Article
Biochemistry & Molecular Biology
Josefa Fernandez-Lopez, Javier Fernandez-Cruz, Beatriz Miguez-Soto
Summary: The study found that European chestnut populations experienced contraction during the Early Pleistocene, splitting into Greek and Italian/Iberian populations. A secondary encounter occurred from the Middle to Late Pleistocene, explaining the hybrid origin of Western Mediterranean populations. Evidence suggests that germplasm translocation may have occurred from Italy to Central Iberian Range, resulting in high diversity in naturalized populations.
Article
Computer Science, Artificial Intelligence
Jinhee Park, Junseok Kwon
Summary: In this study, novel visual tracking methods based on the Wasserstein approximate Bayesian computation (ABC) are presented. The proposed methods, including Wasserstein ABC (WABC), time-series WABC (TWABC), and Hilbert TWABC (HTWABC), improve the accuracy and efficiency of visual tracking by approximating likelihood distributions and encoding temporal dependencies. Experimental results demonstrate the superiority of the proposed methods, and ablation studies confirm the effectiveness of individual components.
PATTERN RECOGNITION
(2022)
Article
Biochemistry & Molecular Biology
Francois-David Collin, Ghislain Durif, Louis Raynal, Eric Lombaert, Mathieu Gautier, Renaud Vitalis, Jean-Michel Marin, Arnaud Estoup
Summary: The DIYABC Random Forest v1.0 software package is introduced for analyzing large SNP data sets to make inferences about complex population genetic histories. This package integrates the functionality of simulating different types of molecular data under custom evolutionary scenarios and evaluating the accuracy of inferences.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Biochemistry & Molecular Biology
Asher Moshe, Elya Wygoda, Noa Ecker, Gil Loewenthal, Oren Avram, Omer Israeli, Einat Hazkani-Covo, Itsik Pe'er, Tal Pupko
Summary: This study developed a probabilistic approach to infer genome rearrangement rate parameters and used an Approximate Bayesian Computation framework for inference. The method can help elucidate the role of genome rearrangement in evolution and simulate genomes with empirical dynamics.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Christelle Fraiesse, Iva Popovic, Clement Mazoyer, Bruno Spataro, Stephane Delmotte, Jonathan Romiguier, Etienne Loire, Alexis Simon, Nicolas Galtier, Laurent Duret, Nicolas Bierne, Xavier Vekemans, Camille Roux
Summary: DILS is a deployable statistical analysis platform that conducts demographic inferences with linked selection from population genomic data using an Approximate Bayesian Computation framework, and is also accessible via a Web interface. Its hierarchical analysis method identifies different demographic and genomic models, and identifies loci associated with barriers to gene flow.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Engineering, Industrial
Manuel Chiachio, Ali Saleh, Susannah Naybour, Juan Chiachio, John Andrews
Summary: This paper presents a probabilistic method for accurately defining the structure and parameters of a reduced Petri net model, enabling accurate modeling of engineering systems and processes. The method allows for numerical measurement and selection of the optimal simplified structure.
RELIABILITY ENGINEERING & SYSTEM SAFETY
(2022)
Article
Engineering, Civil
Pinghe Ni, Qiang Han, Xiuli Du, Xiaowei Cheng, Hongyuan Zhou
Summary: This paper presents a data-driven approach for post-earthquake reliability assessments of civil structures. It updates the probability density functions of random variables using measured vibration data, and generates the posterior probability density functions of structural parameters using two approximate Bayesian computation techniques. The updated probability density functions are then used for reliability assessments, and numerical studies verify the accuracy and efficiency of the proposed techniques.
ENGINEERING STRUCTURES
(2022)
Article
Computer Science, Interdisciplinary Applications
Clara Grazian, Luciana Dalla Valle, Brunero Liseo
Summary: Copula models are flexible tools for representing complex dependence structures of multivariate random variables. However, incorporating covariates in these models is challenging due to the lack of unbiased estimators of the conditional copula and the difficulty in selecting the appropriate copula model.
