cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.g6f47
title: Data from: Hybrid sterility locus on Chromosome X controls meiotic recombination rate in mouse

description: Meiotic recombination safeguards proper segregation of homologous
 chromosomes into gametes, affects genetic variation within species, and
 contributes to meiotic chromosome recognition, pairing and synapsis. The
 Prdm9 gene has a dual role, it controls meiotic recombination by
 determining the genomic position of crossover hotspots and, in infertile
 hybrids of house mouse subspecies Mus m. musculus (Mmm) and Mus m.
 domesticus (Mmd), it further functions as the major hybrid sterility gene.
 In the latter role Prdm9 interacts with the hybrid sterility X 2 (Hstx2)
 genomic locus on Chromosome X (Chr X) by a still unknown mechanism. Here
 we investigated the meiotic recombination rate at the genome-wide level
 and its possible relation to hybrid sterility. Using immunofluorescence
 microscopy we quantified the foci of MLH1 DNA mismatch repair protein, the
 cytological counterparts of reciprocal crossovers, in a panel of
 inter-subspecific chromosome substitution strains. Two autosomes, Chr 7
 and Chr 11, significantly modified the meiotic recombination rate, yet the
 strongest modifier, designated meiotic recombination 1, Meir1, emerged in
 the 4.7 Mb Hstx2 genomic locus on Chr X. The male-limited transgressive
 effect of Meir1 on recombination rate parallels the male-limited
 transgressive role of Hstx2 in hybrid male sterility. Thus, both genetic
 factors, the Prdm9 gene and the Hstx2/Meir1 genomic locus, indicate a link
 between meiotic recombination and hybrid sterility. A strong
 female-specific modifier of meiotic recombination rate with the effect
 opposite to Meir1 was localized on Chr X, distally to Meir1. Mapping Meir1
 to a narrow candidate interval on Chr X is an important first step towards
 positional cloning of the respective gene(s) responsible for variation in
 the global recombination rate between closely related mouse subspecies.
description: Balcova - raw
 dataThe file structure is
 the same for all of .csv files. Each column represents one individiual
 mouse of the genotype stated in the header. Each cell of the column
 represents MLH1 or RAD51/DMC1 (according to the file name) count of
 analyzed cell of the given mouse. Strain abbreviation: D# is B6.PWD-Chr#;
 D7F1 is B6.PWD-Chr7 x B6 F1 The data were analyzed in R 3.2.2 and using
 its packages as is declared in Materials and Methods of the published
 paper.data_DRYAD.zip
DOI: 10.5061/dryad.mv02k
title: Data from: Exact Bayesian inference for animal movement in continuous time

description: It is natural to regard most animal movement as a continuous-time process,
 generally observed at discrete times. Most existing statistical methods
 for movement data ignore this; the remainder mostly use discrete-time
 approximations, the statistical properties of which have not been widely
 studied, or are limited to special cases. We aim to facilitate wider use
 of continuous-time modelling for realistic problems. We develop novel
 methodology which allows exact Bayesian statistical analysis for a rich
 class of movement models with behavioural switching in continuous time,
 without any need for time discretization error. We represent the times of
 changes in behaviour as forming a thinned Poisson process, allowing exact
 simulation and Markov chain Monte Carlo inference. The methodology applies
 to data that are regular or irregular in time, with or without missing
 values. We apply these methods to GPS data from two animals, a fisher
 (Pekania [Martes] pennanti) and a wild boar (Sus scrofa), using models
 with both spatial and temporal heterogeneity. We are able to identify and
 describe differences in movement behaviour across habitats and over time.
 Our methods allow exact fitting of realistically complex movement models,
 incorporating environmental information. They also provide an essential
 point of reference for evaluating other existing and future approximate
 methods for continuous-time inference.
description: GPS locations for an
 adult female wild boarSequence of locations
 for an adult female wild boar fitted with a GPS collar. Values are times
 in minutes and co-ordinates in metres (from an arbitrary origin). Data are
 extracted from the study described in Quy, R. J., Massei, G., Lambert, M.
 S., Coats, J., Miller, L. A., and Cowan, D. P. (2014) Effects of a GnRH
 vaccine on the movement and activity of free-living wild boar (Sus
 scrofa), Wildlife Research 41, 185-193.WildBoarMEE.txt
DOI: 10.5061/dryad.2gt86
title: Data from: Patterns of genetic differentiation at MHC class I genes and microsatellites identify conservation units in the giant panda

