cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ht76hdrg3
title: Low-coverage whole-genome sequencing reveals molecular markers for spawning season and sex identification in Gulf of Maine Atlantic cod (Gadus morhua, Linnaeus 1758)

description: Atlantic cod (Gadus morhua, Linnaeus 1758) in the western Gulf of Maine
 are managed as a single stock despite several lines of evidence supporting
 two spawning groups (spring and winter) that overlap spatially, while
 exhibiting seasonal spawning isolation. Low-coverage whole genome
 sequencing was used to evaluate the genomic population structure of
 Atlantic cod spawning groups in the western Gulf of Maine and Georges Bank
 using 222 individuals collected over multiple years. Results indicated low
 total genomic differentiation, while also showing strong differentiation
 between spring and winter spawning groups at specific regions of the
 genome. Guided regularized random forest and ranked F­ST methods were used
 to select panels of single nucleotide polymorphisms (SNPs) that could
 reliably distinguish spring and winter-spawning Atlantic cod (88.5%
 assignment rate), as well as males and females (95.0% assignment rate)
 collected in the western Gulf of Maine. These SNP panels represent a
 valuable tool for fisheries research and management of Atlantic cod in the
 western Gulf of Maine that will aid investigations of stock production and
 support accuracy of future assessments.
DOI: 10.57841/casdc.0007103
title: 烯基醚氢烷基化反应过程数据和测试表征数据
DOI: 10.5061/dryad.4xgxd2598
title: Chain length, growth rate and clearance rate of Thalassiosira Rotula, Chaetoceros Curvisetus, and Chaetoceros Affinis when exposed to copepodamides.

description: Colony formation is common feature among non-motile marine
 phytoplankton. Several theories exist around the potential benefits of
 larger colonies. Here we test the hypothesis that predation is one of the
 drivers behind colony formation and chain length
 plasticity. We exposed cultures of Thalassiosira rotula,
 Chaetoceros curvisetus and Chaetoceros
 affinis to copepodamides, a
 chemical alarm cue released by copepods and perceived as an indicator of predation threat by their prey. This was coupled with a grazing experiment which compared copepod grazing rates on different chain lengths. Our results show that T. rotula and C. curvisetus decreased their chain lengths by 79% and 49%, respectively, in response to copepodamides. Single cells and short chains were grazed at lower rates compared to long chains and the copepodamide driven size shift led to 30% and 12% lower grazing in T. rotula and C. curvisetus respectively. In contrast, C. affinis showed a slight increased chain length in response to copepodamides although non-significant. We found that 2 of 3 studied species reduce their chain length in response to the presence copepod grazers. Altered size structure has implications for the route of carbon in the marine food webs and carbon export to deeper strata.
DOI: 10.5061/dryad.h18931zm1
title: Comparison of serological and molecular assays for Bartonella species in dogs with hemangiosarcoma

description: Currently, a gold standard diagnostic test for Bartonella infection in
 dogs is lacking. This represents a critical limitation for the development
 and evaluation of new diagnostic tests, as well as for the diagnosis of,
 and research on, bartonellosis in dogs. This retrospective observational
 study aims to compare the results of commonly performed and newly-reported
 Bartonella spp. diagnostic tests in banked clinical specimens from 90 dogs
 with hemangiosarcoma (HSA) using composite reference standard (CRS) and
 random effects latent class analysis (RE-LCA) techniques. Samples from
 each dog were tested using six serological or molecular diagnostic assays,
 including indirect fluorescent antibody (IFA) and Western blot (WB) for
 the detection of antibodies in serum, and qPCR and droplet digital PCR
 (ddPCR) in blood and fresh frozen tissue biopsy samples (mainly splenic
 HSA tumors and histopathologically normal spleen or skin/adipose tissue).
 Bartonella infection prevalence was estimated to be 78% based on the CRS
 (parallel testing with all six assays), and 64% based on the RE-LCA model.
 The assay with the highest diagnostic accuracy was qPCR performed on fresh
 frozen tissue biopsy samples (sensitivity: 94% by RE-LCA and 80% by CRS;
 specificity: 100%). When comparing newly-reported to traditional
 Bartonella diagnostic assays, ddPCR was more sensitive for the detection
 of Bartonella DNA than qPCR when testing blood samples (36% vs. 0%, p
 &lt; 0.0001). Dogs that were positive on serological assays alone with
 negative molecular assays were highly unlikely (&lt;3%) to be
 classified as infected by the RE-LCA model. These data indicate that
 Bartonella spp. DNA can be PCR amplified from fresh frozen tissues from a
 majority of dogs with HSA using both qPCR and ddPCR, supporting the use of
 these methods for future controlled studies comparing the prevalence of
 Bartonella spp. DNA in the tissue of dogs with HSA to that of unaffected
 controls.
description: Please see
 published manuscript for description of methods used for data
 collection.
DOI: 10.5061/dryad.ksn02v74h
title: Projected impacts of climate and land use changes on the habitat of Atlantic Forest plants in Brazil

