cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3v6f25v
title: Data from: A homeotic shift late in development drives mimetic color variation in a bumble bee

description: Natural phenotypic radiations, with their high diversity and convergence,
 are well-suited for informing how genomic changes translate to natural
 phenotypic variation. New genomic tools enable discovery in such
 traditionally non-model systems. Here, we characterize the genomic basis
 of color pattern variation in bumble bees (Hymenoptera, Apidae, Bombus), a
 group that has undergone extensive convergence of setal color patterns as
 a result of Müllerian mimicry. In western North America, multiple species
 converge on local mimicry patterns through parallel shifts of
 mid-abdominal segments from red to black. Using genome-wide association we
 establish that a cis-regulatory locus between the abdominal
 fate-determining Hox genes, abd-A and Abd-B, controls the red-black color
 switch in a western species, Bombus melanopygus. Gene expression analysis
 reveals distinct shifts in Abd-B aligned with the duration of setal
 pigmentation at the pupal-adult transition. This results in atypical
 anterior Abd-B expression, a late developmental homeotic shift. Changing
 expression of Hox genes can have widespread effects given their important
 role across segmental phenotypes, however, the late timing reduces this
 pleiotropy, making Hox genes suitable targets. Analysis of this locus
 across mimics and relatives reveals that other species follow independent
 genetic routes to obtain the same phenotypes.
description: qPCR Raw
 DataqPCR_Data_final.xlsxDraft genome assemblies for B. melanopygus color formsdraft_genome_assemblies.zipSequence files used in mVISTA plotsequence_files_mVISTA.zipPopulation Genomics ScriptspopgenCodes.txtRaw Sanger Sequence FilesRawSangerSeqFiles.zipGenotyping Table from Sanger DataGenotyping_information_final.xlsxReference Sequence for mapping Sanger data.geneiousRefer Sequence for mapping Sanger data in geneious formatBombusRawVariants40.vcfRaw variant calls from all genomic samples in vcf formatplink.assoc.fisherAssoc file for GWAS analysis
DOI: 10.5061/dryad.b2g21j1
title: Data from: Parasite resource manipulation drives bimodal variation in infection duration

description: Over a billion people on earth are infected with helminth parasites and
 show remarkable variation in parasite burden and chronicity. These
 parasite distributions are captured well by classic statistics, such as
 the negative binomial distribution. But the within-host processes
 underlying this variation are not well understood. In this study, we
 explain variation in macroparasite infection outcomes on the basis of
 resource flows within hosts. Resource flows realize the interactions
 between parasites and host immunity and metabolism. When host metabolism
 is modulated by parasites, we find a positive feedback of parasites on
 their own resources. While this positive feedback results in parasites
 improving their resource availability at high burdens, giving rise to
 chronic infections, it also results in a threshold biomass required for
 parasites to establish in the host, giving rise to acute infections when
 biomass fails to clear the threshold. Our finding of chronic and acute
 outcomes in bistability contrasts with classic theory, yet is congruent
 with the variation in helminth burdens observed in human and wildlife
 populations.
description: Rewilding mouse study
 data - Figure ESM1Data from rewilding
 mouse study including parasite biomass, irreversible biomass, reversible
 biomass, induced immunity, and parasite load data.SF Feeding Experiment - Data
 for dryad.xlsx
DOI: 10.5061/dryad.833qr19
title: Data from: Evidence of stress imprinting with population-level differences in two moss species

