Article
Multidisciplinary Sciences
Brandon Legried, Jonathan Terhorst
Summary: Louca and Pennell recently demonstrated that a large class of phylogenetic birth-death models is statistically unidentifiable from lineage-through-time (LTT) data, while an alternative and widely used class of birth-death models is indeed identifiable. They further show that any unidentifiable birth-death model class can be arbitrarily closely approximated by a class of identifiable models, with specific sampling requirements that are expected to be met in many contexts such as the phylodynamic analysis of a global pandemic.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Leo A. Featherstone, Sebastian Duchene, Timothy G. Vaughan
Summary: Despite its increasing role in understanding infectious disease transmission, phylodynamics lacks clarity on ideal data and optimal sampling. This study introduces a method to visualize and quantify the impact of pathogen genome sequence and sampling times on phylodynamic inference. By applying the method to simulated and real-world data, the study provides insights and guidelines for maximizing the use of sequence data in phylodynamic analyses. The continued research on phylodynamic data and inference is crucial for targeted and efficient responses to infectious disease threats.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biology
Brandon Legried, Jonathan Terhorst
Summary: Recent theoretical work reveals differing perspectives on the estimation of phylogenetic birth-death models with lineage-through-time data. While Louca and Pennell (2020) argue that models with continuously differentiable rate functions are nonidentifiable, Legried and Terhorst (2022) show that identifiability can be restored by considering piecewise constant rate functions. In this study, we contribute new theoretical results to this ongoing discussion. We prove that models based on piecewise polynomial rate functions, regardless of the order or number of pieces, are statistically identifiable, including spline-based models with arbitrary knots. However, we also highlight the challenge of rate function estimation, even when identifiability is achieved, by presenting information-theoretic lower bounds for hypothesis testing using birth-death models.
JOURNAL OF THEORETICAL BIOLOGY
(2023)
Article
Ecology
Andrew J. Helmstetter, Rosana Zenil-Ferguson, Herve Sauquet, Sarah P. Otto, Marcos Mendez, Mario Vallejo-Marin, Juerg Schoenenberger, Concetta Burgarella, Bruce Anderson, Hugo de Boer, Sylvain Glemin, Jos Kafer
Summary: This study synthesized data from 152 studies on angiosperm clades using state-dependent speciation and extinction models, and found that intrinsic traits related to reproduction and morphology are often linked to species diversification. However, a set of universal drivers did not emerge as these traits had inconsistent effects across clades. Additionally, the study found that data set properties such as tree size, age, and sampling quality were correlated to SSE model results, and provided best practices for study design and reporting.
Article
Virology
Jeremie Scire, Joelle Barido-Sottani, Denise Kuehnert, Timothy G. Vaughan, Tanja Stadler
Summary: The multi-type birth-death model with sampling is an evolution dynamic model that quantifies past population dynamics in structured populations based on phylogenetic trees, implemented using the bdmm package. Important algorithmic changes to bdmm allows for the analysis of more genetic samples, improving numerical robustness and efficiency, leading to increased precision of parameter estimates, particularly for structured models with a high number of inferred parameters.
Article
Multidisciplinary Sciences
Michael J. Landis, Ignacio Quintero, Martha M. Munoz, Felipe Zapata, Michael J. Donoghue
Summary: Geographical features have an impact on species dispersal, extinction, and speciation. This study uses a Bayesian hierarchical modeling framework to transform regional features into evolutionary rates. The results show that distance between regions affects dispersal rates and speciation rates.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Evolutionary Biology
Ailene MacPherson, Stilianos Louca, Angela McLaughlin, Jeffrey B. Joy, Matthew W. Pennell
Summary: Birth-death stochastic processes are fundamental to many phylogenetic models, but there are various model variants that are difficult to understand and derive. This paper unifies these models into a single framework, showing their relationships and providing a straightforward procedure for deriving likelihood functions for complex models.
SYSTEMATIC BIOLOGY
(2022)
Article
Biology
Sophie Seidel, Tanja Stadler
Summary: This study proposes a phylodynamic inference approach based on single-cell lineage recorder data to estimate time-scaled single-cell trees and cell population dynamics. The performance and comparability of the method are validated and benchmarked against state-of-the-art methods. The practical application of TiDeTree is demonstrated using a public dataset.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Oncology
Antonia Chroni, Sayaka Miura, Lauren Hamilton, Tracy Vu, Stephen G. Gaffney, Vivian Aly, Sajjad Karim, Maxwell Sanderford, Jeffrey P. Townsend, Sudhir Kumar
Summary: By analyzing the genetic heterogeneity of tumors in cancer patients, we found that the migration histories of metastasis are often best described by a hybrid model of metastatic tumor evolution. We discovered that new tumor seedings arise from clones of pre-existing metastases as frequently as they do from clones from primary tumors. Additionally, there were many clone exchanges between the source and recipient tumors.
