cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.g79cnp5m9
title: Exploring whole-genome duplicate gene retention with complex genetic interaction analysis

description: Whole-genome duplication has played a central role in genome evolution of
 many organisms, including the human genome. Most duplicated genes are
 eliminated and factors that influence the retention of persisting
 duplicates remain poorly understood. Here, we describe a systematic
 complex genetic interaction analysis with yeast paralogs derived from the
 whole-genome duplication event. Mapping digenic interactions for a
 deletion mutant of each paralog and trigenic interactions for the double
 mutant provides insight into their roles and a quantitative measure of
 their functional redundancy. Trigenic interaction analysis distinguishes
 two classes of paralogs, a more functionally divergent subset and another
 that retained more functional overlap. Gene feature analysis and modeling
 suggest that evolutionary trajectories of duplicated genes are dictated by
 combined functional and structural entanglement factors.
DOI: 10.5061/dryad.7pvmcvdpv
title: Data for: Angels in disguise: Sympatric hybridization in the marine angelfishes is widespread and occurs between deeply divergent lineages

description: Hybridization is not uncommon in marine environments where physical
 barriers are attenuated. Research conducted on hybridization in coral
 reefs has grown rapidly, but the majority of studies have focused on
 parapatric species along biogeographical suture zones. Comparatively
 little attention has been directed towards sympatric hybridization on
 coral reefs, despite the large amount of biogeographical overlap that
 occurs among coral reef species. Here we investigate if the propensity for
 hybridization along suture zones represents a general phenomenon among
 coral reef fishes, by focusing on the marine angelfishes (Pomacanthidae).
 Although hybridization has been reported for this family, it has not been
 thoroughly surveyed, with more recent hybridization studies focusing
 instead on closely related species from a population genetics perspective.
 Here we provide a comprehensive survey of hybridization among the
 angelfishes, characterize the upper limits of genetic divergences between
 hybridizing species, and investigate the occurrence of sympatric
 hybridization within this group. Our results indicate that the marine
 angelfishes are among the groups of coral reef fishes with the highest
 incidences of hybridization, not only between sympatric species, but also
 between deeply divergent, sympatric lineages.
DOI: 10.5061/dryad.9ghx3ffdk
title: Representation and complementarity of the long-term coral monitoring on the Great Barrier Reef

description: Effective environmental management hinges on efficient and targeted
 monitoring, which in turn should adapt to increasing disturbance regimes
 that now characterize most ecosystems. Habitats and biodiversity of
 Australia’s Great Barrier Reef (GBR) - the world’s largest coral reef
 ecosystem - are in declining condition, prompting a review of the
 effectiveness of existing coral monitoring programs. Applying a regional
 model of coral cover (i.e., the most widely used proxy for coral reef
 condition globally) within major benthic communities, we assess the
 representation and complementarity of existing long-term coral reef
 monitoring programs on the GBR. We show that existing monitoring has
 captured up to 45% of the environmental diversity on the GBR, while some
 geographic areas (including major hotspots of cyclone activity over the
 last 30 years) have remained unmonitored. Further, we identified
 complementary groups of reefs characterized by similar benthic community
 composition and similar coral cover trajectories since 1996. The mosaic of
 their distribution across the GBR reflects spatial variation in the
 cumulative impact of multiple acute disturbances, as well as spatial
 gradients in coral recovery potential. Representation and complementarity,
 in combination with other performance assessment criteria, can inform the
 cost-effective design and stratification of future surveys. Based on these
 results, we formulate recommendations to assist with the design of future
 long-term coral reef monitoring programs.
description: This dataset contains all high-resolution environmental and
 disturbance data as previously published in Matthews et al. (2019), as
 well as model outputs from the coral cover developed by Mellin et al.
 (2019). Both were re-analyzed in the present study to determine the
 representation and complementarity of the long-term coral monitoring, as
 described in the corresponding Ecological Applications
 manuscript. Matthews S, Mellin C, MacNeil MA, Heron S,
 Puotinen ML, Pratchett M. High-resolution characterization of the abiotic
 environment and disturbances regimes on the Great Barrier Reef; 1985-2017.
 Ecology. 2019;100(2):e02574. Mellin C, Matthews S,
 Anthony KRN, Brown SC, Caley MJ, Johns K, et al. Spatial resilience of the
 Great Barrier Reef under cumulative disturbance impacts. Global Change
 Biology. 2019;25(7):2431-45.
description: The RIMREP_ms.R script contains all analyses described in Mellin
 et al. 2020 Ecological Applications based on these data (also embedded in
 the RIMREP_ms.RData data file for convenience).
DOI: 10.5061/dryad.1g1jwstrn
title: The genus Cycas may have diversified from Indochina and occupied its current ranges through vicariance and dispersal events

