What Is a Hologenomic Adaptation? Emergent Individuality and Inter-Identity in Multispecies Systems

Contemporary biological research has suggested that some host-microbiome multispecies systems (referred to as "holobionts") can in certain circumstances evolve as unique biological individual, thus being a unit of selection in evolution. If this is so, then it is arguably the case that some biological adaptations have evolved at the level of the multispecies system, what we call hologenomic adaptations. However, no research has yet been devoted to investigating their nature, or how these adaptations can be distinguished from adaptations at the species-level (genomic adaptations). In this paper, we cover this gap by investigating the nature of hologenomic adaptations. By drawing on the case of the evolution of sanguivory diet in vampire bats, we argue that a trait constitutes a hologenomic adaptation when its evolution can only be explained if the holobiont is considered the biological individual that manifests this adaptation, while the bacterial taxa that bear the trait are only opportunistic beneficiaries of it. We then use the philosophical notions of emergence and inter-identity to explain the nature of this form of individuality and argue why it is special of holobionts. Overall, our paper illustrates how the use of philosophical concepts can illuminate scientific discussions, in the trend of what has recently been called metaphysics of biology.

Symbiont type and environmental factors affect transcriptome-wide gene expression in the coral Montipora capitata

Reef-building corals may harbor genetically distinct lineages of endosymbiotic dinoflagellates in the genus Symbiodinium, which have been shown to affect important colony properties, including growth rates and resilience against environmental stress. However, the molecular processes underlying these differences are not well understood. In this study, we used whole transcriptome sequencing (RNA-seq) to assess gene expression differences between 27 samples of the coral Montipora capitata predominantly hosting two different Symbiodinium types in clades C and D. The samples were further characterized by their origin from two field sites on Hawai'i Island with contrasting environmental conditions. We found that transcriptome-wide gene expression profiles clearly separated by field site first, and symbiont clade second. With 273 differentially expressed genes (DEGs, 1.3% of all host transcripts), symbiont clade had a measurable effect on host gene expression, but the effect of field site proved almost an order of magnitude higher (1,957 DEGs, 9.6%). According to SNP analysis, we found moderate evidence for host genetic differentiation between field sites (F ST = 0.046) and among corals harboring alternative symbiont clades (F ST = 0.036), suggesting that site-related gene expression differences are likely due to a combination of local adaptation and acclimatization to environmental factors. The correlation between host gene expression and symbiont clade may be due to several factors, including host genotype or microhabitat selecting for alternative clades, host physiology responding to different symbionts, or direct modulation of host gene expression by Symbiodinium. However, the magnitude of these effects at the level of transcription was unexpectedly small considering the contribution of symbiont type to holobiont phenotype.

Towards a Dynamic Interaction Network of Life to unify and expand the evolutionary theory

The classic Darwinian theory and the Synthetic evolutionary theory and their linear models, while invaluable to study the origins and evolution of species, are not primarily designed to model the evolution of organisations, typically that of ecosystems, nor that of processes. How could evolutionary theory better explain the evolution of biological complexity and diversity? Inclusive network-based analyses of dynamic systems could retrace interactions between (related or unrelated) components. This theoretical shift from a Tree of Life to a Dynamic Interaction Network of Life, which is supported by diverse molecular, cellular, microbiological, organismal, ecological and evolutionary studies, would further unify evolutionary biology.

The organism as ontological go-between: hybridity, boundaries and degrees of reality in its conceptual history

The organism is neither a discovery like the circulation of the blood or the glycogenic function of the liver, nor a particular biological theory like epigenesis or preformationism. It is rather a concept which plays a series of roles--sometimes overt, sometimes masked--throughout the history of biology, and frequently in very normative ways, also shifting between the biological and the social. Indeed, it has often been presented as a key-concept in life science and the 'theorization' of Life, but conversely has also been the target of influential rejections: as just an instrument of transmission for the selfish gene, but also, historiographically, as part of an outdated 'vitalism'. Indeed, the organism, perhaps because it is experientially closer to the 'body' than to the 'molecule', is often the object of quasi-affective theoretical investments presenting it as essential, sometimes even as the pivot of a science or a particular approach to nature, while other approaches reject or attack it with equal force, assimilating it to a mysterious 'vitalist' ontology of extra-causal forces, or other pseudo-scientific doctrines. This paper does not seek to adjudicate between these debates, either in terms of scientific validity or historical coherence; nor does it return to the well-studied issue of the organism-mechanism tension in biology. Recent scholarship has begun to focus on the emergence and transformation of the concept of organism, but has not emphasized so much the way in which organism is a shifting, 'go-between' concept-invoked as 'natural' by some thinkers to justify their metaphysics, but then presented as value-laden by others, over and against the natural world. The organism as go-between concept is also a hybrid, a boundary concept or an epistemic limit case, all of which partly overlap with the idea of 'nomadic concepts'. Thereby the concept of organism continues to function in different contexts--as a heuristic, an explanatory challenge, a model of order, of regulation, etc.--despite having frequently been pronounced irrelevant and reduced to molecules or genes. Yet this perpetuation is far removed from any 'metaphysics of organism', or organismic biology.

Origins of evolution: non-acquired characters dominates over acquired characters in changing environment

Natural Selection is so ubiquitous that we never wonder how it appeared as the evolution rule driving Life. We usually wonder how Life appeared, and seldom do we make an explicit distinction between Life and natural selection. Here, we apply the evolution concept commonly used for studying Life to evolution itself. More precisely, we developed two models aiming at selecting among different evolution rules competing for their supremacy. We explored competition between acquired (AQ) versus non-acquired (NAQ) character inheritance. The first model is parsimonious and non-spatial, in order to understand relationships between environmental forcings and rule selection. The second model is spatially explicit and studies the adaptation differences between AQ and NAQ populations. We established that NAQ evolution rule is dominating in case of changing environment. Furthermore, we observed that a more adapted population better fits its environmental constraints, but fails in rapidly changing environments. NAQ principle and less adapted populations indeed act as a reservoir of traits that helps populations to survive in rapidly changing environments, such as the ones that probably Life experienced at its origins. Although perfectible, our modeling approaches will certainly help us to improve our understanding of origins of Life and Evolution, on Earth or elsewhere.

Darwinism without populations: a more inclusive understanding of the "Survival of the Fittest"

Following Wallace's suggestion, Darwin framed his theory using Spencer's expression "survival of the fittest". Since then, fitness occupies a significant place in the conventional understanding of Darwinism, even though the explicit meaning of the term 'fitness' is rarely stated. In this paper I examine some of the different roles that fitness has played in the development of the theory. Whereas the meaning of fitness was originally understood in ecological terms, it took a statistical turn in terms of reproductive success throughout the 20th Century. This has lead to the ever-increasing importance of sexually reproducing organisms and the populations they compose in evolutionary explanations. I will argue that, moving forward, evolutionary theory should look back at its ecological roots in order to be more inclusive in the type of systems it examines. Many biological systems (e.g. clonal species, colonial species, multi-species communities) can only be satisfactorily accounted for by offering a non-reproductive account of fitness. This argument will be made by examining biological systems with very small or transient population structures. I argue this has significant consequences for how we define Darwinism, increasing the significance of survival (or persistence) over that of reproduction.