cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.573n5tb6c
title: By animal, water, or wind: can dispersal mode predict genetic connectivity in riverine plant species?

description: Seed dispersal is crucial to gene flow among plant populations. Although
 the effects of geographic distance and barriers to gene flow are well
 studied in many systems, it is unclear how seed dispersal mediates gene
 flow in conjunction with interacting effects of geographic distance and
 barriers. To test whether distinct seed dispersal modes (i.e. hydrochory,
 anemochory, and zoochory) have a consistent effect on the level of genetic
 connectivity (i.e., gene flow) among populations of riverine plant
 species, we used unlinked single-nucleotide polymorphisms (SNPs) for eight
 co-distributed plant species sampled across the Rio Branco, a putative
 biogeographic barrier in the Amazon Basin. We found that animal-dispersed
 plant species exhibited higher levels of genetic diversity and lack of
 inbreeding as a result of the stronger genetic connectivity than plant
 species whose seeds are dispersed by water or wind. Interestingly, our
 results also indicated that the Rio Branco facilitates gene dispersal for
 all plant species analyzed, irrespective of their mode of dispersal. Our
 findings indicate that seed dispersal mode and riverscape features can
 greatly impact genetic structure, representing reliable predictors of
 genetic connectivity in riverine plant species. These results may help
 improve conservation and management policies in Amazonian riparian
 forests, where degradation and deforestation rates are high.
description: The dataset was generated by using a ddRADseq methodology.
description: Each file contains the genotype based on SNP markers for all
 individuals.
DOI: 10.57760/sciencedb.36314
title: Highly Efficient Upgrading of 1-Butanol into 2‐Ethyl‐1‐Hexanol Catalyzed by Nickel Pincer Complexes
title: Highly Efficient Upgrading of 1-Butanol into 2‐Ethyl‐1‐Hexanol Catalyzed by Nickel Pincer Complexes

description: About Highly Efficient Upgrading of 1-Butanol into 2‐Ethyl‐1‐Hexanol Catalyzed by Nickel Pincer Complexes Related data 
description: About Highly Efficient Upgrading of 1-Butanol into 2‐Ethyl‐1‐Hexanol Catalyzed by Nickel Pincer Complexes Related data
DOI: 10.5061/dryad.4xgxd2580
title: Supplementary material for: Phylogenomics and historical biogeography of seahorses, dragonets, goatfishes, and allies (Teleostei: Syngnatharia): Assessing factors driving uncertainty in biogeographic inferences

description: The charismatic trumpetfishes, goatfishes, dragonets, flying gurnards,
 seahorses, and pipefishes encompass a recently defined yet extraordinarily
 diverse clade of percomorph fishes—the series Syngnatharia. This group is
 widely distributed in tropical and warm-temperate regions, with a great
 proportion of its extant diversity occurring in the Indo-Pacific. Because
 most syngnatharians feature long-range dispersal capabilities, tracing
 their biogeographic origins is challenging. Here, we applied an
 integrative phylogenomic approach to elucidate the evolutionary
 biogeography of syngnatharians. We built upon a recently published
 phylogenomic study that examined ultraconserved elements by adding 62
 species (total 169 species) and one family (Draconettidae), to cover ca.
 25% of the species diversity and all 10 families in the group. We inferred
 a set of time-calibrated trees and conducted ancestral range estimations.
 We also examined the sensitivity of these analyses to phylogenetic
 uncertainty (estimated from multiple genomic subsets), area delimitation,
 and biogeographic models that include or exclude the jump-dispersal
 parameter (j). Of the three factors examined, we found that the j
 parameter has the strongest effect in ancestral range estimates, followed
 by number of areas defined, and tree topology and divergence times. After
 accounting for these uncertainties, our results reveal that syngnatharians
 originated in the ancient Tethys Sea ca. 87 Ma (84­–94 Ma; Late
 Cretaceous) and subsequently occupied the Indo-Pacific. Throughout
 syngnatharian history, multiple independent lineages colonized the eastern
 Pacific (6–8 times) and the Atlantic (6–14 times) from their center of
 origin, with most events taking place following an east-to-west route
 prior to the closure of the Tethys Seaway ca. 12–18 Ma. Ultimately, our
 study highlights the importance of accounting for different factors
 generating uncertainty in macroevolutionary and biogeographic inferences.
DOI: 10.5061/dryad.rfj6q578p
title: Age predicts risky investment better than residual reproductive value

