A field guide for teaching evolution in the social sciences

The theory of evolution by natural selection has begun to revolutionize our understanding of perception, cognition, language, social behavior, and cultural practices. Despite the centrality of evolutionary theory to the social sciences, many students, teachers, and even scientists struggle to understand how natural selection works. Our goal is to provide a field guide for social scientists on teaching evolution, based on research in cognitive psychology, developmental psychology, and education. We synthesize what is known about the psychological obstacles to understanding evolution, methods for assessing evolution understanding, and pedagogical strategies for improving evolution understanding. We review what is known about teaching evolution about nonhuman species and then explore implications of these findings for the teaching of evolution about humans. By leveraging our knowledge of how to teach evolution in general, we hope to motivate and equip social scientists to begin teaching evolution in the context of their own field.     

A pocket guide to host-parasite models

Mathematical models have been used to describe the population dynamics of a wide range of host-parasite interactions. Mick Roberts here discusses mathematical models for the dynamics of helminth endoparasites of non-human mammalian hosts, paying particular attention to the density-dependent factors that regulate the parasite populations, and the interaction between parasite and wild or feral animal host populations.     

A conceptual guide to measuring species diversity

Three metrics of species diversity – species richness, the Shannon index and the Simpson index – are still widely used in ecology, despite decades of valid critiques leveled against them. Developing a robust diversity metric has been challenging because, unlike many variables ecologists measure, the diversity of a community often cannot be estimated in an unbiased way based on a random sample from that community. Over the past decade, ecologists have begun to incorporate two important tools for estimating diversity: coverage and Hill diversity. Coverage is a method for equalizing samples that is, on theoretical grounds, preferable to other commonly used methods such as equal-effort sampling, or rarefying datasets to equal sample size. Hill diversity comprises a spectrum of diversity metrics and is based on three key insights. First, species richness and variants of the Shannon and Simpson indices are all special cases of one general equation. Second, richness, Shannon and Simpson can be expressed on the same scale and in units of species. Third, there is no way to eliminate the effect of relative abundance from estimates of any of these diversity metrics, including species richness. Rather, a researcher must choose the relative sensitivity of the metric towards rare and common species, a concept which we describe as ‘leverage.' In this paper we explain coverage and Hill diversity, provide guidelines for how to use them together to measure species diversity, and demonstrate their use with examples from our own data. We show why researchers will obtain more robust results when they estimate the Hill diversity of equal-coverage samples, rather than using other methods such as equal-effort sampling or traditional sample rarefaction.     

A field guide to cultivating computational biology

Evolving in sync with the computation revolution over the past 30 years, computational biology has emerged as a mature scientific field. While the field has made major contributions toward improving scientific knowledge and human health, individual computational biology practitioners at various institutions often languish in career development. As optimistic biologists passionate about the future of our field, we propose solutions for both eager and reluctant individual scientists, institutions, publishers, funding agencies, and educators to fully embrace computational biology. We believe that in order to pave the way for the next generation of discoveries, we need to improve recognition for computational biologists and better align pathways of career success with pathways of scientific progress. With 10 outlined steps, we call on all adjacent fields to move away from the traditional individual, single-discipline investigator research model and embrace multidisciplinary, data-driven, team science.

Do you want to attract computational biologists to your project or to your department? Despite the major contributions of computational biology, those attempting to bridge the interdisciplinary gap often languish in career advancement, publication, and grant review. Here, sixteen computational biologists around the globe present "A field guide to cultivating computational biology," focusing on solutions.

