Climate change, adaptation, and phenotypic plasticity: the problem and the evidence

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The evolution of plasticity of dauer larva developmental arrest in the nematode Caenorhabditis elegans.

Organisms can end up in unfavourable conditions and to survive this they have evolved various strategies. Some organisms, including nematodes, survive unfavourable conditions by undergoing developmental arrest. The model nematode Caenorhabditis elegans has a developmental choice between two larval forms, and it chooses to develop into the arrested dauer larva form in unfavourable conditions (specifically, a lack of food and high population density, indicated by the concentration of a pheromone). Wild C. elegans isolates vary extensively in their dauer larva arrest phenotypes, and this prompts the question of what selective pressures maintain such phenotypic diversity? To investigate this we grew C. elegans in four different environments, consisting of different combinations of cues that can induce dauer larva development: two combinations of food concentration (high and low) in the presence or absence of a dauer larva-inducing pheromone. Five generations of artificial selection of dauer larvae resulted in an overall increase in dauer larva formation in most selection regimes. The presence of pheromone in the environment selected for twice the number of dauer larvae, compared with environments not containing pheromone. Further, only a high food concentration environment containing pheromone increased the plasticity of dauer larva formation. These evolutionary responses also affected the timing of the worms' reproduction. Overall, these results give an insight into the environments that can select for different plasticities of C. elegans dauer larva arrest phenotypes, suggesting that different combinations of environmental cues can select for the diversity of phenotypically plastic responses seen in C. elegans.We would like to thank Henrique Teotonio for the gift of the G140.A population, Louise Hughes and Laura Weldon for technical help, two anonymous reviewers for their comments, and NERC for funding.This is the final published version of the article. It was originally published in Ecology and Evolution (Diaz SA, Viney M, Ecology and Evolution 2015, 5(6), 1343–1353, doi:10.1002/ece3.1436) http://dx.doi.org/10.1002/ece3.143

Shaping Robust System through Evolution

Biological functions are generated as a result of developmental dynamics that form phenotypes governed by genotypes. The dynamical system for development is shaped through genetic evolution following natural selection based on the fitness of the phenotype. Here we study how this dynamical system is robust to noise during development and to genetic change by mutation. We adopt a simplified transcription regulation network model to govern gene expression, which gives a fitness function. Through simulations of the network that undergoes mutation and selection, we show that a certain level of noise in gene expression is required for the network to acquire both types of robustness. The results reveal how the noise that cells encounter during development shapes any network's robustness, not only to noise but also to mutations. We also establish a relationship between developmental and mutational robustness through phenotypic variances caused by genetic variation and epigenetic noise. A universal relationship between the two variances is derived, akin to the fluctuation-dissipation relationship known in physics

Grounding knowledge and normative valuation in agent-based action and scientific commitment

Philosophical investigation in synthetic biology has focused on the knowledge-seeking questions pursued, the kind of engineering techniques used, and on the ethical impact of the products produced. However, little work has been done to investigate the processes by which these epistemological, metaphysical, and ethical forms of inquiry arise in the course of synthetic biology research. An attempt at this work relying on a particular area of synthetic biology will be the aim of this chapter. I focus on the reengineering of metabolic pathways through the manipulation and construction of small DNA-based devices and systems synthetic biology. Rather than focusing on the engineered products or ethical principles that result, I will investigate the processes by which these arise. As such, the attention will be directed to the activities of practitioners, their manipulation of tools, and the use they make of techniques to construct new metabolic devices. Using a science-in-practice approach, I investigate problems at the intersection of science, philosophy of science, and sociology of science. I consider how practitioners within this area of synthetic biology reconfigure biological understanding and ethical categories through active modelling and manipulation of known functional parts, biological pathways for use in the design of microbial machines to solve problems in medicine, technology, and the environment. We might describe this kind of problem-solving as relying on what Helen Longino referred to as “social cognition” or the type of scientific work done within what Hasok Chang calls “systems of practice”. My aim in this chapter will be to investigate the relationship that holds between systems of practice within metabolic engineering research and social cognition. I will attempt to show how knowledge and normative valuation are generated from this particular network of practitioners. In doing so, I suggest that the social nature of scientific inquiry is ineliminable to both knowledge acquisition and ethical evaluations

