cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9ghx3ffmc
title: Repeatable randomness, invariant properties, and the design of biological signatures of identity

description: What makes a perfect signature? Optimal signatures should be consistent
 within individuals and distinctive between individuals. In defence against
 avian brood parasitism, some host species have evolved ‘signatures’ of
 identity on their eggs, comprising inter-individual variation in colour
 and pattern. Tawny-flanked prinia (Prinia subflava) egg signatures
 facilitate recognition and rejection of parasitic cuckoo finch
 (Anomalospiza imberbis) eggs. Here, we show that consistency and
 distinctiveness of pattern are negatively correlated in prinia eggs,
 perhaps because non-random, repeatable pattern generation mechanisms
 increase consistency but limit distinctiveness. We hypothesise that
 pattern properties which are repeatable within individuals but random
 between individuals (‘invariant properties’) allow hosts to circumvent
 this trade-off. To find invariant properties, we develop a method to
 quantify entire egg phenotypes from images taken from different
 perspectives. We find that marking scale (a fine-grained measure of size),
 but not marking orientation or position, is an invariant property in
 prinias. Hosts should therefore use differences in marking scale in egg
 recognition, but instead field experiments show that these differences do
 not predict rejection of conspecific eggs by prinias. Overall, we show
 that invariant properties allow consistency and distinctiveness to
 coexist, yet receiver behaviour is not optimally tuned to make use of this
 information.
description: Dataset consists of pattern metrics extracted from egg images,
 and egg rejection data, from field experiments conducted from
 2018-2020.
DOI: 10.5061/dryad.2bvq83btd
title: Data from: Domain-specific neural networks improve automated bird sound recognition already with small amount of local data

description: An automatic bird sound recognition system is a useful tool for collecting
 data of different bird species for ecological analysis. Together with
 autonomous recording units (ARUs), such a system provides a possibility to
 collect bird observations on a scale that no human observer could ever
 match. During the last decades progress has been made in the field of
 automatic bird sound recognition, but recognizing bird species from
 untargeted soundscape recordings remains a challenge. In this article we
 demonstrate the workflow for building a global identification model and
 adjusting it to perform well on the data of autonomous recorders from a
 specific region. We show how data augmentation and a combination of global
 and local data can be used to train a convolutional neural network to
 classify vocalizations of 101 bird species. We construct a model and train
 it with a global data set to obtain a base model. The base model is then
 fine-tuned with local data from Southern Finland in order to adapt it to
 the sound environment of a specific location and tested with two data
 sets: one originating from the same Southern Finnish region and another
 originating from a different region in German Alps. Our results suggest
 that fine-tuning with local data significantly improves the network
 performance. Classification accuracy was improved for test recordings from
 the same area as the local training data (Southern Finland) but not for
 recordings from a different region (German Alps). Data augmentation
 enables training with a limited number of training data and even with few
 local data samples significant improvement over the base model can be
 achieved. Our model outperforms the current state-of-the-art tool for
 automatic bird sound classification. Using local data to adjust the
 recognition model for the target domain leads to improvement over general
 non-tailored solutions. The process introduced in this article can be
 applied to build a fine-tuned bird sound classification model for a
 specific environment.
description: This repository contains data and recognition models described in
 paper Domain-specific neural networks improve automated bird sound
 recognition already with small amount of local data. (Lauha et al.,
 2022).
description: Models and codes are written in Python and published as Jupyter
 Notebooks. Audio files are in .mp3 and .wav format and can be opened with
 any standard audio software.
DOI: 10.5061/dryad.v9s4mw703
title: A specimen-level dataset of functional traits and DNA barcodes for Chinese bees

