cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.p48f7
title: Data from: Anthropogenic debris ingestion by avifauna in eastern Australia

description: Anthropogenic debris in the world’s oceans and coastal environments is a
 pervasive global issue that has both direct and indirect impacts on
 avifauna. The number of bird species affected, the feeding ecologies
 associated with an increased risk of debris ingestion, and selectivity of
 ingested debris have yet to be investigated in most of Australia’s coastal
 and marine birds. With this study we aim to address the paucity of data
 regarding marine debris ingestion in Australian coastal and marine bird
 species. We investigated which Australian bird groups ingest marine
 debris, and whether debris-ingesting groups exhibit selectivity associated
 with their taxonomy, habitat or foraging methods. Here we present the
 largest multispecies study of anthropogenic debris ingestion in
 Australasian avifauna to date. We necropsied and investigated the
 gastrointestinal contents of 378 birds across 61 species, collected dead
 across eastern Australia. These species represented nine taxonomic orders,
 five habitat groups and six feeding strategies. Among investigated
 species, thirty percent had ingested debris, though ingestion did not
 occur uniformly within the orders of birds surveyed. Debris ingestion was
 found to occur in orders Procellariiformes, Suliformes, Charadriiformes
 and Pelecaniformes, across all surveyed habitats, and among birds that
 foraged by surface feeding, pursuit diving and search-by-sight.
 Procellariiformes, birds in pelagic habitats, and surface feeding marine
 birds ingested debris with the greatest frequency. Among birds which were
 found to ingest marine debris, we investigated debris selectivity and
 found that marine birds were selective with respect to both type and
 colour of debris. Selectivity for type and colour of debris significantly
 correlated with taxonomic order, habitat and foraging strategy. This study
 highlights the significant impact of feeding ecology on debris ingestion
 among Australia’s avifauna.
description: Ingested Plastics
 DataCleaned plastics
 ingestion dataDATA FOR
 PAPER.csv
DOI: 10.5061/dryad.066v4476
title: Data from: Infection intensity and infectivity of the tick-borne pathogen Borrelia afzelii

description: The ‘trade-off’ hypothesis for virulence evolution assumes that
 between-host transmission rate is a positive and saturating function of
 pathogen exploitation and virulence, but there are as yet few tests of
 this assumption, in particular for vector-borne pathogens. Here, I show
 that the infectivity (probability of transmission) of the tick-borne
 bacterium Borrelia afzelii from two of its natural rodent hosts (bank vole
 and yellow-necked mouse) to its main tick vector increases asymptotically
 with increasing exploitation (measured as bacterial load in skin
 biopsies). Hence, this result provides support for one of the basic
 assumptions of the ‘trade-off hypothesis’. Moreover, there was no
 difference in infectivity between bank voles and yellow-necked mice
 despite bacterial loads being on average an order of magnitude higher in
 bank voles, most likely because ticks took larger blood meals from mice.
 This shows that interspecific variation in host resistance does not
 necessarily translate into a difference in infectivity.
description: Raberg2012JEBFile contains data on infection intensity of Borrelia afzelii (as measured by qpcr) in bank voles and yellow-necked mice, and infection status (infected or not) of ticks collected from these animals.
DOI: 10.5061/dryad.vt280
title: Data from: Sticta deyana: a new endemic photomorphic lichen from the imperiled Mid-Atlantic Coastal Plain of eastern North America

description: An intensive lichen biodiversity inventory of the imperiled Mid-Atlantic
 Coastal Plain of eastern North America resulted in the discovery of a new
 species of the ecologically sensitive macrolichen genus Sticta. The
 species is formally described as S. deyana based on a combination of
 molecular and morphological data. It is most similar to the southern
 Appalachian endemic S. fragilinata, differing in its diminutive thallus,
 narrower lobes, and allopatric distribution. All but one population of S.
 deyana occurs within the Dare Regional Biodiversity Hotspot of coastal
 North Carolina and within the most conservative estimated sea-level rise
 by 2100.
description: Sticta_deyana_DATASETSThis is a zipped folder containing the input files used for Bayesian Inference and Maximum Likelihood analyses conducted for this study. An appendix from the manuscript is also included to facilitate translation of isolate numbers to GenBank accession numbers in the datasets.
DOI: 10.15468/dl.2xcdrx
title: Occurrence Download

description: A dataset containing 456 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cryptoblabes gnidiella"
 ]
}

