cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tb2rbp048
title: The origins of climate-diversity relationships and richness patterns in Chinese plants

description: A major goal of ecology and evolutionary biology is to explain geographic
 patterns of species richness. Richness is often correlated with climatic
 variables. However, the processes underlying these climate-diversity
 relationships remain poorly understood. Two potential hypotheses to
 explain these relationships involve: (i) faster diversification rates
 (speciation minus extinction) in high-richness climates, and (ii) earlier
 colonization of high-richness climates, allowing more time for speciation
 to build up richness. Few studies have tested these hypotheses directly,
 and most focused on animal clades with limited richness. In this study we
 test these hypotheses in Chinese angiosperms, encompassing ~10% of Earth’s
 plant species, using large-scale phylogenetic, climatic, and
 distributional data including 26,977 species. We find that climatic zones
 that were colonized earlier have higher species richness. In contrast,
 relationships between diversification rates and richness of climatic zones
 are often non-significant or negative. Our study reveals that even when
 richness is strongly correlated with climate, the underlying explanation
 may still be rooted in phylogenetic history. We also show that the timing
 of colonization can be crucial for explaining richness patterns. Yet, most
 recent studies have ignored this explanation and instead have focused
 solely on rates of speciation and diversification as drivers of diversity
 gradients.
DOI: 10.5061/dryad.t1g1jwt60
title: Pollinator and host sharing lead to hybridization and introgression in Panamanian free-standing figs, but not in their pollinator wasps

description: Obligate pollination mutualisms, in which plant and pollinator lineages
 depend on each other for reproduction, often exhibit high levels of
 species-specificity. However, cases in which two or more pollinator
 species share a single host species (host sharing), or two or more host
 species share a single pollinator species (pollinator sharing), are known
 to occur in the current ecological time. Further, evidence for host
 switching in evolutionary time is increasingly being recognized in these
 systems. The degree to which departures from strict specificity
 differentially affect the potential for hybridization and introgression in
 the associated host or pollinator is unclear. We addressed this question
 using genome-wide sequence data from five sympatric Panamanian
 free-standing fig species (Ficus subgenus Pharmacosycea,
 section Pharmacosycea) and their six associated fig pollinator
 wasp species (Tetrapus). Two of the five fig species, F.
 glabrata and F. maxima, were found to regularly share
 pollinators. In these species, ongoing hybridization was demonstrated by
 the detection of several first-generation (F1) hybrid individuals, and
 historical introgression was indicated by phylogenetic network analysis.
 In contrast, although two of the pollinator species regularly share hosts,
 all six species were genetically distinct and deeply divergent, with no
 evidence for either hybridization or introgression. This pattern is
 consistent with results from other obligate pollination mutualisms,
 suggesting that, in contrast to their host plants, pollinators appear to
 be reproductively isolated, even when different species of pollinators
 mate in shared hosts.
description: Please see the associated manuscript for details.
DOI: 10.5061/dryad.pzgmsbcr0
title: Systemic infection of Bryoria (Lecanoromycetes, Ascomycota) by Athelia (Agaricomycetes, Basidiomycota) in western North America

description: Bryoria (Parmeliaceae, Ascomycota) is one of the dominant genera of hair
 lichens in western North America and is characteristic of high-elevation
 conifer forest ecosystems. In areas where Bryoria is abundant, it is
 common to find thalli in which the thalline filaments become
 conglutinated, forming brittle dead zones. After sampling Bryoria thalli
 across western Canada and the northwestern United States at different
 times of the year, we found this dieback phenomenon is associated with the
 winter growth of a mold-forming basidiomycete. We report that this fungus
 belongs to Athelia (Atheliaceae, Basidiomycota) a genus known to contain
 lichen pathogens, most notably A. arachnoidea. By sequencing a combination
 of genetic markers – nuc rDNA ITS1-5.8S-ITS2 (ITS), partial nuc 28S rDNA
 (28S), and partial translation elongation factor 1-α (TEF1) – paired with
 morphometric analyses, we reveal the involvement of at least three
 additional lineages of lichen-associated Athelia and describe one as a new
 species, Athelia abscondita. A. abscondita is morphologically
 distinguished from other Athelia species by its basidia and basidiospores,
 was found to frequently infect members of Bryoria sect. Implexae, and was
 occasionally on other foliose and fruticose species within Parmeliaceae.
DOI: 10.5061/dryad.95x69p8pm
title: Data from: Mate choice for body size leads to size assortative mating in the Ryukyu Scops Owl Otus elegans

