cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6078/d13t3m
title: Diet sensitivity in field crickets

description: Animals adjust resource acquisition throughout life to meet changing
 physiological demands of growth, reproduction, activity, and somatic
 maintenance. Wing-polymorphic crickets invest in either dispersal or
 reproduction during early adulthood, providing a system in which to
 determine how variation in physiological demands, determined by sex and
 life history strategy, impact nutritional targets, plus the consequences
 of nutritionally imbalanced diets across life stages. We hypothesized that
 high demands of biosynthesis (especially oogenesis in females) drive
 elevated resource acquisition requirements and confer vulnerability to
 imbalanced diets. Nutrient targets and allocation into key tissues
 associated with life history investments were determined for juvenile and
 adult male and female field crickets (Gryllus lineaticeps)  when
 given a choice between two calorically equivalent but nutritionally
 imbalanced (protein- or carbohydrate-biased) artificial diets, or when
 restricted to one imbalanced diet. Flight muscle synthesis drove elevated
 general caloric requirements for juveniles investing in dispersal, but
 flight muscle quality was robust to imbalanced diets. Testes synthesis was
 not costly, and life history investments by males were insensitive to diet
 composition. In contrast, costs of ovarian synthesis drove elevated
 caloric and protein requirements for adult females. When constrained to a
 carbohydrate-biased diet, ovary synthesis was reduced in reproductive
 females, eliminating their advantage in early life fecundity over the
 dispersal morph. Our findings demonstrate that nutrient acquisition
 modulates dispersal-reproduction trade-offs in an age- and sex-specific
 manner. Declines in food quality will thus disproportionately affect
 specific cohorts, potentially driving demographic shifts and altering
 patterns of life history evolution.
DOI: 10.5061/dryad.j6q573ncw
title: Data for: Nectar-dwelling microbes of common tansy are attractive to its mosquito pollinator, Culex pipiens

description: There is widespread interkingdom signalling between insects and microbes.
 For example, microbes found in floral nectar may modify its nutritional
 composition and produce odorants that alter the floral odor bouquet which
 may attract insect pollinators. Mosquitoes consume nectar and can
 pollinate flowers. We identified microbes isolated from nectar of common
 tansy, Tanacetum vulgare , identified the microbial odorants, and tested
 their effect on attracting the common house mosquito, Culex pipiens .
 Results We collected 19 microbial isolates from T. vulgare nectar,
 representing at least 12 different taxa which we identified with 16S or
 26S rDNA sequencing as well as by biochemical and physiological tests.
 Three microorganisms, Lachancea thermotolerans, Micrococcus lactis ,
 Micrococcus luteus , were grown on culture medium and tested in bioassays.
 L. thermotolerans grown on nectar, malt extract agar, or in synthetic
 nectar broth significantly attracted C. pipiens females. The odorant
 profile produced by L. thermotolerans varied depending on the composition
 of the culture medium used. Surprisingly, all three microbes grown
 separately, but presented concurrently, attracted fewer C. pipiens females
 than L. thermotolerans by itself. Conclusions Floral nectar of T. vulgare
 contains various microbes whose odorants contribute to the odor profile of
 inflorescences. In addition, one of the microbes, the yeast L.
 thermotolerans, produced odorants that attract Cx. pipiens females. As the
 odor profile of L. thermotolerans varied with the composition of the
 culture medium, we hypothesize that microbe odorants inform
 nectar-foraging mosquitoes about the availability of certain
 macronutrients which, in turn, affect foraging decisions by mosquitoes.
DOI: 10.5061/dryad.5x69p8d26
title: Growth genes are implicated in the evolutionary divergence of sympatric piscivorous and insectivorous rainbow trout (Oncorhynchus mykiss)