Biology in the digital era requires computation and collaboration. A modern research project may include multiple model systems, use multiple assay technologies, collect varying data types, and require complex computational strategies, which together make effective design and execution difficult or impossible for any individual scientist. While some labs, institutions, funding bodies, publishers, and other educators have already embraced a team science model in computational biology and thrived [1–7], others who have not yet fully adopted it risk severely lagging behind the cutting edge. We propose a general solution: “deep integration” between biology and the computational sciences. Many different collaborative models can yield deep integration, and different problems require different approaches (Fig 1).Open in a separate windowFig 1Supporting interdisciplinary team science will accelerate biological discoveries.Scientists who have little exposure to different fields build silos, in which they perform science without external input. To solve hard problems and to extend your impact, collaborate with diverse scientists, communicate effectively, recognize the importance of core facilities, and embrace research parasitism. In biologically focused parasitism, wet lab biologists use existing computational tools to solve problems; in computationally focused parasitism, primarily dry lab biologists analyze publicly available data. Both strategies maximize the use and societal benefit of scientific data.In this article, we define computational science extremely broadly to include all quantitative approaches such as computer science, statistics, machine learning, and mathematics. We also define biology broadly, including any scientific inquiry pertaining to life and its many complications. A harmonious deep integration between biology and computer science requires action—we outline 10 immediate calls to action in this article and aim our speech directly at individual scientists, institutions, funding agencies, and publishers in an attempt to shift perspectives and enable action toward accepting and embracing computational biology as a mature, necessary, and inevitable discipline (Box 1).Box 1. Ten calls to action for individual scientists, funding bodies, publishers, and institutions to cultivate computational biology. Many actions require increased funding support, while others require a perspective shift. For those actions that require funding, we believe convincing the community of need is the first step toward agencies and systems allocating sufficient support

1. Respect collaborators’ specific research interests and motivationsProblem: Researchers face conflicts when their goals do not align with collaborators. For example, projects with routine analyses provide little benefit for computational biologists.Solution: Explicit discussion about interests/expertise/goals at project onset.Opportunity: Clearly defined expectations identify gaps, provide commitment to mutual benefit.
2. Seek necessary input during project design and throughout the project life cycleProblem: Modern research projects require multiple experts spanning the project’s complexity.Solution: Engage complementary scientists with necessary expertise throughout the entire project life cycle.Opportunity: Better designed and controlled studies with higher likelihood for success.
3. Provide and preserve budgets for computational biologists’ workProblem: The perception that analysis is “free” leads to collaborator budget cuts.Solution: When budget cuts are necessary, ensure that they are spread evenly.Opportunity: More accurate, reproducible, and trustworthy computational analyses.
4. Downplay publication author order as an evaluation metric for computational biologistsProblem: Computational biologist roles on publications are poorly understood and undervalued.Solution: Journals provide more equitable opportunities, funding bodies and institutions improve understanding of the importance of team science, scientists educate each other.Opportunity: Engage more computational biologist collaborators, provide opportunities for more high-impact work.
5. Value software as an academic productProblem: Software is relatively undervalued and can end up poorly maintained and supported, wasting the time put into its creation.Solution: Scientists cite software, and funding bodies provide more software funding opportunities.Opportunity: More high-quality maintainable biology software will save time, reduce reimplementation, and increase analysis reproducibility.
6. Establish academic structures and review panels that specifically reward team scienceProblem: Current mechanisms do not consistently reward multidisciplinary work.Solution: Separate evaluation structures to better align peer review to reward indicators of team science.Opportunity: More collaboration to attack complex multidisciplinary problems.
7. Develop and reward cross-disciplinary training and mentoringProblem: Academic labs and institutions are often insufficiently equipped to provide training to tackle the next generation of biological problems, which require computational skills.Solution: Create better training programs aligned to necessary on-the-job skills with an emphasis on communication, encourage wet/dry co-mentorship, and engage younger students to pursue computational biology.Opportunity: Interdisciplinary students uncover important insights in their own data.
8. Support computing and experimental infrastructure to empower computational biologistsProblem: Individual computational labs often fund suboptimal cluster computing systems and lack access to data generation facilities.Solution: Institutions can support centralized compute and engage core facilities to provide data services.Opportunity: Time and cost savings for often overlooked administrative tasks.
9. Provide incentives and mechanisms to share open data to empower discovery through reanalysisProblem: Data are often siloed and have untapped potential.Solution: Provide institutional data storage with standardized identifiers and provide separate funding mechanisms and publishing venues for data reuse.Opportunity: Foster new breed of researchers, “research parasites,” who will integrate multimodal data and enhance mechanistic insights.
10. Consider infrastructural, ethical, and cultural barriers to clinical data accessProblem: Identifiable health data, which include sensitive information that must be kept hidden, are distributed and disorganized, and thus underutilized.Solution: Leadership must enforce policies to share deidentifiable data with interoperable metadata identifiers.Opportunity: Derive new insights from multimodal data integration and build datasets with increased power to make biological discoveries.

