cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.h1s7b
title: Data from: Differences in patterns of reproductive allocation between the sexes in Nicrophorus orbicollis

description: Organisms are selected to maximize lifetime reproductive success by
 balancing the costs of current reproduction with costs to future survival
 and fecundity. Males and females typically face different reproductive
 costs, which makes comparisons of their reproductive strategies difficult.
 Burying beetles provide a unique system that allows us to compare the
 costs of reproduction between the sexes because males and females are
 capable of raising offspring together or alone and carcass preparation and
 offspring care represent the majority of reproductive costs for both
 sexes. Because both sexes perform the same functions of carcass
 preparation and offspring care, we predict that they would experience
 similar costs and have similar life history patterns. In this study we
 assess the cost of reproduction in male Nicrophorus orbicollis and compare
 to patterns observed in females. We compare the reproductive strategies of
 single males and females that provided pre- and post-hatching parental
 care. There is a cost to reproduction for both males and females, but the
 sexes respond to these costs differently. Females match brood size with
 carcass size, and thus maximize the lifetime number of offspring on a
 given size carcass. Males cull proportionately more offspring on all
 carcass sizes, and thus have a lower lifetime number of offspring compared
 to females. Females exhibit an adaptive reproductive strategy based on
 resource availability, but male reproductive strategies are not adaptive
 in relation to resource availability.
description: Plos Paper Lifetime
 DataIn this data file,
 Treatment 1 = 20g control carcasses, 2 = 30g control carcasses, 3 =
 30g-&gt;20g experimental carcasses, 4 = 20g-&gt;30g experimental
 carcasses, and 7 = non breeding individuals.Plos Paper Within
 Lifetime DataIn this data file,
 carcass 1 = 20g control, carcass 2 = 30g control, carcass 3 = 30g-&gt;20g
 experimental, and carcass 4 = 20g-&gt;30g experimental. Age is the number
 of the reproductive bout. Start brood is the number of first install
 larvae, and final brood is the number of eclosed adult offspring.
 Mindoffmass is the mean individual offspring mass for each reproductive
 bout.
DOI: 10.5061/dryad.h63k2
title: Data from: Density-dependent energy use contributes to the self-thinning relationship of cohorts

description: In resource-limited populations, an increase in average body size can
 occur only with a decline in abundance. This is known as self-thinning,
 and the decline in abundance in food-limited populations is considered
 proportional to the scaling of metabolism with body mass. This popular
 hypothesis may be inaccurate, because self-thinning populations can also
 experience density-dependent competition, which could alter their energy
 use beyond the predictions of metabolic scaling. This study tested whether
 density-dependent competition has an energetic role in self-thinning, by
 manipulating the abundance of the fish Macquaria novemaculeata and tank
 size to partition the effects of competition from metabolic scaling. We
 found that self-thinning can be density dependent and that changes in
 intraspecific competition may be more influential than metabolic scaling
 on self-thinning relationships. The energetic mechanism we propose is that
 density-dependent competition causes variation in the allocation of energy
 to growth, which alters the energetic efficiency of self-thinning cohorts.
 The implication is that food-limited cohorts and populations with
 competitive strategies that encourage fast-growing individuals will have
 less body mass at equilibrium and higher mortality rates. This finding
 sheds light on the processes structuring populations and can be used to
 explain inconsistencies in the mass-abundance scaling of assemblages and
 communities (the energetic-equivalence rule).
description: WeightsWeekly fish weights (grams) for the three experiments (1,2a,2b), for each feeding treatment ("DDR": increasing food; "STR": limiting food), and for each tank abundance treatment ("density"). Between 5 and 12 replicates.DeathsWeekly number of deaths (or pseudo-mortality rates - see publication) during each of the three experiments (1,2a,2b) in each tank, and the total number of fish remaining at the end of each experiment. Feeding treatments - "DDR": increasing food; "STR": limiting food.Activity ratesSwimming speed data for experiment 1. Between 3 and 5 replicate fish followed per tank to measure speed (cm/s), average body length measured (cm), and average speed for each tank calculated (body lengths per s; "Av. BL/s"). Feeding treatments "DDR": increasing food; "STR": limiting food. "Density" refers to the tank abundance treatment.
DOI: 10.5061/dryad.482tn
title: Data from: Geometry of wave-formed orbital ripples in coarse sand