description: Identifying ecologically significant phenotypic traits and the genomic
 mechanisms that underly them are crucial steps in understanding the traits
 associated with population divergence. We used genome-wide data to
 identify genomic regions associated with a key trait that distinguishes
 two ecotypes of rainbow trout (Oncorhynchus mykiss) – insectivores and
 piscivores – that coexist in Kootenay Lake, southeastern British Columbia,
 for the non-breeding portion of the year. "Gerrards" are
 large-bodied (breeding maturity at &gt;60cm) piscivores that spawn
 50km north of Kootenay Lake in the Lardeau River, in contrast to the
 insectivorous populations that are on average smaller in body size, mainly
 forage on aquatic insects, and spawn in tributaries immediately
 surrounding Kootenay Lake. We used pool-seq data covering 60 percent of
 the genome to assess the level of genomic divergence between ecotypes,
 test for genotype-phenotype associations, and identify loci that may play
 functional or selective roles in their divergence. Analysis of nearly
 seven million SNPs provided a genome-wide mean FST estimate of 0.18,
 indicating a high level of reproductive isolation between populations. The
 window-based FST analysis did not reveal “islands” of genomic
 differentiation; however, the window with highest FST estimate did include
 a gene associated with insulin secretion. Although we explored the use of
 the “Local score” approach to identify genomic outlier regions, this
 method was ultimately not used because simulations revealed a high false
 discovery rate (20 percent). Gene Ontology (GO) analysis identified
 several growth processes as enriched in genes occurring in the 200 most
 divergent genomic windows, indicating the importance of genetically-based
 growth and growth-related metabolic functions in the divergence of these
 ecotypes. In spite of their sympatric coexistence, a high degree of
 genomic differentiation separates the populations of piscivores and
 insectivores, indicating little to no contemporary genetic exchange
 between ecotypes. Our results further indicate that the large body
 piscivorous 27 phenotype is likely not due to one or a few loci of large
 effect, rather it may be controlled by several loci of small effect, thus
 highlighting the power of whole-genome low-coverage sequencing in
 phenotypic association studies.
description: Pool-seq data, 80 individuals were population, three
 populations.
description: Individuals are not barcoded, so sequence data per population
 represents a random sampling of individuals that were in the
 library.
DOI: 10.5061/dryad.zcrjdfn9s
title: Validating eDNA Measurements of the Richness and Abundance of Anurans at a Large Scale

description: In some situations, environmental DNA (eDNA) metabarcoding is a more
 accurate tool for measuring species richness of a taxon than
 conventional methods. Whether this tool can reliably estimate the
 abundance of a taxon remains unresolved. We examined the
 reliability of metabarcoding for measuring anuran diversity
 compared to a commonly used traditional line transect method (TLTM)
 through the replicate sampling of three visits across 71 waterbodies
 (ponds or reservoirs) in Liuheng, China. We also investigated the relative
 contributions of species-specific characteristics and the physiochemical
 properties of a waterbody on the relative read count across species and
 waterbodies. We found that eDNA metabarcoding had a higher detection
 probability for each of seven anuran species found in the sampling region
 than TLTM. Furthermore, the relative read count estimated by metabarcoding
 was positively correlated with the density or relative density of
 individuals identified with the TLTM across waterbodies for every
 species. Species-specific characteristics of anurans, such as density,
 relative density, body mass, biomass and relative biomass, accounted for
 substantial variations in the read count across species and waterbodies,
 while physiochemical factors, including pH, temperature, water volume,
 vegetation and elevation, had little effect on the read count. Our results
 based on robust sampling suggest that metabarcoding enables more reliable
 and efficient measurements of anuran occurrence
 at a large scale during a short-term survey (within 15 days) than
 that obtained by the TLTM, and offers an alternative tool for
 quantifications of anuran abundance. Density or biomass is better
 and more reliable indicator of anuran abundance associated with read count
 than relative density or relative biomass.
DOI: 10.5061/dryad.3xsj3txfr
title: The effects of resource subsidy duration in a detritus-based stream ecosystem: a mesocosm experiment

