cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rf2qk
title: Data from: Adaptation in a variable environment: phenotypic plasticity and bet-hedging during egg diapause and hatching in an annual killifish

description: Two ways in which organisms adapt to variable environments are phenotypic
 plasticity and bet-hedging. Theory suggests that bet-hedging is expected
 to evolve in unpredictable environments for which reliable cues indicative
 of future conditions (or season length) are lacking. Alternatively, if
 reliable cues exist indicating future conditions, organisms will be under
 selection to produce the most appropriate phenotype – that is, adaptive
 phenotypic plasticity. Here we experimentally test which of these modes of
 adaptation are at play in killifish that have evolved an annual life
 cycle. These fish persist in ephemeral pools that completely dry each
 season through the production of eggs that can remain in developmental
 arrest, or diapause, buried in the soil, until the following rainy season.
 Consistent with diversified bet-hedging (a risk spreading strategy), we
 demonstrate that the eggs of the annual killifish Nothobranchius furzeri
 exhibit variation at multiple levels - whether or not different stages of
 diapause are entered, for how long diapause is entered, and the timing of
 hatching - and this variation persists after controlling for both genetic
 and environmental sources of variation. However, we show that phenotypic
 plasticity is also present in that the proportion of eggs that enter
 diapause is influenced by environmental factors (temperature and light
 level) that vary seasonally. In nature there is typically a large
 parameter zone where environmental cues are somewhat correlated with
 seasonality, but not perfectly so, such that it may be advantageous to
 have a combination of both bet-hedging and plasticity.
description: Bet-hedging data
 setData set documenting
 that Nothobranchius furzeri embryos (of known parentage incubated under
 common garden laboratory conditions: 25 degrees Celsius, in the dark, on
 moist peat moss) are capable of following either the diapause or
 direct-developing pathway, and once fully-developed embryos exhibit
 variation in hatching time.Phenotypic plasticity
 data setData set documenting
 that the proportion of Nothobranchius furzeri embryos that enter diapause
 is influenced by environmental factors (temperature and light
 level).
DOI: 10.5061/dryad.r8p5m
title: Data from: Climatic stress during stand development alters the sign and magnitude of age-related growth responses in a subtropical mountain pine

description: The modification of typical age-related growth by environmental changes is
 poorly understood, In part because there is a lack of consensus at
 individual tree level regarding age-dependent growth responses to climate
 warming as stands develop. To increase our current understanding about how
 multiple drivers of environmental change can modify growth responses as
 trees age we used tree ring data of a mountain subtropical pine species
 along an altitudinal gradient covering more than 2,200 m of altitude. We
 applied mixed-linear models to determine how absolute and relative
 age-dependent growth varies depending on stand development; and to
 quantify the relative importance of tree age and climate on individual
 tree growth responses. Tree age was the most important factor for tree
 growth in models parameterised using data from all forest developmental
 stages. Contrastingly, the relationship found between tree age and growth
 became non-significant in models parameterised using data corresponding to
 mature stages. These results suggest that although absolute tree growth
 can continuously increase along tree size when trees reach maturity age
 had no effect on growth. Tree growth was strongly reduced under increased
 annual temperature, leading to more constant age-related growth responses.
 Furthermore, young trees were the most sensitive to reductions in relative
 growth rates, but absolute growth was strongly reduced under increased
 temperature in old trees. Our results help to reconcile previous
 contrasting findings of age-related growth responses at the individual
 tree level, suggesting that the sign and magnitude of age-related growth
 responses vary with stand development. The different responses found to
 climate for absolute and relative growth rates suggest that young trees
 are particularly vulnerable under warming climate, but reduced absolute
 growth in old trees could alter the species’ potential as a carbon sink in
 the future.
description: PinusTaiwanensisThis is the original data for each tree (treeid) in each study site (site id; B: bottom, L: low, M: medium, H:high, t: top) from 1960. The variables include: year (yr), basal area increment (BAI, mm2 yr-1), relative tree growth (RTG, % yr-1), tree age (ta, No. years), mean annual temperature (MAT, ºC), annual precipitation (PP, mm).
DOI: 10.5061/dryad.vb850
title: Data from: Fruit evolution and diversification in campanulid angiosperms

