cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jwstqjq8f
title: A recovery network leads to the natural recolonization of an archipelago and a potential trailing edge refuge

description: Rapid environmental change is reshaping ecosystems and driving species
 loss globally. Carnivore populations have declined and retracted rapidly
 and have been the target of numerous translocation projects. Success,
 however, is complicated when these efforts occur in novel ecosystems.
 Identifying refuges, locations that are resistant to environmental change,
 within a translocation framework should improve population recovery and
 persistence. American martens (Martes americana) are the most frequently
 translocated carnivore in North America. As elsewhere, martens were
 extirpated across much of the Great Lakes region by the 1930s and, despite
 multiple translocations beginning in the 1950s, martens remain of regional
 conservation concern. Surprisingly, martens were rediscovered in 2014 on
 the Apostle Islands of Lake Superior after a putative absence of
 &gt;40 years. To identify the source of martens to the islands and
 understand connectivity of the reintroduction network, we collected
 genetic data on martens from the archipelago and from all regional
 reintroduction sites. In total, we genotyped 483 individual martens, 43 of
 which inhabited the Apostle Islands (densities 0.42-1.46/km2). Coalescent
 analyses supported the contemporary recolonization of the Apostle Islands
 with progenitors likely originating from Michigan, which were sourced from
 Ontario. We also identified movements by a first-order relative between
 the Apostle Islands and the recovery network. We detected some regional
 gene flow, but in an unexpected direction: individuals moving from the
 islands to the mainland. Our findings suggest that the Apostle Islands
 were naturally recolonized by progeny of translocated individuals and now
 act as a source back to the reintroduction sites on the mainland. We
 suggest that the Apostle Islands, given its protection from disturbance,
 complex forest structure, and reduced carnivore competition, will act as a
 potential refuge for marten along their trailing range boundary and a
 central node for regional recovery. Our work reveals that translocations,
 even those occurring along southern range boundaries, can create recovery
 networks that function like natural metapopulations. Identifying refuges,
 locations that are resistant to environmental change, within these
 recovery networks can further improve species recovery, even within novel
 environments. Future translocation planning should a priori identify
 potential refuges and sources to improve short-term recovery and long-term
 persistence.
DOI: 10.5061/dryad.2v6wwpzmv
title: Phenotypic plasticity and genetic diversity elucidate rarity and vulnerability of an endangered riparian plant

description: Anthropogenic environmental change threatens many species and can be
 especially challenging for rare species given their potentially limited
 capacity for migration and adaptation relative to more common species. The
 ability to acclimate via phenotypic plasticity could provide an important
 path to persistence, especially for rare species. We investigated the
 responses of an endangered plant species endemic to a highly dynamic
 riparian habitat in southeastern Tennessee, USA, and its most widespread
 congener to environmental change to elucidate their current statuses and
 future vulnerability. Specifically, we compared the population- and
 species-level plasticity of rare Pityopsis ruthii and common P.
 graminifolia to contrasting light, temperature, and water conditions in a
 growth chamber experiment to evaluate their potential to acclimate to
 environmental change. Contrary to our expectations, P. ruthii had greater
 phenotypic plasticity than its common congener in response to both altered
 light and water availability. But this plasticity was not associated with
 increased fitness, suggesting that it was not adaptive. Concurrently, we
 genotyped these individuals at nine putatively neutral microsatellite loci
 to contrast genetic diversity across the range of each species. As
 expected, P. ruthii exhibited reduced genetic diversity relative to its
 more common congener. Overall, our findings accord with the narrow range
 and current habitat specificity of P. ruthii, especially its tolerance of
 highly variable water, and highlight its potential vulnerability to future
 environmental change.
DOI: 10.5061/dryad.bnzs7h4b3
title: Data and R scripts from: Which factors determine the long-term effect of poor early-life nutrition? A meta-analytic review

