cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2ngf1vhmw
title: DNA barcoding of native Caucasus herbal plants: potentials and limitations in complex groups and implications for phylogeographic patterns

description: DNA barcoding rapidly became a useful complementary tool in floristic
 investigations particularly for identifying specimens that lack diagnostic
 characters. Here we assess the capability of three DNA barcode markers
 (chloroplast rpoB, accD and nuclear ITS) in
 correctly species assignment in a floristic survey on Caucasus. We focused
 on two herbal groups with potential for ornamental applications, namely
 orchids and asterids. On these two plant groups we tested whether our
 selection of barcode markers allows identification of the “barcoding gap”
 in sequence identity and to distinguish between monophyletic species when
 employing distance-based methods. All markers successfully amplified most
 specimens, but we found that rate of species-level resolution among
 selected markers largely varied in the two plant groups. Overall, for both
 lineages, plastid markers had a species-level assignment success rate
 lower that nuclear ITS marker. The latter confirmed in orchids both the
 existence of a barcoding gap and that all accessions of same species
 clustered together in monophyletic groups. Further, it also allowed the
 detection of a phylogeographic signal. ITS marker resulted to be the best
 performing barcode for asterids; however, none of the three tested markers
 showed high discriminatory ability. Even if ITS revealed as the
 most promising plant barcode marker we argue that the ability of this
 barcode for species assignment is strongly dependent on the evolutionary
 history of the investigated plant lineage.
description: Generated sequences were aligned by using MUSCLE program in Mega
 X.
DOI: 10.15468/dl.5uy87v
title: Occurrence Download

description: A dataset containing 381925 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "TaxonKey is Piranga olivacea",
 "Year 2023-2025"
 ]
}

 The dataset includes 381925 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002723-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.gqnk98sm8
title: Castela senticosa (Simaroubaceae: Sapindales), a new species from the Caribbean clade endemic to seasonally dry tropical forest on Hispaniola

description: Recent fieldwork in the Sierra Martín García in southwestern Dominican
 Republic has yielded a new species of the American
 clade Castela (Simaroubaceae), Castela
 senticosa sp. nov., from seasonally dry tropical forest. This
 species has been collected from two separate localities, including Môle
 St. Nicolas in northwestern Haiti in 1929, but until now fertile material
 with both flowers and fruit was unknown. We provide a photographic plate
 and illustration, place it phylogenetically using plastome data, and
 compare it morphologically with close relatives. This increases the number
 of known species of Castela on Hispaniola from one to
 two, both of which are endemic but from different clades, and yields
 another species for the Greater Antilles, a known biodiversity hotspot and
 clear center of diversification for this group of arid-adapted, thorny
 shrubs. This work emphasizes that seasonally dry tropical forest, although
 often understudied, house as yet undiscovered biodiversity and deserve far
 more comprehensive studies.
description: This dataset was generated from genome skimming raw reads that
 were mapped to the <em>Ailanthus altissima</em> chloroplast
 genome (NC_037696.1) in Geneious. All raw reads were trimmed with an error
 probability limit of 0.05% before being mapped. A majority consensus
 sequence was then generated, one copy of the inverted repeat was trimmed
 (IRb), and the sequences were aligned in MAFFT yielding an alignment of
 139,323 bp, including gaps.
DOI: 10.5061/dryad.q573n5thg
title: Combined secondary compounds naturally found in nectars enhance honeybee cognition and survival

description: The alkaloid caffeine and the amino acid arginine are present as secondary
 compounds in nectars of some flower species visited by pollinators. Each
 of these compounds affects honeybee appetitive behaviors by improving its
 foraging activity and learning. While caffeine potentiates responses of
 mushroom body neurons involved in honeybee learning processes, arginine
 acts as precursor of nitric oxide enhancing the protein synthesis involved
 in memory formation. Despite existing evidence on how these compounds
 affect honeybee cognitive abilities individually, the effect of their
 mixtures on this matter is still unknown. We evaluated acquisition and
 memory retention in classical olfactory conditioning procedure, in which
 reward (sucrose solution) contained traces of caffeine, arginine or
 mixtures of both. The results indicate that the presence of the single
 compounds and their most concentrated mixture increases bees’ learning
 performance. However, memory retention, measured at short- and long-term,
 increases significantly only in those treatments offering mixtures in the
 reward. Additionally, the most concentrated mixture triggers a significant
 survival rate in the conditioned bees. Thus, some nectar compounds, when
 combined, show synergistic effects on cognitive abilities and survival in
 an insect.
DOI: 10.5061/dryad.t4b8gtj16
title: Variation of foliar silicon concentrations in temperate forbs: effects of soil silicon, phylogeny and habitat