 The dataset includes 456 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001355-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.b9d2cg7
title: Data from: Onosma lhokaensis (Boraginaceae), a new species from Xizang, China

description: A new species of Boraginaceae, Onosma lhokaensis, is described and
 illustrated from Xizang, China. The new species closely resembles O.
 waddellii and O. waltonii in having azure corollas, coherent anthers and
 glabrous filaments, but differs in having particularly bristly indumentum,
 observably narrow corolla, longer calyxes and anthers, and remarkable
 nutlets with stipitate cicatrix. An updated key to the species of Onosma
 from Xizang is also provided.
description: distribution data for
 three Onomsa speciesOriginal data for
 measuring mophological characters
DOI: 10.5061/dryad.9v43h
title: Data from: Multilocus coalescent analyses reveal the demographic history and speciation patterns of mouse lemur sister species

description: Background: Debate continues as to whether allopatric speciation or
 peripatric speciation through a founder effect is the predominant force
 driving evolution in vertebrates. The mouse lemurs of Madagascar are a
 system in which evolution has generated a large number of species over a
 relatively recent time frame. Here, we examine speciation patterns in a
 pair of sister species of mouse lemur, Microcebus murinus and M.
 griseorufus. These two species have ranges that are disparately
 proportioned in size, with M. murinus showing a much more extensive range
 that marginally overlaps that of M. griseorufus. Given that these two
 species are sister taxa, the asymmetric but overlapping geographic ranges
 are consistent with a model of peripatric speciation. To test this
 hypothesis, we analyze DNA sequence data from four molecular markers using
 coalescent methods. If the peripatric speciation model is supported, we
 predict substantially greater genetic diversity in M. murinus, relative to
 M. griseorufus. Further, we expect a larger effective population size in
 M. murinus and in the common ancestor of the two species than in M.
 griseorufus, with a concomitant decrease in gene tree/species tree
 incongruence in the latter and weak signs of demographic expansion in M.
 murinus. Results: Our results reject a model of peripatric divergence.
 Coalescent effective population size estimates were similar for both
 extant species and larger than that estimated for their most recent common
 ancestor. Gene tree results show similar levels of incomplete lineage
 sorting within species with respect to the species tree, and
 locus-specific estimates of genetic diversity are concordant for both
 species. Multilocus demographic analyses suggest range expansions for M.
 murinus, with this species also experiencing more recent population
 declines over the past 160 thousand years. Conclusions: Results suggest
 that speciation occurred in allopatry from a common ancestor narrowly
 distributed throughout southwest Madagascar, with subsequent range
 expansion for M. murinus. Population decline in M. murinus is likely
 related to patterns of climate change in Madagascar throughout the
 Pleistocene, potentially exacerbated by continual anthropogenic
 perturbation. Genome-level data are needed to quantify the role of niche
 specialization and adaptation in shaping the current ranges of these
 species.
description: Multiple sequence
 alignmentsMultiple sequence
 alignments for each locus used in this study. The mtDNA data consist of
 concatenated sequences from cytb and COII.Blair_alignments.zip
DOI: 10.5061/dryad.fg4v1
title: Data from: Naiveté is not forever: responses of a vulnerable native rodent to its long term alien predators