description: Plants are often repeatedly exposed to stresses during their lives and
 have a mechanism called stress imprinting that provides ‘memories’ of
 stresses they experience and increases their ability to cope with later
 stresses. To test hypotheses that primed bryophytes can preserve their
 stress imprinting after 6 days of recovery and induce higher levels of
 osmolytes and ROS-scavenging activities upon later stress exposure, and
 there exist population-level differentiation in their desiccation
 defenses, we transplanted samples of two populations of each of two moss
 species, Hypnum plumaeforme and Pogonatum cirratum, in a nature reserve in
 southern China. After 16 months of acclimation, sets of each population
 were subjected to control, one-time desiccation stress, duplicated
 desiccation stress and cross-stress (low temperature stress followed by
 desiccation stress) treatments. Levels of oxidant enzymes, osmolytes and
 phytohormones in the samples were then determined. The desiccation stress
 generally led to increases in activities or contents of superoxide
 dismutase, guaiacol peroxidase, catalase, proline, soluble sugars, soluble
 proteins, and stress hormones including abscisic acid (ABA), jasmonates
 (JA) and salicylic acid (SA), with differences between both species and
 populations. After a 6-day recovery period, contents of phytohormones
 (including ABA, JA, SA and cytokinins) in stressed H. plumaeforme had
 substantially fallen towards control levels. The duplicated and
 cross-stress treatments generally led to further accumulation of proline,
 soluble sugars and soluble proteins, with further increases in activities
 of antioxidant enzymes in some cases. Furthermore, significant differences
 between allochthonous and native populations were found in contents of
 malondialdehyde and osmolytes, as well as antioxidant enzyme activities.
 Our results confirm the hypotheses, and highlight the importance of
 osmolytes in mosses’ stress responses.
description: Stress
 imprinting_dataData of ROS, osmolytes
 and phytohormones used in this manuscript
DOI: 10.5061/dryad.15nd8v3
title: Data from: Signatures of divergence, invasiveness and terrestralization revealed by four apple snail genomes

description: The family Ampullariidae includes both aquatic and amphibious apple
 snails. They are an emerging model for evolutionary studies due to the
 high diversity, ancient history and wide geographical distribution.
 Insight into drivers of ampullariid evolution is hampered, however, by the
 lack of genomic resources. Here we report the genomes of four ampullariids
 spanning the Old World (Lanistes nyassanus) and New World (Pomacea
 canaliculata, Pomacea maculata and Marisa cornuarietis) clades. The
 ampullariid genomes have conserved ancient bilaterial karyotype features
 and a novel Hox gene cluster rearrangement, making them valuable in
 comparative genomic studies. They have expanded gene families related to
 environmental sensing and cellulose digestion, which may have facilitated
 some ampullarids to become notorious invasive pests. In the amphibious
 Pomacea, novel acquision of an egg neurotoxin and a protein for making the
 calcareous eggshell may have been key adaptations enabling their
 transition from underwater to terrestrial egg deposition.
description: Marisa cornuarietis
 genome v2.0Assembled genome and
 annotation (GFF, transcripts and protein sequence)Marisa_cornuarietis_genome_v2.0.zipLanistes nyassanus genome_v1.0Assembled genome and annotation (GFF, transcripts and protein sequence)Lanistes_nyassanus_genome_v1.0.zipPomacea maculata genome_v1.0Assembled genome and annotation (GFF, transcripts and protein sequence)Pomacea_maculata_genome_v1.0.zipPomacea canaliculata genome_v1.5Assembled genome and annotation (GFF, transcripts and protein sequence)Pomacea_canaliculata_genome_v1.5.zip
DOI: 10.5281/zenodo.18391416
title: CHAQIRUVGA QADAR BOSHLANG'ICH TAYYORGARLIK FANIDAN SAF TAYYORGARLIGI MASHG'ULOTINI O'TISH USLUBI

description: Ushbu maqolada O‘zbekiston Respublikasi umumiy o‘rta, o‘rta maxsus va boshlang‘ich professional ta’lim muassasalarida, Temurbeklar maktablari, Yosh chegarachilar va Jaloliddin Manguberdi nomidagi harbiy- akademik litseylarida chaqiruvga qadar boshlang‘ich tayyorgarlik o‘qituvchilari tomonidan saf tayyorgarlik mashg‘ulotlarini orgatish uchun qolaniladigan usul va uslublar haqida ma’lumotlar yoritilgan.
DOI: 10.5281/zenodo.18391415
title: CHAQIRUVGA QADAR BOSHLANG'ICH TAYYORGARLIK FANIDAN SAF TAYYORGARLIGI MASHG'ULOTINI O'TISH USLUBI

description: Ushbu maqolada O‘zbekiston Respublikasi umumiy o‘rta, o‘rta maxsus va boshlang‘ich professional ta’lim muassasalarida, Temurbeklar maktablari, Yosh chegarachilar va Jaloliddin Manguberdi nomidagi harbiy- akademik litseylarida chaqiruvga qadar boshlang‘ich tayyorgarlik o‘qituvchilari tomonidan saf tayyorgarlik mashg‘ulotlarini orgatish uchun qolaniladigan usul va uslublar haqida ma’lumotlar yoritilgan.
DOI: 10.5061/dryad.h8k61kk
title: Data from: Children can control the expression of masculinity and femininity through the voice

