cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6p394rh
title: Data from: Screening sticky cards as a simple method for improving efficiency of Diaphorina citri (Hemiptera: Liviidae) monitoring and reducing non-target organisms

description: Management of Diaphorina citri Kuwayama (Hemiptera: Liviidae) populations
 is one of the major strategies for reducing the spread and incidence of
 huanglongbing (HLB). HLB is putatively caused by Candidatus Liberibacter
 spp. (Rhizobiales: Phyllopbacteriaceae) that are transmitted to citrus by
 psyllid vectors. Diaphorina citri population monitoring is done to detect
 its presence and inform on management decisions. Various methods are used
 for detecting and estimating D. citri densities but trapping with yellow
 or lime-green sticky cards has proven to be the most effective method.
 These sticky cards rely on the color preference of adult D. citri, but
 many flying organisms are attracted to the same color spectrum as
 psyllids. Hence, in field situations, sticky traps are hampered by large
 numbers of bycatches of nontarget organisms and debris. Here, we described
 a method using a mesh laid on the surface of traps as a sift to catch
 mainly psyllids, while reducing bycatches. By filtering D. citri through
 this mesh, they can be counted more rapidly and accurately. Although
 mesh-covered traps captured 5–15% less D. citri relative to uncovered ACP
 traps, both types of traps statistically agreed on D. citri detection and
 population densities. The effectiveness of mesh-covered traps did not vary
 with season. In addition, mesh-covered traps eliminated &gt;90% of
 nontarget organisms and allowed for quicker enumeration of D. citri. We
 expect this method will become an important component of redesigning
 integrated pest management programs in citrus groves by reducing
 unintended impacts of beneficial arthropods during large scale D. citri
 monitoring.
description: Data on types of mesh
 and validation1. Comparison of D.
 citri caught with screened traps with three types of mesh and unscreened
 traps; 2. Trap cleanness based on type; 3. data on validation
 studyDryad_Mesh
 types.xlsx
DOI: 10.5281/zenodo.18348443
title: KEYS_BRAND7_5F_1_23C_0k_EDLC_single

description: MetSuperCap Project Dataset 

5F SC sample 1

Keysight

Part of the Constant Temperature DataBase
DOI: 10.5281/zenodo.18348442
title: KEYS_BRAND7_5F_1_23C_0k_EDLC_single

description: MetSuperCap Project Dataset 

5F SC sample 1

Keysight

Part of the Constant Temperature DataBase
DOI: 10.5061/dryad.pd8612j
title: Data from: Accounting for kin sampling reveals genetic connectivity in Tasmanian and New Zealand school sharks, Galeorhinus galeus

description: Fishing represents a major problem for conservation of chondrichthyans,
 with a quarter of all species being overexploited. School sharks,
 Galeorhinus galeus, are targeted by commercial fisheries in Australia and
 New Zealand. The Australian stock has been depleted to below 20% of its
 virgin biomass, and the species is recorded as Conservation Dependent
 within Australia. Individuals are known to move between both countries,
 but it is disputed whether the stocks are reproductively linked. Accurate
 and unbiased determination of stock and population connectivity is crucial
 to inform effective management. In this study, we assess the genetic
 composition and population connectivity between Australian and New Zealand
 school sharks using genome‐wide SNPs, while accounting for non‐random kin
 sampling. Between 2009 and 2013, 88 neonate and juvenile individuals from
 Tasmanian and New Zealand nurseries were collected and genotyped. Neutral
 loci were analyzed to detect fine‐scale signals of reproductive
 connectivity. Seven full‐sibling groups were identified and removed for
 unbiased analysis. Based on 6,587 neutral SNPs, pairwise genetic
 differentiation from Tasmanian and New Zealand neonates was
 non‐significant (FST = 0.0003, CI95 = [−0.0002, 0.0009], p = 0.1163; Dest
 = 0.0006 ± 0.0002). This pattern was supported by clustering results. In
 conclusion, we show a significant effect of non‐random sampling of kin and
 identify fine‐scale reproductive connectivity between Australian and New
 Zealand school sharks.
description: Raw and filtered SNPs
 with associated metadataRaw DArTseq SNP data and
 metadata to repeat the complete analysis following "Devloo-Delva et
 al. Supporting Information S1". Additionally, filtered .Rdata (with
 and without full sibling) and supplementary material have been provided as
 well.Devloo-Delva_et_al._2019_DRYAD_data.zip
DOI: 10.5061/dryad.j348s75
title: Data from: Are there synergistic or antagonistic effects of multiple maternally-derived egg components (antibodies and testosterone) on offspring phenotype?

