cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25349/d91030
title: Dynamics of seal bomb use in Channel Islands and Monterey Bay National Marine Sanctuaries

description: The Channel Islands and Monterey Bay National Marine Sanctuaries seek to
 preserve the biodiversity, cultural history, scenic beauty, and economic
 productivity of California’s most precious ocean treasures. Both
 sanctuaries are visited annually by a plethora of migratory cetaceans,
 pelagic fish, and seabirds. Unfortunately, oceans are facing increasing
 anthropogenic pressures, and noise pollution is a growing concern.
 Exposure to acute sound sources poses a significant risk to acoustically
 sensitive cetacean species protected under the Marine Mammal Protection
 Act and the Endangered Species Act. This project will provide a targeted
 analysis of the acoustic impacts of a legal marine mammal acoustic
 deterrent known as a “seal bomb”. These deterrents are underwater
 explosives used in purse seine fisheries, such as the California market
 squid fishery, to deter marine mammals from interfering with commercial
 fishing operations. Seal bombs alter the natural ocean soundscape and are
 believed to cause indirect acoustic impacts to cetaceans within the same
 vicinity. Therefore, this project will analyze squid fishing dynamics and
 associated seal bomb use through passive acoustic monitoring systems
 within both sanctuaries. Spatial overlap between recorded seal bomb
 explosions and existing cetacean habitat distribution  will
 elucidate times and regions where cetaceans may be experiencing increased
 risk. Our analysis will also assess the dynamics of seal bomb use by
 overlaying squid fishing activity with confirmed seal bomb detonations. We
 aim to provide recommendations to the National Marine Fisheries Service,
 Office of National Marine Sanctuaries, and the State of California by
 outlining best management practices to mitigate the impact on cetaceans
 within Monterey Bay and Channel Islands National Marine Sanctuaries,
 highlighting regions where seal bombs can be used with minimal impacts to
 marine organisms and where use should be monitored or restricted.
description: Data was provided from a variety of different sources:
 Squid Ticket Landings, California Department of Fish
 & Wildlife Seal Bomb Detections, NOAA
 SanctSound & Monterey Bay Aquarium Research Institute
 Fishing Vessel Detections, NOAA ONMS, model output from VIIRs
 Satellite Data Cetacean Distrubution Data, NOAA
 Fisheries Cetacean Biologically Important Areas, NOAA
 CetSound Data was pre-processed to align
 spatial and temporal resolution of datasets and then analyzed using R, and
 ArcGIS.
DOI: 10.15468/dl.xkmwaz
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((55.55795 9.19759,154.23123 9.19759,154.23123 58.50833,55.55795 58.50833,55.55795 9.19759))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Notopterygium franchetii"
 ]
}

 The dataset includes 13 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003122-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.63xsj3v4t
title: Sexually but not parthenogenetically produced females benefit from mating in a stick insect

description: In facultatively parthenogenetic populations, the prevalence of sexual
 reproduction depends on whether females mate and therefore produce sons
 and daughters or avoid mating and produce daughters only. The relative
 advantage of mating in such species may depend on a female’s own
 reproductive origin (i.e., development from a fertilised or unfertilised
 egg) if parthenogenesis reduces heterozygosity similarly to sexual
 inbreeding, or if it inhibits mating, sperm storage or fertilisation. But
 effects of reproductive origin on development and performance are poorly
 understood. Using the facultatively parthenogenetic stick insect,
 Extatosoma tiaratum, we quantified morphology, mating probability, and
 reproductive success in mated versus unmated females of sexual versus
 automictic (parthenogenetic) origin. We found strong evidence that
 increased homozygosity negatively impacted some traits in
 parthenogenetically produced females: compared to sexually produced
 females, parthenogenetically produced females were smaller and more prone
 to deformities in vestigial wings, but not more prone to fluctuating
 asymmetry in their legs. Parthenogenetically produced females received
 fewer mating attempts and avoided mating more often than sexually produced
 females. Yet, contrary to the expectation that sex should rescue
 parthenogenetic lineages from the detrimental effects of increased
 homozygosity, parthenogenetically produced females gained no net
 reproductive benefit from mating, suggesting that physiological
 constraints limit fitness returns of sexual reproduction for these
 females. Our findings indicate that advantages of mating in this species
 depend on female reproductive origin. These results could help to explain
 spatial distributions of sex in facultatively parthenogenetic animals and
 evolutionary transitions to obligate asexuality.
description: A README file is provided with the data
DOI: 10.15468/dl.fg8f3t
title: Occurrence Download

