradual but started before (~7 kya versus 800 ya), and was much stronger
 with current population size ten times lower than in the Alps. In the
 Alps, the low genetic structure and limited evidence for isolation by
 distance suggest a non-equilibrium metapopulation functioning. The core
 Apollo population experienced cycles of contraction-expansion with climate
 fluctuations with largely inter-connected populations over time according
 to a ‘metapopulation-pulsar’ functioning. This study demonstrates the
 power of combining demographic inferences and SDMs to determine past and
 future evolutionary trajectories of an endangered species at a regional
 scale.
DOI: 10.5061/dryad.7pvmcvdtd
title: RAD-seq of Ash individuals

description: Ash (Fraxinus spp.) is one of the most widely distributed tree genera in
 North America. Populations of ash in the United States and Canada have
 been decimated by the introduced pest Agrilus planipennis (Coleoptera:
 Buprestidae; emerald ash borer), having negative impacts on both forest
 ecosystems and economic interests. The majority of trees succumb to attack
 by A. planipennis, but some trees have been found to be tolerant to
 infestation despite years of exposure. Restriction site-associated DNA
 (RAD) sequencing was used to sequence ash individuals, both tolerant and
 susceptible to A. planipennis attack, in order to identify single
 nucleotide polymorphism (SNP) patterns related to tolerance and health
 declines. Understanding the mechanisms of host tolerance through
 genome-wide association has the potential to restore populations with
 cultivars that are able to withstand A. planipennis infestation. We were
 successful in using RAD-sequencing in order to identify SNPs that could
 contribute to tolerance of A. planipennis. This was a first step toward
 uncovering the genetic basis for host tolerance to A. planipennis.
description: RAD-seq was used to assemble a <em>de novo</em>
 reference genome of green (<em>Fraxinus pennsylvanica</em>)
 and white (<em>F. americana</em>) ash<em>
 </em>individuals to idenitfy SNPs that are associated with tolerance
 to emerald ash borer (<em>Agrilus planipennis</em>)
 infestation.
description: AshSNPmetadata.csv includes full field assessments for all
 <em>Fraxinus </em>individuals included in this study
 (10.1002/ece3.8163). SSR Run IDs associated with files in AshSNPdata.zip.
 Field assessments include location (included in study 10.1002/ece3.8163)
 and species identification (G = F. pennsylvanica; W = F. americana),
 diameter at breast height (DBH; cm), vigor rating, percent crown dieback,
 and presence or absence of bark splits (BS), exit holes (EH), woodpecker
 damage (WP), and epicormics sprouts. Overall classification of tolerant or
 susceptible was determine using criteria from both vigor and
 dieback.