Editorial Material
Multidisciplinary Sciences
Stefan Glasauer, Hans Straka
Summary: Analyzing fossil specimens of the inner ear helps determine the timeframe of when our mammal-like ancestors started regulating body temperature, providing insights into vertebrate evolution.
Editorial Material
Multidisciplinary Sciences
Simone Hoffmann
Summary: Newly discovered fossil evidence has prompted a re-evaluation of the transition of bones of the lower jaw into those of the middle ear, shedding new light on the evolution of the middle ear in mammals.
Editorial Material
Multidisciplinary Sciences
Matt Friedman
Summary: Scarce evidence suggests that important evolutionary developments for jawed vertebrates may have taken place during or prior to the Silurian period. Fossil discoveries unveil insights into this particular interval.
Editorial Material
Multidisciplinary Sciences
Jorge Mondejar Fernandez, Philippe Janvier
Summary: Scientists have been studying a fossil of an aquatic vertebrate for over a century and debated about what species it represents. Newly analyzed specimens may provide a solution to this mystery.
Editorial Material
Multidisciplinary Sciences
Zhikun Gai, Philip C. J. Donoghue
Summary: An analysis of a 458-million-year-old fossil fish sheds light on the evolution of vertebrate skull organization and provides anatomical insights into the transition from ancestral early vertebrates to jawed vertebrates.
Editorial Material
Multidisciplinary Sciences
Kevin Padian
Summary: Our knowledge about the origin of birds significantly advanced in 1998 with the discovery of a fossilized dinosaur with feathers, which caused a sensation in scientific publications that year.
News Item
Multidisciplinary Sciences
Max Kozlov
Summary: The Canadian fossil has the potential to rewrite the history of animal life, although some paleontologists are skeptical.
Editorial Material
Multidisciplinary Sciences
Fabien Kenig
Summary: A newly discovered fossil record spanning 1.64 billion years suggests that ancient organisms in the eukaryotic domain were only capable of early steps in the synthesis of sterol molecules.
News Item
Multidisciplinary Sciences
Ewen Callaway, Heidi Ledford
Summary: Svante Paabo's discoveries using ancient DNA have had a significant impact on our understanding of human evolution and have played a key role in the development of the field of palaeogenomics.
Article
Biochemistry & Molecular Biology
Mahan Ghafari, Louis du Plessis, Jayna Raghwani, Samir Bhatt, Bo Xu, Oliver G. Pybus, Aris Katzourakis
Summary: High-throughput sequencing allows rapid genome sequencing during outbreaks, providing insight into pathogen evolution dynamics. Evolutionary analyses over short timescales are challenging due to the time-dependent nature of evolutionary rate estimates. The study on SARS-CoV-2 and pH1N1 influenza found that inferred evolutionary parameters decline over time, with growth rates and emergence dates stable after 4 months. Terminal branches exhibit elevated substitution rates, correlated with purifying selection generating time dependency in evolutionary parameters.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Mauro B. S. Lacerda, Jonathas S. Bittencourt, John R. Hutchinson
Summary: The study analyzed the macroevolution of the locomotor system in early Theropoda, with a focus on Megalosauroidea. By scoring Spinosaurus and mapping the modifications onto a phylogeny, the researchers studied the disparities in the evolution of Megalosauroidea. The findings provide a stronger foundation for future studies on pelvic/appendicular musculature and locomotor function.
ROYAL SOCIETY OPEN SCIENCE
(2023)
Article
Multidisciplinary Sciences
Andrea Baucon, Annalisa Ferretti, Chiara Fioroni, Luca Pandolfi, Enrico Serpagli, Armando Piccinini, Carlos Neto de Carvalho, Mario Cachao, Thomas Linley, Fernando Muniz, Zain Belaustegui, Alan Jamieson, Girolamo Lo Russo, Filippo Guerrini, Sara Ferrando, Imants Priede
Summary: This study reveals that fish have been inhabiting the deep seafloor since the Early Cretaceous, using various techniques to feed on prey. These findings shed light on the evolutionary history of deep-seafloor fishes and the availability of new food sources in the deep sea.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biology
Cedric Aria
Summary: The rise of arthropods in different ecosystems has significantly impacted ecological networks. Recent discoveries of well-preserved Palaeozoic fossils have shed light on the appearance of extant arthropods during the Cambrian explosion and the role of plankton and hard integuments in their diversification. The understanding of arthropod evolution has been altered, and important questions have been raised, such as cephalic plasticity and the development of specialized appendages for suspension-feeding.