description: Early-life conditions can have long-lasting effects (experiential
 legacies) on an individual’s performance. Experiential legacies are an
 important source of variation among mature individuals because responses
 to early-life environments vary widely. Yet, the factors influencing the
 magnitudes and directions of phenotypic responses to experiential legacies
 are poorly understood, hindering our ability to predict adult phenotypes
 and population-level consequences of environmental stressors. To better
 understand these issues, we examined how experiential legacies varied with
 the type of phenotypic response (e.g., reproduction, longevity),
 characteristics of the individual, and characteristics of the stressful
 conditions imposed. We conducted a meta-analytic review (nspecies = 65,
 nstudies = 81), examining experiential legacies of early-life nutritional
 restriction. We found generally consistent negative or neutral impacts of
 early nutritional stress on later-life phenotypes, indicating that
 positive responses to early nutritional restriction may be rare among
 organisms. Our results also demonstrated differences in how experiential
 legacies were expressed in specific dimensions of an individual’s
 phenotype; for example, magnitude and direction differed among responses
 in development rate (weak negative response), offspring quality and
 quantity (strong negative), and longevity (neutral response). We also
 found that the harsher the early-life nutritional stress, the stronger the
 negative nutritional legacy. Our results emphasize the complicated
 interactions among a suite of phenotypic responses in determining
 individual performance. Given the potential for individual performance to
 inform the demography and dynamics of populations, we offer avenues for
 future research that can improve our understanding of how experiential
 legacies of nutrition or other early-life conditions affect populations.
description: The primary data are contained in the file titled
 "Almeida_et_at_Data_Ecosphere_final.csv". These data were
 extracted from the primary literature and, within the R scripts included,
 were used to calculate effect sizes and within meta-regressions.
 Additional data files include phylogenetic correlation matrices and shared
 control covariance matrices that are used within the
 meta-regressions.
description: The metadata file
 "Almeida_et_al_Metadata_Ecosphere_final.txt" contains general
 information about the R scripts and the data files, including definitions
 for the variables within the main datafile. Each R script file also
 includes brief metadata at the top of the script and comments throughout
 the script explaining the analyses and data manipulation.
DOI: 10.5061/dryad.kd51c5b5c
title: Exceptional multifunctionality in the feeding apparatus of a mid-Cambrian radiodont

description: Radiodonts (stem Euarthropoda) were ecologically diverse, but species
 generally displayed limited functional specialization of appendages along
 the body axis compared to crown group euarthropods. This is puzzling
 because such functional specialization is considered to have been an
 important driver of euarthropod ecological diversification. One way to
 circumvent this constraint could have been the functional specialization
 of different parts of the frontal appendages, known to have been
 ecologically important in radiodonts. This hypothesis has yet to be tested
 explicitly. Here we redescribe the poorly known mid-Cambrian hurdiid
 radiodont Stanleycaris hirpex from the Burgess Shale (Stephen Formation)
 and quantitatively assess appendage functional specialization in stem
 euarthropods. The appendages of Stanleycaris are composed of fourteen
 podomeres, variously differentiated by their possession of pectinate
 endites, mono- to trifurcate medial gnathites, and outer spines. The oral
 cone is tetraradially organized and can be uniquely distinguished from
 other hurdiids by the presence of 28 rather than 32 smooth tridentate
 plates. Our phylogenetic analysis finds Stanleycaris in a grade of
 hurdiids retaining plesiomorphic raptorial appendicular functionality
 alongside derived adaptations for sweep feeding and large, bilaterally
 opposed gnathites. We conclude that the latter performed a masticatory
 function, convergent with gnathal structures like mandibles in various
 panarthropods. In combination, our results demonstrate that Stanleycaris
 and similar hurdiids provide an extreme example of the evolution of
 division of labour within the appendage of a stem euarthropod and suggest
 that this innovation may have facilitated the functional transition, from
 raptorial to sweep feeding, at the origin of the hurdiid clade.
DOI: 10.5061/dryad.1c59zw3v7
title: Automated, quantitative pupillometry in the critically ill: a systematic review of the literature: online supplementary data