description: Background: Evaluating patterns of genetic variation is important to
 identify conservation units (i.e., evolutionarily significant units
 [ESUs], management units [MUs], and adaptive units [AUs]) in endangered
 species. While neutral markers could be used to infer population history,
 their application in the estimation of adaptive variation is limited. The
 capacity to adapt to various environments is vital for the long-term
 survival of endangered species. Hence, analysis of adaptive loci, such as
 the major histocompatibility complex (MHC) genes, is critical for
 conservation genetics studies. Here, we investigated 4 classical MHC class
 I genes (Aime-C, Aime-F, Aime-I, and Aime-L) and 8 microsatellites to
 infer patterns of genetic variation in the giant panda (Ailuropoda
 melanoleuca) and to further define conservation units. Results: Overall,
 we identified 24 haplotypes (9 for Aime-C, 1 for Aime-F, 7 for Aime-I, and
 7 for Aime-L) from 218 individuals obtained from 6 populations of giant
 panda. We found that the Xiaoxiangling population had the highest genetic
 variation at microsatellites among the 6 giant panda populations and
 higher genetic variation at Aime-MHC class I genes than other larger
 populations (Qinling, Qionglai, and Minshan populations). Differentiation
 index (FST)-based phylogenetic and Bayesian clustering analyses for
 Aime-MHC-I and microsatellite loci both supported that most populations
 were highly differentiated. The Qinling population was the most
 genetically differentiated. Conclusions: The giant panda showed a
 relatively higher level of genetic diversity at MHC class I genes compared
 with endangered felids. Using all of the loci, we found that the 6 giant
 panda populations fell into 2 ESUs: Qinling and non-Qinling populations.
 We defined 3 MUs based on microsatellites: Qinling, Minshan-Qionglai, and
 Daxiangling-Xiaoxiangling-Liangshan. We also recommended 3 possible AUs
 based on MHC loci: Qinling, Minshan-Qionglai, and
 Daxiangling-Xiaoxiangling-Liangshan. Furthermore, we recommend that a
 captive breeding program be considered for the Qinling panda population.
description: Microsatellite data in 6
 wild giant panda populationsCollected from six
 mountain ranges
DOI: 10.5061/dryad.1fc37c3r
title: Data from: Multiplicity of infection does not accelerate infectivity evolution of viral parasites in laboratory microcosms

description: Coinfection with multiple parasite genotypes (multiplicity of infection)
 creates within-host competition and opportunities for parasite
 recombination, and is therefore predicted to be important for both
 parasite and host evolution. We tested for a difference in the infectivity
 of viral parasites (lytic phage Φ2) and resistance of their bacterial
 hosts (Pseudomonas fluorescens SBW25) under both high and low multiplicity
 of infection (MOI) during coevolution in laboratory microcosms. Results
 show that MOI has no effect on infectivity and resistance evolution during
 coevolution over approximately 80 generations of host growth, and this is
 true when the experiment is initiated with wild-type viruses and hosts, or
 with viruses and hosts that have already been coevolving for ~330
 generations. This suggests that MOI does not have a net effect of
 accelerating parasite adaptation to hosts through recombination, or
 retarding adaptation to hosts through between-parasite conflict in this
 system.
description: MOI_data_T0-12Infectivity and resistance data from coevolving communities of phage and bacteria over 12 experimental transfers. Infectivity and resistance measured using a pairwise design as described in the paper; sympatric infectivity and sympatric resistance measured against hosts and phages from the same community at the same time point.MOI_data_T50-62Infectivity and resistance data from coevolving communities at high and low MOI during transfers 50-62. Phage infectivity and bacterial resistance measured using a pairwise design as described in the paper. Sympatric infectivity and sympatric resistance measured against hosts and phages from the same community at the same time point.
DOI: 10.5061/dryad.mq725
title: Data from: The unexpected mating system of the androdioecious barnacle Chelonibia testudinaria (Linnaeus, 1758)

