cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.70bs72s
title: Data from: Exaggerated heterochiasmy in a fish with sex-linked male coloration polymorphisms

description: It is often stated that polymorphisms for mutations affecting fitness of
 males and females in opposite directions [sexually antagonistic (SA)
 polymorphisms] are the main selective force for the evolution of
 recombination suppression between sex chromosomes. However, empirical
 evidence to discriminate between different hypotheses is difficult to
 obtain. We report genetic mapping results in laboratory-raised families of
 the guppy (Poecilia reticulata), a sexually dimorphic fish with SA
 polymorphisms for male coloration genes, mostly on the sex chromosomes.
 Comparison of the genetic and physical maps shows that crossovers are
 distributed very differently in the two sexes (heterochiasmy); in male
 meiosis, they are restricted to the termini of all four chromosomes
 studied, including chromosome 12, which carries the sex-determining locus.
 Genome resequencing of male and female guppies from a population also
 indicates sex linkage of variants across almost the entire chromosome 12.
 More than 90% of the chromosome carrying the male-determining locus is
 therefore transmitted largely through the male lineage. A lack of
 heterochiasmy in a related fish species suggests that it originated
 recently in the lineage leading to the guppy. Our findings do not support
 the hypothesis that suppressed recombination evolved in response to the
 presence of SA polymorphisms. Instead, a low frequency of recombination on
 a chromosome that carries a male-determining locus and has not undergone
 genetic degeneration has probably facilitated the establishment of
 male-beneficial coloration polymorphisms.
description: genetic
 dataGenotypes of molecular
 markers in guppies F1 familiesgenetic_data_dryad.xlsxmapping summary resultsSummary results for all families usedmapping_summary_results.xlsx
DOI: 10.5061/dryad.390js8n
title: Data from: Out of the Mediterranean? post-glacial colonisation pathways varied among cold-water coral species

description: Aim. To infer cold-water corals' post-glacial phylogeography and
 assess the role of Mediterranean Sea glacial refugia as origins for the
 recolonisation of the northeastern Atlantic Ocean. Location. Northeastern
 Atlantic Ocean and Mediterranean Sea. Taxon. Lophelia pertusa, Madrepora
 oculata. Methods. We sampled cold-water corals using remotely operated
 vehicles and one sediment core for coral and sediment dating. We
 characterized spatial genetic patterns (microsatellites and a nuclear gene
 fragment) using networks, clustering and measures of genetic
 differentiation. Results. Inferences from microsatellite and sequence data
 were congruent, and showed a contrast between the two cold-water coral
 species. Populations of L. pertusa present a dominant pioneer haplotype,
 local haplotype radiations and a majority of endemic variation in lower
 latitudes. M. oculata populations are differentiated across the
 northeastern Atlantic and genetic lineages are poorly admixed even among
 neighbouring sites. Conclusions. Our study shows contrasting post-glacial
 colonisation pathways for two key habitat-forming species in the deep-sea.
 The cold-water coral L. pertusa has likely undertaken a long-range
 (post-glacial) recolonisation of the northeastern Atlantic directly from
 refugia located along southern Europe (Mediterranean Sea or Gulf of
 Cadiz). In contrast, the stronger genetic differentiation of M. oculata
 populations mirrors the effects of long-term isolation in multiple
 refugia. We suggest that the distinct and genetically divergent, refugial
 populations initiated the post-glacial recolonisation of the northeastern
 Atlantic margins, leading to a secondary contact in the northern range and
 reaching higher latitudes much later, in the late Holocene. This study
 highlights the need to disentangle the influences of present-day dispersal
 and evolutionary processes on the distribution of genetic polymorphisms,
 to unravel the influence of past and future environmental changes on the
 connectivity of cosmopolitan deep-sea ecosystems associated with
 cold-water corals.
description: lophelia_8loci_13popsThe samples originate from numerous sampling campaigns, in the Mediterranean Sea, Northeast Atlantic (Bay of Biscay, Irish Sea and South of Iceland). 13 populations in total. Samples were genotyped with 8 microsatelite markers (D3, C44, A105, C91, C61, ,C120, C142, A5). The geographical coordinates are provided in columns X,Y.madrepora_genalexThe samples originate from numerous sampling campaigns, in the Mediterranean Sea, Northeast Atlantic (Azores, Bay of Biscay, Irish Sea and South of Iceland). 13 populations in total. Samples were genotyped with 6 microsatelite markers (c016, g028, g025, g016, C7, C6). The geographical coordinates are provided in columns X,Y.
DOI: 10.5061/dryad.h6980d8
title: Data from: Male-mediated prenatal loss: functions and mechanisms