description: Pre-pubertal boys and girls speak with acoustically different voices
 despite the absence of a clear anatomical dimorphism in the vocal
 apparatus, suggesting that a strong component of the expression of gender
 through the voice is behavioural. Initial evidence for this hypothesis was
 found in a previous study showing that they can alter their voice to sound
 like a boy or like a girl. However, whether children can spontaneously
 modulate these voice components within their own gender in order to vary
 the expression of their masculinity and femininity remained to be
 investigated. Here, seventy-two English-speaking children aged 6 to 10
 were asked to give voice to child characters varying in masculine and
 feminine stereo-typicality to investigate whether primary school children
 spontaneously adjust their voices sex-related cues in the voice –
 fundamental frequency (F0) and formant spacing (ΔF) – along gender
 stereotypical lines. Boys and girls masculinised their voice, by lowering
 F0 and ΔF, when impersonating stereotypically masculine child characters
 of the same sex. Girls and older boys also feminised their voice, by
 raising their F0 and ΔF, when impersonating stereotypically feminine
 same-sex child characters. These findings reveal that children have some
 knowledge of the sexually dimorphic acoustic cues underlying the
 expression of gender, and are capable of controlling them to modulate
 gender-related attributes, paving the way for the use of the voice as an
 implicit, objective measure of the development of gender stereotypes and
 behaviour.
description: S3 final dataset in
 repositoryData file for the
 acoustic analyses
DOI: 10.5061/dryad.200pk95
title: Data from: Density-dependent population dynamics of a high Arctic capital breeder, the barnacle goose

description: 1. Density regulation of the population growth rate occurs through
 negative feedbacks on underlying vital rates, in response to increasing
 population size. Here, we examine in a capital breeder how vital rates of
 different life history stages, their elasticities, and population growth
 rates are affected by changes in population size. 2. We developed an
 integrated population model for a local population of Svalbard barnacle
 geese, Branta leucopsis, using counts, reproductive data and
 individual-based mark-recapture data (1990-2017) to model age
 class-specific survival, reproduction and number of individuals. Based on
 these estimates, we quantified the changes in demographic structure and
 the effect of population size on age class-specific vital rates and
 elasticities, as well as the population growth rate. 3. Local density
 regulation at the breeding grounds acted to reduce population growth
 through negative effects on reproduction; however, population size could
 not explain substantial variation in survival rates, although there was
 some support for density-dependent first year survival. 4. With the use of
 prospective perturbation analysis of the density-dependent projection
 matrix, we show that the elasticities to different vital rates changed as
 population size increased. As population size approached carrying
 capacity, the influence of reproductive rates and early life-survival on
 the population growth rate were reduced, whereas the influence of adult
 survival increased. A retrospective perturbation analysis revealed that
 density dependence resulted in a positive contribution of reproductive
 rates, and a negative contribution of the numbers of individuals in the
 adult age class, to the realised population growth rate. 5. The patterns
 of density dependence in this population of barnacle geese were different
 from those recorded in income breeding birds, where density regulation
 mainly occurs through an effect on early life survival. This indicates
 that the population dynamics of capital breeders, such as the barnacle
 goose, are likely to be more reproduction-driven than is the case for
 income breeders.
description: Parameter estimates for
 DD regressions_JAEParameter estimates for
 fitting the density dependence regressions. Includes annual estimates of
 age-class specific survival (and sex-specific recapture rates),
 reproduction, population sizes and population growth rates. Survival,
 recapture and population growth rates are from t to
 t+1.datafordryad_JAE.xlsxIPM_script_JAER script for fitting the integrated population modelIPMscript_JAE_appendix7.txt
DOI: 10.5061/dryad.990m8h3
title: Data from: Symbolic representation of numerosity by honeybees (Apis mellifera): matching characters to small quantities

