Evolution: Biology's next top model?

Not just a cousin of the naked mole-rat: Damaraland mole-rats offer unique insights into biomedicine

Evolutionary medicine has been a fast-growing field of biological research in the past decade. One of the strengths of evolutionary medicine is to use non-traditional model organisms which often exhibit unusual characteristics shaped by natural selection. Studying these unusual traits could provide valuable insight to understand biomedical questions, since natural selection likely discovers solutions to those complex biological problems. Because of many unusual traits, the naked mole-rat (NMR) has attracted attention from different research areas such as aging, cancer, and hypoxia- and hypercapnia-related disorders. However, such uniqueness of NMR physiology may sometimes make the translational study to human research difficult. Damaraland mole-rat (DMR) shares multiple characteristics in common with NMR, but shows higher degree of similarity with human in some aspects of their physiology. Research on DMR could therefore offer alternative insights and might bridge the gap between experimental findings from NMR to human biomedical research. In this review, we discuss studies of DMR as an extension of the current set of model organisms to help better understand different aspects of human biology and disease. We hope to encourage researchers to consider studying DMR together with NMR. By studying these two similar but evolutionarily distinct species, we can harvest the power of convergent evolution and avoid the potential biased conclusions based on life-history of a single species.

Collecting eco-evolutionary data in the dark: Impediments to subterranean research and how to overcome them

Caves and other subterranean habitats fulfill the requirements of experimental model systems to address general questions in ecology and evolution. Yet, the harsh working conditions of these environments and the uniqueness of the subterranean organisms have challenged most attempts to pursuit standardized research.Two main obstacles have synergistically hampered previous attempts. First, there is a habitat impediment related to the objective difficulties of exploring subterranean habitats and our inability to access the network of fissures that represents the elective habitat for the so-called "cave species." Second, there is a biological impediment illustrated by the rarity of most subterranean species and their low physiological tolerance, often limiting sample size and complicating laboratory experiments.We explore the advantages and disadvantages of four general experimental setups (in situ, quasi in situ, ex situ, and in silico) in the light of habitat and biological impediments. We also discuss the potential of indirect approaches to research. Furthermore, using bibliometric data, we provide a quantitative overview of the model organisms that scientists have exploited in the study of subterranean life.Our over-arching goal is to promote caves as model systems where one can perform standardized scientific research. This is important not only to achieve an in-depth understanding of the functioning of subterranean ecosystems but also to fully exploit their long-discussed potential in addressing general scientific questions with implications beyond the boundaries of this discipline.

Let research on subterranean habitats resonate!

Whereas scientists interested in subterranean life typically insist that their research is exciting, adventurous, and important to answer general questions, this enthusiasm and potential often fade when the results are translated into scientific publications. This is because cave research is often written by cave scientists for cave scientists; thus, it rarely “leaves the cave”. However, the status quo is changing rapidly. We analysed 21,486 articles focused on subterranean ecosystems published over the last three decades and observed a recent, near-exponential increase in their annual citations and impact factor. Cave research is now more often published in non-specialized journals, thanks to a number of authors who are exploiting subterranean habitats as model systems for addressing important scientific questions. Encouraged by this positive trend, we here propose a few personal ideas for improving the generality of subterranean literature, including tips for framing broadly scoped research and making it accessible to a general audience, even when published in cave-specialized journals. Hopefully, this small contribution will succeed in condensing and broadcasting even further the collective effort taken by the subterranean biology community to bring their research “outside the cave”.

Record breaking achievements by spiders and the scientists who study them

Organismal biology has been steadily losing fashion in both formal education and scientific research. Simultaneous with this is an observable decrease in the connection between humans, their environment, and the organisms with which they share the planet. Nonetheless, we propose that organismal biology can facilitate scientific observation, discovery, research, and engagement, especially when the organisms of focus are ubiquitous and charismatic animals such as spiders. Despite being often feared, spiders are mysterious and intriguing, offering a useful foundation for the effective teaching and learning of scientific concepts and processes. In order to provide an entryway for teachers and students-as well as scientists themselves-into the biology of spiders, we compiled a list of 99 record breaking achievements by spiders (the "Spider World Records"). We chose a world-record style format, as this is known to be an effective way to intrigue readers of all ages. We highlighted, for example, the largest and smallest spiders, the largest prey eaten, the fastest runners, the highest fliers, the species with the longest sperm, the most venomous species, and many more. We hope that our compilation will inspire science educators to embrace the biology of spiders as a resource that engages students in science learning. By making these achievements accessible to non-arachnologists and arachnologists alike, we suggest that they could be used: (i) by educators to draw in students for science education, (ii) to highlight gaps in current organismal knowledge, and (iii) to suggest novel avenues for future research efforts. Our contribution is not meant to be comprehensive, but aims to raise public awareness on spiders, while also providing an initial database of their record breaking achievements.