description: Silicon (Si) accumulation is known to alleviate various biotic and abiotic
 stressors in plants with potential ecological consequences. However, for
 dicotyledonous plants our understanding of Si variation remains limited.
 We conducted a comparative experimental study to investigate (1)
 interspecific variation of foliar Si concentrations across 37
 dicotyledonous forbs of temperate grasslands, (2) intraspecific variation
 in foliar Si concentration in response to soil Si availability, the
 influence of (3) phylogenetic relatedness, and (4) habitat association to
 moisture. Foliar Si differed markedly (approx. 70-fold) across the
 investigated forbs, with some species exhibiting Si accumulation similar
 to grasses. Foliar Si increased with soil Si availability, but the
 response varied across species: species with higher Si accumulation
 capacity showed a stronger response, indicating that they did not actively
 upregulate Si uptake under low soil Si availability. Foliar Si showed a
 pronounced phylogenetic signal, i.e. closely related species exhibited
 more similar foliar Si concentrations than distantly related species.
 Significant differences in foliar Si concentration within closely related
 species pairs nevertheless support that active Si uptake and associated
 high Si concentrations has evolved multiple times in forbs. Foliar Si was
 not higher in species associated with drier habitats, implying that in
 dicotyledonous forbs of temperate grasslands high foliar inter- and
 intraspecific variation in foliar Si concentration in temperate forbs.
 This variation should have pervasive, but so far understudied, ecological
 consequences for community composition and functioning of temperate
 grasslands under land-use and climate change.
DOI: 10.5061/dryad.15dv41nwg
title: Genetic diversity in two insular populations of bobcats (Lynx rufus)

description: We documented changes in genetic diversity in an isolated, reintroduced
 population of bobcats on Cumberland Island (CUIS), Georgia, USA, compared
 to another bobcat population on Kiawah Island, South Carolina, USA, that
 was naturally established and experiences limited immigration from the
 mainland. We compared the predictions of a novel population viability
 analysis (PVA) to empirical estimates of abundance and genetic diversity
 on CUIS and used our PVA to identify management actions that are likely to
 support long-term viability.
description: Tissue samples and scats from bobcat were collected on Cumberland
 Island, Georgia, USA and Kiawah Island, South Carolina, USA to obtain DNA.
 The DNA samples were used to investigate inbreeding, genetic diversity,
 immigration rates, abundance, and survival rates. A
 population viability analysis was conducted using program VORTEX (version
 10.0.7.0; Lacy and Pollak 2014). Full description of
 methods are provided in: Miller-Butterworth, C. M., D.
 R. Diefenbach, J. E. Edson, L. A. Hansen, J. D. Jordan, T. M. Gingery, and
 A. L. Russell. 2021. Demography and loss of genetic diversity in two
 insular populations of the bobcat (<i>Lynx rufus</i>). Global
 Ecology and Conservation. Literature Cited
 Lacy, R.C., and J.P. Pollak. 2020. Vortex: A stochastic
 simulation of the extinction process. Version 10.3.8. Chicago Zoological
 Society, Brookfield, Illinois, USA.
description: 1. Filename = Bobcats_KW_SC.txt An IMa2 input
 file of 13 biallelic microsatellite loci from individuals from Kiawah
 Island, South Carolina, USA and individuals from mainland South Carolina.
 Allele fragment sizes were converted to numbers of repeats by designating
 the smallest detected fragment size as being equivalent to, arbitrarily,
 10 repeats. 2. Filename = Bobcats_CUIS.txt
 An IMa2 input file of 13 biallelic microsatellite loci from
 founder and current individuals from Cumberland Island, Georgia, USA.
 Allele fragment sizes were converted to numbers of repeats by designating
 the smallest detected fragment size as being equivalent to, arbitrarily,
 10 repeats. 3. Filename =
 Bobcat_alleles_Dryad.txt Fragment sizes of alleles
 amplified from 14 microsatellite loci. Data are presented as biallelic
 genotypes for each bobcat individual, at each locus. Bobcats are
 identified by sampling location, as
 follows:                                                  
 FOUNDER = Founder Cumberland Island (CUIS) bobcats and first
 generation of kittens born on CUIS KW = Kiawah Island
 bobcats SC = South Carolina Mainland bobcats
 CUIS = current population of bobcats on CUIS (sampled in
 2012,2016, 2018, and 2019) 4. Filename =
 Bobcat.xml This is the .xml input file for program
 VORTEX (version 10.0.7.9) that contains all PVA scenarios presented in
 Miller-Butterworth et al. (2021). 5. Filename =
 Founders.allelefreq_Vortex.txt A text file contain the
 allele frequencies of the founder population of bobcats called by program
 VORTEX from the project file "Bobcat.xml"
DOI: 10.5061/dryad.brv15dv8f
title: Behavioural variation among workers promotes feed-forward loops in a simulated insect colony

