cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dv41ns22z
title: Data from: A phylogenomic analysis of Lonicera and its bearing on the evolution of organ fusion

description: PREMISE: The ~140 species of Lonicera are characterized by variously fused
 leaves, bracteoles, and ovaries, making it a model system for studying the
 evolution and development of organ fusion. However, previous phylogenetic
 analyses, based mainly on chloroplast DNA markers, have yielded uncertain
 and conflicting results. A well-supported phylogeny of Lonicera will allow
 us to trace the evolutionary history of organ fusion. METHODS: We inferred
 the phylogeny of Lonicera using Restriction-site Associated DNA Sequencing
 (RADSeq), sampling all major clades and 18 of the 23 subsections. This
 provided the basis for inferring the evolution of five fusion-related
 traits.  RESULTS: RADSeq data yielded a well-resolved and
 well-supported phylogeny. The two traditionally recognized subgenera
 (Periclymenum and Chamaecerasus), three of the four sections
 (Isoxylosteum, Coeloxylosteum, and Nintooa), and half of the subsections
 sampled were recovered as monophyletic. However, the large and
 heterogeneous section Isika was strongly supported as paraphyletic.
 Nintooa, a clade of ~22 mostly vine-forming species, including L.
 japonica, was recovered in a novel position, raising the possibility of
 cytonuclear discordance. We document the parallel evolution of fused
 leaves, bracteoles, and ovaries, with rare reversals. Most strikingly,
 complete cupules, in which four fused bracteoles completely enclose two
 unfused ovaries, arose at least three times. Surprisingly, these appear to
 have evolved directly from ancestors with free bracteoles instead of
 partial cupules. CONCLUSIONS: We provide the most comprehensive and
 well-supported phylogeny of Lonicera to date. Our inference of multiple
 evolutionary shifts in organ fusion provides a solid foundation for
 in-depth developmental and functional analyses.
description: Raw RADSeq sequences are available on NCBI (SRA). Link to the
 files is provided in the paper. Zipfile contains a
 README.md file that provides overview of the contents.
DOI: 10.6086/d1m67c
title: Spatial distributions of Tribrachidium, Rugoconites, and Obamus from the Ediacara Member (Rawnsley Quartzite), South Australia

description: The spatial distribution of in situ sessile organisms, including those
 from the fossil record, provides information about life histories, such as
 possible dispersal and/or settlement mechanisms, and how taxa are
 interacting with each other and their local environments. At Nilpena
 Ediacara National Park (NENP), South Australia, the exquisite preservation
 and excavation of 33 fossiliferous bedding planes from the Ediacara Member
 of the Rawnsley Quartzite reveals in situ communities of the Ediacara
 Biota. Here, the spatial distributions of three relatively common taxa,
 Tribrachidium, Rugoconites, and Obamus, occurring on excavated surfaces
 were analyzed using spatial point pattern analysis. Tribrachidium have a
 variable spatial distribution, implying that settlement or post-settlement
 conditions/preferences had an effect on populations. Rugoconites display
 aggregation, possibly related to their reproductive methods in combination
 with settlement location availability at the time of dispersal and/or
 settlement. Additionally, post-settlement environmental controls could be
 affecting Rugoconites on other surfaces, resulting in lower populations
 and densities. Both Tribrachidium and Rugoconites also commonly occur as
 individuals on a number of beds constraining possible reproductive
 strategies and environmental/substrate preferences. The distribution of
 Obamus is consistent with selective settlement, aggregating near
 conspecifics and on substrates of mature microbial mat. This dispersal
 process is the first example of substrate selective dispersal amongst the
 Ediacara Biota, thus making Obamus similar to numerous modern sessile
 invertebrates with similar dispersal and settlement strategies.
description: Please see the README document
 ("README_TribRugoObam.txt") and the accompanying published
 article: Boan, Evans, Hall, and Droser (in press). Spatial distributions
 of Tribrachidium, Rugoconites, and Obamus from the Ediacara Member
 (Rawnsley Quartzite), South Australia
DOI: 10.5061/dryad.vq83bk3xs
title: Data and toolkit for: SoundScape learning: An automatic method for separating fish chorus in marine soundscapes