description: Biogeographically, cycads were once widely distributed but the extant
 cycads are restricted to tropical and subtropical regions. They originated
 ~ 300 Ma and re-diversified recently around 12 Ma, with the genus Cycas
 being the most rapidly diversified and largely distributed lineage.
 However, the forces that shaped the diversification and biogeography of
 the genus remain to be fully understood. Here, we first retrieved and used
 DNA sequences from Genbank (nuclear: PHYP, RPB1, HZP, AC3, F3H, SAMS and
 GTP; chloroplasts: plant barcode trnH-psbA, trnL-trnF, trnS-trnG and
 psbM-trnD) to assemble a complete dated phylogeny of Cycas. Then, we
 employed the Bayesian Binary Method to reconstruct the historical
 biogeography of the extant Cycas and finally, using the Bayesian approach
 for diversification analysis, we explored the evolutionary events that
 might have shaped the rapid diversification and large distribution of
 Cycas across the Pacific Islands. Our analysis pointed to Indo-China as
 the origin of the genus, which may have dispersed firstly across the
 Pacific Islands during the late Miocene aided by multiple excursions of
 sea levels and the development of a key innovation, i.e. a spongy endocarp
 particularly in the seeds of the subsection Rumphiae. The colonization of
 South China, which was thought to be the origin of the genus, may have
 occurred more recently aided by both dispersal and vicariance events.
 However, no significant shifts in the evolutionary events (speciation,
 extinction, mass extinction) that shaped the diversity of the genus were
 observed. Overall, our study re-clarifies the historical biogeography and
 the evolutionary forces that shaped the current diversity of the genus
 Cycas.
description: This data was retrieved from GenBank/EBI.
DOI: 10.15468/dl.8mtys2
title: Occurrence Download

description: A dataset containing 837 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Adenanthera pavonina",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 837 records from 141 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002209-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.4tmpg4f62
title: Towards ecologically valid biomarkers:real-life gait assessment in cerebellar ataxia

