cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.72s5r1t
title: Data from: Older males are not only attractive to but also aggressive toward females in Gnatocerus cornutus

description: In theory, a male should change the allocation of fighting and mating
 efforts in relation to his age. Thus, the consequences of sexual selection
 may be complicated by changes in the male resource allocation due to
 aging. However, previous studies have focused on changes in female mate
 choice and male-male competition with aging separately, and the impact of
 aging on the relationship between mate choice and male competition is
 unknown. Here, we examined how male competitiveness and attractiveness and
 their relationship changes over male lifespan in Gnatocerus cornutus. In
 this species, males perform courtship displays and fight rival males for
 mates. Older males are more competitive in male fighting and aggressive
 toward females than younger males. The aggression is also directed toward
 females. Almost all older males who attacked a female failed to copulate,
 while younger males never attacked the females. As a result, copulation
 success decreased with age. When an older male did not mistake a female
 for a male, he exhibited more frequent courtship. However, mating with
 older males imposed direct costs on females in terms of both fecundity and
 lifespan, with no offsetting indirect benefits for her offspring. The
 courtship behavior of older males does not supply females with cues for
 mate-choice benefits but are used to coerce females into mating. Our
 results suggest that male–male competition constrains female preference
 for older males. Thus, female choice and male–male competition may not be
 reinforcing in older G. cornutus males.
description: Raw data for Older males are more competitive in male fights and more
 aggressive toward females in the broad-horned flour beetle Gnatocerus
 cornutus
DOI: 10.5061/dryad.6bg5473
title: Data from: Similarity in mycorrhizal communities associating with two widespread terrestrial orchids decays with distance

description: Aim: Interactions with mycorrhizal fungi are increasingly recognized as an
 important factor underlying the distribution and abundance of orchid
 species. However, the geographic distribution of orchid mycorrhizal fungi
 (OMF) and how their communities vary over large geographical areas are
 less well understood. Because climatic and environmental similarity may
 decrease with geographical distance or because some OMF have limited
 dispersal capabilities, similarities in orchid mycorrhizal communities can
 be expected to decrease with increasing distances separating orchid
 populations. However, up till now empirical evidence is largely lacking.
 Location: Eurasia Taxa: Gymnadenia conopsea (L.) R. Brown and Epipactis
 helleborine (L.) Crantz Methods: High-throughput sequencing was used to
 perform a cross-continental comparison of OMF that associate with two
 widespread Eurasian terrestrial orchids, Epipactis helleborine and
 Gymnadenia conopsea. Both phylogenetic and non-phylogenetic measures of
 community dissimilarity and their components were calculated and related
 to geographic distances using Mantel tests. Results: Our results showed
 that in both orchid species similarity in mycorrhizal communities
 decreased significantly with geographical distance. Decomposing the
 contribution of spatial turnover and nestedness to overall dissimilarity
 showed that the observed dissimilarity was mainly the result of species
 replacement between regions, and not of species loss. Similarly, a strong
 relationship was observed between phylogenetic community dissimilarity and
 geographic distance. Decomposing PCD values into a nonphylogenetic and
 phylogenetic component showed that orchid populations located closely next
 to each other were likely to contain the same OTUs, but that the
 non-shared taxa came from different phylogenetic clades. Species indicator
 analyses showed that the majority of OMF OTUs were restricted to
 particular geographic areas. However, some OTUs occurred in both
 continents, indicating that some fungi have very wide distributions. Main
 conclusions: Overall, these results demonstrate that orchid mycorrhizal
 communities differ substantially across large geographic areas, but that
 the distribution of orchids is not necessarily restricted by the
 distribution of particular OMF. Hence, widespread orchid species can be
 considered mycorrhizal generalists that are flexible in the OMF with which
 they associate across large geographic areas.
description: Xing et al
 dataRaw data for mycorrhizal
 community dissimilarity analysis of Epipactis helleborine and Gymnadenia
 conopsea
DOI: 10.5061/dryad.pv4097s
title: Data from: A functionally conserved mechanism of modulation via a vestibule site in pentameric ligand-gated ion channels

