cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.n5rj9
title: Data from: The genetic covariance between life-cycle stages separated by metamorphosis.

description: Metamorphosis is common in animals, yet the genetic associations between
 life cycle stages are poorly understood. Given the radical changes that
 occur at metamorphosis, selection may differ before and after
 metamorphosis, and the extent that genetic associations between pre- and
 post-metamorphic traits constrain evolutionary change is a subject of
 considerable interest. In some instances, metamorphosis may allow the
 genetic decoupling of life cycle stages, whereas in others, metamorphosis
 could allow complementary responses to selection across the life cycle.
 Using a diallel breeding design, we measured viability at four ontogenetic
 stages (embryo, larval, juvenile and adult viability), in the ascidian
 Ciona intestinalis and examined the orientation of additive genetic
 variation with respect to the metamorphic boundary. We found support for
 one eigenvector of G (gobsmax), which contrasted larval viability against
 embryo viability and juvenile viability. Target matrix rotation confirmed
 that while gobsmax shows genetic associations can extend beyond
 metamorphosis, there is still considerable scope for decoupled phenotypic
 evolution. Therefore, although genetic associations across metamorphosis
 could limit that range of phenotypes that are attainable, traits on either
 side of the metamorphic boundary are capable of some independent
 evolutionary change in response to the divergent conditions encountered
 during each life cycle stage.
description: viability_data_Aguirre.et.alData from: The genetic covariance between life-cycle stages separated by metamorphosis., Aguirre, J. David, Blows, Mark, Marshall, Dustin
DOI: 10.5061/dryad.gf54q
title: Data from:Insight into the durability of plant resistance to aphids from a demo-genetic study of Aphis gossypii in melon crops

description: Resistance breakdown has been observed following the deployment of plant
 cultivars resistant to pests. Assessing the durability of a resistance
 requires long-term experiments at least at a regional scale. We collected
 such data for melon resistance conferred by the Vat gene cluster to melon
 aphids. We examined landscape-level populations of Aphis gossypii
 collected in 2004–2015, from melon-producing regions with and without the
 deployment of Vat resistance and with different climates. We conducted
 demo-genetic analyses of the aphid populations on Vat and non-Vat plants
 during the cropping seasons. The Vat resistance decreased the density of
 aphid populations in all areas and changed the genetic structure and
 composition of these populations. Two bottlenecks were identified in the
 dynamics of adapted clones, due to the low levels of production of
 dispersal morphs and winter extinction. Our results suggest that (i) Vat
 resistance will not be durable in the Lesser Antilles, where no bottleneck
 affected the dynamics of adapted clones, (ii) Vat resistance will be
 durable in south-west France, where both bottlenecks affected the dynamics
 of adapted clones and (iii) Vat resistance will be less durable in
 south-east France, where only one of the two bottlenecks was observed.
description: Genetic data_Spring
 migrants Aphis gossypii on melon cropsAphis gossypii spring
 migrants- collected during the 3 weeks following transplantation- on melon
 crops in France. MLG= MultiLocus Genotype based on 8 SSR
 markersGenetic data_Wingless
 Aphis gossypii on melon cropsDemographic data_Aphis
 gossypii on melon cropsMLG Aphis
 gossypii_Allelic composition at 8 SRRSize of Amplification
 product at each locus. 999 = missing data
DOI: 10.5061/dryad.6kp1m6r2
title: Data from: Environmental and biological controls on the diversity and ecology of Late Cretaceous through early Paleogene marine ecosystems in the U.S. Gulf Coastal Plain