description: Aim: To provide novel evidence on the average impact of climate and land
 use changes on habitat suitability for tropical plants and to test
 previous conclusions on the relative importance of these two drivers in
 shaping future availability of habitat for tropical plant species.
 Location: Brazil’s Atlantic Forest domain. Time period: Plant occurrences
 recorded between 1960 and 2014. Baseline climate from 1960-2000 and land
 use from 2015. Projected scenarios of climate for 2041-2060 and land use
 for 2050. Major taxa studied: Angiosperms. Results: Our results suggest
 that climate change alone will, surprisingly, have only a modest negative
 impact on the mean habitat suitability, decreasing it by 2% (median = -5%
 to -7%, variation associated with scenarios). Land use change alone had a
 more consistent negative impact on habitat suitability, causing mean and
 median reductions of 4% to 6%. When the effects of climate and land use
 are combined, the mean habitat suitability was reduced by 4% (median = -9%
 to -11%). Main conclusions:  The combined impacts of climate and
 land use changes were substantial, although smaller than expected. Habitat
 suitability decreased for most species, but it increased substantially for
 some species, suggesting that the distribution of impacts across species
 is markedly right skewed. The impacts were typically detrimental to
 small-ranged species and neutral or beneficial to widespread species. Land
 use change rather than climate change will likely cause more losses to the
 habitat of Atlantic Forest plant species within the next several decades.
description: We modelled the habitat suitability of 2,232 species of
 angiosperms from the Atlantic Forest domain, endemic to Brazil, and
 estimated how future climate and land use may affect species-level habitat
 suitability under a moderate (SSP2-RCP4.5) and a business-as-usual
 (SSP5-RCP8.5) scenario for the year 2050.
DOI: 10.5061/dryad.m0cfxpp47
title: Plastic adjustments of biparental care behaviour across embryonic development under elevated temperature in a marine ectotherm

description: Phenotypic plasticity in parental care investment allows organisms to
 promptly respond to rapid environmental changes by potentially benefiting
 offspring survival and thus parental fitness. To date, a knowledge gap
 exists on whether plasticity in parental care behaviours can mediate
 responses to climate change in marine ectotherms. Here, we assessed the
 plasticity of parental care investment under elevated temperatures in a
 gonochoric marine annelid with bi-parental care, Ophryotrocha labronica,
 and investigated its role in maintaining the reproductive success of this
 species in a warming ocean. We measured the time individuals spent
 carrying out parental care activities across three phases of embryonic
 development, as well as the hatching success of the offspring as a proxy
 for reproductive success, at control (24°C) and elevated (27°C)
 temperature conditions. Under elevated temperature we observed: (i) a
 significant decrease in total parental care activity, underpinned by a
 decreased in male and simultaneous parental care activity, in the late
 stage of embryonic development; and ii) a reduction of hatching success,
 that was however not significantly related to changes in parental-care
 activity levels. These findings, along with the observed unaltered somatic
 growth of parents and decreased brood size, suggest that potential
 cost-benefit trade-offs between offspring survival (i.e. immediate
 fitness) and parents somatic condition (i.e. longer-term fitness
 potential) may occur under ongoing ocean warming. Finally, our results
 suggest that plasticity in parental care behaviour is a mechanism able to
 partially mitigate the negative effects of temperature-dependent impacts.
DOI: 10.5061/dryad.59zw3r27g
title: Using 2D dental geometric morphometrics to identify modern Perognathus and Chaetodipus specimens (Rodentia, Heteromyidae)