description: Pentameric ligand-gated ion channels (pLGICs) belong to a class of ion
 channels involved in fast synaptic signaling in the central and peripheral
 nervous systems. Molecules acting as allosteric modulators target binding
 sites that are remote from the neurotransmitter binding site, but
 functionally affect coupling of ligand binding to channel opening. Here,
 we investigated an allosteric binding site in the ion channel vestibule,
 which has converged from a series of studies on prokaryote and eukaryote
 channel homologs. We discovered single domain antibodies, called
 nanobodies, which are functionally active as allosteric modulators, and
 solved co-crystal structures of the prokaryote channel ELIC bound either
 to a positive (PAM) or a negative (NAM) allosteric modulator. We
 extrapolate the functional importance of the vestibule binding site to
 eukaryote ion channels, suggesting a conserved mechanism of allosteric
 modulation. This work identifies key elements of allosteric binding sites
 and extends drug design possibilities in pLGICs using nanobodies.
description: X-ray diffraction images
 for ELIC-NAM Nb data setThis files contains a
 sweep of 900 diffraction images collected from a single
 crystal.ert_1374_F10_2a.tarX-ray diffraction images for ELIC-PAM Nb data setThis file contains images 1-49922711-B11a-run2-part1.tarX-ray diffraction images for ELIC-PAM Nb data setThis file contains images 500-99922711-B11a-run2-part2.tarX-ray diffraction images for ELIC-PAM Nb data setThis file contains images 1000-149922711-B11a-run2-part3.tarX-ray diffraction images for ELIC-PAM Nb data setThis file contains images 1500-199922711-B11a-run2-part4.tarX-ray diffraction images for ELIC+PAM-Nb data setThis file contains images 2000-250022711-B11a-run2-part5.tar
DOI: 10.5061/dryad.900ng75
title: Data from: Developmental constraints do not influence long-term phenotypic evolution of marsupial forelimbs as revealed by interspecific disparity and integration patterns

description: Marsupials show a smaller range of forelimb ecomorphologies than placental
 mammals, and it is hypothesized that this results from macroevolutionary
 constraints imposed by the specialised reproductive biology of marsupials.
 Specifically, the accelerated development of the marsupial forelimb allows
 neonates to crawl to the mother’s pouch, but may constrain adult
 morphology. This hypothesis makes three main predictions: (i) that
 marsupial forelimbs should show less interspecific disparity than their
 hindlimbs; (ii) that morphological integration within the marsupial
 forelimb is stronger than integration between limbs; and (iii) that these
 patterns should be strongest in diprotodontians, which undergo the most
 rigorous crawls as neonates. We use a three-dimensional geometric
 morphometric dataset of limb bones for 51 marsupial species to tests these
 predictions. We find that (i) marsupial forelimbs and hindlimbs show
 similar disparities, (ii) no clear differences in integration exist either
 within or between limbs, and (iii) the same patterns occur in
 diprotodontians as in other marsupials, even correcting for lineage age.
 Therefore, there is currently little evidence that the developmental
 biology of marsupials has constrained their macroevolutionary patterns.
 Possibly, functional selection can overcome the effects of developmental
 constraint on macroevolutionary timescales. Our findings suggest that the
 role of developmental constraints in explaining the limited phenotypic
 variability of marsupials (compared with placentals) should be
 reconsidered.
description: Morphometric data and
 scripts This file includes all
 the main data and analyses of the paper: Centroid size and Procrustes
 coordinates of each of the seven elements analyzed (csv files), phylogeny
 of the marsupials included (nexus file) and script of the disparity and
 integration analyses (R files). In addition, data obtained form
 evolutionary rates analyses (txt files), phyogeny (nexus file), script and
 list of this analyses (R files). Marsupial analysis
 Martin-Serra&Benson.rar
DOI: 10.5061/dryad.c5c7601
title: Data from: Synchrotron-X-ray absorption spectroscopy of melanosomes in vertebrates and cephalopods: implications for the affinity of Tullimonstrum

