Natural selection. II. Developmental variability and evolutionary rate

In classical evolutionary theory, genetic variation provides the source of heritable phenotypic variation on which natural selection acts. Against this classical view, several theories have emphasized that developmental variability and learning enhance nonheritable phenotypic variation, which in turn can accelerate evolutionary response. In this paper, I show how developmental variability alters evolutionary dynamics by smoothing the landscape that relates genotype to fitness. In a fitness landscape with multiple peaks and valleys, developmental variability can smooth the landscape to provide a directly increasing path of fitness to the highest peak. Developmental variability also allows initial survival of a genotype in response to novel or extreme environmental challenge, providing an opportunity for subsequent adaptation. This initial survival advantage arises from the way in which developmental variability smooths and broadens the fitness landscape. Ultimately, the synergism between developmental processes and genetic variation sets evolutionary rate

Organic Selection and Social Heredity: The Original Baldwin Effect Revisited

The so-called “Baldwin Effect” has been studied for years in the fields of Artificial Life, Cognitive Science, and Evolutionary Theory across disciplines. This idea is often conflated with genetic assimilation, and has raised controversy in trans-disciplinary scientific discourse due to the many interpretations it has. This paper revisits the “Baldwin Effect” in Baldwin’s original spirit from a joint historical, theoretical and experimental approach. Social Heredity – the inheritance of cultural knowledge via non-genetic means in Baldwin’s term – is also taken into consideration. I shall argue that the Baldwin Effect can occur via social heredity without necessity for genetic assimilation. Computational experiments are carried out to show that when social heredity is permitted with high fidelity, there is no need for the assimilation of acquired characteristics; instead the Baldwin Effect occurs as promoting more plasticity to facilitate future intelligence. The role of mind and intelligence in evolution and its implications in an extended synthesis of evolution are briefly discussed

The Role of Social Learning in the Evolution on a Rugged Fitness Landscape

The role and importance of social learning have been investigated by many researchers because it is observed in many animals and is expected to play a significant role in cultural phenomena. We explore the coevolution between individual learning and social learning on a rugged fitness landscape as a realistic condition in which they can interact with each other. We demonstrate that social learning allows individuals not to have adaptive traits innately, and thus, has two important roles to enhance individual fitness. First, social learning spreads and keeps the adaptive phenotypes acquired by individual learning. Second, social learning enables individuals to explore a wide range of fitness landscape by the increased population diversity. Based on the difference of the roles of individual and social learning, they can work complementarily in the course of adaptive evolution on the rugged fitness landscape

Product Development Teams Formation:Effects of Organizational and Product Related Factors

While teams are an essential means for developing products in organizations, how to assemble product development teams remains largely unexplored. According to the social network research, teams might be arranged in either closely connected or sparse structures. Conceptualizing a product development project as collective problem solving endeavour, we develop a computational model of these projects in which a number of designers, who are arranged in teams with a particular structure, conduct search over an NK(C) performance landscape. Simulation of this model enables us to compare the design performance of teams with either closely connected or sparse structures. Our results indicate that how effectively organizations can integrate design solutions determines which of these two structures results in higher development performance. In addition, with our simulation model, design performance of strategies that employ both closely connected and sparse teams, is contrasted with that of those policies which solely use either of these structures. We find that, regardless of product development project integration capability, strategies that simultaneously utilize both closely connected and sparse teams are likely to achieve higher development performance than the other strategies that only use teams with one particular structure. We discuss the implications of our findings in managing product development project

