cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.836fg6bn
title: Data from: Multiple scales of genetic connectivity in a brooding coral on isolated reefs following catastrophic bleaching

description: Understanding the pattern of connectivity among populations is crucial for
 the development of realistic and spatially explicit population models in
 marine systems. Here we analysed variation at eight microsatellite loci to
 assess the genetic structure and to infer patterns of larval dispersal for
 a brooding coral, Seriatopora hystrix, at an isolated system of reefs in
 northern Western Australia. Spatial autocorrelation analyses show that
 populations are locally subdivided, and that the majority of larvae
 recruit to within 100 m of their natal colony. Further, a combination of
 F- and R- statistics showed significant differentiation at larger spatial
 scales (2–60 km) between sites, and this pattern was clearly not
 associated with distance. However, Bayesian analysis demonstrated that
 recruitment has been supplemented by less frequent but recent input of
 larvae from outside the local area; 2–6% of colonies were excluded from
 the site at which they were sampled. Individual assignments of these
 migrants to the most likely populations suggest that the majority of
 migrants were produced at the only site that was not decimated by a recent
 and catastrophic coral bleaching event. Furthermore, the only site that
 recovered to prebleaching levels received most of these immigrants. We
 conclude that the genetic structure of this brooding coral reflects its
 highly opportunistic life history, in which prolific, philopatric
 recruitment is occasionally supplemented by exogenously produced larvae.
description: multiple scales of
 connectivity_Shystrix@scott_rawdata
DOI: 10.5061/dryad.r01j0
title: Data from: Odour cues influence predation risk at artificial bat roosts in urban bushland

description: Odours that accumulate from roosting can attract predators and increase
 predation risk. Consequently, selection should favour strategies that
 allow prey to evade detection by predators, including changing roosts.
 Insectivorous bats that roost in tree hollows regularly switch roosts and
 roost in different sized groups: strategies that would alter the
 accumulation of roost odours and are hypothesized to reduce predation
 risk. We experimentally manipulated the amount and refresh rate of
 roosting odour cues at 90 artificial bat roosts in Sydney, Australia, to
 test the hypothesis that odours increase predator visitation. Predators
 visited roosts with bat faeces significantly more often than untreated
 control roosts. Roosts with small amounts of faeces mimicking sites used
 by solitary bats had the greatest rate of visitation. This suggests that
 bats roosting alone, rather than in groups, have a greater likelihood of
 disturbance or predation. Roost switching likely decreases the
 predictability of finding occupied roosts, however we show that all roosts
 (those currently or recently occupied) were visited by predators,
 suggesting generalist urban predators readily investigate potential
 roosts. This is the first demonstration that bat odours are attractive to
 predators that use olfactory cues, showing that bats are at risk of
 predation in visually cryptic roosts.
description: CThrelfall_DATA_Nest_Predation_2010Raw data collected in the field from a nest predation experiment. The metadata tab describes more detail about when and how the data was collected.
DOI: 10.5061/dryad.04vh7
title: Data from: Pathogen growth in insect hosts: inferring the importance of different mechanisms using stochastic models and response time data

description: Pathogen population dynamics within individual hosts can alter disease
 epidemics and pathogen evolution, but our understanding of the mechanisms
 driving within-host dynamics is weak. Mathematical models have provided
 useful insights, but existing models have only rarely been subjected to
 rigorous tests, and their reliability is therefore open to question. Most
 models assume that initial pathogen population sizes are so large that
 stochastic effects due to small population sizes, so-called demographic
 stochasticity, are negligible, but whether this assumption is reasonable
 is unknown. Most models also assume that the dynamic effects of a host’s
 immune system strongly affect pathogen incubation times or “response
 times,” but whether such effects are important in real host-pathogen
 interactions is likewise unknown. Here we use data for a baculovirus of
 the gypsy moth to test models of within-host pathogen growth. By using
 Bayesian statistical techniques and formal model-selection procedures, we
 are able to show that the response time of the gypsy moth virus is
 strongly affected by both demographic stochasticity and a dynamic response
 of the host immune system. Our results imply that not all response-time
 variability can be explained by host and pathogen variability, and that
 immune system responses to infection may have important effects on
 population-level disease dynamics.
description: 6-22-08
 experimentData from a dose
 response experiment using gypsy moths exposed to the gypsy moth
 baculovirus. Fraction of virus-induced mortality and speed of kill were
 recorded for 5 different doses.
DOI: 10.5061/dryad.487db24
title: Data from: Mating opportunity increases with synchrony of flowering among years more than synchrony within years in a nonmasting perennial

