Increasing morphological disparity and decreasing optimality for jaw speed and strength during the radiation of jawed vertebrates

The Siluro-Devonian adaptive radiation of jawed vertebrates, which underpins almost all living vertebrate biodiversity, is characterized by the evolutionary innovation of the lower jaw. Multiple lines of evidence have suggested that the jaw evolved from a rostral gill arch, but when the jaw took on a feeding function remains unclear. We quantified the variety of form in the earliest jaws in the fossil record from which we generated a theoretical morphospace that we then tested for functional optimality. By drawing comparisons with the real jaw data and reconstructed jaw morphologies from phylogenetically inferred ancestors, our results show that the earliest jaw shapes were optimized for fast closure and stress resistance, inferring a predatory feeding function. Jaw shapes became less optimal for these functions during the later radiation of jawed vertebrates. Thus, the evolution of jaw morphology has continually explored previously unoccupied morphospace and accumulated disparity through time, laying the foundation for diverse feeding strategies and the success of jawed vertebrates

Geometric morphometrics in ammonoids based on virtual modelling

Linear morphometrics is the most widely applied technique to study the variationof the conch morphology in ammonoids and other ectocochleate cephalopods. However,because this method frequently relies upon a few linear measurements, it lacksthe explanatory power to accurately characterize the shape of the whorl cross-section,which is instead discussed solely in descriptive terms, e.g., elliptical, triangular, or subquadrate.Here, we introduce a landmark-based geometric morphometric approach tostudy ammonoid whorl cross-sections, derived from the regularly used morphometricparameters in cephalopods. This new technique uses virtual modelling to generatesemi-landmark configurations and virtual models of whorl cross-sections. We applied itto study 50 ammonoid specimens belonging to 48 genera exhibiting a wide range ofmorphologies and ages. Results indicate that this new method is appropriate todescribe the shape of ammonoid whorl cross-sections, allowing us to construct a morphospaceshowing several biological patterns (e.g., clustering and homeomorphy), andcomplex morphological transformations that, in some cases, correlate with evolutionarytendencies described by previous authors. Further, this technique can be used togenerate the basic segment required for the elaboration of the virtual models employedin hydrostatic and hydrodynamic studies.Fil: Moron Alfonso, Daniel Andres. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Estudios Andinos "Don Pablo Groeber". Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Estudios Andinos "Don Pablo Groeber"; ArgentinaFil: Hoffmann, René. Ruhr Universität Bochum; AlemaniaFil: Cichowolski, Marcela. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Estudios Andinos "Don Pablo Groeber". Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Estudios Andinos "Don Pablo Groeber"; Argentin

Variational principles and optimality in biological systems

The aim of this thesis is to investigate the signatures of evolutionary optimization in biological systems, such as in proteins, human behaviours and transport tissues in vascular plants (xylems), by means of the Pareto optimality analysis and the calculus of variations. In the first part of this thesis, we address multi-objective optimization problems with tradeoffs through the Pareto optimality analysis ( [132],[69]), according which the best tradeoff solutions correspond to the optimal species, enclosed onto low-dimensional geometrical polytopes, defined as Pareto optimal fronts, in the space of physical traits, called morphospace. Chapter 3 is devoted to the Pareto optimality analysis in the Escherichia coli proteome by projecting proteins onto the space of solubility and hydrophobicity. In chapter 4 we analyze the HCP dataset of cognitive and behavioral scores in 1206 humans, in order to identify any signature of Pareto optimization in the space of Delay Discounting Task (DDT), which measures the tendency for people to prefer smaller, immediate monetary rewards over larger, delayed rewards. The second part of this thesis is devoted to solving an optimization problem regarding xylems, which are the internal conduits in angiosperms that deliver water and other nutrients from roots to petioles in plants. Based on the optimization criteria of minimizing the energy dissipated in a fluid flow, we propose in chapter 5 a biophysical model with the goal of explaining the underlying physical mechanism that affects the structure of xylem conduits in vascular plants, which results in tapered xylem profiles [104, 105, 117, 164]. We address this optimization problem by formulating the model in the context of the calculus of variations. The results of these investigations, besides providing quantitative support to previous theories of natural selection, demonstrate how processes of optimization can be identified in different biological systems by applying statistical methods such as the Pareto optimality and the variational one, showing the relevance of employing these statistical approaches to various biological systems

Soft trade-offs and the stochastic emergence of diversification in E. coli evolution experiments

