A simple model of unbounded evolutionary versatility as a largest-scale trend in organismal evolution

The idea that there are any large-scale trends in the evolution of biological organisms is highly controversial. It is commonly believed, for example, that there is a large-scale trend in evolution towards increasing complexity, but empirical and theoretical arguments undermine this belief. Natural selection results in organisms that are well adapted to their local environments, but it is not clear how local adaptation can produce a global trend. In this paper, I present a simple computational model, in which local adaptation to a randomly changing environment results in a global trend towards increasing evolutionary versatility. In this model, for evolutionary versatility to increase without bound, the environment must be highly dynamic. The model also shows that unbounded evolutionary versatility implies an accelerating evolutionary pace. I believe that unbounded increase in evolutionary versatility is a large-scale trend in evolution. I discuss some of the testable predictions about organismal evolution that are suggested by the model

Open-ended Search through Minimal Criterion Coevolution

Search processes guided by objectives are ubiquitous in machine learning. They iteratively reward artifacts based on their proximity to an optimization target, and terminate upon solution space convergence. Some recent studies take a different approach, capitalizing on the disconnect between mainstream methods in artificial intelligence and the field\u27s biological inspirations. Natural evolution has an unparalleled propensity for generating well-adapted artifacts, but these artifacts are decidedly non-convergent. This new class of non-objective algorithms induce a divergent search by rewarding solutions according to their novelty with respect to prior discoveries. While the diversity of resulting innovations exhibit marked parallels to natural evolution, the methods by which search is driven remain unnatural. In particular, nature has no need to characterize and enforce novelty; rather, it is guided by a single, simple constraint: survive long enough to reproduce. The key insight is that such a constraint, called the minimal criterion, can be harnessed in a coevolutionary context where two populations interact, finding novel ways to satisfy their reproductive constraint with respect to each other. Among the contributions of this dissertation, this approach, called minimal criterion coevolution (MCC), is the primary (1). MCC is initially demonstrated in a maze domain (2) where it evolves increasingly complex mazes and solutions. An enhancement to the initial domain (3) is then introduced, allowing mazes to expand unboundedly and validating MCC\u27s propensity for open-ended discovery. A more natural method of diversity preservation through resource limitation (4) is introduced and shown to maintain population diversity without comparing genetic distance. Finally, MCC is demonstrated in an evolutionary robotics domain (5) where it coevolves increasingly complex bodies with brain controllers to achieve principled locomotion. The overall benefit of these contributions is a novel, general, algorithmic framework for the continual production of open-ended dynamics without the need for a characterization of behavioral novelty

Diversity and Diversification Across the Global Radiation of Extant Bats

Diversity is not distributed equally across the tree of life. This fundamental observation is central to ecology and evolutionary biology, and spans both spatial and temporal scales. Species richness, for example, is unevenly distributed both within and across clades. Biodiversity is often spatially concentrated in the tropics, with lower richness in temperate biomes. Some clades are characterized by extremely high ecological and morphological diversity, while others remain static across geologic timescales. This dissertation highlights these patterns of diversity across extant bats, the Order Chiroptera, and seeks to understand the evolutionary processes of diversification that govern them. Chapter 1 serves as both an introduction to the major questions of the dissertation and an overview of extant bat diversity, and how it varies spatially, phylogenetically, and ecologically across the globe. In this chapter, I primarily focus on spatial variation in regional richness patterns, and on the major differences between temperate and tropical bat diversity. In Chapter 2, I assemble a species-level molecular phylogeny of the order that is time-calibrated with fossil data. Using this phylogeny, I infer speciation dynamics across the order, and find that despite the imbalances in species richness, speciation rates are relatively homogeneous. I only infer strong evidence for more rapid rates within the subfamily Stenodermatinae, a clade of Neotropical phyllostomid bats. In Chapter 3, I develop models to test whether bat species co-occurrence is constrained by relatedness or ecomorphological similarity. Contrary to theoretical predictions and results from other major clades, I find that neither of these metrics of divergence controls co-occurrence in sympatry across most bats and realms. The only exception is the Neotropical realm, where bat species are most likely to co-occur when they are the most ecomorphologically similar to one another. This potentially indicates that Neotropical bat communities and species pools, at broad regional scales, are sorted by filtering processes that cluster bats with similar ecologies together in space. For Chapters 4 and 5, I assess how ecology and morphology are linked in New World bats. Chapter 4 describes an open-access, X-ray computed microtomography database of bat skulls, and how this resource can be used by the broader scientific and educational community. Chapter 5 combines crania from that database with diet data across New World bats, and tests whether ecological and morphological evolution are correlated in this group. Surprisingly, I find that patterns of ecological, trophic evolution are largely decoupled from morphological evolution. There is considerable heterogeneity in how readily different clades transition among trophic guilds, yet cranial shape evolution is surprisingly homogeneous. This decoupled pattern is potentially driven by underestimated trophic plasticity and omnivory among noctilionoid bats, as well as high lability among bat crania. Finally, in Chapter 6, I conclude with a summary of our major findings, and some thoughts on ecological and macroevolutionary inference both within bats and across the tree of life.PHDEcology and Evolutionary BiologyUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/145993/1/jeffjshi_1.pd