description: The late Mesozoic through early Cenozoic is an interval of significant
 biologic turnover and ecologic reorganization within marine assemblages,
 but the timing and causes of these changes remain poorly understood. Here,
 we quantify the pattern and timing of changes in the diversity (richness
 and evenness) and ecology of local (i.e., sample level) mollusk-dominated
 assemblages during this critical interval using field-collected and
 published datasets from the US Gulf Coastal Plain. We test whether the
 biologic and ecologic changes observed primarily at the global level
 during this time are also expressed at the local level, and whether the
 end Cretaceous (K/Pg) mass extinction and recovery moderated these trends.
 To explore whether environment had any effect on these patterns, we
 examine data from shallow subtidal and offshore settings. Assemblages from
 both settings recovered to pre-extinction diversity levels rapidly, in
 less than 7 million years. Following initial recovery, diversity remained
 relatively unchanged in both settings. The trajectory of ecological
 restructuring was distinct for each setting in the wake of the K/Pg
 extinction. In offshore assemblages, the abundance and number of predatory
 carnivorous taxa dramatically increased, and surficial sessile suspension
 feeders were replaced by more active suspension feeders. In contrast,
 shallow subtidal assemblages did not experience ecological reorganization
 following the K/Pg extinction. The distinct ecological patterns displayed
 in each environment follow onshore-offshore patterns of innovation,
 whereby evolutionary novelties first appear in onshore settings relative
 to offshore habitats. Increased predation pressure may explain the
 significant ecological restructuring of offshore assemblages, whereby the
 explosive radiation of predators drove changes in their prey.
 Habitat-specific ecological restructuring, and its occurrence solely
 during the recovery interval, implies that disturbance and incumbency were
 also key in mediating these ecological changes.
description: Sessa et al. 2012
 supplement
DOI: 10.5061/dryad.h8d0n
title: Data from: Seasonally varying contributions to urban CO2 in the Chicago, IL, USA region: insights from a high-resolution CO2 concentration and δ13C record

description: Understanding urban carbon cycling is essential given that cities sustain
 54% of the global population and contribute 70% of anthropogenic CO2
 emissions. When combined with CO2 concentration measurements ([CO2]),
 stable carbon isotope analyses (δ13C) can differentiate sources of CO2,
 including ecosystem respiration and combustion of fossil fuels, such as
 petroleum and natural gas. In this study, we used a wavelength
 scanned-cavity ringdown spectrometer to collect ~2x106 paired measurements
 for [CO2] and δ13C values in Evanston, IL for August 2011 through February
 2012. Evanston is located immediately north of Chicago, IL, the third
 largest city in the United States. The measurements represent one of the
 longest records of urban [CO2] and δ13C values thus far reported. We also
 compiled local meteorological information, as well as complementary [CO2]
 and δ13C data for background sites in Park Falls, WI and Mauna Loa, HI. We
 use the dataset to examine how ecosystem processes, fossil fuel usage,
 wind speed, and wind direction control local atmospheric [CO2] and δ13C in
 a midcontinent urban setting on a seasonal to daily basis. On average,
 [CO2] and δ13C values in Evanston were 16–23 ppm higher and 0.97–1.13‰
 lower than the background sites. While seasonal [CO2] and δ13C values
 generally followed broader northern hemisphere trends, the difference
 between Evanston and the background sites was larger in winter versus
 summer. Mixing calculations suggest that ecosystem respiration and
 petroleum combustion equally contributed CO2 in excess of background
 during the summer and that natural gas combustion contributed 80%–94% of
 the excess CO2 in winter. Wind speed and direction strongly influenced
 [CO2] and δ13C values on an hourly time scale. The highest [CO2] and
 lowest δ13C values occurred at wind speeds &lt;3 m s−1 and when winds
 blew from the northwest, west, and south over densely populated
 neighborhoods.
description: moore_jacobson_co2_d13C_meteo_dataThis file contains hourly averages for concentrations and d13C of atmospheric CO2 measured in Evanston, IL from Aug. 2011 to early March 2012. Concentration and d13C values were measured with a Picarro G1101-i wavelength scanned-cavity ring down spectrometer. Wind direction, wind speed, and other supporting meteorological data are from the Illinois Environmental Protection Agency and the US National Weather Service. For more information, see the ReadMe file.
DOI: 10.5061/dryad.gh721
title: Data from: Gene flow from domesticated escapes alters the life history of wild Atlantic salmon

