cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5bh0587
title: Data from: Joint estimation of survival and breeding probability in female dolphins and calves with uncertainty in state assignment

description: While the population growth rate in long-lived species is highly sensitive
 to adult survival, reproduction can also significantly drive population
 dynamics. Reproductive parameters can be challenging to estimate as
 breeders and non-breeders may vary in resighting probability and
 reproductive status may be difficult to assess. We extended
 capture–recapture (CR) models previously fitted for data on other
 long-lived marine mammals to estimate demographic parameters while
 accounting for detection heterogeneity between individuals and state
 uncertainty regarding reproductive status. We applied this model to data
 on 106 adult female bottlenose dolphins observed over 13 years. The
 detection probability differed depending on breeding status. Concerning
 state uncertainty, offspring were not always sighted with their mother,
 and older calves were easier to detect than young-of-the-year (YOY),
 respectively 0.79 (95% CI 0.59–0.90) and 0.58 (95% CI 0.46–0.68). This
 possibly led to inaccurate reproductive status assignment of females.
 Adult female survival probability was high (0.97 CI 95% 0.96–0.98) and did
 not differ according to breeding status. Young-of-the-year and 1-year-old
 calves had a significantly higher survival rate than 2-year-old
 (respectively 0.66 CI 95% 0.50-0.78 and 0.45 CI 95% 0.29–0.61). This
 reduced survival is probably related to weaning, a period during which
 young are exposed to more risks since they lose protection and feeding
 from the mother. The probability of having a new YOY was high for breeding
 females that had raised a calf to the age of 3 or lost a 2-year-old calf
 (0.71, CI 95% 0.45– 0.88). Yet this probability was much lower for
 non-breeding females and breeding females that had lost a YOY or a
 1-year-old calf (0.33, 95% CI 0.26–0.42). The multievent CR framework we
 used is highly flexible and could be easily modified for other study
 questions or taxa (marine or terrestrial) aimed at modelling reproductive
 parameters.
description: Couet2019_Capture_histories_2004_2016
DOI: 10.5061/dryad.s5f6j9h
title: Data from: Agonist-specific voltage-dependent gating of lysosomal Two-Pore Na + Channels

description: Mammalian Two-Pore-Channels (TPC1, 2; TPCN1, TPCN2) are
 ubiquitously-expressed cation channels in the endosomes and lysosomes that
 regulate luminal pH homeostasis, membrane trafficking, and Ebola viral
 infection. Lysosomal patch-clamp studies and high-resolution structural
 determinations have demonstrated that TPCs are Na+-selective channels
 activated by lysosome-localized PI(3,5)P2. Whereas the channel activity of
 TPC1 is strongly dependent on membrane voltage, TPC2 lacks such voltage
 dependence despite the presence of several positively-charged amino acid
 (AA) residues in the presumed “S4 voltage-sensing” domains. By performing
 a Ca2+-imaging-based high-throughput screening followed by lysosomal
 electrophysiology, here we identified a class of tri-cyclic
 anti-depressants (TCAs) as small-molecule agonists of TPC channels. TCAs
 activate both TPC1 and TPC2 in a voltage-dependent manner, so we refer to
 them as Lysosomal Na+ channel Voltage-dependent Activators (LyNa-VAs). We
 also identified another compound which, like PI(3,5)P2, activates TPC2
 independent of voltage, suggesting the existence of agonist-specific
 gating mechanisms. Our identification of small-molecule TPC agonists
 should facilitate the studies of the cell biological roles of TPCs, and
 can also readily explain the reported effects of TCAs in the modulation of
 autophagy and lysosomal function.
description: LOPAC High-throughput
 Screening on TPC2Ca2+ imaging-based HTS
 using the Library of Pharmacologically Active Compounds (LOPAC)1280
 collection (Sigma) was conducted as described previously. Briefly, HEK293
 cells stably expressing TPC2 and TRPML1 were loaded with a Ca2+ detection
 dye (Fluo-4). The kinetic of Ca2+ flux was measured using a kinetic plate
 reader FDSS-7000. Compounds that were positive in the TPC2 assay, but not
 in the TRPML1 assay, were considered to be positive hits for potential
 TPC2 agonists.tpc2-o1-data.xlsx
DOI: 10.5061/dryad.rr4g39b
title: Data from: Seabirds vary responses to supplemental food under dynamic natural prey availability and feeding aggregation composition

