Review
Psychology, Mathematical
Jorge N. Tendeiro, Henk A. L. Kiers
Summary: In this paper, the relationship between null hypothesis Bayesian testing (NHBT) and Bayesian estimation is explained, with an emphasis on the spike-and-slab prior. The study shows that NHBT results can be well approximated by using a strongly peaked prior, which offers not only posterior odds but also effect size information. This research offers a transparent perspective on the NHBT approach and provides a method to approximate NHBT results.
PSYCHONOMIC BULLETIN & REVIEW
(2023)
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
Computer Science, Artificial Intelligence
Jireh Huang, Qing Zhou
Summary: We propose a novel hybrid method called partitioned hybrid greedy search (pHGS) for Bayesian network structure learning, which consists of three distinct yet compatible algorithms: Partitioned PC (pPC), p-value adjacency thresholding (PATH), and hybrid greedy initialization (HGI). We validate the consistency of our algorithms and demonstrate their effectiveness through extensive numerical comparisons. Our empirical results show that pHGS achieves competitive performance against state-of-the-art structure learning algorithms, reducing computational complexity without sacrificing the accuracy of structure estimation.
Article
Cell Biology
Hengye Chen, Hungyo Kharerin, Archana Dhasarathy, Michael Kladde, Lu Bai
Summary: This study systematically investigates the interplay between nucleosome-displacing-factors (NDFs) and ATP-dependent chromatin remodelers (CRs) using a high-throughput method. The results show that CRs are not required for nucleosome invasion by NDFs, but they function downstream of NDF binding to modulate the length of nucleosome-depleted regions (NDRs). Some CRs exhibit high specificity towards certain NDFs, while most CRs are recruited in a factor-nonspecific and NDR length-dependent manner.
Article
Statistics & Probability
Harlan Campbell, Paul Gustafson
Summary: This article points out that there may be contradictions between conclusions obtained from Bayes factor and Bayesian posterior estimation, but these contradictions can be resolved if one consistently defines their priors and posteriors. The key is to use the same prior model odds for testing and estimation. The recommendation is to report posterior estimates along with Bayes factor to acknowledge the uncertainty regarding the correct model.
AMERICAN STATISTICIAN
(2023)
Article
Entomology
Huifeng Zhao, Ye Chen, Zitong Wang, Haifeng Chen, Yaoguang Qin
Summary: Chalcididae is a moderate-sized family within the superfamily Chalcidoidea in Hymenoptera, with 1548 species worldwide. Phylogenetic analysis based on mitogenomes supports the basal position and monophyly of Chalcididae within Chalcidoidea. The newly sequenced mitochondrial genomes of two Chalcididae species show similarities in structure and feature, providing insights into the evolutionary relationships among families in the Chalcidoidea superfamily.
Article
Automation & Control Systems
Shailesh Garg, Souvik Chakraborty
Summary: VB-DeepONet is a Bayesian operator learning framework that addresses the challenges faced by the deterministic DeepONet architecture. It provides better resistance against overfitting, improved generalization, and allows for the quantification of predictive uncertainty. The results from various mechanics problems demonstrate the effectiveness of VB-DeepONet in uncertainty quantification.
ENGINEERING APPLICATIONS OF ARTIFICIAL INTELLIGENCE
(2023)
Article
Entomology
Gavin R. Broad, Julia Stigenberg
Summary: Orionis Shaw, 1987, previously thought to be mainly Neotropical, has been found to be more diverse in the Old World. DNA analysis and morphology have led to the discovery of species previously believed to only exist in the Far Eastern Palaearctic region in Europe.
JOURNAL OF HYMENOPTERA RESEARCH
(2021)
Article
Psychology, Multidisciplinary
Daniel J. Schad, Bruno Nicenboim, Paul-Christian Burkner, Michael Betancourt, Shravan Vasishth
Summary: In this article, the authors examine how Bayes factors behave under different conditions. They explore errors in Bayes factor estimation, test the accuracy and bias of Bayes factor estimates using bridge sampling, study the stability of Bayes factors against different sampling variation in the data, and examine the variability of decisions based on Bayes factors. They outline a Bayes factor workflow for researchers to assess the robustness of Bayes factors in their individual analyses.
