The rise to dominance of genetic model organisms and the decline of curiosity-driven organismal research

The reference genome of Macropodus opercularis (the paradise fish)

Amongst fishes, zebrafish (Danio rerio) has gained popularity as a model system over most other species and while their value as a model is well documented, their usefulness is limited in certain fields of research such as behavior. By embracing other, less conventional experimental organisms, opportunities arise to gain broader insights into evolution and development, as well as studying behavioral aspects not available in current popular model systems. The anabantoid paradise fish (Macropodus opercularis), an "air-breather" species has a highly complex behavioral repertoire and has been the subject of many ethological investigations but lacks genomic resources. Here we report the reference genome assembly of M. opercularis using long-read sequences at 150-fold coverage. The final assembly consisted of 483,077,705 base pairs (~483 Mb) on 152 contigs. Within the assembled genome we identified and annotated 20,157 protein coding genes and assigned ~90% of them to orthogroups.

Model worms: knowledge gains and risks associated with the use of model species in parasitological research

Model parasite species, whose entire life cycle can be completed in the laboratory and maintained for multiple generations, have played a fundamental role in our understanding of host–parasite interactions. Yet, keeping parasites in laboratory conditions may expose them to unnatural evolutionary pressures, and using laboratory cultures for research is therefore not without limitations. Using 2 widely-used model helminth species, the cestode Hymenolepis diminuta and the nematode Heligmosomoides polygyrus, I illustrate the caution needed when interpreting experimental results on model species. I first review more than 1200 experimental studies published on these species in the past 4 decades, to determine which research areas they have contributed to. This is followed by an examination of the institutional laboratory cultures that have provided the parasites used in these studies. Some of these have persisted for decades and accounted for a substantial proportion of published studies, whereas others have been short-lived. Using information provided by the curators of active cultures, I summarize data on their origins and maintenance conditions. Finally, I discuss how laboratory cultures may have been subject to the influence of evolutionary genetic processes, such as founder effects, genetic drift and inbreeding. I also address the possibility that serial passage through laboratory hosts across multiple generations has exerted artificial selection on several parasite traits, resulting in genetic and phenotypic divergence among laboratory cultures, and between these cultures and natural parasite populations. I conclude with recommendations for the continued usage of laboratory helminth cultures aimed at maximizing their important contribution to parasitological research.

SEED: A framework for integrating ecological stoichiometry and eco-evolutionary dynamics

Characterising the extent and sources of intraspecific variation and their ecological consequences is a central challenge in the study of eco-evolutionary dynamics. Ecological stoichiometry, which uses elemental variation of organisms and their environment to understand ecosystem patterns and processes, can be a powerful framework for characterising eco-evolutionary dynamics. However, the current emphasis on the relative content of elements in the body (i.e. organismal stoichiometry) has constrained its application. Intraspecific variation in the rates at which elements are acquired, assimilated, allocated or lost is often greater than the variation in organismal stoichiometry. There is much to gain from studying these traits together as components of an 'elemental phenotype'. Furthermore, each of these traits can have distinct ecological effects that are underappreciated in the current literature. We propose a conceptual framework that explores how microevolutionary change in the elemental phenotype occurs, how its components interact with each other and with other traits, and how its changes can affect a wide range of ecological processes. We demonstrate how the framework can be used to generate novel hypotheses and outline pathways for future research that enhance our ability to explain, analyse and predict eco-evolutionary dynamics.

The reference genome of the paradise fish (Macropodus opercularis)

Over the decades, a small number of model species, each representative of a larger taxa, have dominated the field of biological research. Amongst fishes, zebrafish (Danio rerio) has gained popularity over most other species and while their value as a model is well documented, their usefulness is limited in certain fields of research such as behavior. By embracing other, less conventional experimental organisms, opportunities arise to gain broader insights into evolution and development, as well as studying behavioral aspects not available in current popular model systems. The anabantoid paradise fish (Macropodus opercularis), an "air-breather" species from Southeast Asia, has a highly complex behavioral repertoire and has been the subject of many ethological investigations, but lacks genomic resources. Here we report the reference genome assembly of Macropodus opercularis using long-read sequences at 150-fold coverage. The final assembly consisted of ≈483 Mb on 152 contigs. Within the assembled genome we identified and annotated 20,157 protein coding genes and assigned ≈90% of them to orthogroups. Completeness analysis showed that 98.5% of the Actinopterygii core gene set (ODB10) was present as a complete ortholog in our reference genome with a further 1.2 % being present in a fragmented form. Additionally, we cloned multiple genes important during early development and using newly developed in situ hybridization protocols, we showed that they have conserved expression patterns.