description: While foraging, a predator can feed solitarily or in a group. The net
 energy gain of joining a group is predicted to vary with prey patch
 quality, species-specific prey capture behavior and the size and species
 composition of the predator group. In coastal Newfoundland, Canada,
 capelin (Mallotus villosus), a key forage fish, migrates inshore to spawn
 during the summer, resulting in a dramatic shift in prey availability.
 During July-August, 2015-2017, we examined the numerical and behavioral
 responses of procellarid (Great Shearwater Ardenna gravis, Sooty
 Shearwater A. grisea, Northern Fulmar Fulmarus glacialis) and gull species
 (Herring Gull Larus argentatus, Great Black-backed Gull L. marinus) to
 fish offal under varying capelin availability as well as flock size and
 composition using an at-sea experiment on the northeast Newfoundland
 coast. The experiment consisted of providing a offal every 30 s (10-min
 experimental period), along with 10-min control periods before and after.
 We recorded the species-specific number of birds on the water, the number
 of birds simultaneously attempting to capture offal, and the number of
 successful attempts (‘foraging success’). The number of birds on the water
 was lower during high capelin availability for all species, except for
 Northern Fulmar. The number of conspecifics simultaneously attempting
 increased with the number of conspecifics on the water, but plateaued at
 different numbers (4-17) for each species. The species-specific proportion
 of successful attempts (i.e. ‘foraging success’) varied with flock size
 and composition (i.e. number of conspecifics, heterospecifics, species).
 Foraging success of Herring Gulls and fulmars were moderately affected by
 flock size and composition, suggesting that they may be dominant
 competitors. Findings suggest that seabirds rely more heavily on
 supplemental food sources, such as fisheries discards and offal, when
 natural prey availability declines, potentially resulting in a higher risk
 of by-catch during fisheries activities as forage fish stocks decline.
description: Maynard_et al._2019_The
 AukMaynard_etal._2019_dryad.csv
DOI: 10.5061/dryad.n34h180
title: Data from: Combined transcriptome and metabolome analysis identifies defence responses in spider-mite infested pepper

description: Plants regulate responses towards herbivory through fine-tuning of
 defence-related hormone production, expression of defence genes and
 production of secondary metabolites. Jasmonic acid (JA) plays a key role
 in plant-herbivorous arthropod interactions. To understand how pepper
 responds to herbivory, leaf transcriptomes and metabolomes of two
 genotypes different in their susceptibility to spider mites, were studied.
 Mites induced both JA and salicylic acid (SA) signalling. However, mite
 infestation and exogenous JA resulted in distinct transcriptome profiles.
 Compared with JA, mites induced less differentially expressed genes
 involved in metabolic processes (except for genes involved in the
 phenylpropanoid pathway) and lipid metabolic processes. Furthermore,
 pathogen-related defence responses including WRKY transcription factors,
 were stronger induced upon mite infestation, likely as result of induced
 SA signalling. Untargeted analysis of secondary metabolites confirmed that
 JA treatment induced larger changes in metabolism than spider-mite
 infestation, resulting in a higher terpenoid and flavonoid production. The
 more resistant genotype exhibited a larger increase in endogenous JA and
 volatile and non-volatile secondary metabolites upon infestation, which
 could explain its stronger defence. Reasoning that in JA-SA antagonizing
 crosstalk, SA-defences are prioritized over JA-defences, we hypothesize
 that lack of SA-mediated repression of JA-induced defences could result in
 gain-of-resistance towards spider mites in pepper.
description: Genes and metabolites
 associated with spider-mite induced responses in pepper <strong>Gene
 transcripts, hormone and metabolite analysis</strong>
DOI: 10.5061/dryad.rm8k9q0
title: Data from: Predicting evolutionary responses to interspecific interference in the wild

description: Many interspecifically territorial species interfere with each other
 reproductively, and in some cases, aggression toward heterospecifics may
 be an adaptive response to interspecific mate competition. This hypothesis
 was recently formalized in an agonistic character displacement (ACD) model
 which predicts that species should evolve to defend territories against
 heterospecific rivals above a threshold level of reproductive
 interference. To test this prediction, we parameterized the model with
 field estimates of reproductive interference for 32 sympatric damselfly
 populations and ran evolutionary simulations. Asymmetries in reproductive
 interference made the outcome inherently unpredictable in some cases, but
 80% of the model’s stable outcomes matched levels of heterospecific
 aggression in the field, significantly exceeding chance expectations. In
 addition to bolstering the evidence for ACD, this paper introduces a new,
 predictive approach to testing character displacement theory that, if
 applied to other systems, could help resolve longstanding questions about
 the importance of character displacement processes in nature.
description: Male tethering
 dataData from simulated
 territory intrusion tests in which territory holders were presented with
 tethered male intruders. Edited to include only complete tests, in which
 territory holders were presented with both conspecific and heterospecific
 males and responded aggressively to at least one of them. These data are
 the source of the observed chase duration and attack rate
 ratios.Male_tethering.csvObserved and predicted meansObserved and predicted mean heterospecific aggression ratios and patristic distances.Observed_and_predicted_means.csv
DOI: 10.5061/dryad.d59cq77
title: Data from: Landscape genetics reveals unique and shared effects of urbanization for two sympatric pool-breeding amphibians

