cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vq83bk3ws
title: Assessing the effects of native and alien plant ash on mosquito abundance

description: Plant invasions have been linked to displacement of native vegetation and
 altering of fire regimes and might influence vector mosquito populations
 by altering habitats or nutrient inputs. Whereas wildfire effects on
 terrestrial ecosystems are relatively well-studied, ash depositions into
 aquatic ecosystems and effects on semi-aquatic taxa such as mosquitoes
 have remained overlooked. Here, we investigated mosquito colonization in
 water treated with ash from native plants [quinine tree (Rauvolfia
 caffra), Transvaal milk plum (Englerophytum magalismontanum), apple leaf
 (Philenoptera violacea)] and invasive alien plants [i.e., lantana (Lantana
 camara), guava (Psidium guajava), red river gum (Eucalyptus
 camaldulensis)] in containers at two ash concentrations (i.e., 1 g L-1, 2
 g L-1). Overall, there was no statistically clear difference in
 colonization between ash from native and alien species. We recorded
 colonization by two mosquito genera (Culex spp. and Anopheles spp.), with
 Culex generally much more abundant than Anopheles. Few differences were
 identified among the plants, with statistically clear effects of ash type
 and concentration on larval and pupal stages. High Culex egg and larval
 abundances were shown in lantana and apple leaf treatments compared to
 controls, and milkplum versus controls for pupae of both genera. Further
 research is required to elucidate the influence of nutrient inputs from
 different ash species on vector mosquito population dynamics.
DOI: 10.5061/dryad.5tb2rbp76
title: Data for: Inferring spatially-varying animal movement characteristics using a hierarchical continuous-time velocity model

description: Understanding the spatial dynamics of animal movement is an essential
 component of maintaining ecological connectivity, conserving key habitats,
 and mitigating the impacts of anthropogenic disturbance. Altered movement
 and migratory patterns are often an early warning sign of the effects of
 environmental disturbance, and a precursor to population declines. Here,
 we present a hierarchical Bayesian framework based on Gaussian processes
 for analysing the spatial characteristics of animal movement. At the heart
 of our approach is a novel covariance kernel that links the
 spatially-varying parameters of a continuous-time velocity model with GPS
 locations from multiple individuals. We demonstrate the effectiveness of
 our framework by first applying it to a synthetic dataset, then by
 analysing telemetry data from the Serengeti wildebeest migration. Through
 application of our approach, we are able to identify the key pathways of
 the wildebeest migration as well as revealing the impacts of environmental
 features on movement behaviour.
DOI: 10.5061/dryad.t76hdr840
title: Holocene climate changes explain the spatial pattern in genetic diversity in populations of Cyperus papyrus from Southeast Africa wetlands

description: Wetlands are one of the most threatened ecosystems in the world because
 more than 70% of the area worldwide has been lost since 1900. Wetland
 plant species rely greatly on water for seeds and propagules, which may
 lead to a downstream unidirectional dispersal and accumulation of genetic
 diversity downstream. However, several species show no support for
 unidirectional genetic diversity, revealing the complexity of population
 dynamics and gene flow in wetlands. Here, we used microsatellite loci to
 address how the past demographic dynamics shaped the contemporary spatial
 pattern in genetic diversity and population structure of Cyperus papyrus
 in wetlands of Southeast Africa. Using spatially explicit analysis and
 coalescent modelling we found no support for unidirectional dispersal.
 Instead, we found higher genetic diversity in populations upstream than
 downstream in the river basin. We also found high admixture among
 populations, most likely due to connections between adjacent river basins
 during sporadic floods, and ongoing gene flow due to bird-mediated seed
 dispersal. Our results suggest stepping-stone migration due to strong
 isolation-by-distance, but not necessarily unidirectional. Moreover, the
 past demographic dynamics in the Holocene shaped the current pattern of
 genetic diversity and structure, leading to higher genetic diversity in
 populations upstream of the Zambezi river basin. Our results also point to
 the very low genetic diversity of C. papyrus populations in Southeast
 Africa and the need for management and conservation strategies to
 guarantee the long-term persistence of the species in the region.
DOI: 10.5061/dryad.dv41ns229
title: 144 prioritized genes of flooding-tolerance (FTgenes) in soybean