description: The assignment of a symbolic representation to a specific numerosity is a
 fundamental requirement for humans solving complex mathematical
 calculations used in diverse applications such as algebra, accounting,
 physics, and everyday commerce. Here we show that honeybees are able to
 learn to match a sign to a numerosity, or a numerosity to a sign and
 subsequently transfer this knowledge to novel numerosity stimuli changed
 in colour properties, shape, and configuration. While honeybees learnt the
 associations between two quantities (two; three) and two signs (N-shape;
 inverted T-shape), they failed at reversing their specific task of
 sign-to-numerosity-matching to numerosity-to-sign-matching and vice-versa
 (i.e. a honeybee that learnt to match a sign to a number of elements was
 not able to invert this learning to match the numerosity of elements to a
 sign). Thus, while bees could learn the association between a symbol and
 numerosity, it was linked to the specific task and bees could not
 spontaneously extrapolate the association to a novel, reversed task. Our
 study therefore reveals that the basic requirement for numerical symbolic
 representation can be fulfilled by an insect brain suggesting that the
 absence of its spontaneous emergence in animals is not due to cognitive
 limitation.
description: Training phase
 dataThe choice of each bee
 during each trial in the training phase.Learning_Phase.csvTesting phaseThe individual choice of each bee during each test.Test_Phase.csv
DOI: 10.5061/dryad.34n4t78
title: Data from: Pollen on stigmas of herbarium specimens: a window into the impacts of a century of environmental disturbance on pollen transfer

description: Pollination is necessary for plant reproduction, but often highly
 susceptible to disruption, e.g., by habitat fragmentation and climate
 change. Here, we evaluated on a century time scale pollination
 interactions for species in one of the historically most disturbed
 habitats on earth-- tropical dry forests of Hawai’i. We employed a novel
 method for acquiring a historical perspective on temporal change in
 pollination by characterizing pollen on stigmas of herbarium specimens
 from six remnant native species collected from 1909-2002. We determine
 whether temporal shifts occurred in 1) pollination quantity and quality,
 or 2) the composition of species interacting via pollen transfer. While
 pollen quantity remained constant, these remnant species interact with
 different species in modern times via pollen transfer than they did nearly
 100 years ago. Species which are resilient to long-term environmental
 change may also be the ones subject to changes in pollination
 interactions.
description: Herbarium stigma sample
 pollen countsPollen counts and
 identifications for each stigma sampled from an herbarium sheet from the
 Herbarium Pacificum (BISH) collection used in this
 publication.Johnsonetal_HerbariumSamplingData.xlsxPollen reference collection imagesImages of pollen morphospecies encountered during course of study. Most pollen species were identified and confirmed based on anther collections from the field, while other morphospecies were encountered on stigmas and identification attempts were made based on Selling 1947. See the accompanying uploaded excel document in this data package for proposed species identification, when available, for unknown morphospecies. All images are taken of acetoylized pollen grains at 400x magnification, using a compound light microscope, as described in the associated paper (Johnson et al. 2019).PollenRefImages.pdfCode_forPaperFiguresR code to recreate Figure 2 and 3 in this paper, and conduct underlying analyses. Relies on the Herbarium stigma sample pollen counts.xlsx data file.
DOI: 10.5061/dryad.ng3q1s0
title: Data from: Invasive species reduces parasite prevalence and neutralizes negative environmental effects on parasitism in a native mosquito

description: 1.Invasive species research often focuses on direct effects of invasion on
 native ecosystems and less so on complex effects such as those influencing
 host‐parasite interactions. However, invaders could have important effects
 on native host‐parasite dynamics. Where infectious stages are ubiquitous
 and native host‐pathogen specificity is strong, invasive less‐competent
 hosts may reduce the pool of infectious stages, effectively reducing
 native host‐parasite encounter rate. Alternatively, invasive species could
 alter transmission via changes in native species abundance. 2.Biotic and
 abiotic environmental factors can also impact disease dynamics by altering
 host or parasite condition. However, little is known about potential
 interactive effects of invasion and environmental context on native
 species disease dynamics. Moreover, experimental examinations of the
 mechanisms driving dilution effects are limited, but serve to provide
 tests of predictions leading to diversity‐disease relationships. 3.Using
 field and laboratory experiments, we tested competing hypotheses that an
 invasive species reduces the prevalence of a native parasite in its host
 by removing infectious propagules from the environment or by reducing
 native host abundance. In addition, we evaluated the role of detritus
 quantity as a resource base in mediating effects of the invasive species.
 4.Native parasite prevalence was reduced when the invasive species was
 present. Prevalence was also higher in high detritus habitats, although
 this effect was lost when the invasive species was present. The invasive
 species significantly reduced infectious propagules from the aquatic
 habitats. Presence of the invasive species had no effect on the native
 species abundance; thus, the reduction in parasitism was not due to
 changes in host density but through a reduction in infectious propagule
 encounters. 5.We conclude that an invasive species can facilitate a native
 species by reducing parasite prevalence via a dilution effect and that
 these effects can be modified by resource level. Reductions in parasitism
 may have ripple effects throughout the community, altering the strength of
 competitive interactions, predation rates, or coinfection with other
 pathogens. We advocate considering potential positive effects of invasive
 species on recipient communities, in addition to effects of invasions on
 host‐parasite interactions to gain a broader understanding of the complex
 consequences of invasion.
description: This file contains all
 data collected and used for this manuscript.Data for
 Dryad.xlsx
DOI: 10.5061/dryad.2bm34c2
title: Data from: Specialist foragers in forest bee communities are small, social or emerge early

