cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.15dv41nw7
title: The cost of ectoparasitism in cliff swallows declines over 35 years

description: Host-parasite dynamics often vary over time, brought about by changes in
 the parasite’s virulence or the host’s ability to resist or tolerate the
 parasite.  Although virulence evolution in microparasites is well
 studied, we know little about temporal change in the pathogenicity of
 macroparasites such as blood-feeding insects.  Using data
 collected over 35 years, we report a reduction in pathogenicity of the
 hematophagous swallow bug (Cimex vicarius) on its cliff swallow
 (Petrochelidon pyrrhonota) host.  Relative to experimentally
 fumigated, parasite-free nests, the negative effects of bugs on nestling
 swallow body mass and survival were less in the later years of the study
 than in the earlier years, and the negative relationship between nestling
 body mass and bug abundance became weaker over time.  The
 survival of adult birds exposed to swallow bugs increased throughout the
 study, while survival of birds from parasite-free nests decreased over
 time.  Swallow bug abundance per nest, bug body size, and bug age
 ratios did not change during the study.  Between-colony
 transmission of bugs shifted toward greater immigration into smaller
 colonies than in earlier studies, but there was no net change in
 transmission.  Cliff swallows did not reduce their exposure to
 bugs over time by being more likely to avoid infested nest or colony
 sites.  Parents increased the number of food deliveries to their
 offspring over time in the presence of parasites, but the total amount of
 food delivered was unchanged.  The reduced cost of swallow bug
 ectoparasitism does not seem related to changes in parasite narrow-sense
 virulence, the host’s avoidance of parasites, the presence of alternative
 hosts for bugs, or climate-driven phenological mismatches.  The
 results probably reflect the cliff swallow’s evolving of greater tolerance
 to swallow bugs, brought about by the bird’s shift from natural cliff
 nesting sites to artificial structures that may harbor more bugs than
 natural cliffs.  This study shows that hosts can respond
 relatively rapidly to high levels of parasitism, and provides support for
 models that suggest the evolution of tolerance should be expected in some
 host-parasite systems. 
description: README file describes each dataset, which is cross-referenced to
 each analysis in the paper.
DOI: 10.5061/dryad.547d7wm6t
title: Resources for gasAcu1-4, a new stickleback reference genome

description: gasAcu1-4 is a new version of the stickleback reference genome. It only
 minorly differs from the 2017 Hi-C guided assembly by Peichel, Sullivan,
 Liachko, and White (https://doi.org/10.1093/jhered/esx058) to improve the
 subtelomeric Pitx1 locus and the mitochondrial genome.
 We here present basic resources for utilizing this version of the
 reference genome: the fasta sequence of the assembly and liftOver chains
 for converting coordinates between this reference version and the
 original (Broad S1) gasAcu1
 assembly (https://www.nature.com/articles/nature10944). This
 assembly can be visualized and other data downloaded via the
 Table Browser of the UCSC Genome Browser by copying the following track
 hub URL into the “My Hubs” tab at
 https://genome.ucsc.edu/cgi-bin/hgHubConnect:
 https://sbwdev.stanford.edu/kingsleyAssemblyHub/hub.txt.
description: The 2017 Hi-C guided assembly by Peichel, Sullivan, Liachko, and
 White (https://doi.org/10.1093/jhered/esx058) was modified to address two
 long-standing issues that have persisted throughout several versions of
 the stickleback reference genome: First, the
 subtelomeric region of chrVII is of great biological interest due to its
 well-documented role in controlling pelvic spine development (Shapiro et
 al. 2004). However, due to its highly repetitive nature, it is
 extremely difficult to assemble and many important sequences, including
 the key gene Pitx1, are missing entirely from existing genome assemblies,
 while other sequences in the region are scattered in small unassembled
 scaffolds. We address this issue by including the sequence from Salmon
 River BAC clones (Genbank GU130435) (Chan et al. 2010) as chrP and removing overlapping fragmented sequences from chrUn and the end of chrVII. We note that chrP is derived from a marine population, while the rest of the genome is from a freshwater population (Bear Paw Lake), so all analyses concerning this chromosome must be interpreted with care.  Second, the mitochondrial genome was previously split into two fragments buried within chrUn, while a separate mitochondrial genome sequence from Northern Japan was added as chrM. We corrected these issues by removing the duplicated Bear Paw Lake mitochondrial genome from chrUn and using it to replace the exogenous chrM sequence, resulting in a single copy of the mitochondrial genome derived entirely from Bear Paw Lake. The Peichel et al. 2017 reference genome was not modified in any other ways.
DOI: 10.5068/d1zd5s
title: Single cell transcriptomic analyses reveal the impact of bHLH factors on human retinal organoid development

