cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9p8cz8wgd
title: Body size variation in polyplacophoran mollusks: geographic clines and community structure along the Southeastern Pacific

description: Aim: To evaluate the latitudinal pattern of body size within and among
 chiton species employing phylogenetically structured analyses, and to
 examine the role of geographic variation in temperature, productivity and
 oxygen availability as potential environmental drivers. Location: Coastal
 habitats of the Southeastern Pacific along a latitudinal range of nearly
 6,000 km, from the Equator to Patagonia (~ 2º to 56º S). Time Period:
 Present (2011 – 2017). Major taxa: 31 species of polyplacophoran mollusks.
 Methods: We measured the body length of 6,162 individuals collected in 62
 sites, and reconstructed the phylogeny of this group based on two
 mitochondrial and one nuclear gene regions. We combined this information
 with data of sea surface temperature, chlorophyll-a concentration –as a
 proxy of primary productivity– and dissolved oxygen, and assessed which
 variables best explain the variation in size both within and among species
 employing phylogenetic generalised least squares (PGLS) and a model
 comparison approach. Main conclusions: Our analyses show that body size
 increases consistently with latitude, both within and among species,
 following Bergmann’s rule. Variation in sea surface temperature along the
 latitudinal gradient provided a substantially better fit than
 chlorophyll-a and dissolved oxygen. Our results support the
 temperature-size rule for this lineage and suggest that similar processes
 could underlie the emergence of intra and interspecific gradients in body
 size of polyplacophorans. At the community level, chiton species richness
 was higher at intermediate latitudes and positively correlated with body
 size variation, suggesting that heterogeneity in size may reduce
 interspecific competition and contribute to species coexistence in this
 group. Overall, our study demonstrates that historical events,
 macroecological adaptive trends and local processes at the community level
 contribute to the distribution and size variation of polyplacophoran
 species along the Southeastern Pacific.
description: <b>Chitons sampling
 </b> Field samplings were conducted in 62
 localities ranging from the equator (~ 2.3 °S) to the Magellan strait (~
 56 °S), along the Southeastern Pacific (SEP) (Figure 1A). Sampling was
 conducted mostly in the spring-summer period between July 2011 and January
 2017. We collected a total of 6,162 individuals belonging to 31 chiton
 species (Table S1). Chitons were collected by hand during low tide at
 intertidal habitats, and in shallow subtidal habitats by snorkeling and/or
 SCUBA (2 – 10 m). All surveys were performed during at least two-hour
 intervals at each location in order to homogenize sampling efforts.
 Specimens were identified to the species-level following different
 taxonomic guides (e.g. Kaas & Van Belle, 1987; Schwabe et al.,
 2006; Kaas, Van Belle, & Stack, 2006; Schwabe, 2009). Body length
 (BL, mm) –including the girdle– was measured for each specimen using a
 digital caliper (to the nearest 0.1 mm).
DOI: 10.5061/dryad.66t1g1k25
title: Data for: Reproductive success of captive-reared Allegheny Woodrats (Neotoma magister) released into genetically depauperate populations

description: Habitat fragmentation and degradation have led to a proliferation of small
 and isolated populations that are vulnerable to genetic erosion. Reduction
 in habitat and concomitant declines in population connectivity can
 expediate the collapse of species that exist as natural metapopulations.
 In recent years, Allegheny woodrats (Neotoma magister) have experienced
 local extirpations and declines in genetic diversity across their range
 due to disease-related mortality, reduced food availability, and
 disruption of connectivity among subpopulations. In response, we developed
 a captive-breeding program to facilitate genetic management of isolated
 woodrat populations in Indiana. Between 2010 and 2012, 27 captive-reared
 individuals were released to four sites with declining woodrat abundance.
 We used 99 single nucleotide polymorphisms and 11 microsatellite loci to
 genotype sympatric woodrats from the four sites, sampled before and after
 the release of captive-reared individuals, to: 1) evaluate the
 post-release reproductive success of captive-reared individuals and 2)
 characterize changes in genetic diversity. A minimum of five of the 27
 captive-reared woodrats produced at least 20 offspring, 11 of which were
 sired by a single male. One site exhibited increased abundance by the end
 of the monitoring period, although genetic variability decreased. Two
 sites experienced population declines in concert with fluctuating genetic
 variability. The last site showed comparable abundance at the beginning
 and end of the monitoring period, with an increase in observed
 heterozygosity. Our results indicate that captive-reared woodrats were, in
 some cases, able to reproduce in the wild, interbreed with residents and
 increase genetic diversity and abundance among small, isolated
 subpopulations.
DOI: 10.6084/m9.figshare.31165934
title: Additional file 4 of Metabolomic and proteomic differences in susceptible and benzimidazole-resistant adult females and males of Haemonchus contortus

