cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.280gb5mkw
title: Ecologically diverse clades dominate the oceans via extinction resistance

description: Ecological differentiation is correlated with taxonomic diversity in many
 clades, and ecological divergence is often assumed to be a cause and/or
 consequence of high speciation rate. However, an analysis of 30,074 genera
 of living marine animals and 19,992 genera of fossil marine animals
 indicates that greater ecological differentiation in the modern oceans is
 actually associated with lower rates of origination over evolutionary
 time. Ecologically differentiated clades became taxonomically diverse over
 time because they were better buffered against extinction, particularly
 during mass extinctions, which primarily affected genus-rich, ecologically
 homogeneous clades. The relationship between ecological differentiation
 and taxonomic richness was weak early in the evolution of animals but has
 strengthened over geological time as successive extinction events reshaped
 the marine fauna.
DOI: 10.5061/dryad.bzkh1894f
title: Data from: Mid-Cretaceous amber inclusions reveal morphogenesis of extinct rachis-dominated feathers

description: We describe three-dimensionally preserved feathers in mid-Cretaceous
 Burmese amber that share macro-morphological similarities (e.g.,
 proportionally wide rachis with a “medial stripe”) with lithic,
 two-dimensionally preserved rachis-dominated feathers. These feathers in
 amber reveal a unique ventrally concave and dorsoventrally thin rachis,
 and a dorsal groove (sometimes pigmented) that we identify as the “medial
 stripe” visible in many rachis-dominated rectrices of Mesozoic birds. The
 distally pennaceous portion of these feathers shows differentiated
 proximal and distal barbules, the latter with hooklets forming
 interlocking barbs. Micro-CT scans and transverse sections demonstrate the
 absence of histodifferentiated cortex and medullary pith of the rachis and
 barb rami. The highly differentiated barbules combined with the lack of
 obvious histodifferentiation of the barb rami or rachis suggests that
 these feathers could have been formed without the full suite and
 developmental interplay of intermediate filament alpha keratins and
 corneous beta-proteins that is employed in the cornification process of
 modern feathers. This study thus highlights how the development of these
 feathers might have differed from that of their modern counterparts,
 namely in the morphogenesis of the ventral components of the rachis and
 barb rami. We suggest that the concave ventral surface of the rachis of
 these Cretaceous feathers is not homologous with the ventral groove of
 modern rachises. Our study of these Burmese feathers also confirms
 previous claims, based on two-dimensional fossils, that they correspond to
 an extinct morphotype and it cautions about the common practice of
 extrapolating developmental aspects (and mechanical attributes) of modern
 feathers to those of stem birds (and their dinosaurian outgroups) because
 the latter need not to have developed through identical pathways.
DOI: 10.5061/dryad.nzs7h44mg
title: The eye size of the bluefin killifish (Lucania goodei) varies from springs to swamps

description: Variation in lighting environments creates different demands of visual
 systems for the successful detection and interpretation of visual signals
 in a given setting. Eye size is a critical property of the visual system
 as it is has strong effects on visual acuity and visual sensitivity. While
 many comparative studies have examined eye size across fishes that live in
 disparate lighting environments (i.e., caves versus surface habitats,
 mesopelagic versus pelagic depths, turbid versus clear water), fewer have
 investigated differences in eye size as a function of water clarity at the
 among population - within species level. Here, we compared relative eye
 size (eye size residuals on standard length) between wild-caught
 individuals from swamps and springs and across four drainages in Florida.
 We also performed a laboratory experiment where we reared animals in clear
 or tea-stained water, which mimic spring and swamp conditions to determine
 whether phenotypic plasticity as a function of lighting conditions
 influences relative eye size. Field caught animals greatly varied in
 relative eye size among populations, but there was no clear relationship
 with lighting environment. Fish from southern populations (where swamps
 are common) had greater relative eye size than those from northern
 populations (where springs are common). However, in North Florida, bluefin
 killifish from swamps had smaller eyes than those from springs. This is
 consistent with the results of our laboratory rearing experiment, which
 indicated that animals raised in tea-stained water had slightly smaller
 eyes than those raised in clear water conditions. These two disparate
 patterns suggest that the determinants of eye size are currently unknown.
DOI: 10.5061/dryad.s1rn8pk3h
title: Data from: Gene expression response to a nematode parasite in novel and native eel hosts

