Article
Ecology
Bruno do Rosario Petrucci, Matheus Januario, Tiago Quental
Summary: Simulations are important tools for investigating evolutionary questions, particularly in the analysis of diversification and fossil sampling rates. paleobuddy is a flexible R package that allows for simulations of birth-death processes, fossil records, and phylogenetic trees, providing a more general framework for investigating complex inference models. It expands the available parameter space and increases our understanding of the differences between palaeontological and neontological approaches.
METHODS IN ECOLOGY AND EVOLUTION
(2022)
Article
Evolutionary Biology
Giovanni Laudanno, Bart Haegeman, Daniel L. Rabosky, Rampal S. Etienne
Summary: This article introduces different models and inference methods for phylogenetic trees with varying diversification rates, proposing a new framework for calculating likelihood that has been shown to be more accurate through simulations. The corrected likelihood can also be applied to models with multiple rate shifts, resolving the recent debate on unobserved shifts in diversification rates.
SYSTEMATIC BIOLOGY
(2021)
Article
Biology
Anna L. Wisniewski, Graeme T. Lloyd, Graham J. Slater
Summary: This study investigated the historical biogeography of Primates and their relatives using a novel meta-analytical phylogeny. The results showed that ancestral range estimates for young nodes were largely congruent with molecular phylogeny, but node age had a significant effect on the congruence of ancestral range estimates, with lower probability of congruent inference for older nodes.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Review
Geosciences, Multidisciplinary
Karma Nanglu, Thomas M. Cullen
Summary: Quantitative studies of fossil data have played a critical role in major macroevolutionary and macro-ecological discoveries, but issues such as bias, preservation, sampling, and taxonomy can affect the interpretative resolution and obscure biological signals. This study provides two case studies that illustrate the impact of biases on ecological reconstructions and analysis, and proposes recommendations for future paleoecological and macroecological studies.
EARTH-SCIENCE REVIEWS
(2023)
Article
Ecology
Peng Li, John J. Wiens
Summary: This study provides a comprehensive comparison of the types of traits that can drive diversification in lizard and snake families. It shows that the rate of range expansion is the most important variable for explaining diversification rates and richness patterns in squamates.
JOURNAL OF BIOGEOGRAPHY
(2022)
Article
Biology
R. Weppe, M. J. Orliac, G. Guinot, F. L. Condamine
Summary: The study explores the diversity dynamics of the mammal clade, Cainotherioidea, during the Eocene-Oligocene transition, revealing fluctuations in diversity, extinction events, and a burst of speciation. Adaptability to environmental changes played a key role in the survival and success of the clade, with speciation positively associated with temperature and continental fragmentation, while extinction synchronized with environmental changes. Interactions within the clade negatively affected diversification, and inter-clade competition potentially led to the decline of the group during the late Oligocene.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Ecology
Jiri Smid
Summary: This study identifies hotspots with the most unsampled vertebrate species, mainly in tropical regions. It also suggests that the socio-economic development of a country may be indicative of its sampling completeness.
JOURNAL OF BIOGEOGRAPHY
(2022)
Article
Ecology
Chinmay Hemant Joshi, John J. Wiens
Summary: Understanding the evolution of eusociality in insects, specifically the role of haplodiploidy, has remained a long-standing and unsolved challenge in evolutionary biology. This study conducted large-scale phylogenetic tests across 874 hexapod families, using three different methods, and found mixed support for the hypothesis that haplodiploidy drives the evolution of eusociality. While two methods supported the association between haplodiploidy and eusociality, there were also discordant patterns and one test was non-significant, indicating that eusociality can also evolve without haplodiploidy in certain groups.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
David Cerny, Rossy Natale
Summary: The study presents the most comprehensive non-supertree phylogeny of shorebirds to date, clarifying the timeline of charadriiform evolution by time-scaling with a set of 14 up-to-date fossil calibrations. It also assembles a taxonomically restricted 100-locus dataset specifically designed to resolve outstanding problems in higher-level charadriiform phylogeny. The results are largely congruent with previous studies but highlight the challenges involved in estimating a comprehensively sampled and carefully calibrated time tree for a diverse avian clade.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Ecology
Nicholas M. A. Crouch, Joseph A. Tobias
Summary: Episodic pulses of morphological diversification are a prominent feature of evolutionary history. By analyzing global phylogenetic and morphological data for birds, we found that these pulses tend to occur independently and are associated with habitat niche stability. Our results highlight the potential of functional trait data sets in refining macroevolutionary models.