PSYCHOLOGICAL METHODS
(2022)
Article
Biochemistry & Molecular Biology
Xiao-Yu Zheng, Li-Jun Cao, Peng-Yan Chen, Xue-Xin Chen, Kees van Achterberg, Ary Anthony Hoffmann, Jing-Xian Liu, Shu-Jun Wei
Summary: This study explored the mitochondrial genomes of 23 species in the Aculeata suborder, revealing variations in genomic features and their impact on phylogenetic relationships. Different patterns of gene rearrangements and tRNA rearrangements were observed across species, with some conservation in certain groups. Phylogenetic inference showed the influence of unusual genomic features on the evolutionary relationships within the Aculeata suborder.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Mathematics
Liangjun Yu, Shengfeng Gan, Yu Chen, Dechun Luo
Summary: This paper introduces Naive Bayes and its improved model IWHNB, which combines the improved HNB model with instance weights to achieve significant improvements in classification performance.
Article
Statistics & Probability
Michele Peruzzi, Sudipto Banerjee, Andrew O. Finley
Summary: We introduce a class of scalable Bayesian hierarchical models for the analysis of massive geostatistical datasets. The models combine ideas on high-dimensional geostatistics, partitioning the spatial domain, and sparsity-inducing directed acyclic graphs (DAGs). A major contribution is the development of a meshed Gaussian process (MGP) on tessellated domains, along with a Gibbs sampler for efficient recovery of spatial random effects. The cubic MGP (Q-MGP) improves mixing and computing time by executing large-scale operations in parallel within the Gibbs sampler.
JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION
(2022)
Article
Evolutionary Biology
Wesley D. Colombo, Carly M. Tribull, Cecilia Waichert, Celso O. Azevedo
Summary: We applied integrative taxonomy to resolve a taxonomic issue in a group of flat wasps (Hymenoptera, Bethylidae). By analyzing molecular markers and morphological characters, we constructed the phylogeny of Epyrinae and discovered new genera. The study also investigated important taxonomic characters for Epyrinae and provided a checklist of all species and a taxonomic key for the genera.
SYSTEMATIC ENTOMOLOGY
(2022)
Article
Zoology
Daercio A. A. Lucena, Eduardo A. B. Almeida
Summary: The study integrated multiple datasets to reconstruct the evolutionary history of cuckoo wasps through morphological and phylogenetic analyses. Results suggest monophyly of Chrysididae and major lineages diverged during the Early Cretaceous, with subfamily differentiation occurring in the Paleogene and Neogene. Current southern disjunctions are attributed to more recent dispersals and extinctions during the Neogene due to colder climates in northern continents.
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2022)
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
Entomology
Matt N. Krosch, Francesca Strutt, Mark J. Blacket, Jana Batovska, Melissa Starkie, Anthony R. Clarke, Stephen L. Cameron, Mark K. Schutze
Article
Microbiology
Hua-Ling Wang, Teng Lei, Xiao-Wei Wang, M. N. Maruthi, Dan-Tong Zhu, Stephen L. Cameron, Qiong Rao, Hong-Wei Shan, John Colvin, Yin-Quan Liu, Shu-Sheng Liu
ENVIRONMENTAL MICROBIOLOGY
(2020)
Article
Multidisciplinary Sciences
Kaomud Tyagi, Rajasree Chakraborty, Stephen L. Cameron, Andrew D. Sweet, Kailash Chandra, Vikas Kumar
SCIENTIFIC REPORTS
(2020)
Article
Evolutionary Biology
Min Jee Kim, Iksoo Kim, Stephen L. Cameron
SYSTEMATIC ENTOMOLOGY
(2020)
Article
Multidisciplinary Sciences
Andrew D. Sweet, Kevin P. Johnson, Stephen L. Cameron
Article
Genetics & Heredity
Andrew D. Sweet, Kevin P. Johnson, Yanghui Cao, Robert S. de Moya, Rachel K. Skinner, Milton Tan, Stephany Virrueta Herrera, Stephen L. Cameron
Summary: Parasitic lice have unique mitochondrial genomes characterized by rearranged gene orders, variable structures, and less AT content compared to other insects. The mitochondrial genomes of Amblycera are highly rearranged and AT-biased, with genus-level phylogenetic relationships being consistent with large nuclear datasets but gene order data being unreliable in recovering these relationships. Overall, the mt genomes of lice are more variable than previously thought.
