cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4bk8312
title: Data from: Transcriptome analysis reveals nutrition‐ and age‐related patterns of gene expression in the fat body of pre‐overwintering bumble bee queens

description: Many diapausing insects undergo a nutrient storage period prior to their
 entry into diapause. Bumble bee queens diapause as adults in the winter
 preceding their spring nest initiation period. Before diapause, they
 sequester glycogen and lipids, which they metabolize during the
 overwintering period. We used RNA sequencing to examine how age and nectar
 diet (specifically, the concentration of sucrose in nectar) impact gene
 expression in the pre-overwintering bumble bee queen fat body, the
 “liver-like” organ in insects with broad functions related to nutrient
 storage and metabolism. We found that diet on its own, and in combination
 with age, impacts the expression of genes involved in detoxification. Age
 was also a strong driver of gene expression, especially at earlier ages
 (up to 3 days). In addition to these molecular correlates of diet and age,
 we also found a putative molecular signature of diapause entry or
 preparation in adult queens in the oldest age group (12 days) fed the most
 sucrose-rich diet, based on comparisons between our data set and another
 transcriptome data set from bumble bee queens. This transcriptomic pattern
 suggests that preparation for (or entry into) diapause might be in part
 mediated by nutritional state in bumble bee queens. Collectively, these
 findings show that there are molecular processes in the fat body that are
 responsive to sucrose levels in the diet and/or associated with
 age-related maturational changes. A better understanding of these
 processes may shed light on important aspects of bumble bee biology, such
 as queen responses to nutritional and other forms of stress, and the
 factors that regulate their entrance into diapause.
description: Readcounts Read counts table was generated
 using featureCount v1.5.0-p3 (Liao et al. 2014), wherein it determines the
 number of reads uniquely mapping to exons and summed at the gene level
 using gene features annotated in the B. impatiens OGSv1.0.
DOI: 10.5061/dryad.f0t7jd2
title: Data from: The intake pattern and feed preference of layer hens selected for high or low feed conversion ratio

description: Feed accounts for the greatest proportion of laying hen egg production
 costs and there is substantial variation in feed to egg conversion (FCR)
 efficiency between individual hens. Despite this understanding, there is a
 paucity of information regarding layer hen feeding behaviour, diet
 selection and its impact on feed efficiency. It was hypothesised that
 variation in feed to egg conversion efficiency between hens may be
 influenced by feeding behaviour. For this experiment, two 35- bird groups
 of ISA Brown layers were selected from 450 individually caged hens at
 25-30 weeks of age for either low feed conversion ratio FCR &lt; 1.8 ±
 0.02 (high feed efficiency (HFE))) or high FCR &gt;2.1 ± 0.02 (low
 feed efficiency (LFE)). For each of these 70 hens, intake of an ad-libitum
 mash diet at 2-minute time intervals, 24 h a day, for 7 days was
 determined alongside behavioural assessment and estimation of the
 selection of components of thethis mash. The group selected for HFE had a
 lower feed intake, similar egg mass and associated lower FCR when compared
 with the LFE group. Whilst feed intake patterns were similar between HFE
 and LFE hens, there was a distinct intake pattern for all layer hens with
 intake rate increasing from 0300 to 1700 h with a sharp decline to
 22002100 h. High feed efficiencyFE hens selected a diet with 25% more ash
 and 4% less gross energy than LFE hens. The LFE hens also spent more time
 eating with more walking events, but less time spent resting, drinking,
 preening and cage pecking events as compared with HFE hens. In summary,
 there was no contrasting diurnal pattern of feed consumption behaviour
 between the groups ranked on feed efficiency, howeverIn summary, high feed
 efficiency hens consumed less feed and selected a diet with greater ash
 content and lower gross energy as compared with LFE hens. Our work is now
 focused on individual hen diet selection from mash diets with an aim of
 formulating precision, targeted diets for greater feed efficiency.
description: PlosOne Clark et al
 Layer Hen FCRIntake, diet composition
 and behaviour dataPlosOne Clark et al
 Poultry.xlsx
DOI: 10.5061/dryad.j2k683s
title: Data from: Vocal divergence is concordant with genomic evidence for strong reproductive isolation in grasshopper mice (Onychomys)

