cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kh189325b
title: Data from: A bird’s eye view on turbulence: Seabird foraging associations with evolving surface flow features

description: Understanding physical mechanisms underlying seabird foraging is
 fundamental to predict responses to coastal change. For instance,
 turbulence in the water arising from natural or anthropogenic structures
 can affect foraging opportunities in tidal seas. Yet, identifying
 ecologically important localised turbulence features (e.g. upwellings
 ~10-100 m) is limited by observational scale and this knowledge gap is
 magnified in volatile predators. Here, using a drone-based approach, we
 present the tracking of surface-foraging terns (143 trajectories belonging
 to three tern species) and dynamic turbulent surface flow features in
 synchrony. We thereby provide the earliest evidence that localised
 turbulence features can provide physical foraging cues. Incorporating
 evolving vorticity and upwelling features within a hidden Markov model, we
 show that terns were more likely to actively forage as the strength of the
 underlying vorticity feature increased, while conspicuous upwellings ahead
 of the flight path presented a strong physical cue to stay in transit
 behaviour. This clearly encapsulates the importance of prevalent
 turbulence features as localised foraging cues. Our quantitative approach
 therefore offers the opportunity to unlock knowledge gaps in seabird
 sensory and foraging ecology on hitherto unobtainable scales. Finally, it
 lays the foundation to predict responses to coastal change to inform
 sustainable ocean development. 
description: The processed input dataset (.csv) includes the tern tracking
 data and associated environmental data. The R code (.txt) contains the
 statistical analysis (HMM - hidden Marcov model) and plotting code
 (ggplot) for the figures supporting the article’s results. 
 The R code has been run in the R version R-3.5.2 and requires the
 following packages: library(moveHMM)<br>
 library(mvtnorm)<br> library(ggplot2)<br>
 library(patchwork)<br>
DOI: 10.5061/dryad.v41ns1rvr
title: Scripts from: Inversions and genomic differentiation after secondary contact: When drift contributes to maintenance, not loss, of differentiation

description: Due to their effects on reducing recombination, chromosomal inversions may
 play an important role in speciation by establishing and/or maintaining
 linked blocks of genes causing reproductive isolation (RI) between
 populations. This view fits empirical data indicating that inversions
 typically harbor loci involved in RI. However, previous computer
 simulations of infinite populations with two to four loci involved in RI
 implied that, even with gene flux as low as 10–8 per gamete, per
 generation between alternative arrangements, inversions may not have
 large, qualitative advantages over collinear regions in maintaining
 population differentiation after secondary contact. Here, we report that
 finite population sizes can help counteract the homogenizing consequences
 of gene flux, especially when several fitness-related loci reside within
 the inversion. In these cases, the persistence time of differentiation
 after secondary contact can be similar to when gene flux is absent and
 notably longer than the persistence time without inversions. Thus, despite
 gene flux, population differentiation may be maintained for up to 100,000
 generations, during which time new incompatibilities and/or local
 adaptations might accumulate and facilitate progress toward speciation.
 How often these conditions are met in nature remains to be determined.
description: Custom-made codes in Matlab. 
description: # Scripts from: Inversions and genomic differentiation after secondary
 contact: When drift contributes to maintenance, not loss, of
 differentiation by Rafajlovic et al. (2021; Evolution). Data DOI link
 [https://doi.org/10.5061/dryad.v41ns1rvr](https://doi.org/10.5061/dryad.v41ns1rvr) **Code File Names:** There are four versions of the main code, each version being reserved for a separate model version. “Model2_ConsecArray.m” simulates Model 2, consecutive array version. “Model2_HalfHalfArray.m” simulates Model 2, half-half array version. “Model4_ConsecArray.m” simulates Model 4, consecutive array version. “Model4_HalfHalfArray.m” simulates Model 4, half-half array version. Each code has preset parameter values, and they can easily be changed by the user. All parameters are explained in the form of comments in the code files. **Output and data analysis** The main output, as presented in the publication, is the average weighted time of differentiation. To perform this calculation, one can run the following .m file: “Analyze_WeightedTime.m” (computes the average weighted time of differentiation, based on multiple model realisations). ## Code/Software Matlab
DOI: 10.5061/dryad.r4xgxd2c0
title: Data files for: Hazardous loss of genetic diversity through selective sweeps in asexual populations