description: Sexually selected infanticide has been the subject of intense empirical
 and theoretical study for decades; a related phenomenon, male-mediated
 prenatal loss, has received much less attention in evolutionary studies.
 Male-mediated prenatal loss occurs when inseminated or pregnant females
 terminate reproductive effort following exposure to a non-sire male,
 either through implantation failure or pregnancy termination.
 Male-mediated prenatal loss encompasses two sub-phenomena: sexually
 selected feticide and the Bruce effect. In this review, we lay out a
 framework that explains the relationship between feticide and the Bruce
 effect and describes what is currently known about the proximate and
 ultimate mechanisms involved in each. Using a simple model, we demonstrate
 that male-mediated prenatal loss can provide greater reproductive benefits
 to males than infanticide. We therefore suggest that, compared to
 infanticide, male-mediated prenatal loss may be more prevalent in
 mammalian species and may have played a greater role in their social
 evolution than has previously been documented.
description: Species demonstrating
 male-mediated prenatal lossThis table lists all
 species in which male-mediated prenatal loss has been documented and
 includes appropriate references.Dryad
 Submit.docx
DOI: 10.5061/dryad.57pv818
title: Data from: Thalamocortical synapses in the cat visual system in vivo are weak and unreliable

description: The thalamocortical synapse of the visual system has been central to our
 understanding of sensory computations in the cortex. Although we have a
 fair understanding of the functional properties of the pre and
 post-synaptic populations, little is known about their synaptic
 properties, particularly in vivo. We used simultaneous recordings in LGN
 and V1 in cat in vivo to characterize the dynamic properties of
 thalamocortical synaptic transmission in monosynaptically connected LGN-V1
 neurons. We found that thalamocortical synapses in vivo are unreliable,
 highly variable and exhibit short-term plasticity. Using biologically
 constrained models, we found that variable and unreliable synapses serve
 to increase cortical firing by means of increasing membrane fluctuations,
 similar to high conductance states. Thus, synaptic variability and
 unreliability, rather than acting as system noise, do serve a
 computational function. Our characterization of LGN-V1 synaptic properties
 constrains existing mathematical models, and mechanistic hypotheses, of a
 fundamental circuit in computational neuroscience.
description: Sarvestani et al.
 DataFiles
DOI: 10.5061/dryad.jj174p1
title: Data from: Behavioural patterns of vocal greeting production in four primate species

description: Social animals have evolved a range of signals to avoid aggressive and
 facilitate affiliative interactions. Vocal behaviour is especially
 important in this respect with many species, including various primates,
 producing acoustically distinct ‘greeting calls’ when two individuals
 approach each other. While the ultimate function of greeting calls has
 been explored in several species, little effort has been made to
 understand the mechanisms of this behaviour across species. The aim of
 this study was to explore how differences in individual features
 (individual dominance rank), dyadic relationships (dominance distance and
 social bond strength), and audience composition (presence of high-ranking
 or strongly bonded individuals in proximity), determined vocal greeting
 production during approaches between two individuals in the philopatric
 sex of four primate species: female olive baboons (Papio anubis), male
 chimpanzees (Pan troglodytes), female sooty mangabeys (Cercocebus atys),
 and female vervet monkeys (Chlorocebus pygerythrus). We found that female
 vervet monkeys did not produce greeting calls, while in the other three
 species, low-ranking individuals were more likely to call than
 high-ranking ones. The effects of dyadic dominance relationships differed
 in species-specific ways, with calling being positively associated with
 rank distance between two individuals in baboons and chimpanzees, but
 negatively in mangabeys. In none of the tested species did we find strong
 evidence for an effect of dyadic affiliative relationships or audience on
 call production. These results likely reflect deeper evolutionary layers
 of species-specific peculiarities in social style. We conclude that a
 comparative approach to investigate vocal behaviour has the potential to
 not only better understand the mechanisms mediating social signal
 production, but also to shed light on their evolutionary trajectories.
description: Data
 setData
 setcomparativegreetings-1.txtR codeR codecomparativegreetings-analysis(1).R
DOI: 10.5061/dryad.cg10jn5
title: Data from: Local cod (Gadus morhua) revealed by egg surveys and population genetic analysis after longstanding depletion on the Swedish Skagerrak coast

