cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2547d7wvq
title: Using inbreeding to test the contribution of non-additive genetic effects to additive genetic variance: A case study in Drosophila serrata

description: Additive genetic variance, VA, is the key parameter for predicting
 adaptive and neutral phenotypic evolution. Changes in demography (e.g.,
 increased close-relative inbreeding) can alter VA, but how depends on the,
 typically unknown, gene action and allele frequencies across many loci.
 For example, VA increases proportionally with the inbreeding coefficient
 when allelic effects are additive, but larger (or smaller) increases can
 occur when allele frequencies are unequal at causal loci with dominance
 effects. Here, we describe an experimental approach to assess the
 potential for rare, recessive alleles to inflate VA under inbreeding.
 Applying a powerful paired pedigree design in Drosophila serrata, we
 measured 11 wing traits on half-sibling families bred via either random or
 sibling mating, differing only in homozygosity (not allele frequency).
 Despite close inbreeding and substantial power to detect small VA, we
 detected no deviation from the expected additive effect of inbreeding on
 genetic (co)variances. Our results suggest the average dominance
 coefficient is very small relative to the additive effect, or that allele
 frequencies are relatively equal at loci affecting wing traits. We outline
 the further opportunities for this paired pedigree approach to reveal the
 characteristics of VA, providing insight into historical selection and
 future evolutionary potential.
DOI: 10.5061/dryad.63xsj3v6g
title: A big data–model integration approach for predicting epizootics and population recovery in a keystone species

description: Infectious diseases pose a significant threat to global health and
 biodiversity. Yet, predicting the spatiotemporal dynamics of wildlife
 epizootics remains challenging. Disease outbreaks result from complex
 non-linear interactions among a large collection of variables that rarely
 adhere to the assumptions of parametric regression modeling. We adopted a
 non-parametric machine learning approach to model wildlife epizootics and
 population recovery, using the disease system of colonial black-tailed
 prairie dogs (BTPD, Cynomys ludovicianus) and sylvatic plague as an
 example. We synthesized colony data between 2001–2020 from eight USDA
 Forest Service National Grasslands across the range of BTPD in central
 North America. We then modeled extinctions due to plague and colony
 recovery of BTPD in relation to complex interactions among climate,
 topoedaphic variables, colony characteristics, and disease history.
 Extinctions due to plague occurred more frequently when BTPD colonies were
 spatially clustered, in closer proximity to colonies decimated by plague
 during the previous year, following cooler than average temperatures the
 previous summer, and when wetter winter/springs were preceded by drier
 summer/falls. Rigorous cross-validations and spatial predictions indicated
 that our final models predicted plague outbreaks and colony recovery in
 BTPD with high accuracy (e.g., AUC generally &gt; 0.80). Thus, these
 spatially-explicit models can reliably predict the spatial and temporal
 dynamics of wildlife epizootics and subsequent population recovery in a
 highly complex host-pathogen system. Our models can be used to support
 strategic management planning (e.g., plague mitigation) to optimize
 benefits of this keystone species to associated wildlife communities and
 ecosystem functioning. This optimization can reduce conflicts among
 different landowners and resource managers, as well as economic losses to
 the ranching industry. More broadly, our big data–model integration
 approach provides a general framework for spatially-explicit forecasting
 of disease-induced population fluctuations, for use in natural resource
 management decision-making.
description: All methodological information can be found in the attached
 metadata files entitled
 "README_EAP22-0433_Colony-Growth_FinalDataset" and
 "README_EAP22-0433_Plague-Model_FinalDataset". 
description: No special programs and/or software are required to open our data
 files. We used Program R to format and analyze data in the manuscript. All
 R packages and functions needed to interpret the data are cited in the
 manuscript.
DOI: 10.6078/d1vt6k
title: Data for: Characterization, comparison, and optimization of lattice light sheets (Part 1/3)

