cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j9kd51cdz
title: Invader abundance and contraction of niche breadth during replacement of a native gammarid amphipod

description: The introduction of non-native species to new locations is a growing
 global phenomenon with major negative effects on native species and
 biodiversity. Such introductions potentially bring competitors into
 contact leading to partial or total species replacements. This creates an
 opportunity to study novel species interactions as they occur, with the
 potential to address the strength of inter- and intraspecific
 interactions, most notably competition. Such potential has often not been
 realized, however, due to the difficulties inherent in detecting rapid and
 spatially expansive species interactions under natural field conditions.
 The invasive amphipod crustacean Gammarus pulex has replaced a native
 species, Gammarus duebeni celticus, in river and lake systems across
 Europe. This replacement process is at least partially driven by
 differential parasitism, cannibalism and intraguild predation, but the
 role of interspecific competition has yet to be resolved. Here, we examine
 how abundance of an invasive species may affect spatial niche breadth of a
 native congeneric species. We base our analyses of niche breadth
 on ordination and factor analysis of biological community and physical
 parameters, respectively, constituting a summative, multidimensional
 approach to niche breadth along environmental gradients. Results derived
 from biological and environmental niche criteria were consistent, although
 interspecific effects were stronger using the biological niche approach.
 We show that the niche breadth of the native species is constrained as
 abundance of the invader increases, but the converse effect does not
 occur. We conclude that the interaction between invasive G. pulex and
 native G. d. celticus under natural conditions is consistent with strong
 interspecific competition whereby a native, weaker competitor is replaced
 by a superior invasive competitor. This study indicates a strong role of
 interspecific competition, alongside other known interactions such as
 differential intraguild predation, in rapid and expansive species
 replacements following biological invasions.
description: 26 sites with 30 samples at each site taken at 5 m intervals.
 Environmental variable related to river structure and surrounding habitat
 780 samples in total. Identified and counted to family level except for
 gammarids which were identified to species and also
 adult/juvenile.
DOI: 10.5061/dryad.v41ns1rxs
title: Data for figures and stats in the paper: The effects of locomotion on sensory-evoked haemodynamic responses in the cortex of awake mice

description: Investigating neurovascular coupling in awake rodents is becoming ever
 more popular due, in part, to our increasing knowledge of the profound
 impacts that anaesthesia can have upon brain physiology. Although awake
 imaging brings with it many advantages, we still do not fully understand
 how voluntary locomotion during imaging affects sensory-evoked
 haemodynamic responses. In this study we investigated how evoked
 haemodynamic responses can be affected by the amount and timing of
 locomotion. Using an awake imaging set up, we used 2D-Optical Imaging
 Spectroscopy (2D-OIS) to measure changes in cerebral haemodynamics within
 the sensory cortex of the brain during either 2s whisker stimulation or
 spontaneous (no whisker stimulation) experiments, whilst animals could
 walk on a spherical treadmill. We show that locomotion alters haemodynamic
 responses. The amount and timing of locomotion relative to whisker
 stimulation is important, and can significantly impact sensory-evoked
 haemodynamic responses. If locomotion occurred before or during whisker
 stimulation, the amplitude of the stimulus-evoked haemodynamic response
 was significantly altered. Therefore, monitoring of locomotion during
 awake imaging is necessary to ensure that conclusions based on comparisons
 of evoked haemodynamic responses (e.g., between control and disease
 groups) are not confounded by the effects of locomotion.
DOI: 10.25349/d9d90c
title: Data from: Effectiveness of antifungal treatments during chytridiomycosis epizootics in populations of an endangered frog