description: Interbreeding between domesticated and wild animals occurs in several
 species. This gene flow has long been anticipated to induce genetic
 changes in life-history traits of wild populations, thereby influencing
 population dynamics and viability. Here, we show that individuals with
 high levels of introgression (domesticated ancestry) have altered age and
 size at maturation in 62 wild Atlantic salmon Salmo salar populations,
 including seven ancestral populations to breeding lines of the
 domesticated salmon. This study documents widespread changes to
 life-history traits in wild animal populations following gene flow from
 selectively bred, domesticated conspecifics. The continued high abundance
 of escaped, domesticated Atlantic salmon thus threatens wild Atlantic
 salmon populations by inducing genetic changes in fitness-related traits.
 Our results represent key evidence and a timely warning concerning the
 potential ecological impacts of the globally increasing use of
 domesticated animals.
description: Dataset_Bolstad_et_al_2017_Nature_Ecology_and_EvolutionR code used in Bolstad et al. (2017, Nature Ecology & Evolution)R_code_Bolstad_et_al_2017_Nature_Ecology_and_Evolution.rC++ code needed for running R codeseaAge_analysis.cpp
DOI: 10.5061/dryad.f2452v97
title: Data from: Phylogenetic analyses unravel the evolutionary history of NAC proteins in plants

description: NAC (NAM/ATAF/CUC) proteins are one of the largest groups of transcription
 factors in plants. Although many NAC proteins based on Arabidopsis and
 rice genomes have been reported in a number of species, a complete survey
 and classification of all NAC genes in plant species from disparate
 evolutionary groups is lacking. In this study, we analyzed whole-genome
 sequences from nine major lineages of land plants in order to unveil the
 relationships between these proteins. Our results show that there are
 fewer than 30 NAC proteins present in both mosses and lycophytes, whereas
 more than 100 were found in most of the angiosperms. Phylogenetic analyses
 suggest that NAC proteins consist of 21 subfamilies, most of which have
 highly conserved non-NAC domain motifs. Six of these subfamilies existed
 in early-diverged land plants, while the remainder diverged only within
 the angiosperms. We hypothesize that NAC proteins probably originated
 sometime more than 400 million years ago and expanded together with the
 differentiation of plants into organisms of increasing complexity possibly
 after the divergence of lycophytes from the other vascular plants.
description: Data_NAC
DOI: 10.5061/dryad.c5b7t
title: Data from: Modification of wheat gluten for improvement of binding capacity with keratin in hair

description: In this study, enzymatic hydrolysis and cationization with
 epoxypropyldodecyldimethylammonium chloride of wheat protein, an economic
 protein complex containing great amount of disulfide bonds, were conducted
 to improve properties such as solubility and disassociation behaviour for
 recovery of damaged hair when used in shampoo. The optimal conditions for
 enzymatic hydrolysis were pH 8.2, 55°C with Alcalase for 60 min. After the
 selected hydrolysis, the degree of hydrolysis, nitrogen solubility index,
 foaming capacity index, foam stability index, emulsifying activity index
 and emulsion stability index of hydrolysate with 58.71% of short-chain
 peptides (less than 1000 Da) were 8.81%, 39.07%, 225%, 56.67%, 9.62 m2 g−1
 and 49.08, respectively. The cationization was followed to raise the
 isoelectric point of wheat protein hydrolysate from 7.0 to 10.0, which
 could facilitate the quaternized protein hydrolysate to adhere to the
 surface of hair at the range of pH 5–6 of hair care products to form more
 disulfide bonds. The results show that a shampoo with quaternized wheat
 proteins hydrolysate possesses excellent properties in recovering damaged
 hair, making the surface of hair smooth and compact.
description: These are the data in
 origin program for the paper titled Modification of Wheat Gluten for
 Improvement of Binding Capacity with Keratin in Hairdata.rar
DOI: 10.5061/dryad.t3b18
title: Data from: Spatial and temporal unpredictability of colony size in cliff swallows across 30 years