description: A dataset containing 388811 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is New Zealand",
 "OccurrenceStatus is Present",
 "PublishingOrg is one of (1bfac9af-cc42-4b4f-9d9c-1b456dd804d3, 6b2f029b-7823-4b84-9c30-31ff364238fe, 2760d7b0-767c-11d8-a198-b8a03c50a862, c58ac019-b413-4613-8772-39e57acbeb8e)",
 "TaxonKey is Animalia",
 "Year 2016-2026"
 ]
}

 The dataset includes 388811 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003125-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.jsxksn0c9
title: Burrowing Constrains Patterns of Skull Shape Evolution in Wrasses

description: The evolution of behavioral and ecological specialization can have marked
 effects on the tempo and mode of phenotypic evolution. Head-first
 burrowing has been shown to exert powerful selective pressures on the head
 and body shapes of many vertebrate and invertebrate taxa. In wrasses,
 burrowing behaviors have evolved multiple times independently, and are
 commonly used in foraging and predator avoidance behaviors. While recent
 studies have examined the kinematics and body shape morphology associated
 with this behavior, no study to-date has examined the macroevolutionary
 implications of burrowing on patterns of phenotypic diversification in
 this clade. Here, we use three-dimensional geometric morphometrics and
 phylogenetic comparative methods to study the evolution of skull shape in
 fossorial wrasses and their relatives. We test for skull shape differences
 between burrowing and non-burrowing wrasses and evaluate hypotheses of
 shape convergence among the burrowing wrasses. We also quantify rates of
 skull shape evolution between burrowing and non-burrowing wrasses to test
 for whether burrowing constrains or accelerates rates of skull shape
 evolution in this clade. We find that while burrowing and non-burrowing
 wrasses exhibit similar degrees of morphological disparity, for burrowing
 wrasses, it took nearly twice as long to amass this disparity.
 Furthermore, while the disparities between groups are evenly matched, we
 find that most burrowing species are confined to a particular region of
 shape space with most species exhibiting narrower heads than many
 non-burrowing species. These results suggest head-first burrowing
 constrains patterns of skull shape diversification in wrasses by
 potentially restricting the range of phenotypes that can perform this
 behavior.
description: Three-dimensional meshes were collected via micro-CT scanning for
 all 184 specimens. Shape data were collected using three dimensional
 geometric morphometrics.
description: All analyses were run in R and data files are saved as .R
 files
DOI: 10.5061/dryad.cjsxksn7v
title: Differential effects of ecosystem engineering by the superb lyrebird Menura novaehollandiae and herbivory by large mammals on floristic regeneration and structure in wet eucalypt forests