description: The recently-emerged amphibian chytrid fungus Batrachochytrium
 dendrobatidis (Bd) has had an unprecedented impact on global amphibian
 populations, and highlights the urgent need to develop effective
 mitigation strategies. We conducted in-situ antifungal treatment
 experiments in wild populations of the endangered mountain yellow-legged
 frog during or immediately after Bd-caused mass die-off events. The
 objective of treatments was to reduce Bd infection intensity
 ("load") and in doing so alter frog-Bd dynamics and increase the
 probability of frog population persistence despite ongoing Bd infection.
 Experiments included treatment of early life stages (tadpoles and
 subadults) with the antifungal drug itraconazole, treatment of adults with
 itraconazole, and augmentation of the skin microbiome of subadults with
 Janthinobacterium lividum, a commensal bacterium with antifungal
 properties. All itraconazole treatments caused immediate reductions in Bd
 load, and produced longer-term effects that differed between life stages.
 In experiments focused on early life stages, Bd load was reduced in the
 two months immediately following treatment and was associated with
 increased survival of subadults. However, Bd load and frog survival
 returned to pre-treatment levels in less than one year, and treatment had
 no effect on population persistence. In adults, treatment reduced Bd load
 and increased frog survival over the entire three-year post-treatment
 period, consistent with frogs having developed an effective adaptive
 immune response against Bd. Despite this protracted period of reduced
 impacts of Bd on adults, recruitment into the adult population was limited
 and the population eventually declined to near-extirpation. In the
 microbiome augmentation experiment, exposure of subadults to a solution of
 J. lividum increased concentrations of this potentially protective
 bacterium on frogs. However, concentrations declined to baseline levels
 within one month and did not have a protective effect against Bd
 infection. Collectively, these results indicate that our mitigation
 efforts were ineffective in causing long-term changes in frog-Bd dynamics
 and increasing population persistence, due largely to the inability of
 early life stages to mount an effective immune response against Bd. This
 results in repeated recruitment failure and a low probability of
 population persistence in the face of ongoing Bd infection.
description: These datasets were collected before, during, and after six
 antifungal treatments conducted in lakes and ponds in Kings Canyon
 National Park and the Inyo National Forest (California, USA). Frogs were
 captured, tagged, swabbed, treated, and surveyed using standard methods,
 as described in the associated paper. The data were thoroughly
 error-checked prior to use in statistical analyses.
description: The associated README.md file provides a general description of
 each dataset, and a specific description of the fields in each
 dataset.
DOI: 10.5061/dryad.kprr4xh61
title: Soil nitrogen mediates the effect of distance from climatic center on herbivory rates in a tropical herb

description: The center-periphery hypothesis predicts that species are most abundant at
 the center of their range. Differential herbivory rates between center and
 periphery populations can explain this variation in species abundance.
 However, if the geographic center of a species distribution coincides with
 its ecological optimum, the resource availability hypothesis predicts
 higher herbivory rates and tolerances at the center compared to the
 periphery. Biogeographic studies on herbivory have treated these two
 mechanisms separately, limiting our mechanistic understanding of the role
 of herbivory in shaping species range limits. We analyzed the role of
 resource availability on herbivory variation from center to periphery
 using data collected across the distribution of Thunberbia
 atacorensis, a range limited species of West Africa. We used two
 types of distances: geographic distance (the distance from each plot to
 the geographic center of all populations) and climatic distance (the
 distance from each plot to the preferendum of the species). We found no
 increase in herbivory toward the periphery of the climatic and geographic
 ranges. However, herbivory rates increased with soil nitrogen. Nitrogen in
 soil decrease from center to periphery of climatic range. Phylogenetic
 diversity and surrounding plants' competition did not affect
 herbivory rates. Our study provides insights into how nutrient limitation
 can shape species center-periphery distribution by altering spatial
 variation in herbivory rates.
description: We randomly established five 5 m x 5 m permanent plots to
 collect data on herbivory rate, interspecific competition among
 surrounding species, species diversity and abiotic soil data in
 12 populations of <i>Thunbergia</i> atacorensis.
description: <strong>1. R Scripts</strong> This includes an R markdown file showing how the statistical analysis was performed. <b>2. Datasets</b> The dataset consists of three data: metadata<b>:</b> This data includes 54 observations for 12 variables. The variables represent the population (Population), the plot in which there were collected, the average herbivory rate per plot (herbivory), the concentration of soils elements per plot such as N (Nitrogen), P (Phosphorus), K (Potassium), pH, the distance from the plot to the geographic center (Distance.center), soil moisture per plot (Soil.moisture), the quantity of light available for plant (PAR), interspecific competition of plants per plot (SRU), the distance from the climate center to each plot (mhd). Herbivory.glm: This data includes 3037 observations for three variables. The variables represent the identity (ID), the herbivory rate per leave (Herbivory.rate), the type of insect (specialist or generalist). species_richness: This data includes 1633 observations for four variables. The variables represent the population (Population), the plot in which there were collected (Plot), the species (Species), and the abundance of the species per plot (Abundance).
DOI: 10.6078/d1440w
title: Cricket thermal preferences and starvation