description: Metapopulation-structured species can be negatively affected when
 landscape fragmentation impairs connectivity. We investigated the effects
 of urbanization on genetic diversity and gene flow for two sympatric
 amphibian species, spotted salamanders (Ambystoma maculatum) and wood
 frogs (Lithobates sylvaticus), across a large (&gt;35,000 km2)
 landscape in Maine, USA, containing numerous natural and anthropogenic
 gradients. Isolation by distance (IBD) patterns differed between the
 species. Spotted salamanders showed a linear and relatively high variance
 relationship between genetic and geographic distance (r = 0.057; p
 &lt; 0.001); whereas, wood frogs exhibited a strongly non-linear and
 lower variance relationship (r = 0.429; p &lt; 0.001). Scale
 dependence analysis of IBD found gene flow has its most predictable
 influence (strongest IBD correlations) at distances up to 9 km for spotted
 salamanders and up to 6 km for wood frogs. Estimated effective migration
 surfaces revealed contrasting patterns of high and low genetic diversity
 and gene flow between the two species. Population isolation, quantified as
 the mean IBD residuals for each population, was associated with local
 urbanization and less genetic diversity in both species. The influence of
 geographic proximity and urbanization on population connectivity was
 further supported by distance-based redundancy analysis and multiple
 matrix regression with randomization. Resistance surface modelling found
 interpopulation connectivity to be influenced by developed land cover,
 light roads, interstates, and topography for both species, plus secondary
 roads and rivers for wood frogs. Our results highlight the influence of
 anthropogenic landscape features within the context of natural features
 and broad spatial genetic patterns, in turn supporting the premise that
 while urbanization significantly restricts interpopulation connectivity
 for wood frogs and spotted salamanders, specific landscape elements have
 unique effects on these two sympatric species.
description: SS -
 FilteredQuality filtered spotted
 salamander microsatellite genotypes in GenePop formatWF -
 FilteredQuality filtered wood
 frog microsatellite genotypes in GenePop formatenvData.SSEnvironmental data for spotted salamander breeding sites included in analyses.envData.WFEnvironmental data for wood frog breeding sites included in analyses.SS_lat_longLatitude and longitude for spotted salamander breeding sites included in analyses.WF_lat_longLatitude and longitude for spotted salamander breeding sites included in analyses.
DOI: 10.5281/zenodo.18393640
title: OʻZBEKISTON INNOVATSION MENEJMENT TAMOYILLARI ASOSIDA PEDAGOGIK KADRLAR TAYYORLASH

description: Mazkur tezisda asosiy gʻoya Oʻzbekiston Respublikasining pedagogik kadrlar tayyorlash tizimini innovatsion menejment tamoyillari asosida takomillashtirish masalalari yoritilgan.Asosan bu tezisda innovatsion menejment tushunchasining ahamiyati, bilim sohasida qoʻllanish majburiyatlari, pedagogik ta'lim tizimini zamonaviylashtirish zarurati hamda boshqaruv yondashuvlarining ahamiyati chuqur tahlil qilinadi.E'tiborli jihati shundaki, pedagogik kadrlar tayyorlash jarayoniga raqamli texnologiyalarni tatbiq etish,kompetensiyaviy yondashuvni tatbiq etish,ilmiy faoliyatini integratsiyalash va dunyoga tajribalarni joriy etish masalalariga alohida ahamiyat beriladi.Bu tezisda Oʻzbekistonda ta'lim islohotlari doirasida menejment tamoyillari ahamiyatli asoslab berilgan.
DOI: 10.5281/zenodo.18393641
title: OʻZBEKISTON INNOVATSION MENEJMENT TAMOYILLARI ASOSIDA PEDAGOGIK KADRLAR TAYYORLASH