Incorporating Human Beliefs and Behaviors into Wildlife Ecology

Like much of the global biosphere, wildlife species have experienced rapid declines during the Anthropocene. Wildlife ecologists have responded to these crises by developing a range of technologies, techniques, and large datasets, which together have revolutionized the field, provided novel insights into the movements and behaviors of animals, and identified new risks and impacts to wildlife in a human-dominated world. While these advances have been vitally important, wildlife ecology has been slower to recognize and incorporate humans themselves into its new research domains. The chapters of this dissertation explore methods for better incorporating human behaviors, beliefs, actions, and infrastructure into the theories and approaches in wildlife ecology that have flourished in the last two decades. The research presented here demonstrates the importance of linking human beliefs and behaviors to wildlife ecology both by presenting novel findings and by showing the opportunities missed when narrow approaches are applied to complex socio-ecological problems.In Chapter 1, I provide a general introduction on the theories underlying this research, contextualize the research questions in light of the loss and recovery of large predators, and describe the research site where I collected much of the data for this dissertation. In Chapter 2, I apply the methods of movement ecology to some of the first fine-scale telemetry data collected on rifle hunters. I draw conclusions about their individual, site-level, and regional-level hunting behaviors and discuss the broad implications of these findings for hunting management. In Chapter 3, I examine livestock-predator conflict using approaches from both ecology and the social sciences. I describe a form of selection bias that is likely widespread but unreported due to the omission of social data from ecological models of conflict, and I offer guidelines for combining and translating ecological and social research on conflict. In Chapter 4, I explore the ecological impacts of one of the most globally widespread human constructions, the fence. I show for the first time the potential extent of fencing at large scales and discuss the wide variety of ecological effects of fences for both humans and ecosystems. I further highlight biases and gaps in fence research that have thus far limited a complete understanding of the environmental effects of these features. In Chapter 5, I conclude by making recommendations regarding how research might better incorporate human perceptions, decisions, and actions into ecology