COMPUTATIONAL STATISTICS & DATA ANALYSIS
(2022)
Article
Biochemistry & Molecular Biology
Cesar A. Fortes-Lima, Romain Laurent, Valentin Thouzeau, Bruno Toupance, Paul Verdu
Summary: Admixture is a fundamental evolutionary process that has influenced genetic patterns in numerous species. Maximum-likelihood approaches have limitations in reconstructing complex admixture histories, leading to the development of an Approximate Bayesian Computation (ABC) framework that integrates machine-learning algorithms to investigate admixture history accurately. The study showed that random forest ABC scenario-choice accurately distinguished complex admixture scenarios, while neural network ABC posterior parameter estimation was accurate and conservative under complex admixture scenarios. This approach provides a promising method for reconstructing detailed admixture histories in populations with multiple admixture pulses.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Automation & Control Systems
Yuexi Wang, Tetsuya Kaji, Veronika Rockova
Summary: Approximate Bayesian Computation (ABC) is a method that enables statistical inference in simulator-based models with difficult likelihood calculations but easy simulation. This study constructs a kernel-type approximation of the posterior distribution in ABC by comparing summary statistics of real and simulated data, and uses contrastive learning to directly compare empirical distributions. The research demonstrates the usefulness of this approach in simulated examples and real data analysis in the context of stock volatility estimation.
JOURNAL OF MACHINE LEARNING RESEARCH
(2022)
Article
Biology
Cengiz Kaya, Tomas N. Generalovic, Gunilla Stahls, Martin Hauser, Ana C. Samayoa, Carlos G. Nunes-Silva, Heather Roxburgh, Jens Wohlfahrt, Ebenezer A. Ewusie, Marc Kenis, Yupa Hanboonsong, Jesus Orozco, Nancy Carrejo, Satoshi Nakamura, Laura Gasco, Santos Rojo, Chrysantus M. Tanga, Rudolf Meier, Clint Rhode, Christine J. Picard, Chris D. Jiggins, Florian Leiber, Jeffery K. Tomberlin, Martin Hasselmann, Wolf U. Blanckenhorn, Martin Kapun, Christoph Sandrock
Summary: The study provides the first comprehensive genetic characterization of black soldier fly populations, revealing 16 well-distinguished genetic clusters with significant global population structure. It highlights the dynamic population genetic history and ongoing domestication of black soldier flies, with implications for future research on this emerging insect-livestock model.
Article
Computer Science, Interdisciplinary Applications
Bach Do, Makoto Ohsaki
Summary: This study presents Bayesian optimization-assisted approximate Bayesian computation (BO-assisted ABC) and showcases its application to identifying the approximate posteriors of parameters for known statistical models and of cyclic elastoplastic parameters for structural steels. ABC bypasses likelihood evaluations by generating prior samples that are assigned as samples constituting the posterior if discrepancies between the experimental dataset and the corresponding simulated datasets do not exceed a small, positive threshold. With a modest number of costly simulations, BO facilitates ABC by intelligently constructing a Gaussian process model that approximates the discrepancy mean function.
COMPUTERS & STRUCTURES
(2023)
Article
Ecology
Charlotte Baey, Henrik G. Smith, Maj Rundlof, Ola Olsson, Yann Clough, Ullrika Sahlin
Summary: In this study, alternative strategies for handling high-dimensional data in ABC calibration were investigated. Regression adjustment and machine learning approaches were compared in terms of model estimate coverage and true parameter values. The results showed that random forest-based approaches performed better, and nonlinear regression adjustment outperformed linear ones.
ECOLOGICAL MODELLING
(2023)
Article
Engineering, Mechanical
Joao Pedro Valeriano, Pedro Henrique Cintra, Gustavo Libotte, Igor Reis, Felipe Fontinele, Renato Silva, Sandra Malta
Summary: The long duration of COVID-19 pandemic has led to multiple bursts in infection and death rates, known as epidemic waves. Traditional compartmental models are no longer effective, necessitating more sophisticated mathematical techniques for analyzing epidemic data and making reliable forecasts. In this study, a framework is proposed for analyzing complex dynamical systems by dividing the data into consecutive time-windows for separate analysis. Parameters are estimated for each window using an approximate Bayesian computation (ABC) algorithm, with the posterior distribution from one window serving as the prior distribution for the next. The Bayesian learning approach is tested using COVID-19 case data from various countries, showing improved ABC performance and producing accurate short-term forecasts.
