Implementing code review in the scientific workflow: Insights from ecology and evolutionary biology.

Code review increases reliability and improves reproducibility of research. As such, code review is an inevitable step in software development and is common in fields such as computer science. However, despite its importance, code review is noticeably lacking in ecology and evolutionary biology. This is problematic as it facilitates the propagation of coding errors and a reduction in reproducibility and reliability of published results. To address this, we provide a detailed commentary on how to effectively review code, how to set up your project to enable this form of review and detail its possible implementation at several stages throughout the research process. This guide serves as a primer for code review, and adoption of the principles and advice here will go a long way in promoting more open, reliable, and transparent ecology and evolutionary biology.

Advice for improving the reproducibility of data extraction in meta-analysis.

Extracting data from studies is the norm in meta-analyses, enabling researchers to generate effect sizes when raw data are otherwise not available. While there has been a general push for increased reproducibility in meta-analysis, the transparency and reproducibility of the data extraction phase is still lagging behind. Unfortunately, there is little guidance of how to make this process more transparent and shareable. To address this, we provide several steps to help increase the reproducibility of data extraction in meta-analysis. We also provide suggestions of R software that can further help with reproducible data policies: the shinyDigitise and juicr packages. Adopting the guiding principles listed here and using the appropriate software will provide a more transparent form of data extraction in meta-analyses.

Counter culture: causes, extent and solutions of systematic bias in the analysis of behavioural counts.

We often quantify the rate at which a behaviour occurs by counting the number of times it occurs within a specific, short observation period. Measuring behaviour in such a way is typically unavoidable but induces error. This error acts to systematically reduce effect sizes, including metrics of particular interest to behavioural and evolutionary ecologists such as R2 , repeatability (intra-class correlation, ICC) and heritability. Through introducing a null model, the Poisson process, for modelling the frequency of behaviour, we give a mechanistic explanation of how this problem arises and demonstrate how it makes comparisons between studies and species problematic, because the magnitude of the error depends on how frequently the behaviour has been observed as well as how biologically variable the behaviour is. Importantly, the degree of error is predictable and so can be corrected for. Using the example of parental provisioning rate in birds, we assess the applicability of our null model for modelling the frequency of behaviour. We then survey recent literature and demonstrate that the error is rarely accounted for in current analyses. We highlight the problems that arise from this and provide solutions. We further discuss the biological implications of deviations from our null model, and highlight the new avenues of research that they may provide. Adopting our recommendations into analyses of behavioural counts will improve the accuracy of estimated effect sizes and allow meaningful comparisons to be made between studies.

Decomposing phenotypic skew and its effects on the predicted response to strong selection.

The major frameworks for predicting evolutionary change assume that a phenotype's underlying genetic and environmental components are normally distributed. However, the predictions of these frameworks may no longer hold if distributions are skewed. Despite this, phenotypic skew has never been decomposed, meaning the fundamental assumptions of quantitative genetics remain untested. Here we demonstrate that the substantial phenotypic skew in the body size of juvenile blue tits (Cyanistes caeruleus) is driven by environmental factors. Although skew had little impact on our predictions of selection response in this case, our results highlight the impact of skew on the estimation of inheritance and selection. Specifically, the nonlinear parent-offspring regressions induced by skew, alongside selective disappearance, can strongly bias estimates of heritability. The ubiquity of skew and strong directional selection on juvenile body size imply that heritability is commonly overestimated, which may in part explain the discrepancy between predicted and observed trait evolution.

The role of maternally transferred antibodies in maternal performance in red deer.

Maternal effects are ubiquitous. Yet, the pathways through which maternal effects occur in wild mammals remain largely unknown. We hypothesise that maternal immune transfer is a key mechanism by which mothers can affect their offspring fitness, and that individual variation in maternally derived antibodies mainly depends on a mother's characteristics and the environmental conditions she experiences. To test this, we assayed six colostrum-derived antibodies in the plasma of 1447 neonates in a wild red deer population. Neonatal antibody levels were mainly affected by maternal genes, environmental variation and costs of prior reproductive investment. We found consistent heterogeneity in maternal performance across traits, with mothers producing the heaviest calves also having calves with more antibodies. Unexpectedly, antibody levels were not associated with calf survival. We provide a unique example of how evolutionary theory on maternal effects can be used to gain insight into the causes of maternal effects in wild populations.