description: Screening pigments are essential for vision in animals. Vertebrates
 utilise melanins bound in melanosomes as screening pigments, whereas
 cephalopods are assumed to use ommochromes. Preserved eye melanosomes in
 the controversial fossil Tullimonstrum (Mazon Creek, Illinois) display
 size-and/or shape-specific are present in geometrically distinct layers
 that resemble tissue-specific melanosome populations considered unique to
 the vertebrate eye. Here, we show that extant cephalopod eyes also show
 tissue-specific size- and/or shape-specific partitioning of melanosomes;
 these differ from vertebrate melanosomes in the relative abundance of
 trace metals and in the binding environment of Cu. Chemical signatures of
 melanosomes in the eyes of Tullimonstrum more closely resemble those of
 modern cephalopods than those of vertebrates, suggesting that an
 invertebrate affinity for Tullimonstrum is plausible. Melanosome chemistry
 may thus provide insights into the phylogenetic affinities of enigmatic
 fossils where melanosome size and/or shape is are equivocal.
description: Raw data for Rogers et
 al.Raw data supporting the
 conclusions presented in Rogers et al. including measurements of
 vertebrate and cephalopod melanosomes, and xrf concentration data and
 normalized XANES spectra data for modern and fossil
 melanosomes.
DOI: 10.5061/dryad.0gs7410
title: Data from: Comparative transcriptomics provides insights into reticulate and adaptive evolution of a butterfly radiation

description: Butterfly eyes are complex organs that are composed of a diversity of
 proteins and they play a central role in visual signaling and ultimately,
 speciation and adaptation. Here, we utilized the whole eye transcriptome
 to obtain a more holistic view of the evolution of the butterfly eye while
 accounting for speciation events that co-occur with ancient hybridization.
 We sequenced and assembled transcriptomes from adult female eyes of eight
 species representing all major clades of the Heliconius genus and an
 additional outgroup species, Dryas iulia. We identified 4042 orthologous
 genes shared across all transcriptome datasets and constructed a
 transcriptome-wide phylogeny, which revealed topological discordance with
 the mitochondrial phylogenetic tree in the Heliconius pupal mating clade.
 We then estimated introgression among lineages using additional genome
 data and found evidence for ancient hybridization leading to the common
 ancestor of H. hortense and H. clysonymus. We estimated the Ka/Ks ratio
 for each orthologous cluster and performed further tests to demonstrate
 genes showing evidence of adaptive protein evolution. Furthermore, we
 characterized patterns of expression for a subset of these positively
 selected orthologs using qRT-PCR. Taken together, we identified candidate
 eye genes that show signatures of adaptive molecular evolution and provide
 evidence of their expression divergence between species, tissues and
 sexes. Taken together, our results demonstrate: 1) greater evolutionary
 changes in younger Heliconius lineages, i.e., more positively selected
 genes in the cydno – melpomene – hecale group as opposed to the sara –
 hortense – erato group, and 2) suggest an ancient hybridization leading to
 speciation among Heliconius pupal-mating species.
description: DiuliaTrinity.fastaDe novo assembled eye transcriptome data for D. ilulia.HcydnoTrinity.fastaDe novo assembled eye transcriptome data for H. cydno.HdorisTrinity.fastaDe novo assembled eye transcriptome data for H. doris.HeratoTrinity.fastaDe novo assembled eye transcriptome data for H. erato.HhecaleTrinity.fastaDe novo assembled eye transcriptome data for H. hecale.HhortenseTrinity.fastaDe novo assembled eye transcriptome data for H. hortense.HmelpomeneTrinity.fastaDe novo assembled eye transcriptome data for H. melpomene.HsaraTrinity.fastaDe novo assembled eye transcriptome data for H. sara.
DOI: 10.5061/dryad.7s75p25
title: Data from: Neuron-specific knockouts indicate the importance of network communication to Drosophila rhythmicity