description: The developing retina expresses multiple bHLH transcription
 factors. Their precise functions and interactions in uncommitted
 retinal progenitors remain to be fully elucidated. Here, we
 investigate the roles of bHLH factors ATOH7 and Neurog2 in human ES
 cell-derived retinal organoids.  Single-cell transcriptome
 analyses identify three states of proliferating retinal progenitors:
 pre-neurogenic, neurogenic, and cell cycle-exiting
 progenitors. Each shows different expression profile of bHLH
 factors. The cell cycle-exiting progenitors feed into a
 postmitotic heterozygous neuroblast pool that gives rise to early born
 neuronal lineages. Elevating ATOH7 or Neurog2 expression
 accelerates the transition from the pre-neurogenic to the neurogenic
 state, and expands the exiting progenitor and neuroblast
 populations. In addition, ATOH7 and Neurog2 significantly, yet
 differentially, enhance retinal ganglion cell and cone photoreceptor
 production. Moreover, single-cell transcriptome analyses reveal
 that ATOH7 and Neurog2 assert positive autoregulation, suppress key bHLH
 factors associated with the neurogenic progenitors, and elevate bHLH
 factors expressed by exiting progenitors and differentiating
 neuroblasts. This study thus provides novel insight regarding how
 ATOH7 and Neurog2 impact human retinal progenitor behaviors and neuroblast
 fate choices.
description: The datasets were collected by performing single-cell
 RNA-sequencing of human ESC-derived retinal organoids transduced by
 lentiviral vectors expressing EGFP, ATOH7, or Neurog2. Viral transduced
 cells were FACS sorted and subjected to 10X Genomics single-cell barcoding
 and cDNA library construction. Illumina NovaSeq6000 S2 paired-end 2x50bp
 mode was used to sequence the libraries. Spliced Transcripts Alignment
 to a Reference (STAR) version 2.5.1b (cellranger
 count) was used to perform sequence alignments to the reference human
 genome (GRCh38), barcode counts, and UMI counts to yield summary reports
 and t-Stochastic Neighboring Embedding (t-SNE) dimensionality
 reduction. For downstream analyses, cells with a number of unique molecular identifiers
 (UMI) &gt; 2500 per cell and &lt; 0.1 % mitochondrial
 gene expression were used. For LV-GFP, LV-AEP, LV-NEP samples, the mean
 reads per cell ranged from 139,000-195,000, with mean gene per cell
 ranging from 2935-3079. The resulting total single-cell counts used for
 analysis were 3004 for LV-EGFP, 2063 for LV-AEP, and 3909 for LV-NEP
 infected samples.
DOI: 10.25338/b8xw63
title: Injury alters motivational trade-offs in calves during the healing period

description: Injury can produce long-lasting motivational changes that may alter
 decisions made under risk. Our objective was to determine whether a
 routine painful husbandry procedure, hot-iron disbudding, affects how
 calves trade off risk avoidance against a competing motivation (i.e.,
 feeding), and whether this response depends on time since injury. We used
 a startle test to evaluate this trade-off in calves disbudded 0 or 21 days
 previously and non-injured control calves. For 3 days, calves were
 individually habituated to the testing arena in which they received a 0.5
 L milk meal via a rubber teat. On the 4th day, upon approaching the milk
 reward, the calf was startled by a sudden noise. We assessed the duration
 and magnitude of the calf’s startle response, their latency to return to
 the milk bottle, and duration spent suckling after startling. No treatment
 differences were observed in the duration and magnitude of the startle
 response or in the probability of returning to the bottle after startling.
 However, among those who did return, disbudded calves spent longer
 suckling, indicating they accepted more risk in order to feed compared to
 controls. In addition, calves with 21-day-old injuries tended to return to
 the bottle faster compared to newly disbudded calves and controls. We
 suggest that hot-iron disbudding increases calves’ motivation to suckle,
 as they were more likely to prioritize this behaviour over risk avoidance
 compared to control calves. This effect was most evident 21 days after
 disbudding, indicating that injury can produce long-term changes in
 motivational state.
description: See methods in associated
 publication
description: Data were collected from the
 University of California Davis Dairy Facility on 36 calves in 2018.
 Variables are defined in Sheet 2 of the Excel file. The R script used to
 analyze the dataset is provided.
DOI: 10.5061/dryad.6t1g1jwxh
title: Widely assumed phenotypic associations in Cannabis sativa lack a shared genetic basis

