cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.11r1j
title: Data from: Selection analysis on the rapid evolution of a secondary sexual trait

description: Evolutionary analyses of population translocations (experimental or
 accidental) have been important in demonstrating speed of evolution
 because they subject organisms to abrupt environmental changes that create
 an episode of selection. However, the strength of selection in such
 studies is rarely measured, limiting our understanding of the evolutionary
 process. This contrasts with long-term, mark–recapture studies of
 unmanipulated populations that measure selection directly, yet rarely
 reveal evolutionary change. Here, we present a study of experimental
 evolution of male colour in Trinidadian guppies where we tracked both
 evolutionary change and individual-based measures of selection. Guppies
 were translocated from a predator-rich to a low-predation environment
 within the same stream system. We used a combination of common garden
 experiments and monthly sampling of individuals to measure the phenotypic
 and genetic divergence of male coloration between ancestral and derived
 fish. Results show rapid evolutionary increases in orange coloration in
 both populations (1 year or three generations), replicating the results of
 previous studies. Unlike previous studies, we linked this evolution to an
 individual-based analysis of selection. By quantifying individual
 reproductive success and survival, we show, for the first time, that males
 with more orange and black pigment have higher reproductive success, but
 males with more black pigment also have higher risk of mortality. The net
 effect of selection is thus an advantage of orange but not black
 coloration, as reflected in the evolutionary response. This highlights the
 importance of considering all components of fitness when understanding the
 evolution of sexually selected traits in the wild.
description: Individual Based Male
 Data from the WildMonthly individual guppy
 data on color, survival and reproductive success from the Upper and Lower
 La Laja introduction experiments. March 2008-2009.Gordon_WildData.csvCommon Garden F2 Male DataColor data on F2 common garden males from ancestral (Guanapo HP) and derived (La Laja) populations one year after introduction.Gordon_WildData.csv
DOI: 10.6084/m9.figshare.31153966
title: Additional file 3 of The intracellular localization and the ionic permeation of TRPV6 triggers chronic pancreatitis, skeletal dysplasia and is connected to mucolipidosis type II

description: Supplementary Material 3.
DOI: 10.6084/m9.figshare.31153966.v1
title: Additional file 3 of The intracellular localization and the ionic permeation of TRPV6 triggers chronic pancreatitis, skeletal dysplasia and is connected to mucolipidosis type II

description: Supplementary Material 3.
DOI: 10.5061/dryad.5p67b
title: Data from: Species but not genotype diversity strongly impacts the establishment of rare colonisers

description: 1. Understanding species coexistence and regulation of biodiversity are
 major research challenges, yet there is no consensus on the effects of
 diversity on diversity, including their mediation through plant–plant
 interactions. 2. We examined how the diversity of recipient communities
 impacted on the establishment of colonising species. We ran a
 greenhouse-based community experiment, creating artificial arable crop
 communities with varying levels of barley genotype and weed species
 diversity, analysed with structural equation modelling of responses across
 trophic levels. 3. Colonising arable weed species establishment was
 significantly reduced when the recipient communities’ weed species
 richness, but not barley genotype richness, increased. Recipient plant
 communities with higher species richness occupied more total niche space
 and showed stronger competition with colonising species. In contrast,
 recipient plant communities with higher genotype richness, even though
 they had slightly greater niche space occupancy, had no significant
 effects on the colonisation of additional species. 4. Responses were
 species-specific: colonising common weed species establishment was less
 affected by the recipient plant communities than that of colonising rare
 weed species. Strong responses of colonising rare species were related to
 the abiotic rather than the biotic environment created by the recipient
 communities. The stronger response of colonising rare species suggests
 greater niche overlap with and competitive inferiority to the recipient
 plant community, whereas the relative independence of colonising common
 species indicates less niche overlap and/or competitive equality or
 superiority. 5. We observed a negative species diversity effect on
 colonising species, with the effect size increasing with increasing rarity
 of the colonising species. This differential responsiveness of colonising
 rare and common arable weed species to the presence of and diversity in
 the recipient arable plant communities may be crucial in understanding
 rarity and may result from differential evolutionary pathways in response
 to interactions.
description: datasheet for plot-level
 measurementsData file containing
 contrast coding of the experimental treatments, trait metrics of the
 recipient communities, resource measurements and principal component of
 the microbial communities of all plots and abundance of the colonising
 weed species. The file also contains a meta data sheet for further
 information.database_20160516.xlsxR code for all the calculations, analyses and figuresR code to run all the calculations, analyses and figures using the datasheet providedRcode.R
DOI: 10.5061/dryad.rm230
title: Data from: The functional syndrome: linking individual trait variability to ecosystem functioning