description: Lattice light sheet microscopy excels at the non-invasive imaging of
 three-dimensional (3D) dynamic processes at high spatiotemporal resolution
 within cells and developing embryos. Recently, several papers have called
 into question the performance of lattice light sheets relative to the
 Gaussian sheets most common in light sheet microscopy. Here we undertake a
 comprehensive theoretical and experimental analysis of various forms of
 light sheet microscopy which both demonstrates and explains why lattice
 light sheets provide significant improvements in resolution and
 photobleaching reduction. The analysis provides a procedure to select the
 correct light sheet for a desired experiment and specifies the processing
 that maximizes the use of all fluorescence generated within the light
 sheet excitation envelope for optimal resolution while minimizing image
 artifacts and photodamage. Development of a new type of “harmonic
 balanced” lattice light sheet is shown to improve performance at all
 spatial frequencies within its 3D resolution limits and maintains this
 performance over lengthened propagation distances allowing for expanded
 fields of view.
description: The dataset was collected with homemade lattice light sheet
 microscope with different light sheets and different parameters. The light
 sheet name and the parameters are contained within the zip file name for
 the light sheet.  The dataset has been processed with
 LLSM5DTools (https://github.com/abcucberkeley/LLSM5DTools/tree/dev).
description: The files can be opened with any 3D image visualization tools
 (i.e., Fiji, napari, Imaris and Amira) with support for tiff
 format.
DOI: 10.5061/dryad.000000071
title: Data from: Distinctive microbial community and genome structure in coastal seawater from a human-made port and nearby offshore island in northern Taiwan facing the Northwestern Pacific Ocean

description: Pollution in human-made fishing ports caused by petroleum from boats, dead
 fish, toxic chemicals, and effluent poses a challenge to the organisms in
 seawater. To decipher the impact of pollution on the microbiome, we
 collected surface water from a fishing port and a nearby offshore island
 in northern Taiwan facing the Northwestern Pacific Ocean. By employing 16S
 rRNA gene amplicon sequencing and whole-genome shotgun sequencing, we
 discovered that Rhodobacteraceae, Vibrionaceae, and Oceanospirillaceae
 emerged as the dominant species in the fishing port, where we found many
 genes harboring the functions of antibiotic resistance (ansamycin,
 nitroimidazole, and aminocoumarin), metal tolerance (copper, chromium,
 iron and multimetal), virulence factors (chemotaxis, flagella, T3SS1),
 carbohydrate metabolism (biofilm formation and remodeling of bacterial
 cell walls), nitrogen metabolism (denitrification, N2 fixation, and
 ammonium assimilation), and ABC transporters (phosphate,
 lipopolysaccharide, and branched-chain amino acids). The dominant bacteria
 at the nearby offshore island (Alteromonadaceae, Cryomorphaceae,
 Flavobacteriaceae, Litoricolaceae, and Rhodobacteraceae) were partly
 similar to those in the South China Sea and the East China Sea.
 Furthermore, we inferred that the microbial community network of the
 cooccurrence of dominant bacteria on the offshore island was connected to
 dominant bacteria in the fishing port by mutual exclusion. By examining
 the assembled microbial genomes collected from the coastal seawater of the
 fishing port, we revealed four genomic islands containing large
 gene-containing sequences, including phage integrase, DNA invertase,
 restriction enzyme, DNA gyrase inhibitor, and antitoxin HigA-1. In this
 study, we provided clues for the possibility of genomic islands as the
 units of horizontal transfer and as the tools of microbes for facilitating
 adaptation in a human-made port environment.
description: 1. Microbial samples were collected from the seawater from a human-made port and nearby offshore
 island in northern Taiwan facing the Northwestern Pacific
 Ocean. 2. Next-generation sequencing method was
 employed to discover the genome sequences of the
 microbes. 3. Genome sequences were analyzed for the coding
 sequences and biological functions.
DOI: 10.5061/dryad.80gb5mkv3
title: Dogs take into account the actions of a human partner in a cooperative task

