cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1vn0f13
title: Data from: miR-122, small RNA annealing and sequence mutations alter the predicted structure of the Hepatitis C virus 5′ UTR RNA to stabilize and promote viral RNA accumulation

description: Annealing of the liver-specific microRNA, miR-122, to the Hepatitis C
 virus (HCV) 5′ UTR is required for efficient virus replication. By using
 siRNAs to pressure escape mutations, 30 replication-competent HCV genomes
 having nucleotide changes in the conserved 5′ untranslated region (UTR)
 were identified. In silico analysis predicted that miR-122 annealing
 induces canonical HCV genomic 5′ UTR RNA folding, and mutant 5′ UTR
 sequences that promoted miR-122-independent HCV replication favored the
 formation of the canonical RNA structure, even in the absence of miR-122.
 Additionally, some mutant viruses adapted to use the siRNA as a
 miR-122-mimic. We further demonstrate that small RNAs that anneal with
 perfect complementarity to the 5′ UTR stabilize and promote HCV genome
 accumulation. Thus, HCV genome stabilization and life-cycle promotion does
 not require the specific annealing pattern demonstrated for miR-122 nor 5′
 end annealing or 3′ overhanging nucleotides. Replication promotion by
 perfect-match siRNAs was observed in Ago2 knockout cells revealing that
 other Ago isoforms can support HCV replication. At last, we present a
 model for miR-122 promotion of the HCV life cycle in which miRNA annealing
 to the 5′ UTR, in conjunction with any Ago isoform, modifies the 5′ UTR
 structure to stabilize the viral genome and promote HCV RNA accumulation.
description: Mutant Hepatitis C virus
 5' UTR sequences selected by siRNA induced mutagenesis by siRNAs that
 target the miR-122 binding region.This file contains raw
 sequence data of HCV 5' UTR cDNAs derived from siRNA knockdown
 pressured viruses. Infected cells were treated with virus targeting siRNAs
 to select for viruses having escape mutants that protect the virus from
 knockdown.siRNA selected HCV 5' UTR
 sequences.zip
DOI: 10.15468/dl.y2tppy
title: Occurrence Download

description: A dataset containing 12846 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "GadmGid is CHN.18.12_1",
 "OccurrenceStatus is Present",
 "Year 2000-2024"
 ]
}

 The dataset includes 12846 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000987-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2v0hj
title: Data from: The behavior and reproductive physiology of a solitary progressive provisioning vespid wasp: evidence for a solitary-cycle origin of reproductive castes

description: The emergence of queens and workers from solitary antecedents mark a major
 evolutionary transition in the history of life. The solitary progressive
 provisioning wasp Synagris cornuta, a member of the subfamily basal to
 eusocial vespid wasps (Eumeninae), alternates between behavioral states
 characterized as queen-like and worker-like. Akin to a queen in eusocial
 wasps, a S. cornuta female initiates construction of a cell into which she
 oviposits, and then, similar to a worker, she cares for the brood as it
 develops. The Ovarian Groundplan (OGP) hypothesis for caste origins
 predicts that these behavioral states are associated with cyclical changes
 in ovarian status, where females performing queen-like tasks have eggs and
 those performing worker-like tasks possess only small oocytes. Our
 findings show strong support for the OGP hypothesis: the ovaries of S.
 cornuta females undergo differential oogenesis depending on the behavioral
 phase: the largest oocyte in the ovaries of females building a cell
 progress faster compared to that of females attending brood. Yet contrary
 to the OGP hypothesis, neither juvenile hormone nor ecdysteroids are
 associated with the reproductive cycle. Finally, the cuticular hydrocarbon
 profile showed no link with ovarian status, suggesting that fertility
 signals evolved subsequent to the emergence of group living.
description: Hormones, ovaries and
 CHCsSelf explanatory data
 for hormone titers in hemolymph (radioimmunoassay for juvenile hormone and
 ecdysteroids), measurements of oocyte area for all females (using ImageJ)
 and the cuticular hydrocarbon proportions for all individuals in study.
 The latter data was log transformed for analyses in paper (see
 methods).Synagris_DATA.xlsx
DOI: 10.5061/dryad.s5j72
title: Data from: Divergent plant–soil feedbacks could alter future elevation ranges and ecosystem dynamics