description: Phenotypic variability is increasingly assessed through functional
 response and effect traits, which provide a mechanistic framework for
 investigating how an organism responds to varying ecological factors and
 how these responses affect ecosystem functioning. Covariation between
 response and effect traits has been poorly examined at the intraspecific
 level, thus hampering progress in understanding how phenotypic variability
 alters the role of organisms in ecosystems. Using a multi-trait approach
 and a nine-month longitudinal monitoring of individual red-swamp crayfish
 (Procambarus clarkii), we demonstrated that most of the measured response
 and effect traits were partially stable during the ontogeny of
 individuals. Suites of response and effect traits were associated with a
 response syndrome and an effect syndrome, respectively, which were
 correlated to form a functional syndrome. Using a bioenergetic model, we
 predicted that differences in the response syndrome composition of
 hypothetical populations had important ecological effects on a key
 ecosystem process (i.e. whole-lake litter decomposition) to a level
 similar to those induced by doubling population size. Demonstrating the
 existence of a functional syndrome is likely to improve our understanding
 of the ecological impacts of phenotypic variation among individuals in
 wild populations across levels of biological organization, and the linkage
 between ecosystem and evolutionary ecology.
description: Table_data_raffard
DOI: 10.6084/m9.figshare.31153975
title: Additional file 2 of MicroRNA profiling in serum and humor vitreous of patients affected by vitreoretinal diseases

description: Supplementary material 2
DOI: 10.6084/m9.figshare.31153975.v1
title: Additional file 2 of MicroRNA profiling in serum and humor vitreous of patients affected by vitreoretinal diseases

description: Supplementary material 2
DOI: 10.5061/dryad.3885sv0
title: Data from: Ecological conditions alter cooperative behaviour and its costs in a chemically defended sawfly

description: The evolution of cooperation and social behaviour is often studied in
 isolation from the ecology of organisms. Yet, the selective environment
 under which individuals evolve is much more complex in nature, consisting
 of ecological and abiotic interactions in addition to social ones. Here we
 measured the life-history costs of cooperative chemical defence in a
 gregarious social herbivore, Diprion pini pine sawfly larvae, and how
 these costs vary under different ecological conditions. We ran a rearing
 experiment where we manipulated diet (resin content) and attack intensity
 by repeatedly harassing larvae to produce a chemical defence. We show that
 forcing individuals to allocate more to cooperative defence (high attack
 intensity) incurred a clear cost by decreasing individual survival and
 potency of chemical defence. Cooperative behaviour and the magnitude of
 its costs were further shaped by host plant quality. Number of individuals
 participating in group defence, immune responses, and female growth
 decreased on a high resin diet under high attack intensity. We also found
 some benefits of cheating: non-defending males had higher growth rates
 across treatments. Together these results suggest that ecological
 interactions can shape the adaptive value of cooperative behaviour and
 maintain variation in the frequency of cooperation and cheating.
description: Grouprearing_early
 instars_rawdata_Lindstedt et al.2017Data from the defensive
 behaviour and potency of the chemical defende during the group rearing
 stage of the experiment.Individual_rearing_later_instars_rawdata_Lindstedt_et_al._2017Data file of life-history traits, defensive behaviour and potency of chemical defence from the individual rearing stage of the experiment.
DOI: 10.5061/dryad.mg5mk
title: Data from: Laying sequence interacts with incubation temperature to influence rate of embryonic development and hatching synchrony in a precocial bird