description: Understanding evolutionary phenomena that involve size assortative mating,
 requires elucidating the generating mechanisms on which assortment is
 based. Although various mechanisms have been suggested, their relative
 importance may differ across taxonomic groups. Males selecting for large,
 fecund females combined with the dominance of large males in the
 competition for females, has been suggested as a major mechanism in
 specific groups. However, raptors do not appear to conform to this,
 because the selection for smallness among males (assumed in a theory of
 reversed sexual size dimorphism) and the selection for largeness among
 males (assumed in the theory of size assortative mating) are in opposite
 directions. We studied the assortative mating during a long-term study of
 the Ryukyu Scops Owls Otus elegans interpositus. Significant assortative
 mating was found for culmen length (from the base to the tip of the bill)
 and wing length (from the bend of the wing to the tip of the longest
 primary). Statistical control of the spatial and temporal accessibility of
 potential mates did not affect the assortment. Males with short wings had
 slightly higher fitness components than those with long wings, and females
 settling early tended to have small wings. Considering that early-settling
 females can preferentially choose their mates, these results suggest that
 smaller females have an advantage when choosing smaller males with good
 reproductive performance. Improved flying and hunting ability of smaller
 individuals may be the background of choosing smaller individuals. We
 propose that, not passive process like similarity between individuals and
 their potential mates, but active mate choice for small individuals is an
 explanation for the assortative mating in this owl.
description: This dataset was collected during a long-term study of the Ryukyu
 Scops Owls <em>Otus elegans</em> on Minami-daito Island,
 Japan.
description: Statistical software R and statisitical progamming language Stan
 are required for opening the files in this dataset and for reproducing the
 analyses in the paper. Arbitarary graphics software is
 also required to open figures in eps format. 
 Arbitarary spreadsheet software is also helpful to handle tables
 in csv format.
DOI: 10.5061/dryad.v6wwpzh0m
title: X, Y, and Z: A bird's eye view on light pollution

description: 1. The global increase in light pollution is being viewed with growing
 concern, as it has been reported to have negative effects ranging from the
 individual to the ecosystem level. 2. Unlike movement on the ground,
 flying and swimming allows vertical motion. Here, we demonstrate flight
 altitude change is crucial to the perception and susceptibility of
 artificial light at night of airborne organisms. Because airborne species
 can propagate through the airspace and easily across ecotones, effects
 might not be small-scale. Therefore, we propose including airspace as a
 vital habitat in the concept of ecological light pollution. 3. The
 interplay between flight altitude and the effects of light pollution may
 not only be crucial for understanding flying species but may also provide
 valuable insights into the mechanisms of responses to artificial light at
 night in general.
description: The digital camera images were taken by Canon EOS 6D camera at
 the four principal directions and the zenith. Camera settings: ISO 6400,
 f/3.5, 30s exposure time. The images were processed by the author"s
 DiCaLum software (dicalum.eu) The spectra
 (ksee_spectrum1.d and ksee_spectrum2.d) were measured by a Konica-Minolta
 CS-2000A spectroradiometer. The nightly data were averaged to reduce
 measurement noise.
description: Most image processing and viewer software can open Canon CR2
 files (e.g. gimp, dcraw). Any plotting program or text
 editor opens the spectral data. We provide a CC0
 license-compatible simple Gnuplot script
 (ksee_spectra.plt) that we used to make the figure. Gnuplot is an
 open-source plotting software.
DOI: 10.15468/dl.8kb79m
title: Occurrence Download

description: A dataset containing 15267 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Bryophyte herbarium TRH, NTNU University Museum",
 "Country is Sweden"
 ]
}

 The dataset includes 15267 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003381-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.98sf7m0nc
title: Data for: Should females cannibalise with or without mating in the facultatively parthenogenetic springbok mantis

description: Non-copulatory cannibalism, which occurs when females attack and consume
 males instead of mating with them, could persist if it enhances female
 fecundity more than it exacerbates reproductive failure. However, females
 that are facultatively parthenogenetic may be able to cannibalise
 indiscriminately since securing a mate is not necessary for reproduction
 when parthenogenesis is possible. We used an experimental approach to
 examine the economics of cannibalism with and without mating for female
 Miomantis caffra—a facultatively parthenogenetic mantis that shows high
 rates of non-copulatory cannibalism. If non-copulatory cannibalism is
 maintained by fecundity enhancement, we predicted that eating a male would
 boost female fitness regardless of mating status. If non-copulatory
 cannibalism persists by facilitating total mating avoidance, then we
 predicted that mating would be costly, and females would perform better
 via parthenogenesis than via sex. Contrary to our predictions, we found
 that mating once led to dramatically higher fitness than not mating, and
 cannibalising a single male provided no overall fitness benefit to either
 mated or unmated females. Our results suggest that precopulatory
 cannibalism persists in M. caffra for reasons other than fecundity
 enhancement or total mating avoidance.
DOI: 10.5061/dryad.2z34tmpqk
title: Optogenetic activation of visual thalamus generates artificial visual percepts