A comprehensive analysis of autocorrelation and bias in home range estimation

Home range estimation is routine practice in ecological research. While advances in animal tracking technology have increased our capacity to collect data to support home range analysis, these same advances have also resulted in increasingly autocorrelated data. Consequently, the question of which home range estimator to use on modern, highly autocorrelated tracking data remains open. This question is particularly relevant given that most estimators assume independently sampled data. Here, we provide a comprehensive evaluation of the effects of autocorrelation on home range estimation. We base our study on an extensive data set of GPS locations from 369 individuals representing 27 species distributed across five continents. We first assemble a broad array of home range estimators, including Kernel Density Estimation (KDE) with four bandwidth optimizers (Gaussian reference function, autocorrelated-Gaussian reference function [AKDE], Silverman´s rule of thumb, and least squares cross-validation), Minimum Convex Polygon, and Local Convex Hull methods. Notably, all of these estimators except AKDE assume independent and identically distributed (IID) data. We then employ half-sample cross-validation to objectively quantify estimator performance, and the recently introduced effective sample size for home range area estimation ((Formula presented.)) to quantify the information content of each data set. We found that AKDE 95% area estimates were larger than conventional IID-based estimates by a mean factor of 2. The median number of cross-validated locations included in the hold-out sets by AKDE 95% (or 50%) estimates was 95.3% (or 50.1%), confirming the larger AKDE ranges were appropriately selective at the specified quantile. Conversely, conventional estimates exhibited negative bias that increased with decreasing (Formula presented.). To contextualize our empirical results, we performed a detailed simulation study to tease apart how sampling frequency, sampling duration, and the focal animal´s movement conspire to affect range estimates. Paralleling our empirical results, the simulation study demonstrated that AKDE was generally more accurate than conventional methods, particularly for small (Formula presented.). While 72% of the 369 empirical data sets had >1,000 total observations, only 4% had an (Formula presented.) >1,000, where 30% had an (Formula presented.) <30. In this frequently encountered scenario of small (Formula presented.), AKDE was the only estimator capable of producing an accurate home range estimate on autocorrelated data.Fil: Noonan, Michael J.. National Zoological Park; Estados Unidos. University of Maryland; Estados UnidosFil: Tucker, Marlee A.. Senckenberg Gesellschaft Für Naturforschung; . Goethe Universitat Frankfurt; AlemaniaFil: Fleming, Christen H.. University of Maryland; Estados Unidos. National Zoological Park; Estados UnidosFil: Akre, Thomas S.. National Zoological Park; Estados UnidosFil: Alberts, Susan C.. University of Duke; Estados UnidosFil: Ali, Abdullahi H.. Hirola Conservation Programme. Garissa; KeniaFil: Altmann, Jeanne. University of Princeton; Estados UnidosFil: Antunes, Pamela Castro. Universidade Federal do Mato Grosso do Sul; BrasilFil: Belant, Jerrold L.. State University of New York; Estados UnidosFil: Beyer, Dean. Universitat Phillips; AlemaniaFil: Blaum, Niels. Universitat Potsdam; AlemaniaFil: Böhning Gaese, Katrin. Senckenberg Gesellschaft Für Naturforschung; Alemania. Goethe Universitat Frankfurt; AlemaniaFil: Cullen Jr., Laury. Instituto de Pesquisas Ecológicas; BrasilFil: de Paula, Rogerio Cunha. National Research Center For Carnivores Conservation; BrasilFil: Dekker, Jasja. Jasja Dekker Dierecologie; Países BajosFil: Drescher Lehman, Jonathan. George Mason University; Estados Unidos. National Zoological Park; Estados UnidosFil: Farwig, Nina. Michigan State University; Estados UnidosFil: Fichtel, Claudia. German Primate Center; AlemaniaFil: Fischer, Christina. Universitat Technical Zu Munich; AlemaniaFil: Ford, Adam T.. University of British Columbia; CanadáFil: Goheen, Jacob R.. University of Wyoming; Estados UnidosFil: Janssen, René. Bionet Natuuronderzoek; Países BajosFil: Jeltsch, Florian. Universitat Potsdam; AlemaniaFil: Kauffman, Matthew. University Of Wyoming; Estados UnidosFil: Kappeler, Peter M.. German Primate Center; AlemaniaFil: Koch, Flávia. German Primate Center; AlemaniaFil: LaPoint, Scott. Max Planck Institute für Ornithologie; Alemania. Columbia University; Estados UnidosFil: Markham, A. Catherine. Stony Brook University; Estados UnidosFil: Medici, Emilia Patricia. Instituto de Pesquisas Ecológicas (IPE) ; BrasilFil: Morato, Ronaldo G.. Institute For Conservation of The Neotropical Carnivores; Brasil. National Research Center For Carnivores Conservation; BrasilFil: Nathan, Ran. The Hebrew University of Jerusalem; IsraelFil: Oliveira Santos, Luiz Gustavo R.. Universidade Federal do Mato Grosso do Sul; BrasilFil: Olson, Kirk A.. Wildlife Conservation Society; Estados Unidos. National Zoological Park; Estados UnidosFil: Patterson, Bruce. Field Museum of National History; Estados UnidosFil: Paviolo, Agustin Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Puerto Iguazú | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Puerto Iguazú; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste; ArgentinaFil: Ramalho, Emiliano Esterci. Institute For Conservation of The Neotropical Carnivores; Brasil. Instituto de Desenvolvimento Sustentavel Mamirauá; BrasilFil: Rösner, Sascha. Michigan State University; Estados UnidosFil: Schabo, Dana G.. Michigan State University; Estados UnidosFil: Selva, Nuria. Institute of Nature Conservation of The Polish Academy of Sciences; PoloniaFil: Sergiel, Agnieszka. Institute of Nature Conservation of The Polish Academy of Sciences; PoloniaFil: Xavier da Silva, Marina. Parque Nacional do Iguaçu; BrasilFil: Spiegel, Orr. Universitat Tel Aviv; IsraelFil: Thompson, Peter. University of Maryland; Estados UnidosFil: Ullmann, Wiebke. Universitat Potsdam; AlemaniaFil: Ziḝba, Filip. Tatra National Park; PoloniaFil: Zwijacz Kozica, Tomasz. Tatra National Park; PoloniaFil: Fagan, William F.. University of Maryland; Estados UnidosFil: Mueller, Thomas. Senckenberg Gesellschaft Für Naturforschung; . Goethe Universitat Frankfurt; AlemaniaFil: Calabrese, Justin M.. National Zoological Park; Estados Unidos. University of Maryland; Estados Unido