description: Coordinated responses in eusocial insect colonies arise from worker
 interaction networks that enable collective processing of ecologically
 relevant information. Previous studies have detected a structural motif in
 these networks known as the feed-forward loop, which functions to process
 information in other biological regulatory networks (e.g., transcriptional
 networks). However, the processes that generate feed-forward loops among
 workers and the consequences for information flow within the colony remain
 largely unexplored. We constructed an agent-based model to investigate how
 individual variation in activity and movement shaped production of
 feed-forward loops in a simulated insect colony. We hypothesised that
 individual variation along these axes would generate feed-forward loops by
 driving variation in interaction frequency among workers. We found that
 among-individual variation in activity drove overrepresentation of
 feed-forward loops in the interaction networks by determining the
 directionality of interactions. However, despite previous work linking
 feed-forward loops with efficient information transfer, activity variation
 did not promote faster or more efficient information flow, thus providing
 no support for the hypothesis that feed-forward loops reflect selection
 for enhanced collective functioning. Conversely, individual variation in
 movement trajectory, despite playing no role in generating feed-forward
 loops, promoted fast and efficient information flow by linking together
 unconnected regions of the nest.
description: Data was collected using the Netlogo agent-based simulation
 available from the Zenodo software repository: https://doi.org/10.5281/zenodo.5931784 Using this model, we examined how among-individual variations in activity and turning indices influenced the production of feed-forward loops within the population social network. This dataset includes all the data and R code required to reproduce our analysis and figures. Full details on the analysis can be found in the manuscript. 
description: The agent-based model can be downloaded from the Zenodo software
 repository: https://doi.org/10.5281/zenodo.5931784 Please refer to README file for usage information and additional details.
DOI: 10.5061/dryad.z08kprrbr
title: Sex differences in laterality are associated with reproduction in three-spine stickleback