description: Additional file 4: TMT experimental design (S1). Complete list of proteins identified and quantified in H. contortus adults (S2). Differential expression analyses of their levels (S3) between resistant and susceptible females (S3a), resistant and susceptible males S3b), sensitive males and females (S3c), and resistant males and females (S3d). KEGG pathway analysis of detected metabolites against C. elegans genome (S4a). Homologous relationships for H. contortus proteins identified using BLAST bidirectional best hits (S4b).
DOI: 10.6084/m9.figshare.31165934.v1
title: Additional file 4 of Metabolomic and proteomic differences in susceptible and benzimidazole-resistant adult females and males of Haemonchus contortus

description: Additional file 4: TMT experimental design (S1). Complete list of proteins identified and quantified in H. contortus adults (S2). Differential expression analyses of their levels (S3) between resistant and susceptible females (S3a), resistant and susceptible males S3b), sensitive males and females (S3c), and resistant males and females (S3d). KEGG pathway analysis of detected metabolites against C. elegans genome (S4a). Homologous relationships for H. contortus proteins identified using BLAST bidirectional best hits (S4b).
DOI: 10.5061/dryad.gmsbcc2nb
title: Limitations of using surrogates for behaviour classification of accelerometer data: refining methods using random forest models in Caprids

description: Animal-attached devices can be used on cryptic species to measure their
 movement and behaviour, enabling unprecedented insights into fundamental
 aspects of animal ecology and behaviour. However, direct observations of
 subjects are often still necessary to translate biologging data accurately
 into meaningful behaviours. As many elusive species cannot easily be
 observed in the wild, captive or domestic surrogates are typically used to
 calibrate data from devices. However, the utility of this approach remains
 equivocal.  Here, we assess the validity of using captive
 conspecifics, and phylogenetically-similar domesticated counterparts
 (surrogate species) for calibrating behaviour classification. Tri-axial
 accelerometers and tri-axial magnetometers were used with behavioural
 observations to build random forest models to predict the behaviours. We
 applied these methods using captive Alpine ibex (Capra ibex) and a
 domestic counterpart, pygmy goats (Capra aegagrus hircus), to predict the
 behaviour including terrain slope for locomotion behaviours of captive
 Alpine ibex.  Behavioural classification of captive Alpine ibex
 and domestic pygmy goats was highly accurate (&gt; 98%). Model
 performance was reduced when using data split per individual, i.e.,
 classifying behaviour of individuals not used to train models
 (mean ± sd = 56.1 ± 11%). Behavioural classifications using domestic
 counterparts, i.e., pygmy goat observations to predict ibex behaviour,
 however, were not sufficient to predict all behaviours of a
 phylogenetically similar species accurately (&gt; 55%). We demonstrate
 methods to refine the use of random forest models to classify behaviours
 of both captive and free-living animal species. We suggest there are two
 main reasons for reduced accuracy when using a domestic counterpart to
 predict the behaviour of a wild species in captivity; domestication
 leading to morphological differences and the terrain of the environment in
 which the animals were observed. We also identify limitations when
 behaviour is predicted in individuals that are not used to train models.
 Our results demonstrate that biologging device calibration needs to be
 conducted using: (i) with similar conspecifics, and (ii) in an area where
 they can perform behaviours on terrain that reflects that of species in
 the wild.
description: Collar attached daily diary tags were deployed on pygmy goats and
 Alpine ibex. Behaviour observations were then used to label data for
 specific behaviours, which was processed and then exported from Daily
 Diary Multiple Trace (DDMT). Further processing was conducted in R version
 3.6.
description: NA in first row for smVEDBA. NA first 4 rows for PSD and maz
 frequency variables. NA's in terrain slope column for behaviours
 without terrain slope labelled.
DOI: 10.6084/m9.figshare.31165940
title: Additional file 1 of Daphnia magna diapause-interrupted embryogenesis has changes in histone modifications at H3K9

description: Supplementary material 1
DOI: 10.6084/m9.figshare.31165940.v1
title: Additional file 1 of Daphnia magna diapause-interrupted embryogenesis has changes in histone modifications at H3K9