description: Plant–soil feedbacks (PSF) are important interactions that may influence
 range dynamics in a changing world. What remains largely unknown is the
 generality of plant–soil biotic interactions across populations and the
 potential role of specific soil biota, both of which are key for
 understanding how PSF might change future communities and ecosystems. We
 combined landscape-level field observations and experimental soil
 treatments to test whether a dominant tree alters soil environments to
 impact its own performance and range shifts towards higher elevations. We
 show: (1) soil conditioning by trees varies with elevation, (2) soil biota
 relate to PSF, (3) under simulated conditions, biotic PSF constrain range
 shifts at lower elevations but allow for expansions at higher elevations,
 and (4) differences in soil conditioning predict feedback outcomes in
 specific range-shift scenarios. These results suggest that variable
 plant–soil biotic interactions may influence the migration and
 fragmentation of tree species, and that models incorporating soil
 parameters will more accurately predict future species distributions.
description: Soil_conditioning_dataData used to calculated soil conditioning effects.Biomass_growth_dataData used to analyze growth differences and calculate plant-soil feedback effects.
DOI: 10.5061/dryad.nb320
title: Data from: Long term on-farm participatory maize breeding by stratified mass selection retains molecular diversity while improving agronomic performance

description: Modern maize breeding programs gave rise to genetically uniform varieties
 that can affect maize's capacity to cope with increasing climate
 unpredictability. Maize populations, genetically more heterogeneous, can
 evolve and better adapt to a broader range of edaphic-climatic conditions.
 These populations usually suffer from low yields; it is therefore
 desirable to improve their agronomic performance while maintaining their
 valuable diversity levels. With this objective, a long-term participatory
 breeding/on-farm conservation program was established in Portugal. In this
 program maize populations were subject to stratified mass selection. The
 current work aims to estimate the effect of on-farm stratified mass
 selection on the agronomic performance, quality, and molecular diversity
 of two historical maize populations. Multi-location field trials,
 comparing the initial populations with the derived selection cycles,
 showed that this selection methodology led to agronomic improvement for
 one of the populations. The molecular diversity analysis, using
 microsatellites, revealed that overall genetic diversity in both
 populations was maintained throughout selection. The comparison of quality
 parameters between the initial populations and the derived selection
 cycles was done using kernel from a common garden experiment. This
 analysis showed that the majority of the quality traits evaluated
 progressed erratically over time. In conclusion, this breeding approach,
 through simple and low-cost methodologies, proved to be an alternative
 strategy for genetic resources’ on-farm conservation.
description: Agronomic and molecular
 data on two historical maize poulation across a long-term participatory
 breeding programANNEX I. Data on the
 agronomic performance of two historical maize populations, Amiúdo and
 Castro Verde, and their derived selection cycles from multi-location field
 trials. ANNEX II. Genotypic matrix of the alleles per individual plant,
 scored in base pairs. Thirty random individual plants from each cycle
 (initial populations and selection cycles) were genotyped with 20
 microsatellite markers.Annex data to
 49347782EVA-2017-122-OA.R1.xlsx
DOI: 10.5061/dryad.fm3j82j
title: Data from: Navigating infection risk during oviposition and cannibalistic foraging in a holometabolous insect