Artificial selection reveals the role of transcriptional constraints in the maintenance of life history variation.

The trade-off between reproduction and self-maintenance is a cornerstone of life history theory, yet its proximate underpinnings are elusive. Here, we used an artificial selection approach to create replicated lines of Japanese quail (Coturnix japonica) that differ genetically in their reproductive investment. Whole transcriptome sequencing revealed that females from lines selected for high reproductive output show a consistent upregulation of genes associated with reproduction but a simultaneous downregulation of immune genes. Concordant phenotypic differences in immune function (i.e., specific antibody response against keyhole limpet hemocyanin) were observed between the selection lines, even in males who do not provide parental care. Our findings demonstrate the key role of obligate transcriptional constraints in the maintenance of life history variation. These constraints set fundamental limits to productivity and health in natural and domestic animal populations.

The more you get, the more you give: Positive cascading effects shape the evolutionary potential of prenatal maternal investment.

Maternal effects are prevalent in nature and significantly contribute to variation in phenotypic trait expression. However, little attention has been paid to the factors shaping variation in the traits mediating these effects (maternal effectors). Specific maternal effectors are often not identified, and typically they are assumed to be inherited in an additive genetic and autosomal manner. Given that these effectors can cause long-lasting effects on offspring phenotype, it is likely that they may also affect themselves in the next generation. Although the existence of such cascading maternal effects has been discussed and modeled, empirical examples of such effects are rare, let alone quantitative estimates of their strength and evolutionary consequences. Here, we demonstrate that the investment a mother makes in her eggs positively affects the egg investment of her daughters. Through reciprocally crossing artificially selected lines for divergent prenatal maternal investment in Japanese quail (Coturnix japonica), we demonstrate that the size of eggs daughters lay resembles the egg size of their maternal line significantly more than that of their paternal line, highlighting that egg size is in part maternally inherited. Correspondingly, we find that variation in the daughters' egg size is in part determined by maternal identity, in addition to substantial additive genetic effects. Furthermore, this maternal variance in offspring egg size is fully explained by maternal egg size, demonstrating the presence of a positive cascading effect of maternal egg size on offspring egg size. Finally, we use an evolutionary model to quantify the consequences of covariance between cascading maternal and additive genetic effects for both maternal effector and offspring body mass evolution. Our study demonstrates that by amplifying the amount of variation available for selection to act on, positive cascading maternal effects can significantly enhance the evolutionary potential of maternal effectors and the offspring traits that they affect.

Divide and conquer? Size adjustment with allometry and intermediate outcomes.

Many trait measurements are size-dependent, and while we often divide these traits by size before fitting statistical models to control for the effect of size, this approach does not account for allometry and the intermediate outcome problem. We describe these problems and outline potential solutions.

Divergent artificial selection for female reproductive investment has a sexually concordant effect on male reproductive success.

Depending on the genetic architecture of male and female fitness, sex-specific selection can have negative, positive, or neutral consequences for the opposite sex. Theory predicts that conflict between male and female function may drive the breakdown of intrasexual genetic correlations, allowing sexual dimorphism in sexually antagonistic traits. Reproductive traits are the epitome of this, showing highly differentiated proximate functions between the sexes. Here we use divergent artificial selection lines for female reproductive investment to test how female-specific selection on a sex-limited trait affects male reproductive success in a precocial bird, the Japanese quail (Coturnix japonica). We demonstrate that selection for increased egg investment in females positively affects male reproductive success both in competitive and non-competitive mating situations. This increased reproductive success was linked to a relatively larger left testis in males originating from lines selected for high female reproductive investment. Given that female quail have functional gonads only on their left side, this correlated response indicates that selection has acted on the shared developmental basis of male and female gonads. Our study thereby provides evidence for a positive genetic correlation between key reproductive traits in males and females despite a high degree of sexual dimorphism, and suggests that, in this system, selection on reproductive function is sexually concordant.

A trade-off between reproductive investment and maternal cerebellum size in a precocial bird.

