cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ksn02v71w
title: Species identity and diversity effects on invasion resistance of tropical freshwater plant communities

description: Biotic resistance mediated by native plant diversity has long been
 hypothesized to reduce the success of invading plant species in
 terrestrial systems in temperate regions. However, still little is known
 about the mechanisms driving invasion patterns in other biomes or
 latitudes. We help to fill this gap by investigating how native plant
 community presence and diversity, and the presence of native
 phylogenetically closely related species to an invader, would affect
 invader Hydrilla verticillata establishment success in
 tropical freshwater submerged plant communities. The presence of a native
 community suppressed the growth of H. verticillata, but did not
 prevent its colonisation. Invader growth was negatively affected by native
 plant productivity, but independent of native species richness and
 phylogenetic relatedness to the invader. Native plant production was not
 related to native species richness in our study. We show that resistance
 in these tropical aquatic submerged plant communities is mainly driven by
 the presence and biomass of a native community independent of native
 species diversity. Our study illustrates that resistance provided by these
 tropical freshwater submerged plant communities to invasive species
 contrasts to resistance described for other ecosystems. This emphasizes
 the need to include understudied systems when predicting patterns of
 species invasiveness and ecosystem invasibility across
 biomes.
DOI: 10.5061/dryad.cz8w9gj15
title: Data from: Antagonistic interactions subdue inter‐species green‐beard cooperation in bacteria

description: Cooperation can be favored through the green-beard mechanism, where a set
 of linked genes encodes both a cooperative trait and a phenotypic marker
 (green beard), which allows carriers of the trait to selectively direct
 cooperative acts to other carriers. In theory, the green-beard mechanism
 should favor cooperation even when interacting partners are totally
 unrelated at the genome level. Here, we explore such an extreme
 green-beard scenario between two unrelated bacterial species – Pseudomonas
 aeruginosa and Burkholderia cenocepacia, which share a cooperative locus
 encoding the public good pyochelin (an iron-scavenging siderophore) and
 its cognate receptor (green beard) required for iron-pyochelin uptake. We
 show that pyochelin, when provided in cell-free supernatants, can be
 mutually exchanged between species and provide fitness benefits under iron
 limitation. However, in co-culture we observed that these cooperative
 benefits vanished and communities were dominated by P. aeruginosa,
 regardless of strain background and species starting frequencies. Our
 results further suggest that P. aeruginosa engages in interference
 competition to suppress B. cenocepacia, indicating that inter-species
 conflict arising from dissimilarities at the genome level overrule the
 aligned cooperative interests at the pyochelin locus. Thus, green-beard
 cooperation is subdued by competition, indicating that inter-specific
 siderophore cooperation is difficult to evolve and to be maintained.
DOI: 10.5061/dryad.hmgqnk9dk
title: Data from: The vertical distribution and control of microbial necromass carbon in forest soils

description: Aim: Forest soils contain large amounts of terrestrial organic carbon (C),
 but the formation pathway of soil organic C (SOC) remains unclear. Recent
 evidence suggests that microbial necromass is a significant source of SOC,
 yet a global quantitative assessment across the whole-soil profile is
 lacking. We aimed to assess the vertical distribution and control of
 microbial-derived SOC in forest soils. Location: Global forests. Time
 period: 1996-2019. Major taxa studied: Soil microbial necromass carbon.
 Methods: We evaluated the proportions of fungal and bacterial necromass C
 in total SOC in the litter layer, O horizon soil, and various depths of
 mineral soil in forests using microbial biomarker (glucosamine and muramic
 acid) data. Results: The total microbial necromass C increased
 significantly with soil depth, ranging from 30% of SOC in O horizon soil
 to 62% of SOC in mineral soils below 50 cm. However, only bacterial
 necromass C followed this increasing trend with soil depth; fungal
 necromass C showed little variation across the whole-soil profile. Higher
 fungal and bacterial necromass C was observed in soils with lower C/N
 ratios and smaller aggregate sizes. Soil C/N ratio and microbial biomass C
 dominantly determined microbial necromass C in surface soil (above 20 cm),
 but soil clay content was the primary factor in subsoil (below 20 cm).
 Main conclusions: Microbial necromass C accounted for high percentages of
 the total SOC in forest soils (particularly at depths &gt;20 cm), but
 its long-term stabilization may be governed by different mechanisms at
 different soil horizons. Substrate quality regulates microbial activity
 and then controls biomass turnover in surface soil, while aggregate
 occlusion could facilitate mineral protection of microbial necromass C in
 subsoil. These differential controls of microbial-derived organic C could
 be applied in Earth system studies for predicting soil organic C dynamics
 in forests.
DOI: 10.5281/zenodo.11433383
title: DIVINE: Andalusia Agroclimatic Information Network Historic Datasets - MALAGA - (June 23 - May 24)

