Article
Biochemistry & Molecular Biology
Xavier Didelot, Igor Siveroni, Erik M. Volz
Summary: Phylogenetic dating is a powerful method for drawing epidemiological interpretations from pathogen genomic data. However, commonly used relaxed clock models may not be compatible with biological expectations, leading to estimates with low precision and biased confidence intervals. A new additive relaxed clock model has been proposed to address this issue, providing more accurate estimates of evolutionary rates and ancestral dates.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Zoology
Corentin Jouault, Arthur Marechal, Fabien L. Condamine, Bo Wang, Andre Nel, Frederic Legendre, Vincent Perrichot
Summary: A new phylogeny of the superfamily Evanioidea is proposed using a fossilized birth-death model, estimating divergence times and proving the monophyly of Evanioidea. Additionally, three new othniodellithid wasps are described in this study.
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2022)
Article
Biochemical Research Methods
Yasamin Tabatabaee, Kowshika Sarker, Tandy Warnow
Summary: This article presents Quintet Rooting (QR), a method for rooting species trees based on a proof of identifiability of the rooted species tree under the multi-species coalescent model. The method is shown to be generally more accurate than other rooting methods, except under extreme levels of gene tree estimation error.
Article
Multidisciplinary Sciences
Nathan A. Jud, Sarah E. Allen, Chris W. Nelson, Carolina L. Bastos, Joyce G. Chery
Summary: This study describes anatomically preserved fossils of Paullinieae for the first time and re-evaluates other macrofossils attributed to the tribe through comparisons with extant plants. The fossils provide direct evidence of the origin of Paullinieae and suggest the diversification of this group in the tropics around 18.5-19 million years ago.
Article
Multidisciplinary Sciences
Hanzhang Song, Luliang Huang, Helanlin Xiang, Cheng Quan, Jianhua Jin
Summary: This study reports the discovery of Engelhardia fossil winged fruits with detailed anatomical structures from the Miocene Erzitang Formation of Guangxi, South China, suggesting that Engelhardia had reached its modern distribution during the Miocene. The unique anatomical and morphological features of the new fossils clearly distinguish them from other fossil genera and show unambiguously their attribution to the genus Engelhardia.
Article
Geology
Ben Thuy, Larry Knox, Lea D. Numberger-Thuy, Nicholas S. Smith, Colin D. Sumrall
Summary: Fossil-informed molecular phylogenies have revealed new findings of brittle-star fossils from deep-water sediments in southern Oklahoma, USA. Despite being preserved as disarticulated microscopic ossicles, the skeletal microstructure allows for accurate identification. Comparative anatomical and phylogenetic analyses confirm the presence of basal representatives of extant ophiuroid orders and support the hypothesis that a significant part of crown-group diversification in ophiuroids occurred in deep-water settings before the end-Permian mass extinction.
Article
Evolutionary Biology
Alexander A. Fisher, Xiang Ji, Zhenyu Zhang, Philippe Lemey, Marc A. Suchard
Summary: Relaxed random walk (RRW) models introduce branch-specific rate multipliers to modulate the variance of a standard Brownian diffusion process to accurately model overdispersed biological data. A scalable method in a Bayesian framework is presented to efficiently fit RRWs and infer branch-specific variation. The Hamiltonian Monte Carlo sampler approximates the high-dimensional posterior and achieves computational complexity that scales linearly with the number of taxa studied.
SYSTEMATIC BIOLOGY
(2021)
Article
Computer Science, Hardware & Architecture
Tinghuan Chen, Bingqing Lin, Hao Geng, Shiyan Hu, Bei Yu
Summary: Sensor drift is a challenging obstacle in temperature measurement in smart buildings. The proposed framework utilizes a sensor spatial correlation model and MAP estimation to calibrate drifts, with an alternating-based method to solve the nonconvex problem. Experimental results show that the framework achieves better accuracy and runtime tradeoff compared to state-of-the-art methods.
IEEE TRANSACTIONS ON COMPUTER-AIDED DESIGN OF INTEGRATED CIRCUITS AND SYSTEMS
(2021)
Article
Biodiversity Conservation
C. Henrik Woolley, Jeffrey R. Thompson, Yun-Hsin Wu, David J. Bottjer, Nathan D. Smith
Summary: The fossil record is often incomplete and biased, making it difficult to place fossils in an evolutionary context. This study focuses on the incompleteness bias in a large dataset of fossil squamates. Despite the bias, the most frequently occurring skeletal parts in the fossil record retain similar levels of phylogenetic signal as rarer parts. These findings indicate that the biased squamate fossil record still contains reliable phylogenetic information.
Article
Instruments & Instrumentation
K. H. Phung, J. A. Romero, T. Roche, TAE Team
Summary: The magnetic diagnostics of TAE Technologies' fusion device involve various internal and external sensors for measuring poloidal flux and axial field strength. Bayesian approach is used for calibration to account for errors in the signals, resulting from imperfect construction and physical constraints. The calibration process utilizes model-based predictions and Bayesian inference to achieve accurate measurements and identify instrument malfunctions or errors in database maintenance.