description: OBJECTIVES: With disease-modifying drugs on the horizon for degenerative
 ataxias, ecologically valid motor biomarkers are highly warranted. In this
 observational study, we aimed to unravel and validate markers of ataxic
 gait in real life by using wearable sensors.   METHODS: We
 assessed gait characteristics of 43 patients with degenerative cerebellar
 disease (SARA:9.4±3.9) compared to 35 controls by 3 body-worn inertial
 sensors in three conditions: (1) laboratory-based walking; (2) supervised
 free walking; (3) real-life walking during everyday living (subgroup
 n=21). Movement analysis focussed on measures of spatio-temporal step
 variability and movement smoothness. RESULTS: A set of gait variability
 measures was identified which allowed to consistently identify ataxic gait
 changes in all three conditions. Lateral step deviation and a compound
 measure of step length categorized patients against controls with a
 discrimination accuracy of 0.86 in real life. Both were highly correlated
 with clinical ataxia severity (effect size ρ=0.76). These measures allowed
 detecting group differences even for patients who differed only 1 point in
 the clinical SARAposture&gait subscore, with highest effect sizes
 for real-life walking (d=0.67). CONCLUSIONS: We identified measures of
 ataxic gait that allowed not only to capture the gait variability inherent
 in ataxic gait in real life, but also demonstrate  high
 sensitivity to small differences in disease severity - with highest effect
 sizes in real-life walking. They thus represent promising candidates for
 motor markers for natural history and treatment trials in ecologically
 valid contexts.
description: Walking movements were recorded in three different conditions,
 namely: (i) <b>L</b>ab-<b>b</b>ased
 <b>w</b>alking (LBW condition): walking was constrained by a
 specified walking distance of 50m in a specific quiet non-public indoor
 floor within an institutional setting (hospital), and supervised by a
 study assessor watching the walking performance; patients were instructed
 to walk normally at a self-selected speed;  (ii)
 <b>S</b>upervised <b>F</b>ree
 <b>W</b>alking (SFW condition): unconstrained walking in
 public indoor floor and outdoor spaces  on an institutional (hospital)
 compound where subjects were free to choose and change the floors and
 indoor and outdoor spaces where they wished to walk (complete walking
 time: 5 minutes) with all spaces being open to public, but still
 supervised by a study assessor watching subject’s walking performance;
   (iii)  <b>R</b>eal-<b>L</b>ife
 <b>W</b>alking (RLW condition): unconstrained walking during
 subjects’ everyday living where subjects where free to move how they
 wanted and were used to in their  individual daily life, without
 supervision by any study personnel (total recording time: 4-6 hours).
DOI: 10.5061/dryad.rxwdbrv4v
title: Data from: Insect herbivory in novel Quercus ilex L. forests: the role of landscape attributes, forest composition and host traits

description: Context Understanding the intrinsic and extrinsic drivers of herbivory in
 novel expanding forests is essential to envisage their role for
 biodiversity conservation. Aims: To analyze the effects of landscape
 attributes, forest composition, genetic relatedness, ontogeny and leaf
 traits on insect herbivory in novel Q. ilex forest stands. Methods: In 15
 forest patches, we examined effects of patch size and connectivity, forest
 composition, and tree height, specific leaf area (SLA) and nitrogen
 content on herbivory. In 3 forest patches, we assessed effects of tree
 genetic relatedness, ontogeny and spatial distribution. Results: Herbivory
 was lower in pine-oak than in mixed-oak forests owing to the shorter tree
 height in the former with no effects of patch size or connectivity.
 Herbivory increased with SLA whereas nitrogen content had no effect.
 Within patches, herbivory differed among genetic clusters and was reduced
 in saplings growing near mature oaks and individuals near the forest
 edge.  Conclusion We illustrate the strong context and scale
 dependence of tree-herbivore interactions that renders predictions for
 dynamic systems such as novel oak forests extremely challenging. It
 implies, however, that the structural heterogeneity of such unmanaged
 forests allows their function as stepping stones for insect herbivore
 diversity in fragmented landscapes.
description: The data corresponds to two studies (study I and Study II) on the
 influence of landscape characteristics, genetic relatedness, ontogeny and
 intra-patch position of the host in herbivory damage in Quercus ilex
 individuals.
description: See the Metadata file
DOI: 10.15468/dl.und687
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lestidiops affinis",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2015"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002208-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.v6wwpzgrt
title: Generalists versus specialists in fluctuating environments: a bet‐hedging perspective

