In a 1982 paper, Gould and Vrba argue that a conflation of the two components of adaptation of a feature, historical development of the feature and present utility, has caused evolutionists to overlook a missing term in the science of form, which they call 'exaptation'. In the present project, I show that evolutionary biology still contains a confusion in the use of 'adaptation' due to an inappropriate perception of the interaction between the two components of adaptation. Because of the confusion, evolutionists have missed another term in the science of form. Evolutionary theory, specifically the treatment of adaptation, would profit from the introduction of a term referring to features that have a selective history which causes them to appear overly well adapted to their present function. I suggest we refer to these features as hyperadaptations, since they appear to be hyperbolized adaptations. By introducing hyperadaptation into the conceptual framework of adaptation, we can sharpen our understanding of related concepts (adaptation to function, exaptation, maladaptation, etc.) and remove or reduce some confusion regarding the interplay between analysis of historical pathways and ascriptions of (current) function in the diagnosis of adaptation. Furthermore, the improved framework should allow evolutionists to more adequately explain biological phenomena. / Master of Arts

Thesis advisor: Welkin E. Johnson / Endogenous retroviruses (ERVs) make up a significant portion of vertebrate genomes, and serve as a fossil record of past retroviral infections. Although most ERV genes acquire inactivating mutations over time, some loci retain open reading frames (ORFs) across one or more of the viral genes. The ERV-Fc family, for example, endogenized in multiple mammalian hosts 10 to 30 million years ago, yet many copies maintain intact ORFs corresponding to the env gene, including loci in humans (HERV-Fc1-env) and baboons (babERV-Fc2-env). We previously identified intact ERV-Fc-related env sequences in eight additional mammalian species: chimpanzee, bonobo, aardvark, grey mouse lemur, squirrel monkey, marmoset, dog, and panda. Here we present the results of our assays of expression of these full-length Env proteins. We found that most of the precursors were not cleaved to form the functional surface (SU) and transmembrane (TM) subunits, even when a canonical furin cleavage site was still intact. An exception was babERV-Fc2, in which reconstruction of the cleavage site led to cleavage into SU and TM subunits. Furthermore, removal of 22 residues from the C-terminus of the cytoplasmic tail of babERV-Fc2 enhanced syncytia formation and the ability of babERV-Fc2 pseudotyped virions to infect 293T cells, suggesting the presence of an R-peptide cleavage mechanism. A survey of a small panel of cells revealed that only human cell lines were infectable by babERV-Fc2 pseudotyped murine leukemia virus (MLV) particles, whereas cells of old world monkey, canine, feline and chicken origin were not susceptible to infection. Ectopic expression of native Env codon optimized babERV-Fc2 Env can also inhibit infection by reconstructed babERV-Fc2 pseudotyped virus, raising the possibility that the endogenous glycoprotein encoded in the baboon genome may function as a viral entry inhibitor. Our results suggest that exaptation of ERV Env proteins as antiviral defense genes involves a combination of selective pressures: selection to preserve the receptor-binding and receptor interference functions of Env, but also selection to eliminate the membrane fusion related functions. / Thesis (PhD) — Boston College, 2018. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

Among terrestrial orchids, and particularly among the subtribe Orchidinae, flies are underrepresented as pollinators. The European Neotinea ustulata, which developed specialized pollination by tachinid flies, is known to produce high relative concentrations of the floral cuticular alkenes (Z)-11-tricosene and (Z)-11-pentacosene (referred to as (Z)-11-C23/C25enes), which seem to be uncommon among orchid flowers. If the evolution of tachinid pollination is related to that of (Z)-11-C23/C25enes, we can expect that closely related species have a different floral chemical pattern and significantly small or no production of (Z)-11-C23/C25enes, independently of their pollinator guild identity (e.g., bees, flies, moths). We chemically compared the floral cuticular composition among Neotinea species, performed electrophysiological analyses, reconstructed the phylogenetic Orchidinae tree, and identified the evolutionary history of pollinator guild and (Z)-11-C23/C25enes production within the Orchidinae. Neotinea ustulata has evolved a markedly different floral cuticular composition compared to other Neotinea and produces both compounds ((Z)-11-C23/C25enes) in high relative quantities (i.e., above 8% in combination), which are detectable by tachinid antennae. Moreover, most Orchidinae taxa have minimal or no production of these alkenes, independently of the identity of their pollinator guild. Our ancestral reconstruction suggested that (Z)-11-C23/C25enes production was an evolutionary exaptation in Neotinea, whereas tachinid pollination was a unique evolutionary innovation for N. ustulata. Floral cuticular composition and, in particular, the combined production of (Z)-11-C23/C25enes at relatively high concentrations is intimately linked to the evolution of tachinid pollination within the Orchidinae.

L’objet de cette recherche revient à interroger le rôle du hasard dans le processus d’individuation tel qu’il est théorisé par Gilbert Simondon. Dans cette perspective, le hasard, élaboré à partir du concept darwinien de chance, doit être considéré comme opérateur théorique et concept explicatif d’une théorie des processus de genèse de forme individuelle, et non comme un principe métaphysique ou une mesure de l’ignorance. Il qualifie dans l’individuation la modalité de la rencontre entre la singularité, qui donne forme à l’être individuel, et le milieu métastable individuel, susceptible de transformations. Suivant cette perspective, le hasard devient un des opérateurs de l’invention des structures individuelles singulières, plurielles, et novatrices, formes de vie et manières d’exister, qui sont élaborées comme solution à des problèmes par le processus d’individuation. Cette analyse de la pensée simondonienne va permettre de mettre en place les linéaments d’une théorie de la rencontre individuante, induisant une conception particulière de l’individualité humaine, qui est susceptible d’entrer en dialogue avec les thèses de la sociologie dispositionnelle (P. Bourdieu, B. Lahire). Comme invention, l’opération d’individuation sera alors analysable à partir du concept biologique d’exaptation (S. J. Gould), qui explicite dans l’évolution l’invention de couples structuro-fonctionnels nouveaux, à partir d’un jeu entre hasard et invention vitale. / This research aims to question the role of chance in the individuation process as it was theorized by Gilbert Simondon. In this context, chance, which was drawn up based on the Darwinian concept of chance, must be considered as a theoretical operator and as an explanatory concept of the genesis of individual form, and not as a metaphysical principle or as a measure of ignorance. It characterises within the individuation the modality of the encounter between the singularity which shapes the individual being and the individual metastable environment which is capable of being transformed. From this point of view, chance turns out to be one of the invention operators of singular, individual, plural and innovative structures which are ways of existing, created as solutions to problems by the individuation process itself. This analysis of Simondon’s philosophy allows us to outline a theory of the individuating encounter leading us to think of human individuality through a specific approach which enters into dialogue with the theses of the dispositional sociology (P. Bourdieu, B. Lahire). From an invention point of view, the individuation operation can thus be analysed using the biological concept of exaptation (S. J. Gould) which makes very explicit the invention of new structure-function couples in evolution based on an articulation between chance and vital invention.