cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8w9ghx3jk
title: Bayesian mimicry in the non-rewarding saprophytic orchid Danxiaorchis yangii

description: Bayesian mimicry, a type of deceptive pollination, is a complicated
 strategy used by non-rewarding plants to attract pollinators, but some
 hypotheses concerning this phenomenon have not been systematically
 verified. In order to show in detail a case of Bayesian mimicry on
 saprophytic orchid Danxiaorchis yangii in this study, we compared
 floral characteristics of Danxiaorchis yangii and Lysimachia alfredi as
 well as the pollination behavior of the insect Dufourea
 sp. towards the two species. Lysimachia alfredi can
 provide a reward to Dufourea sp., whereas Danxiaorchis yangii
 cannot. The flowering phenology and geographical distribution of these two
 plants are highly overlapping. Statistical analysis of quadrat and L.
 alfredi transplanting test data revealed that the fruit set rate
 of Danxiaorchis yangii was significantly positively correlated with the
 number of nearby L. alfredi individuals. In a glass cylinder experiment,
 Danxiaorchis yangii and L. alfredi attracted Dufourea sp. through visual
 signals, but the insect could not distinguish between flowers of the two
 plants before landing on flowers. We observed that the ultraviolet
 reflection spectra of Danxiaorchis yangii and L. alfredi are highly
 similar. In addition, we found that the hexagonal color models of the two
 plants are consistent with the bee’s visual characteristics, thus
 indicating that the visual signals of the flowers of the two plants are
 greatly similar. All of these results provide evidence that Danxiaorchis
 yangii simulates the visual signals of L. alfredi through
 Batesian mimicry, thereby deceivingly attracting Dufourea sp.
DOI: 10.5061/dryad.rjdfn2z7v
title: Geographic allele frequency variation in the 1000 Genomes hg38 NYGC dataset

description: A key challenge in human genetics is to describe and understand the
 distribution of human genetic variation. Often genetic variation is
 described by showing rela tionships among populations or
 individuals, in each case drawing inferences over a large number
 of variants. Here, we present an alternative representation of human
 genetic variation that reveals the relative abundance of different allele
 frequency patterns across populations. This approach allows viewers to
 easily see several features of human genetic structure: (1) most variants
 are rare and geographically localized, (2) variants that are common in a
 single geographic region are more likely to be shared across the globe
 than to be private to that region, and (3) where two individuals differ,
 it is most often due to variants that are common globally, regardless of
 whether the individuals are from the same region or different regions. To
 guide interpretation of the results, we also apply the visualization to
 contrasting theoretical scenarios with varying levels of divergence and
 gene flow. Our variant-centric visualization clarifies the major
 geographic patterns of human variation and can be used to help correct
 potential misconceptions about the extent and nature of genetic
 differentiation among populations.
description: This data has been processed using a reproduceable pipeline that
 can be found at the repository : https://github.com/aabiddanda/geovar_rep_paper. The dataset was processed by downloading VCF files from the New York Genome Center, filtered to biallelic single-nucleotide polymorphisms, and those that "PASS" in the filter column. We then calculated the allele frequency in separate populations using PLINK v1.90
description: Please see attached README.md for additional information.
DOI: 10.5061/dryad.tb2rbnzxq
title: Experimental evidence of warming-induced disease emergence and its prediction by a trait-based mechanistic model

description: Predicting the effects of seasonality and climate change on the emergence
 and spread of infectious disease remains difficult, in part because of
 poorly understood connections between warming and the mechanisms driving
 disease. Trait-based mechanistic models combined with thermal performance
 curves arising from the Metabolic Theory of Ecology (MTE) have been
 highlighted as a promising approach going forward; however, this framework
 has not been tested under controlled experimental conditions that isolate
 the role of gradual temporal warming on disease dynamics and emergence.
 Here, we provide experimental evidence that a slowly warming host –
 parasite system can be pushed through a critical transition into an
 epidemic state. We then show that a trait-based mechanistic model with MTE
 functional forms can predict the critical temperature for disease
 emergence, subsequent disease dynamics through time, and final infection
 prevalence in an experimentally warmed system of Daphnia and a
 microsporidian parasite. Our results serve as a proof of principle that
 trait-based mechanistic models using MTE sub-functions can predict
 warming-induced disease emergence in data-rich systems – a critical step
 towards generalizing the approach to other systems.
description: readme file attached
DOI: 10.5061/dryad.j3tx95xb2
title: Monitoring and traceability of genetically modified soybean event GTS 40-3-2 during soybean protein concentrate and isolate preparation