Modeling and Simulation in Engineering

This book provides an open platform to establish and share knowledge developed by scholars, scientists, and engineers from all over the world, about various applications of the modeling and simulation in the design process of products, in various engineering fields. The book consists of 12 chapters arranged in two sections (3D Modeling and Virtual Prototyping), reflecting the multidimensionality of applications related to modeling and simulation. Some of the most recent modeling and simulation techniques, as well as some of the most accurate and sophisticated software in treating complex systems, are applied. All the original contributions in this book are jointed by the basic principle of a successful modeling and simulation process: as complex as necessary, and as simple as possible. The idea is to manipulate the simplifying assumptions in a way that reduces the complexity of the model (in order to make a real-time simulation), but without altering the precision of the results

The evolution, modifications and interactions of proteins and RNAs

Proteins and RNAs are two of the most versatile macromolecules that carry out almost all functions within living organisms. In this thesis I have explored evolutionary and regulatory aspects of proteins and RNAs by studying their structures, modifications and interactions. In the first chapter of my thesis I investigate domain atrophy, a term I coined to describe large-scale deletions of core structural elements within protein domains. By looking into truncated domain boundaries across several domain families using Pfam, I was able to identify rare cases of domains that showed atrophy. Given that even point mutations can be deleterious, it is surprising that proteins can tolerate such large-scale deletions. Some of the structures of atrophied domains show novel protein-protein interaction interfaces that appear to compensate and stabilise their folds. Protein-protein interactions are largely influenced by the surface and charge complementarity, while RNA-RNA interactions are governed by base-pair complementarity; both interaction types are inherently different and these differences might be observed in their interaction networks. Based on this hypothesis I have explored the protein-protein, RNA-protein and the RNA-RNA interaction networks of yeast in the second chapter. By analysing the three networks I found no major differences in their network properties, which indicates an underlying uniformity in their interactomes despite their individual differences. In the third chapter I focus on RNA-protein interactions by investigating post-translational modifications (PTMs) in RNA-binding proteins (RBPs). By comparing occurrences of PTMs, I observe that RBPs significantly undergo more PTMs than non-RBPs. I also found that within RBPs, PTMs are more frequently targeted at regions that directly interact with RNA compared to regions that do not. Moreover disorderedness and amino acid composition were not observed to significantly influence the differential PTMs observed between RBPs and nonRBPs. The results point to a direct regulatory role of PTMs in RNA-protein interactions of RBPs. In the last chapter, I explore regulatory RNA-RNA interactions. Using differential expression data of mRNAs and lncRNAs from mouse models of hereditary hemochromatosis, I investigated competing regulatory interactions between mRNA, lncRNA and miRNA. A mutual interaction network was created from the predicted miRNA interaction sites on mRNAs and lncRNAs to identify regulatory RNAs in the disease. I also observed interesting relations between the sense-antisense mRNA-lncRNA pairs that indicate mutual regulation of expression levels through a yet unknown mechanism