description: Androdioecy was first described by Darwin in his seminal work on barnacle
 diversity; he identified males and hermaphrodites in the same reproductive
 population. Today, we realize that many androdioecious plants and animals
 share astonishing similarities, particularly with regard to their
 evolutionary history and mating system. Notably, these species were
 ancestrally dioecious, and their mating system has the following
 characteristics: hermaphrodites self-fertilize frequently, males are more
 successful in large mating groups, and males have a mating advantage. A
 male mating advantage makes androdioecy more likely to persist over
 evolutionary times. Androdioecious barnacles, however, appear to persist
 as an outlier with a different evolutionary trajectory: they originate
 from hermaphroditic species. Although sexual systems of androdioecious
 barnacles are known, no information on the mating system of androdioecious
 barnacles is available. This study assessed the mating system of the
 androdioecious barnacle Chelonibia testudinaria. In contrast to other
 androdioecious species, C. testudinaria does not self-fertilize, males do
 not have a mating advantage over hermaphrodites, and the average mating
 group is quite small, averaging only three individuals. Mating success is
 increased by proximity to the mate and penis length. Taken together, the
 mating system of C. testudinaria is unusual in comparison with other
 androdioecious plants and animals, and the lack of a male mating advantage
 suggests that the mating system alone does not provide an explanation for
 the maintenance of androdioecy in this species. Instead, we propose that
 sex-specific life history equalizes male and hermaphroditic overall
 fitness.
description: Information to potential
 mating groups used to characterize mating system of C.
 testudinariaTab-delimited file.
 Column headers are described and explained in the ReadMe
 file.DataDryad_Table.csv
DOI: 10.5061/dryad.8405j
title: Data from: Species-specific patterns of nonapeptide brain gene expression relative to pair-bonding behaviour in grouping and non-grouping cichlids

description: Comparative studies have revealed that vasopressin-oxytocin pathways are
 associated with both pair bonding and grouping behaviour. However, the
 relationship between pair bonding and grouping behaviourremains unclear.In
 this study,our aim was to identify whether two species that differ in
 grouping behaviourdisplay a corresponding difference in their pair bonds,
 and in the underlying vasopressin-oxytocinhormonal pathways. Using two
 species of cichlid fishes, the highly social Neolamprologuspulcher and the
 non-social Telmatochromis temporalis, we measuredproximity of pairs during
 pair bond formation, and then measured social behaviors (proximity,
 aggression, submission,affiliation)and brain gene expression of isotocin
 and arginine vasotocin (the teleost homologues of oxytocin and
 vasopressin, respectively), as well as their receptors, after a temporary
 separation and subsequent reunion of the bonded pairs. Pairs of the social
 species spent more time in close proximity relative to the non-social
 species. Rates of aggression increased in both species following the
 separation and reunion treatment, relative to controls that were not
 separated.Overall, whole brain expression of isotocin was higher in the
 social species relative to the non-social species, and correlated with
 proximity, submission, and affiliation, but only in the social species.
 Our results suggest that both a social and a non-social cichlid species
 have similar behavioural responses to a temporary separation from a mate,
 and we found no differencein the brain gene expression of measured
 hormones and receptors based on our separation-reunion treatment. However,
 our results highlight the importance of isotocin in mediating submissive
 and affiliativebehaviourin cichlid fishes, and demonstrate thatisotocinhas
 species-specific correlations with socially relevantbehaviours.
description: Cichlid pair bonding IT
 AVT dataRT-qPCR values and
 behavioral scores
DOI: 10.5281/zenodo.17103694
title: Integrated CNT–Co Honeycomb Metamaterial Platform for Broadband RF Energy Harvesting and Self-Powered Electronics