description: Invasive parasites are involved in population declines of new host species
 worldwide. The high susceptibilities observed in many novel hosts have
 been attributed to the lack of protective immunity to the parasites which
 native hosts acquired during their shared evolution. We experimentally
 infected Japanese eels (Anguilla japonica) and European eels (A. anguilla)
 with Anguillicola crassus, a nematode parasite that is native to the
 Japanese eel and invasive in the European eel. We inferred gene expression
 changes in head kidney tissue from both species, using RNA-seq data to
 determine the responses at two time points during the early stages of
 infection (3 and 23 days post-infection). At both time points, the novel
 host modified the expression of a larger and functionally more diverse set
 of genes than the native host. Strikingly, the native host regulated
 immune gene expression only at the earlier time point and to a small
 extent while the novel host regulated these genes at both time points. A
 low number of differentially expressed immune genes, especially in the
 native host, suggests that a systemic immune response was of minor
 importance during the early stages of infection. Transcript abundance of
 genes involved in cell respiration was reduced in the novel host which may
 affect its ability to cope with harsh conditions and energetically
 demanding activities. The observed gene expression changes in response to
 a novel parasite that we observed in a fish follow a general pattern
 observed in amphibians and mammals, and suggest that the disruption of
 physiological processes, rather than the absence of an immediate immune
 response, are responsible for the higher susceptibility of the novel host.
description: European eels and Japanese eels were experimentally infected with
 Anguillicola crassus larvae or sham-infected with PBS and sampled at 3
 days post-infection or 23 days post-infection (n = 5 for each species,
 time point, and treatment).<br> mRNA was paired-end sequenced on an
 Illumina HiSeq2500 or HiSeq4000 and reads were de novo assembled with
 Trinity. Raw reads and assemblies used to create the the count data are
 available from the BioProjects PRJNA419718 (European eel 3 dpi),
 PRJNA546508 (European eel 23 dpi & assembly), and PRJNA546510
 (Japanese eel 3 & 23 dpi & assembly).<br>
 Differentially expressed genes between infected and control eels were
 identified separately for species and time points using DESeq2 v.1.14.0 on
 read counts obtained with RSEM v.1.3.0 and a mean coverage cut-off
 &gt;= 10.<br> GO term enrichment analysis was done with GOstats
 v2.48.0 using custom background annotations obtained by blasting against
 UniProt/Swiss-Prot and searching the Pfam database integrated in Trinotate
 v3.2.0.
DOI: 10.5061/dryad.41ns1rn96
title: Gene flow limits adaptation along steep environmental gradients

description: When environmental variation is spatially continuous, dispersing
 individuals move among nearby sites with similar habitat conditions. But
 as an environmental gradient becomes steeper, gene flow may connect more
 divergent habitats, and this is predicted to reduce the slope of the
 adaptive cline that evolves. We compared quantitative genetic divergence
 of Rana temporaria frog populations along a 2000-m elevational gradient in
 eastern Switzerland (new experimental results) with divergence along a
 1550-km latitudinal gradient in Fennoscandia (previously published
 results). Both studies found significant countergradient variation in
 larval development rate (i.e., animals from cold climates developed more
 rapidly). The cline was weaker with elevation than with latitude. Animals
 collected on both gradients were genotyped at ~2000 SNP markers, revealing
 that dispersal distance was 30% farther on the latitudinal gradient but
 3.9 times greater with respect to environmental conditions on the
 elevational gradient. A meta-analysis on 19 experimental studies of anuran
 populations spanning temperature gradients revealed that countergradient
 variation in larval development, while significant overall, was weaker
 when measured on steeper gradients. These findings support the prediction
 that adaptive population divergence is less pronounced, and maladaptation
 more pervasive, on steep environmental gradients.
DOI: 10.5061/dryad.hx3ffbg98
title: Data from: Endovascular treatment in older adults with acute ischemic stroke in the MR CLEAN Registry