description: Behavioral barriers to gene flow often evolve faster than intrinsic
 incompatibilities, and can eliminate the opportunity for hybridization
 between interfertile species. While acoustic signal divergence is a common
 driver of premating isolation in birds and insects, its contribution to
 speciation in mammals is less studied. Here we characterize the incidence
 of, and potential barriers to, hybridization among three closely related
 species of grasshopper mice (genus Onychomys). All three species use
 long-distance acoustic signals to attract and localize mates; O. arenicola
 and O. torridus are acoustically similar and morphologically cryptic
 whereas O. leucogaster is larger and acoustically distinct. We used
 genotyping-by-sequencing (GBS) to test for evidence of introgression in
 227 mice from allopatric and sympatric localities in the western United
 States and northern Mexico. We conducted laboratory mating trials for all
 species pairs to assess reproductive compatibility, and recorded
 vocalizations from O. arenicola and O. torridus in sympatry and allopatry
 to test for evidence of acoustic character displacement. Hybridization was
 rare in nature and, contrary to prior evidence for O. torridus/O.
 arenicola hybrids, only involved O. leucogaster and O. arenicola. In
 contrast, lab crosses between O. torridus
description: Onychomys
 genotypesZip file containing two
 data files with SNP genotypes from GBS and an Excel file with associated
 metadata and informationOnychomys_genotypes.zip
DOI: 10.5061/dryad.595c22m
title: Data from: Phylotranscriptomics resolves interspecific relationships and indicates multiple historical out-of-North America dispersals through the Bering Land Bridge for the genus Picea (Pinaceae)

description: A robust phylogeny is prerequisite to understand the evolution and
 biogeography of organisms. However, ancient and recent evolutionary
 radiations occurred in many plant lineages, which pose great challenges
 for phylogenetic analysis, especially for conifers characterized by large
 effective population sizes and long generation times. Picea is an
 important component of the dark coniferous forests in the Northern
 Hemisphere. Previous studies improved our understanding of its
 evolutionary history, but its interspecific relationships and
 biogeographic history remain largely unresolved. In the present study, we
 reconstructed a well-resolved phylogeny of Picea by comparative
 transcriptomic analysis based on a complete species sampling. The
 phylogenetic analysis, together with molecular dating and ancestral area
 reconstruction, further supports the North American origin hypothesis for
 Picea, and indicates that this genus experienced multiple out-of-North
 America dispersals by the Bering Land Bridge. We also found that spruces
 in the Japanese Archipelago have multiple origins, and P. morrisonicola
 from the Taiwan Island has a close relationship with species from the
 Qinghai-Tibetan Plateau and adjacent regions. Our study provides the first
 complete phylogeny of Picea at the genomic level, which is important for
 future studies of this genus.
description: 1141_AA_datasetsAA_TreesAA_Tree.zipAA_concatenation.fas1141OG-AA-dataset-FcC_supermatrix.fas1141_CDS_datasetsCDS_treeCDS_Tree.zipCDS_concatenation_data.fas1141OG-CDSdataset-FcC_supermatrix.fas1141_CDS12_datasetsCDS12_treeCDS12_Tree.zipCDS12_concatenation.fas1141OG-CDS12dataset-FcC_supermatrix.fasMolecular Clock result1141-CDS12-30YI-CIPRES-beast-treeannotator.tre
DOI: 10.5061/dryad.1cg2dq2
title: Data from: High-content imaging of unbiased chemical perturbations reveals that the phenotypic plasticity of the actin cytoskeleton is constrained

description: Although F-actin has a large number of binding partners and regulators,
 the number of phenotypic states available to the actin cytoskeleton is
 unknown. Here, we quantified 74 features defining F-actin and cellular
 morphology in &gt;25 million cells after treatment with a library of
 114,400 structurally diverse compounds. After reducing the dimensionality
 of these data, we found that only ~25 recurrent F-actin phenotypes
 emerged, each defined by distinct quantitative features that could be
 machine learned. We identified 2003 unknown compounds as inducers of
 actin-related phenotypes, including two that directly bind talin, a core
 regulator of integrin activity. Moreover, we observed that compounds with
 distinct molecular mechanisms could induce equivalent phenotypes and that
 initially divergent cellular responses could converge over time. These
 findings suggest a conceptual parallel between the actin cytoskeleton and
 gene regulatory networks; where the theoretical plasticity of interactions
 is nearly infinite, yet phenotypes observed in vivo are constrained into a
 limited subset of practicable configurations.
description: Bryce_et_al_Quantitative_Data
DOI: 10.5061/dryad.22c54m5
title: Data from: Mid-sized groups perform best in a collective decision task in sticklebacks

