cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.zgmsbcc6t
title: Data from: Estimating density from presence/absence data in clustered populations

description: 1. Inventories of plant populations are fundamental in ecological research
 and monitoring, but such surveys are often prone to field assessment
 errors. Presence/absence (P/A) sampling may have advantages over plant
 cover assessments for reducing such errors. However, the linking between
 P/A data and plant density depends on model assumptions for plant spatial
 distributions. Previous studies have shown, for example, how that plant
 density can be estimated under Poisson model assumptions on the plant
 locations. In this study new methods are developed and evaluated for
 linking P/A data with plant density assuming that plants occur in
 clustered spatial patterns. 2. New theory was derived for estimating plant
 density under Neyman-Scott type cluster models such as the Matérn and
 Thomas cluster processes. Suggested estimators, corresponding confidence
 intervals, and a proposed goodness-of-fit test were evaluated in a
 Monte-Carlo simulation study assuming a Matérn cluster process. Further,
 the estimators were applied to plant data from environmental monitoring in
 Sweden to demonstrate their empirical application. 3. The simulation study
 showed that our methods work well for large enough sample sizes. The
 judgment of what is "large enough'' is often difficult, but
 simulations indicate that a sample size is large enough when the sampling
 distributions of the parameter estimators are symmetric or mildly skewed.
 Bootstrap may be used to check whether this is true. The empirical results
 suggests that the derived methodology may be useful for estimating density
 of plants such as Leucanthemum vulgare and Scorzonera humilis. 4.
 By developing estimators of plant density from P/A data under realistic
 model assumptions about plants' spatial distributions, P/A sampling
 will become a more useful tool for inventories of plant populations. Our
 new theory is an important step in this direction.
description: <strong>Presence/absence data from environmental
 monitoring</strong> This file contains observed
 frequencies for the species <em>Leucanthemum
 vulgare</em>, <em>Pimpinella saxifraga</em>,
 and <em>Scorzonera humilis</em>. The data were obtained from
 three monitoring projects associated with the National Inventory of
 Landscapes in Sweden (NILS), where presence/absence-data of plants were
 recorded in nine subplots per plot. See Section 2.4.2 of the paper for
 detailed information about the data. The observed
 frequencies, <em>n<sub>0</sub>, ...,
 n<sub>7</sub></em>, in the data file are from a
 "multinomial experiment" described in our paper (see Example 2
 and the first paragraph of Section 2 for details), and were used for
 estimating parameters of Matérn cluster processes (Section 3.2; Table
 5).
DOI: 10.5061/dryad.tmpg4f4v8
title: Dominant native and non-native graminoids differ in key leaf traits irrespective of nutrient availability

description: Aim Nutrient enrichment is associated with plant invasions and
 biodiversity loss. Functional trait advantages may predict the ascendancy
 of invasive plants following nutrient enrichment but this is rarely
 tested. Here, we investigate 1) whether dominant native and non-native
 plants differ in important morphological and physiological leaf traits, 2)
 how their traits respond to nutrient addition, and 3) whether responses
 are consistent across functional groups. Location Australia, Europe, North
 America and South Africa Time period 2007 - 2014 Major taxa studied
 Graminoids and forbs Methods We focused on two types of leaf traits
 connected to resource acquisition: morphological features relating to
 light-foraging surfaces and investment in tissue (Specific Leaf Area, SLA)
 and physiological features relating to internal leaf chemistry as the
 basis for producing and utilizing photosynthate. We measured these traits
 on 503 leaves from 151 dominant species across 27 grasslands on four
 continents. We used an identical nutrient addition treatment of nitrogen
 (N), phosphorus (P) and potassium (K) at all sites. Sites represented a
 broad range of grasslands that varied widely in climatic and edaphic
 conditions. Results We found evidence that non-native graminoids invest in
 leaves with higher nutrient concentrations than native graminoids,
 particularly at sites where native and non-native species both dominate.
 We found little evidence that native and non-native forbs differed in the
 measured leaf traits. These results were consistent in natural soil
 fertility levels and nutrient enriched conditions, with dominant species
 responding similarly to nutrient addition regardless of whether they were
 native or non-native.  Main conclusions Our work identifies the
 inherent physiological trait advantages that can be used to predict
 non-native graminoid establishment; potentially because of higher
 efficiency at taking up crucial nutrients into their leaves. Most
 importantly, these inherent advantages are already present at natural soil
 fertility levels and are maintained following nutrient enrichment.
description: Missing values are left blank but should be read as NA for
 analysis purposes
DOI: 10.5061/dryad.547d7wm4f
title: Rapid and cost-effective generation of single specimen multilocus barcoding data from whole arthropod communities by multiple levels of multiplexing

