cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2hr77
title: Data from: Tempo and mode of multicellular adaptation in experimentally evolved Saccharomyces cerevisiae

description: Multicellular complexity is a central topic in biology, but the
 evolutionary processes underlying its origin are difficult to study and
 remain poorly understood. Here we use experimental evolution to
 investigate the tempo and mode of multicellular adaptation during a de
 novo evolutionary transition to multicellularity. Multicelled “snowflake”
 yeast evolved from a unicellular ancestor after 7 days of selection for
 faster settling through liquid media. Over the next 220 days, snowflake
 yeast evolved to settle 44% more quickly. Throughout the experiment the
 clusters evolved faster settling by three distinct modes. The number of
 cells per cluster increased from a mean of 42 cells after 7 days of
 selection to 114 cells after 227 days. Between days 28 and 65, larger
 clusters evolved via a twofold increase in the mass of individual cells.
 By day 227, snowflake yeast evolved to form more hydrodynamic clusters
 that settle more quickly for their size than ancestral strains. The timing
 and nature of adaptation in our experiment suggests that costs associated
 with large cluster size favor novel multicellular adaptations, increasing
 organismal complexity.
description: Cell
 volumeVolume of individual
 cells from 7-227d of evolution.cells per
 cluster# cells per cluster,
 from 7-227d of evolution.Cluster buoyant
 densityBuoyant density of yeast
 from 7-227d of evolution.Roundness
 dataRoundness of individual
 clusters from 7-227d of evolution.settling survival
 compiled dataChange in cluster
 survival as we increased the strength of settling
 selection.Size and Settling
 velocityCluster size and
 settling velocity data of yeast from 7-227 days of
 evolution.
DOI: 10.5061/dryad.08fc8
title: Data from: Recreational harvest and incident-response management reduce human-carnivore conflicts in an anthropogenic landscape

description: Conserving viable large carnivore populations requires managing their
 interactions with humans in increasingly anthropogenic landscapes. Faced
 with declining budgets and escalating wildlife conflicts, agencies in
 North America continue to grapple with uncertainty surrounding the
 efficacy of socially divisive management actions such as harvest to reduce
 conflict. We used multistate capture–reencounter methods to estimate
 cause-specific mortality for a large sample (&gt;3500) of American
 black bears Ursus americanus in north-western New Jersey, USA over a
 33-year period. Specifically, we focused on factors that might influence
 the probability of bears being harvested, lethally managed, or dying from
 other causes. We further analysed temporal correlations between &gt;26
 000 human–black bear incidents reported between 2001 and 2013 and
 estimates of total mortality rates, and specifically, rates of harvest
 from newly implemented public hunts and lethal management. Adult females
 were twice as likely (0·163 ± 0·014) as adult males (0·087 ± 0·012) to be
 harvested during the study period. Cubs (0·444 ± 0·025) and yearlings
 (0·372 ± 0·022) had a higher probability of dying from other causes,
 primarily vehicle strikes, than adults (0·199 ± 0·008). Reports of
 nuisance behaviours in year t + 1 declined with increasing mortality
 resulting from harvest plus lethal management in year t (P = 0·028, R2 =
 0·338). Adult bears previously designated as a nuisance and/or threat were
 more likely to be harvested (0·176 ± 0·025) than those never identified as
 a problem (0·109 ± 0·010). Across age classes, individuals assigned
 problem status, were significantly more likely to be lethally controlled.
 Synthesis and applications. Given continuing failures in conserving
 exploited carnivores, their recreational harvest and lethal management
 remain polarizing. Within this social-ecological system, the
 well-regulated harvest of carefully monitored black bear populations
 represents a pragmatic approach to achieve population objectives.
 Furthermore, the integration of harvest and incident-response management
 (both lethal and non-lethal practices) with educational programmes aimed
 at reducing anthropogenic attractants can result in subsequent reductions
 in problem behaviours reported.
description: NJ black bear encounter
 histories for multistate modelsIndividual black bear
 capture histories from northwestern NJ between 1981-2014. States are:
 A=Alive; H=Harvested; M=Management Mortality; D=Dead All Other. Class at
 first capture: c=cub (0-1); y=yearling (1-2); a=adult (2+). Sex: f=female;
 m=male. Behavior: b=normal bear; p=nuisance or threatening
 bear.Raithel-JAPPL-2016-00639_bear_encounter_histories.txt
DOI: 10.5061/dryad.7h9p04r
title: Data from: A new species of trionychid turtle from the Upper Cretaceous (Campanian) Fruitland Formation of New Mexico, U.S.A.