     

Pollen and resource limitation in a gynodioecious species

Differences between plant sex morphs in pollen or resource availability may affect their relative fitness and thereby the sex ratio of dimorphic species. In gynodioecious species, in which hermaphroditic and female plants coexist, a variety of factors (e.g., hermaphrodite self-fertility or rarity or pollinator discrimination against females) might be expected to lead to stronger pollen limitation in females than in hermaphrodites. On the other hand, females have been found to be superior compared to hermaphrodites in low-nutrient conditions. The effects of supplemental hand-pollination and resource addition on the reproductive output of the self-fertile gynodioecious perennial Geranium sylvaticum (Geraniaceae) were tested for several populations that differ in their female frequency (4.4-23.0%). Both pollen and resource availability limited fruit set and the number of seeds produced per plant; however, seed set (i.e., the number of seeds produced per fruit) was limited only by resources. Because pollen limitation in females did not correlate with female frequency, our results suggest that pollen limitation in females does not depend on the frequency of the pollen-producing hermaphrodites. Furthermore, because pollen and resource availability limited reproductive output of both sex morphs, these factors may not contribute significantly to maintenance and evolution of gynodioecy in G. sylvaticum.     

A chemical field guide to histone nonenzymatic modifications

Histone nonenzymatic covalent modifications (NECMs) have recently emerged as an understudied class of posttranslational modifications that regulate chromatin structure and function. These NECMs alter the surface topology of histone proteins, their interactions with DNA and chromatin regulators, as well as compete for modification sites with enzymatic posttranslational modifications. NECM formation depends on the chemical compatibility between a reactive molecule and its target site, in addition to their relative stoichiometries. Here we survey the chemical reactions and conditions that govern the addition of NECMs onto histones as a manual to guide the identification of new physiologically relevant chemical adducts. Characterizing NECMs on chromatin is critical to attain a comprehensive understanding of this new chapter of the so-called “histone code”.     

The evolution of autosomal suppressors of sex-ratio drive in Drosophila simulans

Sex-ratio drive, which results in males siring female-biased progeny, has been reported in several Drosophila species, including D. simulans. It is caused by X-linked drivers that prevent the production of Y-bearing sperm. In natural populations of D. simulans, the drivers are usually cryptic, because their spread has elicited the evolution of drive suppressors. We investigated autosomal suppression in flies from Madagascar, Réunion and Kenya. Autosomal suppressors were found in all three places, indicating that they are a regular component of drive suppression over this geographic area, where strong Y-linked suppressors also occur. These suppressors were suspected of being polymorphic in Madagascar and Réunion and proved to be polymorphic in Kenya. We developed a model simulating the evolution of neutral autosomal suppressors in order to explore the effects of the number of suppressor genes, their relative strength and the co-occurrence of Y-linked suppressors. The most interesting prediction of the model is that when suppression is multigenic, suppressor loci can remain polymorphic despite the absence of balancing selection if an equal sex-ratio is restored in the population before the suppressor alleles become fixed at all loci. The model also emphasises the importance of the sterility of distorters sons in suppressor dynamics.     

Dinosaurs: a field guide/The Princeton field guide to dinosaurs

Eggshells from the three extant crocodilian species Crocodylus mindorensis (Philippine Crocodile), Paleosuchus palpebrosus (Cuvier's Smooth-fronted Caiman or Musky Caiman) and Alligator mississippiensis (American Alligator or Common Alligator) were prepared for thin section and scanning electron microscope analyses and are described in order to improve the knowledge on crocodilian eggs anatomy and microstructure, and to find new apomorphies that can be used for identification. Both extant and fossil crocodilian eggs present an ornamentation that vary as anastomo-, ramo- or the here newly described rugosocavate type. The angusticaniculate pore system is a shared character for Crocodylomorpha eggshells and some dinosaurian and avian groups. Previously reported signs of incubated crocodilian eggs were found also on our only fertilised and hatched egg. Paleosuchus palpebrosus presents unique organization and morphology of the three eggshell layers, with a relatively thin middle layer characterised by dense and compact tabular microstructure.     