REVIEW OF SCIENTIFIC INSTRUMENTS
(2022)
Article
Biology
Nicolas Mongiardino Koch, Jeffrey R. Thompson, Avery S. Hiley, Marina F. McCowin, A. Frances Armstrong, Simon E. Coppard, Felipe Aguilera, Omri Bronstein, Andreas Kroh, Rich Mooi, Greg W. Rouse
Summary: Echinoids, including sand dollars, are crucial components of modern marine ecosystems. However, their early history and the origin of sand dollars have remained uncertain. In this study, we generated genomic data from 18 species of echinoids and used them to reconstruct the phylogeny and divergence times of echinoids. We also introduced a new concept called chronospace to explore different methodological decisions in calibrating phylogenies. Our results revealed that crown group echinoids originated in the Permian and diversified rapidly in the Triassic. We also clarified the relationships between sand dollars and their relatives and confidently dated their origin to the Cretaceous.
Article
Biology
Nicolas Mongiardino Koch, Russell J. Garwood, Luke A. Parry
Summary: Fossils provide a direct window into evolutionary events in the distant past. Incorporating fossils into phylogenetic hypotheses of living clades can help time-calibrate divergences and elucidate macroevolutionary dynamics. Additionally, fossils improve the accuracy of phylogenetic analysis of morphological datasets and increase the number of resolved nodes.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Ecology
Jose Barba-Montoya, Qiqing Tao, Sudhir Kumar
Summary: Morphological matrices are commonly used for dating species divergence times in systematics, either by combining morphological and molecular character data from extant taxa, or by including morphological characters from extinct taxa. Our analysis of three empirical datasets showed a high correlation between divergence time estimates from molecular and discrete morphological data of extant taxa, despite a poor linear relationship between branch lengths. Averaging effects over multiple branches may explain the discrepancy, indicating that nodes with a large number of taxa benefit from this averaging. Discordance between time estimates from molecules and morphology may still occur, particularly at intermediate nodes. It is suggested that node- and tip-calibration approaches may be better suited for nodes with many taxa, emphasizing the importance of evaluating the concordance of intrinsic time structure in morphological and molecular data before conducting dating analysis using combined datasets.
BMC ECOLOGY AND EVOLUTION
(2021)
Article
Evolutionary Biology
Jakub Truszkowski, Allison Perrigo, David Broman, Fredrik Ronquist, Alexandre Antonelli
Summary: Bayesian phylogenetics faces challenges due to its computational expense and the increasing amount of genomic data. However, new approaches such as online phylogenetics and alternatives to Markov chain Monte Carlo (MCMC) offer potential solutions to scale up Bayesian analyses. Collaborative efforts are needed to develop methods for real-time tree expansion through online phylogenetics.
SYSTEMATIC BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Daniele Salvi, Catarina Pinho, Joana Mendes, D. James Harris
Summary: Podarcis wall lizards are endemic to the Mediterranean Basin, with their diversification occurring rapidly during the Middle Miocene, associated with European climate changes and geological history. Multiple dispersal and vicariant events at different time frames are needed to explain current allopatric distributions and Mediterranean biota assembly, cautioning against biogeographic calibrations based on the assumption of vicariance.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Milan Malinsky, Michael Matschiner, Hannes Svardal
Summary: Dsuite is an efficient software package that allows genome scale calculations of the D and f(4)-ratio statistics from VCF files, enabling evaluation of all combinations of multiple populations or species, particularly suited for larger genomic data sets.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Multidisciplinary Sciences
Fabrizia Ronco, Michael Matschiner, Astrid Boehne, Anna Boila, Heinz H. Buescher, Athimed El Taher, Adrian Indermaur, Milan Malinsky, Virginie Ricci, Ansgar Kahmen, Sissel Jentoft, Walter Salzburger
Summary: This text provides a detailed examination of the adaptive radiation of cichlid fishes in Lake Tanganyika, demonstrating empirical support for two theoretical predictions of how adaptive radiations proceed and revealing a positive correlation between species richness and per-individual heterozygosity. The study highlights the rapid morphological diversification through trait-specific pulses of accelerated evolution within the confines of the lake.
Article
Ecology
Martin Hluben, Lukas Kratochvil, Lumir Gvozdik, Zuzana Starostova
Summary: Research on eyelid geckos showed that body size influences metabolic rate, body surface, and scale morphology, complicating the analysis of adaptive changes in total evaporative water loss (TEWL). Evolutionary shifts in TEWL were strongly correlated with habitat aridity, suggesting a crucial role of skin permeability in adaptation. Comparing intra- and interspecific scaling can help detect body size-dependent mechanisms of adaptive changes in ecophysiological traits.
