cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.k1rd0
title: Data from: Experimental evolution reveals balancing selection underlying coexistence of alternative male reproductive phenotypes

description: Heritable alternative reproductive phenotypes (ARPs), which differ in
 traits associated with competition for mates, occur across taxa. If
 polymorphism in the genes underlying ARPs is maintained by balancing
 selection, selection should return ARP proportions to their equilibrium if
 that equilibrium is perturbed. Here, we used an experimental evolution
 approach to directly test this prediction in male Rhizoglyphus robini, in
 which two heritable morphs occur: armoured fighters and more female-like,
 benign scramblers. Using selection lines nearly fixed for male morph, we
 constructed replicate populations consisting of 50% or 94% fighters, and
 allowed them to evolve for 14 generations in two types of environment:
 simple or spatially complex. We found that in both types of populations,
 the proportion of fighters converged on values within a narrow range of
 0.70-0.83, although the rate of convergence was slower in the complex
 environment. Our results thus demonstrate balancing selection acting on
 polymorphism(s) underlying ARPs
description: R.robini male morph
 number counted after experimental evolution in two types of
 environment.Number of alternative
 male morphs assessed after 14 generations of experimental evolution in two
 types of environment differing in complexity level (simple and complex).
 Two levels of initial morph ratio were used (low and high) which gives 4
 combinations of factors in total (simple/complex; low/high). Each
 combination were replicate 5 times (lines nested within combination of
 factors). Data were obtained by counting alternative male morphs after 1
 generation of common garden conditions. Abbreviations used in column
 names: Line_id - number of line within combination of factors;
 Envir_complexity - environment complexity (simple/complex);
 Fighter_start_prop - initial proportion of fighters (low-50%/ high-94%);
 Fighters_end - number of fighters after 14 generations of evolution in
 conditions mentioned above; Scramblers_end - number of fighters after 14
 generations of evolution in conditions mentioned above.Skrzynecka&Radwan_Evolution_2016.xlsx
DOI: 10.5061/dryad.p8cv8
title: Data from: The geography of spatial synchrony

description: Spatial synchrony, defined as correlated temporal fluctuations among
 populations, is a fundamental feature of population dynamics, but many
 aspects of synchrony remain poorly understood. Few studies have examined
 detailed geographical patterns of synchrony; instead most focus on how
 synchrony declines with increasing linear distance between locations,
 making the simplifying assumption that distance decay is isotropic. By
 synthesising and extending prior work, we show how geography of synchrony,
 a term which we use to refer to detailed spatial variation in patterns of
 synchrony, can be leveraged to understand ecological processes including
 identification of drivers of synchrony, a long-standing challenge. We
 focus on three main objectives: (1) showing conceptually and theoretically
 four mechanisms that can generate geographies of synchrony; (2)
 documenting complex and pronounced geographies of synchrony in two
 important study systems; and (3) demonstrating a variety of methods
 capable of revealing the geography of synchrony and, through it,
 underlying organism ecology. For example, we introduce a new type of
 network, the synchrony network, the structure of which provides ecological
 insight. By documenting the importance of geographies of synchrony,
 advancing conceptual frameworks, and demonstrating powerful methods, we
 aim to help elevate the geography of synchrony into a mainstream area of
 study and application.
description: gypsy_moth_defoliation_time_seriesThe file "gypsy_moth_defoliation.csv" contains area defoliated (in units of square kilometers) by the gypsy moth from 1975 to 2014 in 64 x 64 km grid cells spanning the area considered "generally infested" by the gypsy moth (i.e., where gypsy moth populations were established) as of 1975. Defoliated area is based on aerial surveys.gypsy_moth_defoliation.csv
DOI: 10.5061/dryad.7nf43
title: Data from: Phylogenetic context determines the role of competition in adaptive radiation