description: Objective: A systematic literature search has been performed to identify
 potential confounders for outcome prediction using pupillary light reflex
 in adult critically ill patients, as measured by handheld automated
 pupillometry devices. Methods: Three digital databases (PubMed, EmBase,
 Cochrane) were systematically searched. Articles published between
 1990-2019 in adult patients, using monocular automated handheld devices
 were considered. Studies were classified according to the OCEBM
 classification (level 1 represents the highest, level 5 the lowest level
 of evidence). Case reports, original research and systematic reviews were
 included and cross-referenced.  Results: Using 202 search terms,
 58 eligible articles reporting on the use of handheld pupillometry in the
 critically ill could be identified, considering 3246 patients. The highest
 level of evidence came from 10 randomized trials and 19 prospective
 observational studies. The level of evidence was mostly 2 to 3 and highest
 with studies regarding the potential confounding effects of pain, the use
 of opioids and increased intracranial pressure. Additional potential
 confounders found are SSRIs, α2-adregenic receptor agonists and NMDA
 antagonists. Conclusions: The pupillary light reflex is susceptible to
 factors resulting from underlying comorbidities and effects of treatment
 regimes. Scenarios frequently encountered in critical care, such as pain,
 the use of opioids, and proof of increased intracranial pressure have
 potential confounding effects on outcome and pupillary reflexes. When
 treatment is guided by pupillary metrics, such confounders put patients at
 risk of over- or undertreatment. Future research should validate and
 identify additional confounders, as our review suggests that even more
 unexplored confounders may exist.
DOI: 10.5061/dryad.cnp5hqc4g
title: Linking alternative reproductive tactics and habitat selection in Northern chamois

description: In polygynous ungulates, males may achieve fertilization through the use
 of alternative reproductive tactics (ARTs), discrete phenotypic variations
 evolved to maximize fitness. ARTs are often associated with different male
 spatial strategies during the rut, from territoriality to
 female-following. Although variation in space use patterns of rutting male
 ungulates is known to be largely affected by the spatial distribution of
 females, information on the year-round habitat selection of alternative
 reproductive types is scant. Here, we investigate the seasonal variation
 in habitat choice of a large mammal with ARTs (territoriality and
 non-territoriality), the Northern chamois Rupicapra rupicapra. Global
 Positioning System (GPS) data on 28 adult males were collected between
 February 2010 and December 2013 in the Gran Paradiso National Park
 (Italy), and used to fit resource selection functions to explore the
 ART-specific use of key topographic features such as elevation, aspect and
 slope, and vegetation phenology expressed as NDVI values. Territorial and
 non-territorial chamois profoundly differed in their habitat selection not
 only during the rutting season. Compared to non-territorial males,
 territorial males used lower elevations in summer and autumn, preferred
 southern slopes in spring and summer, and used steeper areas in summer but
 not in winter. We found no difference in seasonal selection of NDVI values
 between males adopting ARTs. Our results suggest that territorial males
 tend to occupy warmer, lower-food-quality habitats in late spring and
 summer, whereas non-territorial males are free to follow and exploit
 vegetation phenology and more favourable temperatures. Different patterns
 of habitat selection may reflect different trade-offs between the
 optimisation of energy balances throughout the year and the increase of
 mating opportunities during the rut in males adopting alternative
 reproductive tactics.
DOI: 10.48689/22a7b897-7023-41c7-b0f5-fd0b1c4090a4
title: BCMCA Marine Mammal Feature Counts

description: Number of bcmca marine mammal features used in the Marxan analysis that are found in each 2 km x 2 km planning unit.
DOI: 10.48689/e74a508a-74d8-47ed-874f-80740f351520
title: BCMCA Invertebrate Fishery Feature Counts, 2010

description: Number of bcmca marine fish and invertebrate features used in the Marxan analysis that are found in each 2km x 2 km planning unit.
DOI: 10.5061/dryad.pvmcvdnkr
title: Organelle calcium-derived voltage oscillations in pacemaker neurons drive the motor program for food-seeking behavior in Aplysia