description: Alien predators have wreaked havoc on isolated endemic and island fauna
 worldwide, a phenomenon generally attributed to prey naiveté, or a failure
 to display effective antipredator behaviour due to a lack of experience.
 While the failure to recognise and/or respond to a novel predator has
 devastating impacts in the short term after predators are introduced, few
 studies have asked whether medium to long term experience with alien
 predators enables native species to overcome their naiveté. In Australia,
 introduced dogs (Canis lupus familiaris), foxes (Vulpes vulpes) and cats
 (Felis catus) have caused rapid extinctions and declines in small-medium
 sized native mammals since they were introduced ~150 years ago. However,
 native wildlife have had ~4000 years experience with another dog – the
 dingo (Canis lupus dingo). Native bush rats (Rattus fuscipes) remain
 common despite predation from these predators. We predicted that prior
 experience with dingoes would mean that bush rats recognise and respond to
 dogs, but suspect that hundreds of years experience may not be enough for
 effective responses to cats and foxes. To test these predictions, we
 combined the giving-up density (GUD) with analysis of remote camera
 footage to measure bush rat foraging and behavioural responses to body
 odour from dogs, foxes, cats and native spotted-tail quolls (Dasyurus
 maculatus). Bush rats responded strongly to dogs with increased GUDs,
 increased vigilance and decreased foraging. However, mixed responses to
 foxes and cats suggest that at least some individuals remain naïve towards
 these predators. Naiveté is not necessarily forever: alien predators
 devastate many native prey species, but others may learn or adapt to the
 new threat.
description: Data for
 DryadData used to create
 Figures 1 and 2.
DOI: 10.5061/dryad.k2qc4
title: Data from: Histology and affinity of anaspids, and the early evolution of the vertebrate dermal skeleton

description: The assembly of the gnathostome bodyplan constitutes a formative episode
 in vertebrate evolutionary history, an interval in which the mineralized
 skeleton and its canonical suite of cell and tissue types originated.
 Fossil jawless fishes, assigned to the gnathostome stem-lineage, provide
 an unparalleled insight into the origin and evolution of the skeleton,
 hindered only by uncertainty over the phylogenetic position and
 evolutionary significance of key clades. Chief among these are the jawless
 anaspids, whose skeletal composition, a rich source of phylogenetic
 information, is poorly characterized. Here we survey the histology of
 representatives spanning anaspid diversity and infer their generalized
 skeletal architecture. The anaspid dermal skeleton is composed of
 odontodes comprising spheritic dentine and enameloid, overlying a basal
 layer of acellular parallel fibre bone containing an extensive shallow
 canal network. A recoded and revised phylogenetic analysis using equal and
 implied weights parsimony resolves anaspids as monophyletic, nested among
 stem-gnathostomes. Our results suggest the anaspid dermal skeleton is a
 degenerate derivative of a histologically more complex ancestral
 vertebrate skeleton, rather than reflecting primitive simplicity.
 Hypotheses that anaspids are ancestral skeletonizing lampreys, or a
 derived lineage of jawless vertebrates with paired fins, are rejected.
description: Anaspid
 matrix
DOI: 10.5061/dryad.qc395
title: Data from: Urban landscapes can change virus gene flow and evolution in a fragmentation-sensitive carnivore

description: Urban expansion has widespread impacts on wildlife species globally,
 including the transmission and emergence of infectious diseases. However,
 there is almost no information about how urban landscapes shape
 transmission dynamics in wildlife. Using an innovative phylodynamic
 approach combining host and pathogen molecular data with landscape
 characteristics and host traits, we untangle the complex factors that
 drive transmission networks of Feline Immunodeficiency Virus (FIV) in
 bobcats (Lynx rufus). We found that the urban landscape played a
 significant role in shaping FIV transmission. Even though bobcats were
 often trapped within the urban matrix, FIV transmission events were more
 likely to occur in areas with more natural habitat elements. Urban
 fragmentation also resulted in lower rates of pathogen evolution, possibly
 owing to a narrower range of host genotypes in the fragmented area.
 Combined, our findings show that urban landscapes can have impacts on a
 pathogen and its evolution in a carnivore living in one of the most
 fragmented and urban systems in North America. The analytical approach
 used here can be broadly applied to other host-pathogen systems, including
 humans.
description: Landscape and host data
 and bobcat sample datesLandscape and host data
 tab: Landscape and host variables calculated for each bobcat FIV sample
 (X21 - X240). See the paper for a description of each of each variable.
 Bobcat sample dates tab: Year each bobcat FIV sample was
 taken.Dryad
 landscape and host data.xlsx
DOI: 10.5061/dryad.t3g1vc3
title: Data from: Global methylation in relation to methotrexate-induced oral mucositis in children with acute lymphoblastic leukemia