description: With the two-fold cost of sex, derived asexual organisms have an immediate
 reproductive advantage over their sexual sisters.  Yet the
 "twiggy'' phylogenetic distribution of asexual lineages
 implies that they go extinct relatively quickly over evolutionary time.
  Meanwhile, bacteria and archaea have persisted for billions of
 years without requiring sexual reproduction. A simple explanation for this
 difference is that prokaryotes have very large population sizes that are
 not subject to the accumulation of deleterious mutations, but this implies
 that drift and mutational meltdown dominate derived asexual populations.
   We explored a different hazard, quantifying the degree to which
 genetic variation is lost in asexual populations experiencing selective
 sweeps.  Even though large populations generate diversity by
 mutation during sweeps, we find that populations that are safe from
 mutational meltdown may still be reduced to dangerous effective population
 sizes by sweeps.  Thus, ironically, adaptation itself reduces
 further adaptive potential and may predispose asexual populations to
 extinction.  Our data give results for the probability of
 mutational meltdown across various population sizes, the critical
 population size required to avoid meltdown, and the effect of selective
 sweeps on heterozygosity.  Analytical predictions are confirmed
 by simulation. We also derive a simple approximation for the effective
 population size after a hard sweep, and quantify the impact of
 recent sweeps on evolutionary rescue. These factors may help to explain
 the phylogenetic twigginess of asexuals, the maintenance of sex and
 recombination, and the evolutionary persistence of prokaryotes.
description: See github repository for code to both create and use these
 data.  https://github.com/lmwahl/loss_of_diversity
description: Please see the README.txt file for details regarding each data
 file.
DOI: 10.5061/dryad.cvdncjt3v
title: Behavioral interactions between bacterivorous nematodes and predatory bacteria in a synthetic community

description: Theory and empirical studies in metazoans predict that apex predators
 should shape the behavior and ecology of mesopredators and prey at lower
 trophic levels. Despite the ecological importance of microbial
 communities, few studies of predatory microbes examine such behavioral
 res-ponses and the multiplicity of trophic interactions. Here, we sought
 to assemble a three-level microbial food chain and to test for behavioral
 interactions between the predatory nematode Caenorhabditis elegans and the
 predatory social bacterium Myxococcus xanthus when cultured together with
 two basal prey bacteria that both predators can eat—Escherichia coli and
 Flavobacterium johnsoniae. We found that &gt;90% of C. elegans worms
 failed to interact with M. xanthus even when it was the only potential
 prey species available, whereas most worms were attracted to pure patches
 of E. coli and F. johnsoniae. In addition, M. xanthus altered nematode
 predatory behavior on basal prey, repelling C. elegans from two-species
 patches that would be attractive without M. xanthus, an effect similar to
 that of C. elegans pathogens. The nematode also influenced the behavior of
 the bacterial predator: M. xanthus increased its predatory swarming rate
 in response to C. elegans in a manner dependent both on basal-prey
 identity and on worm density. Our results suggest that M. xanthus is an
 unattractive prey for some soil nematodes and is actively avoided when
 other prey are available. Most broadly, we found that nematode and
 bacterial predators mutually influence one another’s predatory behavior,
 with likely consequences for coevolution within complex microbial food
 webs.
description: Please refer to README file and R markdown documents.
DOI: 10.5061/dryad.d2547d82d
title: Data from: Song type and song type matching are important for joint territorial defense in a duetting songbird

