cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.67891086
title: Data from: Sex at the origin: an Asian population of the rice blast fungus Magnaporthe oryzae reproduces sexually.

description: Sexual reproduction may be cryptic or facultative in fungi and therefore
 difficult to detect. Magnaporthe oryzae, which causes blast, the most
 damaging fungal disease of rice, is thought to originate from South-East
 Asia. It reproduces asexually in all rice-growing regions. Sexual
 reproduction has been suspected in limited areas of South-East Asia, but
 has never been demonstrated in contemporary populations. We characterized
 several M. oryzae populations worldwide both biologically and genetically,
 to identify candidate populations for sexual reproduction. The sexual
 cycle of M. oryzae requires two strains of opposite mating types, at least
 one of which is female-fertile, to come into contact. In one Chinese
 population, the two mating types were found to be present at similar
 frequencies and almost all strains were female-fertile. Compatible strains
 from this population completed the sexual cycle in vitro and produced
 viable progenies. Genotypic richness and linkage disequilibrium data also
 supported the existence of sexual reproduction in this population. We
 resampled this population the following year, and the data obtained
 confirmed the presence of all the biological and genetic characteristics
 of sexual reproduction. In particular, a considerable genetic reshuffling
 of alleles was observed between the two years. Computer simulations
 confirmed that the observed genetic characteristics were unlikely to have
 arisen in the absence of recombination. We therefore concluded that a
 contemporary population of M. oryzae, pathogenic on rice, reproduces
 sexually in natura in South-East Asia. Our findings provide evidence for
 the loss of sexual reproduction by a fungal plant pathogen outside its
 centre of origin.
description: Dataset Saleh et
 al
DOI: 10.5061/dryad.279n4
title: Data from: Gigantic lion, (Panthera leo), from the Pleistocene of Natodomeri, eastern Africa

description: The partial skull of a lion from Natodomeri, northwest Kenya is described.
 The Natodomeri sites are correlated with Member I of the Kibish Formation,
 dated to between 195 ka and ∼205 ka. The skull is remarkable for its very
 great size, equivalent to the largest cave lions (Panthera spelaea) of
 Pleistocene Eurasia and much larger than any previously known lion from
 Africa, living or fossil. We hypothesize that this individual represents a
 previously unknown population or subspecies of lion present in the late
 Middle and Late Pleistocene of eastern Africa rather than being an
 indication of climate-driven size increase in lions of that time. This
 raises questions regarding the extent of our understanding of the pattern
 and causes of lion evolution in the Late Pleistocene.
description: Natodomeri lion
 measurements SI_Manthi et alExcel file with
 measurements used in comparative analyses of this paper
DOI: 10.5061/dryad.5tm76
title: Data from: Leaf photosynthetic, economics and hydraulic traits are decoupled among genotypes of a widespread species of eucalypt grown under ambient and elevated CO2

description: Leaf economics and hydraulic traits strongly influence photosynthesis.
 While the level of coordination among these traits can differ between sets
 of species, leaf functional trait coordination within species remains
 poorly understood. Furthermore, elevated concentrations of atmospheric CO2
 commonly influence the expression of leaf photosynthetic, economics and
 hydraulic traits in contrasting ways, yet the effect of variable
 concentrations of atmospheric CO2 on patterns of trait coordination within
 species remains largely untested. We examined the relationships among key
 leaf photosynthetic (e.g. net photosynthesis and photosynthetic
 biochemistry), economics and water-use (e.g. leaf mass per unit area and
 stomatal conductance) and hydraulic traits (e.g. vein density) in 14
 genotypes of Eucalyptus camaldulensis grown in ambient (aCO2) and elevated
 (eCO2) [CO2]. We examined the level of coordination among leaf traits in
 aCO2 and then assessed whether growth in eCO2 altered that coordination.
 We found that leaf traits related to photosynthetic capacity, economics
 and water-use, and hydraulics were decoupled among genotypes grown in
 aCO2, yet strong relationships were generally observed among suites of
 traits within each ‘functional group’. Significant responses to growth in
 eCO2 were observed for most leaf photosynthetic and economics and
 water-use traits, with the magnitude and direction of the response varying
 among traits. In contrast, leaf hydraulics traits were unaffected by
 variable growth CO2. Despite this, growth in eCO2 did not substantially
 alter patterns of leaf trait coordination observed in aCO2. These results
 suggest suites of leaf traits associated with photosynthetic capacity,
 economics and water-use and hydraulics, respectively, can form independent
 axes of variation among genotypes of a single species, regardless of
 growth CO2. Although growth in eCO2 did not substantially alter patterns
 of trait coordination, decoupling of leaf functional traits among
 genotypes may allow genetically distinct populations to produce novel
 combinations of traits that may be adaptive in response to changes in
 their local environment.
description: Blackman et al
 2016_FE-2015-01039.R1_raw data file_traitsLeaf functional trait
 data for individual replicates of 14 Eucalyptus camaldulensis genotypes
 grown under ambient (400ppm) and elevated (640ppm) CO2.Blackman et al
 2016_FE-2015-01039.R1_raw data file_stomatal traitsStomatal traits of
 replicates of 14 Eucalyptus camaldulensis genotypes grown under ambient
 (400ppm) and elevated (640ppm) CO2
DOI: 10.5281/zenodo.16920203
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 20 August, 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.07668
title: Data from: First report of ostracods (Crustacea) associated with Bithynian (Anisian, Middle Triassic) Tubiphytes-microbial reef in the North Dobrogean Orogen (Romania)