description: Supplementary material 1
DOI: 10.6084/m9.figshare.31165943
title: Additional file 2 of Daphnia magna diapause-interrupted embryogenesis has changes in histone modifications at H3K9

description: Supplementary material 2.
DOI: 10.6084/m9.figshare.31165943.v1
title: Additional file 2 of Daphnia magna diapause-interrupted embryogenesis has changes in histone modifications at H3K9

description: Supplementary material 2.
DOI: 10.5061/dryad.9w0vt4bfp
title: Evolution and phylogeny of the deep-sea isopod families Desmosomatidae Sars, 1897 and Nannoniscidae Hansen, 1916 (Isopoda: Asellota)

description: In the deep sea, the phylogeny and biogeography of only a few taxa have
 been well studied. Although more than 200 species in 32 genera have been
 described for the asellote isopod families Desmosomatidae Sars, 1897 and
 Nannoniscidae Hansen, 1916 from all ocean basins, their phylogenetic
 relationships are not completely understood. There is little doubt about
 the close relationship of these families, but the taxonomic position of a
 number of genera is so far unknown. Based on a combined morphological
 phylogeny using the Hennigian method with a dataset of 107 described
 species and a molecular phylogeny based on three markers (COI, 16S, and
 18S) with 75 species (most new to science), we could separate
 Desmosomatidae and Nannoniscidae as separate families. However, we could
 not support the concept of the subfamilies Eugerdellatinae Hessler, 1970
 and Desmosomatinae Hessler, 1970. Most genera of both families were well
 supported, but several genera appear as para- or even polyphyletic. Within
 both families, convergent evolution and analogies caused difficulty in
 defining apomorphies for phylogenetic reconstructions and this is
 reflected in the results of the concatenated molecular tree. There is no
 biogeographic pattern in the distribution as the genera occur over the
 entire Atlantic and Pacific Ocean, showing no specific phylogeographical
 pattern. Poor resolution at deep desmosomatid nodes may reflect the long
 evolutionary history of the family and rapid evolutionary radiations.
description: All sequences were obtained by single-gene PCR and sequencing on
 individual vouchered specimens collected at sea and preserved in
 ethanol. 18S and 16S sequences were aligned separately
 in MAFFT v.7 using default settings. Those outputs were then filtered
 through Gblocks v0.91b using all 3 options for a less stringent selection
 to create these final alignments. COI sequences were
 aligned as DNA codons in BioEdit using the CLUSTAL algorithm.
DOI: 10.5061/dryad.gtht76hm8
title: Positive interactions between an exotic invader and moss biocrusts vary across life-stage and correspond with the effect of water pulses on soil nitrogen

description:  The size and frequency of resource pulses can affect plant
 interactions and increase the abundance of invasive species relative to
 native species.  We examined resource pulses generated
 during desiccation and rehydration of communities of native biological
 soil crust (biocrust) forming mosses, in the context of positive
 associations between biocrusts and the invasive forb, Centaurea stoebe. We
 surveyed Centaurea and biocrust cover and evaluated how interactions among
 Centaurea, biocrusts, and water pulses influenced plant biomass and soil
 nitrogen in a field experiment.  Centaurea seedling and
 biocrust interactions were also compared in a greenhouse experiment to
 evaluate differences related to life-stage. In field surveys, Centaurea
 and biocrusts were positively associated.  Across water pulse
 treatments, biocrust biomass decreased when Centaurea was removed,
 indicating that Centaurea facilitated biocrusts. Biocrusts did not affect
 adult Centaurea in the field, but Centaurea seedling biomass was greater
 when grown with biocrusts in the greenhouse.  Water
 pulses did not affect plant biomass, but interactions between Centaurea
 and biocrusts corresponded with variation in the effect of water pulses on
 soil nitrogen which were not evident when Centaurea or biocrusts were
 grown alone.  Twenty-four hours after large water pulses
 were added, soil NO3- was nine times higher in plots where biocrusts and
 Centaurea co-occurred compared with small water pulse
 plots.  In these same plots, soil NH4+ tended to be
 lower at the end of the experiment. These results highlight positive
 interactions between an invasive forb and native moss biocrust.
  Water pulses influenced soil nitrogen availability when both
 plants co-occurred, but did not affect plant biomass, suggesting that
 resource pulses and species interactions can interact to affect ecosystem
 processes.
description: There are three datasets. The first dataset was collected during
 field surveys (SlateCover). The second dataset is associated with a
 two-year field study (SlateFieldExp). The third dataset is associated with
 our greenhouse experiment (SlateGHouseExp).  All data
 are raw and unprocessed. 
description: See README for information on each dataset and variables
 within.
DOI: 10.6084/m9.figshare.31165960
title: Additional file 2 of MicroRNA-29a-5p contributes to neuroinflammation through TLR7