description: The lateral geniculate nucleus (LGN), a retinotopic relay center where
 visual inputs from the retina are processed and relayed to the visual
 cortex, has been proposed as a potential target for artificial vision. At
 present, it is unknown whether optogenetic LGN stimulation is sufficient
 to elicit behaviorally relevant percepts, and the properties of LGN neural
 responses relevant for artificial vision have not been thoroughly
 characterized. Here, we demonstrate that tree shrews pre-trained on a
 visual detection task can detect optogenetic LGN activation using an
 AAV2-CamKIIα-ChR2 construct and readily generalize from visual to
 optogenetic detection. Simultaneous recordings of LGN spiking activity and
 primary visual cortex (V1) local field potentials (LFP) during optogenetic
 LGN stimulation show that LGN neurons reliably follow optogenetic
 stimulation at frequencies up to 60 Hz, and uncovered a striking phase
 locking between the V1 local field potential (LFP) and the evoked spiking
 activity in LGN. These phase relationships were maintained over a broad
 range of LGN stimulation frequencies, up to 80 Hz, with spike field
 coherence values favoring higher frequencies, indicating the ability to
 relay temporally precise information to V1 using light activation of the
 LGN. Finally, V1 LFP responses showed sensitivity values to LGN
 optogenetic activation that were similar to the animal’s behavioral
 performance. Taken together, our findings confirm the LGN as a potential
 target for visual prosthetics in a highly visual mammal closely related to
 primates.
DOI: 10.5281/zenodo.17722737
title: Charge Injection and Inter-Fiber Electrical Conduction in Cable Bacteria

description: Cable bacteria are multicellular microorganisms capable of charge transport over centimeterscale distances through a network of conductive fibers embedded in the periplasm. Understanding the charge injection mechanism in cable bacteria is essential to form a complete picture of their long-distance charge transport, and a crucial step for their application in bio-based electronics. To this aim, we fabricated ”crosses” of two filaments, either native bacteria or extracted fiber skeletons, placed one on top of each other. By probing charge transport both through single cables and in cross-cable configurations, i.e., with current flowing from one filament to the other, it is possible to isolate the charge injection contribution. The results indicate that charge transfer between two contacting fibers is possible, albeit with increased resistance. We characterized the crosses at different temperatures, from 300 down to 50 K, observing thermally activated Arrhenius behavior both for single cables and crossconduction.The corresponding activation energy for cable-to-cable transport ranged from 15 to 40 meV, slightly smaller than that of individual cable bacteria filaments. We conclude that charge injection into the fibers must rely on the same mechanism of charge transport along the fibers. A structural model of the fibers is proposed in which the conductive channels are embedded in a protein matrix but can locally reach the surface of the fibers, where they establish electrical contact with the external environment.
DOI: 10.5061/dryad.stqjq2c6t
title: Migration direction in a songbird explained by two loci

description: Migratory routes and remote wintering quarters in birds are often species
 and even population specific. It has been known for decades that songbirds
 mainly migrate solitarily and that the migration direction is genetically
 controlled. Yet, the underlying genetic mechanisms remain unknown. To
 investigate the genetic basis of migration direction, we track genotyped
 willow warblers Phylloscopus trochilus from a migratory divide in Sweden,
 where South-West migrating and South-East migrating subspecies form a
 hybrid swarm. We find that migration direction follows a dominant
 inheritance pattern with epistatic interaction between the two loci
 explaining 74% of variation. Consequently, most hybrids migrate similarly
 to one of the parental subspecies and therefore do not suffer from the
 cost of following an inferior, intermediate route. This has significant
 implications for understanding the selection processes that maintain
 narrow migratory divides.
description: We deployed geolocators across Sweden, retrevied the loggers from
 the birds that returne3d and used R package geolight to proces raw light
 data.
DOI: 10.5281/zenodo.18347037
title: GLORiA: Fish Farm Escape Identification Dataset

description: This repository contains version 1.0 of the GLORiA dataset, designed for training and evaluating computer vision models for the identification of fish farm escapees, particularly those resulting from aquaculture cage failures during sea storms.

Escaped fish are identified based on visual appearance differences observed under controlled laboratory conditions, in comparison with farmed and wild specimens. The dataset includes images from three origin categories:



C – Fish raised in captivity (aquaculture)

E – Escaped fish

S – Wild fish captured at sea


For each category, images are provided for three commercially relevant Mediterranean species:



Mediterranean sea bream (Sparus aurata)

European sea bass (Dicentrarchus labrax)

Meagre (Argyrosomus regius)


The dataset is organized into three main folders:



High-resolution laboratory images (Pending Update)Original images captured under controlled laboratory conditions.

Preprocessed laboratory images (224×224) (main dataset folder)Cropped and resized images centered on the fish body, intended for direct use in deep learning pipelines.

