cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1c59zw3wx
title: Data for the article: Coupling of leaf elemental traits with root fungal community composition reveals a plant resource acquisition strategy in a desert ecosystem

description: Purpose: Plant-associated microbes enhance nutrient access and stress
 tolerance of the host species, and therefore, are crucial for plant traits
 and resource strategies. However, the links between aboveground plant
 traits and belowground microbes related to plant resource strategies under
 stressful conditions remain poorly understood. Methods: We tested the
 relationships between leaf traits linked to water (carbon isotopic
 composition, δ13C) and nutrient use (elemental concentrations and
 stoichiometry) with microbial compositions in roots and rhizospheres of
 two dominant species (Artemisia ordosica and Leymus secalinus) in the Mu
 Us Desert, northern China. Results: L. secalinus exhibited higher Mg and
 Mn concentrations, N:P ratios, stoichiometric flexibility, and root
 fungi:bacteria ratios, but lower foliar K and Ca concentrations and δ13C
 values than A. ordosica. The leaf N:P of L. secalinus increased with the
 root fungi:bacteria ratios, whereas the leaf N:P of A. ordosica decreased
 with the root fungi:bacteria ratios. The plant elemental levels (P, N, K,
 Ca, Mn, and δ13C) of L. secalinus but not A. ordosica were significantly
 related to their root fungal composition. Additionally, the random forest
 model identified four key fungal families in predicting leaf elemental
 traits for both plant species. Conclusion: The results suggested tight
 coupling and coordination between leaf elemental traits and root microbial
 compositions (especially fungal communities) related to plant resource
 acquisition strategies. By regulating aboveground and belowground feedback
 loops through trait flexibility and root microbial compositions, the
 studied plant species can sustain their resource strategies under
 stressful environmental conditions.
description: Please see the README document
 ("README.md") and the accompanying published article: Qiao Y,
 Liu L, Miao C, Zhu G, Miao L, She W, Qin S, and Zhang Y. 2022. Coupling of
 leaf elemental traits with root fungal community composition reveals a
 plant resource acquisition strategy in a desert
 ecosystem. Plant and Soil. Accepted. DOI:
 10.1007/s11104-022-05777-8
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DOI: 10.5061/dryad.pg4f4qrrg
title: Data from: Nitrogen enrichment and warming shift community functional composition via distinct mechanisms: the role of intraspecific trait variability and species turnover

description: 1. Global change factors may shift community functional composition by
 driving species turnover (species occurrence and species relative
 abundance) and intraspecific trait variability. However, their relative
 contribution in determining the functional response of community to global
 change, especially nitrogen enrichment and warming, remains unclear. 2. We
 conducted a fully factorial field experiment in a Tibetan alpine meadow to
 examine responses of plant community functional composition to nitrogen
 enrichment and warming by quantifying seven plant functional traits in
 each plot. Using the sum of squares decomposition, we further disentangled
 the relative contribution of intraspecific trait variability and species
 turnover to changes in community functional composition. 3. We found that
 nitrogen enrichment caused a shift of plant community toward a more
 resource-acquisitive strategy, while warming resulted in a shift toward a
 more resource-conservative strategy. Plant intraspecific trait variability
 controls shifts in community functional composition in response to
 nitrogen enrichment, whereas species turnover (especially change in
 species relative abundance) mainly explains warming-induced shifts.
 Nitrogen enrichment and warming did not show significant interactive
 effects on plant functional composition. 4. These findings suggest that
 nitrogen enrichment and warming can alter community functional composition
 of alpine meadow through distinct mechanisms. Plant intraspecific trait
 variability confers functional resilience of Tibetan alpine meadows under
 nitrogen enrichment, but warming could induce significant turnover of
 species that pronouncedly impacts community functioning in this highland
 ecosystem.
DOI: 10.5061/dryad.9w0vt4bhb
title: Adaptive divergence generates distinct plastic responses in two closely related Senecio species