description: Eggs are multivariate in that they contain multiple maternally-derived egg
 components (e.g. hormones, antibodies, mRNA, antioxidants) which are
 thought to influence offspring phenotype. However, most studies have
 focused on single egg components and on short-term effects. Here, we
 simultaneously manipulated two egg components, maternally-derived
 antibodies (MAb) and yolk testosterone (T) to assess potential synergistic
 or antagonistic effects on offspring phenotype from hatching to sexual
 maturity. We found no evidence for short-or long-term effects of either
 MAb or yolk T alone, or their interaction, on hatching mass, size at
 fledging (tarsus), body mass at sexual maturity (day 82), chick survival,
 humoral immune function, or any measured female reproductive trait at
 sexual maturity. There was a positive effect of yolk T, but not MAb, on
 offspring PHA response at 26 days of age but at 82 days of age MAb, but
 not yolk T, had a positive effect on PHA response. There was also a MAbsex
 interaction on 30 day chick mass, and a positive effect of yolk T on male
 courtship behaviour at sexual maturity. However, we found no evidence for
 synergy, i.e. where offspring treated both with MAb and yolk T had higher
 trait values than offspring treated with either MAb or yolk T alone for
 any measured trait. Similarly, evidence for antagonistic (compensatory)
 effects, where offspring treated both with MAb and yolk T had intermediate
 trait values compared with offspring treated with either MAb or yolk T
 alone, was equivocal.
description: Mom_reproMothers breeding data (1st generation)Chick_growthChick growth dataChick_immuneChick immune data (LPS and MAb)Daughter_breeding_181018Daughter (2nd generation) reproduction dataDaughter_rep.prnMatingMale (son, 2nd generation) mating trial data
DOI: 10.5061/dryad.3708bv1
title: Data from: Evolution of an insect immune barrier through horizontal gene transfer mediated by a parasitic wasp

description: Genome sequencing data have recently demonstrated that eukaryote evolution
 has been remarkably influenced by the acquisition of a large number of
 genes by horizontal gene transfer (HGT) across different kingdoms.
 However, in depth-studies on the physiological traits conferred by these
 accidental DNA acquisitions are largely lacking. Here we elucidate the
 functional role of Sl gasmin, a gene of a symbiotic virus of a parasitic
 wasp that has been transferred to an ancestor of the moth species
 Spodoptera littoralis and domesticated. This gene is highly expressed in
 circulating immune cells (haemocytes) of larval stages, where its
 transcription is rapidly boosted by injection of microorganisms into the
 body cavity. RNAi silencing of Sl gasmin generated a phenotype
 characterized by a precocious suppression of phagocytic activity by
 haemocytes, which was rescued when these immune cells were incubated in
 plasma samples of control larvae, containing high levels of the encoded
 protein. Proteomic analysis demonstrated that the protein Sl gasmin is
 released by haemocytes into the haemolymph, where it opsonizes the
 invading bacteria to promote their phagocytosis, both in vitro and in
 vivo. Our results show that important physiological traits do not
 necessarily originate from evolution of pre-existing genes, but can be
 acquired by HGT events, through unique pathways of symbiotic evolution.
 These findings indicate that insects can paradoxically acquire selective
 advantages with the help of their natural enemies.
description: Raw data Di Lelio et
 al., 2019Numerical data that
 underlies tables and graphs (figures 1-7, 9, 10; table 1) and statistics
 of the PLOS Genetics article from di Lelio et al.,
 2019.Data
 sets Di Lelio et al.xlsx
DOI: 10.5061/dryad.pv93760
title: Data from: Decline in abundance and apparent survival rates of fin whales (Balaenoptera physalus) in the northern Gulf of St. Lawrence