description: Animal circadian rhythms persist in constant darkness and are driven by
 intracellular transcription-translation feedback loops. Although these
 cellular oscillators communicate, isolated mammalian cellular clocks
 continue to tick away in darkness without
 intercellular communication. To investigate these issues
 in Drosophila, we assayed behavior as well as molecular rhythms
 within individual brain clock neurons while
 blocking communication within the ca.
 150 neuron clock network. We also generated
 CRISPR-mediated neuron-specific circadian
 clock knockouts. The results point to two key
 clock neuron groups: loss of the clock within both
 regions but neither one alone has a strong behavioral phenotype in
 darkness; communication between these regions also
 contributes to circadian period determination. Under these dark
 conditions, the clock within one region persists
 without network communication. The clock within the
 famous PDF-expressing s-LNv neurons however was strongly dependent
 on network communication, likely because clock gene
 expression within these vulnerable sLNvs depends on neuronal firing or
 light
description:
DOI: 10.15468/dl.qwkf4m
title: Occurrence Download

description: A dataset listing the 2 species recorded in GBIF matching the query:
{
 "TaxonKey" : [
 "is Calcarius ornatus"
 ]
}

 The dataset's 2 records were derived from 112 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001895-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7c01654
title: Data from: Limited evidence for spatial resource partitioning across temperate grassland biodiversity experiments

description: Locally, plant species richness supports many ecosystem functions. Yet,
 the mechanisms driving these often-positive biodiversity–ecosystem
 functioning relationships are not well understood. Spatial resource
 partitioning across vertical resource gradients is one of the main
 hypothesized causes for enhanced ecosystem functioning in more biodiverse
 grasslands. Spatial resource partitioning occurs if species differ in
 where they acquire resources and can happen both above- and belowground.
 However, studies investigating spatial resource partitioning in grasslands
 provide inconsistent evidence. We present the results of a meta-analysis
 of 21 datasets from experimental species-richness gradients in grasslands.
 We test the hypothesis that increasing spatial resource partitioning along
 vertical resource gradients enhances ecosystem functioning in diverse
 grassland plant communities above- and belowground. To test this
 hypothesis, we asked three questions: 1. Does species richness enhance
 biomass production or community resource uptake across sites? 2. Is there
 evidence of spatial resource partitioning as indicated by resource tracer
 uptake and biomass allocation above- and belowground? 3. Is evidence of
 spatial resource partitioning correlated with increased biomass production
 or community resource uptake? Although plant species richness enhanced
 community nitrogen and potassium uptake and biomass production above- and
 belowground, we found that plant communities did not meet our criteria for
 spatial resource partitioning, though they did invest in significantly
 more aboveground biomass in higher canopy layers in mixture relative to
 monoculture. Furthermore, the extent of spatial resource partitioning
 across studies was not positively correlated with either biomass
 production or community resource uptake. Our results suggest that spatial
 resource partitioning across vertical resource gradients alone does not
 offer a general explanation for enhanced ecosystem functioning in more
 diverse temperate grasslands.
description: Barry.et.al-2019-Ecology-Data for meta-analysis in main figuresData used in main figures of Barry et al. 2019 - EcologyBarry.et.al-2019-Ecology-DataforMeta-analysisFigS1Data used in the supplemental analysis for Figure S1 in Barry et al. 2019 - EcologyBarry.et.al-2019-Ecology-Resource partitioning grasslands - Main figuresData used for the main figures in Barry et al. 2019 EcologyBarry.et.al-2019-Ecology-DataForFigureS1Data for figure S1 in Barry et al. 2019 EcologyREADMEThis readme contains all of the meta-data for all data files as well as a note from the author. This information is also contained in the R markdown file associated with this data package.Barry.et.al-2019-EcologyThis file contains the code in R Markdown format for the meta-analyses and figures for Barry et al. 2019 Ecology as well as the figure captions and some brief notes and explanations.
DOI: 10.5061/dryad.r2h6h33
title: Data from: Helianthus maximiliani and species fine-scale spatial pattern affect diversity interactions in reconstructed tallgrass prairies

