Article
Biodiversity Conservation
Emma K. Roberts, Emily A. Wright, Asha E. Worsham, Daniel M. Hardy, Robert D. Bradley
Summary: The extraordinary morphological diversity among extant mammals poses challenges for studies of speciation, adaptation, molecular evolution, and reproductive isolation. Despite molecular studies, uncertainties remain regarding divergence events. A phylogenetic tool based on a single reproductive molecular marker provides a solution to this longstanding issue.
Article
Microbiology
Adriano de Bernardi Schneider, Carla Osiowy, Reilly Hostager, Henrik Krarup, Malene Borresen, Yasuhito Tanaka, Taylor Morriseau, Joel O. Wertheim
Summary: A study found that a high percentage of Greenland's Inuit population are chronically infected with HBV, with 39 novel HBV/D sequences forming a new quasi-subgenotype that differs from traditional HBV sequences.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biodiversity Conservation
Daijiang Li
Summary: Despite the availability of phylogenetic hypotheses for many taxonomic groups, most do not include all species. In phylogenetic ecology, there is a demand for phylogenies that encompass all species in a study. Existing software tools for grafting species to megatrees are limited to specific taxonomic groups. The new R package 'rtrees' aims to provide an easy, flexible, and reliable way to assemble phylogenies from megatrees, facilitating progress in phylogenetic ecology.
Article
Biodiversity Conservation
Jarod Meecham, T. Heath Ogden
Summary: Coloburiscidae consists of three living genera from Australia, New Zealand, and Chile, and this study presents the first phylogenetic analysis using extensive genomic data to resolve the evolutionary relationships within this family, revealing its monophyly.
Article
Biotechnology & Applied Microbiology
Saoirse Foley, Anna Vlasova, Marina Marcet-Houben, Toni Gabaldon, Veronica F. Hinman
Summary: This study utilizes phylogenomic approaches to identify conserved genes in echinoderms and suggests that the ancestral genes required to form a phylum may be present across broad taxonomic depths.
Article
Biochemistry & Molecular Biology
Frank E. Anderson, Annie R. Lindgren
Summary: Despite decades of research, the phylogenetic relationships among squids and cuttlefishes have remained unclear. This study re-evaluates these relationships using higher-quality genome and transcriptome data, and identifies key clade relationships such as the grouping of closed-eye squid, cuttlefishes, and open-eye squid, as well as the position of pygmy squids as the sister group to all sampled decapodiform lineages. Further research with improved taxon sampling and additional genomic data is needed to rigorously test these novel hypotheses.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Paleontology
Silvia Castiglione, Carmela Serio, Alessandro Mondanaro, Marina Melchionna, Pasquale Raia, Robert Sansom
Summary: This article introduces a new interactive software for the fast production of large, time-calibrated informal supertrees, which allows the merging of different phylogenetic information from various sources. The software automatically implements time calibration and has been applied to two case studies with efficient results.
Article
Mathematics
Ruriko Yoshida
Summary: When applying comparative phylogenetic analyses to genome data, the problem of missing genes in given species/taxa poses a challenge. This paper proposes a novel method to infer the missing part of a gene tree using tropical geometry and a linear regression approach. By considering a tropical polytope, the method guarantees an estimated tree's RF distance of at most four from the ground truth, as demonstrated through computational experiments on simulated and empirical data.
Article
Biochemical Research Methods
Max Hill, Sebastien Roch
Summary: This study investigates the impact of intralocus recombination on species tree estimation from multiple loci, revealing that intralocus recombination can create an inconsistency zone which may amplify the effects of incomplete lineage sorting and lead to inconsistency in inference.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sudhir Kumar, Sudip Sharma
Summary: Evolutionary Sparse Learning (ESL) is a supervised machine learning approach with sparsity constraints that builds models using only the most important genomic loci to explain phylogenetic hypotheses or trait presence/absence. ESL does not involve traditional parameters, but directly utilizes sequence variation concordance. ESL offers a natural way to combine different data types and has the potential to drive the development of new computational methods.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Evolutionary Biology
Andrew H. Moeller
Summary: Bacteria inhabiting the human body exhibit a wide range of genome sizes, with gut bacteria showing larger genomes compared to other body sites. The gut microbiome promotes expansions of bacterial genomes, leading to an average size difference of 127 kb between gut bacteria and their closest relatives in other body sites. Additionally, genome size and relative abundance are positively associated within the gut but negatively associated at other body sites.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Max R. Bangs, Scott J. Steppan
Summary: A genomic probe set optimized for rodents was designed and successfully obtained alignments for 416 of the 418 target loci. The genomic data set performed well in phylogenetic analyses, especially in recent phylogenetic splits.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Plant Sciences
Fei Zhao, Yi-Wen Wu, Bryan T. Drew, Gang Yao, Ya-Ping Chen, Jie Cai, En-De Liu, Bo Li, Chun-Lei Xiang
Summary: Paralamium is a monotypic genus within the subfamily Lamioideae, belonging to the tribe Pogostemoneae and sister to the monotypic genus Craniotome. The study also discusses the generic-level phylogenetic relationships within Pogostemoneae and provides a dichotomous key for genera within the tribe.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Sebastian Burgstaller-Muehlbacher, Stephen M. Crotty, Heiko A. Schmidt, Franziska Reden, Tamara Drucks, Arndt von Haeseler
Summary: This article introduces ModelRevelator, a model selection tool utilizing deep neural networks. By inputting MSA, the tool can quickly recommend evolutionary models and provide estimates for rate heterogeneity and alpha values, thereby saving computational resources.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Plant Sciences
Alexa S. Tyszka, Eric C. Bretz, Holly M. Robertson, Miles D. Woodcock-Girard, Karolis Ramanauskas, Drew A. Larson, Gregory W. Stull, Joseph F. Walker
Summary: Chloroplasts and mitochondria have their own genomes and have been important for inferring land plant phylogeny. This study examined the genomes of 226 land plants to investigate the similarity between the evolutionary histories of these organelles. The results showed mostly concordant topologies, except for a few conflicting relationships that need further investigation. The findings suggest significant differences in molecular evolution between the chloroplast and mitochondrial genomes, indicating the need for separate evolutionary models.
FRONTIERS IN PLANT SCIENCE
(2023)