description: In light of the current biodiversity crisis, molecular barcoding has
 developed into an irreplaceable tool. Barcoding has been considerably
 simplified by developments in high throughput sequencing technology, but
 still can be prohibitively expensive and laborious when community samples
 of thousands of specimens need to be processed. Here, we outline an
 Illumina amplicon sequencing approach to generate multilocus data from
 large collections of arthropods. We reduce cost and effort up to 50-fold,
 by combining multiplex PCRs and DNA extractions from pools of presorted
 and morphotyped specimens and using two levels of sample indexing. We test
 our protocol by generating a comprehensive, community wide dataset of
 barcode sequences for several thousand Hawaiian arthropods from 14 orders,
 which were collected across the archipelago using various trapping
 methods. We explore patterns of diversity across the Archipelago and
 compare the utility of different arthropod trapping methods for
 biodiversity explorations on Hawaii, highlighting undergrowth beating as
 highly efficient method. Moreover, we show the effects of barcode marker,
 taxonomy and relative biomass of the targeted specimens and sequencing
 coverage on taxon recovery. Our protocol enables rapid and inexpensive
 explorations of diversity patterns and the generation of multilocus
 barcode reference libraries across whole ecosystems.
DOI: 10.5061/dryad.63xsj3tzp
title: Insecticide exposure during brood or early-adult development reduces brain growth and impairs adult learning in bumblebees

description: For social bees, an understudied step in evaluating pesticide risk is how
 contaminated food entering colonies affects residing offspring development
 and maturation. For instance, neurotoxic insecticide compounds in food
 could affect central nervous system development predisposing individuals
 to become poorer task performers later-in-life. Studying bumblebee
 colonies provisioned with neonicotinoid spiked nectar substitute, we
 measured brain volume and learning behaviour of 3 or 12-day old adults
 that had experienced in-hive exposure during brood and/or early-stage
 adult development. Micro-computed tomography (µCT) scanning and
 segmentation of multiple brain neuropils showed exposure during either
 developmental stage caused reduced mushroom body calycal growth relative
 to unexposed workers. Associated with this, was a lower probability of
 responding to a sucrose reward and lower learning performance in an
 olfactory conditioning test. Whilst calycal volume of control workers
 positively correlated with learning score, this relationship was absent
 for exposed workers indicating neuropil functional impairment. Comparison
 of 3 and 12-day adults exposed during brood development showed a similar
 degree of reduced calycal volume and impaired behaviour highlighting
 lasting and irrecoverable effects from exposure despite no adult exposure.
 Our findings help explain how the onset of pesticide exposure to whole
 colonies can lead to lag-effects on growth and resultant dysfunction.
DOI: 10.15468/dl.kq6b5f
title: Occurrence Download

description: A dataset containing 282 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Colombia",
 "OccurrenceStatus is Present",
 "TaxonKey is Scaptotrigona"
 ]
}

 The dataset includes 282 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002134-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.crjdfn31b
title: A major locus controls a biologically active pheromone component in Heliconius melpomene

description: Understanding the production, response, and genetics of signals used in
 mate choice can inform our understanding of the evolution of both
 intraspecific mate choice and reproductive isolation. Sex pheromones are
 important for courtship and mate choice in many insects, but we know
 relatively little of their role in butterflies. The butterfly Heliconius
 melpomene uses a complex blend of wing androconial compounds during
 courtship. Electroantennography in H. melpomene and its close relative H.
 cydno showed that responses to androconial extracts were not
 species-specific. Females of both species responded equally strongly to
 extracts of both species, suggesting conservation of peripheral nervous
 system elements across the two species. Individual blend components
 provoked little to no response, with the exception of octadecanal, a major
 component of the H. melpomene blend. Supplementing octadecanal on the
 wings of octadecanal-rich H. melpomene males led to an increase in the
 time until mating, demonstrating the bioactivity of octadecanal in
 Heliconius. Using quantitative trait locus (QTL) mapping, we identified a
 single locus on chromosome 20 responsible for 41% of the parental species’
 difference in octadecanal production. This QTL does not overlap with any
 of the major wing color or mate choice loci, nor does it overlap with
 known regions of elevated or reduced FST. A set of 16 candidate fatty acid
 biosynthesis genes lies underneath the QTL. Pheromones in Heliconius carry
 information relevant for mate choice and are under simple genetic control,
 suggesting they could be important during speciation.
description: This dataset consists of 4 major data subsets: pheromone analysis
 of parent species <em>Heliconius cydno</em> and <em>H.
 melpomene </em>(raw GC-MS output files and data tables);
 electroantennogram responses of both species (raw electroantennogram
 output and data tables); behavioral results (data table); QTL mapping
 information (linkage maps and QTL analysis scripts). GC-MS data were
 analyzed with AMDIS to produce data tables with compound amounts.
 Electroantennogram response strengths were manually marked in GcEad and
 peak heights exported to text files which were then put into data tables
 and analyzed with included scripts. Behavioral results were manually
 entered into data tables. QTL linkage maps were produced from whole genome
 data (separately archived on ENA under project PRJEB34160) and scripts for
 analysis of QTL using the R/qtl2 package are included.
description: Raw GC-MS files may be viewed and analyzed in the free analysis
 software AMDIS, and raw electroantennogram files in the free analysis
 software GcEad. "MP" in files and filenames refers
 to <em>H. melpomene</em> (MP from
 "<em>melpomene </em>Panama") and "CP"
 to <em>H. cydno</em>.
DOI: 10.5061/dryad.k3j9kd540
title: Detection of freshwater mussels (Unionidae) using environmental DNA in riverine systems