description: Dramatic and persistent reductions in Atlantic cod (Gadus morhua) are
 common in many coastal areas. While offshore cod stocks still were
 abundant and productive, the Swedish west coast showed signs of
 diminishing adult cod abundance at the beginning of the 1980s, where the
 local cod component was considered to be extirpated. To survey the present
 cod spawning activity and stock composition, we initiated egg trawling
 over two consecutive years (203 hauls in total) in combination with
 population genetic analyses (425 individually genotyped eggs). Here, we
 provide evidence of cod spawning at the Swedish Skagerrak coast,
 suggesting recolonization or that local cod has recovered from a nearly
 depleted state. Early stage eggs were found inside fjords too far to have
 been transported by oceanic drift from offshore spawning areas. The cod
 eggs were genetically similar in early to late life-stages and cluster
 mainly with the local adult cod, indicating that eggs and adults belong to
 the same genetic unit. The cod eggs were genetically differentiated from
 adult North Sea cod, and, to a lesser degree, also from the Kattegat and
 Öresund cod, i.e. indicating a possible recovery of local coastal stock.
 The patterns of the genetic structure in the inshore areas are, however,
 difficult to fully disentangle, as Atlantic cod in the North Sea-Skagerrak
 area seem to be a mixture of co-existing forms: local cod completing their
 entire life cycle in fjords and sheltered areas, and oceanic populations
 showing homing behaviours. The egg abundances are considerably lower
 compared with what is found in similar studies along the Norwegian
 Skagerrak coast. Nevertheless, the discovery of locally spawning cod along
 the Swedish west coast—although at low biomasses—is an encouraging finding
 that highlights the needs for endurance in protective measures and of
 detailed surveys to secure intraspecific biodiversity and ecosystem
 services.
description: Svedäng et al 2018 Cod
 samplesGenotype
 list.Svedäng et al 2018 genotype
 data.txt
DOI: 10.5061/dryad.1m7n014
title: Reconciling supertramps, great speciators and relict species with the taxon cycle stages of a large island radiation (Aves: Campephagidae)

description: Aim: The taxon cycle concept provides a geographically explicit and
 testable set of hypotheses for exploring the evolutionary processes
 underlying the distribution of species in space and time. Here, we test
 taxon cycle predictions within a large avian island radiation, the core
 Campephagidae and explicitly integrate the concepts of ‘supertramps’,
 ‘great speciators’ and relictualization. Location: The Indo-Pacific,
 Australia, Asia and Africa. Taxon: Corvoid passerine birds. Methods: We
 constructed a new time-calibrated molecular phylogeny of the core
 Campephagidae (cuckoo-shrikes, cicadabirds and trillers) using Bayesian
 phylogenetic methods. Ancestral range estimation methods and
 diversification rate analyses were used to explore the dispersal and
 diversification history of the group. We used an extensive dataset on wing
 morphology and range distributions to test for correlations between
 evolutionary age of species and dispersal capacity, diversification and
 distribution, while accounting for phylogenetic non-independence. Results:
 The core Campephagidae represents an ecologically homogeneous radiation
 distributed across the Indo-Pacific, Australia, South-East Asia and
 Africa. Its members represent a continuum of dispersal abilities; some
 species are widespread and undifferentiated (‘supertramps’) or show strong
 differentiation of local populations (‘great speciators’), and a few are
 endemic to single islands (relicts). We show that older species relative
 to younger species inhabit fewer and larger islands at higher elevations.
 The level of intraspecific variation measured as the number of subspecies
 also decreases with species age, and is highest in ‘great speciators’ with
 intermediate levels of dispersal abilities (as per hand-wing index). Main
 conclusions: Based on trait correlations with species age, we infer phases
 of range expansion and contraction over millions of years (taxon cycles),
 within a single monophyletic group of birds. These observations
 demonstrate reconciliation of the concepts of ‘supertramps’, ‘great
 speciators’ and relictual paleo-endemics within the temporal stages of the
 taxon cycle.
description: Campephagidae
 alignmentSee details in Table
 S1.1 in Appendix S1 in the online Supporting
 Information.Pepke_etal_2019_Campephagidae_align.PAUCampephagidae alignment txtSee details in Table S1.1 in Appendix S1 in the online Supporting Information.Pepke_etal_2019_Campephagidae_align.PAU.txt
DOI: 10.5061/dryad.3bd5rr4
title: Data from: How to survive a glaciation: the challenge of estimating biologically realistic potential distributions under freezing conditions

