cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.g69c080
title: Data from: The cost of infection: Argulus foliaceus and its impact on the swimming performance of the three-spined stickleback (Gasterosteus aculeatus)

description: For fish, there can be multiple consequences of parasitic infections,
 including the physical impacts on swimming and the pathological costs of
 infection. This study utilised the three-spined stickleback (Gasterosteus
 aculeatus) and the ectoparasitic fish louse, Argulus foliaceus, to assess
 both physical (including form drag and mass) and pathological effects of
 infection. Both sustained (prolonged swimming within an open channel
 flume) and burst (C-start) swimming performance were measured on
 individual fish before (Trials 1-2) and after infection (Trials 3-5).
 Experimental infection occurred shortly before the third trial, when the
 physical impacts of infection could be separated from any subsequent
 pathology as transmission of adult parasites causes instantaneous drag
 effects prior to observable pathology. Despite the relatively large size
 of the parasite and corresponding increase in hydrodynamic drag for the
 host, there were no observable physical effects of infection on either
 sustained or burst host swimming. In contrast, parasite-induced pathology
 reduced swimming performance across both tests. All sticklebacks displayed
 a preference for flow refugia, swimming in low velocity regions of the
 flume, and this preference increased with both flow rate and infection
 time. This study suggests that even with large, physically demanding
 parasites their induced pathology is of greater concern than direct
 physical impact.
description: Upstream
 swimmingRecorded data for
 upstream swimming across various flow trailsUpstream.csvPushBackRecorded data for when fish were pushed backwards by flow across various flow trailsStationHoldingRecorded data for station holding across various flow trailsDownstreamRecorded data for downstream swimming across various flow trailsc-startc-start raw data across all trialsRaw data sustained swimmingThe raw data for sustained swimming across trials and flow speedsRaw data.csvproucrit(2)Proportional time fish spent swimming, including projected area valuesProportianal analysisTime fish spent in various areas of the flume as a proportion
DOI: 10.5061/dryad.80f66
title: Data from: Nuclear internal transcribed spacer-1 as a sensitive genetic marker for environmental DNA studies in common carp Cyprinus carpio

description: The recently developed environmental DNA (eDNA) analysis has been used to
 estimate the distribution of aquatic vertebrates by using mitochondrial
 DNA (mtDNA) as a genetic marker. However, mtDNA markers have certain
 drawbacks such as variable copy number and maternal inheritance. In this
 study, we investigated the potential of using nuclear DNA (ncDNA) as a
 more reliable genetic marker for eDNA analysis by using common carp
 (Cyprinus carpio). We measured the copy numbers of cytochrome b (CytB)
 gene region of mtDNA and internal transcribed spacer 1 (ITS1) region of
 ribosomal DNA of ncDNA in various carp tissues and then compared the
 detectability of these markers in eDNA samples. In the DNA extracted from
 the brain and gill tissues and intestinal contents, CytB was detected at
 95.1 ± 10.7 (mean ± 1 standard error), 29.7 ± 1.59 and 24.0 ± 4.33 copies
 per cell, respectively, and ITS1 was detected at 1760 ± 343, 2880 ± 503
 and 1910 ± 352 copies per cell, respectively. In the eDNA samples from
 mesocosm, pond and lake water, the copy numbers of ITS1 were about 160,
 300 and 150 times higher than those of CytB, respectively. The minimum
 volume of pond water required for quantification was 33 and 100 mL for
 ITS1 and CytB, respectively. These results suggested that ITS1 is a more
 sensitive genetic marker for eDNA studies of C. carpio.
description: qPCR_resultsThree Excel files for the results of qPCRs. Each file corresponds to one of three figures.Minamoto_MER.zip
DOI: 10.5281/zenodo.18136451
title: SNAC-DB: Structural NANOBODY® (VHH) and Antibody (VH-VL) Complex Database

description: ***Please use the latest version. Access to earlier version can be requested directly from the authors.***

Welcome to the SNAC-DB — a comprehensive and curated resource of antibody and NANOBODY® VHH structures designed to support computational modeling, machine learning, structural biology research, and available in ML-ready formats. This release includes dataset curated by using the SNAC-DB pipeline (https://github.com/Sanofi-Public/SNAC-DB) on protein structures sourced from the RCSB PDB (https://www.rcsb.org/), as well as a benchmarking dataset for evaluation.