description: New shell material of a trionychid turtle from the Upper Cretaceous (upper
 Campanian) Fossil Forest Member of the Fruitland Formation of northwestern
 New Mexico represents a new species, Gilmoremys gettyspherensis. The
 material consists of right costals I–III, V, VI, and VIII, left costals V,
 VII, and VIII, the left half of the entoplastron, the right hypo- and
 xiphiplastron, and the left hyo-, hypo-, and xiphiplastron. The specimen
 shows great similarities with the Late Cretaceous (Maastrichtian)
 trionychid Gilmoremys lancensis by having a relatively thin shell,
 carapacial sculpturing consisting of fine pits combined with extended
 sinusoidal ridges or grooves, free costal rib ends, presence of a
 preneural, a distally constricted costal I and distally expanded costal
 II, two lateral hyoplastral processes, low hyoplastral shoulders, and full
 midline contact of the elongate xiphiplastra, but differs by being
 smaller, having raised sinusoidal ridges on the carapace instead of
 grooves, less distally expanded costals II, and less elongate
 xiphiplastra. Phylogenetic analysis places Gilmoremys gettyspherensis as
 sister to Gilmoremys lancensis near the base of the clade Plastomenidae.
 Like the majority of previously described plastomenid materials, the type
 specimen of Gilmoremys gettyspherensis was collected from a mudstone
 horizon, suggesting a preference for ponded environments.
description: Supplementary data set
 1Character/taxon matrix
 used in study.Supplementary data set
 2Strict consensus trees
 resulting from the analysis and common synapomorphies.
DOI: 10.5061/dryad.29254rn
title: Data from: Clinical correlates of quantitative EEG in Parkinson’s disease: a systematic review

description: OBJECTIVE To assess the relevance of Quantitative electroencephalography
 (qEEG) measures as outcomes of disease severity and progression in PD.
 METHODS Main databases were systematically searched (January 2018) for
 studies of sufficient methodological quality that examined correlations
 between clinical symptoms of idiopathic PD and cortical (surface) qEEG
 metrics. RESULTS Thirty-six out of 605 identified studied were included.
 Results were classified into four domains: cognition (23 studies), motor
 function (13 studies), effect of treatment (7 studies), and other (10
 studies). In cross-sectional studies, EEG slowing correlated with global
 cognitive impairment and with diffuse deterioration in other domains. In
 longitudinal studies, decreased dominant frequency and increased θ power,
 reflecting EEG slowing, were biomarkers of cognitive deterioration at an
 individual level. Results on motor dysfunction and treatment yielded
 contrasting findings. Studies on functional connectivity at an individual
 level, longitudinal studies on other domains or on connectivity measures,
 were lacking. CONCLUSION QEEG parameters reflecting EEG slowing,
 particularly decreased dominant frequency and increased θ power, correlate
 with cognitive impairment and predict future cognitive deterioration. QEEG
 could provide reliable and widely available biomarkers for non-motor
 disease severity and progression in PD, potentially promoting early
 diagnosis of non-motor symptoms and an objective monitoring of
 progression. More studies are needed to clarify the role of functional
 connectivity and network analyses.
description: PRISMA checklist
 appendix 106.06.2018 Neurology PRISMA
 checklist appendix 1.docxsearch strategy appendix
 206.06.2018
 Neurology search strategy appendix
 2.docxpiloted forms appendix
 306.06.2018
 Neurology piloted forms appendix
 3.docxRisk of bias assessment
 appendix 406.06.2018 Neurology risk of
 bias assessment appendix 4.docxSupplementary
 tablesSupplementary table 1:
 Correlation of qEEG and cognition; Supplementary table 2: Longitudinal
 assessments; Supplementary table 3: Motor function; Supplementary table 4:
 Treatment; Supplementary table 5: Other06.06.2018 Neurology
 supplementary tables.docx
DOI: 10.5061/dryad.7jv49
title: Data from: Little evidence for intralocus sexual conflict over the optimal intake of nutrients for lifespan and reproduction in the black field cricket Teleogryllus commodus