Article
Zoology
Shasta C. Henry, Stephen L. Cameron, Adam Smolenski, Peter McQuillan
Summary: The paper describes a new species of Tasmanian cockroach, Polyzosteria yingina, and uses evidence from morphology, biogeography, and molecular analysis to distinguish it from related Australian taxa. The species has two distinct populations in different environments. The study also speculates on potential reasons for the unusual distribution of this charismatic insect.
Article
Genetics & Heredity
Manuela Moreno-Carmona, Stephen L. Cameron, Carlos Fernando Prada Quiroga
Summary: The evolution of the Hexapoda mitochondrial genome has been a focus of recent genetic and evolutionary studies. By analyzing 1198 Hexapoda species from 32 taxonomic orders, it was discovered that there is a significant variation in the rate of mitochondrial gene rearrangements. Additionally, 24 convergence events in genetic order between different taxonomic orders were identified, indicating a high level of evolutionary dynamics within Hexapoda.
Article
Zoology
Liang Wang, Shuangmei Ding, Stephen L. Cameron, Xin Li, Yue Liu, Gang Yao, Ding Yang
Summary: Vermileonidae is an odd and rarely collected dipteran family, with larvae famous for their unique prey behavior and adults rarely seen. Researchers have sequenced the complete mitochondrial genome of Vermileonidae for the first time, providing insights into its phylogenetic relationships with other flies. By combining mitochondrial genome data with morphology, geographical distribution, and geological history, researchers propose that Vermileonidae originated in India and spread to Africa, the Palaearctic, and the Nearctic through land bridges.
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
Avas Pakrashi, Vikas Kumar, David A. C. Stanford-Beale, Stephen L. Cameron, Kaomud Tyagi
Summary: This study provides new insights into the mitogenomic features, gene arrangement, phylogeny, and divergence time estimation of thrips belonging to the order Thysanoptera.
MOLECULAR BIOLOGY REPORTS
(2022)
Article
Biochemistry & Molecular Biology
M. L. Starkie, S. L. Cameron, M. N. Krosch, M. J. Phillips, J. E. Royer, M. K. Schutze, F. Strutt, A. D. Sweet, M. P. Zalucki, A. R. Clarke
Summary: This study reconstructed the phylogenetic relationships of Dacini tribe by analyzing species from Australia, the Pacific, and Southeast Asia. The results showed that the Australian fauna has high levels of endemism and the divergence time of the tribe is younger than previously reported. The evolution of male lure response exhibited a strong signal, while the signal for host breadth evolution was weaker.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Biology
Andrew D. Sweet, Kevin P. Johnson, Stephen L. Cameron
Summary: The fragmentation of mitochondrial genomes in parasitic lice has evolved multiple times and is highly variable, showing associations with relaxed selection and lower AT% composition. These findings provide important insights into mitochondrial evolution.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biology
Robert S. de Moya, Julie M. Allen, Andrew D. Sweet, Kimberly K. O. Walden, Ricardo L. Palma, Vincent S. Smith, Stephen L. Cameron, Michel P. Valim, Terry D. Galloway, Jason D. Weckstein, Kevin P. Johnson
COMMUNICATIONS BIOLOGY
(2019)
Article
Entomology
Matt N. Krosch, Mark K. Schutze, Francesca Strutt, Anthony R. Clarke, Stephen L. Cameron
AUSTRAL ENTOMOLOGY
(2019)
Article
Entomology
Mengjie Jin, Tom Weir, Stephen L. Cameron, Catherine Lemann, Adam Slipinski, Hong Pang
AUSTRAL ENTOMOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Markus Osaland Fjelde, Einar Timdal, Reidar Haugan, Mika Bendiksby
Summary: This study investigated the taxonomy of the crustose lichen genus Calvitimela using molecular phylogenetics and morphological observations. The results revealed evolutionarily old and deeply divergent lineages within Calvitimela, with overlapping morphological characters between different subgenera. Chemical characters were informative at the level of subgenera but often homoplastic at the species level. A practical taxonomy of Calvitimela was proposed based on these findings.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Bo-Yang Shi, Da Pan, Kang-Qin Zhang, Tian-Yu Gu, Darren C. J. Yeo, Peter K. L. Ng, Neil Cumberlidge, Hong-Ying Sun
Summary: This study investigates the evolutionary history and speciation mechanisms of montane potamids in the Hengduan Mountains Region. The results suggest that the vicariance events of these crabs are correlated with the emergence of sky islands due to the uplift of the mountains. The mountain ridges provided corridors for their dispersal and past climatic conditions played a crucial role in their evolutionary history. The mechanisms isolating sky islands are reinforced by the climatic features of dry-hot valleys and continue to affect local diversification.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Attila Nemeth, Edvard Mizsei, Levente Laczko, David Czaban, Zsolt Hegyeli, Szabolcs Lengyel, Gabor Csorba, Gabor Sramko