description: Understanding ecological mechanisms regulating the evolution of
 biodiversity is of much interest to ecologists and evolutionary
 biologists. Adaptive radiation constitutes an important evolutionary
 process that generates biodiversity. Competition has long been thought to
 influence adaptive radiation, but the directionality of its effect and
 associated mechanisms remain ambiguous. Here, we report a rigorous
 experimental test of the role of competition on adaptive radiation using
 the rapidly evolving bacterium Pseudomonas fluorescens SBW25 interacting
 with multiple bacterial species that differed in their phylogenetic
 distance to the diversifying bacterium. We showed that the inhibitive
 effect of competitors on the adaptive radiation of P. fluorescens
 decreased as their phylogenetic distance increased. To explain this
 phylogenetic dependency of adaptive radiation, we linked the phylogenetic
 distance between P. fluorescens and its competitors to their niche and
 competitive fitness differences. Competitive fitness differences, which
 showed weak phylogenetic signal, reduced P. fluorescens abundance and thus
 diversification, whereas phylogenetically conserved niche differences
 promoted diversification. These results demonstrate the context dependency
 of competitive effects on adaptive radiation, and highlight the importance
 of past evolutionary history for ongoing evolutionary processes.
description: SBW25 density and
 richness
DOI: 10.5061/dryad.7hn64
title: Data from: Feces nitrogen release induced by different large herbivores in a dry grassland

description: Large herbivores have pronounced effects on nutrient cycling in
 grasslands. These organisms are known to alter the quality and quantity of
 plant production as well as the amounts and quality of plant litter and
 animal wastes. The generalization that the relative quality of detritus
 inputs is enhanced by herbivores is well known, but how this process is
 affected by diet selection processing and feces production of different
 large herbivores remains largely unstudied. Here, we measured how these
 differences for cattle and sheep on a dry grassland might influence
 nitrogen (N) mineralization from feces. We found that cattle of larger
 body size tended to select low quality grass Stipa grandis as the major
 food source. In contrast, the subdominant grass Leymus chinensis with
 relatively high N content was a majority in the diet of smaller sheep,
 when palatable forbs were insufficient in the field. This diverse diet
 quality resulted in a C/N ratio of cattle feces that was higher than that
 of sheep feces. Relatively higher labile C availability in the cattle
 feces, namely relatively higher cellulose/hemicellulose contents, promoted
 microbial growth and in turn accelerated cattle feces decomposition. A
 surprise finding was that the feces from cattle mineralized about twice as
 much N as feces from sheep, despite the latter having slightly higher N
 content. From a grassland productivity perspective, increasing the
 proportion of large body-sized species in grazing herbivore assemblages
 perhaps is beneficial to forage productivity and nutrient recycling by the
 rapid degradation of feces.
description: Diet selection of
 herbivoresProportions of each
 plant species foraged by herbivores.Diet_Selection.CSVFeces nutrient releaseFeces C loss (CR), N loss (NR), C release rates (CRR) and N release rates (NRR) during decomposition.Feces_C_N_Release.CSVThe chemical composition of fresh fecesThe chemical composition and fiber contents of fresh feces. The data include fecal C, N, hemicellulose, cellulose, lignin (ADL) and lignin/N ratios.Feces_Chem_Fiber.CSVFeces C/N RatiosDynamics of fecal C/N ratios during decomposition.Feces_CN_Ratio.CSVFeces remaining and water contentDynamics of feces remaining ratio (dry matter) and water content during decomposition.Feces_Mass_Moisture.CSVFeces microbial biomass carbonDynamics of feces microbial biomass carbon during decomposition.Feces_MBC.CSVThe chemical composition of plantsThe C and N contents of plants foraged by herbivores.Plant_C_N.CSVSoil mineral N and water contentsThe mineral N contents and water contents of soil under feces bags at day 0 and day 30 during decomposition.Soil.CSVC/N ratios of dietC/N ratios of herbivores diet.Diet_C_N.CSVREADMEIntroductions for data files.
DOI: 10.5061/dryad.3gt37
title: Data from: Plastic responses of bryozoans to ocean acidification