No personality without experience? A test on Rana dalmatina tadpoles

While the number of studies reporting the presence of individual behavioral consistency (animal personality, behavioral syndrome) has boomed in the recent years, there is still much controversy about the proximate and ultimate mechanisms resulting in the phenomenon. For instance, direct environmental effects during ontogeny (phenotypic plasticity) as the proximate mechanism behind the emergence of consistent individual differences in behavior are usually overlooked compared to environmental effects operating across generations (genetic adaptation). Here, we tested the effects of sociality and perceived predation risk during ontogeny on the strength of behavioral consistency in agile frog (Rana dalmatina) tadpoles in a factorial common garden experiment. Tadpoles reared alone and without predatory cues showed zero repeatability within (i.e., lack of personality) and zero correlation between (i.e., lack of syndrome) activity and risk‐taking. On the other hand, cues from predators alone induced both activity and risk‐taking personalities, while cues from predators and conspecifics together resulted in an activity – risk‐taking behavioral syndrome. Our results show that individual experience has an unequivocal role in the emergence of behavioral consistency. In this particular case, the development of behavioral consistency was most likely the result of genotype × environment interactions, or with other words, individual variation in behavioral plasticity

The Question of Questions: What is a Gene? Comments on Rolston and Griffths & Stotz

If the question “What is a gene?” proves to be worth asking it must be able to elicit an answer which both recognizes and address the reasons why the concept of the gene ever seemed to be something worth getting excited about in the first place as well analyzing and evaluating the latest develops in the molecular biology of DNA. Each of the preceding papers fails to do one of these and sufferrs the consequences. Where Rolston responds to the apparent failure of molecular biology to make good on the desideratum of the classical gene by veering off into fanciful talk about “cybernetic genes,” Griffiths and Stotz lose themselves in the molecular fine print and forget to ask themselves why “genes” should be of any special interst anyway

The ecology of sex explains patterns of helping in arthropod societies

Authors thank the Natural Sciences and Engineering Research Council of Canada (NGD), the Clarendon Fund (NGD) and the Natural Environment Research Council (LR, NE/K009516/1; AG, NE/K009524/1) for funding.Across arthropod societies, sib-rearing (e.g. nursing or nest defence) may be provided by females, by males or by both sexes. According to Hamilton's ‘haplodiploidy hypothesis’, this diversity reflects the relatedness consequences of diploid vs. haplodiploid inheritance. However, an alternative ‘preadaptation hypothesis’ instead emphasises an interplay of ecology and the co-option of ancestral, sexually dimorphic traits for sib-rearing. The preadaptation hypothesis has recently received empirical support, but remains to be formalised. Here, we mathematically model the coevolution of sex-specific helping and sex allocation, contrasting these hypotheses. We find that ploidy per se has little effect. Rather, the ecology of sex shapes patterns of helping: sex-specific preadaptation strongly influences who helps; a freely adjustable sex ratio magnifies sex biases and promotes helping; and sib-mating, promiscuity, and reproductive autonomy also modulate the sex and abundance of helpers. An empirical survey reveals that patterns of sex-specific helping in arthropod taxa are consistent with the preadaptation hypothesis.Publisher PDFPeer reviewe

Intelligence as inference or forcing Occam on the world

We propose to perform the optimization task of Universal Artificial Intelligence (UAI) through learning a reference machine on which good programs are short. Further, we also acknowledge that the choice of reference machine that the UAI objective is based on is arbitrary and, therefore, we learn a suitable machine for the environment we are in. This is based on viewing Occam’s razor as an imperative instead of as a proposition about the world. Since this principle cannot be true for all reference machines, we need to find a machine that makes the principle true. We both want good policies and the environment to have short implementations on the machine. Such a machine is learnt iteratively through a procedure that generalizes the principle underlying the Expectation-Maximization algorithm

Conserved genes underlie phenotypic plasticity in an incipiently social bee

Despite a strong history of theoretical work on the mechanisms of social evolution, relatively little is known of the molecular genetic changes that accompany transitions from solitary to eusocial forms. Here we provide the first genome of an incipiently social bee that shows both solitary and social colony organization in sympatry, the Australian carpenter bee Ceratina australensis. Through comparative analysis, we provide support for the role of conserved genes and cis-regulation of gene expression in the phenotypic plasticity observed in nest-sharing, a rudimentary form of sociality. Additionally, we find that these conserved genes are associated with caste differences in advanced eusocial species, suggesting these types of mechanisms could pave the molecular pathway from solitary to eusocial living. Genes associated with social nesting in this species show signatures of being deeply conserved, in contrast to previous studies in other bees showing novel and faster-evolving genes are associated with derived sociality. Our data provide support for the idea that the earliest social transitions are driven by changes in gene regulation of deeply conserved genes