description: The timing and synchrony of mating activity in a population may vary both
 within and among years. With the exception of masting species, in which
 reproductive activity fluctuates dramatically among years, mating
 synchrony is typically studied within years. However, opportunities to
 mate also vary among years in non-masting iteroparous species. We
 demonstrate that studying only within-year flowering synchrony fails to
 accurately quantify mating opportunity in an experimental population (n =
 286) of a non-masting species, Echinacea angustifolia. We quantified
 individuals' synchrony of flowering within and among years and
 partitioned the contribution of each measure to mean daily mating
 potential, the number of potential mates per individual per day averaged
 over every day it flowered during the 11-year study period. Individual
 within- and among-year synchrony displayed wide variation and were weakly
 correlated. Each contributed to mean daily mating potential to differing
 extents, indicating that consequences of flowering synchrony, such as mate
 availability, vary in magnitude between temporal scales. In particular,
 among-year synchrony explained 39% more variation in mean daily mating
 potential than did within-year synchrony. Thus, among-year synchrony
 likely has underappreciated significance for mating dynamics in
 non-masting species.
description: data_waananen_etal_2018data and R scripts associated with Waananen, Kiefer, Ison, and Wagenius 2018 (see README)
DOI: 10.5061/dryad.m900b
title: Data from: Nitrogen, phosphorus, and cation use efficiency in stands of regenerating tropical dry forest

description: Plants on infertile soils exhibit physiological and morphological traits
 that support conservative internal nutrient cycling. However, potential
 trade-offs among use efficiencies for N, P, and cations are not well
 explored in species-rich habitats where multiple elements may limit plant
 production. We examined uptake efficiency and use efficiency of N, P, K,
 Ca, Mg, Al, and Na in plots of regenerating tropical dry forests spanning
 a gradient of soil fertility. Our aim was to determine whether plant
 responses to multiple elements are correlated, or whether there are
 trade-offs among exploitation strategies across stands varying in
 community composition, soil quality, and successional stage. For all
 elements, both uptake efficiency and use efficiency decreased as
 availability of the corresponding element increased. Plant responses to N,
 Na, and Al were uncoupled from uptake and use efficiencies for P and
 essential base cations, which were tightly correlated. N and P use
 efficiencies were associated with shifts in plant species composition
 along the soil fertility gradient, and there was also a trend towards
 increasing N use efficiency with stand age. N uptake efficiency was
 positively correlated with the abundance of tree species that associate
 with ectomycorrhizal fungi. Taken together, our results suggest that
 successional processes and local species composition interact to regulate
 plant responses to availability of multiple resources. Successional
 tropical dry forests appear to employ different strategies to maximize
 response to N vs. P and K.
description: NUE_plant trait data_for
 Dryad_27Sept2015This dataset contains
 plot-level nutrient concentration data in leaf litter and fine roots for
 18 plots of regenerating tropical dry forest in Guanacaste, Costa Rica.
 The nutrients measured include: aluminum, calcium, potassium, magnesium,
 sodium, phosphorus, and nitrogen. In addition, we report concentrations of
 these same elements in branchwood of 31 species that are common in the
 plots. All methods used to sample these tissues and quantify element
 concentrations are described in the paper.
DOI: 10.3535/5sb-85t-f3j
title: Specimen from Tallinn University of Technology