description: Objective: To explore clinical outcomes in older adults with acute
 ischemic stroke treated with endovascular thrombectomy (EVT). Methods: We
 included consecutive patients (2014–2016) with an anterior circulation
 occlusion undergoing EVT from the MR CLEAN Registry. We assessed the
 effect of age (dichotomized at ≥80 years, and as continuous variable) on
 the modified Rankin Scale [mRS] score at 90 days, symptomatic intracranial
 hemorrhage (sICH), and reperfusion rate. The association between age and
 mRS was assessed with multivariable ordinal logistic regression, and a
 multiplicative interaction term was added to the model to assess
 modification of reperfusion by age on outcome. Results: 380/1526 (25%) of
 patients were 80 years or older (=older adults). Older adults had a worse
 functional outcome than younger patients (adjusted common OR for an mRS
 shift towards better outcome: 0.31, 95%CI 0.24–0.39). Mortality was also
 higher in older adults (51% vs. 22%, aOR 3.12, 95%CI 2.33–4.19). There
 were no differences in proportion of patients with mRS 4-5, sICH, or
 reperfusion rates. Successful reperfusion was more strongly associated
 with a shift towards good functional outcome in older adults than in
 younger patients (acOR 3.22, 95%CI 2.04–5.10 vs. 2.00, 95%CI 1.56–2.57,
 Pinteraction=0.026). Conclusion: Older age is associated with an increased
 absolute risk of poor clinical outcome, while the relative benefit of
 successful reperfusion seems to be higher in these patients. These results
 should be taken into consideration when selecting older adults for EVT.
DOI: 10.5061/dryad.80gb5mkmx
title: Data from: Network-scale effects of invasive species on spatially-structured amphibian populations

description: Understanding the factors affecting the dynamics of spatially-structured
 populations (SSP) is a central topic of conservation and landscape
 ecology. Invasive alien species are increasingly important drivers of the
 dynamics of native species. However, the impacts of invasives are often
 assessed at the patch scale, while their effects on SSP dynamics are
 rarely considered. We used long-term abundance data to test whether the
 impact of invasive crayfish on subpopulations can also affect the whole
 SSP dynamics, through their influence on source populations. From 2010 to
 2018, we surveyed a network of 58 ponds and recorded the abundance of
 Italian agile frog clutches, the occurrence of an invasive crayfish, and
 environmental features. Using Bayesian hierarchical models, we assessed
 relationships between frog abundance in ponds and a) environmental
 features; b) connectivity within the SSP; c) occurrence of invasive
 species at both the patch- and the SSP-levels. If spatial relationships
 between ponds were overlooked, we did not detect effects of crayfish
 presence on frog abundance or trends. When we jointly considered habitat,
 subpopulation, and SSP features, processes acting at all these levels
 affected frog abundance. At the subpopulation scale, frog abundance in a
 year was related to habitat features, but was unrelated to crayfish
 occurrence at that site during the previous year. However, when we
 considered the SSP level, we found a strong negative relationship between
 frog abundance in a given site and crayfish frequency in surrounding
 wetlands during the previous year. Hence, SSP-level analyses can identify
 effects that would remain unnoticed when focussing on single patches.
 Invasive species can affect population dynamics even in not invaded
 patches, through the degradation of subpopulation networks. Patch-scale
 assessments of the impact of invasive species can thus be insufficient:
 predicting the long-term interplay between invasive and native populations
 requires landscape-level approaches accounting for the complexity of
 spatial interactions.
description: Data collected from 2010 to 2018.  The data are available also in
 the paper supporting information.
DOI: 10.5061/dryad.fttdz08nd
title: Strong evidence of an Information-Theoretical Conservation Principle linking all discrete systems