description: BACKGROUND Children with acute lymphoblastic leukemia (ALL) often suffer
 from toxicity of chemotherapeutic drugs such as Methotrexate (MTX).
 Previously, we reported that 20% of patients receiving high-dose MTX
 developed oral mucositis. MTX inhibits folate metabolism, which is
 essential for DNA methylation. We hypothesize that MTX inhibits DNA
 methylation, which results into adverse effects. We studied DNA
 methylation markers during high-dose methotrexate treatment in pediatric
 acute lymphoblastic leukemia (ALL) in relation to developing oral
 mucositis. MATERIALS & METHODS S-Adenosyl-Methionine (SAM) and
 S-Adenosyl-Homocysteine (SAH) levels and LINE1 DNA methylation were
 measured prospectively before and after high-dose methotrexate (HD-MTX 4 x
 5g/m2) therapy in 82 children with ALL. Methotrexate-induced oral
 mucositis was registered prospectively. Oral mucositis (grade ≥ 3 National
 Cancer Institute Criteria) was used as clinical endpoint. RESULTS SAM
 levels decreased significantly during methotrexate therapy (-16.1 nmol/L
 (-144.0 - +46.0), p&lt;0.001), while SAH levels and the SAM:SAH ratio
 did not change significantly. LINE1 DNA methylation (+1.4% (-1.1 - +6.5),
 p&lt;0.001) increased during therapy. SAM and SAH levels were not
 correlated to LINE1 DNA methylation status. No association was found
 between DNA methylation markers with developing oral mucositis.
 CONCLUSIONS This was the first study that assessed DNA methylation in
 relation to MTX-induced oral mucositis in children with ALL. Although
 global methylation markers did change during methotrexate therapy,
 methylation status was not associated with developing oral mucositis.
description: 20180516 Database - DNA
 methylation LINE1 - MTX oral mucositisPatientStudyID:
 anonymized patient number; Gender: 1 = male, 2 = female; AGE_Dx: age at
 diagnosis (in years); Code_immu: 1 = pre-B-ALL, 2 = T-ALL; Code_protRx:
 SRG = standard risk group ALL, MRG = medium risk group ALL; SAM_T0: SAM at
 T0; SAH_T0: SAH at T0; X58075_LINE1_CpG_1_T0: LINE1 CpG1 T0 in percentage;
 X58075_LINE1_CpG_2_T0: LINE1 CpG2 at T0 in percentage;
 X58075_LINE1_CpG_3_T0: LINE1 CpG3 at T0 in percentage;
 X58075_LINE1_CpG_5_T0; LINE1 CpG5 at T0 in percentage;
 X58075_LINE1_CpG_6.7_T0: LINE1 CpG6.7 at T0 in percentage;
 X58075_LINE1_CpG_8.9_T0: LINE1 CpG8.9 at T0 in percentage;
 X58075_LINE1_CpG_11.12_T0: LINE1 CpG11.12 at T0 in percentage;
 X58075_LINE1_total_methylation_T0: LINE1 mean of all CpGs (total
 methylation) at T0 in percentage; all DNA methylation markers at T0 also
 at T1; Mucositis_NCI3_T1_T4; 0 = mucositis absent (NCI CTCAE grade 0 - 1 -
 2), 1 = mucositis present (NCI CTCAE 3 - 4)20180516 Database - DNA
 methylation - MTX oral mucositis.csv
DOI: 10.5061/dryad.m23g6
title: Data from: Foraging modality and plasticity in foraging traits determine the strength of competitive interactions among carnivorous plants, spiders, and toads