description: The full potential for using DNA barcodes for profiling functional trait
 diversity has yet to be determined in plants and animals, thus we outline
 a general framework for quantifying functional trait diversity of insect
 community DNA and propose and assess the accuracy of three methods for
 achieving this.  We built a novel dataset of traits and DNA
 barcodes for wild bees in China. An informatics framework was developed
 for phylogeny-based integration of these data and prediction of traits for
 any subject barcodes, and compared to two Blast-based methods of trait
 assignment.  Under the specimen-level dataset, rate and accuracy
 of trait assigned dropped with an increase in distance between the query
 and its nearest reference member, though phylogenetic assignment was found
 to perform best under several criteria. For a wider range of compiled
 traits, conservative life-history traits showing the highest rates of
 assignment, for example sociality was predicted with confidence at 53%,
 parasitism at 44%, and nest location at 33%.  Bayesian
 phylogenetic assignment of traits showed particular advantage over
 distance-based methods in the much lower rate that it would return
 incorrect state predictions when the query lacked relatives in the
 reference data. Automated, taxon-independent trait assignment might be
 applied at scale to either barcodes or metabarcodes in any invertebrates.
 With the further generation of integrated barcode and trait data, the
 assignment accuracy of the method is likely to increase. 
description: For the newly created specimen-level database, morphological
 traits were measured using either a Motic SMZ-161-BLED stereomicroscope
 with an eyepiece ruler or a Zeiss Discovery V20 stereomicroscope. If the
 length exceeded microscope range, we used a digital caliper to perform
 measurements. Body length was measured as the distance between the
 antennal socket and metasomal apex in lateral view; head width was taken
 as the widest point between the outer margins of compound eyes in frontal
 view; the tongue length was the distance between the prementum base and
 glossa tip; hind leg length was measured as the sum of the lengths of
 coxa, trochanter, femur, tibia and tarsus (including distitarsus); ITD was
 measured as the distance between the nearest inner edges of the tegulae in
 dorsal view; the hairs on the mesonotum were used as a proxy for hair
 length; forewing length was recoded as the distance between wing base and
 anal angle. In addition to the specimen-level dataset,
 we collated data for a set of functional life history traits.
description: Excel
DOI: 10.5061/dryad.18931zd19
title: Data for: TE positions and expression levels in Macrotermes natalensis

description: Transposable elements (TEs) are mobile genetic sequences, which can cause
 the accumulation of genomic damage in the life time of an organism. The
 regulation of TEs, for instance via the piRNA-pathway, is an important
 mechanism to protect the integrity of genomes, especially in the germ-line
 where mutations can be transmitted to offspring. In eusocial insects soma
 and germ-line are divided among worker and reproductive castes, so one may
 expect caste-specific differences in TE regulation to exist. To test this,
 we compared whole-genome levels of repeat element transcription in the fat
 body of female workers, kings, and five different queen stages of the
 higher termite, Macrotermes natalensis. In this species, queens can live
 over 20 years, maintaining near maximum reproductive output, while sterile
 workers only live weeks or months. We found a strong, positive correlation
 between TE expression and the expression of neighbouring genes in all
 castes. However, we found substantially higher TE activity in workers than
 in reproductives. Furthermore, TE expression did not increase with age in
 queens, despite a seven-fold increase in gene expression, due to a
 significant upregulation of the piRNA-pathway in 20-year-old queens. Our
 results suggest a caste- and age-specific regulation of the piRNA-pathway
 has evolved in higher termites that is analogous to germline-specific
 activity in individual organisms. In the fat body of these termite queens,
 an important metabolic tissue for maintaining their extreme longevity and
 reproductive output, an efficient regulation of TEs likely protects genome
 integrity, thus further promoting reproductive fitness even at high age.
DOI: 10.5061/dryad.2jm63xssm
title: Environmental drivers of local abundance-mass scaling in soil animal communities

description: The relationship between species’ body masses and densities is strongly
 conserved around a three-quarter power law when pooling data across
 communities. However, studies of local within-community relationships have
 revealed major deviations from this general pattern, which has profound
 implications for their stability and functioning. Despite multiple
 contributions of soil communities to people, there is limited knowledge on
 the drivers of body mass-abundance relationships in these communities. We
 compiled a dataset comprising 155 soil-animal communities across four
 countries (Canada, Germany, Indonesia, USA), all sampled using the same
 methodology. We tested if variation in local climatic and edaphic
 conditions drives differences in local body mass-abundance scaling
 relationships. We found substantial variation in the slopes of this
 power-law relationship across local communities. Structural equation
 modeling showed that soil temperature and water content have a positive
 and negative net effect, respectively, on soil communities. These effects
 are mediated by changes in local edaphic conditions (soil pH and carbon
 content) and the body-mass range of the communities. These results
 highlight ways in which alterations of soil climatic and edaphic
 conditions interactively impact the distribution of abundance between
 populations of small and large animals. These quantitative mechanistic
 relationships facilitate our understanding of how global changes in
 environmental conditions, such as temperature and precipitation, will
 affect community-abundance distributions and thus the stability and
 functioning of soil-animal communities.
DOI: 10.6086/d18x0v
title: Driving data from multi-human-in-the-loop simulation experiments