description: 1. Most resource subsidies are temporally variable, dynamically affecting
 the consumer populations, community structures, and ecosystem functions of
 recipient ecosystems. Temporally variable resource subsidies are
 characterized by the duration, magnitude, timing, and frequency of
 resource subsidy inputs. These different characteristics may have
 different mechanisms by which to affect recipient ecosystems. 2. Few
 studies have examined the duration of resource subsidy inputs on recipient
 ecosystems, although there exist previous studies focusing on magnitude,
 timing, and frequency. 3. We provide the first experimental test of the
 effects of subsidy duration on a stream ecosystem by using an outdoor
 mesocosm experiment, in which we directly manipulated the subsidy duration
 (pulsed vs. prolonged) of terrestrial invertebrate input into the
 mesocosm. 4. Given the same overall amount of terrestrial invertebrate
 subsidy were added, a prolonged subsidy allowed large-stage fish to
 effectively monopolize the subsidy over small-stage fish, which led
 small-stage fish to maintain their predation pressure on in-situ prey,
 i.e., benthic invertebrates. On the other hand, a pulsed subsidy allowed
 small-stage fish to increase their feeding rate of the subsidy and to
 become away from foraging in-situ prey. Consequently, weaker indirect
 positive effects on in-situ benthic prey and leaf breakdown rate were
 found with the prolonged versus pulsed subsidy. However, these indirect
 effects varied by the dominant benthic prey species, which differed in
 edibility for fish. Such predator-specific vulnerability of benthic prey
 can be important in mediating trophic cascades in detritus-based stream
 food webs. 5. Phenological events that generate temporal subsidies (e.g.,
 salmon spawning run and arthropod emergence) can be synchronized (pulsed)
 or desynchronized (prolonged) within and among species, depending on the
 degree of spatial and temporal environmental heterogeneity. The effects of
 subsidy duration would thus be important to better understand ecological
 processes in spatially and temporally coupled ecosystems.
description: All data were collected in the field mesocosm experiment that was
 done in this study.
description: All raw data are provided: Fish and fishcv
 files are for the all analyses related with fish growth, body size and its
 CV. Benthic file is for the analyses related with the
 abundance of benthic invertebrates. Litter file is for
 the analyses related with the leaf break-down rate. R
 codes were not included because all statistical analyses specified in the
 methods are originally implemented in R.
DOI: 10.5061/dryad.cjsxksn5b
title: Evolution of honey resistance in experimental populations of bacteria depends on the type of honey, and has no major side effects for antibiotic susceptibility

description: With rising antibiotic resistance, alternative treatments for communicable
 diseases are increasingly relevant. One possible alternative for some
 types of infections is honey, used in wound care since before 2000 BCE and
 more recently in licensed, medical-grade products. However, it is unclear
 whether medical application of honey results in the evolution of bacterial
 honey resistance, and whether this has collateral effects on other
 bacterial traits such as antibiotic resistance. Here, we used single-step
 screening assays and serial transfer at increasing concentrations to
 isolate honey-resistant mutants of Escherichia coli. We only
 detected bacteria with consistently increased resistance to the honey they
 evolved in with two of the four tested honey products, and the observed
 increases were small (maximum two-fold increase in IC90). Genomic
 sequencing and experiments with single-gene knockouts showed a key
 mechanism by which bacteria increased their honey resistance was by
 mutating genes involved in detoxifying methylglyoxal, which contributes to
 the antibacterial activity of Leptospermum honeys.
 Crucially, we found no evidence that honey adaptation conferred
 cross-resistance or collateral sensitivity against nine antibiotics from
 six different classes. These results reveal constraints on bacterial
 adaptation to different types of honey, improving our ability to predict
 downstream consequences of wider honey application in medicine.
description: See readme file.
DOI: 10.5061/dryad.g4f4qrfpp
title: A group of ectomycorrhizal fungi restricts organic matter accumulation in boreal forest

description: Boreal forest soils are important global carbon sinks, with significant
 storage in the organic topsoil. Decomposition of these stocks requires
 oxidative enzymes, uniquely produced by fungi. Across Swedish boreal
 forests, we found that local carbon storage in the organic topsoil was 33%
 lower in the presence of a group of closely related species of
 ectomycorrhizal fungi – Cortinarius acutus s.l.. This observation
 challenges the prevailing view that ectomycorrhizal fungi generally act to
 increase carbon storage in soils but supports the idea that certain
 ectomycorrhizal fungi can complement free-living decomposers, maintaining
 organic matter turnover, nutrient cycling and tree productivity under
 nutrient-poor conditions. The indication that a narrow group of fungi may
 exert a major influence on carbon cycling questions the prevailing dogma
 of functional redundancy among microbial decomposers. Cortinarius acutus
 s.l. responds negatively to stand-replacing disturbance, and associated
 population declines are likely to increase soil carbon sequestration while
 impeding long-term nutrient cycling.
DOI: 10.5061/dryad.80gb5mkqh
title: Evaluation of solid state of rice flours produced by different milling processes using ATR-FTIR spectroscopy