description: The flowering plant Cannabis sativa, cultivated for centuries for multiple
 purposes, displays extensive variation in phenotypic traits in addition to
 its wide array of secondary metabolite production. Notably, Cannabis
 produces two well-known secondary-metabolite cannabinoids: cannabidiolic
 acid (CBDA) and delta-9-tetrahydrocannabinolic acid (THCA), which are the
 main products sought by consumers in the medical and recreational market.
 Cannabis has several suggested subspecies which have been shown to differ
 in chemistry, branching patterns, leaf morphology and other traits. In
 this study we obtained measurements related to phytochemistry,
 reproductive traits, growth architecture, and leaf morphology from 297
 hybrid individuals from a cross between two diverse lineages. We explored
 correlations among these characteristics to inform our understanding of
 which traits may be causally associated. Many of the traits widely assumed
 to be strongly correlated did not show any relationship in this hybrid
 population. The current taxonomy and legal regulation within Cannabis is
 based on phenotypic and chemical characteristics. However, we find these
 traits are not associated when lineages are inter-crossed, which is a
 common breeding practice and forms the basis of most modern marijuana and
 hemp germplasms. Our results suggest naming conventions based on leaf
 morphology do not correspond to the chemical properties in plants with
 hybrid ancestry. Therefore, a new system for identifying variation within
 Cannabis is warranted that will provide reliable identifiers of the
 properties important for recreational and, especially, medical use.
DOI: 10.5061/dryad.8cz8w9gnz
title: Spatially anonymized data for: Multistate Ornstein-Uhlenbeck approach for practical estimation of movement and resource selection around central places

description: 1. Home range dynamics and movement are central to a species' ecology
 and strongly mediate both intra- and interspecific interactions. Numerous
 methods have been introduced to describe animal home ranges, but most lack
 predictive ability and cannot capture effects of dynamic environmental
 patterns, such as the impacts of air and water flow on movement. 2. Here,
 we develop a practical, multi-stage approach for statistical inference
 into the behavioral mechanisms underlying how habitat and dynamic energy
 landscapes---in this case how airflow increases or decreases the energetic
 efficiency of flight---shape animal home ranges based around central
 places. We validated the new approach using simulations, then applied it
 to a sample of 12 adult golden eagles (Aquila chrysaetos) tracked
 with satellite telemetry.  3. The application to golden eagles
 revealed effects of habitat variables that align with predicted behavioral
 ecology. Further, we found that males and females partition their home
 ranges dynamically based on uplift. Specifically, changes in wind
 and sun angle drove differential space use between sexes, especially later
 in the breeding season when energetic demands of growing nestlings require
 both parents to forage more widely.   4. This method is easily
 implemented using widely available programming languages and is based on a
 hierarchical multistate Ornstein-Uhlenbeck space use process that
 incorporates habitat and energy landscapes. The underlying
 mathematical properties of the model allow straightforward computation of
 predicted utilization distributions, permitting estimation of home range
 size and visualization of space use patterns under varying conditions.
description: ID: individual tag identifier phen: indicator
 for early or late breeding season k: number of home
 range cores mumu: time series of core
 switches mux: spatially anymonized core center
 location muy: spatially anymonized core center
 location x: spatially anymonized locations
 y: spatially anymonized locations aniso:
 regression covariate for esitmation remaining columns:
 the moajority of remaining columns are environmental covairiates and
 they're centered/scaled equivalents
DOI: 10.5061/dryad.gmsbcc2kt
title: Kin-mediated plasticity in alternative reproductive tactics