description: Diverse discrete systems share common global properties that lack a
 unifying theoretical explanation. However, constraining the simplest
 measure of total information (Hartley-Shannon) in a statistical mechanics
 framework reveals a principle, the Conservation of Hartley-Shannon
 Information (CoHSI) that directly predicts both known and unsuspected
 common properties of discrete systems, as borne out in the diverse systems
 of computer software, proteins and music.  Discrete systems fall
 into two categories distinguished by their structure: heterogeneous
 systems in which there is a distinguishable order of assembly of the
 system's components from an alphabet of  unique tokens (e.g.
 proteins assembled from an alphabet of amino acids), and homogeneous
 systems in which unique tokens are simply binned, counted and rank
 ordered. Heterogeneous systems are characterized by an implicit
 distribution of component lengths, with sharp unimodal peak (containing
 the majority of components) and a power-law tail, whereas homogeneous
 systems reduce naturally to Zipf's Law but with a drooping tail in
 the distribution.  We also confirm predictions that very long
 components are inevitable for heterogeneous systems; that discrete systems
 can exhibit simultaneously both heterogeneous and homogeneous behavior;
 and that in systems with more than one consistent token alphabet (e.g.
 digital music), the alphabets themselves show a power-law relationship.
DOI: 10.5061/dryad.3xsj3tx9s
title: Immuno-competence data

description: The exposure of yolk androgens can positively stimulate chick growth and
 competitive ability but may negatively affect immunity. It has been
 hypothesized that only chicks from immunologically superior fathers can
 bear the cost of prenatal exposure to high androgen levels. To test this
 hypothesis we paired roosters from two selection lines, one up- and one
 down-selected for natural antibodies, with hens from a control line. We
 measured yolk testosterone and androstenedione levels, and we injected the
 treatment group  of  eggs of each female with
 testosterone suspended in sesame oil and the control group with sesame oil
 only. We then measured hatching success, growth, and characterised the
 humoral and cellular immune responses using three different challenges: a
 PHA, an LPS, and an SRBC challenge. We found that the hatching success,
 body mass, initial levels of natural antibodies, and the chicks
 immunological responses to the three different challenges development were
 affected neither by paternal immune-competence nor by treatment. These
 results do not support the hypothesis that chicks from low quality fathers
 are more sensitive to testosterone exposure during embryonic development
 than chicks from high quality fathers.
description: The exposure of yolk androgen can positively stimulate chicks
 growth and competitive ability but may negatively affect immunity. It has
 been hypothesized that only chicks from an immunologically superior father
 can bear the cost of parental exposure to high androgen levels. To test
 this hypothesis we paired roosters from two selection lines, one up- and
 one down-selected for natural antibodies, with hens from a control line.
 We measured yolk testosterone and androstenedione levels, and we injected
 the treatment group  of  eggs of each female with testosterone suspended
 in sesame oil and the control group with sesame oil only. We then measured
 hatching success, growth, and characterised the humoral and cellular
 immune responses using three different challenges: a PHA, an LPS, and an
 SRBC challenge. We found that the hatching success, body mass, initial
 levels of natural antibodies, and the chicks immunological responses to
 the three different challenges development were affected neither by
 paternal immune-competence nor by treatment. These results do not support
 the hypothesis that chicks from low quality fathers are more sensitive to
 testosterone exposure during embryonic development than chicks from high
 quality fathers.<b> </b>
DOI: 10.5061/dryad.2ngf1vhhz
title: Are you what you eat? A highly transient and prey-influenced gut microbiome in the grey house spider Badumna longinqua