description: Marine soundscapes provide the opportunity to non-invasively learn about,
 monitor, and conserve ecosystems. Some fishes produce sound in chorus,
 often in association with mating, and there is much to learn about fish
 choruses and the species producing them. Manually analyzing years of
 acoustic data is increasingly unfeasible, and is especially challenging
 with fish chorus, as multiple fish choruses can co-occur in time and
 frequency and can overlap with vessel noise and other transient sounds.
 SoundScape Learning (SSL) is a novel unsupervised automated method, to
 separate fish chorus from soundscape. SSL is an integrated technique that
 makes use of randomized robust principal component analysis (RRPCA),
 unsupervised clustering, and a neural network. SSL was applied to 14
 recording locations off southern and central California and was able to
 detect a single fish chorus of interest in 5.3 yrs of acoustically diverse
 soundscapes. Through application of SSL, the chorus of interest was found
 to be nocturnal, increased in intensity at sunset and sunrise, and was
 seasonally present from late Spring to late Fall. Further application of
 SSL will improve understanding of fish behavior, essential habitat,
 species distribution, and potential human and climate change impacts, and
 thus allow for protection of vulnerable fish species. This repository
 provides example data and code for the JASA paper: SoundScape
 Learning: an automatic method for separating fish chorus in marine
 soundscapes.
description: See Kim et al. 2023 for methods on dataset collection and
 processing. 
description: R studio, MATLAB.
DOI: 10.5281/zenodo.10803759
title: Data Part 1: Megascale tomography of a quantum detector

description: This contains the raw time tag data which is used for the megascale tomography. 

The processed data can be found here: https://doi.org/10.5281/zenodo.10810148
description: Funded by the European Union (ERC, QuESADILLA, 101042399). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council Executive Agency. Neither the European Union nor the granting authority can be held responsible for them.The authors gratefully acknowledge the computing time provided to them on the high-performance computer Noctua 2 at the NHR Center PC2. These are funded by the Federal Ministry of Education and Research, and the state governments participate on the basis of the resolutions of the GWK for the national high-performance computing at universities (www.nhr-verein.de/unsere-partner).
DOI: 10.5281/zenodo.10803758
title: Data Part 1: Megascale tomography of a quantum detector

description: This contains the raw time tag data which is used for the megascale tomography. 

The processed data can be found here: https://doi.org/10.5281/zenodo.10810148
description: Funded by the European Union (ERC, QuESADILLA, 101042399). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council Executive Agency. Neither the European Union nor the granting authority can be held responsible for them.The authors gratefully acknowledge the computing time provided to them on the high-performance computer Noctua 2 at the NHR Center PC2. These are funded by the Federal Ministry of Education and Research, and the state governments participate on the basis of the resolutions of the GWK for the national high-performance computing at universities (www.nhr-verein.de/unsere-partner).
DOI: 10.5061/dryad.vdncjsxzs
title: Genetic variation in sexual size dimorphism is associated with variation in sex-specific plasticity in Drosophila