description: Insects behaviorally thermoregulate across the diel cycle and their
 preferred microhabitats change based on current resource availabilities
 and the thermal performance optima of traits. Specific combinations of
 traits being prioritized are set by life history strategies, making life
 history an important intrinsic determinant of thermal preferences.
 However, we do not know how life history strategies shape plasticity of
 behavioral thermoregulation, limiting our ability to predict responses to
 environmental variability. We compared female variable field crickets
 (Gryllus lineaticeps) that are flight-capable (long-winged) and flightless
 (short-winged) to test the hypothesis that life history strategy
 determines plasticity of thermal preferences across the diel cycle and
 following starvation. Thermal preferences were elevated during the
 nocturnal activity period, and long-winged crickets preferred warmer
 temperatures compared to short-winged crickets across the diel cycle when
 fully fed. However, thermal preferences of starved crickets were reduced
 compared to fed crickets. The reduction in thermal preferences was greater
 in long-winged crickets, resulting in similar thermal preferences between
 starved long- and short-winged individuals and reflecting a more plastic
 response. Thus, life history does determine plasticity in thermoregulatory
 behaviors following resource limitations and effects of life history on
 thermal preferences are context dependent.
DOI: 10.5061/dryad.k98sf7m75
title: Performance results from species distribution models considering historical occurrences and variables of varying persistency

description: Occurrence data used to build species distribution models often include
 historical records from locations in which the species no longer exists.
 When these records are paired with contemporary environmental values that
 no longer represent the conditions the species experienced, the model
 creates false associations that hurt predictive performance. The extent of
 mismatching increases with the number of historical occurrences and with
 inclusion of environmental variables that are prone to change over time.
 Indeed, the mismatch between occurrence data and contemporaneous
 environmental variables is a common dilemma when modeling rare or cryptic
 species, especially those of conservation concern that were once more
 abundant. Herein, we assess (1) the impact of historical occurrences on
 model performance across three sets of environmental variables of
 increasing persistency, and (2) the performance of models built using
 selected-historical occurrences from locations that showed evidence of
 limited environmental change over time. Concepts are tested on federally
 listed flatwoods salamanders, reflecting real-world conservation
 management efforts. We predicted that, compared to other occurrence sets,
 (1) historical occurrences would perform best with environmental variables
 that were more persistent, (2) recent occurrences would perform best when
 the environmental variables were more impersistent, and that (3) our
 selected-historical occurrences would perform best with a combination of
 persistent and impersistent variables. Our results showed the expected
 inversion of model performance of recent and historical occurrences across
 environmental variables of increasing persistency when evaluated by
 correct predictions. However, the inversion was not seen in AUC
 performance, in which historical occurrences outperformed recent
 occurrence models across all variable sets. Selected-historical
 occurrences did not notably improve performance over all-historical
 occurrences in any metric or variable set. To maximize utility and
 performance, modelers could acknowledge potential tradeoffs from inclusion
 of historical occurrences and consider number and age of recent and
 historical occurrences available, the persistency of environmental
 variables considered, and how their conservation goals are reflected in
 model design and evaluation, particularly with respect to sensitivity vs.
 specificity. Our study lends support for inclusion of historical
 occurrences, with the potential exception of mostly impersistent variables
 when sensitivity is the highest priority.
DOI: 10.5061/dryad.zw3r2288z
title: A timeframe for mint evolution: Towards a better understanding of trait evolution and historical biogeography in Lamiaceae