description: 1. Individual pollinators that specialize on one plant species within a
 foraging bout transfer more conspecific and less heterospecific pollen,
 positively affecting plant reproduction. However, we know much less about
 pollinator specialization at the scale of a foraging bout compared to
 specialization at the species level. 2. In this study, we measured the
 diversity of pollen carried by individual bees foraging in forest plant
 communities in the mid-Atlantic United States. 3. We found that
 individuals frequently carried low-diversity pollen loads, suggesting that
 specialization at the scale of the foraging bout is common. Individuals of
 solitary bee species carried higher diversity pollen loads than did
 individuals of social bee species; the latter have been better studied
 with respect to foraging specialization, but account for a small minority
 of the world’s bee species. Bee body size was positively correlated with
 pollen load diversity and individuals of generalist (but not specialist)
 species carried increasingly diverse pollen loads as the season
 progressed, likely reflecting an increase in the diversity of flowers in
 bloom. Furthermore, the seasonal increase in pollen load diversity was
 stronger for bees visiting trees and shrubs than for bees visiting
 herbaceous plants. 4. Overall, our results showed that both species’
 traits and community-level patterns of flowering phenology are likely to
 be important determinants of individual-level interactions in
 plant-pollinator communities.
description: Forest bee pollen load
 diversityPollen load diversity,
 bee species, plant species and traits dataForestBeePollenLoads.csv
DOI: 10.5061/dryad.rr2vp6g
title: Data from: Invertebrate biodiversity in cold groundwater fissures in Iceland

description: Iceland has an abundance of fissures that are parallel to the Mid-Atlantic
 ridge where bedrock cracks as a result of continental rifting. Some
 fissures penetrate the aquifer and expose the groundwater within the
 bedrock, becoming springs. As such, groundwater fissures have uniform and
 constant physical and chemical environment but they can differ greatly in
 morphology. In addition, there is often great variation in depth within
 fissures and substrate types contrast between vertical rock wall and more
 heterogenous horizontal bottom. The variation in morphological environment
 may create dissimilar habitats with unique characteristics and/or
 influence distribution of resources. Our objective was to study
 macrozoobenthos communities in cold groundwater fissures in Iceland in
 relation to physical habitat by comparing invertebrate diversity and
 density both between fissures with different morphological characteristics
 as well as between substrate types and depths within fissures. Samples
 were collected in two fissures in SW Iceland, Silfra and Flosagjá.
 Assemblages were similar between fissures except for higher densities of
 cladocerans in Flosagjá fissure. Within fissures, there was significant
 difference in Shannon diversity between substrate types in Flosgjá and
 ostracods were found in significantly higher densities on bottom. The
 distribution of all other taxa groups was homogenous in both fissures
 regardless of depth gradient and substrate. Invertebrates were found to be
 living within and around a biofilm that covered the entire substrate.
 These biofilm mats are made from Cyanobacteria and benthic diatoms, which
 are successful under low light conditions and may minimize any effect of
 the heterogeneous habitat creating a uniform and suitable microhabitat for
 invertebrates regardless of depth and substrate type.
description: Ólafsdóttir_Inv.Biodiv.Icel.FisFile contains macrozoobenthos density data from four groundwater fissure in Iceland collected at various depths within fissures and identified to the lowest taxonomic level possible. Also included is information about the location of sampling sites.