NONLINEAR DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Joao Carvalho, Hernan E. Morales, Rui Faria, Roger K. Butlin, Vitor C. Sousa
Summary: In this study, a new Approximate Bayesian Computation (ABC) method was developed to infer the demographic history using pool-seq data. The results showed that pool-seq data can distinguish between general scenarios of ecotype formation and infer relevant demographic parameters.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemistry & Molecular Biology
Sabine Urban, Alexander Nater, Axel Meyer, Claudius F. Kratochwil
Summary: In this study, researchers found that in Lake Malawi, the melanic horizontal stripes in cichlid fish are associated with recent de novo mutations near the agrp2 gene, whereas in Lake Victoria, the stripes are linked to two intronic regions. The haplotypes associated with these traits predate the Lake Victoria radiation and indicate a standing genetic variation driving phenotypic divergence. Both new and ancient allelic variation at the same locus fueled rapid and convergent phenotypic evolution.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Veterinary Sciences
Silke Pfitzer, Leith Meyer, Liesel Laubscher, Kristin Warren, Rebecca Vaughan-Higgins, Jacobus P. Raath, Michael Laurence
Summary: The study compared the cardiopulmonary effects of etorphine and thiafentanil in immobilizing blesbok. Results showed that while thiafentanil caused more significant hypertension, it led to less severe hypoxemia compared to etorphine. Ventilation was adequate for both drugs during immobilization.
VETERINARY ANAESTHESIA AND ANALGESIA
(2021)
Article
Veterinary Sciences
Silke Pfitzer, Leith Meyer, Liesel Laubscher, Kristin Warren, Rebecca Vaughan-Higgins, Jacobus P. Raath, Michael Laurence
Summary: Thiafentanil resulted in faster recumbency time compared to etorphine, but also caused more severe bradypnea at 5 minutes. Etorphine led to a significant decrease in heart rate over time, while thiafentanil induced more profound hypertension and ventilatory effects.
VETERINARY ANAESTHESIA AND ANALGESIA
(2021)
Article
Biochemistry & Molecular Biology
Peiwen Xiong, C. Darrin Hulsey, Carmelo Fruciano, Wai Y. Wong, Alexander Nater, Andreas F. Kautt, Oleg Simakov, Martin Pippel, Shigehiro Kuraku, Axel Meyer, Paolo Franchini
Summary: This study compared two closely related Neotropical cichlid fish lineages using 40 resequenced genomes and two de novo assembled genomes. Despite inhabiting similar ecological environments, the evolutionary outcomes of the two lineages were markedly different.
Article
Multidisciplinary Sciences
Chunyan Li, Melisa Olave, Yali Hou, Geng Qin, Ralf F. Schneider, Zexia Gao, Xiaolong Tu, Xin Wang, Furong Qi, Alexander Nater, Andreas F. Kautt, Shiming Wan, Yanhong Zhang, Yali Liu, Huixian Zhang, Bo Zhang, Hao Zhang, Meng Qu, Shuaishuai Liu, Zeyu Chen, Jia Zhong, He Zhang, Lingfeng Meng, Kai Wang, Jianping Yin, Liangmin Huang, Byrappa Venkatesh, Axel Meyer, Xuemei Lu, Qiang Lin
Summary: Seahorses have a global distribution in tropical to temperate coastal waters and show many adaptations for a sedentary, cryptic lifestyle. New genome assembly and re-sequenced genomes of 21 other species shed light on the evolutionary origin and global dispersal routes of seahorses, revealing that rafting via ocean currents compensates for poor dispersal and bony spines likely evolved multiple times through independent substitutions in a key developmental gene.