description: This dataset contains high-resolution daily agroclimatic data from the RIA (Red de Información Agroclimática de Andalucía) the andalusian agroclimatic information network, managed by IFAPA. The data has been collected as part of the DIVINE project to support research in precision agriculture, water management, and climate adaptation in Southern Spain.

The dataset covers the period from June 1, 2023, to May 31, 2024, providing key parameters such as temperature (mean, max, min), humidity, wind speed, solar radiation, precipitation, and calculated ETo (Evapotranspiration) using the Penman-Monteith method.

Geographic Coverage and Station Distribution: The dataset includes part of the processed records from 123 monitoring stations distributed across the 8 provinces of Andalusia. In this case the data includes the ones in Málaga:

Data Format:





Format: JSON (JavaScript Object Notation).




Naming Convention: 34 [Province_ID] [Station_ID] DIVINE [Station_Name] ([Province]).json




Coordinate System: WGS84 (included within the metadata of individual station files).



Source: Data retrieved from the official IFAPA RIAWS API (Junta de Andalucía).
DOI: 10.5068/d1mx0z
title: Data from: Large-scale assessment of intra- and inter-annual breeding success using a remote camera network

description: Changes in the physical environment along the Antarctic Peninsula have
 been among the most rapid anywhere on the planet. In concert with
 environmental change, the potential for direct human disturbance resulting
 from tourism, scientific programs, and commercial fisheries continues to
 rise in the region. While seabirds, such as the gentoo penguin Pygoscelis
 papua, are commonly used to assess the impact of these disturbances on
 natural systems, research efforts are often hampered by limited spatial
 coverage and lack of temporal resolution. Using a large‐scale remote
 time‐lapse camera network and a modeling framework adapted from
 capture‐recapture studies, we assess drivers of intra‐ and inter‐annual
 dynamics in gentoo penguin breeding success across nearly the entire
 species’ range in the Atlantic sector of the Southern Ocean. We quantify
 the precise timing of egg/chick mortality within each season and examine
 the role of precipitation events, tourism visitation, and fishing activity
 for Antarctic krill Euphausia superba (a principal prey resource in the
 Antarctic) in these processes. We find that nest failure rates are higher
 in the egg than the chick stage and that neither krill fishing nor tourism
 visitation had a strong effect on gentoo penguin breeding success. While
 precipitation events had, on average, little effect on nest mortality,
 results suggest that extreme weather events can precipitate sharp
 increases in nest failure. This study highlights the importance of
 continuous ecosystem monitoring, facilitated here by remote time‐lapse
 cameras, in understanding ecological responses to environmental stressors,
 particularly with regard to the timing of events such as extreme weather.
description: See Usage Notes, README, and associated publication.
description: This dataset contains all files to produce analyses presented in
 the associated manuscript, with the exception of the tourism data, which
 is available upon request from IAATO (https://iaato.org/). The code
 associated with these data can be found here:
 https://github.com/Penguin-Watch/penguin_watch_model. Data include the
 number of gentoo penguin chicks observed at individual nests for a number
 of time points over the course of the breeding season at breeding colonies
 across the Southern Ocean region. These data were obtained from
 annotations of images obtained from a remote time-lapse camera network.
 Precipitation data, obtained from annotations of camera images, are also
 included. .shp files and data on krill catch used in analyses are also
 included, but were obtained from existing sources. See metadata README
 file and associated publication for detailed information.
DOI: 10.5281/zenodo.11433382
title: DIVINE: Andalusia Agroclimatic Information Network Historic Datasets - MALAGA - (June 23 - May 24)

description: This dataset contains high-resolution daily agroclimatic data from the RIA (Red de Información Agroclimática de Andalucía) the andalusian agroclimatic information network, managed by IFAPA. The data has been collected as part of the DIVINE project to support research in precision agriculture, water management, and climate adaptation in Southern Spain.