description: The difference in body size between females and males, or sexual
 size dimorphism (SSD), is ubiquitous, and yet we have a poor
 understanding of the developmental-genetic mechanisms that generate it,
 and how these mechanisms may vary within and among species. Such an
 understanding of the genetic architecture of SSD is important if we are to
 evaluate alternative models of SSD evolution, but is difficult to describe
 because SSD is a characteristic of populations, not individuals. Here, we
 overcome this challenge by using isogenic lineages
 of Drosophila to measure SSD for 196 genotypes. We
 demonstrate extensive genetic variation for SSD, primarily driven by
 higher levels of genetic variation for body size among females than males.
 While we observe a general increase in SSD with sex-averaged body size
 (pooling for sex) among lineages, the vast majority of variation in SSD is
 independent of sex-averaged body size, and shows a strong genetic
 correlation with sex-specific plasticity, such that increased
 female-biased SSD is associated with increased body-size plasticity in
 females. Our data are consistent with the condition-dependence hypothesis
 of sexual dimorphism, and suggest that SSD
 in Drosophila is a consequence of selection on the
 developmental-genetic mechanisms that regulate the plasticity of body
 size.  
description: We collected data from 196
 DGRP lineages. For each lineage, flies were reared following previously
 publish protocols. Eggs were collected over 12-20 h, transferred in lots
 of 50 into 7ml fly food, and the larvae were reared at 22˚C, in standard
 cornmeal-molasses medium until the starvation treatment was applied.
 Larvae were removed from food at precisely timed developmental stages and
 starved starting at either 0–24 h or 24-48h before pupation to generate
 variation in body size. Because larvae stop feeding approximately 24h
 before pupation, larvae removed from the food 0–24 h before pupation were
 essentially allowed to feed <em>ad libitum</em> and are
 referred to as <em>fed</em> flies. In contrast, larvae removed
 from the food 24-48h before pupation were starved during the period when
 adult body size is affected by nutrition, and are referred to
 as <em>starved</em> flies. After being removed from the food,
 larvae were transferred to an empty vial containing a wet cotton plug and
 left until pupariation. To allow us to associate each adult fly with its
 pupal case post-eclosion, pupae were transferred to individual 2.5 mL
 Eppendorf tubes with a small puncture in the top for gas exchange. After
 flies emerged from their pupal cases, they were sexed and the pupal case
 was imaged and size quantified using semi-automated software developed in
 the Shingleton lab. We used area of the pupal silhouette (dorsal view) as
 a proxy for adult body size. Flies were collected in nine temporal blocks,
 with five lineages repeated across blocks to serve as a
 control.
DOI: 10.6071/m3h67f
title: Heritability of plastic trait changes in drought-exposed ponderosa pine seedlings

description: Climate change is imposing new selective pressures on forest tree
 populations. Evolutionary responses may be important for trees, despite
 long generation times, since many populations harbor significant genetic
 variation in environmentally relevant traits. However, the heritability of
 climate responses (e.g. how much growth differs under drought) has been
 investigated in only one tree species previously. Here, we quantify
 heritable variation in environmental response traits of Pinus ponderosa
 using a greenhouse trial. Five seedlings from each maternal family were
 exposed to either wet or dry treatments for four months. Traits measured
 include height and root length, root:shoot mass ratios, and stomatal
 density and number of rows. Narrow-sense heritability for all traits was
 estimated using a half-sib analysis. Many traits varied by treatment, and
 some also differed along gradients of “home” climate. Dry treatment
 root-to-shoot dry mass ratio was associated with survival in that
 treatment. Estimated heritability for drought responsiveness ranged from
 0.15 to 0.65, with the highest values occurring in height growth
 responses. Variation was particularly high for shoot growth under drought
 conditions. Our results suggest that increasingly arid conditions could
 result in strong responses to selection.
DOI: 10.5061/dryad.s1rn8pkcj
title: Experimental evidence root-associated microbes mediate seagrass response to environmental stress

description: Below-ground microbiota play an important role in mediating environmental
 conditions with important consequences for plant
 performance. Microorganisms involved in
 plant-soil interactions may be associated with roots or
 bulk-soil; however, the relative influence of these below-ground microbial
 assemblages on plant performance is poorly known, particularly for marine
 plants.  We separately manipulated the root and sediment
 microbial assemblages of the seagrass Zostera
 muelleri in a fully factorial experiment to determine how these
 assemblages determined plant response (e.g., growth) to nutrient
 enrichment, a major stressor in marine systems.  Under ambient
 nutrient conditions, seagrass growth was maintained regardless of root
 microbial assemblage disruption. Under high nutrient stress, however,
 seagrasses with disrupted root microbiota had reduced growth, whereas
 growth was maintained in seagrasses with an intact root microbiota.
 Disruption of bulk-sediment microbiota did not affect seagrass
 growth. Nutrient elevation was correlated to enhanced abundances
 of several putatively beneficial microbial taxa (e.g.
 sulfide-oxidizing
 Beggiatoaceae and denitrifying Geofilum
 rubicundum) associated with roots.  Synthesis: Our
 results suggest that under ambient nutrient conditions, microorganisms
 play a reduced role in influencing plant performance, but under more
 stressful conditions positive plant-root microorganism interactions
 strengthened. These results are among the first to experimentally
 determine that interactions between marine plants and the root-associated
 microbiota are key drivers of seagrass performance under human-induced
 environmental changes. This suggests that as in terrestrial systems,
 marine plant resilience depends on the stress-mitigating functions of
 their root-associated microbiota and disturbance to those plant-microbiota
 interactions can be deleterious for plant performance. Improving our
 understanding of these plant-microorganism interactions may be critical
 for understanding the functioning and resilience of threatened marine
 plants and developing more effective restoration strategies for them.
DOI: 10.5061/dryad.31zcrjdqp
title: Soil and census data of Heishiding plot

