cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4xgxd259q
title: Condition-dependent sexual reproduction is driven by benefits, not costs of sex

description: Facultative sexual organisms must allocate resources to both asexual and
 sexual reproduction. Optimal patterns of investment in sex depend on the
 relative costs and benefits of each reproductive mode, and may
 consequently be context- and condition-dependent. Two proposed
 explanations for the observed variation in investment in sex among
 facultative sexual lineages invoke alternative condition-dependent
 scenarios. Under the ‘fitness-associated sex’ hypothesis, sex is predicted
 when individuals are in poor condition or experience stressful
 environments. Under the ‘resource-demanding sex’ hypothesis, sex is only
 affordable to individuals in good condition experiencing favourable
 environments. Direct tests of these contrasting hypotheses are rare;
 moreover, investment in different components of sexual reproduction
 responds differently to cues promoting sex, and may be subject to
 different energetic constraints. Using genotypes of facultative sexual
 Daphnia carinata that differ in their level of investment in sex, we
 manipulated resource availability while accounting for day length (a
 seasonal cue for sex) to evaluate these hypotheses. The sexual response to
 day length depended on resource availability: increased day lengths and
 reduced food availability increased the production of sexual eggs, and
 relative investment in males, in a manner consistent with the
 fitness-associated sex hypothesis. The pattern of condition-dependence was
 specific to each component of reproductive investment – while male
 production covaried with asexual fecundity across genotypes, increased
 sexual egg production was associated with reduced asexual reproduction.
 Our results suggest that investment in sex is determined largely by its
 context-dependent advantages, and that this investment is not moderated by
 immediate costs to asexual reproduction.
DOI: 10.5061/dryad.612jm6443
title: Detection, quantification and classification of ripened tomatoes: a comparative analysis of image processing and machine learning

description: In this study, specifically for the detection of ripe/unripe tomatoes
 with/without defects in the crop field, two distinct methods are described
 and compared from captured images by a camera mounted on a mobile robot.
 One is a machine learning approach, known as ‘Cascaded Object Detector’
 (COD) and the other is a composition of traditional customised methods,
 individually known as ‘Colour Transformation’: ‘Colour Segmentation’ and
 ‘Circular Hough Transformation’. The (Viola-Jones) COD generates
 ‘histogram of oriented gradient’ (HOG) features to detect tomatoes. For
 ripeness checking, the RGB mean is calculated with a set of rules.
 However, for traditional methods, colour thresholding is applied to detect
 tomatoes either from natural or solid background and RGB colour is
 adjusted to identify ripened tomatoes. This algorithm is shown to be
 optimally feasible for any micro-controller based miniature electronic
 devices in terms of its run time complexity of O(n3) for a
 traditional method in best and average cases. Comparisons show that the
 accuracy of the machine learning method is 95%, better than that of the
 Colour Segmentation Method using MATLAB.
DOI: 10.5061/dryad.n5tb2rbwk
title: Waste not, want not: microsatellites remain an economical and informative technology for conservation genetics