Cichlid fishes as a model to understand normal and clinical craniofacial variation

We have made great strides towards understanding the etiology of craniofacial disorders, especially for 'simple' Mendelian traits. However, the facial skeleton is a complex trait, and the full spectrum of genetic, developmental, and environmental factors that contribute to its final geometry remain unresolved. Forward genetic screens are constrained with respect to complex traits due to the types of genes and alleles commonly identified, developmental pleiotropy, and limited information about the impact of environmental interactions. Here, we discuss how studies in an evolutionary model - African cichlid fishes - can complement traditional approaches to understand the genetic and developmental origins of complex shape. Cichlids exhibit an unparalleled range of natural craniofacial morphologies that model normal human variation, and in certain instances mimic human facial dysmorphologies. Moreover, the evolutionary history and genomic architecture of cichlids make them an ideal system to identify the genetic basis of these phenotypes via quantitative trait loci (QTL) mapping and population genomics. Given the molecular conservation of developmental genes and pathways, insights from cichlids are applicable to human facial variation and disease. We review recent work in this system, which has identified lbh as a novel regulator of neural crest cell migration, determined the Wnt and Hedgehog pathways mediate species-specific bone morphologies, and examined how plastic responses to diet modulate adult facial shapes. These studies have not only revealed new roles for existing pathways in craniofacial development, but have identified new genes and mechanisms involved in shaping the craniofacial skeleton. In all, we suggest that combining work in traditional laboratory and evolutionary models offers significant potential to provide a more complete and comprehensive picture of the myriad factors that are involved in the development of complex traits.

Nature is (a) mine: conceptions of nature in the Dutch ecogenomics community

Every field of science, but especially biology, contains particular conceptions of nature. These conceptions are not merely epistemological or ontological, but also have normative dimensions; they provide an ethos, a framework for moral orientation. These normative dimensions, whilst often remaining 'hidden' and inarticulate, influence the way in which biologists practice their profession. In this paper, I explore what happens when different versions of these implicit normative frameworks collide. To do so, I will focus on a case study from the field of ecological genomics as it has evolved in one particular country, namely the Netherlands. During an important inaugural meeting, the director of one of the most sizeable Dutch ecogenomics centres gave a presentation in which he introduced the term 'nature mining'. Part of the audience immediately embraced the term, but others were very reluctant. This mixed response is generally explained as a culmination of growing tension about the future direction of the field: due to new funding demands, a shift had occurred from fundamental research to research more interested in 'valorisation'.In addition to this current interpretation, I will argue that the turmoil caused by the use of the term 'nature mining' also reveals a more fundamental difference between the various parties involved in the Dutch ecogenomics community. This term is part of a vocabulary that emphasises the beneficial 'goods' produced by nature. Whereas part of the audience saw no harm in this commodification of nature, others had difficulties with the reduction of nature to a reservoir to be exploited using the latest technologies. I will conclude by arguing that, although at present, the core of Dutch ecogenomics research reflects a more or less instrumental attitude towards nature, the field also harbours other interpretations of nature as a significant and meaningful order. For instance, ecogenomics might further develop the image of land as a 'collective organism', as proposed by Aldo Leopold.

Characterization of Toll-like receptor gene expression and the pathogen agonist response in the antarctic bullhead notothen Notothenia coriiceps

Notothenia coriiceps, a typical Antarctic notothenioid teleost, has evolved to adapt to the extreme Antarctic marine environment. We previously reported an extensive analysis of the Antarctic notothenioid transcriptome. In this study, we focused on a key component of the innate immune system, the Toll-like receptors (TLRs). We cloned the full-length sequence of 12 TLRs of N. coriiceps. The N. coriiceps transcriptome for TLR homologue (ncTLR) genes encode a typical TLR structure, with multiple extracellular leucine-rich regions and an intracellular Toll/IL-1 receptor (TIR) domain. Using phylogenetic analysis, we established that all of the cloned ncTLR genes could be classified into the same orthologous clade with other teleost TLRs. ncTLRs were widely expressed in various organs, with the highest expression levels observed in immune-related tissues, such as the skin, spleen, and kidney. A subset of the ncTLR genes was expressed at higher levels in fish exposed to pathogen-mimicking agonists, heat-killed Escherichia coli, and polyinosinic-polycytidylic acid (poly(I:C)). However, the mechanism involved in the upregulation of TLR expression following pathogen exposure in fish is currently unknown. Further research is required to elucidate these mechanisms and to thereby increase our understanding of vertebrate immune system evolution.