description: Freeway ramp merging involves conflict of vehicle movements that may lead
 to traffic bottlenecks or accidents. Thanks to advances in connected and
 automated vehicle (CAV) technology, a number of efficient ramp merging
 strategies have been developed. However, most of the existing CAV-based
 ramp merging strategies assume that all the vehicles are CAVs or do not
 differentiate vehicle type (i.e., passenger cars vs. heavy-duty trucks).
 In this study, we propose a decentralized cooperative ramp merging
 application for connected vehicles (both connected trucks and connected
 cars) in a mixed-traffic environment. In addition, we develop a
 multi-human-in-the-loop (MHuiL) simulation platform that integrates SUMO
 traffic simulator with two game engine-based driving simulators, allowing
 us to investigate the interactions between two human drivers under various
 traffic scenarios. The case study shows that the decentralized cooperative
 ramp merging application, which provides speed guidance to the connected
 vehicles involved in ramp merging, helps increase the time headways of the
 involved vehicles and smooths their speed profiles. With the speed
 guidance, the median minimum time headway for the yielding car on the
 mainline increases by 57%. Also, its speed variation decreases by 17%
 while the speed variation of the merging truck from the on-ramp decreases
 by 19%. These results demonstrate the potential for the proposed
 application to improve the safety and efficiency of ramp merging for
 heavy-duty trucks, which will be particularly useful at on-ramps with
 relatively short merging lanes. The experiments conducted also validate
 the effectiveness of the developed MHuiL platform for human factor
 research.
description: The dataset was collected from the custom-built
 multi-human-in-the-loop simulation platform by the research team. This
 platform consists of a microscopic traffic simulator, SUMO, and two game
 engine-based driving simulators (one for trucks and the other for
 passenger cars) using Unity. The data has been processed with Python code
 to capture detailed driving information and surrounding vehicles (with
 respect to the two driving simulators) information.
description: The trajectories of each driver and the surrounding vehicles are
 saved in a txt file using JSON format, which should be easily accessible
 by most programs/software.
DOI: 10.15468/dl.sct3sd
title: Occurrence Download

description: A dataset containing 72 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Englerodendron triplisomere",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 72 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003278-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.5mkkwh78r
title: Pollen limitation of native plant reproduction in an urban landscape

description: Premise: Evidence suggests that bees may benefit from moderate levels of
 human development. However, the effects of human development on
 pollination and reproduction of bee-pollinated plants are less well
 understood. Studies have measured natural variation in pollination and
 plant reproduction as a function of urbanization, but few have
 experimentally measured the magnitude of pollen limitation in urban versus
 non-urban sites. Doing so is important to unambiguously link changes in
 pollination to plant reproduction. Previous work in the Southeastern US
 found that urban sites supported twice the abundance of bees compared to
 non-urban sites. We tested the hypothesis that greater bee abundance in
 some of the same urban sites translates into reduced pollen limitation
 compared to non-urban sites. Methods: We manipulated pollination to three
 native, wild-growing, bee-pollinated plants: Gelsemium sempervirens,
 Oenothera fruticosa, and Campsis radicans. Using supplemental
 pollinations, we tested for pollen limitation of three components of
 female reproduction in paired urban and non-urban sites. We also measured
 pollen receipt as a proxy for pollinator visitation. Results: We found
 that all three plant species were pollen-limited for some measures of
 female reproduction. However, opposite to our original hypothesis, two of
 the three species were more pollen-limited in urban relative to non-urban
 sites. We found that open-pollinated flowers in urban sites received less
 conspecific and more heterospecific pollen on average than those in
 non-urban sites. Conclusions: These results suggest that even when urban
 sites have more abundant pollinators, this may not alleviate pollen
 limitation of native plant reproduction in urban landscapes.
description: Data are fruit and seed data from pollen supplementation
 experiments (hand-pollinated and open-pollinated control flowers) and
 pollen deposition data (both conspecific and heterospecific pollen
 receipt).
description: No specific software is required.
DOI: 10.5061/dryad.05qfttf5z
title: The legacies of land-clearance and trophic downgrading accumulate to affect structure and function of kelp forests

description: Aotearoa New Zealand is the last major landmass settled by people, and
 therefore provides a recent record of ecological legacy effects in the
 coastal zone. Large-scale land clearances of forests accelerated over the
 last century, affecting the concentration of suspended sediments, light
 environment and nutrient composition on rocky reefs, and consequently the
 distribution, abundance and composition of algal forests. Environmental
 effects were compounded in many places by overfishing and long-term
 declines of large predatory species, often leading to proliferation and
 extensive grazing by sea urchins. Here we examine these processes in three
 biogeographic regions that have been differentially affected by ecological
 legacy effects. The study was based on the depth-specific associations
 between sea urchins (Evechinus chloroticus) and the common kelp (Ecklonia
 radiata) from multiple sites within each region, some of which were
 sampled over two decades within no-take marine reserves and in actively
 fished areas. Satellite-derived estimates of water column properties were
 used as proxies for the relative effects of coastal sedimentation on kelp
 forest habitats. We then used an information-theoretic framework to assess
 the relative factor weightings of marine reserve effects on urchin
 density, total suspended solids and regional urchin density on the
 depth-specific density of E. radiata. Fishing effects were significant
 within and outside of reserves in the Northern and Central regions, but
 the effect-sizes were by far strongest in the Northern region. In the
 Central region characterised by extensive land clearance and forestry
 combined with high coastal retention of water, the concentration of total
 suspended solids had a major influence on the depth distribution of kelp,
 confining it to shallow water (&lt;10m depth) in small patches where
 urchins did not overgraze. These patterns are in sharp contrast to the
 small marine reserve effects and deep distribution of E. radiata in the
 Southern region, which has intact native forested catchments,
 comparatively low fishing pressure and a large regional network of marine
 reserves. The results highlight important differences in how centuries-old
 legacies of land clearance and exploitation affect regional-scale dynamics
 of sea urchins and kelp, and define the appropriate spatial scale of
 ecosystem-based management of kelp forest habitats.
DOI: 10.5061/dryad.4b8gthtg8
title: Size of an interspecific competitor may be a source of information in reproductive decisions