description: Most colonially breeding animals occupy colonies that range in size from a
 few pairs to thousands of individuals, but the causes of colony size
 variation are largely unknown. Three general hypotheses are: (1) that
 variation in colony size is maintained by fluctuating selection via
 spatial and temporal changes in fitness associated with different colony
 sizes; (2) that colony formation reflects heterogeneity in habitat, with
 some sites having resources to support more individuals than others; and
 (3) that individuals assess the presence or annual reproductive success of
 current colony residents at each site and aggregate preferentially at
 high-quality sites. These hypotheses make predictions about how consistent
 colony size should be across sites and among years. We examined temporal
 and spatial variability of colony size for &gt;200 Cliff Swallow
 (Petrochelidon pyrrhonota) colony sites in western Nebraska across a
 30-year period. A colony's substrate type, annual population size in
 the study area, and whether the nesting season was relatively warm or
 cool, influenced average annual colony size. While some Cliff Swallow
 colony sites hosted perennially large colonies and others perennially
 small ones, between-year variability in colony size at most sites was
 high. Annual colony size distributions were relatively stable over 30
 years and provided no evidence for long-term directional changes in colony
 size. The only ecological characteristic that was strongly associated with
 Cliff Swallow colony size at a site was the type of nesting substrate,
 with bridges tending to have larger colonies and being more frequently
 occupied than other substrates. Some sites showed annual changes in colony
 size consistent with the birds' basing their choice of colony on the
 presence or success of conspecifics, but many sites did not conform to a
 pattern expected if coloniality is a by-product of traditional
 aggregation. Colony size in Cliff Swallows was temporally and spatially
 unpredictable when viewed across the 30 years of this study. Each of the
 three hypotheses to explain size variation may have applied at certain
 sites, but the pattern of colony size variability leant the most support
 to the hypothesis that fluctuating selection on group size maintains
 colonies of widely different sizes.
description: COLONIES
 1Original data used in
 analyses for this paper.
DOI: 10.5061/dryad.dh777
title: Data from: Experimental manipulation of avian social structure reveals segregation is carried over across contexts

description: Our current understanding of animal social networks is largely based on
 observations or experiments that do not directly manipulate associations
 between individuals. Consequently, evidence relating to the causal
 processes underlying such networks is limited. By imposing specified rules
 controlling individual access to feeding stations, we directly manipulated
 the foraging social network of a wild bird community, thus demonstrating
 how external factors can shape social structure. We show that
 experimentally imposed constraints were carried over into patterns of
 association at unrestricted, ephemeral food patches, as well as at nesting
 sites during breeding territory prospecting. Hence, different social
 contexts can be causally linked, and constraints at one level may have
 consequences that extend into other aspects of sociality. Finally, the
 imposed assortment was lost following the cessation of the experimental
 manipulation, indicating the potential for previously perturbed social
 networks of wild animals to recover from segregation driven by external
 constraints.
description: figure2data_wholenetworksSee Description in file - "1) id.info - the names of the vector represent the names of the individuals making up the networks in all other files, the vector values give whether the individual has an odd (=1) or even (=0) pit tag","2) whole.networks - this list contains the whole networks as given as points in figure 2 (see names on list)"figure3data_6daynetworksSee description in file - "1) list.6.day.networks - list contains the networks of the 6 day periods shown in Figure 3, in chronological order"Table1_contextcomparisonsSee description in file - "1) sites.vs.patches - the 3 parts of the list give the networks used in table 3 for comparing the selective feeder sites with the open patches, and spatial cooccurences. Networks in chronological order.","2) sites.vs.boxes - same as (1) but for networks at nestboxes instead of the open patches"
DOI: 10.5061/dryad.b13f4
title: Data from: Natural and experimental evolution of sexual conflict within Caenorhabditis nematodes