Article
Biology
Scott Lidgard, Emanuela Di Martino, Kamil Zagorsek, Lee Hsiang Liow
Summary: Studying the role of local-scale competition in macroevolutionary patterns is a familiar goal in fossil biodiversity research, but faces challenges such as ecological equivalence confirmation, clade interactions, sampling biases, and lack of appropriate statistical tools. Research indicates that clade displacement is not driven by simple correlations or unidirectional relationships, but rather by a complex feedback relationship between inter-clade genus origination and extinction rates.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Physics, Multidisciplinary
Larissa Lubiana Botelho, Flavia Maria Darcie Marquitti, Marcus A. M. de Aguiar
Summary: This study examines the processes of speciation, extinction, and hybridization using a genetically and spatially explicit neutral model. The results show that genome size plays a key role, affecting extinction and hybridization rates. Most hybridization events occur between relatively abundant species.
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL
(2022)
Article
Biochemistry & Molecular Biology
Manon Bucher, Fabien L. Condamine, Yang Luo, Menglin Wang, Thierry Bourgoin
Summary: This study provides a phylogenetic and dating analysis of Fulgoromorpha, covering 531 taxa and representing 80% of the currently described diversity in this group. The results reveal the unexpected paraphyly of Delphacidae, the sister relationship of Meenoplidae-Kinnaridae with other Fulgoroidea families, and the early branching node of Tettigometridae. Additionally, the study emphasizes the importance of high-quality molecular sequences and large sampling in analyzing the phylogeny of this group.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Zhiliang Zhang, Zhifei Zhang, Junye Ma, Paul D. Taylor, Luke C. Strotz, Sarah M. Jacquet, Christian B. Skovsted, Feiyang Chen, Jian Han, Glenn A. Brock
Summary: Bryozoans, also known as ectoprocts or moss animals, are aquatic, primarily sessile, filter-feeding lophophorates that construct an organic or calcareous colonial exoskeleton. Fossils of Protomelission gatehousei from the early Cambrian of Australia and South China have been identified as potential stem-group bryozoans, pushing back the origin of the phylum Bryozoa by approximately 35 million years and aligning it with other skeletonized phyla in the Cambrian Age 3. This discovery reconciles the fossil record with molecular clock estimations of an early Cambrian origin and subsequent Ordovician radiation of Bryozoa following the acquisition of a carbonate skeleton.
Article
Biology
Elaine A. Corbett, L. Alexandra Martinez-Rodriguez, Cian Judd, Redmond G. O'Connell, Simon P. Kelly
Summary: Perceptual decisions are biased toward higher-value options and are influenced by anticipation, detection, and discrimination processes. Motor preparation for higher-value actions begins earlier, providing a starting point advantage, while slower preparation for lower-value actions creates a value-opposed buildup-rate bias. However, this bias is countered by a transient deflection towards the higher-value action during stimulus detection. A neural process model incorporating anticipatory urgency, biased detection, and accumulation of stimulus-discriminating evidence successfully captures both behavior and motor preparation dynamics.