description: Incubation starts during egg laying for many bird species and causes
 developmental asynchrony within clutches. Faster development of late-laid
 eggs can help reduce developmental differences and synchronize hatching,
 which is important for precocial species whose young must leave the nest
 soon after hatching. In this study, we examined the effect of egg laying
 sequence on length of the incubation period in Wood Ducks (Aix sponsa).
 Because incubation temperature strongly influences embryonic development
 rates, we tested the interactive effects of laying sequence and incubation
 temperature on the ability of late-laid eggs to accelerate development and
 synchronize hatching. We also examined the potential cost of faster
 development on duckling body condition. Fresh eggs were collected and
 incubated at three biologically relevant temperatures (Low: 34.9°C,
 Medium: 35.8°C, and High: 37.6°C), and egg laying sequences from 1 to 12
 were used. Length of the incubation period declined linearly as laying
 sequence advanced, but the relationship was strongest at medium
 temperatures followed by low temperatures and high temperatures. There was
 little support for including fresh egg mass in models of incubation
 period. Estimated differences in length of the incubation period between
 eggs 1 and 12 were 2.7 d, 1.2 d, and 0.7 d at medium, low and high
 temperatures, respectively. Only at intermediate incubation temperatures
 did development rates of late-laid eggs increase sufficiently to
 completely compensate for natural levels of developmental asynchrony that
 have been reported in Wood Duck clutches at the start of full incubation.
 Body condition of ducklings was strongly affected by fresh egg mass and
 incubation temperature but declined only slightly as laying sequence
 progressed. Our findings show that laying sequence and incubation
 temperature play important roles in helping to shape embryo development
 and hatching synchrony in a precocial bird.
description: Wood Duck laying
 sequenceComma delimited file
 used to examine effects of incubation temperature and egg laying sequence
 of wood ducks (Aix sponsa) on length of the incubation period and body
 condition of day-old ducklings.WODU laying
 sequence.csvLaying sequence and
 parasitized nestsComma delimited file
 used to test whether daily parasitism of nests across the laying sequence
 differed between incubation temperature treatments.
DOI: 10.5061/dryad.6pr03
title: Data from: Nitrous oxide emission by the non-denitrifying, nitrite ammonifier Bacillus licheniformis

description: Background: Firmicutes have the capacity to remove excess nitrate from the
 environment via either denitrification, dissimilatory nitrate reduction to
 ammonium or both. The recent renewed interest in their nitrogen metabolism
 has revealed many interesting features, the most striking being their wide
 variety of dissimilatory nitrate reduction pathways. In the present study,
 nitrous oxide production from Bacillus licheniformis, a ubiquitous
 Gram-positive, spore-forming species with many industrial applications, is
 investigated. Results: B. licheniformis has long been considered a
 denitrifier but physiological experiments on three different strains
 demonstrated that nitrous oxide is not produced from nitrate in
 stoichiometric amounts, rather ammonium is the most important end-product,
 produced during fermentation. Significant strain dependency in end-product
 ratios, attributed to nitrite and ammonium, and medium dependency in
 nitrous oxide production were also observed. Genome analyses confirmed the
 lack of a nitrite reductase to nitric oxide, the key enzyme of
 denitrification. Based on the gene inventory and building on knowledge
 from other non-denitrifying nitrous oxide emitters, hypothetical pathways
 for nitrous oxide production, involving NarG, NirB, qNor and Hmp, are
 proposed. In addition, all publically available genomes of B.
 licheniformis demonstrated similar gene inventories, with specific
 duplications of the nar operon, narK and hmp genes as well as NarG
 phylogeny supporting the evolutionary separation of previously described
 distinct BALI1 and BALI2 lineages. Conclusions: Using physiological and
 genomic data we have demonstrated that the common soil bacterium B.
 licheniformis does not denitrify but is capable of fermentative
 dissimilatory nitrate/nitrite reduction to ammonium (DNRA) with
 concomitant production of N2O. Considering its ubiquitous nature and
 non-fastidious growth in the lab, B. licheniformis is a suitable candidate
 for further exploration of the actual mechanism of N2O production in DNRA
 bacteria and its relevance in situ.
description: narG_alignmentAlignment of full length NarG used for phylogenetic tree. Sequences were taken from genomes included in the manuscript as well as from all publically available B. licheniformis genomes (dd June 2014) and genomes from other Bacillus species, protein ID or locus tag is given.narK_alignment_trimmedTrimmed alignment of full length NarK sequences used for phylogenetic tree. Sequences were taken from several Bacillus species, as well as reference genomes, locus tag is given.
DOI: 10.6084/m9.figshare.31153984
title: Additional file 2 of Synaptic changes contribute to persistent extra-motor behaviour deficits in amyotrophic lateral sclerosis