description: Humans stand out for their capacity to flexibly cooperate, possibly
 because they understand their partners’ role. Researchers have explored if
 such understanding is unique to humans by assessing whether non-human
 species wait to manipulate a cooperative apparatus until a delayed partner
 arrives. If animals do wait, then it is assumed that they recognize the
 need for a partner. However, success in these tasks may be the result of
 social facilitation, while failure may be due to poor inhibitory control.
 Moreover, this approach does not test if animals take their partners’
 actions into account. Here we trained dogs to press a button
 simultaneously with their human partner. Afterwards, we tested them in
 several conditions to disentangle which elements of their partner’s
 behaviour they take into account. Dogs waited to press the button until:
 the arrival of a delayed partner, the button was available to the partner,
 and the partner acted (pressed the button). We found no relationship
 between inhibitory control and success. We conclude that dogs are not
 merely reacting to the presence of their human partners, but are also
 taking their actions into account when coordinating with them.
DOI: 10.5061/dryad.mgqnk993p
title: Data for: Sexual dimorphism in ichneumonine parasitic wasps (Hymenoptera: Ichneumonidae: Ichneumoninae) and the neglected influence of the ecological niche

description: Sexual dimorphism is a ubiquitous phenomenon, but its ecological role and
 evolutionary significance are still poorly understood in many hyperdiverse
 lineages. We used geometric morphometrics to characterize and quantify
 sexual dimorphism in the head and mesosoma of 24 species in the wasp
 subfamily Ichneumoninae (Hymenoptera: Ichneumonidae). Our results show
 that sexual dimorphism varies substantially among species but is generally
 more pronounced on the head, with males occupying a noticeably smaller
 region of the morphospace than females. Phenotypic trajectory analyses
 showed a trend towards conserved trajectories in the difference between
 males and females, indicating that dimorphism seems to manifest as
 predictable shape changes across species. Species parasitizing pupae,
 particularly in concealed substrates, were found to have higher sexual
 dimorphism for the head than species parasitizing more exposed hosts such
 as larvae. For the mesosoma, this difference was not significant, with the
 degree of sexual dimorphism more influenced by phylogenetic history. We
 hypothesize that female head shape has adapted to the demands related to
 finding hosts in concealed habitats, whereas species that attack exposed
 or weakly concealed hosts have kept a generalized head shape in both
 sexes. These results highlight the importance of investigating intersex
 ecological differences as drivers of sexual dimorphism.
description: This dataset consists of photos of the mesosoma and lateral view
 and head in front view for 24 species of Ichneumoninae (Hymenoptera,
 Ichneumonidae), with 10 males and 10 females of each species photographed.
 Standardized photographs of the head in front view and the mesosoma in
 lateral view taxa were produced using the extended-focus system EntoVision
 (GTVision, Hagerstown, Maryland), consisting of a Leica MZ16 zoom lens
 attached to a JVC KY-75U 3-CCD digital video camera that feeds image data
 to a desktop computer. The program Archimed 5.3.1 is then used to merge an
 image series (representing typically 15–30 focal planes) into a single
 in-focus image. Lighting was provided by an EntoVision dome
 light.
description: Any image-related software can open the files; landmarks for
 geometric morphometrics can be generated through the freely available
 software ImageJ: https://imagej.nih.gov/ij/download.html
DOI: 10.5061/dryad.dv41ns230
title: Occurrences of Echinococcus multilocularis in Europe