description: Soybean [Glycine max (L.) Merr.] is one of the most important legume crops
 abundant in edible protein and oil in the world. Due to the drastic
 climate change, flooding, drought and unevenly distributed rainfall have
 gradually increased in terms of the frequency and intensity worldwide. In
 particular, severe flooding has caused extensive losses to soybean
 production. In light of the harsh situation, there has been an urge to
 breed strong soybean seeds with high flooding tolerance. We collected and
 integrated genetic data that relevant to flooding-tolerant responses in
 soybean from multiple dimensional data sources. A step-function adjusted
 factor prioritization algorithm was proposed to prioritize these
 integrated genetic data. A total of 144 candidate genes of
 flooding-tolerance (FTgenes) in soybean were prioritized, using a
 cut-off threshold of combined score of 42, from 36,705 test genes
 that collected from multidimensional genomic features linking to soybean
 flooding tolerance. Several validation results using independent
 samples from SoyNet, GWAS, SoyBase, GO database and transcriptome
 databases all exhibited excellent agreement, suggesting these 144 FTgenes
 were significantly superior than others. Our results provide valuable
 information, meaningful insight, and contribution to varieties selection
 of soybean. The FTgenes demonstrated the potential for uncovering
 important insights underlying flooding-tolerant response in soybean in
 systems biology stuydies.
description: We collected genetic data from nine data platforms, including genome-wide association study (GWAS),
 association mapping, linkage mapping, gene expression,
 pathway regulation, protein-protein interaction networks (PPIN), network
 analysis, proteomes, text mining, and functional genomic data from model
 plants. An evidence-based scoring and a step-function adjusted
 factor weighting system was proposed to integrate these genomic data
 across multidimensional data sources and prioritize these integrated
 genetic data. To avoid false positive results, all positive and negative
 results were considered and integrated to give a real value for every
 genetic locus to construct evidence-based genes pool (denoted as test
 genes). We computed a weighted combined score summarized from multiple
 data sources for each of the test genes. Similarly, a set of core genes
 was established for prioritizing the test genes. A clear separation
 between the test genes and the core genes was determined to identify
 prioritized FTgenes.
description: Each of the FTgenes provides a combined score, which summed over
 their magnitude of association or response change to the stress from multiple data sources. The gene
 version is in Glyma v2.0.
DOI: 10.5061/dryad.2v6wwpzs5
title: Fungicides Cuprozin Progress and SWITCH Modulate Primary and Specialized Metabolites of Strawberry Fruits

description: Numerous pesticides, including fungicides, are applied every year to crop
 plants. However, such application may affect the plant metabolism and
 thereby impact crop quality. Strawberry is an economically important crop,
 but the fruits are highly susceptible, especially to fungal diseases. In
 the present study, the effects of two fungicides on primary and
 specialized metabolites determining the fruit aroma were tested in two
 strawberry cultivars and the wild strawberry. Fruit extracts were analyzed
 using HPLC (amino acids), GC-MS (organic acids, sugars, flavor
 metabolites) and photometric quantification (total phenolics). Various
 metabolites were either significantly higher or lower in fruits of plants
 exposed to fungicides compared to those of control plants, with
 differences between strawberry cultivars and species, as well as used
 fungicides. Given the various changes in metabolites in response to the
 treatments, the taste and quality of the strawberries may pronouncedly
 change when plants are treated with fungicides.
description: Cultivated strawberry plants
 (<em>Fragaria x
 ananassa</em>,
 Rosaceae) and the wild strawberry (<em>F.
 vesca</em>) were treated with two commonly used systemic fungicides,
 one for conventional and one for organic cultivation. Minor fungicide
 amounts were applied before, during, and after the flowering stage
 according to the manufacturer's instructions. Extracts of ripe fruits
 were derivatized and analyzed using HPLC (amino acids), GC-MS (organic
 acids, sugars, aroma compounds), and photometric quantification (total
 phenolics).
DOI: 10.5061/dryad.vhhmgqnxf
title: Data for: Adaptive, maladaptive, neutral, or absent plasticity: Hidden caveats of reaction norms

description: Adaptive phenotypic plasticity may improve the response of individuals
 when faced with new environmental conditions. Typically, empirical
 evidence for plasticity is based on phenotypic reaction norms obtained in
 reciprocal transplant experiments. In such experiments, individuals from
 their native environment are transplanted into a different environment,
 and a number of trait values, potentially implicated in individuals’
 response to the new environment, are measured. However, the
 interpretations of reaction norms may differ depending on the nature of
 the assessed traits, which may not be known beforehand. For example, for
 traits that contribute to local adaptation, adaptive plasticity implies
 non-zero slopes of reaction norms. By contrast, for traits that are
 correlated to fitness, high tolerance to different environments (possibly
 due to adaptive plasticity in traits that contribute to adaptation) may,
 instead, result in flat reaction norms. Here we
 investigate reaction norms for adaptive versus fitness-correlated traits,
 and how they may affect the conclusions regarding the contribution of
 plasticity. To this end, we first simulate range expansion along an
 environmental gradient where plasticity evolves to different values
 locally and then perform reciprocal transplant experiments in
 silico. We show that reaction norms alone cannot inform us whether the
 assessed trait exhibits locally adaptive, maladaptive, neutral or no
 plasticity, without any additional knowledge of the traits assessed and
 species’ biology. We use the insights from the model to analyse and
 interpret empirical data from reciprocal transplant experiments involving
 the marine isopod Idotea balthica sampled from
 two geographical locations with different salinities,
 concluding that the low-salinity population likely has reduced adaptive
 plasticity relative to the high-salinity population. Overall, we conclude
 that, when interpreting results from reciprocal transplant experiments, it
 is necessary to consider whether traits assessed are locally adaptive with
 respect to the environmental variable accounted for in the experiments, or
 correlated to fitness.
description: Matlab
DOI: 10.5061/dryad.qv9s4mwjc
title: Raw Sanger sequences of the tyr fragment from crispant and control zebrafish embryos