description: Life-history theory predicts that investment into reproduction should
 increase as future reproductive opportunities (i.e., residual reproductive
 value, RRV) decrease. Researchers have thus intuitively used age as a
 proxy for RRV and assume RRV decreases with age when interpreting
 age-specific investment. Yet, age is an imperfect proxy for RRV and may
 even be a poor correlate in some systems. We used a 30-year study of the
 nesting ecology of painted turtles ( Chrysemys picta ) to assess how age
 and RRV compare in explaining variation in a risky investment behavior. We
 predicted that RRV would be a better predictor of risky investment than
 age because RRV accounts for variation in future reproductive potential
 across life. We found that RRV was high in early life, slowly decreased
 until midlife, and then steadily decreased to terminal reproduction.
 However, age predicted risky behavior better than RRV. This finding
 suggests stronger correlates of age (e.g., size) may be more responsible
 for this behavior in turtles. This study highlights that researchers
 should not assume that age-specific investment is driven by RRV and that
 future work should quantify RRV to more directly test this key element of
 life-history theory.
description: The bulk of analysis was conducted on the dataset labelled,
 "AnalyzedDataset". Survival rates used to calculate age-specific
 residual reproductive value were derived from the dataset labelled,
 "CondensedMarkDataset". These are both derived from Fred
 Janzen's long-term dataset on the nesting ecology of painted turtles
 along the Mississippi River. See the paper for full methods.
description: List of Column names: Date = Date of
 observation Year = Year of observation
 Nest = Within-year number assigned to a nest
 Sex = Sex of the individual of the observation
 PL = Plastron length (mm) SoilType = Type of
 soil the nest was constructed in TrueID = Unique ID
 number assigned to an individual YearDayLaid = Unique
 nest number across all years Age = Age of
 female ClutchSize = number of eggs laid
 ClutchMass = mass of clutch DTW = Distance to
 water of nest The rest of the variables are calculated
 metrics and/or transformed variables that can be read with the following
 labelling guide: 1. RRV prefix denotes that the trait
 is the calculated residual reproductive value for the trait name that
 follows. 2. BC denotes that the variable is Box-Cox
 transformed.  3. 2 at the end denotes that variable was
 squared to assess quadratic variation. 4. C at the end
 denotes that variable was standardized to a mean of 0 and unit
 variance.
DOI: 10.5061/dryad.p8cz8w9pc
title: Asymmetric, but opposing reductions in immigrant viability and fecundity promote reproductive isolation among host-associated populations of an insect herbivore

description: Immigrant inviability can contribute to reproductive isolation (RI) during
 ecological speciation by reducing the survival of immigrants in non-native
 environments. However, studies that assess the fitness consequence of
 immigrants moving from native to non-native environments typically fail to
 explore the potential role of concomitant reductions in immigrant
 fecundity despite recent evidence suggesting its prominent role during
 local adaptation. Here, we evaluate the directionality and magnitude of
 both immigrant viability and fecundity to RI in a host specific
 gall-forming wasp, Belonocnema treatae. Using reciprocal transplant
 experiments replicated across sites, we measure immigrant viability and
 fecundity by comparing differences in the incidence of gall formation
 (viability) and predicted number of eggs per female (fecundity) between
 residents and immigrants in each of two host-plant environments. Reduced
 immigrant viability was found in one environment while reduced immigrant
 fecundity was found in the other. Such habitat-dependent barriers resulted
 in asymmetric RI between populations. By surveying recent literature on
 local adaptation, we find that asymmetry in immigrant viability and
 fecundity are widespread across disparate taxa, which highlights the need
 to combine estimates of both common and overlooked barriers in cases of
 potential bi-directional gene flow to create a more comprehensive view of
 the evolution of RI.
DOI: 10.57760/sciencedb.36311
title: **Effects of fermented strawberry pomace on the cecal microbiota of laying hens
title: 发酵草莓果渣对蛋鸡盲肠微生物的影响