description: The Heteromyidae (pocket mice and kangaroo rats) are a group of extant
 small rodents abundant in western North America, as well as in fossil
 assemblages over the last 20 million years. Two genera of heteromyids,
 Chaetodipus and Perognathus, share similar tooth morphology and teeth are
 the primary fossil remains. Previous genetic studies show these extant
 sister genera likely diverged in the middle Miocene (~16 million years
 ago); however, the Chaetodipus fossil record starts in the Pleistocene (~2
 million years ago). In this study, we asked whether two-dimensional
 geometric morphometrics on complete dentition and isolated premolars can
 accurately identify Chaetodipus and Perognathus specimens at the genus and
 species level. We landmarked the occlusal surface of the upper and lower
 tooth rows of modern Chaetodipus (n = 83) and Perognathus specimens (n =
 80), including 12 of the 26 extant species across the two genera. We ran a
 canonical variates analysis to investigate whether principal component
 variation could predict known taxonomic identifications. The morphospace
 using complete dentition can identify specimens to genus with 90 – 92%
 accuracy and to species with more variable accuracy. We found an isolated
 premolar provides sufficient information for genus-level identification
 (69 – 84% accuracy), but not for species-level identification (26 – 56%
 accuracy). This morphospace of modern specimens can be used to identify
 the skeletal remains of Chaetodipus and Perognathus in museum collections,
 raptor pellets, or middens, to refine our existing knowledge of heteromyid
 evolutionary history.
DOI: 10.5061/dryad.9w0vt4bg0
title: Gene-drive suppression of mosquito populations in large cages as a bridge between lab and field

description: CRISPR-based gene-drives targeting the gene doublesex in the malaria
 vector Anopheles gambiae effectively suppressed the reproductive
 capability of mosquito populations reared in small laboratory cages. To
 bridge the gap between laboratory and the field, this gene-drive
 technology must be challenged with vector ecology. Here we report the
 suppressive activity of the gene-drive in age-structured An. gambiae
 populations in large indoor cages that permit complex feeding and
 reproductive behaviours. The gene-drive element spreads rapidly through
 the populations, fully supresses the population within one year and
 without selecting for resistance to the gene drive. Approximate Bayesian
 computation allowed retrospective inference of life-history parameters
 from the large cages and a more accurate prediction of gene-drive
 behaviour under more ecologically-relevant settings. Generating data to
 bridge laboratory and field studies for invasive technologies is
 challenging. Our study represents a paradigm for the stepwise and sound
 development of vector control tools based on gene-drive.
DOI: 10.5061/dryad.2ngf1vhnr
title: Data from: Trait‐based signatures of cloud base height in a tropical cloud forest

description: Clouds have profound consequences for ecosystem structure and function.
 Yet, the direct monitoring of clouds and their effects on biota is
 challenging especially in remote and topographically complex tropical
 cloud forests. We argue that known relationships between climate and the
 taxonomic and functional composition of plant communities may provide a
 fingerprint of cloud base height, thus providing a rapid and
 cost-effective assessment in remote tropical cloud forests. To detect
 cloud base height, we compared species turnover and functional trait
 values among herbaceous and woody plant communities in an ecosystem
 dominated by cloud formation. We measured soil and air temperature, soil
 nutrient concentrations, and extracellular enzyme activity. We
 hypothesized that woody and herbaceous plants would provide signatures of
 cloud base height, as evidenced by abrupt shifts in both taxonomic
 composition and plant function. We demonstrated abrupt changes in
 taxonomic composition and the community-weighted mean of a key functional
 trait, specific leaf area, across elevation for both woody and herbaceous
 species, consistent with our predictions. However, abrupt taxonomic and
 functional changes occurred 100 m higher in elevation for herbaceous
 plants compared to woody ones. Soil temperature abruptly decreased where
 herbaceous taxonomic and functional turnover was high. Other environmental
 variables including soil biogeochemistry did not explain the abrupt change
 observed for woody plant communities. We provide evidence that a
 trait-based approach can be used to estimate cloud base height. We outline
 how rises in cloud base height and differential environmental requirements
 between growth forms can be distinguished using this approach.
description: Climatic, edaphic, and functional trait data collected across
 elevation in Santa Elena Peninsula, Costa Rica.
DOI: 10.6084/m9.figshare.31166614
title: <b>Soft computing-based hybrid heuristic optimization of wear performance in friction stir-processed composites</b>