At the moment, we have processed all PDBs released up until 31 December, 2025. 

Paper: https://www.researchgate.net/publication/393900649_SNAC-DB_The_Hitchhiker's_Guide_to_Building_Better_Predictive_Models_of_Antibody_NANOBODY_R_VHH-Antigen_Complexes
DOI: 10.5061/dryad.bt211nm
title: Data from: Determining diet from faeces: selection of metabarcoding primers for the insectivore Pyrenean desman (Galemys pyrenaicus)

description: Molecular techniques allow non-invasive dietary studies from faeces,
 providing an invaluable tool to unveil ecological requirements of
 endangered or elusive species. They contribute to progress on important
 issues such as genomics, population genetics, dietary studies or
 reproductive analyses, essential knowledge for conservation biology.
 Nevertheless, these techniques require general methods to be tailored to
 the specific research objectives, as well as to substrate- and
 species-specific constraints. In this pilot study we test a range of
 available primers to optimise diet analysis from metabarcoding of faeces
 of a generalist aquatic insectivore, the endangered Pyrenean desman
 (Galemys pyrenaicus, É. Geoffroy Saint-Hilaire, 1811, Talpidae), as a step
 to improve the knowledge of the conservation biology of this species.
 Twenty-four faeces were collected in the field, DNA was extracted from
 them, and fragments of the standard barcode region (COI) were PCR
 amplified by using five primer sets (Brandon-Mong, Gillet, Leray, Meusnier
 and Zeale). PCR outputs were sequenced on the Illumina MiSeq platform,
 sequences were processed, clustered into OTUs (Operational Taxonomic
 Units) using UPARSE algorithm and BLASTed against the NCBI database.
 Although all primer sets successfully amplified their target fragments,
 they differed considerably in the amounts of sequence reads, rough OTUs,
 and taxonomically assigned OTUs. Primer sets consistently identified a few
 abundant prey taxa, probably representing the staple food of the Pyrenean
 desman. However, they differed in the less common prey groups. Overall,
 the combination of Gillet and Zeale primer sets were most cost-effective
 to identify the widest taxonomic range of prey as well as the desman
 itself, which could be further improved stepwise by adding sequentially
 the outputs of Leray, Brandon-Mong and Meusnier primers. These results are
 relevant for the conservation biology of this endangered species as they
 allow a better characterization of its food and habitat requirements.
description: OTU
 tableOTU table built from
 amplicons of DNA extracted from faeces of Galemys pyrenaicus to identify
 its diet. Table includes OTUs, read numbers, sequences and species
 assignations by Blast with query cover values, pairwise identities and
 e-values.Esnaola.et.al_PLoS.ONE.xlsx
DOI: 10.5061/dryad.14mt7
title: Data from: Quantifying apart what belongs together: a multi-state species distribution modeling framework for species using distinct habitats