description: Using new large-scale wave-flume experiments we examine the cross-section
 and planform geometry of wave-formed ripples in coarse sand (median grain
 size D50 = 430 μm) under high-energy shoaling and plunging random waves.
 We find that the ripples remain orbital for the full range of encountered
 conditions, even for wave forcing when in finer sand the ripple length λr
 is known to become independent of the near-bed orbital diameter ds
 (anorbital ripples). The proportionality between λr and ds is not
 constant, but decreases from about 0.55 for ds / D50 ≈ 1400 to about 0.27
 for ds / D50 ≈ 11 , 500 . Analogously, ripple height ηr increases with ds,
 but the constant of proportionally decreases from about 0.08 for ds / D50
 ≈ 1400 to about 0.02 for ds / D50 &gt; 8000 . In contrast to earlier
 observations of coarse-grained two-dimensional wave ripples under mild
 wave conditions, the ripple planform changes with the wave Reynolds number
 from quasi two-dimensional vortex ripples, through oval mounds with
 ripples attached from different directions, to strongly subdued
 hummocky-type features. Finally, we combine our data with existing
 mild-wave coarse-grain ripple data to develop new equilibrium predictors
 for ripple length, height and steepness suitable for a wide range of wave
 conditions and a D50 larger than about 300 μm.
description: Wave-ripple and
 hydrodynamical data for a coarse-sand beachBardexII_CoarseSandRippleData.zip
DOI: 10.5061/dryad.kc1q1
title: Data from: Signatures of natural selection between life cycle stages separated by metamorphosis in European eel

description: Background: Species showing complex life cycles provide excellent
 opportunities to study the genetic associations between life cycle stages,
 as selective pressures may differ before and after metamorphosis. The
 European eel presents a complex life cycle with two metamorphoses, a first
 metamorphosis from larvae into glass eels (juvenile stage) and a second
 metamorphosis into silver eels (adult stage). We tested the hypothesis
 that different genes and gene pathways will be under selection at
 different life stages when comparing the genetic associations between
 glass eels and silver eels. Results: We used two sets of markers to test
 for selection: first, we genotyped individuals using a panel of 80
 coding-gene single nucleotide polymorphisms (SNPs) developed in American
 eel; second, we investigated selection at the genome level using a total
 of 153,423 RAD-sequencing generated SNPs widely distributed across the
 genome. Using the RAD approach, outlier tests identified a total of 2413
 (1.57 %) potentially selected SNPs. Functional annotation analysis
 identified signal transduction pathways as the most over-represented group
 of genes, including MAPK/Erk signalling, calcium signalling and GnRH
 (gonadotropin-releasing hormone) signalling. Many of the over-represented
 pathways were related to growth, while others could result from the
 different conditions that eels inhabit during their life cycle.
 Conclusions: The observation of different genes and gene pathways under
 selection when comparing glass eels vs. silver eels supports the adaptive
 decoupling hypothesis for the benefits of metamorphosis. Partitioning the
 life cycle into discrete morphological phases may be overall beneficial
 since it allows the different life stages to respond independently to
 their unique selection pressures. This might translate into a more
 effective use of food and niche resources and/or performance of
 phase-specific tasks (e.g. feeding in the case of glass eels, migrating
 and reproducing in the case of silver eels).
description: SNP raw
 dataExcel file containing
 all SNP raw data for 113 individualsSNP_Table_BMCGenomicspaper.xlsx
DOI: 10.5061/dryad.c83j2
title: Data from: Research design considerations to ensure detection of all species in an avian community

description: 1.Recent advances in the estimation of species richness from count data
 have allowed avian ecologists to incorporate incomplete detectability of
 species when comparing richness across space or time. Raw counts from
 single or repeated visits to sample point(s) are nonetheless still used
 for assessing community composition, and the failure to account for
 detectability when making these evaluations may lead to incorrect
 inferences about the community. 2.We estimated detection probabilities (p)
 for a suite of bird species and used these detection probabilities to
 determine the minimum number of visits at a single point and the minimum
 number of points in a grid required to confidently (≥ 90%) detect the full
 community of birds for rare, moderately rare, and common species. We used
 occupancy modeling to estimate the detection probabilities for species
 from two study sites in Nebraska and Saskatchewan. 3.Some common or highly
 detectable species were confidently detected in a single visit to a point,
 whereas others with low detection probabilities (p &lt; 0.20) required
 more than ten visits to be confidently detected at a point. The grid size
 required to detect a species in an area varied from a single point for a
 common highly detectable species to over 30 points for a rare species with
 low detectability. 4.Detection probabilities of the least detectable
 species in a study area can be used to determine the number of visits to a
 single point or the number of points in a grid to be confident that the
 full community is detected. Biologists can conclude that a species is most
 likely absent from the community if it remains undetected using the
 appropriate sampling effort.
description: Occupancy
 dataThis file contains two
 tabs with occupancy data (0 = not detected, 1 = detected) from Nebraska
 and from Saskatchewan. Data are from upland grassland sites using
 5-minute, 100-m radius point counts. Each row specifies a single visit to
 a single plot.rarity
 simThis file contains the
 SAS code used to simulate detection across a grid of
 points.
DOI: 10.15468/dl.s237nw
title: Occurrence Download

description: A dataset containing 36010 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Nasturtium officinale"
 ]
}

