Reconstructing weighted phylogenetic trees and phylogenetic networks using answer set programming

Evolutionary relationships between species can be modeled as a tree (called a phylogeny) whose nodes represent the species, internal vertices represent their ancestors and edges represent genetic relationships. If there are borrowings between species, then a small number of edges that denote such borrowings can be added to phylogenies turning them into (phylogenetic) networks. However, there are too many such trees/networks for a given family of species but no phylogenetic system to automatically analyze them. This thesis fulfills this need in phylogenetics, by introducing novel computational methods and tools for computing weighted phylogenies/networks, using Answer Set Programming (ASP). The main idea is to define a weight function for phylogenies/networks that characterizes their plausibility, and to reconstruct phylogenies/networks whose weights are over a given threshold using ASP solvers. We have studied computational problems related to reconstructing weighted phylogenies/networks based on the compatibility criterion, analyzed their computational complexity, and introduced two sorts of ASP-based methods (representation-based and search-based) for computing weighted phylogenies/networks. Utilizing these methods, we have introduced a novel divide-and-conquer algorithm for computing large weighted phylogenies, and implemented a phylogenetic system (Phylo-ASP) based on it. We have also implemented a phylogenetic system (PhyloNet-ASP) for reconstructing weighted networks. We have shown the applicability and the effectiveness of our methods by performing experiments on two real datasets: Indo European languages, and Quercus species in Turkey. Moreover, we have extended our methods to computing weighted solutions in ASP and modified an ASP solver accordingly, providing a useful tool (CLASP-W) for various ASP applications

Music in Evolution and Evolution in Music

Music in Evolution and Evolution in Music by Steven Jan is a comprehensive account of the relationships between evolutionary theory and music. Examining the ‘evolutionary algorithm’ that drives biological and musical-cultural evolution, the book provides a distinctive commentary on how musicality and music can shed light on our understanding of Darwin’s famous theory, and vice-versa. Comprised of seven chapters, with several musical examples, figures and definitions of terms, this original and accessible book is a valuable resource for anyone interested in the relationships between music and evolutionary thought. Jan guides the reader through key evolutionary ideas and the development of human musicality, before exploring cultural evolution, evolutionary ideas in musical scholarship, animal vocalisations, music generated through technology, and the nature of consciousness as an evolutionary phenomenon. A unique examination of how evolutionary thought intersects with music, Music in Evolution and Evolution in Music is essential to our understanding of how and why music arose in our species and why it is such a significant presence in our lives

The development and application of metaheuristics for problems in graph theory: A computational study

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.It is known that graph theoretic models have extensive application to real-life discrete optimization problems. Many of these models are NP-hard and, as a result, exact methods may be impractical for large scale problem instances. Consequently, there is a great interest in developing e±cient approximate methods that yield near-optimal solutions in acceptable computational times. A class of such methods, known as metaheuristics, have been proposed with success. This thesis considers some recently proposed NP-hard combinatorial optimization problems formulated on graphs. In particular, the min- imum labelling spanning tree problem, the minimum labelling Steiner tree problem, and the minimum quartet tree cost problem, are inves- tigated. Several metaheuristics are proposed for each problem, from classical approximation algorithms to novel approaches. A compre- hensive computational investigation in which the proposed methods are compared with other algorithms recommended in the literature is reported. The results show that the proposed metaheuristics outper- form the algorithms recommended in the literature, obtaining optimal or near-optimal solutions in short computational running times. In addition, a thorough analysis of the implementation of these methods provide insights for the implementation of metaheuristic strategies for other graph theoretic problems

Barbed bone and antler technologies: cultural transmission and variation in the Gulf of Georgia, Northwest North America

Although archaeologists have long discussed the evolution of the social stratification and complex group interactions of the hunter-gatherer-fishers of the Northwest Coast (e.g. Matson and Coupland 1994; Ames 1994), few have examined the implied interactions between material culture and the development of complexity in the Gulf of Georgia postulated to have occurred approximately 2600 years ago. When viewed from a Darwinian perspective, specifically Boyd and Richerson\u27s (1985) dual inheritance theory, the development of social stratification and systems of deference may influence the contexts of social learning. I hypothesize that prestige bias (Henrich and Henrich 2007) emerged as a factor in the social learning of technologies tied to systems of resource procurement and prestige-based status, as complexity developed. Barbed bone and antler points are examined in this analysis as a technology tied to these resource systems and prestige-based status. A total of 593 artifacts were examined from 56 archaeological sites from the collections at Western Washington University, the Burke Museum, the Royal British Columbia Museum, and Simon Fraser University. McMurdo\u27s (1972) typology was used as a basis for the examination of attributes. Cladistics was employed using models developed by Eerkens and his coauthors. (2006) in order to detect prestige bias, represented by a branching phylogeny of descent with modification as opposed to a stochastic pattern. Dunnell\u27s (1978) definition of stylistic and functional traits coupled with cluster analyses were utilized in the examination of attributes to select traits that would not result in a \u27false\u27 phylogenetic signal due to artifact functional constraints. In addition to examining the cultural transmission of barbed bone and antler points, the data set was also used to assess previous interpretations of artifact function (e.g. Carlson 1954). Four functional classes (retrievable points, fixed points, leisters, fish hooks) were constructed for this purpose and to determine if there were distinctions in metric attributes between classes. Variation within fixed points was also examined to determine if there were detectable distinctions in attributes hypothesized to be linked to functions such as a fish spears or arrow points (e.g. Carlson 1954, Clark 1975) such as barb morphology, crosssection, and base length. The cultural-historical significance of attributes such as the transition from bilateral to unilateral barb application and line attachments through time and the trend towards squared, enclosed, barbs in later periods were also assessed (Drucker 1943; McMurdo 1972). Cladistics analysis, using geographically and chronologically outlying assemblages as an outgroup, revealed a stochastic pattern of cultural transmission, implying highly individualized (guided variation) or peer based learning (horizontal transmission) rather than prestige bias. Cluster analyses demonstrate considerable geographic homogeneity in the morphological attributes of barbed points, indicating that similar barbed point styles were present throughout the Gulf of Georgia over the past 3500 years. Barb morphological attributes, as indicated by the frequencies of barb paradigmatic classes, also demonstrate considerable continuity over the past 3500 years. Clear distinctions were detected in the metric attributes of morphologically defined functional classes. Variation in the morphology of fixed points, indicative of possible function as a fish spear or bird arrow was also detected. Attributes McMurdo (1972) argued had culture-historic significance, with the exception of those tied to barb morphology, were found to be chronologically sensitive

