Exploring Hierarchical Visualization Designs Using Phylogenetic Trees

Ongoing research on information visualization has produced an ever-increasing number of visualization designs. Despite this activity, limited progress has been made in categorizing this large number of information visualizations. This makes understanding their common design features challenging, and obscures the yet unexplored areas of novel designs. With this work, we provide categorization from an evolutionary perspective, leveraging a computational model to represent evolutionary processes, the phylogenetic tree. The result — a phylogenetic tree of a design corpus of hierarchical visualizations — enables better understanding of the various design features of hierarchical information visualizations, and further illuminates the space in which the visualizations lie, through support for interactive clustering and novel design suggestions. We demonstrate these benefits with our software system, where a corpus of two-dimensional hierarchical visualization designs is constructed into a phylogenetic tree. This software system supports visual interactive clustering and suggesting for novel designs; the latter capacity is also demonstrated via collaboration with an artist who sketched new designs using our system

Characters as Groups: A New Approach to Morphological Characters in Phylogenetic Analysis

A new method for working with morphological characters is described and explored in experiments using human participants. The method uses direct comparison and sorting of images to produce hierarchical character-cladograms. A character-cladogram is a graphical representation of a single character that serves as a hypothesis of phylogeny based on that character. Each dichotomy in the character-cladogram represents a character state. Character states are unnamed, thus avoiding problems that arise through the application of verbal labels. Experiments with human participants are used to explore the conditions under which direct comparison produces reliable (consistent from investigator to investigator) and valid (in agreement with an independent estimate of phylogeny) characters. Participants were drawn from students taking a course in plant diversity at UNC Greensboro, and professional plant morphologists attending the Botany 2004 meetings. The students were randomly assigned to trained and untrained groups. Training was carried out using a method that has been shown to change a participant‘s mode of visual processing from analytic (the mode used by visual novices) to holistic (an additional mode only employed by visual experts). Morphologists (no specialists of the taxonomic group) were included in the study to investigate the effects of disciplinary expertise on the ability to describe character-cladograms. They received no additional training beyond that available to them as disciplinary experts. The results suggest an improvement in both reliability and validity after the training regime. We found no support for the idea that the morphologists differed from untrained students in their ability to produce reliable or valid character-cladograms. Disciplinary expertise may not translate into the ability to make reliable and valid assessments of similarity in an unfamiliar visual domain. Based on these results, we suggest a method for creating morphological characters and character states

Comparative plastome genomics and phylogenomics of Brachypodium: flowering time signatures, introgression and recombination in recently diverged ecotypes

Few pan-genomic studies have been conducted in plants, and none of them have focused on the intraspecific diversity and evolution of their plastid genomes. We address this issue in Brachypodium distachyon and its close relatives B. stacei and B. hybridum, for which a large genomic data set has been compiled. We analyze inter- and intraspecific plastid comparative genomics and phylogenomic relationships within a family-wide framework. Major indel differences were detected between Brachypodium plastomes. Within B. distachyon, we detected two main lineages, a mostly Extremely Delayed Flowering (EDF+) clade and a mostly Spanish (S+) – Turkish (T+) clade, plus nine chloroplast capture and two plastid DNA (ptDNA) introgression and micro-recombination events. Early Oligocene (30.9 million yr ago (Ma)) and Late Miocene (10.1 Ma) divergence times were inferred for the respective stem and crown nodes of Brachypodium and a very recent Mid-Pleistocene (0.9 Ma) time for the B. distachyon split. Flowering time variation is a main factor driving rapid intraspecific divergence in B. distachyon, although it is counterbalanced by repeated introgression between previously isolated lineages. Swapping of plastomes between the three different genomic groups, EDF+, T+, S+, probably resulted from random backcrossing followed by stabilization through selection pressure

Genetic and morphological analyses of historic and contemporary populations of western lowland gorilla: a multidisciplinary approach for the conservation of a critically endangered primate