description: Thanks to the amenability to genetic modifications, the minimal or
 non-invasive phenotyping possibilities in early embryos and larvae and the
 presence of a high percentage of genes orthologous to humans, zebrafish is
 a successful alternative vertebrate to validate new disease genes and
 variants and to study mechanisms underlying human diseases. We developed
 an optimized method allowing early and gentle genotype detection to reduce
 further possible suffering associated with the generation of genetically
 modified zebrafish and valid to strategize the employment of “surplus”
 animals (e.g., those needed solely for line generation or without the
 desired genotype). The method is based on minimally-invasive tissue (fin)
 scratching (FS) to obtain genomic DNA material and perform genotyping in
 early zebrafish embryos. We showcase the method's usefulness for
 various genotyping needs, including screening both F0 and stable
 CRISPR/Cas9 lines and obtaining genomic material compatible with Sanger
 sequencing. Here we provide the raw sequences obtained from FS-derived
 genomic DNA of single mutant F0 embryos carrying mutations in the tyr gene
 generated with Base editor (BE) CRISPR/Cas9 technology. We compared the
 sequencing outcome of FS- vs whole embryos (WE)-based genomic DNA
 preparation (the WE sequencing results are also provided here). Sequences
 show the successful C&gt;T (G&gt;A) conversion generating crispant
 tyr mutants that FS-derived genomic DNA can capture. The resulting dataset
 demonstrates the compatibility of the method developed with
 sequencing-based genotyping of early crispant embryos.
   
description: The data were obtained by Sanger sequencing using
 a 3500 Genetic Analyzer (Applied Biosystems). Data provided are not
 processed.
description: To view the files common sequences analysis software are
 sufficient (Ape, Snapgene and Finch).
DOI: 10.15468/dl.c32mbq
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((105 20,170 20,170 70,105 70,105 20))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Festuca probatoviae"
 ]
}

 The dataset includes 5 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003279-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.vq83bk3wt
title: Data from: Quantifying and linking mechanism scenarios to invasive species impact

description: Plant species invasion represents one of the major drivers of biodiversity
 change globally, yet there is confusion about the nature of non-indigenous
 species (NIS) impact. This stems from differing notions of what
 constitutes invasive species impact and the scales at which it should be
 assessed. At local scales, the mechanisms of impact on local competitors
 can be classified into four scenarios: 1) minimal impact from NIS
 inhabiting unique niches; 2) neutral impact spread across the community
 and proportional to NIS abundance; 3) targeted impact on a small number of
 competitors with overlapping niches; and 4) pervasive impact that is
 disproportionate to NIS abundance and caused by modifications that filter
 out other species. I developed a statistical test to distinguish these
 four mechanism scenarios based on plant community rank-abundance curves
 and then created a scale-independent standardized impact score. Using an
 example long-term dataset, that has high native plant diversity and an
 abundance gradient of the invasive vine, Vincetoxicum rossicum, I show
 that impact resulted in either targeted or pervasive extirpations.
 Regardless of whether NIS impact is neutral, targeted, or pervasive, the
 net outcome will be the homogenization of ecosystems and reduced
 biodiversity at larger scales, perhaps reducing ecosystem resilience. The
 framework and statistical evaluation of impact presented in this paper
 provide researchers and managers with an objective approach to quantifying
 NIS impact and prioritizing species for further management actions.
description: Twenty-five, 1x1 m<sup>2</sup> plots at each of 14
 sites at the Rouge Urban National Park in Canada. We estimated percent
 cover and identify plant species in 2013 and 2019. (for methodological
 details, see: Livingstone et al. 2020). Livingstone,
 Stuart; Isaac, Marney; Cadotte, Marc (2020), Data from: Invasive dominance
 and resident diversity: unpacking the impact of plant invasion on
 biodiversity and ecosystem function, Dryad, Dataset, https://doi.org/10.5061/dryad.dncjsxkwz
DOI: 10.5061/dryad.3j9kd51nb
title: Eusociality and the transition from biparental to alloparental care in termites