description: Estimates of abundance and survivorship provide quantifiable measures to
 monitor populations and to define and understand their conservation
 status. This study investigated changes in abundance and survival rates of
 fin whales (Balaenoptera physalus) in the northern Gulf of St. Lawrence
 (GSL) in the context of anthropogenic pressures and changing environmental
 conditions. A long-term data set, consisting of 35 years of
 photo-identification surveys and comprising more than 5,000
 identifications of 507 individuals, formed the basis of this
 mark-recapture study. Based on model selection using corrected Akaike
 Information Criterion, the most parsimonious Cormack-Jolly-Seber model
 included a linear temporal trend in non-calf apparent survival rates with
 a sharp decline in the last five years of the study and a median survival
 rate of 0.946 (95% confidence interval (CI) 0.910-0.967). To account for
 capture heterogeneity due to divergent patterns of site fidelity,
 agglomerative hierarchical cluster (AHC) analysis was employed to
 categorise individuals based on their annual and survey site fidelity
 indices. However, the negative trend in survivorship remained and was
 corroborated by a significant decline in the estimated super-population
 size from 335 (95% CI 321-348) individuals in 2004-2010 to 291 (95% CI
 270-312) individuals in 2010-2016. Concurrently, a negative trend was
 estimated in recruitment to the population, supported by a sharp decrease
 in the number of observed calves. Ship strikes and changes in prey
 availability are potential drivers of the observed decline in fin whale
 abundance. The combination of clustering methods with mark-recapture
 represents a flexible way to investigate the effects of site fidelity on
 demographic variables and is broadly applicable to other individual-based
 studies.
description: All data and R-code
 filesCapture-recapture
 histories and R-code are provided to replicate results and
 figures.Schleimer_et_al_2019_fin_whale_mark_recapture_data_code.zip
DOI: 10.5061/dryad.6jc8jd1
title: Data from: Life table invasion models: spatial progression and species-specific partitioning

description: Biological invasions are increasingly being considered important spatial
 processes that drive global changes, threatening biodiversity, regional
 economies, and ecosystem functions. A unifying conceptual model of the
 invasion dynamics could serve as a useful tool for comparison and
 classification of invasion processes involving different species across
 large geographic ranges. By dividing these geographic ranges that are
 subject to invasions into discrete spatial units we here conceptualize the
 invasion process as the transition from pristine to invaded spatial units.
 We use California cities as the spatial units and a long-term database of
 invasive tropical tephritids to characterize the invasion patterns. A new
 life-table method based on insect demography, including the progression
 model of invasion stage transition and the species-specific partitioning
 model of multispecies invasions, was developed to analyze the invasion
 patterns. The progression model allows us to estimate the probability and
 rate of transition, for individual cities, from pristine to infested
 stages and subsequently differentiate first year of detection from
 detection recurrences. Importantly, we show that the interval of invasive
 tephritid recurrence in a city declines with increasing invasion stages of
 the city. The species-specific partitioning model revealed profound
 difference in invasion outcome depending on which tephritid species was
 first detected (and then locally eradicated) in the early stage of
 invasion. Taken together, we discuss how these two life-table invasion
 models can cast new light on existing invasion concepts; in particular, on
 formulating invasion dynamics as the state transition of cities and
 partitioning species-specific role during multispecies invasions. These
 models provide a new set of tools for predicting the spatiotemporal
 progression of invasion and providing early warnings of recurrent
 invasions for efficient management.
description: Tephritid captures in
 CaliforniaDetection records of
 alien tephritids in California from 1950-2017. The dataset includes the
 following variables: Species (scientific name of detected tephritids in
 California). Common Name (the common name of detected tephritids in
 California). Date (the detection date as month/day/year). City (location
 information of detected tephritids in California). Total (the detected
 number of alien tephritids in California). Latitude (detected location, a
 geographic coordinate that specifies the north–south position of a point
 on the Earth's surface). Longitude (detected location, a geographic
 coordinate that specifies the east–west position of a point on the
 Earth's surface). Please NOTE: These data are also available from
 Ecology in CSV format. They have been uploaded as supporting information
 for the corresponding publication.raw
 data.xlsx
DOI: 10.5061/dryad.mt5q8m2
title: Data from: Numbers and distribution of the Great Cormorant in Iceland: limitation at the regional and metapopulation level