description: Phenotypic plasticity has the potential to allow organisms to respond
 rapidly to global environmental change, but the range and effectiveness of
 these responses are poorly understood across taxa and growth strategies.
 Colonial organisms might be particularly resilient to environmental
 stressors, as organizational modularity and successive asexual generations
 can allow for distinctively flexible responses in the aggregate form. We
 performed laboratory experiments to examine the effects of increasing
 dissolved carbon dioxide (i.e. ocean acidification) on the colonial
 bryozoan Celleporella cornuta sampled from two source populations within a
 coastal upwelling region of the northern California coast. Bryozoan
 colonies were remarkably plastic under these carbon dioxide (CO2)
 treatments. Colonies raised under high CO2 grew more quickly, investing
 less in reproduction and producing lighter skeletons when compared to
 genetically identical clones raised under current atmospheric values.
 Bryozoans held in high CO2 conditions also changed the Mg/Ca ratio of
 skeletal walls and increased the expression of organic coverings in new
 growth, which may serve as protection against acidified water. We also
 observed strong differences between populations in reproductive investment
 and organic covering reaction norms, consistent with adaptive responses to
 persistent spatial variation in local oceanographic conditions. Our
 results demonstrate that phenotypic plasticity and energetic trade-offs
 can mediate ecological responses to global environmental change, and
 highlight the broad range of strategies available to colonial organisms.
description: JEB_Bryo_DataPrimary bryozoan growth dataset from Swezey et al. 2017.
DOI: 10.5061/dryad.d4196
title: Data from: Individual repeatability in laying behaviour does not support the migratory carry-over effect hypothesis of egg-size dimorphism in Eudyptes penguins

description: Penguins of the genus Eudyptes are unique among birds in that their
 first-laid A-egg is 54–85% the mass of their second-laid B-egg. Although
 the degree of intra-clutch egg-size dimorphism varies greatly among the
 seven species of the genus, obligate brood reduction is typical of each,
 with most fledged chicks resulting from the larger B-egg. Many authors
 have speculated upon why Eudyptes penguins have evolved and maintained a
 highly dimorphic 2-egg clutch, and why it is the first-laid egg that is so
 much smaller than the second, but only recently has a testable, proximate
 mechanism been proposed. In most species of Eudyptes penguins females
 appear to initiate egg-formation at sea during return migration to
 breeding colonies. In macaroni penguins E. chrysolophus, females with a
 shorter pre-laying interval ashore (and thus presumably greater overlap
 between migration and egg-formation) lay more dimorphic eggs, suggesting a
 physiological conflict may constrain growth of the earlier-initiated
 A-egg. This migratory carry-over effect hypothesis (MCEH) was tested in
 eastern rockhopper penguins E. chrysocome filholi on Campbell Island, New
 Zealand, by recording the arrival and lay dates, body sizes, and egg
 masses of transponder-tagged females over two years. Females with longer
 pre-laying intervals laid less dimorphic clutches, as predicted by the
 MCEH. However, repeated measures of individual females revealed that
 within-individual variation in egg-size dimorphism between years was
 unrelated to within-individual variation in pre-laying interval. Egg
 masses, and to a lesser extent egg-size dimorphism, were highly repeatable
 traits related to body size and body mass. These results and a detailed
 consideration of the MCEH suggest that egg-size dimorphism in Eudyptes
 penguins is unlikely to be caused by a migratory carry-over effect.
description: Morrison 2016 Eastern
 Rockhopper Penguin laying dataAll data used in
 Morrison 2016 (Journal of Avian Biology
 doi:10.1111_jav.00740).Morrison penguin lay
 data.csv
DOI: 10.5061/dryad.33d5s
title: Data from: Ecological novelty by hybridization: experimental evidence for increased thermal tolerance by transgressive segregation in Tigriopus californicus