description: Background: Although males and females need one another in order to
 reproduce, they often have different reproductive interests, which can
 lead to conflict between the sexes. The intensity and frequency of
 male-male competition for fertilization opportunities is thought to be an
 important contributor to this conflict. The nematode genus Caenorhabditis
 provides an opportunity to test this hypothesis because the frequency of
 males varies widely among species with different mating systems. Results:
 We find evidence that there is strong inter- and intra-sexual conflict
 within C. remanei, a dioecious species composed of equal frequencies of
 males and females. In particular, some C. remanei males greatly reduce
 female lifespan following mating, and their sperm have a strong
 competitive advantage over the sperm of other males. In contrast, our
 results suggest that both types of conflict have been greatly reduced
 within C. elegans, which is an androdioecious species that is composed of
 self-fertilizing hermaphrodites and rare males. Using experimental
 evolution in mutant C. elegans populations in which sperm production is
 blocked in hermaphrodites (effectively converting them to females), we
 find that the consequences of sexual conflict observed within C. remanei
 evolve rapidly within C. elegans populations experiencing high levels of
 male-male competition. Conclusions: Together, these complementary data
 sets support the hypothesis that the intensity of intersexual conflict
 varies with the intensity of competition among males, and that
 male-induced collateral damage to mates can evolve very rapidly within
 populations.
description: Palopoli_remanei_lifehistoryTotal reproduction and lifespan (age at death) for three different stains of C. remanei mated in a series of factorial crosses. Includes lifespans for virgin females.Palopoli_remanei_spermcompetitionSperm competition among three strains of C. remanei mated against three female backgrounds.Palopoli_remanei_sperm_sizeSperm size measurements for three strains of C. remaneiPalopoli_elegans_spermcompetitionSperm competition results for C. elegans lines evolved in the presence of high and low male-male competitionPalopoli_elegans_hermaphroditemortalitySurvival of hermaphrodites living with males evolved under conditions of high and low male-male competitionPalopoli_elegans_sperm_sizeSperm size measures for C. elegans males evolved under conditions of high and low male-male competitionPalopoli_elegans_spiculeinsertionDuration of spicule insertion for C. elegans males evolved under conditions of high and low male-male competition.
DOI: 10.5061/dryad.d4m3986
title: Data from: Context-dependent scaling of kinematics and energetics during contests and feeding in mantis shrimp

description: Measurements of energy use, and its scaling with size, are critical to
 understanding how organisms accomplish myriad tasks. For example, energy
 budgets are central to game theory models of assessment during contests
 and underlie patterns of feeding behavior. Clear tests connecting energy
 to behavioral theory require measurements of the energy use of single
 individuals for particular behaviors. Many species of mantis shrimp
 (Stomatopoda: Crustacea) use elastic energy storage to power high-speed
 strikes that they deliver to opponents during territorial contests and to
 hard-shelled prey while feeding. We compared the scaling of strike
 kinematics and energetics between feeding and contests in the mantis
 shrimp Neogonodactylus bredini. We filmed strikes with high-speed video,
 measured strike velocity, and used a mathematical model to calculate
 strike energy. During contests, strike velocity did not scale with body
 size but strike energy scaled positively with size. Conversely, while
 feeding, strike velocity decreased with increasing size and strike energy
 did not vary according to body size. Individuals most likely achieved this
 strike variation through differential compression of their exoskeletal
 spring prior to the strike. Post-hoc analyses found that N. bredini used
 greater velocity and energy when striking larger opponents, yet variation
 in prey size was not accompanied by varying strike velocity or energetics.
 Our estimates of energetics inform prior tests of contest and feeding
 behavior in this species. More broadly, our findings elucidate the role
 behavioral context plays in measurements of animal performance.
description: analysis_dataset_FINALFinal analysis dataset (see README for details)PAGetal_analysis_code_FINALAnalysis code R Markdown file (see README for details).PAGetal_analysis_code_FINALR Markdown code output file (see README for details).
DOI: 10.5061/dryad.rk775
title: Data from: Are species’ responses to global change predicted by past niche evolution?

description: Predicting how and when adaptive evolution might rescue species from
 global change, and integrating this process into tools of biodiversity
 forecasting, has now become an urgent task. Here we explored whether
 recent population trends of species can be explained by their past rate of
 niche evolution, which can be inferred from increasingly available
 phylogenetic and niche data. We examined the assemblage of 409 European
 bird species for which estimates of demographic trends between 1970 and
 2000 are available, along with a species-level phylogeny and data on
 climatic, habitat, and trophic niches. We found that species’ proneness to
 demographic decline is associated with slow evolution of the habitat niche
 in the past, in addition to certain current-day life history and
 ecological traits. A similar result was found at a higher taxonomic level,
 where families prone to decline have had a history of slower evolution of
 climatic and habitat niches. Our results support the view that niche
 conservatism can prevent some species from coping with environmental
 change. Thus, linking patterns of past niche evolution and contemporary
 species dynamics for large species samples may provide insights into how
 niche evolution may rescue certain lineages in the face of global change.
description: Birds_100chronogramsPhylogenetic trees (100 best ML chronograms) of all study speciesBirdsClassificationTrendDataClassification and demographic trend data for all study species.BirdsNicheData_updated