Adventures in Invariant Theory

We provide an introduction to enumerating and constructing invariants of group representations via character methods. The problem is contextualised via two case studies arising from our recent work: entanglement measures, for characterising the structure of state spaces for composite quantum systems; and Markov invariants, a robust alternative to parameter-estimation intensive methods of statistical inference in molecular phylogenetics.Comment: 12 pp, includes supplementary discussion of example

Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis

The multi-species coalescent provides an elegant theoretical framework for estimating species trees and species demographics from genetic markers. Practical applications of the multi-species coalescent model are, however, limited by the need to integrate or sample over all gene trees possible for each genetic marker. Here we describe a polynomial-time algorithm that computes the likelihood of a species tree directly from the markers under a finite-sites model of mutation, effectively integrating over all possible gene trees. The method applies to independent (unlinked) biallelic markers such as well-spaced single nucleotide polymorphisms (SNPs), and we have implemented it in SNAPP, a Markov chain Monte-Carlo sampler for inferring species trees, divergence dates, and population sizes. We report results from simulation experiments and from an analysis of 1997 amplified fragment length polymorphism (AFLP) loci in 69 individuals sampled from six species of {\em Ourisia} (New Zealand native foxglove)

Introgressive Hybridization and the Evolution of Lake-Adapted Catostomid Fishes.

Hybridization has been identified as a significant factor in the evolution of plants as groups of interbreeding species retain their phenotypic integrity despite gene exchange among forms. Recent studies have identified similar interactions in animals; however, the role of hybridization in the evolution of animals has been contested. Here we examine patterns of gene flow among four species of catostomid fishes from the Klamath and Rogue rivers using molecular and morphological traits. Catostomus rimiculus from the Rogue and Klamath basins represent a monophyletic group for nuclear and morphological traits; however, the Klamath form shares mtDNA lineages with other Klamath Basin species (C. snyderi, Chasmistes brevirostris, Deltistes luxatus). Within other Klamath Basin taxa, D. luxatus was largely fixed for alternate nuclear alleles relative to C. rimiculus, while Ch. brevirostris and C. snyderi exhibited a mixture of these alleles. Deltistes luxatus was the only Klamath Basin species that exhibited consistent covariation of nuclear and mitochondrial traits and was the primary source of mismatched mtDNA in Ch. brevirostris and C. snyderi, suggesting asymmetrical introgression into the latter species. In Upper Klamath Lake, D. luxatus spawning was more likely to overlap spatially and temporally with C. snyderi and Ch. brevirostris than either of those two with each other. The latter two species could not be distinguished with any molecular markers but were morphologically diagnosable in Upper Klamath Lake, where they were largely spatially and temporally segregated during spawning. We examine parallel evolution and syngameon hypotheses and conclude that observed patterns are most easily explained by introgressive hybridization among Klamath Basin catostomids

WordSup: Exploiting Word Annotations for Character based Text Detection

Imagery texts are usually organized as a hierarchy of several visual elements, i.e. characters, words, text lines and text blocks. Among these elements, character is the most basic one for various languages such as Western, Chinese, Japanese, mathematical expression and etc. It is natural and convenient to construct a common text detection engine based on character detectors. However, training character detectors requires a vast of location annotated characters, which are expensive to obtain. Actually, the existing real text datasets are mostly annotated in word or line level. To remedy this dilemma, we propose a weakly supervised framework that can utilize word annotations, either in tight quadrangles or the more loose bounding boxes, for character detector training. When applied in scene text detection, we are thus able to train a robust character detector by exploiting word annotations in the rich large-scale real scene text datasets, e.g. ICDAR15 and COCO-text. The character detector acts as a key role in the pipeline of our text detection engine. It achieves the state-of-the-art performance on several challenging scene text detection benchmarks. We also demonstrate the flexibility of our pipeline by various scenarios, including deformed text detection and math expression recognition.Comment: 2017 International Conference on Computer Visio

Landscape History and Theory: from Subject Matter to Analytic Tool

This essay explores how landscape history can engage methodologically with the adjacent disciplines of art history and visual/cultural studies. Central to the methodological problem is the mapping of the beholder � spatially, temporally and phenomenologically. In this mapping process, landscape history is transformed from subject matter to analytical tool. As a result, landscape history no longer simply imports and applies ideas from other disciplines but develops its own methodologies to engage and influence them. Landscape history, like art history, thereby takes on a creative cultural presence. Through that process, landscape architecture and garden design regain the cultural power now carried by the arts and museum studies, and has an effect on the innovative capabilities of contemporary landscape design

Phylogeny and biogeography of Croton alabamensis (Euphorbiaceae), a rare shrub from Texas and Alabama, using DNA sequence and AFLP data