 The dataset includes 36010 records from 929 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001070-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.qr3t2
title: Data from: Genetic mapping of two components of reproductive isolation between two sibling species of moths, Ostrinia nubilalis and O. scapulalis

description: We report the quantitative trait loci (QTL) mapping of reproductive
 isolation traits between Ostrinia nubilalis (the European corn borer) and
 its sibling species O. scapulalis (the Adzuki bean borer), focusing on two
 traits: mating isolation (mi) and pheromone production (Pher). Four
 genetic maps were generated from two backcross families, with two maps
 (one chromosomal map and one linkage map) per backcross. We located
 165–323 AFLP markers on these four maps, resulting in the identification
 of 27–31 linkage groups, depending on the map considered. No-choice mating
 experiments with the offspring of each backcross led to the detection of
 at least two QTLs for mi in different linkage groups. QTLs underlying Pher
 were located in a third linkage group. The Z heterochromosome was
 identified by a specific marker (Tpi) and did not carry any of these QTLs.
 Finally, we considered the global divergence between the two sibling
 species, distortions of segregation throughout the genome, and the
 location and effect of mi and Pher QTLs in light of the known candidate
 genes for reproductive isolation within the genus Ostrinia and, more
 broadly, in phytophagous insects.
description: ArchiveThe archive contains 6 files corresponding to genotypic and phenotypic data for the QTL mapping. Each file corresponds to the data of one pedigree (NR_P10, R_P10, NR_C04 and R_C04, see material and methods of the manuscript), and one phenotypic trait associated (Pher and mi for NR_P10 and R_P10, mi for R_C04 and NR_C04). The columns correspond to F2 (backcross) progenies. Lines correspond to AFLP markers (e.g. CbPbeACbAgg207.97) and Tpi marker, followed by one phenotypic trait (Pher or mi). The AFLP phenotypes are coded “a” for the absence of a band, and “h” for the presence of a band. Each AFLP marker has been coded twice, in the observed configuration (e.g. CbPbeACbAgg207.97) and in the reverse one (e.g. CbPbeACbAgg207.97R) because of the unknown linkage phase. The “mi” phenotypes are coded “1” for “mated” and “0” for “non-mated”. The female “pher” phenotypes are coded “0” for “pure E” and “1” for “E/Z” pheromone (no data for males). “-” is for missing data.
DOI: 10.5061/dryad.1s88t
title: Data from: Cryptic diversity in black rats Rattus rattus of the Galápagos Islands, Ecuador

description: Human activity has facilitated the introduction of a number of alien
 mammal species to the Galápagos Archipelago. Understanding the
 phylogeographic history and population genetics of invasive species on the
 Archipelago is an important step in predicting future spread and designing
 effective management strategies. In this study, we describe the invasion
 pathway of Rattus rattus across the Galápagos using microsatellite data,
 coupled with historical knowledge. Microsatellite genotypes were generated
 for 581 R. rattus sampled from 15 islands in the archipelago. The genetic
 data suggest that there are at least three genetic lineages of R. rattus
 present on the Galápagos Islands. The spatial distributions of these
 lineages correspond to the main centers of human settlement in the
 archipelago. There was limited admixture among these three lineages, and
 these finding coupled with low rates of gene flow among island populations
 suggests that interisland movement of R. rattus is rare. The low migration
 among islands recorded for the species will have a positive impact on
 future eradication efforts.
description: R. rattus
 alleles_genepop formatMicrosatellite data for
 study species in Genpop format
DOI: 10.5061/dryad.vb665
title: Data from: How do algae form multicellular groups?

description: Background: Theory suggests that how groups are formed can be a major
 influence on the evolution of cooperation, and whether cooperative groups
 make the major transition to a higher level individual. The formation of
 clonal groups, by remaining with parents (subsocial group formation) leads
 to a greater kin selected benefit of cooperation, compared with formation
 of groups by aggregating, with potential non- relatives (semisocial).
 Freshwater algae form multicellular groups in response to the presence of
 predators, but it is not clear whether they form groups by remaining
 together (subsocial) or by aggregation (semisocial). Organisms: The
 freshwater algae Chlorella sorokiniana, Chlorella vulgaris and Scenedesmus
 obliquus, and the freshwater crustacean predator Daphnia magna. Results:
 Fluorescence microscopy and time-lapse photography revealed that, in
 response to predator supernatant/live predators, these algae form groups
 both subsocially and semisocially. Additionally, different algal species
 form mixed-species multicellular groups in response to predation.
 Conclusion: The observation of semisocial, and even between species, group
 formation in these facultatively multicellular algae: (i) emphasises the
 direct fitness benefits of forming groups to avoid predation; and (ii)
 strengthens the across species correlation between the method of group
 formation and whether multicellularity is facultative or obligate.
description: Data_How do algae form
 multicellular groups?
DOI: 10.5061/dryad.2sp38
title: Data from: Plasticity in ploidy underlies plant fitness compensation to herbivore damage