description: With increases in both the size and scope of phylogenetic trees, we are
 afforded a renewed opportunity to address long standing comparative
 questions, such as whether particular fruit characters account for much of
 the variation in diversity among flowering plant clades. Studies to date
 have reported conflicting results, largely as a consequence of taxonomic
 scale and a reliance on potentially conservative statistical measures.
 Here we examine a larger and older angiosperm clade, the Campanulidae, and
 infer the rates of character transitions among the major fruit types,
 emphasizing the evolution of the achene fruits that are most frequently
 observed within the group. Our analyses imply that campanulids likely
 originated bearing capsules, and that all subsequent fruit diversity was
 derived from various modifications of this dry fruit type. We also found
 that the preponderance of lineages bearing achenes is a consequence of not
 only being a fruit type that is somewhat irreversible once it evolves, but
 one that also seems to have a positive association with diversification
 rates. While these results imply the achene fruit type is a significant
 correlate of diversity patterns observed across campanulids, we conclude
 that it remains difficult to confidently and directly view this character
 state as the actual cause of increased diversification rates.
description: BeaulieuDonoghueFruitThe fruit character scoring matrix
DOI: 10.5061/dryad.kt145km5
title: Data from: Genetic diversity and population structure in contemporary house sparrow populations along an urbanization gradient.

description: House sparrow (Passer domesticus) populations have suffered major declines
 in urban as well as rural areas, while remaining relatively stable in
 suburban ones. Yet, to date no exhaustive attempt has been made to examine
 how, and to what extent, spatial variation in population demography is
 reflected in genetic population structuring along contemporary
 urbanization gradients. Here we use putatively neutral microsatellite loci
 to study if and how genetic variation can be partitioned in a hierarchical
 way among different urbanization classes. Principal coordinate analyses
 did not support the hypothesis that urban/suburban and rural populations
 comprise two distinct genetic clusters. Comparison of FST values at
 different hierarchical scales revealed drift as an important force of
 population differentiation. Redundancy analyses revealed that genetic
 structure was strongly affected by both spatial variation and level of
 urbanization. The results shown here can be used as baseline information
 for future genetic monitoring programmes and provide additional insights
 into contemporary house sparrow dynamics along urbanization gradients.
description: Dryad Data Vangestel et
 al
DOI: 10.5061/dryad.vk43j
title: Data from: Independent domestications of cultivated tree peonies from different wild peony species

description: An understanding of plant domestication history provides insights into
 general mechanisms of plant adaptation and diversification and can guide
 breeding programs that aim to improve cultivated species. Cultivated tree
 peonies (genus Paeonia L.) are among the most popular ornamental plants in
 the world, yet the history of their domestication is still unresolved.
 Here, we explored whether the domestication in China of historically
 cultivated peonies, i.e., the common and flare cultivated tree peonies,
 was a single event or whether independent domestications occurred. We used
 14 nuclear microsatellite markers and a comprehensive set of 553 tree
 peonies collected across China, including common tree peonies, flare tree
 peonies and the wild species or subspecies that are potential contributors
 to the cultivated tree peonies, i.e., Paeonia rockii ssp. rockii, P.
 rockii ssp. atava, P. jishanensis and P. decomposita. Assignment methods,
 a principal component analysis and approximate Bayesian computations
 provided clear evidence for independent domestications of these common
 tree and flare tree peonies from two distinct and allopatric wild species,
 P. jishanensis and P. rockii ssp. atava, respectively. This study provides
 the first example of independent domestications of cultivated trees from
 distinct species and locations. This work also yields crucial insight into
 the history of domestication of one of the most popular woody ornamental
 plants. The cultivated peonies represent an interesting case of parallel
 and convergent evolution. The information obtained in this study will be
 valuable both for improving current tree peony breeding strategies and for
 understanding the mechanisms of domestication, diversification and
 adaptation in plants.
description: Table_S1 Description of
 the cultivated common tree peony, flare tree peony and wild tree peony
 species accessions, with their geographic origin, providers，latitude (N),
 longitude (E), altitude and sampling size.Note: Mt, mountain; Prr,
 P. rockii ssp. rockii; Pra, P. rockii ssp. atava; Size, the number of
 samples of the full dataset, Size*, the number of samples of the pruned
 dataset, the details in Table S3.Table_S1.xlsThe genotypes at 14 microsatellite loci of the 553 accessions.Note: Pj, Paeonia jishanensis, Pd, P. decomposita, Prr, P. rockii ssp. rockii; Pra, P. rockii ssp. atava. CTP: common tree peony; FTP: flare tree peony.Size*, the number of samples of theTable_S3.xls
DOI: 10.5061/dryad.8sj63
title: Data from: Mating affects resource selection and modulates associational effects between neighbouring resources