description: Supplementary Material 2. Table S1. List of reagents (antibodies, primers, cell lines, chemicals, and proteins) used in experimental procedures.
DOI: 10.6084/m9.figshare.31165960.v1
title: Additional file 2 of MicroRNA-29a-5p contributes to neuroinflammation through TLR7

description: Supplementary Material 2. Table S1. List of reagents (antibodies, primers, cell lines, chemicals, and proteins) used in experimental procedures.
DOI: 10.6084/m9.figshare.31165963
title: Additional file 3 of MicroRNA-29a-5p contributes to neuroinflammation through TLR7

description: Supplementary Material 3. Table S2. Excel file containing complete data for differentially expressed genes in WT and APP/PS1 mice, mouse characteristics, mRNA gene targets of miR-29a-5p, and cyto-/chemokine analysis.
DOI: 10.6084/m9.figshare.31165963.v1
title: Additional file 3 of MicroRNA-29a-5p contributes to neuroinflammation through TLR7

description: Supplementary Material 3. Table S2. Excel file containing complete data for differentially expressed genes in WT and APP/PS1 mice, mouse characteristics, mRNA gene targets of miR-29a-5p, and cyto-/chemokine analysis.
DOI: 10.5061/dryad.vdncjsxv2
title: Desiccation amelioration and climate risk on rocky shores

description: A large fraction of global biodiversity resides within biogenic habitats
 that ameliorate physical stresses. In most cases, details of how physical
 conditions within facilitative habitats respond to external climate
 forcing remain unknown, hampering climate change predictions for many of
 the world’s species. Using intertidal mussel beds as a model system, we
 characterize relationships among external climate conditions and
 within-microhabitat heat and desiccation conditions. We use these data,
 along with physiological tolerances of two common inhabitant taxa (the
 isopod Cirolana harfordi and the porcelain crab Petrolisthes cinctipes),
 to examine the magnitude of climate risk inside and outside biogenic
 habitat, applying an empirically derived model of evaporation to simulate
 mortality risk under a high-emissions climate-warming scenario. We found
 that biogenic microhabitat conditions responded so weakly to external
 climate parameters that mortality risk was largely unaffected by climate
 warming. We also found that desiccation outside the biogenic habitat drove
 substantial mortality in both species at temperatures 4.4 to 8.6 ºC below
 their hydrated thermal tolerances. This finding emphasizes the importance
 of warming-exacerbated desiccation to climate-change risk and the role of
 biogenic habitats in buffering this less-appreciated stressor. Our results
 suggests that, when biogenic habitats remain intact, climate
 warming may have weak direct effects on organisms within them.
 Instead, risk to such taxa is likely to be indirect and tightly coupled
 with the fate of habitat-forming populations. Our findings emphasize that
 conserving and/or restoring biogenic habitats that offer climate
 refugia could support biodiversity conservation in the face of climate
 warming.
description: Full description of Methods is included in the associated
 publication.
description: Metadata details with definitions of field (column) headers are
 given in the ReadMe file titled
 READMe_Jurgens_FacilitationClimate.txt and in the file
 titled File_Fields_Metadata.csv. Files include field
 trial data for 2 species in the file
 Animal_trials.csv and agar experiment data in the file
 Agar_data.csv. Data included in Figure 4 of the paper,
 which were used to calculate present day (2012) and future (2099)
 distributions of high-end evaporation stress for each species and which
 include environmental data with resampling for 2012 (measured) and 2099
 (simulated; see Methods for details) are given by focal species
 <em>C. harfordi</em> and <em>P. cinctipes</em> and
 microhabitat. In each file, data were measured or calculated for
 intertidal microhabitats and species given in the file name using
 equations and methods described in Methods. These data are contained in
 the files: C.harfordi_MusselBed_EvapCalc_Fig4.csv,
 C.harfordi_Rock_EvapCalc_Fig4.csv,
 P.cinctipes_MusselBed_EvapCalc_Fig4.csv,
 P.cinctipes_Rock_EvapCalc_Fig4.csv
DOI: 10.6071/m3wq1r
title: Near-term modeled forest fire area and fuel aridity projections