description: We studied a metapopulation of great cormorant (Phalacrocorax carbo) in
 Iceland, using complete aerial censuses of nests in 25 years during
 1975–2015. Age composition was estimated in 1998–2014 by ground surveys in
 September and February. Brood size was estimated from aerial photographs
 in 2007–2015. Weather, food, breeding habitat, and density were considered
 as explanatory variables when examining numerical and distributional
 changes in the cormorant metapopulation. In 1975–1990 total nest numbers
 changed little, very low numbers about 1992 were followed by an annual
 increase of 3.5% in 1994–2015. Total nest numbers were positively
 correlated with estimates of spawning stocks of cod and saithe and
 inversely related to the subpolar gyre index (SPG‐I). During the increase
 in 1994–2015, average colony size at first increased and then declined.
 Habitat use also changed: the proportion of nests on small rocky islets
 (skerries) at first declined, from 69% to 44% in 1995–2003 and then
 increased again to about 58% in 2012–2014. Habitat changes were probably a
 response to changed patterns of human disturbance. Breeding density, as
 nests per km2 sea &lt;20 m deep, was rather uniform among five defined
 regions in 1975–1996. Thereafter, densities became much higher in two
 sheltered regions with kelp forests and in one mostly exposed region. A
 second exposed region remained low and in the third nest numbers declined
 markedly. Thus, carrying capacity was higher in sheltered regions where
 cormorant breeding had historically been depressed by human disturbance.
 Brood size varied little among regions but declined with the years from
 about 2.5 to 1.8. The proportion of juveniles in September (fecundity)
 declined in 1998–2015 from over 0.4 to 0.3 and was inversely correlated
 with year and nest numbers, if outlier years were excluded, suggesting
 resource limitation. Survival of juvenile cormorants in September–February
 was estimated at 0.471 ± 0.066 SE. Commercial fish stocks and climate
 indices were not correlated with the proportion of juveniles. Annual
 survival of adults (breeding and nonbreeding) was estimated from nest
 counts and age composition 1999–2014, as 0.850 ± 0.026 SE and showed no
 trend in 1998–2014. We conclude that the metapopulation of cormorants in
 Iceland was resource‐limited at two levels: fecundity at the regional and
 winter survival at the total level.
description: dryad-data-skarfur-2019The data are comprised of total nests numbers of cormorant in Iceland 1994-2015, proportion of juveniles in september surveys, recruitment stocks of cod and saithe (from the Icelandic Marine Research Institute), as well as mean monthly temperatures for January and February (Stykkisholmur, Iceland) and finally the climate indices sub-polar gyre index (SPG-I; Berx and Payne), NAO (Hurrel) and Atlantic Multi-decadal Oscillation index AMO (Trenberth).
DOI: 10.5281/zenodo.18390250
title: LINF_320010200

description: Ras-related protein Rab4; Leishmania infantum (strain JPCM5)
DOI: 10.5281/zenodo.18390251
title: LINF_320010200

description: Ras-related protein Rab4; Leishmania infantum (strain JPCM5)
DOI: 10.5061/dryad.n222q81
title: Data from: Effects of body plan evolution on the hydrodynamic drag and energy requirements of swimming in ichthyosaurs

description: Ichthyosaurs are an extinct group of fully marine tetrapods that were well
 adapted to aquatic locomotion. During their ~160-million-year existence,
 they evolved from elongate and serpentine forms into stockier, fish-like
 animals, convergent with sharks and dolphins. Here, we use computational
 fluid dynamics (CFD) to quantify the impact of this transition on the
 energy demands of ichthyosaur swimming for the first time. We run
 computational simulations of water flow using three-dimensional digital
 models of nine ichthyosaurs and an extant functional analogue, a
 bottlenose dolphin, providing the first comparison of ichthyosaur
 hydrodynamics across phylogeny. Our results show that morphology did not
 have a major effect on the drag coefficient or the energy cost of steady
 swimming through geological time. We show that even the early ichthyosaurs
 produced low levels of drag for a given volume, comparable to those of a
 modern dolphin, and that deep “torpedo-shaped” bodies did not reduce the
 cost of locomotion. Our analysis also provides important insight into the
 choice of scaling parameters for CFD applied to swimming mechanics and
 underlines the great influence of body size evolution on ichthyosaur
 locomotion. A combination of large bodies and efficient swimming modes
 lowered the cost of steady swimming as ichthyosaurs became increasingly
 adapted to a pelagic existence.
description: 3D
 models
DOI: 10.5061/dryad.md888qr
title: Data from: Noninvasive sub-organ ultrasound stimulation for targeted neuromodulation