description: Bet‐hedging evolves in fluctuating environments because long‐term genotype
 success is determined by geometric (rather than arithmetic) mean fitness
 across generations. Diversifying bet‐hedging produces different specialist
 offspring, whereas conservative bet‐hedging produces similar generalist
 offspring. However, many fields, such as behavioral ecology and thermal
 physiology, typically consider specialist versus generalist strategies
 only in terms of maximizing arithmetic mean fitness benefits to
 individuals. Here we model how environmental variability affects optimal
 amounts of phenotypic variation within and among individuals to maximise
 genotype fitness, and we disentangle the effects of individual‐level
 optimization and genotype‐level bet‐hedging by comparing long‐term
 arithmetic versus geometric mean fitness. For traits with additive fitness
 effects within lifetimes (e.g. foraging‐related traits), genotypes of
 similar generalists or diversified specialists perform equally well.
 However, if fitness effects are multiplicative within lifetimes (e.g.
 sequential survival probabilities), generalist individuals are always
 favored. In this case, geometric mean fitness optimization requires even
 more within‐individual phenotypic variation than does arithmetic mean
 fitness, causing individuals to be more generalist than required to simply
 maximize their own expected fitness. In contrast to previous results in
 the bet‐hedging literature, this generalist conservative bet‐hedging
 effect is always favored over diversifying bet‐hedging. These results link
 the evolution of behavioral and ecological specialization with earlier
 models of bet‐hedging, and we apply our framework to a range of natural
 phenomena from habitat choice to host specificity in parasites.
description: This is the R code used for the fitness calculations and
 producing the figures in the paper and supplementary material.
description: The code should contain the necessary information to reproduce
 the results from the paper. If anything is unclear, please do not hesitate
 to contact Thomas Haaland (corresponding author).
DOI: 10.5061/dryad.08kprr4zr
title: Evolution in interacting species alters predator life history traits, behavior and morphology in experimental microbial communities

description: Predator-prey interactions are key for the dynamics of many ecosystems. An
 increasing body of evidence suggests that rapid evolution and co-evolution
 can alter these interactions, with important ecological implications, by
 acting on traits determining fitness, including reproduction,
 anti-predatory defense and foraging efficiency. However, most studies to
 date have focused only on evolution in the prey species, and the predator
 traits in (co-)evolving systems remain poorly understood. Here we
 investigated changes in predator traits after ~600 generations in a
 predator-prey (ciliate-bacteria) evolutionary experiment. Predators
 independently evolved on seven different prey species, allowing
 generalization of the predator’s evolutionary response. We used highly
 resolved automated image analysis to quantify changes in predator life
 history, morphology and behavior. Consistent with previous studies, we
 found that prey evolution impaired growth of the predator, although the
 effect depended on the prey species. In contrast, predator evolution did
 not cause a clear increase in predator growth when feeding on ancestral
 prey. However, predator evolution affected morphology and behavior,
 increasing size, speed and directionality of movement, which have all been
 linked to higher prey search efficiency. These results show that in
 (co-)evolving systems, predator adaptation can occur in traits relevant to
 foraging efficiency without translating into an increased ability of the
 predator to grow on the ancestral prey type.
description: Protist population densities, morphological traits and movement
 traits have been collected through video-analysis of samples filmed under
 a Leica M165FC stereomicroscope with circular lighting and mounted
 Hamamatsu Orca Flash 4.0 camera. The videos were analysed using the BEMOVI
 R-package. Bacterial densities were measured using Flow
 cytometry using a BD AccuriTM C6 flow cytometer, as well as though optical
 density measurements at 600 nm using a SpectroMax 190 plate
 reader. For details on the protocols for protist and
 bacterial measurements, see associated protocol.
DOI: 10.5061/dryad.4xgxd255p
title: The Pantophysin gene and its relationship with survival in Atlantic cod

description: Distinction between highly migratory Northeast Arctic cod and stationary
 Norwegian Coastal cod represents an important management issue. They
 overlap on the same spawning grounds where they are harvested, but display
 highly different abundences. This necessitates alternative management
 strategies. The bi-allelic genetic marker, pantophysin (Pan I), has been
 widely used as a diagnostic marker to discriminate between these two
 stocks. However, it has been proposed that this locus, or another gene(s)
 on chromosome 1 where it is located, may be under strong divergent
 selection between these two stocks. In order to address this, we compared
 relative survival rates between different Pan I genotypes in common garden
 pedigree-controlled experiments conducted in a temperature-controlled
 laboratory facility, and mesocosms. We found no evidence of departure from
 the expected 1:2:1 mendelian ratio for any of the three genotypes during
 the egg stage, while both the 6 and 12 °C temperature regimes in the
 laboratory experiment weakly favoured the Pan IAA genotype thereafter. No
 difference was observed between genotype survival in the mesocosm
 experiments. These results demonstrate that there are no clear advantages
 of certain Pan I genotypes under the experimental conditions observed.
description: Data from biological experiment with fish from larval to juvenile
 stage. Data contains grouping code, genotype for Pantophysin, length and
 weight.
DOI: 10.5061/dryad.vmcvdncpr
title: Maintenance of hindgut reabsorption during cold exposure is a key adaptation for Drosophila cold tolerance