description: There is often large divergence in the effects of key nutrients on
 lifespan and reproduction in the sexes, yet nutrient intake is regulated
 in the same way in males and females given dietary choice. This suggests
 that the sexes are constrained from feeding to their sex-specific
 nutritional optima for these traits. Here we examine the potential for
 intralocus sexual conflict (IASC) over optimal protein and carbohydrate
 intake for lifespan and reproduction to constrain the evolution of
 sex-specific nutrient regulation in the field cricket, Teleogryllus
 commodus. We show clear sex differences in the effects of protein and
 carbohydrate intake on lifespan and reproduction and strong positive
 genetic correlations between the sexes for the regulated intake of these
 nutrients. However, the between-sex additive genetic covariance matrix had
 very little effect on the predicted evolutionary response of nutrient
 regulation in the sexes. Thus, IASC appears unlikely to act as an
 evolutionary constraint on sex-specific nutrient regulation in T.
 commodus. This finding is supported by clear sexual dimorphism in the
 regulated intake of these nutrients under dietary choice. However,
 nutrient regulation did not coincide with the nutritional optima for
 lifespan or reproduction in either sex suggesting that IASC is not
 completely resolved in T. commodus.
description: Evolution 17-0280.R1
 Rapkin et alFeeding data and
 pedigree information for the three experiments conducted in Rapkin et al
 "Little evidence for intralocus sexual conflict over the optimal
 intake of nutrients for lifespan and reproduction in the black field
 cricket Teleogryllus commodus". The sheet called
 'Landscapes' contains data from Experiment 1. The sheet called
 'IASC' contains data from Experiment 2.The sheet called
 'Choice' contains data from Experiment 3.Rapkin et
 al.xlsx
DOI: 10.5061/dryad.s3031
title: Data from: Detrital production in Nova Scotian kelp beds: patterns and processes

description: Connectivity via the transport of detrital material from areas of high to
 low productivity may be an important determinant of secondary productivity
 and biodiversity in receiving communities. On the Atlantic coast of Nova
 Scotia, detritus exported from subtidal kelp beds contributes to food webs
 in communities inhabiting deeper waters offshore. To estimate the amount
 of energy available via this pathway, we measured rates of detrital
 production via erosion of kelp blades in kelp beds at 5 sites varying in
 wave exposure. Specifically, we measured productivity and erosion of the 2
 dominant species of kelp, Laminaria digitata and Saccharina longicruris,
 over 16 mo. We also examined the effect of environmental and biological
 factors on erosion rates, including temperature, wave exposure, grazing by
 snails and cover by the invasive bryozoan Membranipora membranacea. We
 observed clear seasonal and spatial patterns in productivity, with the
 highest production in spring. Erosion rate was highly variable across
 sites and seasons, and was strongly related to the cover of M. membranacea
 and the intensity of snail grazing at the distal end of kelp blades. Both
 factors cause tissue degradation, abrasions and perforations that weaken
 blades. Erosion rate was also positively related to water temperature and
 site exposure. Annual detrital production from the erosion of kelp blades
 increased linearly with kelp bed biomass, and ranged from 0.5 to 1.71 kg
 dry weight m–2 (150–513 g C m–2) across sites. These rates equal or exceed
 annual phytoplankton production off the Atlantic coast of Nova Scotia and
 estimates of detrital production in seagrass beds in North America.
description: Kelp growth and erosion.
 A Canadian Healthy Oceans Network Ecosystem Function Project,
 EF-11Data on individual kelp
 growth, erosion, and biomass from all sites and all sampling periods in
 the data set. Also included are data on the % of kelp blade area covered
 by Membranipora membranacea and % of the distal 1/3 of the kelp blade
 grazed by Lacuna vincta.Kelp growth and
 erosion.xlsxKelp Biomass and
 Density. A Canadian Healthy Oceans Network Ecosystem Function Project,
 EF-11Kelp biomass and density
 measured in quadrats at each site during each sampling
 period.Kelp
 Biomass Density.xlsx
DOI: 10.5061/dryad.57h24
title: Data from: Human activity reduces niche partitioning among three widespread mesocarnivores