description: Sequencing and analysis of the cecal microbiota were carried out by Shanghai Personal Biotechnology Co., Ltd. (Shanghai, China). Total microbial DNA was isolated from cecal digesta, and PCR amplification targeted the bacterial 16S rRNA gene V3–V4 region, employing universal primer pairs (forward: 5ʹ-ACTCCTACGGGAGGCA-3ʹ; reverse: 5ʹ-GGACTACHVGGGTWTCTAAT-3ʹ). The resulting PCR amplicons were purified before sequencing and subjected to paired-end sequencing on an Illumina NovaSeq system (Illumina, San Diego, CA, USA). The raw sequences were processed by filtering for quality, removing chimera, and clustering into amplicon sequence variants (ASVs), which using Greengenes as the taxonomic reference database. Indices of α and β diversity were calculated to characterize microbial richness, overall diversity, and between-sample dissimilarity. Differences in genus-level abundance among groups were tested with the Kruskal–Wallis nonparametric test. Discriminant taxa among treatments were screened using LEfSe (LDA score ≥ 2, P &lt; 0.05) in combination with random forest modeling. Finally, KEGG pathway prediction was carried out with PICRUSt2, which reconstructs community functions based on phylogenetic information.
description: Sequencing and analysis of the cecal microbiota were carried out by Shanghai Personal Biotechnology Co., Ltd. (Shanghai, China). Total microbial DNA was isolated from cecal digesta, and PCR amplification targeted the bacterial 16S rRNA gene V3–V4 region, employing universal primer pairs (forward: 5ʹ-ACTCCTACGGGAGGCA-3ʹ; reverse: 5ʹ-GGACTACHVGGGTWTCTAAT-3ʹ). The resulting PCR amplicons were purified before sequencing and subjected to paired-end sequencing on an Illumina NovaSeq system (Illumina, San Diego, CA, USA). The raw sequences were processed by filtering for quality, removing chimera, and clustering into amplicon sequence variants (ASVs), which using Greengenes as the taxonomic reference database. Indices of α and β diversity were calculated to characterize microbial richness, overall diversity, and between-sample dissimilarity. Differences in genus-level abundance among groups were tested with the Kruskal–Wallis nonparametric test. Discriminant taxa among treatments were screened using LEfSe (LDA score ≥ 2, P &lt; 0.05) in combination with random forest modeling. Finally, KEGG pathway prediction was carried out with PICRUSt2, which reconstructs community functions based on phylogenetic information.
DOI: 10.5061/dryad.7d7wm37t6
title: A role for myosin II cluster and membrane energy in cortex rupture for Dictyostelium discoideum cells

description: Blebs, pressure driven protrusions of the cell membrane, facilitate the
 movement of eukaryotic cells such as the soil amoeba Dictyostelium
 discoideum, white blood cells and cancer cells. Blebs initiate when the
 cell membrane separates from the underlying cortex. A local rupture of the
 cortex, has been suggested as a mechanism by which blebs are initiated.
 However, much clarity is still needed about how cells inherently regulate
 rupture of the cortex in locations where blebs are expected to form. In
 this work, we examine the role of membrane energy and the motor protein
 myosin II (myosin) in facilitating the cell driven rupture of the cortex.
 We perform under-agarose chemotaxis experiments, using Dictyostelium
 discoideum cells, to visualize the dynamics of myosin and calculate
 changes in membrane energy in the blebbing region. To facilitate a rapid
 detection of blebs and analysis of the energy and myosin distribution at
 the cell front, we introduce an autonomous bleb detection algorithm that
 takes in discrete cell boundaries and returns the coordinate location of
 blebs with its shape characteristics. We are able to identify by
 microscopy naturally occurring gaps in the cortex prior to membrane
 detachment at sites of bleb nucleation. These gaps form at positions
 calculated to have high membrane energy, and are associated with areas of
 myosin enrichment. Myosin is also shown to accumulate in the cortex prior
 to bleb initiation and just before the complete disassembly of the cortex.
 Together our findings provide direct spatial and temporal evidence to
 support cortex rupture as an intrinsic bleb initiation mechanism and
 suggests that myosin clusters are associated with regions of high membrane
 energy where its contractile activity leads to a rupture of the cortex at
 points of maximal energy.
description: Aggregation competent<em> Dictyostelium
 discoideum</em> cells (Ax2 expressing LifeAct-GFP and Ax2 expressing
 myosin-GFP/Life-Act RFP) chomotaxing towards 4 micromolar CAMP under a
 block of agarose gel (0.7%) were imaged for 30 seconds using a spinning
 disk confocal microscope. Images were adjusted for brightness and contrast
 using <em>Image J.</em> See the Methods section our manuscript
 for more details.
DOI: 10.6076/d1h01z
title: Emperor penguin air sac oxygen