NATURE COMMUNICATIONS
(2021)
Article
Genetics & Heredity
Andrea Patrizia Salzmann, Natasha Arora, Giancarlo Russo, Susanne Kreutzer, Lars Snipen, Cordula Haas
Summary: The study revealed compositional changes in body fluids exposed to outdoor conditions after 4 weeks, primarily due to accumulation of environmental bacteria. Indoor samples showed relatively stable RNA composition, with changes in bacterial orders enabling TsD prediction.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Marta Pla-Diaz, Leonor Sanchez-Buso, Lorenzo Giacani, David Smajs, Philipp P. Bosshard, Homayoun C. Bagheri, Verena J. Schuenemann, Kay Nieselt, Natasha Arora, Fernando Gonzalez-Candelas
Summary: The incidence of syphilis is increasing globally, and recombination and selection among the Treponema pallidum subspecies play an important role in the evolution and spread of the bacteria causing syphilis.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Claudius F. Kratochwil, Andreas F. Kautt, Alexander Nater, Andreas Harer, Yipeng Liang, Frederico Henning, Axel Meyer
Summary: This study uncovers the genetic basis of the gold/dark polymorphism in Midas cichlid fish by identifying a transposon insertion in the gene goldentouch.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Camila L. Nacif, Claudius F. Kratochwil, Andreas F. Kautt, Alexander Nater, Gonzalo Machado-Schiaffino, Axel Meyer, Frederico Henning
Summary: The evolution and differentiation of sex chromosomes is a significant event in genome evolution, and the repeated evolution and variability of sex-determination mechanisms in fishes make them a suitable model for studying general patterns in evolution. This study used forward-genetics, long-read sequencing, and optical mapping to determine that sex in Midas cichlids is determined by an XY system and identified and assembled the sex-determining region. The study also found that the male-specific region on chromosome 4 contains transposable elements and a Y-specific duplicate of the anti-Mullerian receptor 2 gene, which has evolved as a master sex-determining gene. The duplication of anti-Mullerian genes is a common mechanism for establishing new sex determiners, highlighting the importance of molecular parallelism in the evolution of sex determination.
Article
Multidisciplinary Sciences
Melisa Olave, Alexander Nater, Andreas F. Kautt, Axel Meyer
Summary: This study presents a rare example of sympatric homoploid hybrid speciation in Midas cichlid fishes from Nicaragua. The hybrid lineage has diverged from its parental species both genomically and phenotypically, and occupies a different trophic niche facilitated by body shape adaptations.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Natasha Arora, Joao F. Matias Rodrigues, Meghna Swayambhu, Pim Witlox
Summary: Microbial communities in biological stains can be used to predict bodily origin, assisting forensic scientists in identifying body fluids/tissues. A new online database and data-mining platform customized for forensic scientists investigating body fluids/tissues has been developed. Users can download data from the platform to train predictive models.
FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES
(2022)
Review
Biotechnology & Applied Microbiology
Meghna Swayambhu, Rolf Kuemmerli, Natasha Arora
Summary: Recent advancements in next-generation sequencing technologies combined with machine learning have shown the potential of microbiome-based analyses in various fields such as clinical diagnostics and forensic sciences. In the field of forensics, microbial markers found in biological stains left at crime scenes can provide crucial information for crime scene reconstruction, including the bodily origin, time since deposition, and donor(s) of the stain. Despite the promising results, there is a need to address the gaps in comprehensive assessment of the method's limitations and the establishment of a standard operating procedure before integrating microbiome-based analyses into routine forensic casework.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Tobias Hasler, Leticia Tavares-Gomes, Sereina Gut, Meghna Swayambhu, Mario Gysi, Martin Hausmann, Natasha Arora, Thierry Hennet
Summary: The availability of carbohydrates in the gastrointestinal tract influences the gut microbiota composition. Bacterial glycoside hydrolases play a role in carbohydrate foraging and can alter the properties of host glycans. Increased sialidase activity exacerbates acute colitis severity by remodeling surface sialylation.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Letter
Ecology
Cyril C. Grueter, Xiaoguang Qi, Dietmar Zinner, Thore Bergman, Ming Li, Zuofu Xiang, Pingfen Zhu, Alex Miller, Michael Krutzen, Julia Fischer, Daniel I. Rubenstein, T. N. C. Vidya, Baoguo Li, Mauricio Cantor, Larissa Swedell
TRENDS IN ECOLOGY & EVOLUTION
(2021)
Article
Ecology
Sam Rycken, Jill M. Shephard, Lian Yeap, Rebecca Vaughan-Higgins, Manda Page, Rick Dawson, Karen Smith, Peter R. Mawson, Kristin S. Warren
Summary: The research aimed to identify key foraging and roosting habitat for Baudin's cockatoos and compare flock movements in Urban, Peri-urban, and Forest regions using telemetry data. Results showed significant differences in flock movements and habitat preferences between the Forest region and the Urban/Peri-urban regions, emphasizing the importance of maintaining vegetation connectivity for the conservation of this endangered species.