description: The evolution of plastic responses to external cues allows species to
 maintain fitness in response to the environmental variation they regularly
 experience. However, it remains unclear how plasticity evolves during
 adaptation. To test whether distinct patterns of plasticity are associated
 with adaptive divergence, we quantified plasticity for two closely related
 but ecologically divergent Sicilian daisy species (Senecio, Asteraceae).
 We sampled c.40 representative genotypes of each species from their native
 range on Mt Etna and then reciprocally transplanted multiple clones of
 each genotype into four field sites along an elevational gradient that
 included the native elevational range of each species, and two
 intermediate elevations. At each elevation we quantified survival and
 measured leaf traits that included investment (specific leaf area),
 morphology, chlorophyll fluorescence, pigment content and gene expression.
 Traits and differentially expressed genes that changed with elevation in
 one species often showed little change in the other species, or changed in
 the opposite direction. As evidence of adaptive divergence, both species
 performed better at their native site and better than the species from the
 other habitat. Adaptive divergence is therefore associated with the
 evolution of distinct plastic responses to environmental variation,
 despite these two species sharing a recent common ancestor.
description: To determine how two ecologically divergent Senecio species
 respond to an elevational gradient, we undertook field experiments and
 transplanted multiple clones of 20-40 genotypes of each species across an
 elevational gradient representing the native range of each species and two
 intermediate eleavations. We transplanted cuttings that allowed us to
 quantify the response of each genotype by measuring survival and leaf
 characteristics (pigment content and leaf morphology). We used the
 software Lamina to quantify leaf shape, and we used a Dualex instrument to
 quantify leaf pigments (chlorophyll and flavonols). In
 as separate laboratory experiment, we grew seeds of each species and
 tested whether they differed in physiological parameters that included
 intrinsic water use efficiency, pigment content of their leaves and their
 ability to regulate heat.
description: Missing values in the transplant data represent plants that died
 and therefore have survival data but no morphology data.
DOI: 10.5061/dryad.4j0zpc8d8
title: Wild zebra finches are attracted towards acoustic cues from conspecific social groups

description: Social information gathered by observing others often supplements personal
 information collected from direct interactions with the physical
 environment during decision making. Social information use may be
 particularly beneficial in harsh environments or if resources are
 distributed patchily, ephemeral and unpredictable, and hence difficult to
 locate. We experimentally tested the use of acoustic cues in wild zebra
 finches (Taeniopygia guttata) as they flew around their arid habitat as a
 way of locating conspecifics on the ground, and potentially accessing
 useful social information. Joining a conspecific group may reduce the
 predation risk, and if they are foraging may also improve foraging
 efficiency, as the distribution of zebra finch food (grass seed) is
 scattered and unpredictable in their natural habitat, the Australian arid
 zone. We conducted playback experiments along vegetated creek lines
 radiating out from an artificial dam where all birds in the population
 were coming for drinking water. We broadcast recordings of vocalizations
 from foraging conspecific groups to birds using these creek lines to move
 to or from the water into the wider habitat. Zebra finches were more
 likely to land near the loudspeaker when conspecific vocalizations were
 broadcast compared to white noise. Birds flying low and close to the
 loudspeaker were most likely to land. Our results indicate that zebra
 finches use acoustic cues of conspecifics as a source of social
 information for grouping decisions. Use of such information may also
 enhance foraging efficiency in environments with unpredictable and scarce
 foraging locations, and reduce predation risk for calling and responding
 individuals.
DOI: 10.25338/b8f93r
title: Cosumnes river floodplain fish outmigration cues

description: This dataset includes 6 data files used to create cumulative catch figures
 and bayseian models: fish catch data, environmental variables (flow,
 temperature, dissolved oxygen). They are structured as csv files. The
 models were all created with the file:
 cosumnes_floodplain_model_dataframe. The remaining 5 files were used to
 create the other figures in the paper (cummulative catch, temperature), as
 well as compiled into the model file. See the README file for more
 detailed information on each of the included files.
DOI: 10.5061/dryad.tmpg4f50v
title: Data from: Historical mitochondrial genome introgression confounds species delimitation—evidence from phylogenetic inference in the Odorrana grahami species complex