description: Comparisons of microsatellite and single-nucleotide polymorphisms (SNPs)
 have found that SNPs outperform microsatellites in population genetic
 analyses, calling into question the continued utility of microsatellites
 in population and landscape genetics. Yet highly polymorphic markers may
 be of value in species that have reduced genetic variation. This study
 repeated analyses previously done using microsatellites with SNPs
 developed from ddRAD sequencing in the black-capped vireo source-sink
 system. SNPs provided greater resolution of genetic diversity, population
 differentiation, and migrant detection but could not reconstruct parentage
 relationships due to insufficient heterozygosities. The biological
 inferences made by both sets of markers were similar: asymmetrical gene
 flow from source sites to the remaining sink sites. With the landscape
 genetic analyses, we found different results between the two molecular
 markers, but associations of the top environmental features (riparian,
 open habitat, agriculture, and human development) with dispersal estimates
 were shared between marker types. Despite the higher precision of SNPs, we
 find that microsatellites effectively uncover population processes and
 patterns and are superior for parentage analyses in this species with
 reduced genetic diversity. This study illustrates the continued
 applicability and relevance of microsatellites in population genetic
 research.
description: # Waste not, want not: microsatellites remain an economical and
 informative technology for conservation genetics
 [https://doi.org/10.5061/dryad.n5tb2rbwk](https://doi.org/10.5061/dryad.n5tb2rbwk) ## Description of the data and file structure The same 185 black-capped vireo samples are represented in both the microsatellite (micro) and SNP genotype datasets below. * BCVI\_Micro\_Genotypes.csv: genepop file format * BCVI\_SNP\_Genotypes\_90GenotypeRate.vcf * BCVI\_SNP\_Genotypes.vcf Landscape data includes * a) At-site predictor variables: elevation, Euclidean distance, water, development, forest, scrub, open, agriculture, riparian, the proportion of scrub habitat, and brown-headed cowbird (BHCO) management * b) Between-site variables: elevation, Euclidean distance, water, development, forest, scrub, open, agri-culture, and riparian BCVI\_Micro\_LandscapeGeneticData.csv BCVI\_SNP\_LandscapeGeneticData.csv Code files included: * BCVI\_ANOVA.R * LG\_HybridApproach.R * LG\_UnivarModel\_opt.R ## Sharing/Access information Microsatellite data is also featured in related articles: https://doi.org/10.1007/s10592-020-01314-1 [https://doi.org/10.1002/ece3.4764](https://doi.org/10.1002/ece3.4764) <br>
DOI: 10.25338/b8792h
title: United States recycled content standards for lithium-ion batteries

description: Lithium-ion battery recycling can decrease life cycle environmental
 impacts of electric vehicles (EVs) and assist in securing domestic supply
 chains. However, the US, the third largest market for EVs, has no policies
 for recycling of batteries at their end-of-life. The European Union has
 proposed recycled content standards (RCSs) to help drive a circular
 battery ecosystem. This analysis calculates feasible RCSs for the US based
 on future sale projections, techno-economic assessment, life cycle
 assessment, and material flow analysis. Using a 95% confidence interval,
 results show that 11–12% of cobalt, 7–8% of lithium, and 10–12% of nickel
 demand in 2030 and 15–18%, 9–11%, and 15–17%, respectively, in 2035, could
 be met by retired supply assuming closed-loop recycling. While domestic
 recycling can be profitable at scale and reduce environmental impacts, it
 is more expensive than exporting to China for recycling. Consequently,
 policy is likely needed to ensure critical materials are recycled
 domestically.
description: The data used in this analysis is taken from the 2020 Global
 Electric Vehicle Outlook from the International Energy Agency, EV Volumes,
 and Xu et al. (2020). The full citations are in the manuscript.
DOI: 10.6076/d16c77
title: Oceanic particle size distributions for the PacAtl and Arctic datasets

description: A dataset of nearly 400 measurements of the particle size distribution
 (PSD) compiled from the Pacific, Atlantic, and Arctic Oceans is used to
 examine variability in the magnitude and shape of the PSD, and to
 characterize the partitioning of particle number, cross-sectional area,
 and volume concentration among defined size intervals. The results
 indicate that the relative contributions of three size classes based upon
 the pico-, nano-, and microplankton size range exhibit substantial changes
 among measures of particle size and between oceanic environments. The
 single slope power law model commonly employed to characterize the PSD in
 aquatic studies is demonstrated to have significant limitations in
 capturing the complexity of PSD shapes observed for natural particle
 assemblages, and in consequence poorly predicts the relative contributions
 of these different size intervals. We show that specific percentile
 diameters derived from the cumulative distributions of particle size are
 strongly correlated with the contributions of these three size classes,
 and that these non-parametric descriptors of the cumulative distribution
 provide superior performance for estimating their contributions while
 requiring no assumption of underlying PSD shape. A comparison of these
 predictive relationships with independent field measurements suggests that
 this approach is generally robust for particle assemblages representing a
 wide diversity of marine environments.
description: Particle size distributions measured on discrete seawater samples
 using a Coulter Counter (Beckman-Coulter MultiSizer III) or HIAC/Royco
 3001 (Pacific Scientific) particle sizer. Further details in uploaded file
 Reynolds_PSD_Readme.txt
description: See uploaded file Reynolds_PSD_Readme.txt
DOI: 10.5061/dryad.nvx0k6dt2
title: Divergent responses of symbiotic and asymbiotic N2 fixation to seawater additions