description: Birds have a diverse acoustic communication system, with species specific
 repertoires facilitating more complex behaviors in terms of both within-
 and between-pair communications. Certain song types are produced for
 specific functions, such as aggressive encounters. In addition, song
 matching behaviors, whereby neighboring individuals match song types, can
 be used in aggressive interactions as a sophisticated acoustic behavior.
 In this study, we examined the functions of song types, in a duet context,
 of male yellow-breasted boubous (Laniarius atroflavus), an Afromontane
 bush-shrike with a vocal sexual dimorphism. We aimed at assessing whether,
 structurally, certain song types elicited a heightened reaction than
 others, and also whether song matching affected response behavior. A dual
 speaker playback procedure was performed for 18 pairs of boubous, each
 pair being exposed to duets with three different male song types. We found
 differences in response towards the different duet types but these
 differences resulted from the amount at which males matched different song
 types. Pairs responded stronger when a focal male matched the playback
 type, and matching was significantly more often found in cases where the
 rarest type of male song was used. We found no sex differences in terms of
 response strength to playback type. Our results indicate a two-level way
 of coding aggression toward intruding pairs. The yellow-breasted boubous
 utilize their repertoires, linking matching with structure in order to
 show aggression in terms of territory defense and sexual conflict. This
 study also confirms joint territorial defense as a main function of duets
 in this species.
description: Data was collected between 13 Nov and 1 Dec 2016 in in the
 Bamenda Highlands in Cameroon (6°5’-6°8’ N and 10°17’-10°20 E). To create
 this data we used Raven Pro (Cornell Lab of Ornithology), and IBM SPSS
 Statistics v. 27 (IBM Corp, Chicago, IL, USA). The final version is
 created in Microsoft Excel file. Column heading are describe in worksheet
 called ‘legend’.
DOI: 10.5061/dryad.zpc866t80
title: How latex film formation and adhesion at the nanoscale correlate to performance of pressure sensitive adhesives with cellulose nanocrystals

description: Emulsion polymerized latex-based pressure sensitive adhesives (PSAs) are
 more environmentally benign because they are synthesized in water but
 often underperform compared to their solution polymerized counterparts.
 Studies have shown a simultaneous improvement in the tack, and peel and
 shear strength of various acrylic PSAs upon the addition of cellulose
 nanocrystals (CNCs). This work uses atomic force microscopy (AFM) to
 examine the role of CNCs in (i) the coalescence of hydrophobic 2‐ethyl
 hexyl acrylate/n‐butyl acrylate/methyl methacrylate (EHA/BA/MMA) latex
 films, and (ii) as adhesion modifiers over multiple length scales.
 EHA/BA/MMA. Thin films with varying solids content and CNC loading were
 prepared by spin coating. AFM revealed that CNCs lowered the solids
 content threshold for latex particle coalescence during film formation.
 This improved the cohesive strength of the films, which was directly
 reflected in the increased shear strength of the EHA/BA/MMA PSAs with
 increasing CNC loading. Colloidal probe AFM indicated that the
 nano-adhesion of thicker continuous latex films increased with CNC loading
 when measured over small contact areas where the effect of surface
 roughness was negligible. Conversely, the beneficial effects of the CNCs
 on macroscopic PSA tack and peel strength were outweighed by the effects
 of increased surface roughness with increasing CNC loading over larger
 surface areas. This highlights that CNCs can improve both cohesive and
 adhesive PSA properties, however, the effects are most pronounced when the
 CNCs interact favorably with the latex polymer and are uniformly dispersed
 throughout the adhesive film.
description: MFP-3D Atomic Force Microscope (Asylum Research –
 Oxford Instruments, Santa Barbara, CA, USA) Igor Pro
 6.0 running Asylum Research AFM software (version 13.17)
DOI: 10.5281/zenodo.18333254
title: Microbial communities data for manuscript: Microbial Communities, Volatile Flavor Profiles and Metabolomic Characteristics during Traditional Hakka Huangjiu Fermentation

description: This dataset is part of raw data of manuscript: Microbial Communities, Volatile Flavor Profiles and Metabolomic Characteristics during Traditional Hakka Huangjiu Fermentation, contains sequence data and analysis results.

 

This dataset will be used in other manuscripts.

 

For other parts of raw data of the manuscript, please visit: 

 10.5281/zenodo.18358381

 10.5281/zenodo.18357407
DOI: 10.5281/zenodo.18333255
title: Microbial communities data for manuscript: Microbial Communities, Volatile Flavor Profiles and Metabolomic Characteristics during Traditional Hakka Huangjiu Fermentation

description: This dataset is part of raw data of manuscript: Microbial Communities, Volatile Flavor Profiles and Metabolomic Characteristics during Traditional Hakka Huangjiu Fermentation, contains sequence data and analysis results.