description: Early generations of hybrids can express both genetic incompatibilities
 and phenotypic novelty. Insights into whether these conflicting
 interactions between intrinsic and extrinsic selection persist after a few
 generations of recombination require experimental studies. To address this
 question, we use interpopulation crosses and recombinant inbred lines
 (RILs) of the copepod Tigriopus californicus, and focus on two traits that
 are relevant for the diversification of this species: survivorship during
 development and tolerance to thermal stress. Experimental crosses between
 two population pairs show that most RILs between two heat-tolerant
 populations show enhanced tolerance to temperatures that are lethal to the
 respective parentals, whereas RILs between a heat-tolerant and a
 heat-sensitive population are intermediate. Although interpopulation
 crosses are affected by intrinsic selection at early generational hybrids,
 most of the sampled F9 RILs have recovered fitness to the level of their
 parentals. Together, these results suggest that a few generations of
 recombination allows for an independent segregation of the genes
 underlying thermal tolerance and cytonuclear incompatibilities, permitting
 certain recombinant lineages to survive in niches previously unused by
 parental taxa (i.e., warmer thermal environments) without incurring
 intrinsic selection.
description: Extrinsic
 fitnessTable showing the
 survivorship (percentage) 3 days after heat stress essay. The data is
 divided into separate files for each temperature and experimental cross.
 BR- Bird Rock; SC- Santa Cruz; SD- San Diego.Intrinsic
 fitnessSurvivorship
 (percentage) 14 days after hatching. The data is divided into separate
 files for each experimental cross and inbred parental lines. BR- Bird
 Rock; SC- Santa Cruz; SD- San Diego.
DOI: 10.5061/dryad.q4t65
title: Data from: Theoretical constraints on the precision and age range of rehydroxylation dating

description: Accurate and precise dating methods are of central importance to
 archaeology, palaeontology and earth science. This paper investigates the
 expected precision and age range of rehydroxylation dating, a recently
 proposed technique for fired clays. An expression for combined measurement
 uncertainty is presented, which takes into account all significant sources
 of experimental uncertainty. Numerical simulations are performed for
 comparison. Combined measurement uncertainties of approximately 5% with
 respect to the age of the ceramic should be possible given well-designed
 experiments. In this case, the most significant contribution to combined
 measurement uncertainty is from effective lifetime temperature. In
 addition, it is shown that precision should be acceptable for recently
 fired material (less than 1 year). Mismatch of balance resolution to
 sample mass results in large variation in combined relative uncertainties,
 which vary by four orders of magnitude (approx. 1–1160%) across recent
 experimental studies, rendering some recently reported dates meaningless.
 It is recommended that this ratio be less than 10−6 for a combined
 relative uncertainty of less than 1%. The age limits of the technique are
 set by the value of the rate constant and individual sample mineralogy.
 This theoretical framework should help future interlaboratory comparison
 as well as optimizing instrument design.
description: RHX_Uncertainties-1.0MATLAB (2014a) code and supplementary data for Hare, VJ (2015) Theoretical constraints on the precision and age range of rehydroxylation dating. R. Soc. open sci.
DOI: 10.5061/dryad.3st56j0
title: Data from: Lifespan bias explains live-dead discordance in abundance of two common bivalves

description: Lifespan bias potentially alters species abundance in death assemblages
 through the overrepresentation of short-lived organisms compared to their
 long-lived counterparts. Although previous work found that lifespan bias
 did not contribute significantly to live-dead discordance in bivalve
 assemblages, lifespan bias better explained discordance in two groups:
 longer-lived bivalve species and species with known lifespans. More
 studies using local, rather than global, species-wide, lifespans and
 mortality rates would help to determine the prevalence of lifespan bias,
 especially for long-lived species with known lifespans. Here, we conducted
 a field study at two sites in North Carolina to assess potential lifespan
 bias between Mercenaria mercenaria and Chione elevata, two long-lived
 bivalve species that can be aged directly. We compared the ability of
 directly measured local lifespans to that of regional and global lifespans
 to predict live-dead discordance between these two species. The
 shorter-lived species (C. elevata) was overrepresented in the death
 assemblage compared to its live abundance, and local lifespan data largely
 predicted the amount of live-dead discordance; local lifespans predicted
 43% to 88% of discordance. Furthermore, the global maximum lifespan for M.
 mercenaria resulted in substantial overpredictions of discordance (1.4 to
 1.6 times the observed live-dead discordance). The results of this study
 suggest that lifespan bias should be considered as a factor affecting
 proportional abundances of species in death assemblages, and that using
 lifespan estimates appropriate to the study locality improves predictions
 of discordance based on lifespan compared to using global lifespan
 estimates.
description: CroninEtAl_R_Script_and_Data.zip file contains R script for all calculations in the manuscript and the data files needed to run it. .csv files include counts for each site, global; regional, and local maximum ages; and ages and measurements for all individuals collected that were at least one year old.
DOI: 10.5061/dryad.h588kh6
title: Data from: Extrinsic and intrinsic constraints interact to drive extra-pair paternities in the Alpine marmot

