Article
Biochemical Research Methods
Merce Llabres, Francesc Rossello, Gabriel Valiente
Summary: The Generalized Robinson-Foulds (GRF) distance is a metric for comparing structures with high resolution and can be computed in linear time, distinct from the RF distance.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2021)
Article
Microbiology
Min Wang, Cong-Jian Li, Zhen Zhang, Pan-Pan Li, Ling-Ling Yang, Xiao-Yang Zhi
Summary: This study evaluated the distribution of development-related genes in Streptomyces genomes and found that most of these genes were ubiquitous. Furthermore, the congruence between development-related genes and the species tree of Streptomyces was higher compared to other strict orthologous genes. These results suggest that morphological development follows the same pattern as species divergence.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemical Research Methods
Chao Zhang, Siavash Mirarab
Summary: ASTRAL-Pro 2 is a more efficient version of ASTRAL-Pro, which enhances scalability while maintaining accuracy by adopting a placement-based optimization algorithm.
Article
Plant Sciences
Jeffrey P. Rose, Ricardo Kriebel, Larissa Kahan, Alexa DiNicola, Jesus G. Gonzalez-Gallegos, Ferhat Celep, Emily M. Lemmon, Alan R. Lemmon, Kenneth J. Sytsma, Bryan T. Drew
Summary: Advancements in next-generation sequencing technologies have allowed for new phylogenomic approaches to clarify relationships within Salvia. Despite gene tree discordance, nuclear and plastid genomes exhibit congruence in delineating Salvia's relationships at both broad and species levels. Horizontal gene flow has been identified as an important factor in Salvia's evolutionary history.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemical Research Methods
Md. Shamsuzzoha Bayzid
Summary: This article proposes a new dynamic programming algorithm for accurately inferring species trees when gene trees are unrooted. The algorithm can also solve constrained problems in polynomial time. The researchers have also proven important structural properties of the algorithm and presented a linear time algorithm for finding the optimal rooted version of unrooted gene trees.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2023)
Article
Biodiversity Conservation
Ziyan Liao, Jin Zhou, Tsung-Jen Shen, Youhua Chen
Summary: This study recommends using the symmetric Dirichlet-multinomial (SDM) distribution to model aggregation patterns in quadrat sampling data. Numerical simulations and empirical tests demonstrate that the SDM model is more accurate in describing aggregation trends compared to the negative binomial distribution (NBD) model.
ECOLOGICAL INDICATORS
(2023)
Article
Biochemistry & Molecular Biology
Marcin Gorniak, Dariusz L. Szlachetko, Natalia Oledrzynska, Aleksandra M. Naczk, Agata Mieszkowska, Lidia Boss, Marek S. Zietara
Summary: The phylogeny of the genus Paphiopedilum based on the plastome is consistent with morphological analysis, but nuclear markers have not confirmed this. There is topology incongruence among different nuclear markers, affecting entire sections of the subgenus Paphiopedilum. The low-copy nuclear protein-coding gene PHYC supports the nuclear-based phylogeny, indicating ancestral homoploid hybridization might be the cause of incongruence in nuclear gene trees.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Computer Science, Artificial Intelligence
Kongjing Gu, Xiaojun Duan, Mingze Qi, Liang Yan
Summary: Interactions and dynamics are crucial for achieving complex intelligence in multi-agent systems. However, inferring these interactions remains a common and open problem. This paper introduces a novel method called K-similarity for measuring global relative similarities and inferring interactions among multiple agents. The method shows promising results in accuracy and stability, outperforming benchmark methods in various scenarios.
COMPLEX & INTELLIGENT SYSTEMS
(2023)
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
Biochemistry & Molecular Biology
Louxin Zhang, Niloufar Abhari, Caroline Colijn, Yufeng Wu
Summary: The reconstruction of phylogenetic networks is a challenging task due to the vastness of the network space. One approach is to solve the minimum phylogenetic network problem by inferring phylogenetic trees first and then computing the smallest network that displays all the trees. A new method, named ALTS, was developed to infer the minimum tree-child network by aligning lineage taxon strings in the phylogenetic trees, overcoming the limitations of existing programs. ALTS is fast enough to handle large-scale networks with reticulations for a set of up to 50 phylogenetic trees with 50 taxa in about 15 minutes on average.
Article
Genetics & Heredity
Nicolas M. Ayala, Maximilian Genetti, Russell Corbett-Detig
Summary: The exchange of genetic information between distinct source populations, known as admixture, is considered a major source of adaptive genetic variation. Admixture introduces many selected alleles simultaneously, which may have pronounced effects on linkage between selected alleles. Existing tools for identifying selected mutations within admixed populations only account for selection at a single site, ignoring the linkage among proximal selected alleles. In this study, a method was developed and validated to identify and quantify the individual effects of multiple linked selected sites on a chromosome in admixed populations. The method accurately detected the number of sites and predicted their selection coefficients even when they were in linkage. The inferred selection coefficients of selected sites in linkage were found to be overestimated if the effects of linkage were ignored. The results suggest that linkage among selected sites may be an important evolutionary force in admixed populations. The developed tool provides a powerful method to investigate these crucial phenomena in diverse populations.
Article
Acoustics
Axel Ahrens, Kasper Duemose Lund
Summary: This study investigates how listeners analyze audio-visual scenes with varying complexity and finds that room reverberation and the number of talkers in a scene can influence the accuracy and response time of analyzing an auditory scene.
JOURNAL OF THE ACOUSTICAL SOCIETY OF AMERICA
(2022)
Proceedings Paper
Computer Science, Hardware & Architecture
Alvin Chon, Pawel Gorecki, Oliver Eulenstein, Xiaoqiu Huang, Ali Jannesari
Summary: This paper presents a method called BFHRF for computing the average RF between different binary evolutionary tree collections. BFHRF is faster and uses less memory compared to existing methods. It can also be modified to accommodate different RF variants and variable taxa in the tree collection, and provides an easy-to-use installation and interface.
2022 IEEE 36TH INTERNATIONAL PARALLEL AND DISTRIBUTED PROCESSING SYMPOSIUM WORKSHOPS (IPDPSW 2022)
(2022)
Article
Plant Sciences
Hailing Chen, Shangli Liu, Quanqing Ye, Yongbin Lu, Shaoqing Tang
Summary: The study suggests that Camellia chrysanthoides, C. micrantha, and C. parvipetala should be recognized as three independent conservation units due to their genetic and morphological differences.
PLANT SPECIES BIOLOGY
(2021)
Article
Evolutionary Biology
Zhi Yan, Huw A. Ogilvie, Luay Nakhleh
Summary: The evolutionary histories of individual loci in a genome can be estimated independently, but this approach is prone to errors due to limited sequence data for each gene. Various gene tree error correction methods have been developed to reduce the distance between gene trees and species trees. We evaluated the performance of two representative methods: TRACTION and TreeFix. Our findings suggest that gene tree error correction often increases the errors in gene tree topologies, even when the true gene and species trees are discordant. Full Bayesian inference of gene trees under the multispecies coalescent model is more accurate than independent inference. Future gene tree correction methods should incorporate realistic models of evolution instead of relying on oversimplified heuristics.
GENOME BIOLOGY AND EVOLUTION
(2023)