description: 1. Foraging modalities (e.g., passive, sit-and-wait, active) and traits
 are plastic in some species, but the extent to which this plasticity
 affects interspecific competition remains unclear. 2. Using a long-term
 laboratory mesocosm experiment, we quantified competition strength and the
 plasticity of foraging traits in a guild of generalist predators of
 arthropods with a range of foraging modalities. 3. Each mesocosm contained
 eight passively foraging pink sundews, and we employed an experimental
 design where treatments were the presence or absence of a sit-and-wait
 foraging spider and actively foraging toad crossed with five levels of
 prey abundance. We hypothesized that actively foraging toads would
 outcompete the other species at low prey abundance, but that spiders and
 sundews would exhibit plasticity in foraging traits to compensate for
 strong competition when prey were limited. 4. Results generally supported
 our hypotheses. Toads had a greater effect on sundews at low prey
 abundances, and toad presence caused spiders to locate webs higher above
 the ground. Additionally, the closer large spider webs were to the ground,
 the greater the trichome densities produced by sundews. Also, spider webs
 were larger with than without toads and as sundew numbers increased, and
 these effects were more prominent as resources became limited. Finally,
 spiders negatively affected toad growth only at low prey abundance. 5.
 These findings highlight the long-term importance of foraging modality and
 plasticity of foraging traits in determining the strength of competition
 within and across taxonomic kingdoms. Future research should assess
 whether plasticity in foraging traits helps to maintain coexistence within
 this guild and whether foraging modality can be used as a trait to
 reliably predict the strength of competitive interactions.
description: Spider prey consumption
 and trait response dataData collected from
 funnel-web-building wolf spiders (Sosippus floridanus) in laboratory
 mesocosms. Units of measurement are: web area (cm2), web height (cm),
 difference in trichome density (number of trichomes/cm2), difference in
 trapping area (cm2), and sum trapping area (cm2).spiders.csvSundew prey consumption and trait response dataData collected from pink sundews (Drosera capillaris) in laboratory mesocosms. Units of measurement are: web area (cm2), web height (cm), difference in trichome density (number of trichomes/cm2), difference in trapping area (cm2), and sum trapping area (cm2).sundews.csvToad prey consumption and trait response dataData collected from oak toads (Anaxyrus quercicus) in laboratory mesocosms. Units of measurement are: web area (cm2), web height (cm), toad growth (g), difference in trichome density (number of trichomes/cm2), difference in trapping area (cm2), and sum trapping area (cm2).toads.csv
DOI: 10.5061/dryad.4kh60
title: Data from: Egg chemoattractants moderate intraspecific sperm competition

description: Interactions among eggs and sperm are often assumed to generate
 intraspecific variation in reproductive fitness, but the specific
 gamete-level mechanisms underlying competitive fertilization success
 remain elusive in most species. Sperm chemotaxis–the attraction of sperm
 by egg-derived chemicals—is a ubiquitous form of gamete signaling,
 occurring throughout the animal and plant kingdoms. The chemical cues
 released by eggs are known to act at the interspecific level (e.g.,
 facilitating species recognition), but recent studies have suggested that
 they could have roles at the intraspecific level by moderating sperm
 competition. Here, we exploit the experimental tractability of a broadcast
 spawning marine invertebrate to test this putative mechanism of
 gamete-level sexual selection. We use a fluorescently labeled
 mitochondrial dye in mussels to track the real-time success of sperm as
 they compete to fertilize eggs, and provide the first direct evidence in
 any species that competitive fertilization success is moderated by
 differential sperm chemotaxis. Furthermore, our data are consistent with
 the idea that egg chemoattractants selectively attract ejaculates from
 genetically compatible males, based on relationships inferred from both
 nuclear and mitochondrial genetic markers. These findings for a species
 that exhibits the ancestral reproductive strategy of broadcast spawning
 have important implications for the numerous species that also rely on egg
 chemoattractants to attract sperm, including humans, and have potentially
 important implications for our understanding of the evolutionary cascade
 of sexual selection.
description: Fertilization success,
 genetic relatedness and mitochondrial lineage estimates from competitive
 sperm chemotaxis experimentSheet 1 contains the
 results of multi-step sperm competition laboratory trials in the presence
 of egg chemoattractants in the mussel Mytilus galloprovincialis. Columns
 included are experimental block number, focal male (sperm donor) ID, focal
 female (egg chemoattractant donor) ID, replicate (two for each focal
 male-female cross), focal male fertilization success, focal male failures
 (eggs not fertilized), and total eggs counted. Sheet 2 contains similar
 data, but with the two replicate fertilization success measures for each
 focal male-female cross combined into a single measure. This sheet also
 contains estimates of nuclear genetic relatedness of male-female pairs,
 and a column specifying whether males and females belong to different (0)
 or the same (1) phylogenetic mitochondrial lineage.Lymbery_et_al_Evolution_Letters_data.xlsx
DOI: 10.15468/dl.n7vjfa
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Convolvulus steppicola"
 ]
}

 The dataset includes 29 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001357-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.