The dataset covers the period from June 1, 2023, to May 31, 2024, providing key parameters such as temperature (mean, max, min), humidity, wind speed, solar radiation, precipitation, and calculated ETo (Evapotranspiration) using the Penman-Monteith method.

Geographic Coverage and Station Distribution: The dataset includes part of the processed records from 123 monitoring stations distributed across the 8 provinces of Andalusia. In this case the data includes the ones in Málaga:

Data Format:





Format: JSON (JavaScript Object Notation).




Naming Convention: 34 [Province_ID] [Station_ID] DIVINE [Station_Name] ([Province]).json




Coordinate System: WGS84 (included within the metadata of individual station files).



Source: Data retrieved from the official IFAPA RIAWS API (Junta de Andalucía).
DOI: 10.5061/dryad.fqz612jqk
title: Data from: Habitat selection of Rusty blackbirds during stopover varies with scale and function

description: The Rusty Blackbird (Euphagus carolinus) is a widespread, uncommon migrant
 that has experienced heavy population declines over the last century. This
 species can spend over a quarter of their annual cycle on migration, so it
 is important to determine their habitat requirements during stopover
 events to inform effective conservation planning. Here, we assess their
 habitat selection at an important stopover site in northern Ohio during
 both fall and spring migration. Since stopover habitat selection is
 scale-dependent, we investigate both patch-scale (between patches) and
 fine-scale (within a patch) selection using radio telemetry to home in on
 foraging and roosting flocks, and compare habitat variables between used
 and available points across the study site. At the patch scale, we found
 that birds preferred dogwood-willow swamp, low-lying forest patches, and
 areas of greater habitat complexity for foraging in both seasons. At the
 fine scale, spring migrants foraged closer to habitat edges than random,
 and preferred areas with more wet leaf litter and shallow water, and less
 grass cover. Fall migrants also preferred shallow water and leaf litter
 cover, and avoided areas with dense grass, forbs, and herbaceous shrub
 cover. By contrast, birds consistently roosted in dense stands of emergent
 Phragmites or Typha marsh, suggesting that the best stopover or staging
 sites are those with a matrix of different wetland habitats. Although the
 migratory range of Rusty Blackbirds is currently dominated by agricultural
 development, our results suggest that fragmented landscapes can still
 provide adequate habitat for migrants if the available land is managed for
 a variety of wet habitat types.
DOI: 10.5061/dryad.f7m0cfxss
title: Data from: The genomic view of diversification

description: The process of species diversification is traditionally summarized by a
 tree, the species tree, whose reconstruction from molecular data is
 hindered by frequent conflicts between gene genealogies. Here, we argue
 that instead of seeing these conflicts as nuisances, we can exploit them
 to inform the diversification process itself. We adopt a gene-based view
 of diversification to model the ubiquitous presence of gene flow among
 diverging lineages, one of the most important processes explaining
 disagreements among gene trees. We propose a new framework for modeling
 the joint evolution of gene and species lineages relaxing the hierarchy
 between the species tree and gene trees inherent to the standard view, as
 embodied in a popular model known as the multi-species coalescent (MSC).
 We implement this framework in two alternative models called the
 gene-based diversification models (GBD): 1) GBD-forward following all
 evolving genomes through time and 2) GBD-backward based on coalescent
 theory. They feature four parameters tuning colonization, gene flow,
 genetic drift and genetic differentiation. We propose a quick inference
 method based on differences between gene trees. Applied to two empirical
 data-sets prone to gene flow, we find better support for the GBD-backward
 model than for the MSC model. Along with the increasing awareness of the
 extent of gene flow, this work shows the importance of considering the
 richer signal contained in genomic histories, rather than in the mere
 species tree, to better apprehend the complex evolutionary history of
 species.
description: Instructions to use the GBD-backward and GBD-forward models are
 given in the read.me file.
DOI: 10.5061/dryad.9s4mw6mcx
title: Data from: Edge effects and mating patterns in a bumblebee-pollinated plant