description: Soft computing methods are now powerful aids for optimizing the parameters of material processing and improving wear resistance. This research proposes a hybrid heuristic method for optimizing Friction Stir Processing (FSP) parameters for improved wear properties. This research started by examining the key processing parameters of tool rotation speed, traverse speed, and number of passes using a face-centered central composite design (FCCCD) under response surface methodology (RSM).To determine and optimally wear resistance, an integrated computational approach using RSM, Genetic Algorithm (GA), Artificial Neural Networks (ANN), and Adaptive Neuro-Fuzzy Inference System (ANFIS) was used. The GA-ANN model obtained an accuracy of 95.48%, while the GA-ANFIS model yielded an accuracy of 92.9%, confirming that the two models proved to be appropriate predictive models of wear behavior. Microstructural analysis using Field Emission Scanning Electron Microscopy (FESEM) showed that when using the optimized conditions for FSP, the reinforcement particles dispersed uniformly, reduced the formation of wear debris, and improved wear resistance and tribological properties. The morphology of the worn surfaces demonstrated a change from severe delamination and deep plowing for the lower performing surface to a refined abrasive to explain the reduction in material loss and improved performance. Furthermore, three-dimensional response surface plots illustrated the significant role of rotational speed and the number of passes on wear resistance, underlining the importance of parameter selection for superior tribological performance.
DOI: 10.6084/m9.figshare.31166614.v1
title: <b>Soft computing-based hybrid heuristic optimization of wear performance in friction stir-processed composites</b>

description: Soft computing methods are now powerful aids for optimizing the parameters of material processing and improving wear resistance. This research proposes a hybrid heuristic method for optimizing Friction Stir Processing (FSP) parameters for improved wear properties. This research started by examining the key processing parameters of tool rotation speed, traverse speed, and number of passes using a face-centered central composite design (FCCCD) under response surface methodology (RSM).To determine and optimally wear resistance, an integrated computational approach using RSM, Genetic Algorithm (GA), Artificial Neural Networks (ANN), and Adaptive Neuro-Fuzzy Inference System (ANFIS) was used. The GA-ANN model obtained an accuracy of 95.48%, while the GA-ANFIS model yielded an accuracy of 92.9%, confirming that the two models proved to be appropriate predictive models of wear behavior. Microstructural analysis using Field Emission Scanning Electron Microscopy (FESEM) showed that when using the optimized conditions for FSP, the reinforcement particles dispersed uniformly, reduced the formation of wear debris, and improved wear resistance and tribological properties. The morphology of the worn surfaces demonstrated a change from severe delamination and deep plowing for the lower performing surface to a refined abrasive to explain the reduction in material loss and improved performance. Furthermore, three-dimensional response surface plots illustrated the significant role of rotational speed and the number of passes on wear resistance, underlining the importance of parameter selection for superior tribological performance.
DOI: 10.5061/dryad.2jm63xspw
title: Data for: Plant host domestication and soil nutrient availability determine positive plant microbial response across the Solanum genus