description: Escalating burned area in western US forests has heightened the need to
 refine near-term forest fire projections. One critical knowledge gap is
 how fire-fuel feedbacks may constrain such projections. We use both static
 climate-fire models and dynamic models that incorporate feedbacks to
 project future western US forest-fire area. Compared to 1991-2020, static
 models for 2021-2050 project a doubling in forest-fire area, increased
 year-to-year variability, and increased occurrence of years with
 forest-fire area exceeding the 2020 fire season. Dynamic models that
 incorporate fire-fuel feedbacks project more moderate increases, but still
 show a 46-90% increase in forest-fire area compared to 1991-2020. Our
 results emphasize the need to mitigate against the negative
 effects of more fire in the coming decades.
DOI: 10.6078/d1799z
title: Accepted marine Diptera from world register of marine species and aquatic annotations

description: List of Fly Families from Wiegmann et al. 2011 and annotations of marine
 and aquatic life histories based on World Register of Marine Species and
 other peer-reviewed sources.
description: These datasets are based on several peer-reviewed sources. We
 combined these peer reviewed sources into our dataset. Sources include
 Wiegmann et al. 2011, Adler and Courtney 2019, and records from the World
 Register of Marine Species (Downloaded file from Dec 2020).
description: Not all infraorders/superfamilies are labeled.  Blank cells under
 the marine, brackish, fresh, and terrestrial were replaced as
 NAs.
DOI: 10.6084/m9.figshare.31165969
title: Additional file 1 of Curation of the Fasciola hepatica kinome as a resource for drug target discovery

description: Additional file 1: Supplementary data 1. XLSX file containing supplementary tables 1–12 presenting the Fasciola hepatica kinome. Table S1: The F. hepatica kinome, kinome classification, amino acid sequences as well as functional annotations with InterPro, Pfam and SUPERFAMILY domain ID and their description, KEGG terms as well as their definitions. Table S2: Curated F. hepatica protein sequences with assignment of PK families based on phylogenetic analysis. Tables S3−12: Closest homolog of F. hepatica in S. mansoni, S. haematobium and H. sapiens kinomes based on global pairwise analysis results via EMBOSS needle for the PK domains in the PK groups AGC (S3), Atypical PKs (S4), CAMK (S5), CK1 (S6), CMGC (S7), Others (S8), RGC (S9), STE (S10), TK (S11), TKL (12). Identity and similarity (in %) of similar regions in the protein kinase domain sequences of genes with highest bit-scores compared to the F. hepatica gene are indicated, with an exception of using full length sequences instead of PK domains for Atypical PKs. Note that the genes are not necessarily orthologous genes. In case no homolog was identified (NA), results of an additional BLAST search with full-length kinase sequences are presented.
DOI: 10.6084/m9.figshare.31165969.v1
title: Additional file 1 of Curation of the Fasciola hepatica kinome as a resource for drug target discovery

description: Additional file 1: Supplementary data 1. XLSX file containing supplementary tables 1–12 presenting the Fasciola hepatica kinome. Table S1: The F. hepatica kinome, kinome classification, amino acid sequences as well as functional annotations with InterPro, Pfam and SUPERFAMILY domain ID and their description, KEGG terms as well as their definitions. Table S2: Curated F. hepatica protein sequences with assignment of PK families based on phylogenetic analysis. Tables S3−12: Closest homolog of F. hepatica in S. mansoni, S. haematobium and H. sapiens kinomes based on global pairwise analysis results via EMBOSS needle for the PK domains in the PK groups AGC (S3), Atypical PKs (S4), CAMK (S5), CK1 (S6), CMGC (S7), Others (S8), RGC (S9), STE (S10), TK (S11), TKL (12). Identity and similarity (in %) of similar regions in the protein kinase domain sequences of genes with highest bit-scores compared to the F. hepatica gene are indicated, with an exception of using full length sequences instead of PK domains for Atypical PKs. Note that the genes are not necessarily orthologous genes. In case no homolog was identified (NA), results of an additional BLAST search with full-length kinase sequences are presented.
DOI: 10.6084/m9.figshare.31165975
title: Additional file 3 of Curation of the Fasciola hepatica kinome as a resource for drug target discovery

description: Additional file 3: Supplementary data 3. KEGG pathway reconstruction for the kinases in the F. hepatica kinome.