description: 1. Species distribution models (SDMs) have been used to inform scientists
 and conservationists about the status and change of occurrence patterns in
 threatened species. Many mobile species use multiple functionally distinct
 habitats, and cannot occupy one habitat type without the other being
 within a reachable distance. For such species, classical applications of
 SDMs might lead to erroneous representations of habitat suitability, as
 the complex relationships between predictors are lost when merging
 occurrence information across multiple habitats. To better account for the
 spatial arrangement of complementary—yet mandatory—habitat types, it is
 important to implement modeling strategies that partition occurrence
 information according to habitat use in a spatial context. Here, we
 address this issue by introducing a multi-state SDM framework. 2. The
 multi-state SDM framework stratifies occurrences according to the temporal
 or behavioral use of distinct habitat types, referred to as “states.”
 Multiple SDMs are then run for each state and statistical thresholds of
 presence are used to combine these separate predictions. To identify
 suitable sites that account for distance between habitats, two optional
 modules are proposed where the thresholded output is aggregated and
 filtered by minimum area size, or through moving windows across maximum
 reachable distances. 3. We illustrate the full use of this framework by
 modeling the dynamic terrestrial breeding habitat preferences of the New
 Zealand sea lion (NZSL; Phocarctos hookeri), using Maxent and trialing
 both modules to identify suitable sites for possible recolonization. 4.
 The Maxent predictions showed excellent performance, and the multi-state
 SDM framework highlighted 36 to 77 potential suitable breeding sites in
 the study area. 5. This framework can be applied to inform management when
 defining habitat suitability for species with complex changes in habitat
 use. It accounts for temporal and behavioral changes in distribution,
 maintains the individuality of each partitioned SDM, and considers
 distance between distinct habitat types. It also yields one final,
 easy-to-understand output for stakeholders and managers.
description: NZ-Sea-Lion_Enderby_GPS_locations-2001-03This is an excel file that contains daily GPS locations of breeding branded New Zealand sea lion females that were obtained manually at the breeding aggregation on Enderby Island over the breeding period (Dec-March) for 2 years (for more details on methodology see Augé et al. 2009 DOI: 10.1163/15683909X427687). Tag is the brand number. Lat and Long are in NZGD2000.
DOI: 10.5061/dryad.84397
title: Data from: The role of bryophytes for tree seedling responses to winter climate change: implications for the stress gradient hypothesis

description: 1.When tree seedlings establish beyond the current tree line due to
 climate warming, they encounter existing vegetation, such as bryophytes
 that often dominate in arctic and alpine tundra. The stress gradient
 hypothesis (SGH) predicts that plant interactions in tundra become
 increasingly negative as climate warms and conditions become less harsh.
 However, for seedlings climate warming might not result in lower winter
 stress, if insulating snow cover is reduced. 2.We aimed to understand to
 if bryophytes facilitate seedling survival in a changing winter climate
 and if these effects of bryophytes on tree seedlings comply with the SGH
 along elevational gradients under contrasting snow conditions. 3.In the
 Swedish subarctic, we transplanted intact bryophyte cores covered by each
 of three bryophyte species and bryophyte-free control soil from above the
 tree line to two field common-garden sites, representing current and
 future tree line air temperature conditions (i.e. current tree line
 elevation and a lower, warmer, elevation below the tree line). We planted
 seedlings of Betula pubescens and Pinus sylvestris into these cores and
 subjected them to experimental manipulation of snow cover during one
 winter. 4.In agreement with the SGH, milder conditions caused by increased
 snow cover enhanced the generally negative or neutral effects of
 bryophytes on seedlings immediately after winter. Further, survival of P.
 sylvestris seedlings after one full year was higher at lower elevation,
 especially when snow cover was thinner. However, in contrast with the SGH,
 impacts of bryophytes on over-winter survival of seedlings did not differ
 between elevations, and impacts on survival of B. pubescens seedlings
 after one year was more negative at lower elevation. Bryophyte species
 differed in their effect on seedling survival after winter, but these
 differences were not related to their insulating capacity. 5.Synthesis:
 Our study demonstrates that interactions from bryophytes can modify the
 impacts of winter climate change on tree seedlings, and vice versa. These
 responses do not always comply with SGH, but could ultimately have
 consequences for large-scale ecological processes such as tree-line
 shifts. These new insights need to be taken into account in predictions of
 plant species responses to climate change.
description: Seedling winter survival
 in 4 bryophyte treatment under different snow treatments and
 elevationsField experimental data
 of winter survival of transplanted seedlings. Experiment had two
 elevational sites to which bryophytes cores were transplanted. These were
 subjected to snow treatments(addition, control, reduction). Seedling were
 transplanted into bryophyte cores in at the end of 2013 growing season and
 survival was assessed in june and august 2014. See published article for
 full description of the experimental detailsData for Lett et
 al.xls
DOI: 10.5061/dryad.cv0tr
title: Data from: Components of reproductive isolation between Orchis mascula and O. pauciflora