description: How plants mitigate damage by animal herbivores is a fundamental
 ecological and evolutionary question of plant-animal interactions. Some
 plants can increase their fitness when damaged in a phenomenon termed
 “overcompensation.” Despite overcompensation being observed in a variety
 of plant species, its mechanistic basis remains elusive. Recent research
 has shown that the Arabidopsis thaliana genotype Columbia-4 employs
 endoreduplication, the replication of the genome without mitosis,
 following damage and that it overcompensates for seed yield. The related
 genotype Landsberg erecta, in contrast, does not increase its
 endoreduplication following damage and suffers reduced seed yield. While
 these results suggest that a plant's ability to plastically increase
 its ploidy during regrowth may promote its mitigation of damage, no
 studies have explicitly linked the endoreduplication genetic pathway to
 the regrowth and fitness of damaged plants. By comparing fitness and
 ploidy between undamaged and damaged plants of Columbia-4, Landsberg
 erecta, and their offspring, we provide evidence that endoreduplication is
 directly involved in compensatory performance. We then overexpressed an
 endoreduplication regulator and compared this mutant's
 endoreduplication and compensation with its background genotype
 Columbia-0, an undercompensator. Enhancing Columbia-0's ability to
 endoreduplicate during regrowth led to the complete mitigation of the
 otherwise detrimental effects of damage on its fitness. These results
 suggest that the ability of these plants to increase their ploidy via
 endoreduplication directly impacts their abilities to compensate for
 damage, providing a novel mechanism by which some plants can mitigate or
 even benefit from apical damage with potential across the wide range of
 plant taxa that endoreduplicate.
description: Fitness and cycle value
 dataFitness and cycle value
 dataData.xlsx
DOI: 10.5061/dryad.vm6dh
title: Data from: Environmental fluctuations restrict eco-evolutionary dynamics in predator-prey system

description: Environmental fluctuations, species interactions and rapid evolution are
 all predicted to affect community structure and their temporal dynamics.
 Although the effects of the abiotic environment and prey evolution on
 ecological community dynamics have been studied separately, these factors
 can also have interactive effects. Here we used bacteria–ciliate microcosm
 experiments to test for eco-evolutionary dynamics in fluctuating
 environments. Specifically, we followed population dynamics and a prey
 defence trait over time when populations were exposed to regular changes
 of bottom-up or top-down stressors, or combinations of these. We found
 that the rate of evolution of a defence trait was significantly lower in
 fluctuating compared with stable environments, and that the defence trait
 evolved to lower levels when two environmental stressors changed
 recurrently. The latter suggests that top-down and bottom-up changes can
 have additive effects constraining evolutionary response within
 populations. The differences in evolutionary trajectories are explained by
 fluctuations in population sizes of the prey and the predator, which
 continuously alter the supply of mutations in the prey and strength of
 selection through predation. Thus, it may be necessary to adopt an
 eco-evolutionary perspective on studies concerning the evolution of traits
 mediating species interactions.
description: FluctEnv_DataPopulation and trait data
DOI: 10.5061/dryad.h4b48
title: Data from: Epigenetic estimation of age in humpback whales

description: Age is a fundamental aspect of animal ecology, but is difficult to
 determine in many species. Humpback whales exemplify this as they have a
 lifespan comparable to humans, mature sexually as early as four years and
 have no reliable visual age indicators after their first year. Current
 methods for estimating humpback age cannot be applied to all individuals
 and populations. Assays for human age have recently been developed
 recently based on age-induced changes in DNA methylation of specific
 genes. We used information on age-associated DNA methylation in human and
 mouse genes to identify homologous gene regions in humpbacks. Humpback
 skin samples were obtained from individuals with a known year of birth and
 employed to calibrate relationships between cytosine methylation and age.
 Seven of 37 cytosines assayed for methylation level in humpback skin had
 significant age-related profiles. The three most age-informative cytosine
 markers were selected for a humpback epigenetic age assay. The assay has
 an R2 of 0.787 (p = 3.04e-16) and predicts age from skin samples with a
 standard deviation of 2.991 years. The epigenetic method correctly
 determined which of parent-offspring pairs is the parent in more than 93%
 of cases. To demonstrate the potential of this technique, we constructed
 the first modern age profile of humpback whales off eastern Australia and
 compared the results to population structure five decades earlier. This is
 the first epigenetic age estimation method for a wild animal species and
 the approach we took for developing it can be applied to many other non
 model organisms.
description: HEAA_MER_Data+ScriptsThis .zip archive contains two directories. The 'Data' directory contains the measured levels of CpG methylation at various places in the humpback whale genome. The 'Scripts' directory contains the R scripts used to analyse this data.