description: Conditional strategies occur when the fitness payoff an individual
 receives from expressing a given phenotype (from a range of two or more
 possible phenotypes) is contingent upon that individual’s environmental
 circumstances. This conditional strategy model underlies many cases of
 alternative reproductive tactics, in which individuals of one sex employ
 different means to obtain reproductive opportunities. How genetic
 relatedness and indirect fitness effects could affect the expression of
 alternative reproductive tactics remains unexplored. Here, we address this
 gap using the Acarid mite Rhizoglyphus echinopus, in which large males
 develop into aggressive ‘fighters’ and small males develop into
 non-aggressive ‘scramblers.’ Because fighters kill their rivals whereas
 scramblers do not, fighters should incur a greater indirect fitness cost
 when competing with their relatives, and thus the expression of the
 fighter phenotype could be reduced in the presences of relatives. To test
 this, we raised mites in full-sibling or mixed-sibship groups and found
 that fighters were more common in full-sibling groups, not less common as
 we predicted. This apparently counter-intuitive result could be explained
 if relatedness and cue variability are interpreted as a signal of
 population density, since fighters are more common at low densities in
 this species. Alternatively, our results may indicate that males compete
 more intensely with relatives than non-relatives in this species. Our
 study provides the first evidence of kin-mediated plasticity in the
 expression of alternative reproductive tactics.
DOI: 10.5061/dryad.4f4qrfj9p
title: Data for degrees earned by faculty teaching in soil science preparatory programs at universities in the USA

description: In the early 2000s some were concerned that few soil science graduate
 students were receiving their bachelor’s degrees in soil science. However,
 no studies were conducted to investigate this or how it may have changed
 over time. Information available on university webpages for faculty in the
 USA was used to determine the faculty’s bachelor’s, master’s, and doctoral
 degree disciplines. Faculty rank was used to determine if a change had
 occurred in the percent of faculty who received their bachelor’s degrees
 in soil science over time. Only 16% of faculty teaching in programs that
 prepare graduates to work as soil scientists received their bachelor’s
 degrees in soil science. This percentage increased to 56% and 67% who
 received their master’s and doctoral degrees, respectively, in soil
 science, but about 26% of faculty who teach in soil science preparatory
 programs did not have any degrees that could be identified as a “soil
 science” degree. The degrees that faculty received their training in also
 differed by their current soil science specialty area. About 13% of
 assistant professors and 20% of full professors received their bachelor’s
 degrees in soil science, so the percentage of students entering soil
 science graduate programs with a bachelor’s degree in soil science appears
 to have declined with time. However, a majority of soil science graduate
 students having bachelor’s degrees from other fields also appears to have
 been common going back at least several decades.
description: Data was collected through online searches of the faculty pages
 at universities known to offer undergraduate training leading to careers
 as soil scientists for their graduates.
DOI: 10.5061/dryad.j9kd51cb0
title: Deafness in Australian Cattle Dogs associated to QTL on chromosome 20 in GWAS analyses

description: Pigment-associated deafness is a common hereditary condition in a range of
 dog breeds. The aim of this study was to perform a genome-wide association
 analysis to investigate the genetic architecture of deafness in Australian
 Cattle Dogs. Genotypes for 104,757 polymorphisms in 96 Australian dogs
 were available for analyses after quality control and included here.
 Further samples from US and UK are available here
 (https://doi.org/10.5061/dryad.sf7m0cg2n). A genomic relationship matrix
 was used in the mixed model analyses to account for polygenic effects, as
 we tested each polymorphism for its association with deafness, in a
 case/control experimental design. Three approaches were used to code the
 genotypes and test for additive, recessive and dominant SNP effects.
 Analysing all samples together, GWAS analyses identified a clear
 association peak on CFA20, with the most significant SNPs on this
 chromosome (-log10 p value = 3.89) in the vicinity of MITF. Mutations in
 MITF have been associated with white pigmentation in dogs and with
 deafness in humans and other species, supporting the premise that canine
 deafness is associated with mutations in or near this gene.  A
 recessive inheritance for the peak in CFA20 is possible given the
 significant results in the recessive model; however, the estimated
 heritability was low (4.54 x10-5). Further validation, identification of
 mutations and testing in other dog breeds are needed.
description: Hearing status was confirmed in Australian Cattle Dogs by means
 of the brainstem auditory evoked response (BAER). In Australia, blood
 samples were collected into EDTA at the time of BAER testing. Samples were
 genotyped using the Illumina CanineHD BeadChip array. This array is a chip
 that contains more than 170,000 single nucleotide polymorphisms (SNPs) and
 was mapped to the CanFam3.1 reference genome. SNPs with a call rate lower
 than 0.8 or a minor allele frequency (MAF) lower than 0.05 were removed
 from the analyses.
description: Phenotypes are indicated in the sample ID:
 D=bilaterally deaf, L=unilaterally deaf in left ear;
 R=unilaterally deaf in right ear; N=not deaf i.e. hearing.
DOI: 10.5061/dryad.80gb5mkpv
title: Plant-plant communication and community of herbivores on tall goldenrod (dataset)