description: Studies of the strength and nature of reproductive isolation (RI) between
 species can greatly contribute to our understanding of speciation.
 Although the role of RI in speciation is well recognized, there is a
 dearth of information on the contributions of different barriers between
 related plant species. Here, we estimated multiple components of RI
 between two Mediterranean orchid sister species (Orchis mascula and Orchis
 pauciflora), disentangling the strength and absolute contributions of
 seven different isolating mechanisms. Our survey includes one
 prepollination, two postpollination prezygotic (pollen–stigma
 incompatibility, conspecific pollen precedence), two intrinsic postzygotic
 (embryo mortality and hybrid sterility) and two extrinsic postzygotic
 (hybrid habitat differentiation and hybrid pollination) isolating
 mechanisms. We found strong RI between the investigated species, although
 none of the barriers were able to completely impede gene flow. Five
 isolating mechanisms contributed positively to the maintenance of species
 boundaries. Contrary to most surveys of isolating mechanisms, our data
 speak against a clear predominance of prepollination or of prezygotic
 barriers but confirm the emerging pattern of multiple barriers
 contributing to the maintenance of species integrity. These findings
 suggest an allopatric condition during early phases of species divergence.
 We discuss our data in the wider context of previous studies carried out
 in this orchid group by using a comparative approach.
description: Reproductive isolation
 dataData and formulas used
 for the calculation of the reproductive isolation
 indicesScopece et al. Reproductive
 isolation data.xls
DOI: 10.5061/dryad.n4709m8
title: Data from: Ancient plants with ancient fungi: liverworts associate with early-diverging arbuscular mycorrhizal fungi

description: Arbuscular mycorrhizas are widespread in land plants including liverworts,
 some of the closest living relatives of the first plants to colonise land
 500 MYA. Previous investigations reported near-exclusive colonisation of
 liverworts by the most recently evolved arbuscular mycorrhizal fungi, the
 Glomeraceae, indicating a recent acquisition from flowering plants at odds
 with the widely-held notion that arbuscular mycorrhizal-like associations
 in liverworts represent the ancestral symbiotic condition in land plants.
 We performed an analysis of symbiotic fungi in 674 globally-collected
 liverworts using molecular phylogenetics and electron microscopy. Here we
 show every order of arbuscular mycorrhizal fungi colonises early-diverging
 liverworts, with non-Glomeraceae being at least ten times more common than
 in flowering plants. Arbuscular mycorrhizal fungi in liverworts and other
 ancient plant lineages (hornworts, lycopods and ferns) were delimited into
 58 taxa and 36 singletons, of which at least 43 are novel and specific to
 liverworts. The discovery that early plant lineages are colonised by
 early-diverging fungi supports the hypothesis that arbuscular mycorrhizas
 are an ancestral symbiosis for all land plants.
description: Figure_1_alignmentAlignment of Glomeromycotina fungi sequences used to produce phylogenetic tree presented in Figure 1. Sequence alignment was performed using MUSCLE algorithms within MEGA7.Figure_1_treeMaximum likelihood phylogenetic tree of Glomeromycotina fungi that can be seen in Figure 1. Tree is in Newick format, having been produced in MEGA7 using the generalised time reversible model with invariant gamma rates and 1,000 bootstrap replicates.
DOI: 10.5061/dryad.q2hn2
title: Data from: Human children rely more on social information than chimpanzees

description: Human societies are characterized by more cultural diversity than
 chimpanzee communities. However, it is currently unclear what mechanism
 might be driving this difference. Since reliance on social information is
 a pivotal characteristic of culture, we investigated individual and social
 information reliance in children and chimpanzees. We repeatedly presented
 subjects with a reward-retrieval task on which they had collected
 conflicting individual and social information of equal accuracy in
 counterbalanced order. While both species relied mostly on their
 individual information, children but not chimpanzees searched for the
 reward at the socially demonstrated location more than at a random
 location. Moreover, only children used social information adaptively when
 individual knowledge on the location of the reward had not yet been
 obtained. These results support the interpretation that a heightened
 tendency to absorb social information may help explain why humans are more
 culturally diversified than chimpanzees.
description: Children's
 information preferencesChimpanzees'
 information preferencesCombined data children
 chimpanzees information preferences_for R
DOI: 10.5061/dryad.dg73kb6
title: Data from: High level of extrapair fertilizations in individual Tibetan azure-winged magpies and their adaptive responses