description: Sea level rise-associated seawater intrusion exerts substantial impacts on
 the structure and function of coastal ecosystems. As nitrogen (N)
 availability is closely related to the structure and function of
 ecosystems, it is crucial to understand how seawater intrusion impacts
 biological N2 fixation, a major pathway of new N input to natural
 ecosystems. Here, a seawater addition experiment with two
 N2-fixing plant species (Acacia auriculiformis and Casuarina
 equisetifolia) and ten non-N2-fixing plant species was conducted to
 simulate sea level rise-associated seawater intrusion. The experiment
 included control (0 mm seawater yr-1), low seawater addition (LSW, 200 mm
 seawater yr-1), and high seawater addition (HSW, 400 mm seawater
 yr-1).  Symbiotic N2 fixation (SNF) rate of A. auriculiformis was
 significantly higher under LSW (but not for HSW) than the control. For C.
 equisetifolia, SNF rates under LSW and HSW significantly increased by 8.0
 and 19.5 times, respectively, compared with the control. In contrast,
 asymbiotic N2 fixation rates under LSW and HSW significantly decreased by
 18.5% and 30.4%, respectively, across all the plant species. Our findings
 suggest that the responses of biological N2 fixation to seawater intrusion
 are divergent either among different N2-fixing plant species or between
 symbiotic and asymbiotic forms, which should be considered in terrestrial
 ecosystem models in order to improve the prediction of N dynamics under
 climate changes.
DOI: 10.7291/d15q4x
title: On the spread of microbes that manipulate reproduction in marine invertebrates

description: Bacterial symbionts are functionally integral to animal reproduction and
 development, some of which have evolved additional mechanisms to override
 these host programs. One habitat that is increasingly recognized to
 contain phylogenetically related lineages of reproductive manipulators is
 the ocean. The reproduction of marine invertebrates often occurs by
 free-spawning instead of by the physical contact of copulation in
 terrestrial systems. We developed an integrated model to understand
 whether and when microbes that manipulate host reproduction by cytoplasmic
 incompatibility, feminization, and male killing spread within populations
 of free-spawning marine invertebrates. Our model support three primary
 findings. First, sex ratio distortion leads to suboptimal fertilization
 and zygote production in planktotrophs (feeding larvae), but enhance these
 processes in lecithotrophs (nonfeeding larvae). Second, feminization and a
 combination of male killing plus enhanced growth are effective at
 spreading reproductive manipulators while also inducing a female-biased
 sex ratio. Third, the majority of free-spawning marine invertebrates could
 be infected across a range of life-history combinations, with infections
 harming species with smaller eggs and longer pelagic durations while
 benefiting species with larger eggs and shorter pelagic durations.
 Together, this supports the general premise that microbes may manipulate
 the reproduction of free-spawning marine invertebrates (e.g., by inducing
 changes in developmental life-history) and that these types of
 manipulations overlap considerably with terrestrial systems.
description: Data used in the analyses as well as files generated by
 simulations. The code that uses and/or produces these data files is found
 in Zenodo and/or GitHub.
DOI: 10.5061/dryad.0cfxpnw30
title: Experimental evolution reveals sex-specific dominance for surviving bacterial infection in laboratory populations of Drosophila melanogaster