On the value of diverse organisms in auditory research: From fish to flies to humans

Historically, diverse organisms have contributed to our understanding of auditory function. In recent years, the laboratory mouse has become the prevailing non-human model in auditory research, particularly for biomedical studies. There are many questions in auditory research for which the mouse is the most appropriate (or the only) model system available. But mice cannot provide answers for all auditory problems of basic and applied importance, nor can any single model system provide a synthetic understanding of the diverse solutions that have evolved to facilitate effective detection and use of acoustic information. In this review, spurred by trends in funding and publishing and inspired by parallel observations in other domains of neuroscience, we highlight a few examples of the profound impact and lasting benefits of comparative and basic organismal research in the auditory system. We begin with the serendipitous discovery of hair cell regeneration in non-mammalian vertebrates, a finding that has fueled an ongoing search for pathways to hearing restoration in humans. We then turn to the problem of sound source localization - a fundamental task that most auditory systems have been compelled to solve despite large variation in the magnitudes and kinds of spatial acoustic cues available, begetting varied direction-detecting mechanisms. Finally, we consider the power of work in highly specialized organisms to reveal exceptional solutions to sensory problems - and the diverse returns of deep neuroethological inquiry - via the example of echolocating bats. Throughout, we consider how discoveries made possible by comparative and curiosity-driven organismal research have driven fundamental scientific, biomedical, and technological advances in the auditory field.

Wikidata and the bibliography of life

Biological taxonomy rests on a long tail of publications spanning nearly three centuries. Not only is this literature vital to resolving disputes about taxonomy and nomenclature, for many species it represents a key source-indeed sometimes the only source-of information about that species. Unlike other disciplines such as biomedicine, the taxonomic community lacks a centralised, curated literature database (the "bibliography of life"). This article argues that Wikidata can be that database as it has flexible and sophisticated models of bibliographic information, and an active community of people and programs ("bots") adding, editing, and curating that information.

Bisphenols impact hormone levels in animals: A meta-analysis

Bisphenols are used in the manufacture of plastics and are endocrine disrupting compounds detectable in free living organisms and environments globally. The original bisphenol, bisphenol A (BPA), is best known as a xenoestrogen, but it also disrupts other steroid hormones and other classes of hormones including thyroid and pituitary hormones. When its toxicity became better known, BPA was replaced by presumably less toxic alternatives, including bisphenols S, F, and AF. However, recent data suggest that all bisphenols can have endocrine disrupting effects, although their impacts remain unresolved particularly in non-human animals. Our aim was to establish the current state-of-knowledge of the effects of different bisphenols on circulating hormone levels in non-human animals. Our meta-analysis showed that a diverse range of hormones (including thyroid hormones, corticosterone, follicle stimulating hormone, luteinizing hormone, and estradiol) are strongly impacted by exposure to any bisphenol type, and that in laboratory rats (Rattus norvegicus) the effect was modified by life-stage. Although there were qualitative differences, BPA alternatives had as great or greater effects on hormone levels as BPA. However, data coverage across hormones was uneven, and most studies measured the effects of BPA on vertebrate reproductive hormones. Similarly, taxonomic coverage was poor. Over 80% of data originated from laboratory rats and zebrafish (Danio rerio) and there are no data for whole classes of invertebrates and vertebrates (e.g., amphibians). Our results show that all bisphenols alter circulating levels of a broad range of hormones. However, the current state-of-knowledge is incomplete so that the ecological impacts of bisphenols are difficult to gauge, although based on the available data bisphenols are likely to be detrimental to a broad range of taxa and ecosystems.

Government funding of research beyond biomedicine: challenges and opportunities for neuroethology

Curiosity-driven research is fundamental for neuroethology and depends crucially on governmental funding. Here, we highlight similarities and differences in funding of curiosity-driven research across countries by comparing two major funding agencies—the National Science Foundation (NSF) in the United States and the German Research Foundation (Deutsche Forschungsgemeinschaft, DFG). We interviewed representatives from each of the two agencies, focusing on general funding trends, levels of young investigator support, career-life balance, and international collaborations. While our analysis revealed a negative trend in NSF funding of biological research, including curiosity-driven research, German researchers in these areas have benefited from a robust positive trend in DFG funding. The main reason for the decrease in curiosity-driven research in the US is that the NSF has only partially been able to compensate for the funding gap resulting from the National Institutes of Health restricting their support to biomedical research using select model organisms. Notwithstanding some differences in funding programs, particularly those relevant for scientists in the postdoctoral phase, both the NSF and DFG clearly support curiosity-driven research.

March Mammal Madness and the power of narrative in science outreach

March Mammal Madness is a science outreach project that, over the course of several weeks in March, reaches hundreds of thousands of people in the United States every year. We combine four approaches to science outreach - gamification, social media platforms, community event(s), and creative products - to run a simulated tournament in which 64 animals compete to become the tournament champion. While the encounters between the animals are hypothetical, the outcomes rely on empirical evidence from the scientific literature. Players select their favored combatants beforehand, and during the tournament scientists translate the academic literature into gripping "play-by-play" narration on social media. To date ~1100 scholarly works, covering almost 400 taxa, have been transformed into science stories. March Mammal Madness is most typically used by high-school educators teaching life sciences, and we estimate that our materials reached ~1% of high-school students in the United States in 2019. Here we document the intentional design, public engagement, and magnitude of reach of the project. We further explain how human psychological and cognitive adaptations for shared experiences, social learning, narrative, and imagery contribute to the widespread use of March Mammal Madness.