description: The mint family (Lamiaceae) is one of the largest and most economically
 important families of flowering plants. Despite focused study on
 relationships within subclades, higher-level relationships have been
 understudied. Moreover, the herbaceous habit of much of the family has
 resulted in a poor fossil record and has hampered estimates of divergence
 times. Using a new dataset of five plastid loci from 178 Lamiaceae
 representing all subfamilies and nearly all tribes, we clarify major
 infrafamilial relationships and present a robust set of divergence times.
 We use this phylogenetic hypothesis as a platform to test prior hypotheses
 regarding the historical biogeography and evolution of major traits within
 the family. We confirm the placement of subfamily Nepetoideae, show
 continued uncertainty in the placement of subfamilies Ajugoideae and
 Premnoideae, and highlight extreme discordance with recent results from
 nuclear data. Lamiaceae originated during the Late Cretaceous as a woody
 plant with a nutlet fruit and four stamens, probably in Southeast Asia.
 Most subfamilies diverged during the Eocene, perhaps facilitated by
 climatic cooling. Our results provide a valuable set of secondary dates
 for Lamiaceae and highlight the need for focused study of subfamilies
 Callicarpoideae and Viticoideae. Our results also provide several
 hypotheses regarding trait or range-dependent diversification.
DOI: 10.5061/dryad.mw6m905z3
title: Data from: Community assembly and metaphylogeography of soil biodiversity: insights from haplotype-level community DNA metabarcoding within an oceanic island

description: Most of our understanding of island diversity comes from the study of
 aboveground systems, while the patterns and processes of diversification
 and community assembly for belowground biotas remain poorly understood.
 Here we take advantage of a relatively young and dynamic oceanic island to
 advance our understanding of eco-evolutionary processes driving community
 assembly within soil mesofauna. Using whole organism community DNA
 (wocDNA) metabarcoding and the recently developed metaMATE pipeline, we
 have generated spatially explicit and reliable haplotype-level DNA
 sequence data for soil mesofauna assemblages sampled across the four main
 habitats within the island of Tenerife. Community ecological and
 metaphylogeographic analyses have been performed at multiple levels of
 genetic similarity, from haplotypes to species and supraspecific
 groupings. Broadly consistent patterns of local-scale species richness
 across different insular habitats have been found, whereas local insular
 richness is lower than in continental settings. Our results reveal an
 important role for niche conservatism as a driver of insular community
 assembly of soil mesofauna, with only limited evidence for habitat shifts
 promoting diversification. Furthermore, support is found for a fundamental
 role of habitat in the assembly of soil mesofauna, where habitat
 specialism is mainly due to colonisation and the establishment of
 preadapted species. Hierarchical patterns of distance decay at the
 community level and metaphylogeographical analyses support a pattern of
 geographic structuring over limited spatial scales, from the level of
 haplotypes through to species and lineages, as expected for taxa with
 strong dispersal limitations. Our results demonstrate the potential for
 wocDNA metabarcoding to advance our understanding of biodiversity.
description: Table in Excel format including (i) geographical coordinates and
 habitat type for the 52 sites sampled, (ii) ASV name, ASV sequence, and
 ASV classification into 3% similarity OTUs and 15% similarity lineages,
 and (iii) presence-absence data for each ASV across the 52 sampled
 sites.
DOI: 10.6084/m9.figshare.31119297
title: Diagnostic value of 18F-FDG PET/CT and MRI in patients suspected of cancer of unknown primary in the head and neck