description: Intransitive competition has long been acknowledged as a potential
 mechanism favoring species coexistence. However, its prevalence, variance
 along environmental gradients, and possible underlying mechanisms
 (trade-offs) in plant communities (especially in forests)
 has seldomly been examined. A recently developed
 “reverse-engineering” approach based on Markov Chain allows us to
 estimate competitive transition matrices and competitive intransitivity
 from observational abundance data. Using this approach, we
 estimated competitive intransitivity of five dominant species in
 a subtropical forest and then related it to soil fertility (soil organic
 matter and soil pH) and demographic trade-offs (growth-survival
 and stature-recruitment trade-offs). In our forest plot,
 intransitive competition was common among the dominant species and peaked
 at the intermediate level of soil organic matter. Neither the
 growth-survival trade-off nor the stature-recruitment trade-off was
 positively related to competitive intransitivity. Our study for the
 first time empirically supported the unimodal
 intransitivity-fertility relationship in forests, which, however,
 was not mediated by the two demographic trade-offs in our plot.
DOI: 10.5061/dryad.51c59zwch
title: Non-reproductive dispersal: An important driver of migratory range dynamics and connectivity

description: Dispersal is the primary ecological process underpinning spatial dynamics
 in motile species by generating flux in reproductive locations over time.
 In migratory species, dispersal can also occur around non-breeding ranges,
 but this form currently lacks a unifying theoretical framework. We present
 a novel conceptual model for dispersal in migrants that builds upon
 existing literature, differentiating ‘reproductive’ dispersal (i.e.
 changes in breeding locations) from ‘non-reproductive’ dispersal, which we
 define as movements resulting in inter-annual or inter-generational
 changes in non-breeding locations. Crucially, unlike reproductive
 dispersal where movement outcomes are naturally propagated between
 generations, the outcomes of non-reproductive dispersal can be
 non-heritable even if dispersers survive to reproduce. We simulate a
 non-social migratory population with a genetically-determined migratory
 programme to model how heritability of this program influences both
 migratory connectivity and range shift propensity. When exposed to
 spatially-uncoupled shifts in habitable ranges (i.e. seasonal climate
 niches shifting at different rates), long-term persistence of simulated
 populations required changes in migratory programmes to arise through
 heritable forms of non-reproductive dispersal (e.g. mutations in migratory
 gene complexes). By contrast, non-heritable dispersal mechanisms (e.g.
 weather drift, navigation errors) did not drive long-term shifts in
 non-breeding ranges, despite being a major component of realised dispersal
 and migratory connectivity patterns. Migratory connectivity metrics
 conflate these heritable and non-heritable drivers of non-reproductive
 dispersal and therefore have limited power in predicting spatial
 population responses to environmental change. Our models provide a
 framework for improving our understanding of spatial dynamics in migratory
 populations and highlight the importance of teasing apart the genetic or
 cultural mechanisms that drive inter-generational migratory variability in
 order to evaluate and predict range plasticity in migrants.
DOI: 10.5061/dryad.8pk0p2ns4
title: First unravelling of the hidden and intricate evolutionary history of a bacterial group II intron family