description: Researchers have long assumed that plant spatial location influences plant
 reproductive success and pollinator foraging behavior. For example, many
 flowering plant populations have small, linear, or irregular shapes that
 increase the proportion of plants on the edge, which may reduce mating
 opportunities through both male and female function. Additionally, plants
 that rely on pollinators may be particularly vulnerable to edge effects if
 those pollinators exhibit restricted foraging and pollen carryover is
 limited. To explore the effects of spatial location (edge vs. interior) on
 siring success, seed production, pollinator foraging patterns, and
 pollen-mediated gene dispersal, we established a square experimental array
 of 49 Mimulus ringens (monkeyflower) plants. We observed foraging patterns
 of pollinating bumblebees and used paternity analysis to quantify male and
 female reproductive success and mate diversity for plants on the edge vs.
 interior. We found no significant differences between edge and interior
 plants in the number of seeds sired, mothered, or the number sires per
 fruit. However, we found strong differences in pollinator behavior based
 on plant location, including 15% lower per flower visitation rates and
 substantially longer interplant moves for edge plants. This translated
 into 40% greater pollen-mediated gene dispersal for edge than for interior
 plants. Overall, our results suggest that edge effects are not as strong
 as is commonly assumed, and that different plant reproduction parameters
 respond to spatial location independently.
description: Data included: seeds mothered, seeds sired, mate number, gene
 dispersal distances, pollinator flight distances
 Genetic data collected via genotyped progeny arrays
 Pollinator data collected via field observations
DOI: 10.5061/dryad.ns1rn8pq1
title: Quantitative profiling of protease specificity

description: Proteases comprise an important class of enzymes, whose activity is
 central to many physiologic and pathologic processes. Detailed knowledge
 of protease specificity is key to understanding their function. Although
 many methodologies have been developed to profile specificities of
 proteases, few have the diversity and quantitative grasp necessary to
 fully define specificity of a protease both in terms of substrate numbers
 and their catalytic efficiencies. We have developed a concept of
 “selectome”, which defines the set of substrates that uniquely represents
 specificity of a protease. We applied it to two closely related members of
 the Matrixin family – MMP-2 and MMP-9 by using substrate phage display
 coupled with Next Generation Sequencing and information theory-based data
 analysis. We have also derived a quantitative measure of substrate
 specificity, which accounts for both the numbers and relative catalytic
 efficiencies of substrates. Using these advances greatly facilitates
 uncovering selectivity between closely related members of protease
 families and provides insight into to the degree of contribution of
 catalytic cleft specificity to protein substrate recognition, thus
 providing basis to overcoming two of the major challenges in the field of
 proteolysis: 1) development of highly selective activity probes and
 inhibitors for studying proteases with overlapping specificities, and 2)
 distinguishing targeted proteolysis from bystander proteolytic events.
description: This dataset was preprocessed data from next generation
 sequencing of phage display data. The data has been
 preprocessed by linux shell scripts and Fortran programs.
description: See information included in the text of our manuscript being
 submitted to Plos Computational Biology. There are no
 missing values.
DOI: 10.5061/dryad.fttdz08qd
title: Interspecific allometry for sexual shape dimorphism: macroevolution of multivariate sexual phenotypes with application to Rensch's rule