description: Species delimitation is essential to informing conservation policy and
 understanding ecological and evolutionary processes. Most of our recent
 gains in knowledge on animal diversity rely on morphological
 characteristics and mitochondrial (mt) DNA variation. Concordant results
 based on both have led to an unprecedented acceleration in the
 identification of new species and enriched the field of taxonomy. However,
 discordances are also found commonly between morphological and mtDNA
 evidence. This confounds species delimitation, especially when gene flow
 or mitochondrial genome introgression has occurred. Here we illustrate how
 mitochondrial genome introgression among species of the Odorrana grahami
 complex confounds species delimitation using the combined evidence of
 morphological characters, mitochondrial variation, and thousands of
 nuclear single nucleotide polymorphisms (SNPs) from
 genotyping-by-sequencing (GBS). Fifty-eight samples across the
 distribution of the O. grahami complex were included. The mtDNA
 matrilineal genealogy indicated two clades, with O. grahami and O.
 junlianensis clustered together. In contrast, all nuclear evidence
 including gene trees, species trees, and genetic structure analyses based
 on GBS data support three species with distinct genetic clusters. These
 three distinct genetic clusters also correspond to distinct morphological
 characters. They affirm the distinct taxonomic entities of both O. grahami
 and O. junlianensis, as well as a third clade distinct from either. Which
 species the third clade belongs to remains unclear and will require
 further testing. The nuclear genomic loci contradict the COI evidence,
 with indications of rampant historical mitochondrial genome introgression
 among the species of the O. grahami complex. These discordant signals
 previously confused species delimitation efforts in this group. Based on
 these findings, we recommend the integration of independent data,
 especially nuclear genomic evidence, in species delimitation so as to be
 robust against the pitfalls of mitochondrial introgression.
DOI: 10.5061/dryad.cc2fqz67g
title: Importance of maternal resources in pollen limitation studies with pollinator gradients: A case study with sunflower

description: Pollen limitation studies are scarce in entomophilous crops, as it can be
 very tedious to supplement plants with hand pollination at the relevant
 plant scale. To overcome this, recent studies have used pollinator
 gradients over several fields to assess whether crops were pollen-limited.
 But the plant maternal resources and thus the yield potential may vary
 between fields of the same crop. If these resources are not properly
 controlled, it may affect the conclusions of the study We investigated the
 relationship between yield, measured as seed number, seed mass, and seed
 oil content per head, and pollinator density in sunflower (Helianthus
 annuus L.) by using a gradient of pollinator densities set both across and
 within fields. We analysed the yield and the % of yield potential, the
 latter being assessed with pollen supplementations applied at the whole
 plant scale. We analysed the data both with and without random effects
 including year, cultivar, field, and sampling plot. We also compared the
 yields of open and pollen-supplemented sunflowers to sunflowers isolated
 under tulle bags to assess autonomous self-fertilization and
 self-production rates in each field. Without random effects included in
 models, yields increased with pollinator density but only up to 0.3 bees
 per head, implying pollen limitation only below this threshold, while with
 random effects included, the yields were marginally pollen-limited across
 the whole range of pollinator densities observed (P = 0.072 and 0.037).
 Yet, on the other hand, there was no relationship between bee density and
 % of yield potential (assessed with pollen supplementation treatments),
 with or without random effects included, implying no pollen limitation
 across the complete range of bee densities observed in our study (0.1-1
 bees per sunflower head). These last results are explained by variation in
 the yield potential between and within fields, and by the positive
 correlation found between yield potential and pollinator density. Insect
 pollination contributed on average to 53.7% and 42.8% of the seed number
 and mass per head, respectively, and also increased the seed oil content
 by 5.5% on average. Our study showed that plant maternal resources and
 random effects are crucial to consider when quantifying pollen limitation
 using pollinator gradients and yields. Pollinator gradients on a
 per-flower basis are a useful tool to identify target pollinator densities
 to maximise yields, but should be combined with pollen supplementation
 treatments at the relevant scale in order to correctly assess pollen
 limitation.
DOI: 10.5061/dryad.p8cz8w9s4
title: A chromosome-level genome assembly of Paracymoriza distinctalis (Lepidoptera: Crambidae: Acentropinae)