description: 1. The volatiles from damaged plants induce defense in neighboring plants.
 The phenomenon is called plant-plant communication, plant talk or plant
 eavesdropping. Plant-plant communication has been reported to be stronger
 between kin plants than genetically far plants in sagebrush. 2. Why do
 plants distinguish volatiles from kin or genetically far plants? We
 hypothesize that plants respond only to important conditions; the induced
 defense is not free of cost for the plant. To clarify the hypothesis, we
 conducted experiments and investigations using goldenrod of 4 different
 genotypes. 3. The arthropods community on tall goldenrods were different
 among 4 genotypes. The response to volatiles was stronger from genetically
 close plants to the emitter than from genetically distant plants from the
 emitter. The volatiles from each genotype of goldenrods were different;
 and they were categorized accordingly. Moreover, the arthropod community
 on each genotype of goldenrods were different. 4. Synthesis: Our results
 support the hypothesis: goldenrods respond to volatiles from genetically
 close plants because they would have similar arthropod species. These
 results are important clues elucidating adaptive significance of
 plant-plant communication.
DOI: 10.5061/dryad.02v6wwq22
title: Sequence alignment for 7 gene regions for new Phytophthora species in clade 2a

description: Five new taxa from Phytophthora ITS Clade 2a are described from Cinnamomum
 cassia plantations and adjacent waterways in Van Yen, Vietnam, and
 disturbed rainforest in the Hela Province of Papua New Guinea and from
 disturbed forest on Christmas Island. Phylogenetic analyses were performed
 using data from nuclear regions (ITS, β-tubulin; Heat shock protein 90)
 and mitochondrial regions (cytochrome c oxidase subunit 1; cytochrome c
 oxidase subunit2; NADH dehydrogenase subunit 1; ribosomal protein L10).
 The molecular data supported recognition of three species: Phytophthora
 insulinativitatica, P. multibullata and P. x vanyenensis and two informal
 taxa, P. sp. germisporangia and P. sp. awatangi. P. x vanyenensis appears
 to be a hybrid between P. sp. mekongensis and an unknown species. P.
 multibullata and P. sp. germisporangia are phylogenetically close to P.
 citrophthora, but morphologically distinct. P. insulinativitatica is most
 closely related to P. botryosa but has different morphology. P. sp.
 germisporangia and P. sp. awatangi were morphologically distinct and
 separated in the phylogeny based on mitochondrial sequences, but their
 nuclear sequences were identical. When comparing the sequences of these
 new species to that available on GenBank, it became evident that some of
 these species shared similarity with isolates submitted to GenBank under
 other species names and a re-evaluation of all P. meadii and P. colocasiae
 ITS sequence data identified an additional 7 putatively new species all
 isolated from Asia. The results support the view that many more
 Phytophthora species remain to be discovered in the Asia-Pacific region.
description: To confirm the new species gene regions were amplified and
 sequenced in both directions; the internal transcribed spacer region
 (ITS), cytochrome oxidase subunit 1 (<i>cox</i>1), cytochrome
 c oxidase subunit2 <i>cox</i>2, NADH dehydrogenase subunit 1
 (<i>nadh1)</i> ribosomal protein L10
 (<i>rps10),</i> β-tubulin and heat shock protein 90
 (<i>hsp</i>90) The sequence data of
 <i>Phytophthora</i> isolates used in this study were compared
 with other closely related species (ITS clade 2a) that were either
 sequenced for this study or taken from GenBank (http://www.ncbi.nlm.nih.gov/) or the <i>Phytophthora </i>database (http://www.phytophthoradb.org/) or the IDphy online resource (http://idtools.org/id/phytophthora/index.php). Sequence data were compiled in Geneious Prime 2019 (Biomatters; available from http://www.geneious.com/). The most appropriate substitution model was determined using jModelTest (Posada 2008). Bayesian analysis with MrBayes (Ronquist et al. 2011) and Maximum Likelihood (ML) analysis using RAxML (Stamatakis 2014) were performed as a plugins within the Geneious software.
description: There are seven nexus sequence alignment files that can be
 directly uploaded