BIOLOGICAL REVIEWS
(2022)
Article
Zoology
Steven E. Jasinski
Summary: The study reveals the diversity of painted turtles in North America and the discovery of a new species provides new data on their evolution and species diversity. The new fossil species represents a basal morphology in the turtle family and suggests the occurrence of multiple evolutionary events with similar basal morphologies. Additionally, the increase in turtle species after a period of optimal climate conditions may be influenced by lower temperatures.
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2023)
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
Biochemistry & Molecular Biology
Asif U. Tamuri, Mario dos Reis
Summary: The study utilizes population genetics principles to model protein evolution under persistent positive selection, finding it to be an irreversible Markov process with strongly asymmetrical distribution of selection coefficients. The authors suggest that the omega > 1 criteria for detecting positive selection is conservative and arbitrary due to highly deleterious mutations being removed even at positively selected sites in real proteins. This research demonstrates the successful detection of persistent positive selection in plant RuBisCO and influenza HA proteins using a penalized-likelihood implementation of the model, highlighting the improved ability to detect molecular adaptation in proteins by directly estimating selection coefficients at protein sites.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Ellen J. Coombs, Ryan N. Felice, Julien Clavel, Travis Park, Rebecca F. Bennion, Morgan Churchill, Jonathan H. Geisler, Brian Beatty, Anjali Goswami
Summary: The evolution of cetaceans from terrestrial mammals to highly specialized aquatic animals is characterized by significant anatomical changes in feeding, respiratory, and sensory structures of the cranium. The evolution of cetaceans occurred through three periods of rapid evolution, with diet and echolocation playing the strongest roles in shaping cranial morphology.
Article
Biochemistry & Molecular Biology
Ziheng Yang, Tomas Flouri
Summary: This study investigates the issue of unidentifiability in multispecies coalescent models with introgression, using full-likelihood methods. The unidentifiability of the bidirectional introgression model is characterized, and novel algorithms for addressing label-switching problems are developed. Real and synthetic data analyses demonstrate the utility of these models and algorithms, and guidelines for using them to infer gene flow with genomic data are provided.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Tianqi Zhu, Tomas Flouri, Ziheng Yang
Summary: This study conducted a computer simulation to examine the impact of recombination on several Bayesian analyses of multilocus sequence data. The results showed that recombination has little impact on species tree estimation, species delimitation, and estimation of population parameters, while higher recombination rates may affect parameter estimation, causing positive biases in introgression times and ancestral population sizes. However, species divergence times and cross-species introgression probabilities are estimated with little bias.
Article
Biochemistry & Molecular Biology
Tomas Flouri, Jun Huang, Xiyun Jiao, Paschalia Kapli, Bruce Rannala, Ziheng Yang
Summary: The multispecies coalescent model provides a natural framework for phylogenetic analysis of genomic data, allowing estimation of species divergence times and ancestral population sizes. Clock violation should be considered, and the relaxed-clock models can extract valuable phylogenetic information from gene-tree branch lengths.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biology
Agnese Lanzetti, Ellen J. Coombs, Roberto Portela Miguez, Vincent Fernandez, Anjali Goswami
Summary: Through studying the asymmetry and shape changes of the skull during prenatal and postnatal ontogeny in five genera of toothed whales, it was found that asymmetry starts low in early development, increases with age, and converges to comparable levels among different taxa. Porpoises maintain low levels of asymmetry and exhibit a decelerated growth rate, possibly retained from the ancestral condition. Ancestral state reconstruction shows that both paedomorphism and peramorphism contribute to cranial shape diversity across odontocetes, highlighting how divergent developmental pathways can lead to convergent ecological adaptations even in the most unusual phenotypes exhibited among vertebrates.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biology
Jelmer W. Poelstra, B. Karina Montero, Jan Luedemann, Ziheng Yang, S. Jacques Rakotondranary, Paul Hohenlohe, Nadine Stetter, Joerg U. Ganzhorn, Anne D. Yoder
Summary: Microsatellites are commonly used in evolutionary genetic studies, but their high mutation rate leads to uncertainty in deeper evolutionary comparisons. In this study, RADseq data was used to re-examine hybridization patterns in two mouse lemur species in Madagascar, and it was found that previously inferred hybrids were false positives, providing new insights into the reproductive isolation of these species.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Jun Huang, Yuttapong Thawornwattana, Tomas Flouri, James Mallet, Ziheng Yang
Summary: Genomic sequence data are valuable for studying species divergence and gene flow. However, when the model of gene flow is misspecified, estimation bias and interpretation issues may arise. Despite this, the simple introgression model can still be useful for extracting information about between-species gene flow and divergence.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Evolutionary Biology
Jiayi Ji, Donavan J. Jackson, Adam D. Leache, Ziheng Yang
Summary: Over the past two decades, genomic data have been widely used for detecting historical gene flow between species. The Tamias quadrivittatus group of chipmunks in North America, which originated through rapid speciation events, show extensive mitochondrial introgression. However, a recent analysis of targeted nuclear loci found no evidence for cross-species introgression, suggesting cytonuclear discordance.