description: Deciding where to eat and raise offspring carries important fitness
 consequences for all animals, especially if foraging, feeding and
 reproduction increase pathogen exposure. In insects with complete
 metamorphosis, foraging mainly occurs during the larval stage, while
 oviposition decisions are made by adult females. Selection for infection
 avoidance behaviours may therefore be developmentally uncoupled. Using a
 combination of experimental infections and behavioral choice assays, we
 tested if Drosophila melanogaster fruit flies avoid infectious
 environments at distinct developmental stages. When given conspecific fly
 carcasses as a food source, larvae did not discriminate between carcasses
 that were clean or infected with the pathogenic Drosophila C Virus (DCV),
 even though cannibalism was a viable route of DCV transmission. When
 laying eggs, DCV-infected females did not discriminate between infectious
 and non-infectious carcasses. Healthy mothers however, laid more eggs near
 a clean rather than an infectious carcass. Avoidance during oviposition
 changed over time: after an initial oviposition period, healthy mothers
 stopped avoiding infectious carcasses. We attribute this to a trade-off
 between infection risk and reproduction. Laying eggs near potentially
 infectious carcasses was always preferred to sites containing only fly
 food. Our findings suggest infection avoidance contributes to how mothers
 provision their offspring and underline the need to consider infection
 avoidance behaviors at multiple life-stages.
description: Navigating Infection
 Risk DataData gathered from 2
 behavioral choice experiments on distinct developmental stages of
 Drosophila. Both experiments were conducted under laboratory conditions.
 Larvae were given the choice of cannibalising an infectious or
 non-infectious carcass and infected or healthy mated females were given
 the choice of laying eggs on 3 potential oviposition sites containing:
 food, food and a dead fly or food and a dead infected fly. Following these
 choice assays we measured the developmental and pathological consequences
 of these decisions, in the form of egg-to-adult viability and pathogen
 load.Navigating Infection Risk MS
 Data.xlsx
DOI: 10.5061/dryad.s3s7p
title: Data from: Variable drivers of primary versus secondary nesting: density-dependence and drought effects on greater sage-grouse

description: Organisms seek to maximize fitness by balancing reproductive allocations
 against mortality risk, given selection pressures inherent to the
 environment. However, environmental conditions are often dynamic and
 unpredictable, which complicates the ability to achieve such a balance,
 and may require reproductive adjustments depending on prevailing
 conditions. We evaluated the effects of density-dependent,
 density-independent (drought), and individual (age, body condition)
 factors on nesting decisions of female greater sage-grouse in the American
 Great Basin. We obtained relocations and recorded reproductive histories
 from 287 radio-marked females over a period of 10 yr, and applied these
 data to a multi-state model that estimated probabilities of initiating a
 first nest (primary nesting rate) or a second nest, given loss of a first
 (secondary nesting rate). This approach allowed us to evaluate the
 relative association between nesting rates and covariates while accounting
 for imperfect detection of nests. Sage-grouse primary and secondary
 nesting were influenced differently by density dependence and drought.
 Primary nesting was high and relatively constant among years despite
 variable drought conditions, but was negatively associated with population
 size (density dependence). Secondary nesting was lower and more variable
 compared to primary nesting, was similarly influenced by
 density-dependence, and was also sensitive to drought conditions. Females
 known to initiate second nests were in better body condition than females
 that only initiated first nests, and females of intermediate age had
 higher primary nesting rates, whereas secondary nesting was unaffected by
 age. Our results suggest that females were more flexible and responded
 more readily to changing conditions when allocating resources to second
 nests. These results are consistent with patterns that have been
 demonstrated for female allocation to clutch size in this system, and
 suggest that when conditions are poor second nests reflect a tipping point
 where reproductive costs (increased mortality) outweigh benefits
 (offspring reproductive value).
description: Multistate input file
 and body condition data - Blomberg et al.This text file contains
 the .inp file necessary to run our multi-state survival analysis in
 Program MARK, as well as body condition data for females as a comma
 separated file.Blomberg et al.
 Data.txt
DOI: 10.5061/dryad.q5v77
title: Data from: Shape variation in the least killifish: ecological associations of phenotypic variation and the effects of a common garden