description: Global change is expected to have complex effects on the distribution and
 transmission patterns of zoonotic parasites. Modelling habitat suitability
 for parasites with complex life cycles is essential to further our
 understanding of how disease systems respond to environmental changes, and
 to make spatial predictions of their future distributions. However, the
 limited availability of high-quality occurrence data with high spatial
 resolution often constrains these investigations. Using 449 reliable
 occurrence records for Echinococcus multilocularis from across Europe
 published over the last 35 years, we modelled habitat suitability for this
 parasite, the aetiological agent of alveolar echinococcosis, in order to
 describe its environmental niche, predict its current and future
 distribution under three global change scenarios, and quantify the
 probability of occurrence for each European country. Using a machine
 learning approach, we developed large-scale (25x25 km) species
 distribution models based on seven sets of predictors, each set
 representing a distinct biological hypothesis supported by current
 knowledge of the autecology of the parasite. The best-supported hypothesis
 included climatic, orographic and land-use/land-cover variables such as
 the temperature of the coldest quarter, forest cover, urban cover and the
 precipitation seasonality. Future projections suggested the appearance of
 highly suitable areas for E. multilocularis towards northern latitudes and
 in the whole Alpine region under all scenarios, while decreases in habitat
 suitability were predicted for central Europe. Our spatially explicit
 predictions of habitat suitability shed light on the complex responses of
 parasites to ongoing global changes.
DOI: 10.5061/dryad.fbg79cp03
title: Data and codes for: Experimental evolution of evolutionary potential in fluctuating environments

description: This supplementary data contains raw data for a publication:
 "Experimental evolution of evolutionary potential in fluctuating
 environments." 1) Raw data of optical density measurements (10 .csv
 files), 2) R-code for obtaining maximal growth rate and maximum biomass
 yield from measurements. 3) resulting data file 4) R-code for Bayesian
 analysis of the data.
description: Data was collected by repeated bioscreen spectrophotometer
 measurements of clones evolved in constant or in two different fluctuating
 environments. 
description: Codes are freely usable for any purposes (CC0 license)
DOI: 10.5061/dryad.p8cz8w9v7
title: Secondary ion mass spectrometry, a powerful tool for revealing ink formulations and animal skins in medieval manuscripts

description: Book production by medieval scriptoria has gained growing interest in
 recent studies. In this context, identifying ink compositions and
 parchment animal species from illuminated manuscripts is of great
 importance. Here, we introduce time-of-flight secondary ion mass
 spectrometry (ToF-SIMS) as a non-invasive tool to identify both inks and
 animal skins in manuscripts, at the same time. For this purpose, both
 positive and negative ion spectra in inked and non-inked areas were
 recorded. Chemical compositions of pigments (decoration) or black inks
 (text) were determined by searching for characteristic ion mass peaks.
 Animal skins were identified by data processing of raw ToF-SIMS spectra
 using principal component analysis (PCA). In illuminated manuscripts from
 the fifteenth to sixteenth century, malachite (green), azurite (blue),
 cinnabar (red) inorganic pigments, as well as iron-gall black ink, were
 identified. Carbon black and indigo (blue) organic pigments were also
 identified. Animal skins were identified in modern parchments of known
 animal species by a two-step PCA procedure. We believe the proposed method
 will find extensive application in material studies of medieval
 manuscripts, as it is non-invasive, highly sensitive and able to identify
 both inks and animal skins at the same time, even from traces of pigments
 and tiny scanned areas.
description: Analytical and data processing methods can be found in the
 associated article.
description: In-house PCA algorithm requires python.
 ToF-SIMS raw data require SurfaceLab software.
 ATR-FTIR raw data (.0) can be read with free-licence software
 (Fityk). XRD diffractograms are directly exported in
 .txt from .xyz files.
DOI: 10.5061/dryad.f7m0cfz1j
title: Data for: Assessment of the accuracy of counting large ungulate species (red deer Cervus elaphus) with UAV-mounted thermal infrared cameras during night flights