description: Associational effects occur when the attack rate on a resource depends on
 neighbouring resources in the environment. These effects are predicted to
 result from mismatches experienced by the consumer organism in resource
 selection along hierarchical search levels. As resource selection depends
 on sensory information used during search behaviour, we expected that
 different physiological states of an insect might modulate the outcome of
 associational effects due to differences in resource selection. We used
 Drosophila melanogaster, as a model organism for olfactory-guided
 behaviour in insects, to study the effects of mating induced behavioural
 changes on associational effects between two alternative resources. We
 found that mating has no effect on the ability of D. melanogaster to
 locate resource patches, but rather affects the perception of the
 resources within the patch. Consequently, we only found associational
 effects in the experiments with unmated females and not in the experiments
 with mated females. Our results suggest that the lack of associational
 effects for mated females resulted from changes in the use of short-range
 olfactory cues, leading to random selection among the resources. In
 conclusion, our results suggest that the physiological state of an insect
 modulates associational effects by affecting resource selection rates
 within the patch.
description: 1_one_choice_experimentData file contains the landing rate of unmated and mated Drosophila melanogaster females per odour source treatment. Data is presented in a binomial format.2_two_choice_experimentData file contains the attraction and landing rates of unmated and mated Drosophila melanogaster females on individual odour-point sources in the two-odour point source experiments. Data is presented in a binomial format.3_four_choice_experimentData file contains the attraction and landing rates of unmated and mated Drosophila melanogaster females on individual odour-point sources in the four-odour point source patches. Data is presented in a binomial format.4_patch_attraction_ratesData file contains the attraction rates of unmated and mated Drosophila melanogaster females to patches of different resource frequencies. Data is presented in a binomial format.5_flight_durationData file contains the flight durations of unmated and mated Drosophila melanogaster females in the four-odour point source patches measured in seconds.
DOI: 10.5061/dryad.8j0g0
title: Data from: The effects of stress intensity and stress type on inbreeding depression in Silene vulgaris

description: Inbreeding depression (ID) is generally assumed to increase under
 stressful conditions, but a number of studies have found the opposite
 pattern, i.e. that crossed offspring were more capable of exploiting
 benign conditions. Alternatively, the phenotypic variation hypothesis
 predicts that not stress intensity, but enhanced phenotypic variation in
 an environment leads to increased ID. We subjected inbred and crossed
 offspring of Silene vulgaris to drought, simulated herbivory, copper
 contamination, and two levels of nutrient deficiency and shade. In
 contrast to the predominant expectation, most stress treatments decreased
 inbreeding depression. With increasing nutrient limitation, ID decreased
 strongly, whereas under increasing shade ID did not change. These
 differences may be due to purging in the population of origin where
 conditions are nutrient-poor and dry, but not shaded. In contrast to the
 greenhouse experiment, ID was higher in a field site than in a more benign
 common garden. However, the predictions of the phenotypic variation
 hypothesis were met in both the greenhouse and the field vs. garden
 experiment. The results suggest that there may be no general relationship
 between ID and stress intensity, but specific effects of stress type and
 the novelty and variability of the environment.
description: Data on inbreeding
 depression and stress in Silene vulgarisThis document contains
 data on seed set and germination after self- and cross-pollination of
 Silene vulgaris and on the performance of the resulting seedlings grown
 under different stress conditions.Data Sandner & Matthies
 2016.xls
DOI: 10.5061/dryad.c96md
title: Data from: Evolution in eggs and phases: experimental evolution of fecundity and reproductive timing in Caenorhabditis elegans

description: To examine the role of natural selection in fecundity in a variety of
 Caenorhabditis elegans genetic backgrounds, we used an experimental
 evolution protocol to evolve 14 distinct genetic strains over 15–20
 generations. We were able to generate 790 distinct genealogies, which
 provided information on both the effects of natural selection and the
 evolvability of each strain. Among these genotypes are a wild-type (N2)
 and a collection of mutants with targeted mutations in the daf-c, daf-d
 and AMPK pathways. Differences are observed in reproductive fitness along
 with related changes in reproductive timing. The majority of selective
 effects on fecundity occur during the first few generations of evolution,
 while the negative selection for reproductive timing occurs on longer time
 scales. In addition, positive selection on fecundity results in positive
 and negative strain-dependent selection on reproductive timing. A
 derivative of population size per generation called reproductive
 carry-over (RCO) may be informative in terms of developmental selection.
 While these findings transcend mutations in a specific gene, changes in
 the RCO measure may nevertheless be products of selection. In conclusion,
 the broader implications of these findings are discussed, particularly in
 the context of genotype-fitness maps and the role of uncharacterized
 mutations in individual variation and evolvability.
description: Strain Catalogue and
 Reproductive Data per GenerationStrain catalogue with
 full genotypes, data for all genealogies (offspring per generation and RCO
 measures), and data for control conditions and heat map
 analysis.Supplemental-File-1.xlsxDesign for Genetic Crosses Unique to ExperimentMethod of multi-generational crosses for construction of selected mutant strains. Page 1 features daf-7; AMPK method, and Page 2 features daf-7; daf-16 method.Supplemental-File-2.pptx
DOI: 10.5061/dryad.83tg7
title: Data from: Expression of sexual ornaments in a polymorphic species: phenotypic variation in response to environmental risk