description: Males and females are subjected to distinct kinds of selection pressures,
 often leading to the evolution of sex-specific genetic architecture, an
 example being sex-specific dominance. Sex-specific dominance reversals
 (SSDRs), where alleles at sexually antagonistic loci are at least
 partially dominant in the sex they benefit, have been documented in
 Atlantic salmon, rainbow trout and beetles. Another interesting feature of
 many sexually reproducing organisms is the asymmetric inheritance pattern
 of X chromosomes, which often leads to distinct evolutionary outcomes on X
 chromosomes compared to autosomes. Examples include, the higher efficacy
 of sexually concordant selection on X chromosomes, and X chromosomes being
 more conducive to the maintenance of sexually antagonistic polymorphisms
 under certain conditions. Immunocompetence is a trait that has been
 extensively investigated for sexual dimorphism with growing evidence for
 sex-specific or sexually antagonistic variation. X chromosomes have been
 shown to harbour substantial immunity-related genetic variation in the
 fruit-fly, Drosophila melanogaster. Here, using interpopulation crosses
 and cytogenetic cloning, we investigated sex-specific dominance and the
 role of the X chromosome in improved post-infection survivorship of
 laboratory populations of D. melanogaster selected against pathogenic
 challenge by Pseudomonas entomophila. We could not detect any contribution
 of the X chromosome to the evolved immunocompetence of our selected
 populations as well as to within population variation in immunocompetence.
 However, we found strong evidence of sex-specific dominance related to
 surviving bacterial infection. Our results indicate that alleles that
 confer a survival advantage to the selected populations are, on average,
 partially dominant in females but partially recessive in males. This could
 also imply a sex-specific dominance reversal for overall fitness, given
 the putative evidence for sexually antagonistic selection affecting
 immunocompetence in Drosophila melanogaster. We also highlight
 sex-specific dominance as a potential mechanism of sex differences in
 immunocompetence, with population-level sex differences primarily driven
 by sex differences in heterozygotes.
description: See Readme files.
DOI: 10.5061/dryad.sf7m0cg73
title: Data for: Predation risk and the evolution of a vertebrate stress response: parallel evolution of stress reactivity and sexual dimorphism

description: Predation risk is often invoked to explain variation in stress responses.
 Yet, the answers to several key questions remain elusive, including: 1)
 how predation risk influences the evolution of stress phenotypes, 2) the
 relative importance of environmental versus genetic factors in stress
 reactivity, and 3) sexual dimorphism in stress physiology. To address
 these questions, we explored variation in stress reactivity
 (ventilation frequency) in a post-Pleistocene radiation of live-bearing
 fish, where Bahamas mosquitofish (Gambusia hubbsi) inhabit isolated blue
 holes that differ in predation risk. Individuals of populations coexisting
 with predators exhibited similar, relatively low stress reactivity as
 compared to low-predation populations. We suggest that this dampened
 stress reactivity has evolved to reduce energy expenditure in environments
 with frequent and intense stressors, such as piscivorous fish.
 Importantly, the magnitude of stress responses exhibited by fish from
 high-predation sites in the wild changed very little after two generations
 of laboratory rearing in the absence of predators. By comparison,
 low-predation populations exhibited greater among-population variation and
 larger changes subsequent to laboratory rearing. These low-predation
 populations appear to have evolved more dampened stress responses in blue
 holes with lower food availability. Moreover, females showed a lower
 ventilation frequency, and this sexual dimorphism was stronger in
 high-predation populations. This may reflect a greater premium placed on
 energy efficiency in live-bearing females, especially under high predation
 risk where females show higher fecundities. Altogether, by demonstrating
 parallel adaptive divergence in stress reactivity, we highlight how
 energetic trade-offs may mould the evolution of the vertebrate stress
 response under varying predation risk and resource availability.
DOI: 10.5061/dryad.g1jwstqrm
title: Developmental timing of Drosophila pachea pupae is robust to temperature changes

description: Rearing temperature is correlated with the timing and speed of development
 in a wide range of poikiloterm animals that do not regulate their body
 temperature. However, exceptions exist, especially in species that live in
 environments with high temperature extremes or oscillations. Drosophila
 pachea is endemic to the Sonoran desert in Mexico, in which temperatures
 and temperature variations are extreme. We wondered if the developmental
 timing in D. pachea may be sensitive to differing rearing temperatures or
 if it remains constant. We determined the overall timing of the Drosophila
 pachea life-cycle at different temperatures. The duration of pupal
 development was similar at 25 °C, 29 °C and
 32 °C, although the relative progress differed at particular
 stages. Thus, D. pachea may have evolved mechanisms to buffer temperature
 effects on developmental speed, potentially to ensure proper development
 and individual's fitness in desert climate conditions.
DOI: 10.5061/dryad.tht76hf0f
title: Data for: Quantifying patch-specific seed dispersal and local population dynamics to estimate population spread of an endangered plant species