description: An atypical neuronal pacemaker mechanism, based on rhythmic intracellular
 calcium store release in an identified pair of interneurons (B63) and
 resulting oscillation of the neurons’ membrane potential, acts as an
 autonomous releaser for the irregular occurrences of the motor program for
 food-seeking behavior in Aplysia. The rhythmic variations of the membrane
 potential in B63 neurons were analyzed by Fast Fourier Transform (FFT)
 analysis in a cycle period bandwidth of 512 s to 8 s. The resulting power
 spectral density periodograms were used to identify oscillation periods of
 peak magnitude. The periodograms were computed from the FFT frequency
 spectrograms by converting the frequency band (in Hz) to its reciprocal,
 period (in secs). These analysis were performed in isolated buccal ganglia
 preparations bathed in artifical sea water (ASW), in ‘Low Ca+Co’ saline to
 block chemical synapses, or in ‘Low Ca+Co’ saline and after an
 intracellular injection of organelle membrane calcium channel blocker
 heparin into either the bilateral B63 or B31 neurons. The oscillations of
 B63 membrane potential that were recorded in ASW persisted in ‘Low Ca+Co’,
 but were suppressed after heparin injection specifically into B63.
DOI: 10.48689/75f3e0c5-0cdb-44c3-966d-7ce79334d08f
title: BCMCA Giant Kelp (Macrocystis integrifolia) presence as of 2008

description: Areal extents of Giant Kelp (Macrocystis intergrifolia)
DOI: 10.5061/dryad.r2280gbcg
title: Maize tassel detection from UAV imagery using deep learning

description: Dataset associated with paper titled "Maize Tassel Detection from UAV
 Imagery Using Deep Learning" published on the journal
 of Frontiers in Robotics and AI (DOI: 10.3389/frobt.2021.600410).
 The timing of flowering plays a critical role in determining the
 productivity of agricultural crops. If the crops flower too
 early, the crop would mature before the end of the
 growing season, losing the opportunity to capture and use large
 amounts of light energy. If the crops flower too late, the crop
 may be killed by the change of seasons before it is ready
 to harvest. Maize flowering is one of the most important periods
 where even small amounts of stress can significantly alter yield.
 In this work, we developed and compared two methods for automatic
 tassel detection based on the imagery collected from an unmanned
 aerial vehicle, using deep learning models. The first approach
 was a customized framework for tassel detection based on
 convolutional neural network (TD-CNN). The other method was a
 state-of-the-art object detection technique of the faster region-based CNN
 (Faster R-CNN), serving as baseline detection accuracy. The
 evaluation criteria for tassel detection were customized to
 correctly reflect the needs of tassel detection in an agricultural
 setting. Although detecting thin tassels in the aerial imagery is
 challenging, our results showed promising accuracy: the TD-CNN
 had an F1 score of 95.9% and the Faster R-CNN had 97.9% F1 score.
 More CNN-based model structures can be investigated in the future
 for improved accuracy, speed, and generalizability on
 aerial-based tassel detection.  The dataset including raw images
 and labelled images are here. The code are available on Dr. Aziza
 Alzadjali's GitHub account "azizanajeeb"
 (github.com). 
description: The aerial RGB imagery was collected by a UAV (DJI Phantom 3 Pro)
 over a maize breeding field located in Mead, Nebraska, in late July, 2017.
 The UAV was flying at a low altitude (20 m AGL). The field has a large
 number of different varieties. Some of them were
 flowering/tasseling.  The maize tassels were later
 labelled and used to train CNN models to automatically detect the
 tassels. 
description: There are three folders when you download and unzip the file here
 named "Maize_Tassels_Recognition.zip": 
 1_ReadMe
 2_Raw_RGB_Images_Collected_by_UAV
 3_Labels_for_CNN In the 1_ReadMe
 filder, there is a "readme.txt" file with brief descriptions for
 the labels in the folder 3_Labels_for_CNN: a) xml files
 are annotated images used to generate the labels, they are used as an
 input to xml_to_csv.py script which is going to generate a csv
 file.<br> b) The generated csv file is used as an input to generate
 the tfrecord files using the generate_tfrecord.py script as shown in below
 example:<br> # Create train data:  python generate_tfrecord.py
 --csv_input='path to csv file’  --output_path=’path to output
 tfrecord file’<br>
DOI: 10.48689/80d366b4-5339-4868-a452-fa660ea5b53e
title: BCMCA Bird Feature Count, 2010