description: Numerous studies have reported functional improvements in collective
 behaviour with increasing group size, however the possibility that such
 improvements may saturate or even decline as group size continues to grow
 have seldom been tested experimentally. Here, we tested the ability of
 solitary three-spined sticklebacks and those in groups, ranging from 2 to
 29 fish, to leave an unfavourable patch of habitat. Our results replicate
 the findings of previous studies at low group sizes, with the fish
 initially showing a reduction in their latency to leave the unfavourable
 habitat as group size increased. As group size continued to increase,
 however, latency to leave the habitat increased, so that the functional
 relationship between group size and latency to depart was U-shaped. Our
 results suggest an optimum group size in this context of between 12 and 20
 fish. Underlying this group-level trend was a similar U-shaped
 relationship between group size and the first fish to leave the habitat,
 suggesting that at larger group sizes, social conformity to the behaviour
 of the majority can stifle the ability of fish to innovate - in this case,
 to induce a collective movement from the unfavourable habitat.
description:
DOI: 10.5061/dryad.g7j45sn
title: Data from: Effects of restoration on tree communities and carbon storage in rainforest fragments of the Western Ghats, India

description: Ecological restoration is a leading strategy for reversing biodiversity
 losses and enhancing terrestrial carbon sequestration in degraded tropical
 forests. There have been few comprehensive assessments of recovery
 following restoration in fragmented forest landscapes, and the efficacy of
 active versus passive (i.e., natural regeneration) restoration remains
 unclear. We examined 11 indicators of forest structure, tree diversity and
 composition (adult and sapling), and aboveground carbon storage in 25
 pairs of actively restored (AR; 7–15 yr after weed removal and
 mixed-native tree species planting) and naturally regenerating (NR) plots
 within degraded rainforest fragments, and in 17 less-disturbed benchmark
 (BM) rainforest plots in the Western Ghats, India. We assessed the effects
 of active restoration on the 11 indicators and tested the hypothesis that
 active restoration effects increase with isolation from contiguous and
 relatively intact rainforests. Active restoration significantly increased
 canopy cover, adult tree and sapling density, adult and sapling species
 density (overall and late successional), compositional similarity to
 benchmarks, and aboveground carbon storage, which recovered 14–82% toward
 BM targets relative to NR baselines. By contrast, tree height–diameter
 ratios and the proportion of native saplings did not recover consistently
 in actively restored forests. The effects of active restoration on canopy
 cover, species density (adult), late successional species density (adult
 and sapling), and species composition, but not carbon storage, increased
 with isolation across the fragmented landscape. Our findings show that
 active restoration can promote recovery of forest structure, composition,
 and carbon storage within 7–15 yr of restoration in degraded tropical
 rainforest fragments, although the benefits of active over passive
 restoration across fragmented landscapes would depend on indicator type
 and may increase with site isolation. These findings on early stages of
 recovery suggest that active restoration in ubiquitous fragmented
 landscapes of the tropics could complement passive restoration of degraded
 forests in less fragmented landscapes, and protection of intact forests,
 as a key strategy for conserving biodiversity and mitigating climate
 change.
description: Plot and traits data
 from restored rainforests, Anamalai Hills, IndiaPlot data on adult
 trees, seedlings and saplings from actively restored, naturally
 regenerating, and benchmark rainforests in the Anamalai Hills,
 IndiaOsuri
 et al_data_scripts.zip
DOI: 10.5281/zenodo.18393611
title: O'ZBEKISTON UMUMTA'LIM MAKTABLARIDA TA'LIM MENEJMENTI TIZIMINI TAKOMILLASHTIRISH: BOSHQARUV SAMARADORLIGI VA INNOVATSION YONDASHUVLAR

description: Mazkur maqolada O‘zbekiston umumta’lim maktablarida ta’lim menejmenti tizimini takomillashtirish masalalari boshqaruv samaradorligi va innovatsion yondashuvlar nuqtayi nazaridan tahlil qilinadi. Ta’limni boshqarishda strategik rejalashtirish, raqamli boshqaruv, maktab rahbarlarining menejerlik kompetensiyalarini rivojlantirish hamda xalqaro tajribadan foydalanish masalalari yoritiladi. Tadqiqotda normativ-huquqiy hujjatlar, rasmiy statistik ma’lumotlar va ilmiy manbalarga asoslanilgan.
DOI: 10.5061/dryad.q361k5p
title: Data from: Neotropical migratory and resident birds occurring in sympatry during winter have distinct haemosporidian parasite assemblages