description: Secondary sexual traits may evolve under the antagonistic context of
 sexual and natural selection. In some polymorphic species, these traits
 are only expressed during the breeding period and are differently
 expressed in alternative phenotypes. However, it is unknown whether such
 phenotypes exhibit phenotypic plasticity of seasonal ornamentations in
 response to environmental pressures such as in the presence of fish
 (predation risk). This is an important question to understand the
 evolution of polyphenisms. We used facultative paedomorphosis in newts as
 a model system because it involves the coexistence of paedomorphs that
 retain gills in the adult stage with metamorphs that have undergone
 metamorphosis, but also because newts exhibit seasonal sexual traits. Our
 aim was therefore to determine the influence of fish on the development of
 seasonal ornamentation in the two phenotypes of the palmate newt
 (Lissotriton helveticus). During the entire newt breeding period, we
 assessed the importance of phenotype and fish presence with an
 information-theoretic approach. Our results showed that paedomorphs
 presented much less developed ornamentation than metamorphs and those
 ornamentations varied over time. Fish inhibited the development of sexual
 traits but differently between phenotypes: in contrast to metamorphs,
 paedomorphs lack the phenotypic plasticity of sexual traits to
 environmental risk. This study points out that internal and external
 parameters act in complex ways in the expression of seasonal sexual
 ornamentations and that similar environmental pressure can induce a
 contrasted evolution in alternative phenotypes.
description: Data used for the
 statistical analyses on secondary sexual traits in palmate
 newtData.pdf
DOI: 10.5061/dryad.p0b6b
title: Data from: Strong linkages between depth, longevity and demographic stability across marine sessile species

description: Understanding the role of the environment in shaping the evolution of life
 histories remains a major challenge in ecology and evolution. We
 synthesize longevity patterns of marine sessile species and find strong
 positive relationships between depth and maximum lifespan across multiple
 sessile marine taxa, including corals, bivalves, sponges and macroalgae.
 Using long-term demographic data on marine sessile and terrestrial plant
 species, we show that extreme longevity leads to strongly dampened
 population dynamics. We also used detailed analyses of Mediterranean red
 coral, with a maximum lifespan of 532 yr, to explore the life-history
 patterns of long-lived taxa and the vulnerability to external mortality
 sources that these characteristics can create. Depth-related environmental
 gradients – including light, food availability, temperature, and
 disturbance intensity –drive highly predictable distributions of life
 histories that, in turn, have predictable ecological consequences for the
 dynamics of natural populations.
description: C_rubrum_demographySize-based individual demographic data of Mediterranean red coral (Corallium rubrum) populations in the NW Mediterranean Sea.Data_C_rubrum_demography_1.csv
DOI: 10.5061/dryad.nt91j
title: Data from: Relating trophic resources to community structure: a predictive index of food availability

description: The abundance and the distribution of trophic resources available for
 consumers influence the productivity and the diversity of natural
 communities. Nevertheless, assessment of the actual abundance of food
 items available for individual trophic groups has been constrained by
 differences in methods and metrics used by various authors. Here we
 develop an index of food abundance, the framework of which can be adapted
 for different ecosystems. The relative available food index (RAFI) is
 computed by considering standard resource conditions of a habitat and the
 influence of various generalized anthropogenic and natural factors. RAFI
 was developed using published literature on food abundance and validated
 by comparison of predictions versus observed trophic resources across
 various marine sites. RAFI tables here proposed can be applied to a range
 of marine ecosystems for predictions of the potential abundance of food
 available for each trophic group, hence permitting exploration of
 ecological theories by focusing on the deviation from the observed to the
 expected.
description: Table
 S_1Table S_1. Literature
 used to rank the abundance of trophic resources among ecosystems. The last
 section (biotope typologies) has been used principally to detect natural
 or anthropogenic pressures influencing the basic patterns of food
 availability. Reference numbers indicated in Tables 1 and 6 refer to the
 papers listed here.Table S_2_ RAFI
 Evaluation for sitesTable S_2. a) Original
 spreadsheets used to evaluate RAFI in the ecosystems considered in the
 manuscript; b) User spreadsheets to be filled with own data for computing
 the Relative Abundance of Trophic Resources (RAFI) in other ecosystems.
 Please fill only the white cells: other cells must not be modified. Do not
 consider empty stations: they all initially result equal to
 "1.0" due to lack of data until your data will be
 present