A Theory of Conceptual Advance: Explaining Conceptual Change in Evolutionary, Molecular, and Evolutionary Developmental Biology

The theory of concepts advanced in the dissertation aims at accounting for a) how a concept makes successful practice possible, and b) how a scientific concept can be subject to rational change in the course of history. Traditional accounts in the philosophy of science have usually studied concepts in terms only of their reference; their concern is to establish a stability of reference in order to address the incommensurability problem. My discussion, in contrast, suggests that each scientific concept consists of three components of content: 1) reference, 2) inferential role, and 3) the epistemic goal pursued with the concept's use. I argue that in the course of history a concept can change in any of these three components, and that change in one component—including change of reference—can be accounted for as being rational relative to other components, in particular a concept's epistemic goal.This semantic framework is applied to two cases from the history of biology: the homology concept as used in 19th and 20th century biology, and the gene concept as used in different parts of the 20th century. The homology case study argues that the advent of Darwinian evolutionary theory, despite introducing a new definition of homology, did not bring about a new homology concept (distinct from the pre-Darwinian concept) in the 19th century. Nowadays, however, distinct homology concepts are used in systematics/evolutionary biology, in evolutionary developmental biology, and in molecular biology. The emergence of these different homology concepts is explained as occurring in a rational fashion. The gene case study argues that conceptual progress occurred with the transition from the classical to the molecular gene concept, despite a change in reference. In the last two decades, change occurred internal to the molecular gene concept, so that nowadays this concept's usage and reference varies from context to context. I argue that this situation emerged rationally and that the current variation in usage and reference is conducive to biological practice.The dissertation uses ideas and methodological tools from the philosophy of mind and language, the philosophy of science, the history of science, and the psychology of concepts

Diversity and phylogenetic structure of two complex marine microbial communities

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 2004.Includes bibliographical references (p. 102-103).(cont.) competitive mechanisms are too weak to purge diversity from within them.Molecular surveys have revealed that microbial communities are extraordinarily diverse. Yet, two important questions remain unanswered: how many bacterial types co-exist, and do such types form phylogenetically discrete units of potential ecological relevance? This thesis explores these questions by investigating bacterial diversity in two complex marine communities (coastal bacterioplankton and sediment sulfate-reducing bacteria) by (i) comprehensive analysis of large 16S rRNA clone libraries, and (ii) refinement and application of parametric diversity estimators. Identification and correction of sequence artifacts demonstrated their potentially significant contribution to diversity estimates. Still, hundreds of unique rRNA sequences (ribotypes) were detected in the corrected libraries, and extrapolation to community diversity with commonly used non-parametric diversity estimators suggested at least thousands of co-existing ribotypes in the two communities. However, close inspection revealed that the non-parametric estimators likely lead to underestimation of ribotype diversity in the clone libraries. Thus, an improved parametric method was developed and shown to closely fit the data. The extrapolated total ribotype diversity in the sample by the improved method was up to one order of magnitude higher than estimated with common non-parametric approaches. Most significantly, the compensation for artifacts and improved estimation revealed that the vast majority of ribotypes fall into microdiverse clusters containing <1% sequence divergence. It is proposed that the observed microdiverse clusters form important units of differentiation in microbial communities. They are hypothesized to arise by selective sweeps and contain high diversity becauseby Vanja Klepac-Ceraj.Ph.D

Everything Flows

This collection of essays explores the metaphysical thesis that the living world is not ontologically made up of substantial particles or things, as has often been assumed, but is rather constituted by processes. The biological domain is organized as an interdependent hierarchy of processes, which are stabilized and actively maintained at different timescales. Even entities that intuitively appear to be paradigms of things, such as organisms, are actually better understood as processes. Unlike previous attempts to articulate processual views of biology, which have tended to use Alfred North Whitehead’s panpsychist metaphysics as a foundation, this book takes a naturalistic approach to metaphysics. It submits that the main motivations for replacing an ontology of substances with one of processes are to be looked for in the empirical findings of science. Biology provides compelling reasons for thinking that the living realm is fundamentally dynamic and that the existence of things is always conditional on the existence of processes. The phenomenon of life cries out for theories that prioritize processes over things, and it suggests that the central explanandum of biology is not change but rather stability—or, more precisely, stability attained through constant change. This multicontributor volume brings together philosophers of science and metaphysicians interested in exploring the consequences of a processual philosophy of biology. The contributors draw on an extremely wide range of biological case studies and employ a process perspective to cast new light on a number of traditional philosophical problems such as identity, persistence, and individuality