description: Ecosystem engineers that modify soil and ground-layer properties exert a
 strong influence on vegetation communities in ecosystems worldwide.
 Understanding the interactions between animal engineers and vegetation is
 challenging when in the presence of large herbivores, as many vegetation
 communities are simultaneously affected by both engineering and herbivory.
 The superb lyrebird Menura novaehollandiae, an ecosystem engineer in wet
 forests of south-eastern Australia, extensively modifies litter and soil
 on the forest floor. The aim of this study was to disentangle the impacts
 of engineering by lyrebirds and herbivory by large mammals on the
 composition and structure of ground-layer vegetation. We carried out a
 two-year, manipulative exclusion experiment in the Central Highlands of
 Victoria, Australia. We compared three treatments: fenced plots with
 simulated lyrebird foraging; fenced plots excluding herbivores and
 lyrebirds; and open controls. This design allowed assessment of the
 relative impacts of engineering and herbivory on germination rates,
 seedling density, vegetation cover and structure, and community
 composition. Engineering by lyrebirds enhanced the germination of seeds in
 the litter layer. After two years, more than double the number of
 germinants were present in ‘engineered’ than ‘non-engineered’ plots.
 Engineering did not affect the density of seedlings, but herbivory had
 strong detrimental effects. Herbivory also reduced the floristic richness
 and structural complexity (&lt; 0.5 m) of forest vegetation, including
 the cover of herbs. Neither process altered the floristic composition of
 the vegetation within the 2-year study period. Ecosystem engineering by
 lyrebirds and herbivory by large mammals both influence the structure of
 forest-floor vegetation. The two-fold increase in seeds stimulated to
 germinate by engineering may contribute to the evolutionary adaptation of
 plants by allowing greater phenotypic expression and selection than would
 otherwise occur. Over long timescales, engineering and herbivory likely
 combine to maintain a more-open forest floor conducive to ongoing
 ecosystem engineering by lyrebirds.
description: We compared three treatments: fenced plots with simulated
 lyrebird foraging; fenced plots excluding herbivores and lyrebirds; and
 open controls. This design allowed assessment of the relative impacts of
 engineering and herbivory on germination rates, seedling density,
 vegetation cover and structure, and community composition, measured in the
 field.
DOI: 10.5061/dryad.95x69p8nc
title: Evolutionary change in metabolic rate of Daphnia pulicaria following invasion by the predator Bythotrephes longimanus

description: Metabolic rate is a trait that may evolve in response to the direct and
 indirect effects of predator-induced mortality. Predators may indirectly
 alter selection by lowering prey densities and increasing resource
 availability or by intensifying resource limitation through changes in
 prey behaviour (e.g. use of less productive areas). In the current study
 we quantify evolution of metabolic rate in the zooplankton Daphnia
 pulicaria following an invasive event by the predator Bythotrephes
 longimanus in Lake Mendota, Wisconsin, US. This invasion has been shown to
 dramatically impact D. pulicaria, causing a ~60% decline in their
 biomass. Using a resurrection ecology approach, we compared the metabolic
 rate of D. pulicaria clones originating from prior to the Bythotrephes
 invasion with that of clones having evolved in the presence of
 Bythotrephes. We observed a 7.4% reduction in metabolic rate among
 post-invasive clones compared to pre-invasive clones, and discuss the
 potential roles of direct and indirect selection in driving this change.
description: See the file "README_file.txt" for an explanation of
 data file structure and variable names
DOI: 10.5061/dryad.dbrv15f3m
title: Mandrill mothers associate with infants who look like their own offspring using phenotype matching

description: Behavioral discrimination of kin is a key process structuring social
 relationships in animals. In this study, we provide a first example of
 discrimination towards non-kin by third-parties through a mechanism of
 phenotype matching. In mandrills, we recently demonstrated increased
 facial resemblance among paternally-related juvenile and adult females
 indicating adaptive opportunities for paternal kin recognition. Here, we
 hypothesize that mothers use offspring’s facial resemblance with other
 infants to guide offspring’s social opportunities towards
 similarly-looking ones. Using deep learning for face recognition in 80
 wild mandrill infants, we first show that infants born to the same father
 or conceived during the tenure of the same alpha male resemble each other
 the most, independently of their age, sex or maternal origin, extending
 previous results to the youngest age class. Using long-term behavioral
 observations on association patterns and controlling for matrilineal
 origin, maternal relatedness and infant age and sex, we then demonstrate
 that, as hypothesized, mothers are spatially closer to infants that
 resemble their own offspring more, thereby facilitating associations among
 similar-looking infants. Using theoretical modeling, we describe a
 plausible evolutionary process whereby mothers gain fitness benefits by
 promoting nepotism among paternally related infants. This mechanism, that
 we call “second order kin selection”, may extend beyond mother-infant
 interactions and has the potential to explain cooperative behaviors among
 non-kin in social species, including humans.
description: Field data (behavior and pictures) and AI methods.
DOI: 10.5061/dryad.80gb5mkt4
title: Epigenetic regulation of autonomous pathway mediates polymorphism of flowering time in Arabidopsis