description: Cancer of unknown primary (CUP) is diagnostically challenging. Diagnostic strategy remains controversial. The aim of this retrospective study was to evaluate the diagnostic value of FDG-PET/CT and MRI in detecting primary tumours in patients presenting with suspected CUP. Patients referred to FDG-PET/CT for suspected CUP were included retrospectively. Data on demographics, diagnostic tests and imaging was collected. Sensitivity and specificity for FDG-PET/CT and MRI were compared using McNemar’s test. In a four year period a total of 329 patients were included, 226 (68.7%) with malignant and 103 (31.3%) with benign pathology. Of the 226 with malignant tumours, 150 (66.4%) had head and neck cancer, the majority of which were with oropharyngeal origin 114 (76.0%). In a subgroup of 80 patients who had both FDG-PET/CT and MRI scans (53.3%), MRI did not significantly increase sensitivity (<i>p</i> = 0.092) in identifying tumour site There was no significant difference in the sensitivity between FDG-PET/CT and MRI in patients with head and neck cancer or CUP. Adding MRI to the diagnostic workup in occult cancer did not significantly improve detection of primary tumours. In case of malignant tumours, 50% were oropharyngeal cancer and required MRI for preoperative planning.
DOI: 10.6084/m9.figshare.31119297.v2
title: Diagnostic value of 18F-FDG PET/CT and MRI in patients suspected of cancer of unknown primary in the head and neck

description: Cancer of unknown primary (CUP) is diagnostically challenging. Diagnostic strategy remains controversial. The aim of this retrospective study was to evaluate the diagnostic value of FDG-PET/CT and MRI in detecting primary tumours in patients presenting with suspected CUP. Patients referred to FDG-PET/CT for suspected CUP were included retrospectively. Data on demographics, diagnostic tests and imaging was collected. Sensitivity and specificity for FDG-PET/CT and MRI were compared using McNemar’s test. In a four year period a total of 329 patients were included, 226 (68.7%) with malignant and 103 (31.3%) with benign pathology. Of the 226 with malignant tumours, 150 (66.4%) had head and neck cancer, the majority of which were with oropharyngeal origin 114 (76.0%). In a subgroup of 80 patients who had both FDG-PET/CT and MRI scans (53.3%), MRI did not significantly increase sensitivity (<i>p</i> = 0.092) in identifying tumour site There was no significant difference in the sensitivity between FDG-PET/CT and MRI in patients with head and neck cancer or CUP. Adding MRI to the diagnostic workup in occult cancer did not significantly improve detection of primary tumours. In case of malignant tumours, 50% were oropharyngeal cancer and required MRI for preoperative planning.
DOI: 10.6084/m9.figshare.31119297.v1
title: Diagnostic value of 18F-FDG PET/CTand MRI in patients suspected of cancer of unknown primary in the head and neck

description: Cancer of unknown primary (CUP) is diagnostically challenging. Diagnostic strategy remains controversial. The aim of this retrospective study was to evaluate the diagnostic value of FDG-PET/CT and MRI in detecting primary tumours in patients presenting with suspected CUP. Patients referred to FDG-PET/CT for suspected CUP were included retrospectively. Data on demographics, diagnostic tests and imaging was collected. Sensitivity and specificity for FDG-PET/CT and MRI were compared using McNemar’s test. In a four year period a total of 329 patients were included, 226 (68.7%) with malignant and 103 (31.3%) with benign pathology. Of the 226 with malignant tumours, 150 (66.4%) had head and neck cancer, the majority of which were with oropharyngeal origin 114 (76.0%). In a subgroup of 80 patients who had both FDG-PET/CT and MRI scans (53.3%), MRI did not significantly increase sensitivity (<i>p</i> = 0.092) in identifying tumour site There was no significant difference in the sensitivity between FDG-PET/CT and MRI in patients with head and neck cancer or CUP. Adding MRI to the diagnostic workup in occult cancer did not significantly improve detection of primary tumours. In case of malignant tumours, 50% were oropharyngeal cancer and required MRI for preoperative planning.