description: Domestication of crops has changed how crops shape their associated
 microbial communities compared to their progenitors. However, studies
 testing how crop domestication-driven differences in rhizosphere microbial
 communities affect plant health are limited mostly to specific symbiont
 pairings. By conducting a soil manipulation greenhouse study, we examined
 plant growth and yield in response to differences in microbial communities
 and nutrient availability across a variety of wild, landrace, and
 cultivated potatoes. Coupled with this, we conducted 16S and ITS amplicon
 sequencing to examine plant host and soil treatment-driven differences in
 microbial community composition on potato plant roots. Our results found
 the plant response to microbes (PRM) is context-dependent. In low nutrient
 conditions, landraces responded positively to the presence of live soil
 microbial inocula. Conversely, modern potato varieties positively
 responded in high nutrient conditions. Amplicon sequencing found
 differences in bacterial communities due to environmental and temporal
 factors. However, potato clade (e.g. Andigenum, Chiletanum, S. berthaulti,
 and Modern) alone did not lead to differences in microbial communities
 that accounted for PRM differences. Differences in PRM between landraces
 and modern potatoes, and the correlation of PRM to microbial diversity,
 suggest that domestication has altered the S. tuberosum response to
 rhizosphere microbiomes.
DOI: 10.5061/dryad.bzkh18991
title: Dataset for chromosome-level genome assembly of Scapharca kagoshimensis

description: Ark shells are commercially important clam species that inhabit in muddy
 sediments of shallow coasts in East Asia. For a long time, the
 lack of genome resources has hindered scientific research of ark shells.
 Here, we reported a high-quality chromosome-level genome assembly
 of Scapharca kagoshimensis, with an aim to
 unravel the molecular basis of heme biosynthesis,
 and develop genomic resources for genetic breeding and population
 genetics in ark shells.
DOI: 10.5061/dryad.80gb5mkr6
title: Abundance of Drosophila suzukii in the agricultural landscape

description: We sampled the abundance of males and females in the agricultural
 landscape in Slovenia. We selected 10 locations in the central part of
 Slovenia, five of which were closer than 200 m from the forest edge and
 five of which were more than 200 m from the forest edge. We collected SWD
 adults in three habitat types per location from the end of June until the
 end of October 2020. Also the actual distance is taken into account. We
 have two datasets in which the abundance is pooled for the whole period
 and one in which the sampling period is every two weeks. In the analysis
 of the article the number of SWD were standardized to number of SWD per 14
 days.
description: There are two datasets. Details are written in the ReadMe
 file.
DOI: 10.5061/dryad.stqjq2c3t
title: Phenology of Lupinus polyphyllus from Central to Northern Europe

description: Plant phenology, i. e. the timing of life cycle events, is related to
 individual fitness and species distribution ranges. Among the
 environmental factors, phenology is mostly driven by temperature and day
 length. Rapid adaptation of their phenology may also be important for the
 success of invasive plant species. Our main aim was to understand how the
 performance, timing, and temperature dependence of the phenology of the
 invasive legume Lupinus polyphyllus varies with latitude. L. polyphyllus
 is one of the most frequent invasive species in Europe, and the gained
 information may help to make management more effective by adjustments to
 latitude and phenology.
description: We quantified variation in phenology across a &gt;2000 km
 latitudinal gradient from Central to Northern Europe. We sampled data of
 flowering and fruiting of <em>L. polyphyllus </em>using
 &gt;1600 digital photos of inflorescences from 220 individual plants
 observed weekly at 22 locations. We calculated the accumulated growing
 degree days for each observation date at each site from the temperature
 data of the meteorological stations, which are listed in the metadata of
 the dataset.
DOI: 10.57841/casdc.0007104
title: 含硅烯烃氢烷基化反应过程数据和测试表征数据
DOI: 10.5061/dryad.wpzgmsbn9
title: Conservation of birds in fragmented landscapes requires protected areas

description: For successful conservation of biodiversity, it is vital to know whether
 protected areas in increasingly fragmented landscapes effectively conserve
 species. However, how large habitat fragments must be and what level of
 protection is required to sustain species, remains poorly known. We
 compiled a global dataset on almost 2000 bird species in 741 forest
 fragments varying in size and protection status, and show that protection
 is associated with higher bird occurrence, especially for threatened
 species. Protection becomes increasingly important with increasing size of
 forest fragments. For forest fragments &gt;50 ha our results show that
 strict protection (IUCN cat. I-IV) is strongly associated with higher bird
 occurrences, whereas fragments should be at least 175 ha to observe a
 positive effect of moderate protection (cat. V-VI). This meta-analysis
 quantifies the importance of fragment size, protection status, and their
 interaction for the conservation of bird species communities, and stresses
 that protection should not be limited to large pristine areas.