description: Correlative ecological niche models are increasingly used to estimate
 potential distributions during the Last Glacial Maximum (LGM) for
 biogeographical research. In the case of
 presence-background/pseudoabsences techniques, cold environments that are
 poorly represented in existing geography can complicate the process of
 model calibration and transfer into more extreme cold environments that
 were very common during the LGM (non-analog conditions). This may lead to
 biologically unrealistic estimations. Using one cold-adapted North
 American mammal, we explore a real scenario to better understand the
 effect of restricting the range of environmental conditions over which
 niche models are calibrated and then transferred to LGM conditions. We
 performed two sets of experiments in MAXENT: (1) we calibrated models in
 the context of only present‐day climate conditions, which is the most
 common practice, and compared predictions under LGM conditions based on
 two extrapolation methods (clamping vs unconstrained); (2) we calibrated
 single models using both present‐day and LGM conditions as part of the
 same background in order to include more extreme environments in the model
 calibration. Our experiments led to dramatically different estimates of
 species’ potential distributions, showing notable differences with respect
 to latitudinal and elevational shifts during the LGM. Models calibrated
 using present‐day climates yielded biologically unrealistic estimations,
 suggesting that species survived in the glaciers during the LGM. Even more
 unrealistic estimations were achieved when clamping was enforced as the
 method to extrapolate. Models calibrated in the context of both modern and
 past climates reduced the required degree of extrapolation and allowed
 more realistic potential distributions, suggesting that the species
 avoided extremely cold conditions during the LGM. This study alerts to the
 possibility of obtaining implausible potential distributions during the
 LGM due to restricted background datasets and offers recommendations that
 should promote better strategies to estimate distributional changes during
 glaciations.
description: Raw data used in
 constructing ecological niche modelsThis excel file contains
 (sheet 1): the background points for Experiment 1; (sheet 2): the
 background points for Experiment 2; (sheet 3): the occurrence data for
 Ochotona princeps filtered at 10 km; (sheet 4): the occurrence data for
 Ochotona princeps filtered at 20 km; (sheet 5): the occurrence data for
 Ochotona princeps filtered at 30 kmRawData_GeorreferencesXY.xlsR code used to create ecological niche modelsThis code was used to filter occurrences data and tune models using spThin and ENMeval packages. It also was used to predict the geographic distributions across time using optimal settings.Rcode_Guevara&Leon-Paniagua2019.R
DOI: 10.5281/zenodo.18384044
title: Near Real Time Automatic Extraction of CME Properties From LASCO C2 Coronagraph Images Using Deep Learning

description: seeds_monthly_2023_2025_merged_process.txt is the CME catalog text produced by the SEEDS method. ours.txt is the CME catalog generated by our method. univ_all_CDAW_process.txt is the CDAW catalog, and comb_qkl_CACTUS_process.txt is the catalog produced by the CACTus method.