Sex inheritance in gynodioecious species: a polygenic view

Gynodioecy is defined as the coexistence of two different sexual morphs in a population: females and hermaphrodites. This breeding system is found among many different families of angiosperms and is usually under nucleo-cytoplasmic inheritance, with maternally inherited genes causing male sterility and nuclear factors restoring male fertility. Numerous theoretical models have investigated the conditions for the stable coexistence of females and hermaphrodites. To date, all models rest on the assumption that restoration of a given male sterile genotype is controlled by a single Mendelian factor. Here, we review data bearing on the genetic determinism of sex inheritance in three gynodiecious plant species. We suggest that restoration of male fertility is probably best viewed as a quantitative trait controlled by many loci. We develop a threshold model that accommodates an underlying polygenic trait, which is resolved at the phenotypic level in discrete sexual morphs. We use this model to reanalyse data in Thymus vulgaris, Silene vulgaris and Plantago coronopus. A simple Mendelian inheritance of sex determinism is unlikely in all three species. We discuss how our model can shed additional light on the genetics of restoration and point towards future efforts in the modelling of gynodioecy.     

A cost of restoration of male fertility in a gynodioecious species,Lobelia siphilitica

Abstract.— Models allowing the coexistence of females and hermaphrodites in gynodioecious populations assume a simple genetic system of sex determination, a seed fitness advantage of females (compensation), and a negative pleiotropic effect of nuclear sex-determining genes on fitness (cost of restoration). In Lobelia siphilitica , sex is determined by both mitochondrial genes causing cytoplasmic male sterility (CMS) and nuclear genes that restore fertility when present with specific CMS haplotypes (nuclear restorers). I tested for a cost of restoration in L. siphilitica by measuring restored hermaphrodites for five fitness components and estimating the number of nuclear restorers by crosses with females carrying CMS1 and CMS2. A cost of restoration appears as a significant negative coefficient (B) in the regression model explaining fitness. I found that hermaphrodites carrying more nuclear restorer genes for CMS2 (or restorer genes of greater effect) have lower pollen viability (B =– 1.08, P = 0.001). This pollen viability cost of restoration in L. siphilitica supports the theoretical prediction that negative pleiotropic effects of restorers will exist in populations of gynodioecious species containing females. The existence of such a cost supports the view that gynodioecy can be a stable breeding system in nature.     

Pollen-stigma interference in two gynodioecious species of Lamiaceae with intermediate individuals

BACKGROUND AND AIMS: Intermediate individuals (perfect flowers with very high degree of pollen abortion) in a gynodioecious plant species are very rare. A study is made of male-female relationships in each flower type and how floral characters can enhance the avoidance of 'pollen discounting' and 'self-pollination' in two gynodioecious species, Teucrium capitatum and Origanum syriacum. METHODS: The relationship between stigma receptivity and pollen viability was studied in two gynodioecious protandrous species of Lamiaceae, in addition to measuring some floral morphological characters over the life span of the flowers. KEY RESULTS: Three plant types in each species were found: plants bearing hermaphrodite (or male fertile) flowers (MF), female (or male sterile) flowers (MS) and intermediate flowers (INT). Plant types differed in flower size, with MS types being shorter than the other two types. There was no difference in style length among plant types in T. capitatum. Stigma receptivity decayed with floral age and was negative and significantly correlated with pollen viability in the two species, and positive and significantly correlated with style length in O. syriacum but only in MS flowers of T. capitatum. CONCLUSIONS: Reduction in size of floral characters is associated with male sterility, except style length in T. capitatum. MF flowers have two successive reproductive impediments: self-pollination and pollen-stigma interference. In both species, self-pollination is avoided by dichogamy (negative correlation between stigma receptivity and pollen viability), and pollen-stigma interference shows two different patterns: (1) style elongation in O. syriacum is characterized by a significant length increase, final MF dimensions are greater than those of MS dimensions, and style length is positively and significantly correlated with stigma receptivity; and (2) style movement in T. capitatum is characterized by a non-significant increase in style length, final MF floral dimensions are similar to those of MS dimensions, and there is no correlation between style length and stigma receptivity.     

Local population structure and sex ratio: evolution in gynodioecious plants

Although the influence of population structure on evolution has been explored previously in a variety of theoretical studies, there are few examples of specific traits whose fitness is likely to be modified by the local structure. Here we focus on a specific trait, sex expression in gynodioecious plants, and derive a model in which the fitness of females and hermaphrodites is a function of the local sex ratio. By using the concept d genes. As a consequence, when local demes vary in sex ratio, a polymorphism for a cytoplasmic male sterility (CMS) allele can be maintained in the absence of nuclear alleles that restore male function. When of subjective frequencies, it is shown that among-deme variance in the local sex ratio reduces the average fitness of females when pollen availability limits fertility. In contrast, sex ratio variance increases the fitness of hermaphrodites from the perspective of maternally inherited genes and lessens the negative impact of pollen limitation on hermaphrodite fitness when it is measured from the perspective of biparentally inheriterestorer alleles are introduced into the model, polymorphism cannot be maintained simultaneously at both the cytoplasmic and nuclear loci. In that case, the CMS allele spreads to fixation, and the equilibrium frequency of females is an inverse function of the equilibrium frequency of the restorer allele, which increases with increased structure. The results exemplify how population structure can greatly alter the fitness and evolution of a frequency-dependent trait.     