JOURNAL OF EVOLUTIONARY BIOLOGY
(2021)
Review
Biology
Matthias Stoeck, Dmitrij Dedukh, Radka Reifova, Dunja K. Lamatsch, Zuzana Starostova, Karel Janko
Summary: The roles of sex chromosomes in vertebrate hybridization and speciation are dependent on the level of divergence, affecting the degree of reproductive isolation. Undifferentiated sex chromosomes are more susceptible to introgression and may give rise to new sex chromosome systems.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Ecology
Michael Matschiner, Julia Maria Isis Barth, Ole Kristian Torresen, Bastiaan Star, Helle Tessand Baalsrud, Marine Servane Ono Brieuc, Christophe Pampoulie, Ian Bradbury, Kjetill Sigurd Jakobsen, Sissel Jentoft
Summary: This study investigates the origin and evolution of four megabase-scale supergenes in Atlantic cod. The results show that these supergenes are formed through chromosomal inversions at different time points. Furthermore, gene conversion and double crossover play important roles in the maintenance and evolution of supergenes.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Physiology
Brandon Meter, Lukas Kratochvil, Lukas Kubicka, Zuzana Starostova
Summary: Previous belief of indeterminate growth in lizards has been challenged by recent studies showing bone growth plate closure as a stoppage of bone prolongation. This has significant consequences for understanding the causes of sexual size dimorphism in squamate reptiles.
FRONTIERS IN PHYSIOLOGY
(2022)
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
Multidisciplinary Sciences
Iliana Bista, Jonathan M. D. Wood, Thomas Desvignes, Shane A. McCarthy, Michael Matschiner, Zemin Ning, Alan Tracey, James Torrance, Ying Sims, William Chow, Michelle Smith, Karen Oliver, Leanne Haggerty, Walter Salzburger, John H. Postlethwait, Kerstin Howe, Melody S. Clark, H. William Detrich, C. -H. Christina Cheng, Eric A. Miska, Richard Durbin
Summary: To understand the evolution of notothenioids, researchers generated and analyzed new genome assemblies for 24 species, finding that the radiation of this fish group started approximately 10.7 million years ago. They also discovered a two-fold variation in genome size, driven by expansion of transposable element families, and reconstructed two important gene family loci using long-read data.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Stanislaw Bury, Lukas Kratochvil, Zuzana Starostova
Summary: Small erythrocytes contribute less to blood viscosity than large erythrocytes, and larger erythrocytes may have relatively smaller nucleus size and rounder shape, allowing higher flexibility. However, nucleus size and erythrocyte area, as well as cell width and cell length, exhibit linear relationships, indicating proportional mutual changes. The commonly used N : C ratio and elongation ratio might be mathematically trivial scaling rather than reflecting adaptive or maladaptive changes, which warns against misinterpretation of evolutionary processes.
ROYAL SOCIETY OPEN SCIENCE
(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)
Correction
Plant Sciences
Lei Yu, Marina Khachaturyan, Michael Matschiner, Adam Healey, Diane Bauer, Brenda Cameron, Mathieu Cusson, J. Emmett Duffy, F. Joel Fodrie, Diana Gill, Jane Grimwood, Masakazu Hori, Kevin Hovel, A. Randall Hughes, Marlene Jahnke, Jerry Jenkins, Keykhosrow Keymanesh, Claudia Kruschel, Sujan Mamidi, Damian M. M. Menning, Per-Olav Moksnes, Masahiro Nakaoka, Christa Pennacchio, Katrin Reiss, Francesca Rossi, Jennifer L. L. Ruesink, Stewart T. T. Schultz, Sandra Talbot, Richard Unsworth, David H. H. Ward, Tal Dagan, Jeremy Schmutz, Jonathan A. Eisen, John J. Stachowicz, Yves Van de Peer, Jeanine L. Olsen, Thorsten B. H. Reusch
Article
Plant Sciences
Lei Yu, Marina Khachaturyan, Michael Matschiner, Adam Healey, Diane Bauer, Brenda Cameron, Mathieu Cusson, J. Emmett Duffy, F. Joel Fodrie, Diana Gill, Jane Grimwood, Masakazu Hori, Kevin Hovel, A. Randall Hughes, Marlene Jahnke, Jerry Jenkins, Keykhosrow Keymanesh, Claudia Kruschel, Sujan Mamidi, Damian M. Menning, Per-Olav Moksnes, Masahiro Nakaoka, Christa Pennacchio, Katrin Reiss, Francesca Rossi, Jennifer L. Ruesink, Stewart T. Schultz, Sandra Talbot, Richard Unsworth, David H. Ward, Tal Dagan, Jeremy Schmutz, Jonathan A. Eisen, John J. Stachowicz, Yves van de Peer, Jeanine L. Olsen, Thorsten B. H. Reusch
Summary: Ocean currents play a crucial role in the distribution of marine coastal species. In this study, the nuclear and chloroplast genomes of eelgrass (Zostera marina L.) were used to trace its colonization history from its origin in the Northwest Pacific. The study revealed two divergent Pacific clades, evidence of admixture along the East Pacific coast, and the key role of the North Pacific Current in the trans-Pacific colonization events. The arrival of eelgrass in the Atlantic was estimated to be around 243,000 years ago, and the recent colonization and low genomic diversity in the Atlantic compared to the Pacific raises concerns about its response to warming coastal oceans.