description: 1. Biodiversity and Ecosystem Function analyses aim to explain how
 individual species and their interactions affect ecosystem function. With
 this study we asked in what ways do species interact, are these
 interactions affected by species planting pattern, and are initial
 (planted) proportions or previous year (realized) proportions a better
 reference point for characterizing grassland diversity effects? 2. We
 addressed these questions with experimental communities compiled from a
 pool of 16 tallgrass prairie species. We planted all species in
 monocultures and mixtures that varied in their species richness, evenness,
 and spatial pattern. We recorded species-specific biomass production over
 three growing seasons and fitted Diversity-Interactions (DI) models to
 annual plot biomass yields. 3. In the establishment season, all species
 interacted equally to form the diversity effect. In years 2 and 3, each
 species contributed a unique additive coefficient to its interaction with
 every other species to form the diversity effect. These interactions were
 affected by H. maximiliani and the species planting pattern. Models based
 on species planted proportions better-fit annual plot yields than models
 based on species previous contributions to plot biomass. 4. Outcomes
 suggest that efforts to plant tallgrass prairies to maximize diversity
 effects should focus on the specific species present and in what
 arrangement they are planted. Furthermore, for particularly diverse
 grasslands, the effort of collecting annual species biomass data may not
 be necessary when quantifying diversity effects with
 Diversity-Interactions models.
description: Total biomass with
 planted and realized proportionsThe plant community
 structureMcKenna_et_al_Data_for_archive.csv
DOI: 10.5061/dryad.bg167bq
title: Shift in bacterial taxa precedes morphological plasticity in a larval echinoid

description: Morphological plasticity is an adaptive response to heterogenous
 environments when a fitness advantage is conferred. Larval sea urchins,
 for example, increase individual fitness in dilute feeding environments by
 elongating their feeding structure. Morphological plasticity for larval
 sea urchins is also coupled with significant shifts in the associated
 bacterial community, but whether this response occurs before, during, or
 following the expression of plasticity is unclear. Using the sea urchin
 Lytechinus variegatus, we define the temporal pattern of the associated
 bacterial community throughout the expression of morphological plasticity.
 From prefeeding through plasticity, we observed that L. variegatus larvae
 exhibit a four-stage successional pattern and the relatedness of the
 larval-associated bacterial community directly reflects morphological
 plasticity and does so prior to expression of the environmental-specific
 morphology. Based on the structure of the larval-associated bacterial
 communities, the expression of morphological plasticity correlates
 short-arm larvae deviating from the microbial trajectory of pre-plastic
 siblings. Taken together, these data suggest that a holobiont may exhibit
 shifts in the associated bacterial community corresponding with the
 environmental variation in absence or anticipation of morphological
 plasticity.
description: CarrierReitzel_RawSeq1First half of data corresponding with this manuscript.CarrierReitzel_RawSeq2Second half of data corresponding with this manuscript.
DOI: 10.5061/dryad.02ts21t
title: Data from: Canine sense of quantity: evidence for numerical ratio-dependent activation in parietotemporal cortex

description: The approximate number system (ANS), which supports the rapid estimation
 of quantity, emerges early in human development and is widespread across
 species. Neural evidence from both human and non-human primates suggests
 the parietal cortex as a primary locus of numerical estimation, but it is
 unclear whether the numerical competencies observed across non-primate
 species are subserved by similar neural mechanisms. Moreover, because
 studies with non-human animals typically involve extensive training,
 little is known about the spontaneous numerical capacities of non-human
 animals. To address these questions, we examined the neural underpinnings
 of number perception using awake canine functional magnetic resonance
 imaging. Dogs passively viewed dot arrays that varied in ratio and,
 critically, received no task-relevant training or exposure prior to
 testing. We found evidence of ratio-dependent activation, which is a key
 feature of the ANS, in canine parietotemporal cortex in the majority of
 dogs tested. This finding is suggestive of a neural mechanism for quantity
 perception that has been conserved across mammalian evolution.
description: Dog Numerosity
 Train/Test Model DataAFNI-format files. Each
 dog contains: a mean fMRI image for underlay; GLM train/test model results
 (GAM...); and final cluster mask. For both the train and test briks, the
 [0] is the main effect and the [1] is the effect modulated by the numeric
 ratio. ROIS were identified by the positive contrast of the train set, and
 then probed with the test set.dog_numerosity.zip