description: This study evaluated the influence of the milling process on solid state
 of rice flours according to water activity using ATR-FTIR. A band at 1740
 cm-1 attributed to the C=O stretching of lipids was detected for
 crystalline samples, and it disappeared at a high aw range. The CH band at
 2930 cm-1 of crystalline samples gradually shifted to a higher wavenumber
 with aw. This band of the α-formed and wet-milled samples shifted to
 higher wavenumbers above 0.8 aw. A band due to OH stretching mode in the
 3500–3000 cm-1 region did not shift with aw. The result obtained from IR
 spectra suggests that the parameter K calculated by Guggenheim–Anderson–de
 Boar (GAB) model reflected not only the interaction between water
 molecules but also the changes of state in solids. Consequently, the
 results from this study provide insights about the adsorption properties
 of non-ideal solids such as rice flour.
DOI: 10.5061/dryad.c2fqz6177
title: Primary ciliary dyskinesia multigene NGS diagnostic testing in Cyprus

description: The dataset describes the genetic diagnosis in the national PCD
 cohort of Cyprus, an island with a high disease prevalence. Targeted
 next-generation sequencing (NGS) of 39 known PCD genes was
 carried out in samples from 48 patients of Greek-Cypriot and other
 ancestries. Molecular diagnosis was achived in 74% of the unrelated
 families tested (68% of Greek-Cypriot and 90% of non-Greek-Cypriot origin
 respectively). A total of 24 different mutations in 11 genes, 12
 of which are novel were identified. These were categorized as
 nonsense (n= 9), splice-site (7), frameshift (n= 4), and missense (n= 3)
 mutations, and small deletions (n= 1). Homozygosity was more common in
 Greek-Cypriot than non-Greek-Cypriot patients (88% vs 46.2%, p =0.016).
 Four mutations (DNAH11:c.5095-2A&gt;G, CFAP300:c.95_103delGCCGGCTCC,
 TTC25:c.716G&gt;A, RSPH9: c.670+2T&gt;C,) were found in 74% of the
 diagnosed Greek-Cypriot families, usually appearing in homozygosity and
 regional clusters. Patients with RSPH9 mutations demonstrated higher nasal
 nitric oxide production (57nL/min Vs 15 nL/min, p &lt;0.001), higher
 FEV1 (-0.89 vs -2.37, p=0.018) and FVC (-1.00 vs -2.16, p=0.029) z-scores
 than the rest of the cohort. Targeted multigene-panel NGS diagnosis is an
 efficient single test for early diagnosis of PCD, providing insight to
 disease genetic epidemiology in isolated populations and improved patient
 stratification.
description: Diagnostic tests for PCD
 were performed as described previously (https://doi.org/10.1016/j.pupt.2017.10.010).  The performance of nNO measurement, HSVM and TEM evaluation were performed as described previously (Kouis et al., 2018). To discriminate abnormally low nNO, a cut-off of 77 nl/min was used (https://doi.org/10.1513/AnnalsATS.201305-110OC). HSVM analysis was performed and Ciliary Beat Frequency was quantified with the use of SAVA system. Ciliary Beat Pattern was determined with slow motion video playbacks (https://doi.org/10.1046/j.1365-2818.2003.01209.x). For classification of ciliary ultrastructure defects by TEM, the international consensus guideline for reporting transmission electron microscopy findings in the diagnosis of PCD (BEAT PCD TEM Criteria) was employed (Shoemark et al., 2020). Data on clinical manifestations were collected through a specific questionnaire and were routinely uploaded to the international PCD registry (DOI: 10.1183/13993003.00776-2015). Genetic screening of the known PCD-related genes was performed using a custom, targeted, 39-gene Next Generation Screening panel. Enrichment for the genomic regions of interest was performed using Agilent’s SureSelect<sup>QXT</sup> Target Enrichment System (Agilent Technologies, Santa Clara, CA, USA) following the manufacturer’s protocol. Libraries were sequenced on an Illumina MiSeq® platform following the manufacturer’s instructions. 
description: No specific instructions are required. No missing
 values. Please refer to the ReadMe files for the
 complete list of sequenced genes.
DOI: 10.5061/dryad.w3r2280pz
title: Rear-edge populations are important for understanding climate change risk and adaptation potential of threatened species