description: Some marine birds and mammals can perform dives of extraordinary duration
 and depth. Such dive performance is dependent on many factors, including
 total body oxygen (O2) stores. For diving penguins, the respiratory system
 (air sacs and lungs) constitutes 30-50% of the total body O2 store. To
 better understand the role and mechanism of parabronchial ventilation and
 O2 utilization in penguins both on the surface and during the dive, we
 examined air sac partial pressures of O2 (PO2) in emperor penguins
 (Aptenodytes forsteri) equipped with backpack PO2 recorders. Cervical air
 sac PO2s at rest were lower than in other birds, while the cervical air
 sac to posterior thoracic air sac PO2 difference was larger. Pre-dive
 cervical air sac PO2s were often greater than those at rest, but had a
 wide range and were not significantly different from those at rest. The
 maximum respiratory O2 store and total body O2 stores calculated with
 representative anterior and posterior air sac PO2 data did not differ from
 prior estimates. The mean calculated anterior air sac O2 depletion rate
 for dives up to 11 min was approximately one-tenth that of the posterior
 air sacs.  Low cervical air sac PO2s at rest may be secondary to
 a low ratio of parabronchial ventilation to parabronchial blood O2
 extraction. During dives, overlap of simultaneously recorded cervical and
 posterior thoracic air sac PO2 profiles supported the concept of
 maintenance of parabronchial ventilation during a dive by air movement
 through the lungs.
description: Data set was collected at a research camp in Antarctica at which
 emperor penguins voluntarily dove beneath the sea ice to forage.  While
 under anesthesia, birds were equipped withmicrocpocessor-based backpack
 recorders to collect data on depth, wing stroke rate (via accelerometry),
 and air sac oxygen levels (with an indwellling oxygen electrode).  Birds
 were allowed to dive over a one to two-day period after overnight recovery
 from anesthesia.  Devices were removed under anesthesia.  The birds were
 released back to to sea at the ice edge. Data were
 downloaded into computers and analyzed with excel software to assemble the
 csv files in this repository.  These data files were then analyzed with
 custom programs for the anlayses and graphs detailed in the manuscript. 
 These files are the basis for all the analyses.
description: These files do not have any missing values.  The data sets are
 ready for export or copy into any analysis program.
DOI: 10.57760/sciencedb.36231
title: Brain Network Characteristics and Behavioral Correlations in Global Developmental Delay Based on Functional Near-Infrared Spectroscopy
title: Brain Network Characteristics and Behavioral Correlations in Global Developmental Delay Based on Functional Near-Infrared Spectroscopy