description: Mazkur tezisda asosiy gʻoya Oʻzbekiston Respublikasining pedagogik kadrlar tayyorlash tizimini innovatsion menejment tamoyillari asosida takomillashtirish masalalari yoritilgan.Asosan bu tezisda innovatsion menejment tushunchasining ahamiyati, bilim sohasida qoʻllanish majburiyatlari, pedagogik ta'lim tizimini zamonaviylashtirish zarurati hamda boshqaruv yondashuvlarining ahamiyati chuqur tahlil qilinadi.E'tiborli jihati shundaki, pedagogik kadrlar tayyorlash jarayoniga raqamli texnologiyalarni tatbiq etish,kompetensiyaviy yondashuvni tatbiq etish,ilmiy faoliyatini integratsiyalash va dunyoga tajribalarni joriy etish masalalariga alohida ahamiyat beriladi.Bu tezisda Oʻzbekistonda ta'lim islohotlari doirasida menejment tamoyillari ahamiyatli asoslab berilgan.
DOI: 10.5061/dryad.m7q37nv
title: Data from: Mechanical feedback and robustness of apical constrictions in Drosophila embryo ventral furrow formation

description: Formation of the ventral furrow in the Drosophila embryo relies on the
 apical constriction of cells in the ventral region to produce bending
 forces that drive tissue invagination. Recently [J Phys Condens Matter.
 2016;28(41):414021], we observed that apical constrictions during the
 initial phase of ventral furrow formation produce elongated patterns of
 cellular constriction chains prior to invagination, and argued that these
 are indicative of tensile stress feedback. Here, we quantitatively analyze
 the constriction patterns preceding ventral furrow formation and find that
 they are consistent with the predictions of our active-granular-fluid
 model of a monolayer of mechanically coupled stress-sensitive constricting
 particles. Our model shows that tensile feedback causes constriction
 chains to develop along underlying precursor tensile stress chains that
 gradually strengthen with subsequent cellular constrictions. As seen in
 both our model and available optogenetic experiments, this mechanism
 allows constriction chains to penetrate or circumvent zones of reduced
 cell contractility, thus increasing the robustness of ventral furrow
 formation to spatial variation of cell contractility by rescuing cellular
 constrictions in the disrupted regions.
description: Ventral Furrow Formation
 Embryo 1 Time-lapse image series
 of gastrulating Drosophila melanogaster embryos, ventral surface,
 wild-type embryos carrying Spider-GFP, three planes separated by 1 micron,
 collected every 15 seconds, embryo 1. Embryo 1.zip
 
 Ventral Furrow
 Formation Embryo 2 Time-lapse image series
 of gastrulating Drosophila melanogaster embryos, ventral surface,
 wild-type embryos carrying Spider-GFP, three planes separated by 1 micron,
 collected every 15 seconds, embryo 2. Embryo 2.zip
 
 Ventral Furrow
 Formation Embryo 3 Time-lapse image series
 of gastrulating Drosophila melanogaster embryos, ventral surface,
 wild-type embryos carrying Spider-GFP, three planes separated by 1 micron,
 collected every 15 seconds, embryo 3. Embryo 3.zip
 
 Ventral Furrow
 Formation Embryo 4 Time-lapse image series
 of gastrulating Drosophila melanogaster embryos, ventral surface,
 wild-type embryos carrying Spider-GFP, three planes separated by 1 micron,
 collected every 15 seconds, embryo 4. Embryo 4.zip
 
 Ventral Furrow
 Formation Embryo 5 Time-lapse image series
 of gastrulating Drosophila melanogaster embryos, ventral surface,
 wild-type embryos carrying Spider-GFP, three planes separated by 1 micron,
 collected every 15 seconds, embryo 5. Embryo 5.zip
DOI: 10.5061/dryad.0716vc7
title: Data from: Experimental migration upward in elevation is associated with strong selection on life history traits

description: One of the strongest biological impacts of climate change has been the
 movement of species poleward and upward in elevation. Yet, what is not
 clear, is the extent to which the spatial distribution of locally adapted
 lineages and ecologically important traits may also shift with continued
 climate change. Here, we take advantage of a transplant experiment
 mimicking up-slope seed dispersal for a suite of ecologically-diverse
 populations of yellow monkeyflower (Mimulus guttatus sensu lato) into a
 high-elevation common garden during an extreme drought period in the
 Sierra Nevada mountains, California, USA. We use a demographic approach to
 quantify fitness and test for selection on life history traits in local
 vs. lower-elevation populations and in normal vs. drought years to test
 the potential for up-slope migration and phenotypic selection to alter the
 distribution of key life history traits in montane environments. We find
 that lower-elevation populations tend to outperform local populations,
 confirming the potential for up-slope migration. Although selection
 generally favored some local montane traits, including larger flowers and
 larger stem size at flowering, drought conditions tended to select for
 earlier flowering typical of lower elevation genotypes. Taken together,
 this suggests that monkeyflower lineages moving upward in elevation could
 experience selection for novel trait combinations, particularly under
 warmer and drier conditions that are predicted to occur with continued
 climate change.
description: Common garden
 dataDemographic and life
 history traits for Mimulus guttatus individuals sown in a common garden
 experiment in Stanislaus National Forest, CA from
 2012-2013
DOI: 10.5061/dryad.ms33h5h
title: Data from: Divergent color signals from homologous unfeathered ornaments in two congeneric grouse