Understanding Innovation as a Collaborative, Co-Evolutionary Process

La innovació, que ha estat durant molt de temps el resultat, a vegades heroic, de la tasca d'un emprenedor solitari, està esdevenint progressivament una tasca col·lectiva que troba una descripció més acurada quan es presenta com el resultat d'un procés complex amb múltiples actors. Aquesta tesi vol explorar aquest aspecte col·lectiu de la innovació, tot aprofundint en dues línies de recerca. Una, que utilitza el modelatge basat en agents per a la creació de model teòrics. L'altre, que es basa en l'ús de l'anàlisi qualitatiu per a esbrinar algunes de les claus d'unes organitzacions ‐els Living Labs ‐ que cerquen involucrar els usuaris en el procés d'innovació. Ara bé, malgrat presentem la innovació com un procés obert, aquesta entesa com un procés tancat sembla també tenir èxit. De fet, tant els telèfons mòbils molt simples o molt complexos, semblen seguir aquest enfocament. En quines condicions el procés d'innovació es beneficia de ser un procés obert i quan és possible obtenir millors resultats retenint el control de la totalitat del procés, és la nostra primera pregunta de recerca. D'altra banda, aquest procés de col·laboració, característic d'un enfocament obert, és considerat normalment a un nivell micro com el resultat de la interacció diàdica entre agents. Existeix però, un altre nivell, un nivell macro que ve caracteritzat per la funció d'institucions com les Escoles de Negocis, que juguen un paper important en destil·lar les millors pràctiques i crear hipòtesis a partir d'elles que si es revelen exitoses seran adoptades per la totalitat dels agents. La comprensió del funcionament d'aquest procés, del nombre de casos que cal considerar i de quan extensius han de ser, entendre fins a quin punt les empreses poden confiar en l'assessorament de les Escoles de Negoci i quan es necessari aventurar‐se en l'exploració de noves possibilitats, és també quelcom necessari per a caracteritzar la innovació com un procés col·lectiu. Malauradament, la nostra comprensió dels mecanismes col·laboratius és encara escassa. Sabem però, que la innovació ja no és quelcom exclusiu dels laboratoris d'I+D o d'organitzacions capdavanteres, sinó que els usuaris juguen no solament un paper rellevant sinó que són percebuts com a actors amb un gran potencial. Els Living Labs és una de les tentatives per proporcionar estructura i governança a la involucració dels usuaris en el procés d'innovació. En aquest aspecte, examinarem quina és la contribució d'aquests usuaris i com els Living Labs busquen capturar‐ne el seu coneixement i aplicar‐lo i quant tenen èxit en aquest procés.La innovación, que se ha presentado muchas veces como el resultado de un proceso, muchas veces heroico, de emprendedores excepcionales, se está convirtiendo de una forma progresiva en un proceso colectivo que se describe con más acierto cuando se presenta como el resultado de un proceso complejo con multitud de actores. Esta tesis, pretende explorar este aspecto colectivo del proceso de innovación, profundizando en dos líneas de investigación. Una que utiliza el modelado basado en agentes para la construcción de modelos teóricos. Otra que se basa en el análisis cualitativo para profundizar en las claves de unas organizaciones ¬los Living Labs ‐ que buscan involucrar a los usuarios en los procesos de innovación. Ahora bien, a pesar de que la innovación se presente como un proceso abierto, ésta entendida como un proceso cerrado, parece también tener éxito. De hecho, los teléfonos móviles muy simples o muy complejos, parecen seguir este enfoque. En qué condiciones el proceso de innovación se beneficia de ser un proceso abierto y cuando es posible obtener mejores resultados reteniendo el control de la totalidad del proceso, es nuestra primera pregunta de investigación. Por otro lado, este proceso de colaboración, característico de un enfoque abierto, es considerado normalmente a un nivel micro, como el resultado de la interacción diádica entre agentes. Existe pero, otro nivel, un nivel macro, caracterizado por la función de instituciones como las Escuelas de Negocios, que juegan un papel importante destilando las mejores prácticas y creando hipótesis a partir de ellas que si se revelan exitosas serán masivamente adoptadas. La comprensión del funcionamiento de este proceso, del número de casos a considerar y de su extensión, comprender hasta qué punto las empresas pueden confiar en el asesoramiento de las Escuelas de Negocios y cuando es necesario aventurarse en un proceso de exploración de nuevas posibilidades, es también algo imprescindible para caracterizar la innovación como un proceso colectivo. Desgraciadamente nuestra comprensión de los mecanismos colaborativos en la innovación es aún escasa. Sin embargo sabemos que la innovación ya no es algo exclusivo de los laboratorios de I+D o de grandes empresas, los usuarios juegan no sólo un papel relevante sino que son percibidos como actores con un alto potencial. Los Living Labs es una de las tentativas que buscan proporcionar estructura y gobierno a la involucración de los usuarios en el proceso de innovación. En este aspecto, examinaremos cuál es la contribución de los usuarios, cómo los Living Labs buscan capturar su conocimiento y aplicarlo y cuando tienen éxito en su intento.Innovation, which used to be the result of a single, sometimes heroic, entrepreneur, is progressively turning into a collaborative endeavor, better described as the result of a complex process with multiple actors. This thesis aims to explore this collaborative aspect of innovation by digging into two strands of research. One uses Agent‐Based Modeling to create theoretical models, where the other one uses qualitative analysis to devise some insights from organizations ‐Living Labs ‐that aim to involve users in innovation. In addition to understanding innovation as an open process, a closed one seems sometimes to be equally successful. In fact, very simple and very complex mobile phones seem to follow this later approach. Under what conditions innovation benefits from being open and when better results can be obtained from retaining control of the whole process is our first research question. This process of collaboration, characteristic of the open approach, is normally considered at a micro level, as a result of a dyadic interaction between agents. Nevertheless, there is a macro level characterized by institutions, such as Business Schools, that play an important role in uncovering Best Practices and building hypothesis that, if successful, will be adopted by the agents. Understanding how this process works; how many cases should be collected and how comprehensive they should be; how much companies can rely on the insights of Business Schools; and when it is necessary to engage in exploration, is also necessary when characterizing innovation as a collective process. The mechanisms of collaboration are, however, not all well‐understood. Innovation is no longer in the solely hands of R&D laboratories or even organizations, users play an increasingly significant role and are being perceived as holding vast potential. Living Labs is one attempt to provide structure and governance to user involvement in innovation. Here, we will examine what is the contribution of users, how Living Labs aim to capture relevant knowledge and apply it, and when and how this proves successful