description: Studies of the adaptive significance of variation among conspecific
 populations often focus on a single ecological factor. However, habitats
 rarely differ in only a single ecological factor, creating a challenge for
 identifying the relative importance of the various ecological factors that
 might be maintaining local adaptation. Here we investigate the ecological
 factors associated with male body shape variation among nine populations
 of the poeciliid fish, Heterandria formosa, from three distinct habitats
 and combine those results with a laboratory study of three of those
 populations to assess the contributions of genetic and environmental
 influences to shape variation. Field-collected animals varied principally
 in three ways: the orientation of the gonopodium, the intromittent organ;
 the degree of body depth and streamlining; and the shape of the tail
 musculature. Fish collected in the spring season were larger and had a
 more anteriorly positioned gonopodium than fish collected in autumn. Fish
 collected from lotic springs were larger and more streamlined than those
 collected from lentic ponds or tidal marshes. Some of the variation in
 male shape among populations within habitats was associated with
 population-level variation in species richness, adult density, vegetative
 cover, predation risk, and female standard length. Population-level
 differences among males in body size, position of the gonopodium, and
 shape of the tail musculature were maintained among males reared in a
 common environment. In contrast, population variation in the degree of
 streamlining was eliminated when males were reared in a common
 environment. These results illustrate the complicated construction of
 multivariate phenotypic variation and suggest that different agents of
 selection have acted on different components of shape.
description: EcoDataAllThis file contains mean morphometric variables for each population as well as mean female standard length and ecological variables.RelativeWarpsAnalysisRelative Warp Analysis data. Includes RW 1-10 and centroid size.F1 RWACommon garden RWA
DOI: 10.5061/dryad.nn831
title: Data from: How important is thermal history? Evidence for lasting effects of developmental temperature on upper thermal limits in Drosophila melanogaster

description: A common practice in thermal biology is to take individuals directly from
 the field and estimate a range of thermal traits. These estimates are then
 used in studies aiming to understand broad scale distributional patterns,
 understanding and predicting the evolution of phenotypic plasticity, and
 generating predictions for climate change risk. However, the use of
 field-caught individuals in such studies ignores the fact that many traits
 are phenotypically plastic and will be influenced by the thermal history
 of the focal individuals. The current study aims to determine the extent
 to which estimates of upper thermal limits (CTmax), a frequently used
 measure for climate change risk, are sensitive to developmental and adult
 acclimation temperatures and whether these two forms of plasticity are
 reversible. Examining a temperate and tropical population of Drosophila
 melanogaster we show that developmental acclimation has a larger and more
 lasting effect on CTmax than adult acclimation. We also find evidence for
 an interaction between developmental and adult acclimation, particularly
 when flies are acclimated for a longer period, and that these effects can
 be population specific. These results suggest that thermal history can
 have lasting effects on estimates of CTmax. In addition, we provide
 evidence that developmental and/or adult acclimation are unlikely to
 contribute to substantial shifts in CTmax and that acclimation capacity
 may be constrained at higher temperatures.
description: 5 day and 23 day
 acclimation data5 day and 23 day
 developmental and adult acclimation data.for
 dryad.xlsx
DOI: 10.5061/dryad.35j39r8
title: Data from: Evolution of patterned plumage as a sexual signal in estrildid finches

description: Colour patterns, such as bars or dots, that cover the body surface of
 animals are generally thought to play roles in signalling and camouflage.
 In birds, however, the macroscopic aspects of plumage colouration are less
 well understood, as past studies typically described plumage colourations
 by using spectrophotometric analyses. To provide insight into the
 evolution of plumage patterns as sexual signals, we characterised
 interspecific and intersexual variations in the plumage patterns of
 estrildid finches and tested their associations with other courtship
 signals and life-history traits using a comparative phylogenetic approach.
 Our results support the idea that plumage patterns in estrildids are
 favoured by sexual selection because large-sized conspicuous plumage
 patterns are possessed by species with an elaborate courtship dance. These
 plumage patterns may also play roles in social signalling because patterns
 are more conspicuous in species with intraspecific brood parasitism. We
 predict that pattern traits can be favoured by mate choice or intra-sexual
 competition when they can serve as honest indicators of individual
 condition. As our results are consistent between the sexes, we suggest
 that the same selective force is acting on the evolution of plumage
 patterns in males and females in parallel. Finally, we also found a
 trade-off between large size and vivid colour patterns, suggesting that
 too conspicuous patterns are costly, presumably because of the risk of
 catching the eyes of potential predators. Therefore, plumage patterns are
 also shaped by natural selection.
description: Plumage pattern
 characteristics of Estrildid finchesGeometric features of
 plumage patterns and PCA outcomes are shown for each sex of each
 species.PCA_MF.xlsx
DOI: 10.5061/dryad.3h7s9
title: Data from: Functional genotypes are associated with commensal Escherichia coli strain abundance within host individuals and populations