description: Animals use interspecific cues as a source of information in
 decision-making, but the full costs and benefits of interspecific
 information use are unknown. We tested whether pied flycatchers use the
 body size and clutch size of great tits as cues in their reproductive
 decisions and what are the possible fitness consequences as a function of
 great tit size. The size of great tit females was positively associated
 with flycatchers’ probability to settle near a tit nest over a territory
 further away. Flycatcher egg mass was positively correlated with great tit
 female size regardless of flycatcher territory choice. However, in
 flycatchers that had chosen to nest near great tits, the size of nestlings
 decreased in relation to increasing great tit female size. Our results
 demonstrate the use of size of interspecifics as a cue in reproductive
 decisions and the trade-off between the value of information and costs of
 competition information users face when using interspecific information in
 decision-making.
DOI: 10.5061/dryad.m63xsj45f
title: Chemistry-weather interacted model system GRAPES_Meso5.1/CUACE CW V1.0

description: The Chinese Meteorology Administration chemistry model CUACE is online
 integrated into the mesoscale operational weather prediction (NWP) model
 (GRAPES_Meso5.1) and aerosol-cloud-radiation interaction is achieved to
 establish the first version (V1) of chemistry-weather (CW) interacted
 model GRAPES-Meso5.1/CUACE CW V1. The most polluted winter 2016-2017 is
 selected to study the meteorology impacts on haze/fog prediction, the
 impact of aerosol-radiation, aerosol-cloud, and CW interaction (ARI, ACI,
 CWI) on haze/fog prediction, and NWP. Single way model without CWI
 displays reasonable PM2.5 and visibility prediction in general. However,
 modeled PM2.5 peaks are underestimated and visibility valleys are
 overestimated during haze/fog pollution, the underestimation of relative
 humidity (RH) contributes major to this misestimation; CWI model cut the
 negative errors of PM2.5 peaks and the positive errors of visibility
 valleys. The improvement of 5km and 3km low visibility by CWI during
 severe haze/fog period is more obvious than that of 10 km, which just
 compensates for the largest deficiency in low visibility prediction
 related to severe haze/fog by single way model; The NWP including sea
 level pressures, relative humidity(RH), temperature, wind speed are also
 improved by CWI from surface to upper troposphere; ARI contributes larger
 to the predicted PM2.5, visibility and NWP improvement than that of ACI,
 their relative contributions varies with model vertical height and the
 overlapping condition of cloud and aerosols. Due to the joint contribution
 of RH and PM2.5, CWI’s improvement in visibility is larger than PM2.5.
 This study illustrates the importance of including CWI in the air quality
 prediction model.
DOI: 10.5061/dryad.hqbzkh1kc
title: Personality predicts mode of attack in a generalist ground spider predator

description: Personality traits, such as boldness and/or aggressiveness, have long been
 accepted to have a profound influence on many aspects of the lives of
 animals, including foraging. However, little is known about how
 personality traits shape the use of a particular attack strategy. Ground
 spiders use either venom or silk attack to immobilise prey. In this study,
 we tested the hypothesis that behavioural differences among individuals
 (namely boldness, measured as the time spent exploring a novel
 environment; and aggressiveness, measured as the number of killed but not
 consumed prey) drive the use of a particular attack strategy. We used a
 generalist ground spider, Drassodes lapidosus, and recorded the mode of
 attack on two types of prey, dangerous and safe. Moreover, we measured the
 size of the venom gland to test the relationship between the size of venom
 volume and the personality, as well as the mode of attack. Drassodes
 individuals showed consistent behavioural differences in the way they
 attacked prey. Venom attack was significantly related to increased
 aggressiveness when attacking spider (dangerous) prey and to increased
 boldness when attacking cricket (safe) prey. Silk attack was more
 frequently used by shy (for cricket prey) and docile  (for spider
 prey). The volume of venom was not related to the attack strategy. We
 conclude that personality traits are important drivers of prey capture
 behaviour in generalist ground spiders.
description: Details are included in the material and methods of the
 manuscript.
description: MS Excel