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.31153984.v1
title: Additional file 2 of Synaptic changes contribute to persistent extra-motor behaviour deficits in amyotrophic lateral sclerosis

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.31153987
title: Additional file 3 of Synaptic changes contribute to persistent extra-motor behaviour deficits in amyotrophic lateral sclerosis

description: Supplementary Material 3
DOI: 10.6084/m9.figshare.31153987.v1
title: Additional file 3 of Synaptic changes contribute to persistent extra-motor behaviour deficits in amyotrophic lateral sclerosis

description: Supplementary Material 3
DOI: 10.5061/dryad.8594
title: Data from: Comparing the differential filling of morphospace and allometric space through time: the morphological and developmental dynamics of early Jurassic ammonoids

description: The evolutionary history of shell geometry of Early Jurassic ammonoids
 during the Pliensbachian–Toarcian second-order mass extinction is explored
 at both adult and ontogenetic levels. The ontogenetic approach builds on
 the concept of allometric space to get insights into the developmental
 aspects of morphological evolution. Investigation of the deployment of
 taxa in adult morphospace and allometric space allows the appraisal of the
 temporal evolution of morphological and allometric disparities. Curves of
 taxonomic diversity, adult morphological disparity, allometric disparity,
 and average adult size are contrasted. Results show that during the
 Pliensbachian–Toarcian interval, ammonoids underwent two successive and
 drastic declines in taxonomic diversity. Patterns of morphospace and
 allometric space occupancy suggest nonselective extinction at both
 morphological and developmental levels. Another measure of allometric
 disparity suggests the occurrence of two heterochronic trends, a
 peramorphocline followed by a paedomorphocline, during the Toarcian. These
 trends are concomitant with changes in average adult size that compensate
 for the heterochronic effects and explain the striking stability of
 morphological disparity despite changes in diversity. The results also
 emphasize the existence of two contrasted evolutionary dynamics in
 Pliensbachian and Toarcian ammonoids. Methodologically, the allometric
 disparity approach appears to be a fruitful tool to analyze the rather
 understudied clade-wide ontogenetic aspects of morphological evolution.
 Combining multiple approaches to describe clade morphological dynamics
 leads to a better characterization and understanding of the
 diversity-disparities relationships and a better distinction of the
 potential processes driving these macroevolutionary patterns.
description: Morphological data of
 early Jurassic ammonoidsThe following table
 provides the list of the 164 species used as representative of the 164
 Pliensbachian-Toarcian genera, their stratigraphic occurrences, their
 values for Raup’s (1966, 1967) parameters WR (whorl expansion) and DR
 (distance of the generating curve to the coiling axis), their relative
 warp coordinates (RW1, RW2) and their scores on the two principal
 components of the allometric space (PC1, PC2). Chronostratigraphic
 abbreviations are as follows: 1, Jamesoni; 2, Ibex; 3, Davoei; 4,
 Margaritatus; 5, Spinatum; 6, Tenuicostatum; 7, Falciferum; 8, Bifrons; 9,
 Variabilis; 10, Thouarsense; 11, Dispansum; 12, Pseudoradiosa; 13,
 Aalensis.Appendix.xls
DOI: 10.6084/m9.figshare.31153999
title: Additional file 2 of Visual ERP-based brain–computer interface use with severe physical, speech and eye movement impairments: case studies

description: Additional file 2.. Decoding performance per participant. Description: Full table of decoding target selection accuracies per participant, decoder and VSA condition
DOI: 10.6084/m9.figshare.31153999.v1
title: Additional file 2 of Visual ERP-based brain–computer interface use with severe physical, speech and eye movement impairments: case studies