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.5061/dryad.t8h9553
title: Data from: Population genetics and speciation of yellow-bellied, red-naped, and red-breasted sapsuckers (Sphyrapicus varius, S. nuchalis, and S. ruber)

description: The root of understanding speciation lies in determining the forces which
 drive it. In many closely-related species, including Sphyrapicus varius,
 S. nuchalis, and S. ruber, it is assumed that speciation occurred due to
 isolation in multiple Pleistocene refugia. We used genetic data from 457
 samples at the control region, COI, and CHD1Z to examine rangewide
 population genetic structure and differentiation amongst these three
 species across each species’ breeding range. In addition, we modelled
 these species’ ecological niches for the Holocene (~6,000 ya), Last
 Glacial Maximum (~22,000 ya), and Last Interglacial (~120,000-140,000 ya)
 to determine if Pleistocene glaciations could have contributed to
 allopatric distributions, therefore allowing these groups to
 differentiate. Population genetic data show a potential Pleistocene
 refugium in Haida Gwaii, an east-west split among S. varius, and low
 genetic differentiation within each species. Our control region data show
 some polyphyly, while COI and CHD1Z data show differentiation among
 species using composite genotypes. Ecological Niche Modelling shows a
 large amount of niche overlap at each time period suggesting that S.
 varius, S. nuchalis, and S. ruber may not have been completely allopatric,
 and these species likely had repeated intermittent contact. Our data
 support the growing body of research that suggests differentiation despite
 gene flow.
description: Voucher Specimen
 DataSource museums and
 identification numbers for all museum specimens used in study. Museum
 samples from the Royal British Columbia Museum (RBCM), University of
 British Columbia (UNBC), Queen’s University (QU), University of Michigan
 (UMich) Museum of Southwest Biology (MSB), American Museum of Natural
 History (AMNH), University of Washington Burke Museum (UWBM), Royal
 Alberta Museum (RABM), Field Museum Natural History (FMNH), New Brunswick
 Museum (NBM), Canadian Museum of Nature (CMN), Smithsonian (Smith) and
 Royal Saskatchewan Museum (RSKM).VoucherSpecimenData_Dryad.xlsxGeographic dataCoordinate data for all samples used in study.GeographicData_Dryad.xlsxCladesSNPIndelControl region clades, COI SNPs, and CHD1Z Indel loci for each bird in the study.
DOI: 10.5061/dryad.8935834
title: Data from: Autoimmune encephalitis: a costly condition

description: Objective: To assess the inpatient hospitalization burden and costs of
 patients with autoimmune encephalitis (AE) at a tertiary care institution.
 Methods: Adult inpatients with AE were identified retrospectively from
 July 1, 2005 – June 30, 2015. Demographic and clinical data were collected
 and analyzed. Billing data were compared to that of patients with herpes
 simplex encephalitis (HSE). Charges were adjusted for inflation. Results:
 Of 244 admissions for encephalitis reviewed, 63 patients met criteria for
 probable or definite AE. Thirty-one (49%) patients were antibody-positive,
 and twenty-seven (43%) were admitted to the intensive care unit (ICU).
 Median hospital charges per AE patient were over $70k, median length of
 stay (LOS) was 15 days, and in hospital mortality was 6%. ICU patients had
 substantially higher median hospital charges (ICU $173k/ admission vs.
 non-ICU $50k/ admission, p&lt;0.001). LOS was strongly associated with
 charges and was driven by delay in diagnosis of AE, prolonged treatment
 courses, and lack of response to therapy. In comparison with HSE, median
 hospital charges per AE patient were nearly 4 times higher, median AE LOS
 was 3 times higher, and total charges over the study period were nearly
 twice as high. Conclusions: AE patients utilized more inpatient healthcare
 resources per patient during a ten-year period than HSE at our
 institution. ICU-admitted AE patients were responsible for a substantially
 higher financial burden than non-ICU-admitted AE patients. Our data
 underscore the need for the development of novel diagnostic and
 therapeutic modalities to improve patient outcomes and decrease hospital
 burden in AE.
description: AE burden supplementary
 informationSupplemental Figures and
 TablesAE
 burden supplementary_figures.docx
DOI: 10.5061/dryad.nt60p
title: Data from: Cyfip1 regulates presynaptic activity during development

