Why don't we share data and code? Perceived barriers and benefits to public archiving practices

The biological sciences community is increasingly recognizing the value ofopen, reproducible and transparent research practices for science and societyat large. Despite this recognition, many researchers fail to share their dataand code publicly. This pattern may arise from knowledge barriers abouthow to archive data and code, concerns about its reuse, and misalignedcareer incentives. Here, we define, categorize and discuss barriers to dataand code sharing that are relevant to many research fields. We explorehow real and perceived barriers might be overcome or reframed in thelight of the benefits relative to costs. By elucidating these barriers and thecontexts in which they arise, we can take steps to mitigate them and alignour actions with the goals of open science, both as individual scientistsand as a scientific community

Sex bias in mortality risk changes over the lifespan of bottlenose dolphins.

Research on sex biases in longevity in mammals often assumes that male investment in competition results in a female survival advantage that is constant throughout life. We use 35 years of longitudinal data on 1003 wild bottlenose dolphins (Tursiops aduncus) to examine age-specific mortality, demonstrating a time-varying effect of sex on mortality hazard over the five-decade lifespan of a social mammal. Males are at higher risk of mortality than females during the juvenile period, but the gap between male and female mortality hazard closes in the mid-teens, coincident with the onset of female reproduction. Female mortality hazard is non-significantly higher than male mortality hazard in adulthood, resulting in a moderate male bias in the oldest age class. Bottlenose dolphins have an intensely male-competitive mating system, and juvenile male mortality has been linked to social competition. Contrary to predictions from sexual selection theory, however, male–male competition does not result in sustained male-biased mortality. As female dolphins experience high costs of sexual coercion in addition to long and energetically expensive periods of gestation and lactation, this suggests that substantial female investment in reproduction can elevate female mortality risk and impact sex biases in lifespan

SimulatedGenotypeData

Genotypes simulated using the program Conancestry (Wang 2011) for 100 pairs at each of 6 levels of relatedness. Allele frequencies and genotyping error are set to match those found in the real dolphin genotype data in the study

DolphinGenotypeData

Genotypes for 272 individual Tursiops aduncus at 4235 loc

Data from: Quality and quantity of genetic relatedness data affect the analysis of social structure

Kinship plays a fundamental role in the evolution of social systems and is considered a key driver of group living. To understand the role of kinship in the formation and maintenance of social bonds, accurate measures of genetic relatedness are critical. Genotype-by-sequencing technologies are rapidly advancing the accuracy and precision of genetic relatedness estimates for wild populations. The ability to assign kinship from genetic data varies depending on a species’ or population’s mating system and pattern of dispersal, and empirical data from longitudinal studies are crucial to validate these methods. We use data from a long-term behavioral study of a polygynandrous, bisexually philopatric marine mammal to measure accuracy and precision of parentage and genetic relatedness estimation against a known partial pedigree. We show that with moderate but obtainable sample sizes of approximately 4235 SNPs and 272 individuals, highly accurate parentage assignments and genetic relatedness coefficients can be obtained. Additionally, we subsample our data to quantify how data availability affects relatedness estimation and kinship assignment. Lastly, we conduct a social network analysis to investigate the extent to which accuracy and precision of relatedness estimation improve statistical power to detect an effect of relatedness on social structure. Our results provide practical guidance for minimum sample sizes and sequencing depth for future studies, as well as thresholds for post hoc interpretation of previous analyses

Cooperation and strategic complementarity: An experiment with two voluntary contribution mechanism games with interior equilibria

In public goods game experiments, designs implementing non-linearities in the production are less common than the standard linear setting, especially so under the assumption that the private goods production and public goods aggregation function are both non-linear. We study a voluntary contribution game (VCM) in which returns from the private project have diminishing marginal benefits and the contributions to the joint project exhibit pairwise strategic complementarities. As a control, we use a public goods game with an identical private production technology, but with the standard linear public goods aggregation. In addition to the aggregation technology, we manipulate the group size variable: In both treatments, the subjects will first play a VCM game in groups of five for 20 rounds, after which the group size is reduced to two, and the game is played for another 20 rounds. A significant over-contribution is observed in both settings when the group size is five. The rate of over-contribution is much higher under the complementary technology, but as predicted by theory, the contributions drop drastically when the group size is reduced from n = 5 to n = 2 within this treatment. Our experiment also provides empirical evidence that the so-called group size effect is present in both treatments, but it is much weaker under the standard aggregation technology

Data from: Quality and quantity of genetic relatedness data affect the analysis of social structure

Kinship plays a fundamental role in the evolution of social systems and is considered a key driver of group living. To understand the role of kinship in the formation and maintenance of social bonds, accurate measures of genetic relatedness are critical. Genotype-by-sequencing technologies are rapidly advancing the accuracy and precision of genetic relatedness estimates for wild populations. The ability to assign kinship from genetic data varies depending on a species’ or population’s mating system and pattern of dispersal, and empirical data from longitudinal studies are crucial to validate these methods. We use data from a long-term behavioral study of a polygynandrous, bisexually philopatric marine mammal to measure accuracy and precision of parentage and genetic relatedness estimation against a known partial pedigree. We show that with moderate but obtainable sample sizes of approximately 4235 SNPs and 272 individuals, highly accurate parentage assignments and genetic relatedness coefficients can be obtained. Additionally, we subsample our data to quantify how data availability affects relatedness estimation and kinship assignment. Lastly, we conduct a social network analysis to investigate the extent to which accuracy and precision of relatedness estimation improve statistical power to detect an effect of relatedness on social structure. Our results provide practical guidance for minimum sample sizes and sequencing depth for future studies, as well as thresholds for post hoc interpretation of previous analyses

Rôles et limites de la psychologie dans la formation des enseignants d'après les <i>Conférences sur l'éducation</i> de W. James

National audienc

Study of intracellular deposition of the anti-leprosy drug clofazimine in mouse spleen using laser microprobe mass analysis

R code - custom functions for use with creation of dolphin mode