description: Number of bcmca marine bird features used in the Marxan analysis that are found in each 2 km x 2km planning unit.
DOI: 10.48689/f9d14838-9fb0-4448-b82a-cb73f32d965c
title: Associations Between Arthropods and the Supralittoral Ecotone: Dependence of Aquatic and Terrestrial Taxa on Riparian Vegetation

description: In this paper we present a structural analysis of the abundance and distribution of arthropods in relation to supralittoral vegetation in the ecotone between the sea and the land. We evaluated the family-level richness and abundance of aquatic and terrestrial arthropods in marine supralittoral habitats and related arthropod assemblages to the presence and composition of supralittoral vegetation. Our results suggest that removal of supralittoral vegetation may have cascading effects on supralittoral arthropod communities and may adversely affect the productivity of both aquatic and terrestrial arthropods.
DOI: 10.5061/dryad.jsxksn08t
title: Soil microbial biomass and enzyme kinetics for the assessment of temporal diversification in agroecosystems

description: In agroecosystems, temporal diversification creates a sequence of
 short-lived habitats through time. Crop species as well as the diversity
 of crops grown in sequence might affect soil biodiversity and nutrient
 cycling processes. In the present study, we focused on a long-term crop
 rotation established in 2006 in Lower Saxony, Germany on a Luvisol. Winter
 wheat (WW) and silage maize (SM) were grown in continuous cultivation as
 well as in rotations. WW rotations span up to six years (including silage
 maize, sugar beet, winter rape and/or grain pea). Over two years,
 microbial biomass carbon (MBC) as well as kinetics (Michaelis-Menten Vmax
 and Km) of extracellular hydrolytic enzymes (b-glucosidase (BG),
 N-acetyl-b-glucosaminidase (NAG) and acid phosphomonoesterase (AP)) were
 measured in topsoil (0-10 cm depth) three times during the growing season.
 Continuous wheat increased soil microbial parameters compared to
 continuous maize as indicated by the higher microbial biomass to soil
 organic carbon ratio and higher potential enzymes activities involved in
 the C- and N-cycles (Vmax of BG and NAG). The efficiency of these enzymes
 was lowest in continuous maize (highest Km of BG and NAG). Maize and sugar
 beet as preceding crop of WW significantly decreased MBC in the 1st year
 but not in the 2nd year WW. Sugar beet decreased BG activity as well as
 its substrate affinity (increased Km). The effect of sugar beet on MBC and
 enzyme kinetics depended on the preceding crop and lessened with grain pea
 as the preceding crop. Soil microorganisms in the wheat phase benefited
 from winter rape as the preceding crop, shown by an increased biomass and
 efficiency to turn over chitin and peptidoglycan (decreased Km of NAG).
 Differences between cultivated crops, cropping history and fluctuations
 within the year in soil microbial biomass and enzyme kinetics are shown.
DOI: 10.48689/69c22223-f091-4b2a-b154-323ffa9fcca0
title: Assessing eelgrass (Zostera marina) restoration in the Squamish River estuary, British Columbia

description: Shallow, protected estuarine areas have often been used for log storage in coastal British Columbia. Eelgrass habitats, however, often coincide with these same environments and have been negatively impacted by biophysical changes caused, in part, by these industrial activities. In order to determine the restoration potential of eelgrass communities impacted by industrial activities and changing biophysical conditions in the Squamish River Estuary, a community-based restoration assessment was commenced in the summer of 2004.
DOI: 10.48689/22f71a88-0ddd-4ad1-b74f-c510f6f49904
title: Assessing Potential Habitat Impacts of Commercial Geoduck Harvest (1994 ongoing)

description: The UHA worked with DFO and other industry partners to complete a large scale investigation of the potential effects of commercial geoduck harvesting on the ocean floor and surrounding sensitive habitats like eelgrass meadows. These studies indicate that the commercial geoduck harvest has no significant, long-term effects on the structure of the ocean floor, the small organisms that live in the sediment or the plants and animals on the surface of the floor. Click here for the summary of this research.