description: Climate change disproportionately threatens alpine species, by reducing
 available habitat and by isolating their populations. These pressures are
 particularly relevant for rear-edge populations, which typically occupy
 more marginal habitat compared to populations at the core of species’
 ranges. We studied Caucasian grouse Lyrurus mlokosiewiczi in the Caucasus
 ecoregion, a global biodiversity hotspot where this species is endemic, to
 understand potential climate change impacts on the species. Specifically,
 we assessed how climate change impacts rear-edge populations and how
 important these populations are for understanding range shifts and
 adaptive capacity under climate change. We used maximum entropy modelling
 to assess changes in the distribution of climatically-suitable habitat
 under present and 2070 climate conditions for the representative
 concentration pathways 8.5 (RCP8.5). Our results revealed that ignoring
 rear-edge populations leads to a significant underestimation of the future
 range (by about 14,700 km²). Rear-edge populations were better adapted to
 warmer climates compared to core populations, and ignoring them therefore
 also underestimates adaptive capacity. Preventing the loss of rear-edge
 populations should therefore be a priority for conservation planning in
 the face of climate change. Because the Caucasian grouse is associated
 with alpine mountain tops, conservation should focus on establishing
 connectivity between rear-edge and core populations (e.g., via
 transboundary corridors or assisted colonizations). Our study reveals how
 species distribution modelling can highlight the importance of rear-edge
 populations for mitigating climate change impacts on species of
 conservation concern.
description: Three datasets are provided: 1. A table of
 Caucasiain grouse (Lyrurus mlokosiewiczi) occurence locations used as
 input to the species dsitribution modelling
 (Caucasian-grouse-occurence-points.zip) 2. Maps of the
 current distribution of climatically-suitable areas for the Caucasian
 grouse using all occurence points for the full mode and core-population
 model (Current-habitat-distribution.zip) 3. A map of
 the future distribution of climatically-suitable areas for the Caucasian
 grouse using all occurence points for the full mode and core-population
 model (Future-habitat-distribution.zip) Distributional
 maps were generated using Maxent, with future conditions represented by
 bioclimateic variables derived for 2070 using the Representative
 Concentration Pathway (RCP) 8.5 scenario and the Community Climate System
 Model version 4 (CCSM4). Each ZIP-file contains a readme file with further
 detail. We refer to the methods section and supporting information of the
 paper for a full description of the data collection and processing
 methods.
DOI: 10.5061/dryad.7pvmcvdrz
title: Areas of endemism of selected seed plants in southcentral/southwestern USA

description: Areas of endemism (AEs) are fundamental entities of analysis in
 biogeography and a key step for biogeographical regionalization. Even
 though many studies have contributed to the biogeographical knowledge of
 southern USA flora, no endemicity analysis (EA) has been conducted that
 would include a large number of native seed plant species from different
 families. A new analysis of plant spatial patterns is important as a first
 step for a future updated floristic regionalization of North America North
 of Mexico. It has become easier to accomplish owing to the increased
 availability of large-scale digitized distributional data and statistical
 methods of biogeographic analysis. Here we identify the AEs in SC/SW USA
 using digitized plant specimen data available from IDigBio. We built a
 database with 81,851-specimen point records of 400 selected mostly
 angiosperm species and applied the NDM/VNDM method of endemicity analysis.
 We then compare the established 26 AEs in the area of study with the
 floristic provinces in two comparatively recent regionalization systems of
 USA. To understand the spatial patterns, we pay some attention to the
 information on relationships of the endemic species found in phylogenetic
 literature.
description: Digitized herbarium data were downloaded from the Integrated
 Digitized Biocollections (iDigBio accessed January –April 2020), cleaned
 to eliminate duplicates and other erroneous records, and contrasted with
 those documented by the Biota of North America Project (BONAP;
 https://bonap.org, accessed April–May 2020), online databases (EOL: https://eol.org/), and literature (Turner at al., 2003; FNA).