 

This dataset will be used in other manuscripts.

 

For other parts of raw data of the manuscript, please visit: 

 10.5281/zenodo.18358381

 10.5281/zenodo.18357407
DOI: 10.5061/dryad.mcvdnck0p
title: Selection for phage resistance reduces virulence of Shigella flexneri

description: There is increasing interest in phage therapy as an alternative to
 chemical antibiotics for treating bacterial infections, especially using
 phages that select for evolutionary trade-offs between increased phage
 resistance and decreased fitness traits such as virulence in target
 bacteria. A vast repertoire of virulence factors allows the opportunistic
 bacterial pathogen, Shigella flexneri, to invade human gut epithelial
 cells, to replicate intracellularly, and to evade host immunity through
 intercellular spread; the latter is an infection stage that causes tissue
 damage, contributing to host mortality. It is previously shown that outer
 membrane porin OmpA of S. flexneri is necessary for polar localization of
 virulence factor IcsA, which polymerizes host actin and results in
 bacterial motility within infected cells. We hypothesized that a phage
 which uses OmpA as a receptor to recognize, bind and infect S. flexneri,
 should select for phage-resistant mutants with attenuated intercellular
 spread.  Here we show that a naturally-isolated Myoviridae virus,
 phage A1-1, requires OmpA as a receptor, and selects for reduced virulence
 in S. flexneri. We characterized five phage-resistant mutants by measuring
 their phenotypic changes relative to wildtype bacteria in various traits:
 cell-membrane permeability, total lipopolysaccharide (LPS), sensitivity to
 four antibiotics, and susceptibility to infection by phages T7 and 60B.
 Results separated the mutants into two groups: R1 and R2 phenotypically
 resembled ompA knockouts, whereas R3, R4 and R5 were similar to
 LPS-deficient strains. Whole genome sequencing confirmed that R1 and R2
 had mutations in ompA, while R3, R4 and R5 showed mutations in LPS
 inner-core biosynthesis genes gmhA and gmhC. Bacterial plaque assays in
 Vero cells confirmed that all five phage-resistant mutants were incapable
 of intercellular spread. We concluded that selection for S. flexneri
 resistance to phage A1-1 generally reduced the virulence trait
 intercellular spread, but this trade-off could be mediated either by
 mutations in ompA or those in LPS-core genes that likely altered OmpA
 conformation.
DOI: 10.5061/dryad.9ghx3ffh1
title: Data and code for: Replay of innate vocal patterns during sleep in suboscines

description: Activation of forebrain circuitry during sleep has been variably
 characterized as ‘pre- or replay’ and has been linked to memory
 consolidation. The evolutionary origins of this mechanism, however, are
 unknown. Sleep activation of the sensori-motor pathways of learned
 birdsong is a particularly useful model system because the muscles
 controlling the vocal organ are activated, revealing syringeal activity
 patterns for direct comparison with those of day-time vocal activity. Here
 we show that suboscine birds, which develop their species-typical songs
 innately without the elaborate forebrain-thalamic circuitry of the vocal
 learning taxa, also engage in replay during sleep. In two tyrannid species
 the characteristic syringeal activation patterns of song could also be
 identified during sleep. Similar to song-learning oscines, the burst
 structure was more variable during sleep than day-time song production. In
 kiskadees (Pitangus sulphuratus), a second vocalization, which is part of
 a multi-modal display, was also replayed during sleep along with one
 component of the visual display. These data show unambiguously that
 variable ‘replay’ of stereotyped motor programs is not restricted to
 programs confined within forebrain circuitry. The proposed effects on
 vocal motor program maintenance are therefore building on a pre-existing
 neural mechanism that predates the evolution of learned vocal motor
 behavior.
DOI: 10.5061/dryad.6m905qfzv
title: Supplemental data for: Three-dimensional kinematics of euchelicerate limbs uncover functional specialisation in eurypterid appendages