Article
Virology
Anthony Lam, Sebastian Duchene
Summary: Phylodynamic inference is crucial in understanding the transmission dynamics of viral outbreaks, with estimating the molecular evolutionary rate being an essential first step. The birth-death model outperforms the coalescent exponential model in estimating epidemiological parameters when faced with low diversity sequence data, while the coalescent model requires additional samples and sequence variability for accurate estimates. This was supported by empirical data analyses of SARS-CoV-2 outbreaks in Australia and New Zealand, emphasizing the importance of considering the birth-death model for future viral outbreak investigations with low sequence diversity.
Article
Biochemistry & Molecular Biology
Sudip Sharma, Sudhir Kumar
Summary: The study discovers that using subsample-upsample approach can significantly reduce the computational costs in analyzing long sequence alignments in molecular evolution, while still recovering the correct optimal substitution model. An adaptive protocol called ModelTamer is proposed, which can select the optimal models in much shorter time and with much less memory usage.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Stilianos Louca, Angela McLaughlin, Ailene MacPherson, Jeffrey B. Joy, Matthew W. Pennell
Summary: Viral phylogenies are crucial for understanding infectious disease spread, but extracting information from them is complex due to uncertainties and sampling issues. Current methods may not reliably reconstruct the true epidemiological dynamics, requiring further research and strategies.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Evolutionary Biology
Michael R. May, Carl J. Rothfels
Summary: Time-calibrated phylogenetic trees are important for studying evolutionary, ecological, and epidemiological phenomena, but comparing different tree models has been problematic. By treating the tree parameter as a parameter and ignoring the data component, the ability to accurately compare tree models is compromised, which has broad implications for applications based on time-calibrated trees. Potential remedies and guidance for assessing tree model fit are provided.
SYSTEMATIC BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Valentin Rineau, Jan Smycka, David Storch
Summary: Biodiversity on Earth is influenced by abiotic perturbations and rapid diversifications, as well as biotic interactions. Analysis of the fossil record reveals that diversity has a universal impact on origination and extinction rates, although the precise mechanisms are complex. The global regulation of diversity through negative diversity dependence seems to be a common feature in the biosphere, with significant implications for understanding the current biodiversity crisis.
Article
Neurosciences
Thomas Maullin-Sapey, Thomas E. Nichols
Summary: Large-scale, shared datasets in neuroimaging pose challenges to existing tools in terms of scale and complexity. To address these challenges, researchers have developed the BLMM toolbox, an efficient tool for large-scale fMRI linear mixed models analysis.
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
Evolutionary Biology
Huw A. Ogilvie, Fabio K. Mendes, Timothy G. Vaughan, Nicholas J. Matzke, Tanja Stadler, David Welch, Alexei J. Drummond
Summary: Evolutionary models usually focus on either population-level or species-level processes, but not both. In this study, a new model called FBD-MSC is introduced, which integrates genealogical and fossilization phenomena using the multispecies coalescent (MSC) and fossilized birth-death (FBD) processes. This model allows for the reconstruction of phylogenies and estimation of speciation event times. The study also addresses known issues with divergence time estimates and proposes a solution using the FBD-MSC model. The new integrative method and empirical results have important implications for probabilistic total evidence analyses in evolutionary biology.
SYSTEMATIC BIOLOGY
(2022)
Review
Ecology
Claire Guinat, Timothee Vergne, Arthur Kocher, Debapryio Chakraborty, Mathilde C. Paul, Mariette Ducatez, Tanja Stadler
Summary: Infectious diseases pose a major burden on global economies, public health, and animal health. Phylodynamic techniques, which infer pathogen transmission dynamics from genetic data, have shown promise in enhancing disease management and informing more effective control strategies. These techniques can address fundamental epidemiological questions and quantify spillover events at the wildlife-livestock interface.
TRENDS IN ECOLOGY & EVOLUTION
(2021)
Article
Infectious Diseases
Julija Pecerska, Denise Kuehnert, Conor J. Meehan, Mireia Coscolla, Bouke C. de Jong, Sebastien Gagneux, Tanja Stadler
Summary: The study introduces a method for phylodynamic analysis of Mycobacterium tuberculosis, showing that drug-resistant strains incur a transmission fitness cost. The estimates are robust to different prior distributions on resistance acquisition rate, but are affected by dataset size.
Article
Biochemical Research Methods
Chaoran Chen, Sarah Nadeau, Michael Yared, Philippe Voinov, Ning Xie, Cornelius Roemer, Tanja Stadler
Summary: The CoV-Spectrum website provides support for identifying and tracking new SARS-CoV-2 variants, with flexible mutation search capabilities and analysis on various data sources to understand characteristics and transmission of different variants.