description: Paracymoriza distinctalis is a semi-aquatic lepidopteran insect, which is
 of great value for studying the differentiation of the Pyraloidea super
 family. However, the understanding of heredity, evolution, and functional
 genomics of P. distinctalis are limited by few genome-wide resources.
 Here, we applied PacBio sequencing and the chromosome capture technique to
 assemble the first P. distinctalis genome from a single female individual.
 The genome size is 1.2 Gb with 32 chromosomes and the N50 is 38.91 Mb.
 Approximately 576.37 Mb, accounting for 48.93% of the genome, was
 identified as repeats. The genome comprises 39,003 protein-coding genes,
 66.56% of which were functionally annotated. Comparative genomics analysis
 suggested that the common ancestor of P. distinctalis and Chilo
 suppressalis lived ~83.5 million years ago. This chromosome-level genome
 assembly work is not only conducive to the understanding of P.
 distinctalis, but also may promote the study of the genomes of other
 lepidopteran species.
DOI: 10.5061/dryad.qbzkh18jv
title: Data for collected samples and mating experiment of Acilius Japonicus

description: Previous studies have predicted that antagonistic intraspecific evolution
 of sexually dimorphic characters causing rapid speciation can be driven by
 demographic history and environmental variations. However, researchers
 have rarely examined this issue in the wild. Here, we examined
 intraspecific evolution of sexually dimorphic characters and its driving
 force by using a diving beetle, Acilius japonicus, which has very marked
 sexually dimorphic characters. Males with wider big suction cups could
 copulate with females with a higher success rate, whereas the mating
 durations of females with more hairs on their pronota were shorter.
 Females in a region with greater interpopulation genetic differentiation
 had more pronotal hairs. Considering that a previous study showed that
 less continuity among populations leads to a higher female cost of mating,
 this result suggests a greater female cost of mating in this region.
 Females at warmer sites also had more pronotal hairs. In light of the
 increase in O2 consumption in warmer water, our result suggests that more
 pronotal hairs in females at warmer sites have been maintained to prevent
 prolonged underwater mating at higher O2 demand. These findings suggest
 that demographic history and temperature can direct the evolution of
 sexually dimorphic characters related to sexual conflict in females.
DOI: 10.5061/dryad.hmgqnk9jp
title: Supplementary Data - The Paris Biota decapod (Arthropoda) fauna and the diversity of Triassic decapods

description: We describe here the early Spathian (Early Triassic) Paris Biota decapod
 fauna from the western USA basin. This fauna contains two taxa of
 Aegeridae (Dendobranchiata), namely Anisaeger longirostrus n. sp. and
 Aeger sp. that are the oldest known representatives of their family, thus
 extending its temporal range by 5 Myr back into the Early Triassic. This
 fauna also includes two representatives of Glypheida (Pleocyemata) with
 Litogaster turnbullensis Schram, 1971 and Pemphix krumenackeri n. sp.,
 comforting for the former, and extending for the latter, the temporal
 range of their respective superfamily back to the Early Triassic. Overall,
 the Paris Biota decapods are some of the oldest known representatives of
 Decapoda, filling in an important gap in the evolutionary history of this
 group, especially during the Triassic that marks the early diversification
 of this clade. Additionally, we overview and compile all known Triassic
 decapods, which leads to the revision of four species of Middle and Late
 Triassic Aegeridae, and to a revised family assignment of a Middle
 Triassic Glypheida. Based on this refined dataset, we also investigate
 decapod diversity throughout the Triassic. We show that the apparent
 increase in decapod taxonomic richness is probably driven by the
 heterogeneity of the fossil record and/or sampling effort, and that the
 decapod alpha diversity is actually relatively high as soon as the Early
 Triassic and remains rather stable throughout the Triassic.
DOI: 10.5061/dryad.x0k6djhmb
title: Delimiting the cryptic diversity and host preferences of Sycophila parasitoid wasps associated with oak galls using phylogenomic data