description: To reproduce, animals have to form pairs and large variations in the
 degree of mate switching are observed. Extrinsic and intrinsic factors can
 constrain individual’s mate switching. Among intrinsic factors, genes
 involved in pair-bonding, such as Avpr-1a, receive increasing attention.
 The length of microsatellites present in the regulatory region of Avpr-1a
 determines the neural densities and distributions of the vasopressin
 receptors known to impact pair-bonding behaviours. For the first time, we
 investigated if and how the genetic makeup at Avpr-1a, an intrinsic
 factor, and the social context, an extrinsic factor, experienced by wild
 Alpine marmot (Marmota marmota) females affect the proportion of
 extra-pair young. This proportion was positively correlated with the
 length of their Avpr-1a regulatory region but only when the social
 constraints were relaxed, i.e. when mature male subordinates were present.
 When ignoring the interactive effect between the length of their Avpr-1a
 regulatory region and the social constraints, the genetic makeup at
 Avpr-1a was not associated with the proportion of extra-pair young. Under
 natural conditions, the genetic regulation of pair-bonding could be hidden
 by extrinsic factors constraining mate choice.
description: avpr-1a lengths of
 Alpine marmot females and extra-pair behaviourFemale avpr-1a lengths,
 extra-pair paternity occurence, social pair genetic relatedness and
 presence-absence of male subordinatesavpr1_DRYAD.csv
DOI: 10.5061/dryad.hb84g
title: Data from: Rapid loss of behavioural plasticity and immunocompetence under intense sexual selection

description: Phenotypic plasticity allows animals to maximise fitness by conditionally
 expressing the phenotype best adapted to their environment. While evidence
 for such adjustment in reproductive tactics is common, little is known
 about how phenotypic plasticity evolves in response to sexual selection.
 We examined the effect of sexual selection intensity on phenotypic
 plasticity in mating behaviour using the beetle Callosobruchus maculatus.
 Male genital spines harm females during mating and females exhibit
 copulatory kicking, an apparent resistance trait aimed to dislodge mating
 males. After exposing individuals from male- and female-biased
 experimental evolution lines to male- and female-biased sociosexual
 environments, we examined behavioural plasticity in matings with standard
 partners. While females from female-biased lines kicked sooner after
 exposure to male-biased sociosexual contexts, in male-biased lines this
 plasticity was lost. Ejaculate size did not diverge in response to
 selection history, but males from both treatments exhibited plasticity
 consistent with sperm competition intensity models, reducing size as the
 number of competitors increased. Analysis of immunocompetence revealed
 reduced immunity in both sexes in male-biased lines, pointing to increased
 reproductive costs under high sexual selection. These results highlight
 how male and female reproductive strategies are shaped by interactions
 between phenotypically plastic and genetic mechanisms of sexual trait
 expression.
description: dataTwo csv files,
 containing the main experimental data (data-main.csv) and the data from
 the lytic activity assay (data-lytic.csv).
DOI: 10.5061/dryad.r4g3g
title: Data from: Assessing differences between ancestral recombination graphs

description: Ancestral recombination graphs (ARGs) represent the history of portions of
 a genome with recombination. Attempts to infer ARGs have been hampered by
 the lack of an ARG comparison metric which could be used to measure how
 well inference succeeded. We propose a simple ARG comparison framework
 based on averaging standard tree comparison measures across sites. Using
 simulated data we show that this framework, instantiated with an
 appropriate tree comparison measure, can distinguish better from worse
 inferences of an ARG.
description: Python ARG-comparison
 programsTar gzip archive of
 Python programs used to implement the ARG comparison framework and to
 perform the simulations in the paper.arg_comparison.tgz