description: Laterality, the partitioning of information processing into specific brain
 hemispheres, is widespread across animal taxa. Substantial unexplained
 variation in this trait exists, particularly between the sexes, despite
 multiple identified advantages of lateralisation. Here, we demonstrate a
 relationship between laterality (measured as directional biases),
 reproduction and experience of mating and parenting. Using three-spine
 sticklebacks Gasterosteus aculeatus, a species with uniparental male care,
 we showed that individuals of the caring sex (males) were more strongly
 lateralised than the non-caring sex (females) during reproduction, and
 that laterality was reduced outside the breeding season in males.
 Additionally, males with experience of mating and parenting were more
 strongly lateralised than males without this experience. Our findings
 suggest that fitness related behaviours that vary between the sexes, such
 as reproductive behaviours including courtship, spawning and parenting,
 are significant but previously unidentified sources of variation in
 laterality.
description: ID: Unique individual ID used to account for repeated
 measures. Sex: Sex of the fish (male or
 female). Stage: Stage of reproduction. This describes
 what reproductive behaviours individuals fish had performed when each
 measurement was taken.  Right turns: Number of turns to
 the right side out of a total of 10 in a standard detour test.
 Left turns: Number of turns to the left side out of a total of 10
 in a standard detour test. Relative laterality index:
 Relative laterality index, L<sub>R</sub>, is calculated as
 [(right detours – left detours) / (right detours + left detours) x 100]
 and assesses directional biases of fish at the population level.
 L<sub>R</sub> ranges from -100 to +100, representing a
 population that detoured consistently leftward or rightward
 respectively. Absolute laterality index: Absolute
 laterality index, L<sub>A</sub>, is calculated as
 |L<sub>R</sub>| and assesses the strength of laterality at the
 individual level. L<sub>A</sub> ranges from 0, individuals
 that turned left and right an equal number of times, to 100, individuals
 that turned consistently in one direction.  Detours:
 Total number of detours in a single trial (10). Notes:
 Any additional notes for individual fish e.g. deaths etc. 
 Treatment: Describes whether fish were in the treatment group
 (reproductive breeding males) or control treatment (non-breeding
 males).  Order: The order in which repeated measures
 occured for each individual. Body size: Standard length
 of each individual (cm).
DOI: 10.5061/dryad.6hdr7sr01
title: Data from: Interspecific variation in post-disturbance growth responses of a savanna tree community and its implications for escaping the fire trap

description: Vegetation states in savannas are highly sensitive to tree growth rates,
 which determine whether individual trees can ‘escape’ periodic
 disturbances. Resprouting trees have lopsided shoot:root ratios and are
 often multi-stemmed, and these variables can modify post-disturbance
 growth rates and therefore the probability of escape. To date, few studies
 have systematically examined the implications of interspecific variation
 in these factors for escape. We conducted a two-year field experiment in
 lowveld savanna in South Africa and quantified post-disturbance growth
 characteristics of topkilled trees among 16 species. We examined the
 dependence of growth on pre-disturbance stem size across species, and the
 relationship between growth rates and the tendency of trees to produce a
 few large vs. many small resprouts following disturbance. We found that
 resprout growth was strongly influenced by pre-disturbance size, but the
 relationship did not vary among species. In contrast, our results showed
 that fast-growing species tend to allocate resources towards a few
 dominant stems, while slow-growing species allocated new biomass towards
 many smaller stems. Tree species that produced a few large stems also
 tended to produce individual stems that were tall and thin, further
 suggesting that the “few large vs. many small” axis is linked to intrinsic
 species attributes. These findings have implications for understanding how
 interspecific variation in savanna tree communities may influence their
 ability to escape disturbance traps.
description: <strong>Tree data from the Wits Rural Facility in Limpopo,
 South Africa</strong> One file containing data
 for all trees in the study including GPS locations, heights, mean gap
 fractions, and initial and final stem diameters and stem counts.
 One README.txt file containing the associated metadata.
DOI: 10.5061/dryad.jsxksn087
title: Associations between metabolic traits and growth rate in brown trout (Salmo trutta) depend on thermal regime

description: Metabolism defines the energetic cost of life, yet we still know
 relatively little about why intraspecific variation in metabolic rate
 arises and persists. Spatiotemporal variation in selection potentially
 maintains differences, but relationships between metabolic traits
 (standard metabolic rate (SMR), maximum metabolic rate (MMR), and aerobic
 scope) and fitness across contexts are unresolved. We show that
 associations between SMR, MMR, and growth rate (a key fitness-related
 trait) vary depending on thermal regime (a potential selective agent) in
 offspring of wild-sampled brown trout from two populations reared for ~15
 months in either a cool or warm (+ 1.8°C) regime. SMR was
 positively related to growth in the cool, but negatively related in the
 warm regime. The opposite patterns were found for MMR and growth
 associations (positive in warm, negative in cool regime). Mean SMR, but
 not MMR, was lower in warm regimes within both populations (i.e., basal
 metabolic costs were reduced at higher temperatures), consistent with an
 adaptive acclimation response that optimises growth. Metabolic
 phenotypes thus exhibited a thermally sensitive metabolic ‘floor’
 and a less flexible metabolic ‘ceiling’. Our findings suggest a
 role for growth-related fluctuating selection in shaping patterns of
 metabolic variation that is likely important in adapting to climate
 change.
description: See associated README.txt file for detailed overview on datasets,
 including variables and allowable values.
DOI: 10.5061/dryad.vhhmgqns3
title: Wing plasticity and associated gene expression varies across the pea aphid biotype complex