Croton alabamensis (Euphorbiaceae s.s. ) is a rare plant species known from several populations in Texas and Alabama that have been assigned to var. texensis and var. alabamensis , respectively. We performed maximum parsimony, maximum likelihood, and Bayesian analyses of DNA sequences from the nuclear ribosomal internal transcribed spacer (ITS) and 5.8S regions and chloroplast trn L- trn F regions from collections of the two varieties of C. alabamensis and from outgroup taxa. C. alabamensis emerges alone on a long branch that is sister to Croton section Corylocroton and the Cuban endemic genus Moacroton . Molecular clock analysis estimates the split of C. alabamensis from its closest relatives in sect. Corylocroton at 41 million years ago, whereas the split of the two varieties of C. alabamensis occurred sometime in the Quaternary. Amplified fragment length polymorphism (AFLP) analyses were performed using two selective primer pairs on a larger sampling of accessions (22 from Texas, 17 from Alabama) to further discriminate phylogenetic structure and quantify genetic diversity. Using both neighbour joining and minimum evolution, the populations from the Cahaba and Black Warrior watersheds in Alabama form two well-separated groups, and in Texas, geographically distinct populations are recovered from Fort Hood, Balcones Canyonlands, and Pace Bend Park. Most of the molecular variance is accounted for by variance within populations. Approximately equal variance is found among populations within states and between states (varieties). Genetic distance between the Texas populations is significantly less than genetic distance between the Alabama populations. Both sequence and AFLP data support the same relationships between the varieties of C. alabamensis and their outgroup, while the AFLP data provide better resolution among the different geographical regions where C. alabamensis occurs. The conservation implications of these findings are discussed.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72311/1/j.1365-294X.2006.02970.x.pd

Phylogeny, biogeography and diversification patterns of side-necked turtles (Testudines: Pleurodira)

Pleurodires or side-necked turtles are today restricted to freshwater environments of South America, Africa– Madagascar and Australia, but in the past they were distributed much more broadly, being found also on Eurasia, India and North America, and marine environments. Two hypotheses were proposed to explain this distribution; in the first, vicariance would have shaped the current geographical distribution and, in the second, extinctions constrained a previously widespread distribution. Here, we aim to reconstruct pleurodiran biogeographic history and diversification patterns based on a new phylogenetic hypothesis recovered from the analysis of the largest morphological dataset yet compiled for the lineage, testing which biogeographical process prevailed during its evolutionary history. The resulting topology generally agrees with previous hypotheses of the group and shows that most diversification shifts were related to the exploration of new niches, e.g. littoral or marine radiations. In addition, as other turtles, pleurodires do not seem to have been much affected by either the Cretaceous– Palaeogene or the Eocene–Oligocene mass extinctions. The biogeographic analyses highlight the predominance of both anagenetic and cladogenetic dispersal events and support the importance of transoceanic dispersals as a more common driver of area changes than previously thought, agreeing with previous studies with other non-turtle lineages.Fil: Ferreira, Gabriel S.. Universidade de Sao Paulo; Brasil. Senckenberg Centre For Human Evolution And Palaeoenvironment; Alemania. Universität Tübingen; AlemaniaFil: Bronzati Filho, Mario. Bayerische Staatssammlung für Paläontologie und Geologie; AlemaniaFil: Langer, Max C.. Universidade de Sao Paulo; BrasilFil: Sterli, Juliana. Museo Paleontológico Egidio Feruglio; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Coalescent-based genome analyses resolve the early branches of the euarchontoglires

Despite numerous large-scale phylogenomic studies, certain parts of the mammalian tree are extraordinarily difficult to resolve. We used the coding regions from 19 completely sequenced genomes to study the relationships within the super-clade Euarchontoglires (Primates, Rodentia, Lagomorpha, Dermoptera and Scandentia) because the placement of Scandentia within this clade is controversial. The difficulty in resolving this issue is due to the short time spans between the early divergences of Euarchontoglires, which may cause incongruent gene trees. The conflict in the data can be depicted by network analyses and the contentious relationships are best reconstructed by coalescent-based analyses. This method is expected to be superior to analyses of concatenated data in reconstructing a species tree from numerous gene trees. The total concatenated dataset used to study the relationships in this group comprises 5,875 protein-coding genes (9,799,170 nucleotides) from all orders except Dermoptera (flying lemurs). Reconstruction of the species tree from 1,006 gene trees using coalescent models placed Scandentia as sister group to the primates, which is in agreement with maximum likelihood analyses of concatenated nucleotide sequence data. Additionally, both analytical approaches favoured the Tarsier to be sister taxon to Anthropoidea, thus belonging to the Haplorrhine clade. When divergence times are short such as in radiations over periods of a few million years, even genome scale analyses struggle to resolve phylogenetic relationships. On these short branches processes such as incomplete lineage sorting and possibly hybridization occur and make it preferable to base phylogenomic analyses on coalescent methods