description: Unmanned Aerial Vehicles (UAVs) are increasingly used in wildlife
 surveying, including estimation of population densities. It is essential
 that we evaluate and test new survey methods to guide optimal sampling
 strategies. This study aimed to assess the accuracy of using a UAV-mounted
 thermal infrared (TIR) camera to count red deer Cervus elaphus
 populations, and how this was influenced by flight season, height and
 velocity, in order to help guide future census design. We flew 57 flights
 across a captive population of red deer in a 13 ha deer park enclosure of
 semi-natural habitat, representative of the species’ range in northern
 Germany. Flights and image assessments were performed with no prior
 knowledge of actual population size. Accuracy was quantified by comparing
 real population size (known only to deer park staff) and independently
 estimated population sizes from UAV TIR images. Accuracy was significantly
 influenced by ecological season (early and late winter, spring and early
 summer) and height. Across all seasons, lower flights (100 m) performed
 better than higher ones (120 m), with lower flights in early winter and
 early summer being on average accurate to within 1% of actual population
 counts. For the season where we had the largest range of temperatures
 between flights (late winter) we found that accuracy was highest when
 temperatures were lowest. Flights were also able to identify all five
 stags (defined as a male deer ≥2 years old) present in early summer, but
 not in spring. Deer appeared to avoid the landing/take-off area, but there
 were no noted behavioural responses to drones flying over animals when at
 constant height and velocity during surveys. Our results indicate that
 UAV-mounted TIR camera have the potential to accurately count populations
 of large ungulate species, but that flight season, height and potentially
 temperature need to be taken into account to maximise accuracy. This
 approach has the potential to be scaled up to more accurately estimate
 densities of wild populations compared to existing approaches.
DOI: 10.5061/dryad.qz612jmkt
title: Adult branchiosaurid temnospondyls: The life cycle of Xerodromeus gracilis

description: The Branchiosauridae form a clade of tiny newt-like, extinct amphibians of
 overall larval appearance. While their status as neotenic
 (perennibranchiate) forms had long been universally accepted, adult
 specimens are known from only one taxon that was hitherto referred to
 as Melanerpeton (Apateon) gracile. Here we
 study this life cycle in depth, which includes the only well-documented
 metamorphosis-like transformation in an early tetrapod outside
 Lisssamphibia. Based on various newly recognized
 features, Melanerpeton gracile is attributed to
 a new genus, Xerodromeus. X. gracilis is
 characterized by a short postorbital skull table, wide supratemporal,
 quadrate condyles well posterior to the occipital ones, ossified
 endocranial elements, carpals, coracoid and pelvis as well as wedge-shaped
 intercentra and cylindrical pleurocentra, of which the latter are
 identified for the first time in branchiosaurids. The studied size classes
 are referred to four phases: (A) integration of jaw and cheek, longer
 snout, (B) stronger teeth, robust limbs, incipient ossification of
 exoccipital, coracoid, and pelvis, change in dermal ornament), (C) larger
 gape, wider skull, polygonal ornament) and (D) quadrate, coracoid,
 carpals, and vertebral centra ossified, during which a probably
 terrestrial adult morph developed. Adult X. gracilis is
 more massively built than amphibamids, and its non-pedicellate dentition
 indicates that it was probably feeding on different prey.
description: The morphological data were acquired by first-hand examination
 and literature review of morphological characters in the studied taxa. The
 character-states were coded by the senior author.
description: TNT 1.5.
DOI: 10.5061/dryad.r4xgxd2hp
title: Native diversity contributes to composition heterogeneity of exotic floras

description: Variation in species composition among sites (beta diversity) is generally
 thought to be driven by environmental filtering and dispersal limitation
 but the role of biotic interactions has not been sufficiently addressed.
 Specifically, the early species in a local community may contribute to
 subsequent beta diversity patterns. Exotic assemblages within native
 communities provide a unique opportunity to study biotic interaction
 mechanisms. In this study, we conducted a field survey of plants over a
 ~1800 km transect in the middle and lower Yangtze River valley in China to
 study how native communities influence exotic beta diversity. The survey
 included 459 plots in 51 local plant communities with 40 exotic species
 and 103 co-occurring native species. We also investigated how 11
 environmental factors involving climate conditions, soil properties and
 human activity regulate the interaction between native and exotic plants.
 The results showed that native diversity (Shannon-Wiener index) increased
 exotic beta diversity. Environmental conditions, especially monthly
 minimum temperature, influenced exotic beta diversity indirectly through
 native diversity rather than directly. Our results suggest that lower
 native diversity driven by environmental conditions, especially warmer
 temperatures, led to a decrease in composition heterogeneity of the exotic
 flora. Our results will help to incorporate biotic interactions into the
 framework of beta diversity mechanisms for local community assembly.