description: Additional file 2.. Decoding performance per participant. Description: Full table of decoding target selection accuracies per participant, decoder and VSA condition
DOI: 10.6084/m9.figshare.31154002
title: Additional file 3 of Visual ERP-based brain–computer interface use with severe physical, speech and eye movement impairments: case studies

description: Additional file 3.. Cross-condition decoding performance per participant. Description: Full table of cross-validated, cross-condition decoding target selection accuracies per participant and decoder.
DOI: 10.6084/m9.figshare.31154002.v1
title: Additional file 3 of Visual ERP-based brain–computer interface use with severe physical, speech and eye movement impairments: case studies

description: Additional file 3.. Cross-condition decoding performance per participant. Description: Full table of cross-validated, cross-condition decoding target selection accuracies per participant and decoder.
DOI: 10.5061/dryad.rt214
title: Data from: Long antibody persistence and transgenerational transfer of immunity in a long-lived vertebrate

description: Although little studied in natural populations, the persistence of
 immunoglobulins may dramatically affect the dynamics of immunity and the
 ecology and evolution of host-pathogen interactions involving vertebrate
 hosts. By means of a multiple-year vaccination design against Newcastle
 disease virus, we experimentally addressed whether levels of specific
 antibodies can persist over several years in females of a long-lived
 procellariiform seabird—Cory’s shearwater—and whether maternal antibodies
 against that antigen could persist over a long period in offspring several
 years after the mother was exposed. We found that a single vaccination led
 to high levels of antibodies for several years and that the females
 transmitted antibodies to their offspring that persisted for several weeks
 after hatching even 5 years after a single vaccination. The temporal
 persistence of maternally transferred antibodies in nestlings was highly
 dependent on the level at hatching. A second vaccination boosted
 efficiently the level of antibodies in females and thus their transfer to
 offspring. Overall, these results stress the need to consider the temporal
 dynamics of immune responses if we are to understand the evolutionary
 ecology of host-parasite interactions and trade-offs between immunity and
 other life-history characteristics, in particular in long-lived species.
 They also have strong implications for conservation when vaccination may
 be used in natural populations facing disease threats.
description: female_dataFemale datachick_dataChick data
DOI: 10.5061/dryad.j94s2
title: Data from: Contrasting patterns of clonality and fine-scale genetic structure in two rare sedges with differing geographic distributions

description: For plants with mixed reproductive capabilities, asexual reproduction is
 more frequent in rare species and is considered a strategy for persistence
 when sexual recruitment is limited. We investigate whether asexual
 reproduction contributes to the persistence of two co-occurring, rare
 sedges that both experience irregular seed set and if their differing
 geographic distributions have a role in the relative contribution of
 clonality. Genotypic richness was high (R=0.889±0.02) across the clustered
 populations of Lepidosperma sp. Mt Caudan and, where detected, clonal
 patches were small, both in ramet numbers (less than or equal to3
 ramets/genet) and physical size (1.3±0.1 m). In contrast, genotypic
 richness was lower in the isolated L. sp. Parker Range populations, albeit
 more variable (R=0.437±0.13), with genets as large as 17 ramets and up to
 5.8 m in size. Aggregated clonal growth generated significant fine-scale
 genetic structure in both species but to a greater spatial extent and with
 additional genet-level structure in L. sp. Parker Range that is likely due
 to restricted seed dispersal. Despite both species being rare, asexual
 reproduction clearly has a more important role in the persistence of L.
 sp. Parker Range than L. sp. Mt Caudan. This is consistent with our
 prediction that limitations to sexual reproduction, via geographic
 isolation to effective gene exchange, can lead to greater contributions of
 asexual reproduction. These results demonstrate the role of population
 isolation in affecting the balance of alternate reproductive modes and the
 contextual nature of asexual reproduction in rare species.
description: LPR
 GenotypesAll raw genotypes for
 Lepidosperma sp. Parker Range, sorted into shared multi-locus
 genotypes.LMC
 GenotypesAll raw genotypes for
 Lepidosperma sp. Mt Caudan, sorted into shared multi-locus
 genotypes.