description: Sea scorpions (Eurypterida; Euchelicerata) explored the extreme limits of
 the aquatic euchelicerate body plan. Indeed, the group contains the
 largest known marine euarthropods. Inferences on eurypterid life modes—in
 particular walking and eating—are commonly made by comparing the group to
 horseshoe crabs (Xiphosura; Euchelicerata). However, no models have been
 presented to test these hypotheses. Here, we reconstruct prosomal
 appendages of two exceptionally well-preserved eurypterids Eurypterus
 tetragonophthalmus and Pentecopterus decorahensis and kinematically model
 the flexure and extension of these appendages in 3D. We compare these
 models to 3D kinematic models of Limulus polyphemus prosomal appendages.
 This comparison highlights that the examined eurypterid prosomal
 appendages could not have effectively moved prey items to the gnathal
 edges, and therefore would not have emulated the motion of a L. polyphemus
 walking leg. It seems that these eurypterid appendages were primarily used
 to walk or grab prey and other appendages would have moved prey for
 mastication. Such 3D kinematic modelling highlights how eurypterid
 appendage morphologies placed substantial limits on their function,
 suggesting a high degree of specialisation, especially when compared to
 horseshoe crabs. 3D kinematic modelling of these extinct groups also
 presents an innovative approach to understanding the position of these
 animals within their respective paleoecosystems.
DOI: 10.5061/dryad.9w0vt4bf9
title: Coordination of movement via complementary interactions of leaders and followers in termite mating pairs.

description: Leadership of animal group movements depends on social feedback, hence
 leader’s signals and follower’s responses should be attuned to each other.
 However, leader and follower roles are difficult to disentangle in species
 with high levels of coordination. To overcome this challenge, we
 investigated a simple case of movement coordination: termite pairs in
 which a female leads a male as they search for a nest site. To tease apart
 leader and follower roles, we created conspecific and heterospecific pairs
 of Coptotermes gestroi and C. formosanus, which share a pairing pheromone
 so that males follow females of either species. Conspecific pairs were
 stable for both species, even though C. gestroi females produce less
 pheromone than C. formosanus. Heterospecific pairs with C. gestroi males
 were also stable, but not those with C. formosanus males. We attributed
 this difference to the C. gestroi male’s unique capacity to follow females
 that release small amounts of pheromone; C. formosanus males cannot follow
 or reject C. gestroi females as unsuitable. This conclusion was supported
 by an information-theoretic analysis that detected information flow from
 female to male in only stable tandems. Despite their following ability, C.
 gestroi males lost to C. formosanus males in competitions to follow C.
 formosanus females. Thus, partner selection has shaped the
 species-specific association of mating pairs. Our results demonstrate that
 a similar level of coordination can emerge from distinct sets of
 complementary sender-receiver interactions.
description: All data were generated from video analysis (tracking of
 individuals in tandem) using UMATracker. For processing, please read the
 readme files.
DOI: 10.5061/dryad.1g1jwstvq
title: Data from: High-performance resistive humidity sensor based on Ag nanoparticles decorated with graphene quantum dots

description: In this work, we present a low-cost, fast and simple fabrication of
 resistive-type humidity sensors based on the graphene quantum dots (GQDs)
 and silver nanoparticles (AgNPs) nanocomposites. The GQDs and AgNPs were
 synthesized by hydrothermal method and green reducing agent route,
 respectively. UV/Vis spectrophotometer, X-ray photoelectron spectroscopy
 and field emission transmission electron microscopy were used to
 characterize quality, chemical bonding states and morphology of the
 nanocomposite materials and confirm the successful formation of
 core/shell-like AgNPs/GQDs structure. According to sensing humidity
 results, the ratio of GQDs/AgNPs 1:1 nanocomposite exhibits the best
 humidity response of 98.14% with exponential relation in the humidity
 range of 25 - 95% RH at room temperature as well as faster
 response/recovery times than commercial one at the same condition. The
 sensing mechanism of the high-performance GQDs/AgNPs humidity sensor is
 proposed via Schottky junction formation and intrinsic synergistic effects
 of GQDs and AgNPs.