description: Tools for noninvasively modulating neural signaling in peripheral organs
 will advance the study of nerves and their effect on homeostasis and
 disease. Herein, we demonstrate a noninvasive method to modulate specific
 signaling pathways within organs using ultrasound (US). US is first
 applied to spleen to modulate the cholinergic anti-inflammatory pathway
 (CAP), and US stimulation is shown to reduce cytokine response to
 endotoxin to the same levels as implant-based vagus nerve stimulation
 (VNS). Next, hepatic US stimulation is shown to modulate pathways that
 regulate blood glucose and is as effective as VNS in suppressing the
 hyperglycemic effect of endotoxin exposure. This response to hepatic US is
 only found when targeting specific sub-organ locations known to contain
 glucose sensory neurons, and both molecular (i.e. neurotransmitter
 concentration and cFOS expression) and neuroimaging results indicate US
 induced signaling to metabolism-related hypothalamic sub-nuclei. These
 data demonstrate that US stimulation within organs provides a new method
 for site-selective neuromodulation to regulate specific physiological
 functions.
description: Images associated with
 Nature Comm article "Noninvasive sub-organ ultrasound stimulation for
 targeted neuromodulation"The file contains images
 associated with Nature Comm article "Noninvasive sub-organ ultrasound
 stimulation for targeted neuromodulation"; refer to article for
 description and materials and methods.Additional cFOS
 Images.pdf
DOI: 10.5061/dryad.np44k70
title: Data from: Extinction debt and delayed colonization have had comparable but unique effects on plant community-climate lags since the Last Glacial Maximum

description: Aim: Plant communities typically exhibit lagged responses to climate
 change due to poorly-understood effects of colonization and local
 extinction. Here, we quantify rates of change in mean cold tolerances, and
 contributions of colonization and local extinction to those rates,
 recorded in plant macrofossil assemblages from North American hot deserts
 over the last 30,000 years. Location: Mojave, Sonoran and Chihuahuan
 Deserts Time period: 30-0 thousand years before present (kybp) Major taxa
 studied: Vascular plants Methods: Colonization and local extinction dates
 for 269 plant species were approximated from macrofossils in 15 packrat
 (Neotoma) midden series. Cold tolerances estimated from contemporary
 climate were used to quantify assemblage-mean cold tolerances through
 time. Rates of colonization and local extinction, and their effects on
 rates of change in assemblage-mean cold tolerances, were estimated for
 30-20 kybp (Late Pleistocene, no directional warming), 20-10 kybp
 (deglaciation, rapid warming), and 10-0 kybp (Holocene, no directional
 warming). Results: Rates of change in all metrics were negligible during
 the Late Pleistocene. Rates of change in assemblage-mean cold tolerances
 (mean 1.0 ⁰C x10-4 yr-1) lagged behind warming during deglaciation, and
 continued at similar rates (1.2 ⁰C x10-4 yr-1) throughout the Holocene.
 Colonization and local extinction contributed equally to delayed responses
 to warming, but their dynamics differed through time: Colonization by
 warm-adapted species predominated during deglaciation, while the most
 heat-adapted species exhibited long delays in colonization. Only the most
 cold-adapted species went locally extinct during deglaciation, followed by
 slow repayment of the extinction debt of cool-adapted species during the
 Holocene. Conclusions: Responses to rapid warming can persist for
 millennia, even after cessation of warming. Consistent patterns from
 different midden series across the region support a metacommunity model in
 which dispersal interacts with environmental filters and buffers against
 local extinction to drive community-climate disequilibrium during and
 after periods of warming.
description: TableS01 - Colonization
 and extinction dates for each species and siteTableS01.csvTableS02 - Climatic tolerance estimates of speciesSuffix '05' refers to species 5th percentile, '95' to the 95th percentile. NAs for species with insufficient number of occurrence recordsTableS02.csv