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 …

Functional horizontal gene transfer from bacteria to eukaryotes

F Husnik, JP McCutcheon - Nature Reviews Microbiology, 2018 - nature.com
Bacteria influence eukaryotic biology as parasitic, commensal or beneficial symbionts. Aside
from these organismal interactions, bacteria have also been important sources of new …

Genome-based phylogeny and taxonomy of the 'Enterobacteriales': proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae …

M Adeolu, S Alnajar, S Naushad… - … journal of systematic …, 2016 - microbiologyresearch.org
Understanding of the phylogeny and interrelationships of the genera within the order
'Enterobacteriales' has proven difficult using the 16S rRNA gene and other single-gene or …

A rooted phylogeny resolves early bacterial evolution

GA Coleman, AA Davín, TA Mahendrarajah… - Science, 2021 - science.org
INTRODUCTION Bacteria are the most diverse and abundant cellular organisms on Earth,
and in recent years environmental genomics has revealed the existence of an enormous …

Divergent evolutionary trajectories of bryophytes and tracheophytes from a complex common ancestor of land plants

BJ Harris, JW Clark, D Schrempf, GJ Szöllősi… - Nature Ecology & …, 2022 - nature.com
The origin of plants and their colonization of land fundamentally transformed the terrestrial
environment. Here we elucidate the basis of this formative episode in Earth history through …

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

M García-López, JP Meier-Kolthoff, BJ Tindall… - Frontiers in …, 2019 - frontiersin.org
Although considerable progress has been made in recent years regarding the classification
of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify …

Insights into the phylogeny and coding potential of microbial dark matter

C Rinke, P Schwientek, A Sczyrba, NN Ivanova… - Nature, 2013 - nature.com
Genome sequencing enhances our understanding of the biological world by providing
blueprints for the evolutionary and functional diversity that shapes the biosphere. However …

Phylogenomics provides robust support for a two-domains tree of life

TA Williams, CJ Cox, PG Foster, GJ Szöllősi… - Nature ecology & …, 2020 - nature.com
Hypotheses about the origin of eukaryotic cells are classically framed within the context of a
universal 'tree of life'based on conserved core genes. Vigorous ongoing debate about …

Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology

PA Goloboff, A Torres, JS Arias - Cladistics, 2018 - Wiley Online Library
One of the lasting controversies in phylogenetic inference is the degree to which specific
evolutionary models should influence the choice of methods. Model‐based approaches to …

Lipid biomarkers: molecular tools for illuminating the history of microbial life

RE Summons, PV Welander, DA Gold - Nature Reviews Microbiology, 2022 - nature.com
Fossilized lipids preserved in sedimentary rocks offer singular insights into the Earth's
palaeobiology. These 'biomarkers' encode information pertaining to the oxygenation of the …