Divergence in skeletal mass and bone morphology in antarctic notothenioid fishes

Although notothenioid fishes lack swim bladders, some species live temporarily or permanently in the water column. Given its relatively high density, skeletal mass is a key determinant of buoyancy. Notothenioids have reduced skeletal ossification, but there is little quantitative data on the phylogenetic distribution of this trait. We obtained dry skeletal masses for 54 specimens representing 20 species from six notothenioid families. Although comparative data are sparse, notothenioid skeletons comprise a smaller percentage of body mass, <3.5%, than those of three non-notothenioid perciforms. With relatively high skeletal mass, the non-Antarctic Bovichtus diacanthus is similar in skeletal mass to some non-notothenioids. Eleginops maclovinus, the non-Antarctic sister group of the Antarctic clade, has a relatively light skeleton (<2% of body mass) similar to many species in the Antarctic clade. Low skeletal mass is therefore a synapomorphy shared by Eleginops plus the Antarctic clade. We provide gross, histological, and micro-CT documentation of the structure and location of bone and cartilage in skulls, pectoral girdles, and vertebrae, with emphasis on the bovichtid B. diacanthus, the eleginopsid E. maclovinus, and the channichthyid Chaenodraco wilsoni. In Eleginops and the Antarctic clade, most bone is spongy and most species have persisting cartilage in the skull and appendicular skeleton. We also measured the relative size of the notochordal canal in adult vertebral centra of 38 species representing all eight families. There is considerable interspecific variation in this pedomorphic trait and all species show an ontogenetic reduction in the relative size of the canal. However, large persisting canals are present in adults of the Antarctic clade, especially in the nototheniids Pleuragramma and Aethotaxis and in a number of bathydraconid and channichthyid genera.

What makes a model organism?

This article explains the key role of model organisms within contemporary research, while at the same time acknowledging their limitations as biological models. We analyse the epistemic and social characteristics of model organism biology as a form of "big science", which includes the development of large, centralised infrastructures, a shared ethos and a specific long-term vision about the "right way" to do research. In order to make wise use of existing resources, researchers now find themselves committed to carrying out this vision with its accompanying assumptions. By clarifying the specific characteristics of model organism work, we aim to provide a framework to assess how much funding should be allocated to such research. On the one hand, it is imperative to exploit the resources and knowledge accumulated using these models to study more diverse groups of organisms. On the other hand, this type of research may be inappropriate for research programmes where the processes of interest are much more delimited, can be usefully studied in isolation and/or are simply not captured by model organism biology.

Model systems, taxonomic bias, and sexual selection: beyond Drosophila

Although model systems are useful in entomology, allowing generalizations based on a few well-known species, they also have drawbacks. It can be difficult to know how far to generalize from information in a few species: Are all flies like Drosophila? The use of model systems is particularly problematic in studying sexual selection, where variability among taxa is key to the evolution of different behaviors. A bias toward the use of a few insect species, particularly from the genus Drosophila, is evident in the sexual selection and sexual conflict literature over the past several decades, although the diversity of study organisms has increased more recently. As the number of model systems used to study sexual conflict increased, support for the idea that sexual interactions resulted in harm to females decreased. Future work should choose model systems thoughtfully, combining well-known species with those that can add to the variation that allows us to make more meaningful generalizations.

Re-thinking organisms: The impact of databases on model organism biology

Community databases have become crucial to the collection, ordering and retrieval of data gathered on model organisms, as well as to the ways in which these data are interpreted and used across a range of research contexts. This paper analyses the impact of community databases on research practices in model organism biology by focusing on the history and current use of four community databases: FlyBase, Mouse Genome Informatics, WormBase and The Arabidopsis Information Resource. We discuss the standards used by the curators of these databases for what counts as reliable evidence, acceptable terminology, appropriate experimental set-ups and adequate materials (e.g., specimens). On the one hand, these choices are informed by the collaborative research ethos characterising most model organism communities. On the other hand, the deployment of these standards in databases reinforces this ethos and gives it concrete and precise instantiations by shaping the skills, practices, values and background knowledge required of the database users. We conclude that the increasing reliance on community databases as vehicles to circulate data is having a major impact on how researchers conduct and communicate their research, which affects how they understand the biology of model organisms and its relation to the biology of other species.

Anhydrobiosis: the model worm as a model?

New work now shows that the dauer larvae of Caenorhabditis elegans can survive anhydrobiotically. The genetic tractability of this model organism may be useful in studying how organisms survive when losing most or all of their water.

Selectable genetic markers for nematode transgenesis

The nematode Caenorhabditis elegans has been used to study genetics and development since the mid-1970s. Over the years, the arsenal of techniques employed in this field has grown steadily in parallel with the number of researchers using this model. Since the introduction of C. elegans transgenesis, nearly 20 years ago, this system has been extensively used in areas such as rescue experiments, gene expression studies, and protein localization. The completion of the C. elegans genome sequence paved the way for genome-wide studies requiring higher throughput and improved scalability than provided by traditional genetic markers. The development of antibiotic selection systems for nematode transgenesis addresses these requirements and opens the possibility to apply transgenesis to investigate biological functions in other nematode species for which no genetic markers had been developed to date.

The Flexible Organism Ecological Developmental Biology Integrating Epigenetics, Medicine, and Evolution by Scott F. Gilbert and David Epel Sinauer Associates, Sunderland, MA, 2009. 496 pp. $49.95. ISBN 9780878932993

Gilbert and Epel focus on embryonic and larval development of metazoans to explore where "embryology meets the real world."