description: Dataset on seed dispersal and population spread for the paper Quantifying
 patch-specific seed dispersal and local population dynamics to estimate
 population spread of an endangered plant species Jinlei Zhu1, 2, *,
 Karolína Hrušková1, 3, Hana Pánková1, Zuzana Münzbergová1, 3 1Institute of
 Botany, Czech Academy of Sciences, Průhonice, Czech Republic 2Institute of
 Landscape and Plant Ecology, University of Hohenheim, Stuttgart, Germany
 3Department of Botany, Faculty of Science, Charles University, Prague,
 Czech Republic *Corresponding author: jinlei.zhu@uni-hohenheim.de
 Institute of Landscape and Plant Ecology University of Hohenheim
 Ottilie-Zeller-Weg 2, 70599 Stuttgart, Germany
description: Seed dispersal data was from simulation using the mechanistic
 dispersal model WALD (Katul et al. 2005, American Naturalist).
 Population spread data was from simulation by combining the
 analytical wavespeed model of Neubert and Caswell (2000) with a
 demographic matrix model with integrodifference equations describing
 dispersal (Gilbert et al., 2014).
DOI: 10.5061/dryad.f4qrfj6wn
title: Supplementary to "A stable foraging polymorphism buffers Galápagos sea lions against environmental change"

description: All vibrissae photographs, measured relative vibrissae length and raw data
 of the reproductive history of females used for "A foraging
 polymorphism buffers Galápagos sea lions against climate change".
description: Relative_vibrissae_length: Information of all females with their
 age, measured relative vibrissae length etc.
 pupping_rate: Information of each female and each year on if
 the had a pup (0 no pup in a given year, 1 pup born in given year), with
 SST, age etc. body_condition: Information of the pups
 body condition of all included females, with SST, age etc.
 first_year_survival: Information if the pups of a given year
 survived to an age of one year (0 pup died, 1 pup survived) with SST, age
 etc. relative_vibrissae_length_first: All pictures of
 vibrissae and how relative vibrissae length were calculated during the
 first field season
 relative_vibrissae_length_within_season: All pictures of
 vibrissae from females that got a second pictures taken within the same
 field season
DOI: 10.5061/dryad.3r2280gh2
title: Dataset female gregariousness in bonobos and chimpanzees

description: Spatial association between females often mirrors pattern and strength of
 social relationships and cooperation within groups. Here we test for
 proposed differences in female-female associations and the role of sexual
 signaling between the two species of the genus Pan that have been linked
 to difference in female cooperation. Unlike previous studies, we found
 only limited evidence for a higher female-female gregariousness in
 bonobos. While bonobo females exhibited a slightly higher average number
 of females in their parties, there was neither a species difference in the
 time females spent alone, nor in the number of female party members in the
 absence of sexually attractive females. We found that the more frequent
 presence of maximally tumescent females in bonobos was associated with a
 significantly stronger increase in the number of female party members,
 independent of variation in food abundance. This indicates that conditions
 leading to changes in female sexual signaling ultimately affect female
 associations, potentially leading to marked behavioural differences
 between chimpanzees and bonobos. Our findings refute the idea that the
 higher gregariousness among bonobo females is driven by ecological factors
 alone and highlight that the temporal distribution of female sexual
 receptivity is an important factor to consider when studying mammal
 sociality.
description: This dataset has been collected at the field sites of LuiKotale,
 DRC and Taï, Cȏte d’Ivoire , between February 2015 and December 2017. We
 relied on female focal individual follows to reduce the bias towards
 larger groups stemming from party follows and be better able to quantify
 the durations individuals spend alone. We followed focal animals daily in
 two chimpanzee communities (Taï East and Taï South) and one bonobo
 community (Bompusa). We included all adult parous females at the start of
 our study period as our focal individuals (estimated older than 13 years).
 In the dataset there are the following columns: Focal
 id, species, date (as character), halfday of follow, average number of
 female party members during focal follow, number party observation
 (conducted cumulative over 30 min), number of maximal tumescence females
 present in categories (see manuscript for categorization), percentage time
 spent in party with at least one maximally tumescent female, percentage of
 time spent with only females, percentage alone, monthly proportion of
 awake time spent feeding.