CDAW_matched_1.txt contains the catalog entries from CDAW that were matched with our detections, and ours_cdaw_matched_1.txt contains the corresponding entries from our catalog that match CDAW.

public_data_1.tar contains the processing outputs of our method for CMEs from 2023 to 2025, including segmentation, tracking, linear speed fitting, and the final exported catalog.
DOI: 10.5281/zenodo.18384043
title: Near Real Time Automatic Extraction of CME Properties From LASCO C2 Coronagraph Images Using Deep Learning

description: seeds_monthly_2023_2025_merged_process.txt is the CME catalog text produced by the SEEDS method. ours.txt is the CME catalog generated by our method. univ_all_CDAW_process.txt is the CDAW catalog, and comb_qkl_CACTUS_process.txt is the catalog produced by the CACTus method.

CDAW_matched_1.txt contains the catalog entries from CDAW that were matched with our detections, and ours_cdaw_matched_1.txt contains the corresponding entries from our catalog that match CDAW.

public_data_1.tar contains the processing outputs of our method for CMEs from 2023 to 2025, including segmentation, tracking, linear speed fitting, and the final exported catalog.
DOI: 10.5061/dryad.7q294p8
title: Data from: A novel biomechanical approach for animal behaviour recognition using accelerometers

description: Data from animal‐borne inertial sensors are widely used to investigate
 several aspects of an animal's life, such as energy expenditure,
 daily activity patterns and behaviour. Accelerometer data used in
 conjunction with machine learning algorithms have been the tool of choice
 for characterising animal behaviour. Although machine learning models
 perform reasonably well, they may not rely on meaningful features, nor
 lend themselves to physical interpretation of the classification rules.
 This lack of interpretability and control over classification outcomes is
 of particular concern where different behaviours have different frequency
 of occurrence and duration, as in most natural systems, and calls for the
 development of alternative methods. Biomechanical approaches to human
 activity classification could overcome these shortcomings, yet their full
 potential remains untapped for animal studies. We propose a general
 framework for behaviour recognition using accelerometers, and develop a
 hybrid model where (a) biomechanical features characterise movement
 dynamics, and (b) a node‐based hierarchical classification scheme employs
 simple machine learning algorithms at each node to find feature‐value
 thresholds separating different behaviours. Using triaxial accelerometer
 data collected on 10 wild Kalahari meerkats, and annotated video
 recordings of each individual as groundtruth, this hybrid model was
 validated in three scenarios: (a) when each behaviour was equally
 represented (EQDIST), (b) when naturally imbalanced datasets were
 considered (STRAT) and (c) when data from new individuals were considered
 (LOIO). A linear‐kernel Support Vector Machine at each node of our
 classification scheme yielded an overall accuracy of &gt;95% for each
 scenario. Our hybrid approach had a 2.7% better average overall accuracy
 than top‐performing classical machine learning approaches. Further, we
 showed that not all models with high overall accuracy returned accurate
 behaviour‐specific performance, and good performance during EQDIST did not
 always generalise to STRAT and LOIO. Our hybrid model took advantage of
 robust machine learning algorithms for automatically estimating decision
 boundaries between behavioural classes. This not only achieved high
 classification performance but also permitted biomechanical interpretation
 of classification outcomes. The framework presented here provides the
 flexibility to adapt models to required levels of behavioural resolution,
 and has the potential to facilitate meaningful model sharing between
 studies.
description: Labelled3DaccDataFeature MatricesFeatureMatrices_Chakravarty_et_al_2019_MEE.rar
DOI: 10.5061/dryad.62dt334
title: Data from: A split sex ratio in solitary and social nests of a facultatively social bee

description: A classic prediction of kin selection theory is that a mixed population of
 social and solitary nests of haplodiploid insects should exhibit a split
 sex ratio among offspring: female biased in social nests, male biased in
 solitary nests. Here we provide the first evidence of a solitary-social
 split sex ratio, using the sweat bee Megalopta genalis (Halictidae). Data
 from 2502 offspring collected from naturally occurring nests across six
 years spanning the range of the M. genalis reproductive season show that
 despite significant yearly and seasonal variation, the offspring sex ratio
 of social nests is consistently more female biased than in solitary nests.
 This suggests that split sex ratios may facilitate the evolutionary
 origins of cooperation based on reproductive altruism via kin selection.
description: Data from: A split sex
 ratio in solitary and social nests of a facultatively social
 beeData from: A split sex
 ratio in solitary and social nests of a facultatively social
 beesex
 ratio data for upload to dryad.xlsx