Reconstructing Phylogenies with Memetic Algorithms and Branch-and-Bound

A phylogenetic tree represents the evolutionary history for a collection of organisms. We consider the problem of inferring such a tree given a certain set of data (genomic, proteomic, or even morphological). Given the computational hardness of this problem, exact approaches are inherently limited. However, exact techniques can still be useful to endow heuristic approaches with problem-awareness. We analyze this hybridization in the context of memetic algorithms and branch-and-bound techniques. Focusing in the ultrametric model for phylogenetic inference, we show that this combination can be synergetic. We analyze the parameters involved in this hybrid model, and determine a robust setting for these. A summary of related work is also provided.

Evolution: From Big Bang to Nanorobots

The present volume is the fourth issue of the Yearbook series entitled ‘Evolution’. The title of the present volume is ‘From Big Bang to Nanorobots’. In this way we demonstrate that all phases of evolution and Big History are covered in the articles of the present Yearbook. Several articles also present the forecasts about future development. The main objective of our Yearbook as well as of the previous issues is the creation of a unified interdisciplinary field of research in which the scientists specializing in different disciplines could work within the framework of unified or similar paradigms, using the common terminology and searching for common rules, tendencies and regularities. At the same time for the formation of such an integrated field one should use all available opportunities: theories, laws and methods. In the present volume, a number of such approaches are used

Evolution: From Big Bang to Nanorobots

The present volume is the fourth issue of the Yearbook series entitled ‘Evolution’. The title of the present volume is ‘From Big Bang to Nanorobots’. In this way we demonstrate that all phases of evolution and Big History are covered in the articles of the present Yearbook. Several articles also present the forecasts about future development. The main objective of our Yearbook as well as of the previous issues is the creation of a unified interdisciplinary field of research in which the scientists specializing in different disciplines could work within the framework of unified or similar paradigms, using the common terminology and searching for common rules, tendencies and regularities. At the same time for the formation of such an integrated field one should use all available opportunities: theories, laws and methods. In the present volume, a number of such approaches are used

Evolution of bow-arrow technology.

This thesis examines the development of bow-arrow technology in terms of modem evolutionary theory. Previous approaches that propose functional-adaptive technological trajectories are critiqued. Different theoretical approaches towards technology and associated units of analysis are examined. Behavioural ecology, evolutionary archaeology, and dual inheritance theory are shown to hold most promise for explaining trait-lineages in a given technological tradition. Previous approaches to bow-arrow technology are analysed, and an evolutionary archaeological methodology appropriate for examining lithic armatures is presented. Environment, historical contingency, selection, drift, population dynamics and social learning mechanisms are seen as key complex factors requiring case by case examination. An evolutionary case study with nine temporally, geographically, and culturally related stratigraphic phases containing a total of 3600 complete lithic armatures from the south Scandinavian middle Mesolithic (c. 6600-5400 BC) is presented. The phases are described in terms of associated fine-grained archaeological data and previous interpretations. A Bayesian chronological framework is constructed for the case study, using modelling facilities in the OxCal calibration package. This method time-steps and calculates relative occupation durations of point bearing phases in terms of available archaeological and radiometric data. The chronological model covers the culture-historical periods termed Blak, Kongemose and Early Ertebolle phases. The validity of previous typological interpretations of projectile point sequences is questioned in light of these results. The nine time-stepped lithic armature assemblages are then analysed to describe inter- and intra-site point trait variation. A linked series of descriptive and multivariate statistical techniques identify key morphological attributes that summarise trait variation within and between phases. Variation is graphically represented and related to different social learning populations, reduction strategies, and engineering constraints. A remarkably long-term homogenous pattern of complex projectile point manufacture is found for the Kongemose phases, compared to the temporally bracketing Blak and Ertebolle phases. Faunal, climatic, and population level factors are then modelled to account for variation and stability of the case study's armature traits. Faunal data from the Tagerup and Segebro sites, spanning the case study period, are examined for possible diet breadth changes, in relation to point-trait variation. No functional relationship is found between point-shape and potential target-prey. A population model is then constructed in OxCal using all published south Scandinavian radiometric data from the final Maglemose to the final Ertebolle cultural phases. A simple model of landmass reduction, forestation cover and mammalian population density levels demonstrates reduced land mass alone would not significantly affect human population levels - even with relatively high human population densities. Holocene 5180 and A14C data is used as a proxy for contemporaneous climatic fluctuations. These proxies are plotted and superimposed onto the population graph. A correlation between climate change, population fluctuation, and projectile point technology is found. As changes in point morphology and lithic reduction strategies coincide with apparent regional drops in population, drift processes may account for some variation in point-shape