A field guide to the proteomics of post-translational modifications in DNA repair

All cells incur DNA damage from exogenous and endogenous sources and possess pathways to detect and repair DNA damage. Post-translational modifications (PTMs), in the past 20 years, have risen to ineluctable importance in the study of the regulation of DNA repair mechanisms. For example, DNA damage response kinases are critical in both the initial sensing of DNA damage as well as in orchestrating downstream activities of DNA repair factors. Mass spectrometry-based proteomics revolutionized the study of the role of PTMs in the DNA damage response and has canonized PTMs as central modulators of nearly all aspects of DNA damage signaling and repair. This review provides a biologist-friendly guide for the mass spectrometry analysis of PTMs in the context of DNA repair and DNA damage responses. We reflect on the current state of proteomics for exploring new mechanisms of PTM-based regulation and outline a roadmap for designing PTM mapping experiments that focus on the DNA repair and DNA damage responses.     

A field guide to the Mps1 family of protein kinases

Cell cycle events must be faithfully executed and properly integrated to ensure genetic stability. The Mps1 family of protein kinases has recently emerged as a critical regulator of genetic stability, because they regulate several processes central to mitotic fidelity. The spindle checkpoint monitors alignment of mitotic chromosomes, and centrosomes control cell cycle entry, mitotic spindle assembly, and cytokinesis. Several studies have shown that vertebrate orthologues of budding yeast Mps1p regulate the spindle checkpoint. More recently it has been demonstrated that human Mps1 is also required for centrosome duplication, normal mitotic progression, and cytokinesis.     

Brood-size and sex-ratio variation in field populations of three species of solitary aphid parasitoids (Hymenoptera: Braconidae, Aphidiinae)

Solitary parasitoids of colony-forming hosts may produce quasi-gregarious broods, which favours sibmating on the natal patch and local mate competition (LMC). We examined seasonal variations in brood size and sex ratio in three species of solitary parasitoids of aphids associated with trophobiotic ants. Adialytus arvicola, a parasitoid of Sipha agropyrella on grasses, had the smallest broods (mean=4.2, maximum 19), while Lysiphlebus hirticornis, a parasitoid of Metopeurum fuscoviride on tansy, had the largest broods (mean=32.0, maximum 265). In Pauesia pini, a parasitoid of Cinara piceicola on Norway spruce, broods comprised an average of 5.8 (maximum 41) individuals; brood size increased during early summer when hosts became more available but remained the same later in the season. In all three species the sex ratio at eclosion was female-biased, with broods containing approximately two daughters for each son in both A. arvicola and L. hirticornis; the degree of female-bias was least in P. pini. The sex ratio did not vary with brood size. In A. arvicola, the variance of the number of sons declined with an increase in brood size, consistent with "precise" sex allocation. In contrast, in L. hirticornis, the overall sex-ratio variance was greater than its binomial expectation, while it did not differ from binomial in P. pini. A large proportion of broods contained only sons or only daughters, especially in A. arvicola. An excess of male-only broods is expected if constrained females (which can produce only sons) contribute offspring prior to mating. The number of male-only broods, however, did not differ from the number expected if all females are mated and allocate offspring sexes binomially, except in P. pini. In the latter species, broods with two daughters (as opposed to two sons) exceeded binomial expectations. We propose that P. pini is largely outbreeding, while the strongly female-biased sex ratio in A. arvicola and L. hirticornis is consistent with partial sibmating and LMC. Ant-parasitoid interactions could account for a different population mating structure in the three parasitoid species. Both A. arvicola and L. hirticornis mimic the epicuticular hydrocarbon pattern of their aphid hosts. Eclosing wasps are ignored by honeydew-collecting ants and hence can mate and forage on the natal patch. In contrast, P. pini generally depart the mummy area to avoid attacks by trophobiotic ants and mate off patch.