description: Plant flowering time is affected by endogenous and exogenous factors, but
 its polymorphism among different populations of a species has not been
 fully explained yet. Here, 27 Arabidopsis thaliana populations were used
 to determine how autonomous pathway gene methylation affects flowering
 differences by regulating gene expression patterns. DNA methylation
 analysis, qPCR and transgenic verification showed that polymorphism in the
 flowering time among the Arabidopsis populations ranged from 19 to 55 days
 was significantly correlated with methylation of the coding regions of six
 upstream genes in the autonomous pathway, FVE, FY, FLD, PEP, HDA5 and PPR
 39-1 and their relative expression levels (P &lt; 0.05). Expression of
 selected FVE and FVE(CS) separately through codon degeneracy substitution
 of cytosine led to earlier flowering of transgenic plants by 8 days and 25
 days, respectively. An accurate determination of methylated sites of FVE
 and FVE(CS) among those transgenic plants and recipient Col-0 verified the
 close relationship between their methylation number, expression and the
 flowering times. Our findings firstly suggest that the methylation
 variation of those six key upstream transcription factors regulates the
 gene expression level of the autonomous pathway, leading to phenotypic
 differences in flowering time of Arabidopsis. The FVE(CS) and FVE genes in
 transgenic plants tend to be hypermethylated, and this could be a
 protective mechanism for plants. However, modification of gene sequence
 through codon degeneracy substitution to reduce cytosine can avoid
 hypermethylated transferred-genes in transgenic plants. It may be possible
 to partially regulate the flowering of plants by modified trans-epigenetic
 technology.
DOI: 10.5061/dryad.h44j0zpnr
title: Processed microphysical profiles of convective cloud scenes from satellite over ATTO

description: We present a new approach of analyzing and interpreting vertical profiles
 of cloud microstructure obtained by satellite remote sensing. The method
 is based on a spectral bin microphysics adiabatic parcel model and aims to
 elucidate the effects of aerosols on the evolution of convective clouds
 and related microphysical processes, including the activation of cloud
 condensation nuclei (CCN), the growth of cloud droplets, and the formation
 of precipitation. Characteristic features in the vertical profiles of
 effective radius (re) and temperature (T) reveal different microphysical
 zones in convective clouds related to the change increase of re with
 decreasing T. The classification of the different microphysical zones
 includes the (1) condensational growth of droplets, (2) growth by
 coalescence, (3) rainout, (4) secondary droplet activation zone (SAZ), (5)
 mixed-phase of ice particles and water droplets and (6) glaciation of the
 cloud. The detection of the SAZ is introduced here for the first time.
 This method allows us to identify the activation of aerosol particles
 above cloud base and their role in the invigoration of deep convective
 clouds.
DOI: 10.5061/dryad.0k6djhb2h
title: Data from: Variation in red fox Vulpes vulpes diet in five continents