Market imagesImages acquired in real-world market conditions, enabling evaluation under more realistic and challenging visual scenarios.


In addition, the repository includes two PDF documents providing expert-guided morphological descriptions to help distinguish between Sparus aurata and Dicentrarchus labrax. These documents are intended as reference material to support both human interpretation and the design of domain-aware visual models.

All 224×224 images were generated from the original high-resolution laboratory images using the provided Python preprocessing scripts, which perform fish-centered cropping and resizing.

 

This dataset extends the dataset "The GLORiA2 fish farm escapes identification dataset"

Zenodo record: 10.5281/zenodo.7082807

AcknowledgementsThe study was funded by the project “GLObal change Resilience in Aquaculture-TOOls for Long-term Sustainability (GLORiA-TOOLS),” supported by the Bio-diversity Foundation of the Spanish Ministry for the Ecological Transition and Demographic Challenge through the Pleamar Program and co-financed by the European Maritime, Fisheries and Aquaculture Fund (EMFAF).
DOI: 10.5061/dryad.2v6wwpzsk
title: Body mass and triglycerides predict departure of free-living nomadic pine siskins

description: 1. Facultative migrations are observed across vertebrate taxa, include
 irruptive and nomadic movements, and occur in response to ephemeral and
 unpredictably variable resources. While the physiology underlying
 seasonal, obligate migrations is thoroughly studied, much less is known
 about the physiological mechanisms of facultative movements. We test two
 hypotheses in a free-living, nomadic bird, the pine siskin (Spinus pinus).
 2. The Prepare Hypothesis predicts that, like obligate migrants, siskins
 increase fuel stores to prepare for migratory movements and elevations of
 baseline corticosterone (CORT) support departure. The Escape Hypothesis
 predicts that siskins do not prepare for departure, body condition
 declines as food availability declines, and stress-related levels of CORT
 induce escape from resource-poor areas. 3. Under the controlled lab
 conditions of previous studies, food restriction induces declines in body
 condition and increases in CORT and locomotor activity, supporting the
 Escape Hypothesis. This study evaluates the ecological relevance of these
 captive findings by testing the Prepare and Escape Hypotheses in the field
 for the first time. 4. During two fall field seasons, we radio-tagged
 siskins and tracked their local movements using handheld and automated
 telemetry. We assess how body condition and CORT relate to feeding
 behavior (estimated via plasma triglycerides (TRIG)), space use, and
 departure. 5. We do not find support for either the Prepare or Escape
 Hypothesis, but rather observe an intermediate pattern. Birds with higher
 TRIG, and therefore greater food intake, are more likely to depart. Birds
 in poor condition stay longer near the field site; however, above a
 threshold body mass, body condition does not predict departure. 6. These
 findings suggest moderate energy stores are necessary for departure but
 movement decisions depend on other factors among birds with sufficient
 fuel. Siskin movements are physiologically distinct from both obligate and
 fugitive movements, and we discuss how food availability and body
 condition interact to drive different types of movement.
description: See manuscript for details: DeSimone, JG, Domschot, BS, Fylling,
 MA, Blake, WM, and Breuner, CW. 2022. Body mass and triglycerides predict
 departure of free-living nomadic pine siskins. Functional Ecology.
 Accepted.
description: See READme file for details
DOI: 10.5061/dryad.r2280gbh5
title: Mutualistic coevolution and community diversity favor persistence in metacommunities under environmental changes

description: Linking local to regional ecological and evolutionary processes is key to
 understand the response of Earth's biodiversity to environmental
 changes. Here we integrate evolution and mutualistic coevolution in a
 model of metacommunity dynamics to understand how coevolution can shape
 species distribution and persistence in landscapes varying in space and
 time. Using simulations, we show that coevolution and species richness can
 synergistically shape distribution patterns by increasing colonization and
 reducing extinction of populations in metacommunities. Although
 conflicting selective pressures emerging from mutualisms may increase
 mismatches with the local environment and the rate of local extinctions,
 coevolution increases trait matching among mutualists at the landscape
 scale, counteracting local maladaptation and favoring colonization and
 range expansions. Our results show that by facilitating colonization,
 coevolution can also buffer the effects of environmental changes,
 preventing species extinctions and the collapse of metacommunities. Our
 findings reveal the mechanisms whereby coevolution can favor persistence
 under environmental changes and highlight that these positive effects are
 greater in more diverse systems that retain landscape connectivity.
description: The dataset consists of the dataset resulting from numerical
 simulations, code and scripts to perform the model numerical simulations
 for the manuscript <em>Mutualistic coevolution and community
 diversity favor persistence in metacommunities under environmental
 changes.</em>
description: For usage instructions, please refer to the README file.