description: Maintaining extracellular osmotic and ionic homeostasis is crucial for
 organismal function.  In insects, hemolymph volume and ion
 content is regulated by the secretory Malpighian tubules and reabsorptive
 hindgut. When exposed to stressful cold, homeostasis is gradually
 disrupted, characterized by a debilitating increase in extracellular K+
 concentration (hyperkalemia). Accordingly, studies have found a strong
 link between the species-specific cold tolerance and their ability to
 maintain ion and water homeostasis at low temperature. This is also true
 for drosophilids where inter- and intra-specific differences in cold
 tolerance are linked to the secretory capacity of Malpighian tubules.
 There is, however, little information on the reabsorptive capacity of the
 hindgut in Drosophila. To address this, we developed a novel method that
 permits continued measurements of hindgut ion and fluid reabsorption in
 Drosophila. We demonstrate that this assay is temporally stable (~ 2
 hours) and responsive to cAMP stimulation and pharmacological intervention
 in accordance with the current insect hindgut reabsorption model. We then
 investigated how cold acclimation or cold adaptation affected hindgut
 reabsorption at benign (24°C) and low temperature (3°C). Cold
 tolerant Drosophila species and
 cold-acclimated D. melanogaster maintain superior fluid
 and Na+ reabsorption at low temperature. Furthermore, cold
 adaptation and acclimation caused a relative reduction in
 K+ reabsorption at low temperature. These characteristic
 responses of cold adaptation/ acclimation will promote maintenance of ion
 and water homeostasis at low temperature. Our study of hindgut function
 therefore provides evidence to suggest that adaptations in osmoregulatory
 capacity of insects are critical for their ability to tolerate
 cold.
DOI: 10.5281/zenodo.18394500
title: Jeu de données pour TD d'initiation aux SIG avec QGIS

description: Ce jeu de données est utilisé pour s'initier aux Systèmes d'Information Géographiques (SIG) en utilisant le logiciel QGIS. Il est destiné à un public de grand débutant et permet de découvrir les principales fonctionnalités d'un SIG en passant par la découverte des formats de fichiers dédiés et des systèmes de coordonnées de référence. Le support PDF accompagne le dossier. Le support peut se lire accompagné de la documentation en ligne Les Briques de Géomatique.

Le support peut également être téléchargé à ce lien : https://hal.science/hal-05480695v1

Le support peut être cité comme ceci : Paul Passy, Poullo Baidy Ba, Vincent Viel, Mathilde Resch, Mélody Dumont, et Théophile Piau. Initiation aux SIG - Travaux Dirigés. Licence. Initiation à la télédétection et aux SIG, Paris, France. 2026, pp.73
DOI: 10.5281/zenodo.18394499
title: Jeu de données pour TD d'initiation aux SIG avec QGIS

description: Ce jeu de données est utilisé pour s'initier aux Systèmes d'Information Géographiques (SIG) en utilisant le logiciel QGIS. Il est destiné à un public de grand débutant et permet de découvrir les principales fonctionnalités d'un SIG en passant par la découverte des formats de fichiers dédiés et des systèmes de coordonnées de référence. Le support PDF accompagne le dossier. Le support peut se lire accompagné de la documentation en ligne Les Briques de Géomatique.

Le support peut également être téléchargé à ce lien : https://hal.science/hal-05480695v1

Le support peut être cité comme ceci : Paul Passy, Poullo Baidy Ba, Vincent Viel, Mathilde Resch, Mélody Dumont, et Théophile Piau. Initiation aux SIG - Travaux Dirigés. Licence. Initiation à la télédétection et aux SIG, Paris, France. 2026, pp.73