Article
Genetics & Heredity
Gizem Kaya, Chisom Ezekannagha, Dominik Heider, Georges Hattab
Summary: Sustained efforts in next-generation sequencing technologies are changing the field of taxonomy. In order to support evolutionary and taxonomic studies, researchers have developed an interactive web tool called Context-Aware Phylogenetic Trees (CAPT). This tool enhances the traditional phylogenetic tree view with taxonomic icicle view, providing context and interactive techniques for exploring and validating the data.
FRONTIERS IN GENETICS
(2022)
Article
Biochemical Research Methods
Luna L. Sanchez-Reyes, Martha Kandziora, Emily Jane McTavish
Summary: Physcraper is a tool that automates the update of published phylogenies by adding public DNA sequences to underlying alignments, facilitating non-specialists in generating phylogenetic hypotheses and specialists in gathering molecular datasets and comparing alternative phylogenetic hypotheses.
BMC BIOINFORMATICS
(2021)
Article
Biology
Theo Sanderson
Summary: The COVID-19 pandemic has generated an unprecedented amount of sequencing data for SARS-CoV-2, leading to the need for a scalable tool for exploring phylogenetic trees. Taxonium is a new tool that uses WebGL to enable the exploration of large trees with millions of nodes in the browser. This article describes the insights gained from analyzing a tree of five million sequences and provides a tool for exploring a public tree of over five million SARS-CoV-2 sequences.
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
Biochemistry & Molecular Biology
Benoit Morel, Paul Schade, Sarah Lutteropp, Tom A. Williams, Gergely J. Szollosi, Alexandros Stamatakis
Summary: SpeciesRax is a maximum likelihood method that can infer a rooted species tree from a set of gene family trees and can account for gene duplication, loss, and transfer events. It leverages the phylogenetic rooting signal in gene trees and infers species tree branch lengths and support values through paralogy-aware quartets extracted from the gene family trees. It is faster and at least as accurate as the best competing methods.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
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)
Article
Plant Sciences
Rebeca Hernandez-Gutierrez, Cassio van den Berg, Carolina Granados Mendoza, Marcia Penafiel Cevallos, M. Efrain Freire, Emily Moriarty Lemmon, Alan R. Lemmon, Susana Magallon
Summary: This study aims to generate a phylogenetic hypothesis of the cotton and cacao family using nuclear genes, and analyzes the discordance among different methods and gene histories.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Mathematics, Applied
Zemin Jin, Xueyao Gui, Kaijun Wang
Summary: The paper discusses the problem of using up to k colors in the edge coloring of graphs, and determines the color number for trees.
APPLIED MATHEMATICS AND COMPUTATION
(2021)
Article
Multidisciplinary Sciences
Yannick Woudstra, Juan Viruel, Martin Fritzsche, Thomas Bleazard, Ryan Mate, Caroline Howard, Nina Ronsted, Olwen M. Grace
Summary: Plant molecular identification studies have been limited by the use of highly conserved markers, reducing resolution in diverse plant clades, while low-copy nuclear genes can overcome this limitation but are difficult to sequence and require high-quality DNA. Aloe vera and its relatives face conservation issues, necessitating a molecular identification tool for trade regulation. The development of a customised RNA-bait panel targeting low-copy nuclear genes has shown efficacy in obtaining high-coverage sequence data for phylogenetic relationships of Aloe vera and related species.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Chao Zhang, Siavash Mirarab
Summary: This paper introduces a threshold-free weighting scheme for quartet-based species tree inference, which improves the utility of summary methods and reduces incongruence with gene concatenation.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Mathematics, Applied
Kinkar Chandra Das, Ivan Gutman
Summary: This paper focuses on the recently introduced Sombor index SO, and presents bounds on SO values of trees in relation to order, independence number, and number of pendent vertices, while characterizing extremal cases. Additionally, analogous results for quasi-trees are established.
APPLIED MATHEMATICS AND COMPUTATION
(2022)
Article
Biochemical Research Methods
Thien Le, Aaron Sy, Erin K. Molloy, Qiuyi Zhang, Satish Rao, Tandy Warnow
Summary: Incremental tree building (INC) is a fast converging phylogeny estimation method, but has poor accuracy for gene tree estimation; Constrained-INC approaches the accuracy of the best methods for species tree estimation and is faster.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2021)
Article
Plant Sciences
Ting Wang, Ting-Zhang Li, Si-Si Chen, Tuo Yang, Jiang-Ping Shu, Yu-Nong Mu, Kang-Lin Wang, Jian-Bing Chen, Jian-Ying Xiang, Yue-Hong Yan
Summary: This study resolves the phylogeny of Dennstaedtiaceae by analyzing plastid genomes. By generating new plastid genomes and combining them with publicly available data, the study establishes a robust phylogenetic backbone for future research on the classification, evolution, and diversification of Dennstaedtiaceae. The study also suggests considering plastid phylogenomic conflict and using amino acid sequences as a comparison to verify nucleotide-based trees.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Forestry
Olga Cholewinska, Andrzej Keczynski, Barbara Kusinska, Bogdan Jaroszewicz
Summary: The study found that the species of large trees have a significant impact on the diversity, distance, and frequency of adjacent trees, and as the diameter of the large tree increases, the distance between neighboring trees and the large tree also increases.
Article
Biochemical Research Methods
Benoit Morel, Tom A. Williams, Alexandros Stamatakis
Summary: Asteroid is a novel algorithm that infers an unrooted species tree from a set of unrooted gene trees. It is more accurate than ASTRAL and ASTRID for very high proportions (>80%) of missing data and much faster for datasets with thousands of genes. Asteroid offers advanced features such as parallelization, support value computation, and support for multi-copy and multifurcating gene trees.
