Incongruence in the phylogenomics era

JL Steenwyk, Y Li, X Zhou, XX Shen… - Nature Reviews Genetics, 2023 - nature.com
Genome-scale data and the development of novel statistical phylogenetic approaches have
greatly aided the reconstruction of a broad sketch of the tree of life and resolved many of its …

Common methods for phylogenetic Tree Construction and their implementation in R

Y Zou, Z Zhang, Y Zeng, H Hu, Y Hao, S Huang, B Li - Bioengineering, 2024 - mdpi.com
A phylogenetic tree can reflect the evolutionary relationships between species or gene
families, and they play a critical role in modern biological research. In this review, we …

Weighted ASTRID: fast and accurate species trees from weighted internode distances

B Liu, T Warnow - Algorithms for Molecular Biology, 2023 - Springer
Background Species tree estimation is a basic step in many biological research projects, but
is complicated by the fact that gene trees can differ from the species tree due to processes …

Rapid Evolution of Host Repertoire and Geographic Range in a Young and Diverse Genus of Montane Butterflies

S Mo, Y Zhu, MP Braga, DJ Lohman, S Nylin… - Systematic …, 2024 - academic.oup.com
Evolutionary changes in geographic distribution and larval host plants may promote the
rapid diversification of montane insects, but this scenario has been rarely investigated. We …

Phylogenomics of Neogastropoda: the backbone hidden in the bush

AE Fedosov, P Zaharias, T Lemarcis… - Systematic …, 2024 - academic.oup.com
The molluskan order Neogastropoda encompasses over 15,000 almost exclusively marine
species playing important roles in benthic communities and in the economies of coastal …

Pangenomic analysis of the bacterial cellulose-producing genera Komagataeibacter and Novacetimonas

BA Akhoon, Q Qiao, A Stewart, J Chen… - International Journal of …, 2025 - Elsevier
Bacterial cellulose (BC) holds significant commercial potential due to its unique structural
and chemical properties, making it suitable for applications in electronics, medicine, and …

Phylogenomic workflow for uncultivable microbial eukaryotes using single-cell RNA sequencing− A case study with planktonic ciliates (Ciliophora, Oligotrichea)

SUA Shazib, R Ahsan, M Leleu, GB McManus… - Molecular Phylogenetics …, 2025 - Elsevier
Phylogenetic analyses increasingly rely on genomic and transcriptomic data to produce
better supported inferences on the evolutionary relationships among microbial eukaryotes …

Integrating phylogenies with chronology to assemble the tree of life

J Barba-Montoya, JM Craig, S Kumar - bioRxiv, 2024 - pmc.ncbi.nlm.nih.gov
Reconstructing the global Tree of Life necessitates computational approaches to integrate
numerous molecular phylogenies with limited species overlap into a comprehensive …

Terraces in species tree inference from gene trees

M Habib, K Roy, S Hasan, AH Rahman… - BMC Ecology and …, 2024 - Springer
A terrace in a phylogenetic tree space is a region where all trees contain the same set of
subtrees, due to certain patterns of missing data among the taxa sampled, resulting in an …

Advances in lineage sorting theories and their detection methods

Y Lv, Z Wang, Y **ao, Z He, C Wu… - Biodiversity Science, 2024 - biodiversity-science.net
Background & Aims: Lineage sorting (LS) refers to the process in which multiple populations
are descended from a common ancestral population or species and are now reproductively …