description: In eusocial organisms, cooperative brood care within a colony represents a
 situation where the ancestral parental care duties have shifted away from
 the reproductive parent(s) towards their own offspring. The shift to
 alloparental care was often instrumental in the initial emergence of
 eusociality, as it ultimately contributed to the establishment of
 reproductive division of labor. Remarkably, eusocial taxa such as ants and
 termites, which still display an ancestral independent colony foundation
 phase, must go through an obligatory parental care period, as a temporary
 subsocial family unit. In termites specifically, an incipient colony
 inherently remains a woodroach family unit until alloparental care is
 established. Colony foundation success can then be limited by a series of
 factors that may include environmental, behavioral, symbiotic, and
 physiological constraints. In this study, 450 incipient termite colonies
 (Coptotermes gestroi) were established to investigate the timing of
 physiological changes in founders during the transition from biparental to
 alloparental care. Results showed that the finite initial internal
 nutritional resources that alates carry during the dispersal flight are a
 primary limiting factor for successful colony establishment. The
 Coptotermes queen and king must rapidly establish (&lt; 150 d) their
 first cohort of offspring to reach alloparental care or simply run out of
 resources and die. Alates, therefore, carry just enough internal resources
 to produce the first few alloparents (&lt; 15 workers) to prime the
 system toward colony ergonomic growth, with a definitive shift to solely
 reproductive functions. Eusocial insect primary reproductive traits were
 optimized for three successive functions within the life cycle of a
 colony: alate dispersal (sexual reproduction), colony foundation (parental
 care), and colony growth (increased egg production toward colony
 maturity). However, results suggest that trade-offs involving these
 functions appear to primarily favor dispersal ones (quantity vs. quality
 of alates), as founder(s) carry minimal resources and have no room for
 parental care inefficiency, and as they then fully rely on their
 alloparents for further reproductive output. The transition toward
 alloparental care during colony foundation of eusocial insects may
 therefore reflect on the initial evolutionary transition from ancestral
 subsociality to eusociality.
description: See M&M in original article.
description: Excel file for raw data, and PDF for R analysis output and
 supplementary figure SF1
DOI: 10.15468/dl.dgjvwp
title: Occurrence Download

description: A dataset containing 80 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is ITA.16_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Canis lupus",
 "Year 2005-2026"
 ]
}

 The dataset includes 80 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003281-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xkvrp6
title: Occurrence Download

description: A dataset containing 22 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((105 20,170 20,170 70,105 70,105 20))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Trisetum spicatum alascanum"
 ]
}

 The dataset includes 22 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003280-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6071/m35x0x
title: LSU Bioinformatics Workshop course materials

description: RNA sequencing (RNA-Seq) is a powerful tool that captures information
 about how organisms respond to stimuli in their environment at the
 molecular level. A common RNA-Seq approach involves isolating and
 sequencing all of the messenger RNA (mRNA) in a tissue sample taken from
 an organism. Researchers can compare patterns observed in RNA-Seq data to
 understand how individuals respond to the environment over minutes, hours,
 or days and how populations evolve in response to the environment over
 millions of years. The materials in this repository will guide
 users through an analysis of RNA-Seq data collected from two California
 populations of a copepod crustacean, Tigriopus californicus, that were
 exposed to different levels of salinity. Users will examine the contents
 of a fastq file that contains raw RNA-Seq data, determine the quality of
 the RNA-Seq data using a web-server, and test for significant differences
 in gene expression between the copepod populations using the R packages
 DESeq2, edgeR, and VennDiagram. The course materials were developed for
 the 2022 LSU Bioinformatics Workshop held at Louisiana State University,
 Baton Rouge, LA on July 17-22, hosted by Melissa DeBiasse and Morgan
 Kelly.
DOI: 10.15468/dl.2bvsa3
title: Occurrence Download

description: A dataset containing 702 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Nemipterus japonicus"
 ]
}

 The dataset includes 702 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003282-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8cz8w9gv4
title: Ranavirus infection-induced avoidance behavior in wood frog juveniles: Do amphibians socially distance?

description: Hosts may limit exposure to pathogens through changes in behavior, such as
 avoiding infected individuals or contaminated areas. Here, we tested for a
 behavioral response to ranavirus infection in juvenile wood frogs (Rana
 sylvatica) because the majority of dispersal between populations occurs
 during this life stage. We hypothesized that if infections are
 transmissible and detectable at this life stage, then susceptibles would
 display avoidance behaviors when introduced to an infected conspecific.
 Despite no apparent signs of infection, we observed a greater distance
 between susceptible-infected pairs, compared to pairs of either two
 infected or two susceptible animals. Further, distances between
 susceptible-infected pairs were positively related to the infection
 intensity of the focal exposed frog, suggesting the cue to avoid infected
 conspecifics may become more detectable with more intense infections.
 Although we did not quantify whether transmission was affected by their
 distancing, our findings suggest that juvenile frogs have the potential to
 reduce terrestrial transmission of ranaviruses through avoidance
 behaviors.