description: Color-based visual signals are important aspects of communication
 throughout the animal kingdom. Individuals evaluate color to obtain
 information about age and condition and to behave accordingly. Birds
 display a variety of striking, conspicuous colors and make ideal subjects
 for the study of color signaling. While most studies of avian color focus
 on plumage, bare unfeathered body parts also display a wide range of color
 signals. Mate choice and intrasexual competitive interactions are easily
 observed in lekking grouse, which also signal with prominent unfeathered
 color patches. Most male grouse have one pair of colorful bare part
 ornaments (combs), and males of several species also have inflatable air
 sacs in their throat. Previous studies have mostly focused on comb color
 and size, but little is known about the signaling role of air sac color.
 We measured comb size and the color properties of combs and air sacs in
 the Lesser and Greater Prairie-Chicken (Tympanuchus pallidicinctus and T.
 cupido, respectively), and investigated whether these properties varied
 with age and mass. We found that mass predicted color properties of air
 sacs and that age predicted comb size in the Greater Prairie-Chicken,
 suggesting that these ornaments indicate condition-dependence. No
 conclusive relationships between color and age or size were detected in
 the Lesser Prairie-Chicken. Color properties of both ornaments differed
 between the two species. Further research is needed to determine
 mechanisms that link condition to color and whether the information
 advertised by color signals from these ornaments is intended for males,
 females, or both.
description: Ornament Color and Size
 for Lesser and Greater Prairie-ChickensThis data set consists
 of the mass, age class, capture date, comb size, and air sac and comb
 color variables for Lesser and Greater Prairie-Chickens captured in
 western Kansas in 2012-2013 and 2016-2018. The color variables were
 generated using visual models of tetrahedral color space with reflectance
 data from a spectrometer acting as the input. They consist of total
 saturation, total brightness, and hue in the visible and UV portions of
 the spectrum. The leks were coded to avoid association with private
 landowners. The units for mass are grams, and square millimeters for comb
 area. Coding for age is SY (second year) for yearling birds and ASY (after
 second year) for adults.Dryad
 Data.csv
DOI: 10.5061/dryad.0qv86b5
title: Data from: Variable effects of a changing climate on lay dates and productivity across the range of the Red-cockaded Woodpecker

description: Many temperate bird species are breeding earlier in response to warming
 temperatures. We examined the effects of climate on breeding phenology and
 productivity in 19 populations across the range of the Red-cockaded
 Woodpecker (Picoides borealis), an endangered species endemic to pine
 (Pinus spp.) forests in the southeastern United States. Red-cockaded
 Woodpeckers nested earlier in warmer springs and delayed nesting in wetter
 springs. Earlier nesting and larger group sizes resulted in higher
 productivity. Spring temperatures have warmed over time across the range,
 but this has not led to range-wide advances in nesting date over time.
 Coastal and northern populations have exhibited a trend of earlier nesting
 over time, but the response of inland populations has been variable,
 including some populations in which nesting has become later over time.
 Geographic patterns included high and increasing productivity at higher
 latitudes, and declining productivity in the southwestern portion of the
 range, suggesting a possible shift in acceptable climate conditions for
 the species. Earlier nesting over time was associated with increasing
 productivity at higher latitudes, while elsewhere earlier nesting over
 time was associated with declining or stable productivity, suggesting that
 populations differ in their ability to adjust to a changing climate. The
 Red-cockaded Woodpecker is a habitat specialist heavily reliant on habitat
 management and has little capacity to shift its range, so its long-term
 viability will depend on its ability to adjust in place to changing local
 conditions.
description: RCW Climate Change
 DataData used for boosted
 regression tree models of climate effects on Red-cockaded woodpecker
 reproductionClimateChangeDataDryad.xlsxRCW Climate Change R Code: Boosted RegressionTreesR Code to run boosted regression trees models describing climate effects on Red-cockaded woodpecker reproductionBoostedRegressionClimateScriptDryad.R