Article
Endocrinology & Metabolism
Stuart J. McGurnaghan, Amanda Weir, Jen Bishop, Sharon Kennedy, Luke A. K. Blackbourn, David A. McAllister, Sharon Hutchinson, Thomas M. Caparrotta, Joseph Mellor, Anita Jeyam, Joseph E. O'Reilly, Sarah H. Wild, Sara Hatam, Andreas Hoehn, Marco Colombo, Chris Robertson, Nazir Lone, Janet Murray, Elaine Butterly, John Petrie, Brian Kennon, Rory McCrimmon, Robert Lindsay, Ewan Pearson, Naveed Sattar, John McKnight, Sam Philip, Andrew Collier, Jim McMenamin, Alison Smith-Palmer, David Goldberg, Paul M. McKeigue, Helen M. Colhoun
Summary: The study aimed to compare the risk of fatal or critical care unit-treated COVID-19 between people with and without diabetes, and developed a predictive model. Results showed that people with diabetes had a higher risk of developing the disease, with several related factors, and the predictive model demonstrated good accuracy.
LANCET DIABETES & ENDOCRINOLOGY
(2021)
Article
Paleontology
Jodie L. Murphy, Mark N. Puttick, Joseph E. O'Reilly, Davide Pisani, Philip C. J. Donoghue
Summary: The study investigated 486 tetrapod morphological cladistic datasets to establish an empirical distribution of consistency among characters and datasets. It was found that the consistency between phylogenetic history and individual character histories has a bearing on the evolutionary process, with the most significant decreases resulting from the addition of taxa rather than characters. This research challenges the conjecture that high quality phylogenetic characters are quickly exhausted in the search for phylogenetic resolution.
Article
Ecology
Hans P. Puschel, Ornella C. Bertrand, Joseph E. O'Reilly, Rene Bobe, Thomas A. Puschel
Summary: The study applied a Bayesian total evidence dating approach to hominin phylogeny, estimating the origin of Homo probably occurred 4.3-2.56 million years ago. Ancestral state reconstructions revealed a trend towards increasing body mass and accelerating encephalization evolution. The results provide a rigorous temporal framework for human evolution.
NATURE ECOLOGY & EVOLUTION
(2021)
Article
Endocrinology & Metabolism
Joseph E. O'Reilly, Anita Jeyam, Thomas M. Caparrotta, Joseph Mellor, Andreas Hohn, Paul M. McKeigue, Stuart J. McGurnaghan, Luke A. K. Blackbourn, Rory McCrimmon, Sarah H. Wild, John R. Petrie, John A. McKnight, Brian Kennon, John Chalmers, Sam Phillip, Graham Leese, Robert S. Lindsay, Naveed Sattar, Fraser W. Gibb, Helen M. Colhoun
Summary: The study found that the incidence of DKA among individuals with type 1 diabetes in Scotland has increased since 2004, except in the 10-19 age group. There are strong and widening socioeconomic disparities in DKA outcomes, indicating a need for efforts to prevent DKA in vulnerable groups.
Article
Paleontology
Thomas J. Smith, Mark N. Puttick, Joseph E. O'Reilly, Davide Pisani, Philip C. J. Donoghue
Summary: Cladistic character matrices are often used in analyses of morphological disparity, but their sampling may lead to biases in morphospace occupation. Differences in tree shape can predict genuine differences in morphospace occupation, cautioning against uncritical repurposing of cladistic datasets in disparity analyses. Uniformity in lineage sampling across time and topology is important for distinguishing evolutionary phenomena from artefactual signals.
Article
Paleontology
Joseph E. O'Reilly, Philip C. J. Donoghue
Summary: The impact of systematically distributed missing data resulting from taphonomic processes on clade age estimates is negative, with different stages of taphonomy introducing greater differences in age estimates. However, the general influence of missing data is weak, likely due to the compensatory effect of extensive morphological data from extant taxa.
Article
Endocrinology & Metabolism
Anita Jeyam, Fraser W. Gibb, John A. McKnight, Joseph E. O'Reilly, Thomas M. Caparrotta, Andreas Hohn, Stuart J. McGurnaghan, Luke A. K. Blackbourn, Sara Hatam, Brian Kennon, Rory J. McCrimmon, Graham Leese, Sam Philip, Naveed Sattar, Paul M. McKeigue, Helen M. Colhoun
Summary: Results of the study showed that for type 1 diabetes patients using flash monitors, there was a significant reduction in HbA(1c) levels and a noticeable decrease in DKA rates after FM initiation. The use of FM has important implications for improving blood sugar management in diabetic patients.