Ecology and Evolution of Social Information Use

Sociality is a strategy many animals employ to cope with their environments, enabling them to survive and reproduce more successfully than would otherwise be possible. When navigating their environments and making decisions, social individuals often use information provided by conspecifics (in the form of social cues and signals), thereby increasing the scope and reliability of the information they can gather. However, social information use may be influenced by many factors, including key differences in context across the physical and social environment. My thesis asks and answers a series of questions regarding the trade-offs in social information use across different contexts, with particular focus on signals (chapters 1 and 2) and movement (chapters 3 and 4). Using experimental manipulations of the highly social terrestrial hermit crab (Coenobita compressus) and the less social marine hermit crab (Pagurus bernhardus) I explored social information use across four key areas of behaviour critical to the success of most social organisms: (1) communication, (2) signal evolution, (3) movement, and (4) information transmission. For (1) communication, I tested the production of and response to threat displays across species, examining the evolutionary loss of these displays in species from dramatically different physical and social environments. For (2) signal evolution, I tested the correlation between red colouration and resource holding potential (RHP) across body parts with different signalling potential, based on whether they are exposed or covered by surrounding shell architecture. For (3) movement, I tested whether individuals were biased in their movement by their social group, and whether the level of movement bias changed in different contexts, with individuals having their own private source of protection—a shell—that supersedes the group. Finally, for (4) information transmission, I tested the capacity for information gathering via antennal contact, experimentally seeding social information in the wild to examine whether social information is beneficial to receive and costly to bear. Ultimately, by synthesising social information use across these four important contexts, I have addressed key questions about how and why social context modifies behaviour, and the ways in which a highly valuable and limiting resource—architecturally remodelled shells—shape social behaviours

Macroevolution: Explanation, Interpretation and Evidence

info:eu-repo/semantics/publishedVersio

Characterising fitness landscapes of protein evolution by next-generation sequencing

A protein’s amino acid sequence determines its structural, chemical and physical properties, yet how sequence variation influences protein function is still incompletely understood. Protein fitness landscapes powerfully describe the sequence-function relationship by dividing sequence space into functional hills and valleys. This representation is often invoked yet lacks experimental evidence; the immense vastness of possible sequence space makes comprehensive high-quality datasets difficult to obtain. Laboratory directed evolution has focused on optimal utilisation of substitution libraries, however examination of functional innovation in Nature shows that short insertions and deletions (InDels) also play a key role. Beyond rare targeted studies of specific InDels, high-throughput data on fitness landscape for mutations other than substitutions are lacking entirely. In my PhD, I worked towards experimentally describing the fitness landscapes of InDels and substitutions in three systems: GFP, phosphotriesterase (PTE) and the kinase MKK1 docking domain. Towards this goal, I established two experimental assays (GFP, PTE) for deep mutational scanning and a new software toolkit, InDelScanner, for interpreting resulting data that contain InDels. With GFP, I sorted the deletions and substitution libraries into three activity fractions using FACS, then deep sequenced them with Illumina MiSeq to obtain a pilot dataset. The comparison of deletion effects between different lengths of deletions (-3, -6 and -9 bp) indicates that deletions are partially tolerated in eGFP, with tolerance improved for short deletions and in the stabilised starting point GFP8. Further interpretation of data was complicated by limited resolution in the sequencing dataset stemming from poor FACS separation, so I optimised the conditions for better sorting resolution using the mKate2 fluorescent protein as an expression reporter. In the second iteration of the activity sorting I additionally included UMIs in the plasmid design to improve the utilisation of NGS capacity. In the case of PTE, I performed proof-of-concept experiments for microfluidic droplet sorting in an integrated device with an in-line incubation line and a fluorescent sorting design. In parallel, testing of solubility and activity of random InDel variants showed that functional InDels do not necessarily suffer from a stability handicap, making InDel mutagenesis a viable strategy for gene randomisation in directed evolution. One challenge of InDel library data analysis is that InDels are not compatible with existing, substitution-focused software. Using the GFP deletions dataset, I developed the InDelScanner scripts which accurately detect, aggregate and filter insertions, deletions and substitutions. Using the scripts for composition analysis of TRIAD libraries in PTE showed these libraries are well balanced and highly diverse. Finally, I used the InDelScanner scripts to interpret a deep mutational scanning dataset that recorded the sequence preferences in the MKK1 docking domain, acting to activate ERK2. This experiment showed that the fitness landscape in this kinase pair is shaped by the activating effect of hydrophobic residues in the docking groove, as well as widespread positive epistasis. Together, the projects in this thesis demonstrate that deep mutational scanning experiments are a powerful method for exploring the sequence-function relationship in proteins, which can extend into comparison of different types of mutations as well as probing their (epistatic) interactions.BBSRC BB/M011194/