description: The Mahmudia Quarry is located in the North Dobrogean Orogen (Romania),
 representing the western tip of the Palaeotethys-issued Cimmeride Orogenic
 System. One sample from the Tubiphytes-microbial reef exposed in the
 quarry yielded an abundant well-preserved ostracod assemblage of
 Bithynian, early Middle Anisian, Middle Triassic age. We report the
 occurrence of 56 ostracod species distributed among 23 genera. Ten species
 are newly described: Acratia caeracella sp. nov., Bairdia mandruella sp.
 nov., B. liviae sp. nov., Hungarella mahmudiaensis sp. nov., Kempfina
 tineriella sp. nov., Liuzhinia antalyaformis sp. nov., L. bithynica sp.
 nov., L. edvardgriegi sp. nov., Microcheilinella contrariella sp. nov.,
 Paracypris oanaella sp. nov. One species is renamed, Bairdia monostorii
 nom. nov. and the diagnosis of the genus Palaeocypridina is emended to
 include the central muscle scars pattern. The Tubiphytes ecosystem is a
 complex with a multi-layer food chain as shown by the presence of
 diversified carnivorous nekton-benthic ostracods, being both preys and
 predators of other organisms. The palaeoenvironmental requirements of the
 main ostracod taxa indicate a deposition in an open marine environment, on
 the outer platform-upper slope zone, in accordance with information
 provided by other proxies. We discuss the relationship of ostracods and
 microbial mats during the Triassic and conclude that the composition of
 assemblages are rather related both to the characteristics of this
 chemosynthetically-driven habitat and to bathymetry. However, some taxa,
 such as the genus Liuzhinia, are typical of Triassic microbial ecosystems.
 We perform the first analysis of ostracods provincialism during the
 Anisian and identify a distinct peri-Palaeo-Tethyan province.
description: APPENDICESAppendix 1, complete list of the ostracods species occurring in the Anisian, Middle Triassic of North Dobrogea, Romania (Mirăuță et al. 1993; Crasquin-Soleau & Grădinaru 1996; Sebe 2013; Sebe et al. 2013; this work).; appendix 2, matrix of ostracod species distribution during the Anisian, Middle Triassic; appendix 3, matrix of ostracod genera distribution during the Anisian, Middle Triassic.
DOI: 10.5061/dryad.24610
title: Data from: Predictable food supplies induce plastic shifts in avian scaled body mass

description: Urbanization constitutes one of the most profound forms of land-use change
 and strongly affects global biodiversity and ecosystem functioning.
 Expansion of urban areas typically leads to species loss but may also
 induce more subtle changes in species dynamics through selection or
 plasticity. Using a dual correlative (field) and experimental (aviary)
 approach, we here show that free-ranging urban house sparrows in southern
 France were smaller and lighter than their rural counterparts after
 allometric scaling, whereas 2 independent indices of nutritional (feather
 growth rates) and developmental (feather asymmetry) stress did not vary
 with urbanization. When subjecting these individuals to urban or rural
 diets in a highly predictable, controlled setting, rural but not urban
 sparrows decreased their body mass, independent of diet type, to the
 extent that initial scaled mass differences between urban and rural birds
 disappeared by the end of the captive period. By integrating field- and
 aviary measurements of body size and mass with indices of nutritional and
 developmental stress, we conclude that the lower scaled body masses of
 urban birds likely reflect a plastic response to predictable food
 supplies, possibly mediated through predation. Urban environments
 therefore do not necessarily constitute nutritionally stressful
 environments for species that typically cohabit with humans, such as house
 sparrows.
description: Biometric measurements,
 ptilochronology and fluctuating asymmetry of house sparrows from urban and
 rural areas in FranceThe database consists of
 biometric measurements (body mass, tarsus length, wing length, bill height
 and bill length) and scores of feather moulting stage collected during
 field sampling and body mass obtained from experiment. Data on
 ptilochronology were yielded through manual measurement of feather growth
 bar width. Fluctuating asymmetry data consist of two times measurements of
 feather length which were used to estimate fluctuating
 asymmetry.Noraine et
 al.xlsx
DOI: 10.5061/dryad.5ps58
title: Data from: Coevolution between positive reciprocity, punishment, and partner switching in repeated interactions