Natural selection favours increased investment in reproduction, yet considerable variation in parental investment is observed in natural populations. Life-history theory predicts that this variation is maintained by a trade-off between the benefits of increased reproductive investment and its associated costs for the parents. The nature of these costs of reproduction, however, remains poorly understood. The brain is an energetically highly expensive organ and increased reproductive investment may, therefore, negatively affect brain maintenance. Using artificial selection lines for high and low prenatal maternal investment in a precocial bird, the Japanese quail (Coturnix japonica), we provide experimental evidence for this hypothesis by showing that increased prenatal provisioning negatively affects the size of a particular brain region of the mother, the cerebellum. Our finding suggests that cognitive demands may constrain the evolution of parental investment, and vice versa, contributing to the maintenance of variation in reproductive behaviour in animal populations.

Disentangling Genetic and Prenatal Maternal Effects on Offspring Size and Survival.

Organizational processes during prenatal development can have long-term effects on an individual's phenotype. Because these early developmental stages are sensitive to environmental influences, mothers are in a unique position to alter their offspring's phenotype by differentially allocating resources to their developing young. However, such prenatal maternal effects are difficult to disentangle from other forms of parental care, additive genetic effects, and/or other forms of maternal inheritance, hampering our understanding of their evolutionary consequences. Here we used divergent selection lines for high and low prenatal maternal investment and their reciprocal line crosses in a precocial bird-the Japanese quail (Coturnix japonica)-to quantify the relative importance of genes and prenatal maternal effects in shaping offspring phenotype. Maternal but not paternal origin strongly affected offspring body size and survival throughout development. Although the effects of maternal egg investment faded over time, they were large at key life stages. Additionally, there was evidence for other forms of maternal inheritance affecting offspring phenotype at later stages of development. Our study is among the first to successfully disentangle prenatal maternal effects from all other sources of confounding variation and highlights the important role of prenatal maternal provisioning in shaping offspring traits closely linked to fitness.

House sparrows.

Shinichi Nakagawa and Joel Pick introduce what we can learn from house sparrows.

Matrilineal inheritance of a key mediator of prenatal maternal effects.

Sex-linkage is predicted to evolve in response to sex-specific or sexually antagonistic selection. In line with this prediction, most sex-linked genes are associated with reproduction in the respective sex. In addition to traits directly involved in fertility and fecundity, mediators of maternal effects may be predisposed to evolve sex-linkage, because they indirectly affect female fitness through their effect on offspring phenotype. Here, we test for sex-linked inheritance of a key mediator of prenatal maternal effects in oviparous species, the transfer of maternally derived testosterone to the eggs. Consistent with maternal inheritance, we found that in Japanese quail (Coturnix japonica) granddaughters resemble their maternal (but not their paternal) grandmother in yolk testosterone deposition. This pattern of resemblance was not due to non-genetic priming effects of testosterone exposure during prenatal development, as an experimental manipulation of yolk testosterone levels did not affect the females' testosterone transfer to their own eggs later in life. Instead, W chromosome and/or mitochondrial variation may underlie the observed matrilineal inheritance pattern. Ultimately, the inheritance of mediators of maternal effects along the maternal line will allow for a fast and direct response to female-specific selection, thereby affecting the dynamics of evolutionary processes mediated by maternal effects.

Artificial selection reveals the energetic expense of producing larger eggs.

BACKGROUND: The amount of resources provided by the mother before birth has important and long-lasting effects on offspring fitness. Despite this, there is a large amount of variation in maternal investment seen in natural populations. Life-history theory predicts that this variation is maintained through a trade-off between the benefits of high maternal investment for the offspring and the costs of high investment for the mother. However, the proximate mechanisms underlying these costs of reproduction are not well understood. Here we used artificial selection for high and low maternal egg investment in a precocial bird, the Japanese quail (Coturnix japonica) to quantify costs of maternal reproductive investment. RESULTS: We show that females from the high maternal investment lines had significantly larger reproductive organs, which explained their overall larger body mass, and resulted in a higher resting metabolic rate (RMR). Contrary to our expectations, this increase in metabolic activity did not lead to a higher level of oxidative damage. CONCLUSIONS: This study is the first to provide experimental evidence for metabolic costs of increased per offspring investment.