description: Understanding variation in the diet of widely distributed species can help
 us to predict how they respond to future environmental and anthropogenic
 changes. We studied the diet of the red fox Vulpes vulpes, one of the
 world’s most widely distributed carnivores. We compiled dietary data from
 217 studies at 276 locations in five continents to assess how fox diet
 composition varied according to geographic location, climate,
 anthropogenic impact and sampling method. The diet of foxes showed
 substantial variation throughout the species’ range, but with a general
 trend for small mammals and invertebrates to be the most frequently
 occurring dietary items. The incidence of small and large mammals and
 birds in fox diets was greater away from the equator. The incidence of
 invertebrates and fruits increased with mean elevation, while the
 occurrence of medium-sized mammals and birds decreased.  Fox diet
 differed according to climatic and anthropogenic variables. Diet richness
 decreased with increasing temperature and precipitation. The incidence of
 small and large mammals decreased with increasing temperature. The
 incidence of birds and invertebrates decreased with increasing mean annual
 precipitation. Higher Human Footprint Index was associated with lower
 incidence of large mammals and higher incidence of birds and fruit in fox
 diet.  Sampling method influenced fox diet estimation: estimated
 percentage of small and medium-sized mammals and fruit was lower in
 studies based on stomach contents, while large mammals were more likely to
 be recorded in studies of stomach contents than in studies of scats. Our
 study confirms the flexible and opportunistic dietary behaviour of foxes
 at the global scale. This behavioural trait allows them to thrive in a
 range of climatic conditions, and in areas with different degrees of
 human-induced habitat change. This knowledge can help place the results of
 local-scale fox diet studies into a broader context and to predict how
 foxes will respond to future environmental changes.
description: Castañeda et al. 2022 Mammal Review (Variation in red fox Vulpes
 vulpes diet in five continents)
DOI: 10.5061/dryad.p8cz8w9sm
title: Molecular phenotyping uncovers differences in basic housekeeping functions among closely related species of hares (Lepus spp., Lagomorpha: Leporidae)

description: Speciation is a fundamental evolutionary process, which results in genetic
 differentiation of populations and manifests as discrete morphological,
 physiological as well as behavioral differences. Each species has had its
 own evolutionary trajectory, formed by many types of selection pressures
 and random drift, making it extremely complicated to associate genetic
 differences between the species with the phenotypic differences. In the
 present study, we have used an in vitro model to analyze in depth the
 genetic and gene regulation differences between fibroblasts of two closely
 related mammals, arctic/subarctic mountain hare (Lepus timidus Linnaeus)
 and a temperate, steppe-like climate adapted brown hare (Lepus europaeus
 Pallas). We discovered the existence of a species-specific expression
 pattern of 1,623 genes, manifesting in differences in cell growth,
 respiration, and metabolism. Interspecific differences in the housekeeping
 functions of fibroblast cells suggest speciation acts on fundamental
 processes, even in these two interfertile species. Our results help to
 understand the molecular constituents of a species difference on a
 cellular level, which could contribute to the maintenance of the species
 boundary.
DOI: 10.5061/dryad.sj3tx9674
title: Provenance rather than nitrogen addition dominate the phenotypes and plasticity of Ambrosia artemisiifolia in China

description: Phenotypic plasticity, which differs between species, populations,
 individuals, even traits, is considered as one of the mechanisms of plant
 invasion. We conducted a common garden experiment with six provenances
 (HRB, CC, HG, ML, MZ, LB) of Ambrosia artemisiifolia and three nitrogen
 addition treatments to test their performance response. In order to
 explore the adaptation strategies of A. artemisiifolia towards
 heterogeneous habitats, phenotypic plasticity indexes were calculated to
 analyze among different provenances and traits. All traits were
 significantly influenced (P&lt;0.05) by provenance, except for number
 of inflorescences, inflorescences length and intercellular CO2
 concentration. Nitrogen addition notably affected on seed length, root
 biomass ratio, root-shoot ratio and four physiological traits (Pn, Tr, Gs,
 Ci). Among six provenances, the phenotypic plasticity index differed
 significantly (P&lt;0.05), but there were no significant differences
 of plasticity among nitrogen treatments. And biomass phenotypic plasticity
 was relatively higher both in response to prevenance and to nitrogen. We
 also found that only the plasticity of 100-seed weight was closely related
 to latitude, climate and genetic factors. In summary, provenances had a
 greater impact on the phenotype and plasticity of A. artemisiifolia than
 nitrogen addition, indicating the potential for further evolution of
 plasticity. Differences in plasticity among provenances and traits are
 important in predicting the invasion trend of A. artemisiifolia in the
 future.