description: Extrapair fertilizations (EPFs) occur widely in socially monogamous birds
 and result in mixed parentage in the brood. The response of an individual
 to these EPFs of its social mate remains poorly investigated in terms of
 parental care for the mixed brood. We addressed this question in a
 cooperatively-breeding corvid, the azure-winged magpie Cyanopica cyana.
 Parentage analysis indicated that 45% of females and 37% of males engaged
 in EPFs. There were 49% of cooperative groups and 36% of bi-parental nests
 with extrapair paternity (EPP) offspring, and 22% of cooperative groups
 and 19% of bi-parental nests with extrapair maternity (EPM) offspring.
 Based on the identity of offspring, we classified adults into four types:
 EPP offspring fathers/mothers, EPM offspring fathers/mothers, cuckolded
 males/females, and faithful males/females. A comparison of provisioning
 rates among all four types of breeders showed that 1) EPM offspring
 fathers had the highest provisioning rate; 2) cuckolded males did not
 reduce parental care, compared to faithful males and EPP offspring
 fathers; and 3) females of different types did not differ in their
 provisioning rates. Our findings suggest that a combination of frequent
 opportunities, low costs of cuckoldry, and the benefits of establishing a
 cooperative neighbourhood can explain why EPFs occur frequently in the
 Tibetan population of azure-winged magpie.
description: data used in the paper
 10.1111-jav.01739
DOI: 10.5061/dryad.666sn
title: Data from: High genetic diversity in the offshore island populations of the tephritid fruit fly Bactrocera dorsalis

description: Background: Geographic isolation is an important factor that limit species
 dispersal and thereby affects genetic diversity. Because islands are often
 small and surrounded by a natural water barrier to dispersal, they
 generally form discrete isolated habitats. Therefore, islands may play a
 key role in the distribution of the genetic diversity of insects,
 including flies. Results: To characterize the genetic structure of island
 populations of Bactrocera dorsalis, we analyzed a dataset containing both
 microsatellite and mtDNA loci of B. dorsalis samples collected from six
 offshore islands in Southern China. The microsatellite data revealed a
 high level of genetic diversity among these six island populations based
 on observed heterozygosity (Ho), expected heterozygosity (HE), Nei’s
 standard genetic distance (D), genetic identity (I) and the percentage of
 polymorphic loci (PIC). These island populations had low F ST values (F ST
 = 0.04161), and only 4.16 % of the total genetic variation in the species
 was found on these islands, as determined by an analysis of molecular
 variance. Based on the mtDNA COI data, high nucleotide diversity (0.9655)
 and haplotype diversity (0.00680) were observed in all six island
 populations. F-statistics showed that the six island populations exhibited
 low or medium levels of genetic differentiation among some island
 populations. To investigate the population differentiation between the
 sampled locations, a factorial correspondence analysis and both the
 unweighted pair-group method with arithmetic mean and Bayesian clustering
 methods were used to analyze the microsatellite data. The results showed
 that Hebao Island, Weizhou Island and Dong’ao Island were grouped together
 in one clade. Another clade consisted of Shangchuan Island and Naozhou
 Island, and a final, separate clade contained only the Wailingding Island
 population. Phylogenetic analysis of the mtDNA COI sequences revealed that
 the populations on each of these six islands were closely related to
 different populations on mainland China. Conclusions: Our study suggests
 that these island populations have high genetic diversity, experience
 frequent gene flow and exhibit low or medium levels of genetic
 differentiation among some island populations. Therefore, the geographic
 isolation of the six islands does not appear to be a major dispersal
 barrier to B. dorsalis. Such knowledge is helpful for a better
 understanding of evolutionary processes of the species of island
 populations.
description: SSR Data of Bactocera
 dorsalisAll samples were
 collected from six island of South China, genotyped 120 individuals using
 8 microsatellite loci.COI sequences of six
 island populations of Bactocera dorsalisIdentified 120 COI
 sequences in six islands using mitochondria DNA.