description: Stable core microbial communities have been described in numerous animal
 species and are commonly associated with fitness benefits for their hosts.
 Recent research, however, highlights examples of species whose microbiota
 are transient and environmentally derived. Here, we test the effect of
 diet on gut microbial community assembly in the spider Badumna longinqua.
 Using 16S rRNA gene amplicon sequencing combined with quantitative PCR, we
 analyze diversity and abundance of the spider’s gut microbes, and
 simultaneously characterize its prey communities using nuclear rRNA
 markers. We find a clear correlation between community similarity of the
 spider’s insect prey and gut microbial DNA, suggesting that microbiome
 assembly is primarily diet-driven . This assumption is supported by a
 feeding experiment, in which two types of prey – crickets and fruit flies
 – both substantially altered microbial diversity and community similarity
 between spiders, but did so in different ways. After cricket consumption,
 numerous cricket-derived microbes appeared in the spider’s gut, resulting
 in a rapid homogenization of microbial communities among spiders. In
 contrast, few prey-associated bacteria were detected after consumption of
 fruit flies; instead, the microbial community was remodeled by
 environmentally sourced microbes, or abundance shifts of rare taxa in the
 spider’s gut. The reshaping of the microbiota by both prey taxa mimicked a
 stable core microbiome in the spiders for several weeks post feeding. Our
 results suggest that the spider’s gut microbiome undergoes pronounced
 temporal fluctuations, that its assembly is dictated by the consumed prey,
 and that different prey taxa may remodel the microbiota in drastically
 different ways.
DOI: 10.5061/dryad.jh9w0vt6d
title: Manipulation of photoperiod perception advances gonadal growth but not laying date in the great tit

description: In seasonal environments, organisms use biotic and abiotic cues to time
 various biological processes that are crucial for growth, survival and
 reproductive success. Photoperiod is the best-known cue used to regulate
 gonadal development, migration and moult of many animal species. In birds,
 the relationship between photoperiod and gonadal development is clearly
 established, but we have little understanding on whether photoperiod also
 regulates actual timing of egg laying under natural conditions.
 Elucidating the link between photoperiod and timing of breeding is however
 key to understand whether an evolutionary change in sensitivity to
 photoperiod is a possible mechanism through which organisms could adjust
 their seasonal timing in response to climate warming. Here, we
 investigated the causal relationship between photoperiod, gonadal growth
 and laying date in wild female great tits. We experimentally increased the
 photoperiod perceived by the birds in spring by clipping head feathers,
 and we subsequently monitored gonadal development in the lab and egg
 laying dates in the wild. We show that our manipulation increased the
 photoperiod perceived by the birds to a level that approximately
 corresponds to an advancement of ten calendar days. This increase in
 perceived photoperiod led to an acceleration of gonadal development, but
 not to an advancement of egg laying dates. Our results indicate that
 photoperiod sensitivity is not constraining the advancement of laying date
 under current environmental conditions and suggest that evolution of
 sensitivity to other supplementary cues is necessary to advance
 reproduction under global warming.
description: Data collection and analysis is decribed in the materials and
 methods section of the corresponding paper. Light
 trasmission data were collected in 3 individuals and then averaged. The
 average was used for plotting in figure 2.
DOI: 10.5061/dryad.n02v6wwsb
title: Hydroxyacetophenone defenses in white spruce against spruce budworm

description: We review a recently discovered white spruce (Picea glauca) chemical
 defense against spruce budworm (Choristoneura fumiferana) involving
 hydroxyacetophenones. These defense metabolites detected in the foliage
 accumulate variably as the aglycons, piceol and pungenol, or the
 corresponding glucosides, picein and pungenin. We summarize current
 knowledge of the genomic, molecular and biochemical as well as genetic
 underpinnings of this defense and its effects on C. fumiferana. We present
 an update with new results on the ontogenic variation and the phenological
 window of this defense, including analysis of transcript responses in P.
 glauca to C. fumiferana herbivory. We also discuss this chemical defense
 from an evolutionary and a breeding context.
description: Gene counts and metadata for each library results presented in
 the "Induction of hydroxyacetophenone defense in the current year
 foliage of mature grafts of <i>Picea glauca" </i>section
 of the article. Files are in DESeq2 format. More
 details are provided in the method section within the article and the
 supplementary material. For more information, please contact
 genevieve.parent@dfo-mpo.gc.ca.
DOI: 10.5281/zenodo.18393714
title: Results of the project "The evaluation of skills and the development of cognitive abilities regarding History in Compulsory Secondary Education (EDU2015-65621-C3-2-R)
DOI: 10.5281/zenodo.18393713
title: Results of the project "The evaluation of skills and the development of cognitive abilities regarding History in Compulsory Secondary Education (EDU2015-65621-C3-2-R)