This study investigates the morphology and genetic diversity of the critically endangered sub-species, the western lowland gorilla (Gorilla gorilla gorilla). Regional variation of a historic wild population was assessed morphologically and genetically, and genetic comparisons between this and a contemporary captive population were made to assess the genetic fitness of the contemporary population with the aim of assisting future conservation planning. Geometric morphometric analyses were applied to skulls and mandibles of both sexes in the historic population of gorillas to assess regional variation in relation to size and shape. No significant difference was found for regional size comparisons but shape variation between regions did find significant variation in skull morphology, particularly for males. MtDNA and nuclear markers were employed to detect regional differentiation in the historic population of gorillas, and to compare genetic diversity between historic and contemporary populations. The mtDNA results were hindered by nuclear insertions (numts) yet 30 sequences of the mitochondrial Control Region Hypervariable Region I (HVI) were obtained and haplogroups identified, which revealed potential differences in the historic distribution of haplogroups than current literature reports. Nuclear analysis based on microsatellites confirmed that all the gorillas used in this study were western lowland gorillas. Furthermore, the paternity of individuals in the contemporary population was confirmed. Comparisons between the historical population and the captive US population showed that genetic diversity of the contemporary population had been retained at similar levels to wild populations and the US captive population thus concluding that the contemporary population is genetically sustainable for the foreseeable future

EvoMiner: Frequent Subtree Mining in Phylogenetic Databases

The problem of mining collections of trees to identify common patterns, called frequent subtrees (FSTs), arises often when trying to interpret the results of phylogenetic analysis. FST mining generalizes the well-known maximum agreement subtree problem. Here we present EvoMiner, a new algorithm for mining frequent subtrees in collections of phylogenetic trees. EvoMiner is an Apriori-like level-wise method, which uses a novel phylogeny-specific constant-time candidate generation scheme, an efficient fingerprinting-based technique for downward closure, and a lowest common ancestor based support counting step that requires neither costly subtree operations nor database traversal. Our algorithm achieves speed-ups of up to 100 times or more over Phylominer, the current state-of-the-art algorithm for mining phylogenetic trees. EvoMiner can also work in depth first enumeration mode, to use less memory at the expense of speed. We demonstrate the utility of FST mining as a way to extract meaningful phylogenetic information from collections of trees when compared to maximum agreement subtrees and majority rule trees --- two commonly used approaches in phylogenetic analysis for extracting consensus information from a collection of trees over a common leaf set

Phylogenomic, Biogeographic, and Evolutionary Research Trends in Arachnology

This book focuses on systematics, biogeography, and evolution of arachnids, a group of ancient chelicerate lineages that have taken on terrestrial lifestyles. The book opens with the questions of what arachnology represents, and where the field should go in the future. Twelve original contributions then dissect the current state-of-the-art in arachnological research. These papers provide innovative phylogenomic, evolutionary and biogeographic analyses and interpretations of new data and/or synthesize our knowledge to offer new directions for the future of arachnology

Using phylogenetic trees to generate semantic meaningful edge bundles

Graphs have been successfully applied in a range of problems and applications. It is the object of study of different areas, from modeling and analysis to the construction of visual representations. Different approaches exist for graph visualization, however, most of them suffer from the severe clutter when the number of nodes or edges is large. Amongst the techniques of graph visualization that handle such problem, Edge-bundling techniques attained relative success on improving the quality of the visual representations by bending and aggregating edges in order to reduce overlapping. Despite this success, most of them just perform the bundle based only on the visual space information, that is, there is no explicit connection between the produced bundled visual representation and the data. Some of them look upon edge information as a complement to the visual information, but it is just an additional measure, not their main goal. In this paper, we present a novel edge-bundling technique, called Neighbor Joining Bundling (NJB), for graph visualization that tackles this problem by considering the similarity between the nodes when performing the edges bending.FAPESP (#2014/18665-1 and #2011/22749-8)CapesCNP