description: To evaluate DNA fragmentation and GMO quantification during soybean
 protein concentrate and isolate preparation, genetically modified soybean
 event GTS 40-3-2 (RRS) was blended with conventional soybeans at mass
 percentages of 0.9%, 2%, 3%, 5%, and 10%. Qualitative PCR and real-time
 PCR were used to monitor the taxon-specific lectin and exogenous cp4 epsps
 target levels in all of the main products and by-products, which has
 practical significance for RRS labelling threshold and traceability. Along
 the preparation chain, the majority of DNA was distributed in main
 products, and the DNA degradation was noticed. From a holistic
 perspective, the lectin target degraded more than cp4 epsps target during
 both of the two soybean proteins preparations. Therefore, the transgenic
 contents in the final protein products were higher than the actual mass
 percentages of RRS in raw materials. Our results are beneficial to the
 improvement of GMO labelling legislation and the protection of consumer
 rights.
DOI: 10.5061/dryad.18931zctk
title: Stereo video files used for 3d tracking horsefly trajectories

description: Of all hypotheses advanced for why zebras have stripes, avoidance of
 biting fly attack receives by far the most support, yet the mechanisms by
 which stripes thwart landings are not yet understood. A logical and
 popular hypothesis is that stripes interfere with optic flow patterns
 needed by flying insects to execute controlled landings. This could occur
 through disrupting the radial symmetry of optic flow via the aperture
 effect (i.e. generation of false motion cues by straight edges), or
 through spatiotemporal aliasing (i.e. misregistration of repeated
 features) of evenly spaced stripes. By recording and reconstructing
 tabanid fly behaviour around horses wearing differently patterned rugs, we
 could tease out these hypotheses using realistic target stimuli. We found
 that flies avoided landing on, flew faster near, and did not approach as
 close to striped and checked rugs compared to grey. Our observations that
 flies avoided checked patterns in a similar way to stripes refutes the
 hypothesis that stripes disrupt optic flow via the aperture effect, which
 critically demands parallel striped patterns. Our data narrow the menu of
 fly-equid visual interactions that form the basis for the extraordinary
 coloration of zebras.
description: Filming was conducted using
 a custom-built stereo camera rig consisting of two digital video cameras
 (Hero 5, GoPro, San Mateo, USA) affixed at either end of a 1.0 m metal bar
 mounted on a tripod. Cameras were triggered simultaneously by a single
 wireless remote and temporally synchronized using the audio channel. The
 relative position of each camera and the distortive effects of the camera
 optics were determined via a calibration routine involving a flat
 checkerboard standard and the stereo camera toolbox in Matlab (2018a,
 Mathworks, Natick, USA). Fly activity around horses was filmed at 60
 frames per second, at a resolution of 2704 x1520 pixels. Horsefly
 (<i>Haematopota pluvialis</i> and <i>Tabanus
 bromius</i>) trajectories were manually extracted from the stereo
 video recordings, first by identifying tabanids approaching the horse,
 then by manually digitising the fly’s location frame-by-frame in the pair
 of stereo images using a custom-written script in Matlab. Finally, the
 moment-to-moment position of the fly was extracted using the built-in
 functions of the stereo camera toolbox. To place the trajectory data in
 the context of the target host, a three dimensional mesh model of an
 average-sized horse was placed in the virtual space alongside the fly
 trajectory and manoeuvred to align with markers digitised on the front and
 rear regions of the original horse. Care was taken to sample the 100 or so
 trajectories from each rug type across as many horses as possible, over as
 wide time intervals as possible to further reduce the unlikely event of
 digitizing the same fly.
DOI: 10.5061/dryad.mcvdncjz1
title: Data from: Female-limited X-chromosome evolution effects on male pre- and post-copulatory success