Article
Biochemistry & Molecular Biology
Ugne Stolz, Tanja Stadler, Nicola F. Mueller, Timothy G. Vaughan
Summary: The study introduces an extended structured coalescent method to investigate migration patterns between viral subpopulations, particularly for segmented viruses that can undergo reassortment. Through simulated data analysis, this method can accurately estimate subpopulation dependent effective population sizes, reassortment, and migration rates. Additionally, analyses of avian influenza A/H5N1 sequences show that accounting for segment reassortment and using sequencing data from multiple viral segments for joint phylodynamic inference leads to different estimates.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Infectious Diseases
Chaoran Chen, Sarah Ann Nadeau, Ivan Topolsky, Marc Manceau, Jana S. Huisman, Kim Philipp Jablonski, Lara Fuhrmann, David Dreifuss, Katharina Jahn, Christiane Beckmann, Maurice Redondo, Christoph Noppen, Lorenz Risch, Martin Risch, Nadia Wohlwend, Sinem Kas, Thomas Bodmer, Tim Roloff, Madlen Stange, Adrian Egli, Isabella Eckerle, Laurent Kaiser, Rebecca Denes, Mirjam Feldkamp, Ina Nissen, Natascha Santacroce, Elodie Burcklen, Catharine Aquino, Andreia Cabral de Gouvea, Maria Domenica Moccia, Simon Grueter, Timothy Sykes, Lennart Opitz, Griffin White, Laura Neff, Doris Popovic, Andrea Patrignani, Jay Tracy, Ralph Schlapbach, Emmanouil T. Dermitzakis, Keith Harshman, Ioannis Xenarios, Henri Pegeot, Lorenzo Cerutti, Deborah Penet, Anthony Blin, Melyssa Elies, Christian L. Althaus, Christian Beisel, Niko Beerenwinkel, Martin Ackermann, Tanja Stadler
Summary: The study estimated that the B.1.1.7 variant had a transmission fitness advantage of about 43-52% in Switzerland, and showed a reproductive number above 1 from January 2021 until the end of the study period. Switzerland implemented more non-pharmaceutical interventions on January 18, 2021 and lifted some measures on March 1, 2021.
Article
Microbiology
Jelissa Katharina Peter, Fanny Wegner, Severin Gsponer, Fabrice Helfenstein, Tim Roloff, Rahel Tarnutzer, Kerstin Grosheintz, Moritz Back, Carla Schaubhut, Sabina Wagner, Helena M. B. Seth-Smith, Patrick Scotton, Maurice Redondo, Christiane Beckmann, Tanja Stadler, Andrea Salzmann, Henriette Kurth, Karoline Leuzinger, Stefano Bassetti, Roland Bingisser, Martin Siegemund, Maja Weisser, Manuel Battegay, Sarah Tschudin Sutter, Aitana Lebrand, Hans H. Hirsch, Simon Fuchs, Adrian Egli
Summary: Breakthrough infections in fully vaccinated individuals are rare and mild, but can occur early post-vaccination. Lower risk factors include age and previous COVID-19 infection, while higher risk factors include vaccination with Pfizer/BioNTech, chronic disease, and being a healthcare worker. Continuous monitoring of breakthrough infections is crucial due to emerging new variants.
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
Virology
Evelyn Kuhlmeier, Tatjana Chan, Cecilia Valenzuela Agui, Barbara Willi, Aline Wolfensberger, Christian Beisel, Ivan Topolsky, Niko Beerenwinkel, Tanja Stadler, Sarah Jones, Grace Tyson, Margaret J. Hosie, Katja Reitt, Julia Huttl, Marina L. Meli, Regina Hofmann-Lehmann
Summary: This study aims to investigate SARS-CoV-2 infections in companion animals in close contact with COVID-19-positive owners, with a focus on the Delta variant. The results show that 11 cats and 3 dogs in 9 COVID-19-positive households tested positive for the SARS-CoV-2 Delta variant. NGS data identified SNPs in the viral sequences of companion animals that occur at a higher frequency than in viral sequences of humans, as well as SNPs exclusively found in the animals investigated in this study.
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)
Article
Ecology
Fabienne Benz, Jana S. Huisman, Erik Bakkeren, Joana A. Herter, Tanja Stadler, Martin Ackermann, Mederic Diard, Adrian Egli, Alex R. Hall, Wolf-Dietrich Hardt, Sebastian Bonhoeffer
Summary: This study found that clinical Escherichia coli strains associated with ESBL-producing plasmids could conjugate with other E. coli and Salmonella strains in the absence of antibiotics, with transconjugant frequencies influenced by plasmid properties, donor and recipient strains, as well as the presence of transfer genes on ESBL-plasmids and plasmid incompatibility. The results suggest that plasmid spread in the complex gut environment of animals and humans can be predicted based on in vitro testing and genetic data.