description: Copy number variations encompassing the gene encoding Cyfip1 have been
 associated with a variety of human diseases, including autism and
 schizophrenia. Here we show that juvenile mice hemizygous for Cyfip1 have
 altered presynaptic function, enhanced protein translation, and increased
 levels of F-actin. In developing hippocampus, reduced Cyfip1 levels serve
 to decrease paired pulse facilitation and increase miniature EPSC
 frequency without a change in amplitude. Higher-resolution examination
 shows these changes to be caused primarily by an increase in presynaptic
 terminal size and enhanced vesicle release probability. Short
 hairpin-mediated knockdown of Cyfip1 coupled with expression of mutant
 Cyfip1 proteins indicates that the presynaptic alterations are caused by
 dysregulation of the WAVE regulatory complex. Such dysregulation occurs
 downstream of Rac1 as acute exposure to Rac1 inhibitors rescues
 presynaptic responses in culture and in hippocampal slices. The data serve
 to highlight an early and essential role for Cyfip1 in the generation of
 normally functioning synapses and suggest a means by which changes in
 Cyfip1 levels could impact the generation of neural networks and
 contribute to abnormal and maladaptive behaviors.
description: Hsiao_Statistical_Summary_JNChart of the assays, measurements, n's, values, statistical tests and p values for the data presented in figures in this paper.
DOI: 10.5061/dryad.r80d3
title: Data from: Changing climate cues differentially alter zooplankton dormancy dynamics across latitudes

description: 1. In seasonal climates, dormancy is a common strategy that structures
 biodiversity and is necessary for the persistence of many species. Climate
 change will likely alter dormancy dynamics in zooplankton, the basis of
 aquatic food webs, by altering two important hatching cues: mean
 temperatures during the ice-free season, and mean day length when lakes
 become ice free. Theory suggests that these changes could alter diversity,
 hatchling abundances and phenology within lakes, and that these responses
 may diverge across latitudes due to differences in optimal hatching cues
 and strategies. 2. To examine the role of temperature and day length on
 hatching dynamics, we collected sediment from 25 lakes across a 1800 km
 latitudinal gradient and exposed sediment samples to a factorial
 combination of two photoperiods (12 and 16 hours) and two temperatures
 (8°C and 12 °C) representative of historical southern (short photoperiod,
 warm) and northern (long photoperiod, cool) lake conditions. We tested
 whether sensitivity to these hatching cues varies by latitudinal origin
 and differs among taxa. 3. Higher temperatures advanced phenology for all
 taxa, and these advances were greatest for cladocerans followed by
 copepods and rotifers. Although phenology differed among taxa, the effect
 of temperature did not vary with latitude. The latitudinal origin of the
 egg bank influenced egg abundance and hatchling abundance and diversity,
 with these latter effects varying with taxa, temperature and photoperiod.
 4. Copepod hatchling abundances peaked at mid latitudes in the high
 temperature and long photoperiod treatments, whereas hatchling abundances
 of other zooplankton were greatest at low latitudes and high temperature.
 The overall diversity of crustacean zooplankton (copepods and cladocerans)
 also reflected distinct responses of each taxa to our treatments, with the
 greatest diversity occurring at mid latitudes (~56° N) in the shorter
 photoperiod treatment. 5. Our results demonstrate that hatching cues
 differ for broad taxonomic groups that vary in developmental and
 life-history strategies. These differences are predicted to drive
 latitude-specific shifts in zooplankton emergence with climate change, and
 could alter the base of aquatic food webs.
description: Data for egg number,
 phenology, abundance, diversity and lake characteristics
 analysisThis data file includes
 zooplankton diversity data that were provided by K. Patalas and pelagic
 samples that we collected from from lakes in 2011. The data file also
 includes lake chemistry data that we collected from the field in 2011. The
 remainder of the data is the results from the hatching experiment we
 conducted, which is the focus of this manuscript.Jones & Gilbert JAE - Data
 for Dryad.xlsx
DOI: 10.3535/fra-mjr-xrh
title: Cephalopoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.5061/dryad.725m1
title: Data from: What was old is new again: thermal adaptation within clonal lineages during range expansion in a fungal pathogen