description: In our article, entitled “Female-limited X-chromosome evolution effects on
 male pre- and post-copulatory success”, we carried out a female-limited X
 chromosome evolution experiment to study the effect of X-linked sexually
 antagonistic genetic variance on male reproductive traits. By limiting
 expression of the X chromosome to females for multiple generations, we
 removed male selective constraints, which should allow X-linked
 female-beneficial alleles to increase in frequency.  As a result,
 expressing the experimentally evolved X chromosome in males, we found a
 small reduction in male fitness caused by the trade-off between male
 attractiveness and sperm competitiveness. These results indicate
 that the X chromosome in D. melanogaster harbors
 sexually antagonistic genetic variance for pre- and post- copulatory
 success in males.
description: The dataset name is Manat Y. et.al,2021, FLXexperimental
 evolution.xlsx. The data were collected from several
 experimentally evolved <em>D.melanogster </em>populations.
 More information can be found  the manuscript entitled "Female-limited X-chromosome
 evolution effects on male pre- and post-copulatory
 success" by
 Yesbol Manat, Katrine K.
 Lund-Hansen, Georgios Katsianis, Jessica K.
 Abbott. 
description: The R script name is R script.
DOI: 10.5061/dryad.51c59zw5s
title: Control of the anterior pituitary cell lineage regulator POU1F1 by the stem cell determinant Musashi

description: The cytokine leptin regulates energy homeostasis through ubiquitously
 expressed leptin receptors.  Leptin has a number of
 major signaling targets in the brain, including cells of the anterior
 pituitary (AP).  We have previously reported that mice
 lacking leptin receptors in AP somatotropes display growth hormone (GH)
 deficiency, metabolic dysfunction and adult onset
 obesity.  Amongst other targets, leptin signaling
 promotes increased levels of the pituitary transcription factor POU1F1
 (also referred to as Pit1) which, in turn, regulates the specification of
 somatotrope, lactotrope and thyrotrope cell lineages within the anterior
 pituitary.  Leptin’s mechanism of action on somatotropes
 is sex-dependent, with females demonstrating post-transcriptional
 control of Pou1f1 mRNA
 translation.  In this study, we have investigated the
 mechanism that regulates Pou1f1 mRNA translational
 control and report that the stem cell marker and mRNA translational
 control protein, Musashi1, exerts repression of
 the Pou1f1 mRNA. In FACS-purified female
 somatotropes, Msi1 mRNA levels and Musashi1 protein
 levels are increased in the mouse model that lacks leptin signaling
 (Gh-CRE Lepr-null), coincident with lack of POU1f1 protein,
 despite normal levels of Pou1f1 mRNA. Single-cell RNA
 sequencing of pituitary cells from control female animals indicates that
 both Msi1 and Pou1f1 mRNAs are
 expressed in Gh-expressing somatrotropes and immunocytochemistry
 analyses of these cells confirms that Musashi1 protein is present in the
 somatotrope population. We demonstrate that Musashi interacts directly
 with the Pou1f1 mRNA 3’ untranslated region and exerts
 translational repression of a Pou1f1 mRNA
 translation reporter in a leptin-sensitive
 manner.  Musashi immunoprecipitation from whole
 pituitary reveals
 co-associated Pou1f1 mRNA.  These
 findings suggest a mechanism in which leptin stimulation is required to
 reverse Musashi-mediated Pou1f1 mRNA translational
 control to coordinate AP somatotrope function with metabolic status.
description: Publically accessible databases queried for author specific
 genes/processes as noted in accompanying Table and Figure legends.
   Author generated single cell RNA sequencing data (see
 Gene Expression Omnibus (GEO) under accession number GSE153045) with
 differential gene expression analysis between clusters performed as
 described in accompanying Figure legend and primary manuscript
 Individual luciferase reporter assay experiments performed as
 described in theprimary manuscript that were aggregated to generate teh
 composite graph Figure 6D in the primary manuscript
 EMSA (RNA binding assays) essentially as described in the primary
 manuscript (see figure 6A and 6B) except full length forms of human
 Musashi1 and Musashi2 were employed
DOI: 10.5061/dryad.0gb5mkkzc
title: Data from: Landscape-dependent effects of varietal mixtures on insect pest control and implications for farmer profits