description: Environmental DNA (eDNA) methods are being developed for use in
 conservation biology to improve upon conventional species survey
 techniques. Validation of eDNA methods in different environmental contexts
 is required if they are to be widely adopted. One potential application of
 eDNA methods is for the detection of freshwater mussels (Bivalvia:
 Unionidae), which are among the most imperiled species in North America.
 Conventional unionid survey methods are highly invasive and can be
 difficult to conduct due to issues with morphological identification and
 their cryptic use of habitat. eDNA methods can potentially provide a
 non-invasive, extremely specific, and highly sensitive alternative. Here
 we examine the effectiveness of eDNA methods at detecting an imperiled
 unionid, the wavy-rayed lampmussel (Lampsilis fasciola), in lotic systems
 with moderate discharge. We developed a novel qPCR assay for the detection
 of L. fasciola eDNA, which included a custom internal positive control to
 check for PCR inhibition. We used different experimental densities of
 caged L. fasciola specimens as a point source of eDNA within two rivers of
 the Grand River watershed in Southern Ontario. Sampling occurred at set
 distances downstream of the cage using purpose built sampling equipment.
 Detection was obtained at the cage (i.e., point of eDNA shedding) but not
 downstream at distances ≥10 meters during stream discharges of
 approximately 1632 – 2332 L/s. The results indicate that eDNA is diluted
 rapidly in rivers with moderate discharge and that high resolution spatial
 sampling efforts may be necessary to obtain meaningful eDNA-based
 distribution data of unionids, and other sessile organisms, present at low
 density in lotic systems.
description: See associated publication
DOI: 10.5061/dryad.66t1g1jz4
title: Prehistoric baseline reveals substantial decline of oyster reef condition in a Gulf of Mexico conservation priority area

description: This dataset contains oyster shell height measurements for prehistoric and
 modern oysters collected near Crystal River, Florida, USA. Oxygen and
 carbon stable isotope values for large prehistoric and modern oysters are
 also reported.
description: See methods in article: https://doi.org/10.1098/rsbl.2019.0865
DOI: 10.5066/p13luw6k
title: Soil carbon and plant cover data for uninvaded and cheatgrass invaded sites in Grand Junction, Colorado and Rock Springs, Wyoming

description: Soil data includes carbon (total, organic, mineral-associated, particulate-organic) and texture. Bulk density data includes bulk density values used to calculate carbon stocks. Plant data includes microsite coverage percents and sagebrush demographics. Data is from uninvaded and cheatgrass invaded points near Grand Junction, Colorado and Rock Springs, Wyoming in October and November 2023.
DOI: 10.6075/j05t3hvt
title: Bacteriophage lambda overcomes a perturbation in its host‐viral genetic network through mutualism and evolution of life history traits

description: An important driver of viral evolution is natural selection to optimize
 the use of their hosts’ genetic network. To learn how viruses respond to
 this pressure, we disrupted the genetic network of Escherichia
 coli to inhibit replication of its virus, bacteriophage lambda,
 and then observed how λ evolved to compensate. We deleted E.
 coli's dnaJ gene, which lambda uses to initiate DNA
 replication. Lambda partially restored its ability to reproduce with just
 two adaptive mutations associated with
 genes J and S. The location of the mutations
 was unexpected because they were not in genes that directly interact with
 DnaJ, rather they affected seemingly unrelated life history traits. A
 nonsynonymous J mutation increased λ’s adsorption rate
 and an S regulatory mutation delayed lysis timing. λ
 also recovered some of its reproductive potential through intracellular
 mutualism. This study offers two important lessons: first, viruses can
 rapidly adapt to disruptive changes in their host's genetic network.
 Second, organisms can employ mechanisms thought to operate at the
 population scale, such as evolution of life history traits and social
 interactions, in order to overcome hurdles at the molecular level. As life
 science research progresses and new fields become increasingly
 specialized, these results remind us of the importance of multiscale and
 interdisciplinary approaches to understanding adaptation.
description: 1. ‘Figure data_main text_DRYAD.xlsx’ contains raw data for all
 the figures in the main text of the paper. Different sheets in the excel
 file correspond to different figure numbers in the paper. Likewise,
 ‘Figure data_supp info_DRYAD.xlsx’ contains data for figures in
 Supplementary Information. 2.
 ‘final_cooperationModel.m’ is the MATLAB script file which was used to
 generate density dependent dynamics in Figure 4c. 3.
 The paired-end raw sequencing data for whole genome sequencing of DNAJ1,
 DNAJ2 and 6 WT clones (listed in Supplementary Table 2) are in the
 compressed file ‘Raw whole genome sequencing data for mutualism
 paper.zip’.<br>
DOI: 10.5061/dryad.8w9ghx3h9
title: Transcriptomics illuminate the phylogenetic backbone of tiger beetles