Summary: Species delimitation of European blind mole rats is challenging due to their small morphological differences and complex chromosomal evolution. This study provides a comprehensive framework to improve understanding of their evolutionary history and revise their taxonomy. The results reveal the presence of multiple superspecies and species, with distinct geographic patterns and rapid chromosomal evolution.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Ying Qi, Zhaoyan Zhong, Xu Liu, Xing He, Yadong Zhou, Lili Zhang, Chong Chen, Katrin Linse, Jian-Wen Qiu, Jin Sun
Summary: This study investigates the phylogenetic relationships among patellogastropod families using mitochondrial and phylogenomic data. The results show that the mitochondrial phylogeny recovers monophyly of most families, but the relationships among families are still contentious. However, a more robust family-level topology consistent with morphology is achieved by phylogenomics. Additionally, the mainly deep-water families are found to be monophyletic, suggesting a single colonization of the deep water during the Jurassic.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Yu-Jie Shi, Jin -Liang Huang, Jia-Xuan Mi, Jing Li, Fan-Yu Meng, Yu Zhong, Fang He, Fei -Fei Tian, Fan Zhang, Liang-Hua Chen, Han-Bo Yang, Hong-Lin Hu, Xue-Qin Wan
Summary: Despite numerous studies on hybrid speciation, our understanding of this process remains limited. In this study, we conducted an 18-year systematic investigation on Populus taxa on the Qinghai-Tibet Plateau and discovered three new taxa that originated from distant hybridization between two different sections. These hybrid taxa demonstrate greater ecological adaptability than their ancestral species due to heterosis. We propose a hybrid speciation process model that can explain important evolutionary concerns.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Anna Cho, Denis Tikhonenkov, Gordon Lax, Kristina I. Prokina, Patrick J. Keeling
Summary: Unlike conspicuous ochrophytes, many small and overlooked flagellates belonging to basally branching stramenopiles remain poorly characterized at the cellular or genomic level. This study describes four new species, including two new genera, of sediment-dwelling MAST-6 and provides updated phylogenomic tree of stramenopiles. The characterization of these flagellates is important due to their phylogenetic diversity and abundance in various environments.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Tian-Tian Xue, Steven B. Janssens, Bin-Bin Liu, Sheng-Xiang Yu
Summary: Phylogenomic conflicts are widespread among genomic data, with most previous studies primarily focusing on nuclear datasets instead of organellar genomes. In this study, we investigated the phylogenetic conflicts within and between plastid and mitochondrial genomes using Potentilla as a case study. We found that both plastid and mitochondrial genomes divided Potentilla into eight highly supported clades, with two newly identified clades. Our results demonstrate that mitochondrial genes can fully resolve phylogenetic relationships among major clades of Potentilla and are not always linked with plastomes in evolutionary history.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Alexandra A. Grossi, Chunpo Tian, Mengjiao Ren, Fasheng Zou, Daniel R. Gustafsson
Summary: This study suggests that the coevolutionary relationships between chewing lice, endosymbiotic bacteria, and birds are not independent, but the patterns vary depending on the analysis method used. Additionally, louse host-switching does not seem to affect bacterial strains.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Ingrid Olivares, Sergio Tusso, Maria Jose Sanin, Marylaure de La Harpe, Oriane Loiseau, Jonathan Rolland, Nicolas Salamin, Michael Kessler, Kentaro K. Shimizu, Margot Paris
Summary: Traditionally, differences between species have been associated with morphological variation. However, the discovery of cryptic diversity suggests that the evolution of distinct lineages can occur without morphological differences. Through genetic analysis, we found that a tropical montane plant lineage is composed of numerous unrecognized genetic groups that are not morphologically distinct. Geographic distance and topography play a crucial role in determining the genetic divergence of these groups.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)