description: Intraspecific plant diversity can significantly impact insect herbivore
 populations in natural systems. Yet, its role as an insect pest control
 strategy in agriculture has received less attention, and little is known
 about which crop traits are important to herbivores in different landscape
 contexts. Moreover, empirical economic analyses on the cost-effectiveness
 of varietal mixtures is lacking. We used varietal mixtures of Brassica
 oleracea crops on working farms to examine how two metrics of
 intraspecific crop diversity—varietal richness and number of plant colors
 (color richness)—affect crop damage and the incidence and abundance of two
 insect pest species, Pieris rapae and Phyllotreta spp. We evaluated the
 context-dependency of varietal mixtures by sampling early and late season
 plantings of B. oleracea crops in farms across a gradient of landscape
 composition. We developed crop budgets and used a net present value
 analysis to assess the impact of varietal mixtures on input and labor
 costs, crop revenues, and profit. We found context-dependent effects of
 varietal mixtures on both pests. In early season plantings, color richness
 did not affect Phyllotreta spp. populations. However, increasing varietal
 richness reduced Phyllotreta spp. incidence in simple landscapes dominated
 by cropland, but this trend was reversed in complex landscapes dominated
 by natural habitats. In late season plantings, color richness reduced the
 incidence and abundance of P. rapae larvae, but only in complex landscapes
 where their populations were highest. Varietal richness had the same
 effect on P. rapae larvae as color richness. Unexpectedly, we consistently
 found lower pest pressure and reduced crop damage in simple landscapes.
 Although varietal mixtures did not affect crop damage, increasing color
 richness corresponded with increased profits, due to increased revenue and
 a marginal reduction in labor and input costs. We demonstrate varietal
 mixtures can significantly impact pest populations, and this effect can be
 mediated by intraspecific variation in crop color. However, the strength
 and direction of these effects vary by season, landscape composition, and
 pest species. The association between varietal color richness and
 profitability indicates farmers could design mixtures to enhance economic
 returns. We recommend additional research on the benefits of intraspecific
 trait variation for farmers.
DOI: 10.5061/dryad.wdbrv15kt
title: Data from: Inducing seed dispersal by generalist frugivores: A new technique to overcome dispersal limitation in restoration

description: 1. Dispersal limitation severely impairs the trajectory of restoration,
 mainly due to the lack of seed vectors bringing seeds from nearby
 habitats; a role played by many frugivorous vertebrates that can be absent
 or reduced in restored or degraded sites. 2. Here we propose a new
 technique named Induced Seed Dispersal, that amplifies the role that many
 generalist frugivores have in seed dispersal. It consists in the offering
 of seeds embedded in the pulp of commercial fruits or whole native fleshy
 fruits in feeders to generalist frugivores, which ingest the seeds and
 defecate them elsewhere. We set feeders in a restored site and monitored
 the visiting pattern of these frugivores with cameras-traps. We also set
 seed traps to retrieve seeds dispersed by frugivores and offered around
 1500 seeds of Cecropia hololeuca (Urticaceae) per week for one year. 3. We
 recorded at least 24 generalist frugivore species of terrestrial mammals,
 bats, and birds, which ingested/removed the seeds/fruits from the feeders.
 Seeds of C. hololeuca dispersed by marmosets were retrieved in the seed
 traps and germinated. We estimated a potential seed rain of more than 600
 C. hololeuca seeds ha-1 mo-1. 4. Synthesis and applications. Our study
 demonstrates that this new technique can make use of generalist frugivores
 to assist restoration or regeneration into sites where seed dispersal is
 compromised by the lack of dispersers or limited seed arrival. Inducing
 seed dispersal by generalist frugivores is a low-cost and easy-managed
 technique that can be applied year-round in restoration and forest
 enrichments at all scales.
description: Visits of frugivorous vertebrates to feeders were recorded by
 camera-traps in a restoration site in Southeastern Brazil from April 2016
 to July 2018. Recordings consisted of video sequences of 20 s long. All
 video sequences with recordings of fruit consumption by frugivores were
 analyzed to obtain data on feeding behavior. Measurements of bills (birds)
 and mandibles (mammals) were made in a museum vertebrate collection to
 elaborate an index of pulp consumption by each species.
description: All necessary information for data reusing is available in the
 manuscript text and datasheets.
DOI: 10.5061/dryad.0rxwdbrx3
title: Data from: Plant protection services mediated by extrafloral nectaries decline with aridity but are not influenced by chronic anthropogenic disturbance in Brazilian Caatinga