description: Phylogenomics is progressing rapidly, allowing large strides forward into
 our understanding of the tree of life. In this study, we generated
 transcriptomes from ethanol-preserved specimens of 13 tiger beetle species
 (Coleoptera: Cicindelinae) and one Scaritinae outgroup. From these 14
 transcriptomes and seven publicly available transcriptomes, we recovered
 an average of 2538 loci for phylogenetic analysis. We constructed an
 evolutionary tree of tiger beetles to examine deep-level relationships and
 examined the extent to which the composition of the dataset, missing data,
 gene tree inconsistency and codon position saturation impacted
 phylogenetic accuracy. Ethanol-preserved specimens yielded similar numbers
 of loci to specimens originally preserved in costly reagents, showcasing
 more flexibility in transcriptomics than anticipated. The number of loci
 and gene tree inconsistency had less impact on downstream results than
 third codon position saturation and missing data. Our results recovered
 tiger beetles as sister to Carabidae with strong support, confirming their
 taxonomic status as an independent family within Adephaga. Within tiger
 beetles, phylogenetic relationships were robust across all nodes. This new
 phylogenomic backbone represents a useful framework for future endeavours
 in tiger beetle systematics and serves as a starting point for the
 development of less costly target capture toolkits to expand the taxonomic
 breadth of the future tiger beetle tree of life.
description: For complete information on collection, extraction and sequencing
 see (Gough et al. 2020).
DOI: 10.15468/dl.tua9hw
title: Occurrence Download

description: A dataset containing 1038 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Zehneria scabra",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 1038 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002133-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.pvmcvdngx
title: Metabolic rate is negatively linked to adult survival but does not explain latitudinal differences in songbirds

description: Survival rates vary dramatically among species and predictably across
 latitudes, but causes of this variation are unclear. The rate of living
 hypothesis posits that physiological damage from metabolism causes species
 with faster metabolic rates to exhibit lower survival rates. However,
 whether increased survival commonly observed in tropical and south
 temperate latitudes is associated with slower metabolic rate remains
 unclear. We compared metabolic rates and annual survival rates across 46
 species that we measured, and 147 species from literature data across
 northern, southern, and tropical latitudes. High metabolic rates were
 associated with lower survival but latitude had substantial direct effects
 on survival independent of metabolism. The inability of metabolic rate to
 explain latitudinal variation in survival suggests 1) that species may
 evolve physiological mechanisms that mitigate physiological damage from
 cellular metabolism, and 2) a larger role of extrinsic environmental,
 rather than intrinsic metabolic, causes of latitudinal differences in
 mortality.
description: Metabolic data in our field dataset were collected via
 respiromtery. Adult survival data were collected via several consecutive
 years of mark-recapture-resight protocols and cormack-jolly-seber
 models. 
description: These datasets include a) RMR and adult
 survival proability data collected by the authors at sites in Sabah,
 Malaysia, Western Cape, South Africa, and the Coconino National Forest,
 Arizona, USA.  b) BMR and adult survival probability
 data compiled from the literature across all songbirds.
DOI: 10.15468/dl.3qtuqr
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hemerocoetes monopterygius",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 2014"
 ]
}

 The dataset includes 28 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002129-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.kkwh70s1v
title: Data from: Low-dimensional spatio-temporal dynamics underlie cortex-wide neural activity

description: Cognition arises from the dynamic flow of neural activity through the
 brain. To capture these dynamics, we used mesoscale calcium imaging to
 record neural activity across the dorsal cortex of awake mice. We found
 that the large majority of variance in cortex-wide activity (~75%) could
 be explained by a limited set of ~14 ‘motifs’ of neural activity. Each
 motif captured a unique spatio-temporal pattern of neural activity across
 the cortex. These motifs generalized across animals and were seen in
 multiple behavioral environments. Motif expression differed across
 behavioral states and specific motifs were engaged by sensory processing,
 suggesting the motifs reflect core cortical computations. Together, our
 results show that cortex-wide neural activity is highly dynamic, but that
 these dynamics are restricted to a low-dimensional set of motifs,
 potentially allowing for efficient control of behavior.