description: The rapid deployment of renewable energy systems is reshaping global power infrastructure, yet life-cycle analyses reveal persistent carbon emissions associated with their manufacture and deployment. In parallel, the proliferation of wireless networks has saturated modern environments with ambient radiofrequency (RF) fields, which are increasingly recognized both as a pollutant and as an untapped energy resource. Here we report a 3D-printed CNT-Co metamaterial antenna that converts far-field RF radiation into usable electrical power with broadband efficiency. By integrating carbon nanotubes and cobalt nanoparticles into a UV-curable resin, we achieved strong conduction and magnetic losses that, when combined with a honeycomb metamaterial architecture, delivered absorption efficiencies up to 99.9% across dual frequency bands (3.35-4.59 GHz and 9.45-16.57 GHz). The system outperformed a commercial Wi-Fi antenna by factors of up to three under low input powers, maintained stable operation in ambient environments, and powered practical devices including LEDs, medical sensors, and wireless trackers. These results establish CNT-Co metamaterial antennas as a scalable platform for harvesting energy from the electromagnetic environment, opening new pathways toward sustainable, battery-free electronics.
DOI: 10.5061/dryad.jr82b
title: Data from: Hibernation alters the diversity and composition of mucosa-associated bacteria while enhancing antimicrobial defense in the gut of 13-lined ground squirrels

description: The gut microbiota plays important roles in animal nutrition and health.
 This relationship is particularly dynamic in hibernating mammals where
 fasting drives the gut community to rely on host-derived nutrients instead
 of exogenous substrates. We used 16S rRNA pyrosequencing and cecal tissue
 protein analysis to investigate the effects of hibernation on the
 mucosa-associated bacterial microbiota and host responses in 13-lined
 ground squirrels. The mucosal microbiota was less diverse in winter
 hibernators than in actively feeding spring and summer squirrels. UniFrac
 analysis revealed distinct summer and late winter microbiota clusters,
 while spring and early winter clusters overlapped slightly, consistent
 with their transitional structures. Communities in all seasons were
 dominated by Firmicutes and Bacteroidetes, with lesser contributions from
 Proteobacteria, Verrucomicrobia, Tenericutes and Actinobacteria.
 Hibernators had lower relative abundances of Firmicutes, which include
 genera that prefer plant polysaccharides, and higher abundances of
 Bacteroidetes and Verrucomicrobia, some of which can survive solely on
 host-derived mucins. A core mucosal assemblage of nine operational
 taxonomic units shared among all individuals was identified with an
 average total sequence abundance of 60.2%. This core community, together
 with moderate shifts in specific taxa, indicates that the mucosal
 microbiota remains relatively stable over the annual cycle yet responds to
 substrate changes while potentially serving as a pool for “seeding” the
 microbiota once exogenous substrates return in spring. Relative to summer,
 hibernation reduced cecal crypt length and increased MUC2 expression in
 early winter and spring. Hibernation also decreased cecal TLR4 and
 increased TLR5 expression, suggesting a protective response that minimizes
 inflammation.
description: MEC-14-0588MUC2.csvMUC2 Protein ExpressionMEC-14-0588TLR4.csvTLR4 Protein ExpressionMEC-14-0588TLR5.csvTLR5 Protein ExpressionMEC-14-0588Histology.csvCecal HistologyMEC-14-0588 Cecal Histology.csv
DOI: 10.5281/zenodo.17103693
title: Integrated CNT–Co Honeycomb Metamaterial Platform for Broadband RF Energy Harvesting and Self-Powered Electronics

description: The rapid deployment of renewable energy systems is reshaping global power infrastructure, yet life-cycle analyses reveal persistent carbon emissions associated with their manufacture and deployment. In parallel, the proliferation of wireless networks has saturated modern environments with ambient radiofrequency (RF) fields, which are increasingly recognized both as a pollutant and as an untapped energy resource. Here we report a 3D-printed CNT-Co metamaterial antenna that converts far-field RF radiation into usable electrical power with broadband efficiency. By integrating carbon nanotubes and cobalt nanoparticles into a UV-curable resin, we achieved strong conduction and magnetic losses that, when combined with a honeycomb metamaterial architecture, delivered absorption efficiencies up to 99.9% across dual frequency bands (3.35-4.59 GHz and 9.45-16.57 GHz). The system outperformed a commercial Wi-Fi antenna by factors of up to three under low input powers, maintained stable operation in ambient environments, and powered practical devices including LEDs, medical sensors, and wireless trackers. These results establish CNT-Co metamaterial antennas as a scalable platform for harvesting energy from the electromagnetic environment, opening new pathways toward sustainable, battery-free electronics.
DOI: 10.5061/dryad.80mq6
title: Data from: Deadly competition and life-saving predation: the potential for alternative stable states in a stage-structured predator–prey system

