Second CLIPS Conference Proceedings, volume 1

Topics covered at the 2nd CLIPS Conference held at the Johnson Space Center, September 23-25, 1991 are given. Topics include rule groupings, fault detection using expert systems, decision making using expert systems, knowledge representation, computer aided design and debugging expert systems

Evolutionary Inference from Admixed Genomes: Implications of Hybridization for Biodiversity Dynamics and Conservation

Hybridization as a macroevolutionary mechanism has been historically underappreciated among vertebrate biologists. Yet, the advent and subsequent proliferation of next-generation sequencing methods has increasingly shown hybridization to be a pervasive agent influencing evolution in many branches of the Tree of Life (to include ancestral hominids). Despite this, the dynamics of hybridization with regards to speciation and extinction remain poorly understood. To this end, I here examine the role of hybridization in the context of historical divergence and contemporary decline of several threatened and endangered North American taxa, with the goal to illuminate implications of hybridization for promoting—or impeding—population persistence in a shifting adaptive landscape. Chapter I employed population genomic approaches to examine potential effects of habitat modification on species boundary stability in co-occurring endemic fishes of the Colorado River basin (Gila robusta and G. cypha). Results showed how one potential outcome of hybridization might drive species decline: via a breakdown in selection against interspecific heterozygotes and subsequent genetic erosion of parental species. Chapter II explored long-term contributions of hybridization in an evolutionarily recent species complex (Gila) using a combination of phylogenomic and phylogeographic modelling approaches. Massively parallel computational methods were developed (and so deployed) to categorize sources of phylogenetic discordance as drivers of systematic bias among a panel of species tree inference algorithms. Contrary to past evidence, we found that hypotheses of hybrid origin (excluding one notable example) were instead explained by gene-tree discordance driven by a rapid radiation. Chapter III examined patterns of local ancestry in the endangered red wolf genome (Canis rufus) – a controversial taxon of a long-standing debate about the origin of the species. Analyses show how pervasive autosomal introgression served to mask signatures of prior isolation—in turn misleading analyses that led the species to be interpreted as of recent hybrid origin. Analyses also showed how recombination interacts with selection to create a non-random, structured genomic landscape of ancestries with, in the case of the red wolf, the ‘original’ species tree being retained only in low-recombination ‘refugia’ of the X chromosome. The final three chapters present bioinformatic software that I developed for my dissertation research to facilitate molecular approaches and analyses presented in Chapters I–III. Chapter IV details an in-silico method for optimizing similar genomic methods as used herein (RADseq of reduced representation libraries) for other non-model organisms. Chapter V describes a method for parsing genomic datasets for elements of interest, either as a filtering mechanism for downstream analysis, or as a precursor to targeted-enrichment reduced-representation genomic sequencing. Chapter VI presents a rapid algorithm for the definition of a ‘most parsimonious’ set of recombinational breakpoints in genomic datasets, as a method promoting local ancestry analyses as utilized in Chapter III. My three case studies and accompanying software promote three trajectories in modern hybridization research: How does hybridization impact short-term population persistence? How does hybridization drive macroevolutionary trends? and How do outcomes of hybridization vary in the genome? In so doing, my research promotes a deeper understanding of the role that hybridization has and will continue to play in governing the evolutionary fates of lineages at both contemporary and historic timescales

Phylogeny of the Viral Hemorrhagic Septicemia Virus in European Aquaculture

<p>One of the most valuable aquaculture fish in Europe is the rainbow trout, Oncorhynchus mykiss, but the profitability of trout production is threatened by a highly lethal infectious disease, viral hemorrhagic septicemia (VHS), caused by the VHS virus (VHSV). For the past few decades, the subgenogroup Ia of VHSV has been the main cause of VHS outbreaks in European freshwater-farmed rainbow trout. Little is currently known, however, about the phylogenetic radiation of this Ia lineage into subordinate Ia clades and their subsequent geographical spread routes. We investigated this topic using the largest Ia-isolate dataset ever compiled, comprising 651 complete G gene sequences: 209 GenBank Ia isolates and 442 Ia isolates from this study. The sequences come from 11 European countries and cover the period 1971-2015. Based on this dataset, we documented the extensive spread of the Ia population and the strong mixing of Ia isolates, assumed to be the result of the Europe-wide trout trade. For example, the Ia lineage underwent a radiation into nine Ia clades, most of which are difficult to allocate to a specific geographic distribution. Furthermore, we found indications for two rapid, large-scale population growth events, and identified three polytomies among the Ia clades, both of which possibly indicate a rapid radiation. However, only about 4% of Ia haplotypes (out of 398) occur in more than one European country. This apparently conflicting finding regarding the Europe-wide spread and mixing of Ia isolates can be explained by the high mutation rate of VHSV. Accordingly, the mean period of occurrence of a single Ia haplotype was less than a full year, and we found a substitution rate of up to 7.813 × 10^-4 nucleotides per site per year. Finally, we documented significant differences between Germany and Denmark regarding their VHS epidemiology, apparently due to those countries' individual handling of VHS.</p

Managing conflict in national parks: the case of encroachment in Kerinci Seblat, Indonesia