description: 1. Most terrestrial species occur in human-modified landscapes that are
 experiencing climate change. In addition to direct impacts on species,
 both anthropogenic disturbance and climate change can have important
 effects through changes in species interactions, including the disruption
 of ecological services provided by them. 2. Here we investigate how
 chronic anthropogenic disturbance (CAD) and aridity affect the
 effectiveness of plant protection services provided by ants to plants
 bearing extrafloral nectaries (EFNs). 3. The study was conducted across 13
 01-ha plots distributed along CAD and aridity gradients in Caatinga
 vegetation of northeastern Brazil. We focused on Pityrocarpa moniliformis,
 the most abundant and widely distributed EFN-bearing tree species
 occurring in our study area, and used experimental attack rates on
 termites as a measure of effectiveness of ant protection services. We
 investigated the relative roles of nectar production (volume and
 concentration) and ant species composition in mediating the effects of CAD
 and aridity on the effectiveness of protection services. 4. Attack rates
 by ants declined with increasing aridity but were not related to CAD. The
 volume of extrafloral nectar declined with increasing CAD but was not
 affected by aridity, whereas the concentration was not related to either
 CAD or aridity. The composition of attendant ant species varied with
 aridity but not with CAD. 5. Synthesis: The decline in ant-protection
 services with increased aridity was therefore mediated by changes in the
 composition of attendant ant species rather than by changes in the
 production of extrafloral nectar. Our findings suggest that CAD does not
 affect plant-protection services provided by ants but highlights the
 vulnerability of EFN-bearing plants to climate change through decreased
 predation of herbivores.
DOI: 10.5061/dryad.18931zctm
title: Data from: Variations of mesozoic feathers: insights from the morphogenesis of extant feather rachises

description: The rachises of extant feathers, composed of dense cortex and spongy
 internal medulla, are flexible and light, yet stiff enough to withstand
 the load required for flight, among other functions. Incomplete knowledge
 of early feathers prevents a full understanding of how cylindrical
 rachises have evolved. Bizarre feathers with unusually wide and
 flattened rachises, known as “rachis-dominated feathers” (RDFs)
 have been observed in fossil non-avian and avian theropods. Newly
 discovered RDFs embedded in early Late Cretaceous Burmese ambers (~99 Ma)
 suggest the unusually wide and flattened rachises mainly consist of a
 dorsal cortex, lacking a medulla and a ventral cortex. Coupled with
 findings on extant feather morphogenesis, known fossil RDFs were
 categorized into three morphotypes based on their rachidial
 configurations. For each morphotype, potential developmental scenarios
 were depicted by referring to the rachidial development in chickens, and
 relative stiffness of each morphotype was estimated through functional
 simulations. The results suggest rachises of RDFs are
 developmentally equivalent to a variety of immature stages of cylindrical
 rachises. Similar rachidial morphotypes documented in extant penguins
 suggest that the RDFs are not unique to Mesozoic theropods, though they
 are likely to have evolved independently in extant penguins.
description: Electronic Supplementary Information to "Variations of
 mesozoic feathers: insights from the morphogenesis of extant feather
 rachises"
DOI: 10.5061/dryad.8w9ghx3jm
title: Data from: The genetic architecture of fitness drives population viability during rapid environmental change

description: The rapid global loss of biodiversity calls for improved predictions of
 how populations will evolve and respond demographically to ongoing
 environmental change. The heritability (h2) of selected traits has long
 been known to affect evolutionary and demographic responses to
 environmental change. However, effects of the genetic architecture
 underlying the h2 of a selected trait on population responses to selection
 are less well understood. We use deterministic models and stochastic
 simulations to show that the genetic architecture underlying h2 can
 dramatically affect population viability during environmental change.
 Polygenic trait architectures (many loci, each with a small phenotypic
 effect) conferred higher population viability than genetic architectures
 with the same initial h2 and large-effect loci under a wide range of
 scenarios. Population viability also depended strongly on the initial
 frequency of large-effect beneficial alleles, with moderately low initial
 allele frequencies conferring higher viability than rare or
 already-frequent large-effect alleles. Greater population viability
 associated with polygenic architectures appears to be due to higher short
 term evolutionary potential compared to architectures with large-effect
 loci. These results suggest that integrating information on the trait
 genetic architecture into quantitiative genetic analysis will
 substantially improve our understanding and prediction of evolutionary and
 demographic responses to environmental change.