description: Predators often undergo complete ontogenetic diet shifts, engaging in
 resource competition with species that become their prey during later
 developmental stages. Theory posits that this mix of stage-specific
 competition and predation, termed life-history intraguild predation
 (LHIGP), can lead to alternative stable states. In one state, prey exclude
 predators through competition (i.e. juvenile competitive bottleneck),
 while in the alternative, adult predators control prey density to limit
 competition and foster coexistence. Nevertheless, the interactions leading
 to these states have not been demonstrated in an empirical LHIGP system.
 To address this gap, we manipulated densities of cannibalistic adult
 cyclopoid copepods (Mesocyclops edax) and their cladoceran prey (Daphnia
 pulex) in a response-surface design and measured the maturation and
 survival of juvenile copepods (nauplii). We found that Daphnia reduced and
 even precluded both nauplii maturation and survival through depletion of a
 shared food resource. As predicted, adult copepods enhanced nauplii
 maturation and survival through Daphnia consumption, yet this positive
 effect was dependent on the relative abundance of Daphnia as well as the
 absolute density of adult copepods. Adult copepods reduced nauplii
 survival through cannibalism at low Daphnia densities and at the highest
 copepod density. This work demonstrates that predation can relax a strong
 juvenile competitive bottleneck in freshwater zooplankton, though
 cannibalism can reduce predator recruitment. Thus, our results highlight a
 key role for cannibalism in LHIGP dynamics and provide evidence for the
 interactions that drive alternative stable states in such systems.
description: Toscano_et_al_final_densitiesInitial and final densities of all animals used in experiments. Experiment was run in 3 temporal blocks.Toscano_et_al_copepod_reproduction_dataAdult copepod egg production data. Experiment was run in 3 temporal blocks.
DOI: 10.5061/dryad.62sm982
title: Data from: Sex chromosome turnovers and genetic drift: a simulation study

description: The recent advances of new genomic technologies has enabled to identify
 and characterize sex chromosomes in an increasing number of non-model
 species, revealing that many plants and animals undergo frequent sex
 chromosome turnovers. What evolutionary forces drive these turnovers
 remains poorly understood, but it was recently proposed that drift might
 play a more important role than generally assumed. We analyzed the
 dynamics of different types of turnovers using individual-based
 simulations, and show that when mediated by genetic drift, turnovers are
 usually easier to achieve than substitutions at neutral markers, but that
 their dynamics and relative likelihoods vary with the type of the resident
 and emergent sex chromosome system (XY and/or ZW), and the dominance
 relationships among the sex-determining factors. Focusing on turnovers
 driven by epistatically dominant mutations, we find that drift-mediated
 turnovers that preserve the heterogamety pattern are 2-4x more likely than
 those along which the heterogametic sex changes. This ratio nevertheless
 decreases along with effective population size, and can even reverse in
 case of extreme polygyny. This can be attributed to a “drift-induced”
 selective force, known to influence transitions between male and female
 heterogamety, but which according to our study, does not affect turnovers
 that preserve the heterogametic sex.
description: simulation_filesThis is the Dryad data submission corresponding to "Sex chromosome turnovers and genetic drift: a simulation study" by Saunders, Neuenschwander and Perrin, Journal of Evolutionary Biology It contains two folders: * a folder with the input files for the simulations with information on all parameters. * a folder with the allelic value files, necessary to specify the type to turnover studied in a simulation (or set of simulations). All informations and download links for quantiNemo executable and corresponding manual can be found at http://www2.unil.ch/popgen/softwares/quantinemo