description: Cryptic species diversity is a major challenge for the species-rich
 community of parasitoids attacking oak gall wasps due to a high degree of
 sexual dimorphism, morphological plasticity, small size, and poorly known
 biology. As such, we know very little about the number of species present,
 nor the evolutionary forces responsible for generating this diversity. One
 hypothesis is that trait diversity in the gall wasps, including the
 morphology of the galls they induce, has evolved in response to selection
 imposed by the parasitoid community, with reciprocal selection driving
 diversification of the parasitoids. Using a rare, continental-scale data
 set of Sycophila parasitoid wasps reared from 44 species of cynipid galls
 from 18 species of oak across the US, we combined mitochondrial DNA
 barcodes, Ultraconserved Elements (UCEs), morphological, and natural
 history data to delimit putative species. Using these results, we generate
 the first large-scale assessment of ecological specialization and host
 association in this species-rich group, with implications for evolutionary
 ecology and biocontrol. We find most Sycophila target specific subsets of
 available cynipid host galls with similar morphologies, and
 generally attack larger galls. Our results suggest that parasitoid wasps
 such as Sycophila have adaptations allowing them to exploit particular
 host trait combinations, while hosts with contrasting traits are resistant
 to attack. These findings support the tritrophic niche concept for the
 structuring of plant-herbivore-parasitoid communities.
DOI: 10.5061/dryad.v9s4mw6xs
title: Telomere length correlates with physiological and behavioural responses of a long-lived seabird to an ecologically-relevant challenge

description: Determinants of individual variation in reallocation of limited resources
 towards self-maintenance versus reproduction are not well known. We tested
 the hypothesis that individual heterogeneity in long-term “somatic state”
 a) explains variation in endocrine and behavioural responses to
 environmental challenges, and b) is associated with variation in
 strategies for allocating to self-maintenance versus reproduction. We used
 relative telomere length as an indicator of somatic state and
 experimentally generated an abrupt short-term reduction of food
 availability (withdrawal of food supplementation) for free-living seabirds
 (Black-legged kittiwakes, Rissa tridactyla). Incubating male kittiwakes
 responded to withdrawal by increasing circulating corticosterone and
 losing more weight compared to continuously supplemented controls. Males
 with longer telomeres increased time in directed travel regardless of
 treatment, while experiencing smaller increases in corticosterone. Males
 with longer telomeres fledged more chicks in the control group and tended
 to be more likely to return regardless of treatment. This study supports
 the hypothesis that somatic state can explain variation in short-term
 physiological and behavioural responses to challenges, and longer-term
 consequences for fitness. Male kittiwakes with longer telomeres appear to
 have prioritized investment in self over investment in offspring under
 challenging conditions.
description: This data accompanies the paper "Telomere length correlates
 with physiological and behavioural responses of a long-lived seabird to an
 ecologically-relevant challenge" in Proceedings of the Royal Society
 of London, Series B (2022; open access). Details about data collection and
 analyses can be found in the methods; R code for analysis and figures is
 included as an electronic supplement. See accompanying ReadMe file
 associated with this dataset for more information.
description: All data were analyzed in R (Version 3.4.1). Code (including
 relevant packages/libraries) is included in the electronic supplemental
 material associated with the publication (open access). See associated
 "ReadMe" file.