description: Allometric trends in the degree of sexual dimorphism with body size have
 long fascinated evolutionary biologists. Many male-biased clades display
 more prominent sexual dimorphism in larger taxa (Rensch’s rule), with most
 examples documenting this pattern for body size dimorphism. While sexual
 dimorphism in traits other than body size is equally functionally
 relevant, characterizing allometric patterns of sexual dimorphism in such
 traits is hampered by lack of an analytical framework that can accommodate
 multivariate phenotypes. In this paper we derive a multivariate
 equivalency for investigating trends in sexual dimorphism – relative to
 overall body size – across taxa and provide a generalized test to
 determine whether such allometric patterns correspond with Rensch's
 rule. For univariate linear traits like body size, our approach yields
 equivalent results to those from standard procedures, but our test is also
 capable of detecting trends in multivariate datasets like shape. Computer
 simulations reveal the method displays appropriate statistical properties,
 and an empirical example in Mediterranean lizards provides the first
 demonstration of Rensch’s rule in a multivariate phenotype (head shape).
 Our generalized procedure substantially extends the analytical toolkit for
 investigating macroevolutionary patterns of sexual dimorphism and seeking
 a better understanding of the processes that underlie them.
DOI: 10.5061/dryad.bvq83bk67
title: Data from: Developmental loss of neurofibromin across distributed neuronal circuits drives excessive grooming in Drosophila

description: Neurofibromatosis type 1 is a monogenetic disorder that predisposes
 individuals to tumor formation and cognitive and behavioral
 symptoms.  The neuronal circuitry and developmental events
 underlying these neurological symptoms are unknown.  To better
 understand how mutations of the underlying gene (NF1) drive behavioral
 alterations, we have examined grooming in the Drosophila neurofibromatosis
 1 model.  Mutations of the fly NF1 ortholog drive excessive
 grooming, and increased grooming was observed in adults when Nf1 was
 knocked down during development.  Furthermore, intact Nf1 Ras
 GAP-related domain signaling was required to maintain normal grooming.
  The requirement for Nf1 was distributed across neuronal
 circuits, which were additive when targeted in parallel, rather than
 mapping to discrete microcircuits.  Overall, these data suggest
 that broadly-distributed alterations in neuronal function during
 development, requiring intact Ras signaling, drive key Nf1-mediated
 behavioral alterations.  Thus, global developmental alterations
 in brain circuits/systems function may contribute to behavioral phenotypes
 in neurofibromatosis type 1.
description: 5-minute videos were recorded of individual flies grooming in an
 open field, and the grooming of each body part was scored by a blind
 observer.  For most analyses, grooming bouts were pooled across all body
 parts to calculate the total grooming duration across the video.  The
 percentage of time spent grooming was then calculated for each
 subject/video.  This data set contains Excel (.xls) files with genotypes
 labeled, as well as some comma-delimited (.csv) files, in which cases the
 genotypes are listed in an accompanying text file.
DOI: 10.5061/dryad.qrfj6q5cv
title: Efficient removal of pharmaceuticals from water using graphene nanoplatelets as adsorbent

description: Recently, pharmaceutical pollutants in water emerge as global concern as
 they give threat to human health and environment. In this study, graphene
 nanoplatelets (GNPs) were used to efficiently remove antibiotics
 sulfamethoxazole (SMX) and analgesic acetaminophen (ACM) as pharmaceutical
 pollutants from water by adsorption process. GNPs; C750, C300, M15, and M5
 were characterized by high-resolution transmission electron microscopy,
 Raman spectroscopy, X-Ray diffraction and Brunauer-Emmett-Teller. The
 effects of several parameters; viz., solution pH, adsorbent amount,
 initial concentration and contact time were studied. The parameters were
 optimized by batch adsorption process and the maximum removal efficiency
 for both pharmaceuticals were 99%. The adsorption kinetics and isotherms
 model were employed, and the experimental data were best analysed with
 pseudo-second kinetic and Langmuir isotherm with maximum adsorption
 capacity (Qm) of 210.08 mg g-1 for sulfamethoxazole and
 56.21 mg g-1 for acetaminophen. Regeneration study were applied
 using different eluents; 5% ethanol-deionized water 0.005 M NaOH and HCl.
 GNP C300 were able to remove most of both pollutants
 from environmental water samples. Molecular docking was
 used to simulate the adsorption mechanism of GNP C300 towards
 sulfamethoxazole and acetaminophen with free binding energy of
 -7.54 kcal mol-1 and -5.29 kcal mol-1 respectively which revealed
 adsorption occurred spontaneously.