Article
Biochemical Research Methods
Merce Llabres, Francesc Rossello, Gabriel Valiente
Summary: The Generalized Robinson-Foulds (GRF) distance is a metric for comparing structures with high resolution and can be computed in linear time, distinct from the RF distance.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2021)
Article
Microbiology
Min Wang, Cong-Jian Li, Zhen Zhang, Pan-Pan Li, Ling-Ling Yang, Xiao-Yang Zhi
Summary: This study evaluated the distribution of development-related genes in Streptomyces genomes and found that most of these genes were ubiquitous. Furthermore, the congruence between development-related genes and the species tree of Streptomyces was higher compared to other strict orthologous genes. These results suggest that morphological development follows the same pattern as species divergence.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Ecology
Yan Wong, James Rosindell
Summary: The text discusses the availability of the complete tree of life and the need for methods to visualize it for research and teaching. They have developed an effective visualization engine through automated data processing and dynamic population of metadata. Additionally, it mentions some achievements of the project and future challenges to be addressed.
METHODS IN ECOLOGY AND EVOLUTION
(2022)
Proceedings Paper
Computer Science, Hardware & Architecture
Alvin Chon, Pawel Gorecki, Oliver Eulenstein, Xiaoqiu Huang, Ali Jannesari
Summary: This paper presents a method called BFHRF for computing the average RF between different binary evolutionary tree collections. BFHRF is faster and uses less memory compared to existing methods. It can also be modified to accommodate different RF variants and variable taxa in the tree collection, and provides an easy-to-use installation and interface.
2022 IEEE 36TH INTERNATIONAL PARALLEL AND DISTRIBUTED PROCESSING SYMPOSIUM WORKSHOPS (IPDPSW 2022)
(2022)
Article
Plant Sciences
David A. Rasmussen, Niklaus J. Grunwald
Summary: Phylogeography combines geographic information with phylogenetic and population genomic approaches to infer the evolutionary history of a species or population in a geographic context. It is particularly useful for understanding the emergence, spread, and evolution of plant pathogens. Phylogeography can provide insights into questions about the origin, native status, and frequency of introductions of pathogens.
Article
Biochemical Research Methods
Kaari Landry, Aivee Teodocio, Manuel Lafond, Olivier Tremblay-Savard
Summary: In phylogenetic networks, cherry-picking operations have been shown to have structural and algorithmic applications. They can be used to determine reconstructibility, solve network hybridization and network containment problems, and measure similarity between networks. This paper introduces four novel distances on networks based on cherry picking and their reverse operation, providing new comparative measures for phylogenetic trees. While computing these distances is NP-hard, they can be efficiently computed in quadratic time on two trees.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Biology
Robert J. Driver, Susan B. McRae
Summary: The Hardy-Weinberg principle is crucial in population genetics, shedding light on the preservation of variation during evolution and the impact of natural and sexual selection on traits. It is a fundamental topic in introductory biology courses in the United States, where students need sufficient time to grasp the foundations of population genetics with clear information presented to ensure accurate understanding. Misconceptions regarding the HWP are common and pose a risk to students' comprehension, as highlighted through examples from university and AP-level standardized tests.
AMERICAN BIOLOGY TEACHER
(2021)
Article
Biology
Joan Carles Pons, Charles Semple, Mike Steel
JOURNAL OF MATHEMATICAL BIOLOGY
(2019)
Article
Biology
Lina Herbst, Heyang Li, Mike Steel
JOURNAL OF MATHEMATICAL BIOLOGY
(2019)
Article
Multidisciplinary Sciences
Mike Steel, Wim Hordijk, Joana C. Xavier
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2019)
Article
Evolutionary Biology
Tanja Stadler, Mike Steel
SYSTEMATIC BIOLOGY
(2019)
Editorial Material
Ecology
Mike Steel
THEORETICAL POPULATION BIOLOGY
(2020)
Article
Biology
Kristina Wicke, Mike Steel
JOURNAL OF MATHEMATICAL BIOLOGY
(2020)
Article
Biology
Mike Steel, Wim Hordijk, Stuart A. Kauffman
JOURNAL OF THEORETICAL BIOLOGY
(2020)
Article
Biology
Oliver Weller-Davies, Mike Steel, Jotun Hein
MATHEMATICAL BIOSCIENCES
(2020)
Article
Multidisciplinary Sciences
Mike Steel, Joana C. Xavier, Daniel H. Huson
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2020)
Article
Biology
Allan Bai, Peter L. Erdos, Charles Semple, Mike Steel
Summary: Rooted phylogenetic networks provide a more comprehensive representation of ancestral relationships, especially in instances of reticulate evolutionary processes. Unique determinations within the class of orchard networks are only maintained when an additional stack-free restriction is in place. However, if this restriction is lifted, uniqueness within orchard networks is subject to high in-degree vertex resolutions.
MATHEMATICAL BIOSCIENCES
(2021)
Article
Biology
Wim Hordijk, Mike Steel, Stuart Kauffman
Summary: The study investigates the emergence of autocatalytic sets in chemical evolution theory, providing theoretical results and comparing them with computer simulations. This research may offer insights into possible pathways towards the origin of life.
Article
Biology
Andrew Francis, Mike Steel
Summary: In this paper, a new class of phylogenetic networks called "labellable" is defined, which are in bijection with the set of "expanding covers" of finite sets. This generalizes the encoding method of phylogenetic forests by partitions of finite sets. Labellable networks can be characterized by a simple combinatorial condition, and their relationship with other commonly studied classes is described. Furthermore, it is shown that all phylogenetic networks have a quotient network that is labellable.
BULLETIN OF MATHEMATICAL BIOLOGY
(2023)
Article
Mathematical & Computational Biology
Mike Steel
Summary: The emergence of an autocatalytic network from a set of available elements is crucial in early evolutionary processes. By studying the reactions between elements and their catalytic effects, we can identify and classify autocatalytic sets. Although this process may be more complex in large systems, some generic results regarding autocatalytic sets have been obtained.
ACTA BIOTHEORETICA
(2023)
Article
Biology
Marcus Overwater, Daniel Pelletier, Mike Steel
Summary: The rapid extinction of species not only leads to their loss, but also results in the disappearance of their unique features. By studying the relationship between phylogenetic diversity and feature diversity, we found that the impact of extinction events on feature diversity is different from that on phylogenetic diversity.
JOURNAL OF MATHEMATICAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Liane Gabora, Mike Steel
Summary: Natural selection explains adaptive change in organisms, but certain domains like cultural evolution and early life retain acquired traits. The lack of transmission of acquired traits is due to the use of a self-assembly code in germ cells. Cumulative, adaptive change in these domains is attributed to a lower-fidelity evolutionary process known as self-other reorganization (SOR).
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2021)