Kerinci Seblat National Park (KSNP) is the largest national park in Indonesia. It surrounds Kerinci District, the biggest enclave inside any comparable national park in the world. For these reasons the people-park problems are potentially the most complex among all parks in Indonesia.The greatest threat to the integrity of KSNP comes from encroachment which is largely aimed at the cultivation of cinnamon trees. Traditional approaches to park management and enforcement activities to exclude local people from the park have been unable to solve this problem. This study attempts to fill gaps in our knowledge of people-park interactions in KSNP and aims to incorporate encroachment problems in the park’s management plan.The objectives of this study were: (1) to examine characteristics of encroachment systems, people’s attitude towards the Park and encroachment; (2) to measure the degree of people pressure on the park and analyse impacts of encroachment on soil properties; (3) to model historical land use dynamics in an attempt to predict future encroachment; and (4) to provide alternative management options for the Park using a multi-criteria decision making (MCDM) model, and define the trade-offs that will exist between economic, environmental and social variables associated with alternative optionsThe results demonstrate that shortage of land and people’s perception of cinnamon are significant factors influencing encroachment activities in KSNP. Land use dynamics in the District are strongly influenced by the twin processes of encroachment and forest degradation. The most critical zone for encroachment in the District is the area in the elevation between 500-1500 m with slope less than 40 percent. Due to human encroachment, the Park is now under serious population pressure. Therefore, four scenarios of land allocation for buffer and traditional use zones were produced to lessen the pressure. A model was developed for identifying the area most likely to be encroached in the future. These results were utilised in order to develop eleven alternative management options for resolving conflict between encroachment and sustainable park management

Transformational maintenance by reuse of design histories

This thesis provides theory and procedures for modifying software artifacts implemented by a formal transformation process. Installing modifications requires knowing not only what transformations were applied (a derivation history) to construct the artifact, but also why the application sequence ensures that the artifact meets its specification. The derivation history and the justification are collectively called a design history. A Design Maintenance System (DMS), when provided with a formal change called a maintenance delta, revises a design history to guide construction of a new artifact. A DMS can be used to integrate a stream of deltas into a history, providing implementations as a side effect, leading to an incremental-evolution model for software construction.We provide a broadly applicable formal model of transformation systems in which specifications are performance predicates, subsuming the functional specifications which are traditional for transformation systems. Such performance predicates provide vocabulary used in the design history to describe the effect of applying sets of transformations.A nonprocedural, performance-goal-oriented Transformation Control Language (TCL) is defined to control navigation of the design space for a transformation system. Recording the execution of a TCL metaprogram directly provides a design history.A complete classification of, and representation for, the set of possible maintenance deltas is given in terms of the inputs defined by the transformation system model. Such deltas include not only specification changes, but also changes to implementation support technologies. Delta integration procedures for revising derivation histories given functional or support technology deltas are provided, based on rearranging the order of transformations in the design space. Building on these operations, integration procedures that revise the design history for each type of delta are described. An agenda-oriented TCL execution process dovetails smoothly with the integration procedures.Our DMS is compared to a number of other maintenance systems. By using an explicit delta and verified commutativity, our DMS often reuses transformations correctly when others fail

A heuristic-based approach to code-smell detection

Encapsulation and data hiding are central tenets of the object oriented paradigm. Deciding what data and behaviour to form into a class and where to draw the line between its public and private details can make the difference between a class that is an understandable, flexible and reusable abstraction and one which is not. This decision is a difficult one and may easily result in poor encapsulation which can then have serious implications for a number of system qualities. It is often hard to identify such encapsulation problems within large software systems until they cause a maintenance problem (which is usually too late) and attempting to perform such analysis manually can also be tedious and error prone. Two of the common encapsulation problems that can arise as a consequence of this decomposition process are data classes and god classes. Typically, these two problems occur together – data classes are lacking in functionality that has typically been sucked into an over-complicated and domineering god class. This paper describes the architecture of a tool which automatically detects data and god classes that has been developed as a plug-in for the Eclipse IDE. The technique has been evaluated in a controlled study on two large open source systems which compare the tool results to similar work by Marinescu, who employs a metrics-based approach to detecting such features. The study provides some valuable insights into the strengths and weaknesses of the two approache

Genomic studies of sex differences : On mutations, recombination, and sexual antagonism in songbirds

Many organisms have separate sexes, i.e., males and females. The presence of separate sexes causes sex-specific selection regimes and sexual antagonism, which can lead to sex differences in morphology, physiology, and behaviours. Sex and sex differences can be genetically governed and regulated by a pair of sex chromosomes (e.g., X and Y, or Z and W), on which there often are regions without recombination. In this thesis, I used genomic approaches to study sex differences in a songbird, the great reed warbler (Acrocephalus arundinaceus), in which male and females are monochromatic and genetically determined by a pair of sex chromosomes. The thesis starts with a study presenting and evaluating two alternative phylogenetic approaches (the expected likelihood weight (ELW) and the BEAST approach) to determine when different parts of the sex chromosomes stop recombining. My findings highlight the benefits of using fixed topologies to estimate the timing of recombination cessation as done by these approaches. Thereafter, I focus on molecular sex differences using genomic and bioinformatic methods to specifically investigate sex biases in de novo mutations and in recombination patterns, and search for sexually antagonistic loci in the genome.By using whole genome sequencing data from a three-generation pedigree of the great reed warbler, I found a strong sex bias in the numbers of de novo mutations, with males having three times as many mutations as females. Regarding recombination, I found no statistical support for sex-specific recombination rates, but the recombination landscape differed between sexes, with males having more crossovers towards the chromosome ends compared to females. Besides, I developed an interactive R application, RecView ShinyApp, to implement the methodology of locating recombination for future studies within similar topic.Finally, I used statistical approaches based on allele frequency differences and associations with sex per se to search for sexually antagonistic loci with whole genome sequencing data from 100 old great reed warblers that aged between 3 and 5 years. By comparing the top 100 SNPs with the strongest allelic differentiation between the sexes, and the most significant associations with sex, I discovered 50 overlapping SNPs that constitute candidates for future studies of sexual antagonistic selection. To conclude, this thesis has improved the methodology for studying the timing of recombination cessation on sex chromosomes as well as to study recombination per se, identified sex-specific de novo mutation rates and sexually dimorphic recombination landscapes, and obtained candidate loci for sexual antagonism