description: Cooperation based on mutual investments can occur between unrelated
 individuals when they are engaged in repeated interactions. Individuals
 then need to use a conditional strategy to deter their interaction
 partners from defecting. Responding to defection such that the future
 payoff of a defector is reduced relative to cooperating with it is called
 a partner control mechanism. Three main partner control mechanisms are (i)
 to switch from cooperation to defection when being defected (‘positive
 reciprocity’), (ii) to actively reduce the payoff of a defecting partner
 (‘punishment’), or (iii) to stop interacting and switch partner (‘partner
 switching’). However, such mechanisms to stabilize cooperation are often
 studied in isolation from each other. In order to better understand the
 conditions under which each partner control mechanism tends to be favoured
 by selection, we here analyse by way of individual-based simulations the
 coevolution between positive reciprocity, punishment, and partner
 switching. We show that random interactions in an unstructured population
 and a high number of rounds increase the likelihood that selection favours
 partner switching. In contrast, interactions localized in small groups
 (without genetic structure) increase the likelihood that selection favours
 punishment and/or positive reciprocity. This study thus highlights the
 importance of comparing different control mechanisms for cooperation under
 different conditions.
description: simulation
 codeThis file contains C++
 code which can be compiled in order to run the simulations described in
 the paper.pd_code5.cpp
DOI: 10.5061/dryad.p15h2
title: Data from: Temporal stability of genetic variability and differentiation in the three-spined stickleback (Gasterosteus aculeatus)

description: Temporal variation in allele frequencies, whether caused by deterministic
 or stochastic forces, can inform us about interesting demographic and
 evolutionary phenomena occurring in wild populations. In spite of the
 continued surge of interest in the genetics of three-spined stickleback
 (Gasterosteus aculeatus) populations, little attention has been paid
 towards the temporal stability of allele frequency distributions, and
 whether there are consistent differences in effective size (Ne) of local
 populations. We investigated temporal stability of genetic variability and
 differentiation in 15 microsatellite loci within and among eight
 collection sites of varying habitat type, surveyed twice over a six-year
 time period. In addition, Nes were estimated with the expectation that
 they would be lowest in isolated ponds, intermediate in larger lakes and
 largest in open marine sites. In spite of the marked differences in
 genetic variability and differentiation among the study sites, the
 temporal differences in allele frequencies, as well as measures of genetic
 diversity and differentiation, were negligible. Accordingly, the Ne
 estimates were temporally stable, but tended to be lower in ponds than in
 lake or marine habitats. Hence, we conclude that allele frequencies in
 putatively neutral markers in three-spined sticklebacks seem to be
 temporally stable – at least over periods of few generations – across a
 wide range of habitat types differing markedly in levels of genetic
 variability, effective population size and gene flow.
description: Genetic
 dataMicrosatellite data for
 the four Baltic Sea populations (2003) and four Fennoscandian freshwater
 populations (2003 and 2009)Temporal
 data_PLoS.txt
DOI: 10.15468/dl.ntggm7
title: Occurrence Download

description: A dataset containing 389 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Fendlerella utahensis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 389 records from 54 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001052-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.77tm4
title: Data from: Postcranial morphology and the locomotor habits of living and extinct carnivorans

description: Members of the order Carnivora display a broad range of locomotor habits,
 including cursorial, scansorial, arboreal, semiaquatic, aquatic, and
 semifossorial species from multiple families. Ecomorphological analyses
 from osteological measurements have been used successfully in prior
 studies of carnivorans and rodents to accurately infer the locomotor
 habits of extinct species. This study uses 20 postcranial measurements
 that have been shown to be effective indicators of locomotor habits in
 rodents and incorporates an extensive sample of over 300 individuals from
 more than 100 living carnivoran species. We performed statistical
 analyses, including analysis of variance (ANOVA) and stepwise discriminant
 function analysis, using a set of 16 functional indices (ratios). Our
 ANOVA results reveal consistent differences in postcranial skeletal
 morphology among locomotor groups. Cursorial species display distal
 elongation of the limbs, gracile limb elements, and relatively narrow
 humeral and femoral epicondyles. Aquatic and semiaquatic species display
 relatively robust, shortened femora and elongate metatarsals.
 Semifossorial species display relatively short, robust limbs with enlarged
 muscular attachment sites and elongate claws. Both semiaquatic and
 semifossorial species have relatively elongate olecranon process of the
 ulna and enlarged humeral and femoral epicondyles. Terrestrial,
 scansorial, and arboreal species are characterized by having primarily
 intermediate features, but arboreal species do show relatively elongate
 manual digits. Morphological indices effectively discriminate locomotor
 groups, with cursorial and arboreal species more accurately classified
 than terrestrial, scansorial, or semiaquatic species. Both within and
 between families, species with similar locomotor habits converge toward
 similar postcranial morphology despite their independent evolutionary
 histories. The discriminant analysis worked particularly well to correctly
 classify members of the Canidae, but not as well for members of the
 Mustelidae or Ursidae. Results are used to infer the locomotor habits of
 extinct carnivorans, including members of several extinct families, and
 also 12 species from the Pleistocene of Rancho La Brea.
description: Carnivore Postcranial
 Morphology Data Samuels et al. 2013
DOI: 10.5061/dryad.v286m
title: Data from: The context dependence of assortative mating: a demonstration with conspecific salmonid populations