description: Anthropogenic disturbances can constrain the realized niche space of
 wildlife by inducing avoidance behaviors and altering community dynamics.
 Human activity might contribute to reduced partitioning of niche space by
 carnivores that consume similar resources, both by promoting tolerant
 species while also altering behavior of species (e.g. activity patterns).
 We investigated the influence of anthropogenic disturbance on habitat and
 dietary niche breadth and overlap among competing carnivores, and explored
 if altered resource partitioning could be explained by human-induced
 activity shifts. To describe the diets of coyotes, bobcat, and gray foxes,
 we designed a citizen science program to collect carnivore scat samples in
 low- (“wildland”) and high- (“interface”) human-use open space preserves,
 and obtained diet estimates using a DNA metabarcoding approach. Habitat
 use was determined at scat locations. We found that coyotes expanded
 habitat and dietary niche breadth in interface preserves, whereas bobcats
 and foxes narrowed both niche breadth measures. High human use was related
 to increased dietary niche overlap among all mesocarnivore pairs,
 increased coyote habitat overlap with bobcats and foxes, and a small
 reduction in habitat overlap between bobcats and foxes. The strongest
 increase in diet overlap was among coyotes and foxes, which was smaller in
 magnitude than their habitat overlap increase. Finally, coyote scats were
 more likely to contain nocturnal prey in interface preserves, whereas
 foxes appeared to reduce consumption of nocturnal prey. Our results
 suggest that dominant and generalist mesocarnivores may encroach on the
 niche space of subordinate mesocarnivores in areas with high human
 activity, and that patterns in resource use may be related to
 human-induced activity shifts.
description: Predator Sample by
 OTUSequence counts in
 individual scat samples matching reference sequences of extant carnivores
 in the Santa Cruz Mountains. Scat samples were collected by citizen
 scientists on trails in seven Midpeninsula Open Space preserves and were
 all less than one week old.Appendix 1 - Predator Sample by
 OTU.xlsxPrey Sample by
 OTUSequence counts in
 individual scat samples matching reference sequences of extant vertebrates
 (potential prey species of mesocarnivores) in the Santa Cruz Mountains.
 Scat samples were collected by citizen scientists on trails in seven
 Midpeninsula Open Space preserves and were all less than one week
 old.Appendix 2 - Prey Sample by
 OTU.xlsx
DOI: 10.5061/dryad.8350667
title: Data from: On the interplay among ambient temperature, basal metabolic rate and body mass

description: One of the most generalized conclusions arising from studies analyzing the
 ecological variation of energy metabolism in endotherms is the apparent
 negative correlation between ambient temperature and mass-independent
 basal metabolic rate (residual BMR). As a consequence, ambient temperature
 has been considered the most important external factor driving the
 evolution of residual BMR. It is not clear, however, if this relationship
 is size dependent, and artifacts such as the biased sampling of body
 masses in physiological data sets could cause us to overstate the ubiquity
 of the relationship. Accordingly, here we used published data on body mass
 (mb), BMR, and annual mean temperature (Tmean) for 458 mammal species
 (and/or subspecies) to examine the size-dependence of the relationship
 between temperature and BMR. We found a significant interaction between mb
 and Tmean, such that the effect of Tmean on residual BMR decreases as a
 function of mb. In line with this, the amount of residual variance in BMR
 explained by Tmean decreased with mb, from 20 - 30% at body sizes &lt;
 100 g to almost zero at body size &gt; 1,000 g. These data suggest
 that our current understanding of the importance of broad-scale variation
 in ambient temperature as a driver of metabolic evolution in endotherms
 probably is affected by the large number of small species in both nature
 and physiological datasets.
description: Naya_et_al_DataSetsBasal metabolic rate, together with geographic coordinates and climatic data, for 458 mammal species (or sub-species)
DOI: 10.5061/dryad.vf62744
title: Data from: Diet complementation as a frequency‐dependent mechanism conferring advantages to rare plants via dispersal

description: 1. We used an agent-based model to test the hypothesis that diet
 complementation by frugivores can promote the persistence of rare plant
 species in communities (DCH). 2. Models simulated bird movement,
 frugivory, seed-dispersal, and plant recruitment on landscapes that
 differed in their degree of fragmentation and in their degree of fruiting
 species mixing at the scale of frugivores’ foraging decisions. 3. Diet
 complementation promoted the dispersal of rare-species without the need of
 a priori preference from birds. The effects of landscape structure on the
 dispersal of rare plants were small (&lt;5%) compared to positive
 effects of diet complementation because birds tracked the nutrients
 contained in rare fruits to balance their diets. However,
 resource-tracking of rare fruits increased foraging costs up to 20% of net
 energy intakes. 4. During post-dispersal stages, density-dependent
 mortality only conferred advantages to rare plants when located within
 hetero-specific plant patches. Still, thanks to rare-biased dispersal,
 rare plants showed the highest seed dispersal effectiveness irrespectively
 of landscape configuration. 5. Our theoretical approach presents a
 behavioral mechanism by which fruit choice can act as a
 frequency-dependent mechanism conferring rare-species advantages as
 important as classic post-dispersal density-dependent processes. 6. We
 hope that this study stimulates future work aimed at evaluating the
 importance of diet complementation in structuring the composition and
 spatial patterning of plant communities.
description: Diet_complementation_model_ouputsExcel file containing main model outputs- Changes in plant species relative abundance in the seed availability-seed rain transition (Rsp2), resource provisioning effectiveness (RPE) and seed dispersal effectiveness of focal species (SDE). All datas have a read_me sheet with variables information
DOI: 10.5061/dryad.q8m165t
title: Data from: Fine scale waterbody data improve prediction of waterbird occurrence despite coarse species data

