Evolutionary distances in the twilight zone -- a rational kernel approach

Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly. Alignment-free methods, on the other hand, are based on abstract string comparisons and avoid potential alignment problems. However, in general they are not biologically motivated and ignore our knowledge about the evolution of sequences. Thus, it is still a major open question how to define an evolutionary distance metric between divergent sequences that makes use of indel information and known substitution models without the need for a multiple alignment. Here we propose a new evolutionary distance metric to close this gap. It uses finite-state transducers to create a biologically motivated similarity score which models substitutions and indels, and does not depend on a multiple sequence alignment. The sequence similarity score is defined in analogy to pairwise alignments and additionally has the positive semi-definite property. We describe its derivation and show in simulation studies and real-world examples that it is more accurate in reconstructing phylogenies than competing methods. The result is a new and accurate way of determining evolutionary distances in and beyond the twilight zone of sequence alignments that is suitable for large datasets.Comment: to appear in PLoS ON

Two Refinements of the Template-Guided DNA Recombination Model of Ciliate Computing

To solve the mystery of the intricate gene unscrambling mechanism in ciliates, various theoretical models for this process have been proposed from the point of view of computation. Two main models are the reversible guided recombination system by Kari and Landweber and the template-guided recombination (TGR) system by Prescott, Ehrenfeucht and Rozenberg, based on two categories of DNA recombination: the pointer guided and the template directed recombination respectively. The latter model has been generalized by Daley and McQuillan. In this thesis, we propose a new approach to generate regular languages using the iterated TGR system with a finite initial language and a finite set of templates, that reduces the size of the template language and the alphabet compared to that of the Daley-McQuillan model. To achieve computational completeness using only finite components we also propose an extension of the contextual template-guided recombination system (CTGR system) by Daley and McQuillan, by adding an extra control called permitting contexts on the usage of templates. Then we prove that our proposed system, the CTGR system using permitting contexts, has the capability to characterize the family of recursively enumerable languages using a finite initial language and a finite set of templates. Lastly, we present a comparison and analysis of the computational power of the reversible guided recombination system and the TGR system. Keywords: ciliates, gene unscrambling, in vivo computing, DNA computing, cellular computing, reversible guided recombination, template-guided recombination

Law of Genome Evolution Direction : Coding Information Quantity Grows

The problem of the directionality of genome evolution is studied. Based on the analysis of C-value paradox and the evolution of genome size we propose that the function-coding information quantity of a genome always grows in the course of evolution through sequence duplication, expansion of code, and gene transfer from outside. The function-coding information quantity of a genome consists of two parts, p-coding information quantity which encodes functional protein and n-coding information quantity which encodes other functional elements except amino acid sequence. The evidences on the evolutionary law about the function-coding information quantity are listed. The needs of function is the motive force for the expansion of coding information quantity and the information quantity expansion is the way to make functional innovation and extension for a species. So, the increase of coding information quantity of a genome is a measure of the acquired new function and it determines the directionality of genome evolution.Comment: 16 page

Meiofauna Biodiversity and Ecology

Meiofauna are small organisms ranging 30–500 μm in body size, inhabiting marine sediments and other substrata all over the world, even the most extreme ones. We can find many different meiofaunal species in a very small handful of sediment, with the most varied and curious shapes, that share peculiar lifestyles, ecological relationships, and evolutionary traits. They contribute significantly to the processes and functioning of marine ecosystems, thanks to their high abundance and taxonomical diversity, fast turnover and metabolic rates. Some meiofaunal taxa have also revealed their considerable utility in the evaluation of the ecological quality of coastal marine sediments in accordance with European Directives. Therefore, understanding the distribution patterns of their biodiversity and identifying the factors that control it at a global level and in different types of habitats is of great importance. Due to their very small morphological characteristics utilized for the taxonomical identification of these taxa, the suite of necessary skills in taxonomy, and the general taxonomic crisis, many young scientists have been discouraged to tackle meiofauna systematics. The papers collected in this book, however, bring together important themes on the biology, taxonomy, systematics, and ecology of meiofauna, thanks to the contribution of researchers from around the world from the USA, Brazil, Costa Rica, Mexico, Cuba, Italy, Belgium, France, Denmark, Russia, Kuwait, Vietnam, and South Korea. This was certainly an additional opportunity to build a more solid network among experts in this field and contribute to increasing the visibility of these tiny organisms. A special thanks to Prof. Wonchoel Lee for the wonderful taxonomic drawings of the species described in this volume that contribute to make our cover unique

Meiofauna Biodiversity and Ecology

Sedimentary habitats cover the vast majority of the ocean floor and constitute the largest ecosystem on Earth. These systems supply fundamental services to human beings, such as food production and nutrient recycling. It is well known that meiofauna are an abundant and ubiquitous component of sediments, even though their biodiversity and importance in marine ecosystem functioning remain to be fully investigated. In this book, the meiofaunal biodiversity trends in marine habitats worldwide are documented, along with the collection of empirical evidence on their role in ecosystem services, such as the production, consumption, and decomposition of organic matter, and energy transfer to higher and lower trophic levels. Meiofaunal activities, like feeding and bioturbation, induce changes in several physico-chemical and biological properties of sediments, and might increase the resilience of the benthic ecosystem processes that are essential for the supply of ecosystem goods and services required by humans. As a key component of marine habitats, the taxonomical and functional aspects of the meiofaunal community are also used for the ecological assessment of the sediments’ quality status, providing important information on the anthropogenic impact of benthos

Summer Research Fellowship Project Descriptions 2022

A summary of research done by Smith College’s 2021 Summer Research Fellowship (SURF) Program participants. Ever since its 1967 start, SURF has been a cornerstone of Smith’s science education. Supervised by faculty mentor-advisors drawn from the Clark Science Center and connected to its eighteen science, mathematics, and engineering departments and programs and associated centers and units. At summer’s end, SURF participants were asked to summarize their research experiences for this publication.https://scholarworks.smith.edu/clark_womeninscience/1012/thumbnail.jp

Particle Computation: Complexity, Algorithms, and Logic

We investigate algorithmic control of a large swarm of mobile particles (such as robots, sensors, or building material) that move in a 2D workspace using a global input signal (such as gravity or a magnetic field). We show that a maze of obstacles to the environment can be used to create complex systems. We provide a wide range of results for a wide range of questions. These can be subdivided into external algorithmic problems, in which particle configurations serve as input for computations that are performed elsewhere, and internal logic problems, in which the particle configurations themselves are used for carrying out computations. For external algorithms, we give both negative and positive results. If we are given a set of stationary obstacles, we prove that it is NP-hard to decide whether a given initial configuration of unit-sized particles can be transformed into a desired target configuration. Moreover, we show that finding a control sequence of minimum length is PSPACE-complete. We also work on the inverse problem, providing constructive algorithms to design workspaces that efficiently implement arbitrary permutations between different configurations. For internal logic, we investigate how arbitrary computations can be implemented. We demonstrate how to encode dual-rail logic to build a universal logic gate that concurrently evaluates and, nand, nor, and or operations. Using many of these gates and appropriate interconnects, we can evaluate any logical expression. However, we establish that simulating the full range of complex interactions present in arbitrary digital circuits encounters a fundamental difficulty: a fan-out gate cannot be generated. We resolve this missing component with the help of 2x1 particles, which can create fan-out gates that produce multiple copies of the inputs. Using these gates we provide rules for replicating arbitrary digital circuits.Comment: 27 pages, 19 figures, full version that combines three previous conference article