description: Bacterial group II introns are large RNA enzymes that self-splice from
 primary transcripts. Following excision, they can invade various DNA
 target sites using RNA-based mobility pathways. As fast-evolving
 retromobile elements that move between genetic loci within and across
 species, their evolutionary history was proved difficult to study and
 infer. Here we identified several homologs of Ll.LtrB, the model group II
 intron from Lactococcus lactis, and traced back their
 evolutionary relationship through phylogenetic analyses. Our data
 demonstrate that the Ll.LtrB homologs in Lactococci originate from a
 single and recent lateral transfer event of Ef.PcfG
 from Enterococcus faecalis. We also show that
 these introns disseminated
 in Lactococci following recurrent episodes of
 independent mobility events in conjunction with occurences of lateral
 transfer. Our phylogenies identified additional lateral transfer events
 from the environmental clade of the more diverged Lactococci introns to a
 series of low GC gram-positive bacterial species including E.
 faecalis. We also determined that functional intron adaptation occurred
 early in Lactococci following Ef.PcfG acquisition from E.
 faecalis and that two of the more diverged Ll.LtrB homologs remain
 proficient mobile elements despite the significant number of mutations
 acquired. This study describes the first
 comprehensive evolutionary history of a bacterial group II intron
 family.
DOI: 10.5061/dryad.9cnp5hqp2
title: Manganese Enhanced Magnetic Resonance Imaging reveals light-induced brain asymmetry in embryo

description: The idea that sensory stimulation to the embryo (in utero or in ovo) may
 be crucial for brain development is widespread. Unfortunately, up to now
 evidence was only indirect because mapping of embryonic brain activity in
 vivo is challenging. Here we applied for the first time Manganese Enhanced
 Magnetic Resonance Imaging (MEMRI), a functional imaging method, to the
 eggs of domestic chicks. We revealed both spontaneous and light-induced
 brain asymmetry by comparing embryonic brain activity in vivo of eggs that
 were stimulated by light or maintained in the darkness. Our protocol paves
 the way to investigation of the effects of a variety of sensory
 stimulations on brain activity in embryo.
DOI: 10.17632/fcsy8bxz2k
title: Biochar increases rill erosion risk during the short term following its application to distinct loess textures

description: The core hypothesis of this study was that short-term biochar amendment would, contrary to its long-term benefits, exacerbate rill erosion risk in loess soils by increasing soil detachment capacity (Dc) and rill erodibility (Kr), with this effect being significantly modulated by soil texture.To test this hypothesis, a dataset was established through flume experiments and soil physicochemical analyses.
The first part comprises raw data from flume scour experiments. The experiments were conducted in a recirculating flume under controlled hydrodynamic conditions, combining two slope gradients (15° and 25°) with three flow discharge rates (12, 24, and 36 L min⁻¹). All experimental runs were performed following a 2-week incubation period after biochar application, during which both amended and control soils were maintained under identical open-air conditions. A total of 240 experimental runs were performed, covering five loess soils of distinct textures (from Yangling, Changwu, Ansai, Dingbian, and Shenmu) each under two treatments: untreated control and amended with 3% corn straw biochar. For each run, primary data on hydraulic parameters (flow velocity, temperature) and erosion response (dry weight of collected sediment and corresponding scouring duration) were recorded directly. These primary measurements were then used to calculate key hydrodynamic stress indicators—including shear stress, stream power, and unit stream power—applying standard hydraulic formulas. The fundamental response variable, soil detachment capacity (Dc), was subsequently determined from these calculations.
The second part is the supporting soil physicochemical property dataset. This component involves standardized laboratory analyses performed on all soil samples used in the flume experiments (both control and biochar-amended). This dataset is intended to elucidate the controlling mechanisms of intrinsic soil properties on the erosion process.
The dataset clearly reveals several key findings. Firstly, the data directly demonstrates that short-term biochar amendment consistently and significantly increased soil detachment capacity (Dc) across all tested soil textures and hydrodynamic conditions, and generally raised rill erodibility (Kr). Secondly, data analysis indicates that the finest-textured clay loess was the most sensitive to this biochar-induced erosion exacerbation. Most critically, the data identifies soil organic carbon (SOC) as the dominant factor controlling Dc and Kr. Finally, the data confirms that stream power (ω) serves as the optimal hydrodynamic predictor for Dc. This foundation successfully supported the development of high-fidelity multivariate predictive models that integrate hydraulic forcing (stream power) with key soil attributes (e.g., SOC, MWD, porosity).