description: Global developmental delay (GDD) involves disruptions in early brain development, yet its underlying functional neurobiology is not fully characterized. Using functional near-infrared spectroscopy (fNIRS) during naturalistic stimulation in 49 children with GDD and 45 healthy controls (HC) aged 2–4 years, we investigated functional brain network organization and local neural activity. We found that children with GDD revealed significant reductions in Eglobal Elocal, CC, and functional connectivity strength within bilateral prefrontal networks, including the dorsolateral prefrontal cortex (DLPFC) and medial prefrontal cortex (mPFC). Additionally, local activity patterns were altered, with hypoactivity in prefrontal and hyperactivity in temporal regions. Network metrics correlated positively with developmental measures of motor, adaptive, and social functions. These findings demonstrate disrupted brain network organization and abnormal neural activity underlying cognitive and motor delays in GDD, highlighting the potential of these neurofunctional markers for early diagnosis and personalized intervention strategies.
description: Global developmental delay (GDD) involves disruptions in early brain development, yet its underlying functional neurobiology is not fully characterized. Using functional near-infrared spectroscopy (fNIRS) during naturalistic stimulation in 49 children with GDD and 45 healthy controls (HC) aged 2–4 years, we investigated functional brain network organization and local neural activity. We found that children with GDD revealed significant reductions in Eglobal Elocal, CC, and functional connectivity strength within bilateral prefrontal networks, including the dorsolateral prefrontal cortex (DLPFC) and medial prefrontal cortex (mPFC). Additionally, local activity patterns were altered, with hypoactivity in prefrontal and hyperactivity in temporal regions. Network metrics correlated positively with developmental measures of motor, adaptive, and social functions. These findings demonstrate disrupted brain network organization and abnormal neural activity underlying cognitive and motor delays in GDD, highlighting the potential of these neurofunctional markers for early diagnosis and personalized intervention strategies.
DOI: 10.15468/dl.dmw4ab
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((100.85002 -1.59013,102.24532 -1.59013,102.24532 -0.21773,100.85002 -0.21773,100.85002 -1.59013))",
 "HasGeospatialIssue is false",
 "IucnRedListCategory is CR",
 "OccurrenceStatus is Present",
 "Year 2015-2026"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002701-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25338/b8p614
title: Data from: A phylogeny for the Drosophila montium species group: a model clade for comparative analyses

description: The Drosophila montium species group is a clade of 94 named species
 closely related to the model D. melanogaster species group. The montium
 species group is distributed over a broad geographic range throughout
 Asia, Africa, and Australasia. Species of this group possess a wide range
 of morphologies, mating behaviors, and endosymbiont associations, making
 this clade useful for comparative analyses. We use genomic data from 42
 available species to estimate the phylogeny and relative divergence times
 within the montium species group, and its relative divergence time from
 the melanogaster group. To assess the robustness of our phylogenetic
 inferences, we use 3 non-overlapping sets of 20 single-copy coding
 sequences and analyze all 60 genes with both Bayesian and maximum
 likelihood methods. Our analyses support monophyly of the group. Apart
 from the uncertain placement of a single species, D. baimaii, our analyses
 also support the monophyly of all seven subgroups proposed within the
 montium group. Our phylograms and relative chronograms provide a highly
 resolved species tree, with discordance restricted to estimates of
 relatively short branches deep in the tree. In contrast, age estimates for
 the montium crown group, relative to its divergence from D. melanogaster,
 depend critically on prior assumptions concerning variation in rates of
 molecular evolution across branches, and hence have not been reliably
 determined. We discuss methodological issues that limit phylogenetic
 resolution – even when complete genome sequences are available ­– as well
 as the utility of the current phylogeny for understanding the evolutionary
 and biogeographic history of this clade.
description: This dataset consists of assemblies of the Drosophila montium
 species group and the scripts used for the phylogenetic analyses in the
 associated paper. Further information is available in the README
 file.
DOI: 10.5061/dryad.rv15dv476
title: Supporting information for Rensch’s rule – definitions and statistics

description: Issue: Sexual size dimorphism is thought to vary predictable manner with
 overall body size, a pattern named ‘Rensch’s rule’. The rule is thought to
 suggest different predictions for taxa with female- and male- biased
 dimorphism. This leaves taxa where both types of dimorphism are common in
 limbo. Rensch’s rule is usually estimated using the reduced major axis
 (RMA) slope of a regression of male size on female size. A slope steeper
 than one shows support for the rule. Evidence: We show that the
 predictions of Rensch’s rule for male- and female- biased taxa are in fact
 the same and offer a unified definition of the rule. Using numerical
 examples, and literature data, we show that RMA and ordinary least square
 (OLS) methods of line fitting can produce conflicting results, suggesting
 that RMA is less conservative a way to test the rule. Conclusion: We
 recommend that both line fitting methods are used to estimate Rensch’s
 rule with strong support claimed only when results of both agree with each
 other. Alternatively, we suggest tests are conducted in a way that agree
 with the rule’s definition, i.e. that size dimorphism is regressed on the
 mean size of males and females of species.