description: Assortative mating is thought to play a key role in reproductive
 isolation. However, most experimental studies of assortative mating do not
 take place in multiple natural environments and, hence, they ignore its
 potential context dependence. We implemented an experiment in which two
 populations of brown trout (Salmo trutta) with different natural flow
 regimes were placed into semi-natural stream channels under two different
 artificial flow regimes. Natural reproduction was allowed and reproductive
 isolation was measured by means of parentage assignment to compare
 within-population versus between-population male-female mating and
 relative offspring production. For both metrics, reproductive isolation
 was highly context dependent: no isolation was evident under one flow
 regime but strong isolation was evident under the other flow regime. These
 patterns were fully driven by variance in the mating success of males from
 one of the two populations. Our results highlight how reproductive
 isolation through assortative mating can be strongly context dependent,
 which could have dramatic consequences for patterns of gene flow and
 speciation under environmental change.
description: Traits and
 characteristics of fishThis table present the
 traits (sex, body size, weight, origin, ID, offspring number) and
 experimental treatment of brown trout spawners used for the experiment
 described in the associated reference. The experimental treatment is flow
 manipulation (constant versus stochastic), and fish originate from two
 rivers (Bastan, France, and Urumea, Spain).Gauthey et al - 2016 -
 Supplementary Information 3 - AXIOS -
 JEB.xlsxMating success
 matricesThis parental table
 describes mating success between pairs of possible parents in each of the
 two experimental treatment (constant versus stochastic flow). The mating
 success is either equal to zero if no offspring were found, or equal to
 one if at least one offspring was found. The number of offspring was
 assigned to parental pairs using genetic assignation.Gauthey et al - 2016 -
 Supplementary Information 5 - corrected - AXIOS -
 JEB.xlsxReproductive success
 matrices.This table describes the
 number of offspring produced by possible parental pairs in each of the
 experimental treatment (constant versus stochastic flow). The number of
 offspring was estimated using genetic assignation based on microsatellite
 markers (see associated reference).Gauthey et al - 2016 -
 Supplementary Information 6 - AXIOS -
 JEB.xlsx
DOI: 10.5061/dryad.qc297
title: Data from: Sex-specific inbreeding depression depends on the strength of male-male competition

description: Inbreeding depression has become a central theme in evolutionary biology
 and is considered to be a driving force for the evolution of reproductive
 morphology, physiology, behavior, and mating systems. Despite the
 overwhelming body of empirical work on the reproductive consequences of
 inbreeding, relatively little is known on whether inbreeding depresses
 male and female fitness to the same extent. However, sex-specific
 inbreeding depression has been argued to affect the evolution of selfing
 rates in simultaneous hermaphrodites and provides a powerful approach to
 test whether selection is stronger in males than in females, which is
 predicted to be the consequence of sexual selection. We tested for
 sex-specific inbreeding depression in the simultaneously hermaphroditic
 freshwater snail Physa acuta by comparing the reproductive performance of
 both sex functions between selfed and outcrossed focal individuals under
 different levels of male–male competition. We found that inbreeding
 impaired both male and female reproductive success and that the magnitude
 of male inbreeding depression exceeded female inbreeding depression when
 the opportunity for sperm competition was highest. Our study provides the
 first evidence for sex-specific inbreeding depression in a hermaphroditic
 animal and highlights the importance of considering the level of male–male
 competition when assessing sex differences in inbreeding depression.
description: DATA TABLE 1
 Reproductive performance and body weightMeasurements of
 reproductive performance and body weight of inbred and outbred snails
 assessed under controlled laboratory conditions. For column abbreviations
 see data sheet 'DATA TABLE 1 Legend'.Janicke_et_al_DATA_TABLE_1.xlsxDATA TABLE 2 Early survival of focal snailsMeasurements of early survival of inbred and outbred focal snails assessed under controlled laboratory conditions. For column abbreviations see data sheet 'DATA TABLE 2 Legend'.Janicke_et_al_DATA_TABLE_2.xlsx