description: The selective pressures that determine genotype abundance and distribution
 frequently vary between ecological levels. Thus, it is often unclear
 whether the same functional genotypes will become abundant at different
 levels and how selection acting at these different scales are linked. In
 this study, we examined whether particular functional genotypes, defined
 by the presence or absence of 34 genes, of commensal E. coli strains were
 associated with within-host abundance and/or host population abundance in
 a wild population of 54 adult mountain brushtail possums (Trichosurus
 cunninghami). Our results revealed that there was a positive correlation
 between a strain’s relative abundance within individuals and the strain’s
 abundance in the host population. We also found that strain abundance at
 both ecological levels was predicted by the same group of functional genes
 (agn43, focH, micH47, iroN, ygiL, ompT, kspmT2 and K1) that had associated
 patterns of occurrence. We propose that direct selection on the same
 functional genes at both levels may in part be responsible for the
 observed correlation between the ecological levels. However, a potential
 link between abundance within the host and excretion rate may also
 contribute.
description: Strain
 DataColumns F-T indicate the
 presence or absence of each functional gene. Columns U-AB provide the
 coordinates of each strain on the axes of the correspondence analysis
 performed in the computer program TANAGRA on the strains functional
 genotypes.Data for
 DRYAD.xlsx
DOI: 10.5061/dryad.rg15p
title: Data from: Explaining large mitochondrial sequence differences within a population sample

description: Mitochondrial DNA sequence is frequently used to infer species'
 boundaries, as divergence is relatively rapid when populations are
 reproductively isolated. However, the shared history of a non-recombining
 gene naturally leads to correlation of pairwise differences, resulting in
 mtDNA clusters that might be mistaken for evidence of multiple species.
 There are four distinct processes that can explain high levels of mtDNA
 sequence difference within a single sample. Here, we examine one case in
 detail as an exemplar to distinguish among competing hypotheses. Within
 our sample of tree wētā (Hemideina crassidens; Orthoptera), we found
 multiple mtDNA haplotypes for a protein-coding region (cytb/ND1) that
 differed by a maximum of 7.9%. From sequencing the whole mitochondrial
 genome of two representative individuals, we found evidence of
 constraining selection. Heterozygotes were as common as expected under
 random mating at five nuclear loci. Morphological traits and nuclear
 markers did not resolve the mtDNA groupings of individuals. We concluded
 that the large differences found among our sample of mtDNA sequences were
 simply owing to a large population size over an extended period of time
 allowing an equilibrium between mutation and drift to retain a great deal
 of genetic diversity within a single species.
description: Cytb-ND_rangi_29specimensShort (519 bp) mtDNA sequences from a population sample of the tree weta Hemideina crassidens.Cytb-ND_rangi_29.phyPhenotype and genotypes for pop sample_nuclear markers_tableExcel table with two morphological traits and genotypes at five nuclear loci provided for 29 tree weta (Hemideina crassidens) collected from the same locationnuclear markers_table.xlsxHemideina_crassidens_mtDNAgenomes.fastaWhole mitochondrial genome sequences from two tree weta (Hemideina crassidens) representing two clades observed within a single population sample