description: Developmental phenotypic plasticity is a widespread phenomenon that allows
 organisms to produce different adult phenotypes in response to different
 environments. Investigating the molecular mechanisms underlying plasticity
 has the potential to reveal the precise changes that lead to the evolution
 of plasticity as a phenotype. Here, we study wing plasticity in multiple
 host-plant adapted populations of pea aphids as a model for understanding
 adaptation to different environments within a single species. We describe
 the wing plasticity response of different ‘biotypes’ to a crowded
 environment and find differences within as well as among biotypes. We then
 use transcriptome profiling to compare a highly plastic pea aphid genotype
 to one that shows no plasticity and find that the latter exhibits no gene
 expression differences between environments. We conclude that the loss of
 plasticity has been accompanied by a loss of differential gene expression
 and therefore that genetic assimilation has occurred. Our gene expression
 results generalize previous studies that have shown a correlation between
 plasticity in morphology and gene expression.
description: Tab 1: Data associated with Figure 1. Aphid genotype and biotype
 are shown in the first two columns. The number of Unwinged and Winged
 aphids from each plant are shown in the third and fourth columns,
 respectively. Tab 2: Data associated with Figure 2.
 Genotype is shown in the first column (either 319 or 74). The Treatment
 (whether an aphid was exposed to solitary or crowded conditions) is shown
 in the second column. As above, the number of Unwinged and Winged aphids
 from each plant are shown in the third and fourth columns,
 respectively.
DOI: 10.5061/dryad.18931zcw9
title: NanoString nCounter copy number variation assay

description: The sex chromosomes often follow unusual evolutionary trajectories. In
 particular, the sex-limited Y and W chromosomes frequently exhibit a small
 but unusual gene content in numerous species, where many genes have
 undergone massive gene amplification. The reasons for this remain elusive
 with a number of recent studies implicating meiotic drive, sperm
 competition, genetic drift and gene conversion in the expansion of gene
 families. However, our understanding is primarily based on Y chromosome
 studies, and the W chromosome has been largely overlooked. Here, we
 conduct a comprehensive investigation into the abundance, variability, and
 evolution of ampliconic genes on the W both across and within avian
 species. We find a striking deficit of gene families on the duck W
 chromosome, as well as conservation in W-linked gene copy number across
 duck breeds, indicating that gene amplification may not be such a general
 feature of sex chromosome evolution as Y studies would initially suggest.
 Furthermore, we show that gene families have expanded independently in the
 duck and chicken. In particular, using contrasts between modern chicken
 and duck breeds selected for different female-specific selection regimes
 and their wild ancestors, we investigate the factors driving the expansion
 of HINTW, a prominent ampliconic gene family hypothesized to play a role
 in female reproduction and oogenesis. While we find that HINTW is
 ampliconic in both species, our results support a role of female-specific
 selection in driving gene amplification in the chicken but not the duck,
 challenging the assumption that HINTW is key for female fecundity across
 the avian phylogeny.
description: The NanoString nCounter assay was
 performed according to standard protocol. Briefly, at least 300ng of
 DNA per sample was fragmented via AluI digestion and then
 hybridized to the custom CNV CodeSet. Samples included three females and
 two males from each of the selectively bred chicken and duck breeds, and
 two female and two male samples from each of the modern ancestor breeds.
 Samples were distributed randomly over the CNV CodeSets to avoid batch
 effects. The nCounter
 Digital Analyzer was used to count and quantify signals of reporter
 probes. Data analysis was performed using the nSolver
 Analysis Software.