description: While modelling habitat suitability and species distribution, ecologists
 must deal with issues related to the spatial resolution of species
 occurrence and environmental data. Indeed, given that the spatial
 resolution of species and environmental datasets range from centimeters to
 hundreds of kilometers, it underlines the importance of choosing the
 optimal combination of resolutions to achieve the highest possible
 modelling prediction accuracy. We evaluated how the spatial resolution of
 land cover/waterbody datasets (meters to 1 km) affect waterbird habitat
 suitability models based on atlas data (grid cell of 12×11 km). We
 hypothesized that the area, perimeter and number of waterbodies computed
 from high resolution datasets would explain distributions of waterbirds
 better because coarse resolution datasets omit small waterbodies affecting
 species occurrence. Specifically, we investigated which spatial resolution
 of waterbodies better explain the distribution of seven waterbirds nesting
 on ponds/lakes with areas ranging from 0.1 ha to hundreds of hectares. Our
 results show that the area and perimeter of waterbodies derived from high
 resolution datasets (raster data with 30 m resolution, vector data
 corresponding with map scale 1:10,000) explain the distribution of the
 waterbirds better than those calculated using less accurate datasets
 despite the coarse grain of the species data. Taking into account the
 spatial extent (global vs regional) of the datasets, we found the Global
 Inland Waterbody Dataset to be the most suitable for modelling
 distribution of waterbirds. In general, we recommend using land cover data
 of a resolution sufficient to capture the smallest patches of the habitat
 suitable for a given species’ presence for both fine and coarse grain
 habitat suitability and distribution modelling.
description: WaterbirdDataCount, perimeter, and area of water bodies within mapping squares of Atlas of Breeding Birds in the Czech Republic 2001–2003. The values were derived from five datasets: clc - Corine Land Cover, gcl - Global Consensus Land Cover, giw - Global Inland Water, osm - Open Street Map, dib - Dibavod. IdSquare - ID of the atlas mapping square. PA - Presence/absence of the species (species name is included in the file name.
DOI: 10.5061/dryad.r1f08nt
title: Data from: A rangewide herbarium-derived dataset indicates high levels of gene flow in black cherry (Prunus serotina)

description: Aim: Isolation by Distance (IBD) is a genetic pattern in which populations
 geographically closer to one another are more genetically similar to each
 other than populations which are farther apart. Black cherry (Prunus
 serotina Ehrh.) (Rosaceae) is a forest tree species widespread in eastern
 North America, and found sporadically in the southwestern United States,
 Mexico, and Guatemala. IBD has been studied in relatively few North
 American plant taxa, and no study has rigorously sampled across the range
 of such a widespread species. In this study, IBD and overall genetic
 structure were assessed in eastern black cherry (P. serotina Ehrh. subsp.
 serotina), the widespread subspecies of eastern North America. Location:
 Eastern North America Taxon: Prunus serotina Ehrh. Rosaceae Methods: Dense
 sampling across the entire range of eastern black cherry was made possible
 by genotyping 15 microsatellite loci in 439 herbarium samples from all
 portions of the range. Mantel tests and STRUCTURE analyses were performed
 to evaluate the hypothesis of IBD and genetic structure. Results: Mantel
 tests demonstrated significant but weak IBD, while STRUCTURE analyses
 revealed no clear geographic pattern of genetic groups. Main conclusions:
 The modest geographic/genetic structure across the eastern black cherry
 range suggests widespread gene flow in this taxon. This is consistent with
 P. serotina's status as a disturbance-associated species. Further
 studies should similarly evaluate IBD in species characteristic of
 low-disturbance forests.
description: P_serotina_genotypesMicrosatellite genotypes for individuals examined in this studyPrunus_serotina_localityLocality data from herbarium sheets of individuals examined in this study