SYSTEMATIC BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Sandra Alvarez-Carretero, Paschalia Kapli, Ziheng Yang
Summary: The CODEML program in the PAML package is widely used to analyze protein-coding gene sequences, estimate synonymous and nonsynonymous rates, and detect positive selection driving protein evolution. This article provides a step-by-step protocol for commonly used tests in CODEML, including branch models, site models, and branch-site models. It also discusses a new feature that allows users to perform positive selection tests for multiple genes in genome-sequencing projects. The PAML package is distributed under the GNU license and supported at its discussion site. Data files used in this protocol are available at the provided link.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biology
Anjali Goswami, Eve Noirault, Ellen J. Coombs, Julien Clavel, Anne-Claire Fabre, Thomas J. D. Halliday, Morgan Churchill, Abigail Curtis, Akinobu Watanabe, Nancy B. Simmons, Brian L. Beatty, Jonathan H. Geisler, David L. Fox, Ryan N. Felice
Summary: The evolution of the skull's major skeletal elements was assessed in this study, using a dataset of 322 living and extinct placental mammals and their relatives. The results revealed distinct macroevolutionary patterns across different cranial elements and highlighted the influence of ecological adaptations. Elements derived from neural crest showed the fastest rates of evolution, while developmental origin had an impact on evolutionary tempo but not specialization capacity.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Biology
Matilda Brindle, Henry Ferguson-Gow, Joseph Williamson, Ruth Thomsen, Volker Sommer
Summary: Masturbation is a widely observed behavior in the animal kingdom, and its adaptive benefits have been a subject of debate. This study presents new data on primate masturbation and uses phylogenetic comparative methods to examine its evolutionary pathways and correlates. The findings support the hypotheses that masturbation aids fertilization and helps reduce the risk of infection, suggesting that it may be an adaptive trait at a macroevolutionary scale.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Yuttapong Thawornwattana, Jun Huang, Tomas Flouri, James Mallet, Ziheng Yang
Summary: Genomic data provide valuable information for studying species divergence and gene flow between species, including the direction, timing, and strength of gene flow. However, inferring the direction of gene flow is challenging due to similar patterns generated by gene flow in opposite directions. This study uses likelihood-based methods and simulation to investigate the information about the direction of gene flow present in genomic sequence data. The results show that it is easier to infer gene flow from a small population to a large one and from outgroup species to ingroup species than in the opposite direction, and a longer time of separate evolution between divergence and introgression makes gene flow inference easier.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Evolutionary Biology
Paschalia Kapli, Ioanna Kotari, Maximilian J. Telford, Nick Goldman, Ziheng Yang
Summary: Inference of deep phylogenies has primarily used protein sequences, but our analysis shows that DNA sequences may be just as useful and should not be excluded. We conducted a simulation study and analyzed empirical data, which suggest that DNA sequences can recover the correct tree as often as protein sequences. Using DNA data has computational advantages and allows for advanced models that account for heterogeneity in the nucleotide-substitution process.
SYSTEMATIC BIOLOGY
(2023)
Article
Ecology
Sergio Ferreira-Cardoso, Julien Claude, Anjali Goswami, Frederic Delsuc, Lionel Hautier
Summary: The cranial modularity of myrmecophagous placental mammals is similar to that of non-myrmecophagous placentals, but changes in integration have occurred due to extreme functional and morphological features, which may be related to their myrmecophagous diet.
BMC ECOLOGY AND EVOLUTION
(2022)