description: Range-expanding species are expected to gain an increasing importance in
 the context of global change. They provide a great opportunity to study
 contemporary evolutionary changes and to unravel the mechanisms of
 evolution. Cryphonectria parasitica, the causal agent of chestnut blight,
 originating from Asia, has been spread since the beginning of the 20th
 century into different continents. We took advantage of the C. parasitica
 recent emergence in northern France to study the changes in population
 genetic structure and in phenotypic traits along this colonization and
 climatic gradient. Four hundred twenty-seven C. parasitica isolates were
 sampled in 47 chestnut sites in northern France. The C. parasitica
 outbreak in the north was found to be due to the expansion of five
 dominant clonal groups from southern France and to the emergence of a few
 rare recombined genotypes. The evolutionary changes during C. parasitica
 range expansion were studied by analyzing phenotypic changes in isolates
 from the same clonal lineage, with or without a geographic shift. Growth
 rates were assessed in vitro, at four temperatures. The northern isolates
 grew faster at 12 and 15°C and more slowly at 28 and 32°C than the
 southern isolates. These results strongly suggest local adaptation to low
 temperatures in C. parasitica, with a trade-off of slower growth at high
 temperatures. They also reflect the high evolutionary potential of C.
 parasitica along a colonization gradient and show that clonal evolution is
 not a limitation for the rapid thermal adaptation of this invasive fungal
 species.
description: geneticdataC. parasitica isolates were genotyped with 10 microsatellite markers data. The file contains genotypes of the studied isolates and the genotypes found in Francephenotypic dataThe file contains mean growth rate of C.parasitica in vitro at four temperatures, and minimal and maximal temperatures at their sampling site.
DOI: 10.5061/dryad.g1hf29c
title: Data from: Increased male bias in eider ducks can be explained by sex-specific survival of prime-age breeders

description: In contrast to theoretical predictions of even adult sex ratios, males are
 dominating in many bird populations. Such bias among adults may be
 critical to population growth and viability. Nevertheless, demographic
 mechanisms for biased adult sex ratios are still poorly understood. Here,
 we examined potential demographic mechanisms for the recent dramatic shift
 from a slight female bias among adult eider ducks (Somateria mollissima)
 to a male bias (about 65% males) in the Baltic Sea, where the species is
 currently declining. We analysed a nine-year dataset on offspring sex
 ratio at hatching based on molecularly sexed ducklings of individually
 known mothers. Moreover, using demographic data from long-term
 individual-based capture-recapture records, we investigated how
 sex-specific survival at different ages after fledgling can modify the
 adult sex ratio. More specifically, we constructed a stochastic two-sex
 matrix population model and simulated scenarios of different survival
 probabilities for males and females. We found that sex ratio at hatching
 was slightly female-biased (52.8%) and therefore unlikely to explain the
 observed male bias among adult birds. Our stochastic simulations with
 higher survival for males than for females revealed that despite a slight
 female bias at hatching, study populations shifted to a male-biased adult
 sex ratio (&gt; 60% males) in a few decades. This shift that was
 driven by prime reproductive-age individuals (≥5-year-old), with
 sex-specific survival of younger age classes playing a minor role. Hence,
 different age classes contributed disproportionally to population
 dynamics. We argue that an alternative explanation for the observed male
 dominance among adults - sex-biased dispersal - can be considered
 redundant and is unlikely, given the ecology of the species. The present
 study highlights the importance of considering population structure and
 age-specific vital rates when assessing population dynamics and management
 targets.
description: Duckling sex
 ratioThis data file contains
 the duckling sex ratio of individually known female eiders during
 2005-2013.duckling sex_Ramula et
 al.csv