description: Aim: We compared the parasite assemblages of over-wintering migratory
 birds and permanent residents on the wintering grounds. We determined
 whether parasite sharing between migratory and resident birds is
 influenced by host phylogenetic relatedness. We then inferred whether
 migratory birds transport haemosporidian parasite lineages between the
 breeding and wintering grounds. Location: Sierra de Bahoruco National
 Park, Dominican Republic, Hispaniola Taxa: Migratory and resident birds
 (primarily Aves: Passeriformes) and their haemosporidian parasites (order
 Haemosporida, Plasmodium, Haemoproteus and Parahaemoproteus). Methods: We
 used mist nets to capture birds in thorn scrub, broadleaf dry forests, and
 pine forests during midwinter. We used molecular methods to recognize
 haemosporidian parasites in blood samples, and genotyped infections based
 on the nucleotide differences in a region of the parasite cytochrome b
 gene. Results and Main Conclusion: We identified 505 infections by 32
 haemosporidian parasite lineages in 1780 blood samples from 37 resident
 species, and in 901 blood samples from 14 overwintering migratory species,
 over five years at the same sites. Infection prevalence varied among
 migratory species from zero to 13%, whereas infection prevalence among
 resident species ranged up to 77%. Host relatedness did not predict
 parasite assemblage similarity. We discuss four hypotheses for the rarity
 of haemosporidian infections in migratory birds during winter, and for the
 infrequency of parasite sharing between migratory and resident birds: 1)
 relative abundance and host preferences of dipteran vectors lower parasite
 transmission to migratory birds; 2) parasite lineages adapted to infect
 endemic Caribbean hosts are unable to infect migratory species; 3) the
 physiology of migratory birds after migration and during winter reduces
 parasite survival; and 4) infected individuals suffer more pronounced
 rates during migration. We highlight the link between host-parasite
 coevolution and the physiological adaptations associated with avian
 seasonal migration.
description: Haemosporidian Dominican
 Republic 2014-2017Band numbers, four code
 species ID and haemosporidian lineage detected in birds sampled in the
 Dominican Republic, 2014, 2015 and 2017.DR_dataavailability.csv
DOI: 10.5281/zenodo.18393610
title: O'ZBEKISTON UMUMTA'LIM MAKTABLARIDA TA'LIM MENEJMENTI TIZIMINI TAKOMILLASHTIRISH: BOSHQARUV SAMARADORLIGI VA INNOVATSION YONDASHUVLAR

description: Mazkur maqolada O‘zbekiston umumta’lim maktablarida ta’lim menejmenti tizimini takomillashtirish masalalari boshqaruv samaradorligi va innovatsion yondashuvlar nuqtayi nazaridan tahlil qilinadi. Ta’limni boshqarishda strategik rejalashtirish, raqamli boshqaruv, maktab rahbarlarining menejerlik kompetensiyalarini rivojlantirish hamda xalqaro tajribadan foydalanish masalalari yoritiladi. Tadqiqotda normativ-huquqiy hujjatlar, rasmiy statistik ma’lumotlar va ilmiy manbalarga asoslanilgan.
DOI: 10.5061/dryad.7034412
title: Data from: Effects of rhizoma peanut cultivars (Arachis glabrata Benth.) on the soil bacterial diversity and predicted function in nitrogen fixation

description: There is a growing awareness of the importance of soil microorganisms in
 agricultural management practices. Currently, much less is known about
 whether different crop cultivar has an effect on the taxonomic structure
 and diversity, and specific functions of soil bacterial communities. Here
 we examined the changes of the diversity and composition and
 enzyme-encoding nitrogenase genes in a long-term field experiment with
 seven different rhizoma peanut cultivars in southeastern USA, coupling
 high-throughput 16S rRNA gene sequencing and the sequence-based function
 prediction with Tax4Fun. Of the 32 phyla detected (Proteobacteria class),
 13 were dominant: Acidobacteria, Alphaproteobacteria, Actinobacteria,
 Betaproteobacteria, Bacteroidetes, Verrucomicrobia, Gammaproteobacteria,
 Deltaproteobacteria, Gemmatimonadetes, Firmicutes, Nitrospirae,
 Chloroflexi and Planctomycetes (relative abundance &gt;1%). We found
 no evidence that the diversity and composition of bacterial communities
 was significantly different among different cultivars, but the abundance
 of some dominant bacterial groups that have N-fixation potentials (at
 broad or fine taxonomic level) and predicted abundances of some
 enzyme-encoding nitrogenase genes showed significant across-cultivar
 differences. The nitrogenase genes were notably abundant in Florigraze and
 Latitude soils while remarkably lower in Arbook and UF_TITO soils when
 compared with other cultivars, indicating different nitrogen fixation
 potentials among different cultivars. The findings also suggest that the
 abundance of certain bacterial taxa and the specific function bacteria
 perform in ecosystems can have an inherent association. Our study is
 helpful to understand how microbiological responses and feedback to
 different plant genotypes through the variation in structure and function
 of their communities in the rhizosphere.
description: Bacterial 16s amplicons
 sequencing OTU TableTable
 S3.xlsxFunctional
 profilesFunctional profiles
 based on Tax4Fun.Table
 S4.xlsx
DOI: 10.5061/dryad.n8v4v6d
title: Data from: Adapterama II: universal amplicon sequencing on Illumina platforms (TaggiMatrix)