Laboratory experiments of bacterial colonies (e.g., \emph{Escherichia coli}) under well-controlled conditions often lead to evolutionary diversification in which (at least) two ecotypes, each one specialized in the consumption of a different set of metabolic resources, branch out from an initially monomorphic population. Empirical evidence suggests that, even under fixed and stable conditions, such an ``evolutionary branching'' occurs in a stochastic way, meaning that: (i) it is observed in a significant fraction, but not all, of the experimental repetitions, (ii) it may emerge at broadly diverse times, and (iii) the relative abundances of the resulting subpopulations are variable across experiments. Theoretical approaches shedding light on the possible emergence of evolutionary branching in this type of conditions have been previously developed within the theory of ``adaptive dynamics''. Such approaches are typically deterministic -- or incorporate at most demographic or finite-size fluctuations which become negligible for the extremely large populations of these experiments -- and, thus, do not permit to reproduce the empirically observed large degree of variability. Here, we make further progress and shed new light on the stochastic nature of evolutionary outcomes by introducing the idea of ``soft'' trade-offs (as opposed to ``hard'' ones). This introduces a natural new source of stochasticity which allows one to account for the empirically observed variability as well as to make predictions for the likelihood of evolutionary branching to be observed, thus helping to bridge the gap between theory and experiments

CONSTRAINTS OF THE IMAGINATION: HOW PHENOTYPES ARE SHAPED THROUGH GENETICS, THE ENVIRONMENT, AND DEVELOPMENT

Phenotypic constraints are ubiquitous throughout nature, being found throughout all stages of life and at multiple different biological levels including cellular, genetic, environmental, behavioral, evolutionary, and developmental. These constraints have shaped, not only the natural world, but the way that we perceive what is possible, or impossible, an observation made clear by François Jacob in his 1977 paper “Evolution and Tinkering”. This is reflected in the literature, repeatedly, by the regular occurrence of densely packed visualization of phenotypic space that seemingly always have large areas that go unoccupied. Despite constrained regions of space being observable across countless taxa, identifying the mechanisms of those constraints remains elusive. Given that constraints are widespread and have influenced how evolution may work, my aim was to identify mechanisms of constraint throughout multiple biological levels. Chapter one is divided into two parts, sections A and B, but largely focuses on how constraints are influenced by genetics. For this, we investigated crocc2, a protein that encodes for a structural component of the ciliary rootlet which in turn plays a major role as a mechanosensory for nearly all cells. We found dysfunctional crocc2 resulted in both dysmorphic bone development and a decrease in the plastic response potential of zebrafish (section A), as well as altered developmental trajectories in juvenile morphology, presumably due to alterations in cellular polarity and inadequate extracellular communication. Importantly, all results from this chapter point toward crocc2 play a canalizing role in the production of phenotypes at multiple life-history stages. Chapter 2 takes a different approach into understanding constrains by looking at broad ecological alterations and how those alterations may alter morphology of resident taxa. Here, we utilized the heavily altered habitat of the Tocantins River in the Amazon and the existing museum collections to evaluate how select representatives of the cichlid community had responded to such change. We found significant changes in contemporary morphology across all included cichlid species compared to their historical counterparts. These data show that alterations to the environment have resulted in changes to the local resident species, and possibly an alteration to their future evolutionary trajectories. Among the species included, one was found to have the most substantial morphological changes, which is what we followed up in the next chapter. Chapter 3 dug into the morphological changes of Satanoperca, a Geophagine cichlid with a unique feeding mechanism known as winnowing. Winnowing is a poorly understood mechanical process involving substrate manipulation. Given that anthropogenic alterations to local hydrology oft result in changes to the benthic sediment composition, we wanted to know if differing substrates was enough to induce a plastic response in winnowing fishes, and if so which traits were effected. We found significant differences across our experimental populations in both shape and disparity and present evidence in support of wide-spread integration across craniofacial traits. In addition, these data suggest that the novel anatomical structure, the epibranchial lobe, is more modular than other craniofacial traits involved in the winnowing process. Chapters 4 and 5 utilize a unique lineage of fishes, the Bramidae, to understand how developmental and evolutionary constraints are broken to produce morphological novelties. We used a combination of DNA sequences from GenBank and numerous museum specimens to illuminate constraints and determine how constraints are broken to produce complex phenotypic novelties. In Chapter 4, we found that the fanfishes had experienced greater rates of morphological evolution than other members of the Bramidae family, resulting in their occupation of an entirely novel region of phenotypic space. In Chapter 5, we elaborated on this by investigating the developmental processes involved in producing an extreme morphological novelty. The data presented in Chapter 5 provide evidence suggesting that the fanfishes have broken various constraints, resulting in prominent anatomical and morphological changes to accommodate their novel phenotype. In all, my dissertation provides examples of how constraints have shaped the variability that we see throughout life and shows examples of how constraints can be identified, what happens when they are broken, and how they work to control the pace and trajectory of evolutionary processes