Article
Biology
Alexander Pohle, Bjoern Kroeger, Rachel C. M. Warnock, Andy H. King, David H. Evans, Martina Aubrechtova, Marcela Cichowolski, Xiang Fang, Christian Klug
Summary: Despite the excellent fossil record of cephalopods, their early evolution remains poorly understood. In this study, researchers conducted a comprehensive phylogenetic analysis of Cambrian and Ordovician cephalopods and resolved existing controversies. The results revealed three major monophyletic groups, and clarified the evolutionary pathways. The study also provided insights into the application of Bayesian phylogenetic inference on morphological datasets, suggesting the use of quartet similarity metrics and posterior pruned maximum clade credibility trees for assessing support for phylogenetic relationships among relevant taxa.
Article
Multidisciplinary Sciences
Andreas Hohn, Stuart J. McGurnaghan, Thomas M. Caparrotta, Anita J. Jeyam, Joseph E. O'Reilly, Luke A. K. Blackbourn, Sara J. Hatam, Christian Dudel, Rosie J. R. Seaman, Joseph Mellor, Naveed M. Sattar, Rory J. M. McCrimmon, Brian Kennon, John R. Petrie, Sarah Wild, Paul M. McKeigue, Helen M. Colhoun
Summary: This study examines the impact of socioeconomic disparities on life expectancy and years lived without complications among individuals with type 1 diabetes in Scotland. The results demonstrate that patients with higher levels of socioeconomic deprivation experience shorter life expectancy and fewer years without complications. The study highlights the importance of tailored support for individuals from low socioeconomic backgrounds in diabetes management and complication prevention.
Editorial Material
Ecology
Hans P. Puschel, Ornella C. Bertrand, Joseph E. O'Reilly, Rene Bobe, Thomas A. Puschel
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Biology
Laura P. A. Mulvey, Rachel C. M. Warnock, Kenneth De Baets
Summary: Parasites play a major role in shaping community structure and their extinction could have massive cascading effects across ecosystems. Estimating their extinction risk is crucial, and we propose a novel metric that incorporates the evolutionary history of parasites and hosts using cophylogenetic methods. By analyzing polystome parasites and their anuran hosts, we show that different methods have a significant impact on extinction risk estimation and that model-based approaches offer greater insights into cophylogenetic history and extinction risk.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Ecology
Sam Giles, Kara Feilich, Rachel C. M. Warnock, Stephanie E. Pierce, Matt Friedman
Summary: An exceptionally preserved fossil from 7 million years before the end-Devonian mass extinction reveals unexpected anatomical features. This suggests complex patterns of divergence and diversification around the Devonian/Carboniferous boundary, as well as conspicuous feeding and locomotor structure diversification in the Carboniferous.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Paleontology
Joelle Barido-Sottani, Alexander Pohle, Kenneth De Baets, Duncan Murdock, Rachel C. M. Warnock
Summary: The fossilized birth-death (FBD) process is used to infer phylogenies and divergence times from both extant and fossil taxa. This study compares two different approaches to place fossils in the tree: using topological constraints based on established taxonomy, or using total-evidence analyses which incorporate morphological data. The results show that both approaches are reliable in recovering the extant topology and divergence times, although topological constraints with errors can lead to higher errors in divergence times. The study also demonstrates that trees recovered under the FBD model are more accurate than those estimated using non-time calibrated inference.
Meeting Abstract
Endocrinology & Metabolism
A. Hohn, S. J. McGurnaghan, T. M. Caparrotta, A. Jeyam, J. E. O'Reilly, L. A. K. Blackbourn, S. Hatam, C. Dudel, P. M. McKeigue, H. M. Colhoun
Meeting Abstract
Endocrinology & Metabolism
J. E. O'Reilly, A. Jeyam, T. M. Caparrotta, P. McKeigue, H. Colhoun