description: Next-generation sequencing (NGS) of amplicons is used in a wide variety of
 contexts. In many cases, NGS amplicon sequencing remains overly expensive
 and inflexible, with library preparation strategies relying upon the
 fusion of locus-specific primers to full-length adapter sequences with a
 single identifying sequence or ligating adapters onto PCR products. In
 Adapterama I, we presented universal stubs and primers to produce
 thousands of unique index combinations and a modifiable system for
 incorporating them into Illumina libraries. Here, we describe multiple
 ways to use the Adapterama system and other approaches for amplicon
 sequencing on Illumina instruments. In the variant we use most frequently
 for large-scale projects, we fuse partial adapter sequences (TruSeq or
 Nextera) onto the 5’ end of locus-specific PCR primers with
 variable-length tag sequences between the adapter and locus-specific
 sequences. These fusion primers can be used combinatorially to amplify
 samples within a 96-well plate (eight forward primers + 12 reverse primers
 yield 8 x 12 = 96 combinations), and the resulting amplicons can be
 pooled. The initial PCR products then serve as template for a second round
 of PCR with dual-indexed iTru or iNext primers (also used combinatorially)
 to make full-length libraries. The resulting quadruple-indexed amplicons
 have diversity at most base positions and can be pooled with any standard
 Illumina library for sequencing. The number of sequencing reads from the
 amplicon pools can be adjusted, facilitating deep sequencing when required
 or reducing sequencing costs per sample to an economically trivial amount
 when deep coverage is not needed. We demonstrate the utility and
 versatility of our approaches with results from six projects using
 different implementations of our protocols. Thus, we show that these
 methods facilitate amplicon library construction for Illumina instruments
 at reduced cost with increased flexibility. A simple web page to design
 fusion primers compatible with iTru primers is available at:
 http://baddna.uga.edu/tools-taggi.html. A fast and easy to use program to
 demultiplex amplicon pools with internal indexes is available at:
 https://github.com/lefeverde/Mr_Demuxy.
description: Bacterial_MetabarcodingMap file and sample information for the bacterial metabarcoding dataset from Adapterama IIKissing_Bug_Blood-MealAll necessary scripts for analyses and results from the kissing bug blood-meal characterization dataset from Adapterama IIPathogenic_Fungi_on_TreesAll necessary scripts for analyses and results from the pathogenic tree fungi dataset from Adapterama IISalamander_eDNA_MetabarcodingAll necessary scripts for analyses and results from the plethodontid salamander environmental DNA dataset from Adapterama IIDNA_MethylationAll necessary scripts for analyzing the DNA methylation dataset from Adapterama II.
DOI: 10.5061/dryad.42jb0t4
title: Data from: Behavioural laterality in foraging bottlenose dolphins (Tursiops truncatus)

description: Lateralized behaviour is found in humans and wide variety of other
 species. At a population level, lateralization of behaviour suggests
 hemispheric specialization may underlie this behaviour. As in other
 cetaceans, dolphins exhibit a strong right-side bias in foraging
 behaviour. Common bottlenose dolphins in The Bahamas utilise a foraging
 technique termed ‘crater feeding,’ in which they swim slowly along the
 ocean floor, scanning the substrate using echolocation, and then bury
 their rostrums into the sand to obtain prey. The bottlenose dolphins off
 Bimini, The Bahamas, frequently execute a sharp turn before burying their
 rostrums in the sand. Based on data collected from 2012 – 2018, we report
 a significant right-side (left turn) bias in these dolphins. Out of 709
 turns recorded from at least 27 different individuals, 99.44% (n = 705)
 were to the left (right side and right eye down) [z=3.275, p=0.001]. Only
 one individual turned right (left side and left eye down, 4/4 turns). We
 hypothesize that this right-side bias may be due in part to the possible
 laterization of echolocation production mechanisms, the dolphins’ use of
 the right set of phonic lips to produce echolocation clicks, and a right
 eye (left hemisphere) advantage in visual discrimination and visuospatial
 processing.
description: DataSet_BehaviouralLateralityBottlenose